diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 47233250a3..59a937faba 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -37,7 +37,8 @@ src/MESONT/* @iafoss src/ML-HDNNP/* @singraber src/ML-IAP/* @athomps src/ML-PACE/* @yury-lysogorskiy -src/ML-POD/* @exapde @rohskopf +src/ML-POD/* @exapde +src/ML-UF3/* @monk-04 src/MOFFF/* @hheenen src/MOLFILE/* @akohlmey src/NETCDF/* @pastewka @@ -58,7 +59,8 @@ src/VTK/* @rbberger # individual files in packages src/GPU/pair_vashishta_gpu.* @andeplane -src/KOKKOS/pair_vashishta_kokkos.* @andeplane +src/KOKKOS/pair_vashishta_kokkos.* @andeplane @stanmoore1 +src/KOSSOS/pair_pod_kokkos.* @exapde @stanmoore1 src/MANYBODY/pair_vashishta_table.* @andeplane src/MANYBODY/pair_atm.* @sergeylishchuk src/MANYBODY/pair_nb3b_screened.* @flodesani @@ -72,6 +74,8 @@ src/MC/fix_sgcmc.* @athomps src/REAXFF/compute_reaxff_atom.* @rbberger src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger src/REPLICA/fix_pimd_langevin.* @Yi-FanLi +src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud +src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud # core LAMMPS classes src/lammps.* @sjplimp @@ -83,7 +87,7 @@ src/bond.* @sjplimp src/comm*.* @sjplimp src/compute.* @sjplimp src/dihedral.* @sjplimp -src/domain.* @sjplimp +src/domain.* @sjplimp @stanmoore1 src/dump*.* @sjplimp src/error.* @sjplimp src/finish.* @sjplimp diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml index f9c2a838d6..b0bc4b2727 100644 --- a/.github/workflows/unittest-macos.yml +++ b/.github/workflows/unittest-macos.yml @@ -15,7 +15,7 @@ jobs: build: name: MacOS Unit Test if: ${{ github.repository == 'lammps/lammps' }} - runs-on: macos-latest + runs-on: macos-13 env: CCACHE_DIR: ${{ github.workspace }}/.ccache @@ -43,6 +43,8 @@ jobs: working-directory: build run: | ccache -z + python3 -m venv macosenv + source macosenv/bin/activate python3 -m pip install numpy python3 -m pip install pyyaml cmake -C ../cmake/presets/clang.cmake \ diff --git a/.gitignore b/.gitignore index 4faef4b8db..d96f0b4b5f 100644 --- a/.gitignore +++ b/.gitignore @@ -43,12 +43,12 @@ Thumbs.db #cmake /build* -/CMakeCache.txt -/CMakeFiles/ -/Testing +CMakeCache.txt +CMakeFiles /Makefile -/Testing -/cmake_install.cmake +Testing +Temporary +cmake_install.cmake /lmp out/Debug out/RelWithDebInfo @@ -60,3 +60,4 @@ src/Makefile.package.settings-e /cmake/build/x64-Debug-Clang /install/x64-GUI-MSVC /install +.Rhistory diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f87c92396f..d8b4f0a4f6 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -23,6 +23,7 @@ project(lammps CXX) set(SOVERSION 0) get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) +include(GNUInstallDirs) get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE) get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE) # collect all executables and shared libs in the top level build folder @@ -208,7 +209,7 @@ else() unset(CMAKE_CXX_CLANG_TIDY CACHE) endif() -include(GNUInstallDirs) + file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp) list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES}) @@ -256,6 +257,7 @@ set(STANDARD_PACKAGES DRUDE EFF ELECTRODE + EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX @@ -281,10 +283,11 @@ set(STANDARD_PACKAGES ML-HDNNP ML-IAP ML-PACE + ML-POD ML-QUIP ML-RANN ML-SNAP - ML-POD + ML-UF3 MOFFF MOLECULE MOLFILE @@ -689,7 +692,7 @@ endif() # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### -foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU) +foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() diff --git a/cmake/Modules/OpenCLLoader.cmake b/cmake/Modules/OpenCLLoader.cmake index 4b5c5a1200..411058e0b1 100644 --- a/cmake/Modules/OpenCLLoader.cmake +++ b/cmake/Modules/OpenCLLoader.cmake @@ -1,6 +1,6 @@ message(STATUS "Downloading and building OpenCL loader library") -set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball") -set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" CACHE STRING "MD5 checksum of OpenCL loader tarball") +set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball") +set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball") mark_as_advanced(OPENCL_LOADER_URL) mark_as_advanced(OPENCL_LOADER_MD5) diff --git a/cmake/Modules/Packages/DPD-BASIC.cmake b/cmake/Modules/Packages/DPD-BASIC.cmake new file mode 100644 index 0000000000..b92d4b56a1 --- /dev/null +++ b/cmake/Modules/Packages/DPD-BASIC.cmake @@ -0,0 +1,9 @@ +# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed +if(NOT PKG_KSPACE) + get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR) + list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h) + set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}") + get_target_property(LAMMPS_SOURCES lammps SOURCES) + list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp) + set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}") +endif() diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index e1da77c6d0..3776d18a3e 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -45,8 +45,8 @@ if(DOWNLOAD_KOKKOS) list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}") list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}") include(ExternalProject) - set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball") - set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball") + set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball") + set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" CACHE STRING "MD5 checksum of KOKKOS tarball") mark_as_advanced(KOKKOS_URL) mark_as_advanced(KOKKOS_MD5) GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK) @@ -71,7 +71,7 @@ if(DOWNLOAD_KOKKOS) add_dependencies(LAMMPS::KOKKOSCORE kokkos_build) add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build) elseif(EXTERNAL_KOKKOS) - find_package(Kokkos 4.2.00 REQUIRED CONFIG) + find_package(Kokkos 4.3.01 REQUIRED CONFIG) target_link_libraries(lammps PRIVATE Kokkos::kokkos) else() set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) @@ -139,12 +139,9 @@ if(PKG_KSPACE) message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.") target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS) elseif(FFT_KOKKOS STREQUAL "CUFFT") - find_library(CUFFT_LIBRARY cufft) - if (CUFFT_LIBRARY STREQUAL "CUFFT_LIBRARY-NOTFOUND") - message(FATAL_ERROR "Required cuFFT library not found. Check your environment or set CUFFT_LIBRARY to its location") - endif() + find_package(CUDAToolkit REQUIRED) target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT) - target_link_libraries(lammps PRIVATE ${CUFFT_LIBRARY}) + target_link_libraries(lammps PRIVATE CUDA::cufft) endif() elseif(Kokkos_ENABLE_HIP) if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT"))) diff --git a/cmake/Modules/Packages/ML-IAP.cmake b/cmake/Modules/Packages/ML-IAP.cmake index d6059c44b8..91b772efb5 100644 --- a/cmake/Modules/Packages/ML-IAP.cmake +++ b/cmake/Modules/Packages/ML-IAP.cmake @@ -10,6 +10,14 @@ endif() option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT}) +# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP +set(MLIAP_ENABLE_ACE_DEFAULT OFF) +if(PKG_ML-PACE) + set(MLIAP_ENABLE_ACE_DEFAULT ON) +endif() + +option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT}) + if(MLIAP_ENABLE_PYTHON) find_package(Cythonize REQUIRED) find_package(Python COMPONENTS NumPy REQUIRED) @@ -36,3 +44,10 @@ if(MLIAP_ENABLE_PYTHON) target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON) target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR}) endif() + +if(MLIAP_ENABLE_ACE) + if(NOT PKG_ML-PACE) + message(FATAL_ERROR "Must enable ML-PACE package for including ACE support in ML-IAP") + endif() + target_compile_definitions(lammps PRIVATE -DMLIAP_ACE) +endif() diff --git a/cmake/Modules/Packages/PLUMED.cmake b/cmake/Modules/Packages/PLUMED.cmake index b1a4f3cc72..8312589478 100644 --- a/cmake/Modules/Packages/PLUMED.cmake +++ b/cmake/Modules/Packages/PLUMED.cmake @@ -1,5 +1,9 @@ # Plumed2 support for PLUMED package +# for supporting multiple concurrent plumed2 installations for debugging and testing +set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library") +mark_as_advanced(PLUMED_SUFFIX) + if(BUILD_MPI) set(PLUMED_CONFIG_MPI "--enable-mpi") set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER}) @@ -21,9 +25,11 @@ else() set(PLUMED_CONFIG_OMP "--disable-openmp") endif() -set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz" +# Note: must also adjust check for supported API versions in +# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y +set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz" CACHE STRING "URL for PLUMED tarball") -set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball") +set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball") mark_as_advanced(PLUMED_URL) mark_as_advanced(PLUMED_MD5) @@ -151,15 +157,15 @@ else() file(MAKE_DIRECTORY ${INSTALL_DIR}/include) else() find_package(PkgConfig REQUIRED) - pkg_check_modules(PLUMED REQUIRED plumed) + pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX}) add_library(LAMMPS::PLUMED INTERFACE IMPORTED) if(PLUMED_MODE STREQUAL "STATIC") - include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static) + include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static) elseif(PLUMED_MODE STREQUAL "SHARED") - include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared) + include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared) elseif(PLUMED_MODE STREQUAL "RUNTIME") - set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") - include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime) + set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}") + include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime) endif() set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}") set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}") diff --git a/cmake/packaging/build_linux_tgz.sh b/cmake/packaging/build_linux_tgz.sh index 48e3017f61..ea2fb7fb10 100755 --- a/cmake/packaging/build_linux_tgz.sh +++ b/cmake/packaging/build_linux_tgz.sh @@ -59,12 +59,14 @@ done echo "Set up wrapper script" MYDIR=$(dirname "$0") +cp ${MYDIR}/xdg-open ${DESTDIR}/bin cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin for s in ${DESTDIR}/bin/* do \ EXE=$(basename $s) test ${EXE} = linux_wrapper.sh && continue test ${EXE} = qt.conf && continue + test ${EXE} = xdg-open && continue ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE} done diff --git a/cmake/packaging/linux_wrapper.sh b/cmake/packaging/linux_wrapper.sh index a679030188..b777c09eb1 100755 --- a/cmake/packaging/linux_wrapper.sh +++ b/cmake/packaging/linux_wrapper.sh @@ -4,15 +4,17 @@ # reset locale to avoid problems with decimal numbers export LC_ALL=C -BASEDIR=$(dirname "$0") -EXENAME=$(basename "$0") +BASEDIR="$(dirname "$0")" +EXENAME="$(basename "$0")" + +PATH="${BASEDIR}/bin:${PATH}" # append to LD_LIBRARY_PATH to prefer local (newer) libs -LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib +LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib" # set some environment variables for LAMMPS etc. -LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials -MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files -export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY +LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials" +MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files" +export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH exec "${BASEDIR}/bin/${EXENAME}" "$@" diff --git a/cmake/packaging/xdg-open b/cmake/packaging/xdg-open new file mode 100755 index 0000000000..d282bb3d11 --- /dev/null +++ b/cmake/packaging/xdg-open @@ -0,0 +1,1074 @@ +#!/usr/bin/sh +#--------------------------------------------- +# xdg-open +# +# Utility script to open a URL in the registered default application. +# +# Refer to the usage() function below for usage. +# +# Copyright 2009-2010, Fathi Boudra +# Copyright 2009-2016, Rex Dieter +# Copyright 2006, Kevin Krammer +# Copyright 2006, Jeremy White +# +# LICENSE: +# +# Permission is hereby granted, free of charge, to any person obtaining a +# copy of this software and associated documentation files (the "Software"), +# to deal in the Software without restriction, including without limitation +# the rights to use, copy, modify, merge, publish, distribute, sublicense, +# and/or sell copies of the Software, and to permit persons to whom the +# Software is furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included +# in all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR +# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, +# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR +# OTHER DEALINGS IN THE SOFTWARE. +# +#--------------------------------------------- + +NEW_LIBRARY_PATH="/usr/local/lib64" +for s in $(echo $LD_LIBRARY_PATH | sed -e 's/:/ /g') +do \ + echo $s | grep LAMMPS_GUI > /dev/null || NEW_LIBRARY_PATH="${NEW_LIBRARY_PATH}:$s" +done +export LD_LIBRARY_PATH="${NEW_LIBRARY_PATH}" +unset NEW_LIBRARY_PATH + +manualpage() +{ +cat << _MANUALPAGE +Name + + xdg-open - opens a file or URL in the user's preferred + application + +Synopsis + + xdg-open { file | URL } + + xdg-open { --help | --manual | --version } + +Description + + xdg-open opens a file or URL in the user's preferred + application. If a URL is provided the URL will be opened in the + user's preferred web browser. If a file is provided the file + will be opened in the preferred application for files of that + type. xdg-open supports file, ftp, http and https URLs. + + xdg-open is for use inside a desktop session only. It is not + recommended to use xdg-open as root. + +Options + + --help + Show command synopsis. + + --manual + Show this manual page. + + --version + Show the xdg-utils version information. + +Exit Codes + + An exit code of 0 indicates success while a non-zero exit code + indicates failure. The following failure codes can be returned: + + 1 + Error in command line syntax. + + 2 + One of the files passed on the command line did not + exist. + + 3 + A required tool could not be found. + + 4 + The action failed. + +See Also + + xdg-mime(1), xdg-settings(1), MIME applications associations + specification + +Examples + +xdg-open 'http://www.freedesktop.org/' + + Opens the freedesktop.org website in the user's default + browser. + +xdg-open /tmp/foobar.png + + Opens the PNG image file /tmp/foobar.png in the user's default + image viewing application. +_MANUALPAGE +} + +usage() +{ +cat << _USAGE + xdg-open - opens a file or URL in the user's preferred + application + +Synopsis + + xdg-open { file | URL } + + xdg-open { --help | --manual | --version } + +_USAGE +} + +#@xdg-utils-common@ + +#---------------------------------------------------------------------------- +# Common utility functions included in all XDG wrapper scripts +#---------------------------------------------------------------------------- + +DEBUG() +{ + [ -z "${XDG_UTILS_DEBUG_LEVEL}" ] && return 0; + [ ${XDG_UTILS_DEBUG_LEVEL} -lt $1 ] && return 0; + shift + echo "$@" >&2 +} + +# This handles backslashes but not quote marks. +first_word() +{ + read first rest + echo "$first" +} + +#------------------------------------------------------------- +# map a binary to a .desktop file +binary_to_desktop_file() +{ + search="${XDG_DATA_HOME:-$HOME/.local/share}:${XDG_DATA_DIRS:-/usr/local/share:/usr/share}" + binary="`which "$1"`" + binary="`readlink -f "$binary"`" + base="`basename "$binary"`" + IFS=: + for dir in $search; do + unset IFS + [ "$dir" ] || continue + [ -d "$dir/applications" ] || [ -d "$dir/applnk" ] || continue + for file in "$dir"/applications/*.desktop "$dir"/applications/*/*.desktop "$dir"/applnk/*.desktop "$dir"/applnk/*/*.desktop; do + [ -r "$file" ] || continue + # Check to make sure it's worth the processing. + grep -q "^Exec.*$base" "$file" || continue + # Make sure it's a visible desktop file (e.g. not "preferred-web-browser.desktop"). + grep -Eq "^(NoDisplay|Hidden)=true" "$file" && continue + command="`grep -E "^Exec(\[[^]=]*])?=" "$file" | cut -d= -f 2- | first_word`" + command="`which "$command"`" + if [ x"`readlink -f "$command"`" = x"$binary" ]; then + # Fix any double slashes that got added path composition + echo "$file" | sed -e 's,//*,/,g' + return + fi + done + done +} + +#------------------------------------------------------------- +# map a .desktop file to a binary +desktop_file_to_binary() +{ + search="${XDG_DATA_HOME:-$HOME/.local/share}:${XDG_DATA_DIRS:-/usr/local/share:/usr/share}" + desktop="`basename "$1"`" + IFS=: + for dir in $search; do + unset IFS + [ "$dir" ] && [ -d "$dir/applications" ] || [ -d "$dir/applnk" ] || continue + # Check if desktop file contains - + if [ "${desktop#*-}" != "$desktop" ]; then + vendor=${desktop%-*} + app=${desktop#*-} + if [ -r $dir/applications/$vendor/$app ]; then + file_path=$dir/applications/$vendor/$app + elif [ -r $dir/applnk/$vendor/$app ]; then + file_path=$dir/applnk/$vendor/$app + fi + fi + if test -z "$file_path" ; then + for indir in "$dir"/applications/ "$dir"/applications/*/ "$dir"/applnk/ "$dir"/applnk/*/; do + file="$indir/$desktop" + if [ -r "$file" ]; then + file_path=$file + break + fi + done + fi + if [ -r "$file_path" ]; then + # Remove any arguments (%F, %f, %U, %u, etc.). + command="`grep -E "^Exec(\[[^]=]*])?=" "$file_path" | cut -d= -f 2- | first_word`" + command="`which "$command"`" + readlink -f "$command" + return + fi + done +} + +#------------------------------------------------------------- +# Exit script on successfully completing the desired operation + +exit_success() +{ + if [ $# -gt 0 ]; then + echo "$@" + echo + fi + + exit 0 +} + + +#----------------------------------------- +# Exit script on malformed arguments, not enough arguments +# or missing required option. +# prints usage information + +exit_failure_syntax() +{ + if [ $# -gt 0 ]; then + echo "xdg-open: $@" >&2 + echo "Try 'xdg-open --help' for more information." >&2 + else + usage + echo "Use 'man xdg-open' or 'xdg-open --manual' for additional info." + fi + + exit 1 +} + +#------------------------------------------------------------- +# Exit script on missing file specified on command line + +exit_failure_file_missing() +{ + if [ $# -gt 0 ]; then + echo "xdg-open: $@" >&2 + fi + + exit 2 +} + +#------------------------------------------------------------- +# Exit script on failure to locate necessary tool applications + +exit_failure_operation_impossible() +{ + if [ $# -gt 0 ]; then + echo "xdg-open: $@" >&2 + fi + + exit 3 +} + +#------------------------------------------------------------- +# Exit script on failure returned by a tool application + +exit_failure_operation_failed() +{ + if [ $# -gt 0 ]; then + echo "xdg-open: $@" >&2 + fi + + exit 4 +} + +#------------------------------------------------------------ +# Exit script on insufficient permission to read a specified file + +exit_failure_file_permission_read() +{ + if [ $# -gt 0 ]; then + echo "xdg-open: $@" >&2 + fi + + exit 5 +} + +#------------------------------------------------------------ +# Exit script on insufficient permission to write a specified file + +exit_failure_file_permission_write() +{ + if [ $# -gt 0 ]; then + echo "xdg-open: $@" >&2 + fi + + exit 6 +} + +check_input_file() +{ + if [ ! -e "$1" ]; then + exit_failure_file_missing "file '$1' does not exist" + fi + if [ ! -r "$1" ]; then + exit_failure_file_permission_read "no permission to read file '$1'" + fi +} + +check_vendor_prefix() +{ + file_label="$2" + [ -n "$file_label" ] || file_label="filename" + file=`basename "$1"` + case "$file" in + [[:alpha:]]*-*) + return + ;; + esac + + echo "xdg-open: $file_label '$file' does not have a proper vendor prefix" >&2 + echo 'A vendor prefix consists of alpha characters ([a-zA-Z]) and is terminated' >&2 + echo 'with a dash ("-"). An example '"$file_label"' is '"'example-$file'" >&2 + echo "Use --novendor to override or 'xdg-open --manual' for additional info." >&2 + exit 1 +} + +check_output_file() +{ + # if the file exists, check if it is writeable + # if it does not exists, check if we are allowed to write on the directory + if [ -e "$1" ]; then + if [ ! -w "$1" ]; then + exit_failure_file_permission_write "no permission to write to file '$1'" + fi + else + DIR=`dirname "$1"` + if [ ! -w "$DIR" ] || [ ! -x "$DIR" ]; then + exit_failure_file_permission_write "no permission to create file '$1'" + fi + fi +} + +#---------------------------------------- +# Checks for shared commands, e.g. --help + +check_common_commands() +{ + while [ $# -gt 0 ] ; do + parm="$1" + shift + + case "$parm" in + --help) + usage + echo "Use 'man xdg-open' or 'xdg-open --manual' for additional info." + exit_success + ;; + + --manual) + manualpage + exit_success + ;; + + --version) + echo "xdg-open 1.1.3+" + exit_success + ;; + esac + done +} + +check_common_commands "$@" + +[ -z "${XDG_UTILS_DEBUG_LEVEL}" ] && unset XDG_UTILS_DEBUG_LEVEL; +if [ ${XDG_UTILS_DEBUG_LEVEL-0} -lt 1 ]; then + # Be silent + xdg_redirect_output=" > /dev/null 2> /dev/null" +else + # All output to stderr + xdg_redirect_output=" >&2" +fi + +#-------------------------------------- +# Checks for known desktop environments +# set variable DE to the desktop environments name, lowercase + +detectDE() +{ + # see https://bugs.freedesktop.org/show_bug.cgi?id=34164 + unset GREP_OPTIONS + + if [ -n "${XDG_CURRENT_DESKTOP}" ]; then + case "${XDG_CURRENT_DESKTOP}" in + # only recently added to menu-spec, pre-spec X- still in use + Cinnamon|X-Cinnamon) + DE=cinnamon; + ;; + ENLIGHTENMENT) + DE=enlightenment; + ;; + # GNOME, GNOME-Classic:GNOME, or GNOME-Flashback:GNOME + GNOME*) + DE=gnome; + ;; + KDE) + DE=kde; + ;; + DEEPIN|Deepin|deepin) + DE=deepin; + ;; + LXDE) + DE=lxde; + ;; + LXQt) + DE=lxqt; + ;; + MATE) + DE=mate; + ;; + XFCE) + DE=xfce + ;; + X-Generic) + DE=generic + ;; + esac + fi + + if [ x"$DE" = x"" ]; then + # classic fallbacks + if [ x"$KDE_FULL_SESSION" != x"" ]; then DE=kde; + elif [ x"$GNOME_DESKTOP_SESSION_ID" != x"" ]; then DE=gnome; + elif [ x"$MATE_DESKTOP_SESSION_ID" != x"" ]; then DE=mate; + elif `dbus-send --print-reply --dest=org.freedesktop.DBus /org/freedesktop/DBus org.freedesktop.DBus.GetNameOwner string:org.gnome.SessionManager > /dev/null 2>&1` ; then DE=gnome; + elif xprop -root _DT_SAVE_MODE 2> /dev/null | grep ' = \"xfce4\"$' >/dev/null 2>&1; then DE=xfce; + elif xprop -root 2> /dev/null | grep -i '^xfce_desktop_window' >/dev/null 2>&1; then DE=xfce + elif echo $DESKTOP | grep -q '^Enlightenment'; then DE=enlightenment; + elif [ x"$LXQT_SESSION_CONFIG" != x"" ]; then DE=lxqt; + fi + fi + + if [ x"$DE" = x"" ]; then + # fallback to checking $DESKTOP_SESSION + case "$DESKTOP_SESSION" in + gnome) + DE=gnome; + ;; + LXDE|Lubuntu) + DE=lxde; + ;; + MATE) + DE=mate; + ;; + xfce|xfce4|'Xfce Session') + DE=xfce; + ;; + esac + fi + + if [ x"$DE" = x"" ]; then + # fallback to uname output for other platforms + case "$(uname 2>/dev/null)" in + CYGWIN*) + DE=cygwin; + ;; + Darwin) + DE=darwin; + ;; + esac + fi + + if [ x"$DE" = x"gnome" ]; then + # gnome-default-applications-properties is only available in GNOME 2.x + # but not in GNOME 3.x + which gnome-default-applications-properties > /dev/null 2>&1 || DE="gnome3" + fi + + if [ -f "$XDG_RUNTIME_DIR/flatpak-info" ]; then + DE="flatpak" + fi +} + +#---------------------------------------------------------------------------- +# kfmclient exec/openURL can give bogus exit value in KDE <= 3.5.4 +# It also always returns 1 in KDE 3.4 and earlier +# Simply return 0 in such case + +kfmclient_fix_exit_code() +{ + version=`LC_ALL=C.UTF-8 kde-config --version 2>/dev/null | grep '^KDE'` + major=`echo $version | sed 's/KDE.*: \([0-9]\).*/\1/'` + minor=`echo $version | sed 's/KDE.*: [0-9]*\.\([0-9]\).*/\1/'` + release=`echo $version | sed 's/KDE.*: [0-9]*\.[0-9]*\.\([0-9]\).*/\1/'` + test "$major" -gt 3 && return $1 + test "$minor" -gt 5 && return $1 + test "$release" -gt 4 && return $1 + return 0 +} + +#---------------------------------------------------------------------------- +# Returns true if there is a graphical display attached. + +has_display() +{ + if [ -n "$DISPLAY" ] || [ -n "$WAYLAND_DISPLAY" ]; then + return 0 + else + return 1 + fi +} + +# This handles backslashes but not quote marks. +last_word() +{ + read first rest + echo "$rest" +} + +# Get the value of a key in a desktop file's Desktop Entry group. +# Example: Use get_key foo.desktop Exec +# to get the values of the Exec= key for the Desktop Entry group. +get_key() +{ + local file="${1}" + local key="${2}" + local desktop_entry="" + + IFS_="${IFS}" + IFS="" + while read line + do + case "$line" in + "[Desktop Entry]") + desktop_entry="y" + ;; + # Reset match flag for other groups + "["*) + desktop_entry="" + ;; + "${key}="*) + # Only match Desktop Entry group + if [ -n "${desktop_entry}" ] + then + echo "${line}" | cut -d= -f 2- + fi + esac + done < "${file}" + IFS="${IFS_}" +} + +# Returns true if argument is a file:// URL or path +is_file_url_or_path() +{ + if echo "$1" | grep -q '^file://' \ + || ! echo "$1" | grep -Eq '^[[:alpha:]][[:alpha:][:digit:]+\.\-]*:'; then + return 0 + else + return 1 + fi +} + +# If argument is a file URL, convert it to a (percent-decoded) path. +# If not, leave it as it is. +file_url_to_path() +{ + local file="$1" + if echo "$file" | grep -q '^file://\(localhost\)\?/'; then + file=${file#file://localhost} + file=${file#file://} + file=${file%%#*} + file=$(echo "$file" | sed -r 's/\?.*$//') + local printf=printf + if [ -x /usr/bin/printf ]; then + printf=/usr/bin/printf + fi + file=$($printf "$(echo "$file" | sed -e 's@%\([a-f0-9A-F]\{2\}\)@\\x\1@g')") + fi + echo "$file" +} + +open_cygwin() +{ + cygstart "$1" + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_darwin() +{ + open "$1" + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_kde() +{ + if [ -n "${KDE_SESSION_VERSION}" ]; then + case "${KDE_SESSION_VERSION}" in + 4) + kde-open "$1" + ;; + 5) + kde-open${KDE_SESSION_VERSION} "$1" + ;; + esac + else + kfmclient exec "$1" + kfmclient_fix_exit_code $? + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_deepin() +{ + if dde-open -version >/dev/null 2>&1; then + dde-open "$1" + else + open_generic "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_gnome3() +{ + if gio help open 2>/dev/null 1>&2; then + gio open "$1" + elif gvfs-open --help 2>/dev/null 1>&2; then + gvfs-open "$1" + else + open_generic "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_gnome() +{ + if gio help open 2>/dev/null 1>&2; then + gio open "$1" + elif gvfs-open --help 2>/dev/null 1>&2; then + gvfs-open "$1" + elif gnome-open --help 2>/dev/null 1>&2; then + gnome-open "$1" + else + open_generic "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_mate() +{ + if gio help open 2>/dev/null 1>&2; then + gio open "$1" + elif gvfs-open --help 2>/dev/null 1>&2; then + gvfs-open "$1" + elif mate-open --help 2>/dev/null 1>&2; then + mate-open "$1" + else + open_generic "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_xfce() +{ + if exo-open --help 2>/dev/null 1>&2; then + exo-open "$1" + elif gio help open 2>/dev/null 1>&2; then + gio open "$1" + elif gvfs-open --help 2>/dev/null 1>&2; then + gvfs-open "$1" + else + open_generic "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_enlightenment() +{ + if enlightenment_open --help 2>/dev/null 1>&2; then + enlightenment_open "$1" + else + open_generic "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_flatpak() +{ + gdbus call --session \ + --dest org.freedesktop.portal.Desktop \ + --object-path /org/freedesktop/portal/desktop \ + --method org.freedesktop.portal.OpenURI.OpenURI \ + "" "$1" {} + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +#----------------------------------------- +# Recursively search .desktop file + +search_desktop_file() +{ + local default="$1" + local dir="$2" + local target="$3" + + local file="" + # look for both vendor-app.desktop, vendor/app.desktop + if [ -r "$dir/$default" ]; then + file="$dir/$default" + elif [ -r "$dir/`echo $default | sed -e 's|-|/|'`" ]; then + file="$dir/`echo $default | sed -e 's|-|/|'`" + fi + + if [ -r "$file" ] ; then + command="$(get_key "${file}" "Exec" | first_word)" + command_exec=`which $command 2>/dev/null` + icon="$(get_key "${file}" "Icon")" + # FIXME: Actually LC_MESSAGES should be used as described in + # http://standards.freedesktop.org/desktop-entry-spec/latest/ar01s04.html + localised_name="$(get_key "${file}" "Name")" + set -- $(get_key "${file}" "Exec" | last_word) + # We need to replace any occurrence of "%f", "%F" and + # the like by the target file. We examine each + # argument and append the modified argument to the + # end then shift. + local args=$# + local replaced=0 + while [ $args -gt 0 ]; do + case $1 in + %[c]) + replaced=1 + arg="${localised_name}" + shift + set -- "$@" "$arg" + ;; + %[fFuU]) + replaced=1 + arg="$target" + shift + set -- "$@" "$arg" + ;; + %[i]) + replaced=1 + shift + set -- "$@" "--icon" "$icon" + ;; + *) + arg="$1" + shift + set -- "$@" "$arg" + ;; + esac + args=$(( $args - 1 )) + done + [ $replaced -eq 1 ] || set -- "$@" "$target" + "$command_exec" "$@" + + if [ $? -eq 0 ]; then + exit_success + fi + fi + + for d in "$dir/"*/; do + [ -d "$d" ] && search_desktop_file "$default" "$d" "$target" + done +} + + +open_generic_xdg_mime() +{ + filetype="$2" + default=`xdg-mime query default "$filetype"` + if [ -n "$default" ] ; then + xdg_user_dir="$XDG_DATA_HOME" + [ -n "$xdg_user_dir" ] || xdg_user_dir="$HOME/.local/share" + + xdg_system_dirs="$XDG_DATA_DIRS" + [ -n "$xdg_system_dirs" ] || xdg_system_dirs=/usr/local/share/:/usr/share/ + +DEBUG 3 "$xdg_user_dir:$xdg_system_dirs" + for x in `echo "$xdg_user_dir:$xdg_system_dirs" | sed 's/:/ /g'`; do + search_desktop_file "$default" "$x/applications/" "$1" + done + fi +} + +open_generic_xdg_file_mime() +{ + filetype=`xdg-mime query filetype "$1" | sed "s/;.*//"` + open_generic_xdg_mime "$1" "$filetype" +} + +open_generic_xdg_x_scheme_handler() +{ + scheme="`echo $1 | sed -n 's/\(^[[:alnum:]+\.-]*\):.*$/\1/p'`" + if [ -n $scheme ]; then + filetype="x-scheme-handler/$scheme" + open_generic_xdg_mime "$1" "$filetype" + fi +} + +has_single_argument() +{ + test $# = 1 +} + +open_envvar() +{ + local oldifs="$IFS" + local browser browser_with_arg + + IFS=":" + for browser in $BROWSER; do + IFS="$oldifs" + + if [ -z "$browser" ]; then + continue + fi + + if echo "$browser" | grep -q %s; then + # Avoid argument injection. + # See https://bugs.freedesktop.org/show_bug.cgi?id=103807 + # URIs don't have IFS characters spaces anyway. + has_single_argument $1 && $(printf "$browser" "$1") + else + $browser "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + fi + done +} + +open_generic() +{ + if is_file_url_or_path "$1"; then + local file="$(file_url_to_path "$1")" + + check_input_file "$file" + + if has_display; then + filetype=`xdg-mime query filetype "$file" | sed "s/;.*//"` + open_generic_xdg_mime "$file" "$filetype" + fi + + if which run-mailcap 2>/dev/null 1>&2; then + run-mailcap --action=view "$file" + if [ $? -eq 0 ]; then + exit_success + fi + fi + + if has_display && mimeopen -v 2>/dev/null 1>&2; then + mimeopen -L -n "$file" + if [ $? -eq 0 ]; then + exit_success + fi + fi + fi + + if has_display; then + open_generic_xdg_x_scheme_handler "$1" + fi + + if [ -n "$BROWSER" ]; then + open_envvar "$1" + fi + + # if BROWSER variable is not set, check some well known browsers instead + if [ x"$BROWSER" = x"" ]; then + BROWSER=www-browser:links2:elinks:links:lynx:w3m + if has_display; then + BROWSER=x-www-browser:firefox:iceweasel:seamonkey:mozilla:epiphany:konqueror:chromium:chromium-browser:google-chrome:$BROWSER + fi + fi + + open_envvar "$1" + + exit_failure_operation_impossible "no method available for opening '$1'" +} + +open_lxde() +{ + + # pcmanfm only knows how to handle file:// urls and filepaths, it seems. + if pcmanfm --help >/dev/null 2>&1 && is_file_url_or_path "$1"; then + local file="$(file_url_to_path "$1")" + + # handle relative paths + if ! echo "$file" | grep -q ^/; then + file="$(pwd)/$file" + fi + + pcmanfm "$file" + else + open_generic "$1" + fi + + if [ $? -eq 0 ]; then + exit_success + else + exit_failure_operation_failed + fi +} + +open_lxqt() +{ + open_generic "$1" +} + +[ x"$1" != x"" ] || exit_failure_syntax + +url= +while [ $# -gt 0 ] ; do + parm="$1" + shift + + case "$parm" in + -*) + exit_failure_syntax "unexpected option '$parm'" + ;; + + *) + if [ -n "$url" ] ; then + exit_failure_syntax "unexpected argument '$parm'" + fi + url="$parm" + ;; + esac +done + +if [ -z "${url}" ] ; then + exit_failure_syntax "file or URL argument missing" +fi + +detectDE + +if [ x"$DE" = x"" ]; then + DE=generic +fi + +DEBUG 2 "Selected DE $DE" + +# sanitize BROWSER (avoid calling ourselves in particular) +case "${BROWSER}" in + *:"xdg-open"|"xdg-open":*) + BROWSER=$(echo $BROWSER | sed -e 's|:xdg-open||g' -e 's|xdg-open:||g') + ;; + "xdg-open") + BROWSER= + ;; +esac + +case "$DE" in + kde) + open_kde "$url" + ;; + + deepin) + open_deepin "$url" + ;; + + gnome3|cinnamon) + open_gnome3 "$url" + ;; + + gnome) + open_gnome "$url" + ;; + + mate) + open_mate "$url" + ;; + + xfce) + open_xfce "$url" + ;; + + lxde) + open_lxde "$url" + ;; + + lxqt) + open_lxqt "$url" + ;; + + enlightenment) + open_enlightenment "$url" + ;; + + cygwin) + open_cygwin "$url" + ;; + + darwin) + open_darwin "$url" + ;; + + flatpak) + open_flatpak "$url" + ;; + + generic) + open_generic "$url" + ;; + + *) + exit_failure_operation_impossible "no method available for opening '$url'" + ;; +esac diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index e078879f70..1ed5c0acd7 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -26,8 +26,9 @@ set(ALL_PACKAGES DPD-REACT DPD-SMOOTH DRUDE - ELECTRODE EFF + ELECTRODE + EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX @@ -60,6 +61,7 @@ set(ALL_PACKAGES ML-QUIP ML-RANN ML-SNAP + ML-UF3 MOFFF MOLECULE MOLFILE diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 3f44a863f7..c4345470e5 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -28,8 +28,9 @@ set(ALL_PACKAGES DPD-REACT DPD-SMOOTH DRUDE - ELECTRODE EFF + ELECTRODE + EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX @@ -62,6 +63,7 @@ set(ALL_PACKAGES ML-QUIP ML-RANN ML-SNAP + ML-UF3 MOFFF MOLECULE MOLFILE diff --git a/cmake/presets/kokkos-hip.cmake b/cmake/presets/kokkos-hip.cmake index ffc259a225..38bf27092f 100644 --- a/cmake/presets/kokkos-hip.cmake +++ b/cmake/presets/kokkos-hip.cmake @@ -13,7 +13,7 @@ set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE) set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE) # If KSPACE is also enabled, use CUFFT for FFTs -set(FFT_KOKKOS "HIPFFT" CACHE STRING FORCE) +set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE) # hide deprecation warnings temporarily for stable release set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index f3565668b2..100ce13632 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -22,8 +22,9 @@ set(WIN_PACKAGES DPD-REACT DPD-SMOOTH DRUDE - ELECTRODE EFF + ELECTRODE + EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX @@ -32,7 +33,6 @@ set(WIN_PACKAGES FEP GPU GRANULAR - INTEL INTERLAYER KSPACE LEPTON @@ -50,6 +50,7 @@ set(WIN_PACKAGES ML-POD ML-RANN ML-SNAP + ML-UF3 MOFFF MOLECULE MOLFILE diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 2356e24764..d01642f94d 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -26,6 +26,7 @@ set(ALL_PACKAGES DRUDE EFF ELECTRODE + EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX @@ -45,6 +46,7 @@ set(ALL_PACKAGES ML-IAP ML-POD ML-SNAP + ML-UF3 MOFFF MOLECULE OPENMP diff --git a/cmake/presets/windows.cmake b/cmake/presets/windows.cmake index 9655134e7f..403d40efa4 100644 --- a/cmake/presets/windows.cmake +++ b/cmake/presets/windows.cmake @@ -22,6 +22,7 @@ set(WIN_PACKAGES DRUDE EFF ELECTRODE + EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX @@ -42,6 +43,7 @@ set(WIN_PACKAGES ML-IAP ML-POD ML-SNAP + ML-UF3 MOFFF MOLECULE MOLFILE @@ -50,8 +52,8 @@ set(WIN_PACKAGES ORIENT PERI PHONON - POEMS PLUGIN + POEMS PTM QEQ QTB diff --git a/doc/lammps.1 b/doc/lammps.1 index 0c7c9a0354..a66083ed07 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,7 +1,7 @@ -.TH LAMMPS "1" "7 February 2024" "2024-02-07" +.TH LAMMPS "1" "27 June 2024" "2024-06-27" .SH NAME .B LAMMPS -\- Molecular Dynamics Simulator. Version 7 February 2024 +\- Molecular Dynamics Simulator. Version 27 June 2024 .SH SYNOPSIS .B lmp @@ -297,7 +297,7 @@ the chapter on errors in the manual gives some additional information about error messages, if possible. .SH COPYRIGHT -© 2003--2022 Sandia Corporation +© 2003--2024 Sandia Corporation This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 1f643a9d14..f66238c3c9 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -533,9 +533,6 @@ They must be specified in uppercase. * - A64FX - HOST - ARMv8.2 with SVE Support - * - WSM - - HOST - - Intel Westmere CPU (SSE 4.2) * - SNB - HOST - Intel Sandy/Ivy Bridge CPU (AVX 1) @@ -566,18 +563,15 @@ They must be specified in uppercase. * - KNL - HOST - Intel Knights Landing Xeon Phi - * - BGQ - - HOST - - IBM Blue Gene/Q CPU - * - POWER7 - - HOST - - IBM POWER7 CPU * - POWER8 - HOST - IBM POWER8 CPU * - POWER9 - HOST - IBM POWER9 CPU + * - RISCV_SG2042 + - HOST + - SG2042 (RISC-V) CPU * - KEPLER30 - GPU - NVIDIA Kepler generation CC 3.0 GPU @@ -666,7 +660,7 @@ They must be specified in uppercase. - GPU - Intel GPU Ponte Vecchio -This list was last updated for version 4.2 of the Kokkos library. +This list was last updated for version 4.3.0 of the Kokkos library. .. tabs:: diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index ef36b6b7c4..73235cf3c6 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -27,7 +27,7 @@ OPT. * :doc:`none ` * :doc:`zero ` - * :doc:`hybrid ` + * :doc:`hybrid (k) ` * * * @@ -89,6 +89,7 @@ OPT. * :doc:`cosine/shift (o) ` * :doc:`cosine/shift/exp (o) ` * :doc:`cosine/squared (o) ` + * :doc:`cosine/squared/restricted (o) ` * :doc:`cross ` * :doc:`dipole (o) ` * :doc:`fourier (o) ` @@ -127,6 +128,7 @@ OPT. * :doc:`charmmfsw (k) ` * :doc:`class2 (ko) ` * :doc:`cosine/shift/exp (o) ` + * :doc:`cosine/squared/restricted ` * :doc:`fourier (io) ` * :doc:`harmonic (iko) ` * :doc:`helix (o) ` diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 0352ad5374..2e8f291c77 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -108,6 +108,10 @@ KOKKOS, o = OPENMP, t = OPT. * :doc:`pe/mol/tally ` * :doc:`pe/tally ` * :doc:`plasticity/atom ` + * :doc:`pod/atom ` + * :doc:`podd/atom ` + * :doc:`pod/local ` + * :doc:`pod/global ` * :doc:`pressure ` * :doc:`pressure/alchemy ` * :doc:`pressure/uef ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 9bbe216dec..f83f2539a3 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -25,16 +25,16 @@ OPT. * :doc:`none ` * :doc:`zero ` - * :doc:`hybrid (k) ` - * :doc:`hybrid/overlay (k) ` - * :doc:`hybrid/scaled ` + * :doc:`hybrid (ko) ` + * :doc:`hybrid/molecular (o) ` + * :doc:`hybrid/overlay (ko) ` + * :doc:`hybrid/scaled (o) ` * :doc:`kim ` * :doc:`list ` * :doc:`tracker ` * * * - * * :doc:`adp (ko) ` * :doc:`agni (o) ` * :doc:`aip/water/2dm (t) ` @@ -94,9 +94,10 @@ OPT. * :doc:`coul/wolf (ko) ` * :doc:`coul/wolf/cs ` * :doc:`dpd (giko) ` - * :doc:`dpd/fdt ` + * :doc:`dpd/coul/slater/long (g) ` * :doc:`dpd/ext (ko) ` * :doc:`dpd/ext/tstat (ko) ` + * :doc:`dpd/fdt ` * :doc:`dpd/fdt/energy (k) ` * :doc:`dpd/tstat (gko) ` * :doc:`dsmc ` @@ -245,7 +246,8 @@ OPT. * :doc:`oxrna2/coaxstk ` * :doc:`pace (k) ` * :doc:`pace/extrapolation (k) ` - * :doc:`pod ` + * :doc:`pedone (o) ` + * :doc:`pod (k) ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` @@ -268,7 +270,7 @@ OPT. * :doc:`smd/ulsph ` * :doc:`smtbq ` * :doc:`snap (ik) ` - * :doc:`soft (go) ` + * :doc:`soft (gko) ` * :doc:`sph/heatconduction (g) ` * :doc:`sph/idealgas ` * :doc:`sph/lj (g) ` @@ -302,6 +304,7 @@ OPT. * :doc:`tip4p/long/soft (o) ` * :doc:`tri/lj ` * :doc:`ufm (got) ` + * :doc:`uf3 (k) ` * :doc:`vashishta (gko) ` * :doc:`vashishta/table (o) ` * :doc:`wf/cut ` diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 0ade07af64..4955bc6f0b 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -148,6 +148,14 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS and the :ref:`GPU package ` are maintained and allow running LAMMPS with GPU acceleration. +i-PI tool +--------- + +.. versionchanged:: 27June2024 + +The i-PI tool has been removed from the LAMMPS distribution. Instead, +instructions to install i-PI from PyPI via pip are provided. + restart2data tool ----------------- diff --git a/doc/src/Developer_updating.rst b/doc/src/Developer_updating.rst index cd61eaa5a1..83491ac095 100644 --- a/doc/src/Developer_updating.rst +++ b/doc/src/Developer_updating.rst @@ -18,6 +18,7 @@ Available topics in mostly chronological order are: - `Setting flags in the constructor`_ - `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_ - `Use ev_init() to initialize variables derived from eflag and vflag`_ +- `Use utils::count_words() functions instead of atom->count_words()`_ - `Use utils::numeric() functions instead of force->numeric()`_ - `Use utils::open_potential() function to open potential files`_ - `Use symbolic Atom and AtomVec constants instead of numerical values`_ @@ -130,6 +131,41 @@ Not applying this change will not cause a compilation error, but can lead to inconsistent behavior and incorrect tallying of energy or virial. +Use utils::count_words() functions instead of atom->count_words() +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 2Jun2020 + +The "count_words()" functions for parsing text have been moved from the +Atom class to the :doc:`utils namespace `. The +"count_words()" function in "utils" uses the Tokenizer class internally +to split a line into words and count them, thus it will not modify the +argument string as the function in the Atoms class did and thus had a +variant using a copy buffer. Unlike the old version, the new version +does not remove comments. For that you can use the +:cpp:func:`utils::trim_comment() function +` as shown in the example below. + +Old: + +.. code-block:: c++ + + nwords = atom->count_words(line); + int nwords = atom->count_words(buf); + +New: + +.. code-block:: c++ + + nwords = utils::count_words(line); + int nwords = utils::count_words(utils::trim_comment(buf)); + +.. seealso:: + + :cpp:func:`utils::count_words() `, + :cpp:func:`utils::trim_comments() ` + + Use utils::numeric() functions instead of force->numeric() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -137,11 +173,12 @@ Use utils::numeric() functions instead of force->numeric() The "numeric()" conversion functions (including "inumeric()", "bnumeric()", and "tnumeric()") have been moved from the Force class to -the utils namespace. Also they take an additional argument that selects -whether the ``Error::all()`` or ``Error::one()`` function should be -called in case of an error. The former should be used when *all* MPI -processes call the conversion function and the latter *must* be used -when they are called from only one or a subset of the MPI processes. +the :doc:`utils namespace `. Also they take an +additional argument that selects whether the ``Error::all()`` or +``Error::one()`` function should be called in case of an error. The +former should be used when *all* MPI processes call the conversion +function and the latter *must* be used when they are called from only +one or a subset of the MPI processes. Old: diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 625ce15202..2923e5b29c 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -211,6 +211,9 @@ Argument processing .. doxygenfunction:: bounds :project: progguide +.. doxygenfunction:: bounds_typelabel + :project: progguide + .. doxygenfunction:: expand_args :project: progguide @@ -635,10 +638,10 @@ Tohoku University (under MIT license) ---------- -.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) +.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort) :project: progguide -.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) +.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort) :project: progguide --------------------------- diff --git a/doc/src/Developer_write_pair.rst b/doc/src/Developer_write_pair.rst index d70f8ec50b..c286b9e1dd 100644 --- a/doc/src/Developer_write_pair.rst +++ b/doc/src/Developer_write_pair.rst @@ -50,6 +50,30 @@ We are looking at the following cases: - `Case 3: a potential requiring communication`_ - `Case 4: potentials without a compute() function`_ +Package and build system considerations +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +In general, new pair styles should be added to the :ref:`EXTRA-PAIR +package ` unless they are an accelerated pair style and +then they should be added to the corresponding accelerator package +(:ref:`GPU `, :ref:`INTEL `, :ref:`KOKKOS +`, :ref:`OPENMP `, :ref:`OPT `). If +you feel that your contribution should be added to a different package, +please consult with the LAMMPS developers first. + +The contributed code needs to support the :doc:`traditional GNU make +build process ` **and** the :doc:`CMake build process +`. For the GNU make process and if the package has an +``Install.sh`` file, most likely that file needs to be updated to +correctly copy the sources when installing the package and properly +delete them when uninstalling. This is particularly important when +added a new pair style that is a derived class from an existing pair +style in a package, so that its installation depends on the the +installation status of the package of the derived class. For the CMake +process, it is sometimes necessary to make changes to the package +specific CMake scripting in ``cmake/Modules/Packages``. + + ---- Case 1: a pairwise additive model diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index b63d80a9ae..c798784106 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -13,15 +13,44 @@ discussions of such cases. Unknown identifier in data file ------------------------------- -This error happens when LAMMPS encounters a line of text in an unexpected format -while reading a data file. This is most commonly cause by inconsistent header and -section data. The header section informs LAMMPS how many entries or lines are expected in the -various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file. -If there is a mismatch, LAMMPS will either keep reading beyond the end of a section -or stop reading before the section has ended. +This error happens when LAMMPS encounters a line of text with an +unexpected keyword while :doc:`reading a data file `. This +would be either header keywords or section header keywords. This is +most commonly due to a mistyped keyword or due to a keyword that is +inconsistent with the :doc:`atom style ` used. -Such a mismatch can happen unexpectedly when the first line of the data -is *not* a comment as required by the format. That would result in -LAMMPS expecting, for instance, 0 atoms because the "atoms" header line -is treated as a comment. +The header section informs LAMMPS how many entries or lines are expected +in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of +the data file. If there is a mismatch, LAMMPS will either keep reading +beyond the end of a section or stop reading before the section has +ended. In that case the next line will not contain a recognized keyword. +Such a mismatch can also happen when the first line of the data +is *not* a comment as required by the format, but a line with a valid +header keyword. That would result in LAMMPS expecting, for instance, +0 atoms because the "atoms" header line is the first line and thus +treated as a comment. + +Another possibility to trigger this error is to have a keyword in the +data file that corresponds to a fix (e.g. :doc:`fix cmap `) +but the :doc:`read_data ` command is missing the (optional) +arguments that identify the fix and the header keyword and section +keyword or those arguments are inconsistent with the keywords in the +data file. + +.. _err0002: + +Incorrect format in ... section of data file +-------------------------------------------- + +This error happens when LAMMPS reads the contents of a section of a +:doc:`data file ` and the number of parameters in the line +differs from what is expected. This most commonly happens, when the +atom style is different from what is expected for a specific data file +since changing the atom style usually changes the format of the line. + +This error can also happen when the number of entries indicated in the +header of a data file (e.g. the number of atoms) is larger than the +number of lines provided (e.g. in the corresponding Atoms section) +and then LAMMPS will continue reading into the next section and that +would have a completely different format. diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index bfdba4f6a1..2a146a9184 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -7883,12 +7883,6 @@ keyword to allow for additional bonds to be formed Fix poems cannot (yet) work with coupled bodies whose joints connect the bodies in a tree structure. -*Triclinic box skew is too large* - The displacement in a skewed direction must be less than half the box - length in that dimension. E.g. the xy tilt must be between -half and - +half of the x box length. This constraint can be relaxed by using - the box tilt command. - *Tried to convert a double to int, but input_double > INT_MAX* Self-explanatory. diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index b0fa2e2173..d244818cc9 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -752,13 +752,6 @@ This will most likely cause errors in kinetic fluctuations. More than the maximum # of neighbors was found multiple times. This was unexpected. -*Triclinic box skew is large* - The displacement in a skewed direction is normally required to be less - than half the box length in that dimension. E.g. the xy tilt must be - between -half and +half of the x box length. You have relaxed the - constraint using the box tilt command, but the warning means that a - LAMMPS simulation may be inefficient as a result. - *Use special bonds = 0,1,1 with bond style fene* Most FENE models need this setting for the special_bonds command. diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst index 64fca57a02..cea70dd3af 100644 --- a/doc/src/Fortran.rst +++ b/doc/src/Fortran.rst @@ -305,6 +305,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS. :ftype extract_setting: function :f extract_global: :f:func:`extract_global` :ftype extract_global: function + :f map_atom: :f:func:`map_atom` + :ftype map_atom: function :f extract_atom: :f:func:`extract_atom` :ftype extract_atom: function :f extract_compute: :f:func:`extract_compute` @@ -1255,8 +1257,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type three elements of the global vector calculated by fix recenter into the variables *dx*, *dy*, and *dz*, respectively. - If asked for per-atom or local data, :f:func:`extract_compute` returns a - pointer to actual LAMMPS data. The pointer so returned will have the + If asked for per-atom or local data, :f:func:`extract_fix` returns a + pointer to actual LAMMPS data. The pointer returned will have the appropriate size to match the internal data, and will be type/kind/rank-checked at the time of the assignment. For example, diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index ae58711063..d02cfc0814 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -1,42 +1,112 @@ -2d simulations -============== +================ + 2d simulations +================ -Use the :doc:`dimension ` command to specify a 2d simulation. +You must use the :doc:`dimension ` command to specify a 2d +simulation. The default is 3d. -Make the simulation box periodic in z via the :doc:`boundary ` -command. This is the default. +A 2d simulation box must be periodic in z as set by the :doc:`boundary +` command. This is the default. -If using the :doc:`create_box ` command to define a -simulation box, set the z dimensions narrow, but finite, so that the -:doc:`create_atoms ` command will fill the 3d simulation -box with a single z plane of atoms - e.g. +Simulation boxes in LAMMPS can be either orthogonal or triclinic in +shape. Orthogonal boxes in 2d are a rectangle with 4 edges that are +each perpendicular to either the x or y coordinate axes. Triclinic +boxes in 2d are a parallelogram with opposite pairs of faces parallel +to each other. LAMMPS supports two forms of triclinic boxes, +restricted and general, which for 2d differ in how the box is oriented +with respect to the xy coordinate axes. See the :doc:`Howto triclinic +` for a detailed description of all 3 kinds of +simulation boxes. + +Here are examples of using the :doc:`create_box ` command +to define the simulation box for a 2d system. .. code-block:: LAMMPS - create_box 1 -10 10 -10 10 -0.25 0.25 + # 2d orthogonal box using a block-style region + region mybox block -10 10 0 10 -0.5 0.5 + create_box 1 mybox -If using the :doc:`read_data ` command to read in a file of -atom coordinates, set the "zlo zhi" values to be finite but narrow, -similar to the create_box command settings just described. For each -atom in the file, assign a z coordinate so it falls inside the -z-boundaries of the box - e.g. 0.0. + # 2d restricted triclinic box using a prism-style region with only xy tilt + region mybox prism 0 10 0 10 -0.5 0.5 2.0 0.0 0.0 + create_box 1 mybox -Use the :doc:`fix enforce2d ` command as the last -defined fix to ensure that the z-components of velocities and forces -are zeroed out every timestep. The reason to make it the last fix is -so that any forces induced by other fixes will be zeroed out. + # 2d general triclinic box using a primitive cell for a 2d hex lattice + lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 & + a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general + create_box 1 NULL 0 5 0 5 -0.5 0.5 -Many of the example input scripts included in the LAMMPS distribution +Note that for 2d orthogonal or restricted triclinic boxes, the box has +a 3rd dimension which must straddle z = 0.0 in the z dimension. +Typically the width of box in the z dimension should be narrow, +e.g. -0.5 to 0.5, but that is not required. For a 2d general +triclinic box, the *a3* vector defined by the :doc:`lattice ` +command must be (0.0,0.0,1.0), which is its default value. Also the +*clo* and *chi* arguments of the :doc:`create_box ` +command must be -0.5 and 0.5. + +Here are examples of using the :doc:`read_data ` command +to define the simulation box for a 2d system via keywords in the +header section of the data file. These are the same boxes as the examples +for the :doc:`create_box ` command + +.. code-block:: LAMMPS + + # 2d orthogonal box + -10 10 xlo xhi + 0 10 ylo yhi + -0.5 0.5 zlo zhi # this is the default, so no need to specify + + # 2d restricted triclinic box with only xy tilt + -10 10 xlo xhi + 0 10 ylo yhi + -0.5 0.5 zlo zhi # this is the default, so no need to specify + 2.0 0.0 0.0 xy xz yz + + # 3d general triclinic box using a primitive cell for a 2d hex lattice + 5 0 0 avec + 2.5 4.3301270189 0 bvec + 0 0 1 cvec # this is the default, so no need to specify + 0 0 -0.5 abc origin # this is the default for 2d, so no need to specify + +Note that for 2d orthogonal or restricted triclinic boxes, the box has +a 3rd dimension specified by the *zlo zhi* values, which must straddle +z = 0.0. Typically the width of box in the z dimension should be +narrow, e.g. -0.5 to 0.5, but that is not required. For a 2d general +triclinic box, the z component of *avec* and *bvec* must be zero, and +*cvec* must be (0,0,1), which is the default. The z component of *abc +origin* must also be -0.5, which is the default. + +If using the :doc:`create_atoms ` command to create +atoms in the 2d simulation box, all the z coordinates of created atoms +will be zero. + +If using the :doc:`read_data ` command to read in a data +file of atom coordinates for a 2d system, the z coordinates of all +atoms should be zero. A value within epsilon of zero is also allowed +in case the data file was generated by another program with finite +numeric precision, in which case the z coord for the atom will be set +to zero. + +Use the :doc:`fix enforce2d ` command as the last fix +defined in the input script. It ensures that the z-components of +velocities and forces are zeroed out every timestep. The reason to +make it the last fix is so that any forces added by other fixes will +also be zeroed out. + +Many of the example input scripts included in the examples directory are for 2d models. .. note:: Some models in LAMMPS treat particles as finite-size spheres, as - opposed to point particles. See the :doc:`atom_style sphere ` and :doc:`fix nve/sphere ` - commands for details. By default, for 2d simulations, such particles - will still be modeled as 3d spheres, not 2d discs (circles), meaning + opposed to point particles. See the :doc:`atom_style sphere + ` and :doc:`fix nve/sphere ` commands + for details. By default, for 2d simulations, such particles will + still be modeled as 3d spheres, not 2d discs (circles), meaning their moment of inertia will be that of a sphere. If you wish to - model them as 2d discs, see the :doc:`set density/disc ` command - and the *disc* option for the :doc:`fix nve/sphere `, - :doc:`fix nvt/sphere `, :doc:`fix nph/sphere `, :doc:`fix npt/sphere ` - commands. + model them as 2d discs, see the :doc:`set density/disc ` + command and the *disc* option for the :doc:`fix nve/sphere + `, :doc:`fix nvt/sphere `, + :doc:`fix nph/sphere `, :doc:`fix npt/sphere + ` commands. diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 8899f7520c..7418a43861 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -1,6 +1,10 @@ CHARMM, AMBER, COMPASS, and DREIDING force fields ================================================= +A compact summary of the concepts, definitions, and properties of +force fields with explicit bonded interactions (like the ones discussed +in this HowTo) is given in :ref:`(Gissinger) `. + A force field has 2 parts: the formulas that define it and the coefficients used for a particular system. Here we only discuss formulas implemented in LAMMPS that correspond to formulas commonly used @@ -11,12 +15,42 @@ commands like :doc:`pair_coeff ` or :doc:`bond_coeff ` and so on. See the :doc:`Tools ` doc page for additional tools that can use CHARMM, AMBER, or Materials Studio generated files to assign force field coefficients and convert their -output into LAMMPS input. +output into LAMMPS input. LAMMPS input scripts can also be generated by +`charmm-gui.org `_. -See :ref:`(MacKerell) ` for a description of the CHARMM -force field. See :ref:`(Cornell) ` for a description of -the AMBER force field. See :ref:`(Sun) ` for a description -of the COMPASS force field. +CHARMM and AMBER +---------------- + +The `CHARMM force field +`_ :ref:`(MacKerell) +` and `AMBER force field +`_ :ref:`(Cornell) ` +have potential energy function of the form + +.. math:: + + V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{ + \text{charmm} \\ + \text{charmmfsw} + }} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em] + & \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{ + \text{lj/charmm/coul/charmm} \\ + \text{lj/charmm/coul/charmm/implicit} \\ + \text{lj/charmm/coul/long} \\ + \text{lj/charmm/coul/msm} \\ + \text{lj/charmmfsw/coul/charmmfsh} \\ + \text{lj/charmmfsw/coul/long} + }} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)} + + +The terms are computed by bond styles (relationship between 2 atoms), +angle styles (between 3 atoms) , dihedral/improper styles (between 4 +atoms), pair styles (non-covalently bonded pair interactions) and +special bonds. The CMAP term (see :doc:`fix cmap ` command for +details) corrects for pairs of dihedral angles ("Correction MAP") to +significantly improve the structural and dynamic properties of proteins +in crystalline and solution environments :ref:`(Brooks) +`. The AMBER force field does not include the CMAP term. The interaction styles listed below compute force field formulas that are consistent with common options in CHARMM or AMBER. See each @@ -31,10 +65,81 @@ command's documentation for the formula it computes. * :doc:`pair_style ` lj/charmm/coul/charmm * :doc:`pair_style ` lj/charmm/coul/charmm/implicit * :doc:`pair_style ` lj/charmm/coul/long - * :doc:`special_bonds ` charmm * :doc:`special_bonds ` amber +The pair styles compute Lennard Jones (LJ) and Coulombic interactions +with additional switching or shifting functions that ramp the energy +and/or force smoothly to zero between an inner :math:`(a)` and outer +:math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or +*charmmfsh*\ ) in their name compute the LJ and Coulombic interactions +with an energy switching function (esw) S(r) which ramps the energy +smoothly to zero between the inner and outer cutoff. This can cause +irregularities in pairwise forces (due to the discontinuous second +derivative of energy at the boundaries of the switching region), which +in some cases can result in complications in energy minimization and +detectable artifacts in MD simulations. + +.. grid:: 1 1 2 2 + + .. grid-item:: + + .. math:: + + LJ(r) &= 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^6 \right]\\[.6em] + C(r) &= \frac{C q_i q_j}{ \epsilon r}\\[.6em] + S(r) &= \frac{ \left(b^2 - r^2\right)^2 \left(b^2 + 2r^2 - 3{a^2}\right)} + { \left(b^2 - a^2\right)^3 }\\[.6em] + E_{LJ}(r) &= \begin{cases} + LJ(r), & r \leq a \\ + LJ(r) S(r), & a < r \leq b \\ + 0, &r > b + \end{cases} \\[.6em] + E_{coul}(r) &= \begin{cases} + C(r), & r \leq a \\ + C(r) S(r), & a < r \leq b \\ + 0, & r > b + \end{cases} + + .. grid-item:: + + .. image:: img/howto_charmm_ELJ.png + :align: center + +The newer styles with *charmmfsw* or *charmmfsh* in their name replace +energy switching with force switching (fsw) for LJ interactions and +force shifting (fsh) functions for Coulombic interactions +:ref:`(Steinbach) ` + +.. grid:: 1 1 2 2 + + .. grid-item:: + + .. math:: + + E_{LJ}(r) = & \begin{cases} + 4 \epsilon \sigma^6 \left(\frac{\displaystyle\sigma + ^6-r^6}{\displaystyle r^{12}}-\frac{\displaystyle\sigma ^6}{\displaystyle a^6 + b^6}+\frac{\displaystyle 1}{\displaystyle a^3 b^3}\right) & r\leq a \\ + \frac{\displaystyle 4 \epsilon \sigma^6 \left(\sigma ^6 + \left(b^6-r^6\right)^2-b^3 r^6 \left(a^3+b^3\right) + \left(b^3-r^3\right)^2\right)}{\displaystyle b^6 r^{12} + \left(b^6-a^6\right)} & ab + \end{cases}\\[.6em] + E_{coul}(r) & = \begin{cases} + C(r) \frac{\displaystyle (b-r)^2}{\displaystyle r b^2}, & r \leq b \\ + 0, & r > b + \end{cases} + + .. grid-item:: + .. image:: img/howto_charmmfsw_ELJ.png + :align: center + +These styles are used by LAMMPS input scripts generated by +https://charmm-gui.org/ :ref:`(Brooks) `. + .. note:: For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in @@ -43,17 +148,33 @@ command's documentation for the formula it computes. ` and :doc:`dihedral charmm ` doc pages. +.. note:: + + The TIP3P water model is strongly recommended for use with the CHARMM + force field. In fact, `"using the SPC model with CHARMM parameters is + a bad idea" + `_ and `"to + enable TIP4P style water in CHARMM, you would have to write a new pair + style" + `_ + . LAMMPS input scripts generated by Solution Builder on https://charmm-gui.org + use TIP3P molecules for solvation. Any other water model can and + probably will lead to false conclusions. + +COMPASS +------- + COMPASS is a general force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers which was -developed using ab initio and empirical parameterization techniques. -See the :doc:`Tools ` page for the msi2lmp tool for creating -LAMMPS template input and data files from BIOVIA's Materials Studio -files. Please note that the msi2lmp tool is very old and largely -unmaintained, so it does not support all features of Materials Studio -provided force field files, especially additions during the last decade. -You should watch the output carefully and compare results, where -possible. See :ref:`(Sun) ` for a description of the COMPASS force -field. +developed using ab initio and empirical parameterization techniques +:ref:`(Sun) `. See the :doc:`Tools ` page for the +msi2lmp tool for creating LAMMPS template input and data files from +BIOVIA's Materials Studio files. Please note that the msi2lmp tool is +very old and largely unmaintained, so it does not support all features +of Materials Studio provided force field files, especially additions +during the last decade. You should watch the output carefully and +compare results, where possible. See :ref:`(Sun) ` for a +description of the COMPASS force field. These interaction styles listed below compute force field formulas that are consistent with the COMPASS force field. See each command's @@ -70,14 +191,21 @@ documentation for the formula it computes. * :doc:`special_bonds ` lj/coul 0 0 1 -DREIDING is a generic force field developed by the `Goddard group `_ at Caltech and is useful for -predicting structures and dynamics of organic, biological and main-group -inorganic molecules. The philosophy in DREIDING is to use general force -constants and geometry parameters based on simple hybridization -considerations, rather than individual force constants and geometric -parameters that depend on the particular combinations of atoms involved -in the bond, angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond term ` to describe interactions involving a -hydrogen atom on very electronegative atoms (N, O, F). +DREIDING +-------- + +DREIDING is a generic force field developed by the `Goddard group +`_ at Caltech and is useful for predicting +structures and dynamics of organic, biological and main-group inorganic +molecules. The philosophy in DREIDING is to use general force constants +and geometry parameters based on simple hybridization considerations, +rather than individual force constants and geometric parameters that +depend on the particular combinations of atoms involved in the bond, +angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond +term ` to describe interactions involving a +hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM +or AMBER, the DREIDING force field has not been parameterized for +considering solvents (like water). See :ref:`(Mayo) ` for a description of the DREIDING force field @@ -110,21 +238,31 @@ documentation for the formula it computes. ---------- +.. _Typelabel2: + +**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024). + .. _howto-MacKerell: -**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). +**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998). J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f .. _howto-Cornell: -**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). +**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman (1995). JACS 117, 5179-5197. https://doi.org/10.1021/ja00124a002 + +.. _howto-Steinbach: + +**(Steinbach)** Steinbach, Brooks (1994). J Comput Chem, 15, 667. https://doi.org/10.1002/jcc.540150702 + +.. _howto-Brooks: + +**(Brooks)** Brooks, et al (2009). J Comput Chem, 30, 1545. https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287 .. _howto-Sun: -**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998). +**(Sun)** Sun (1998). J. Phys. Chem. B, 102, 7338-7364. https://doi.org/10.1021/jp980939v .. _howto-Mayo: -**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). +**(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010 + diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 968e10edd8..23d0e1019d 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -102,8 +102,19 @@ particles of different styles | :doc:`dump image ` | output body particle attributes as an image | +------------------------------------------------+-----------------------------------------------------+ -The pair styles defined for use with specific body styles are listed -in the sections below. +The pair styles currently defined for use with specific body styles +are listed in the sections below. + +Note that for all the body styles, if the data file defines a general +triclinic box, then the orientation of the body particle and its +corresponding 6 moments of inertia and other orientation-dependent +values should reflect the fact the body is defined withing a general +triclinic box with edge vectors **A**,**B**,**C**. LAMMPS will rotate +the box to convert it to a restricted triclinic box. This operation +will also rotate the orientation of the body particles. See the +:doc:`Howto triclinic ` doc page for more details. +The sections below highlight the orientation-dependent values specific +to each body style. ---------- @@ -154,12 +165,18 @@ values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. + The coordinates of each sub-particle are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the *Atoms* section of the data file, as is the total mass of the body particle. +Note that if the data file defines a general triclinic simulation box, +these sub-particle displacements are orientation-dependent and, as +mentioned above, should reflect the body particle's orientation within +the general triclinic box. + The :doc:`pair_style body/nparticle ` command can be used with this body style to compute body/body and body/non-body interactions. @@ -226,6 +243,7 @@ values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. + The coordinates of each vertex are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the @@ -270,6 +288,11 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows: 0 0 0 3.0 +Note that if the data file defines a general triclinic simulation box, +these polygon vertex displacements are orientation-dependent and, as +mentioned above, should reflect the body particle's orientation within +the general triclinic box. + The :doc:`pair_style body/rounded/polygon ` command can be used with this body style to compute body/body interactions. The :doc:`fix wall/body/polygon ` @@ -366,6 +389,7 @@ values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. + The coordinates of each vertex are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the @@ -435,6 +459,11 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: The number of edges and faces for a rod or sphere must be listed, but is ignored. +Note that if the data file defines a general triclinic simulation box, +these polyhedron vertex displacements are orientation-dependent and, +as mentioned above, should reflect the body particle's orientation +within the general triclinic box. + The :doc:`pair_style body/rounded/polhedron ` command can be used with this body style to compute body/body interactions. The :doc:`fix diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst index 0ca4e85fbb..5aa277275d 100644 --- a/doc/src/Howto_bpm.rst +++ b/doc/src/Howto_bpm.rst @@ -15,7 +15,8 @@ orientation for rotational models. This produces a stress-free initial state. Furthermore, bonds are allowed to break under large strains, producing fracture. The examples/bpm directory has sample input scripts for simulations of the fragmentation of an impacted plate and the -pouring of extended, elastic bodies. +pouring of extended, elastic bodies. See :ref:`(Clemmer) ` +for more general information on the approach and the LAMMPS implementation. ---------- @@ -150,3 +151,9 @@ the following are currently compatible with BPM bond styles: interactions, one will need to switch between different *special_bonds* settings in the input script. An example is found in ``examples/bpm/impact``. + +---------- + +.. _howto-Clemmer: + +**(Clemmer)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024). diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 2983d013c6..3529579d65 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -2,43 +2,195 @@ Triclinic (non-orthogonal) simulation boxes =========================================== By default, LAMMPS uses an orthogonal simulation box to encompass the -particles. The :doc:`boundary ` command sets the boundary -conditions of the box (periodic, non-periodic, etc). The orthogonal -box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors -starting from the origin given by **a** = (xhi-xlo,0,0); **b** = -(0,yhi-ylo,0); **c** = (0,0,zhi-zlo). The 6 parameters +particles. The orthogonal box has its "origin" at (xlo,ylo,zlo) and +extends to (xhi,yhi,zhi). Conceptually it is defined by 3 edge +vectors starting from the origin given by **A** = (xhi-xlo,0,0); **B** += (0,yhi-ylo,0); **C** = (0,0,zhi-zlo). The :doc:`boundary +` command sets the boundary conditions for the 6 faces of +the box (periodic, non-periodic, etc). The 6 parameters (xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the :doc:`create_box ` or -:doc:`read_data ` or :doc:`read_restart ` -commands. Additionally, LAMMPS defines box size parameters lx,ly,lz -where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the -:doc:`thermo_style custom ` command. +is created by one of these commands: -LAMMPS also allows simulations to be performed in triclinic -(non-orthogonal) simulation boxes shaped as a parallelepiped with -triclinic symmetry. The parallelepiped has its "origin" at -(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the -origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** = -(xz,yz,zhi-zlo). *xy,xz,yz* can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. In LAMMPS the triclinic -simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary -vectors. As indicated, **a** must lie on the positive x axis. **b** must -lie in the xy plane, with strictly positive y component. **c** may have -any orientation with strictly positive z component. The requirement -that **a**, **b**, and **c** have strictly positive x, y, and z components, -respectively, ensures that **a**, **b**, and **c** form a complete -right-handed basis. These restrictions impose no loss of generality, -since it is possible to rotate/invert any set of 3 crystal basis -vectors so that they conform to the restrictions. +* :doc:`create_box ` +* :doc:`read_data ` +* :doc:`read_restart ` +* :doc:`read_dump ` -For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge -vectors of a general parallelepiped, where there is no restriction on -**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e. -**A** x **B** . **C** > 0. The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear -rotation of **A**, **B**, and **C** and can be computed as follows: +Internally, LAMMPS defines box size parameters lx,ly,lz where lx = +xhi-xlo, and similarly in the y and z dimensions. The 6 parameters, as +well as lx,ly,lz, can be output via the :doc:`thermo_style custom +` command. See the :doc:`Howto 2d ` doc page +for info on how zlo and zhi are defined for 2d simulations. + +---------- + +Triclinic simulation boxes +"""""""""""""""""""""""""" + +LAMMPS also allows simulations to be performed using triclinic +(non-orthogonal) simulation boxes shaped as a 3d parallelepiped with +triclinic symmetry. For 2d simulations a triclinic simulation box is +effectively a parallelogram; see the :doc:`Howto 2d ` doc +page for details. + +One use of triclinic simulation boxes is to model solid-state crystals +with triclinic symmetry. The :doc:`lattice ` command can be +used with non-orthogonal basis vectors to define a lattice that will +tile a triclinic simulation box via the :doc:`create_atoms +` command. + +A second use is to run Parrinello-Rahman dynamics via the :doc:`fix +npt ` command, which will adjust the xy, xz, yz tilt factors +to compensate for off-diagonal components of the pressure tensor. The +analog for an :doc:`energy minimization ` is the :doc:`fix +box/relax ` command. + +A third use is to shear a bulk solid to study the response of the +material. The :doc:`fix deform ` command can be used for +this purpose. It allows dynamic control of the xy, xz, yz tilt +factors as a simulation runs. This is discussed in the :doc:`Howto +NEMD ` doc page on non-equilibrium MD (NEMD) simulations. + +Conceptually, a triclinic parallelepiped is defined with an "origin" +at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** = +(bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long +as they are non-zero, distinct, and not co-planar. In addition, they +must define a right-handed system, such that (**A** cross **B**) +points in the direction of **C**. Note that a left-handed system can +be converted to a right-handed system by simply swapping the order of +any pair of the **A**, **B**, **C** vectors. + +The 4 commands listed above for defining orthogonal simulation boxes +have triclinic options which allow for specification of the origin and +edge vectors **A**, **B**, **C**. For each command, this can be done +in one of two ways, for what LAMMPS calls a *general* triclinic box or +a *restricted* triclinic box. + +A *general* triclinic box is specified by an origin (xlo, ylo, zlo) +and arbitrary edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), and +**C** = (cx,cy,cz). So there are 12 parameters in total. + +A *restricted* triclinic box also has an origin (xlo,ylo,zlo), but its +edge vectors are of the following restricted form: **A** = +(xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So +there are 9 parameters in total. Note that the restricted form +requires **A** to be along the x-axis, **B** to be in the xy plane +with a y-component in the +y direction, and **C** to have its +z-component in the +z direction. Note that a restricted triclinic box +is *right-handed* by construction since (**A** cross **B**) points in +the direction of **C**. + +The *xy,xz,yz* values can be zero or positive or negative. They are +called "tilt factors" because they are the amount of displacement +applied to edges of faces of an orthogonal box to change it into a +restricted triclinic parallelepiped. + +.. note:: + + Any right-handed general triclinic box (i.e. solid-state crystal + basis vectors) can be rotated in 3d around its origin in order to + conform to the LAMMPS definition of a restricted triclinic box. + See the discussion in the next sub-section about general triclinic + simulation boxes in LAMMPS. + +Note that the :doc:`thermo_style custom ` command has +keywords for outputting the various parameters that define the size +and shape of orthogonal, restricted triclinic, and general triclinic +simulation boxes. + +For orthogonal boxes there 6 thermo keywords (xlo,ylo,zlo) and +(xhi,yhi,zhi). + +For restricted triclinic boxes there are 9 thermo keywords for +(xlo,ylo,zlo), (xhi,yhi,zhi), and the (xy,xz,yz) tilt factors. + +For general triclinic boxes there are 12 thermo keywords for +(xlo,ylo,zhi) and the components of the **A**, **B**, **C** edge +vectors, namely (avecx,avecy,avecz), (bvecx,bvecy,bvecz), and +(cvecx,cvecy,cvecz), + +The remainder of this doc page explains (a) how LAMMPS operates with +general triclinic simulation boxes, (b) mathematical transformations +between general and restricted triclinic boxes which may be useful +when creating LAMMPS inputs or interpreting outputs for triclinic +simulations, and (c) how LAMMPS uses tilt factors for restricted +triclinic simulation boxes. + +---------- + +General triclinic simulation boxes in LAMMPS +"""""""""""""""""""""""""""""""""""""""""""" + +LAMMPS allows specification of general triclinic simulation boxes with +their atoms as a convenience for users who may be converting data from +solid-state crystallographic representations or from DFT codes for +input to LAMMPS. Likewise it allows output of dump files, data files, +and thermodynamic data (e.g. pressure tensor) in a general triclinic +format. + +However internally, LAMMPS only uses restricted triclinic simulation +boxes. This is for parallel efficiency and to formulate partitioning +of the simulation box across processors, neighbor list building, and +inter-processor communication of per-atom data with methods similar to +those used for orthogonal boxes. + +This means 4 things which are important to understand: + +* Input of a general triclinic system is immediately converted to a + restricted triclinic system. +* If output of per-atom data for a general triclinic system is + requested (e.g. for atom coordinates in a dump file), + conversion from a restricted to general triclinic system is done at + the time of output. +* The conversion of the simulation box and per-atom data from general + triclinic to restricted triclinic (and vice versa) is a 3d rotation + operation around an origin, which is the lower left corner of the + simulation box. This means an input data file for a general + triclinic system should specify all per-atom quantities consistent + with the general triclinic box and its orientation relative to the + standard x,y,z coordinate axes. For example, atom coordinates + should be inside the general triclinic simulation box defined by the + edge vectors **A**, **B**, **C** and its origin. Likewise per-atom + velocities should be in directions consistent with the general + triclinic box orientation. E.g. a velocity vector which will be in + the +x direction once LAMMPS converts from a general to restricted + triclinic box, should be specified in the data file in the direction + of the **A** edge vector. See the :doc:`read_data ` doc + page for info on all the per-atom vector quantities to which this + rule applies when a data file for a general triclinic box is input. +* If commands such as :doc:`write_data ` or :doc:`dump + custom ` are used to output general triclinic information, it + is effectively the inverse of the operation described in the + preceding bullet. +* Other LAMMPS commands such as :doc:`region ` or + :doc:`velocity ` or :doc:`set `, operate on a + restricted triclinic system even if a general triclinic system was + defined initially. + +This is the list of commands which have general triclinic options: + +* :doc:`create_box ` - define a general triclinic box +* :doc:`create_atoms ` - add atoms to a general triclinic box +* :doc:`lattice ` - define a custom lattice consistent with the **A**, **B**, **C** edge vectors of a general triclinic box +* :doc:`read_data ` - read a data file for a general triclinic system +* :doc:`write_data ` - write a data file for a general triclinic system +* :doc:`dump atom, dump custom ` - output dump snapshots in general triclinic format +* :doc:`dump_modify triclinic/general ` - select general triclinic format for dump output +* :doc:`thermo_style ` - output the pressure tensor in + general triclinic format +* :doc:`thermo_modify triclinic/general ` - select general triclinic format for thermo output +* :doc:`read_restart ` - read a restart file for a general triclinic system +* :doc:`write_restart ` - write a restart file for a general triclinic system + +---------- + +Transformation from general to restricted triclinic boxes +""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Let **A**,\ **B**,\ **C** be the right-handed edge vectors of a +general triclinic simulation box. The equivalent LAMMPS **a**,\ +**b**,\ **c** for a restricted triclinic box are a 3d rotation of +**A**, **B**, and **C** and can be computed as follows: .. math:: @@ -55,23 +207,17 @@ rotation of **A**, **B**, and **C** and can be computed as follows: c_y = & \mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})} \times \mathbf{\hat{A}} \quad = \quad \frac{\mathbf{B} \cdot \mathbf{C} - b_x c_x}{b_y} \\ c_z = & |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2} -where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^) -indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles -between the vectors described below. Note that by construction, -**a**, **b**, and **c** have strictly positive x, y, and z components, respectively. -If it should happen that -**A**, **B**, and **C** form a left-handed basis, then the above equations -are not valid for **c**\ . In this case, it is necessary -to first apply an inversion. This can be achieved -by interchanging two basis vectors or by changing the sign of one of them. +where A = \| **A** \| indicates the scalar length of **A**\ . The hat +symbol (\^) indicates the corresponding unit vector. :math:`\beta` and +:math:`\gamma` are angles between the **A**, **B**, **C** vectors +as described below. -For consistency, the same rotation/inversion applied to the basis vectors -must also be applied to atom positions, velocities, -and any other vector quantities. -This can be conveniently achieved by first converting to -fractional coordinates in the -old basis and then converting to distance coordinates in the new basis. -The transformation is given by the following equation: +For consistency, the same rotation applied to the triclinic box edge +vectors can also be applied to atom positions, velocities, and other +vector quantities. This can be conveniently achieved by first +converting to fractional coordinates in the general triclinic +coordinates and then converting to coordinates in the restricted +triclinic basis. The transformation is given by the following equation: .. math:: @@ -82,87 +228,24 @@ The transformation is given by the following equation: \mathbf{A \times B} \end{pmatrix} \cdot \mathbf{X} -where *V* is the volume of the box, **X** is the original vector quantity and -**x** is the vector in the LAMMPS basis. +where *V* is the volume of the box (same in either basis), **X** is +the fractional vector in the general triclinic basis and **x** is the +resulting vector in the restricted triclinic basis. -There is no requirement that a triclinic box be periodic in any -dimension, though it typically should be in at least the second dimension -of the tilt (y in xy) if you want to enforce a shift in periodic -boundary conditions across that boundary. Some commands that work -with triclinic boxes, e.g. the :doc:`fix deform ` and :doc:`fix npt ` commands, require periodicity or non-shrink-wrap -boundary conditions in specific dimensions. See the command doc pages -for details. +---------- -The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simulation box is created. This happens in one of 3 ways. -If the :doc:`create_box ` command is used with a region of -style *prism*, then a triclinic box is setup. See the -:doc:`region ` command for details. If the -:doc:`read_data ` command is used to define the simulation -box, and the header of the data file contains a line with the "xy xz -yz" keyword, then a triclinic box is setup. See the -:doc:`read_data ` command for details. Finally, if the -:doc:`read_restart ` command reads a restart file which -was written from a simulation using a triclinic box, then a triclinic -box will be setup for the restarted simulation. +Crystallographic general triclinic representation of a simulation box +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Note that you can define a triclinic box with all 3 tilt factors = -0.0, so that it is initially orthogonal. This is necessary if the box -will become non-orthogonal, e.g. due to the :doc:`fix npt ` or -:doc:`fix deform ` commands. Alternatively, you can use the -:doc:`change_box ` command to convert a simulation box from -orthogonal to triclinic and vice versa. - -As with orthogonal boxes, LAMMPS defines triclinic box size parameters -lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. -The 9 parameters, as well as lx,ly,lz, can be output via the -:doc:`thermo_style custom ` command. - -To avoid extremely tilted boxes (which would be computationally -inefficient), LAMMPS normally requires that no tilt factor can skew -the box more than half the distance of the parallel box length, which -is the first dimension in the tilt factor (x for xz). This is required -both when the simulation box is created, e.g. via the -:doc:`create_box ` or :doc:`read_data ` commands, -as well as when the box shape changes dynamically during a simulation, -e.g. via the :doc:`fix deform ` or :doc:`fix npt ` -commands. - -For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are geometrically all equivalent. If the box tilt exceeds this -limit during a dynamics run (e.g. via the :doc:`fix deform ` -command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the :doc:`fix deform ` page for further details. - -One exception to this rule is if the first dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient, due to the highly skewed simulation box. - -Box flips that may occur using the :doc:`fix deform ` or -:doc:`fix npt ` commands can be turned off using the *flip no* -option with either of the commands. - -Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped subdomain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -Triclinic crystal structures are often defined using three lattice -constants *a*, *b*, and *c*, and three angles :math:`\alpha`, -:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, -the a, b, and c lattice constants are the scalar lengths of the edge +General triclinic crystal structures are often defined using three +lattice constants *a*, *b*, and *c*, and three angles :math:`\alpha`, +:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the +a, b, and c lattice constants are the scalar lengths of the edge vectors **a**, **b**, and **c** defined above. The relationship between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`, -:math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) = -(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: +:math:`\gamma`) and the LAMMPS restricted triclinic box sizes +(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is +as follows: .. math:: @@ -186,15 +269,19 @@ The inverse relationship can be written as follows: The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and :math:`\gamma` can be printed out or accessed by computes using the -:doc:`thermo_style custom ` keywords -*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*, -respectively. +:doc:`thermo_style custom ` keywords *cella*, *cellb*, +*cellc*, *cellalpha*, *cellbeta*, *cellgamma*, respectively. + +---------- + +Output of restricted and general triclinic boxes in a dump file +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" As discussed on the :doc:`dump ` command doc page, when the BOX -BOUNDS for a snapshot is written to a dump file for a triclinic box, -an orthogonal bounding box which encloses the triclinic simulation box -is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic -box, formatted as follows: +BOUNDS for a snapshot is written to a dump file for a restricted +triclinic box, an orthogonal bounding box which encloses the triclinic +simulation box is output, along with the 3 tilt factors (xy, xz, yz) of +the restricted triclinic box, formatted as follows: .. parsed-literal:: @@ -204,7 +291,7 @@ box, formatted as follows: zlo_bound zhi_bound yz This bounding box is convenient for many visualization programs and is -calculated from the 9 triclinic box parameters +calculated from the 9 restricted triclinic box parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: .. parsed-literal:: @@ -217,22 +304,66 @@ calculated from the 9 triclinic box parameters zhi_bound = zhi These formulas can be inverted if you need to convert the bounding box -back into the triclinic box parameters, e.g. xlo = xlo_bound - -MIN(0.0,xy,xz,xy+xz). +back into the restricted triclinic box parameters, e.g. xlo = +xlo_bound - MIN(0.0,xy,xz,xy+xz). -One use of triclinic simulation boxes is to model solid-state crystals -with triclinic symmetry. The :doc:`lattice ` command can be -used with non-orthogonal basis vectors to define a lattice that will -tile a triclinic simulation box via the -:doc:`create_atoms ` command. +---------- -A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt ` command, which will adjust the xy, xz, yz tilt -factors to compensate for off-diagonal components of the pressure -tensor. The analog for an :doc:`energy minimization ` is -the :doc:`fix box/relax ` command. +Periodicity and tilt factors for triclinic simulation boxes +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -A third use is to shear a bulk solid to study the response of the -material. The :doc:`fix deform ` command can be used for -this purpose. It allows dynamic control of the xy, xz, yz tilt -factors as a simulation runs. This is discussed in the next section -on non-equilibrium MD (NEMD) simulations. +There is no requirement that a triclinic box be periodic in any +dimension, though it typically should be in y or z if you wish to +enforce a shift in coordinates due to periodic boundary conditions +across the y or z boundaries. See the doc page for the :doc:`boundary +` command for an explanation of shifted coordinates for +restricted triclinic boxes which are periodic. + +Some commands that work with triclinic boxes, e.g. the :doc:`fix +deform ` and :doc:`fix npt ` commands, require +periodicity or non-shrink-wrap boundary conditions in specific +dimensions. See the command doc pages for details. + +A restricted triclinic box can be defined with all 3 tilt factors = +0.0, so that it is initially orthogonal. This is necessary if the box +will become non-orthogonal, e.g. due to use of the :doc:`fix npt +` or :doc:`fix deform ` commands. Alternatively, +you can use the :doc:`change_box ` command to convert a +simulation box from orthogonal to restricted triclinic and vice versa. + +.. note:: + + Highly tilted restricted triclinic simulation boxes can be + computationally inefficient. This is due to the large volume of + communication needed to acquire ghost atoms around a processor's + irregular-shaped subdomain. For extreme values of tilt, LAMMPS may + also lose atoms and generate an error. + +LAMMPS will issue a warning if you define a restricted triclinic box +with a tilt factor which skews the box more than half the distance of +the parallel box length, which is the first dimension in the tilt +factor (e.g. x for xz). + +For example, if xlo = 2 and xhi = 12, then the x box length is 10 and +the xy tilt factor should be between -5 and 5 to avoid the warning. +Similarly, both xz and yz should be between -(xhi-xlo)/2 and ++(yhi-ylo)/2. Note that these are not limitations, since if the +maximum tilt factor is 5 (as in this example), then simulations boxes +and atom configurations with tilt = ..., -15, -5, 5, 15, 25, ... are +all geometrically equivalent. + +If the box tilt exceeds this limit during a dynamics run (e.g. due to +the :doc:`fix deform ` command), then by default the box +is "flipped" to an equivalent shape with a tilt factor within the +warning bounds, and the run continues. See the :doc:`fix deform +` page for further details. Box flips that would normally +occur using the :doc:`fix deform ` or :doc:`fix npt +` commands can be suppressed using the *flip no* option with +either of the commands. + +One exception to box flipping is if the first dimension in the tilt +factor (e.g. x for xy) is non-periodic. In that case, the limits on +the tilt factor are not enforced, since flipping the box in that +dimension would not change the atom positions due to non-periodicity. +In this mode, if the system tilts to large angles, the simulation will +simply become inefficient, due to the highly skewed simulation box. diff --git a/doc/src/Howto_type_labels.rst b/doc/src/Howto_type_labels.rst index 8f03f45ef9..6b734f5c8d 100644 --- a/doc/src/Howto_type_labels.rst +++ b/doc/src/Howto_type_labels.rst @@ -14,16 +14,17 @@ wherever they appear in LAMMPS input or output files. The total number Ntypes for each interaction is "locked in" when the simulation box is created. -A recent addition to LAMMPS is the option to use strings - referred -to as type labels - as an alternative. Using type labels instead of +A recent addition to LAMMPS is the option to use strings - referred to +as type labels - as an alternative. Using type labels instead of numeric types can be advantageous in various scenarios. For example, -type labels can make inputs more readable and generic (i.e. usable through -the :doc:`include command ` for different systems with different -numerical values assigned to types. This generality also applies to -other inputs like data files read by :doc:`read_data ` or -molecule template files read by the :doc:`molecule ` -command. See below for a list of other commands that can use -type labels in different ways. +type labels can make inputs more readable and generic (i.e. usable +through the :doc:`include command ` for different systems with +different numerical values assigned to types. This generality also +applies to other inputs like data files read by :doc:`read_data +` or molecule template files read by the :doc:`molecule +` command. A discussion of the current type label support can +be found in :ref:`(Gissinger) `. See below for a list of +other commands that can use type labels in different ways. LAMMPS will *internally* continue to use numeric types, which means that many previous restrictions still apply. For example, the total @@ -124,3 +125,9 @@ between the files. The creation of simulation-ready reaction templates for :doc:`fix bond/react ` is much simpler when using type labels, and results in templates that can be used without modification in multiple simulations or different systems. + +----------- + +.. _Typelabel24: + +**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024). diff --git a/doc/src/Intro_citing.rst b/doc/src/Intro_citing.rst index 69ccab6162..8b906bb725 100644 --- a/doc/src/Intro_citing.rst +++ b/doc/src/Intro_citing.rst @@ -47,6 +47,8 @@ In addition there are DOIs generated for individual stable releases: - 3 March 2020 version: `DOI:10.5281/zenodo.3726417 `_ - 29 October 2020 version: `DOI:10.5281/zenodo.4157471 `_ - 29 September 2021 version: `DOI:10.5281/zenodo.6386596 `_ +- 23 June 2022 version: `DOI:10.5281/zenodo.10806836 `_ +- 2 August 2023 version: `DOI:10.5281/zenodo.10806852 `_ Home page ^^^^^^^^^ diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index f7b4dd319b..98e9d981ed 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -29,7 +29,7 @@ General features * spatial decomposition of simulation domain for MPI parallelism * particle decomposition inside spatial decomposition for OpenMP and GPU parallelism * GPLv2 licensed open-source distribution -* highly portable C++-11 +* highly portable C++-11 (optional packages may require C++17) * modular code with most functionality in optional packages * only depends on MPI library for basic parallel functionality, MPI stub for serial compilation * other libraries are optional and only required for specific packages @@ -81,7 +81,7 @@ commands) * pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted * charged pairwise potentials: Coulombic, point-dipole * many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta -* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN +* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN, SNAP * interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP * long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS * polarization models: :doc:`QEq `, :doc:`core/shell model `, :doc:`Drude dipole model ` diff --git a/doc/src/Library_properties.rst b/doc/src/Library_properties.rst index 005bfaeea5..73abcbbe1b 100644 --- a/doc/src/Library_properties.rst +++ b/doc/src/Library_properties.rst @@ -13,6 +13,7 @@ This section documents the following functions: - :cpp:func:`lammps_extract_setting` - :cpp:func:`lammps_extract_global_datatype` - :cpp:func:`lammps_extract_global` +- :cpp:func:`lammps_map_atom` -------------------- @@ -120,3 +121,8 @@ subdomains and processors. .. doxygenfunction:: lammps_extract_global :project: progguide +----------------------- + +.. doxygenfunction:: lammps_map_atom + :project: progguide + diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index a3d65d9d65..e759e3bd18 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -52,6 +52,7 @@ page gives those details. * :ref:`DRUDE ` * :ref:`EFF ` * :ref:`ELECTRODE ` + * :ref:`EXTRA-COMMAND ` * :ref:`EXTRA-COMPUTE ` * :ref:`EXTRA-DUMP ` * :ref:`EXTRA-FIX ` @@ -84,6 +85,7 @@ page gives those details. * :ref:`ML-QUIP ` * :ref:`ML-RANN ` * :ref:`ML-SNAP ` + * :ref:`ML-UF3 ` * :ref:`MOFFF ` * :ref:`MOLECULE ` * :ref:`MOLFILE ` @@ -403,6 +405,7 @@ and :ref:`ASPHERE ` packages are installed. * :doc:`bond_style oxdna2/\* ` * :doc:`bond_style oxrna2/\* ` * :doc:`fix nve/dotc/langevin ` +* examples/PACKAGES/cgdna ---------- @@ -676,7 +679,12 @@ DPD-BASIC package Pair styles for the basic dissipative particle dynamics (DPD) method and DPD thermostatting. -**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP) +Pair style :doc:`dpd/coul/slater/long ` also +includes smeared charges for coulomb interactions and thus requires the +:ref:`KSPACE ` package to be installed to handle the long-range +Coulomb part of the interactions. + +**Authors:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP), Eddy Barraud (IFPEN) **Supporting info:** @@ -685,6 +693,7 @@ and DPD thermostatting. * :doc:`pair_style dpd/tstat ` * :doc:`pair_style dpd/ext ` * :doc:`pair_style dpd/ext/tstat ` +* :doc:`pair_style dpd/coul/slater/long ` * examples/PACKAGES/dpd-basic ---------- @@ -886,6 +895,22 @@ This package has :ref:`specific installation instructions ` on the ---------- +.. _PKG-EXTRA-COMMAND: + +EXTRA-COMMAND package +--------------------- + +**Contents:** + +Additional command styles that are less commonly used. + +**Supporting info:** + +* src/EXTRA-COMMAND: filenames -> commands +* :doc:`general commands ` + +---------- + .. _PKG-EXTRA-COMPUTE: EXTRA-COMPUTE package @@ -1925,6 +1950,31 @@ computes which analyze attributes of the potential. ---------- +.. _PKG-ML-UF3: + +ML-UF3 package +-------------- + +**Contents:** + +A pair style for the ultra-fast force field potentials (UF3). UF3 is a +methodology for deriving a highly accurate classical potential which is +fast to evaluate and is fitted to a large archives of quantum mechanical +(DFT) data. The use of b-spline basis set in UF3 enables the rapid +evaluation of 2-body and 3-body interactions. + +**Authors:** Ajinkya C Hire (University of Florida), +Hendrik Krass (University of Constance), +Matthias Rupp (Luxembourg Institute of Science and Technology), +Richard Hennig (University of Florida) + +**Supporting info:** + +* src/ML-UF3: filenames -> commands +* :doc:`pair_style uf3 ` +* examples/uf3 +* https://github.com/uf3/uf3 + .. _PKG-MOFFF: MOFFF package diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index c0a1164513..d1422c5f09 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -158,6 +158,11 @@ whether an extra library is needed to build and use the package: - :doc:`fix electrode/conp ` - PACKAGES/electrode - no + * - :ref:`EXTRA-COMMAND ` + - additional command styles + - :doc:`general commands ` + - n/a + - no * - :ref:`EXTRA-COMPUTE ` - additional compute styles - :doc:`compute ` @@ -318,6 +323,11 @@ whether an extra library is needed to build and use the package: - :doc:`pair_style snap ` - snap - no + * - :ref:`ML-UF3 ` + - quantum-fitted ultra fast potentials + - :doc:`pair_style uf3 ` + - PACKAGES/uf3 + - no * - :ref:`MOFFF ` - styles for `MOF-FF `_ force field - :doc:`pair_style buck6d/coul/gauss ` diff --git a/doc/src/Python_scatter.rst b/doc/src/Python_scatter.rst index 002a36cc98..e4444fabe7 100644 --- a/doc/src/Python_scatter.rst +++ b/doc/src/Python_scatter.rst @@ -54,8 +54,21 @@ like this: x[3] = x coord of atom with ID 2 ... x[n3-1] = z coord of atom with ID natoms - lmp.scatter_atoms("x",1,3,x) + lmp.scatter_atoms("x", 1, 3, x) + +The coordinates can also be provided as arguments to the initializer of x: + +.. code-block:: python + + from ctypes import c_double + natoms = 2 + n3 = 3*natoms + # init in constructor + x = (n3*c_double)(0.0, 0.0, 0.0, 1.0, 1.0, 1.0) + lmp.scatter_atoms("x", 1, 3, x) + # or using a list + coords = [1.0, 2.0, 3.0, -3.0, -2.0, -1.0] + x = (c_double*len(coords))(*coords) Alternatively, you can just change values in the vector returned by the gather methods, since they are also ctypes vectors. - diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 49022a4ee9..0732398e53 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -90,7 +90,7 @@ Miscellaneous tools * :ref:`LAMMPS coding standards ` * :ref:`emacs ` - * :ref:`i-pi ` + * :ref:`i-PI ` * :ref:`kate ` * :ref:`LAMMPS shell ` * :ref:`LAMMPS GUI ` @@ -376,21 +376,40 @@ See README file in the tools/fep directory. .. _ipi: -i-pi tool +i-PI tool ------------------- -The tools/i-pi directory contains a version of the i-PI package, with -all the LAMMPS-unrelated files removed. It is provided so that it can -be used with the :doc:`fix ipi ` command to perform -path-integral molecular dynamics (PIMD). +.. versionchanged:: 27June2024 + +The tools/i-pi directory used to contain a bundled version of the i-PI +software package for use with LAMMPS. This version, however, was +removed in 06/2024. The i-PI package was created and is maintained by Michele Ceriotti, michele.ceriotti at gmail.com, to interface to a variety of molecular dynamics codes. -See the tools/i-pi/manual.pdf file for an overview of i-PI, and the -:doc:`fix ipi ` page for further details on running PIMD -calculations with LAMMPS. +i-PI is now available via PyPI using the pip package manager at: +https://pypi.org/project/ipi/ + +Here are the commands to set up a virtual environment and install +i-PI into it with all its dependencies. + +.. code-block:: sh + + python -m venv ipienv + source ipienv/bin/activate + pip install --upgrade pip + pip install ipi + +To install the development version from GitHub, please use: + +.. code-block:: sh + + pip install git+https://github.com/i-pi/i-pi.git + +For further information, please consult the [i-PI home +page](https://ipi-code.org). ---------- @@ -709,8 +728,8 @@ CMake is required. The LAMMPS GUI has been successfully compiled and tested on: - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12 -- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS -- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS +- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS +- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.5LTS - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS - Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS @@ -752,22 +771,23 @@ if necessary. When both, Qt5 and Qt6 are available, Qt6 will be preferred unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set. It should be possible to build the LAMMPS GUI as a standalone -compilation (e.g. when LAMMPS has been compiled with traditional make), -then the CMake configuration needs to be told where to find the LAMMPS +compilation (e.g. when LAMMPS has been compiled with traditional make). +Then the CMake configuration needs to be told where to find the LAMMPS headers and the LAMMPS library, via ``-D LAMMPS_SOURCE_DIR=/path/to/lammps/src``. CMake will try to guess a build folder with the LAMMPS library from that path, but it can also be set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``. Rather than linking to the LAMMPS library during compilation, it is also -possible to compile the GUI with a plugin loader library that will load +possible to compile the GUI with a plugin loader that will load the LAMMPS library dynamically at runtime during the start of the GUI from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or ``liblammps.dll`` (depending on the operating system). This has the -advantage that the LAMMPS library can be updated LAMMPS without having -to recompile the GUI. The ABI of the LAMMPS C-library interface is very -stable and generally backward compatible. This feature is enabled by -setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D +advantage that the LAMMPS library can be built from updated or modified +LAMMPS source without having to recompile the GUI. The ABI of the +LAMMPS C-library interface is very stable and generally backward +compatible. This feature is enabled by setting +``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this would be the ``examples/COUPLE/plugin`` folder of the LAMMPS distribution. @@ -779,8 +799,8 @@ macOS """"" When building on macOS, the build procedure will try to manufacture a -drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg' -target (i.e. ``cmake --build --target dmg`` or ``make dmg``. +drag-n-drop installer, ``LAMMPS-macOS-multiarch.dmg``, when using the +'dmg' target (i.e. ``cmake --build --target dmg`` or ``make dmg``. To build multi-arch executables that will run on both, arm64 and x86_64 architectures natively, it is necessary to set the CMake variable ``-D @@ -819,12 +839,12 @@ and LAMMPS GUI can be launched from anywhere from the command line. The standard CMake build procedure can be applied and the ``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake -command will automatically include a suitable CMake toolset file (the -regular cmake command can be used after that). After building the -libraries and executables, you can build the target 'zip' -(i.e. ``cmake --build --target zip`` or ``make zip`` -to stage all installed files into a LAMMPS_GUI folder and then -run a script to copy all required dependencies, some other files, +command will automatically include a suitable CMake toolchain file (the +regular cmake command can be used after that to modify the configuration +settings, if needed). After building the libraries and executables, +you can build the target 'zip' (i.e. ``cmake --build --target zip`` +or ``make zip`` to stage all installed files into a LAMMPS_GUI folder +and then run a script to copy all required dependencies, some other files, and create a zip file from it. Linux diff --git a/doc/src/angle_cosine_squared_restricted.rst b/doc/src/angle_cosine_squared_restricted.rst new file mode 100644 index 0000000000..008ebfebeb --- /dev/null +++ b/doc/src/angle_cosine_squared_restricted.rst @@ -0,0 +1,80 @@ +.. index:: angle_style cosine/squared/restricted +.. index:: angle_style cosine/squared/restricted/omp + +angle_style cosine/squared/restricted command +============================================= + +Accelerator Variants: *cosine/squared/restricted/omp* + +Syntax +"""""" + +.. code-block:: LAMMPS + + angle_style cosine/squared/restricted + +Examples +"""""""" + +.. code-block:: LAMMPS + + angle_style cosine/squared/restricted + angle_coeff 2*4 75.0 100.0 + +Description +""""""""""" + +.. versionadded:: 17Apr2024 + +The *cosine/squared/restricted* angle style uses the potential + +.. math:: + + E = K [\cos(\theta) - \cos(\theta_0)]^2 / \sin^2(\theta) + +, which is commonly used in the MARTINI force field, +where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` +is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. + +See :ref:`(Bulacu) ` for a description of the restricted angle for the MARTINI force field. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* :math:`K` (energy) +* :math:`\theta_0` (degrees) + +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally. + +---------- + +.. include:: accel_styles.rst + +---------- + +Restrictions +"""""""""""" + +This angle style can only be used if LAMMPS was built with the +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page +for more info. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +Default +""""""" + +none + +---------- + +.. _restricted-Bulacu: + +**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292 +(2013). diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 1f1ae72647..eeb174e772 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -10,7 +10,7 @@ Syntax angle_style style -* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table* +* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cosine/squared/restricted* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table* Examples """""""" @@ -84,6 +84,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`cosine/shift ` - angle cosine with a shift * :doc:`cosine/shift/exp ` - cosine with shift and exponential term in spring constant * :doc:`cosine/squared ` - angle with cosine squared term +* :doc:`cosine/squared/restricted ` - angle with restricted cosine squared term * :doc:`cross ` - cross term coupling angle and bond lengths * :doc:`dipole ` - angle that controls orientation of a point dipole * :doc:`fourier ` - angle with multiple cosine terms diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index 21590e6680..0d750f1755 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -71,11 +71,11 @@ all atoms, e.g. in a data or restart file. atom IDs are required, due to how neighbor lists are built. The *map* keyword determines how atoms with specific IDs are found -when required. An example are the bond (angle, etc) methods which -need to find the local index of an atom with a specific global ID -which is a bond (angle, etc) partner. LAMMPS performs this operation -efficiently by creating a "map", which is either an *array* or *hash* -table, as described below. +when required. For example, the bond (angle, etc) methods need to +find the local index of an atom with a specific global ID which is a +bond (angle, etc) partner. LAMMPS performs this operation efficiently +by creating a "map", which is either an *array* or *hash* table, as +described below. When the *map* keyword is not specified in your input script, LAMMPS only creates a map for :doc:`atom_styles ` for molecular @@ -83,34 +83,39 @@ systems which have permanent bonds (angles, etc). No map is created for atomic systems, since it is normally not needed. However some LAMMPS commands require a map, even for atomic systems, and will generate an error if one does not exist. The *map* keyword thus -allows you to force the creation of a map. The *yes* value will -create either an *array* or *hash* style map, as explained in the next -paragraph. The *array* and *hash* values create an array-style or -hash-style map respectively. +allows you to force the creation of a map. -For an *array*\ -style map, each processor stores a lookup table of -length N, where N is the largest atom ID in the system. This is a -fast, simple method for many simulations, but requires too much memory -for large simulations. For a *hash*\ -style map, a hash table is -created on each processor, which finds an atom ID in constant time -(independent of the global number of atom IDs). It can be slightly -slower than the *array* map, but its memory cost is proportional to -the number of atoms owned by a processor, i.e. N/P when N is the total -number of atoms in the system and P is the number of processors. +Specifying a value of *yes* will create either an array-style or +hash-style map, depending on the size of the system. If no atom ID is +larger than 1 million, then an array-style map is used, otherwise a +hash-style map is used. Specifying a value of *array* or *hash* +creates an array-style or hash-style map respectively, regardless of +the size of the system. -The *first* keyword allows a :doc:`group ` to be specified whose -atoms will be maintained as the first atoms in each processor's list -of owned atoms. This in only useful when the specified group is a -small fraction of all the atoms, and there are other operations LAMMPS -is performing that will be sped-up significantly by being able to loop -over the smaller set of atoms. Otherwise the reordering required by -this option will be a net slow-down. The :doc:`neigh_modify include ` and :doc:`comm_modify group ` -commands are two examples of commands that require this setting to -work efficiently. Several :doc:`fixes `, most notably time -integration fixes like :doc:`fix nve `, also take advantage of -this setting if the group they operate on is the group specified by -this command. Note that specifying "all" as the group-ID effectively -turns off the *first* option. +For an array-style map, each processor stores a lookup table of length +N, where N is the largest atom ID in the system. This is a fast, +simple method for many simulations, but requires too much memory for +large simulations. For a hash-style map, a hash table is created on +each processor, which finds an atom ID in constant time (independent +of the global number of atom IDs). It can be slightly slower than the +*array* map, but its memory cost is proportional to the number of +atoms owned by a processor, i.e. N/P when N is the total number of +atoms in the system and P is the number of processors. + +The *first* keyword allows a :doc:`group ` to be specified +whose atoms will be maintained as the first atoms in each processor's +list of owned atoms. This in only useful when the specified group is +a small fraction of all the atoms, and there are other operations +LAMMPS is performing that will be sped-up significantly by being able +to loop over the smaller set of atoms. Otherwise the reordering +required by this option will be a net slow-down. The +:doc:`neigh_modify include ` and :doc:`comm_modify group +` commands are two examples of commands that require this +setting to work efficiently. Several :doc:`fixes `, most notably +time integration fixes like :doc:`fix nve `, also take +advantage of this setting if the group they operate on is the group +specified by this command. Note that specifying "all" as the group-ID +effectively turns off the *first* option. It is OK to use the *first* keyword with a group that has not yet been defined, e.g. to use the atom_modify first command at the beginning of @@ -148,15 +153,16 @@ cache locality will be undermined. .. note:: - Running a simulation with sorting on versus off should not - change the simulation results in a statistical sense. However, a - different ordering will induce round-off differences, which will lead - to diverging trajectories over time when comparing two simulations. - Various commands, particularly those which use random numbers - (e.g. :doc:`velocity create `, and :doc:`fix langevin `), may generate (statistically identical) - results which depend on the order in which atoms are processed. The - order of atoms in a :doc:`dump ` file will also typically change - if sorting is enabled. + Running a simulation with sorting on versus off should not change + the simulation results in a statistical sense. However, a + different ordering will induce round-off differences, which will + lead to diverging trajectories over time when comparing two + simulations. Various commands, particularly those which use random + numbers (e.g. :doc:`velocity create `, and :doc:`fix + langevin `), may generate (statistically identical) + results which depend on the order in which atoms are processed. + The order of atoms in a :doc:`dump ` file will also typically + change if sorting is enabled. .. note:: @@ -183,12 +189,13 @@ Default By default, *id* is yes. By default, atomic systems (no bond topology info) do not use a map. For molecular systems (with bond topology -info), a map is used. The default map style is array if no atom ID is -larger than 1 million, otherwise the default is hash. By default, a -"first" group is not defined. By default, sorting is enabled with a -frequency of 1000 and a binsize of 0.0, which means the neighbor -cutoff will be used to set the bin size. If no neighbor cutoff is -defined, sorting will be turned off. +info), the default is to use a map of either *array* or *hash* style +depending on the size of the sustem, as explained above for the *map +yes* keyword/value option. By default, a *first* group is not +defined. By default, sorting is enabled with a frequency of 1000 and +a binsize of 0.0, which means the neighbor cutoff will be used to set +the bin size. If no neighbor cutoff is defined, sorting will be turned +off. ---------- diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 60a85e0bcb..f11cdf54b9 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -283,21 +283,22 @@ Note that there may be additional arguments required along with the arguments are described on the :doc:`Howto body ` doc page. For the *dielectric* style, each particle can be either a physical -particle (e.g. an ion), or an interface particle representing a boundary -element between two regions of different dielectric constant. For -interface particles, in addition to the properties associated with -atom_style full, each particle also should be assigned a normal unit -vector (defined by normx, normy, normz), an area (area/patch), the +particle (e.g. an ion), or an interface particle representing a +boundary element between two regions of different dielectric +constant. For interface particles, in addition to the properties +associated with atom_style full, each particle also should be assigned +a unit dipole vector (mu) representing the direction of the induced +dipole moment at each interface particle, an area (area/patch), the difference and mean of the dielectric constants of two sides of the interface along the direction of the normal vector (ed and em), the -local dielectric constant at the boundary element (epsilon), and a mean -local curvature (curv). Physical particles must be assigned these -values, as well, but only their local dielectric constants will be used; -see documentation for associated :doc:`pair styles ` -and :doc:`fixes `. The distinction between the physical -and interface particles is only meaningful when :doc:`fix polarize -` commands are applied to the interface particles. This -style is part of the DIELECTRIC package. +local dielectric constant at the boundary element (epsilon), and a +mean local curvature (curv). Physical particles must be assigned +these values, as well, but only their local dielectric constants will +be used; see documentation for associated :doc:`pair styles +` and :doc:`fixes `. The distinction +between the physical and interface particles is only meaningful when +:doc:`fix polarize ` commands are applied to the +interface particles. This style is part of the DIELECTRIC package. For the *dipole* style, a point dipole vector mu is defined for each point particle. Note that if you wish the particles to be finite-size diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 1ffd4a1c98..ea90ed2b57 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -1,8 +1,11 @@ .. index:: bond_style hybrid +.. index:: bond_style hybrid/kk bond_style hybrid command ========================= +Accelerator Variants: *hybrid/kk* + Syntax """""" @@ -15,7 +18,7 @@ Syntax Examples """""""" -.. code-block: LAMMPS +.. code-block:: LAMMPS bond_style hybrid harmonic fene bond_coeff 1 harmonic 80.0 1.2 @@ -60,6 +63,10 @@ bond types. ---------- +.. include:: accel_styles.rst + +---------- + Restrictions """""""""""" diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 1bce606da7..f395634b0b 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -27,6 +27,7 @@ Examples .. code-block:: LAMMPS + # LJ units bond_style oxdna/fene bond_coeff * 2.0 0.25 0.7525 @@ -36,6 +37,32 @@ Examples bond_style oxrna2/fene bond_coeff * 2.0 0.25 0.76107 + bond_style oxdna/fene + bond_coeff * oxdna_lj.cgdna + + # Real units + bond_style oxdna/fene + bond_coeff * 11.92337812042065 2.1295 6.409795 + + bond_style oxdna2/fene + bond_coeff * 11.92337812042065 2.1295 6.4430152 + + bond_style oxrna2/fene + bond_coeff * 11.92337812042065 2.1295 6.482800913 + + bond_style oxrna2/fene + bond_coeff * oxrna2_real.cgdna + +.. note:: + + The coefficients in the above examples have to be kept fixed and + cannot be changed without reparameterizing the entire model. They are + provided in forms compatible with both *units lj* and *units real* + (see documentation of :doc:`units `). These can also be read + from a potential file with correct unit style by specifying the name + of the file. Several potential files for each unit style are included + in the ``potentials`` directory of the LAMMPS distribution. + Description """"""""""" @@ -46,15 +73,14 @@ The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right] to define a modified finite extensible nonlinear elastic (FENE) -potential :ref:`(Ouldridge) ` to model the connectivity of the -phosphate backbone in the oxDNA/oxRNA force field for coarse-grained +potential :ref:`(Ouldridge) ` to model the connectivity of +the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained modelling of DNA/RNA. The following coefficients must be defined for the bond type via the :doc:`bond_coeff ` command as given in the above example, or -in the data file or restart files read by the -:doc:`read_data ` or :doc:`read_restart ` -commands: +in the data file or restart files read by the :doc:`read_data +` or :doc:`read_restart ` commands: * :math:`\epsilon` (energy) * :math:`\Delta` (distance) @@ -62,41 +88,40 @@ commands: .. note:: - The oxDNA bond style has to be used together with the - corresponding oxDNA pair styles for excluded volume interaction - *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and - coaxial stacking interaction *oxdna/coaxstk* as well as - hydrogen-bonding interaction *oxdna/hbond* (see also documentation of - :doc:`pair_style oxdna/excv `). For the oxDNA2 - :ref:`(Snodin) ` bond style the analogous pair styles - *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* , - *oxdna2/hbond* and an additional Debye-Hueckel pair style - *oxdna2/dh* have to be defined. The same applies to the oxRNA2 - :ref:`(Sulc1) ` styles. - The coefficients in the above example have to be kept fixed and cannot - be changed without reparameterizing the entire model. + The oxDNA bond style has to be used together with the corresponding + oxDNA pair styles for excluded volume interaction *oxdna/excv* , + stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial + stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding + interaction *oxdna/hbond* (see also documentation of :doc:`pair_style + oxdna/excv `). For the oxDNA2 :ref:`(Snodin) ` + bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* , + *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional + Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same + applies to the oxRNA2 :ref:`(Sulc1) ` styles. .. note:: - This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna* - (see documentation of :doc:`atom_style `). The *atom_style oxdna* - stores the 3'-to-5' polarity of the nucleotide strand, which is set through - the bond topology in the data file. The first (second) atom in a bond definition - is understood to point towards the 3'-end (5'-end) of the strand. + This bond style has to be used with the *atom_style hybrid bond + ellipsoid oxdna* (see documentation of :doc:`atom_style + `). The *atom_style oxdna* stores the 3'-to-5' polarity + of the nucleotide strand, which is set through the bond topology in + the data file. The first (second) atom in a bond definition is + understood to point towards the 3'-end (5'-end) of the strand. .. warning:: - If data files are produced with :doc:`write_data `, then the - :doc:`newton ` command should be set to *newton on* or *newton off on*. - Otherwise the data files will not have the same 3'-to-5' polarity as the - initial data file. This limitation does not apply to binary restart files - produced with :doc:`write_restart `. + If data files are produced with :doc:`write_data `, then + the :doc:`newton ` command should be set to *newton on* or + *newton off on*. Otherwise the data files will not have the same + 3'-to-5' polarity as the initial data file. This limitation does not + apply to binary restart files produced with :doc:`write_restart + `. Example input and data files for DNA and RNA duplexes can be found in -examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python -setup tool which creates single straight or helical DNA strands, DNA/RNA -duplexes or arrays of DNA/RNA duplexes can be found in -examples/PACKAGES/cgdna/util/. +``examples/PACKAGES/cgdna/examples/oxDNA/`, `.../oxDNA2/`` and +``.../oxRNA2/``. A simple python setup tool which creates single +straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA +duplexes can be found in ``examples/PACKAGES/cgdna/util/``. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. An updated documentation that contains general information @@ -113,6 +138,39 @@ and for sequence-specific hydrogen-bonding and stacking interactions ---------- +Potential file reading +"""""""""""""""""""""" + +For each style oxdna, oxdna2 and oxrna2, the first parameter argument +can be a filename, and if it is, no further arguments should be +supplied. Therefore the following command: + +.. code-block:: LAMMPS + + bond_style oxdna/fene + bond_coeff * oxdna_lj.cgdna + +will be interpreted as a request to read the (FENE) potential +:ref:`(Ouldridge) ` parameters from the file with the given +name. The file can define multiple potential parameters for both bonded +and pair interactions, but for the above bonded interactions there must +exist in the file a line of the form: + +.. code-block:: LAMMPS + + * fene epsilon delta r0 + +There are sample potential files for each unit style in the +``potentials`` directory of the LAMMPS distribution. The potential file +unit system must align with the units defined via the :doc:`units +` command. For conversion between different *LJ* and *real* unit +systems for oxDNA, the python tool *lj2real.py* located in the +``examples/PACKAGES/cgdna/util/`` directory can be used. This tool +assumes similar file structure to the examples found in +``examples/PACKAGES/cgdna/examples/``. + +---------- + Restrictions """""""""""" diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index 8e019e801c..06f125ed4f 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -42,8 +42,10 @@ commands. The style *p* means the box is periodic, so that particles interact across the boundary, and they can exit one end of the box and re-enter the other end. A periodic dimension can change in size due to -constant pressure boundary conditions or box deformation (see the :doc:`fix npt ` and :doc:`fix deform ` commands). The *p* -style must be applied to both faces of a dimension. +constant pressure boundary conditions or box deformation (see the +:doc:`fix npt ` and :doc:`fix deform ` commands). +The *p* style must be applied to both faces of a dimension. For 2d +simulations the z dimension must be periodic (which is the default). The styles *f*, *s*, and *m* mean the box is non-periodic, so that particles do not interact across the boundary and do not move from one @@ -76,28 +78,44 @@ atoms becomes less than 50.0. This can be useful if you start a simulation with an empty box or if you wish to leave room on one side of the box, e.g. for atoms to evaporate from a surface. -For triclinic (non-orthogonal) simulation boxes, if the second dimension -of a tilt factor (e.g. y for xy) is periodic, then the periodicity is -enforced with the tilt factor offset. If the first dimension is -shrink-wrapped, then the shrink wrapping is applied to the tilted box -face, to encompass the atoms. E.g. for a positive xy tilt, the xlo -and xhi faces of the box are planes tilting in the +y direction as y -increases. These tilted planes are shrink-wrapped around the atoms to -determine the x extent of the box. - +LAMMPS also allows use of triclinic (non-orthogonal) simulation boxes. See the :doc:`Howto triclinic ` page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. +description of both general and restricted triclinic boxes and how to +define them. General triclinic boxes (arbitrary edge vectors **A**, +**B**, and **C**) are converted internally to restricted triclinic +boxes with tilt factors (xy,xz,yz) which skew an otherwise orthogonal +box. + +The boundary command settings explained above for the 6 +faces of an orthogonal box also apply in similar manner to the 6 faces +of a restricted triclinic box (and thus to the corresponding 6 faces +of a general triclinic box), with the following context. + +if the second dimension of a tilt factor (e.g. y for xy) is periodic, +then the periodicity is enforced with the tilt factor offset. This +means that for y periodicity a particle which exits the lower y +boundary is displaced in the x-direction by xy before it re-enters the +upper y boundary. And vice versa if a particle exits the upper y +boundary. Likewise the ghost atoms surrounding a particle near the +lower y boundary include images of particles near the upper y-boundary +which are displaced in the x-direction by xy. Similar rules apply for +z-periodicity and the xz and/or yz tilt factors. + +If the first dimension of a tilt factor is shrink-wrapped, then the +shrink wrapping is applied to the tilted box face, to encompass the +atoms. E.g. for a positive xy tilt, the xlo and xhi faces of the box +are planes tilting in the +y direction as y increases. The position +of these tilted planes are adjusted dynamically to shrink-wrap around +the atoms to determine the xlo and xhi extents of the box. Restrictions """""""""""" This command cannot be used after the simulation box is defined by a -:doc:`read_data ` or :doc:`create_box ` command or -:doc:`read_restart ` command. See the -:doc:`change_box ` command for how to change the simulation -box boundaries after it has been defined. +:doc:`read_data ` or :doc:`create_box ` command +or :doc:`read_restart ` command. See the +:doc:`change_box ` command for how to change the +simulation box boundaries after it has been defined. For 2d simulations, the z dimension must be periodic. diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 7b620deed7..05181b9e7e 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -272,6 +272,10 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`pe/mol/tally ` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism * :doc:`pe/tally ` - potential energy between two groups of atoms via the tally callback mechanism * :doc:`plasticity/atom ` - Peridynamic plasticity for each atom +* :doc:`pod/atom ` - POD descriptors for each atom +* :doc:`podd/atom ` - derivative of POD descriptors for each atom +* :doc:`pod/local ` - local POD descriptors and their derivatives +* :doc:`pod/global ` - global POD descriptors and their derivatives * :doc:`pressure ` - total pressure and pressure tensor * :doc:`pressure/alchemy ` - mixed system total pressure and pressure tensor for :doc:`fix alchemy ` runs * :doc:`pressure/uef ` - pressure tensor in the reference frame of an applied flow field diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index fc1ad1ae0a..a43a10207c 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -204,8 +204,23 @@ angles per atom satisfying the ADF criteria. Restrictions """""""""""" -This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +By default, the ADF is not computed for distances longer than the +largest force cutoff, since the neighbor list creation will only contain +pairs up to that distance (plus neighbor list skin). If you use outer +cutoffs larger than that, you must use :doc:`neighbor style 'bin' or +'nsq' `. + +If you want an ADF for a larger outer cutoff, you can also use the +:doc:`rerun ` command to post-process a dump file, use :doc:`pair +style zero ` and set the force cutoff to be larger in the +rerun script. Note that in the rerun context, the force cutoff is +arbitrary and with pair style zero you are not computing any forces, and +since you are not running dynamics you are not changing the model that +generated the trajectory. The ADF is not computed for neighbors outside the force cutoff, since processors (in parallel) don't know about atom coordinates for diff --git a/doc/src/compute_ave_sphere_atom.rst b/doc/src/compute_ave_sphere_atom.rst index ecb67ae7b5..4640b8534a 100644 --- a/doc/src/compute_ave_sphere_atom.rst +++ b/doc/src/compute_ave_sphere_atom.rst @@ -102,6 +102,8 @@ This compute is part of the EXTRA-COMPUTE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +This compute requires :doc:`neighbor styles 'bin' or 'nsq' `. + Related commands """""""""""""""" diff --git a/doc/src/compute_composition_atom.rst b/doc/src/compute_composition_atom.rst index e973eaa234..c3e6fb7c60 100644 --- a/doc/src/compute_composition_atom.rst +++ b/doc/src/compute_composition_atom.rst @@ -107,6 +107,8 @@ This compute is part of the EXTRA-COMPUTE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +This compute requires :doc:`neighbor styles 'bin' or 'nsq' `. + Related commands """""""""""""""" diff --git a/doc/src/compute_count_type.rst b/doc/src/compute_count_type.rst index ca3b02ecdb..5fbe6175a3 100644 --- a/doc/src/compute_count_type.rst +++ b/doc/src/compute_count_type.rst @@ -12,7 +12,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * count/type = style name of this compute command -* mode = {atom} or {bond} or {angle} or {dihedral} or {improper} +* mode = *atom* or *bond* or *angle* or *dihedral* or *improper* Examples """""""" @@ -69,29 +69,42 @@ for each type: ---------- -If the {mode} setting is {atom} then the count of atoms for each atom +If the *mode* setting is *atom* then the count of atoms for each atom type is tallied. Only atoms in the specified group are counted. -If the {mode} setting is {bond} then the count of bonds for each bond +The atom count for each type can be normalized by the total number of +atoms like so: + +.. code-block:: LAMMPS + + compute typevec all count/type atom # number of atoms of each type + variable normtypes vector c_typevec/atoms # divide by total number of atoms + variable ntypes equal extract_setting(ntypes) # number of atom types + thermo_style custom step v_normtypes[*${ntypes}] # vector variable needs upper limit + +Similarly, bond counts can be normalized by the total number of bonds. +The same goes for angles, dihedrals, and impropers (see below). + +If the *mode* setting is *bond* then the count of bonds for each bond type is tallied. Only bonds with both atoms in the specified group are counted. -For {mode} = {bond}, broken bonds with a bond type of zero are also +For *mode* = *bond*, broken bonds with a bond type of zero are also counted. The :doc:`bond_style quartic ` and :doc:`BPM -bond styles ` break bonds by doing this. See the :doc:` -Howto broken bonds ` doc page for more details. +bond styles ` break bonds by doing this. See the +:doc:`Howto broken bonds ` doc page for more details. Note that the group setting is ignored for broken bonds; all broken bonds in the system are counted. -If the {mode} setting is {angle} then the count of angles for each +If the *mode* setting is *angle* then the count of angles for each angle type is tallied. Only angles with all 3 atoms in the specified group are counted. -If the {mode} setting is {dihedral} then the count of dihedrals for +If the *mode* setting is *dihedral* then the count of dihedrals for each dihedral type is tallied. Only dihedrals with all 4 atoms in the specified group are counted. -If the {mode} setting is {improper} then the count of impropers for +If the *mode* setting is *improper* then the count of impropers for each improper type is tallied. Only impropers with all 4 atoms in the specified group are counted. @@ -101,18 +114,19 @@ Output info """"""""""" This compute calculates a global vector of counts. If the mode is -{atom} or {bond} or {angle} or {dihedral} or {improper}, then the +*atom* or *bond* or *angle* or *dihedral* or *improper*, then the vector length is the number of atom types or bond types or angle types or dihedral types or improper types, respectively. -If the mode is {bond} this compute also calculates a global scalar +If the mode is *bond* this compute also calculates a global scalar which is the number of broken bonds with type = 0, as explained above. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar and vector values calculated by this compute are "extensive". +The scalar and vector values calculated by this compute are both +"intensive". Restrictions """""""""""" diff --git a/doc/src/compute_efield_wolf_atom.rst b/doc/src/compute_efield_wolf_atom.rst index 1a709dc9f2..93bfa55151 100644 --- a/doc/src/compute_efield_wolf_atom.rst +++ b/doc/src/compute_efield_wolf_atom.rst @@ -106,6 +106,8 @@ Restrictions This compute is part of the EXTRA-COMPUTE package. It is only enabled if LAMMPS was built with that package. +This compute requires :doc:`neighbor styles 'bin' or 'nsq' `. + Related commands """""""""""""""" diff --git a/doc/src/compute_mliap.rst b/doc/src/compute_mliap.rst index 6abd3e5a6b..4bd5194bfd 100644 --- a/doc/src/compute_mliap.rst +++ b/doc/src/compute_mliap.rst @@ -20,7 +20,7 @@ Syntax *model* values = style style = *linear* or *quadratic* or *mliappy* *descriptor* values = style filename - style = *sna* + style = *sna* or *ace* filename = name of file containing descriptor definitions *gradgradflag* value = 0/1 toggle gradgrad method for force gradient @@ -31,6 +31,7 @@ Examples .. code-block:: LAMMPS compute mliap model linear descriptor sna Ta06A.mliap.descriptor + compute mliap model linear descriptor ace H_N_O_ccs.yace gradgradflag 1 Description """"""""""" @@ -40,18 +41,15 @@ of machine-learning interatomic potentials with respect to model parameters. It is used primarily for calculating the gradient of energy, force, and stress components with respect to model parameters, which is useful when training :doc:`mliap pair_style ` models to match target data. -It provides separate -definitions of the interatomic potential functional form (*model*) -and the geometric quantities that characterize the atomic positions -(*descriptor*). By defining *model* and *descriptor* separately, +It provides separate definitions of the interatomic potential functional +form (*model*) and the geometric quantities that characterize the atomic +positions (*descriptor*). By defining *model* and *descriptor* separately, it is possible to use many different models with a given descriptor, -or many different descriptors with a given model. Currently, the -compute supports just two models, *linear* and *quadratic*, -and one descriptor, *sna*, the SNAP descriptor used by -:doc:`pair_style snap `, including the linear, quadratic, -and chem variants. Work is currently underway to extend -the interface to handle neural network energy models, -and it is also straightforward to add new descriptor styles. +or many different descriptors with a given model. Currently, the compute +supports *linear* and *quadratic* SNAP descriptor computes used in +:doc:`pair_style snap `, *linear* SO3 descriptor computes, and +*linear* ACE descriptor computes used in :doc:`pair_style pace `, +and it is straightforward to add new descriptor styles. The compute *mliap* command must be followed by two keywords *model* and *descriptor* in either order. @@ -60,19 +58,31 @@ The *model* keyword is followed by the model style (*linear*, *quadratic* or *mliappy*). The *mliappy* model is only available if LAMMPS is built with the *mliappy* Python module. There are :ref:`specific installation instructions ` for that module. +For the *mliap* compute, specifying a *linear* model will compute the +specified descriptors and gradients with respect to linear model parameters +whereas *quadratic* will do the same, but for the quadratic products of +descriptors. The *descriptor* keyword is followed by a descriptor style, and -additional arguments. The compute currently supports two descriptor -styles *sna* and *so3*, but it is is straightforward to add additional -descriptor styles. The SNAP descriptor style *sna* is the same as that -used by :doc:`pair_style snap `, including the linear, -quadratic, and chem variants. A single additional argument specifies -the descriptor filename containing the parameters and setting used by -the SNAP descriptor. The descriptor filename usually ends in the +additional arguments. The compute currently supports three descriptor +styles: *sna*, *so3*, and *ace*, but it is is straightforward to add +additional descriptor styles. The SNAP descriptor style *sna* is the +same as that used by :doc:`pair_style snap `, including the +linear, quadratic, and chem variants. A single additional argument +specifies the descriptor filename containing the parameters and setting used +by the SNAP descriptor. The descriptor filename usually ends in the *.mliap.descriptor* extension. The format of this file is identical to the descriptor file in the :doc:`pair_style mliap `, and is described in detail there. +The ACE descriptor style *ace* is the same as :doc:`pair_style pace `. +A single additional argument specifies the *ace* descriptor filename +that contains parameters and settings for the ACE descriptors. This file +format differs from the SNAP or SO3 descriptor files, and has a *.yace* or +*.ace* extension. However, as with other mliap descriptor styles, this file +is identical to the ace descriptor file in :doc:`pair_style mliap `, +where it is described in further detail. + .. note:: The number of LAMMPS atom types (and the value of *nelems* in the model) @@ -172,8 +182,10 @@ This compute is part of the ML-IAP package. It is only enabled if LAMMPS was built with that package. In addition, building LAMMPS with the ML-IAP package requires building LAMMPS with the ML-SNAP package. The *mliappy* model also requires building LAMMPS with the PYTHON -package. See the :doc:`Build package ` page for more -info. +package. The *ace* descriptor also requires building LAMMPS with the +ML-PACE package. See the :doc:`Build package ` page for +more info. Note that `kk` (KOKKOS) accelerated variants of SNAP and +ACE descriptors are not compatible with `mliap descriptor`. Related commands """""""""""""""" diff --git a/doc/src/compute_pod_atom.rst b/doc/src/compute_pod_atom.rst new file mode 100644 index 0000000000..caa70dfa2c --- /dev/null +++ b/doc/src/compute_pod_atom.rst @@ -0,0 +1,145 @@ +.. index:: compute pod/atom +.. index:: compute podd/atom +.. index:: compute pod/local +.. index:: compute pod/global + +compute pod/atom command +======================== + +compute podd/atom command +========================= + +compute pod/local command +========================= + +compute pod/global command +========================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + compute ID group-ID pod/atom param.pod coefficients.pod + compute ID group-ID podd/atom param.pod coefficients.pod + compute ID group-ID pod/local param.pod coefficients.pod + compute ID group-ID pod/global param.pod coefficients.pod + +* ID, group-ID are documented in :doc:`compute ` command +* pod/atom = style name of this compute command +* param.pod = the parameter file specifies parameters of the POD descriptors +* coefficients.pod = the coefficient file specifies coefficients of the POD potential + +Examples +"""""""" + +.. code-block:: LAMMPS + + compute d all pod/atom Ta_param.pod + compute dd all podd/atom Ta_param.pod + compute ldd all pod/local Ta_param.pod + compute gdd all podd/global Ta_param.pod + compute d all pod/atom Ta_param.pod Ta_coefficients.pod + compute dd all podd/atom Ta_param.pod Ta_coefficients.pod + compute ldd all pod/local Ta_param.pod Ta_coefficients.pod + compute gdd all podd/global Ta_param.pod Ta_coefficients.pod + +Description +""""""""""" + +.. versionadded:: 27June2024 + +Define a computation that calculates a set of quantities related to the +POD descriptors of the atoms in a group. These computes are used +primarily for calculating the dependence of energy and force components +on the linear coefficients in the :doc:`pod pair_style `, +which is useful when training a POD potential to match target data. POD +descriptors of an atom are characterized by the radial and angular +distribution of neighbor atoms. The detailed mathematical definition is +given in the papers by :ref:`(Nguyen and Rohskopf) `, +:ref:`(Nguyen2023) `, :ref:`(Nguyen2024) `, +and :ref:`(Nguyen and Sema) `. + +Compute *pod/atom* calculates the per-atom POD descriptors. + +Compute *podd/atom* calculates derivatives of the per-atom POD +descriptors with respect to atom positions. + +Compute *pod/local* calculates the per-atom POD descriptors and their +derivatives with respect to atom positions. + +Compute *pod/global* calculates the global POD descriptors and their +derivatives with respect to atom positions. + +Examples how to use Compute POD commands are found in the directory +``examples/PACKAGES/pod``. + + +.. warning:: + + All of these compute styles produce *very* large per-atom output + arrays that scale with the total number of atoms in the system. + This will result in *very* large memory consumption for systems + with a large number of atoms. + +---------- + +Output info +""""""""""" + +Compute *pod/atom* produces an 2D array of size :math:`N \times M`, +where :math:`N` is the number of atoms and :math:`M` is the number of +descriptors. Each column corresponds to a particular POD descriptor. + +Compute *podd/atom* produces an 2D array of size :math:`N \times (M * 3 +N)`. Each column corresponds to a particular derivative of a POD +descriptor. + +Compute *pod/local* produces an 2D array of size :math:`(1 + 3N) \times +(M * N)`. The first row contains the per-atom descriptors, and the last +3N rows contain the derivatives of the per-atom descriptors with respect +to atom positions. + +Compute *pod/global* produces an 2D array of size :math:`(1 + 3N) \times +(M)`. The first row contains the global descriptors, and the last 3N +rows contain the derivatives of the global descriptors with respect to +atom positions. + +Restrictions +"""""""""""" + +These computes are part of the ML-POD package. They are only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +Related commands +"""""""""""""""" + +:doc:`fitpod `, +:doc:`pair_style pod ` + + +Default +""""""" + +none + +---------- + +.. _Nguyen20222c: + +**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023). + +.. _Nguyen20232c: + +**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023). + +.. _Nguyen20242c: + +**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024). + +.. _Nguyen20243c: + +**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024). + + diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index ed73800f82..1330c6f300 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -13,8 +13,8 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * rdf = style name of this compute command * Nbin = number of RDF bins -* itypeN = central atom type for Nth RDF histogram (see asterisk form below) -* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) +* itypeN = central atom type for Nth RDF histogram (integer, type label, or asterisk form) +* jtypeN = distribution atom type for Nth RDF histogram (integer, type label, or asterisk form) * zero or more keyword/value pairs may be appended * keyword = *cutoff* @@ -96,14 +96,16 @@ is computed for :math:`g(r)` between all atom types. If one or more pairs are listed, then a separate histogram is generated for each *itype*,\ *jtype* pair. -The *itypeN* and *jtypeN* settings can be specified in one of two -ways. An explicit numeric value can be used, as in the fourth example -above. Or a wild-card asterisk can be used to specify a range of atom -types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If -:math:`N` is the number of atom types, then an asterisk with no numeric values -means all types from 1 to :math:`N`. A leading asterisk means all types from 1 -to n (inclusive). A trailing asterisk means all types from m to :math:`N` -(inclusive). A middle asterisk means all types from m to n (inclusive). +The *itypeN* and *jtypeN* settings can be specified in one of three +ways. One or both of the types in the I,J pair can be a +:doc:`type label `. Or an explicit numeric value can be +used, as in the fourth example above. Or a wild-card asterisk can be used +to specify a range of atom types. This takes the form "\*" or "\*n" or +"m\*" or "m\*n". If :math:`N` is the number of atom types, then an asterisk +with no numeric values means all types from 1 to :math:`N`. A leading +asterisk means all types from 1 to n (inclusive). A trailing asterisk +means all types from m to :math:`N` (inclusive). A middle asterisk means +all types from m to n (inclusive). If both *itypeN* and *jtypeN* are single values, as in the fourth example above, this means that a :math:`g(r)` is computed where atoms of type *itypeN* @@ -176,22 +178,29 @@ also numbers :math:`\ge 0.0`. Restrictions """""""""""" -The RDF is not computed for distances longer than the force cutoff, -since processors (in parallel) do not know about atom coordinates for -atoms further away than that distance. If you want an RDF for larger -distances, you can use the :doc:`rerun ` command to post-process -a dump file and set the cutoff for the potential to be longer in the +By default, the RDF is not computed for distances longer than the +largest force cutoff, since the neighbor list creation will only contain +pairs up to that distance (plus neighbor list skin). This distance can +be increased using the *cutoff* keyword but this keyword is only valid +with :doc:`neighbor styles 'bin' and 'nsq' `. + +If you want an RDF for larger distances, you can also use the +:doc:`rerun ` command to post-process a dump file, use :doc:`pair +style zero ` and set the force cutoff to be longer in the rerun script. Note that in the rerun context, the force cutoff is -arbitrary, since you are not running dynamics and thus are not changing -your model. The definition of :math:`g(r)` used by LAMMPS is only appropriate -for characterizing atoms that are uniformly distributed throughout the -simulation cell. In such cases, the coordination number is still -correct and meaningful. As an example, if a large simulation cell -contains only one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)` -will register an arbitrarily large spike at whatever distance they -happen to be at, and zero everywhere else. -The function :math:`\text{coord}(r)` will show a step -change from zero to one at the location of the spike in :math:`g(r)`. +arbitrary and with pair style zero you are not computing any forces, and +you are not running dynamics you are not changing the model that +generated the trajectory. + +The definition of :math:`g(r)` used by LAMMPS is only appropriate for +characterizing atoms that are uniformly distributed throughout the +simulation cell. In such cases, the coordination number is still correct +and meaningful. As an example, if a large simulation cell contains only +one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)` will +register an arbitrarily large spike at whatever distance they happen to +be at, and zero everywhere else. The function :math:`\text{coord}(r)` +will show a step change from zero to one at the location of the spike in +:math:`g(r)`. .. note:: diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index 6630c7171f..b4779b8bf3 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -126,7 +126,7 @@ These styles are part of the EXTRA-COMPUTE package. They are only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page on for more info. -The method is only implemented for 3d orthogonal simulation boxes whose +The method is implemented for orthogonal simulation boxes whose size does not change in time, and axis-aligned planes. The method only works with two-body pair interactions, because it diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 7f67670506..44f569548b 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -10,7 +10,7 @@ Syntax create_atoms type style args keyword values ... -* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) +* type = atom type (1-Ntypes or type label) of atoms to create (offset for molecule creation) * style = *box* or *region* or *single* or *mesh* or *random* .. parsed-literal:: @@ -37,7 +37,7 @@ Syntax seed = random # seed (positive integer) *basis* values = M itype M = which basis atom - itype = atom type (1-N) to assign to this basis atom + itype = atom type (1-Ntypes or type label) to assign to this basis atom *ratio* values = frac seed frac = fraction of lattice sites (0 to 1) to populate randomly seed = random # seed (positive integer) @@ -74,6 +74,13 @@ Examples .. code-block:: LAMMPS create_atoms 1 box + + labelmap atom 1 Pt + create_atoms Pt box + + labelmap atom 1 C 2 Si + create_atoms C region regsphere basis Si C + create_atoms 3 region regsphere basis 2 3 create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637 create_atoms 3 single 0 0 5 @@ -86,25 +93,46 @@ Description """"""""""" This command creates atoms (or molecules) within the simulation box, -either on a lattice, or a single atom (or molecule), or on a surface -defined by a triangulated mesh, or a random collection of atoms (or -molecules). It is an alternative to reading in atom coordinates +either on a lattice, or at random points, or on a surface defined by a +triangulated mesh. Or it creates a single atom (or molecule) at a +specified point. It is an alternative to reading in atom coordinates explicitly via a :doc:`read_data ` or :doc:`read_restart -` command. A simulation box must already exist, which is +` command. + +To use this command a simulation box must already exist, which is typically created via the :doc:`create_box ` command. -Before using this command, a lattice must also be defined using the -:doc:`lattice ` command, unless you specify the *single* style -with units = box or the *random* style. For the remainder of this doc -page, a created atom or molecule is referred to as a "particle". +Before using this command, a lattice must typically also be defined +using the :doc:`lattice ` command, unless you specify the +*single* or *mesh* style with units = box or the *random* style. To +create atoms on a lattice for general triclinic boxes, see the +discussion below. + +For the remainder of this doc page, a created atom or molecule is +referred to as a "particle". If created particles are individual atoms, they are assigned the specified atom *type*, though this can be altered via the *basis* keyword as discussed below. If molecules are being created, the type -of each atom in the created molecule is specified in the file read by -the :doc:`molecule ` command, and those values are added to -the specified atom *type* (e.g., if *type* = 2 and the file specifies -atom types 1, 2, and 3, then each created molecule will have atom types -3, 4, and 5). +of each atom in the created molecule is specified in a specified file +read by the :doc:`molecule ` command, and those values are +added to the specified atom *type* (e.g., if *type* = 2 and the file +specifies atom types 1, 2, and 3, then each created molecule will have +atom types 3, 4, and 5). + +.. note:: + + You cannot use this command to create atoms that are outside the + simulation box; they will just be ignored by LAMMPS. This is true + even if you are using shrink-wrapped box boundaries, as specified + by the :doc:`boundary ` command. However, you can first + use the :doc:`change_box ` command to temporarily + expand the box, then add atoms via create_atoms, then finally use + change_box command again if needed to re-shrink-wrap the new atoms. + See the :doc:`change_box ` doc page for an example of + how to do this, using the create_atoms *single* style to insert a + new atom outside the current simulation box. + +---------- For the *box* style, the create_atoms command fills the entire simulation box with particles on the lattice. If your simulation box @@ -126,10 +154,117 @@ periodic boundaries. If this is desired, you should either use the *box* style, or tweak the region size to get precisely the particles you want. +---------- + +If the simulation box is formulated as a general triclinic box defined +by arbitrary edge vectors **A**, **B**, **C**, then the *box* and +*region* styles will create atoms on a lattice commensurate with those +edge vectors. See the :doc:`Howto_triclinic ` doc +page for a detailed explanation of orthogonal, restricted triclinic, +and general triclinic simulation boxes. As with the :doc:`create_box +` command, the :doc:`lattice ` command used by +this command must be of style *custom* and use its *triclinic/general* +option. The *a1, *a2*, *a3* settings of the :doc:`lattice ` +command define the edge vectors of a unit cell of the general +triclinic lattice. The :doc:`create_box ` command creates +a simulation box which replicates that unit cell along each of the +**A**, **B**, **C** edge vectors. + +.. note:: + + LAMMPS allows specification of general triclinic simulation boxes + as a convenience for users who may be converting data from + solid-state crystallographic representations or from DFT codes for + input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally, + LAMMPS only uses restricted triclinic simulation boxes. This means + the box created by the :doc:`create_box ` command as + well as the atoms created by this command with their per-atom + information (e.g. coordinates, velocities) are converted (rotated) + from general to restricted triclinic form when the two commands are + invoked. The ` doc page also discusses other + LAMMPS commands which can input/output general triclinic + representations of the simulation box and per-atom data. + +The *box* style will fill the entire general triclinic box with +particles on the lattice, as explained above. + +.. note:: + + The *region* style also operates as explained above, but the check + for particles inside the region is performed *after* the particle + coordinates have been converted to the restricted triclinic box. + This means the region must also be defined with respect to the + restricted triclinic box, not the general triclinic box. + +If the simulation box is general triclinic, the *single*, *random*, +and *mesh* styles described next operate on the box *after* it has +been converted to restricted triclinic. So all the settings for those +styles should be made in that context. + +---------- + For the *single* style, a single particle is added to the system at the specified coordinates. This can be useful for debugging purposes or to create a tiny system with a handful of particles at specified -positions. +positions. For a 2d simulation the specified z coordinate must be +0.0. + +.. versionchanged:: 2Jun2022 + +The *porosity* style has been renamed to *random* with added functionality. + +For the *random* style, *N* particles are added to the system at +randomly generated coordinates, which can be useful for generating an +amorphous system. For 2d simulations, the z coordinates of all added +atoms will be 0.0. + +The particles are created one by one using the specified random number +*seed*, resulting in the same set of particle coordinates, independent +of how many processors are being used in the simulation. Unless the +*overlap* keyword is specified, particles created by the *random* +style will typically be highly overlapped. Various additional +criteria can be used to accept or reject a random particle insertion; +see the keyword discussion below. Multiple attempts per particle are +made (see the *maxtry* keyword) until the insertion is either +successful or fails. If this command fails to add all requested *N* +particles, a warning will be output. + +If the *region-ID* argument is specified as NULL, then the randomly +created particles will be anywhere in the simulation box. If a +*region-ID* is specified, a geometric volume is filled that is both +inside the simulation box and is also consistent with the region +volume. See the :doc:`region ` command for details. Note +that a region can be specified so that its "volume" is either inside +or outside its geometric boundary. + +Note that the create_atoms command adds particles to those that +already exist. This means it can be used to add particles to a system +previously read in from a data or restart file. Or the create_atoms +command can be used multiple times, to add multiple sets of particles +to the simulation. For example, grain boundaries can be created, by +interleaving the create_atoms command with :doc:`lattice ` +commands specifying different orientations. + +When this command is used, care should be taken to ensure the +resulting system does not contain particles that are highly +overlapped. Such overlaps will cause many interatomic potentials to +compute huge energies and forces, leading to bad dynamics. There are +several strategies to avoid this problem: + +* Use the :doc:`delete_atoms overlap ` command after + create_atoms. For example, this strategy can be used to overlay and + surround a large protein molecule with a volume of water molecules, + then delete water molecules that overlap with the protein atoms. + +* For the *random* style, use the optional *overlap* keyword to avoid + overlaps when each new particle is created. + +* Before running dynamics on an overlapped system, perform an + :doc:`energy minimization `. Or run initial dynamics with + :doc:`pair_style soft ` or with :doc:`fix nve/limit + ` to un-overlap the particles, before running normal + dynamics. .. figure:: img/marble_race.jpg :figwidth: 33% @@ -189,73 +324,6 @@ to the area of that triangle. beneficial to exclude computing interactions between the created particles using :doc:`neigh_modify exclude `. -.. versionchanged:: 2Jun2022 - -The *porosity* style has been renamed to *random* with added functionality. - -For the *random* style, *N* particles are added to the system at -randomly generated coordinates, which can be useful for generating an -amorphous system. The particles are created one by one using the -specified random number *seed*, resulting in the same set of particle -coordinates, independent of how many processors are being used in the -simulation. Unless the *overlap* keyword is specified, particles -created by the *random* style will typically be highly overlapped. -Various additional criteria can be used to accept or reject a random -particle insertion; see the keyword discussion below. Multiple -attempts per particle are made (see the *maxtry* keyword) until the -insertion is either successful or fails. If this command fails to add -all requested *N* particles, a warning will be output. - -If the *region-ID* argument is specified as NULL, then the randomly -created particles will be anywhere in the simulation box. If a -*region-ID* is specified, a geometric volume is filled that is both -inside the simulation box and is also consistent with the region -volume. See the :doc:`region ` command for details. Note -that a region can be specified so that its "volume" is either inside -or outside its geometric boundary. - -Note that the create_atoms command adds particles to those that -already exist. This means it can be used to add particles to a system -previously read in from a data or restart file. Or the create_atoms -command can be used multiple times, to add multiple sets of particles -to the simulation. For example, grain boundaries can be created, by -interleaving the create_atoms command with :doc:`lattice ` -commands specifying different orientations. - -When this command is used, care should be taken to ensure the -resulting system does not contain particles that are highly -overlapped. Such overlaps will cause many interatomic potentials to -compute huge energies and forces, leading to bad dynamics. There are -several strategies to avoid this problem: - -* Use the :doc:`delete_atoms overlap ` command after - create_atoms. For example, this strategy can be used to overlay and - surround a large protein molecule with a volume of water molecules, - then delete water molecules that overlap with the protein atoms. - -* For the *random* style, use the optional *overlap* keyword to avoid - overlaps when each new particle is created. - -* Before running dynamics on an overlapped system, perform an - :doc:`energy minimization `. Or run initial dynamics with - :doc:`pair_style soft ` or with :doc:`fix nve/limit - ` to un-overlap the particles, before running normal - dynamics. - -.. note:: - - You cannot use any of the styles explained above to create atoms - that are outside the simulation box; they will just be ignored by - LAMMPS. This is true even if you are using shrink-wrapped box - boundaries, as specified by the :doc:`boundary ` command. - However, you can first use the :doc:`change_box ` - command to temporarily expand the box, then add atoms via - create_atoms, then finally use change_box command again if needed - to re-shrink-wrap the new atoms. See the :doc:`change_box - ` doc page for an example of how to do this, using the - create_atoms *single* style to insert a new atom outside the - current simulation box. - ---------- Individual atoms are inserted by this command, unless the *mol* @@ -407,12 +475,13 @@ to. The *overlap* keyword only applies to the *random* style. It prevents newly created particles from being created closer than the specified -*Doverlap* distance from any other particle. When the particles being -created are molecules, the radius of the molecule (from its geometric -center) is added to *Doverlap*. If particles have finite size (see -:doc:`atom_style sphere ` for example) *Doverlap* should -be specified large enough to include the particle size in the -non-overlapping criterion. +*Doverlap* distance from any other particle. If particles have finite +size (see :doc:`atom_style sphere ` for example) *Doverlap* +should be specified large enough to include the particle size in the +non-overlapping criterion. If molecules are being randomly inserted, then +an insertion is only accepted if each particle in the molecule meets the +overlap criterion with respect to other particles (not including particles +in the molecule itself). .. note:: @@ -469,12 +538,19 @@ on a single CPU core. ----- The *units* keyword determines the meaning of the distance units used -to specify the coordinates of the one particle created by the *single* -style, or the overlap distance *Doverlap* by the *overlap* keyword. A -*box* value selects standard distance units as defined by the -:doc:`units ` command (e.g., :math:`\AA` for -units = *real* or *metal*\ . A *lattice* value means the distance units are in -lattice spacings. +by parameters for various styles. A *box* value selects standard +distance units as defined by the :doc:`units ` command (e.g., +:math:`\AA` for units = *real* or *metal*\ . A *lattice* value means +the distance units are in lattice spacings. These are affected settings: + +* for *single* style: coordinates of the particle created +* for *random* style: overlap distance *Doverlap* by the *overlap* keyword +* for *mesh* style: *bisect* threshold value for *meshmode* = *bisect* +* for *mesh* style: *radthresh* value for *meshmode* = *bisect* +* for *mesh* style: *density* value for *meshmode* = *qrand* + +Since *density* represents an area (distance ^2), the lattice spacing +factor is also squared. ---------- diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index f930ecea83..062fa2b360 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -9,9 +9,11 @@ Syntax .. code-block:: LAMMPS create_box N region-ID keyword value ... + create_box N NULL alo ahi blo bhi clo chi keyword value ... * N = # of atom types to use in this simulation -* region-ID = ID of region to use as simulation domain +* region-ID = ID of region to use as simulation domain or NULL for general triclinic box +* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc"`lattice ` command (only when region-ID = NULL) * zero or more keyword/value pairs may be appended * keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* @@ -32,121 +34,204 @@ Examples .. code-block:: LAMMPS + # orthogonal or restricted triclinic box using regionID = mybox create_box 2 mybox create_box 2 mybox bond/types 2 extra/bond/per/atom 1 +.. code-block:: LAMMPS + + # 2d general triclinic box using primitive cell for 2d hex lattice + lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 & + a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general + create_box 1 NULL 0 5 0 5 -0.5 0.5 + +.. code-block:: LAMMPS + + # 3d general triclinic box using primitive cell for 3d fcc lattice + lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general + create box 1 NULL -5 5 -10 10 0 20 + Description """"""""""" -This command creates a simulation box based on the specified region. -Thus a :doc:`region ` command must first be used to define a -geometric domain. It also partitions the simulation box into a -regular 3d grid of rectangular bricks, one per processor, based on the -number of processors being used and the settings of the -:doc:`processors ` command. The partitioning can later be -changed by the :doc:`balance ` or :doc:`fix balance ` commands. +This command creates a simulation box. It also partitions the box into +a regular 3d grid of smaller sub-boxes, one per processor (MPI task). +The geometry of the partitioning is based on the size and shape of the +simulation box, the number of processors being used and the settings +of the :doc:`processors ` command. The partitioning can +later be changed by the :doc:`balance ` or :doc:`fix balance +` commands. -The argument N is the number of atom types that will be used in the +Simulation boxes in LAMMPS can be either orthogonal or triclinic in +shape. Orthogonal boxes are a brick in 3d (rectangle in 2d) with 6 +faces that are each perpendicular to one of the standard xyz +coordinate axes. Triclinic boxes are a parallelepiped in 3d +(parallelogram in 2d) with opposite pairs of faces parallel to each +other. LAMMPS supports two forms of triclinic boxes, restricted and +general, which differ in how the box is oriented with respect to the +xyz coordinate axes. See the :doc:`Howto triclinic ` +for a detailed description of all 3 kinds of simulation boxes. + +The argument *N* is the number of atom types that will be used in the simulation. +Orthogonal and restricted triclinic boxes are created by specifying a +region ID previously defined by the :doc:`region ` command. +General triclinic boxes are discussed below. + If the region is not of style *prism*, then LAMMPS encloses the region (block, sphere, etc.) with an axis-aligned orthogonal bounding box -which becomes the simulation domain. +which becomes the simulation domain. For a 2d simulation, the zlo and +zhi values of the simulation box must straddle zero. If the region is of style *prism*, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. As defined by the :doc:`region prism ` command, the -parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by three -edge vectors starting from the origin given by -:math:`\vec a = (x_\text{hi}-x_\text{lo},0,0)`; -:math:`\vec b = (xy,y_\text{hi}-y_\text{lo},0)`; and -:math:`\vec c = (xz,yz,z_\text{hi}-z_\text{lo})`. -The parameters *xy*\ , *xz*\ , and *yz* can be 0.0 or -positive or negative values and are called "tilt factors" because they -are the amount of displacement applied to faces of an originally -orthogonal box to transform it into the parallelepiped. +parallelepiped has an "origin" at (xlo,ylo,zlo) and three edge vectors +starting from the origin given by :math:`\vec a = +(x_\text{hi}-x_\text{lo},0,0)`; :math:`\vec b = +(xy,y_\text{hi}-y_\text{lo},0)`; and :math:`\vec c = +(xz,yz,z_\text{hi}-z_\text{lo})`. In LAMMPS lingo, this is a +restricted triclinic box because the three edge vectors cannot be +defined in arbitrary (general) directions. The parameters *xy*\ , +*xz*\ , and *yz* can be 0.0 or positive or negative values and are +called "tilt factors" because they are the amount of displacement +applied to faces of an originally orthogonal box to transform it into +the parallelepiped. For a 2d simulation, the zlo and zhi values of +the simulation box must straddle zero. -By default, a *prism* region used with the create_box command must have -tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half -the distance of the parallel box length. For example, if -:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x` -box length is 10 and the :math:`xy` tilt factor must be between -:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz` -must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and +Typically a *prism* region used with the create_box command should +have tilt factors :math:`(xy,xz,yz)` that do not skew the box more +than half the distance of the parallel box length. For example, if +:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the +:math:`x` box length is 10 and the :math:`xy` tilt factor must be +between :math:`-5` and :math:`5`. Similarly, both :math:`xz` and +:math:`yz` must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and :math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this example), -then configurations with tilt :math:`= \dots, -15`, :math:`-5`, -:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically -equivalent. Simulations with large tilt factors will run inefficiently, -since they require more ghost atoms and thus more communication. With -very large tilt factors, LAMMPS will eventually produce incorrect -trajectories and stop with errors due to lost atoms or similar. +limitation, since if the maximum tilt factor is 5 (as in this +example), then configurations with tilt :math:`= \dots, -15`, +:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots` are all +geometrically equivalent. -See the :doc:`Howto triclinic ` page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. +LAMMPS will issue a warning if the tilt factors of the created box do +not meet this criterion. This is because simulations with large tilt +factors may run inefficiently, since they require more ghost atoms and +thus more communication. With very large tilt factors, LAMMPS may +eventually produce incorrect trajectories and stop with errors due to +lost atoms or similar issues. -When a prism region is used, the simulation domain should normally be periodic -in the dimension that the tilt is applied to, which is given by the second -dimension of the tilt factor (e.g., :math:`y` for :math:`xy` tilt). This is so -that pairs of atoms interacting across that boundary will have one of them -shifted by the tilt factor. Periodicity is set by the -:doc:`boundary ` command. For example, if the :math:`xy` tilt factor -is non-zero, then the :math:`y` dimension should be periodic. Similarly, the -:math:`z` dimension should be periodic if :math:`xz` or :math:`yz` is non-zero. -LAMMPS does not require this periodicity, but you may lose atoms if this is not -the case. +See the :doc:`Howto triclinic ` page for geometric +descriptions of triclinic boxes and tilt factors, as well as how to +transform the restricted triclinic parameters to and from other +commonly used triclinic representations. + +When a prism region is used, the simulation domain should normally be +periodic in the dimension that the tilt is applied to, which is given +by the second dimension of the tilt factor (e.g., :math:`y` for +:math:`xy` tilt). This is so that pairs of atoms interacting across +that boundary will have one of them shifted by the tilt factor. +Periodicity is set by the :doc:`boundary ` command. For +example, if the :math:`xy` tilt factor is non-zero, then the :math:`y` +dimension should be periodic. Similarly, the :math:`z` dimension +should be periodic if :math:`xz` or :math:`yz` is non-zero. LAMMPS +does not require this periodicity, but you may lose atoms if this is +not the case. Note that if your simulation will tilt the box (e.g., via the -:doc:`fix deform ` command), the simulation box must be set up to -be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by +:doc:`fix deform ` command), the simulation box must be +created as triclinic, even if the tilt factors are initially 0.0. You +can also change an orthogonal box to a triclinic box or vice versa by using the :doc:`change box ` command with its *ortho* and *triclinic* options. .. note:: - If the system is non-periodic (in a dimension), then you should - not make the lo/hi box dimensions (as defined in your - :doc:`region ` command) radically smaller/larger than the extent - of the atoms you eventually plan to create (e.g., via the - :doc:`create_atoms ` command). For example, if your atoms - extend from 0 to 50, you should not specify the box bounds as :math:`-10000` - and :math:`10000`. This is because as described above, LAMMPS uses the - specified box size to lay out the 3d grid of processors. A huge - (mostly empty) box will be sub-optimal for performance when using - "fixed" boundary conditions (see the :doc:`boundary ` - command). When using "shrink-wrap" boundary conditions (see the - :doc:`boundary ` command), a huge (mostly empty) box may cause - a parallel simulation to lose atoms the first time that LAMMPS - shrink-wraps the box around the atoms. + If the system is non-periodic (in a dimension), then you should not + make the lo/hi box dimensions (as defined in your :doc:`region + ` command) radically smaller/larger than the extent of the + atoms you eventually plan to create (e.g., via the + :doc:`create_atoms ` command). For example, if your + atoms extend from 0 to 50, you should not specify the box bounds as + :math:`-10000` and :math:`10000`. This is because as described + above, LAMMPS uses the specified box size to lay out the 3d grid of + processors. A huge (mostly empty) box will be sub-optimal for + performance when using "fixed" boundary conditions (see the + :doc:`boundary ` command). When using "shrink-wrap" + boundary conditions (see the :doc:`boundary ` command), a + huge (mostly empty) box may cause a parallel simulation to lose + atoms the first time that LAMMPS shrink-wraps the box around the + atoms. + +---------- + +As noted above, general triclinic boxes in LAMMPS allow the box to +have arbitrary edge vectors **A**, **B**, **C**. The only +restrictions are that the three vectors be distinct, non-zero, and not +co-planar. They must also define a right-handed system such that +(**A** x **B**) points in the direction of **C**. Note that a +left-handed system can be converted to a right-handed system by simply +swapping the order of any pair of the **A**, **B**, **C** vectors. + +To create a general triclinic boxes, the region is specified as NULL +and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three +edge vectors **A**, **B**, **C** using additional information +previously defined by the :doc:`lattice ` command. + +The lattice must be of style *custom* and use its *triclinic/general* +option. This insures the lattice satisfies the restrictions listed +above. The *a1, *a2*, *a3* settings of the :doc:`lattice ` +command define the edge vectors of a unit cell of the general +triclinic lattice. This command uses them to define the three edge +vectors and origin of the general triclinic box as: + +* **A** = (ahi-alo) * *a1* +* **B** = (bhi-blo) * *a2* +* **C** = (chi-clo) * *a3* +* origin = (alo*a1 + blo*a2 + clo*a3) + +For 2d general triclinic boxes, clo = -0.5 and chi = 0.5 is required. + +.. note:: + + LAMMPS allows specification of general triclinic simulation boxes + as a convenience for users who may be converting data from + solid-state crystallographic representations or from DFT codes for + input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally, + LAMMPS only uses restricted triclinic simulation boxes. This means + the box defined by this command and per-atom information + (e.g. coordinates, velocities) defined by the :doc:`create_atoms + ` command are converted (rotated) from general to + restricted triclinic form when the two commands are invoked. The + ` doc page also discusses other LAMMPS commands + which can input/output general triclinic representations of the + simulation box and per-atom data. ---------- The optional keywords can be used to create a system that allows for bond (angle, dihedral, improper) interactions, or for molecules with -special 1--2, 1--3, or 1--4 neighbors to be added later. These optional -keywords serve the same purpose as the analogous keywords that can be -used in a data file which are recognized by the +special 1--2, 1--3, or 1--4 neighbors to be added later. These +optional keywords serve the same purpose as the analogous keywords +that can be used in a data file which are recognized by the :doc:`read_data ` command when it sets up a system. Note that if these keywords are not used, then the create_box command creates an atomic (non-molecular) simulation that does not allow bonds -between pairs of atoms to be defined, or a -:doc:`bond potential ` to be specified, or for molecules with -special neighbors to be added to the system by commands such as -:doc:`create_atoms mol `, :doc:`fix deposit ` -or :doc:`fix pour `. +between pairs of atoms to be defined, or a :doc:`bond potential +` to be specified, or for molecules with special neighbors +to be added to the system by commands such as :doc:`create_atoms mol +`, :doc:`fix deposit ` or :doc:`fix pour +`. As an example, see the examples/deposit/in.deposit.molecule script, which deposits molecules onto a substrate. Initially there are no -molecules in the system, but they are added later by the -:doc:`fix deposit ` command. The create_box command in the -script uses the bond/types and extra/bond/per/atom keywords to allow -this. If the added molecule contained more than one special bond -(allowed by default), an extra/special/per/atom keyword would also -need to be specified. +molecules in the system, but they are added later by the :doc:`fix +deposit ` command. The create_box command in the script +uses the bond/types and extra/bond/per/atom keywords to allow this. +If the added molecule contained more than one special bond (allowed by +default), an extra/special/per/atom keyword would also need to be +specified. ---------- diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index 0b30ae5588..e03c4b3ac7 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -43,6 +43,9 @@ Examples delete_bonds all bond 0*3 special delete_bonds all stats + labelmap atom 4 hc + delete_bonds all atom hc special + Description """"""""""" @@ -59,19 +62,20 @@ For all styles, by default, an interaction is only turned off (or on) if all the atoms involved are in the specified group. See the *any* keyword to change the behavior. -Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, -*improper*\ ) take a *type* as an argument. The specified *type* should -be an integer from 0 to :math:`N`, where :math:`N` is the number of relevant +Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, *improper*\ ) +take a *type* as an argument. The specified *type* can be a +:doc:`type label `. Otherwise, the type should be an +integer from 0 to :math:`N`, where :math:`N` is the number of relevant types (atom types, bond types, etc.). A value of 0 is only relevant for -style *bond*\ ; see details below. In all cases, a wildcard asterisk +style *bond*\ ; see details below. For numeric types, a wildcard asterisk can be used in place of or in conjunction with the *type* argument to specify a range of types. This takes the form "\*" or "\*n" or "m\*" or -"m\*n". If :math:`N` is the number of types, then an asterisk with no numeric -values means all types from 0 to :math:`N`. A leading asterisk means all -types from 0 to n (inclusive). A trailing asterisk means all types -from m to N (inclusive). A middle asterisk means all types from m to -n (inclusive). Note that it is fine to include a type of 0 for -non-bond styles; it will simply be ignored. +"m\*n". If :math:`N` is the number of types, then an asterisk with no +numeric values means all types from 0 to :math:`N`. A leading asterisk +means all types from 0 to n (inclusive). A trailing asterisk means all +types from m to N (inclusive). A middle asterisk means all types from m to +n (inclusive). Note that it is fine to include a type of 0 for non-bond +styles; it will simply be ignored. For style *multi* all bond, angle, dihedral, and improper interactions of any type, involving atoms in the group, are turned off. diff --git a/doc/src/dihedral_cosine_squared_restricted.rst b/doc/src/dihedral_cosine_squared_restricted.rst new file mode 100644 index 0000000000..c402c983ab --- /dev/null +++ b/doc/src/dihedral_cosine_squared_restricted.rst @@ -0,0 +1,71 @@ +.. index:: dihedral_style cosine/squared/restricted + +dihedral_style cosine/squared/restricted command +================================================ + + +Syntax +"""""" + +.. code-block:: LAMMPS + + dihedral_style cosine/squared/restricted + +Examples +"""""""" + +.. code-block:: LAMMPS + + dihedral_style cosine/squared/restricted + dihedral_coeff 1 10.0 120 + +Description +""""""""""" + +.. versionadded:: 17Apr2024 + +The *cosine/squared/restricted* dihedral style uses the potential + +.. math:: + + E = K [\cos(\phi) - \cos(\phi_0)]^2 / \sin^2(\phi) + +, which is commonly used in the MARTINI force field. + +See :ref:`(Bulacu) ` for a description of the restricted dihedral for the MARTINI force field. + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* :math:`K` (energy) +* :math:`\phi_0` (degrees) + +:math:`\phi_0` is specified in degrees, but LAMMPS converts it to radians internally. + +---------- + +Restrictions +"""""""""""" + +This dihedral style can only be used if LAMMPS was built with the +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page +for more info. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +Default +""""""" + +none + +---------- + +.. _restricted-Bul: + +**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292 +(2013). diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 45dd66e750..56b8ff5226 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -10,7 +10,7 @@ Syntax dihedral_style style -* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut* +* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *cosine/squared/restricted* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut* Examples """""""" @@ -105,6 +105,7 @@ exist. * :doc:`charmmfsw ` - CHARMM dihedral with force switching * :doc:`class2 ` - COMPASS (class 2) dihedral * :doc:`cosine/shift/exp ` - dihedral with exponential in spring constant +* :doc:`cosine/squared/restricted ` - squared cosine dihedral with restricted term * :doc:`fourier ` - dihedral with multiple cosine terms * :doc:`harmonic ` - harmonic dihedral * :doc:`helix ` - helix dihedral diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 82faba6c81..a8175fa612 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -114,6 +114,7 @@ Syntax proc = ID of processor that owns atom procp1 = ID+1 of processor that owns atom type = atom type + typelabel = atom :doc:`type label ` element = name of atom element, as defined by :doc:`dump_modify ` command mass = atom mass x,y,z = unscaled atom coordinates @@ -275,16 +276,20 @@ format ` command and its options. Format of native LAMMPS format dump files: The *atom*, *custom*, *grid*, and *local* styles create files in a -simple LAMMPS-specific text format that is self-explanatory when -viewing a dump file. Many post-processing tools either included with -LAMMPS or third-party tools can read this format, as does the +simple LAMMPS-specific text format that is mostly self-explanatory +when viewing a dump file. Many post-processing tools either included +with LAMMPS or third-party tools can read this format, as does the :doc:`rerun ` command. See tools described on the :doc:`Tools ` doc page for examples, including `Pizza.py `_. For all these styles, the dimensions of the simulation box are -included in each snapshot. For an orthogonal simulation box this -information is formatted as: +included in each snapshot. The simulation box in LAMMPS can be +defined in one of 3 ways: orthogonal, restricted triclinic, and +general triclinic. See the :doc:`Howto triclinic ` +doc page for a detailed description of all 3 options. + +For an orthogonal simulation box the box information is formatted as: .. parsed-literal:: @@ -301,10 +306,10 @@ the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap), or *m* (shrink wrapped with a minimum value). See the :doc:`boundary ` command for details. -For triclinic simulation boxes (non-orthogonal), an orthogonal -bounding box which encloses the triclinic simulation box is output, -along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box, -formatted as follows: +For a restricted triclinic simulation box, an orthogonal bounding box +which encloses the restricted triclinic simulation box is output, +along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic +box, formatted as follows: .. parsed-literal:: @@ -326,6 +331,10 @@ bounding box extents (xlo_bound, xhi_bound, etc.) are calculated from the triclinic parameters, and how to transform those parameters to and from other commonly used triclinic representations. +For a general triclinic simulation box, see the "General triclinic" +section below for a description of the ITEM: BOX BOUNDS format as well +as how per-atom coordinates and per-atom vector quantities are output. + The *atom* and *custom* styles output a "ITEM: NUMBER OF ATOMS" line with the count of atoms in the snapshot. Likewise they output an "ITEM: ATOMS" line which includes column descriptors for the per-atom @@ -397,7 +406,6 @@ command. Dump files in other popular formats: - .. note:: This section only discusses file formats relevant to this doc page. @@ -463,8 +471,9 @@ followed by one line per atom with the atom type and the :math:`x`-, :math:`y`-, and :math:`z`-coordinate of that atom. You can use the :doc:`dump_modify element ` option to change the output from using the (numerical) atom type to an element name (or some other -label). This will help many visualization programs to guess bonds and -colors. +label). This option will help many visualization programs to guess bonds +and colors. You can use the :doc:`dump_modify types labels ` +option to replace numeric atom types with :doc:`type labels `. .. versionadded:: 22Dec2022 @@ -653,6 +662,87 @@ how to control the compression level in both variants. ---------- +General triclinic simulation box output for the *atom* and *custom* styles: + +As mentioned above, the simulation box can be defined as a general +triclinic box, which means that 3 arbitrary box edge vectors **A**, +**B**, **C** can be specified. See the :doc:`Howto triclinic +` doc page for a detailed description of general +triclinic boxes. + +This option is provided as a convenience for users who may be +converting data from solid-state crystallographic representations or +from DFT codes for input to LAMMPS. However, as explained on the +:doc:`Howto_triclinic ` doc page, internally, LAMMPS +only uses restricted triclinic simulation boxes. This means the box +and per-atom information (e.g. coordinates, velocities) LAMMPS stores +are converted (rotated) from general to restricted triclinic form when +the system is created. + +For dump output, if the :doc:`dump_modify triclinic/general +` command is used, the box description and per-atom +coordinates and other per-atom vectors will be converted (rotated) +from restricted to general form when each dump file snapshots is +output. This option can only be used if the simulation box was +initially created as general triclinic. If the option is not used, +and the simulation box is general triclinic, then the dump file +snapshots will reflect the internal restricted triclinic geometry. + +The dump_modify triclinic/general option affects 3 aspects of the dump +file output. + +First, the format for the BOX BOUNDS is as follows + +.. parsed-literal:: + + ITEM: BOX BOUNDS abc origin + ax ay az originx + bx by bz originy + cx cy cz originz + +where the **A** edge vector of the box is (ax,ay,az) and similarly +for **B** and **C**. The origin of all 3 edge vectors is (originx, +originy, originz). + +Second, the coordinates of each atom are converted (rotated) so that +the atom is inside (or near) the general triclinic box defined by the +**A**, **B**, **C** edge vectors. For style *atom*, this only alters +output for unscaled atom coords, via the :doc:`dump_modify scaled no +` setting. For style *custom*, this alters output for +either unscaled or unwrapped output of atom coords, via the *x,y,z* or +*xu,yu,zu* attributes. For output of scaled atom coords by both +styles, there is no difference between restricted and general +triclinic values. + +Third, the output for any attribute of the *custom* style which +represents a per-atom vector quantity will be converted (rotated) to +be oriented consistent with the general triclinic box and its +orientation relative to the standard xyz coordinate axes. + +This applies to the following *custom* style attributes: + +* vx,vy,vz = atom velocities +* fx,fy,fz = forces on atoms +* mux,muy,muz = orientation of dipole moment of atom +* omegax,omegay,omegaz = angular velocity of spherical particle +* angmomx,angmomy,angmomz = angular momentum of aspherical particle +* tqx,tqy,tqz = torque on finite-size particles + +For example, if the velocity of an atom in a restricted triclinic box +is along the x-axis, then it will be output for a general triclinic +box as a vector along the **A** edge vector of the box. + +.. note:: + + For style *custom*, the :doc:`dump_modify thresh ` + command may access per-atom attributes either directly or + indirectly through a compute or variable. If the attribute is an + atom coordinate or one of the vectors mentioned above, its value + will *NOT* be a general triclinic (rotated) value. Rather it will + be a restricted triclinic value. + +---------- + Arguments for different styles: The sections below describe per-atom, local, and per grid cell @@ -686,21 +776,21 @@ command creates a per-atom array with six columns: Per-atom attributes used as arguments to the *custom* and *cfg* styles: -The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*, -*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory. +The *id*, *mol*, *proc*, *procp1*, *type*, *typelabel*, *element*, *mass*, +*vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory. -*Id* is the atom ID. *Mol* is the molecule ID, included in the data -file for molecular systems. *Proc* is the ID of the processor (0 to +*Id* is the atom ID. *Mol* is the molecule ID, included in the data file +for molecular systems. *Proc* is the ID of the processor (0 to :math:`N_\text{procs}-1`) that currently owns the atom. *Procp1* is the proc ID+1, which can be convenient in place of a *type* attribute (1 to :math:`N_\text{types}`) for coloring atoms in a visualization program. -*Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is -typically the chemical name of an element, which you must assign to each -type via the :doc:`dump_modify element ` command. More -generally, it can be any string you wish to associated with an atom -type. *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*, -*fy*, *fz*, and *q* are components of atom velocity and force and atomic -charge. +*Type* is the atom type (1 to :math:`N_\text{types}`). *Typelabel* is the +atom :doc:`type label `. *Element* is typically the +chemical name of an element, which you must assign to each type via the +:doc:`dump_modify element ` command. More generally, it can +be any string you wish to associated with an atom type. *Mass* is the atom +mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are +components of atom velocity and force and atomic charge. There are several options for outputting atom coordinates. The *x*, *y*, and *z* attributes write atom coordinates "unscaled", in the diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 2d84f28836..79fdf2cc3e 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -17,7 +17,7 @@ Syntax * one or more keyword/value pairs may be appended * these keywords apply to various dump styles -* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap* +* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *triclinic/general* or *types* or *units* or *unwrap* .. parsed-literal:: @@ -74,12 +74,14 @@ Syntax -N = sort per-atom lines in descending order by the Nth column *tfactor* arg = time scaling factor (> 0.0) *thermo* arg = *yes* or *no* - *time* arg = *yes* or *no* *thresh* args = attribute operator value attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^" value = numeric value to compare to, or LAST these 3 args can be replaced by the word "none" to turn off thresholding + *time* arg = *yes* or *no* + *triclinic/general* arg = *yes* or *no* + *types* value = *numeric* or *labels* *units* arg = *yes* or *no* *unwrap* arg = *yes* or *no* @@ -802,8 +804,9 @@ region since the last dump. dump_modify ... thresh v_charge |^ LAST This will dump atoms whose charge has changed from an absolute value -less than :math:`\frac12` to greater than :math:`\frac12` (or vice versa) since the last dump (e.g., due to reactions and subsequent charge equilibration in a -reactive force field). +less than :math:`\frac12` to greater than :math:`\frac12` (or vice +versa) since the last dump (e.g., due to reactions and subsequent +charge equilibration in a reactive force field). The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "\|\^". @@ -811,6 +814,18 @@ In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is "true" and the threshold criterion is met. Otherwise it is not met. +.. note:: + + For style *custom*, the *triclinic/general* keyword can alter dump + output for general triclinic simulation boxes and their atoms. See + the :doc:`dump ` command for details of how this changes the + format of dump file snapshots. The thresh keyword may access + per-atom attributes either directly or indirectly through a compute + or variable. If the attribute is an atom coordinate or a per-atom + vector (such as velocity, force, or dipole moment), its value will + *NOT* be a general triclinic (rotated) value. Rather it will be a + restricted triclinic value. + ---------- The *time* keyword only applies to the dump *atom*, *custom*, *local*, @@ -835,6 +850,36 @@ The default setting is *no*\ . ---------- +The *types* keyword applies only to the dump xyz style. If this keyword is +used with a value of *numeric*, then numeric atom types are printed in the +xyz file (default). If the value *labels* is specified, then +:doc:`type labels ` are printed for atom types. + +---------- + +The *triclinic/general* keyword only applies to the dump *atom* and +*custom* styles. It can only be used with a value of *yes* if the +simulation box was created as a general triclinic box. See the +:doc:`Howto_triclinic ` doc page for a detailed +explanation of orthogonal, restricted triclinic, and general triclinic +simulation boxes. + +If this keyword is used with a value of *yes*, the box information at +the beginning of each snapshot will include information about the 3 +arbitrary edge vectors **A**, **B**, **C** that define the general +triclinic box as well as their origin. The format is described on the +:doc:`dump ` doc page. + +The coordinates of each atom will likewise be output as values in (or +near) the general triclinic box. Likewise, per-atom vector quantities +such as velocity, omega, dipole moment, etc will have orientations +consistent with the general triclinic box, meaning they will be +rotated relative to the standard xyz coordinate axes. See the +:doc:`dump ` doc page for a full list of which dump attributes +this affects. + +---------- + The *units* keyword only applies to the dump *atom*, *custom*, and *local* styles (and their COMPRESS package versions *atom/gz*, *custom/gz* and *local/gz*\ ). If set to *yes*, each individual dump @@ -922,10 +967,12 @@ The option defaults are * sort = off for dump styles *atom*, *custom*, *cfg*, and *local* * sort = id for dump styles *dcd*, *xtc*, and *xyz* * thresh = none +* time = no +* triclinic/general = no +* types = numeric * units = no * unwrap = no * compression_level = 9 (gz variants) * compression_level = 0 (zstd variants) * checksum = yes (zstd variants) - diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst index 28afb990ff..3b348fa339 100644 --- a/doc/src/fitpod_command.rst +++ b/doc/src/fitpod_command.rst @@ -1,18 +1,19 @@ .. index:: fitpod fitpod command -====================== +============== Syntax """""" .. code-block:: LAMMPS - fitpod Ta_param.pod Ta_data.pod + fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod * fitpod = style name of this command * Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs) * Ta_data.pod = an input file that specifies DFT data used to fit a POD potential +* Ta_coefficients.pod (optional) = an input file that specifies trainable coefficients of a POD potential Examples """""""" @@ -20,20 +21,26 @@ Examples .. code-block:: LAMMPS fitpod Ta_param.pod Ta_data.pod + fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Description """"""""""" .. versionadded:: 22Dec2022 Fit a machine-learning interatomic potential (ML-IAP) based on proper -orthogonal descriptors (POD). Two input files are required for this -command. The first input file describes a POD potential parameter -settings, while the second input file specifies the DFT data used for -the fitting procedure. +orthogonal descriptors (POD); please see :ref:`(Nguyen and Rohskopf) +`, :ref:`(Nguyen2023) `, :ref:`(Nguyen2024) +`, and :ref:`(Nguyen and Sema) ` for details. +The fitted POD potential can be used to run MD simulations via +:doc:`pair_style pod `. -The table below has one-line descriptions of all the keywords that can -be used in the first input file (i.e. ``Ta_param.pod`` in the example -above): +Two input files are required for this command. The first input file +describes a POD potential parameter settings, while the second input +file specifies the DFT data used for the fitting procedure. All keywords +except *species* have default values. If a keyword is not set in the +input file, its default value is used. The table below has one-line +descriptions of all the keywords that can be used in the first input +file (i.e. ``Ta_param.pod``) .. list-table:: :header-rows: 1 @@ -52,7 +59,7 @@ above): - INT - three integer constants specify boundary conditions * - rin - - 1.0 + - 0.5 - REAL - a real number specifies the inner cut-off radius * - rcut @@ -60,46 +67,75 @@ above): - REAL - a real number specifies the outer cut-off radius * - bessel_polynomial_degree - - 3 + - 4 - INT - the maximum degree of Bessel polynomials * - inverse_polynomial_degree - - 6 + - 8 - INT - the maximum degree of inverse radial basis functions + * - number_of_environment_clusters + - 1 + - INT + - the number of clusters for environment-adaptive potentials + * - number_of_principal_components + - 2 + - INT + - the number of principal components for dimensionality reduction * - onebody - 1 - BOOL - turns on/off one-body potential * - twobody_number_radial_basis_functions - - 6 + - 8 - INT - number of radial basis functions for two-body potential * - threebody_number_radial_basis_functions - - 5 + - 6 - INT - number of radial basis functions for three-body potential - * - threebody_number_angular_basis_functions + * - threebody_angular_degree - 5 - INT - - number of angular basis functions for three-body potential - * - fourbody_snap_twojmax + - angular degree for three-body potential + * - fourbody_number_radial_basis_functions + - 4 + - INT + - number of radial basis functions for four-body potential + * - fourbody_angular_degree + - 3 + - INT + - angular degree for four-body potential + * - fivebody_number_radial_basis_functions - 0 - INT - - band limit for SNAP bispectrum components (0,2,4,6,8... allowed) - * - fourbody_snap_chemflag + - number of radial basis functions for five-body potential + * - fivebody_angular_degree - 0 - - BOOL - - turns on/off the explicit multi-element variant of the SNAP bispectrum components - * - quadratic_pod_potential + - INT + - angular degree for five-body potential + * - sixbody_number_radial_basis_functions - 0 - - BOOL - - turns on/off quadratic POD potential + - INT + - number of radial basis functions for six-body potential + * - sixbody_angular_degree + - 0 + - INT + - angular degree for six-body potential + * - sevenbody_number_radial_basis_functions + - 0 + - INT + - number of radial basis functions for seven-body potential + * - sevenbody_angular_degree + - 0 + - INT + - angular degree for seven-body potential + +Note that both the number of radial basis functions and angular degree +must decrease as the body order increases. The next table describes all +keywords that can be used in the second input file (i.e. ``Ta_data.pod`` +in the example above): -All keywords except *species* have default values. If a keyword is not -set in the input file, its default value is used. The next table -describes all keywords that can be used in the second input file -(i.e. ``Ta_data.pod`` in the example above): .. list-table:: :header-rows: 1 @@ -125,6 +161,10 @@ describes all keywords that can be used in the second input file - "" - STRING - specifies the path to test data files in double quotes + * - path_to_environment_configuration_set + - "" + - STRING + - specifies the path to environment configuration files in double quotes * - fraction_training_data_set - 1.0 - REAL @@ -133,6 +173,14 @@ describes all keywords that can be used in the second input file - 0 - BOOL - turns on/off randomization of the training set + * - fraction_test_data_set + - 1.0 + - REAL + - a real number (<= 1.0) specifies the fraction of the test set used to validate POD + * - randomize_test_data_set + - 0 + - BOOL + - turns on/off randomization of the test set * - fitting_weight_energy - 100.0 - REAL @@ -161,6 +209,10 @@ describes all keywords that can be used in the second input file - 8 - INT - number of digits after the decimal points for numbers in the coefficient file + * - group_weights + - global + - STRING + - ``table`` uses group weights defined for each group named by filename All keywords except *path_to_training_data_set* have default values. If a keyword is not set in the input file, its default value is used. After @@ -172,14 +224,44 @@ successful training, a number of output files are produced, if enabled: * ``_test_analysis.pod`` reports detailed errors for all test configurations * ``_coefficients.pod`` contains the coefficients of the POD potential -After training the POD potential, ``Ta_param.pod`` and ``_coefficients.pod`` -are the two files needed to use the POD potential in LAMMPS. See -:doc:`pair_style pod ` for using the POD potential. Examples -about training and using POD potentials are found in the directory -lammps/examples/PACKAGES/pod. +After training the POD potential, ``Ta_param.pod`` and +``_coefficients.pod`` are the two files needed to use the POD +potential in LAMMPS. See :doc:`pair_style pod ` for using the +POD potential. Examples about training and using POD potentials are +found in the directory lammps/examples/PACKAGES/pod and the Github repo +https://github.com/cesmix-mit/pod-examples. -Parameterized Potential Energy Surface -"""""""""""""""""""""""""""""""""""""" +Loss Function Group Weights +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The *group_weights* keyword in the ``data.pod`` file is responsible for +weighting certain groups of configurations in the loss function. For +example: + +.. code-block:: LAMMPS + + group_weights table + Displaced_A15 100.0 1.0 + Displaced_BCC 100.0 1.0 + Displaced_FCC 100.0 1.0 + Elastic_BCC 100.0 1.0 + Elastic_FCC 100.0 1.0 + GSF_110 100.0 1.0 + GSF_112 100.0 1.0 + Liquid 100.0 1.0 + Surface 100.0 1.0 + Volume_A15 100.0 1.0 + Volume_BCC 100.0 1.0 + Volume_FCC 100.0 1.0 + +This will apply an energy weight of ``100.0`` and a force weight of +``1.0`` for all groups in the ``Ta`` example. The groups are named by +their respective filename. If certain groups are left out of this table, +then the globally defined weights from the ``fitting_weight_energy`` and +``fitting_weight_force`` keywords will be used. + +POD Potential +""""""""""""" We consider a multi-element system of *N* atoms with :math:`N_{\rm e}` unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n` @@ -187,535 +269,82 @@ position vector and type of an atom *n* in the system, respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e} \}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots, \boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1, -Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface -(PES) of the system can be expressed as a many-body expansion of the -form +Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the +POD potential is expressed as :math:`E(\boldsymbol R, \boldsymbol Z) = +\sum_{i=1}^N E_i(\boldsymbol R_i, \boldsymbol Z_i)`, where .. math:: - E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)}) \\ - & + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots - -where :math:`V^{(1)}` is the one-body potential often used for -representing external field or energy of isolated elements, and the -higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric, -uniquely defined, and zero if two or more indices take identical values. -The superscript on each potential denotes its body order. Each *q*-body -potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which -are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu` -is a collection of all potential parameters :math:`\boldsymbol -\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol -\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of -hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and -outer cut-off radius :math:`r_{\rm cut}`. - -Interatomic potentials rely on parameters to learn relationship between -atomic environments and interactions. Since interatomic potentials are -approximations by nature, their parameters need to be set to some -reference values or fitted against data by necessity. Typically, -potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`, -to minimize a certain loss function of the predicted quantities and -data. Since the fitted potential depends on the data set used to fit it, -different data sets will yield different optimal parameters and thus -different fitted potentials. When fitting the same functional form on -*Q* different data sets, we would obtain *Q* different optimized -potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta, -\boldsymbol \mu_q^*), 1 \le q \le Q`. Consequently, there exist many -different sets of optimized parameters for empirical interatomic -potentials. - -Instead of optimizing the potential parameters, inspired by the reduced -basis method :ref:`(Grepl) ` for parameterized partial -differential equations, we view the parameterized PES as a parametric -manifold of potential energies - -.. math:: - - \mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \ \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \} - -where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which -:math:`\boldsymbol \mu` resides. The parametric manifold -:math:`\mathcal{M}` contains potential energy surfaces for all values of -:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`. Therefore, the -parametric manifold yields a much richer and more transferable atomic -representation than any particular individual PES :math:`E(\boldsymbol -R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`. - -We propose specific forms of the parameterized potentials for one-body, -two-body, and three-body interactions. We apply the Karhunen-Loeve -expansion to snapshots of the parameterized potentials to obtain sets of -orthogonal basis functions. These basis functions are aggregated -according to the chemical elements of atoms, thus leading to -multi-element proper orthogonal descriptors. - -Proper Orthogonal Descriptors -""""""""""""""""""""""""""""" - -Proper orthogonal descriptors are finger prints characterizing the -radial and angular distribution of a system of atoms. The detailed -mathematical definition is given in the paper by Nguyen and Rohskopf -:ref:`(Nguyen) `. - -The descriptors for the one-body interaction are used to capture energy -of isolated elements and defined as follows - -.. math:: - - D_{ip}^{(1)} = \left\{ - \begin{array}{ll} - 1, & \mbox{if } Z_i = p \\ - 0, & \mbox{if } Z_i \neq p - \end{array} - \right. - -for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body -descriptors per atom is equal to the number of elements. The one-body -descriptors are independent of atom positions, but dependent on atom -types. The one-body descriptors are active only when the keyword -*onebody* is set to 1. - -We adopt the usual assumption that the direct interaction between two -atoms vanishes smoothly when their distance is greater than the outer -cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two -atoms can not get closer than the inner cutoff distance :math:`r_{\rm -in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in}, -r_{\rm cut})`, we introduce the following parameterized radial functions - -.. math:: - - \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad \varphi(r, \gamma) = \frac{1}{r^\gamma} , - -where the scaled distance function :math:`x` is defined below to enrich the two-body manifold - -.. math:: - - x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} . - -We introduce the following function as a convex combination of the two functions - -.. math:: - - \psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa) = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa) \varphi(r, \gamma) . - -We see that :math:`\psi` is a function of distance :math:`r`, cut-off -distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters -:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow -the function :math:`\psi` to characterize a diverse spectrum of two-body -interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm -cut})`. - -Next, we introduce the following parameterized potential - -.. math:: - - W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) - -where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} = -\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and -:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm -c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the -smooth vanishing of the potential and its derivative for :math:`r_{ij} -\ge r_{\rm cut}`: - -.. math:: - - f_{\rm c}(r_{ij}, r_{\rm in}, r_{\rm cut}) = \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right) - -Based on the parameterized potential, we form a set of snapshots as -follows. We assume that we are given :math:`N_{\rm s}` parameter tuples -:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We -introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm -cut})`: - -.. math:: - - \xi_\ell(r_{ij}, \boldsymbol \eta) = W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell), \quad \ell = 1, \ldots, N_{\rm s} . - -To ensure adequate sampling of the PES for different parameters, we -choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol -\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1 -\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1, -N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where -:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for -:math:`\alpha` and :math:`\gamma`, respectively. We next choose -:math:`N_\beta` different values of :math:`\beta` in the interval -:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and -:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either -0 or 1. Hence, the total number of parameter points is :math:`N_{\rm s} -= N_\alpha N_\beta + N_\gamma`. Although :math:`N_\alpha, N_\beta, -N_\gamma` can be chosen conservatively large, we find that -:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most -problems. Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to -*bessel_polynomial_degree* and *inverse_polynomial_degree*, -respectively. - -We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal -basis set which is known to be optimal for representation of the -snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body -orthogonal basis functions are computed as follows - -.. math:: - - U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \, \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} , - -where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times -N_{\rm s}}` consists of eigenvectors of the eigenvalue problem - -.. math:: - - \boldsymbol C \boldsymbol a = \lambda \boldsymbol a - -with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by - -.. math:: - - C_{ij} = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s} - -Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm -s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge -\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is -pe-computed and stored for any given :math:`\boldsymbol \eta`. Owing to -the rapid convergence of the KL expansion, only a small number of -orthogonal basis functions is needed to obtain accurate -approximation. The value of :math:`N_{\rm 2b}` corresponds to -*twobody_number_radial_basis_functions*. - -The two-body proper orthogonal descriptors at each atom *i* are computed -by summing the orthogonal basis functions over the neighbors of atom *i* -and numerating on the atom types as follows - -.. math:: - - D^{(2)}_{im l(p, q) }(\boldsymbol \eta) = \left\{ - \begin{array}{ll} - \displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij}, \boldsymbol \eta), & \mbox{if } Z_i = p \\ - 0, & \mbox{if } Z_i \neq p - \end{array} - \right. - -for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm -e}`. Here :math:`l(p,q)` is a symmetric index mapping such that - -.. math:: - - l(p,q) = \left\{ - \begin{array}{ll} - q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\ - p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p . - \end{array} - \right. - -The number of two-body descriptors per atom is thus :math:`N_{\rm 2b} -N_{\rm e}(N_{\rm e}+1)/2`. - -It is important to note that the orthogonal basis functions do not -depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the -cost of evaluating the basis functions and their derivatives with -respect to :math:`r_{ij}` is independent of the number of elements -:math:`N_{\rm e}`. Consequently, even though the two-body proper -orthogonal descriptors depend on :math:`\boldsymbol Z`, their -computational complexity is independent of :math:`N_{\rm e}`. - -In order to provide proper orthogonal descriptors for three-body -interactions, we need to introduce a three-body parameterized -potential. In particular, the three-body potential is defined as a -product of radial and angular functions as follows - -.. math:: - - W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)}) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\ - \psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\ - \cos (\sigma \theta_{ijk} + \zeta) - -where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the -equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta, -\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an -angular fingerprint of the atomic environment through the bond angles -:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and -:math:`k`. Compared to the two-body potential, the three-body potential -has two extra parameters :math:`(\sigma, \zeta)` associated with the -angular component. - -Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We -assume that we are given :math:`L_{\rm r}` parameter tuples -:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`. We -introduce the following set of snapshots on :math:`(r_{\min}, -r_{\max})`: - -.. math:: - - \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} . - -We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to -obtain orthogonal basis functions as follows - -.. math:: - - U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \, \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} , - -where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists -of eigenvectors of the eigenvalue problem. For the parameterized angular function, -we consider angular basis functions - -.. math:: - - U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad n = 1,\ldots, N_{\rm a}, - -where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal -basis functions for the parameterized potential are computed as follows - -.. math:: - - U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}), - -for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body -orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and -independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to -*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to -*threebody_number_angular_basis_functions*. - -The three-body proper orthogonal descriptors at each atom *i* -are obtained by summing over the neighbors *j* and *k* of atom *i* as - -.. math:: - - D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta) = \left\{ - \begin{array}{ll} - \displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\ - 0, & \mbox{if } Z_i \neq p - \end{array} - \right. - -for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`, -where - -.. math:: - - \ell(p,q,s) = \left\{ - \begin{array}{ll} - s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\ - q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q . - \end{array} - \right. - -The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`. -While the number of three-body PODs is cubic function of the number of elements, -the computational complexity of the three-body PODs is independent of the number of elements. - -Four-Body SNAP Descriptors -"""""""""""""""""""""""""" - -In addition to the proper orthogonal descriptors described above, we also employ -the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components -to characterize the local neighborhood of each atom in a very general way. The mathematical definition -of the bispectrum calculation and its derivatives w.r.t. atom positions is described in -:doc:`compute snap `. In SNAP, the -total energy is decomposed into a sum over atom energies. The energy of -atom *i* is expressed as a weighted sum over bispectrum components. - -.. math:: - - E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)} - - -where the SNAP descriptors are related to the bispectrum components by - -.. math:: - - D^{(4)}_{ikp} = \left\{ - \begin{array}{ll} - \displaystyle B_{ik}, & \mbox{if } Z_i = p \\ - 0, & \mbox{if } Z_i \neq p - \end{array} - \right. - -Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of -bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}` -and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0 -then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`. -If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`. -The bispectrum calculation is described in more detail in :doc:`compute sna/atom `. - -Linear Proper Orthogonal Descriptor Potentials -"""""""""""""""""""""""""""""""""""""""""""""" - -The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies -in the following expansion - -.. math:: - - E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}} \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}} \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta), - -where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the one-body, two-body, three-body, four-body descriptors, -respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion -coefficients. In a more compact notation that implies summation over descriptor indices -the atomic energies can be written as - -.. math:: - - E_i(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im} - -where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`, -:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and -:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are -the number of two-body, three-body, and four-body descriptors, respectively. - -The potential energy is then obtained by summing local atomic energies :math:`E_i` -for all atoms :math:`i` in the system - -.. math:: - - E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta) - -Because the descriptors are one-body, two-body, and three-body terms, -the resulting POD potential is a three-body PES. We can express the potential -energy as a linear combination of the global descriptors as follows - -.. math:: - - E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m} - -where the global descriptors are given by - -.. math:: - - d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta) - -Hence, we obtain the atomic forces as - -.. math:: - - \boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m \nabla d_m^{(4)} - -where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body -three-body, and four-body global descriptors with respect to atom positions, respectively. -Note that since the first-body global descriptors are constant, their derivatives are zero. - -Quadratic Proper Orthogonal Descriptor Potentials -""""""""""""""""""""""""""""""""""""""""""""""""" - -We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`, -and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`, -with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and -:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being -the number of descriptors per atom for the two-body PODs and three-body PODs, -respectively. We employ them to define a new set of atomic descriptors as follows - -.. math:: - - D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk} \right) - -for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. -The new descriptors are four-body because they involve central atom :math:`i` together -with three neighbors :math:`j, k` and :math:`l`. The total number of new descriptors per atom is equal to - -.. math:: - - N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 . - -The new global descriptors are calculated as - -.. math:: - - d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m, - -for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient -of the new global descriptors with respect to atom positions is calculated as - -.. math:: - - \nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k} + d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} . - -The quadratic POD potential is defined as a linear combination of the -original and new global descriptors as follows - -.. math:: - - E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} . - -It thus follows that - -.. math:: - - E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)} , - -which is simplified to - -.. math:: - - E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b_m^{(3)} d_m^{(3)} - -where - -.. math:: - - b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\ - b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} . - -The quadratic POD potential results in the following atomic forces - -.. math:: - - \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} \nabla d^{(2*3)}_{km} . - -It can be shown that - -.. math:: - - \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b^{(3)}_m \nabla d_m^{(3)} . - -The calculation of the atomic forces for the quadratic POD potential -only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible. -As a result, the quadratic POD potential does not increase the computational complexity. - + E_i(\boldsymbol R_i, \boldsymbol Z_i) \ = \ \sum_{m=1}^M c_m \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i) + + +Here :math:`c_m` are trainable coefficients and +:math:`\mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)` are per-atom +POD descriptors. Summing the per-atom descriptors over :math:`i` yields +the global descriptors :math:`d_m(\boldsymbol R, \boldsymbol Z) = +\sum_{i=1}^N \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)`. It +thus follows that :math:`E(\boldsymbol R, \boldsymbol Z) = \sum_{m=1}^M +c_m d_m(\boldsymbol R, \boldsymbol Z)`. + +The per-atom POD descriptors include one, two, three, four, five, six, +and seven-body descriptors, which can be specified in the first input +file. Furthermore, the per-atom POD descriptors also depend on the +number of environment clusters specified in the first input file. +Please see :ref:`(Nguyen2024) ` and :ref:`(Nguyen and Sema) +` for the detailed description of the per-atom POD +descriptors. Training """""""" -POD potentials are trained using the least-squares regression against +A POD potential is trained using the least-squares regression against density functional theory (DFT) data. Let :math:`J` be the number of training configurations, with :math:`N_j` being the number of atoms in -the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and -:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and -forces for :math:`J` configurations. Next, we calculate the global -descriptors and their derivatives for all training configurations. Let -:math:`d_{jm}, 1 \le m \le M`, be the global descriptors associated with -the j-th configuration, where :math:`M` is the number of global -descriptors. We then form a matrix :math:`\boldsymbol A \in -\mathbb{R}^{J \times M}` with entries :math:`A_{jm} = d_{jm}/ N_j` for -:math:`j=1,\ldots,J` and :math:`m=1,\ldots,M`. Moreover, we form a -matrix :math:`\boldsymbol B \in \mathbb{R}^{\mathcal{N} \times M}` by -stacking the derivatives of the global descriptors for all training -configurations from top to bottom, where :math:`\mathcal{N} = -3\sum_{j=1}^{J} N_j`. +the j-th configuration. The training configurations are extracted from +the extended XYZ files located in a directory (i.e., +path_to_training_data_set in the second input file). Let +:math:`\{E^{\star}_j\}_{j=1}^{J}` and :math:`\{\boldsymbol +F^{\star}_j\}_{j=1}^{J}` be the DFT energies and forces for :math:`J` +configurations. Next, we calculate the global descriptors and their +derivatives for all training configurations. Let :math:`d_{jm}, 1 \le m +\le M`, be the global descriptors associated with the j-th +configuration, where :math:`M` is the number of global descriptors. We +then form a matrix :math:`\boldsymbol A \in \mathbb{R}^{J \times M}` +with entries :math:`A_{jm} = d_{jm}/ N_j` for :math:`j=1,\ldots,J` and +:math:`m=1,\ldots,M`. Moreover, we form a matrix :math:`\boldsymbol B +\in \mathbb{R}^{\mathcal{N} \times M}` by stacking the derivatives of +the global descriptors for all training configurations from top to +bottom, where :math:`\mathcal{N} = 3\sum_{j=1}^{J} N_j`. The coefficient vector :math:`\boldsymbol c` of the POD potential is found by solving the following least-squares problem .. math:: - {\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2, + {\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2, where :math:`w_E` and :math:`w_F` are weights for the energy (*fitting_weight_energy*) and force (*fitting_weight_force*), -respectively; and :math:`w_R` is the regularization parameter (*fitting_regularization_parameter*). Here :math:`\bar{\boldsymbol E}^{\star} \in -\mathbb{R}^{J}` is a vector of with entries :math:`\bar{E}^{\star}_j = -E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of -:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol -F^{\star}_j\}_{j=1}^{J}` from top to bottom. +respectively; and :math:`w_R` is the regularization parameter +(*fitting_regularization_parameter*). Here :math:`\bar{\boldsymbol +E}^{\star} \in \mathbb{R}^{J}` is a vector of with entries +:math:`\bar{E}^{\star}_j = E^{\star}_j/N_j` and :math:`\boldsymbol +F^{\star}` is a vector of :math:`\mathcal{N}` entries obtained by +stacking :math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` from top to +bottom. -The training procedure is the same for both the linear and quadratic POD -potentials. However, since the quadratic POD potential has a -significantly larger number of the global descriptors, it is more -expensive to train the linear POD potential. This is because the -training of the quadratic POD potential still requires us to calculate -and store the quadratic global descriptors and their -gradient. Furthermore, the quadratic POD potential may require more -training data in order to prevent over-fitting. In order to reduce the -computational cost of fitting the quadratic POD potential and avoid -over-fitting, we can use subsets of two-body and three-body PODs for -constructing the new descriptors. +Validation +"""""""""" +POD potential can be validated on a test dataset in a directory +specified by setting path_to_test_data_set in the second input file. It +is possible to validate the POD potential after the training is +complete. This is done by providing the coefficient file as an input to +:doc:`fitpod `, for example, + +.. code-block:: LAMMPS + + fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Restrictions """""""""""" @@ -727,7 +356,11 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair_style pod ` +:doc:`pair_style pod `, +:doc:`compute pod/atom `, +:doc:`compute podd/atom `, +:doc:`compute pod/local `, +:doc:`compute pod/global ` Default """"""" @@ -736,10 +369,20 @@ The keyword defaults are also given in the description of the input files. ---------- -.. _Grepl20072: +.. _Nguyen20222a: -**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007). +**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023). + +.. _Nguyen20232a: + +**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023). + +.. _Nguyen20242a: + +**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024). + +.. _Nguyen20243a: + +**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024). -.. _Nguyen20222: -**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022). diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index f857a6333c..03aef12a6c 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -21,17 +21,17 @@ Syntax *pair* args = pstyle pparam I J v_name pstyle = pair style name (e.g., lj/cut) pparam = parameter to adapt over time - I,J = type pair(s) to set parameter for + I,J = type pair(s) to set parameter for (integer or type label) v_name = variable with name that calculates value of pparam *bond* args = bstyle bparam I v_name bstyle = bond style name (e.g., harmonic) bparam = parameter to adapt over time - I = type bond to set parameter for + I = type bond to set parameter for (integer or type label) v_name = variable with name that calculates value of bparam *angle* args = astyle aparam I v_name astyle = angle style name (e.g., harmonic) aparam = parameter to adapt over time - I = type angle to set parameter for + I = type angle to set parameter for (integer or type label) v_name = variable with name that calculates value of aparam *kspace* arg = v_name v_name = variable with name that calculates scale factor on :math:`k`-space terms @@ -67,6 +67,9 @@ Examples variable ramp_up equal "ramp(0.01,0.5)" fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up + labelmap atom 1 c1 + fix 1 all adapt 1 pair soft a c1 c1 v_prefactor + Description """"""""""" @@ -254,10 +257,12 @@ should be specified to indicate which type pairs to apply it to. If a global parameter is specified, the :math:`I` and :math:`J` settings still need to be specified, but are ignored. -Similar to the :doc:`pair_coeff command `, :math:`I` and :math:`J` -can be specified in one of two ways. Explicit numeric values can be used for -each, as in the first example above. :math:`I \le J` is required. LAMMPS sets -the coefficients for the symmetric :math:`J,I` interaction to the same values. +Similar to the :doc:`pair_coeff command `, :math:`I` and +:math:`J` can be specified in one of several ways. Explicit numeric values +can be used for each, as in the first example above. Or, one or both of +the types in the I,J pair can be a :doc:`type label `. +LAMMPS sets the coefficients for the symmetric :math:`J,I` interaction to +the same values. A wild-card asterisk can be used in place of or in conjunction with the :math:`I,J` arguments to set the coefficients for multiple pairs of atom @@ -266,8 +271,9 @@ is the number of atom types, then an asterisk with no numeric values means all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N` (inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with :math:`I \le J` are considered; if -asterisks imply type pairs where :math:`J < I`, they are ignored. +(inclusive). For the asterisk syntax, note that only type pairs with +:math:`I \le J` are considered; if asterisks imply type pairs where +:math:`J < I`, they are ignored. IMPORTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 474fc799de..3bcdfc5035 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -21,13 +21,13 @@ Syntax *pair* args = pstyle pparam I J v_name pstyle = pair style name (e.g., lj/cut) pparam = parameter to adapt over time - I,J = type pair(s) to set parameter for + I,J = type pair(s) to set parameter for (integer or type label) v_name = variable with name that calculates value of pparam *kspace* arg = v_name v_name = variable with name that calculates scale factor on K-space terms *atom* args = aparam v_name aparam = parameter to adapt over time - I = type(s) to set parameter for + I = type(s) to set parameter for (integer or type label) v_name = variable with name that calculates value of aparam * zero or more keyword/value pairs may be appended @@ -56,6 +56,9 @@ Examples fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes fix 1 all adapt/fep 10 atom diameter 1 v_size + labelmap atom 1 c1 + fix 1 all adapt/fep 1 pair soft a c1 c1 v_prefactor + Example input scripts available: examples/PACKAGES/fep @@ -218,10 +221,12 @@ be specified to indicate which type pairs to apply it to. If a global parameter is specified, the *I* and *J* settings still need to be specified, but are ignored. -Similar to the :doc:`pair_coeff command `, I and J can be -specified in one of two ways. Explicit numeric values can be used for -each, as in the first example above. :math:`I \le J` is required. LAMMPS sets -the coefficients for the symmetric J,I interaction to the same values. +Similar to the :doc:`pair_coeff command `, :math:`I` and +:math:`J` can be specified in one of several ways. Explicit numeric values +can be used for each, as in the first example above. Or, one or both of +the types in the I,J pair can be a :doc:`type label `. +LAMMPS sets the coefficients for the symmetric :math:`J,I` interaction to +the same values. A wild-card asterisk can be used in place of or in conjunction with the :math:`I,J` arguments to set the coefficients for multiple pairs of atom @@ -230,8 +235,9 @@ the number of atom types, then an asterisk with no numeric values means all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N` (inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with :math:`I \le J` are considered; if -asterisks imply type pairs where :math:`J < I`, they are ignored. +(inclusive). For the asterisk syntax, note that only type pairs with +:math:`I \le J` are considered; if asterisks imply type pairs where +:math:`J < I`, they are ignored. IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify diff --git a/doc/src/fix_amoeba_bitorsion.rst b/doc/src/fix_amoeba_bitorsion.rst index a9abaf19ce..057c5cf550 100644 --- a/doc/src/fix_amoeba_bitorsion.rst +++ b/doc/src/fix_amoeba_bitorsion.rst @@ -35,7 +35,11 @@ the implementation of AMOEBA and HIPPO in LAMMPS. Bitorsion interactions add additional potential energy contributions to pairs of overlapping phi-psi dihedrals of amino-acids, which are -important to properly represent their conformational behavior. +important to properly represent their conformational behavior. Each +bitorsion interaction is thus defined for a 5-tuple of atoms +:math:`IJKLM` with bonds between successive atoms in the list, +i.e. two overlapping dihedral interactions for atoms :math:`IJKL` and +:math:`JKLM`. The examples/amoeba directory has a sample input script and data file for ubiquitin, which illustrates use of the fix amoeba/bitorsion @@ -68,14 +72,15 @@ lines: [...] N 3 314 315 317 318 330 -The first column is an index from 1 to :math:`N` to enumerate the bitorsion -5-atom tuples; it is ignored by LAMMPS. The second column is the -*type* of the interaction; it is an index into the bitorsion force -field file. The remaining 5 columns are the atom IDs of the atoms in -the two 4-atom dihedrals that overlap to create the bitorsion 5-body -interaction. Note that the *bitorsions* and *BiTorsions* keywords for -the header and body sections match those specified in the -:doc:`read_data ` command following the data file name. +The first column is an index from 1 to :math:`N` to enumerate the +bitorsion 5-atom tuples; it is ignored by LAMMPS. The second column +is the *type* of the interaction; it is an index into the bitorsion +force field file. The remaining 5 columns are the atom IDs of the +atoms (in order) for the 5-tuple :math:`IJKLM`, as described above. + +Note that the *bitorsions* and *BiTorsions* keywords for the header +and body sections match those specified in the :doc:`read_data +` command following the data file name. The data file should be generated by using the tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS diff --git a/doc/src/fix_amoeba_pitorsion.rst b/doc/src/fix_amoeba_pitorsion.rst index 484c1015c8..936eba762d 100644 --- a/doc/src/fix_amoeba_pitorsion.rst +++ b/doc/src/fix_amoeba_pitorsion.rst @@ -57,7 +57,7 @@ should have two lines like these in its header section: M pitorsion types N pitorsions -where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is +where :math:`N` is the number of pitorsion 6-body interactions and :math:`M` is the number of pitorsion types. It should also have two sections in the body of the data file like these with :math:`M` and :math:`N` lines each: @@ -74,21 +74,20 @@ of the data file like these with :math:`M` and :math:`N` lines each: PiTorsions - 1 1 8 10 12 18 20 - 2 5 18 20 22 25 27 + 1 1 2 4 3 20 21 24 + 2 5 21 23 22 37 38 41 [...] - N 3 314 315 317 318 330 + N 7 27 29 28 30 35 36 -For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` to -enumerate the pitorsion types. The second column is the single +For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` +to enumerate the pitorsion types. The second column is the single prefactor coefficient needed for each type. -For PiTorsions, the first column is an index from 1 to :math:`N` to enumerate -the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second -column is the "type" of the interaction; it is an index into the -PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the -atoms in the two 4-atom dihedrals that overlap to create the pitorsion -5-body interaction. +For PiTorsions, the first column is an index from 1 to :math:`N` to +enumerate the pitorsion 6-atom tuples; it is ignored by LAMMPS. The +second column is the "type" of the interaction; it is an index into +the PiTorsion Coeffs. The remaining 6 columns are the atom IDs of the +atoms (in order) for the 6-tuple :math:`IJKLMN`, as described above. Note that the *pitorsion types* and *pitorsions* and *PiTorsion Coeffs* and *PiTorsions* keywords for the header and body sections of diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index aa8127561c..6cd6fa2f56 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -21,7 +21,7 @@ Syntax .. parsed-literal:: - *types* values = two or more atom types + *types* values = two or more atom types (1-Ntypes or type label) *mu* values = chemical potential of swap types (energy units) *ke* value = *no* or *yes* *no* = no conservation of kinetic energy after atom swaps @@ -168,7 +168,7 @@ the following global cumulative quantities: * 1 = swap attempts * 2 = swap accepts -The vector values calculated by this fix are "extensive". +The vector values calculated by this fix are "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index adbfb43d72..449b9b8208 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -31,7 +31,7 @@ Syntax v_name = per-atom vector calculated by an atom-style variable with name * zero or more keyword/arg pairs may be appended -* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *format* or *title1* or *title2* or *title3* +* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *append* or *overwrite* or *format* or *title1* or *title2* or *title3* .. parsed-literal:: @@ -51,6 +51,8 @@ Syntax dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation *file* arg = filename filename = file to write results to + *append* arg = filename + filename = file to append results to *overwrite* arg = none = overwrite output file with only latest output *format* arg = string string = C-style format string @@ -433,15 +435,21 @@ molecule. ---------- -The *file* keyword allows a filename to be specified. Every -:math:`N_\text{freq}` timesteps, a section of chunk info will be written to a -text file in the following format. A line with the timestep and number of -chunks is written. Then one line per chunk is written, containing the chunk -ID :math:`(1-N_\text{chunk}),` an optional original ID value, optional -coordinate values for chunks that represent spatial bins, the number of atoms -in the chunk, and one or more calculated values. More explanation of the -optional values is given below. The number of values in each line -corresponds to the number of values specified in the fix ave/chunk +.. versionadded:: 17Apr2024 + new keyword *append* + +The *file* or *append* keywords allow a filename to be specified. If +*file* is used, then the filename is overwritten if it already exists. +If *append* is used, then the filename is appended to if it already +exists, or created if it does not exist. Every :math:`N_\text{freq}` +timesteps, a section of chunk info will be written to a text file in the +following format. A line with the timestep and number of chunks is +written. Then one line per chunk is written, containing the chunk ID +:math:`(1-N_\text{chunk}),` an optional original ID value, optional +coordinate values for chunks that represent spatial bins, the number of +atoms in the chunk, and one or more calculated values. More explanation +of the optional values is given below. The number of values in each +line corresponds to the number of values specified in the fix ave/chunk command. The number of atoms and the value(s) are summed or average quantities, as explained above. diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 1aff749048..659e15105c 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -65,7 +65,6 @@ Examples fix 1 all ave/correlate 1 50 10000 & c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] & type upper ave running title1 "My correlation data" - fix 1 all ave/correlate 1 50 10000 c_thermo_press[*] Description diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index e2b23248f2..003bdf897d 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -20,11 +20,11 @@ Syntax .. parsed-literal:: c_ID = global scalar calculated by a compute with ID - c_ID[I] = Ith component of global vector calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) f_ID = global scalar calculated by a fix with ID - f_ID[I] = Ith component of global vector calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) v_name = global value calculated by an equal-style variable with name - v_name[I] = Ith component of global vector calculated by a vector-style variable with name + v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below) * zero or more keyword/arg pairs may be appended * keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount* @@ -63,6 +63,7 @@ Examples fix 1 all ave/correlate/long 1 10000 & c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] & type upper title1 "My correlation data" nlen 15 ncount 3 + fix 1 all ave/correlate/long 1 10000 c_thermo_press[*] Description """"""""""" @@ -80,8 +81,10 @@ specified values may represent calculations performed by computes and fixes which store their own "group" definitions. Each listed value can be the result of a compute or fix or the -evaluation of an equal-style variable. See the -:doc:`fix ave/correlate ` page for details. +evaluation of an equal-style or vector-style variable. For +vector-style variables, the specified indices can include a wildcard +character. See the :doc:`fix ave/correlate ` page +for details. The *Nevery* and *Nfreq* arguments specify on what time steps the input values will be used to calculate correlation data and the frequency diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 9699e4238c..ac3b77086e 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -35,7 +35,7 @@ Syntax v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below) * zero or more keyword/arg pairs may be appended -* keyword = *mode* or *kind* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3* +* keyword = *mode* or *kind* or *file* or *append* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3* .. parsed-literal:: @@ -45,6 +45,8 @@ Syntax *kind* arg = *global* or *peratom* or *local* *file* arg = filename filename = name of file to output histogram(s) to + *append* arg = filename + filename = name of file to append histogram(s) to *ave* args = *one* or *running* or *window* one = output a new average value every Nfreq steps running = output cumulative average of all previous Nfreq steps @@ -317,19 +319,25 @@ on. The default is step 0. Often input values can be 0.0 at time 0, so setting *start* to a larger value can avoid including a 0.0 in a running or windowed histogram. -The *file* keyword allows a filename to be specified. Every *Nfreq* -steps, one histogram is written to the file. This includes a leading -line that contains the timestep, number of bins, the total count of -values contributing to the histogram, the count of values that were -not histogrammed (see the *beyond* keyword), the minimum value -encountered, and the maximum value encountered. The min/max values -include values that were not histogrammed. Following the leading -line, one line per bin is written into the file. Each line contains -the bin #, the coordinate for the center of the bin (between *lo* and -*hi*\ ), the count of values in the bin, and the normalized count. The -normalized count is the bin count divided by the total count (not -including values not histogrammed), so that the normalized values sum -to 1.0 across all bins. +.. versionadded:: 17Apr2024 + new keyword *append* + +The *file* or *append* keywords allow a filename to be specified. If +*file* is used, then the filename is overwritten if it already exists. +If *append* is used, then the filename is appended to if it already +exists, or created if it does not exist. Every *Nfreq* steps, one +histogram is written to the file. This includes a leading line that +contains the timestep, number of bins, the total count of values +contributing to the histogram, the count of values that were not +histogrammed (see the *beyond* keyword), the minimum value encountered, +and the maximum value encountered. The min/max values include values +that were not histogrammed. Following the leading line, one line per +bin is written into the file. Each line contains the bin #, the +coordinate for the center of the bin (between *lo* and *hi*\ ), the +count of values in the bin, and the normalized count. The normalized +count is the bin count divided by the total count (not including values +not histogrammed), so that the normalized values sum to 1.0 across all +bins. The *overwrite* keyword will continuously overwrite the output file with the latest output, so that it only contains one timestep worth of diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index aa82e676ea..cb05b8a5ab 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -28,7 +28,7 @@ Syntax v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below) * zero or more keyword/arg pairs may be appended -* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3* +* keyword = *mode* or *file* or *append* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3* .. parsed-literal:: @@ -45,6 +45,8 @@ Syntax M = value # from 1 to Nvalues *file* arg = filename filename = name of file to output time averages to + *append* arg = filename + filename = name of file to append time averages to *overwrite* arg = none = overwrite output file with only latest output *format* arg = string string = C-style format string @@ -270,16 +272,21 @@ are effectively constant or are simply current values (e.g., they are being written to a file with other time-averaged values for purposes of creating well-formatted output). -The *file* keyword allows a filename to be specified. Every *Nfreq* -steps, one quantity or vector of quantities is written to the file for -each input value specified in the fix ave/time command. For *mode* = -scalar, this means a single line is written each time output is -performed. Thus the file ends up to be a series of lines, i.e. one -column of numbers for each input value. For *mode* = vector, an array -of numbers is written each time output is performed. The number of rows -is the length of the input vectors, and the number of columns is the -number of values. Thus the file ends up to be a series of these array -sections. +.. versionadded:: 17Apr2024 + new keyword *append* + +The *file* or *append* keywords allow a filename to be specified. If +*file* is used, then the filename is overwritten if it already exists. +If *append* is used, then the filename is appended to if it already +exists, or created if it does not exist. Every *Nfreq* steps, one +quantity or vector of quantities is written to the file for each input +value specified in the fix ave/time command. For *mode* = scalar, this +means a single line is written each time output is performed. Thus the +file ends up to be a series of lines, i.e. one column of numbers for +each input value. For *mode* = vector, an array of numbers is written +each time output is performed. The number of rows is the length of the +input vectors, and the number of columns is the number of values. Thus +the file ends up to be a series of these array sections. .. versionadded:: 4May2022 diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 0672a05470..3065707dc7 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -14,15 +14,15 @@ Syntax * balance = style name of this fix command * Nfreq = perform dynamic load balancing every this many steps * thresh = imbalance threshold that must be exceeded to perform a re-balance -* style = *shift* or *rcb* - +* style = *shift* or *rcb* or *report* .. parsed-literal:: - shift args = dimstr Niter stopthresh + *shift* args = dimstr Niter stopthresh dimstr = sequence of letters containing *x* or *y* or *z*, each not more than once Niter = # of times to iterate within each dimension of dimstr sequence stopthresh = stop balancing when this imbalance threshold is reached *rcb* args = none + *report* args = none * zero or more keyword/arg pairs may be appended * keyword = *weight* or *out* @@ -70,6 +70,13 @@ re-balancing is performed periodically during the simulation. To perform "static" balancing, before or between runs, see the :doc:`balance ` command. +.. versionadded:: 17Apr2024 + +The *report* balance style only computes the load imbalance but +does not attempt any re-balancing. This way the load imbalance +information can be used otherwise, for instance for stopping a +run with :doc:`fix halt `. + Load-balancing is typically most useful if the particles in the simulation box have a spatially-varying density distribution or where the computational cost varies significantly between different diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index a0f7fad581..cfa29d8275 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * bond/break = style name of this fix command * Nevery = attempt bond breaking every this many steps -* bondtype = type of bonds to break +* bondtype = type of bonds to break (integer or type label) * Rmax = bond longer than Rmax can break (distance units) * zero or more keyword/value pairs may be appended * keyword = *prob* diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index bc5e1b83f8..0d818b2eae 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -17,9 +17,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * bond/create = style name of this fix command * Nevery = attempt bond creation every this many steps -* itype,jtype = atoms of itype can bond to atoms of jtype +* itype,jtype = atoms of itype can bond to atoms of jtype (1-Ntypes or type label) * Rmin = 2 atoms separated by less than Rmin can bond (distance units) -* bondtype = type of created bonds +* bondtype = type of created bonds (integer or type label) * zero or more keyword/value pairs may be appended to args * keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain* @@ -27,19 +27,19 @@ Syntax *iparam* values = maxbond, newtype maxbond = max # of bonds of bondtype the itype atom can have - newtype = change the itype atom to this type when maxbonds exist + newtype = change the itype atom to this type when maxbonds exist (1-Ntypes or type label) *jparam* values = maxbond, newtype maxbond = max # of bonds of bondtype the jtype atom can have - newtype = change the jtype atom to this type when maxbonds exist + newtype = change the jtype atom to this type when maxbonds exist (1-Ntypes or type label) *prob* values = fraction seed fraction = create a bond with this probability if otherwise eligible seed = random number seed (positive integer) *atype* value = angletype - angletype = type of created angles + angletype = type of created angles (integer or type label) *dtype* value = dihedraltype - dihedraltype = type of created dihedrals + dihedraltype = type of created dihedrals (integer or type label) *itype* value = impropertype - impropertype = type of created impropers + impropertype = type of created impropers (integer or type label) *aconstrain* value = amin amax amin = minimal angle at which new bonds can be created amax = maximal angle at which new bonds can be created @@ -54,6 +54,10 @@ Examples fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2 fix 5 all bond/create/angle 10 1 2 1.122 1 aconstrain 120 180 prob 1 4928459 iparam 2 1 jparam 2 2 + labelmap atom 1 c1 2 n2 + labelmap bond 1 c1-n2 + fix 5 all bond/create 10 c1 n2 0.8 c1-n2 + Description """"""""""" diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index 091eeae417..fe77deb91e 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -13,8 +13,8 @@ Syntax * ID, group-ID are documented in fix command * charge/regulation = style name of this fix command -* cation_type = atom type of free cations -* anion_type = atom type of free anions +* cation_type = atom type of free cations (integer or type label) +* anion_type = atom type of free anions (integer or type label) * zero or more keyword/value pairs may be appended @@ -27,8 +27,8 @@ Syntax *pIp* value = activity (effective concentration) of free cations (in the -log10 representation) *pIm* value = activity (effective concentration) of free anions (in the -log10 representation) *pKs* value = solvent self-dissociation constant (in the -log10 representation) - *acid_type* = atom type of acid groups - *base_type* = atom type of base groups + *acid_type* = atom type of acid groups (integer or type label) + *base_type* = atom type of base groups (integer or type label) *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers) *temp* value = temperature *tempfixid* value = fix ID of temperature thermostat @@ -51,6 +51,9 @@ Examples fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5.0 pKb 6.0 pH 7.0 pIp 3.0 pIm 3.0 nevery 200 nmc 200 seed 123 tempfixid fT fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0 + labelmap atom 1 H+ 2 OH- + fix chareg all charge/regulation H+ OH- pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0 + Description """"""""""" diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 9146b987c8..2c76463369 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -64,6 +64,8 @@ Syntax effectively an engineering shear strain rate *erate* value = R R = engineering shear strain rate (1/time units) + *erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure ` command) + R = engineering shear strain rate (1/time units) *trate* value = R R = true shear strain rate (1/time units) *wiggle* values = A Tp diff --git a/doc/src/fix_deform_pressure.rst b/doc/src/fix_deform_pressure.rst index f85ad37238..25ad5bfeca 100644 --- a/doc/src/fix_deform_pressure.rst +++ b/doc/src/fix_deform_pressure.rst @@ -29,10 +29,12 @@ Syntax NOTE: All other styles are documented by the :doc:`fix deform ` command *xy*, *xz*, *yz* args = style value - style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* + style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale* *pressure* values = target gain target = target pressure (pressure units) gain = proportional gain constant (1/(time * pressure) or 1/time units) + *erate/rescale* value = R + R = engineering shear strain rate (1/time units) NOTE: All other styles are documented by the :doc:`fix deform ` command *box* = style value @@ -69,7 +71,7 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 17Apr2024 This fix is an extension of the :doc:`fix deform ` command, which allows all of its options to be used as well as new @@ -91,7 +93,7 @@ corresponding component of the pressure tensor. This option attempts to maintain a specified target pressure using a linear controller where the box length :math:`L` evolves according to the equation -.. parsed-literal:: +.. math:: \frac{d L(t)}{dt} = L(t) k (P_t - P) @@ -159,6 +161,21 @@ details of a simulation and testing different values is recommended. One can also apply a maximum limit to the magnitude of the applied strain using the :ref:`max/rate ` option. +The *erate/rescale* style operates similarly to the *erate* style with +a specified strain rate in units of 1/time. The difference is that +the change in the tilt factor will depend on the current length of +the box perpendicular to the shear direction, L, instead of the +original length, L0. The tilt factor T as a function of time will +change as + +.. parsed-literal:: + + T(t) = T(t-1) + L\*erate\* \Delta t + +where T(t-1) is the tilt factor on the previous timestep and :math:`\Delta t` +is the timestep size. This option may be useful in scenarios where +L changes in time. + ---------- The *box* parameter provides an additional control over the *x*, *y*, @@ -294,6 +311,10 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` +page for more info. + You cannot apply x, y, or z deformations to a dimension that is shrink-wrapped via the :doc:`boundary ` command. diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 5264999839..8f88717a00 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * deposit = style name of this fix command * N = # of atoms or molecules to insert -* type = atom type to assign to inserted atoms (offset for molecule insertion) +* type = atom type (1-Ntypes or type label) to assign to inserted atoms (offset for molecule insertion) * M = insert a single atom or molecule every M steps * seed = random # seed (positive integer) * one or more keyword/value pairs may be appended to args @@ -76,6 +76,9 @@ Examples fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box + labelmap atom 1 Au + fix 4 sputter deposit 1000 Au 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice + Description """"""""""" diff --git a/doc/src/fix_electrode.rst b/doc/src/fix_electrode.rst index 99e098db31..fad2b19022 100644 --- a/doc/src/fix_electrode.rst +++ b/doc/src/fix_electrode.rst @@ -253,23 +253,26 @@ be enabled if any electrode particle has the same type as any electrolyte particle (which would be unusual in a typical simulation) and the fix will issue an error in that case. -.. versionchanged:: qtotal +.. versionadded:: 17Apr2024 -The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo* -to add an overall potential to all electrodes so that the total charge on -the electrodes is a specified amount (which may be an equal-style variable). -For example, if a user wanted to simulate a solution of excess cations -such that the total electrolyte charge is +2, setting *qtotal -2* would cause -the total electrode charge to be -2, so that the simulation box remains overall -electroneutral. Since *fix electrode/conq* constrains the total charges of -individual electrodes, and since *symm on* constrains the total charge of all -electrodes to be zero, either option is incompatible with the *qtotal* keyword -(even if *qtotal* is set to zero). +The keyword *qtotal* causes *fix electrode/conp* and *fix +electrode/thermo* to add an overall potential to all electrodes so that +the total charge on the electrodes is a specified amount (which may be +an equal-style variable). For example, if a user wanted to simulate a +solution of excess cations such that the total electrolyte charge is +2, +setting *qtotal -2* would cause the total electrode charge to be -2, so +that the simulation box remains overall electroneutral. Since *fix +electrode/conq* constrains the total charges of individual electrodes, +and since *symm on* constrains the total charge of all electrodes to be +zero, either option is incompatible with the *qtotal* keyword (even if +*qtotal* is set to zero). -The keyword *eta* takes the name of a custom double vector defined via fix -property/atom. The values will be used instead of the standard eta value. The -property/atom fix must be for vector of double values and use the *ghost on* -option. +.. versionadded:: 17Apr2024 + +The keyword *eta* takes the name of a custom double vector defined via +fix property/atom. The values will be used instead of the standard eta +value. The property/atom fix must be for vector of double values and +use the *ghost on* option. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index a21e85d803..aee8bdc90b 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -15,7 +15,7 @@ Syntax * N = invoke this fix every N steps * X = average number of GCMC exchanges to attempt every N steps * M = average number of MC moves to attempt every N steps -* type = atom type for inserted atoms (must be 0 if mol keyword used) +* type = atom type (1-Ntypes or type label) for inserted atoms (must be 0 if mol keyword used) * seed = random # seed (positive integer) * T = temperature of the ideal gas reservoir (temperature units) * mu = chemical potential of the ideal gas reservoir (energy units) @@ -45,7 +45,7 @@ Syntax *group* value = group-ID group-ID = group-ID for inserted atoms (string) *grouptype* values = type group-ID - type = atom type (int) + type = atom type (1-Ntypes or type label) group-ID = group-ID for inserted atoms (string) *intra_energy* value = intramolecular energy (energy units) *tfac_insert* value = scale up/down temperature of inserted atoms (unitless) @@ -62,52 +62,47 @@ Examples fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk + labelmap atom 1 Li + fix 2 ion gcmc 10 1000 1000 Li 29494 298.0 -0.5 0.01 + Description """"""""""" -This fix performs grand canonical Monte Carlo (GCMC) exchanges of -atoms or molecules with an imaginary ideal gas -reservoir at the specified T and chemical potential (mu) as discussed -in :ref:`(Frenkel) `. It also -attempts Monte Carlo (MC) moves (translations and molecule -rotations) within the simulation cell or -region. If used with the :doc:`fix nvt ` +This fix performs grand canonical Monte Carlo (GCMC) exchanges of atoms or +molecules with an imaginary ideal gas reservoir at the specified T and +chemical potential (mu) as discussed in :ref:`(Frenkel) `. It +also attempts Monte Carlo (MC) moves (translations and molecule rotations) +within the simulation cell or region. If used with the :doc:`fix nvt ` command, simulations in the grand canonical ensemble (muVT, constant chemical potential, constant volume, and constant temperature) can be performed. Specific uses include computing isotherms in microporous materials, or computing vapor-liquid coexistence curves. -Every N timesteps the fix attempts both GCMC exchanges -(insertions or deletions) and MC moves of gas atoms or molecules. -On those timesteps, the average number of attempted GCMC exchanges is X, -while the average number of attempted MC moves is M. -For GCMC exchanges of either molecular or atomic gasses, -these exchanges can be either deletions or insertions, -with equal probability. +Every N timesteps the fix attempts both GCMC exchanges (insertions or +deletions) and MC moves of gas atoms or molecules. On those timesteps, the +average number of attempted GCMC exchanges is X, while the average number +of attempted MC moves is M. For GCMC exchanges of either molecular or +atomic gasses, these exchanges can be either deletions or insertions, with +equal probability. -The possible choices for MC moves are translation of an atom, -translation of a molecule, and rotation of a molecule. -The relative amounts of each are determined by the optional -*mcmoves* keyword (see below). -The default behavior is as follows. -If the *mol* keyword is used, only molecule translations -and molecule rotations are performed with equal probability. -Conversely, if the *mol* keyword is not used, only atom -translations are performed. -M should typically be -chosen to be approximately equal to the expected number of gas atoms -or molecules of the given type within the simulation cell or region, -which will result in roughly one MC move per atom or molecule -per MC cycle. +The possible choices for MC moves are translation of an atom, translation +of a molecule, and rotation of a molecule. The relative amounts of each are +determined by the optional *mcmoves* keyword (see below). The default +behavior is as follows. If the *mol* keyword is used, only molecule +translations and molecule rotations are performed with equal probability. +Conversely, if the *mol* keyword is not used, only atom translations are +performed. M should typically be chosen to be approximately equal to the +expected number of gas atoms or molecules of the given type within the +simulation cell or region, which will result in roughly one MC move per +atom or molecule per MC cycle. -All inserted particles are always added to two groups: the default -group "all" and the fix group specified in the fix command. -In addition, particles are also added to any groups -specified by the *group* and *grouptype* keywords. If inserted -particles are individual atoms, they are assigned the atom type given -by the type argument. If they are molecules, the type argument has no -effect and must be set to zero. Instead, the type of each atom in the -inserted molecule is specified in the file read by the +All inserted particles are always added to two groups: the default group +"all" and the fix group specified in the fix command. In addition, +particles are also added to any groups specified by the *group* and +*grouptype* keywords. If inserted particles are individual atoms, they are +assigned the atom type given by the type argument. If they are molecules, +the type argument has no effect and must be set to zero. Instead, the type +of each atom in the inserted molecule is specified in the file read by the :doc:`molecule ` command. .. note:: @@ -427,7 +422,7 @@ the following global cumulative quantities: * 7 = rotation attempts * 8 = rotation successes -The vector values calculated by this fix are "extensive". +The vector values calculated by this fix are "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 76b17cddc4..54a4516fd1 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -512,8 +512,7 @@ Value 27 computes the average boost for biased bonds only on this step. Value 28 is the count of bonds with an absolute value of strain >= q on this step. -The scalar value is an "extensive" quantity since it grows with the -system size; the vector values are all "intensive". +The scalar value and vector values are all "intensive". This fix also computes a local vector of length the number of bonds currently in the system. The value for each bond is its :math:`C_{ij}` diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index 15790e15d0..e041f9f29b 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -8,33 +8,44 @@ Syntax .. code-block:: LAMMPS - fix ID group-ID indent K keyword values ... + fix ID group-ID indent K gstyle args keyword value ... * ID, group-ID are documented in :doc:`fix ` command * indent = style name of this fix command * K = force constant for indenter surface (force/distance\^2 units) -* one or more keyword/value pairs may be appended -* keyword = *sphere* or *cylinder* or *plane* or *side* or *units* +* gstyle = *sphere* or *cylinder* or *cone* or *plane* .. parsed-literal:: *sphere* args = x y z R - x,y,z = position of center of indenter (distance units) + x, y, z = position of center of indenter (distance units) R = sphere radius of indenter (distance units) - any of x,y,z,R can be a variable (see below) + any of x, y, z, R can be a variable (see below) *cylinder* args = dim c1 c2 R dim = *x* or *y* or *z* = axis of cylinder - c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) + c1, c2 = coords of cylinder axis in other 2 dimensions (distance units) R = cylinder radius of indenter (distance units) any of c1,c2,R can be a variable (see below) + *cone* args = dim c1 c2 radlo radhi lo hi + dim = *x* or *y* or *z* = axis of cone + c1, c2 = coords of cone axis in other 2 dimensions (distance units) + radlo,radhi = cone radii at lo and hi end (distance units) + lo,hi = bounds of cone in dim (distance units) + any of c1, c2, radlo, radhi, lo, hi can be a variable (see below) *plane* args = dim pos side dim = *x* or *y* or *z* = plane perpendicular to this dimension pos = position of plane in dimension x, y, or z (distance units) pos can be a variable (see below) side = *lo* or *hi* + +* zero or more keyword/value pairs may be appended +* keyword = *side* or *units* + + .. parsed-literal:: + *side* value = *in* or *out* - *in* = the indenter acts on particles inside the sphere or cylinder - *out* = the indenter acts on particles outside the sphere or cylinder + *in* = the indenter acts on particles inside the sphere or cylinder or cone + *out* = the indenter acts on particles outside the sphere or cylinder or cone *units* value = *lattice* or *box* lattice = the geometry is defined in lattice units box = the geometry is defined in simulation box units @@ -53,12 +64,12 @@ Description Insert an indenter within a simulation box. The indenter repels all atoms in the group that touch it, so it can be used to push into a -material or as an obstacle in a flow. Or it can be used as a +material or as an obstacle in a flow. Alternatively, it can be used as a constraining wall around a simulation; see the discussion of the *side* keyword below. -The indenter can either be spherical or cylindrical or planar. You -must set one of those 3 keywords. +The *gstyle* geometry of the indenter can either be a sphere, a +cylinder, a cone, or a plane. A spherical indenter exerts a force of magnitude @@ -75,15 +86,20 @@ A cylindrical indenter exerts the same force, except that *r* is the distance from the atom to the center axis of the cylinder. The cylinder extends infinitely along its axis. -Spherical and cylindrical indenters account for periodic boundaries in -two ways. First, the center point of a spherical indenter (x,y,z) or -axis of a cylindrical indenter (c1,c2) is remapped back into the -simulation box, if the box is periodic in a particular dimension. -This occurs every timestep if the indenter geometry is specified with -a variable (see below), e.g. it is moving over time. Second, the -calculation of distance to the indenter center or axis accounts for -periodic boundaries. Both of these mean that an indenter can -effectively move through and straddle one or more periodic boundaries. +A conical indenter is similar to a cylindrical indenter except that it +has a finite length (between *lo* and *hi*), and that two different +radii (one at each end, *radlo* and *radhi*) can be defined. + +Spherical, cylindrical, and conical indenters account for periodic +boundaries in two ways. First, the center point of a spherical +indenter (x,y,z) or axis of a cylindrical/conical indenter (c1,c2) is +remapped back into the simulation box, if the box is periodic in a +particular dimension. This occurs every timestep if the indenter +geometry is specified with a variable (see below), e.g. it is moving +over time. Second, the calculation of distance to the indenter center +or axis accounts for periodic boundaries. Both of these mean that an +indenter can effectively move through and straddle one or more +periodic boundaries. A planar indenter is really an axis-aligned infinite-extent wall exerting the same force on atoms in the system, where *R* is the @@ -97,9 +113,13 @@ is specified as *hi*\ . Any of the 4 quantities defining a spherical indenter's geometry can be specified as an equal-style :doc:`variable `, namely *x*, -*y*, *z*, or *R*\ . Similarly, for a cylindrical indenter, any of *c1*, -*c2*, or *R*, can be a variable. For a planar indenter, *pos* can be -a variable. If the value is a variable, it should be specified as +*y*, *z*, or *R*\ . For a cylindrical indenter, any of the 3 +quantities *c1*, *c2*, or *R*, can be a variable. For a conical +indenter, any of the 6 quantities *c1*, *c2*, *radlo*, *radhi*, *lo*, +or *hi* can be a variable. For a planar indenter, the single value +*pos* can be a variable. + +If any of these values is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to define the indenter geometry. @@ -110,7 +130,8 @@ command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify indenter properties that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the -:doc:`run ` command and the *elaplong* keyword of :doc:`thermo_style custom ` for details. +:doc:`run ` command and the *elaplong* keyword of +:doc:`thermo_style custom ` for details. For example, if a spherical indenter's x-position is specified as v_x, then this variable definition will keep it's center at a relative @@ -141,12 +162,13 @@ rate. If the *side* keyword is specified as *out*, which is the default, then particles outside the indenter are pushed away from its outer -surface, as described above. This only applies to spherical or -cylindrical indenters. If the *side* keyword is specified as *in*, -the action of the indenter is reversed. Particles inside the indenter -are pushed away from its inner surface. In other words, the indenter -is now a containing wall that traps the particles inside it. If the -radius shrinks over time, it will squeeze the particles. +surface, as described above. This only applies to spherical, +cylindrical, and conical indenters. If the *side* keyword is +specified as *in*, the action of the indenter is reversed. Particles +inside the indenter are pushed away from its inner surface. In other +words, the indenter is now a containing wall that traps the particles +inside it. If the radius shrinks over time, it will squeeze the +particles. The *units* keyword determines the meaning of the distance units used to define the indenter geometry. A *box* value selects standard @@ -166,10 +188,10 @@ lattice spacings in a variable formula. The force constant *K* is not affected by the *units* keyword. It is always in force/distance\^2 units where force and distance are defined -by the :doc:`units ` command. If you wish K to be scaled by the -lattice spacing, you can define K with a variable whose formula -contains *xlat*, *ylat*, *zlat* keywords of the -:doc:`thermo_style ` command, e.g. +by the :doc:`units ` command. If you wish K to be scaled by +the lattice spacing, you can define K with a variable whose formula +contains *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style +` command, e.g. .. code-block:: LAMMPS diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index 7705f211e8..2e19363f33 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -35,23 +35,24 @@ Description """"""""""" This fix enables LAMMPS to be run as a client for the i-PI Python -wrapper :ref:`(IPI) ` for performing a path integral molecular dynamics -(PIMD) simulation. The philosophy behind i-PI is described in the -following publication :ref:`(IPI-CPC) `. +wrapper :ref:`(IPI) `. i-PI is a universal force engine, +designed to perform advanced molecular simulations, with a special +focus on path integral molecular dynamics (PIMD) simulation. +The philosophy behind i-PI is to separate the evaluation of the +energy and forces, which is delegated to the client, and the evolution +of the dynamics, that is the responsibility of i-PI. This approach also +simplifies combining energies computed from different codes, which +can for instance be useful to mix first-principles calculations, +empirical force fields or machine-learning potentials. +The following publication :ref:`(IPI-CPC-2014) ` discusses the +overall implementation of i-PI, and focuses on path-integral techniques, +while a later release :ref:`(IPI-CPC-2019) ` introduces several +additional features and simulation schemes. -A version of the i-PI package, containing only files needed for use -with LAMMPS, is provided in the tools/i-pi directory. See the -tools/i-pi/manual.pdf for an introduction to i-PI. The -examples/PACKAGES/i-pi directory contains example scripts for using i-PI -with LAMMPS. - -In brief, the path integral molecular dynamics is performed by the -Python wrapper, while the client (LAMMPS in this case) simply computes -forces and energy for each configuration. The communication between -the two components takes place using sockets, and is reduced to the -bare minimum. All the parameters of the dynamics are specified in the -input of i-PI, and all the parameters of the force field must be -specified as LAMMPS inputs, preceding the *fix ipi* command. +The communication between i-PI and LAMMPS takes place using sockets, +and is reduced to the bare minimum. All the parameters of the dynamics +are specified in the input of i-PI, and all the parameters of the force +field must be specified as LAMMPS inputs, preceding the *fix ipi* command. The server address must be specified by the *address* argument, and can be either the IP address, the fully-qualified name of the server, @@ -75,6 +76,20 @@ If the cell varies too wildly, it may be advisable to re-initialize these interactions at each call. This behavior can be requested by setting the *reset* switch. +Obtaining i-PI +"""""""""""""" + +Here are the commands to set up a virtual environment and install +i-PI into it with all its dependencies via the PyPI repository and +the pip package manager. + +.. code-block:: sh + + python -m venv ipienv + source ipienv/bin/activate + pip install --upgrade pip + pip install ipi + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" @@ -111,9 +126,14 @@ Related commands .. _IPICPC: -**(IPI-CPC)** Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, +**(IPI-CPC-2014)** Ceriotti, More and Manolopoulos, Comp Phys Comm 185, 1019-1026 (2014). +.. _IPICPC2: + +**(IPI-CPC-2019)** Kapil et al., Comp Phys Comm 236, 214-223 (2019). + + .. _ipihome: **(IPI)** diff --git a/doc/src/fix_mol_swap.rst b/doc/src/fix_mol_swap.rst index b344b9c0e6..d437a6c2fe 100644 --- a/doc/src/fix_mol_swap.rst +++ b/doc/src/fix_mol_swap.rst @@ -14,7 +14,7 @@ Syntax * atom/swap = style name of this fix command * N = invoke this fix every N steps * X = number of swaps to attempt every N steps -* itype,jtype = two atom types to swap with each other +* itype,jtype = two atom types (1-Ntypes or type label) to swap with each other * seed = random # seed (positive integer) * T = scaling temperature of the MC swaps (temperature units) * zero or more keyword/value pairs may be appended to args @@ -34,6 +34,9 @@ Examples fix 2 all mol/swap 100 1 2 3 29494 300.0 ke no fix mySwap fluid mol/swap 500 10 1 2 482798 1.0 + labelmap atom 1 A 2 B + fix mySwap fluid mol/swap 500 10 A B 482798 1.0 + Description """"""""""" @@ -146,7 +149,7 @@ the following global cumulative quantities: * 1 = swap attempts * 2 = swap accepts -The vector values calculated by this fix are "extensive". +The vector values calculated by this fix are "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during diff --git a/doc/src/fix_nonaffine_displacement.rst b/doc/src/fix_nonaffine_displacement.rst index c6dfbc2e49..fd9830cc48 100644 --- a/doc/src/fix_nonaffine_displacement.rst +++ b/doc/src/fix_nonaffine_displacement.rst @@ -8,7 +8,7 @@ Syntax .. parsed-literal:: - fix ID group nonaffine/displacement style args reference/style nstep + fix ID group nonaffine/displacement style args reference/style nstep keyword values * ID, group are documented in :doc:`fix ` command * nonaffine/displacement = style name of this fix command @@ -32,6 +32,13 @@ Syntax *update* = update the reference frame every *nstep* timesteps *offset* = update the reference frame *nstep* timesteps before calculating the nonaffine displacement +* zero or more keyword/value pairs may be appended + + .. parsed-literal:: + + *z/min* values = zmin + zmin = minimum coordination number to calculate D2min + Examples """""""" @@ -76,6 +83,12 @@ is the identity tensor. This calculation is only performed on timesteps that are a multiple of *nevery* (including timestep zero). Data accessed before this occurs will simply be zeroed. +For particles with low coordination numbers, calculations of :math:`D^2_\mathrm{min}` +may not be accurate. An optional minimum coordination number can be defined using +the *z/min* keyword. If any particle has fewer than the specified number of particles +in the cutoff distance or in contact, the above calculations will be skipped and the +corresponding peratom array entries will be zero. + The *integrated* style simply integrates the velocity of particles every timestep to calculate a displacement. This style only works if used in conjunction with another fix that deforms the box and displaces @@ -86,8 +99,8 @@ Both of these methods require defining a reference state. With the *fixed* refer style, the user picks a specific timestep *nstep* at which particle positions are saved. If peratom data is accessed from this compute prior to this timestep, it will simply be zeroed. The *update* reference style implies the reference state will be updated every -*nstep* timesteps. The *offset* reference only applies to the *d2min* metric and will -update the reference state *nstep* timesteps before a multiple of *nevery* timesteps. +*nstep* timesteps. The *offset* reference will update the reference state *nstep* +timesteps before a multiple of *nevery* timesteps. ---------- diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst index 9bf1a82933..fba7fcaa93 100644 --- a/doc/src/fix_reaxff_species.rst +++ b/doc/src/fix_reaxff_species.rst @@ -20,7 +20,7 @@ Syntax * Nfreq = calculate average bond-order every this many timesteps * filename = name of output file * zero or more keyword/value pairs may be appended -* keyword = *cutoff* or *element* or *position* or *delete* +* keyword = *cutoff* or *element* or *position* or *delete* or *delete_rate_limit* .. parsed-literal:: @@ -110,10 +110,10 @@ all types from 1 to :math:`N`. A leading asterisk means all types from The optional keyword *element* can be used to specify the chemical symbol printed for each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types and each symbol must consist of -1 or 2 alphanumeric characters. Normally, these symbols should be -chosen to match the chemical identity of each LAMMPS atom type, as -specified using the :doc:`reaxff pair_coeff ` command and -the ReaxFF force field file. +1 or 2 alphanumeric characters. By default, these symbols are the same +as the chemical identity of each LAMMPS atom type, as specified by the +:doc:`ReaxFF pair_coeff ` command and the ReaxFF force +field file. The optional keyword *position* writes center-of-mass positions of each identified molecules to file *filepos* every *posfreq* timesteps. @@ -134,36 +134,34 @@ value. For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc. .. versionadded:: 3Aug2022 -The optional keyword *delete* enables the periodic removal of -molecules from the system. Criteria for deletion can be either a list -of specific chemical formulae or a range of molecular weights. -Molecules are deleted every *Nfreq* timesteps, and bond connectivity -is determined using the *Nevery* and *Nrepeat* keywords. The -*filedel* argument is the name of the output file that records the -species that are removed from the system. The *specieslist* keyword -permits specific chemical species to be deleted. The *Nspecies* -argument specifies how many species are eligible for deletion and is -followed by a list of chemical formulae, whose strings are compared to -species identified by this fix. For example, "specieslist 2 CO CO2" -deletes molecules that are identified as "CO" and "CO2" in the species -output file. When using the *specieslist* keyword, the *filedel* file -has the following format: the first line lists the chemical formulae -eligible for deletion, and each additional line contains the timestep -on which a molecule deletion occurs and the number of each species -deleted on that timestep. The *masslimit* keyword permits deletion of -molecules with molecular weights between *massmin* and *massmax*. -When using the *masslimit* keyword, each line of the *filedel* file -contains the timestep on which deletions occurs, followed by how many -of each species are deleted (with quantities preceding chemical -formulae). The *specieslist* and *masslimit* keywords cannot both be -used in the same *reaxff/species* fix. The *delete_rate_limit* -keyword can enforce an upper limit on the overall rate of molecule -deletion. The number of deletion occurrences is limited to Nlimit -within an interval of Nsteps timesteps. Nlimit can be specified with -an equal-style :doc:`variable `. When using the -*delete_rate_limit* keyword, no deletions are permitted to occur -within the first Nsteps timesteps of the first run (after reading a -either a data or restart file). +The optional keyword *delete* enables the periodic removal of molecules +from the system :ref:`(Gissinger) `. Criteria for deletion can +be either a list of specific chemical formulae or a range of molecular +weights. Molecules are deleted every *Nfreq* timesteps, and bond +connectivity is determined using the *Nevery* and *Nrepeat* keywords. The +*filedel* argument is the name of the output file that records the species +that are removed from the system. The *specieslist* keyword permits +specific chemical species to be deleted. The *Nspecies* argument specifies +how many species are eligible for deletion and is followed by a list of +chemical formulae, whose strings are compared to species identified by this +fix. For example, "specieslist 2 CO CO2" deletes molecules that are +identified as "CO" and "CO2" in the species output file. When using the +*specieslist* keyword, the *filedel* file has the following format: the +first line lists the chemical formulae eligible for deletion, and each +additional line contains the timestep on which a molecule deletion occurs +and the number of each species deleted on that timestep. The *masslimit* +keyword permits deletion of molecules with molecular weights between +*massmin* and *massmax*. When using the *masslimit* keyword, each line of +the *filedel* file contains the timestep on which deletions occurs, +followed by how many of each species are deleted (with quantities preceding +chemical formulae). The *specieslist* and *masslimit* keywords cannot both +be used in the same *reaxff/species* fix. The *delete_rate_limit* keyword +can enforce an upper limit on the overall rate of molecule deletion. The +number of deletion occurrences is limited to Nlimit within an interval of +Nsteps timesteps. Nlimit can be specified with an equal-style +:doc:`variable `. When using the *delete_rate_limit* keyword, no +deletions are permitted to occur within the first Nsteps timesteps of the +first run (after reading a either a data or restart file). ---------- @@ -233,5 +231,9 @@ Default """"""" The default values for bond-order cutoffs are 0.3 for all I-J pairs. -The default element symbols are C, H, O, N. +The default element symbols are taken from the ReaxFF pair_coeff command. Position files are not written by default. + +.. _Delete: + +**(Gissinger)** Jacob R. Gissinger, Scott R. Zavada, Joseph G. Smith, Josh Kemppainen, Ivan Gallegos, Gregory M. Odegard, Emilie J. Siochi, and Kristopher E. Wise, Carbon, 202, 336-347 (2023). diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 3174a0929c..0277793d0f 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -171,14 +171,15 @@ Examples of large rigid bodies are a colloidal particle, or portions of a biomolecule such as a protein. Example of small rigid bodies are patchy nanoparticles, such as those -modeled in :ref:`this paper ` by Sharon Glotzer's group, clumps of -granular particles, lipid molecules consisting of one or more point -dipoles connected to other spheroids or ellipsoids, irregular -particles built from line segments (2d) or triangles (3d), and -coarse-grain models of nano or colloidal particles consisting of a -small number of constituent particles. Note that the :doc:`fix shake ` command can also be used to rigidify small -molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats -the constituent atoms as point masses. +modeled in :ref:`this paper ` by Sharon Glotzer's group, +clumps of granular particles, lipid molecules consisting of one or +more point dipoles connected to other spheroids or ellipsoids, +irregular particles built from line segments (2d) or triangles (3d), +and coarse-grain models of nano or colloidal particles consisting of a +small number of constituent particles. Note that the :doc:`fix shake +` command can also be used to rigidify small molecules of +2, 3, or 4 atoms, e.g. water molecules. That fix treats the +constituent atoms as point masses. These fixes also update the positions and velocities of the atoms in each rigid body via time integration, in the NVE, NVT, NPT, or NPH @@ -212,13 +213,14 @@ processors when ghost atom info is accumulated. .. note:: - To use the *rigid/small* styles the ghost atom cutoff must be - large enough to span the distance between the atom that owns the body - and every other atom in the body. This distance value is printed out - when the rigid bodies are defined. If the - :doc:`pair_style ` cutoff plus neighbor skin does not span - this distance, then you should use the :doc:`comm_modify cutoff ` command with a setting epsilon larger than - the distance. + To use the *rigid/small* styles the ghost atom cutoff must be large + enough to span the distance between the atom that owns the body and + every other atom in the body. This distance value is printed out + when the rigid bodies are defined. If the :doc:`pair_style + ` cutoff plus neighbor skin does not span this + distance, then you should use the :doc:`comm_modify cutoff + ` command with a setting epsilon larger than the + distance. Which of the two variants is faster for a particular problem is hard to predict. The best way to decide is to perform a short test run. @@ -229,49 +231,54 @@ differences may accumulate to produce divergent trajectories. .. note:: You should not update the atoms in rigid bodies via other - time-integration fixes (e.g. :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix npt `, :doc:`fix move `), - or you will have conflicting updates to positions and velocities - resulting in unphysical behavior in most cases. When performing a hybrid - simulation with some atoms in rigid bodies, and some not, a separate - time integration fix like :doc:`fix nve ` or :doc:`fix nvt ` should be used for the non-rigid particles. + time-integration fixes (e.g. :doc:`fix nve `, :doc:`fix + nvt `, :doc:`fix npt `, :doc:`fix move + `), or you will have conflicting updates to positions and + velocities resulting in unphysical behavior in most cases. When + performing a hybrid simulation with some atoms in rigid bodies, and + some not, a separate time integration fix like :doc:`fix nve + ` or :doc:`fix nvt ` should be used for the + non-rigid particles. .. note:: - These fixes are overkill if you simply want to hold a collection - of atoms stationary or have them move with a constant velocity. A - simpler way to hold atoms stationary is to not include those atoms in - your time integration fix. E.g. use "fix 1 mobile nve" instead of - "fix 1 all nve", where "mobile" is the group of atoms that you want to - move. You can move atoms with a constant velocity by assigning them - an initial velocity (via the :doc:`velocity ` command), - setting the force on them to 0.0 (via the :doc:`fix setforce ` command), and integrating them as usual - (e.g. via the :doc:`fix nve ` command). + These fixes are overkill if you simply want to hold a collection of + atoms stationary or have them move with a constant velocity. A + simpler way to hold atoms stationary is to not include those atoms + in your time integration fix. E.g. use "fix 1 mobile nve" instead + of "fix 1 all nve", where "mobile" is the group of atoms that you + want to move. You can move atoms with a constant velocity by + assigning them an initial velocity (via the :doc:`velocity + ` command), setting the force on them to 0.0 (via the + :doc:`fix setforce ` command), and integrating them + as usual (e.g. via the :doc:`fix nve ` command). .. warning:: - The aggregate properties of each rigid body are - calculated at the start of a simulation run and are maintained in - internal data structures. The properties include the position and - velocity of the center-of-mass of the body, its moments of inertia, and - its angular momentum. This is done using the properties of the - constituent atoms of the body at that point in time (or see the *infile* - keyword option). Thereafter, changing these properties of individual - atoms in the body will have no effect on a rigid body's dynamics, unless - they effect any computation of per-atom forces or torques. If the - keyword *reinit* is set to *yes* (the default), the rigid body data - structures will be recreated at the beginning of each *run* command; - if the keyword *reinit* is set to *no*, the rigid body data structures - will be built only at the very first *run* command and maintained for - as long as the rigid fix is defined. For example, you might think you - could displace the atoms in a body or add a large velocity to each atom - in a body to make it move in a desired direction before a second run is - performed, using the :doc:`set ` or - :doc:`displace_atoms ` or :doc:`velocity ` - commands. But these commands will not affect the internal attributes - of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no* - (or using the *infile* option, which implies *reinit* *no*\ ) the position - and velocity of individual atoms in the body will be reset when time - integration starts again. + The aggregate properties of each rigid body are calculated at the + start of a simulation run and are maintained in internal data + structures. The properties include the position and velocity of the + center-of-mass of the body, its moments of inertia, and its angular + momentum. This is done using the properties of the constituent + atoms of the body at that point in time (or see the *infile* + keyword option). Thereafter, changing these properties of + individual atoms in the body will have no effect on a rigid body's + dynamics, unless they effect any computation of per-atom forces or + torques. If the keyword *reinit* is set to *yes* (the default), the + rigid body data structures will be recreated at the beginning of + each *run* command; if the keyword *reinit* is set to *no*, the + rigid body data structures will be built only at the very first + *run* command and maintained for as long as the rigid fix is + defined. For example, you might think you could displace the atoms + in a body or add a large velocity to each atom in a body to make it + move in a desired direction before a second run is performed, using + the :doc:`set ` or :doc:`displace_atoms ` or + :doc:`velocity ` commands. But these commands will not + affect the internal attributes of the body unless *reinit* is set + to *yes*\ . With *reinit* set to *no* (or using the *infile* + option, which implies *reinit* *no*\ ) the position and velocity of + individual atoms in the body will be reset when time integration + starts again. ---------- @@ -316,17 +323,17 @@ to be part of rigid bodies. .. note:: - To compute the initial center-of-mass position and other - properties of each rigid body, the image flags for each atom in the - body are used to "unwrap" the atom coordinates. Thus you must ensure - that these image flags are consistent so that the unwrapping creates a + To compute the initial center-of-mass position and other properties + of each rigid body, the image flags for each atom in the body are + used to "unwrap" the atom coordinates. Thus you must ensure that + these image flags are consistent so that the unwrapping creates a valid rigid body (one where the atoms are close together), - particularly if the atoms in a single rigid body straddle a periodic - boundary. This means the input data file or restart file must define - the image flags for each atom consistently or that you have used the - :doc:`set ` command to specify them correctly. If a dimension is - non-periodic then the image flag of each atom must be 0 in that - dimension, else an error is generated. + particularly if the atoms in a single rigid body straddle a + periodic boundary. This means the input data file or restart file + must define the image flags for each atom consistently or that you + have used the :doc:`set ` command to specify them correctly. + If a dimension is non-periodic then the image flag of each atom + must be 0 in that dimension, else an error is generated. The *force* and *torque* keywords discussed next are only allowed for the *rigid* styles. @@ -362,12 +369,13 @@ settings from the final keyword are used. .. note:: - For computational efficiency, you may wish to turn off pairwise - and bond interactions within each rigid body, as they no longer - contribute to the motion. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` - commands are used to do this. If the rigid bodies have strongly - overlapping atoms, you may need to turn off these interactions to - avoid numerical problems due to large equal/opposite intra-body forces + For computational efficiency, you may wish to turn off pairwise and + bond interactions within each rigid body, as they no longer + contribute to the motion. The :doc:`neigh_modify exclude + ` and :doc:`delete_bonds ` commands are + used to do this. If the rigid bodies have strongly overlapping + atoms, you may need to turn off these interactions to avoid + numerical problems due to large equal/opposite intra-body forces swamping the contribution of small inter-body forces. For computational efficiency, you should typically define one fix @@ -379,7 +387,8 @@ is more expensive. The constituent particles within a rigid body can be point particles (the default in LAMMPS) or finite-size particles, such as spheres or -ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri ` commands for more +ellipsoids or line segments or triangles. See the :doc:`atom_style +sphere and ellipsoid and line and tri ` commands for more details on these kinds of particles. Finite-size particles contribute differently to the moment of inertia of a rigid body than do point particles. Finite-size particles can also experience torque (e.g. due @@ -389,7 +398,8 @@ orientation. These contributions are accounted for by these fixes. Forces between particles within a body do not contribute to the external force or torque on the body. Thus for computational efficiency, you may wish to turn off pairwise and bond interactions -between particles within each rigid body. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` +between particles within each rigid body. The :doc:`neigh_modify +exclude ` and :doc:`delete_bonds ` commands are used to do this. For finite-size particles this also means the particles can be highly overlapped when creating the rigid body. @@ -401,16 +411,17 @@ perform constant NVE time integration. They are referred to below as the 4 NVE rigid styles. The only difference is that the *rigid* and *rigid/small* styles use an integration technique based on Richardson iterations. The *rigid/nve* and *rigid/small/nve* styles uses the -methods described in the paper by :ref:`Miller `, which are thought -to provide better energy conservation than an iterative approach. +methods described in the paper by :ref:`Miller `, which are +thought to provide better energy conservation than an iterative +approach. The *rigid/nvt* and *rigid/nvt/small* styles performs constant NVT integration using a Nose/Hoover thermostat with chains as described -originally in :ref:`(Hoover) ` and :ref:`(Martyna) `, which -thermostats both the translational and rotational degrees of freedom -of the rigid bodies. They are referred to below as the 2 NVT rigid -styles. The rigid-body algorithm used by *rigid/nvt* is described in -the paper by :ref:`Kamberaj `. +originally in :ref:`(Hoover) ` and :ref:`(Martyna) +`, which thermostats both the translational and rotational +degrees of freedom of the rigid bodies. They are referred to below as +the 2 NVT rigid styles. The rigid-body algorithm used by *rigid/nvt* +is described in the paper by :ref:`Kamberaj `. The *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small* styles perform constant NPT or NPH integration using a Nose/Hoover @@ -436,12 +447,12 @@ The target pressures for each of the 6 components of the stress tensor can be specified independently via the *x*, *y*, *z* keywords, which correspond to the 3 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped -value during the run from *Pstart* to *Pstop*\ . If a target pressure is -specified for a component, then the corresponding box dimension will -change during a simulation. For example, if the *y* keyword is used, -the y-box length will change. A box dimension will not change if that -component is not specified, although you have the option to change -that dimension via the :doc:`fix deform ` command. +value during the run from *Pstart* to *Pstop*\ . If a target pressure +is specified for a component, then the corresponding box dimension +will change during a simulation. For example, if the *y* keyword is +used, the y-box length will change. A box dimension will not change +if that component is not specified, although you have the option to +change that dimension via the :doc:`fix deform ` command. For all barostat keywords, the *Pdamp* parameter operates like the *Tdamp* parameter, determining the time scale on which pressure is @@ -525,11 +536,11 @@ discussed below. The *langevin* keyword applies a Langevin thermostat to the constant NVE time integration performed by any of the 4 NVE rigid styles: -*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot be -used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . The -desired temperature at each timestep is a ramped value during the run -from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in time -units and determines how rapidly the temperature is relaxed. For +*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot +be used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . +The desired temperature at each timestep is a ramped value during the +run from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in +time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time units (:math:`\tau` or fs or ps - see the :doc:`units ` command). The random # *seed* must be a positive @@ -564,29 +575,30 @@ used. *Tchain* is the number of thermostats in the Nose Hoover chain. This value, along with *Tdamp* can be varied to dampen undesirable oscillations in temperature that can occur in a simulation. As a rule of thumb, increasing the chain length should lead to smaller -oscillations. The keyword *pchain* specifies the number of -thermostats in the chain thermostatting the barostat degrees of -freedom. +oscillations. The keyword *pchain* specifies the number of thermostats +in the chain thermostatting the barostat degrees of freedom. .. note:: There are alternate ways to thermostat a system of rigid bodies. - You can use :doc:`fix langevin ` to treat the individual - particles in the rigid bodies as effectively immersed in an implicit - solvent, e.g. a Brownian dynamics model. For hybrid systems with both - rigid bodies and solvent particles, you can thermostat only the - solvent particles that surround one or more rigid bodies by - appropriate choice of groups in the compute and fix commands for - temperature and thermostatting. The solvent interactions with the - rigid bodies should then effectively thermostat the rigid body - temperature as well without use of the Langevin or Nose/Hoover options - associated with the fix rigid commands. + You can use :doc:`fix langevin ` to treat the + individual particles in the rigid bodies as effectively immersed in + an implicit solvent, e.g. a Brownian dynamics model. For hybrid + systems with both rigid bodies and solvent particles, you can + thermostat only the solvent particles that surround one or more + rigid bodies by appropriate choice of groups in the compute and fix + commands for temperature and thermostatting. The solvent + interactions with the rigid bodies should then effectively + thermostat the rigid body temperature as well without use of the + Langevin or Nose/Hoover options associated with the fix rigid + commands. ---------- The *mol* keyword can only be used with the *rigid/small* styles. It -must be used when other commands, such as :doc:`fix deposit ` or :doc:`fix pour `, add rigid -bodies on-the-fly during a simulation. You specify a *template-ID* +must be used when other commands, such as :doc:`fix deposit +` or :doc:`fix pour `, add rigid bodies +on-the-fly during a simulation. You specify a *template-ID* previously defined using the :doc:`molecule ` command, which reads a file that defines the molecule. You must use the same *template-ID* that the other fix which is adding rigid bodies uses. @@ -670,16 +682,16 @@ cross periodic boundaries during the simulation. .. note:: - If you use the *infile* or *mol* keywords and write restart - files during a simulation, then each time a restart file is written, - the fix also write an auxiliary restart file with the name - rfile.rigid, where "rfile" is the name of the restart file, + If you use the *infile* or *mol* keywords and write restart files + during a simulation, then each time a restart file is written, the + fix also write an auxiliary restart file with the name rfile.rigid, + where "rfile" is the name of the restart file, e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary - file is in the same format described above. Thus it can be used in a - new input script that restarts the run and re-specifies a rigid fix - using an *infile* keyword and the appropriate filename. Note that the - auxiliary file will contain one line for every rigid body, even if the - original file only listed a subset of the rigid bodies. + file is in the same format described above. Thus it can be used in + a new input script that restarts the run and re-specifies a rigid + fix using an *infile* keyword and the appropriate filename. Note + that the auxiliary file will contain one line for every rigid body, + even if the original file only listed a subset of the rigid bodies. If the system has rigid bodies with finite-size overlapping particles and the model uses the :doc:`fix gravity ` command to @@ -728,10 +740,11 @@ also accounted for by this fix. ---------- -If your simulation is a hybrid model with a mixture of rigid bodies and -non-rigid particles (e.g. solvent) there are several ways these rigid -fixes can be used in tandem with :doc:`fix nve `, :doc:`fix nvt -`, :doc:`fix npt `, and :doc:`fix nph `. +If your simulation is a hybrid model with a mixture of rigid bodies +and non-rigid particles (e.g. solvent) there are several ways these +rigid fixes can be used in tandem with :doc:`fix nve `, +:doc:`fix nvt `, :doc:`fix npt `, and :doc:`fix nph +`. If you wish to perform NVE dynamics (no thermostatting or barostatting), use one of 4 NVE rigid styles to integrate the rigid @@ -741,14 +754,14 @@ particles. If you wish to perform NVT dynamics (thermostatting, but no barostatting), you can use one of the 2 NVT rigid styles for the rigid bodies, and any thermostatting fix for the non-rigid particles -(:doc:`fix nvt `, :doc:`fix langevin `, :doc:`fix -temp/berendsen `). You can also use one of the 4 -NVE rigid styles for the rigid bodies and thermostat them using -:doc:`fix langevin ` on the group that contains all the -particles in the rigid bodies. The net force added by :doc:`fix -langevin ` to each rigid body effectively thermostats its -translational center-of-mass motion. Not sure how well it does at -thermostatting its rotational motion. +(:doc:`fix nvt `, :doc:`fix langevin `, +:doc:`fix temp/berendsen `). You can also use one +of the 4 NVE rigid styles for the rigid bodies and thermostat them +using :doc:`fix langevin ` on the group that contains +all the particles in the rigid bodies. The net force added by +:doc:`fix langevin ` to each rigid body effectively +thermostats its translational center-of-mass motion. Not sure how +well it does at thermostatting its rotational motion. If you wish to perform NPT or NPH dynamics (barostatting), you cannot use both :doc:`fix npt ` and the NPT or NPH rigid styles. This @@ -774,12 +787,12 @@ to the global pressure and the box is scaled the same by any of the barostatting fixes. You could even use the second and third options for a non-hybrid -simulation consisting of only rigid bodies, assuming you give :doc:`fix -npt ` an empty group, though it's an odd thing to do. The -barostatting fixes (:doc:`fix npt ` and :doc:`fix press/berensen -`) will monitor the pressure and change the box -dimensions, but not time integrate any particles. The integration of -the rigid bodies will be performed by fix rigid/nvt. +simulation consisting of only rigid bodies, assuming you give +:doc:`fix npt ` an empty group, though it's an odd thing to +do. The barostatting fixes (:doc:`fix npt ` and :doc:`fix +press/berensen `) will monitor the pressure and +change the box dimensions, but not time integrate any particles. The +integration of the rigid bodies will be performed by fix rigid/nvt. ---------- @@ -824,10 +837,10 @@ various :doc:`output commands `. The scalar value calculated by these fixes is "intensive". The scalar is the current temperature of the collection of rigid bodies. This is averaged over all rigid bodies and their translational and rotational degrees of -freedom. The translational energy of a rigid body is 1/2 m v\^2, where -m = total mass of the body and v = the velocity of its center of mass. -The rotational energy of a rigid body is 1/2 I w\^2, where I = the -moment of inertia tensor of the body and w = its angular velocity. +freedom. The translational energy of a rigid body is 1/2 m v\^2, +where m = total mass of the body and v = the velocity of its center of +mass. The rotational energy of a rigid body is 1/2 I w\^2, where I = +the moment of inertia tensor of the body and w = its angular velocity. Degrees of freedom constrained by the *force* and *torque* keywords are removed from this calculation, but only for the *rigid* and *rigid/nve* fixes. diff --git a/doc/src/fix_sgcmc.rst b/doc/src/fix_sgcmc.rst index bcdbdf2736..51ec572a47 100644 --- a/doc/src/fix_sgcmc.rst +++ b/doc/src/fix_sgcmc.rst @@ -15,7 +15,7 @@ Syntax * every_nsteps = number of MD steps between MC cycles * swap_fraction = fraction of a full MC cycle carried out at each call (a value of 1.0 will perform as many trial moves as there are atoms) * temperature = temperature that enters Boltzmann factor in Metropolis criterion (usually the same as MD temperature) -* deltamu = chemical potential difference(s) (`N-1` values must be provided, with `N` being the number of elements) +* deltamu = `N-1` chemical potential differences :math:`\mu_1-\mu_2, \ldots, \mu_1-\mu_N` (`N` is the number of atom types) * Zero or more keyword/value pairs may be appended to fix definition line: .. parsed-literal:: @@ -23,7 +23,7 @@ Syntax keyword = *variance* or *randseed* or *window_moves* or *window_size* *variance* kappa conc1 [conc2] ... [concN] kappa = variance constraint parameter - conc1,conc2,... = target concentration(s) in the range 0.0-1.0 (*N-1* values must be provided, with *N* being the number of elements) + `c_2`, `c_3`,..., `c_N` = `N-1` target concentration fractions *randseed* N N = seed for pseudo random number generator *window_moves* N @@ -90,11 +90,10 @@ the simulation, e.g., to speed up equilibration at low temperatures. ------------ -The parameter *deltamu* is used to set the chemical potential difference -in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 `). By -convention it is the difference of the chemical potentials of elements -`B`, `C` ..., with respect to element A. When the simulation includes -`N` elements, `N-1` values must be specified. +The parameter *deltamu* is used to set the chemical potential differences +in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 `). +The `N-1` differences are defined as :math:`\mu_1-\mu_2, \ldots, \mu_1-\mu_N`, +where `N` is the number of atom types. ------------ @@ -104,12 +103,12 @@ the effective average constraint in the parallel VC-SGC MC algorithm (parameter :math:`\delta\mu_0` in Eq. (20) of :ref:`Sadigh1 `). The parameter *kappa* specifies the variance constraint (see Eqs. (20-21) in :ref:`Sadigh1 `). - -The parameter *conc* sets the target concentration (parameter -:math:`c_0` in Eqs. (20-21) of :ref:`Sadigh1 `). The atomic -concentrations refer to components `B`, `C` ..., with `A` being set -automatically. When the simulation includes `N` elements, `N-1` -concentration values must be specified. +The parameter *conc* sets the `N-1` target atomic concentration +fractions (parameter :math:`c_0` in Eqs. (20-21) of :ref:`Sadigh1 `) +:math:`0 \le c_2, \ldots, c_N \le 1`, with +:math:`c_1 = 1 - \Sigma_{i=2}^N c_i`. +When the simulation includes `N` atom types (elements), +`N-1` concentration values must be specified. ------------ @@ -143,10 +142,12 @@ components of the vector represent the following quantities: * 1 = The absolute number of accepted trial swaps during the last MC step * 2 = The absolute number of rejected trial swaps during the last MC step -* 3 = The current global concentration of species *A* (= number of atoms of type 1 / total number of atoms) -* 4 = The current global concentration of species *B* (= number of atoms of type 2 / total number of atoms) +* 3 = Current global concentration `c_1` (= number of atoms of type 1 / total number of atoms) +* 4 = Current global concentration `c_2` (= number of atoms of type 2 / total number of atoms) * ... -* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms) +* N+2: Current global concentration `c_N` (= number of atoms of type *N* / total number of atoms) + +The vector values calculated by this fix are "intensive". Restrictions """""""""""" diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index ccf7f16554..f3e6a08d61 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -96,11 +96,11 @@ each processor, which is acceptable when the overall grid is reasonably small. For larger grids you should use fix *ttm/grid* instead. Fix *ttm/mod* adds options to account for external heat sources (e.g. at -a surface) and for specifying parameters that allow the electronic -heat capacity to depend strongly on electronic temperature. It is -more expensive computationally than fix *ttm* because it treats the -thermal diffusion equation as non-linear. More details on fix *ttm/mod* -are given below. +a surface) and for specifying parameters that allow the electronic heat +capacity to depend strongly on electronic temperature. It is more +expensive computationally than fix *ttm* because it treats the thermal +diffusion equation as non-linear. More details on fix *ttm/mod* are +given below. Heat transfer between the electronic and atomic subsystems is carried out via an inhomogeneous Langevin thermostat. Only atoms in the fix @@ -136,23 +136,23 @@ transfer between the subsystems: \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' -where C_e is the specific heat, rho_e is the density, kappa_e is the -thermal conductivity, T is temperature, the "e" and "a" subscripts -represent electronic and atomic subsystems respectively, g_p is the -coupling constant for the electron-ion interaction, and g_s is the -electron stopping coupling parameter. C_e, rho_e, and kappa_e are -specified as parameters to the fix. The other quantities are derived. -The form of the heat diffusion equation used here is almost the same -as that in equation 6 of :ref:`(Duffy) `, with the exception that the -electronic density is explicitly represented, rather than being part -of the specific heat parameter. +where :math:`C_e` is the specific heat, :math:`\rho_e` is the density, +:math:`\kappa_e` is the thermal conductivity, *T* is temperature, the +"e" and "a" subscripts represent electronic and atomic subsystems +respectively, :math:`g_p` is the coupling constant for the electron-ion +interaction, and :math:`g_s` is the electron stopping coupling +parameter. :math:`C_e`, :math:`\rho_e`, and :math:`\kappa_e` are +specified as parameters to the fix *ttm* or *ttm/grid*. The other +quantities are derived. The form of the heat diffusion equation used +here is almost the same as that in equation 6 of :ref:`(Duffy) `, +with the exception that the electronic density is explicitly +represented, rather than being part of the specific heat parameter. Currently, the TTM fixes assume that none of the user-supplied -parameters will vary with temperature. Note that :ref:`(Duffy) -` used a tanh() functional form for the temperature dependence -of the electronic specific heat, but ignored temperature dependencies -of any of the other parameters. See more discussion below for fix -ttm/mod. +parameters will vary with temperature. Note that :ref:`(Duffy) ` +used a tanh() functional form for the temperature dependence of the +electronic specific heat, but ignored temperature dependencies of any of +the other parameters. See more discussion below for fix *ttm/mod*. .. note:: @@ -265,27 +265,27 @@ heat sources (e.g. laser heating in ablation simulations): \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin}) -where theta is the Heaviside step function, I_0 is the (absorbed) -laser pulse intensity for ablation simulations, l_skin is the depth -of skin-layer, and all other designations have the same meaning as in -the former equation. The duration of the pulse is set by the parameter -*tau* in the *init_file*. +where :math:`\theta` is the Heaviside step function, :math:`I_0` is the +(absorbed) laser pulse intensity for ablation simulations, +:math:`l_{skin}` is the depth of the skin-layer, and all other +designations have the same meaning as in the former equation. The +duration of the pulse is set by the parameter *tau* in the *init_file*. -Fix ttm/mod also allows users to specify the dependencies of C_e and -kappa_e on the electronic temperature. The specific heat is expressed -as +Fix *ttm/mod* also allows users to specify the dependencies of +:math:`C_e` and :math:`\kappa_e` on the electronic temperature. The +specific heat is expressed as .. math:: C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2) -where *X* = T_e/1000, and the thermal conductivity is defined as -kappa_e = D_e\*rho_e\*C_e, where D_e is the thermal diffusion -coefficient. +where :math:`X = \frac{T_e}{1000}`, and the thermal conductivity is +defined as :math:`\kappa_e = D_e \cdot rho_e \cdot C_e`, where +:math:`D_e` is the thermal diffusion coefficient. -Electronic pressure effects are included in the TTM model to account -for the blast force acting on ions because of electronic pressure -gradient (see :ref:`(Chen) `, :ref:`(Norman) `). The total force +Electronic pressure effects are included in the TTM model to account for +the blast force acting on ions because of electronic pressure gradient +(see :ref:`(Chen) `, :ref:`(Norman) `). The total force acting on an ion is: .. math:: @@ -293,25 +293,26 @@ acting on an ion is: {\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec F}_{langevin} - \nabla P_e/n_{ion} -where F_langevin is a force from Langevin thermostat simulating -electron-phonon coupling, and nabla P_e/n_ion is the electron blast -force. +where :math:`F_{langevin}` is a force from Langevin thermostat +simulating electron-phonon coupling, and :math:`\nabla P_e/n_{ion}` is +the electron blast force. -The electronic pressure is taken to be P_e = B\*rho_e\*C_e\*T_e +The electronic pressure is taken to be :math:`P_e = B \cdot rho_e \cdot +C_e \cdot T_e` -The current fix ttm/mod implementation allows TTM simulations with a +The current fix *ttm/mod* implementation allows TTM simulations with a vacuum. The vacuum region is defined as the grid cells with zero electronic temperature. The numerical scheme does not allow energy exchange with such cells. Since the material can expand to previously -unoccupied region in some simulations, the vacuum border can be -allowed to move. It is controlled by the *surface_movement* parameter -in the *init_file*. If it is set to 1, then "vacuum" cells can be -changed to "electron-filled" cells with the temperature *T_e_min* if -atoms move into them (currently only implemented for the case of -1-dimensional motion of flat surface normal to the X axis). The -initial borders of vacuum can be set in the *init_file* via *lsurface* -and *rsurface* parameters. In this case, electronic pressure gradient -is calculated as +unoccupied region in some simulations, the vacuum border can be allowed +to move. It is controlled by the *surface_movement* parameter in the +*init_file*. If it is set to 1, then "vacuum" cells can be changed to +"electron-filled" cells with the temperature *T_e_min* if atoms move +into them (currently only implemented for the case of 1-dimensional +motion of a flat surface normal to the X axis). The initial locations of +the interfaces of the electron density to the vacuum can be set in the +*init_file* via *lsurface* and *rsurface* parameters. In this case, +electronic pressure gradient is calculated as .. math:: @@ -319,10 +320,10 @@ is calculated as \frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta x}-(C_e{}T_e)_{x}}{\Delta x} \right] -where lambda is the electron mean free path (see :ref:`(Norman) `, -:ref:`(Pisarev) `) +where :math:`\lambda` is the electron mean free path (see :ref:`(Norman) +`, :ref:`(Pisarev) `) -The fix ttm/mod parameter file *init_file* has the following syntax. +The fix *ttm/mod* parameter file *init_file* has the following syntax. Every line with an odd number is considered as a comment and ignored. The lines with the even numbers are treated as follows: diff --git a/doc/src/fix_wall_flow.rst b/doc/src/fix_wall_flow.rst index b40ba9697f..d498e57c63 100644 --- a/doc/src/fix_wall_flow.rst +++ b/doc/src/fix_wall_flow.rst @@ -40,7 +40,7 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 17Apr2024 This fix implements flow boundary conditions (FBC) introduced in :ref:`(Pavlov1) ` and :ref:`(Pavlov2) `. diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index f6465d1159..25d659241c 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -115,6 +115,18 @@ friction and twisting friction supported by the :doc:`pair_style granular `. +.. note:: + When *fstyle* *granular* is specified, the associated *fstyle_params* are taken as + those for a wall/particle interaction. For example, for the *hertz/material* normal + contact model with :math:`E = 960` and :math:`\nu = 0.2`, the effective Young's + modulus for a wall/particle interaction is computed as + :math:`E_{eff} = \frac{960}{2(1-0.2^2)} = 500`. Any pair coefficients defined by + :doc:`pair_style granular ` are not taken into consideration. To + model different wall/particle interactions for particles of different material + types, the user may define multiple fix wall/gran commands operating on separate + groups (e.g. based on particle type) each with a different wall/particle effective + Young's modulus. + Note that you can choose a different force styles and/or different values for the wall/particle coefficients than for particle/particle interactions. E.g. if you wish to model the wall as a different diff --git a/doc/src/fix_widom.rst b/doc/src/fix_widom.rst index 43e081800f..e9cffcba88 100644 --- a/doc/src/fix_widom.rst +++ b/doc/src/fix_widom.rst @@ -14,7 +14,7 @@ Syntax * widom = style name of this fix command * N = invoke this fix every N steps * M = number of Widom insertions to attempt every N steps -* type = atom type for inserted atoms (must be 0 if mol keyword used) +* type = atom type (1-Ntypes or type label) for inserted atoms (must be 0 if mol keyword used) * seed = random # seed (positive integer) * T = temperature of the system (temperature units) * zero or more keyword/value pairs may be appended to args @@ -38,6 +38,9 @@ Examples fix 2 gas widom 1 50000 1 19494 2.0 fix 3 water widom 1000 100 0 29494 300.0 mol h2omol full_energy + labelmap atom 1 Li + fix 2 ion widom 1 50000 Li 19494 2.0 + Description """"""""""" @@ -179,7 +182,7 @@ the following global cumulative quantities: * 2 = average difference in potential energy on each timestep * 3 = volume of the insertion region -The vector values calculated by this fix are "extensive". +The vector values calculated by this fix are "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during diff --git a/doc/src/group.rst b/doc/src/group.rst index fb1e0fb157..15ab0c9dc8 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -20,13 +20,13 @@ Syntax *empty* = no args *region* args = region-ID *type* or *id* or *molecule* - args = list of one or more atom types, atom IDs, or molecule IDs - any entry in list can be a sequence formatted as A:B or A:B:C where + args = list of one or more atom types (1-Ntypes or type label), atom IDs, or molecule IDs + any numeric entry in list can be a sequence formatted as A:B or A:B:C where A = starting index, B = ending index, C = increment between indices, 1 if not specified args = logical value logical = "<" or "<=" or ">" or ">=" or "==" or "!=" - value = an atom type or atom ID or molecule ID (depending on *style*\ ) + value = an atom type (1-Ntypes or type label) or atom ID or molecule ID (depending on *style*\ ) args = logical value1 value2 logical = "<>" value1,value2 = atom types or atom IDs or molecule IDs (depending on *style*\ ) @@ -52,6 +52,7 @@ Examples group edge region regstrip group water type 3 4 + group water type OW HT group sub id 10 25 50 group sub id 10 25 50 500:1000 group sub id 100:10000:10 @@ -119,7 +120,7 @@ three styles can use arguments specified in one of two formats. The first format is a list of values (types or IDs). For example, the second command in the examples above puts all atoms of type 3 or 4 into -the group named *water*\ . Each entry in the list can be a +the group named *water*\ . Each numeric entry in the list can be a colon-separated sequence ``A:B`` or ``A:B:C``, as in two of the examples above. A "sequence" generates a sequence of values (types or IDs), with an optional increment. The first example with ``500:1000`` has the @@ -135,7 +136,8 @@ except ``<>`` take a single argument. The third example above adds all atoms with IDs from 1 to 150 to the group named *sub*\ . The logical ``<>`` means "between" and takes 2 arguments. The fourth example above adds all atoms belonging to molecules with IDs from 50 to 250 (inclusive) to -the group named polyA. +the group named polyA. For the *type* style, type labels are converted into +numeric types before being evaluated. The *variable* style evaluates a variable to determine which atoms to add to the group. It must be an :doc:`atom-style variable ` diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 077f88e3e8..19c472e109 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -34,32 +34,66 @@ Description Write or read a Gromacs style index file in text format that associates atom IDs with the corresponding group definitions. This index file can be used with in combination with Gromacs analysis tools or to import group -definitions into the :doc:`fix colvars ` input file. It can -also be used to save and restore group definitions for static groups. +definitions into the :doc:`fix colvars ` input file. + +It can also be used to save and restore group definitions for static groups +using the individual atom IDs. This may be important if the original +group definition depends on a region or otherwise on the geometry and thus +cannot be easily recreated. + +Another application would be to import atom groups defined for Gromacs +simulation into LAMMPS. When translating Gromacs topology and geometry +data to LAMMPS. The *group2ndx* command will write group definitions to an index file. -Without specifying any group IDs, all groups will be written to the index -file. When specifying group IDs, only those groups will be written to the -index file. In order to follow the Gromacs conventions, the group *all* -will be renamed to *System* in the index file. +Without specifying any group IDs, all groups will be written to the +index file. When specifying group IDs, only those groups will be +written to the index file. In order to follow the Gromacs conventions, +the group *all* will be renamed to *System* in the index file. -The *ndx2group* command will create of update group definitions from those -stored in an index file. Without specifying any group IDs, all groups except -*System* will be read from the index file and the corresponding groups -recreated. If a group of the same name already exists, it will be completely -reset. When specifying group IDs, those groups, if present, will be read -from the index file and restored. +The *ndx2group* command will create of update group definitions from +those stored in an index file. Without specifying any group IDs, all +groups except *System* will be read from the index file and the +corresponding groups recreated. If a group of the same name already +exists, it will be completely reset. When specifying group IDs, those +groups, if present, will be read from the index file and restored. + +File Format +""""""""""" + +The file format is equivalent and compatible with what is produced by +the `Gromacs make_ndx command `_. +and follows the `Gromacs definition of an ndx file `_ + +Each group definition begins with the group name in square brackets with +blanks, e.g. \[ water \] and is then followed by the list of atom +indices, which may be spread over multiple lines. Here is a small +example file: + +.. code-block:: ini + + [ Oxygen ] + 1 4 7 + [ Hydrogen ] + 2 3 5 6 + 8 9 + [ Water ] + 1 2 3 4 5 6 7 8 9 + +The index file defines 3 groups: Oxygen, Hydrogen, and Water and the +latter happens to be the union of the first two. ---------- Restrictions """""""""""" -This command requires that atoms have atom IDs, since this is the +These commands require that atoms have atom IDs, since this is the information that is written to the index file. -These commands are part of the COLVARS package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +These commands are part of the EXTRA-COMMAND package. They are only +enabled if LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/img/howto_charmm_ELJ.png b/doc/src/img/howto_charmm_ELJ.png new file mode 100644 index 0000000000..f55e553ef9 Binary files /dev/null and b/doc/src/img/howto_charmm_ELJ.png differ diff --git a/doc/src/img/howto_charmmfsw_ELJ.png b/doc/src/img/howto_charmmfsw_ELJ.png new file mode 100644 index 0000000000..6c08eb98cf Binary files /dev/null and b/doc/src/img/howto_charmmfsw_ELJ.png differ diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index 27cb6e5538..75c14cbc44 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -64,8 +64,8 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc -page for more info. +EXTRA-MOLECULE package. See the :doc:`Build package ` +doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index 545222e0a3..73953785c4 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -54,8 +54,8 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc -page for more info. +EXTRA-MOLECULE package. See the :doc:`Build package ` +doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 5852a57038..bde584fb87 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -60,8 +60,8 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc -page for more info. +EXTRA-MOLECULE package. See the :doc:`Build package ` +doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index 99eed00b90..4bad4c9656 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -72,8 +72,8 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc -page for more info. +EXTRA-MOLECULE package. See the :doc:`Build package ` +doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/labelmap.rst b/doc/src/labelmap.rst index 9e3d705101..2374116509 100644 --- a/doc/src/labelmap.rst +++ b/doc/src/labelmap.rst @@ -24,6 +24,7 @@ Examples .. code-block:: LAMMPS + labelmap atom 1 c1 2 hc 3 cp 4 nt labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#" labelmap atom $(label2type(atom,carbon)) C # change type label from 'carbon' to 'C' labelmap clear @@ -43,7 +44,8 @@ The label map can also be defined by the :doc:`read_data ` command when it reads these sections in a data file: Atom Type Labels, Bond Type Labels, etc. See the :doc:`Howto type labels ` doc page for a general discussion of how type -labels can be used. +labels can be used. See :ref:`(Gissinger) ` for a +discussion of the type label implementation in LAMMPS and its uses. Valid type labels can contain any alphanumeric character, but must not start with a number, a '#', or a '*' character. They can contain other @@ -98,3 +100,9 @@ Default """"""" none + +----------- + +.. _Typelabel1: + +**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024). diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index 7dc9c579e5..99d954e43d 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -19,7 +19,7 @@ Syntax scale = lattice constant in distance units (for all other units) * zero or more keyword/value pairs may be appended -* keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis* +* keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis* or *triclinic/general* .. parsed-literal:: @@ -34,6 +34,7 @@ Syntax x,y,z = primitive vector components that define unit cell *basis* values = x y z x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) + *triclinic/general* values = no values Examples """""""" @@ -44,7 +45,7 @@ Examples lattice hex 0.85 lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0 lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 & - basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 + basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 triclinic/general lattice none 2.0 Description @@ -129,10 +130,13 @@ and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you can specify them to be of any length and non-orthogonal to each other, so that they describe a tilted parallelepiped. Via the *basis* keyword you add atoms, one at a time, to the unit cell. Its arguments -are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector -x of a basis atom within the unit cell is thus a linear combination of -the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, -where bx,by,bz are the 3 values specified for the *basis* keyword. +are fractional coordinates (0.0 <= x,y,z < 1.0). For 2d simulations, +the fractional z coordinate for any basis atom must be 0.0. + +The position vector x of a basis atom within the unit cell is a linear +combination of the unit cell's 3 edge vectors, i.e. x = bx a1 + by +a2 + bz a3, where bx,by,bz are the 3 values specified for the *basis* +keyword. ---------- @@ -168,18 +172,21 @@ The *origin* option specifies how the unit cell will be shifted or translated when mapping it into the simulation box. The x,y,z values are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice by a fraction of the lattice spacing in each dimension. The meaning -of "lattice spacing" is discussed below. +of "lattice spacing" is discussed below. For 2d simulations, the +*origin* z value must be 0.0. The *orient* option specifies how the unit cell will be rotated when mapping it into the simulation box. The *dim* argument is one of the 3 coordinate axes in the simulation box. The other 3 arguments are the crystallographic direction in the lattice that you want to orient along that axis, specified as integers. E.g. "orient x 2 1 0" means -the x-axis in the simulation box will be the [210] lattice -direction, and similarly for y and z. The 3 lattice directions you -specify do not have to be unit vectors, but they must be mutually -orthogonal and obey the right-hand rule, i.e. (X cross Y) points in -the Z direction. +the x-axis in the simulation box will be the [210] lattice direction, +and similarly for y and z. The 3 lattice directions you specify do +not have to be unit vectors, but they must be mutually orthogonal and +obey the right-hand rule, i.e. (X cross Y) points in the Z direction. +For 2d simulations, the *orient* x and y vectors must define 0 for +their 3rd component. Similarly the *orient* z vector must define 0 +for its 1st and 2nd components. .. note:: @@ -193,6 +200,59 @@ the Z direction. ---------- +The *triclinic/general* option specifies that the defined lattice is +for use with a general triclinic simulation box, as opposed to an +orthogonal or restricted triclinic box. The :doc:`Howto triclinic +` doc page explains all 3 kinds of simulation boxes +LAMMPS supports. + +If this option is specified, a *custom* lattice style must be used. +The *a1*, *a2*, *a3* vectors should define the edge vectors of a +single unit cell of the lattice with one or more basis atoms. They +edge vectors can be arbitrary so long as they are non-zero, distinct, +and not co-planar. In addition, they must define a right-handed +system, such that (*a1* cross *a2*) points in the direction of *a3*. +Note that a left-handed system can be converted to a right-handed +system by simply swapping the order of any pair of the *a1*, *a2*, +*a3* vectors. For 2d simulations, the *a3* vector must be specified +as (0.0,0.0,1.0), which is its default value. + +If this option is used, the *origin* and *orient* settings must have +their default values. Namely (0.0,0.0,0.0) for the *origin* and +(100), (010), (001) for the *orient* vectors. + +The :doc:`create_box ` command can be used to create a +general triclinic box that replicates the *a1*, *a2*, *a3* unit cell +vectors in each direction to create the 3 arbitrary edge vectors of +the overall simulation box. It requires a lattice with the +*triclinic/general* option. + +Likewise, the :doc:`create_atoms ` command can be used +to add atoms (or molecules) to a general triclinic box which lie on +the lattice points defined by *a1*, *a2*, *a3* and the unit cell basis +atoms. To do this, it also requires a lattice with the +*triclinic/general* option. + +.. note:: + + LAMMPS allows specification of general triclinic lattices and + simulation boxes as a convenience for users who may be converting + data from solid-state crystallographic representations or from DFT + codes for input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally, + LAMMPS only uses restricted triclinic simulation boxes. This means + the box and per-atom information (e.g. coordinates, velocities) + defined by the :doc:`create_box ` and + :doc:`create_atoms ` commands are converted from + general to restricted triclinic form when the two commands are + invoked. It also means that any other commands which use lattice + spacings from this command (e.g. the region command), will be + operating on a restricted triclinic simulation box, even if the + *triclinic/general* option was used to define the lattice. See the + next section for details. + +---------- + Several LAMMPS commands have the option to use distance units that are inferred from "lattice spacings" in the x,y,z box directions. E.g. the :doc:`region ` command can create a block of size @@ -216,6 +276,18 @@ coordinates of the 8 corner points of the modified unit cell (4 in 2d). Similarly, the Y and Z lattice spacings are defined as the difference in the min/max of the y and z coordinates. +.. note:: + + If the *triclinic/general* option is specified, the unit cell + defined by *a1*, *a2*, *a3* edge vectors is first converted to a + restricted triclinic orientation, which is a rotation operation. + The min/max extent of the 8 corner points is then determined, as + described in the preceding paragraph, to set the lattice + spacings. As explained for the *triclinic/general* option above, + this is because any use of the lattice spacings by other commands + will be for a restricted triclinic simulation box, not a general + triclinic box. + Note that if the unit cell is orthogonal with axis-aligned edges (no rotation via the *orient* keyword), then the lattice spacings in each dimension are simply the scale factor (described above) multiplied by diff --git a/doc/src/package.rst b/doc/src/package.rst index 2fe4baaae7..8be6639e72 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -576,7 +576,7 @@ changed to *no* since the *sort* keyword does not support *host* mode. Not all fix styles with extra atom data support *device* mode and in that case a warning will be given and atom sorting will run in *no* mode instead. -.. versionadded:: TBD +.. versionadded:: 17Apr2024 The *atom/map* keyword determines whether the host or device builds the atom_map, see the :doc:`atom_modify map ` command. The diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index 30b03ad872..15ed40e0ec 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -112,26 +112,22 @@ Description These pair styles compute Lennard Jones (LJ) and Coulombic interactions with additional switching or shifting functions that ramp the energy and/or force smoothly to zero between an inner and outer -cutoff. They are implementations of the widely used CHARMM force -field used in the `CHARMM `_ MD code (and -others). See :ref:`(MacKerell) ` for a description of the -CHARMM force field. +cutoff. They implement the widely used CHARMM force field, see +:doc:`Howto discussion on biomolecular force fields ` for +details. The styles with *charmm* (not *charmmfsw* or *charmmfsh*\ ) in their name are the older, original LAMMPS implementations. They compute the -LJ and Coulombic interactions with an energy switching function (esw, -shown in the formula below as S(r)), which ramps the energy smoothly -to zero between the inner and outer cutoff. This can cause -irregularities in pairwise forces (due to the discontinuous second -derivative of energy at the boundaries of the switching region), which -in some cases can result in detectable artifacts in an MD simulation. +LJ and Coulombic interactions with an energy switching function which +ramps the energy smoothly to zero between the inner and outer cutoff. +This can cause irregularities in pairwise forces (due to the discontinuous +second derivative of energy at the boundaries of the switching region), +which in some cases can result in detectable artifacts in an MD simulation. The newer styles with *charmmfsw* or *charmmfsh* in their name replace the energy switching with force switching (fsw) and force shifting (fsh) functions, for LJ and Coulombic interactions respectively. -These follow the formulas and description given in -:ref:`(Steinbach) ` and :ref:`(Brooks) ` to minimize these -artifacts. + .. note:: @@ -152,26 +148,6 @@ artifacts. the CHARMM force field energies and forces, when using one of these two CHARMM pair styles. -.. math:: - - E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\ - = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ - E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\ - = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ - LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] \\ - C(r) = & \frac{C q_i q_j}{ \epsilon r} \\ - S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} - { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } - -where S(r) is the energy switching function mentioned above for the -*charmm* styles. See the :ref:`(Steinbach) ` paper for the -functional forms of the force switching and force shifting functions -used in the *charmmfsw* and *charmmfsh* styles. - When using the *lj/charmm/coul/charmm styles*, both the LJ and Coulombic terms require an inner and outer cutoff. They can be the same for both formulas or different depending on whether 2 or 4 diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index f22bc974b0..14cc4851f6 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -379,10 +379,11 @@ These pair styles can only be used via the *pair* keyword of the Restrictions """""""""""" -The *coul/cut/global*, *coul/long*, *coul/msm*, *coul/streitz*, and *tip4p/long* styles -are part of the KSPACE package. They are only enabled if LAMMPS was built -with that package. See the :doc:`Build package ` doc page -for more info. +The *coul/long*, *coul/msm*, *coul/streitz*, and *tip4p/long* styles are +part of the KSPACE package. The *coul/cut/global* and *coul/exclude* are +part of the EXTRA-PAIR package. A pair style is only enabled if LAMMPS was +built with its corresponding package. See the :doc:`Build package ` +doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_dpd_coul_slater_long.rst b/doc/src/pair_dpd_coul_slater_long.rst new file mode 100644 index 0000000000..069c34c018 --- /dev/null +++ b/doc/src/pair_dpd_coul_slater_long.rst @@ -0,0 +1,196 @@ +.. index:: pair_style dpd/coul/slater/long +.. index:: pair_style dpd/coul/slater/long/gpu + +pair_style dpd/coul/slater/long command +======================================= + +Accelerator Variants: *dpd/coul/slater/long/gpu* + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style dpd/coul/slater/long T cutoff_DPD seed lambda cutoff_coul + +* T = temperature (temperature units) +* cutoff_DPD = global cutoff for DPD interactions (distance units) +* seed = random # seed (positive integer) +* lambda = decay length of the charge (distance units) +* cutoff_coul = global cutoff for Coulombic interactions (distance units) + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style dpd/coul/slater/long 1.0 2.5 34387 0.25 3.0 + + pair_coeff 1 1 78.0 4.5 # not charged by default + pair_coeff 2 2 78.0 4.5 yes + + +Description +""""""""""" + +.. versionadded:: 27June2024 + +Style *dpd/coul/slater/long* computes a force field for dissipative +particle dynamics (DPD) following the exposition in :ref:`(Groot) +`. It also allows for the use of charged particles in the +model by adding a long-range Coulombic term to the DPD interactions. +The short-range portion of the Coulombics is calculated by this pair +style. The long-range Coulombics are computed by use of the +:doc:`kspace_style ` command, e.g. using the Ewald or +PPPM styles. + +Coulombic forces in mesoscopic models such as DPD employ potentials +without explicit excluded-volume interactions. The goal is to prevent +artificial ionic pair formation by including a charge distribution in +the Coulomb potential, following the formulation in :ref:`(Melchor1) +`. + +.. note:: + + This pair style is effectively the combination of the + :doc:`pair_style dpd ` and :doc:`pair_style + coul/slater/long ` commands, but should be more + efficient (especially on GPUs) than using :doc:`pair_style + hybrid/overlay dpd coul/slater/long `. That is + particularly true for the GPU package version of the pair style since + this version is compatible with computing neighbor lists on the GPU + instead of the CPU as is required for hybrid styles. + +In the charged DPD model, the force on bead I due to bead J is given +as a sum of 4 terms: + +.. math:: + + \vec{f} = & (F^C + F^D + F^R + F^E) \hat{r_{ij}} \\ + F^C = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_{DPD} \\ + F^D = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_{DPD} \\ + F^R = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_{DPD} \\ + w(r) = & 1 - \frac{r}{r_{DPD}} \\ + F^E = & \frac{C q_iq_j}{\epsilon r^2} \left( 1- exp\left( \frac{2r_{ij}}{\lambda} \right) \left( 1 + \frac{2r_{ij}}{\lambda} \left( 1 + \frac{r_{ij}}{\lambda} \right)\right) \right) + +where :math:`F^C` is a conservative force, :math:`F^D` is a +dissipative force, :math:`F^R` is a random force, and :math:`F^E` is +an electrostatic force. :math:`\hat{r_{ij}}` is a unit vector in the +direction :math:`r_i - r_j`, :math:`\vec{v}_{ij}` is the vector +difference in velocities of the two atoms :math:`\vec{v}_i - +\vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean +and unit variance, *dt* is the timestep size, and :math:`w(r)` is a +weighting factor that varies between 0 and 1. + +:math:`\sigma` is set equal to :math:`\sqrt{2 k_B T \gamma}`, where +:math:`k_B` is the Boltzmann constant and *T* is the temperature +parameter in the pair_style command. + +:math:`r_{DPD}` is the pairwise cutoff for the first 3 DPD terms in +the formula as specified by *cutoff_DPD*. For the :math:`F^E` term, +pairwise interactions within the specified *cutoff_coul* distance are +computed directly; interactions beyond that distance are computed in +reciprocal space. *C* is the same Coulomb conversion factor used in +the Coulombic formulas described on the :doc:`pair_coul ` +doc page. + +The following parameters must be defined for each pair of atoms types +via the :doc:`pair_coeff ` command as in the examples +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* A (force units) +* :math:`\gamma` (force/velocity units) +* is_charged (optional boolean, default = no) + +The *is_charged* parameter is optional and can be specified as *yes* or +*no*. *Yes* should be used for interactions between two types of +charged particles. *No* is the default and should be used for +interactions between two types of particles when one or both are +uncharged. + +---------- + +.. include:: accel_styles.rst + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +This pair style does not support the :doc:`pair_modify ` +shift option for the energy of the pair interaction. + +The :doc:`pair_modify ` table option is not relevant +for this pair style. + +This pair style does not support the :doc:`pair_modify ` +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style writes its information to :doc:`binary restart files +`, so pair_style and pair_coeff commands do not need to be +specified in an input script that reads a restart file. Note that the +user-specified random number seed is stored in the restart file, so +when a simulation is restarted, each processor will re-initialize its +random number generator the same way it did initially. This means the +random forces will be random, but will not be the same as they would +have been if the original simulation had continued past the restart +time. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*, *middle*, *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This style is part of the DPD-BASIC package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +The default frequency for rebuilding neighbor lists is every 10 steps +(see the :doc:`neigh_modify ` command). This may be too +infrequent since particles move rapidly and can overlap by large +amounts. If this setting yields a non-zero number of "dangerous" +reneighborings (printed at the end of a simulation), you should +experiment with forcing reneighboring more often and see if system +energies/trajectories change. + +This pair style requires use of the :doc:`comm_modify vel yes +` command so that velocities are stored by ghost atoms. + +This pair style also requires use of a long-range solvers from the +KSPACE package. + +This pair style will not restart exactly when using the +:doc:`read_restart ` command, though they should provide +statistically similar results. This is because the forces they compute +depend on atom velocities. See the :doc:`read_restart ` +command for more details. + +Related commands +"""""""""""""""" + +:doc:`pair_style dpd `, :doc:`pair_style coul/slater/long `, + +Default +""""""" + +For the pair_coeff command, the default is is_charged = no. + +---------- + +.. _Groot5: + +**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). + +.. _Melchor1: + +**(Melchor)** Gonzalez-Melchor, Mayoral, Velazquez, and Alejandre, J Chem Phys, 125, 224107 (2006). diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 654f49c166..cdb6487981 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -140,6 +140,21 @@ The OpenKIM Project at provides EAM potentials that can be used directly in LAMMPS with the :doc:`kim command ` interface. +.. warning:: + + The EAM potential files tabulate the embedding energy as a function + of the local electron density :math:`\rho`. When atoms get too + close, this electron density may exceed the range for which the + embedding energy was tabulated for. To avoid crashes, LAMMPS will + assume a linearly increasing embedding energy for electron densities + beyond the maximum tabulated value. LAMMPS will print a warning when + this happens. It may be acceptable at the beginning of an + equilibration (e.g. when using randomized coordinates) but would be a + big concern for accuracy if it happens during production runs. The + EAM potential file triggering the warning during production is thus + not a good choice, and the EAM model in general not likely a good + model for the kind of system under investigation. + ---------- For style *eam*, potential values are read from a file that is in the diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index bc469412d9..dca85d8be1 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -111,7 +111,7 @@ For the *hertz* model, the normal component of force is given by: \mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} -Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective +Here, :math:`R_{eff} = R = \frac{R_i R_j}{R_i + R_j}` is the effective radius, denoted for simplicity as *R* from here on. For *hertz*, the units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or equivalently *pressure*\ . @@ -120,13 +120,14 @@ For the *hertz/material* model, the force is given by: .. math:: - \mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} + \mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R^{1/2}\delta_{ij}^{3/2} \mathbf{n} -Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}` is the effective Young's -modulus, with :math:`\nu_i, \nu_j` the Poisson ratios of the particles of -types *i* and *j*\ . Note that if the elastic modulus and the shear -modulus of the two particles are the same, the *hertz/material* model -is equivalent to the *hertz* model with :math:`k_n = 4/3 E_{eff}` +Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}` +is the effective Young's modulus, with :math:`\nu_i, \nu_j` the Poisson ratios +of the particles of types *i* and *j*. :math:`E_{eff}` is denoted as *E* from here on. +Note that if the elastic modulus and the shear modulus of the two particles are the +same, the *hertz/material* model is equivalent to the *hertz* model with +:math:`k_n = 4/3 E` The *dmt* model corresponds to the :ref:`(Derjaguin-Muller-Toporov) ` cohesive model, where the force @@ -187,6 +188,7 @@ for the damping model currently supported are: 2. *mass_velocity* 3. *viscoelastic* 4. *tsuji* +5. *coeff_restitution* If the *damping* keyword is not specified, the *viscoelastic* model is used by default. @@ -248,6 +250,30 @@ The dimensionless coefficient of restitution :math:`e` specified as part of the normal contact model parameters should be between 0 and 1, but no error check is performed on this. +The *coeff_restitution* model is useful when a specific normal coefficient of +restitution :math:`e` is required. In these models, the normal coefficient of +restitution :math:`e` is specified as an input. Following the approach of +:ref:`(Brilliantov et al) `, when using the *hooke* normal model, +*coeff_restitution* calculates the damping coefficient as: + +.. math:: + + \eta_n = \sqrt{\frac{4m_{eff}k_n}{1+\left( \frac{\pi}{\log(e)}\right)^2}} , + +For any other normal model, e.g. the *hertz* and *hertz/material* models, the damping +coefficient is: + +.. math:: + + \eta_n = -2\sqrt{\frac{5}{6}}\frac{\log(e)}{\sqrt{\pi^2+(\log(e))^2}}(R_{eff} \delta_{ij})^{\frac{1}{4}}\sqrt{\frac{3}{2}k_n m_{eff}} , + +where :math:`k_n = \frac{4}{3} E_{eff}` for the *hertz/material* model. Since +*coeff_restitution* accounts for the effective mass, effective radius, and +pairwise overlaps (except when used with the *hooke* normal model) when calculating +the damping coefficient, it accurately reproduces the specified coefficient of +restitution for both monodisperse and polydisperse particle pairs. This damping +model is not compatible with cohesive normal models such as *JKR* or *DMT*. + The total normal force is computed as the sum of the elastic and damping components: @@ -417,11 +443,11 @@ discussion above. To match the Mindlin solution, one should set G_{eff} = \left(\frac{2-\nu_i}{G_i} + \frac{2-\nu_j}{G_j}\right)^{-1} -where :math:`G` is the shear modulus, related to Young's modulus :math:`E` -and Poisson's ratio :math:`\nu` by :math:`G = E/(2(1+\nu))`. This can also be -achieved by specifying *NULL* for :math:`k_t`, in which case a -normal contact model that specifies material parameters :math:`E` and -:math:`\nu` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this +where :math:`G_i` is the shear modulus of a particle of type :math:`i`, related to Young's +modulus :math:`E_i` and Poisson's ratio :math:`\nu_i` by :math:`G_i = E_i/(2(1+\nu_i))`. +This can also be achieved by specifying *NULL* for :math:`k_t`, in which case a +normal contact model that specifies material parameters :math:`E_i` and +:math:`\nu_i` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this case, mixing of the shear modulus for different particle types *i* and *j* is done according to the formula above. @@ -551,7 +577,7 @@ opposite torque on each particle, according to: .. math:: - \tau_{roll,i} = R_{eff} \mathbf{n} \times \mathbf{F}_{roll} + \tau_{roll,i} = R \mathbf{n} \times \mathbf{F}_{roll} .. math:: diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index a33991e43e..634717f8a8 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -1,28 +1,41 @@ .. index:: pair_style hybrid .. index:: pair_style hybrid/kk +.. index:: pair_style hybrid/omp +.. index:: pair_style hybrid/molecular +.. index:: pair_style hybrid/molecular/omp .. index:: pair_style hybrid/overlay +.. index:: pair_style hybrid/overlay/omp .. index:: pair_style hybrid/overlay/kk .. index:: pair_style hybrid/scaled +.. index:: pair_style hybrid/scaled/omp pair_style hybrid command ========================= -Accelerator Variants: *hybrid/kk* +Accelerator Variants: *hybrid/kk*, *hybrid/omp* + +pair_style hybrid/molecular command +=================================== + +Accelerator Variant: *hybrid/molecular/omp* pair_style hybrid/overlay command ================================= -Accelerator Variants: *hybrid/overlay/kk* +Accelerator Variants: *hybrid/overlay/kk*, *hybrid/overlay/omp* pair_style hybrid/scaled command ================================== +Accelerator Variant: *hybrid/scaled/omp* + Syntax """""" .. code-block:: LAMMPS pair_style hybrid style1 args style2 args ... + pair_style hybrid/molecular factor1 style1 args factor2 style 2 args pair_style hybrid/overlay style1 args style2 args ... pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ... @@ -47,6 +60,10 @@ Examples pair_coeff * * tersoff Si.tersoff Si pair_coeff * * sw Si.sw Si + pair_style hybrid/molecular lj/cut 2.5 lj/cut 2.5 + pair_coeff * * lj/cut 1 1.0 1.0 + pair_coeff * * lj/cut 2 1.5 1.0 + variable one equal ramp(1.0,0.0) variable two equal 1.0-v_one pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5 @@ -56,17 +73,26 @@ Examples Description """"""""""" -The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the -use of multiple pair styles in one simulation. With the *hybrid* style, -exactly one pair style is assigned to each pair of atom types. With the -*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can -be assigned to each pair of atom types. The assignment of pair styles -to type pairs is made via the :doc:`pair_coeff ` command. -The major difference between the *hybrid/overlay* and *hybrid/scaled* -styles is that the *hybrid/scaled* adds a scale factor for each -sub-style contribution to forces, energies and stresses. Because of the -added complexity, the *hybrid/scaled* style has more overhead and thus -may be slower than *hybrid/overlay*. +The *hybrid*, *hybrid/overlay*, *hybrid/molecular*, and *hybrid/scaled* +styles enable the use of multiple pair styles in one simulation. With +the *hybrid* style, exactly one pair style is assigned to each pair of +atom types. With the *hybrid/overlay* and *hybrid/scaled* styles, one +or more pair styles can be assigned to each pair of atom types. With +the hybrid/molecular style, pair styles are assigned to either intra- +or inter-molecular interactions. + +The assignment of pair styles to type pairs is made via the +:doc:`pair_coeff ` command. The major difference between +the *hybrid/overlay* and *hybrid/scaled* styles is that the +*hybrid/scaled* adds a scale factor for each sub-style contribution to +forces, energies and stresses. Because of the added complexity, the +*hybrid/scaled* style has more overhead and thus may be slower than +*hybrid/overlay*. + +The *hybrid/molecular* pair style accepts *only* two sub-styles: the +first is assigned to intra-molecular interactions (i.e. both atoms +have the same molecule ID), the second to inter-molecular interactions +(i.e. interacting atoms have different molecule IDs). Here are two examples of hybrid simulations. The *hybrid* style could be used for a simulation of a metal droplet on a LJ surface. The metal @@ -476,6 +502,8 @@ the same or else LAMMPS will generate an error. Pair style *hybrid/scaled* currently only works for non-accelerated pair styles and pair styles from the OPT package. +Pair style *hybrid/molecular* is not compatible with manybody potentials. + When using pair styles from the GPU package they must not be listed multiple times. LAMMPS will detect this and abort. diff --git a/doc/src/pair_mliap.rst b/doc/src/pair_mliap.rst index fcb9c7881e..e325de0aa6 100644 --- a/doc/src/pair_mliap.rst +++ b/doc/src/pair_mliap.rst @@ -22,7 +22,7 @@ Syntax style = *linear* or *quadratic* or *nn* or *mliappy* filename = name of file containing model definitions *descriptor* values = style filename - style = *sna* or *so3* + style = *sna* or *so3* or *ace* filename = name of file containing descriptor definitions *unified* values = filename ghostneigh_flag filename = name of file containing serialized unified Python object @@ -36,6 +36,7 @@ Examples pair_style mliap model linear InP.mliap.model descriptor sna InP.mliap.descriptor pair_style mliap model quadratic W.mliap.model descriptor sna W.mliap.descriptor pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor + pair_style mliap model mliappy ACE_NN_Pytorch.pt descriptor ace ccs_single_element.yace pair_style mliap unified mliap_unified_lj_Ar.pkl 0 pair_coeff * * In P @@ -49,8 +50,8 @@ quantities that characterize the atomic positions (*descriptor*). By defining *model* and *descriptor* separately, it is possible to use many different models with a given descriptor, or many different -descriptors with a given model. The pair style currently supports only -*sna* and *so3* descriptor styles, but it is straightforward to add new +descriptors with a given model. The pair style currently supports *sna*, +*so3* and *ace* descriptor styles, but it is straightforward to add new descriptor styles. By using the *unified* keyword, it is possible to define a Python model that combines functionalities of both *model* and *descriptor*. @@ -72,6 +73,26 @@ the smooth SO(3) power spectrum with the explicit inclusion of a radial basis :ref:`(Bartok) ` and :ref:`(Zagaceta) `. The available models are *linear* and *nn*. +.. versionadded:: 17Apr2024 + +The descriptor style *ace* is a class of highly general atomic +descriptors, atomic cluster expansion descriptors (ACE) from +:ref:`(Drautz) `, that include a radial basis, an angular +basis, and bases for other variables (such as chemical species) if +relevant. In descriptor style *ace*, the *ace* descriptors may be +defined up to an arbitrary body order. This descriptor style is the same +as that used in :doc:`pair_style pace ` and :doc:`compute +pace `. The available models with *ace* in ML-IAP are +*linear* and *mliappy*. The *ace* descriptors and models require +building LAMMPS with the ML-PACE package (see below). The *mliappy* +model style may be used with *ace* descriptors, but it requires that +LAMMPS is also built with the PYTHON package. As with other model +styles, the *mliappy* model style can be used to couple arbitrary python +models that use the *ace* descriptors such as Pytorch NNs. Note that +*ALL* mliap model styles with *ace* descriptors require that descriptors +and hyperparameters are supplied in a `.yace` or `.ace` file, similar to +:doc:`compute pace `. + The pair_style *mliap* command must be followed by two keywords *model* and *descriptor* in either order, or the one keyword *unified*. A single *pair_coeff* command is also required. The first 2 arguments @@ -136,7 +157,7 @@ The detail of *nn* module implementation can be found at :ref:`(Yanxon) `. Note that unlike the potential file, the + Clebsch-Gordan coefficients in the descriptor file supplied should *NOT* be + multiplied by linear or square root embedding terms. + + The SNAP descriptor file closely follows the format of the :doc:`pair_style snap ` parameter file. The file can contain blank and comment lines (start with #) anywhere. Each non-blank @@ -169,6 +200,24 @@ contains a few more arguments (e.g., *nmax* and *alpha*). The preparation of SO3 descriptor and model files can be done with the `Pyxtal_FF `_ package. +The ACE descriptor file differs from the SNAP and SO3 files. It more +closely resembles the potential file format for linear or square-root +embedding ACE potentials used in the :doc:`pair_style pace `. +As noted above, the key difference is that the Clebsch-Gordan +coefficients in the descriptor file with *mliap descriptor ace* are +*NOT* multiplied by linear or square root embedding terms. In other +words,the model is separated from the descriptor definitions and +hyperparameters. In :doc:`pair_style pace `, they are +combined. The ACE descriptor files required by *mliap* are generated +automatically in `FitSNAP `_ during +linear, pytorch, etc. ACE model fitting. Additional tools are provided +there to prepare *ace* descriptor files and hyperparameters before model +fitting. The *ace* descriptor files can also be extracted from ACE +model fits in `python-ace. `_. It +is important to note that order of the types listed in :doc:`pair_coeff +` must match the order of the elements/types listed in the +ACE descriptor file for all *mliap* styles when using *ace* descriptors. + See the :doc:`pair_coeff ` page for alternate ways to specify the path for these *model* and *descriptor* files. @@ -245,7 +294,10 @@ This pair style is part of the ML-IAP package. It is only enabled if LAMMPS was built with that package. In addition, building LAMMPS with the ML-IAP package requires building LAMMPS with the ML-SNAP package. The *mliappy* model requires building LAMMPS with the PYTHON package. -See the :doc:`Build package ` page for more info. +The *ace* descriptor requires building LAMMPS with the ML-PACE package. +See the :doc:`Build package ` page for more info. Note +that `pair_mliap/kk` acceleration will *not* invoke the `kk` +accelerated variants of SNAP or ACE descriptors. Related commands @@ -271,5 +323,3 @@ none .. _Yanxon2020: **(Yanxon2020)** Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020). - - diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index dab1c2a230..6d78bc531b 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -37,18 +37,19 @@ Syntax *oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) - T = temperature (oxDNA units, 0.1 = 300 K) - xi = 1.3448 (temperature-independent coefficient in stacking strength) - kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength) + T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) + xi = 1.3448 (LJ units) or 8.01727944817084 (real units), temperature-independent coefficient in stacking strength + kappa = 2.6568 (LJ units) or 0.005279604 (real units), coefficient of linear temperature dependence in stacking strength *oxdna/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) - eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) + eps = 1.077 (LJ units) or 6.42073911784652 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs Examples """""""" .. code-block:: LAMMPS + # LJ units pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 @@ -58,55 +59,105 @@ Examples pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk + pair_coeff * * oxdna/excv oxdna_lj.cgdna + pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna + pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna + pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna + pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna + pair_coeff * * oxdna/xstk oxdna_lj.cgdna + pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna + + # Real units + pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk + pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 + pair_coeff * * oxdna/stk seqdep 300.0 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 + pair_coeff * * oxdna/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + pair_coeff 1 4 oxdna/hbond seqdep 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + pair_coeff 2 3 oxdna/hbond seqdep 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 + pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 -0.65 2.0 -0.65 + + pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk + pair_coeff * * oxdna/excv oxdna_real.cgdna + pair_coeff * * oxdna/stk seqav 300.0 8.01727944817084 0.005279604 oxdna_real.cgdna + pair_coeff * * oxdna/hbond seqav oxdna_real.cgdna + pair_coeff 1 4 oxdna/hbond seqav oxdna_real.cgdna + pair_coeff 2 3 oxdna/hbond seqav oxdna_real.cgdna + pair_coeff * * oxdna/xstk oxdna_real.cgdna + pair_coeff * * oxdna/coaxstk oxdna_real.cgdna + +.. note:: + + The coefficients in the above examples are provided in forms + compatible with both *units lj* and *units real* (see documentation + of :doc:`units `). These can also be read from a potential + file with correct unit style by specifying the name of the + file. Several potential files for each unit style are included in the + ``potentials`` directory of the LAMMPS distribution. + Description """"""""""" -The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*, cross-stacking *oxdna/xstk* -and coaxial stacking interaction *oxdna/coaxstk* as well -as the hydrogen-bonding interaction *oxdna/hbond* between complementary pairs of nucleotides on -opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths -are supported :ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can be achieved by using -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases -up and down along the backbone. +The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA +force field for coarse-grained modelling of DNA. The effective +interaction between the nucleotides consists of potentials for the +excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*, +cross-stacking *oxdna/xstk* and coaxial stacking interaction +*oxdna/coaxstk* as well as the hydrogen-bonding interaction +*oxdna/hbond* between complementary pairs of nucleotides on opposite +strands. Average sequence or sequence-dependent stacking and +base-pairing strengths are supported :ref:`(Sulc) `. Quasi-unique +base-pairing between nucleotides can be achieved by using more +complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, +13-16 and 14-15, etc. This prevents the hybridization of in principle +complementary bases within Ntypes/4 bases up and down along the +backbone. -The exact functional form of the pair styles is rather complex. -The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. -We refer to :ref:`(Ouldridge-DPhil) ` and :ref:`(Ouldridge) ` -for a detailed description of the oxDNA force field. +The exact functional form of the pair styles is rather complex. The +individual potentials consist of products of modulation factors, which +themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic +smoothing and modulation terms. We refer to :ref:`(Ouldridge-DPhil) +` and :ref:`(Ouldridge) ` for a detailed +description of the oxDNA force field. .. note:: - These pair styles have to be used together with the related oxDNA bond style - *oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond_style oxdna/fene `). Most of the coefficients - in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. - Exceptions are the first four coefficients after *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example) - and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example). - When using a Langevin thermostat, e.g. through :doc:`fix langevin ` - or :doc:`fix nve/dotc/langevin ` - the temperature coefficients have to be matched to the one used in the fix. + These pair styles have to be used together with the related oxDNA + bond style *oxdna/fene* for the connectivity of the phosphate + backbone (see also documentation of :doc:`bond_style oxdna/fene + `). Most of the coefficients in the above example have to + be kept fixed and cannot be changed without reparameterizing the + entire model. Exceptions are the first four coefficients after + *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 and + corresponding *real unit* equivalents in the above examples) and the + first coefficient after *oxdna/hbond* (seq=seqdep in the above + example). When using a Langevin thermostat, e.g. through :doc:`fix + langevin ` or :doc:`fix nve/dotc/langevin + ` the temperature coefficients have to be + matched to the one used in the fix. .. note:: - These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* - (see documentation of :doc:`atom_style `). The *atom_style oxdna* - stores the 3'-to-5' polarity of the nucleotide strand, which is set through - the bond topology in the data file. The first (second) atom in a bond definition - is understood to point towards the 3'-end (5'-end) of the strand. + These pair styles have to be used with the *atom_style hybrid bond + ellipsoid oxdna* (see documentation of :doc:`atom_style + `). The *atom_style oxdna* stores the 3'-to-5' polarity + of the nucleotide strand, which is set through the bond topology in + the data file. The first (second) atom in a bond definition is + understood to point towards the 3'-end (5'-end) of the strand. -Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. +Example input and data files for DNA duplexes can be found in +``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A +simple python setup tool which creates single straight or helical DNA +strands, DNA duplexes or arrays of DNA duplexes can be found in +``examples/PACKAGES/cgdna/util/``. Please cite :ref:`(Henrich) ` in any publication that uses -this implementation. An updated documentation that contains general information -on the model, its implementation and performance as well as the structure of -the data and input file can be found `here `_. +this implementation. An updated documentation that contains general +information on the model, its implementation and performance as well as +the structure of the data and input file can be found `here +`_. Please cite also the relevant oxDNA publications :ref:`(Ouldridge) `, @@ -115,6 +166,57 @@ and :ref:`(Sulc) `. ---------- +Potential file reading +"""""""""""""""""""""" + +For each pair style above the first non-modifiable argument can be a +filename, and if it is, no further arguments should be +supplied. Therefore the following command: + +.. code-block:: LAMMPS + + pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna + +will be interpreted as a request to read the corresponding hydrogen +bonding potential parameters from the file with the given name. The file +can define multiple potential parameters for both bonded and pair +interactions, but for the example pair interaction above there must +exist in the file a line of the form: + +.. code-block:: LAMMPS + + 1 4 hbond + +If potential customization is required, the potential file reading can +be mixed with the manual specification of the potential parameters. For +example, the following command: + +.. code-block:: LAMMPS + + pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk + pair_coeff * * oxdna/excv oxdna_lj.cgdna + pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 + pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna + pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna + pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna + pair_coeff * * oxdna/xstk oxdna_lj.cgdna + pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +will read the stacking and coaxial stacking potential parameters from +the manual specification and all others from the potential file +*oxdna_lj.cgdna*. + +There are sample potential files for each unit style in the +``potentials`` directory of the LAMMPS distribution. The potential file +unit system must align with the units defined via the :doc:`units +` command. For conversion between different *LJ* and *real* unit +systems for oxDNA, the python tool *lj2real.py* located in the +``examples/PACKAGES/cgdna/util/`` directory can be used. This tool +assumes similar file structure to the examples found in +``examples/PACKAGES/cgdna/examples/``. + +---------- + Restrictions """""""""""" diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 5cac7d8f77..c91f991a71 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -41,14 +41,14 @@ Syntax *oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) - T = temperature (oxDNA units, 0.1 = 300 K) - xi = 1.3523 (temperature-independent coefficient in stacking strength) - kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength) + T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) + xi = 1.3523 (LJ units) or 8.06199211612242 (real units), temperature-independent coefficient in stacking strength + kappa = 2.6717 (LJ units) or 0.005309213 (real units), coefficient of linear temperature dependence in stacking strength *oxdna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) - eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs) + eps = 1.0678 (LJ units) or 6.36589157849259 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs *oxdna2/dh* args = T rhos qeff - T = temperature (oxDNA units, 0.1 = 300 K) + T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) rhos = salt concentration (mole per litre) qeff = 0.815 (effective charge in elementary charges) @@ -57,6 +57,7 @@ Examples .. code-block:: LAMMPS + # LJ units pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 @@ -67,61 +68,169 @@ Examples pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 pair_coeff * * oxdna2/dh 0.1 0.5 0.815 + pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh + pair_coeff * * oxdna2/excv oxdna2_lj.cgdna + pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna + pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna + pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna + pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna + pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna + pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna + pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2_lj.cgdna + + # Real units + pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh + pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 + pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 + pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 + pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 40.0 3.116592653589793 + pair_coeff * * oxdna2/dh 300.0 0.5 0.815 + + pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh + pair_coeff * * oxdna2/excv oxdna2_real.cgdna + pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna + pair_coeff * * oxdna2/hbond seqdep oxdna2_real.cgdna + pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_real.cgdna + pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_real.cgdna + pair_coeff * * oxdna2/xstk oxdna2_real.cgdna + pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna + pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2_real.cgdna + +.. note:: + + The coefficients in the above examples are provided in forms + compatible with both *units lj* and *units real* (see documentation + of :doc:`units `). These can also be read from a potential + file with correct unit style by specifying the name of the + file. Several potential files for each unit style are included in the + ``potentials`` directory of the LAMMPS distribution. + Description """"""""""" -The *oxdna2* pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*, cross-stacking *oxdna2/xstk* -and coaxial stacking interaction *oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh* -as well as the hydrogen-bonding interaction *oxdna2/hbond* between complementary pairs of nucleotides on -opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths -are supported :ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can be achieved by using -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +The *oxdna2* pair styles compute the pairwise-additive parts of the +oxDNA force field for coarse-grained modelling of DNA. The effective +interaction between the nucleotides consists of potentials for the +excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*, +cross-stacking *oxdna2/xstk* and coaxial stacking interaction +*oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh* as +well as the hydrogen-bonding interaction *oxdna2/hbond* between +complementary pairs of nucleotides on opposite strands. Average sequence +or sequence-dependent stacking and base-pairing strengths are supported +:ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can +be achieved by using more complementary pairs of atom types like 5-8 and +6-7, 9-12 and 10-11, 13-16 and 14-15, etc. This prevents the +hybridization of in principle complementary bases within Ntypes/4 bases up and down along the backbone. -The exact functional form of the pair styles is rather complex. -The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. -We refer to :ref:`(Snodin) ` and the original oxDNA publications :ref:`(Ouldridge-DPhil) ` -and :ref:`(Ouldridge) ` for a detailed description of the oxDNA2 force field. +The exact functional form of the pair styles is rather complex. The +individual potentials consist of products of modulation factors, which +themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic +smoothing and modulation terms. We refer to :ref:`(Snodin) ` +and the original oxDNA publications :ref:`(Ouldridge-DPhil) +` and :ref:`(Ouldridge) ` for a detailed +description of the oxDNA2 force field. .. note:: - These pair styles have to be used together with the related oxDNA2 bond style - *oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond_style oxdna2/fene `). Most of the coefficients - in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. - Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example), - the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients - after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat - e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` - the temperature coefficients have to be matched to the one used in the fix. + These pair styles have to be used together with the related oxDNA2 + bond style *oxdna2/fene* for the connectivity of the phosphate + backbone (see also documentation of :doc:`bond_style oxdna2/fene + `). Most of the coefficients in the above example have to + be kept fixed and cannot be changed without reparameterizing the + entire model. Exceptions are the first four coefficients after + *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 and + corresponding *real unit* equivalents in the above examples). the + first coefficient after *oxdna2/hbond* (seq=seqdep in the above + example) and the three coefficients after *oxdna2/dh* (T=0.1, + rhos=0.5, qeff=0.815 in the above example). When using a Langevin + thermostat e.g. through :doc:`fix langevin ` or + :doc:`fix nve/dotc/langevin ` the temperature + coefficients have to be matched to the one used in the fix. .. note:: - These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* - (see documentation of :doc:`atom_style `). The *atom_style oxdna* - stores the 3'-to-5' polarity of the nucleotide strand, which is set through - the bond topology in the data file. The first (second) atom in a bond definition - is understood to point towards the 3'-end (5'-end) of the strand. + These pair styles have to be used with the *atom_style hybrid bond + ellipsoid oxdna* (see documentation of :doc:`atom_style + `). The *atom_style oxdna* stores the 3'-to-5' polarity + of the nucleotide strand, which is set through the bond topology in + the data file. The first (second) atom in a bond definition is + understood to point towards the 3'-end (5'-end) of the strand. -Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. +Example input and data files for DNA duplexes can be found in +``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A +simple python setup tool which creates single straight or helical DNA +strands, DNA duplexes or arrays of DNA duplexes can be found in +``examples/PACKAGES/cgdna/util/``. Please cite :ref:`(Henrich) ` in any publication that uses -this implementation. An updated documentation that contains general information -on the model, its implementation and performance as well as the structure of -the data and input file can be found `here `_. +this implementation. An updated documentation that contains general +information on the model, its implementation and performance as well as +the structure of the data and input file can be found `here +`_. Please cite also the relevant oxDNA2 publications :ref:`(Snodin) ` and :ref:`(Sulc) `. ---------- +Potential file reading +"""""""""""""""""""""" + +For each pair style above the first non-modifiable argument can be a +filename (with exception of Debye-Hueckel, for which the effective +charge argument can be a filename), and if it is, no further arguments +should be supplied. Therefore the following command: + +.. code-block:: LAMMPS + + pair_coeff 1 4 oxdna2/hbond seqdep oxdna_real.cgdna + +will be interpreted as a request to read the corresponding hydrogen +bonding potential parameters from the file with the given name. The +file can define multiple potential parameters for both bonded and pair +interactions, but for the example pair interaction above there must +exist in the file a line of the form: + +.. code-block:: LAMMPS + + 1 4 hbond + +If potential customization is required, the potential file reading can +be mixed with the manual specification of the potential parameters. For +example, the following command: + +.. code-block:: LAMMPS + + pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh + pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 + pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna + pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna + pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna + pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna + pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna + pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna + pair_coeff * * oxdna2/dh 0.1 0.5 0.815 + +will read the excluded volume and Debye-Hueckel effective charge *qeff* +parameters from the manual specification and all others from the +potential file *oxdna2_lj.cgdna*. + +There are sample potential files for each unit style in the ``potentials`` +directory of the LAMMPS distribution. The potential file unit system +must align with the units defined via the :doc:`units ` +command. For conversion between different *LJ* and *real* unit systems +for oxDNA, the python tool *lj2real.py* located in the +``examples/PACKAGES/cgdna/util/`` directory can be used. This tool assumes +similar file structure to the examples found in +``examples/PACKAGES/cgdna/examples/``. + +---------- + Restrictions """""""""""" diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 7b8220740c..6fd99bc33d 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -41,14 +41,14 @@ Syntax *oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) - T = temperature (oxDNA units, 0.1 = 300 K) - xi = 1.40206 (temperature-independent coefficient in stacking strength) - kappa = 2.77 (coefficient of linear temperature dependence in stacking strength) + T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) + xi = 1.40206 (LJ units) or 8.35864576375849 (real units), temperature-independent coefficient in stacking strength + kappa = 2.77 (LJ units) or 0.005504556 (real units), coefficient of linear temperature dependence in stacking strength *oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) - eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs) + eps = 0.870439 (LJ units) or 5.18928666388042 (real units), average hydrogen bonding strength between A-U and C-G Watson-Crick and G-U wobble base pairs, 0 between all other pairs *oxrna2/dh* args = T rhos qeff - T = temperature (oxDNA units, 0.1 = 300 K) + T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) rhos = salt concentration (mole per litre) qeff = 1.02455 (effective charge in elementary charges) @@ -57,6 +57,7 @@ Examples .. code-block:: LAMMPS + # LJ units pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 @@ -68,58 +69,168 @@ Examples pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 + pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + pair_coeff * * oxrna2/excv oxrna2_lj.cgdna + pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna + pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna + pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna + pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2_lj.cgdna + + # Real units + pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 + pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 + pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 + pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 + pair_coeff * * oxrna2/dh 300.0 0.5 1.02455 + + pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + pair_coeff * * oxrna2/excv oxrna2_real.cgdna + pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2_real.cgdna + pair_coeff * * oxrna2/hbond seqdep oxrna2_real.cgdna + pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_real.cgdna + pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_real.cgdna + pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_real.cgdna + pair_coeff * * oxrna2/xstk oxrna2_real.cgdna + pair_coeff * * oxrna2/coaxstk oxrna2_real.cgdna + pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2_real.cgdna + +.. note:: + + The coefficients in the above examples are provided in forms + compatible with both *units lj* and *units real* (see documentation + of :doc:`units `). These can also be read from a potential + file with correct unit style by specifying the name of the + file. Several potential files for each unit style are included in the + ``potentials`` directory of the LAMMPS distribution. + Description """"""""""" -The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, cross-stacking *oxrna2/xstk* -and coaxial stacking interaction *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* -as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on -opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths -are supported :ref:`(Sulc2) `. Quasi-unique base-pairing between nucleotides can be achieved by using -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +The *oxrna2* pair styles compute the pairwise-additive parts of the +oxDNA force field for coarse-grained modelling of RNA. The effective +interaction between the nucleotides consists of potentials for the +excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, +cross-stacking *oxrna2/xstk* and coaxial stacking interaction +*oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* as +well as the hydrogen-bonding interaction *oxrna2/hbond* between +complementary pairs of nucleotides on opposite strands. Average sequence +or sequence-dependent stacking and base-pairing strengths are supported +:ref:`(Sulc2) `. Quasi-unique base-pairing between nucleotides +can be achieved by using more complementary pairs of atom types like 5-8 +and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. This prevents the +hybridization of in principle complementary bases within Ntypes/4 bases up and down along the backbone. -The exact functional form of the pair styles is rather complex. -The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. -We refer to :ref:`(Sulc1) ` and the original oxDNA publications :ref:`(Ouldridge-DPhil) ` -and :ref:`(Ouldridge) ` for a detailed description of the oxRNA2 force field. +The exact functional form of the pair styles is rather complex. The +individual potentials consist of products of modulation factors, which +themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic +smoothing and modulation terms. We refer to :ref:`(Sulc1) ` and +the original oxDNA publications :ref:`(Ouldridge-DPhil) +` and :ref:`(Ouldridge) ` for a detailed +description of the oxRNA2 force field. .. note:: - These pair styles have to be used together with the related oxDNA2 bond style - *oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond_style oxrna2/fene `). Most of the coefficients - in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. - Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example), - the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients - after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat - e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` - the temperature coefficients have to be matched to the one used in the fix. + These pair styles have to be used together with the related oxDNA2 + bond style *oxrna2/fene* for the connectivity of the phosphate + backbone (see also documentation of :doc:`bond_style oxrna2/fene + `). Most of the coefficients in the above example have to + be kept fixed and cannot be changed without reparameterizing the + entire model. Exceptions are the first four coefficients after + *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 and + corresponding *real unit* equivalents in the above examples), the + first coefficient after *oxrna2/hbond* (seq=seqdep in the above + example) and the three coefficients after *oxrna2/dh* (T=0.1, + rhos=0.5, qeff=1.02455 in the above example). When using a Langevin + thermostat e.g. through :doc:`fix langevin ` or + :doc:`fix nve/dotc/langevin ` the temperature + coefficients have to be matched to the one used in the fix. .. note:: - These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* - (see documentation of :doc:`atom_style `). The *atom_style oxdna* - stores the 3'-to-5' polarity of the nucleotide strand, which is set through - the bond topology in the data file. The first (second) atom in a bond definition - is understood to point towards the 3'-end (5'-end) of the strand. + These pair styles have to be used with the *atom_style hybrid bond + ellipsoid oxdna* (see documentation of :doc:`atom_style + `). The *atom_style oxdna* stores the 3'-to-5' polarity + of the nucleotide strand, which is set through the bond topology in + the data file. The first (second) atom in a bond definition is + understood to point towards the 3'-end (5'-end) of the strand. -Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. +Example input and data files for DNA duplexes can be found in +``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A simple python +setup tool which creates single straight or helical DNA strands, DNA +duplexes or arrays of DNA duplexes can be found in +``examples/PACKAGES/cgdna/util/``. Please cite :ref:`(Henrich) ` in any publication that uses -this implementation. The article contains general information -on the model, its implementation and performance as well as the structure of -the data and input file. The preprint version of the article can be found -`here `_. -Please cite also the relevant oxRNA2 publications -:ref:`(Sulc1) ` and :ref:`(Sulc2) `. +this implementation. The article contains general information on the +model, its implementation and performance as well as the structure of +the data and input file. The preprint version of the article can be +found `here `_. Please cite also the relevant oxRNA2 +publications :ref:`(Sulc1) ` and :ref:`(Sulc2) `. + +---------- + +Potential file reading +"""""""""""""""""""""" + +For each pair style above the first non-modifiable argument can be a +filename (with exception of Debye-Hueckel, for which the effective +charge argument can be a filename), and if it is, no further arguments +should be supplied. Therefore the following command: + +.. code-block:: LAMMPS + + pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna + +will be interpreted as a request to read the corresponding hydrogen +bonding potential parameters from the file with the given name. The +file can define multiple potential parameters for both bonded and pair +interactions, but for the example pair interaction above there must +exist in the file a line of the form: + +.. code-block:: LAMMPS + + 3 4 hbond + +If potential customization is required, the potential file reading can +be mixed with the manual specification of the potential parameters. For +example, the following command: + +.. code-block:: LAMMPS + + pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 + pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna + pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna + pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna + pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna + pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 + +will read the excluded volume and Debye-Hueckel effective charge *qeff* +parameters from the manual specification and all others from the +potential file *oxrna2_lj.cgdna*. + +There are sample potential files for each unit style in the +``potentials`` directory of the LAMMPS distribution. The potential file +unit system must align with the units defined via the :doc:`units +` command. For conversion between different *LJ* and *real* unit +systems for oxDNA, the python tool *lj2real.py* located in the +``examples/PACKAGES/cgdna/util/`` directory can be used. This tool +assumes similar file structure to the examples found in +``examples/PACKAGES/cgdna/examples/``. ---------- diff --git a/doc/src/pair_pedone.rst b/doc/src/pair_pedone.rst new file mode 100644 index 0000000000..10fcb63e2e --- /dev/null +++ b/doc/src/pair_pedone.rst @@ -0,0 +1,137 @@ +.. index:: pair_style pedone +.. index:: pair_style pedone/omp + +pair_style pedone command +========================= + +Accelerator Variants: *pedone/omp* + + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style args + +* style = pedone* +* args = list of arguments for a particular style + +.. parsed-literal:: + + *pedone* args = cutoff + cutoff = global cutoff for Pedone interactions (distance units) + +Examples +"""""""" + +.. code-block:: LAMMPS + +pair_style hybrid/overlay pedone 15.0 coul/long 15.0 +kspace_style pppm 1.0e-5 + +pair_coeff * * coul/long +pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 +pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + +Used in input scripts: + + .. parsed-literal:: + + examples/PACKAGES/pedone/in.pedone.relax + examples/PACKAGES/pedone/in.pedone.melt + + + +Description +""""""""""" + +.. versionadded:: 17Apr2024 + +Pair style *pedone* computes the **non-Coulomb** interactions of the Pedone +(or PMMCS) potential :ref:`(Pedone) ` which combines Coulomb +interactions, Morse potential, and repulsive :math:`r^{-12}` +Lennard-Jones terms (see below). The *pedone* pair style is meant +to be used in addition to a :doc:`Coulomb pair style ` via +pair style :doc:`hybrid/overlay ` (see example above). +Using *coul/long* or *could/dsf* (for solids) is recommended. + +The full Pedone potential function from :ref:`(Pedone) ` for each +pair of atoms is: + +.. math:: + + E = \frac{C q_i q_j}{\epsilon r} + + D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] + + \frac{B_0}{r^{12}} \qquad r < r_c + +:math:`r_c` is the cutoff and :math:`C` is a conversion factor that is +specific to the choice of :doc:`units ` so that the entire +Coulomb term is in energy units with :math:`q_i` and :math:`q_j` as the +assigned charges in multiples of the elementary charge. + +The following coefficients must be defined for the selected pairs of +atom types via the :doc:`pair_coeff ` command as in the +example above: + +* :math:`D_0` (energy units) +* :math:`\alpha` (1/distance units) +* :math:`r_0` (distance units) +* :math:`C_0` (energy units) +* cutoff (distance units) + +The last coefficient is optional. If not specified, the global *pedone* +cutoff is used. + +---------- + +.. include:: accel_styles.rst + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This pair style does not support mixing. + +This pair style support the :doc:`pair_modify ` shift +option for the energy of the pair interaction. + +This pair style does not support the :doc:`pair_modify ` +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style writes its information to :doc:`binary restart files `, +so pair_style and pair_coeff commands does not need to be specified in an input +script that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*, *middle*, or *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +The *pedone* pair style is only enabled if LAMMPS was built with the +EXTRA-PAIR package. See the :doc:`Build package ` page +for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff `, :doc:`pair_style `, +:doc:`pair style coul/long and coul/dsf `, +:doc:`pair style morse ` + +Default +""""""" + +none + +------------- + +.. _Pedone: + +**(Pedone)** A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006) diff --git a/doc/src/pair_pod.rst b/doc/src/pair_pod.rst index cb4edcb9e9..0c7f188b3f 100644 --- a/doc/src/pair_pod.rst +++ b/doc/src/pair_pod.rst @@ -1,8 +1,11 @@ .. index:: pair_style pod +.. index:: pair_style pod/kk pair_style pod command ======================== +Accelerator Variants: *pod/kk* + Syntax """""" @@ -24,29 +27,33 @@ Description .. versionadded:: 22Dec2022 Pair style *pod* defines the proper orthogonal descriptor (POD) -potential :ref:`(Nguyen) `. The mathematical definition of -the POD potential is described from :doc:`fitpod `, which is -used to fit the POD potential to *ab initio* energy and force data. +potential :ref:`(Nguyen and Rohskopf) `, +:ref:`(Nguyen2023) `, :ref:`(Nguyen2024) `, +and :ref:`(Nguyen and Sema) `. The :doc:`fitpod +` is used to fit the POD potential. Only a single pair_coeff command is used with the *pod* style which -specifies a POD parameter file followed by a coefficient file. +specifies a POD parameter file followed by a coefficient file, a +projection matrix file, and a centroid file. -The coefficient file (``Ta_coefficients.pod``) contains coefficients for the -POD potential. The top of the coefficient file can contain any number of -blank and comment lines (start with #), but follows a strict format -after that. The first non-blank non-comment line must contain: +The POD parameter file (``Ta_param.pod``) can contain blank and comment +lines (start with #) anywhere. Each non-blank non-comment line must +contain one keyword/value pair. See :doc:`fitpod ` for +the description of all the keywords that can be assigned in the +parameter file. -* POD_coefficients: *ncoeff* +The coefficient file (``Ta_coefficients.pod``) contains coefficients for +the POD potential. The top of the coefficient file can contain any +number of blank and comment lines (start with #), but follows a strict +format after that. The first non-blank non-comment line must contain: -This is followed by *ncoeff* coefficients, one per line. The coefficient +* model_coefficients: *ncoeff* *nproj* *ncentroid* + +This is followed by *ncoeff* coefficients, *nproj* projection matrix entries, +and *ncentroid* centroid coordinates, one per line. The coefficient file is generated after training the POD potential using :doc:`fitpod `. -The POD parameter file (``Ta_param.pod``) can contain blank and comment lines -(start with #) anywhere. Each non-blank non-comment line must contain -one keyword/value pair. See :doc:`fitpod ` for the description -of all the keywords that can be assigned in the parameter file. - As an example, if a LAMMPS indium phosphide simulation has 4 atoms types, with the first two being indium and the third and fourth being phophorous, the pair_coeff command would look like this: @@ -67,7 +74,33 @@ the *hybrid* pair style. The NULL values are placeholders for atom types that will be used with other potentials. Examples about training and using POD potentials are found in the -directory lammps/examples/PACKAGES/pod. +directory lammps/examples/PACKAGES/pod and the Github repo https://github.com/cesmix-mit/pod-examples. + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS with +user-specifiable parameters as described above. You never need to +specify a pair_coeff command with I != J arguments for this style. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential files. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*, *middle*, *outer* keywords. + +---------- + +.. include:: accel_styles.rst ---------- @@ -78,12 +111,14 @@ This style is part of the ML-POD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -This pair style does not compute per-atom energies and per-atom stresses. - Related commands """""""""""""""" :doc:`fitpod `, +:doc:`compute pod/atom `, +:doc:`compute podd/atom `, +:doc:`compute pod/local `, +:doc:`compute pod/global ` Default """"""" @@ -92,6 +127,20 @@ none ---------- -.. _Nguyen20221: +.. _Nguyen20222b: + +**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023). + +.. _Nguyen20232b: + +**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023). + +.. _Nguyen20242b: + +**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024). + +.. _Nguyen20243b: + +**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024). + -**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022). diff --git a/doc/src/pair_rebomos.rst b/doc/src/pair_rebomos.rst index 9f4b8006c1..05be473256 100644 --- a/doc/src/pair_rebomos.rst +++ b/doc/src/pair_rebomos.rst @@ -28,7 +28,7 @@ Example input scripts available: examples/threebody/ Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 17Apr2024 The *rebomos* pair style computes the interactions between molybdenum and sulfur atoms :ref:`(Stewart) ` utilizing an adaptive diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index e21ae28432..1405cb8101 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -1,11 +1,12 @@ .. index:: pair_style soft .. index:: pair_style soft/gpu +.. index:: pair_style soft/kk .. index:: pair_style soft/omp pair_style soft command ======================= -Accelerator Variants: *soft/gpu*, *soft/omp* +Accelerator Variants: *soft/gpu*, *soft/kk*, *soft/omp* Syntax """""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 53bf269e1c..75157d6127 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -108,6 +108,7 @@ accelerated styles exist. * :doc:`none ` - turn off pairwise interactions * :doc:`hybrid ` - multiple styles of pairwise interactions +* :doc:`hybrid/molecular ` - different pair styles for intra- and inter-molecular interactions * :doc:`hybrid/overlay ` - multiple styles of superposed pairwise interactions * :doc:`hybrid/scaled ` - multiple styles of scaled superposed pairwise interactions * :doc:`zero ` - neighbor list but no interactions @@ -171,6 +172,7 @@ accelerated styles exist. * :doc:`coul/wolf ` - Coulomb via Wolf potential * :doc:`coul/wolf/cs ` - Coulomb via Wolf potential with core/shell adjustments * :doc:`dpd ` - dissipative particle dynamics (DPD) +* :doc:`dpd/coul/slater/long ` - dissipative particle dynamics (DPD) with electrostatic interactions * :doc:`dpd/ext ` - generalized force field for DPD * :doc:`dpd/ext/tstat ` - pairwise DPD thermostatting with generalized force field * :doc:`dpd/fdt ` - DPD for constant temperature and pressure @@ -275,30 +277,30 @@ accelerated styles exist. * :doc:`lj/smooth/linear ` - linear smoothed LJ potential * :doc:`lj/switch3/coulgauss/long ` - smoothed LJ vdW potential with Gaussian electrostatics * :doc:`lj96/cut ` - Lennard-Jones 9/6 potential -* :doc:`local/density ` - generalized basic local density potential -* :doc:`lubricate ` - hydrodynamic lubrication forces -* :doc:`lubricate/poly ` - hydrodynamic lubrication forces with polydispersity -* :doc:`lubricateU ` - hydrodynamic lubrication forces for Fast Lubrication Dynamics -* :doc:`lubricateU/poly ` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity +* :doc:`local/density ` - Generalized basic local density potential +* :doc:`lubricate ` - Hydrodynamic lubrication forces +* :doc:`lubricate/poly ` - Hydrodynamic lubrication forces with polydispersity +* :doc:`lubricateU ` - Hydrodynamic lubrication forces for Fast Lubrication Dynamics +* :doc:`lubricateU/poly ` - Hydrodynamic lubrication forces for Fast Lubrication with polydispersity * :doc:`mdpd ` - mDPD particle interactions * :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density -* :doc:`meam ` - modified embedded atom method (MEAM) -* :doc:`meam/ms ` - multi-state modified embedded atom method (MS-MEAM) -* :doc:`meam/spline ` - splined version of MEAM -* :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term -* :doc:`mesocnt ` - mesoscopic vdW potential for (carbon) nanotubes -* :doc:`mesocnt/viscous ` - mesoscopic vdW potential for (carbon) nanotubes with friction -* :doc:`mgpt ` - simplified model generalized pseudopotential theory (MGPT) potential +* :doc:`meam ` - Modified embedded atom method (MEAM) +* :doc:`meam/ms ` - Multi-state modified embedded atom method (MS-MEAM) +* :doc:`meam/spline ` - Splined version of MEAM +* :doc:`meam/sw/spline ` - Splined version of MEAM with a Stillinger-Weber term +* :doc:`mesocnt ` - Mesoscopic vdW potential for (carbon) nanotubes +* :doc:`mesocnt/viscous ` - Mesoscopic vdW potential for (carbon) nanotubes with friction +* :doc:`mgpt ` - Simplified model generalized pseudopotential theory (MGPT) potential * :doc:`mie/cut ` - Mie potential -* :doc:`mm3/switch3/coulgauss/long ` - smoothed MM3 vdW potential with Gaussian electrostatics +* :doc:`mm3/switch3/coulgauss/long ` - Smoothed MM3 vdW potential with Gaussian electrostatics * :doc:`momb ` - Many-Body Metal-Organic (MOMB) force field * :doc:`morse ` - Morse potential -* :doc:`morse/smooth/linear ` - linear smoothed Morse potential +* :doc:`morse/smooth/linear ` - Linear smoothed Morse potential * :doc:`morse/soft ` - Morse potential with a soft core * :doc:`multi/lucy ` - DPD potential with density-dependent force * :doc:`multi/lucy/rx ` - reactive DPD potential with density-dependent force -* :doc:`nb3b/harmonic ` - non-bonded 3-body harmonic potential -* :doc:`nb3b/screened ` - non-bonded 3-body screened harmonic potential +* :doc:`nb3b/harmonic ` - Non-bonded 3-body harmonic potential +* :doc:`nb3b/screened ` - Non-bonded 3-body screened harmonic potential * :doc:`nm/cut ` - N-M potential * :doc:`nm/cut/coul/cut ` - N-M potential with cutoff Coulomb * :doc:`nm/cut/coul/long ` - N-M potential with long-range Coulomb @@ -322,21 +324,22 @@ accelerated styles exist. * :doc:`oxrna2/xstk ` - * :doc:`pace ` - Atomic Cluster Expansion (ACE) machine-learning potential * :doc:`pace/extrapolation ` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades +* :doc:`pedone ` - Pedone (PMMCS) potential (non-Coulomb part) * :doc:`pod ` - Proper orthogonal decomposition (POD) machine-learning potential -* :doc:`peri/eps ` - peridynamic EPS potential -* :doc:`peri/lps ` - peridynamic LPS potential -* :doc:`peri/pmb ` - peridynamic PMB potential -* :doc:`peri/ves ` - peridynamic VES potential -* :doc:`polymorphic ` - polymorphic 3-body potential +* :doc:`peri/eps ` - Peridynamic EPS potential +* :doc:`peri/lps ` - Peridynamic LPS potential +* :doc:`peri/pmb ` - Peridynamic PMB potential +* :doc:`peri/ves ` - Peridynamic VES potential +* :doc:`polymorphic ` - Polymorphic 3-body potential * :doc:`python ` - * :doc:`quip ` - * :doc:`rann ` - * :doc:`reaxff ` - ReaxFF potential -* :doc:`rebo ` - second generation REBO potential of Brenner +* :doc:`rebo ` - Second generation REBO potential of Brenner * :doc:`rebomos ` - REBOMoS potential for MoS2 * :doc:`resquared ` - Everaers RE-Squared ellipsoidal potential -* :doc:`saip/metal ` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces -* :doc:`sdpd/taitwater/isothermal ` - smoothed dissipative particle dynamics for water at isothermal conditions +* :doc:`saip/metal ` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces +* :doc:`sdpd/taitwater/isothermal ` - Smoothed dissipative particle dynamics for water at isothermal conditions * :doc:`smatb ` - Second Moment Approximation to the Tight Binding * :doc:`smatb/single ` - Second Moment Approximation to the Tight Binding for single-element systems * :doc:`smd/hertz ` - @@ -381,6 +384,7 @@ accelerated styles exist. * :doc:`tracker ` - monitor information about pairwise interactions * :doc:`tri/lj ` - LJ potential between triangles * :doc:`ufm ` - +* :doc:`uf3 ` - UF3 machine-learning potential * :doc:`vashishta ` - Vashishta 2-body and 3-body potential * :doc:`vashishta/table ` - * :doc:`wf/cut ` - Wang-Frenkel Potential for short-ranged interactions diff --git a/doc/src/pair_uf3.rst b/doc/src/pair_uf3.rst new file mode 100644 index 0000000000..b6bb990385 --- /dev/null +++ b/doc/src/pair_uf3.rst @@ -0,0 +1,213 @@ +.. index:: pair_style uf3 +.. index:: pair_style uf3/kk + +pair_style uf3 command +====================== + +Accelerator Variants: *uf3/kk* + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style BodyFlag + +* style = *uf3* or *uf3/kk* + + .. parsed-literal:: + + BodyFlag = Indicates whether to calculate only 2-body or 2 and 3-body interactions. Possible values: 2 or 3 + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style uf3 3 + pair_coeff * * Nb.uf3 Nb + + pair_style uf3 2 + pair_coeff * * NbSn.uf3 Nb Sn + + pair_style uf3 3 + pair_coeff * * NbSn.uf3 Nb Sn + +Description +""""""""""" + +.. versionadded:: 27June2024 + +The *uf3* style computes the :ref:`Ultra-Fast Force Fields (UF3) +` potential, a machine-learning interatomic potential. In UF3, +the total energy of the system is defined via two- and three-body +interactions: + +.. math:: + + E & = \sum_{i,j} V_2(r_{ij}) + \sum_{i,j,k} V_3 (r_{ij},r_{ik},r_{jk}) \\ + V_2(r_{ij}) & = \sum_{n=0}^N c_n B_n(r_{ij}) \\ + V_3 (r_{ij},r_{ik},r_{jk}) & = \sum_{l=0}^{N_l} \sum_{m=0}^{N_m} \sum_{n=0}^{N_n} c_{l,m,n} B_l(r_{ij}) B_m(r_{ik}) B_n(r_{jk}) + +where :math:`V_2(r_{ij})` and :math:`V_3 (r_{ij},r_{ik},r_{jk})` are the +two- and three-body interactions, respectively. For the two-body the +summation is over all neighbors J and for the three-body the summation +is over all neighbors J and K of atom I within a cutoff distance +determined from the potential files. :math:`B_n(r_{ij})` are the cubic +b-spline basis, :math:`c_n` and :math:`c_{l,m,n}` are the machine-learned +interaction parameters and :math:`N`, :math:`N_l`, :math:`N_m`, and +:math:`N_n` denote the number of basis functions per spline or tensor +spline dimension. + +With *uf3* style only a single pair_coeff command is used to indicate the +UF3 LAMMPS potential file containing all the two- and three-body interactions +followed by N additional arguments specifying the mapping of UF3 elements to +LAMMPS atom types, where N is the number of LAMMPS atom types: + +* UF3 LAMMPS potential file +* N elements names = mapping of UF3 elements to atom types + +As an example, if a LAMMPS simulation contains 2 atom types (elements +'A' and 'B'), the pair_coeff command will be: + +.. code-block:: LAMMPS + + pair_style uf3 3 + pair_coeff * * AB.uf3 A B + +The AB.uf3 file should contain all two-body (A-A, A-B, B-B) and three-body +(A-A-A, A-A-B, A-B-B, B-A-A, B-A-B, B-B-B). + +If a value of "2" is specified in the :code:`pair_style uf3` command, +only the two-body potentials are needed. For 3-body interaction the +first atom type is the central atom. We recommend using the +:code:`generate_uf3_lammps_pots.py` script (found `here +`_) for +generating the UF3 LAMMPS potential file from the UF3 JSON potentials. + +---------- + +UF3 LAMMPS potential file in the *potentials* directory of the LAMMPS +distribution have a ".uf3" suffix. The interaction block in UF3 LAMMPS potential +file should start with :code:`#UF3 POT` and end with :code:`#` characters. +Following shows the format of a generic 2-body and 3-body potential block in +UF3 LAMMPS potential file- + +.. code-block:: LAMMPS + + #UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE + 2B ELEMENT1 ELEMENT2 LEADING_TRIM TRAILING_TRIM + Rij_CUTOFF NUM_OF_KNOTS + BSPLINE_KNOTS + NUM_OF_COEFF + COEFF + # + #UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE + 3B ELEMENT1 ELEMENT2 ELEMENT3 LEADING_TRIM TRAILING_TRIM + Rjk_CUTOFF Rik_CUTOFF Rij_CUTOFF NUM_OF_KNOTS_JK NUM_OF_KNOTS_IK NUM_OF_KNOTS_IJ + BSPLINE_KNOTS_FOR_JK + BSPLINE_KNOTS_FOR_IK + BSPLINE_KNOTS_FOR_IJ + SHAPE_OF_COEFF_MATRIX[I][J][K] + COEFF_MATRIX[0][0][K] + COEFF_MATRIX[0][1][K] + COEFF_MATRIX[0][2][K] + . + . + . + COEFF_MATRIX[1][0][K] + COEFF_MATRIX[1][1][K] + COEFF_MATRIX[1][2][K] + . + . + . + # + +The second line indicates whether the block contains data for 2-body +(:code:`2B`) or 3-body (:code:`3B`) interaction. This is followed by element +combination interaction, :code:`LEADING_TRIM` and :code:`TRAILING_TRIM` +number on the same line. The current implementation is only tested for +:code:`LEADING_TRIM=0` and :code:`TRAILING_TRIM=3`. +If other values are used LAMMPS is terminated after issuing an error message. +The :code:`Rij_CUTOFF` sets the 2-body cutoff for the interaction described +by the potential block. :code:`NUM_OF_KNOTS` is the number of knots +(or the length of the knot vector) present on the very next line. The +:code:`BSPLINE_KNOTS` line should contain all the knots in ascending order. +:code:`NUM_OF_COEFF` is the number of coefficients in the :code:`COEFF` line. +All the numbers in the BSPLINE_KNOTS and COEFF line should be space-separated. +Similar to the 2-body potential block, the third line sets the cutoffs and +length of the knots. The cutoff distance between atom-type I and J is +:code:`Rij_CUTOFF`, atom-type I and K is :code:`Rik_CUTOFF` and between +J and K is :code:`Rjk_CUTOFF`. + +.. note:: + + The current implementation only works for UF3 potentials with cutoff + distances for 3-body interactions that follows + :code:`2Rij_CUTOFF=2Rik_CUTOFF=Rjk_CUTOFF` relation. + +The :code:`BSPLINE_KNOTS_FOR_JK`, :code:`BSPLINE_KNOTS_FOR_IK`, and +:code:`BSPLINE_KNOTS_FOR_IJ` lines (note the order) contain the knots in +increasing order for atoms J and K, I and K, and atoms I and J +respectively. The number of knots is defined by the +:code:`NUM_OF_KNOTS_*` characters in the previous line. The shape of +the coefficient matrix is defined on the +:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` line followed by the columns of +the coefficient matrix, one per line, as shown above. For example, if +the coefficient matrix has the shape of 8x8x13, then +:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` will be :code:`8 8 13` followed +by 64 (8x8) lines each containing 13 coefficients separated by space. + +---------- + +.. include:: accel_styles.rst + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as described +above from values in the potential file. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*, *middle*, *outer* keywords. + +Restrictions +"""""""""""" + +The 'uf3' pair style is part of the ML-UF3 package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +This pair style requires the :doc:`newton ` setting to be "on". + +The UF3 LAMMPS potential file provided with LAMMPS (see the potentials +directory) are parameterized for metal :doc:`units `. + +The single() function of 'uf3' pair style only return the 2-body +interaction energy. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + +Default +""""""" + +none + +---------- + +.. _Xie23: + +**(Xie23)** Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7 diff --git a/doc/src/processors.rst b/doc/src/processors.rst index 921bbcc667..f909790304 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -25,6 +25,8 @@ Syntax *numa* params = none *custom* params = infile infile = file containing grid layout + *numa_nodes* arg = Nn + Nn = number of numa domains per node *map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx* cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 @@ -157,26 +159,30 @@ surface-to-volume ratio of each processor's subdomain. for most MPI implementations, but some MPIs provide options for this ordering, e.g. via environment variable settings. -The *numa* style operates similar to the *twolevel* keyword except -that it auto-detects which cores are running on which nodes. -Currently, it does this in only 2 levels, but it may be extended in -the future to account for socket topology and other non-uniform memory -access (NUMA) costs. It also uses a different algorithm than the -*twolevel* keyword for doing the two-level factorization of the -simulation box into a 3d processor grid to minimize off-node -communication, and it does its own MPI-based mapping of nodes and -cores to the regular 3d grid. Thus it may produce a different layout -of the processors than the *twolevel* options. +The *numa* style operates similar to the *twolevel* keyword except that +it auto-detects which cores are running on which nodes. It will also +subdivide the cores into numa domains. Currently, the number of numa +domains is not auto-detected and must be specified using the +*numa_nodes* keyword; otherwise, the default value is used. The *numa* +style uses a different algorithm than the *twolevel* keyword for doing +the two-level factorization of the simulation box into a 3d processor +grid to minimize off-node communication and communication across numa +domains. It does its own MPI-based mapping of nodes and cores to the +regular 3d grid. Thus it may produce a different layout of the +processors than the *twolevel* options. The *numa* style will give an error if the number of MPI processes is not divisible by the number of cores used per node, or any of the Px -or Py of Pz values is greater than 1. +or Py or Pz values is greater than 1. .. note:: Unlike the *twolevel* style, the *numa* style does not require - any particular ordering of MPI ranks i norder to work correctly. This + any particular ordering of MPI ranks in order to work correctly. This is because it auto-detects which processes are running on which nodes. + However, it assumes that the lowest ranks are in the first numa + domain, and so forth. MPI rank orderings that do not preserve this + property might result in more intra-node communication between CPUs. The *custom* style uses the file *infile* to define both the 3d factorization and the mapping of processors to the grid. @@ -207,6 +213,14 @@ any order, but no processor ID should appear more than once. ---------- +The *numa_nodes* keyword is used to specify the number of numa domains +per node. It is currently only used by the *numa* style for two-level +factorization to reduce the amount of MPI communications between CPUs. +A good setting for this will typically be equal to the number of CPU +sockets per node. + +---------- + The *map* keyword affects how the P processor IDs (from 0 to P-1) are mapped to the 3d grid of processors. It is only used by the *onelevel* and *twolevel* grid settings. @@ -356,5 +370,5 @@ Related commands Default """"""" -The option defaults are Px Py Pz = \* \* \*, grid = onelevel, and map = -cart. +The option defaults are Px Py Pz = \* \* \*, grid = onelevel, map = +cart, and numa_nodes = 2. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 0ecd2b6fa2..dd2f42e2a8 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -63,11 +63,16 @@ Description Read in a data file containing information LAMMPS needs to run a simulation. The file can be ASCII text or a gzipped text file -(detected by a .gz suffix). This is one of 3 ways to specify initial -atom coordinates; see the :doc:`read_restart ` and -:doc:`create_atoms ` commands for alternative methods. -Also see the explanation of the :doc:`-restart command-line switch -` which can convert a restart file to a data file. +(detected by a .gz suffix). + +This is one of 3 ways to specify the simulation box: see the +:doc:`create_box ` and :doc:`read_restart ` +and commands for alternative methods. It is also one of 3 ways to +specify initial atom coordinates: see the :doc:`create_atoms +` and :doc:`read_restart ` and commands +for alternative methods. Also see the explanation of the +:doc:`-restart command-line switch ` which can convert a +restart file to a data file. This command can be used multiple times to add new atoms and their properties to an existing system by using the *add*, *offset*, and @@ -122,37 +127,55 @@ keyword must be used. .. note:: - The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in - the new data file will be merged with the existing simulation box to - create a large enough box in each dimension to contain both the - existing and new atoms. Each box dimension never shrinks due to this - merge operation, it only stays the same or grows. Care must be used if - you are growing the existing simulation box in a periodic dimension. - If there are existing atoms with bonds that straddle that periodic - boundary, then the atoms may become far apart if the box size grows. - This will separate the atoms in the bond, which can lead to "lost" - bond atoms or bad dynamics. + If the first read_data command defined an orthogonal or restricted + triclinic or general triclinic simulation box (see the sub-section + below on header keywords), then subsequent data files must define + the same kind of simulation box. For orthogonal boxes, the new box + can be a different size; see the next Note. For a restricted + triclinic box, the 3 new tilt factors ("xy xz yz" keyword) must + have the same values as in the original data file. For a general + triclinic box, the new avec, bvec, cvec, and "abc origin" keywords + must have the same values in the original data file. files. Also + the *shift* keyword cannot be used in subsequent read_data commands + for a general triclinic box. + +.. note:: + + For orthogonal boxes, the simulation box size in the new data file + will be merged with the existing simulation box to create a large + enough box in each dimension to contain both the existing and new + atoms. Each box dimension never shrinks due to this merge + operation, it only stays the same or grows. Care must be used if + you are growing the existing simulation box in a periodic + dimension. If there are existing atoms with bonds that straddle + that periodic boundary, then the atoms may become far apart if the + box size grows. This will separate the atoms in the bond, which + can lead to "lost" bond atoms or bad dynamics. The three choices for the *add* argument affect how the atom IDs and -molecule IDs of atoms in the data file are treated. If *append* is -specified, atoms in the data file are added to the current system, -with their atom IDs reset so that an atom-ID = M in the data file -becomes atom-ID = N+M, where N is the largest atom ID in the current -system. This rule is applied to all occurrences of atom IDs in the -data file, e.g. in the Velocity or Bonds section. This is also done -for molecule IDs, if the atom style does support molecule IDs or -they are enabled via fix property/atom. If *IDoffset* is specified, -then *IDoffset* is a numeric value is given, e.g. 1000, so that an -atom-ID = M in the data file becomes atom-ID = 1000+M. For systems -with enabled molecule IDs, another numerical argument *MOLoffset* -is required representing the equivalent offset for molecule IDs. -If *merge* is specified, the data file atoms -are added to the current system without changing their IDs. They are -assumed to merge (without duplication) with the currently defined -atoms. It is up to you to ensure there are no multiply defined atom -IDs, as LAMMPS only performs an incomplete check that this is the case -by ensuring the resulting max atom-ID >= the number of atoms. For -molecule IDs, there is no check done at all. +molecule IDs of atoms in the data file are treated. + +If *append* is specified, atoms in the data file are added to the +current system, with their atom IDs reset so that an atom-ID = M in +the data file becomes atom-ID = N+M, where N is the largest atom ID in +the current system. This rule is applied to all occurrences of atom +IDs in the data file, e.g. in the Velocity or Bonds section. This is +also done for molecule IDs, if the atom style does support molecule +IDs or they are enabled via fix property/atom. + +If *IDoffset* is specified, then *IDoffset* is a numeric value is +given, e.g. 1000, so that an atom-ID = M in the data file becomes +atom-ID = 1000+M. For systems with enabled molecule IDs, another +numerical argument *MOLoffset* is required representing the equivalent +offset for molecule IDs. + +If *merge* is specified, the data file atoms are added to the current +system without changing their IDs. They are assumed to merge (without +duplication) with the currently defined atoms. It is up to you to +ensure there are no multiply defined atom IDs, as LAMMPS only performs +an incomplete check that this is the case by ensuring the resulting +max atom-ID >= the number of atoms. For molecule IDs, there is no +check done at all. The *offset* and *shift* keywords can only be used if the *add* keyword is also specified. @@ -288,13 +311,16 @@ Format of the header of a data file """"""""""""""""""""""""""""""""""" These are the recognized header keywords. Header lines can come in -any order. The value(s) are read from the beginning of the line. +any order. Each keyword takes a single value unless noted in this +list. The value(s) are read from the beginning of the line. Thus the keyword *atoms* should be in a line like "1000 atoms"; the keyword *ylo yhi* should be in a line like "-10.0 10.0 ylo yhi"; the keyword *xy xz yz* should be in a line like "0.0 5.0 6.0 xy xz yz". -All these settings have a default value of 0, except the lo/hi box -size defaults are -0.5 and 0.5. A line need only appear if the value -is different than the default. + +All these settings have a default value of 0, except for the +simulation box size settings; their defaults are explained below. A +keyword line need only appear if its value is different than the +default. * *atoms* = # of atoms in system * *bonds* = # of bonds in system @@ -315,81 +341,178 @@ is different than the default. * *lines* = # of line segments in system * *triangles* = # of triangles in system * *bodies* = # of bodies in system -* *xlo xhi* = simulation box boundaries in x dimension -* *ylo yhi* = simulation box boundaries in y dimension -* *zlo zhi* = simulation box boundaries in z dimension -* *xy xz yz* = simulation box tilt factors for triclinic system +* *xlo xhi* = simulation box boundaries in x dimension (2 values) +* *ylo yhi* = simulation box boundaries in y dimension (2 values) +* *zlo zhi* = simulation box boundaries in z dimension (2 values) +* *xy xz yz* = simulation box tilt factors for triclinic system (3 values) +* *avec* = first edge vector of a general triclinic simulation box (3 values) +* *bvec* = second edge vector of a general triclinic simulation box (3 values) +* *cvec* = third edge vector of a general triclinic simulation box (3 values) +* *abc origin* = origin of a general triclinic simulation box (3 values) -The initial simulation box size is determined by the lo/hi settings. -In any dimension, the system may be periodic or non-periodic; see the -:doc:`boundary ` command. When the simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the :doc:`processors ` command. The -partitioning can later be changed by the :doc:`balance ` or -:doc:`fix balance ` commands. +---------- -If the *xy xz yz* line does not appear, LAMMPS will set up an -axis-aligned (orthogonal) simulation box. If the line does appear, -LAMMPS creates a non-orthogonal simulation domain shaped as a -parallelepiped with triclinic symmetry. The parallelepiped has its -"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting -from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = -(xz,yz,zhi-zlo). *Xy,xz,yz* can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. +Header specification of the simulation box size and shape +""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -The tilt factors (xy,xz,yz) should not skew the box more than half the -distance of the corresponding parallel box length. For example, if -:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x` -box length is 10 and the :math:`xy` tilt factor must be between -:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz` -must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and -:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this example), -then configurations with tilt :math:`= \dots, -15`, :math:`-5`, -:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically -equivalent. Simulations with large tilt factors will run inefficiently, -since they require more ghost atoms and thus more communication. With -very large tilt factors, LAMMPS will eventually produce incorrect -trajectories and stop with errors due to lost atoms or similar. +The last 8 keywords in the list of header keywords are for simulation +boxes of 3 kinds which LAMMPS supports: -See the :doc:`Howto triclinic ` page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. +* orthogonal box = faces are perpendicular to the xyz coordinate axes +* restricted triclinic box = a parallelepiped defined by 3 edge vectors oriented in a constrained manner +* general triclinic box = a parallelepiped defined by 3 arbitrary edge vectors -When a triclinic system is used, the simulation domain should normally -be periodic in the dimension that the tilt is applied to, which is -given by the second dimension of the tilt factor (e.g. y for xy tilt). -This is so that pairs of atoms interacting across that boundary will -have one of them shifted by the tilt factor. Periodicity is set by -the :doc:`boundary ` command. For example, if the xy tilt -factor is non-zero, then the y dimension should be periodic. -Similarly, the z dimension should be periodic if xz or yz is non-zero. -LAMMPS does not require this periodicity, but you may lose atoms if -this is not the case. +For restricted and general triclinic boxes, see the +:doc:`Howto_triclinic ` doc page for a fuller +description than is given here. -Also note that if your simulation will tilt the box, e.g. via the -:doc:`fix deform ` command, the simulation box must be setup -to be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by using -the :doc:`change box ` command with its *ortho* and -*triclinic* options. +The units of the values for all 8 keywords in in distance units; see +the :doc:`units ` command for details. -For 2d simulations, the *zlo zhi* values should be set to bound the z -coords for atoms that appear in the file; the default of -0.5 0.5 is -valid if all z coords are 0.0. For 2d triclinic simulations, the xz -and yz tilt factors must be 0.0. +For all 3 kinds of simulation boxes, the system may be periodic or +non-periodic in any dimension; see the :doc:`boundary ` +command for details. + +When the simulation box is created by the read_data command, it is +also partitioned into a regular 3d grid of subdomains, one per +processor, based on the number of processors being used and the +settings of the :doc:`processors ` command. For each kind +of simulation box the subdomains have the same shape as the simulation +box, i.e. smaller orthogonal bricks for orthogonal boxes, smaller +parallelepipeds for triclinic boxes. The partitioning can later be +changed by the :doc:`balance ` or :doc:`fix balance +` commands. + +For an orthogonal box, only the *xlo xhi*, *ylo yhi*, *zlo zhi* +keywords are used. They define the extent of the simulation box in +each dimension so that the resulting edge vectors of an orthogonal box +are: + +* **A** = (xhi-xlo,0,0) +* **B** = (0,yhi-ylo,0) +* **C** = (0,0,zhi-zlo) + +The origin (lower left corner) of the orthogonal box is at +(xlo,ylo,zlo). The default values for these 3 keywords are -0.5 and +0.5 for each lo/hi pair. For a 2d simulation, the zlo and zhi values +must straddle zero. The default zlo/zhi values do this, so that +keyword is not needed in 2d. + +For a restricted triclinic box, the *xy xz yz* keyword is used in +addition to the *xlo xhi*, *ylo yhi*, *zlo zhi* keywords. The three +*xy,xz,yz* values can be 0.0 or positive or negative, and are called +"tilt factors" because they are the amount of displacement applied to +edges of faces of an orthogonal box to transform it into a restricted +triclinic parallelepiped. + +The :doc:`Howto_triclinic ` doc page discusses the +tilt factors in detail and explains that the resulting edge vectors of +a restricted triclinic box are: + +* **A** = (xhi-xlo,0,0) +* **B** = (xy,yhi-ylo,0) +* **C** = (xz,yz,zhi-zlo) + +This restricted form of edge vectors requires that **A** be in the +direction of the x-axis, **B** be in the xy plane with its y-component +in the +y direction, and **C** have its z-component in the +z +direction. The origin (lower left corner) of the restricted triclinic +box is at (xlo,ylo,zlo). + +For a 2d simulation, the zlo and zhi values must straddle zero. The +default zlo/zhi values do this, so that keyword is not needed in 2d. +The xz and yz values must also be zero in 2d. The shape of the 2d +restricted triclinic simulation box is effectively a parallelogram. + +.. note:: + + When a restricted triclinic box is used, the simulation domain + should normally be periodic in any dimensions that tilt is applied + to, which is given by the second dimension of the tilt factor + (e.g. y for xy tilt). This is so that pairs of atoms interacting + across that boundary will have one of them shifted by the tilt + factor. Periodicity is set by the :doc:`boundary ` + command which also describes the shifting by the tilt factor. For + example, if the xy tilt factor is non-zero, then the y dimension + should be periodic. Similarly, the z dimension should be periodic + if xz or yz is non-zero. LAMMPS does not require this periodicity, + but you may lose atoms if this is not the case. + +.. note:: + + Normally, the specified tilt factors (xy,xz,yz) should not skew the + simulation box by more than half the distance of the corresponding + parallel box length for computational efficiency. For example, if + :math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the + :math:`x` box length is 10 and the :math:`xy` tilt factor should be + between :math:`-5` and :math:`5`. LAMMPS will issue a warning if + this is not the case. See the last sub-section of the + :doc:`Howto_triclinic ` doc page for more details. + +.. note:: + + If a simulation box is initially orthogonal, but will tilt during a + simulation, e.g. via the :doc:`fix deform ` command, + then the box should be defined as restricted triclinic with all 3 + tilt factors = 0.0. Alternatively, the :doc:`change box + ` command can be used to convert an orthogonal box to a + restricted triclinic box. + +For a general triclinic box, the *avec*, *bvec*, *cvec*, and *abc +origin* keywords are used. The *xlo xhi*, *ylo yhi*, *zlo zhi*, and +*xy xz yz* keywords are NOT used. The first 3 keywords define the 3 +edge vectors **A**, **B**, **C** of the general triclinic box. They +can be arbitrary vectors so long as they are distinct, non-zero, and +not co-planar. They must also define a right-handed system such that +(**A** x **B**) points in the direction of **C**. Note that a +left-handed system can be converted to a right-handed system by simply +swapping the order of any pair of the **A**, **B**, **C** vectors. +The origin of the box (origin of the 3 edge vectors) is set by the +*abc origin* keyword. + +The default values for these 4 keywords are as follows: + +* avec = (1,0,0) +* bvec = (0,1,0) +* cvec = (0,0,1) +* abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d + +For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of +*abc origin* must be -0.5. These are the default values, so the +*cvec* keyword is not needed in 2d. + +.. note:: + + LAMMPS allows specification of general triclinic simulation boxes + as a convenience for users who may be converting data from + solid-state crystallographic representations or from DFT codes for + input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally, + LAMMPS only uses restricted triclinic simulation boxes. This means + the box and per-atom information (e.g. coordinates, velocities) in + the data file are converted (rotated) from general to restricted + triclinic form when the file is read. Other sections of the data + file must also list their per-atom data appropriately if vector + quantities are specified. This requirement is explained below for + the relevant sections. The :doc:`Howto_triclinic + ` doc page also discusses other LAMMPS commands + which can input/output general triclinic representations of the + simulation box and per-atom data. + +The following explanations apply to all 3 kinds of simulation boxes: +orthogonal, restricted triclinic, and general triclinic. If the system is periodic (in a dimension), then atom coordinates can be outside the bounds (in that dimension); they will be remapped (in a -periodic sense) back inside the box. Note that if the *add* option is -being used to add atoms to a simulation box that already exists, this -periodic remapping will be performed using simulation box bounds that -are the union of the existing box and the box boundaries in the new -data file. +periodic sense) back inside the box. For triclinic boxes, periodicity +in x,y,z refers to the faces of the parallelepiped defined by the +**A**,**B**,**C** edge vectors of the simulation box. See the +:doc:`boundary ` command doc page for a fuller discussion. + +Note that if the *add* option is being used to add atoms to a +simulation box that already exists, this periodic remapping will be +performed using simulation box bounds that are the union of the +existing box and the box boundaries in the new data file. If the system is non-periodic (in a dimension), then an image flag for that direction has no meaning, since there cannot be periodic images @@ -406,7 +529,6 @@ individually back into the principal unit cell in that direction. This operation is equivalent to the behavior of the :doc:`change_box command ` when used to change periodicity. - If those atoms with non-zero image flags are involved in bonded interactions, this reset can lead to undesired changes, when the image flag values differ between the atoms, i.e. the bonded interaction @@ -421,73 +543,81 @@ needed, so that the image flag would be zero. .. note:: - If the system is non-periodic (in a dimension), then all atoms in the - data file must have coordinates (in that dimension) that are "greater - than or equal to" the lo value and "less than or equal to" the hi - value. If the non-periodic dimension is of style "fixed" (see the - :doc:`boundary ` command), then the atom coords must be - strictly "less than" the hi value, due to the way LAMMPS assign atoms - to processors. Note that you should not make the lo/hi values - radically smaller/larger than the extent of the atoms. For example, - if your atoms extend from 0 to 50, you should not specify the box - bounds as -10000 and 10000 unless you also use the :doc:`processors - command `. This is because LAMMPS uses the specified box - size to layout the 3d grid of processors. A huge (mostly empty) box - will be sub-optimal for performance when using "fixed" boundary - conditions (see the :doc:`boundary ` command). When using - "shrink-wrap" boundary conditions (see the :doc:`boundary ` - command), a huge (mostly empty) box may cause a parallel simulation - to lose atoms when LAMMPS shrink-wraps the box around the atoms. The - read_data command will generate an error in this case. + If the system is non-periodic (in a dimension), then all atoms in + the data file must have coordinates (in that dimension) that are + "greater than or equal to" the lo value and "less than or equal to" + the hi value. If the non-periodic dimension is of style "fixed" + (see the :doc:`boundary ` command), then the atom coords + must be strictly "less than" the hi value, due to the way LAMMPS + assign atoms to processors. Note that you should not make the + lo/hi values radically smaller/larger than the extent of the atoms. + For example, if atoms extend from 0 to 50, you should not specify + the box bounds as -10000 and 10000 unless you also use the + :doc:`processors command `. This is because LAMMPS + uses the specified box size to layout the 3d grid of processors. A + huge (mostly empty) box will be sub-optimal for performance when + using "fixed" boundary conditions (see the :doc:`boundary + ` command). When using "shrink-wrap" boundary conditions + (see the :doc:`boundary ` command), a huge (mostly empty) + box may cause a parallel simulation to lose atoms when LAMMPS + shrink-wraps the box around the atoms. The read_data command will + generate an error in this case. + +---------- + +Meaning of other header keywords +"""""""""""""""""""""""""""""""" The "extra bond per atom" setting (angle, dihedral, improper) is only needed if new bonds (angles, dihedrals, impropers) will be added to -the system when a simulation runs, e.g. by using the :doc:`fix bond/create ` command. Using this header flag -is deprecated; please use the *extra/bond/per/atom* keyword (and +the system when a simulation runs, e.g. by using the :doc:`fix +bond/create ` command. Using this header flag is +deprecated; please use the *extra/bond/per/atom* keyword (and correspondingly for angles, dihedrals and impropers) in the read_data command instead. Either will pre-allocate space in LAMMPS data structures for storing the new bonds (angles, dihedrals, impropers). The "extra special per atom" setting is typically only needed if new -bonds/angles/etc will be added to the system, e.g. by using the :doc:`fix bond/create ` command. Or if entire new molecules -will be added to the system, e.g. by using the -:doc:`fix deposit ` or :doc:`fix pour ` commands, -which will have more special 1-2,1-3,1-4 neighbors than any other -molecules defined in the data file. Using this header flag is -deprecated; please use the *extra/special/per/atom* keyword instead. -Using this setting will pre-allocate space in the LAMMPS data -structures for storing these neighbors. See the -:doc:`special_bonds ` and :doc:`molecule ` doc -pages for more discussion of 1-2,1-3,1-4 neighbors. +bonds/angles/etc will be added to the system, e.g. by using the +:doc:`fix bond/create ` command. Or if entire new +molecules will be added to the system, e.g. by using the :doc:`fix +deposit ` or :doc:`fix pour ` commands, which +will have more special 1-2,1-3,1-4 neighbors than any other molecules +defined in the data file. Using this header flag is deprecated; +please use the *extra/special/per/atom* keyword instead. Using this +setting will pre-allocate space in the LAMMPS data structures for +storing these neighbors. See the :doc:`special_bonds ` +and :doc:`molecule ` doc pages for more discussion of +1-2,1-3,1-4 neighbors. .. note:: - All of the "extra" settings are only applied in the first data - file read and when no simulation box has yet been created; as soon as + All of the "extra" settings are only applied in the first data file + read and when no simulation box has yet been created; as soon as the simulation box is created (and read_data implies that), these settings are *locked* and cannot be changed anymore. Please see the - description of the *add* keyword above for reading multiple data files. - If they appear in later data files, they are ignored. + description of the *add* keyword above for reading multiple data + files. If they appear in later data files, they are ignored. The "ellipsoids" and "lines" and "triangles" and "bodies" settings are -only used with :doc:`atom_style ellipsoid or line or tri or body ` and specify how many of the atoms are -finite-size ellipsoids or lines or triangles or bodies; the remainder -are point particles. See the discussion of ellipsoidflag and the -*Ellipsoids* section below. See the discussion of lineflag and the -*Lines* section below. See the discussion of triangleflag and the -*Triangles* section below. See the discussion of bodyflag and the -*Bodies* section below. +only used with :doc:`atom_style ellipsoid or line or tri or body +` and specify how many of the atoms are finite-size +ellipsoids or lines or triangles or bodies; the remainder are point +particles. See the discussion of ellipsoidflag and the *Ellipsoids* +section below. See the discussion of lineflag and the *Lines* section +below. See the discussion of triangleflag and the *Triangles* section +below. See the discussion of bodyflag and the *Bodies* section below. .. note:: - For :doc:`atom_style template `, the molecular - topology (bonds,angles,etc) is contained in the molecule templates - read-in by the :doc:`molecule ` command. This means you - cannot set the *bonds*, *angles*, etc header keywords in the data - file, nor can you define *Bonds*, *Angles*, etc sections as discussed + For :doc:`atom_style template `, the molecular topology + (bonds,angles,etc) is contained in the molecule templates read-in + by the :doc:`molecule ` command. This means you cannot + set the *bonds*, *angles*, etc header keywords in the data file, + nor can you define *Bonds*, *Angles*, etc sections as discussed below. You can set the *bond types*, *angle types*, etc header - keywords, though it is not necessary. If specified, they must match - the maximum values defined in any of the template molecules. + keywords, though it is not necessary. If specified, they must + match the maximum values defined in any of the template molecules. ---------- @@ -680,6 +810,19 @@ appended to it, which indicate which image of a periodic simulation box the atom is in. These may be important to include for some kinds of analysis. +.. note:: + + For orthogonal and restricted and general triclinic simulation + boxes, the atom coordinates (x,y,z) listed in this section should + be inside the corresponding simulation box. For restricted + triclinic boxes that means the parallelepiped defined by the *xlo + xhi*, *ylo yhi*, *zlo zhi*, and *xy xz yz*, keywords. For general + triclinic boxes that means the parallelepiped defined by the 3 edge + vectors and origin specified by the *avec*, *bvec*, *cvec*, and + *abc origin* header keywords. See the discussion in the header + section above about how atom coordinates outside the simulation box + are (or are not) remapped to be inside the box. + .. list-table:: * - angle @@ -690,10 +833,12 @@ of analysis. - atom-ID atom-type bodyflag mass x y z * - bond - atom-ID molecule-ID atom-type x y z + * - bpm/sphere + - atom-ID molecule-ID atom-type diameter density x y z * - charge - atom-ID atom-type q x y z * - dielectric - - atom-ID atom-type q x y z normx normy normz area ed em epsilon curvature + - atom-ID atom-type q x y z mux muy muz area ed em epsilon curvature * - dipole - atom-ID atom-type q x y z mux muy muz * - dpd @@ -720,8 +865,6 @@ of analysis. - atom-ID atom-type rho esph cv x y z * - sphere - atom-ID atom-type diameter density x y z - * - bpm/sphere - - atom-ID molecule-ID atom-type diameter density x y z * - spin - atom-ID atom-type x y z spx spy spz sp * - tdpd @@ -757,24 +900,42 @@ The per-atom values have these meanings and units, listed alphabetically: * lineflag = 1 for line segment particles, 0 for point or spherical particles * mass = mass of particle (mass units) * molecule-ID = integer ID of molecule the atom belongs to -* mux,muy,muz = components of dipole moment of atom (dipole units) +* mux,muy,muz = components of dipole moment of atom (dipole units) (see general triclinic note below) * q = charge on atom (charge units) * rho = density (need units) for SPH particles * sp = magnitude of magnetic spin of atom (Bohr magnetons) -* spx,spy,spz = components of magnetic spin of atom (unit vector) +* spx,spy,spz = components of magnetic spin of atom (unit vector) (see general triclinic note below) * template-atom = which atom within a template molecule the atom is * template-index = which molecule within the molecule template the atom is part of * theta = internal temperature of a DPD particle * triangleflag = 1 for triangular particles, 0 for point or spherical particles * volume = volume of Peridynamic particle (distance\^3 units) * x,y,z = coordinates of atom (distance units) -* x0,y0,z0 = original (strain-free) coordinates of atom (distance units) +* x0,y0,z0 = original (strain-free) coordinates of atom (distance + units) (see general triclinic note below) The units for these quantities depend on the unit style; see the :doc:`units ` command for details. -For 2d simulations specify z as 0.0, or a value within the *zlo zhi* -setting in the data file header. +For 2d simulations, the atom coordinate z must be specified as 0.0. +If the data file is created by another program, then z values for a 2d +simulation can be within epsilon of 0.0, and LAMMPS will force them to +zero. + +.. note:: + + If the data file defines a general triclinic box, then the + following per-atom values in the list above are per-atom vectors + which imply an orientation: (mux,muy,muz) and (spx,spy,spz). This + means they should be specified consistent with the general + triclinic box and its orientation relative to the standard x,y,z + coordinate axes. For example a dipole moment vector which will be + in the +x direction once LAMMPS converts from a general to + restricted triclinic box, should be specified in the data file in + the direction of the **A** edge vector. Likewise the (x0,y0,z0) + per-atom strain-free coordinates should be inside the general + triclinic simulation box as explained in the note above. See the + :doc:`Howto triclinic ` doc page for more details. The atom-ID is used to identify the atom throughout the simulation and in dump files. Normally, it is a unique value from 1 to Natoms for @@ -922,9 +1083,8 @@ that use unwrapped coordinates internally are as follows: Atom velocities and other atom quantities not defined above are set to 0.0 when the *Atoms* section is read. Velocities can be set later by -a *Velocities* section in the data file or by a -:doc:`velocity ` or :doc:`set ` command in the input -script. +a *Velocities* section in the data file or by a :doc:`velocity +` or :doc:`set ` command in the input script. ---------- @@ -963,8 +1123,9 @@ the "bodies" keyword. Each body can have a variable number of integer and/or floating-point values. The number and meaning of the values is defined by the body -style, as described in the :doc:`Howto body ` doc page. The -body style is given as an argument to the :doc:`atom_style body ` command. +style, as described in the :doc:`Howto body ` doc page. +The body style is given as an argument to the :doc:`atom_style body +` command. The Ninteger and Ndouble values determine how many integer and floating-point values are specified for this particle. Ninteger and @@ -1179,10 +1340,10 @@ and a general discussion of how type labels can be used. 12 1 2 1 1 0 0 0 -The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid ` is used and any atoms are listed in the -*Atoms* section with an ellipsoidflag = 1. The number of ellipsoids -should be specified in the header section via the "ellipsoids" -keyword. +The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid +` is used and any atoms are listed in the *Atoms* section +with an ellipsoidflag = 1. The number of ellipsoids should be +specified in the header section via the "ellipsoids" keyword. The 3 shape values specify the 3 diameters or aspect ratios of a finite-size ellipsoidal particle, when it is oriented along the 3 @@ -1200,6 +1361,12 @@ the quaternion that represents its new orientation is given by LAMMPS normalizes each atom's quaternion in case (a,b,c) is not specified as a unit vector. +If the data file defines a general triclinic box, then the quaternion +for each ellipsoid should be specified for its orientation relative to +the standard x,y,z coordinate axes. When the system is converted to a +restricted triclinic box, the ellipsoid quaternions will be altered to +reflect the new orientation of the ellipsoid. + The *Ellipsoids* section must appear after the *Atoms* section. ---------- @@ -1316,13 +1483,24 @@ is used and any atoms are listed in the *Atoms* section with a lineflag = 1. The number of lines should be specified in the header section via the "lines" keyword. -The 2 end points are the end points of the line segment. The ordering -of the 2 points should be such that using a right-hand rule to cross -the line segment with a unit vector in the +z direction, gives an -"outward" normal vector perpendicular to the line segment. +The 2 end points are the end points of the line segment. They should +be values close to the center point of the line segment specified in +the Atoms section of the data file, even if individual end points are +outside the simulation box. + +The ordering of the 2 points should be such that using a right-hand +rule to cross the line segment with a unit vector in the +z direction, +gives an "outward" normal vector perpendicular to the line segment. I.e. normal = (c2-c1) x (0,0,1). This orientation may be important for defining some interactions. +If the data file defines a general triclinic box, then the x1,y1 and +x2,y2 values for each line segment should be specified for its +orientation relative to the standard x,y,z coordinate axes. When the +system is converted to a restricted triclinic box, the x1,y1,x2,y2 +values will be altered to reflect the new orientation of the line +segment. + The *Lines* section must appear after the *Atoms* section. ---------- @@ -1444,15 +1622,27 @@ via the :doc:`pair_coeff ` command in the input script. 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 -The *Triangles* section must appear if :doc:`atom_style tri ` is used and any atoms are listed in the *Atoms* -section with a triangleflag = 1. The number of lines should be -specified in the header section via the "triangles" keyword. +The *Triangles* section must appear if :doc:`atom_style tri +` is used and any atoms are listed in the *Atoms* section +with a triangleflag = 1. The number of lines should be specified in +the header section via the "triangles" keyword. -The 3 corner points are the corner points of the triangle. The -ordering of the 3 points should be such that using a right-hand rule -to go from point1 to point2 to point3 gives an "outward" normal vector -to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This -orientation may be important for defining some interactions. +The 3 corner points are the corner points of the triangle. They +should be values close to the center point of the triangle specified +in the Atoms section of the data file, even if individual corner +points are outside the simulation box. + +The ordering of the 3 points should be such that using a right-hand +rule to go from point1 to point2 to point3 gives an "outward" normal +vector to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). +This orientation may be important for defining some interactions. + +If the data file defines a general triclinic box, then the x1,y1,z1 +and x2,y2,z2 and x3,y3,z3 values for each triangle should be specified +for its orientation relative to the standard x,y,z coordinate axes. +When the system is converted to a restricted triclinic box, the +x1,y1,z1,x2,y2,z2,x3,y3,z3 values will be altered to reflect the new +orientation of the triangle. The *Triangles* section must appear after the *Atoms* section. @@ -1493,6 +1683,12 @@ Vx, vy, vz, and ervel are in :doc:`units ` of velocity. Lx, ly, lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, Wz are in units of angular velocity (radians/time). +If the data file defines a general triclinic box, then each of the 3 +vectors (translational velocity, angular momentum, angular velocity) +should be specified for the rotated coordinate axes of the general +triclinic box. See the :doc:`Howto triclinic ` doc +page for more details. + For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the @@ -1513,8 +1709,8 @@ fields: atom-ID vx vy vz ervel wx wy wz -Translational velocities can also be set by the -:doc:`velocity ` command in the input script. +Translational velocities can also be (re)set by the :doc:`velocity +` command in the input script. ---------- diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst index 6bfbeab891..8713ea2f95 100644 --- a/doc/src/replicate.rst +++ b/doc/src/replicate.rst @@ -8,56 +8,118 @@ Syntax .. code-block:: LAMMPS - replicate nx ny nz *keyword* + replicate nx ny nz keyword ... nx,ny,nz = replication factors in each dimension -* optional *keyword* = *bbox* +* zero or more keywords may be appended +* keyword = *bbox* or *bond/periodic* .. parsed-literal:: - *bbox* = only check atoms in replicas that overlap with a processor's subdomain + *bbox* = use a bounding-box algorithm which is faster for large proc counts + *bond/periodic* = use an algorithm that correctly replicates periodic bond loops Examples """""""" +For examples of replicating simple linear polymer chains (periodic or +non-periodic) or periodic carbon nanotubes, see examples/replicate. + .. code-block:: LAMMPS replicate 2 3 2 + replicate 2 3 2 bbox + replicate 2 3 2 bond/periodic Description """"""""""" -Replicate the current simulation one or more times in each dimension. -For example, replication factors of 2,2,2 will create a simulation -with 8x as many atoms by doubling the simulation domain in each -dimension. A replication factor of 1 in a dimension leaves the -simulation domain unchanged. When the new simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the :doc:`processors ` command. The -partitioning can later be changed by the :doc:`balance ` or -:doc:`fix balance ` commands. +Replicate the current system one or more times in each dimension. For +example, replication factors of 2,2,2 will create a simulation with 8x +as many atoms by doubling the size of the simulation box in each +dimension. A replication factor of 1 leaves the simulation domain +unchanged in that dimension. -All properties of the atoms are replicated, including their -velocities, which may or may not be desirable. New atom IDs are -assigned to new atoms, as are molecule IDs. Bonds and other topology -interactions are created between pairs of new atoms as well as between -old and new atoms. This is done by using the image flag for each atom -to "unwrap" it out of the periodic box before replicating it. +When the new simulation box is created it is partitioned into a +regular 3d grid of rectangular bricks, one per processor, based on the +number of processors being used and the settings of the +:doc:`processors ` command. The partitioning can be +changed by subsequent :doc:`balance ` or :doc:`fix balance +` commands. -This means that any molecular bond you specify in the original data -file that crosses a periodic boundary should be between two atoms with -image flags that differ by 1. This will allow the bond to be -unwrapped appropriately. +All properties of each atom are replicated (except per-atom fix data, +see the Restrictions section below). This includes their velocities, +which may or may not be desirable. New atom IDs are assigned to new +atoms, as are new molecule IDs. Bonds and other topology interactions +are created between pairs of new atoms as well as between old and new +atoms. -The optional keyword *bbox* uses a bounding box to only check atoms in -replicas that overlap with a processor's subdomain when assigning -atoms to processors. It typically results in a substantial speedup -when using the replicate command on a large number of processors. It -does require temporary use of more memory, specifically that each -processor can store all atoms in the entire system before it is -replicated. +.. note:: + + The bond discussion which follows only refers to models with + permanent covalent bonds typically defined in LAMMPS via a data + file. It is not relevant to systems modeled with many-body + potentials which can define bonds on-the-fly, based on the current + positions of nearby atoms, e.g. models using the :doc:`AIREBO + ` or :doc:`ReaxFF ` potentials. + +If the *bond/periodic* keyword is not specified, bond replication is +done by using the image flag for each atom to "unwrap" it out of the +periodic box before replicating it. After replication is performed, +atoms outside the new periodic box are wrapped back into it. This +assigns correct images flags to all atoms in the system. For this to +work, all original atoms in the original simulation box must have +consistent image flags. This means that if two atoms have a bond +between them which crosses a periodic boundary, their respective image +flags will differ by 1 in that dimension. + +Image flag consistency is not possible if a system has a periodic bond +loop, meaning there is a chain of bonds which crosses an entire +dimension and re-connects to itself across a periodic boundary. In +this case you MUST use the *bond/periodic* keyword to correctly +replicate the system. This option zeroes the image flags for all +atoms and uses a different algorithm to find new (nearby) bond +neighbors in the replicated system. In the final replicated system +all image flags are zero (in each dimension). + +.. note:: + + LAMMPS does not check for image flag consistency before performing + the replication (it does issue a warning about this before a + simulation is run). If the original image flags are inconsistent, + the replicated system will also have inconsistent image flags, but + will otherwise be correctly replicated. This is NOT the case if + there is a periodic bond loop. See the next note. + +.. note:: + + LAMMPS does not check for periodic bond loops. If you use the + *bond/periodic* keyword for a system without periodic bond loops, + the system will be correctly replicated, but image flag information + will be lost (which may or may not be important to your model). If + you do not use the *bond/periodic* keyword for a system with + periodic bond loops, the replicated system will have invalid bonds + (typically very long), resulting in bad dynamics. + +If possible, the *bbox* keyword should be used when running on a large +number of processors, as it can result in a substantial speed-up for +the replication operation. It uses a bounding box to only check atoms +in replicas that overlap with each processor's new subdomain when +assigning atoms to processors. It also preserves image flag +information. The only drawback to the *bbox* option is that it +requires a temporary use of more memory. Each processor must be able +to store all atoms (and their per-atom data) in the original system, +before it is replicated. + +.. note:: + + The algorithm used by the *bond/periodic* keyword builds on the + algorithm used by the *bbox* keyword and thus has the same memory + requirements. If you specify only the *bond/peridoic* keyword it + will internally set the *bbox* keyword as well. + +---------- Restrictions """""""""""" @@ -65,49 +127,30 @@ Restrictions A 2d simulation cannot be replicated in the z dimension. If a simulation is non-periodic in a dimension, care should be used -when replicating it in that dimension, as it may put atoms nearly on -top of each other. - -.. note:: - - You cannot use the replicate command on a system which has a - molecule that spans the box and is bonded to itself across a periodic - boundary, so that the molecule is effectively a loop. A simple - example would be a linear polymer chain that spans the simulation box - and bonds back to itself across the periodic boundary. More realistic - examples would be a CNT (meant to be an infinitely long CNT) or a - graphene sheet or a bulk periodic crystal where there are explicit - bonds specified between near neighbors. (Note that this only applies - to systems that have permanent bonds as specified in the data file. A - CNT that is just atoms modeled with the :doc:`AIREBO potential ` has no such permanent bonds, so it can be - replicated.) The reason replication does not work with those systems - is that the image flag settings described above cannot be made - consistent. I.e. it is not possible to define images flags so that - when every pair of bonded atoms is unwrapped (using the image flags), - they will be close to each other. The only way the replicate command - could work in this scenario is for it to break a bond, insert more - atoms, and re-connect the loop for the larger simulation box. But it - is not clever enough to do this. So you will have to construct a - larger version of your molecule as a pre-processing step and input a - new data file to LAMMPS. +when replicating it in that dimension, as it may generate atoms nearly +on top of each other. If the current simulation was read in from a restart file (before a -run is performed), there must not be any fix information stored in -the file for individual atoms. Similarly, no fixes can be defined at -the time the replicate command is used that require vectors of atom +run is performed), there must not be any fix information stored in the +file for individual atoms. Similarly, no fixes can be defined at the +time the replicate command is used that require vectors of atom information to be stored. This is because the replicate command does not know how to replicate that information for new atoms it creates. -To work around this restriction, restart files may be converted into -data files and fixes may be undefined via the :doc:`unfix ` -command before and redefined after the replicate command. + +To work around this restriction two options are possible. (1) Fixes +which use the stored data in the restart file can be defined before +replication and then deleted via the :doc:`unfix ` command and +re-defined after it. Or (2) the restart file can be converted to a +data file (which deletes the stored fix information) and fixes defined +after the replicate command. In both these scenarios, the per-atom +fix information in the restart file is lost. Related commands """""""""""""""" none - Default """"""" -none +No settings for using the *bbox* or *bond/periodic* algorithms. diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index d2e47c0884..c06cef4296 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -327,10 +327,12 @@ Restrictions """""""""""" The *verlet/split* style can only be used if LAMMPS was built with the -REPLICA package. Correspondingly the *respa/omp* style is available +REPLICA package. Correspondingly the *respa/omp* style is available only if the OPENMP package was included. See the :doc:`Build package -` page for more info. It is not compatible with -kspace styles from the INTEL package. +` page for more info. + +Run style *verlet/split* is not compatible with kspace styles from +the INTEL package and it is not compatible with any TIP4P styles. Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 3d2c19614e..dcbe313508 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -11,7 +11,7 @@ Syntax thermo_modify keyword value ... * one or more keyword/value pairs may be listed -* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press* +* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press* or *triclinic/general* .. parsed-literal:: @@ -32,6 +32,8 @@ Syntax *or* a thermo keyword or reference to compute, fix, property or variable. *temp* value = compute ID that calculates a temperature *press* value = compute ID that calculates a pressure + *triclinic/general* arg = *yes* or *no* + Examples """""""" @@ -240,6 +242,19 @@ command, thermo output uses a default compute for pressure with ID = keyword, then the new pressure compute specified by the *press* keyword will be unaffected by the *temp* setting. +The *triclinic/general* keyword can only be used with a value of *yes* +if the simulation box was created as a general triclinic box. See the +:doc:`Howto_triclinic ` doc page for a detailed +explanation of orthogonal, restricted triclinic, and general triclinic +simulation boxes. + +If this keyword is *yes*, the output of the simulation box edge +vectors and the pressure tensor components for the system are +affected. These are specified by the *avec,bvec,cvec* and +*pxx,pyy,pzz,pxy,pxz,pyz* keywords of the :doc:`thermo_style +` command. See the :doc:`thermo_style ` +doc page for details. + Restrictions """""""""""" none @@ -253,8 +268,9 @@ Default """"""" The option defaults are lost = error, warn = 100, norm = yes for unit -style of *lj*, norm = no for unit style of *real* and *metal*, -flush = no, and temp/press = compute IDs defined by thermo_style. +style of *lj*, norm = no for unit style of *real* and *metal*, flush = +no, temp/press = compute IDs defined by thermo_style, and +triclinic/general = no. The defaults for the line and format options depend on the thermo style. For styles "one" and "custom", the line and format defaults are "one", diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 89a2c0b740..fa90a45b0e 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -25,12 +25,18 @@ Syntax evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail, enthalpy, ecouple, econserve, - vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, - xy, xz, yz, xlat, ylat, zlat, - bonds, angles, dihedrals, impropers, - pxx, pyy, pzz, pxy, pxz, pyz, - fmax, fnorm, nbuild, ndanger, + vol, density, + xlo, xhi, ylo, yhi, zlo, zhi, + xy, xz, yz, + avecx, avecy, avecz, + bvecx, bvecy, bvecz, + cvecx, cvecy, cvecz, + lx, ly, lz, + xlat, ylat, zlat, cella, cellb, cellc, cellalpha, cellbeta, cellgamma, + pxx, pyy, pzz, pxy, pxz, pyz, + bonds, angles, dihedrals, impropers, + fmax, fnorm, nbuild, ndanger, c_ID, c_ID[I], c_ID[I][J], f_ID, f_ID[I], f_ID[I][J], v_name, v_name[I] @@ -66,18 +72,21 @@ Syntax econserve = pe + ke + ecouple = etotal + ecouple vol = volume density = mass density of system - lx,ly,lz = box lengths in x,y,z xlo,xhi,ylo,yhi,zlo,zhi = box boundaries - xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes + xy,xz,yz = box tilt for restricted triclinic (non-orthogonal) simulation boxes + avecx,avecy,avecz = components of edge vector A of the simulation box + bvecx,bvecy,bvecz = components of edge vector B of the simulation box + cvecx,cvecy,cvecz = components of edge vector C of the simulation box + lx,ly,lz = box lengths in x,y,z xlat,ylat,zlat = lattice spacings as calculated by :doc:`lattice ` command - bonds,angles,dihedrals,impropers = # of these interactions defined + cella,cellb,cellc = periodic cell lattice constants a,b,c + cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor + bonds,angles,dihedrals,impropers = # of these interactions defined fmax = max component of force on any atom in any dimension fnorm = length of force vector for all atoms nbuild = # of neighbor list builds ndanger = # of dangerous neighbor list builds - cella,cellb,cellc = periodic cell lattice constants a,b,c - cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma c_ID = global scalar value calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) c_ID[I][J] = I,J component of global array calculated by a compute with ID @@ -102,8 +111,11 @@ Examples Description """"""""""" -Set the style and content for printing thermodynamic data to the screen -and log files. +Set the style and content for printing thermodynamic data to the +screen and log files. The units for each column of output +corresponding to the list of keywords is determined by the :doc:`units +` command for the simulation. E.g. energies will be in energy +units, temperature in temperature units, pressure in pressure units. Style *one* prints a single line of thermodynamic info that is the equivalent of "thermo_style custom step temp epair emol etotal press". @@ -245,7 +257,7 @@ and *pxx*, *pyy*, etc. ---------- Here is more information on other keywords whose meaning may not be -clear: +clear. The *step*, *elapsed*, and *elaplong* keywords refer to timestep count. *Step* is the current timestep, or iteration count when a @@ -319,6 +331,63 @@ thermostatting or barostatting to their coupling reservoirs -- that is, the NVT, NPH, or NPT ensembles, the *econserve* quantity should remain constant over time even though *etotal* may change. +In LAMMPS, the simulation box can be defined as orthogonal or +triclinic (non-orthogonal). See the :doc:`Howto_triclinic +` doc page for a detailed explanation of orthogonal, +restricted triclinic, and general triclinic simulation boxes and how +LAMMPS rotates a general triclinic box to be restricted triclinic +internally. + +The *lx*, *ly*, *lz* keywords are the extent of the simulation box in +each dimension. The *xlo*, *xhi*, *ylo*, *yhi*, *zlo*, *zhi* keywords +are the lower and upper bounds of the simulation box in each dimension. +I.e. *lx* = *xhi* - *xlo*). These 9 values are the same for all 3 kinds +of boxes. I.e. for a restricted triclinic box, they are the values as +if the box were not tilted. For a general triclinic box, they are the +values after it is internally rotated to be a restricted triclinic box. + +The *xy*, *xz*, *yz* are the current tilt factors for a triclinic box. +They are the same for restricted and general triclinic boxes. + +The *avecx*, *avecy*, *avecz*, *bvecx*, *bvecy*, *bvecz*, *cvecx*, +*cvecy*, *cvecz* are the components of the 3 edge vectors of the +current general simulation box. If it is an orthogonal box the +vectors are along the x, y, z coordinate axes. If it is a restricted +triclinic box, the **A** vector is along the x axis, the **B** vector +is in the xy plane with a +y coordinate, and the **C** vector has a +z +coordinate, as explained on the :doc:`Howto_triclinic +` doc page. If the :doc:`thermo_modify +triclinic/general ` option is set then they are the +**A**, **B**, **C** vector which define the general triclinic box. + +The *cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma* +keywords correspond to the usual crystallographic quantities that +define the periodic simulation box of a crystalline system. See the +:doc:`Howto triclinic ` page for a precise definition +of these quantities in terms of the LAMMPS representation of a +restricted triclinic simulation box via *lx*, *ly*, *lz*, *yz*, *xz*, +*xy*\ . + +The *pxx,pyy,pzz,pxy,pxz,pyz* keywords are the 6 components of the +symmetric pressure tensor for the system. See the :doc:`compute +pressure ` command doc page for details of how it is +calculated. + +If the :doc:`thermo_modify triclinic/general ` option +is set then the 6 components will be output as values consistent with +the orientation of the general triclinic box relative to the standard +xyz coordinate axes. If this keyword is not used, the values will be +consistent with the orientation of the restricted triclinic box (which +aligns with the xyz coordinate axes). As explained on the +:doc:`Howto_triclinic ` doc page, even if the +simulation box is created as a general triclinic box, internally +LAMMPS uses a restricted triclinic box. + +Note that because the pressure tensor components are computed using +force vectors and atom coordinates, both of which are rotated in the +general versus restricted triclinic representation, the values will +typically be different for the two cases. + The *fmax* and *fnorm* keywords are useful for monitoring the progress of an :doc:`energy minimization `. The *fmax* keyword calculates the maximum force in any dimension on any atom in the @@ -338,14 +407,6 @@ to reduce the delay factor to ensure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place. -The keywords *cella*, *cellb*, *cellc*, *cellalpha*, -*cellbeta*, *cellgamma*, correspond to the usual crystallographic -quantities that define the periodic unit cell of a crystal. See the -:doc:`Howto triclinic ` page for a geometric -description of triclinic periodic cells, including a precise -definition of these quantities in terms of the internal LAMMPS cell -dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ . - ---------- For output values from a compute or fix or variable, the bracketed diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 1cd96543f5..330e44139e 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -67,7 +67,7 @@ Syntax bound(group,dir,region), gyration(group,region), ke(group,reigon), angmom(group,dim,region), torque(group,dim,region), inertia(group,dimdim,region), omega(group,dim,region) - special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) + special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout() feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id) atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz @@ -279,9 +279,9 @@ This means the variable can then be evaluated as many times as desired and will return those values. There are two ways to cause the next set of per-atom values from the file to be read: use the :doc:`next ` command or the next() function in an atom-style -variable, as discussed below. Unlike most variable styles -atomfile-style variables are **deleted** during a :doc:`clear ` -command. +variable, as discussed below. Unlike most variable styles, which +remain defined, atomfile-style variables are **deleted** during a +:doc:`clear ` command. The rules for formatting the file are as follows. Each time a set of per-atom values is read, a non-blank line is searched for in the file. @@ -289,23 +289,37 @@ The file is read line by line but only up to 254 characters are used. The rest are ignored. A comment character "#" can be used anywhere on a line and all text following and the "#" character are ignored; text starting with the comment character is stripped. Blank lines -are skipped. The first "word" of a non-blank line, delimited by -white-space, is read as the count N of per-atom lines to immediately -follow. N can be the total number of atoms in the system, or only a -subset. The next N lines have the following format - -.. parsed-literal:: - - ID value - -where ID is an atom ID and value is the per-atom numeric value that -will be assigned to that atom. IDs can be listed in any order. +are skipped. The first non-blank line is expected to contain a single +integer number as the count *N* of per-atom lines to follow. *N* can +be the total number of atoms in the system or less, indicating that data +for a subset is read. The next N lines must consist of two numbers, +the atom-ID of the atom for which a value is set followed by a floating +point number with the value. The atom-IDs may be listed in any order. .. note:: - Every time a set of per-atom lines is read, the value for all - atoms is first set to 0.0. Thus values for atoms whose ID does not - appear in the set, will remain 0.0. + Every time a set of per-atom lines is read, the value of the atomfile + variable for **all** atoms is first initialized to 0.0. Thus values + for atoms whose ID do not appear in the set in the file will remain + at 0.0. + +Below is a small example for the atomfile variable file format: + + .. parsed-literal:: + + # first set + 4 + # atom-ID value + 3 1 + 4 -4 + 1 0.5 + 2 -0.5 + + # second set + 2 + + 2 1.0 + 4 -1.0 ---------- @@ -533,7 +547,7 @@ variables. +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) | +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) | +| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout() | +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) | +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ @@ -899,23 +913,27 @@ Special Functions Special functions take specific kinds of arguments, meaning their arguments cannot be formulas themselves. -The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions -each take 1 argument which is of the form "c_ID" or "c_ID[N]" or -"f_ID" or "f_ID[N]" or "v_name". The first two are computes and the -second two are fixes; the ID in the reference should be replaced by -the ID of a compute or fix defined elsewhere in the input script. The -compute or fix must produce either a global vector or array. If it -produces a global vector, then the notation without "[N]" should be -used. If it produces a global array, then the notation with "[N]" -should be used, when N is an integer, to specify which column of the -global array is being referenced. The last form of argument "v_name" -is for a vector-style variable where "name" is replaced by the name of -the variable. +The sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), and +rsort(x) functions each take 1 argument which is of the form "c_ID" or +"c_ID[N]" or "f_ID" or "f_ID[N]" or "v_name". The first two are +computes and the second two are fixes; the ID in the reference should be +replaced by the ID of a compute or fix defined elsewhere in the input +script. The compute or fix must produce either a global vector or +array. If it produces a global vector, then the notation without "[N]" +should be used. If it produces a global array, then the notation with +"[N]" should be used, where N is an integer, to specify which column of +the global array is being referenced. The last form of argument +"v_name" is for a vector-style variable where "name" is replaced by the +name of the variable. -These functions operate on a global vector of inputs and reduce it to -a single scalar value. This is analogous to the operation of the -:doc:`compute reduce ` command, which performs similar -operations on per-atom and local vectors. +The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions +operate on a global vector of inputs and reduce it to a single scalar +value. This is analogous to the operation of the :doc:`compute reduce +` command, which performs similar operations on per-atom +and local vectors. + +The sort(x) and rsort(x) functions operate on a global vector of inputs +and return a global vector of the same length. The sum() function calculates the sum of all the vector elements. The min() and max() functions find the minimum and maximum element @@ -939,6 +957,12 @@ of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2), length N. The returned value is the slope of the line. If the line has a single point or is vertical, it returns 1.0e20. +.. versionadded:: 27June2024 + +The sort(x) and rsort(x) functions sort the data of the input vector by +their numeric value: sort(x) sorts in ascending order, rsort(x) sorts +in descending order. + The gmask(x) function takes 1 argument which is a group ID. It can only be used in atom-style variables. It returns a 1 for atoms that are in the group, and a 0 for atoms that are not. @@ -1018,6 +1042,20 @@ label2type(), but returns 1 if the type label has been assigned, otherwise it returns 0. This function can be used to check if a particular type label already exists in the simulation. +.. versionadded:: TBD + +The is_timeout() function returns 1 when the :doc:`timer timeout +` has expired otherwise it returns 0. This function can be used +to check inputs in combination with the :doc:`if command ` to +execute commands after the timer has expired. Example: + +.. code-block:: LAMMPS + + variable timeout equal is_timeout() + timer timeout 0:10:00 every 10 + run 10000 + if ${timeout} then "print 'Timer has expired'" + ---------- Feature Functions @@ -1174,12 +1212,17 @@ custom atom properties are the same; just replace the leading "i" with +--------+---------------+------------------------------------------+ | equal | i_name[I] | element of per-atom vector (I = atom ID) | ++--------+---------------+------------------------------------------+ | equal | i2_name[I][J] | element of per-atom array (I = atom ID) | +--------+---------------+------------------------------------------+ ++--------+---------------+------------------------------------------+ | vector | i_name[I] | element of per-atom vector (I = atom ID) | ++--------+---------------+------------------------------------------+ | vector | i2_name[I][J] | element of per-atom array (I = atom ID) | +--------+---------------+------------------------------------------+ ++--------+---------------+------------------------------------------+ | atom | i_name | per-atom vector | ++--------+---------------+------------------------------------------+ | atom | i2_name[I] | column of per-atom array | +--------+---------------+------------------------------------------+ @@ -1222,15 +1265,23 @@ table: +--------+------------+------------------------------------------+ | equal | c_ID | global scalar | ++--------+------------+------------------------------------------+ | equal | c_ID[I] | element of global vector | ++--------+------------+------------------------------------------+ | equal | c_ID[I][J] | element of global array | ++--------+------------+------------------------------------------+ | equal | C_ID[I] | element of per-atom vector (I = atom ID) | ++--------+------------+------------------------------------------+ | equal | C_ID[I][J] | element of per-atom array (I = atom ID) | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | vector | c_ID | global vector | ++--------+------------+------------------------------------------+ | vector | c_ID[I] | column of global array | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | atom | c_ID | per-atom vector | ++--------+------------+------------------------------------------+ | atom | c_ID[I] | column of per-atom array | +--------+------------+------------------------------------------+ @@ -1286,15 +1337,23 @@ and atom-style variables are listed in the following table: +--------+------------+------------------------------------------+ | equal | f_ID | global scalar | ++--------+------------+------------------------------------------+ | equal | f_ID[I] | element of global vector | ++--------+------------+------------------------------------------+ | equal | f_ID[I][J] | element of global array | ++--------+------------+------------------------------------------+ | equal | F_ID[I] | element of per-atom vector (I = atom ID) | ++--------+------------+------------------------------------------+ | equal | F_ID[I][J] | element of per-atom array (I = atom ID) | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | vector | f_ID | global vector | ++--------+------------+------------------------------------------+ | vector | f_ID[I] | column of global array | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | atom | f_ID | per-atom vector | ++--------+------------+------------------------------------------+ | atom | f_ID[I] | column of per-atom array | +--------+------------+------------------------------------------+ @@ -1365,17 +1424,27 @@ per-atom vector. +--------+-----------+-----------------------------------------------------------------------------------+ | equal | v_name | global scalar from an equal-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | equal | v_name[I] | element of global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | equal | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable | +--------+-----------+-----------------------------------------------------------------------------------+ ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name | global scalar from an equal-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name | global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name[I] | element of global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable | +--------+-----------+-----------------------------------------------------------------------------------+ ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name | global scalar from an equal-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name | per-atom vector from an atom-style or atomfile-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name[I] | element of global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable | +--------+-----------+-----------------------------------------------------------------------------------+ diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index c598ebe481..e1e5b04953 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -12,13 +12,14 @@ Syntax * file = name of data file to write out * zero or more keyword/value pairs may be appended -* keyword = *pair* or *nocoeff* or *nofix* or *nolabelmap* +* keyword = *nocoeff* or *nofix* or *nolabelmap* or *triclinic/general* or *types* or *pair* .. parsed-literal:: *nocoeff* = do not write out force field info *nofix* = do not write out extra sections read by fixes *nolabelmap* = do not write out type labels + *triclinic/general* = write data file in general triclinic format *types* value = *numeric* or *labels* *pair* value = *ii* or *ij* *ii* = write one line of pair coefficient info per atom type @@ -31,6 +32,7 @@ Examples write_data data.polymer write_data data.* + write_data data.solid triclinic/general Description """"""""""" @@ -85,10 +87,11 @@ using the :doc:`-r command-line switch `. :doc:`fixes ` are stored. :doc:`Binary restart files ` store more information. -Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake ` or :doc:`delete_bonds ` command will -be written to a data file as if they are turned on. This means they -will need to be turned off again in a new run after the data file is -read. +Bond interactions (angle, etc) that have been turned off by the +:doc:`fix shake ` or :doc:`delete_bonds ` +command will be written to a data file as if they are turned on. This +means they will need to be turned off again in a new run after the +data file is read. Bonds that are broken (e.g. by a bond-breaking potential) are not written to the data file. Thus these bonds will not exist when the @@ -122,6 +125,23 @@ not written to the data file. By default, they are written if they exist. A type label must be defined for every numeric type (within a given type-kind) to be written to the data file. +Use of the *triclinic/general* keyword will output a data file which +specifies a general triclinic simulation box as well as per-atom +quantities consistent with the general triclinic box. The latter means +that per-atom vectors, such as velocities and dipole moments will be +oriented consistent with the 3d rotation implied by the general +triclinic box (relative to the associated restricted triclinic box). + +This option can only be requested if the simulation box was initially +defined to be general triclinic. If if was and the +*triclinic/general* keyword is not used, then the data file will +specify a restricted triclinic box, since that is the internal format +LAMMPS uses for both general and restricted triclinic simulations. +See the :doc:`Howto triclinic ` doc page for more +explanation of how general triclinic simulation boxes are supported by +LAMMPS. And see the :doc:`read_data ` doc page for details +of how the format is altered for general triclinic data files. + The *types* keyword determines how atom types, bond types, angle types, etc are written into these data file sections: Atoms, Bonds, Angles, etc. The default is the *numeric* setting, even if type label @@ -169,4 +189,4 @@ Related commands Default """"""" -The option defaults are pair = ii and types_style = numeric. +The option defaults are pair = ii and types = numeric. diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index a35adffe56..6205f24faf 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -55,21 +55,22 @@ alter the number of files written. Restart files can be read by a :doc:`read_restart ` command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on -another machine. In this case, you can use the :doc:`-r command-line switch ` to convert a restart file to a data file. +another machine. In this case, you can use the :doc:`-r command-line +switch ` to convert a restart file to a data file. .. note:: Although the purpose of restart files is to enable restarting a simulation from where it left off, not all information about a - simulation is stored in the file. For example, the list of fixes that - were specified during the initial run is not stored, which means the - new input script must specify any fixes you want to use. Even when - restart information is stored in the file, as it is for some fixes, - commands may need to be re-specified in the new input script, in order - to re-use that information. Details are usually given in the - documentation of the respective command. Also, see the - :doc:`read_restart ` command for general information about - what is stored in a restart file. + simulation is stored in the file. For example, the list of fixes + that were specified during the initial run is not stored, which + means the new input script must specify any fixes you want to use. + Even when restart information is stored in the file, as it is for + some fixes, commands may need to be re-specified in the new input + script, in order to re-use that information. Details are usually + given in the documentation of the respective command. Also, see the + :doc:`read_restart ` command for general information + about what is stored in a restart file. ---------- diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index 5bb8e3911d..83d4999dd7 100644 --- a/doc/utils/requirements.txt +++ b/doc/utils/requirements.txt @@ -1,6 +1,7 @@ Sphinx >= 5.3.0, <8.0 sphinxcontrib-spelling sphinxcontrib-jquery +sphinx-design git+https://github.com/akohlmey/sphinx-fortran@parallel-read sphinx-tabs>=3.4.1 breathe diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index c0805ba6b1..337485e689 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -57,6 +57,7 @@ extensions = [ 'table_from_list', 'tab_or_note', 'breathe', + 'sphinx_design' ] images_config = { diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 030c80d30c..c300cf608d 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -50,6 +50,7 @@ agilio Agilio agni Agnolin +ahi Ahrens Ai Aidan @@ -86,6 +87,7 @@ allocator allocators allosws AlO +alo Alonso Alperen alphak @@ -187,6 +189,10 @@ automagically Auvergne Avalos avalue +avec +avecx +avecy +avecz aveforce Avendano Averett @@ -194,11 +200,14 @@ avi AVX awpmd AWPMD +ax Axel Axilrod Ay +ay Ayton Az +az Azevedo azimuthal Azuri @@ -271,6 +280,7 @@ Bext Bfrac bgq Bh +bhi Bialke biaxial bicrystal @@ -307,6 +317,7 @@ Bkappa blabel Blaise blanchedalmond +blo blocksize blueviolet bn @@ -380,12 +391,17 @@ btype buckPlusAttr buf builtin +Bulacu Bulatov Bureekaew burlywood Bussi Buturigakkwaishi Buyl +bvec +bvecx +bvecy +bvecz Bybee bz Cadarache @@ -476,6 +492,7 @@ ChiralIDs chirality Cho Chodera +Choi ChooseOffset chris Christoph @@ -617,6 +634,7 @@ cstdlib cstring cstyle csvr +ctilde ctrl ctrn ctypes @@ -648,14 +666,21 @@ cv Cv Cval cvar +cvec +cvecx +cvecy +cvecz cvff cwiggle +cx +cy cygwin Cygwin cylindrically Cyrot cyrstals cython +cz Daivis Dammak dampflag @@ -947,6 +972,7 @@ elastance Electroneg electronegative electronegativity +electroneutral electroneutrality Eleftheriou ElementN @@ -966,6 +992,7 @@ emax Emax Embt emi +Emilie Emmrich emol eN @@ -1146,6 +1173,7 @@ finitecutflag Finnis Fiorin fitpod +fivebody fixID fj Fji @@ -1301,6 +1329,7 @@ gmres gname gneb GNEB +Goga Goldfarb Gompper Gonzalez-Melchor @@ -1406,6 +1435,7 @@ Hendrik Henin Henkelman Henkes +Hennig henrich Henrich Hermitian @@ -1478,6 +1508,7 @@ hydroxyl Hynninen Hyoungki hyperdynamics +hyperparameters hyperplane hyperradius hyperspherical @@ -1566,6 +1597,7 @@ interlayer intermolecular interoperable Interparticle +interpretable interstitials intertube Intr @@ -1704,6 +1736,7 @@ Kalia Kamberaj Kantorovich Kapfer +Kapil Karhunen Karls Karlsruhe @@ -1735,8 +1768,10 @@ keflag Keir Kelchner Kelkar +Kemppainen Kemper kepler +Kemppainen keV Keyes keyfile @@ -1785,6 +1820,7 @@ Koziol Kp kradius Kraker +Krass Kraus Kremer Kress @@ -2039,6 +2075,7 @@ Makefiles makelist makepkg Makse +Malavasi malloc Malolepsza Manby @@ -2148,6 +2185,7 @@ membered memcheck Mendelev Menon +Menziani mer Meremianin Mersenne @@ -2258,6 +2296,7 @@ Montalenti Monterey Montero Monti +Monticelli Mora Morefoo Morfill @@ -2452,6 +2491,7 @@ Nevery newfile Newns newtype +nextsort Neyts Nf nfft @@ -2641,6 +2681,7 @@ nzlo ocl octahedral octants +Odegard Ohara O'Hearn ohenrich @@ -2685,6 +2726,9 @@ organometallic orientational orientationsFile orientorder +originx +originy +originz Orlikowski ornl Ornstein @@ -2728,6 +2772,7 @@ papayawhip paquay Paquay parallelepiped +parallelepipeds Parallelizable parallelization parallelized @@ -2771,6 +2816,8 @@ Peachey peachpuff Pearlman Pedersen +pedone +Pedone peID PEigenDense Peng @@ -2784,6 +2831,7 @@ peridynamic Peridynamic peridynamics Peridynamics +Periole perl permittivity perp @@ -2850,6 +2898,7 @@ Pmolrotate Pmoltrans pN png +podd Podhorszki Poiseuille poisson @@ -2915,6 +2964,7 @@ Priya proc Proc procs +procgrid progguide Prony ps @@ -3199,6 +3249,7 @@ Ronevich Rosati Rosato Rosenberger +Rossi Rossky rosybrown rotationally @@ -3213,6 +3264,7 @@ rRESPA Rsi Rso Rspace +rsort rsq rst rstyle @@ -3225,6 +3277,7 @@ Rudranarayan Rudzinski Runge runtime +Rupp Rutuparna rx rxd @@ -3248,6 +3301,7 @@ Saidi saip Salanne Salles +sametag sandia Sandia sandybrown @@ -3318,6 +3372,7 @@ setmask Setmask setpoint setvel +sevenbody sfftw sfree Sg @@ -3365,8 +3420,10 @@ sinh sinusoid sinusoidally SiO +Siochi Sirk Sival +sixbody sizeI sizeJ sizex @@ -3412,6 +3469,7 @@ solvated solvation someuser Sorensen +sortfreq soundspeed sourceforge Souza @@ -3642,6 +3700,7 @@ thrid ThunderX thylakoid THz +Tieleman Tigran Tij Tildesley @@ -3680,7 +3739,6 @@ tokyo tol tomic toolchain -toolset topologies Toporov Torder @@ -3758,6 +3816,7 @@ typeJ typelabel typeN typesafe +typestr Tz Tzou ub @@ -3770,6 +3829,8 @@ uChem uCond uef UEF +uf +uf3 ufm Uhlenbeck Ui @@ -4109,6 +4170,7 @@ yy yz Zagaceta Zannoni +Zavada Zavattieri zbl ZBL @@ -4122,6 +4184,7 @@ zenodo Zepeda zflag Zhang +Zhao Zhen zhi Zhigilei diff --git a/examples/COUPLE/plugin/liblammpsplugin.c b/examples/COUPLE/plugin/liblammpsplugin.c index 011c320254..81dcf2cd50 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.c +++ b/examples/COUPLE/plugin/liblammpsplugin.c @@ -101,6 +101,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(extract_setting); ADDSYM(extract_global_datatype); ADDSYM(extract_global); + ADDSYM(map_atom); ADDSYM(extract_atom_datatype); ADDSYM(extract_atom); diff --git a/examples/COUPLE/plugin/liblammpsplugin.h b/examples/COUPLE/plugin/liblammpsplugin.h index 1d647e8e93..ea00277083 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.h +++ b/examples/COUPLE/plugin/liblammpsplugin.h @@ -146,6 +146,7 @@ struct _liblammpsplugin { int (*extract_setting)(void *, const char *); int *(*extract_global_datatype)(void *, const char *); void *(*extract_global)(void *, const char *); + void *(*map_atom)(void *, const void *); int *(*extract_atom_datatype)(void *, const char *); void *(*extract_atom)(void *, const char *); diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/data.duplex1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex1/data.duplex1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/data.duplex1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/in.duplex1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/in.duplex1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/data.duplex2 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex2/data.duplex2 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/data.duplex2 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/in.duplex2 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/in.duplex2 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/data.duplex1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/data.duplex1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/data.duplex1 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/in.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/in.duplex1 new file mode 100644 index 0000000000..64d3cd0adf --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/in.duplex1 @@ -0,0 +1,70 @@ +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + +set atom * mass 3.1575 + +group all type 1 4 + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * oxdna_lj.cgdna +special_bonds lj 0 1 1 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv oxdna_lj.cgdna +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna +pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna +pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna +pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna +pair_coeff * * oxdna/xstk oxdna_lj.cgdna +pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/log.19May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/log.19May24.duplex1.g++.1 new file mode 100644 index 0000000000..6bee219ed2 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/log.19May24.duplex1.g++.1 @@ -0,0 +1,1113 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.005 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna.lj with DATE: 2024-04-21 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (stk) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (xstk) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (coaxstk) file oxdna.lj with DATE: 2024-04-21 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.9560004 + ghost atom cutoff = 3.8 + binsize = 1.4780002, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 1e-05 +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -13.0576219534369 | etot = -9.13334913094246 +Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3488546 0.043092397 -1.1949086 -4.6816211e-05 64000 +1000 ekin = 1.08024346604046 | erot = 2.90873406534668 | epot = -13.1223266626202 | etot = -9.13334913123308 +2000 ekin = 1.05028450914437 | erot = 2.98006324808558 | epot = -13.1636968886591 | etot = -9.13334913142915 +3000 ekin = 1.01964458529397 | erot = 3.02592193798632 | epot = -13.1789156547658 | etot = -9.13334913148547 +4000 ekin = 0.989515033089539 | erot = 3.04428486059471 | epot = -13.1671490250724 | etot = -9.13334913138813 +5000 ekin = 0.961283929687833 | erot = 3.03510855539557 | epot = -13.1297416162282 | etot = -9.1333491311448 +6000 ekin = 0.936412193404256 | erot = 3.00022299571975 | epot = -13.0699843199583 | etot = -9.13334913083425 +7000 ekin = 0.916233699107968 | erot = 2.9427713444016 | epot = -12.9923541739966 | etot = -9.13334913048708 +8000 ekin = 0.901760662506268 | erot = 2.86671228744164 | epot = -12.9018220800865 | etot = -9.13334913013854 +9000 ekin = 0.893571390067878 | erot = 2.77649686780604 | epot = -12.8034173876806 | etot = -9.13334912980663 +10000 ekin = 0.891805685056846 | erot = 2.67686855006733 | epot = -12.7020233645915 | etot = -9.13334912946735 +11000 ekin = 0.896243557993589 | erot = 2.57266042063118 | epot = -12.6022531078194 | etot = -9.13334912919463 +12000 ekin = 0.906416039154816 | erot = 2.46827537271555 | epot = -12.5080405408347 | etot = -9.13334912896432 +13000 ekin = 0.92170409177849 | erot = 2.36760645470833 | epot = -12.4226596752787 | etot = -9.13334912879187 +14000 ekin = 0.941405275130076 | erot = 2.27374941641175 | epot = -12.3485038202328 | etot = -9.13334912869097 +15000 ekin = 0.964770892951774 | erot = 2.18876720165113 | epot = -12.2868872232635 | etot = -9.1333491286606 +16000 ekin = 0.991029016801085 | erot = 2.11380018376645 | epot = -12.2381783292304 | etot = -9.13334912866287 +17000 ekin = 1.01940907375712 | erot = 2.04893605182119 | epot = -12.2016942543554 | etot = -9.13334912877713 +18000 ekin = 1.04917923728265 | erot = 1.99335017578102 | epot = -12.1758785419804 | etot = -9.13334912891671 +19000 ekin = 1.07969247848165 | erot = 1.94569933362972 | epot = -12.158740941176 | etot = -9.13334912906464 +20000 ekin = 1.11043268152286 | erot = 1.90411175657085 | epot = -12.1478935672811 | etot = -9.13334912918742 +21000 ekin = 1.14104909735584 | erot = 1.86695882979252 | epot = -12.1413570564146 | etot = -9.13334912926621 +22000 ekin = 1.171368218481 | erot = 1.83313674901907 | epot = -12.1378540967919 | etot = -9.13334912929187 +23000 ekin = 1.20137634097694 | erot = 1.80222523558988 | epot = -12.1369507058331 | etot = -9.13334912926625 +24000 ekin = 1.23117249622901 | erot = 1.77451266102198 | epot = -12.1390342864515 | etot = -9.13334912920046 +25000 ekin = 1.26089526640646 | erot = 1.75088411697602 | epot = -12.1451285124968 | etot = -9.13334912911432 +26000 ekin = 1.29063712254633 | erot = 1.73259428379513 | epot = -12.1565805353675 | etot = -9.13334912902604 +27000 ekin = 1.32035987087031 | erot = 1.72114061671182 | epot = -12.174849616541 | etot = -9.13334912895886 +28000 ekin = 1.349804606588 | erot = 1.71795709927862 | epot = -12.2011108348018 | etot = -9.13334912893516 +29000 ekin = 1.37841624051165 | erot = 1.72414013785746 | epot = -12.2359055073441 | etot = -9.13334912897504 +30000 ekin = 1.40529015727357 | erot = 1.74019656639673 | epot = -12.2788358527638 | etot = -9.13334912909354 +31000 ekin = 1.42915801743401 | erot = 1.76583252336954 | epot = -12.3283396701 | etot = -9.13334912929648 +32000 ekin = 1.44843712560546 | erot = 1.79982181745345 | epot = -12.3816080726339 | etot = -9.13334912957502 +33000 ekin = 1.46136904668685 | erot = 1.84000474140077 | epot = -12.4347229179884 | etot = -9.13334912990075 +34000 ekin = 1.4662594078552 | erot = 1.88346459856621 | epot = -12.4830731366474 | etot = -9.13334913022599 +35000 ekin = 1.46179739484312 | erot = 1.92688889524942 | epot = -12.5220354205851 | etot = -9.1333491304926 +36000 ekin = 1.44738855724081 | erot = 1.96705754746498 | epot = -12.5477952353503 | etot = -9.13334913064453 +37000 ekin = 1.42340054468554 | erot = 2.00129614949928 | epot = -12.5580458249024 | etot = -9.13334913071753 +38000 ekin = 1.39122781542986 | erot = 2.02761655303766 | epot = -12.5521934990546 | etot = -9.13334913058709 +39000 ekin = 1.35313842096822 | erot = 2.04547852103605 | epot = -12.5319660723435 | etot = -9.13334913033923 +40000 ekin = 1.31193587699368 | erot = 2.05554364627561 | epot = -12.5008286533154 | etot = -9.1333491300461 +41000 ekin = 1.27054093924549 | erot = 2.05894429581373 | epot = -12.4628343648331 | etot = -9.13334912977385 +42000 ekin = 1.23161000992333 | erot = 2.0569489325571 | epot = -12.4219080720067 | etot = -9.13334912952632 +43000 ekin = 1.197239697595 | erot = 2.0508575807566 | epot = -12.3814464076994 | etot = -9.13334912934785 +44000 ekin = 1.16880185864005 | erot = 2.0417223836063 | epot = -12.3438733714903 | etot = -9.13334912924393 +45000 ekin = 1.14690787175727 | erot = 2.03029950061775 | epot = -12.3105565015798 | etot = -9.13334912920477 +46000 ekin = 1.13147919636059 | erot = 2.01712256175377 | epot = -12.2819508873242 | etot = -9.13334912920983 +47000 ekin = 1.1218930049273 | erot = 2.00264798837259 | epot = -12.257890122535 | etot = -9.13334912923509 +48000 ekin = 1.11716788112736 | erot = 1.98739120721195 | epot = -12.2379082176345 | etot = -9.1333491292952 +49000 ekin = 1.11615794795258 | erot = 1.97187368108376 | epot = -12.2213807583349 | etot = -9.13334912929852 +50000 ekin = 1.11772326336409 | erot = 1.95708534394627 | epot = -12.2081577365825 | etot = -9.13334912927216 +51000 ekin = 1.12084924497886 | erot = 1.94437394210217 | epot = -12.1985723162996 | etot = -9.13334912921861 +52000 ekin = 1.12470549785263 | erot = 1.93529800314869 | epot = -12.1933526301508 | etot = -9.13334912914952 +53000 ekin = 1.12864556674986 | erot = 1.93145365271658 | epot = -12.1934483485496 | etot = -9.13334912908316 +54000 ekin = 1.13216113523098 | erot = 1.934302748755 | epot = -12.199813013012 | etot = -9.13334912902602 +55000 ekin = 1.13481106600243 | erot = 1.94490436967235 | epot = -12.213064564702 | etot = -9.13334912902726 +56000 ekin = 1.13614343535825 | erot = 1.96361884590779 | epot = -12.233111410353 | etot = -9.13334912908696 +57000 ekin = 1.13563178311291 | erot = 1.99002978527238 | epot = -12.2590106975985 | etot = -9.13334912921317 +58000 ekin = 1.13263976908255 | erot = 2.02286978616489 | epot = -12.2888586846525 | etot = -9.13334912940509 +59000 ekin = 1.12642426113443 | erot = 2.060044134417 | epot = -12.3198175252028 | etot = -9.13334912965135 +60000 ekin = 1.11618536041545 | erot = 2.09876774945537 | epot = -12.3483022398004 | etot = -9.13334912992961 +61000 ekin = 1.10116810417879 | erot = 2.13581434618261 | epot = -12.3703315805683 | etot = -9.13334913020688 +62000 ekin = 1.08081637521816 | erot = 2.16786879318294 | epot = -12.3820342988433 | etot = -9.13334913044215 +63000 ekin = 1.05497014428163 | erot = 2.19194503254428 | epot = -12.3802643074575 | etot = -9.13334913063164 +64000 ekin = 1.0240860160317 | erot = 2.20562384873122 | epot = -12.3630589954179 | etot = -9.13334913065501 +65000 ekin = 0.989434415807808 | erot = 2.20769180278649 | epot = -12.3304753491251 | etot = -9.13334913053076 +66000 ekin = 0.953195593563941 | erot = 2.19842250482619 | epot = -12.2849672286538 | etot = -9.13334913026364 +67000 ekin = 0.918366365968281 | erot = 2.17942400884171 | epot = -12.2311395047047 | etot = -9.13334912989468 +68000 ekin = 0.888467814666263 | erot = 2.15321364358189 | epot = -12.1750305877199 | etot = -9.13334912947174 +69000 ekin = 0.867150037001592 | erot = 2.1228863370436 | epot = -12.1233855031206 | etot = -9.13334912907539 +70000 ekin = 0.857579951604684 | erot = 2.09151913845136 | epot = -12.0824482188428 | etot = -9.13334912878676 +71000 ekin = 0.861815425267379 | erot = 2.06157004239544 | epot = -12.0567345963616 | etot = -9.1333491286988 +72000 ekin = 0.880191815685361 | erot = 2.03435275439347 | epot = -12.0478936988729 | etot = -9.13334912879405 +73000 ekin = 0.911201453876568 | erot = 2.00982694750386 | epot = -12.0543775304376 | etot = -9.13334912905722 +74000 ekin = 0.951849895585039 | erot = 1.98685418272612 | epot = -12.0720532077343 | etot = -9.13334912942315 +75000 ekin = 0.998151008641185 | erot = 1.96362530027594 | epot = -12.0951254387262 | etot = -9.13334912980909 +76000 ekin = 1.04581734271591 | erot = 1.93821700241349 | epot = -12.1173834752669 | etot = -9.13334913013746 +77000 ekin = 1.09091996835708 | erot = 1.90910715282282 | epot = -12.1333762515352 | etot = -9.13334913035526 +78000 ekin = 1.13037631927927 | erot = 1.87551578135384 | epot = -12.139241231075 | etot = -9.13334913044189 +79000 ekin = 1.16219588597798 | erot = 1.8375058018326 | epot = -12.1330508182184 | etot = -9.13334913040778 +80000 ekin = 1.18548972632247 | erot = 1.79585942669989 | epot = -12.1146982833063 | etot = -9.13334913028394 +81000 ekin = 1.20030605718972 | erot = 1.75181365939749 | epot = -12.0854688466957 | etot = -9.13334913010848 +82000 ekin = 1.20737786492213 | erot = 1.70676694760221 | epot = -12.047493942439 | etot = -9.1333491299147 +83000 ekin = 1.2078605140209 | erot = 1.66205278152632 | epot = -12.0032624252718 | etot = -9.13334912972458 +84000 ekin = 1.20310991572493 | erot = 1.61882913247322 | epot = -11.9552881777461 | etot = -9.13334912954799 +85000 ekin = 1.19452073297182 | erot = 1.5780804300242 | epot = -11.905950292382 | etot = -9.13334912938601 +86000 ekin = 1.18342100682573 | erot = 1.54069268896239 | epot = -11.8574628250236 | etot = -9.13334912923547 +87000 ekin = 1.17100858957359 | erot = 1.50755090689522 | epot = -11.8119086255618 | etot = -9.13334912909303 +88000 ekin = 1.15831377551695 | erot = 1.47961680456726 | epot = -11.7712797090418 | etot = -9.13334912895759 +89000 ekin = 1.14617682817411 | erot = 1.457963781289 | epot = -11.7374897382939 | etot = -9.13334912883077 +90000 ekin = 1.13523447969431 | erot = 1.44376438030035 | epot = -11.712347988711 | etot = -9.13334912871638 +91000 ekin = 1.12591345720559 | erot = 1.43823772500959 | epot = -11.6975003108348 | etot = -9.13334912861964 +92000 ekin = 1.11843099489294 | erot = 1.44256930748531 | epot = -11.6943494309247 | etot = -9.13334912854649 +93000 ekin = 1.11280329634823 | erot = 1.457815248145 | epot = -11.7039676729954 | etot = -9.13334912850221 +94000 ekin = 1.10886209127347 | erot = 1.48480045701892 | epot = -11.7270116767845 | etot = -9.13334912849208 +95000 ekin = 1.10627886010347 | erot = 1.5239622064756 | epot = -11.7635901951108 | etot = -9.13334912853173 +96000 ekin = 1.10459509814429 | erot = 1.57519859223443 | epot = -11.8131428189846 | etot = -9.13334912860591 +97000 ekin = 1.1032594376991 | erot = 1.63800664193819 | epot = -11.8746152083619 | etot = -9.13334912872459 +98000 ekin = 1.10166959581649 | erot = 1.71130689804988 | epot = -11.946325622754 | etot = -9.13334912888766 +99000 ekin = 1.09921849385165 | erot = 1.79339905630377 | epot = -12.0259666792472 | etot = -9.1333491290918 +100000 ekin = 1.09534596880107 | erot = 1.88196872528585 | epot = -12.1106638234162 | etot = -9.13334912932927 +101000 ekin = 1.08959720755117 | erot = 1.97415616931463 | epot = -12.197102506452 | etot = -9.13334912958621 +102000 ekin = 1.08168751154814 | erot = 2.06670282185183 | epot = -12.2817394632425 | etot = -9.13334912984254 +103000 ekin = 1.07156932342311 | erot = 2.15618192508065 | epot = -12.3611003785772 | etot = -9.13334913007339 +104000 ekin = 1.05949237996068 | erot = 2.23930158373566 | epot = -12.4321430939484 | etot = -9.13334913025201 +105000 ekin = 1.04604342224872 | erot = 2.31323902285842 | epot = -12.4926315754928 | etot = -9.1333491303857 +106000 ekin = 1.03224316318554 | erot = 2.37579242095975 | epot = -12.541384714564 | etot = -9.13334913041871 +107000 ekin = 1.01951120148926 | erot = 2.42585603740555 | epot = -12.5787163692799 | etot = -9.13334913038511 +108000 ekin = 1.00875017477202 | erot = 2.46348952984478 | epot = -12.6055888348731 | etot = -9.13334913025634 +109000 ekin = 1.00109573552388 | erot = 2.48980806114952 | epot = -12.6242529267274 | etot = -9.13334913005404 +110000 ekin = 0.997931591358029 | erot = 2.50673918610782 | epot = -12.6380199072771 | etot = -9.13334912981121 +111000 ekin = 1.00076792351311 | erot = 2.51665915373025 | epot = -12.6507762068071 | etot = -9.13334912956377 +112000 ekin = 1.01109610479917 | erot = 2.52200701599638 | epot = -12.6664522501387 | etot = -9.13334912934312 +113000 ekin = 1.03019016817874 | erot = 2.52496101252873 | epot = -12.6885003099858 | etot = -9.13334912927836 +114000 ekin = 1.05821017520618 | erot = 2.52722573627506 | epot = -12.7187850407013 | etot = -9.13334912922008 +115000 ekin = 1.09472530400135 | erot = 2.53003930448821 | epot = -12.758113737719 | etot = -9.13334912922949 +116000 ekin = 1.13884650903327 | erot = 2.53414832430443 | epot = -12.8063439626437 | etot = -9.13334912930599 +117000 ekin = 1.18909444999481 | erot = 2.53980839277131 | epot = -12.8622519722148 | etot = -9.13334912944873 +118000 ekin = 1.24341490970474 | erot = 2.54678348242636 | epot = -12.9235475217869 | etot = -9.13334912965575 +119000 ekin = 1.29923662064194 | erot = 2.55432909401013 | epot = -12.986914844573 | etot = -9.13334912992098 +120000 ekin = 1.35358959215651 | erot = 2.56118615921801 | epot = -13.0481248816038 | etot = -9.1333491302293 +121000 ekin = 1.40329803815458 | erot = 2.56563135861663 | epot = -13.1022785273256 | etot = -9.13334913055438 +122000 ekin = 1.44524692196622 | erot = 2.56562448409229 | epot = -13.1442205369175 | etot = -9.13334913085895 +123000 ekin = 1.4766954080484 | erot = 2.55906317998206 | epot = -13.1691077191312 | etot = -9.1333491311007 +124000 ekin = 1.49558302658171 | erot = 2.54411105943722 | epot = -13.1730432172613 | etot = -9.13334913124241 +125000 ekin = 1.50076122489749 | erot = 2.51952798471309 | epot = -13.1536383408714 | etot = -9.13334913126079 +126000 ekin = 1.49214728684723 | erot = 2.4851593310352 | epot = -13.1106557490374 | etot = -9.13334913115499 +127000 ekin = 1.47053410713964 | erot = 2.44174480075129 | epot = -13.0456280388476 | etot = -9.13334913095664 +128000 ekin = 1.43743445323513 | erot = 2.39059049317552 | epot = -12.9613740770759 | etot = -9.13334913066526 +129000 ekin = 1.3950110970706 | erot = 2.33380120125824 | epot = -12.8621614286436 | etot = -9.13334913031473 +130000 ekin = 1.34584042016758 | erot = 2.27401545397182 | epot = -12.7532050040793 | etot = -9.13334912993989 +131000 ekin = 1.29268930786596 | erot = 2.2141013411123 | epot = -12.6401397785508 | etot = -9.13334912957252 +132000 ekin = 1.2383231561683 | erot = 2.15686384200892 | epot = -12.5285361274154 | etot = -9.13334912923819 +133000 ekin = 1.18535267681206 | erot = 2.10479906741765 | epot = -12.4235008731853 | etot = -9.13334912895557 +134000 ekin = 1.13612155562825 | erot = 2.05991346428636 | epot = -12.3293841486506 | etot = -9.13334912873599 +135000 ekin = 1.09263262326068 | erot = 2.02360952444373 | epot = -12.2495912762906 | etot = -9.13334912858618 +136000 ekin = 1.05650575788366 | erot = 1.99662030668691 | epot = -12.1864751930782 | etot = -9.13334912850765 +137000 ekin = 1.02895878679478 | erot = 1.97899212834894 | epot = -12.1413000436435 | etot = -9.13334912849981 +138000 ekin = 1.0108038899587 | erot = 1.97013512172241 | epot = -12.1142881402334 | etot = -9.13334912855233 +139000 ekin = 1.0024545939537 | erot = 1.96888144460883 | epot = -12.1046851672405 | etot = -9.13334912867798 +140000 ekin = 1.00393780740644 | erot = 1.97333010973461 | epot = -12.110617046003 | etot = -9.13334912886192 +141000 ekin = 1.01490973367059 | erot = 1.98104530944803 | epot = -12.1293041722138 | etot = -9.13334912909522 +142000 ekin = 1.03468044934444 | erot = 1.98917872502442 | epot = -12.1572083037338 | etot = -9.13334912936495 +143000 ekin = 1.06225104646203 | erot = 1.99463134790795 | epot = -12.1902315240234 | etot = -9.1333491296534 +144000 ekin = 1.09636709127279 | erot = 1.9944122031841 | epot = -12.2241284243806 | etot = -9.13334912992374 +145000 ekin = 1.1355904536215 | erot = 1.98572590466022 | epot = -12.2546654884645 | etot = -9.13334913018273 +146000 ekin = 1.1783885412212 | erot = 1.96612892354273 | epot = -12.2778665951537 | etot = -9.13334913038977 +147000 ekin = 1.22300699749208 | erot = 1.93405129394994 | epot = -12.2904074219631 | etot = -9.13334913052107 +148000 ekin = 1.26785677863045 | erot = 1.88891621350862 | epot = -12.2901221226999 | etot = -9.13334913056081 +149000 ekin = 1.31170551487325 | erot = 1.83123494690888 | epot = -12.2762895922886 | etot = -9.13334913050644 +150000 ekin = 1.35361858091221 | erot = 1.76263607509631 | epot = -12.2496037863729 | etot = -9.13334913036435 +151000 ekin = 1.39299848911448 | erot = 1.68572491420626 | epot = -12.2120725334744 | etot = -9.13334913015366 +152000 ekin = 1.42958376961927 | erot = 1.60381549112353 | epot = -12.1667483906421 | etot = -9.13334912989935 +153000 ekin = 1.46340801747606 | erot = 1.52060159601926 | epot = -12.1173587431247 | etot = -9.13334912962937 +154000 ekin = 1.4947265022457 | erot = 1.43981503875283 | epot = -12.0678906703689 | etot = -9.13334912937039 +155000 ekin = 1.52392161825085 | erot = 1.36491657683223 | epot = -12.0221873242284 | etot = -9.13334912914536 +156000 ekin = 1.55140022159557 | erot = 1.29884972381831 | epot = -11.9835990743855 | etot = -9.13334912897165 +157000 ekin = 1.57749707056585 | erot = 1.24387068637234 | epot = -11.9547168857973 | etot = -9.13334912885913 +158000 ekin = 1.60239506185777 | erot = 1.20145363967825 | epot = -11.9371978303525 | etot = -9.13334912881648 +159000 ekin = 1.62604462003778 | erot = 1.1722643676051 | epot = -11.9316581164849 | etot = -9.13334912884202 +160000 ekin = 1.64813303486535 | erot = 1.15619534708328 | epot = -11.9376775108799 | etot = -9.13334912893126 +161000 ekin = 1.66807327612965 | erot = 1.15245312716206 | epot = -11.9538755323661 | etot = -9.13334912907436 +162000 ekin = 1.68501875283039 | erot = 1.15969471512819 | epot = -11.9780625972159 | etot = -9.13334912925728 +163000 ekin = 1.69790620824654 | erot = 1.17620989126117 | epot = -12.0074652289691 | etot = -9.13334912946137 +164000 ekin = 1.70552711798372 | erot = 1.20014309389839 | epot = -12.0390193415465 | etot = -9.13334912966439 +165000 ekin = 1.70662691809321 | erot = 1.22974121417727 | epot = -12.0697172621124 | etot = -9.1333491298419 +166000 ekin = 1.70002908026818 | erot = 1.26360423252414 | epot = -12.0969824427628 | etot = -9.13334912997051 +167000 ekin = 1.6847768395585 | erot = 1.30090518403763 | epot = -12.1190311536263 | etot = -9.13334913003016 +168000 ekin = 1.66027923283153 | erot = 1.34154370359067 | epot = -12.1351720664304 | etot = -9.13334913000821 +169000 ekin = 1.62644124957695 | erot = 1.38619810991384 | epot = -12.1459884893936 | etot = -9.13334912990284 +170000 ekin = 1.58375251890743 | erot = 1.43625221626174 | epot = -12.1533538648943 | etot = -9.13334912972516 +171000 ekin = 1.53331003043897 | erot = 1.49359459893387 | epot = -12.1602537588717 | etot = -9.13334912949887 +172000 ekin = 1.47676106161376 | erot = 1.56031583407019 | epot = -12.1704260249395 | etot = -9.13334912925556 +173000 ekin = 1.41695754705503 | erot = 1.63848249765388 | epot = -12.188789173044 | etot = -9.13334912833514 +174000 ekin = 1.35937684304463 | erot = 1.72968793645213 | epot = -12.2224139078248 | etot = -9.13334912832799 +175000 ekin = 1.30537540818794 | erot = 1.83369980102236 | epot = -12.2724243375748 | etot = -9.1333491283645 +176000 ekin = 1.25571357800289 | erot = 1.94952726339923 | epot = -12.3385899698484 | etot = -9.1333491284463 +177000 ekin = 1.21104692225301 | erot = 2.07558802224364 | epot = -12.4199840730635 | etot = -9.13334912856686 +178000 ekin = 1.17189512057028 | erot = 2.20976079574622 | epot = -12.5150050450636 | etot = -9.13334912874708 +179000 ekin = 1.13864315857366 | erot = 2.3494989013287 | epot = -12.621491188811 | etot = -9.13334912890866 +180000 ekin = 1.1115662183559 | erot = 2.49234008539987 | epot = -12.7372554328242 | etot = -9.1333491290684 +181000 ekin = 1.09087167613583 | erot = 2.63567357536121 | epot = -12.8598943807494 | etot = -9.13334912925234 +182000 ekin = 1.07675226579839 | erot = 2.77693577183311 | epot = -12.9870371670188 | etot = -9.13334912938731 +183000 ekin = 1.0694229423415 | erot = 2.91405263083417 | epot = -13.1168247026758 | etot = -9.13334912950008 +184000 ekin = 1.06913488705837 | erot = 3.04520163111631 | epot = -13.2476856477696 | etot = -9.13334912959493 +185000 ekin = 1.0761434592279 | erot = 3.1687577292989 | epot = -13.3782503182119 | etot = -9.13334912968511 +186000 ekin = 1.09060563376751 | erot = 3.28317984154817 | epot = -13.5071346051096 | etot = -9.13334912979391 +187000 ekin = 1.11239929858152 | erot = 3.38683780589046 | epot = -13.6325862344238 | etot = -9.13334912995179 +188000 ekin = 1.14088837562649 | erot = 3.47780595660469 | epot = -13.752043462419 | etot = -9.1333491301878 +189000 ekin = 1.17469755695859 | erot = 3.55369218298205 | epot = -13.8617388704563 | etot = -9.13334913051562 +190000 ekin = 1.21158961983354 | erot = 3.61161008256034 | epot = -13.9565488333125 | etot = -9.13334913091859 +191000 ekin = 1.24837558083747 | erot = 3.64780345127522 | epot = -14.0295281634879 | etot = -9.13334913137525 +192000 ekin = 1.28102311682986 | erot = 3.65810395428969 | epot = -14.072476202787 | etot = -9.13334913166741 +193000 ekin = 1.30598320817013 | erot = 3.64139295006481 | epot = -14.0807252900248 | etot = -9.1333491317899 +194000 ekin = 1.32049648836661 | erot = 3.59844552363031 | epot = -14.0522911436922 | etot = -9.13334913169526 +195000 ekin = 1.32298604774318 | erot = 3.53212928134951 | epot = -13.9884644604293 | etot = -9.13334913133662 +196000 ekin = 1.31323645162616 | erot = 3.44751612705317 | epot = -13.8941017095236 | etot = -9.13334913084423 +197000 ekin = 1.2922893469819 | erot = 3.35072340322514 | epot = -13.7763618804991 | etot = -9.13334913029208 +198000 ekin = 1.26212633786675 | erot = 3.24789114382014 | epot = -13.6433666114233 | etot = -9.13334912973641 +199000 ekin = 1.22527047461754 | erot = 3.14483705467229 | epot = -13.5034566585633 | etot = -9.1333491292735 +200000 ekin = 1.18441799207269 | erot = 3.04594245963017 | epot = -13.3637095806219 | etot = -9.13334912891904 +201000 ekin = 1.14216630511971 | erot = 2.95390025492375 | epot = -13.2294156887273 | etot = -9.13334912868379 +202000 ekin = 1.10084220211764 | erot = 2.86987712396365 | epot = -13.1040684546434 | etot = -9.13334912856213 +203000 ekin = 1.06240856569024 | erot = 2.79366067226848 | epot = -12.9894183664997 | etot = -9.13334912854095 +204000 ekin = 1.02841768821225 | erot = 2.72389144275529 | epot = -12.8856582595718 | etot = -9.13334912860426 +205000 ekin = 0.999988405220766 | erot = 2.65832732458335 | epot = -12.7916648585388 | etot = -9.13334912873468 +206000 ekin = 0.977799621225092 | erot = 2.59412391514213 | epot = -12.7052726652796 | etot = -9.13334912891242 +207000 ekin = 0.962105653965326 | erot = 2.52813792126146 | epot = -12.6235927043397 | etot = -9.13334912911289 +208000 ekin = 0.952783648018753 | erot = 2.45726642892344 | epot = -12.5433992062486 | etot = -9.13334912930642 +209000 ekin = 0.949416945748423 | erot = 2.37882137049759 | epot = -12.4615874457066 | etot = -9.13334912946056 +210000 ekin = 0.951402263215106 | erot = 2.29090939419268 | epot = -12.3756607869543 | etot = -9.13334912954655 +211000 ekin = 0.958051952077502 | erot = 2.19275562021938 | epot = -12.2841567018438 | etot = -9.13334912954694 +212000 ekin = 0.968659667700392 | erot = 2.08489619855889 | epot = -12.1869049957199 | etot = -9.1333491294606 +213000 ekin = 0.982515908119897 | erot = 1.96918422281075 | epot = -12.0850492602326 | etot = -9.133349129302 +214000 ekin = 0.998888701919718 | erot = 1.84860041862004 | epot = -11.9808382496358 | etot = -9.13334912909602 +215000 ekin = 1.01700134912567 | erot = 1.72690897492254 | epot = -11.8772594529195 | etot = -9.1333491288713 +216000 ekin = 1.03603050122455 | erot = 1.60822693577902 | epot = -11.7776065656588 | etot = -9.1333491286552 +217000 ekin = 1.05512477228475 | erot = 1.49657917533865 | epot = -11.6850530760952 | etot = -9.13334912847181 +218000 ekin = 1.07342860744192 | erot = 1.39550092670239 | epot = -11.6022786624838 | etot = -9.13334912833947 +219000 ekin = 1.09009860355586 | erot = 1.30773521951603 | epot = -11.531182951341 | etot = -9.13334912826909 +220000 ekin = 1.10431207607362 | erot = 1.23505496062922 | epot = -11.4727161649658 | etot = -9.13334912826295 +221000 ekin = 1.1152771799306 | erot = 1.17821867809274 | epot = -11.4268449863378 | etot = -9.13334912831449 +222000 ekin = 1.12225437592988 | erot = 1.13704823944158 | epot = -11.3926517437815 | etot = -9.13334912841 +223000 ekin = 1.12459297621428 | erot = 1.11060060825111 | epot = -11.3685427129971 | etot = -9.13334912853171 +224000 ekin = 1.12177911879634 | erot = 1.09739625543922 | epot = -11.352524502896 | etot = -9.1333491286604 +225000 ekin = 1.11348637905772 | erot = 1.09566402531927 | epot = -11.3424995331557 | etot = -9.13334912877874 +226000 ekin = 1.09961800000724 | erot = 1.10360909760937 | epot = -11.336576226485 | etot = -9.13334912886838 +227000 ekin = 1.08033165066238 | erot = 1.11952730043402 | epot = -11.3332080800318 | etot = -9.13334912893538 +228000 ekin = 1.056046028728 | erot = 1.14187865421858 | epot = -11.3312738119169 | etot = -9.13334912897035 +229000 ekin = 1.02742418663527 | erot = 1.16938489301674 | epot = -11.3301582086284 | etot = -9.13334912897636 +230000 ekin = 0.995339184991783 | erot = 1.20102048198616 | epot = -11.3297087959367 | etot = -9.13334912895879 +231000 ekin = 0.960829492708881 | erot = 1.23597735762307 | epot = -11.3301559792542 | etot = -9.13334912892228 +232000 ekin = 0.925050432735401 | erot = 1.27360958612393 | epot = -11.3320091477352 | etot = -9.13334912887592 +233000 ekin = 0.889225435959866 | erot = 1.31337910210641 | epot = -11.3359536668891 | etot = -9.13334912882285 +234000 ekin = 0.854600006628788 | erot = 1.35483402381932 | epot = -11.3427831592146 | etot = -9.13334912876651 +235000 ekin = 0.822390924845208 | erot = 1.39757430015849 | epot = -11.3533143537192 | etot = -9.13334912871546 +236000 ekin = 0.793732848711787 | erot = 1.4412143339908 | epot = -11.3682963113761 | etot = -9.13334912867351 +237000 ekin = 0.769632191219323 | erot = 1.48535644446078 | epot = -11.3883377643262 | etot = -9.13334912864607 +238000 ekin = 0.75091899336586 | erot = 1.52956143549222 | epot = -11.4138295574954 | etot = -9.13334912863731 +239000 ekin = 0.738206267496961 | erot = 1.57333361162157 | epot = -11.4448890077674 | etot = -9.13334912864883 +240000 ekin = 0.731862193743725 | erot = 1.6161314997423 | epot = -11.4813428221651 | etot = -9.13334912867903 +241000 ekin = 0.731999328001734 | erot = 1.6574109045686 | epot = -11.522759361293 | etot = -9.13334912872263 +242000 ekin = 0.738482620156991 | erot = 1.69669130986306 | epot = -11.5685230587936 | etot = -9.1333491287736 +243000 ekin = 0.750955042325049 | erot = 1.73364929482319 | epot = -11.6179534659678 | etot = -9.13334912881953 +244000 ekin = 0.768877080466275 | erot = 1.76822360275613 | epot = -11.6704498120764 | etot = -9.13334912885403 +245000 ekin = 0.791573929294317 | erot = 1.8006804512131 | epot = -11.7256035093787 | etot = -9.13334912887131 +246000 ekin = 0.818282914271255 | erot = 1.83164107445169 | epot = -11.7832731175934 | etot = -9.13334912887047 +247000 ekin = 0.848193621601422 | erot = 1.8620509655523 | epot = -11.8435937160095 | etot = -9.13334912885574 +248000 ekin = 0.880474358635257 | erot = 1.89308546777779 | epot = -11.9069089552494 | etot = -9.13334912883634 +249000 ekin = 0.914280881219071 | erot = 1.92599713223872 | epot = -11.9736271422835 | etot = -9.13334912882575 +250000 ekin = 0.94874673071633 | erot = 1.96192054843713 | epot = -12.0440164079935 | etot = -9.13334912884 +251000 ekin = 0.982959063854246 | erot = 2.00165977259888 | epot = -12.1179679653479 | etot = -9.13334912889475 +252000 ekin = 1.0159294824985 | erot = 2.04549252396353 | epot = -12.1947711354629 | etot = -9.13334912900091 +253000 ekin = 1.04657777483982 | erot = 2.0930344130595 | epot = -12.2729613170591 | etot = -9.13334912915976 +254000 ekin = 1.0737354175508 | erot = 2.14319803018439 | epot = -12.3502825770981 | etot = -9.13334912936293 +255000 ekin = 1.09620163163036 | erot = 2.1943096672054 | epot = -12.4238604284173 | etot = -9.1333491295815 +256000 ekin = 1.11287206428163 | erot = 2.24438579427434 | epot = -12.4906069883387 | etot = -9.1333491297827 +257000 ekin = 1.12287782510643 | erot = 2.29146665865411 | epot = -12.5476936136919 | etot = -9.13334912993136 +258000 ekin = 1.12572293500286 | erot = 2.33396623628278 | epot = -12.5930383012896 | etot = -9.13334913000396 +259000 ekin = 1.12139026023667 | erot = 2.37095948468564 | epot = -12.625698874911 | etot = -9.13334912998872 +260000 ekin = 1.11036122819352 | erot = 2.40229658115407 | epot = -12.6460069392476 | etot = -9.13334912990001 +261000 ekin = 1.09354805445105 | erot = 2.42847877902947 | epot = -12.6553759632427 | etot = -9.13334912976214 +262000 ekin = 1.07216031825818 | erot = 2.45046938603056 | epot = -12.6559788338926 | etot = -9.13334912960391 +263000 ekin = 1.04754368718327 | erot = 2.46943297797226 | epot = -12.6503257946122 | etot = -9.13334912945668 +264000 ekin = 1.02102495133862 | erot = 2.4864784463718 | epot = -12.6408525270506 | etot = -9.13334912934016 +265000 ekin = 0.993788783443946 | erot = 2.5024706313643 | epot = -12.629608544077 | etot = -9.13334912926878 +266000 ekin = 0.966800247930228 | erot = 2.51790683905048 | epot = -12.6180562162305 | etot = -9.13334912924975 +267000 ekin = 0.94078424945952 | erot = 2.53283827184844 | epot = -12.6069716505897 | etot = -9.13334912928175 +268000 ekin = 0.916272152394679 | erot = 2.54684612152533 | epot = -12.5964674032731 | etot = -9.13334912935312 +269000 ekin = 0.893722172477494 | erot = 2.55907244306974 | epot = -12.5861437450346 | etot = -9.13334912948737 +270000 ekin = 0.873709285129105 | erot = 2.56799722891236 | epot = -12.5750556436018 | etot = -9.13334912956034 +271000 ekin = 0.857156433251675 | erot = 2.57226369508363 | epot = -12.5627692579079 | etot = -9.13334912957259 +272000 ekin = 0.845541083724106 | erot = 2.57096110909458 | epot = -12.5498513223267 | etot = -9.13334912950806 +273000 ekin = 0.840983736969804 | erot = 2.56364270819377 | epot = -12.5379755745175 | etot = -9.13334912935396 +274000 ekin = 0.846103061110532 | erot = 2.55054497183587 | epot = -12.5299971620894 | etot = -9.13334912914304 +275000 ekin = 0.863570741244998 | erot = 2.53260377851043 | epot = -12.5295236486812 | etot = -9.13334912892575 +276000 ekin = 0.895419299415327 | erot = 2.5111464501477 | epot = -12.5399148783705 | etot = -9.13334912880747 +277000 ekin = 0.942302359418886 | erot = 2.48734970425681 | epot = -12.5630011925122 | etot = -9.13334912883649 +278000 ekin = 1.002990699416 | erot = 2.46199112036415 | epot = -12.5983309488098 | etot = -9.13334912902969 +279000 ekin = 1.07434561589273 | erot = 2.43529774590776 | epot = -12.6429924911398 | etot = -9.13334912933935 +280000 ekin = 1.15182340984047 | erot = 2.40711596365535 | epot = -12.6922885031803 | etot = -9.13334912968444 +281000 ekin = 1.23030856581836 | erot = 2.37726964751256 | epot = -12.7409273433239 | etot = -9.13334912999297 +282000 ekin = 1.30483974879791 | erot = 2.34551973870794 | epot = -12.7837086176988 | etot = -9.13334913019294 +283000 ekin = 1.37151257999464 | erot = 2.31231452819903 | epot = -12.8171762384381 | etot = -9.13334913024448 +284000 ekin = 1.42789685319405 | erot = 2.27901843146221 | epot = -12.8402644148115 | etot = -9.13334913015527 +285000 ekin = 1.47299679574484 | erot = 2.24762833985835 | epot = -12.8539742655638 | etot = -9.1333491299606 +286000 ekin = 1.50701906587717 | erot = 2.22050056283345 | epot = -12.8608687584215 | etot = -9.13334912971088 +287000 ekin = 1.53099472144781 | erot = 2.19999584806517 | epot = -12.864339698972 | etot = -9.13334912945897 +288000 ekin = 1.54636449768891 | erot = 2.18811490987512 | epot = -12.8678285368147 | etot = -9.13334912925069 +289000 ekin = 1.5546116349122 | erot = 2.18618804174371 | epot = -12.8741488057733 | etot = -9.13334912911742 +290000 ekin = 1.55699428674689 | erot = 2.19466879450611 | epot = -12.8850122103266 | etot = -9.13334912907358 +291000 ekin = 1.55439775255667 | erot = 2.21306131818002 | epot = -12.9008081998533 | etot = -9.13334912911663 +292000 ekin = 1.54729960240284 | erot = 2.23998314422001 | epot = -12.9206318758538 | etot = -9.133349129231 +293000 ekin = 1.53582108608433 | erot = 2.27333490842391 | epot = -12.9425051239025 | etot = -9.13334912939425 +294000 ekin = 1.51982864506212 | erot = 2.31049721096887 | epot = -12.9636749856262 | etot = -9.13334912959518 +295000 ekin = 1.49905154213373 | erot = 2.34851873983962 | epot = -12.9809194117667 | etot = -9.13334912979334 +296000 ekin = 1.4731936480285 | erot = 2.38443281021098 | epot = -12.9909755882221 | etot = -9.13334912998259 +297000 ekin = 1.44203124546029 | erot = 2.41536854589973 | epot = -12.9907489215099 | etot = -9.13334913014992 +298000 ekin = 1.40549976702148 | erot = 2.43867409046127 | epot = -12.9775229877653 | etot = -9.13334913028256 +299000 ekin = 1.36377241662864 | erot = 2.4520487180048 | epot = -12.9491702650004 | etot = -9.13334913036692 +300000 ekin = 1.31732711912216 | erot = 2.45368408092609 | epot = -12.9043603304391 | etot = -9.13334913039084 +301000 ekin = 1.26699022414775 | erot = 2.44240353914634 | epot = -12.8427428936402 | etot = -9.13334913034613 +302000 ekin = 1.21394210637208 | erot = 2.41777278593002 | epot = -12.7650640225336 | etot = -9.13334913023146 +303000 ekin = 1.15967414429375 | erot = 2.38015189683698 | epot = -12.6731751711849 | etot = -9.13334913005414 +304000 ekin = 1.1058972625133 | erot = 2.33066939618209 | epot = -12.5699157885246 | etot = -9.13334912982919 +305000 ekin = 1.05441504199289 | erot = 2.27111808933752 | epot = -12.4588822609065 | etot = -9.13334912957608 +306000 ekin = 1.00698421397174 | erot = 2.20379218514098 | epot = -12.3441255284277 | etot = -9.13334912931499 +307000 ekin = 0.965188337627758 | erot = 2.13129764385454 | epot = -12.2298351105455 | etot = -9.13334912906317 +308000 ekin = 0.930345631944655 | erot = 2.05636814615613 | epot = -12.1200629069335 | etot = -9.13334912883274 +309000 ekin = 0.903461768093119 | erot = 1.98167791132915 | epot = -12.0184888080546 | etot = -9.13334912863236 +310000 ekin = 0.885228515008137 | erot = 1.90967870211614 | epot = -11.928256345589 | etot = -9.13334912846471 +311000 ekin = 0.876047647700593 | erot = 1.84263812610081 | epot = -11.8520349021336 | etot = -9.1333491283322 +312000 ekin = 0.876068182199119 | erot = 1.78248869456911 | epot = -11.7919060050066 | etot = -9.13334912823841 +313000 ekin = 0.885223985970029 | erot = 1.73072892882235 | epot = -11.7493020429815 | etot = -9.13334912818911 +314000 ekin = 0.903258342515253 | erot = 1.68832066988359 | epot = -11.7249281405904 | etot = -9.13334912819159 +315000 ekin = 0.929731391718592 | erot = 1.65558558099713 | epot = -11.7186661009688 | etot = -9.13334912825309 +316000 ekin = 0.964013828970858 | erot = 1.63211973509021 | epot = -11.7294826924394 | etot = -9.1333491283783 +317000 ekin = 1.00527629211699 | erot = 1.61675326466453 | epot = -11.7553786853479 | etot = -9.1333491285664 +318000 ekin = 1.05248736450163 | erot = 1.60758570940549 | epot = -11.7934222027153 | etot = -9.13334912880819 +319000 ekin = 1.1044333286817 | erot = 1.60212494474497 | epot = -11.8399074025109 | etot = -9.13334912908421 +320000 ekin = 1.1597692492087 | erot = 1.59754526105393 | epot = -11.8906636396272 | etot = -9.13334912936456 +321000 ekin = 1.2171035230572 | erot = 1.5910555451816 | epot = -11.9415081978521 | etot = -9.13334912961331 +322000 ekin = 1.27510751189521 | erot = 1.58033324923083 | epot = -11.9887898909203 | etot = -9.13334912979421 +323000 ekin = 1.33263084645762 | erot = 1.56394390937339 | epot = -12.0299238857107 | etot = -9.13334912987968 +324000 ekin = 1.38879590712265 | erot = 1.54164678485237 | epot = -12.063791821834 | etot = -9.13334912985893 +325000 ekin = 1.44304623679759 | erot = 1.51450056885262 | epot = -12.0908959353912 | etot = -9.13334912974094 +326000 ekin = 1.49513435445731 | erot = 1.48473073066047 | epot = -12.1132142146707 | etot = -9.13334912955292 +327000 ekin = 1.54505065938393 | erot = 1.4553840086034 | epot = -12.1337837973215 | etot = -9.13334912933419 +328000 ekin = 1.59290981434296 | erot = 1.42984788209339 | epot = -12.1561068255639 | etot = -9.13334912912751 +329000 ekin = 1.63881860975664 | erot = 1.41133335467791 | epot = -12.1835010934064 | etot = -9.1333491289718 +330000 ekin = 1.68274896183131 | erot = 1.40240729591343 | epot = -12.218505386642 | etot = -9.13334912889729 +331000 ekin = 1.72443467169599 | erot = 1.40463116342023 | epot = -12.2624149640395 | etot = -9.1333491289233 +332000 ekin = 1.76330533674359 | erot = 1.41833479327455 | epot = -12.3149892590745 | etot = -9.1333491290564 +333000 ekin = 1.79846823309319 | erot = 1.44253834966228 | epot = -12.3743557120445 | etot = -9.13334912928905 +334000 ekin = 1.82874900591132 | erot = 1.47503277033862 | epot = -12.4371309058477 | etot = -9.13334912959778 +335000 ekin = 1.8527961611585 | erot = 1.51263570197517 | epot = -12.4987809930765 | etot = -9.1333491299428 +336000 ekin = 1.86927630558798 | erot = 1.55160162438179 | epot = -12.5542270602388 | etot = -9.13334913026902 +337000 ekin = 1.87711735413951 | erot = 1.58820049773354 | epot = -12.5986669823879 | etot = -9.13334913051487 +338000 ekin = 1.87574840923178 | erot = 1.61938868722965 | epot = -12.6284862270854 | etot = -9.13334913062394 +339000 ekin = 1.86534866362725 | erot = 1.64338736517895 | epot = -12.642085159367 | etot = -9.13334913056081 +340000 ekin = 1.84695798886992 | erot = 1.66009075059819 | epot = -12.6403978697906 | etot = -9.13334913032249 +341000 ekin = 1.82243969076641 | erot = 1.67114820362656 | epot = -12.6269370243339 | etot = -9.13334912994089 +342000 ekin = 1.79428655955863 | erot = 1.67969211618972 | epot = -12.6073278052237 | etot = -9.13334912947535 +343000 ekin = 1.76531632972518 | erot = 1.68978090506938 | epot = -12.5884463637906 | etot = -9.13334912899607 +344000 ekin = 1.73833039739252 | erot = 1.70570000747066 | epot = -12.5773795334329 | etot = -9.13334912856973 +345000 ekin = 1.71580589060231 | erot = 1.73127559556374 | epot = -12.5804306144146 | etot = -9.13334912824853 +346000 ekin = 1.69966353097544 | erot = 1.76931234934783 | epot = -12.6023250083902 | etot = -9.13334912806694 +347000 ekin = 1.69112042623226 | erot = 1.82120184302293 | epot = -12.645671397299 | etot = -9.13334912804384 +348000 ekin = 1.69061396982694 | erot = 1.88669704033623 | epot = -12.7106601383494 | etot = -9.13334912818626 +349000 ekin = 1.69777681788133 | erot = 1.96382926866199 | epot = -12.794955215034 | etot = -9.13334912849066 +350000 ekin = 1.71145115010181 | erot = 2.04895591402545 | epot = -12.8937561930696 | etot = -9.13334912894229 +351000 ekin = 1.72974629646103 | erot = 2.13695636910498 | epot = -13.0000517950758 | etot = -9.13334912950983 +352000 ekin = 1.75015893903866 | erot = 2.22162008456598 | epot = -13.1051281537444 | etot = -9.13334913013976 +353000 ekin = 1.76978034905491 | erot = 2.29627029645961 | epot = -13.1993997762708 | etot = -9.13334913075623 +354000 ekin = 1.78560210911906 | erot = 2.35462017023395 | epot = -13.2735714106196 | etot = -9.13334913126658 +355000 ekin = 1.79489785472806 | erot = 2.39176336004141 | epot = -13.3200103463507 | etot = -9.13334913158127 +356000 ekin = 1.79561393246573 | erot = 2.40509186859492 | epot = -13.3340549326994 | etot = -9.13334913163879 +357000 ekin = 1.78667091072634 | erot = 2.39487614134892 | epot = -13.3148961835031 | etot = -9.13334913142788 +358000 ekin = 1.76810167230531 | erot = 2.36429897994129 | epot = -13.2657497831711 | etot = -9.13334913092448 +359000 ekin = 1.74170569044722 | erot = 2.31907684809606 | epot = -13.1941316689281 | etot = -9.13334913038481 +360000 ekin = 1.70943632676222 | erot = 2.26611368397256 | epot = -13.1088991405414 | etot = -9.13334912980664 +361000 ekin = 1.67315005965478 | erot = 2.21234166615806 | epot = -13.018840855099 | etot = -9.13334912928617 +362000 ekin = 1.63480994001595 | erot = 2.16376887379898 | epot = -12.9319279427065 | etot = -9.13334912889153 +363000 ekin = 1.59622606057555 | erot = 2.12469986683813 | epot = -12.8542750560706 | etot = -9.13334912865692 +364000 ekin = 1.5589020583379 | erot = 2.09734631559819 | epot = -12.7895975025215 | etot = -9.13334912858545 +365000 ekin = 1.52397421076772 | erot = 2.08181308416711 | epot = -12.7391364235913 | etot = -9.13334912865645 +366000 ekin = 1.49221260734006 | erot = 2.07639009796189 | epot = -12.701951834135 | etot = -9.13334912883309 +367000 ekin = 1.46405952364948 | erot = 2.07805510122142 | epot = -12.6754637539433 | etot = -9.13334912907236 +368000 ekin = 1.43967726932382 | erot = 2.08307216057574 | epot = -12.6560985592331 | etot = -9.13334912933359 +369000 ekin = 1.41899010811481 | erot = 2.08756917147258 | epot = -12.6399084091724 | etot = -9.13334912958505 +370000 ekin = 1.40171557356767 | erot = 2.08800173652873 | epot = -12.6230664399019 | etot = -9.13334912980549 +371000 ekin = 1.38739280854876 | erot = 2.08146226240639 | epot = -12.6022042009371 | etot = -9.13334912998193 +372000 ekin = 1.375423403086 | erot = 2.06585193702358 | epot = -12.5746244702138 | etot = -9.13334913010421 +373000 ekin = 1.36513752357924 | erot = 2.03996886737186 | epot = -12.5384555211132 | etot = -9.13334913016208 +374000 ekin = 1.35583949105185 | erot = 2.00351975772513 | epot = -12.4927083789465 | etot = -9.13334913016951 +375000 ekin = 1.3469415771146 | erot = 1.95716038268622 | epot = -12.4374510898688 | etot = -9.13334913006802 +376000 ekin = 1.33814968105267 | erot = 1.90258032253411 | epot = -12.374079133484 | etot = -9.1333491298972 +377000 ekin = 1.32936261120809 | erot = 1.84227265725305 | epot = -12.3049843981379 | etot = -9.13334912967674 +378000 ekin = 1.32063159991346 | erot = 1.77926043319111 | epot = -12.2332411625435 | etot = -9.13334912943897 +379000 ekin = 1.31208340368852 | erot = 1.71672941783702 | epot = -12.1621619507414 | etot = -9.13334912921587 +380000 ekin = 1.30384179784202 | erot = 1.65764204155844 | epot = -12.0948329684338 | etot = -9.13334912903333 +381000 ekin = 1.29657917475819 | erot = 1.60487100826734 | epot = -12.0347993118452 | etot = -9.1333491288197 +382000 ekin = 1.29092190134678 | erot = 1.56061067707121 | epot = -11.9848817072432 | etot = -9.13334912882517 +383000 ekin = 1.28620909068409 | erot = 1.52536833770036 | epot = -11.9449265572231 | etot = -9.13334912883862 +384000 ekin = 1.28205683099616 | erot = 1.49922806168849 | epot = -11.9146340215161 | etot = -9.13334912883142 +385000 ekin = 1.27850478017856 | erot = 1.48216189144843 | epot = -11.8940158004142 | etot = -9.13334912878723 +386000 ekin = 1.27603762173984 | erot = 1.47423730493031 | epot = -11.8836240553802 | etot = -9.13334912871007 +387000 ekin = 1.27548287271899 | erot = 1.47565716104753 | epot = -11.8844891623902 | etot = -9.13334912862373 +388000 ekin = 1.27780044585774 | erot = 1.48660964097436 | epot = -11.8977592153985 | etot = -9.13334912856639 +389000 ekin = 1.28381262703564 | erot = 1.50697425852414 | epot = -11.9241360141384 | etot = -9.13334912857858 +390000 ekin = 1.29393930260842 | erot = 1.5359803506825 | epot = -11.9632687819857 | etot = -9.13334912869483 +391000 ekin = 1.30800074456097 | erot = 1.57190984924444 | epot = -12.0132597227344 | etot = -9.13334912892897 +392000 ekin = 1.32513099179446 | erot = 1.61197584867697 | epot = -12.0704559697433 | etot = -9.13334912927191 +393000 ekin = 1.34382543000147 | erot = 1.65241448883368 | epot = -12.1295890485249 | etot = -9.13334912968977 +394000 ekin = 1.36212102398643 | erot = 1.68881012624722 | epot = -12.1842802803624 | etot = -9.13334913012874 +395000 ekin = 1.37788072140321 | erot = 1.7166159305402 | epot = -12.2278457824674 | etot = -9.133349130524 +396000 ekin = 1.3891315451241 | erot = 1.73181112618322 | epot = -12.2542918021046 | etot = -9.13334913079729 +397000 ekin = 1.39439357479747 | erot = 1.73153617599057 | epot = -12.2592788817204 | etot = -9.13334913093237 +398000 ekin = 1.39293904659196 | erot = 1.71441550438758 | epot = -12.2407036818553 | etot = -9.13334913087581 +399000 ekin = 1.38493174777447 | erot = 1.68094766350892 | epot = -12.1992285419451 | etot = -9.13334913066174 +400000 ekin = 1.37142116074107 | erot = 1.63330764197893 | epot = -12.1380779330254 | etot = -9.13334913030538 +401000 ekin = 1.35412991252456 | erot = 1.57501044311705 | epot = -12.0624894855338 | etot = -9.13334912989223 +402000 ekin = 1.33517991856915 | erot = 1.51048364980033 | epot = -11.9790126977739 | etot = -9.13334912940442 +403000 ekin = 1.31709653187286 | erot = 1.44458891478893 | epot = -11.8950345756002 | etot = -9.1333491289384 +404000 ekin = 1.30234590493894 | erot = 1.38198365576712 | epot = -11.8176786892411 | etot = -9.13334912853505 +405000 ekin = 1.29301391716292 | erot = 1.32673455588809 | epot = -11.7530976012888 | etot = -9.13334912823777 +406000 ekin = 1.2906546746281 | erot = 1.28204116436323 | epot = -11.7060449670169 | etot = -9.13334912802553 +407000 ekin = 1.29643237294816 | erot = 1.25006436588362 | epot = -11.6798458667507 | etot = -9.13334912791893 +408000 ekin = 1.31094700615268 | erot = 1.23190986721473 | epot = -11.6762060012832 | etot = -9.13334912791582 +409000 ekin = 1.33422438303379 | erot = 1.2276348975221 | epot = -11.6952084085706 | etot = -9.13334912801469 +410000 ekin = 1.36572014154963 | erot = 1.23628017302459 | epot = -11.7353494427862 | etot = -9.13334912821197 +411000 ekin = 1.40432668760761 | erot = 1.25592548503539 | epot = -11.7936013011441 | etot = -9.13334912850106 +412000 ekin = 1.44839088645853 | erot = 1.28379672627828 | epot = -11.8655367416044 | etot = -9.1333491288676 +413000 ekin = 1.49576795241833 | erot = 1.31646032748912 | epot = -11.9455774091907 | etot = -9.13334912928325 +414000 ekin = 1.54394920889439 | erot = 1.35014055217853 | epot = -12.0274388907764 | etot = -9.13334912970352 +415000 ekin = 1.59029421705134 | erot = 1.38116660571177 | epot = -12.1048099528334 | etot = -9.1333491300703 +416000 ekin = 1.63235973909082 | erot = 1.40649922749302 | epot = -12.1722080969089 | etot = -9.13334913032505 +417000 ekin = 1.66825800489195 | erot = 1.42422016761186 | epot = -12.2258273029357 | etot = -9.13334913043192 +418000 ekin = 1.69693219837217 | erot = 1.43381449957501 | epot = -12.2640958283216 | etot = -9.13334913037439 +419000 ekin = 1.71824951894772 | erot = 1.43620625779646 | epot = -12.2878049069281 | etot = -9.13334913018396 +420000 ekin = 1.73288337430552 | erot = 1.43350825350801 | epot = -12.2997407577245 | etot = -9.13334912991093 +421000 ekin = 1.74204129532364 | erot = 1.42856028674966 | epot = -12.3039507116832 | etot = -9.13334912960995 +422000 ekin = 1.747137018077 | erot = 1.42445618730832 | epot = -12.3049423347126 | etot = -9.13334912932731 +423000 ekin = 1.74949063384699 | erot = 1.42413436044387 | epot = -12.306974123395 | etot = -9.1333491291041 +424000 ekin = 1.75009754642992 | erot = 1.43005641925135 | epot = -12.3135030946279 | etot = -9.13334912894662 +425000 ekin = 1.74947257256707 | erot = 1.444124008023 | epot = -12.3269457094739 | etot = -9.13334912888379 +426000 ekin = 1.69664946387304 | erot = 1.40011304962389 | epot = -12.2301116345961 | etot = -9.13334912109913 +427000 ekin = 1.76448154346204 | erot = 1.46695774970338 | epot = -12.3647884699843 | etot = -9.13334917681884 +428000 ekin = 1.77864040382746 | erot = 1.51204937412204 | epot = -12.4240389057571 | etot = -9.13334912780757 +429000 ekin = 1.77744254090666 | erot = 1.55645173379844 | epot = -12.4672434028093 | etot = -9.13334912810418 +430000 ekin = 1.7686448171393 | erot = 1.60567169371135 | epot = -12.5076656392882 | etot = -9.13334912843752 +431000 ekin = 1.75041443993065 | erot = 1.656556385141 | epot = -12.5403199538331 | etot = -9.13334912876141 +432000 ekin = 1.72143753020943 | erot = 1.70559294341285 | epot = -12.5603796026436 | etot = -9.13334912902135 +433000 ekin = 1.68129756274214 | erot = 1.74934007551085 | epot = -12.5639867674179 | etot = -9.13334912916489 +434000 ekin = 1.63077650979966 | erot = 1.78490039303256 | epot = -12.5490260319869 | etot = -9.13334912915467 +435000 ekin = 1.57198882084486 | erot = 1.81033246556167 | epot = -12.515670415387 | etot = -9.13334912898049 +436000 ekin = 1.50828072851469 | erot = 1.82489908961086 | epot = -12.4665289467905 | etot = -9.13334912866496 +437000 ekin = 1.44388315301224 | erot = 1.82908776307999 | epot = -12.4063200443506 | etot = -9.13334912825842 +438000 ekin = 1.38337900429711 | erot = 1.82441107452547 | epot = -12.3411392066475 | etot = -9.13334912782494 +439000 ekin = 1.33110407576218 | erot = 1.81306694504111 | epot = -12.2775201482279 | etot = -9.13334912742462 +440000 ekin = 1.29061754888995 | erot = 1.797574755084 | epot = -12.221541431074 | etot = -9.1333491271001 +441000 ekin = 1.26434687832149 | erot = 1.7804860060744 | epot = -12.178182011266 | etot = -9.13334912687011 +442000 ekin = 1.25344985037915 | erot = 1.76421040799475 | epot = -12.1510093851077 | etot = -9.13334912673382 +443000 ekin = 1.25787308938395 | erot = 1.7509340047674 | epot = -12.1421562208302 | etot = -9.13334912667889 +444000 ekin = 1.27654491138783 | erot = 1.74256727852053 | epot = -12.1524613166015 | etot = -9.13334912669317 +445000 ekin = 1.30762960642458 | erot = 1.74066161517062 | epot = -12.1816403483642 | etot = -9.13334912676901 +446000 ekin = 1.34878485335209 | erot = 1.74626611357119 | epot = -12.2284000938274 | etot = -9.13334912690415 +447000 ekin = 1.39739993763723 | erot = 1.75974793458104 | epot = -12.2904969993182 | etot = -9.13334912709987 +448000 ekin = 1.45076649190894 | erot = 1.78060717934165 | epot = -12.3647227986027 | etot = -9.13334912735207 +449000 ekin = 1.50623999605352 | erot = 1.80738848344728 | epot = -12.4469776071503 | etot = -9.13334912764947 +450000 ekin = 1.56138908054594 | erot = 1.83773497344371 | epot = -12.5324731819605 | etot = -9.13334912797084 +451000 ekin = 1.61412412964519 | erot = 1.86859865234448 | epot = -12.6160719102763 | etot = -9.13334912828666 +452000 ekin = 1.66280931630107 | erot = 1.896585480364 | epot = -12.6927439252279 | etot = -9.13334912856284 +453000 ekin = 1.70634971637084 | erot = 1.91837476586823 | epot = -12.7580736110105 | etot = -9.13334912877139 +454000 ekin = 1.74423056750362 | erot = 1.93111374790659 | epot = -12.8086934443054 | etot = -9.13334912889515 +455000 ekin = 1.77648988409882 | erot = 1.93270291378201 | epot = -12.8425419268134 | etot = -9.13334912893253 +456000 ekin = 1.80361911556738 | erot = 1.92192628287829 | epot = -12.8588945273419 | etot = -9.1333491288962 +457000 ekin = 1.8264001670622 | erot = 1.89842961389973 | epot = -12.8581789097702 | etot = -9.13334912880823 +458000 ekin = 1.84570455025944 | erot = 1.86259298695776 | epot = -12.8416466659122 | etot = -9.13334912869503 +459000 ekin = 1.86229070170956 | erot = 1.8153534231518 | epot = -12.8109932534391 | etot = -9.13334912857775 +460000 ekin = 1.87663848085872 | erot = 1.75803306182823 | epot = -12.7680206711605 | etot = -9.13334912847359 +461000 ekin = 1.88883864523193 | erot = 1.6921974638434 | epot = -12.7143852374645 | etot = -9.13334912838912 +462000 ekin = 1.89856203652303 | erot = 1.61956678027482 | epot = -12.6514779451224 | etot = -9.13334912832454 +463000 ekin = 1.90510221764477 | erot = 1.54196437877891 | epot = -12.5804157246998 | etot = -9.13334912827614 +464000 ekin = 1.90747686786656 | erot = 1.4612799319853 | epot = -12.5021059280867 | etot = -9.13334912823483 +465000 ekin = 1.9045797735616 | erot = 1.37946070091786 | epot = -12.4173896026653 | etot = -9.1333491281858 +466000 ekin = 1.89536572152326 | erot = 1.29851485172206 | epot = -12.3272297013668 | etot = -9.13334912812148 +467000 ekin = 1.87901831709977 | erot = 1.22048659414433 | epot = -12.23285403928 | etot = -9.13334912803586 +468000 ekin = 1.85509917792058 | erot = 1.14739126284092 | epot = -12.1358395686896 | etot = -9.13334912792812 +469000 ekin = 1.82366605107319 | erot = 1.08110787535124 | epot = -12.0381230542268 | etot = -9.13334912780234 +470000 ekin = 1.7853521607561 | erot = 1.02324127043709 | epot = -11.9419425588574 | etot = -9.13334912766423 +471000 ekin = 1.7414105151338 | erot = 0.974982090043943 | epot = -11.8497417326969 | etot = -9.13334912751916 +472000 ekin = 1.69372019705931 | erot = 0.937000644455253 | epot = -11.7640699688863 | etot = -9.13334912737171 +473000 ekin = 1.6447363277097 | erot = 0.909402534932154 | epot = -11.6874879898691 | etot = -9.13334912722722 +474000 ekin = 1.5973499517736 | erot = 0.891755018431853 | epot = -11.6224540973011 | etot = -9.13334912709562 +475000 ekin = 1.55462885495252 | erot = 0.883174765260568 | epot = -11.5711527472047 | etot = -9.13334912699162 +476000 ekin = 1.51944866261163 | erot = 0.882459888569966 | epot = -11.5352576781134 | etot = -9.1333491269318 +477000 ekin = 1.49408243529036 | erot = 0.888250161717261 | epot = -11.5156817239355 | etot = -9.1333491269279 +478000 ekin = 1.47985622585634 | erot = 0.899197335533166 | epot = -11.5124026883716 | etot = -9.13334912698206 +479000 ekin = 1.47695373952855 | erot = 0.914115348457805 | epot = -11.5244182150803 | etot = -9.13334912709393 +480000 ekin = 1.48439477575462 | erot = 0.932072516621168 | epot = -11.5498164196182 | etot = -9.13334912724239 +481000 ekin = 1.50022741217527 | erot = 0.952423999184411 | epot = -11.5860005387821 | etot = -9.13334912742244 +482000 ekin = 1.52172985963446 | erot = 0.97475421184665 | epot = -11.6298331991077 | etot = -9.13334912762659 +483000 ekin = 1.54567018241534 | erot = 0.998770450814866 | epot = -11.6777897610761 | etot = -9.13334912784592 +484000 ekin = 1.5685861472313 | erot = 1.02419763510865 | epot = -11.7261329104088 | etot = -9.1333491280688 +485000 ekin = 1.58707346955127 | erot = 1.05070585623149 | epot = -11.7711284540624 | etot = -9.13334912827961 +486000 ekin = 1.59807103603154 | erot = 1.07788995424692 | epot = -11.8093101187385 | etot = -9.13334912845999 +487000 ekin = 1.59911980804505 | erot = 1.10529931942179 | epot = -11.8377682560599 | etot = -9.13334912859303 +488000 ekin = 1.58856342116736 | erot = 1.13249736396222 | epot = -11.8544099137967 | etot = -9.13334912866709 +489000 ekin = 1.56566142904791 | erot = 1.15911683125798 | epot = -11.8581273889847 | etot = -9.13334912867881 +490000 ekin = 1.53060268554749 | erot = 1.18488502427328 | epot = -11.8488368384543 | etot = -9.13334912863355 +491000 ekin = 1.48443427069566 | erot = 1.20959914015976 | epot = -11.8273825393281 | etot = -9.13334912847264 +492000 ekin = 1.42930345354542 | erot = 1.23291829593324 | epot = -11.7955708778628 | etot = -9.13334912838418 +493000 ekin = 1.3674956414523 | erot = 1.25438544605066 | epot = -11.7552302157787 | etot = -9.13334912827576 +494000 ekin = 1.30137262988138 | erot = 1.27348228002512 | epot = -11.7082040380618 | etot = -9.13334912815528 +495000 ekin = 1.23360970817057 | erot = 1.28954660636107 | epot = -11.6565054425592 | etot = -9.13334912802759 +496000 ekin = 1.16375548640953 | erot = 1.30023195608579 | epot = -11.5973366205401 | etot = -9.13334917804474 +497000 ekin = 1.02574644939849 | erot = 1.24927230426271 | epot = -11.4083678755035 | etot = -9.13334912184225 +498000 ekin = 1.13339044616365 | erot = 1.24939677704376 | epot = -11.5161363891151 | etot = -9.13334916590768 +499000 ekin = 1.1643476239325 | erot = 1.25864673154937 | epot = -11.5563434800381 | etot = -9.13334912455626 +500000 ekin = 1.16768486506762 | erot = 1.25769344443886 | epot = -11.5587274345815 | etot = -9.13334912507499 +501000 ekin = 1.1755989549752 | erot = 1.2503891544258 | epot = -11.559337234304 | etot = -9.13334912490305 +502000 ekin = 1.18926606273897 | erot = 1.23784323633022 | epot = -11.5604584237503 | etot = -9.13334912468111 +503000 ekin = 1.20982408114902 | erot = 1.22204157664311 | epot = -11.565214782232 | etot = -9.13334912443988 +504000 ekin = 1.23811782736999 | erot = 1.20572865378421 | epot = -11.5771956053585 | etot = -9.13334912420434 +505000 ekin = 1.27460966228739 | erot = 1.19199209322131 | epot = -11.59995087951 | etot = -9.13334912400132 +506000 ekin = 1.31928047819545 | erot = 1.18393687677876 | epot = -11.6365664788295 | etot = -9.13334912385525 +507000 ekin = 1.3715770090045 | erot = 1.18435118386581 | epot = -11.6892773166538 | etot = -9.13334912378344 +508000 ekin = 1.43042502721483 | erot = 1.19541187481579 | epot = -11.7591860258242 | etot = -9.13334912379356 +509000 ekin = 1.49431413372792 | erot = 1.21846596295654 | epot = -11.846129220568 | etot = -9.13334912388354 +510000 ekin = 1.56143815899919 | erot = 1.25390781315394 | epot = -11.9486950961969 | etot = -9.13334912404381 +511000 ekin = 1.62985405359467 | erot = 1.30115550673995 | epot = -12.0643586845959 | etot = -9.13334912426124 +512000 ekin = 1.69760948238373 | erot = 1.35871536004307 | epot = -12.1896739669509 | etot = -9.1333491245241 +513000 ekin = 1.76279412854719 | erot = 1.42431355746776 | epot = -12.32045681084 | etot = -9.13334912482506 +514000 ekin = 1.82349978434154 | erot = 1.49507387317791 | epot = -12.4519227826782 | etot = -9.13334912515872 +515000 ekin = 1.87772649131677 | erot = 1.56773414236142 | epot = -12.5788097591923 | etot = -9.1333491255141 +516000 ekin = 1.92332299298482 | erot = 1.63891274675915 | epot = -12.69558486561 | etot = -9.13334912586601 +517000 ekin = 1.95805681102052 | erot = 1.70543998934056 | epot = -12.7968459265345 | etot = -9.1333491261734 +518000 ekin = 1.97984991947006 | erot = 1.76473849815274 | epot = -12.8779375440109 | etot = -9.1333491263881 +519000 ekin = 1.98711819296696 | erot = 1.81518192784922 | epot = -12.9356492472873 | etot = -9.13334912647111 +520000 ekin = 1.97908911077209 | erot = 1.85632478175102 | epot = -12.9687630189357 | etot = -9.13334912641256 +521000 ekin = 1.95594858056403 | erot = 1.88892760796725 | epot = -12.978225314758 | etot = -9.13334912622669 +522000 ekin = 1.91881161738194 | erot = 1.91475582237519 | epot = -12.9669165657085 | etot = -9.1333491259514 +523000 ekin = 1.86954045343306 | erot = 1.93620351350347 | epot = -12.9390930925726 | etot = -9.13334912563611 +524000 ekin = 1.81047332181718 | erot = 1.95582271022186 | epot = -12.8996451573712 | etot = -9.13334912533215 +525000 ekin = 1.74413482435723 | erot = 1.97582576721634 | epot = -12.8533097166606 | etot = -9.13334912508703 +526000 ekin = 1.67297434024948 | erot = 1.99761678040473 | epot = -12.8039402455928 | etot = -9.13334912493856 +527000 ekin = 1.59916865616217 | erot = 2.02141684187625 | epot = -12.7539346229455 | etot = -9.13334912490706 +528000 ekin = 1.52452149634667 | erot = 2.04605877912579 | epot = -12.7039294004615 | etot = -9.13334912498898 +529000 ekin = 1.4504814163804 | erot = 2.06903286947785 | epot = -12.6528634110109 | etot = -9.13334912515263 +530000 ekin = 1.37827485203354 | erot = 2.08683821123061 | epot = -12.5984621886057 | etot = -9.1333491253415 +531000 ekin = 1.30911544825154 | erot = 2.09562136598167 | epot = -12.53808593972 | etot = -9.13334912548683 +532000 ekin = 1.24441932206878 | erot = 2.09198653946278 | epot = -12.4697549870582 | etot = -9.13334912552664 +533000 ekin = 1.18594679653148 | erot = 2.07377924595488 | epot = -12.3930751679106 | etot = -9.13334912542429 +534000 ekin = 1.13581312461376 | erot = 2.04062941960208 | epot = -12.3097916693946 | etot = -9.13334912517874 +535000 ekin = 1.09635528031422 | erot = 1.99411201499615 | epot = -12.2238164201335 | etot = -9.13334912482314 +536000 ekin = 1.06988655695605 | erot = 1.93750945181515 | epot = -12.1407451331851 | etot = -9.13334912441391 +537000 ekin = 1.05839509271265 | erot = 1.87547351818717 | epot = -12.0672177348934 | etot = -9.1333491239936 +538000 ekin = 1.06323891385521 | erot = 1.81331424698605 | epot = -12.0099022845203 | etot = -9.13334912367902 +539000 ekin = 1.08487929969981 | erot = 1.75562392314816 | epot = -11.9738523463418 | etot = -9.13334912349383 +540000 ekin = 1.12268189022981 | erot = 1.70611667318581 | epot = -11.9621476868903 | etot = -9.13334912347465 +541000 ekin = 1.17481105395874 | erot = 1.66717481230911 | epot = -11.9753349899066 | etot = -9.13334912363877 +542000 ekin = 1.23824417790952 | erot = 1.63956314455245 | epot = -12.0111564464417 | etot = -9.13334912397975 +543000 ekin = 1.30892832432068 | erot = 1.62236761446663 | epot = -12.0646450632504 | etot = -9.13334912446311 +544000 ekin = 1.38208514507537 | erot = 1.61318872881518 | epot = -12.1286229989214 | etot = -9.1333491250308 +545000 ekin = 1.45263801176084 | erot = 1.60857948401539 | epot = -12.1945666213831 | etot = -9.1333491256069 +546000 ekin = 1.51570974605567 | erot = 1.60467377472626 | epot = -12.2537326468929 | etot = -9.133349126111 +547000 ekin = 1.56711452712117 | erot = 1.59788800381426 | epot = -12.2983516574103 | etot = -9.13334912647489 +548000 ekin = 1.60376221827898 | erot = 1.58554162816415 | epot = -12.3226529730993 | etot = -9.13334912665618 +549000 ekin = 1.6239104162608 | erot = 1.56625626420984 | epot = -12.3235158071168 | etot = -9.13334912664616 +550000 ekin = 1.62723358008838 | erot = 1.54012357328336 | epot = -12.3007062798175 | etot = -9.13334912644577 +551000 ekin = 1.61471889891529 | erot = 1.50851459570431 | epot = -12.2565826207644 | etot = -9.13334912614485 +552000 ekin = 1.58843016682267 | erot = 1.47348936383955 | epot = -12.1952686564325 | etot = -9.13334912577033 +553000 ekin = 1.55120098109845 | erot = 1.43753302718781 | epot = -12.122083133656 | etot = -9.13334912536972 +554000 ekin = 1.50631636213089 | erot = 1.40318755322937 | epot = -12.0428530403387 | etot = -9.13334912497846 +555000 ekin = 1.4572287898642 | erot = 1.37279698199754 | epot = -11.9633748964818 | etot = -9.13334912462009 +556000 ekin = 1.40732293285075 | erot = 1.3483759063889 | epot = -11.8890479635463 | etot = -9.13334912430663 +557000 ekin = 1.35973750772758 | erot = 1.33157707038824 | epot = -11.8246637021589 | etot = -9.13334912404312 +558000 ekin = 1.31723590732834 | erot = 1.32371628032663 | epot = -11.7743013114869 | etot = -9.13334912383197 +559000 ekin = 1.28211028309013 | erot = 1.32580526483731 | epot = -11.741264671604 | etot = -9.1333491236766 +560000 ekin = 1.25610590404742 | erot = 1.33855626265929 | epot = -11.7280112902901 | etot = -9.13334912358343 +561000 ekin = 1.24035844263181 | erot = 1.36234138770408 | epot = -11.7360489538967 | etot = -9.13334912356079 +562000 ekin = 1.23534624012527 | erot = 1.39711468447578 | epot = -11.7658100482175 | etot = -9.13334912361642 +563000 ekin = 1.24087113988324 | erot = 1.44233150298486 | epot = -11.8165517666192 | etot = -9.13334912375111 +564000 ekin = 1.25609129142956 | erot = 1.4969187586782 | epot = -11.8863591740616 | etot = -9.13334912395381 +565000 ekin = 1.27963015842528 | erot = 1.55937933471346 | epot = -11.9723586173274 | etot = -9.13334912418865 +566000 ekin = 1.30976945418407 | erot = 1.62795664726333 | epot = -12.0710752258958 | etot = -9.13334912444839 +567000 ekin = 1.344698735113 | erot = 1.70073738337239 | epot = -12.1787852431764 | etot = -9.13334912469102 +568000 ekin = 1.38275779930764 | erot = 1.77591787230402 | epot = -12.2920247965167 | etot = -9.13334912490504 +569000 ekin = 1.42260294142294 | erot = 1.85183127902069 | epot = -12.4077833455384 | etot = -9.1333491250948 +570000 ekin = 1.46311433096022 | erot = 1.92670412004672 | epot = -12.5231675763748 | etot = -9.13334912536789 +571000 ekin = 1.50327753328857 | erot = 1.99853100880341 | epot = -12.6351576677733 | etot = -9.13334912568128 +572000 ekin = 1.54192966726581 | erot = 2.06497613729518 | epot = -12.7402549304361 | etot = -9.13334912587511 +573000 ekin = 1.57823855406838 | erot = 2.12427016696112 | epot = -12.835857846987 | etot = -9.13334912595753 +574000 ekin = 1.61207502224081 | erot = 2.17570201380447 | epot = -12.9211261619157 | etot = -9.13334912587043 +575000 ekin = 1.64402582173477 | erot = 2.22028441013993 | epot = -12.9976593575004 | etot = -9.13334912562575 +576000 ekin = 1.67538587678027 | erot = 2.26042238856247 | epot = -13.0691573906338 | etot = -9.13334912529101 +577000 ekin = 1.70789209378595 | erot = 2.29915883242291 | epot = -13.1404000511767 | etot = -9.13334912496781 +578000 ekin = 1.74326819508035 | erot = 2.33909725076145 | epot = -13.2157145705905 | etot = -9.13334912474872 +579000 ekin = 1.7827223183793 | erot = 2.38182643841946 | epot = -13.2978978814936 | etot = -9.13334912469486 +580000 ekin = 1.82652189372618 | erot = 2.42751679139504 | epot = -13.3873878099544 | etot = -9.13334912483318 +581000 ekin = 1.87370675175069 | erot = 2.47480205693684 | epot = -13.4818579338617 | etot = -9.13334912517416 +582000 ekin = 1.92197052578215 | erot = 2.52092715153037 | epot = -13.5762468029727 | etot = -9.13334912566015 +583000 ekin = 1.96774925896673 | erot = 2.56227660801418 | epot = -13.6633749932215 | etot = -9.13334912624057 +584000 ekin = 2.0065737454006 | erot = 2.59498886542612 | epot = -13.7349117376471 | etot = -9.13334912682034 +585000 ekin = 2.03371871575598 | erot = 2.61566274200138 | epot = -13.7827305850398 | etot = -9.1333491272824 +586000 ekin = 2.04507827703247 | erot = 2.62214006251252 | epot = -13.8005674670615 | etot = -9.13334912751656 +587000 ekin = 2.03806243485687 | erot = 2.6141199488886 | epot = -13.7855315112053 | etot = -9.13334912745978 +588000 ekin = 2.01223115184467 | erot = 2.59335030111899 | epot = -13.7389305800891 | etot = -9.13334912712544 +589000 ekin = 1.96942837554751 | erot = 2.56324673362657 | epot = -13.6660242357784 | etot = -9.13334912660433 +590000 ekin = 1.91334419959251 | erot = 2.52801524733212 | epot = -13.5747085729566 | etot = -9.13334912603195 +591000 ekin = 1.84865383331094 | erot = 2.49158313368622 | epot = -13.4735860925327 | etot = -9.13334912553558 +592000 ekin = 1.78006004420174 | erot = 2.45674050608108 | epot = -13.370149675468 | etot = -9.13334912518518 +593000 ekin = 1.71159279762799 | erot = 2.42478693108793 | epot = -13.2697288536947 | etot = -9.13334912497879 +594000 ekin = 1.6463494640605 | erot = 2.39569805900865 | epot = -13.1753966479402 | etot = -9.13334912487103 +595000 ekin = 1.58659479949651 | erot = 2.36854432556728 | epot = -13.088488249883 | etot = -9.13334912481918 +596000 ekin = 1.53398103552138 | erot = 2.34182175784987 | epot = -13.0091519181817 | etot = -9.13334912481045 +597000 ekin = 1.48969441623305 | erot = 2.31355286210216 | epot = -12.9365964031866 | etot = -9.13334912485139 +598000 ekin = 1.45449014891121 | erot = 2.28129539495559 | epot = -12.8691346688093 | etot = -9.13334912494246 +599000 ekin = 1.42868283606617 | erot = 2.24230571379428 | epot = -12.8043376749212 | etot = -9.1333491250608 +600000 ekin = 1.41215819513413 | erot = 2.19421771508927 | epot = -12.7397250351208 | etot = -9.13334912489744 +601000 ekin = 1.40437980064227 | erot = 2.13675092848109 | epot = -12.674479854184 | etot = -9.1333491250606 +602000 ekin = 1.4044246685369 | erot = 2.06863595764279 | epot = -12.6064097512979 | etot = -9.13334912511825 +603000 ekin = 1.41112302449957 | erot = 1.98998056957538 | epot = -12.5344527191462 | etot = -9.13334912507128 +604000 ekin = 1.42310135152474 | erot = 1.90274524322857 | epot = -12.4591957196977 | etot = -9.13334912494436 +605000 ekin = 1.43883447822767 | erot = 1.81030632011133 | epot = -12.3824899231105 | etot = -9.13334912477148 +606000 ekin = 1.45673760095441 | erot = 1.71684240504894 | epot = -12.3069291305871 | etot = -9.1333491245837 +607000 ekin = 1.47529863713372 | erot = 1.62672298753086 | epot = -12.2353707490674 | etot = -9.13334912440278 +608000 ekin = 1.49323166610551 | erot = 1.54399943869127 | epot = -12.1705802290369 | etot = -9.1333491242401 +609000 ekin = 1.50961256615932 | erot = 1.47208306433965 | epot = -12.1150447546085 | etot = -9.13334912410951 +610000 ekin = 1.52396039431504 | erot = 1.41350705715129 | epot = -12.0708165754609 | etot = -9.13334912399459 +611000 ekin = 1.53622860047253 | erot = 1.36992443741221 | epot = -12.0395021618086 | etot = -9.13334912392381 +612000 ekin = 1.54668536626352 | erot = 1.3420536287302 | epot = -12.022088118904 | etot = -9.13334912391032 +613000 ekin = 1.55571309695795 | erot = 1.32960894335998 | epot = -12.0186711642892 | etot = -9.13334912397123 +614000 ekin = 1.56356369221823 | erot = 1.33131277562582 | epot = -12.0282255919648 | etot = -9.1333491241207 +615000 ekin = 1.57013881826772 | erot = 1.34494539761769 | epot = -12.0484333402228 | etot = -9.1333491243374 +616000 ekin = 1.57485681904011 | erot = 1.36757312206254 | epot = -12.0757790657607 | etot = -9.13334912465809 +617000 ekin = 1.57672646781302 | erot = 1.39546251366762 | epot = -12.1055381065033 | etot = -9.13334912502266 +618000 ekin = 1.57456346737885 | erot = 1.42448013453559 | epot = -12.1323927272923 | etot = -9.13334912537787 +619000 ekin = 1.56732946470188 | erot = 1.45059208152766 | epot = -12.1512706718918 | etot = -9.13334912566229 +620000 ekin = 1.55451321753947 | erot = 1.47039334455551 | epot = -12.1582556879147 | etot = -9.13334912581971 +621000 ekin = 1.53644782338443 | erot = 1.48161304590915 | epot = -12.1514099951067 | etot = -9.13334912581315 +622000 ekin = 1.51447783518411 | erot = 1.48347710481868 | epot = -12.1313040656377 | etot = -9.13334912563487 +623000 ekin = 1.4909296073309 | erot = 1.47683215248821 | epot = -12.1011108851279 | etot = -9.13334912530878 +624000 ekin = 1.46886130170089 | erot = 1.46422198591475 | epot = -12.0664324125264 | etot = -9.13334912491077 +625000 ekin = 1.45155188812702 | erot = 1.44918251594185 | epot = -12.034083528553 | etot = -9.1333491244841 +626000 ekin = 1.44224748157969 | erot = 1.43533399591641 | epot = -12.0109306015691 | etot = -9.13334912407302 +627000 ekin = 1.44381530880042 | erot = 1.42638005354647 | epot = -12.003544486083 | etot = -9.13334912373614 +628000 ekin = 1.4583308162018 | erot = 1.42560824875086 | epot = -12.0172881884907 | etot = -9.13334912353806 +629000 ekin = 1.48676985537134 | erot = 1.43535417576979 | epot = -12.0554731546297 | etot = -9.13334912348854 +630000 ekin = 1.52866417049231 | erot = 1.45689184513358 | epot = -12.1189051392522 | etot = -9.13334912362626 +631000 ekin = 1.58193413339033 | erot = 1.49015054897492 | epot = -12.2054338063838 | etot = -9.1333491240185 +632000 ekin = 1.64234851055789 | erot = 1.53357750658868 | epot = -12.3092751416895 | etot = -9.13334912454295 +633000 ekin = 1.70466841197193 | erot = 1.58426390210063 | epot = -12.4222814392228 | etot = -9.13334912515021 +634000 ekin = 1.76318354699534 | erot = 1.63860587790572 | epot = -12.5351385506359 | etot = -9.13334912573484 +635000 ekin = 1.81242625034957 | erot = 1.6930662732065 | epot = -12.6388416497418 | etot = -9.13334912618573 +636000 ekin = 1.84805557838285 | erot = 1.74492785470072 | epot = -12.7263325594988 | etot = -9.13334912641528 +637000 ekin = 1.86755595284879 | erot = 1.79286465559239 | epot = -12.7937697348522 | etot = -9.13334912641101 +638000 ekin = 1.87047357468901 | erot = 1.83697965057398 | epot = -12.8408023514706 | etot = -9.13334912620759 +639000 ekin = 1.85817220593361 | erot = 1.87849437006589 | epot = -12.8700157018816 | etot = -9.13334912588206 +640000 ekin = 1.83325502874958 | erot = 1.91930247136563 | epot = -12.885906625629 | etot = -9.13334912551383 +641000 ekin = 1.79889805051541 | erot = 1.96149522932208 | epot = -12.8937424049962 | etot = -9.13334912515873 +642000 ekin = 1.75833330344853 | erot = 2.00701454517116 | epot = -12.8986969734754 | etot = -9.13334912485567 +643000 ekin = 1.7145240073858 | erot = 2.05742054585042 | epot = -12.9052936778327 | etot = -9.13334912459647 +644000 ekin = 1.67006045206594 | erot = 2.11379950766605 | epot = -12.9172090841632 | etot = -9.13334912443116 +645000 ekin = 1.6271016919367 | erot = 2.17652829047733 | epot = -12.9369791067725 | etot = -9.13334912435849 +646000 ekin = 1.58731920571063 | erot = 2.24499987972293 | epot = -12.9656682098048 | etot = -9.13334912437124 +647000 ekin = 1.55192879849992 | erot = 2.31774723145711 | epot = -13.0030251544506 | etot = -9.1333491244936 +648000 ekin = 1.52155547404462 | erot = 2.39216849405107 | epot = -13.0470730928249 | etot = -9.13334912472924 +649000 ekin = 1.49615701172559 | erot = 2.46459269466501 | epot = -13.0940988314669 | etot = -9.13334912507634 +650000 ekin = 1.47495820408152 | erot = 2.53042613107585 | epot = -13.1387334606775 | etot = -9.13334912552013 +651000 ekin = 1.45644758275942 | erot = 2.58442104122347 | epot = -13.1742177500117 | etot = -9.13334912602884 +652000 ekin = 1.43848054670144 | erot = 2.62109720356023 | epot = -13.1929268768094 | etot = -9.13334912654773 +653000 ekin = 1.41853538646796 | erot = 2.63533318879136 | epot = -13.1872177022577 | etot = -9.13334912699843 +654000 ekin = 1.39414099594742 | erot = 2.6231144598761 | epot = -13.1506045831159 | etot = -9.13334912729234 +655000 ekin = 1.36342278664596 | erot = 2.58232798191637 | epot = -13.079099895894 | etot = -9.13334912733166 +656000 ekin = 1.32754554560004 | erot = 2.5134399730674 | epot = -12.9743346448115 | etot = -9.13334912614407 +657000 ekin = 1.0773875979354 | erot = 2.44669612963344 | epot = -12.6574327808031 | etot = -9.1333490532343 +658000 ekin = 1.00652014229837 | erot = 2.49084781646746 | epot = -12.6307170433245 | etot = -9.1333490845587 +659000 ekin = 1.0724008501772 | erot = 2.42929901831599 | epot = -12.6350489837806 | etot = -9.13334911528737 +660000 ekin = 1.09381648980751 | erot = 2.30102308261678 | epot = -12.5281886879207 | etot = -9.13334911549642 +661000 ekin = 1.11701334337948 | erot = 2.16959631554218 | epot = -12.4199587738168 | etot = -9.13334911489519 +662000 ekin = 1.14263894057925 | erot = 2.04231481245762 | epot = -12.3183028674869 | etot = -9.13334911444999 +663000 ekin = 1.17093665277013 | erot = 1.92510458369694 | epot = -12.2293903506443 | etot = -9.13334911417719 +664000 ekin = 1.20146324496735 | erot = 1.82207009510847 | epot = -12.1568824541656 | etot = -9.13334911408975 +665000 ekin = 1.23289032447861 | erot = 1.73564836427598 | epot = -12.1018878027966 | etot = -9.13334911404202 +666000 ekin = 1.2634046445509 | erot = 1.66702592668068 | epot = -12.0637796854962 | etot = -9.13334911426459 +667000 ekin = 1.29102574814457 | erot = 1.61488086820359 | epot = -12.0392557309122 | etot = -9.13334911456403 +668000 ekin = 1.31376054134788 | erot = 1.57649712773579 | epot = -12.0236067839909 | etot = -9.13334911490723 +669000 ekin = 1.32989404565327 | erot = 1.54828621181468 | epot = -12.0115293726975 | etot = -9.13334911522951 +670000 ekin = 1.33826340890624 | erot = 1.52640844797349 | epot = -11.9980209723658 | etot = -9.13334911548607 +671000 ekin = 1.33847461323227 | erot = 1.50724764864701 | epot = -11.9790713775213 | etot = -9.13334911564201 +672000 ekin = 1.3310196955457 | erot = 1.48781306139119 | epot = -11.9521818726164 | etot = -9.13334911567954 +673000 ekin = 1.31737035051081 | erot = 1.46610228052956 | epot = -11.916821746603 | etot = -9.13334911556259 +674000 ekin = 1.29992521798111 | erot = 1.44131241760667 | epot = -11.8745867509648 | etot = -9.13334911537702 +675000 ekin = 1.28129254582443 | erot = 1.41347048294432 | epot = -11.8281121439055 | etot = -9.13334911513675 +676000 ekin = 1.26413925333674 | erot = 1.38336835396468 | epot = -11.780856722188 | etot = -9.13334911488654 +677000 ekin = 1.25080949629945 | erot = 1.35227525692334 | epot = -11.7364338679145 | etot = -9.13334911469175 +678000 ekin = 1.24240325883856 | erot = 1.32122246363524 | epot = -11.6969748370321 | etot = -9.13334911455833 +679000 ekin = 1.23935164124742 | erot = 1.2912444646096 | epot = -11.6639452203564 | etot = -9.1333491144994 +680000 ekin = 1.24151057851686 | erot = 1.26358348831183 | epot = -11.638443181175 | etot = -9.13334911434632 +681000 ekin = 1.24810791985327 | erot = 1.2399896630032 | epot = -11.6214466973226 | etot = -9.13334911446615 +682000 ekin = 1.25738088472489 | erot = 1.22073219170612 | epot = -11.6114621910613 | etot = -9.13334911463026 +683000 ekin = 1.26715254864019 | erot = 1.2055490969498 | epot = -11.6060507604005 | etot = -9.13334911481056 +684000 ekin = 1.27521936884227 | erot = 1.1939299525669 | epot = -11.6024984363882 | etot = -9.13334911497905 +685000 ekin = 1.27965818657898 | erot = 1.18525667281205 | epot = -11.5982639744954 | etot = -9.13334911510434 +686000 ekin = 1.27906445706477 | erot = 1.17887846190965 | epot = -11.5912920341658 | etot = -9.13334911519141 +687000 ekin = 1.27268261753878 | erot = 1.17407129022315 | epot = -11.5801030230226 | etot = -9.13334911526067 +688000 ekin = 1.26041914406529 | erot = 1.17007604783625 | epot = -11.5638443071302 | etot = -9.13334911522864 +689000 ekin = 1.24287938495418 | erot = 1.16656725574487 | epot = -11.542795755857 | etot = -9.1333491151579 +690000 ekin = 1.22118240404812 | erot = 1.16336387131318 | epot = -11.5178953904215 | etot = -9.1333491150602 +691000 ekin = 1.19679867225218 | erot = 1.1603733923323 | epot = -11.4905211795315 | etot = -9.13334911494706 +692000 ekin = 1.17139142555508 | erot = 1.15758648593198 | epot = -11.4623270263156 | etot = -9.13334911482852 +693000 ekin = 1.14685376597351 | erot = 1.15519232867503 | epot = -11.43539520919 | etot = -9.13334911454148 +694000 ekin = 1.12537035278837 | erot = 1.15368599836397 | epot = -11.412405465606 | etot = -9.13334911445361 +695000 ekin = 1.10824764597647 | erot = 1.15324052660653 | epot = -11.3948372869662 | etot = -9.13334911438318 +696000 ekin = 1.09641524899318 | erot = 1.15407441364792 | epot = -11.3838387769767 | etot = -9.13334911433562 +697000 ekin = 1.09040706959969 | erot = 1.15645735234579 | epot = -11.3802135362638 | etot = -9.13334911431836 +698000 ekin = 1.09030542376423 | erot = 1.16063392710817 | epot = -11.3842884652019 | etot = -9.13334911432953 +699000 ekin = 1.09552536142149 | erot = 1.16669639941964 | epot = -11.3955708752043 | etot = -9.13334911436317 +700000 ekin = 1.10527379803376 | erot = 1.17478862116044 | epot = -11.413411533631 | etot = -9.13334911443681 +701000 ekin = 1.11851271408306 | erot = 1.18492470948339 | epot = -11.4367865380917 | etot = -9.13334911452528 +702000 ekin = 1.13395549372905 | erot = 1.19694667251844 | epot = -11.4642512808785 | etot = -9.13334911463097 +703000 ekin = 1.15018285433436 | erot = 1.2105705597151 | epot = -11.4941025287949 | etot = -9.13334911474541 +704000 ekin = 1.16576673458005 | erot = 1.22535908060259 | epot = -11.524474930041 | etot = -9.13334911485839 +705000 ekin = 1.1793891550362 | erot = 1.24076765314177 | epot = -11.5535059231369 | etot = -9.13334911495895 +706000 ekin = 1.18994261306461 | erot = 1.25622348494723 | epot = -11.5795152130483 | etot = -9.13334911503649 +707000 ekin = 1.19660107195649 | erot = 1.27122780267428 | epot = -11.601177989713 | etot = -9.13334911508226 +708000 ekin = 1.19885615186834 | erot = 1.28546332267772 | epot = -11.617668589637 | etot = -9.13334911509095 +709000 ekin = 1.19651981509624 | erot = 1.29888532038569 | epot = -11.6287542505429 | etot = -9.13334911506102 +710000 ekin = 1.1896995749728 | erot = 1.31177606554515 | epot = -11.6348247555135 | etot = -9.13334911499554 +711000 ekin = 1.17875387602993 | erot = 1.32474791483259 | epot = -11.6368509057646 | etot = -9.1333491149021 +712000 ekin = 1.16423391784039 | erot = 1.33868945229385 | epot = -11.6362724849257 | etot = -9.13334911479148 +713000 ekin = 1.14681758773241 | erot = 1.35466305350979 | epot = -11.634829755921 | etot = -9.13334911467886 +714000 ekin = 1.12724173590803 | erot = 1.37373509014099 | epot = -11.6343259406274 | etot = -9.13334911457843 +715000 ekin = 1.10624050750102 | erot = 1.39681075797783 | epot = -11.636400379983 | etot = -9.13334911450419 +716000 ekin = 1.08449847089099 | erot = 1.42446438144571 | epot = -11.642311966804 | etot = -9.13334911446735 +717000 ekin = 1.06262586730388 | erot = 1.45678801963117 | epot = -11.6527630014097 | etot = -9.13334911447468 +718000 ekin = 1.0411605651787 | erot = 1.49328580499053 | epot = -11.6677954846958 | etot = -9.13334911452653 +719000 ekin = 1.02059756446753 | erot = 1.53283565406685 | epot = -11.6867823331507 | etot = -9.13334911461631 +720000 ekin = 1.00144276091413 | erot = 1.57373478107905 | epot = -11.7085266567238 | etot = -9.13334911473058 +721000 ekin = 0.984282698240148 | erot = 1.61383653731177 | epot = -11.7314683504017 | etot = -9.13334911484982 +722000 ekin = 0.969856334574313 | erot = 1.65076935458844 | epot = -11.7539748041187 | etot = -9.13334911495596 +723000 ekin = 0.959109074095741 | erot = 1.68219090540859 | epot = -11.7746490945272 | etot = -9.1333491150229 +724000 ekin = 0.953206498551791 | erot = 1.70610525280311 | epot = -11.7926608663937 | etot = -9.13334911503875 +725000 ekin = 0.953487871457924 | erot = 1.72112406445268 | epot = -11.8079610509099 | etot = -9.13334911499929 +726000 ekin = 0.961348420447912 | erot = 1.72664218756335 | epot = -11.8213397229241 | etot = -9.1333491149128 +727000 ekin = 0.97805518699853 | erot = 1.72290320032706 | epot = -11.8343075021228 | etot = -9.13334911479718 +728000 ekin = 1.0045258249759 | erot = 1.71095374107079 | epot = -11.8488286807208 | etot = -9.1333491146741 +729000 ekin = 1.04110137579816 | erot = 1.69252215340752 | epot = -11.8669726437755 | etot = -9.13334911456981 +730000 ekin = 1.08735958690232 | erot = 1.66981008957876 | epot = -11.8905187909885 | etot = -9.13334911450745 +731000 ekin = 1.14200418374975 | erot = 1.64524141705888 | epot = -11.9205947153133 | etot = -9.13334911450468 +732000 ekin = 1.20285318014156 | erot = 1.62119095712991 | epot = -11.9573932518439 | etot = -9.13334911457242 +733000 ekin = 1.26692596391395 | erot = 1.5997652890977 | epot = -12.0000403677157 | etot = -9.13334911470405 +734000 ekin = 1.3306440641792 | erot = 1.58254289880402 | epot = -12.0465360778929 | etot = -9.13334911490972 +735000 ekin = 1.3901348438841 | erot = 1.57032898633128 | epot = -12.0938129453762 | etot = -9.13334911516082 +736000 ekin = 1.44157509139514 | erot = 1.56317476788492 | epot = -12.1380989747094 | etot = -9.1333491154293 +737000 ekin = 1.48157845589663 | erot = 1.56044545881387 | epot = -12.1753730303891 | etot = -9.13334911567864 +738000 ekin = 1.50757504378022 | erot = 1.56100911666954 | epot = -12.2019332763196 | etot = -9.13334911586983 +739000 ekin = 1.51813561812344 | erot = 1.56352092529404 | epot = -12.2150056593848 | etot = -9.13334911596734 +740000 ekin = 1.51318914849279 | erot = 1.56675183784976 | epot = -12.2132901022895 | etot = -9.13334911594693 +741000 ekin = 1.494088658301 | erot = 1.56989906103947 | epot = -12.1973368351411 | etot = -9.13334911580064 +742000 ekin = 1.46350061535639 | erot = 1.57280025700594 | epot = -12.1696499879049 | etot = -9.13334911554256 +743000 ekin = 1.42512524133893 | erot = 1.57593310600626 | epot = -12.1344074625137 | etot = -9.13334911516847 +744000 ekin = 1.38338487585334 | erot = 1.5805436127817 | epot = -12.0972776034334 | etot = -9.1333491147984 +745000 ekin = 1.34281951274038 | erot = 1.58823582840455 | epot = -12.0644044556013 | etot = -9.13334911445635 +746000 ekin = 1.30747334765451 | erot = 1.60047096980636 | epot = -12.0412934316595 | etot = -9.13334911419865 +747000 ekin = 1.28046646005545 | erot = 1.61821768665577 | epot = -12.0320332608048 | etot = -9.13334911409364 +748000 ekin = 1.2636795592375 | erot = 1.64132893143221 | epot = -12.0383576048404 | etot = -9.13334911417067 +749000 ekin = 1.2574293442015 | erot = 1.66831440024257 | epot = -12.0590928588826 | etot = -9.1333491144385 +750000 ekin = 1.26047795507978 | erot = 1.69628448614573 | epot = -12.090111556077 | etot = -9.13334911485146 +751000 ekin = 1.27026186447295 | erot = 1.72133386885839 | epot = -12.1249448486719 | etot = -9.13334911534054 +752000 ekin = 1.28339547086523 | erot = 1.73919075505692 | epot = -12.1559353417316 | etot = -9.13334911580946 +753000 ekin = 1.29635957466786 | erot = 1.74596876191851 | epot = -12.1756774528061 | etot = -9.13334911621977 +754000 ekin = 1.30599158741058 | erot = 1.73885024063263 | epot = -12.1781909444319 | etot = -9.13334911638871 +755000 ekin = 1.31024888116237 | erot = 1.71683511468117 | epot = -12.1604331121855 | etot = -9.13334911634191 +756000 ekin = 1.30846938321599 | erot = 1.68097972249568 | epot = -12.122798221804 | etot = -9.13334911609235 +757000 ekin = 1.30124985041447 | erot = 1.63419006476499 | epot = -12.0687890308692 | etot = -9.1333491156897 +758000 ekin = 1.29019641090577 | erot = 1.58073563388991 | epot = -12.0042811600005 | etot = -9.13334911520485 +759000 ekin = 1.27761222227675 | erot = 1.52554636406469 | epot = -11.9365077010407 | etot = -9.13334911469927 +760000 ekin = 1.26609069506809 | erot = 1.47348693038545 | epot = -11.8729267397129 | etot = -9.1333491142594 +761000 ekin = 1.25808964011679 | erot = 1.4286955046248 | epot = -11.8201342586658 | etot = -9.13334911392424 +762000 ekin = 1.25572222200592 | erot = 1.39407442311272 | epot = -11.783145758868 | etot = -9.13334911374938 +763000 ekin = 1.26054534569765 | erot = 1.37090045944091 | epot = -11.7647949188348 | etot = -9.13334911369624 +764000 ekin = 1.27353435439959 | erot = 1.35887199086233 | epot = -11.7657554590542 | etot = -9.13334911379228 +765000 ekin = 1.29496682599886 | erot = 1.35616457698051 | epot = -11.7844805169728 | etot = -9.13334911399346 +766000 ekin = 1.32454629042167 | erot = 1.35977679502717 | epot = -11.8176721997125 | etot = -9.1333491142637 +767000 ekin = 1.36163954271813 | erot = 1.36618632223691 | epot = -11.8611749795106 | etot = -9.13334911455553 +768000 ekin = 1.40531019892548 | erot = 1.37181010083209 | epot = -11.9104694145872 | etot = -9.13334911482959 +769000 ekin = 1.45446512869009 | erot = 1.37353498051008 | epot = -11.9613492242412 | etot = -9.133349115041 +770000 ekin = 1.50793050152268 | erot = 1.36921125649596 | epot = -12.0104908732554 | etot = -9.13334911523675 +771000 ekin = 1.56389616693286 | erot = 1.35775090660939 | epot = -12.0549961888008 | etot = -9.13334911525855 +772000 ekin = 1.62113703504456 | erot = 1.33970323504921 | epot = -12.0941893852832 | etot = -9.1333491151894 +773000 ekin = 1.67872851569461 | erot = 1.31702982988939 | epot = -12.1291074606468 | etot = -9.13334911506284 +774000 ekin = 1.73569257108714 | erot = 1.29264163250421 | epot = -12.1616833185143 | etot = -9.13334911492296 +775000 ekin = 1.79085656133396 | erot = 1.26988000052048 | epot = -12.1940856766665 | etot = -9.13334911481206 +776000 ekin = 1.84276100467974 | erot = 1.25197534038132 | epot = -12.2280854598203 | etot = -9.13334911475925 +777000 ekin = 1.88967118603443 | erot = 1.24159765891606 | epot = -12.2646179597232 | etot = -9.13334911477269 +778000 ekin = 1.92971622260319 | erot = 1.2405758321466 | epot = -12.3036411695912 | etot = -9.13334911484138 +779000 ekin = 1.96113164254476 | erot = 1.24980912493539 | epot = -12.3442898824213 | etot = -9.13334911494117 +780000 ekin = 1.98254203385816 | erot = 1.26932045667053 | epot = -12.385211605573 | etot = -9.13334911504432 +781000 ekin = 1.99321406405247 | erot = 1.29840823518634 | epot = -12.424971414369 | etot = -9.13334911513024 +782000 ekin = 1.99321095940316 | erot = 1.33580885492091 | epot = -12.4623689295127 | etot = -9.13334911518861 +783000 ekin = 1.98342491293014 | erot = 1.37983642298321 | epot = -12.4966104511316 | etot = -9.13334911521824 +784000 ekin = 1.96551238429564 | erot = 1.42849371621145 | epot = -12.5273552156776 | etot = -9.13334911517052 +785000 ekin = 1.94195910111626 | erot = 1.47961348821668 | epot = -12.5549217044948 | etot = -9.13334911516186 +786000 ekin = 1.91549982325751 | erot = 1.53087711626559 | epot = -12.5797260546598 | etot = -9.13334911513665 +787000 ekin = 1.8890291593285 | erot = 1.5799756597558 | epot = -12.6023539341779 | etot = -9.13334911509364 +788000 ekin = 1.86553746553843 | erot = 1.624786460251 | epot = -12.6236730408275 | etot = -9.13334911503805 +789000 ekin = 1.84793067284063 | erot = 1.6635057242642 | epot = -12.6447855120696 | etot = -9.13334911496478 +790000 ekin = 1.83884831412084 | erot = 1.6947732587169 | epot = -12.6669706877328 | etot = -9.13334911489506 +791000 ekin = 1.84038435201475 | erot = 1.71768127848555 | epot = -12.6914147453562 | etot = -9.13334911485594 +792000 ekin = 1.85374621231288 | erot = 1.73169683790445 | epot = -12.7187921650957 | etot = -9.13334911487841 +793000 ekin = 1.87892178729818 | erot = 1.73653576924259 | epot = -12.7488066715272 | etot = -9.13334911498642 +794000 ekin = 1.91440510045617 | erot = 1.73204169928025 | epot = -12.7797959149158 | etot = -9.1333491151794 +795000 ekin = 1.9572669787266 | erot = 1.71818976217474 | epot = -12.8088058563225 | etot = -9.13334911542115 +796000 ekin = 2.00360851779916 | erot = 1.69525335459208 | epot = -12.8322109880396 | etot = -9.13334911564835 +797000 ekin = 2.04914358120658 | erot = 1.66405946741855 | epot = -12.8465521644156 | etot = -9.13334911579048 +798000 ekin = 2.08995546227692 | erot = 1.6262374595251 | epot = -12.8495420376053 | etot = -9.13334911580325 +799000 ekin = 2.12309292251422 | erot = 1.58427028116194 | epot = -12.8407123193635 | etot = -9.13334911568735 +800000 ekin = 2.14682990847686 | erot = 1.54126138559232 | epot = -12.8214404095517 | etot = -9.13334911548252 +801000 ekin = 2.16058282772883 | erot = 1.50048202046929 | epot = -12.7944139634446 | etot = -9.13334911524647 +802000 ekin = 2.16461511109508 | erot = 1.4648661550268 | epot = -12.7628303811528 | etot = -9.13334911503096 +803000 ekin = 2.15969104316568 | erot = 1.43661335441871 | epot = -12.7296535124535 | etot = -9.13334911486915 +804000 ekin = 2.14679128687981 | erot = 1.41698988507951 | epot = -12.6971302867191 | etot = -9.1333491147598 +805000 ekin = 2.12692065944037 | erot = 1.40638520514516 | epot = -12.6666549793105 | etot = -9.13334911472493 +806000 ekin = 2.10099028263577 | erot = 1.40422932574766 | epot = -12.6385687231448 | etot = -9.13334911476135 +807000 ekin = 2.06982763841923 | erot = 1.40909451158422 | epot = -12.6122712648422 | etot = -9.13334911483878 +808000 ekin = 2.03419092297893 | erot = 1.41919422166591 | epot = -12.5867342595742 | etot = -9.13334911492934 +809000 ekin = 1.99478586656104 | erot = 1.43238858340905 | epot = -12.5605235650235 | etot = -9.1333491150534 +810000 ekin = 1.95230744546777 | erot = 1.44625258192922 | epot = -12.5319091425729 | etot = -9.1333491151759 +811000 ekin = 1.90747094188883 | erot = 1.45847148723609 | epot = -12.4992915444085 | etot = -9.13334911528359 +812000 ekin = 1.86102893102719 | erot = 1.46703963548782 | epot = -12.4614176818789 | etot = -9.13334911536387 +813000 ekin = 1.81416432243589 | erot = 1.4704986890784 | epot = -12.4180121266511 | etot = -9.13334911513678 +814000 ekin = 1.76902926167611 | erot = 1.46826739311543 | epot = -12.3706457700776 | etot = -9.13334911528603 +815000 ekin = 1.71533069952235 | erot = 1.45797598424652 | epot = -12.3066557947939 | etot = -9.13334911102499 +816000 ekin = 1.68468183702939 | erot = 1.43935942019659 | epot = -12.2573903676342 | etot = -9.13334911040824 +817000 ekin = 1.67569540451429 | erot = 1.4202275919336 | epot = -12.2292721045971 | etot = -9.13334910814921 +818000 ekin = 1.65431804078162 | erot = 1.40071144600318 | epot = -12.1883785945462 | etot = -9.13334910776142 +819000 ekin = 1.63740188371065 | erot = 1.38256931717011 | epot = -12.153320308267 | etot = -9.13334910738622 +820000 ekin = 1.62512170450081 | erot = 1.36928168853139 | epot = -12.1277525000567 | etot = -9.1333491070245 +821000 ekin = 1.61915909097092 | erot = 1.36404110716092 | epot = -12.11654930484 | etot = -9.13334910670812 +822000 ekin = 1.62172343975808 | erot = 1.36925913747897 | epot = -12.1243316837552 | etot = -9.1333491065182 +823000 ekin = 1.63427494812446 | erot = 1.38616632190815 | epot = -12.1537903765421 | etot = -9.13334910650952 +824000 ekin = 1.65698382617878 | erot = 1.41459711185232 | epot = -12.2049300447245 | etot = -9.1333491066934 +825000 ekin = 1.68854753273546 | erot = 1.45301631841537 | epot = -12.2749129581896 | etot = -9.13334910703881 +826000 ekin = 1.72638863496051 | erot = 1.49875661579281 | epot = -12.3584943582419 | etot = -9.13334910748853 +827000 ekin = 1.76710423380876 | erot = 1.54839439233899 | epot = -12.4488477341244 | etot = -9.13334910797666 +828000 ekin = 1.80698482334325 | erot = 1.59818184901007 | epot = -12.5385157807984 | etot = -9.13334910844504 +829000 ekin = 1.84246939970613 | erot = 1.64447465717755 | epot = -12.6202931657296 | etot = -9.13334910884588 +830000 ekin = 1.87048980344135 | erot = 1.68412933438833 | epot = -12.6879682469707 | etot = -9.133349109141 +831000 ekin = 1.88871335828747 | erot = 1.7148664541795 | epot = -12.7369289217676 | etot = -9.13334910930059 +832000 ekin = 1.89569916792697 | erot = 1.73558694751866 | epot = -12.764635224751 | etot = -9.13334910930536 +833000 ekin = 1.89096344936422 | erot = 1.74659447551969 | epot = -12.7709070340386 | etot = -9.13334910915468 +834000 ekin = 1.87493429545542 | erot = 1.74964392180539 | epot = -12.7579273261507 | etot = -9.13334910888991 +835000 ekin = 1.84878280514662 | erot = 1.74762027308213 | epot = -12.7297521867536 | etot = -9.13334910852485 +836000 ekin = 1.81414476909893 | erot = 1.74421722088884 | epot = -12.6917110981285 | etot = -9.13334910814076 +837000 ekin = 1.7727787546756 | erot = 1.74335285139652 | epot = -12.6494807138765 | etot = -9.1333491078044 +838000 ekin = 1.72624445531611 | erot = 1.74841404792743 | epot = -12.6080076108106 | etot = -9.1333491075671 +839000 ekin = 1.67568816110943 | erot = 1.76165550554581 | epot = -12.570692774111 | etot = -9.1333491074558 +840000 ekin = 1.62179135099532 | erot = 1.78387657045993 | epot = -12.539017028912 | etot = -9.13334910745679 +841000 ekin = 1.56488441151317 | erot = 1.8145657394287 | epot = -12.5127992584805 | etot = -9.13334910753866 +842000 ekin = 1.50517399563021 | erot = 1.85205645864973 | epot = -12.4905795619779 | etot = -9.133349107698 +843000 ekin = 1.44300548283947 | erot = 1.89358112522319 | epot = -12.4699357158698 | etot = -9.13334910780714 +844000 ekin = 1.3790662063083 | erot = 1.93639685186287 | epot = -12.4488121660428 | etot = -9.13334910787166 +845000 ekin = 1.31446352833072 | erot = 1.97812996436346 | epot = -12.4259426005661 | etot = -9.13334910787188 +846000 ekin = 1.25068692329101 | erot = 2.01700234953533 | epot = -12.4010383806301 | etot = -9.13334910780379 +847000 ekin = 1.18947724707585 | erot = 2.05204320491572 | epot = -12.3748695596675 | etot = -9.1333491076759 +848000 ekin = 1.13265732504311 | erot = 2.08314733277938 | epot = -12.3491537653274 | etot = -9.13334910750494 +849000 ekin = 1.08197657769554 | erot = 2.11099249694411 | epot = -12.3263181819498 | etot = -9.13334910731013 +850000 ekin = 1.03899924537585 | erot = 2.13684654284267 | epot = -12.3091948953317 | etot = -9.13334910711322 +851000 ekin = 1.00503792489241 | erot = 2.1623061869887 | epot = -12.3006932188161 | etot = -9.13334910693494 +852000 ekin = 0.981116857867558 | erot = 2.18901371773059 | epot = -12.3034796823913 | etot = -9.13334910679312 +853000 ekin = 0.967947652219077 | erot = 2.21839549971936 | epot = -12.319692258642 | etot = -9.13334910670357 +854000 ekin = 0.965908910684845 | erot = 2.25145766400305 | epot = -12.3507156813619 | etot = -9.13334910667397 +855000 ekin = 0.975031148289229 | erot = 2.28866143867603 | epot = -12.3970416936717 | etot = -9.13334910670648 +856000 ekin = 0.994993726115382 | erot = 2.32988587265752 | epot = -12.4582287055698 | etot = -9.13334910679695 +857000 ekin = 1.02514000045782 | erot = 2.37447147763668 | epot = -12.5329605850303 | etot = -9.13334910693584 +858000 ekin = 1.06451194042942 | erot = 2.4213258126328 | epot = -12.6191868601726 | etot = -9.13334910711038 +859000 ekin = 1.11189872921004 | erot = 2.46906217646423 | epot = -12.7143100129823 | etot = -9.13334910730799 +860000 ekin = 1.16588800432633 | erot = 2.51613734356883 | epot = -12.8153744554142 | etot = -9.13334910751906 +861000 ekin = 1.22490604809684 | erot = 2.56095681692958 | epot = -12.9192119727658 | etot = -9.13334910773933 +862000 ekin = 1.28723632580519 | erot = 2.60192847235763 | epot = -13.0225139061331 | etot = -9.1333491079703 +863000 ekin = 1.35101431938172 | erot = 2.63746581474587 | epot = -13.1218292423438 | etot = -9.13334910821618 +864000 ekin = 1.41420820518621 | erot = 2.66596355873972 | epot = -13.213520872406 | etot = -9.1333491084801 +865000 ekin = 1.474605629288 | erot = 2.68578195463931 | epot = -13.2937366926875 | etot = -9.13334910876019 +866000 ekin = 1.52983303720862 | erot = 2.69527584727287 | epot = -13.3584579935269 | etot = -9.13334910904543 +867000 ekin = 1.57743376517003 | erot = 2.69288933096463 | epot = -13.4036722054498 | etot = -9.13334910931511 +868000 ekin = 1.61502389037619 | erot = 2.67731200501023 | epot = -13.4256850049263 | etot = -9.13334910953988 +869000 ekin = 1.64053051308626 | erot = 2.64766625528208 | epot = -13.4215458780546 | etot = -9.1333491096863 +870000 ekin = 1.65249590025612 | erot = 2.60367561916686 | epot = -13.3895206291465 | etot = -9.13334910972348 +871000 ekin = 1.65040511754571 | erot = 2.54576053414804 | epot = -13.3295147613243 | etot = -9.13334910963058 +872000 ekin = 1.63497077371797 | erot = 2.47502461263687 | epot = -13.2433444957577 | etot = -9.13334910940288 +873000 ekin = 1.60829551087388 | erot = 2.39312864671266 | epot = -13.1347732666412 | etot = -9.13334910905463 +874000 ekin = 1.57383856498918 | erot = 2.30208675136389 | epot = -13.009274424972 | etot = -9.13334910861897 +875000 ekin = 1.53613967513714 | erot = 2.20404109164996 | epot = -12.8735298749316 | etot = -9.13334910814452 +876000 ekin = 1.50030007472729 | erot = 2.10106901468676 | epot = -12.7347181971028 | etot = -9.13334910768871 +877000 ekin = 1.47128183651296 | erot = 1.99505592487128 | epot = -12.5996868686922 | etot = -9.13334910730796 +878000 ekin = 1.45315269236055 | erot = 1.88764504253869 | epot = -12.4741468419449 | etot = -9.13334910704562 +879000 ekin = 1.44845009593538 | erot = 1.78026193724959 | epot = -12.3620611401048 | etot = -9.13334910691979 +880000 ekin = 1.45783397195063 | erot = 1.67420503622105 | epot = -12.2653881150899 | etot = -9.13334910691825 +881000 ekin = 1.48012455417224 | erot = 1.57078382964539 | epot = -12.1842574908196 | etot = -9.13334910700192 +882000 ekin = 1.5127001573733 | erot = 1.47147015192622 | epot = -12.1175194164183 | etot = -9.13334910711883 +883000 ekin = 1.55211568291855 | erot = 1.37801244883281 | epot = -12.0634772389729 | etot = -9.13334910722158 +884000 ekin = 1.59475301549602 | erot = 1.29246300163248 | epot = -12.0205651244085 | etot = -9.13334910727997 +885000 ekin = 1.63734681491989 | erot = 1.21709221485478 | epot = -11.9877881370596 | etot = -9.13334910728496 +886000 ekin = 1.6773121129974 | erot = 1.15420415260773 | epot = -11.9648653728496 | etot = -9.1333491072445 +887000 ekin = 1.71288068344983 | erot = 1.1059016506412 | epot = -11.9521314412663 | etot = -9.13334910717523 +888000 ekin = 1.74309500656233 | erot = 1.07385834531352 | epot = -11.9503024589725 | etot = -9.13334910709663 +889000 ekin = 1.7677096909044 | erot = 1.05913784424729 | epot = -11.9601966421798 | etot = -9.13334910702809 +890000 ekin = 1.78703240995309 | erot = 1.06207375035544 | epot = -11.9824552672965 | etot = -9.13334910698797 +891000 ekin = 1.80172329223837 | erot = 1.08220747466607 | epot = -12.0172798738974 | etot = -9.133349106993 +892000 ekin = 1.81257293681694 | erot = 1.11828058018496 | epot = -12.0642026240581 | etot = -9.13334910705617 +893000 ekin = 1.82028982710525 | erot = 1.16828769625244 | epot = -12.1219266305388 | etot = -9.13334910718111 +894000 ekin = 1.82533649727321 | erot = 1.22960280171717 | epot = -12.1882884063516 | etot = -9.13334910736122 +895000 ekin = 1.82785071658659 | erot = 1.2991877547125 | epot = -12.2603875788756 | etot = -9.13334910757654 +896000 ekin = 1.82766966747087 | erot = 1.373875833364 | epot = -12.3348946086321 | etot = -9.13334910779723 +897000 ekin = 1.8244460380743 | erot = 1.45069893544176 | epot = -12.4084940815062 | etot = -9.13334910799018 +898000 ekin = 1.81781661005142 | erot = 1.52720356356303 | epot = -12.4783692817419 | etot = -9.13334910812749 +899000 ekin = 1.80756915108884 | erot = 1.60168843028469 | epot = -12.5426066895668 | etot = -9.13334910819328 +900000 ekin = 1.79375843955228 | erot = 1.67330364931061 | epot = -12.600411197052 | etot = -9.13334910818907 +901000 ekin = 1.7767431847529 | erot = 1.74197941465417 | epot = -12.6520717075394 | etot = -9.1333491081323 +902000 ekin = 1.75714245727952 | erot = 1.80819394408218 | epot = -12.6986855094136 | etot = -9.13334910805189 +903000 ekin = 1.73573344440651 | erot = 1.8726332599149 | epot = -12.7417158123012 | etot = -9.13334910797977 +904000 ekin = 1.71332625907696 | erot = 1.93582474193256 | epot = -12.7825001089525 | etot = -9.13334910794303 +905000 ekin = 1.69065428569544 | erot = 1.99783248440657 | epot = -12.8218358780583 | etot = -9.13334910795628 +906000 ekin = 1.66831072855338 | erot = 2.05808381418786 | epot = -12.8597436507616 | etot = -9.13334910802032 +907000 ekin = 1.64674588303224 | erot = 2.11535919822829 | epot = -12.895454189381 | etot = -9.1333491081205 +908000 ekin = 1.62631907113484 | erot = 2.16793324011555 | epot = -12.9276014194855 | etot = -9.13334910823515 +909000 ekin = 1.60738004100026 | erot = 2.21381581982329 | epot = -12.9545449691648 | etot = -9.13334910834128 +910000 ekin = 1.59034402491222 | erot = 2.25102295600224 | epot = -12.9747160893366 | etot = -9.1333491084221 +911000 ekin = 1.57572782710918 | erot = 2.277814880823 | epot = -12.9868918164009 | etot = -9.13334910846875 +912000 ekin = 1.56413054683344 | erot = 2.29287003003948 | epot = -12.9903496853528 | etot = -9.1333491084799 +913000 ekin = 1.55616398737713 | erot = 2.29539983334109 | epot = -12.9849129291763 | etot = -9.1333491084581 +914000 ekin = 1.55235379274339 | erot = 2.28522760386805 | epot = -12.9709305050182 | etot = -9.13334910840677 +915000 ekin = 1.55303636075823 | erot = 2.26284508696911 | epot = -12.949230556057 | etot = -9.13334910832969 +916000 ekin = 1.5582700337317 | erot = 2.22943339360568 | epot = -12.9210525355706 | etot = -9.13334910823322 +917000 ekin = 1.56776924055646 | erot = 2.18681551598596 | epot = -12.8879338646704 | etot = -9.13334910812794 +918000 ekin = 1.58086450735377 | erot = 2.13731406706591 | epot = -12.8515276824491 | etot = -9.13334910802945 +919000 ekin = 1.59649190921214 | erot = 2.08351907894052 | epot = -12.8133600961064 | etot = -9.13334910795375 +920000 ekin = 1.61321892883211 | erot = 2.02800735916828 | epot = -12.7745753959137 | etot = -9.13334910791327 +921000 ekin = 1.62931395437318 | erot = 1.97307497751045 | epot = -12.7357380397974 | etot = -9.13334910791372 +922000 ekin = 1.64286104746273 | erot = 1.92053870341358 | epot = -12.6967488588275 | etot = -9.13334910795121 +923000 ekin = 1.65191234390639 | erot = 1.87163759208555 | epot = -12.6568990440064 | etot = -9.13334910801449 +924000 ekin = 1.65466206200986 | erot = 1.82703710613807 | epot = -12.6150482762349 | etot = -9.13334910808699 +925000 ekin = 1.64962158355783 | erot = 1.78691680128999 | epot = -12.5698874929983 | etot = -9.13334910815045 +926000 ekin = 1.63577435705576 | erot = 1.75111283231246 | epot = -12.5202362975557 | etot = -9.13334910818743 +927000 ekin = 1.61269412580611 | erot = 1.71928618608352 | epot = -12.4653294200734 | etot = -9.13334910818379 +928000 ekin = 1.58061327338008 | erot = 1.6910938751334 | epot = -12.4050562566434 | etot = -9.1333491081299 +929000 ekin = 1.54043465718159 | erot = 1.66634444993994 | epot = -12.3401282151427 | etot = -9.13334910802119 +930000 ekin = 1.49368612296493 | erot = 1.64511875929571 | epot = -12.2721539901209 | etot = -9.13334910786024 +931000 ekin = 1.44242020035224 | erot = 1.62783092394303 | epot = -12.2036002319534 | etot = -9.13334910765818 +932000 ekin = 1.38906420477439 | erot = 1.61520048768146 | epot = -12.1376137998919 | etot = -9.13334910743607 +933000 ekin = 1.33622958395717 | erot = 1.6081156841027 | epot = -12.0776943752833 | etot = -9.1333491072234 +934000 ekin = 1.2864948698263 | erot = 1.60739378972857 | epot = -12.0272377666101 | etot = -9.13334910705527 +935000 ekin = 1.24218246525151 | erot = 1.61347919083391 | epot = -11.9890107630505 | etot = -9.1333491069651 +936000 ekin = 1.20515312897653 | erot = 1.62614770365951 | epot = -11.964649939614 | etot = -9.13334910697793 +937000 ekin = 1.17664231216556 | erot = 1.64429583354665 | epot = -11.9542872528177 | etot = -9.13334910710546 +938000 ekin = 1.15716006420695 | erot = 1.66588444175091 | epot = -11.9563936132983 | etot = -9.13334910734043 +939000 ekin = 1.14647171711249 | erot = 1.68810326831496 | epot = -11.9679240930752 | etot = -9.13334910764771 +940000 ekin = 1.14367004081528 | erot = 1.70771457433425 | epot = -11.9847337231466 | etot = -9.13334910799707 +941000 ekin = 1.14733884563713 | erot = 1.72149292699604 | epot = -12.0021808809557 | etot = -9.13334910832257 +942000 ekin = 1.15580134680936 | erot = 1.7268730043979 | epot = -12.0160234597704 | etot = -9.1333491085631 +943000 ekin = 1.16743729513902 | erot = 1.72249936624965 | epot = -12.0232857700545 | etot = -9.13334910866583 +944000 ekin = 1.18103106475074 | erot = 1.70858712463335 | epot = -12.0229672979861 | etot = -9.13334910860203 +945000 ekin = 1.19606804454282 | erot = 1.68696892706269 | epot = -12.0163860799892 | etot = -9.13334910838369 +946000 ekin = 1.21284058109939 | erot = 1.6607587024864 | epot = -12.0069483916586 | etot = -9.13334910807286 +947000 ekin = 1.23222210572639 | erot = 1.63367011138998 | epot = -11.9992413248881 | etot = -9.1333491077717 +948000 ekin = 1.25509690715378 | erot = 1.60916358071506 | epot = -11.997609595456 | etot = -9.13334910758714 +949000 ekin = 1.28167104220527 | erot = 1.58969080393641 | epot = -12.0047109537222 | etot = -9.13334910758053 +950000 ekin = 1.31105510037785 | erot = 1.57628415674534 | epot = -12.0206883648616 | etot = -9.13334910773845 +951000 ekin = 1.34140314928201 | erot = 1.56859135849962 | epot = -12.043343615765 | etot = -9.13334910798332 +952000 ekin = 1.37054117668376 | erot = 1.56526000759508 | epot = -12.0691502925007 | etot = -9.13334910822188 +953000 ekin = 1.39670348101113 | erot = 1.56444621742767 | epot = -12.0944988068314 | etot = -9.13334910839263 +954000 ekin = 1.4189752923736 | erot = 1.56423287015354 | epot = -12.1165572710098 | etot = -9.13334910848266 +955000 ekin = 1.43729048069879 | erot = 1.56287479953591 | epot = -12.1335143887467 | etot = -9.13334910851205 +956000 ekin = 1.4521106633202 | erot = 1.55892938548409 | epot = -12.1443891573107 | etot = -9.13334910850645 +957000 ekin = 1.46402190622609 | erot = 1.55132217596935 | epot = -12.1486931906794 | etot = -9.13334910848397 +958000 ekin = 1.47342593725099 | erot = 1.53954965712517 | epot = -12.1463247028127 | etot = -9.13334910843657 +959000 ekin = 1.48038578494467 | erot = 1.52394133602027 | epot = -12.1376762293246 | etot = -9.13334910835967 +960000 ekin = 1.48460604033713 | erot = 1.50575363437733 | epot = -12.1237087829604 | etot = -9.13334910824597 +961000 ekin = 1.48549975935824 | erot = 1.48721075412757 | epot = -12.106059621579 | etot = -9.13334910809315 +962000 ekin = 1.48229853496176 | erot = 1.47141202583608 | epot = -12.087059668705 | etot = -9.1333491079072 +963000 ekin = 1.47417603271992 | erot = 1.46210240867559 | epot = -12.0696275490978 | etot = -9.13334910770234 +964000 ekin = 1.46036644524951 | erot = 1.46332191689092 | epot = -12.0570374696377 | etot = -9.13334910749723 +965000 ekin = 1.44026662181988 | erot = 1.47896324786461 | epot = -12.0525789770028 | etot = -9.13334910731835 +966000 ekin = 1.41351583400694 | erot = 1.51227943251762 | epot = -12.059144373716 | etot = -9.13334910719145 +967000 ekin = 1.38005134112423 | erot = 1.56539665062614 | epot = -12.0787970988913 | etot = -9.13334910714088 +968000 ekin = 1.34025482724925 | erot = 1.63885686277268 | epot = -12.112460797199 | etot = -9.13334910717708 +969000 ekin = 1.29476921982041 | erot = 1.73132793710645 | epot = -12.1594462642505 | etot = -9.13334910732368 +970000 ekin = 1.2444200539345 | erot = 1.83972520712468 | epot = -12.2174943685998 | etot = -9.13334910754062 +971000 ekin = 1.19046696427998 | erot = 1.95943091409337 | epot = -12.2832469861702 | etot = -9.13334910779685 +972000 ekin = 1.13463097114403 | erot = 2.08475088502484 | epot = -12.352730964219 | etot = -9.13334910805015 +973000 ekin = 1.07911059568601 | erot = 2.20953944501925 | epot = -12.4219991489639 | etot = -9.13334910825864 +974000 ekin = 1.02657367042271 | erot = 2.32774347840179 | epot = -12.4876662572494 | etot = -9.13334910842495 +975000 ekin = 0.979977932774985 | erot = 2.43392801404294 | epot = -12.5472550553053 | etot = -9.13334910848734 +976000 ekin = 0.942304887107112 | erot = 2.52399013955702 | epot = -12.5996441351383 | etot = -9.13334910847414 +977000 ekin = 0.916335295713485 | erot = 2.59517570124226 | epot = -12.644860105367 | etot = -9.13334910841129 +978000 ekin = 0.904316422898909 | erot = 2.64601698757917 | epot = -12.6836825188106 | etot = -9.13334910833249 +979000 ekin = 0.907654941515727 | erot = 2.67612704045912 | epot = -12.7171310902444 | etot = -9.1333491082696 +980000 ekin = 0.926700183442384 | erot = 2.6859274466418 | epot = -12.7459767383294 | etot = -9.13334910824517 +981000 ekin = 0.960659745244906 | erot = 2.67638285527738 | epot = -12.7703917087897 | etot = -9.13334910826743 +982000 ekin = 1.00766017971614 | erot = 2.64879736701335 | epot = -12.7898066550607 | etot = -9.13334910833125 +983000 ekin = 1.06493892794418 | erot = 2.60470505316654 | epot = -12.8029930895288 | etot = -9.13334910841807 +984000 ekin = 1.12913508942183 | erot = 2.54586103456153 | epot = -12.8083452324841 | etot = -9.1333491085007 +985000 ekin = 1.19663599745585 | erot = 2.47431116852799 | epot = -12.8042962745337 | etot = -9.13334910854988 +986000 ekin = 1.26393164267519 | erot = 2.39249159639496 | epot = -12.7897723476107 | etot = -9.13334910854057 +987000 ekin = 1.3279291023599 | erot = 2.30329384118472 | epot = -12.7645720520045 | etot = -9.13334910845984 +988000 ekin = 1.38618594051206 | erot = 2.21003704542634 | epot = -12.7295720942485 | etot = -9.13334910831007 +989000 ekin = 1.43703663164584 | erot = 2.11631776637386 | epot = -12.6867035061281 | etot = -9.13334910810837 +990000 ekin = 1.47960743025514 | erot = 2.02574976477812 | epot = -12.6387063029151 | etot = -9.13334910788184 +991000 ekin = 1.513737246519 | erot = 1.94164272478426 | epot = -12.5887290789645 | etot = -9.13334910766121 +992000 ekin = 1.53983818592076 | erot = 1.86668512517543 | epot = -12.5398724185702 | etot = -9.133349107474 +993000 ekin = 1.55873490673373 | erot = 1.80268982006506 | epot = -12.4947738341386 | etot = -9.13334910733986 +994000 ekin = 1.57151651514655 | erot = 1.7504391420723 | epot = -12.4553047644872 | etot = -9.13334910726838 +995000 ekin = 1.57942173435936 | erot = 1.70964079470146 | epot = -12.4224116363212 | etot = -9.1333491072604 +996000 ekin = 1.58376261672678 | erot = 1.67898574513841 | epot = -12.396097469174 | etot = -9.13334910730886 +997000 ekin = 1.58587878575657 | erot = 1.65629050261323 | epot = -12.3755183957718 | etot = -9.13334910740197 +998000 ekin = 1.58710748471771 | erot = 1.63870906511802 | epot = -12.3591656573593 | etot = -9.13334910752362 +999000 ekin = 1.58875603199946 | erot = 1.62299637539018 | epot = -12.3451015150474 | etot = -9.13334910765779 +1000000 ekin = 1.59207001215674 | erot = 1.60581739808023 | epot = -12.3312365180193 | etot = -9.13334910778229 + 1000000 0.11793111 -1.2674127 0.034288999 -1.0739167 -1.3883882e-05 64000 +Loop time of 9.89878 on 1 procs for 1000000 steps with 10 atoms + +Performance: 87283.501 tau/day, 101022.571 timesteps/s, 1.010 Matom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.6716 | 7.6716 | 7.6716 | 0.0 | 77.50 +Bond | 0.40131 | 0.40131 | 0.40131 | 0.0 | 4.05 +Neigh | 0.012519 | 0.012519 | 0.012519 | 0.0 | 0.13 +Comm | 0.26996 | 0.26996 | 0.26996 | 0.0 | 2.73 +Output | 0.11986 | 0.11986 | 0.11986 | 0.0 | 1.21 +Modify | 1.1336 | 1.1336 | 1.1336 | 0.0 | 11.45 +Other | | 0.2899 | | | 2.93 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:09 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/log.19May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/log.19May24.duplex1.g++.4 new file mode 100644 index 0000000000..38553ab177 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/log.19May24.duplex1.g++.4 @@ -0,0 +1,1113 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.008 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna.lj with DATE: 2024-04-21 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (stk) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (xstk) file oxdna.lj with DATE: 2024-04-21 +Reading oxdna potential (coaxstk) file oxdna.lj with DATE: 2024-04-21 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.9560004 + ghost atom cutoff = 3.8 + binsize = 1.4780002, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 1e-05 +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -13.057621953437 | etot = -9.13334913094248 +Per MPI rank memory allocation (min/avg/max) = 7.105 | 7.11 | 7.116 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3488546 0.043092397 -1.1949086 -4.6816211e-05 64000 +1000 ekin = 1.08024346604046 | erot = 2.90873406534668 | epot = -13.1223266626202 | etot = -9.13334913123309 +2000 ekin = 1.05028450914436 | erot = 2.98006324808558 | epot = -13.1636968886591 | etot = -9.13334913142917 +3000 ekin = 1.01964458529397 | erot = 3.02592193798631 | epot = -13.1789156547658 | etot = -9.13334913148549 +4000 ekin = 0.989515033089522 | erot = 3.04428486059471 | epot = -13.1671490250723 | etot = -9.13334913138808 +5000 ekin = 0.961283929687805 | erot = 3.03510855539557 | epot = -13.1297416162282 | etot = -9.13334913114478 +6000 ekin = 0.936412193404224 | erot = 3.00022299571977 | epot = -13.0699843199583 | etot = -9.13334913083427 +7000 ekin = 0.916233699107934 | erot = 2.94277134440163 | epot = -12.9923541739966 | etot = -9.13334913048703 +8000 ekin = 0.901760662506231 | erot = 2.86671228744168 | epot = -12.9018220800865 | etot = -9.13334913013854 +9000 ekin = 0.893571390067841 | erot = 2.77649686780611 | epot = -12.8034173876806 | etot = -9.13334912980665 +10000 ekin = 0.89180568505681 | erot = 2.6768685500674 | epot = -12.7020233645916 | etot = -9.13334912946735 +11000 ekin = 0.896243557993558 | erot = 2.57266042063126 | epot = -12.6022531078195 | etot = -9.13334912919466 +12000 ekin = 0.906416039154792 | erot = 2.46827537271563 | epot = -12.5080405408348 | etot = -9.13334912896439 +13000 ekin = 0.921704091778471 | erot = 2.3676064547084 | epot = -12.4226596752788 | etot = -9.13334912879193 +14000 ekin = 0.941405275130066 | erot = 2.27374941641182 | epot = -12.3485038202329 | etot = -9.13334912869102 +15000 ekin = 0.964770892951772 | erot = 2.18876720165118 | epot = -12.2868872232636 | etot = -9.13334912866064 +16000 ekin = 0.991029016801091 | erot = 2.11380018376647 | epot = -12.2381783292305 | etot = -9.13334912866296 +17000 ekin = 1.01940907375713 | erot = 2.04893605182118 | epot = -12.2016942543555 | etot = -9.13334912877723 +18000 ekin = 1.04917923728266 | erot = 1.99335017578097 | epot = -12.1758785419805 | etot = -9.13334912891687 +19000 ekin = 1.07969247848164 | erot = 1.94569933362964 | epot = -12.1587409411761 | etot = -9.13334912906482 +20000 ekin = 1.11043268152285 | erot = 1.90411175657075 | epot = -12.1478935672812 | etot = -9.13334912918763 +21000 ekin = 1.14104909735581 | erot = 1.8669588297924 | epot = -12.1413570564147 | etot = -9.13334912926643 +22000 ekin = 1.17136821848097 | erot = 1.83313674901893 | epot = -12.137854096792 | etot = -9.13334912929212 +23000 ekin = 1.2013763409769 | erot = 1.80222523558974 | epot = -12.1369507058332 | etot = -9.13334912926651 +24000 ekin = 1.23117249622896 | erot = 1.77451266102185 | epot = -12.1390342864516 | etot = -9.13334912920075 +25000 ekin = 1.2608952664064 | erot = 1.75088411697588 | epot = -12.1451285124969 | etot = -9.13334912911462 +26000 ekin = 1.29063712254627 | erot = 1.732594283795 | epot = -12.1565805353676 | etot = -9.13334912902628 +27000 ekin = 1.32035987087023 | erot = 1.7211406167117 | epot = -12.174849616541 | etot = -9.13334912895908 +28000 ekin = 1.34980460658792 | erot = 1.71795709927852 | epot = -12.2011108348018 | etot = -9.13334912893533 +29000 ekin = 1.37841624051157 | erot = 1.72414013785738 | epot = -12.2359055073442 | etot = -9.13334912897525 +30000 ekin = 1.40529015727349 | erot = 1.74019656639667 | epot = -12.2788358527639 | etot = -9.13334912909374 +31000 ekin = 1.42915801743393 | erot = 1.7658325233695 | epot = -12.3283396701001 | etot = -9.1333491292967 +32000 ekin = 1.44843712560538 | erot = 1.79982181745342 | epot = -12.3816080726341 | etot = -9.13334912957528 +33000 ekin = 1.46136904668678 | erot = 1.84000474140075 | epot = -12.4347229179886 | etot = -9.13334912990108 +34000 ekin = 1.46625940785513 | erot = 1.88346459856619 | epot = -12.4830731366476 | etot = -9.13334913022629 +35000 ekin = 1.46179739484305 | erot = 1.9268888952494 | epot = -12.5220354205853 | etot = -9.1333491304929 +36000 ekin = 1.44738855724074 | erot = 1.96705754746495 | epot = -12.5477952353505 | etot = -9.1333491306448 +37000 ekin = 1.42340054468546 | erot = 2.00129614949924 | epot = -12.5580458249025 | etot = -9.13334913071781 +38000 ekin = 1.39122781542977 | erot = 2.02761655303762 | epot = -12.5521934990548 | etot = -9.13334913058742 +39000 ekin = 1.35313842096812 | erot = 2.04547852103599 | epot = -12.5319660723437 | etot = -9.13334913033961 +40000 ekin = 1.31193587699358 | erot = 2.05554364627555 | epot = -12.5008286533156 | etot = -9.13334913004651 +41000 ekin = 1.27054093924537 | erot = 2.05894429581367 | epot = -12.4628343648333 | etot = -9.13334912977423 +42000 ekin = 1.23161000992319 | erot = 2.05694893255704 | epot = -12.4219080720069 | etot = -9.13334912952672 +43000 ekin = 1.19723969759484 | erot = 2.05085758075654 | epot = -12.3814464076996 | etot = -9.13334912934826 +44000 ekin = 1.16880185863986 | erot = 2.04172238360624 | epot = -12.3438733714904 | etot = -9.13334912924432 +45000 ekin = 1.14690787175705 | erot = 2.03029950061771 | epot = -12.3105565015799 | etot = -9.13334912920515 +46000 ekin = 1.13147919636034 | erot = 2.01712256175374 | epot = -12.2819508873243 | etot = -9.13334912921019 +47000 ekin = 1.12189300492702 | erot = 2.00264798837259 | epot = -12.2578901225351 | etot = -9.13334912923549 +48000 ekin = 1.11716788112706 | erot = 1.98739120721198 | epot = -12.2379082176347 | etot = -9.13334912929562 +49000 ekin = 1.11615794795226 | erot = 1.97187368108381 | epot = -12.221380758335 | etot = -9.13334912929889 +50000 ekin = 1.11772326336375 | erot = 1.95708534394636 | epot = -12.2081577365827 | etot = -9.13334912927259 +51000 ekin = 1.1208492449785 | erot = 1.94437394210229 | epot = -12.1985723162998 | etot = -9.13334912921904 +52000 ekin = 1.12470549785227 | erot = 1.93529800314884 | epot = -12.1933526301511 | etot = -9.13334912914995 +53000 ekin = 1.12864556674951 | erot = 1.93145365271676 | epot = -12.1934483485499 | etot = -9.13334912908359 +54000 ekin = 1.13216113523062 | erot = 1.93430274875519 | epot = -12.1998130130122 | etot = -9.13334912902642 +55000 ekin = 1.13481106600208 | erot = 1.94490436967254 | epot = -12.2130645647023 | etot = -9.13334912902767 +56000 ekin = 1.1361434353579 | erot = 1.96361884590798 | epot = -12.2331114103532 | etot = -9.13334912908732 +57000 ekin = 1.13563178311256 | erot = 1.99002978527255 | epot = -12.2590106975987 | etot = -9.13334912921356 +58000 ekin = 1.13263976908221 | erot = 2.02286978616504 | epot = -12.2888586846527 | etot = -9.13334912940548 +59000 ekin = 1.1264242611341 | erot = 2.06004413441712 | epot = -12.319817525203 | etot = -9.13334912965174 +60000 ekin = 1.11618536041514 | erot = 2.09876774945547 | epot = -12.3483022398006 | etot = -9.13334912993001 +61000 ekin = 1.1011681041785 | erot = 2.13581434618267 | epot = -12.3703315805685 | etot = -9.13334913020729 +62000 ekin = 1.0808163752179 | erot = 2.16786879318298 | epot = -12.3820342988434 | etot = -9.13334913044257 +63000 ekin = 1.05497014428139 | erot = 2.1919450325443 | epot = -12.3802643074577 | etot = -9.133349130632 +64000 ekin = 1.02408601603151 | erot = 2.20562384873123 | epot = -12.363058995418 | etot = -9.1333491306553 +65000 ekin = 0.989434415807667 | erot = 2.20769180278651 | epot = -12.3304753491252 | etot = -9.13334913053104 +66000 ekin = 0.953195593563851 | erot = 2.19842250482622 | epot = -12.284967228654 | etot = -9.13334913026394 +67000 ekin = 0.918366365968241 | erot = 2.17942400884177 | epot = -12.231139504705 | etot = -9.13334912989501 +68000 ekin = 0.88846781466627 | erot = 2.15321364358197 | epot = -12.1750305877204 | etot = -9.13334912947211 +69000 ekin = 0.867150037001639 | erot = 2.12288633704371 | epot = -12.123385503121 | etot = -9.13334912907568 +70000 ekin = 0.857579951604763 | erot = 2.09151913845149 | epot = -12.0824482188433 | etot = -9.13334912878702 +71000 ekin = 0.86181542526747 | erot = 2.06157004239559 | epot = -12.0567345963622 | etot = -9.13334912869911 +72000 ekin = 0.880191815685442 | erot = 2.0343527543936 | epot = -12.0478936988734 | etot = -9.13334912879437 +73000 ekin = 0.911201453876623 | erot = 2.00982694750396 | epot = -12.0543775304381 | etot = -9.13334912905754 +74000 ekin = 0.951849895585052 | erot = 1.98685418272619 | epot = -12.0720532077347 | etot = -9.13334912942345 +75000 ekin = 0.998151008641142 | erot = 1.96362530027596 | epot = -12.0951254387265 | etot = -9.13334912980944 +76000 ekin = 1.04581734271581 | erot = 1.93821700241347 | epot = -12.1173834752671 | etot = -9.13334913013781 +77000 ekin = 1.09091996835692 | erot = 1.90910715282276 | epot = -12.1333762515352 | etot = -9.13334913035557 +78000 ekin = 1.13037631927904 | erot = 1.87551578135374 | epot = -12.139241231075 | etot = -9.13334913044224 +79000 ekin = 1.1621958859777 | erot = 1.83750580183249 | epot = -12.1330508182183 | etot = -9.13334913040809 +80000 ekin = 1.18548972632215 | erot = 1.79585942669976 | epot = -12.1146982833062 | etot = -9.13334913028424 +81000 ekin = 1.20030605718936 | erot = 1.75181365939736 | epot = -12.0854688466955 | etot = -9.1333491301088 +82000 ekin = 1.20737786492176 | erot = 1.70676694760209 | epot = -12.0474939424388 | etot = -9.13334912991494 +83000 ekin = 1.20786051402051 | erot = 1.66205278152621 | epot = -12.0032624252715 | etot = -9.1333491297248 +84000 ekin = 1.20310991572454 | erot = 1.6188291324731 | epot = -11.9552881777459 | etot = -9.13334912954824 +85000 ekin = 1.19452073297143 | erot = 1.57808043002408 | epot = -11.9059502923817 | etot = -9.13334912938621 +86000 ekin = 1.18342100682536 | erot = 1.54069268896226 | epot = -11.8574628250233 | etot = -9.1333491292357 +87000 ekin = 1.17100858957323 | erot = 1.50755090689507 | epot = -11.8119086255615 | etot = -9.13334912909325 +88000 ekin = 1.15831377551661 | erot = 1.47961680456709 | epot = -11.7712797090415 | etot = -9.13334912895782 +89000 ekin = 1.1461768281738 | erot = 1.4579637812888 | epot = -11.7374897382936 | etot = -9.13334912883096 +90000 ekin = 1.13523447969402 | erot = 1.44376438030013 | epot = -11.7123479887107 | etot = -9.13334912871654 +91000 ekin = 1.12591345720532 | erot = 1.43823772500936 | epot = -11.6975003108345 | etot = -9.13334912861983 +92000 ekin = 1.11843099489269 | erot = 1.44256930748506 | epot = -11.6943494309244 | etot = -9.1333491285466 +93000 ekin = 1.112803296348 | erot = 1.45781524814474 | epot = -11.7039676729951 | etot = -9.13334912850232 +94000 ekin = 1.10886209127324 | erot = 1.48480045701866 | epot = -11.7270116767841 | etot = -9.13334912849224 +95000 ekin = 1.10627886010325 | erot = 1.52396220647535 | epot = -11.7635901951105 | etot = -9.13334912853194 +96000 ekin = 1.10459509814408 | erot = 1.57519859223418 | epot = -11.8131428189843 | etot = -9.13334912860609 +97000 ekin = 1.1032594376989 | erot = 1.63800664193795 | epot = -11.8746152083616 | etot = -9.13334912872477 +98000 ekin = 1.10166959581631 | erot = 1.71130689804966 | epot = -11.9463256227538 | etot = -9.1333491288878 +99000 ekin = 1.0992184938515 | erot = 1.79339905630356 | epot = -12.025966679247 | etot = -9.13334912909191 +100000 ekin = 1.09534596880096 | erot = 1.88196872528567 | epot = -12.110663823416 | etot = -9.13334912932934 +101000 ekin = 1.08959720755109 | erot = 1.97415616931449 | epot = -12.1971025064518 | etot = -9.13334912958625 +102000 ekin = 1.08168751154809 | erot = 2.06670282185173 | epot = -12.2817394632424 | etot = -9.13334912984258 +103000 ekin = 1.07156932342309 | erot = 2.15618192508059 | epot = -12.3611003785771 | etot = -9.1333491300734 +104000 ekin = 1.0594923799607 | erot = 2.23930158373565 | epot = -12.4321430939483 | etot = -9.13334913025199 +105000 ekin = 1.04604342224879 | erot = 2.31323902285846 | epot = -12.492631575493 | etot = -9.13334913038572 +106000 ekin = 1.03224316318565 | erot = 2.37579242095985 | epot = -12.5413847145642 | etot = -9.13334913041871 +107000 ekin = 1.01951120148941 | erot = 2.42585603740569 | epot = -12.5787163692802 | etot = -9.13334913038506 +108000 ekin = 1.00875017477221 | erot = 2.46348952984496 | epot = -12.6055888348734 | etot = -9.13334913025625 +109000 ekin = 1.00109573552412 | erot = 2.48980806114974 | epot = -12.6242529267278 | etot = -9.13334913005397 +110000 ekin = 0.997931591358304 | erot = 2.50673918610807 | epot = -12.6380199072775 | etot = -9.13334912981118 +111000 ekin = 1.00076792351343 | erot = 2.5166591537305 | epot = -12.6507762068076 | etot = -9.13334912956365 +112000 ekin = 1.01109610479951 | erot = 2.52200701599662 | epot = -12.6664522501391 | etot = -9.133349129343 +113000 ekin = 1.0301901681791 | erot = 2.52496101252893 | epot = -12.6885003099863 | etot = -9.13334912927822 +114000 ekin = 1.05821017520655 | erot = 2.52722573627522 | epot = -12.7187850407016 | etot = -9.13334912921986 +115000 ekin = 1.09472530400172 | erot = 2.5300393044883 | epot = -12.7581137377193 | etot = -9.13334912922923 +116000 ekin = 1.13884650903364 | erot = 2.53414832430445 | epot = -12.8063439626438 | etot = -9.13334912930572 +117000 ekin = 1.18909444999517 | erot = 2.53980839277126 | epot = -12.8622519722148 | etot = -9.1333491294484 +118000 ekin = 1.24341490970508 | erot = 2.54678348242624 | epot = -12.9235475217867 | etot = -9.13334912965538 +119000 ekin = 1.29923662064227 | erot = 2.55432909400996 | epot = -12.9869148445729 | etot = -9.13334912992068 +120000 ekin = 1.35358959215683 | erot = 2.5611861592178 | epot = -13.0481248816036 | etot = -9.13334913022902 +121000 ekin = 1.40329803815488 | erot = 2.5656313586164 | epot = -13.1022785273253 | etot = -9.13334913055406 +122000 ekin = 1.44524692196652 | erot = 2.56562448409207 | epot = -13.1442205369173 | etot = -9.13334913085867 +123000 ekin = 1.47669540804869 | erot = 2.55906317998187 | epot = -13.169107719131 | etot = -9.13334913110044 +124000 ekin = 1.49558302658199 | erot = 2.54411105943705 | epot = -13.1730432172612 | etot = -9.13334913124216 +125000 ekin = 1.50076122489775 | erot = 2.51952798471295 | epot = -13.1536383408713 | etot = -9.13334913126062 +126000 ekin = 1.49214728684746 | erot = 2.48515933103509 | epot = -13.1106557490374 | etot = -9.13334913115489 +127000 ekin = 1.47053410713985 | erot = 2.44174480075121 | epot = -13.0456280388476 | etot = -9.13334913095659 +128000 ekin = 1.43743445323531 | erot = 2.39059049317546 | epot = -12.961374077076 | etot = -9.13334913066526 +129000 ekin = 1.39501109707075 | erot = 2.3338012012582 | epot = -12.8621614286437 | etot = -9.13334913031472 +130000 ekin = 1.34584042016769 | erot = 2.27401545397177 | epot = -12.7532050040794 | etot = -9.13334912993992 +131000 ekin = 1.29268930786602 | erot = 2.21410134111225 | epot = -12.6401397785509 | etot = -9.1333491295726 +132000 ekin = 1.23832315616831 | erot = 2.15686384200886 | epot = -12.5285361274155 | etot = -9.13334912923836 +133000 ekin = 1.18535267681202 | erot = 2.10479906741759 | epot = -12.4235008731853 | etot = -9.13334912895568 +134000 ekin = 1.13612155562816 | erot = 2.05991346428629 | epot = -12.3293841486505 | etot = -9.133349128736 +135000 ekin = 1.09263262326054 | erot = 2.02360952444367 | epot = -12.2495912762905 | etot = -9.13334912858628 +136000 ekin = 1.05650575788347 | erot = 1.99662030668685 | epot = -12.1864751930781 | etot = -9.13334912850776 +137000 ekin = 1.02895878679454 | erot = 1.97899212834891 | epot = -12.1413000436434 | etot = -9.13334912849995 +138000 ekin = 1.01080388995842 | erot = 1.9701351217224 | epot = -12.1142881402332 | etot = -9.13334912855242 +139000 ekin = 1.00245459395339 | erot = 1.96888144460886 | epot = -12.1046851672404 | etot = -9.13334912867811 +140000 ekin = 1.0039378074061 | erot = 1.97333010973467 | epot = -12.1106170460029 | etot = -9.13334912886208 +141000 ekin = 1.01490973367025 | erot = 1.98104530944812 | epot = -12.1293041722138 | etot = -9.13334912909543 +142000 ekin = 1.03468044934409 | erot = 1.98917872502454 | epot = -12.1572083037338 | etot = -9.13334912936515 +143000 ekin = 1.06225104646168 | erot = 1.99463134790809 | epot = -12.1902315240234 | etot = -9.13334912965366 +144000 ekin = 1.09636709127245 | erot = 1.99441220318426 | epot = -12.2241284243807 | etot = -9.13334912992396 +145000 ekin = 1.13559045362118 | erot = 1.98572590466038 | epot = -12.2546654884646 | etot = -9.13334913018302 +146000 ekin = 1.17838854122089 | erot = 1.96612892354289 | epot = -12.2778665951539 | etot = -9.13334913039009 +147000 ekin = 1.2230069974918 | erot = 1.9340512939501 | epot = -12.2904074219633 | etot = -9.13334913052135 +148000 ekin = 1.2678567786302 | erot = 1.88891621350878 | epot = -12.2901221227001 | etot = -9.1333491305611 +149000 ekin = 1.31170551487303 | erot = 1.83123494690903 | epot = -12.2762895922888 | etot = -9.13334913050675 +150000 ekin = 1.35361858091203 | erot = 1.76263607509644 | epot = -12.2496037863731 | etot = -9.13334913036465 +151000 ekin = 1.39299848911433 | erot = 1.68572491420637 | epot = -12.2120725334746 | etot = -9.13334913015392 +152000 ekin = 1.42958376961915 | erot = 1.60381549112362 | epot = -12.1667483906424 | etot = -9.13334912989958 +153000 ekin = 1.46340801747597 | erot = 1.52060159601931 | epot = -12.1173587431249 | etot = -9.13334912962961 +154000 ekin = 1.49472650224564 | erot = 1.43981503875285 | epot = -12.0678906703691 | etot = -9.1333491293706 +155000 ekin = 1.52392161825082 | erot = 1.36491657683223 | epot = -12.0221873242286 | etot = -9.13334912914557 +156000 ekin = 1.55140022159559 | erot = 1.29884972381827 | epot = -11.9835990743857 | etot = -9.1333491289718 +157000 ekin = 1.57749707056591 | erot = 1.24387068637226 | epot = -11.9547168857974 | etot = -9.13334912885921 +158000 ekin = 1.60239506185786 | erot = 1.20145363967816 | epot = -11.9371978303525 | etot = -9.13334912881648 +159000 ekin = 1.62604462003791 | erot = 1.17226436760499 | epot = -11.931658116485 | etot = -9.13334912884206 +160000 ekin = 1.64813303486552 | erot = 1.15619534708316 | epot = -11.93767751088 | etot = -9.13334912893129 +161000 ekin = 1.66807327612987 | erot = 1.15245312716193 | epot = -11.9538755323662 | etot = -9.13334912907437 +162000 ekin = 1.68501875283066 | erot = 1.15969471512808 | epot = -11.978062597216 | etot = -9.13334912925728 +163000 ekin = 1.69790620824686 | erot = 1.17620989126109 | epot = -12.0074652289693 | etot = -9.13334912946133 +164000 ekin = 1.7055271179841 | erot = 1.20014309389834 | epot = -12.0390193415467 | etot = -9.13334912966428 +165000 ekin = 1.70662691809365 | erot = 1.22974121417727 | epot = -12.0697172621128 | etot = -9.13334912984184 +166000 ekin = 1.70002908026867 | erot = 1.26360423252418 | epot = -12.0969824427633 | etot = -9.13334912997049 +167000 ekin = 1.68477683955904 | erot = 1.30090518403772 | epot = -12.1190311536269 | etot = -9.1333491300301 +168000 ekin = 1.66027923283209 | erot = 1.34154370359082 | epot = -12.1351720664311 | etot = -9.13334913000816 +169000 ekin = 1.62644124957751 | erot = 1.38619810991404 | epot = -12.1459884893943 | etot = -9.13334912990279 +170000 ekin = 1.58375251890797 | erot = 1.43625221626198 | epot = -12.153353864895 | etot = -9.13334912972505 +171000 ekin = 1.53331003043946 | erot = 1.49359459893415 | epot = -12.1602537588723 | etot = -9.13334912949871 +172000 ekin = 1.47676106161418 | erot = 1.56031583407051 | epot = -12.17042602494 | etot = -9.13334912925535 +173000 ekin = 1.41695754705538 | erot = 1.63848249765424 | epot = -12.1887891730445 | etot = -9.13334912833489 +174000 ekin = 1.3593768430449 | erot = 1.72968793645253 | epot = -12.2224139078251 | etot = -9.13334912832771 +175000 ekin = 1.30537540818815 | erot = 1.83369980102279 | epot = -12.2724243375751 | etot = -9.13334912836421 +176000 ekin = 1.25571357800303 | erot = 1.94952726339969 | epot = -12.3385899698488 | etot = -9.13334912844608 +177000 ekin = 1.21104692225308 | erot = 2.07558802224412 | epot = -12.4199840730639 | etot = -9.13334912856671 +178000 ekin = 1.1718951205703 | erot = 2.20976079574673 | epot = -12.5150050450639 | etot = -9.13334912874691 +179000 ekin = 1.13864315857365 | erot = 2.34949890132923 | epot = -12.6214911888114 | etot = -9.13334912890848 +180000 ekin = 1.11156621835588 | erot = 2.49234008540043 | epot = -12.7372554328246 | etot = -9.13334912906826 +181000 ekin = 1.09087167613581 | erot = 2.63567357536181 | epot = -12.8598943807499 | etot = -9.13334912925225 +182000 ekin = 1.07675226579837 | erot = 2.77693577183374 | epot = -12.9870371670193 | etot = -9.13334912938722 +183000 ekin = 1.0694229423415 | erot = 2.91405263083485 | epot = -13.1168247026763 | etot = -9.13334912949999 +184000 ekin = 1.06913488705839 | erot = 3.04520163111703 | epot = -13.2476856477703 | etot = -9.13334912959484 +185000 ekin = 1.07614345922792 | erot = 3.16875772929967 | epot = -13.3782503182127 | etot = -9.13334912968508 +186000 ekin = 1.09060563376754 | erot = 3.28317984154898 | epot = -13.5071346051103 | etot = -9.1333491297938 +187000 ekin = 1.11239929858156 | erot = 3.38683780589129 | epot = -13.6325862344245 | etot = -9.13334912995164 +188000 ekin = 1.14088837562652 | erot = 3.47780595660551 | epot = -13.7520434624197 | etot = -9.13334913018771 +189000 ekin = 1.17469755695859 | erot = 3.55369218298284 | epot = -13.861738870457 | etot = -9.13334913051552 +190000 ekin = 1.21158961983351 | erot = 3.61161008256105 | epot = -13.9565488333131 | etot = -9.1333491309185 +191000 ekin = 1.24837558083739 | erot = 3.64780345127581 | epot = -14.0295281634884 | etot = -9.13334913137519 +192000 ekin = 1.28102311682972 | erot = 3.65810395429013 | epot = -14.0724762027872 | etot = -9.1333491316674 +193000 ekin = 1.3059832081699 | erot = 3.64139295006508 | epot = -14.0807252900248 | etot = -9.13334913178983 +194000 ekin = 1.32049648836629 | erot = 3.59844552363041 | epot = -14.0522911436919 | etot = -9.13334913169516 +195000 ekin = 1.32298604774279 | erot = 3.53212928134945 | epot = -13.9884644604287 | etot = -9.1333491313365 +196000 ekin = 1.31323645162571 | erot = 3.44751612705298 | epot = -13.8941017095228 | etot = -9.13334913084408 +197000 ekin = 1.29228934698143 | erot = 3.35072340322484 | epot = -13.7763618804982 | etot = -9.13334913029193 +198000 ekin = 1.26212633786626 | erot = 3.24789114381976 | epot = -13.6433666114223 | etot = -9.13334912973633 +199000 ekin = 1.22527047461707 | erot = 3.14483705467186 | epot = -13.5034566585623 | etot = -9.1333491292734 +200000 ekin = 1.18441799207224 | erot = 3.04594245962971 | epot = -13.3637095806209 | etot = -9.133349128919 +201000 ekin = 1.14216630511931 | erot = 2.95390025492329 | epot = -13.2294156887263 | etot = -9.13334912868374 +202000 ekin = 1.10084220211731 | erot = 2.86987712396318 | epot = -13.1040684546426 | etot = -9.13334912856206 +203000 ekin = 1.06240856568998 | erot = 2.79366067226801 | epot = -12.9894183664989 | etot = -9.13334912854089 +204000 ekin = 1.02841768821206 | erot = 2.7238914427548 | epot = -12.8856582595711 | etot = -9.13334912860425 +205000 ekin = 0.999988405220642 | erot = 2.65832732458283 | epot = -12.7916648585382 | etot = -9.1333491287347 +206000 ekin = 0.977799621225039 | erot = 2.59412391514158 | epot = -12.7052726652791 | etot = -9.13334912891246 +207000 ekin = 0.96210565396534 | erot = 2.52813792126086 | epot = -12.6235927043392 | etot = -9.13334912911298 +208000 ekin = 0.952783648018826 | erot = 2.4572664289228 | epot = -12.5433992062482 | etot = -9.13334912930654 +209000 ekin = 0.949416945748555 | erot = 2.37882137049688 | epot = -12.4615874457061 | etot = -9.13334912946071 +210000 ekin = 0.951402263215277 | erot = 2.2909093941919 | epot = -12.3756607869538 | etot = -9.13334912954662 +211000 ekin = 0.95805195207771 | erot = 2.19275562021856 | epot = -12.2841567018434 | etot = -9.13334912954713 +212000 ekin = 0.968659667700622 | erot = 2.08489619855804 | epot = -12.1869049957195 | etot = -9.1333491294608 +213000 ekin = 0.982515908120138 | erot = 1.96918422280988 | epot = -12.0850492602323 | etot = -9.13334912930225 +214000 ekin = 0.998888701919955 | erot = 1.84860041861919 | epot = -11.9808382496354 | etot = -9.13334912909625 +215000 ekin = 1.0170013491259 | erot = 1.72690897492172 | epot = -11.8772594529192 | etot = -9.13334912887158 +216000 ekin = 1.03603050122475 | erot = 1.60822693577827 | epot = -11.7776065656585 | etot = -9.13334912865547 +217000 ekin = 1.05512477228492 | erot = 1.496579175338 | epot = -11.6850530760951 | etot = -9.13334912847215 +218000 ekin = 1.07342860744204 | erot = 1.39550092670185 | epot = -11.6022786624837 | etot = -9.13334912833986 +219000 ekin = 1.09009860355593 | erot = 1.30773521951561 | epot = -11.531182951341 | etot = -9.13334912826951 +220000 ekin = 1.10431207607363 | erot = 1.23505496062892 | epot = -11.4727161649659 | etot = -9.13334912826336 +221000 ekin = 1.11527717993055 | erot = 1.17821867809255 | epot = -11.426844986338 | etot = -9.13334912831486 +222000 ekin = 1.12225437592976 | erot = 1.1370482394415 | epot = -11.3926517437816 | etot = -9.13334912841031 +223000 ekin = 1.1245929762141 | erot = 1.11060060825111 | epot = -11.3685427129973 | etot = -9.13334912853205 +224000 ekin = 1.12177911879611 | erot = 1.0973962554393 | epot = -11.3525245028961 | etot = -9.13334912866071 +225000 ekin = 1.11348637905745 | erot = 1.0956640253194 | epot = -11.3424995331558 | etot = -9.133349128779 +226000 ekin = 1.09961800000694 | erot = 1.10360909760954 | epot = -11.3365762264851 | etot = -9.13334912886863 +227000 ekin = 1.08033165066207 | erot = 1.1195273004342 | epot = -11.3332080800319 | etot = -9.13334912893563 +228000 ekin = 1.0560460287277 | erot = 1.14187865421875 | epot = -11.331273811917 | etot = -9.13334912897058 +229000 ekin = 1.02742418663498 | erot = 1.16938489301688 | epot = -11.3301582086284 | etot = -9.13334912897658 +230000 ekin = 0.995339184991514 | erot = 1.20102048198626 | epot = -11.3297087959369 | etot = -9.13334912895908 +231000 ekin = 0.960829492708653 | erot = 1.23597735762313 | epot = -11.3301559792544 | etot = -9.13334912892258 +232000 ekin = 0.925050432735229 | erot = 1.27360958612392 | epot = -11.3320091477354 | etot = -9.13334912887625 +233000 ekin = 0.889225435959757 | erot = 1.31337910210636 | epot = -11.3359536668893 | etot = -9.1333491288232 +234000 ekin = 0.854600006628753 | erot = 1.35483402381923 | epot = -11.3427831592148 | etot = -9.13334912876681 +235000 ekin = 0.822390924845247 | erot = 1.39757430015836 | epot = -11.3533143537194 | etot = -9.1333491287158 +236000 ekin = 0.793732848711906 | erot = 1.44121433399065 | epot = -11.3682963113763 | etot = -9.13334912867375 +237000 ekin = 0.76963219121953 | erot = 1.48535644446062 | epot = -11.3883377643265 | etot = -9.13334912864631 +238000 ekin = 0.750918993366152 | erot = 1.52956143549206 | epot = -11.4138295574958 | etot = -9.13334912863755 +239000 ekin = 0.738206267497332 | erot = 1.57333361162144 | epot = -11.4448890077678 | etot = -9.13334912864905 +240000 ekin = 0.731862193744161 | erot = 1.61613149974219 | epot = -11.4813428221655 | etot = -9.1333491286792 +241000 ekin = 0.731999328002225 | erot = 1.65741090456852 | epot = -11.5227593612935 | etot = -9.13334912872278 +242000 ekin = 0.738482620157526 | erot = 1.69669130986301 | epot = -11.5685230587944 | etot = -9.13334912877383 +243000 ekin = 0.75095504232561 | erot = 1.73364929482317 | epot = -11.6179534659685 | etot = -9.13334912881975 +244000 ekin = 0.768877080466842 | erot = 1.76822360275613 | epot = -11.6704498120771 | etot = -9.13334912885415 +245000 ekin = 0.79157392929488 | erot = 1.80068045121312 | epot = -11.7256035093795 | etot = -9.13334912887146 +246000 ekin = 0.818282914271808 | erot = 1.8316410744517 | epot = -11.7832731175941 | etot = -9.13334912887063 +247000 ekin = 0.84819362160195 | erot = 1.86205096555233 | epot = -11.8435937160101 | etot = -9.13334912885584 +248000 ekin = 0.880474358635757 | erot = 1.89308546777779 | epot = -11.90690895525 | etot = -9.13334912883643 +249000 ekin = 0.914280881219526 | erot = 1.9259971322387 | epot = -11.9736271422841 | etot = -9.13334912882583 +250000 ekin = 0.948746730716735 | erot = 1.96192054843707 | epot = -12.0440164079939 | etot = -9.13334912884008 +251000 ekin = 0.982959063854598 | erot = 2.00165977259877 | epot = -12.1179679653482 | etot = -9.13334912889487 +252000 ekin = 1.01592948249879 | erot = 2.04549252396337 | epot = -12.1947711354631 | etot = -9.13334912900098 +253000 ekin = 1.04657777484006 | erot = 2.09303441305928 | epot = -12.2729613170592 | etot = -9.13334912915986 +254000 ekin = 1.07373541755098 | erot = 2.14319803018411 | epot = -12.350282577098 | etot = -9.13334912936295 +255000 ekin = 1.0962016316305 | erot = 2.19430966720506 | epot = -12.4238604284171 | etot = -9.13334912958158 +256000 ekin = 1.11287206428172 | erot = 2.24438579427395 | epot = -12.4906069883384 | etot = -9.13334912978273 +257000 ekin = 1.12287782510647 | erot = 2.29146665865368 | epot = -12.5476936136915 | etot = -9.13334912993139 +258000 ekin = 1.12572293500287 | erot = 2.33396623628233 | epot = -12.5930383012892 | etot = -9.133349130004 +259000 ekin = 1.12139026023665 | erot = 2.37095948468519 | epot = -12.6256988749106 | etot = -9.13334912998877 +260000 ekin = 1.11036122819349 | erot = 2.40229658115363 | epot = -12.6460069392472 | etot = -9.13334912990009 +261000 ekin = 1.09354805445101 | erot = 2.42847877902905 | epot = -12.6553759632423 | etot = -9.13334912976222 +262000 ekin = 1.07216031825813 | erot = 2.45046938603018 | epot = -12.6559788338922 | etot = -9.13334912960391 +263000 ekin = 1.04754368718323 | erot = 2.46943297797192 | epot = -12.6503257946119 | etot = -9.13334912945675 +264000 ekin = 1.02102495133859 | erot = 2.4864784463715 | epot = -12.6408525270504 | etot = -9.13334912934026 +265000 ekin = 0.993788783443924 | erot = 2.50247063136404 | epot = -12.6296085440768 | etot = -9.13334912926887 +266000 ekin = 0.966800247930213 | erot = 2.51790683905026 | epot = -12.6180562162303 | etot = -9.1333491292498 +267000 ekin = 0.940784249459517 | erot = 2.53283827184827 | epot = -12.6069716505896 | etot = -9.13334912928181 +268000 ekin = 0.916272152394691 | erot = 2.5468461215252 | epot = -12.5964674032731 | etot = -9.13334912935317 +269000 ekin = 0.893722172477521 | erot = 2.55907244306963 | epot = -12.5861437450347 | etot = -9.13334912948752 +270000 ekin = 0.873709285129145 | erot = 2.56799722891229 | epot = -12.5750556436019 | etot = -9.13334912956044 +271000 ekin = 0.857156433251724 | erot = 2.57226369508359 | epot = -12.562769257908 | etot = -9.13334912957266 +272000 ekin = 0.845541083724155 | erot = 2.57096110909456 | epot = -12.5498513223268 | etot = -9.13334912950808 +273000 ekin = 0.840983736969839 | erot = 2.56364270819375 | epot = -12.5379755745176 | etot = -9.13334912935399 +274000 ekin = 0.846103061110545 | erot = 2.55054497183583 | epot = -12.5299971620895 | etot = -9.13334912914318 +275000 ekin = 0.863570741244989 | erot = 2.53260377851036 | epot = -12.5295236486812 | etot = -9.13334912892586 +276000 ekin = 0.895419299415286 | erot = 2.51114645014759 | epot = -12.5399148783703 | etot = -9.13334912880747 +277000 ekin = 0.942302359418826 | erot = 2.48734970425668 | epot = -12.563001192512 | etot = -9.13334912883648 +278000 ekin = 1.00299069941595 | erot = 2.46199112036399 | epot = -12.5983309488096 | etot = -9.13334912902968 +279000 ekin = 1.0743456158927 | erot = 2.4352977459076 | epot = -12.6429924911397 | etot = -9.13334912933943 +280000 ekin = 1.15182340984049 | erot = 2.4071159636552 | epot = -12.6922885031802 | etot = -9.13334912968449 +281000 ekin = 1.23030856581844 | erot = 2.37726964751242 | epot = -12.7409273433238 | etot = -9.13334912999295 +282000 ekin = 1.30483974879804 | erot = 2.34551973870782 | epot = -12.7837086176988 | etot = -9.13334913019296 +283000 ekin = 1.37151257999484 | erot = 2.31231452819892 | epot = -12.8171762384383 | etot = -9.1333491302445 +284000 ekin = 1.42789685319431 | erot = 2.27901843146214 | epot = -12.8402644148117 | etot = -9.13334913015527 +285000 ekin = 1.47299679574515 | erot = 2.24762833985833 | epot = -12.8539742655641 | etot = -9.13334912996062 +286000 ekin = 1.50701906587751 | erot = 2.2205005628335 | epot = -12.8608687584219 | etot = -9.13334912971089 +287000 ekin = 1.53099472144815 | erot = 2.19999584806531 | epot = -12.8643396989725 | etot = -9.133349129459 +288000 ekin = 1.54636449768925 | erot = 2.18811490987536 | epot = -12.8678285368153 | etot = -9.13334912925072 +289000 ekin = 1.55461163491252 | erot = 2.18618804174404 | epot = -12.874148805774 | etot = -9.13334912911742 +290000 ekin = 1.5569942867472 | erot = 2.19466879450655 | epot = -12.8850122103273 | etot = -9.13334912907358 +291000 ekin = 1.55439775255695 | erot = 2.21306131818056 | epot = -12.9008081998541 | etot = -9.13334912911663 +292000 ekin = 1.54729960240307 | erot = 2.23998314422064 | epot = -12.9206318758547 | etot = -9.13334912923097 +293000 ekin = 1.53582108608452 | erot = 2.27333490842462 | epot = -12.9425051239033 | etot = -9.13334912939421 +294000 ekin = 1.51982864506225 | erot = 2.31049721096962 | epot = -12.963674985627 | etot = -9.13334912959509 +295000 ekin = 1.4990515421338 | erot = 2.34851873984041 | epot = -12.9809194117674 | etot = -9.13334912979322 +296000 ekin = 1.47319364802849 | erot = 2.38443281021178 | epot = -12.9909755882228 | etot = -9.13334912998248 +297000 ekin = 1.44203124546021 | erot = 2.41536854590052 | epot = -12.9907489215106 | etot = -9.13334913014987 +298000 ekin = 1.40549976702133 | erot = 2.438674090462 | epot = -12.9775229877658 | etot = -9.13334913028248 +299000 ekin = 1.36377241662842 | erot = 2.45204871800543 | epot = -12.9491702650007 | etot = -9.13334913036682 +300000 ekin = 1.31732711912188 | erot = 2.4536840809266 | epot = -12.9043603304393 | etot = -9.13334913039078 +301000 ekin = 1.2669902241474 | erot = 2.44240353914669 | epot = -12.8427428936401 | etot = -9.13334913034601 +302000 ekin = 1.21394210637168 | erot = 2.41777278593021 | epot = -12.7650640225331 | etot = -9.13334913023125 +303000 ekin = 1.1596741442933 | erot = 2.380151896837 | epot = -12.6731751711843 | etot = -9.13334913005402 +304000 ekin = 1.10589726251281 | erot = 2.33066939618196 | epot = -12.5699157885238 | etot = -9.13334912982902 +305000 ekin = 1.05441504199238 | erot = 2.27111808933726 | epot = -12.4588822609056 | etot = -9.13334912957594 +306000 ekin = 1.00698421397122 | erot = 2.20379218514064 | epot = -12.3441255284267 | etot = -9.13334912931484 +307000 ekin = 0.965188337627229 | erot = 2.13129764385414 | epot = -12.2298351105443 | etot = -9.13334912906297 +308000 ekin = 0.930345631944139 | erot = 2.05636814615571 | epot = -12.1200629069324 | etot = -9.13334912883259 +309000 ekin = 0.903461768092625 | erot = 1.98167791132874 | epot = -12.0184888080534 | etot = -9.13334912863207 +310000 ekin = 0.885228515007679 | erot = 1.90967870211578 | epot = -11.9282563455879 | etot = -9.13334912846441 +311000 ekin = 0.876047647700181 | erot = 1.84263812610051 | epot = -11.8520349021326 | etot = -9.13334912833191 +312000 ekin = 0.876068182198755 | erot = 1.78248869456891 | epot = -11.7919060050058 | etot = -9.13334912823816 +313000 ekin = 0.88522398596972 | erot = 1.73072892882223 | epot = -11.7493020429808 | etot = -9.13334912818882 +314000 ekin = 0.903258342515012 | erot = 1.68832066988356 | epot = -11.7249281405897 | etot = -9.13334912819118 +315000 ekin = 0.929731391718417 | erot = 1.65558558099718 | epot = -11.7186661009682 | etot = -9.1333491282526 +316000 ekin = 0.964013828970745 | erot = 1.63211973509034 | epot = -11.7294826924389 | etot = -9.1333491283778 +317000 ekin = 1.00527629211694 | erot = 1.61675326466471 | epot = -11.7553786853475 | etot = -9.13334912856588 +318000 ekin = 1.05248736450164 | erot = 1.60758570940571 | epot = -11.7934222027149 | etot = -9.13334912880761 +319000 ekin = 1.10443332868176 | erot = 1.60212494474522 | epot = -11.8399074025106 | etot = -9.13334912908365 +320000 ekin = 1.1597692492088 | erot = 1.5975452610542 | epot = -11.890663639627 | etot = -9.133349129364 +321000 ekin = 1.21710352305734 | erot = 1.59105554518188 | epot = -11.941508197852 | etot = -9.13334912961278 +322000 ekin = 1.2751075118954 | erot = 1.58033324923112 | epot = -11.9887898909202 | etot = -9.13334912979368 +323000 ekin = 1.33263084645785 | erot = 1.56394390937369 | epot = -12.0299238857107 | etot = -9.1333491298792 +324000 ekin = 1.38879590712293 | erot = 1.54164678485268 | epot = -12.0637918218341 | etot = -9.13334912985847 +325000 ekin = 1.44304623679791 | erot = 1.51450056885294 | epot = -12.0908959353913 | etot = -9.13334912974046 +326000 ekin = 1.49513435445767 | erot = 1.4847307306608 | epot = -12.1132142146709 | etot = -9.13334912955244 +327000 ekin = 1.54505065938433 | erot = 1.45538400860376 | epot = -12.1337837973218 | etot = -9.13334912933371 +328000 ekin = 1.59290981434341 | erot = 1.4298478820938 | epot = -12.1561068255642 | etot = -9.133349129127 +329000 ekin = 1.63881860975713 | erot = 1.41133335467837 | epot = -12.1835010934069 | etot = -9.13334912897138 +330000 ekin = 1.68274896183183 | erot = 1.40240729591395 | epot = -12.2185053866427 | etot = -9.13334912889693 +331000 ekin = 1.72443467169651 | erot = 1.40463116342082 | epot = -12.2624149640402 | etot = -9.1333491289229 +332000 ekin = 1.7633053367441 | erot = 1.41833479327521 | epot = -12.3149892590753 | etot = -9.13334912905599 +333000 ekin = 1.79846823309365 | erot = 1.44253834966298 | epot = -12.3743557120453 | etot = -9.13334912928862 +334000 ekin = 1.82874900591171 | erot = 1.47503277033936 | epot = -12.4371309058484 | etot = -9.13334912959735 +335000 ekin = 1.85279616115881 | erot = 1.5126357019759 | epot = -12.498780993077 | etot = -9.13334912994232 +336000 ekin = 1.8692763055882 | erot = 1.55160162438249 | epot = -12.5542270602391 | etot = -9.13334913026845 +337000 ekin = 1.8771173541396 | erot = 1.5882004977342 | epot = -12.5986669823881 | etot = -9.1333491305143 +338000 ekin = 1.87574840923173 | erot = 1.61938868723024 | epot = -12.6284862270853 | etot = -9.13334913062332 +339000 ekin = 1.86534866362707 | erot = 1.64338736517947 | epot = -12.6420851593667 | etot = -9.13334913056018 +340000 ekin = 1.84695798886959 | erot = 1.66009075059862 | epot = -12.64039786979 | etot = -9.1333491303218 +341000 ekin = 1.82243969076597 | erot = 1.67114820362691 | epot = -12.6269370243332 | etot = -9.13334912994032 +342000 ekin = 1.79428655955809 | erot = 1.67969211618998 | epot = -12.6073278052229 | etot = -9.13334912947479 +343000 ekin = 1.76531632972456 | erot = 1.68978090506957 | epot = -12.5884463637896 | etot = -9.13334912899551 +344000 ekin = 1.73833039739185 | erot = 1.70570000747079 | epot = -12.5773795334318 | etot = -9.1333491285692 +345000 ekin = 1.7158058906016 | erot = 1.73127559556382 | epot = -12.5804306144134 | etot = -9.13334912824796 +346000 ekin = 1.69966353097473 | erot = 1.76931234934788 | epot = -12.6023250083889 | etot = -9.13334912806627 +347000 ekin = 1.69112042623157 | erot = 1.82120184302299 | epot = -12.6456713972978 | etot = -9.1333491280432 +348000 ekin = 1.69061396982628 | erot = 1.88669704033633 | epot = -12.7106601383482 | etot = -9.13334912818561 +349000 ekin = 1.69777681788073 | erot = 1.96382926866215 | epot = -12.7949552150328 | etot = -9.13334912848994 +350000 ekin = 1.71145115010129 | erot = 2.04895591402571 | epot = -12.8937561930686 | etot = -9.13334912894162 +351000 ekin = 1.72974629646061 | erot = 2.13695636910536 | epot = -13.0000517950752 | etot = -9.13334912950918 +352000 ekin = 1.75015893903836 | erot = 2.22162008456652 | epot = -13.105128153744 | etot = -9.13334913013911 +353000 ekin = 1.76978034905474 | erot = 2.29627029646031 | epot = -13.1993997762706 | etot = -9.13334913075554 +354000 ekin = 1.78560210911901 | erot = 2.35462017023483 | epot = -13.2735714106197 | etot = -9.13334913126588 +355000 ekin = 1.79489785472813 | erot = 2.39176336004244 | epot = -13.3200103463512 | etot = -9.13334913158058 +356000 ekin = 1.7956139324659 | erot = 2.40509186859607 | epot = -13.3340549327001 | etot = -9.13334913163815 +357000 ekin = 1.78667091072658 | erot = 2.39487614135014 | epot = -13.3148961835039 | etot = -9.13334913142721 +358000 ekin = 1.7681016723056 | erot = 2.3642989799425 | epot = -13.2657497831719 | etot = -9.13334913092383 +359000 ekin = 1.74170569044756 | erot = 2.31907684809719 | epot = -13.1941316689289 | etot = -9.13334913038417 +360000 ekin = 1.70943632676256 | erot = 2.26611368397356 | epot = -13.1088991405421 | etot = -9.13334912980602 +361000 ekin = 1.67315005965508 | erot = 2.2123416661589 | epot = -13.0188408550996 | etot = -9.13334912928563 +362000 ekin = 1.63480994001619 | erot = 2.16376887379963 | epot = -12.9319279427068 | etot = -9.13334912889101 +363000 ekin = 1.5962260605757 | erot = 2.1246998668386 | epot = -12.8542750560708 | etot = -9.13334912865646 +364000 ekin = 1.55890205833795 | erot = 2.09734631559849 | epot = -12.7895975025214 | etot = -9.133349128585 +365000 ekin = 1.52397421076766 | erot = 2.08181308416726 | epot = -12.7391364235909 | etot = -9.13334912865599 +366000 ekin = 1.49221260733989 | erot = 2.07639009796191 | epot = -12.7019518341345 | etot = -9.13334912883268 +367000 ekin = 1.4640595236492 | erot = 2.07805510122135 | epot = -12.6754637539425 | etot = -9.133349129072 +368000 ekin = 1.43967726932343 | erot = 2.08307216057558 | epot = -12.6560985592322 | etot = -9.13334912933319 +369000 ekin = 1.41899010811432 | erot = 2.08756917147235 | epot = -12.6399084091713 | etot = -9.13334912958465 +370000 ekin = 1.4017155735671 | erot = 2.08800173652844 | epot = -12.6230664399006 | etot = -9.13334912980506 +371000 ekin = 1.38739280854812 | erot = 2.08146226240604 | epot = -12.6022042009356 | etot = -9.13334912998148 +372000 ekin = 1.3754234030853 | erot = 2.06585193702315 | epot = -12.5746244702122 | etot = -9.13334913010378 +373000 ekin = 1.36513752357851 | erot = 2.03996886737135 | epot = -12.5384555211115 | etot = -9.13334913016165 +374000 ekin = 1.35583949105109 | erot = 2.00351975772453 | epot = -12.4927083789448 | etot = -9.13334913016913 +375000 ekin = 1.34694157711384 | erot = 1.95716038268554 | epot = -12.437451089867 | etot = -9.13334913006761 +376000 ekin = 1.33814968105194 | erot = 1.90258032253335 | epot = -12.374079133482 | etot = -9.13334912989673 +377000 ekin = 1.32936261120742 | erot = 1.84227265725224 | epot = -12.3049843981359 | etot = -9.13334912967628 +378000 ekin = 1.32063159991288 | erot = 1.77926043319027 | epot = -12.2332411625417 | etot = -9.13334912943852 +379000 ekin = 1.31208340368805 | erot = 1.71672941783618 | epot = -12.1621619507397 | etot = -9.13334912921549 +380000 ekin = 1.30384179784167 | erot = 1.65764204155762 | epot = -12.0948329684323 | etot = -9.13334912903296 +381000 ekin = 1.29657917475797 | erot = 1.60487100826659 | epot = -12.0347993118439 | etot = -9.13334912881932 +382000 ekin = 1.29092190134667 | erot = 1.56061067707055 | epot = -11.9848817072419 | etot = -9.13334912882472 +383000 ekin = 1.28620909068407 | erot = 1.52536833769981 | epot = -11.9449265572222 | etot = -9.13334912883829 +384000 ekin = 1.28205683099622 | erot = 1.49922806168804 | epot = -11.9146340215154 | etot = -9.13334912883115 +385000 ekin = 1.27850478017866 | erot = 1.48216189144808 | epot = -11.8940158004137 | etot = -9.13334912878696 +386000 ekin = 1.27603762173996 | erot = 1.47423730493007 | epot = -11.8836240553798 | etot = -9.13334912870974 +387000 ekin = 1.27548287271909 | erot = 1.47565716104739 | epot = -11.8844891623898 | etot = -9.13334912862331 +388000 ekin = 1.2778004458578 | erot = 1.4866096409743 | epot = -11.8977592153981 | etot = -9.13334912856596 +389000 ekin = 1.28381262703566 | erot = 1.50697425852415 | epot = -11.9241360141379 | etot = -9.13334912857811 +390000 ekin = 1.29393930260839 | erot = 1.53598035068258 | epot = -11.9632687819853 | etot = -9.1333491286943 +391000 ekin = 1.30800074456088 | erot = 1.5719098492446 | epot = -12.013259722734 | etot = -9.13334912892847 +392000 ekin = 1.32513099179432 | erot = 1.61197584867722 | epot = -12.0704559697429 | etot = -9.13334912927137 +393000 ekin = 1.3438254300013 | erot = 1.65241448883401 | epot = -12.1295890485245 | etot = -9.13334912968923 +394000 ekin = 1.36212102398624 | erot = 1.68881012624764 | epot = -12.1842802803621 | etot = -9.13334913012818 +395000 ekin = 1.37788072140303 | erot = 1.71661593054073 | epot = -12.2278457824672 | etot = -9.13334913052342 +396000 ekin = 1.38913154512392 | erot = 1.73181112618384 | epot = -12.2542918021045 | etot = -9.13334913079678 +397000 ekin = 1.3943935747973 | erot = 1.73153617599127 | epot = -12.2592788817204 | etot = -9.13334913093185 +398000 ekin = 1.39293904659178 | erot = 1.71441550438834 | epot = -12.2407036818554 | etot = -9.1333491308753 +399000 ekin = 1.38493174777428 | erot = 1.68094766350971 | epot = -12.1992285419453 | etot = -9.13334913066127 +400000 ekin = 1.37142116074086 | erot = 1.6333076419797 | epot = -12.1380779330255 | etot = -9.13334913030493 +401000 ekin = 1.35412991252432 | erot = 1.57501044311775 | epot = -12.0624894855338 | etot = -9.13334912989174 +402000 ekin = 1.33517991856886 | erot = 1.51048364980092 | epot = -11.9790126977736 | etot = -9.13334912940385 +403000 ekin = 1.31709653187253 | erot = 1.44458891478936 | epot = -11.8950345755997 | etot = -9.13334912893783 +404000 ekin = 1.30234590493855 | erot = 1.38198365576739 | epot = -11.8176786892404 | etot = -9.13334912853445 +405000 ekin = 1.29301391716251 | erot = 1.32673455588818 | epot = -11.7530976012879 | etot = -9.13334912823722 +406000 ekin = 1.29065467462767 | erot = 1.28204116436315 | epot = -11.7060449670158 | etot = -9.133349128025 +407000 ekin = 1.29643237294773 | erot = 1.2500643658834 | epot = -11.6798458667495 | etot = -9.13334912791839 +408000 ekin = 1.31094700615227 | erot = 1.23190986721439 | epot = -11.6762060012819 | etot = -9.13334912791524 +409000 ekin = 1.33422438303342 | erot = 1.22763489752168 | epot = -11.6952084085692 | etot = -9.13334912801405 +410000 ekin = 1.36572014154933 | erot = 1.23628017302415 | epot = -11.7353494427848 | etot = -9.13334912821129 +411000 ekin = 1.4043266876074 | erot = 1.25592548503495 | epot = -11.7936013011427 | etot = -9.13334912850032 +412000 ekin = 1.44839088645843 | erot = 1.28379672627791 | epot = -11.8655367416032 | etot = -9.13334912886682 +413000 ekin = 1.49576795241837 | erot = 1.31646032748887 | epot = -11.9455774091897 | etot = -9.13334912928247 +414000 ekin = 1.54394920889458 | erot = 1.35014055217844 | epot = -12.0274388907757 | etot = -9.13334912970263 +415000 ekin = 1.5902942170517 | erot = 1.38116660571189 | epot = -12.104809952833 | etot = -9.13334913006945 +416000 ekin = 1.63235973909137 | erot = 1.40649922749338 | epot = -12.172208096909 | etot = -9.13334913032422 +417000 ekin = 1.66825800489265 | erot = 1.42422016761247 | epot = -12.2258273029362 | etot = -9.13334913043104 +418000 ekin = 1.69693219837303 | erot = 1.43381449957587 | epot = -12.2640958283224 | etot = -9.13334913037349 +419000 ekin = 1.7182495189487 | erot = 1.43620625779753 | epot = -12.2878049069294 | etot = -9.13334913018312 +420000 ekin = 1.7328833743066 | erot = 1.43350825350923 | epot = -12.2997407577259 | etot = -9.13334912991011 +421000 ekin = 1.74204129532477 | erot = 1.42856028675097 | epot = -12.3039507116849 | etot = -9.1333491296092 +422000 ekin = 1.74713701807814 | erot = 1.42445618730966 | epot = -12.3049423347143 | etot = -9.13334912932652 +423000 ekin = 1.74949063384811 | erot = 1.42413436044518 | epot = -12.3069741233966 | etot = -9.13334912910334 +424000 ekin = 1.75009754643101 | erot = 1.43005641925257 | epot = -12.3135030946294 | etot = -9.13334912894587 +425000 ekin = 1.74947257256809 | erot = 1.4441240080241 | epot = -12.3269457094753 | etot = -9.13334912888314 +426000 ekin = 1.69664946387641 | erot = 1.40011304962925 | epot = -12.2301116346042 | etot = -9.13334912109858 +427000 ekin = 1.76448154345776 | erot = 1.46695774969997 | epot = -12.3647884699761 | etot = -9.13334917681841 +428000 ekin = 1.7786404038279 | erot = 1.51204937412251 | epot = -12.4240389057576 | etot = -9.13334912780716 +429000 ekin = 1.77744254090706 | erot = 1.55645173379881 | epot = -12.4672434028096 | etot = -9.13334912810371 +430000 ekin = 1.76864481713971 | erot = 1.60567169371162 | epot = -12.5076656392884 | etot = -9.13334912843703 +431000 ekin = 1.75041443993107 | erot = 1.6565563851412 | epot = -12.5403199538332 | etot = -9.13334912876093 +432000 ekin = 1.72143753020987 | erot = 1.70559294341302 | epot = -12.5603796026437 | etot = -9.13334912902085 +433000 ekin = 1.68129756274263 | erot = 1.74934007551102 | epot = -12.5639867674181 | etot = -9.13334912916441 +434000 ekin = 1.63077650980017 | erot = 1.78490039303275 | epot = -12.5490260319871 | etot = -9.13334912915421 +435000 ekin = 1.57198882084538 | erot = 1.81033246556191 | epot = -12.5156704153873 | etot = -9.13334912897997 +436000 ekin = 1.50828072851522 | erot = 1.82489908961114 | epot = -12.4665289467908 | etot = -9.13334912866448 +437000 ekin = 1.44388315301276 | erot = 1.82908776308031 | epot = -12.4063200443509 | etot = -9.13334912825785 +438000 ekin = 1.38337900429759 | erot = 1.82441107452581 | epot = -12.3411392066477 | etot = -9.13334912782426 +439000 ekin = 1.33110407576258 | erot = 1.81306694504145 | epot = -12.277520148228 | etot = -9.13334912742398 +440000 ekin = 1.29061754889026 | erot = 1.79757475508433 | epot = -12.221541431074 | etot = -9.13334912709939 +441000 ekin = 1.26434687832171 | erot = 1.7804860060747 | epot = -12.1781820112658 | etot = -9.13334912686943 +442000 ekin = 1.25344985037928 | erot = 1.76421040799502 | epot = -12.1510093851073 | etot = -9.13334912673305 +443000 ekin = 1.25787308938399 | erot = 1.75093400476763 | epot = -12.1421562208298 | etot = -9.13334912667816 +444000 ekin = 1.27654491138777 | erot = 1.74256727852075 | epot = -12.1524613166011 | etot = -9.13334912669253 +445000 ekin = 1.30762960642446 | erot = 1.74066161517084 | epot = -12.1816403483637 | etot = -9.13334912676842 +446000 ekin = 1.34878485335192 | erot = 1.74626611357143 | epot = -12.2284000938269 | etot = -9.13334912690351 +447000 ekin = 1.39739993763702 | erot = 1.75974793458134 | epot = -12.2904969993176 | etot = -9.13334912709922 +448000 ekin = 1.45076649190871 | erot = 1.78060717934201 | epot = -12.3647227986021 | etot = -9.13334912735142 +449000 ekin = 1.5062399960533 | erot = 1.80738848344772 | epot = -12.4469776071498 | etot = -9.13334912764873 +450000 ekin = 1.56138908054573 | erot = 1.83773497344423 | epot = -12.5324731819601 | etot = -9.13334912797012 +451000 ekin = 1.61412412964502 | erot = 1.86859865234508 | epot = -12.616071910276 | etot = -9.13334912828589 +452000 ekin = 1.66280931630096 | erot = 1.89658548036465 | epot = -12.6927439252276 | etot = -9.13334912856203 +453000 ekin = 1.70634971637078 | erot = 1.91837476586891 | epot = -12.7580736110103 | etot = -9.13334912877057 +454000 ekin = 1.74423056750361 | erot = 1.93111374790724 | epot = -12.8086934443052 | etot = -9.13334912889435 +455000 ekin = 1.77648988409887 | erot = 1.9327029137826 | epot = -12.8425419268132 | etot = -9.13334912893172 +456000 ekin = 1.80361911556749 | erot = 1.92192628287876 | epot = -12.8588945273416 | etot = -9.13334912889534 +457000 ekin = 1.82640016706236 | erot = 1.89842961390005 | epot = -12.8581789097698 | etot = -9.13334912880743 +458000 ekin = 1.84570455025966 | erot = 1.86259298695791 | epot = -12.8416466659118 | etot = -9.13334912869422 +459000 ekin = 1.86229070170983 | erot = 1.81535342315176 | epot = -12.8109932534385 | etot = -9.13334912857691 +460000 ekin = 1.87663848085905 | erot = 1.75803306182803 | epot = -12.7680206711598 | etot = -9.13334912847276 +461000 ekin = 1.88883864523233 | erot = 1.69219746384304 | epot = -12.7143852374636 | etot = -9.13334912838823 +462000 ekin = 1.89856203652349 | erot = 1.61956678027435 | epot = -12.6514779451215 | etot = -9.13334912832368 +463000 ekin = 1.9051022176453 | erot = 1.54196437877836 | epot = -12.5804157246989 | etot = -9.13334912827526 +464000 ekin = 1.90747686786717 | erot = 1.46127993198471 | epot = -12.5021059280858 | etot = -9.1333491282339 +465000 ekin = 1.90457977356229 | erot = 1.37946070091726 | epot = -12.4173896026645 | etot = -9.13334912818491 +466000 ekin = 1.89536572152405 | erot = 1.29851485172146 | epot = -12.3272297013661 | etot = -9.13334912812057 +467000 ekin = 1.87901831710062 | erot = 1.22048659414375 | epot = -12.2328540392793 | etot = -9.13334912803494 +468000 ekin = 1.85509917792147 | erot = 1.14739126284037 | epot = -12.135839568689 | etot = -9.13334912792715 +469000 ekin = 1.8236660510741 | erot = 1.08110787535072 | epot = -12.0381230542261 | etot = -9.13334912780131 +470000 ekin = 1.785352160757 | erot = 1.02324127043659 | epot = -11.9419425588568 | etot = -9.1333491276632 +471000 ekin = 1.74141051513467 | erot = 0.974982090043445 | epot = -11.8497417326962 | etot = -9.13334912751811 +472000 ekin = 1.69372019706013 | erot = 0.937000644454747 | epot = -11.7640699688855 | etot = -9.13334912737064 +473000 ekin = 1.64473632771046 | erot = 0.909402534931637 | epot = -11.6874879898683 | etot = -9.13334912722617 +474000 ekin = 1.59734995177427 | erot = 0.891755018431329 | epot = -11.6224540973001 | etot = -9.13334912709447 +475000 ekin = 1.55462885495311 | erot = 0.883174765260048 | epot = -11.5711527472037 | etot = -9.1333491269905 +476000 ekin = 1.51944866261213 | erot = 0.882459888569459 | epot = -11.5352576781123 | etot = -9.13334912693073 +477000 ekin = 1.49408243529076 | erot = 0.888250161716788 | epot = -11.5156817239344 | etot = -9.13334912692685 +478000 ekin = 1.47985622585666 | erot = 0.899197335532742 | epot = -11.5124026883704 | etot = -9.13334912698098 +479000 ekin = 1.47695373952882 | erot = 0.914115348457448 | epot = -11.5244182150791 | etot = -9.13334912709281 +480000 ekin = 1.48439477575485 | erot = 0.932072516620887 | epot = -11.549816419617 | etot = -9.13334912724127 +481000 ekin = 1.50022741217548 | erot = 0.952423999184216 | epot = -11.5860005387809 | etot = -9.13334912742123 +482000 ekin = 1.52172985963465 | erot = 0.974754211846534 | epot = -11.6298331991066 | etot = -9.13334912762538 +483000 ekin = 1.54567018241554 | erot = 0.998770450814832 | epot = -11.6777897610751 | etot = -9.13334912784471 +484000 ekin = 1.56858614723153 | erot = 1.0241976351087 | epot = -11.7261329104078 | etot = -9.13334912806762 +485000 ekin = 1.58707346955154 | erot = 1.05070585623162 | epot = -11.7711284540615 | etot = -9.1333491282783 +486000 ekin = 1.59807103603186 | erot = 1.07788995424715 | epot = -11.8093101187377 | etot = -9.13334912845869 +487000 ekin = 1.59911980804544 | erot = 1.10529931942212 | epot = -11.8377682560593 | etot = -9.1333491285917 +488000 ekin = 1.58856342116781 | erot = 1.13249736396266 | epot = -11.8544099137963 | etot = -9.13334912866581 +489000 ekin = 1.56566142904843 | erot = 1.15911683125853 | epot = -11.8581273889845 | etot = -9.13334912867754 +490000 ekin = 1.53060268554808 | erot = 1.18488502427396 | epot = -11.8488368384543 | etot = -9.13334912863223 +491000 ekin = 1.48443427069631 | erot = 1.20959914016058 | epot = -11.8273825393282 | etot = -9.13334912847127 +492000 ekin = 1.42930345354614 | erot = 1.23291829593421 | epot = -11.7955708778632 | etot = -9.13334912838287 +493000 ekin = 1.36749564145311 | erot = 1.25438544605179 | epot = -11.7552302157793 | etot = -9.13334912827441 +494000 ekin = 1.30137262988227 | erot = 1.27348228002641 | epot = -11.7082040380627 | etot = -9.133349128154 +495000 ekin = 1.23360970817153 | erot = 1.28954660636253 | epot = -11.6565054425604 | etot = -9.13334912802634 +496000 ekin = 1.16375548641149 | erot = 1.30023195608786 | epot = -11.597336620543 | etot = -9.13334917804361 +497000 ekin = 1.02574644939893 | erot = 1.24927230426525 | epot = -11.4083678755046 | etot = -9.13334912184043 +498000 ekin = 1.13339044616149 | erot = 1.24939677704534 | epot = -11.5161363891128 | etot = -9.13334916590599 +499000 ekin = 1.16434762393305 | erot = 1.25864673155132 | epot = -11.5563434800389 | etot = -9.13334912455449 +500000 ekin = 1.16768486506821 | erot = 1.2576934444408 | epot = -11.5587274345822 | etot = -9.13334912507316 +501000 ekin = 1.17559895497582 | erot = 1.25038915442767 | epot = -11.5593372343047 | etot = -9.1333491249012 +502000 ekin = 1.18926606273961 | erot = 1.23784323633194 | epot = -11.5604584237508 | etot = -9.13334912467929 +503000 ekin = 1.20982408114966 | erot = 1.22204157664462 | epot = -11.5652147822324 | etot = -9.13334912443811 +504000 ekin = 1.23811782737063 | erot = 1.20572865378543 | epot = -11.5771956053586 | etot = -9.13334912420251 +505000 ekin = 1.27460966228801 | erot = 1.19199209322219 | epot = -11.5999508795096 | etot = -9.1333491239994 +506000 ekin = 1.31928047819605 | erot = 1.18393687677926 | epot = -11.6365664788287 | etot = -9.1333491238534 +507000 ekin = 1.37157700900509 | erot = 1.18435118386592 | epot = -11.6892773166525 | etot = -9.13334912378151 +508000 ekin = 1.43042502721541 | erot = 1.1954118748155 | epot = -11.7591860258226 | etot = -9.1333491237917 +509000 ekin = 1.49431413372851 | erot = 1.21846596295587 | epot = -11.8461292205661 | etot = -9.1333491238817 +510000 ekin = 1.56143815899979 | erot = 1.25390781315292 | epot = -11.9486950961947 | etot = -9.13334912404201 +511000 ekin = 1.62985405359528 | erot = 1.30115550673861 | epot = -12.0643586845933 | etot = -9.13334912425937 +512000 ekin = 1.69760948238436 | erot = 1.35871536004144 | epot = -12.189673966948 | etot = -9.13334912452224 +513000 ekin = 1.76279412854786 | erot = 1.42431355746588 | epot = -12.320456810837 | etot = -9.13334912482321 +514000 ekin = 1.82349978434223 | erot = 1.49507387317583 | epot = -12.4519227826749 | etot = -9.1333491251568 +515000 ekin = 1.87772649131747 | erot = 1.56773414235918 | epot = -12.5788097591887 | etot = -9.13334912551208 +516000 ekin = 1.92332299298554 | erot = 1.63891274675679 | epot = -12.6955848656063 | etot = -9.13334912586395 +517000 ekin = 1.95805681102128 | erot = 1.70543998933813 | epot = -12.7968459265308 | etot = -9.13334912617134 +518000 ekin = 1.97984991947085 | erot = 1.76473849815031 | epot = -12.8779375440072 | etot = -9.13334912638607 +519000 ekin = 1.98711819296778 | erot = 1.81518192784685 | epot = -12.9356492472837 | etot = -9.1333491264691 +520000 ekin = 1.97908911077294 | erot = 1.85632478174878 | epot = -12.9687630189323 | etot = -9.13334912641058 +521000 ekin = 1.95594858056491 | erot = 1.8889276079652 | epot = -12.9782253147548 | etot = -9.13334912622471 +522000 ekin = 1.91881161738285 | erot = 1.9147558223734 | epot = -12.9669165657056 | etot = -9.13334912594938 +523000 ekin = 1.86954045343398 | erot = 1.93620351350197 | epot = -12.93909309257 | etot = -9.13334912563406 +524000 ekin = 1.8104733218181 | erot = 1.9558227102207 | epot = -12.8996451573689 | etot = -9.13334912533007 +525000 ekin = 1.74413482435815 | erot = 1.97582576721553 | epot = -12.8533097166586 | etot = -9.1333491250849 +526000 ekin = 1.67297434025038 | erot = 1.99761678040426 | epot = -12.8039402455911 | etot = -9.13334912493644 +527000 ekin = 1.59916865616304 | erot = 2.02141684187611 | epot = -12.7539346229441 | etot = -9.133349124905 +528000 ekin = 1.52452149634748 | erot = 2.04605877912595 | epot = -12.7039294004604 | etot = -9.13334912498693 +529000 ekin = 1.4504814163811 | erot = 2.06903286947822 | epot = -12.6528634110099 | etot = -9.13334912515059 +530000 ekin = 1.37827485203411 | erot = 2.08683821123111 | epot = -12.5984621886047 | etot = -9.13334912533946 +531000 ekin = 1.30911544825195 | erot = 2.09562136598219 | epot = -12.5380859397189 | etot = -9.13334912548476 +532000 ekin = 1.24441932206898 | erot = 2.09198653946324 | epot = -12.4697549870569 | etot = -9.13334912552464 +533000 ekin = 1.18594679653143 | erot = 2.07377924595515 | epot = -12.3930751679089 | etot = -9.13334912542228 +534000 ekin = 1.13581312461343 | erot = 2.04062941960209 | epot = -12.3097916693922 | etot = -9.13334912517671 +535000 ekin = 1.09635528031359 | erot = 1.99411201499583 | epot = -12.2238164201305 | etot = -9.13334912482111 +536000 ekin = 1.06988655695511 | erot = 1.93750945181444 | epot = -12.1407451331814 | etot = -9.13334912441183 +537000 ekin = 1.05839509271139 | erot = 1.87547351818609 | epot = -12.067217734889 | etot = -9.13334912399155 +538000 ekin = 1.06323891385367 | erot = 1.8133142469846 | epot = -12.0099022845153 | etot = -9.13334912367703 +539000 ekin = 1.08487929969803 | erot = 1.75562392314644 | epot = -11.9738523463361 | etot = -9.13334912349166 +540000 ekin = 1.12268189022786 | erot = 1.70611667318395 | epot = -11.9621476868843 | etot = -9.13334912347248 +541000 ekin = 1.17481105395673 | erot = 1.66717481230729 | epot = -11.9753349899007 | etot = -9.13334912363666 +542000 ekin = 1.23824417790755 | erot = 1.63956314455092 | epot = -12.0111564464361 | etot = -9.13334912397767 +543000 ekin = 1.30892832431888 | erot = 1.62236761446567 | epot = -12.0646450632456 | etot = -9.13334912446102 +544000 ekin = 1.38208514507386 | erot = 1.61318872881507 | epot = -12.1286229989176 | etot = -9.13334912502866 +545000 ekin = 1.45263801175973 | erot = 1.60857948401639 | epot = -12.1945666213809 | etot = -9.13334912560476 +546000 ekin = 1.51570974605503 | erot = 1.60467377472855 | epot = -12.2537326468924 | etot = -9.13334912610883 +547000 ekin = 1.56711452712105 | erot = 1.5978880038179 | epot = -12.2983516574116 | etot = -9.13334912647268 +548000 ekin = 1.60376221827936 | erot = 1.58554162816907 | epot = -12.3226529731024 | etot = -9.13334912665393 +549000 ekin = 1.62391041626163 | erot = 1.56625626421581 | epot = -12.3235158071214 | etot = -9.13334912664393 +550000 ekin = 1.62723358008958 | erot = 1.54012357329004 | epot = -12.3007062798231 | etot = -9.13334912644349 +551000 ekin = 1.61471889891675 | erot = 1.50851459571133 | epot = -12.2565826207707 | etot = -9.13334912614266 +552000 ekin = 1.58843016682431 | erot = 1.47348936384652 | epot = -12.195268656439 | etot = -9.13334912576819 +553000 ekin = 1.5512009811002 | erot = 1.43753302719441 | epot = -12.1220831336622 | etot = -9.13334912536755 +554000 ekin = 1.50631636213267 | erot = 1.4031875532353 | epot = -12.0428530403443 | etot = -9.13334912497632 +555000 ekin = 1.45722878986597 | erot = 1.37279698200258 | epot = -11.9633748964865 | etot = -9.13334912461799 +556000 ekin = 1.40732293285248 | erot = 1.34837590639291 | epot = -11.88904796355 | etot = -9.13334912430461 +557000 ekin = 1.35973750772925 | erot = 1.3315770703911 | epot = -11.8246637021615 | etot = -9.13334912404111 +558000 ekin = 1.31723590732991 | erot = 1.32371628032827 | epot = -11.7743013114881 | etot = -9.13334912382991 +559000 ekin = 1.28211028309157 | erot = 1.32580526483769 | epot = -11.7412646716038 | etot = -9.13334912367457 +560000 ekin = 1.25610590404874 | erot = 1.33855626265837 | epot = -11.7280112902885 | etot = -9.13334912358135 +561000 ekin = 1.24035844263297 | erot = 1.36234138770184 | epot = -11.7360489538933 | etot = -9.13334912355851 +562000 ekin = 1.23534624012624 | erot = 1.39711468447221 | epot = -11.7658100482125 | etot = -9.13334912361409 +563000 ekin = 1.24087113988399 | erot = 1.44233150297995 | epot = -11.8165517666127 | etot = -9.13334912374876 +564000 ekin = 1.25609129143005 | erot = 1.49691875867199 | epot = -11.8863591740536 | etot = -9.13334912395155 +565000 ekin = 1.2796301584255 | erot = 1.55937933470603 | epot = -11.972358617318 | etot = -9.13334912418645 +566000 ekin = 1.30976945418403 | erot = 1.62795664725485 | epot = -12.0710752258852 | etot = -9.13334912444628 +567000 ekin = 1.34469873511273 | erot = 1.70073738336314 | epot = -12.1787852431648 | etot = -9.13334912468897 +568000 ekin = 1.38275779930725 | erot = 1.77591787229441 | epot = -12.2920247965046 | etot = -9.13334912490297 +569000 ekin = 1.4226029414226 | erot = 1.85183127901131 | epot = -12.4077833455266 | etot = -9.1333491250927 +570000 ekin = 1.46311433096011 | erot = 1.92670412003824 | epot = -12.5231675763641 | etot = -9.13334912536576 +571000 ekin = 1.50327753328895 | erot = 1.99853100879653 | epot = -12.6351576677648 | etot = -9.13334912567935 +572000 ekin = 1.54192966726684 | erot = 2.06497613729043 | epot = -12.7402549304304 | etot = -9.13334912587309 +573000 ekin = 1.57823855407023 | erot = 2.12427016695884 | epot = -12.8358578469846 | etot = -9.13334912595553 +574000 ekin = 1.61207502224351 | erot = 2.17570201380467 | epot = -12.9211261619166 | etot = -9.13334912586839 +575000 ekin = 1.64402582173823 | erot = 2.22028441014227 | epot = -12.9976593575043 | etot = -9.13334912562384 +576000 ekin = 1.67538587678429 | erot = 2.26042238856638 | epot = -13.0691573906398 | etot = -9.13334912528911 +577000 ekin = 1.70789209379029 | erot = 2.29915883242772 | epot = -13.1404000511839 | etot = -9.1333491249659 +578000 ekin = 1.74326819508472 | erot = 2.33909725076652 | epot = -13.2157145705981 | etot = -9.13334912474687 +579000 ekin = 1.7827223183835 | erot = 2.38182643842429 | epot = -13.2978978815009 | etot = -9.13334912469309 +580000 ekin = 1.82652189373004 | erot = 2.42751679139928 | epot = -13.3873878099607 | etot = -9.13334912483141 +581000 ekin = 1.87370675175411 | erot = 2.47480205694032 | epot = -13.4818579338668 | etot = -9.13334912517237 +582000 ekin = 1.92197052578507 | erot = 2.52092715153303 | epot = -13.5762468029763 | etot = -9.13334912565824 +583000 ekin = 1.96774925896911 | erot = 2.56227660801606 | epot = -13.6633749932238 | etot = -9.13334912623863 +584000 ekin = 2.00657374540242 | erot = 2.59498886542731 | epot = -13.7349117376481 | etot = -9.13334912681841 +585000 ekin = 2.03371871575722 | erot = 2.61566274200203 | epot = -13.7827305850397 | etot = -9.13334912728048 +586000 ekin = 2.04507827703309 | erot = 2.62214006251279 | epot = -13.8005674670606 | etot = -9.13334912751474 +587000 ekin = 2.03806243485681 | erot = 2.61411994888867 | epot = -13.7855315112034 | etot = -9.13334912745792 +588000 ekin = 2.01223115184381 | erot = 2.59335030111902 | epot = -13.7389305800864 | etot = -9.13334912712354 +589000 ekin = 1.96942837554574 | erot = 2.56324673362673 | epot = -13.6660242357749 | etot = -9.13334912660243 +590000 ekin = 1.91334419958977 | erot = 2.52801524733261 | epot = -13.5747085729524 | etot = -9.13334912603005 +591000 ekin = 1.8486538333072 | erot = 2.49158313368731 | epot = -13.4735860925282 | etot = -9.1333491255337 +592000 ekin = 1.78006004419711 | erot = 2.45674050608303 | epot = -13.3701496754634 | etot = -9.13334912518328 +593000 ekin = 1.71159279762265 | erot = 2.42478693109097 | epot = -13.2697288536906 | etot = -9.13334912497694 +594000 ekin = 1.64634946405468 | erot = 2.39569805901288 | epot = -13.1753966479367 | etot = -9.1333491248691 +595000 ekin = 1.58659479949042 | erot = 2.3685443255726 | epot = -13.0884882498803 | etot = -9.13334912481725 +596000 ekin = 1.53398103551517 | erot = 2.34182175785605 | epot = -13.0091519181797 | etot = -9.13334912480847 +597000 ekin = 1.4896944162268 | erot = 2.31355286210882 | epot = -12.936596403185 | etot = -9.13334912484939 +598000 ekin = 1.45449014890496 | erot = 2.28129539496237 | epot = -12.8691346688077 | etot = -9.13334912494036 +599000 ekin = 1.42868283605997 | erot = 2.24230571380088 | epot = -12.8043376749196 | etot = -9.13334912505876 +600000 ekin = 1.41215819512801 | erot = 2.19421771509534 | epot = -12.7397250351187 | etot = -9.13334912489538 +601000 ekin = 1.40437980063629 | erot = 2.13675092848644 | epot = -12.6744798541813 | etot = -9.1333491250586 +602000 ekin = 1.40442466853112 | erot = 2.06863595764755 | epot = -12.6064097512949 | etot = -9.13334912511623 +603000 ekin = 1.41112302449405 | erot = 1.98998056957968 | epot = -12.5344527191431 | etot = -9.13334912506935 +604000 ekin = 1.42310135151954 | erot = 1.90274524323251 | epot = -12.4591957196945 | etot = -9.13334912494249 +605000 ekin = 1.43883447822283 | erot = 1.81030632011497 | epot = -12.3824899231074 | etot = -9.13334912476965 +606000 ekin = 1.45673760094997 | erot = 1.71684240505229 | epot = -12.3069291305841 | etot = -9.13334912458189 +607000 ekin = 1.47529863712971 | erot = 1.62672298753391 | epot = -12.2353707490645 | etot = -9.13334912440092 +608000 ekin = 1.49323166610194 | erot = 1.54399943869403 | epot = -12.1705802290343 | etot = -9.13334912423836 +609000 ekin = 1.5096125661562 | erot = 1.47208306434206 | epot = -12.115044754606 | etot = -9.13334912410772 +610000 ekin = 1.52396039431241 | erot = 1.41350705715335 | epot = -12.0708165754585 | etot = -9.13334912399274 +611000 ekin = 1.53622860047036 | erot = 1.3699244374139 | epot = -12.0395021618062 | etot = -9.13334912392191 +612000 ekin = 1.54668536626181 | erot = 1.34205362873153 | epot = -12.0220881189018 | etot = -9.13334912390848 +613000 ekin = 1.55571309695671 | erot = 1.32960894336099 | epot = -12.0186711642871 | etot = -9.13334912396935 +614000 ekin = 1.56356369221744 | erot = 1.33131277562655 | epot = -12.0282255919628 | etot = -9.13334912411877 +615000 ekin = 1.57013881826736 | erot = 1.34494539761822 | epot = -12.048433340221 | etot = -9.13334912433545 +616000 ekin = 1.57485681904016 | erot = 1.36757312206296 | epot = -12.0757790657592 | etot = -9.13334912465612 +617000 ekin = 1.57672646781345 | erot = 1.39546251366801 | epot = -12.1055381065021 | etot = -9.13334912502063 +618000 ekin = 1.57456346737962 | erot = 1.42448013453604 | epot = -12.1323927272915 | etot = -9.13334912537588 +619000 ekin = 1.56732946470294 | erot = 1.45059208152824 | epot = -12.1512706718915 | etot = -9.1333491256603 +620000 ekin = 1.55451321754076 | erot = 1.47039334455628 | epot = -12.1582556879148 | etot = -9.13334912581774 +621000 ekin = 1.53644782338588 | erot = 1.48161304591014 | epot = -12.1514099951073 | etot = -9.13334912581127 +622000 ekin = 1.51447783518566 | erot = 1.48347710481991 | epot = -12.1313040656385 | etot = -9.13334912563293 +623000 ekin = 1.49092960733246 | erot = 1.47683215248968 | epot = -12.1011108851291 | etot = -9.13334912530692 +624000 ekin = 1.46886130170239 | erot = 1.46422198591643 | epot = -12.0664324125277 | etot = -9.13334912490889 +625000 ekin = 1.45155188812839 | erot = 1.44918251594374 | epot = -12.0340835285544 | etot = -9.13334912448225 +626000 ekin = 1.44224748158087 | erot = 1.4353339959185 | epot = -12.0109306015706 | etot = -9.13334912407122 +627000 ekin = 1.44381530880132 | erot = 1.42638005354872 | epot = -12.0035444860845 | etot = -9.1333491237345 +628000 ekin = 1.45833081620235 | erot = 1.42560824875323 | epot = -12.0172881884922 | etot = -9.13334912353658 +629000 ekin = 1.48676985537149 | erot = 1.43535417577217 | epot = -12.0554731546308 | etot = -9.13334912348712 +630000 ekin = 1.528664170492 | erot = 1.4568918451359 | epot = -12.1189051392527 | etot = -9.13334912362481 +631000 ekin = 1.58193413338957 | erot = 1.49015054897711 | epot = -12.2054338063838 | etot = -9.13334912401709 +632000 ekin = 1.64234851055675 | erot = 1.53357750659073 | epot = -12.3092751416891 | etot = -9.13334912454161 +633000 ekin = 1.70466841197052 | erot = 1.58426390210257 | epot = -12.4222814392219 | etot = -9.13334912514886 +634000 ekin = 1.76318354699381 | erot = 1.63860587790759 | epot = -12.535138550635 | etot = -9.13334912573357 +635000 ekin = 1.8124262503481 | erot = 1.69306627320837 | epot = -12.638841649741 | etot = -9.13334912618454 +636000 ekin = 1.84805557838161 | erot = 1.74492785470264 | epot = -12.7263325594983 | etot = -9.13334912641409 +637000 ekin = 1.86755595284793 | erot = 1.79286465559443 | epot = -12.7937697348522 | etot = -9.13334912640983 +638000 ekin = 1.87047357468866 | erot = 1.83697965057618 | epot = -12.8408023514712 | etot = -9.13334912620637 +639000 ekin = 1.85817220593381 | erot = 1.87849437006827 | epot = -12.8700157018828 | etot = -9.13334912588074 +640000 ekin = 1.83325502875035 | erot = 1.91930247136817 | epot = -12.885906625631 | etot = -9.13334912551248 +641000 ekin = 1.79889805051669 | erot = 1.96149522932472 | epot = -12.8937424049988 | etot = -9.13334912515733 +642000 ekin = 1.75833330345023 | erot = 2.0070145451738 | epot = -12.8986969734783 | etot = -9.13334912485424 +643000 ekin = 1.7145240073878 | erot = 2.05742054585298 | epot = -12.9052936778359 | etot = -9.1333491245951 +644000 ekin = 1.67006045206809 | erot = 2.11379950766841 | epot = -12.9172090841662 | etot = -9.13334912442973 +645000 ekin = 1.62710169193889 | erot = 2.17652829047939 | epot = -12.9369791067753 | etot = -9.13334912435698 +646000 ekin = 1.58731920571272 | erot = 2.24499987972462 | epot = -12.9656682098071 | etot = -9.13334912436974 +647000 ekin = 1.5519287985018 | erot = 2.31774723145838 | epot = -13.0030251544523 | etot = -9.13334912449209 +648000 ekin = 1.52155547404621 | erot = 2.3921684940519 | epot = -13.0470730928258 | etot = -9.13334912472772 +649000 ekin = 1.49615701172682 | erot = 2.46459269466547 | epot = -13.0940988314671 | etot = -9.13334912507481 +650000 ekin = 1.47495820408236 | erot = 2.53042613107603 | epot = -13.138733460677 | etot = -9.1333491255186 +651000 ekin = 1.4564475827599 | erot = 2.58442104122353 | epot = -13.1742177500108 | etot = -9.13334912602733 +652000 ekin = 1.43848054670156 | erot = 2.62109720356034 | epot = -13.1929268768081 | etot = -9.13334912654621 +653000 ekin = 1.41853538646776 | erot = 2.63533318879173 | epot = -13.1872177022564 | etot = -9.1333491269969 +654000 ekin = 1.39414099594694 | erot = 2.62311445987691 | epot = -13.1506045831147 | etot = -9.13334912729084 +655000 ekin = 1.36342278664523 | erot = 2.58232798191781 | epot = -13.0790998958933 | etot = -9.13334912733024 +656000 ekin = 1.32754554559948 | erot = 2.51343997306954 | epot = -12.9743346448116 | etot = -9.13334912614261 +657000 ekin = 1.07738759791682 | erot = 2.44669612964251 | epot = -12.6574327807916 | etot = -9.13334905323232 +658000 ekin = 1.00652014230921 | erot = 2.49084781648346 | epot = -12.6307170433487 | etot = -9.13334908455601 +659000 ekin = 1.07240085018084 | erot = 2.42929901832081 | epot = -12.6350489837861 | etot = -9.1333491152845 +660000 ekin = 1.09381648981083 | erot = 2.30102308262149 | epot = -12.5281886879259 | etot = -9.13334911549354 +661000 ekin = 1.11701334338237 | erot = 2.16959631554663 | epot = -12.4199587738214 | etot = -9.13334911489242 +662000 ekin = 1.14263894058173 | erot = 2.04231481246177 | epot = -12.3183028674908 | etot = -9.13334911444725 +663000 ekin = 1.17093665277224 | erot = 1.92510458370076 | epot = -12.2293903506475 | etot = -9.13334911417454 +664000 ekin = 1.20146324496915 | erot = 1.8220700951119 | epot = -12.1568824541682 | etot = -9.13334911408712 +665000 ekin = 1.23289032448006 | erot = 1.73564836427905 | epot = -12.1018878027985 | etot = -9.13334911403939 +666000 ekin = 1.2634046445521 | erot = 1.66702592668336 | epot = -12.0637796854973 | etot = -9.13334911426185 +667000 ekin = 1.29102574814559 | erot = 1.61488086820582 | epot = -12.0392557309127 | etot = -9.13334911456134 +668000 ekin = 1.31376054134881 | erot = 1.57649712773753 | epot = -12.0236067839909 | etot = -9.13334911490453 +669000 ekin = 1.3298940456542 | erot = 1.54828621181595 | epot = -12.011529372697 | etot = -9.13334911522682 +670000 ekin = 1.33826340890721 | erot = 1.5264084479743 | epot = -11.9980209723649 | etot = -9.13334911548336 +671000 ekin = 1.33847461323328 | erot = 1.50724764864746 | epot = -11.9790713775201 | etot = -9.13334911563934 +672000 ekin = 1.33101969554674 | erot = 1.4878130613914 | epot = -11.952181872615 | etot = -9.13334911567686 +673000 ekin = 1.31737035051182 | erot = 1.46610228052969 | epot = -11.9168217466015 | etot = -9.13334911555997 +674000 ekin = 1.299925217982 | erot = 1.44131241760688 | epot = -11.8745867509632 | etot = -9.13334911537436 +675000 ekin = 1.28129254582506 | erot = 1.41347048294476 | epot = -11.828112143904 | etot = -9.13334911513414 +676000 ekin = 1.26413925333698 | erot = 1.38336835396547 | epot = -11.7808567221864 | etot = -9.13334911488393 +677000 ekin = 1.25080949629915 | erot = 1.35227525692454 | epot = -11.7364338679129 | etot = -9.1333491146892 +678000 ekin = 1.2424032588376 | erot = 1.32122246363687 | epot = -11.6969748370303 | etot = -9.13334911455584 +679000 ekin = 1.23935164124574 | erot = 1.29124446461166 | epot = -11.6639452203543 | etot = -9.13334911449693 +680000 ekin = 1.24151057851449 | erot = 1.26358348831428 | epot = -11.6384431811727 | etot = -9.13334911434394 +681000 ekin = 1.24810791985032 | erot = 1.23998966300598 | epot = -11.62144669732 | etot = -9.13334911446373 +682000 ekin = 1.25738088472151 | erot = 1.22073219170914 | epot = -11.6114621910585 | etot = -9.13334911462782 +683000 ekin = 1.26715254863656 | erot = 1.20554909695297 | epot = -11.6060507603977 | etot = -9.13334911480812 +684000 ekin = 1.2752193688386 | erot = 1.19392995257013 | epot = -11.6024984363854 | etot = -9.13334911497663 +685000 ekin = 1.27965818657545 | erot = 1.18525667281522 | epot = -11.5982639744926 | etot = -9.13334911510194 +686000 ekin = 1.27906445706152 | erot = 1.17887846191265 | epot = -11.5912920341632 | etot = -9.13334911518902 +687000 ekin = 1.2726826175359 | erot = 1.17407129022586 | epot = -11.58010302302 | etot = -9.13334911525825 +688000 ekin = 1.26041914406282 | erot = 1.1700760478386 | epot = -11.5638443071276 | etot = -9.1333491152262 +689000 ekin = 1.24287938495211 | erot = 1.16656725574678 | epot = -11.5427957558543 | etot = -9.13334911515544 +690000 ekin = 1.22118240404644 | erot = 1.16336387131462 | epot = -11.5178953904187 | etot = -9.13334911505765 +691000 ekin = 1.19679867225082 | erot = 1.16037339233329 | epot = -11.4905211795285 | etot = -9.13334911494444 +692000 ekin = 1.17139142555397 | erot = 1.15758648593257 | epot = -11.4623270263125 | etot = -9.13334911482593 +693000 ekin = 1.14685376597261 | erot = 1.1551923286753 | epot = -11.4353952091868 | etot = -9.13334911453894 +694000 ekin = 1.12537035278758 | erot = 1.15368599836399 | epot = -11.4124054656026 | etot = -9.13334911445106 +695000 ekin = 1.10824764597567 | erot = 1.15324052660636 | epot = -11.3948372869626 | etot = -9.13334911438055 +696000 ekin = 1.09641524899228 | erot = 1.15407441364761 | epot = -11.3838387769728 | etot = -9.13334911433286 +697000 ekin = 1.0904070695986 | erot = 1.15645735234538 | epot = -11.3802135362596 | etot = -9.13334911431564 +698000 ekin = 1.09030542376286 | erot = 1.16063392710768 | epot = -11.3842884651973 | etot = -9.13334911432678 +699000 ekin = 1.09552536141978 | erot = 1.16669639941913 | epot = -11.3955708751994 | etot = -9.13334911436046 +700000 ekin = 1.1052737980317 | erot = 1.17478862115996 | epot = -11.4134115336258 | etot = -9.13334911443418 +701000 ekin = 1.11851271408066 | erot = 1.18492470948297 | epot = -11.4367865380862 | etot = -9.13334911452258 +702000 ekin = 1.13395549372637 | erot = 1.19694667251813 | epot = -11.4642512808728 | etot = -9.13334911462828 +703000 ekin = 1.15018285433147 | erot = 1.21057055971496 | epot = -11.4941025287891 | etot = -9.13334911474272 +704000 ekin = 1.16576673457706 | erot = 1.22535908060261 | epot = -11.5244749300354 | etot = -9.13334911485575 +705000 ekin = 1.17938915503319 | erot = 1.24076765314193 | epot = -11.5535059231314 | etot = -9.13334911495629 +706000 ekin = 1.18994261306167 | erot = 1.25622348494748 | epot = -11.579515213043 | etot = -9.13334911503388 +707000 ekin = 1.19660107195369 | erot = 1.27122780267454 | epot = -11.601177989708 | etot = -9.13334911507973 +708000 ekin = 1.19885615186576 | erot = 1.28546332267785 | epot = -11.617668589632 | etot = -9.13334911508841 +709000 ekin = 1.1965198150939 | erot = 1.29888532038554 | epot = -11.628754250538 | etot = -9.13334911505853 +710000 ekin = 1.18969957497071 | erot = 1.31177606554453 | epot = -11.6348247555083 | etot = -9.13334911499308 +711000 ekin = 1.17875387602807 | erot = 1.32474791483134 | epot = -11.6368509057591 | etot = -9.13334911489969 +712000 ekin = 1.16423391783875 | erot = 1.33868945229183 | epot = -11.6362724849197 | etot = -9.13334911478913 +713000 ekin = 1.14681758773094 | erot = 1.35466305350686 | epot = -11.6348297559143 | etot = -9.1333491146765 +714000 ekin = 1.12724173590673 | erot = 1.37373509013708 | epot = -11.6343259406199 | etot = -9.13334911457606 +715000 ekin = 1.10624050749987 | erot = 1.39681075797293 | epot = -11.6364003799747 | etot = -9.13334911450186 +716000 ekin = 1.08449847088997 | erot = 1.42446438143983 | epot = -11.6423119667947 | etot = -9.13334911446493 +717000 ekin = 1.062625867303 | erot = 1.45678801962439 | epot = -11.6527630013996 | etot = -9.13334911447222 +718000 ekin = 1.04116056517795 | erot = 1.49328580498299 | epot = -11.667795484685 | etot = -9.13334911452401 +719000 ekin = 1.02059756446694 | erot = 1.53283565405871 | epot = -11.6867823331394 | etot = -9.13334911461372 +720000 ekin = 1.0014427609137 | erot = 1.57373478107053 | epot = -11.7085266567121 | etot = -9.13334911472792 +721000 ekin = 0.984282698239887 | erot = 1.61383653730308 | epot = -11.7314683503902 | etot = -9.13334911484722 +722000 ekin = 0.969856334574209 | erot = 1.65076935457979 | epot = -11.7539748041074 | etot = -9.13334911495343 +723000 ekin = 0.95910907409578 | erot = 1.68219090540018 | epot = -11.7746490945164 | etot = -9.1333491150204 +724000 ekin = 0.953206498551931 | erot = 1.70610525279512 | epot = -11.7926608663832 | etot = -9.13334911503619 +725000 ekin = 0.953487871458107 | erot = 1.72112406444521 | epot = -11.8079610509 | etot = -9.13334911499673 +726000 ekin = 0.961348420448078 | erot = 1.7266421875565 | epot = -11.8213397229149 | etot = -9.13334911491036 +727000 ekin = 0.978055186998605 | erot = 1.72290320032085 | epot = -11.8343075021142 | etot = -9.13334911479471 +728000 ekin = 1.00452582497582 | erot = 1.71095374106527 | epot = -11.8488286807127 | etot = -9.13334911467165 +729000 ekin = 1.04110137579789 | erot = 1.69252215340265 | epot = -11.8669726437678 | etot = -9.13334911456729 +730000 ekin = 1.08735958690186 | erot = 1.66981008957452 | epot = -11.8905187909812 | etot = -9.13334911450487 +731000 ekin = 1.14200418374912 | erot = 1.64524141705526 | epot = -11.9205947153065 | etot = -9.13334911450213 +732000 ekin = 1.20285318014081 | erot = 1.62119095712685 | epot = -11.9573932518376 | etot = -9.13334911456996 +733000 ekin = 1.26692596391318 | erot = 1.59976528909515 | epot = -12.0000403677099 | etot = -9.13334911470158 +734000 ekin = 1.33064406417848 | erot = 1.5825428988019 | epot = -12.0465360778876 | etot = -9.13334911490722 +735000 ekin = 1.39013484388352 | erot = 1.57032898632949 | epot = -12.0938129453713 | etot = -9.13334911515826 +736000 ekin = 1.44157509139475 | erot = 1.56317476788337 | epot = -12.1380989747049 | etot = -9.13334911542673 +737000 ekin = 1.48157845589651 | erot = 1.56044545881246 | epot = -12.1753730303849 | etot = -9.13334911567597 +738000 ekin = 1.50757504378036 | erot = 1.56100911666817 | epot = -12.2019332763157 | etot = -9.13334911586718 +739000 ekin = 1.51813561812383 | erot = 1.56352092529265 | epot = -12.2150056593813 | etot = -9.13334911596481 +740000 ekin = 1.51318914849343 | erot = 1.56675183784834 | epot = -12.2132901022861 | etot = -9.13334911594438 +741000 ekin = 1.49408865830186 | erot = 1.56989906103806 | epot = -12.1973368351381 | etot = -9.13334911579818 +742000 ekin = 1.46350061535747 | erot = 1.5728002570046 | epot = -12.1696499879022 | etot = -9.13334911554011 +743000 ekin = 1.42512524134019 | erot = 1.57593310600514 | epot = -12.1344074625113 | etot = -9.133349115166 +744000 ekin = 1.3833848758548 | erot = 1.58054361278093 | epot = -12.0972776034317 | etot = -9.13334911479593 +745000 ekin = 1.34281951274205 | erot = 1.5882358284043 | epot = -12.0644044556002 | etot = -9.13334911445384 +746000 ekin = 1.30747334765641 | erot = 1.60047096980676 | epot = -12.0412934316593 | etot = -9.13334911419612 +747000 ekin = 1.28046646005764 | erot = 1.61821768665688 | epot = -12.0320332608056 | etot = -9.13334911409104 +748000 ekin = 1.26367955924 | erot = 1.64132893143407 | epot = -12.0383576048422 | etot = -9.13334911416815 +749000 ekin = 1.2574293442043 | erot = 1.66831440024512 | epot = -12.0590928588854 | etot = -9.13334911443597 +750000 ekin = 1.26047795508285 | erot = 1.6962844861488 | epot = -12.0901115560805 | etot = -9.13334911484889 +751000 ekin = 1.27026186447622 | erot = 1.72133386886176 | epot = -12.1249448486758 | etot = -9.13334911533786 +752000 ekin = 1.28339547086858 | erot = 1.73919075506032 | epot = -12.1559353417357 | etot = -9.13334911580678 +753000 ekin = 1.2963595746712 | erot = 1.74596876192164 | epot = -12.1756774528099 | etot = -9.13334911621709 +754000 ekin = 1.3059915874138 | erot = 1.73885024063525 | epot = -12.1781909444351 | etot = -9.13334911638605 +755000 ekin = 1.31024888116544 | erot = 1.7168351146831 | epot = -12.1604331121877 | etot = -9.13334911633919 +756000 ekin = 1.30846938321887 | erot = 1.68097972249687 | epot = -12.1227982218053 | etot = -9.13334911608958 +757000 ekin = 1.30124985041718 | erot = 1.63419006476544 | epot = -12.0687890308696 | etot = -9.13334911568699 +758000 ekin = 1.29019641090838 | erot = 1.58073563388972 | epot = -12.0042811600002 | etot = -9.13334911520213 +759000 ekin = 1.27761222227934 | erot = 1.52554636406397 | epot = -11.9365077010399 | etot = -9.13334911469657 +760000 ekin = 1.26609069507073 | erot = 1.4734869303843 | epot = -11.8729267397118 | etot = -9.13334911425681 +761000 ekin = 1.25808964011953 | erot = 1.42869550462328 | epot = -11.8201342586644 | etot = -9.13334911392157 +762000 ekin = 1.25572222200879 | erot = 1.39407442311085 | epot = -11.7831457588663 | etot = -9.13334911374665 +763000 ekin = 1.26054534570068 | erot = 1.37090045943868 | epot = -11.764794918833 | etot = -9.1333491136936 +764000 ekin = 1.27353435440278 | erot = 1.35887199085961 | epot = -11.765755459052 | etot = -9.13334911378957 +765000 ekin = 1.2949668260023 | erot = 1.35616457697726 | epot = -11.7844805169704 | etot = -9.13334911399081 +766000 ekin = 1.32454629042533 | erot = 1.35977679502324 | epot = -11.8176721997097 | etot = -9.13334911426109 +767000 ekin = 1.36163954272201 | erot = 1.3661863222321 | epot = -11.861174979507 | etot = -9.13334911455294 +768000 ekin = 1.40531019892957 | erot = 1.37181010082622 | epot = -11.9104694145828 | etot = -9.13334911482705 +769000 ekin = 1.45446512869437 | erot = 1.37353498050302 | epot = -11.961349224236 | etot = -9.13334911503857 +770000 ekin = 1.50793050152716 | erot = 1.36921125648765 | epot = -12.0104908732492 | etot = -9.13334911523436 +771000 ekin = 1.5638961669376 | erot = 1.35775090659989 | epot = -12.0549961887936 | etot = -9.1333491152561 +772000 ekin = 1.62113703504958 | erot = 1.33970323503865 | epot = -12.094189385275 | etot = -9.13334911518681 +773000 ekin = 1.67872851569995 | erot = 1.317029829878 | epot = -12.1291074606382 | etot = -9.13334911506024 +774000 ekin = 1.73569257109284 | erot = 1.29264163249231 | epot = -12.1616833185055 | etot = -9.13334911492038 +775000 ekin = 1.79085656134002 | erot = 1.26988000050848 | epot = -12.194085676658 | etot = -9.1333491148095 +776000 ekin = 1.84276100468616 | erot = 1.25197534036964 | epot = -12.2280854598125 | etot = -9.1333491147567 +777000 ekin = 1.88967118604117 | erot = 1.24159765890511 | epot = -12.2646179597164 | etot = -9.13334911477014 +778000 ekin = 1.92971622261019 | erot = 1.24057583213674 | epot = -12.3036411695857 | etot = -9.13334911483877 +779000 ekin = 1.96113164255194 | erot = 1.24980912492691 | epot = -12.3442898824175 | etot = -9.13334911493862 +780000 ekin = 1.98254203386542 | erot = 1.26932045666364 | epot = -12.3852116055708 | etot = -9.13334911504177 +781000 ekin = 1.99321406405968 | erot = 1.29840823518112 | epot = -12.4249714143686 | etot = -9.13334911512778 +782000 ekin = 1.99321095941016 | erot = 1.33580885491735 | epot = -12.4623689295136 | etot = -9.13334911518613 +783000 ekin = 1.98342491293678 | erot = 1.37983642298119 | epot = -12.4966104511338 | etot = -9.13334911521582 +784000 ekin = 1.96551238430177 | erot = 1.42849371621078 | epot = -12.5273552156807 | etot = -9.13334911516811 +785000 ekin = 1.94195910112175 | erot = 1.47961348821713 | epot = -12.5549217044983 | etot = -9.13334911515939 +786000 ekin = 1.91549982326227 | erot = 1.53087711626691 | epot = -12.5797260546635 | etot = -9.13334911513429 +787000 ekin = 1.88902915933248 | erot = 1.57997565975775 | epot = -12.6023539341816 | etot = -9.13334911509139 +788000 ekin = 1.8655374655416 | erot = 1.62478646025336 | epot = -12.6236730408307 | etot = -9.13334911503573 +789000 ekin = 1.84793067284303 | erot = 1.66350572426683 | epot = -12.6447855120723 | etot = -9.13334911496242 +790000 ekin = 1.83884831412254 | erot = 1.69477325871971 | epot = -12.6669706877348 | etot = -9.13334911489259 +791000 ekin = 1.84038435201585 | erot = 1.71768127848849 | epot = -12.6914147453579 | etot = -9.13334911485354 +792000 ekin = 1.85374621231349 | erot = 1.73169683790756 | epot = -12.7187921650971 | etot = -9.13334911487601 +793000 ekin = 1.8789217872984 | erot = 1.73653576924597 | epot = -12.7488066715285 | etot = -9.13334911498412 +794000 ekin = 1.91440510045612 | erot = 1.73204169928402 | epot = -12.7797959149171 | etot = -9.13334911517698 +795000 ekin = 1.95726697872637 | erot = 1.71818976217901 | epot = -12.8088058563243 | etot = -9.13334911541889 +796000 ekin = 2.00360851779882 | erot = 1.69525335459694 | epot = -12.8322109880418 | etot = -9.13334911564608 +797000 ekin = 2.04914358120617 | erot = 1.66405946742404 | epot = -12.8465521644182 | etot = -9.13334911578802 +798000 ekin = 2.08995546227648 | erot = 1.62623745953124 | epot = -12.8495420376086 | etot = -9.1333491158009 +799000 ekin = 2.12309292251377 | erot = 1.58427028116865 | epot = -12.8407123193673 | etot = -9.13334911568487 +800000 ekin = 2.14682990847639 | erot = 1.5412613855995 | epot = -12.821440409556 | etot = -9.13334911548006 +801000 ekin = 2.16058282772835 | erot = 1.50048202047673 | epot = -12.7944139634492 | etot = -9.13334911524412 +802000 ekin = 2.16461511109456 | erot = 1.46486615503426 | epot = -12.7628303811574 | etot = -9.13334911502858 +803000 ekin = 2.15969104316506 | erot = 1.43661335442589 | epot = -12.7296535124577 | etot = -9.13334911486671 +804000 ekin = 2.14679128687906 | erot = 1.41698988508608 | epot = -12.6971302867224 | etot = -9.1333491147573 +805000 ekin = 2.12692065943943 | erot = 1.40638520515076 | epot = -12.6666549793126 | etot = -9.13334911472241 +806000 ekin = 2.10099028263459 | erot = 1.40422932575195 | epot = -12.6385687231454 | etot = -9.13334911475883 +807000 ekin = 2.06982763841779 | erot = 1.40909451158688 | epot = -12.6122712648409 | etot = -9.13334911483622 +808000 ekin = 2.0341909229772 | erot = 1.41919422166664 | epot = -12.5867342595708 | etot = -9.13334911492697 +809000 ekin = 1.99478586655906 | erot = 1.4323885834077 | epot = -12.5605235650179 | etot = -9.13334911505111 +810000 ekin = 1.95230744546565 | erot = 1.44625258192577 | epot = -12.5319091425649 | etot = -9.13334911517351 +811000 ekin = 1.90747094188675 | erot = 1.45847148723069 | epot = -12.4992915443987 | etot = -9.13334911528121 +812000 ekin = 1.86102893102544 | erot = 1.4670396354808 | epot = -12.4614176818678 | etot = -9.13334911536157 +813000 ekin = 1.81416432243492 | erot = 1.47049868907024 | epot = -12.4180121266397 | etot = -9.13334911513457 +814000 ekin = 1.76902926167641 | erot = 1.46826739310675 | epot = -12.3706457700669 | etot = -9.13334911528372 +815000 ekin = 1.71533069952284 | erot = 1.45797598423766 | epot = -12.3066557947832 | etot = -9.13334911102266 +816000 ekin = 1.68468183703544 | erot = 1.43935942018881 | epot = -12.2573903676303 | etot = -9.13334911040601 +817000 ekin = 1.67569540452249 | erot = 1.42022759192753 | epot = -12.229272104597 | etot = -9.13334910814694 +818000 ekin = 1.65431804079221 | erot = 1.40071144599893 | epot = -12.1883785945503 | etot = -9.1333491077592 +819000 ekin = 1.63740188372281 | erot = 1.38256931716781 | epot = -12.1533203082747 | etot = -9.1333491073841 +820000 ekin = 1.62512170451317 | erot = 1.36928168853097 | epot = -12.1277525000666 | etot = -9.13334910702245 +821000 ekin = 1.61915909098214 | erot = 1.36404110716217 | epot = -12.1165493048504 | etot = -9.13334910670606 +822000 ekin = 1.62172343976694 | erot = 1.36925913748166 | epot = -12.1243316837646 | etot = -9.13334910651599 +823000 ekin = 1.63427494813012 | erot = 1.38616632191204 | epot = -12.1537903765495 | etot = -9.13334910650734 +824000 ekin = 1.65698382618083 | erot = 1.41459711185718 | epot = -12.2049300447293 | etot = -9.1333491066913 +825000 ekin = 1.68854753273397 | erot = 1.45301631842097 | epot = -12.2749129581916 | etot = -9.13334910703664 +826000 ekin = 1.72638863495593 | erot = 1.49875661579892 | epot = -12.3584943582411 | etot = -9.1333491074863 +827000 ekin = 1.76710423380173 | erot = 1.54839439234532 | epot = -12.4488477341213 | etot = -9.13334910797425 +828000 ekin = 1.80698482333454 | erot = 1.5981818490163 | epot = -12.5385157807934 | etot = -9.13334910844251 +829000 ekin = 1.84246939969648 | erot = 1.64447465718334 | epot = -12.6202931657233 | etot = -9.13334910884345 +830000 ekin = 1.87048980343148 | erot = 1.68412933439335 | epot = -12.6879682469634 | etot = -9.13334910913854 +831000 ekin = 1.88871335827799 | erot = 1.71486645418346 | epot = -12.7369289217595 | etot = -9.13334910929808 +832000 ekin = 1.89569916791839 | erot = 1.73558694752135 | epot = -12.7646352247427 | etot = -9.13334910930292 +833000 ekin = 1.89096344935692 | erot = 1.74659447552094 | epot = -12.7709070340301 | etot = -9.13334910915223 +834000 ekin = 1.87493429544964 | erot = 1.74964392180512 | epot = -12.7579273261423 | etot = -9.13334910888755 +835000 ekin = 1.84878280514247 | erot = 1.74762027308025 | epot = -12.7297521867453 | etot = -9.13334910852257 +836000 ekin = 1.8141447690964 | erot = 1.74421722088535 | epot = -12.6917110981203 | etot = -9.13334910813853 +837000 ekin = 1.77277875467461 | erot = 1.74335285139141 | epot = -12.6494807138681 | etot = -9.13334910780208 +838000 ekin = 1.7262444553165 | erot = 1.74841404792074 | epot = -12.608007610802 | etot = -9.13334910756481 +839000 ekin = 1.67568816111102 | erot = 1.76165550553764 | epot = -12.5706927741021 | etot = -9.1333491074534 +840000 ekin = 1.62179135099795 | erot = 1.78387657045046 | epot = -12.5390170289028 | etot = -9.13334910745439 +841000 ekin = 1.56488441151669 | erot = 1.81456573941819 | epot = -12.5127992584711 | etot = -9.13334910753619 +842000 ekin = 1.50517399563451 | erot = 1.85205645863854 | epot = -12.4905795619685 | etot = -9.13334910769547 +843000 ekin = 1.44300548284445 | erot = 1.89358112521172 | epot = -12.4699357158607 | etot = -9.13334910780454 +844000 ekin = 1.3790662063139 | erot = 1.93639685185152 | epot = -12.4488121660344 | etot = -9.13334910786901 +845000 ekin = 1.31446352833686 | erot = 1.97812996435259 | epot = -12.4259426005586 | etot = -9.13334910786912 +846000 ekin = 1.25068692329763 | erot = 2.01700234952521 | epot = -12.4010383806239 | etot = -9.13334910780111 +847000 ekin = 1.18947724708284 | erot = 2.0520432049065 | epot = -12.3748695596627 | etot = -9.13334910767339 +848000 ekin = 1.13265732505036 | erot = 2.08314733277112 | epot = -12.3491537653239 | etot = -9.13334910750245 +849000 ekin = 1.08197657770294 | erot = 2.11099249693677 | epot = -12.3263181819474 | etot = -9.13334910730764 +850000 ekin = 1.03899924538329 | erot = 2.13684654283616 | epot = -12.3091948953303 | etot = -9.13334910711086 +851000 ekin = 1.0050379248998 | erot = 2.16230618698294 | epot = -12.3006932188152 | etot = -9.13334910693251 +852000 ekin = 0.981116857874806 | erot = 2.18901371772547 | epot = -12.303479682391 | etot = -9.13334910679072 +853000 ekin = 0.967947652226109 | erot = 2.21839549971482 | epot = -12.3196922586421 | etot = -9.13334910670121 +854000 ekin = 0.965908910691589 | erot = 2.25145766399906 | epot = -12.3507156813621 | etot = -9.13334910667145 +855000 ekin = 0.975031148295586 | erot = 2.28866143867258 | epot = -12.397041693672 | etot = -9.13334910670388 +856000 ekin = 0.994993726121242 | erot = 2.32988587265462 | epot = -12.4582287055702 | etot = -9.13334910679431 +857000 ekin = 1.02514000046305 | erot = 2.37447147763437 | epot = -12.5329605850307 | etot = -9.13334910693331 +858000 ekin = 1.06451194043388 | erot = 2.42132581263115 | epot = -12.619186860173 | etot = -9.133349107108 +859000 ekin = 1.11189872921357 | erot = 2.46906217646335 | epot = -12.7143100129825 | etot = -9.13334910730561 +860000 ekin = 1.16588800432878 | erot = 2.51613734356884 | epot = -12.8153744554145 | etot = -9.13334910751683 +861000 ekin = 1.22490604809807 | erot = 2.56095681693069 | epot = -12.9192119727658 | etot = -9.13334910773705 +862000 ekin = 1.28723632580509 | erot = 2.60192847236006 | epot = -13.0225139061332 | etot = -9.13334910796808 +863000 ekin = 1.35101431938026 | erot = 2.63746581474994 | epot = -13.1218292423441 | etot = -9.13334910821392 +864000 ekin = 1.41420820518342 | erot = 2.66596355874572 | epot = -13.213520872407 | etot = -9.13334910847785 +865000 ekin = 1.47460562928395 | erot = 2.68578195464753 | epot = -13.2937366926894 | etot = -9.13334910875787 +866000 ekin = 1.52983303720344 | erot = 2.69527584728353 | epot = -13.3584579935301 | etot = -9.1333491090431 +867000 ekin = 1.57743376516387 | erot = 2.69288933097783 | epot = -13.4036722054545 | etot = -9.13334910931283 +868000 ekin = 1.61502389036922 | erot = 2.6773120050259 | epot = -13.4256850049327 | etot = -9.13334910953756 +869000 ekin = 1.64053051307865 | erot = 2.64766625530002 | epot = -13.4215458780626 | etot = -9.13334910968391 +870000 ekin = 1.65249590024801 | erot = 2.60367561918667 | epot = -13.3895206291558 | etot = -9.13334910972108 +871000 ekin = 1.65040511753722 | erot = 2.54576053416916 | epot = -13.3295147613346 | etot = -9.13334910962825 +872000 ekin = 1.63497077370924 | erot = 2.47502461265863 | epot = -13.2433444957684 | etot = -9.13334910940055 +873000 ekin = 1.60829551086502 | erot = 2.39312864673435 | epot = -13.1347732666517 | etot = -9.13334910905235 +874000 ekin = 1.57383856498032 | erot = 2.30208675138478 | epot = -13.0092744249818 | etot = -9.13334910861673 +875000 ekin = 1.53613967512839 | erot = 2.20404109166936 | epot = -12.8735298749402 | etot = -9.13334910814241 +876000 ekin = 1.50030007471879 | erot = 2.10106901470409 | epot = -12.7347181971093 | etot = -9.13334910768647 +877000 ekin = 1.47128183650484 | erot = 1.99505592488608 | epot = -12.5996868686966 | etot = -9.13334910730565 +878000 ekin = 1.45315269235295 | erot = 1.88764504255069 | epot = -12.4741468419469 | etot = -9.13334910704327 +879000 ekin = 1.44845009592847 | erot = 1.78026193725866 | epot = -12.3620611401045 | etot = -9.13334910691736 +880000 ekin = 1.4578339719446 | erot = 1.67420503622729 | epot = -12.2653881150876 | etot = -9.13334910691574 +881000 ekin = 1.48012455416729 | erot = 1.57078382964907 | epot = -12.1842574908159 | etot = -9.13334910699952 +882000 ekin = 1.51270015736965 | erot = 1.47147015192771 | epot = -12.1175194164139 | etot = -9.13334910711658 +883000 ekin = 1.55211568291642 | erot = 1.37801244883258 | epot = -12.0634772389683 | etot = -9.13334910721927 +884000 ekin = 1.59475301549556 | erot = 1.29246300163102 | epot = -12.0205651244041 | etot = -9.13334910727755 +885000 ekin = 1.63734681492121 | erot = 1.21709221485257 | epot = -11.9877881370563 | etot = -9.1333491072825 +886000 ekin = 1.67731211300055 | erot = 1.15420415260516 | epot = -11.9648653728478 | etot = -9.1333491072421 +887000 ekin = 1.71288068345475 | erot = 1.10590165063859 | epot = -11.9521314412662 | etot = -9.13334910717285 +888000 ekin = 1.74309500656892 | erot = 1.07385834531108 | epot = -11.9503024589743 | etot = -9.13334910709431 +889000 ekin = 1.76770969091248 | erot = 1.05913784424507 | epot = -11.9601966421833 | etot = -9.13334910702578 +890000 ekin = 1.78703240996246 | erot = 1.06207375035338 | epot = -11.9824552673014 | etot = -9.13334910698558 +891000 ekin = 1.8017232922488 | erot = 1.082207474664 | epot = -12.0172798739034 | etot = -9.13334910699064 +892000 ekin = 1.81257293682823 | erot = 1.11828058018261 | epot = -12.0642026240647 | etot = -9.13334910705388 +893000 ekin = 1.82028982711721 | erot = 1.16828769624953 | epot = -12.1219266305456 | etot = -9.13334910717881 +894000 ekin = 1.8253364972857 | erot = 1.2296028017134 | epot = -12.188288406358 | etot = -9.13334910735892 +895000 ekin = 1.82785071659948 | erot = 1.29918775470761 | epot = -12.2603875788813 | etot = -9.13334910757419 +896000 ekin = 1.82766966748405 | erot = 1.37387583335774 | epot = -12.3348946086366 | etot = -9.13334910779482 +897000 ekin = 1.82444603808765 | erot = 1.45069893543395 | epot = -12.4084940815094 | etot = -9.13334910798781 +898000 ekin = 1.81781661006481 | erot = 1.52720356355353 | epot = -12.4783692817434 | etot = -9.13334910812505 +899000 ekin = 1.80756915110211 | erot = 1.60168843027344 | epot = -12.5426066895664 | etot = -9.13334910819084 +900000 ekin = 1.79375843956525 | erot = 1.67330364929765 | epot = -12.6004111970495 | etot = -9.13334910818656 +901000 ekin = 1.7767431847654 | erot = 1.74197941463959 | epot = -12.6520717075347 | etot = -9.13334910812975 +902000 ekin = 1.75714245729137 | erot = 1.8081939440662 | epot = -12.6986855094068 | etot = -9.13334910804925 +903000 ekin = 1.73573344441754 | erot = 1.8726332598978 | epot = -12.7417158122925 | etot = -9.1333491079772 +904000 ekin = 1.71332625908703 | erot = 1.93582474191466 | epot = -12.7825001089422 | etot = -9.13334910794046 +905000 ekin = 1.69065428570444 | erot = 1.99783248438824 | epot = -12.8218358780465 | etot = -9.13334910795378 +906000 ekin = 1.66831072856122 | erot = 2.05808381416944 | epot = -12.8597436507486 | etot = -9.13334910801792 +907000 ekin = 1.6467458830389 | erot = 2.11535919821009 | epot = -12.895454189367 | etot = -9.13334910811806 +908000 ekin = 1.62631907114034 | erot = 2.16793324009784 | epot = -12.9276014194707 | etot = -9.13334910823256 +909000 ekin = 1.60738004100465 | erot = 2.21381581980632 | epot = -12.9545449691496 | etot = -9.13334910833859 +910000 ekin = 1.59034402491562 | erot = 2.25102295598621 | epot = -12.9747160893212 | etot = -9.13334910841939 +911000 ekin = 1.57572782711176 | erot = 2.27781488080808 | epot = -12.9868918163859 | etot = -9.13334910846606 +912000 ekin = 1.5641305468354 | erot = 2.29287003002579 | epot = -12.9903496853383 | etot = -9.13334910847715 +913000 ekin = 1.55616398737872 | erot = 2.29539983332877 | epot = -12.9849129291629 | etot = -9.13334910845537 +914000 ekin = 1.55235379274487 | erot = 2.28522760385718 | epot = -12.970930505006 | etot = -9.13334910840395 +915000 ekin = 1.55303636075987 | erot = 2.26284508695978 | epot = -12.9492305560465 | etot = -9.13334910832683 +916000 ekin = 1.55827003373375 | erot = 2.22943339359798 | epot = -12.9210525355621 | etot = -9.13334910823033 +917000 ekin = 1.56776924055917 | erot = 2.18681551597995 | epot = -12.8879338646642 | etot = -9.1333491081251 +918000 ekin = 1.58086450735735 | erot = 2.13731406706161 | epot = -12.8515276824457 | etot = -9.13334910802674 +919000 ekin = 1.59649190921672 | erot = 2.08351907893787 | epot = -12.8133600961056 | etot = -9.13334910795102 +920000 ekin = 1.61321892883775 | erot = 2.02800735916717 | epot = -12.7745753959154 | etot = -9.13334910791047 +921000 ekin = 1.62931395437988 | erot = 1.97307497751068 | epot = -12.7357380398015 | etot = -9.1333491079109 +922000 ekin = 1.64286104747039 | erot = 1.92053870341486 | epot = -12.6967488588336 | etot = -9.13334910794835 +923000 ekin = 1.65191234391482 | erot = 1.87163759208753 | epot = -12.6568990440141 | etot = -9.13334910801172 +924000 ekin = 1.65466206201883 | erot = 1.82703710614034 | epot = -12.6150482762435 | etot = -9.13334910808429 +925000 ekin = 1.64962158356706 | erot = 1.78691680129212 | epot = -12.5698874930069 | etot = -9.1333491081477 +926000 ekin = 1.635774357065 | erot = 1.75111283231405 | epot = -12.5202362975638 | etot = -9.13334910818478 +927000 ekin = 1.61269412581515 | erot = 1.71928618608427 | epot = -12.4653294200806 | etot = -9.13334910818114 +928000 ekin = 1.58061327338877 | erot = 1.69109387513308 | epot = -12.4050562566491 | etot = -9.13334910812727 +929000 ekin = 1.5404346571899 | erot = 1.66634444993847 | epot = -12.3401282151469 | etot = -9.13334910801855 +930000 ekin = 1.49368612297294 | erot = 1.64511875929311 | epot = -12.2721539901236 | etot = -9.13334910785752 +931000 ekin = 1.44242020036011 | erot = 1.6278309239394 | epot = -12.2036002319549 | etot = -9.1333491076554 +932000 ekin = 1.38906420478236 | erot = 1.61520048767696 | epot = -12.1376137998927 | etot = -9.13334910743335 +933000 ekin = 1.33622958396548 | erot = 1.60811568409747 | epot = -12.0776943752837 | etot = -9.1333491072207 +934000 ekin = 1.28649486983519 | erot = 1.60739378972276 | epot = -12.0272377666104 | etot = -9.13334910705249 +935000 ekin = 1.24218246526119 | erot = 1.61347919082763 | epot = -11.989010763051 | etot = -9.13334910696217 +936000 ekin = 1.20515312898716 | erot = 1.62614770365281 | epot = -11.964649939615 | etot = -9.13334910697501 +937000 ekin = 1.17664231217722 | erot = 1.64429583353959 | epot = -11.9542872528193 | etot = -9.13334910710245 +938000 ekin = 1.15716006421962 | erot = 1.66588444174352 | epot = -11.9563936133005 | etot = -9.1333491073374 +939000 ekin = 1.14647171712607 | erot = 1.68810326830728 | epot = -11.9679240930781 | etot = -9.13334910764477 +940000 ekin = 1.14367004082956 | erot = 1.70771457432631 | epot = -11.9847337231501 | etot = -9.13334910799423 +941000 ekin = 1.14733884565177 | erot = 1.72149292698786 | epot = -12.0021808809595 | etot = -9.13334910831984 +942000 ekin = 1.15580134682391 | erot = 1.72687300438947 | epot = -12.0160234597736 | etot = -9.13334910856026 +943000 ekin = 1.16743729515297 | erot = 1.72249936624098 | epot = -12.0232857700571 | etot = -9.13334910866313 +944000 ekin = 1.18103106476359 | erot = 1.70858712462445 | epot = -12.0229672979874 | etot = -9.13334910859936 +945000 ekin = 1.19606804455417 | erot = 1.68696892705364 | epot = -12.0163860799888 | etot = -9.13334910838101 +946000 ekin = 1.21284058110907 | erot = 1.66075870247738 | epot = -12.0069483916567 | etot = -9.13334910807027 +947000 ekin = 1.23222210573444 | erot = 1.63367011138129 | epot = -11.9992413248847 | etot = -9.13334910776902 +948000 ekin = 1.25509690716044 | erot = 1.60916358070706 | epot = -11.9976095954519 | etot = -9.13334910758437 +949000 ekin = 1.28167104221087 | erot = 1.58969080392946 | epot = -12.0047109537182 | etot = -9.13334910757788 +950000 ekin = 1.31105510038267 | erot = 1.57628415673981 | epot = -12.0206883648584 | etot = -9.13334910773589 +951000 ekin = 1.34140314928627 | erot = 1.56859135849577 | epot = -12.0433436157629 | etot = -9.13334910798086 +952000 ekin = 1.37054117668759 | erot = 1.56526000759302 | epot = -12.0691502924999 | etot = -9.13334910821928 +953000 ekin = 1.39670348101467 | erot = 1.56444621742743 | epot = -12.0944988068321 | etot = -9.13334910839002 +954000 ekin = 1.418975292377 | erot = 1.56423287015498 | epot = -12.1165572710122 | etot = -9.1333491084802 +955000 ekin = 1.43729048070224 | erot = 1.56287479953881 | epot = -12.1335143887507 | etot = -9.13334910850965 +956000 ekin = 1.45211066332392 | erot = 1.5589293854881 | epot = -12.144389157316 | etot = -9.133349108504 +957000 ekin = 1.46402190623028 | erot = 1.55132217597402 | epot = -12.1486931906856 | etot = -9.13334910848131 +958000 ekin = 1.47342593725582 | erot = 1.53954965712998 | epot = -12.1463247028198 | etot = -9.13334910843402 +959000 ekin = 1.48038578495019 | erot = 1.52394133602467 | epot = -12.1376762293322 | etot = -9.1333491083573 +960000 ekin = 1.48460604034332 | erot = 1.50575363438079 | epot = -12.1237087829676 | etot = -9.13334910824351 +961000 ekin = 1.48549975936494 | erot = 1.48721075412964 | epot = -12.1060596215852 | etot = -9.13334910809064 +962000 ekin = 1.48229853496878 | erot = 1.4714120258364 | epot = -12.08705966871 | etot = -9.13334910790478 +963000 ekin = 1.47417603272701 | erot = 1.46210240867396 | epot = -12.0696275491009 | etot = -9.13334910769994 +964000 ekin = 1.4603664452564 | erot = 1.46332191688728 | epot = -12.0570374696385 | etot = -9.13334910749479 +965000 ekin = 1.44026662182629 | erot = 1.47896324785904 | epot = -12.0525789770013 | etot = -9.13334910731597 +966000 ekin = 1.41351583401261 | erot = 1.51227943251032 | epot = -12.059144373712 | etot = -9.13334910718905 +967000 ekin = 1.38005134112891 | erot = 1.56539665061738 | epot = -12.0787970988848 | etot = -9.1333491071385 +968000 ekin = 1.34025482725276 | erot = 1.63885686276279 | epot = -12.1124607971902 | etot = -9.13334910717463 +969000 ekin = 1.29476921982257 | erot = 1.73132793709573 | epot = -12.1594462642397 | etot = -9.13334910732141 +970000 ekin = 1.24442005393518 | erot = 1.83972520711345 | epot = -12.2174943685871 | etot = -9.13334910753846 +971000 ekin = 1.19046696427907 | erot = 1.95943091408197 | epot = -12.2832469861558 | etot = -9.13334910779477 +972000 ekin = 1.13463097114153 | erot = 2.08475088501359 | epot = -12.3527309642031 | etot = -9.13334910804801 +973000 ekin = 1.07911059568202 | erot = 2.20953944500849 | epot = -12.421999148947 | etot = -9.1333491082565 +974000 ekin = 1.0265736704174 | erot = 2.32774347839194 | epot = -12.4876662572323 | etot = -9.13334910842292 +975000 ekin = 0.979977932768695 | erot = 2.43392801403437 | epot = -12.5472550552884 | etot = -9.13334910848538 +976000 ekin = 0.942304887100263 | erot = 2.52399013955009 | epot = -12.5996441351223 | etot = -9.13334910847197 +977000 ekin = 0.916335295706531 | erot = 2.59517570123723 | epot = -12.644860105353 | etot = -9.1333491084092 +978000 ekin = 0.904316422892292 | erot = 2.6460169875762 | epot = -12.6836825187988 | etot = -9.13334910833034 +979000 ekin = 0.907654941509809 | erot = 2.67612704045827 | epot = -12.7171310902355 | etot = -9.13334910826745 +980000 ekin = 0.926700183437424 | erot = 2.68592744664294 | epot = -12.7459767383234 | etot = -9.13334910824302 +981000 ekin = 0.960659745241031 | erot = 2.67638285528021 | epot = -12.7703917087865 | etot = -9.13334910826521 +982000 ekin = 1.00766017971334 | erot = 2.64879736701747 | epot = -12.7898066550598 | etot = -9.13334910832899 +983000 ekin = 1.06493892794231 | erot = 2.60470505317151 | epot = -12.8029930895296 | etot = -9.13334910841577 +984000 ekin = 1.12913508942066 | erot = 2.54586103456691 | epot = -12.8083452324861 | etot = -9.13334910849851 +985000 ekin = 1.19663599745507 | erot = 2.47431116853344 | epot = -12.8042962745361 | etot = -9.13334910854757 +986000 ekin = 1.2639316426745 | erot = 2.39249159640019 | epot = -12.7897723476129 | etot = -9.13334910853825 +987000 ekin = 1.32792910235901 | erot = 2.30329384118958 | epot = -12.7645720520061 | etot = -9.13334910845755 +988000 ekin = 1.38618594051068 | erot = 2.21003704543074 | epot = -12.7295720942493 | etot = -9.13334910830784 +989000 ekin = 1.4370366316437 | erot = 2.11631776637777 | epot = -12.6867035061275 | etot = -9.13334910810604 +990000 ekin = 1.47960743025201 | erot = 2.02574976478159 | epot = -12.6387063029131 | etot = -9.13334910787949 +991000 ekin = 1.51373724651467 | erot = 1.94164272478737 | epot = -12.5887290789609 | etot = -9.13334910765885 +992000 ekin = 1.53983818591504 | erot = 1.86668512517839 | epot = -12.5398724185651 | etot = -9.13334910747168 +993000 ekin = 1.55873490672647 | erot = 1.80268982006813 | epot = -12.4947738341322 | etot = -9.13334910733764 +994000 ekin = 1.57151651513761 | erot = 1.75043914207588 | epot = -12.4553047644798 | etot = -9.13334910726628 +995000 ekin = 1.57942173434867 | erot = 1.70964079470597 | epot = -12.4224116363129 | etot = -9.13334910725828 +996000 ekin = 1.58376261671428 | erot = 1.67898574514433 | epot = -12.3960974691653 | etot = -9.13334910730674 +997000 ekin = 1.58587878574227 | erot = 1.65629050262104 | epot = -12.3755183957631 | etot = -9.13334910739977 +998000 ekin = 1.58710748470162 | erot = 1.63870906512813 | epot = -12.3591656573512 | etot = -9.13334910752142 +999000 ekin = 1.58875603198164 | erot = 1.62299637540287 | epot = -12.34510151504 | etot = -9.13334910765546 +1000000 ekin = 1.5920700121372 | erot = 1.6058173980956 | epot = -12.3312365180129 | etot = -9.13334910778006 + 1000000 0.11793111 -1.2674127 0.034288999 -1.0739167 -1.3883882e-05 64000 +Loop time of 10.7087 on 4 procs for 1000000 steps with 10 atoms + +Performance: 80681.753 tau/day, 93381.659 timesteps/s, 933.817 katom-step/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.4032 | 4.2397 | 6.1061 | 53.2 | 39.59 +Bond | 0.12793 | 0.18606 | 0.24447 | 11.1 | 1.74 +Neigh | 0.007285 | 0.007333 | 0.007366 | 0.0 | 0.07 +Comm | 2.4191 | 4.544 | 5.5427 | 58.9 | 42.43 +Output | 0.058426 | 0.065905 | 0.08554 | 4.4 | 0.62 +Modify | 0.39789 | 0.48281 | 0.59308 | 12.1 | 4.51 +Other | | 1.183 | | | 11.05 + +Nlocal: 2.5 ave 4 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 9 max 6 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25 ave 19 max 5 min +Histogram: 2 1 0 0 0 0 0 0 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:10 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/oxdna_lj.cgdna b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/oxdna_lj.cgdna new file mode 120000 index 0000000000..fe7ce5cd55 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/oxdna_lj.cgdna @@ -0,0 +1 @@ +../../../../../../../potentials/oxdna_lj.cgdna \ No newline at end of file diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/data.dsring similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/data.dsring diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/in.dsring similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/in.dsring diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/log.2Jul21.dsring.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/log.2Jul21.dsring.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/log.2Jul21.dsring.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/dsring/log.2Jul21.dsring.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/data.duplex1 new file mode 100644 index 0000000000..54eb2beaf5 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file via write_data, version 27 May 2021 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0 +2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0 +3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0 +4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0 +5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0 +6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0 +7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0 +8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0 +9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0 +10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397 +2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385 +3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783 +4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775 +5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883 +6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354 +7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567 +8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627 +9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048 +10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/in.duplex1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/in.duplex1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/log.2Jul21.duplex1.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/log.2Jul21.duplex1.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/log.2Jul21.duplex1.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.2Jul21.duplex1.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/log.2Jul21.duplex1.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/data.duplex2 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/data.duplex2 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/data.duplex2 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/in.duplex2 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/in.duplex2 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/log.2Jul21.duplex2.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/log.2Jul21.duplex2.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/log.2Jul21.duplex2.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.2Jul21.duplex2.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex2/log.2Jul21.duplex2.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/data.duplex3 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/data.duplex3 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/data.duplex3 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/data.duplex3 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/in.duplex3 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/in.duplex3 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/log.2Jul21.duplex3.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/log.2Jul21.duplex3.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/log.2Jul21.duplex3.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.2Jul21.duplex3.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex3/log.2Jul21.duplex3.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/data.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/data.duplex1 new file mode 100644 index 0000000000..54eb2beaf5 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file via write_data, version 27 May 2021 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0 +2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0 +3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0 +4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0 +5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0 +6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0 +7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0 +8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0 +9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0 +10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397 +2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385 +3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783 +4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775 +5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883 +6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354 +7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567 +8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627 +9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048 +10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/in.duplex1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/in.duplex1 new file mode 100644 index 0000000000..061fd9ebf9 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/in.duplex1 @@ -0,0 +1,72 @@ +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + +set atom * mass 3.1575 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * oxdna2_lj.cgdna +special_bonds lj 0 1 1 + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv oxdna2_lj.cgdna +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna +pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna +pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna +pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna +pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna +pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna +pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2_lj.cgdna + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/log.19May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/log.19May24.duplex1.g++.1 new file mode 100644 index 0000000000..7d4a187390 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/log.19May24.duplex1.g++.1 @@ -0,0 +1,1120 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.005 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna2.lj with DATE: 2024-04-21 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (stk) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (xstk) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (coaxstk) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (dh) file oxdna2.lj with DATE: 2024-04-21 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3014979 + ghost atom cutoff = 4.3014979 + binsize = 2.150749, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 1e-05 +WARNING: Communication cutoff adjusted to 4.301497916929199 (src/comm.cpp:739) +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -12.4543859162177 | etot = -8.53011309372317 +Per MPI rank memory allocation (min/avg/max) = 7.467 | 7.467 | 7.467 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3525648 0.10712616 -1.134585 -6.3346859e-05 64000 +1000 ekin = 1.07575988625876 | erot = 2.91276427031684 | epot = -12.5186372505575 | etot = -8.53011309398185 +2000 ekin = 1.05292961692331 | erot = 3.00631080619825 | epot = -12.5893535174382 | etot = -8.53011309431664 +3000 ekin = 1.0404793567822 | erot = 3.09099198685794 | epot = -12.6615844383056 | etot = -8.5301130946655 +4000 ekin = 1.03797149598187 | erot = 3.16182957406825 | epot = -12.7299141650203 | etot = -8.53011309497013 +5000 ekin = 1.04436175992637 | erot = 3.21484050133169 | epot = -12.7893153564536 | etot = -8.53011309519554 +6000 ekin = 1.058261961669 | erot = 3.24734130245542 | epot = -12.8357163594551 | etot = -8.53011309533065 +7000 ekin = 1.07813397987529 | erot = 3.25800057687377 | epot = -12.8662476521273 | etot = -8.5301130953782 +8000 ekin = 1.10242233608904 | erot = 3.2467735191286 | epot = -12.8793089505567 | etot = -8.53011309533902 +9000 ekin = 1.129661928832 | erot = 3.21481512313353 | epot = -12.8745901471786 | etot = -8.53011309521308 +10000 ekin = 1.1585736522661 | erot = 3.16442800302926 | epot = -12.8531147503057 | etot = -8.53011309501037 +11000 ekin = 1.18812580536523 | erot = 3.09887248462025 | epot = -12.8171113847418 | etot = -8.53011309475631 +12000 ekin = 1.21753508254996 | erot = 3.02200194393143 | epot = -12.769650120973 | etot = -8.53011309449156 +13000 ekin = 1.2462058323433 | erot = 2.9377430603182 | epot = -12.714061986917 | etot = -8.53011309425547 +14000 ekin = 1.27363535726518 | erot = 2.84960621277607 | epot = -12.6533546641222 | etot = -8.53011309408095 +15000 ekin = 1.29932429763742 | erot = 2.76035703495641 | epot = -12.5897944265541 | etot = -8.53011309396027 +16000 ekin = 1.32272478678523 | erot = 2.6720937631297 | epot = -12.524931643808 | etot = -8.53011309389307 +17000 ekin = 1.34324184048103 | erot = 2.58606256429308 | epot = -12.4594174987189 | etot = -8.53011309394479 +18000 ekin = 1.36028413036255 | erot = 2.50244725823279 | epot = -12.3928444826193 | etot = -8.53011309402401 +19000 ekin = 1.37335728231339 | erot = 2.42064483701932 | epot = -12.3241152134301 | etot = -8.53011309409738 +20000 ekin = 1.38218242867047 | erot = 2.34004763399705 | epot = -12.2523431568014 | etot = -8.53011309413387 +21000 ekin = 1.38682228720779 | erot = 2.26037911407475 | epot = -12.177314495392 | etot = -8.5301130941095 +22000 ekin = 1.38779551760397 | erot = 2.18193012018469 | epot = -12.0998387317994 | etot = -8.53011309401076 +23000 ekin = 1.38615925697244 | erot = 2.10566093427178 | epot = -12.0219332850808 | etot = -8.53011309383658 +24000 ekin = 1.38353970337949 | erot = 2.03315888827115 | epot = -11.9468116852494 | etot = -8.53011309359879 +25000 ekin = 1.38209065002972 | erot = 1.96646602495005 | epot = -11.878669768302 | etot = -8.53011309332227 +26000 ekin = 1.38436080324083 | erot = 1.90779815728269 | epot = -11.8222720535672 | etot = -8.53011309304368 +27000 ekin = 1.39305591970662 | erot = 1.85918805302253 | epot = -11.7823570655392 | etot = -8.53011309281007 +28000 ekin = 1.41069326836991 | erot = 1.82208843481178 | epot = -11.7628947958561 | etot = -8.53011309267439 +29000 ekin = 1.43917287732209 | erot = 1.79698086203697 | epot = -11.7662668320471 | etot = -8.53011309268808 +30000 ekin = 1.47932849918245 | erot = 1.78306055931658 | epot = -11.7925021513844 | etot = -8.53011309288539 +31000 ekin = 1.53057628219298 | erot = 1.77809666847709 | epot = -11.8387860439325 | etot = -8.53011309326246 +32000 ekin = 1.59082591350721 | erot = 1.77861870572279 | epot = -11.8995577129103 | etot = -8.53011309368031 +33000 ekin = 1.65668666319888 | erot = 1.78084924850009 | epot = -11.9676490059449 | etot = -8.5301130942459 +34000 ekin = 1.72400978324414 | erot = 1.78052778818395 | epot = -12.0346506661702 | etot = -8.53011309474212 +35000 ekin = 1.7886123825629 | erot = 1.77409588873529 | epot = -12.0928213663778 | etot = -8.53011309507956 +36000 ekin = 1.84692171859354 | erot = 1.75957152442153 | epot = -12.1366063382347 | etot = -8.53011309521964 +37000 ekin = 1.89635505211536 | erot = 1.73677582238486 | epot = -12.1632439696813 | etot = -8.53011309518103 +38000 ekin = 1.93537564106391 | erot = 1.70707948670454 | epot = -12.1725682227891 | etot = -8.53011309502064 +39000 ekin = 1.96330319937479 | erot = 1.6728321302729 | epot = -12.1662484244538 | etot = -8.53011309480614 +40000 ekin = 1.98002136738555 | erot = 1.63672123005991 | epot = -12.1468556920407 | etot = -8.53011309459527 +41000 ekin = 1.98570586801292 | erot = 1.60124465405442 | epot = -12.1170636164834 | etot = -8.53011309441608 +42000 ekin = 1.98063892667626 | erot = 1.56840871961079 | epot = -12.079160740572 | etot = -8.5301130942849 +43000 ekin = 1.96512381188785 | erot = 1.53942032547732 | epot = -12.0346572315593 | etot = -8.53011309419408 +44000 ekin = 1.93948381096135 | erot = 1.51506739642158 | epot = -11.984664301514 | etot = -8.53011309413104 +45000 ekin = 1.90411789628636 | erot = 1.49583019895571 | epot = -11.930061189321 | etot = -8.5301130940789 +46000 ekin = 1.85959054249402 | erot = 1.48193663738997 | epot = -11.8716402739046 | etot = -8.53011309402065 +47000 ekin = 1.80673127931967 | erot = 1.47351008731115 | epot = -11.8103544605731 | etot = -8.53011309394226 +48000 ekin = 1.74672194665333 | erot = 1.47069179369331 | epot = -11.7475268341802 | etot = -8.53011309383356 +49000 ekin = 1.681153790432 | erot = 1.47372603796066 | epot = -11.6849929220833 | etot = -8.53011309369066 +50000 ekin = 1.61204360764113 | erot = 1.48300481815587 | epot = -11.6251615193115 | etot = -8.53011309351451 +51000 ekin = 1.54180688827886 | erot = 1.49907572686268 | epot = -11.5709957084487 | etot = -8.53011309330713 +52000 ekin = 1.47319223880804 | erot = 1.52262764796927 | epot = -11.5259329798625 | etot = -8.53011309308518 +53000 ekin = 1.40918336186017 | erot = 1.55438319093874 | epot = -11.4936796456586 | etot = -8.53011309285965 +54000 ekin = 1.35286923285663 | erot = 1.59499333649053 | epot = -11.4779756619988 | etot = -8.53011309265166 +55000 ekin = 1.3072761010404 | erot = 1.64486884964686 | epot = -11.4822580431747 | etot = -8.53011309248741 +56000 ekin = 1.2751604136272 | erot = 1.70395929448973 | epot = -11.509232800514 | etot = -8.53011309239707 +57000 ekin = 1.25877821290722 | erot = 1.77153045261034 | epot = -11.5604217579235 | etot = -8.53011309240593 +58000 ekin = 1.25966981557396 | erot = 1.84600740239507 | epot = -11.6357903104947 | etot = -8.53011309252566 +59000 ekin = 1.27850991703401 | erot = 1.92494493442932 | epot = -11.7335679442149 | etot = -8.53011309275159 +60000 ekin = 1.31505846517354 | erot = 2.00506933713746 | epot = -11.8502408954026 | etot = -8.53011309309164 +61000 ekin = 1.36820967857684 | erot = 2.08251311350662 | epot = -11.9808358855456 | etot = -8.53011309346211 +62000 ekin = 1.43610935375693 | erot = 2.15340897405314 | epot = -12.1196314216668 | etot = -8.5301130938567 +63000 ekin = 1.51630533152245 | erot = 2.2141008432564 | epot = -12.2605192690214 | etot = -8.53011309424256 +64000 ekin = 1.60588594281051 | erot = 2.26150680600727 | epot = -12.3975058434118 | etot = -8.53011309459399 +65000 ekin = 1.70157559823965 | erot = 2.29343173619353 | epot = -12.5251204293296 | etot = -8.53011309489646 +66000 ekin = 1.79977612979946 | erot = 2.3087594351045 | epot = -12.6386486600531 | etot = -8.53011309514917 +67000 ekin = 1.89656896474264 | erot = 2.30747600160479 | epot = -12.7341580617102 | etot = -8.53011309536274 +68000 ekin = 1.98772340358698 | erot = 2.29052837543627 | epot = -12.8083648745724 | etot = -8.53011309554913 +69000 ekin = 2.06877558194363 | erot = 2.25958722526848 | epot = -12.8584759029224 | etot = -8.53011309571026 +70000 ekin = 2.13523440531619 | erot = 2.21681911735293 | epot = -12.8821666185007 | etot = -8.53011309583153 +71000 ekin = 2.18292944014516 | erot = 2.16475080910303 | epot = -12.8777933451316 | etot = -8.53011309588342 +72000 ekin = 2.20845503567845 | erot = 2.10623867450836 | epot = -12.8448068060206 | etot = -8.53011309583374 +73000 ekin = 2.20961374982505 | erot = 2.04448327477864 | epot = -12.784210120232 | etot = -8.53011309562831 +74000 ekin = 2.18583088959709 | erot = 1.98307376954797 | epot = -12.6990177544748 | etot = -8.53011309532969 +75000 ekin = 2.13819357127786 | erot = 1.92577296068263 | epot = -12.5940796268929 | etot = -8.53011309493236 +76000 ekin = 2.06931387379192 | erot = 1.87621391736368 | epot = -12.4756408856272 | etot = -8.53011309447156 +77000 ekin = 1.9831459935215 | erot = 1.83766509006144 | epot = -12.3509241775703 | etot = -8.53011309398734 +78000 ekin = 1.88464003549136 | erot = 1.81276644965514 | epot = -12.2275195786651 | etot = -8.53011309351862 +79000 ekin = 1.77934330540969 | erot = 1.80331865972863 | epot = -12.1127750582401 | etot = -8.53011309310181 +80000 ekin = 1.67297594037631 | erot = 1.81012474896281 | epot = -12.0132137821111 | etot = -8.530113092772 +81000 ekin = 1.57099416873045 | erot = 1.8328690442996 | epot = -11.9339763055923 | etot = -8.53011309256227 +82000 ekin = 1.47816348110906 | erot = 1.87002999045995 | epot = -11.8783065640684 | etot = -8.53011309249942 +83000 ekin = 1.398187784623 | erot = 1.91885160298036 | epot = -11.8471524801993 | etot = -8.5301130925959 +84000 ekin = 1.3334581452956 | erot = 1.97542175599055 | epot = -11.8389929941294 | etot = -8.53011309284326 +85000 ekin = 1.28497532516075 | erot = 2.0349061774483 | epot = -11.8499945958141 | etot = -8.530113093205 +86000 ekin = 1.25246025395582 | erot = 2.09197660059406 | epot = -11.8745499481781 | etot = -8.53011309362821 +87000 ekin = 1.23461285408012 | erot = 2.14137296784411 | epot = -11.9060989159744 | etot = -8.53011309405018 +88000 ekin = 1.22943812073932 | erot = 2.17852719424197 | epot = -11.9380784093963 | etot = -8.53011309441497 +89000 ekin = 1.23455364871357 | erot = 2.20012041252108 | epot = -11.9647871559195 | etot = -8.53011309468488 +90000 ekin = 1.247425805765 | erot = 2.20445455177206 | epot = -11.9819934523813 | etot = -8.53011309484426 +91000 ekin = 1.265533830847 | erot = 2.19157144961211 | epot = -11.9872183753549 | etot = -8.53011309489578 +92000 ekin = 1.28623000858103 | erot = 2.16295140457794 | epot = -11.9792945080807 | etot = -8.53011309492174 +93000 ekin = 1.30692364344383 | erot = 2.12123926047786 | epot = -11.9582759987369 | etot = -8.5301130948152 +94000 ekin = 1.32581527393273 | erot = 2.07018243043928 | epot = -11.9261107990066 | etot = -8.53011309463457 +95000 ekin = 1.34182901778834 | erot = 2.01402433128801 | epot = -11.8859664434698 | etot = -8.53011309439347 +96000 ekin = 1.35474622264798 | erot = 1.95709566330722 | epot = -11.8419549800687 | etot = -8.53011309411347 +97000 ekin = 1.36518588247822 | erot = 1.90343342927418 | epot = -11.7987324055815 | etot = -8.53011309382905 +98000 ekin = 1.37438024241765 | erot = 1.85642234303645 | epot = -11.7609156790417 | etot = -8.53011309358764 +99000 ekin = 1.38375494732475 | erot = 1.81846000225616 | epot = -11.7323280430252 | etot = -8.53011309344426 +100000 ekin = 1.39439154293898 | erot = 1.79066261133391 | epot = -11.715167247719 | etot = -8.53011309344614 +101000 ekin = 1.40650610053404 | erot = 1.77268374626497 | epot = -11.7093029404209 | etot = -8.53011309362194 +102000 ekin = 1.41909865539682 | erot = 1.76268825953969 | epot = -11.7119000089018 | etot = -8.53011309396524 +103000 ekin = 1.42990225853186 | erot = 1.75756086568116 | epot = -11.7175762186402 | etot = -8.53011309442723 +104000 ekin = 1.43568960458615 | erot = 1.75339758186002 | epot = -11.7192002813656 | etot = -8.53011309491945 +105000 ekin = 1.43290883108516 | erot = 1.74626770102832 | epot = -11.7092896274385 | etot = -8.530113095325 +106000 ekin = 1.41854295074815 | erot = 1.73316545657386 | epot = -11.6818215028412 | etot = -8.53011309551917 +107000 ekin = 1.39103174229079 | erot = 1.71299001598405 | epot = -11.6341348536725 | etot = -8.53011309539768 +108000 ekin = 1.35105252774001 | erot = 1.68731521419139 | epot = -11.5684808368427 | etot = -8.53011309491129 +109000 ekin = 1.30192293440573 | erot = 1.66066055824567 | epot = -11.4926965867505 | etot = -8.53011309409914 +110000 ekin = 1.24955692632171 | erot = 1.64004235665915 | epot = -11.4197123754604 | etot = -8.53011309247958 +111000 ekin = 1.20373683101899 | erot = 1.634056606309 | epot = -11.367906529011 | etot = -8.53011309168306 +112000 ekin = 1.17136800050139 | erot = 1.64951573593171 | epot = -11.3509968276174 | etot = -8.53011309118433 +113000 ekin = 1.1564373725265 | erot = 1.69002000568969 | epot = -11.3765704693516 | etot = -8.53011309113541 +114000 ekin = 1.1601666491979 | erot = 1.75506593403395 | epot = -11.4453456747906 | etot = -8.53011309155874 +115000 ekin = 1.18078581898495 | erot = 1.83995213492442 | epot = -11.5508510462439 | etot = -8.53011309233455 +116000 ekin = 1.21421955357384 | erot = 1.93685465219997 | epot = -11.6811872990251 | etot = -8.53011309325133 +117000 ekin = 1.25536144135748 | erot = 2.03668558524402 | epot = -11.8221601206889 | etot = -8.53011309408735 +118000 ekin = 1.29940451384013 | erot = 2.13109010342768 | epot = -11.9606077119492 | etot = -8.5301130946814 +119000 ekin = 1.342774776846 | erot = 2.21397393951699 | epot = -12.0868618113322 | etot = -8.53011309496919 +120000 ekin = 1.38347061820549 | erot = 2.28221236483861 | epot = -12.195796078024 | etot = -8.53011309497985 +121000 ekin = 1.42087086651048 | erot = 2.33551129662523 | epot = -12.2864952579391 | etot = -8.53011309480344 +122000 ekin = 1.4552263897788 | erot = 2.3756429290616 | epot = -12.3609824133927 | etot = -8.53011309455232 +123000 ekin = 1.4870758266584 | erot = 2.40539124222141 | epot = -12.4225801632077 | etot = -8.53011309432789 +124000 ekin = 1.51676676843718 | erot = 2.42751903858622 | epot = -12.4743989012248 | etot = -8.5301130942014 +125000 ekin = 1.54417459772326 | erot = 2.44396324559694 | epot = -12.5182509375273 | etot = -8.53011309420714 +126000 ekin = 1.56863810035605 | erot = 2.4553511272518 | epot = -12.5541023219522 | etot = -8.53011309434435 +127000 ekin = 1.58908101361901 | erot = 2.4608536627413 | epot = -12.5800477709425 | etot = -8.53011309458218 +128000 ekin = 1.6042708388842 | erot = 2.45836168530056 | epot = -12.5927456190491 | etot = -8.53011309486435 +129000 ekin = 1.61315658291869 | erot = 2.44495811201806 | epot = -12.5882277900549 | etot = -8.53011309511816 +130000 ekin = 1.61521763497857 | erot = 2.4176285931953 | epot = -12.5629593234409 | etot = -8.53011309526708 +131000 ekin = 1.61074673258805 | erot = 2.37408565093652 | epot = -12.5149454787753 | etot = -8.53011309525076 +132000 ekin = 1.60099281445321 | erot = 2.31350559905906 | epot = -12.4446115085553 | etot = -8.53011309504302 +133000 ekin = 1.58811839137735 | erot = 2.23695676757674 | epot = -12.3551882536157 | etot = -8.53011309466161 +134000 ekin = 1.57497837856358 | erot = 2.1473790715212 | epot = -12.252470544281 | etot = -8.53011309419617 +135000 ekin = 1.56467799512159 | erot = 2.04902291672221 | epot = -12.1438140054843 | etot = -8.53011309364047 +136000 ekin = 1.56033306064837 | erot = 1.94701578012998 | epot = -12.0374619338905 | etot = -8.53011309311218 +137000 ekin = 1.56479379508625 | erot = 1.84660873227816 | epot = -11.9415156200312 | etot = -8.53011309266677 +138000 ekin = 1.58030314703432 | erot = 1.75245153796743 | epot = -11.8628677773359 | etot = -8.53011309233418 +139000 ekin = 1.60833080358451 | erot = 1.6682660913931 | epot = -11.8067099870999 | etot = -8.53011309212233 +140000 ekin = 1.64949521723192 | erot = 1.59676588041006 | epot = -11.7763741896652 | etot = -8.53011309202317 +141000 ekin = 1.70355355174859 | erot = 1.53975804779895 | epot = -11.7734246915232 | etot = -8.53011309197561 +142000 ekin = 1.76943720118442 | erot = 1.49859523121387 | epot = -11.7981455244592 | etot = -8.5301130920609 +143000 ekin = 1.84530405880862 | erot = 1.47384945852753 | epot = -11.8492666095588 | etot = -8.53011309222263 +144000 ekin = 1.92861465369001 | erot = 1.46549379274654 | epot = -11.9242215388116 | etot = -8.53011309237502 +145000 ekin = 2.01648600784352 | erot = 1.47353305209478 | epot = -12.0201321527194 | etot = -8.5301130927811 +146000 ekin = 2.10458212275704 | erot = 1.49637875129038 | epot = -12.1310739673154 | etot = -8.53011309326793 +147000 ekin = 2.18785677137349 | erot = 1.5314591984994 | epot = -12.2494290636989 | etot = -8.53011309382603 +148000 ekin = 2.26104758516561 | erot = 1.57543986096036 | epot = -12.3666005405508 | etot = -8.53011309442483 +149000 ekin = 2.31910091716379 | erot = 1.62430319702598 | epot = -12.4735172091961 | etot = -8.5301130950063 +150000 ekin = 2.35773821658445 | erot = 1.67365853244669 | epot = -12.5615098445252 | etot = -8.53011309549403 +151000 ekin = 2.37405078100302 | erot = 1.7192672632974 | epot = -12.6234311401175 | etot = -8.53011309581711 +152000 ekin = 2.36692545461634 | erot = 1.75764773901451 | epot = -12.6546862895679 | etot = -8.53011309593708 +153000 ekin = 2.33712749183089 | erot = 1.78656744402825 | epot = -12.6538080317178 | etot = -8.53011309585864 +154000 ekin = 2.28703010669271 | erot = 1.80529001826454 | epot = -12.6224332205718 | etot = -8.53011309561459 +155000 ekin = 2.22017210957738 | erot = 1.81456905274742 | epot = -12.5648542575675 | etot = -8.53011309524267 +156000 ekin = 2.1408721665017 | erot = 1.81646017186521 | epot = -12.4874454331416 | etot = -8.53011309477465 +157000 ekin = 2.05398632051146 | erot = 1.81400844427825 | epot = -12.3981078590399 | etot = -8.53011309425016 +158000 ekin = 1.96465269026301 | erot = 1.81075171604371 | epot = -12.305517500103 | etot = -8.53011309379623 +159000 ekin = 1.87738211880319 | erot = 1.80975809034341 | epot = -12.2172533025062 | etot = -8.53011309335963 +160000 ekin = 1.79637755657175 | erot = 1.81368342474274 | epot = -12.1401740743796 | etot = -8.53011309306516 +161000 ekin = 1.72479660822492 | erot = 1.82417298786657 | epot = -12.0790826890673 | etot = -8.53011309297584 +162000 ekin = 1.66403255347616 | erot = 1.84141406703866 | epot = -12.0355597136254 | etot = -8.53011309311057 +163000 ekin = 1.61344211817627 | erot = 1.86416684407897 | epot = -12.0077220556812 | etot = -8.53011309342599 +164000 ekin = 1.57053136480639 | erot = 1.89024538669855 | epot = -11.990889845331 | etot = -8.53011309382611 +165000 ekin = 1.53158684055262 | erot = 1.91735211282816 | epot = -11.9790520475667 | etot = -8.53011309418588 +166000 ekin = 1.49257533008373 | erot = 1.94405290672945 | epot = -11.9667413312082 | etot = -8.53011309439505 +167000 ekin = 1.45004739614814 | erot = 1.9705428218327 | epot = -11.9507033123727 | etot = -8.53011309439191 +168000 ekin = 1.40180339426578 | erot = 1.99893184094575 | epot = -11.9308483293895 | etot = -8.53011309417795 +169000 ekin = 1.34719230179007 | erot = 2.03295603374789 | epot = -11.9102614293485 | etot = -8.53011309381054 +170000 ekin = 1.28704969495272 | erot = 2.07721655562314 | epot = -11.8943793439504 | etot = -8.53011309337457 +171000 ekin = 1.22340120606629 | erot = 2.13620458401901 | epot = -11.8897188830155 | etot = -8.53011309293021 +172000 ekin = 1.15916399135854 | erot = 2.21333149138595 | epot = -11.9026085753701 | etot = -8.5301130926256 +173000 ekin = 1.09731722457336 | erot = 2.31014635554186 | epot = -11.9375766725986 | etot = -8.53011309248333 +174000 ekin = 1.04063961884127 | erot = 2.42581098119803 | epot = -11.9965636925781 | etot = -8.53011309253885 +175000 ekin = 0.991434959332988 | erot = 2.55687374585407 | epot = -12.0784217979906 | etot = -8.53011309280354 +176000 ekin = 0.951286219743537 | erot = 2.69734247997581 | epot = -12.1787417929831 | etot = -8.53011309326378 +177000 ekin = 0.920906931255968 | erot = 2.83907560795418 | epot = -12.2900956330861 | etot = -8.530113093876 +178000 ekin = 0.900110889875814 | erot = 2.97251922257665 | epot = -12.4027432070179 | etot = -8.53011309456542 +179000 ekin = 0.887921283965376 | erot = 3.08778217993959 | epot = -12.5058165591358 | etot = -8.53011309523079 +180000 ekin = 0.882819894460815 | erot = 3.17595008457009 | epot = -12.5888830747921 | etot = -8.53011309576116 +181000 ekin = 0.883094662246449 | erot = 3.23041576817405 | epot = -12.6436235264849 | etot = -8.53011309606437 +182000 ekin = 0.887197266497044 | erot = 3.24791323274169 | epot = -12.6652235953324 | etot = -8.53011309609369 +183000 ekin = 0.894005517566804 | erot = 3.22896613968051 | epot = -12.6530847531087 | etot = -8.53011309586139 +184000 ekin = 0.902922567053578 | erot = 3.17763362003998 | epot = -12.610669282523 | etot = -8.53011309542945 +185000 ekin = 0.913819897430199 | erot = 3.10068233612809 | epot = -12.5446153284403 | etot = -8.53011309488204 +186000 ekin = 0.926892274386944 | erot = 3.00648382594885 | epot = -12.4634891947413 | etot = -8.53011309440549 +187000 ekin = 0.942359343467903 | erot = 2.90341264008055 | epot = -12.3758850774298 | etot = -8.53011309388138 +188000 ekin = 0.960415128419174 | erot = 2.7995023321508 | epot = -12.2900305539847 | etot = -8.53011309341473 +189000 ekin = 0.981336580896324 | erot = 2.702219690544 | epot = -12.2136693644689 | etot = -8.53011309302854 +190000 ekin = 1.00543372733298 | erot = 2.61771835557185 | epot = -12.1532651756636 | etot = -8.53011309275873 +191000 ekin = 1.03305642669588 | erot = 2.55042331784814 | epot = -12.1135928371337 | etot = -8.53011309258972 +192000 ekin = 1.06458819978575 | erot = 2.502951492612 | epot = -12.0976527849401 | etot = -8.53011309254235 +193000 ekin = 1.10043008600686 | erot = 2.4759146106301 | epot = -12.1064577892569 | etot = -8.53011309261996 +194000 ekin = 1.14095348227996 | erot = 2.46790659075146 | epot = -12.1389731658498 | etot = -8.53011309281836 +195000 ekin = 1.18642396462085 | erot = 2.47566002440274 | epot = -12.1921970821463 | etot = -8.53011309312271 +196000 ekin = 1.2369145605392 | erot = 2.49438862695288 | epot = -12.2614162809965 | etot = -8.53011309350438 +197000 ekin = 1.29223924615382 | erot = 2.51832160491041 | epot = -12.3406739449846 | etot = -8.53011309392038 +198000 ekin = 1.35193471466299 | erot = 2.54139178285267 | epot = -12.4234395918359 | etot = -8.53011309432024 +199000 ekin = 1.41529957065347 | erot = 2.55798242673134 | epot = -12.5033950920399 | etot = -8.53011309465512 +200000 ekin = 1.481473900578 | erot = 2.56359779441153 | epot = -12.5751847898788 | etot = -8.53011309488927 +201000 ekin = 1.54952685169028 | erot = 2.55533485734996 | epot = -12.6349748040457 | etot = -8.53011309500544 +202000 ekin = 1.61852368373095 | erot = 2.53209551772288 | epot = -12.6807322964589 | etot = -8.53011309500508 +203000 ekin = 1.68755981245379 | erot = 2.49462961612359 | epot = -12.7123025234438 | etot = -8.53011309486638 +204000 ekin = 1.75576103234987 | erot = 2.44539440890692 | epot = -12.7312685359473 | etot = -8.53011309469053 +205000 ekin = 1.82226727517107 | erot = 2.38780081716033 | epot = -12.7401811867913 | etot = -8.53011309445995 +206000 ekin = 1.88619984147264 | erot = 2.32611076719096 | epot = -12.7424237028677 | etot = -8.53011309420411 +207000 ekin = 1.94660231588624 | erot = 2.26504166017975 | epot = -12.7417570700272 | etot = -8.5301130939612 +208000 ekin = 2.00235042264584 | erot = 2.20925458967812 | epot = -12.7417181061045 | etot = -8.5301130937805 +209000 ekin = 2.05203134834761 | erot = 2.16271925047937 | epot = -12.7448636925487 | etot = -8.53011309372176 +210000 ekin = 2.09381524344858 | erot = 2.12796343491006 | epot = -12.7518917722037 | etot = -8.53011309384504 +211000 ekin = 2.12537929046187 | erot = 2.10530160183663 | epot = -12.760793986487 | etot = -8.53011309418849 +212000 ekin = 2.14398845109537 | erot = 2.09226506761566 | epot = -12.7663666134465 | etot = -8.53011309473546 +213000 ekin = 2.14685083920782 | erot = 2.08357075606551 | epot = -12.7605346906603 | etot = -8.530113095387 +214000 ekin = 2.1317793355869 | erot = 2.07198437940519 | epot = -12.7338768105377 | etot = -8.53011309554561 +215000 ekin = 2.09740576159844 | erot = 2.05243678649467 | epot = -12.6799556440651 | etot = -8.53011309597196 +216000 ekin = 2.04414786569907 | erot = 2.01980811255998 | epot = -12.5940690742957 | etot = -8.53011309603668 +217000 ekin = 1.97496281847612 | erot = 1.97035714827555 | epot = -12.4754330625051 | etot = -8.53011309575345 +218000 ekin = 1.8948373238438 | erot = 1.90369037051482 | epot = -12.3286407894934 | etot = -8.53011309513472 +219000 ekin = 1.81041467830664 | erot = 1.82278463149711 | epot = -12.1633124040823 | etot = -8.5301130942786 +220000 ekin = 1.72938454080915 | erot = 1.73330150874472 | epot = -11.9927991427904 | etot = -8.53011309323654 +221000 ekin = 1.65959820381305 | erot = 1.64273176790434 | epot = -11.8324430640329 | etot = -8.53011309231554 +222000 ekin = 1.60845034453789 | erot = 1.55815968235264 | epot = -11.6967231184019 | etot = -8.53011309151133 +223000 ekin = 1.58228239188915 | erot = 1.48580466478771 | epot = -11.5982001475875 | etot = -8.53011309091067 +224000 ekin = 1.5856976551694 | erot = 1.43046423809878 | epot = -11.5462749838454 | etot = -8.5301130905772 +225000 ekin = 1.62100953317662 | erot = 1.39504063224572 | epot = -11.5461632559814 | etot = -8.53011309055906 +226000 ekin = 1.68783126437479 | erot = 1.38020176396467 | epot = -11.5981461192339 | etot = -8.53011309089441 +227000 ekin = 1.78271150290518 | erot = 1.38413372943446 | epot = -11.6969583246211 | etot = -8.53011309228148 +228000 ekin = 1.89495289262362 | erot = 1.40258789217287 | epot = -11.8276538782981 | etot = -8.53011309350161 +229000 ekin = 2.01170607721849 | erot = 1.42820655801896 | epot = -11.9700257301876 | etot = -8.53011309495016 +230000 ekin = 2.11989887159659 | erot = 1.4523540971715 | epot = -12.1023660650346 | etot = -8.53011309626653 +231000 ekin = 2.20759782077804 | erot = 1.46730876356808 | epot = -12.2050196815073 | etot = -8.53011309716122 +232000 ekin = 2.26562589153242 | erot = 1.46886009000392 | epot = -12.2645990789947 | etot = -8.53011309745836 +233000 ekin = 2.28822506975746 | erot = 1.45787535434379 | epot = -12.2762135212095 | etot = -8.53011309710823 +234000 ekin = 2.27464524977865 | erot = 1.43990370669335 | epot = -12.2446620527941 | etot = -8.53011309632208 +235000 ekin = 2.22825507530892 | erot = 1.42328017859116 | epot = -12.1816483492739 | etot = -8.53011309537382 +236000 ekin = 2.15494106311511 | erot = 1.41661045699289 | epot = -12.1016646145796 | etot = -8.53011309447159 +237000 ekin = 2.06197124561426 | erot = 1.42677729192205 | epot = -12.0188616312522 | etot = -8.53011309371585 +238000 ekin = 1.95733575736116 | erot = 1.45790014382963 | epot = -11.9453489943268 | etot = -8.53011309313597 +239000 ekin = 1.84937348817275 | erot = 1.51100787616932 | epot = -11.8904944570919 | etot = -8.53011309274985 +240000 ekin = 1.74634948667573 | erot = 1.58401675949076 | epot = -11.8604793387578 | etot = -8.53011309259134 +241000 ekin = 1.65579840431705 | erot = 1.67182932722843 | epot = -11.8577408242433 | etot = -8.53011309269777 +242000 ekin = 1.58370704114946 | erot = 1.76665328809221 | epot = -11.8804734223153 | etot = -8.53011309307363 +243000 ekin = 1.53379082409438 | erot = 1.85876363932185 | epot = -11.9226675570786 | etot = -8.53011309366237 +244000 ekin = 1.50713311675996 | erot = 1.93781479613261 | epot = -11.9750610072396 | etot = -8.53011309434702 +245000 ekin = 1.50232523408853 | erot = 1.99453085491372 | epot = -12.0269691839801 | etot = -8.53011309497784 +246000 ekin = 1.51606904510282 | erot = 2.02239007086936 | epot = -12.0685722113878 | etot = -8.53011309541565 +247000 ekin = 1.54406668998835 | erot = 2.01887471172768 | epot = -12.0930544972697 | etot = -8.53011309555362 +248000 ekin = 1.58197270416977 | erot = 1.9860852549186 | epot = -12.0981710544434 | etot = -8.53011309535498 +249000 ekin = 1.62609171467958 | erot = 1.93029875238694 | epot = -12.0865035619571 | etot = -8.53011309489059 +250000 ekin = 1.67387536281809 | erot = 1.86081409573892 | epot = -12.0648025528069 | etot = -8.53011309424987 +251000 ekin = 1.72391096985858 | erot = 1.78844826295717 | epot = -12.0424723264225 | etot = -8.5301130936067 +252000 ekin = 1.7753819071169 | erot = 1.7236719123789 | epot = -12.0291669125776 | etot = -8.53011309308178 +253000 ekin = 1.82754829280947 | erot = 1.67492092834063 | epot = -12.0325823139111 | etot = -8.53011309276105 +254000 ekin = 1.87961881561723 | erot = 1.64770020961713 | epot = -12.0574321179074 | etot = -8.53011309267301 +255000 ekin = 1.93045785731808 | erot = 1.64434942869014 | epot = -12.1049203788171 | etot = -8.5301130928089 +256000 ekin = 1.97849877464051 | erot = 1.66421751998761 | epot = -12.1728293877676 | etot = -8.53011309313951 +257000 ekin = 2.0217566179138 | erot = 1.70407398948232 | epot = -12.2559437010212 | etot = -8.53011309362509 +258000 ekin = 2.05791961396887 | erot = 1.75862748975153 | epot = -12.3466601979401 | etot = -8.53011309421969 +259000 ekin = 2.08450645969242 | erot = 1.82109836581008 | epot = -12.4357179203749 | etot = -8.53011309487241 +260000 ekin = 2.09907285067837 | erot = 1.88382726111915 | epot = -12.5130132073275 | etot = -8.53011309552994 +261000 ekin = 2.09944572596161 | erot = 1.93893768787249 | epot = -12.5684965099611 | etot = -8.53011309612699 +262000 ekin = 2.08396569038711 | erot = 1.97908462797729 | epot = -12.5931634149734 | etot = -8.53011309660901 +263000 ekin = 2.05172676882021 | erot = 1.9982090888738 | epot = -12.580048954553 | etot = -8.53011309685898 +264000 ekin = 2.00296719649569 | erot = 1.9928343917862 | epot = -12.5259146850348 | etot = -8.53011309675296 +265000 ekin = 1.93948872899132 | erot = 1.96339266268781 | epot = -12.4329944878833 | etot = -8.53011309620415 +266000 ekin = 1.86494390143915 | erot = 1.91505343003299 | epot = -12.3101104266354 | etot = -8.53011309516322 +267000 ekin = 1.78505719746833 | erot = 1.85721593585793 | epot = -12.1723862273132 | etot = -8.53011309398698 +268000 ekin = 1.70605852586669 | erot = 1.80175587067256 | epot = -12.0379274893394 | etot = -8.53011309280011 +269000 ekin = 1.63387234043008 | erot = 1.76055577812986 | epot = -11.9245412104251 | etot = -8.53011309186521 +270000 ekin = 1.57342106955824 | erot = 1.74281009478432 | epot = -11.8463442556698 | etot = -8.53011309132727 +271000 ekin = 1.52797485202415 | erot = 1.75341085935497 | epot = -11.8114988026157 | etot = -8.53011309123661 +272000 ekin = 1.49894876525735 | erot = 1.79234603399532 | epot = -11.8214078908094 | etot = -8.53011309155678 +273000 ekin = 1.48604758198122 | erot = 1.85507402496715 | epot = -11.8712346991386 | etot = -8.5301130921902 +274000 ekin = 1.48766345157073 | erot = 1.93349346053598 | epot = -11.9512700051694 | etot = -8.53011309306265 +275000 ekin = 1.50135017863795 | erot = 2.01723774122155 | epot = -12.0487010137587 | etot = -8.5301130938992 +276000 ekin = 1.52425343307295 | erot = 2.09653669779255 | epot = -12.1509032254467 | etot = -8.53011309458124 +277000 ekin = 1.55417046599777 | erot = 2.16339336358524 | epot = -12.2476769246678 | etot = -8.53011309508482 +278000 ekin = 1.58883002210858 | erot = 2.21269572879347 | epot = -12.3316388462086 | etot = -8.53011309530658 +279000 ekin = 1.62657848626996 | erot = 2.24273575291771 | epot = -12.3994273344821 | etot = -8.53011309529447 +280000 ekin = 1.6662646237581 | erot = 2.25488508621539 | epot = -12.4512628051112 | etot = -8.53011309513769 +281000 ekin = 1.70666329888322 | erot = 2.2528781375611 | epot = -12.4896545313672 | etot = -8.5301130949229 +282000 ekin = 1.74606224489442 | erot = 2.24193390477342 | epot = -12.5181092443714 | etot = -8.53011309470351 +283000 ekin = 1.78229604375783 | erot = 2.22773335199481 | epot = -12.5401424902721 | etot = -8.53011309451947 +284000 ekin = 1.81303392681889 | erot = 2.21528431693992 | epot = -12.5584313381479 | etot = -8.53011309438912 +285000 ekin = 1.83626784551359 | erot = 2.20859920573473 | epot = -12.5749801456019 | etot = -8.53011309435358 +286000 ekin = 1.85056798130881 | erot = 2.20962029353652 | epot = -12.5903013692877 | etot = -8.53011309444239 +287000 ekin = 1.8550635304434 | erot = 2.21784540833844 | epot = -12.6030220334124 | etot = -8.53011309463059 +288000 ekin = 1.8494233981353 | erot = 2.23075201933167 | epot = -12.6102885123078 | etot = -8.53011309484083 +289000 ekin = 1.8339088801736 | erot = 2.24488012942888 | epot = -12.6089021045818 | etot = -8.53011309497935 +290000 ekin = 1.80943255390652 | erot = 2.2572237152992 | epot = -12.5967693641603 | etot = -8.53011309495454 +291000 ekin = 1.77754353319109 | erot = 2.26619423186307 | epot = -12.57385085985 | etot = -8.53011309479584 +292000 ekin = 1.74029196122666 | erot = 2.27170357096951 | epot = -12.5421086267524 | etot = -8.5301130945562 +293000 ekin = 1.6999754354036 | erot = 2.27474290666544 | epot = -12.5048314363832 | etot = -8.53011309431417 +294000 ekin = 1.65879913990678 | erot = 2.27646633894027 | epot = -12.4653785730009 | etot = -8.53011309415386 +295000 ekin = 1.61857194087987 | erot = 2.27728965532028 | epot = -12.4259746903009 | etot = -8.53011309410079 +296000 ekin = 1.58063856927617 | erot = 2.27661684716244 | epot = -12.387368510527 | etot = -8.5301130940884 +297000 ekin = 1.54603085638124 | erot = 2.27331893745141 | epot = -12.3494628879054 | etot = -8.53011309407273 +298000 ekin = 1.51552933019762 | erot = 2.26654381109844 | epot = -12.3121862352837 | etot = -8.53011309398763 +299000 ekin = 1.48978666564629 | erot = 2.25633296635495 | epot = -12.2762327258636 | etot = -8.53011309386239 +300000 ekin = 1.46918272389791 | erot = 2.24345468614642 | epot = -12.242750503802 | etot = -8.53011309375768 +301000 ekin = 1.45354278560875 | erot = 2.22882911340882 | epot = -12.2124849927865 | etot = -8.5301130937689 +302000 ekin = 1.44183301629794 | erot = 2.21276714678519 | epot = -12.1847132569687 | etot = -8.53011309388561 +303000 ekin = 1.43225770121122 | erot = 2.19458092752688 | epot = -12.1569517228355 | etot = -8.53011309409737 +304000 ekin = 1.42259637356991 | erot = 2.17276750288897 | epot = -12.1254769707815 | etot = -8.53011309432262 +305000 ekin = 1.41064586326832 | erot = 2.14566468388069 | epot = -12.0864236416132 | etot = -8.5301130944642 +306000 ekin = 1.39473877107246 | erot = 2.11230934515816 | epot = -12.0371612106968 | etot = -8.53011309446616 +307000 ekin = 1.3740115615447 | erot = 2.07305527676066 | epot = -11.9771799326147 | etot = -8.53011309430936 +308000 ekin = 1.3485247052802 | erot = 2.02957445559338 | epot = -11.9082122549388 | etot = -8.53011309406522 +309000 ekin = 1.31899505489831 | erot = 1.9842726911903 | epot = -11.8333808399303 | etot = -8.53011309384171 +310000 ekin = 1.28628826657229 | erot = 1.93930156456122 | epot = -11.7557029248838 | etot = -8.53011309375026 +311000 ekin = 1.25093726244378 | erot = 1.89525998935024 | epot = -11.6763103458619 | etot = -8.53011309406784 +312000 ekin = 1.21290642809376 | erot = 1.84947048977035 | epot = -11.5924900122399 | etot = -8.53011309437575 +313000 ekin = 1.1714184611298 | erot = 1.79876682021561 | epot = -11.5002983761237 | etot = -8.53011309477825 +314000 ekin = 1.07288272942862 | erot = 1.70848696881406 | epot = -11.311482847552 | etot = -8.5301131493093 +315000 ekin = 0.929305233250754 | erot = 1.46737286493929 | epot = -10.9267911417344 | etot = -8.53011304354439 +316000 ekin = 1.3343895371699 | erot = 1.37623199915563 | epot = -11.2407347047628 | etot = -8.53011316843732 +317000 ekin = 1.400093717002 | erot = 1.31826590785373 | epot = -11.2484727303605 | etot = -8.53011310550475 +318000 ekin = 1.4311535991829 | erot = 1.25971123043266 | epot = -11.2209779347353 | etot = -8.53011310511977 +319000 ekin = 1.45754379434808 | erot = 1.20520642772615 | epot = -11.1928633267497 | etot = -8.53011310467545 +320000 ekin = 1.48149893345566 | erot = 1.15864569690776 | epot = -11.17025773465 | etot = -8.53011310428661 +321000 ekin = 1.50513128439723 | erot = 1.1235040010055 | epot = -11.1587483894097 | etot = -8.53011310400692 +322000 ekin = 1.52997806002378 | erot = 1.10223049025858 | epot = -11.1623216541776 | etot = -8.53011310389523 +323000 ekin = 1.55672107909495 | erot = 1.09578101873747 | epot = -11.182615201786 | etot = -8.53011310395358 +324000 ekin = 1.58511366200745 | erot = 1.10363080456385 | epot = -11.2188575707121 | etot = -8.53011310414085 +325000 ekin = 1.61412294527432 | erot = 1.12419697508963 | epot = -11.2684330247499 | etot = -8.5301131043859 +326000 ekin = 1.64224941760032 | erot = 1.15551879655626 | epot = -11.327881318772 | etot = -8.53011310461539 +327000 ekin = 1.66792915391916 | erot = 1.19590561828287 | epot = -11.3939478769661 | etot = -8.53011310476403 +328000 ekin = 1.68988361976014 | erot = 1.24442310373763 | epot = -11.4644198283235 | etot = -8.53011310482578 +329000 ekin = 1.70729453548122 | erot = 1.30088738083626 | epot = -11.5382950211521 | etot = -8.53011310483462 +330000 ekin = 1.71977920215653 | erot = 1.36542606219528 | epot = -11.6153183691923 | etot = -8.53011310484046 +331000 ekin = 1.7271994815718 | erot = 1.43788972641168 | epot = -11.6952023128944 | etot = -8.53011310491089 +332000 ekin = 1.72935048705178 | erot = 1.51741015576131 | epot = -11.7768737478656 | etot = -8.53011310505251 +333000 ekin = 1.72589292388536 | erot = 1.60231164706421 | epot = -11.8583176761893 | etot = -8.53011310523976 +334000 ekin = 1.71641096845526 | erot = 1.69042382797069 | epot = -11.9369479018441 | etot = -8.53011310541811 +335000 ekin = 1.70061954221322 | erot = 1.77963047985444 | epot = -12.010363127601 | etot = -8.5301131055333 +336000 ekin = 1.67861266632182 | erot = 1.86835013660108 | epot = -12.0770759084894 | etot = -8.53011310556652 +337000 ekin = 1.65104084371354 | erot = 1.95564880215523 | epot = -12.1368027514031 | etot = -8.5301131055343 +338000 ekin = 1.61919653971752 | erot = 2.04088006325108 | epot = -12.190189708458 | etot = -8.53011310548938 +339000 ekin = 1.58494018858508 | erot = 2.12306951704665 | epot = -12.238122811097 | etot = -8.53011310546525 +340000 ekin = 1.55068751498696 | erot = 2.20045691490743 | epot = -12.2812575353507 | etot = -8.53011310545628 +341000 ekin = 1.51939352315548 | erot = 2.27052960843886 | epot = -12.3200362370415 | etot = -8.53011310544716 +342000 ekin = 1.49422831422776 | erot = 2.33048372011776 | epot = -12.3548251398142 | etot = -8.53011310546866 +343000 ekin = 1.47765440209368 | erot = 2.37774277923671 | epot = -12.3855102869164 | etot = -8.53011310558606 +344000 ekin = 1.47024986717927 | erot = 2.41039440931555 | epot = -12.4107573822795 | etot = -8.53011310578464 +345000 ekin = 1.4703254442581 | erot = 2.42787360989988 | epot = -12.4283121600592 | etot = -8.53011310590122 +346000 ekin = 1.47497435411168 | erot = 2.43200037641058 | epot = -12.4370878362722 | etot = -8.53011310574992 +347000 ekin = 1.48176297397457 | erot = 2.42757307622205 | epot = -12.4394491555202 | etot = -8.53011310532358 +348000 ekin = 1.48960567691877 | erot = 2.42152466454833 | epot = -12.4412434462867 | etot = -8.53011310481961 +349000 ekin = 1.49842206767879 | erot = 2.42094801211174 | epot = -12.449483184191 | etot = -8.53011310440048 +350000 ekin = 1.50804667267444 | erot = 2.43083585672827 | epot = -12.4689956337612 | etot = -8.53011310435853 +351000 ekin = 1.51733539244436 | erot = 2.45275056185542 | epot = -12.5001990588662 | etot = -8.53011310456645 +352000 ekin = 1.52440681732 | erot = 2.48551818836661 | epot = -12.5400381105947 | etot = -8.53011310490808 +353000 ekin = 1.52713336973071 | erot = 2.52632890408686 | epot = -12.5835753790747 | etot = -8.53011310525712 +354000 ekin = 1.52372188533753 | erot = 2.57191593401478 | epot = -12.6257509248866 | etot = -8.53011310553432 +355000 ekin = 1.51309115687089 | erot = 2.61929569219585 | epot = -12.6624999548058 | etot = -8.53011310573909 +356000 ekin = 1.49483332847629 | erot = 2.66580549560282 | epot = -12.690751930001 | etot = -8.53011310592193 +357000 ekin = 1.46901113664047 | erot = 2.70863650615431 | epot = -12.7077607489362 | etot = -8.5301131061414 +358000 ekin = 1.43592917031781 | erot = 2.74427787084649 | epot = -12.7103201475722 | etot = -8.53011310640789 +359000 ekin = 1.39610164165407 | erot = 2.76842107185796 | epot = -12.6946358201685 | etot = -8.5301131066565 +360000 ekin = 1.3504767265446 | erot = 2.77663698694861 | epot = -12.6572268202645 | etot = -8.53011310677133 +361000 ekin = 1.30076611042313 | erot = 2.76564868782872 | epot = -12.5965279049014 | etot = -8.53011310664958 +362000 ekin = 1.24961928501762 | erot = 2.73457480734076 | epot = -12.5143071986249 | etot = -8.53011310626656 +363000 ekin = 1.20045386452402 | erot = 2.68545051258155 | epot = -12.4160174827976 | etot = -8.530113105692 +364000 ekin = 1.157102610977 | erot = 2.62295556817078 | epot = -12.3101712839486 | etot = -8.53011310480086 +365000 ekin = 1.12337541340606 | erot = 2.55368748907328 | epot = -12.2071760067613 | etot = -8.53011310428193 +366000 ekin = 1.10127753424493 | erot = 2.48317695958238 | epot = -12.1145675977517 | etot = -8.53011310392434 +367000 ekin = 1.09158671746534 | erot = 2.41562896418526 | epot = -12.0373287854038 | etot = -8.53011310375322 +368000 ekin = 1.09395460107056 | erot = 2.35367302017297 | epot = -11.9777407249947 | etot = -8.53011310375121 +369000 ekin = 1.10707029824331 | erot = 2.29842564871272 | epot = -11.9356090508305 | etot = -8.53011310387444 +370000 ekin = 1.12891021359741 | erot = 2.24980412691876 | epot = -11.9088274446063 | etot = -8.53011310409015 +371000 ekin = 1.15702393729329 | erot = 2.20683986953329 | epot = -11.8939769111755 | etot = -8.53011310434893 +372000 ekin = 1.1888151292629 | erot = 2.16808122068957 | epot = -11.8870094545637 | etot = -8.53011310461122 +373000 ekin = 1.22180472347242 | erot = 2.13193560462625 | epot = -11.8838534329408 | etot = -8.5301131048421 +374000 ekin = 1.25386446213045 | erot = 2.0969644455036 | epot = -11.8809420126469 | etot = -8.53011310501288 +375000 ekin = 1.2834073568592 | erot = 2.06212828826987 | epot = -11.8756487502314 | etot = -8.53011310510234 +376000 ekin = 1.30952081504534 | erot = 2.02696442652639 | epot = -11.8665983466716 | etot = -8.53011310509989 +377000 ekin = 1.33202999726286 | erot = 1.99167753887158 | epot = -11.8538206411415 | etot = -8.53011310500704 +378000 ekin = 1.35148382625458 | erot = 1.95712256046334 | epot = -11.8387194915564 | etot = -8.5301131048385 +379000 ekin = 1.369064102421 | erot = 1.92466782261762 | epot = -11.82384502966 | etot = -8.53011310462137 +380000 ekin = 1.38611586816741 | erot = 1.89583861081395 | epot = -11.8120675838441 | etot = -8.53011310486269 +381000 ekin = 1.40217385032451 | erot = 1.87134526426162 | epot = -11.803632219315 | etot = -8.53011310472886 +382000 ekin = 1.41800173053399 | erot = 1.85196748545548 | epot = -11.8000823206103 | etot = -8.53011310462078 +383000 ekin = 1.43471626247799 | erot = 1.83825951701721 | epot = -11.8030888840428 | etot = -8.53011310454761 +384000 ekin = 1.45338249836178 | erot = 1.8303714900458 | epot = -11.8138670929096 | etot = -8.53011310450204 +385000 ekin = 1.47500130812885 | erot = 1.82815692745039 | epot = -11.8332713400434 | etot = -8.53011310446414 +386000 ekin = 1.50055250094717 | erot = 1.83139934862293 | epot = -11.8620649539819 | etot = -8.5301131044118 +387000 ekin = 1.53104646326555 | erot = 1.84005108459159 | epot = -11.9012106521924 | etot = -8.53011310433528 +388000 ekin = 1.56751609348179 | erot = 1.85434854378498 | epot = -11.9519777415169 | etot = -8.53011310425013 +389000 ekin = 1.61088446669801 | erot = 1.87469764895861 | epot = -12.0156952198589 | etot = -8.53011310420226 +390000 ekin = 1.66167288139125 | erot = 1.90128526220805 | epot = -12.0930712478648 | etot = -8.53011310426552 +391000 ekin = 1.71956364223298 | erot = 1.93346596746207 | epot = -12.1831427142166 | etot = -8.5301131045216 +392000 ekin = 1.78290672529176 | erot = 1.96909292130231 | epot = -12.2821127516394 | etot = -8.53011310504532 +393000 ekin = 1.84827871010929 | erot = 2.00406071425718 | epot = -12.3824525302018 | etot = -8.53011310583528 +394000 ekin = 1.91039848955051 | erot = 2.03249756432607 | epot = -12.4730091606569 | etot = -8.53011310678034 +395000 ekin = 1.9626508412109 | erot = 2.04794740083118 | epot = -12.540711349686 | etot = -8.53011310764391 +396000 ekin = 1.99833003479206 | erot = 2.0454869435874 | epot = -12.5739300865153 | etot = -8.53011310813587 +397000 ekin = 2.0123250581197 | erot = 2.02401360401976 | epot = -12.5664517701983 | etot = -8.53011310805884 +398000 ekin = 2.00252306207336 | erot = 1.98743944257818 | epot = -12.5200756120851 | etot = -8.53011310743354 +399000 ekin = 1.9701718559996 | erot = 1.94392108511941 | epot = -12.4442060476114 | etot = -8.5301131064924 +400000 ekin = 1.91900875366626 | erot = 1.90345223754713 | epot = -12.3525740967566 | etot = -8.53011310554319 +401000 ekin = 1.85370867757513 | erot = 1.87511245492143 | epot = -12.2589342373134 | etot = -8.53011310481684 +402000 ekin = 1.77849786328493 | erot = 1.86519132439144 | epot = -12.1738022920808 | etot = -8.53011310440448 +403000 ekin = 1.69647765085585 | erot = 1.87662651194791 | epot = -12.1032172670431 | etot = -8.53011310423931 +404000 ekin = 1.60979304525873 | erot = 1.90948179463012 | epot = -12.0493879441535 | etot = -8.53011310426464 +405000 ekin = 1.52031831980354 | erot = 1.96148591335594 | epot = -12.0119173375337 | etot = -8.53011310437419 +406000 ekin = 1.43052069774053 | erot = 2.02884810423333 | epot = -11.9894819063522 | etot = -8.53011310437832 +407000 ekin = 1.34451311631117 | erot = 2.10762662358732 | epot = -11.9822528435709 | etot = -8.53011310367242 +408000 ekin = 1.27105659597624 | erot = 2.19486129527893 | epot = -11.9960309945651 | etot = -8.53011310330992 +409000 ekin = 1.13887966167889 | erot = 2.29455518643042 | epot = -11.9635479631131 | etot = -8.5301131150038 +410000 ekin = 1.06340398971496 | erot = 2.43839727639424 | epot = -12.0319143782641 | etot = -8.53011311215495 +411000 ekin = 1.12994363439163 | erot = 2.56530077013229 | epot = -12.2253575154564 | etot = -8.53011311093251 +412000 ekin = 1.18303314251565 | erot = 2.647961367565 | epot = -12.3611076219087 | etot = -8.53011311182804 +413000 ekin = 1.26155297788366 | erot = 2.71721639006694 | epot = -12.5088824809558 | etot = -8.5301131130052 +414000 ekin = 1.3509234915351 | erot = 2.76712696986896 | epot = -12.6481635756115 | etot = -8.53011311420743 +415000 ekin = 1.43876511602364 | erot = 2.79254621486906 | epot = -12.7614244458774 | etot = -8.53011311498468 +416000 ekin = 1.51568555880255 | erot = 2.79087249527984 | epot = -12.8366711691915 | etot = -8.53011311510912 +417000 ekin = 1.5774627292708 | erot = 2.76317937782424 | epot = -12.8707552217669 | etot = -8.53011311467188 +418000 ekin = 1.62492964319337 | erot = 2.71407200335297 | epot = -12.8691147604605 | etot = -8.53011311391414 +419000 ekin = 1.66144511720312 | erot = 2.6494832898614 | epot = -12.8410415202834 | etot = -8.53011311321891 +420000 ekin = 1.69059185762612 | erot = 2.57483616462589 | epot = -12.7955411349095 | etot = -8.53011311265746 +421000 ekin = 1.71537831168895 | erot = 2.4944848692942 | epot = -12.7399762932607 | etot = -8.53011311227753 +422000 ekin = 1.73777830628493 | erot = 2.41134366235769 | epot = -12.6792350807076 | etot = -8.53011311206497 +423000 ekin = 1.75875042276785 | erot = 2.32696083577665 | epot = -12.6158243705244 | etot = -8.5301131119799 +424000 ekin = 1.77846413727746 | erot = 2.24181259776204 | epot = -12.5503898470151 | etot = -8.53011311197561 +425000 ekin = 1.79665710139619 | erot = 2.15579348528976 | epot = -12.4825636984917 | etot = -8.53011311180572 +426000 ekin = 1.81317574252429 | erot = 2.0690861526654 | epot = -12.4123750070692 | etot = -8.53011311187953 +427000 ekin = 1.82711019090163 | erot = 1.98123134137931 | epot = -12.3384546442035 | etot = -8.53011311192255 +428000 ekin = 1.83751691854821 | erot = 1.89199984736734 | epot = -12.2596298778276 | etot = -8.53011311191205 +429000 ekin = 1.84368310695259 | erot = 1.80177215302921 | epot = -12.1755683718219 | etot = -8.53011311184013 +430000 ekin = 1.84519909790049 | erot = 1.71159843544078 | epot = -12.0869106450535 | etot = -8.53011311171223 +431000 ekin = 1.8419824729196 | erot = 1.62310758133309 | epot = -11.9952031657953 | etot = -8.53011311154265 +432000 ekin = 1.83426509469808 | erot = 1.5384228551188 | epot = -11.9028010611701 | etot = -8.53011311135323 +433000 ekin = 1.82255993369577 | erot = 1.46009341020983 | epot = -11.8127664550844 | etot = -8.53011311117885 +434000 ekin = 1.8075108581923 | erot = 1.39007773702003 | epot = -11.7277017062243 | etot = -8.53011311101194 +435000 ekin = 1.78989394282613 | erot = 1.32998390314055 | epot = -11.6499909568369 | etot = -8.53011311087023 +436000 ekin = 1.77056724604991 | erot = 1.28100064172276 | epot = -11.5816809985409 | etot = -8.53011311076826 +437000 ekin = 1.75036829512574 | erot = 1.24377047064084 | epot = -11.5242518764822 | etot = -8.53011311071567 +438000 ekin = 1.73003454471314 | erot = 1.21832954508395 | epot = -11.4784772005229 | etot = -8.53011311072585 +439000 ekin = 1.71009916119256 | erot = 1.20407719866515 | epot = -11.444289470637 | etot = -8.53011311077925 +440000 ekin = 1.6909660003284 | erot = 1.19975997138874 | epot = -11.4208390825869 | etot = -8.53011311086975 +441000 ekin = 1.67263636924185 | erot = 1.20336882729014 | epot = -11.4061183077393 | etot = -8.5301131112073 +442000 ekin = 1.65454003555858 | erot = 1.21209014500598 | epot = -11.3967432919143 | etot = -8.5301131113497 +443000 ekin = 1.63689233562187 | erot = 1.22351444913945 | epot = -11.3905198962988 | etot = -8.5301131115375 +444000 ekin = 1.61963083195094 | erot = 1.23489712396683 | epot = -11.3846410676151 | etot = -8.53011311169732 +445000 ekin = 1.60286309976439 | erot = 1.24366705310612 | epot = -11.3766432646847 | etot = -8.53011311181423 +446000 ekin = 1.58694903183935 | erot = 1.24767642065071 | epot = -11.3647385643679 | etot = -8.53011311187784 +447000 ekin = 1.57243059659248 | erot = 1.24537195304132 | epot = -11.3479156615357 | etot = -8.53011311190193 +448000 ekin = 1.56000091269129 | erot = 1.23594098261454 | epot = -11.3260550071527 | etot = -8.53011311184687 +449000 ekin = 1.55055832679574 | erot = 1.21941073242635 | epot = -11.3000821709566 | etot = -8.53011311173451 +450000 ekin = 1.54505171747098 | erot = 1.19665850060397 | epot = -11.2718233296474 | etot = -8.53011311157245 +451000 ekin = 1.54440025802266 | erot = 1.16936613900744 | epot = -11.2438795084035 | etot = -8.53011311137341 +452000 ekin = 1.54941604020834 | erot = 1.13989972058507 | epot = -11.2194288719472 | etot = -8.5301131111538 +453000 ekin = 1.56073218733759 | erot = 1.11111895993854 | epot = -11.2019642583116 | etot = -8.5301131110355 +454000 ekin = 1.57840116510927 | erot = 1.08594835310017 | epot = -11.1944626290754 | etot = -8.53011311086592 +455000 ekin = 1.601995726954 | erot = 1.06716100526496 | epot = -11.1992698429482 | etot = -8.53011311072925 +456000 ekin = 1.63102931523391 | erot = 1.05734777204784 | epot = -11.2184901979328 | etot = -8.53011311065108 +457000 ekin = 1.66465491829929 | erot = 1.05859720823486 | epot = -11.25336523717 | etot = -8.53011311063581 +458000 ekin = 1.70170935167593 | erot = 1.07231891092448 | epot = -11.3041413732864 | etot = -8.53011311068599 +459000 ekin = 1.7407794029015 | erot = 1.09914653783994 | epot = -11.3700390515413 | etot = -8.53011311079982 +460000 ekin = 1.78028759701322 | erot = 1.13890397190042 | epot = -11.4493046798752 | etot = -8.5301131109616 +461000 ekin = 1.81860197242949 | erot = 1.19067102876365 | epot = -11.539386112353 | etot = -8.53011311115989 +462000 ekin = 1.85415391005744 | erot = 1.25289584358374 | epot = -11.6371628650211 | etot = -8.53011311137988 +463000 ekin = 1.88554792944948 | erot = 1.3235024717984 | epot = -11.739163512856 | etot = -8.53011311160815 +464000 ekin = 1.91164681845144 | erot = 1.40002350523732 | epot = -11.8417834355221 | etot = -8.5301131118333 +465000 ekin = 1.93162421638187 | erot = 1.47973907161313 | epot = -11.9414764000402 | etot = -8.5301131120452 +466000 ekin = 1.94498500126989 | erot = 1.55982523463937 | epot = -12.0349233481435 | etot = -8.53011311223423 +467000 ekin = 1.95156193454112 | erot = 1.63751691044159 | epot = -12.1191919573735 | etot = -8.53011311239078 +468000 ekin = 1.95150012931985 | erot = 1.71026532451092 | epot = -12.1918785663379 | etot = -8.53011311250716 +469000 ekin = 1.94523738406744 | erot = 1.7759064103245 | epot = -12.2512569069617 | etot = -8.53011311256974 +470000 ekin = 1.93348412613007 | erot = 1.83286583557099 | epot = -12.2964630742777 | etot = -8.53011311257661 +471000 ekin = 1.91719298127392 | erot = 1.88021093656515 | epot = -12.3275170303717 | etot = -8.53011311253268 +472000 ekin = 1.89750254537298 | erot = 1.91763317251143 | epot = -12.3452488303327 | etot = -8.53011311244833 +473000 ekin = 1.87564239828497 | erot = 1.94536290421053 | epot = -12.3511184148396 | etot = -8.53011311234412 +474000 ekin = 1.85280042951765 | erot = 1.96399915053207 | epot = -12.3469126922909 | etot = -8.53011311224115 +475000 ekin = 1.82997212692377 | erot = 1.9743433684352 | epot = -12.3344286075125 | etot = -8.53011311215353 +476000 ekin = 1.80782991664007 | erot = 1.97731520040876 | epot = -12.3152582291305 | etot = -8.53011311208166 +477000 ekin = 1.78665653477381 | erot = 1.97399991971349 | epot = -12.2907695664986 | etot = -8.53011311201126 +478000 ekin = 1.76636958091236 | erot = 1.9658140143465 | epot = -12.2622967071795 | etot = -8.5301131119206 +479000 ekin = 1.74662905134933 | erot = 1.95469632259907 | epot = -12.2314384857418 | etot = -8.53011311179338 +480000 ekin = 1.72698437878123 | erot = 1.9431887679411 | epot = -12.2002862583526 | etot = -8.53011311163024 +481000 ekin = 1.70700474377422 | erot = 1.93430214046924 | epot = -12.1714199956951 | etot = -8.53011311145166 +482000 ekin = 1.68635525356891 | erot = 1.93116021406649 | epot = -12.147628578926 | etot = -8.53011311129063 +483000 ekin = 1.66481678021135 | erot = 1.93652118160286 | epot = -12.1314510729945 | etot = -8.53011311118025 +484000 ekin = 1.6422770599304 | erot = 1.95232513145262 | epot = -12.124715302525 | etot = -8.53011311114202 +485000 ekin = 1.61901562080308 | erot = 1.97931073968796 | epot = -12.1284394716016 | etot = -8.53011311111052 +486000 ekin = 1.59577228279584 | erot = 2.01691499832701 | epot = -12.1428003923466 | etot = -8.53011311122377 +487000 ekin = 1.5726976073156 | erot = 2.06349128121944 | epot = -12.166302000014 | etot = -8.53011311147895 +488000 ekin = 1.54979615320385 | erot = 2.11629853285763 | epot = -12.1962077977342 | etot = -8.53011311167275 +489000 ekin = 1.52793571893382 | erot = 2.17194986392789 | epot = -12.2299986947139 | etot = -8.53011311185218 +490000 ekin = 1.50872304470115 | erot = 2.22662776559679 | epot = -12.2654639222932 | etot = -8.53011311199526 +491000 ekin = 1.49451121745785 | erot = 2.27632252256503 | epot = -12.3009468521215 | etot = -8.53011311209864 +492000 ekin = 1.48823109411415 | erot = 2.31702824482111 | epot = -12.3353724511176 | etot = -8.53011311218238 +493000 ekin = 1.49518318209271 | erot = 2.34597345237406 | epot = -12.3712697461198 | etot = -8.53011311165304 +494000 ekin = 1.51845501165919 | erot = 2.36107283299034 | epot = -12.4096409568443 | etot = -8.53011311219474 +495000 ekin = 1.55341225536929 | erot = 2.35806327093555 | epot = -12.4415886369949 | etot = -8.53011311069005 +496000 ekin = 1.60682048122344 | erot = 2.3340672304928 | epot = -12.4710008246549 | etot = -8.53011311293862 +497000 ekin = 1.66595753312185 | erot = 2.29001283524384 | epot = -12.4860834812982 | etot = -8.53011311293247 +498000 ekin = 1.73079985976382 | erot = 2.22455469203371 | epot = -12.4854676647411 | etot = -8.53011311294352 +499000 ekin = 1.79938231063312 | erot = 2.13975923972669 | epot = -12.4692546631917 | etot = -8.53011311283187 +500000 ekin = 1.86459078890622 | erot = 2.04085817004223 | epot = -12.4355620715728 | etot = -8.53011311262434 +501000 ekin = 1.92273434830708 | erot = 1.93494769033077 | epot = -12.3877951508818 | etot = -8.53011311224398 +502000 ekin = 1.97166638935067 | erot = 1.83018302876625 | epot = -12.3319625299275 | etot = -8.53011311181053 +503000 ekin = 2.01030983363916 | erot = 1.73409537515224 | epot = -12.2745183201332 | etot = -8.53011311134178 +504000 ekin = 2.03852387656583 | erot = 1.65386645969169 | epot = -12.2225034472042 | etot = -8.53011311094666 +505000 ekin = 2.05672143890249 | erot = 1.5951695431987 | epot = -12.182004092794 | etot = -8.53011311069283 +506000 ekin = 2.06541322369564 | erot = 1.56133329124062 | epot = -12.1568596255599 | etot = -8.53011311062362 +507000 ekin = 2.06489683747097 | erot = 1.55298683202232 | epot = -12.1479967802499 | etot = -8.53011311075663 +508000 ekin = 2.05510409508288 | erot = 1.56796083678997 | epot = -12.1531780429542 | etot = -8.53011311108135 +509000 ekin = 2.03562755335735 | erot = 1.6014641311663 | epot = -12.1672047960773 | etot = -8.53011311155361 +510000 ekin = 2.0059290836208 | erot = 1.64659845424943 | epot = -12.1826406499626 | etot = -8.53011311209234 +511000 ekin = 1.9656968001201 | erot = 1.69527026509278 | epot = -12.1910801777999 | etot = -8.53011311258698 +512000 ekin = 1.91525552531113 | erot = 1.73945419950567 | epot = -12.1848228377404 | etot = -8.53011311292356 +513000 ekin = 1.85587746893783 | erot = 1.77257277562009 | epot = -12.1585633575815 | etot = -8.53011311302363 +514000 ekin = 1.78983987134752 | erot = 1.79060149181183 | epot = -12.1105544760337 | etot = -8.53011311287438 +515000 ekin = 1.72017129591416 | erot = 1.7925412010645 | epot = -12.0428256095076 | etot = -8.53011311252899 +516000 ekin = 1.65040042950193 | erot = 1.78043480915809 | epot = -11.9609483505948 | etot = -8.53011311193474 +517000 ekin = 1.58404068014581 | erot = 1.75852731252286 | epot = -11.8726811041263 | etot = -8.5301131114576 +518000 ekin = 1.52414481737364 | erot = 1.73170053428691 | epot = -11.7859584626124 | etot = -8.53011311095184 +519000 ekin = 1.47366796925332 | erot = 1.70507688462324 | epot = -11.7088579644956 | etot = -8.53011311061909 +520000 ekin = 1.4336537817973 | erot = 1.68280907302141 | epot = -11.646575965153 | etot = -8.53011311033426 +521000 ekin = 1.40489785043721 | erot = 1.66827026613384 | epot = -11.6032812266553 | etot = -8.53011311008428 +522000 ekin = 1.38811259815573 | erot = 1.66372628764844 | epot = -11.5819519960241 | etot = -8.53011311021994 +523000 ekin = 1.38336778490129 | erot = 1.66945534863268 | epot = -11.58293624363 | etot = -8.53011311009606 +524000 ekin = 1.3913126502459 | erot = 1.68543796397887 | epot = -11.6068637243454 | etot = -8.53011311012059 +525000 ekin = 1.41205700478391 | erot = 1.71025646512276 | epot = -11.6524265802486 | etot = -8.53011311034194 +526000 ekin = 1.44455820368128 | erot = 1.7408487288601 | epot = -11.7155200433033 | etot = -8.5301131107619 +527000 ekin = 1.48642955052829 | erot = 1.77280714509435 | epot = -11.7893498069414 | etot = -8.53011311131872 +528000 ekin = 1.53418163870907 | erot = 1.80110112523955 | epot = -11.8653958758444 | etot = -8.53011311189574 +529000 ekin = 1.58386362601825 | erot = 1.82112172078186 | epot = -11.9350984591552 | etot = -8.53011311235511 +530000 ekin = 1.63189696415521 | erot = 1.82978202390416 | epot = -11.9917921006438 | etot = -8.53011311258448 +531000 ekin = 1.67581590193207 | erot = 1.82633306141048 | epot = -12.0322620756507 | etot = -8.5301131123082 +532000 ekin = 1.7158553823674 | erot = 1.81520910325175 | epot = -12.0611775977952 | etot = -8.53011311217609 +533000 ekin = 1.75284097660823 | erot = 1.80146596914443 | epot = -12.0844200576741 | etot = -8.53011311192148 +534000 ekin = 1.78745390743537 | erot = 1.78869315999008 | epot = -12.1062601790962 | etot = -8.53011311167072 +535000 ekin = 1.8206503812731 | erot = 1.780275917528 | epot = -12.1310394103256 | etot = -8.53011311152449 +536000 ekin = 1.85299611868859 | erot = 1.77858522848976 | epot = -12.1616944587211 | etot = -8.53011311154276 +537000 ekin = 1.88407496145215 | erot = 1.78428087125629 | epot = -12.1984689444103 | etot = -8.53011311170191 +538000 ekin = 1.91279454454533 | erot = 1.79686892929592 | epot = -12.2397765856266 | etot = -8.53011311178537 +539000 ekin = 1.93839394839969 | erot = 1.81622314390843 | epot = -12.2847302042266 | etot = -8.53011311191852 +540000 ekin = 1.95998962534144 | erot = 1.84168603209833 | epot = -12.3317887694832 | etot = -8.53011311204347 +541000 ekin = 1.97685104517888 | erot = 1.87234426277005 | epot = -12.3793084201202 | etot = -8.53011311217123 +542000 ekin = 1.98798216003479 | erot = 1.90711972835206 | epot = -12.4252150005513 | etot = -8.53011311216449 +543000 ekin = 1.99396475052983 | erot = 1.945576946181 | epot = -12.4696548087713 | etot = -8.53011311206048 +544000 ekin = 1.99659195334791 | erot = 1.98768793524451 | epot = -12.5143930004874 | etot = -8.53011311189503 +545000 ekin = 1.99841939299606 | erot = 2.03351546468472 | epot = -12.5620479694138 | etot = -8.53011311173304 +546000 ekin = 2.00223379008667 | erot = 2.0827823942969 | epot = -12.6151292960316 | etot = -8.53011311164803 +547000 ekin = 2.01043375036019 | erot = 2.13441666463564 | epot = -12.674963526692 | etot = -8.53011311169613 +548000 ekin = 2.02454142532241 | erot = 2.18636947292415 | epot = -12.7410240101592 | etot = -8.53011311191265 +549000 ekin = 2.04472650265224 | erot = 2.23524716352228 | epot = -12.8100867784561 | etot = -8.53011311228159 +550000 ekin = 2.06971706084028 | erot = 2.27669143349774 | epot = -12.8765216070943 | etot = -8.53011311275624 +551000 ekin = 2.09694987343594 | erot = 2.30602592213473 | epot = -12.9330889088326 | etot = -8.53011311326193 +552000 ekin = 2.12288123765233 | erot = 2.31896388909698 | epot = -12.9719582404551 | etot = -8.53011311370584 +553000 ekin = 2.14351313995335 | erot = 2.31240753793649 | epot = -12.9860337918829 | etot = -8.53011311399303 +554000 ekin = 2.15523965907907 | erot = 2.28547313898653 | epot = -12.9708259121304 | etot = -8.53011311406476 +555000 ekin = 2.15534485410926 | erot = 2.23961985935181 | epot = -12.9250778273599 | etot = -8.53011311389882 +556000 ekin = 2.14242415869296 | erot = 2.17853141058428 | epot = -12.8510686828015 | etot = -8.53011311352426 +557000 ekin = 2.11652525560435 | erot = 2.1075590112211 | epot = -12.7541973798358 | etot = -8.5301131130104 +558000 ekin = 2.07899262360117 | erot = 2.03287016333855 | epot = -12.6419758993834 | etot = -8.53011311244369 +559000 ekin = 2.0320952570691 | erot = 1.96055588826784 | epot = -12.5227642572393 | etot = -8.53011311190237 +560000 ekin = 1.97856970493128 | erot = 1.89593544894334 | epot = -12.4046182653067 | etot = -8.5301131114321 +561000 ekin = 1.92120586059015 | erot = 1.84318662679526 | epot = -12.2945055984573 | etot = -8.53011311107193 +562000 ekin = 1.86248053377607 | erot = 1.8052511136239 | epot = -12.1978447582136 | etot = -8.53011311081363 +563000 ekin = 1.8044056602921 | erot = 1.78397358726299 | epot = -12.1184923582038 | etot = -8.53011311064866 +564000 ekin = 1.74859757239431 | erot = 1.78025486278411 | epot = -12.0589655457279 | etot = -8.53011311054952 +565000 ekin = 1.69697420506686 | erot = 1.79398971152769 | epot = -12.0210770271779 | etot = -8.53011311058339 +566000 ekin = 1.64969612949606 | erot = 1.82405026339996 | epot = -12.0038595036661 | etot = -8.53011311077008 +567000 ekin = 1.60592346389133 | erot = 1.86815174766649 | epot = -12.0041883226168 | etot = -8.53011311105901 +568000 ekin = 1.56447342355334 | erot = 1.9229510651846 | epot = -12.017537600017 | etot = -8.5301131112791 +569000 ekin = 1.5249189399058 | erot = 1.9848167243289 | epot = -12.0398487760181 | etot = -8.53011311178338 +570000 ekin = 1.48563885354617 | erot = 2.04789795967133 | epot = -12.0636499255003 | etot = -8.5301131122828 +571000 ekin = 1.44514780819869 | erot = 2.10567642130785 | epot = -12.0809373422384 | etot = -8.53011311273184 +572000 ekin = 1.40265340711305 | erot = 2.15189441844554 | epot = -12.0846609385934 | etot = -8.53011311303485 +573000 ekin = 1.35831475977169 | erot = 2.18135236040309 | epot = -12.0697802333439 | etot = -8.53011311316915 +574000 ekin = 1.31325665398762 | erot = 2.19054857027398 | epot = -12.033918337377 | etot = -8.53011311311536 +575000 ekin = 1.26941751353478 | erot = 2.17808969341531 | epot = -11.9776203199914 | etot = -8.53011311304127 +576000 ekin = 1.22896606046744 | erot = 2.14379444928284 | epot = -11.9028736225321 | etot = -8.53011311278182 +577000 ekin = 1.19393185424958 | erot = 2.08947552578937 | epot = -11.8135204923717 | etot = -8.53011311233275 +578000 ekin = 1.16652110218135 | erot = 2.01971345754357 | epot = -11.7163476715595 | etot = -8.53011311183457 +579000 ekin = 1.14855907858584 | erot = 1.94028096237537 | epot = -11.6189531523163 | etot = -8.53011311135512 +580000 ekin = 1.14121418715426 | erot = 1.85735567591632 | epot = -11.5286829740285 | etot = -8.53011311095796 +581000 ekin = 1.14478819464611 | erot = 1.7767355740351 | epot = -11.4516368793735 | etot = -8.53011311069233 +582000 ekin = 1.15860725310189 | erot = 1.70317164276779 | epot = -11.391892006456 | etot = -8.53011311058632 +583000 ekin = 1.18104542316811 | erot = 1.63989823949237 | epot = -11.3510567733034 | etot = -8.53011311064297 +584000 ekin = 1.20969611011887 | erot = 1.58840206182665 | epot = -11.3282112827866 | etot = -8.53011311084111 +585000 ekin = 1.24168069892305 | erot = 1.54843600705948 | epot = -11.3202298171212 | etot = -8.53011311113868 +586000 ekin = 1.2740546840078 | erot = 1.51825728966861 | epot = -11.3224250851562 | etot = -8.53011311147982 +587000 ekin = 1.30424737194179 | erot = 1.49504623591216 | epot = -11.3294067196582 | etot = -8.53011311180426 +588000 ekin = 1.33045790147862 | erot = 1.47543949669554 | epot = -11.336010510232 | etot = -8.53011311205788 +589000 ekin = 1.35193228855922 | erot = 1.45609131903564 | epot = -11.3381367197977 | etot = -8.53011311220281 +590000 ekin = 1.3690637353216 | erot = 1.43416814795309 | epot = -11.3333449954988 | etot = -8.53011311222415 +591000 ekin = 1.38329049901086 | erot = 1.40769463798183 | epot = -11.3210982491251 | etot = -8.53011311213237 +592000 ekin = 1.39680526625229 | erot = 1.37570509646357 | epot = -11.3026234746754 | etot = -8.5301131119595 +593000 ekin = 1.41212834900077 | erot = 1.33820418780231 | epot = -11.2804456485532 | etot = -8.53011311175016 +594000 ekin = 1.43162615781853 | erot = 1.295986417953 | epot = -11.2577256873211 | etot = -8.53011311154953 +595000 ekin = 1.45706677221744 | erot = 1.250391132337 | epot = -11.2375710159481 | etot = -8.53011311139362 +596000 ekin = 1.48935058064689 | erot = 1.20330184638379 | epot = -11.222765538265 | etot = -8.53011311123432 +597000 ekin = 1.52837107420579 | erot = 1.15683058607483 | epot = -11.2153147714789 | etot = -8.53011311119825 +598000 ekin = 1.57294993725724 | erot = 1.11287817711154 | epot = -11.2159412255862 | etot = -8.53011311121744 +599000 ekin = 1.62105272044028 | erot = 1.07333264838417 | epot = -11.2244984800962 | etot = -8.5301131112717 +600000 ekin = 1.67007785978927 | erot = 1.04007259181371 | epot = -11.2402635629414 | etot = -8.53011311133838 +601000 ekin = 1.71718069772665 | erot = 1.01497757077084 | epot = -11.2622713798937 | etot = -8.53011311139617 +602000 ekin = 1.75956754279021 | erot = 0.999928377461801 | epot = -11.2896090316898 | etot = -8.53011311143777 +603000 ekin = 1.79477210700253 | erot = 0.996719273887856 | epot = -11.3216044923427 | etot = -8.53011311145232 +604000 ekin = 1.82082157915211 | erot = 1.00697983034402 | epot = -11.3579145210094 | etot = -8.53011311151329 +605000 ekin = 1.83582223390645 | erot = 1.03147611611005 | epot = -11.3974114615043 | etot = -8.53011311148779 +606000 ekin = 1.8387140851627 | erot = 1.07115549980537 | epot = -11.4399826962261 | etot = -8.53011311125804 +607000 ekin = 1.83011347633669 | erot = 1.1264712109122 | epot = -11.4866977985761 | etot = -8.53011311132725 +608000 ekin = 1.8102394194917 | erot = 1.19707781561461 | epot = -11.537430346509 | etot = -8.53011311140273 +609000 ekin = 1.77867265022502 | erot = 1.28228554239947 | epot = -11.5910713041089 | etot = -8.53011311148444 +610000 ekin = 1.73547793526514 | erot = 1.38091511477527 | epot = -11.6465061616037 | etot = -8.53011311156333 +611000 ekin = 1.68128247270891 | erot = 1.49134780299442 | epot = -11.7027433873263 | etot = -8.53011311162298 +612000 ekin = 1.61741095621708 | erot = 1.6116145640346 | epot = -11.7591386318972 | etot = -8.53011311164548 +613000 ekin = 1.54603198036209 | erot = 1.73948721912068 | epot = -11.8156323111033 | etot = -8.53011311162058 +614000 ekin = 1.47024512206905 | erot = 1.87249022213823 | epot = -11.8728484558906 | etot = -8.53011311168336 +615000 ekin = 1.39417329366749 | erot = 2.00621352658744 | epot = -11.9304999319624 | etot = -8.53011311170745 +616000 ekin = 1.32190082987795 | erot = 2.13583847737815 | epot = -11.9878524190141 | etot = -8.53011311175805 +617000 ekin = 1.25724259788341 | erot = 2.25683214183279 | epot = -12.044187851591 | etot = -8.53011311187476 +618000 ekin = 1.20346368463748 | erot = 2.36421640891362 | epot = -12.0977932056388 | etot = -8.53011311208765 +619000 ekin = 1.1627837357839 | erot = 2.45267600796726 | epot = -12.1455728561444 | etot = -8.53011311239321 +620000 ekin = 1.13605929310698 | erot = 2.51695592467634 | epot = -12.1831283305324 | etot = -8.53011311274907 +621000 ekin = 1.12273498783652 | erot = 2.5525832487945 | epot = -12.2054313497004 | etot = -8.53011311306935 +622000 ekin = 1.12111468633955 | erot = 2.55686207164847 | epot = -12.2080898712351 | etot = -8.53011311324703 +623000 ekin = 1.12887388452668 | erot = 2.52989511158575 | epot = -12.1888821093023 | etot = -8.53011311318982 +624000 ekin = 1.14366711341982 | erot = 2.47526890170086 | epot = -12.1490491279779 | etot = -8.53011311285719 +625000 ekin = 1.16365333268032 | erot = 2.40007033438084 | epot = -12.0938367793385 | etot = -8.53011311227731 +626000 ekin = 1.1877796889279 | erot = 2.31409540899866 | epot = -12.0319882094815 | etot = -8.53011311155492 +627000 ekin = 1.21575247625636 | erot = 2.22841508882912 | epot = -11.974280675903 | etot = -8.53011311081753 +628000 ekin = 1.24777701345755 | erot = 2.15375689269322 | epot = -11.9316470163397 | etot = -8.53011311018898 +629000 ekin = 1.28416743273269 | erot = 2.0990785591541 | epot = -11.9133591016497 | etot = -8.53011310976295 +630000 ekin = 1.3249536049168 | erot = 2.07058701615878 | epot = -11.9256537306725 | etot = -8.53011310959688 +631000 ekin = 1.36955506517704 | erot = 2.07123416093218 | epot = -11.970902335822 | etot = -8.53011310971283 +632000 ekin = 1.41660411980783 | erot = 2.10067869858403 | epot = -12.0473959281541 | etot = -8.53011310976226 +633000 ekin = 1.46471660335937 | erot = 2.15728920673495 | epot = -12.1521189203372 | etot = -8.53011311024285 +634000 ekin = 1.5116423330738 | erot = 2.23677755842588 | epot = -12.2785330023927 | etot = -8.53011311089301 +635000 ekin = 1.55431486763673 | erot = 2.33246650108445 | epot = -12.4168944816116 | etot = -8.5301131128904 +636000 ekin = 1.58749795609299 | erot = 2.43289415005748 | epot = -12.5505052200571 | etot = -8.53011311390666 +637000 ekin = 1.60559044461902 | erot = 2.52510908162173 | epot = -12.6608126409174 | etot = -8.53011311467662 +638000 ekin = 1.60593314361717 | erot = 2.60108258773675 | epot = -12.7371288464172 | etot = -8.53011311506329 +639000 ekin = 1.58800768940635 | erot = 2.65612694656144 | epot = -12.7742477510045 | etot = -8.53011311503675 +640000 ekin = 1.55357432529172 | erot = 2.68914087075659 | epot = -12.7728283107672 | etot = -8.53011311471885 +641000 ekin = 1.50594258808403 | erot = 2.70186118673875 | epot = -12.7379168890284 | etot = -8.53011311420558 +642000 ekin = 1.44931462465822 | erot = 2.69765625484959 | epot = -12.6770839931722 | etot = -8.53011311366437 +643000 ekin = 1.38808387569846 | erot = 2.68019687245753 | epot = -12.5983938613571 | etot = -8.53011311320107 +644000 ekin = 1.32616709544766 | erot = 2.65251028990018 | epot = -12.5087904982142 | etot = -8.53011311286636 +645000 ekin = 1.26675082971288 | erot = 2.61647581101856 | epot = -12.4133397533931 | etot = -8.53011311266169 +646000 ekin = 1.21233854698239 | erot = 2.57274112824624 | epot = -12.3151927877793 | etot = -8.53011311255063 +647000 ekin = 1.16530705824513 | erot = 2.5217462541534 | epot = -12.2171664245162 | etot = -8.53011311211771 +648000 ekin = 1.12796239477798 | erot = 2.46431327603398 | epot = -12.122388782996 | etot = -8.53011311218402 +649000 ekin = 1.10135546654543 | erot = 2.39865320679758 | epot = -12.0301217854793 | etot = -8.53011311213631 +650000 ekin = 1.08691260033709 | erot = 2.32393477717278 | epot = -11.9409604894842 | etot = -8.53011311197434 +651000 ekin = 1.08628079617831 | erot = 2.24073961887863 | epot = -11.8571335268109 | etot = -8.53011311175398 +652000 ekin = 1.10075131990634 | erot = 2.15085977532613 | epot = -11.7817242067922 | etot = -8.53011311155974 +653000 ekin = 1.13059734565321 | erot = 2.05677047633761 | epot = -11.7174809334498 | etot = -8.53011311145893 +654000 ekin = 1.17466906494936 | erot = 1.96105944317186 | epot = -11.6658416195893 | etot = -8.53011311146811 +655000 ekin = 1.23047347721873 | erot = 1.86606271801435 | epot = -11.6266493067841 | etot = -8.53011311155106 +656000 ekin = 1.29470000779083 | erot = 1.77378178161793 | epot = -11.5985949010557 | etot = -8.53011311164694 +657000 ekin = 1.36393161431824 | erot = 1.68598333612987 | epot = -11.5800280621529 | etot = -8.53011311170483 +658000 ekin = 1.46427470176043 | erot = 1.51772157409014 | epot = -11.5121093881302 | etot = -8.53011311227959 +659000 ekin = 1.64802750939022 | erot = 1.39327336689376 | epot = -11.5714140171067 | etot = -8.53011314082273 +660000 ekin = 1.73185850257778 | erot = 1.3295411594665 | epot = -11.5915127822407 | etot = -8.53011312019639 +661000 ekin = 1.80627684680885 | erot = 1.27623279768931 | epot = -11.6126227646866 | etot = -8.53011312018847 +662000 ekin = 1.87475382732446 | erot = 1.23350073992408 | epot = -11.6383676874432 | etot = -8.53011312019471 +663000 ekin = 1.93633534016178 | erot = 1.20171441189947 | epot = -11.6681628722886 | etot = -8.53011312022732 +664000 ekin = 1.99014964301494 | erot = 1.18083533498295 | epot = -11.7010980982892 | etot = -8.53011312029132 +665000 ekin = 2.03529479420636 | erot = 1.17046521671664 | epot = -11.735873131308 | etot = -8.53011312038497 +666000 ekin = 2.07079068067167 | erot = 1.16992318050101 | epot = -11.7708269816743 | etot = -8.5301131205016 +667000 ekin = 2.09559163008676 | erot = 1.17833553455765 | epot = -11.8040402852757 | etot = -8.53011312063128 +668000 ekin = 2.10864748671423 | erot = 1.19472204260171 | epot = -11.8334826500796 | etot = -8.53011312076368 +669000 ekin = 2.10899520333026 | erot = 1.21806343010007 | epot = -11.8571717543206 | etot = -8.53011312089023 +670000 ekin = 2.09586141354525 | erot = 1.24733872817407 | epot = -11.8733132627235 | etot = -8.53011312100421 +671000 ekin = 2.068762787098 | erot = 1.28153124625685 | epot = -11.8804071544553 | etot = -8.5301131211004 +672000 ekin = 2.02760595017448 | erot = 1.31961745604762 | epot = -11.8773365273931 | etot = -8.53011312117098 +673000 ekin = 1.97280574595705 | erot = 1.36056605412237 | epot = -11.8634849212816 | etot = -8.53011312120221 +674000 ekin = 1.90544539354424 | erot = 1.40337348376535 | epot = -11.8389319984827 | etot = -8.53011312117309 +675000 ekin = 1.82748035868504 | erot = 1.44714139190344 | epot = -11.8047348716492 | etot = -8.53011312106071 +676000 ekin = 1.74193854032682 | erot = 1.49116973847738 | epot = -11.7632213996555 | etot = -8.53011312085132 +677000 ekin = 1.65301515488034 | erot = 1.53501856941755 | epot = -11.7181468448497 | etot = -8.53011312055176 +678000 ekin = 1.56597364723852 | erot = 1.57850581645581 | epot = -11.6745925833963 | etot = -8.53011311970194 +679000 ekin = 1.48964066739842 | erot = 1.62216732403127 | epot = -11.6419211112302 | etot = -8.53011311980047 +680000 ekin = 1.41474111992769 | erot = 1.66316827970068 | epot = -11.608022522731 | etot = -8.53011312310264 +681000 ekin = 1.3875618080501 | erot = 1.70006441987859 | epot = -11.6177393496769 | etot = -8.5301131217482 +682000 ekin = 1.41176839058057 | erot = 1.74149456084064 | epot = -11.6833760730977 | etot = -8.53011312167646 +683000 ekin = 1.4347859017671 | erot = 1.78362921084864 | epot = -11.74852823407 | etot = -8.53011312145429 +684000 ekin = 1.47724360907987 | erot = 1.82441599450683 | epot = -11.8317727257632 | etot = -8.53011312217646 +685000 ekin = 1.53305607829933 | erot = 1.86370343685203 | epot = -11.9268726374703 | etot = -8.53011312231898 +686000 ekin = 1.5999920369516 | erot = 1.90117320867556 | epot = -12.0312783681521 | etot = -8.53011312252495 +687000 ekin = 1.67585532676896 | erot = 1.93616514336694 | epot = -12.1421335928676 | etot = -8.5301131227317 +688000 ekin = 1.75824359228939 | erot = 1.96747116978299 | epot = -12.2558278850929 | etot = -8.53011312302057 +689000 ekin = 1.84428806109397 | erot = 1.99331990889021 | epot = -12.3677210933648 | etot = -8.53011312338067 +690000 ekin = 1.93038830487381 | erot = 2.01163201954795 | epot = -12.4721334481824 | etot = -8.53011312376062 +691000 ekin = 2.0124388124024 | erot = 2.02053622466786 | epot = -12.563088161158 | etot = -8.53011312408775 +692000 ekin = 2.08628029307014 | erot = 2.01896054467736 | epot = -12.6353539620466 | etot = -8.53011312429905 +693000 ekin = 2.14819565616757 | erot = 2.00704872931776 | epot = -12.6853575098526 | etot = -8.53011312436728 +694000 ekin = 2.19527915053926 | erot = 1.98620471483403 | epot = -12.7115969896827 | etot = -8.53011312430943 +695000 ekin = 2.22558662019519 | erot = 1.95872876712409 | epot = -12.7144285114953 | etot = -8.530113124176 +696000 ekin = 2.23807939046259 | erot = 1.92719459917365 | epot = -12.6953871136599 | etot = -8.53011312402367 +697000 ekin = 2.23245491258998 | erot = 1.89382427549971 | epot = -12.6563923119818 | etot = -8.5301131238921 +698000 ekin = 2.20898166045956 | erot = 1.86009447102955 | epot = -12.5991892552733 | etot = -8.53011312378417 +699000 ekin = 2.16842192915358 | erot = 1.82670876840176 | epot = -12.5252438212486 | etot = -8.53011312369329 +700000 ekin = 2.11206718079843 | erot = 1.79377149364874 | epot = -12.4359517980247 | etot = -8.53011312357757 +701000 ekin = 2.04183510230187 | erot = 1.76109647800014 | epot = -12.3330447037309 | etot = -8.53011312342893 +702000 ekin = 1.9603063691051 | erot = 1.72840134027956 | epot = -12.2188208326314 | etot = -8.53011312324677 +703000 ekin = 1.87071986578067 | erot = 1.69529695521636 | epot = -12.0961299440382 | etot = -8.53011312304119 +704000 ekin = 1.77689930890354 | erot = 1.6611057765389 | epot = -11.9681182082896 | etot = -8.53011312284715 +705000 ekin = 1.68305722563765 | erot = 1.62461573119795 | epot = -11.8377860795182 | etot = -8.53011312268258 +706000 ekin = 1.59370733728767 | erot = 1.58419230640585 | epot = -11.7080127662152 | etot = -8.53011312252172 +707000 ekin = 1.51408760177217 | erot = 1.53852435757229 | epot = -11.5827250817791 | etot = -8.53011312243462 +708000 ekin = 1.44811612149855 | erot = 1.48556130217597 | epot = -11.4637905459337 | etot = -8.53011312225917 +709000 ekin = 1.39918507090357 | erot = 1.42450216552995 | epot = -11.3538003584163 | etot = -8.53011312198281 +710000 ekin = 1.37013904497866 | erot = 1.35650265895892 | epot = -11.2567548255768 | etot = -8.53011312163919 +711000 ekin = 1.36293784710523 | erot = 1.28452294871087 | epot = -11.177573917118 | etot = -8.53011312130192 +712000 ekin = 1.37810571334542 | erot = 1.21275926767383 | epot = -11.1209781019579 | etot = -8.53011312093868 +713000 ekin = 1.41539111506379 | erot = 1.1462528512795 | epot = -11.0917570870382 | etot = -8.53011312069488 +714000 ekin = 1.47330237310361 | erot = 1.09011154668932 | epot = -11.0935270405084 | etot = -8.53011312071543 +715000 ekin = 1.54871417396785 | erot = 1.04700633005665 | epot = -11.1258336248984 | etot = -8.53011312087386 +716000 ekin = 1.63763638283809 | erot = 1.01816315230752 | epot = -11.1859126562794 | etot = -8.53011312113384 +717000 ekin = 1.73566547228712 | erot = 1.00365944746308 | epot = -11.2694380412112 | etot = -8.53011312146104 +718000 ekin = 1.83830978287828 | erot = 1.00261452540746 | epot = -11.3710374301145 | etot = -8.53011312182876 +719000 ekin = 1.94121801685678 | erot = 1.01337618099033 | epot = -11.4847073200663 | etot = -8.53011312221914 +720000 ekin = 2.04031989970054 | erot = 1.0336756329226 | epot = -11.6041086552424 | etot = -8.5301131226193 +721000 ekin = 2.13191426653948 | erot = 1.06076519451606 | epot = -11.7227925840712 | etot = -8.53011312301563 +722000 ekin = 2.21272563482337 | erot = 1.09108188128853 | epot = -11.8339206397588 | etot = -8.53011312364686 +723000 ekin = 2.27980497539282 | erot = 1.1198830983019 | epot = -11.929801197718 | etot = -8.53011312402331 +724000 ekin = 2.33074458889845 | erot = 1.14401404987369 | epot = -12.0048717630048 | etot = -8.53011312423261 +725000 ekin = 2.36404026188179 | erot = 1.16137515755472 | epot = -12.0555285437419 | etot = -8.53011312430541 +726000 ekin = 2.37921817082242 | erot = 1.17112079793551 | epot = -12.0804520929896 | etot = -8.53011312423162 +727000 ekin = 2.37683377543408 | erot = 1.17363131590977 | epot = -12.0805782153631 | etot = -8.53011312401923 +728000 ekin = 2.35838505905363 | erot = 1.17045679634039 | epot = -12.0589549790964 | etot = -8.53011312370242 +729000 ekin = 2.3261061343185 | erot = 1.16404528412633 | epot = -12.0202645417651 | etot = -8.53011312332028 +730000 ekin = 2.28270056427543 | erot = 1.15738479164455 | epot = -11.9701984788421 | etot = -8.53011312292208 +731000 ekin = 2.23120367718931 | erot = 1.15355872123357 | epot = -11.9148755209223 | etot = -8.53011312249944 +732000 ekin = 2.17470227949417 | erot = 1.15522777871211 | epot = -11.8600431804118 | etot = -8.53011312220553 +733000 ekin = 2.11571523134037 | erot = 1.16431239937572 | epot = -11.8101407526813 | etot = -8.53011312196517 +734000 ekin = 2.05656428236166 | erot = 1.18217764585344 | epot = -11.7688550500047 | etot = -8.53011312178957 +735000 ekin = 1.99938712968247 | erot = 1.20940907181726 | epot = -11.7389093231742 | etot = -8.53011312167449 +736000 ekin = 1.94615450234839 | erot = 1.24582378057203 | epot = -11.7220914045337 | etot = -8.53011312161325 +737000 ekin = 1.89868408609312 | erot = 1.2905472824522 | epot = -11.7193444901454 | etot = -8.53011312160005 +738000 ekin = 1.8586330040137 | erot = 1.3421107223096 | epot = -11.7308568479547 | etot = -8.53011312163138 +739000 ekin = 1.82745784098469 | erot = 1.39854613747351 | epot = -11.7561171001662 | etot = -8.53011312170797 +740000 ekin = 1.80633906931732 | erot = 1.45733644211442 | epot = -11.7937886333266 | etot = -8.53011312189481 +741000 ekin = 1.79607780004651 | erot = 1.51536575546308 | epot = -11.8415566775877 | etot = -8.53011312207814 +742000 ekin = 1.79696493223211 | erot = 1.56951628226472 | epot = -11.8965943368768 | etot = -8.53011312237996 +743000 ekin = 1.80846594325561 | erot = 1.6163304464024 | epot = -11.9549095123419 | etot = -8.53011312268386 +744000 ekin = 1.82931777589884 | erot = 1.65249323454789 | epot = -12.0119241334618 | etot = -8.53011312301508 +745000 ekin = 1.85761408802979 | erot = 1.67511504714017 | epot = -12.0628422585089 | etot = -8.53011312333896 +746000 ekin = 1.89090050882387 | erot = 1.68206656301284 | epot = -12.1030801954477 | etot = -8.530113123611 +747000 ekin = 1.92640401789238 | erot = 1.67240004233478 | epot = -12.1289171840141 | etot = -8.53011312378691 +748000 ekin = 1.96133145904701 | erot = 1.64668719346329 | epot = -12.1381317763454 | etot = -8.5301131238351 +749000 ekin = 1.9931847828739 | erot = 1.60714989956533 | epot = -12.1304478061854 | etot = -8.53011312374616 +750000 ekin = 2.0200355789032 | erot = 1.55750382538372 | epot = -12.107652527823 | etot = -8.53011312353607 +751000 ekin = 2.04071538033916 | erot = 1.50252212963145 | epot = -12.0733506332106 | etot = -8.53011312324001 +752000 ekin = 2.05490285137441 | erot = 1.4474147433058 | epot = -12.0324307175831 | etot = -8.53011312290288 +753000 ekin = 2.06311311777681 | erot = 1.39717761208881 | epot = -11.9904038524287 | etot = -8.53011312256307 +754000 ekin = 2.06660147050372 | erot = 1.35603065032696 | epot = -11.9527452431002 | etot = -8.5301131222695 +755000 ekin = 2.06719659825846 | erot = 1.32693138051867 | epot = -11.9242411008192 | etot = -8.53011312204203 +756000 ekin = 2.0671036998156 | erot = 1.3113988140042 | epot = -11.9086156357185 | etot = -8.53011312189868 +757000 ekin = 2.06866724415208 | erot = 1.3094625281623 | epot = -11.9082428938087 | etot = -8.53011312149428 +758000 ekin = 2.07499396292543 | erot = 1.32035089931502 | epot = -11.925457983815 | etot = -8.5301131215746 +759000 ekin = 2.08841045515532 | erot = 1.34191093708327 | epot = -11.96043451401 | etot = -8.53011312177144 +760000 ekin = 2.10963645109489 | erot = 1.37032699691538 | epot = -12.0100765700779 | etot = -8.53011312206764 +761000 ekin = 2.13857799102783 | erot = 1.40109303382923 | epot = -12.0697841472857 | etot = -8.53011312242866 +762000 ekin = 2.17432662718611 | erot = 1.42956057102255 | epot = -12.1340003210162 | etot = -8.53011312280759 +763000 ekin = 2.2153033445177 | erot = 1.45159579145362 | epot = -12.1970122591095 | etot = -8.53011312313819 +764000 ekin = 2.25988007753059 | erot = 1.46444731772141 | epot = -12.2544405178094 | etot = -8.53011312255735 +765000 ekin = 2.30943589560724 | erot = 1.46853530580971 | epot = -12.3080843239992 | etot = -8.5301131225823 +766000 ekin = 2.36332281187347 | erot = 1.46534946813803 | epot = -12.3587854024957 | etot = -8.53011312248424 +767000 ekin = 2.42035196934608 | erot = 1.45783003509466 | epot = -12.4082951267389 | etot = -8.53011312229817 +768000 ekin = 2.47581566548054 | erot = 1.44854904096221 | epot = -12.4544778288911 | etot = -8.5301131224483 +769000 ekin = 2.5236329914572 | erot = 1.44004118153085 | epot = -12.4937872952374 | etot = -8.53011312224932 +770000 ekin = 2.56270533135524 | erot = 1.43704014071487 | epot = -12.5298585941748 | etot = -8.5301131221047 +771000 ekin = 2.59209730116264 | erot = 1.44343459837348 | epot = -12.5656450216346 | etot = -8.53011312209843 +772000 ekin = 2.61072906203368 | erot = 1.46130008818214 | epot = -12.6021422725227 | etot = -8.53011312230689 +773000 ekin = 2.61709469190311 | erot = 1.49008956149496 | epot = -12.6372973761744 | etot = -8.53011312277635 +774000 ekin = 2.6090964566865 | erot = 1.5261853113214 | epot = -12.6653948914977 | etot = -8.53011312348982 +775000 ekin = 2.58418075699894 | erot = 1.56310881844526 | epot = -12.6774026997542 | etot = -8.53011312430998 +776000 ekin = 2.54009174823719 | erot = 1.59267184116488 | epot = -12.6628767144435 | etot = -8.53011312504144 +777000 ekin = 2.47580451030859 | erot = 1.60710708459036 | epot = -12.6130247202843 | etot = -8.53011312538531 +778000 ekin = 2.39287500139183 | erot = 1.60165568863609 | epot = -12.5246438151509 | etot = -8.53011312512302 +779000 ekin = 2.29635110870132 | erot = 1.57655114307824 | epot = -12.4030153760378 | etot = -8.53011312425821 +780000 ekin = 2.19432865476922 | erot = 1.53718068405292 | epot = -12.2616224618999 | etot = -8.5301131230778 +781000 ekin = 2.09599445127249 | erot = 1.49202506838098 | epot = -12.1181326417003 | etot = -8.53011312204685 +782000 ekin = 2.01067959044775 | erot = 1.44954049914492 | epot = -11.9903332112136 | etot = -8.53011312162094 +783000 ekin = 1.94134953218635 | erot = 1.4142221223979 | epot = -11.8856847763454 | etot = -8.53011312176118 +784000 ekin = 1.88557673990069 | erot = 1.38612068275655 | epot = -11.8018105449661 | etot = -8.53011312230882 +785000 ekin = 1.8382125158826 | erot = 1.36190678416234 | epot = -11.7302324230318 | etot = -8.53011312298688 +786000 ekin = 1.79361791903349 | erot = 1.33665294680265 | epot = -11.6603839893739 | etot = -8.53011312353779 +787000 ekin = 1.74765651997725 | erot = 1.30572681397029 | epot = -11.5834964577365 | etot = -8.53011312378899 +788000 ekin = 1.69893980453935 | erot = 1.26627175391768 | epot = -11.4953246821149 | etot = -8.53011312365785 +789000 ekin = 1.64926102871369 | erot = 1.21811104686223 | epot = -11.3974851988071 | etot = -8.53011312323117 +790000 ekin = 1.60278391128869 | erot = 1.16409864378586 | epot = -11.2969956774873 | etot = -8.53011312241278 +791000 ekin = 1.56615980927194 | erot = 1.10959117745814 | epot = -11.2058641081802 | etot = -8.53011312145014 +792000 ekin = 1.54703734324897 | erot = 1.06142547772204 | epot = -11.1385759415279 | etot = -8.53011312055688 +793000 ekin = 1.55198521112706 | erot = 1.02650367069295 | epot = -11.1086020017646 | etot = -8.53011311994463 +794000 ekin = 1.58477896414495 | erot = 1.01030347984837 | epot = -11.1251955637503 | etot = -8.53011311975694 +795000 ekin = 1.64530503793607 | erot = 1.0157995055352 | epot = -11.1912176634937 | etot = -8.5301131200224 +796000 ekin = 1.72945610306449 | erot = 1.04308507626302 | epot = -11.3026542999848 | etot = -8.5301131206573 +797000 ekin = 1.83001099514718 | erot = 1.08968689108651 | epot = -11.4498110077441 | etot = -8.53011312151045 +798000 ekin = 1.93812374531269 | erot = 1.15131252104657 | epot = -11.6195493887796 | etot = -8.53011312242032 +799000 ekin = 2.04497054169321 | erot = 1.22278827268487 | epot = -11.7978719376079 | etot = -8.53011312322978 +800000 ekin = 2.14336798474912 | erot = 1.29926771175094 | epot = -11.9727488204676 | etot = -8.53011312396754 +801000 ekin = 2.22727301807807 | erot = 1.3753304782639 | epot = -12.132716620907 | etot = -8.53011312456501 +802000 ekin = 2.29233025372734 | erot = 1.44569167636572 | epot = -12.2681350550915 | etot = -8.5301131249984 +803000 ekin = 2.33601370069085 | erot = 1.50574813524509 | epot = -12.3718749611944 | etot = -8.53011312525848 +804000 ekin = 2.35746789192217 | erot = 1.55190067907921 | epot = -12.4394816963513 | etot = -8.53011312534996 +805000 ekin = 2.35725821081217 | erot = 1.58176758445585 | epot = -12.4691389205546 | etot = -8.53011312528653 +806000 ekin = 2.33708958181609 | erot = 1.59429980420554 | epot = -12.4615025111052 | etot = -8.53011312508358 +807000 ekin = 2.29933748330709 | erot = 1.58976408842292 | epot = -12.419214696614 | etot = -8.53011312488397 +808000 ekin = 2.24664197364469 | erot = 1.56989950315772 | epot = -12.3466546012196 | etot = -8.53011312441723 +809000 ekin = 2.1825349798202 | erot = 1.53842514359652 | epot = -12.251073247252 | etot = -8.5301131238353 +810000 ekin = 2.11065804207626 | erot = 1.50058136870816 | epot = -12.1413525344378 | etot = -8.53011312365334 +811000 ekin = 2.03314489473095 | erot = 1.46124027742313 | epot = -12.0244982952517 | etot = -8.53011312309758 +812000 ekin = 1.95235452668761 | erot = 1.42640454804181 | epot = -11.9088721972944 | etot = -8.53011312256503 +813000 ekin = 1.87042476526586 | erot = 1.40255580938068 | epot = -11.8030936967653 | etot = -8.53011312211877 +814000 ekin = 1.78881788399123 | erot = 1.39558114783999 | epot = -11.7145121536357 | etot = -8.53011312180448 +815000 ekin = 1.70830262134368 | erot = 1.41006409307363 | epot = -11.6484798360531 | etot = -8.53011312163576 +816000 ekin = 1.62913132400075 | erot = 1.44882680729612 | epot = -11.6080712528942 | etot = -8.53011312159728 +817000 ekin = 1.55135581922303 | erot = 1.51275412295674 | epot = -11.5942230638405 | etot = -8.5301131216607 +818000 ekin = 1.47515646825021 | erot = 1.6008108113837 | epot = -11.6060804014367 | etot = -8.5301131218028 +819000 ekin = 1.4010559904149 | erot = 1.71014259913742 | epot = -11.641311711565 | etot = -8.53011312201267 +820000 ekin = 1.32995993550542 | erot = 1.83623765525366 | epot = -11.6963107130399 | etot = -8.53011312228078 +821000 ekin = 1.26306525352047 | erot = 1.97322574609999 | epot = -11.766404122207 | etot = -8.5301131225865 +822000 ekin = 1.20173310116911 | erot = 2.11438661281973 | epot = -11.8462328368839 | etot = -8.53011312289509 +823000 ekin = 1.14740078104335 | erot = 2.25282523513454 | epot = -11.9303391393447 | etot = -8.53011312316681 +824000 ekin = 1.10154739191156 | erot = 2.38216838200903 | epot = -12.013828897289 | etot = -8.53011312336843 +825000 ekin = 1.06568617705408 | erot = 2.49713206508732 | epot = -12.0929313656228 | etot = -8.53011312348143 +826000 ekin = 1.04135225335478 | erot = 2.59387442827314 | epot = -12.1653398051303 | etot = -8.53011312350241 +827000 ekin = 1.0300690753039 | erot = 2.67011598052409 | epot = -12.2302981792697 | etot = -8.53011312344172 +828000 ekin = 1.03328978432075 | erot = 2.72505389606421 | epot = -12.2884568037043 | etot = -8.53011312331935 +829000 ekin = 1.05231294056933 | erot = 2.75912544456951 | epot = -12.3415515083008 | etot = -8.53011312316197 +830000 ekin = 1.08816877276041 | erot = 2.7736892067289 | epot = -12.3919711024882 | etot = -8.53011312299886 +831000 ekin = 1.14147021989246 | erot = 2.77068822984812 | epot = -12.4422715726009 | etot = -8.53011312286037 +832000 ekin = 1.21222920790235 | erot = 2.75233425304545 | epot = -12.4946765837238 | etot = -8.53011312277601 +833000 ekin = 1.29965444893424 | erot = 2.72082561150635 | epot = -12.5505931832145 | etot = -8.53011312277386 +834000 ekin = 1.40196412281876 | erot = 2.67809188941165 | epot = -12.610169135109 | etot = -8.53011312287861 +835000 ekin = 1.51625524420434 | erot = 2.6255598705884 | epot = -12.6719282378992 | etot = -8.53011312310646 +836000 ekin = 1.63847039446473 | erot = 2.56396340709026 | epot = -12.7325469250142 | etot = -8.53011312345919 +837000 ekin = 1.76350003260508 | erot = 2.49326751329086 | epot = -12.7868806698075 | etot = -8.53011312391161 +838000 ekin = 1.88545581841659 | erot = 2.41282706135739 | epot = -12.8283960041697 | etot = -8.53011312439575 +839000 ekin = 1.99811239252423 | erot = 2.32192717675838 | epot = -12.8501526941075 | etot = -8.53011312482491 +840000 ekin = 2.09569613381754 | erot = 2.22044440711267 | epot = -12.8462536659934 | etot = -8.53011312506321 +841000 ekin = 2.17372526458142 | erot = 2.10989077519493 | epot = -12.8137291647737 | etot = -8.53011312499732 +842000 ekin = 2.22978701489745 | erot = 1.99424893653508 | epot = -12.7541490760042 | etot = -8.53011312457168 +843000 ekin = 2.26403143579391 | erot = 1.88022583110555 | epot = -12.674370390718 | etot = -8.53011312381855 +844000 ekin = 2.27916623050959 | erot = 1.77673401952997 | epot = -12.5860133728978 | etot = -8.5301131228582 +845000 ekin = 2.27988872464566 | erot = 1.69367250750107 | epot = -12.5036743540144 | etot = -8.5301131218677 +846000 ekin = 2.27183600928308 | erot = 1.64035007883682 | epot = -12.4422992091634 | etot = -8.53011312104352 +847000 ekin = 2.26027572817844 | erot = 1.6239672341206 | epot = -12.4143560828269 | etot = -8.53011312052791 +848000 ekin = 2.24926761303696 | erot = 1.64823314902357 | epot = -12.4276138824767 | etot = -8.53011312041621 +849000 ekin = 2.2409304996373 | erot = 1.7127191869587 | epot = -12.4837628073227 | etot = -8.53011312072673 +850000 ekin = 2.23528630972878 | erot = 1.81271493779141 | epot = -12.5781143689312 | etot = -8.53011312141102 +851000 ekin = 2.23059418781143 | erot = 1.93958610382867 | epot = -12.7002934140097 | etot = -8.53011312236962 +852000 ekin = 2.22400796081198 | erot = 2.08159933081266 | epot = -12.8357204149898 | etot = -8.53011312336517 +853000 ekin = 2.21277994498023 | erot = 2.22526716129808 | epot = -12.9681602307806 | etot = -8.53011312450228 +854000 ekin = 2.19416370961739 | erot = 2.35673636874866 | epot = -13.0810132038027 | etot = -8.53011312543664 +855000 ekin = 2.16598116515109 | erot = 2.46372761528164 | epot = -13.159821906468 | etot = -8.53011312603531 +856000 ekin = 2.12753272380137 | erot = 2.53738513635797 | epot = -13.1950309863878 | etot = -8.53011312622846 +857000 ekin = 2.07957021480506 | erot = 2.5733641191515 | epot = -13.1830474599809 | etot = -8.53011312602436 +858000 ekin = 2.02398845904357 | erot = 2.57205351926334 | epot = -13.1261551038021 | etot = -8.53011312549514 +859000 ekin = 1.96347606560471 | erot = 2.538301329127 | epot = -13.0318905195264 | etot = -8.53011312479471 +860000 ekin = 1.90079123527623 | erot = 2.47952673186276 | epot = -12.9104310912327 | etot = -8.53011312409367 +861000 ekin = 1.83808336626078 | erot = 2.40350575738459 | epot = -12.771702247107 | etot = -8.53011312346161 +862000 ekin = 1.7769226964898 | erot = 2.31773605221603 | epot = -12.6247718716715 | etot = -8.53011312296563 +863000 ekin = 1.71824491583962 | erot = 2.22850238053643 | epot = -12.4768604189972 | etot = -8.53011312262119 +864000 ekin = 1.66247784195644 | erot = 2.14047748401912 | epot = -12.3330684483814 | etot = -8.53011312240586 +865000 ekin = 1.60977147001189 | erot = 2.05677487411754 | epot = -12.1966594664085 | etot = -8.53011312227909 +866000 ekin = 1.5602354279003 | erot = 1.97927297432111 | epot = -12.0696215244206 | etot = -8.53011312219923 +867000 ekin = 1.5141162515596 | erot = 1.90904243445895 | epot = -11.95327180815 | etot = -8.53011312213141 +868000 ekin = 1.47188909913906 | erot = 1.84677021416781 | epot = -11.8487724353568 | etot = -8.53011312204993 +869000 ekin = 1.43450342551766 | erot = 1.79302433223088 | epot = -11.7576408796875 | etot = -8.53011312193895 +870000 ekin = 1.40309125560257 | erot = 1.74850970124891 | epot = -11.6817140786662 | etot = -8.53011312181474 +871000 ekin = 1.37958721284379 | erot = 1.71440263903883 | epot = -11.6241029734475 | etot = -8.53011312156489 +872000 ekin = 1.36659086815741 | erot = 1.69146102325433 | epot = -11.5881650131034 | etot = -8.53011312169162 +873000 ekin = 1.36373253533302 | erot = 1.68047336436782 | epot = -11.5743190213543 | etot = -8.53011312165341 +874000 ekin = 1.37056306917168 | erot = 1.68272728098881 | epot = -11.5834034718139 | etot = -8.53011312165341 +875000 ekin = 1.3864192230475 | erot = 1.69919412002808 | epot = -11.6157264647898 | etot = -8.53011312171422 +876000 ekin = 1.41041928725535 | erot = 1.73002723125778 | epot = -11.6705596403935 | etot = -8.53011312188036 +877000 ekin = 1.44135762457885 | erot = 1.77412255949985 | epot = -11.7455933061831 | etot = -8.53011312210442 +878000 ekin = 1.47769632418173 | erot = 1.82989689230891 | epot = -11.8377063388571 | etot = -8.53011312236644 +879000 ekin = 1.51786971939981 | erot = 1.89513519880948 | epot = -11.9431180408527 | etot = -8.53011312264339 +880000 ekin = 1.56043024313837 | erot = 1.96714021039869 | epot = -12.0576835764586 | etot = -8.53011312292149 +881000 ekin = 1.60413749600546 | erot = 2.04284304208084 | epot = -12.1770936612861 | etot = -8.53011312319976 +882000 ekin = 1.64798530769034 | erot = 2.11880523098331 | epot = -12.2969036621876 | etot = -8.53011312351396 +883000 ekin = 1.69122698488457 | erot = 2.19098801160399 | epot = -12.4123281203044 | etot = -8.53011312381588 +884000 ekin = 1.73324713426401 | erot = 2.25513555685009 | epot = -12.518495815234 | etot = -8.5301131241199 +885000 ekin = 1.77353313459879 | erot = 2.30696174268605 | epot = -12.6106080016839 | etot = -8.53011312439907 +886000 ekin = 1.81168812334986 | erot = 2.34253084485012 | epot = -12.6843320928115 | etot = -8.53011312461151 +887000 ekin = 1.84747843477679 | erot = 2.35884841151242 | epot = -12.7364399709989 | etot = -8.53011312470974 +888000 ekin = 1.8809005510878 | erot = 2.35429714156542 | epot = -12.765310817859 | etot = -8.53011312520577 +889000 ekin = 1.91199067528862 | erot = 2.32652877039544 | epot = -12.768632570677 | etot = -8.53011312499295 +890000 ekin = 1.94125303800117 | erot = 2.27732909895155 | epot = -12.748695261539 | etot = -8.53011312458633 +891000 ekin = 1.96982663207205 | erot = 2.21178980997174 | epot = -12.7117295661083 | etot = -8.53011312406448 +892000 ekin = 1.99917310247387 | erot = 2.13642241819792 | epot = -12.6657086442081 | etot = -8.53011312353632 +893000 ekin = 2.03065310417621 | erot = 2.05798315745513 | epot = -12.6187493847446 | etot = -8.53011312311324 +894000 ekin = 2.06504907974643 | erot = 1.98231723802894 | epot = -12.5774794406568 | etot = -8.53011312288139 +895000 ekin = 2.1021701839369 | erot = 1.91347939811021 | epot = -12.5457627049308 | etot = -8.53011312288371 +896000 ekin = 2.14066929405318 | erot = 1.85328312216171 | epot = -12.5240655391746 | etot = -8.53011312295969 +897000 ekin = 2.178881820565 | erot = 1.80140384588356 | epot = -12.5103987897421 | etot = -8.53011312329356 +898000 ekin = 2.21472564822659 | erot = 1.75594910479886 | epot = -12.5007878767186 | etot = -8.53011312369316 +899000 ekin = 2.24569847682448 | erot = 1.71401610886598 | epot = -12.4898277097489 | etot = -8.53011312405846 +900000 ekin = 2.26993925536076 | erot = 1.67248576848322 | epot = -12.4725381481436 | etot = -8.53011312429966 +901000 ekin = 2.28606210285319 | erot = 1.62859738727852 | epot = -12.4447726152915 | etot = -8.53011312515978 +902000 ekin = 2.29042230831636 | erot = 1.5793253202287 | epot = -12.3998607538073 | etot = -8.53011312526226 +903000 ekin = 2.28273813410943 | erot = 1.52313711845165 | epot = -12.3359883777638 | etot = -8.53011312520276 +904000 ekin = 2.26413659223501 | erot = 1.45995102717232 | epot = -12.2542007444324 | etot = -8.53011312502506 +905000 ekin = 2.23616199953194 | erot = 1.3908814816503 | epot = -12.1571566059684 | etot = -8.53011312478611 +906000 ekin = 2.20025203977182 | erot = 1.31795883319974 | epot = -12.0483239975002 | etot = -8.53011312452868 +907000 ekin = 2.15741247689603 | erot = 1.2438599330396 | epot = -11.9313855341998 | etot = -8.53011312426417 +908000 ekin = 2.10821372462424 | erot = 1.1717580431236 | epot = -11.8100848916697 | etot = -8.53011312392188 +909000 ekin = 2.0533959765881 | erot = 1.1052361371856 | epot = -11.6887452373732 | etot = -8.53011312359954 +910000 ekin = 1.9943738863817 | erot = 1.04840591874189 | epot = -11.5728929279094 | etot = -8.53011312278585 +911000 ekin = 1.93472408693351 | erot = 1.00596121880683 | epot = -11.4707984281725 | etot = -8.5301131224322 +912000 ekin = 1.87571848813277 | erot = 0.981792282316895 | epot = -11.3876238925624 | etot = -8.53011312211272 +913000 ekin = 1.81824273788001 | erot = 0.979441553334138 | epot = -11.3277974130229 | etot = -8.53011312180879 +914000 ekin = 1.76344481711691 | erot = 1.00191943330251 | epot = -11.2954773719654 | etot = -8.53011312154602 +915000 ekin = 1.7126576881857 | erot = 1.05137542112642 | epot = -11.2941462307085 | etot = -8.53011312139635 +916000 ekin = 1.66711519083649 | erot = 1.12858220203734 | epot = -11.3258105142236 | etot = -8.53011312134976 +917000 ekin = 1.62763655706369 | erot = 1.23302216364502 | epot = -11.3907718421526 | etot = -8.53011312144387 +918000 ekin = 1.59455865390118 | erot = 1.36258552106968 | epot = -11.4872572966706 | etot = -8.53011312169973 +919000 ekin = 1.56762589341053 | erot = 1.51336619450293 | epot = -11.6111052100433 | etot = -8.53011312212986 +920000 ekin = 1.5459315744459 | erot = 1.67955640230889 | epot = -11.7556010994845 | etot = -8.5301131227297 +921000 ekin = 1.52794851746671 | erot = 1.85350715088319 | epot = -11.9115687918171 | etot = -8.53011312346721 +922000 ekin = 1.51169520995972 | erot = 2.02606206722181 | epot = -12.067870401454 | etot = -8.5301131242725 +923000 ekin = 1.4950738423225 | erot = 2.18724898577061 | epot = -12.2124359531328 | etot = -8.53011312503965 +924000 ekin = 1.47635971360147 | erot = 2.3273137721574 | epot = -12.3337866114077 | etot = -8.53011312564884 +925000 ekin = 1.45471560014799 | erot = 2.43791688064627 | epot = -12.4227456067991 | etot = -8.53011312600481 +926000 ekin = 1.43051136688473 | erot = 2.51317740630618 | epot = -12.473801899265 | etot = -8.5301131260741 +927000 ekin = 1.40525402734709 | erot = 2.5502684120006 | epot = -12.4856355652394 | etot = -8.53011312589176 +928000 ekin = 1.38111941156276 | erot = 2.54946754684865 | epot = -12.4607000839444 | etot = -8.53011312553295 +929000 ekin = 1.3599258527227 | erot = 2.51283593008147 | epot = -12.4028749085046 | etot = -8.53011312570039 +930000 ekin = 1.34158304398879 | erot = 2.44241099548171 | epot = -12.3141071645525 | etot = -8.53011312508201 +931000 ekin = 1.32656952525849 | erot = 2.34647203270355 | epot = -12.2031546823254 | etot = -8.53011312436339 +932000 ekin = 1.31543664435648 | erot = 2.23535488464011 | epot = -12.0809046526125 | etot = -8.53011312361596 +933000 ekin = 1.30881286163193 | erot = 2.11983848401906 | epot = -11.95876446856 | etot = -8.53011312290906 +934000 ekin = 1.30745813481004 | erot = 2.01001812957095 | epot = -11.847589386687 | etot = -8.53011312230597 +935000 ekin = 1.31220098075813 | erot = 1.9144462159354 | epot = -11.7567603185262 | etot = -8.53011312183264 +936000 ekin = 1.32391210171741 | erot = 1.83958727483052 | epot = -11.6936124980695 | etot = -8.53011312152155 +937000 ekin = 1.34332477770944 | erot = 1.78957436751403 | epot = -11.6630122666068 | etot = -8.53011312138337 +938000 ekin = 1.37084792782475 | erot = 1.76617827878338 | epot = -11.6671393280291 | etot = -8.53011312142099 +939000 ekin = 1.40642931156935 | erot = 1.76890798114243 | epot = -11.7054504143274 | etot = -8.53011312161567 +940000 ekin = 1.44952186396214 | erot = 1.79522267831962 | epot = -11.7748576642577 | etot = -8.53011312197589 +941000 ekin = 1.49902948237103 | erot = 1.84063576443025 | epot = -11.8697783692815 | etot = -8.53011312248019 +942000 ekin = 1.55333690858857 | erot = 1.89898447953926 | epot = -11.9824345112207 | etot = -8.53011312309283 +943000 ekin = 1.61046155751663 | erot = 1.96285592643144 | epot = -12.1034306077032 | etot = -8.53011312375517 +944000 ekin = 1.66830779522798 | erot = 2.02424654682829 | epot = -12.2226674664441 | etot = -8.53011312438782 +945000 ekin = 1.72497649037036 | erot = 2.07544351226215 | epot = -12.3305331275389 | etot = -8.53011312490634 +946000 ekin = 1.77904739723341 | erot = 2.10999554440733 | epot = -12.4191560668842 | etot = -8.53011312524345 +947000 ekin = 1.82974878179447 | erot = 2.1235525324349 | epot = -12.4834144395953 | etot = -8.53011312536594 +948000 ekin = 1.87696379691168 | erot = 2.11435368830262 | epot = -12.5214306113984 | etot = -8.53011312618414 +949000 ekin = 1.91868968736917 | erot = 2.08113041335485 | epot = -12.5299332268206 | etot = -8.5301131260966 +950000 ekin = 1.9525004135901 | erot = 2.02444704715869 | epot = -12.5070605866164 | etot = -8.5301131258676 +951000 ekin = 1.97786377860527 | erot = 1.94836556912359 | epot = -12.4563424732691 | etot = -8.53011312554024 +952000 ekin = 1.9944032290504 | erot = 1.85836147892453 | epot = -12.3828778331274 | etot = -8.53011312515246 +953000 ekin = 2.00183985525881 | erot = 1.76077654422277 | epot = -12.2927295242209 | etot = -8.53011312473928 +954000 ekin = 1.99994520547877 | erot = 1.66230521855966 | epot = -12.1923635483737 | etot = -8.53011312433531 +955000 ekin = 1.98848781981187 | erot = 1.56949886940344 | epot = -12.0880998131888 | etot = -8.53011312397347 +956000 ekin = 1.96719248394502 | erot = 1.48830066036356 | epot = -11.9856062679853 | etot = -8.53011312367672 +957000 ekin = 1.93576585488627 | erot = 1.42368152914648 | epot = -11.8895605074794 | etot = -8.53011312344665 +958000 ekin = 1.89410745234003 | erot = 1.37950780385348 | epot = -11.8037283792177 | etot = -8.53011312302418 +959000 ekin = 1.84388200430519 | erot = 1.35926323940579 | epot = -11.7332583666525 | etot = -8.53011312294155 +960000 ekin = 1.78600307796804 | erot = 1.36453982266578 | epot = -11.6806560234787 | etot = -8.5301131228449 +961000 ekin = 1.72147601474392 | erot = 1.39572572980377 | epot = -11.6473148672821 | etot = -8.53011312273439 +962000 ekin = 1.65221748522298 | erot = 1.4524380059047 | epot = -11.634768613771 | etot = -8.53011312264331 +963000 ekin = 1.58085937428924 | erot = 1.53327574296057 | epot = -11.6442482398661 | etot = -8.5301131226163 +964000 ekin = 1.51040322860342 | erot = 1.63556392925408 | epot = -11.6760802805373 | etot = -8.53011312267978 +965000 ekin = 1.44386585375724 | erot = 1.75533146867227 | epot = -11.7293104452584 | etot = -8.53011312282892 +966000 ekin = 1.38401833471973 | erot = 1.88762696925973 | epot = -11.8017584270141 | etot = -8.53011312303459 +967000 ekin = 1.33323855953349 | erot = 2.02706397428321 | epot = -11.8904156570798 | etot = -8.53011312326314 +968000 ekin = 1.29343485248817 | erot = 2.16835538295901 | epot = -11.9919033589444 | etot = -8.5301131234972 +969000 ekin = 1.26598521106734 | erot = 2.30662029880419 | epot = -12.1027186336141 | etot = -8.53011312374257 +970000 ekin = 1.25166332225621 | erot = 2.43738938129169 | epot = -12.2191658275689 | etot = -8.53011312402102 +971000 ekin = 1.25055917700305 | erot = 2.55639826953469 | epot = -12.3370705708916 | etot = -8.53011312435386 +972000 ekin = 1.26202503907091 | erot = 2.65935818610938 | epot = -12.4514963499266 | etot = -8.53011312474633 +973000 ekin = 1.28468152304165 | erot = 2.7419011912667 | epot = -12.5566958394848 | etot = -8.53011312517645 +974000 ekin = 1.31650940090302 | erot = 2.79983470555576 | epot = -12.64645723205 | etot = -8.5301131255912 +975000 ekin = 1.35503678006273 | erot = 2.82973569321423 | epot = -12.7148855991916 | etot = -8.53011312591465 +976000 ekin = 1.39761106498719 | erot = 2.82978989838473 | epot = -12.757514089437 | etot = -8.53011312606513 +977000 ekin = 1.44171682389421 | erot = 2.80065378127379 | epot = -12.7724837311485 | etot = -8.53011312598046 +978000 ekin = 1.48527676990002 | erot = 2.74603610444877 | epot = -12.7614259999919 | etot = -8.53011312564306 +979000 ekin = 1.52686311961727 | erot = 2.67272089285715 | epot = -12.7296971376689 | etot = -8.53011312519452 +980000 ekin = 1.56541539899103 | erot = 2.58979180874379 | epot = -12.6853203322416 | etot = -8.53011312450682 +981000 ekin = 1.60047076755278 | erot = 2.50776375788484 | epot = -12.6383476492396 | etot = -8.53011312380203 +982000 ekin = 1.63230110544612 | erot = 2.4371358709238 | epot = -12.5995500991041 | etot = -8.53011312273413 +983000 ekin = 1.66203103419979 | erot = 2.38850313754454 | epot = -12.5806472942433 | etot = -8.53011312249895 +984000 ekin = 1.68995499845883 | erot = 2.36799213713314 | epot = -12.5880602580152 | etot = -8.53011312242327 +985000 ekin = 1.71562347305687 | erot = 2.37731939437886 | epot = -12.6230559899602 | etot = -8.5301131225245 +986000 ekin = 1.73850018165221 | erot = 2.41550202449183 | epot = -12.6841153289477 | etot = -8.53011312280364 +987000 ekin = 1.75791457125372 | erot = 2.47889412323631 | epot = -12.7669218177375 | etot = -8.53011312324744 +988000 ekin = 1.77306329674351 | erot = 2.56140924190709 | epot = -12.8645856624799 | etot = -8.53011312382927 +989000 ekin = 1.78306912448162 | erot = 2.65491288897562 | epot = -12.9680951379619 | etot = -8.53011312450465 +990000 ekin = 1.78711020292118 | erot = 2.74980403799705 | epot = -13.0670273661277 | etot = -8.53011312520947 +991000 ekin = 1.78462774609367 | erot = 2.83581968224401 | epot = -13.1505605541974 | etot = -8.53011312585969 +992000 ekin = 1.77558737009051 | erot = 2.9030532797661 | epot = -13.2087537762222 | etot = -8.53011312636561 +993000 ekin = 1.76071115996797 | erot = 2.94306881053661 | epot = -13.2338930971609 | etot = -8.53011312665633 +994000 ekin = 1.74155803531838 | erot = 2.94987789379559 | epot = -13.2215490558191 | etot = -8.53011312670518 +995000 ekin = 1.7203663536266 | erot = 2.92053034159358 | epot = -13.171009821755 | etot = -8.53011312653484 +996000 ekin = 1.69928711841057 | erot = 2.85461248857379 | epot = -13.0840127336349 | etot = -8.53011312665052 +997000 ekin = 1.67961730933121 | erot = 2.75367224451106 | epot = -12.963402680013 | etot = -8.53011312617073 +998000 ekin = 1.66320821768275 | erot = 2.62336921200245 | epot = -12.8166905552899 | etot = -8.53011312560465 +999000 ekin = 1.65140969902045 | erot = 2.47137959793784 | epot = -12.652902421993 | etot = -8.5301131250347 +1000000 ekin = 1.64474900328077 | erot = 2.30633529340389 | epot = -12.481197421207 | etot = -8.53011312452231 + 1000000 0.12183326 -1.2831408 0.035021017 -1.0836448 3.258552e-05 64000 +Loop time of 11.8041 on 1 procs for 1000000 steps with 10 atoms + +Performance: 73194.863 tau/day, 84716.277 timesteps/s, 847.163 katom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.445 | 9.445 | 9.445 | 0.0 | 80.01 +Bond | 0.46517 | 0.46517 | 0.46517 | 0.0 | 3.94 +Neigh | 0.006341 | 0.006341 | 0.006341 | 0.0 | 0.05 +Comm | 0.2823 | 0.2823 | 0.2823 | 0.0 | 2.39 +Output | 0.12112 | 0.12112 | 0.12112 | 0.0 | 1.03 +Modify | 1.1786 | 1.1786 | 1.1786 | 0.0 | 9.98 +Other | | 0.3055 | | | 2.59 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:11 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/log.19May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/log.19May24.duplex1.g++.4 new file mode 100644 index 0000000000..17a927bae2 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/log.19May24.duplex1.g++.4 @@ -0,0 +1,1120 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.008 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna2.lj with DATE: 2024-04-21 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (stk) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (hbond) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (xstk) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (coaxstk) file oxdna2.lj with DATE: 2024-04-21 +Reading oxdna potential (dh) file oxdna2.lj with DATE: 2024-04-21 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3014979 + ghost atom cutoff = 4.3014979 + binsize = 2.150749, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 1e-05 +WARNING: Communication cutoff adjusted to 4.301497916929199 (src/comm.cpp:739) +0 ekin = 1.10853632272819 | erot = 2.81573649976629 | epot = -12.4543859162177 | etot = -8.5301130937232 +Per MPI rank memory allocation (min/avg/max) = 7.451 | 7.452 | 7.453 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0.082113802 -1.3525648 0.10712616 -1.134585 -6.3346859e-05 64000 +1000 ekin = 1.07575988625876 | erot = 2.91276427031684 | epot = -12.5186372505574 | etot = -8.53011309398184 +2000 ekin = 1.05292961692331 | erot = 3.00631080619826 | epot = -12.5893535174382 | etot = -8.53011309431666 +3000 ekin = 1.0404793567822 | erot = 3.09099198685795 | epot = -12.6615844383057 | etot = -8.53011309466551 +4000 ekin = 1.03797149598187 | erot = 3.16182957406827 | epot = -12.7299141650203 | etot = -8.53011309497019 +5000 ekin = 1.04436175992636 | erot = 3.21484050133171 | epot = -12.7893153564538 | etot = -8.53011309519572 +6000 ekin = 1.05826196166896 | erot = 3.24734130245545 | epot = -12.8357163594552 | etot = -8.53011309533081 +7000 ekin = 1.07813397987524 | erot = 3.25800057687381 | epot = -12.8662476521274 | etot = -8.53011309537834 +8000 ekin = 1.10242233608897 | erot = 3.24677351912865 | epot = -12.8793089505568 | etot = -8.53011309533922 +9000 ekin = 1.12966192883192 | erot = 3.21481512313357 | epot = -12.8745901471787 | etot = -8.53011309521326 +10000 ekin = 1.15857365226601 | erot = 3.16442800302929 | epot = -12.8531147503058 | etot = -8.53011309501054 +11000 ekin = 1.18812580536513 | erot = 3.09887248462026 | epot = -12.8171113847419 | etot = -8.53011309475649 +12000 ekin = 1.21753508254985 | erot = 3.02200194393141 | epot = -12.7696501209729 | etot = -8.53011309449164 +13000 ekin = 1.24620583234319 | erot = 2.93774306031816 | epot = -12.7140619869169 | etot = -8.53011309425555 +14000 ekin = 1.27363535726507 | erot = 2.84960621277601 | epot = -12.6533546641221 | etot = -8.53011309408098 +15000 ekin = 1.29932429763731 | erot = 2.76035703495632 | epot = -12.5897944265539 | etot = -8.53011309396028 +16000 ekin = 1.32272478678513 | erot = 2.67209376312961 | epot = -12.5249316438079 | etot = -8.53011309389312 +17000 ekin = 1.34324184048093 | erot = 2.58606256429299 | epot = -12.4594174987188 | etot = -8.53011309394488 +18000 ekin = 1.36028413036245 | erot = 2.5024472582327 | epot = -12.3928444826192 | etot = -8.53011309402405 +19000 ekin = 1.3733572823133 | erot = 2.42064483701924 | epot = -12.32411521343 | etot = -8.53011309409746 +20000 ekin = 1.38218242867039 | erot = 2.34004763399698 | epot = -12.2523431568013 | etot = -8.53011309413396 +21000 ekin = 1.38682228720772 | erot = 2.26037911407471 | epot = -12.177314495392 | etot = -8.53011309410961 +22000 ekin = 1.38779551760391 | erot = 2.18193012018468 | epot = -12.0998387317995 | etot = -8.53011309401088 +23000 ekin = 1.38615925697238 | erot = 2.10566093427181 | epot = -12.021933285081 | etot = -8.53011309383678 +24000 ekin = 1.38353970337944 | erot = 2.03315888827121 | epot = -11.9468116852497 | etot = -8.530113093599 +25000 ekin = 1.38209065002968 | erot = 1.96646602495015 | epot = -11.8786697683023 | etot = -8.53011309332244 +26000 ekin = 1.38436080324078 | erot = 1.90779815728283 | epot = -11.8222720535675 | etot = -8.53011309304391 +27000 ekin = 1.39305591970655 | erot = 1.8591880530227 | epot = -11.7823570655396 | etot = -8.53011309281036 +28000 ekin = 1.41069326836982 | erot = 1.82208843481197 | epot = -11.7628947958564 | etot = -8.53011309267462 +29000 ekin = 1.43917287732197 | erot = 1.79698086203717 | epot = -11.7662668320475 | etot = -8.53011309268833 +30000 ekin = 1.47932849918231 | erot = 1.78306055931677 | epot = -11.7925021513846 | etot = -8.53011309288555 +31000 ekin = 1.53057628219279 | erot = 1.77809666847726 | epot = -11.8387860439327 | etot = -8.53011309326269 +32000 ekin = 1.59082591350698 | erot = 1.77861870572293 | epot = -11.8995577129104 | etot = -8.53011309368051 +33000 ekin = 1.65668666319862 | erot = 1.78084924850019 | epot = -11.967649005945 | etot = -8.53011309424617 +34000 ekin = 1.72400978324383 | erot = 1.78052778818401 | epot = -12.0346506661702 | etot = -8.53011309474232 +35000 ekin = 1.78861238256258 | erot = 1.77409588873529 | epot = -12.0928213663776 | etot = -8.53011309507968 +36000 ekin = 1.84692171859322 | erot = 1.75957152442149 | epot = -12.1366063382344 | etot = -8.53011309521972 +37000 ekin = 1.89635505211505 | erot = 1.73677582238477 | epot = -12.1632439696809 | etot = -8.53011309518106 +38000 ekin = 1.93537564106362 | erot = 1.70707948670443 | epot = -12.1725682227887 | etot = -8.53011309502064 +39000 ekin = 1.96330319937453 | erot = 1.67283213027277 | epot = -12.1662484244534 | etot = -8.53011309480613 +40000 ekin = 1.98002136738534 | erot = 1.63672123005977 | epot = -12.1468556920403 | etot = -8.53011309459515 +41000 ekin = 1.98570586801275 | erot = 1.60124465405429 | epot = -12.117063616483 | etot = -8.53011309441591 +42000 ekin = 1.98063892667616 | erot = 1.56840871961068 | epot = -12.0791607405716 | etot = -8.53011309428474 +43000 ekin = 1.9651238118878 | erot = 1.53942032547724 | epot = -12.0346572315589 | etot = -8.53011309419391 +44000 ekin = 1.93948381096139 | erot = 1.51506739642153 | epot = -11.9846643015137 | etot = -8.53011309413079 +45000 ekin = 1.90411789628647 | erot = 1.49583019895569 | epot = -11.9300611893209 | etot = -8.53011309407871 +46000 ekin = 1.85959054249419 | erot = 1.48193663738999 | epot = -11.8716402739047 | etot = -8.53011309402051 +47000 ekin = 1.80673127931988 | erot = 1.47351008731121 | epot = -11.8103544605731 | etot = -8.53011309394205 +48000 ekin = 1.74672194665358 | erot = 1.47069179369341 | epot = -11.7475268341804 | etot = -8.53011309383339 +49000 ekin = 1.6811537904323 | erot = 1.47372603796079 | epot = -11.6849929220836 | etot = -8.53011309369055 +50000 ekin = 1.61204360764145 | erot = 1.48300481815601 | epot = -11.6251615193119 | etot = -8.5301130935144 +51000 ekin = 1.54180688827919 | erot = 1.49907572686282 | epot = -11.5709957084491 | etot = -8.53011309330705 +52000 ekin = 1.47319223880838 | erot = 1.52262764796941 | epot = -11.525932979863 | etot = -8.53011309308517 +53000 ekin = 1.40918336186051 | erot = 1.55438319093886 | epot = -11.4936796456592 | etot = -8.53011309285979 +54000 ekin = 1.35286923285696 | erot = 1.59499333649063 | epot = -11.4779756619993 | etot = -8.5301130926517 +55000 ekin = 1.30727610104069 | erot = 1.64486884964692 | epot = -11.4822580431751 | etot = -8.53011309248744 +56000 ekin = 1.27516041362746 | erot = 1.70395929448975 | epot = -11.5092328005143 | etot = -8.53011309239705 +57000 ekin = 1.25877821290744 | erot = 1.7715304526103 | epot = -11.5604217579236 | etot = -8.53011309240586 +58000 ekin = 1.25966981557414 | erot = 1.84600740239498 | epot = -11.6357903104947 | etot = -8.53011309252561 +59000 ekin = 1.27850991703415 | erot = 1.92494493442919 | epot = -11.733567944215 | etot = -8.53011309275162 +60000 ekin = 1.31505846517362 | erot = 2.00506933713728 | epot = -11.8502408954026 | etot = -8.53011309309171 +61000 ekin = 1.36820967857689 | erot = 2.08251311350642 | epot = -11.9808358855455 | etot = -8.53011309346224 +62000 ekin = 1.43610935375694 | erot = 2.15340897405292 | epot = -12.1196314216667 | etot = -8.53011309385685 +63000 ekin = 1.51630533152243 | erot = 2.21410084325619 | epot = -12.2605192690213 | etot = -8.5301130942427 +64000 ekin = 1.60588594281046 | erot = 2.26150680600709 | epot = -12.3975058434117 | etot = -8.53011309459412 +65000 ekin = 1.70157559823958 | erot = 2.2934317361934 | epot = -12.5251204293295 | etot = -8.53011309489655 +66000 ekin = 1.79977612979936 | erot = 2.30875943510443 | epot = -12.638648660053 | etot = -8.53011309514926 +67000 ekin = 1.8965689647425 | erot = 2.30747600160478 | epot = -12.7341580617101 | etot = -8.53011309536285 +68000 ekin = 1.98772340358679 | erot = 2.29052837543634 | epot = -12.8083648745723 | etot = -8.53011309554919 +69000 ekin = 2.06877558194337 | erot = 2.25958722526862 | epot = -12.8584759029223 | etot = -8.53011309571028 +70000 ekin = 2.13523440531587 | erot = 2.21681911735311 | epot = -12.8821666185006 | etot = -8.5301130958316 +71000 ekin = 2.18292944014475 | erot = 2.16475080910326 | epot = -12.8777933451315 | etot = -8.53011309588345 +72000 ekin = 2.20845503567797 | erot = 2.10623867450861 | epot = -12.8448068060203 | etot = -8.53011309583374 +73000 ekin = 2.20961374982451 | erot = 2.04448327477891 | epot = -12.7842101202317 | etot = -8.53011309562828 +74000 ekin = 2.18583088959651 | erot = 1.98307376954826 | epot = -12.6990177544744 | etot = -8.53011309532966 +75000 ekin = 2.13819357127726 | erot = 1.92577296068293 | epot = -12.5940796268925 | etot = -8.5301130949323 +76000 ekin = 2.06931387379133 | erot = 1.87621391736399 | epot = -12.4756408856268 | etot = -8.53011309447153 +77000 ekin = 1.98314599352095 | erot = 1.83766509006174 | epot = -12.3509241775701 | etot = -8.53011309398736 +78000 ekin = 1.8846400354909 | erot = 1.81276644965543 | epot = -12.227519578665 | etot = -8.53011309351871 +79000 ekin = 1.77934330540936 | erot = 1.80331865972891 | epot = -12.1127750582402 | etot = -8.53011309310191 +80000 ekin = 1.67297594037611 | erot = 1.81012474896306 | epot = -12.0132137821112 | etot = -8.530113092772 +81000 ekin = 1.57099416873038 | erot = 1.83286904429981 | epot = -11.9339763055925 | etot = -8.53011309256232 +82000 ekin = 1.47816348110911 | erot = 1.87002999046013 | epot = -11.8783065640687 | etot = -8.53011309249949 +83000 ekin = 1.39818778462314 | erot = 1.91885160298051 | epot = -11.8471524801997 | etot = -8.53011309259605 +84000 ekin = 1.33345814529582 | erot = 1.97542175599065 | epot = -11.8389929941299 | etot = -8.53011309284345 +85000 ekin = 1.28497532516104 | erot = 2.03490617744834 | epot = -11.8499945958147 | etot = -8.53011309320533 +86000 ekin = 1.25246025395615 | erot = 2.09197660059405 | epot = -11.8745499481787 | etot = -8.53011309362848 +87000 ekin = 1.23461285408046 | erot = 2.14137296784406 | epot = -11.9060989159749 | etot = -8.53011309405039 +88000 ekin = 1.22943812073966 | erot = 2.17852719424188 | epot = -11.9380784093967 | etot = -8.53011309441514 +89000 ekin = 1.23455364871389 | erot = 2.20012041252095 | epot = -11.9647871559198 | etot = -8.53011309468496 +90000 ekin = 1.2474258057653 | erot = 2.20445455177191 | epot = -11.9819934523816 | etot = -8.53011309484435 +91000 ekin = 1.26553383084727 | erot = 2.19157144961194 | epot = -11.9872183753551 | etot = -8.53011309489588 +92000 ekin = 1.28623000858128 | erot = 2.16295140457774 | epot = -11.9792945080808 | etot = -8.53011309492179 +93000 ekin = 1.30692364344404 | erot = 2.12123926047763 | epot = -11.9582759987369 | etot = -8.53011309481527 +94000 ekin = 1.32581527393291 | erot = 2.07018243043902 | epot = -11.9261107990066 | etot = -8.53011309463468 +95000 ekin = 1.34182901778851 | erot = 2.01402433128774 | epot = -11.8859664434698 | etot = -8.53011309439352 +96000 ekin = 1.35474622264815 | erot = 1.95709566330696 | epot = -11.8419549800687 | etot = -8.5301130941136 +97000 ekin = 1.3651858824784 | erot = 1.90343342927394 | epot = -11.7987324055814 | etot = -8.53011309382907 +98000 ekin = 1.37438024241784 | erot = 1.85642234303625 | epot = -11.7609156790417 | etot = -8.53011309358765 +99000 ekin = 1.38375494732497 | erot = 1.818460002256 | epot = -11.7323280430253 | etot = -8.53011309344429 +100000 ekin = 1.39439154293922 | erot = 1.7906626113338 | epot = -11.7151672477191 | etot = -8.53011309344611 +101000 ekin = 1.4065061005343 | erot = 1.77268374626491 | epot = -11.7093029404211 | etot = -8.53011309362191 +102000 ekin = 1.41909865539709 | erot = 1.76268825953967 | epot = -11.7119000089019 | etot = -8.53011309396517 +103000 ekin = 1.42990225853212 | erot = 1.75756086568118 | epot = -11.7175762186405 | etot = -8.53011309442716 +104000 ekin = 1.43568960458639 | erot = 1.75339758186005 | epot = -11.7192002813658 | etot = -8.53011309491935 +105000 ekin = 1.43290883108536 | erot = 1.74626770102834 | epot = -11.7092896274386 | etot = -8.5301130953249 +106000 ekin = 1.41854295074829 | erot = 1.73316545657385 | epot = -11.6818215028411 | etot = -8.53011309551901 +107000 ekin = 1.39103174229088 | erot = 1.71299001598399 | epot = -11.6341348536724 | etot = -8.53011309539752 +108000 ekin = 1.35105252774005 | erot = 1.68731521419128 | epot = -11.5684808368424 | etot = -8.5301130949111 +109000 ekin = 1.30192293440572 | erot = 1.6606605582455 | epot = -11.4926965867502 | etot = -8.53011309409895 +110000 ekin = 1.24955692632168 | erot = 1.64004235665893 | epot = -11.41971237546 | etot = -8.5301130924794 +111000 ekin = 1.20373683101898 | erot = 1.63405660630875 | epot = -11.3679065290106 | etot = -8.53011309168286 +112000 ekin = 1.17136800050142 | erot = 1.64951573593143 | epot = -11.3509968276171 | etot = -8.53011309118424 +113000 ekin = 1.15643737252659 | erot = 1.6900200056894 | epot = -11.3765704693513 | etot = -8.53011309113527 +114000 ekin = 1.16016664919805 | erot = 1.75506593403365 | epot = -11.4453456747902 | etot = -8.53011309155847 +115000 ekin = 1.18078581898516 | erot = 1.83995213492409 | epot = -11.5508510462435 | etot = -8.53011309233425 +116000 ekin = 1.21421955357408 | erot = 1.93685465219959 | epot = -11.6811872990248 | etot = -8.53011309325109 +117000 ekin = 1.25536144135774 | erot = 2.03668558524356 | epot = -11.8221601206883 | etot = -8.53011309408699 +118000 ekin = 1.29940451384038 | erot = 2.13109010342711 | epot = -11.9606077119486 | etot = -8.53011309468107 +119000 ekin = 1.34277477684622 | erot = 2.2139739395163 | epot = -12.0868618113314 | etot = -8.53011309496886 +120000 ekin = 1.38347061820567 | erot = 2.28221236483783 | epot = -12.195796078023 | etot = -8.53011309497945 +121000 ekin = 1.42087086651062 | erot = 2.33551129662439 | epot = -12.286495257938 | etot = -8.53011309480299 +122000 ekin = 1.45522638977893 | erot = 2.37564292906074 | epot = -12.3609824133916 | etot = -8.53011309455193 +123000 ekin = 1.48707582665851 | erot = 2.40539124222057 | epot = -12.4225801632066 | etot = -8.53011309432755 +124000 ekin = 1.51676676843729 | erot = 2.42751903858547 | epot = -12.4743989012238 | etot = -8.53011309420102 +125000 ekin = 1.5441745977234 | erot = 2.44396324559633 | epot = -12.5182509375264 | etot = -8.53011309420666 +126000 ekin = 1.56863810035623 | erot = 2.45535112725137 | epot = -12.5541023219514 | etot = -8.53011309434382 +127000 ekin = 1.58908101361922 | erot = 2.4608536627411 | epot = -12.580047770942 | etot = -8.53011309458164 +128000 ekin = 1.60427083888446 | erot = 2.4583616853006 | epot = -12.592745619049 | etot = -8.5301130948639 +129000 ekin = 1.61315658291899 | erot = 2.44495811201836 | epot = -12.5882277900551 | etot = -8.53011309511771 +130000 ekin = 1.61521763497892 | erot = 2.41762859319586 | epot = -12.5629593234414 | etot = -8.53011309526658 +131000 ekin = 1.61074673258845 | erot = 2.37408565093732 | epot = -12.514945478776 | etot = -8.53011309525019 +132000 ekin = 1.60099281445362 | erot = 2.31350559906005 | epot = -12.4446115085561 | etot = -8.53011309504247 +133000 ekin = 1.58811839137776 | erot = 2.23695676757785 | epot = -12.3551882536167 | etot = -8.5301130946611 +134000 ekin = 1.57497837856398 | erot = 2.14737907152235 | epot = -12.2524705442819 | etot = -8.53011309419559 +135000 ekin = 1.56467799512196 | erot = 2.04902291672334 | epot = -12.1438140054853 | etot = -8.53011309363996 +136000 ekin = 1.5603330606487 | erot = 1.94701578013103 | epot = -12.0374619338914 | etot = -8.53011309311163 +137000 ekin = 1.56479379508655 | erot = 1.84660873227908 | epot = -11.9415156200319 | etot = -8.53011309266624 +138000 ekin = 1.58030314703457 | erot = 1.75245153796817 | epot = -11.8628677773364 | etot = -8.53011309233368 +139000 ekin = 1.60833080358471 | erot = 1.66826609139363 | epot = -11.8067099871002 | etot = -8.53011309212189 +140000 ekin = 1.64949521723208 | erot = 1.59676588041037 | epot = -11.7763741896652 | etot = -8.53011309202271 +141000 ekin = 1.70355355174871 | erot = 1.53975804779902 | epot = -11.773424691523 | etot = -8.53011309197523 +142000 ekin = 1.76943720118451 | erot = 1.49859523121373 | epot = -11.7981455244588 | etot = -8.53011309206051 +143000 ekin = 1.84530405880869 | erot = 1.4738494585272 | epot = -11.8492666095581 | etot = -8.53011309222225 +144000 ekin = 1.92861465369007 | erot = 1.46549379274605 | epot = -11.9242215388109 | etot = -8.53011309237475 +145000 ekin = 2.01648600784357 | erot = 1.47353305209417 | epot = -12.0201321527186 | etot = -8.53011309278083 +146000 ekin = 2.1045821227571 | erot = 1.49637875128969 | epot = -12.1310739673145 | etot = -8.53011309326768 +147000 ekin = 2.18785677137355 | erot = 1.53145919849867 | epot = -12.2494290636981 | etot = -8.53011309382584 +148000 ekin = 2.26104758516568 | erot = 1.57543986095963 | epot = -12.3666005405499 | etot = -8.53011309442461 +149000 ekin = 2.31910091716388 | erot = 1.62430319702527 | epot = -12.4735172091952 | etot = -8.53011309500607 +150000 ekin = 2.35773821658458 | erot = 1.67365853244602 | epot = -12.5615098445244 | etot = -8.53011309549382 +151000 ekin = 2.37405078100319 | erot = 1.71926726329679 | epot = -12.6234311401169 | etot = -8.53011309581693 +152000 ekin = 2.36692545461656 | erot = 1.75764773901397 | epot = -12.6546862895674 | etot = -8.5301130959369 +153000 ekin = 2.33712749183116 | erot = 1.78656744402779 | epot = -12.6538080317174 | etot = -8.53011309585849 +154000 ekin = 2.28703010669305 | erot = 1.80529001826418 | epot = -12.6224332205717 | etot = -8.5301130956145 +155000 ekin = 2.2201721095778 | erot = 1.81456905274717 | epot = -12.5648542575676 | etot = -8.53011309524261 +156000 ekin = 2.14087216650219 | erot = 1.8164601718651 | epot = -12.4874454331419 | etot = -8.53011309477457 +157000 ekin = 2.05398632051204 | erot = 1.81400844427827 | epot = -12.3981078590404 | etot = -8.53011309425007 +158000 ekin = 1.96465269026368 | erot = 1.81075171604387 | epot = -12.3055175001036 | etot = -8.53011309379607 +159000 ekin = 1.87738211880393 | erot = 1.8097580903437 | epot = -12.2172533025071 | etot = -8.53011309335947 +160000 ekin = 1.79637755657255 | erot = 1.81368342474314 | epot = -12.1401740743807 | etot = -8.53011309306501 +161000 ekin = 1.72479660822577 | erot = 1.82417298786708 | epot = -12.0790826890685 | etot = -8.53011309297568 +162000 ekin = 1.66403255347704 | erot = 1.84141406703924 | epot = -12.0355597136267 | etot = -8.53011309311038 +163000 ekin = 1.61344211817714 | erot = 1.86416684407958 | epot = -12.0077220556825 | etot = -8.53011309342581 +164000 ekin = 1.57053136480723 | erot = 1.89024538669912 | epot = -11.9908898453323 | etot = -8.53011309382591 +165000 ekin = 1.53158684055339 | erot = 1.91735211282864 | epot = -11.9790520475678 | etot = -8.53011309418574 +166000 ekin = 1.49257533008441 | erot = 1.94405290672982 | epot = -11.9667413312092 | etot = -8.53011309439499 +167000 ekin = 1.4500473961487 | erot = 1.97054282183292 | epot = -11.9507033123734 | etot = -8.53011309439173 +168000 ekin = 1.40180339426623 | erot = 1.99893184094582 | epot = -11.9308483293898 | etot = -8.53011309417774 +169000 ekin = 1.34719230179042 | erot = 2.03295603374783 | epot = -11.9102614293486 | etot = -8.53011309381032 +170000 ekin = 1.28704969495297 | erot = 2.07721655562297 | epot = -11.8943793439503 | etot = -8.53011309337434 +171000 ekin = 1.22340120606645 | erot = 2.13620458401877 | epot = -11.8897188830152 | etot = -8.53011309293002 +172000 ekin = 1.15916399135863 | erot = 2.21333149138569 | epot = -11.9026085753698 | etot = -8.53011309262547 +173000 ekin = 1.09731722457339 | erot = 2.31014635554163 | epot = -11.9375766725982 | etot = -8.5301130924832 +174000 ekin = 1.04063961884125 | erot = 2.42581098119786 | epot = -11.9965636925778 | etot = -8.53011309253868 +175000 ekin = 0.991434959332931 | erot = 2.556873745854 | epot = -12.0784217979903 | etot = -8.53011309280332 +176000 ekin = 0.951286219743454 | erot = 2.69734247997586 | epot = -12.1787417929829 | etot = -8.53011309326361 +177000 ekin = 0.920906931255869 | erot = 2.83907560795435 | epot = -12.290095633086 | etot = -8.53011309387581 +178000 ekin = 0.900110889875705 | erot = 2.97251922257693 | epot = -12.4027432070177 | etot = -8.53011309456511 +179000 ekin = 0.887921283965262 | erot = 3.08778217993997 | epot = -12.5058165591357 | etot = -8.53011309523047 +180000 ekin = 0.882819894460704 | erot = 3.17595008457056 | epot = -12.5888830747921 | etot = -8.53011309576086 +181000 ekin = 0.883094662246339 | erot = 3.23041576817458 | epot = -12.643623526485 | etot = -8.53011309606404 +182000 ekin = 0.887197266496938 | erot = 3.24791323274223 | epot = -12.6652235953326 | etot = -8.5301130960934 +183000 ekin = 0.894005517566709 | erot = 3.22896613968099 | epot = -12.6530847531088 | etot = -8.53011309586114 +184000 ekin = 0.902922567053486 | erot = 3.17763362004039 | epot = -12.6106692825231 | etot = -8.53011309542923 +185000 ekin = 0.913819897430119 | erot = 3.10068233612839 | epot = -12.5446153284403 | etot = -8.53011309488181 +186000 ekin = 0.926892274386875 | erot = 3.00648382594899 | epot = -12.4634891947411 | etot = -8.53011309440524 +187000 ekin = 0.942359343467852 | erot = 2.90341264008053 | epot = -12.3758850774295 | etot = -8.53011309388114 +188000 ekin = 0.960415128419152 | erot = 2.79950233215061 | epot = -12.2900305539843 | etot = -8.53011309341452 +189000 ekin = 0.981336580896334 | erot = 2.70221969054365 | epot = -12.2136693644683 | etot = -8.53011309302835 +190000 ekin = 1.00543372733302 | erot = 2.61771835557138 | epot = -12.153265175663 | etot = -8.53011309275858 +191000 ekin = 1.03305642669596 | erot = 2.55042331784757 | epot = -12.113592837133 | etot = -8.53011309258951 +192000 ekin = 1.06458819978588 | erot = 2.50295149261136 | epot = -12.0976527849393 | etot = -8.53011309254206 +193000 ekin = 1.10043008600705 | erot = 2.47591461062942 | epot = -12.1064577892561 | etot = -8.53011309261967 +194000 ekin = 1.14095348228018 | erot = 2.46790659075077 | epot = -12.1389731658491 | etot = -8.53011309281815 +195000 ekin = 1.18642396462111 | erot = 2.47566002440206 | epot = -12.1921970821457 | etot = -8.53011309312254 +196000 ekin = 1.23691456053948 | erot = 2.49438862695221 | epot = -12.2614162809959 | etot = -8.53011309350423 +197000 ekin = 1.29223924615411 | erot = 2.51832160490974 | epot = -12.3406739449842 | etot = -8.53011309392031 +198000 ekin = 1.3519347146633 | erot = 2.54139178285202 | epot = -12.4234395918354 | etot = -8.53011309432009 +199000 ekin = 1.41529957065379 | erot = 2.55798242673069 | epot = -12.5033950920395 | etot = -8.530113094655 +200000 ekin = 1.48147390057833 | erot = 2.56359779441088 | epot = -12.5751847898783 | etot = -8.53011309488911 +201000 ekin = 1.54952685169063 | erot = 2.55533485734931 | epot = -12.6349748040453 | etot = -8.53011309500533 +202000 ekin = 1.61852368373135 | erot = 2.53209551772225 | epot = -12.6807322964585 | etot = -8.53011309500488 +203000 ekin = 1.68755981245424 | erot = 2.49462961612296 | epot = -12.7123025234434 | etot = -8.53011309486622 +204000 ekin = 1.75576103235039 | erot = 2.44539440890628 | epot = -12.731268535947 | etot = -8.53011309469034 +205000 ekin = 1.82226727517167 | erot = 2.3878008171597 | epot = -12.7401811867911 | etot = -8.53011309445972 +206000 ekin = 1.88619984147331 | erot = 2.32611076719035 | epot = -12.7424237028676 | etot = -8.53011309420394 +207000 ekin = 1.94660231588698 | erot = 2.26504166017917 | epot = -12.7417570700271 | etot = -8.53011309396097 +208000 ekin = 2.00235042264665 | erot = 2.20925458967758 | epot = -12.7417181061045 | etot = -8.53011309378024 +209000 ekin = 2.0520313483485 | erot = 2.16271925047888 | epot = -12.7448636925489 | etot = -8.53011309372154 +210000 ekin = 2.09381524344954 | erot = 2.12796343490961 | epot = -12.751891772204 | etot = -8.53011309384484 +211000 ekin = 2.12537929046287 | erot = 2.10530160183622 | epot = -12.7607939864875 | etot = -8.53011309418839 +212000 ekin = 2.1439884510964 | erot = 2.0922650676153 | epot = -12.766366613447 | etot = -8.53011309473533 +213000 ekin = 2.14685083920888 | erot = 2.08357075606521 | epot = -12.760534690661 | etot = -8.53011309538686 +214000 ekin = 2.13177933558798 | erot = 2.07198437940492 | epot = -12.7338768105384 | etot = -8.53011309554549 +215000 ekin = 2.09740576159951 | erot = 2.0524367864944 | epot = -12.6799556440657 | etot = -8.5301130959718 +216000 ekin = 2.04414786570014 | erot = 2.0198081125597 | epot = -12.5940690742963 | etot = -8.5301130960365 +217000 ekin = 1.97496281847719 | erot = 1.97035714827525 | epot = -12.4754330625057 | etot = -8.53011309575328 +218000 ekin = 1.89483732384485 | erot = 1.9036903705145 | epot = -12.3286407894939 | etot = -8.53011309513458 +219000 ekin = 1.81041467830767 | erot = 1.82278463149675 | epot = -12.1633124040828 | etot = -8.53011309427844 +220000 ekin = 1.72938454081015 | erot = 1.73330150874432 | epot = -11.9927991427908 | etot = -8.53011309323634 +221000 ekin = 1.65959820381403 | erot = 1.64273176790391 | epot = -11.8324430640332 | etot = -8.53011309231531 +222000 ekin = 1.60845034453884 | erot = 1.55815968235219 | epot = -11.6967231184021 | etot = -8.5301130915111 +223000 ekin = 1.58228239189008 | erot = 1.48580466478726 | epot = -11.5982001475877 | etot = -8.53011309091036 +224000 ekin = 1.58569765517033 | erot = 1.43046423809837 | epot = -11.5462749838456 | etot = -8.5301130905769 +225000 ekin = 1.62100953317755 | erot = 1.39504063224538 | epot = -11.5461632559818 | etot = -8.53011309055883 +226000 ekin = 1.68783126437574 | erot = 1.38020176396443 | epot = -11.5981461192342 | etot = -8.530113090894 +227000 ekin = 1.78271150290612 | erot = 1.38413372943434 | epot = -11.6969583246216 | etot = -8.53011309228119 +228000 ekin = 1.89495289262447 | erot = 1.40258789217286 | epot = -11.8276538782986 | etot = -8.53011309350131 +229000 ekin = 2.01170607721918 | erot = 1.42820655801903 | epot = -11.9700257301881 | etot = -8.53011309494986 +230000 ekin = 2.11989887159711 | erot = 1.45235409717163 | epot = -12.102366065035 | etot = -8.53011309626622 +231000 ekin = 2.20759782077834 | erot = 1.46730876356824 | epot = -12.2050196815075 | etot = -8.53011309716089 +232000 ekin = 2.26562589153249 | erot = 1.46886009000409 | epot = -12.2645990789946 | etot = -8.53011309745806 +233000 ekin = 2.2882250697573 | erot = 1.45787535434396 | epot = -12.2762135212093 | etot = -8.53011309710803 +234000 ekin = 2.2746452497783 | erot = 1.43990370669354 | epot = -12.2446620527937 | etot = -8.5301130963219 +235000 ekin = 2.22825507530842 | erot = 1.42328017859139 | epot = -12.1816483492734 | etot = -8.53011309537358 +236000 ekin = 2.15494106311448 | erot = 1.41661045699318 | epot = -12.1016646145791 | etot = -8.53011309447141 +237000 ekin = 2.06197124561353 | erot = 1.4267772919224 | epot = -12.0188616312515 | etot = -8.53011309371556 +238000 ekin = 1.95733575736037 | erot = 1.45790014383004 | epot = -11.9453489943261 | etot = -8.53011309313565 +239000 ekin = 1.84937348817194 | erot = 1.51100787616977 | epot = -11.8904944570913 | etot = -8.53011309274963 +240000 ekin = 1.74634948667495 | erot = 1.58401675949126 | epot = -11.8604793387574 | etot = -8.53011309259121 +241000 ekin = 1.65579840431634 | erot = 1.67182932722897 | epot = -11.857740824243 | etot = -8.53011309269764 +242000 ekin = 1.58370704114883 | erot = 1.76665328809278 | epot = -11.8804734223152 | etot = -8.53011309307357 +243000 ekin = 1.53379082409385 | erot = 1.85876363932242 | epot = -11.9226675570786 | etot = -8.53011309366233 +244000 ekin = 1.50713311675952 | erot = 1.93781479613316 | epot = -11.9750610072397 | etot = -8.53011309434701 +245000 ekin = 1.50232523408817 | erot = 1.9945308549142 | epot = -12.0269691839801 | etot = -8.53011309497775 +246000 ekin = 1.51606904510254 | erot = 2.02239007086975 | epot = -12.0685722113879 | etot = -8.53011309541558 +247000 ekin = 1.54406668998812 | erot = 2.01887471172796 | epot = -12.0930544972696 | etot = -8.53011309555354 +248000 ekin = 1.58197270416959 | erot = 1.98608525491879 | epot = -12.0981710544433 | etot = -8.53011309535488 +249000 ekin = 1.62609171467947 | erot = 1.93029875238705 | epot = -12.086503561957 | etot = -8.5301130948905 +250000 ekin = 1.67387536281804 | erot = 1.86081409573898 | epot = -12.0648025528068 | etot = -8.53011309424979 +251000 ekin = 1.7239109698586 | erot = 1.78844826295721 | epot = -12.0424723264224 | etot = -8.53011309360662 +252000 ekin = 1.775381907117 | erot = 1.72367191237892 | epot = -12.0291669125776 | etot = -8.53011309308168 +253000 ekin = 1.82754829280966 | erot = 1.67492092834061 | epot = -12.0325823139112 | etot = -8.5301130927609 +254000 ekin = 1.87961881561752 | erot = 1.64770020961706 | epot = -12.0574321179075 | etot = -8.53011309267291 +255000 ekin = 1.93045785731848 | erot = 1.64434942868997 | epot = -12.1049203788172 | etot = -8.53011309280879 +256000 ekin = 1.97849877464101 | erot = 1.66421751998728 | epot = -12.1728293877678 | etot = -8.53011309313946 +257000 ekin = 2.02175661791442 | erot = 1.70407398948181 | epot = -12.2559437010213 | etot = -8.53011309362504 +258000 ekin = 2.05791961396963 | erot = 1.75862748975079 | epot = -12.34666019794 | etot = -8.53011309421958 +259000 ekin = 2.08450645969332 | erot = 1.82109836580911 | epot = -12.4357179203747 | etot = -8.5301130948723 +260000 ekin = 2.0990728506794 | erot = 1.88382726111794 | epot = -12.5130132073272 | etot = -8.53011309552988 +261000 ekin = 2.09944572596275 | erot = 1.93893768787103 | epot = -12.5684965099607 | etot = -8.53011309612693 +262000 ekin = 2.08396569038833 | erot = 1.9790846279756 | epot = -12.5931634149729 | etot = -8.53011309660893 +263000 ekin = 2.05172676882149 | erot = 1.99820908887188 | epot = -12.5800489545523 | etot = -8.53011309685892 +264000 ekin = 2.00296719649698 | erot = 1.99283439178409 | epot = -12.5259146850339 | etot = -8.53011309675287 +265000 ekin = 1.93948872899256 | erot = 1.96339266268558 | epot = -12.4329944878823 | etot = -8.53011309620413 +266000 ekin = 1.8649439014403 | erot = 1.91505343003071 | epot = -12.3101104266342 | etot = -8.53011309516323 +267000 ekin = 1.78505719746936 | erot = 1.85721593585567 | epot = -12.1723862273119 | etot = -8.53011309398687 +268000 ekin = 1.70605852586759 | erot = 1.80175587067043 | epot = -12.0379274893381 | etot = -8.53011309280003 +269000 ekin = 1.63387234043083 | erot = 1.76055577812795 | epot = -11.924541210424 | etot = -8.53011309186518 +270000 ekin = 1.57342106955886 | erot = 1.7428100947827 | epot = -11.8463442556687 | etot = -8.53011309132713 +271000 ekin = 1.52797485202463 | erot = 1.7534108593537 | epot = -11.8114988026148 | etot = -8.53011309123648 +272000 ekin = 1.49894876525771 | erot = 1.79234603399444 | epot = -11.8214078908088 | etot = -8.53011309155661 +273000 ekin = 1.48604758198147 | erot = 1.85507402496668 | epot = -11.8712346991381 | etot = -8.53011309218999 +274000 ekin = 1.48766345157087 | erot = 1.93349346053591 | epot = -11.9512700051693 | etot = -8.53011309306249 +275000 ekin = 1.50135017863801 | erot = 2.01723774122183 | epot = -12.0487010137588 | etot = -8.53011309389898 +276000 ekin = 1.52425343307294 | erot = 2.09653669779313 | epot = -12.1509032254471 | etot = -8.530113094581 +277000 ekin = 1.55417046599772 | erot = 2.16339336358605 | epot = -12.2476769246684 | etot = -8.53011309508459 +278000 ekin = 1.58883002210849 | erot = 2.21269572879442 | epot = -12.3316388462093 | etot = -8.53011309530637 +279000 ekin = 1.62657848626988 | erot = 2.2427357529187 | epot = -12.3994273344828 | etot = -8.53011309529425 +280000 ekin = 1.66626462375805 | erot = 2.25488508621636 | epot = -12.4512628051118 | etot = -8.53011309513739 +281000 ekin = 1.70666329888323 | erot = 2.25287813756201 | epot = -12.4896545313678 | etot = -8.53011309492257 +282000 ekin = 1.74606224489453 | erot = 2.24193390477425 | epot = -12.5181092443719 | etot = -8.5301130947031 +283000 ekin = 1.78229604375805 | erot = 2.22773335199554 | epot = -12.5401424902727 | etot = -8.53011309451915 +284000 ekin = 1.81303392681924 | erot = 2.21528431694055 | epot = -12.5584313381487 | etot = -8.53011309438886 +285000 ekin = 1.83626784551407 | erot = 2.20859920573524 | epot = -12.5749801456027 | etot = -8.53011309435334 +286000 ekin = 1.8505679813094 | erot = 2.20962029353691 | epot = -12.5903013692885 | etot = -8.53011309444215 +287000 ekin = 1.85506353044408 | erot = 2.21784540833872 | epot = -12.6030220334131 | etot = -8.53011309463028 +288000 ekin = 1.84942339813604 | erot = 2.23075201933183 | epot = -12.6102885123084 | etot = -8.53011309484051 +289000 ekin = 1.83390888017438 | erot = 2.24488012942893 | epot = -12.6089021045823 | etot = -8.53011309497904 +290000 ekin = 1.80943255390731 | erot = 2.25722371529918 | epot = -12.5967693641607 | etot = -8.53011309495422 +291000 ekin = 1.77754353319189 | erot = 2.26619423186302 | epot = -12.5738508598504 | etot = -8.53011309479552 +292000 ekin = 1.74029196122747 | erot = 2.27170357096947 | epot = -12.5421086267528 | etot = -8.53011309455589 +293000 ekin = 1.69997543540441 | erot = 2.27474290666544 | epot = -12.5048314363837 | etot = -8.53011309431389 +294000 ekin = 1.65879913990757 | erot = 2.27646633894028 | epot = -12.4653785730015 | etot = -8.53011309415364 +295000 ekin = 1.61857194088063 | erot = 2.2772896553203 | epot = -12.4259746903014 | etot = -8.5301130941005 +296000 ekin = 1.58063856927687 | erot = 2.27661684716242 | epot = -12.3873685105274 | etot = -8.53011309408813 +297000 ekin = 1.54603085638188 | erot = 2.27331893745131 | epot = -12.3494628879057 | etot = -8.53011309407249 +298000 ekin = 1.51552933019819 | erot = 2.26654381109825 | epot = -12.3121862352838 | etot = -8.53011309398736 +299000 ekin = 1.4897866656468 | erot = 2.25633296635467 | epot = -12.2762327258637 | etot = -8.53011309386228 +300000 ekin = 1.46918272389837 | erot = 2.24345468614606 | epot = -12.242750503802 | etot = -8.53011309375758 +301000 ekin = 1.45354278560917 | erot = 2.22882911340837 | epot = -12.2124849927863 | etot = -8.53011309376879 +302000 ekin = 1.44183301629828 | erot = 2.21276714678466 | epot = -12.1847132569685 | etot = -8.53011309388556 +303000 ekin = 1.43225770121149 | erot = 2.1945809275263 | epot = -12.1569517228351 | etot = -8.53011309409729 +304000 ekin = 1.42259637357009 | erot = 2.17276750288833 | epot = -12.1254769707811 | etot = -8.53011309432264 +305000 ekin = 1.41064586326838 | erot = 2.14566468387999 | epot = -12.0864236416126 | etot = -8.53011309446427 +306000 ekin = 1.39473877107242 | erot = 2.11230934515746 | epot = -12.0371612106961 | etot = -8.53011309446626 +307000 ekin = 1.37401156154455 | erot = 2.07305527676002 | epot = -11.977179932614 | etot = -8.53011309430942 +308000 ekin = 1.34852470527996 | erot = 2.02957445559285 | epot = -11.908212254938 | etot = -8.53011309406523 +309000 ekin = 1.31899505489798 | erot = 1.98427269118996 | epot = -11.8333808399297 | etot = -8.53011309384175 +310000 ekin = 1.2862882665719 | erot = 1.93930156456111 | epot = -11.7557029248833 | etot = -8.53011309375026 +311000 ekin = 1.25093726244332 | erot = 1.89525998935032 | epot = -11.6763103458614 | etot = -8.5301130940678 +312000 ekin = 1.21290642809322 | erot = 1.84947048977057 | epot = -11.5924900122396 | etot = -8.53011309437579 +313000 ekin = 1.17141846112916 | erot = 1.79876682021589 | epot = -11.5002983761234 | etot = -8.5301130947783 +314000 ekin = 1.07288272942441 | erot = 1.70848696881221 | epot = -11.311482847546 | etot = -8.5301131493094 +315000 ekin = 0.929305233254205 | erot = 1.46737286493799 | epot = -10.9267911417366 | etot = -8.53011304354436 +316000 ekin = 1.33438953717469 | erot = 1.37623199915606 | epot = -11.2407347047679 | etot = -8.53011316843718 +317000 ekin = 1.40009371700333 | erot = 1.31826590785411 | epot = -11.2484727303621 | etot = -8.53011310550466 +318000 ekin = 1.43115359918425 | erot = 1.25971123043315 | epot = -11.2209779347371 | etot = -8.5301131051197 +319000 ekin = 1.45754379434943 | erot = 1.20520642772675 | epot = -11.1928633267516 | etot = -8.5301131046754 +320000 ekin = 1.48149893345698 | erot = 1.15864569690845 | epot = -11.170257734652 | etot = -8.53011310428657 +321000 ekin = 1.5051312843985 | erot = 1.12350400100625 | epot = -11.1587483894116 | etot = -8.53011310400684 +322000 ekin = 1.52997806002497 | erot = 1.10223049025935 | epot = -11.1623216541795 | etot = -8.5301131038952 +323000 ekin = 1.55672107909604 | erot = 1.09578101873819 | epot = -11.1826152017877 | etot = -8.53011310395352 +324000 ekin = 1.5851136620084 | erot = 1.10363080456445 | epot = -11.2188575707136 | etot = -8.53011310414072 +325000 ekin = 1.61412294527511 | erot = 1.12419697509005 | epot = -11.268433024751 | etot = -8.5301131043858 +326000 ekin = 1.64224941760094 | erot = 1.15551879655647 | epot = -11.3278813187727 | etot = -8.53011310461526 +327000 ekin = 1.66792915391961 | erot = 1.19590561828286 | epot = -11.3939478769664 | etot = -8.53011310476391 +328000 ekin = 1.68988361976044 | erot = 1.24442310373742 | epot = -11.4644198283235 | etot = -8.53011310482566 +329000 ekin = 1.70729453548138 | erot = 1.30088738083589 | epot = -11.5382950211518 | etot = -8.53011310483453 +330000 ekin = 1.71977920215656 | erot = 1.36542606219482 | epot = -11.6153183691918 | etot = -8.5301131048404 +331000 ekin = 1.72719948157173 | erot = 1.43788972641118 | epot = -11.6952023128938 | etot = -8.53011310491092 +332000 ekin = 1.72935048705161 | erot = 1.51741015576086 | epot = -11.7768737478651 | etot = -8.53011310505263 +333000 ekin = 1.72589292388511 | erot = 1.60231164706384 | epot = -11.8583176761888 | etot = -8.53011310523986 +334000 ekin = 1.71641096845493 | erot = 1.69042382797046 | epot = -11.9369479018436 | etot = -8.53011310541824 +335000 ekin = 1.70061954221282 | erot = 1.7796304798544 | epot = -12.0103631276007 | etot = -8.53011310553347 +336000 ekin = 1.67861266632134 | erot = 1.86835013660124 | epot = -12.0770759084893 | etot = -8.53011310556669 +337000 ekin = 1.65104084371297 | erot = 1.95564880215561 | epot = -12.136802751403 | etot = -8.53011310553446 +338000 ekin = 1.61919653971688 | erot = 2.04088006325167 | epot = -12.1901897084582 | etot = -8.53011310548962 +339000 ekin = 1.58494018858436 | erot = 2.12306951704741 | epot = -12.2381228110973 | etot = -8.53011310546556 +340000 ekin = 1.55068751498618 | erot = 2.2004569149083 | epot = -12.2812575353511 | etot = -8.53011310545662 +341000 ekin = 1.51939352315465 | erot = 2.27052960843975 | epot = -12.320036237042 | etot = -8.53011310544755 +342000 ekin = 1.4942283142269 | erot = 2.33048372011859 | epot = -12.3548251398146 | etot = -8.53011310546907 +343000 ekin = 1.47765440209276 | erot = 2.37774277923742 | epot = -12.3855102869167 | etot = -8.53011310558656 +344000 ekin = 1.47024986717826 | erot = 2.41039440931609 | epot = -12.4107573822795 | etot = -8.53011310578515 +345000 ekin = 1.47032544425693 | erot = 2.42787360990024 | epot = -12.4283121600589 | etot = -8.53011310590172 +346000 ekin = 1.47497435411031 | erot = 2.43200037641079 | epot = -12.4370878362715 | etot = -8.53011310575041 +347000 ekin = 1.48176297397304 | erot = 2.42757307622222 | epot = -12.4394491555193 | etot = -8.53011310532408 +348000 ekin = 1.48960567691712 | erot = 2.42152466454856 | epot = -12.4412434462858 | etot = -8.53011310482014 +349000 ekin = 1.49842206767709 | erot = 2.4209480121121 | epot = -12.4494831841902 | etot = -8.53011310440098 +350000 ekin = 1.50804667267274 | erot = 2.43083585672876 | epot = -12.4689956337606 | etot = -8.53011310435906 +351000 ekin = 1.5173353924427 | erot = 2.45275056185602 | epot = -12.5001990588657 | etot = -8.53011310456693 +352000 ekin = 1.52440681731839 | erot = 2.48551818836727 | epot = -12.5400381105944 | etot = -8.5301131049087 +353000 ekin = 1.52713336972915 | erot = 2.52632890408748 | epot = -12.5835753790744 | etot = -8.53011310525773 +354000 ekin = 1.523721885336 | erot = 2.57191593401525 | epot = -12.6257509248862 | etot = -8.530113105535 +355000 ekin = 1.51309115686939 | erot = 2.61929569219605 | epot = -12.6624999548052 | etot = -8.53011310573978 +356000 ekin = 1.4948333284748 | erot = 2.66580549560263 | epot = -12.6907519300001 | etot = -8.53011310592265 +357000 ekin = 1.46901113663898 | erot = 2.70863650615366 | epot = -12.7077607489347 | etot = -8.53011310614211 +358000 ekin = 1.43592917031632 | erot = 2.74427787084531 | epot = -12.7103201475703 | etot = -8.53011310640863 +359000 ekin = 1.39610164165262 | erot = 2.76842107185624 | epot = -12.6946358201661 | etot = -8.53011310665726 +360000 ekin = 1.35047672654323 | erot = 2.77663698694642 | epot = -12.6572268202617 | etot = -8.53011310677201 +361000 ekin = 1.3007661104219 | erot = 2.76564868782621 | epot = -12.5965279048983 | etot = -8.53011310665023 +362000 ekin = 1.24961928501658 | erot = 2.73457480733808 | epot = -12.5143071986218 | etot = -8.53011310626714 +363000 ekin = 1.20045386452323 | erot = 2.68545051257892 | epot = -12.4160174827948 | etot = -8.53011310569261 +364000 ekin = 1.1571026109765 | erot = 2.62295556816838 | epot = -12.3101712839462 | etot = -8.53011310480137 +365000 ekin = 1.12337541340586 | erot = 2.55368748907124 | epot = -12.2071760067595 | etot = -8.53011310428242 +366000 ekin = 1.10127753424505 | erot = 2.48317695958081 | epot = -12.1145675977507 | etot = -8.53011310392482 +367000 ekin = 1.09158671746577 | erot = 2.41562896418422 | epot = -12.0373287854036 | etot = -8.53011310375364 +368000 ekin = 1.09395460107129 | erot = 2.3536730201725 | epot = -11.9777407249954 | etot = -8.53011310375157 +369000 ekin = 1.1070702982443 | erot = 2.29842564871278 | epot = -11.9356090508318 | etot = -8.53011310387475 +370000 ekin = 1.12891021359863 | erot = 2.24980412691932 | epot = -11.9088274446084 | etot = -8.5301131040904 +371000 ekin = 1.15702393729471 | erot = 2.20683986953429 | epot = -11.8939769111781 | etot = -8.53011310434907 +372000 ekin = 1.18881512926452 | erot = 2.16808122069092 | epot = -11.8870094545668 | etot = -8.53011310461133 +373000 ekin = 1.22180472347423 | erot = 2.13193560462788 | epot = -11.8838534329442 | etot = -8.53011310484212 +374000 ekin = 1.25386446213246 | erot = 2.09696444550541 | epot = -11.8809420126508 | etot = -8.53011310501295 +375000 ekin = 1.28340735686141 | erot = 2.06212828827176 | epot = -11.8756487502356 | etot = -8.53011310510241 +376000 ekin = 1.30952081504778 | erot = 2.02696442652824 | epot = -11.866598346676 | etot = -8.53011310509994 +377000 ekin = 1.33202999726555 | erot = 1.99167753887332 | epot = -11.8538206411461 | etot = -8.53011310500719 +378000 ekin = 1.35148382625757 | erot = 1.95712256046493 | epot = -11.8387194915612 | etot = -8.53011310483868 +379000 ekin = 1.36906410242434 | erot = 1.92466782261904 | epot = -11.8238450296649 | etot = -8.53011310462152 +380000 ekin = 1.38611586817106 | erot = 1.89583861081519 | epot = -11.8120675838491 | etot = -8.53011310486282 +381000 ekin = 1.40217385032836 | erot = 1.87134526426269 | epot = -11.80363221932 | etot = -8.53011310472898 +382000 ekin = 1.41800173053803 | erot = 1.85196748545645 | epot = -11.8000823206153 | etot = -8.53011310462087 +383000 ekin = 1.43471626248222 | erot = 1.83825951701816 | epot = -11.8030888840481 | etot = -8.53011310454774 +384000 ekin = 1.45338249836618 | erot = 1.83037149004682 | epot = -11.8138670929151 | etot = -8.53011310450216 +385000 ekin = 1.4750013081334 | erot = 1.82815692745157 | epot = -11.8332713400492 | etot = -8.53011310446425 +386000 ekin = 1.50055250095182 | erot = 1.83139934862436 | epot = -11.8620649539881 | etot = -8.53011310441195 +387000 ekin = 1.53104646327023 | erot = 1.84005108459331 | epot = -11.9012106521991 | etot = -8.53011310433554 +388000 ekin = 1.56751609348646 | erot = 1.85434854378703 | epot = -11.9519777415238 | etot = -8.53011310425033 +389000 ekin = 1.61088446670257 | erot = 1.87469764896096 | epot = -12.0156952198659 | etot = -8.53011310420239 +390000 ekin = 1.66167288139561 | erot = 1.90128526221067 | epot = -12.0930712478719 | etot = -8.53011310426566 +391000 ekin = 1.71956364223701 | erot = 1.93346596746484 | epot = -12.1831427142236 | etot = -8.53011310452177 +392000 ekin = 1.78290672529534 | erot = 1.96909292130509 | epot = -12.282112751646 | etot = -8.53011310504553 +393000 ekin = 1.84827871011224 | erot = 2.00406071425975 | epot = -12.3824525302076 | etot = -8.53011310583559 +394000 ekin = 1.91039848955262 | erot = 2.03249756432822 | epot = -12.4730091606615 | etot = -8.53011310678065 +395000 ekin = 1.962650841212 | erot = 2.04794740083273 | epot = -12.5407113496889 | etot = -8.53011310764422 +396000 ekin = 1.99833003479199 | erot = 2.04548694358824 | epot = -12.5739300865163 | etot = -8.53011310813611 +397000 ekin = 2.01232505811841 | erot = 2.02401360401992 | epot = -12.5664517701974 | etot = -8.5301131080591 +398000 ekin = 2.0025230620709 | erot = 1.98743944257781 | epot = -12.5200756120825 | etot = -8.53011310743375 +399000 ekin = 1.97017185599611 | erot = 1.94392108511877 | epot = -12.4442060476074 | etot = -8.53011310649254 +400000 ekin = 1.91900875366194 | erot = 1.90345223754646 | epot = -12.3525740967518 | etot = -8.53011310554345 +401000 ekin = 1.85370867757018 | erot = 1.87511245492095 | epot = -12.2589342373083 | etot = -8.53011310481718 +402000 ekin = 1.77849786327956 | erot = 1.86519132439128 | epot = -12.1738022920757 | etot = -8.53011310440484 +403000 ekin = 1.69647765085025 | erot = 1.87662651194813 | epot = -12.103217267038 | etot = -8.5301131042396 +404000 ekin = 1.60979304525306 | erot = 1.90948179463073 | epot = -12.0493879441487 | etot = -8.5301131042649 +405000 ekin = 1.52031831979797 | erot = 1.96148591335689 | epot = -12.0119173375293 | etot = -8.53011310437441 +406000 ekin = 1.43052069773525 | erot = 2.02884810423451 | epot = -11.9894819063482 | etot = -8.53011310437844 +407000 ekin = 1.34451311630643 | erot = 2.1076266235887 | epot = -11.9822528435678 | etot = -8.53011310367264 +408000 ekin = 1.27105659597284 | erot = 2.1948612952805 | epot = -11.9960309945634 | etot = -8.5301131033101 +409000 ekin = 1.1388796616568 | erot = 2.29455518643573 | epot = -11.963547963097 | etot = -8.53011311500446 +410000 ekin = 1.06340398972402 | erot = 2.43839727640636 | epot = -12.0319143782863 | etot = -8.53011311215586 +411000 ekin = 1.12994363439476 | erot = 2.56530077013481 | epot = -12.2253575154631 | etot = -8.53011311093354 +412000 ekin = 1.18303314251998 | erot = 2.64796136756708 | epot = -12.3611076219161 | etot = -8.53011311182907 +413000 ekin = 1.26155297788784 | erot = 2.71721639006832 | epot = -12.5088824809625 | etot = -8.53011311300633 +414000 ekin = 1.35092349153842 | erot = 2.76712696986951 | epot = -12.6481635756166 | etot = -8.53011311420862 +415000 ekin = 1.43876511602559 | erot = 2.79254621486869 | epot = -12.7614244458802 | etot = -8.53011311498593 +416000 ekin = 1.51568555880285 | erot = 2.79087249527856 | epot = -12.8366711691918 | etot = -8.53011311511038 +417000 ekin = 1.57746272926947 | erot = 2.76317937782222 | epot = -12.8707552217649 | etot = -8.53011311467321 +418000 ekin = 1.62492964319063 | erot = 2.71407200335048 | epot = -12.8691147604566 | etot = -8.53011311391544 +419000 ekin = 1.66144511719922 | erot = 2.64948328985865 | epot = -12.8410415202781 | etot = -8.53011311322023 +420000 ekin = 1.69059185762129 | erot = 2.57483616462309 | epot = -12.7955411349031 | etot = -8.53011311265877 +421000 ekin = 1.7153783116834 | erot = 2.49448486929148 | epot = -12.7399762932537 | etot = -8.53011311227883 +422000 ekin = 1.73777830627883 | erot = 2.41134366235516 | epot = -12.6792350807003 | etot = -8.53011311206633 +423000 ekin = 1.7587504227613 | erot = 2.32696083577434 | epot = -12.6158243705169 | etot = -8.53011311198125 +424000 ekin = 1.77846413727057 | erot = 2.24181259775995 | epot = -12.5503898470075 | etot = -8.53011311197693 +425000 ekin = 1.79665710138905 | erot = 2.15579348528792 | epot = -12.482563698484 | etot = -8.53011311180703 +426000 ekin = 1.81317574251695 | erot = 2.0690861526638 | epot = -12.4123750070616 | etot = -8.53011311188084 +427000 ekin = 1.82711019089416 | erot = 1.98123134137793 | epot = -12.3384546441959 | etot = -8.53011311192384 +428000 ekin = 1.83751691854066 | erot = 1.89199984736615 | epot = -12.2596298778201 | etot = -8.53011311191326 +429000 ekin = 1.84368310694498 | erot = 1.8017721530282 | epot = -12.1755683718145 | etot = -8.53011311184129 +430000 ekin = 1.84519909789286 | erot = 1.71159843543995 | epot = -12.0869106450462 | etot = -8.53011311171339 +431000 ekin = 1.84198247291198 | erot = 1.62310758133244 | epot = -11.9952031657882 | etot = -8.53011311154377 +432000 ekin = 1.83426509469049 | erot = 1.53842285511833 | epot = -11.9028010611632 | etot = -8.53011311135434 +433000 ekin = 1.82255993368825 | erot = 1.46009341020954 | epot = -11.8127664550778 | etot = -8.53011311117997 +434000 ekin = 1.80751085818488 | erot = 1.39007773701991 | epot = -11.7277017062178 | etot = -8.53011311101305 +435000 ekin = 1.78989394281882 | erot = 1.32998390314058 | epot = -11.6499909568307 | etot = -8.53011311087133 +436000 ekin = 1.77056724604275 | erot = 1.28100064172295 | epot = -11.581680998535 | etot = -8.53011311076935 +437000 ekin = 1.75036829511875 | erot = 1.24377047064117 | epot = -11.5242518764766 | etot = -8.53011311071664 +438000 ekin = 1.73003454470636 | erot = 1.21832954508443 | epot = -11.4784772005177 | etot = -8.53011311072691 +439000 ekin = 1.71009916118602 | erot = 1.20407719866578 | epot = -11.4442894706321 | etot = -8.53011311078034 +440000 ekin = 1.69096600032215 | erot = 1.1997599713895 | epot = -11.4208390825825 | etot = -8.53011311087082 +441000 ekin = 1.67263636923596 | erot = 1.20336882729106 | epot = -11.4061183077354 | etot = -8.53011311120842 +442000 ekin = 1.65454003555309 | erot = 1.21209014500703 | epot = -11.396743291911 | etot = -8.53011311135084 +443000 ekin = 1.63689233561682 | erot = 1.22351444914061 | epot = -11.3905198962961 | etot = -8.53011311153863 +444000 ekin = 1.61963083194638 | erot = 1.23489712396808 | epot = -11.3846410676129 | etot = -8.53011311169845 +445000 ekin = 1.60286309976038 | erot = 1.24366705310744 | epot = -11.3766432646832 | etot = -8.53011311181542 +446000 ekin = 1.58694903183592 | erot = 1.24767642065206 | epot = -11.364738564367 | etot = -8.530113111879 +447000 ekin = 1.57243059658971 | erot = 1.24537195304266 | epot = -11.3479156615355 | etot = -8.53011311190312 +448000 ekin = 1.56000091268923 | erot = 1.23594098261579 | epot = -11.3260550071531 | etot = -8.53011311184805 +449000 ekin = 1.55055832679442 | erot = 1.21941073242742 | epot = -11.3000821709575 | etot = -8.53011311173565 +450000 ekin = 1.54505171747041 | erot = 1.19665850060475 | epot = -11.2718233296487 | etot = -8.53011311157355 +451000 ekin = 1.54440025802286 | erot = 1.16936613900785 | epot = -11.2438795084052 | etot = -8.53011311137454 +452000 ekin = 1.54941604020931 | erot = 1.13989972058501 | epot = -11.2194288719492 | etot = -8.5301131111549 +453000 ekin = 1.56073218733935 | erot = 1.11111895993793 | epot = -11.2019642583138 | etot = -8.53011311103654 +454000 ekin = 1.57840116511174 | erot = 1.08594835309889 | epot = -11.1944626290776 | etot = -8.53011311086696 +455000 ekin = 1.60199572695718 | erot = 1.067161005263 | epot = -11.1992698429505 | etot = -8.5301131107303 +456000 ekin = 1.63102931523779 | erot = 1.0573477720452 | epot = -11.2184901979352 | etot = -8.53011311065218 +457000 ekin = 1.66465491830386 | erot = 1.05859720823158 | epot = -11.2533652371723 | etot = -8.53011311063683 +458000 ekin = 1.70170935168118 | erot = 1.07231891092067 | epot = -11.3041413732889 | etot = -8.53011311068709 +459000 ekin = 1.74077940290741 | erot = 1.0991465378357 | epot = -11.370039051544 | etot = -8.53011311080086 +460000 ekin = 1.78028759701974 | erot = 1.13890397189591 | epot = -11.4493046798783 | etot = -8.53011311096265 +461000 ekin = 1.81860197243655 | erot = 1.190671028759 | epot = -11.5393861123564 | etot = -8.53011311116083 +462000 ekin = 1.85415391006496 | erot = 1.25289584357914 | epot = -11.6371628650249 | etot = -8.53011311138083 +463000 ekin = 1.88554792945735 | erot = 1.32350247179401 | epot = -11.7391635128605 | etot = -8.53011311160914 +464000 ekin = 1.91164681845957 | erot = 1.40002350523331 | epot = -11.8417834355271 | etot = -8.53011311183422 +465000 ekin = 1.93162421639016 | erot = 1.47973907160968 | epot = -11.941476400046 | etot = -8.53011311204611 +466000 ekin = 1.94498500127825 | erot = 1.55982523463663 | epot = -12.0349233481501 | etot = -8.53011311223519 +467000 ekin = 1.95156193454946 | erot = 1.63751691043975 | epot = -12.1191919573808 | etot = -8.53011311239157 +468000 ekin = 1.95150012932807 | erot = 1.71026532451013 | epot = -12.1918785663461 | etot = -8.53011311250794 +469000 ekin = 1.94523738407549 | erot = 1.77590641032492 | epot = -12.2512569069708 | etot = -8.53011311257044 +470000 ekin = 1.93348412613791 | erot = 1.83286583557274 | epot = -12.296463074288 | etot = -8.53011311257733 +471000 ekin = 1.91719298128153 | erot = 1.88021093656836 | epot = -12.3275170303833 | etot = -8.53011311253336 +472000 ekin = 1.89750254538035 | erot = 1.91763317251617 | epot = -12.3452488303456 | etot = -8.53011311244905 +473000 ekin = 1.87564239829209 | erot = 1.94536290421679 | epot = -12.3511184148537 | etot = -8.53011311234486 +474000 ekin = 1.85280042952451 | erot = 1.96399915053982 | epot = -12.3469126923062 | etot = -8.53011311224187 +475000 ekin = 1.82997212693037 | erot = 1.97434336844431 | epot = -12.334428607529 | etot = -8.53011311215432 +476000 ekin = 1.80782991664635 | erot = 1.97731520041903 | epot = -12.3152582291479 | etot = -8.53011311208248 +477000 ekin = 1.78665653477972 | erot = 1.97399991972465 | epot = -12.2907695665165 | etot = -8.53011311201214 +478000 ekin = 1.76636958091782 | erot = 1.96581401435826 | epot = -12.2622967071976 | etot = -8.53011311192151 +479000 ekin = 1.74662905135426 | erot = 1.95469632261111 | epot = -12.2314384857597 | etot = -8.5301131117943 +480000 ekin = 1.7269843787855 | erot = 1.94318876795314 | epot = -12.2002862583696 | etot = -8.53011311163097 +481000 ekin = 1.70700474377776 | erot = 1.93430214048104 | epot = -12.1714199957112 | etot = -8.53011311145243 +482000 ekin = 1.68635525357164 | erot = 1.93116021407784 | epot = -12.1476285789408 | etot = -8.53011311129136 +483000 ekin = 1.66481678021318 | erot = 1.9365211816136 | epot = -12.1314510730077 | etot = -8.53011311118095 +484000 ekin = 1.6422770599313 | erot = 1.95232513146263 | epot = -12.1247153025367 | etot = -8.53011311114272 +485000 ekin = 1.619015620803 | erot = 1.97931073969716 | epot = -12.1284394716114 | etot = -8.53011311111128 +486000 ekin = 1.59577228279478 | erot = 2.01691499833533 | epot = -12.1428003923546 | etot = -8.53011311122449 +487000 ekin = 1.57269760731357 | erot = 2.06349128122684 | epot = -12.16630200002 | etot = -8.53011311147963 +488000 ekin = 1.54979615320087 | erot = 2.11629853286408 | epot = -12.1962077977383 | etot = -8.53011311167333 +489000 ekin = 1.52793571892999 | erot = 2.17194986393337 | epot = -12.2299986947161 | etot = -8.5301131118527 +490000 ekin = 1.50872304469661 | erot = 2.22662776560131 | epot = -12.2654639222937 | etot = -8.53011311199583 +491000 ekin = 1.49451121745273 | erot = 2.27632252256859 | epot = -12.3009468521205 | etot = -8.53011311209918 +492000 ekin = 1.48823109410857 | erot = 2.31702824482369 | epot = -12.3353724511152 | etot = -8.53011311218297 +493000 ekin = 1.4951831820869 | erot = 2.34597345237573 | epot = -12.3712697461163 | etot = -8.53011311165363 +494000 ekin = 1.51845501165305 | erot = 2.36107283299099 | epot = -12.4096409568393 | etot = -8.53011311219529 +495000 ekin = 1.55341225536275 | erot = 2.35806327093511 | epot = -12.4415886369885 | etot = -8.5301131106906 +496000 ekin = 1.60682048121588 | erot = 2.33406723049124 | epot = -12.4710008246463 | etot = -8.5301131129392 +497000 ekin = 1.66595753311319 | erot = 2.29001283524094 | epot = -12.4860834812872 | etot = -8.5301131129331 +498000 ekin = 1.73079985975399 | erot = 2.22455469202947 | epot = -12.4854676647277 | etot = -8.53011311294429 +499000 ekin = 1.79938231062206 | erot = 2.13975923972116 | epot = -12.4692546631759 | etot = -8.53011311283265 +500000 ekin = 1.864590788894 | erot = 2.04085817003559 | epot = -12.4355620715547 | etot = -8.53011311262514 +501000 ekin = 1.92273434829387 | erot = 1.93494769032325 | epot = -12.3877951508618 | etot = -8.53011311224467 +502000 ekin = 1.97166638933671 | erot = 1.83018302875813 | epot = -12.3319625299061 | etot = -8.53011311181124 +503000 ekin = 2.01030983362468 | erot = 1.73409537514378 | epot = -12.274518320111 | etot = -8.53011311134249 +504000 ekin = 2.03852387655111 | erot = 1.65386645968326 | epot = -12.2225034471818 | etot = -8.53011311094747 +505000 ekin = 2.0567214388878 | erot = 1.59516954319063 | epot = -12.1820040927721 | etot = -8.53011311069366 +506000 ekin = 2.0654132236812 | erot = 1.56133329123323 | epot = -12.1568596255387 | etot = -8.53011311062431 +507000 ekin = 2.06489683745696 | erot = 1.5529868320159 | epot = -12.1479967802301 | etot = -8.53011311075727 +508000 ekin = 2.05510409506943 | erot = 1.56796083678471 | epot = -12.1531780429361 | etot = -8.53011311108195 +509000 ekin = 2.03562755334453 | erot = 1.60146413116227 | epot = -12.167204796061 | etot = -8.5301131115542 +510000 ekin = 2.00592908360857 | erot = 1.64659845424657 | epot = -12.1826406499481 | etot = -8.53011311209294 +511000 ekin = 1.96569680010841 | erot = 1.69527026509092 | epot = -12.1910801777868 | etot = -8.53011311258751 +512000 ekin = 1.91525552529987 | erot = 1.73945419950455 | epot = -12.1848228377285 | etot = -8.53011311292405 +513000 ekin = 1.85587746892691 | erot = 1.77257277561938 | epot = -12.1585633575704 | etot = -8.53011311302411 +514000 ekin = 1.78983987133691 | erot = 1.79060149181125 | epot = -12.110554476023 | etot = -8.53011311287486 +515000 ekin = 1.7201712959039 | erot = 1.79254120106384 | epot = -12.0428256094973 | etot = -8.53011311252956 +516000 ekin = 1.65040042949212 | erot = 1.7804348091573 | epot = -11.9609483505847 | etot = -8.53011311193526 +517000 ekin = 1.5840406801366 | erot = 1.75852731252202 | epot = -11.8726811041166 | etot = -8.53011311145803 +518000 ekin = 1.52414481736526 | erot = 1.73170053428619 | epot = -11.7859584626037 | etot = -8.53011311095221 +519000 ekin = 1.4736679692459 | erot = 1.70507688462286 | epot = -11.7088579644883 | etot = -8.5301131106195 +520000 ekin = 1.43365378179093 | erot = 1.68280907302155 | epot = -11.6465759651473 | etot = -8.53011311033478 +521000 ekin = 1.40489785043186 | erot = 1.66827026613465 | epot = -11.6032812266512 | etot = -8.53011311008469 +522000 ekin = 1.38811259815129 | erot = 1.66372628765001 | epot = -11.5819519960218 | etot = -8.53011311022052 +523000 ekin = 1.38336778489754 | erot = 1.66945534863506 | epot = -11.5829362436293 | etot = -8.53011311009666 +524000 ekin = 1.3913126502426 | erot = 1.68543796398208 | epot = -11.6068637243459 | etot = -8.53011311012124 +525000 ekin = 1.41205700478085 | erot = 1.71025646512686 | epot = -11.6524265802503 | etot = -8.53011311034254 +526000 ekin = 1.44455820367828 | erot = 1.74084872886512 | epot = -11.715520043306 | etot = -8.53011311076257 +527000 ekin = 1.48642955052526 | erot = 1.77280714510033 | epot = -11.7893498069451 | etot = -8.53011311131948 +528000 ekin = 1.53418163870598 | erot = 1.80110112524649 | epot = -11.8653958758489 | etot = -8.53011311189648 +529000 ekin = 1.58386362601508 | erot = 1.82112172078969 | epot = -11.9350984591607 | etot = -8.53011311235592 +530000 ekin = 1.63189696415197 | erot = 1.82978202391273 | epot = -11.9917921006499 | etot = -8.53011311258521 +531000 ekin = 1.67581590192871 | erot = 1.82633306141955 | epot = -12.0322620756572 | etot = -8.53011311230891 +532000 ekin = 1.71585538236368 | erot = 1.8152091032606 | epot = -12.0611775978011 | etot = -8.53011311217683 +533000 ekin = 1.75284097660429 | erot = 1.80146596915312 | epot = -12.0844200576796 | etot = -8.53011311192222 +534000 ekin = 1.78745390743137 | erot = 1.7886931599987 | epot = -12.1062601791015 | etot = -8.53011311167139 +535000 ekin = 1.82065038126921 | erot = 1.7802759175367 | epot = -12.1310394103311 | etot = -8.53011311152523 +536000 ekin = 1.85299611868502 | erot = 1.77858522849865 | epot = -12.1616944587272 | etot = -8.53011311154351 +537000 ekin = 1.88407496144919 | erot = 1.7842808712656 | epot = -12.1984689444174 | etot = -8.53011311170263 +538000 ekin = 1.91279454454315 | erot = 1.79686892930563 | epot = -12.2397765856348 | etot = -8.53011311178604 +539000 ekin = 1.93839394839843 | erot = 1.81622314391844 | epot = -12.284730204236 | etot = -8.53011311191909 +540000 ekin = 1.95998962534122 | erot = 1.84168603210851 | epot = -12.3317887694937 | etot = -8.53011311204393 +541000 ekin = 1.97685104517971 | erot = 1.8723442627802 | epot = -12.3793084201316 | etot = -8.53011311217171 +542000 ekin = 1.98798216003657 | erot = 1.90711972836194 | epot = -12.4252150005635 | etot = -8.53011311216495 +543000 ekin = 1.99396475053246 | erot = 1.94557694619036 | epot = -12.4696548087837 | etot = -8.53011311206087 +544000 ekin = 1.99659195335123 | erot = 1.98768793525312 | epot = -12.5143930004997 | etot = -8.53011311189537 +545000 ekin = 1.99841939299989 | erot = 2.03351546469238 | epot = -12.5620479694254 | etot = -8.53011311173315 +546000 ekin = 2.00223379009079 | erot = 2.08278239430349 | epot = -12.6151292960425 | etot = -8.53011311164824 +547000 ekin = 2.01043375036443 | erot = 2.13441666464114 | epot = -12.6749635267018 | etot = -8.53011311169627 +548000 ekin = 2.0245414253266 | erot = 2.18636947292862 | epot = -12.7410240101681 | etot = -8.5301131119129 +549000 ekin = 2.04472650265624 | erot = 2.23524716352582 | epot = -12.8100867784639 | etot = -8.53011311228183 +550000 ekin = 2.06971706084401 | erot = 2.27669143350054 | epot = -12.876521607101 | etot = -8.53011311275642 +551000 ekin = 2.09694987343936 | erot = 2.30602592213695 | epot = -12.9330889088384 | etot = -8.53011311326205 +552000 ekin = 2.1228812376554 | erot = 2.31896388909875 | epot = -12.9719582404603 | etot = -8.53011311370618 +553000 ekin = 2.14351313995611 | erot = 2.31240753793797 | epot = -12.9860337918876 | etot = -8.53011311399348 +554000 ekin = 2.15523965908159 | erot = 2.28547313898784 | epot = -12.9708259121345 | etot = -8.53011311406508 +555000 ekin = 2.15534485411163 | erot = 2.23961985935309 | epot = -12.9250778273638 | etot = -8.53011311389909 +556000 ekin = 2.14242415869529 | erot = 2.17853141058563 | epot = -12.8510686828054 | etot = -8.53011311352449 +557000 ekin = 2.11652525560679 | erot = 2.10755901122257 | epot = -12.75419737984 | etot = -8.5301131130106 +558000 ekin = 2.07899262360386 | erot = 2.03287016334017 | epot = -12.6419758993878 | etot = -8.53011311244374 +559000 ekin = 2.03209525707211 | erot = 1.96055588826955 | epot = -12.5227642572441 | etot = -8.53011311190243 +560000 ekin = 1.97856970493465 | erot = 1.89593544894508 | epot = -12.4046182653117 | etot = -8.53011311143199 +561000 ekin = 1.92120586059386 | erot = 1.84318662679696 | epot = -12.2945055984625 | etot = -8.53011311107173 +562000 ekin = 1.86248053378004 | erot = 1.80525111362544 | epot = -12.197844758219 | etot = -8.53011311081349 +563000 ekin = 1.80440566029618 | erot = 1.78397358726431 | epot = -12.1184923582089 | etot = -8.53011311064843 +564000 ekin = 1.74859757239829 | erot = 1.78025486278517 | epot = -12.0589655457327 | etot = -8.53011311054927 +565000 ekin = 1.69697420507052 | erot = 1.79398971152847 | epot = -12.0210770271823 | etot = -8.53011311058327 +566000 ekin = 1.64969612949923 | erot = 1.8240502634005 | epot = -12.0038595036696 | etot = -8.53011311076992 +567000 ekin = 1.60592346389383 | erot = 1.86815174766682 | epot = -12.0041883226195 | etot = -8.53011311105886 +568000 ekin = 1.56447342355498 | erot = 1.92295106518469 | epot = -12.0175376000187 | etot = -8.53011311127902 +569000 ekin = 1.5249189399064 | erot = 1.98481672432871 | epot = -12.0398487760184 | etot = -8.53011311178333 +570000 ekin = 1.48563885354576 | erot = 2.0478979596709 | epot = -12.0636499254993 | etot = -8.53011311228265 +571000 ekin = 1.44514780819736 | erot = 2.10567642130719 | epot = -12.0809373422362 | etot = -8.53011311273169 +572000 ekin = 1.40265340711092 | erot = 2.15189441844465 | epot = -12.0846609385903 | etot = -8.53011311303474 +573000 ekin = 1.35831475976892 | erot = 2.18135236040197 | epot = -12.0697802333399 | etot = -8.53011311316902 +574000 ekin = 1.31325665398436 | erot = 2.19054857027259 | epot = -12.0339183373723 | etot = -8.53011311311537 +575000 ekin = 1.26941751353119 | erot = 2.17808969341363 | epot = -11.9776203199862 | etot = -8.53011311304134 +576000 ekin = 1.22896606046371 | erot = 2.14379444928078 | epot = -11.9028736225264 | etot = -8.53011311278191 +577000 ekin = 1.1939318542458 | erot = 2.08947552578693 | epot = -11.8135204923656 | etot = -8.53011311233291 +578000 ekin = 1.16652110217761 | erot = 2.01971345754074 | epot = -11.7163476715532 | etot = -8.53011311183482 +579000 ekin = 1.1485590785822 | erot = 1.94028096237221 | epot = -11.6189531523097 | etot = -8.53011311135534 +580000 ekin = 1.14121418715078 | erot = 1.85735567591289 | epot = -11.5286829740217 | etot = -8.53011311095804 +581000 ekin = 1.14478819464287 | erot = 1.77673557403154 | epot = -11.4516368793669 | etot = -8.53011311069244 +582000 ekin = 1.15860725309894 | erot = 1.70317164276424 | epot = -11.3918920064496 | etot = -8.5301131105864 +583000 ekin = 1.18104542316549 | erot = 1.63989823948895 | epot = -11.3510567732975 | etot = -8.53011311064311 +584000 ekin = 1.20969611011658 | erot = 1.58840206182349 | epot = -11.3282112827813 | etot = -8.53011311084127 +585000 ekin = 1.24168069892109 | erot = 1.54843600705662 | epot = -11.3202298171165 | etot = -8.53011311113879 +586000 ekin = 1.27405468400613 | erot = 1.51825728966608 | epot = -11.3224250851521 | etot = -8.53011311147993 +587000 ekin = 1.30424737194037 | erot = 1.49504623590991 | epot = -11.3294067196548 | etot = -8.53011311180455 +588000 ekin = 1.33045790147737 | erot = 1.47543949669353 | epot = -11.3360105102291 | etot = -8.53011311205818 +589000 ekin = 1.35193228855807 | erot = 1.45609131903373 | epot = -11.338136719795 | etot = -8.53011311220317 +590000 ekin = 1.36906373532047 | erot = 1.43416814795119 | epot = -11.3333449954962 | etot = -8.53011311222451 +591000 ekin = 1.38329049900968 | erot = 1.40769463797985 | epot = -11.3210982491223 | etot = -8.53011311213273 +592000 ekin = 1.396805266251 | erot = 1.37570509646141 | epot = -11.3026234746724 | etot = -8.53011311195998 +593000 ekin = 1.41212834899936 | erot = 1.33820418779995 | epot = -11.2804456485499 | etot = -8.53011311175062 +594000 ekin = 1.43162615781701 | erot = 1.29598641795047 | epot = -11.2577256873175 | etot = -8.53011311155 +595000 ekin = 1.45706677221587 | erot = 1.25039113233439 | epot = -11.2375710159443 | etot = -8.53011311139409 +596000 ekin = 1.48935058064536 | erot = 1.20330184638127 | epot = -11.2227655382613 | etot = -8.53011311123466 +597000 ekin = 1.52837107420443 | erot = 1.15683058607257 | epot = -11.2153147714756 | etot = -8.53011311119857 +598000 ekin = 1.57294993725619 | erot = 1.11287817710978 | epot = -11.2159412255837 | etot = -8.53011311121776 +599000 ekin = 1.62105272043967 | erot = 1.07333264838314 | epot = -11.2244984800949 | etot = -8.53011311127213 +600000 ekin = 1.67007785978922 | erot = 1.04007259181364 | epot = -11.2402635629416 | etot = -8.53011311133876 +601000 ekin = 1.71718069772722 | erot = 1.0149775707719 | epot = -11.2622713798956 | etot = -8.53011311139647 +602000 ekin = 1.75956754279139 | erot = 0.99992837746411 | epot = -11.2896090316937 | etot = -8.53011311143815 +603000 ekin = 1.79477210700428 | erot = 0.996719273891467 | epot = -11.3216044923485 | etot = -8.53011311145271 +604000 ekin = 1.82082157915429 | erot = 1.00697983034891 | epot = -11.3579145210169 | etot = -8.5301131115137 +605000 ekin = 1.83582223390883 | erot = 1.03147611611613 | epot = -11.3974114615132 | etot = -8.53011311148824 +606000 ekin = 1.83871408516499 | erot = 1.07115549981242 | epot = -11.439982696236 | etot = -8.5301131112586 +607000 ekin = 1.83011347633852 | erot = 1.12647121092001 | epot = -11.4866977985863 | etot = -8.53011311132778 +608000 ekin = 1.81023941949276 | erot = 1.19707781562292 | epot = -11.537430346519 | etot = -8.53011311140329 +609000 ekin = 1.77867265022505 | erot = 1.28228554240803 | epot = -11.5910713041181 | etot = -8.53011311148498 +610000 ekin = 1.73547793526389 | erot = 1.38091511478385 | epot = -11.6465061616115 | etot = -8.53011311156377 +611000 ekin = 1.68128247270621 | erot = 1.49134780300283 | epot = -11.7027433873325 | etot = -8.53011311162347 +612000 ekin = 1.61741095621286 | erot = 1.61161456404272 | epot = -11.7591386319015 | etot = -8.53011311164596 +613000 ekin = 1.54603198035631 | erot = 1.73948721912843 | epot = -11.8156323111056 | etot = -8.53011311162087 +614000 ekin = 1.47024512206181 | erot = 1.8724902221456 | epot = -11.872848455891 | etot = -8.53011311168358 +615000 ekin = 1.39417329365892 | erot = 2.00621352659441 | epot = -11.9304999319609 | etot = -8.53011311170756 +616000 ekin = 1.32190082986828 | erot = 2.13583847738475 | epot = -11.9878524190112 | etot = -8.53011311175813 +617000 ekin = 1.25724259787289 | erot = 2.25683214183905 | epot = -12.0441878515868 | etot = -8.53011311187485 +618000 ekin = 1.20346368462638 | erot = 2.36421640891954 | epot = -12.0977932056336 | etot = -8.53011311208768 +619000 ekin = 1.1627837357725 | erot = 2.45267600797282 | epot = -12.1455728561386 | etot = -8.53011311239324 +620000 ekin = 1.13605929309554 | erot = 2.51695592468145 | epot = -12.183128330526 | etot = -8.53011311274904 +621000 ekin = 1.12273498782525 | erot = 2.55258324879902 | epot = -12.2054313496935 | etot = -8.53011311306925 +622000 ekin = 1.12111468632864 | erot = 2.55686207165221 | epot = -12.2080898712278 | etot = -8.53011311324693 +623000 ekin = 1.12887388451623 | erot = 2.5298951115885 | epot = -12.1888821092945 | etot = -8.53011311318977 +624000 ekin = 1.14366711340987 | erot = 2.47526890170239 | epot = -12.1490491279694 | etot = -8.53011311285711 +625000 ekin = 1.1636533326709 | erot = 2.40007033438096 | epot = -12.093836779329 | etot = -8.53011311227714 +626000 ekin = 1.18777968891899 | erot = 2.31409540899725 | epot = -12.0319882094711 | etot = -8.53011311155485 +627000 ekin = 1.21575247624791 | erot = 2.22841508882612 | epot = -11.9742806758914 | etot = -8.53011311081738 +628000 ekin = 1.2477770134495 | erot = 2.15375689268861 | epot = -11.931647016327 | etot = -8.53011311018884 +629000 ekin = 1.28416743272501 | erot = 2.09907855914796 | epot = -11.9133591016357 | etot = -8.53011310976274 +630000 ekin = 1.32495360490945 | erot = 2.07058701615122 | epot = -11.9256537306572 | etot = -8.53011310959653 +631000 ekin = 1.36955506517005 | erot = 2.07123416092344 | epot = -11.9709023358059 | etot = -8.53011310971242 +632000 ekin = 1.4166041198013 | erot = 2.10067869857442 | epot = -12.0473959281377 | etot = -8.530113109762 +633000 ekin = 1.46471660335347 | erot = 2.15728920672483 | epot = -12.1521189203209 | etot = -8.53011311024257 +634000 ekin = 1.51164233306884 | erot = 2.2367775584158 | epot = -12.2785330023773 | etot = -8.53011311089267 +635000 ekin = 1.55431486763314 | erot = 2.33246650107505 | epot = -12.4168944815982 | etot = -8.53011311289006 +636000 ekin = 1.58749795609154 | erot = 2.4328941500499 | epot = -12.5505052200478 | etot = -8.53011311390632 +637000 ekin = 1.60559044462006 | erot = 2.52510908161638 | epot = -12.6608126409127 | etot = -8.53011311467626 +638000 ekin = 1.60593314362082 | erot = 2.60108258773354 | epot = -12.7371288464172 | etot = -8.53011311506288 +639000 ekin = 1.58800768941235 | erot = 2.6561269465598 | epot = -12.7742477510085 | etot = -8.53011311503639 +640000 ekin = 1.55357432529951 | erot = 2.68914087075556 | epot = -12.7728283107735 | etot = -8.53011311471843 +641000 ekin = 1.50594258809282 | erot = 2.70186118673738 | epot = -12.7379168890354 | etot = -8.53011311420525 +642000 ekin = 1.4493146246673 | erot = 2.69765625484718 | epot = -12.6770839931786 | etot = -8.53011311366408 +643000 ekin = 1.38808387570727 | erot = 2.68019687245386 | epot = -12.5983938613618 | etot = -8.53011311320068 +644000 ekin = 1.32616709545583 | erot = 2.65251028989558 | epot = -12.5087904982175 | etot = -8.53011311286604 +645000 ekin = 1.26675082972023 | erot = 2.61647581101387 | epot = -12.4133397533956 | etot = -8.53011311266147 +646000 ekin = 1.21233854698878 | erot = 2.5727411282426 | epot = -12.3151927877818 | etot = -8.53011311255044 +647000 ekin = 1.16530705825035 | erot = 2.52174625415196 | epot = -12.2171664245199 | etot = -8.53011311211762 +648000 ekin = 1.12796239478171 | erot = 2.46431327603586 | epot = -12.1223887830015 | etot = -8.53011311218397 +649000 ekin = 1.10135546654711 | erot = 2.39865320680352 | epot = -12.0301217854869 | etot = -8.53011311213631 +650000 ekin = 1.08691260033598 | erot = 2.32393477718293 | epot = -11.9409604894932 | etot = -8.5301131119743 +651000 ekin = 1.08628079617365 | erot = 2.24073961889261 | epot = -11.8571335268201 | etot = -8.53011311175385 +652000 ekin = 1.10075131989762 | erot = 2.15085977534316 | epot = -11.7817242068004 | etot = -8.53011311155963 +653000 ekin = 1.13059734564037 | erot = 2.05677047635677 | epot = -11.717480933456 | etot = -8.53011311145884 +654000 ekin = 1.17466906493285 | erot = 1.96105944319222 | epot = -11.6658416195931 | etot = -8.53011311146804 +655000 ekin = 1.23047347719944 | erot = 1.86606271803509 | epot = -11.6266493067855 | etot = -8.53011311155101 +656000 ekin = 1.29470000776986 | erot = 1.77378178163835 | epot = -11.5985949010552 | etot = -8.53011311164695 +657000 ekin = 1.36393161429671 | erot = 1.68598333614943 | epot = -11.5800280621511 | etot = -8.53011311170499 +658000 ekin = 1.46427470172726 | erot = 1.5177215741261 | epot = -11.5121093881332 | etot = -8.53011311227979 +659000 ekin = 1.64802750935634 | erot = 1.39327336691684 | epot = -11.5714140170961 | etot = -8.53011314082295 +660000 ekin = 1.73185850255149 | erot = 1.32954115948652 | epot = -11.5915127822348 | etot = -8.53011312019675 +661000 ekin = 1.80627684678466 | erot = 1.27623279770698 | epot = -11.6126227646805 | etot = -8.53011312018888 +662000 ekin = 1.87475382730263 | erot = 1.23350073993935 | epot = -11.6383676874372 | etot = -8.53011312019518 +663000 ekin = 1.93633534014241 | erot = 1.2017144119124 | epot = -11.6681628722826 | etot = -8.53011312022775 +664000 ekin = 1.99014964299795 | erot = 1.18083533499367 | epot = -11.7010980982835 | etot = -8.53011312029191 +665000 ekin = 2.03529479419155 | erot = 1.17046521672532 | epot = -11.7358731313024 | etot = -8.53011312038551 +666000 ekin = 2.07079068065876 | erot = 1.16992318050786 | epot = -11.7708269816687 | etot = -8.53011312050209 +667000 ekin = 2.09559163007541 | erot = 1.1783355345629 | epot = -11.8040402852701 | etot = -8.53011312063184 +668000 ekin = 2.10864748670405 | erot = 1.19472204260561 | epot = -11.8334826500739 | etot = -8.53011312076428 +669000 ekin = 2.10899520332087 | erot = 1.21806343010287 | epot = -11.8571717543145 | etot = -8.53011312089073 +670000 ekin = 2.09586141353625 | erot = 1.24733872817599 | epot = -11.8733132627168 | etot = -8.5301131210046 +671000 ekin = 2.06876278708906 | erot = 1.28153124625808 | epot = -11.880407154448 | etot = -8.53011312110084 +672000 ekin = 2.0276059501653 | erot = 1.3196174560483 | epot = -11.8773365273852 | etot = -8.53011312117159 +673000 ekin = 1.97280574594745 | erot = 1.36056605412265 | epot = -11.8634849212729 | etot = -8.53011312120279 +674000 ekin = 1.90544539353419 | erot = 1.40337348376535 | epot = -11.8389319984731 | etot = -8.53011312117355 +675000 ekin = 1.82748035867474 | erot = 1.44714139190333 | epot = -11.8047348716393 | etot = -8.53011312106128 +676000 ekin = 1.74193854031676 | erot = 1.49116973847737 | epot = -11.7632213996459 | etot = -8.53011312085182 +677000 ekin = 1.65301515487123 | erot = 1.53501856941789 | epot = -11.7181468448415 | etot = -8.53011312055241 +678000 ekin = 1.56597364723133 | erot = 1.57850581645678 | epot = -11.6745925833905 | etot = -8.5301131197024 +679000 ekin = 1.48964066739432 | erot = 1.62216732403317 | epot = -11.6419211112285 | etot = -8.53011311980098 +680000 ekin = 1.4147411199256 | erot = 1.66316827970309 | epot = -11.6080225227317 | etot = -8.53011312310305 +681000 ekin = 1.3875618080588 | erot = 1.70006441988288 | epot = -11.6177393496906 | etot = -8.53011312174889 +682000 ekin = 1.41176839058291 | erot = 1.74149456084656 | epot = -11.6833760731068 | etot = -8.53011312167729 +683000 ekin = 1.43478590176895 | erot = 1.78362921085527 | epot = -11.7485282340794 | etot = -8.53011312145515 +684000 ekin = 1.47724360908045 | erot = 1.82441599451412 | epot = -11.8317727257719 | etot = -8.53011312217729 +685000 ekin = 1.53305607829824 | erot = 1.86370343685993 | epot = -11.926872637478 | etot = -8.53011312231985 +686000 ekin = 1.59999203694875 | erot = 1.9011732086841 | epot = -12.0312783681585 | etot = -8.53011312252567 +687000 ekin = 1.67585532676464 | erot = 1.93616514337617 | epot = -12.1421335928733 | etot = -8.53011312273246 +688000 ekin = 1.75824359228375 | erot = 1.96747116979292 | epot = -12.2558278850981 | etot = -8.53011312302143 +689000 ekin = 1.84428806108725 | erot = 1.99331990890081 | epot = -12.3677210933695 | etot = -8.53011312338147 +690000 ekin = 1.93038830486633 | erot = 2.01163201955911 | epot = -12.4721334481869 | etot = -8.53011312376144 +691000 ekin = 2.0124388123945 | erot = 2.02053622467935 | epot = -12.5630881611624 | etot = -8.53011312408858 +692000 ekin = 2.08628029306208 | erot = 2.01896054468879 | epot = -12.6353539620508 | etot = -8.53011312429993 +693000 ekin = 2.14819565615959 | erot = 2.00704872932862 | epot = -12.6853575098564 | etot = -8.53011312436814 +694000 ekin = 2.19527915053153 | erot = 1.98620471484385 | epot = -12.7115969896857 | etot = -8.5301131243103 +695000 ekin = 2.22558662018778 | erot = 1.95872876713241 | epot = -12.7144285114969 | etot = -8.53011312417675 +696000 ekin = 2.23807939045553 | erot = 1.92719459918016 | epot = -12.6953871136602 | etot = -8.53011312402447 +697000 ekin = 2.23245491258329 | erot = 1.89382427550433 | epot = -12.6563923119805 | etot = -8.5301131238929 +698000 ekin = 2.2089816604532 | erot = 1.8600944710324 | epot = -12.5991892552706 | etot = -8.53011312378496 +699000 ekin = 2.16842192914749 | erot = 1.82670876840315 | epot = -12.5252438212447 | etot = -8.53011312369402 +700000 ekin = 2.1120671807926 | erot = 1.79377149364922 | epot = -12.4359517980202 | etot = -8.53011312357841 +701000 ekin = 2.04183510229625 | erot = 1.76109647800035 | epot = -12.3330447037266 | etot = -8.53011312342996 +702000 ekin = 1.96030636909966 | erot = 1.72840134028024 | epot = -12.2188208326276 | etot = -8.5301131232477 +703000 ekin = 1.87071986577536 | erot = 1.6952969552183 | epot = -12.0961299440358 | etot = -8.53011312304212 +704000 ekin = 1.77689930889829 | erot = 1.66110577654282 | epot = -11.9681182082892 | etot = -8.53011312284807 +705000 ekin = 1.68305722563238 | erot = 1.62461573120443 | epot = -11.8377860795203 | etot = -8.53011312268345 +706000 ekin = 1.59370733728226 | erot = 1.58419230641528 | epot = -11.7080127662202 | etot = -8.5301131225227 +707000 ekin = 1.51408760176651 | erot = 1.53852435758473 | epot = -11.5827250817869 | etot = -8.53011312243563 +708000 ekin = 1.44811612149248 | erot = 1.48556130219114 | epot = -11.4637905459439 | etot = -8.53011312226029 +709000 ekin = 1.39918507089688 | erot = 1.42450216554722 | epot = -11.3538003584281 | etot = -8.53011312198401 +710000 ekin = 1.37013904497115 | erot = 1.35650265897742 | epot = -11.256754825589 | etot = -8.53011312164041 +711000 ekin = 1.36293784709674 | erot = 1.28452294872962 | epot = -11.1775739171295 | etot = -8.53011312130316 +712000 ekin = 1.37810571333588 | erot = 1.2127592676919 | epot = -11.1209781019676 | etot = -8.53011312093986 +713000 ekin = 1.41539111505309 | erot = 1.14625285129577 | epot = -11.0917570870448 | etot = -8.53011312069598 +714000 ekin = 1.47330237309178 | erot = 1.09011154670301 | epot = -11.0935270405112 | etot = -8.53011312071644 +715000 ekin = 1.54871417395516 | erot = 1.04700633006755 | epot = -11.1258336248975 | etot = -8.5301131208748 +716000 ekin = 1.63763638282486 | erot = 1.01816315231564 | epot = -11.1859126562753 | etot = -8.53011312113476 +717000 ekin = 1.73566547227376 | erot = 1.00365944746866 | epot = -11.2694380412044 | etot = -8.53011312146196 +718000 ekin = 1.83830978286523 | erot = 1.00261452541088 | epot = -11.3710374301057 | etot = -8.53011312182958 +719000 ekin = 1.94121801684452 | erot = 1.0133761809921 | epot = -11.4847073200566 | etot = -8.53011312221999 +720000 ekin = 2.04031989968954 | erot = 1.03367563292332 | epot = -11.604108655233 | etot = -8.53011312262012 +721000 ekin = 2.13191426653015 | erot = 1.06076519451637 | epot = -11.722792584063 | etot = -8.53011312301647 +722000 ekin = 2.21272563481609 | erot = 1.09108188128938 | epot = -11.8339206397532 | etot = -8.53011312364771 +723000 ekin = 2.2798049753879 | erot = 1.11988309830396 | epot = -11.929801197716 | etot = -8.53011312402416 +724000 ekin = 2.3307445888961 | erot = 1.14401404987743 | epot = -12.0048717630069 | etot = -8.5301131242334 +725000 ekin = 2.36404026188201 | erot = 1.16137515756009 | epot = -12.0555285437483 | etot = -8.53011312430622 +726000 ekin = 2.37921817082508 | erot = 1.17112079794218 | epot = -12.0804520929998 | etot = -8.53011312423249 +727000 ekin = 2.37683377543891 | erot = 1.17363131591717 | epot = -12.0805782153761 | etot = -8.53011312402005 +728000 ekin = 2.35838505906028 | erot = 1.17045679634781 | epot = -12.0589549791114 | etot = -8.53011312370335 +729000 ekin = 2.32610613432665 | erot = 1.16404528413303 | epot = -12.0202645417809 | etot = -8.53011312332125 +730000 ekin = 2.28270056428477 | erot = 1.15738479164984 | epot = -11.9701984788577 | etot = -8.53011312292305 +731000 ekin = 2.23120367719957 | erot = 1.15355872123693 | epot = -11.9148755209369 | etot = -8.53011312250044 +732000 ekin = 2.17470227950519 | erot = 1.15522777871328 | epot = -11.860043180425 | etot = -8.53011312220656 +733000 ekin = 2.11571523135208 | erot = 1.16431239937464 | epot = -11.8101407526929 | etot = -8.5301131219662 +734000 ekin = 2.05656428237398 | erot = 1.18217764585023 | epot = -11.7688550500147 | etot = -8.53011312179045 +735000 ekin = 1.99938712969537 | erot = 1.20940907181223 | epot = -11.738909323183 | etot = -8.5301131216754 +736000 ekin = 1.94615450236175 | erot = 1.24582378056569 | epot = -11.7220914045417 | etot = -8.53011312161425 +737000 ekin = 1.89868408610683 | erot = 1.29054728244519 | epot = -11.7193444901531 | etot = -8.53011312160107 +738000 ekin = 1.85863300402756 | erot = 1.34211072230266 | epot = -11.7308568479626 | etot = -8.53011312163242 +739000 ekin = 1.82745784099844 | erot = 1.39854613746744 | epot = -11.7561171001749 | etot = -8.53011312170898 +740000 ekin = 1.80633906933064 | erot = 1.45733644211004 | epot = -11.7937886333365 | etot = -8.53011312189581 +741000 ekin = 1.79607780005903 | erot = 1.51536575546117 | epot = -11.8415566775994 | etot = -8.53011312207919 +742000 ekin = 1.79696493224339 | erot = 1.56951628226599 | epot = -11.8965943368904 | etot = -8.53011312238097 +743000 ekin = 1.80846594326523 | erot = 1.61633044640747 | epot = -11.9549095123576 | etot = -8.53011312268487 +744000 ekin = 1.82931777590634 | erot = 1.6524932345571 | epot = -12.0119241334793 | etot = -8.53011312301591 +745000 ekin = 1.85761408803469 | erot = 1.67511504715363 | epot = -12.0628422585281 | etot = -8.53011312333981 +746000 ekin = 1.89090050882572 | erot = 1.68206656303043 | epot = -12.103080195468 | etot = -8.5301131236118 +747000 ekin = 1.9264040178908 | erot = 1.67240004235613 | epot = -12.1289171840346 | etot = -8.53011312378763 +748000 ekin = 1.9613314590417 | erot = 1.64668719348782 | epot = -12.1381317763653 | etot = -8.53011312383578 +749000 ekin = 1.99318478286464 | erot = 1.60714989959232 | epot = -12.1304478062039 | etot = -8.53011312374693 +750000 ekin = 2.02003557888993 | erot = 1.55750382541237 | epot = -12.1076525278393 | etot = -8.53011312353702 +751000 ekin = 2.04071538032199 | erot = 1.50252212966086 | epot = -12.0733506332239 | etot = -8.53011312324101 +752000 ekin = 2.05490285135359 | erot = 1.44741474333511 | epot = -12.0324307175925 | etot = -8.53011312290377 +753000 ekin = 2.06311311775271 | erot = 1.3971776121172 | epot = -11.9904038524337 | etot = -8.53011312256377 +754000 ekin = 2.06660147047687 | erot = 1.35603065035366 | epot = -11.9527452431008 | etot = -8.5301131222703 +755000 ekin = 2.06719659822953 | erot = 1.32693138054303 | epot = -11.9242411008154 | etot = -8.53011312204286 +756000 ekin = 2.06710369978537 | erot = 1.31139881402575 | epot = -11.9086156357105 | etot = -8.53011312189937 +757000 ekin = 2.06866724412146 | erot = 1.30946252818078 | epot = -11.9082428937971 | etot = -8.53011312149487 +758000 ekin = 2.07499396289555 | erot = 1.32035089933049 | epot = -11.925457983801 | etot = -8.53011312157492 +759000 ekin = 2.08841045512732 | erot = 1.34191093709598 | epot = -11.9604345139953 | etot = -8.53011312177199 +760000 ekin = 2.10963645106986 | erot = 1.37032699692581 | epot = -12.010076570064 | etot = -8.53011312206832 +761000 ekin = 2.13857799100674 | erot = 1.40109303383798 | epot = -12.0697841472741 | etot = -8.53011312242933 +762000 ekin = 2.17432662716976 | erot = 1.42956057103018 | epot = -12.1340003210081 | etot = -8.5301131228082 +763000 ekin = 2.21530334450661 | erot = 1.45159579146069 | epot = -12.1970122591061 | etot = -8.5301131231388 +764000 ekin = 2.25988007752543 | erot = 1.46444731772858 | epot = -12.254440517812 | etot = -8.53011312255798 +765000 ekin = 2.30943589560879 | erot = 1.46853530581777 | epot = -12.3080843240095 | etot = -8.53011312258293 +766000 ekin = 2.3633228118817 | erot = 1.46534946814755 | epot = -12.3587854025141 | etot = -8.53011312248485 +767000 ekin = 2.42035196936083 | erot = 1.45783003510621 | epot = -12.4082951267659 | etot = -8.53011312229886 +768000 ekin = 2.47581566549893 | erot = 1.44854904097506 | epot = -12.4544778289231 | etot = -8.5301131224491 +769000 ekin = 2.52363299147821 | erot = 1.44004118154502 | epot = -12.4937872952733 | etot = -8.53011312225009 +770000 ekin = 2.5627053313779 | erot = 1.43704014073028 | epot = -12.5298585942135 | etot = -8.53011312210536 +771000 ekin = 2.59209730118586 | erot = 1.44343459838975 | epot = -12.5656450216748 | etot = -8.53011312209923 +772000 ekin = 2.61072906205615 | erot = 1.46130008819838 | epot = -12.6021422725622 | etot = -8.5301131223077 +773000 ekin = 2.61709469192326 | erot = 1.49008956150967 | epot = -12.6372973762101 | etot = -8.53011312277716 +774000 ekin = 2.60909645670254 | erot = 1.5261853113325 | epot = -12.6653948915257 | etot = -8.53011312349066 +775000 ekin = 2.584180757009 | erot = 1.56310881845028 | epot = -12.6774026997703 | etot = -8.53011312431102 +776000 ekin = 2.54009174823966 | erot = 1.59267184116151 | epot = -12.6628767144439 | etot = -8.53011312504277 +777000 ekin = 2.47580451030283 | erot = 1.60710708457714 | epot = -12.6130247202665 | etot = -8.53011312538657 +778000 ekin = 2.39287500137842 | erot = 1.60165568861311 | epot = -12.5246438151158 | etot = -8.53011312512425 +779000 ekin = 2.29635110868226 | erot = 1.5765511430474 | epot = -12.4030153759893 | etot = -8.53011312425959 +780000 ekin = 2.19432865474743 | erot = 1.53718068401753 | epot = -12.2616224618442 | etot = -8.53011312307929 +781000 ekin = 2.09599445125154 | erot = 1.49202506834476 | epot = -12.1181326416448 | etot = -8.53011312204848 +782000 ekin = 2.01067959043123 | erot = 1.44954049911078 | epot = -11.9903332111645 | etot = -8.53011312162245 +783000 ekin = 1.94134953217387 | erot = 1.41422212236663 | epot = -11.8856847763031 | etot = -8.53011312176256 +784000 ekin = 1.88557673989061 | erot = 1.38612068272764 | epot = -11.8018105449286 | etot = -8.53011312231031 +785000 ekin = 1.83821251587275 | erot = 1.36190678413453 | epot = -11.7302324229957 | etot = -8.53011312298836 +786000 ekin = 1.79361791902195 | erot = 1.3366529467747 | epot = -11.6603839893359 | etot = -8.53011312353925 +787000 ekin = 1.74765651996289 | erot = 1.30572681394152 | epot = -11.5834964576949 | etot = -8.53011312379047 +788000 ekin = 1.69893980452203 | erot = 1.26627175388825 | epot = -11.4953246820696 | etot = -8.53011312365928 +789000 ekin = 1.64926102869428 | erot = 1.21811104683314 | epot = -11.3974851987599 | etot = -8.53011312323247 +790000 ekin = 1.60278391126891 | erot = 1.16409864375872 | epot = -11.2969956774418 | etot = -8.53011312241422 +791000 ekin = 1.56615980925356 | erot = 1.10959117743484 | epot = -11.20586410814 | etot = -8.5301131214516 +792000 ekin = 1.54703734323363 | erot = 1.0614254777043 | epot = -11.1385759414963 | etot = -8.53011312055839 +793000 ekin = 1.55198521111592 | erot = 1.02650367068198 | epot = -11.1086020017441 | etot = -8.5301131199462 +794000 ekin = 1.58477896413844 | erot = 1.01030347984465 | epot = -11.1251955637415 | etot = -8.53011311975843 +795000 ekin = 1.64530503793388 | erot = 1.01579950553846 | epot = -11.1912176634959 | etot = -8.53011312002353 +796000 ekin = 1.72945610306576 | erot = 1.04308507627236 | epot = -11.3026542999965 | etot = -8.5301131206584 +797000 ekin = 1.8300109951507 | erot = 1.08968689110058 | epot = -11.4498110077628 | etot = -8.53011312151148 +798000 ekin = 1.93812374531718 | erot = 1.15131252106377 | epot = -11.6195493888024 | etot = -8.53011312242143 +799000 ekin = 2.04497054169758 | erot = 1.22278827270361 | epot = -11.797871937632 | etot = -8.53011312323085 +800000 ekin = 2.14336798475252 | erot = 1.29926771176965 | epot = -11.9727488204909 | etot = -8.5301131239687 +801000 ekin = 2.22727301807979 | erot = 1.37533047828101 | epot = -12.1327166209271 | etot = -8.5301131245663 +802000 ekin = 2.29233025372697 | erot = 1.44569167637999 | epot = -12.2681350551068 | etot = -8.53011312499983 +803000 ekin = 2.33601370068831 | erot = 1.50574813525576 | epot = -12.371874961204 | etot = -8.53011312525998 +804000 ekin = 2.35746789191767 | erot = 1.55190067908611 | epot = -12.4394816963551 | etot = -8.53011312535132 +805000 ekin = 2.35725821080623 | erot = 1.58176758445941 | epot = -12.4691389205536 | etot = -8.53011312528795 +806000 ekin = 2.33708958180946 | erot = 1.59429980420671 | epot = -12.4615025111012 | etot = -8.53011312508503 +807000 ekin = 2.29933748330018 | erot = 1.58976408842282 | epot = -12.4192146966084 | etot = -8.53011312488541 +808000 ekin = 2.24664197363816 | erot = 1.56989950315781 | epot = -12.3466546012147 | etot = -8.53011312441874 +809000 ekin = 2.18253497981478 | erot = 1.53842514359824 | epot = -12.2510732472497 | etot = -8.53011312383664 +810000 ekin = 2.11065804207247 | erot = 1.50058136871252 | epot = -12.1413525344396 | etot = -8.53011312365459 +811000 ekin = 2.03314489472902 | erot = 1.46124027743061 | epot = -12.0244982952586 | etot = -8.53011312309894 +812000 ekin = 1.95235452668751 | erot = 1.42640454805233 | epot = -11.9088721973062 | etot = -8.53011312256636 +813000 ekin = 1.87042476526723 | erot = 1.40255580939367 | epot = -11.8030936967812 | etot = -8.53011312212027 +814000 ekin = 1.78881788399355 | erot = 1.39558114785454 | epot = -11.7145121536541 | etot = -8.53011312180602 +815000 ekin = 1.70830262134635 | erot = 1.4100640930887 | epot = -11.6484798360723 | etot = -8.53011312163725 +816000 ekin = 1.62913132400324 | erot = 1.44882680731072 | epot = -11.6080712529127 | etot = -8.53011312159876 +817000 ekin = 1.55135581922497 | erot = 1.51275412297016 | epot = -11.5942230638573 | etot = -8.5301131216622 +818000 ekin = 1.47515646825142 | erot = 1.6008108113956 | epot = -11.6060804014516 | etot = -8.53011312180456 +819000 ekin = 1.40105599041545 | erot = 1.71014259914793 | epot = -11.6413117115776 | etot = -8.53011312201426 +820000 ekin = 1.32995993550557 | erot = 1.83623765526334 | epot = -11.6963107130513 | etot = -8.53011312228234 +821000 ekin = 1.2630652535206 | erot = 1.97322574610967 | epot = -11.7664041222185 | etot = -8.53011312258819 +822000 ekin = 1.20173310116966 | erot = 2.11438661283038 | epot = -11.8462328368969 | etot = -8.53011312289682 +823000 ekin = 1.14740078104478 | erot = 2.25282523514708 | epot = -11.9303391393603 | etot = -8.53011312316844 +824000 ekin = 1.10154739191426 | erot = 2.38216838202414 | epot = -12.0138288973085 | etot = -8.53011312337014 +825000 ekin = 1.06568617705835 | erot = 2.49713206510535 | epot = -12.092931365647 | etot = -8.53011312348325 +826000 ekin = 1.04135225336083 | erot = 2.59387442829393 | epot = -12.1653398051589 | etot = -8.53011312350415 +827000 ekin = 1.03006907531184 | erot = 2.67011598054695 | epot = -12.2302981793023 | etot = -8.53011312344346 +828000 ekin = 1.03328978433061 | erot = 2.7250538960879 | epot = -12.2884568037396 | etot = -8.5301131233211 +829000 ekin = 1.05231294058107 | erot = 2.75912544459229 | epot = -12.341551508337 | etot = -8.53011312316364 +830000 ekin = 1.08816877277396 | erot = 2.7736892067486 | epot = -12.3919711025229 | etot = -8.53011312300031 +831000 ekin = 1.14147021990776 | erot = 2.77068822986241 | epot = -12.4422715726318 | etot = -8.53011312286164 +832000 ekin = 1.21222920791932 | erot = 2.75233425305209 | epot = -12.4946765837488 | etot = -8.53011312277737 +833000 ekin = 1.29965444895282 | erot = 2.72082561150348 | epot = -12.5505931832315 | etot = -8.53011312277522 +834000 ekin = 1.40196412283888 | erot = 2.67809188939794 | epot = -12.6101691351166 | etot = -8.53011312287981 +835000 ekin = 1.51625524422594 | erot = 2.62555987056327 | epot = -12.6719282378969 | etot = -8.53011312310766 +836000 ekin = 1.63847039448776 | erot = 2.56396340705378 | epot = -12.7325469250018 | etot = -8.53011312346027 +837000 ekin = 1.76350003262958 | erot = 2.49326751324379 | epot = -12.7868806697862 | etot = -8.53011312391279 +838000 ekin = 1.88545581844262 | erot = 2.4128270613012 | epot = -12.8283960041408 | etot = -8.53011312439698 +839000 ekin = 1.99811239255192 | erot = 2.32192717669508 | epot = -12.8501526940733 | etot = -8.53011312482625 +840000 ekin = 2.09569613384735 | erot = 2.22044440704456 | epot = -12.8462536659563 | etot = -8.53011312506442 +841000 ekin = 2.173725264614 | erot = 2.10989077512463 | epot = -12.8137291647372 | etot = -8.53011312499862 +842000 ekin = 2.22978701493361 | erot = 1.99424893646548 | epot = -12.7541490759721 | etot = -8.53011312457298 +843000 ekin = 2.26403143583444 | erot = 1.88022583103963 | epot = -12.6743703906942 | etot = -8.53011312382014 +844000 ekin = 2.27916623055503 | erot = 1.77673401947053 | epot = -12.5860133728853 | etot = -8.53011312285977 +845000 ekin = 2.27988872469615 | erot = 1.69367250745041 | epot = -12.5036743540158 | etot = -8.53011312186927 +846000 ekin = 2.27183600933847 | erot = 1.64035007879627 | epot = -12.4422992091798 | etot = -8.5301131210451 +847000 ekin = 2.26027572823778 | erot = 1.62396723409051 | epot = -12.4143560828578 | etot = -8.53011312052946 +848000 ekin = 2.24926761309835 | erot = 1.64823314900325 | epot = -12.4276138825195 | etot = -8.53011312041792 +849000 ekin = 2.24093049969823 | erot = 1.71271918694617 | epot = -12.4837628073727 | etot = -8.5301131207283 +850000 ekin = 2.2352863097863 | erot = 1.81271493778336 | epot = -12.5781143689823 | etot = -8.53011312141266 +851000 ekin = 2.23059418786245 | erot = 1.9395861038207 | epot = -12.7002934140546 | etot = -8.53011312237144 +852000 ekin = 2.22400796085368 | erot = 2.08159933079985 | epot = -12.8357204150204 | etot = -8.53011312336684 +853000 ekin = 2.21277994501012 | erot = 2.22526716127566 | epot = -12.9681602307897 | etot = -8.53011312450391 +854000 ekin = 2.19416370963483 | erot = 2.35673636871339 | epot = -13.0810132037864 | etot = -8.53011312543816 +855000 ekin = 2.16598116515685 | erot = 2.46372761523239 | epot = -13.1598219064261 | etot = -8.53011312603689 +856000 ekin = 2.12753272379751 | erot = 2.53738513629609 | epot = -13.1950309863236 | etot = -8.53011312623 +857000 ekin = 2.07957021479449 | erot = 2.57336411908054 | epot = -13.1830474599009 | etot = -8.53011312602585 +858000 ekin = 2.02398845902938 | erot = 2.57205351918814 | epot = -13.1261551037142 | etot = -8.53011312549671 +859000 ekin = 1.96347606559006 | erot = 2.53830132905375 | epot = -13.0318905194401 | etot = -8.5301131247963 +860000 ekin = 1.90079123526298 | erot = 2.47952673179557 | epot = -12.9104310911536 | etot = -8.53011312409506 +861000 ekin = 1.83808336624989 | erot = 2.40350575732642 | epot = -12.7717022470392 | etot = -8.53011312346292 +862000 ekin = 1.77692269648157 | erot = 2.31773605216886 | epot = -12.6247718716174 | etot = -8.53011312296695 +863000 ekin = 1.71824491583397 | erot = 2.22850238050143 | epot = -12.476860418958 | etot = -8.53011312262258 +864000 ekin = 1.66247784195313 | erot = 2.1404774839969 | epot = -12.3330684483573 | etot = -8.53011312240726 +865000 ekin = 1.60977147001079 | erot = 2.05677487410831 | epot = -12.1966594663994 | etot = -8.53011312228031 +866000 ekin = 1.56023542790143 | erot = 1.97927297432476 | epot = -12.0696215244265 | etot = -8.53011312220029 +867000 ekin = 1.51411625156317 | erot = 1.90904243447512 | epot = -11.9532718081708 | etot = -8.5301131221325 +868000 ekin = 1.47188909914546 | erot = 1.84677021419571 | epot = -11.8487724353921 | etot = -8.5301131220509 +869000 ekin = 1.43450342552722 | erot = 1.79302433226931 | epot = -11.7576408797363 | etot = -8.53011312193975 +870000 ekin = 1.40309125561533 | erot = 1.74850970129618 | epot = -11.681714078727 | etot = -8.53011312181552 +871000 ekin = 1.37958721285951 | erot = 1.7144026390927 | epot = -11.6241029735179 | etot = -8.53011312156574 +872000 ekin = 1.36659086817592 | erot = 1.6914610233121 | epot = -11.5881650131805 | etot = -8.53011312169251 +873000 ekin = 1.36373253535392 | erot = 1.68047336442592 | epot = -11.5743190214342 | etot = -8.53011312165436 +874000 ekin = 1.37056306919445 | erot = 1.68272728104334 | epot = -11.5834034718922 | etot = -8.53011312165442 +875000 ekin = 1.38641922307153 | erot = 1.69919412007513 | epot = -11.6157264648621 | etot = -8.53011312171546 +876000 ekin = 1.41041928728016 | erot = 1.7300272312922 | epot = -11.6705596404538 | etot = -8.53011312188148 +877000 ekin = 1.44135762460335 | erot = 1.77412255951791 | epot = -11.7455933062268 | etot = -8.53011312210553 +878000 ekin = 1.47769632420485 | erot = 1.8298968923088 | epot = -11.8377063388812 | etot = -8.53011312236755 +879000 ekin = 1.51786971942077 | erot = 1.89513519879109 | epot = -11.9431180408563 | etot = -8.53011312264443 +880000 ekin = 1.56043024315676 | erot = 1.96714021036355 | epot = -12.057683576443 | etot = -8.53011312292266 +881000 ekin = 1.60413749602127 | erot = 2.04284304203179 | epot = -12.1770936612538 | etot = -8.53011312320076 +882000 ekin = 1.64798530770388 | erot = 2.11880523092398 | epot = -12.2969036621429 | etot = -8.53011312351505 +883000 ekin = 1.69122698489641 | erot = 2.1909880115382 | epot = -12.4123281202516 | etot = -8.53011312381701 +884000 ekin = 1.73324713427492 | erot = 2.2551355567814 | epot = -12.5184958151774 | etot = -8.53011312412103 +885000 ekin = 1.77353313460965 | erot = 2.30696174261745 | epot = -12.6106080016274 | etot = -8.53011312440027 +886000 ekin = 1.81168812336169 | erot = 2.34253084478391 | epot = -12.6843320927583 | etot = -8.53011312461273 +887000 ekin = 1.84747843479067 | erot = 2.35884841145035 | epot = -12.7364399709521 | etot = -8.53011312471107 +888000 ekin = 1.88090055110488 | erot = 2.35429714150869 | epot = -12.7653108178208 | etot = -8.5301131252072 +889000 ekin = 1.91199067531012 | erot = 2.32652877034522 | epot = -12.7686325706498 | etot = -8.53011312499449 +890000 ekin = 1.94125303802836 | erot = 2.27732909890954 | epot = -12.7486952615258 | etot = -8.53011312458792 +891000 ekin = 1.96982663210601 | erot = 2.21178980993948 | epot = -12.7117295661116 | etot = -8.53011312406609 +892000 ekin = 1.99917310251531 | erot = 2.13642241817651 | epot = -12.6657086442298 | etot = -8.53011312353799 +893000 ekin = 2.03065310422525 | erot = 2.05798315744505 | epot = -12.6187493847851 | etot = -8.53011312311476 +894000 ekin = 2.06504907980253 | erot = 1.98231723802983 | epot = -12.5774794407153 | etot = -8.53011312288296 +895000 ekin = 2.10217018399877 | erot = 1.91347939812078 | epot = -12.5457627050049 | etot = -8.5301131228854 +896000 ekin = 2.14066929411878 | erot = 1.85328312217968 | epot = -12.5240655392598 | etot = -8.53011312296133 +897000 ekin = 2.17888182063151 | erot = 1.80140384590578 | epot = -12.5103987898324 | etot = -8.5301131232951 +898000 ekin = 2.21472564829072 | erot = 1.7559491048214 | epot = -12.500787876807 | etot = -8.53011312369491 +899000 ekin = 2.24569847688266 | erot = 1.71401610888441 | epot = -12.4898277098273 | etot = -8.53011312406028 +900000 ekin = 2.26993925540951 | erot = 1.67248576849309 | epot = -12.4725381482042 | etot = -8.53011312430161 +901000 ekin = 2.28606210288977 | erot = 1.62859738727612 | epot = -12.4447726153278 | etot = -8.53011312516187 +902000 ekin = 2.29042230833931 | erot = 1.57932532021181 | epot = -12.3998607538154 | etot = -8.53011312526431 +903000 ekin = 2.28273813411885 | erot = 1.52313711842009 | epot = -12.3359883777437 | etot = -8.53011312520473 +904000 ekin = 2.26413659223255 | erot = 1.45995102712811 | epot = -12.2542007443878 | etot = -8.53011312502713 +905000 ekin = 2.23616199952034 | erot = 1.39088148159727 | epot = -12.1571566059059 | etot = -8.5301131247883 +906000 ekin = 2.20025203975427 | erot = 1.31795883314273 | epot = -12.048323997428 | etot = -8.53011312453098 +907000 ekin = 2.15741247687551 | erot = 1.24385993298354 | epot = -11.9313855341255 | etot = -8.53011312426642 +908000 ekin = 2.10821372460307 | erot = 1.17175804307284 | epot = -11.8100848916 | etot = -8.5301131239241 +909000 ekin = 2.05339597656793 | erot = 1.10523613714342 | epot = -11.6887452373131 | etot = -8.53011312360174 +910000 ekin = 1.99437388636401 | erot = 1.04840591871054 | epot = -11.5728929278626 | etot = -8.53011312278807 +911000 ekin = 1.93472408691892 | erot = 1.00596121878728 | epot = -11.4707984281407 | etot = -8.53011312243452 +912000 ekin = 1.87571848812107 | erot = 0.981792282309055 | epot = -11.3876238925452 | etot = -8.53011312211502 +913000 ekin = 1.81824273787103 | erot = 0.979441553337294 | epot = -11.3277974130193 | etot = -8.53011312181098 +914000 ekin = 1.76344481711065 | erot = 1.00191943331552 | epot = -11.2954773719745 | etot = -8.53011312154833 +915000 ekin = 1.71265768818243 | erot = 1.05137542114792 | epot = -11.2941462307294 | etot = -8.53011312139905 +916000 ekin = 1.66711519083679 | erot = 1.12858220206574 | epot = -11.325810514255 | etot = -8.53011312135242 +917000 ekin = 1.62763655706833 | erot = 1.23302216367853 | epot = -11.3907718421935 | etot = -8.53011312144669 +918000 ekin = 1.59455865391094 | erot = 1.36258552110633 | epot = -11.4872572967196 | etot = -8.53011312170233 +919000 ekin = 1.56762589342604 | erot = 1.51336619454063 | epot = -11.6111052100989 | etot = -8.5301131221322 +920000 ekin = 1.54593157446753 | erot = 1.67955640234537 | epot = -11.7556010995449 | etot = -8.53011312273205 +921000 ekin = 1.52794851749444 | erot = 1.85350715091608 | epot = -11.9115687918801 | etot = -8.5301131234696 +922000 ekin = 1.51169520999303 | erot = 2.02606206724868 | epot = -12.0678704015167 | etot = -8.53011312427499 +923000 ekin = 1.49507384236035 | erot = 2.18724898578918 | epot = -12.2124359531917 | etot = -8.53011312504216 +924000 ekin = 1.47635971364226 | erot = 2.3273137721656 | epot = -12.3337866114592 | etot = -8.53011312565137 +925000 ekin = 1.4547156001897 | erot = 2.43791688064256 | epot = -12.4227456068396 | etot = -8.53011312600731 +926000 ekin = 1.43051136692512 | erot = 2.51317740628974 | epot = -12.4738018992913 | etot = -8.53011312607646 +927000 ekin = 1.40525402738398 | erot = 2.55026841197154 | epot = -12.4856355652497 | etot = -8.53011312589415 +928000 ekin = 1.38111941159435 | erot = 2.54946754680809 | epot = -12.4607000839378 | etot = -8.53011312553534 +929000 ekin = 1.35992585274761 | erot = 2.51283593003105 | epot = -12.4028749084815 | etot = -8.53011312570288 +930000 ekin = 1.34158304400649 | erot = 2.44241099542427 | epot = -12.3141071645153 | etot = -8.53011312508453 +931000 ekin = 1.32656952526936 | erot = 2.34647203264279 | epot = -12.203154682278 | etot = -8.53011312436587 +932000 ekin = 1.31543664436151 | erot = 2.23535488457966 | epot = -12.0809046525596 | etot = -8.5301131236184 +933000 ekin = 1.30881286163248 | erot = 2.11983848396202 | epot = -11.9587644685058 | etot = -8.53011312291131 +934000 ekin = 1.30745813480763 | erot = 2.01001812951955 | epot = -11.8475893866352 | etot = -8.53011312230804 +935000 ekin = 1.31220098075424 | erot = 1.91444621589099 | epot = -11.7567603184798 | etot = -8.53011312183458 +936000 ekin = 1.32391210171335 | erot = 1.83958727479365 | epot = -11.6936124980305 | etot = -8.53011312152353 +937000 ekin = 1.34332477770633 | erot = 1.7895743674847 | epot = -11.6630122665762 | etot = -8.53011312138513 +938000 ekin = 1.37084792782356 | erot = 1.76617827876127 | epot = -11.6671393280075 | etot = -8.53011312142264 +939000 ekin = 1.40642931157091 | erot = 1.76890798112712 | epot = -11.7054504143154 | etot = -8.53011312161738 +940000 ekin = 1.44952186396718 | erot = 1.79522267831072 | epot = -11.7748576642556 | etot = -8.53011312197768 +941000 ekin = 1.49902948238017 | erot = 1.84063576442742 | epot = -11.8697783692894 | etot = -8.53011312248181 +942000 ekin = 1.55333690860234 | erot = 1.89898447954219 | epot = -11.9824345112389 | etot = -8.53011312309434 +943000 ekin = 1.61046155753537 | erot = 1.96285592643975 | epot = -12.1034306077316 | etot = -8.53011312375651 +944000 ekin = 1.66830779525176 | erot = 2.02424654684136 | epot = -12.2226674664823 | etot = -8.53011312438917 +945000 ekin = 1.72497649039889 | erot = 2.07544351227897 | epot = -12.3305331275858 | etot = -8.53011312490793 +946000 ekin = 1.77904739726597 | erot = 2.10999554442641 | epot = -12.4191560669373 | etot = -8.53011312524495 +947000 ekin = 1.82974878182985 | erot = 2.12355253245418 | epot = -12.4834144396516 | etot = -8.53011312536752 +948000 ekin = 1.87696379694816 | erot = 2.11435368831943 | epot = -12.5214306114532 | etot = -8.53011312618566 +949000 ekin = 1.91868968740517 | erot = 2.08113041336664 | epot = -12.52993322687 | etot = -8.53011312609818 +950000 ekin = 1.95250041362345 | erot = 2.02444704716244 | epot = -12.5070605866549 | etot = -8.53011312586905 +951000 ekin = 1.9778637786337 | erot = 1.94836556911643 | epot = -12.4563424732917 | etot = -8.53011312554161 +952000 ekin = 1.99440322907185 | erot = 1.85836147890427 | epot = -12.38287783313 | etot = -8.53011312515385 +953000 ekin = 2.00183985527172 | erot = 1.76077654418835 | epot = -12.2927295242009 | etot = -8.5301131247408 +954000 ekin = 1.99994520548227 | erot = 1.66230521851151 | epot = -12.1923635483307 | etot = -8.53011312433688 +955000 ekin = 1.98848781980585 | erot = 1.56949886934363 | epot = -12.0880998131247 | etot = -8.53011312397522 +956000 ekin = 1.96719248393008 | erot = 1.4883006602956 | epot = -11.9856062679043 | etot = -8.53011312367857 +957000 ekin = 1.93576585486353 | erot = 1.42368152907481 | epot = -11.8895605073869 | etot = -8.53011312344858 +958000 ekin = 1.89410745231055 | erot = 1.37950780378272 | epot = -11.8037283791194 | etot = -8.53011312302612 +959000 ekin = 1.84388200426958 | erot = 1.35926323934016 | epot = -11.7332583665532 | etot = -8.53011312294347 +960000 ekin = 1.7860030779281 | erot = 1.36453982260963 | epot = -11.6806560233844 | etot = -8.5301131228467 +961000 ekin = 1.72147601470138 | erot = 1.39572572976078 | epot = -11.6473148671986 | etot = -8.53011312273643 +962000 ekin = 1.65221748517946 | erot = 1.45243800587786 | epot = -11.6347686137028 | etot = -8.53011312264547 +963000 ekin = 1.5808593742463 | erot = 1.53327574295208 | epot = -11.6442482398169 | etot = -8.53011312261852 +964000 ekin = 1.51040322856247 | erot = 1.6355639292653 | epot = -11.6760802805099 | etot = -8.5301131226821 +965000 ekin = 1.4438658537195 | erot = 1.75533146870353 | epot = -11.7293104452544 | etot = -8.53011312283137 +966000 ekin = 1.38401833468609 | erot = 1.88762696931008 | epot = -11.8017584270335 | etot = -8.5301131230373 +967000 ekin = 1.33323855950443 | erot = 2.0270639743502 | epot = -11.8904156571205 | etot = -8.53011312326589 +968000 ekin = 1.29343485246359 | erot = 2.16835538303868 | epot = -11.9919033590023 | etot = -8.53011312350007 +969000 ekin = 1.26598521104654 | erot = 2.30662029889123 | epot = -12.1027186336833 | etot = -8.53011312374556 +970000 ekin = 1.25166332223789 | erot = 2.4373893813798 | epot = -12.2191658276418 | etot = -8.53011312402409 +971000 ekin = 1.25055917698537 | erot = 2.55639826961706 | epot = -12.3370705709594 | etot = -8.53011312435701 +972000 ekin = 1.2620250390517 | erot = 2.6593581861793 | epot = -12.4514963499806 | etot = -8.53011312474964 +973000 ekin = 1.2846815230187 | erot = 2.74190119131833 | epot = -12.5566958395169 | etot = -8.53011312517987 +974000 ekin = 1.31650940087453 | erot = 2.79983470558498 | epot = -12.6464572320542 | etot = -8.53011312559467 +975000 ekin = 1.35503678002767 | erot = 2.82973569321932 | epot = -12.7148855991652 | etot = -8.53011312591824 +976000 ekin = 1.39761106494576 | erot = 2.8297898983668 | epot = -12.7575140893814 | etot = -8.5301131260688 +977000 ekin = 1.44171682384798 | erot = 2.80065378123681 | epot = -12.772483731069 | etot = -8.53011312598422 +978000 ekin = 1.48527676985186 | erot = 2.74603610439897 | epot = -12.7614259998977 | etot = -8.53011312564688 +979000 ekin = 1.52686311957103 | erot = 2.6727208928021 | epot = -12.7296971375713 | etot = -8.53011312519821 +980000 ekin = 1.56541539895159 | erot = 2.58979180869151 | epot = -12.6853203321536 | etot = -8.53011312451051 +981000 ekin = 1.60047076752442 | erot = 2.50776375784216 | epot = -12.6383476491722 | etot = -8.53011312380564 +982000 ekin = 1.63230110543246 | erot = 2.43713587089594 | epot = -12.5995500990661 | etot = -8.53011312273768 +983000 ekin = 1.66203103420328 | erot = 2.38850313753443 | epot = -12.5806472942403 | etot = -8.53011312250262 +984000 ekin = 1.68995499848083 | erot = 2.36799213714196 | epot = -12.5880602580497 | etot = -8.53011312242695 +985000 ekin = 1.71562347309754 | erot = 2.37731939440605 | epot = -12.6230559900315 | etot = -8.53011312252794 +986000 ekin = 1.73850018171065 | erot = 2.41550202453549 | epot = -12.6841153290532 | etot = -8.53011312280707 +987000 ekin = 1.75791457132817 | erot = 2.47889412329359 | epot = -12.7669218178726 | etot = -8.53011312325089 +988000 ekin = 1.77306329683152 | erot = 2.56140924197459 | epot = -12.8645856626387 | etot = -8.53011312383259 +989000 ekin = 1.78306912458022 | erot = 2.65491288904962 | epot = -12.9680951381379 | etot = -8.53011312450809 +990000 ekin = 1.7871102030269 | erot = 2.74980403807363 | epot = -13.0670273663133 | etot = -8.53011312521283 +991000 ekin = 1.78462774620252 | erot = 2.83581968231897 | epot = -13.1505605543846 | etot = -8.53011312586315 +992000 ekin = 1.77558737019808 | erot = 2.903053279835 | epot = -13.2087537764021 | etot = -8.53011312636903 +993000 ekin = 1.7607111600695 | erot = 2.94306881059492 | epot = -13.2338930973241 | etot = -8.53011312665972 +994000 ekin = 1.74155803540902 | erot = 2.94987789383902 | epot = -13.2215490559567 | etot = -8.53011312670862 +995000 ekin = 1.7203663537019 | erot = 2.92053034161859 | epot = -13.1710098218588 | etot = -8.53011312653833 +996000 ekin = 1.69928711846718 | erot = 2.85461248857855 | epot = -13.0840127336996 | etot = -8.5301131266539 +997000 ekin = 1.67961730936722 | erot = 2.75367224449579 | epot = -12.9634026800371 | etot = -8.53011312617413 +998000 ekin = 1.66320821769785 | erot = 2.62336921196973 | epot = -12.8166905552758 | etot = -8.53011312560823 +999000 ekin = 1.65140969901601 | erot = 2.47137959789259 | epot = -12.6529024219469 | etot = -8.53011312503827 +1000000 ekin = 1.64474900325961 | erot = 2.3063352933529 | epot = -12.4811974211383 | etot = -8.53011312452577 + 1000000 0.12183326 -1.2831408 0.035021017 -1.0836448 3.258552e-05 64000 +Loop time of 11.3718 on 4 procs for 1000000 steps with 10 atoms + +Performance: 75977.257 tau/day, 87936.641 timesteps/s, 879.366 katom-step/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.222 | 4.604 | 6.7099 | 60.2 | 40.49 +Bond | 0.14199 | 0.20499 | 0.26671 | 11.1 | 1.80 +Neigh | 0.004255 | 0.0043152 | 0.004356 | 0.1 | 0.04 +Comm | 2.4232 | 4.8228 | 6.2203 | 65.4 | 42.41 +Output | 0.055097 | 0.058013 | 0.063725 | 1.4 | 0.51 +Modify | 0.41435 | 0.49065 | 0.58017 | 10.8 | 4.31 +Other | | 1.187 | | | 10.44 + +Nlocal: 2.5 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 8 max 7 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25 ave 18 max 3 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:11 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/oxdna2_lj.cgdna b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/oxdna2_lj.cgdna new file mode 120000 index 0000000000..7df48263bc --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/oxdna2_lj.cgdna @@ -0,0 +1 @@ +../../../../../../../potentials/oxdna2_lj.cgdna \ No newline at end of file diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/data.duplex4.4type similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/data.duplex4.4type diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/data.duplex4.8type similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/data.duplex4.8type diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/generate_unique.py similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/generate_unique.py diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/in.duplex4.4type similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/in.duplex4.4type diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/in.duplex4.8type similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/in.duplex4.8type diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.4type.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/unique_bp/log.2Jul21.duplex4.8type.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/data.duplex2 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2 rename to examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/data.duplex2 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/in.duplex2 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/in.duplex2 rename to examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/in.duplex2 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/log.2Jul21.duplex2.g++.1 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.1 rename to examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/log.2Jul21.duplex2.g++.1 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/log.2Jul21.duplex2.g++.4 similarity index 100% rename from examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.2Jul21.duplex2.g++.4 rename to examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/duplex2/log.2Jul21.duplex2.g++.4 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/data.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/data.duplex2 new file mode 100644 index 0000000000..8c985708ca --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file via write_data, version 27 May 2021 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-20 20 xlo xhi +-20 20 ylo yhi +-20 20 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0 +2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0 +3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0 +4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0 +5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0 +6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0 +7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0 +8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0 +9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0 +10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0 +11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0 +12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0 +13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0 +14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0 +15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0 +16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0 + +Velocities + +1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725 +2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215 +3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625 +4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877 +5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292 +6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776 +7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357 +8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032 +9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696 +10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506 +11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418 +12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697 +13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132 +14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759 +15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106 +16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/in.duplex2 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/in.duplex2 new file mode 100644 index 0000000000..de2d1e462d --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/in.duplex2 @@ -0,0 +1,73 @@ +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.5 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + +set atom * mass 3.1575 + +group all type 1 4 + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * oxrna2_lj.cgdna +special_bonds lj 0 1 1 + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv oxrna2_lj.cgdna +pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna +pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna +pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna +pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna +pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna +pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna +pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna +pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2_lj.cgdna + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/log.19May24.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/log.19May24.duplex2.g++.1 new file mode 100644 index 0000000000..dc66a95ea7 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/log.19May24.duplex2.g++.1 @@ -0,0 +1,1121 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.005 seconds +Setting atom values ... + 16 settings made for mass +16 atoms in group all +Reading oxdna potential (fene) file oxrna2.lj with DATE: 2024-04-19 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (stk) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (xstk) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (coaxstk) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (dh) file oxrna2.lj with DATE: 2024-04-19 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3014979 + ghost atom cutoff = 4.3014979 + binsize = 2.150749, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 1e-05 +WARNING: Communication cutoff adjusted to 4.301497916929199 (src/comm.cpp:739) +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -11.1349465280231 | etot = -5.62847186873665 +Per MPI rank memory allocation (min/avg/max) = 7.592 | 7.592 | 7.592 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -0.7299505 0.034016337 -0.52688704 5.1214421e-05 64000 +1000 ekin = 2.74425239815418 | erot = 2.79065458610894 | epot = -11.163378852689 | etot = -5.62847186842591 +2000 ekin = 2.78841691867037 | erot = 2.77992540099535 | epot = -11.1968141877249 | etot = -5.62847186805919 +3000 ekin = 2.83938215410024 | erot = 2.77185117591642 | epot = -11.2397051978033 | etot = -5.62847186778665 +4000 ekin = 2.89876217830266 | erot = 2.76816783884241 | epot = -11.295401884792 | etot = -5.62847186764698 +5000 ekin = 2.96742170720772 | erot = 2.76919345829433 | epot = -11.3650870331989 | etot = -5.62847186769686 +6000 ekin = 3.04563007371043 | erot = 2.77376672268246 | epot = -11.4478686641706 | etot = -5.62847186777771 +7000 ekin = 3.13407886898542 | erot = 2.78065913591454 | epot = -11.5432098726294 | etot = -5.6284718677294 +8000 ekin = 3.23400863287747 | erot = 2.78938863934855 | epot = -11.651869139893 | etot = -5.62847186766701 +9000 ekin = 3.34625998930262 | erot = 2.80019523753782 | epot = -11.7749270943235 | etot = -5.62847186748302 +10000 ekin = 3.47220350616338 | erot = 2.8146462281528 | epot = -11.9153216015116 | etot = -5.6284718671954 +11000 ekin = 3.61341090096022 | erot = 2.83541090219848 | epot = -12.0772936703878 | etot = -5.62847186722913 +12000 ekin = 3.76971728921065 | erot = 2.8651661044909 | epot = -12.2633552607298 | etot = -5.62847186702827 +13000 ekin = 3.9410557771447 | erot = 2.90597306806357 | epot = -12.4755007121565 | etot = -5.6284718669482 +14000 ekin = 4.1273074489676 | erot = 2.95952862137382 | epot = -12.7153079373022 | etot = -5.6284718669608 +15000 ekin = 4.32776706381553 | erot = 3.02701108512254 | epot = -12.9832500158853 | etot = -5.62847186694726 +16000 ekin = 4.54139695680688 | erot = 3.10924468066181 | epot = -13.2791135046205 | etot = -5.6284718671518 +17000 ekin = 4.76575661763827 | erot = 3.20604355373096 | epot = -13.6002720389201 | etot = -5.62847186755087 +18000 ekin = 4.99700491214688 | erot = 3.31611869568271 | epot = -13.9415954758898 | etot = -5.62847186806023 +19000 ekin = 5.23048108112193 | erot = 3.43700077146765 | epot = -14.2959537213472 | etot = -5.62847186875764 +20000 ekin = 5.46074742513059 | erot = 3.56463156086408 | epot = -14.6538508556014 | etot = -5.6284718696067 +21000 ekin = 5.68087058007136 | erot = 3.6925677668172 | epot = -15.0019102179231 | etot = -5.62847187103453 +22000 ekin = 5.88327619983878 | erot = 3.81252322503561 | epot = -15.3242712967755 | etot = -5.62847187190114 +23000 ekin = 6.06249979951991 | erot = 3.91720950057676 | epot = -15.6081811728147 | etot = -5.62847187271807 +24000 ekin = 6.21449712377435 | erot = 4.00104081543186 | epot = -15.8440098121105 | etot = -5.62847187290428 +25000 ekin = 6.33853277809253 | erot = 4.06184542619887 | epot = -16.0288500769829 | etot = -5.62847187269146 +26000 ekin = 6.43627737187009 | erot = 4.10076278430849 | epot = -16.1655120283939 | etot = -5.62847187221528 +27000 ekin = 6.51092447972025 | erot = 4.12134483746815 | epot = -16.2607411888241 | etot = -5.62847187163574 +28000 ekin = 6.56622100976682 | erot = 4.12827111510821 | epot = -16.3229639959506 | etot = -5.62847187107561 +29000 ekin = 6.60587340002393 | erot = 4.12622173833904 | epot = -16.3605670089492 | etot = -5.62847187058621 +30000 ekin = 6.63335580501828 | erot = 4.11921545444656 | epot = -16.3810431296794 | etot = -5.62847187021455 +31000 ekin = 6.65211888589272 | erot = 4.10999678317533 | epot = -16.3905875389834 | etot = -5.62847186991536 +32000 ekin = 6.66584763664876 | erot = 4.10024297795102 | epot = -16.3945624842072 | etot = -5.62847186960746 +33000 ekin = 6.67923227191032 | erot = 4.09129207413366 | epot = -16.398996215263 | etot = -5.62847186921904 +34000 ekin = 6.69756137216835 | erot = 4.08414768607663 | epot = -16.4101809271347 | etot = -5.62847186888967 +35000 ekin = 6.72589628312086 | erot = 4.07950228497946 | epot = -16.4338704366878 | etot = -5.62847186858743 +36000 ekin = 6.76908557113719 | erot = 4.07778615492108 | epot = -16.4753435944362 | etot = -5.62847186837788 +37000 ekin = 6.83097506213408 | erot = 4.07899014040663 | epot = -16.5384370708783 | etot = -5.62847186833763 +38000 ekin = 6.91354703253176 | erot = 4.08242106390417 | epot = -16.6244399649597 | etot = -5.62847186852377 +39000 ekin = 7.01626065739838 | erot = 4.08652171942787 | epot = -16.7312542457772 | etot = -5.62847186895094 +40000 ekin = 7.13573792258334 | erot = 4.08884404540009 | epot = -16.8530538375759 | etot = -5.62847186959249 +41000 ekin = 7.26614194134518 | erot = 4.08627042537775 | epot = -16.9808842370344 | etot = -5.62847187031148 +42000 ekin = 7.40051154120591 | erot = 4.07546023443116 | epot = -17.1044436466278 | etot = -5.62847187099075 +43000 ekin = 7.53157437143692 | erot = 4.05344655359659 | epot = -17.2134927965851 | etot = -5.62847187155156 +44000 ekin = 7.65268317567645 | erot = 4.01819177227258 | epot = -17.2993468198235 | etot = -5.62847187187444 +45000 ekin = 7.75845343306887 | erot = 3.96898510895803 | epot = -17.3559104142067 | etot = -5.62847187217978 +46000 ekin = 7.84504377034638 | erot = 3.90454903064828 | epot = -17.3780646733318 | etot = -5.62847187233719 +47000 ekin = 7.91002390820626 | erot = 3.82478596555232 | epot = -17.3632817459108 | etot = -5.62847187215224 +48000 ekin = 7.95195705456501 | erot = 3.73154439390041 | epot = -17.311973320413 | etot = -5.62847187194754 +49000 ekin = 7.97001825706861 | erot = 3.6275200729508 | epot = -17.2260102016186 | etot = -5.62847187159922 +50000 ekin = 7.96375756700422 | erot = 3.51726958365139 | epot = -17.1094990215453 | etot = -5.62847187088966 +51000 ekin = 7.93280761300431 | erot = 3.40827188497864 | epot = -16.9695513688031 | etot = -5.62847187082019 +52000 ekin = 7.87656811744183 | erot = 3.30207418532557 | epot = -16.8071141735587 | etot = -5.62847187079128 +53000 ekin = 7.79531012541898 | erot = 3.19839984815428 | epot = -16.6221818441147 | etot = -5.62847187054148 +54000 ekin = 7.68952609570325 | erot = 3.09980185481829 | epot = -16.4177998208246 | etot = -5.62847187030301 +55000 ekin = 7.55966222141086 | erot = 3.00897426989539 | epot = -16.1971083614499 | etot = -5.62847187014369 +56000 ekin = 7.4059412450799 | erot = 2.92802865182258 | epot = -15.9624417669772 | etot = -5.62847187007475 +57000 ekin = 7.2281659814198 | erot = 2.85836584281787 | epot = -15.7150036943479 | etot = -5.62847187011025 +58000 ekin = 7.02573051397596 | erot = 2.80066522322027 | epot = -15.4548676074194 | etot = -5.62847187022315 +59000 ekin = 6.80455077165109 | erot = 2.75651944712021 | epot = -15.1895420860965 | etot = -5.62847186732517 +60000 ekin = 6.57760251691503 | erot = 2.72731501678723 | epot = -14.9333893991692 | etot = -5.62847186546695 +61000 ekin = 5.99884053189999 | erot = 2.65010269791689 | epot = -14.2774150331152 | etot = -5.6284718032983 +62000 ekin = 5.82217958652223 | erot = 2.65058478195176 | epot = -14.1012361774608 | etot = -5.6284718089868 +63000 ekin = 6.00993174210236 | erot = 2.71143483466413 | epot = -14.3498384845185 | etot = -5.62847190775202 +64000 ekin = 5.85096985050355 | erot = 2.7117391762473 | epot = -14.1911809366076 | etot = -5.62847190985675 +65000 ekin = 5.67959801442723 | erot = 2.70731630130169 | epot = -14.0153862253964 | etot = -5.62847190966753 +66000 ekin = 5.49812382731694 | erot = 2.69646895132519 | epot = -13.8230646880633 | etot = -5.62847190942114 +67000 ekin = 5.31011188753136 | erot = 2.67901331172419 | epot = -13.6175971082585 | etot = -5.62847190900291 +68000 ekin = 5.11964229582578 | erot = 2.65622197273437 | epot = -13.4043361770529 | etot = -5.62847190849276 +69000 ekin = 4.93067975207842 | erot = 2.63014135225731 | epot = -13.1892930124932 | etot = -5.62847190815746 +70000 ekin = 4.74697386617474 | erot = 2.60347312706344 | epot = -12.9789189008753 | etot = -5.62847190763708 +71000 ekin = 4.57222133259557 | erot = 2.57971589798969 | epot = -12.7804091377446 | etot = -5.62847190715932 +72000 ekin = 4.40959648507772 | erot = 2.56228295922529 | epot = -12.6003513510618 | etot = -5.62847190675876 +73000 ekin = 4.26170009573894 | erot = 2.55406076080147 | epot = -12.4442327629951 | etot = -5.62847190645466 +74000 ekin = 4.13052949790808 | erot = 2.557131558412 | epot = -12.3161329625868 | etot = -5.62847190626671 +75000 ekin = 4.01588192828862 | erot = 2.56608801434098 | epot = -12.2104419139899 | etot = -5.62847197136028 +76000 ekin = 3.95904625854757 | erot = 2.44184942386042 | epot = -12.0293675901712 | etot = -5.62847190776322 +77000 ekin = 4.02755960266353 | erot = 2.46007159499071 | epot = -12.116103109804 | etot = -5.62847191214981 +78000 ekin = 3.98785439943804 | erot = 2.49596945534623 | epot = -12.1122957670967 | etot = -5.62847191231245 +79000 ekin = 3.96575767721416 | erot = 2.54200842335471 | epot = -12.1362380131156 | etot = -5.62847191254671 +80000 ekin = 3.95961954869541 | erot = 2.59604589435614 | epot = -12.1841373558851 | etot = -5.62847191283359 +81000 ekin = 3.96734100032327 | erot = 2.6557706223237 | epot = -12.2515835357819 | etot = -5.62847191313495 +82000 ekin = 3.98651997822105 | erot = 2.71892569307102 | epot = -12.3339175847232 | etot = -5.62847191343116 +83000 ekin = 4.01459300302725 | erot = 2.78352190390217 | epot = -12.4265868206362 | etot = -5.62847191370674 +84000 ekin = 4.04956210608531 | erot = 2.84796629664438 | epot = -12.5260003165346 | etot = -5.62847191380496 +85000 ekin = 4.09049341026844 | erot = 2.91104365381121 | epot = -12.6300089781182 | etot = -5.62847191403855 +86000 ekin = 4.13484812560025 | erot = 2.9720116541911 | epot = -12.7353316940206 | etot = -5.62847191422921 +87000 ekin = 4.18003829184629 | erot = 3.03078479878308 | epot = -12.8392950049956 | etot = -5.62847191436619 +88000 ekin = 4.22360704724714 | erot = 3.08796574000345 | epot = -12.9400447017004 | etot = -5.62847191444985 +89000 ekin = 4.26326024607304 | erot = 3.14481288279509 | epot = -13.0365450433362 | etot = -5.62847191446803 +90000 ekin = 4.29588111790597 | erot = 3.20341713777037 | epot = -13.1277701703303 | etot = -5.62847191465392 +91000 ekin = 4.31697784577794 | erot = 3.26736040230181 | epot = -13.212810162646 | etot = -5.62847191456621 +92000 ekin = 4.32507837347559 | erot = 3.33931601944585 | epot = -13.2928663075904 | etot = -5.62847191466898 +93000 ekin = 4.31872212432177 | erot = 3.42036541916803 | epot = -13.3675594581782 | etot = -5.62847191468837 +94000 ekin = 4.29660005793274 | erot = 3.5120569475443 | epot = -13.4371289201543 | etot = -5.62847191467728 +95000 ekin = 4.25789021838825 | erot = 3.6160647566687 | epot = -13.5024268896673 | etot = -5.62847191461038 +96000 ekin = 4.20253661926483 | erot = 3.73412422729693 | epot = -13.5651327610316 | etot = -5.62847191446987 +97000 ekin = 4.13146529060001 | erot = 3.8680303743933 | epot = -13.6279675793422 | etot = -5.6284719143489 +98000 ekin = 4.04669071975339 | erot = 4.01885670334765 | epot = -13.6940193371957 | etot = -5.62847191409463 +99000 ekin = 3.95128630061884 | erot = 4.187728400135 | epot = -13.767486614563 | etot = -5.62847191380918 +100000 ekin = 3.84921784883049 | erot = 4.37558821791318 | epot = -13.8532779802878 | etot = -5.62847191354417 +101000 ekin = 3.74501223923277 | erot = 4.58258429231828 | epot = -13.956068444915 | etot = -5.62847191336391 +102000 ekin = 3.64330024870546 | erot = 4.80764134110159 | epot = -14.0794135031378 | etot = -5.62847191333073 +103000 ekin = 3.54831662006249 | erot = 5.04811575607592 | epot = -14.2249042896179 | etot = -5.62847191347951 +104000 ekin = 3.46349772064904 | erot = 5.29960820358542 | epot = -14.3915778382041 | etot = -5.62847191396964 +105000 ekin = 3.39136254536235 | erot = 5.55507704360083 | epot = -14.5749115034255 | etot = -5.62847191446236 +106000 ekin = 3.33356403744374 | erot = 5.8071875932503 | epot = -14.7692235454844 | etot = -5.62847191479038 +107000 ekin = 3.29209861353668 | erot = 6.0490668738685 | epot = -14.9696374027459 | etot = -5.6284719153407 +108000 ekin = 3.26748487341083 | erot = 6.27418243659812 | epot = -15.1701392258635 | etot = -5.62847191585455 +109000 ekin = 3.25930506886586 | erot = 6.4758541724443 | epot = -15.3636311580698 | etot = -5.62847191675962 +110000 ekin = 3.2656827282909 | erot = 6.64602097208043 | epot = -15.5401756176992 | etot = -5.62847191732783 +111000 ekin = 3.2852005917262 | erot = 6.77857539600456 | epot = -15.6922479055275 | etot = -5.62847191779676 +112000 ekin = 3.31659315707444 | erot = 6.86862760564094 | epot = -15.8136926809258 | etot = -5.62847191821046 +113000 ekin = 3.35860144230948 | erot = 6.91335224014968 | epot = -15.9004256006584 | etot = -5.6284719181992 +114000 ekin = 3.41073468124698 | erot = 6.91406610981346 | epot = -15.9532727088349 | etot = -5.62847191777451 +115000 ekin = 3.47381531534301 | erot = 6.87643065686537 | epot = -15.9787178894085 | etot = -5.62847191720015 +116000 ekin = 3.54886437558797 | erot = 6.80711139529244 | epot = -15.984447687959 | etot = -5.62847191707857 +117000 ekin = 3.63467409204973 | erot = 6.71320827683705 | epot = -15.9763542854639 | etot = -5.62847191657716 +118000 ekin = 3.72815555523582 | erot = 6.60276001485677 | epot = -15.9593874864274 | etot = -5.62847191633482 +119000 ekin = 3.82420980363939 | erot = 6.48288858478363 | epot = -15.93557030497 | etot = -5.62847191654703 +120000 ekin = 3.91797748357234 | erot = 6.35662792089918 | epot = -15.9030773212286 | etot = -5.62847191675707 +121000 ekin = 4.00591742044046 | erot = 6.22468993027114 | epot = -15.8590792676436 | etot = -5.62847191693197 +122000 ekin = 4.08550270322376 | erot = 6.08676575288909 | epot = -15.8007403736375 | etot = -5.62847191752465 +123000 ekin = 4.15433540908381 | erot = 5.94071572290349 | epot = -15.7235230494649 | etot = -5.62847191747758 +124000 ekin = 4.21272085203604 | erot = 5.7859073386943 | epot = -15.6271001078555 | etot = -5.62847191712512 +125000 ekin = 4.26325970413184 | erot = 5.62467373686559 | epot = -15.5164053575236 | etot = -5.62847191652619 +126000 ekin = 4.30880597980507 | erot = 5.46113290467094 | epot = -15.3984108007453 | etot = -5.62847191626933 +127000 ekin = 4.35136313111025 | erot = 5.29960307371332 | epot = -15.2794381205815 | etot = -5.62847191575791 +128000 ekin = 4.39391383900502 | erot = 5.14386269106641 | epot = -15.1662484454475 | etot = -5.62847191537605 +129000 ekin = 4.43858036063656 | erot = 4.99693296064706 | epot = -15.0639852363967 | etot = -5.6284719151131 +130000 ekin = 4.48619887382537 | erot = 4.86092637377905 | epot = -14.9755971627249 | etot = -5.62847191512053 +131000 ekin = 4.53629967746117 | erot = 4.7355227995548 | epot = -14.9002943921708 | etot = -5.62847191515479 +132000 ekin = 4.58794392436765 | erot = 4.62012473201898 | epot = -14.8365405715617 | etot = -5.62847191517503 +133000 ekin = 4.63977927970876 | erot = 4.51475331813975 | epot = -14.7830045130172 | etot = -5.62847191516872 +134000 ekin = 4.69096227444651 | erot = 4.41936571520131 | epot = -14.738799904783 | etot = -5.62847191513517 +135000 ekin = 4.74083332632072 | erot = 4.33399770983653 | epot = -14.7033029512384 | etot = -5.6284719150812 +136000 ekin = 4.78901374177403 | erot = 4.25873574864823 | epot = -14.6762214054338 | etot = -5.62847191501159 +137000 ekin = 4.8351903396627 | erot = 4.19345584709314 | epot = -14.6571181018645 | etot = -5.62847191510868 +138000 ekin = 4.87857190019245 | erot = 4.13759960010499 | epot = -14.6446434153654 | etot = -5.628471915068 +139000 ekin = 4.9193390426862 | erot = 4.09041841408156 | epot = -14.6382293717812 | etot = -5.62847191501339 +140000 ekin = 4.9580213261069 | erot = 4.05108530565772 | epot = -14.6375785467333 | etot = -5.62847191496867 +141000 ekin = 4.99519923255321 | erot = 4.01864210163627 | epot = -14.6423132491267 | etot = -5.62847191493722 +142000 ekin = 5.03134031865355 | erot = 3.99210960072451 | epot = -14.6519218343064 | etot = -5.62847191492836 +143000 ekin = 5.06663282814573 | erot = 3.97056100872237 | epot = -14.6656657518146 | etot = -5.62847191494651 +144000 ekin = 5.10088003253933 | erot = 3.9531838593664 | epot = -14.6825358068963 | etot = -5.6284719149906 +145000 ekin = 5.13347728619374 | erot = 3.93933318432643 | epot = -14.7012823855751 | etot = -5.62847191505492 +146000 ekin = 5.16346418936991 | erot = 3.92856945833561 | epot = -14.7205055628364 | etot = -5.62847191513091 +147000 ekin = 5.18962884502066 | erot = 3.92067778970094 | epot = -14.7387785499312 | etot = -5.62847191520956 +148000 ekin = 5.21063630104988 | erot = 3.91566839447772 | epot = -14.7547766108102 | etot = -5.62847191528256 +149000 ekin = 5.22515818277256 | erot = 3.91376203384928 | epot = -14.7673921319648 | etot = -5.628471915343 +150000 ekin = 5.23199081771384 | erot = 3.91536756918841 | epot = -14.7758303022869 | etot = -5.62847191538467 +151000 ekin = 5.23025857434836 | erot = 3.92102977399535 | epot = -14.7797602637291 | etot = -5.62847191538541 +152000 ekin = 5.21970456277572 | erot = 3.93136599417286 | epot = -14.7795424723185 | etot = -5.62847191536996 +153000 ekin = 5.20020715643885 | erot = 3.94729684642981 | epot = -14.775975918157 | etot = -5.62847191528831 +154000 ekin = 5.17219962280842 | erot = 3.96989664945391 | epot = -14.7705681875095 | etot = -5.6284719152472 +155000 ekin = 5.13597939415144 | erot = 4.00025654377857 | epot = -14.7647078530824 | etot = -5.62847191515234 +156000 ekin = 5.09227456538744 | erot = 4.03969792967839 | epot = -14.7604444100923 | etot = -5.62847191502649 +157000 ekin = 5.04214374655757 | erot = 4.08965648366349 | epot = -14.7602721451213 | etot = -5.62847191490026 +158000 ekin = 4.98664076893659 | erot = 4.15175637520604 | epot = -14.7668690589132 | etot = -5.62847191477057 +159000 ekin = 4.92656708226313 | erot = 4.22693785976679 | epot = -14.7819768568009 | etot = -5.62847191477094 +160000 ekin = 4.86235166664928 | erot = 4.31524574981736 | epot = -14.8060693313523 | etot = -5.62847191488569 +161000 ekin = 4.79340744408358 | erot = 4.41634192155675 | epot = -14.8382212806371 | etot = -5.62847191499678 +162000 ekin = 4.71931679137137 | erot = 4.52911647420282 | epot = -14.8769051807422 | etot = -5.62847191516803 +163000 ekin = 4.6396517883786 | erot = 4.65170333188703 | epot = -14.919827035611 | etot = -5.62847191534539 +164000 ekin = 4.55406399624263 | erot = 4.7816630174031 | epot = -14.964198929296 | etot = -5.62847191565023 +165000 ekin = 4.46213996067388 | erot = 4.91530272158869 | epot = -15.0059145982043 | etot = -5.62847191594171 +166000 ekin = 4.36388109534803 | erot = 5.04805357548557 | epot = -15.0404065870402 | etot = -5.62847191620659 +167000 ekin = 4.25995046842371 | erot = 5.1751106852223 | epot = -15.0635330700689 | etot = -5.62847191642292 +168000 ekin = 4.15154354282065 | erot = 5.29182746831876 | epot = -15.0718429277117 | etot = -5.62847191657225 +169000 ekin = 4.04026084727433 | erot = 5.39411747728063 | epot = -15.0628502412096 | etot = -5.62847191665469 +170000 ekin = 3.9279772383829 | erot = 5.47890367159884 | epot = -15.0353528265938 | etot = -5.62847191661206 +171000 ekin = 3.81680551395789 | erot = 5.5446021996112 | epot = -14.989879630019 | etot = -5.62847191644987 +172000 ekin = 3.70912194360857 | erot = 5.59119877272674 | epot = -14.928792632495 | etot = -5.62847191615971 +173000 ekin = 3.60767008609973 | erot = 5.62020496676 | epot = -14.8563469686163 | etot = -5.62847191575655 +174000 ekin = 3.51593123142691 | erot = 5.63484613588081 | epot = -14.7792492818561 | etot = -5.62847191454834 +175000 ekin = 3.43946966413885 | erot = 5.64148825119104 | epot = -14.7094298295818 | etot = -5.62847191425188 +176000 ekin = 3.38149964340037 | erot = 5.64304584979616 | epot = -14.6530174072225 | etot = -5.62847191402599 +177000 ekin = 3.34426304280352 | erot = 5.64075589500562 | epot = -14.6134908517397 | etot = -5.62847191393054 +178000 ekin = 3.32907821318153 | erot = 5.6342917192535 | epot = -14.5918418466211 | etot = -5.62847191418611 +179000 ekin = 3.33553286829373 | erot = 5.62088708741521 | epot = -14.5848918700478 | etot = -5.62847191433888 +180000 ekin = 3.36333384277269 | erot = 5.59827011329204 | epot = -14.5900758706831 | etot = -5.62847191461841 +181000 ekin = 3.4111832274471 | erot = 5.5636994923285 | epot = -14.6033546347483 | etot = -5.62847191497266 +182000 ekin = 3.47666657813938 | erot = 5.51442909119382 | epot = -14.6195675846752 | etot = -5.62847191534198 +183000 ekin = 3.5564662729713 | erot = 5.44847615754742 | epot = -14.6334143461254 | etot = -5.62847191560665 +184000 ekin = 3.64671110623906 | erot = 5.36528131962488 | epot = -14.6404643416901 | etot = -5.62847191582612 +185000 ekin = 3.7429424385425 | erot = 5.26596644090105 | epot = -14.6373807953573 | etot = -5.62847191591374 +186000 ekin = 3.84064021177422 | erot = 5.15359326678908 | epot = -14.6227053944198 | etot = -5.62847191585649 +187000 ekin = 3.93563840595015 | erot = 5.03296537332406 | epot = -14.5970756949479 | etot = -5.6284719156737 +188000 ekin = 4.024443084093 | erot = 4.91004205202575 | epot = -14.56295705154 | etot = -5.62847191542127 +189000 ekin = 4.1043748157031 | erot = 4.7910115792593 | epot = -14.5238583101449 | etot = -5.62847191518247 +190000 ekin = 4.1734883261999 | erot = 4.68117061833012 | epot = -14.4831308595833 | etot = -5.62847191505332 +191000 ekin = 4.23028845394438 | erot = 4.58386192798764 | epot = -14.4426222970223 | etot = -5.62847191509028 +192000 ekin = 4.27358054060648 | erot = 4.49984530057482 | epot = -14.401897756479 | etot = -5.62847191529769 +193000 ekin = 4.24592911993921 | erot = 4.46741799187519 | epot = -14.3418190226908 | etot = -5.62847191087637 +194000 ekin = 4.19994174150923 | erot = 4.47173701960612 | epot = -14.3001506793666 | etot = -5.62847191825126 +195000 ekin = 4.19981139522172 | erot = 4.4036551359031 | epot = -14.2319384423484 | etot = -5.62847191122363 +196000 ekin = 4.18831859749936 | erot = 4.32821378408509 | epot = -14.1450042928944 | etot = -5.62847191130993 +197000 ekin = 4.16445522600476 | erot = 4.24686919663338 | epot = -14.0397963337818 | etot = -5.62847191114364 +198000 ekin = 4.13074920372937 | erot = 4.15919636754533 | epot = -13.9184174820229 | etot = -5.62847191074818 +199000 ekin = 4.09062074736166 | erot = 4.06700829109793 | epot = -13.7861009486901 | etot = -5.62847191023052 +200000 ekin = 4.04792338687192 | erot = 3.97356549445309 | epot = -13.649960790969 | etot = -5.628471909644 +201000 ekin = 4.0066824491976 | erot = 3.88277215508942 | epot = -13.5179265133893 | etot = -5.62847190910232 +202000 ekin = 3.97063392471701 | erot = 3.79828207702051 | epot = -13.3973879104091 | etot = -5.6284719086716 +203000 ekin = 3.94283665189344 | erot = 3.72290259923721 | epot = -13.2942111595165 | etot = -5.62847190838587 +204000 ekin = 3.92540743372103 | erot = 3.65835216262312 | epot = -13.2122315045943 | etot = -5.62847190825014 +205000 ekin = 3.91946432177235 | erot = 3.60562062220839 | epot = -13.1535568521694 | etot = -5.62847190818865 +206000 ekin = 3.92515912499344 | erot = 3.56510062726484 | epot = -13.1187316605127 | etot = -5.62847190825447 +207000 ekin = 3.94166066189477 | erot = 3.53643554884964 | epot = -13.1065681191255 | etot = -5.62847190838107 +208000 ekin = 3.96741904659518 | erot = 3.5190928531884 | epot = -13.114983808319 | etot = -5.62847190853542 +209000 ekin = 3.99456273872549 | erot = 3.50083315850336 | epot = -13.1238678065883 | etot = -5.6284719093595 +210000 ekin = 4.04796401860086 | erot = 3.49168954890742 | epot = -13.168125481534 | etot = -5.62847191402569 +211000 ekin = 4.09773342715845 | erot = 3.4930481201277 | epot = -13.2192534546312 | etot = -5.6284719073451 +212000 ekin = 4.14205596974194 | erot = 3.50221111647712 | epot = -13.272738993685 | etot = -5.62847190746594 +213000 ekin = 4.18461227969058 | erot = 3.51992604962276 | epot = -13.3330102373193 | etot = -5.62847190800596 +214000 ekin = 4.22291801220809 | erot = 3.54318058637816 | epot = -13.3945705067352 | etot = -5.62847190814894 +215000 ekin = 4.2563906994383 | erot = 3.570186348328 | epot = -13.4550489560022 | etot = -5.62847190823593 +216000 ekin = 4.2851705613054 | erot = 3.59920416165248 | epot = -13.5128466312758 | etot = -5.62847190831795 +217000 ekin = 4.30951457891106 | erot = 3.62862634730446 | epot = -13.5666128346039 | etot = -5.6284719083884 +218000 ekin = 4.33022749097326 | erot = 3.6563911824752 | epot = -13.6150905819273 | etot = -5.62847190847882 +219000 ekin = 4.34822739188537 | erot = 3.68015661121711 | epot = -13.6568559116855 | etot = -5.62847190858298 +220000 ekin = 4.36437280258125 | erot = 3.69755509928731 | epot = -13.6903998105138 | etot = -5.62847190864523 +221000 ekin = 4.37954317243207 | erot = 3.70660976824576 | epot = -13.7146248493696 | etot = -5.62847190869182 +222000 ekin = 4.39451292716876 | erot = 3.70596363375701 | epot = -13.7289484695945 | etot = -5.62847190866875 +223000 ekin = 4.41008213188782 | erot = 3.69513355487823 | epot = -13.7336875953401 | etot = -5.62847190857404 +224000 ekin = 4.42678943726031 | erot = 3.67466536393953 | epot = -13.7299267097399 | etot = -5.62847190854008 +225000 ekin = 4.44460701700765 | erot = 3.64600909388441 | epot = -13.7190880192614 | etot = -5.6284719083693 +226000 ekin = 4.47380092381616 | erot = 3.58830814099361 | epot = -13.69058097804 | etot = -5.62847191323027 +227000 ekin = 4.56056009802499 | erot = 3.47269306832995 | epot = -13.6617250773531 | etot = -5.62847191099815 +228000 ekin = 4.61083327531008 | erot = 3.40803816011441 | epot = -13.6473433475484 | etot = -5.62847191212392 +229000 ekin = 4.63150013167911 | erot = 3.35898149000892 | epot = -13.6189535337052 | etot = -5.62847191201718 +230000 ekin = 4.65431068143946 | erot = 3.31343017818568 | epot = -13.5962127716265 | etot = -5.62847191200139 +231000 ekin = 4.67934821404752 | erot = 3.27332737527216 | epot = -13.5811475014857 | etot = -5.62847191216602 +232000 ekin = 4.70592354946218 | erot = 3.23944506667555 | epot = -13.5738405284598 | etot = -5.62847191232205 +233000 ekin = 4.73271416122442 | erot = 3.21144788525773 | epot = -13.5726339590415 | etot = -5.62847191255935 +234000 ekin = 4.75943444984945 | erot = 3.19078729233504 | epot = -13.5786936545765 | etot = -5.62847191239206 +235000 ekin = 4.78642241817988 | erot = 3.18021193976644 | epot = -13.5951062703926 | etot = -5.62847191244628 +236000 ekin = 4.81315037988122 | erot = 3.1801732533471 | epot = -13.6217955456949 | etot = -5.62847191246663 +237000 ekin = 4.83923297185456 | erot = 3.19145400453184 | epot = -13.6591588888775 | etot = -5.62847191249107 +238000 ekin = 4.86487585931703 | erot = 3.21481908800045 | epot = -13.7081668597312 | etot = -5.6284719124137 +239000 ekin = 4.8906393171484 | erot = 3.25114955281718 | epot = -13.7702607826794 | etot = -5.6284719127138 +240000 ekin = 4.91656145052454 | erot = 3.29901781218542 | epot = -13.8440511754868 | etot = -5.62847191277685 +241000 ekin = 4.94245255089272 | erot = 3.35699698381213 | epot = -13.9279214477077 | etot = -5.62847191300285 +242000 ekin = 4.9676738034608 | erot = 3.42365009425621 | epot = -14.0197958109172 | etot = -5.62847191320015 +243000 ekin = 5.00573446223301 | erot = 3.47030260471464 | epot = -14.1045089792072 | etot = -5.6284719122595 +244000 ekin = 5.06987350319691 | erot = 3.50985787352737 | epot = -14.2082032932914 | etot = -5.62847191656711 +245000 ekin = 5.0840511595776 | erot = 3.57323736718629 | epot = -14.2857604930724 | etot = -5.62847196630849 +246000 ekin = 5.1386728156871 | erot = 3.53022410786619 | epot = -14.2973688418925 | etot = -5.62847191833917 +247000 ekin = 5.24446071734938 | erot = 3.63707192639368 | epot = -14.5100045566448 | etot = -5.62847191290176 +248000 ekin = 5.23528120841874 | erot = 3.74023330973652 | epot = -14.6039864311631 | etot = -5.62847191300786 +249000 ekin = 5.2126007843532 | erot = 3.83729795659792 | epot = -14.6783706538224 | etot = -5.62847191287131 +250000 ekin = 5.1783908125047 | erot = 3.92749000333375 | epot = -14.7343527284444 | etot = -5.62847191260599 +251000 ekin = 5.13586036334126 | erot = 4.01108345357157 | epot = -14.7754157290627 | etot = -5.62847191214983 +252000 ekin = 5.08918292106614 | erot = 4.09018694183985 | epot = -14.8078417745552 | etot = -5.62847191164922 +253000 ekin = 5.04264218495584 | erot = 4.16759058211337 | epot = -14.8387046782764 | etot = -5.62847191120718 +254000 ekin = 4.99116344079271 | erot = 4.24248912287346 | epot = -14.8621245493485 | etot = -5.62847198568235 +255000 ekin = 4.72637462800591 | erot = 4.24407837663544 | epot = -14.5989249326067 | etot = -5.62847192796535 +256000 ekin = 4.59834109997945 | erot = 4.36369782208908 | epot = -14.5905108364758 | etot = -5.62847191440726 +257000 ekin = 4.77089539877071 | erot = 4.60066315313584 | epot = -15.0000305289667 | etot = -5.62847197706018 +258000 ekin = 4.85704242990276 | erot = 4.66807324375475 | epot = -15.15358758141 | etot = -5.62847190775251 +259000 ekin = 4.89901811472448 | erot = 4.72718635920299 | epot = -15.2546763808506 | etot = -5.62847190692317 +260000 ekin = 4.94107094739493 | erot = 4.79406863685127 | epot = -15.3636114914047 | etot = -5.62847190715847 +261000 ekin = 4.98242309075064 | erot = 4.86508628580449 | epot = -15.4759812846147 | etot = -5.62847190805952 +262000 ekin = 5.01659840998678 | erot = 4.93871137847133 | epot = -15.5837816973583 | etot = -5.62847190890018 +263000 ekin = 5.0398266119465 | erot = 5.00983839411183 | epot = -15.6781369155651 | etot = -5.62847190950679 +264000 ekin = 5.04732696350029 | erot = 5.07389667598189 | epot = -15.7496955495877 | etot = -5.62847191010551 +265000 ekin = 5.03448807085276 | erot = 5.12688367712678 | epot = -15.7898436586171 | etot = -5.62847191063758 +266000 ekin = 4.99773438959841 | erot = 5.16480683531284 | epot = -15.7910131359598 | etot = -5.62847191104857 +267000 ekin = 4.93508497406515 | erot = 5.18388050749872 | epot = -15.7474373928659 | etot = -5.62847191130205 +268000 ekin = 4.84654531471177 | erot = 5.18063468558716 | epot = -15.655651911682 | etot = -5.62847191138309 +269000 ekin = 4.73423214274983 | erot = 5.15198859731787 | epot = -15.5146926513571 | etot = -5.62847191128937 +270000 ekin = 4.60224202248884 | erot = 5.0954068881696 | epot = -15.3261208188956 | etot = -5.62847190823717 +271000 ekin = 4.45636876655286 | erot = 5.00923317388324 | epot = -15.094073848202 | etot = -5.62847190776593 +272000 ekin = 4.30375505735806 | erot = 4.89315778304422 | epot = -14.8253847474981 | etot = -5.62847190709586 +273000 ekin = 4.15244061480226 | erot = 4.74862648123577 | epot = -14.5295390022984 | etot = -5.62847190626042 +274000 ekin = 4.01137482334719 | erot = 4.57896672456709 | epot = -14.2188134532273 | etot = -5.62847190531298 +275000 ekin = 3.87388872892913 | erot = 4.3895080579543 | epot = -13.8918687169958 | etot = -5.6284719301124 +276000 ekin = 3.70828148350437 | erot = 4.18975567950365 | epot = -13.5265090654718 | etot = -5.62847190246383 +277000 ekin = 3.74025187940247 | erot = 3.9889440521083 | epot = -13.3576678645683 | etot = -5.6284719330575 +278000 ekin = 3.74221760775476 | erot = 3.77038543692233 | epot = -13.141074947917 | etot = -5.62847190323991 +279000 ekin = 3.75220115766733 | erot = 3.55790331815025 | epot = -12.9385763794584 | etot = -5.62847190364078 +280000 ekin = 3.77561814014455 | erot = 3.35781654492889 | epot = -12.761906588381 | etot = -5.62847190330753 +281000 ekin = 3.81272927484615 | erot = 3.17409695196621 | epot = -12.615298129818 | etot = -5.62847190300567 +282000 ekin = 3.8650198803656 | erot = 3.00952640155287 | epot = -12.5030181842053 | etot = -5.62847190228687 +283000 ekin = 3.93628900406623 | erot = 2.86613168182149 | epot = -12.4308925881233 | etot = -5.62847190223561 +284000 ekin = 4.02702703049906 | erot = 2.74480306500276 | epot = -12.4003019978982 | etot = -5.62847190239635 +285000 ekin = 4.14139706639541 | erot = 2.64599110157975 | epot = -12.4158600691614 | etot = -5.62847190118625 +286000 ekin = 4.28525774917777 | erot = 2.5695076248925 | epot = -12.4832372763168 | etot = -5.62847190224656 +287000 ekin = 4.44987555795207 | erot = 2.51493810068279 | epot = -12.593285560952 | etot = -5.62847190231719 +288000 ekin = 4.63520922264523 | erot = 2.48100112555547 | epot = -12.7446822515429 | etot = -5.62847190334219 +289000 ekin = 4.83125797005403 | erot = 2.46527241539456 | epot = -12.9250022896833 | etot = -5.6284719042347 +290000 ekin = 5.02763799219358 | erot = 2.46542435681751 | epot = -13.1215342540964 | etot = -5.62847190508529 +291000 ekin = 5.21465468575785 | erot = 2.47913524144451 | epot = -13.3222618329661 | etot = -5.62847190576375 +292000 ekin = 5.38472348790201 | erot = 2.50416430328942 | epot = -13.5173596974294 | etot = -5.62847190623798 +293000 ekin = 5.53302487062945 | erot = 2.53823701976243 | epot = -13.6997337969532 | etot = -5.62847190656128 +294000 ekin = 5.65718701899543 | erot = 2.57877496352923 | epot = -13.8644338893352 | etot = -5.62847190681054 +295000 ekin = 5.75652780496729 | erot = 2.62269919784018 | epot = -14.0076989098362 | etot = -5.62847190702875 +296000 ekin = 5.83139499491568 | erot = 2.66652171228923 | epot = -14.1263886144125 | etot = -5.62847190720756 +297000 ekin = 5.882823563323 | erot = 2.70675614330057 | epot = -14.2180516139338 | etot = -5.62847190731017 +298000 ekin = 5.91239748765333 | erot = 2.74048494300737 | epot = -14.2813543379694 | etot = -5.62847190730872 +299000 ekin = 5.92208198046601 | erot = 2.76585299302064 | epot = -14.3164068806918 | etot = -5.62847190720516 +300000 ekin = 5.9139094201893 | erot = 2.78233336188598 | epot = -14.3247146891002 | etot = -5.62847190702494 +301000 ekin = 5.8896213351144 | erot = 2.79074353675919 | epot = -14.3088367786675 | etot = -5.62847190679387 +302000 ekin = 5.85048781421133 | erot = 2.79307875791735 | epot = -14.2720384786508 | etot = -5.62847190652211 +303000 ekin = 5.79743517877185 | erot = 2.79223225552608 | epot = -14.2181393405071 | etot = -5.62847190620919 +304000 ekin = 5.73124340760708 | erot = 2.79262915089302 | epot = -14.152344464163 | etot = -5.62847190566291 +305000 ekin = 5.65258268469947 | erot = 2.79940899091141 | epot = -14.0804635809917 | etot = -5.62847190538081 +306000 ekin = 5.56254653523144 | erot = 2.81503734235102 | epot = -14.0060557827401 | etot = -5.62847190515761 +307000 ekin = 5.46251129680771 | erot = 2.8407589238596 | epot = -13.9317421257007 | etot = -5.62847190503336 +308000 ekin = 5.35391293499841 | erot = 2.87633235163905 | epot = -13.8587171916691 | etot = -5.6284719050316 +309000 ekin = 5.23805007411562 | erot = 2.91996940722861 | epot = -13.7864913863792 | etot = -5.62847190503493 +310000 ekin = 5.1161387582238 | erot = 2.96880482959449 | epot = -13.7134154931036 | etot = -5.62847190528531 +311000 ekin = 4.98925852659244 | erot = 3.01839769775032 | epot = -13.6361281298098 | etot = -5.62847190546702 +312000 ekin = 4.85867326622229 | erot = 3.06421411592692 | epot = -13.5513592877705 | etot = -5.62847190562128 +313000 ekin = 4.72585112667392 | erot = 3.10236590329129 | epot = -13.4566889356282 | etot = -5.62847190566301 +314000 ekin = 4.5929342104636 | erot = 3.13002199528236 | epot = -13.3514281113021 | etot = -5.62847190555609 +315000 ekin = 4.46270669971744 | erot = 3.14588950386823 | epot = -13.2370681089026 | etot = -5.62847190531692 +316000 ekin = 4.33845457034406 | erot = 3.15016989317518 | epot = -13.1170963685036 | etot = -5.62847190498433 +317000 ekin = 4.22370149067494 | erot = 3.14429402986633 | epot = -12.9964674251473 | etot = -5.62847190460606 +318000 ekin = 4.12188681800985 | erot = 3.13056754977697 | epot = -12.8809262720118 | etot = -5.62847190422498 +319000 ekin = 4.03607214172158 | erot = 3.11184182786797 | epot = -12.7763858734595 | etot = -5.62847190386996 +320000 ekin = 3.96873641009138 | erot = 3.09128048611575 | epot = -12.6884887997592 | etot = -5.62847190355207 +321000 ekin = 3.92167797369667 | erot = 3.07226107993859 | epot = -12.6224109569052 | etot = -5.62847190326996 +322000 ekin = 3.89600971422886 | erot = 3.05833648374322 | epot = -12.5828181009992 | etot = -5.62847190302713 +323000 ekin = 3.89216326552237 | erot = 3.05323078720034 | epot = -12.5738659555586 | etot = -5.62847190283586 +324000 ekin = 3.90971752721021 | erot = 3.06065920137141 | epot = -12.5988486315804 | etot = -5.62847190299879 +325000 ekin = 3.94474197767314 | erot = 3.08325557842132 | epot = -12.6564694593425 | etot = -5.62847190324804 +326000 ekin = 3.99225791211577 | erot = 3.12131666195312 | epot = -12.74204647784 | etot = -5.62847190377106 +327000 ekin = 4.04715751818396 | erot = 3.1727757387251 | epot = -12.8484051614822 | etot = -5.6284719045731 +328000 ekin = 4.10306827948901 | erot = 3.23289809100399 | epot = -12.9644382760934 | etot = -5.62847190560038 +329000 ekin = 4.15294077796041 | erot = 3.29460254685698 | epot = -13.0760152314909 | etot = -5.62847190667349 +330000 ekin = 4.1904608637735 | erot = 3.34957314358157 | epot = -13.1685059148568 | etot = -5.62847190750169 +331000 ekin = 4.21187936703383 | erot = 3.38989153265768 | epot = -13.2302428076589 | etot = -5.62847190796742 +332000 ekin = 4.21589857652203 | erot = 3.41075094374301 | epot = -13.2551214281195 | etot = -5.62847190785443 +333000 ekin = 4.20485265998752 | erot = 3.41174399824678 | epot = -13.2450685654283 | etot = -5.628471907194 +334000 ekin = 4.18435368274816 | erot = 3.39692225044427 | epot = -13.2097478393505 | etot = -5.62847190615809 +335000 ekin = 4.16205455860123 | erot = 3.37367623594531 | epot = -13.1642026995331 | etot = -5.62847190498657 +336000 ekin = 4.14609491419202 | erot = 3.35093309666816 | epot = -13.1254999147641 | etot = -5.62847190390388 +337000 ekin = 4.14364358929798 | erot = 3.33736964606269 | epot = -13.1094851384318 | etot = -5.6284719030711 +338000 ekin = 4.15982493121391 | erot = 3.33968220643224 | epot = -13.1279790403763 | etot = -5.62847190273014 +339000 ekin = 4.19714166714036 | erot = 3.36120406394876 | epot = -13.1868176336954 | etot = -5.62847190260627 +340000 ekin = 4.25518474379064 | erot = 3.40394456534699 | epot = -13.2876012119366 | etot = -5.628471902799 +341000 ekin = 4.33079125357956 | erot = 3.46797257818277 | epot = -13.4272357350008 | etot = -5.62847190323849 +342000 ekin = 4.41854745256192 | erot = 3.55173943759763 | epot = -13.5987587940061 | etot = -5.62847190384659 +343000 ekin = 4.5115386483586 | erot = 3.65250494550388 | epot = -13.7925154984096 | etot = -5.6284719045471 +344000 ekin = 4.60219231315277 | erot = 3.76671918647586 | epot = -13.9973834048833 | etot = -5.62847190525472 +345000 ekin = 4.68312343517509 | erot = 3.89042211424083 | epot = -14.2020174553193 | etot = -5.6284719059034 +346000 ekin = 4.74786790537578 | erot = 4.01955036383248 | epot = -14.3958901756503 | etot = -5.628471906442 +347000 ekin = 4.79150376884344 | erot = 4.15019529883455 | epot = -14.570170974473 | etot = -5.62847190679502 +348000 ekin = 4.81117855584063 | erot = 4.27877359763513 | epot = -14.718424060525 | etot = -5.6284719070492 +349000 ekin = 4.80564918858235 | erot = 4.40205662691375 | epot = -14.8361777226639 | etot = -5.6284719071678 +350000 ekin = 4.77545945328399 | erot = 4.51714564004313 | epot = -14.9210770005203 | etot = -5.62847190719314 +351000 ekin = 4.72262273321761 | erot = 4.62116010887444 | epot = -14.9722547492962 | etot = -5.62847190720411 +352000 ekin = 4.65007958814115 | erot = 4.71078593019996 | epot = -14.989337425621 | etot = -5.62847190727985 +353000 ekin = 4.56109157465486 | erot = 4.7818033558294 | epot = -14.971366837947 | etot = -5.6284719074627 +354000 ekin = 4.45876151246803 | erot = 4.8289597964644 | epot = -14.9161932166554 | etot = -5.62847190772297 +355000 ekin = 4.34584612945877 | erot = 4.84663553107962 | epot = -14.8209535684629 | etot = -5.62847190792453 +356000 ekin = 4.22495470321376 | erot = 4.83038190908079 | epot = -14.6838085201839 | etot = -5.62847190788934 +357000 ekin = 4.09903296595215 | erot = 4.77873075093123 | epot = -14.5062356243656 | etot = -5.62847190748225 +358000 ekin = 3.97178667556377 | erot = 4.69444561049166 | epot = -14.2947041927644 | etot = -5.62847190670902 +359000 ekin = 3.84767298929744 | erot = 4.58431182213364 | epot = -14.0604567171835 | etot = -5.6284719057524 +360000 ekin = 3.73136439808791 | erot = 4.4574661315761 | epot = -13.817302434422 | etot = -5.62847190475798 +361000 ekin = 3.62758093165424 | erot = 4.3237906450543 | epot = -13.5798434807399 | etot = -5.62847190403139 +362000 ekin = 3.54294892306402 | erot = 4.19358097114648 | epot = -13.3650017978878 | etot = -5.62847190367727 +363000 ekin = 3.47837311690952 | erot = 4.07207692082501 | epot = -13.1789219412918 | etot = -5.6284719035573 +364000 ekin = 3.43225009805526 | erot = 3.96193194141973 | epot = -13.0226539430622 | etot = -5.62847190358719 +365000 ekin = 3.40198388462799 | erot = 3.86460642705559 | epot = -12.8950622153685 | etot = -5.62847190368494 +366000 ekin = 3.38451833851579 | erot = 3.78104622244878 | epot = -12.7940364647457 | etot = -5.62847190378114 +367000 ekin = 3.37682483157396 | erot = 3.71218000857552 | epot = -12.7174767439907 | etot = -5.62847190384127 +368000 ekin = 3.37625204137715 | erot = 3.65912147822917 | epot = -12.6638454234593 | etot = -5.628471903853 +369000 ekin = 3.380746367259 | erot = 3.62312680344518 | epot = -12.6323450745294 | etot = -5.62847190382522 +370000 ekin = 3.3889463669779 | erot = 3.60538856637072 | epot = -12.6228068371684 | etot = -5.62847190381979 +371000 ekin = 3.40011634059004 | erot = 3.60672333637875 | epot = -12.6353115807155 | etot = -5.62847190374667 +372000 ekin = 3.41430323561842 | erot = 3.62748920223738 | epot = -12.6702643415539 | etot = -5.62847190369808 +373000 ekin = 3.43217624794534 | erot = 3.66740997408251 | epot = -12.7280581255706 | etot = -5.62847190354274 +374000 ekin = 3.45538314685052 | erot = 3.7253207076594 | epot = -12.809175758137 | etot = -5.62847190362708 +375000 ekin = 3.48458983102283 | erot = 3.79950576965501 | epot = -12.9125675044332 | etot = -5.62847190375535 +376000 ekin = 3.51994630862302 | erot = 3.88772077540614 | epot = -13.036138987954 | etot = -5.62847190392486 +377000 ekin = 3.56162263238158 | erot = 3.98718032085896 | epot = -13.1772748573335 | etot = -5.62847190409292 +378000 ekin = 3.61009229017818 | erot = 4.09470007580354 | epot = -13.3332642702852 | etot = -5.62847190430351 +379000 ekin = 3.6662193925075 | erot = 4.20668278514851 | epot = -13.5013740820978 | etot = -5.62847190444178 +380000 ekin = 3.73222313433561 | erot = 4.31893025304286 | epot = -13.6796252922566 | etot = -5.62847190487811 +381000 ekin = 3.80656943721869 | erot = 4.42661769093369 | epot = -13.8616590336024 | etot = -5.62847190544999 +382000 ekin = 3.88594558524316 | erot = 4.52459411504536 | epot = -14.0390116063713 | etot = -5.62847190608281 +383000 ekin = 3.96695089997732 | erot = 4.60747433893913 | epot = -14.2028971456399 | etot = -5.62847190672346 +384000 ekin = 4.04619645065851 | erot = 4.66967915256757 | epot = -14.3443475105221 | etot = -5.62847190729599 +385000 ekin = 4.12092029135741 | erot = 4.70599192061983 | epot = -14.4553841196463 | etot = -5.62847190766905 +386000 ekin = 4.18945537161052 | erot = 4.71237691680779 | epot = -14.5303041965239 | etot = -5.62847190810561 +387000 ekin = 4.24770733743672 | erot = 4.6853187164418 | epot = -14.5614979619324 | etot = -5.62847190805387 +388000 ekin = 4.29400518231241 | erot = 4.62433064766082 | epot = -14.5468077376836 | etot = -5.62847190771033 +389000 ekin = 4.32973751034516 | erot = 4.53230747816488 | epot = -14.490516895674 | etot = -5.62847190716399 +390000 ekin = 4.35696496431934 | erot = 4.41432356916916 | epot = -14.3997604400568 | etot = -5.62847190656826 +391000 ekin = 4.37768888460328 | erot = 4.27672755002634 | epot = -14.2828883405661 | etot = -5.62847190593644 +392000 ekin = 4.39398588700305 | erot = 4.12625191226902 | epot = -14.1487097046515 | etot = -5.62847190537946 +393000 ekin = 4.40738241117814 | erot = 3.96936593197269 | epot = -14.0052202479737 | etot = -5.62847190482285 +394000 ekin = 4.41937568155273 | erot = 3.81285278688638 | epot = -13.8607003731014 | etot = -5.62847190466234 +395000 ekin = 4.429887681643 | erot = 3.66065946576785 | epot = -13.7190190519414 | etot = -5.62847190453055 +396000 ekin = 4.43847476589413 | erot = 3.51525603215846 | epot = -13.5822027024437 | etot = -5.6284719043911 +397000 ekin = 4.44517728397444 | erot = 3.37891512777923 | epot = -13.4525643159698 | etot = -5.62847190421616 +398000 ekin = 4.45064950026545 | erot = 3.25392386318522 | epot = -13.3330452674466 | etot = -5.62847190399591 +399000 ekin = 4.45613851378025 | erot = 3.14269651880886 | epot = -13.2273069363872 | etot = -5.62847190379807 +400000 ekin = 4.46297608306431 | erot = 3.04745583064105 | epot = -13.1389038172501 | etot = -5.62847190354471 +401000 ekin = 4.47275546002442 | erot = 2.97053701409529 | epot = -13.0717643774788 | etot = -5.62847190335911 +402000 ekin = 4.48672336701788 | erot = 2.91396522578301 | epot = -13.029160496141 | etot = -5.62847190334015 +403000 ekin = 4.50482841073211 | erot = 2.87870251807445 | epot = -13.0120028324215 | etot = -5.62847190361493 +404000 ekin = 4.524843257315 | erot = 2.86379686212345 | epot = -13.0171120236897 | etot = -5.6284719042513 +405000 ekin = 4.54178669954638 | erot = 2.8653512056657 | epot = -13.0356098106887 | etot = -5.62847190547664 +406000 ekin = 4.54812186978994 | erot = 2.8756562345168 | epot = -13.0522500109031 | etot = -5.62847190659635 +407000 ekin = 4.53567765664406 | erot = 2.88781666331989 | epot = -13.0519662273854 | etot = -5.62847190742146 +408000 ekin = 4.49806839875085 | erot = 2.89717319273749 | epot = -13.0237134991376 | etot = -5.62847190764926 +409000 ekin = 4.43289041828323 | erot = 2.9029317342836 | epot = -12.9642940598422 | etot = -5.62847190727535 +410000 ekin = 4.34222243514944 | erot = 2.90784571762389 | epot = -12.8785400593187 | etot = -5.62847190654535 +411000 ekin = 4.23122328985304 | erot = 2.91632332328884 | epot = -12.7760185189366 | etot = -5.62847190579472 +412000 ekin = 4.10591302472356 | erot = 2.93234263224213 | epot = -12.6667275622006 | etot = -5.62847190523494 +413000 ekin = 3.97147909139366 | erot = 2.95826875335732 | epot = -12.5582197496564 | etot = -5.62847190490539 +414000 ekin = 3.83169645331895 | erot = 2.99487215437993 | epot = -12.4550405124416 | etot = -5.62847190474269 +415000 ekin = 3.68915556889422 | erot = 3.04191716150965 | epot = -12.3595446350688 | etot = -5.62847190466496 +416000 ekin = 3.54575553260147 | erot = 3.09878213610582 | epot = -12.2730095733191 | etot = -5.62847190461177 +417000 ekin = 3.40315271148973 | erot = 3.16484246788968 | epot = -12.1964670839311 | etot = -5.62847190455169 +418000 ekin = 3.26306253875921 | erot = 3.23960054551429 | epot = -12.1311349887461 | etot = -5.62847190447262 +419000 ekin = 3.12743539448628 | erot = 3.32265867808808 | epot = -12.0785659769468 | etot = -5.62847190437241 +420000 ekin = 2.99854685250536 | erot = 3.41362396343085 | epot = -12.0406427201918 | etot = -5.62847190425557 +421000 ekin = 2.87901712494606 | erot = 3.5119788037687 | epot = -12.0194678328506 | etot = -5.62847190413584 +422000 ekin = 2.77174596054379 | erot = 3.61690112201243 | epot = -12.0171189865972 | etot = -5.62847190404102 +423000 ekin = 2.67973794666689 | erot = 3.72700827484235 | epot = -12.0352181255237 | etot = -5.62847190401442 +424000 ekin = 2.60579870930555 | erot = 3.84002717526432 | epot = -12.074297788682 | etot = -5.62847190411217 +425000 ekin = 2.55208954529187 | erot = 3.95244167891433 | epot = -12.1330031286045 | etot = -5.62847190439832 +426000 ekin = 2.51954653046236 | erot = 4.05920212805388 | epot = -12.2072205634457 | etot = -5.62847190492948 +427000 ekin = 2.50725893892059 | erot = 4.15363681828261 | epot = -12.2893676629178 | etot = -5.62847190571456 +428000 ekin = 2.51210485176412 | erot = 4.22782399612785 | epot = -12.3684007545411 | etot = -5.62847190664909 +429000 ekin = 2.52911833234268 | erot = 4.27377369071121 | epot = -12.4313639305338 | etot = -5.62847190747988 +430000 ekin = 2.55284926702148 | erot = 4.28551618825896 | epot = -12.4668373631688 | etot = -5.6284719078884 +431000 ekin = 2.57924139421313 | erot = 4.26142412036458 | epot = -12.4691374222602 | etot = -5.62847190768247 +432000 ekin = 2.60692475468281 | erot = 4.20541068246078 | epot = -12.4408073440803 | etot = -5.62847190693669 +433000 ekin = 2.63712842984009 | erot = 4.12604912501212 | epot = -12.3916494607877 | etot = -5.62847190593547 +434000 ekin = 2.67245542243098 | erot = 4.03405948921194 | epot = -12.3349868166311 | etot = -5.62847190498821 +435000 ekin = 2.71543854641988 | erot = 3.93961255970513 | epot = -12.2835230104087 | etot = -5.62847190428369 +436000 ekin = 2.76760991343117 | erot = 3.85063248522731 | epot = -12.2467143025347 | etot = -5.62847190387622 +437000 ekin = 2.82920515673023 | erot = 3.77223859649696 | epot = -12.2299156569534 | etot = -5.62847190372624 +438000 ekin = 2.89929820059969 | erot = 3.70707509974139 | epot = -12.2348452041086 | etot = -5.62847190376755 +439000 ekin = 2.97609334156257 | erot = 3.65590372387851 | epot = -12.2604689693811 | etot = -5.62847190394 +440000 ekin = 3.0572090661351 | erot = 3.61815200782515 | epot = -12.3038329781603 | etot = -5.62847190420003 +441000 ekin = 3.13989672829312 | erot = 3.5923230239825 | epot = -12.360691656793 | etot = -5.62847190451741 +442000 ekin = 3.2211992751893 | erot = 3.57626892518592 | epot = -12.4259401052482 | etot = -5.62847190487303 +443000 ekin = 3.29807867302227 | erot = 3.56737972994689 | epot = -12.4939303082158 | etot = -5.62847190524664 +444000 ekin = 3.36753883944179 | erot = 3.56276348926254 | epot = -12.5587742343224 | etot = -5.62847190561804 +445000 ekin = 3.42676046581367 | erot = 3.55942025918075 | epot = -12.6146526309594 | etot = -5.62847190596496 +446000 ekin = 3.47324383647347 | erot = 3.55443462308445 | epot = -12.6561503658264 | etot = -5.62847190626847 +447000 ekin = 3.50497354376933 | erot = 3.54511419619531 | epot = -12.6785596464708 | etot = -5.62847190650619 +448000 ekin = 3.52056213084159 | erot = 3.5297410071025 | epot = -12.678775044464 | etot = -5.62847190651992 +449000 ekin = 3.51939696591908 | erot = 3.50705904511348 | epot = -12.6549279176377 | etot = -5.6284719066051 +450000 ekin = 3.50164536054644 | erot = 3.47565071066506 | epot = -12.605767977811 | etot = -5.62847190659949 +451000 ekin = 3.46824790708968 | erot = 3.434721512032 | epot = -12.5314413256229 | etot = -5.62847190650123 +452000 ekin = 3.42090312737986 | erot = 3.38414558730049 | epot = -12.433520620992 | etot = -5.62847190631168 +453000 ekin = 3.36201791829813 | erot = 3.32449206046166 | epot = -12.3149818847957 | etot = -5.62847190603594 +454000 ekin = 3.29463316061968 | erot = 3.2570173981978 | epot = -12.1801224645013 | etot = -5.62847190568382 +455000 ekin = 3.22233274900136 | erot = 3.18360703277462 | epot = -12.034411687045 | etot = -5.62847190526907 +456000 ekin = 3.14914248629959 | erot = 3.10666992198597 | epot = -11.884284313096 | etot = -5.62847190481048 +457000 ekin = 3.07939737174129 | erot = 3.02894564058933 | epot = -11.7368149166696 | etot = -5.62847190433899 +458000 ekin = 3.01756413268935 | erot = 2.95322108562861 | epot = -11.5992571221695 | etot = -5.62847190385151 +459000 ekin = 2.96810632524382 | erot = 2.88249754736357 | epot = -11.4790757760119 | etot = -5.62847190340455 +460000 ekin = 2.93513889003322 | erot = 2.81955267521 | epot = -11.3831634682776 | etot = -5.6284719030344 +461000 ekin = 2.92205746388576 | erot = 2.76669234907988 | epot = -11.3172217157448 | etot = -5.62847190277913 +462000 ekin = 2.93114290150317 | erot = 2.72556812595781 | epot = -11.2851829301332 | etot = -5.62847190267221 +463000 ekin = 2.96319319680066 | erot = 2.69703193761399 | epot = -11.2886970371507 | etot = -5.62847190273605 +464000 ekin = 3.01726238568611 | erot = 2.68105615130189 | epot = -11.326790439963 | etot = -5.62847190297497 +465000 ekin = 3.09058398932049 | erot = 2.67674994759099 | epot = -11.3958058402812 | etot = -5.62847190336969 +466000 ekin = 3.17872270900206 | erot = 2.68248866700377 | epot = -11.4896832798861 | etot = -5.62847190388032 +467000 ekin = 3.27594114496115 | erot = 2.69614045585657 | epot = -11.6005535052724 | etot = -5.62847190445465 +468000 ekin = 3.37571282133917 | erot = 2.7153402624028 | epot = -11.7195249887813 | etot = -5.62847190503931 +469000 ekin = 3.47128178262938 | erot = 2.73774679763355 | epot = -11.8375004858527 | etot = -5.62847190558975 +470000 ekin = 3.55617737699295 | erot = 2.76123628661555 | epot = -11.9458855696824 | etot = -5.62847190607386 +471000 ekin = 3.6246330939994 | erot = 2.78402790004091 | epot = -12.0371329005091 | etot = -5.62847190646883 +472000 ekin = 3.67190559892769 | erot = 2.80477124778906 | epot = -12.1051487534733 | etot = -5.62847190675652 +473000 ekin = 3.69451868441339 | erot = 2.82263116141129 | epot = -12.1456217527447 | etot = -5.62847190691997 +474000 ekin = 3.690457463319 | erot = 2.83737882568697 | epot = -12.1563081959514 | etot = -5.62847190694547 +475000 ekin = 3.65932116351354 | erot = 2.84946541726914 | epot = -12.1372584876075 | etot = -5.62847190682481 +476000 ekin = 3.60242486139365 | erot = 2.86004016498472 | epot = -12.0909369329381 | etot = -5.62847190655976 +477000 ekin = 3.52282746240941 | erot = 2.87088465735228 | epot = -12.0221840259233 | etot = -5.62847190616159 +478000 ekin = 3.42525452631152 | erot = 2.88424967269603 | epot = -11.9379761046733 | etot = -5.62847190566571 +479000 ekin = 3.31588349740451 | erot = 2.90254646895417 | epot = -11.8469018714746 | etot = -5.62847190511589 +480000 ekin = 3.20192949247412 | erot = 2.92801081389738 | epot = -11.7584122109498 | etot = -5.62847190457828 +481000 ekin = 3.09102106842349 | erot = 2.962275100393 | epot = -11.68176807295 | etot = -5.6284719041335 +482000 ekin = 2.99039932402913 | erot = 3.00590839367439 | epot = -11.6247796215674 | etot = -5.62847190386392 +483000 ekin = 2.90605693346212 | erot = 3.0579980296226 | epot = -11.5925268669205 | etot = -5.62847190383583 +484000 ekin = 2.84200171526081 | erot = 3.11586840861443 | epot = -11.586342027954 | etot = -5.62847190407872 +485000 ekin = 2.81072036469033 | erot = 3.03665546470463 | epot = -11.4758477219315 | etot = -5.62847189253652 +486000 ekin = 2.99172671784441 | erot = 2.89028588609549 | epot = -11.5104845146674 | etot = -5.6284719107275 +487000 ekin = 3.04661020883305 | erot = 2.89516257154732 | epot = -11.5702446860141 | etot = -5.62847190563374 +488000 ekin = 3.02813445461909 | erot = 2.91755814175032 | epot = -11.5741645019042 | etot = -5.62847190553475 +489000 ekin = 3.0291817318923 | erot = 2.94703274342082 | epot = -11.6046863809146 | etot = -5.62847190560147 +490000 ekin = 3.04920929974356 | erot = 2.98299921438345 | epot = -11.6606804199472 | etot = -5.62847190582018 +491000 ekin = 3.08564623420881 | erot = 3.02458607701207 | epot = -11.7387042173395 | etot = -5.62847190611864 +492000 ekin = 3.13426650213357 | erot = 3.07113014036676 | epot = -11.8338685489377 | etot = -5.62847190643739 +493000 ekin = 3.19024782354288 | erot = 3.12246736374614 | epot = -11.9411870939343 | etot = -5.62847190664525 +494000 ekin = 3.24418110399159 | erot = 3.17757093523865 | epot = -12.0502240477464 | etot = -5.62847200851614 +495000 ekin = 3.12930691881805 | erot = 3.12025770000067 | epot = -11.8780365336473 | etot = -5.62847191482857 +496000 ekin = 3.38154400856943 | erot = 3.12702216680609 | epot = -12.1370381395841 | etot = -5.62847196420855 +497000 ekin = 3.5379633430085 | erot = 3.2134524018408 | epot = -12.3798876660854 | etot = -5.62847192123606 +498000 ekin = 3.54725242242046 | erot = 3.31274815694437 | epot = -12.4884725006184 | etot = -5.62847192125361 +499000 ekin = 3.54686752390257 | erot = 3.42936350671392 | epot = -12.6047029519614 | etot = -5.62847192134493 +500000 ekin = 3.53611629142107 | erot = 3.5621447184912 | epot = -12.7267329314238 | etot = -5.62847192151152 +501000 ekin = 3.51474019582421 | erot = 3.7083124006301 | epot = -12.8515245182113 | etot = -5.62847192175698 +502000 ekin = 3.48291543615832 | erot = 3.86351597858801 | epot = -12.9749033367362 | etot = -5.62847192198988 +503000 ekin = 3.44167367983497 | erot = 4.02200657195978 | epot = -13.0921521741415 | etot = -5.62847192234678 +504000 ekin = 3.3916656193754 | erot = 4.17733332043199 | epot = -13.1974708625473 | etot = -5.6284719227399 +505000 ekin = 3.33344269450503 | erot = 4.32266370128013 | epot = -13.2845783189161 | etot = -5.62847192313095 +506000 ekin = 3.26726906279279 | erot = 4.45157764164499 | epot = -13.347318627836 | etot = -5.62847192339819 +507000 ekin = 3.19388361649229 | erot = 4.55898983229981 | epot = -13.3813453722761 | etot = -5.62847192348402 +508000 ekin = 3.1146272404848 | erot = 4.64207406472587 | epot = -13.3851732285439 | etot = -5.62847192333327 +509000 ekin = 3.03154551889222 | erot = 4.70083202644274 | epot = -13.3608494682894 | etot = -5.62847192295445 +510000 ekin = 2.94513058610523 | erot = 4.73730594222444 | epot = -13.3109084508144 | etot = -5.62847192248476 +511000 ekin = 2.85640718493158 | erot = 4.75516581382911 | epot = -13.2400449206807 | etot = -5.62847192192004 +512000 ekin = 2.7685448252352 | erot = 4.75962991523576 | epot = -13.1566466618343 | etot = -5.62847192136329 +513000 ekin = 2.68465921481286 | erot = 4.75599513194568 | epot = -13.0691262676556 | etot = -5.62847192089705 +514000 ekin = 2.60745568312153 | erot = 4.74870168660043 | epot = -12.9846292903035 | etot = -5.62847192058154 +515000 ekin = 2.53899080261884 | erot = 4.74082869238916 | epot = -12.908291415412 | etot = -5.62847192040399 +516000 ekin = 2.48057862894501 | erot = 4.73416754063572 | epot = -12.8432180899358 | etot = -5.62847192035506 +517000 ekin = 2.43281299018052 | erot = 4.72933651073029 | epot = -12.7906214213124 | etot = -5.62847192040158 +518000 ekin = 2.39567246198618 | erot = 4.72611868195944 | epot = -12.7502630644488 | etot = -5.6284719205032 +519000 ekin = 2.36868008075511 | erot = 4.72386163460508 | epot = -12.7210136359791 | etot = -5.6284719206189 +520000 ekin = 2.3510906803018 | erot = 4.72186744280268 | epot = -12.7014300438176 | etot = -5.62847192071307 +521000 ekin = 2.34207426122853 | erot = 4.71970227704795 | epot = -12.690248459041 | etot = -5.62847192076452 +522000 ekin = 2.3408585839593 | erot = 4.717351137329 | epot = -12.6866816420599 | etot = -5.62847192077156 +523000 ekin = 2.34541603964687 | erot = 4.65571671275286 | epot = -12.62960468288 | etot = -5.62847193048032 +524000 ekin = 2.39460269537327 | erot = 4.5440923968237 | epot = -12.5671670124743 | etot = -5.6284719202773 +525000 ekin = 2.51755565343829 | erot = 4.49060445329404 | epot = -12.6366320324554 | etot = -5.6284719257231 +526000 ekin = 2.63891940338083 | erot = 4.49670026133261 | epot = -12.7640916024971 | etot = -5.62847193778366 +527000 ekin = 2.68130557079429 | erot = 4.50503337382341 | epot = -12.81481087471 | etot = -5.62847193009234 +528000 ekin = 2.71450795012238 | erot = 4.51098798635674 | epot = -12.8539678666714 | etot = -5.62847193019227 +529000 ekin = 2.74727192396273 | erot = 4.51402301148384 | epot = -12.8897668657089 | etot = -5.6284719302623 +530000 ekin = 2.77952118316763 | erot = 4.51256666257441 | epot = -12.9205597760307 | etot = -5.62847193028861 +531000 ekin = 2.81130699781853 | erot = 4.50555264770735 | epot = -12.9453315757932 | etot = -5.62847193026728 +532000 ekin = 2.84274553230611 | erot = 4.49253106983451 | epot = -12.9637485323479 | etot = -5.62847193020728 +533000 ekin = 2.87393313772675 | erot = 4.47361780235876 | epot = -12.9760228702139 | etot = -5.62847193012842 +534000 ekin = 2.90486933810437 | erot = 4.4492884461776 | epot = -12.982629714336 | etot = -5.62847193005404 +535000 ekin = 2.93541519867713 | erot = 4.42010482065887 | epot = -12.983991949336 | etot = -5.62847192999997 +536000 ekin = 2.96529830149696 | erot = 4.38649798395868 | epot = -12.9802682154263 | etot = -5.62847192997066 +537000 ekin = 2.9941546715244 | erot = 4.34867665836289 | epot = -12.9713032598383 | etot = -5.62847192995098 +538000 ekin = 3.02158801650267 | erot = 4.30669342609435 | epot = -12.9567533725476 | etot = -5.62847192995063 +539000 ekin = 3.04722844373896 | erot = 4.26048951904726 | epot = -12.9361898927328 | etot = -5.62847192994659 +540000 ekin = 3.07077963643902 | erot = 4.21000980478417 | epot = -12.9092613711529 | etot = -5.62847192992969 +541000 ekin = 3.09204730616454 | erot = 4.15535061585166 | epot = -12.8758698519111 | etot = -5.62847192989485 +542000 ekin = 3.11094831332973 | erot = 4.09682671838095 | epot = -12.8362469615525 | etot = -5.62847192984182 +543000 ekin = 3.12750284882097 | erot = 4.03499383130383 | epot = -12.7909686098982 | etot = -5.62847192977342 +544000 ekin = 3.14181233917186 | erot = 3.9706269261982 | epot = -12.7409111950686 | etot = -5.6284719296985 +545000 ekin = 3.15402369277355 | erot = 3.9046220841584 | epot = -12.6871177065573 | etot = -5.62847192962532 +546000 ekin = 3.16427777376567 | erot = 3.8380946572635 | epot = -12.6308443605863 | etot = -5.62847192955709 +547000 ekin = 3.17263245314417 | erot = 3.7724854223622 | epot = -12.5735898050362 | etot = -5.62847192952988 +548000 ekin = 3.17905114127017 | erot = 3.70842416474136 | epot = -12.5159472355486 | etot = -5.62847192953704 +549000 ekin = 3.18335924851677 | erot = 3.646194434218 | epot = -12.4580256122719 | etot = -5.62847192953711 +550000 ekin = 3.18506506659257 | erot = 3.58603484427266 | epot = -12.3995718405164 | etot = -5.62847192965112 +551000 ekin = 3.18354118865646 | erot = 3.52751972613024 | epot = -12.3395328445766 | etot = -5.62847192978987 +552000 ekin = 3.17814056099685 | erot = 3.46973317227459 | epot = -12.2763456632029 | etot = -5.62847192993142 +553000 ekin = 3.16816249047943 | erot = 3.4118771629193 | epot = -12.2085115834413 | etot = -5.62847193004256 +554000 ekin = 3.152974640569 | erot = 3.35363386891104 | epot = -12.1350804395661 | etot = -5.62847193008603 +555000 ekin = 3.13218065543358 | erot = 3.29554931590148 | epot = -12.0562019013624 | etot = -5.62847193002736 +556000 ekin = 3.10581995744964 | erot = 3.23932890453177 | epot = -11.9736207918255 | etot = -5.62847192984405 +557000 ekin = 3.07457883900136 | erot = 3.18795403306235 | epot = -11.8910048015923 | etot = -5.62847192952859 +558000 ekin = 3.0399826265664 | erot = 3.14553707334498 | epot = -11.8139916290184 | etot = -5.62847192910703 +559000 ekin = 3.00450378989002 | erot = 3.1169371283537 | epot = -11.7499128468228 | etot = -5.62847192857912 +560000 ekin = 2.97145203627554 | erot = 3.10758181984466 | epot = -11.7075057841409 | etot = -5.62847192802067 +561000 ekin = 2.94451934107631 | erot = 3.12267269752084 | epot = -11.6956639661595 | etot = -5.62847192756238 +562000 ekin = 2.92714140963741 | erot = 3.16633554920152 | epot = -11.7219488860852 | etot = -5.62847192724623 +563000 ekin = 2.9220614763248 | erot = 3.24077054351229 | epot = -11.7913039470345 | etot = -5.62847192719737 +564000 ekin = 2.93031627661537 | erot = 3.34563410952266 | epot = -11.904422313636 | etot = -5.62847192749801 +565000 ekin = 2.95068712298472 | erot = 3.47751232959147 | epot = -12.0566713807284 | etot = -5.62847192815217 +566000 ekin = 2.97962685527569 | erot = 3.62985521352484 | epot = -12.2379539979236 | etot = -5.62847192912305 +567000 ekin = 3.01171593581948 | erot = 3.79324477334104 | epot = -12.4334326394742 | etot = -5.6284719303137 +568000 ekin = 3.04054477454128 | erot = 3.95610049169994 | epot = -12.6251171978273 | etot = -5.62847193158611 +569000 ekin = 3.05981811086283 | erot = 4.10576505731969 | epot = -12.7940551009638 | etot = -5.62847193278128 +570000 ekin = 3.06446758305144 | erot = 4.22987220708192 | epot = -12.922811723873 | etot = -5.62847193373966 +571000 ekin = 3.05159191048677 | erot = 4.31782950105469 | epot = -12.9978933458657 | etot = -5.62847193432422 +572000 ekin = 3.02108996846969 | erot = 4.36217384040604 | epot = -13.0117357433222 | etot = -5.62847193444643 +573000 ekin = 2.97589592653743 | erot = 4.35953364445579 | epot = -12.9639015050781 | etot = -5.62847193408484 +574000 ekin = 2.9217726095476 | erot = 4.31098813645812 | epot = -12.8612326793025 | etot = -5.62847193329677 +575000 ekin = 2.86675845152662 | erot = 4.22206447601689 | epot = -12.7172948575799 | etot = -5.62847193003638 +576000 ekin = 2.82238695050776 | erot = 4.11002108698041 | epot = -12.5608799670038 | etot = -5.62847192951559 +577000 ekin = 2.79586021294431 | erot = 3.98405314231564 | epot = -12.4083852843453 | etot = -5.62847192908532 +578000 ekin = 2.7906267865537 | erot = 3.84816173897867 | epot = -12.2672604543784 | etot = -5.62847192884604 +579000 ekin = 2.80727876771314 | erot = 3.70630768395844 | epot = -12.1420583805015 | etot = -5.6284719288299 +580000 ekin = 2.84308800290578 | erot = 3.56147502220943 | epot = -12.033034954412 | etot = -5.62847192929679 +581000 ekin = 2.89275945174584 | erot = 3.4167770803592 | epot = -11.9380084614761 | etot = -5.62847192937104 +582000 ekin = 2.94948274103276 | erot = 3.2785263562891 | epot = -11.8564810267625 | etot = -5.62847192944067 +583000 ekin = 3.00600312784595 | erot = 3.15339507865486 | epot = -11.7878701359251 | etot = -5.62847192942433 +584000 ekin = 3.05615870305645 | erot = 3.04800743031942 | epot = -11.7326380626758 | etot = -5.62847192929997 +585000 ekin = 3.09596263910765 | erot = 2.96828908152132 | epot = -11.6927236497189 | etot = -5.6284719290899 +586000 ekin = 3.1240729820118 | erot = 2.91878541589529 | epot = -11.6713303267329 | etot = -5.62847192882581 +587000 ekin = 3.14174614222812 | erot = 2.90225430094425 | epot = -11.6724723717087 | etot = -5.62847192853628 +588000 ekin = 3.1524003162434 | erot = 2.91960613645308 | epot = -11.7004783809564 | etot = -5.62847192825996 +589000 ekin = 3.16081808259293 | erot = 2.97006448177757 | epot = -11.7593544924097 | etot = -5.62847192803921 +590000 ekin = 3.17204827388567 | erot = 3.05134069932488 | epot = -11.8518609011252 | etot = -5.62847192791469 +591000 ekin = 3.19150299843264 | erot = 3.16015018738911 | epot = -11.9801251138133 | etot = -5.6284719279916 +592000 ekin = 3.22264872307499 | erot = 3.29204057523907 | epot = -12.1431612266306 | etot = -5.62847192831653 +593000 ekin = 3.26585695468827 | erot = 3.44092346946795 | epot = -12.3352523530142 | etot = -5.62847192885796 +594000 ekin = 3.31918005201003 | erot = 3.59965335610763 | epot = -12.5473053376812 | etot = -5.62847192956349 +595000 ekin = 3.37897127087938 | erot = 3.76045843951374 | epot = -12.7679016406818 | etot = -5.62847193028864 +596000 ekin = 3.43824068583499 | erot = 3.91359738335248 | epot = -12.9803100018114 | etot = -5.62847193262389 +597000 ekin = 3.48744876802532 | erot = 4.04782437870026 | epot = -13.1637450799831 | etot = -5.62847193325755 +598000 ekin = 3.52187002174033 | erot = 4.1569858043421 | epot = -13.3073277596942 | etot = -5.62847193361181 +599000 ekin = 3.53831455075583 | erot = 4.23767846718814 | epot = -13.4044649516274 | etot = -5.62847193368348 +600000 ekin = 3.53510970432726 | erot = 4.28920847112016 | epot = -13.452790108963 | etot = -5.62847193351559 +601000 ekin = 3.51191041819736 | erot = 4.31320178201164 | epot = -13.4535841333868 | etot = -5.62847193317776 +602000 ekin = 3.46937521147322 | erot = 4.31295152745267 | epot = -13.4107986716704 | etot = -5.62847193274446 +603000 ekin = 3.40882221241426 | erot = 4.29270411933321 | epot = -13.3299982640245 | etot = -5.62847193227706 +604000 ekin = 3.33194570981526 | erot = 4.25705245868206 | epot = -13.2174701003137 | etot = -5.62847193181633 +605000 ekin = 3.24062643786331 | erot = 4.21052248041457 | epot = -13.0796208496601 | etot = -5.62847193138225 +606000 ekin = 3.13683319323927 | erot = 4.15735875798811 | epot = -12.9226638822062 | etot = -5.62847193097882 +607000 ekin = 3.02259481107608 | erot = 4.10146703774399 | epot = -12.7525337794202 | etot = -5.62847193060012 +608000 ekin = 2.90001652258154 | erot = 4.04645475157649 | epot = -12.574943204394 | etot = -5.62847193023597 +609000 ekin = 2.77131728805922 | erot = 3.99571460781224 | epot = -12.3955038257476 | etot = -5.62847192987615 +610000 ekin = 2.63886938888048 | erot = 3.95250622990976 | epot = -12.2198475483046 | etot = -5.62847192951437 +611000 ekin = 2.50524882247892 | erot = 3.92003293777695 | epot = -12.0537536891167 | etot = -5.62847192886078 +612000 ekin = 2.37382087279007 | erot = 3.90218869853792 | epot = -11.9044814998599 | etot = -5.62847192853195 +613000 ekin = 2.24769613360656 | erot = 3.90186788749861 | epot = -11.7780359493281 | etot = -5.62847192822294 +614000 ekin = 2.12975142860572 | erot = 3.92103062115479 | epot = -11.6792539777365 | etot = -5.62847192797597 +615000 ekin = 2.02283676461716 | erot = 3.96080056830067 | epot = -11.6121092607438 | etot = -5.62847192782593 +616000 ekin = 1.92967019041878 | erot = 4.02099162186615 | epot = -11.579133740091 | etot = -5.62847192780604 +617000 ekin = 1.85273791857026 | erot = 4.09974474408036 | epot = -11.5809545905959 | etot = -5.62847192794533 +618000 ekin = 1.79420296290766 | erot = 4.19322703626905 | epot = -11.6159019274337 | etot = -5.62847192825703 +619000 ekin = 1.75583197424195 | erot = 4.29552606651499 | epot = -11.6798299694835 | etot = -5.62847192872651 +620000 ekin = 1.73895870094446 | erot = 4.39891672379093 | epot = -11.7663473540351 | etot = -5.62847192929971 +621000 ekin = 1.74449834712895 | erot = 4.49462250669986 | epot = -11.8675927837139 | etot = -5.62847192988505 +622000 ekin = 1.77300875725232 | erot = 4.57403518095986 | epot = -11.9755158685887 | etot = -5.62847193037655 +623000 ekin = 1.82476626665333 | erot = 4.63011744399526 | epot = -12.0833556413381 | etot = -5.62847193068951 +624000 ekin = 1.89980556096372 | erot = 4.65854151397894 | epot = -12.1868190057356 | etot = -5.62847193079293 +625000 ekin = 1.99788931008649 | erot = 4.65817060165253 | epot = -12.2845318424541 | etot = -5.6284719307151 +626000 ekin = 2.11841939009616 | erot = 4.63077870087959 | epot = -12.3776700214989 | etot = -5.62847193052312 +627000 ekin = 2.26034340502548 | erot = 4.58024268390528 | epot = -12.4690580192171 | etot = -5.62847193028638 +628000 ekin = 2.42211143985386 | erot = 4.51161612045591 | epot = -12.5621994903691 | etot = -5.6284719300593 +629000 ekin = 2.60047669415179 | erot = 4.43316974500275 | epot = -12.6621183685534 | etot = -5.62847192939883 +630000 ekin = 2.7503574900296 | erot = 4.3100390573783 | epot = -12.6888685131096 | etot = -5.62847196570167 +631000 ekin = 2.81471524142744 | erot = 4.11774535981825 | epot = -12.560932537004 | etot = -5.6284719357583 +632000 ekin = 2.95867552219892 | erot = 4.07926707204035 | epot = -12.6664145271043 | etot = -5.62847193286502 +633000 ekin = 3.21010693597188 | erot = 4.20581326818235 | epot = -13.0443921662251 | etot = -5.62847196207084 +634000 ekin = 3.41641131498702 | erot = 4.25928215922315 | epot = -13.3041654105749 | etot = -5.62847193636469 +635000 ekin = 3.57385274074614 | erot = 4.24018711593412 | epot = -13.4425117938152 | etot = -5.62847193713496 +636000 ekin = 3.71894531192207 | erot = 4.21896102694803 | epot = -13.5663782768412 | etot = -5.62847193797114 +637000 ekin = 3.84555962848383 | erot = 4.19009538983304 | epot = -13.6641269569835 | etot = -5.62847193866661 +638000 ekin = 3.94874232725405 | erot = 4.14881281916048 | epot = -13.72602708545 | etot = -5.62847193903547 +639000 ekin = 4.02564653203983 | erot = 4.09271382108853 | epot = -13.7468322921298 | etot = -5.62847193900142 +640000 ekin = 4.07582551371721 | erot = 4.02260436107351 | epot = -13.7269018134047 | etot = -5.628471938614 +641000 ekin = 4.10019063769985 | erot = 3.94203419554565 | epot = -13.6706967717062 | etot = -5.62847193846072 +642000 ekin = 4.09923586000013 | erot = 3.85569636498804 | epot = -13.5834041628699 | etot = -5.6284719378817 +643000 ekin = 4.07616079985079 | erot = 3.76850329621968 | epot = -13.4731360334278 | etot = -5.62847193735732 +644000 ekin = 4.03483546311363 | erot = 3.68428538400513 | epot = -13.3475927840616 | etot = -5.62847193694285 +645000 ekin = 3.97939693539872 | erot = 3.60521279235852 | epot = -13.2130816643787 | etot = -5.62847193662148 +646000 ekin = 3.91424157398736 | erot = 3.53197746505452 | epot = -13.0746909753807 | etot = -5.62847193633883 +647000 ekin = 3.84412108358933 | erot = 3.46430751165856 | epot = -12.9369005314278 | etot = -5.62847193617996 +648000 ekin = 3.77442093454335 | erot = 3.40030625090033 | epot = -12.8031991213061 | etot = -5.62847193586241 +649000 ekin = 3.71064844406707 | erot = 3.33902116852718 | epot = -12.6781415481349 | etot = -5.62847193554064 +650000 ekin = 3.65777288966146 | erot = 3.28036981753718 | epot = -12.5666146424668 | etot = -5.62847193526817 +651000 ekin = 3.61962254756271 | erot = 3.22458240428293 | epot = -12.4726768869373 | etot = -5.62847193509165 +652000 ekin = 3.5983886698494 | erot = 3.17201593039475 | epot = -12.3988765352733 | etot = -5.62847193502919 +653000 ekin = 3.59447660063664 | erot = 3.12302902486399 | epot = -12.3459775605649 | etot = -5.62847193506423 +654000 ekin = 3.60674141926213 | erot = 3.07797678372087 | epot = -12.3131901381398 | etot = -5.62847193515675 +655000 ekin = 3.63298841319899 | erot = 3.03728497083513 | epot = -12.298745319302 | etot = -5.62847193526783 +656000 ekin = 3.67052655538393 | erot = 3.00147990307841 | epot = -12.3004783938467 | etot = -5.62847193538435 +657000 ekin = 3.71734630715188 | erot = 2.97084073563873 | epot = -12.3166589781819 | etot = -5.62847193539126 +658000 ekin = 3.75778663152406 | erot = 2.94872940868083 | epot = -12.3349879989909 | etot = -5.62847195878602 +659000 ekin = 3.70128994157181 | erot = 2.99267200690746 | epot = -12.3224338842044 | etot = -5.62847193572512 +660000 ekin = 3.77980484703633 | erot = 3.05081678610233 | epot = -12.4590935972117 | etot = -5.62847196407309 +661000 ekin = 3.87674047152168 | erot = 3.0204372245258 | epot = -12.5256496414073 | etot = -5.62847194535981 +662000 ekin = 3.96189665332223 | erot = 2.97294510662936 | epot = -12.5633137062543 | etot = -5.62847194630273 +663000 ekin = 4.0323399214187 | erot = 2.90724728967078 | epot = -12.5680591574168 | etot = -5.62847194632729 +664000 ekin = 4.08703350805266 | erot = 2.8237107412405 | epot = -12.5392161951014 | etot = -5.62847194580827 +665000 ekin = 4.13016908298482 | erot = 2.72591755760377 | epot = -12.4845585856393 | etot = -5.62847194505068 +666000 ekin = 4.16485763716588 | erot = 2.62158318056137 | epot = -12.4149127617997 | etot = -5.6284719440724 +667000 ekin = 4.19388444256735 | erot = 2.52048046545659 | epot = -12.3428368513381 | etot = -5.62847194331417 +668000 ekin = 4.2197011138852 | erot = 2.43117566524618 | epot = -12.279348721894 | etot = -5.62847194276262 +669000 ekin = 4.24419480087444 | erot = 2.35970998738712 | epot = -12.2323767306649 | etot = -5.62847194240331 +670000 ekin = 4.26650932865956 | erot = 2.31009212963202 | epot = -12.205073400566 | etot = -5.6284719422744 +671000 ekin = 4.28028750606661 | erot = 2.28394068936243 | epot = -12.1927001376509 | etot = -5.62847194222186 +672000 ekin = 4.28604953841681 | erot = 2.28087700932289 | epot = -12.1953984899257 | etot = -5.62847194218603 +673000 ekin = 4.28538321009053 | erot = 2.29981058102313 | epot = -12.2136657332555 | etot = -5.62847194214187 +674000 ekin = 4.28032637914606 | erot = 2.33931519983992 | epot = -12.2481135210873 | etot = -5.62847194210128 +675000 ekin = 4.27310613172282 | erot = 2.39770546325545 | epot = -12.2992835370902 | etot = -5.62847194211198 +676000 ekin = 4.26563141872319 | erot = 2.47283047848192 | epot = -12.3669338394774 | etot = -5.62847194227226 +677000 ekin = 4.25873601051767 | erot = 2.56159475129278 | epot = -12.4488027044409 | etot = -5.62847194263047 +678000 ekin = 4.25154383433598 | erot = 2.65951246655273 | epot = -12.5395282441259 | etot = -5.62847194323716 +679000 ekin = 4.24120573486625 | erot = 2.76057514742513 | epot = -12.6302528263285 | etot = -5.62847194403713 +680000 ekin = 4.22320051199589 | erot = 2.8577068909422 | epot = -12.7093793478055 | etot = -5.62847194486737 +681000 ekin = 4.19242845467527 | erot = 2.94400272534198 | epot = -12.7649031255142 | etot = -5.6284719454969 +682000 ekin = 4.14477706350661 | erot = 3.01435956371948 | epot = -12.7876085729696 | etot = -5.62847194574355 +683000 ekin = 4.07850194590293 | erot = 3.0666968929119 | epot = -12.7736707843732 | etot = -5.62847194555838 +684000 ekin = 3.98766788586786 | erot = 3.09062770629772 | epot = -12.7067675425492 | etot = -5.62847195038364 +685000 ekin = 3.87609976038648 | erot = 3.07213118833004 | epot = -12.5767028923904 | etot = -5.6284719436739 +686000 ekin = 3.78865422808705 | erot = 3.0537998251476 | epot = -12.4709259955823 | etot = -5.62847194234768 +687000 ekin = 3.72885638141783 | erot = 3.0512831038631 | epot = -12.4086114325096 | etot = -5.62847194722862 +688000 ekin = 3.6548808547633 | erot = 3.04382149752739 | epot = -12.3271742986283 | etot = -5.62847194633765 +689000 ekin = 3.57606770161188 | erot = 3.03834252490863 | epot = -12.2428821721519 | etot = -5.62847194563136 +690000 ekin = 3.51634425581226 | erot = 3.04775260785467 | epot = -12.1925688087854 | etot = -5.62847194511852 +691000 ekin = 3.47971445769588 | erot = 3.07622358472064 | epot = -12.1844099872813 | etot = -5.62847194486478 +692000 ekin = 3.46765181287758 | erot = 3.12642449714008 | epot = -12.2225482549492 | etot = -5.62847194493155 +693000 ekin = 3.47854301587009 | erot = 3.19918358098635 | epot = -12.3061985421888 | etot = -5.62847194533241 +694000 ekin = 3.50760869836038 | erot = 3.29340441047934 | epot = -12.4294850548493 | etot = -5.62847194600957 +695000 ekin = 3.54747029199626 | erot = 3.40637947909001 | epot = -12.5823217179315 | etot = -5.62847194684524 +696000 ekin = 3.58927155200529 | erot = 3.53441505490595 | epot = -12.7521585546129 | etot = -5.6284719477017 +697000 ekin = 3.62399868557745 | erot = 3.67347767301628 | epot = -12.9259483070505 | etot = -5.62847194845679 +698000 ekin = 3.64429609790095 | erot = 3.81929275594453 | epot = -13.0920608029479 | etot = -5.62847194910241 +699000 ekin = 3.64411727683406 | erot = 3.96826912288242 | epot = -13.2408583492345 | etot = -5.62847194951805 +700000 ekin = 3.61972386507404 | erot = 4.11779628913867 | epot = -13.3659921038979 | etot = -5.62847194968518 +701000 ekin = 3.57045543159744 | erot = 4.26605645121247 | epot = -13.4649838325435 | etot = -5.62847194973359 +702000 ekin = 3.49917622974374 | erot = 4.4103702949508 | epot = -13.5380184743033 | etot = -5.62847194960877 +703000 ekin = 3.41079978170358 | erot = 4.54773448474831 | epot = -13.5870062158287 | etot = -5.62847194937682 +704000 ekin = 3.31149657270676 | erot = 4.6756046408261 | epot = -13.6155731626141 | etot = -5.62847194908128 +705000 ekin = 3.20807903060945 | erot = 4.79162132878981 | epot = -13.628172308179 | etot = -5.62847194877975 +706000 ekin = 3.10702043908999 | erot = 4.89365607492231 | epot = -13.6291484625546 | etot = -5.62847194854233 +707000 ekin = 3.01353531422026 | erot = 4.97967086403023 | epot = -13.6216781266884 | etot = -5.62847194843788 +708000 ekin = 2.93091332956849 | erot = 5.04739802040307 | epot = -13.6067832984855 | etot = -5.62847194851397 +709000 ekin = 2.86026033884964 | erot = 5.09399325374139 | epot = -13.5827255413625 | etot = -5.62847194877149 +710000 ekin = 2.80069789546349 | erot = 5.11589857272134 | epot = -13.5450684173414 | etot = -5.62847194915653 +711000 ekin = 2.74994326412216 | erot = 5.10911210204212 | epot = -13.4875273157305 | etot = -5.62847194956624 +712000 ekin = 2.7050985703084 | erot = 5.06990681725726 | epot = -13.403477337442 | etot = -5.62847194987633 +713000 ekin = 2.66343594245662 | erot = 4.9958228255835 | epot = -13.2877307180213 | etot = -5.62847194998114 +714000 ekin = 2.62297982869924 | erot = 4.8865841179905 | epot = -13.1380358965202 | etot = -5.62847194983045 +715000 ekin = 2.58275404761751 | erot = 4.74456650492436 | epot = -12.9557925019884 | etot = -5.62847194944654 +716000 ekin = 2.5426793398065 | erot = 4.57461726448396 | epot = -12.7457685531992 | etot = -5.62847194890871 +717000 ekin = 2.50334692016308 | erot = 4.38348005438083 | epot = -12.5152989225401 | etot = -5.62847194799621 +718000 ekin = 2.4686718204679 | erot = 4.18280619282889 | epot = -12.2799499610364 | etot = -5.62847194773966 +719000 ekin = 2.44027484657121 | erot = 3.97913844266094 | epot = -12.047885236721 | etot = -5.62847194748881 +720000 ekin = 2.41790751023352 | erot = 3.77617089290506 | epot = -11.8225503503867 | etot = -5.62847194724809 +721000 ekin = 2.40130900313552 | erot = 3.57751641362776 | epot = -11.6072973637835 | etot = -5.62847194702017 +722000 ekin = 2.39001969432109 | erot = 3.38620933336079 | epot = -11.4047009746952 | etot = -5.62847194701334 +723000 ekin = 2.3828880820704 | erot = 3.20447847597663 | epot = -11.215838504763 | etot = -5.62847194671593 +724000 ekin = 2.38038137247374 | erot = 3.03585463087247 | epot = -11.0447079497915 | etot = -5.62847194644529 +725000 ekin = 2.38334904374461 | erot = 2.88343528873249 | epot = -10.8952562786821 | etot = -5.62847194620497 +726000 ekin = 2.39277988809285 | erot = 2.74974572525579 | epot = -10.7709975593489 | etot = -5.62847194600029 +727000 ekin = 2.40968215734596 | erot = 2.63676770304837 | epot = -10.6749218062317 | etot = -5.6284719458374 +728000 ekin = 2.42515138001133 | erot = 2.54412147904229 | epot = -10.5977448184035 | etot = -5.62847195934989 +729000 ekin = 2.40297855341014 | erot = 2.51475999942454 | epot = -10.5462104922609 | etot = -5.62847193942621 +730000 ekin = 2.46310039281923 | erot = 2.5408883826841 | epot = -10.6324607144775 | etot = -5.62847193897412 +731000 ekin = 2.53308642093335 | erot = 2.54954386945207 | epot = -10.7111022294503 | etot = -5.62847193906488 +732000 ekin = 2.61398262091125 | erot = 2.58024874604495 | epot = -10.8227033062294 | etot = -5.62847193927323 +733000 ekin = 2.70404858445246 | erot = 2.63167940200761 | epot = -10.9641999261022 | etot = -5.62847193964217 +734000 ekin = 2.8005195006671 | erot = 2.70132929845247 | epot = -11.1303207393381 | etot = -5.6284719402185 +735000 ekin = 2.89941283718647 | erot = 2.78510796768852 | epot = -11.3129927459065 | etot = -5.62847194103148 +736000 ekin = 2.99560133061641 | erot = 2.87741009023027 | epot = -11.5014833619395 | etot = -5.6284719410928 +737000 ekin = 3.08481605487795 | erot = 2.97524489367303 | epot = -11.6885328905302 | etot = -5.62847194197919 +738000 ekin = 3.16217862823363 | erot = 3.07317374877312 | epot = -11.8638243198038 | etot = -5.62847194279704 +739000 ekin = 3.22336037224067 | erot = 3.16493875129828 | epot = -12.0167710668836 | etot = -5.62847194334467 +740000 ekin = 3.26585131631857 | erot = 3.24522139638509 | epot = -12.1395446571316 | etot = -5.62847194442793 +741000 ekin = 3.28375382521718 | erot = 3.29991441197048 | epot = -12.2121401816134 | etot = -5.62847194442576 +742000 ekin = 3.27631313169807 | erot = 3.32408611724281 | epot = -12.2288711928783 | etot = -5.62847194393738 +743000 ekin = 3.24737724828938 | erot = 3.32046927292841 | epot = -12.1963184644142 | etot = -5.62847194319645 +744000 ekin = 3.20210603641817 | erot = 3.29401551212441 | epot = -12.1245934909575 | etot = -5.62847194241491 +745000 ekin = 3.14567705928071 | erot = 3.25033567037431 | epot = -12.0244846713649 | etot = -5.62847194170993 +746000 ekin = 3.08279906313083 | erot = 3.19521988723091 | epot = -11.9064908912242 | etot = -5.62847194086242 +747000 ekin = 3.01768881776059 | erot = 3.13473855348665 | epot = -11.7808993116274 | etot = -5.62847194038016 +748000 ekin = 2.95302867468964 | erot = 3.07321432178736 | epot = -11.65471493642 | etot = -5.62847193994298 +749000 ekin = 2.89104396170422 | erot = 3.01469856730411 | epot = -11.5342144685365 | etot = -5.62847193952822 +750000 ekin = 2.8337941745466 | erot = 2.96315742678199 | epot = -11.4254235404597 | etot = -5.62847193913107 +751000 ekin = 2.78329891305071 | erot = 2.9224177747446 | epot = -11.3341886265558 | etot = -5.62847193876044 +752000 ekin = 2.741568463393 | erot = 2.89600799339186 | epot = -11.2660483952193 | etot = -5.62847193843442 +753000 ekin = 2.71056677649853 | erot = 2.88693753466555 | epot = -11.2259762493407 | etot = -5.62847193817665 +754000 ekin = 2.69212502670267 | erot = 2.89743125968375 | epot = -11.218028224405 | etot = -5.62847193801856 +755000 ekin = 2.68776538370963 | erot = 2.92849871107142 | epot = -11.2447360328523 | etot = -5.62847193807124 +756000 ekin = 2.69845743039874 | erot = 2.97938409378287 | epot = -11.3063134624135 | etot = -5.6284719382319 +757000 ekin = 2.72458496416934 | erot = 3.04788425638831 | epot = -11.4009411591918 | etot = -5.62847193863418 +758000 ekin = 2.76540921280869 | erot = 3.12962823296902 | epot = -11.5235093850925 | etot = -5.62847193931481 +759000 ekin = 2.8186834205833 | erot = 3.21794575409103 | epot = -11.6651011149324 | etot = -5.62847194025804 +760000 ekin = 2.8805374646865 | erot = 3.30429272415793 | epot = -11.8133021301886 | etot = -5.62847194134417 +761000 ekin = 2.94600007659666 | erot = 3.37947250569254 | epot = -11.9539445246123 | etot = -5.62847194232311 +762000 ekin = 3.01037281067103 | erot = 3.43568700397793 | epot = -12.0745317575364 | etot = -5.62847194288743 +763000 ekin = 3.07103775515989 | erot = 3.46881600104856 | epot = -12.1683256990494 | etot = -5.62847194284092 +764000 ekin = 3.12866395059387 | erot = 3.47975039732283 | epot = -12.2368862901505 | etot = -5.62847194223379 +765000 ekin = 3.18696433111039 | erot = 3.47390232202085 | epot = -12.2893385944614 | etot = -5.62847194133016 +766000 ekin = 3.25112146440173 | erot = 3.45917589119073 | epot = -12.3387692960395 | etot = -5.62847194044708 +767000 ekin = 3.32577328193089 | erot = 3.44357056068677 | epot = -12.3978157824358 | etot = -5.62847193981815 +768000 ekin = 3.41341833371836 | erot = 3.43342634992446 | epot = -12.4753166231942 | etot = -5.62847193955134 +769000 ekin = 3.51361597939465 | erot = 3.43258837748851 | epot = -12.5746762965394 | etot = -5.62847193965622 +770000 ekin = 3.62296220600081 | erot = 3.44225950977127 | epot = -12.6936936558521 | etot = -5.62847194008001 +771000 ekin = 3.67754209852463 | erot = 3.42051682733498 | epot = -12.7265308936653 | etot = -5.62847196780573 +772000 ekin = 3.59351734061991 | erot = 3.35849685513247 | epot = -12.580486129291 | etot = -5.62847193353866 +773000 ekin = 3.58504863477517 | erot = 3.48413941982102 | epot = -12.6976599878645 | etot = -5.62847193326836 +774000 ekin = 3.69556246711488 | erot = 3.75600381605852 | epot = -13.0800382519706 | etot = -5.62847196879722 +775000 ekin = 3.75799647040695 | erot = 3.87395641028272 | epot = -13.2604248532319 | etot = -5.6284719725422 +776000 ekin = 3.7651493106552 | erot = 3.89275295626045 | epot = -13.2863742396306 | etot = -5.62847197271492 +777000 ekin = 3.74852837996943 | erot = 3.88975944412788 | epot = -13.2667597964422 | etot = -5.62847197234492 +778000 ekin = 3.71300754083808 | erot = 3.86527182205757 | epot = -13.2067513345255 | etot = -5.62847197162988 +779000 ekin = 3.66665793138621 | erot = 3.82295167572417 | epot = -13.1180815776383 | etot = -5.62847197052793 +780000 ekin = 3.61972773205039 | erot = 3.76957330513283 | epot = -13.0177730064674 | etot = -5.62847196928414 +781000 ekin = 3.58276242580336 | erot = 3.71368279695867 | epot = -12.9249171909595 | etot = -5.6284719681975 +782000 ekin = 3.56434384335661 | erot = 3.66344621629536 | epot = -12.8562620271603 | etot = -5.62847196750834 +783000 ekin = 3.56907083418469 | erot = 3.62459601370177 | epot = -12.8221388153382 | etot = -5.62847196745174 +784000 ekin = 3.59655578207864 | erot = 3.59908724254982 | epot = -12.8241149924364 | etot = -5.6284719678079 +785000 ekin = 3.64263842905025 | erot = 3.58559579665692 | epot = -12.8567061941961 | etot = -5.62847196848889 +786000 ekin = 3.70061363584185 | erot = 3.5803271427736 | epot = -12.9094127478978 | etot = -5.62847196928234 +787000 ekin = 3.7629028954063 | erot = 3.57827846475705 | epot = -12.9696533302076 | etot = -5.6284719700443 +788000 ekin = 3.82230691252267 | erot = 3.57432079320563 | epot = -13.0250996764001 | etot = -5.62847197067175 +789000 ekin = 3.87288356008586 | erot = 3.56402750500699 | epot = -13.0653830361963 | etot = -5.62847197110343 +790000 ekin = 3.91054381119323 | erot = 3.54422213321065 | epot = -13.0832379156691 | etot = -5.62847197126525 +791000 ekin = 3.93344679994591 | erot = 3.51333982549555 | epot = -13.0752585966227 | etot = -5.62847197118128 +792000 ekin = 3.94193166989336 | erot = 3.47142235448868 | epot = -13.0418259952844 | etot = -5.62847197090236 +793000 ekin = 3.93805337474175 | erot = 3.41982689816554 | epot = -12.9863522434094 | etot = -5.62847197050213 +794000 ekin = 3.92496167512552 | erot = 3.36081973449906 | epot = -12.9142533796758 | etot = -5.62847197005125 +795000 ekin = 3.90631843210397 | erot = 3.29713731804311 | epot = -12.8319277197525 | etot = -5.62847196960539 +796000 ekin = 3.88587920101549 | erot = 3.23158100779698 | epot = -12.7459321780137 | etot = -5.62847196920121 +797000 ekin = 3.86724402833238 | erot = 3.1666803762435 | epot = -12.6623963734357 | etot = -5.62847196885983 +798000 ekin = 3.85371944463732 | erot = 3.1044622070207 | epot = -12.5866536202458 | etot = -5.62847196858778 +799000 ekin = 3.84821326134452 | erot = 3.0463740685037 | epot = -12.5230592982317 | etot = -5.62847196838352 +800000 ekin = 3.85308746123986 | erot = 2.99338091108245 | epot = -12.4749403405621 | etot = -5.62847196823983 +801000 ekin = 3.86994742123277 | erot = 2.94620265037627 | epot = -12.44462203976 | etot = -5.62847196815095 +802000 ekin = 3.89938743558651 | erot = 2.90559564193987 | epot = -12.4334550456423 | etot = -5.62847196811593 +803000 ekin = 3.94077451984869 | erot = 2.87255363133981 | epot = -12.4418001193271 | etot = -5.62847196813862 +804000 ekin = 3.99217445544446 | erot = 2.84833794120658 | epot = -12.4689843648722 | etot = -5.62847196822119 +805000 ekin = 4.0504882902739 | erot = 2.83432176416712 | epot = -12.513282022804 | etot = -5.628471968363 +806000 ekin = 4.11178329751802 | erot = 2.83170980297367 | epot = -12.5719650690503 | etot = -5.6284719685586 +807000 ekin = 4.17172086392056 | erot = 2.84122318400431 | epot = -12.641416016727 | etot = -5.62847196880214 +808000 ekin = 4.22595471217704 | erot = 2.86283161226543 | epot = -12.7172582935313 | etot = -5.62847196908883 +809000 ekin = 4.27041103460948 | erot = 2.89559061356835 | epot = -12.7944736175914 | etot = -5.62847196941361 +810000 ekin = 4.3014357915985 | erot = 2.93761851633603 | epot = -12.8675262777001 | etot = -5.62847196976555 +811000 ekin = 4.31585912495264 | erot = 2.98622782351587 | epot = -12.9305589185916 | etot = -5.6284719701231 +812000 ekin = 4.31104963141284 | erot = 3.03819974711332 | epot = -12.9777213489804 | etot = -5.62847197045424 +813000 ekin = 4.28501152869628 | erot = 3.09015837057483 | epot = -13.0036418699911 | etot = -5.62847197071994 +814000 ekin = 4.23653530272657 | erot = 3.13897206713297 | epot = -13.0039793407427 | etot = -5.62847197088318 +815000 ekin = 4.16537042791397 | erot = 3.18209773828538 | epot = -12.9759401371178 | etot = -5.62847197091842 +816000 ekin = 4.0723651750119 | erot = 3.21779646402385 | epot = -12.9186336098534 | etot = -5.62847197081764 +817000 ekin = 3.95951977467803 | erot = 3.2451838025511 | epot = -12.8331755478221 | etot = -5.62847197059292 +818000 ekin = 3.82991762721696 | erot = 3.26412066867229 | epot = -12.7225102661653 | etot = -5.62847197027605 +819000 ekin = 3.687533567486 | erot = 3.27498902901603 | epot = -12.5909945664016 | etot = -5.62847196989961 +820000 ekin = 3.5369910682491 | erot = 3.27842149088493 | epot = -12.4438845286404 | etot = -5.62847196950641 +821000 ekin = 3.3832361389577 | erot = 3.27505502168988 | epot = -12.2867631297766 | etot = -5.62847196912897 +822000 ekin = 3.23123737473759 | erot = 3.26537695363164 | epot = -12.1250862971552 | etot = -5.62847196878592 +823000 ekin = 3.0857411631345 | erot = 3.24970236680904 | epot = -11.9639154984254 | etot = -5.62847196848185 +824000 ekin = 2.9510991987633 | erot = 3.22828590291375 | epot = -11.8078570698846 | etot = -5.62847196820759 +825000 ekin = 2.83117167310576 | erot = 3.20152981109227 | epot = -11.6611734521472 | etot = -5.62847196794913 +826000 ekin = 2.7292944893361 | erot = 3.17021233047786 | epot = -11.5279787875067 | etot = -5.62847196769275 +827000 ekin = 2.64828540291044 | erot = 3.13564460973056 | epot = -11.4124019800765 | etot = -5.62847196743546 +828000 ekin = 2.59045268672873 | erot = 3.0996802790463 | epot = -11.3186049329633 | etot = -5.62847196718826 +829000 ekin = 2.55756748880607 | erot = 3.06454892074378 | epot = -11.2505883765264 | etot = -5.62847196697658 +830000 ekin = 2.55077388252505 | erot = 3.03254604901289 | epot = -11.2117918983721 | etot = -5.62847196683417 +831000 ekin = 2.57043725889653 | erot = 3.0056609749316 | epot = -11.2045702006219 | etot = -5.62847196679376 +832000 ekin = 2.61596870917374 | erot = 2.98524787975124 | epot = -11.2296885558022 | etot = -5.62847196687719 +833000 ekin = 2.68568117628702 | erot = 2.97182255716636 | epot = -11.2859757005432 | etot = -5.62847196708978 +834000 ekin = 2.77673677891606 | erot = 2.96502424351085 | epot = -11.370232989845 | etot = -5.62847196741807 +835000 ekin = 2.88522064072264 | erot = 2.96372965232095 | epot = -11.477422260878 | etot = -5.62847196783445 +836000 ekin = 3.00633984363646 | erot = 2.9662686057928 | epot = -11.6010804177332 | etot = -5.62847196830389 +837000 ekin = 3.13471078705654 | erot = 2.9706713329556 | epot = -11.7338540888042 | etot = -5.6284719687921 +838000 ekin = 3.26467976824324 | erot = 2.97489019137264 | epot = -11.8680419288866 | etot = -5.62847196927074 +839000 ekin = 3.39062361970843 | erot = 2.97696578941869 | epot = -11.9960613788464 | etot = -5.62847196971931 +840000 ekin = 3.50719614041285 | erot = 2.97513773521714 | epot = -12.1108058457538 | etot = -5.62847197012383 +841000 ekin = 3.6095143027186 | erot = 2.96792302707412 | epot = -12.205909300265 | etot = -5.62847197047228 +842000 ekin = 3.69330308228449 | erot = 2.95419217547664 | epot = -12.2759672285131 | etot = -5.62847197075196 +843000 ekin = 3.75502927937468 | erot = 2.93326273057532 | epot = -12.3167639808958 | etot = -5.62847197094577 +844000 ekin = 3.79205095648075 | erot = 2.90501003368086 | epot = -12.3255329611959 | etot = -5.62847197103429 +845000 ekin = 3.8027882689469 | erot = 2.8699770841502 | epot = -12.3012373240957 | etot = -5.62847197099859 +846000 ekin = 3.78689078296352 | erot = 2.82944607252066 | epot = -12.2448088263123 | etot = -5.62847197082816 +847000 ekin = 3.74534923703212 | erot = 2.78543388012331 | epot = -12.1592550876821 | etot = -5.62847197052666 +848000 ekin = 3.68048960874458 | erot = 2.74058491245749 | epot = -12.0495464913185 | etot = -5.62847197011638 +849000 ekin = 3.59580402255087 | erot = 2.69795473495838 | epot = -11.9222307271489 | etot = -5.62847196963968 +850000 ekin = 3.49561211002082 | erot = 2.660698263175 | epot = -11.7847823423459 | etot = -5.62847196915008 +851000 ekin = 3.38460421171663 | erot = 2.63169879010079 | epot = -11.6447749705228 | etot = -5.62847196870538 +852000 ekin = 3.26735834636956 | erot = 2.61319105498462 | epot = -11.5090213697088 | etot = -5.62847196835459 +853000 ekin = 3.14792970844458 | erot = 2.60644045977848 | epot = -11.3828421363496 | etot = -5.62847196812652 +854000 ekin = 3.02961721509545 | erot = 2.61155167727597 | epot = -11.2696408603924 | etot = -5.62847196802096 +855000 ekin = 2.91497870669537 | erot = 2.62749311915792 | epot = -11.1709437938701 | etot = -5.6284719680168 +856000 ekin = 2.80592683673044 | erot = 2.65229723530302 | epot = -11.0866960401081 | etot = -5.62847196807466 +857000 ekin = 2.703943231405 | erot = 2.68342637135654 | epot = -11.0158415709137 | etot = -5.62847196815217 +858000 ekin = 2.61028085054562 | erot = 2.71820874454616 | epot = -10.9569615633078 | etot = -5.62847196821602 +859000 ekin = 2.52608469719978 | erot = 2.754234598628 | epot = -10.9087912640763 | etot = -5.62847196824853 +860000 ekin = 2.45241725372545 | erot = 2.78962480113721 | epot = -10.8705140231101 | etot = -5.6284719682474 +861000 ekin = 2.39021948360179 | erot = 2.82313150333694 | epot = -10.8418229551612 | etot = -5.62847196822247 +862000 ekin = 2.34025129588246 | erot = 2.85407946372215 | epot = -10.8228027277946 | etot = -5.62847196819004 +863000 ekin = 2.30304188879519 | erot = 2.88219277624658 | epot = -10.8137066332093 | etot = -5.62847196816755 +864000 ekin = 2.27886006118591 | erot = 2.90737073863019 | epot = -10.8147027679861 | etot = -5.62847196817005 +865000 ekin = 2.26770197293632 | erot = 2.92947677463961 | epot = -10.8256507157835 | etot = -5.62847196820762 +866000 ekin = 2.26929189352837 | erot = 2.94819404235521 | epot = -10.8459579041654 | etot = -5.62847196828177 +867000 ekin = 2.28309242287195 | erot = 2.96298089303998 | epot = -10.8745452842981 | etot = -5.62847196838621 +868000 ekin = 2.30832281778756 | erot = 2.97313399092797 | epot = -10.9099287772236 | etot = -5.62847196850803 +869000 ekin = 2.34398135241071 | erot = 2.97793980535769 | epot = -10.9503931263996 | etot = -5.62847196863116 +870000 ekin = 2.38886744836853 | erot = 2.97686809825971 | epot = -10.9942075153696 | etot = -5.62847196874141 +871000 ekin = 2.44159861884558 | erot = 2.9697417543727 | epot = -11.0398123420501 | etot = -5.62847196883177 +872000 ekin = 2.5006196168482 | erot = 2.95681803718454 | epot = -11.0859096229375 | etot = -5.62847196890477 +873000 ekin = 2.56420808222993 | erot = 2.9387461409749 | epot = -11.1314261921749 | etot = -5.62847196897009 +874000 ekin = 2.63049127112492 | erot = 2.9164190583251 | epot = -11.1753822984876 | etot = -5.62847196903761 +875000 ekin = 2.69749664540251 | erot = 2.8907906907097 | epot = -11.216759305222 | etot = -5.62847196910977 +876000 ekin = 2.76325740973805 | erot = 2.86275138640014 | epot = -11.2544807653133 | etot = -5.62847196917512 +877000 ekin = 2.82597857166378 | erot = 2.83312911709584 | epot = -11.2875796579688 | etot = -5.62847196920921 +878000 ekin = 2.88426506134625 | erot = 2.8028296012945 | epot = -11.3155666317744 | etot = -5.62847196913367 +879000 ekin = 2.93899285599508 | erot = 2.77402557800297 | epot = -11.3414904029069 | etot = -5.62847196890886 +880000 ekin = 2.9907442958877 | erot = 2.74904466450902 | epot = -11.368260929336 | etot = -5.6284719689393 +881000 ekin = 3.03734869075307 | erot = 2.72816458142423 | epot = -11.3939852409551 | etot = -5.62847196877785 +882000 ekin = 3.07935286425336 | erot = 2.71303253571348 | epot = -11.420857368578 | etot = -5.62847196861113 +883000 ekin = 3.11756797182064 | erot = 2.7051773190194 | epot = -11.4512172593177 | etot = -5.62847196847765 +884000 ekin = 3.15280252947099 | erot = 2.70569769661966 | epot = -11.4869721944935 | etot = -5.62847196840282 +885000 ekin = 3.18571613305558 | erot = 2.71504911595383 | epot = -11.5292372174093 | etot = -5.62847196839988 +886000 ekin = 3.21676773489322 | erot = 2.73290580106824 | epot = -11.5781455044355 | etot = -5.62847196847404 +887000 ekin = 3.24623562526992 | erot = 2.758066691363 | epot = -11.6327742852617 | etot = -5.62847196862876 +888000 ekin = 3.2742594211583 | erot = 2.78837179693705 | epot = -11.6911031869626 | etot = -5.62847196886727 +889000 ekin = 3.30086478990684 | erot = 2.8206406849913 | epot = -11.7499774440861 | etot = -5.62847196918797 +890000 ekin = 3.3259692497401 | erot = 2.85071439964589 | epot = -11.8051556189558 | etot = -5.62847196956976 +891000 ekin = 3.34941253341091 | erot = 2.87373382356758 | epot = -11.8516183269375 | etot = -5.62847196995899 +892000 ekin = 3.37107523663489 | erot = 2.88476437033503 | epot = -11.8843115772387 | etot = -5.62847197026882 +893000 ekin = 3.39111185206228 | erot = 2.87974242650533 | epot = -11.8993262489684 | etot = -5.62847197040083 +894000 ekin = 3.41023213017078 | erot = 2.8565082941896 | epot = -11.8952123946463 | etot = -5.6284719702859 +895000 ekin = 3.4298773096595 | erot = 2.81553499415925 | epot = -11.8738842737409 | etot = -5.6284719699221 +896000 ekin = 3.45214149069667 | erot = 2.7600121308389 | epot = -11.8406255909169 | etot = -5.62847196938128 +897000 ekin = 3.47941735704329 | erot = 2.6952146635652 | epot = -11.8031039893885 | etot = -5.62847196878006 +898000 ekin = 3.51352962135538 | erot = 2.62737086745297 | epot = -11.7693724702135 | etot = -5.62847198140512 +899000 ekin = 3.4889391156295 | erot = 2.56291214099395 | epot = -11.6803232260754 | etot = -5.62847196945197 +900000 ekin = 3.45535689424771 | erot = 2.5501598516678 | epot = -11.633988708263 | etot = -5.62847196234745 +901000 ekin = 3.50186288216171 | erot = 2.58894159291876 | epot = -11.7192764508551 | etot = -5.62847197577464 +902000 ekin = 3.56610213671591 | erot = 2.58196928732591 | epot = -11.7765433965905 | etot = -5.62847197254872 +903000 ekin = 3.6281487590088 | erot = 2.56232070445125 | epot = -11.8189414363827 | etot = -5.62847197292267 +904000 ekin = 3.69112394802224 | erot = 2.55247638510122 | epot = -11.872072306533 | etot = -5.62847197340955 +905000 ekin = 3.75091280522258 | erot = 2.54985569761219 | epot = -11.9292404767528 | etot = -5.62847197391804 +906000 ekin = 3.80322506696776 | erot = 2.55191272482583 | epot = -11.9836097661385 | etot = -5.62847197434491 +907000 ekin = 3.84434228912085 | erot = 2.55683360498905 | epot = -12.0296478687135 | etot = -5.62847197460356 +908000 ekin = 3.87190064221287 | erot = 2.56394104721686 | epot = -12.064313664082 | etot = -5.62847197465227 +909000 ekin = 3.88547927316326 | erot = 2.57365301108526 | epot = -12.0876042587557 | etot = -5.62847197450716 +910000 ekin = 3.88680450854636 | erot = 2.58702435686882 | epot = -12.1023008396463 | etot = -5.62847197423115 +911000 ekin = 3.87951720170576 | erot = 2.60508796278979 | epot = -12.1130771384011 | etot = -5.62847197390549 +912000 ekin = 3.868592335706 | erot = 2.62827701350561 | epot = -12.1253413228164 | etot = -5.62847197360479 +913000 ekin = 3.85955913201886 | erot = 2.65612234920028 | epot = -12.1441534546053 | etot = -5.62847197338611 +914000 ekin = 3.85765974257593 | erot = 2.68725904764579 | epot = -12.173390762903 | etot = -5.62847197268133 +915000 ekin = 3.86988559037046 | erot = 2.72155495965703 | epot = -12.2199125228843 | etot = -5.62847197285679 +916000 ekin = 3.89721211274706 | erot = 2.75899199765551 | epot = -12.2846760836652 | etot = -5.62847197326266 +917000 ekin = 3.93597306522694 | erot = 2.79756616674688 | epot = -12.3620112056762 | etot = -5.62847197370238 +918000 ekin = 3.98211349921921 | erot = 2.83523643983055 | epot = -12.4458219131976 | etot = -5.62847197414785 +919000 ekin = 4.03109884668079 | erot = 2.86939983290182 | epot = -12.5289706551609 | etot = -5.62847197557833 +920000 ekin = 4.07575007330476 | erot = 2.89203459399706 | epot = -12.596256643198 | etot = -5.62847197589616 +921000 ekin = 4.11121320741237 | erot = 2.89963706006279 | epot = -12.6393222441106 | etot = -5.62847197663542 +922000 ekin = 4.12946329710173 | erot = 2.8910149144705 | epot = -12.6489501884791 | etot = -5.6284719769069 +923000 ekin = 4.12574552179452 | erot = 2.86656720117553 | epot = -12.6207846998621 | etot = -5.62847197689209 +924000 ekin = 4.09806256168754 | erot = 2.82817436967983 | epot = -12.5547089079965 | etot = -5.62847197662916 +925000 ekin = 4.04683813422561 | erot = 2.77889165963382 | epot = -12.4542017700762 | etot = -5.62847197621676 +926000 ekin = 3.97415981056844 | erot = 2.72240485359097 | epot = -12.3250366399212 | etot = -5.62847197576179 +927000 ekin = 3.88290109696565 | erot = 2.6624723921107 | epot = -12.173845464402 | etot = -5.62847197532566 +928000 ekin = 3.77619172594752 | erot = 2.60258196870239 | epot = -12.0072456695555 | etot = -5.62847197490555 +929000 ekin = 3.65741733873877 | erot = 2.54590495895918 | epot = -11.8317942721553 | etot = -5.62847197445737 +930000 ekin = 3.53056331260239 | erot = 2.49545263068043 | epot = -11.6544879172217 | etot = -5.62847197393891 +931000 ekin = 3.40054525763448 | erot = 2.45429284513148 | epot = -11.4833100757944 | etot = -5.62847197302846 +932000 ekin = 3.27351307152582 | erot = 2.42812142558973 | epot = -11.3301064697454 | etot = -5.62847197262981 +933000 ekin = 3.1547941266228 | erot = 2.42017428531859 | epot = -11.2034403841693 | etot = -5.62847197222788 +934000 ekin = 3.04934557068947 | erot = 2.43124949633132 | epot = -11.1090670388962 | etot = -5.62847197187545 +935000 ekin = 2.96178382601915 | erot = 2.46165171489738 | epot = -11.0519075125338 | etot = -5.62847197161731 +936000 ekin = 2.89581269285815 | erot = 2.51113391183748 | epot = -11.0354185761747 | etot = -5.62847197147905 +937000 ekin = 2.85385879438853 | erot = 2.57889786087473 | epot = -11.0612286267285 | etot = -5.62847197146526 +938000 ekin = 2.83694342952909 | erot = 2.66364816258385 | epot = -11.1290635636777 | etot = -5.62847197156476 +939000 ekin = 2.84476696228394 | erot = 2.76369076809427 | epot = -11.2369297021307 | etot = -5.62847197175248 +940000 ekin = 2.87595320499146 | erot = 2.87707538000882 | epot = -11.3815005569944 | etot = -5.62847197199412 +941000 ekin = 2.92838858204786 | erot = 3.0017815987521 | epot = -11.5586421530512 | etot = -5.62847197225125 +942000 ekin = 2.99958691563851 | erot = 3.13593595651889 | epot = -11.7639948446456 | etot = -5.62847197248821 +943000 ekin = 3.08701486180388 | erot = 3.27802584214522 | epot = -11.9935126766285 | etot = -5.6284719726794 +944000 ekin = 3.18658687306184 | erot = 3.42629435889835 | epot = -12.2413532058483 | etot = -5.62847197388816 +945000 ekin = 3.29120912256844 | erot = 3.57701253555209 | epot = -12.4966936325289 | etot = -5.62847197440832 +946000 ekin = 3.39621217516328 | erot = 3.72637389468479 | epot = -12.7510580448496 | etot = -5.62847197500155 +947000 ekin = 3.49687303191433 | erot = 3.86977321215332 | epot = -12.9951182197596 | etot = -5.62847197569197 +948000 ekin = 3.58827211298237 | erot = 4.00151346909816 | epot = -13.218257558562 | etot = -5.62847197648142 +949000 ekin = 3.66536645499313 | erot = 4.1147510611234 | epot = -13.4085894934499 | etot = -5.62847197733334 +950000 ekin = 3.72323941968076 | erot = 4.20180191728634 | epot = -13.5535133151338 | etot = -5.62847197816666 +951000 ekin = 3.75754185590692 | erot = 4.25489778144033 | epot = -13.640911616207 | etot = -5.62847197885974 +952000 ekin = 3.76507381529323 | erot = 4.26734583439933 | epot = -13.6608916289676 | etot = -5.62847197927499 +953000 ekin = 3.74438822193795 | erot = 4.23487585238769 | epot = -13.6077360536211 | etot = -5.62847197929546 +954000 ekin = 3.69625242722009 | erot = 4.15681815053726 | epot = -13.4815425566211 | etot = -5.62847197886375 +955000 ekin = 3.62380419976425 | erot = 4.0367317136519 | epot = -13.2890078914231 | etot = -5.6284719780069 +956000 ekin = 3.52555336266068 | erot = 3.88073804767679 | epot = -13.0347633899736 | etot = -5.62847197963612 +957000 ekin = 3.39894638487826 | erot = 3.70474137393303 | epot = -12.7321597333898 | etot = -5.62847197457856 +958000 ekin = 3.27782879007273 | erot = 3.53760737143124 | epot = -12.4439081344594 | etot = -5.62847197295542 +959000 ekin = 3.1783502835544 | erot = 3.38602207592145 | epot = -12.1928443342853 | etot = -5.62847197480943 +960000 ekin = 3.09019087590765 | erot = 3.23509493268237 | epot = -11.9537577850406 | etot = -5.62847197645055 +961000 ekin = 3.00426258992433 | erot = 3.0824813330516 | epot = -11.7152158985205 | etot = -5.62847197554455 +962000 ekin = 2.92693479637486 | erot = 2.94805480632257 | epot = -11.5034615780285 | etot = -5.6284719753311 +963000 ekin = 2.85972055351158 | erot = 2.83488454341514 | epot = -11.3230770719522 | etot = -5.62847197502553 +964000 ekin = 2.80427359226685 | erot = 2.74583972995613 | epot = -11.1785852970698 | etot = -5.62847197484687 +965000 ekin = 2.76170821849677 | erot = 2.68249826029499 | epot = -11.0726784535849 | etot = -5.62847197479316 +966000 ekin = 2.73254763760849 | erot = 2.64503832947664 | epot = -11.0060579419568 | etot = -5.62847197487166 +967000 ekin = 2.71665522017441 | erot = 2.63218922342262 | epot = -10.9773164186843 | etot = -5.62847197508732 +968000 ekin = 2.71315992420235 | erot = 2.64124364193297 | epot = -10.9828755415621 | etot = -5.62847197542673 +969000 ekin = 2.72046614638018 | erot = 2.66825860669117 | epot = -11.0171967289234 | etot = -5.62847197585206 +970000 ekin = 2.73639579035357 | erot = 2.70848274170002 | epot = -11.073350508363 | etot = -5.62847197630937 +971000 ekin = 2.75849383273491 | erot = 2.75695664231006 | epot = -11.1439224517037 | etot = -5.62847197665877 +972000 ekin = 2.78540546423872 | erot = 2.80984083790062 | epot = -11.2237182790709 | etot = -5.62847197693153 +973000 ekin = 2.81581409029779 | erot = 2.86412704793782 | epot = -11.3084131153518 | etot = -5.62847197711619 +974000 ekin = 2.84847995223966 | erot = 2.91762904313292 | epot = -11.394580972579 | etot = -5.62847197720637 +975000 ekin = 2.88260770883418 | erot = 2.9692077422299 | epot = -11.4802874282683 | etot = -5.62847197720426 +976000 ekin = 2.90702473613829 | erot = 3.01964919146321 | epot = -11.555145929188 | etot = -5.62847200158652 +977000 ekin = 2.82994036412631 | erot = 3.10467596021963 | epot = -11.5630883021957 | etot = -5.62847197784979 +978000 ekin = 2.82908362121548 | erot = 3.2254663925878 | epot = -11.6830220175211 | etot = -5.62847200371779 +979000 ekin = 2.83706100054281 | erot = 3.25481872941685 | epot = -11.7203517200298 | etot = -5.62847199007014 +980000 ekin = 2.83601345062761 | erot = 3.27042511438439 | epot = -11.7349105551174 | etot = -5.62847199010541 +981000 ekin = 2.82679467427683 | erot = 3.27908745939339 | epot = -11.7343541238172 | etot = -5.62847199014698 +982000 ekin = 2.80889456989795 | erot = 3.28090658202195 | epot = -11.7182731421114 | etot = -5.62847199019147 +983000 ekin = 2.78208898547456 | erot = 3.27578646990667 | epot = -11.6863474455989 | etot = -5.62847199021772 +984000 ekin = 2.74660136779493 | erot = 3.26353952214283 | epot = -11.6386128801286 | etot = -5.62847199019088 +985000 ekin = 2.70333214312677 | erot = 3.24411390807002 | epot = -11.5759180412707 | etot = -5.62847199007386 +986000 ekin = 2.65408912624307 | erot = 3.2178652626592 | epot = -11.5004263787422 | etot = -5.62847198983991 +987000 ekin = 2.57871632758182 | erot = 3.17247279232543 | epot = -11.3796611142273 | etot = -5.62847199432008 +988000 ekin = 2.53018925473336 | erot = 3.15315339683742 | epot = -11.3118146535091 | etot = -5.62847200193829 +989000 ekin = 2.49566277922967 | erot = 3.12952117136867 | epot = -11.2536559425352 | etot = -5.62847199193689 +990000 ekin = 2.46227182208794 | erot = 3.09741757527421 | epot = -11.1881613887439 | etot = -5.6284719913817 +991000 ekin = 2.44592298947839 | erot = 3.07158094759995 | epot = -11.1459759281972 | etot = -5.62847199111885 +992000 ekin = 2.45174281271621 | erot = 3.05611048227045 | epot = -11.1363252859054 | etot = -5.62847199091873 +993000 ekin = 2.48099671405936 | erot = 3.05281517933321 | epot = -11.1622838841579 | etot = -5.6284719907653 +994000 ekin = 2.53415669983384 | erot = 3.06359154200859 | epot = -11.2262202325221 | etot = -5.62847199067972 +995000 ekin = 2.61088853092033 | erot = 3.09015398394547 | epot = -11.3295145055374 | etot = -5.62847199067165 +996000 ekin = 2.7101181952278 | erot = 3.13378298566575 | epot = -11.4723731716367 | etot = -5.62847199074318 +997000 ekin = 2.83015603167808 | erot = 3.1951526760491 | epot = -11.6537806986213 | etot = -5.62847199089407 +998000 ekin = 2.96878571572636 | erot = 3.2742319127211 | epot = -11.8714896195807 | etot = -5.62847199113322 +999000 ekin = 3.12322522668413 | erot = 3.37022004661284 | epot = -12.1219172647843 | etot = -5.62847199148729 +1000000 ekin = 3.28990650620536 | erot = 3.48146010670929 | epot = -12.399838604914 | etot = -5.62847199199935 + 1000000 0.14621807 -0.83009398 0.055104069 -0.56937076 4.8223734e-05 64000 +Loop time of 19.3831 on 1 procs for 1000000 steps with 16 atoms + +Performance: 44574.879 tau/day, 51591.295 timesteps/s, 825.461 katom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.183 | 16.183 | 16.183 | 0.0 | 83.49 +Bond | 0.69138 | 0.69138 | 0.69138 | 0.0 | 3.57 +Neigh | 0.007921 | 0.007921 | 0.007921 | 0.0 | 0.04 +Comm | 0.27135 | 0.27135 | 0.27135 | 0.0 | 1.40 +Output | 0.17337 | 0.17337 | 0.17337 | 0.0 | 0.89 +Modify | 1.767 | 1.767 | 1.767 | 0.0 | 9.12 +Other | | 0.2889 | | | 1.49 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 106 ave 106 max 106 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 106 +Ave neighs/atom = 6.625 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:19 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/log.19May24.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/log.19May24.duplex2.g++.4 new file mode 100644 index 0000000000..d957078bdc --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/log.19May24.duplex2.g++.4 @@ -0,0 +1,1121 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.008 seconds +Setting atom values ... + 16 settings made for mass +16 atoms in group all +Reading oxdna potential (fene) file oxrna2.lj with DATE: 2024-04-19 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (stk) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (hbond) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (xstk) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (coaxstk) file oxrna2.lj with DATE: 2024-04-19 +Reading oxdna potential (dh) file oxrna2.lj with DATE: 2024-04-19 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3014979 + ghost atom cutoff = 4.3014979 + binsize = 2.150749, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 1e-05 +WARNING: Communication cutoff adjusted to 4.301497916929199 (src/comm.cpp:739) +0 ekin = 2.70475393009871 | erot = 2.80172072918779 | epot = -11.1349465280232 | etot = -5.62847186873667 +Per MPI rank memory allocation (min/avg/max) = 7.577 | 7.606 | 7.69 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0.12021129 -0.7299505 0.034016337 -0.52688704 5.1214421e-05 64000 +1000 ekin = 2.74425239815417 | erot = 2.79065458610893 | epot = -11.1633788526891 | etot = -5.62847186842597 +2000 ekin = 2.78841691867035 | erot = 2.77992540099535 | epot = -11.196814187725 | etot = -5.62847186805933 +3000 ekin = 2.83938215410022 | erot = 2.77185117591642 | epot = -11.2397051978034 | etot = -5.62847186778672 +4000 ekin = 2.89876217830263 | erot = 2.76816783884241 | epot = -11.295401884792 | etot = -5.62847186764698 +5000 ekin = 2.96742170720769 | erot = 2.76919345829435 | epot = -11.3650870331989 | etot = -5.62847186769689 +6000 ekin = 3.0456300737104 | erot = 2.77376672268248 | epot = -11.4478686641706 | etot = -5.62847186777773 +7000 ekin = 3.13407886898538 | erot = 2.78065913591457 | epot = -11.5432098726294 | etot = -5.62847186772942 +8000 ekin = 3.23400863287743 | erot = 2.78938863934858 | epot = -11.651869139893 | etot = -5.62847186766703 +9000 ekin = 3.34625998930258 | erot = 2.80019523753785 | epot = -11.7749270943235 | etot = -5.62847186748304 +10000 ekin = 3.47220350616334 | erot = 2.81464622815282 | epot = -11.9153216015116 | etot = -5.62847186719547 +11000 ekin = 3.61341090096018 | erot = 2.83541090219849 | epot = -12.0772936703879 | etot = -5.62847186722922 +12000 ekin = 3.76971728921063 | erot = 2.8651661044909 | epot = -12.26335526073 | etot = -5.62847186702843 +13000 ekin = 3.94105577714468 | erot = 2.90597306806356 | epot = -12.4755007121567 | etot = -5.62847186694845 +14000 ekin = 4.12730744896758 | erot = 2.95952862137381 | epot = -12.7153079373025 | etot = -5.62847186696111 +15000 ekin = 4.32776706381551 | erot = 3.02701108512252 | epot = -12.9832500158855 | etot = -5.62847186694746 +16000 ekin = 4.54139695680685 | erot = 3.10924468066178 | epot = -13.2791135046207 | etot = -5.62847186715204 +17000 ekin = 4.76575661763823 | erot = 3.20604355373091 | epot = -13.6002720389201 | etot = -5.62847186755099 +18000 ekin = 4.99700491214683 | erot = 3.31611869568265 | epot = -13.9415954758899 | etot = -5.62847186806046 +19000 ekin = 5.23048108112189 | erot = 3.43700077146758 | epot = -14.2959537213473 | etot = -5.62847186875783 +20000 ekin = 5.46074742513055 | erot = 3.56463156086399 | epot = -14.6538508556015 | etot = -5.62847186960696 +21000 ekin = 5.68087058007131 | erot = 3.69256776681709 | epot = -15.0019102179231 | etot = -5.62847187103471 +22000 ekin = 5.88327619983871 | erot = 3.81252322503548 | epot = -15.3242712967755 | etot = -5.62847187190132 +23000 ekin = 6.06249979951982 | erot = 3.91720950057661 | epot = -15.6081811728146 | etot = -5.6284718727182 +24000 ekin = 6.21449712377427 | erot = 4.00104081543169 | epot = -15.8440098121103 | etot = -5.62847187290435 +25000 ekin = 6.33853277809242 | erot = 4.06184542619867 | epot = -16.0288500769827 | etot = -5.62847187269159 +26000 ekin = 6.43627737186998 | erot = 4.10076278430829 | epot = -16.1655120283937 | etot = -5.62847187221544 +27000 ekin = 6.51092447972012 | erot = 4.12134483746795 | epot = -16.2607411888239 | etot = -5.62847187163586 +28000 ekin = 6.56622100976667 | erot = 4.12827111510804 | epot = -16.3229639959505 | etot = -5.62847187107576 +29000 ekin = 6.60587340002377 | erot = 4.12622173833889 | epot = -16.360567008949 | etot = -5.62847187058635 +30000 ekin = 6.63335580501812 | erot = 4.11921545444644 | epot = -16.3810431296792 | etot = -5.62847187021468 +31000 ekin = 6.65211888589255 | erot = 4.10999678317525 | epot = -16.3905875389832 | etot = -5.62847186991539 +32000 ekin = 6.66584763664858 | erot = 4.10024297795097 | epot = -16.3945624842072 | etot = -5.62847186960762 +33000 ekin = 6.67923227191015 | erot = 4.09129207413363 | epot = -16.398996215263 | etot = -5.62847186921926 +34000 ekin = 6.69756137216819 | erot = 4.08414768607663 | epot = -16.4101809271346 | etot = -5.62847186888976 +35000 ekin = 6.7258962831207 | erot = 4.07950228497947 | epot = -16.4338704366877 | etot = -5.62847186858755 +36000 ekin = 6.76908557113703 | erot = 4.07778615492108 | epot = -16.4753435944362 | etot = -5.6284718683781 +37000 ekin = 6.83097506213393 | erot = 4.07899014040663 | epot = -16.5384370708784 | etot = -5.62847186833782 +38000 ekin = 6.91354703253162 | erot = 4.08242106390416 | epot = -16.6244399649597 | etot = -5.62847186852396 +39000 ekin = 7.01626065739823 | erot = 4.08652171942784 | epot = -16.7312542457771 | etot = -5.62847186895107 +40000 ekin = 7.13573792258319 | erot = 4.08884404540002 | epot = -16.8530538375758 | etot = -5.62847186959262 +41000 ekin = 7.26614194134504 | erot = 4.08627042537764 | epot = -16.9808842370343 | etot = -5.62847187031164 +42000 ekin = 7.40051154120577 | erot = 4.07546023443099 | epot = -17.1044436466276 | etot = -5.62847187099086 +43000 ekin = 7.53157437143679 | erot = 4.05344655359637 | epot = -17.2134927965847 | etot = -5.6284718715515 +44000 ekin = 7.65268317567636 | erot = 4.01819177227231 | epot = -17.299346819823 | etot = -5.62847187187438 +45000 ekin = 7.75845343306881 | erot = 3.96898510895771 | epot = -17.3559104142061 | etot = -5.62847187217961 +46000 ekin = 7.84504377034637 | erot = 3.90454903064792 | epot = -17.3780646733313 | etot = -5.62847187233703 +47000 ekin = 7.9100239082063 | erot = 3.82478596555195 | epot = -17.3632817459104 | etot = -5.6284718721521 +48000 ekin = 7.95195705456511 | erot = 3.73154439390002 | epot = -17.3119733204125 | etot = -5.62847187194738 +49000 ekin = 7.97001825706878 | erot = 3.62752007295042 | epot = -17.2260102016183 | etot = -5.62847187159909 +50000 ekin = 7.96375756700447 | erot = 3.51726958365103 | epot = -17.109499021545 | etot = -5.62847187088952 +51000 ekin = 7.93280761300463 | erot = 3.4082718849783 | epot = -16.969551368803 | etot = -5.62847187082006 +52000 ekin = 7.8765681174422 | erot = 3.30207418532529 | epot = -16.8071141735586 | etot = -5.62847187079111 +53000 ekin = 7.7953101254194 | erot = 3.19839984815406 | epot = -16.6221818441148 | etot = -5.62847187054135 +54000 ekin = 7.68952609570371 | erot = 3.09980185481814 | epot = -16.4177998208248 | etot = -5.6284718703029 +55000 ekin = 7.55966222141136 | erot = 3.00897426989528 | epot = -16.1971083614502 | etot = -5.62847187014354 +56000 ekin = 7.40594124508042 | erot = 2.92802865182251 | epot = -15.9624417669776 | etot = -5.62847187007466 +57000 ekin = 7.22816598142032 | erot = 2.85836584281784 | epot = -15.7150036943484 | etot = -5.62847187011025 +58000 ekin = 7.02573051397646 | erot = 2.80066522322026 | epot = -15.4548676074198 | etot = -5.62847187022312 +59000 ekin = 6.80455077165157 | erot = 2.7565194471202 | epot = -15.1895420860968 | etot = -5.62847186732506 +60000 ekin = 6.57760251691547 | erot = 2.7273150167872 | epot = -14.9333893991696 | etot = -5.62847186546689 +61000 ekin = 5.9988405319016 | erot = 2.65010269791703 | epot = -14.2774150331164 | etot = -5.62847180329775 +62000 ekin = 5.82217958652129 | erot = 2.6505847819514 | epot = -14.1012361774593 | etot = -5.6284718089866 +63000 ekin = 6.00993174210264 | erot = 2.71143483466393 | epot = -14.3498384845184 | etot = -5.62847190775186 +64000 ekin = 5.85096985050382 | erot = 2.71173917624701 | epot = -14.1911809366074 | etot = -5.62847190985654 +65000 ekin = 5.6795980144275 | erot = 2.70731630130132 | epot = -14.0153862253962 | etot = -5.62847190966738 +66000 ekin = 5.49812382731721 | erot = 2.69646895132475 | epot = -13.8230646880629 | etot = -5.6284719094209 +67000 ekin = 5.31011188753164 | erot = 2.67901331172367 | epot = -13.617597108258 | etot = -5.62847190900273 +68000 ekin = 5.11964229582607 | erot = 2.6562219727338 | epot = -13.4043361770524 | etot = -5.62847190849251 +69000 ekin = 4.93067975207874 | erot = 2.63014135225669 | epot = -13.1892930124926 | etot = -5.62847190815713 +70000 ekin = 4.74697386617509 | erot = 2.6034731270628 | epot = -12.9789189008746 | etot = -5.62847190763674 +71000 ekin = 4.57222133259595 | erot = 2.57971589798904 | epot = -12.780409137744 | etot = -5.62847190715903 +72000 ekin = 4.40959648507812 | erot = 2.56228295922466 | epot = -12.6003513510612 | etot = -5.62847190675846 +73000 ekin = 4.26170009573938 | erot = 2.55406076080087 | epot = -12.4442327629946 | etot = -5.62847190645434 +74000 ekin = 4.13052949790856 | erot = 2.55713155841143 | epot = -12.3161329625864 | etot = -5.62847190626636 +75000 ekin = 4.0158819282893 | erot = 2.56608801434125 | epot = -12.2104419139906 | etot = -5.62847197136006 +76000 ekin = 3.95904625854645 | erot = 2.44184942386113 | epot = -12.0293675901706 | etot = -5.62847190776307 +77000 ekin = 4.02755960266396 | erot = 2.46007159499044 | epot = -12.1161031098039 | etot = -5.62847191214949 +78000 ekin = 3.98785439943849 | erot = 2.49596945534602 | epot = -12.1122957670966 | etot = -5.62847191231205 +79000 ekin = 3.96575767721464 | erot = 2.54200842335455 | epot = -12.1362380131154 | etot = -5.62847191254623 +80000 ekin = 3.95961954869592 | erot = 2.59604589435599 | epot = -12.184137355885 | etot = -5.62847191283309 +81000 ekin = 3.9673410003238 | erot = 2.65577062232356 | epot = -12.2515835357819 | etot = -5.62847191313457 +82000 ekin = 3.98651997822158 | erot = 2.71892569307088 | epot = -12.3339175847233 | etot = -5.62847191343081 +83000 ekin = 4.01459300302777 | erot = 2.78352190390201 | epot = -12.4265868206362 | etot = -5.62847191370641 +84000 ekin = 4.0495621060858 | erot = 2.8479662966442 | epot = -12.5260003165346 | etot = -5.62847191380463 +85000 ekin = 4.09049341026889 | erot = 2.91104365381099 | epot = -12.6300089781181 | etot = -5.62847191403819 +86000 ekin = 4.13484812560063 | erot = 2.97201165419083 | epot = -12.7353316940204 | etot = -5.62847191422892 +87000 ekin = 4.18003829184661 | erot = 3.03078479878275 | epot = -12.8392950049953 | etot = -5.6284719143659 +88000 ekin = 4.22360704724739 | erot = 3.08796574000306 | epot = -12.9400447017 | etot = -5.6284719144496 +89000 ekin = 4.26326024607321 | erot = 3.14481288279462 | epot = -13.0365450433356 | etot = -5.62847191446776 +90000 ekin = 4.29588111790608 | erot = 3.20341713776984 | epot = -13.1277701703296 | etot = -5.62847191465366 +91000 ekin = 4.31697784577799 | erot = 3.26736040230122 | epot = -13.2128101626451 | etot = -5.62847191456589 +92000 ekin = 4.3250783734756 | erot = 3.33931601944521 | epot = -13.2928663075894 | etot = -5.62847191466861 +93000 ekin = 4.31872212432174 | erot = 3.42036541916733 | epot = -13.3675594581772 | etot = -5.62847191468809 +94000 ekin = 4.29660005793268 | erot = 3.51205694754354 | epot = -13.4371289201532 | etot = -5.62847191467697 +95000 ekin = 4.25789021838815 | erot = 3.61606475666788 | epot = -13.5024268896661 | etot = -5.62847191461011 +96000 ekin = 4.2025366192647 | erot = 3.73412422729603 | epot = -13.5651327610303 | etot = -5.62847191446958 +97000 ekin = 4.13146529059983 | erot = 3.86803037439235 | epot = -13.6279675793408 | etot = -5.62847191434867 +98000 ekin = 4.04669071975317 | erot = 4.01885670334665 | epot = -13.6940193371941 | etot = -5.62847191409431 +99000 ekin = 3.95128630061856 | erot = 4.18772840013396 | epot = -13.7674866145613 | etot = -5.6284719138088 +100000 ekin = 3.84921784883014 | erot = 4.37558821791212 | epot = -13.8532779802861 | etot = -5.62847191354385 +101000 ekin = 3.74501223923234 | erot = 4.5825842923172 | epot = -13.9560684449131 | etot = -5.62847191336357 +102000 ekin = 3.64330024870495 | erot = 4.80764134110052 | epot = -14.0794135031359 | etot = -5.62847191333045 +103000 ekin = 3.54831662006189 | erot = 5.04811575607487 | epot = -14.2249042896159 | etot = -5.62847191347916 +104000 ekin = 3.46349772064836 | erot = 5.29960820358442 | epot = -14.3915778382021 | etot = -5.62847191396929 +105000 ekin = 3.39136254536159 | erot = 5.5550770435999 | epot = -14.5749115034235 | etot = -5.628471914462 +106000 ekin = 3.33356403744289 | erot = 5.80718759324942 | epot = -14.7692235454824 | etot = -5.62847191479007 +107000 ekin = 3.29209861353571 | erot = 6.04906687386761 | epot = -14.9696374027438 | etot = -5.62847191534052 +108000 ekin = 3.2674848734097 | erot = 6.27418243659718 | epot = -15.1701392258613 | etot = -5.62847191585437 +109000 ekin = 3.25930506886458 | erot = 6.4758541724433 | epot = -15.3636311580673 | etot = -5.62847191675944 +110000 ekin = 3.26568272828949 | erot = 6.64602097207931 | epot = -15.5401756176965 | etot = -5.62847191732771 +111000 ekin = 3.28520059172467 | erot = 6.77857539600323 | epot = -15.6922479055245 | etot = -5.62847191779661 +112000 ekin = 3.31659315707279 | erot = 6.86862760563939 | epot = -15.8136926809225 | etot = -5.62847191821031 +113000 ekin = 3.35860144230777 | erot = 6.91335224014795 | epot = -15.9004256006548 | etot = -5.62847191819904 +114000 ekin = 3.41073468124525 | erot = 6.91406610981162 | epot = -15.9532727088313 | etot = -5.62847191777438 +115000 ekin = 3.47381531534132 | erot = 6.87643065686351 | epot = -15.9787178894049 | etot = -5.62847191720006 +116000 ekin = 3.54886437558636 | erot = 6.80711139529066 | epot = -15.9844476879556 | etot = -5.62847191707855 +117000 ekin = 3.63467409204824 | erot = 6.71320827683544 | epot = -15.9763542854608 | etot = -5.6284719165771 +118000 ekin = 3.72815555523451 | erot = 6.60276001485538 | epot = -15.9593874864246 | etot = -5.62847191633475 +119000 ekin = 3.8242098036383 | erot = 6.48288858478252 | epot = -15.9355703049679 | etot = -5.62847191654706 +120000 ekin = 3.91797748357147 | erot = 6.35662792089839 | epot = -15.9030773212269 | etot = -5.62847191675705 +121000 ekin = 4.00591742043981 | erot = 6.22468993027065 | epot = -15.8590792676424 | etot = -5.62847191693198 +122000 ekin = 4.08550270322333 | erot = 6.08676575288889 | epot = -15.8007403736368 | etot = -5.62847191752457 +123000 ekin = 4.15433540908357 | erot = 5.94071572290355 | epot = -15.7235230494647 | etot = -5.62847191747755 +124000 ekin = 4.21272085203595 | erot = 5.78590733869454 | epot = -15.6271001078556 | etot = -5.62847191712511 +125000 ekin = 4.26325970413181 | erot = 5.62467373686594 | epot = -15.516405357524 | etot = -5.62847191652626 +126000 ekin = 4.30880597980493 | erot = 5.46113290467127 | epot = -15.3984108007456 | etot = -5.62847191626943 +127000 ekin = 4.3513631311099 | erot = 5.29960307371356 | epot = -15.2794381205815 | etot = -5.62847191575806 +128000 ekin = 4.39391383900439 | erot = 5.14386269106642 | epot = -15.166248445447 | etot = -5.62847191537622 +129000 ekin = 4.43858036063557 | erot = 4.99693296064673 | epot = -15.0639852363956 | etot = -5.62847191511328 +130000 ekin = 4.48619887382404 | erot = 4.86092637377837 | epot = -14.9755971627232 | etot = -5.62847191512077 +131000 ekin = 4.53629967745958 | erot = 4.73552279955379 | epot = -14.9002943921684 | etot = -5.62847191515504 +132000 ekin = 4.58794392436588 | erot = 4.62012473201771 | epot = -14.8365405715589 | etot = -5.62847191517533 +133000 ekin = 4.63977927970688 | erot = 4.51475331813831 | epot = -14.7830045130142 | etot = -5.62847191516899 +134000 ekin = 4.69096227444458 | erot = 4.41936571519981 | epot = -14.7387999047798 | etot = -5.62847191513542 +135000 ekin = 4.74083332631883 | erot = 4.33399770983505 | epot = -14.7033029512355 | etot = -5.62847191508162 +136000 ekin = 4.78901374177222 | erot = 4.25873574864683 | epot = -14.6762214054312 | etot = -5.62847191501212 +137000 ekin = 4.83519033966102 | erot = 4.19345584709188 | epot = -14.6571181018621 | etot = -5.62847191510917 +138000 ekin = 4.87857190019093 | erot = 4.13759960010392 | epot = -14.6446434153633 | etot = -5.62847191506846 +139000 ekin = 4.91933904268488 | erot = 4.09041841408072 | epot = -14.6382293717793 | etot = -5.62847191501367 +140000 ekin = 4.95802132610577 | erot = 4.05108530565712 | epot = -14.6375785467319 | etot = -5.62847191496898 +141000 ekin = 4.99519923255229 | erot = 4.01864210163592 | epot = -14.6423132491258 | etot = -5.62847191493756 +142000 ekin = 5.03134031865286 | erot = 3.9921096007244 | epot = -14.651921834306 | etot = -5.62847191492874 +143000 ekin = 5.06663282814527 | erot = 3.97056100872247 | epot = -14.6656657518147 | etot = -5.6284719149469 +144000 ekin = 5.10088003253911 | erot = 3.9531838593667 | epot = -14.6825358068967 | etot = -5.62847191499091 +145000 ekin = 5.13347728619377 | erot = 3.93933318432689 | epot = -14.7012823855759 | etot = -5.62847191505523 +146000 ekin = 5.16346418937017 | erot = 3.92856945833623 | epot = -14.7205055628377 | etot = -5.62847191513127 +147000 ekin = 5.18962884502114 | erot = 3.9206777897017 | epot = -14.7387785499329 | etot = -5.62847191521003 +148000 ekin = 5.21063630105058 | erot = 3.91566839447859 | epot = -14.7547766108122 | etot = -5.62847191528303 +149000 ekin = 5.22515818277348 | erot = 3.91376203385023 | epot = -14.7673921319672 | etot = -5.6284719153435 +150000 ekin = 5.23199081771498 | erot = 3.91536756918944 | epot = -14.7758303022896 | etot = -5.62847191538518 +151000 ekin = 5.2302585743497 | erot = 3.92102977399639 | epot = -14.7797602637321 | etot = -5.62847191538598 +152000 ekin = 5.21970456277725 | erot = 3.93136599417393 | epot = -14.7795424723217 | etot = -5.62847191537049 +153000 ekin = 5.20020715644055 | erot = 3.94729684643089 | epot = -14.7759759181602 | etot = -5.62847191528876 +154000 ekin = 5.17219962281025 | erot = 3.96989664945499 | epot = -14.7705681875129 | etot = -5.62847191524761 +155000 ekin = 5.13597939415339 | erot = 4.00025654377964 | epot = -14.7647078530859 | etot = -5.62847191515283 +156000 ekin = 5.09227456538948 | erot = 4.03969792967945 | epot = -14.7604444100958 | etot = -5.6284719150269 +157000 ekin = 5.04214374655968 | erot = 4.08965648366453 | epot = -14.7602721451249 | etot = -5.62847191490065 +158000 ekin = 4.98664076893875 | erot = 4.15175637520707 | epot = -14.7668690589168 | etot = -5.62847191477102 +159000 ekin = 4.92656708226531 | erot = 4.22693785976786 | epot = -14.7819768568045 | etot = -5.62847191477136 +160000 ekin = 4.86235166665144 | erot = 4.31524574981851 | epot = -14.8060693313562 | etot = -5.62847191488621 +161000 ekin = 4.79340744408571 | erot = 4.41634192155802 | epot = -14.8382212806409 | etot = -5.62847191499721 +162000 ekin = 4.71931679137345 | erot = 4.52911647420422 | epot = -14.8769051807461 | etot = -5.62847191516839 +163000 ekin = 4.63965178838057 | erot = 4.65170333188857 | epot = -14.9198270356149 | etot = -5.6284719153458 +164000 ekin = 4.55406399624446 | erot = 4.78166301740476 | epot = -14.9641989292998 | etot = -5.62847191565063 +165000 ekin = 4.46213996067549 | erot = 4.9153027215904 | epot = -15.005914598208 | etot = -5.62847191594211 +166000 ekin = 4.36388109534935 | erot = 5.04805357548725 | epot = -15.0404065870436 | etot = -5.62847191620698 +167000 ekin = 4.25995046842471 | erot = 5.17511068522386 | epot = -15.0635330700719 | etot = -5.62847191642331 +168000 ekin = 4.15154354282127 | erot = 5.29182746832013 | epot = -15.0718429277141 | etot = -5.6284719165727 +169000 ekin = 4.04026084727452 | erot = 5.39411747728171 | epot = -15.0628502412115 | etot = -5.62847191665525 +170000 ekin = 3.92797723838266 | erot = 5.47890367159956 | epot = -15.0353528265949 | etot = -5.62847191661267 +171000 ekin = 3.81680551395721 | erot = 5.54460219961154 | epot = -14.9898796300193 | etot = -5.62847191645055 +172000 ekin = 3.70912194360746 | erot = 5.59119877272667 | epot = -14.9287926324946 | etot = -5.62847191616047 +173000 ekin = 3.60767008609825 | erot = 5.62020496675955 | epot = -14.8563469686151 | etot = -5.62847191575734 +174000 ekin = 3.51593123142515 | erot = 5.63484613588001 | epot = -14.7792492818543 | etot = -5.62847191454913 +175000 ekin = 3.43946966413688 | erot = 5.64148825118996 | epot = -14.7094298295795 | etot = -5.62847191425268 +176000 ekin = 3.38149964339828 | erot = 5.64304584979489 | epot = -14.6530174072199 | etot = -5.62847191402674 +177000 ekin = 3.34426304280142 | erot = 5.64075589500425 | epot = -14.613490851737 | etot = -5.62847191393132 +178000 ekin = 3.32907821317954 | erot = 5.63429171925213 | epot = -14.5918418466184 | etot = -5.62847191418678 +179000 ekin = 3.33553286829191 | erot = 5.62088708741392 | epot = -14.5848918700454 | etot = -5.62847191433961 +180000 ekin = 3.3633338427711 | erot = 5.59827011329087 | epot = -14.590075870681 | etot = -5.62847191461902 +181000 ekin = 3.41118322744577 | erot = 5.56369949232745 | epot = -14.6033546347466 | etot = -5.6284719149734 +182000 ekin = 3.47666657813831 | erot = 5.51442909119293 | epot = -14.6195675846739 | etot = -5.62847191534263 +183000 ekin = 3.55646627297049 | erot = 5.44847615754669 | epot = -14.6334143461245 | etot = -5.62847191560728 +184000 ekin = 3.64671110623847 | erot = 5.36528131962425 | epot = -14.6404643416894 | etot = -5.62847191582671 +185000 ekin = 3.7429424385421 | erot = 5.26596644090051 | epot = -14.637380795357 | etot = -5.62847191591437 +186000 ekin = 3.84064021177397 | erot = 5.15359326678864 | epot = -14.6227053944198 | etot = -5.62847191585718 +187000 ekin = 3.93563840595001 | erot = 5.03296537332374 | epot = -14.5970756949481 | etot = -5.62847191567436 +188000 ekin = 4.02444308409296 | erot = 4.91004205202559 | epot = -14.5629570515405 | etot = -5.62847191542198 +189000 ekin = 4.10437481570314 | erot = 4.79101157925938 | epot = -14.5238583101457 | etot = -5.62847191518321 +190000 ekin = 4.17348832620003 | erot = 4.68117061833053 | epot = -14.4831308595846 | etot = -5.62847191505407 +191000 ekin = 4.2302884539446 | erot = 4.5838619279884 | epot = -14.442622297024 | etot = -5.62847191509104 +192000 ekin = 4.2735805406068 | erot = 4.49984530057596 | epot = -14.4018977564812 | etot = -5.62847191529842 +193000 ekin = 4.24592911994321 | erot = 4.46741799187356 | epot = -14.341819022694 | etot = -5.62847191087726 +194000 ekin = 4.19994174151085 | erot = 4.47173701960621 | epot = -14.3001506793693 | etot = -5.62847191825224 +195000 ekin = 4.19981139522261 | erot = 4.40365513590485 | epot = -14.2319384423521 | etot = -5.62847191122465 +196000 ekin = 4.18831859750035 | erot = 4.328213784087 | epot = -14.1450042928984 | etot = -5.62847191131101 +197000 ekin = 4.16445522600586 | erot = 4.24686919663538 | epot = -14.0397963337859 | etot = -5.62847191114469 +198000 ekin = 4.1307492037306 | erot = 4.15919636754741 | epot = -13.9184174820272 | etot = -5.62847191074922 +199000 ekin = 4.09062074736305 | erot = 4.06700829110004 | epot = -13.7861009486946 | etot = -5.6284719102315 +200000 ekin = 4.04792338687347 | erot = 3.97356549445519 | epot = -13.6499607909737 | etot = -5.62847190964504 +201000 ekin = 4.00668244919937 | erot = 3.88277215509152 | epot = -13.5179265133942 | etot = -5.62847190910329 +202000 ekin = 3.97063392471906 | erot = 3.79828207702263 | epot = -13.3973879104142 | etot = -5.6284719086725 +203000 ekin = 3.94283665189579 | erot = 3.72290259923935 | epot = -13.2942111595221 | etot = -5.62847190838693 +204000 ekin = 3.92540743372375 | erot = 3.65835216262531 | epot = -13.2122315046004 | etot = -5.62847190825132 +205000 ekin = 3.91946432177547 | erot = 3.60562062221061 | epot = -13.1535568521759 | etot = -5.62847190818981 +206000 ekin = 3.92515912499702 | erot = 3.56510062726708 | epot = -13.1187316605198 | etot = -5.62847190825566 +207000 ekin = 3.94166066189883 | erot = 3.53643554885193 | epot = -13.106568119133 | etot = -5.62847190838225 +208000 ekin = 3.96741904659975 | erot = 3.51909285319074 | epot = -13.1149838083271 | etot = -5.62847190853662 +209000 ekin = 3.99456273873009 | erot = 3.50083315850435 | epot = -13.1238678065952 | etot = -5.62847190936073 +210000 ekin = 4.04796401860738 | erot = 3.49168954891013 | epot = -13.1681254815447 | etot = -5.62847191402719 +211000 ekin = 4.09773342716367 | erot = 3.49304812012984 | epot = -13.2192534546401 | etot = -5.62847190734662 +212000 ekin = 4.14205596974759 | erot = 3.50221111647932 | epot = -13.2727389936944 | etot = -5.62847190746751 +213000 ekin = 4.18461227969667 | erot = 3.51992604962506 | epot = -13.3330102373293 | etot = -5.62847190800754 +214000 ekin = 4.22291801221457 | erot = 3.54318058638054 | epot = -13.3945705067456 | etot = -5.62847190815054 +215000 ekin = 4.25639069944512 | erot = 3.57018634833026 | epot = -13.4550489560127 | etot = -5.62847190823736 +216000 ekin = 4.28517056131255 | erot = 3.59920416165437 | epot = -13.5128466312863 | etot = -5.62847190831941 +217000 ekin = 4.30951457891845 | erot = 3.6286263473057 | epot = -13.5666128346141 | etot = -5.62847190838996 +218000 ekin = 4.33022749098081 | erot = 3.65639118247548 | epot = -13.6150905819366 | etot = -5.62847190848033 +219000 ekin = 4.34822739189298 | erot = 3.68015661121616 | epot = -13.6568559116936 | etot = -5.62847190858443 +220000 ekin = 4.3643728025888 | erot = 3.69755509928487 | epot = -13.6903998105203 | etot = -5.62847190864662 +221000 ekin = 4.37954317243948 | erot = 3.7066097682417 | epot = -13.7146248493744 | etot = -5.6284719086932 +222000 ekin = 4.39451292717598 | erot = 3.70596363375132 | epot = -13.7289484695975 | etot = -5.62847190867022 +223000 ekin = 4.41008213189481 | erot = 3.69513355487105 | epot = -13.7336875953414 | etot = -5.62847190857551 +224000 ekin = 4.42678943726707 | erot = 3.67466536393115 | epot = -13.7299267097397 | etot = -5.6284719085415 +225000 ekin = 4.4446070170142 | erot = 3.64600909387524 | epot = -13.7190880192601 | etot = -5.62847190837067 +226000 ekin = 4.47380092383422 | erot = 3.58830814096065 | epot = -13.6905809780265 | etot = -5.6284719132316 +227000 ekin = 4.56056009805432 | erot = 3.47269306830543 | epot = -13.6617250773591 | etot = -5.62847191099938 +228000 ekin = 4.61083327531231 | erot = 3.40803816010519 | epot = -13.6473433475428 | etot = -5.62847191212525 +229000 ekin = 4.63150013168163 | erot = 3.35898149000111 | epot = -13.6189535337013 | etot = -5.62847191201853 +230000 ekin = 4.65431068144238 | erot = 3.31343017817962 | epot = -13.5962127716248 | etot = -5.62847191200278 +231000 ekin = 4.67934821405078 | erot = 3.27332737526791 | epot = -13.5811475014861 | etot = -5.62847191216744 +232000 ekin = 4.70592354946585 | erot = 3.23944506667347 | epot = -13.5738405284628 | etot = -5.62847191232351 +233000 ekin = 4.73271416122856 | erot = 3.21144788525789 | epot = -13.5726339590472 | etot = -5.62847191256077 +234000 ekin = 4.75943444985412 | erot = 3.19078729233751 | epot = -13.5786936545851 | etot = -5.62847191239346 +235000 ekin = 4.78642241818518 | erot = 3.18021193977121 | epot = -13.595106270404 | etot = -5.62847191244762 +236000 ekin = 4.81315037988696 | erot = 3.18017325335413 | epot = -13.6217955457091 | etot = -5.62847191246801 +237000 ekin = 4.83923297186064 | erot = 3.19145400454097 | epot = -13.6591588888941 | etot = -5.62847191249251 +238000 ekin = 4.86487585932329 | erot = 3.21481908801147 | epot = -13.7081668597499 | etot = -5.62847191241512 +239000 ekin = 4.89063931715455 | erot = 3.25114955282969 | epot = -13.7702607826994 | etot = -5.6284719127152 +240000 ekin = 4.91656145053025 | erot = 3.29901781219886 | epot = -13.8440511755073 | etot = -5.62847191277818 +241000 ekin = 4.94245255089761 | erot = 3.35699698382585 | epot = -13.9279214477277 | etot = -5.62847191300429 +242000 ekin = 4.9676738034646 | erot = 3.42365009426975 | epot = -14.0197958109359 | etot = -5.62847191320155 +243000 ekin = 5.00573446226822 | erot = 3.47030260467981 | epot = -14.104508979209 | etot = -5.62847191226097 +244000 ekin = 5.06987350322707 | erot = 3.50985787352213 | epot = -14.2082032933178 | etot = -5.62847191656865 +245000 ekin = 5.08405115957498 | erot = 3.57323736718823 | epot = -14.2857604930734 | etot = -5.62847196631014 +246000 ekin = 5.13867281569357 | erot = 3.53022410787181 | epot = -14.297368841906 | etot = -5.62847191834066 +247000 ekin = 5.24446071734615 | erot = 3.63707192640274 | epot = -14.5100045566521 | etot = -5.62847191290324 +248000 ekin = 5.23528120841445 | erot = 3.74023330974589 | epot = -14.6039864311697 | etot = -5.62847191300932 +249000 ekin = 5.21260078434817 | erot = 3.837297956608 | epot = -14.6783706538289 | etot = -5.62847191287273 +250000 ekin = 5.17839081249927 | erot = 3.92749000334494 | epot = -14.7343527284516 | etot = -5.62847191260741 +251000 ekin = 5.13586036333573 | erot = 4.01108345358421 | epot = -14.7754157290713 | etot = -5.62847191215138 +252000 ekin = 5.08918292106074 | erot = 4.09018694185419 | epot = -14.8078417745656 | etot = -5.62847191165069 +253000 ekin = 5.04264218495073 | erot = 4.16759058212955 | epot = -14.8387046782889 | etot = -5.62847191120863 +254000 ekin = 4.99116344077593 | erot = 4.24248912288695 | epot = -14.8621245493469 | etot = -5.62847198568401 +255000 ekin = 4.72637462796507 | erot = 4.24407837664817 | epot = -14.5989249325811 | etot = -5.62847192796782 +256000 ekin = 4.59834109997933 | erot = 4.36369782213481 | epot = -14.5905108365242 | etot = -5.62847191441005 +257000 ekin = 4.77089539877043 | erot = 4.60066315318934 | epot = -15.0000305290225 | etot = -5.62847197706276 +258000 ekin = 4.85704242988894 | erot = 4.66807324378547 | epot = -15.1535875814296 | etot = -5.62847190775515 +259000 ekin = 4.89901811471773 | erot = 4.72718635922983 | epot = -15.2546763808734 | etot = -5.62847190692585 +260000 ekin = 4.94107094738753 | erot = 4.79406863687931 | epot = -15.3636114914281 | etot = -5.62847190716125 +261000 ekin = 4.9824230907422 | erot = 4.86508628583352 | epot = -15.475981284638 | etot = -5.62847190806228 +262000 ekin = 5.01659840997744 | erot = 4.93871137850052 | epot = -15.5837816973808 | etot = -5.62847190890283 +263000 ekin = 5.03982661193641 | erot = 5.00983839413939 | epot = -15.6781369155853 | etot = -5.62847190950953 +264000 ekin = 5.0473269634892 | erot = 5.07389667600714 | epot = -15.7496955496047 | etot = -5.62847191010834 +265000 ekin = 5.03448807084051 | erot = 5.12688367714911 | epot = -15.7898436586299 | etot = -5.62847191064033 +266000 ekin = 4.99773438958486 | erot = 5.16480683533175 | epot = -15.791013135968 | etot = -5.62847191105136 +267000 ekin = 4.93508497405026 | erot = 5.18388050751387 | epot = -15.747437392869 | etot = -5.62847191130489 +268000 ekin = 4.84654531469559 | erot = 5.1806346855983 | epot = -15.6556519116799 | etot = -5.62847191138598 +269000 ekin = 4.73423214273252 | erot = 5.1519885973249 | epot = -15.5146926513497 | etot = -5.62847191129228 +270000 ekin = 4.60224202247072 | erot = 5.09540688817256 | epot = -15.3261208188833 | etot = -5.62847190824006 +271000 ekin = 4.45636876653434 | erot = 5.00923317388234 | epot = -15.0940738481856 | etot = -5.62847190776888 +272000 ekin = 4.30375505733966 | erot = 4.89315778303985 | epot = -14.8253847474784 | etot = -5.62847190709885 +273000 ekin = 4.15244061478458 | erot = 4.74862648122846 | epot = -14.5295390022765 | etot = -5.62847190626348 +274000 ekin = 4.01137482333106 | erot = 4.5789667245575 | epot = -14.2188134532047 | etot = -5.62847190531616 +275000 ekin = 3.87388872891049 | erot = 4.3895080579432 | epot = -13.8918687169693 | etot = -5.6284719301156 +276000 ekin = 3.70828148349361 | erot = 4.18975567949233 | epot = -13.5265090654534 | etot = -5.62847190246743 +277000 ekin = 3.74025187939912 | erot = 3.98894405209637 | epot = -13.3576678645567 | etot = -5.62847193306118 +278000 ekin = 3.74221760775116 | erot = 3.77038543691051 | epot = -13.1410749479052 | etot = -5.62847190324349 +279000 ekin = 3.75220115766653 | erot = 3.55790331813957 | epot = -12.9385763794507 | etot = -5.62847190364464 +280000 ekin = 3.77561814014657 | erot = 3.35781654491971 | epot = -12.7619065883777 | etot = -5.62847190331142 +281000 ekin = 3.81272927485115 | erot = 3.17409695195876 | epot = -12.6152981298196 | etot = -5.62847190300969 +282000 ekin = 3.86501988037386 | erot = 3.00952640154724 | epot = -12.503018184212 | etot = -5.62847190229088 +283000 ekin = 3.93628900407809 | erot = 2.8661316818177 | epot = -12.4308925881356 | etot = -5.62847190223979 +284000 ekin = 4.0270270305153 | erot = 2.74480306500081 | epot = -12.4003019979166 | etot = -5.62847190240049 +285000 ekin = 4.14139706641422 | erot = 2.64599110157996 | epot = -12.4158600691845 | etot = -5.62847190119033 +286000 ekin = 4.28525774919445 | erot = 2.56950762489452 | epot = -12.4832372763396 | etot = -5.62847190225059 +287000 ekin = 4.44987555796749 | erot = 2.51493810068656 | epot = -12.5932855609754 | etot = -5.62847190232132 +288000 ekin = 4.63520922265897 | erot = 2.48100112556068 | epot = -12.744682251566 | etot = -5.6284719033463 +289000 ekin = 4.83125797006575 | erot = 2.46527241540077 | epot = -12.9250022897052 | etot = -5.62847190423864 +290000 ekin = 5.02763799220291 | erot = 2.4654243568242 | epot = -13.1215342541163 | etot = -5.62847190508923 +291000 ekin = 5.21465468576449 | erot = 2.47913524145117 | epot = -13.3222618329834 | etot = -5.6284719057677 +292000 ekin = 5.38472348790597 | erot = 2.50416430329569 | epot = -13.5173596974435 | etot = -5.62847190624189 +293000 ekin = 5.5330248706311 | erot = 2.53823701976809 | epot = -13.6997337969643 | etot = -5.62847190656515 +294000 ekin = 5.65718701899536 | erot = 2.57877496353416 | epot = -13.864433889344 | etot = -5.6284719068145 +295000 ekin = 5.75652780496621 | erot = 2.62269919784431 | epot = -14.007698909843 | etot = -5.62847190703252 +296000 ekin = 5.83139499491419 | erot = 2.6665217122924 | epot = -14.1263886144181 | etot = -5.6284719072115 +297000 ekin = 5.88282356332146 | erot = 2.70675614330257 | epot = -14.2180516139381 | etot = -5.62847190731405 +298000 ekin = 5.91239748765179 | erot = 2.74048494300791 | epot = -14.2813543379722 | etot = -5.62847190731251 +299000 ekin = 5.92208198046436 | erot = 2.76585299301949 | epot = -14.3164068806928 | etot = -5.62847190720895 +300000 ekin = 5.91390942018729 | erot = 2.78233336188307 | epot = -14.324714689099 | etot = -5.6284719070286 +301000 ekin = 5.88962133511172 | erot = 2.79074353675468 | epot = -14.3088367786641 | etot = -5.62847190679768 +302000 ekin = 5.8504878142078 | erot = 2.79307875791172 | epot = -14.2720384786454 | etot = -5.6284719065259 +303000 ekin = 5.79743517876747 | erot = 2.79223225552008 | epot = -14.2181393405006 | etot = -5.62847190621301 +304000 ekin = 5.7312434076019 | erot = 2.79262915088754 | epot = -14.1523444641561 | etot = -5.62847190566669 +305000 ekin = 5.65258268469364 | erot = 2.79940899090737 | epot = -14.0804635809857 | etot = -5.62847190538469 +306000 ekin = 5.56254653522508 | erot = 2.81503734234927 | epot = -14.0060557827357 | etot = -5.62847190516136 +307000 ekin = 5.46251129680086 | erot = 2.84075892386076 | epot = -13.9317421256988 | etot = -5.62847190503716 +308000 ekin = 5.35391293499096 | erot = 2.87633235164342 | epot = -13.8587171916696 | etot = -5.62847190503525 +309000 ekin = 5.23805007410738 | erot = 2.91996940723619 | epot = -13.7864913863822 | etot = -5.6284719050386 +310000 ekin = 5.11613875821451 | erot = 2.96880482960497 | epot = -13.7134154931085 | etot = -5.62847190528902 +311000 ekin = 4.98925852658179 | erot = 3.01839769776313 | epot = -13.6361281298157 | etot = -5.62847190547077 +312000 ekin = 4.85867326621007 | erot = 3.06421411594136 | epot = -13.5513592877764 | etot = -5.62847190562498 +313000 ekin = 4.72585112666007 | erot = 3.1023659033067 | epot = -13.4566889356335 | etot = -5.62847190566677 +314000 ekin = 4.59293421044821 | erot = 3.13002199529812 | epot = -13.3514281113063 | etot = -5.62847190555992 +315000 ekin = 4.46270669970081 | erot = 3.14588950388386 | epot = -13.2370681089054 | etot = -5.62847190532072 +316000 ekin = 4.3384545703267 | erot = 3.15016989319031 | epot = -13.1170963685052 | etot = -5.62847190498817 +317000 ekin = 4.22370149065743 | erot = 3.14429402988067 | epot = -12.996467425148 | etot = -5.62847190460986 +318000 ekin = 4.12188681799284 | erot = 3.13056754979034 | epot = -12.8809262720121 | etot = -5.62847190422894 +319000 ekin = 4.03607214170579 | erot = 3.11184182788027 | epot = -12.77638587346 | etot = -5.62847190387392 +320000 ekin = 3.96873641007762 | erot = 3.09128048612704 | epot = -12.6884887997606 | etot = -5.62847190355594 +321000 ekin = 3.92167797368586 | erot = 3.07226107994919 | epot = -12.6224109569088 | etot = -5.62847190327372 +322000 ekin = 3.89600971422213 | erot = 3.05833648375385 | epot = -12.5828181010071 | etot = -5.62847190303107 +323000 ekin = 3.89216326552103 | erot = 3.05323078721206 | epot = -12.5738659555728 | etot = -5.62847190283971 +324000 ekin = 3.90971752721543 | erot = 3.06065920138556 | epot = -12.5988486316037 | etot = -5.62847190300271 +325000 ekin = 3.94474197768388 | erot = 3.08325557843867 | epot = -12.6564694593744 | etot = -5.62847190325185 +326000 ekin = 3.99225791213231 | erot = 3.1213166619738 | epot = -12.7420464778809 | etot = -5.62847190377475 +327000 ekin = 4.04715751820597 | erot = 3.17277573874842 | epot = -12.8484051615311 | etot = -5.6284719045767 +328000 ekin = 4.10306827951536 | erot = 3.23289809102827 | epot = -12.9644382761474 | etot = -5.6284719056038 +329000 ekin = 4.1529407779893 | erot = 3.29460254687961 | epot = -13.0760152315458 | etot = -5.62847190667689 +330000 ekin = 4.19046086380311 | erot = 3.34957314359943 | epot = -13.1685059149075 | etot = -5.628471907505 +331000 ekin = 4.21187936706255 | erot = 3.3898915326679 | epot = -13.2302428077012 | etot = -5.62847190797073 +332000 ekin = 4.21589857654889 | erot = 3.410750943744 | epot = -13.2551214281506 | etot = -5.62847190785773 +333000 ekin = 4.20485266001253 | erot = 3.4117439982385 | epot = -13.2450685654485 | etot = -5.62847190719748 +334000 ekin = 4.18435368277225 | erot = 3.39692225042827 | epot = -13.2097478393621 | etot = -5.62847190616153 +335000 ekin = 4.16205455862581 | erot = 3.37367623592429 | epot = -13.1642026995401 | etot = -5.62847190499001 +336000 ekin = 4.14609491421859 | erot = 3.3509330966453 | epot = -13.1254999147712 | etot = -5.62847190390733 +337000 ekin = 4.14364358932779 | erot = 3.33736964604109 | epot = -13.1094851384434 | etot = -5.62847190307457 +338000 ekin = 4.15982493124777 | erot = 3.33968220641345 | epot = -13.1279790403949 | etot = -5.62847190273368 +339000 ekin = 4.19714166717843 | erot = 3.36120406393393 | epot = -13.1868176337222 | etot = -5.62847190260982 +340000 ekin = 4.2551847438325 | erot = 3.4039445653371 | epot = -13.2876012119721 | etot = -5.62847190280253 +341000 ekin = 4.33079125362424 | erot = 3.46797257817826 | epot = -13.4272357350448 | etot = -5.62847190324226 +342000 ekin = 4.41854745260805 | erot = 3.55173943759857 | epot = -13.598758794057 | etot = -5.62847190385035 +343000 ekin = 4.51153864840457 | erot = 3.65250494550999 | epot = -13.7925154984656 | etot = -5.62847190455105 +344000 ekin = 4.60219231319681 | erot = 3.76671918648665 | epot = -13.997383404942 | etot = -5.62847190525855 +345000 ekin = 4.68312343521548 | erot = 3.89042211425568 | epot = -14.2020174553784 | etot = -5.62847190590722 +346000 ekin = 4.74786790541098 | erot = 4.01955036385073 | epot = -14.3958901757075 | etot = -5.6284719064458 +347000 ekin = 4.79150376887216 | erot = 4.1501952988555 | epot = -14.5701709745265 | etot = -5.62847190679885 +348000 ekin = 4.81117855586204 | erot = 4.27877359765812 | epot = -14.7184240605732 | etot = -5.62847190705307 +349000 ekin = 4.80564918859609 | erot = 4.4020566269382 | epot = -14.8361777227061 | etot = -5.62847190717178 +350000 ekin = 4.7754594532902 | erot = 4.51714564006845 | epot = -14.9210770005556 | etot = -5.62847190719693 +351000 ekin = 4.72262273321685 | erot = 4.62116010890004 | epot = -14.9722547493249 | etot = -5.62847190720796 +352000 ekin = 4.65007958813433 | erot = 4.71078593022506 | epot = -14.989337425643 | etot = -5.62847190728361 +353000 ekin = 4.56109157464307 | erot = 4.78180335585299 | epot = -14.9713668379626 | etot = -5.62847190746653 +354000 ekin = 4.45876151245249 | erot = 4.82895979648526 | epot = -14.9161932166645 | etot = -5.6284719077268 +355000 ekin = 4.34584612944072 | erot = 4.84663553109637 | epot = -14.8209535684655 | etot = -5.62847190792837 +356000 ekin = 4.22495470319457 | erot = 4.83038190909228 | epot = -14.68380852018 | etot = -5.62847190789319 +357000 ekin = 4.09903296593331 | erot = 4.77873075093692 | epot = -14.5062356243563 | etot = -5.6284719074861 +358000 ekin = 3.97178667554692 | erot = 4.69444561049185 | epot = -14.2947041927515 | etot = -5.62847190671276 +359000 ekin = 3.84767298928416 | erot = 4.58431182212931 | epot = -14.0604567171694 | etot = -5.62847190575592 +360000 ekin = 3.73136439807966 | erot = 4.45746613156864 | epot = -13.8173024344097 | etot = -5.62847190476144 +361000 ekin = 3.62758093165255 | erot = 4.32379064504548 | epot = -13.5798434807329 | etot = -5.62847190403486 +362000 ekin = 3.54294892306986 | erot = 4.19358097113779 | epot = -13.3650017978886 | etot = -5.6284719036809 +363000 ekin = 3.47837311692254 | erot = 4.07207692081703 | epot = -13.1789219413003 | etot = -5.62847190356078 +364000 ekin = 3.43225009807465 | erot = 3.96193194141269 | epot = -13.0226539430779 | etot = -5.62847190359055 +365000 ekin = 3.40198388465267 | erot = 3.86460642704947 | epot = -12.8950622153906 | etot = -5.62847190368841 +366000 ekin = 3.38451833854459 | erot = 3.78104622244357 | epot = -12.7940364647728 | etot = -5.62847190378467 +367000 ekin = 3.37682483160575 | erot = 3.7121800085712 | epot = -12.7174767440217 | etot = -5.6284719038448 +368000 ekin = 3.37625204141101 | erot = 3.65912147822589 | epot = -12.6638454234932 | etot = -5.62847190385628 +369000 ekin = 3.38074636729424 | erot = 3.62312680344321 | epot = -12.6323450745658 | etot = -5.62847190382834 +370000 ekin = 3.38894636701411 | erot = 3.60538856637043 | epot = -12.6228068372074 | etot = -5.62847190382282 +371000 ekin = 3.40011634062708 | erot = 3.60672333638067 | epot = -12.6353115807575 | etot = -5.62847190374974 +372000 ekin = 3.41430323565628 | erot = 3.62748920224198 | epot = -12.6702643415996 | etot = -5.62847190370131 +373000 ekin = 3.43217624798381 | erot = 3.66740997409027 | epot = -12.7280581256201 | etot = -5.62847190354598 +374000 ekin = 3.45538314688893 | erot = 3.72532070767081 | epot = -12.8091757581902 | etot = -5.62847190363042 +375000 ekin = 3.48458983106171 | erot = 3.79950576967025 | epot = -12.9125675044908 | etot = -5.62847190375884 +376000 ekin = 3.519946308663 | erot = 3.88772077542516 | epot = -13.0361389880165 | etot = -5.62847190392834 +377000 ekin = 3.56162263242343 | erot = 3.98718032088155 | epot = -13.1772748574015 | etot = -5.62847190409652 +378000 ekin = 3.6100922902232 | erot = 4.09470007582941 | epot = -13.3332642703601 | etot = -5.62847190430747 +379000 ekin = 3.66621939255748 | erot = 4.20668278517705 | epot = -13.5013740821801 | etot = -5.62847190444559 +380000 ekin = 3.73222313439189 | erot = 4.31893025307307 | epot = -13.6796252923471 | etot = -5.62847190488211 +381000 ekin = 3.80656943727892 | erot = 4.42661769096398 | epot = -13.8616590336969 | etot = -5.62847190545403 +382000 ekin = 3.88594558530565 | erot = 4.52459411507408 | epot = -14.0390116064667 | etot = -5.62847190608696 +383000 ekin = 3.96695090004012 | erot = 4.60747433896425 | epot = -14.2028971457321 | etot = -5.62847190672769 +384000 ekin = 4.0461964507197 | erot = 4.66967915258677 | epot = -14.3443475106066 | etot = -5.62847190730011 +385000 ekin = 4.12092029141552 | erot = 4.70599192063093 | epot = -14.4553841197197 | etot = -5.62847190767323 +386000 ekin = 4.18945537166368 | erot = 4.71237691680877 | epot = -14.5303041965821 | etot = -5.62847190810968 +387000 ekin = 4.24770733747877 | erot = 4.68531871642997 | epot = -14.5614979619664 | etot = -5.62847190805767 +388000 ekin = 4.29400518234331 | erot = 4.624330647637 | epot = -14.5468077376945 | etot = -5.62847190771423 +389000 ekin = 4.32973751036583 | erot = 4.53230747813147 | epot = -14.4905168956653 | etot = -5.62847190716798 +390000 ekin = 4.35696496433089 | erot = 4.41432356912958 | epot = -14.3997604400326 | etot = -5.62847190657214 +391000 ekin = 4.37768888460709 | erot = 4.27672754998431 | epot = -14.2828883405318 | etot = -5.62847190594035 +392000 ekin = 4.39398588700049 | erot = 4.12625191222807 | epot = -14.1487097046122 | etot = -5.6284719053836 +393000 ekin = 4.40738241117029 | erot = 3.96936593193603 | epot = -14.0052202479334 | etot = -5.62847190482706 +394000 ekin = 4.41937568154045 | erot = 3.81285278685682 | epot = -13.8607003730639 | etot = -5.62847190466665 +395000 ekin = 4.42988768162593 | erot = 3.66065946574567 | epot = -13.7190190519064 | etot = -5.62847190453479 +396000 ekin = 4.43847476587206 | erot = 3.5152560321435 | epot = -13.582202702411 | etot = -5.62847190439546 +397000 ekin = 4.44517728394754 | erot = 3.37891512777114 | epot = -13.4525643159392 | etot = -5.62847190422053 +398000 ekin = 4.45064950023435 | erot = 3.25392386318359 | epot = -13.3330452674182 | etot = -5.62847190400029 +399000 ekin = 4.45613851374602 | erot = 3.14269651881333 | epot = -13.2273069363619 | etot = -5.62847190380256 +400000 ekin = 4.46297608302819 | erot = 3.04745583065118 | epot = -13.1389038172284 | etot = -5.62847190354901 +401000 ekin = 4.47275545998799 | erot = 2.97053701411079 | epot = -13.0717643774621 | etot = -5.62847190336335 +402000 ekin = 4.4867233669823 | erot = 2.91396522580327 | epot = -13.0291604961298 | etot = -5.62847190334424 +403000 ekin = 4.50482841069757 | erot = 2.87870251809813 | epot = -13.0120028324148 | etot = -5.62847190361907 +404000 ekin = 4.52484325728014 | erot = 2.86379686214802 | epot = -13.0171120236836 | etot = -5.6284719042554 +405000 ekin = 4.54178669950829 | erot = 2.86535120568894 | epot = -13.035609810678 | etot = -5.62847190548074 +406000 ekin = 4.54812186974468 | erot = 2.87565623453592 | epot = -13.052250010881 | etot = -5.62847190660039 +407000 ekin = 4.53567765658788 | erot = 2.88781666333265 | epot = -13.0519662273462 | etot = -5.62847190742564 +408000 ekin = 4.49806839868194 | erot = 2.89717319274415 | epot = -13.0237134990795 | etot = -5.62847190765341 +409000 ekin = 4.4328904182026 | erot = 2.90293173428735 | epot = -12.9642940597694 | etot = -5.62847190727948 +410000 ekin = 4.34222243506053 | erot = 2.90784571762984 | epot = -12.8785400592398 | etot = -5.6284719065494 +411000 ekin = 4.23122328976019 | erot = 2.91632332330227 | epot = -12.7760185188611 | etot = -5.62847190579869 +412000 ekin = 4.10591302463055 | erot = 2.9323426322671 | epot = -12.6667275621366 | etot = -5.62847190523896 +413000 ekin = 3.97147909130296 | erot = 2.9582687533961 | epot = -12.5582197496086 | etot = -5.62847190490952 +414000 ekin = 3.83169645323166 | erot = 2.99487215443308 | epot = -12.4550405124112 | etot = -5.62847190474651 +415000 ekin = 3.68915556881038 | erot = 3.04191716157642 | epot = -12.3595446350554 | etot = -5.62847190466862 +416000 ekin = 3.54575553252049 | erot = 3.09878213618451 | epot = -12.2730095733204 | etot = -5.62847190461537 +417000 ekin = 3.40315271141066 | erot = 3.164842467978 | epot = -12.196467083944 | etot = -5.62847190455536 +418000 ekin = 3.26306253868106 | erot = 3.23960054560962 | epot = -12.1311349887671 | etot = -5.62847190447641 +419000 ekin = 3.12743539440816 | erot = 3.32265867818775 | epot = -12.0785659769723 | etot = -5.62847190437633 +420000 ekin = 2.99854685242666 | erot = 3.41362396353234 | epot = -12.0406427202186 | etot = -5.62847190425955 +421000 ekin = 2.87901712486664 | erot = 3.51197880386987 | epot = -12.0194678328765 | etot = -5.62847190413994 +422000 ekin = 2.77174596046411 | erot = 3.61690112211165 | epot = -12.0171189866207 | etot = -5.62847190404499 +423000 ekin = 2.67973794658802 | erot = 3.72700827493852 | epot = -12.035218125545 | etot = -5.62847190401841 +424000 ekin = 2.60579870922907 | erot = 3.84002717535674 | epot = -12.0742977887019 | etot = -5.62847190411612 +425000 ekin = 2.55208954521947 | erot = 3.95244167900237 | epot = -12.1330031286242 | etot = -5.62847190440239 +426000 ekin = 2.51954653039535 | erot = 4.05920212813651 | epot = -12.2072205634654 | etot = -5.62847190493355 +427000 ekin = 2.5072589388593 | erot = 4.15363681835807 | epot = -12.2893676629362 | etot = -5.62847190571882 +428000 ekin = 2.51210485170757 | erot = 4.22782399619353 | epot = -12.3684007545544 | etot = -5.62847190665333 +429000 ekin = 2.52911833228889 | erot = 4.27377369076429 | epot = -12.4313639305373 | etot = -5.62847190748416 +430000 ekin = 2.55284926696839 | erot = 4.28551618829766 | epot = -12.4668373631587 | etot = -5.62847190789266 +431000 ekin = 2.5792413941596 | erot = 4.26142412038931 | epot = -12.4691374222357 | etot = -5.62847190768682 +432000 ekin = 2.60692475462905 | erot = 4.20541068247442 | epot = -12.4408073440443 | etot = -5.62847190694087 +433000 ekin = 2.63712842978732 | erot = 4.12604912501915 | epot = -12.391649460746 | etot = -5.62847190593952 +434000 ekin = 2.67245542238064 | erot = 4.03405948921703 | epot = -12.3349868165901 | etot = -5.62847190499243 +435000 ekin = 2.71543854637315 | erot = 3.93961255971203 | epot = -12.2835230103731 | etot = -5.62847190428796 +436000 ekin = 2.7676099133887 | erot = 3.85063248523838 | epot = -12.2467143025076 | etot = -5.62847190388056 +437000 ekin = 2.82920515669222 | erot = 3.77223859651331 | epot = -12.229915656936 | etot = -5.62847190373046 +438000 ekin = 2.89929820056594 | erot = 3.70707509976307 | epot = -12.2348452041008 | etot = -5.62847190377184 +439000 ekin = 2.9760933415326 | erot = 3.65590372390477 | epot = -12.2604689693817 | etot = -5.6284719039443 +440000 ekin = 3.05720906610823 | erot = 3.61815200785468 | epot = -12.3038329781675 | etot = -5.62847190420454 +441000 ekin = 3.13989672826847 | erot = 3.59232302401357 | epot = -12.3606916568039 | etot = -5.62847190452184 +442000 ekin = 3.22119927516582 | erot = 3.57626892521649 | epot = -12.4259401052597 | etot = -5.62847190487744 +443000 ekin = 3.29807867299877 | erot = 3.56737972997483 | epot = -12.4939303082247 | etot = -5.62847190525111 +444000 ekin = 3.36753883941706 | erot = 3.56276348928583 | epot = -12.5587742343254 | etot = -5.6284719056225 +445000 ekin = 3.4267604657865 | erot = 3.5594202591977 | epot = -12.6146526309536 | etot = -5.62847190596943 +446000 ekin = 3.4732438364428 | erot = 3.55443462309391 | epot = -12.6561503658096 | etot = -5.6284719062729 +447000 ekin = 3.50497354373429 | erot = 3.54511419619686 | epot = -12.6785596464417 | etot = -5.62847190651056 +448000 ekin = 3.52056213080159 | erot = 3.52974100709658 | epot = -12.6787750444224 | etot = -5.62847190652427 +449000 ekin = 3.51939696587387 | erot = 3.50705904510086 | epot = -12.654927917584 | etot = -5.62847190660929 +450000 ekin = 3.5016453604961 | erot = 3.47565071064701 | epot = -12.6057679777469 | etot = -5.6284719066038 +451000 ekin = 3.46824790703459 | erot = 3.43472151201005 | epot = -12.5314413255503 | etot = -5.62847190650569 +452000 ekin = 3.42090312732073 | erot = 3.38414558727626 | epot = -12.4335206209132 | etot = -5.62847190631618 +453000 ekin = 3.36201791823597 | erot = 3.32449206043664 | epot = -12.314981884713 | etot = -5.62847190604043 +454000 ekin = 3.2946331605557 | erot = 3.2570173981732 | epot = -12.1801224644173 | etot = -5.62847190568836 +455000 ekin = 3.22233274893701 | erot = 3.18360703275134 | epot = -12.034411686962 | etot = -5.62847190527366 +456000 ekin = 3.14914248623648 | erot = 3.1066699219646 | epot = -11.8842843130161 | etot = -5.62847190481507 +457000 ekin = 3.07939737168114 | erot = 3.02894564057018 | epot = -11.7368149165949 | etot = -5.62847190434356 +458000 ekin = 3.01756413263389 | erot = 2.95322108561181 | epot = -11.5992571221015 | etot = -5.62847190385585 +459000 ekin = 2.96810632519469 | erot = 2.88249754734906 | epot = -11.4790757759526 | etot = -5.62847190340889 +460000 ekin = 2.93513888999174 | erot = 2.81955267519756 | epot = -11.3831634682281 | etot = -5.62847190303883 +461000 ekin = 2.92205746385285 | erot = 2.76669234906914 | epot = -11.3172217157053 | etot = -5.62847190278331 +462000 ekin = 2.93114290147914 | erot = 2.72556812594822 | epot = -11.2851829301037 | etot = -5.62847190267634 +463000 ekin = 2.96319319678514 | erot = 2.69703193760489 | epot = -11.2886970371302 | etot = -5.62847190274017 +464000 ekin = 3.01726238567802 | erot = 2.68105615129255 | epot = -11.3267904399496 | etot = -5.62847190297905 +465000 ekin = 3.09058398931814 | erot = 2.67674994758071 | epot = -11.3958058402727 | etot = -5.62847190337382 +466000 ekin = 3.17872270900337 | erot = 2.68248866699199 | epot = -11.4896832798798 | etot = -5.6284719038844 +467000 ekin = 3.27594114496388 | erot = 2.69614045584313 | epot = -11.6005535052654 | etot = -5.62847190445843 +468000 ekin = 3.37571282134116 | erot = 2.71534026238797 | epot = -11.7195249887722 | etot = -5.6284719050431 +469000 ekin = 3.47128178262872 | erot = 2.73774679761809 | epot = -11.8375004858403 | etot = -5.62847190559353 +470000 ekin = 3.55617737698809 | erot = 2.76123628660059 | epot = -11.9458855696663 | etot = -5.62847190607764 +471000 ekin = 3.62463309398908 | erot = 2.7840279000278 | epot = -12.0371329004895 | etot = -5.62847190647262 +472000 ekin = 3.6719055989109 | erot = 2.80477124777919 | epot = -12.1051487534503 | etot = -5.62847190676026 +473000 ekin = 3.69451868438929 | erot = 2.8226311614059 | epot = -12.1456217527189 | etot = -5.62847190692371 +474000 ekin = 3.69045746328685 | erot = 2.83737882568705 | epot = -12.1563081959231 | etot = -5.62847190694923 +475000 ekin = 3.6593211634728 | erot = 2.84946541727549 | epot = -12.137258487577 | etot = -5.62847190682866 +476000 ekin = 3.60242486134417 | erot = 2.86004016499793 | epot = -12.0909369329056 | etot = -5.6284719065635 +477000 ekin = 3.52282746235149 | erot = 2.87088465737282 | epot = -12.0221840258896 | etot = -5.6284719061653 +478000 ekin = 3.42525452624621 | erot = 2.88424967272427 | epot = -11.9379761046398 | etot = -5.62847190566935 +479000 ekin = 3.31588349733366 | erot = 2.90254646899046 | epot = -11.8469018714438 | etot = -5.6284719051197 +480000 ekin = 3.20192949240033 | erot = 2.92801081394181 | epot = -11.7584122109241 | etot = -5.62847190458198 +481000 ekin = 3.09102106834982 | erot = 2.96227510044524 | epot = -11.6817680729323 | etot = -5.62847190413723 +482000 ekin = 2.99039932395874 | erot = 3.00590839373353 | epot = -11.6247796215598 | etot = -5.62847190386749 +483000 ekin = 2.90605693339778 | erot = 3.057998029687 | epot = -11.5925268669243 | etot = -5.62847190383955 +484000 ekin = 2.84200171520451 | erot = 3.11586840868176 | epot = -11.5863420279687 | etot = -5.62847190408239 +485000 ekin = 2.81072036470337 | erot = 3.03665546450253 | epot = -11.4758477217461 | etot = -5.62847189254017 +486000 ekin = 2.99172671803144 | erot = 2.8902858860562 | epot = -11.5104845148187 | etot = -5.6284719107311 +487000 ekin = 3.04661020878249 | erot = 2.8951625715582 | epot = -11.570244685978 | etot = -5.62847190563732 +488000 ekin = 3.02813445458055 | erot = 2.91755814176744 | epot = -11.5741645018864 | etot = -5.62847190553838 +489000 ekin = 3.02918173187053 | erot = 2.94703274344757 | epot = -11.6046863809234 | etot = -5.62847190560528 +490000 ekin = 3.04920929974131 | erot = 2.98299921442212 | epot = -11.6606804199871 | etot = -5.62847190582362 +491000 ekin = 3.08564623422607 | erot = 3.02458607706386 | epot = -11.738704217412 | etot = -5.6284719061221 +492000 ekin = 3.1342665021678 | erot = 3.07113014043047 | epot = -11.8338685490392 | etot = -5.62847190644092 +493000 ekin = 3.19024782358984 | erot = 3.1224673638186 | epot = -11.9411870940572 | etot = -5.62847190664872 +494000 ekin = 3.24418110409375 | erot = 3.17757093534113 | epot = -12.0502240479546 | etot = -5.62847200851974 +495000 ekin = 3.12930691892923 | erot = 3.12025770016925 | epot = -11.8780365339305 | etot = -5.62847191483198 +496000 ekin = 3.38154400840661 | erot = 3.12702216687179 | epot = -12.1370381394914 | etot = -5.62847196421296 +497000 ekin = 3.53796334308702 | erot = 3.21345240190075 | epot = -12.3798876662285 | etot = -5.62847192124069 +498000 ekin = 3.54725242248558 | erot = 3.31274815699891 | epot = -12.4884725007429 | etot = -5.62847192125837 +499000 ekin = 3.54686752395165 | erot = 3.42936350676291 | epot = -12.6047029520642 | etot = -5.62847192134968 +500000 ekin = 3.53611629145284 | erot = 3.56214471853519 | epot = -12.7267329315047 | etot = -5.62847192151662 +501000 ekin = 3.51474019583872 | erot = 3.70831240067005 | epot = -12.8515245182709 | etot = -5.62847192176214 +502000 ekin = 3.48291543615718 | erot = 3.8635159786248 | epot = -12.9749033367771 | etot = -5.62847192199511 +503000 ekin = 3.44167367982098 | erot = 4.02200657199432 | epot = -13.0921521741673 | etot = -5.62847192235205 +504000 ekin = 3.39166561935164 | erot = 4.17733332046514 | epot = -13.1974708625621 | etot = -5.62847192274537 +505000 ekin = 3.33344269447494 | erot = 4.32266370131248 | epot = -13.2845783189239 | etot = -5.62847192313651 +506000 ekin = 3.26726906275998 | erot = 4.45157764167683 | epot = -13.3473186278406 | etot = -5.62847192340378 +507000 ekin = 3.19388361646075 | erot = 4.55898983233121 | epot = -13.3813453722816 | etot = -5.62847192348966 +508000 ekin = 3.11462724045838 | erot = 4.64207406475665 | epot = -13.385173228554 | etot = -5.62847192333901 +509000 ekin = 3.03154551887422 | erot = 4.70083202647248 | epot = -13.360849468307 | etot = -5.6284719229603 +510000 ekin = 2.94513058609306 | erot = 4.73730594225058 | epot = -13.3109084508342 | etot = -5.62847192249056 +511000 ekin = 2.85640718492639 | erot = 4.75516581384965 | epot = -13.2400449207019 | etot = -5.62847192192582 +512000 ekin = 2.76854482523754 | erot = 4.75962991524841 | epot = -13.1566466618552 | etot = -5.62847192136923 +513000 ekin = 2.68465921482265 | erot = 4.75599513194798 | epot = -13.0691262676736 | etot = -5.62847192090298 +514000 ekin = 2.60745568313821 | erot = 4.74870168659019 | epot = -12.984629290316 | etot = -5.62847192058764 +515000 ekin = 2.53899080264135 | erot = 4.74082869236398 | epot = -12.9082914154155 | etot = -5.62847192041015 +516000 ekin = 2.48057862897191 | erot = 4.73416754059327 | epot = -12.8432180899264 | etot = -5.62847192036126 +517000 ekin = 2.43281299021006 | erot = 4.72933651066864 | epot = -12.7906214212866 | etot = -5.62847192040792 +518000 ekin = 2.39567246201647 | erot = 4.72611868187727 | epot = -12.7502630644033 | etot = -5.62847192050952 +519000 ekin = 2.36868008078425 | erot = 4.72386163450201 | epot = -12.7210136359116 | etot = -5.62847192062535 +520000 ekin = 2.351090680328 | erot = 4.72186744267955 | epot = -12.7014300437272 | etot = -5.62847192071969 +521000 ekin = 2.34207426125026 | erot = 4.71970227690684 | epot = -12.6902484589283 | etot = -5.62847192077116 +522000 ekin = 2.34085858397537 | erot = 4.71735113717328 | epot = -12.6866816419269 | etot = -5.62847192077827 +523000 ekin = 2.34541603966011 | erot = 4.65571671246147 | epot = -12.6296046826087 | etot = -5.62847193048713 +524000 ekin = 2.39460269545043 | erot = 4.54409239654082 | epot = -12.5671670122753 | etot = -5.62847192028407 +525000 ekin = 2.51755565356127 | erot = 4.49060445310787 | epot = -12.6366320323991 | etot = -5.62847192572995 +526000 ekin = 2.63891940342127 | erot = 4.49670026119053 | epot = -12.7640916024026 | etot = -5.62847193779077 +527000 ekin = 2.68130557076811 | erot = 4.5050333736858 | epot = -12.8148108745534 | etot = -5.62847193009947 +528000 ekin = 2.71450795008385 | erot = 4.51098798623258 | epot = -12.8539678665158 | etot = -5.62847193019934 +529000 ekin = 2.74727192391268 | erot = 4.51402301137498 | epot = -12.889766865557 | etot = -5.62847193026936 +530000 ekin = 2.77952118310714 | erot = 4.51256666248204 | epot = -12.9205597758847 | etot = -5.62847193029555 +531000 ekin = 2.81130699774894 | erot = 4.50555264763214 | epot = -12.9453315756554 | etot = -5.62847193027431 +532000 ekin = 2.84274553222903 | erot = 4.49253106977664 | epot = -12.9637485322199 | etot = -5.62847193021427 +533000 ekin = 2.87393313764405 | erot = 4.47361780231794 | epot = -12.9760228700973 | etot = -5.62847193013535 +534000 ekin = 2.90486933801811 | erot = 4.4492884461532 | epot = -12.9826297142323 | etot = -5.62847193006102 +535000 ekin = 2.9354151985895 | erot = 4.42010482065 | epot = -12.9839919492465 | etot = -5.62847193000696 +536000 ekin = 2.96529830141012 | erot = 4.38649798396423 | epot = -12.980268215352 | etot = -5.62847192997765 +537000 ekin = 2.99415467144036 | erot = 4.34867665838155 | epot = -12.9713032597798 | etot = -5.62847192995786 +538000 ekin = 3.02158801642316 | erot = 4.30669342612465 | epot = -12.9567533725053 | etot = -5.62847192995749 +539000 ekin = 3.04722844366539 | erot = 4.26048951908749 | epot = -12.9361898927062 | etot = -5.62847192995329 +540000 ekin = 3.07077963637244 | erot = 4.21000980483243 | epot = -12.9092613711412 | etot = -5.62847192993634 +541000 ekin = 3.09204730610561 | erot = 4.15535061590596 | epot = -12.8758698519132 | etot = -5.62847192990163 +542000 ekin = 3.11094831327871 | erot = 4.0968267184393 | epot = -12.8362469615667 | etot = -5.62847192984872 +543000 ekin = 3.12750284877782 | erot = 4.0349938313643 | epot = -12.7909686099225 | etot = -5.62847192978037 +544000 ekin = 3.14181233913617 | erot = 3.97062692625898 | epot = -12.7409111951006 | etot = -5.62847192970544 +545000 ekin = 3.15402369274461 | erot = 3.90462208421789 | epot = -12.6871177065949 | etot = -5.62847192963236 +546000 ekin = 3.16427777374247 | erot = 3.83809465732085 | epot = -12.6308443606275 | etot = -5.62847192956418 +547000 ekin = 3.17263245312541 | erot = 3.77248542241658 | epot = -12.5735898050789 | etot = -5.62847192953695 +548000 ekin = 3.1790511412543 | erot = 3.70842416479202 | epot = -12.5159472355905 | etot = -5.62847192954419 +549000 ekin = 3.18335924850198 | erot = 3.64619443426463 | epot = -12.4580256123109 | etot = -5.62847192954424 +550000 ekin = 3.18506506657657 | erot = 3.58603484431588 | epot = -12.3995718405506 | etot = -5.62847192965811 +551000 ekin = 3.18354118863699 | erot = 3.52751972617015 | epot = -12.339532844604 | etot = -5.62847192979682 +552000 ekin = 3.17814056097155 | erot = 3.46973317231156 | epot = -12.2763456632213 | etot = -5.62847192993822 +553000 ekin = 3.16816249044583 | erot = 3.41187716295382 | epot = -12.208511583449 | etot = -5.62847193004933 +554000 ekin = 3.1529746405247 | erot = 3.35363386894367 | epot = -12.1350804395611 | etot = -5.62847193009276 +555000 ekin = 3.13218065537644 | erot = 3.2955493159329 | epot = -12.0562019013434 | etot = -5.6284719300341 +556000 ekin = 3.10581995737785 | erot = 3.23932890456271 | epot = -11.9736207917914 | etot = -5.62847192985081 +557000 ekin = 3.07457883891359 | erot = 3.18795403309369 | epot = -11.8910048015426 | etot = -5.62847192953529 +558000 ekin = 3.03998262646176 | erot = 3.14553707337718 | epot = -11.8139916289527 | etot = -5.62847192911379 +559000 ekin = 3.0045037897678 | erot = 3.11693712838727 | epot = -11.749912846741 | etot = -5.62847192858597 +560000 ekin = 2.97145203613503 | erot = 3.1075818198801 | epot = -11.7075057840427 | etot = -5.62847192802759 +561000 ekin = 2.94451934091812 | erot = 3.12267269755829 | epot = -11.6956639660457 | etot = -5.62847192756929 +562000 ekin = 2.92714140946132 | erot = 3.16633554924112 | epot = -11.7219488859557 | etot = -5.62847192725328 +563000 ekin = 2.92206147613056 | erot = 3.24077054355409 | epot = -11.7913039468894 | etot = -5.6284719272047 +564000 ekin = 2.93031627640334 | erot = 3.34563410956691 | epot = -11.9044223134757 | etot = -5.62847192750548 +565000 ekin = 2.95068712275629 | erot = 3.47751232963896 | epot = -12.0566713805547 | etot = -5.62847192815944 +566000 ekin = 2.97962685503355 | erot = 3.62985521357708 | epot = -12.2379539977413 | etot = -5.62847192913063 +567000 ekin = 3.0117159355677 | erot = 3.7932447734004 | epot = -12.433432639289 | etot = -5.62847193032094 +568000 ekin = 3.04054477428489 | erot = 3.95610049176935 | epot = -12.6251171976474 | etot = -5.62847193159311 +569000 ekin = 3.05981811060729 | erot = 4.10576505740202 | epot = -12.7940551007975 | etot = -5.62847193278818 +570000 ekin = 3.06446758280182 | erot = 4.2298722071793 | epot = -12.9228117237277 | etot = -5.62847193374654 +571000 ekin = 3.05159191024699 | erot = 4.31782950116782 | epot = -12.997893345746 | etot = -5.62847193433116 +572000 ekin = 3.02108996824198 | erot = 4.36217384053392 | epot = -13.0117357432293 | etot = -5.62847193445341 +573000 ekin = 2.97589592632213 | erot = 4.35953364459578 | epot = -12.9639015050098 | etot = -5.62847193409191 +574000 ekin = 2.92177260934326 | erot = 4.31098813660637 | epot = -12.8612326792533 | etot = -5.62847193330371 +575000 ekin = 2.86675845133009 | erot = 4.22206447616752 | epot = -12.7172948575409 | etot = -5.62847193004325 +576000 ekin = 2.82238695031475 | erot = 4.11002108712494 | epot = -12.560879966962 | etot = -5.62847192952236 +577000 ekin = 2.79586021275311 | erot = 3.98405314245172 | epot = -12.4083852842971 | etot = -5.62847192909222 +578000 ekin = 2.79062678636397 | erot = 3.84816173910418 | epot = -12.2672604543212 | etot = -5.62847192885309 +579000 ekin = 2.80727876752649 | erot = 3.70630768407174 | epot = -12.1420583804352 | etot = -5.62847192883696 +580000 ekin = 2.84308800272595 | erot = 3.56147502231061 | epot = -12.0330349543403 | etot = -5.62847192930378 +581000 ekin = 2.89275945157798 | erot = 3.41677708044794 | epot = -11.9380084614041 | etot = -5.62847192937814 +582000 ekin = 2.94948274088248 | erot = 3.27852635636522 | epot = -11.8564810266952 | etot = -5.62847192944751 +583000 ekin = 3.00600312771789 | erot = 3.15339507871819 | epot = -11.7878701358669 | etot = -5.62847192943084 +584000 ekin = 3.05615870295294 | erot = 3.04800743036932 | epot = -11.7326380626285 | etot = -5.62847192930623 +585000 ekin = 3.09596263902806 | erot = 2.96828908155645 | epot = -11.6927236496809 | etot = -5.62847192909636 +586000 ekin = 3.12407298195256 | erot = 2.91878541591358 | epot = -11.6713303266982 | etot = -5.62847192883209 +587000 ekin = 3.1417461421833 | erot = 2.90225430094311 | epot = -11.672472371669 | etot = -5.62847192854258 +588000 ekin = 3.15240031620553 | erot = 2.91960613642982 | epot = -11.7004783809018 | etot = -5.62847192826648 +589000 ekin = 3.16081808255434 | erot = 2.97006448172946 | epot = -11.7593544923294 | etot = -5.62847192804564 +590000 ekin = 3.17204827383965 | erot = 3.05134069925084 | epot = -11.8518609010118 | etot = -5.6284719279213 +591000 ekin = 3.19150299837461 | erot = 3.16015018729065 | epot = -11.9801251136635 | etot = -5.62847192799819 +592000 ekin = 3.22264872300333 | erot = 3.29204057512014 | epot = -12.1431612264465 | etot = -5.62847192832309 +593000 ekin = 3.26585695460439 | erot = 3.44092346933461 | epot = -12.3352523528035 | etot = -5.62847192886452 +594000 ekin = 3.31918005191763 | erot = 3.59965335596714 | epot = -12.5473053374549 | etot = -5.62847192957014 +595000 ekin = 3.37897127078336 | erot = 3.76045843937389 | epot = -12.7679016404524 | etot = -5.62847193029511 +596000 ekin = 3.4382406857396 | erot = 3.91359738321914 | epot = -12.980310001589 | etot = -5.62847193263027 +597000 ekin = 3.48744876793451 | erot = 4.0478243785771 | epot = -13.1637450797755 | etot = -5.62847193326394 +598000 ekin = 3.52187002165693 | erot = 4.15698580423063 | epot = -13.3073277595056 | etot = -5.62847193361804 +599000 ekin = 3.53831455068156 | erot = 4.23767846708786 | epot = -13.4044649514591 | etot = -5.6284719336897 +600000 ekin = 3.53510970426307 | erot = 4.28920847102939 | epot = -13.4527901088142 | etot = -5.62847193352171 +601000 ekin = 3.51191041814396 | erot = 4.31320178192835 | epot = -13.453584133256 | etot = -5.62847193318372 +602000 ekin = 3.46937521143132 | erot = 4.3129515273753 | epot = -13.410798671557 | etot = -5.6284719327504 +603000 ekin = 3.40882221238478 | erot = 4.29270411926118 | epot = -13.3299982639291 | etot = -5.62847193228318 +604000 ekin = 3.33194570979922 | erot = 4.2570524586158 | epot = -13.2174701002375 | etot = -5.62847193182252 +605000 ekin = 3.2406264378616 | erot = 4.21052248035532 | epot = -13.0796208496054 | etot = -5.62847193138844 +606000 ekin = 3.13683319325246 | erot = 4.15735875793748 | epot = -12.9226638821749 | etot = -5.62847193098499 +607000 ekin = 3.02259481110418 | erot = 4.1014670377034 | epot = -12.7525337794138 | etot = -5.62847193060621 +608000 ekin = 2.90001652262392 | erot = 4.04645475154674 | epot = -12.5749432044128 | etot = -5.62847193024212 +609000 ekin = 2.77131728811454 | erot = 3.99571460779313 | epot = -12.3955038257901 | etot = -5.62847192988241 +610000 ekin = 2.63886938894673 | erot = 3.95250622989986 | epot = -12.219847548367 | etot = -5.62847192952046 +611000 ekin = 2.50524882255296 | erot = 3.92003293777274 | epot = -12.0537536891925 | etot = -5.6284719288668 +612000 ekin = 2.37382087286659 | erot = 3.9021886985327 | epot = -11.9044814999374 | etot = -5.62847192853806 +613000 ekin = 2.24769613368194 | erot = 3.9018678874881 | epot = -11.7780359493991 | etot = -5.62847192822908 +614000 ekin = 2.12975142867636 | erot = 3.92103062113487 | epot = -11.6792539777934 | etot = -5.62847192798222 +615000 ekin = 2.02283676467958 | erot = 3.96080056826795 | epot = -11.61210926078 | etot = -5.62847192783249 +616000 ekin = 1.92967019046992 | erot = 4.02099162181975 | epot = -11.5791337401025 | etot = -5.62847192781281 +617000 ekin = 1.85273791860752 | erot = 4.09974474402214 | epot = -11.5809545905817 | etot = -5.62847192795206 +618000 ekin = 1.794202962929 | erot = 4.1932270362042 | epot = -11.615901927397 | etot = -5.62847192826377 +619000 ekin = 1.75583197424594 | erot = 4.29552606645212 | epot = -11.6798299694312 | etot = -5.62847192873316 +620000 ekin = 1.73895870093018 | erot = 4.39891672374147 | epot = -11.7663473539779 | etot = -5.62847192930629 +621000 ekin = 1.7444983470959 | erot = 4.49462250667638 | epot = -11.867592783664 | etot = -5.62847192989172 +622000 ekin = 1.7730087572002 | erot = 4.57403518097385 | epot = -11.9755158685574 | etot = -5.62847193038335 +623000 ekin = 1.82476626658183 | erot = 4.63011744405485 | epot = -12.0833556413331 | etot = -5.62847193069639 +624000 ekin = 1.89980556087252 | erot = 4.65854151408734 | epot = -12.1868190057596 | etot = -5.62847193079971 +625000 ekin = 1.99788930997527 | erot = 4.65817060180771 | epot = -12.284531842505 | etot = -5.62847193072199 +626000 ekin = 2.11841938996492 | erot = 4.63077870107517 | epot = -12.3776700215701 | etot = -5.62847193053003 +627000 ekin = 2.26034340487478 | erot = 4.58024268413209 | epot = -12.4690580193001 | etot = -5.62847193029324 +628000 ekin = 2.42211143968505 | erot = 4.51161612070374 | epot = -12.5621994904549 | etot = -5.62847193006612 +629000 ekin = 2.60047669397099 | erot = 4.43316974525301 | epot = -12.6621183686296 | etot = -5.62847192940563 +630000 ekin = 2.75035748976938 | erot = 4.3100390575377 | epot = -12.6888685130155 | etot = -5.62847196570841 +631000 ekin = 2.81471524115763 | erot = 4.11774535995794 | epot = -12.5609325368805 | etot = -5.62847193576491 +632000 ekin = 2.95867552203419 | erot = 4.07926707228417 | epot = -12.6664145271904 | etot = -5.628471932872 +633000 ekin = 3.21010693586428 | erot = 4.2058132684618 | epot = -13.0443921664052 | etot = -5.62847196207909 +634000 ekin = 3.41641131483616 | erot = 4.25928215940961 | epot = -13.3041654106185 | etot = -5.62847193637274 +635000 ekin = 3.57385274060691 | erot = 4.24018711613006 | epot = -13.44251179388 | etot = -5.62847193714308 +636000 ekin = 3.71894531180235 | erot = 4.21896102715994 | epot = -13.5663782769414 | etot = -5.62847193797916 +637000 ekin = 3.84555962838986 | erot = 4.1900953900669 | epot = -13.6641269571315 | etot = -5.62847193867471 +638000 ekin = 3.94874232718941 | erot = 4.14881281942018 | epot = -13.7260270856532 | etot = -5.62847193904357 +639000 ekin = 4.02564653200494 | erot = 4.09271382137468 | epot = -13.7468322923892 | etot = -5.62847193900963 +640000 ekin = 4.07582551370951 | erot = 4.02260436138313 | epot = -13.7269018137147 | etot = -5.62847193862206 +641000 ekin = 4.10019063770968 | erot = 3.9420341958717 | epot = -13.6706967720501 | etot = -5.62847193846869 +642000 ekin = 4.09923586001873 | erot = 3.85569636532128 | epot = -13.5834041632297 | etot = -5.62847193788973 +643000 ekin = 4.07616079987132 | erot = 3.76850329654985 | epot = -13.4731360337866 | etot = -5.62847193736548 +644000 ekin = 4.03483546313061 | erot = 3.68428538432172 | epot = -13.3475927844035 | etot = -5.62847193695118 +645000 ekin = 3.97939693540902 | erot = 3.60521279265152 | epot = -13.2130816646903 | etot = -5.62847193662975 +646000 ekin = 3.91424157399056 | erot = 3.53197746531507 | epot = -13.0746909756527 | etot = -5.62847193634712 +647000 ekin = 3.84412108358683 | erot = 3.46430751188328 | epot = -12.9369005316585 | etot = -5.62847193618836 +648000 ekin = 3.77442093453599 | erot = 3.40030625109366 | epot = -12.8031991215005 | etot = -5.62847193587081 +649000 ekin = 3.71064844405663 | erot = 3.33902116868532 | epot = -12.6781415482909 | etot = -5.62847193554899 +650000 ekin = 3.65777288964813 | erot = 3.28036981765667 | epot = -12.5666146425814 | etot = -5.62847193527658 +651000 ekin = 3.61962254754419 | erot = 3.22458240436025 | epot = -12.4726768870043 | etot = -5.6284719350999 +652000 ekin = 3.59838866982073 | erot = 3.17201593042627 | epot = -12.3988765352844 | etot = -5.62847193503738 +653000 ekin = 3.59447660059077 | erot = 3.12302902484626 | epot = -12.3459775605094 | etot = -5.62847193507238 +654000 ekin = 3.60674141919119 | erot = 3.07797678365128 | epot = -12.3131901380073 | etot = -5.62847193516482 +655000 ekin = 3.6329884130958 | erot = 3.03728497071295 | epot = -12.2987453190845 | etot = -5.62847193527574 +656000 ekin = 3.67052655524344 | erot = 3.00147990290593 | epot = -12.3004783935418 | etot = -5.62847193539242 +657000 ekin = 3.71734630696999 | erot = 2.97084073542309 | epot = -12.3166589777923 | etot = -5.6284719353992 +658000 ekin = 3.75778663136606 | erot = 2.94872940841724 | epot = -12.3349879985774 | etot = -5.62847195879406 +659000 ekin = 3.70128994133686 | erot = 2.99267200660902 | epot = -12.322433883679 | etot = -5.62847193573312 +660000 ekin = 3.77980484666389 | erot = 3.05081678588696 | epot = -12.459093596632 | etot = -5.62847196408119 +661000 ekin = 3.87674047113916 | erot = 3.02043722437581 | epot = -12.5256496408831 | etot = -5.62847194536809 +662000 ekin = 3.96189665293746 | erot = 2.9729451065493 | epot = -12.5633137057978 | etot = -5.62847194631105 +663000 ekin = 4.03233992104381 | erot = 2.90724728968081 | epot = -12.5680591570602 | etot = -5.62847194633553 +664000 ekin = 4.08703350769439 | erot = 2.82371074134662 | epot = -12.5392161948574 | etot = -5.62847194581638 +665000 ekin = 4.13016908264132 | erot = 2.72591755779726 | epot = -12.4845585854975 | etot = -5.62847194505895 +666000 ekin = 4.1648576368289 | erot = 2.62158318082323 | epot = -12.414912761733 | etot = -5.62847194408083 +667000 ekin = 4.19388444222523 | erot = 2.52048046577159 | epot = -12.3428368513194 | etot = -5.62847194332254 +668000 ekin = 4.21970111352808 | erot = 2.43117566558869 | epot = -12.2793487218878 | etot = -5.62847194277106 +669000 ekin = 4.24419480049408 | erot = 2.35970998773563 | epot = -12.2323767306416 | etot = -5.62847194241189 +670000 ekin = 4.26650932826211 | erot = 2.31009212997052 | epot = -12.2050734005156 | etot = -5.62847194228301 +671000 ekin = 4.28028750565683 | erot = 2.28394068968216 | epot = -12.1927001375696 | etot = -5.62847194223062 +672000 ekin = 4.28604953799413 | erot = 2.28087700961919 | epot = -12.195398489808 | etot = -5.62847194219469 +673000 ekin = 4.28538320965501 | erot = 2.29981058129386 | epot = -12.2136657330995 | etot = -5.62847194215067 +674000 ekin = 4.28032637869879 | erot = 2.33931520008498 | epot = -12.2481135208938 | etot = -5.62847194211004 +675000 ekin = 4.27310613126655 | erot = 2.39770546347679 | epot = -12.299283536864 | etot = -5.62847194212067 +676000 ekin = 4.26563141826313 | erot = 2.47283047868407 | epot = -12.3669338392281 | etot = -5.62847194228089 +677000 ekin = 4.25873601006311 | erot = 2.56159475148419 | epot = -12.4488027041865 | etot = -5.62847194263915 +678000 ekin = 4.25154383389769 | erot = 2.65951246674432 | epot = -12.5395282438879 | etot = -5.62847194324589 +679000 ekin = 4.24120573445568 | erot = 2.76057514762954 | epot = -12.630252826131 | etot = -5.62847194404578 +680000 ekin = 4.2232005116225 | erot = 2.85770689117101 | epot = -12.7093793476694 | etot = -5.62847194487586 +681000 ekin = 4.19242845434314 | erot = 2.94400272560173 | epot = -12.7649031254502 | etot = -5.62847194550537 +682000 ekin = 4.14477706321235 | erot = 3.01435956400889 | epot = -12.7876085729734 | etot = -5.62847194575211 +683000 ekin = 4.07850194563539 | erot = 3.06669689322157 | epot = -12.7736707844239 | etot = -5.62847194556698 +684000 ekin = 3.98766788563961 | erot = 3.0906277066639 | epot = -12.7067675426958 | etot = -5.62847195039226 +685000 ekin = 3.87609976013985 | erot = 3.07213118871214 | epot = -12.5767028925343 | etot = -5.62847194368236 +686000 ekin = 3.78865422776275 | erot = 3.05379982547376 | epot = -12.4709259955926 | etot = -5.62847194235608 +687000 ekin = 3.72885638105159 | erot = 3.05128310414022 | epot = -12.4086114324289 | etot = -5.62847194723706 +688000 ekin = 3.65488085441971 | erot = 3.04382149778312 | epot = -12.327174298549 | etot = -5.62847194634615 +689000 ekin = 3.57606770123459 | erot = 3.0383425251152 | epot = -12.2428821719897 | etot = -5.6284719456399 +690000 ekin = 3.51634425539962 | erot = 3.04775260801092 | epot = -12.1925688085377 | etot = -5.62847194512715 +691000 ekin = 3.47971445724813 | erot = 3.07622358482834 | epot = -12.1844099869499 | etot = -5.62847194487341 +692000 ekin = 3.46765181239654 | erot = 3.12642449720365 | epot = -12.2225482545402 | etot = -5.62847194494003 +693000 ekin = 3.47854301535925 | erot = 3.19918358101293 | epot = -12.3061985417131 | etot = -5.6284719453409 +694000 ekin = 3.50760869782508 | erot = 3.29340441047875 | epot = -12.4294850543218 | etot = -5.628471946018 +695000 ekin = 3.54747029144369 | erot = 3.40637947907432 | epot = -12.5823217173717 | etot = -5.62847194685366 +696000 ekin = 3.58927155144407 | erot = 3.53441505488866 | epot = -12.7521585540429 | etot = -5.62847194771015 +697000 ekin = 3.62399868501821 | erot = 3.67347767301132 | epot = -12.9259483064947 | etot = -5.6284719484652 +698000 ekin = 3.64429609735003 | erot = 3.81929275596897 | epot = -13.0920608024297 | etot = -5.62847194911072 +699000 ekin = 3.64411727630314 | erot = 3.96826912294918 | epot = -13.2408583487786 | etot = -5.62847194952627 +700000 ekin = 3.61972386457296 | erot = 4.11779628925705 | epot = -13.3659921035235 | etot = -5.62847194969347 +701000 ekin = 3.57045543113338 | erot = 4.26605645138673 | epot = -13.4649838322621 | etot = -5.62847194974201 +702000 ekin = 3.49917622932028 | erot = 4.41037029517899 | epot = -13.5380184741164 | etot = -5.62847194961714 +703000 ekin = 3.4107997813188 | erot = 4.54773448502706 | epot = -13.587006215731 | etot = -5.62847194938518 +704000 ekin = 3.31149657235527 | erot = 4.67560464114877 | epot = -13.6155731625935 | etot = -5.62847194908948 +705000 ekin = 3.20807903028367 | erot = 4.79162132914824 | epot = -13.6281723082198 | etot = -5.62847194878786 +706000 ekin = 3.10702043878188 | erot = 4.89365607530917 | epot = -13.6291484626414 | etot = -5.62847194855037 +707000 ekin = 3.01353531392337 | erot = 4.97967086444126 | epot = -13.6216781268107 | etot = -5.62847194844611 +708000 ekin = 2.93091332927947 | erot = 5.04739802083869 | epot = -13.6067832986402 | etot = -5.62847194852201 +709000 ekin = 2.86026033856888 | erot = 5.09399325420687 | epot = -13.5827255415552 | etot = -5.62847194877949 +710000 ekin = 2.80069789519474 | erot = 5.11589857322537 | epot = -13.5450684175845 | etot = -5.62847194916438 +711000 ekin = 2.74994326387124 | erot = 5.10911210259413 | epot = -13.4875273160395 | etot = -5.62847194957416 +712000 ekin = 2.70509857008142 | erot = 5.06990681786419 | epot = -13.40347733783 | etot = -5.62847194988441 +713000 ekin = 2.66343594225847 | erot = 4.99582282624686 | epot = -13.2877307184944 | etot = -5.62847194998911 +714000 ekin = 2.62297982853256 | erot = 4.88658411870471 | epot = -13.1380358970756 | etot = -5.6284719498383 +715000 ekin = 2.58275404748242 | erot = 4.7445665056767 | epot = -12.9557925026135 | etot = -5.62847194945441 +716000 ekin = 2.54267933970092 | erot = 4.57461726525615 | epot = -12.7457685538738 | etot = -5.62847194891675 +717000 ekin = 2.50334692008347 | erot = 4.38348005515169 | epot = -12.5152989232394 | etot = -5.62847194800429 +718000 ekin = 2.46867182041133 | erot = 4.18280619357873 | epot = -12.2799499617377 | etot = -5.62847194774766 +719000 ekin = 2.44027484653412 | erot = 3.97913844337086 | epot = -12.0478852374019 | etot = -5.62847194749693 +720000 ekin = 2.41790751021186 | erot = 3.77617089355823 | epot = -11.8225503510262 | etot = -5.62847194725612 +721000 ekin = 2.40130900312515 | erot = 3.57751641421023 | epot = -11.6072973643638 | etot = -5.62847194702837 +722000 ekin = 2.39001969431688 | erot = 3.38620933386067 | epot = -11.4047009751991 | etot = -5.62847194702158 +723000 ekin = 2.3828880820675 | erot = 3.20447847638599 | epot = -11.2158385051777 | etot = -5.62847194672426 +724000 ekin = 2.38038137246863 | erot = 3.03585463118768 | epot = -11.0447079501099 | etot = -5.62847194645357 +725000 ekin = 2.38334904373452 | erot = 2.88343528895326 | epot = -10.8952562789009 | etot = -5.62847194621316 +726000 ekin = 2.39277988807573 | erot = 2.74974572538476 | epot = -10.770997559469 | etot = -5.6284719460085 +727000 ekin = 2.40968215732026 | erot = 2.63676770309079 | epot = -10.6749218062566 | etot = -5.62847194584551 +728000 ekin = 2.42515137975779 | erot = 2.5441214789684 | epot = -10.5977448180843 | etot = -5.62847195935808 +729000 ekin = 2.40297855327853 | erot = 2.51475999964849 | epot = -10.5462104923613 | etot = -5.62847193943428 +730000 ekin = 2.46310039280251 | erot = 2.5408883826994 | epot = -10.6324607144842 | etot = -5.62847193898228 +731000 ekin = 2.53308642092932 | erot = 2.54954386945172 | epot = -10.7111022294541 | etot = -5.6284719390731 +732000 ekin = 2.61398262091984 | erot = 2.5802487460378 | epot = -10.8227033062391 | etot = -5.62847193928148 +733000 ekin = 2.70404858447065 | erot = 2.63167940199874 | epot = -10.9641999261199 | etot = -5.62847193965049 +734000 ekin = 2.8005195006875 | erot = 2.70132929844069 | epot = -11.1303207393551 | etot = -5.62847194022687 +735000 ekin = 2.89941283719614 | erot = 2.78510796766437 | epot = -11.3129927459004 | etot = -5.62847194103986 +736000 ekin = 2.99560133060157 | erot = 2.87741009018683 | epot = -11.5014833618896 | etot = -5.62847194110119 +737000 ekin = 3.08481605483121 | erot = 2.97524489361586 | epot = -11.6885328904346 | etot = -5.62847194198753 +738000 ekin = 3.16217862814305 | erot = 3.07317374869036 | epot = -11.8638243196388 | etot = -5.6284719428054 +739000 ekin = 3.2233603721011 | erot = 3.16493875118342 | epot = -12.0167710666374 | etot = -5.62847194335292 +740000 ekin = 3.26585131612077 | erot = 3.24522139621343 | epot = -12.1395446567704 | etot = -5.62847194443622 +741000 ekin = 3.2837538249289 | erot = 3.29991441167503 | epot = -12.2121401810381 | etot = -5.62847194443414 +742000 ekin = 3.27631313133045 | erot = 3.32408611683988 | epot = -12.2288711921161 | etot = -5.6284719439458 +743000 ekin = 3.24737724786071 | erot = 3.32046927244631 | epot = -12.1963184635118 | etot = -5.62847194320475 +744000 ekin = 3.20210603594743 | erot = 3.2940155115945 | epot = -12.124593489965 | etot = -5.62847194242307 +745000 ekin = 3.14567705878359 | erot = 3.250335669825 | epot = -12.0244846703266 | etot = -5.62847194171797 +746000 ekin = 3.08279906261887 | erot = 3.19521988668621 | epot = -11.9064908901754 | etot = -5.62847194087029 +747000 ekin = 3.01768881724062 | erot = 3.13473855296553 | epot = -11.7808993105941 | etot = -5.62847194038797 +748000 ekin = 2.95302867416643 | erot = 3.07321432130338 | epot = -11.6547149354205 | etot = -5.62847193995069 +749000 ekin = 2.89104396118233 | erot = 3.01469856686716 | epot = -11.5342144675854 | etot = -5.62847193953596 +750000 ekin = 2.83379417403106 | erot = 2.96315742639844 | epot = -11.4254235395683 | etot = -5.62847193913884 +751000 ekin = 2.78329891254728 | erot = 2.92241777441717 | epot = -11.3341886257327 | etot = -5.62847193876824 +752000 ekin = 2.74156846290812 | erot = 2.89600799311955 | epot = -11.2660483944698 | etot = -5.6284719384421 +753000 ekin = 2.71056677603929 | erot = 2.88693753444364 | epot = -11.2259762486671 | etot = -5.62847193818419 +754000 ekin = 2.6921250262768 | erot = 2.89743125950373 | epot = -11.2180282238068 | etot = -5.62847193802625 +755000 ekin = 2.68776538332655 | erot = 2.92849871092333 | epot = -11.2447360323289 | etot = -5.62847193807897 +756000 ekin = 2.6984574300686 | erot = 2.97938409365199 | epot = -11.3063134619601 | etot = -5.62847193823949 +757000 ekin = 2.72458496390267 | erot = 3.04788425625457 | epot = -11.4009411587989 | etot = -5.62847193864169 +758000 ekin = 2.76540921261669 | erot = 3.12962823280928 | epot = -11.5235093847483 | etot = -5.6284719393223 +759000 ekin = 2.8186834204767 | erot = 3.21794575388076 | epot = -11.665101114623 | etot = -5.62847194026549 +760000 ekin = 2.88053746467355 | erot = 3.30429272387349 | epot = -11.8133021298986 | etot = -5.62847194135151 +761000 ekin = 2.94600007668104 | erot = 3.37947250531428 | epot = -11.9539445243258 | etot = -5.6284719423305 +762000 ekin = 3.01037281085116 | erot = 3.4356870034939 | epot = -12.0745317572401 | etot = -5.62847194289507 +763000 ekin = 3.07103775543011 | erot = 3.46881600045824 | epot = -12.1683256987372 | etot = -5.62847194284888 +764000 ekin = 3.12866395094601 | erot = 3.47975039663874 | epot = -12.2368862898265 | etot = -5.62847194224175 +765000 ekin = 3.186964331534 | erot = 3.47390232126689 | epot = -12.289338594139 | etot = -5.62847194133806 +766000 ekin = 3.25112146488291 | erot = 3.45917589039751 | epot = -12.3387692957354 | etot = -5.62847194045498 +767000 ekin = 3.32577328245099 | erot = 3.44357055988634 | epot = -12.3978157821634 | etot = -5.62847193982605 +768000 ekin = 3.41341833425398 | erot = 3.43342634914627 | epot = -12.4753166229595 | etot = -5.6284719395593 +769000 ekin = 3.51361597991924 | erot = 3.43258837675694 | epot = -12.5746762963404 | etot = -5.62847193966423 +770000 ekin = 3.62296220648689 | erot = 3.44225950910434 | epot = -12.6936936556792 | etot = -5.62847194008801 +771000 ekin = 3.67754210046274 | erot = 3.42051682780157 | epot = -12.7265308960792 | etot = -5.62847196781485 +772000 ekin = 3.59351734265618 | erot = 3.35849685511311 | epot = -12.5804861313175 | etot = -5.62847193354824 +773000 ekin = 3.58504863491028 | erot = 3.48413941777935 | epot = -12.6976599859675 | etot = -5.62847193327789 +774000 ekin = 3.69556246628016 | erot = 3.75600381412234 | epot = -13.0800382492094 | etot = -5.62847196880686 +775000 ekin = 3.75799647008904 | erot = 3.87395641041514 | epot = -13.2604248530579 | etot = -5.62847197255368 +776000 ekin = 3.76514931022827 | erot = 3.89275295650614 | epot = -13.2863742394607 | etot = -5.62847197272632 +777000 ekin = 3.74852837945355 | erot = 3.88975944446788 | epot = -13.2667597962775 | etot = -5.62847197235611 +778000 ekin = 3.71300754026299 | erot = 3.86527182247719 | epot = -13.2067513343813 | etot = -5.62847197164114 +779000 ekin = 3.66665793078762 | erot = 3.82295167621109 | epot = -13.118081577538 | etot = -5.62847197053928 +780000 ekin = 3.61972773146591 | erot = 3.76957330567891 | epot = -13.0177730064403 | etot = -5.62847196929548 +781000 ekin = 3.58276242526532 | erot = 3.7136827975555 | epot = -12.9249171910297 | etot = -5.62847196820893 +782000 ekin = 3.56434384288602 | erot = 3.66344621693003 | epot = -12.8562620273358 | etot = -5.62847196751975 +783000 ekin = 3.56907083378379 | erot = 3.62459601435148 | epot = -12.8221388155981 | etot = -5.62847196746287 +784000 ekin = 3.59655578173696 | erot = 3.59908724318581 | epot = -12.8241149927414 | etot = -5.62847196781863 +785000 ekin = 3.64263842874967 | erot = 3.58559579725084 | epot = -12.8567061945 | etot = -5.62847196849948 +786000 ekin = 3.7006136355618 | erot = 3.58032714330354 | epot = -12.9094127481587 | etot = -5.62847196929335 +787000 ekin = 3.76290289512677 | erot = 3.57827846521126 | epot = -12.9696533303932 | etot = -5.62847197005519 +788000 ekin = 3.82230691222562 | erot = 3.57432079358343 | epot = -13.0250996764915 | etot = -5.62847197068247 +789000 ekin = 3.87288355975678 | erot = 3.56402750531758 | epot = -13.0653830361885 | etot = -5.62847197111416 +790000 ekin = 3.91054381082331 | erot = 3.54422213347088 | epot = -13.08323791557 | etot = -5.62847197127583 +791000 ekin = 3.93344679953294 | erot = 3.51333982572675 | epot = -13.0752585964514 | etot = -5.62847197119174 +792000 ekin = 3.94193166944081 | erot = 3.47142235471328 | epot = -13.0418259950669 | etot = -5.62847197091279 +793000 ekin = 3.93805337425617 | erot = 3.41982689840428 | epot = -12.986352243173 | etot = -5.62847197051252 +794000 ekin = 3.92496167461381 | erot = 3.36081973476922 | epot = -12.9142533794446 | etot = -5.62847197006157 +795000 ekin = 3.90631843157168 | erot = 3.29713731835807 | epot = -12.8319277195454 | etot = -5.62847196961569 +796000 ekin = 3.88587920046634 | erot = 3.23158100816642 | epot = -12.7459321778441 | etot = -5.62847196921137 +797000 ekin = 3.86724402776889 | erot = 3.16668037667399 | epot = -12.6623963733129 | etot = -5.62847196886996 +798000 ekin = 3.85371944406203 | erot = 3.10446220751623 | epot = -12.5866536201763 | etot = -5.62847196859802 +799000 ekin = 3.84821326076136 | erot = 3.04637406906617 | epot = -12.5230592982213 | etot = -5.62847196839378 +800000 ekin = 3.85308746065549 | erot = 2.99338091171213 | epot = -12.4749403406177 | etot = -5.62847196825011 +801000 ekin = 3.86994742065734 | erot = 2.94620265107237 | epot = -12.4446220398909 | etot = -5.62847196816119 +802000 ekin = 3.8993874350338 | erot = 2.90559564270117 | epot = -12.4334550458614 | etot = -5.62847196812642 +803000 ekin = 3.9407745193352 | erot = 2.87255363216513 | epot = -12.4418001196493 | etot = -5.62847196814892 +804000 ekin = 3.99217445498752 | erot = 2.84833794209498 | epot = -12.4689843653142 | etot = -5.62847196823168 +805000 ekin = 4.05048828988904 | erot = 2.83432176511747 | epot = -12.5132820233799 | etot = -5.6284719683734 +806000 ekin = 4.11178329721603 | erot = 2.83170980398372 | epot = -12.5719650697689 | etot = -5.62847196856918 +807000 ekin = 4.17172086370491 | erot = 2.8412231850695 | epot = -12.6414160175871 | etot = -5.6284719688127 +808000 ekin = 4.22595471204195 | erot = 2.86283161337761 | epot = -12.7172582945189 | etot = -5.62847196909934 +809000 ekin = 4.27041103453903 | erot = 2.89559061471501 | epot = -12.7944736186782 | etot = -5.62847196942413 +810000 ekin = 4.30143579156689 | erot = 2.93761851750008 | epot = -12.8675262788428 | etot = -5.62847196977579 +811000 ekin = 4.31585912492563 | erot = 2.98622782467629 | epot = -12.9305589197353 | etot = -5.62847197013339 +812000 ekin = 4.31104963135019 | erot = 3.03819974824636 | epot = -12.9777213500609 | etot = -5.62847197046432 +813000 ekin = 4.28501152855523 | erot = 3.09015837165568 | epot = -13.0036418709409 | etot = -5.62847197072996 +814000 ekin = 4.23653530246598 | erot = 3.13897206813755 | epot = -13.0039793414967 | etot = -5.62847197089316 +815000 ekin = 4.1653704274989 | erot = 3.1820977391918 | epot = -12.975940137619 | etot = -5.62847197092834 +816000 ekin = 4.07236517441846 | erot = 3.21779646481347 | epot = -12.9186336100596 | etot = -5.62847197082768 +817000 ekin = 3.95951977389787 | erot = 3.24518380320904 | epot = -12.8331755477101 | etot = -5.62847197060317 +818000 ekin = 3.82991762626086 | erot = 3.26412066918763 | epot = -12.7225102657349 | etot = -5.62847197028639 +819000 ekin = 3.68753356638624 | erot = 3.27498902938163 | epot = -12.5909945656778 | etot = -5.62847196990993 +820000 ekin = 3.53699106705929 | erot = 3.278421491097 | epot = -12.4438845276731 | etot = -5.62847196951684 +821000 ekin = 3.38323613774945 | erot = 3.27505502174732 | epot = -12.2867631286362 | etot = -5.62847196913939 +822000 ekin = 3.23123737359429 | erot = 3.26537695353517 | epot = -12.1250862959258 | etot = -5.62847196879639 +823000 ekin = 3.08574116214281 | erot = 3.24970236656038 | epot = -11.9639154971954 | etot = -5.62847196849219 +824000 ekin = 2.95109919800351 | erot = 3.22828590251511 | epot = -11.8078570687366 | etot = -5.62847196821798 +825000 ekin = 2.83117167264324 | erot = 3.20152981054634 | epot = -11.6611734511487 | etot = -5.62847196795915 +826000 ekin = 2.72929448921519 | erot = 3.1702123297884 | epot = -11.5279787867064 | etot = -5.62847196770285 +827000 ekin = 2.64828540315214 | erot = 3.13564460890332 | epot = -11.4124019795009 | etot = -5.62847196744548 +828000 ekin = 2.59045268733176 | erot = 3.09968027809008 | epot = -11.3186049326203 | etot = -5.62847196719851 +829000 ekin = 2.55756748975069 | erot = 3.064548919671 | epot = -11.2505883764086 | etot = -5.62847196698692 +830000 ekin = 2.5507738837779 | erot = 3.0325460478396 | epot = -11.2117918984618 | etot = -5.62847196684431 +831000 ekin = 2.57043726041525 | erot = 3.0056609736767 | epot = -11.2045702008956 | etot = -5.62847196680369 +832000 ekin = 2.61596871091072 | erot = 2.98524787843516 | epot = -11.229688556233 | etot = -5.62847196688709 +833000 ekin = 2.68568117819201 | erot = 2.97182255580954 | epot = -11.2859757011011 | etot = -5.62847196709954 +834000 ekin = 2.77673678093812 | erot = 2.96502424213231 | epot = -11.3702329904984 | etot = -5.62847196742795 +835000 ekin = 2.88522064281158 | erot = 2.96372965093723 | epot = -11.4774222615931 | etot = -5.62847196784434 +836000 ekin = 3.00633984574425 | erot = 2.96626860441722 | epot = -11.6010804184754 | etot = -5.62847196831393 +837000 ekin = 3.13471078913859 | erot = 2.9706713315979 | epot = -11.7338540895385 | etot = -5.62847196880199 +838000 ekin = 3.26467977025951 | erot = 2.97489019003885 | epot = -11.8680419295789 | etot = -5.62847196928059 +839000 ekin = 3.39062362162418 | erot = 2.97696578811114 | epot = -11.9960613794644 | etot = -5.6284719697291 +840000 ekin = 3.507196142199 | erot = 2.9751377339346 | epot = -12.1108058462673 | etot = -5.62847197013369 +841000 ekin = 3.60951430435165 | erot = 2.96792302581209 | epot = -12.2059093006459 | etot = -5.62847197048216 +842000 ekin = 3.69330308374611 | erot = 2.95419217422804 | epot = -12.2759672287361 | etot = -5.62847197076192 +843000 ekin = 3.75502928065118 | erot = 2.93326272933157 | epot = -12.3167639809386 | etot = -5.62847197095582 +844000 ekin = 3.79205095756263 | erot = 2.90501003243346 | epot = -12.3255329610403 | etot = -5.62847197104421 +845000 ekin = 3.80278826982853 | erot = 2.86997708289261 | epot = -12.3012373237297 | etot = -5.62847197100856 +846000 ekin = 3.78689078364321 | erot = 2.82944607125015 | epot = -12.2448088257316 | etot = -5.62847197083821 +847000 ekin = 3.74534923751239 | erot = 2.78543387884246 | epot = -12.1592550868916 | etot = -5.62847197053678 +848000 ekin = 3.68048960903234 | erot = 2.74058491117485 | epot = -12.0495464903338 | etot = -5.62847197012659 +849000 ekin = 3.59580402265742 | erot = 2.69795473368827 | epot = -11.9222307259957 | etot = -5.62847196964997 +850000 ekin = 3.49561210996146 | erot = 2.66069826193653 | epot = -11.7847823410584 | etot = -5.62847196916039 +851000 ekin = 3.38460421150981 | erot = 2.63169878891611 | epot = -11.6447749691419 | etot = -5.62847196871596 +852000 ekin = 3.26735834603567 | erot = 2.61319105387691 | epot = -11.5090213682777 | etot = -5.62847196836509 +853000 ekin = 3.14792970800198 | erot = 2.60644045876884 | epot = -11.3828421349078 | etot = -5.62847196813696 +854000 ekin = 3.02961721456353 | erot = 2.61155167638246 | epot = -11.2696408589775 | etot = -5.6284719680315 +855000 ekin = 2.91497870609257 | erot = 2.62749311839419 | epot = -11.1709437925141 | etot = -5.62847196802735 +856000 ekin = 2.80592683607162 | erot = 2.6522972346767 | epot = -11.0866960388335 | etot = -5.62847196808521 +857000 ekin = 2.70394323070065 | erot = 2.68342637086871 | epot = -11.015841569732 | etot = -5.62847196816267 +858000 ekin = 2.61028084980153 | erot = 2.71820874419168 | epot = -10.9569615622196 | etot = -5.62847196822636 +859000 ekin = 2.52608469641724 | erot = 2.75423459839653 | epot = -10.9087912630729 | etot = -5.62847196825908 +860000 ekin = 2.45241725290201 | erot = 2.78962480101476 | epot = -10.8705140221748 | etot = -5.62847196825805 +861000 ekin = 2.39021948273227 | erot = 2.82313150330722 | epot = -10.8418229542727 | etot = -5.62847196823325 +862000 ekin = 2.34025129495987 | erot = 2.85407946376761 | epot = -10.822802726928 | etot = -5.62847196820057 +863000 ekin = 2.30304188781159 | erot = 2.88219277634858 | epot = -10.813706632338 | etot = -5.62847196817783 +864000 ekin = 2.27886006013276 | erot = 2.90737073876856 | epot = -10.8147027670818 | etot = -5.62847196818052 +865000 ekin = 2.26770197180472 | erot = 2.92947677479193 | epot = -10.8256507148148 | etot = -5.6284719682181 +866000 ekin = 2.26929189230923 | erot = 2.94819404249625 | epot = -10.8459579030977 | etot = -5.62847196829218 +867000 ekin = 2.28309242155635 | erot = 2.96298089314197 | epot = -10.874545283095 | etot = -5.62847196839671 +868000 ekin = 2.30832281636741 | erot = 2.97313399096203 | epot = -10.9099287758479 | etot = -5.62847196851846 +869000 ekin = 2.34398135087991 | erot = 2.97793980529636 | epot = -10.9503931248177 | etot = -5.62847196864144 +870000 ekin = 2.38886744672429 | erot = 2.97686809808026 | epot = -10.9942075135562 | etot = -5.6284719687517 +871000 ekin = 2.44159861708973 | erot = 2.96974175406055 | epot = -11.0398123399925 | etot = -5.6284719688422 +872000 ekin = 2.50061961498804 | erot = 2.95681803673566 | epot = -11.0859096206388 | etot = -5.62847196891511 +873000 ekin = 2.56420808027826 | erot = 2.93874614039664 | epot = -11.1314261896553 | etot = -5.6284719689804 +874000 ekin = 2.63049126909912 | erot = 2.91641905763502 | epot = -11.1753822957821 | etot = -5.628471969048 +875000 ekin = 2.69749664332261 | erot = 2.89079068993249 | epot = -11.2167593023751 | etot = -5.62847196912 +876000 ekin = 2.76325740762409 | erot = 2.8627513855634 | epot = -11.2544807623728 | etot = -5.62847196918535 +877000 ekin = 2.82597856953319 | erot = 2.83312911622589 | epot = -11.2875796549786 | etot = -5.62847196921951 +878000 ekin = 2.88426505921199 | erot = 2.80282960041362 | epot = -11.3155666287694 | etot = -5.6284719691438 +879000 ekin = 2.93899285381861 | erot = 2.77402557710308 | epot = -11.3414903998404 | etot = -5.62847196891873 +880000 ekin = 2.99074429370243 | erot = 2.74904466361883 | epot = -11.3682609262703 | etot = -5.62847196894903 +881000 ekin = 3.03734868856232 | erot = 2.72816458055542 | epot = -11.3939852379052 | etot = -5.62847196878747 +882000 ekin = 3.07935286205246 | erot = 2.71303253487346 | epot = -11.4208573655467 | etot = -5.62847196862081 +883000 ekin = 3.11756796960435 | erot = 2.70517731821704 | epot = -11.4512172563087 | etot = -5.62847196848731 +884000 ekin = 3.15280252723544 | erot = 2.70569769586684 | epot = -11.4869721915149 | etot = -5.62847196841262 +885000 ekin = 3.18571613079919 | erot = 2.71504911526553 | epot = -11.5292372144745 | etot = -5.62847196840978 +886000 ekin = 3.21676773261692 | erot = 2.73290580046188 | epot = -11.5781455015627 | etot = -5.62847196848389 +887000 ekin = 3.24623562297705 | erot = 2.75806669085735 | epot = -11.6327742824729 | etot = -5.62847196863852 +888000 ekin = 3.27425941885426 | erot = 2.78837179655079 | epot = -11.6911031842822 | etot = -5.62847196887713 +889000 ekin = 3.30086478759873 | erot = 2.82064068474087 | epot = -11.7499774415375 | etot = -5.62847196919789 +890000 ekin = 3.32596924743585 | erot = 2.8507143995424 | epot = -11.8051556165578 | etot = -5.62847196957959 +891000 ekin = 3.34941253111799 | erot = 2.87373382361226 | epot = -11.8516183246993 | etot = -5.62847196996901 +892000 ekin = 3.37107523435862 | erot = 2.88476437051389 | epot = -11.8843115751514 | etot = -5.62847197027888 +893000 ekin = 3.39111184980405 | erot = 2.87974242678446 | epot = -11.8993262469996 | etot = -5.62847197041106 +894000 ekin = 3.41023212792719 | erot = 2.85650829451306 | epot = -11.8952123927364 | etot = -5.62847197029618 +895000 ekin = 3.42987730742305 | erot = 2.81553499445148 | epot = -11.873884271807 | etot = -5.62847196993249 +896000 ekin = 3.45214148845859 | erot = 2.76001213101189 | epot = -11.8406255888621 | etot = -5.62847196939163 +897000 ekin = 3.47941735479851 | erot = 2.69521466352953 | epot = -11.8031039871185 | etot = -5.62847196879047 +898000 ekin = 3.51352961892427 | erot = 2.62737086711433 | epot = -11.7693724674547 | etot = -5.6284719814161 +899000 ekin = 3.48893911158129 | erot = 2.56291214052526 | epot = -11.6803232215692 | etot = -5.6284719694627 +900000 ekin = 3.45535689137436 | erot = 2.55015985198085 | epot = -11.6339887057135 | etot = -5.62847196235833 +901000 ekin = 3.50186288051208 | erot = 2.58894159273042 | epot = -11.719276449028 | etot = -5.62847197578548 +902000 ekin = 3.56610213509042 | erot = 2.58196928558468 | epot = -11.7765433932355 | etot = -5.62847197256043 +903000 ekin = 3.62814875790769 | erot = 2.56232070257317 | epot = -11.8189414334154 | etot = -5.6284719729345 +904000 ekin = 3.69112394769311 | erot = 2.5524763832157 | epot = -11.8720723043302 | etot = -5.62847197342134 +905000 ekin = 3.75091280592953 | erot = 2.54985569583922 | epot = -11.9292404756987 | etot = -5.62847197392995 +906000 ekin = 3.8032250689438 | erot = 2.55191272324046 | epot = -11.9836097665412 | etot = -5.6284719743569 +907000 ekin = 3.84434229250825 | erot = 2.5568336035953 | epot = -12.0296478707192 | etot = -5.62847197461568 +908000 ekin = 3.871900647008 | erot = 2.56394104594644 | epot = -12.0643136676191 | etot = -5.62847197466464 +909000 ekin = 3.88547927918536 | erot = 2.57365300982679 | epot = -12.0876042635317 | etot = -5.62847197451959 +910000 ekin = 3.88680451544102 | erot = 2.58702435551622 | epot = -12.1023008452009 | etot = -5.62847197424369 +911000 ekin = 3.87951720898021 | erot = 2.60508796128714 | epot = -12.1130771441854 | etot = -5.62847197391802 +912000 ekin = 3.86859234278359 | erot = 2.62827701186852 | epot = -12.1253413282694 | etot = -5.62847197361728 +913000 ekin = 3.85955913829983 | erot = 2.65612234750808 | epot = -12.1441534592065 | etot = -5.62847197339855 +914000 ekin = 3.85765974744707 | erot = 2.68725904601637 | epot = -12.1733907661574 | etot = -5.62847197269395 +915000 ekin = 3.86988559284798 | erot = 2.72155495759146 | epot = -12.2199125233092 | etot = -5.62847197286973 +916000 ekin = 3.89721211304123 | erot = 2.75899199516187 | epot = -12.2846760814788 | etot = -5.62847197327566 +917000 ekin = 3.93597306343169 | erot = 2.79756616380009 | epot = -12.3620112009473 | etot = -5.6284719737155 +918000 ekin = 3.98211349531499 | erot = 2.83523643636804 | epot = -12.445821905844 | etot = -5.62847197416096 +919000 ekin = 4.03109884083907 | erot = 2.86939982935091 | epot = -12.5289706457807 | etot = -5.62847197559067 +920000 ekin = 4.07575006581286 | erot = 2.89203459117052 | epot = -12.5962566328921 | etot = -5.62847197590877 +921000 ekin = 4.11121319883197 | erot = 2.89963705809888 | epot = -12.6393222335791 | etot = -5.62847197664822 +922000 ekin = 4.12946328833856 | erot = 2.89101491350044 | epot = -12.6489501787586 | etot = -5.62847197691959 +923000 ekin = 4.12574551357268 | erot = 2.86656720131328 | epot = -12.6207846917908 | etot = -5.62847197690484 +924000 ekin = 4.0980625546228 | erot = 2.82817437101463 | epot = -12.5547089022792 | etot = -5.6284719766418 +925000 ekin = 4.04683812875273 | erot = 2.77889166219992 | epot = -12.4542017671822 | etot = -5.62847197622952 +926000 ekin = 3.97415980690535 | erot = 2.7224048573368 | epot = -12.3250366400166 | etot = -5.6284719757744 +927000 ekin = 3.88290109511714 | erot = 2.66247239688044 | epot = -12.1738454673358 | etot = -5.6284719753382 +928000 ekin = 3.77619172574108 | erot = 2.60258197423891 | epot = -12.0072456748983 | etot = -5.6284719749183 +929000 ekin = 3.65741733987843 | erot = 2.54590496492842 | epot = -11.831794279277 | etot = -5.62847197447012 +930000 ekin = 3.53056331472612 | erot = 2.49545263670913 | epot = -11.6544879253869 | etot = -5.62847197395165 +931000 ekin = 3.40054526036444 | erot = 2.454292850849 | epot = -11.4833100842546 | etot = -5.62847197304114 +932000 ekin = 3.27351307450537 | erot = 2.42812143066844 | epot = -11.3301064778166 | etot = -5.62847197264279 +933000 ekin = 3.15479412953591 | erot = 2.4201742894763 | epot = -11.2034403912531 | etot = -5.62847197224091 +934000 ekin = 3.04934557327881 | erot = 2.43124949935863 | epot = -11.109067044526 | etot = -5.62847197188859 +935000 ekin = 2.96178382809207 | erot = 2.46165171666485 | epot = -11.0519075163873 | etot = -5.62847197163034 +936000 ekin = 2.89581269428724 | erot = 2.51113391229723 | epot = -11.0354185780765 | etot = -5.62847197149205 +937000 ekin = 2.8538587951087 | erot = 2.57889786005817 | epot = -11.0612286266452 | etot = -5.62847197147829 +938000 ekin = 2.8369434295325 | erot = 2.66364816059609 | epot = -11.1290635617065 | etot = -5.62847197157791 +939000 ekin = 2.84476696161334 | erot = 2.76369076510542 | epot = -11.2369296984843 | etot = -5.62847197176559 +940000 ekin = 2.87595320373246 | erot = 2.87707537624185 | epot = -11.3815005519813 | etot = -5.62847197200697 +941000 ekin = 2.92838858032047 | erot = 3.00178159446771 | epot = -11.5586421470521 | etot = -5.62847197226393 +942000 ekin = 2.99958691358805 | erot = 3.13593595199803 | epot = -11.7639948380871 | etot = -5.62847197250098 +943000 ekin = 3.08701485959176 | erot = 3.27802583767079 | epot = -11.9935126699548 | etot = -5.62847197269224 +944000 ekin = 3.18658687084634 | erot = 3.42629435473283 | epot = -12.2413531994801 | etot = -5.62847197390095 +945000 ekin = 3.29120912050651 | erot = 3.577012531924 | epot = -12.4966936268516 | etot = -5.62847197442111 +946000 ekin = 3.39621217340276 | erot = 3.7263738917811 | epot = -12.7510580401981 | etot = -5.62847197501423 +947000 ekin = 3.4968730305855 | erot = 3.86977321011431 | epot = -12.9951182164045 | etot = -5.62847197570464 +948000 ekin = 3.58827211219312 | erot = 4.00151346801785 | epot = -13.2182575567051 | etot = -5.6284719764941 +949000 ekin = 3.66536645482548 | erot = 4.11475106105357 | epot = -13.4085894932251 | etot = -5.62847197734605 +950000 ekin = 3.72323942018895 | erot = 4.20180191824226 | epot = -13.5535133166105 | etot = -5.62847197817932 +951000 ekin = 3.75754185711642 | erot = 4.25489778340543 | epot = -13.6409116193944 | etot = -5.62847197887252 +952000 ekin = 3.76507381720016 | erot = 4.26734583732727 | epot = -13.6608916338152 | etot = -5.62847197928779 +953000 ekin = 3.74438822450871 | erot = 4.23487585620145 | epot = -13.6077360600182 | etot = -5.62847197930807 +954000 ekin = 3.6962524303913 | erot = 4.15681815512645 | epot = -13.4815425643942 | etot = -5.62847197887646 +955000 ekin = 3.62380420344389 | erot = 4.03673171887103 | epot = -13.2890079003346 | etot = -5.62847197801971 +956000 ekin = 3.52555337106034 | erot = 3.8807380542249 | epot = -13.0347634049366 | etot = -5.62847197965134 +957000 ekin = 3.39894639548186 | erot = 3.704741379357 | epot = -12.7321597494327 | etot = -5.6284719745938 +958000 ekin = 3.27782879701388 | erot = 3.53760737302324 | epot = -12.4439081430079 | etot = -5.62847197297078 +959000 ekin = 3.17835028698373 | erot = 3.3860220764187 | epot = -12.1928443382271 | etot = -5.62847197482472 +960000 ekin = 3.09019087998482 | erot = 3.23509493738875 | epot = -11.9537577938396 | etot = -5.62847197646608 +961000 ekin = 3.00426259412953 | erot = 3.08248133846111 | epot = -11.7152159081467 | etot = -5.62847197555611 +962000 ekin = 2.92693480006865 | erot = 2.94805481108402 | epot = -11.5034615864953 | etot = -5.62847197534258 +963000 ekin = 2.85972055652158 | erot = 2.83488454740043 | epot = -11.3230770789589 | etot = -5.62847197503687 +964000 ekin = 2.80427359444853 | erot = 2.74583973307705 | epot = -11.1785853023839 | etot = -5.62847197485834 +965000 ekin = 2.76170821974625 | erot = 2.68249826250847 | epot = -11.0726784570591 | etot = -5.62847197480438 +966000 ekin = 2.73254763787259 | erot = 2.64503833078586 | epot = -11.0060579435413 | etot = -5.62847197488283 +967000 ekin = 2.71665521945761 | erot = 2.63218922387602 | epot = -10.977316418432 | etot = -5.62847197509839 +968000 ekin = 2.71315992256797 | erot = 2.6412436416193 | epot = -10.9828755396252 | etot = -5.62847197543791 +969000 ekin = 2.72046614394445 | erot = 2.66825860572991 | epot = -11.0171967255374 | etot = -5.62847197586305 +970000 ekin = 2.73639578727365 | erot = 2.70848274022898 | epot = -11.073350503823 | etot = -5.62847197632035 +971000 ekin = 2.7584938291987 | erot = 2.75695664047694 | epot = -11.1439224463452 | etot = -5.62847197666954 +972000 ekin = 2.78540546045377 | erot = 2.80984083585929 | epot = -11.2237182732553 | etot = -5.62847197694225 +973000 ekin = 2.81581408645962 | erot = 2.86412704583047 | epot = -11.3084131094169 | etot = -5.62847197712684 +974000 ekin = 2.84847994853285 | erot = 2.91762904109419 | epot = -11.394580966844 | etot = -5.62847197721695 +975000 ekin = 2.88260770542579 | erot = 2.96920774038639 | epot = -11.480287423027 | etot = -5.62847197721485 +976000 ekin = 2.90702474892291 | erot = 3.0196491884248 | epot = -11.5551459389487 | etot = -5.62847200160094 +977000 ekin = 2.82994038022815 | erot = 3.10467594136529 | epot = -11.5630882994573 | etot = -5.62847197786387 +978000 ekin = 2.82908361926504 | erot = 3.22546638455035 | epot = -11.6830220075474 | etot = -5.628472003732 +979000 ekin = 2.83706100134503 | erot = 3.2548187323809 | epot = -11.720351723827 | etot = -5.62847199010104 +980000 ekin = 2.83601345165634 | erot = 3.27042511751412 | epot = -11.7349105593066 | etot = -5.62847199013615 +981000 ekin = 2.82679467553623 | erot = 3.27908746265508 | epot = -11.734354128369 | etot = -5.62847199017766 +982000 ekin = 2.80889457138308 | erot = 3.28090658537119 | epot = -11.7182731469763 | etot = -5.62847199022204 +983000 ekin = 2.78208898717251 | erot = 3.27578647329014 | epot = -11.6863474507109 | etot = -5.62847199024828 +984000 ekin = 2.74660136968689 | erot = 3.26353952550221 | epot = -11.6386128854104 | etot = -5.62847199022127 +985000 ekin = 2.70333214519072 | erot = 3.24411391134697 | epot = -11.575918046642 | etot = -5.62847199010433 +986000 ekin = 2.65408912845627 | erot = 3.21786526580058 | epot = -11.5004263841271 | etot = -5.62847198987027 +987000 ekin = 2.57871631765271 | erot = 3.17247278893129 | epot = -11.3796611009394 | etot = -5.62847199435536 +988000 ekin = 2.53018926708017 | erot = 3.15315340977068 | epot = -11.3118146788246 | etot = -5.62847200197374 +989000 ekin = 2.49566278306744 | erot = 3.12952117448782 | epot = -11.2536559495158 | etot = -5.62847199196056 +990000 ekin = 2.46227182596968 | erot = 3.09741757832303 | epot = -11.1881613956981 | etot = -5.62847199140542 +991000 ekin = 2.44592299332381 | erot = 3.07158095055821 | epot = -11.1459759350248 | etot = -5.62847199114281 +992000 ekin = 2.45174281643038 | erot = 3.05611048511796 | epot = -11.1363252924909 | etot = -5.62847199094254 +993000 ekin = 2.4809967175337 | erot = 3.05281518204759 | epot = -11.1622838903702 | etot = -5.62847199078888 +994000 ekin = 2.53415670294871 | erot = 3.06359154456191 | epot = -11.2262202382137 | etot = -5.62847199070311 +995000 ekin = 2.61088853355121 | erot = 3.09015398630347 | epot = -11.3295145105498 | etot = -5.62847199069511 +996000 ekin = 2.71011819725457 | erot = 3.13378298778989 | epot = -11.4723731758111 | etot = -5.62847199076662 +997000 ekin = 2.83015603299592 | erot = 3.19515267790156 | epot = -11.653780701815 | etot = -5.62847199091748 +998000 ekin = 2.96878571625672 | erot = 3.27423191427181 | epot = -11.8714896216853 | etot = -5.62847199115672 +999000 ekin = 3.12322522638366 | erot = 3.37022004784673 | epot = -12.1219172657411 | etot = -5.6284719915107 +1000000 ekin = 3.28990650507131 | erot = 3.4814601076319 | epot = -12.3998386047259 | etot = -5.62847199202267 + 1000000 0.14621807 -0.83009398 0.055104069 -0.56937076 4.8223734e-05 64000 +Loop time of 14.5271 on 4 procs for 1000000 steps with 16 atoms + +Performance: 59474.862 tau/day, 68836.646 timesteps/s, 1.101 Matom-step/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.9496 | 6.919 | 8.139 | 48.5 | 47.63 +Bond | 0.17781 | 0.27579 | 0.35519 | 12.1 | 1.90 +Neigh | 0.004968 | 0.0050075 | 0.005068 | 0.1 | 0.03 +Comm | 4.3521 | 5.4851 | 7.6042 | 55.8 | 37.76 +Output | 0.06127 | 0.06555 | 0.074377 | 2.0 | 0.45 +Modify | 0.58934 | 0.65958 | 0.71877 | 7.1 | 4.54 +Other | | 1.117 | | | 7.69 + +Nlocal: 4 ave 4 max 4 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 12 ave 12 max 12 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 26.5 ave 47 max 9 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 106 +Ave neighs/atom = 6.625 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/oxrna2_lj.cgdna b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/oxrna2_lj.cgdna new file mode 120000 index 0000000000..61a572f605 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/oxrna2_lj.cgdna @@ -0,0 +1 @@ +../../../../../../../potentials/oxrna2_lj.cgdna \ No newline at end of file diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/data.duplex1 new file mode 100644 index 0000000000..a368cef424 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0 +2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0 +3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0 +4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0 +5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0 +6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0 +7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0 +8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0 +9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0 +10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618 +2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161 +3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145 +4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535 +5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021 +6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764 +7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955 +8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736 +9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246 +10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/in.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/in.duplex1 new file mode 100644 index 0000000000..cc5e11b43b --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/in.duplex1 @@ -0,0 +1,71 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.1 new file mode 100644 index 0000000000..a8cb9b5d68 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.1 @@ -0,0 +1,1176 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 25.179212 + ghost atom cutoff = 32.4 + binsize = 12.589606, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8453746587949 | etot = -54.4567170072638 +Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -80.414409 2.5690347 -71.238502 -0.031164646 39304000 +1000 ekin = 6.43820783118127 | erot = 17.3362198819252 | epot = -78.2311447221034 | etot = -54.4567170089969 +2000 ekin = 6.25962757371398 | erot = 17.7614951323061 | epot = -78.4778397161865 | etot = -54.4567170101664 +3000 ekin = 6.07700556573588 | erot = 18.0349356633584 | epot = -78.568658239597 | etot = -54.4567170105028 +4000 ekin = 5.89744395525129 | erot = 18.144460931621 | epot = -78.4986218967948 | etot = -54.4567170099226 +5000 ekin = 5.72921700410326 | erot = 18.0898077153686 | epot = -78.2757417280193 | etot = -54.4567170085474 +6000 ekin = 5.58103231328821 | erot = 17.8818838137361 | epot = -77.9196331337201 | etot = -54.4567170066957 +7000 ekin = 5.46083908443389 | erot = 17.5394286863637 | epot = -77.4569847754236 | etot = -54.456717004626 +8000 ekin = 5.37466806168184 | erot = 17.086045740889 | epot = -76.9174308051193 | etot = -54.4567170025485 +9000 ekin = 5.32596283558547 | erot = 16.5482758509796 | epot = -76.3309556871347 | etot = -54.4567170005696 +10000 ekin = 5.31555310057087 | erot = 15.9544038907651 | epot = -75.7266739899446 | etot = -54.4567169986086 +11000 ekin = 5.34212439127906 | erot = 15.33325110042 | epot = -75.1320924886816 | etot = -54.4567169969825 +12000 ekin = 5.40287885250685 | erot = 14.7110726721716 | epot = -74.570668520288 | etot = -54.4567169956095 +13000 ekin = 5.49412472240381 | erot = 14.1110805159141 | epot = -74.0619222328998 | etot = -54.4567169945818 +14000 ekin = 5.6116733967227 | erot = 13.5517285104402 | epot = -73.6201189011436 | etot = -54.4567169939806 +15000 ekin = 5.75106060199928 | erot = 13.0453082210511 | epot = -73.2530858167914 | etot = -54.4567169937411 +16000 ekin = 5.9076835700648 | erot = 12.5986044578508 | epot = -72.9630050218526 | etot = -54.4567169939369 +17000 ekin = 6.07694775533401 | erot = 12.2121295946254 | epot = -72.745794344578 | etot = -54.4567169946187 +18000 ekin = 6.2544900101667 | erot = 11.8809581167544 | epot = -72.5921651219471 | etot = -54.456716995026 +19000 ekin = 6.43645340088853 | erot = 11.5970728654625 | epot = -72.4902432622587 | etot = -54.4567169959077 +20000 ekin = 6.61976225801504 | erot = 11.3493123188075 | epot = -72.4257915734619 | etot = -54.4567169966394 +21000 ekin = 6.80232746725453 | erot = 11.12797043509 | epot = -72.3870148994525 | etot = -54.456716997108 +22000 ekin = 6.98311688717135 | erot = 10.9264751205881 | epot = -72.3663090050195 | etot = -54.4567169972601 +23000 ekin = 7.16205079775862 | erot = 10.7423327849975 | epot = -72.3611005798626 | etot = -54.4567169971065 +24000 ekin = 7.33972059294137 | erot = 10.5772758543376 | epot = -72.3737134439925 | etot = -54.4567169967136 +25000 ekin = 7.51695157931204 | erot = 10.4365899375964 | epot = -72.410258513139 | etot = -54.4567169962305 +26000 ekin = 7.69429229269129 | erot = 10.3277639309844 | epot = -72.4787732193795 | etot = -54.4567169957038 +27000 ekin = 7.87150951743587 | erot = 10.2597304033277 | epot = -72.5879569160672 | etot = -54.4567169953037 +28000 ekin = 8.04705135555601 | erot = 10.2410352171346 | epot = -72.7448035678545 | etot = -54.456716995164 +29000 ekin = 8.21759746027588 | erot = 10.2782041594724 | epot = -72.9525186151519 | etot = -54.4567169954035 +30000 ekin = 8.37774171245007 | erot = 10.3742403796591 | epot = -73.2086990882218 | etot = -54.4567169961126 +31000 ekin = 8.51990909585299 | erot = 10.5273666264231 | epot = -73.503992719602 | etot = -54.4567169973259 +32000 ekin = 8.63465262126945 | erot = 10.7302431095271 | epot = -73.8216127297857 | etot = -54.4567169989892 +33000 ekin = 8.71148334085703 | erot = 10.9699651918536 | epot = -74.1381655336434 | etot = -54.4567170009328 +34000 ekin = 8.74030392010885 | erot = 11.2291223208267 | epot = -74.4261432438069 | etot = -54.4567170028714 +35000 ekin = 8.71331622899753 | erot = 11.4879560434145 | epot = -74.6579892768899 | etot = -54.4567170044778 +36000 ekin = 8.6270054941397 | erot = 11.7272789104034 | epot = -74.8110014099219 | etot = -54.4567170053788 +37000 ekin = 8.48360146994024 | erot = 11.9311520187442 | epot = -74.8714704944482 | etot = -54.4567170057638 +38000 ekin = 8.29145725510879 | erot = 12.0877651508229 | epot = -74.8359394109127 | etot = -54.456717004981 +39000 ekin = 8.06412808157086 | erot = 12.1939490782825 | epot = -74.7147941632556 | etot = -54.4567170034022 +40000 ekin = 7.8183491672969 | erot = 12.2536811005695 | epot = -74.5287472695195 | etot = -54.4567170016531 +41000 ekin = 7.57153983107151 | erot = 12.2737166637664 | epot = -74.3019734948458 | etot = -54.4567170000079 +42000 ekin = 7.33952905244385 | erot = 12.2616299907504 | epot = -74.0578760417282 | etot = -54.4567169985339 +43000 ekin = 7.13479707854096 | erot = 12.2251663434275 | epot = -73.8166804194407 | etot = -54.4567169974722 +44000 ekin = 6.96549624172411 | erot = 12.1705863869632 | epot = -73.5927996255427 | etot = -54.4567169968554 +45000 ekin = 6.83524241842684 | erot = 12.1023865846985 | epot = -73.3943459997491 | etot = -54.4567169966237 +46000 ekin = 6.74353977237873 | erot = 12.0237417555818 | epot = -73.2239985246163 | etot = -54.4567169966557 +47000 ekin = 6.68665226743047 | erot = 11.9373741846297 | epot = -73.0807434488668 | etot = -54.4567169968066 +48000 ekin = 6.65871295716605 | erot = 11.8463562055031 | epot = -72.9617861597101 | etot = -54.4567169970409 +49000 ekin = 6.65288229900589 | erot = 11.7538080029642 | epot = -72.8634072990292 | etot = -54.4567169970592 +50000 ekin = 6.66236312881733 | erot = 11.6656641757333 | epot = -72.7847443014512 | etot = -54.4567169969006 +51000 ekin = 6.68111060961778 | erot = 11.5899788256564 | epot = -72.7278064318541 | etot = -54.4567169965799 +52000 ekin = 6.7041802474988 | erot = 11.5360562910265 | epot = -72.696953534693 | etot = -54.4567169961677 +53000 ekin = 6.72772366359015 | erot = 11.5134142818732 | epot = -72.6978549412364 | etot = -54.456716995773 +54000 ekin = 6.74871337970471 | erot = 11.5307585185416 | epot = -72.7361888937386 | etot = -54.4567169954923 +55000 ekin = 6.76451852991647 | erot = 11.5943746539851 | epot = -72.815610179404 | etot = -54.4567169955025 +56000 ekin = 6.77243985440047 | erot = 11.7063710780976 | epot = -72.9355279283601 | etot = -54.456716995862 +57000 ekin = 6.76933053582512 | erot = 11.8642156230109 | epot = -73.0902631554544 | etot = -54.4567169966185 +58000 ekin = 6.75138726809175 | erot = 12.0602974501204 | epot = -73.2684017159796 | etot = -54.4567169977675 +59000 ekin = 6.71417128126918 | erot = 12.2820751409027 | epot = -73.4529634214104 | etot = -54.4567169992384 +60000 ekin = 6.65290992288017 | erot = 12.5129009338982 | epot = -73.6225278576777 | etot = -54.4567170008993 +61000 ekin = 6.56310682197025 | erot = 12.7335144723087 | epot = -73.7533382968305 | etot = -54.4567170025516 +62000 ekin = 6.44146338255561 | erot = 12.9241509619395 | epot = -73.8223313484456 | etot = -54.4567170039505 +63000 ekin = 6.28705781387306 | erot = 13.0670338389574 | epot = -73.8108086578462 | etot = -54.4567170050157 +64000 ekin = 6.10266169757214 | erot = 13.1477809820694 | epot = -73.7071596847869 | etot = -54.4567170051453 +65000 ekin = 5.89591130160378 | erot = 13.1592635961187 | epot = -73.5118919021165 | etot = -54.456717004394 +66000 ekin = 5.67987143865612 | erot = 13.1032095066899 | epot = -73.2397979480396 | etot = -54.4567170026935 +67000 ekin = 5.47246439370461 | erot = 12.9892907727309 | epot = -72.9184721669219 | etot = -54.4567170004864 +68000 ekin = 5.29471721365622 | erot = 12.8325811063881 | epot = -72.5840153180084 | etot = -54.456716997964 +69000 ekin = 5.16838716298711 | erot = 12.6515610640471 | epot = -72.2766652226397 | etot = -54.4567169956055 +70000 ekin = 5.1123024949134 | erot = 12.464558608656 | epot = -72.0335780974641 | etot = -54.4567169938946 +71000 ekin = 5.13863171719959 | erot = 12.2861676510959 | epot = -71.8815163616864 | etot = -54.456716993391 +72000 ekin = 5.24921766817571 | erot = 12.1241146960812 | epot = -71.8300493582313 | etot = -54.4567169939744 +73000 ekin = 5.43495114762194 | erot = 11.9780651684539 | epot = -71.8697333116311 | etot = -54.4567169955553 +74000 ekin = 5.67787386257412 | erot = 11.8411579566087 | epot = -71.9757488169253 | etot = -54.4567169977424 +75000 ekin = 5.95416182625046 | erot = 11.7025717830519 | epot = -72.113450609344 | etot = -54.4567170000417 +76000 ekin = 6.2382481878043 | erot = 11.5508489468467 | epot = -72.2458141366446 | etot = -54.4567170019935 +77000 ekin = 6.50675110372134 | erot = 11.376960643443 | epot = -72.3404287504467 | etot = -54.4567170032824 +78000 ekin = 6.7413670315104 | erot = 11.1763239765949 | epot = -72.3744080118938 | etot = -54.4567170037885 +79000 ekin = 6.93031685727 | erot = 10.9493830401345 | epot = -72.3364169009795 | etot = -54.456717003575 +80000 ekin = 7.06838579021362 | erot = 10.7008558180281 | epot = -72.2259586110715 | etot = -54.4567170028298 +81000 ekin = 7.15593174989378 | erot = 10.4381486680532 | epot = -72.0507974197271 | etot = -54.4567170017802 +82000 ekin = 7.19737561193852 | erot = 10.1696078110448 | epot = -71.8237004236075 | etot = -54.4567170006242 +83000 ekin = 7.19963709941819 | erot = 9.90317661788338 | epot = -71.5595307167926 | etot = -54.4567169994911 +84000 ekin = 7.17081556671144 | erot = 9.64574605090055 | epot = -71.273278616051 | etot = -54.456716998439 +85000 ekin = 7.11922963823867 | erot = 9.40317461807844 | epot = -70.9791212537907 | etot = -54.4567169974735 +86000 ekin = 7.05279272914885 | erot = 9.18074070207743 | epot = -70.6902504278029 | etot = -54.4567169965767 +87000 ekin = 6.97863676438221 | erot = 8.98372361344457 | epot = -70.4190773735549 | etot = -54.4567169957281 +88000 ekin = 6.9028911125576 | erot = 8.81786450432949 | epot = -70.1774726118083 | etot = -54.4567169949212 +89000 ekin = 6.83054970527891 | erot = 8.68957087135389 | epot = -69.9768375707985 | etot = -54.4567169941657 +90000 ekin = 6.76539137201421 | erot = 8.60583796049187 | epot = -69.8279463259915 | etot = -54.4567169934854 +91000 ekin = 6.70994198518223 | erot = 8.57393232143089 | epot = -69.7405912995239 | etot = -54.4567169929108 +92000 ekin = 6.66547828037124 | erot = 8.60091153028055 | epot = -69.7231068031287 | etot = -54.4567169924769 +93000 ekin = 6.63207907276869 | erot = 8.69305218260925 | epot = -69.7818482475942 | etot = -54.4567169922162 +94000 ekin = 6.60872467795709 | erot = 8.85524213295501 | epot = -69.920683803072 | etot = -54.4567169921598 +95000 ekin = 6.59344191188652 | erot = 9.09002892498404 | epot = -70.1401878292941 | etot = -54.4567169924236 +96000 ekin = 6.58348503117511 | erot = 9.39676155295883 | epot = -70.4369635770044 | etot = -54.4567169928704 +97000 ekin = 6.57555779040114 | erot = 9.77238659111696 | epot = -70.8046613751019 | etot = -54.4567169935838 +98000 ekin = 6.56606406506479 | erot = 10.2104006447577 | epot = -71.2331817043831 | etot = -54.4567169945606 +99000 ekin = 6.55138371755748 | erot = 10.7005955684093 | epot = -71.7086962817498 | etot = -54.456716995783 +100000 ekin = 6.52818215156319 | erot = 11.229104804122 | epot = -72.2140039528875 | etot = -54.4567169972023 +101000 ekin = 6.49376016387468 | erot = 11.7788216139172 | epot = -72.7292987765279 | etot = -54.456716998736 +102000 ekin = 6.44644131665652 | erot = 12.3302826834051 | epot = -73.2334410003245 | etot = -54.4567170002629 +103000 ekin = 6.38597185526512 | erot = 12.8630533051893 | epot = -73.7057421620888 | etot = -54.4567170016345 +104000 ekin = 6.31387792328204 | erot = 13.3575416630676 | epot = -74.1281365890417 | etot = -54.456717002692 +105000 ekin = 6.23369870065412 | erot = 13.7969859266863 | epot = -74.4874016306526 | etot = -54.4567170033122 +106000 ekin = 6.15159087577179 | erot = 14.168347479028 | epot = -74.7766553580931 | etot = -54.4567170032933 +107000 ekin = 6.07597686979475 | erot = 14.4651876627012 | epot = -74.9978815355769 | etot = -54.456717003081 +108000 ekin = 6.01223234716995 | erot = 14.6879971316708 | epot = -75.1569464811428 | etot = -54.456717002302 +109000 ekin = 5.96716606188232 | erot = 14.843544289216 | epot = -75.2674273521871 | etot = -54.4567170010888 +110000 ekin = 5.94905536831921 | erot = 14.9434041692657 | epot = -75.3491765372227 | etot = -54.4567169996377 +111000 ekin = 5.96691720967362 | erot = 15.0017805706305 | epot = -75.4254147784671 | etot = -54.456716998163 +112000 ekin = 6.02963996568461 | erot = 15.0332074410399 | epot = -75.5195644035762 | etot = -54.4567169968517 +113000 ekin = 6.1447355794934 | erot = 15.0506276935639 | epot = -75.6520802691281 | etot = -54.4567169960708 +114000 ekin = 6.31295582028789 | erot = 15.0641514071762 | epot = -75.8338242231953 | etot = -54.4567169957312 +115000 ekin = 6.53172798600582 | erot = 15.0811124191474 | epot = -76.069557400948 | etot = -54.4567169957948 +116000 ekin = 6.79568089093934 | erot = 15.1059058197088 | epot = -76.3583037069064 | etot = -54.4567169962582 +117000 ekin = 7.09592407299118 | erot = 15.1399966271433 | epot = -76.692637697252 | etot = -54.4567169971175 +118000 ekin = 7.42014276685631 | erot = 15.1819125959108 | epot = -77.0587723611274 | etot = -54.4567169983602 +119000 ekin = 7.75294827199695 | erot = 15.2271422568037 | epot = -77.4368075287489 | etot = -54.4567169999482 +120000 ekin = 8.07659193886436 | erot = 15.2681028416293 | epot = -77.801411782285 | etot = -54.4567170017913 +121000 ekin = 8.37212580399467 | erot = 15.2944516166555 | epot = -78.1232944243814 | etot = -54.4567170037313 +122000 ekin = 8.62100116395937 | erot = 15.2939804912635 | epot = -78.3716986607659 | etot = -54.456717005543 +123000 ekin = 8.80694171731996 | erot = 15.254150000928 | epot = -78.5178087252231 | etot = -54.4567170069752 +124000 ekin = 8.91776467099479 | erot = 15.1640535889468 | epot = -78.5385352677475 | etot = -54.4567170078059 +125000 ekin = 8.9467480094793 | erot = 15.0163836749129 | epot = -78.4198486922921 | etot = -54.4567170078999 +126000 ekin = 8.89353650631002 | erot = 14.8103820375823 | epot = -78.1606355511996 | etot = -54.4567170073073 +127000 ekin = 8.7629508625392 | erot = 14.5505189841093 | epot = -77.7701868527587 | etot = -54.4567170061102 +128000 ekin = 8.56410993715709 | erot = 14.2447035162366 | epot = -77.2655304577559 | etot = -54.4567170043622 +129000 ekin = 8.30998017116567 | erot = 13.9055852316428 | epot = -76.6722824050741 | etot = -54.4567170022657 +130000 ekin = 8.0159653369684 | erot = 13.5489606027688 | epot = -76.0216429397662 | etot = -54.456717000029 +131000 ekin = 7.69857959330988 | erot = 13.1919558696584 | epot = -75.3472524608086 | etot = -54.4567169978403 +132000 ekin = 7.37430715049019 | erot = 12.8512838848574 | epot = -74.6823080311994 | etot = -54.4567169958518 +133000 ekin = 7.0586935021734 | erot = 12.5417841519133 | epot = -74.0571946482606 | etot = -54.4567169941739 +134000 ekin = 6.76568000840989 | erot = 12.275351752871 | epot = -73.4977487541533 | etot = -54.4567169928724 +135000 ekin = 6.50716750003369 | erot = 12.0602618213868 | epot = -73.0241463134093 | etot = -54.4567169919888 +136000 ekin = 6.29276806012063 | erot = 11.9007845740719 | epot = -72.6502696257233 | etot = -54.4567169915308 +137000 ekin = 6.12969309854731 | erot = 11.7970866991162 | epot = -72.383496789158 | etot = -54.4567169914945 +138000 ekin = 6.02273320867752 | erot = 11.7455527096574 | epot = -72.2250029101791 | etot = -54.4567169918441 +139000 ekin = 5.97430093912997 | erot = 11.7390915567029 | epot = -72.1701094884367 | etot = -54.4567169926038 +140000 ekin = 5.98450304637459 | erot = 11.7662502093753 | epot = -72.2074702494607 | etot = -54.4567169937108 +141000 ekin = 6.05123669074409 | erot = 11.8124070325092 | epot = -72.320360718363 | etot = -54.4567169951097 +142000 ekin = 6.17033803011812 | erot = 11.8605042646628 | epot = -72.4875592915039 | etot = -54.456716996723 +143000 ekin = 6.33580648591466 | erot = 11.8920252829288 | epot = -72.6845487670587 | etot = -54.4567169982153 +144000 ekin = 6.54012675510817 | erot = 11.8891823611258 | epot = -72.8860261161641 | etot = -54.4567169999301 +145000 ekin = 6.77470074055122 | erot = 11.835329124418 | epot = -73.0667468664361 | etot = -54.4567170014669 +146000 ekin = 7.03037496397094 | erot = 11.7160243954403 | epot = -73.2031163621668 | etot = -54.4567170027555 +147000 ekin = 7.29665364400722 | erot = 11.5220998483009 | epot = -73.2754704958303 | etot = -54.4567170035221 +148000 ekin = 7.56413207766539 | erot = 11.2503161699918 | epot = -73.271165251398 | etot = -54.4567170037408 +149000 ekin = 7.82550108771502 | erot = 10.9039474189432 | epot = -73.186165510058 | etot = -54.4567170033997 +150000 ekin = 8.07523421780289 | erot = 10.4929157971078 | epot = -73.0248670174494 | etot = -54.4567170025387 +151000 ekin = 8.30981632230252 | erot = 10.0329247877175 | epot = -72.7994581112926 | etot = -54.4567170012726 +152000 ekin = 8.52773011311519 | erot = 9.54384337569265 | epot = -72.5282904885591 | etot = -54.4567169997513 +153000 ekin = 8.72920635330005 | erot = 9.04773752673777 | epot = -72.2336608781799 | etot = -54.4567169981421 +154000 ekin = 8.91578242577526 | erot = 8.56683521279765 | epot = -71.9393346351766 | etot = -54.4567169966037 +155000 ekin = 9.08973687645378 | erot = 8.12169369348659 | epot = -71.6681475652115 | etot = -54.4567169952711 +156000 ekin = 9.25347765694827 | erot = 7.72974563990293 | epot = -71.4399402910981 | etot = -54.4567169942469 +157000 ekin = 9.40896984476625 | erot = 7.40429996452383 | epot = -71.2699868028787 | etot = -54.4567169935887 +158000 ekin = 9.55725976319915 | erot = 7.15399036856882 | epot = -71.1679671251158 | etot = -54.4567169933478 +159000 ekin = 9.69799996758358 | erot = 6.98263031177209 | epot = -71.1373472728688 | etot = -54.4567169935132 +160000 ekin = 9.82927262106836 | erot = 6.88943240362223 | epot = -71.175422018748 | etot = -54.4567169940574 +161000 ekin = 9.94752627639203 | erot = 6.86953876421339 | epot = -71.2737820355257 | etot = -54.4567169949203 +162000 ekin = 10.0476688890864 | erot = 6.91484346813018 | epot = -71.4192293532338 | etot = -54.4567169960172 +163000 ekin = 10.1233289285869 | erot = 7.01508857895246 | epot = -71.5951345047758 | etot = -54.4567169972365 +164000 ekin = 10.167286691898 | erot = 7.15919485891927 | epot = -71.7831985492619 | etot = -54.4567169984446 +165000 ekin = 10.172071480185 | erot = 7.33674388087147 | epot = -71.9655323605532 | etot = -54.4567169994967 +166000 ekin = 10.1307061587134 | erot = 7.53947176071279 | epot = -72.1268949196778 | etot = -54.4567170002516 +167000 ekin = 10.0375550044427 | erot = 7.76257261597526 | epot = -72.2568446210092 | etot = -54.4567170005913 +168000 ekin = 9.88919379240196 | erot = 8.00559837771024 | epot = -72.3515091705549 | etot = -54.4567170004427 +169000 ekin = 9.6851801471051 | erot = 8.27274634403696 | epot = -72.4146434909394 | etot = -54.4567169997973 +170000 ekin = 9.42857099718864 | erot = 8.57239606368005 | epot = -72.4576840595931 | etot = -54.4567169987245 +171000 ekin = 9.12604219834733 | erot = 8.91588733602143 | epot = -72.4986465317349 | etot = -54.4567169973661 +172000 ekin = 8.78753113653861 | erot = 9.31569783313623 | epot = -72.5599459655889 | etot = -54.456716995914 +173000 ekin = 8.43073965990155 | erot = 9.78417932410986 | epot = -72.671635978036 | etot = -54.4567169940246 +174000 ekin = 8.08793433498934 | erot = 10.3304999174786 | epot = -72.875151246456 | etot = -54.4567169939881 +175000 ekin = 7.76668155628905 | erot = 10.9530367882572 | epot = -73.1764353387604 | etot = -54.4567169942141 +176000 ekin = 7.47150671335906 | erot = 11.6457657834608 | epot = -73.5739894915295 | etot = -54.4567169947096 +177000 ekin = 7.20629810214911 | erot = 12.399154012461 | epot = -74.0621691100447 | etot = -54.4567169954346 +178000 ekin = 6.9741272880157 | erot = 13.20044277241 | epot = -74.6312870568994 | etot = -54.4567169964737 +179000 ekin = 6.77726137275677 | erot = 14.0344360010767 | epot = -75.2684143712719 | etot = -54.4567169974384 +180000 ekin = 6.61731488748464 | erot = 14.8864655843919 | epot = -75.9604974702674 | etot = -54.4567169983909 +181000 ekin = 6.49550388720072 | erot = 15.7408909287416 | epot = -76.6931118153551 | etot = -54.4567169994128 +182000 ekin = 6.41296392663574 | erot = 16.5825261501 | epot = -77.4522070769509 | etot = -54.4567170002152 +183000 ekin = 6.3709676834719 | erot = 17.3990430380084 | epot = -78.2267277223659 | etot = -54.4567170008855 +184000 ekin = 6.37100453719247 | erot = 18.179602922008 | epot = -79.0073244606508 | etot = -54.4567170014503 +185000 ekin = 6.41457925655592 | erot = 18.9145289221421 | epot = -79.7858251806889 | etot = -54.4567170019908 +186000 ekin = 6.5025855392 | erot = 19.5946185261353 | epot = -80.5539210679827 | etot = -54.4567170026474 +187000 ekin = 6.63421344627452 | erot = 20.2101022369757 | epot = -81.301032686852 | etot = -54.4567170036018 +188000 ekin = 6.80554165522936 | erot = 20.7494117391994 | epot = -82.0116703994567 | etot = -54.456717005028 +189000 ekin = 7.00820348124499 | erot = 21.1981783931206 | epot = -82.6630988813659 | etot = -54.4567170070004 +190000 ekin = 7.22868521932685 | erot = 21.5391098111504 | epot = -83.2245120398911 | etot = -54.4567170094138 +191000 ekin = 7.4477192848795 | erot = 21.7494170056954 | epot = -83.6538533032724 | etot = -54.4567170126975 +192000 ekin = 7.64125751956296 | erot = 21.8048207783503 | epot = -83.9027953123215 | etot = -54.4567170144082 +193000 ekin = 7.78828740685131 | erot = 21.6991673926867 | epot = -83.9441718146326 | etot = -54.4567170150946 +194000 ekin = 7.87257389701823 | erot = 21.4375246080176 | epot = -83.7668155195165 | etot = -54.4567170144808 +195000 ekin = 7.88499447657079 | erot = 21.0374826850393 | epot = -83.3791941740676 | etot = -54.4567170124575 +196000 ekin = 7.82454827833775 | erot = 20.5296762951829 | epot = -82.8109415830013 | etot = -54.4567170094806 +197000 ekin = 7.69767598869928 | erot = 19.9506603805433 | epot = -82.1050533754265 | etot = -54.4567170061839 +198000 ekin = 7.51633971742497 | erot = 19.3369849795458 | epot = -81.3100416995884 | etot = -54.4567170026176 +199000 ekin = 7.29564326176015 | erot = 18.7231663844438 | epot = -80.4755266460848 | etot = -54.4567169998808 +200000 ekin = 7.05165448325543 | erot = 18.1349004645792 | epot = -79.6432719456297 | etot = -54.4567169977951 +201000 ekin = 6.79980702715855 | erot = 17.5878866996147 | epot = -78.8444107231935 | etot = -54.4567169964203 +202000 ekin = 6.55389674542695 | erot = 17.0887428909489 | epot = -78.0993566320958 | etot = -54.45671699572 +203000 ekin = 6.32553934601966 | erot = 16.6359102128837 | epot = -77.4181665545184 | etot = -54.4567169956151 +204000 ekin = 6.12389931338692 | erot = 16.2210487374615 | epot = -76.8016650468575 | etot = -54.4567169960091 +205000 ekin = 5.95555747604073 | erot = 15.8306192384197 | epot = -76.2428937112594 | etot = -54.4567169967989 +206000 ekin = 5.82447629752483 | erot = 15.4475601715693 | epot = -75.7287534669597 | etot = -54.4567169978656 +207000 ekin = 5.73209725915263 | erot = 15.0531052521605 | epot = -75.2419195103738 | etot = -54.4567169990607 +208000 ekin = 5.67763110960507 | erot = 14.6288167787902 | epot = -74.7631648886021 | etot = -54.4567170002068 +209000 ekin = 5.65856116655301 | erot = 14.1588249337465 | epot = -74.2741031014098 | etot = -54.4567170011102 +210000 ekin = 5.6712828663927 | erot = 13.6320871718379 | epot = -73.7600870398326 | etot = -54.456717001602 +211000 ekin = 5.71170580201836 | erot = 13.0442947184104 | epot = -73.2127175220104 | etot = -54.4567170015816 +212000 ekin = 5.77563179366601 | erot = 12.3989793850675 | epot = -72.6313281797795 | etot = -54.456717001046 +213000 ekin = 5.85883529486916 | erot = 11.7074993993304 | epot = -72.0230516942857 | etot = -54.4567170000862 +214000 ekin = 5.95694378807647 | erot = 10.9878661192832 | epot = -71.4015269062099 | etot = -54.4567169988502 +215000 ekin = 6.06530909503383 | erot = 10.2626621519582 | epot = -70.7846882445011 | etot = -54.4567169975091 +216000 ekin = 6.17900319439905 | erot = 9.55646209151467 | epot = -70.1921822821411 | etot = -54.4567169962274 +217000 ekin = 6.29293379836596 | erot = 8.89318379220723 | epot = -69.6428345857192 | etot = -54.456716995146 +218000 ekin = 6.40198693072017 | erot = 8.29373644846285 | epot = -69.1524403735552 | etot = -54.4567169943722 +219000 ekin = 6.50112265239684 | erot = 7.77424405643487 | epot = -68.732083702802 | etot = -54.4567169939703 +220000 ekin = 6.58542599005467 | erot = 7.34501698346264 | epot = -68.3871599674677 | etot = -54.4567169939504 +221000 ekin = 6.6501699004463 | erot = 7.01032033730907 | epot = -68.1172072320272 | etot = -54.4567169942718 +222000 ekin = 6.69094775781919 | erot = 6.76886488024845 | epot = -67.9165296329197 | etot = -54.4567169948521 +223000 ekin = 6.7038957063633 | erot = 6.61485079073525 | epot = -67.7754634926816 | etot = -54.456716995583 +224000 ekin = 6.68598136532833 | erot = 6.53933986021408 | epot = -67.6820382218934 | etot = -54.456716996351 +225000 ekin = 6.63530548008247 | erot = 6.53171636120422 | epot = -67.6237388382973 | etot = -54.4567169970106 +226000 ekin = 6.55135057790799 | erot = 6.58128483353117 | epot = -67.5893524090246 | etot = -54.4567169975854 +227000 ekin = 6.43512370214418 | erot = 6.67791109033852 | epot = -67.5697517904585 | etot = -54.4567169979758 +228000 ekin = 6.28918970974481 | erot = 6.81247705117115 | epot = -67.5583837590923 | etot = -54.4567169981763 +229000 ekin = 6.1175658806069 | erot = 6.9774347779435 | epot = -67.5517176567548 | etot = -54.4567169982044 +230000 ekin = 5.92551276691973 | erot = 7.16674212049638 | epot = -67.5489718855087 | etot = -54.4567169980926 +231000 ekin = 5.71926565756217 | erot = 7.37564891103254 | epot = -67.551631566466 | etot = -54.4567169978713 +232000 ekin = 5.50574389394972 | erot = 7.60035647333841 | epot = -67.5628173648789 | etot = -54.4567169975908 +233000 ekin = 5.29225977426159 | erot = 7.83770399533277 | epot = -67.5866807668658 | etot = -54.4567169972714 +234000 ekin = 5.0862439206851 | erot = 8.08503631201549 | epot = -67.6279972296364 | etot = -54.4567169969359 +235000 ekin = 4.89494104385069 | erot = 8.33999580227168 | epot = -67.6916538427544 | etot = -54.456716996632 +236000 ekin = 4.72509234581344 | erot = 8.60029924339022 | epot = -67.7821085855883 | etot = -54.4567169963846 +237000 ekin = 4.58266021004047 | erot = 8.86357795327799 | epot = -67.9029551595439 | etot = -54.4567169962255 +238000 ekin = 4.47254260204365 | erot = 9.12720418841258 | epot = -68.0564637866342 | etot = -54.456716996178 +239000 ekin = 4.39833350162634 | erot = 9.38820734227972 | epot = -68.2432578401588 | etot = -54.4567169962527 +240000 ekin = 4.36216127770993 | erot = 9.6433463222102 | epot = -68.462224596357 | etot = -54.4567169964369 +241000 ekin = 4.36462932001241 | erot = 9.88937569308729 | epot = -68.710722009799 | etot = -54.4567169966993 +242000 ekin = 4.40486892553622 | erot = 10.1234451005895 | epot = -68.9850310231314 | etot = -54.4567169970057 +243000 ekin = 4.48069651384233 | erot = 10.3436703820966 | epot = -69.2810838932164 | etot = -54.4567169972774 +244000 ekin = 4.58885218173362 | erot = 10.5497495785183 | epot = -69.5953187577336 | etot = -54.4567169974817 +245000 ekin = 4.7252822690641 | erot = 10.7433460022148 | epot = -69.9253452688599 | etot = -54.456716997581 +246000 ekin = 4.88542118269804 | erot = 10.9282390794557 | epot = -70.2703772597261 | etot = -54.4567169975724 +247000 ekin = 5.06442778965484 | erot = 11.1101246208771 | epot = -70.6312694080142 | etot = -54.4567169974822 +248000 ekin = 5.25733886261363 | erot = 11.2960355852754 | epot = -71.0100914452567 | etot = -54.4567169973676 +249000 ekin = 5.45911617615758 | erot = 11.4934186026626 | epot = -71.4092517761299 | etot = -54.4567169973098 +250000 ekin = 5.66458445083205 | erot = 11.7089626303561 | epot = -71.830264078593 | etot = -54.4567169974049 +251000 ekin = 5.86828470151914 | erot = 11.947332082785 | epot = -72.2723337820484 | etot = -54.4567169977442 +252000 ekin = 6.0643012791257 | erot = 12.2100106162496 | epot = -72.7310288937673 | etot = -54.456716998392 +253000 ekin = 6.24616780492437 | erot = 12.4945137484007 | epot = -73.1973985526759 | etot = -54.4567169993509 +254000 ekin = 6.40690922038606 | erot = 12.7941888151781 | epot = -73.6578150361332 | etot = -54.456717000569 +255000 ekin = 6.53938368546832 | erot = 13.0989475895796 | epot = -74.0950482769172 | etot = -54.4567170018693 +256000 ekin = 6.63705992686419 | erot = 13.3969420757732 | epot = -74.4907190057033 | etot = -54.4567170030659 +257000 ekin = 6.6948413285815 | erot = 13.6765522910167 | epot = -74.828110623551 | etot = -54.4567170039528 +258000 ekin = 6.70989585739565 | erot = 13.9284862768506 | epot = -75.0950991385978 | etot = -54.4567170043516 +259000 ekin = 6.68225912100141 | erot = 14.1474604164198 | epot = -75.2864365416593 | etot = -54.456717004238 +260000 ekin = 6.6149269670595 | erot = 14.3327847112012 | epot = -75.4044286819583 | etot = -54.4567170036976 +261000 ekin = 6.51342916846603 | erot = 14.4875948089515 | epot = -75.4577409802865 | etot = -54.456717002869 +262000 ekin = 6.38502298989667 | erot = 14.6177175279221 | epot = -75.4594575197481 | etot = -54.4567170019294 +263000 ekin = 6.23773151259011 | erot = 14.7300999730227 | epot = -75.4245484866719 | etot = -54.4567170010591 +264000 ekin = 6.07942833310978 | erot = 14.8312906384144 | epot = -75.3674359719007 | etot = -54.4567170003765 +265000 ekin = 5.91711592012144 | erot = 14.9263499746133 | epot = -75.3001828946998 | etot = -54.456716999965 +266000 ekin = 5.75647898919375 | erot = 15.0181250690755 | epot = -75.2313210581342 | etot = -54.456716999865 +267000 ekin = 5.60177946975526 | erot = 15.1067951880379 | epot = -75.1652916578609 | etot = -54.4567170000677 +268000 ekin = 5.45615379098988 | erot = 15.189745234935 | epot = -75.1026160264251 | etot = -54.4567170005002 +269000 ekin = 5.32235014694951 | erot = 15.2617179030208 | epot = -75.0407850514111 | etot = -54.4567170014407 +270000 ekin = 5.20387607982583 | erot = 15.3135128498176 | epot = -74.9741059315067 | etot = -54.4567170018633 +271000 ekin = 5.10637822315521 | erot = 15.3372496535188 | epot = -74.9003448785744 | etot = -54.4567170019004 +272000 ekin = 5.03885187481446 | erot = 15.327624841925 | epot = -74.8231937182271 | etot = -54.4567170014876 +273000 ekin = 5.01411589731618 | erot = 15.2821745715634 | epot = -74.7530074694248 | etot = -54.4567170005452 +274000 ekin = 5.04786741773145 | erot = 15.2025250198948 | epot = -74.7071094368927 | etot = -54.4567169992664 +275000 ekin = 5.15594350432475 | erot = 15.0944700838312 | epot = -74.7071305860956 | etot = -54.4567169979397 +276000 ekin = 5.35014893903236 | erot = 14.9659361282781 | epot = -74.7728020645803 | etot = -54.4567169972699 +277000 ekin = 5.63387543033527 | erot = 14.8238652605351 | epot = -74.9144576883626 | etot = -54.4567169974923 +278000 ekin = 5.99920506254099 | erot = 14.6727240463492 | epot = -75.1286461075833 | etot = -54.4567169986931 +279000 ekin = 6.42692112008751 | erot = 14.513699602506 | epot = -75.3973377231584 | etot = -54.4567170005649 +280000 ekin = 6.88964247825144 | erot = 14.3457897766104 | epot = -75.6921492574821 | etot = -54.4567170026203 +281000 ekin = 7.35680808434941 | erot = 14.1678692303649 | epot = -75.9813943196751 | etot = -54.4567170049608 +282000 ekin = 7.79894530205517 | erot = 13.9783131612805 | epot = -76.2339754694448 | etot = -54.4567170061092 +283000 ekin = 8.19329732426299 | erot = 13.7802856701101 | epot = -76.4303000007414 | etot = -54.4567170063683 +284000 ekin = 8.52584895841313 | erot = 13.5821656429363 | epot = -76.5647316071434 | etot = -54.4567170057939 +285000 ekin = 8.79110175655308 | erot = 13.3960594628864 | epot = -76.6438782240431 | etot = -54.4567170046036 +286000 ekin = 8.99062132696362 | erot = 13.2361225163112 | epot = -76.6834608463776 | etot = -54.4567170031028 +287000 ekin = 9.13075096351798 | erot = 13.116415254778 | epot = -76.7038832199022 | etot = -54.4567170016063 +288000 ekin = 9.2201402060807 | erot = 13.0487281533165 | epot = -76.7255853597818 | etot = -54.4567170003847 +289000 ekin = 9.26758159069276 | erot = 13.0407526423211 | epot = -76.7650512326338 | etot = -54.4567169996199 +290000 ekin = 9.28045458789671 | erot = 13.0948897576293 | epot = -76.8320613449156 | etot = -54.4567169993897 +291000 ekin = 9.26388652304975 | erot = 13.2078630291817 | epot = -76.9284665519076 | etot = -54.4567169996761 +292000 ekin = 9.22058026560232 | erot = 13.3711344770738 | epot = -77.0484317430577 | etot = -54.4567170003816 +293000 ekin = 9.15114447320877 | erot = 13.5719438956012 | epot = -77.1798053701816 | etot = -54.4567170013717 +294000 ekin = 9.05470928641046 | erot = 13.7944688657362 | epot = -77.3058951547296 | etot = -54.4567170025829 +295000 ekin = 8.92962793964649 | erot = 14.0209919623835 | epot = -77.4073369057994 | etot = -54.4567170037694 +296000 ekin = 8.77413837931907 | erot = 14.233755611159 | epot = -77.4646109953774 | etot = -54.4567170048993 +297000 ekin = 8.58694141176308 | erot = 14.4156117991042 | epot = -77.4592702167607 | etot = -54.4567170058934 +298000 ekin = 8.36771464082724 | erot = 14.5507736801853 | epot = -77.3752053276863 | etot = -54.4567170066738 +299000 ekin = 8.11757828386985 | erot = 14.6256180333509 | epot = -77.1999133243813 | etot = -54.4567170071606 +300000 ekin = 7.83948860310585 | erot = 14.6295386097215 | epot = -76.9257442201075 | etot = -54.4567170072802 +301000 ekin = 7.53848779196521 | erot = 14.5557753435651 | epot = -76.5509801425169 | etot = -54.4567170069866 +302000 ekin = 7.22172227244577 | erot = 14.4020558262293 | epot = -76.0804951049512 | etot = -54.4567170062762 +303000 ekin = 6.898170015461 | erot = 14.170873945613 | epot = -75.5257609662701 | etot = -54.4567170051961 +304000 ekin = 6.57808261931137 | erot = 13.8692983759016 | epot = -74.9040979990486 | etot = -54.4567170038356 +305000 ekin = 6.2722234776823 | erot = 13.5083194093946 | epot = -74.2372598893895 | etot = -54.4567170023126 +306000 ekin = 5.99103930572871 | erot = 13.1018578904956 | epot = -73.549614196971 | etot = -54.4567170007467 +307000 ekin = 5.74391705619897 | erot = 12.6656285179261 | epot = -72.8662625733666 | etot = -54.4567169992415 +308000 ekin = 5.53864734382477 | erot = 12.2160468439345 | epot = -72.2114111856259 | etot = -54.4567169978666 +309000 ekin = 5.38115498325946 | erot = 11.7690964633918 | epot = -71.6069684433846 | etot = -54.4567169967334 +310000 ekin = 5.27549820636478 | erot = 11.3394194656315 | epot = -71.0716346677326 | etot = -54.4567169957363 +311000 ekin = 5.22401044242898 | erot = 10.9405074525655 | epot = -70.6212348899484 | etot = -54.4567169949538 +312000 ekin = 5.22752009859842 | erot = 10.58378677297 | epot = -70.2680238659752 | etot = -54.4567169944068 +313000 ekin = 5.2855691102471 | erot = 10.278028711995 | epot = -70.0203148163729 | etot = -54.4567169941308 +314000 ekin = 5.39655367391449 | erot = 10.0287341725483 | epot = -69.8820048406328 | etot = -54.45671699417 +315000 ekin = 5.55776516265216 | erot = 9.83752336502832 | epot = -69.8520055222453 | etot = -54.4567169945648 +316000 ekin = 5.76535304575541 | erot = 9.7016458093175 | epot = -69.9237158504148 | etot = -54.4567169953418 +317000 ekin = 6.01426692501147 | erot = 9.61377206322875 | epot = -70.0847559847325 | etot = -54.4567169964923 +318000 ekin = 6.29825476428649 | erot = 9.56224828023903 | epot = -70.3172200424818 | etot = -54.4567169979563 +319000 ekin = 6.60999451535049 | erot = 9.5319755768407 | epot = -70.5986870918048 | etot = -54.4567169996136 +320000 ekin = 6.94141382334492 | erot = 9.50599899524184 | epot = -70.9041298198703 | etot = -54.4567170012835 +321000 ekin = 7.28420684012922 | erot = 9.46773994831762 | epot = -71.2086637911961 | etot = -54.4567170027492 +322000 ekin = 7.63049375596247 | erot = 9.40359379846618 | epot = -71.4908045582248 | etot = -54.4567170037962 +323000 ekin = 7.97350371439743 | erot = 9.30540350739528 | epot = -71.7356242260599 | etot = -54.4567170042672 +324000 ekin = 8.30812216471307 | erot = 9.17221603058585 | epot = -71.9370551994029 | etot = -54.456717004104 +325000 ekin = 8.63115493817483 | erot = 9.01082149334885 | epot = -72.0986934348921 | etot = -54.4567170033684 +326000 ekin = 8.94122829508797 | erot = 8.83486894707444 | epot = -72.2328142443922 | etot = -54.4567170022298 +327000 ekin = 9.23834163996081 | erot = 8.66273411451702 | epot = -72.3577927554029 | etot = -54.4567170009251 +328000 ekin = 9.52317541128336 | erot = 8.51461710980073 | epot = -72.4945095207944 | etot = -54.4567169997103 +329000 ekin = 9.79629908030493 | erot = 8.40945765597971 | epot = -72.6624737351001 | etot = -54.4567169988154 +330000 ekin = 10.0574197993294 | erot = 8.36217436292908 | epot = -72.8763111606755 | etot = -54.4567169984171 +331000 ekin = 10.3047815002041 | erot = 8.38155728442034 | epot = -73.1430557832487 | etot = -54.4567169986243 +332000 ekin = 10.5347934531664 | erot = 8.46897862472524 | epot = -73.4604890773601 | etot = -54.4567169994685 +333000 ekin = 10.7419525181473 | erot = 8.61799790190843 | epot = -73.8166674209546 | etot = -54.4567170008989 +334000 ekin = 10.9191228829944 | erot = 8.81492290907158 | epot = -74.1907627948314 | etot = -54.4567170027654 +335000 ekin = 11.0582310034198 | erot = 9.04039212108807 | epot = -74.5553401293301 | etot = -54.4567170048223 +336000 ekin = 11.1513905495672 | erot = 9.27198870540517 | epot = -74.880096261711 | etot = -54.4567170067386 +337000 ekin = 11.1923691999822 | erot = 9.48771814311757 | epot = -75.1368043512457 | etot = -54.4567170081459 +338000 ekin = 11.1781584914567 | erot = 9.66988639694834 | epot = -75.3047618971217 | etot = -54.4567170087167 +339000 ekin = 11.1102731632004 | erot = 9.80861367328644 | epot = -75.3756038447372 | etot = -54.4567170082504 +340000 ekin = 10.9953796290097 | erot = 9.90409604937516 | epot = -75.3561926851333 | etot = -54.4567170067484 +341000 ekin = 10.8449930881419 | erot = 9.96693425469746 | epot = -75.268644347256 | etot = -54.4567170044166 +342000 ekin = 10.6742553473784 | erot = 10.0163686561569 | epot = -75.1473410051493 | etot = -54.456717001614 +343000 ekin = 10.5000860602698 | erot = 10.0768729195906 | epot = -75.0336759786219 | etot = -54.4567169987615 +344000 ekin = 10.3391511438798 | erot = 10.1739718598944 | epot = -74.9698400000255 | etot = -54.4567169962514 +345000 ekin = 10.2060562002363 | erot = 10.3301918101587 | epot = -74.9929650047806 | etot = -54.4567169943855 +346000 ekin = 10.1120018691461 | erot = 10.5617784620028 | epot = -75.1304973245115 | etot = -54.4567169933625 +347000 ekin = 10.0639419677441 | erot = 10.8764329835346 | epot = -75.3970919445696 | etot = -54.456716993291 +348000 ekin = 10.0641555603058 | erot = 11.272025732448 | epot = -75.7928982869613 | etot = -54.4567169942075 +349000 ekin = 10.1101145524105 | erot = 11.7361477401435 | epot = -76.3029792886416 | etot = -54.4567169960877 +350000 ekin = 10.194582521887 | erot = 12.2464414545059 | epot = -76.8977409752301 | etot = -54.4567169988372 +351000 ekin = 10.3059767731321 | erot = 12.7718298178684 | epot = -77.5345235932654 | etot = -54.4567170022649 +352000 ekin = 10.4291136841201 | erot = 13.274913313952 | epot = -78.1607440041161 | etot = -54.456717006044 +353000 ekin = 10.5464827220696 | erot = 13.7157870243144 | epot = -78.7189867560916 | etot = -54.4567170097076 +354000 ekin = 10.6401081739569 | erot = 14.057229186967 | epot = -79.1540543736257 | etot = -54.4567170127017 +355000 ekin = 10.6938478547038 | erot = 14.2706326977498 | epot = -79.421197566951 | etot = -54.4567170144975 +356000 ekin = 10.6957117760349 | erot = 14.3414067966632 | epot = -79.4938355874434 | etot = -54.4567170147452 +357000 ekin = 10.6396104112845 | erot = 14.2722652226246 | epot = -79.3685926473052 | etot = -54.4567170133961 +358000 ekin = 10.5262520486628 | erot = 14.0832401802021 | epot = -79.0662092386956 | etot = -54.4567170098307 +359000 ekin = 10.3670012344496 | erot = 13.8092169878378 | epot = -78.6329352288622 | etot = -54.4567170065747 +360000 ekin = 10.1730345911639 | erot = 13.4915235481033 | epot = -78.1212751423934 | etot = -54.4567170031263 +361000 ekin = 9.95554687781761 | erot = 13.1714216600725 | epot = -77.5836855379417 | etot = -54.4567170000515 +362000 ekin = 9.72626696401673 | erot = 12.8843171182331 | epot = -77.0673010799944 | etot = -54.4567169977445 +363000 ekin = 9.49594699775478 | erot = 12.6552376501784 | epot = -76.6079016443334 | etot = -54.4567169964002 +364000 ekin = 9.27348051448134 | erot = 12.4966397003761 | epot = -76.226837210883 | etot = -54.4567169960255 +365000 ekin = 9.06556428138691 | erot = 12.408435956081 | epot = -75.9307172339611 | etot = -54.4567169964932 +366000 ekin = 8.87671568778686 | erot = 12.3798183116159 | epot = -75.7132509969826 | etot = -54.4567169975798 +367000 ekin = 8.70950256436292 | erot = 12.3923063931803 | epot = -75.5585259565717 | etot = -54.4567169990284 +368000 ekin = 8.56482533240977 | erot = 12.4233361953079 | epot = -75.4448785283144 | etot = -54.4567170005967 +369000 ekin = 8.44216266248821 | erot = 12.4496962572909 | epot = -75.3485759218773 | etot = -54.4567170020982 +370000 ekin = 8.33975827582798 | erot = 12.4502709028872 | epot = -75.2467461821219 | etot = -54.4567170034067 +371000 ekin = 8.25479796579994 | erot = 12.4078609325617 | epot = -75.1193759028063 | etot = -54.4567170044447 +372000 ekin = 8.1836687896195 | erot = 12.3101981041707 | epot = -74.9505838989413 | etot = -54.4567170051512 +373000 ekin = 8.12237120101005 | erot = 12.150469466894 | epot = -74.7295576733678 | etot = -54.4567170054638 +374000 ekin = 8.06677539354389 | erot = 11.9273562293618 | epot = -74.4508486283267 | etot = -54.456717005421 +375000 ekin = 8.01350111914578 | erot = 11.6453205219606 | epot = -74.1155386458777 | etot = -54.4567170047713 +376000 ekin = 7.96091572449109 | erot = 11.3149868234321 | epot = -73.7326195516342 | etot = -54.4567170037111 +377000 ekin = 7.90852881943222 | erot = 10.9517029979104 | epot = -73.3169488197141 | etot = -54.4567170023715 +378000 ekin = 7.85672904351673 | erot = 10.5738384909382 | epot = -72.8872845353939 | etot = -54.456717000939 +379000 ekin = 7.80630927768835 | erot = 10.2005458441792 | epot = -72.4635721214806 | etot = -54.456716999613 +380000 ekin = 7.75800079079379 | erot = 9.84945299077856 | epot = -72.0641707801124 | etot = -54.4567169985401 +381000 ekin = 7.71644600863279 | erot = 9.53800624562745 | epot = -71.7111692500986 | etot = -54.4567169958383 +382000 ekin = 7.68441527893159 | erot = 9.2783208983659 | epot = -71.4194531731883 | etot = -54.4567169958909 +383000 ekin = 7.65787566183791 | erot = 9.07303517127919 | epot = -71.1876278290995 | etot = -54.4567169959824 +384000 ekin = 7.63460910810437 | erot = 8.92241188986493 | epot = -71.0137379939128 | etot = -54.4567169959435 +385000 ekin = 7.61495351644065 | erot = 8.82611541869655 | epot = -70.8977859308194 | etot = -54.4567169956822 +386000 ekin = 7.60189486281627 | erot = 8.78441843695726 | epot = -70.8430302950001 | etot = -54.4567169952266 +387000 ekin = 7.6004189110324 | erot = 8.79838942462995 | epot = -70.8555253303877 | etot = -54.4567169947253 +388000 ekin = 7.61622683362077 | erot = 8.86894752211266 | epot = -70.9418913501425 | etot = -54.4567169944091 +389000 ekin = 7.65411397461101 | erot = 8.99508106939632 | epot = -71.1059120385254 | etot = -54.4567169945181 +390000 ekin = 7.71640194413762 | erot = 9.17181221608524 | epot = -71.3449311554783 | etot = -54.4567169952555 +391000 ekin = 7.80179289421792 | erot = 9.38846927313518 | epot = -71.6469791640467 | etot = -54.4567169966936 +392000 ekin = 7.90489667240656 | erot = 9.62803617098395 | epot = -71.9896498421597 | etot = -54.4567169987692 +393000 ekin = 8.01656398897941 | erot = 9.86778742621825 | epot = -72.3410684164707 | etot = -54.456717001273 +394000 ekin = 8.12500523168231 | erot = 10.0813107732258 | epot = -72.6630330087845 | etot = -54.4567170038763 +395000 ekin = 8.21751488333194 | erot = 10.2416672650839 | epot = -72.915899154609 | etot = -54.4567170061932 +396000 ekin = 8.28249369762926 | erot = 10.3253499492638 | epot = -73.0645606546967 | etot = -54.4567170078036 +397000 ekin = 8.31139266032575 | erot = 10.315944912881 | epot = -73.0840545817406 | etot = -54.4567170085339 +398000 ekin = 8.30021982541605 | erot = 10.206034771068 | epot = -72.9629716046318 | etot = -54.4567170081478 +399000 ekin = 8.25031816200888 | erot = 9.99940615795296 | epot = -72.7064413267651 | etot = -54.4567170068033 +400000 ekin = 8.16827445227822 | erot = 9.70970155030778 | epot = -72.3346930072165 | etot = -54.4567170046305 +401000 ekin = 8.06453103741756 | erot = 9.35834706106926 | epot = -71.8795951005915 | etot = -54.4567170021047 +402000 ekin = 7.95192509945215 | erot = 8.9720246874988 | epot = -71.3806667861483 | etot = -54.4567169991973 +403000 ekin = 7.84555125758116 | erot = 8.5797180293817 | epot = -70.8819862834035 | etot = -54.4567169964406 +404000 ekin = 7.76002341839185 | erot = 8.20898478879149 | epot = -70.4257252013545 | etot = -54.4567169941711 +405000 ekin = 7.7073293183604 | erot = 7.88377510171153 | epot = -70.04782141242 | etot = -54.4567169923481 +406000 ekin = 7.69678612080548 | erot = 7.62266799266178 | epot = -69.7761711045927 | etot = -54.4567169911254 +407000 ekin = 7.73513354697874 | erot = 7.43808993656983 | epot = -69.6299404740827 | etot = -54.4567169905341 +408000 ekin = 7.8257165724106 | erot = 7.33617130723373 | epot = -69.6186048702056 | etot = -54.4567169905613 +409000 ekin = 7.9684496970445 | erot = 7.31680539063865 | epot = -69.7419720788775 | etot = -54.4567169911943 +410000 ekin = 8.15983887505972 | erot = 7.37383443939713 | epot = -69.9903903068714 | etot = -54.4567169924145 +411000 ekin = 8.39302325865334 | erot = 7.4953976334531 | epot = -70.345137886285 | etot = -54.4567169941786 +412000 ekin = 8.65789214072952 | erot = 7.66460030904632 | epot = -70.7792094461696 | etot = -54.4567169963938 +413000 ekin = 8.94143674964152 | erot = 7.86072523711258 | epot = -71.2588789856408 | etot = -54.4567169988867 +414000 ekin = 9.2285627397849 | erot = 8.06118997496099 | epot = -71.7464697161277 | etot = -54.4567170013818 +415000 ekin = 9.50353222597935 | erot = 8.24426927837358 | epot = -72.2045185078814 | etot = -54.4567170035285 +416000 ekin = 9.75196200032584 | erot = 8.3922487405301 | epot = -72.6009277458387 | etot = -54.4567170049828 +417000 ekin = 9.96294493861504 | erot = 8.4942852221574 | epot = -72.9139471663141 | etot = -54.4567170055416 +418000 ekin = 10.1306180934849 | erot = 8.54795226111009 | epot = -73.1352873597258 | etot = -54.4567170051309 +419000 ekin = 10.2546096453467 | erot = 8.55936156101576 | epot = -73.2706882103111 | etot = -54.4567170039486 +420000 ekin = 10.3392413847909 | erot = 8.5415094684924 | epot = -73.3374678555834 | etot = -54.4567170023001 +421000 ekin = 10.3918587231878 | erot = 8.51150598433204 | epot = -73.3600817080286 | etot = -54.4567170005087 +422000 ekin = 10.420878514384 | erot = 8.48778665542919 | epot = -73.3653821686562 | etot = -54.456716998843 +423000 ekin = 10.434035033694 | erot = 8.48770021699399 | epot = -73.3784522482256 | etot = -54.4567169975376 +424000 ekin = 10.4370437707889 | erot = 8.52571262941259 | epot = -73.4194733968352 | etot = -54.4567169966337 +425000 ekin = 10.4323779106206 | erot = 8.61252848638848 | epot = -73.5016237919832 | etot = -54.4567173949741 +426000 ekin = 10.102769114069 | erot = 8.3108489099065 | epot = -72.8703349960252 | etot = -54.4567169720496 +427000 ekin = 10.5737761012436 | erot = 8.79661991597064 | epot = -73.8271134052581 | etot = -54.4567173880439 +428000 ekin = 10.6073086148571 | erot = 9.02815734229429 | epot = -74.0921832808582 | etot = -54.4567173237068 +429000 ekin = 10.5962992474403 | erot = 9.29502326253689 | epot = -74.3480398354735 | etot = -54.4567173254963 +430000 ekin = 10.5389640746102 | erot = 9.58950094092139 | epot = -74.5851823430198 | etot = -54.4567173274882 +431000 ekin = 10.424560070762 | erot = 9.89254945457633 | epot = -74.7738268547395 | etot = -54.4567173294012 +432000 ekin = 10.2456183701252 | erot = 10.1831375483455 | epot = -74.8854732493789 | etot = -54.4567173309082 +433000 ekin = 10.0001839880952 | erot = 10.4408608802982 | epot = -74.8977622000937 | etot = -54.4567173317003 +434000 ekin = 9.69355282026506 | erot = 10.6487620299475 | epot = -74.7990321817772 | etot = -54.4567173315646 +435000 ekin = 9.33897175582479 | erot = 10.7957385369256 | epot = -74.5914276232058 | etot = -54.4567173304554 +436000 ekin = 8.95691803308959 | erot = 10.8779295163446 | epot = -74.2915648779558 | etot = -54.4567173285216 +437000 ekin = 8.57292089770475 | erot = 10.8987288383945 | epot = -73.9283670621729 | etot = -54.4567173260737 +438000 ekin = 8.21432291140729 | erot = 10.8675107992394 | epot = -73.5385510341416 | etot = -54.4567173234949 +439000 ekin = 7.90671191649818 | erot = 10.7975744645327 | epot = -73.1610037021698 | etot = -54.4567173211389 +440000 ekin = 7.67083057757437 | erot = 10.704001256365 | epot = -72.8315491531841 | etot = -54.4567173192447 +441000 ekin = 7.52056261879319 | erot = 10.6019893788256 | epot = -72.5792693155341 | etot = -54.4567173179153 +442000 ekin = 7.46221677066932 | erot = 10.5058719364384 | epot = -72.4248060242437 | etot = -54.456717317136 +443000 ekin = 7.49495713473312 | erot = 10.4286506059643 | epot = -72.3803250575354 | etot = -54.456717316838 +444000 ekin = 7.61199665329081 | erot = 10.3816668192493 | epot = -72.4503807894868 | etot = -54.4567173169467 +445000 ekin = 7.80212113163771 | erot = 10.3740565458196 | epot = -72.6328949948784 | etot = -54.4567173174211 +446000 ekin = 8.05121208711611 | erot = 10.4118503345054 | epot = -72.9197797398638 | etot = -54.4567173182423 +447000 ekin = 8.34364339005653 | erot = 10.4968771153949 | epot = -73.2972378248907 | etot = -54.4567173194392 +448000 ekin = 8.66325116931131 | erot = 10.625662516794 | epot = -73.7456310070801 | etot = -54.4567173209747 +449000 ekin = 8.99432108685695 | erot = 10.7889809207854 | epot = -74.2400193304181 | etot = -54.4567173227757 +450000 ekin = 9.32245948923829 | erot = 10.9722541224504 | epot = -74.751430936397 | etot = -54.4567173247083 +451000 ekin = 9.63536145904856 | erot = 11.156898532641 | epot = -75.2489773182818 | etot = -54.4567173265923 +452000 ekin = 9.92347885289157 | erot = 11.3224562063112 | epot = -75.7026523874263 | etot = -54.4567173282236 +453000 ekin = 10.1805354635941 | erot = 11.4491361056663 | epot = -76.0863888986956 | etot = -54.4567173294351 +454000 ekin = 10.4037376220791 | erot = 11.5201500068692 | epot = -76.3806049590792 | etot = -54.4567173301309 +455000 ekin = 10.5935799379761 | erot = 11.5233605384503 | epot = -76.5736578067353 | etot = -54.4567173303089 +456000 ekin = 10.7532157912851 | erot = 11.4519857883943 | epot = -76.6619189097318 | etot = -54.4567173300525 +457000 ekin = 10.8874528211754 | erot = 11.3044013916463 | epot = -76.6485715423183 | etot = -54.4567173294966 +458000 ekin = 11.001535672013 | erot = 11.0833330749799 | epot = -76.5415860757935 | etot = -54.4567173288006 +459000 ekin = 11.0999386292817 | erot = 10.7947718565368 | epot = -76.3514278139082 | etot = -54.4567173280897 +460000 ekin = 11.1853921968857 | erot = 10.4469386378857 | epot = -76.0890481622364 | etot = -54.456717327465 +461000 ekin = 11.2582527529505 | erot = 10.0494375630704 | epot = -75.7644076429835 | etot = -54.4567173269627 +462000 ekin = 11.3163535530699 | erot = 9.61273056585407 | epot = -75.3858014455075 | etot = -54.4567173265835 +463000 ekin = 11.3552901634218 | erot = 9.1478274108088 | epot = -74.959834900532 | etot = -54.4567173263014 +464000 ekin = 11.3690501275205 | erot = 8.66606699696608 | epot = -74.4918344505474 | etot = -54.4567173260608 +465000 ekin = 11.3509395537084 | erot = 8.17907283457056 | epot = -73.9867297140534 | etot = -54.4567173257744 +466000 ekin = 11.2946941726397 | erot = 7.69877194993406 | epot = -73.4501834479707 | etot = -54.4567173253969 +467000 ekin = 11.1954789031865 | erot = 7.23723472359684 | epot = -72.889430951676 | etot = -54.4567173248926 +468000 ekin = 11.0507711892589 | erot = 6.80628316339318 | epot = -72.3137716769111 | etot = -54.456717324259 +469000 ekin = 10.8610622879329 | erot = 6.41684853511032 | epot = -71.7346281465611 | etot = -54.4567173235179 +470000 ekin = 10.6303293037452 | erot = 6.07816222727495 | epot = -71.1652088537213 | etot = -54.4567173227011 +471000 ekin = 10.3662986164649 | erot = 5.79695153505929 | epot = -70.6199674733634 | etot = -54.4567173218392 +472000 ekin = 10.0804738216169 | erot = 5.57685091063635 | epot = -70.1140420532125 | etot = -54.4567173209592 +473000 ekin = 9.78780661767614 | erot = 5.41818349563098 | epot = -69.6627074333982 | etot = -54.4567173200911 +474000 ekin = 9.50580460754672 | erot = 5.31815275508718 | epot = -69.2806746819342 | etot = -54.4567173193003 +475000 ekin = 9.25291327929457 | erot = 5.27138134030385 | epot = -68.9810119382783 | etot = -54.4567173186798 +476000 ekin = 9.04625597797249 | erot = 5.27069575628468 | epot = -68.773669052586 | etot = -54.4567173183288 +477000 ekin = 8.89916818083064 | erot = 5.30806481991686 | epot = -68.6639503190668 | etot = -54.4567173183193 +478000 ekin = 8.81917608291934 | erot = 5.37558721489192 | epot = -68.6514806164727 | etot = -54.4567173186615 +479000 ekin = 8.80688801078544 | erot = 5.46634570345682 | epot = -68.729951033573 | etot = -54.4567173193307 +480000 ekin = 8.85595772732357 | erot = 5.57491529290513 | epot = -68.8875903404655 | etot = -54.4567173202368 +481000 ekin = 8.9542741130118 | erot = 5.69752640400347 | epot = -69.108517838353 | etot = -54.4567173213377 +482000 ekin = 9.0851963959233 | erot = 5.83169305185317 | epot = -69.3736067703566 | etot = -54.4567173225801 +483000 ekin = 9.22914118620107 | erot = 5.97559221268723 | epot = -69.6614507227971 | etot = -54.4567173239088 +484000 ekin = 9.3652821454577 | erot = 6.12746790494848 | epot = -69.9494673756554 | etot = -54.4567173252492 +485000 ekin = 9.47329519940104 | erot = 6.28524325030241 | epot = -70.2152557762067 | etot = -54.4567173265033 +486000 ekin = 9.53507247962912 | erot = 6.44644236438812 | epot = -70.4382321715783 | etot = -54.4567173275611 +487000 ekin = 9.53625700454616 | erot = 6.60839833383176 | epot = -70.6013726667003 | etot = -54.4567173283224 +488000 ekin = 9.46740386001155 | erot = 6.7686126489044 | epot = -70.692733837639 | etot = -54.456717328723 +489000 ekin = 9.32459963448959 | erot = 6.92506407616445 | epot = -70.7063810394037 | etot = -54.4567173287496 +490000 ekin = 9.10947948779674 | erot = 7.07631880463358 | epot = -70.642515620872 | etot = -54.4567173284416 +491000 ekin = 8.82889148608559 | erot = 7.22129660537944 | epot = -70.5069054189546 | etot = -54.4567173274895 +492000 ekin = 8.4962875622067 | erot = 7.35787986415986 | epot = -70.3108847533115 | etot = -54.456717326945 +493000 ekin = 8.12488660028817 | erot = 7.48347573766635 | epot = -70.0650796642411 | etot = -54.4567173262866 +494000 ekin = 7.72897177736132 | erot = 7.59497930547726 | epot = -69.7806684084012 | etot = -54.4567173255626 +495000 ekin = 7.32471897790911 | erot = 7.68843463889095 | epot = -69.469870936463 | etot = -54.4567173196629 +496000 ekin = 6.87941085033666 | erot = 7.73484184190264 | epot = -69.0709701954428 | etot = -54.4567175032035 +497000 ekin = 6.10739678417312 | erot = 7.42313588089451 | epot = -67.9872498480863 | etot = -54.4567171830187 +498000 ekin = 6.8219211726194 | erot = 7.452484020774 | epot = -68.7311226730858 | etot = -54.4567174796924 +499000 ekin = 6.94584861699242 | erot = 7.49830975479282 | epot = -68.9008757168133 | etot = -54.456717345028 +500000 ekin = 6.96878886920507 | erot = 7.49013442211219 | epot = -68.9156406384771 | etot = -54.4567173471599 +501000 ekin = 7.01883264694271 | erot = 7.44447241972525 | epot = -68.9200224127091 | etot = -54.4567173460412 +502000 ekin = 7.10336336312501 | erot = 7.36823892373933 | epot = -68.9283196315699 | etot = -54.4567173447056 +503000 ekin = 7.2289928990578 | erot = 7.27372377747254 | epot = -68.9594340197928 | etot = -54.4567173432625 +504000 ekin = 7.4005994068373 | erot = 7.17755657732697 | epot = -69.0348733260256 | etot = -54.4567173418614 +505000 ekin = 7.62076916489943 | erot = 7.09828995867377 | epot = -69.1757764642378 | etot = -54.4567173406646 +506000 ekin = 7.88922231362651 | erot = 7.05443045706273 | epot = -69.4003701105027 | etot = -54.4567173398134 +507000 ekin = 8.20252308360148 | erot = 7.06244306986031 | epot = -69.7216834928712 | etot = -54.4567173394094 +508000 ekin = 8.55418648389005 | erot = 7.13501434822763 | epot = -70.1459181716127 | etot = -54.456717339495 +509000 ekin = 8.93520489703948 | erot = 7.27978431320932 | epot = -70.6717065503033 | etot = -54.4567173400545 +510000 ekin = 9.33488714865777 | erot = 7.49865655844548 | epot = -71.2902610481323 | etot = -54.4567173410291 +511000 ekin = 9.74177952549099 | erot = 7.7876981022302 | epot = -71.9861949700651 | etot = -54.4567173423439 +512000 ekin = 10.1443709695663 | erot = 8.13755539116802 | epot = -72.7386437046674 | etot = -54.456717343933 +513000 ekin = 10.5313274213558 | erot = 8.5342579999187 | epot = -73.5223027670323 | etot = -54.4567173457578 +514000 ekin = 10.8911959115654 | erot = 8.96029115458747 | epot = -74.3082044139355 | etot = -54.4567173477827 +515000 ekin = 11.2118380805567 | erot = 9.39590833077182 | epot = -75.0644637612635 | etot = -54.456717349935 +516000 ekin = 11.4801433363293 | erot = 9.82076307115846 | epot = -75.7576237595405 | etot = -54.4567173520528 +517000 ekin = 11.6825679425294 | erot = 10.2159470150834 | epot = -76.3552323114897 | etot = -54.4567173538768 +518000 ekin = 11.8066633107561 | erot = 10.5663069186954 | epot = -76.8296875845688 | etot = -54.4567173551172 +519000 ekin = 11.8431596193449 | erot = 10.8625837428753 | epot = -77.1624607177696 | etot = -54.4567173555494 +520000 ekin = 11.7878285859662 | erot = 11.1027186624689 | epot = -77.3472646035601 | etot = -54.456717355125 +521000 ekin = 11.6422563220656 | erot = 11.2918969270452 | epot = -77.3908706030577 | etot = -54.4567173539469 +522000 ekin = 11.4135745678826 | erot = 11.4412270159144 | epot = -77.3115189360506 | etot = -54.4567173522537 +523000 ekin = 11.1132889182013 | erot = 11.565401362665 | epot = -77.1354076312099 | etot = -54.4567173503435 +524000 ekin = 10.7556171647493 | erot = 11.6798233409133 | epot = -76.89215785419 | etot = -54.4567173485274 +525000 ekin = 10.3557495856454 | erot = 11.7976048718282 | epot = -76.6100718045622 | etot = -54.4567173470886 +526000 ekin = 9.92830200952678 | erot = 11.9267761658672 | epot = -76.3117955216386 | etot = -54.4567173462447 +527000 ekin = 9.4861760916393 | erot = 12.0681058739526 | epot = -76.0109993116997 | etot = -54.4567173461077 +528000 ekin = 9.04001720130084 | erot = 12.2139837697124 | epot = -75.7107183176547 | etot = -54.4567173466414 +529000 ekin = 8.59838558982515 | erot = 12.3488494507761 | epot = -75.4039523882436 | etot = -54.4567173476424 +530000 ekin = 8.16860222530235 | erot = 12.4514559330934 | epot = -75.0767755071576 | etot = -54.4567173487618 +531000 ekin = 7.75801650618655 | erot = 12.4988074604703 | epot = -74.7135413162482 | etot = -54.4567173495913 +532000 ekin = 7.37526556650152 | erot = 12.4710301212426 | epot = -74.3030130375125 | etot = -54.4567173497683 +533000 ekin = 7.03105781111155 | erot = 12.355970528863 | epot = -73.8437456890665 | etot = -54.4567173490919 +534000 ekin = 6.73815971498395 | erot = 12.1522682791501 | epot = -73.3471453417086 | etot = -54.4567173475745 +535000 ekin = 6.51053456919657 | erot = 11.8701146968309 | epot = -72.8373666114534 | etot = -54.456717345426 +536000 ekin = 6.36183924354587 | erot = 11.5296683851323 | epot = -72.348224971669 | etot = -54.4567173429908 +537000 ekin = 6.30361425977092 | erot = 11.1591555752721 | epot = -71.9194871756111 | etot = -54.4567173405681 +538000 ekin = 6.34347309062687 | erot = 10.7899247971594 | epot = -71.5901152265502 | etot = -54.456717338764 +539000 ekin = 6.48353756609274 | erot = 10.448864772999 | epot = -71.3891196768483 | etot = -54.4567173377565 +540000 ekin = 6.71929044884142 | erot = 10.1573936013011 | epot = -71.3334013878978 | etot = -54.4567173377553 +541000 ekin = 7.03900384377628 | erot = 9.92878251409714 | epot = -71.4245036967232 | etot = -54.4567173388497 +542000 ekin = 7.42390727691472 | erot = 9.76658171325418 | epot = -71.6472063311494 | etot = -54.4567173409805 +543000 ekin = 7.84922333880294 | erot = 9.66443151246169 | epot = -71.9703721951897 | etot = -54.4567173439251 +544000 ekin = 8.28608576855171 | erot = 9.60741387125949 | epot = -72.3502169871298 | etot = -54.4567173473186 +545000 ekin = 8.70416168565093 | erot = 9.5748381917973 | epot = -72.7357172281471 | etot = -54.4567173506988 +546000 ekin = 9.07464757513591 | erot = 9.54408103804464 | epot = -73.0754459667738 | etot = -54.4567173535932 +547000 ekin = 9.3731666291265 | erot = 9.49472293137369 | epot = -73.3246069161143 | etot = -54.4567173556141 +548000 ekin = 9.58208685808983 | erot = 9.41206012908931 | epot = -73.450864343719 | etot = -54.4567173565398 +549000 ekin = 9.69189882138825 | erot = 9.2892089381751 | epot = -73.4378251159085 | etot = -54.4567173563452 +550000 ekin = 9.70150390326669 | erot = 9.12788542700221 | epot = -73.2861066853078 | etot = -54.4567173550388 +551000 ekin = 9.61749941014082 | erot = 8.93692851360498 | epot = -73.0111452769413 | etot = -54.4567173531955 +552000 ekin = 9.45272119087804 | erot = 8.7288749611758 | epot = -72.6383135030083 | etot = -54.4567173509545 +553000 ekin = 9.22440824207828 | erot = 8.51841746658326 | epot = -72.199543057248 | etot = -54.4567173485864 +554000 ekin = 8.95232614946946 | erot = 8.32031677004921 | epot = -71.7293602658114 | etot = -54.4567173462927 +555000 ekin = 8.65710798386219 | erot = 8.14801655131682 | epot = -71.2618418793792 | etot = -54.4567173442002 +556000 ekin = 8.35889174137027 | erot = 8.01297313100488 | epot = -70.8285822147525 | etot = -54.4567173423774 +557000 ekin = 8.07627835317248 | erot = 7.92452278401225 | epot = -70.4575184780337 | etot = -54.456717340849 +558000 ekin = 7.82557556425423 | erot = 7.89005526871244 | epot = -70.1723481725976 | etot = -54.4567173396309 +559000 ekin = 7.62022949923433 | erot = 7.9151997742857 | epot = -69.9921466122684 | etot = -54.4567173387483 +560000 ekin = 7.47037167198336 | erot = 8.00382469731386 | epot = -69.9309137075372 | etot = -54.45671733824 +561000 ekin = 7.3824437430579 | erot = 8.1577660602575 | epot = -69.9969271414742 | etot = -54.4567173381588 +562000 ekin = 7.35891939627435 | erot = 8.37634747918822 | epot = -70.1919842140091 | etot = -54.4567173385465 +563000 ekin = 7.39821090242522 | erot = 8.65591018978209 | epot = -70.5108384316117 | etot = -54.4567173394044 +564000 ekin = 7.49490249873523 | erot = 8.98967393472835 | epot = -70.9412937741221 | etot = -54.4567173406586 +565000 ekin = 7.64044839043029 | erot = 9.3684279189398 | epot = -71.4655936514438 | etot = -54.4567173420737 +566000 ekin = 7.82436206842929 | erot = 9.78146009418592 | epot = -72.0625395062585 | etot = -54.4567173436433 +567000 ekin = 8.03570817671654 | erot = 10.2171991122977 | epot = -72.7096246341256 | etot = -54.4567173451114 +568000 ekin = 8.26450258147394 | erot = 10.6646881726335 | epot = -73.3859081005311 | etot = -54.4567173464237 +569000 ekin = 8.50263013239494 | erot = 11.1136558316471 | epot = -74.0730033116448 | etot = -54.4567173476028 +570000 ekin = 8.74345958959075 | erot = 11.5533265255301 | epot = -74.7535034642607 | etot = -54.4567173491399 +571000 ekin = 8.98083952020821 | erot = 11.9715855040633 | epot = -75.4091423755824 | etot = -54.4567173513109 +572000 ekin = 9.20828931136966 | erot = 12.3553438318268 | epot = -76.0203504955519 | etot = -54.4567173523555 +573000 ekin = 9.42090854110721 | erot = 12.6948199769556 | epot = -76.5724458709036 | etot = -54.4567173528408 +574000 ekin = 9.61857732717745 | erot = 12.9876096044057 | epot = -77.0629042836973 | etot = -54.4567173521141 +575000 ekin = 9.80559233525979 | erot = 13.2418166844513 | epot = -77.5041263702044 | etot = -54.4567173504934 +576000 ekin = 9.99035771755662 | erot = 13.4731869806674 | epot = -77.9202620466551 | etot = -54.4567173484311 +577000 ekin = 10.1835632722247 | erot = 13.700252686708 | epot = -78.3405333056113 | etot = -54.4567173466786 +578000 ekin = 10.395375100666 | erot = 13.9378911113993 | epot = -78.7899835575509 | etot = -54.4567173454857 +579000 ekin = 10.6324997791282 | erot = 14.1944325431012 | epot = -79.2836496675446 | etot = -54.4567173453152 +580000 ekin = 10.895796940664 | erot = 14.4694129346651 | epot = -79.8219272216207 | etot = -54.4567173462917 +581000 ekin = 11.1787341118753 | erot = 14.7532777796984 | epot = -80.3887292399888 | etot = -54.4567173484151 +582000 ekin = 11.466833292332 | erot = 15.0284724124371 | epot = -80.9520230561641 | etot = -54.4567173513951 +583000 ekin = 11.7383428294357 | erot = 15.2728618931496 | epot = -81.4679220774621 | etot = -54.4567173548768 +584000 ekin = 11.9664778295303 | erot = 15.4633320551032 | epot = -81.8865272429157 | etot = -54.4567173582823 +585000 ekin = 12.1233962794696 | erot = 15.5801019753539 | epot = -82.1602156157369 | etot = -54.4567173609133 +586000 ekin = 12.1854288034105 | erot = 15.6113292070309 | epot = -82.2534753725822 | etot = -54.4567173621408 +587000 ekin = 12.1382875982287 | erot = 15.5565429926688 | epot = -82.1515479525323 | etot = -54.4567173616348 +588000 ekin = 11.9805672635908 | erot = 15.4274086012425 | epot = -81.8646932243601 | etot = -54.4567173595268 +589000 ekin = 11.7241953475014 | erot = 15.2450549080848 | epot = -81.4259676119825 | etot = -54.4567173563962 +590000 ekin = 11.3915332486304 | erot = 15.0345988268882 | epot = -80.8828494285741 | etot = -54.4567173530556 +591000 ekin = 11.0101533181064 | erot = 14.8188164822634 | epot = -80.2856871505942 | etot = -54.4567173502244 +592000 ekin = 10.6073077807329 | erot = 14.6133535707874 | epot = -79.6773786997805 | etot = -54.4567173482602 +593000 ekin = 10.2061141300746 | erot = 14.4250491600689 | epot = -79.0878806372491 | etot = -54.4567173471056 +594000 ekin = 9.8243391782238 | erot = 14.2531987869314 | epot = -78.534255311642 | etot = -54.4567173464868 +595000 ekin = 9.47512062808258 | erot = 14.0920125306519 | epot = -78.0238505049153 | etot = -54.4567173461808 +596000 ekin = 9.16819158314277 | erot = 13.9323441617422 | epot = -77.5572530910253 | etot = -54.4567173461403 +597000 ekin = 8.91059203427263 | erot = 13.7621053819225 | epot = -77.1294147626067 | etot = -54.4567173464115 +598000 ekin = 8.7067730827948 | erot = 13.5663641000571 | epot = -76.7298545298322 | etot = -54.4567173469804 +599000 ekin = 8.55852376879638 | erot = 13.3285545478083 | epot = -76.3437956642939 | etot = -54.4567173476893 +600000 ekin = 8.46506569146732 | erot = 13.0361676653363 | epot = -75.957950704708 | etot = -54.4567173479044 +601000 ekin = 8.42303295999629 | erot = 12.6870523997733 | epot = -75.5668027085597 | etot = -54.4567173487902 +602000 ekin = 8.42685459628099 | erot = 12.2732861398469 | epot = -75.1568580851668 | etot = -54.4567173490389 +603000 ekin = 8.46950143052246 | erot = 11.797057152529 | epot = -74.7232759317285 | etot = -54.4567173486771 +604000 ekin = 8.54270518563639 | erot = 11.2713924783248 | epot = -74.2708150118271 | etot = -54.4567173478659 +605000 ekin = 8.6372873366298 | erot = 10.7173462217388 | epot = -73.81135090518 | etot = -54.4567173468114 +606000 ekin = 8.74373801577756 | erot = 10.1602725630418 | epot = -73.3607279245054 | etot = -54.456717345686 +607000 ekin = 8.85303389946066 | erot = 9.62621357889553 | epot = -72.9359648229882 | etot = -54.456717344632 +608000 ekin = 8.95757126306202 | erot = 9.13896619785316 | epot = -72.5532548046045 | etot = -54.4567173436894 +609000 ekin = 9.05196680864353 | erot = 8.71829532643352 | epot = -72.2269794780304 | etot = -54.4567173429533 +610000 ekin = 9.13352888579933 | erot = 8.37856547529385 | epot = -71.9688117034023 | etot = -54.4567173423091 +611000 ekin = 9.20215106470486 | erot = 8.12901246860289 | epot = -71.7878808752354 | etot = -54.4567173419276 +612000 ekin = 9.25956583878083 | erot = 7.97314000871177 | epot = -71.6894231893825 | etot = -54.4567173418899 +613000 ekin = 9.30811487221598 | erot = 7.90851279250858 | epot = -71.6733450070229 | etot = -54.4567173422983 +614000 ekin = 9.34927530412252 | erot = 7.92684519060762 | epot = -71.7328378379656 | etot = -54.4567173432355 +615000 ekin = 9.38237013823359 | erot = 8.01433182907842 | epot = -71.8534193119359 | etot = -54.4567173446239 +616000 ekin = 9.40383195120778 | erot = 8.15304439800148 | epot = -72.0135936957659 | etot = -54.4567173465567 +617000 ekin = 9.40773875972861 | erot = 8.32048130516021 | epot = -72.1849374136101 | etot = -54.4567173487212 +618000 ekin = 9.38718282197416 | erot = 8.49205380139463 | epot = -72.3359539741626 | etot = -54.4567173507938 +619000 ekin = 9.33634137208887 | erot = 8.64410576159845 | epot = -72.4371644860946 | etot = -54.4567173524073 +620000 ekin = 9.25274239709628 | erot = 8.75706693535131 | epot = -72.4665266856836 | etot = -54.456717353236 +621000 ekin = 9.13908734782551 | erot = 8.81838549167825 | epot = -72.4141901925815 | etot = -54.4567173530778 +622000 ekin = 9.00413159187232 | erot = 8.82453847241603 | epot = -72.2853874161967 | etot = -54.4567173519084 +623000 ekin = 8.86237387264741 | erot = 8.7815904437476 | epot = -72.100681665748 | etot = -54.456717349353 +624000 ekin = 8.73233250271996 | erot = 8.70601363408245 | epot = -71.8950634838493 | etot = -54.4567173470468 +625000 ekin = 8.63352260272379 | erot = 8.61836006913258 | epot = -71.7086000163641 | etot = -54.4567173445077 +626000 ekin = 8.58515687060557 | erot = 8.54022417073196 | epot = -71.5820983834407 | etot = -54.4567173421031 +627000 ekin = 8.60386594899659 | erot = 8.49340879469285 | epot = -71.5539920838688 | etot = -54.4567173401793 +628000 ekin = 8.7012527296389 | erot = 8.49697729760367 | epot = -71.6549473663074 | etot = -54.4567173390648 +629000 ekin = 8.88211046285069 | erot = 8.5641034304371 | epot = -71.9029312321927 | etot = -54.4567173389049 +630000 ekin = 9.14246131283763 | erot = 8.70144773180668 | epot = -72.300626384512 | etot = -54.4567173398677 +631000 ekin = 9.46837458093943 | erot = 8.90764779898328 | epot = -72.8327397225162 | etot = -54.4567173425934 +632000 ekin = 9.83312177173637 | erot = 9.17246776667656 | epot = -73.4623068842293 | etot = -54.4567173458164 +633000 ekin = 10.2047873751213 | erot = 9.47797241849136 | epot = -74.1394771430748 | etot = -54.4567173494621 +634000 ekin = 10.5489934613266 | erot = 9.80262636497442 | epot = -74.8083371791868 | etot = -54.4567173528857 +635000 ekin = 10.8335202630288 | erot = 10.125865527331 | epot = -75.4161031457917 | etot = -54.4567173554318 +636000 ekin = 11.0335668276709 | erot = 10.4324958345062 | epot = -75.9227800187378 | etot = -54.4567173565607 +637000 ekin = 11.1356918483499 | erot = 10.715848515948 | epot = -76.3082577206512 | etot = -54.4567173563533 +638000 ekin = 11.1388069575963 | erot = 10.9775008619026 | epot = -76.573025174505 | etot = -54.456717355006 +639000 ekin = 11.0524003327436 | erot = 11.2253769821821 | epot = -76.7344946679223 | etot = -54.4567173529966 +640000 ekin = 10.8928630382816 | erot = 11.4709640829692 | epot = -76.8205444720415 | etot = -54.4567173507906 +641000 ekin = 10.6795161167761 | erot = 11.7265694567109 | epot = -76.8628029221936 | etot = -54.4567173487066 +642000 ekin = 10.431652152028 | erot = 12.0033863745235 | epot = -76.8917558734979 | etot = -54.4567173469463 +643000 ekin = 10.1667694779383 | erot = 12.3102216339995 | epot = -76.9337084574531 | etot = -54.4567173455153 +644000 ekin = 9.90007447739006 | erot = 12.6530565857471 | epot = -77.009848407728 | etot = -54.4567173445908 +645000 ekin = 9.64408802626263 | erot = 13.0333521361078 | epot = -77.1341575065431 | etot = -54.4567173441727 +646000 ekin = 9.40846495824295 | erot = 13.4468842705586 | epot = -77.3120665731202 | etot = -54.4567173443187 +647000 ekin = 9.20006047028955 | erot = 13.8841334486512 | epot = -77.5409112640701 | etot = -54.4567173451294 +648000 ekin = 9.02208271234192 | erot = 14.3287870732403 | epot = -77.8075871322004 | etot = -54.4567173466181 +649000 ekin = 8.87371560220482 | erot = 14.7582675570506 | epot = -78.0887005080238 | etot = -54.4567173487684 +650000 ekin = 8.74973394437183 | erot = 15.1446190956538 | epot = -78.3510703915072 | etot = -54.4567173514816 +651000 ekin = 8.64055354280855 | erot = 15.4561976746668 | epot = -78.5534685720271 | etot = -54.4567173545518 +652000 ekin = 8.53295942949864 | erot = 15.6603023870304 | epot = -78.649979174163 | etot = -54.456717357634 +653000 ekin = 8.41177726197952 | erot = 15.726842939348 | epot = -78.5953375615667 | etot = -54.4567173602391 +654000 ekin = 8.26255435902931 | erot = 15.63291856528 | epot = -78.3521902861158 | etot = -54.4567173618065 +655000 ekin = 8.07486030841898 | erot = 15.3675533060676 | epot = -77.8991309763139 | etot = -54.4567173618274 +656000 ekin = 7.85584872993325 | erot = 14.9356063836777 | epot = -77.248172899955 | etot = -54.456717786344 +657000 ekin = 6.26705400187039 | erot = 14.5624207623999 | epot = -75.2861920811979 | etot = -54.4567173169276 +658000 ekin = 6.04203621444953 | erot = 14.8338374902579 | epot = -75.3325912844764 | etot = -54.4567175797689 +659000 ekin = 6.38626397398244 | erot = 14.3789536735541 | epot = -75.2219349118071 | etot = -54.4567172642705 +660000 ekin = 6.5182532339776 | erot = 13.6086452150087 | epot = -74.5836157135098 | etot = -54.4567172645234 +661000 ekin = 6.66109617845102 | erot = 12.8240798503781 | epot = -73.9418932898926 | etot = -54.4567172610634 +662000 ekin = 6.81858404115184 | erot = 12.0684544028029 | epot = -73.3437557024629 | etot = -54.4567172585082 +663000 ekin = 6.99165023052044 | erot = 11.3761522151831 | epot = -72.8245197026858 | etot = -54.4567172569822 +664000 ekin = 7.17719978230657 | erot = 10.7706097932657 | epot = -72.4045268320594 | etot = -54.4567172564871 +665000 ekin = 7.36750072100346 | erot = 10.2650050778807 | epot = -72.0892230556958 | etot = -54.4567172568117 +666000 ekin = 7.55090853135322 | erot = 9.86588701349086 | epot = -71.8735128030468 | etot = -54.4567172582027 +667000 ekin = 7.71548675043945 | erot = 9.56433968483975 | epot = -71.7365436952498 | etot = -54.4567172599706 +668000 ekin = 7.84942783246737 | erot = 9.34349379628263 | epot = -71.6496388907829 | etot = -54.4567172620329 +669000 ekin = 7.94275892172798 | erot = 9.18157787770468 | epot = -71.5810540633774 | etot = -54.4567172639448 +670000 ekin = 7.98895216682213 | erot = 9.0554441907046 | epot = -71.5011136229651 | etot = -54.4567172654384 +671000 ekin = 7.98617320847965 | erot = 8.94354459269314 | epot = -71.3864350674871 | etot = -54.4567172663143 +672000 ekin = 7.93791523096266 | erot = 8.82829898981495 | epot = -71.2229314872527 | etot = -54.4567172664751 +673000 ekin = 7.85355743595451 | erot = 8.69824309780591 | epot = -71.0085177991649 | etot = -54.4567172654045 +674000 ekin = 7.74778223221068 | erot = 8.54905666591076 | epot = -70.7535561623749 | etot = -54.4567172642534 +675000 ekin = 7.63634833352537 | erot = 8.38135292477012 | epot = -70.4744185210927 | etot = -54.4567172627972 +676000 ekin = 7.53516290999972 | erot = 8.20022759715558 | epot = -70.1921077684618 | etot = -54.4567172613065 +677000 ekin = 7.45794951913446 | erot = 8.01347239993289 | epot = -69.9281391793291 | etot = -54.4567172602618 +678000 ekin = 7.41073692376308 | erot = 7.82731022276803 | epot = -69.6947644060943 | etot = -54.4567172595631 +679000 ekin = 7.39569395416424 | erot = 7.64806661290669 | epot = -69.5004778263204 | etot = -54.4567172592495 +680000 ekin = 7.41151846312342 | erot = 7.4835380650913 | epot = -69.3517737862698 | etot = -54.456717258055 +681000 ekin = 7.45301960110315 | erot = 7.34389485536555 | epot = -69.2536317152595 | etot = -54.4567172587908 +682000 ekin = 7.50922760715596 | erot = 7.2303462747693 | epot = -69.1962911416981 | etot = -54.4567172597729 +683000 ekin = 7.56703179130107 | erot = 7.14137901612441 | epot = -69.1651280682614 | etot = -54.4567172608359 +684000 ekin = 7.61337845770433 | erot = 7.07402860509472 | epot = -69.1441243245626 | etot = -54.4567172617635 +685000 ekin = 7.63706923549581 | erot = 7.0248092367962 | epot = -69.1185957348405 | etot = -54.4567172625485 +686000 ekin = 7.63012070151843 | erot = 6.98974489725438 | epot = -69.0765828618106 | etot = -54.4567172630378 +687000 ekin = 7.58847196986521 | erot = 6.96451826185643 | epot = -69.0097074950328 | etot = -54.4567172633111 +688000 ekin = 7.51200727212071 | erot = 6.94458821707491 | epot = -68.9133127523039 | etot = -54.4567172631083 +689000 ekin = 7.40470220583609 | erot = 6.92788077436856 | epot = -68.7893002428866 | etot = -54.4567172626819 +690000 ekin = 7.27351140184473 | erot = 6.91313342463168 | epot = -68.6433620885768 | etot = -54.4567172621004 +691000 ekin = 7.12739933242756 | erot = 6.89961683272431 | epot = -68.4837334265833 | etot = -54.4567172614315 +692000 ekin = 6.97639340737162 | erot = 6.88713701598974 | epot = -68.3202476840923 | etot = -54.4567172607309 +693000 ekin = 6.83172646954978 | erot = 6.87668966227034 | epot = -68.1651333908689 | etot = -54.4567172590488 +694000 ekin = 6.70636456505114 | erot = 6.87119415659047 | epot = -68.0342759801781 | etot = -54.4567172585365 +695000 ekin = 6.60796425051828 | erot = 6.87171260019601 | epot = -67.936394108847 | etot = -54.4567172581327 +696000 ekin = 6.54180332236266 | erot = 6.87956193852608 | epot = -67.8780825187599 | etot = -54.4567172578711 +697000 ekin = 6.51072403244211 | erot = 6.89634898359872 | epot = -67.8637902738429 | etot = -54.4567172578021 +698000 ekin = 6.51486325250793 | erot = 6.92352997719595 | epot = -67.895110487963 | etot = -54.4567172582591 +699000 ekin = 6.55040388682853 | erot = 6.96167022069476 | epot = -67.9687913660073 | etot = -54.456717258484 +700000 ekin = 6.6121585282473 | erot = 7.01154258673771 | epot = -68.0804183739173 | etot = -54.4567172589323 +701000 ekin = 6.69364481780753 | erot = 7.07323470972917 | epot = -68.2235967870077 | etot = -54.456717259471 +702000 ekin = 6.7869961028155 | erot = 7.145771194002 | epot = -68.389484556921 | etot = -54.4567172601035 +703000 ekin = 6.88366969335579 | erot = 7.22749691999032 | epot = -68.5678838741235 | etot = -54.4567172607774 +704000 ekin = 6.97518890724708 | erot = 7.31588802326416 | epot = -68.7477941919433 | etot = -54.4567172614321 +705000 ekin = 7.05384046081159 | erot = 7.40783149503236 | epot = -68.9183892178483 | etot = -54.4567172620044 +706000 ekin = 7.11324845192292 | erot = 7.50009403269181 | epot = -69.0700597470489 | etot = -54.4567172624342 +707000 ekin = 7.14876450803415 | erot = 7.58991849146169 | epot = -69.1954002621692 | etot = -54.4567172626734 +708000 ekin = 7.15764928628057 | erot = 7.67564119575133 | epot = -69.2900077447258 | etot = -54.4567172626939 +709000 ekin = 7.13905930511253 | erot = 7.75720447258943 | epot = -69.3529810401927 | etot = -54.4567172624908 +710000 ekin = 7.0938793544147 | erot = 7.83644881069371 | epot = -69.3870454271923 | etot = -54.4567172620839 +711000 ekin = 7.0244446759505 | erot = 7.91710241224327 | epot = -69.3982643497145 | etot = -54.4567172615207 +712000 ekin = 6.93418797428583 | erot = 8.00444137728025 | epot = -69.3953466124244 | etot = -54.4567172608583 +713000 ekin = 6.82724359613114 | erot = 8.10466156445409 | epot = -69.388622420787 | etot = -54.4567172602017 +714000 ekin = 6.70804581029775 | erot = 8.22386653913456 | epot = -69.3886296090599 | etot = -54.4567172596276 +715000 ekin = 6.58096815991289 | erot = 8.36710453057032 | epot = -69.4047899497005 | etot = -54.4567172592173 +716000 ekin = 6.45005603944238 | erot = 8.53736910170365 | epot = -69.4441424001801 | etot = -54.456717259034 +717000 ekin = 6.31889522685289 | erot = 8.73472575132229 | epot = -69.5103382372902 | etot = -54.456717259115 +718000 ekin = 6.19064203155935 | erot = 8.95572089428787 | epot = -69.6030801853046 | etot = -54.4567172594574 +719000 ekin = 6.06821802711044 | erot = 9.19320356818901 | epot = -69.7181388553172 | etot = -54.4567172600177 +720000 ekin = 5.95464760383198 | erot = 9.43665584955481 | epot = -69.8480207140972 | etot = -54.4567172607104 +721000 ekin = 5.85348609830537 | erot = 9.67307075500268 | epot = -69.9832741147241 | etot = -54.4567172614161 +722000 ekin = 5.76925126938931 | erot = 9.88829892323016 | epot = -70.114267454639 | etot = -54.4567172620195 +723000 ekin = 5.70773585553476 | erot = 10.06860213304 | epot = -70.2330552509523 | etot = -54.4567172623776 +724000 ekin = 5.6760645042894 | erot = 10.2025682810442 | epot = -70.335350047752 | etot = -54.4567172624185 +725000 ekin = 5.68237542170082 | erot = 10.2825935057557 | epot = -70.4216861895841 | etot = -54.4567172621276 +726000 ekin = 5.73506597281948 | erot = 10.3058575699355 | epot = -70.4976408043186 | etot = -54.4567172615636 +727000 ekin = 5.84164351928827 | erot = 10.2746192681695 | epot = -70.5729800482991 | etot = -54.4567172608413 +728000 ekin = 6.00736875336289 | erot = 10.1958472010947 | epot = -70.6599332145536 | etot = -54.456717260096 +729000 ekin = 6.23388239567645 | erot = 10.0804050315148 | epot = -70.7710046866801 | etot = -54.4567172594889 +730000 ekin = 6.5181079856077 | erot = 9.94175964622021 | epot = -70.9165848909827 | etot = -54.4567172591548 +731000 ekin = 6.85163923571744 | erot = 9.79445434032455 | epot = -71.1028108352361 | etot = -54.4567172591941 +732000 ekin = 7.22074424891735 | erot = 9.65249486307845 | epot = -71.3299563716612 | etot = -54.4567172596655 +733000 ekin = 7.60696817054733 | erot = 9.52810422851143 | epot = -71.5917896595774 | etot = -54.4567172605186 +734000 ekin = 7.98843781661947 | erot = 9.43013551828111 | epot = -71.8752905967073 | etot = -54.4567172618067 +735000 ekin = 8.34173972939013 | erot = 9.36277858698969 | epot = -72.1612355797255 | etot = -54.4567172633456 +736000 ekin = 8.64402787584928 | erot = 9.32573536298566 | epot = -72.4264805037993 | etot = -54.4567172649644 +737000 ekin = 8.87535498674526 | erot = 9.3146792206772 | epot = -72.6467514738655 | etot = -54.4567172664431 +738000 ekin = 9.0209200187784 | erot = 9.32245328119848 | epot = -72.8000905675264 | etot = -54.4567172675495 +739000 ekin = 9.07295023114234 | erot = 9.34080514541082 | epot = -72.8704726446309 | etot = -54.4567172680777 +740000 ekin = 9.03191800999384 | erot = 9.36236057635137 | epot = -72.8509958542333 | etot = -54.4567172678881 +741000 ekin = 8.90683448949746 | erot = 9.38246134464619 | epot = -72.7460131010873 | etot = -54.4567172669436 +742000 ekin = 8.71448735995827 | erot = 9.40037005966795 | epot = -72.5715746850156 | etot = -54.4567172653894 +743000 ekin = 8.47780203517174 | erot = 9.41934825447453 | epot = -72.3538675527049 | etot = -54.4567172630586 +744000 ekin = 8.2239441336512 | erot = 9.44738079426397 | epot = -72.1280421887358 | etot = -54.4567172608206 +745000 ekin = 7.979957206327 | erot = 9.49389903747194 | epot = -71.930573502561 | etot = -54.4567172587621 +746000 ekin = 7.76976645074965 | erot = 9.56761523721079 | epot = -71.7940989452218 | etot = -54.4567172572613 +747000 ekin = 7.61167419659637 | erot = 9.67422583430891 | epot = -71.7426172875921 | etot = -54.4567172566868 +748000 ekin = 7.51658612862877 | erot = 9.81263188347016 | epot = -71.785935269318 | etot = -54.4567172572191 +749000 ekin = 7.48573262349267 | erot = 9.97339077046083 | epot = -71.9158406528599 | etot = -54.4567172589064 +750000 ekin = 7.51095577908412 | erot = 10.1387308601717 | epot = -72.1064039007001 | etot = -54.4567172614443 +751000 ekin = 7.57621289892419 | erot = 10.2849285861805 | epot = -72.3178587495141 | etot = -54.4567172644094 +752000 ekin = 7.66072006265649 | erot = 10.3863157071405 | epot = -72.5037530370115 | etot = -54.4567172672145 +753000 ekin = 7.74275043504163 | erot = 10.4196294184866 | epot = -72.6190971230344 | etot = -54.4567172695062 +754000 ekin = 7.80325401374395 | erot = 10.3685500609724 | epot = -72.6285213451586 | etot = -54.4567172704423 +755000 ekin = 7.83074135615125 | erot = 10.228246958544 | epot = -72.5157055847655 | etot = -54.4567172700702 +756000 ekin = 7.82164306775544 | erot = 10.0059989462499 | epot = -72.2843592824949 | etot = -54.4567172684896 +757000 ekin = 7.7799505806884 | erot = 9.72007455916815 | epot = -71.9567424058705 | etot = -54.456717266014 +758000 ekin = 7.71576193730277 | erot = 9.39663554338545 | epot = -71.5691147437055 | etot = -54.4567172630173 +759000 ekin = 7.6433560104715 | erot = 9.06548554812045 | epot = -71.1655588186319 | etot = -54.45671726004 +760000 ekin = 7.57812578248301 | erot = 8.75574971039161 | epot = -70.7905927503089 | etot = -54.4567172574342 +761000 ekin = 7.5347738470087 | erot = 8.49179690722462 | epot = -70.4832880097082 | etot = -54.4567172554749 +762000 ekin = 7.52580486699214 | erot = 8.29027904918132 | epot = -70.2728011706086 | etot = -54.4567172544351 +763000 ekin = 7.56027219186238 | erot = 8.157884937744 | epot = -70.1748743837876 | etot = -54.4567172541812 +764000 ekin = 7.64375808862693 | erot = 8.0920934118109 | epot = -70.1925687554821 | etot = -54.4567172550442 +765000 ekin = 7.77732533264697 | erot = 8.08087591863862 | epot = -70.3149185075756 | etot = -54.45671725629 +766000 ekin = 7.95932937982089 | erot = 8.10617755734997 | epot = -70.5222241950778 | etot = -54.456717257907 +767000 ekin = 8.18579174502709 | erot = 8.14683277454142 | epot = -70.7893417792425 | etot = -54.456717259674 +768000 ekin = 8.45095313228628 | erot = 8.18150203238837 | epot = -71.0891724259741 | etot = -54.4567172612995 +769000 ekin = 8.74814097852324 | erot = 8.19192572077826 | epot = -71.3967839618408 | etot = -54.4567172625393 +770000 ekin = 9.06864484878833 | erot = 8.16518273783507 | epot = -71.690544850802 | etot = -54.4567172641786 +771000 ekin = 9.40152051233623 | erot = 8.09534580341989 | epot = -71.9535835800355 | etot = -54.4567172642793 +772000 ekin = 9.74055140010678 | erot = 7.98665030969471 | epot = -72.183918973657 | etot = -54.4567172638555 +773000 ekin = 10.0800699458604 | erot = 7.85110373963236 | epot = -72.3878909486045 | etot = -54.4567172631118 +774000 ekin = 10.4140305141568 | erot = 7.70610726769944 | epot = -72.576855044164 | etot = -54.4567172623078 +775000 ekin = 10.7352090238447 | erot = 7.57137133473538 | epot = -72.763297620266 | etot = -54.4567172616859 +776000 ekin = 11.0347273426194 | erot = 7.46577166842762 | epot = -72.9572162724493 | etot = -54.4567172614022 +777000 ekin = 11.3022272086606 | erot = 7.40478419490276 | epot = -73.1637286650549 | etot = -54.4567172614916 +778000 ekin = 11.526792332514 | erot = 7.39895687130388 | epot = -73.3824664656914 | etot = -54.4567172618736 +779000 ekin = 11.6984431849191 | erot = 7.4534644593814 | epot = -73.6086249067104 | etot = -54.4567172624099 +780000 ekin = 11.8098204310397 | erot = 7.56848658977413 | epot = -73.8350242837535 | etot = -54.4567172629397 +781000 ekin = 11.8576135100472 | erot = 7.74008064722733 | epot = -74.0544114206266 | etot = -54.4567172633521 +782000 ekin = 11.84335462244 | erot = 7.96106713733883 | epot = -74.2611390233815 | etot = -54.4567172636027 +783000 ekin = 11.7734660925532 | erot = 8.2217578563219 | epot = -74.4519412125745 | etot = -54.4567172636994 +784000 ekin = 11.6594880030989 | erot = 8.510684683383 | epot = -74.6268899498919 | etot = -54.4567172634101 +785000 ekin = 11.5166274257283 | erot = 8.81499326200193 | epot = -74.7883379510601 | etot = -54.4567172633298 +786000 ekin = 11.360989591068 | erot = 9.12075819552402 | epot = -74.9384650497693 | etot = -54.4567172631773 +787000 ekin = 11.2098737157826 | erot = 9.41411994883949 | epot = -75.0807109275669 | etot = -54.4567172629449 +788000 ekin = 11.0807838157264 | erot = 9.68217635161522 | epot = -75.2196774299904 | etot = -54.4567172626488 +789000 ekin = 10.9904701398967 | erot = 9.91392462850634 | epot = -75.3611120306953 | etot = -54.4567172622923 +790000 ekin = 10.9537524860448 | erot = 10.1009165691582 | epot = -75.5113863171902 | etot = -54.4567172619872 +791000 ekin = 10.9817979913689 | erot = 10.2372809089182 | epot = -75.6757961621807 | etot = -54.4567172618937 +792000 ekin = 11.0801481532633 | erot = 10.3193115157189 | epot = -75.8561769311678 | etot = -54.4567172621856 +793000 ekin = 11.2467542974172 | erot = 10.3447700002189 | epot = -76.0482415606158 | etot = -54.4567172629796 +794000 ekin = 11.4705768797841 | erot = 10.3123151888631 | epot = -76.2396093328664 | etot = -54.4567172642192 +795000 ekin = 11.7331024077072 | erot = 10.2218576029517 | epot = -76.4116772763255 | etot = -54.4567172656666 +796000 ekin = 12.010452379327 | erot = 10.0755577767683 | epot = -76.5427274230119 | etot = -54.4567172669166 +797000 ekin = 12.2774168644693 | erot = 9.87947565191715 | epot = -76.6136097839571 | etot = -54.4567172675707 +798000 ekin = 12.5118492347159 | erot = 9.64485933478221 | epot = -76.6134258369216 | etot = -54.4567172674235 +799000 ekin = 12.6978284048544 | erot = 9.38805929781137 | epot = -76.5426049692048 | etot = -54.456717266539 +800000 ekin = 12.8267336416874 | erot = 9.12873028581606 | epot = -76.4121811927006 | etot = -54.4567172651972 +801000 ekin = 12.8964017894382 | erot = 8.88689375956078 | epot = -76.2400128127474 | etot = -54.4567172637485 +802000 ekin = 12.9092334834897 | erot = 8.67992468173849 | epot = -76.0458754277123 | etot = -54.4567172624841 +803000 ekin = 12.8701763431678 | erot = 8.52035040790844 | epot = -75.8472440126504 | etot = -54.4567172615742 +804000 ekin = 12.7851658304065 | erot = 8.4150129817737 | epot = -75.6568960731781 | etot = -54.4567172609978 +805000 ekin = 12.6600414871828 | erot = 8.36523459714379 | epot = -75.4819933451723 | etot = -54.4567172608457 +806000 ekin = 12.5000407944914 | erot = 8.3665682915745 | epot = -75.3233263471979 | etot = -54.456717261132 +807000 ekin = 12.3098796732048 | erot = 8.40968834837655 | epot = -75.1762852832235 | etot = -54.4567172616422 +808000 ekin = 12.0938131957704 | erot = 8.48342142268738 | epot = -75.0339518808372 | etot = -54.4567172623793 +809000 ekin = 11.8557464184214 | erot = 8.57397165843714 | epot = -74.8864353400505 | etot = -54.4567172631919 +810000 ekin = 11.5994894992351 | erot = 8.66620690069611 | epot = -74.7224136639258 | etot = -54.4567172639946 +811000 ekin = 11.328949668636 | erot = 8.74571674828224 | epot = -74.5313836816209 | etot = -54.4567172647026 +812000 ekin = 11.0482743074415 | erot = 8.80005767532243 | epot = -74.3050492479917 | etot = -54.4567172652278 +813000 ekin = 10.7652338996024 | erot = 8.82039840378805 | epot = -74.0423495680921 | etot = -54.4567172647017 +814000 ekin = 10.4915993454138 | erot = 8.80333280505509 | epot = -73.751649416073 | etot = -54.4567172656042 +815000 ekin = 10.1506392603296 | erot = 8.72916604607101 | epot = -73.3365225755293 | etot = -54.4567172691287 +816000 ekin = 10.0078569448662 | erot = 8.6078590322417 | epot = -73.0724332558889 | etot = -54.456717278781 +817000 ekin = 9.94168629459043 | erot = 8.48386018506341 | epot = -72.8822637662551 | etot = -54.4567172866013 +818000 ekin = 9.8160254128801 | erot = 8.35562171933562 | epot = -72.6283644162528 | etot = -54.4567172840371 +819000 ekin = 9.7200144970214 | erot = 8.23727756031698 | epot = -72.414009339184 | etot = -54.4567172818457 +820000 ekin = 9.65393768638163 | erot = 8.15065357777833 | epot = -72.2613085437645 | etot = -54.4567172796045 +821000 ekin = 9.62991083870796 | erot = 8.11519232362434 | epot = -72.2018204400825 | etot = -54.4567172777502 +822000 ekin = 9.66070438852946 | erot = 8.14514958893694 | epot = -72.2625712542169 | etot = -54.4567172767505 +823000 ekin = 9.75366113133722 | erot = 8.24729238627225 | epot = -72.4576707944965 | etot = -54.456717276887 +824000 ekin = 9.90784075221045 | erot = 8.41983721973809 | epot = -72.7843952501275 | etot = -54.4567172781789 +825000 ekin = 10.1134132500765 | erot = 8.6528077235256 | epot = -73.222938254008 | etot = -54.4567172804058 +826000 ekin = 10.3532272232195 | erot = 8.92957217380895 | epot = -73.7395166802349 | etot = -54.4567172832064 +827000 ekin = 10.6056861232758 | erot = 9.2291218901548 | epot = -74.2915252996249 | etot = -54.4567172861942 +828000 ekin = 10.8478833100317 | erot = 9.52863932139692 | epot = -74.8332399204523 | etot = -54.4567172890238 +829000 ekin = 11.0582941053422 | erot = 9.80604986037188 | epot = -75.3210612571246 | etot = -54.4567172914105 +830000 ekin = 11.2188022337386 | erot = 10.0424425697406 | epot = -75.7179620966016 | etot = -54.4567172931224 +831000 ekin = 11.316113379123 | erot = 10.2243333144583 | epot = -75.9971639875571 | etot = -54.4567172939758 +832000 ekin = 11.3426219926655 | erot = 10.3456446448561 | epot = -76.144983931386 | etot = -54.4567172938643 +833000 ekin = 11.2966905572863 | erot = 10.4090470942505 | epot = -76.1624549443369 | etot = -54.4567172928 +834000 ekin = 11.182229358983 | erot = 10.4261077170688 | epot = -76.0650543670087 | etot = -54.4567172909569 +835000 ekin = 11.0075161183012 | erot = 10.4150475473378 | epot = -75.8792809542957 | etot = -54.4567172886567 +836000 ekin = 10.7833649095851 | erot = 10.3987463120899 | epot = -75.6388285079792 | etot = -54.4567172863042 +837000 ekin = 10.5209605456082 | erot = 10.4007504685186 | epot = -75.3784282984365 | etot = -54.4567172843097 +838000 ekin = 10.2299052199625 | erot = 10.4407488044951 | epot = -75.1273713074253 | etot = -54.4567172829676 +839000 ekin = 9.91700879954974 | erot = 10.5309577036188 | epot = -74.9046837856552 | etot = -54.4567172824866 +840000 ekin = 9.58612989126957 | erot = 10.6748490697451 | epot = -74.7176962436113 | etot = -54.4567172825966 +841000 ekin = 9.23902247606654 | erot = 10.8680222456528 | epot = -74.5637620048793 | etot = -54.45671728316 +842000 ekin = 8.87682183150687 | erot = 11.0993209653809 | epot = -74.4328600810575 | etot = -54.4567172841697 +843000 ekin = 8.50166697126372 | erot = 11.3515587654951 | epot = -74.3099430215634 | etot = -54.4567172848045 +844000 ekin = 8.11786122482937 | erot = 11.6086450389977 | epot = -74.1832235489656 | etot = -54.4567172851385 +845000 ekin = 7.73224665959471 | erot = 11.856919901106 | epot = -74.0458838457755 | etot = -54.4567172850748 +846000 ekin = 7.35386726308554 | erot = 12.0865858112961 | epot = -73.8971703589925 | etot = -54.4567172846108 +847000 ekin = 6.99310483301922 | erot = 12.2927531540975 | epot = -73.7425752709287 | etot = -54.4567172838119 +848000 ekin = 6.66064227407544 | erot = 12.4755849217792 | epot = -73.5929444786391 | etot = -54.4567172827845 +849000 ekin = 6.36657021968653 | erot = 12.6396628745633 | epot = -73.4629503758916 | etot = -54.4567172816418 +850000 ekin = 6.11978999363782 | erot = 12.7927789147892 | epot = -73.3692861889337 | etot = -54.4567172805067 +851000 ekin = 5.92769059320259 | erot = 12.9443936749531 | epot = -73.328801547648 | etot = -54.4567172794923 +852000 ekin = 5.79598233520181 | erot = 13.1040127665031 | epot = -73.3567123804033 | etot = -54.4567172786984 +853000 ekin = 5.72857612927171 | erot = 13.2797145891451 | epot = -73.4650079966327 | etot = -54.4567172782158 +854000 ekin = 5.72746426148597 | erot = 13.4770198626373 | epot = -73.6612014022069 | etot = -54.4567172780836 +855000 ekin = 5.79262212016434 | erot = 13.6982251276031 | epot = -73.9475645260803 | etot = -54.4567172783128 +856000 ekin = 5.92198051771585 | erot = 13.9422405100411 | epot = -74.3209383066336 | etot = -54.4567172788767 +857000 ekin = 6.11150866267658 | erot = 14.2048890108522 | epot = -74.7731149532471 | etot = -54.4567172797184 +858000 ekin = 6.35541287948108 | erot = 14.4795498831894 | epot = -75.2916800434334 | etot = -54.4567172807629 +859000 ekin = 6.64641352744846 | erot = 14.7579710750208 | epot = -75.8611018844076 | etot = -54.4567172819383 +860000 ekin = 6.97602906179018 | erot = 15.031049493862 | epot = -76.4637958388483 | etot = -54.4567172831961 +861000 ekin = 7.33478689144592 | erot = 15.2894014997161 | epot = -77.0809056756773 | etot = -54.4567172845152 +862000 ekin = 7.71230494061546 | erot = 15.5236284018704 | epot = -77.6926506283928 | etot = -54.4567172859069 +863000 ekin = 8.0972429154566 | erot = 15.7243060787924 | epot = -78.2782662816448 | etot = -54.4567172873958 +864000 ekin = 8.47719156700412 | erot = 15.8818501460864 | epot = -78.8157590020863 | etot = -54.4567172889958 +865000 ekin = 8.83862795339356 | erot = 15.9864762744088 | epot = -79.2818215184876 | etot = -54.4567172906853 +866000 ekin = 9.16709499257563 | erot = 16.0284566448477 | epot = -79.6522689298105 | etot = -54.4567172923871 +867000 ekin = 9.44775496531962 | erot = 15.9987710030364 | epot = -79.9032432623224 | etot = -54.4567172939664 +868000 ekin = 9.6664170744344 | erot = 15.8900978287038 | epot = -80.0132321983787 | etot = -54.4567172952405 +869000 ekin = 9.81104759054265 | erot = 15.697936812546 | epot = -79.9657016990976 | etot = -54.4567172960089 +870000 ekin = 9.87363911507839 | erot = 15.4215512162341 | epot = -79.7519076274087 | etot = -54.4567172960962 +871000 ekin = 9.85215986226453 | erot = 15.0644163888748 | epot = -79.3732935465326 | etot = -54.4567172953932 +872000 ekin = 9.7521666623902 | erot = 14.6339832230399 | epot = -78.8428671793229 | etot = -54.4567172938928 +873000 ekin = 9.58760337521736 | erot = 14.1407822457465 | epot = -78.1851029126663 | etot = -54.4567172917025 +874000 ekin = 9.38036224430972 | erot = 13.597111552683 | epot = -77.4341910860359 | etot = -54.4567172890432 +875000 ekin = 9.15836908048365 | erot = 13.0156613282078 | epot = -76.6307476949113 | etot = -54.4567172862198 +876000 ekin = 8.95224910374833 | erot = 12.4083870186539 | epot = -75.8173534059835 | etot = -54.4567172835813 +877000 ekin = 8.79100811653287 | erot = 11.7858100333708 | epot = -75.0335354313618 | etot = -54.4567172814581 +878000 ekin = 8.69754976341394 | erot = 11.1567995255962 | epot = -74.3110665690975 | etot = -54.4567172800874 +879000 ekin = 8.68509191534171 | erot = 10.5288226081013 | epot = -73.6706318029878 | etot = -54.4567172795448 +880000 ekin = 8.75545564714934 | erot = 9.90861257462188 | epot = -73.1207855014893 | etot = -54.4567172797181 +881000 ekin = 8.89970025386099 | erot = 9.30313444734775 | epot = -72.6595519815518 | etot = -54.4567172803431 +882000 ekin = 9.10082855523646 | erot = 8.72061110508849 | epot = -72.2781569414177 | etot = -54.4567172810928 +883000 ekin = 9.33764332479556 | erot = 8.1712754623967 | epot = -71.9656360688781 | etot = -54.4567172816858 +884000 ekin = 9.58861580334731 | erot = 7.66753088020623 | epot = -71.7128639655093 | etot = -54.4567172819558 +885000 ekin = 9.83488676080902 | erot = 7.22337392461422 | epot = -71.5149779672928 | etot = -54.4567172818695 +886000 ekin = 10.0620352551291 | erot = 6.85319082652144 | epot = -71.3719433631456 | etot = -54.4567172814951 +887000 ekin = 10.2607068157632 | erot = 6.57023940271384 | epot = -71.2876634994279 | etot = -54.4567172809509 +888000 ekin = 10.4264068596052 | erot = 6.38516766531579 | epot = -71.2682918052929 | etot = -54.4567172803719 +889000 ekin = 10.5587552560593 | erot = 6.30481332827294 | epot = -71.3202858642243 | etot = -54.456717279892 +890000 ekin = 10.6604009571512 | erot = 6.3313819173971 | epot = -71.4485001541792 | etot = -54.4567172796309 +891000 ekin = 10.7357341009366 | erot = 6.46201557974538 | epot = -71.6544669603718 | etot = -54.4567172796898 +892000 ekin = 10.7895437608077 | erot = 6.68876199670318 | epot = -71.9350230376444 | etot = -54.4567172801336 +893000 ekin = 10.8258166395542 | erot = 6.99898655746096 | epot = -72.2815204779803 | etot = -54.4567172809652 +894000 ekin = 10.8468969134803 | erot = 7.37628199601942 | epot = -72.6798961916184 | etot = -54.4567172821187 +895000 ekin = 10.8531861940975 | erot = 7.80188530606377 | epot = -73.1117887836164 | etot = -54.4567172834552 +896000 ekin = 10.8434432146178 | erot = 8.25651048988155 | epot = -73.5566709892849 | etot = -54.4567172847856 +897000 ekin = 10.8155751276989 | erot = 8.72237163402597 | epot = -73.9946640476367 | etot = -54.4567172859118 +898000 ekin = 10.7676627830279 | erot = 9.18505046673359 | epot = -74.4094305364376 | etot = -54.4567172866761 +899000 ekin = 10.6988999918464 | erot = 9.63481320600628 | epot = -74.7904304848565 | etot = -54.4567172870038 +900000 ekin = 10.6101778355024 | erot = 10.0670454033516 | epot = -75.1339405257768 | etot = -54.4567172869229 +901000 ekin = 10.5041792336263 | erot = 10.4816537280424 | epot = -75.4425502482243 | etot = -54.4567172865556 +902000 ekin = 10.3850069961677 | erot = 10.8815370479461 | epot = -75.723261330198 | etot = -54.4567172860842 +903000 ekin = 10.2574985062542 | erot = 11.2704782387657 | epot = -75.9846940307208 | etot = -54.4567172857008 +904000 ekin = 10.1264528578434 | erot = 11.6509689579676 | epot = -76.2341391013697 | etot = -54.4567172855587 +905000 ekin = 9.99600212718199 | erot = 12.0224964837307 | epot = -76.4752158966417 | etot = -54.456717285729 +906000 ekin = 9.86930089578128 | erot = 12.3806889296984 | epot = -76.706707111672 | etot = -54.4567172861924 +907000 ekin = 9.74860096930186 | erot = 12.717473329665 | epot = -76.9227915858112 | etot = -54.4567172868443 +908000 ekin = 9.63564731437693 | erot = 13.0221203323681 | epot = -77.1144849342879 | etot = -54.4567172875429 +909000 ekin = 9.53221635088924 | erot = 13.2828159173612 | epot = -77.2717495564014 | etot = -54.456717288151 +910000 ekin = 9.44056511136237 | erot = 13.4883008485944 | epot = -77.3855832485332 | etot = -54.4567172885764 +911000 ekin = 9.36359901015972 | erot = 13.6292002110449 | epot = -77.4495165099879 | etot = -54.4567172887832 +912000 ekin = 9.30468390683423 | erot = 13.6988898091476 | epot = -77.4602910047642 | etot = -54.4567172887824 +913000 ekin = 9.2671667518601 | erot = 13.6939842819807 | epot = -77.41786832244 | etot = -54.4567172885992 +914000 ekin = 9.25375894933545 | erot = 13.6146373108747 | epot = -77.3251135484712 | etot = -54.4567172882611 +915000 ekin = 9.2659424721694 | erot = 13.4647622141686 | epot = -77.1874219741281 | etot = -54.4567172877901 +916000 ekin = 9.3034996705056 | erot = 13.252095142795 | epot = -77.0123121005206 | etot = -54.45671728722 +917000 ekin = 9.36419714228145 | erot = 12.9878926207137 | epot = -76.8088070496062 | etot = -54.456717286611 +918000 ekin = 9.4436196362461 | erot = 12.6860933860155 | epot = -76.5864303083068 | etot = -54.4567172860452 +919000 ekin = 9.53516188539609 | erot = 12.3619660455384 | epot = -76.3538452165503 | etot = -54.4567172856158 +920000 ekin = 9.6302153355846 | erot = 12.0304853675905 | epot = -76.1174179885652 | etot = -54.4567172853901 +921000 ekin = 9.71859337757226 | erot = 11.7047977082043 | epot = -75.8801083711812 | etot = -54.4567172854046 +922000 ekin = 9.7892066721518 | erot = 11.3950992586233 | epot = -75.6410232164054 | etot = -54.4567172856303 +923000 ekin = 9.83094506629074 | erot = 11.1081050699644 | epot = -75.3957674222563 | etot = -54.4567172860011 +924000 ekin = 9.8336730468052 | erot = 10.8471196662819 | epot = -75.1375099995099 | etot = -54.4567172864229 +925000 ekin = 9.78921982201672 | erot = 10.6125977274286 | epot = -74.8585348362305 | etot = -54.4567172867852 +926000 ekin = 9.69224265484151 | erot = 10.4030278881647 | epot = -74.5519878299939 | etot = -54.4567172869877 +927000 ekin = 9.54086684318481 | erot = 10.2159706089149 | epot = -74.2135547390471 | etot = -54.4567172869474 +928000 ekin = 9.33704160544839 | erot = 10.049113171626 | epot = -73.8428720636795 | etot = -54.4567172866051 +929000 ekin = 9.08657260994688 | erot = 9.90122855058418 | epot = -73.4445184464668 | etot = -54.4567172859358 +930000 ekin = 8.79883716652832 | erot = 9.77291303142043 | epot = -73.0284674828996 | etot = -54.4567172849509 +931000 ekin = 8.48619808326945 | erot = 9.6669433018564 | epot = -72.6098586688443 | etot = -54.4567172837184 +932000 ekin = 8.16314309644076 | erot = 9.58807622106468 | epot = -72.2079365998691 | etot = -54.4567172823636 +933000 ekin = 7.84519354305061 | erot = 9.54217917979384 | epot = -71.8440900039073 | etot = -54.4567172810628 +934000 ekin = 7.54765679217323 | erot = 9.53474238375616 | epot = -71.5391164559538 | etot = -54.4567172800244 +935000 ekin = 7.284333071741 | erot = 9.56903045439682 | epot = -71.3100808055868 | etot = -54.456717279449 +936000 ekin = 7.06631285076321 | erot = 9.64428867327643 | epot = -71.1673188035272 | etot = -54.4567172794875 +937000 ekin = 6.9010072120583 | erot = 9.75446862336522 | epot = -71.1121931156352 | etot = -54.4567172802116 +938000 ekin = 6.791541293687 | erot = 9.88787401273449 | epot = -71.1361325880017 | etot = -54.4567172815803 +939000 ekin = 6.73661249445985 | erot = 10.0281331616284 | epot = -71.2214629394807 | etot = -54.4567172833925 +940000 ekin = 6.73087290002795 | erot = 10.1560913569087 | epot = -71.3436815424214 | etot = -54.4567172854848 +941000 ekin = 6.76583136819434 | erot = 10.252418493811 | epot = -71.4749671494792 | etot = -54.4567172874739 +942000 ekin = 6.83124487467581 | erot = 10.3013419690557 | epot = -71.5893041327359 | etot = -54.4567172890045 +943000 ekin = 6.91692812768483 | erot = 10.2938485498701 | epot = -71.6674939673204 | etot = -54.4567172897655 +944000 ekin = 7.01479645632583 | erot = 10.2298584620325 | epot = -71.701372207932 | etot = -54.4567172895736 +945000 ekin = 7.12068760757986 | erot = 10.1186471972992 | epot = -71.696052093349 | etot = -54.4567172884699 +946000 ekin = 7.23514614954191 | erot = 9.97707725562207 | epot = -71.6689406919542 | etot = -54.4567172867903 +947000 ekin = 7.36229609113421 | erot = 9.82579824686105 | epot = -71.644811623109 | etot = -54.4567172851137 +948000 ekin = 7.50666547843035 | erot = 9.68437595382033 | epot = -71.6477587163093 | etot = -54.4567172840586 +949000 ekin = 7.66924616191772 | erot = 9.56691299458701 | epot = -71.692876440489 | etot = -54.4567172839843 +950000 ekin = 7.84507329855829 | erot = 9.47964218457065 | epot = -71.7814327679451 | etot = -54.4567172848161 +951000 ekin = 8.02398780691496 | erot = 9.42110967875665 | epot = -71.9018147717852 | etot = -54.4567172861135 +952000 ekin = 8.19417684165141 | erot = 9.38438008346554 | epot = -72.0352742124693 | etot = -54.4567172873524 +953000 ekin = 8.34626778801213 | erot = 9.35991642812015 | epot = -72.1629015043317 | etot = -54.4567172881995 +954000 ekin = 8.47568923855396 | erot = 9.33789032824472 | epot = -72.270296855398 | etot = -54.4567172885994 +955000 ekin = 8.58250201858603 | erot = 9.30949114580661 | epot = -72.3487104530702 | etot = -54.4567172886776 +956000 ekin = 8.66948436711163 | erot = 9.26761872827085 | epot = -72.3938203840399 | etot = -54.4567172886574 +957000 ekin = 8.73983265750596 | erot = 9.20719774881724 | epot = -72.403747694787 | etot = -54.4567172884638 +958000 ekin = 8.79545874721684 | erot = 9.12647624462242 | epot = -72.3786522799993 | etot = -54.45671728816 +959000 ekin = 8.83619167917057 | erot = 9.02839052830606 | epot = -72.321299495177 | etot = -54.4567172877003 +960000 ekin = 8.8597516775373 | erot = 8.921066131001 | epot = -72.2375350955797 | etot = -54.4567172870414 +961000 ekin = 8.86221391088967 | erot = 8.81796977947868 | epot = -72.1369009765418 | etot = -54.4567172861734 +962000 ekin = 8.83870974709834 | erot = 8.73730143653572 | epot = -72.0327284687628 | etot = -54.4567172851288 +963000 ekin = 8.78419063762297 | erot = 8.70062153324984 | epot = -71.941529454855 | etot = -54.4567172839822 +964000 ekin = 8.69414320505532 | erot = 8.73080443183868 | epot = -71.8816649197466 | etot = -54.4567172828526 +965000 ekin = 8.56518846879808 | erot = 8.84947946882749 | epot = -71.8713852195034 | etot = -54.4567172818779 +966000 ekin = 8.39553184386797 | erot = 9.07419585611561 | epot = -71.9264449812041 | etot = -54.4567172812205 +967000 ekin = 8.18525791183118 | erot = 9.41563515997517 | epot = -72.0576103528196 | etot = -54.4567172810133 +968000 ekin = 7.93667478277496 | erot = 9.87520375458517 | epot = -72.2685958186602 | etot = -54.4567172813001 +969000 ekin = 7.65450207895293 | erot = 10.4432619151597 | epot = -72.554481276342 | etot = -54.4567172822294 +970000 ekin = 7.3444529420773 | erot = 11.099955291077 | epot = -72.9011255166994 | etot = -54.4567172835451 +971000 ekin = 7.01467245168829 | erot = 11.8168528075889 | epot = -73.2882425443265 | etot = -54.4567172850493 +972000 ekin = 6.67605450391219 | erot = 12.5598107323187 | epot = -73.6925825227156 | etot = -54.4567172864848 +973000 ekin = 6.34244769979576 | erot = 13.2923396271009 | epot = -74.0915046146129 | etot = -54.4567172877162 +974000 ekin = 6.03025176751086 | erot = 13.9789096322924 | epot = -74.4658786882448 | etot = -54.4567172884415 +975000 ekin = 5.75716039273076 | erot = 14.5899381418184 | epot = -74.8038158231949 | etot = -54.4567172886457 +976000 ekin = 5.54124167943899 | erot = 15.1033057453066 | epot = -75.1012647131604 | etot = -54.4567172884147 +977000 ekin = 5.39911082454268 | erot = 15.50491198647 | epot = -75.3607400989432 | etot = -54.4567172879305 +978000 ekin = 5.34386272251207 | erot = 15.7880067440631 | epot = -75.5885867539899 | etot = -54.4567172874147 +979000 ekin = 5.3831993070512 | erot = 15.9517029514082 | epot = -75.7916195455258 | etot = -54.4567172870663 +980000 ekin = 5.51814445211147 | erot = 15.9991910955376 | epot = -75.9740528346666 | etot = -54.4567172870175 +981000 ekin = 5.74260488051433 | erot = 15.9361251477774 | epot = -76.1354473155988 | etot = -54.4567172873071 +982000 ekin = 6.04385436985727 | erot = 15.7695224495589 | epot = -76.2700941072881 | etot = -54.4567172878719 +983000 ekin = 6.40384970652226 | erot = 15.5073539290396 | epot = -76.3679209241306 | etot = -54.4567172885687 +984000 ekin = 6.80116238511362 | erot = 15.1588118512124 | epot = -76.4166915255271 | etot = -54.4567172892011 +985000 ekin = 7.213233657274 | erot = 14.7350438439508 | epot = -76.4049947907932 | etot = -54.4567172895684 +986000 ekin = 7.61862562383731 | erot = 14.2499737923036 | epot = -76.3253167056553 | etot = -54.4567172895143 +987000 ekin = 7.99894925435838 | erot = 13.7207610181171 | epot = -76.1764275614454 | etot = -54.45671728897 +988000 ekin = 8.34021171329978 | erot = 13.1675370959009 | epot = -75.9644660971741 | etot = -54.4567172879735 +989000 ekin = 8.63344275565441 | erot = 12.6122920454569 | epot = -75.7024520877672 | etot = -54.456717286656 +990000 ekin = 8.87460950484452 | erot = 12.0770718401663 | epot = -75.4083986302158 | etot = -54.456717285205 +991000 ekin = 9.06396875500343 | erot = 11.581864705789 | epot = -75.102550744612 | etot = -54.4567172838197 +992000 ekin = 9.20509314118759 | erot = 11.1426150699705 | epot = -74.8044254938273 | etot = -54.4567172826692 +993000 ekin = 9.30382170788255 | erot = 10.7697167151334 | epot = -74.5302557048824 | etot = -54.4567172818665 +994000 ekin = 9.36733435636145 | erot = 10.467172113734 | epot = -74.2912237515574 | etot = -54.456717281462 +995000 ekin = 9.40346085609221 | erot = 10.232442639238 | epot = -74.0926207767815 | etot = -54.4567172814512 +996000 ekin = 9.42024172460242 | erot = 10.0569050470709 | epot = -73.9338640534591 | etot = -54.4567172817857 +997000 ekin = 9.42568515137797 | erot = 9.92679732902699 | epot = -73.8091997627901 | etot = -54.4567172823851 +998000 ekin = 9.42763194302568 | erot = 9.8245642652313 | epot = -73.7089134914019 | etot = -54.4567172831449 +999000 ekin = 9.43365149698941 | erot = 9.73053828894017 | epot = -73.6209070698904 | etot = -54.4567172839608 +1000000 ekin = 9.45092723111945 | erot = 9.62486149925983 | epot = -73.532506015067 | etot = -54.4567172846877 + 1000000 352.2878 -75.545604 2.0130979 -64.081579 -0.0098473389 39304000 +Loop time of 16.8981 on 1 procs for 1000000 steps with 10 atoms + +Performance: 87.228 ns/day, 0.275 hours/ns, 59178.314 timesteps/s, 591.783 katom-step/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.505 | 13.505 | 13.505 | 0.0 | 79.92 +Bond | 0.61276 | 0.61276 | 0.61276 | 0.0 | 3.63 +Neigh | 0.038787 | 0.038787 | 0.038787 | 0.0 | 0.23 +Comm | 0.46975 | 0.46975 | 0.46975 | 0.0 | 2.78 +Output | 0.12918 | 0.12918 | 0.12918 | 0.0 | 0.76 +Modify | 1.6798 | 1.6798 | 1.6798 | 0.0 | 9.94 +Other | | 0.4627 | | | 2.74 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:16 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.4 new file mode 100644 index 0000000000..929e921b16 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.4 @@ -0,0 +1,1176 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 25.179212 + ghost atom cutoff = 32.4 + binsize = 12.589606, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8453746587951 | etot = -54.456717007264 +Per MPI rank memory allocation (min/avg/max) = 7.105 | 7.11 | 7.116 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -80.414409 2.5690347 -71.238502 -0.031164646 39304000 +1000 ekin = 6.43820783118129 | erot = 17.3362198819252 | epot = -78.2311447221034 | etot = -54.4567170089969 +2000 ekin = 6.25962757371404 | erot = 17.7614951323062 | epot = -78.4778397161865 | etot = -54.4567170101663 +3000 ekin = 6.07700556573592 | erot = 18.0349356633584 | epot = -78.5686582395969 | etot = -54.4567170105026 +4000 ekin = 5.8974439552513 | erot = 18.144460931621 | epot = -78.498621896795 | etot = -54.4567170099227 +5000 ekin = 5.72921700410324 | erot = 18.0898077153687 | epot = -78.2757417280194 | etot = -54.4567170085474 +6000 ekin = 5.58103231328815 | erot = 17.8818838137361 | epot = -77.9196331337203 | etot = -54.456717006696 +7000 ekin = 5.4608390844338 | erot = 17.5394286863637 | epot = -77.4569847754239 | etot = -54.4567170046264 +8000 ekin = 5.37466806168172 | erot = 17.086045740889 | epot = -76.9174308051194 | etot = -54.4567170025487 +9000 ekin = 5.32596283558534 | erot = 16.5482758509796 | epot = -76.3309556871347 | etot = -54.4567170005697 +10000 ekin = 5.31555310057074 | erot = 15.9544038907651 | epot = -75.7266739899444 | etot = -54.4567169986085 +11000 ekin = 5.34212439127895 | erot = 15.3332511004199 | epot = -75.1320924886814 | etot = -54.4567169969825 +12000 ekin = 5.40287885250677 | erot = 14.7110726721716 | epot = -74.5706685202876 | etot = -54.4567169956093 +13000 ekin = 5.49412472240376 | erot = 14.1110805159141 | epot = -74.0619222328995 | etot = -54.4567169945816 +14000 ekin = 5.61167339672267 | erot = 13.5517285104403 | epot = -73.6201189011433 | etot = -54.4567169939804 +15000 ekin = 5.75106060199931 | erot = 13.0453082210512 | epot = -73.2530858167916 | etot = -54.4567169937411 +16000 ekin = 5.90768357006488 | erot = 12.598604457851 | epot = -72.9630050218527 | etot = -54.4567169939368 +17000 ekin = 6.07694775533413 | erot = 12.2121295946256 | epot = -72.7457943445781 | etot = -54.4567169946184 +18000 ekin = 6.25449001016684 | erot = 11.8809581167547 | epot = -72.592165121947 | etot = -54.4567169950255 +19000 ekin = 6.43645340088868 | erot = 11.5970728654628 | epot = -72.490243262259 | etot = -54.4567169959076 +20000 ekin = 6.6197622580152 | erot = 11.3493123188078 | epot = -72.425791573462 | etot = -54.4567169966391 +21000 ekin = 6.80232746725469 | erot = 11.1279704350903 | epot = -72.3870148994526 | etot = -54.4567169971076 +22000 ekin = 6.98311688717153 | erot = 10.9264751205884 | epot = -72.3663090050199 | etot = -54.45671699726 +23000 ekin = 7.1620507977588 | erot = 10.7423327849978 | epot = -72.3611005798631 | etot = -54.4567169971065 +24000 ekin = 7.33972059294154 | erot = 10.5772758543379 | epot = -72.3737134439929 | etot = -54.4567169967134 +25000 ekin = 7.51695157931217 | erot = 10.4365899375969 | epot = -72.4102585131396 | etot = -54.4567169962306 +26000 ekin = 7.69429229269138 | erot = 10.3277639309848 | epot = -72.4787732193801 | etot = -54.4567169957039 +27000 ekin = 7.87150951743594 | erot = 10.2597304033282 | epot = -72.5879569160679 | etot = -54.4567169953037 +28000 ekin = 8.04705135555603 | erot = 10.2410352171351 | epot = -72.7448035678557 | etot = -54.4567169951646 +29000 ekin = 8.21759746027584 | erot = 10.278204159473 | epot = -72.9525186151527 | etot = -54.4567169954039 +30000 ekin = 8.37774171244999 | erot = 10.3742403796597 | epot = -73.2086990882227 | etot = -54.456716996113 +31000 ekin = 8.51990909585288 | erot = 10.5273666264236 | epot = -73.5039927196028 | etot = -54.4567169973263 +32000 ekin = 8.6346526212693 | erot = 10.7302431095275 | epot = -73.8216127297865 | etot = -54.4567169989897 +33000 ekin = 8.71148334085684 | erot = 10.9699651918539 | epot = -74.1381655336438 | etot = -54.4567170009331 +34000 ekin = 8.7403039201086 | erot = 11.2291223208269 | epot = -74.4261432438071 | etot = -54.4567170028716 +35000 ekin = 8.71331622899725 | erot = 11.4879560434145 | epot = -74.6579892768899 | etot = -54.4567170044781 +36000 ekin = 8.62700549413936 | erot = 11.7272789104032 | epot = -74.811001409922 | etot = -54.4567170053794 +37000 ekin = 8.48360146993983 | erot = 11.9311520187439 | epot = -74.8714704944479 | etot = -54.4567170057642 +38000 ekin = 8.29145725510833 | erot = 12.0877651508225 | epot = -74.8359394109119 | etot = -54.456717004981 +39000 ekin = 8.06412808157037 | erot = 12.193949078282 | epot = -74.714794163255 | etot = -54.4567170034026 +40000 ekin = 7.81834916729639 | erot = 12.253681100569 | epot = -74.5287472695191 | etot = -54.4567170016537 +41000 ekin = 7.57153983107097 | erot = 12.2737166637658 | epot = -74.3019734948451 | etot = -54.4567170000083 +42000 ekin = 7.33952905244331 | erot = 12.2616299907499 | epot = -74.0578760417273 | etot = -54.4567169985341 +43000 ekin = 7.13479707854045 | erot = 12.2251663434269 | epot = -73.8166804194395 | etot = -54.4567169974721 +44000 ekin = 6.96549624172367 | erot = 12.1705863869627 | epot = -73.5927996255415 | etot = -54.4567169968552 +45000 ekin = 6.83524241842647 | erot = 12.102386584698 | epot = -73.3943459997481 | etot = -54.4567169966236 +46000 ekin = 6.74353977237846 | erot = 12.0237417555814 | epot = -73.2239985246156 | etot = -54.4567169966557 +47000 ekin = 6.68665226743031 | erot = 11.9373741846293 | epot = -73.0807434488664 | etot = -54.4567169968068 +48000 ekin = 6.65871295716602 | erot = 11.8463562055027 | epot = -72.9617861597099 | etot = -54.4567169970411 +49000 ekin = 6.65288229900598 | erot = 11.7538080029638 | epot = -72.863407299029 | etot = -54.4567169970592 +50000 ekin = 6.66236312881751 | erot = 11.6656641757329 | epot = -72.7847443014508 | etot = -54.4567169969004 +51000 ekin = 6.68111060961808 | erot = 11.589978825656 | epot = -72.7278064318538 | etot = -54.4567169965796 +52000 ekin = 6.70418024749921 | erot = 11.5360562910261 | epot = -72.6969535346928 | etot = -54.4567169961675 +53000 ekin = 6.72772366359068 | erot = 11.5134142818728 | epot = -72.6978549412363 | etot = -54.4567169957729 +54000 ekin = 6.74871337970537 | erot = 11.5307585185411 | epot = -72.7361888937389 | etot = -54.4567169954924 +55000 ekin = 6.76451852991725 | erot = 11.5943746539845 | epot = -72.8156101794049 | etot = -54.4567169955031 +56000 ekin = 6.77243985440136 | erot = 11.706371078097 | epot = -72.9355279283612 | etot = -54.4567169958628 +57000 ekin = 6.7693305358261 | erot = 11.8642156230101 | epot = -73.0902631554553 | etot = -54.4567169966191 +58000 ekin = 6.75138726809276 | erot = 12.0602974501195 | epot = -73.2684017159808 | etot = -54.4567169977685 +59000 ekin = 6.71417128127022 | erot = 12.2820751409018 | epot = -73.4529634214116 | etot = -54.4567169992396 +60000 ekin = 6.65290992288125 | erot = 12.5129009338972 | epot = -73.6225278576791 | etot = -54.4567170009007 +61000 ekin = 6.56310682197134 | erot = 12.7335144723076 | epot = -73.7533382968318 | etot = -54.4567170025529 +62000 ekin = 6.44146338255673 | erot = 12.9241509619383 | epot = -73.8223313484469 | etot = -54.4567170039518 +63000 ekin = 6.28705781387421 | erot = 13.0670338389562 | epot = -73.8108086578477 | etot = -54.4567170050173 +64000 ekin = 6.10266169757333 | erot = 13.1477809820682 | epot = -73.7071596847884 | etot = -54.4567170051469 +65000 ekin = 5.89591130160499 | erot = 13.1592635961174 | epot = -73.5118919021177 | etot = -54.4567170043953 +66000 ekin = 5.67987143865734 | erot = 13.1032095066886 | epot = -73.2397979480404 | etot = -54.4567170026945 +67000 ekin = 5.47246439370584 | erot = 12.9892907727295 | epot = -72.9184721669227 | etot = -54.4567170004874 +68000 ekin = 5.29471721365746 | erot = 12.8325811063867 | epot = -72.5840153180095 | etot = -54.4567169979654 +69000 ekin = 5.16838716298836 | erot = 12.6515610640457 | epot = -72.2766652226416 | etot = -54.4567169956076 +70000 ekin = 5.11230249491464 | erot = 12.4645586086546 | epot = -72.0335780974658 | etot = -54.4567169938966 +71000 ekin = 5.13863171720077 | erot = 12.2861676510944 | epot = -71.8815163616887 | etot = -54.4567169933935 +72000 ekin = 5.24921766817675 | erot = 12.1241146960797 | epot = -71.8300493582336 | etot = -54.4567169939772 +73000 ekin = 5.43495114762277 | erot = 11.9780651684523 | epot = -71.8697333116332 | etot = -54.4567169955581 +74000 ekin = 5.67787386257464 | erot = 11.8411579566072 | epot = -71.9757488169268 | etot = -54.456716997745 +75000 ekin = 5.95416182625064 | erot = 11.7025717830502 | epot = -72.1134506093456 | etot = -54.4567170000447 +76000 ekin = 6.2382481878041 | erot = 11.5508489468451 | epot = -72.2458141366457 | etot = -54.4567170019965 +77000 ekin = 6.50675110372077 | erot = 11.3769606434414 | epot = -72.3404287504472 | etot = -54.456717003285 +78000 ekin = 6.74136703150947 | erot = 11.1763239765936 | epot = -72.3744080118945 | etot = -54.4567170037914 +79000 ekin = 6.93031685726874 | erot = 10.9493830401333 | epot = -72.3364169009801 | etot = -54.456717003578 +80000 ekin = 7.06838579021211 | erot = 10.7008558180271 | epot = -72.2259586110722 | etot = -54.456717002833 +81000 ekin = 7.1559317498921 | erot = 10.4381486680524 | epot = -72.0507974197279 | etot = -54.4567170017834 +82000 ekin = 7.19737561193674 | erot = 10.1696078110443 | epot = -71.8237004236083 | etot = -54.4567170006273 +83000 ekin = 7.19963709941639 | erot = 9.90317661788295 | epot = -71.5595307167935 | etot = -54.4567169994941 +84000 ekin = 7.17081556670968 | erot = 9.64574605090018 | epot = -71.2732786160521 | etot = -54.4567169984422 +85000 ekin = 7.11922963823702 | erot = 9.40317461807806 | epot = -70.9791212537918 | etot = -54.4567169974768 +86000 ekin = 7.05279272914734 | erot = 9.18074070207699 | epot = -70.6902504278042 | etot = -54.4567169965799 +87000 ekin = 6.97863676438084 | erot = 8.98372361344404 | epot = -70.4190773735564 | etot = -54.4567169957315 +88000 ekin = 6.90289111255646 | erot = 8.81786450432879 | epot = -70.1774726118098 | etot = -54.4567169949245 +89000 ekin = 6.83054970527794 | erot = 8.68957087135301 | epot = -69.9768375708001 | etot = -54.4567169941691 +90000 ekin = 6.76539137201343 | erot = 8.6058379604908 | epot = -69.827946325993 | etot = -54.4567169934887 +91000 ekin = 6.70994198518164 | erot = 8.57393232142963 | epot = -69.7405912995254 | etot = -54.4567169929141 +92000 ekin = 6.66547828037082 | erot = 8.60091153027911 | epot = -69.7231068031299 | etot = -54.4567169924799 +93000 ekin = 6.63207907276839 | erot = 8.6930521826077 | epot = -69.7818482475959 | etot = -54.4567169922198 +94000 ekin = 6.60872467795687 | erot = 8.8552421329534 | epot = -69.9206838030737 | etot = -54.4567169921635 +95000 ekin = 6.59344191188633 | erot = 9.09002892498244 | epot = -70.1401878292959 | etot = -54.4567169924271 +96000 ekin = 6.58348503117488 | erot = 9.39676155295733 | epot = -70.4369635770063 | etot = -54.456716992874 +97000 ekin = 6.57555779040081 | erot = 9.77238659111564 | epot = -70.8046613751035 | etot = -54.456716993587 +98000 ekin = 6.56606406506432 | erot = 10.2104006447566 | epot = -71.2331817043844 | etot = -54.4567169945635 +99000 ekin = 6.55138371755681 | erot = 10.7005955684085 | epot = -71.7086962817511 | etot = -54.4567169957858 +100000 ekin = 6.52818215156233 | erot = 11.2291048041215 | epot = -72.2140039528885 | etot = -54.4567169972047 +101000 ekin = 6.49376016387362 | erot = 11.7788216139169 | epot = -72.7292987765295 | etot = -54.4567169987389 +102000 ekin = 6.44644131665531 | erot = 12.3302826834051 | epot = -73.233441000326 | etot = -54.4567170002657 +103000 ekin = 6.38597185526377 | erot = 12.8630533051894 | epot = -73.7057421620907 | etot = -54.4567170016375 +104000 ekin = 6.31387792328062 | erot = 13.3575416630679 | epot = -74.1281365890436 | etot = -54.456717002695 +105000 ekin = 6.23369870065272 | erot = 13.7969859266867 | epot = -74.4874016306547 | etot = -54.4567170033153 +106000 ekin = 6.15159087577044 | erot = 14.1683474790283 | epot = -74.7766553580954 | etot = -54.4567170032966 +107000 ekin = 6.07597686979351 | erot = 14.4651876627013 | epot = -74.9978815355799 | etot = -54.4567170030851 +108000 ekin = 6.01223234716891 | erot = 14.6879971316708 | epot = -75.1569464811456 | etot = -54.4567170023059 +109000 ekin = 5.9671660618815 | erot = 14.8435442892158 | epot = -75.2674273521902 | etot = -54.4567170010929 +110000 ekin = 5.94905536831868 | erot = 14.9434041692653 | epot = -75.3491765372256 | etot = -54.4567169996416 +111000 ekin = 5.96691720967342 | erot = 15.0017805706299 | epot = -75.4254147784705 | etot = -54.4567169981672 +112000 ekin = 6.02963996568477 | erot = 15.0332074410391 | epot = -75.5195644035797 | etot = -54.4567169968558 +113000 ekin = 6.14473557949392 | erot = 15.050627693563 | epot = -75.6520802691319 | etot = -54.456716996075 +114000 ekin = 6.31295582028862 | erot = 15.0641514071753 | epot = -75.833824223199 | etot = -54.4567169957351 +115000 ekin = 6.5317279860067 | erot = 15.0811124191464 | epot = -76.0695574009521 | etot = -54.456716995799 +116000 ekin = 6.79568089094029 | erot = 15.1059058197079 | epot = -76.3583037069103 | etot = -54.4567169962621 +117000 ekin = 7.09592407299215 | erot = 15.1399966271423 | epot = -76.6926376972559 | etot = -54.4567169971214 +118000 ekin = 7.42014276685719 | erot = 15.1819125959101 | epot = -77.058772361131 | etot = -54.4567169983637 +119000 ekin = 7.75294827199775 | erot = 15.2271422568032 | epot = -77.4368075287532 | etot = -54.4567169999523 +120000 ekin = 8.07659193886498 | erot = 15.268102841629 | epot = -77.8014117822893 | etot = -54.4567170017953 +121000 ekin = 8.37212580399509 | erot = 15.2944516166555 | epot = -78.1232944243858 | etot = -54.4567170037352 +122000 ekin = 8.62100116395953 | erot = 15.2939804912639 | epot = -78.3716986607707 | etot = -54.4567170055472 +123000 ekin = 8.80694171731981 | erot = 15.2541500009288 | epot = -78.517808725228 | etot = -54.4567170069794 +124000 ekin = 8.91776467099437 | erot = 15.164053588948 | epot = -78.5385352677523 | etot = -54.4567170078099 +125000 ekin = 8.94674800947867 | erot = 15.0163836749145 | epot = -78.4198486922972 | etot = -54.456717007904 +126000 ekin = 8.89353650630918 | erot = 14.8103820375844 | epot = -78.1606355512052 | etot = -54.4567170073116 +127000 ekin = 8.7629508625382 | erot = 14.5505189841118 | epot = -77.7701868527644 | etot = -54.4567170061144 +128000 ekin = 8.56410993715598 | erot = 14.2447035162395 | epot = -77.2655304577616 | etot = -54.4567170043662 +129000 ekin = 8.30998017116448 | erot = 13.9055852316459 | epot = -76.67228240508 | etot = -54.4567170022696 +130000 ekin = 8.01596533696713 | erot = 13.5489606027722 | epot = -76.0216429397722 | etot = -54.4567170000329 +131000 ekin = 7.69857959330859 | erot = 13.1919558696619 | epot = -75.347252460815 | etot = -54.4567169978444 +132000 ekin = 7.37430715048895 | erot = 12.851283884861 | epot = -74.6823080312056 | etot = -54.4567169958556 +133000 ekin = 7.05869350217223 | erot = 12.5417841519169 | epot = -74.057194648267 | etot = -54.4567169941778 +134000 ekin = 6.76568000840881 | erot = 12.2753517528745 | epot = -73.4977487541602 | etot = -54.4567169928769 +135000 ekin = 6.50716750003275 | erot = 12.0602618213903 | epot = -73.0241463134165 | etot = -54.4567169919934 +136000 ekin = 6.29276806011983 | erot = 11.9007845740752 | epot = -72.6502696257304 | etot = -54.4567169915353 +137000 ekin = 6.12969309854662 | erot = 11.7970866991193 | epot = -72.3834967891649 | etot = -54.456716991499 +138000 ekin = 6.02273320867693 | erot = 11.7455527096604 | epot = -72.2250029101856 | etot = -54.4567169918483 +139000 ekin = 5.97430093912947 | erot = 11.7390915567055 | epot = -72.170109488443 | etot = -54.456716992608 +140000 ekin = 5.98450304637417 | erot = 11.7662502093776 | epot = -72.2074702494665 | etot = -54.4567169937147 +141000 ekin = 6.05123669074375 | erot = 11.8124070325109 | epot = -72.3203607183682 | etot = -54.4567169951136 +142000 ekin = 6.17033803011782 | erot = 11.8605042646639 | epot = -72.4875592915082 | etot = -54.4567169967265 +143000 ekin = 6.33580648591441 | erot = 11.8920252829291 | epot = -72.6845487670624 | etot = -54.456716998219 +144000 ekin = 6.54012675510799 | erot = 11.8891823611252 | epot = -72.8860261161669 | etot = -54.4567169999337 +145000 ekin = 6.77470074055112 | erot = 11.8353291244163 | epot = -73.0667468664381 | etot = -54.4567170014707 +146000 ekin = 7.03037496397093 | erot = 11.7160243954377 | epot = -73.2031163621673 | etot = -54.4567170027587 +147000 ekin = 7.29665364400731 | erot = 11.5220998482973 | epot = -73.27547049583 | etot = -54.4567170035254 +148000 ekin = 7.56413207766569 | erot = 11.2503161699873 | epot = -73.2711652513975 | etot = -54.4567170037445 +149000 ekin = 7.82550108771552 | erot = 10.9039474189382 | epot = -73.1861655100572 | etot = -54.4567170034035 +150000 ekin = 8.07523421780362 | erot = 10.4929157971022 | epot = -73.0248670174482 | etot = -54.4567170025424 +151000 ekin = 8.3098163223035 | erot = 10.0329247877117 | epot = -72.7994581112916 | etot = -54.4567170012765 +152000 ekin = 8.52773011311644 | erot = 9.54384337568687 | epot = -72.5282904885589 | etot = -54.4567169997555 +153000 ekin = 8.72920635330158 | erot = 9.04773752673217 | epot = -72.2336608781799 | etot = -54.4567169981462 +154000 ekin = 8.91578242577698 | erot = 8.56683521279237 | epot = -71.9393346351768 | etot = -54.4567169966075 +155000 ekin = 9.08973687645563 | erot = 8.1216936934817 | epot = -71.6681475652126 | etot = -54.4567169952753 +156000 ekin = 9.25347765695021 | erot = 7.72974563989849 | epot = -71.4399402910998 | etot = -54.4567169942511 +157000 ekin = 9.40896984476819 | erot = 7.40429996451988 | epot = -71.2699868028811 | etot = -54.456716993593 +158000 ekin = 9.55725976320102 | erot = 7.15399036856533 | epot = -71.1679671251185 | etot = -54.4567169933522 +159000 ekin = 9.69799996758521 | erot = 6.98263031176904 | epot = -71.1373472728716 | etot = -54.4567169935173 +160000 ekin = 9.82927262106972 | erot = 6.88943240361959 | epot = -71.1754220187509 | etot = -54.4567169940616 +161000 ekin = 9.947526276393 | erot = 6.86953876421116 | epot = -71.2737820355287 | etot = -54.4567169949245 +162000 ekin = 10.0476688890869 | erot = 6.91484346812827 | epot = -71.4192293532371 | etot = -54.4567169960219 +163000 ekin = 10.123328928587 | erot = 7.01508857895077 | epot = -71.5951345047789 | etot = -54.4567169972412 +164000 ekin = 10.1672866918974 | erot = 7.15919485891775 | epot = -71.7831985492644 | etot = -54.4567169984493 +165000 ekin = 10.1720714801839 | erot = 7.33674388087005 | epot = -71.9655323605553 | etot = -54.4567169995013 +166000 ekin = 10.1307061587117 | erot = 7.53947176071147 | epot = -72.1268949196792 | etot = -54.4567170002561 +167000 ekin = 10.0375550044402 | erot = 7.76257261597399 | epot = -72.2568446210101 | etot = -54.4567170005959 +168000 ekin = 9.88919379239882 | erot = 8.00559837770909 | epot = -72.3515091705551 | etot = -54.4567170004472 +169000 ekin = 9.68518014710124 | erot = 8.27274634403603 | epot = -72.4146434909393 | etot = -54.456716999802 +170000 ekin = 9.42857099718412 | erot = 8.57239606367951 | epot = -72.4576840595929 | etot = -54.4567169987293 +171000 ekin = 9.12604219834231 | erot = 8.91588733602144 | epot = -72.4986465317343 | etot = -54.4567169973706 +172000 ekin = 8.78753113653312 | erot = 9.31569783313693 | epot = -72.5599459655886 | etot = -54.4567169959186 +173000 ekin = 8.43073965989606 | erot = 9.7841793241114 | epot = -72.6716359780365 | etot = -54.4567169940291 +174000 ekin = 8.08793433498408 | erot = 10.330499917481 | epot = -72.8751512464577 | etot = -54.4567169939927 +175000 ekin = 7.76668155628402 | erot = 10.9530367882605 | epot = -73.1764353387626 | etot = -54.4567169942181 +176000 ekin = 7.47150671335435 | erot = 11.6457657834648 | epot = -73.5739894915328 | etot = -54.4567169947137 +177000 ekin = 7.20629810214466 | erot = 12.3991540124657 | epot = -74.0621691100488 | etot = -54.4567169954385 +178000 ekin = 6.9741272880116 | erot = 13.2004427724153 | epot = -74.6312870569044 | etot = -54.4567169964775 +179000 ekin = 6.777261372753 | erot = 14.0344360010824 | epot = -75.2684143712779 | etot = -54.4567169974425 +180000 ekin = 6.61731488748121 | erot = 14.886465584398 | epot = -75.9604974702741 | etot = -54.4567169983949 +181000 ekin = 6.49550388719761 | erot = 15.740890928748 | epot = -76.6931118153624 | etot = -54.4567169994167 +182000 ekin = 6.4129639266329 | erot = 16.5825261501067 | epot = -77.4522070769592 | etot = -54.4567170002196 +183000 ekin = 6.37096768346922 | erot = 17.3990430380152 | epot = -78.2267277223741 | etot = -54.4567170008897 +184000 ekin = 6.37100453718988 | erot = 18.1796029220147 | epot = -79.007324460659 | etot = -54.4567170014544 +185000 ekin = 6.41457925655334 | erot = 18.9145289221487 | epot = -79.7858251806977 | etot = -54.4567170019957 +186000 ekin = 6.50258553919727 | erot = 19.5946185261417 | epot = -80.5539210679911 | etot = -54.4567170026522 +187000 ekin = 6.63421344627162 | erot = 20.2101022369816 | epot = -81.3010326868601 | etot = -54.4567170036069 +188000 ekin = 6.80554165522624 | erot = 20.7494117392046 | epot = -82.0116703994637 | etot = -54.4567170050328 +189000 ekin = 7.00820348124158 | erot = 21.198178393125 | epot = -82.6630988813723 | etot = -54.4567170070057 +190000 ekin = 7.2286852193232 | erot = 21.5391098111538 | epot = -83.2245120398958 | etot = -54.4567170094187 +191000 ekin = 7.4477192848755 | erot = 21.7494170056975 | epot = -83.6538533032756 | etot = -54.4567170127026 +192000 ekin = 7.64125751955868 | erot = 21.804820778351 | epot = -83.902795312323 | etot = -54.4567170144133 +193000 ekin = 7.78828740684676 | erot = 21.699167392686 | epot = -83.9441718146323 | etot = -54.4567170150995 +194000 ekin = 7.87257389701353 | erot = 21.4375246080157 | epot = -83.7668155195151 | etot = -54.4567170144859 +195000 ekin = 7.88499447656609 | erot = 21.0374826850363 | epot = -83.379194174065 | etot = -54.4567170124625 +196000 ekin = 7.82454827833309 | erot = 20.5296762951792 | epot = -82.8109415829978 | etot = -54.4567170094855 +197000 ekin = 7.69767598869487 | erot = 19.9506603805391 | epot = -82.1050533754226 | etot = -54.4567170061886 +198000 ekin = 7.51633971742089 | erot = 19.3369849795413 | epot = -81.3100416995845 | etot = -54.4567170026223 +199000 ekin = 7.29564326175657 | erot = 18.7231663844391 | epot = -80.475526646081 | etot = -54.4567169998853 +200000 ekin = 7.05165448325243 | erot = 18.1349004645742 | epot = -79.6432719456259 | etot = -54.4567169977993 +201000 ekin = 6.79980702715613 | erot = 17.5878866996096 | epot = -78.8444107231904 | etot = -54.4567169964247 +202000 ekin = 6.55389674542505 | erot = 17.0887428909435 | epot = -78.0993566320929 | etot = -54.4567169957244 +203000 ekin = 6.32553934601821 | erot = 16.635910212878 | epot = -77.4181665545157 | etot = -54.4567169956195 +204000 ekin = 6.12389931338586 | erot = 16.2210487374556 | epot = -76.8016650468549 | etot = -54.4567169960135 +205000 ekin = 5.95555747603993 | erot = 15.8306192384133 | epot = -76.2428937112566 | etot = -54.4567169968033 +206000 ekin = 5.82447629752423 | erot = 15.4475601715623 | epot = -75.7287534669561 | etot = -54.4567169978695 +207000 ekin = 5.73209725915215 | erot = 15.053105252153 | epot = -75.24191951037 | etot = -54.4567169990648 +208000 ekin = 5.67763110960464 | erot = 14.6288167787821 | epot = -74.7631648885979 | etot = -54.4567170002112 +209000 ekin = 5.65856116655253 | erot = 14.1588249337379 | epot = -74.274103101405 | etot = -54.4567170011145 +210000 ekin = 5.67128286639217 | erot = 13.6320871718289 | epot = -73.7600870398271 | etot = -54.456717001606 +211000 ekin = 5.71170580201778 | erot = 13.0442947184013 | epot = -73.2127175220048 | etot = -54.4567170015858 +212000 ekin = 5.77563179366534 | erot = 12.3989793850584 | epot = -72.631328179774 | etot = -54.4567170010502 +213000 ekin = 5.85883529486842 | erot = 11.7074993993216 | epot = -72.0230516942805 | etot = -54.4567170000905 +214000 ekin = 5.95694378807573 | erot = 10.9878661192751 | epot = -71.4015269062056 | etot = -54.4567169988548 +215000 ekin = 6.06530909503309 | erot = 10.2626621519509 | epot = -70.7846882444977 | etot = -54.4567169975137 +216000 ekin = 6.17900319439831 | erot = 9.55646209150858 | epot = -70.1921822821386 | etot = -54.4567169962318 +217000 ekin = 6.29293379836523 | erot = 8.89318379220252 | epot = -69.6428345857182 | etot = -54.4567169951505 +218000 ekin = 6.40198693071945 | erot = 8.29373644845956 | epot = -69.1524403735559 | etot = -54.4567169943768 +219000 ekin = 6.50112265239607 | erot = 7.77424405643308 | epot = -68.7320837028041 | etot = -54.456716993975 +220000 ekin = 6.5854259900538 | erot = 7.34501698346227 | epot = -68.387159967471 | etot = -54.4567169939549 +221000 ekin = 6.65016990044527 | erot = 7.01032033730988 | epot = -68.1172072320316 | etot = -54.4567169942764 +222000 ekin = 6.69094775781806 | erot = 6.76886488025023 | epot = -67.916529632925 | etot = -54.4567169948567 +223000 ekin = 6.70389570636201 | erot = 6.61485079073771 | epot = -67.7754634926876 | etot = -54.4567169955879 +224000 ekin = 6.68598136532681 | erot = 6.53933986021686 | epot = -67.6820382218994 | etot = -54.4567169963558 +225000 ekin = 6.63530548008065 | erot = 6.53171636120698 | epot = -67.6237388383031 | etot = -54.4567169970154 +226000 ekin = 6.55135057790585 | erot = 6.58128483353357 | epot = -67.5893524090299 | etot = -54.4567169975904 +227000 ekin = 6.43512370214175 | erot = 6.67791109034028 | epot = -67.5697517904632 | etot = -54.4567169979811 +228000 ekin = 6.2891897097421 | erot = 6.81247705117203 | epot = -67.5583837590954 | etot = -54.4567169981813 +229000 ekin = 6.11756588060394 | erot = 6.97743477794333 | epot = -67.5517176567565 | etot = -54.4567169982092 +230000 ekin = 5.92551276691658 | erot = 7.16674212049509 | epot = -67.5489718855092 | etot = -54.4567169980975 +231000 ekin = 5.71926565755888 | erot = 7.37564891103015 | epot = -67.5516315664655 | etot = -54.4567169978765 +232000 ekin = 5.50574389394642 | erot = 7.60035647333501 | epot = -67.5628173648775 | etot = -54.4567169975961 +233000 ekin = 5.29225977425841 | erot = 7.83770399532855 | epot = -67.586680766864 | etot = -54.456716997277 +234000 ekin = 5.08624392068214 | erot = 8.08503631201065 | epot = -67.6279972296341 | etot = -54.4567169969414 +235000 ekin = 4.89494104384804 | erot = 8.33999580226642 | epot = -67.6916538427518 | etot = -54.4567169966373 +236000 ekin = 4.72509234581121 | erot = 8.6002992433848 | epot = -67.782108585585 | etot = -54.456716996389 +237000 ekin = 4.58266021003873 | erot = 8.86357795327266 | epot = -67.9029551595412 | etot = -54.4567169962298 +238000 ekin = 4.47254260204247 | erot = 9.12720418840754 | epot = -68.0564637866322 | etot = -54.4567169961822 +239000 ekin = 4.39833350162575 | erot = 9.38820734227518 | epot = -68.2432578401578 | etot = -54.4567169962569 +240000 ekin = 4.36216127770996 | erot = 9.64334632220632 | epot = -68.462224596357 | etot = -54.4567169964407 +241000 ekin = 4.36462932001306 | erot = 9.88937569308421 | epot = -68.7107220098002 | etot = -54.4567169967029 +242000 ekin = 4.40486892553746 | erot = 10.1234451005874 | epot = -68.9850310231344 | etot = -54.4567169970095 +243000 ekin = 4.48069651384412 | erot = 10.3436703820956 | epot = -69.2810838932206 | etot = -54.4567169972809 +244000 ekin = 4.58885218173589 | erot = 10.5497495785184 | epot = -69.5953187577396 | etot = -54.4567169974854 +245000 ekin = 4.72528226906678 | erot = 10.7433460022161 | epot = -69.9253452688674 | etot = -54.4567169975846 +246000 ekin = 4.88542118270109 | erot = 10.9282390794581 | epot = -70.2703772597352 | etot = -54.456716997576 +247000 ekin = 5.06442778965819 | erot = 11.1101246208806 | epot = -70.6312694080245 | etot = -54.4567169974857 +248000 ekin = 5.25733886261718 | erot = 11.29603558528 | epot = -71.010091445268 | etot = -54.4567169973708 +249000 ekin = 5.45911617616127 | erot = 11.4934186026681 | epot = -71.4092517761424 | etot = -54.456716997313 +250000 ekin = 5.66458445083577 | erot = 11.7089626303623 | epot = -71.830264078606 | etot = -54.4567169974079 +251000 ekin = 5.86828470152281 | erot = 11.9473320827919 | epot = -72.272333782062 | etot = -54.4567169977473 +252000 ekin = 6.06430127912922 | erot = 12.2100106162568 | epot = -72.7310288937809 | etot = -54.4567169983949 +253000 ekin = 6.24616780492761 | erot = 12.494513748408 | epot = -73.1973985526896 | etot = -54.4567169993539 +254000 ekin = 6.40690922038896 | erot = 12.7941888151854 | epot = -73.6578150361466 | etot = -54.4567170005723 +255000 ekin = 6.5393836854708 | erot = 13.0989475895866 | epot = -74.09504827693 | etot = -54.4567170018726 +256000 ekin = 6.63705992686618 | erot = 13.3969420757797 | epot = -74.4907190057148 | etot = -54.4567170030689 +257000 ekin = 6.69484132858293 | erot = 13.6765522910225 | epot = -74.8281106235613 | etot = -54.4567170039558 +258000 ekin = 6.70989585739654 | erot = 13.9284862768558 | epot = -75.0950991386068 | etot = -54.4567170043544 +259000 ekin = 6.68225912100175 | erot = 14.1474604164245 | epot = -75.2864365416673 | etot = -54.456717004241 +260000 ekin = 6.61492696705933 | erot = 14.3327847112053 | epot = -75.4044286819652 | etot = -54.4567170037005 +261000 ekin = 6.51342916846536 | erot = 14.4875948089552 | epot = -75.4577409802919 | etot = -54.4567170028714 +262000 ekin = 6.38502298989557 | erot = 14.6177175279255 | epot = -75.4594575197531 | etot = -54.456717001932 +263000 ekin = 6.23773151258861 | erot = 14.730099973026 | epot = -75.4245484866763 | etot = -54.4567170010617 +264000 ekin = 6.07942833310793 | erot = 14.8312906384176 | epot = -75.3674359719046 | etot = -54.456717000379 +265000 ekin = 5.91711592011929 | erot = 14.9263499746167 | epot = -75.3001828947035 | etot = -54.4567169999675 +266000 ekin = 5.7564789891914 | erot = 15.018125069079 | epot = -75.2313210581377 | etot = -54.4567169998673 +267000 ekin = 5.60177946975274 | erot = 15.1067951880419 | epot = -75.1652916578647 | etot = -54.4567170000701 +268000 ekin = 5.45615379098727 | erot = 15.1897452349394 | epot = -75.1026160264288 | etot = -54.4567170005022 +269000 ekin = 5.32235014694693 | erot = 15.2617179030259 | epot = -75.0407850514157 | etot = -54.4567170014429 +270000 ekin = 5.20387607982337 | erot = 15.3135128498233 | epot = -74.9741059315122 | etot = -54.4567170018656 +271000 ekin = 5.10637822315298 | erot = 15.3372496535252 | epot = -74.9003448785808 | etot = -54.4567170019026 +272000 ekin = 5.0388518748126 | erot = 15.327624841932 | epot = -74.8231937182346 | etot = -54.45671700149 +273000 ekin = 5.01411589731478 | erot = 15.2821745715711 | epot = -74.753007469433 | etot = -54.4567170005471 +274000 ekin = 5.04786741773059 | erot = 15.2025250199031 | epot = -74.7071094369017 | etot = -54.456716999268 +275000 ekin = 5.15594350432443 | erot = 15.0944700838399 | epot = -74.7071305861059 | etot = -54.4567169979416 +276000 ekin = 5.35014893903254 | erot = 14.9659361282872 | epot = -74.7728020645917 | etot = -54.456716997272 +277000 ekin = 5.63387543033584 | erot = 14.8238652605444 | epot = -74.9144576883746 | etot = -54.4567169974944 +278000 ekin = 5.9992050625418 | erot = 14.6727240463587 | epot = -75.1286461075964 | etot = -54.4567169986959 +279000 ekin = 6.42692112008834 | erot = 14.5136996025157 | epot = -75.3973377231713 | etot = -54.4567170005673 +280000 ekin = 6.88964247825228 | erot = 14.3457897766202 | epot = -75.6921492574948 | etot = -54.4567170026223 +281000 ekin = 7.35680808435014 | erot = 14.1678692303747 | epot = -75.9813943196878 | etot = -54.4567170049629 +282000 ekin = 7.79894530205569 | erot = 13.97831316129 | epot = -76.233975469457 | etot = -54.4567170061112 +283000 ekin = 8.19329732426334 | erot = 13.7802856701195 | epot = -76.4303000007534 | etot = -54.4567170063705 +284000 ekin = 8.52584895841343 | erot = 13.5821656429456 | epot = -76.5647316071554 | etot = -54.4567170057964 +285000 ekin = 8.79110175655349 | erot = 13.3960594628958 | epot = -76.6438782240551 | etot = -54.4567170046058 +286000 ekin = 8.99062132696418 | erot = 13.236122516321 | epot = -76.6834608463903 | etot = -54.4567170031052 +287000 ekin = 9.13075096351883 | erot = 13.1164152547882 | epot = -76.703883219916 | etot = -54.456717001609 +288000 ekin = 9.22014020608195 | erot = 13.0487281533272 | epot = -76.7255853597968 | etot = -54.4567170003877 +289000 ekin = 9.26758159069438 | erot = 13.0407526423324 | epot = -76.7650512326496 | etot = -54.4567169996229 +290000 ekin = 9.2804545878987 | erot = 13.0948897576411 | epot = -76.8320613449326 | etot = -54.4567169993928 +291000 ekin = 9.26388652305205 | erot = 13.2078630291939 | epot = -76.9284665519251 | etot = -54.4567169996791 +292000 ekin = 9.22058026560491 | erot = 13.371134477086 | epot = -77.0484317430758 | etot = -54.4567170003849 +293000 ekin = 9.15114447321159 | erot = 13.5719438956133 | epot = -77.1798053701999 | etot = -54.456717001375 +294000 ekin = 9.05470928641344 | erot = 13.7944688657478 | epot = -77.3058951547474 | etot = -54.4567170025862 +295000 ekin = 8.92962793964952 | erot = 14.0209919623942 | epot = -77.4073369058163 | etot = -54.4567170037725 +296000 ekin = 8.77413837932213 | erot = 14.2337556111685 | epot = -77.4646109953927 | etot = -54.4567170049021 +297000 ekin = 8.58694141176616 | erot = 14.415611799112 | epot = -77.4592702167747 | etot = -54.4567170058966 +298000 ekin = 8.3677146408304 | erot = 14.5507736801909 | epot = -77.3752053276984 | etot = -54.4567170066771 +299000 ekin = 8.1175782838731 | erot = 14.6256180333538 | epot = -77.199913324391 | etot = -54.4567170071641 +300000 ekin = 7.83948860310923 | erot = 14.6295386097215 | epot = -76.9257442201147 | etot = -54.4567170072839 +301000 ekin = 7.53848779196876 | erot = 14.5557753435617 | epot = -76.5509801425209 | etot = -54.4567170069904 +302000 ekin = 7.22172227244953 | erot = 14.4020558262223 | epot = -76.0804951049517 | etot = -54.4567170062799 +303000 ekin = 6.89817001546493 | erot = 14.1708739456024 | epot = -75.5257609662668 | etot = -54.4567170051995 +304000 ekin = 6.5780826193155 | erot = 13.8692983758872 | epot = -74.9040979990421 | etot = -54.4567170038394 +305000 ekin = 6.2722234776866 | erot = 13.5083194093766 | epot = -74.237259889379 | etot = -54.4567170023159 +306000 ekin = 5.99103930573308 | erot = 13.1018578904741 | epot = -73.5496141969571 | etot = -54.4567170007499 +307000 ekin = 5.74391705620338 | erot = 12.6656285179015 | epot = -72.8662625733495 | etot = -54.4567169992446 +308000 ekin = 5.53864734382918 | erot = 12.2160468439072 | epot = -72.2114111856066 | etot = -54.4567169978702 +309000 ekin = 5.38115498326384 | erot = 11.7690964633624 | epot = -71.6069684433639 | etot = -54.4567169967377 +310000 ekin = 5.27549820636912 | erot = 11.3394194656006 | epot = -71.0716346677099 | etot = -54.4567169957402 +311000 ekin = 5.22401044243336 | erot = 10.9405074525337 | epot = -70.6212348899248 | etot = -54.4567169949577 +312000 ekin = 5.22752009860295 | erot = 10.5837867729379 | epot = -70.2680238659518 | etot = -54.4567169944109 +313000 ekin = 5.28556911025189 | erot = 10.2780287119632 | epot = -70.0203148163499 | etot = -54.4567169941348 +314000 ekin = 5.39655367391962 | erot = 10.0287341725174 | epot = -69.8820048406112 | etot = -54.4567169941742 +315000 ekin = 5.55776516265775 | erot = 9.83752336499865 | epot = -69.8520055222255 | etot = -54.4567169945691 +316000 ekin = 5.7653530457615 | erot = 9.70164580928948 | epot = -69.9237158503973 | etot = -54.4567169953463 +317000 ekin = 6.01426692501809 | erot = 9.61377206320262 | epot = -70.0847559847169 | etot = -54.4567169964962 +318000 ekin = 6.29825476429367 | erot = 9.56224828021495 | epot = -70.3172200424689 | etot = -54.4567169979603 +319000 ekin = 6.60999451535819 | erot = 9.53197557681878 | epot = -70.5986870917947 | etot = -54.4567169996177 +320000 ekin = 6.94141382335311 | erot = 9.50599899522209 | epot = -70.9041298198628 | etot = -54.4567170012876 +321000 ekin = 7.28420684013784 | erot = 9.46773994829997 | epot = -71.2086637911906 | etot = -54.4567170027528 +322000 ekin = 7.63049375597147 | erot = 9.40359379845071 | epot = -71.4908045582218 | etot = -54.4567170037996 +323000 ekin = 7.97350371440688 | erot = 9.30540350738197 | epot = -71.7356242260594 | etot = -54.4567170042706 +324000 ekin = 8.30812216472291 | erot = 9.17221603057476 | epot = -71.9370551994056 | etot = -54.4567170041079 +325000 ekin = 8.63115493818506 | erot = 9.01082149334007 | epot = -72.0986934348975 | etot = -54.4567170033723 +326000 ekin = 8.94122829509857 | erot = 8.83486894706814 | epot = -72.2328142444007 | etot = -54.456717002234 +327000 ekin = 9.2383416399717 | erot = 8.66273411451335 | epot = -72.3577927554137 | etot = -54.4567170009287 +328000 ekin = 9.52317541129448 | erot = 8.51461710979976 | epot = -72.494509520808 | etot = -54.4567169997138 +329000 ekin = 9.79629908031618 | erot = 8.40945765598148 | epot = -72.662473735117 | etot = -54.4567169988193 +330000 ekin = 10.0574197993405 | erot = 8.36217436293344 | epot = -72.8763111606947 | etot = -54.4567169984207 +331000 ekin = 10.3047815002149 | erot = 8.38155728442706 | epot = -73.1430557832698 | etot = -54.4567169986279 +332000 ekin = 10.5347934531765 | erot = 8.46897862473395 | epot = -73.4604890773827 | etot = -54.4567169994722 +333000 ekin = 10.7419525181563 | erot = 8.61799790191855 | epot = -73.8166674209773 | etot = -54.4567170009025 +334000 ekin = 10.9191228830018 | erot = 8.81492290908233 | epot = -74.1907627948531 | etot = -54.456717002769 +335000 ekin = 11.0582310034251 | erot = 9.04039212109867 | epot = -74.5553401293494 | etot = -54.4567170048256 +336000 ekin = 11.1513905495702 | erot = 9.27198870541487 | epot = -74.8800962617268 | etot = -54.4567170067418 +337000 ekin = 11.1923691999824 | erot = 9.48771814312567 | epot = -75.1368043512572 | etot = -54.4567170081491 +338000 ekin = 11.1781584914541 | erot = 9.66988639695432 | epot = -75.304761897128 | etot = -54.4567170087196 +339000 ekin = 11.110273163195 | erot = 9.80861367328994 | epot = -75.3756038447384 | etot = -54.4567170082535 +340000 ekin = 10.9953796290017 | erot = 9.90409604937616 | epot = -75.3561926851294 | etot = -54.4567170067515 +341000 ekin = 10.8449930881317 | erot = 9.96693425469623 | epot = -75.2686443472476 | etot = -54.4567170044196 +342000 ekin = 10.6742553473666 | erot = 10.0163686561537 | epot = -75.1473410051374 | etot = -54.4567170016172 +343000 ekin = 10.5000860602567 | erot = 10.0768729195859 | epot = -75.0336759786075 | etot = -54.4567169987649 +344000 ekin = 10.3391511438661 | erot = 10.1739718598885 | epot = -74.9698400000093 | etot = -54.4567169962547 +345000 ekin = 10.2060562002225 | erot = 10.3301918101523 | epot = -74.9929650047638 | etot = -54.4567169943891 +346000 ekin = 10.1120018691326 | erot = 10.5617784619961 | epot = -75.1304973244953 | etot = -54.4567169933667 +347000 ekin = 10.0639419677312 | erot = 10.8764329835278 | epot = -75.3970919445539 | etot = -54.4567169932949 +348000 ekin = 10.0641555602939 | erot = 11.2720257324416 | epot = -75.7928982869476 | etot = -54.4567169942121 +349000 ekin = 10.1101145523998 | erot = 11.7361477401378 | epot = -76.3029792886303 | etot = -54.4567169960927 +350000 ekin = 10.1945825218777 | erot = 12.2464414545011 | epot = -76.8977409752211 | etot = -54.4567169988423 +351000 ekin = 10.3059767731242 | erot = 12.7718298178647 | epot = -77.5345235932589 | etot = -54.45671700227 +352000 ekin = 10.4291136841137 | erot = 13.2749133139495 | epot = -78.1607440041122 | etot = -54.456717006049 +353000 ekin = 10.5464827220645 | erot = 13.715787024313 | epot = -78.7189867560902 | etot = -54.4567170097128 +354000 ekin = 10.640108173953 | erot = 14.0572291869667 | epot = -79.1540543736269 | etot = -54.4567170127073 +355000 ekin = 10.6938478547007 | erot = 14.2706326977504 | epot = -79.4211975669542 | etot = -54.456717014503 +356000 ekin = 10.6957117760324 | erot = 14.3414067966647 | epot = -79.4938355874482 | etot = -54.4567170147512 +357000 ekin = 10.6396104112823 | erot = 14.2722652226267 | epot = -79.3685926473108 | etot = -54.4567170134019 +358000 ekin = 10.5262520486607 | erot = 14.0832401802047 | epot = -79.066209238702 | etot = -54.4567170098366 +359000 ekin = 10.3670012344474 | erot = 13.8092169878407 | epot = -78.6329352288687 | etot = -54.4567170065806 +360000 ekin = 10.1730345911612 | erot = 13.4915235481061 | epot = -78.1212751423994 | etot = -54.456717003132 +361000 ekin = 9.95554687781411 | erot = 13.1714216600755 | epot = -77.5836855379466 | etot = -54.456717000057 +362000 ekin = 9.72626696401215 | erot = 12.8843171182361 | epot = -77.0673010799981 | etot = -54.4567169977498 +363000 ekin = 9.49594699774894 | erot = 12.6552376501816 | epot = -76.6079016443356 | etot = -54.456716996405 +364000 ekin = 9.27348051447418 | erot = 12.4966397003795 | epot = -76.2268372108837 | etot = -54.45671699603 +365000 ekin = 9.06556428137841 | erot = 12.4084359560849 | epot = -75.9307172339607 | etot = -54.4567169964974 +366000 ekin = 8.8767156877772 | erot = 12.3798183116203 | epot = -75.7132509969821 | etot = -54.4567169975845 +367000 ekin = 8.70950256435238 | erot = 12.3923063931854 | epot = -75.5585259565708 | etot = -54.456716999033 +368000 ekin = 8.56482533239843 | erot = 12.4233361953136 | epot = -75.4448785283136 | etot = -54.4567170006016 +369000 ekin = 8.44216266247639 | erot = 12.4496962572969 | epot = -75.3485759218763 | etot = -54.456717002103 +370000 ekin = 8.33975827581587 | erot = 12.4502709028933 | epot = -75.2467461821205 | etot = -54.4567170034114 +371000 ekin = 8.25479796578774 | erot = 12.407860932567 | epot = -75.1193759028043 | etot = -54.4567170044495 +372000 ekin = 8.1836687896073 | erot = 12.3101981041747 | epot = -74.950583898938 | etot = -54.4567170051561 +373000 ekin = 8.12237120099796 | erot = 12.150469466896 | epot = -74.7295576733628 | etot = -54.4567170054689 +374000 ekin = 8.06677539353194 | erot = 11.9273562293612 | epot = -74.4508486283192 | etot = -54.456717005426 +375000 ekin = 8.01350111913413 | erot = 11.645320521957 | epot = -74.1155386458676 | etot = -54.4567170047766 +376000 ekin = 7.96091572447976 | erot = 11.3149868234253 | epot = -73.7326195516215 | etot = -54.4567170037164 +377000 ekin = 7.90852881942141 | erot = 10.9517029979008 | epot = -73.3169488196991 | etot = -54.4567170023769 +378000 ekin = 7.85672904350658 | erot = 10.5738384909262 | epot = -72.887284535377 | etot = -54.4567170009443 +379000 ekin = 7.80630927767902 | erot = 10.2005458441653 | epot = -72.4635721214624 | etot = -54.4567169996181 +380000 ekin = 7.75800079078551 | erot = 9.8494529907635 | epot = -72.064170780094 | etot = -54.456716998545 +381000 ekin = 7.71644600862591 | erot = 9.53800624561232 | epot = -71.7111692500814 | etot = -54.4567169958432 +382000 ekin = 7.68441527892619 | erot = 9.27832089835142 | epot = -71.4194531731731 | etot = -54.4567169958955 +383000 ekin = 7.65787566183404 | erot = 9.07303517126605 | epot = -71.187627829087 | etot = -54.4567169959869 +384000 ekin = 7.63460910810198 | erot = 8.9224118898537 | epot = -71.0137379939037 | etot = -54.456716995948 +385000 ekin = 7.6149535164395 | erot = 8.82611541868757 | epot = -70.8977859308139 | etot = -54.4567169956869 +386000 ekin = 7.60189486281613 | erot = 8.78441843695066 | epot = -70.8430302949976 | etot = -54.4567169952308 +387000 ekin = 7.60041891103307 | erot = 8.79838942462568 | epot = -70.8555253303886 | etot = -54.4567169947299 +388000 ekin = 7.61622683362204 | erot = 8.86894752211043 | epot = -70.9418913501462 | etot = -54.4567169944138 +389000 ekin = 7.65411397461264 | erot = 8.99508106939575 | epot = -71.1059120385311 | etot = -54.4567169945227 +390000 ekin = 7.71640194413937 | erot = 9.17181221608584 | epot = -71.3449311554853 | etot = -54.4567169952601 +391000 ekin = 7.80179289421955 | erot = 9.38846927313634 | epot = -71.6469791640544 | etot = -54.4567169966985 +392000 ekin = 7.90489667240788 | erot = 9.62803617098498 | epot = -71.9896498421672 | etot = -54.4567169987743 +393000 ekin = 8.01656398898028 | erot = 9.86778742621853 | epot = -72.3410684164769 | etot = -54.4567170012781 +394000 ekin = 8.12500523168265 | erot = 10.0813107732248 | epot = -72.6630330087891 | etot = -54.4567170038816 +395000 ekin = 8.21751488333172 | erot = 10.2416672650812 | epot = -72.9158991546114 | etot = -54.4567170061985 +396000 ekin = 8.2824936976285 | erot = 10.3253499492592 | epot = -73.0645606546968 | etot = -54.456717007809 +397000 ekin = 8.3113926603245 | erot = 10.3159449128745 | epot = -73.0840545817383 | etot = -54.4567170085394 +398000 ekin = 8.30021982541439 | erot = 10.2060347710596 | epot = -72.9629716046272 | etot = -54.4567170081532 +399000 ekin = 8.25031816200703 | erot = 9.99940615794297 | epot = -72.7064413267589 | etot = -54.4567170068089 +400000 ekin = 8.16827445227634 | erot = 9.7097015502967 | epot = -72.3346930072091 | etot = -54.456717004636 +401000 ekin = 8.06453103741583 | erot = 9.35834706105757 | epot = -71.8795951005835 | etot = -54.4567170021101 +402000 ekin = 7.95192509945075 | erot = 8.97202468748702 | epot = -71.3806667861405 | etot = -54.4567169992027 +403000 ekin = 7.84555125758021 | erot = 8.57971802937037 | epot = -70.8819862833966 | etot = -54.456716996446 +404000 ekin = 7.76002341839152 | erot = 8.20898478878102 | epot = -70.425725201349 | etot = -54.4567169941765 +405000 ekin = 7.70732931836054 | erot = 7.8837751017023 | epot = -70.0478214124161 | etot = -54.4567169923533 +406000 ekin = 7.69678612080616 | erot = 7.62266799265398 | epot = -69.7761711045908 | etot = -54.4567169911307 +407000 ekin = 7.73513354697998 | erot = 7.43808993656357 | epot = -69.6299404740833 | etot = -54.4567169905398 +408000 ekin = 7.82571657241241 | erot = 7.33617130722911 | epot = -69.6186048702079 | etot = -54.4567169905664 +409000 ekin = 7.96844969704685 | erot = 7.31680539063558 | epot = -69.7419720788819 | etot = -54.4567169911994 +410000 ekin = 8.15983887506257 | erot = 7.37383443939548 | epot = -69.9903903068786 | etot = -54.4567169924205 +411000 ekin = 8.39302325865663 | erot = 7.4953976334526 | epot = -70.3451378862939 | etot = -54.4567169941847 +412000 ekin = 8.65789214073318 | erot = 7.66460030904681 | epot = -70.7792094461797 | etot = -54.4567169963997 +413000 ekin = 8.94143674964541 | erot = 7.86072523711374 | epot = -71.2588789856516 | etot = -54.4567169988925 +414000 ekin = 9.22856273978891 | erot = 8.06118997496246 | epot = -71.7464697161389 | etot = -54.4567170013875 +415000 ekin = 9.50353222598334 | erot = 8.24426927837509 | epot = -72.2045185078928 | etot = -54.4567170035344 +416000 ekin = 9.75196200032965 | erot = 8.39224874053139 | epot = -72.6009277458497 | etot = -54.4567170049887 +417000 ekin = 9.9629449386187 | erot = 8.49428522215829 | epot = -72.9139471663249 | etot = -54.4567170055479 +418000 ekin = 10.1306180934885 | erot = 8.54795226111053 | epot = -73.1352873597359 | etot = -54.4567170051369 +419000 ekin = 10.2546096453504 | erot = 8.55936156101561 | epot = -73.2706882103206 | etot = -54.4567170039546 +420000 ekin = 10.3392413847947 | erot = 8.54150946849157 | epot = -73.3374678555919 | etot = -54.4567170023057 +421000 ekin = 10.3918587231919 | erot = 8.51150598433048 | epot = -73.3600817080363 | etot = -54.4567170005139 +422000 ekin = 10.4208785143884 | erot = 8.4877866554269 | epot = -73.3653821686634 | etot = -54.4567169988481 +423000 ekin = 10.4340350336987 | erot = 8.48770021699104 | epot = -73.3784522482328 | etot = -54.456716997543 +424000 ekin = 10.4370437707939 | erot = 8.52571262940896 | epot = -73.4194733968421 | etot = -54.4567169966392 +425000 ekin = 10.4323779106235 | erot = 8.61252848638176 | epot = -73.5016237919849 | etot = -54.4567173949797 +426000 ekin = 10.1027691140753 | erot = 8.31084890989174 | epot = -72.8703349960224 | etot = -54.4567169720554 +427000 ekin = 10.5737761012621 | erot = 8.79661991597699 | epot = -73.8271134052882 | etot = -54.4567173880491 +428000 ekin = 10.6073086148619 | erot = 9.02815734228935 | epot = -74.0921832808639 | etot = -54.4567173237126 +429000 ekin = 10.5962992474437 | erot = 9.29502326253138 | epot = -74.3480398354772 | etot = -54.4567173255021 +430000 ekin = 10.5389640746118 | erot = 9.58950094091545 | epot = -74.5851823430212 | etot = -54.4567173274939 +431000 ekin = 10.4245600707616 | erot = 9.89254945457005 | epot = -74.7738268547387 | etot = -54.4567173294071 +432000 ekin = 10.2456183701228 | erot = 10.1831375483389 | epot = -74.8854732493764 | etot = -54.4567173309147 +433000 ekin = 10.0001839880906 | erot = 10.4408608802914 | epot = -74.8977622000884 | etot = -54.4567173317063 +434000 ekin = 9.69355282025833 | erot = 10.6487620299407 | epot = -74.7990321817699 | etot = -54.4567173315709 +435000 ekin = 9.33897175581629 | erot = 10.7957385369187 | epot = -74.5914276231967 | etot = -54.4567173304618 +436000 ekin = 8.95691803307971 | erot = 10.8779295163378 | epot = -74.2915648779456 | etot = -54.4567173285281 +437000 ekin = 8.5729208976939 | erot = 10.8987288383879 | epot = -73.9283670621617 | etot = -54.4567173260799 +438000 ekin = 8.21432291139599 | erot = 10.8675107992332 | epot = -73.5385510341301 | etot = -54.4567173235009 +439000 ekin = 7.90671191648676 | erot = 10.7975744645269 | epot = -73.1610037021589 | etot = -54.4567173211452 +440000 ekin = 7.67083057756313 | erot = 10.7040012563597 | epot = -72.8315491531736 | etot = -54.4567173192507 +441000 ekin = 7.52056261878233 | erot = 10.6019893788208 | epot = -72.5792693155245 | etot = -54.4567173179214 +442000 ekin = 7.46221677065886 | erot = 10.5058719364342 | epot = -72.4248060242353 | etot = -54.4567173171422 +443000 ekin = 7.49495713472296 | erot = 10.4286506059608 | epot = -72.3803250575281 | etot = -54.4567173168443 +444000 ekin = 7.61199665328085 | erot = 10.3816668192465 | epot = -72.4503807894806 | etot = -54.4567173169533 +445000 ekin = 7.80212113162776 | erot = 10.3740565458178 | epot = -72.6328949948733 | etot = -54.4567173174277 +446000 ekin = 8.05121208710603 | erot = 10.4118503345047 | epot = -72.9197797398594 | etot = -54.4567173182487 +447000 ekin = 8.34364339004613 | erot = 10.4968771153954 | epot = -73.2972378248874 | etot = -54.4567173194459 +448000 ekin = 8.66325116930049 | erot = 10.6256625167956 | epot = -73.7456310070778 | etot = -54.4567173209817 +449000 ekin = 8.99432108684567 | erot = 10.788980920788 | epot = -74.2400193304163 | etot = -54.4567173227827 +450000 ekin = 9.32245948922637 | erot = 10.9722541224535 | epot = -74.751430936395 | etot = -54.4567173247151 +451000 ekin = 9.63536145903598 | erot = 11.1568985326443 | epot = -75.2489773182791 | etot = -54.4567173265988 +452000 ekin = 9.92347885287827 | erot = 11.3224562063141 | epot = -75.7026523874227 | etot = -54.4567173282304 +453000 ekin = 10.1805354635802 | erot = 11.4491361056682 | epot = -76.0863888986905 | etot = -54.4567173294422 +454000 ekin = 10.4037376220647 | erot = 11.5201500068694 | epot = -76.3806049590722 | etot = -54.4567173301382 +455000 ekin = 10.5935799379614 | erot = 11.5233605384484 | epot = -76.5736578067262 | etot = -54.4567173303164 +456000 ekin = 10.7532157912704 | erot = 11.45198578839 | epot = -76.6619189097202 | etot = -54.4567173300598 +457000 ekin = 10.8874528211611 | erot = 11.3044013916393 | epot = -76.6485715423045 | etot = -54.456717329504 +458000 ekin = 11.0015356719994 | erot = 11.0833330749703 | epot = -76.5415860757781 | etot = -54.4567173288083 +459000 ekin = 11.0999386292695 | erot = 10.7947718565247 | epot = -76.351427813892 | etot = -54.4567173280978 +460000 ekin = 11.1853921968751 | erot = 10.4469386378716 | epot = -76.08904816222 | etot = -54.4567173274733 +461000 ekin = 11.2582527529419 | erot = 10.0494375630547 | epot = -75.7644076429679 | etot = -54.4567173269713 +462000 ekin = 11.3163535530636 | erot = 9.6127305658376 | epot = -75.3858014454931 | etot = -54.4567173265919 +463000 ekin = 11.3552901634181 | erot = 9.14782741079218 | epot = -74.9598349005202 | etot = -54.4567173263099 +464000 ekin = 11.3690501275197 | erot = 8.66606699695009 | epot = -74.4918344505388 | etot = -54.456717326069 +465000 ekin = 11.3509395537104 | erot = 8.17907283455601 | epot = -73.9867297140495 | etot = -54.4567173257831 +466000 ekin = 11.2946941726445 | erot = 7.69877194992159 | epot = -73.4501834479714 | etot = -54.4567173254054 +467000 ekin = 11.1954789031938 | erot = 7.23723472358706 | epot = -72.8894309516824 | etot = -54.4567173249016 +468000 ekin = 11.0507711892684 | erot = 6.80628316338651 | epot = -72.3137716769225 | etot = -54.4567173242676 +469000 ekin = 10.8610622879441 | erot = 6.41684853510692 | epot = -71.7346281465774 | etot = -54.4567173235264 +470000 ekin = 10.6303293037576 | erot = 6.07816222727485 | epot = -71.1652088537423 | etot = -54.4567173227098 +471000 ekin = 10.3662986164779 | erot = 5.7969515350622 | epot = -70.6199674733878 | etot = -54.4567173218477 +472000 ekin = 10.0804738216297 | erot = 5.57685091064185 | epot = -70.1140420532388 | etot = -54.4567173209673 +473000 ekin = 9.78780661768799 | erot = 5.41818349563855 | epot = -69.6627074334256 | etot = -54.456717320099 +474000 ekin = 9.50580460755706 | erot = 5.31815275509628 | epot = -69.2806746819618 | etot = -54.4567173193084 +475000 ekin = 9.25291327930302 | erot = 5.27138134031401 | epot = -68.9810119383048 | etot = -54.4567173186878 +476000 ekin = 9.04625597797891 | erot = 5.27069575629549 | epot = -68.7736690526116 | etot = -54.4567173183372 +477000 ekin = 8.89916818083511 | erot = 5.30806481992805 | epot = -68.6639503190903 | etot = -54.4567173183271 +478000 ekin = 8.81917608292222 | erot = 5.37558721490333 | epot = -68.651480616495 | etot = -54.4567173186694 +479000 ekin = 8.80688801078725 | erot = 5.46634570346839 | epot = -68.7299510335938 | etot = -54.4567173193382 +480000 ekin = 8.8559577273249 | erot = 5.57491529291688 | epot = -68.8875903404855 | etot = -54.4567173202437 +481000 ekin = 8.95427411301321 | erot = 5.69752640401541 | epot = -69.1085178383731 | etot = -54.4567173213445 +482000 ekin = 9.08519639592524 | erot = 5.83169305186526 | epot = -69.3736067703773 | etot = -54.4567173225868 +483000 ekin = 9.22914118620374 | erot = 5.97559221269923 | epot = -69.6614507228185 | etot = -54.4567173239156 +484000 ekin = 9.36528214546114 | erot = 6.12746790496011 | epot = -69.9494673756776 | etot = -54.4567173252563 +485000 ekin = 9.47329519940515 | erot = 6.28524325031333 | epot = -70.215255776229 | etot = -54.4567173265105 +486000 ekin = 9.53507247963369 | erot = 6.44644236439794 | epot = -70.4382321715999 | etot = -54.4567173275683 +487000 ekin = 9.53625700455088 | erot = 6.60839833384011 | epot = -70.6013726667204 | etot = -54.4567173283294 +488000 ekin = 9.46740386001613 | erot = 6.76861264891106 | epot = -70.6927338376571 | etot = -54.45671732873 +489000 ekin = 9.32459963449382 | erot = 6.92506407616929 | epot = -70.7063810394197 | etot = -54.4567173287566 +490000 ekin = 9.10947948780052 | erot = 7.07631880463668 | epot = -70.6425156208857 | etot = -54.4567173284485 +491000 ekin = 8.82889148608906 | erot = 7.22129660538092 | epot = -70.5069054189664 | etot = -54.4567173274964 +492000 ekin = 8.49628756221007 | erot = 7.35787986415986 | epot = -70.3108847533214 | etot = -54.4567173269515 +493000 ekin = 8.1248866002914 | erot = 7.48347573766511 | epot = -70.0650796642496 | etot = -54.4567173262931 +494000 ekin = 7.72897177736439 | erot = 7.59497930547508 | epot = -69.7806684084087 | etot = -54.4567173255692 +495000 ekin = 7.32471897791198 | erot = 7.68843463888807 | epot = -69.4698709364699 | etot = -54.4567173196699 +496000 ekin = 6.87941085033985 | erot = 7.73484184189949 | epot = -69.0709701954506 | etot = -54.4567175032113 +497000 ekin = 6.1073967841752 | erot = 7.42313588089099 | epot = -67.9872498480929 | etot = -54.4567171830267 +498000 ekin = 6.82192117262335 | erot = 7.452484020769 | epot = -68.7311226730924 | etot = -54.4567174797001 +499000 ekin = 6.94584861699919 | erot = 7.49830975478806 | epot = -68.9008757168235 | etot = -54.4567173450363 +500000 ekin = 6.96878886921288 | erot = 7.49013442210754 | epot = -68.9156406384887 | etot = -54.4567173471683 +501000 ekin = 7.01883264695104 | erot = 7.44447241972064 | epot = -68.9200224127215 | etot = -54.4567173460498 +502000 ekin = 7.10336336313328 | erot = 7.36823892373464 | epot = -68.928319631582 | etot = -54.456717344714 +503000 ekin = 7.22899289906535 | erot = 7.27372377746777 | epot = -68.9594340198038 | etot = -54.4567173432706 +504000 ekin = 7.40059940684358 | erot = 7.17755657732221 | epot = -69.0348733260352 | etot = -54.4567173418694 +505000 ekin = 7.62076916490399 | erot = 7.09828995866922 | epot = -69.1757764642455 | etot = -54.4567173406723 +506000 ekin = 7.88922231362901 | erot = 7.05443045705873 | epot = -69.4003701105086 | etot = -54.4567173398209 +507000 ekin = 8.20252308360173 | erot = 7.06244306985725 | epot = -69.7216834928758 | etot = -54.4567173394168 +508000 ekin = 8.55418648388798 | erot = 7.13501434822598 | epot = -70.1459181716168 | etot = -54.4567173395029 +509000 ekin = 8.93520489703516 | erot = 7.27978431320956 | epot = -70.6717065503075 | etot = -54.4567173400628 +510000 ekin = 9.33488714865156 | erot = 7.49865655844805 | epot = -71.2902610481376 | etot = -54.456717341038 +511000 ekin = 9.74177952548336 | erot = 7.78769810223546 | epot = -71.9861949700715 | etot = -54.4567173423527 +512000 ekin = 10.1443709695578 | erot = 8.1375553911762 | epot = -72.7386437046762 | etot = -54.4567173439422 +513000 ekin = 10.5313274213469 | erot = 8.53425799992997 | epot = -73.5223027670439 | etot = -54.456717345767 +514000 ekin = 10.8911959115567 | erot = 8.96029115460181 | epot = -74.3082044139501 | etot = -54.4567173477916 +515000 ekin = 11.2118380805486 | erot = 9.39590833078901 | epot = -75.0644637612815 | etot = -54.4567173499439 +516000 ekin = 11.480143336322 | erot = 9.8207630711781 | epot = -75.7576237595617 | etot = -54.4567173520616 +517000 ekin = 11.6825679425228 | erot = 10.2159470151048 | epot = -76.3552323115135 | etot = -54.4567173538859 +518000 ekin = 11.8066633107499 | erot = 10.5663069187178 | epot = -76.8296875845938 | etot = -54.4567173551261 +519000 ekin = 11.8431596193386 | erot = 10.8625837428977 | epot = -77.1624607177948 | etot = -54.4567173555585 +520000 ekin = 11.7878285859595 | erot = 11.1027186624904 | epot = -77.3472646035842 | etot = -54.4567173551343 +521000 ekin = 11.642256322058 | erot = 11.2918969270651 | epot = -77.3908706030792 | etot = -54.4567173539561 +522000 ekin = 11.4135745678739 | erot = 11.4412270159323 | epot = -77.3115189360688 | etot = -54.4567173522626 +523000 ekin = 11.1132889181913 | erot = 11.5654013626807 | epot = -77.1354076312241 | etot = -54.456717350352 +524000 ekin = 10.755617164738 | erot = 11.6798233409266 | epot = -76.8921578542007 | etot = -54.4567173485361 +525000 ekin = 10.3557495856328 | erot = 11.7976048718395 | epot = -76.6100718045692 | etot = -54.4567173470969 +526000 ekin = 9.92830200951311 | erot = 11.926776165877 | epot = -76.3117955216426 | etot = -54.4567173462526 +527000 ekin = 9.48617609162457 | erot = 12.0681058739613 | epot = -76.0109993117011 | etot = -54.4567173461153 +528000 ekin = 9.04001720128526 | erot = 12.2139837697204 | epot = -75.7107183176543 | etot = -54.4567173466486 +529000 ekin = 8.59838558980895 | erot = 12.3488494507838 | epot = -75.4039523882422 | etot = -54.4567173476494 +530000 ekin = 8.16860222528581 | erot = 12.451455933101 | epot = -75.0767755071562 | etot = -54.4567173487694 +531000 ekin = 7.75801650616995 | erot = 12.4988074604779 | epot = -74.7135413162469 | etot = -54.4567173495991 +532000 ekin = 7.37526556648521 | erot = 12.4710301212504 | epot = -74.3030130375118 | etot = -54.4567173497761 +533000 ekin = 7.03105781109593 | erot = 12.355970528871 | epot = -73.8437456890664 | etot = -54.4567173490995 +534000 ekin = 6.73815971496944 | erot = 12.1522682791584 | epot = -73.3471453417096 | etot = -54.4567173475817 +535000 ekin = 6.51053456918365 | erot = 11.8701146968395 | epot = -72.8373666114564 | etot = -54.4567173454333 +536000 ekin = 6.36183924353497 | erot = 11.5296683851411 | epot = -72.3482249716737 | etot = -54.4567173429977 +537000 ekin = 6.30361425976245 | erot = 11.1591555752809 | epot = -71.9194871756187 | etot = -54.4567173405753 +538000 ekin = 6.34347309062121 | erot = 10.7899247971681 | epot = -71.5901152265605 | etot = -54.4567173387712 +539000 ekin = 6.48353756609007 | erot = 10.4488647730074 | epot = -71.3891196768614 | etot = -54.456717337764 +540000 ekin = 6.71929044884176 | erot = 10.1573936013085 | epot = -71.3334013879135 | etot = -54.4567173377632 +541000 ekin = 7.03900384377945 | erot = 9.92878251410278 | epot = -71.4245036967398 | etot = -54.4567173388576 +542000 ekin = 7.42390727692028 | erot = 9.766581713257 | epot = -71.6472063311658 | etot = -54.4567173409885 +543000 ekin = 7.84922333881028 | erot = 9.6644315124603 | epot = -71.9703721952034 | etot = -54.4567173439328 +544000 ekin = 8.2860857685601 | erot = 9.60741387125263 | epot = -72.3502169871389 | etot = -54.4567173473261 +545000 ekin = 8.70416168565955 | erot = 9.57483819178386 | epot = -72.7357172281503 | etot = -54.4567173507069 +546000 ekin = 9.07464757514397 | erot = 9.54408103802403 | epot = -73.0754459667689 | etot = -54.4567173536009 +547000 ekin = 9.37316662913337 | erot = 9.49472293134589 | epot = -73.3246069161013 | etot = -54.4567173556221 +548000 ekin = 9.582086858095 | erot = 9.41206012905516 | epot = -73.4508643436985 | etot = -54.4567173565483 +549000 ekin = 9.69189882139144 | erot = 9.28920893813615 | epot = -73.4378251158813 | etot = -54.4567173563537 +550000 ekin = 9.70150390326778 | erot = 9.12788542696047 | epot = -73.2861066852756 | etot = -54.4567173550473 +551000 ekin = 9.61749941013993 | erot = 8.93692851356279 | epot = -73.0111452769067 | etot = -54.4567173532039 +552000 ekin = 9.45272119087526 | erot = 8.72887496113547 | epot = -72.638313502974 | etot = -54.4567173509632 +553000 ekin = 9.22440824207383 | erot = 8.5184174665468 | epot = -72.1995430572152 | etot = -54.4567173485946 +554000 ekin = 8.95232614946355 | erot = 8.3203167700183 | epot = -71.7293602657827 | etot = -54.4567173463009 +555000 ekin = 8.65710798385505 | erot = 8.1480165512927 | epot = -71.2618418793551 | etot = -54.4567173442074 +556000 ekin = 8.35889174136217 | erot = 8.01297313098835 | epot = -70.8285822147343 | etot = -54.4567173423838 +557000 ekin = 8.07627835316373 | erot = 7.92452278400383 | epot = -70.4575184780232 | etot = -54.4567173408556 +558000 ekin = 7.82557556424515 | erot = 7.89005526871232 | epot = -70.1723481725954 | etot = -54.4567173396379 +559000 ekin = 7.62022949922536 | erot = 7.91519977429377 | epot = -69.9921466122746 | etot = -54.4567173387554 +560000 ekin = 7.4703716719749 | erot = 8.00382469732972 | epot = -69.9309137075519 | etot = -54.4567173382473 +561000 ekin = 7.38244374305034 | erot = 8.15776606028061 | epot = -69.9969271414971 | etot = -54.4567173381662 +562000 ekin = 7.35891939626811 | erot = 8.37634747921777 | epot = -70.1919842140397 | etot = -54.4567173385538 +563000 ekin = 7.39821090242063 | erot = 8.6559101898171 | epot = -70.5108384316496 | etot = -54.4567173394119 +564000 ekin = 7.49490249873246 | erot = 8.9896739347677 | epot = -70.9412937741658 | etot = -54.4567173406656 +565000 ekin = 7.64044839042939 | erot = 9.36842791898228 | epot = -71.4655936514913 | etot = -54.4567173420797 +566000 ekin = 7.82436206843023 | erot = 9.7814600942301 | epot = -72.0625395063096 | etot = -54.4567173436493 +567000 ekin = 8.03570817671908 | erot = 10.2171991123419 | epot = -72.7096246341783 | etot = -54.4567173451174 +568000 ekin = 8.26450258147759 | erot = 10.6646881726758 | epot = -73.3859081005832 | etot = -54.4567173464298 +569000 ekin = 8.50263013239885 | erot = 11.113655831685 | epot = -74.073003311693 | etot = -54.4567173476091 +570000 ekin = 8.74345958959415 | erot = 11.5533265255611 | epot = -74.7535034643013 | etot = -54.456717349146 +571000 ekin = 8.98083952020989 | erot = 11.9715855040848 | epot = -75.4091423756117 | etot = -54.456717351317 +572000 ekin = 9.2082893113693 | erot = 12.3553438318372 | epot = -76.0203504955679 | etot = -54.4567173523613 +573000 ekin = 9.42090854110401 | erot = 12.6948199769537 | epot = -76.5724458709045 | etot = -54.4567173528468 +574000 ekin = 9.61857732717091 | erot = 12.9876096043916 | epot = -77.0629042836827 | etot = -54.4567173521202 +575000 ekin = 9.80559233524997 | erot = 13.2418166844266 | epot = -77.5041263701766 | etot = -54.4567173505001 +576000 ekin = 9.99035771754399 | erot = 13.4731869806347 | epot = -77.9202620466162 | etot = -54.4567173484375 +577000 ekin = 10.18356327221 | erot = 13.7002526866703 | epot = -78.3405333055655 | etot = -54.4567173466852 +578000 ekin = 10.39537510065 | erot = 13.9378911113595 | epot = -78.7899835575021 | etot = -54.4567173454925 +579000 ekin = 10.6324997791117 | erot = 14.1944325430615 | epot = -79.2836496674951 | etot = -54.456717345322 +580000 ekin = 10.8957969406474 | erot = 14.4694129346268 | epot = -79.8219272215725 | etot = -54.4567173462984 +581000 ekin = 11.1787341118591 | erot = 14.7532777796623 | epot = -80.3887292399432 | etot = -54.4567173484219 +582000 ekin = 11.4668332923165 | erot = 15.0284724124031 | epot = -80.9520230561213 | etot = -54.4567173514017 +583000 ekin = 11.7383428294213 | erot = 15.2728618931176 | epot = -81.4679220774225 | etot = -54.4567173548836 +584000 ekin = 11.9664778295178 | erot = 15.4633320550726 | epot = -81.8865272428793 | etot = -54.456717358289 +585000 ekin = 12.1233962794599 | erot = 15.5801019753244 | epot = -82.1602156157044 | etot = -54.4567173609202 +586000 ekin = 12.1854288034047 | erot = 15.6113292070022 | epot = -82.253475372555 | etot = -54.4567173621481 +587000 ekin = 12.1382875982282 | erot = 15.5565429926412 | epot = -82.1515479525114 | etot = -54.4567173616419 +588000 ekin = 11.980567263597 | erot = 15.4274086012163 | epot = -81.8646932243473 | etot = -54.4567173595339 +589000 ekin = 11.7241953475155 | erot = 15.2450549080607 | epot = -81.42596761198 | etot = -54.4567173564038 +590000 ekin = 11.3915332486529 | erot = 15.0345988268665 | epot = -80.8828494285826 | etot = -54.4567173530633 +591000 ekin = 11.0101533181373 | erot = 14.8188164822443 | epot = -80.2856871506142 | etot = -54.4567173502326 +592000 ekin = 10.6073077807716 | erot = 14.6133535707705 | epot = -79.6773786998103 | etot = -54.4567173482682 +593000 ekin = 10.20611413012 | erot = 14.4250491600538 | epot = -79.0878806372874 | etot = -54.4567173471136 +594000 ekin = 9.82433917827452 | erot = 14.2531987869176 | epot = -78.5342553116875 | etot = -54.4567173464954 +595000 ekin = 9.47512062813722 | erot = 14.0920125306389 | epot = -78.0238505049661 | etot = -54.45671734619 +596000 ekin = 9.16819158320015 | erot = 13.9323441617294 | epot = -77.5572530910782 | etot = -54.4567173461486 +597000 ekin = 8.91059203433178 | erot = 13.7621053819093 | epot = -77.1294147626611 | etot = -54.45671734642 +598000 ekin = 8.70677308285503 | erot = 13.5663641000429 | epot = -76.7298545298872 | etot = -54.4567173469893 +599000 ekin = 8.55852376885718 | erot = 13.3285545477924 | epot = -76.3437956643477 | etot = -54.4567173476981 +600000 ekin = 8.46506569152837 | erot = 13.0361676653189 | epot = -75.9579507047602 | etot = -54.4567173479129 +601000 ekin = 8.42303296005732 | erot = 12.6870523997539 | epot = -75.5668027086096 | etot = -54.4567173487984 +602000 ekin = 8.42685459634187 | erot = 12.2732861398249 | epot = -75.1568580852133 | etot = -54.4567173490466 +603000 ekin = 8.4695014305831 | erot = 11.7970571525042 | epot = -74.723275931772 | etot = -54.4567173486848 +604000 ekin = 8.54270518569668 | erot = 11.2713924782976 | epot = -74.2708150118676 | etot = -54.4567173478733 +605000 ekin = 8.63728733668962 | erot = 10.7173462217099 | epot = -73.8113509052181 | etot = -54.4567173468186 +606000 ekin = 8.74373801583669 | erot = 10.1602725630121 | epot = -73.3607279245415 | etot = -54.4567173456927 +607000 ekin = 8.85303389951875 | erot = 9.62621357886593 | epot = -72.9359648230231 | etot = -54.4567173446384 +608000 ekin = 8.95757126311852 | erot = 9.13896619782446 | epot = -72.5532548046386 | etot = -54.4567173436956 +609000 ekin = 9.05196680869766 | erot = 8.71829532640637 | epot = -72.2269794780634 | etot = -54.4567173429594 +610000 ekin = 9.13352888585026 | erot = 8.37856547526864 | epot = -71.9688117034343 | etot = -54.4567173423154 +611000 ekin = 9.20215106475175 | erot = 8.12901246857978 | epot = -71.7878808752659 | etot = -54.4567173419343 +612000 ekin = 9.25956583882272 | erot = 7.97314000869066 | epot = -71.68942318941 | etot = -54.4567173418966 +613000 ekin = 9.3081148722521 | erot = 7.90851279248914 | epot = -71.6733450070467 | etot = -54.4567173423054 +614000 ekin = 9.34927530415222 | erot = 7.92684519058937 | epot = -71.7328378379836 | etot = -54.456717343242 +615000 ekin = 9.38237013825649 | erot = 8.0143318290608 | epot = -71.8534193119474 | etot = -54.4567173446301 +616000 ekin = 9.40383195122376 | erot = 8.15304439798393 | epot = -72.0135936957706 | etot = -54.4567173465629 +617000 ekin = 9.4077387597377 | erot = 8.32048130514227 | epot = -72.1849374136078 | etot = -54.4567173487279 +618000 ekin = 9.38718282197665 | erot = 8.49205380137603 | epot = -72.3359539741535 | etot = -54.4567173508008 +619000 ekin = 9.33634137208541 | erot = 8.64410576157911 | epot = -72.4371644860788 | etot = -54.4567173524143 +620000 ekin = 9.25274239708756 | erot = 8.75706693533138 | epot = -72.4665266856622 | etot = -54.4567173532432 +621000 ekin = 9.13908734781248 | erot = 8.81838549165813 | epot = -72.4141901925553 | etot = -54.4567173530847 +622000 ekin = 9.00413159185615 | erot = 8.82453847239636 | epot = -72.2853874161675 | etot = -54.456717351915 +623000 ekin = 8.86237387262931 | erot = 8.78159044372925 | epot = -72.1006816657179 | etot = -54.4567173493594 +624000 ekin = 8.73233250270114 | erot = 8.70601363406663 | epot = -71.8950634838214 | etot = -54.4567173470537 +625000 ekin = 8.63352260270537 | erot = 8.61836006911987 | epot = -71.7086000163401 | etot = -54.4567173445148 +626000 ekin = 8.58515687058863 | erot = 8.54022417072272 | epot = -71.5820983834213 | etot = -54.4567173421099 +627000 ekin = 8.60386594898203 | erot = 8.49340879468718 | epot = -71.5539920838551 | etot = -54.4567173401859 +628000 ekin = 8.70125272962733 | erot = 8.49697729760153 | epot = -71.6549473663013 | etot = -54.4567173390724 +629000 ekin = 8.88211046284254 | erot = 8.56410343043823 | epot = -71.9029312321935 | etot = -54.4567173389128 +630000 ekin = 9.142461312833 | erot = 8.70144773181049 | epot = -72.3006263845185 | etot = -54.456717339875 +631000 ekin = 9.468374580938 | erot = 8.90764779898911 | epot = -72.8327397225276 | etot = -54.4567173426005 +632000 ekin = 9.83312177173734 | erot = 9.17246776668357 | epot = -73.4623068842449 | etot = -54.456717345824 +633000 ekin = 10.2047873751234 | erot = 9.47797241849862 | epot = -74.1394771430913 | etot = -54.4567173494693 +634000 ekin = 10.5489934613283 | erot = 9.80262636498115 | epot = -74.8083371792022 | etot = -54.4567173528927 +635000 ekin = 10.8335202630285 | erot = 10.1258655273367 | epot = -75.4161031458045 | etot = -54.4567173554393 +636000 ekin = 11.0335668276672 | erot = 10.4324958345106 | epot = -75.9227800187459 | etot = -54.4567173565681 +637000 ekin = 11.1356918483419 | erot = 10.7158485159515 | epot = -76.3082577206544 | etot = -54.456717356361 +638000 ekin = 11.1388069575836 | erot = 10.9775008619056 | epot = -76.5730251745032 | etot = -54.456717355014 +639000 ekin = 11.0524003327262 | erot = 11.2253769821853 | epot = -76.7344946679159 | etot = -54.4567173530044 +640000 ekin = 10.8928630382599 | erot = 11.4709640829734 | epot = -76.8205444720317 | etot = -54.4567173507984 +641000 ekin = 10.6795161167506 | erot = 11.7265694567167 | epot = -76.8628029221806 | etot = -54.4567173487133 +642000 ekin = 10.4316521519997 | erot = 12.0033863745313 | epot = -76.8917558734831 | etot = -54.4567173469521 +643000 ekin = 10.1667694779079 | erot = 12.3102216340097 | epot = -76.9337084574385 | etot = -54.4567173455209 +644000 ekin = 9.90007447735835 | erot = 12.6530565857597 | epot = -77.0098484077146 | etot = -54.4567173445965 +645000 ekin = 9.64408802623023 | erot = 13.0333521361229 | epot = -77.1341575065314 | etot = -54.4567173441782 +646000 ekin = 9.40846495821037 | erot = 13.446884270576 | epot = -77.3120665731115 | etot = -54.4567173443251 +647000 ekin = 9.20006047025728 | erot = 13.8841334486704 | epot = -77.5409112640638 | etot = -54.4567173451361 +648000 ekin = 9.02208271231024 | erot = 14.3287870732609 | epot = -77.8075871321958 | etot = -54.4567173466247 +649000 ekin = 8.87371560217377 | erot = 14.7582675570719 | epot = -78.0887005080209 | etot = -54.4567173487753 +650000 ekin = 8.74973394434129 | erot = 15.1446190956748 | epot = -78.3510703915045 | etot = -54.4567173514884 +651000 ekin = 8.64055354277824 | erot = 15.456197674687 | epot = -78.5534685720233 | etot = -54.4567173545581 +652000 ekin = 8.53295942946815 | erot = 15.6603023870487 | epot = -78.6499791741566 | etot = -54.4567173576397 +653000 ekin = 8.41177726194849 | erot = 15.7268429393637 | epot = -78.5953375615569 | etot = -54.4567173602447 +654000 ekin = 8.26255435899738 | erot = 15.6329185652919 | epot = -78.3521902861014 | etot = -54.4567173618121 +655000 ekin = 8.07486030838614 | erot = 15.3675533060751 | epot = -77.8991309762939 | etot = -54.4567173618327 +656000 ekin = 7.85584872990473 | erot = 14.9356063836805 | epot = -77.2481728999348 | etot = -54.4567177863496 +657000 ekin = 6.2670540018988 | erot = 14.5624207623774 | epot = -75.2861920812074 | etot = -54.4567173169312 +658000 ekin = 6.04203621440511 | erot = 14.8338374902085 | epot = -75.332591284386 | etot = -54.4567175797724 +659000 ekin = 6.38626397395935 | erot = 14.3789536735285 | epot = -75.221934911762 | etot = -54.4567172642741 +660000 ekin = 6.51825323395761 | erot = 13.6086452149817 | epot = -74.5836157134663 | etot = -54.456717264527 +661000 ekin = 6.6610961784344 | erot = 12.8240798503498 | epot = -73.9418932898507 | etot = -54.4567172610665 +662000 ekin = 6.81858404113844 | erot = 12.0684544027732 | epot = -73.3437557024229 | etot = -54.4567172585112 +663000 ekin = 6.99165023050995 | erot = 11.3761522151523 | epot = -72.824519702647 | etot = -54.4567172569848 +664000 ekin = 7.17719978229865 | erot = 10.770609793234 | epot = -72.4045268320221 | etot = -54.4567172564894 +665000 ekin = 7.36750072099867 | erot = 10.2650050778477 | epot = -72.08922305566 | etot = -54.4567172568136 +666000 ekin = 7.5509085313514 | erot = 9.86588701345707 | epot = -71.8735128030129 | etot = -54.4567172582044 +667000 ekin = 7.71548675044036 | erot = 9.56433968480603 | epot = -71.7365436952187 | etot = -54.4567172599723 +668000 ekin = 7.84942783247078 | erot = 9.34349379624979 | epot = -71.6496388907549 | etot = -54.4567172620343 +669000 ekin = 7.94275892173366 | erot = 9.18157787767355 | epot = -71.5810540633531 | etot = -54.4567172639459 +670000 ekin = 7.98895216682981 | erot = 9.05544419067568 | epot = -71.5011136229456 | etot = -54.4567172654401 +671000 ekin = 7.98617320848899 | erot = 8.94354459266666 | epot = -71.3864350674714 | etot = -54.4567172663158 +672000 ekin = 7.93791523097339 | erot = 8.82829898979078 | epot = -71.2229314872407 | etot = -54.4567172664766 +673000 ekin = 7.85355743596615 | erot = 8.6982430977836 | epot = -71.0085177991557 | etot = -54.456717265406 +674000 ekin = 7.74778223222283 | erot = 8.54905666588965 | epot = -70.7535561623678 | etot = -54.4567172642553 +675000 ekin = 7.63634833353771 | erot = 8.38135292474944 | epot = -70.4744185210863 | etot = -54.4567172627992 +676000 ekin = 7.53516291001198 | erot = 8.20022759713448 | epot = -70.1921077684553 | etot = -54.4567172613088 +677000 ekin = 7.45794951914645 | erot = 8.01347239991047 | epot = -69.9281391793211 | etot = -54.4567172602642 +678000 ekin = 7.41073692377504 | erot = 7.82731022274383 | epot = -69.6947644060845 | etot = -54.4567172595657 +679000 ekin = 7.3956939541761 | erot = 7.6480666128801 | epot = -69.5004778263083 | etot = -54.4567172592521 +680000 ekin = 7.4115184631352 | erot = 7.48353806506187 | epot = -69.3517737862543 | etot = -54.4567172580573 +681000 ekin = 7.45301960111475 | erot = 7.34389485533304 | epot = -69.2536317152404 | etot = -54.4567172587926 +682000 ekin = 7.5092276071674 | erot = 7.23034627473376 | epot = -69.1962911416763 | etot = -54.4567172597751 +683000 ekin = 7.56703179131234 | erot = 7.14137901608625 | epot = -69.1651280682368 | etot = -54.4567172608383 +684000 ekin = 7.6133784577155 | erot = 7.07402860505464 | epot = -69.1441243245358 | etot = -54.4567172617657 +685000 ekin = 7.6370692355068 | erot = 7.02480923675523 | epot = -69.1185957348129 | etot = -54.4567172625509 +686000 ekin = 7.63012070152936 | erot = 6.98974489721365 | epot = -69.0765828617828 | etot = -54.4567172630398 +687000 ekin = 7.58847196987618 | erot = 6.9645182618173 | epot = -69.0097074950062 | etot = -54.4567172633128 +688000 ekin = 7.51200727213185 | erot = 6.94458821703858 | epot = -68.9133127522802 | etot = -54.4567172631098 +689000 ekin = 7.40470220584746 | erot = 6.92788077433601 | epot = -68.7893002428668 | etot = -54.4567172626833 +690000 ekin = 7.2735114018564 | erot = 6.91313342460364 | epot = -68.6433620885619 | etot = -54.4567172621018 +691000 ekin = 7.1273993324396 | erot = 6.89961683270119 | epot = -68.4837334265735 | etot = -54.4567172614327 +692000 ekin = 6.97639340738409 | erot = 6.88713701597176 | epot = -68.3202476840878 | etot = -54.456717260732 +693000 ekin = 6.83172646956237 | erot = 6.87668966225714 | epot = -68.1651333908689 | etot = -54.4567172590494 +694000 ekin = 6.70636456506374 | erot = 6.87119415658171 | epot = -68.0342759801826 | etot = -54.4567172585371 +695000 ekin = 6.6079642505311 | erot = 6.87171260019125 | epot = -67.9363941088555 | etot = -54.4567172581332 +696000 ekin = 6.54180332237583 | erot = 6.87956193852472 | epot = -67.8780825187723 | etot = -54.4567172578718 +697000 ekin = 6.51072403245576 | erot = 6.89634898360005 | epot = -67.863790273859 | etot = -54.4567172578032 +698000 ekin = 6.51486325252216 | erot = 6.92352997719932 | epot = -67.8951104879818 | etot = -54.4567172582604 +699000 ekin = 6.55040388684346 | erot = 6.96167022069946 | epot = -67.9687913660279 | etot = -54.456717258485 +700000 ekin = 6.6121585282628 | erot = 7.01154258674288 | epot = -68.0804183739391 | etot = -54.4567172589334 +701000 ekin = 6.69364481782336 | erot = 7.07323470973425 | epot = -68.22359678703 | etot = -54.4567172594724 +702000 ekin = 6.78699610283142 | erot = 7.14577119400644 | epot = -68.3894845569424 | etot = -54.4567172601045 +703000 ekin = 6.88366969337153 | erot = 7.22749691999373 | epot = -68.567883874144 | etot = -54.4567172607787 +704000 ekin = 6.97518890726232 | erot = 7.31588802326638 | epot = -68.7477941919628 | etot = -54.4567172614341 +705000 ekin = 7.05384046082615 | erot = 7.40783149503349 | epot = -68.9183892178659 | etot = -54.4567172620063 +706000 ekin = 7.1132484519367 | erot = 7.5000940326921 | epot = -69.0700597470648 | etot = -54.4567172624361 +707000 ekin = 7.14876450804701 | erot = 7.58991849146167 | epot = -69.1954002621842 | etot = -54.4567172626755 +708000 ekin = 7.15764928629245 | erot = 7.67564119575173 | epot = -69.2900077447402 | etot = -54.456717262696 +709000 ekin = 7.13905930512345 | erot = 7.757204472591 | epot = -69.3529810402078 | etot = -54.4567172624933 +710000 ekin = 7.09387935442471 | erot = 7.83644881069707 | epot = -69.3870454272082 | etot = -54.4567172620864 +711000 ekin = 7.0244446759596 | erot = 7.91710241224915 | epot = -69.3982643497324 | etot = -54.4567172615236 +712000 ekin = 6.93418797429413 | erot = 8.0044413772892 | epot = -69.3953466124448 | etot = -54.4567172608615 +713000 ekin = 6.82724359613869 | erot = 8.10466156446648 | epot = -69.3886224208104 | etot = -54.4567172602053 +714000 ekin = 6.70804581030452 | erot = 8.22386653915046 | epot = -69.3886296090861 | etot = -54.4567172596311 +715000 ekin = 6.58096815991889 | erot = 8.36710453058969 | epot = -69.4047899497292 | etot = -54.4567172592206 +716000 ekin = 6.45005603944762 | erot = 8.53736910172616 | epot = -69.4441424002111 | etot = -54.4567172590373 +717000 ekin = 6.31889522685732 | erot = 8.73472575134746 | epot = -69.5103382373227 | etot = -54.4567172591179 +718000 ekin = 6.19064203156286 | erot = 8.95572089431508 | epot = -69.6030801853378 | etot = -54.4567172594598 +719000 ekin = 6.0682180271129 | erot = 9.1932035682174 | epot = -69.7181388553502 | etot = -54.4567172600199 +720000 ekin = 5.95464760383327 | erot = 9.43665584958345 | epot = -69.8480207141297 | etot = -54.456717260713 +721000 ekin = 5.85348609830537 | erot = 9.67307075503052 | epot = -69.9832741147543 | etot = -54.4567172614184 +722000 ekin = 5.76925126938791 | erot = 9.88829892325627 | epot = -70.1142674546659 | etot = -54.4567172620217 +723000 ekin = 5.70773585553192 | erot = 10.0686021330634 | epot = -70.2330552509752 | etot = -54.4567172623799 +724000 ekin = 5.67606450428522 | erot = 10.2025682810643 | epot = -70.3353500477706 | etot = -54.4567172624211 +725000 ekin = 5.68237542169558 | erot = 10.282593505772 | epot = -70.4216861895975 | etot = -54.4567172621299 +726000 ekin = 5.73506597281358 | erot = 10.305857569948 | epot = -70.4976408043275 | etot = -54.4567172615659 +727000 ekin = 5.84164351928237 | erot = 10.2746192681783 | epot = -70.5729800483047 | etot = -54.456717260844 +728000 ekin = 6.0073687533578 | erot = 10.1958472011005 | epot = -70.6599332145571 | etot = -54.4567172600989 +729000 ekin = 6.23388239567308 | erot = 10.0804050315184 | epot = -70.7710046866831 | etot = -54.4567172594917 +730000 ekin = 6.51810798560694 | erot = 9.94175964622273 | epot = -70.9165848909866 | etot = -54.4567172591569 +731000 ekin = 6.85163923572006 | erot = 9.79445434032714 | epot = -71.1028108352439 | etot = -54.4567172591967 +732000 ekin = 7.22074424892383 | erot = 9.65249486308226 | epot = -71.3299563716739 | etot = -54.4567172596678 +733000 ekin = 7.60696817055788 | erot = 9.5281042285174 | epot = -71.5917896595965 | etot = -54.4567172605213 +734000 ekin = 7.98843781663386 | erot = 9.43013551829001 | epot = -71.8752905967343 | etot = -54.4567172618105 +735000 ekin = 8.34173972940781 | erot = 9.36277858700205 | epot = -72.1612355797593 | etot = -54.4567172633495 +736000 ekin = 8.6440278758694 | erot = 9.32573536300172 | epot = -72.4264805038396 | etot = -54.4567172649685 +737000 ekin = 8.87535498676661 | erot = 9.31467922069703 | epot = -72.6467514739115 | etot = -54.4567172664478 +738000 ekin = 9.0209200187997 | erot = 9.32245328122186 | epot = -72.8000905675755 | etot = -54.456717267554 +739000 ekin = 9.0729502311621 | erot = 9.34080514543739 | epot = -72.8704726446821 | etot = -54.4567172680826 +740000 ekin = 9.03191801001054 | erot = 9.36236057638055 | epot = -72.8509958542847 | etot = -54.4567172678936 +741000 ekin = 8.90683448950978 | erot = 9.38246134467714 | epot = -72.7460131011363 | etot = -54.4567172669494 +742000 ekin = 8.7144873599651 | erot = 9.40037005969976 | epot = -72.5715746850596 | etot = -54.4567172653947 +743000 ekin = 8.47780203517238 | erot = 9.41934825450641 | epot = -72.3538675527427 | etot = -54.4567172630639 +744000 ekin = 8.22394413364553 | erot = 9.44738079429509 | epot = -72.1280421887658 | etot = -54.4567172608252 +745000 ekin = 7.97995720631533 | erot = 9.49389903750132 | epot = -71.9305735025832 | etot = -54.4567172587665 +746000 ekin = 7.76976645073265 | erot = 9.56761523723776 | epot = -71.7940989452355 | etot = -54.4567172572651 +747000 ekin = 7.61167419657528 | erot = 9.6742258343332 | epot = -71.7426172875988 | etot = -54.4567172566903 +748000 ekin = 7.51658612860559 | erot = 9.81263188349218 | epot = -71.7859352693208 | etot = -54.456717257223 +749000 ekin = 7.48573262346974 | erot = 9.97339077048108 | epot = -71.915840652861 | etot = -54.4567172589101 +750000 ekin = 7.51095577906381 | erot = 10.138730860191 | epot = -72.106403900703 | etot = -54.4567172614481 +751000 ekin = 7.57621289890869 | erot = 10.2849285861996 | epot = -72.3178587495214 | etot = -54.4567172644132 +752000 ekin = 7.66072006264762 | erot = 10.3863157071598 | epot = -72.5037530370257 | etot = -54.4567172672183 +753000 ekin = 7.74275043504004 | erot = 10.419629418506 | epot = -72.619097123056 | etot = -54.4567172695099 +754000 ekin = 7.80325401374989 | erot = 10.3685500609919 | epot = -72.6285213451875 | etot = -54.4567172704458 +755000 ekin = 7.83074135616447 | erot = 10.228246958563 | epot = -72.5157055848015 | etot = -54.4567172700741 +756000 ekin = 7.8216430677752 | erot = 10.0059989462675 | epot = -72.2843592825357 | etot = -54.456717268493 +757000 ekin = 7.77995058071358 | erot = 9.72007455918367 | epot = -71.9567424059144 | etot = -54.4567172660171 +758000 ekin = 7.71576193733231 | erot = 9.39663554339804 | epot = -71.569114743751 | etot = -54.4567172630207 +759000 ekin = 7.64335601050446 | erot = 9.06548554812967 | epot = -71.1655588186764 | etot = -54.4567172600423 +760000 ekin = 7.57812578251839 | erot = 8.75574971039739 | epot = -70.7905927503519 | etot = -54.4567172574361 +761000 ekin = 7.5347738470458 | erot = 8.49179690722728 | epot = -70.4832880097503 | etot = -54.4567172554773 +762000 ekin = 7.52580486703051 | erot = 8.29027904918141 | epot = -70.2728011706493 | etot = -54.4567172544374 +763000 ekin = 7.56027219190173 | erot = 8.15788493774223 | epot = -70.1748743838271 | etot = -54.4567172541832 +764000 ekin = 7.64375808866712 | erot = 8.09209341180804 | epot = -70.192568755521 | etot = -54.4567172550458 +765000 ekin = 7.77732533268789 | erot = 8.08087591863538 | epot = -70.3149185076153 | etot = -54.456717256292 +766000 ekin = 7.95932937986269 | erot = 8.10617755734732 | epot = -70.5222241951193 | etot = -54.4567172579093 +767000 ekin = 8.18579174507 | erot = 8.1468327745402 | epot = -70.7893417792868 | etot = -54.4567172596766 +768000 ekin = 8.45095313233048 | erot = 8.18150203238947 | epot = -71.0891724260222 | etot = -54.4567172613023 +769000 ekin = 8.74814097856872 | erot = 8.19192572078243 | epot = -71.3967839618926 | etot = -54.4567172625415 +770000 ekin = 9.06864484883337 | erot = 8.16518273784215 | epot = -71.6905448508566 | etot = -54.4567172641811 +771000 ekin = 9.40152051237963 | erot = 8.09534580342965 | epot = -71.9535835800912 | etot = -54.4567172642819 +772000 ekin = 9.74055140014758 | erot = 7.98665030970658 | epot = -72.1839189737122 | etot = -54.456717263858 +773000 ekin = 10.0800699458974 | erot = 7.85110373964542 | epot = -72.3878909486576 | etot = -54.4567172631147 +774000 ekin = 10.4140305141887 | erot = 7.70610726771234 | epot = -72.5768550442126 | etot = -54.4567172623115 +775000 ekin = 10.7352090238702 | erot = 7.57137133474641 | epot = -72.7632976203061 | etot = -54.4567172616894 +776000 ekin = 11.0347273426372 | erot = 7.46577166843489 | epot = -72.9572162724777 | etot = -54.4567172614056 +777000 ekin = 11.3022272086694 | erot = 7.40478419490446 | epot = -73.1637286650686 | etot = -54.4567172614947 +778000 ekin = 11.5267923325131 | erot = 7.39895687129842 | epot = -73.3824664656885 | etot = -54.456717261877 +779000 ekin = 11.6984431849081 | erot = 7.45346445936768 | epot = -73.6086249066891 | etot = -54.4567172624134 +780000 ekin = 11.8098204310185 | erot = 7.56848658975163 | epot = -73.8350242837125 | etot = -54.4567172629423 +781000 ekin = 11.8576135100164 | erot = 7.74008064719624 | epot = -74.0544114205676 | etot = -54.456717263355 +782000 ekin = 11.843354622401 | erot = 7.96106713730013 | epot = -74.261139023307 | etot = -54.4567172636059 +783000 ekin = 11.773466092508 | erot = 8.22175785627727 | epot = -74.4519412124876 | etot = -54.4567172637024 +784000 ekin = 11.6594880030509 | erot = 8.51068468333472 | epot = -74.6268899497988 | etot = -54.4567172634132 +785000 ekin = 11.5166274256803 | erot = 8.81499326195249 | epot = -74.7883379509651 | etot = -54.4567172633323 +786000 ekin = 11.3609895910229 | erot = 9.12075819547596 | epot = -74.9384650496785 | etot = -54.4567172631797 +787000 ekin = 11.2098737157431 | erot = 9.4141199487952 | epot = -75.0807109274858 | etot = -54.4567172629475 +788000 ekin = 11.080783815695 | erot = 9.68217635157661 | epot = -75.2196774299222 | etot = -54.4567172626505 +789000 ekin = 10.9904701398751 | erot = 9.91392462847478 | epot = -75.3611120306443 | etot = -54.4567172622944 +790000 ekin = 10.9537524860344 | erot = 10.1009165691342 | epot = -75.5113863171584 | etot = -54.4567172619898 +791000 ekin = 10.9817979913698 | erot = 10.2372809089016 | epot = -75.6757961621672 | etot = -54.4567172618958 +792000 ekin = 11.0801481532749 | erot = 10.3193115157086 | epot = -75.8561769311707 | etot = -54.4567172621873 +793000 ekin = 11.2467542974375 | erot = 10.344770000213 | epot = -76.0482415606321 | etot = -54.4567172629816 +794000 ekin = 11.4705768798105 | erot = 10.312315188859 | epot = -76.2396093328906 | etot = -54.4567172642211 +795000 ekin = 11.733102407737 | erot = 10.2218576029472 | epot = -76.4116772763532 | etot = -54.456717265669 +796000 ekin = 12.0104523793572 | erot = 10.0755577767611 | epot = -76.5427274230367 | etot = -54.4567172669184 +797000 ekin = 12.2774168644973 | erot = 9.87947565190563 | epot = -76.6136097839764 | etot = -54.4567172675735 +798000 ekin = 12.51184923474 | erot = 9.64485933476574 | epot = -76.6134258369316 | etot = -54.4567172674259 +799000 ekin = 12.6978284048735 | erot = 9.38805929779039 | epot = -76.542604969205 | etot = -54.4567172665411 +800000 ekin = 12.8267336417013 | erot = 9.12873028579183 | epot = -76.4121811926931 | etot = -54.4567172652 +801000 ekin = 12.8964017894472 | erot = 8.88689375953526 | epot = -76.2400128127339 | etot = -54.4567172637514 +802000 ekin = 12.9092334834948 | erot = 8.67992468171397 | epot = -76.0458754276961 | etot = -54.4567172624874 +803000 ekin = 12.8701763431697 | erot = 8.52035040788718 | epot = -75.8472440126345 | etot = -54.4567172615776 +804000 ekin = 12.7851658304062 | erot = 8.41501298175795 | epot = -75.6568960731657 | etot = -54.4567172610016 +805000 ekin = 12.660041487181 | erot = 8.36523459713533 | epot = -75.4819933451657 | etot = -54.4567172608494 +806000 ekin = 12.5000407944888 | erot = 8.36656829157481 | epot = -75.3233263471994 | etot = -54.4567172611358 +807000 ekin = 12.3098796732018 | erot = 8.40968834838668 | epot = -75.1762852832351 | etot = -54.4567172616467 +808000 ekin = 12.0938131957673 | erot = 8.48342142270803 | epot = -75.0339518808583 | etot = -54.456717262383 +809000 ekin = 11.855746418418 | erot = 8.57397165846824 | epot = -74.8864353400818 | etot = -54.4567172631955 +810000 ekin = 11.5994894992308 | erot = 8.66620690073695 | epot = -74.7224136639664 | etot = -54.4567172639987 +811000 ekin = 11.3289496686299 | erot = 8.74571674833127 | epot = -74.5313836816674 | etot = -54.4567172647062 +812000 ekin = 11.0482743074323 | erot = 8.80005767537732 | epot = -74.3050492480417 | etot = -54.4567172652321 +813000 ekin = 10.7652338995879 | erot = 8.82039840384585 | epot = -74.0423495681397 | etot = -54.4567172647059 +814000 ekin = 10.491599345393 | erot = 8.80333280511247 | epot = -73.7516494161139 | etot = -54.4567172656085 +815000 ekin = 10.1506392602966 | erot = 8.72916604612333 | epot = -73.3365225755524 | etot = -54.4567172691325 +816000 ekin = 10.0078569448266 | erot = 8.6078590322844 | epot = -73.072433255896 | etot = -54.456717278785 +817000 ekin = 9.94168629455641 | erot = 8.48386018509532 | epot = -72.8822637662572 | etot = -54.4567172866055 +818000 ekin = 9.81602541284464 | erot = 8.35562171935582 | epot = -72.6283644162418 | etot = -54.4567172840414 +819000 ekin = 9.72001449698606 | erot = 8.23727756032506 | epot = -72.4140093391615 | etot = -54.4567172818503 +820000 ekin = 9.65393768634831 | erot = 8.15065357777487 | epot = -72.2613085437321 | etot = -54.456717279609 +821000 ekin = 9.62991083867892 | erot = 8.11519232361071 | epot = -72.2018204400444 | etot = -54.4567172777548 +822000 ekin = 9.66070438850672 | erot = 8.14514958891508 | epot = -72.2625712541767 | etot = -54.4567172767549 +823000 ekin = 9.75366113132238 | erot = 8.2472923862444 | epot = -72.4576707944586 | etot = -54.4567172768918 +824000 ekin = 9.90784075220442 | erot = 8.41983721970679 | epot = -72.7843952500946 | etot = -54.4567172781834 +825000 ekin = 10.1134132500794 | erot = 8.65280772349328 | epot = -73.2229382539831 | etot = -54.4567172804104 +826000 ekin = 10.3532272232306 | erot = 8.92957217377799 | epot = -73.7395166802203 | etot = -54.4567172832117 +827000 ekin = 10.6056861232938 | erot = 9.22912189012728 | epot = -74.2915252996209 | etot = -54.4567172861998 +828000 ekin = 10.8478833100547 | erot = 9.52863932137444 | epot = -74.8332399204591 | etot = -54.4567172890299 +829000 ekin = 11.0582941053682 | erot = 9.80604986035545 | epot = -75.3210612571405 | etot = -54.4567172914169 +830000 ekin = 11.218802233765 | erot = 10.0424425697305 | epot = -75.7179620966237 | etot = -54.4567172931282 +831000 ekin = 11.3161133791475 | erot = 10.2243333144541 | epot = -75.9971639875828 | etot = -54.4567172939812 +832000 ekin = 11.3426219926857 | erot = 10.3456446448569 | epot = -76.1449839314125 | etot = -54.4567172938699 +833000 ekin = 11.2966905573002 | erot = 10.4090470942552 | epot = -76.1624549443618 | etot = -54.4567172928064 +834000 ekin = 11.1822293589888 | erot = 10.4261077170764 | epot = -76.0650543670288 | etot = -54.4567172909636 +835000 ekin = 11.007516118298 | erot = 10.4150475473475 | epot = -75.8792809543085 | etot = -54.4567172886631 +836000 ekin = 10.7833649095725 | erot = 10.3987463121013 | epot = -75.6388285079847 | etot = -54.456717286311 +837000 ekin = 10.5209605455866 | erot = 10.4007504685316 | epot = -75.3784282984345 | etot = -54.4567172843164 +838000 ekin = 10.2299052199325 | erot = 10.4407488045102 | epot = -75.127371307417 | etot = -54.4567172829743 +839000 ekin = 9.91700879951234 | erot = 10.5309577036362 | epot = -74.9046837856422 | etot = -54.4567172824936 +840000 ekin = 9.58612989122598 | erot = 10.6748490697653 | epot = -74.7176962435954 | etot = -54.4567172826041 +841000 ekin = 9.23902247601797 | erot = 10.8680222456759 | epot = -74.5637620048616 | etot = -54.4567172831678 +842000 ekin = 8.87682183145439 | erot = 11.0993209654069 | epot = -74.4328600810384 | etot = -54.4567172841771 +843000 ekin = 8.50166697120823 | erot = 11.3515587655238 | epot = -74.309943021544 | etot = -54.456717284812 +844000 ekin = 8.11786122477187 | erot = 11.6086450390288 | epot = -74.1832235489468 | etot = -54.4567172851461 +845000 ekin = 7.73224665953605 | erot = 11.8569199011394 | epot = -74.0458838457577 | etot = -54.4567172850822 +846000 ekin = 7.35386726302661 | erot = 12.0865858113318 | epot = -73.8971703589764 | etot = -54.4567172846179 +847000 ekin = 6.99310483296078 | erot = 12.2927531541356 | epot = -73.742575270915 | etot = -54.4567172838186 +848000 ekin = 6.66064227401819 | erot = 12.4755849218195 | epot = -73.5929444786285 | etot = -54.4567172827908 +849000 ekin = 6.36657021963096 | erot = 12.6396628746056 | epot = -73.4629503758848 | etot = -54.4567172816482 +850000 ekin = 6.11978999358428 | erot = 12.7927789148331 | epot = -73.3692861889307 | etot = -54.4567172805133 +851000 ekin = 5.92769059315122 | erot = 12.9443936749977 | epot = -73.3288015476477 | etot = -54.4567172794987 +852000 ekin = 5.79598233515264 | erot = 13.1040127665475 | epot = -73.3567123804052 | etot = -54.4567172787051 +853000 ekin = 5.72857612922473 | erot = 13.2797145891883 | epot = -73.465007996636 | etot = -54.456717278223 +854000 ekin = 5.72746426144119 | erot = 13.4770198626781 | epot = -73.6612014022099 | etot = -54.4567172780906 +855000 ekin = 5.7926221201218 | erot = 13.6982251276403 | epot = -73.9475645260821 | etot = -54.45671727832 +856000 ekin = 5.92198051767567 | erot = 13.9422405100738 | epot = -74.3209383066334 | etot = -54.456717278884 +857000 ekin = 6.11150866263892 | erot = 14.2048890108794 | epot = -74.7731149532434 | etot = -54.456717279725 +858000 ekin = 6.3554128794462 | erot = 14.4795498832106 | epot = -75.2916800434266 | etot = -54.4567172807698 +859000 ekin = 6.64641352741666 | erot = 14.7579710750353 | epot = -75.8611018843973 | etot = -54.4567172819453 +860000 ekin = 6.97602906176176 | erot = 15.0310494938697 | epot = -76.4637958388347 | etot = -54.4567172832033 +861000 ekin = 7.33478689142115 | erot = 15.2894014997167 | epot = -77.0809056756608 | etot = -54.456717284523 +862000 ekin = 7.71230494059453 | erot = 15.5236284018639 | epot = -77.692650628373 | etot = -54.4567172859146 +863000 ekin = 8.09724291543955 | erot = 15.7243060787791 | epot = -78.2782662816227 | etot = -54.4567172874041 +864000 ekin = 8.4771915669909 | erot = 15.8818501460663 | epot = -78.8157590020617 | etot = -54.4567172890045 +865000 ekin = 8.83862795338403 | erot = 15.9864762743823 | epot = -79.2818215184602 | etot = -54.4567172906939 +866000 ekin = 9.16709499256939 | erot = 16.0284566448153 | epot = -79.6522689297808 | etot = -54.4567172923961 +867000 ekin = 9.44775496531617 | erot = 15.9987710029987 | epot = -79.9032432622897 | etot = -54.4567172939749 +868000 ekin = 9.6664170744331 | erot = 15.8900978286616 | epot = -80.0132321983435 | etot = -54.4567172952488 +869000 ekin = 9.81104759054282 | erot = 15.6979368125003 | epot = -79.9657016990601 | etot = -54.456717296017 +870000 ekin = 9.87363911507953 | erot = 15.4215512161863 | epot = -79.7519076273703 | etot = -54.4567172961045 +871000 ekin = 9.85215986226638 | erot = 15.0644163888267 | epot = -79.3732935464946 | etot = -54.4567172954015 +872000 ekin = 9.75216666239265 | erot = 14.6339832229935 | epot = -78.8428671792867 | etot = -54.4567172939006 +873000 ekin = 9.58760337522076 | erot = 14.1407822457039 | epot = -78.1851029126354 | etot = -54.4567172917107 +874000 ekin = 9.38036224431465 | erot = 13.5971115526464 | epot = -77.4341910860126 | etot = -54.4567172890515 +875000 ekin = 9.1583690804909 | erot = 13.0156613281791 | epot = -76.6307476948981 | etot = -54.4567172862282 +876000 ekin = 8.95224910375881 | erot = 12.4083870186345 | epot = -75.8173534059835 | etot = -54.4567172835902 +877000 ekin = 8.79100811654741 | erot = 11.7858100333618 | epot = -75.0335354313758 | etot = -54.4567172814667 +878000 ekin = 8.69754976343306 | erot = 11.1567995255978 | epot = -74.3110665691266 | etot = -54.4567172800958 +879000 ekin = 8.68509191536562 | erot = 10.528822608113 | epot = -73.6706318030318 | etot = -54.4567172795532 +880000 ekin = 8.75545564717777 | erot = 9.90861257464238 | epot = -73.1207855015467 | etot = -54.4567172797265 +881000 ekin = 8.89970025389319 | erot = 9.30313444737478 | epot = -72.6595519816192 | etot = -54.4567172803512 +882000 ekin = 9.10082855527117 | erot = 8.72061110511921 | epot = -72.278156941492 | etot = -54.4567172811017 +883000 ekin = 9.33764332483114 | erot = 8.17127546242785 | epot = -71.9656360689544 | etot = -54.4567172816955 +884000 ekin = 9.58861580338188 | erot = 7.66753088023467 | epot = -71.7128639655819 | etot = -54.4567172819654 +885000 ekin = 9.83488676084092 | erot = 7.22337392463723 | epot = -71.5149779673575 | etot = -54.4567172818793 +886000 ekin = 10.0620352551567 | erot = 6.85319082653713 | epot = -71.3719433631991 | etot = -54.4567172815053 +887000 ekin = 10.2607068157852 | erot = 6.57023940272128 | epot = -71.2876634994672 | etot = -54.4567172809607 +888000 ekin = 10.4264068596208 | erot = 6.38516766531517 | epot = -71.2682918053188 | etot = -54.4567172803829 +889000 ekin = 10.5587552560681 | erot = 6.30481332826537 | epot = -71.3202858642362 | etot = -54.4567172799027 +890000 ekin = 10.660400957153 | erot = 6.33138191738457 | epot = -71.4485001541795 | etot = -54.456717279642 +891000 ekin = 10.7357341009314 | erot = 6.46201557973017 | epot = -71.6544669603625 | etot = -54.456717279701 +892000 ekin = 10.7895437607956 | erot = 6.68876199668767 | epot = -71.9350230376277 | etot = -54.4567172801445 +893000 ekin = 10.8258166395352 | erot = 6.99898655744732 | epot = -72.2815204779588 | etot = -54.4567172809762 +894000 ekin = 10.8468969134544 | erot = 7.3762819960095 | epot = -72.6798961915935 | etot = -54.4567172821296 +895000 ekin = 10.8531861940648 | erot = 7.80188530605902 | epot = -73.1117887835901 | etot = -54.4567172834663 +896000 ekin = 10.8434432145783 | erot = 8.25651048988296 | epot = -73.5566709892582 | etot = -54.4567172847969 +897000 ekin = 10.8155751276529 | erot = 8.72237163403413 | epot = -73.9946640476099 | etot = -54.4567172859228 +898000 ekin = 10.767662782976 | erot = 9.18505046674875 | epot = -74.409430536412 | etot = -54.4567172866873 +899000 ekin = 10.6988999917894 | erot = 9.63481320602856 | epot = -74.790430484832 | etot = -54.456717287014 +900000 ekin = 10.6101778354415 | erot = 10.0670454033808 | epot = -75.1339405257556 | etot = -54.4567172869334 +901000 ekin = 10.5041792335631 | erot = 10.4816537280782 | epot = -75.4425502482074 | etot = -54.456717286566 +902000 ekin = 10.3850069961039 | erot = 10.8815370479879 | epot = -75.7232613301866 | etot = -54.4567172860948 +903000 ekin = 10.2574985061915 | erot = 11.2704782388129 | epot = -75.9846940307164 | etot = -54.456717285712 +904000 ekin = 10.1264528577835 | erot = 11.6509689580187 | epot = -76.2341391013718 | etot = -54.4567172855695 +905000 ekin = 9.99600212712643 | erot = 12.0224964837842 | epot = -76.4752158966507 | etot = -54.4567172857401 +906000 ekin = 9.86930089573122 | erot = 12.3806889297523 | epot = -76.7067071116865 | etot = -54.4567172862029 +907000 ekin = 9.74860096925809 | erot = 12.7174733297172 | epot = -76.92279158583 | etot = -54.4567172868547 +908000 ekin = 9.63564731433989 | erot = 13.0221203324162 | epot = -77.1144849343097 | etot = -54.4567172875536 +909000 ekin = 9.53221635085886 | erot = 13.2828159174028 | epot = -77.2717495564238 | etot = -54.4567172881622 +910000 ekin = 9.44056511133843 | erot = 13.4883008486278 | epot = -77.385583248554 | etot = -54.4567172885878 +911000 ekin = 9.36359901014175 | erot = 13.629200211069 | epot = -77.4495165100058 | etot = -54.456717288795 +912000 ekin = 9.30468390682152 | erot = 13.6988898091622 | epot = -77.4602910047774 | etot = -54.4567172887937 +913000 ekin = 9.26716675185183 | erot = 13.6939842819864 | epot = -77.4178683224487 | etot = -54.4567172886105 +914000 ekin = 9.25375894933069 | erot = 13.6146373108726 | epot = -77.3251135484751 | etot = -54.4567172882718 +915000 ekin = 9.265942472167 | erot = 13.4647622141606 | epot = -77.1874219741286 | etot = -54.456717287801 +916000 ekin = 9.30349967050416 | erot = 13.2520951427828 | epot = -77.0123121005179 | etot = -54.456717287231 +917000 ekin = 9.36419714227949 | erot = 12.9878926206989 | epot = -76.8088070496005 | etot = -54.4567172866221 +918000 ekin = 9.44361963624214 | erot = 12.6860933859995 | epot = -76.5864303082981 | etot = -54.4567172860564 +919000 ekin = 9.53516188538878 | erot = 12.3619660455222 | epot = -76.3538452165377 | etot = -54.4567172856267 +920000 ekin = 9.6302153355728 | erot = 12.0304853675748 | epot = -76.1174179885498 | etot = -54.4567172854022 +921000 ekin = 9.71859337755521 | erot = 11.70479770819 | epot = -75.8801083711618 | etot = -54.4567172854166 +922000 ekin = 9.78920667212906 | erot = 11.3950992586109 | epot = -75.6410232163825 | etot = -54.4567172856426 +923000 ekin = 9.83094506626224 | erot = 11.1081050699541 | epot = -75.39576742223 | etot = -54.4567172860137 +924000 ekin = 9.83367304677115 | erot = 10.8471196662737 | epot = -75.13750999948 | etot = -54.4567172864352 +925000 ekin = 9.78921982197768 | erot = 10.6125977274222 | epot = -74.8585348361976 | etot = -54.4567172867977 +926000 ekin = 9.69224265479811 | erot = 10.4030278881592 | epot = -74.5519878299579 | etot = -54.4567172870006 +927000 ekin = 9.54086684313772 | erot = 10.215970608909 | epot = -74.2135547390065 | etot = -54.4567172869598 +928000 ekin = 9.33704160539799 | erot = 10.049113171618 | epot = -73.842872063634 | etot = -54.456717286618 +929000 ekin = 9.08657260989333 | erot = 9.90122855057232 | epot = -73.4445184464149 | etot = -54.4567172859493 +930000 ekin = 8.79883716647138 | erot = 9.77291303140251 | epot = -73.0284674828389 | etot = -54.4567172849651 +931000 ekin = 8.48619808320862 | erot = 9.66694330183042 | epot = -72.6098586687716 | etot = -54.4567172837326 +932000 ekin = 8.16314309637535 | erot = 9.58807622102903 | epot = -72.207936599781 | etot = -54.4567172823766 +933000 ekin = 7.84519354297996 | erot = 9.54217917974753 | epot = -71.8440900038035 | etot = -54.456717281076 +934000 ekin = 7.54765679209689 | erot = 9.53474238369921 | epot = -71.539116455835 | etot = -54.4567172800389 +935000 ekin = 7.28433307165894 | erot = 9.56903045433067 | epot = -71.3100808054524 | etot = -54.4567172794628 +936000 ekin = 7.066312850676 | erot = 9.64428867320406 | epot = -71.167318803382 | etot = -54.456717279502 +937000 ekin = 6.9010072119673 | erot = 9.75446862329103 | epot = -71.1121931154852 | etot = -54.4567172802269 +938000 ekin = 6.79154129359436 | erot = 9.88787401266418 | epot = -71.1361325878541 | etot = -54.4567172815956 +939000 ekin = 6.73661249436847 | erot = 10.0281331615685 | epot = -71.2214629393441 | etot = -54.4567172834071 +940000 ekin = 6.73087289994123 | erot = 10.156091356866 | epot = -71.3436815423055 | etot = -54.4567172854983 +941000 ekin = 6.76583136811592 | erot = 10.2524184937916 | epot = -71.4749671493956 | etot = -54.4567172874881 +942000 ekin = 6.83124487460903 | erot = 10.3013419690641 | epot = -71.5893041326923 | etot = -54.4567172890192 +943000 ekin = 6.91692812763227 | erot = 10.2938485499083 | epot = -71.6674939673214 | etot = -54.4567172897808 +944000 ekin = 7.01479645628877 | erot = 10.2298584620993 | epot = -71.7013722079767 | etot = -54.4567172895886 +945000 ekin = 7.12068760755787 | erot = 10.11864719739 | epot = -71.6960520934326 | etot = -54.4567172884847 +946000 ekin = 7.23514614953277 | erot = 9.97707725572987 | epot = -71.6689406920673 | etot = -54.4567172868047 +947000 ekin = 7.36229609113449 | erot = 9.82579824697724 | epot = -71.6448116232399 | etot = -54.4567172851282 +948000 ekin = 7.5066654784363 | erot = 9.68437595393612 | epot = -71.6477587164466 | etot = -54.4567172840742 +949000 ekin = 7.66924616192619 | erot = 9.56691299469446 | epot = -71.6928764406203 | etot = -54.4567172839997 +950000 ekin = 7.84507329856733 | erot = 9.47964218466348 | epot = -71.7814327680629 | etot = -54.4567172848321 +951000 ekin = 8.02398780692388 | erot = 9.42110967883054 | epot = -71.9018147718842 | etot = -54.4567172861297 +952000 ekin = 8.1941768416605 | erot = 9.38438008351819 | epot = -72.0352742125472 | etot = -54.4567172873685 +953000 ekin = 8.346267788022 | erot = 9.35991642815096 | epot = -72.1629015043888 | etot = -54.4567172882158 +954000 ekin = 8.47568923856527 | erot = 9.33789032825475 | epot = -72.2702968554351 | etot = -54.4567172886151 +955000 ekin = 8.58250201859919 | erot = 9.30949114579842 | epot = -72.3487104530905 | etot = -54.4567172886929 +956000 ekin = 8.66948436712674 | erot = 9.26761872824813 | epot = -72.3938203840475 | etot = -54.4567172886726 +957000 ekin = 8.739832657523 | erot = 9.20719774878436 | epot = -72.4037476947865 | etot = -54.4567172884791 +958000 ekin = 8.79545874723552 | erot = 9.126476244584 | epot = -72.378652279995 | etot = -54.4567172881754 +959000 ekin = 8.83619167919023 | erot = 9.02839052826676 | epot = -72.3212994951729 | etot = -54.4567172877159 +960000 ekin = 8.85975167755722 | erot = 8.92106613096496 | epot = -72.2375350955793 | etot = -54.4567172870572 +961000 ekin = 8.86221391090885 | erot = 8.81796977944934 | epot = -72.1369009765478 | etot = -54.4567172861896 +962000 ekin = 8.83870974711557 | erot = 8.73730143651553 | epot = -72.0327284687764 | etot = -54.4567172851453 +963000 ekin = 8.78419063763695 | erot = 8.70062153323996 | epot = -71.9415294548756 | etot = -54.4567172839987 +964000 ekin = 8.69414320506481 | erot = 8.73080443183895 | epot = -71.8816649197731 | etot = -54.4567172828693 +965000 ekin = 8.56518846880189 | erot = 8.84947946883654 | epot = -71.8713852195325 | etot = -54.4567172818941 +966000 ekin = 8.395531843865 | erot = 9.07419585613114 | epot = -71.9264449812332 | etot = -54.4567172812371 +967000 ekin = 8.18525791182074 | erot = 9.41563515999431 | epot = -72.0576103528451 | etot = -54.4567172810301 +968000 ekin = 7.93667478275607 | erot = 9.875203754605 | epot = -72.2685958186773 | etot = -54.4567172813162 +969000 ekin = 7.65450207892527 | erot = 10.4432619151776 | epot = -72.5544812763479 | etot = -54.4567172822451 +970000 ekin = 7.34445294204124 | erot = 11.0999552910906 | epot = -72.9011255166925 | etot = -54.4567172835607 +971000 ekin = 7.01467245164451 | erot = 11.8168528075962 | epot = -73.2882425443051 | etot = -54.4567172850644 +972000 ekin = 6.67605450386153 | erot = 12.5598107323186 | epot = -73.69258252268 | etot = -54.4567172864998 +973000 ekin = 6.34244769973959 | erot = 13.292339627092 | epot = -74.0915046145631 | etot = -54.4567172877315 +974000 ekin = 6.03025176745024 | erot = 13.9789096322743 | epot = -74.4658786881816 | etot = -54.4567172884571 +975000 ekin = 5.75716039266692 | erot = 14.5899381417919 | epot = -74.8038158231207 | etot = -54.4567172886618 +976000 ekin = 5.54124167937354 | erot = 15.1033057452736 | epot = -75.1012647130769 | etot = -54.4567172884298 +977000 ekin = 5.39911082447761 | erot = 15.5049119864332 | epot = -75.360740098856 | etot = -54.4567172879452 +978000 ekin = 5.34386272244975 | erot = 15.7880067440261 | epot = -75.5885867539051 | etot = -54.4567172874293 +979000 ekin = 5.38319930699435 | erot = 15.9517029513751 | epot = -75.7916195454502 | etot = -54.4567172870807 +980000 ekin = 5.51814445206285 | erot = 15.9991910955127 | epot = -75.974052834607 | etot = -54.4567172870314 +981000 ekin = 5.74260488047642 | erot = 15.9361251477645 | epot = -76.1354473155615 | etot = -54.4567172873206 +982000 ekin = 6.04385436983203 | erot = 15.7695224495612 | epot = -76.2700941072787 | etot = -54.4567172878855 +983000 ekin = 6.40384970651062 | erot = 15.5073539290585 | epot = -76.3679209241518 | etot = -54.4567172885826 +984000 ekin = 6.80116238511539 | erot = 15.158811851248 | epot = -76.4166915255777 | etot = -54.4567172892143 +985000 ekin = 7.21323365728782 | erot = 14.7350438440015 | epot = -76.4049947908705 | etot = -54.4567172895812 +986000 ekin = 7.61862562386071 | erot = 14.2499737923667 | epot = -76.3253167057545 | etot = -54.4567172895271 +987000 ekin = 7.99894925438823 | erot = 13.7207610181892 | epot = -76.1764275615598 | etot = -54.4567172889824 +988000 ekin = 8.34021171333252 | erot = 13.1675370959784 | epot = -75.9644660972962 | etot = -54.4567172879853 +989000 ekin = 8.63344275568658 | erot = 12.6122920455365 | epot = -75.7024520878918 | etot = -54.4567172866688 +990000 ekin = 8.87460950487308 | erot = 12.0770718402453 | epot = -75.4083986303363 | etot = -54.4567172852179 +991000 ekin = 9.06396875502587 | erot = 11.5818647058656 | epot = -75.1025507447246 | etot = -54.4567172838331 +992000 ekin = 9.20509314120202 | erot = 11.1426150700437 | epot = -74.8044254939285 | etot = -54.4567172826828 +993000 ekin = 9.30382170788786 | erot = 10.7697167152029 | epot = -74.5302557049708 | etot = -54.4567172818801 +994000 ekin = 9.36733435635714 | erot = 10.4671721138003 | epot = -74.2912237516329 | etot = -54.4567172814754 +995000 ekin = 9.40346085607831 | erot = 10.2324426393021 | epot = -74.0926207768454 | etot = -54.456717281465 +996000 ekin = 9.42024172457918 | erot = 10.056905047134 | epot = -73.9338640535126 | etot = -54.4567172817994 +997000 ekin = 9.42568515134584 | erot = 9.92679732909049 | epot = -73.8091997628356 | etot = -54.4567172823993 +998000 ekin = 9.42763194298499 | erot = 9.82456426529677 | epot = -73.7089134914418 | etot = -54.45671728316 +999000 ekin = 9.43365149694049 | erot = 9.73053828900897 | epot = -73.620907069925 | etot = -54.4567172839756 +1000000 ekin = 9.45092723106241 | erot = 9.62486149933323 | epot = -73.5325060150984 | etot = -54.4567172847028 + 1000000 352.2878 -75.545604 2.0130979 -64.081579 -0.0098473389 39304000 +Loop time of 16.7951 on 4 procs for 1000000 steps with 10 atoms + +Performance: 87.763 ns/day, 0.273 hours/ns, 59541.025 timesteps/s, 595.410 katom-step/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.5941 | 6.7707 | 9.5516 | 62.7 | 40.31 +Bond | 0.2092 | 0.2872 | 0.38189 | 13.0 | 1.71 +Neigh | 0.018433 | 0.018502 | 0.018552 | 0.0 | 0.11 +Comm | 3.8835 | 7.1053 | 8.5337 | 70.8 | 42.31 +Output | 0.073525 | 0.077664 | 0.085514 | 1.7 | 0.46 +Modify | 0.58013 | 0.70982 | 0.8931 | 15.7 | 4.23 +Other | | 1.826 | | | 10.87 + +Nlocal: 2.5 ave 4 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 9 max 6 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25 ave 19 max 5 min +Histogram: 2 1 0 0 0 0 0 0 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:16 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/data.duplex2 new file mode 100644 index 0000000000..78a6fdd51a --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0 +2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0 +3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0 +4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0 +5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0 +6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0 +7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0 +8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0 +9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0 +10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0 +11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0 +12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0 +13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0 +14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0 +15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0 +16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447 +2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514 +3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762 +4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703 +5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389 +6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085 +7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256 +8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774 +9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824 +10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333 +11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933 +12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927 +13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526 +14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926 +15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399 +16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/in.duplex2 new file mode 100644 index 0000000000..83474d62e4 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/in.duplex2 @@ -0,0 +1,71 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.1 new file mode 100644 index 0000000000..8254a5535a --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.1 @@ -0,0 +1,1178 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.010 seconds + +set atom * mass 315.8376 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 25.179212 + ghost atom cutoff = 32.4 + binsize = 12.589606, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -131.137679785989 | etot = -98.3191045555159 +Per MPI rank memory allocation (min/avg/max) = 7.322 | 7.322 | 7.322 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -132.72638 1.5886993 -115.01736 0.034438461 39304000 +1000 ekin = 16.0002912584478 | erot = 15.4130110640124 | epot = -130.027520323725 | etot = -98.6142180012648 +2000 ekin = 15.5533535250411 | erot = 14.7917296260752 | epot = -129.046610368884 | etot = -98.7015272177675 +3000 ekin = 15.7337839961821 | erot = 14.6842095726446 | epot = -128.328696192996 | etot = -97.9107026241695 +4000 ekin = 15.3482319530843 | erot = 14.1372237687107 | epot = -127.776261802948 | etot = -98.2908060811534 +5000 ekin = 14.9263694483589 | erot = 12.443938366847 | epot = -127.296202022196 | etot = -99.9258942069904 +6000 ekin = 14.0721574322892 | erot = 14.008279091165 | epot = -126.855924907346 | etot = -98.7754883838923 +7000 ekin = 14.1550430881492 | erot = 12.9264438891654 | epot = -126.709078100902 | etot = -99.6275911235871 +8000 ekin = 14.4700082617388 | erot = 12.7980942938229 | epot = -126.72076237707 | etot = -99.4526598215087 +9000 ekin = 13.7935207810181 | erot = 11.1109944089258 | epot = -126.899837825726 | etot = -101.995322635783 +10000 ekin = 13.8730717933148 | erot = 11.5704248326849 | epot = -127.244033240875 | etot = -101.800536614875 +11000 ekin = 13.3507232443761 | erot = 12.9112263667083 | epot = -127.760111494138 | etot = -101.498161883054 +12000 ekin = 13.4086541156856 | erot = 13.8643429386181 | epot = -128.401057480199 | etot = -101.128060425895 +13000 ekin = 13.7941097212275 | erot = 15.1829473516003 | epot = -128.924634303951 | etot = -99.9475772311232 +14000 ekin = 13.7373019772469 | erot = 16.8593959312396 | epot = -129.287018821105 | etot = -98.6903209126183 +15000 ekin = 14.3775667172534 | erot = 15.5179347513432 | epot = -129.421282945982 | etot = -99.5257814773857 +16000 ekin = 13.8847755684525 | erot = 16.5304656056102 | epot = -129.305608895632 | etot = -98.8903677215693 +17000 ekin = 14.2834170163594 | erot = 18.0673540120274 | epot = -129.01182681491 | etot = -96.6610557865233 +18000 ekin = 13.905752827044 | erot = 18.7376551039341 | epot = -128.621578737511 | etot = -95.9781708065332 +19000 ekin = 14.4760834974064 | erot = 17.7902128999092 | epot = -128.117151475392 | etot = -95.8508550780764 +20000 ekin = 15.3937345783259 | erot = 19.8648992029204 | epot = -127.56855463044 | etot = -92.3099208491937 +21000 ekin = 15.7671119393256 | erot = 19.8430380451201 | epot = -127.124003368253 | etot = -91.5138533838069 +22000 ekin = 15.7994783207316 | erot = 19.4784869721879 | epot = -126.816699306327 | etot = -91.5387340134077 +23000 ekin = 16.3483836601625 | erot = 17.0357673010608 | epot = -126.649700985973 | etot = -93.2655500247493 +24000 ekin = 16.1507594840298 | erot = 15.2693364703422 | epot = -126.685461426128 | etot = -95.2653654717559 +25000 ekin = 16.203184519179 | erot = 14.6059430302144 | epot = -126.807847056136 | etot = -95.9987195067425 +26000 ekin = 16.7507819920595 | erot = 15.3659928707758 | epot = -127.061168325559 | etot = -94.9443934627232 +27000 ekin = 17.3027801847627 | erot = 15.0549761447199 | epot = -127.358431293729 | etot = -95.0006749642463 +28000 ekin = 16.7275411326653 | erot = 14.4833693237958 | epot = -127.72825168154 | etot = -96.5173412250786 +29000 ekin = 16.9331906804681 | erot = 14.1732399680703 | epot = -128.314160300347 | etot = -97.2077296518087 +30000 ekin = 17.3979368845819 | erot = 15.0750861896632 | epot = -129.049441921784 | etot = -96.5764188475391 +31000 ekin = 17.9805518710242 | erot = 15.9147863527506 | epot = -129.875453929081 | etot = -95.9801157053065 +32000 ekin = 18.991749110182 | erot = 16.1051463551532 | epot = -130.726992714223 | etot = -95.6300972488879 +33000 ekin = 20.6032790039669 | erot = 18.2127305854676 | epot = -131.442482248633 | etot = -92.6264726591987 +34000 ekin = 20.7015732844057 | erot = 20.3695139053724 | epot = -132.038212296576 | etot = -90.9671251067976 +35000 ekin = 20.6224774217646 | erot = 19.1826782921038 | epot = -132.36647836209 | etot = -92.5613226482212 +36000 ekin = 20.1520537423062 | erot = 17.8179561641377 | epot = -132.366786362955 | etot = -94.3967764565106 +37000 ekin = 19.6565905262906 | erot = 16.3054808375501 | epot = -132.145922204066 | etot = -96.1838508402256 +38000 ekin = 19.9043964212916 | erot = 15.6056111124709 | epot = -131.77788857791 | etot = -96.2678810441475 +39000 ekin = 19.2882958101298 | erot = 15.4027429551991 | epot = -131.213373717576 | etot = -96.5223349522475 +40000 ekin = 18.5691038706094 | erot = 13.0929098923544 | epot = -130.537124768966 | etot = -98.8751110060019 +41000 ekin = 18.1316081462315 | erot = 13.3149957669955 | epot = -130.010011539913 | etot = -98.5634076266863 +42000 ekin = 16.9837403650448 | erot = 16.7094940454199 | epot = -129.655904971791 | etot = -95.9626705613262 +43000 ekin = 16.6349665476583 | erot = 14.3402625718885 | epot = -129.393776619619 | etot = -98.418547500072 +44000 ekin = 15.8682276051288 | erot = 14.7913358635091 | epot = -129.290903327673 | etot = -98.631339859035 +45000 ekin = 15.374715567058 | erot = 14.977371976636 | epot = -129.432162022537 | etot = -99.0800744788433 +46000 ekin = 16.2897580482644 | erot = 16.2176299382166 | epot = -129.612152759202 | etot = -97.1047647727206 +47000 ekin = 15.7516354593177 | erot = 15.4475115771978 | epot = -129.956141906889 | etot = -98.7569948703731 +48000 ekin = 15.4507690861218 | erot = 14.5236736832187 | epot = -130.3940307148 | etot = -100.419587945459 +49000 ekin = 16.2344750706822 | erot = 13.3047207185633 | epot = -130.84669718433 | etot = -101.307501395085 +50000 ekin = 16.974320381226 | erot = 11.9032594834734 | epot = -131.236179316067 | etot = -102.358599451368 +51000 ekin = 17.2827942073029 | erot = 11.4154864948559 | epot = -131.479776782662 | etot = -102.781496080503 +52000 ekin = 18.1014798851337 | erot = 13.1049523637151 | epot = -131.679246819995 | etot = -100.472814571146 +53000 ekin = 17.8363780895838 | erot = 14.2885179417882 | epot = -131.763708181028 | etot = -99.6388121496565 +54000 ekin = 17.8598848344147 | erot = 13.8728193262606 | epot = -131.772814929948 | etot = -100.040110769273 +55000 ekin = 17.8592413500744 | erot = 14.8949775530269 | epot = -131.788674697824 | etot = -99.0344557947223 +56000 ekin = 17.5814377002229 | erot = 14.5440455332349 | epot = -131.675930178395 | etot = -99.5504469449374 +57000 ekin = 17.5694966593012 | erot = 12.6931336033397 | epot = -131.401500646115 | etot = -101.138870383474 +58000 ekin = 16.8071038576405 | erot = 12.7212915633872 | epot = -131.028272581344 | etot = -101.499877160317 +59000 ekin = 16.1422224289164 | erot = 14.2423694840757 | epot = -130.526951561124 | etot = -100.142359648132 +60000 ekin = 16.1183208468105 | erot = 15.2534297133036 | epot = -129.877962750013 | etot = -98.5062121898987 +61000 ekin = 15.8468789930106 | erot = 15.1008931337113 | epot = -129.107716413246 | etot = -98.1599442865238 +62000 ekin = 15.5108881063089 | erot = 13.2610118920851 | epot = -128.242062813497 | etot = -99.4701628151025 +63000 ekin = 15.6866053841808 | erot = 13.2559649896144 | epot = -127.370136974907 | etot = -98.4275666011119 +64000 ekin = 16.3650311075986 | erot = 13.0247193745828 | epot = -126.81154472196 | etot = -97.4217942397782 +65000 ekin = 16.217921452927 | erot = 12.3591320054664 | epot = -126.401331482561 | etot = -97.8242780241672 +66000 ekin = 15.3952746105419 | erot = 12.3832665394644 | epot = -126.246883127669 | etot = -98.4683419776623 +67000 ekin = 15.3668510897215 | erot = 14.5485753507038 | epot = -126.332363292344 | etot = -96.4169368519185 +68000 ekin = 14.8298516167412 | erot = 12.6826894448494 | epot = -126.499589453513 | etot = -98.9870483919221 +69000 ekin = 14.4197557600489 | erot = 13.0250391104792 | epot = -126.686977344856 | etot = -99.2421824743277 +70000 ekin = 14.4530539036206 | erot = 11.6611565262399 | epot = -126.836765346542 | etot = -100.722554916682 +71000 ekin = 14.4961247230087 | erot = 11.0649797539566 | epot = -127.014655125463 | etot = -101.453550648498 +72000 ekin = 14.9071629587059 | erot = 9.53168845128428 | epot = -127.281977581188 | etot = -102.843126171198 +73000 ekin = 16.0169617863648 | erot = 11.2607729989771 | epot = -127.583014326462 | etot = -100.30527954112 +74000 ekin = 16.2569393274987 | erot = 11.8334160482446 | epot = -127.818314339837 | etot = -99.7279589640935 +75000 ekin = 16.8670757324127 | erot = 12.4213486471541 | epot = -128.029735422439 | etot = -98.7413110428726 +76000 ekin = 17.2976336472792 | erot = 12.879667512141 | epot = -128.139997635216 | etot = -97.9626964757962 +77000 ekin = 18.9931403596589 | erot = 11.9221218276246 | epot = -128.052440626273 | etot = -97.1371784389893 +78000 ekin = 19.394659905772 | erot = 12.1596842130888 | epot = -127.76770141798 | etot = -96.2133572991196 +79000 ekin = 19.7391494083177 | erot = 12.9687576857251 | epot = -127.276778614558 | etot = -94.5688715205149 +80000 ekin = 19.3784743185415 | erot = 10.6322882254241 | epot = -126.796792973285 | etot = -96.7860304293193 +81000 ekin = 19.5852720432779 | erot = 9.69691370921807 | epot = -126.444229916257 | etot = -97.1620441637614 +82000 ekin = 19.2528014767837 | erot = 9.16533538275201 | epot = -126.419751672762 | etot = -98.0016148132264 +83000 ekin = 19.2726394261073 | erot = 10.5733782728441 | epot = -126.649102059466 | etot = -96.8030843605145 +84000 ekin = 19.4901256787956 | erot = 10.2566570330584 | epot = -126.969410464622 | etot = -97.2226277527679 +85000 ekin = 19.3717582209146 | erot = 10.2207007723129 | epot = -127.279479509792 | etot = -97.6870205165645 +86000 ekin = 20.1169646940559 | erot = 12.2331608931121 | epot = -127.669894380001 | etot = -95.3197687928331 +87000 ekin = 19.8199316335769 | erot = 12.6055320729838 | epot = -128.209799664864 | etot = -95.7843359583029 +88000 ekin = 20.1143482830516 | erot = 11.2392321140212 | epot = -129.003860885668 | etot = -97.6502804885948 +89000 ekin = 20.2912810198292 | erot = 10.3771111810482 | epot = -129.862921520447 | etot = -99.1945293195698 +90000 ekin = 21.2385708389402 | erot = 12.5546025693475 | epot = -130.937191073068 | etot = -97.1440176647801 +91000 ekin = 21.2084155909481 | erot = 14.436661012157 | epot = -132.067716247902 | etot = -96.4226396447972 +92000 ekin = 21.71873003754 | erot = 15.8603151651083 | epot = -133.245555158888 | etot = -95.6665099562398 +93000 ekin = 22.1317495382794 | erot = 15.6295367194274 | epot = -134.200273553933 | etot = -96.4389872962266 +94000 ekin = 21.949719023268 | erot = 14.6383852953061 | epot = -134.922496598838 | etot = -98.3343922802639 +95000 ekin = 21.468800110721 | erot = 15.5094419013228 | epot = -135.565235686649 | etot = -98.5869936746055 +96000 ekin = 21.0494524849867 | erot = 16.2349068795399 | epot = -136.032384853513 | etot = -98.7480254889863 +97000 ekin = 20.7022343863734 | erot = 16.3930105482435 | epot = -136.280776864423 | etot = -99.1855319298058 +98000 ekin = 20.0586507158573 | erot = 15.7422390985769 | epot = -136.24083928734 | etot = -100.439949472906 +99000 ekin = 18.9200848479137 | erot = 16.9075669037859 | epot = -136.045266794452 | etot = -100.217615042752 +100000 ekin = 17.8102741519931 | erot = 16.9898477309619 | epot = -135.820697365174 | etot = -101.020575482219 +101000 ekin = 16.7191861190764 | erot = 16.572117698704 | epot = -135.367559627769 | etot = -102.076255809988 +102000 ekin = 15.5604601147527 | erot = 18.7393309186972 | epot = -134.606463333772 | etot = -100.306672300322 +103000 ekin = 15.043766004853 | erot = 18.6887446608384 | epot = -133.629407863476 | etot = -99.8968971977843 +104000 ekin = 14.2309904924867 | erot = 16.7585227469162 | epot = -132.657529916021 | etot = -101.668016676618 +105000 ekin = 13.5307342972836 | erot = 14.2329071196199 | epot = -131.710640738879 | etot = -103.946999321976 +106000 ekin = 12.7588190389982 | erot = 12.5675515841715 | epot = -131.062722179269 | etot = -105.736351556099 +107000 ekin = 12.2848069136798 | erot = 13.8288267188167 | epot = -130.665821320327 | etot = -104.552187687831 +108000 ekin = 12.8978548254809 | erot = 14.6573820266306 | epot = -130.544172595275 | etot = -102.988935743164 +109000 ekin = 12.9066390538737 | erot = 14.2468668334229 | epot = -130.69655634357 | etot = -103.543050456274 +110000 ekin = 13.5825831993828 | erot = 12.0551466952966 | epot = -131.153439888024 | etot = -105.515709993345 +111000 ekin = 14.4468776745219 | erot = 12.4348555024264 | epot = -131.878599317061 | etot = -104.996866140112 +112000 ekin = 15.2148666281821 | erot = 12.2384602080734 | epot = -132.638387064263 | etot = -105.185060228007 +113000 ekin = 15.8160811574652 | erot = 11.0065173851632 | epot = -133.382963297375 | etot = -106.560364754746 +114000 ekin = 16.4085569951633 | erot = 12.3376379377087 | epot = -134.005415783613 | etot = -105.259220850741 +115000 ekin = 16.4020966917755 | erot = 13.1540800498664 | epot = -134.641649425681 | etot = -105.085472684039 +116000 ekin = 16.8996004253809 | erot = 13.296911620848 | epot = -135.229810156526 | etot = -105.033298110297 +117000 ekin = 17.1887029044031 | erot = 14.2289002418826 | epot = -135.754078163037 | etot = -104.336475016752 +118000 ekin = 17.5090683674025 | erot = 13.4749070837834 | epot = -136.19297997047 | etot = -105.209004519284 +119000 ekin = 19.0558350472289 | erot = 13.2667454261941 | epot = -136.458998196109 | etot = -104.136417722686 +120000 ekin = 18.9045500154951 | erot = 13.4435679533703 | epot = -136.568097306505 | etot = -104.219979337639 +121000 ekin = 19.2557939304512 | erot = 14.4339693154683 | epot = -136.569048606398 | etot = -102.879285360479 +122000 ekin = 18.8865007741635 | erot = 13.6663074510193 | epot = -136.587605250461 | etot = -104.034797025279 +123000 ekin = 18.7137166321052 | erot = 11.169333805289 | epot = -136.646720786768 | etot = -106.763670349374 +124000 ekin = 18.3218148265107 | erot = 12.3689492421929 | epot = -136.64304942624 | etot = -105.952285357536 +125000 ekin = 17.9902568889492 | erot = 10.4651260036653 | epot = -136.608097596548 | etot = -108.152714703934 +126000 ekin = 17.6810494767023 | erot = 11.2690108811725 | epot = -136.570395380905 | etot = -107.62033502303 +127000 ekin = 17.8729038850439 | erot = 11.4759215374361 | epot = -136.391207617742 | etot = -107.042382195262 +128000 ekin = 18.2989451975646 | erot = 11.8732548028112 | epot = -136.265155167301 | etot = -106.092955166925 +129000 ekin = 17.9032951218842 | erot = 11.6160534805629 | epot = -136.069640494141 | etot = -106.550291891694 +130000 ekin = 16.9045975355621 | erot = 14.9262955299882 | epot = -135.688547941966 | etot = -103.857654876415 +131000 ekin = 16.2349308565787 | erot = 16.1403468239481 | epot = -135.10681866779 | etot = -102.731540987263 +132000 ekin = 15.6332820235376 | erot = 15.0630053125927 | epot = -134.181800815943 | etot = -103.485513479812 +133000 ekin = 15.7009729678023 | erot = 14.2528271870486 | epot = -132.916499565398 | etot = -102.962699410548 +134000 ekin = 14.9315011699325 | erot = 12.4915114384226 | epot = -131.575630200091 | etot = -104.152617591736 +135000 ekin = 14.8045596171802 | erot = 12.8071231802165 | epot = -130.318367864972 | etot = -102.706685067575 +136000 ekin = 15.0986027791077 | erot = 10.3883791876898 | epot = -129.220547878708 | etot = -103.733565911911 +137000 ekin = 15.3176346759751 | erot = 10.4825340194199 | epot = -128.412442913985 | etot = -102.61227421859 +138000 ekin = 15.0740242341681 | erot = 11.4385668785644 | epot = -127.819127774961 | etot = -101.306536662228 +139000 ekin = 15.3573672627478 | erot = 10.7684531712248 | epot = -127.494497268646 | etot = -101.368676834673 +140000 ekin = 15.6199088724475 | erot = 9.04566079561385 | epot = -127.38675330942 | etot = -102.721183641359 +141000 ekin = 15.5698778978445 | erot = 9.24310378273314 | epot = -127.464223511521 | etot = -102.651241830943 +142000 ekin = 15.0115449600326 | erot = 10.0113260240699 | epot = -127.712250221221 | etot = -102.689379237119 +143000 ekin = 14.8991843032077 | erot = 9.06970244498392 | epot = -128.136878896406 | etot = -104.167992148215 +144000 ekin = 15.1898171101041 | erot = 10.8668122423024 | epot = -128.858201876452 | etot = -102.801572524046 +145000 ekin = 15.3171573114553 | erot = 12.7878827054972 | epot = -129.647569384495 | etot = -101.542529367543 +146000 ekin = 15.9413992219932 | erot = 13.4735306574188 | epot = -130.234770564237 | etot = -100.819840684825 +147000 ekin = 16.0347198576474 | erot = 15.2458163610442 | epot = -130.576336429324 | etot = -99.295800210632 +148000 ekin = 16.7791528014655 | erot = 15.4906262875814 | epot = -130.69472449657 | etot = -98.4249454075234 +149000 ekin = 16.3974490292734 | erot = 13.8758696818836 | epot = -130.734343874237 | etot = -100.46102516308 +150000 ekin = 16.0380854312512 | erot = 14.4637229471481 | epot = -130.553161201443 | etot = -100.051352823044 +151000 ekin = 15.8946438576778 | erot = 14.2701384636695 | epot = -129.365628155838 | etot = -99.2008458344912 +152000 ekin = 15.9244818270971 | erot = 15.1347805649692 | epot = -128.715889634918 | etot = -97.6566272428514 +153000 ekin = 16.1479991430796 | erot = 16.2402011023445 | epot = -129.650834574842 | etot = -97.2626343294183 +154000 ekin = 16.6917314371582 | erot = 16.451832508432 | epot = -130.087230811386 | etot = -96.9436668657962 +155000 ekin = 16.2489098122788 | erot = 17.2157917300678 | epot = -129.559076328912 | etot = -96.0943747865656 +156000 ekin = 15.8423098858465 | erot = 16.5702905283791 | epot = -128.955263004383 | etot = -96.5426625901579 +157000 ekin = 15.2853301639819 | erot = 16.1544241722267 | epot = -128.325555922222 | etot = -96.8858015860138 +158000 ekin = 15.3551884809801 | erot = 16.3192694941534 | epot = -127.806205056443 | etot = -96.1317470813092 +159000 ekin = 15.2508248933275 | erot = 17.4482804319322 | epot = -127.421417710431 | etot = -94.7223123851718 +160000 ekin = 15.1833265141526 | erot = 16.7226535455955 | epot = -127.059746301972 | etot = -95.153766242224 +161000 ekin = 14.7380410492237 | erot = 17.329552553938 | epot = -126.786115621944 | etot = -94.7185220187828 +162000 ekin = 15.0014487927904 | erot = 15.3205308979557 | epot = -126.5574162697 | etot = -96.2354365789538 +163000 ekin = 15.0312059815085 | erot = 14.803202250397 | epot = -126.515068752591 | etot = -96.6806605206855 +164000 ekin = 15.0902427307857 | erot = 13.9580872796748 | epot = -126.642563682153 | etot = -97.594233671693 +165000 ekin = 15.481282446002 | erot = 12.6743787504216 | epot = -126.905859153793 | etot = -98.750197957369 +166000 ekin = 16.0608755355545 | erot = 12.3086848707364 | epot = -127.24911338436 | etot = -98.8795529780688 +167000 ekin = 16.2282316088892 | erot = 12.6143211413337 | epot = -127.683675953027 | etot = -98.8411232028041 +168000 ekin = 16.3389435120181 | erot = 12.8827177881545 | epot = -128.23863628333 | etot = -99.0169749831576 +169000 ekin = 16.9532736782907 | erot = 11.7574256374146 | epot = -128.746548281825 | etot = -100.035848966119 +170000 ekin = 18.2540588255421 | erot = 11.4722914498663 | epot = -129.244632914848 | etot = -99.5182826394401 +171000 ekin = 19.1497515906143 | erot = 9.49869493296074 | epot = -129.744877695631 | etot = -101.096431172056 +172000 ekin = 20.0681191250966 | erot = 9.95519996138493 | epot = -130.152728743129 | etot = -100.129409656648 +173000 ekin = 20.3331863851461 | erot = 11.2046910177818 | epot = -130.438278432724 | etot = -98.9004010297965 +174000 ekin = 20.6529243059645 | erot = 11.7240396464557 | epot = -130.610859886778 | etot = -98.2338959343579 +175000 ekin = 20.7286579041432 | erot = 9.29182363661769 | epot = -130.472756798948 | etot = -100.452275258187 +176000 ekin = 19.1181096676417 | erot = 9.23346759201931 | epot = -130.161831508159 | etot = -101.810254248498 +177000 ekin = 18.6791037094626 | erot = 7.67821204772778 | epot = -129.600557171612 | etot = -103.243241414421 +178000 ekin = 18.2871156893105 | erot = 7.56184967577425 | epot = -128.974796857575 | etot = -103.125831492491 +179000 ekin = 18.043015789403 | erot = 9.37993265109908 | epot = -128.33568973733 | etot = -100.912741296828 +180000 ekin = 18.0964905790507 | erot = 9.99801977043647 | epot = -127.679401629723 | etot = -99.5848912802359 +181000 ekin = 17.0120997756123 | erot = 10.4535491853832 | epot = -127.217825960243 | etot = -99.7521769992471 +182000 ekin = 16.3473936279656 | erot = 10.761354749287 | epot = -126.905304899434 | etot = -99.7965565221812 +183000 ekin = 16.4609643727092 | erot = 10.8354988012549 | epot = -126.556207283471 | etot = -99.2597441095067 +184000 ekin = 16.0469067177505 | erot = 11.109442164242 | epot = -126.247810862301 | etot = -99.0914619803086 +185000 ekin = 15.6202500798552 | erot = 12.3669619352056 | epot = -126.096968425562 | etot = -98.109756410501 +186000 ekin = 15.1924452621001 | erot = 12.8295056259982 | epot = -125.968901879549 | etot = -97.946950991451 +187000 ekin = 14.7771944109672 | erot = 12.6493832440545 | epot = -126.106569826735 | etot = -98.6799921717135 +188000 ekin = 14.3207779227598 | erot = 13.6116854714263 | epot = -126.402203973973 | etot = -98.4697405797871 +189000 ekin = 13.385260119371 | erot = 13.8479820839096 | epot = -126.775222723285 | etot = -99.5419805200042 +190000 ekin = 13.5514846421718 | erot = 14.6728282356554 | epot = -127.365057872334 | etot = -99.140744994507 +191000 ekin = 14.2360401850254 | erot = 15.8334204771094 | epot = -127.88954605325 | etot = -97.8200853911154 +192000 ekin = 14.0394062170729 | erot = 18.6498901434561 | epot = -128.443582464875 | etot = -95.754286104346 +193000 ekin = 13.9057228894394 | erot = 18.8750739063564 | epot = -128.948119462078 | etot = -96.1673226662823 +194000 ekin = 14.1078589447328 | erot = 22.3833421748141 | epot = -129.3945413397 | etot = -92.9033402201531 +195000 ekin = 13.5757179047645 | erot = 25.2041428404574 | epot = -129.660083110115 | etot = -90.8802223648927 +196000 ekin = 13.4159639631571 | erot = 25.0155233968615 | epot = -129.591217872059 | etot = -91.1597305120399 +197000 ekin = 12.7331825620695 | erot = 23.6181766985819 | epot = -129.274693665 | etot = -92.9233344043489 +198000 ekin = 12.5238727214166 | erot = 20.6772199687304 | epot = -128.852316296547 | etot = -95.6512236064 +199000 ekin = 12.3353111593904 | erot = 18.0354427762159 | epot = -128.513210124739 | etot = -98.1424561891331 +200000 ekin = 12.3733317169889 | erot = 18.8116130335414 | epot = -128.331355786181 | etot = -97.1464110356508 +201000 ekin = 13.2940290718405 | erot = 15.9786030977858 | epot = -128.411423714828 | etot = -99.1387915452015 +202000 ekin = 13.2038790800745 | erot = 16.1428217321254 | epot = -128.572901959575 | etot = -99.2262011473754 +203000 ekin = 13.6834241382204 | erot = 14.7859534761891 | epot = -128.748093246908 | etot = -100.278715632499 +204000 ekin = 13.4726523769991 | erot = 14.9049225906812 | epot = -128.999005210395 | etot = -100.621430242714 +205000 ekin = 14.312738708907 | erot = 15.6330075134966 | epot = -129.273568080049 | etot = -99.3278218576454 +206000 ekin = 14.9985564010157 | erot = 15.2142768714429 | epot = -129.499986068484 | etot = -99.2871527960254 +207000 ekin = 15.2486951661946 | erot = 13.8132121356488 | epot = -129.843774815407 | etot = -100.781867513563 +208000 ekin = 15.5979820144755 | erot = 12.5704782835112 | epot = -129.908177320465 | etot = -101.739717022479 +209000 ekin = 15.9388640690578 | erot = 12.489018324278 | epot = -130.201081837909 | etot = -101.773199444573 +210000 ekin = 16.8762349462909 | erot = 12.7190509274418 | epot = -131.145026574916 | etot = -101.549740701184 +211000 ekin = 17.4220344404586 | erot = 12.6471677876529 | epot = -132.519387999437 | etot = -102.450185771325 +212000 ekin = 17.9158339611631 | erot = 14.2816709902002 | epot = -133.564060958952 | etot = -101.366556007588 +213000 ekin = 18.6791844656338 | erot = 14.7410608598078 | epot = -134.521756200711 | etot = -101.10151087527 +214000 ekin = 19.3123062163582 | erot = 14.0028524424837 | epot = -135.374158066027 | etot = -102.058999407186 +215000 ekin = 19.4134189144043 | erot = 13.4900891515746 | epot = -135.986326780715 | etot = -103.082818714736 +216000 ekin = 19.8944087115707 | erot = 13.4198267426885 | epot = -136.475272377482 | etot = -103.161036923223 +217000 ekin = 20.3143700135294 | erot = 14.6569915101503 | epot = -136.826129411951 | etot = -101.854767888271 +218000 ekin = 20.5260831833942 | erot = 14.3225070474492 | epot = -136.955719311893 | etot = -102.107129081049 +219000 ekin = 20.0261261099089 | erot = 14.0855117453547 | epot = -137.045898242291 | etot = -102.934260387027 +220000 ekin = 19.5772178023657 | erot = 14.8079025538451 | epot = -137.035690586438 | etot = -102.650570230227 +221000 ekin = 19.0686644538266 | erot = 15.7270830972781 | epot = -136.797883254277 | etot = -102.002135703172 +222000 ekin = 18.2092174924555 | erot = 15.4615482209608 | epot = -136.39657978212 | etot = -102.725814068703 +223000 ekin = 17.9697270507782 | erot = 16.1464066152582 | epot = -135.801551344766 | etot = -101.68541767873 +224000 ekin = 17.7178255154891 | erot = 16.0656630046494 | epot = -135.167568318264 | etot = -101.384079798125 +225000 ekin = 17.3477532062982 | erot = 16.1544999122399 | epot = -134.802495354868 | etot = -101.30024223633 +226000 ekin = 16.6517061779647 | erot = 15.1979683929058 | epot = -134.798630887109 | etot = -102.948956316239 +227000 ekin = 16.5149238351976 | erot = 13.734679973746 | epot = -135.011165815353 | etot = -104.761562006409 +228000 ekin = 16.5975136787034 | erot = 13.5550357367901 | epot = -135.44882457975 | etot = -105.296275164256 +229000 ekin = 16.4664582112495 | erot = 14.2645570036993 | epot = -135.928480049796 | etot = -105.197464834847 +230000 ekin = 16.9589676053995 | erot = 14.4619844215598 | epot = -136.29006123152 | etot = -104.86910920456 +231000 ekin = 17.444530146953 | erot = 16.5760137368524 | epot = -136.464945197664 | etot = -102.444401313858 +232000 ekin = 17.4720797716795 | erot = 13.9037237803607 | epot = -136.377600567084 | etot = -105.001797015044 +233000 ekin = 17.1305119969797 | erot = 12.9940728716144 | epot = -136.045491235421 | etot = -105.920906366826 +234000 ekin = 17.3941720895486 | erot = 12.3971971519277 | epot = -135.524764844421 | etot = -105.733395602945 +235000 ekin = 17.2222918114377 | erot = 11.1795795703929 | epot = -135.112434520214 | etot = -106.710563138383 +236000 ekin = 16.9622450999128 | erot = 11.50173508147 | epot = -134.562992360186 | etot = -106.099012178803 +237000 ekin = 16.5431140101905 | erot = 11.9685358265296 | epot = -133.810906450387 | etot = -105.299256613667 +238000 ekin = 16.5518547445294 | erot = 11.0722705438122 | epot = -133.199095342347 | etot = -105.574970054005 +239000 ekin = 16.2543912576344 | erot = 10.8806497272305 | epot = -132.982555090604 | etot = -105.847514105739 +240000 ekin = 16.0314195713285 | erot = 12.4496344754948 | epot = -133.046699057712 | etot = -104.565645010888 +241000 ekin = 16.1924009690743 | erot = 14.0898563327293 | epot = -133.406445180049 | etot = -103.124187878245 +242000 ekin = 16.3502244599483 | erot = 16.0736417497567 | epot = -133.977527530223 | etot = -101.553661320518 +243000 ekin = 15.8307360625516 | erot = 18.4098416555442 | epot = -134.768966704509 | etot = -100.528388986413 +244000 ekin = 15.5660987903881 | erot = 18.216424446668 | epot = -135.704771720512 | etot = -101.922248483456 +245000 ekin = 15.0206879832057 | erot = 18.3347125890275 | epot = -136.709866936058 | etot = -103.354466363825 +246000 ekin = 14.5983592669302 | erot = 17.2791372467644 | epot = -137.659912920669 | etot = -105.782416406974 +247000 ekin = 14.1389633248416 | erot = 17.8322351386096 | epot = -138.411568752716 | etot = -106.440370289265 +248000 ekin = 14.0556558873111 | erot = 15.6482142940717 | epot = -138.969271581399 | etot = -109.265401400016 +249000 ekin = 13.9871814152265 | erot = 15.1488259769451 | epot = -139.233103913672 | etot = -110.0970965215 +250000 ekin = 13.0889756322674 | erot = 15.0994464326628 | epot = -139.151301578144 | etot = -110.962879513214 +251000 ekin = 13.1265133320355 | erot = 15.1671673579225 | epot = -138.834287785767 | etot = -110.540607095809 +252000 ekin = 13.6807409207044 | erot = 13.5786302525258 | epot = -138.504314451182 | etot = -111.244943277952 +253000 ekin = 13.3626877424682 | erot = 15.9553236397028 | epot = -138.160123882558 | etot = -108.842112500387 +254000 ekin = 13.1819154618248 | erot = 16.8128591383959 | epot = -137.798880274068 | etot = -107.804105673847 +255000 ekin = 13.0646354839786 | erot = 17.1265318147002 | epot = -137.431415416262 | etot = -107.240248117583 +256000 ekin = 12.5455352336142 | erot = 15.0691738093945 | epot = -137.037269359459 | etot = -109.422560316451 +257000 ekin = 12.4610621922096 | erot = 15.3244442994292 | epot = -136.650137111473 | etot = -108.864630619834 +258000 ekin = 13.0934983821441 | erot = 12.7478447445714 | epot = -136.179917609462 | etot = -110.338574482747 +259000 ekin = 13.1927221115934 | erot = 12.3903494092558 | epot = -135.770628179201 | etot = -110.187556658352 +260000 ekin = 13.2941157489993 | erot = 11.22688430765 | epot = -135.451558075777 | etot = -110.930558019128 +261000 ekin = 13.3169193064141 | erot = 10.1699688960191 | epot = -135.237869432726 | etot = -111.750981230293 +262000 ekin = 14.3711228423067 | erot = 10.4503987705639 | epot = -135.113914031243 | etot = -110.292392418373 +263000 ekin = 15.1617681926543 | erot = 9.76935646696164 | epot = -135.118250431521 | etot = -110.187125771906 +264000 ekin = 15.6249686448438 | erot = 9.54663847149783 | epot = -135.300018145263 | etot = -110.128411028921 +265000 ekin = 15.7070435934641 | erot = 9.62497037452938 | epot = -135.636255277972 | etot = -110.304241309979 +266000 ekin = 15.8792704002142 | erot = 11.3471449824637 | epot = -136.133743198173 | etot = -108.907327815495 +267000 ekin = 16.9884321303562 | erot = 11.7427982683644 | epot = -136.655021558832 | etot = -107.923791160112 +268000 ekin = 17.2245327247186 | erot = 13.3186954001273 | epot = -137.191242260107 | etot = -106.648014135262 +269000 ekin = 17.6491304051601 | erot = 14.088257284035 | epot = -137.597464707406 | etot = -105.860077018211 +270000 ekin = 19.0828861152192 | erot = 13.8308394104387 | epot = -137.711801575054 | etot = -104.798076049396 +271000 ekin = 19.7133229003058 | erot = 13.0047824303646 | epot = -137.668061575719 | etot = -104.949956245049 +272000 ekin = 20.1809313158975 | erot = 13.5694407845615 | epot = -137.453986195083 | etot = -103.703614094624 +273000 ekin = 20.5379119616857 | erot = 13.896572634632 | epot = -137.108139763831 | etot = -102.673655167513 +274000 ekin = 19.6672280108431 | erot = 14.0368019105876 | epot = -136.556049686856 | etot = -102.852019765425 +275000 ekin = 19.1151518991178 | erot = 12.9713100474465 | epot = -135.942867662374 | etot = -103.85640571581 +276000 ekin = 18.9644196866248 | erot = 15.1190182514797 | epot = -135.305761696867 | etot = -101.222323758763 +277000 ekin = 18.1790415654528 | erot = 15.6915033365274 | epot = -134.686290990098 | etot = -100.815746088118 +278000 ekin = 17.2302816699807 | erot = 14.5630186482311 | epot = -134.192212791496 | etot = -102.398912473285 +279000 ekin = 16.369908562734 | erot = 13.9908783510267 | epot = -133.797540061325 | etot = -103.436753147565 +280000 ekin = 16.433782481313 | erot = 14.3147528722557 | epot = -133.452962953684 | etot = -102.704427600115 +281000 ekin = 15.8960625121675 | erot = 13.2178776330307 | epot = -133.399396244585 | etot = -104.285456099387 +282000 ekin = 15.548559273272 | erot = 12.8722007360345 | epot = -133.49732624149 | etot = -105.076566232184 +283000 ekin = 15.4150561563309 | erot = 12.3116409770538 | epot = -133.588854787054 | etot = -105.862157653669 +284000 ekin = 15.1964277060974 | erot = 13.3914179429752 | epot = -133.806054668234 | etot = -105.218209019162 +285000 ekin = 15.2489124117006 | erot = 16.4856490647835 | epot = -134.22065384738 | etot = -102.486092370896 +286000 ekin = 15.550747369737 | erot = 18.8796113679636 | epot = -134.69002569583 | etot = -100.259666958129 +287000 ekin = 14.8603292913743 | erot = 18.8135765008557 | epot = -134.998990769646 | etot = -101.325084977416 +288000 ekin = 14.9073867488869 | erot = 20.8515827516646 | epot = -135.209097506634 | etot = -99.4501280060825 +289000 ekin = 14.580042804101 | erot = 19.9269408519653 | epot = -135.262547507993 | etot = -100.755563851926 +290000 ekin = 14.2667577225128 | erot = 18.5576074022871 | epot = -135.14384414274 | etot = -102.31947901794 +291000 ekin = 14.4608493520139 | erot = 17.020989166249 | epot = -135.100140508514 | etot = -103.618301990251 +292000 ekin = 14.3512951121633 | erot = 16.4441072192349 | epot = -135.176730339777 | etot = -104.381328008378 +293000 ekin = 14.4343768380636 | erot = 15.2817002428186 | epot = -135.340148693332 | etot = -105.62407161245 +294000 ekin = 14.7414214511854 | erot = 17.4317969241924 | epot = -135.463496511849 | etot = -103.290278136471 +295000 ekin = 14.8006885026394 | erot = 15.8578506551645 | epot = -135.633228910137 | etot = -104.974689752333 +296000 ekin = 14.9509290304818 | erot = 15.0968130074849 | epot = -135.846814176395 | etot = -105.799072138428 +297000 ekin = 15.3553412489363 | erot = 16.8227270457587 | epot = -135.965779977314 | etot = -103.787711682618 +298000 ekin = 15.7861548470201 | erot = 15.4994205982361 | epot = -135.923798442612 | etot = -104.638222997356 +299000 ekin = 15.3731178851645 | erot = 14.9134030635961 | epot = -135.788540081438 | etot = -105.502019132677 +300000 ekin = 15.1591467758614 | erot = 14.913706960876 | epot = -135.541047558063 | etot = -105.468193821326 +301000 ekin = 15.1397822527051 | erot = 13.8966200648362 | epot = -135.135635625953 | etot = -106.099233308412 +302000 ekin = 15.159623148571 | erot = 14.0664742347814 | epot = -134.731648984919 | etot = -105.505551601567 +303000 ekin = 15.2175218974919 | erot = 13.4462351632379 | epot = -134.411234683939 | etot = -105.747477623209 +304000 ekin = 14.5374568169516 | erot = 11.5234287916082 | epot = -134.106892875677 | etot = -108.046007267117 +305000 ekin = 14.1500393411098 | erot = 11.9173026853239 | epot = -134.047561404168 | etot = -107.980219377735 +306000 ekin = 13.9196264051666 | erot = 11.6457724597909 | epot = -134.132883888331 | etot = -108.567485023374 +307000 ekin = 14.1005702019832 | erot = 12.5077575778325 | epot = -134.434608932883 | etot = -107.826281153068 +308000 ekin = 14.2585019936264 | erot = 15.3958591359035 | epot = -134.946476601929 | etot = -105.2921154724 +309000 ekin = 14.4850692770863 | erot = 14.9402760560304 | epot = -135.555546751183 | etot = -106.130201418066 +310000 ekin = 15.492391653303 | erot = 17.0903447047106 | epot = -136.088841261877 | etot = -103.506104903864 +311000 ekin = 15.3890643243749 | erot = 19.2610528144109 | epot = -136.416623046967 | etot = -101.766505908181 +312000 ekin = 15.2534523734811 | erot = 20.639433925015 | epot = -136.486497272686 | etot = -100.59361097419 +313000 ekin = 15.2642533521526 | erot = 19.4719026755312 | epot = -136.453193514327 | etot = -101.717037486643 +314000 ekin = 15.9088102113763 | erot = 18.1158097744565 | epot = -136.079284445116 | etot = -102.054664459283 +315000 ekin = 16.3317488039196 | erot = 17.8215548717385 | epot = -135.489614657583 | etot = -101.336310981925 +316000 ekin = 16.7127254665424 | erot = 17.0621123809074 | epot = -134.692922956559 | etot = -100.918085109109 +317000 ekin = 17.5082995775713 | erot = 15.454754479648 | epot = -133.709498409164 | etot = -100.746444351945 +318000 ekin = 17.2770894172302 | erot = 15.0009638702678 | epot = -132.809048322747 | etot = -100.530995035249 +319000 ekin = 17.3853813655136 | erot = 14.6635925801312 | epot = -131.945684244476 | etot = -99.8967102988308 +320000 ekin = 18.3081586199625 | erot = 13.8417925858814 | epot = -131.130097913125 | etot = -98.9801467072811 +321000 ekin = 18.7025012020988 | erot = 12.5254510027626 | epot = -130.554557102668 | etot = -99.3266048978071 +322000 ekin = 19.3729234492728 | erot = 14.6496801700427 | epot = -130.267637027781 | etot = -96.2450334084658 +323000 ekin = 19.305884647827 | erot = 15.108631117722 | epot = -130.280223563659 | etot = -95.86570779811 +324000 ekin = 20.1791746601352 | erot = 12.9595357297034 | epot = -130.560819572515 | etot = -97.4221091826763 +325000 ekin = 19.9229721579764 | erot = 12.6937530782134 | epot = -130.854796864401 | etot = -98.2380716282109 +326000 ekin = 20.1494557071319 | erot = 11.2055252329235 | epot = -131.031149467831 | etot = -99.6761685277753 +327000 ekin = 20.1584272008461 | erot = 12.8758025350741 | epot = -131.233681045978 | etot = -98.1994513100582 +328000 ekin = 20.2643855639433 | erot = 14.5928040377303 | epot = -131.292981088156 | etot = -96.435791486482 +329000 ekin = 20.3915092050716 | erot = 13.323391436832 | epot = -131.131824450461 | etot = -97.416923808557 +330000 ekin = 20.2912600284135 | erot = 12.8991717498625 | epot = -130.672767581113 | etot = -97.4823358028366 +331000 ekin = 18.9233901861363 | erot = 12.4977211780143 | epot = -129.925928506111 | etot = -98.5048171419608 +332000 ekin = 17.7836902793254 | erot = 14.8657125217102 | epot = -129.218240818358 | etot = -96.5688380173225 +333000 ekin = 17.2104765267529 | erot = 13.4490686449807 | epot = -128.531401145493 | etot = -97.8718559737597 +334000 ekin = 16.2590845220449 | erot = 13.9850453847657 | epot = -128.188656013223 | etot = -97.9445261064122 +335000 ekin = 15.9740258843418 | erot = 15.2587829777059 | epot = -128.194625469078 | etot = -96.9618166070303 +336000 ekin = 16.0871088550339 | erot = 15.9231026554215 | epot = -128.442662404935 | etot = -96.4324508944797 +337000 ekin = 15.4081060894536 | erot = 18.6510765846712 | epot = -129.029581276312 | etot = -94.9703986021868 +338000 ekin = 14.9084404652835 | erot = 18.5521822060606 | epot = -129.67002053088 | etot = -96.209397859536 +339000 ekin = 14.2887751325506 | erot = 18.3637986948568 | epot = -130.377076219122 | etot = -97.7245023917149 +340000 ekin = 14.8657804006019 | erot = 17.7641504172419 | epot = -131.02063068338 | etot = -98.3906998655363 +341000 ekin = 14.8960466933512 | erot = 17.2892865665249 | epot = -131.496204140598 | etot = -99.3108708807218 +342000 ekin = 15.0156852076313 | erot = 16.8226002620008 | epot = -131.849716442671 | etot = -100.011430973038 +343000 ekin = 14.829880784036 | erot = 16.2291852975375 | epot = -132.272502245046 | etot = -101.213436163473 +344000 ekin = 15.461309073626 | erot = 16.6968933814696 | epot = -132.490462225244 | etot = -100.332259770148 +345000 ekin = 16.4175355377691 | erot = 16.5679997852715 | epot = -132.518100798509 | etot = -99.5325654754687 +346000 ekin = 16.7873544963258 | erot = 13.9089222946379 | epot = -132.494362386097 | etot = -101.798085595133 +347000 ekin = 17.5341944625862 | erot = 14.8988271783669 | epot = -132.643299258145 | etot = -100.210277617192 +348000 ekin = 17.7040765279244 | erot = 16.3501560162002 | epot = -132.679901962864 | etot = -98.6256694187397 +349000 ekin = 18.6732345768778 | erot = 16.6988217905427 | epot = -132.625569643541 | etot = -97.2535132761207 +350000 ekin = 18.4130575315697 | erot = 17.096873206343 | epot = -132.463584372258 | etot = -96.9536536343456 +351000 ekin = 18.4327090823276 | erot = 15.202701456387 | epot = -132.460712631495 | etot = -98.8253020927801 +352000 ekin = 18.5786729672979 | erot = 13.1442948374853 | epot = -132.422025658642 | etot = -100.699057853859 +353000 ekin = 18.3167584321581 | erot = 13.5377327815225 | epot = -132.307592865039 | etot = -100.453101651358 +354000 ekin = 18.1047840391406 | erot = 13.5953436553486 | epot = -132.195846272543 | etot = -100.495718578054 +355000 ekin = 18.1986897792976 | erot = 13.5583564256669 | epot = -132.091108805341 | etot = -100.334062600376 +356000 ekin = 18.3907444230833 | erot = 13.2933159759753 | epot = -132.00073429578 | etot = -100.316673896722 +357000 ekin = 18.228074400546 | erot = 14.265637563401 | epot = -131.856932329748 | etot = -99.3632203658011 +358000 ekin = 18.905942614608 | erot = 16.1142874028293 | epot = -131.849628069353 | etot = -96.8293980519153 +359000 ekin = 18.8676526001794 | erot = 16.6138177795695 | epot = -131.891754625532 | etot = -96.4102842457828 +360000 ekin = 18.7099054939284 | erot = 15.3718802743092 | epot = -131.997021147589 | etot = -97.9152353793512 +361000 ekin = 18.4905666675549 | erot = 17.3995560989326 | epot = -132.031349470221 | etot = -96.1412267037338 +362000 ekin = 18.1855970132715 | erot = 17.942912738158 | epot = -132.011645615621 | etot = -95.8831358641914 +363000 ekin = 18.2338378875984 | erot = 17.7801397977108 | epot = -131.858096991963 | etot = -95.8441193066534 +364000 ekin = 17.7535711043704 | erot = 18.8250835249016 | epot = -131.66069608376 | etot = -95.0820414544875 +365000 ekin = 17.3695156905276 | erot = 17.9883441026839 | epot = -131.364026405965 | etot = -96.006166612754 +366000 ekin = 16.9850573956501 | erot = 16.6067085347191 | epot = -130.892399012665 | etot = -97.3006330822961 +367000 ekin = 15.997392244026 | erot = 14.7885107777799 | epot = -130.541890303735 | etot = -99.7559872819289 +368000 ekin = 15.8563119798033 | erot = 15.0425885910495 | epot = -130.433580819971 | etot = -99.5346802491183 +369000 ekin = 15.3277171500825 | erot = 12.7447003449411 | epot = -130.381445733827 | etot = -102.309028238804 +370000 ekin = 14.7095470896123 | erot = 13.0656296157977 | epot = -130.483012980666 | etot = -102.707836275256 +371000 ekin = 14.0759895035629 | erot = 14.1359591379551 | epot = -130.384112296464 | etot = -102.172163654946 +372000 ekin = 14.0274743219116 | erot = 11.5530950019089 | epot = -130.161328386178 | etot = -104.580759062357 +373000 ekin = 13.2735786074107 | erot = 11.7624698283845 | epot = -129.929770447592 | etot = -104.893722011797 +374000 ekin = 12.5703680081111 | erot = 14.4470952413483 | epot = -129.713420572473 | etot = -102.695957323014 +375000 ekin = 12.5023514450046 | erot = 15.8497938518021 | epot = -129.637706135675 | etot = -101.285560838869 +376000 ekin = 12.0221432627941 | erot = 17.5431672416675 | epot = -129.715548310157 | etot = -100.150237805695 +377000 ekin = 11.7237507704746 | erot = 18.4106449767234 | epot = -129.779086106179 | etot = -99.6446903589815 +378000 ekin = 11.0789972070929 | erot = 17.5195452694909 | epot = -129.895108316626 | etot = -101.296565840043 +379000 ekin = 10.791187345069 | erot = 17.2671980167644 | epot = -129.974216175833 | etot = -101.915830814 +380000 ekin = 10.3303845891398 | erot = 19.7350662610716 | epot = -129.985033641003 | etot = -99.9195827907913 +381000 ekin = 10.6501452347105 | erot = 17.9096333905339 | epot = -130.048148553028 | etot = -101.488369927783 +382000 ekin = 10.8437625928638 | erot = 19.6245357971332 | epot = -130.162960896156 | etot = -99.6946625061586 +383000 ekin = 11.3542531169641 | erot = 19.2079982598655 | epot = -130.251228617436 | etot = -99.6889772406066 +384000 ekin = 11.0272904963054 | erot = 18.6311518814503 | epot = -129.943258464192 | etot = -100.284816086437 +385000 ekin = 11.4771222018941 | erot = 17.1360629774048 | epot = -129.430781333483 | etot = -100.817596154184 +386000 ekin = 12.4376078364946 | erot = 14.6619087078055 | epot = -130.047233050888 | etot = -102.947716506588 +387000 ekin = 12.8153361806634 | erot = 15.3926488614594 | epot = -130.959137626804 | etot = -102.751152584681 +388000 ekin = 13.1378115586545 | erot = 15.8470409404985 | epot = -131.544384429979 | etot = -102.559531930826 +389000 ekin = 13.1350510873651 | erot = 15.808281971926 | epot = -132.065057931578 | etot = -103.121724872287 +390000 ekin = 13.3617719743925 | erot = 16.6918377695317 | epot = -132.580573672771 | etot = -102.526963928847 +391000 ekin = 13.5851369990731 | erot = 15.4004538175445 | epot = -133.044781890658 | etot = -104.059191074041 +392000 ekin = 13.4438982626802 | erot = 14.1857107746609 | epot = -133.309825877743 | etot = -105.680216840402 +393000 ekin = 14.3296801723329 | erot = 13.6901426487985 | epot = -133.547799958499 | etot = -105.527977137368 +394000 ekin = 14.2177717751005 | erot = 12.0786990382449 | epot = -133.641139399124 | etot = -107.344668585779 +395000 ekin = 14.0616425604673 | erot = 12.7471805398942 | epot = -133.908782967968 | etot = -107.099959867607 +396000 ekin = 14.1032172942454 | erot = 14.0283872031366 | epot = -134.074906003737 | etot = -105.943301506355 +397000 ekin = 13.8378437478735 | erot = 14.2359696883988 | epot = -134.163422059715 | etot = -106.089608623443 +398000 ekin = 13.5940545581343 | erot = 14.6507863495143 | epot = -134.074310654568 | etot = -105.82946974692 +399000 ekin = 13.3759242523696 | erot = 13.1356112226362 | epot = -133.887986258004 | etot = -107.376450782998 +400000 ekin = 13.2095793005716 | erot = 12.5790429567952 | epot = -133.576623692892 | etot = -107.788001435525 +401000 ekin = 13.0396921424937 | erot = 12.2222140410468 | epot = -133.239411997493 | etot = -107.977505813952 +402000 ekin = 12.9124676200662 | erot = 12.802771887062 | epot = -132.749760635641 | etot = -107.034521128513 +403000 ekin = 13.6179554188645 | erot = 13.0476775850248 | epot = -132.374859479026 | etot = -105.709226475137 +404000 ekin = 13.9894231701241 | erot = 12.5074913311586 | epot = -132.071111245917 | etot = -105.574196744634 +405000 ekin = 14.5489181812674 | erot = 11.634731946324 | epot = -131.925777405071 | etot = -105.742127277479 +406000 ekin = 14.976727696514 | erot = 10.9961892206581 | epot = -131.890965998628 | etot = -105.918049081456 +407000 ekin = 14.7146600327761 | erot = 11.6658057798981 | epot = -131.87989514807 | etot = -105.499429335395 +408000 ekin = 15.9530558009153 | erot = 13.4701962947535 | epot = -131.991523588142 | etot = -102.568271492473 +409000 ekin = 15.8818880911976 | erot = 14.1597558336122 | epot = -131.939714559954 | etot = -101.898070635144 +410000 ekin = 15.81619586303 | erot = 14.0248035740244 | epot = -131.84757648489 | etot = -102.006577047836 +411000 ekin = 15.9025579383179 | erot = 13.3878786896913 | epot = -131.767259935917 | etot = -102.476823307908 +412000 ekin = 16.2083664349041 | erot = 12.276906139516 | epot = -131.672975695472 | etot = -103.187703121052 +413000 ekin = 17.4022750179687 | erot = 12.5891828631102 | epot = -131.587541886629 | etot = -101.59608400555 +414000 ekin = 17.6851004318575 | erot = 11.9592267254818 | epot = -131.583004895796 | etot = -101.938677738457 +415000 ekin = 17.5336471811434 | erot = 12.8184792185166 | epot = -131.704230153421 | etot = -101.352103753761 +416000 ekin = 17.9668105672965 | erot = 13.7108633385326 | epot = -132.037460565773 | etot = -100.359786659944 +417000 ekin = 17.8399648024649 | erot = 14.2203301850684 | epot = -132.426256244686 | etot = -100.365961257153 +418000 ekin = 17.4373266510266 | erot = 15.5396524051407 | epot = -132.754253958411 | etot = -99.7772749022435 +419000 ekin = 18.0205796450897 | erot = 15.3126889659148 | epot = -133.005735986312 | etot = -99.672467375307 +420000 ekin = 18.5794007469783 | erot = 13.0784072360516 | epot = -133.261233710656 | etot = -101.603425727626 +421000 ekin = 18.4757093355527 | erot = 14.9535208579566 | epot = -133.799291639828 | etot = -100.370061446318 +422000 ekin = 19.2487771494885 | erot = 16.268026050742 | epot = -134.536311090174 | etot = -99.0195078899435 +423000 ekin = 19.710846898957 | erot = 15.0015583081186 | epot = -135.119946009976 | etot = -100.4075408029 +424000 ekin = 20.1011764905376 | erot = 13.9954970565913 | epot = -135.493941644932 | etot = -101.397268097803 +425000 ekin = 20.4927709508711 | erot = 12.7359618472531 | epot = -135.644203458846 | etot = -102.415470660721 +426000 ekin = 20.2344431180808 | erot = 12.4974029807555 | epot = -135.682241584656 | etot = -102.95039548582 +427000 ekin = 20.20892349886 | erot = 12.4896758256051 | epot = -135.651436139498 | etot = -102.952836815033 +428000 ekin = 19.7621890963077 | erot = 12.1541092473208 | epot = -135.687038886783 | etot = -103.770740543154 +429000 ekin = 19.8396272648528 | erot = 13.6427748903784 | epot = -135.721716464191 | etot = -102.23931430896 +430000 ekin = 19.1242728130447 | erot = 13.3933193323844 | epot = -135.663972003042 | etot = -103.146379857613 +431000 ekin = 19.1762831784107 | erot = 12.6020570852289 | epot = -135.522194472845 | etot = -103.743854209205 +432000 ekin = 18.2266115891595 | erot = 12.6834992627955 | epot = -135.36090839296 | etot = -104.450797541005 +433000 ekin = 18.1788501350975 | erot = 12.6590600202183 | epot = -135.284447049825 | etot = -104.446536894509 +434000 ekin = 17.720384648689 | erot = 12.2966448579521 | epot = -135.171510962613 | etot = -105.154481455972 +435000 ekin = 17.5311827306758 | erot = 13.5626215409125 | epot = -135.015208240923 | etot = -103.921403969335 +436000 ekin = 16.4711775181156 | erot = 12.8102827557078 | epot = -134.842179935764 | etot = -105.560719661941 +437000 ekin = 15.4657901044588 | erot = 10.80418591292 | epot = -134.709837955315 | etot = -108.439861937937 +438000 ekin = 15.2386769334434 | erot = 12.0324207051325 | epot = -134.707049527887 | etot = -107.435951889311 +439000 ekin = 15.0935841802307 | erot = 13.0754089066331 | epot = -134.836060039942 | etot = -106.667066953078 +440000 ekin = 14.3360038839268 | erot = 14.291563980863 | epot = -134.988119560412 | etot = -106.360551695622 +441000 ekin = 14.2694626093034 | erot = 13.1679327831247 | epot = -135.087990978588 | etot = -107.65059558616 +442000 ekin = 13.9397245181093 | erot = 13.5878148151393 | epot = -135.27763911375 | etot = -107.750099780502 +443000 ekin = 13.6891873480654 | erot = 12.7391553909139 | epot = -135.564786299035 | etot = -109.136443560056 +444000 ekin = 13.3446443464529 | erot = 13.499236365613 | epot = -135.849809317035 | etot = -109.005928604969 +445000 ekin = 13.6875995140372 | erot = 13.2030900365622 | epot = -136.086843695633 | etot = -109.196154145034 +446000 ekin = 13.7510820507316 | erot = 13.7935955897445 | epot = -136.319424424693 | etot = -108.774746784217 +447000 ekin = 13.9536756645579 | erot = 12.6323777770505 | epot = -136.507693431303 | etot = -109.921639989694 +448000 ekin = 13.827548811272 | erot = 11.285056587657 | epot = -136.608608530592 | etot = -111.496003131663 +449000 ekin = 14.9136066480825 | erot = 12.7726370410636 | epot = -136.711695112838 | etot = -109.025451423692 +450000 ekin = 15.3130329071512 | erot = 12.937348088392 | epot = -136.734120986225 | etot = -108.483739990681 +451000 ekin = 15.301302701309 | erot = 14.8417359986012 | epot = -136.867644105403 | etot = -106.724605405493 +452000 ekin = 15.3991468229934 | erot = 16.1597910131671 | epot = -136.947934830867 | etot = -105.388996994706 +453000 ekin = 15.3544337424077 | erot = 14.4343236069841 | epot = -136.960688535188 | etot = -107.171931185796 +454000 ekin = 15.9488000063485 | erot = 12.9304684614664 | epot = -136.856618010944 | etot = -107.977349543129 +455000 ekin = 15.2922715833283 | erot = 14.486121405257 | epot = -136.770277576782 | etot = -106.991884588196 +456000 ekin = 16.1315234476418 | erot = 14.4187765377405 | epot = -136.76890079148 | etot = -106.218600806097 +457000 ekin = 15.9303613769982 | erot = 13.9233688633883 | epot = -136.927755091366 | etot = -107.07402485098 +458000 ekin = 16.7129528959658 | erot = 12.4702904353342 | epot = -137.053260145678 | etot = -107.870016814378 +459000 ekin = 17.1862391955335 | erot = 12.622579403626 | epot = -137.11674220014 | etot = -107.30792360098 +460000 ekin = 16.7474694887743 | erot = 11.4402733756922 | epot = -137.064789703783 | etot = -108.877046839317 +461000 ekin = 16.3707132234329 | erot = 11.9667807483365 | epot = -136.909114896434 | etot = -108.571620924665 +462000 ekin = 16.057050749257 | erot = 11.071055260652 | epot = -136.760977151544 | etot = -109.632871141635 +463000 ekin = 15.9960445636137 | erot = 10.2608114523641 | epot = -136.645584443945 | etot = -110.388728427967 +464000 ekin = 15.9839199462213 | erot = 10.8607695443336 | epot = -136.533700257303 | etot = -109.689010766748 +465000 ekin = 16.2497389586414 | erot = 10.5313175008318 | epot = -136.422141283632 | etot = -109.641084824158 +466000 ekin = 16.4518159227467 | erot = 8.66003642684213 | epot = -136.240386445842 | etot = -111.128534096253 +467000 ekin = 16.100799974088 | erot = 8.85502090217157 | epot = -135.945676273344 | etot = -110.989855397085 +468000 ekin = 15.1757358310978 | erot = 8.75786767066468 | epot = -135.561277287738 | etot = -111.627673785976 +469000 ekin = 15.3336805141778 | erot = 10.294151576367 | epot = -135.258770009998 | etot = -109.630937919453 +470000 ekin = 15.1416986121053 | erot = 8.28861239898659 | epot = -134.943369066082 | etot = -111.51305805499 +471000 ekin = 15.0808434941798 | erot = 9.35823693722223 | epot = -134.657084844574 | etot = -110.218004413172 +472000 ekin = 14.8199031521034 | erot = 9.75538519900261 | epot = -134.368392289563 | etot = -109.793103938457 +473000 ekin = 14.4399928658261 | erot = 11.1636383462408 | epot = -134.206329135161 | etot = -108.602697923094 +474000 ekin = 14.935676186505 | erot = 12.4931115595082 | epot = -134.145148601937 | etot = -106.716360855924 +475000 ekin = 14.6384685751387 | erot = 11.0850165170751 | epot = -134.221735909125 | etot = -108.498250816911 +476000 ekin = 13.9153709379498 | erot = 12.0827855450883 | epot = -134.469586713931 | etot = -108.471430230893 +477000 ekin = 14.6563896342164 | erot = 12.0460213856471 | epot = -134.829702895449 | etot = -108.127291875586 +478000 ekin = 14.3931715088047 | erot = 14.4906569380074 | epot = -135.139673364882 | etot = -106.25584491807 +479000 ekin = 13.8400742131686 | erot = 13.8710649509623 | epot = -135.382131827147 | etot = -107.670992663016 +480000 ekin = 14.0424905732934 | erot = 14.0689887089952 | epot = -135.588748807054 | etot = -107.477269524765 +481000 ekin = 13.6170227455239 | erot = 13.1439295606646 | epot = -135.69134424373 | etot = -108.930391937541 +482000 ekin = 13.8439473766551 | erot = 14.4045116666526 | epot = -135.770512223603 | etot = -107.522053180295 +483000 ekin = 13.5424118445011 | erot = 15.2738244947149 | epot = -135.761995151043 | etot = -106.945758811827 +484000 ekin = 14.1849101922232 | erot = 15.8666757145785 | epot = -135.575970226919 | etot = -105.524384320117 +485000 ekin = 14.195940956825 | erot = 15.6114816494057 | epot = -135.39877590756 | etot = -105.591353301329 +486000 ekin = 13.9111457593459 | erot = 14.7215876222303 | epot = -135.223040470219 | etot = -106.590307088643 +487000 ekin = 12.9992191510958 | erot = 16.0593366085531 | epot = -135.161251042679 | etot = -106.10269528303 +488000 ekin = 12.6168795173545 | erot = 15.220417466404 | epot = -135.112432961673 | etot = -107.275135977914 +489000 ekin = 13.201759570014 | erot = 15.5867132105965 | epot = -135.074404157315 | etot = -106.285931376705 +490000 ekin = 13.2265885469164 | erot = 13.3100611495396 | epot = -134.568930622594 | etot = -108.032280926138 +491000 ekin = 13.5709245520791 | erot = 11.2379321911317 | epot = -133.759906399328 | etot = -108.951049656117 +492000 ekin = 15.1091749804628 | erot = 11.7194529548775 | epot = -133.655474302235 | etot = -106.826846366895 +493000 ekin = 16.2076959760405 | erot = 12.441837078746 | epot = -134.249886628433 | etot = -105.600353573647 +494000 ekin = 16.6484098740154 | erot = 10.9573285365692 | epot = -134.403715395303 | etot = -106.797976984718 +495000 ekin = 16.5025641778354 | erot = 10.3597875757963 | epot = -134.308352870214 | etot = -107.446001116582 +496000 ekin = 16.9766321377782 | erot = 9.35188747914268 | epot = -134.281373463348 | etot = -107.952853846427 +497000 ekin = 16.078651039206 | erot = 10.3949908356289 | epot = -134.223609434181 | etot = -107.749967559347 +498000 ekin = 15.6772701233096 | erot = 11.8315398449411 | epot = -134.244125085288 | etot = -106.735315117037 +499000 ekin = 15.7882815478804 | erot = 13.6372268111213 | epot = -134.289867732572 | etot = -104.86435937357 +500000 ekin = 15.6419277561492 | erot = 13.3617656571946 | epot = -134.377671866557 | etot = -105.373978453214 +501000 ekin = 15.4257894818581 | erot = 15.21161110053 | epot = -134.484904618377 | etot = -103.847504035988 +502000 ekin = 15.3486659157681 | erot = 15.4855204602635 | epot = -134.581746159061 | etot = -103.747559783029 +503000 ekin = 16.0150000243146 | erot = 15.3699470263174 | epot = -134.643201434117 | etot = -103.258254383485 +504000 ekin = 16.1490322325749 | erot = 15.6846837800625 | epot = -134.388203436914 | etot = -102.554487424276 +505000 ekin = 16.7723260928518 | erot = 14.0444994484244 | epot = -133.964626020725 | etot = -103.147800479449 +506000 ekin = 16.4475237902167 | erot = 13.5971228003138 | epot = -133.629606075219 | etot = -103.584959484689 +507000 ekin = 16.5024238998181 | erot = 12.429540490011 | epot = -133.299502045104 | etot = -104.367537655275 +508000 ekin = 16.3169089606643 | erot = 13.3198009459649 | epot = -133.005026942353 | etot = -103.368317035724 +509000 ekin = 16.6164955497601 | erot = 14.4826644625662 | epot = -132.746126116551 | etot = -101.646966104225 +510000 ekin = 16.1209406991229 | erot = 13.7477413055598 | epot = -132.592852521091 | etot = -102.724170516408 +511000 ekin = 15.6091977614599 | erot = 13.8436628675437 | epot = -132.380877927575 | etot = -102.928017298572 +512000 ekin = 15.6596479673297 | erot = 12.9299515573588 | epot = -132.048855483892 | etot = -103.459255959204 +513000 ekin = 15.6707994531395 | erot = 13.5959910505632 | epot = -131.731147580255 | etot = -102.464357076552 +514000 ekin = 15.6264137878191 | erot = 14.3727983536369 | epot = -131.520236647057 | etot = -101.521024505601 +515000 ekin = 14.4146997050622 | erot = 15.0596594316434 | epot = -131.342225044141 | etot = -101.867865907436 +516000 ekin = 14.9555651275164 | erot = 16.623536869884 | epot = -130.964505322647 | etot = -99.3854033252465 +517000 ekin = 14.8906196334375 | erot = 15.5851664164921 | epot = -130.510208206423 | etot = -100.034422156494 +518000 ekin = 14.3416366159403 | erot = 15.5365067560293 | epot = -130.130994049642 | etot = -100.252850677672 +519000 ekin = 13.7572803913558 | erot = 13.6198602780253 | epot = -129.803290384483 | etot = -102.426149715102 +520000 ekin = 13.5689181041519 | erot = 13.681926699745 | epot = -129.450948259648 | etot = -102.200103455751 +521000 ekin = 13.4082068826809 | erot = 14.1274743169116 | epot = -129.208824571097 | etot = -101.673143371504 +522000 ekin = 14.0315761677748 | erot = 14.1153864915646 | epot = -129.153644705208 | etot = -101.006682045869 +523000 ekin = 14.166597113974 | erot = 12.7207551535532 | epot = -129.405656319294 | etot = -102.518304051766 +524000 ekin = 14.8887229346385 | erot = 13.3588377354723 | epot = -129.865664477682 | etot = -101.618103807571 +525000 ekin = 14.688902281872 | erot = 14.9972172935593 | epot = -130.367047855264 | etot = -100.680928279832 +526000 ekin = 14.8363870564648 | erot = 15.4274874416849 | epot = -130.737233349362 | etot = -100.473358851212 +527000 ekin = 15.2869545670686 | erot = 16.1904831046063 | epot = -131.085990612593 | etot = -99.6085529409177 +528000 ekin = 15.2918013581306 | erot = 16.5067056449313 | epot = -131.451788517536 | etot = -99.6532815144741 +529000 ekin = 14.8678046515922 | erot = 17.291651478174 | epot = -131.723891935077 | etot = -99.5644358053108 +530000 ekin = 15.2573279172882 | erot = 20.5735211144431 | epot = -131.892883532099 | etot = -96.0620345003679 +531000 ekin = 15.6180440994647 | erot = 20.3297963054759 | epot = -132.105039828192 | etot = -96.157199423251 +532000 ekin = 15.7576388597626 | erot = 19.385030015024 | epot = -132.470818857238 | etot = -97.3281499824516 +533000 ekin = 15.8706341627548 | erot = 18.6066906708007 | epot = -132.905264850299 | etot = -98.4279400167437 +534000 ekin = 15.3696535565231 | erot = 20.3101666824023 | epot = -133.506233176794 | etot = -97.8264129378684 +535000 ekin = 15.2002473385359 | erot = 20.7831933548962 | epot = -134.11565174357 | etot = -98.1322110501384 +536000 ekin = 15.1615571330119 | erot = 20.1952257505014 | epot = -134.713251892966 | etot = -99.3564690094531 +537000 ekin = 14.9999277554404 | erot = 20.8390703164538 | epot = -135.462424885782 | etot = -99.6234268138877 +538000 ekin = 15.2115436578884 | erot = 22.3424857038856 | epot = -136.279383530687 | etot = -98.7253541689125 +539000 ekin = 15.386866594686 | erot = 22.69624463026 | epot = -136.979522583157 | etot = -98.8964113582114 +540000 ekin = 14.9545130224662 | erot = 22.6718649747582 | epot = -136.975604226613 | etot = -99.3492262293885 +541000 ekin = 14.7052299608299 | erot = 20.8759766501206 | epot = -136.170699327884 | etot = -100.589492716934 +542000 ekin = 15.4627037134851 | erot = 18.9043634730505 | epot = -136.392086463158 | etot = -102.025019276622 +543000 ekin = 15.7339524861005 | erot = 18.278149011262 | epot = -137.617204947251 | etot = -103.605103449888 +544000 ekin = 16.4706711523584 | erot = 16.4296713716256 | epot = -138.254480342312 | etot = -105.354137818328 +545000 ekin = 16.5610113459295 | erot = 17.2785208493854 | epot = -138.339071018101 | etot = -104.499538822786 +546000 ekin = 16.5789197609368 | erot = 15.1504740634871 | epot = -138.313871915051 | etot = -106.584478090627 +547000 ekin = 16.7878570141239 | erot = 14.7267570932877 | epot = -138.142446983588 | etot = -106.627832876176 +548000 ekin = 16.6455858796663 | erot = 16.6956992651407 | epot = -137.853579013093 | etot = -104.512293868286 +549000 ekin = 16.4197155196691 | erot = 16.1951837028797 | epot = -137.47646138011 | etot = -104.861562157561 +550000 ekin = 16.0121780135926 | erot = 16.5563179618333 | epot = -137.001885168841 | etot = -104.433389193415 +551000 ekin = 15.7084668677551 | erot = 16.9496657427157 | epot = -136.432267850723 | etot = -103.774135240252 +552000 ekin = 15.8326822462472 | erot = 17.1645099805633 | epot = -135.769947950372 | etot = -102.772755723561 +553000 ekin = 15.5762449855294 | erot = 14.9351507169072 | epot = -134.949512056203 | etot = -104.438116353766 +554000 ekin = 15.2061720137279 | erot = 14.6141329679615 | epot = -134.235489211813 | etot = -104.415184230123 +555000 ekin = 14.8324273580499 | erot = 14.4249898884469 | epot = -133.547214238345 | etot = -104.289796991849 +556000 ekin = 14.5316030200092 | erot = 14.6505308104098 | epot = -132.899169936009 | etot = -103.71703610559 +557000 ekin = 14.0459856506802 | erot = 14.0161608645567 | epot = -132.386383041322 | etot = -104.324236526085 +558000 ekin = 13.7020140248454 | erot = 14.782028582676 | epot = -131.910334835384 | etot = -103.426292227863 +559000 ekin = 13.7432172213168 | erot = 14.5379288254006 | epot = -131.411435046497 | etot = -103.130288999779 +560000 ekin = 13.5764218212111 | erot = 13.2381632256738 | epot = -130.994489577413 | etot = -104.179904530529 +561000 ekin = 13.6694726081568 | erot = 12.6384801319582 | epot = -130.581065186663 | etot = -104.273112446548 +562000 ekin = 13.0725079305121 | erot = 14.7244789763498 | epot = -130.498504712296 | etot = -102.701517805434 +563000 ekin = 13.4441169709271 | erot = 14.3755753345078 | epot = -130.583300492981 | etot = -102.763608187546 +564000 ekin = 14.3355089861334 | erot = 13.3790453196086 | epot = -130.804412145375 | etot = -103.089857839633 +565000 ekin = 14.6463307763696 | erot = 13.5486951094224 | epot = -131.204065969761 | etot = -103.009040083968 +566000 ekin = 14.3164808224567 | erot = 13.1814841428168 | epot = -131.597877349356 | etot = -104.099912384082 +567000 ekin = 14.5801374605908 | erot = 12.6017253683148 | epot = -131.986438794862 | etot = -104.804575965956 +568000 ekin = 14.4596416689885 | erot = 13.0421302262916 | epot = -132.231847146029 | etot = -104.730075250749 +569000 ekin = 14.393036553157 | erot = 12.5269341604941 | epot = -132.421675425711 | etot = -105.50170471206 +570000 ekin = 13.7030235038524 | erot = 12.2078817020517 | epot = -132.56865427436 | etot = -106.657749068456 +571000 ekin = 14.1650035664346 | erot = 12.2664973696732 | epot = -132.662283950982 | etot = -106.230783014874 +572000 ekin = 13.80817038309 | erot = 15.4383237311916 | epot = -132.642462945806 | etot = -103.395968831524 +573000 ekin = 13.7312113229557 | erot = 13.7697915123458 | epot = -132.501933226632 | etot = -105.00093039133 +574000 ekin = 13.2327575645112 | erot = 13.9844401957313 | epot = -132.336703603402 | etot = -105.11950584316 +575000 ekin = 13.8802071791623 | erot = 12.7631149758893 | epot = -132.105424543308 | etot = -105.462102388256 +576000 ekin = 14.2841183967677 | erot = 12.8966359591139 | epot = -131.811456667571 | etot = -104.63070231169 +577000 ekin = 13.955392583855 | erot = 11.5459823908892 | epot = -131.541549476664 | etot = -106.04017450192 +578000 ekin = 12.9003719500766 | erot = 11.5907900539213 | epot = -131.283674188775 | etot = -106.792512184777 +579000 ekin = 12.5310866104434 | erot = 11.5216820056368 | epot = -130.98539489617 | etot = -106.932626280089 +580000 ekin = 11.8973995685346 | erot = 11.6553088676291 | epot = -130.646310809283 | etot = -107.093602373119 +581000 ekin = 11.7065186885648 | erot = 11.869388389168 | epot = -130.358427822785 | etot = -106.782520745052 +582000 ekin = 11.0914180718352 | erot = 11.3567488184505 | epot = -130.22758086689 | etot = -107.779413976605 +583000 ekin = 10.2506360999176 | erot = 11.7568857204028 | epot = -130.336040517298 | etot = -108.328518696977 +584000 ekin = 10.1601197978661 | erot = 10.9760836192065 | epot = -130.620163191849 | etot = -109.483959774776 +585000 ekin = 10.4034716853605 | erot = 12.1580330986388 | epot = -131.093630730313 | etot = -108.532125946314 +586000 ekin = 10.3456966546715 | erot = 10.9642773747521 | epot = -131.662529259606 | etot = -110.352555230183 +587000 ekin = 10.1101055033411 | erot = 12.2604221492255 | epot = -132.202061141041 | etot = -109.831533488475 +588000 ekin = 10.8550854785802 | erot = 12.1180835063843 | epot = -132.721338026939 | etot = -109.748169041974 +589000 ekin = 10.4838288102523 | erot = 12.4652186764336 | epot = -133.094533075413 | etot = -110.145485588727 +590000 ekin = 10.2708605727086 | erot = 12.0832199140329 | epot = -133.373241152813 | etot = -111.019160666072 +591000 ekin = 10.5461874611445 | erot = 13.1100448360533 | epot = -133.560319943383 | etot = -109.904087646185 +592000 ekin = 10.3683190472224 | erot = 13.8143658675337 | epot = -133.721970598625 | etot = -109.539285683869 +593000 ekin = 10.3963603270053 | erot = 14.0225276294655 | epot = -133.713364164402 | etot = -109.294476207931 +594000 ekin = 10.3885184551674 | erot = 11.8366624994157 | epot = -133.432214935383 | etot = -111.207033980799 +595000 ekin = 10.8901100347939 | erot = 12.7293674296796 | epot = -133.490144522074 | etot = -109.870667057601 +596000 ekin = 11.2395722555263 | erot = 13.2248327342833 | epot = -133.796673156416 | etot = -109.332268166606 +597000 ekin = 11.0753436447356 | erot = 13.2536125837525 | epot = -133.948486901648 | etot = -109.619530673159 +598000 ekin = 11.3295624496026 | erot = 14.4195031759415 | epot = -133.954880324906 | etot = -108.205814699362 +599000 ekin = 11.331046112778 | erot = 15.4881855975619 | epot = -134.083362573079 | etot = -107.264130862739 +600000 ekin = 11.787907714726 | erot = 16.2359247840996 | epot = -134.420698276021 | etot = -106.396865777195 +601000 ekin = 11.0674547947287 | erot = 17.1991417694205 | epot = -134.739702452331 | etot = -106.473105888182 +602000 ekin = 11.0658520666972 | erot = 17.8370750074243 | epot = -135.079186592698 | etot = -106.176259518577 +603000 ekin = 11.123025232225 | erot = 16.6582984609292 | epot = -135.353147132872 | etot = -107.571823439718 +604000 ekin = 11.0624256310746 | erot = 17.669693596944 | epot = -135.471225799491 | etot = -106.739106571472 +605000 ekin = 11.3655531984221 | erot = 16.8851075345015 | epot = -135.342771432833 | etot = -107.092110699909 +606000 ekin = 11.790361471117 | erot = 14.5486847318163 | epot = -134.887938817663 | etot = -108.54889261473 +607000 ekin = 11.9947476941859 | erot = 14.6413174773056 | epot = -134.171826699456 | etot = -107.535761527964 +608000 ekin = 12.6872570248572 | erot = 13.7892560118068 | epot = -133.234735764685 | etot = -106.758222728021 +609000 ekin = 12.2978389537806 | erot = 12.6216102709477 | epot = -132.338952096986 | etot = -107.419502872258 +610000 ekin = 12.9319596688048 | erot = 12.8528160105898 | epot = -131.595816421921 | etot = -105.811040742526 +611000 ekin = 13.403950451031 | erot = 14.5703491939065 | epot = -131.024347032422 | etot = -103.050047387485 +612000 ekin = 13.921720677335 | erot = 14.5312432623672 | epot = -130.66128472498 | etot = -102.208320785278 +613000 ekin = 14.8335676341184 | erot = 12.1892650746368 | epot = -130.57911763963 | etot = -103.556284930875 +614000 ekin = 15.6973748522454 | erot = 10.612671055615 | epot = -130.733946081241 | etot = -104.423900173381 +615000 ekin = 16.5193269330944 | erot = 10.4111060862413 | epot = -131.257652843502 | etot = -104.327219824166 +616000 ekin = 17.4182254801146 | erot = 10.6241298247176 | epot = -131.879015462748 | etot = -103.836660157916 +617000 ekin = 18.8060108860562 | erot = 10.6269464192339 | epot = -132.516170710368 | etot = -103.083213405078 +618000 ekin = 19.7521663009964 | erot = 11.7065011338251 | epot = -133.037629576903 | etot = -101.578962142082 +619000 ekin = 20.7319417879726 | erot = 10.5260631750347 | epot = -133.415676264291 | etot = -102.157671301284 +620000 ekin = 20.806112241773 | erot = 11.2973621819735 | epot = -133.777756947299 | etot = -101.674282523553 +621000 ekin = 21.5639010876462 | erot = 11.8815197873692 | epot = -134.077776891501 | etot = -100.632356016486 +622000 ekin = 21.3689926748465 | erot = 10.4000956440602 | epot = -134.021288449876 | etot = -102.25220013097 +623000 ekin = 21.6413407887715 | erot = 10.2158203320462 | epot = -133.796628671815 | etot = -101.939467550998 +624000 ekin = 21.8076351837845 | erot = 10.1265152484649 | epot = -133.459085422801 | etot = -101.524934990551 +625000 ekin = 21.5096831710928 | erot = 9.17825774554449 | epot = -133.038125310673 | etot = -102.350184394036 +626000 ekin = 21.0176216446481 | erot = 8.97744992051248 | epot = -132.607623817873 | etot = -102.612552252713 +627000 ekin = 20.8788365359662 | erot = 9.87058291961609 | epot = -132.164577569461 | etot = -101.415158113879 +628000 ekin = 20.2034168939666 | erot = 10.4444442872214 | epot = -131.678338536356 | etot = -101.030477355168 +629000 ekin = 19.3064563629411 | erot = 10.2499650498306 | epot = -131.144652768321 | etot = -101.58823135555 +630000 ekin = 19.0283822665889 | erot = 11.4607176277001 | epot = -130.715631612411 | etot = -100.226531718122 +631000 ekin = 18.853928236171 | erot = 11.6825333882764 | epot = -130.198991821501 | etot = -99.6625301970532 +632000 ekin = 18.7638574657448 | erot = 11.7839211128261 | epot = -129.872523807162 | etot = -99.3247452285915 +633000 ekin = 19.1642923397429 | erot = 11.9682159332104 | epot = -129.641992518844 | etot = -98.5094842458908 +634000 ekin = 19.011902271626 | erot = 11.9959688493353 | epot = -129.402075848754 | etot = -98.3942047277926 +635000 ekin = 18.4542360070819 | erot = 10.3492575604963 | epot = -129.096467560285 | etot = -100.292973992707 +636000 ekin = 17.4532790638245 | erot = 11.0635840815128 | epot = -128.911926960293 | etot = -100.395063814956 +637000 ekin = 17.3697707632952 | erot = 11.8426124617262 | epot = -128.885602395439 | etot = -99.6732191704177 +638000 ekin = 17.8124685503002 | erot = 15.0406823494439 | epot = -128.862699862875 | etot = -96.0095489631308 +639000 ekin = 16.8245330169191 | erot = 15.3819182323387 | epot = -128.707243154464 | etot = -96.5007919052067 +640000 ekin = 17.1487785956868 | erot = 16.1921496722363 | epot = -128.479723988268 | etot = -95.1387957203447 +641000 ekin = 17.632304741787 | erot = 14.5156274009652 | epot = -128.247653925063 | etot = -96.0997217823104 +642000 ekin = 17.6377005136293 | erot = 14.8918647023334 | epot = -127.7222158562 | etot = -95.1926506402372 +643000 ekin = 17.5995374741385 | erot = 13.0483903667298 | epot = -127.475347763399 | etot = -96.8274199225309 +644000 ekin = 17.2764214454808 | erot = 13.4322078016665 | epot = -127.50241310641 | etot = -96.7937838592628 +645000 ekin = 17.6329098614701 | erot = 14.8201317624595 | epot = -127.370024239851 | etot = -94.9169826159211 +646000 ekin = 17.3427098437108 | erot = 13.7780394339763 | epot = -127.073196149197 | etot = -95.9524468715101 +647000 ekin = 17.3595786850669 | erot = 13.9873874432287 | epot = -126.772558544259 | etot = -95.4255924159632 +648000 ekin = 17.0611431890051 | erot = 13.0626442863658 | epot = -126.584048857572 | etot = -96.4602613822013 +649000 ekin = 16.7266328806953 | erot = 11.9283675008885 | epot = -126.556686003538 | etot = -97.9016856219541 +650000 ekin = 16.6456727674167 | erot = 12.2570663207293 | epot = -126.548172209526 | etot = -97.6454331213801 +651000 ekin = 16.9002856731565 | erot = 13.3933098195866 | epot = -126.720400236418 | etot = -96.4268047436752 +652000 ekin = 16.7932763933177 | erot = 14.7033800305508 | epot = -127.049483045287 | etot = -95.5528266214182 +653000 ekin = 17.7647934818536 | erot = 13.8375007670746 | epot = -127.392270209636 | etot = -95.789975960708 +654000 ekin = 17.209316171397 | erot = 14.2007953575714 | epot = -127.56913405221 | etot = -96.159022523242 +655000 ekin = 17.6084053546657 | erot = 13.9941896781433 | epot = -127.645735987679 | etot = -96.0431409548704 +656000 ekin = 17.2654955511365 | erot = 14.2668455216441 | epot = -127.748066013247 | etot = -96.2157249404664 +657000 ekin = 16.5710486898344 | erot = 14.8882862137457 | epot = -127.842117997841 | etot = -96.3827830942608 +658000 ekin = 16.5743027081066 | erot = 15.6308833553704 | epot = -127.848455858139 | etot = -95.6432697946622 +659000 ekin = 15.8266958160284 | erot = 16.4254782065586 | epot = -127.71822851761 | etot = -95.4660544950226 +660000 ekin = 15.3112771903098 | erot = 15.6235881574271 | epot = -127.557942038109 | etot = -96.6230766903721 +661000 ekin = 15.8077883257459 | erot = 15.6666313122459 | epot = -127.508168696619 | etot = -96.0337490586269 +662000 ekin = 15.3802586792991 | erot = 15.337973703448 | epot = -127.419047017781 | etot = -96.700814635034 +663000 ekin = 14.8214266320984 | erot = 14.2399068140589 | epot = -127.519931099912 | etot = -98.4585976537543 +664000 ekin = 14.9926156053738 | erot = 13.1516722159445 | epot = -127.751223811833 | etot = -99.6069359905142 +665000 ekin = 14.5355886254308 | erot = 14.4330045828586 | epot = -127.860821729608 | etot = -98.8922285213183 +666000 ekin = 13.993202155639 | erot = 15.5478123878428 | epot = -127.957098605449 | etot = -98.4160840619675 +667000 ekin = 13.8245326045681 | erot = 15.3532694542223 | epot = -128.10704925619 | etot = -98.9292471973995 +668000 ekin = 14.0604782799456 | erot = 14.4332737800123 | epot = -128.176648458561 | etot = -99.6828963986028 +669000 ekin = 13.7787536594503 | erot = 13.9395856557243 | epot = -128.348271613639 | etot = -100.629932298465 +670000 ekin = 14.2424674257766 | erot = 14.5981257177606 | epot = -128.431794917609 | etot = -99.5912017740719 +671000 ekin = 14.387062989952 | erot = 15.5143125489868 | epot = -128.778242221573 | etot = -98.876866682634 +672000 ekin = 15.2473568542792 | erot = 15.2152626056923 | epot = -129.394110943278 | etot = -98.931491483307 +673000 ekin = 15.5056041088206 | erot = 17.2342681078165 | epot = -130.048159647237 | etot = -97.3082874305997 +674000 ekin = 16.3082128970751 | erot = 16.8038738415255 | epot = -130.669452416793 | etot = -97.5573656781928 +675000 ekin = 17.3496022950423 | erot = 14.099213708718 | epot = -131.146386881476 | etot = -99.6975708777154 +676000 ekin = 17.4855817054841 | erot = 13.6259419730735 | epot = -131.573074528302 | etot = -100.461550849744 +677000 ekin = 17.9773747000129 | erot = 13.2884946897501 | epot = -131.905198606277 | etot = -100.639329216514 +678000 ekin = 18.756104779453 | erot = 11.5097220147452 | epot = -132.009951932527 | etot = -101.744125138329 +679000 ekin = 19.6534720398864 | erot = 12.5636470497439 | epot = -131.955300256185 | etot = -99.738181166555 +680000 ekin = 20.1148588822356 | erot = 11.9869019758845 | epot = -131.765794686934 | etot = -99.6640338288138 +681000 ekin = 20.6125173098223 | erot = 11.3275556925411 | epot = -131.422403214398 | etot = -99.4823302120342 +682000 ekin = 20.1612020041995 | erot = 10.25296966302 | epot = -130.85139674089 | etot = -100.437225073671 +683000 ekin = 20.4206920530109 | erot = 11.0282007623623 | epot = -130.068105322083 | etot = -98.6192125067094 +684000 ekin = 20.05862830642 | erot = 10.6196531732859 | epot = -129.017037414534 | etot = -98.3387559348276 +685000 ekin = 20.0501427662243 | erot = 9.32187952123111 | epot = -127.900190622709 | etot = -98.5281683352532 +686000 ekin = 19.6532740905757 | erot = 8.65222158893636 | epot = -126.80071547898 | etot = -98.4952197994682 +687000 ekin = 19.6071118679399 | erot = 6.25822222115198 | epot = -125.750923597613 | etot = -99.8855895085213 +688000 ekin = 18.6107517889504 | erot = 6.89943216928201 | epot = -124.767749264565 | etot = -99.2575653063329 +689000 ekin = 17.786165697441 | erot = 7.34415317404528 | epot = -123.934925934202 | etot = -98.804607062716 +690000 ekin = 17.2137917120142 | erot = 6.85316361120009 | epot = -123.304074630627 | etot = -99.2371193074124 +691000 ekin = 17.009061300303 | erot = 8.04723455588605 | epot = -122.926862515605 | etot = -97.8705666594159 +692000 ekin = 16.8427529291393 | erot = 9.64210590522718 | epot = -122.715486115409 | etot = -96.2306272810422 +693000 ekin = 16.6030310253516 | erot = 10.4924589289819 | epot = -122.768020487027 | etot = -95.6725305326935 +694000 ekin = 16.3048528654834 | erot = 12.4471190740222 | epot = -123.022286253553 | etot = -94.270314314047 +695000 ekin = 15.339802993942 | erot = 12.8071087066075 | epot = -123.319286176581 | etot = -95.1723744760314 +696000 ekin = 14.9987332166208 | erot = 15.2635629143938 | epot = -123.644497776405 | etot = -93.3822016453903 +697000 ekin = 14.940762697799 | erot = 14.9244275674713 | epot = -123.960109795361 | etot = -94.0949195300911 +698000 ekin = 14.0997549981025 | erot = 15.7381881754958 | epot = -124.107312815591 | etot = -94.2693696419927 +699000 ekin = 13.7943337632395 | erot = 16.0170549498387 | epot = -123.991134657769 | etot = -94.1797459446904 +700000 ekin = 12.8063636607364 | erot = 12.680481544518 | epot = -123.85162587337 | etot = -98.3647806681157 +701000 ekin = 12.8612106473772 | erot = 12.9911896973119 | epot = -123.747249168771 | etot = -97.8948488240819 +702000 ekin = 12.5373972410767 | erot = 12.6276758774894 | epot = -123.640580341737 | etot = -98.4755072231712 +703000 ekin = 12.6072489563843 | erot = 12.5468539742673 | epot = -123.699321244085 | etot = -98.545218313433 +704000 ekin = 12.6734208156719 | erot = 12.5270514569359 | epot = -123.756584691502 | etot = -98.5561124188939 +705000 ekin = 12.8445978291383 | erot = 12.750222980517 | epot = -123.976213049728 | etot = -98.3813922400731 +706000 ekin = 12.8449829535686 | erot = 13.5171315458091 | epot = -124.316370759914 | etot = -97.9542562605358 +707000 ekin = 12.8620546770194 | erot = 15.0519067703314 | epot = -124.917435471422 | etot = -97.0034740240716 +708000 ekin = 12.9796643069234 | erot = 14.8620447269899 | epot = -125.502317311951 | etot = -97.6606082780378 +709000 ekin = 13.4425028573336 | erot = 15.9332647617992 | epot = -126.272781545451 | etot = -96.8970139263186 +710000 ekin = 13.1547552000127 | erot = 17.8834151113392 | epot = -127.033117464091 | etot = -95.9949471527395 +711000 ekin = 13.4874377372487 | erot = 16.0607910461807 | epot = -127.504754023023 | etot = -97.9565252395938 +712000 ekin = 13.7924126544431 | erot = 15.2920613726707 | epot = -127.815103299365 | etot = -98.7306292722512 +713000 ekin = 13.9907440471021 | erot = 15.8322143325442 | epot = -128.080408121937 | etot = -98.2574497422907 +714000 ekin = 14.6731230864015 | erot = 14.6744003398262 | epot = -128.139315876289 | etot = -98.7917924500613 +715000 ekin = 14.9866978807952 | erot = 14.2251786521101 | epot = -127.99112794836 | etot = -98.7792514154548 +716000 ekin = 15.3347364297118 | erot = 15.1475300811861 | epot = -127.845332694351 | etot = -97.3630661834535 +717000 ekin = 15.7619963336696 | erot = 14.1476757849327 | epot = -127.888362278856 | etot = -97.9786901602535 +718000 ekin = 16.0048893455512 | erot = 15.6262184360819 | epot = -128.122619123465 | etot = -96.4915113418323 +719000 ekin = 16.6349193746809 | erot = 15.1484323248786 | epot = -128.272096588204 | etot = -96.4887448886448 +720000 ekin = 16.0143934659125 | erot = 14.5414311757607 | epot = -128.480047240563 | etot = -97.9242225988903 +721000 ekin = 15.8386507266873 | erot = 14.9433149722159 | epot = -128.906317156562 | etot = -98.1243514576583 +722000 ekin = 15.7282032498829 | erot = 15.9023039697213 | epot = -129.341717518457 | etot = -97.7112102988526 +723000 ekin = 15.731880435534 | erot = 17.749192011007 | epot = -129.777579686607 | etot = -96.2965072400656 +724000 ekin = 15.427042918024 | erot = 16.4686399920709 | epot = -130.116589837276 | etot = -98.2209069271809 +725000 ekin = 15.5672329831503 | erot = 16.0722969231333 | epot = -130.474940539864 | etot = -98.8354106335801 +726000 ekin = 16.1328135687716 | erot = 15.7741216094127 | epot = -130.724853139716 | etot = -98.8179179615313 +727000 ekin = 15.6837398672645 | erot = 16.6270161118848 | epot = -130.86237501229 | etot = -98.5516190331405 +728000 ekin = 14.6858065335577 | erot = 17.7598917766687 | epot = -130.772258770392 | etot = -98.3265604601657 +729000 ekin = 14.9842824776698 | erot = 17.3304276406768 | epot = -130.51834477387 | etot = -98.2036346555234 +730000 ekin = 14.9986618380551 | erot = 16.977161143267 | epot = -130.349888473804 | etot = -98.3740654924819 +731000 ekin = 15.072419946482 | erot = 15.5025002987448 | epot = -130.313937515373 | etot = -99.7390172701463 +732000 ekin = 15.0409370451248 | erot = 16.2573442357521 | epot = -130.274919889256 | etot = -98.9766386083787 +733000 ekin = 15.6185311878005 | erot = 15.0146206472834 | epot = -130.180741386029 | etot = -99.5475895509451 +734000 ekin = 15.7749636780031 | erot = 16.2756923502233 | epot = -130.196950898771 | etot = -98.1462948705443 +735000 ekin = 16.044115826757 | erot = 18.3259275272639 | epot = -130.085814501036 | etot = -95.7157711470153 +736000 ekin = 16.2339951070393 | erot = 16.3221994127835 | epot = -130.005795136695 | etot = -97.4496006168719 +737000 ekin = 16.4642106151448 | erot = 15.5915334244816 | epot = -129.968543990814 | etot = -97.9127999511879 +738000 ekin = 17.7474567806986 | erot = 13.3846078157141 | epot = -130.065858513805 | etot = -98.9337939173927 +739000 ekin = 18.2743829557154 | erot = 12.4537693748626 | epot = -130.333016566357 | etot = -99.6048642357788 +740000 ekin = 19.5421159739048 | erot = 13.9198719736109 | epot = -130.741176612734 | etot = -97.279188665218 +741000 ekin = 20.0405631999331 | erot = 13.8151974831221 | epot = -131.114870812315 | etot = -97.2591101292603 +742000 ekin = 20.1818484809558 | erot = 13.397127844109 | epot = -131.504055759369 | etot = -97.9250794343039 +743000 ekin = 20.0007073391441 | erot = 12.6273491140328 | epot = -132.076033929977 | etot = -99.4479774768002 +744000 ekin = 20.6160415767284 | erot = 13.5049314394245 | epot = -132.559227691432 | etot = -98.4382546752792 +745000 ekin = 20.944556948979 | erot = 13.0220816885235 | epot = -132.956762159222 | etot = -98.9901235217199 +746000 ekin = 21.6545317174542 | erot = 13.685648829312 | epot = -133.287520475787 | etot = -97.9473399290209 +747000 ekin = 21.8754679889551 | erot = 13.1649764213831 | epot = -133.499334676271 | etot = -98.4588902659332 +748000 ekin = 20.9798296230572 | erot = 14.3677983877726 | epot = -133.697635079704 | etot = -98.3500070688744 +749000 ekin = 21.2941195504557 | erot = 12.2988241905264 | epot = -133.964567395955 | etot = -100.371623654973 +750000 ekin = 20.8791041785629 | erot = 12.653626434287 | epot = -134.294471152444 | etot = -100.761740539594 +751000 ekin = 21.0339776589627 | erot = 12.9333552750725 | epot = -134.603899040048 | etot = -100.636566106013 +752000 ekin = 21.0774807924274 | erot = 12.7418232022087 | epot = -134.857220864973 | etot = -101.037916870337 +753000 ekin = 21.1546021542847 | erot = 11.3522599642878 | epot = -135.227146596956 | etot = -102.720284478383 +754000 ekin = 20.5989298905737 | erot = 11.1611855235251 | epot = -135.609613516534 | etot = -103.849498102435 +755000 ekin = 20.3529899217498 | erot = 10.721023454402 | epot = -135.85498251637 | etot = -104.780969140219 +756000 ekin = 19.9366508667302 | erot = 11.8706717129902 | epot = -135.957321057682 | etot = -104.149998477962 +757000 ekin = 19.4492537888836 | erot = 13.3040371984666 | epot = -136.055534015096 | etot = -103.302243027746 +758000 ekin = 18.870441602617 | erot = 13.940907005559 | epot = -135.932113520107 | etot = -103.120764911931 +759000 ekin = 18.4381079682431 | erot = 17.3593158119301 | epot = -135.430914119115 | etot = -99.6334903389415 +760000 ekin = 18.6535478425871 | erot = 16.3778024131385 | epot = -134.384013538437 | etot = -99.3526632827115 +761000 ekin = 18.0084310402216 | erot = 15.1920476092574 | epot = -132.912547865729 | etot = -99.7120692162498 +762000 ekin = 16.6250024488483 | erot = 14.6931539795508 | epot = -131.231500252283 | etot = -99.9133438238835 +763000 ekin = 15.9176228846105 | erot = 14.1239676637626 | epot = -129.548148653073 | etot = -99.5065581046994 +764000 ekin = 14.6501966418504 | erot = 13.2622214975588 | epot = -127.8921214723 | etot = -99.9797033328911 +765000 ekin = 13.9564269642774 | erot = 13.0613675990511 | epot = -126.543459959695 | etot = -99.525665396366 +766000 ekin = 13.6966651105155 | erot = 13.7626226983998 | epot = -125.41601449072 | etot = -97.9567266818045 +767000 ekin = 13.0978987393861 | erot = 12.1472706916983 | epot = -124.506389593956 | etot = -99.2612201628716 +768000 ekin = 12.4142543061902 | erot = 13.4245758119772 | epot = -123.786612364054 | etot = -97.9477822458871 +769000 ekin = 12.289582250433 | erot = 14.4568180345425 | epot = -123.42169845901 | etot = -96.6752981740347 +770000 ekin = 11.9859942037679 | erot = 14.6546247707137 | epot = -123.397779734471 | etot = -96.7571607599892 +771000 ekin = 11.8475710151106 | erot = 14.8012891749296 | epot = -123.869190330419 | etot = -97.220330140379 +772000 ekin = 11.7359793659099 | erot = 16.5883752490396 | epot = -124.768006930615 | etot = -96.4436523156657 +773000 ekin = 12.0733307671956 | erot = 16.5674235924411 | epot = -125.8522838928 | etot = -97.2115295331635 +774000 ekin = 12.5912612730351 | erot = 17.7892613421319 | epot = -127.008516926733 | etot = -96.6279943115656 +775000 ekin = 12.7512581989845 | erot = 19.0144480580651 | epot = -128.283580553391 | etot = -96.5178742963414 +776000 ekin = 13.4059786045676 | erot = 18.2473301169866 | epot = -129.393853982732 | etot = -97.7405452611776 +777000 ekin = 13.5315026296802 | erot = 18.1698856467946 | epot = -130.174580869581 | etot = -98.4731925931059 +778000 ekin = 13.6435316916632 | erot = 18.7285223705771 | epot = -130.610133816236 | etot = -98.2380797539954 +779000 ekin = 14.1728401216417 | erot = 19.3726258416256 | epot = -130.752679341931 | etot = -97.2072133786632 +780000 ekin = 14.3824254384742 | erot = 20.2805423869659 | epot = -130.435745396869 | etot = -95.7727775714289 +781000 ekin = 14.0634521502132 | erot = 20.3041404137273 | epot = -129.692899713134 | etot = -95.3253071491932 +782000 ekin = 13.8997273963854 | erot = 19.7159523322204 | epot = -128.633785263159 | etot = -95.0181055345536 +783000 ekin = 14.5805702964738 | erot = 20.1367377346838 | epot = -127.487731977038 | etot = -92.7704239458805 +784000 ekin = 14.7295631629307 | erot = 18.7608866458735 | epot = -126.409989889347 | etot = -92.9195400805428 +785000 ekin = 14.5790289372303 | erot = 17.4212018507806 | epot = -125.571701429834 | etot = -93.5714706418234 +786000 ekin = 14.2141516435897 | erot = 14.6518199402866 | epot = -124.99579338584 | etot = -96.1298218019636 +787000 ekin = 14.7660420282759 | erot = 14.3914140729782 | epot = -123.862400112953 | etot = -94.704944011699 +788000 ekin = 15.7494797111644 | erot = 12.6417731115525 | epot = -123.487492512329 | etot = -95.0962396896122 +789000 ekin = 16.4321389308584 | erot = 13.473476852771 | epot = -125.223738036691 | etot = -95.3181222530615 +790000 ekin = 17.3944355914136 | erot = 14.2126538098132 | epot = -127.385989262941 | etot = -95.7788998617147 +791000 ekin = 17.542338647832 | erot = 14.3976563853015 | epot = -128.733371193597 | etot = -96.7933761604638 +792000 ekin = 17.6101111277555 | erot = 14.9499923510334 | epot = -129.847480085414 | etot = -97.287376606625 +793000 ekin = 17.2581577551513 | erot = 14.1974755752264 | epot = -130.580364142478 | etot = -99.1247308121006 +794000 ekin = 16.7526133614699 | erot = 13.8636403294348 | epot = -130.973813390232 | etot = -100.357559699328 +795000 ekin = 16.152604382294 | erot = 12.334243547554 | epot = -131.129532088002 | etot = -102.642684158154 +796000 ekin = 15.6349941418492 | erot = 12.4142765623166 | epot = -131.056983721197 | etot = -103.007713017031 +797000 ekin = 14.5293002263362 | erot = 11.759988164135 | epot = -130.813311575391 | etot = -104.524023184919 +798000 ekin = 14.1135420442321 | erot = 10.8474101898055 | epot = -130.507414821542 | etot = -105.546462587504 +799000 ekin = 13.7157706752659 | erot = 9.15130327128856 | epot = -130.090152366231 | etot = -107.223078419677 +800000 ekin = 13.466337314599 | erot = 9.16452060462954 | epot = -129.481458557592 | etot = -106.850600638364 +801000 ekin = 12.8490622653902 | erot = 8.41321946082014 | epot = -128.96939259777 | etot = -107.70711087156 +802000 ekin = 13.7835122772835 | erot = 8.99586275439796 | epot = -128.432235679839 | etot = -105.652860648157 +803000 ekin = 14.0432574044119 | erot = 8.39637796858142 | epot = -128.177607032156 | etot = -105.737971659163 +804000 ekin = 13.8804500627769 | erot = 9.39056778995296 | epot = -128.315756136538 | etot = -105.044738283808 +805000 ekin = 15.0895769357648 | erot = 12.097064628012 | epot = -128.936249613784 | etot = -101.749608050007 +806000 ekin = 16.1350689976413 | erot = 13.8359534948363 | epot = -129.911548037637 | etot = -99.9405255451598 +807000 ekin = 16.6487380381467 | erot = 14.4054222723811 | epot = -131.140263119421 | etot = -100.086102808893 +808000 ekin = 16.8039057643138 | erot = 15.758311021031 | epot = -132.506156082331 | etot = -99.9439392969863 +809000 ekin = 17.2617813404718 | erot = 16.0034253999197 | epot = -133.900332428715 | etot = -100.635125688324 +810000 ekin = 17.4397194922013 | erot = 17.7015647323618 | epot = -135.106809970596 | etot = -99.9655257460327 +811000 ekin = 18.5552016569806 | erot = 15.5843807328861 | epot = -135.96875770198 | etot = -101.829175312113 +812000 ekin = 18.452942576441 | erot = 15.477064826739 | epot = -136.446107523642 | etot = -102.516100120462 +813000 ekin = 18.0113066408674 | erot = 16.4026644740323 | epot = -136.670265971773 | etot = -102.256294856873 +814000 ekin = 17.7868542427568 | erot = 17.3205338046621 | epot = -136.743768644101 | etot = -101.636380596682 +815000 ekin = 17.7754863920035 | erot = 18.7339508013952 | epot = -136.659989345585 | etot = -100.150552152186 +816000 ekin = 17.5065493572092 | erot = 17.1968985200238 | epot = -136.400538862054 | etot = -101.697090984821 +817000 ekin = 17.2588765439722 | erot = 15.6021104078125 | epot = -136.167389858462 | etot = -103.306402906677 +818000 ekin = 16.876373306759 | erot = 15.0018605000463 | epot = -135.870042114207 | etot = -103.991808307402 +819000 ekin = 16.1216438713348 | erot = 11.849282533174 | epot = -135.48669525519 | etot = -107.515768850682 +820000 ekin = 16.0944828339213 | erot = 11.8427524808205 | epot = -135.233140928133 | etot = -107.295905613391 +821000 ekin = 15.2472975456955 | erot = 12.9378009309886 | epot = -134.9979253824 | etot = -106.812826905715 +822000 ekin = 15.0752482356614 | erot = 12.7408900780694 | epot = -134.73675818524 | etot = -106.920619871509 +823000 ekin = 14.3163077300462 | erot = 14.6185288827014 | epot = -134.536623471219 | etot = -105.601786858471 +824000 ekin = 13.8825887049532 | erot = 12.1669825326315 | epot = -134.375629636678 | etot = -108.326058399093 +825000 ekin = 13.4148282268949 | erot = 12.0634646733754 | epot = -134.280881024751 | etot = -108.802588124481 +826000 ekin = 13.0078373334353 | erot = 11.1634559575192 | epot = -134.41845725157 | etot = -110.247163960615 +827000 ekin = 12.8902878621291 | erot = 12.4990264061792 | epot = -134.596703509122 | etot = -109.207389240814 +828000 ekin = 11.5646757522929 | erot = 11.7439684813367 | epot = -134.731964075119 | etot = -111.42331984149 +829000 ekin = 11.4309614137037 | erot = 13.7952087113858 | epot = -134.695440471703 | etot = -109.469270346614 +830000 ekin = 11.2235876454851 | erot = 14.6428741287968 | epot = -134.725488974224 | etot = -108.859027199942 +831000 ekin = 11.3182098379071 | erot = 14.8589328583958 | epot = -134.746515470085 | etot = -108.569372773782 +832000 ekin = 11.0441964839711 | erot = 14.7856408247966 | epot = -134.69527750462 | etot = -108.865440195853 +833000 ekin = 10.682877295527 | erot = 15.2548604731414 | epot = -134.718548488044 | etot = -108.780810719376 +834000 ekin = 10.7039002106542 | erot = 14.579139201353 | epot = -134.735534464464 | etot = -109.452495052457 +835000 ekin = 10.754888995261 | erot = 14.0543937892664 | epot = -134.87402565228 | etot = -110.064742867752 +836000 ekin = 10.1202700043138 | erot = 15.3187790957702 | epot = -134.966464909492 | etot = -109.527415809408 +837000 ekin = 9.36234114773746 | erot = 14.4708358739391 | epot = -135.110181941762 | etot = -111.277004920085 +838000 ekin = 8.87163067670835 | erot = 13.3319755420188 | epot = -135.14565322912 | etot = -112.942047010393 +839000 ekin = 8.26265877207255 | erot = 10.7014626128465 | epot = -134.963344229617 | etot = -115.999222844698 +840000 ekin = 8.65274084856224 | erot = 11.6602884297826 | epot = -134.667798245535 | etot = -114.35476896719 +841000 ekin = 9.09288775627553 | erot = 13.2429300960466 | epot = -134.331535715412 | etot = -111.99571786309 +842000 ekin = 8.73215975376481 | erot = 12.5284564004336 | epot = -133.950833272912 | etot = -112.690217118713 +843000 ekin = 8.65124461219831 | erot = 12.9503805345727 | epot = -133.483565630294 | etot = -111.881940483523 +844000 ekin = 8.92016599758121 | erot = 14.1441235679163 | epot = -133.090855503351 | etot = -110.026565937854 +845000 ekin = 9.24238498531286 | erot = 14.160904310189 | epot = -132.693134649357 | etot = -109.289845353855 +846000 ekin = 9.47094397282618 | erot = 13.9264005793038 | epot = -132.141006784401 | etot = -108.743662232271 +847000 ekin = 9.22691639989 | erot = 13.232116465856 | epot = -131.514293754285 | etot = -109.055260888539 +848000 ekin = 9.81639190741643 | erot = 13.4624778225235 | epot = -131.049818949204 | etot = -107.770949219264 +849000 ekin = 9.87499092114145 | erot = 13.4822095987195 | epot = -130.870134339441 | etot = -107.51293381958 +850000 ekin = 9.83564446645358 | erot = 12.6007895189713 | epot = -131.029439664217 | etot = -108.593005678792 +851000 ekin = 10.5153977481081 | erot = 13.1044039605866 | epot = -131.446208931684 | etot = -107.826407222989 +852000 ekin = 10.5652395268177 | erot = 13.6468476218826 | epot = -132.131050112736 | etot = -107.918962964036 +853000 ekin = 11.262037481661 | erot = 14.446483379253 | epot = -132.979088951229 | etot = -107.270568090315 +854000 ekin = 11.4569649466538 | erot = 17.1991085713483 | epot = -134.009370355524 | etot = -105.353296837522 +855000 ekin = 11.445488750865 | erot = 16.5529047086022 | epot = -134.943555963858 | etot = -106.945162504391 +856000 ekin = 11.2646195062545 | erot = 17.558083039108 | epot = -135.668419945928 | etot = -106.845717400566 +857000 ekin = 11.2354695936597 | erot = 16.7487718857675 | epot = -136.143808419399 | etot = -108.159566939972 +858000 ekin = 10.5439313741143 | erot = 18.2042876178967 | epot = -136.307794363773 | etot = -107.559575371762 +859000 ekin = 10.7672246081709 | erot = 17.9429149428159 | epot = -136.236481879082 | etot = -107.526342328095 +860000 ekin = 11.0765038715224 | erot = 15.1462206889691 | epot = -136.047337276816 | etot = -109.824612716324 +861000 ekin = 11.4922571976088 | erot = 14.5695602895126 | epot = -135.790868771919 | etot = -109.729051284798 +862000 ekin = 12.1881568645894 | erot = 15.0206074004975 | epot = -135.424809146931 | etot = -108.216044881844 +863000 ekin = 12.3866842688664 | erot = 13.1123151530289 | epot = -135.015770553593 | etot = -109.516771131698 +864000 ekin = 12.8632139181769 | erot = 13.7451008182927 | epot = -134.614814546035 | etot = -108.006499809565 +865000 ekin = 12.9638528536504 | erot = 13.6732291585873 | epot = -134.295821517661 | etot = -107.658739505423 +866000 ekin = 12.5285835028733 | erot = 14.008283117103 | epot = -133.888276396547 | etot = -107.351409776571 +867000 ekin = 12.8000471911401 | erot = 14.4698446946666 | epot = -133.467248927542 | etot = -106.197357041736 +868000 ekin = 13.1554690969182 | erot = 13.964610280343 | epot = -133.175453685062 | etot = -106.0553743078 +869000 ekin = 13.7120033028546 | erot = 11.8020589066468 | epot = -132.989469614359 | etot = -107.475407404858 +870000 ekin = 13.9391425121738 | erot = 13.0192309663512 | epot = -133.0787492608 | etot = -106.120375782275 +871000 ekin = 13.3534556427411 | erot = 13.3944244233334 | epot = -133.277418395417 | etot = -106.529538329343 +872000 ekin = 13.7050089765843 | erot = 11.495485697045 | epot = -133.445985589622 | etot = -108.245490915993 +873000 ekin = 13.8738540716938 | erot = 12.2832282136725 | epot = -133.643235472027 | etot = -107.486153186661 +874000 ekin = 13.8212081970824 | erot = 12.1151874051868 | epot = -133.808063577332 | etot = -107.871667975063 +875000 ekin = 14.0946798797608 | erot = 11.7035888290353 | epot = -133.895351646674 | etot = -108.097082937878 +876000 ekin = 14.1819210407418 | erot = 10.0686648643882 | epot = -134.058953727432 | etot = -109.808367822302 +877000 ekin = 13.5901545093495 | erot = 10.9480086211963 | epot = -134.241074066514 | etot = -109.702910935968 +878000 ekin = 13.4971281598819 | erot = 11.1672820818965 | epot = -134.290468904476 | etot = -109.626058662697 +879000 ekin = 13.3086598631466 | erot = 12.7622181194315 | epot = -134.337336158552 | etot = -108.266458175974 +880000 ekin = 12.7541898443434 | erot = 13.6844425966541 | epot = -134.456318873947 | etot = -108.017686432949 +881000 ekin = 12.704424051613 | erot = 12.7860717477841 | epot = -134.506208701955 | etot = -109.015712902558 +882000 ekin = 12.38175129326 | erot = 12.5269482810238 | epot = -134.475617168012 | etot = -109.566917593728 +883000 ekin = 12.8005161905499 | erot = 13.7653440439173 | epot = -134.385992892951 | etot = -107.820132658484 +884000 ekin = 12.3652892075703 | erot = 15.5648473454406 | epot = -134.222776727309 | etot = -106.292640174298 +885000 ekin = 12.0619930057671 | erot = 14.1939231875669 | epot = -134.080051417373 | etot = -107.824135224039 +886000 ekin = 12.2054674734484 | erot = 14.8698901321818 | epot = -133.957603716119 | etot = -106.882246110488 +887000 ekin = 12.1829993268256 | erot = 15.6890235183903 | epot = -133.904222766011 | etot = -106.032199920795 +888000 ekin = 11.8698368140704 | erot = 15.4726957926098 | epot = -134.032299812731 | etot = -106.689767206051 +889000 ekin = 11.8558062660389 | erot = 16.6333316988663 | epot = -134.313150343233 | etot = -105.824012378328 +890000 ekin = 11.7074193256418 | erot = 16.4561079507288 | epot = -134.686433124892 | etot = -106.522905848521 +891000 ekin = 11.8227765090214 | erot = 18.718819634335 | epot = -135.196066326519 | etot = -104.654470183162 +892000 ekin = 11.8650323220337 | erot = 19.9226451035174 | epot = -135.556241115282 | etot = -103.76856368973 +893000 ekin = 12.0470317758748 | erot = 19.3855445494598 | epot = -135.891211989264 | etot = -104.458635663929 +894000 ekin = 12.1250598934591 | erot = 19.2499377433869 | epot = -136.174199472749 | etot = -104.799201835903 +895000 ekin = 11.9703268745587 | erot = 18.9604233891347 | epot = -136.240824123016 | etot = -105.310073859322 +896000 ekin = 10.8580427095038 | erot = 16.9854081129452 | epot = -136.159057957534 | etot = -108.315607135085 +897000 ekin = 10.7026227472956 | erot = 17.4906089849623 | epot = -135.932613786588 | etot = -107.73938205433 +898000 ekin = 10.7568818714307 | erot = 19.3984017753267 | epot = -135.457667467377 | etot = -105.30238382062 +899000 ekin = 11.1540453865913 | erot = 20.6151680986397 | epot = -135.047602655699 | etot = -103.278389170468 +900000 ekin = 11.2175608638145 | erot = 19.8715641919662 | epot = -134.736413488125 | etot = -103.647288432344 +901000 ekin = 11.5101373877627 | erot = 17.8933441490503 | epot = -134.479708180581 | etot = -105.076226643768 +902000 ekin = 11.4087293028101 | erot = 20.4577282287692 | epot = -134.293838000833 | etot = -102.427380469254 +903000 ekin = 11.4178722691804 | erot = 17.4756725453983 | epot = -134.016292968863 | etot = -105.122748154284 +904000 ekin = 11.4124991341652 | erot = 16.9249725788514 | epot = -133.687544123328 | etot = -105.350072410311 +905000 ekin = 11.9954511177595 | erot = 14.3970744281279 | epot = -133.425037879226 | etot = -107.032512333339 +906000 ekin = 12.0771681940923 | erot = 14.9878917468925 | epot = -133.185172444762 | etot = -106.120112503778 +907000 ekin = 12.764164755251 | erot = 16.127921504246 | epot = -132.903026797284 | etot = -104.010940537786 +908000 ekin = 13.2416154546869 | erot = 14.0281141132319 | epot = -132.582508485649 | etot = -105.31277891773 +909000 ekin = 12.771252526275 | erot = 13.0977024687493 | epot = -132.229917788064 | etot = -106.36096279304 +910000 ekin = 12.9561361597062 | erot = 13.2736243804977 | epot = -131.821724501839 | etot = -105.591963961635 +911000 ekin = 12.9068816048144 | erot = 13.6485321023552 | epot = -131.407608343572 | etot = -104.852194636402 +912000 ekin = 13.2772456269506 | erot = 14.5242824475044 | epot = -130.977971232473 | etot = -103.176443158018 +913000 ekin = 13.1306998666374 | erot = 14.7149120267765 | epot = -130.52100490856 | etot = -102.675393015147 +914000 ekin = 12.8093566473286 | erot = 13.8806688643145 | epot = -130.224086240756 | etot = -103.534060729113 +915000 ekin = 12.8745710469366 | erot = 12.6676371277359 | epot = -130.008628800888 | etot = -104.466420626215 +916000 ekin = 13.223678815262 | erot = 13.4318130589697 | epot = -129.849039579721 | etot = -103.19354770549 +917000 ekin = 13.3230372229 | erot = 14.0310965196101 | epot = -129.790699621134 | etot = -102.436565878624 +918000 ekin = 12.4265792123797 | erot = 15.6148707504268 | epot = -129.8169124534 | etot = -101.775462490593 +919000 ekin = 12.220974434008 | erot = 14.1518762580801 | epot = -130.092421038386 | etot = -103.719570346298 +920000 ekin = 11.8569854116187 | erot = 12.9944440715349 | epot = -130.372816939904 | etot = -105.52138745675 +921000 ekin = 11.9745758153479 | erot = 13.7045518397409 | epot = -130.579378399795 | etot = -104.900250744706 +922000 ekin = 11.468261093001 | erot = 13.2111290377418 | epot = -130.67355905795 | etot = -105.994168927208 +923000 ekin = 11.2696141785986 | erot = 14.8033836218883 | epot = -130.604779557645 | etot = -104.531781757158 +924000 ekin = 10.9244534653336 | erot = 13.7528204728959 | epot = -130.350543738113 | etot = -105.673269799883 +925000 ekin = 10.748471352004 | erot = 14.9078929219465 | epot = -130.176002568529 | etot = -104.519638294578 +926000 ekin = 11.3564418867195 | erot = 13.6652442920639 | epot = -130.027164773435 | etot = -105.005478594652 +927000 ekin = 10.4765814318482 | erot = 13.503963295669 | epot = -130.028984607566 | etot = -106.048439880048 +928000 ekin = 10.3151612142982 | erot = 13.4727210163475 | epot = -130.188689943777 | etot = -106.400807713131 +929000 ekin = 10.151015523495 | erot = 13.3951209233371 | epot = -130.553489617275 | etot = -107.007353170443 +930000 ekin = 10.6440405527458 | erot = 13.9301361945634 | epot = -131.189687645539 | etot = -106.61551089823 +931000 ekin = 10.595775497238 | erot = 14.6636196854686 | epot = -132.016296679709 | etot = -106.756901497003 +932000 ekin = 10.5626271885369 | erot = 15.4572471481413 | epot = -133.026095879091 | etot = -107.006221542412 +933000 ekin = 10.6490766959895 | erot = 15.3038627591627 | epot = -134.057954665411 | etot = -108.105015210259 +934000 ekin = 11.1937467149855 | erot = 14.5937452805419 | epot = -134.893443999866 | etot = -109.105952004339 +935000 ekin = 11.3488940339692 | erot = 15.4807492324312 | epot = -135.595176425098 | etot = -108.765533158698 +936000 ekin = 11.3744288823135 | erot = 17.1112970346653 | epot = -135.937168990954 | etot = -107.451443073975 +937000 ekin = 11.1657976751234 | erot = 15.7606154645341 | epot = -135.860030492702 | etot = -108.933617353045 +938000 ekin = 11.1829378761665 | erot = 14.4189121235504 | epot = -135.351180399316 | etot = -109.749330399599 +939000 ekin = 10.5851827305985 | erot = 14.3272900546407 | epot = -134.523380642394 | etot = -109.610907857155 +940000 ekin = 10.4903114388466 | erot = 13.3425812668397 | epot = -133.366179589938 | etot = -109.533286884252 +941000 ekin = 9.52063942115619 | erot = 13.5352915653376 | epot = -132.123237965418 | etot = -109.067306978924 +942000 ekin = 8.74706267981836 | erot = 12.4110030144493 | epot = -130.908618290138 | etot = -109.75055259587 +943000 ekin = 8.9549636255604 | erot = 12.473092229632 | epot = -130.058250494687 | etot = -108.630194639494 +944000 ekin = 8.98821699338599 | erot = 12.3873422546726 | epot = -129.470595306546 | etot = -108.095036058487 +945000 ekin = 9.09403438906677 | erot = 13.3614165234565 | epot = -129.289328427114 | etot = -106.833877514591 +946000 ekin = 9.95513668013973 | erot = 13.1181423396425 | epot = -129.364277357447 | etot = -106.290998337665 +947000 ekin = 10.4725815693779 | erot = 14.4861547677326 | epot = -129.471170334547 | etot = -104.512433997437 +948000 ekin = 10.5412885878304 | erot = 13.3820116775197 | epot = -129.651745198669 | etot = -105.728444933319 +949000 ekin = 11.3390682449021 | erot = 12.8346039395199 | epot = -129.853068461769 | etot = -105.679396277347 +950000 ekin = 11.8794959542905 | erot = 13.7224705305763 | epot = -130.324131082403 | etot = -104.722164597536 +951000 ekin = 12.5217035454997 | erot = 13.7824684702848 | epot = -130.875487062828 | etot = -104.571315047044 +952000 ekin = 12.9654307635086 | erot = 16.0387315207576 | epot = -131.40058602524 | etot = -102.396423740973 +953000 ekin = 13.6692114039146 | erot = 16.0850126958549 | epot = -132.148229978679 | etot = -102.39400587891 +954000 ekin = 14.8931307274368 | erot = 15.0103797716773 | epot = -132.83987069331 | etot = -102.936360194196 +955000 ekin = 15.9734871407686 | erot = 17.0379601351532 | epot = -133.552722143682 | etot = -100.541274867761 +956000 ekin = 17.025406676142 | erot = 17.0899757623241 | epot = -134.234131690523 | etot = -100.118749252057 +957000 ekin = 17.540142645343 | erot = 19.3177114307724 | epot = -134.708519326177 | etot = -97.8506652500616 +958000 ekin = 18.4016736399259 | erot = 18.4240376247552 | epot = -134.751779209151 | etot = -97.9260679444695 +959000 ekin = 18.5940884762891 | erot = 18.347307346037 | epot = -134.358100904725 | etot = -97.4167050823986 +960000 ekin = 17.3247294602177 | erot = 17.9629603679272 | epot = -133.460927708724 | etot = -98.1732378805788 +961000 ekin = 17.2306824725633 | erot = 16.7825045081642 | epot = -132.047541059604 | etot = -98.034354078877 +962000 ekin = 16.2087363183156 | erot = 16.0768499749745 | epot = -130.288840410701 | etot = -98.0032541174114 +963000 ekin = 15.5499262105869 | erot = 14.3007373099541 | epot = -128.435374572404 | etot = -98.5847110518625 +964000 ekin = 14.3795154917121 | erot = 12.9245269567082 | epot = -126.598763146099 | etot = -99.2947206976787 +965000 ekin = 13.9616806865964 | erot = 12.1486231334406 | epot = -124.963453525024 | etot = -98.8531497049867 +966000 ekin = 13.0155517382896 | erot = 12.0708514834773 | epot = -123.798553047858 | etot = -98.7121498260912 +967000 ekin = 12.3914707709181 | erot = 12.6226506849405 | epot = -122.905482106119 | etot = -97.8913606502604 +968000 ekin = 11.8072823696662 | erot = 13.4385266736669 | epot = -122.270775658815 | etot = -97.0249666154823 +969000 ekin = 11.9064670191824 | erot = 12.8382084862548 | epot = -122.129056637682 | etot = -97.384381132245 +970000 ekin = 11.9766530746505 | erot = 13.8039016134453 | epot = -122.193888973048 | etot = -96.4133342849519 +971000 ekin = 12.159620075604 | erot = 15.341662000356 | epot = -122.480873285093 | etot = -94.979591209133 +972000 ekin = 12.5956668716873 | erot = 15.9071846222339 | epot = -122.764232934679 | etot = -94.2613814407573 +973000 ekin = 12.7616925472694 | erot = 16.6414713137862 | epot = -122.899748930094 | etot = -93.4965850690388 +974000 ekin = 12.1483639370037 | erot = 17.4786162173978 | epot = -122.866366650609 | etot = -93.2393864962079 +975000 ekin = 11.4260688976502 | erot = 15.2790586824017 | epot = -122.596269183682 | etot = -95.8911416036296 +976000 ekin = 10.9216516769999 | erot = 15.7519482858511 | epot = -122.319486518036 | etot = -95.6458865551851 +977000 ekin = 10.5216621983397 | erot = 16.0123618137797 | epot = -121.88416826783 | etot = -95.3501442557107 +978000 ekin = 10.3472075940097 | erot = 13.5450182182488 | epot = -121.556550278314 | etot = -97.6643244660555 +979000 ekin = 10.803310231626 | erot = 12.1528830044995 | epot = -121.334850754201 | etot = -98.3786575180758 +980000 ekin = 10.6895825619785 | erot = 10.2559339362194 | epot = -121.109151001193 | etot = -100.163634502995 +981000 ekin = 10.9968022195623 | erot = 9.53919152162597 | epot = -121.208373587714 | etot = -100.672379846526 +982000 ekin = 11.5373240954519 | erot = 10.4706043721691 | epot = -121.620091061045 | etot = -99.6121625934238 +983000 ekin = 11.9172748436564 | erot = 11.8485953609637 | epot = -122.126407301373 | etot = -98.3605370967528 +984000 ekin = 13.0889146402121 | erot = 12.4878324404259 | epot = -122.927779363662 | etot = -97.3510322830236 +985000 ekin = 13.7889356146106 | erot = 13.380892004438 | epot = -123.875604227913 | etot = -96.7057766088645 +986000 ekin = 14.6369741755906 | erot = 12.4272204904535 | epot = -124.920620462043 | etot = -97.856425795999 +987000 ekin = 15.2725809361966 | erot = 13.5313107393271 | epot = -125.964544413027 | etot = -97.1606527375033 +988000 ekin = 15.9394864570637 | erot = 13.7633278728772 | epot = -127.059285682591 | etot = -97.3564713526504 +989000 ekin = 16.7034442412101 | erot = 14.8636845615711 | epot = -128.067821490903 | etot = -96.5006926881219 +990000 ekin = 17.3598679987177 | erot = 16.0856163930444 | epot = -128.903898946066 | etot = -95.4584145543041 +991000 ekin = 18.3664301585912 | erot = 18.399967003844 | epot = -129.448926673439 | etot = -92.6825295110034 +992000 ekin = 18.6308602186873 | erot = 18.749563061417 | epot = -129.691537637601 | etot = -92.3111143574964 +993000 ekin = 18.6355049261452 | erot = 18.5256774093057 | epot = -129.643793449999 | etot = -92.4826111145484 +994000 ekin = 18.5321198188331 | erot = 20.2443491138306 | epot = -129.571189129639 | etot = -90.7947201969756 +995000 ekin = 18.3418410607544 | erot = 21.5710227479243 | epot = -129.467040986364 | etot = -89.5541771776855 +996000 ekin = 18.4398021901266 | erot = 19.2378942069908 | epot = -129.422390629411 | etot = -91.7446942322936 +997000 ekin = 18.0450043136384 | erot = 19.2580344833964 | epot = -129.394444796923 | etot = -92.0914059998885 +998000 ekin = 18.2062986210865 | erot = 19.8852445419398 | epot = -129.196206296319 | etot = -91.1046631332925 +999000 ekin = 18.7341404690777 | erot = 19.3234540065288 | epot = -128.842851529638 | etot = -90.7852570540318 +1000000 ekin = 18.6583620145008 | erot = 16.6848586754118 | epot = -128.346967556883 | etot = -93.0037468669704 + 1000000 417.29959 -129.94144 1.5944718 -109.68861 0.062656806 39304000 +Loop time of 34.4889 on 1 procs for 1000000 steps with 16 atoms + +Performance: 42.738 ns/day, 0.562 hours/ns, 28994.847 timesteps/s, 463.918 katom-step/s +99.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.385 | 27.385 | 27.385 | 0.0 | 79.40 +Bond | 0.89821 | 0.89821 | 0.89821 | 0.0 | 2.60 +Neigh | 0.043138 | 0.043138 | 0.043138 | 0.0 | 0.13 +Comm | 0.47566 | 0.47566 | 0.47566 | 0.0 | 1.38 +Output | 0.20876 | 0.20876 | 0.20876 | 0.0 | 0.61 +Modify | 5.0059 | 5.0059 | 5.0059 | 0.0 | 14.51 +Other | | 0.4721 | | | 1.37 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 105 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 105 +Ave neighs/atom = 6.5625 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:34 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.4 new file mode 100644 index 0000000000..2397997895 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.4 @@ -0,0 +1,1178 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.013 seconds + +set atom * mass 315.8376 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 25.179212 + ghost atom cutoff = 32.4 + binsize = 12.589606, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -131.137679785989 | etot = -98.3191045555159 +Per MPI rank memory allocation (min/avg/max) = 7.232 | 7.264 | 7.344 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -132.72638 1.5886993 -115.01736 0.034438461 39304000 +1000 ekin = 16.0915734242602 | erot = 18.1131907799999 | epot = -129.960758701937 | etot = -95.7559944976768 +2000 ekin = 16.3445512762835 | erot = 14.8147206882645 | epot = -128.691660333568 | etot = -97.5323883690197 +3000 ekin = 16.1759985834646 | erot = 13.3386627579329 | epot = -127.637971683901 | etot = -98.1233103425036 +4000 ekin = 15.6545057241999 | erot = 13.1236462676588 | epot = -126.77586522849 | etot = -97.9977132366311 +5000 ekin = 15.1758404392585 | erot = 13.0857411237448 | epot = -126.165703238772 | etot = -97.9041216757689 +6000 ekin = 15.1413640531156 | erot = 13.3861657435171 | epot = -125.809598527628 | etot = -97.282068730995 +7000 ekin = 15.1774504947436 | erot = 12.9637778426295 | epot = -125.76113527326 | etot = -97.619906935887 +8000 ekin = 14.5595245432668 | erot = 11.3238063810154 | epot = -125.967991017334 | etot = -100.084660093052 +9000 ekin = 14.8927108369538 | erot = 11.4216264838282 | epot = -126.397480899428 | etot = -100.083143578646 +10000 ekin = 15.5221737145433 | erot = 13.8269758172558 | epot = -126.818238777881 | etot = -97.4690892460816 +11000 ekin = 15.0053200181519 | erot = 15.5093678794875 | epot = -127.17066902637 | etot = -96.655981128731 +12000 ekin = 15.0557850237049 | erot = 14.2278865862305 | epot = -127.611853301489 | etot = -98.3281816915534 +13000 ekin = 15.5007975534887 | erot = 14.1582062863706 | epot = -128.190402950814 | etot = -98.5313991109551 +14000 ekin = 15.9123478432744 | erot = 13.2884863097123 | epot = -128.77065424977 | etot = -99.569820096783 +15000 ekin = 16.1874456366003 | erot = 13.1984958116548 | epot = -129.368116004472 | etot = -99.9821745562173 +16000 ekin = 16.987752968205 | erot = 14.5429430611517 | epot = -129.945650295152 | etot = -98.4149542657954 +17000 ekin = 17.5894073729048 | erot = 14.2448280375259 | epot = -130.400289816865 | etot = -98.5660544064342 +18000 ekin = 17.0413568209226 | erot = 14.1346624808112 | epot = -130.57596518431 | etot = -99.3999458825761 +19000 ekin = 16.5319443382977 | erot = 13.947657144873 | epot = -130.450874378105 | etot = -99.9712728949343 +20000 ekin = 15.4026055300823 | erot = 15.2171572465952 | epot = -130.066075567863 | etot = -99.4463127911858 +21000 ekin = 14.9726687525356 | erot = 14.9897963360516 | epot = -129.561873475372 | etot = -99.599408386785 +22000 ekin = 14.8466725545297 | erot = 15.0786863271903 | epot = -128.948825210294 | etot = -99.0234663285742 +23000 ekin = 14.2532915697464 | erot = 13.1592595555267 | epot = -128.266976221893 | etot = -100.85442509662 +24000 ekin = 14.0658797888538 | erot = 11.3521316996468 | epot = -127.585110784609 | etot = -102.167099296108 +25000 ekin = 13.6024746157443 | erot = 11.742533824335 | epot = -127.070880960057 | etot = -101.725872519978 +26000 ekin = 13.0978066432598 | erot = 13.5826324483342 | epot = -126.769055195787 | etot = -100.088616104193 +27000 ekin = 11.9699125238479 | erot = 13.1150613622135 | epot = -126.7844815598 | etot = -101.699507673739 +28000 ekin = 10.976958959255 | erot = 13.6899050629201 | epot = -126.937013027768 | etot = -102.270149005593 +29000 ekin = 11.0368750062285 | erot = 12.709718724462 | epot = -127.369395793738 | etot = -103.622802063048 +30000 ekin = 10.8238378103432 | erot = 14.1297110441393 | epot = -127.987976670544 | etot = -103.034427816061 +31000 ekin = 11.1817723397155 | erot = 13.7202852392807 | epot = -128.851290355668 | etot = -103.949232776672 +32000 ekin = 11.9975217177556 | erot = 14.2657511631903 | epot = -129.880371605081 | etot = -103.617098724135 +33000 ekin = 12.5203490340081 | erot = 15.8304065565672 | epot = -131.014428299273 | etot = -102.663672708697 +34000 ekin = 12.0696862490131 | erot = 16.9564094479006 | epot = -132.324011685246 | etot = -103.297915988333 +35000 ekin = 11.7726407778174 | erot = 17.990672971408 | epot = -133.663597856935 | etot = -103.900284107709 +36000 ekin = 11.9959593870982 | erot = 17.3956522997854 | epot = -134.862973450605 | etot = -105.471361763722 +37000 ekin = 12.3526748777694 | erot = 18.2934291366227 | epot = -135.947502079273 | etot = -105.301398064881 +38000 ekin = 12.2423038130269 | erot = 18.1018836744392 | epot = -136.801871054289 | etot = -106.457683566823 +39000 ekin = 12.3301933819594 | erot = 18.4512027729023 | epot = -137.321697704824 | etot = -106.540301549962 +40000 ekin = 11.9214026505523 | erot = 18.155853425263 | epot = -137.484973787963 | etot = -107.407717712147 +41000 ekin = 12.2283801694364 | erot = 16.5594427515912 | epot = -137.235774487483 | etot = -108.447951566455 +42000 ekin = 12.2314632281809 | erot = 17.0024712401299 | epot = -136.723923546115 | etot = -107.489989077804 +43000 ekin = 11.5473242505992 | erot = 18.1570126474715 | epot = -136.048887123393 | etot = -106.344550225323 +44000 ekin = 11.0056443389832 | erot = 17.5202845883571 | epot = -135.346714231662 | etot = -106.820785304322 +45000 ekin = 10.3089452018478 | erot = 15.5453434092819 | epot = -134.738395816973 | etot = -108.884107205843 +46000 ekin = 9.48705433272769 | erot = 15.6671792391693 | epot = -134.176879085244 | etot = -109.022645513347 +47000 ekin = 9.18503548542159 | erot = 15.8180331675045 | epot = -133.624329948875 | etot = -108.621261295949 +48000 ekin = 9.10761376026737 | erot = 15.2682372491717 | epot = -133.032908706349 | etot = -108.65705769691 +49000 ekin = 8.65668957250512 | erot = 13.0944047989688 | epot = -132.550858027152 | etot = -110.799763655678 +50000 ekin = 8.1737259790025 | erot = 14.1949347253049 | epot = -132.2185709826 | etot = -109.849910278292 +51000 ekin = 8.21916407653718 | erot = 15.2388404404011 | epot = -131.883447609852 | etot = -108.425443092913 +52000 ekin = 8.1845083787042 | erot = 15.788134210059 | epot = -131.669258926228 | etot = -107.696616337465 +53000 ekin = 8.65161111403999 | erot = 17.068486763557 | epot = -131.618869332305 | etot = -105.898771454708 +54000 ekin = 8.90576877224079 | erot = 18.0582236265828 | epot = -131.689941436948 | etot = -104.725949038125 +55000 ekin = 9.24202585479757 | erot = 14.9731119730928 | epot = -131.819084800161 | etot = -107.603946972271 +56000 ekin = 8.88882310600324 | erot = 15.1891758585241 | epot = -131.975081416319 | etot = -107.897082451792 +57000 ekin = 8.94491042496245 | erot = 14.4108327591405 | epot = -132.246801477382 | etot = -108.891058293279 +58000 ekin = 9.57648602676765 | erot = 13.3529125589093 | epot = -132.56882440802 | etot = -109.639425822343 +59000 ekin = 10.3109680181628 | erot = 13.8677646293818 | epot = -132.891622299369 | etot = -108.712889651825 +60000 ekin = 10.0897668833558 | erot = 14.3091845020349 | epot = -133.20939158103 | etot = -108.810440195639 +61000 ekin = 10.290789659164 | erot = 12.5797002428319 | epot = -133.446868280818 | etot = -110.576378378822 +62000 ekin = 10.7068064774009 | erot = 13.2073275266195 | epot = -133.677681123353 | etot = -109.763547119333 +63000 ekin = 10.5676870641081 | erot = 13.735975736358 | epot = -133.826597743211 | etot = -109.522934942745 +64000 ekin = 11.0603266771933 | erot = 13.7863043276276 | epot = -133.950208397973 | etot = -109.103577393152 +65000 ekin = 10.6704349910448 | erot = 11.6124881615164 | epot = -133.950498994477 | etot = -111.667575841916 +66000 ekin = 10.5670030718972 | erot = 10.8876772742217 | epot = -133.847500084089 | etot = -112.39281973797 +67000 ekin = 10.7868181650423 | erot = 11.5085527656524 | epot = -133.790955553073 | etot = -111.495584622378 +68000 ekin = 11.3210825282139 | erot = 12.0516390700809 | epot = -133.788999651569 | etot = -110.416278053274 +69000 ekin = 11.4223846034049 | erot = 11.9043057631203 | epot = -133.879195860376 | etot = -110.552505493851 +70000 ekin = 11.7601725001356 | erot = 11.8946373824682 | epot = -133.974361358016 | etot = -110.319551475413 +71000 ekin = 11.9369565657213 | erot = 12.1587051890993 | epot = -134.06649094326 | etot = -109.970829188439 +72000 ekin = 12.2201356783385 | erot = 13.4203096414169 | epot = -134.148152400829 | etot = -108.507707081074 +73000 ekin = 11.7316097869837 | erot = 15.2661105057596 | epot = -134.197324788334 | etot = -107.199604495591 +74000 ekin = 11.5690454821182 | erot = 13.4185622894577 | epot = -134.084325017159 | etot = -109.096717245583 +75000 ekin = 11.3541437997286 | erot = 12.5773883852486 | epot = -133.907173454644 | etot = -109.975641269667 +76000 ekin = 11.740167238967 | erot = 12.0171543614756 | epot = -133.707208332066 | etot = -109.949886731623 +77000 ekin = 11.5941480714565 | erot = 11.3641007358234 | epot = -133.461741313057 | etot = -110.503492505777 +78000 ekin = 11.7433960085455 | erot = 11.5091759189829 | epot = -133.211758849829 | etot = -109.959186922301 +79000 ekin = 11.6812633246783 | erot = 11.1354353644819 | epot = -132.913438827558 | etot = -110.096740138397 +80000 ekin = 12.4071653100863 | erot = 9.00188979502124 | epot = -132.719598371346 | etot = -111.310543266239 +81000 ekin = 12.6725361317755 | erot = 10.0624404211498 | epot = -132.652952964947 | etot = -109.917976412022 +82000 ekin = 12.5350998837219 | erot = 10.0263772168773 | epot = -132.790356964392 | etot = -110.228879863793 +83000 ekin = 12.7855032943191 | erot = 10.8502686831836 | epot = -132.979108225794 | etot = -109.343336248291 +84000 ekin = 12.7147866504013 | erot = 12.0987110978396 | epot = -133.207699067029 | etot = -108.394201318788 +85000 ekin = 12.4318211562989 | erot = 13.8366282022955 | epot = -133.445467029335 | etot = -107.177017670741 +86000 ekin = 12.9409373725302 | erot = 11.7015118858333 | epot = -133.683038178489 | etot = -109.040588920126 +87000 ekin = 13.354234292103 | erot = 13.3370432943118 | epot = -133.969966837143 | etot = -107.278689250728 +88000 ekin = 13.5612268384264 | erot = 12.836777717707 | epot = -134.226306622826 | etot = -107.828302066693 +89000 ekin = 13.6432048747635 | erot = 12.6826068084665 | epot = -134.529852057328 | etot = -108.204040374098 +90000 ekin = 13.7316673862683 | erot = 13.6890146705956 | epot = -134.865860116451 | etot = -107.445178059587 +91000 ekin = 13.793156118478 | erot = 12.3833233041062 | epot = -135.075133149533 | etot = -108.898653726949 +92000 ekin = 14.149859068654 | erot = 13.335295026605 | epot = -135.149724950008 | etot = -107.664570854749 +93000 ekin = 13.4980981353872 | erot = 15.839915962006 | epot = -135.091526446813 | etot = -105.75351234942 +94000 ekin = 13.5365193696502 | erot = 16.1422521803842 | epot = -134.821112082621 | etot = -105.142340532587 +95000 ekin = 12.8768504224914 | erot = 16.5006661696424 | epot = -134.411357406747 | etot = -105.033840814613 +96000 ekin = 12.7317120655562 | erot = 17.9157627764991 | epot = -133.813467873532 | etot = -103.165993031477 +97000 ekin = 12.3620275480032 | erot = 15.8088677905014 | epot = -133.036335674756 | etot = -104.865440336251 +98000 ekin = 12.6047637501621 | erot = 15.6670590119394 | epot = -132.381652529338 | etot = -104.109829767237 +99000 ekin = 12.772362081575 | erot = 15.8664620748852 | epot = -131.817074700568 | etot = -103.178250544108 +100000 ekin = 12.9540440847007 | erot = 12.4848150466462 | epot = -131.419169306588 | etot = -105.980310175241 +101000 ekin = 12.8094026921687 | erot = 14.2352897206951 | epot = -131.233253678842 | etot = -104.188561265978 +102000 ekin = 12.9075167891449 | erot = 15.7903246648522 | epot = -131.287129201557 | etot = -102.58928774756 +103000 ekin = 12.8268218514855 | erot = 15.2926771721625 | epot = -131.552091540385 | etot = -103.432592516737 +104000 ekin = 12.860831753567 | erot = 15.6609633521036 | epot = -132.011631626406 | etot = -103.489836520735 +105000 ekin = 12.6856584399003 | erot = 15.8393109865105 | epot = -132.442611390941 | etot = -103.91764196453 +106000 ekin = 12.7490296627693 | erot = 16.4923225385789 | epot = -132.819026273508 | etot = -103.57767407216 +107000 ekin = 13.1257231720193 | erot = 15.9047147356431 | epot = -132.9779702812 | etot = -103.947532373538 +108000 ekin = 12.9781624509355 | erot = 16.7386244266203 | epot = -133.008694729617 | etot = -103.291907852061 +109000 ekin = 13.1080842306847 | erot = 17.3246912941556 | epot = -132.846381558103 | etot = -102.413606033263 +110000 ekin = 12.9475997478039 | erot = 16.7850636978276 | epot = -132.497755741303 | etot = -102.765092295671 +111000 ekin = 12.8408247556273 | erot = 14.6321690150569 | epot = -131.894060346807 | etot = -104.421066576123 +112000 ekin = 12.7390861304882 | erot = 15.1117102902424 | epot = -130.984815863023 | etot = -103.134019442292 +113000 ekin = 12.8023139379481 | erot = 14.2324468707309 | epot = -129.882034899179 | etot = -102.8472740905 +114000 ekin = 12.6751738711337 | erot = 13.4254865804269 | epot = -128.756084659542 | etot = -102.655424207982 +115000 ekin = 12.557402062209 | erot = 13.8313460573849 | epot = -127.640176987516 | etot = -101.251428867922 +116000 ekin = 12.2716056143536 | erot = 13.9615225919651 | epot = -126.709200713432 | etot = -100.476072507113 +117000 ekin = 12.2847487950703 | erot = 13.6658123026522 | epot = -125.940464748038 | etot = -99.9899036503155 +118000 ekin = 12.347565234157 | erot = 13.4953928075455 | epot = -125.314722779843 | etot = -99.4717647381409 +119000 ekin = 12.3072829088613 | erot = 11.56019171662 | epot = -125.058806664351 | etot = -101.19133203887 +120000 ekin = 12.6296065527395 | erot = 11.0377809484387 | epot = -125.099637270972 | etot = -101.432249769794 +121000 ekin = 12.9145904443762 | erot = 13.9293169064353 | epot = -125.374907702351 | etot = -98.5310003515397 +122000 ekin = 13.5256452707358 | erot = 14.3717971253563 | epot = -125.827679973218 | etot = -97.9302375771264 +123000 ekin = 13.198802866049 | erot = 13.8107684289809 | epot = -126.275164852546 | etot = -99.2655935575157 +124000 ekin = 13.4518200076391 | erot = 15.4211124799704 | epot = -126.829001981501 | etot = -97.9560694938919 +125000 ekin = 13.6280016089997 | erot = 14.8298658476017 | epot = -127.205034447317 | etot = -98.7471669907156 +126000 ekin = 14.0397253286273 | erot = 16.0000098172294 | epot = -127.428770535868 | etot = -97.3890353900114 +127000 ekin = 13.8129336121093 | erot = 15.8531342695909 | epot = -127.500620517311 | etot = -97.8345526356106 +128000 ekin = 14.5061529689428 | erot = 14.8309580426828 | epot = -127.382851147517 | etot = -98.0457401358917 +129000 ekin = 14.2869042038546 | erot = 12.5620727215151 | epot = -127.305998717116 | etot = -100.457021791747 +130000 ekin = 14.4107502489808 | erot = 10.7964820337384 | epot = -127.311709857223 | etot = -102.104477574504 +131000 ekin = 14.3444673612414 | erot = 10.5888492005681 | epot = -127.326961511477 | etot = -102.393644949667 +132000 ekin = 14.3594541413417 | erot = 10.320464075859 | epot = -127.305521202206 | etot = -102.625602985006 +133000 ekin = 14.1546729294946 | erot = 11.0859672393095 | epot = -127.303615695499 | etot = -102.062975526695 +134000 ekin = 14.0570010332958 | erot = 12.3312282654639 | epot = -127.315060459314 | etot = -100.926831160555 +135000 ekin = 13.8473879798681 | erot = 13.0027980951685 | epot = -127.252918803603 | etot = -100.402732728566 +136000 ekin = 13.4783448344795 | erot = 12.3181728167375 | epot = -127.18263098152 | etot = -101.386113330303 +137000 ekin = 13.3123106942823 | erot = 13.5051604453636 | epot = -127.08518294385 | etot = -100.267711804204 +138000 ekin = 13.4309678557282 | erot = 13.1985799236462 | epot = -127.143176389732 | etot = -100.513628610357 +139000 ekin = 14.0341574099361 | erot = 12.592173678287 | epot = -127.630455692374 | etot = -101.004124604151 +140000 ekin = 13.8065761622945 | erot = 13.5119869120374 | epot = -128.179355103039 | etot = -100.860792028707 +141000 ekin = 13.9214361852354 | erot = 13.3848320157243 | epot = -128.251831418661 | etot = -100.945563217702 +142000 ekin = 13.934909380203 | erot = 11.8831702139305 | epot = -128.331562017751 | etot = -102.513482423617 +143000 ekin = 14.0700905519444 | erot = 10.619272505908 | epot = -128.561461044053 | etot = -103.872097986201 +144000 ekin = 14.3846568066528 | erot = 11.0308870704306 | epot = -128.895057471406 | etot = -103.479513594323 +145000 ekin = 14.9295000268487 | erot = 11.80072002172 | epot = -129.156865883934 | etot = -102.426645835365 +146000 ekin = 15.0588681489582 | erot = 11.6178166529404 | epot = -129.47454946755 | etot = -102.797864665651 +147000 ekin = 15.2106427102622 | erot = 11.0376270042099 | epot = -129.927765438226 | etot = -103.679495723754 +148000 ekin = 15.0876610117964 | erot = 11.9374908285857 | epot = -130.557482212129 | etot = -103.532330371747 +149000 ekin = 14.7490538017439 | erot = 11.9315940063832 | epot = -131.322108511717 | etot = -104.641460703589 +150000 ekin = 15.2657424668262 | erot = 12.1726110910327 | epot = -131.985788180337 | etot = -104.547434622478 +151000 ekin = 14.5781518851264 | erot = 13.9496009411186 | epot = -132.673335698855 | etot = -104.14558287261 +152000 ekin = 14.5777113379811 | erot = 13.4755555746181 | epot = -133.162587051672 | etot = -105.109320139073 +153000 ekin = 14.6773814043059 | erot = 12.9849504561485 | epot = -133.330572771012 | etot = -105.668240910557 +154000 ekin = 14.8598979227303 | erot = 13.0480139509153 | epot = -133.356298154222 | etot = -105.448386280576 +155000 ekin = 14.5658462808371 | erot = 12.7291316324933 | epot = -133.159457277165 | etot = -105.864479363835 +156000 ekin = 14.6072311785003 | erot = 13.4815572745023 | epot = -132.755625124995 | etot = -104.666836671993 +157000 ekin = 14.7186895782839 | erot = 11.514964433911 | epot = -132.443538170593 | etot = -106.209884158398 +158000 ekin = 14.756915811197 | erot = 11.2678012861988 | epot = -132.19840267674 | etot = -106.173685579344 +159000 ekin = 14.5674148933329 | erot = 10.8738418737426 | epot = -131.950323387759 | etot = -106.509066620683 +160000 ekin = 14.0467728438122 | erot = 11.063386097205 | epot = -131.797209529149 | etot = -106.687050588132 +161000 ekin = 14.5555554295251 | erot = 12.8052370294303 | epot = -131.76970435803 | etot = -104.408911899074 +162000 ekin = 14.6977677167711 | erot = 12.2364421421908 | epot = -131.778479435647 | etot = -104.844269576685 +163000 ekin = 14.1196642871595 | erot = 12.9329860305353 | epot = -131.948814514085 | etot = -104.89616419639 +164000 ekin = 13.7898491622463 | erot = 13.0457286661398 | epot = -132.281155651746 | etot = -105.44557782336 +165000 ekin = 14.146767384781 | erot = 15.4611523406016 | epot = -132.760779804613 | etot = -103.15286007923 +166000 ekin = 14.6508841513351 | erot = 17.3890180629077 | epot = -133.236728473221 | etot = -101.196826258978 +167000 ekin = 15.0721587960347 | erot = 17.6227659908065 | epot = -133.680095808284 | etot = -100.985171021443 +168000 ekin = 14.1994828512195 | erot = 15.9037522618147 | epot = -134.055194827403 | etot = -103.951959714369 +169000 ekin = 14.1602341444753 | erot = 18.0296755447982 | epot = -134.449473646656 | etot = -102.259563957382 +170000 ekin = 14.0694306307775 | erot = 19.4725625534463 | epot = -134.692004642621 | etot = -101.150011458397 +171000 ekin = 13.7361512674535 | erot = 18.7505480644722 | epot = -134.786694998901 | etot = -102.299995666975 +172000 ekin = 13.5627257932729 | erot = 18.093237266307 | epot = -134.689962511105 | etot = -103.033999451525 +173000 ekin = 13.6193404079345 | erot = 18.3116904639331 | epot = -134.630527397265 | etot = -102.699496525397 +174000 ekin = 13.8652291607269 | erot = 17.9414686212446 | epot = -134.704751380789 | etot = -102.898053598817 +175000 ekin = 13.6178278396075 | erot = 16.01475083407 | epot = -134.841815041644 | etot = -105.209236367966 +176000 ekin = 14.2818264517968 | erot = 15.7467129433123 | epot = -135.135186152403 | etot = -105.106646757294 +177000 ekin = 13.9605374749723 | erot = 16.9682019434855 | epot = -135.553348493467 | etot = -104.624609075009 +178000 ekin = 14.1719985856751 | erot = 17.9568318814641 | epot = -136.147751073445 | etot = -104.018920606306 +179000 ekin = 14.5848015120145 | erot = 17.0815739296152 | epot = -136.819563786046 | etot = -105.153188344416 +180000 ekin = 14.5317430049169 | erot = 16.515035644651 | epot = -137.453724809158 | etot = -106.40694615959 +181000 ekin = 14.7963541253609 | erot = 15.6683381743307 | epot = -138.009004975563 | etot = -107.544312675871 +182000 ekin = 14.8779441014054 | erot = 14.4395053549216 | epot = -138.44189613322 | etot = -109.124446676893 +183000 ekin = 15.7558270527731 | erot = 12.9184044380285 | epot = -138.693559981229 | etot = -110.019328490427 +184000 ekin = 15.5143742044925 | erot = 13.3181825150061 | epot = -138.800057405125 | etot = -109.967500685627 +185000 ekin = 15.3652686778713 | erot = 14.6676409373754 | epot = -138.908865602223 | etot = -108.875955986977 +186000 ekin = 15.0348400978665 | erot = 15.3231102748848 | epot = -138.945875626631 | etot = -108.58792525388 +187000 ekin = 14.9176766057609 | erot = 16.6599898753524 | epot = -138.88156084498 | etot = -107.303894363866 +188000 ekin = 14.6921621349464 | erot = 18.1602885309884 | epot = -138.60499813301 | etot = -105.752547467075 +189000 ekin = 13.7408076240997 | erot = 16.4479475752207 | epot = -138.155816715908 | etot = -107.967061516588 +190000 ekin = 13.6152992340025 | erot = 17.7725230118411 | epot = -137.628867284981 | etot = -106.241045039138 +191000 ekin = 13.4728687325774 | erot = 18.0823791600731 | epot = -137.091957918931 | etot = -105.53671002628 +192000 ekin = 12.3530399718251 | erot = 19.8393244691615 | epot = -136.481023981569 | etot = -104.288659540582 +193000 ekin = 11.5299273102656 | erot = 19.1824282103537 | epot = -135.946553250796 | etot = -105.234197730177 +194000 ekin = 11.1649895000932 | erot = 18.9423306262241 | epot = -135.561409713864 | etot = -105.454089587546 +195000 ekin = 10.2365038832962 | erot = 16.2974974326929 | epot = -135.016356459364 | etot = -108.482355143375 +196000 ekin = 9.9052405548998 | erot = 15.4114866769535 | epot = -134.379903501341 | etot = -109.063176269488 +197000 ekin = 10.5101662173868 | erot = 13.2519428202659 | epot = -133.773926980255 | etot = -110.011817942602 +198000 ekin = 10.0701100246755 | erot = 12.1224401786724 | epot = -133.192517881119 | etot = -110.999967677771 +199000 ekin = 10.0888815862907 | erot = 14.6060699047979 | epot = -132.831052684003 | etot = -108.136101192915 +200000 ekin = 10.2713328348432 | erot = 14.1677382732657 | epot = -132.499452328271 | etot = -108.060381220162 +201000 ekin = 9.67279836297051 | erot = 17.4741053490013 | epot = -131.99405625743 | etot = -104.847152545458 +202000 ekin = 9.42113475905542 | erot = 15.2416466004391 | epot = -131.442522675496 | etot = -106.779741316001 +203000 ekin = 9.0781733153247 | erot = 15.1373499225716 | epot = -130.854993475045 | etot = -106.639470237149 +204000 ekin = 8.64036139073472 | erot = 17.435031602458 | epot = -130.304718885752 | etot = -104.22932589256 +205000 ekin = 8.66192717162963 | erot = 17.8705703808059 | epot = -129.744393097525 | etot = -103.211895545089 +206000 ekin = 8.18798685710702 | erot = 16.9494530844962 | epot = -129.347297685166 | etot = -104.209857743563 +207000 ekin = 7.88269489811464 | erot = 18.0934252936306 | epot = -128.990899660502 | etot = -103.014779468757 +208000 ekin = 8.12847467633978 | erot = 18.4474275963927 | epot = -128.638908979831 | etot = -102.063006707099 +209000 ekin = 8.26627077414831 | erot = 17.1117207999031 | epot = -128.23848022138 | etot = -102.860488647329 +210000 ekin = 8.57369266047589 | erot = 17.032945225006 | epot = -127.514761594822 | etot = -101.908123709341 +211000 ekin = 8.18082139293309 | erot = 15.8142422862498 | epot = -126.729751967164 | etot = -102.734688287982 +212000 ekin = 9.07705835356712 | erot = 15.9995543237684 | epot = -125.964981789987 | etot = -100.888369112651 +213000 ekin = 9.76583660780628 | erot = 15.8151382659827 | epot = -125.199540834626 | etot = -99.6185659608372 +214000 ekin = 9.73283924990857 | erot = 16.6768685665889 | epot = -124.440549725109 | etot = -98.0308419086116 +215000 ekin = 10.1664065327728 | erot = 16.0847590616496 | epot = -123.79380778278 | etot = -97.5426421883573 +216000 ekin = 10.3574466909358 | erot = 14.6556450781529 | epot = -123.28062097795 | etot = -98.2675292088615 +217000 ekin = 9.99430963257152 | erot = 14.6958322737206 | epot = -123.189352423249 | etot = -98.499210516957 +218000 ekin = 10.1271230685036 | erot = 16.0494811167673 | epot = -123.437228010009 | etot = -97.2606238247383 +219000 ekin = 10.4093264435591 | erot = 17.1225695976585 | epot = -123.698309155169 | etot = -96.1664131139511 +220000 ekin = 10.5602197780445 | erot = 16.2275384087012 | epot = -124.065089165668 | etot = -97.277330978922 +221000 ekin = 10.9045703829906 | erot = 18.0174254671399 | epot = -124.727084208592 | etot = -95.8050883584616 +222000 ekin = 11.040495548172 | erot = 17.5416727186541 | epot = -125.550268118699 | etot = -96.9680998518726 +223000 ekin = 11.1981785017269 | erot = 18.164520187603 | epot = -126.473672051786 | etot = -97.1109733624564 +224000 ekin = 12.3865134633279 | erot = 17.2503270676206 | epot = -127.415472901141 | etot = -97.7786323701921 +225000 ekin = 13.4632742183497 | erot = 16.909295138679 | epot = -128.40622689616 | etot = -98.0336575391309 +226000 ekin = 14.1793039795669 | erot = 16.7746173675137 | epot = -129.250401073249 | etot = -98.2964797261683 +227000 ekin = 14.8975736064985 | erot = 17.3200491535059 | epot = -129.944415508111 | etot = -97.7267927481065 +228000 ekin = 15.2580858632895 | erot = 17.2813783440679 | epot = -130.50979767698 | etot = -97.970333469623 +229000 ekin = 15.2815972995915 | erot = 18.1327345586269 | epot = -130.858522010649 | etot = -97.4441901524304 +230000 ekin = 14.9973822396235 | erot = 17.8215863917617 | epot = -130.974519927144 | etot = -98.1555512957592 +231000 ekin = 15.4944447453545 | erot = 16.2505631688955 | epot = -130.85331196464 | etot = -99.1083040503902 +232000 ekin = 15.5013714729644 | erot = 16.2360267966493 | epot = -130.500978065803 | etot = -98.7635797961897 +233000 ekin = 15.6475288254976 | erot = 15.1355009388718 | epot = -130.001130700983 | etot = -99.2181009366136 +234000 ekin = 14.9928070596118 | erot = 14.4561491773725 | epot = -129.212554811537 | etot = -99.7635985745524 +235000 ekin = 14.1500040050198 | erot = 13.5773795570139 | epot = -128.226927217841 | etot = -100.499543655807 +236000 ekin = 14.4337875956183 | erot = 10.7128375101057 | epot = -127.271678633039 | etot = -102.125053527315 +237000 ekin = 14.5718229916728 | erot = 9.51868813665584 | epot = -126.478805285378 | etot = -102.38829415705 +238000 ekin = 14.5641840406761 | erot = 10.4514244387947 | epot = -125.959186005466 | etot = -100.943577525995 +239000 ekin = 14.7945250169988 | erot = 11.969263456021 | epot = -125.65407099266 | etot = -98.89028251964 +240000 ekin = 14.0676596483411 | erot = 13.0566366120945 | epot = -125.489156131504 | etot = -98.364859871068 +241000 ekin = 14.7580193710404 | erot = 15.6473002667172 | epot = -125.66357027176 | etot = -95.2582506340023 +242000 ekin = 15.0062171423708 | erot = 15.5223047402974 | epot = -126.083825388996 | etot = -95.5553035063272 +243000 ekin = 14.7207315030811 | erot = 18.4914286449845 | epot = -126.572433200165 | etot = -93.3602730520994 +244000 ekin = 15.0653849672011 | erot = 19.6152150630557 | epot = -127.121940701804 | etot = -92.4413406715474 +245000 ekin = 14.5826576895288 | erot = 20.3516097643047 | epot = -127.553594792066 | etot = -92.6193273382324 +246000 ekin = 13.9733910446231 | erot = 19.6995579979128 | epot = -127.855154542609 | etot = -94.182205500073 +247000 ekin = 13.736300165071 | erot = 20.1509121154037 | epot = -127.994211800693 | etot = -94.106999520218 +248000 ekin = 13.4538859747754 | erot = 18.603950634457 | epot = -127.933960738259 | etot = -95.8761241290265 +249000 ekin = 13.297290371713 | erot = 16.5376067949551 | epot = -127.726266783486 | etot = -97.8913696168181 +250000 ekin = 13.0769443442147 | erot = 15.5723980218652 | epot = -127.384478077717 | etot = -98.7351357116367 +251000 ekin = 12.3569665649421 | erot = 14.4296804417377 | epot = -127.05572435213 | etot = -100.26907734545 +252000 ekin = 12.2031777119723 | erot = 12.4241877259964 | epot = -126.724280026054 | etot = -102.096914588085 +253000 ekin = 12.3738435396613 | erot = 14.5862876200654 | epot = -126.430208509831 | etot = -99.4700773501048 +254000 ekin = 12.701123410553 | erot = 11.9848764326328 | epot = -126.255809655633 | etot = -101.569809812447 +255000 ekin = 12.3382365581446 | erot = 12.7694066951398 | epot = -126.233303332426 | etot = -101.125660079142 +256000 ekin = 12.5719056004921 | erot = 11.5455936083012 | epot = -126.375065873605 | etot = -102.257566664812 +257000 ekin = 12.8416394174466 | erot = 10.7766996711506 | epot = -126.680049307901 | etot = -103.061710219303 +258000 ekin = 12.9127876656524 | erot = 10.6100975371551 | epot = -127.056048348568 | etot = -103.533163145761 +259000 ekin = 13.0763581338929 | erot = 12.1546697170536 | epot = -127.528741703229 | etot = -102.297713852282 +260000 ekin = 12.9774755067595 | erot = 11.7128970638702 | epot = -127.854225807735 | etot = -103.163853237105 +261000 ekin = 12.6289865133086 | erot = 11.916003948093 | epot = -128.074160501116 | etot = -103.529170039715 +262000 ekin = 12.7023707694459 | erot = 11.5117802208444 | epot = -128.203484535596 | etot = -103.989333545305 +263000 ekin = 12.6698225025792 | erot = 11.6383988496484 | epot = -128.150951306963 | etot = -103.842729954735 +264000 ekin = 12.7498512344178 | erot = 11.747728649697 | epot = -128.001417548791 | etot = -103.503837664677 +265000 ekin = 12.7016227310984 | erot = 12.8720320892253 | epot = -127.952383302815 | etot = -102.378728482492 +266000 ekin = 12.8942439084782 | erot = 12.8567176427997 | epot = -128.012852928163 | etot = -102.261891376885 +267000 ekin = 13.0340848907472 | erot = 11.6602421677083 | epot = -128.191216268543 | etot = -103.496889210087 +268000 ekin = 13.74589289983 | erot = 11.7671487795819 | epot = -128.563005843981 | etot = -103.049964164569 +269000 ekin = 13.9144500485916 | erot = 12.0904513989345 | epot = -128.873355694132 | etot = -102.868454246606 +270000 ekin = 13.5038302515385 | erot = 13.2027756375057 | epot = -129.228046693482 | etot = -102.521440804438 +271000 ekin = 13.1726853474607 | erot = 14.5028204858769 | epot = -129.509496883975 | etot = -101.833991050637 +272000 ekin = 13.1912017675959 | erot = 13.5128916820094 | epot = -129.700425481901 | etot = -102.996332032296 +273000 ekin = 12.9622515947264 | erot = 12.8466394726389 | epot = -129.921650080588 | etot = -104.112759013222 +274000 ekin = 12.5726481833756 | erot = 13.144678909737 | epot = -130.003176276943 | etot = -104.28584918383 +275000 ekin = 12.2148607636527 | erot = 13.2928615382628 | epot = -129.750232770451 | etot = -104.242510468535 +276000 ekin = 11.5576072728742 | erot = 11.9452733541113 | epot = -129.307440448112 | etot = -105.804559821127 +277000 ekin = 11.0565703290287 | erot = 11.469754008817 | epot = -128.75449578412 | etot = -106.228171446274 +278000 ekin = 10.7140705151042 | erot = 12.8871671766821 | epot = -128.25525823396 | etot = -104.654020542174 +279000 ekin = 10.2324972238429 | erot = 12.7118920306067 | epot = -127.872408298753 | etot = -104.928019044303 +280000 ekin = 9.79931602143696 | erot = 13.8984293718546 | epot = -127.807598666717 | etot = -104.109853273425 +281000 ekin = 9.96767949511765 | erot = 14.9654599630386 | epot = -127.757791381375 | etot = -102.824651923219 +282000 ekin = 9.89651453389989 | erot = 13.5038073340885 | epot = -127.982178238681 | etot = -104.581856370693 +283000 ekin = 9.35876750231768 | erot = 15.0311658542219 | epot = -128.425494240096 | etot = -104.035560883557 +284000 ekin = 8.57796244132644 | erot = 17.1817140478391 | epot = -129.113884013508 | etot = -103.354207524343 +285000 ekin = 9.05859694880589 | erot = 17.9339958923453 | epot = -130.133829218508 | etot = -103.141236377357 +286000 ekin = 9.17556209977891 | erot = 18.2995006002098 | epot = -131.242009857551 | etot = -103.766947157562 +287000 ekin = 9.39155514425713 | erot = 17.9196244698037 | epot = -132.27033351819 | etot = -104.959153904129 +288000 ekin = 9.76851862303189 | erot = 17.6913296641995 | epot = -133.197079996702 | etot = -105.737231709471 +289000 ekin = 10.1309528932397 | erot = 14.7061979034103 | epot = -133.872197861025 | etot = -109.035047064375 +290000 ekin = 10.9195489558526 | erot = 15.1690523778334 | epot = -134.442096043655 | etot = -108.353494709969 +291000 ekin = 11.3604751581556 | erot = 13.153742270531 | epot = -134.942066208005 | etot = -110.427848779318 +292000 ekin = 12.1184001542666 | erot = 12.7399143491585 | epot = -135.347997739513 | etot = -110.489683236088 +293000 ekin = 12.5651917109573 | erot = 13.5564554248973 | epot = -135.657332732208 | etot = -109.535685596353 +294000 ekin = 13.2393207416801 | erot = 11.835377731584 | epot = -135.972747963976 | etot = -110.898049490712 +295000 ekin = 14.0110196704011 | erot = 11.3649738472938 | epot = -136.372700304619 | etot = -110.996706786924 +296000 ekin = 14.7267764120059 | erot = 13.5793475441506 | epot = -136.743277666314 | etot = -108.437153710158 +297000 ekin = 15.2715627348123 | erot = 11.5626347691872 | epot = -137.087873604616 | etot = -110.253676100617 +298000 ekin = 16.0387776845994 | erot = 12.8157712333341 | epot = -137.568618159699 | etot = -108.714069241765 +299000 ekin = 16.587224686565 | erot = 13.5924474386199 | epot = -138.038387602089 | etot = -107.858715476904 +300000 ekin = 16.9700828590548 | erot = 13.2635259234366 | epot = -138.350224271807 | etot = -108.116615489315 +301000 ekin = 17.5403695703678 | erot = 12.344461606446 | epot = -138.564780141525 | etot = -108.679948964711 +302000 ekin = 17.999368780733 | erot = 10.9002774435477 | epot = -138.669984344615 | etot = -109.770338120335 +303000 ekin = 18.5119335743994 | erot = 11.3459589833676 | epot = -138.702590892745 | etot = -108.844698334978 +304000 ekin = 18.9041713193929 | erot = 9.35010741615854 | epot = -138.69532616302 | etot = -110.441047427468 +305000 ekin = 19.4425597436692 | erot = 9.42197838138271 | epot = -138.633141612569 | etot = -109.768603487517 +306000 ekin = 19.6036016605872 | erot = 10.6931976987772 | epot = -138.477912570479 | etot = -108.181113211115 +307000 ekin = 19.3417236015309 | erot = 13.2387828544056 | epot = -138.253199109005 | etot = -105.672692653069 +308000 ekin = 18.6999426944204 | erot = 11.973083632259 | epot = -137.851569596535 | etot = -107.178543269856 +309000 ekin = 18.7265657872805 | erot = 13.0303472217923 | epot = -137.317309351105 | etot = -105.560396342032 +310000 ekin = 17.8195957255941 | erot = 14.0238269204621 | epot = -136.848405156991 | etot = -105.004982510935 +311000 ekin = 17.1255719645332 | erot = 15.2230056343622 | epot = -136.455665695132 | etot = -104.107088096236 +312000 ekin = 17.5406156481837 | erot = 16.4951001106738 | epot = -136.079726861853 | etot = -102.044011102996 +313000 ekin = 17.1670923816363 | erot = 15.0877984771809 | epot = -135.822923328133 | etot = -103.568032469316 +314000 ekin = 16.6423728735091 | erot = 15.2891889046024 | epot = -135.810853367455 | etot = -103.879291589344 +315000 ekin = 16.7627241814776 | erot = 14.6381862323553 | epot = -135.936566495695 | etot = -104.535656081862 +316000 ekin = 16.7205036269676 | erot = 15.3512491017753 | epot = -136.088132270724 | etot = -104.016379541981 +317000 ekin = 17.366695391312 | erot = 15.0403764000411 | epot = -136.090944178317 | etot = -103.683872386964 +318000 ekin = 17.3898541429783 | erot = 14.4562587649093 | epot = -136.029567624113 | etot = -104.183454716225 +319000 ekin = 17.6468368920276 | erot = 13.5657924751129 | epot = -135.837201238631 | etot = -104.62457187149 +320000 ekin = 17.853845424944 | erot = 11.4555633526327 | epot = -135.634795052626 | etot = -106.325386275049 +321000 ekin = 18.4774011194484 | erot = 9.47340321644106 | epot = -135.396484896295 | etot = -107.445680560405 +322000 ekin = 18.5638208747372 | erot = 10.5540356873042 | epot = -135.178405880719 | etot = -106.060549318678 +323000 ekin = 18.3144849132937 | erot = 9.18750574356535 | epot = -135.011277898535 | etot = -107.509287241676 +324000 ekin = 18.2814120547138 | erot = 8.43295922987849 | epot = -134.870516827034 | etot = -108.156145542441 +325000 ekin = 17.6828287811198 | erot = 9.25503886901379 | epot = -134.72004058206 | etot = -107.782172931927 +326000 ekin = 17.5682068543231 | erot = 8.80877184189272 | epot = -134.518753123174 | etot = -108.141774426958 +327000 ekin = 17.563579091233 | erot = 9.26405936905546 | epot = -134.407298439375 | etot = -107.579659979087 +328000 ekin = 17.6947130932733 | erot = 10.1923998064966 | epot = -134.311937694853 | etot = -106.424824795083 +329000 ekin = 17.1881472843045 | erot = 9.42382068529237 | epot = -134.061202456107 | etot = -107.44923448651 +330000 ekin = 16.7033164328865 | erot = 10.5958861015874 | epot = -133.644326190092 | etot = -106.345123655618 +331000 ekin = 16.5614873472988 | erot = 11.0963106255071 | epot = -133.114955864068 | etot = -105.457157891263 +332000 ekin = 15.344800831015 | erot = 10.5204968548347 | epot = -132.655714437217 | etot = -106.790416751368 +333000 ekin = 14.8824601261092 | erot = 11.0665055647672 | epot = -132.381703135978 | etot = -106.432737445102 +334000 ekin = 14.3520097856488 | erot = 11.2693925718679 | epot = -132.234967905192 | etot = -106.613565547675 +335000 ekin = 13.3400126008158 | erot = 11.5365782005848 | epot = -132.005833272039 | etot = -107.129242470638 +336000 ekin = 13.4251377988672 | erot = 12.7016844832713 | epot = -131.693539084324 | etot = -105.566716802185 +337000 ekin = 13.0974476255357 | erot = 10.5699064068532 | epot = -131.267127574954 | etot = -107.599773542565 +338000 ekin = 13.6450169603266 | erot = 11.3468402093231 | epot = -130.910112680268 | etot = -105.918255510618 +339000 ekin = 13.6181925950493 | erot = 12.1076210040202 | epot = -130.557539825855 | etot = -104.831726226786 +340000 ekin = 13.7060735716503 | erot = 12.8412065521541 | epot = -130.462716763992 | etot = -103.915436640188 +341000 ekin = 13.7778063734593 | erot = 13.1174330704424 | epot = -130.531074545887 | etot = -103.635835101985 +342000 ekin = 13.954513538403 | erot = 13.7402525553091 | epot = -130.774043628587 | etot = -103.079277534875 +343000 ekin = 13.6604942473275 | erot = 15.5089663905455 | epot = -131.055721366082 | etot = -101.886260728209 +344000 ekin = 14.2665127121401 | erot = 12.2031321771093 | epot = -131.282570170384 | etot = -104.812925281134 +345000 ekin = 14.982149542259 | erot = 14.1635371069014 | epot = -131.519726557152 | etot = -102.374039907991 +346000 ekin = 14.998876481554 | erot = 13.4617445281837 | epot = -131.723744104871 | etot = -103.263123095133 +347000 ekin = 15.541259245477 | erot = 13.601421487498 | epot = -131.923412477975 | etot = -102.780731745 +348000 ekin = 16.7329536809704 | erot = 15.090740991205 | epot = -132.143772859728 | etot = -100.320078187552 +349000 ekin = 17.3861913016786 | erot = 15.1922827054211 | epot = -132.306356374554 | etot = -99.7278823674542 +350000 ekin = 16.8574823749626 | erot = 18.3600447459492 | epot = -132.445783817605 | etot = -97.2282566966928 +351000 ekin = 16.6164885604699 | erot = 17.7507419907115 | epot = -132.477967998207 | etot = -98.1107374470257 +352000 ekin = 16.3906985693055 | erot = 16.3395128451898 | epot = -132.469143894269 | etot = -99.7389324797738 +353000 ekin = 16.4418561748943 | erot = 15.3428425414812 | epot = -132.543386699625 | etot = -100.758687983249 +354000 ekin = 16.6947592950631 | erot = 15.1610311708645 | epot = -132.725354977831 | etot = -100.869564511904 +355000 ekin = 16.7054244183613 | erot = 15.2739548015032 | epot = -132.888828993417 | etot = -100.909449773552 +356000 ekin = 15.8418260139205 | erot = 15.6343326906158 | epot = -133.092904724418 | etot = -101.616746019881 +357000 ekin = 15.8177678978165 | erot = 15.2776312771737 | epot = -133.349964737571 | etot = -102.254565562581 +358000 ekin = 16.247272467314 | erot = 17.5237438978863 | epot = -133.533290253873 | etot = -99.7622738886724 +359000 ekin = 15.9369501984957 | erot = 16.4723204711401 | epot = -133.373483972013 | etot = -100.964213302377 +360000 ekin = 15.6524039179353 | erot = 16.0917756991532 | epot = -133.088827410712 | etot = -101.344647793623 +361000 ekin = 16.1255813737833 | erot = 14.6043819685595 | epot = -132.682676037011 | etot = -101.952712694669 +362000 ekin = 16.2084060425783 | erot = 15.3061306055287 | epot = -132.004572522378 | etot = -100.490035874271 +363000 ekin = 16.5841147977374 | erot = 13.2870116635265 | epot = -131.206997511749 | etot = -101.335871050485 +364000 ekin = 16.2264175141248 | erot = 13.4839607171259 | epot = -130.301334854897 | etot = -100.590956623646 +365000 ekin = 16.3338338884753 | erot = 11.8882794464809 | epot = -129.439123661589 | etot = -101.217010326633 +366000 ekin = 17.1178313527511 | erot = 10.6429828523485 | epot = -128.636953230029 | etot = -100.876139024929 +367000 ekin = 17.3978780298834 | erot = 10.6214323462969 | epot = -127.896731204461 | etot = -99.8774208282811 +368000 ekin = 18.3422043204519 | erot = 9.4920165520943 | epot = -127.35450483558 | etot = -99.5202839630333 +369000 ekin = 18.4267461523155 | erot = 7.58439614439429 | epot = -126.945478039691 | etot = -100.934335742981 +370000 ekin = 18.2591228784488 | erot = 7.91611442179113 | epot = -126.712837988326 | etot = -100.537600688086 +371000 ekin = 18.2272055256963 | erot = 8.48549388283735 | epot = -126.57487508976 | etot = -99.862175681226 +372000 ekin = 18.0229029350717 | erot = 8.16872677639403 | epot = -126.568133032703 | etot = -100.376503321237 +373000 ekin = 18.0182875091869 | erot = 8.52949424427823 | epot = -126.633731606883 | etot = -100.085949853418 +374000 ekin = 17.5191535636621 | erot = 8.7866303781134 | epot = -126.751870079523 | etot = -100.446086137747 +375000 ekin = 17.5729190729748 | erot = 11.0368009575165 | epot = -127.082054262238 | etot = -98.4723342317464 +376000 ekin = 18.0972024010139 | erot = 12.0869149457635 | epot = -127.446482398761 | etot = -97.2623650519836 +377000 ekin = 17.6238550669767 | erot = 13.7823413485362 | epot = -127.957012085504 | etot = -96.5508156699915 +378000 ekin = 17.1545260492794 | erot = 13.8789438569943 | epot = -128.483574679142 | etot = -97.4501047728679 +379000 ekin = 17.3943043447361 | erot = 15.6128954133663 | epot = -128.994286417227 | etot = -95.9870866591242 +380000 ekin = 16.9345655337106 | erot = 18.1586393022775 | epot = -129.430697636469 | etot = -94.3374928004806 +381000 ekin = 17.8592077966176 | erot = 16.952172224398 | epot = -130.21546363601 | etot = -95.404083614994 +382000 ekin = 17.6738126866299 | erot = 17.8907570066601 | epot = -130.472318203666 | etot = -94.907748510376 +383000 ekin = 17.3598919179248 | erot = 16.8602796085688 | epot = -130.370641785571 | etot = -96.1504702590775 +384000 ekin = 18.2785876510998 | erot = 16.1041146883972 | epot = -130.284480210515 | etot = -95.9017778710178 +385000 ekin = 18.0115952307709 | erot = 16.1845211065083 | epot = -130.175062220429 | etot = -95.9789458831495 +386000 ekin = 18.2027845423779 | erot = 13.5505429677105 | epot = -130.071894452599 | etot = -98.3185669425111 +387000 ekin = 19.0293092080126 | erot = 12.3123326888389 | epot = -130.135076599882 | etot = -98.7934347030301 +388000 ekin = 18.6600110494417 | erot = 12.2331355301054 | epot = -130.332797961397 | etot = -99.4396513818503 +389000 ekin = 18.818884817512 | erot = 12.7152045936026 | epot = -130.592939995127 | etot = -99.0588505840127 +390000 ekin = 18.6974666589397 | erot = 10.8179966323085 | epot = -130.78222296628 | etot = -101.266759675032 +391000 ekin = 18.3414303481244 | erot = 12.2662395181876 | epot = -131.036431663152 | etot = -100.42876179684 +392000 ekin = 18.5329248278577 | erot = 12.6118921508214 | epot = -131.466923523897 | etot = -100.322106545218 +393000 ekin = 18.5931926394875 | erot = 12.8938189916972 | epot = -132.085060887916 | etot = -100.598049256732 +394000 ekin = 18.2689521082511 | erot = 15.0363349114738 | epot = -132.658203470269 | etot = -99.3529164505442 +395000 ekin = 18.6758840400074 | erot = 16.5774071524663 | epot = -133.167812128949 | etot = -97.9145209364753 +396000 ekin = 18.4208033998166 | erot = 16.041020157979 | epot = -133.420028914843 | etot = -98.9582053570477 +397000 ekin = 18.4283974295758 | erot = 17.6803004336543 | epot = -133.424412246365 | etot = -97.3157143831351 +398000 ekin = 18.4760707507248 | erot = 16.8354806241528 | epot = -133.369641128673 | etot = -98.0580897537952 +399000 ekin = 18.0667158930869 | erot = 15.5802846351424 | epot = -133.22438235147 | etot = -99.5773818232405 +400000 ekin = 17.3629932701991 | erot = 14.8051530851039 | epot = -133.239266370825 | etot = -101.071120015522 +401000 ekin = 17.2940999376157 | erot = 16.6455729704891 | epot = -133.275703752707 | etot = -99.3360308446024 +402000 ekin = 17.3373502544325 | erot = 17.3495249767143 | epot = -133.263650452982 | etot = -98.5767752218353 +403000 ekin = 17.0362458779982 | erot = 16.4801854838531 | epot = -133.157361678239 | etot = -99.6409303163881 +404000 ekin = 17.5013218057167 | erot = 17.2356941364713 | epot = -132.956729120098 | etot = -98.2197131779096 +405000 ekin = 17.0802098794189 | erot = 16.960939476204 | epot = -132.73062826728 | etot = -98.6894789116567 +406000 ekin = 17.1407753969823 | erot = 16.5675801382684 | epot = -132.546431302203 | etot = -98.8380757669523 +407000 ekin = 17.5700320840176 | erot = 16.7173366740167 | epot = -132.354385760767 | etot = -98.0670170027328 +408000 ekin = 17.9123282076661 | erot = 15.7372438792219 | epot = -132.093303820899 | etot = -98.4437317340109 +409000 ekin = 18.044290976688 | erot = 16.407264301022 | epot = -131.981012061687 | etot = -97.5294567839774 +410000 ekin = 17.4352926916021 | erot = 16.3490998455989 | epot = -131.999734401999 | etot = -98.2153418647982 +411000 ekin = 17.0403229577767 | erot = 17.0106034249502 | epot = -131.927984341917 | etot = -97.8770579591898 +412000 ekin = 16.3738553108077 | erot = 15.0380907323597 | epot = -131.815285103374 | etot = -100.403339060206 +413000 ekin = 15.6919116030853 | erot = 17.2865003579153 | epot = -131.733742658542 | etot = -98.7553306975415 +414000 ekin = 15.6596268128862 | erot = 18.3746086998306 | epot = -131.584803652767 | etot = -97.5505681400504 +415000 ekin = 14.8929074608614 | erot = 17.7221778643748 | epot = -131.540961193749 | etot = -98.9258758685133 +416000 ekin = 14.4887531949694 | erot = 16.0376591524414 | epot = -131.440311706363 | etot = -100.913899358952 +417000 ekin = 14.1092266063953 | erot = 15.9394824142608 | epot = -131.425898951561 | etot = -101.377189930905 +418000 ekin = 13.5048216543633 | erot = 16.2965565979027 | epot = -131.446662451558 | etot = -101.645284199292 +419000 ekin = 13.3086351919324 | erot = 15.4549783534211 | epot = -131.453449134288 | etot = -102.689835588934 +420000 ekin = 13.0039130784646 | erot = 15.3952024087555 | epot = -131.719273036113 | etot = -103.320157548893 +421000 ekin = 12.9877601419768 | erot = 15.1190337961972 | epot = -132.049830775422 | etot = -103.943036837248 +422000 ekin = 12.554469558493 | erot = 16.7536314378964 | epot = -132.424089805828 | etot = -103.115988809439 +423000 ekin = 12.3222010360323 | erot = 14.8918300268163 | epot = -132.786217773111 | etot = -105.572186710262 +424000 ekin = 12.5012656891908 | erot = 14.7126562690067 | epot = -132.854779708475 | etot = -105.640857750277 +425000 ekin = 12.4166002750664 | erot = 16.1748358263138 | epot = -132.827420051655 | etot = -104.235983950275 +426000 ekin = 12.1981797043573 | erot = 15.3722763039744 | epot = -132.839512680494 | etot = -105.269056672162 +427000 ekin = 12.2165197755212 | erot = 15.2845443324948 | epot = -132.75768742892 | etot = -105.256623320904 +428000 ekin = 13.1144440915078 | erot = 15.6749776075794 | epot = -132.542738612485 | etot = -103.753316913397 +429000 ekin = 13.036052320167 | erot = 15.7209148357586 | epot = -132.22260768664 | etot = -103.465640530715 +430000 ekin = 13.6804158115964 | erot = 14.2380884060342 | epot = -131.771024384698 | etot = -103.852520167068 +431000 ekin = 13.9916031179658 | erot = 14.4553961722166 | epot = -131.156620565525 | etot = -102.709621275343 +432000 ekin = 13.8407074506787 | erot = 14.0482504895216 | epot = -130.497219933366 | etot = -102.608261993166 +433000 ekin = 13.9379330807462 | erot = 14.8523876478218 | epot = -129.700123346572 | etot = -100.909802618004 +434000 ekin = 14.1249100563244 | erot = 14.6514940517254 | epot = -128.827486006554 | etot = -100.051081898504 +435000 ekin = 14.0577137236944 | erot = 14.8667331330112 | epot = -128.014172796523 | etot = -99.0897259398178 +436000 ekin = 14.5305553563525 | erot = 14.077832522527 | epot = -127.226475749873 | etot = -98.6180878709938 +437000 ekin = 15.1830124290822 | erot = 14.1336118031537 | epot = -126.373743476486 | etot = -97.0571192442501 +438000 ekin = 16.1148966247471 | erot = 13.7238250343371 | epot = -125.603706556133 | etot = -95.7649848970485 +439000 ekin = 15.385679382347 | erot = 13.0371901783453 | epot = -125.011554691989 | etot = -96.5886851312965 +440000 ekin = 14.8956016821331 | erot = 13.2387714435016 | epot = -124.533132544974 | etot = -96.3987594193397 +441000 ekin = 15.1065254767362 | erot = 11.8972960070098 | epot = -124.250944728352 | etot = -97.2471232446062 +442000 ekin = 15.3644507419134 | erot = 10.7065439746187 | epot = -124.229899271249 | etot = -98.1589045547165 +443000 ekin = 15.3891963376255 | erot = 10.1101763676241 | epot = -124.493875210453 | etot = -98.9945025052031 +444000 ekin = 16.0632437745756 | erot = 10.4333528402067 | epot = -124.833925383649 | etot = -98.3373287688666 +445000 ekin = 17.2273822876834 | erot = 8.91547796476049 | epot = -125.383423644888 | etot = -99.2405633924442 +446000 ekin = 17.1389184638908 | erot = 9.12523748934503 | epot = -126.015232743036 | etot = -99.7510767898003 +447000 ekin = 17.377575602989 | erot = 8.67259461502235 | epot = -126.729888890992 | etot = -100.67971867298 +448000 ekin = 17.2411873858276 | erot = 10.5843952673172 | epot = -127.469866797344 | etot = -99.6442841441993 +449000 ekin = 16.5447004709401 | erot = 12.6570239249849 | epot = -127.967892349291 | etot = -98.7661679533661 +450000 ekin = 16.6696115448345 | erot = 13.660677404722 | epot = -128.35986377413 | etot = -98.0295748245735 +451000 ekin = 16.5552547561237 | erot = 16.503578149668 | epot = -128.634970955751 | etot = -95.5761380499589 +452000 ekin = 16.2155010684469 | erot = 17.0500352874338 | epot = -128.726789743404 | etot = -95.4612533875228 +453000 ekin = 16.2255379767424 | erot = 16.185189206655 | epot = -128.722337839339 | etot = -96.3116106559417 +454000 ekin = 16.5243165270907 | erot = 16.6985926110523 | epot = -128.556875352001 | etot = -95.3339662138579 +455000 ekin = 16.9760722657111 | erot = 17.8495892261178 | epot = -128.399530068863 | etot = -93.5738685770343 +456000 ekin = 16.9744890299368 | erot = 17.0726018893998 | epot = -128.193610158915 | etot = -94.1465192395783 +457000 ekin = 16.1512954354001 | erot = 16.737623335392 | epot = -127.967910997967 | etot = -95.0789922271744 +458000 ekin = 15.8580429496479 | erot = 16.4857785048016 | epot = -127.751523953145 | etot = -95.407702498695 +459000 ekin = 15.5887403100112 | erot = 15.4749874483398 | epot = -127.617668067827 | etot = -96.5539403094756 +460000 ekin = 15.0949705154881 | erot = 13.2973001244165 | epot = -127.598680189169 | etot = -99.2064095492648 +461000 ekin = 15.0290066467678 | erot = 14.29519361259 | epot = -127.707013966238 | etot = -98.3828137068801 +462000 ekin = 15.8077450100979 | erot = 13.6257527682163 | epot = -127.884476940387 | etot = -98.4509791620729 +463000 ekin = 16.062196194493 | erot = 14.3797480578408 | epot = -127.829474639376 | etot = -97.387530387042 +464000 ekin = 16.1624606718217 | erot = 13.3998051887236 | epot = -127.51699406138 | etot = -97.9547282008342 +465000 ekin = 15.6381101655691 | erot = 12.5725935623154 | epot = -127.066598022852 | etot = -98.8558942949679 +466000 ekin = 15.2407794586003 | erot = 13.3100076426715 | epot = -126.622194820008 | etot = -98.0714077187358 +467000 ekin = 15.0664135855113 | erot = 13.6942009748088 | epot = -126.28954890608 | etot = -97.5289343457599 +468000 ekin = 14.5001274424649 | erot = 15.1357469131307 | epot = -126.07424293658 | etot = -96.4383685809844 +469000 ekin = 13.8148903552505 | erot = 14.223999189392 | epot = -125.858567589752 | etot = -97.8196780451091 +470000 ekin = 12.6907212988909 | erot = 13.6918076668432 | epot = -125.767431927259 | etot = -99.3849029615245 +471000 ekin = 12.4289290086777 | erot = 15.0863192981982 | epot = -125.804921167394 | etot = -98.2896728605182 +472000 ekin = 12.1365487961463 | erot = 15.8579152946744 | epot = -125.988649611677 | etot = -97.9941855208562 +473000 ekin = 13.0961380363004 | erot = 16.1001497266475 | epot = -126.771177224312 | etot = -97.5748894613642 +474000 ekin = 13.3403983346927 | erot = 15.895679725814 | epot = -127.294879744049 | etot = -98.0588016835421 +475000 ekin = 13.3958404060839 | erot = 15.5810145881428 | epot = -127.668448007433 | etot = -98.691593013206 +476000 ekin = 12.8342624195179 | erot = 14.012167697525 | epot = -127.891612353104 | etot = -101.045182236061 +477000 ekin = 13.4994760162231 | erot = 14.5514425266847 | epot = -127.705505124345 | etot = -99.6545865814376 +478000 ekin = 13.0008910137509 | erot = 14.4625603245608 | epot = -127.285952890868 | etot = -99.8225015525561 +479000 ekin = 12.925623431067 | erot = 12.8402234582223 | epot = -126.723146755559 | etot = -100.957299866269 +480000 ekin = 12.6915178381984 | erot = 11.8974174666012 | epot = -126.064725410566 | etot = -101.475790105766 +481000 ekin = 11.9916396192061 | erot = 12.2214430216206 | epot = -125.413028349128 | etot = -101.199945708301 +482000 ekin = 11.3629431274558 | erot = 11.391757186839 | epot = -124.8621930605 | etot = -102.107492746205 +483000 ekin = 11.5689648109245 | erot = 10.144520666394 | epot = -124.438832864686 | etot = -102.725347387368 +484000 ekin = 11.4499537844141 | erot = 11.7371690424975 | epot = -124.381939468864 | etot = -101.194816641953 +485000 ekin = 12.0189710017623 | erot = 11.7434065697059 | epot = -124.614298842439 | etot = -100.851921270971 +486000 ekin = 11.8991797933449 | erot = 13.5151264595704 | epot = -125.077358922215 | etot = -99.6630526693001 +487000 ekin = 12.4219195894054 | erot = 15.6605158990156 | epot = -125.929338188086 | etot = -97.8469026996647 +488000 ekin = 12.8520167671218 | erot = 16.2319523237351 | epot = -126.955871195299 | etot = -97.8719021044424 +489000 ekin = 13.7133618431336 | erot = 18.3140519919298 | epot = -128.237887359736 | etot = -96.2104735246727 +490000 ekin = 14.2146690739332 | erot = 18.9961890015251 | epot = -129.588400932625 | etot = -96.3775428571665 +491000 ekin = 14.808905169883 | erot = 21.5224586397688 | epot = -131.015732216573 | etot = -94.6843684069208 +492000 ekin = 14.750712438806 | erot = 22.5923047841892 | epot = -132.246725890571 | etot = -94.9037086675762 +493000 ekin = 15.1077946421563 | erot = 22.6929093665649 | epot = -133.247303637476 | etot = -95.4465996287548 +494000 ekin = 15.1920275386136 | erot = 23.5057837098355 | epot = -133.917128945417 | etot = -95.2193176969681 +495000 ekin = 15.0480842601332 | erot = 21.4431285606056 | epot = -134.196913391918 | etot = -97.7057005711795 +496000 ekin = 14.801133841351 | erot = 22.137297148718 | epot = -134.202005678487 | etot = -97.2635746884177 +497000 ekin = 14.5566297317389 | erot = 22.9603809009053 | epot = -133.933825890348 | etot = -96.4168152577042 +498000 ekin = 14.6619206915101 | erot = 22.9348589273131 | epot = -133.417393773742 | etot = -95.8206141549183 +499000 ekin = 14.6543962596984 | erot = 18.7924434716854 | epot = -132.757790561971 | etot = -99.3109508305874 +500000 ekin = 14.7948775335471 | erot = 16.8704146240129 | epot = -131.958349808731 | etot = -100.293057651171 +501000 ekin = 14.8212816049331 | erot = 17.2091603638901 | epot = -131.118007497895 | etot = -99.0875655290715 +502000 ekin = 14.2885953758062 | erot = 15.85905487186 | epot = -130.39871612516 | etot = -100.251065877494 +503000 ekin = 14.0762344761913 | erot = 14.1483016387479 | epot = -129.744615024457 | etot = -101.520078909518 +504000 ekin = 14.176212959032 | erot = 14.2350898986543 | epot = -129.207198739059 | etot = -100.795895881373 +505000 ekin = 13.6888052577052 | erot = 14.2289443328037 | epot = -128.696137557374 | etot = -100.778387966865 +506000 ekin = 13.4857007103928 | erot = 11.6555737897757 | epot = -128.364531164014 | etot = -103.223256663846 +507000 ekin = 13.0537719068172 | erot = 10.7795083902701 | epot = -128.193789387401 | etot = -104.360509090314 +508000 ekin = 13.1162062822673 | erot = 11.4121783699166 | epot = -128.279833854618 | etot = -103.751449202435 +509000 ekin = 13.1836336688781 | erot = 11.5863056276099 | epot = -128.45911395506 | etot = -103.689174658572 +510000 ekin = 13.0280622782 | erot = 11.8450610227354 | epot = -128.740981895406 | etot = -103.86785859447 +511000 ekin = 12.3628109385324 | erot = 12.7404715566925 | epot = -128.944512647296 | etot = -103.841230152071 +512000 ekin = 12.3887761509538 | erot = 13.4980201010906 | epot = -128.966759710659 | etot = -103.079963458614 +513000 ekin = 12.6203594119359 | erot = 14.9620317911436 | epot = -128.917294459074 | etot = -101.334903255995 +514000 ekin = 12.416213783629 | erot = 12.5299068441166 | epot = -128.735514185956 | etot = -103.789393558211 +515000 ekin = 12.0294921527753 | erot = 13.3421264250705 | epot = -128.446078796814 | etot = -103.074460218968 +516000 ekin = 11.8441128618075 | erot = 12.277781080756 | epot = -128.103440698687 | etot = -103.981546756123 +517000 ekin = 12.3586706122186 | erot = 12.3670188016377 | epot = -128.082833904249 | etot = -103.357144490393 +518000 ekin = 12.9365280265603 | erot = 11.8762998706373 | epot = -128.22698743522 | etot = -103.414159538022 +519000 ekin = 13.6117924708073 | erot = 13.3273571491215 | epot = -128.635724945509 | etot = -101.69657532558 +520000 ekin = 14.1284257546955 | erot = 14.8580807891771 | epot = -129.210763866088 | etot = -100.224257322215 +521000 ekin = 14.2594823424047 | erot = 15.9120363152587 | epot = -129.920545116455 | etot = -99.7490264587917 +522000 ekin = 14.6923115374459 | erot = 15.7230660161783 | epot = -130.676867164244 | etot = -100.26148961062 +523000 ekin = 15.8340959189976 | erot = 15.7547714850755 | epot = -131.59187880646 | etot = -100.003011402387 +524000 ekin = 15.9462671339903 | erot = 16.1578758631154 | epot = -132.52371992845 | etot = -100.419576931344 +525000 ekin = 15.813201014982 | erot = 14.802508044054 | epot = -133.377920150286 | etot = -102.76221109125 +526000 ekin = 15.9259293672298 | erot = 16.1371214076855 | epot = -134.291592712454 | etot = -102.228541937539 +527000 ekin = 15.9819142520504 | erot = 15.5862790563603 | epot = -135.192735086636 | etot = -103.624541778225 +528000 ekin = 16.1691928695597 | erot = 17.1936054197086 | epot = -136.054848670118 | etot = -102.69205038085 +529000 ekin = 15.8817769138475 | erot = 19.3393060367764 | epot = -136.763310777796 | etot = -101.542227827172 +530000 ekin = 15.5515554360964 | erot = 19.8324657382225 | epot = -137.157056151491 | etot = -101.773034977172 +531000 ekin = 14.9303544336884 | erot = 19.0533857282465 | epot = -137.248602719131 | etot = -103.264862557196 +532000 ekin = 14.6915272773098 | erot = 19.0390414117406 | epot = -136.996143110598 | etot = -103.265574421548 +533000 ekin = 13.9218469991517 | erot = 18.7667814804586 | epot = -136.361439999745 | etot = -103.672811520135 +534000 ekin = 13.4103769437142 | erot = 18.8946707342246 | epot = -135.40463976648 | etot = -103.099592088541 +535000 ekin = 12.6789216861393 | erot = 17.8184136269511 | epot = -134.182890960124 | etot = -103.685555647033 +536000 ekin = 12.590240564203 | erot = 17.6185115266883 | epot = -132.857306433374 | etot = -102.648554342482 +537000 ekin = 12.7801413064203 | erot = 18.0490344965301 | epot = -131.608606294163 | etot = -100.779430491213 +538000 ekin = 12.0877979797428 | erot = 14.9801227270707 | epot = -130.49452729631 | etot = -103.426606589496 +539000 ekin = 12.3249668177085 | erot = 13.0781131963431 | epot = -129.732435692574 | etot = -104.329355678523 +540000 ekin = 12.7893035389578 | erot = 9.75097061835908 | epot = -129.346688800889 | etot = -106.806414643573 +541000 ekin = 12.7487638514656 | erot = 9.97259012466338 | epot = -129.383324148842 | etot = -106.661970172713 +542000 ekin = 13.652289820802 | erot = 10.738186646458 | epot = -129.724457369635 | etot = -105.333980902375 +543000 ekin = 14.4952710603151 | erot = 10.2165874947633 | epot = -130.086121346986 | etot = -105.374262791908 +544000 ekin = 15.416882573394 | erot = 11.4128423966562 | epot = -130.51978905639 | etot = -103.69006408634 +545000 ekin = 16.1991969290116 | erot = 11.8259443121054 | epot = -130.995098171202 | etot = -102.969956930085 +546000 ekin = 16.7458919606058 | erot = 12.4861916085953 | epot = -131.293817426567 | etot = -102.061733857366 +547000 ekin = 17.1167854935215 | erot = 9.90508540311228 | epot = -131.450445770389 | etot = -104.428574873755 +548000 ekin = 17.5980170044881 | erot = 8.59899762550693 | epot = -131.534284690752 | etot = -105.337270060757 +549000 ekin = 18.05716372922 | erot = 9.03817412574295 | epot = -131.461799421632 | etot = -104.36646156667 +550000 ekin = 18.0110025502984 | erot = 8.75474126584266 | epot = -131.197169935683 | etot = -104.431426119542 +551000 ekin = 18.0766639239252 | erot = 8.53967490713076 | epot = -130.876590963895 | etot = -104.260252132839 +552000 ekin = 17.8245432639909 | erot = 8.21111901724959 | epot = -130.613873841209 | etot = -104.578211559969 +553000 ekin = 17.5785562404818 | erot = 8.1637249709468 | epot = -130.411446104862 | etot = -104.669164893433 +554000 ekin = 18.1123880413587 | erot = 9.24690423334698 | epot = -130.275148444209 | etot = -102.915856169503 +555000 ekin = 17.9212552367127 | erot = 9.62912969525877 | epot = -130.169859263365 | etot = -102.619474331394 +556000 ekin = 17.3952054982104 | erot = 10.6263113078829 | epot = -130.010818613481 | etot = -101.989301807388 +557000 ekin = 16.9877102103003 | erot = 9.66426744471381 | epot = -129.86176781953 | etot = -103.209790164516 +558000 ekin = 16.4865425164111 | erot = 10.8347141196074 | epot = -129.73204173083 | etot = -102.410785094812 +559000 ekin = 14.6833363987515 | erot = 13.8364712312426 | epot = -128.194049488042 | etot = -99.674241858048 +560000 ekin = 13.8032704865151 | erot = 16.3621868060878 | epot = -128.630373745615 | etot = -98.4649164530117 +561000 ekin = 15.490294368332 | erot = 14.8483889650737 | epot = -131.674752388104 | etot = -101.336069054698 +562000 ekin = 16.4428741862032 | erot = 17.5475675993354 | epot = -132.990492692958 | etot = -99.0000509074191 +563000 ekin = 17.1003382235047 | erot = 19.640250194249 | epot = -133.976850490626 | etot = -97.2362620728722 +564000 ekin = 16.8297751290314 | erot = 19.1525128665222 | epot = -134.481565057905 | etot = -98.4992770623515 +565000 ekin = 16.3252092422451 | erot = 19.1618918613524 | epot = -134.565272154893 | etot = -99.0781710512954 +566000 ekin = 17.2895019331068 | erot = 16.8462091007505 | epot = -134.327406255376 | etot = -100.191695221518 +567000 ekin = 17.0323906492612 | erot = 16.2918825563585 | epot = -133.70766075318 | etot = -100.383387547561 +568000 ekin = 16.3790772060084 | erot = 15.574422277605 | epot = -132.83958628787 | etot = -100.886086804257 +569000 ekin = 16.2273810520686 | erot = 14.7240543653566 | epot = -131.797679013765 | etot = -100.84624359634 +570000 ekin = 15.9900641522897 | erot = 13.4261011321613 | epot = -130.646318396574 | etot = -101.230153112123 +571000 ekin = 15.7066604174784 | erot = 13.0234217520948 | epot = -129.518264815906 | etot = -100.788182646333 +572000 ekin = 16.0092989285471 | erot = 12.1575559277608 | epot = -128.379111697494 | etot = -100.212256841186 +573000 ekin = 15.9708631343734 | erot = 11.1187133232187 | epot = -127.396033205366 | etot = -100.306456747774 +574000 ekin = 16.4336742572048 | erot = 11.0463709626913 | epot = -126.578179119945 | etot = -99.0981339000487 +575000 ekin = 16.6705776713588 | erot = 10.7073066200581 | epot = -125.724205448364 | etot = -98.3463211569468 +576000 ekin = 16.643261097378 | erot = 12.4216729485139 | epot = -125.152387316774 | etot = -96.0874532708816 +577000 ekin = 15.6029696585245 | erot = 12.0210027469721 | epot = -124.637013618676 | etot = -97.013041213179 +578000 ekin = 15.1217504082973 | erot = 11.4595910442715 | epot = -124.233033278189 | etot = -97.6516918256206 +579000 ekin = 15.0465935734355 | erot = 12.7262115365452 | epot = -123.793441452729 | etot = -96.020636342748 +580000 ekin = 15.0940489280731 | erot = 13.6051774356274 | epot = -123.331749104319 | etot = -94.6325227406182 +581000 ekin = 14.7781331191962 | erot = 13.1159956075504 | epot = -122.898867614539 | etot = -95.0047388877927 +582000 ekin = 15.6100957687545 | erot = 11.534434713536 | epot = -122.427694372763 | etot = -95.283163890472 +583000 ekin = 15.7489992202402 | erot = 11.4364124472658 | epot = -121.985823755297 | etot = -94.8004120877914 +584000 ekin = 15.8254878380624 | erot = 10.2058040644955 | epot = -121.640978549533 | etot = -95.6096866469753 +585000 ekin = 15.8487737856408 | erot = 8.71747367911913 | epot = -121.394720232222 | etot = -96.8284727674621 +586000 ekin = 15.9308434965333 | erot = 6.8128965677088 | epot = -121.46318607434 | etot = -98.7194460100977 +587000 ekin = 15.8799609085446 | erot = 7.01145208775909 | epot = -121.773232683032 | etot = -98.8818196867284 +588000 ekin = 16.4457907771307 | erot = 9.32918579174535 | epot = -122.366046753847 | etot = -96.5910701849708 +589000 ekin = 16.8324168458399 | erot = 9.1361453433059 | epot = -123.120906016409 | etot = -97.1523438272635 +590000 ekin = 17.7155015065396 | erot = 10.8010239309507 | epot = -123.950279101779 | etot = -95.4337536642889 +591000 ekin = 18.582172637572 | erot = 12.1434913540551 | epot = -124.74317051467 | etot = -94.0175065230431 +592000 ekin = 19.7287269455987 | erot = 11.640248069895 | epot = -125.49053884396 | etot = -94.1215638284665 +593000 ekin = 20.2421360449823 | erot = 11.4691273703594 | epot = -125.936877192475 | etot = -94.2256137771328 +594000 ekin = 20.8258968307947 | erot = 11.5067585781664 | epot = -126.003184271851 | etot = -93.6705288628895 +595000 ekin = 20.9016737450791 | erot = 11.1374359774499 | epot = -125.680251813537 | etot = -93.6411420910081 +596000 ekin = 20.5312730467165 | erot = 12.1007665172713 | epot = -125.005964164709 | etot = -92.3739246007213 +597000 ekin = 21.2832040757798 | erot = 11.0271699946615 | epot = -124.018711426703 | etot = -91.7083373562622 +598000 ekin = 21.6040849696085 | erot = 10.0992687087962 | epot = -122.785973741727 | etot = -91.0826200633223 +599000 ekin = 21.1832754570889 | erot = 9.77634716460214 | epot = -121.476563224164 | etot = -90.5169406024733 +600000 ekin = 20.1228831509292 | erot = 9.54773898830651 | epot = -120.17647917022 | etot = -90.5058570309846 +601000 ekin = 19.1118572595483 | erot = 8.11320736376245 | epot = -119.010980700425 | etot = -91.785916077114 +602000 ekin = 18.665680178544 | erot = 7.4830535665545 | epot = -118.045890820527 | etot = -91.8971570754285 +603000 ekin = 18.081995606827 | erot = 7.92648414432153 | epot = -117.479261710445 | etot = -91.4707819592969 +604000 ekin = 17.4910237608208 | erot = 8.46224773004699 | epot = -117.280073334434 | etot = -91.3268018435657 +605000 ekin = 16.4456067890573 | erot = 9.20099509670733 | epot = -117.313042448408 | etot = -91.6664405626436 +606000 ekin = 16.1733601636595 | erot = 11.093246978186 | epot = -117.38446139491 | etot = -90.1178542530648 +607000 ekin = 15.1981680377195 | erot = 13.1805232503445 | epot = -117.510376798243 | etot = -89.1316855101794 +608000 ekin = 14.0081061131211 | erot = 13.7561125379848 | epot = -117.649547699418 | etot = -89.8853290483125 +609000 ekin = 13.818830938552 | erot = 14.2766924193893 | epot = -117.637467628634 | etot = -89.5419442706926 +610000 ekin = 13.1121335077745 | erot = 16.045118377416 | epot = -117.371219818667 | etot = -88.2139679334762 +611000 ekin = 12.0976672808248 | erot = 15.1858927078526 | epot = -116.858556378552 | etot = -89.5749963898744 +612000 ekin = 11.9220029638036 | erot = 13.3855104580498 | epot = -116.373946806847 | etot = -91.066433384994 +613000 ekin = 11.3666160758114 | erot = 13.2728981904756 | epot = -115.771250337883 | etot = -91.1317360715958 +614000 ekin = 11.2524143895935 | erot = 11.9009495049358 | epot = -115.241963454889 | etot = -92.0885995603595 +615000 ekin = 11.1884819806374 | erot = 13.6569860280969 | epot = -114.774782544834 | etot = -89.9293145360998 +616000 ekin = 10.6499975272197 | erot = 15.2013862540199 | epot = -114.309207967121 | etot = -88.4578241858816 +617000 ekin = 10.4138402335121 | erot = 15.0033070762677 | epot = -113.953877170139 | etot = -88.5367298603587 +618000 ekin = 10.3874764562149 | erot = 16.4172186143102 | epot = -113.710134407831 | etot = -86.905439337306 +619000 ekin = 9.99028636695849 | erot = 14.7274727636021 | epot = -113.508001683668 | etot = -88.7902425531073 +620000 ekin = 10.3041883721209 | erot = 13.8526750931187 | epot = -113.308536373256 | etot = -89.1516729080167 +621000 ekin = 10.1555806788994 | erot = 13.963035038534 | epot = -113.272222139053 | etot = -89.1536064216194 +622000 ekin = 10.86693916419 | erot = 14.0813122989611 | epot = -113.376374288736 | etot = -88.4281228255848 +623000 ekin = 11.3859700250509 | erot = 14.8524083294346 | epot = -113.589012852683 | etot = -87.3506344981977 +624000 ekin = 11.6048296639596 | erot = 13.5297803701118 | epot = -113.839931482373 | etot = -88.7053214483019 +625000 ekin = 12.1696847808373 | erot = 13.4945782229098 | epot = -114.125840311987 | etot = -88.4615773082402 +626000 ekin = 13.3063758914076 | erot = 11.0407694649289 | epot = -114.542707544126 | etot = -90.195562187789 +627000 ekin = 14.0513781678418 | erot = 12.9296572169748 | epot = -115.235963654475 | etot = -88.2549282696589 +628000 ekin = 14.7386326295209 | erot = 14.2733655885988 | epot = -116.140527364528 | etot = -87.1285291464083 +629000 ekin = 16.0597037656505 | erot = 14.8674132821056 | epot = -117.325470573689 | etot = -86.3983535259332 +630000 ekin = 17.2708284639223 | erot = 16.7113994079231 | epot = -118.67269157756 | etot = -84.6904637057142 +631000 ekin = 19.0760838890113 | erot = 17.1201987673922 | epot = -120.170898337672 | etot = -83.9746156812687 +632000 ekin = 19.549583469596 | erot = 16.7553102323763 | epot = -121.774107568747 | etot = -85.4692138667745 +633000 ekin = 19.7557365237614 | erot = 19.5052241200048 | epot = -123.382136946336 | etot = -84.1211763025696 +634000 ekin = 20.3758046951383 | erot = 20.4839422619294 | epot = -124.793264832696 | etot = -83.9335178756281 +635000 ekin = 20.5084225289458 | erot = 20.7141390055288 | epot = -126.044346489046 | etot = -84.8217849545716 +636000 ekin = 21.1081835997456 | erot = 21.7042260881149 | epot = -127.030253954489 | etot = -84.2178442666289 +637000 ekin = 21.7890525197018 | erot = 22.3611764197008 | epot = -127.462306332383 | etot = -83.3120773929799 +638000 ekin = 22.8566093419233 | erot = 23.1784344200364 | epot = -127.315216811043 | etot = -81.2801730490835 +639000 ekin = 22.3429920008256 | erot = 22.0459046291129 | epot = -126.706799479394 | etot = -82.3179028494555 +640000 ekin = 22.6953942607299 | erot = 20.8983710819614 | epot = -125.829760713803 | etot = -82.2359953711113 +641000 ekin = 22.8439968772693 | erot = 21.0740721959676 | epot = -124.721138440745 | etot = -80.8030693675081 +642000 ekin = 22.1533451706583 | erot = 21.1494022467433 | epot = -123.447161286469 | etot = -80.144413869067 +643000 ekin = 21.5294868902541 | erot = 20.1256715660592 | epot = -122.008233998322 | etot = -80.3530755420084 +644000 ekin = 20.2303184656479 | erot = 19.3407148019869 | epot = -120.681831167764 | etot = -81.1107979001294 +645000 ekin = 19.4828971696373 | erot = 19.0195806413955 | epot = -119.467917319826 | etot = -80.9654395087931 +646000 ekin = 19.0662621367578 | erot = 18.9888559285631 | epot = -118.272684937573 | etot = -80.2175668722518 +647000 ekin = 18.6861208388155 | erot = 16.4218027074871 | epot = -117.232865439236 | etot = -82.1249418929329 +648000 ekin = 18.418772080989 | erot = 16.1392001141573 | epot = -116.443271389682 | etot = -81.8852991945353 +649000 ekin = 16.9720643990158 | erot = 15.679285405117 | epot = -115.834634277679 | etot = -83.1832844735462 +650000 ekin = 16.637818718134 | erot = 17.4493822417518 | epot = -115.341820195353 | etot = -81.254619235467 +651000 ekin = 16.7043030093967 | erot = 16.7313546097741 | epot = -115.376079299152 | etot = -81.9404216799809 +652000 ekin = 16.4646476925032 | erot = 17.3683673741032 | epot = -115.48194607439 | etot = -81.6489310077834 +653000 ekin = 15.8000469685932 | erot = 17.0265265526311 | epot = -115.746812156879 | etot = -82.9202386356544 +654000 ekin = 15.7743381483674 | erot = 19.3876348309309 | epot = -116.186419410868 | etot = -81.0244464315693 +655000 ekin = 15.6655810278436 | erot = 19.2583049313345 | epot = -116.555885603646 | etot = -81.6319996444684 +656000 ekin = 15.0368233093534 | erot = 20.8003287973529 | epot = -116.82925763844 | etot = -80.9921055317338 +657000 ekin = 15.1977678605749 | erot = 22.5087472235756 | epot = -116.936596984334 | etot = -79.2300819001832 +658000 ekin = 15.0298677342316 | erot = 21.6714000896342 | epot = -116.869137587512 | etot = -80.1678697636462 +659000 ekin = 14.8443959405137 | erot = 20.4195205180262 | epot = -116.673989819183 | etot = -81.410073360643 +660000 ekin = 14.5570644255729 | erot = 19.4853396657641 | epot = -116.400519641973 | etot = -82.3581155506359 +661000 ekin = 14.2956622818766 | erot = 18.7621543659755 | epot = -116.213425951533 | etot = -83.1556093036806 +662000 ekin = 14.4919431565361 | erot = 20.1886485654266 | epot = -115.918921077967 | etot = -81.2383293560043 +663000 ekin = 14.8058643406684 | erot = 20.6580010049446 | epot = -115.546581931323 | etot = -80.0827165857098 +664000 ekin = 14.7871760339976 | erot = 22.1135393371422 | epot = -115.398518278306 | etot = -78.497802907166 +665000 ekin = 15.8458781174239 | erot = 20.1244374174276 | epot = -115.392650343006 | etot = -79.4223348081541 +666000 ekin = 16.0080119400059 | erot = 18.1659687841157 | epot = -115.303268542373 | etot = -81.1292878182515 +667000 ekin = 15.5486521051748 | erot = 18.0884297532321 | epot = -115.256306296413 | etot = -81.6192244380064 +668000 ekin = 15.0598613033583 | erot = 15.4712674184192 | epot = -115.093834281093 | etot = -84.5627055593156 +669000 ekin = 15.3526157137167 | erot = 16.0088825474127 | epot = -115.00952385519 | etot = -83.6480255940608 +670000 ekin = 15.4977592110664 | erot = 14.8092487819138 | epot = -114.862532491762 | etot = -84.5555244987819 +671000 ekin = 15.4000237698432 | erot = 15.1143684799316 | epot = -114.652041425745 | etot = -84.1376491759703 +672000 ekin = 15.9713138534395 | erot = 14.5307653528988 | epot = -114.375144978471 | etot = -83.8730657721329 +673000 ekin = 16.3571505623909 | erot = 14.7153383635329 | epot = -113.918004164911 | etot = -82.8455152389876 +674000 ekin = 16.4861407399183 | erot = 13.3557709857525 | epot = -113.506238187029 | etot = -83.6643264613584 +675000 ekin = 16.4743983981331 | erot = 13.8105719239148 | epot = -113.022350157152 | etot = -82.737379835104 +676000 ekin = 17.3383460372365 | erot = 12.757377551601 | epot = -112.515050263435 | etot = -82.4193266745974 +677000 ekin = 16.9898565100054 | erot = 12.1680687389642 | epot = -112.128350557786 | etot = -82.9704253088166 +678000 ekin = 16.8525966578395 | erot = 13.7263413713123 | epot = -111.889145456694 | etot = -81.3102074275422 +679000 ekin = 16.9505937066578 | erot = 14.8954677234306 | epot = -111.616506596362 | etot = -79.7704451662738 +680000 ekin = 16.6414596570693 | erot = 14.6477182707077 | epot = -111.397557777114 | etot = -80.1083798493368 +681000 ekin = 16.2530255794803 | erot = 13.7865807840322 | epot = -111.318742772779 | etot = -81.2791364092661 +682000 ekin = 16.3185190504211 | erot = 14.6921548981951 | epot = -111.351569076462 | etot = -80.3408951278459 +683000 ekin = 16.2911111923816 | erot = 15.4238571396284 | epot = -111.548791079125 | etot = -79.8338227471145 +684000 ekin = 16.3651768582959 | erot = 14.9055126637841 | epot = -111.716864234947 | etot = -80.4461747128669 +685000 ekin = 15.9554620519382 | erot = 15.0240157618528 | epot = -111.878241765913 | etot = -80.8987639521215 +686000 ekin = 16.4059641913669 | erot = 15.3352984316397 | epot = -111.971770781358 | etot = -80.2305081583519 +687000 ekin = 16.7571821779775 | erot = 16.6079020554036 | epot = -112.02692872915 | etot = -78.6618444957691 +688000 ekin = 16.6415130117968 | erot = 15.8521345488749 | epot = -112.172800950489 | etot = -79.6791533898177 +689000 ekin = 16.7359898215401 | erot = 14.8035884446369 | epot = -112.53523866823 | etot = -80.9956604020534 +690000 ekin = 16.8520545819418 | erot = 14.9597259359453 | epot = -113.117923875801 | etot = -81.3061433579143 +691000 ekin = 17.1386154555738 | erot = 15.3420381306263 | epot = -113.815057780648 | etot = -81.3344041944475 +692000 ekin = 17.3543364338973 | erot = 17.3837703304784 | epot = -114.578602205326 | etot = -79.8404954409507 +693000 ekin = 18.236928358818 | erot = 17.1339159798889 | epot = -115.378509414152 | etot = -80.0076650754447 +694000 ekin = 17.1861910484986 | erot = 18.1297188911614 | epot = -116.139393340963 | etot = -80.8234834013025 +695000 ekin = 17.1237054673681 | erot = 18.1517844517828 | epot = -116.808974183386 | etot = -81.5334842642353 +696000 ekin = 17.4738329836767 | erot = 18.9867781591255 | epot = -117.420473407581 | etot = -80.9598622647786 +697000 ekin = 17.1553618265826 | erot = 19.5068840346769 | epot = -117.886125153115 | etot = -81.223879291855 +698000 ekin = 16.7865903997279 | erot = 19.0601681299166 | epot = -118.19902016553 | etot = -82.3522616358854 +699000 ekin = 16.2934280530717 | erot = 19.0599342090789 | epot = -118.052863064983 | etot = -82.6995008028323 +700000 ekin = 15.4184996147696 | erot = 15.9110837414063 | epot = -117.595973373478 | etot = -86.2663900173019 +701000 ekin = 15.5318785396331 | erot = 14.2265443299337 | epot = -117.037441525618 | etot = -87.2790186560516 +702000 ekin = 15.7357667092624 | erot = 15.1652334280863 | epot = -116.473846536182 | etot = -85.5728463988331 +703000 ekin = 15.2723305471281 | erot = 15.3880906719037 | epot = -115.787949915447 | etot = -85.1275286964155 +704000 ekin = 14.9831548145634 | erot = 16.7463413685097 | epot = -115.05972941091 | etot = -83.330233227837 +705000 ekin = 14.5159504582253 | erot = 16.6398789411266 | epot = -114.297577433871 | etot = -83.1417480345187 +706000 ekin = 14.5872231438258 | erot = 17.5787870360321 | epot = -113.518744454188 | etot = -81.35273427433 +707000 ekin = 14.9278866425061 | erot = 16.6557553871101 | epot = -112.751461632238 | etot = -81.1678196026222 +708000 ekin = 14.4328586823026 | erot = 15.5195587722882 | epot = -111.994936287192 | etot = -82.042518832601 +709000 ekin = 13.8576942695953 | erot = 14.1136534418066 | epot = -111.410050264174 | etot = -83.4387025527717 +710000 ekin = 13.5706587266072 | erot = 13.7463574518263 | epot = -111.040631911948 | etot = -83.7236157335143 +711000 ekin = 13.1978890368118 | erot = 13.1768388142301 | epot = -110.941500879792 | etot = -84.5667730287496 +712000 ekin = 13.3102169421158 | erot = 13.1640922590864 | epot = -110.967842198588 | etot = -84.4935329973858 +713000 ekin = 13.6132122765889 | erot = 12.3364585742912 | epot = -110.879608176168 | etot = -84.9299373252874 +714000 ekin = 14.7428498532989 | erot = 12.0295592979849 | epot = -111.015008669574 | etot = -84.2425995182899 +715000 ekin = 15.3901173158569 | erot = 12.7484723792576 | epot = -111.491503816928 | etot = -83.3529141218137 +716000 ekin = 15.3539152995683 | erot = 15.1814525656434 | epot = -112.277977254205 | etot = -81.7426093889929 +717000 ekin = 15.9160011253634 | erot = 15.8038627550558 | epot = -113.174131044634 | etot = -81.454267164215 +718000 ekin = 16.3504419499244 | erot = 15.4025864539449 | epot = -114.156959448308 | etot = -82.4039310444385 +719000 ekin = 16.549602317868 | erot = 14.5807668603065 | epot = -114.891534334078 | etot = -83.7611651559037 +720000 ekin = 16.699182133157 | erot = 13.8081822822405 | epot = -115.438802283192 | etot = -84.9314378677944 +721000 ekin = 17.1673185529944 | erot = 12.9193605231338 | epot = -115.861508293824 | etot = -85.7748292176956 +722000 ekin = 17.4322438179512 | erot = 12.6776690207364 | epot = -116.375570814202 | etot = -86.2656579755143 +723000 ekin = 18.5581458626413 | erot = 14.2424135829758 | epot = -116.917532631926 | etot = -84.1169731863093 +724000 ekin = 18.9428272620659 | erot = 15.165421285469 | epot = -117.57414912553 | etot = -83.465900577995 +725000 ekin = 19.441432399728 | erot = 15.7836923804543 | epot = -118.074905294794 | etot = -82.8497805146113 +726000 ekin = 20.2132558330506 | erot = 14.7911998387733 | epot = -118.490382568412 | etot = -83.4859268965885 +727000 ekin = 20.9690773603413 | erot = 11.3121249395298 | epot = -118.880706212445 | etot = -86.5995039125738 +728000 ekin = 21.4971860333606 | erot = 10.174445400751 | epot = -119.160483525573 | etot = -87.4888520914613 +729000 ekin = 21.8812710806639 | erot = 10.6840378391884 | epot = -119.399746884653 | etot = -86.8344379648003 +730000 ekin = 21.4809035479769 | erot = 10.7417210007781 | epot = -119.442086082618 | etot = -87.2194615338635 +731000 ekin = 20.4761865270565 | erot = 10.8248255192935 | epot = -119.278005568648 | etot = -87.9769935222981 +732000 ekin = 20.3680589172194 | erot = 10.678516662158 | epot = -119.003139163919 | etot = -87.9565635845412 +733000 ekin = 19.4298841117498 | erot = 11.8407837845394 | epot = -118.616695680095 | etot = -87.346027783806 +734000 ekin = 19.5819429337487 | erot = 12.4147186446835 | epot = -118.117352533724 | etot = -86.1206909552921 +735000 ekin = 19.0632000575252 | erot = 11.5927293968676 | epot = -117.616849772036 | etot = -86.9609203176429 +736000 ekin = 18.297506560165 | erot = 12.7308502117521 | epot = -117.091431606781 | etot = -86.0630748348637 +737000 ekin = 18.0538832577921 | erot = 10.7657920073953 | epot = -116.578648690768 | etot = -87.7589734255808 +738000 ekin = 17.421418619176 | erot = 12.5509163664985 | epot = -116.136132354182 | etot = -86.1637973685077 +739000 ekin = 17.0897370867241 | erot = 13.2088390637356 | epot = -115.640502304353 | etot = -85.3419261538932 +740000 ekin = 16.310117342326 | erot = 13.6200255516858 | epot = -115.050866589654 | etot = -85.1207236956421 +741000 ekin = 15.6365317806195 | erot = 14.019129912876 | epot = -114.449993391252 | etot = -84.7943316977568 +742000 ekin = 14.9732300630273 | erot = 15.7356270066579 | epot = -113.890619494628 | etot = -83.181762424943 +743000 ekin = 14.4083614596627 | erot = 16.5554398771082 | epot = -113.280494362843 | etot = -82.3166930260719 +744000 ekin = 13.03898614748 | erot = 15.4061319404246 | epot = -112.634742954922 | etot = -84.1896248670175 +745000 ekin = 13.1381721908975 | erot = 14.6690692508061 | epot = -112.009444415089 | etot = -84.2022029733852 +746000 ekin = 13.0326251674368 | erot = 13.5725220329178 | epot = -111.333092273034 | etot = -84.7279450726797 +747000 ekin = 12.8821095039388 | erot = 12.0155935329808 | epot = -110.787633139541 | etot = -85.8899301026215 +748000 ekin = 12.9584427751653 | erot = 11.5383896235378 | epot = -110.394048001213 | etot = -85.8972156025098 +749000 ekin = 12.3400213550355 | erot = 10.5815921772998 | epot = -110.143265497353 | etot = -87.221651965018 +750000 ekin = 11.5393734324413 | erot = 10.9845533382395 | epot = -109.959563791501 | etot = -87.4356370208202 +751000 ekin = 10.9222252305684 | erot = 11.6128989794224 | epot = -109.949578832544 | etot = -87.4144546225531 +752000 ekin = 10.8238329042319 | erot = 10.0479136602577 | epot = -110.149993490078 | etot = -89.278246925588 +753000 ekin = 11.4962089358426 | erot = 9.58927029980097 | epot = -110.492110868259 | etot = -89.4066316326155 +754000 ekin = 11.6378196030486 | erot = 9.80908458276957 | epot = -110.821288821443 | etot = -89.3743846356246 +755000 ekin = 12.38505496023 | erot = 8.99090744479519 | epot = -111.249098590009 | etot = -89.8731361849842 +756000 ekin = 12.7731677402928 | erot = 9.77341945625968 | epot = -111.842275371625 | etot = -89.2956881750728 +757000 ekin = 12.8115161379076 | erot = 12.7795055261822 | epot = -112.510161341528 | etot = -86.9191396774381 +758000 ekin = 13.5020359203668 | erot = 14.4715401370259 | epot = -113.210435142659 | etot = -85.2368590852658 +759000 ekin = 13.2381945175707 | erot = 16.983701060954 | epot = -113.881228857596 | etot = -83.6593332790709 +760000 ekin = 13.3246669671446 | erot = 14.6963642691986 | epot = -114.560324803731 | etot = -86.5392935673879 +761000 ekin = 14.0784624928702 | erot = 14.2932107965424 | epot = -115.370367666941 | etot = -86.9986943775289 +762000 ekin = 14.7915513624397 | erot = 13.904714415853 | epot = -116.143777057633 | etot = -87.4475112793401 +763000 ekin = 15.2123522918624 | erot = 15.2465001915023 | epot = -116.81256893766 | etot = -86.3537164542953 +764000 ekin = 14.8052789359422 | erot = 16.1650390125407 | epot = -117.411346708376 | etot = -86.4410287598929 +765000 ekin = 15.5310091315323 | erot = 15.2812812493463 | epot = -117.982434585728 | etot = -87.1701442048491 +766000 ekin = 15.994350647252 | erot = 14.2761412052699 | epot = -118.562864469692 | etot = -88.2923726171706 +767000 ekin = 16.2653623244275 | erot = 13.7064523675545 | epot = -119.093242354204 | etot = -89.121427662222 +768000 ekin = 16.3947126291507 | erot = 14.7588954053121 | epot = -119.6036559285 | etot = -88.450047894037 +769000 ekin = 15.629652360566 | erot = 12.0886911958527 | epot = -119.97790024693 | etot = -92.2595566905108 +770000 ekin = 15.7806956095376 | erot = 12.2052577997901 | epot = -120.284346707973 | etot = -92.2983932986457 +771000 ekin = 16.6370376614557 | erot = 13.2528225497813 | epot = -120.446347401408 | etot = -90.5564871901711 +772000 ekin = 16.9996640417653 | erot = 12.0570296338132 | epot = -120.44856845661 | etot = -91.3918747810311 +773000 ekin = 16.9898540586523 | erot = 10.6185471059335 | epot = -120.369839005892 | etot = -92.7614378413063 +774000 ekin = 16.8919394319844 | erot = 9.77617810301849 | epot = -120.229185976585 | etot = -93.561068441582 +775000 ekin = 16.5524346521886 | erot = 10.4045168893084 | epot = -120.094649134474 | etot = -93.137697592977 +776000 ekin = 16.2101595715457 | erot = 11.2240534564775 | epot = -120.110452870025 | etot = -92.676239842002 +777000 ekin = 16.7785554550484 | erot = 10.1287514469566 | epot = -120.151810661078 | etot = -93.2445037590733 +778000 ekin = 17.1166911974141 | erot = 9.50157485152149 | epot = -120.313848313001 | etot = -93.6955822640657 +779000 ekin = 17.6889693237664 | erot = 9.32976665587914 | epot = -120.610167321774 | etot = -93.5914313421284 +780000 ekin = 17.9806088731003 | erot = 9.33508062594656 | epot = -120.940873026538 | etot = -93.6251835274909 +781000 ekin = 18.5993438310554 | erot = 10.627473857285 | epot = -121.148642480253 | etot = -91.9218247919125 +782000 ekin = 19.2641311336065 | erot = 11.1079291456411 | epot = -121.32487065963 | etot = -90.9528103803828 +783000 ekin = 20.2812434331 | erot = 8.23327550658308 | epot = -121.316369254064 | etot = -92.8018503143813 +784000 ekin = 20.9752118637556 | erot = 8.15469782183701 | epot = -121.272107440927 | etot = -92.1421977553348 +785000 ekin = 21.8924066799283 | erot = 7.70304666368148 | epot = -121.238520205958 | etot = -91.6430668623479 +786000 ekin = 21.7796096028903 | erot = 8.04220753044906 | epot = -121.159628332142 | etot = -91.3378111988023 +787000 ekin = 22.1195259314042 | erot = 6.8282785893581 | epot = -120.922313278572 | etot = -91.9745087578098 +788000 ekin = 21.3828517102018 | erot = 6.99007001840233 | epot = -120.69597980518 | etot = -92.3230580765763 +789000 ekin = 21.936131278614 | erot = 5.79811923390562 | epot = -120.340814667307 | etot = -92.6065641547875 +790000 ekin = 21.8385813428668 | erot = 4.72762778556262 | epot = -120.048164377261 | etot = -93.481955248832 +791000 ekin = 21.8319066908171 | erot = 5.39355344376339 | epot = -119.853156156477 | etot = -92.6276960218966 +792000 ekin = 21.0658428104221 | erot = 5.79436809250518 | epot = -119.743288386152 | etot = -92.8830774832244 +793000 ekin = 19.8199186658772 | erot = 5.82943748935814 | epot = -119.596178428627 | etot = -93.9468222733916 +794000 ekin = 19.7672847441192 | erot = 5.59633501272583 | epot = -119.475585853262 | etot = -94.111966096417 +795000 ekin = 18.6499050116789 | erot = 8.31430007281567 | epot = -119.285414166791 | etot = -92.3212090822962 +796000 ekin = 17.9363655678375 | erot = 9.507008126683 | epot = -119.093130917218 | etot = -91.6497572226971 +797000 ekin = 17.6195070538523 | erot = 11.5281197691252 | epot = -118.913703089804 | etot = -89.7660762668261 +798000 ekin = 16.7416832038213 | erot = 10.8230200177241 | epot = -118.592676023165 | etot = -91.0279728016191 +799000 ekin = 15.9683628681919 | erot = 10.5008188359403 | epot = -118.118213389297 | etot = -91.6490316851645 +800000 ekin = 15.8328009163475 | erot = 10.6678350162836 | epot = -117.620684456068 | etot = -91.1200485234368 +801000 ekin = 15.8815393666215 | erot = 11.8801796924214 | epot = -117.150405220342 | etot = -89.3886861612996 +802000 ekin = 15.2912046436652 | erot = 12.3681708297557 | epot = -116.682465911253 | etot = -89.0230904378323 +803000 ekin = 15.0644332574077 | erot = 13.4381207505363 | epot = -116.228148754426 | etot = -87.7255947464824 +804000 ekin = 14.8698392773217 | erot = 12.3545854788909 | epot = -115.807242252982 | etot = -88.582817496769 +805000 ekin = 14.2149826847359 | erot = 11.5366482534163 | epot = -115.507222545212 | etot = -89.7555916070598 +806000 ekin = 14.1074639425469 | erot = 11.0928417857839 | epot = -115.376020508432 | etot = -90.1757147801011 +807000 ekin = 14.113570534875 | erot = 10.7403809857074 | epot = -115.500754282591 | etot = -90.6468027620081 +808000 ekin = 14.8515656803556 | erot = 9.93484379441975 | epot = -115.742973376619 | etot = -90.9565639018439 +809000 ekin = 15.5106263974934 | erot = 9.46177919939148 | epot = -116.039589606039 | etot = -91.067184009154 +810000 ekin = 15.3650711677996 | erot = 10.9192101328555 | epot = -116.36001113323 | etot = -90.0757298325749 +811000 ekin = 15.6996079985536 | erot = 11.3353249327696 | epot = -116.659308700673 | etot = -89.6243757693493 +812000 ekin = 15.5955589758704 | erot = 9.77769038449703 | epot = -116.933632012428 | etot = -91.5603826520602 +813000 ekin = 15.7905106860366 | erot = 10.0769482126314 | epot = -117.121213114681 | etot = -91.2537542160133 +814000 ekin = 15.836943371153 | erot = 10.4725840830616 | epot = -117.242992703304 | etot = -90.9334652490891 +815000 ekin = 15.7798728273714 | erot = 10.270859520781 | epot = -117.464478160431 | etot = -91.4137458122788 +816000 ekin = 15.5108139706635 | erot = 9.81402764178317 | epot = -117.700565923965 | etot = -92.375724311518 +817000 ekin = 14.9505026726033 | erot = 12.6345228166784 | epot = -117.993099747899 | etot = -90.4080742586175 +818000 ekin = 15.1200903840887 | erot = 12.1447825805719 | epot = -118.351925084352 | etot = -91.0870521196916 +819000 ekin = 14.4311436258796 | erot = 12.6781303279808 | epot = -118.826174003248 | etot = -91.7169000493874 +820000 ekin = 13.5072356830853 | erot = 12.3586951787113 | epot = -119.259399926334 | etot = -93.3934690645378 +821000 ekin = 13.4519855490784 | erot = 13.635560178739 | epot = -119.686972219316 | etot = -92.5994264914982 +822000 ekin = 13.2612756217885 | erot = 12.828076715774 | epot = -120.107052971282 | etot = -94.0177006337199 +823000 ekin = 13.6566874959119 | erot = 12.8519595303742 | epot = -120.692147426794 | etot = -94.183500400508 +824000 ekin = 13.6549705792837 | erot = 13.7641831570978 | epot = -121.262313617144 | etot = -93.8431598807624 +825000 ekin = 13.9319007132007 | erot = 14.8682888426075 | epot = -121.845959741125 | etot = -93.045770185317 +826000 ekin = 14.2062841472185 | erot = 14.0474169899914 | epot = -122.317101839548 | etot = -94.0634007023385 +827000 ekin = 14.6726774871556 | erot = 14.3687000686378 | epot = -122.63996326646 | etot = -93.5985857106662 +828000 ekin = 14.954904414193 | erot = 12.1762478618103 | epot = -122.850502321156 | etot = -95.7193500451532 +829000 ekin = 15.8405253719071 | erot = 12.0065735120163 | epot = -123.014458934709 | etot = -95.167360050786 +830000 ekin = 16.3737927574426 | erot = 11.8470255390997 | epot = -123.203517144017 | etot = -94.982698847475 +831000 ekin = 17.0141828340646 | erot = 11.2463282353398 | epot = -123.352294850051 | etot = -95.0917837806466 +832000 ekin = 17.3349692010058 | erot = 10.0974853526763 | epot = -123.490699679036 | etot = -96.0582451253537 +833000 ekin = 17.6111288592833 | erot = 9.39186517389969 | epot = -123.666551367413 | etot = -96.6635573342296 +834000 ekin = 17.8993253229693 | erot = 9.24560386945977 | epot = -123.969738347961 | etot = -96.824809155532 +835000 ekin = 18.3602247479247 | erot = 9.79891209034335 | epot = -124.198813308332 | etot = -96.0396764700638 +836000 ekin = 18.964054173631 | erot = 11.4834158200508 | epot = -124.485950275745 | etot = -94.0384802820636 +837000 ekin = 19.161629252954 | erot = 10.2394617340205 | epot = -124.746605863583 | etot = -95.3455148766088 +838000 ekin = 19.1740945620472 | erot = 9.13223901034505 | epot = -125.035058601471 | etot = -96.7287250290788 +839000 ekin = 19.7505157589066 | erot = 9.63496380125181 | epot = -125.284451947216 | etot = -95.8989723870572 +840000 ekin = 20.1471792177468 | erot = 9.10187944827153 | epot = -125.534736495681 | etot = -96.2856778296631 +841000 ekin = 19.6027548002793 | erot = 8.52546960166535 | epot = -125.680127019133 | etot = -97.5519026171889 +842000 ekin = 19.4863854237829 | erot = 9.54974707904911 | epot = -125.695704153012 | etot = -96.6595716501799 +843000 ekin = 19.155026075008 | erot = 10.3127317669629 | epot = -125.588742330561 | etot = -96.12098448859 +844000 ekin = 18.7487380479702 | erot = 9.96785575488987 | epot = -125.34545235114 | etot = -96.6288585482803 +845000 ekin = 18.2331914387742 | erot = 9.53282016412031 | epot = -125.057985349926 | etot = -97.2919737470317 +846000 ekin = 18.5216298811579 | erot = 10.6765011499907 | epot = -124.75053142677 | etot = -95.5524003956219 +847000 ekin = 17.6129752038445 | erot = 11.1954358895151 | epot = -124.458389475805 | etot = -95.649978382445 +848000 ekin = 17.8418961529153 | erot = 13.3467675634966 | epot = -124.107460776295 | etot = -92.9187970598832 +849000 ekin = 17.0906867018798 | erot = 14.9412863530835 | epot = -123.797756965365 | etot = -91.7657839104019 +850000 ekin = 16.5565760771884 | erot = 16.3168424817122 | epot = -123.572248019221 | etot = -90.69882946032 +851000 ekin = 16.3630368263058 | erot = 17.241519847228 | epot = -123.335025531801 | etot = -89.7304688582673 +852000 ekin = 15.9752556062866 | erot = 17.7177869526889 | epot = -123.116884707468 | etot = -89.4238421484925 +853000 ekin = 15.8668361896513 | erot = 18.0092422853688 | epot = -122.872128188376 | etot = -88.9960497133555 +854000 ekin = 15.8229688728036 | erot = 18.0711771193 | epot = -122.5253434954 | etot = -88.6311975032962 +855000 ekin = 15.9585783329093 | erot = 18.7102931799029 | epot = -122.021344738748 | etot = -87.3524732259361 +856000 ekin = 15.6873864921224 | erot = 18.1729033343094 | epot = -121.461170358966 | etot = -87.6008805325342 +857000 ekin = 15.4166200885964 | erot = 18.1249802377734 | epot = -120.732895294045 | etot = -87.1912949676752 +858000 ekin = 15.920319634723 | erot = 17.2576511362215 | epot = -119.978117030039 | etot = -86.8001462590944 +859000 ekin = 15.8396762585139 | erot = 18.5696751038999 | epot = -119.31190868098 | etot = -84.9025573185659 +860000 ekin = 15.5827603182971 | erot = 18.7231746346669 | epot = -118.677135587555 | etot = -84.3712006345911 +861000 ekin = 15.1722766838704 | erot = 18.3361843793459 | epot = -118.024779075157 | etot = -84.5163180119404 +862000 ekin = 15.0094595057786 | erot = 18.888095695251 | epot = -117.561240138321 | etot = -83.6636849372913 +863000 ekin = 16.3992141495581 | erot = 19.0270095430012 | epot = -117.158995958539 | etot = -81.7327722659794 +864000 ekin = 17.0456638476167 | erot = 16.7973031691559 | epot = -116.781733582951 | etot = -82.9387665661782 +865000 ekin = 17.6056841777089 | erot = 14.0078111610621 | epot = -116.43066511917 | etot = -84.8171697803986 +866000 ekin = 17.9448372652699 | erot = 14.0693010157328 | epot = -116.126112398458 | etot = -84.1119741174554 +867000 ekin = 18.2732015455461 | erot = 13.244034526719 | epot = -115.888005802281 | etot = -84.3707697300162 +868000 ekin = 18.2849597704299 | erot = 12.9928912198279 | epot = -115.682028470573 | etot = -84.4041774803151 +869000 ekin = 17.7524383551921 | erot = 12.0043148955387 | epot = -115.581878837995 | etot = -85.8251255872641 +870000 ekin = 18.12155333597 | erot = 11.1888007724603 | epot = -115.508894436749 | etot = -86.1985403283188 +871000 ekin = 18.7002477332545 | erot = 11.3537342736374 | epot = -115.469320490239 | etot = -85.4153384833468 +872000 ekin = 18.3281851410687 | erot = 11.3049334382773 | epot = -115.522508538055 | etot = -85.8893899587089 +873000 ekin = 18.9326956575937 | erot = 11.6721180224957 | epot = -115.602256457199 | etot = -84.9974427771099 +874000 ekin = 18.8522970516783 | erot = 11.911050725311 | epot = -115.846744057966 | etot = -85.0833962809767 +875000 ekin = 18.4229796561767 | erot = 11.8729396239959 | epot = -116.074179417696 | etot = -85.7782601375235 +876000 ekin = 18.7082371539651 | erot = 12.516865025384 | epot = -116.343864328932 | etot = -85.1187621495826 +877000 ekin = 18.3022205400887 | erot = 13.6432909766226 | epot = -116.743995963962 | etot = -84.7984844472511 +878000 ekin = 18.6015825941817 | erot = 13.8971846266847 | epot = -117.366355702891 | etot = -84.867588482025 +879000 ekin = 17.9525634287373 | erot = 12.9414239809514 | epot = -118.014864660128 | etot = -87.120877250439 +880000 ekin = 18.3766039136358 | erot = 14.5500115107006 | epot = -118.764298269044 | etot = -85.8376828447072 +881000 ekin = 17.262513355404 | erot = 14.9536600733876 | epot = -119.565385720242 | etot = -87.3492122914507 +882000 ekin = 16.7762235931364 | erot = 14.5097084376052 | epot = -120.289225623202 | etot = -89.0032935924604 +883000 ekin = 15.8395576604101 | erot = 15.8361420619882 | epot = -120.824117258563 | etot = -89.148417536165 +884000 ekin = 15.5937774075175 | erot = 13.8227021338877 | epot = -121.099783610957 | etot = -91.6833040695522 +885000 ekin = 14.9813853737919 | erot = 13.3756451967454 | epot = -121.078780185378 | etot = -92.7217496148406 +886000 ekin = 14.5031068301856 | erot = 13.5060136353071 | epot = -120.843158893017 | etot = -92.8340384275241 +887000 ekin = 14.6650536360114 | erot = 13.7553660443201 | epot = -120.357347236274 | etot = -91.9369275559425 +888000 ekin = 14.1759873663133 | erot = 14.4716353583819 | epot = -119.759474461657 | etot = -91.1118517369617 +889000 ekin = 14.1111904475878 | erot = 12.7620258712917 | epot = -119.106732143149 | etot = -92.2335158242697 +890000 ekin = 13.5338966496054 | erot = 14.264867338732 | epot = -118.366576823951 | etot = -90.567812835614 +891000 ekin = 12.589910875445 | erot = 16.09351402541 | epot = -117.697261254063 | etot = -89.0138363532079 +892000 ekin = 12.367696657161 | erot = 14.8343112464362 | epot = -117.114979792313 | etot = -89.9129718887153 +893000 ekin = 11.8888199540295 | erot = 15.5619355677984 | epot = -116.569736465347 | etot = -89.1189809435189 +894000 ekin = 12.0695922005297 | erot = 14.1768659854505 | epot = -116.193015287478 | etot = -89.9465571014977 +895000 ekin = 12.0137012689767 | erot = 14.7176843341314 | epot = -116.049279411988 | etot = -89.3178938088798 +896000 ekin = 12.0457177984029 | erot = 15.0690385660324 | epot = -116.226063999879 | etot = -89.1113076354438 +897000 ekin = 11.9649944708071 | erot = 16.7585652239991 | epot = -116.547901475597 | etot = -87.8243417807911 +898000 ekin = 12.4125505791435 | erot = 16.0288167842045 | epot = -116.877747709982 | etot = -88.4363803466339 +899000 ekin = 12.7913647101517 | erot = 16.2599665436297 | epot = -117.22389856283 | etot = -88.1725673090489 +900000 ekin = 12.7213203733162 | erot = 15.9346879561939 | epot = -117.525910997654 | etot = -88.8699026681444 +901000 ekin = 13.3925140460675 | erot = 13.0898105027757 | epot = -117.79105806064 | etot = -91.3087335117963 +902000 ekin = 13.5974591701383 | erot = 12.6629036844613 | epot = -118.166495804444 | etot = -91.9061329498441 +903000 ekin = 13.8239248106963 | erot = 12.9097445050843 | epot = -118.503808290443 | etot = -91.7701389746622 +904000 ekin = 13.9003237222555 | erot = 12.7187951249901 | epot = -118.954435028969 | etot = -92.3353161817234 +905000 ekin = 13.8484759023217 | erot = 14.4414990804685 | epot = -119.555904078968 | etot = -91.2659290961777 +906000 ekin = 14.0709567230086 | erot = 17.1395182144883 | epot = -120.256597236867 | etot = -89.0461222993702 +907000 ekin = 13.0525497710419 | erot = 17.0435686835159 | epot = -120.833284821664 | etot = -90.7371663671067 +908000 ekin = 13.5011032375864 | erot = 17.4068087159159 | epot = -121.378539430815 | etot = -90.4706274773124 +909000 ekin = 13.0477752122483 | erot = 17.3551032189452 | epot = -121.944468320843 | etot = -91.5415898896497 +910000 ekin = 13.0734564213323 | erot = 17.7240098890034 | epot = -122.455605036845 | etot = -91.6581387265093 +911000 ekin = 12.9549554196173 | erot = 18.5309639253154 | epot = -122.885520670757 | etot = -91.3996013258247 +912000 ekin = 12.9071827432122 | erot = 19.3038132220738 | epot = -123.295755441277 | etot = -91.0847594759915 +913000 ekin = 12.873639651769 | erot = 17.6447968514768 | epot = -123.591389017518 | etot = -93.0729525142721 +914000 ekin = 13.2090327600462 | erot = 18.6146303397366 | epot = -123.77613155181 | etot = -91.9524684520271 +915000 ekin = 13.7372183863305 | erot = 16.6833035864293 | epot = -123.924888819256 | etot = -93.5043668464961 +916000 ekin = 13.3061011890743 | erot = 15.5577380665692 | epot = -124.029742172947 | etot = -95.1659029173032 +917000 ekin = 12.890908113948 | erot = 15.6377285599624 | epot = -124.171723385822 | etot = -95.6430867119113 +918000 ekin = 13.2538313269488 | erot = 15.4177757921272 | epot = -124.357165714437 | etot = -95.6855585953608 +919000 ekin = 14.0444948242936 | erot = 15.0452292964814 | epot = -124.576101947629 | etot = -95.4863778268544 +920000 ekin = 14.0410127504381 | erot = 13.9634869300633 | epot = -124.738136118335 | etot = -96.7336364378338 +921000 ekin = 14.1551987065811 | erot = 12.3941306059594 | epot = -125.088498782391 | etot = -98.5391694698508 +922000 ekin = 14.2276920732135 | erot = 15.0327547601353 | epot = -125.526288759493 | etot = -96.2658419261437 +923000 ekin = 14.3552438210034 | erot = 14.1363941405235 | epot = -126.12829028672 | etot = -97.6366523251935 +924000 ekin = 14.5041705296654 | erot = 15.9619253409903 | epot = -126.843033999763 | etot = -96.3769381291074 +925000 ekin = 14.5400944209119 | erot = 17.4997296566513 | epot = -127.507177319307 | etot = -95.4673532417434 +926000 ekin = 14.6046327805672 | erot = 17.1373142992145 | epot = -128.134692034914 | etot = -96.392744955132 +927000 ekin = 14.6215715719242 | erot = 16.8724972360635 | epot = -128.740987589665 | etot = -97.2469187816775 +928000 ekin = 14.6396595729414 | erot = 17.1396439909469 | epot = -129.209041498762 | etot = -97.4297379348733 +929000 ekin = 13.808814016571 | erot = 18.5482425791424 | epot = -129.59969540295 | etot = -97.2426388072368 +930000 ekin = 13.3703713100728 | erot = 18.6606507891562 | epot = -129.760150362545 | etot = -97.7291282633159 +931000 ekin = 13.1805297982085 | erot = 19.545741585529 | epot = -129.743156282366 | etot = -97.0168848986289 +932000 ekin = 13.2649592845646 | erot = 17.8574402167804 | epot = -129.645087354661 | etot = -98.5226878533157 +933000 ekin = 12.9607863802779 | erot = 16.307893445402 | epot = -129.63857938217 | etot = -100.36989955649 +934000 ekin = 12.4022727576482 | erot = 17.8774718578769 | epot = -129.637637094327 | etot = -99.3578924788016 +935000 ekin = 12.2995741285428 | erot = 14.8343045174739 | epot = -129.628654926379 | etot = -102.494776280362 +936000 ekin = 12.3522202641654 | erot = 13.1781575590471 | epot = -129.751598147133 | etot = -104.221220323921 +937000 ekin = 12.8178813976735 | erot = 13.3255184079132 | epot = -130.052677130556 | etot = -103.90927732497 +938000 ekin = 13.6621340607039 | erot = 15.3154449818888 | epot = -130.403259068065 | etot = -101.425680025473 +939000 ekin = 14.2055416406367 | erot = 15.7669887777399 | epot = -130.71799989098 | etot = -100.745469472603 +940000 ekin = 14.6172332568569 | erot = 15.1413456776972 | epot = -130.980505941845 | etot = -101.221927007291 +941000 ekin = 14.7993386129929 | erot = 12.9776335555139 | epot = -131.272247687568 | etot = -103.495275519061 +942000 ekin = 15.5335296614623 | erot = 14.077753507083 | epot = -131.64827113102 | etot = -102.036987962475 +943000 ekin = 15.8153674520153 | erot = 13.8900929959998 | epot = -132.104615249043 | etot = -102.399154801027 +944000 ekin = 15.995840679904 | erot = 13.2503963107949 | epot = -132.383467447975 | etot = -103.137230457276 +945000 ekin = 16.9506733718874 | erot = 13.0128057924875 | epot = -132.814341083772 | etot = -102.850861919398 +946000 ekin = 17.2683330453948 | erot = 12.2206111801736 | epot = -133.190147697266 | etot = -103.701203471697 +947000 ekin = 18.2654627390238 | erot = 12.607864411813 | epot = -133.437356622139 | etot = -102.564029471302 +948000 ekin = 18.9247564734275 | erot = 10.7958947548298 | epot = -133.491427845306 | etot = -103.770776617049 +949000 ekin = 19.0156199461051 | erot = 10.4720682695147 | epot = -133.362034264067 | etot = -103.874346048447 +950000 ekin = 18.6246087033182 | erot = 13.6364514367478 | epot = -133.04549769442 | etot = -100.784437554354 +951000 ekin = 18.6927083514433 | erot = 13.6661715172821 | epot = -132.47325327942 | etot = -100.114373410695 +952000 ekin = 18.3844441390729 | erot = 13.8860557825372 | epot = -131.51579451266 | etot = -99.2452945910494 +953000 ekin = 17.8871996339964 | erot = 15.3325866197267 | epot = -130.276129986655 | etot = -97.0563437329319 +954000 ekin = 16.8413865084877 | erot = 14.9334765987234 | epot = -128.903833142085 | etot = -97.1289700348742 +955000 ekin = 15.7491647284399 | erot = 13.5522552230972 | epot = -127.637147734617 | etot = -98.3357277830796 +956000 ekin = 15.0316123603932 | erot = 13.0118712405706 | epot = -126.594426180261 | etot = -98.5509425792974 +957000 ekin = 13.9511166207686 | erot = 12.8079283002139 | epot = -125.829517110607 | etot = -99.0704721896241 +958000 ekin = 13.3400958629755 | erot = 12.8632040396806 | epot = -125.202163021613 | etot = -98.9988631189573 +959000 ekin = 12.3250795668259 | erot = 12.4564269151362 | epot = -124.933673005766 | etot = -100.152166523804 +960000 ekin = 11.692935434419 | erot = 13.0608145327809 | epot = -124.894940531961 | etot = -100.141190564761 +961000 ekin = 11.1176175414437 | erot = 14.4883300738387 | epot = -124.970867463286 | etot = -99.3649198480031 +962000 ekin = 10.411109427009 | erot = 16.3322519853867 | epot = -125.234118963607 | etot = -98.4907575512117 +963000 ekin = 9.3402588646206 | erot = 16.0988706764342 | epot = -125.397678792901 | etot = -99.9585492518461 +964000 ekin = 9.16866022508975 | erot = 17.2216753836534 | epot = -125.348930629784 | etot = -98.9585950210411 +965000 ekin = 8.68918272510296 | erot = 17.3709063020777 | epot = -125.23288520793 | etot = -99.1727961807491 +966000 ekin = 8.81826896074676 | erot = 14.5745151863203 | epot = -125.032911211113 | etot = -101.640127064046 +967000 ekin = 8.9569030293131 | erot = 14.2045669524529 | epot = -124.84250103047 | etot = -101.681031048704 +968000 ekin = 9.54853320838666 | erot = 13.2723352951195 | epot = -124.74515666583 | etot = -101.924288162324 +969000 ekin = 9.4502437687464 | erot = 14.3945740263151 | epot = -124.682399280719 | etot = -100.837581485658 +970000 ekin = 9.21873366215398 | erot = 13.9996220324049 | epot = -124.744791785532 | etot = -101.526436090974 +971000 ekin = 9.99365012208013 | erot = 12.832841266649 | epot = -125.082193628276 | etot = -102.255702239547 +972000 ekin = 10.8531518844497 | erot = 10.1692890940719 | epot = -125.661646459223 | etot = -104.639205480702 +973000 ekin = 12.2157559658085 | erot = 10.8538801407932 | epot = -126.544527982808 | etot = -103.474891876206 +974000 ekin = 12.8260432549802 | erot = 10.3799360087168 | epot = -127.611569187676 | etot = -104.405589923979 +975000 ekin = 13.6580394236602 | erot = 11.9432331482014 | epot = -128.916385945886 | etot = -103.315113374025 +976000 ekin = 14.9533034244138 | erot = 13.0781940579022 | epot = -130.386531138976 | etot = -102.35503365666 +977000 ekin = 16.1302157200235 | erot = 11.728247443694 | epot = -131.809854533652 | etot = -103.951391369934 +978000 ekin = 17.4131006781175 | erot = 12.2883320926868 | epot = -133.127724933689 | etot = -103.426292162884 +979000 ekin = 18.3408340925242 | erot = 12.638307739685 | epot = -134.299556644019 | etot = -103.32041481181 +980000 ekin = 18.486099268637 | erot = 11.4553544827387 | epot = -135.258651277385 | etot = -105.31719752601 +981000 ekin = 18.3977271567707 | erot = 10.6940239109833 | epot = -135.863204035817 | etot = -106.771452968063 +982000 ekin = 18.264195125121 | erot = 11.8519030299459 | epot = -136.325677964425 | etot = -106.209579809358 +983000 ekin = 18.2336771349386 | erot = 11.5789339214239 | epot = -136.608013715885 | etot = -106.795402659523 +984000 ekin = 18.0795330780538 | erot = 10.8886569682827 | epot = -136.787086300594 | etot = -107.818896254257 +985000 ekin = 18.3215007661408 | erot = 11.1826156263063 | epot = -136.893675411741 | etot = -107.389559019294 +986000 ekin = 18.9278184735634 | erot = 10.2084663205533 | epot = -136.842552426241 | etot = -107.706267632124 +987000 ekin = 19.2070490323178 | erot = 10.3450839761618 | epot = -136.728820076786 | etot = -107.176687068307 +988000 ekin = 19.3393384968811 | erot = 13.1094542662134 | epot = -136.487574308696 | etot = -104.038781545602 +989000 ekin = 18.8692607694595 | erot = 10.804304167891 | epot = -136.128710512953 | etot = -106.455145575602 +990000 ekin = 19.1296994352489 | erot = 11.0871442087597 | epot = -135.566590211579 | etot = -105.349746567571 +991000 ekin = 19.2058799885993 | erot = 10.5863233864291 | epot = -134.828724859505 | etot = -105.036521484476 +992000 ekin = 18.6626052074925 | erot = 9.94438664060896 | epot = -134.114003323149 | etot = -105.507011475048 +993000 ekin = 18.2986732324755 | erot = 12.5751167790973 | epot = -133.457845849078 | etot = -102.584055837505 +994000 ekin = 18.9118804426949 | erot = 16.3587861176306 | epot = -132.884788625388 | etot = -97.6141220650621 +995000 ekin = 18.8780869759588 | erot = 14.201731801613 | epot = -132.323032403657 | etot = -99.243213626085 +996000 ekin = 19.0405880064438 | erot = 12.7388574752212 | epot = -131.843357344105 | etot = -100.06391186244 +997000 ekin = 18.2614854697624 | erot = 12.4531767028895 | epot = -131.423862770818 | etot = -100.709200598166 +998000 ekin = 17.4819080210013 | erot = 11.3300069724737 | epot = -130.959892229695 | etot = -102.14797723622 +999000 ekin = 17.0511128282761 | erot = 11.8922913066054 | epot = -130.533301683943 | etot = -101.589897549061 +1000000 ekin = 16.4176868113516 | erot = 10.505891115617 | epot = -130.086633390017 | etot = -103.163055463049 + 1000000 367.18625 -134.96443 4.8777959 -113.66895 -0.029625089 39304000 +Loop time of 26.4037 on 4 procs for 1000000 steps with 16 atoms + +Performance: 55.825 ns/day, 0.430 hours/ns, 37873.477 timesteps/s, 605.976 katom-step/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.0347 | 10.957 | 16.143 | 93.9 | 41.50 +Bond | 0.3256 | 0.38079 | 0.42679 | 6.8 | 1.44 +Neigh | 0.021142 | 0.021313 | 0.021466 | 0.1 | 0.08 +Comm | 5.5113 | 11.003 | 14.141 | 100.0 | 41.67 +Output | 0.091898 | 0.097995 | 0.11134 | 2.5 | 0.37 +Modify | 1.3872 | 1.6961 | 1.9792 | 21.0 | 6.42 +Other | | 2.247 | | | 8.51 + +Nlocal: 4 ave 6 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 12 ave 14 max 10 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 26.25 ave 67 max 8 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 105 +Ave neighs/atom = 6.5625 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:26 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/data.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/data.duplex1 new file mode 100644 index 0000000000..a368cef424 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0 +2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0 +3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0 +4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0 +5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0 +6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0 +7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0 +8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0 +9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0 +10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618 +2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161 +3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145 +4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535 +5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021 +6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764 +7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955 +8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736 +9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246 +10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/in.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/in.duplex1 new file mode 100644 index 0000000000..0cf9f2f12e --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/in.duplex1 @@ -0,0 +1,71 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * oxdna_real.cgdna +special_bonds lj 0 1 1 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv oxdna_real.cgdna +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 oxdna_real.cgdna +pair_coeff * * oxdna/hbond seqav oxdna_real.cgdna +pair_coeff 1 4 oxdna/hbond seqav oxdna_real.cgdna +pair_coeff 2 3 oxdna/hbond seqav oxdna_real.cgdna +pair_coeff * * oxdna/xstk oxdna_real.cgdna +pair_coeff * * oxdna/coaxstk oxdna_real.cgdna + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/log.19May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/log.19May24.duplex1.g++.1 new file mode 100644 index 0000000000..7a84803893 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/log.19May24.duplex1.g++.1 @@ -0,0 +1,1113 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.005 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna.real with DATE: 2024-04-26 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (stk) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (xstk) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (coaxstk) file oxdna.real with DATE: 2024-04-26 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 25.179212 + ghost atom cutoff = 32.4 + binsize = 12.589606, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 0.01706 +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8452930576477 | etot = -54.4566354061166 +Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -80.414328 2.5690347 -71.23842 -0.031164648 39304000 +1000 ekin = 6.43820748574479 | erot = 17.3362209220524 | epot = -78.2310638156466 | etot = -54.4566354078494 +2000 ekin = 6.25962687713456 | erot = 17.7614973153003 | epot = -78.4777596014537 | etot = -54.4566354090188 +3000 ekin = 6.07700448778501 | erot = 18.0349390575316 | epot = -78.5685789546716 | etot = -54.456635409355 +4000 ekin = 5.8974424369014 | erot = 18.1444655563221 | epot = -78.4985434019985 | etot = -54.456635408775 +5000 ekin = 5.72921495795424 | erot = 18.0898135345449 | epot = -78.2756638999 | etot = -54.4566354074009 +6000 ekin = 5.58102962967708 | erot = 17.881890737865 | epot = -77.9195557730913 | etot = -54.4566354055493 +7000 ekin = 5.46083564262923 | erot = 17.5394365844241 | epot = -77.4569076305333 | etot = -54.45663540348 +8000 ekin = 5.37466374419903 | erot = 17.0860544650629 | epot = -76.9173536106644 | etot = -54.4566354014025 +9000 ekin = 5.32595754281569 | erot = 16.5482852541262 | epot = -76.3308781963659 | etot = -54.456635399424 +10000 ekin = 5.31554676342217 | erot = 15.954413846903 | epot = -75.7265960077926 | etot = -54.4566353974674 +11000 ekin = 5.34211698054867 | erot = 15.3332614944559 | epot = -75.132013870846 | etot = -54.4566353958413 +12000 ekin = 5.4028703847121 | erot = 14.711083423083 | epot = -74.5705892022628 | etot = -54.4566353944677 +13000 ekin = 5.49411526233304 | erot = 14.1110915850693 | epot = -74.0618422408422 | etot = -54.4566353934398 +14000 ekin = 5.61166305682735 | erot = 13.5517399019593 | epot = -73.6200383516251 | etot = -54.4566353928384 +15000 ekin = 5.75104953856985 | erot = 13.0453199784599 | epot = -73.2530049096301 | etot = -54.4566353926003 +16000 ekin = 5.90767197595959 | erot = 12.5986167018215 | epot = -72.9629240705716 | etot = -54.4566353927906 +17000 ekin = 6.07693584949005 | erot = 12.2121424091128 | epot = -72.7457136520755 | etot = -54.4566353934727 +18000 ekin = 6.25447802454937 | erot = 11.8809715590397 | epot = -72.5920849774634 | etot = -54.4566353938743 +19000 ekin = 6.43644156574384 | erot = 11.5970868983705 | epot = -72.4901638588709 | etot = -54.4566353947565 +20000 ekin = 6.61975078718414 | erot = 11.3493268347887 | epot = -72.425713017461 | etot = -54.4566353954882 +21000 ekin = 6.80231654537078 | erot = 11.1279852357805 | epot = -72.386937177108 | etot = -54.4566353959567 +22000 ekin = 6.9831066603949 | erot = 10.9264899080746 | epot = -72.3662319645787 | etot = -54.4566353961091 +23000 ekin = 7.16204136914421 | erot = 10.7423471683524 | epot = -72.3610239334525 | etot = -54.4566353959559 +24000 ekin = 7.33971202276034 | erot = 10.5772893708791 | epot = -72.3736367892022 | etot = -54.4566353955627 +25000 ekin = 7.51694389098066 | erot = 10.4366021288186 | epot = -72.4101814148955 | etot = -54.4566353950963 +26000 ekin = 7.69428547961004 | erot = 10.3277743414164 | epot = -72.4786952155962 | etot = -54.4566353945698 +27000 ekin = 7.87150355456813 | erot = 10.2597385959261 | epot = -72.5878775446635 | etot = -54.4566353941693 +28000 ekin = 8.04704621231786 | erot = 10.2410408314318 | epot = -72.7447224377789 | etot = -54.4566353940292 +29000 ekin = 8.21759311371839 | erot = 10.2782069424415 | epot = -72.9524354504287 | etot = -54.4566353942689 +30000 ekin = 8.37773815926491 | erot = 10.3742402092555 | epot = -73.2086137634984 | etot = -54.456635394978 +31000 ekin = 8.5199063606362 | erot = 10.5273635253434 | epot = -73.5039052821707 | etot = -54.4566353961911 +32000 ekin = 8.63465075757977 | erot = 10.7302372452279 | epot = -73.8215234006618 | etot = -54.4566353978541 +33000 ekin = 8.71148242170727 | erot = 10.9699568578568 | epot = -74.1380746793619 | etot = -54.4566353997978 +34000 ekin = 8.74030401673698 | erot = 11.2291118958906 | epot = -74.4260513143637 | etot = -54.4566354017361 +35000 ekin = 8.71331738120299 | erot = 11.4879439611373 | epot = -74.6578967456838 | etot = -54.4566354033435 +36000 ekin = 8.62700768065711 | erot = 11.7272655611848 | epot = -74.8109086460864 | etot = -54.4566354042445 +37000 ekin = 8.48360459165237 | erot = 11.9311379268697 | epot = -74.8713779230666 | etot = -54.4566354045445 +38000 ekin = 8.29146113848086 | erot = 12.0877506878432 | epot = -74.8358472300852 | etot = -54.4566354037611 +39000 ekin = 8.06413250091548 | erot = 12.1939343847315 | epot = -74.7147022878414 | etot = -54.4566354021944 +40000 ekin = 7.81835387769382 | erot = 12.2536662217391 | epot = -74.5286554998782 | etot = -54.4566354004452 +41000 ekin = 7.57154460494701 | erot = 12.2737017000962 | epot = -74.3018817037925 | etot = -54.4566353987493 +42000 ekin = 7.33953370634719 | erot = 12.2616149193725 | epot = -74.0577840229955 | etot = -54.4566353972758 +43000 ekin = 7.13480148719636 | erot = 12.225151124624 | epot = -73.8165880080345 | etot = -54.4566353962141 +44000 ekin = 6.96550034046731 | erot = 12.1705709864264 | epot = -73.5927067224915 | etot = -54.4566353955978 +45000 ekin = 6.83524619732669 | erot = 12.1023709627624 | epot = -73.3942525554551 | etot = -54.456635395366 +46000 ekin = 6.74354326448599 | erot = 12.0237258448777 | epot = -73.2239045047616 | etot = -54.456635395398 +47000 ekin = 6.68665553239008 | erot = 11.9373578617833 | epot = -73.0806487897222 | etot = -54.4566353955488 +48000 ekin = 6.6587160612366 | erot = 11.846339390239 | epot = -72.9616908473448 | etot = -54.4566353958692 +49000 ekin = 6.65288529208964 | erot = 11.7537905708822 | epot = -72.8633112588598 | etot = -54.456635395888 +50000 ekin = 6.66236602673449 | erot = 11.665645731731 | epot = -72.7846471541946 | etot = -54.4566353957291 +51000 ekin = 6.68111338468324 | erot = 11.5899588724776 | epot = -72.7277076525689 | etot = -54.4566353954081 +52000 ekin = 6.70418283073615 | erot = 11.5360342718571 | epot = -72.6968524975893 | etot = -54.456635394996 +53000 ekin = 6.72772596002091 | erot = 11.5133896479182 | epot = -72.6977510025407 | etot = -54.4566353946016 +54000 ekin = 6.74871529529379 | erot = 11.5307308739651 | epot = -72.7360815636092 | etot = -54.4566353943504 +55000 ekin = 6.76452000506484 | erot = 11.5943437358561 | epot = -72.8154991352817 | etot = -54.4566353943608 +56000 ekin = 6.77244089755462 | erot = 11.7063368897022 | epot = -72.9354131819766 | etot = -54.4566353947198 +57000 ekin = 6.76933125218943 | erot = 11.8641785052103 | epot = -73.0901451528759 | etot = -54.4566353954762 +58000 ekin = 6.75138787630661 | erot = 12.0602581117046 | epot = -73.2682813846362 | etot = -54.456635396625 +59000 ekin = 6.71417211137041 | erot = 12.2820346405452 | epot = -73.4528421500119 | etot = -54.4566353980963 +60000 ekin = 6.65291138937908 | erot = 12.5128606065824 | epot = -73.6224073957182 | etot = -54.4566353997567 +61000 ekin = 6.56310936735918 | erot = 12.7334757971162 | epot = -73.7532205658841 | etot = -54.4566354014088 +62000 ekin = 6.4414673896219 | erot = 12.9241153784064 | epot = -73.8222181708359 | etot = -54.4566354028076 +63000 ekin = 6.28706349170015 | erot = 13.0670025811129 | epot = -73.810701476737 | etot = -54.456635403924 +64000 ekin = 6.10266894647869 | erot = 13.1477550766291 | epot = -73.7070594271612 | etot = -54.4566354040534 +65000 ekin = 5.89591961177536 | erot = 13.159243189225 | epot = -73.5117982043027 | etot = -54.4566354033024 +66000 ekin = 5.67987986272269 | erot = 13.1031941166757 | epot = -73.2397093810288 | etot = -54.4566354016304 +67000 ekin = 5.47247153600003 | erot = 12.989279234259 | epot = -72.9183861696828 | etot = -54.4566353994238 +68000 ekin = 5.29472138366934 | erot = 12.8325717552519 | epot = -72.5839285358223 | etot = -54.4566353969011 +69000 ekin = 5.16838664772545 | erot = 12.6515520795185 | epot = -72.2765741217863 | etot = -54.4566353945424 +70000 ekin = 5.11229587755514 | erot = 12.4645483617671 | epot = -72.0334796321543 | etot = -54.456635392832 +71000 ekin = 5.13861822273185 | erot = 12.2861550396877 | epot = -71.8814086546626 | etot = -54.456635392243 +72000 ekin = 5.2491977626994 | erot = 12.1240996085004 | epot = -71.8299327640264 | etot = -54.4566353928266 +73000 ekin = 5.43492595011745 | erot = 11.9780482590895 | epot = -71.8696096036143 | etot = -54.4566353944073 +74000 ekin = 5.67784516722635 | erot = 11.8411405072589 | epot = -71.9756210710801 | etot = -54.4566353965948 +75000 ekin = 5.95413179780696 | erot = 11.7025554045187 | epot = -72.1133226012198 | etot = -54.4566353988942 +76000 ekin = 6.23821902238384 | erot = 11.550835238765 | epot = -72.2456896619949 | etot = -54.456635400846 +77000 ekin = 6.50672473640332 | erot = 11.3769509006249 | epot = -72.3403110391631 | etot = -54.4566354021349 +78000 ekin = 6.74134494190867 | erot = 11.1763190057829 | epot = -72.3742993503321 | etot = -54.4566354026406 +79000 ekin = 6.93029998725147 | erot = 10.9493831098248 | epot = -72.3363184995039 | etot = -54.4566354024276 +80000 ekin = 7.06837455802669 | erot = 10.7008607206279 | epot = -72.2258706803373 | etot = -54.4566354016827 +81000 ekin = 7.15592612862585 | erot = 10.4381578436614 | epot = -72.05071937292 | etot = -54.4566354006327 +82000 ekin = 7.19737523755897 | erot = 10.1696204752438 | epot = -71.8236311122793 | etot = -54.4566353994766 +83000 ekin = 7.19964138072357 | erot = 9.90319185133895 | epot = -71.559468630406 | etot = -54.4566353983435 +84000 ekin = 7.17082378076055 | erot = 9.64576283606949 | epot = -71.2732220141216 | etot = -54.4566353972916 +85000 ekin = 7.11924100547637 | erot = 9.40319183444012 | epot = -70.9790682362424 | etot = -54.4566353963259 +86000 ekin = 7.05280646949636 | erot = 9.18075710620515 | epot = -70.6901989711303 | etot = -54.4566353954288 +87000 ekin = 6.97865213852011 | erot = 8.98373783121374 | epot = -70.4190253643139 | etot = -54.45663539458 +88000 ekin = 6.9029074524998 | erot = 8.8178750532503 | epot = -70.1774178995232 | etot = -54.4566353937731 +89000 ekin = 6.83056643684682 | erot = 8.68957621789659 | epot = -69.9767780477612 | etot = -54.4566353930177 +90000 ekin = 6.76540803039367 | erot = 8.6058366061046 | epot = -69.8278800288353 | etot = -54.456635392337 +91000 ekin = 6.70995822419681 | erot = 8.57392290473256 | epot = -69.7405165206917 | etot = -54.4566353917624 +92000 ekin = 6.66549387606452 | erot = 8.60089293174941 | epot = -69.7230221991425 | etot = -54.4566353913285 +93000 ekin = 6.63209392240901 | erot = 8.69302362042091 | epot = -69.7817529338986 | etot = -54.4566353910687 +94000 ekin = 6.6087387957867 | erot = 8.85520324232614 | epot = -69.9205774291257 | etot = -54.4566353910128 +95000 ekin = 6.5934554231299 | erot = 9.08998001249973 | epot = -70.1400708268608 | etot = -54.4566353912311 +96000 ekin = 6.58349816402809 | erot = 9.39670336712944 | epot = -70.4368369228354 | etot = -54.4566353916779 +97000 ekin = 6.57557086190993 | erot = 9.7723203542983 | epot = -70.8045266085995 | etot = -54.4566353923912 +98000 ekin = 6.56607746070853 | erot = 10.2103280886839 | epot = -71.233040942761 | etot = -54.4566353933686 +99000 ekin = 6.55139785883141 | erot = 10.700518875157 | epot = -71.7085521285789 | etot = -54.4566353945905 +100000 ekin = 6.52819744721324 | erot = 11.2290265012434 | epot = -72.2138593444663 | etot = -54.4566353960097 +101000 ekin = 6.49377694354442 | erot = 11.778744418072 | epot = -72.7291567591596 | etot = -54.4566353975432 +102000 ekin = 6.44645975182924 | erot = 12.3302092947474 | epot = -73.2333044456467 | etot = -54.4566353990701 +103000 ekin = 6.38599188040475 | erot = 12.8629861678417 | epot = -73.7056134486881 | etot = -54.4566354004416 +104000 ekin = 6.31389917689188 | erot = 13.3574827218747 | epot = -74.1280173002654 | etot = -54.4566354014988 +105000 ekin = 6.23372050746404 | erot = 13.7969365030789 | epot = -74.4872924127827 | etot = -54.4566354022397 +106000 ekin = 6.15161195850931 | erot = 14.1683082609505 | epot = -74.7765556218299 | etot = -54.45663540237 +107000 ekin = 6.07599644252674 | erot = 14.4651582362835 | epot = -74.9977900809679 | etot = -54.4566354021577 +108000 ekin = 6.01224980359744 | erot = 14.6879762973639 | epot = -75.1568615023395 | etot = -54.4566354013782 +109000 ekin = 5.96718055298343 | erot = 14.8435302087046 | epot = -75.2673461618523 | etot = -54.4566354001642 +110000 ekin = 5.94906585806739 | erot = 14.9433946245219 | epot = -75.3490958813021 | etot = -54.4566353987129 +111000 ekin = 5.96692254396596 | erot = 15.0017732632798 | epot = -75.4253312044835 | etot = -54.4566353972378 +112000 ekin = 6.02963894580686 | erot = 15.0332002745137 | epot = -75.5194746162464 | etot = -54.4566353959258 +113000 ekin = 6.14472749189881 | erot = 15.0506190089295 | epot = -75.6519818961823 | etot = -54.456635395354 +114000 ekin = 6.31294119125893 | erot = 15.0641400294536 | epot = -75.8337166157274 | etot = -54.4566353950148 +115000 ekin = 6.53170723497726 | erot = 15.0810976270015 | epot = -76.0694402570575 | etot = -54.4566353950787 +116000 ekin = 6.79565473868378 | erot = 15.1058873747025 | epot = -76.3581775089288 | etot = -54.4566353955425 +117000 ekin = 7.09589353296915 | erot = 15.1399747310401 | epot = -76.6925036604113 | etot = -54.4566353964021 +118000 ekin = 7.42010913176814 | erot = 15.1818878453243 | epot = -77.0586323747378 | etot = -54.4566353976454 +119000 ekin = 7.75291308545885 | erot = 15.2271156041089 | epot = -77.436664088802 | etot = -54.4566353992342 +120000 ekin = 8.07655694001114 | erot = 15.2680755527864 | epot = -77.8012678938754 | etot = -54.4566354010778 +121000 ekin = 8.37209283452514 | erot = 15.2944252034468 | epot = -78.1231534409902 | etot = -54.4566354030182 +122000 ekin = 8.62097203571359 | erot = 15.2939565964172 | epot = -78.3715640369608 | etot = -54.45663540483 +123000 ekin = 8.80691805373849 | erot = 15.2541302313802 | epot = -78.5176836913811 | etot = -54.4566354062624 +124000 ekin = 8.91774775140848 | erot = 15.1640393169121 | epot = -78.5384224754137 | etot = -54.4566354070931 +125000 ekin = 8.94673865107599 | erot = 15.0163758445777 | epot = -78.4197499028408 | etot = -54.4566354071871 +126000 ekin = 8.89353504113546 | erot = 14.8103810343862 | epot = -78.1605514820978 | etot = -54.4566354065761 +127000 ekin = 8.76295715660914 | erot = 14.5505246086874 | epot = -77.7701171706756 | etot = -54.4566354053791 +128000 ekin = 8.56412338279211 | erot = 14.2447148868085 | epot = -77.2654736732317 | etot = -54.456635403631 +129000 ekin = 8.30999977775241 | erot = 13.9056008475438 | epot = -76.6722360268308 | etot = -54.4566354015347 +130000 ekin = 8.01598983357869 | erot = 13.5489784634635 | epot = -76.0216036963406 | etot = -54.4566353992984 +131000 ekin = 7.69860752663267 | erot = 13.191973628217 | epot = -75.3472165519593 | etot = -54.4566353971097 +132000 ekin = 7.37433696937952 | erot = 12.8512990204963 | epot = -74.682271384997 | etot = -54.4566353951211 +133000 ekin = 7.05872362614925 | erot = 12.5417941515422 | epot = -74.0571531711344 | etot = -54.4566353934429 +134000 ekin = 6.76570888198983 | erot = 12.2753542959273 | epot = -73.4976985700582 | etot = -54.4566353921411 +135000 ekin = 6.50719363731297 | erot = 12.0602549647526 | epot = -73.0240839933233 | etot = -54.4566353912577 +136000 ekin = 6.29279008475018 | erot = 11.9007669358432 | epot = -72.6501924113932 | etot = -54.4566353907998 +137000 ekin = 6.1297097827656 | erot = 11.797057630299 | epot = -72.3834028038282 | etot = -54.4566353907636 +138000 ekin = 6.02274351233274 | erot = 11.7455123962494 | epot = -72.2248912997163 | etot = -54.4566353911342 +139000 ekin = 5.97430404723505 | erot = 11.7390412107215 | epot = -72.1699806498505 | etot = -54.456635391894 +140000 ekin = 5.98449840319398 | erot = 11.7661921151461 | epot = -72.2073259113408 | etot = -54.4566353930008 +141000 ekin = 6.05122402382853 | erot = 11.8123445028326 | epot = -72.3202039210611 | etot = -54.4566353944 +142000 ekin = 6.17031735772835 | erot = 11.860441511122 | epot = -72.4873942648628 | etot = -54.4566353960124 +143000 ekin = 6.33577810129533 | erot = 11.8919671618459 | epot = -72.6843806606519 | etot = -54.4566353975106 +144000 ekin = 6.5400911832184 | erot = 11.8891339130634 | epot = -72.8858604955073 | etot = -54.4566353992254 +145000 ekin = 6.7746586664194 | erot = 11.8352952468181 | epot = -73.0665893139994 | etot = -54.4566354007619 +146000 ekin = 7.03032727827686 | erot = 11.7160091899344 | epot = -73.2029718703323 | etot = -54.456635402121 +147000 ekin = 7.29660189209642 | erot = 11.5221059419086 | epot = -73.2753432368926 | etot = -54.4566354028876 +148000 ekin = 7.56407690493304 | erot = 11.2503448019254 | epot = -73.2710571099655 | etot = -54.4566354031071 +149000 ekin = 7.82544292003207 | erot = 10.9039979828621 | epot = -73.1860763056619 | etot = -54.4566354027677 +150000 ekin = 8.07517324147418 | erot = 10.4929858681079 | epot = -73.0247945114893 | etot = -54.4566354019072 +151000 ekin = 8.30975251519227 | erot = 10.0330103746793 | epot = -72.7993982905126 | etot = -54.4566354006411 +152000 ekin = 8.52766332329262 | erot = 9.54393934171969 | epot = -72.5282380641322 | etot = -54.4566353991199 +153000 ekin = 8.72913641124913 | erot = 9.04783809538959 | epot = -72.2336099041494 | etot = -54.4566353975106 +154000 ekin = 8.91570927168975 | erot = 8.56693447900063 | epot = -71.9392791466627 | etot = -54.4566353959723 +155000 ekin = 9.08966068414512 | erot = 8.12178607637931 | epot = -71.6680821551646 | etot = -54.4566353946402 +156000 ekin = 9.25339893961253 | erot = 7.72982624258095 | epot = -71.4398605758094 | etot = -54.4566353936159 +157000 ekin = 9.40888952795375 | erot = 7.40436483126651 | epot = -71.2698897521795 | etot = -54.4566353929592 +158000 ekin = 9.5571792388578 | erot = 7.15403664791566 | epot = -71.1678512794925 | etot = -54.456635392719 +159000 ekin = 9.69792111012153 | erot = 6.98265633604475 | epot = -71.1372128390505 | etot = -54.4566353928842 +160000 ekin = 9.82919776336752 | erot = 6.88943769583961 | epot = -71.1752708526347 | etot = -54.4566353934276 +161000 ekin = 9.94745815557448 | erot = 6.8695239744895 | epot = -71.2736175243542 | etot = -54.4566353942902 +162000 ekin = 10.0476105552154 | erot = 6.9148102338052 | epot = -71.4190561844078 | etot = -54.4566353953872 +163000 ekin = 10.1232836123728 | erot = 7.01503930069488 | epot = -71.5949583096737 | etot = -54.4566353966061 +164000 ekin = 10.1672576282715 | erot = 7.15913239145111 | epot = -71.7830254175365 | etot = -54.4566353978139 +165000 ekin = 10.1720616886924 | erot = 7.33667115267699 | epot = -71.9653682402348 | etot = -54.4566353988654 +166000 ekin = 10.130718189882 | erot = 7.53939136045688 | epot = -72.1267449499592 | etot = -54.4566353996203 +167000 ekin = 10.0375906740833 | erot = 7.76248640952837 | epot = -72.2567124835719 | etot = -54.4566353999602 +168000 ekin = 9.88925393885932 | erot = 8.00550722627944 | epot = -72.3513965649499 | etot = -54.4566353998111 +169000 ekin = 9.68526445659958 | erot = 8.27264999921095 | epot = -72.4145498549766 | etot = -54.4566353991661 +170000 ekin = 9.42867794111905 | erot = 8.57229328100177 | epot = -72.4576066202142 | etot = -54.4566353980934 +171000 ekin = 9.12616910816985 | erot = 8.91577619747958 | epot = -72.4985807023847 | etot = -54.4566353967353 +172000 ekin = 8.78767440912354 | erot = 9.31557620898523 | epot = -72.5598860133921 | etot = -54.4566353952833 +173000 ekin = 8.4308902629603 | erot = 9.78404466318918 | epot = -72.6715703175844 | etot = -54.4566353914349 +174000 ekin = 8.08808636305844 | erot = 10.330351924278 | epot = -72.8750736787358 | etot = -54.4566353913993 +175000 ekin = 7.76683289792752 | erot = 10.9528766887196 | epot = -73.1763449782723 | etot = -54.4566353916252 +176000 ekin = 7.47165533673879 | erot = 11.6455953906608 | epot = -73.5738861195206 | etot = -54.456635392121 +177000 ekin = 7.20644207982112 | erot = 12.3989755240462 | epot = -74.0620529967131 | etot = -54.4566353928457 +178000 ekin = 6.974264785072 | erot = 13.2002588275757 | epot = -74.6311590065932 | etot = -54.4566353939455 +179000 ekin = 6.77739061781459 | erot = 14.034248956954 | epot = -75.2682749696791 | etot = -54.4566353949105 +180000 ekin = 6.61743414637729 | erot = 14.8862774181217 | epot = -75.9603469603612 | etot = -54.4566353958622 +181000 ekin = 6.49561144162321 | erot = 15.7407037445572 | epot = -76.6929505832098 | etot = -54.4566353970295 +182000 ekin = 6.41305807095974 | erot = 16.5823414720904 | epot = -77.4520349408826 | etot = -54.4566353978324 +183000 ekin = 6.37104675400492 | erot = 17.3988622631936 | epot = -78.2265444157012 | etot = -54.4566353985027 +184000 ekin = 6.37106698283056 | erot = 18.1794275278873 | epot = -79.0071299097852 | etot = -54.4566353990674 +185000 ekin = 6.41462378113363 | erot = 18.9143606927346 | epot = -79.7856198734752 | etot = -54.456635399607 +186000 ekin = 6.50261133383222 | erot = 19.594459796067 | epot = -80.5537065301622 | etot = -54.456635400263 +187000 ekin = 6.63422049770368 | erot = 20.2099561332676 | epot = -81.3008120321885 | etot = -54.4566354012172 +188000 ekin = 6.80553106495261 | erot = 20.7492823612707 | epot = -82.0114488288671 | etot = -54.4566354026438 +189000 ekin = 7.00817768191868 | erot = 21.1980708186845 | epot = -82.6628839052196 | etot = -54.4566354046164 +190000 ekin = 7.22864796075227 | erot = 21.5390297894768 | epot = -83.2243131572579 | etot = -54.4566354070288 +191000 ekin = 7.44767622618309 | erot = 21.7493732842278 | epot = -83.6536849211036 | etot = -54.4566354106927 +192000 ekin = 7.64121438364656 | erot = 21.8048177890285 | epot = -83.9026675850786 | etot = -54.4566354124035 +193000 ekin = 7.78824892260135 | erot = 21.6992058928577 | epot = -83.9440902285495 | etot = -54.4566354130904 +194000 ekin = 7.87254337485893 | erot = 21.4376021938463 | epot = -83.7667809811825 | etot = -54.4566354124772 +195000 ekin = 7.88497345911822 | erot = 21.0375935324407 | epot = -83.3792024018217 | etot = -54.4566354102629 +196000 ekin = 7.82453658225029 | erot = 20.5298119321328 | epot = -82.8109839217733 | etot = -54.4566354073902 +197000 ekin = 7.69767210841892 | erot = 19.9508117348117 | epot = -82.1051192473244 | etot = -54.4566354040938 +198000 ekin = 7.51634139122171 | erot = 19.3371432855414 | epot = -81.3101200775114 | etot = -54.4566354007483 +199000 ekin = 7.29564803023476 | erot = 18.7233240020312 | epot = -80.4756074302768 | etot = -54.4566353980108 +200000 ekin = 7.05166010690528 | erot = 18.1350524779765 | epot = -79.6433479808066 | etot = -54.4566353959248 +201000 ekin = 6.79981173468669 | erot = 17.5880304600562 | epot = -78.8444775892921 | etot = -54.4566353945492 +202000 ekin = 6.55389933641572 | erot = 17.0888778993458 | epot = -78.0994126296097 | etot = -54.4566353938482 +203000 ekin = 6.32553919621666 | erot = 16.6360378263834 | epot = -77.4182124163434 | etot = -54.4566353937433 +204000 ekin = 6.12389632660999 | erot = 16.221171795851 | epot = -76.8017035165982 | etot = -54.4566353941373 +205000 ekin = 5.95555200640865 | erot = 15.8307416505747 | epot = -76.2429290519105 | etot = -54.4566353949271 +206000 ekin = 5.82446904491665 | erot = 15.4476864597757 | epot = -75.7287909006854 | etot = -54.456635395993 +207000 ekin = 5.73208912867472 | erot = 15.0532400346064 | epot = -75.2419645604691 | etot = -54.4566353971881 +208000 ekin = 5.67762302906586 | erot = 14.6289641823334 | epot = -74.7632226097333 | etot = -54.4566353983341 +209000 ekin = 5.65855387682243 | erot = 14.1589879691225 | epot = -74.2741772451824 | etot = -54.4566353992374 +210000 ekin = 5.67127672991725 | erot = 13.6322671582814 | epot = -73.7601792879283 | etot = -54.4566353997296 +211000 ekin = 5.71170069345446 | erot = 13.0444908839479 | epot = -73.2128269771113 | etot = -54.456635399709 +212000 ekin = 5.77562712092918 | erot = 12.3991887587334 | epot = -72.6314512788358 | etot = -54.4566353991733 +213000 ekin = 5.85883014811268 | erot = 11.7077170437804 | epot = -72.0231825901061 | etot = -54.456635398213 +214000 ekin = 5.95693715945621 | erot = 10.9880856586527 | epot = -71.4016582150861 | etot = -54.4566353969771 +215000 ekin = 6.06530009270273 | erot = 10.2628764798217 | epot = -70.7848119681606 | etot = -54.4566353956361 +216000 ekin = 6.17899119913878 | erot = 9.55666412395529 | epot = -70.1922907174477 | etot = -54.4566353943536 +217000 ekin = 6.29291855291586 | erot = 8.89336715125219 | epot = -69.64292109744 | etot = -54.4566353932719 +218000 ekin = 6.40196857726006 | erot = 8.29389599676029 | epot = -69.1524999665188 | etot = -54.4566353924985 +219000 ekin = 6.50110173408261 | erot = 7.77437623954087 | epot = -68.7321133657201 | etot = -54.4566353920966 +220000 ekin = 6.58540342133091 | erot = 7.34511996775883 | epot = -68.3871587811671 | etot = -54.4566353920774 +221000 ekin = 6.65014690325897 | erot = 7.01039395844385 | epot = -68.1171762541011 | etot = -54.4566353923982 +222000 ekin = 6.69092576193417 | erot = 6.76891043700557 | epot = -67.9164715919184 | etot = -54.4566353929786 +223000 ekin = 6.70387621884996 | erot = 6.61487073126029 | epot = -67.77538234382 | etot = -54.4566353937098 +224000 ekin = 6.6859658221945 | erot = 6.53933741261809 | epot = -67.6819386292908 | etot = -54.4566353944782 +225000 ekin = 6.63529509868518 | erot = 6.53169516027476 | epot = -67.6236256540922 | etot = -54.4566353951323 +226000 ekin = 6.55134622983674 | erot = 6.58124861354781 | epot = -67.5892302390912 | etot = -54.4566353957066 +227000 ekin = 6.43512582373462 | erot = 6.6778633909886 | epot = -67.5696246108205 | etot = -54.4566353960973 +228000 ekin = 6.28919825971956 | erot = 6.81242105498751 | epot = -67.5582547110045 | etot = -54.4566353962974 +229000 ekin = 6.11758034386912 | erot = 6.97737322344776 | epot = -67.5515889636427 | etot = -54.4566353963259 +230000 ekin = 5.92553219663261 | erot = 7.1666772772129 | epot = -67.5488448700593 | etot = -54.4566353962138 +231000 ekin = 5.71928874368776 | erot = 7.37558258297039 | epot = -67.5515067226485 | etot = -54.4566353959904 +232000 ekin = 5.50576904745089 | erot = 7.60029005185252 | epot = -67.5626944950135 | etot = -54.4566353957101 +233000 ekin = 5.29228522016845 | erot = 7.83763848257108 | epot = -67.5865590981304 | etot = -54.4566353953909 +234000 ekin = 5.08626778915082 | erot = 8.0849723575554 | epot = -67.627875541769 | etot = -54.4566353950628 +235000 ekin = 4.89496149390685 | erot = 8.33993380345756 | epot = -67.6915306921237 | etot = -54.4566353947593 +236000 ekin = 4.725107662887 | erot = 8.60023942152078 | epot = -67.7819824789196 | etot = -54.4566353945118 +237000 ekin = 4.58266891059204 | erot = 8.863520450285 | epot = -67.9028247552286 | etot = -54.4566353943516 +238000 ekin = 4.47254352856373 | erot = 9.12714914792354 | epot = -68.0563280707913 | etot = -54.456635394304 +239000 ekin = 4.39832589608058 | erot = 9.38815494537381 | epot = -68.2431162358326 | etot = -54.4566353943782 +240000 ekin = 4.36214482372772 | erot = 9.64329675760556 | epot = -68.4620769758964 | etot = -54.4566353945632 +241000 ekin = 4.36460414736016 | erot = 9.88932905774899 | epot = -68.7105685999353 | etot = -54.4566353948261 +242000 ekin = 4.40483557566032 | erot = 10.123401279054 | epot = -68.9848722498437 | etot = -54.4566353951294 +243000 ekin = 4.48065587113318 | erot = 10.3436288280301 | epot = -69.2809200945657 | etot = -54.4566353954024 +244000 ekin = 4.58880538052794 | erot = 10.5497091929702 | epot = -69.5951499691048 | etot = -54.4566353956067 +245000 ekin = 4.72523059106075 | erot = 10.7433050692471 | epot = -69.925171056014 | etot = -54.4566353957062 +246000 ekin = 4.88536596035895 | erot = 10.9281953102942 | epot = -70.2701966663515 | etot = -54.4566353956983 +247000 ekin = 5.06437032892622 | erot = 11.1100753168529 | epot = -70.6310810413878 | etot = -54.4566353956087 +248000 ekin = 5.2572803931489 | erot = 11.2959779038021 | epot = -71.0098936924448 | etot = -54.4566353954938 +249000 ekin = 5.4590578306858 | erot = 11.4933498885016 | epot = -71.4090431146237 | etot = -54.4566353954363 +250000 ekin = 5.6645272689396 | erot = 11.7088807610481 | epot = -71.8300434255194 | etot = -54.4566353955318 +251000 ekin = 5.86822964772049 | erot = 11.9472357725875 | epot = -72.2721008161787 | etot = -54.4566353958707 +252000 ekin = 6.06424926084265 | erot = 12.2098996244356 | epot = -72.7307842817964 | etot = -54.4566353965181 +253000 ekin = 6.24611969949079 | erot = 12.4943889560454 | epot = -73.1971440530269 | etot = -54.4566353974907 +254000 ekin = 6.4068657770421 | erot = 12.7940520504516 | epot = -73.6575532262015 | etot = -54.4566353987078 +255000 ekin = 6.53934545678292 | erot = 13.0988013252432 | epot = -74.0947821820346 | etot = -54.4566354000085 +256000 ekin = 6.63702718994521 | erot = 13.3967890648194 | epot = -74.4904516559583 | etot = -54.4566354011937 +257000 ekin = 6.69481406277413 | erot = 13.676395236133 | epot = -74.8278447009719 | etot = -54.4566354020648 +258000 ekin = 6.70987363015967 | erot = 13.9283274305685 | epot = -75.0948364631916 | etot = -54.4566354024634 +259000 ekin = 6.68224111902895 | erot = 14.1473011903233 | epot = -75.2861777117026 | etot = -54.4566354023504 +260000 ekin = 6.6149121085381 | erot = 14.3326259136799 | epot = -75.4041734240351 | etot = -54.4566354018171 +261000 ekin = 6.51341628163524 | erot = 14.4874368525599 | epot = -75.4574885351826 | etot = -54.4566354009875 +262000 ekin = 6.38501100285347 | erot = 14.6175606151456 | epot = -75.459207018044 | etot = -54.4566354000449 +263000 ekin = 6.23771961613877 | erot = 14.7299444235434 | epot = -75.4242994388567 | etot = -54.4566353991745 +264000 ekin = 6.07941608333398 | erot = 14.8311371615597 | epot = -75.3671886433855 | etot = -54.4566353984918 +265000 ekin = 5.91710326790405 | erot = 14.926199726942 | epot = -75.2999383929275 | etot = -54.4566353980815 +266000 ekin = 5.75646622878407 | erot = 15.017979690906 | epot = -75.231081317672 | etot = -54.4566353979818 +267000 ekin = 5.60176709254115 | erot = 15.106656765002 | epot = -75.1650592557273 | etot = -54.4566353981841 +268000 ekin = 5.45614222906146 | erot = 15.189616158016 | epot = -75.1023937856933 | etot = -54.4566353986158 +269000 ekin = 5.32233940193201 | erot = 15.2616013239986 | epot = -75.0405761254131 | etot = -54.4566353994824 +270000 ekin = 5.20386526321306 | erot = 15.313412678491 | epot = -74.9739133416087 | etot = -54.4566353999047 +271000 ekin = 5.10636511575734 | erot = 15.3371670926589 | epot = -74.9001676083476 | etot = -54.4566353999314 +272000 ekin = 5.03883267753818 | erot = 15.3275595144062 | epot = -74.8230275914628 | etot = -54.4566353995184 +273000 ekin = 5.01408540358722 | erot = 15.2821242951832 | epot = -74.7528450973462 | etot = -54.4566353985758 +274000 ekin = 5.04781979148557 | erot = 15.2024861316973 | epot = -74.7069413204901 | etot = -54.4566353973072 +275000 ekin = 5.15587366097677 | erot = 15.0944379866221 | epot = -74.70694704358 | etot = -54.4566353959811 +276000 ekin = 5.35005421474681 | erot = 14.9659067954328 | epot = -74.7725964054904 | etot = -54.4566353953107 +277000 ekin = 5.63375697520957 | erot = 14.823836281555 | epot = -74.9142286522973 | etot = -54.4566353955328 +278000 ekin = 5.99906841359137 | erot = 14.6726954109903 | epot = -75.1283992213119 | etot = -54.4566353967302 +279000 ekin = 6.42677541448493 | erot = 14.5136733620313 | epot = -75.3970841751191 | etot = -54.4566353986028 +280000 ekin = 6.88949881397351 | erot = 14.3457690850598 | epot = -75.6919032996898 | etot = -54.4566354006565 +281000 ekin = 7.35667779023817 | erot = 14.1678579049843 | epot = -75.9811710982574 | etot = -54.4566354030349 +282000 ekin = 7.79883836993533 | erot = 13.9783154933866 | epot = -76.2337892675062 | etot = -54.4566354041843 +283000 ekin = 8.19321965983707 | erot = 13.7803017892201 | epot = -76.4301568535012 | etot = -54.456635404444 +284000 ekin = 8.52580258151993 | erot = 13.5821927274771 | epot = -76.5646307128671 | etot = -54.4566354038701 +285000 ekin = 8.79108509960225 | erot = 13.3960919484842 | epot = -76.6438124507659 | etot = -54.4566354026794 +286000 ekin = 8.99063008546271 | erot = 13.2361528285313 | epot = -76.6834183151731 | etot = -54.4566354011791 +287000 ekin = 9.13077921529744 | erot = 13.1164348721714 | epot = -76.7038494871523 | etot = -54.4566353996835 +288000 ekin = 9.22018153921085 | erot = 13.0487287839798 | epot = -76.7255457216523 | etot = -54.4566353984616 +289000 ekin = 9.26763004982218 | erot = 13.0407273170634 | epot = -76.7649927645828 | etot = -54.4566353976972 +290000 ekin = 9.28050533355007 | erot = 13.094833692554 | epot = -76.8319744235714 | etot = -54.4566353974674 +291000 ekin = 9.26393617617635 | erot = 13.2077741770249 | epot = -76.9283457509549 | etot = -54.4566353977536 +292000 ekin = 9.22062696895226 | erot = 13.3710137562639 | epot = -77.0482761236745 | etot = -54.4566353984584 +293000 ekin = 9.15118773751663 | erot = 13.5717951426594 | epot = -77.1796182796241 | etot = -54.4566353994481 +294000 ekin = 9.05474970264756 | erot = 13.7942987417177 | epot = -77.3056838449919 | etot = -54.4566354006267 +295000 ekin = 8.92966682643982 | erot = 14.0208093015831 | epot = -77.4071115298357 | etot = -54.4566354018128 +296000 ekin = 8.7741774127974 | erot = 14.233571023826 | epot = -77.4643838395654 | etot = -54.4566354029419 +297000 ekin = 8.58698226598697 | erot = 14.4154370340303 | epot = -77.4590547039531 | etot = -54.4566354039359 +298000 ekin = 8.36775865344638 | erot = 14.5506208496152 | epot = -77.3750149077777 | etot = -54.456635404716 +299000 ekin = 8.11762616774706 | erot = 14.6254987182126 | epot = -77.1997602911624 | etot = -54.4566354052028 +300000 ekin = 7.83954023620354 | erot = 14.6294629242916 | epot = -76.9256385658176 | etot = -54.4566354053225 +301000 ekin = 7.53854212204199 | erot = 14.5557510868048 | epot = -76.5509286138768 | etot = -54.45663540503 +302000 ekin = 7.22177736042479 | erot = 14.4020878566552 | epot = -76.0805006213996 | etot = -54.4566354043196 +303000 ekin = 6.89822321248548 | erot = 14.1709638782383 | epot = -75.5258224939627 | etot = -54.4566354032389 +304000 ekin = 6.57813083858624 | erot = 13.869444626723 | epot = -74.9042108671878 | etot = -54.4566354018786 +305000 ekin = 6.27226349854785 | erot = 13.5085175341593 | epot = -74.2374164330628 | etot = -54.4566354003557 +306000 ekin = 5.99106804508633 | erot = 13.1021011111619 | epot = -73.5498045550381 | etot = -54.4566353987898 +307000 ekin = 5.74393176217476 | erot = 12.6659083209143 | epot = -72.8664754803728 | etot = -54.4566353972837 +308000 ekin = 5.53864569893524 | erot = 12.2163535665821 | epot = -72.2116346614262 | etot = -54.4566353959089 +309000 ekin = 5.38113513069927 | erot = 11.7694200620306 | epot = -71.6071905875238 | etot = -54.4566353947939 +310000 ekin = 5.27545873877789 | erot = 11.3397497111436 | epot = -71.0718438437192 | etot = -54.4566353937978 +311000 ekin = 5.22395041073499 | erot = 10.9408344797135 | epot = -70.6214202834639 | etot = -54.4566353930154 +312000 ekin = 5.22743903848066 | erot = 10.5841016939956 | epot = -70.2681761249448 | etot = -54.4566353924685 +313000 ekin = 5.28546710256986 | erot = 10.2783241765307 | epot = -70.0204266712923 | etot = -54.4566353921918 +314000 ekin = 5.39643142780609 | erot = 10.0290048888872 | epot = -69.8820717089236 | etot = -54.4566353922303 +315000 ekin = 5.55762409515259 | erot = 9.83776650484665 | epot = -69.8520259926243 | etot = -54.4566353926251 +316000 ekin = 5.76519532362118 | erot = 9.70186120840598 | epot = -69.9236919254295 | etot = -54.4566353934023 +317000 ekin = 6.01409543293347 | erot = 9.61396213871344 | epot = -70.0846929662005 | etot = -54.4566353945536 +318000 ekin = 6.29807297065393 | erot = 9.562417609845 | epot = -70.3171259765173 | etot = -54.4566353960184 +319000 ekin = 6.60980622314066 | erot = 9.53213013021435 | epot = -70.5985717510309 | etot = -54.4566353976759 +320000 ekin = 6.94122281960071 | erot = 9.50614507367243 | epot = -70.9040032926193 | etot = -54.4566353993461 +321000 ekin = 7.28401648903376 | erot = 9.46788297195031 | epot = -71.208534861796 | etot = -54.4566354008119 +322000 ekin = 7.63030660902787 | erot = 9.40373715745484 | epot = -71.4906791683421 | etot = -54.4566354018594 +323000 ekin = 7.97332122461268 | erot = 9.30554772849007 | epot = -71.7355043554331 | etot = -54.4566354023304 +324000 ekin = 8.30794457963839 | erot = 9.17235846962826 | epot = -71.936938451434 | etot = -54.4566354021673 +325000 ekin = 8.63098140949704 | erot = 9.0109566441418 | epot = -72.0985734550708 | etot = -54.456635401432 +326000 ekin = 8.94105719146754 | erot = 8.83498929956515 | epot = -72.232681891326 | etot = -54.4566354002933 +327000 ekin = 9.2381710054864 | erot = 8.66283136635324 | epot = -72.3576377708286 | etot = -54.4566353989889 +328000 ekin = 9.52300348811516 | erot = 8.5146834839797 | epot = -72.4943223698687 | etot = -54.4566353977739 +329000 ekin = 9.79612481313629 | erot = 8.40948710595072 | epot = -72.6622473159659 | etot = -54.4566353968789 +330000 ekin = 10.0572432527195 | erot = 8.362163518333 | epot = -72.876042167532 | etot = -54.4566353964795 +331000 ekin = 10.3046041371655 | erot = 8.38150606119571 | epot = -73.1427455950476 | etot = -54.4566353966864 +332000 ekin = 10.5346182384524 | erot = 8.46889046679764 | epot = -73.4601441027809 | etot = -54.4566353975309 +333000 ekin = 10.7417838215593 | erot = 8.61787963653054 | epot = -73.8162988570504 | etot = -54.4566353989605 +334000 ekin = 10.9189661695317 | erot = 8.81478419867269 | epot = -74.1903857690307 | etot = -54.4566354008263 +335000 ekin = 11.0580923139754 | erot = 9.0402445035637 | epot = -74.5549722204231 | etot = -54.456635402884 +336000 ekin = 11.1512758054914 | erot = 9.27184425622304 | epot = -74.8797554665151 | etot = -54.4566354048006 +337000 ekin = 11.192283410668 | erot = 9.48758788095734 | epot = -75.1365066978345 | etot = -54.4566354062091 +338000 ekin = 11.1781049966217 | erot = 9.66977867524164 | epot = -75.3045190786432 | etot = -54.4566354067799 +339000 ekin = 11.110253074136 | erot = 9.80853289682954 | epot = -75.3754213772802 | etot = -54.4566354063147 +340000 ekin = 10.9953916139861 | erot = 9.90404205087864 | epot = -75.3560690696778 | etot = -54.4566354048131 +341000 ekin = 10.8450335653197 | erot = 9.96690251907776 | epot = -75.2685714868785 | etot = -54.456635402481 +342000 ekin = 10.6743190321388 | erot = 10.0163513349014 | epot = -75.1473057667194 | etot = -54.4566353996792 +343000 ekin = 10.5001667181513 | erot = 10.0768603504225 | epot = -75.0336624654006 | etot = -54.4566353968268 +344000 ekin = 10.3392423699624 | erot = 10.1739542078182 | epot = -74.9698319720972 | etot = -54.4566353943167 +345000 ekin = 10.2061520845065 | erot = 10.3301605013023 | epot = -74.9929479782598 | etot = -54.4566353924511 +346000 ekin = 10.112097481429 | erot = 10.5617272299193 | epot = -75.1304601027765 | etot = -54.4566353914282 +347000 ekin = 10.0640336630298 | erot = 10.8763584969767 | epot = -75.3970275513628 | etot = -54.4566353913564 +348000 ekin = 10.0642411405127 | erot = 11.2719278614799 | epot = -75.7928043942644 | etot = -54.4566353922718 +349000 ekin = 10.1101933212636 | erot = 11.7360295300956 | epot = -76.3028582455116 | etot = -54.4566353941525 +350000 ekin = 10.1946552474004 | erot = 12.2463088365559 | epot = -76.8975994808581 | etot = -54.4566353969019 +351000 ekin = 10.306045543854 | erot = 12.7716910290039 | epot = -77.5343719731872 | etot = -54.4566354003293 +352000 ekin = 10.4291816280409 | erot = 13.2747779707954 | epot = -78.1605950029443 | etot = -54.456635404108 +353000 ekin = 10.5465535663497 | erot = 13.7156648337578 | epot = -78.718853807879 | etot = -54.4566354077714 +354000 ekin = 10.6401856668561 | erot = 14.0571283974516 | epot = -79.1539494750733 | etot = -54.4566354107656 +355000 ekin = 10.6939351373282 | erot = 14.2705585631452 | epot = -79.421129113035 | etot = -54.4566354125615 +356000 ekin = 10.6958108467941 | erot = 14.3413604466876 | epot = -79.4938067062911 | etot = -54.4566354128094 +357000 ekin = 10.639721828255 | erot = 14.2722433045623 | epot = -79.3686005442783 | etot = -54.456635411461 +358000 ekin = 10.5263737986249 | erot = 14.0832351439808 | epot = -79.0662443502861 | etot = -54.4566354076805 +359000 ekin = 10.3671285162277 | erot = 13.8092183812893 | epot = -78.6329823019411 | etot = -54.4566354044241 +360000 ekin = 10.17316577932 | erot = 13.4915210097222 | epot = -78.1213221900177 | etot = -54.4566354009755 +361000 ekin = 9.95567993138924 | erot = 13.1714056563713 | epot = -77.5837209856608 | etot = -54.4566353979003 +362000 ekin = 9.72639985071429 | erot = 12.8842804433114 | epot = -77.067315689619 | etot = -54.4566353955933 +363000 ekin = 9.49607796369749 | erot = 12.6551764253519 | epot = -76.6078897832975 | etot = -54.456635394248 +364000 ekin = 9.27360822633292 | erot = 12.4965538445838 | epot = -76.2267974647912 | etot = -54.4566353938744 +365000 ekin = 9.0656878434669 | erot = 12.4083291366445 | epot = -75.9306523744536 | etot = -54.4566353943422 +366000 ekin = 8.87683460603669 | erot = 12.3796974185334 | epot = -75.7131674199994 | etot = -54.4566353954294 +367000 ekin = 8.7096167114834 | erot = 12.3921806495176 | epot = -75.5584327578787 | etot = -54.4566353968777 +368000 ekin = 8.56493490850766 | erot = 12.4232160321889 | epot = -75.4447863391428 | etot = -54.4566353984462 +369000 ekin = 8.44226817634377 | erot = 12.4495921416358 | epot = -75.348495717927 | etot = -54.4566353999474 +370000 ekin = 8.33986053924033 | erot = 12.450192287463 | epot = -75.2466882279602 | etot = -54.4566354012569 +371000 ekin = 8.25489807014457 | erot = 12.4078154254081 | epot = -75.119348897848 | etot = -54.4566354022953 +372000 ekin = 8.1837680247658 | erot = 12.310190867959 | epot = -74.9505942957263 | etot = -54.4566354030015 +373000 ekin = 8.1224708952436 | erot = 12.1505028141942 | epot = -74.7296091127515 | etot = -54.4566354033137 +374000 ekin = 8.06687702985106 | erot = 11.927429705507 | epot = -74.4509421386789 | etot = -54.4566354033209 +375000 ekin = 8.0136053899695 | erot = 11.645430301628 | epot = -74.1156710942693 | etot = -54.4566354026719 +376000 ekin = 7.96102274026665 | erot = 11.3151262124852 | epot = -73.7327843543635 | etot = -54.4566354016116 +377000 ekin = 7.90863816659117 | erot = 10.9518631003599 | epot = -73.3171366672237 | etot = -54.4566354002726 +378000 ekin = 7.85683990183276 | erot = 10.5740091031991 | epot = -72.8874844038712 | etot = -54.4566353988393 +379000 ekin = 7.80642061178599 | erot = 10.2007165018144 | epot = -72.4637725111139 | etot = -54.4566353975135 +380000 ekin = 7.75811152743384 | erot = 9.8496139866053 | epot = -72.0643609104786 | etot = -54.4566353964394 +381000 ekin = 7.71654925828114 | erot = 9.53814492422012 | epot = -71.7113295774989 | etot = -54.4566353949976 +382000 ekin = 7.68451239863347 | erot = 9.27843266615603 | epot = -71.4195804598395 | etot = -54.45663539505 +383000 ekin = 7.65796830190889 | erot = 9.07311806362129 | epot = -71.1877217606714 | etot = -54.4566353951412 +384000 ekin = 7.63469818489458 | erot = 8.92246566923042 | epot = -71.0137992492274 | etot = -54.4566353951024 +385000 ekin = 7.61503891044967 | erot = 8.82614106516799 | epot = -70.8978153704589 | etot = -54.4566353948413 +386000 ekin = 7.60197533238529 | erot = 8.78441775442624 | epot = -70.8430284811966 | etot = -54.4566353943851 +387000 ekin = 7.60049226510599 | erot = 8.79836488560014 | epot = -70.8554925445896 | etot = -54.4566353938834 +388000 ekin = 7.61629032899055 | erot = 8.8689023697532 | epot = -70.9418280923105 | etot = -54.4566353935667 +389000 ekin = 7.65416483434698 | erot = 8.9950195746858 | epot = -71.1058198027103 | etot = -54.4566353936776 +390000 ekin = 7.71643785888504 | erot = 9.17173992639597 | epot = -71.3448131796954 | etot = -54.4566353944143 +391000 ekin = 7.80181238366649 | erot = 9.38839302764267 | epot = -71.6468408071618 | etot = -54.4566353958526 +392000 ekin = 7.90489923332247 | erot = 9.62796379831632 | epot = -71.9894984295676 | etot = -54.4566353979288 +393000 ekin = 8.01655002691858 | erot = 9.86772713454984 | epot = -72.3409125619011 | etot = -54.4566354004327 +394000 ekin = 8.12497584792011 | erot = 10.0812703662914 | epot = -72.662881617248 | etot = -54.4566354030366 +395000 ekin = 8.2174716208145 | erot = 10.2416533823477 | epot = -72.9157604085161 | etot = -54.4566354053539 +396000 ekin = 8.2824383224774 | erot = 10.3253672880818 | epot = -73.0644410175194 | etot = -54.4566354069602 +397000 ekin = 8.31132698802442 | erot = 10.3159962168273 | epot = -73.0839586125428 | etot = -54.456635407691 +398000 ekin = 8.30014555011519 | erot = 10.206120512026 | epot = -72.9629014694186 | etot = -54.4566354072774 +399000 ekin = 8.2502366708628 | erot = 9.99952429134871 | epot = -72.7063963681449 | etot = -54.4566354059334 +400000 ekin = 8.1681866367312 | erot = 9.70984792287219 | epot = -72.3346699633647 | etot = -54.4566354037613 +401000 ekin = 8.06443767762594 | erot = 9.35851558615808 | epot = -71.8795886650977 | etot = -54.4566354013137 +402000 ekin = 7.95182608081662 | erot = 8.97220739200882 | epot = -71.3806688712322 | etot = -54.4566353984067 +403000 ekin = 7.84544588741641 | erot = 8.57990607062258 | epot = -70.8819873536886 | etot = -54.4566353956496 +404000 ekin = 7.75991092033335 | erot = 8.20916918182752 | epot = -70.4257154955327 | etot = -54.4566353933718 +405000 ekin = 7.70721158904269 | erot = 7.88394698602643 | epot = -70.047793966617 | etot = -54.4566353915479 +406000 ekin = 7.69666260474901 | erot = 7.62282033660503 | epot = -69.7761183316813 | etot = -54.4566353903273 +407000 ekin = 7.7350040209002 | erot = 7.43821712170258 | epot = -69.6298565323385 | etot = -54.4566353897357 +408000 ekin = 7.82558122097257 | erot = 7.33626935411989 | epot = -69.6184859648542 | etot = -54.4566353897618 +409000 ekin = 7.96830915348111 | erot = 7.31687210469156 | epot = -69.7418166485681 | etot = -54.4566353903955 +410000 ekin = 8.15969424373301 | erot = 7.37386951086162 | epot = -69.9901991462101 | etot = -54.4566353916155 +411000 ekin = 8.39287612484659 | erot = 7.49540270153548 | epot = -70.3449142197616 | etot = -54.4566353933795 +412000 ekin = 8.65774455619527 | erot = 7.66457893931484 | epot = -70.7789588911044 | etot = -54.4566353955943 +413000 ekin = 8.94129116530325 | erot = 7.86068273350687 | epot = -71.258609296898 | etot = -54.4566353980879 +414000 ekin = 9.22842184777222 | erot = 8.06113294632612 | epot = -71.7461901946816 | etot = -54.4566354005832 +415000 ekin = 9.50339868561016 | erot = 8.24420492650161 | epot = -72.2042390148415 | etot = -54.4566354027298 +416000 ekin = 9.75183806738326 | erot = 8.39218393331151 | epot = -72.6006574048789 | etot = -54.4566354041842 +417000 ekin = 9.9628320827581 | erot = 8.49422554923714 | epot = -72.9136930367169 | etot = -54.4566354047217 +418000 ekin = 10.1305167323595 | erot = 8.54790138251185 | epot = -73.1350535191826 | etot = -54.4566354043112 +419000 ekin = 10.2545191073023 | erot = 8.55932055564976 | epot = -73.270475066081 | etot = -54.4566354031289 +420000 ekin = 10.3391601305845 | erot = 8.54147699792933 | epot = -73.3372725299946 | etot = -54.4566354014807 +421000 ekin = 10.3917847643115 | erot = 8.51147867525398 | epot = -73.3598988392543 | etot = -54.4566353996888 +422000 ekin = 10.4208099208918 | erot = 8.4877596621653 | epot = -73.3652049810802 | etot = -54.4566353980231 +423000 ekin = 10.4339704342082 | erot = 8.48766818012622 | epot = -73.3782740110689 | etot = -54.4566353967345 +424000 ekin = 10.4369827822117 | erot = 8.52566990469129 | epot = -73.4192880827333 | etot = -54.4566353958303 +425000 ekin = 10.4323601115191 | erot = 8.61251346626977 | epot = -73.5015091924224 | etot = -54.4566356146335 +426000 ekin = 10.1026717198751 | erot = 8.31096137628217 | epot = -72.8702682878912 | etot = -54.4566351917339 +427000 ekin = 10.5734553943682 | erot = 8.79632347543578 | epot = -73.8264144771792 | etot = -54.4566356073752 +428000 ekin = 10.6072422295385 | erot = 9.02803563913991 | epot = -74.0919131525333 | etot = -54.4566352838549 +429000 ekin = 10.5962603681844 | erot = 9.29488255867862 | epot = -74.3477782125074 | etot = -54.4566352856444 +430000 ekin = 10.5389594927131 | erot = 9.58934591829317 | epot = -74.5849406986421 | etot = -54.4566352876359 +431000 ekin = 10.4245953942776 | erot = 9.89238704681948 | epot = -74.7736177306457 | etot = -54.4566352895486 +432000 ekin = 10.245696886456 | erot = 10.1829761184383 | epot = -74.8853082959497 | etot = -54.4566352910554 +433000 ekin = 10.0003056146292 | erot = 10.4407089711134 | epot = -74.8976498775905 | etot = -54.456635291848 +434000 ekin = 9.69371342948773 | erot = 10.6486269472888 | epot = -74.7989756684881 | etot = -54.4566352917115 +435000 ekin = 9.33916315685611 | erot = 10.7956251646109 | epot = -74.5914236120697 | etot = -54.4566352906027 +436000 ekin = 8.95712875742735 | erot = 10.8778397412534 | epot = -74.2916037873504 | etot = -54.4566352886697 +437000 ekin = 8.57313769393175 | erot = 10.8986617406356 | epot = -73.9284347207896 | etot = -54.4566352862222 +438000 ekin = 8.21453260376657 | erot = 10.8674634356771 | epot = -73.5386313230875 | etot = -54.4566352836438 +439000 ekin = 7.90690315351327 | erot = 10.7975428309107 | epot = -73.1610812657124 | etot = -54.4566352812884 +440000 ekin = 7.6709950562787 | erot = 10.7039809990724 | epot = -72.8316113347451 | etot = -54.4566352793941 +441000 ekin = 7.52069557968595 | erot = 10.6019760377327 | epot = -72.5793068954817 | etot = -54.4566352780631 +442000 ekin = 7.46231680922547 | erot = 10.5058607974097 | epot = -72.4248128839192 | etot = -54.4566352772841 +443000 ekin = 7.49502555660675 | erot = 10.4286364553075 | epot = -72.3802972888998 | etot = -54.4566352769855 +444000 ekin = 7.61203666089189 | erot = 10.3816439307591 | epot = -72.4503158687455 | etot = -54.4566352770945 +445000 ekin = 7.80213707906526 | erot = 10.3740191034624 | epot = -72.6327914600963 | etot = -54.4566352775686 +446000 ekin = 8.05120889605329 | erot = 10.411793260142 | epot = -72.9196374345791 | etot = -54.4566352783837 +447000 ekin = 8.34362619155195 | erot = 10.4967971423188 | epot = -73.2970586134515 | etot = -54.4566352795808 +448000 ekin = 8.66322518430969 | erot = 10.6255592268213 | epot = -73.745419692246 | etot = -54.4566352811151 +449000 ekin = 8.99429132589985 | erot = 10.788857275459 | epot = -74.2397838842748 | etot = -54.456635282916 +450000 ekin = 9.32243048437278 | erot = 10.9721164674744 | epot = -74.7511822366959 | etot = -54.4566352848487 +451000 ekin = 9.63533692189911 | erot = 11.156756002054 | epot = -75.2487282106873 | etot = -54.4566352867343 +452000 ekin = 9.92346130381757 | erot = 11.3223196777254 | epot = -75.7024162699076 | etot = -54.4566352883646 +453000 ekin = 10.1805259141491 | erot = 11.4490169495349 | epot = -76.08617815326 | etot = -54.456635289576 +454000 ekin = 10.4037354722937 | erot = 11.5200589234786 | epot = -76.3804296860442 | etot = -54.4566352902719 +455000 ekin = 10.5935831355321 | erot = 11.5233067080518 | epot = -76.573525134034 | etot = -54.4566352904502 +456000 ekin = 10.7532212609292 | erot = 11.4519763299573 | epot = -76.661832881081 | etot = -54.4566352901944 +457000 ekin = 10.8874570866201 | erot = 11.304441066212 | epot = -76.6485334424715 | etot = -54.4566352896394 +458000 ekin = 11.0015355382719 | erot = 11.0834241212114 | epot = -76.541594948426 | etot = -54.4566352889428 +459000 ekin = 11.0999318012795 | erot = 10.7949138906133 | epot = -76.3514809801242 | etot = -54.4566352882314 +460000 ekin = 11.185377739659 | erot = 10.4471286620219 | epot = -76.0891416892845 | etot = -54.4566352876037 +461000 ekin = 11.258231340308 | erot = 10.0496701056143 | epot = -75.7645367330242 | etot = -54.4566352871019 +462000 ekin = 11.3163274976769 | erot = 9.61299797023347 | epot = -75.385960754631 | etot = -54.4566352867206 +463000 ekin = 11.3552632497945 | erot = 9.14812026271252 | epot = -74.9600187989452 | etot = -54.4566352864381 +464000 ekin = 11.3690273085563 | erot = 8.66637468807761 | epot = -74.4920372828284 | etot = -54.4566352861945 +465000 ekin = 11.3509265610548 | erot = 8.17938417024519 | epot = -73.9869460172089 | etot = -54.4566352859089 +466000 ekin = 11.2946971057441 | erot = 7.69907577472872 | epot = -73.4504081660039 | etot = -54.4566352855311 +467000 ekin = 11.1955035374656 | erot = 7.23752069346309 | epot = -72.8896595159555 | etot = -54.4566352850269 +468000 ekin = 11.050822539511 | erot = 6.80654240242827 | epot = -72.3140002263333 | etot = -54.4566352843941 +469000 ekin = 10.86114406671 | erot = 6.41707429380281 | epot = -71.7348536441655 | etot = -54.4566352836527 +470000 ekin = 10.6304433621366 | erot = 6.07835039051584 | epot = -71.1654290354893 | etot = -54.4566352828368 +471000 ekin = 10.3664443931402 | erot = 5.79710085709561 | epot = -70.6201805322111 | etot = -54.4566352819752 +472000 ekin = 10.0806478860474 | erot = 5.57696288908532 | epot = -70.1142460562275 | etot = -54.4566352810949 +473000 ekin = 9.78800246195651 | erot = 5.41826188422999 | epot = -69.6628996264136 | etot = -54.4566352802271 +474000 ekin = 9.50601286877946 | erot = 5.31820281474071 | epot = -69.2808509629562 | etot = -54.456635279436 +475000 ekin = 9.25312250159259 | erot = 5.27140899122385 | epot = -68.981166771632 | etot = -54.4566352788155 +476000 ekin = 9.04645385403574 | erot = 5.27070679329708 | epot = -68.7737959257985 | etot = -54.4566352784657 +477000 ekin = 8.89934302897966 | erot = 5.30806431670584 | epot = -68.664042624141 | etot = -54.4566352784555 +478000 ekin = 8.81931824251968 | erot = 5.37557918610962 | epot = -68.6515327074266 | etot = -54.4566352787973 +479000 ekin = 8.80699076959439 | erot = 5.46633303732314 | epot = -68.7299590863708 | etot = -54.4566352794532 +480000 ekin = 8.85601818726949 | erot = 5.57490002076701 | epot = -68.8875534883974 | etot = -54.4566352803609 +481000 ekin = 8.95429342118332 | erot = 5.69751011508116 | epot = -69.1084388177255 | etot = -54.456635281461 +482000 ekin = 9.08517946645072 | erot = 5.83167729002761 | epot = -69.3734920391816 | etot = -54.4566352827033 +483000 ekin = 9.22909607276365 | erot = 5.97557873339551 | epot = -69.6613100901915 | etot = -54.4566352840323 +484000 ekin = 9.36521899372269 | erot = 6.12745864218488 | epot = -69.9493129212799 | etot = -54.4566352853723 +485000 ekin = 9.47322485683509 | erot = 6.28523994694603 | epot = -70.215100090408 | etot = -54.4566352866269 +486000 ekin = 9.53500494319618 | erot = 6.44644593217249 | epot = -70.4380861630537 | etot = -54.456635287685 +487000 ekin = 9.53619997079524 | erot = 6.60840812030772 | epot = -70.60124337955 | etot = -54.456635288447 +488000 ekin = 9.46736165753982 | erot = 6.76862588122827 | epot = -70.6926228276161 | etot = -54.456635288848 +489000 ekin = 9.32457274797106 | erot = 6.92507571371354 | epot = -70.7062837505591 | etot = -54.4566352888745 +490000 ekin = 9.10946474824588 | erot = 7.07632195430853 | epot = -70.6424219911205 | etot = -54.4566352885661 +491000 ekin = 8.82888029926538 | erot = 7.22128416903702 | epot = -70.5067997559143 | etot = -54.4566352876119 +492000 ekin = 8.49626753098065 | erot = 7.35784727800537 | epot = -70.310750096053 | etot = -54.456635287067 +493000 ekin = 8.1248527430003 | erot = 7.48341898212076 | epot = -70.0649070115298 | etot = -54.4566352864087 +494000 ekin = 7.72891988561606 | erot = 7.594896974988 | epot = -69.7804521462887 | etot = -54.4566352856847 +495000 ekin = 7.32464765069171 | erot = 7.68832902470749 | epot = -69.4696119585252 | etot = -54.456635283126 +496000 ekin = 6.87909737983938 | erot = 7.73460610289615 | epot = -69.0703390393874 | etot = -54.4566355566519 +497000 ekin = 6.10749796783306 | erot = 7.42289860775864 | epot = -67.9870318122161 | etot = -54.4566352366244 +498000 ekin = 6.8223384553338 | erot = 7.45240806496291 | epot = -68.7313820537625 | etot = -54.4566355334658 +499000 ekin = 6.94585811355033 | erot = 7.49819185265535 | epot = -68.9006852433609 | etot = -54.4566352771552 +500000 ekin = 6.96877722036869 | erot = 7.49002786304807 | epot = -68.9154403630746 | etot = -54.4566352796579 +501000 ekin = 7.01880112773725 | erot = 7.44438420076744 | epot = -68.9198206071064 | etot = -54.4566352786017 +502000 ekin = 7.10331622209194 | erot = 7.3681739431656 | epot = -68.9281254425242 | etot = -54.4566352772666 +503000 ekin = 7.22893470364811 | erot = 7.27368415101028 | epot = -68.9592541304816 | etot = -54.4566352758232 +504000 ekin = 7.40053482834623 | erot = 7.17754137262058 | epot = -69.0347114753891 | etot = -54.4566352744222 +505000 ekin = 7.620702806129 | erot = 7.09829571792874 | epot = -69.1756337972824 | etot = -54.4566352732246 +506000 ekin = 7.8891584943945 | erot = 7.05445199996171 | epot = -69.4002457667284 | etot = -54.4566352723722 +507000 ekin = 8.20246554171515 | erot = 7.06247440845856 | epot = -69.7215752221428 | etot = -54.4566352719691 +508000 ekin = 8.55413799383062 | erot = 7.13504955838413 | epot = -70.1458228242684 | etot = -54.4566352720537 +509000 ekin = 8.93516686126007 | erot = 7.27981823673083 | epot = -70.6716203706044 | etot = -54.4566352726135 +510000 ekin = 9.33485927282882 | erot = 7.49868525981083 | epot = -71.2901798062273 | etot = -54.4566352735876 +511000 ekin = 9.74175973587721 | erot = 7.78771907258941 | epot = -71.9861140833685 | etot = -54.4566352749019 +512000 ekin = 10.1443557396928 | erot = 8.13756756500318 | epot = -72.7385585811883 | etot = -54.4566352764922 +513000 ekin = 10.5313126056699 | erot = 8.53426169204685 | epot = -73.5222095760326 | etot = -54.4566352783158 +514000 ekin = 10.8911780109873 | erot = 8.96028799858001 | epot = -74.3081012899077 | etot = -54.4566352803403 +515000 ekin = 11.2118156252179 | erot = 9.39590120044802 | epot = -75.0643521081583 | etot = -54.4566352824925 +516000 ekin = 11.4801179010227 | erot = 9.82075584956387 | epot = -75.7575090351961 | etot = -54.4566352846096 +517000 ekin = 11.6825443563144 | erot = 10.2159440472245 | epot = -76.3551236899727 | etot = -54.4566352864338 +518000 ekin = 11.8066489253373 | erot = 10.5663121117384 | epot = -76.8295963247492 | etot = -54.4566352876736 +519000 ekin = 11.8431629051622 | erot = 10.8625994980096 | epot = -77.1623976912762 | etot = -54.4566352881044 +520000 ekin = 11.7878575690797 | erot = 11.1027449902058 | epot = -77.3472378469657 | etot = -54.4566352876802 +521000 ekin = 11.6423174236629 | erot = 11.29193106552 | epot = -77.3908837756855 | etot = -54.4566352865025 +522000 ekin = 11.4136719884741 | erot = 11.4412637557161 | epot = -77.3115710289993 | etot = -54.4566352848091 +523000 ekin = 11.1134246219281 | erot = 11.5654340582746 | epot = -77.1354939631016 | etot = -54.456635282899 +524000 ekin = 10.7557913149077 | erot = 11.6798454532603 | epot = -76.8922720492505 | etot = -54.4566352810825 +525000 ekin = 10.3559612263718 | erot = 11.7976117586443 | epot = -76.6102082646594 | etot = -54.4566352796433 +526000 ekin = 9.92854976444486 | erot = 11.9267667903689 | epot = -76.3119518336127 | etot = -54.4566352787989 +527000 ekin = 9.48645866346676 | erot = 12.0680840250121 | epot = -76.0111779671406 | etot = -54.4566352786618 +528000 ekin = 9.04033350014003 | erot = 12.2139583839317 | epot = -75.7109271632676 | etot = -54.4566352791959 +529000 ekin = 8.59873443632333 | erot = 12.3488338467362 | epot = -75.4042035632559 | etot = -54.4566352801964 +530000 ekin = 8.16898173779832 | erot = 12.4514660033289 | epot = -75.0770830224439 | etot = -54.4566352813166 +531000 ekin = 7.75842341266217 | erot = 12.4988592010136 | epot = -74.7139178958228 | etot = -54.4566352821471 +532000 ekin = 7.37569471991213 | erot = 12.4711371154282 | epot = -74.3034671176647 | etot = -54.4566352823243 +533000 ekin = 7.03150209878443 | erot = 12.3561420075346 | epot = -73.8442793879667 | etot = -54.4566352816476 +534000 ekin = 6.73861037988931 | erot = 12.1525081131711 | epot = -73.3477537731904 | etot = -54.45663528013 +535000 ekin = 6.51098179615119 | erot = 11.8704212665668 | epot = -72.8380383407013 | etot = -54.4566352779833 +536000 ekin = 6.36227279688875 | erot = 11.5300349542147 | epot = -72.3489430266505 | etot = -54.456635275547 +537000 ekin = 6.30402397008893 | erot = 11.1595690920527 | epot = -71.9202283348878 | etot = -54.4566352727462 +538000 ekin = 6.34384912539326 | erot = 10.7903690893075 | epot = -71.5908534856437 | etot = -54.456635270943 +539000 ekin = 6.48387052849282 | erot = 10.449318947169 | epot = -71.3898247455974 | etot = -54.4566352699356 +540000 ekin = 6.71957140286 | erot = 10.1578313306127 | epot = -71.3340380034084 | etot = -54.4566352699357 +541000 ekin = 7.03922441471471 | erot = 9.92917206920205 | epot = -71.425031754947 | etot = -54.4566352710303 +542000 ekin = 7.42406000054681 | erot = 9.7668871120603 | epot = -71.6475823857676 | etot = -54.4566352731605 +543000 ekin = 7.8493023531804 | erot = 9.66461535275778 | epot = -71.9705529820422 | etot = -54.4566352761041 +544000 ekin = 8.28608775689842 | erot = 9.60744188180074 | epot = -72.3501649181947 | etot = -54.4566352794955 +545000 ekin = 8.70408689278687 | erot = 9.57468499690642 | epot = -72.7354071725678 | etot = -54.4566352828746 +546000 ekin = 9.07450055253648 | erot = 9.54373584492586 | epot = -73.07487168323 | etot = -54.4566352857677 +547000 ekin = 9.37295630422306 | erot = 9.49419334511057 | epot = -73.3237849371211 | etot = -54.4566352877874 +548000 ekin = 9.58182570226534 | erot = 9.41137262818507 | epot = -73.4498336191623 | etot = -54.4566352887119 +549000 ekin = 9.69160120899948 | erot = 9.288405596616 | epot = -73.4366420941315 | etot = -54.4566352885161 +550000 ekin = 9.70118406830511 | erot = 9.12701779123922 | epot = -73.2848371467454 | etot = -54.4566352872011 +551000 ekin = 9.61716955377869 | erot = 8.93605057969941 | epot = -73.0098554188361 | etot = -54.456635285358 +552000 ekin = 9.45239020385166 | erot = 8.72803660183396 | epot = -72.6370620888035 | etot = -54.4566352831179 +553000 ekin = 9.2240812648701 | erot = 8.51766004434715 | epot = -72.1983765899684 | etot = -54.4566352807511 +554000 ekin = 8.95200493899196 | erot = 8.31967116939608 | epot = -71.7283113868479 | etot = -54.4566352784598 +555000 ekin = 8.65679189107807 | erot = 8.14750332104929 | epot = -71.2609304884951 | etot = -54.4566352763678 +556000 ekin = 8.35857893219484 | erot = 8.01260395508868 | epot = -70.8278181618281 | etot = -54.4566352745446 +557000 ekin = 8.07596711126812 | erot = 7.92430276672875 | epot = -70.4569051510142 | etot = -54.4566352730173 +558000 ekin = 7.82526545931107 | erot = 7.88998546795382 | epot = -70.1718861990647 | etot = -54.4566352717999 +559000 ekin = 7.61992228153161 | erot = 7.91527958484657 | epot = -69.9918371372954 | etot = -54.4566352709172 +560000 ekin = 7.47007181068654 | erot = 8.00405379786488 | epot = -69.9307608789601 | etot = -54.4566352704086 +561000 ekin = 7.38215855425466 | erot = 8.15814566484878 | epot = -69.9969394894308 | etot = -54.4566352703273 +562000 ekin = 7.35865871746505 | erot = 8.37688060997226 | epot = -70.192174598151 | etot = -54.4566352707137 +563000 ekin = 7.39798626084945 | erot = 8.65660065502576 | epot = -70.5112221874459 | etot = -54.4566352715707 +564000 ekin = 7.49472571183601 | erot = 8.99052373941851 | epot = -70.9418847240798 | etot = -54.4566352728253 +565000 ekin = 7.64032956783369 | erot = 9.36943411102764 | epot = -71.4663989531132 | etot = -54.4566352742518 +566000 ekin = 7.82430710587938 | erot = 9.78260719502216 | epot = -72.0635495767252 | etot = -54.4566352758236 +567000 ekin = 8.03571605971452 | erot = 10.2184542007834 | epot = -72.7108055377923 | etot = -54.4566352772944 +568000 ekin = 8.26456312039748 | erot = 10.665997223562 | epot = -73.3871956225684 | etot = -54.4566352786089 +569000 ekin = 8.50272301774751 | erot = 11.1149437632744 | epot = -74.0743020608117 | etot = -54.4566352797898 +570000 ekin = 8.74355516144858 | erot = 11.554502920604 | epot = -74.7546933635585 | etot = -54.456635281506 +571000 ekin = 8.98090334155492 | erot = 11.9725583583672 | epot = -75.4100969832648 | etot = -54.4566352833427 +572000 ekin = 9.2082873836897 | erot = 12.356036477509 | epot = -76.0209591455829 | etot = -54.4566352843841 +573000 ekin = 9.42081793455992 | erot = 12.6951950119417 | epot = -76.5726482312271 | etot = -54.4566352847255 +574000 ekin = 9.61839098683161 | erot = 12.987675719223 | epot = -77.0627019900489 | etot = -54.4566352839943 +575000 ekin = 9.8053207114464 | erot = 13.2416249343119 | epot = -77.5035809281287 | etot = -54.4566352823704 +576000 ekin = 9.99002522865977 | erot = 13.4728181322991 | epot = -77.9194786412667 | etot = -54.4566352803078 +577000 ekin = 10.1832012886898 | erot = 13.6997981601504 | epot = -78.3396347273587 | etot = -54.4566352785186 +578000 ekin = 10.3950145220004 | erot = 13.9374358143628 | epot = -78.7890856136916 | etot = -54.4566352773284 +579000 ekin = 10.6321657048067 | erot = 14.1940413546622 | epot = -79.2828423366299 | etot = -54.456635277161 +580000 ekin = 10.8955063623585 | erot = 14.4691297491996 | epot = -79.8212713896975 | etot = -54.4566352781394 +581000 ekin = 11.1784960138876 | erot = 14.7531280290353 | epot = -80.3882593231847 | etot = -54.4566352802618 +582000 ekin = 11.466649890903 | erot = 15.0284667683102 | epot = -80.9517519424562 | etot = -54.456635283243 +583000 ekin = 11.7382109395759 | erot = 15.2729975156372 | epot = -81.46784374194 | etot = -54.4566352867269 +584000 ekin = 11.9663900039709 | erot = 15.4635948123567 | epot = -81.8866201064609 | etot = -54.4566352901333 +585000 ekin = 12.1233421755881 | erot = 15.5804670946604 | epot = -82.160444563015 | etot = -54.4566352927665 +586000 ekin = 12.1853975661735 | erot = 15.6117625736168 | epot = -82.2537954337851 | etot = -54.4566352939948 +587000 ekin = 12.1382713601941 | erot = 15.5570038313302 | epot = -82.1519104850123 | etot = -54.456635293488 +588000 ekin = 11.9805642896439 | erot = 15.4278527969017 | epot = -81.8650523779254 | etot = -54.4566352913799 +589000 ekin = 11.7242102225958 | erot = 15.2454372701353 | epot = -81.4262827809805 | etot = -54.4566352882494 +590000 ekin = 11.3915725976128 | erot = 15.0348737081542 | epot = -80.8830815906766 | etot = -54.4566352849096 +591000 ekin = 11.0102189263756 | erot = 14.8189389013234 | epot = -80.2857931097779 | etot = -54.4566352820789 +592000 ekin = 10.607391880722 | erot = 14.6132844347576 | epot = -79.6773115955935 | etot = -54.456635280114 +593000 ekin = 10.2062007299119 | erot = 14.4247656797278 | epot = -79.0876016885973 | etot = -54.4566352789576 +594000 ekin = 9.8244107941942 | erot = 14.2527059307027 | epot = -78.5337520032326 | etot = -54.4566352783357 +595000 ekin = 9.4751657623942 | erot = 14.0913483028674 | epot = -78.0231493432885 | etot = -54.4566352780269 +596000 ekin = 9.16820839960829 | erot = 13.9315742319822 | epot = -77.556417909575 | etot = -54.4566352779845 +597000 ekin = 8.91058714548235 | erot = 13.7613090155275 | epot = -77.1285314392662 | etot = -54.4566352782563 +598000 ekin = 8.7067575239535 | erot = 13.565617791176 | epot = -76.7290105939553 | etot = -54.4566352788258 +599000 ekin = 8.55850888714088 | erot = 13.3279192983947 | epot = -76.3430634650727 | etot = -54.4566352795371 +600000 ekin = 8.46506040530667 | erot = 13.0357131362851 | epot = -75.9574088200021 | etot = -54.4566352784104 +601000 ekin = 8.42304118578906 | erot = 12.6867916099869 | epot = -75.566468075072 | etot = -54.4566352792961 +602000 ekin = 8.42687753936552 | erot = 12.2731929910378 | epot = -75.1567058099478 | etot = -54.4566352795445 +603000 ekin = 8.4695384899465 | erot = 11.797098713486 | epot = -74.7232724826155 | etot = -54.456635279183 +604000 ekin = 8.54275438847601 | erot = 11.2715335231716 | epot = -74.2709231900193 | etot = -54.4566352783717 +605000 ekin = 8.63734562583982 | erot = 10.7175531247483 | epot = -73.8115340279045 | etot = -54.4566352773163 +606000 ekin = 8.7438013028547 | erot = 10.1605162228263 | epot = -73.3609528018798 | etot = -54.4566352761988 +607000 ekin = 8.85309694757045 | erot = 9.62647077148101 | epot = -72.9362029941963 | etot = -54.4566352751448 +608000 ekin = 8.95762756595134 | erot = 9.13922005193509 | epot = -72.5534828920879 | etot = -54.4566352742015 +609000 ekin = 9.05200869449805 | erot = 8.71853436573584 | epot = -72.2271783337178 | etot = -54.4566352734839 +610000 ekin = 9.13354825725741 | erot = 8.37878256427127 | epot = -71.9689660943683 | etot = -54.4566352728396 +611000 ekin = 9.20214054253594 | erot = 8.1292053216989 | epot = -71.7879811366928 | etot = -54.4566352724579 +612000 ekin = 9.25952066990905 | erot = 7.97330837182916 | epot = -71.6894643141582 | etot = -54.45663527242 +613000 ekin = 9.30803502782429 | erot = 7.90865833531061 | epot = -71.6733286359623 | etot = -54.4566352728274 +614000 ekin = 9.34916711094965 | erot = 7.92697148192955 | epot = -71.732773866643 | etot = -54.4566352737638 +615000 ekin = 9.38224690750502 | erot = 8.01444322716698 | epot = -71.8533254097658 | etot = -54.4566352750938 +616000 ekin = 9.40371294252271 | erot = 8.15314542837713 | epot = -72.0134936479267 | etot = -54.4566352770269 +617000 ekin = 9.40764668982314 | erot = 8.32057787067663 | epot = -72.1848598396912 | etot = -54.4566352791914 +618000 ekin = 9.38714075160868 | erot = 8.49215030180821 | epot = -72.3359263346812 | etot = -54.4566352812643 +619000 ekin = 9.33636921849528 | erot = 8.64420325442949 | epot = -72.437207755803 | etot = -54.4566352828783 +620000 ekin = 9.25285403025117 | erot = 8.75716147301268 | epot = -72.4666507869722 | etot = -54.4566352837083 +621000 ekin = 9.13928884697163 | erot = 8.81846717425121 | epot = -72.4143913047736 | etot = -54.4566352835508 +622000 ekin = 9.00442091794227 | erot = 8.82459164771617 | epot = -72.2856478480408 | etot = -54.4566352823824 +623000 ekin = 8.86274189508419 | erot = 8.78159561803589 | epot = -72.1009727932407 | etot = -54.4566352801206 +624000 ekin = 8.73276401800715 | erot = 8.70595407666082 | epot = -71.8953533724822 | etot = -54.4566352778143 +625000 ekin = 8.63399867890784 | erot = 8.618212469755 | epot = -71.7088464239378 | etot = -54.4566352752749 +626000 ekin = 8.58565910354917 | erot = 8.53996947435426 | epot = -71.5822638507735 | etot = -54.4566352728701 +627000 ekin = 8.60437912917914 | erot = 8.49303514267052 | epot = -71.5540495427944 | etot = -54.4566352709448 +628000 ekin = 8.70176554878871 | erot = 8.49648522566346 | epot = -71.6548860443256 | etot = -54.4566352698734 +629000 ekin = 8.88261620993874 | erot = 8.5635071725507 | epot = -71.9027586522013 | etot = -54.4566352697118 +630000 ekin = 9.14296246573492 | erot = 8.70076359816389 | epot = -72.3003613345725 | etot = -54.4566352706737 +631000 ekin = 9.46887704354127 | erot = 8.90689930706844 | epot = -72.8324116238796 | etot = -54.4566352732699 +632000 ekin = 9.83363185826934 | erot = 9.17168072088574 | epot = -73.4619478556477 | etot = -54.4566352764926 +633000 ekin = 10.2053124154562 | erot = 9.47717112296441 | epot = -74.1391188185588 | etot = -54.4566352801382 +634000 ekin = 10.5495376010831 | erot = 9.80182933657188 | epot = -74.8080022212184 | etot = -54.4566352835635 +635000 ekin = 10.8340816739443 | erot = 10.1250818406842 | epot = -75.4157988007395 | etot = -54.456635286111 +636000 ekin = 11.0341363466738 | erot = 10.4317241828331 | epot = -75.9224958167892 | etot = -54.4566352872823 +637000 ekin = 11.1362536303687 | erot = 10.7150791019426 | epot = -76.3079680193872 | etot = -54.4566352870759 +638000 ekin = 11.1393407345868 | erot = 10.9767172064 | epot = -76.5726932267163 | etot = -54.4566352857295 +639000 ekin = 11.0528857655549 | erot = 11.224562529706 | epot = -76.7340835789804 | etot = -54.4566352837195 +640000 ekin = 10.893283375067 | erot = 11.4701066828315 | epot = -76.8200253394105 | etot = -54.456635281512 +641000 ekin = 10.6798604052081 | erot = 11.7256640733954 | epot = -76.862159758033 | etot = -54.4566352794294 +642000 ekin = 10.4319158115154 | erot = 12.0024358075463 | epot = -76.8909868967299 | etot = -54.4566352776682 +643000 ekin = 10.166953187212 | erot = 12.3092359597876 | epot = -76.9328244231824 | etot = -54.4566352761827 +644000 ekin = 9.90018316847719 | erot = 12.6520525446443 | epot = -77.0088709883795 | etot = -54.4566352752581 +645000 ekin = 9.64412813643454 | erot = 13.0323474006439 | epot = -77.1331108120166 | etot = -54.4566352749382 +646000 ekin = 9.40844464391873 | erot = 13.4458998080393 | epot = -77.3109797269726 | etot = -54.4566352750145 +647000 ekin = 9.1999884291585 | erot = 13.8831906422816 | epot = -77.5398143472699 | etot = -54.4566352758298 +648000 ekin = 9.02196759880059 | erot = 14.327906247855 | epot = -77.8065091239739 | etot = -54.4566352773183 +649000 ekin = 8.87356627779062 | erot = 14.7574673823316 | epot = -78.0876689395909 | etot = -54.4566352794687 +650000 ekin = 8.74956009132211 | erot = 15.1439160026326 | epot = -78.3501113761364 | etot = -54.4566352821817 +651000 ekin = 8.64036637406831 | erot = 15.4556053528726 | epot = -78.552607012193 | etot = -54.456635285252 +652000 ekin = 8.53277201870684 | erot = 15.6598310256854 | epot = -78.6492383327263 | etot = -54.456635288334 +653000 ekin = 8.41160402390922 | erot = 15.7264979165626 | epot = -78.5947372314111 | etot = -54.4566352909393 +654000 ekin = 8.26240952718729 | erot = 15.6326986256784 | epot = -78.3517434454054 | etot = -54.4566352925398 +655000 ekin = 8.07475580658865 | erot = 15.3674488766353 | epot = -77.8988399757855 | etot = -54.4566352925616 +656000 ekin = 7.8558568329232 | erot = 14.9355978465144 | epot = -77.2480902330833 | etot = -54.4566355536457 +657000 ekin = 6.26754941237541 | erot = 14.5622178162966 | epot = -75.2864023129602 | etot = -54.4566350842882 +658000 ekin = 6.04146739777421 | erot = 14.8336076395965 | epot = -75.3317103840911 | etot = -54.4566353467204 +659000 ekin = 6.38604373424062 | erot = 14.3792060567779 | epot = -75.2218852652085 | etot = -54.4566354741899 +660000 ekin = 6.5180692366814 | erot = 13.6089213615818 | epot = -74.5836260719848 | etot = -54.4566354737216 +661000 ekin = 6.66094978027865 | erot = 12.8243584228285 | epot = -73.9419436733274 | etot = -54.4566354702202 +662000 ekin = 6.81847461883994 | erot = 12.0687190077668 | epot = -73.3438290942705 | etot = -54.4566354676637 +663000 ekin = 6.99157703856223 | erot = 11.3763942501093 | epot = -72.824606754809 | etot = -54.4566354661374 +664000 ekin = 7.17716154109503 | erot = 10.7708280861964 | epot = -72.4046250929334 | etot = -54.4566354656419 +665000 ekin = 7.36751346457915 | erot = 10.2651942829233 | epot = -72.0893432136831 | etot = -54.4566354661807 +666000 ekin = 7.55097379427906 | erot = 9.86605911513187 | epot = -71.8736683769829 | etot = -54.456635467572 +667000 ekin = 7.71560064024578 | erot = 9.56451333310551 | epot = -71.7367494426919 | etot = -54.4566354693406 +668000 ekin = 7.84958438765827 | erot = 9.3436894719049 | epot = -71.6499093309659 | etot = -54.4566354714027 +669000 ekin = 7.94295016385616 | erot = 9.1818139048154 | epot = -71.5813995419857 | etot = -54.4566354733142 +670000 ekin = 7.9891684211374 | erot = 9.05573401739516 | epot = -71.5015379133415 | etot = -54.4566354748089 +671000 ekin = 7.98640376800962 | erot = 8.94389368817567 | epot = -71.3869329318708 | etot = -54.4566354756855 +672000 ekin = 7.9381494549713 | erot = 8.8287029853038 | epot = -71.2234879161209 | etot = -54.4566354758458 +673000 ekin = 7.85378610279984 | erot = 8.6986877436715 | epot = -71.0091093212467 | etot = -54.4566354747754 +674000 ekin = 7.74799942744435 | erot = 8.54952007570365 | epot = -70.754154976773 | etot = -54.456635473625 +675000 ekin = 7.63655278417633 | erot = 8.38180900834835 | epot = -70.4749972646932 | etot = -54.4566354721686 +676000 ekin = 7.53535852001204 | erot = 8.20065006866992 | epot = -70.1926440593593 | etot = -54.4566354706773 +677000 ekin = 7.45814475127725 | erot = 8.01383837145264 | epot = -69.9286185924865 | etot = -54.4566354697567 +678000 ekin = 7.41094295256099 | erot = 7.82760230140382 | epot = -69.6951807229993 | etot = -54.4566354690345 +679000 ekin = 7.39592235492869 | erot = 7.64827405779127 | epot = -69.5008318814407 | etot = -54.4566354687208 +680000 ekin = 7.41177806097664 | erot = 7.48365592355626 | epot = -69.3520694527969 | etot = -54.456635468264 +681000 ekin = 7.45331527396897 | erot = 7.34392547755961 | epot = -69.2538762205284 | etot = -54.4566354689998 +682000 ekin = 7.50955937697697 | erot = 7.23029783103104 | epot = -69.1964926779914 | etot = -54.4566354699834 +683000 ekin = 7.56739476561478 | erot = 7.14126315260236 | epot = -69.1652933892642 | etot = -54.456635471047 +684000 ekin = 7.61376409144466 | erot = 7.07385958563683 | epot = -69.1442591490619 | etot = -54.4566354719804 +685000 ekin = 7.63746698432958 | erot = 7.02460383232006 | epot = -69.1187062894153 | etot = -54.4566354727656 +686000 ekin = 7.63051953632514 | erot = 6.98951954535261 | epot = -69.0766745549324 | etot = -54.4566354732546 +687000 ekin = 7.58886140551023 | erot = 6.96428884092867 | epot = -69.0097857199475 | etot = -54.4566354735086 +688000 ekin = 7.5123778443976 | erot = 6.94436871140367 | epot = -68.9133820291076 | etot = -54.4566354733063 +689000 ekin = 7.40504576868385 | erot = 6.92768230556345 | epot = -68.7893635471276 | etot = -54.4566354728803 +690000 ekin = 7.27382130827893 | erot = 6.91296338857061 | epot = -68.6434201691486 | etot = -54.4566354722991 +691000 ekin = 7.12767077385367 | erot = 6.89947861386804 | epot = -68.483784859351 | etot = -54.4566354716293 +692000 ekin = 6.9766239669048 | erot = 6.88703034397747 | epot = -68.3202897818118 | etot = -54.4566354709295 +693000 ekin = 6.83191834520977 | erot = 6.87661243826572 | epot = -68.1651662534466 | etot = -54.4566354699711 +694000 ekin = 6.70652274538362 | erot = 6.87114213828651 | epot = -68.0343003531286 | etot = -54.4566354694585 +695000 ekin = 6.60809645496262 | erot = 6.87168002796421 | epot = -67.9364119519809 | etot = -54.4566354690541 +696000 ekin = 6.54192055188176 | erot = 6.87954258793329 | epot = -67.8780986086068 | etot = -54.4566354687917 +697000 ekin = 6.51083965228446 | erot = 6.89633668058504 | epot = -67.8638118015929 | etot = -54.4566354687234 +698000 ekin = 6.51499125638723 | erot = 6.92351826954681 | epot = -67.8951449951714 | etot = -54.4566354692374 +699000 ekin = 6.550556818564 | erot = 6.96165096856857 | epot = -67.9688432565951 | etot = -54.4566354694625 +700000 ekin = 6.61234823812044 | erot = 7.01150759224098 | epot = -68.0804913002851 | etot = -54.4566354699236 +701000 ekin = 6.69387980257822 | erot = 7.07317762179458 | epot = -68.2236928948352 | etot = -54.4566354704624 +702000 ekin = 6.78728068982377 | erot = 7.14568383977926 | epot = -68.3896000006983 | etot = -54.4566354710953 +703000 ekin = 6.88400379171242 | erot = 7.22737250162029 | epot = -68.5680117651016 | etot = -54.4566354717689 +704000 ekin = 6.97556832835716 | erot = 7.31572261063949 | epot = -68.747926411421 | etot = -54.4566354724243 +705000 ekin = 7.05425772042527 | erot = 7.40762548355635 | epot = -68.9185186769786 | etot = -54.4566354729969 +706000 ekin = 7.11369388310506 | erot = 7.49985325016107 | epot = -69.070182606692 | etot = -54.4566354734259 +707000 ekin = 7.14922746289103 | erot = 7.58965466907766 | epot = -69.1955176056336 | etot = -54.4566354736649 +708000 ekin = 7.15811920574744 | erot = 7.6753716118775 | epot = -69.2901262913103 | etot = -54.4566354736853 +709000 ekin = 7.13952646258542 | erot = 7.75695073870722 | epot = -69.3531126747745 | etot = -54.4566354734819 +710000 ekin = 7.09433523087588 | erot = 7.83623493467486 | epot = -69.3872056386251 | etot = -54.4566354730744 +711000 ekin = 7.02488197437687 | erot = 7.91695244606739 | epot = -69.3984698929541 | etot = -54.4566354725099 +712000 ekin = 6.93460038929036 | erot = 8.00437692967606 | epot = -69.3956127908169 | etot = -54.4566354718505 +713000 ekin = 6.82762548688049 | erot = 8.10469988089882 | epot = -69.3889608389739 | etot = -54.4566354711946 +714000 ekin = 6.70839192371242 | erot = 8.22401944315054 | epot = -69.3890468374827 | etot = -54.4566354706198 +715000 ekin = 6.58127350482036 | erot = 8.36737765962647 | epot = -69.4052866346558 | etot = -54.456635470209 +716000 ekin = 6.45031596780151 | erot = 8.53776210680492 | epot = -69.4447135446327 | etot = -54.4566354700262 +717000 ekin = 6.31910573966021 | erot = 8.73523312779016 | epot = -69.510974337557 | etot = -54.4566354701066 +718000 ekin = 6.19080028786937 | erot = 8.95633319730107 | epot = -69.603768955619 | etot = -54.4566354704485 +719000 ekin = 6.06832299313285 | erot = 9.19390878348299 | epot = -69.7188672476246 | etot = -54.4566354710087 +720000 ekin = 5.95470075028698 | erot = 9.43744070375475 | epot = -69.8487769257427 | etot = -54.4566354717009 +721000 ekin = 5.85349202512459 | erot = 9.67392180064466 | epot = -69.9840492981764 | etot = -54.4566354724072 +722000 ekin = 5.76921811618467 | erot = 9.88920295785366 | epot = -70.1150565470426 | etot = -54.4566354730043 +723000 ekin = 5.70767535089409 | erot = 10.0695468208251 | epot = -70.2338576450814 | etot = -54.4566354733622 +724000 ekin = 5.67599154890781 | erot = 10.203542552663 | epot = -70.3361695749737 | etot = -54.4566354734029 +725000 ekin = 5.68230712443453 | erot = 10.2835870142371 | epot = -70.4225296117833 | etot = -54.4566354731117 +726000 ekin = 5.73502013958263 | erot = 10.3068600066279 | epot = -70.4985156187578 | etot = -54.4566354725473 +727000 ekin = 5.84163680642924 | erot = 10.2756197556135 | epot = -70.573892033868 | etot = -54.4566354718252 +728000 ekin = 6.00741477143184 | erot = 10.1968335781189 | epot = -70.6608838206318 | etot = -54.456635471081 +729000 ekin = 6.23399006285525 | erot = 10.0813630553523 | epot = -70.771988588682 | etot = -54.4566354704744 +730000 ekin = 6.51828052765144 | erot = 9.9426735456021 | epot = -70.9175895433943 | etot = -54.4566354701407 +731000 ekin = 6.85187412405264 | erot = 9.79530805490023 | epot = -71.103817649134 | etot = -54.4566354701812 +732000 ekin = 7.22103408683562 | erot = 9.65327415425518 | epot = -71.3309437117429 | etot = -54.4566354706521 +733000 ekin = 7.60730193027085 | erot = 9.52880121518164 | epot = -71.5927386169427 | etot = -54.4566354714902 +734000 ekin = 7.98880332434209 | erot = 9.43074706131371 | epot = -71.876185858433 | etot = -54.4566354727772 +735000 ekin = 8.34212509373748 | erot = 9.3633098334892 | epot = -72.1620704015425 | etot = -54.4566354743158 +736000 ekin = 8.64442251577016 | erot = 9.32619971932519 | epot = -72.4272577110297 | etot = -54.4566354759344 +737000 ekin = 8.87574972639943 | erot = 9.31509601120067 | epot = -72.6474812150134 | etot = -54.4566354774133 +738000 ekin = 9.02130630169665 | erot = 9.32284410470334 | epot = -72.8007858849193 | etot = -54.4566354785193 +739000 ekin = 9.07331880500993 | erot = 9.34118914837109 | epot = -72.8711434324294 | etot = -54.4566354790484 +740000 ekin = 9.03225763738395 | erot = 9.36274956106376 | epot = -72.8516426773077 | etot = -54.45663547886 +741000 ekin = 8.90713122012936 | erot = 9.3828557688273 | epot = -72.7466224668723 | etot = -54.4566354779156 +742000 ekin = 8.71472462486779 | erot = 9.40075675433865 | epot = -72.5721168556002 | etot = -54.4566354763937 +743000 ekin = 8.47795966699027 | erot = 9.41969955783087 | epot = -72.3542946989564 | etot = -54.4566354741353 +744000 ekin = 8.22400086784026 | erot = 9.44765885710949 | epot = -72.1282951968482 | etot = -54.4566354718985 +745000 ekin = 7.97989641728764 | erot = 9.49406284314719 | epot = -71.9305947302801 | etot = -54.4566354698453 +746000 ekin = 7.76957023230139 | erot = 9.56762699730982 | epot = -71.7938326979343 | etot = -54.4566354683231 +747000 ekin = 7.6113281427264 | erot = 9.67405775028686 | epot = -71.7420213607417 | etot = -54.4566354677284 +748000 ekin = 7.51608906095942 | erot = 9.81227809036011 | epot = -71.7850026195773 | etot = -54.4566354682578 +749000 ekin = 7.48509635035055 | erot = 9.97286752416827 | epot = -71.914599344452 | etot = -54.4566354699332 +750000 ekin = 7.51020628173353 | erot = 10.1380775195895 | epot = -72.1049192737933 | etot = -54.4566354724703 +751000 ekin = 7.57538607462524 | erot = 10.2842078237016 | epot = -72.3162293737607 | etot = -54.4566354754339 +752000 ekin = 7.65985767866269 | erot = 10.3856021559485 | epot = -72.5020953128504 | etot = -54.4566354782391 +753000 ekin = 7.74189887066433 | erot = 10.419001280809 | epot = -72.6175356321296 | etot = -54.4566354806562 +754000 ekin = 7.80244855953598 | erot = 10.3680715765413 | epot = -72.6271556176715 | etot = -54.4566354815942 +755000 ekin = 7.83000162073562 | erot = 10.2279599097075 | epot = -72.5145970116681 | etot = -54.456635481225 +756000 ekin = 7.82097337519573 | erot = 10.0059197104317 | epot = -72.2835285652745 | etot = -54.456635479647 +757000 ekin = 7.77934134712486 | erot = 9.72019517222596 | epot = -71.9561719965242 | etot = -54.4566354771734 +758000 ekin = 7.71519090760764 | erot = 9.3969298917774 | epot = -71.568756273586 | etot = -54.4566354742009 +759000 ekin = 7.64279612364638 | erot = 9.06591672497264 | epot = -71.1653483198422 | etot = -54.4566354712232 +760000 ekin = 7.57755088532868 | erot = 8.75627990045633 | epot = -70.790466254402 | etot = -54.456635468617 +761000 ekin = 7.53416140040996 | erot = 8.49239651707641 | epot = -70.4831933841425 | etot = -54.4566354666561 +762000 ekin = 7.52513654525459 | erot = 8.29092896401282 | epot = -70.2727009748851 | etot = -54.4566354656177 +763000 ekin = 7.55953487192201 | erot = 8.15857993674247 | epot = -70.1747502740267 | etot = -54.4566354653622 +764000 ekin = 7.64294215281726 | erot = 8.0928450780051 | epot = -70.1924226970456 | etot = -54.4566354662233 +765000 ekin = 7.77642284081022 | erot = 8.08170347276273 | epot = -70.3147617810413 | etot = -54.4566354674683 +766000 ekin = 7.95834261066027 | erot = 8.10711564973332 | epot = -70.5220937294794 | etot = -54.4566354690858 +767000 ekin = 8.18472660667583 | erot = 8.14791972848129 | epot = -70.7892818060094 | etot = -54.4566354708523 +768000 ekin = 8.44981765186404 | erot = 8.18277444593156 | epot = -71.0892275702743 | etot = -54.4566354724787 +769000 ekin = 8.74694394959826 | erot = 8.19341027607498 | epot = -71.3969896993911 | etot = -54.4566354737179 +770000 ekin = 9.0674029995204 | erot = 8.16689258700995 | epot = -71.6909310619803 | etot = -54.4566354754499 +771000 ekin = 9.40024405596226 | erot = 8.09727042676162 | epot = -71.9541499582763 | etot = -54.4566354755524 +772000 ekin = 9.73924667677548 | erot = 7.98875570208412 | epot = -72.1846378539895 | etot = -54.4566354751299 +773000 ekin = 10.0787428377665 | erot = 7.85333550370643 | epot = -72.3887138158604 | etot = -54.4566354743875 +774000 ekin = 10.4126881201536 | erot = 7.70839587028075 | epot = -72.5777194640181 | etot = -54.4566354735838 +775000 ekin = 10.7338614307519 | erot = 7.5736395282272 | epot = -72.7641364319404 | etot = -54.4566354729614 +776000 ekin = 11.0333888250078 | erot = 7.46794248962755 | epot = -72.9579667873123 | etot = -54.456635472677 +777000 ekin = 11.3009163259555 | erot = 7.40678795795349 | epot = -73.1643397566749 | etot = -54.4566354727659 +778000 ekin = 11.5255306315622 | erot = 7.40073666279855 | epot = -73.3829027675071 | etot = -54.4566354731464 +779000 ekin = 11.6972525421253 | erot = 7.45497855950837 | epot = -73.6088665753155 | etot = -54.4566354736818 +780000 ekin = 11.8087202601131 | erot = 7.56970994291763 | epot = -73.8350656772418 | etot = -54.456635474211 +781000 ekin = 11.8566181530725 | erot = 7.74100457478778 | epot = -74.0542582024836 | etot = -54.4566354746234 +782000 ekin = 11.8424717374736 | erot = 7.96169824308615 | epot = -74.260805455433 | etot = -54.4566354748733 +783000 ekin = 11.772696068821 | erot = 8.22211610462947 | epot = -74.4514476484202 | etot = -54.4566354749697 +784000 ekin = 11.6588151949699 | erot = 8.51079893968734 | epot = -74.6262496093 | etot = -54.4566354746428 +785000 ekin = 11.5160383797475 | erot = 8.81490190988977 | epot = -74.7875757641991 | etot = -54.4566354745618 +786000 ekin = 11.360467176424 | erot = 9.12050352622298 | epot = -74.9376061770542 | etot = -54.4566354744072 +787000 ekin = 11.2093970331549 | erot = 9.4137436342822 | epot = -75.0797761416126 | etot = -54.4566354741755 +788000 ekin = 11.0803298420605 | erot = 9.68171559587104 | epot = -75.2186809118141 | etot = -54.4566354738826 +789000 ekin = 10.9900153478649 | erot = 9.91340849394794 | epot = -75.3600593153399 | etot = -54.456635473527 +790000 ekin = 10.9532761013338 | erot = 10.1003645461715 | epot = -75.5102761207273 | etot = -54.456635473222 +791000 ekin = 10.9812861942189 | erot = 10.2367032936654 | epot = -75.6746249610122 | etot = -54.4566354731278 +792000 ekin = 11.0795985346102 | erot = 10.3187114954301 | epot = -75.8549455034587 | etot = -54.4566354734184 +793000 ekin = 11.2461815584149 | erot = 10.344147052189 | epot = -76.0469640849238 | etot = -54.4566354743199 +794000 ekin = 11.470010961038 | erot = 10.3116670234561 | epot = -76.2383134600531 | etot = -54.4566354755591 +795000 ekin = 11.7325834354423 | erot = 10.2211808754552 | epot = -76.4103997879038 | etot = -54.4566354770063 +796000 ekin = 12.0100258299387 | erot = 10.0748477066209 | epot = -76.5415090148157 | etot = -54.456635478256 +797000 ekin = 12.277125034995 | erot = 9.87872464390326 | epot = -76.6124851578108 | etot = -54.4566354789125 +798000 ekin = 12.5117241722609 | erot = 9.64405687336503 | epot = -76.6124165243918 | etot = -54.4566354787658 +799000 ekin = 12.6978884572209 | erot = 9.38719424495255 | epot = -76.541718180055 | etot = -54.4566354778816 +800000 ekin = 12.8269839018831 | erot = 9.12779516060063 | epot = -76.4114145390235 | etot = -54.4566354765398 +801000 ekin = 12.8968371081357 | erot = 8.8858893984407 | epot = -76.2393619816671 | etot = -54.4566354750907 +802000 ekin = 12.9098422516114 | erot = 8.67886362140375 | epot = -76.0453413468402 | etot = -54.456635473825 +803000 ekin = 12.8709437099691 | erot = 8.51925810394788 | epot = -75.8468372868319 | etot = -54.4566354729149 +804000 ekin = 12.7860755415072 | erot = 8.41392281570264 | epot = -75.6566338295845 | etot = -54.4566354723747 +805000 ekin = 12.6610782480009 | erot = 8.36419460873407 | epot = -75.4819083289808 | etot = -54.4566354722458 +806000 ekin = 12.5011884973247 | erot = 8.3656329949461 | epot = -75.3234569648034 | etot = -54.4566354725326 +807000 ekin = 12.3111195444882 | erot = 8.40891169869997 | epot = -75.1766667162117 | etot = -54.4566354730235 +808000 ekin = 12.0951213686719 | erot = 8.48285306309104 | epot = -75.034609905525 | etot = -54.456635473762 +809000 ekin = 11.8570912953369 | erot = 8.57364419054096 | epot = -74.8873709604546 | etot = -54.4566354745767 +810000 ekin = 11.6008292339629 | erot = 8.66613366755959 | epot = -74.7235983769046 | etot = -54.4566354753821 +811000 ekin = 11.3302304258252 | erot = 8.74588715342986 | epot = -74.5327530553485 | etot = -54.4566354760934 +812000 ekin = 11.049430435476 | erot = 8.80043497509599 | epot = -74.3065008871933 | etot = -54.4566354766213 +813000 ekin = 10.7661929387732 | erot = 8.820921438455 | epot = -74.0437498529207 | etot = -54.4566354756925 +814000 ekin = 10.4922967616431 | erot = 8.803923684692 | epot = -73.7528559227931 | etot = -54.456635476458 +815000 ekin = 10.1508207490653 | erot = 8.72967512610392 | epot = -73.3371313415199 | etot = -54.4566354663507 +816000 ekin = 10.0080919366075 | erot = 8.6082286816217 | epot = -73.0729560943243 | etot = -54.4566354760951 +817000 ekin = 9.9417663188555 | erot = 8.48405485447215 | epot = -72.882456631768 | etot = -54.4566354584404 +818000 ekin = 9.81594850431016 | erot = 8.35559405938805 | epot = -72.6281780195682 | etot = -54.45663545587 +819000 ekin = 9.71985113501945 | erot = 8.23701168827821 | epot = -72.4134982795899 | etot = -54.4566354562922 +820000 ekin = 9.65376512615121 | erot = 8.1501567306149 | epot = -72.260557310816 | etot = -54.4566354540499 +821000 ekin = 9.62982370507439 | erot = 8.11448531446734 | epot = -72.2009444717374 | etot = -54.4566354521956 +822000 ekin = 9.66077700455577 | erot = 8.14425821637578 | epot = -72.2616706721298 | etot = -54.4566354511983 +823000 ekin = 9.75392749287522 | erot = 8.24624180251047 | epot = -72.4568047467245 | etot = -54.4566354513388 +824000 ekin = 9.90828878172935 | erot = 8.4186513843487 | epot = -72.7835756187113 | etot = -54.4566354526332 +825000 ekin = 10.1139944762006 | erot = 8.65151311650705 | epot = -73.2221430475685 | etot = -54.4566354548608 +826000 ekin = 10.3538759474279 | erot = 8.92820306635602 | epot = -73.738714471444 | etot = -54.4566354576601 +827000 ekin = 10.606338982672 | erot = 9.22772390085596 | epot = -74.2906983441747 | etot = -54.4566354606467 +828000 ekin = 10.8484921435726 | erot = 9.52726891665539 | epot = -74.8323965237032 | etot = -54.4566354634752 +829000 ekin = 11.0588299502289 | erot = 9.80476940803695 | epot = -75.3202348241266 | etot = -54.4566354658608 +830000 ekin = 11.2192526328106 | erot = 10.0413124779635 | epot = -75.7172005783464 | etot = -54.4566354675724 +831000 ekin = 11.3164768757008 | erot = 10.2234037408202 | epot = -75.996516084949 | etot = -54.4566354684279 +832000 ekin = 11.3429029406713 | erot = 10.3449490493039 | epot = -76.1444874582939 | etot = -54.4566354683187 +833000 ekin = 11.2968956967983 | erot = 10.4085990339246 | epot = -76.1621301979783 | etot = -54.4566354672554 +834000 ekin = 11.1823662954395 | erot = 10.4259018262243 | epot = -76.0649035871392 | etot = -54.4566354654754 +835000 ekin = 11.0075932322104 | erot = 10.415064292159 | epot = -75.8792929875455 | etot = -54.4566354631761 +836000 ekin = 10.7833921149831 | erot = 10.3989545533741 | epot = -75.6389821291817 | etot = -54.4566354608245 +837000 ekin = 10.5209501551182 | erot = 10.4011161497682 | epot = -75.3787017637168 | etot = -54.4566354588304 +838000 ekin = 10.2298721897682 | erot = 10.4412405801822 | epot = -75.1277482274376 | etot = -54.4566354574871 +839000 ekin = 9.9169698633829 | erot = 10.5315530525306 | epot = -74.9051583728937 | etot = -54.4566354569802 +840000 ekin = 9.58610156141702 | erot = 10.6755294545289 | epot = -74.7182664730354 | etot = -54.4566354570895 +841000 ekin = 9.23901842927408 | erot = 10.868774358744 | epot = -74.5644282456714 | etot = -54.4566354576533 +842000 ekin = 8.87685056107778 | erot = 11.1001329244142 | epot = -74.4336189440919 | etot = -54.4566354585999 +843000 ekin = 8.50173060234696 | erot = 11.3524188663457 | epot = -74.3107849279275 | etot = -54.4566354592348 +844000 ekin = 8.11795575231061 | erot = 11.6095427521259 | epot = -74.1841339640053 | etot = -54.4566354595688 +845000 ekin = 7.73236361560105 | erot = 11.8578438185536 | epot = -74.0468428936599 | etot = -54.4566354595052 +846000 ekin = 7.35399612874066 | erot = 12.0875238819158 | epot = -73.8981554696971 | etot = -54.4566354590406 +847000 ekin = 6.99323530265824 | erot = 12.2936929401837 | epot = -73.7435637010834 | etot = -54.4566354582415 +848000 ekin = 6.66076569760595 | erot = 12.476513505272 | epot = -73.5939146600918 | etot = -54.4566354572138 +849000 ekin = 6.36668003284545 | erot = 12.6405664289168 | epot = -73.4638819178322 | etot = -54.45663545607 +850000 ekin = 6.11988143343135 | erot = 12.7936422801385 | epot = -73.3701591685048 | etot = -54.4566354549349 +851000 ekin = 5.9277602422565 | erot = 12.9452003506214 | epot = -73.3295960467989 | etot = -54.4566354539209 +852000 ekin = 5.79602796366905 | erot = 13.1047455614325 | epot = -73.3574089782281 | etot = -54.4566354531266 +853000 ekin = 5.72859704152406 | erot = 13.2803568755571 | epot = -73.4655893697262 | etot = -54.4566354526451 +854000 ekin = 5.72746205359738 | erot = 13.4775571123792 | epot = -73.6616546184891 | etot = -54.4566354525126 +855000 ekin = 5.79260154210359 | erot = 13.6986462729226 | epot = -73.9478832677686 | etot = -54.4566354527424 +856000 ekin = 5.92195007057475 | erot = 13.9425386772173 | epot = -74.3211242010997 | etot = -54.4566354533076 +857000 ekin = 6.11148060846784 | erot = 14.2050613164122 | epot = -74.7731773790288 | etot = -54.4566354541488 +858000 ekin = 6.35540247729863 | erot = 14.4795962341537 | epot = -75.2916341666453 | etot = -54.456635455193 +859000 ekin = 6.6464375003053 | erot = 14.7578922330101 | epot = -75.8609651896848 | etot = -54.4566354563695 +860000 ekin = 6.97610349830149 | erot = 15.0308449598478 | epot = -76.4635839157752 | etot = -54.4566354576259 +861000 ekin = 7.3349249363496 | erot = 15.2890679300596 | epot = -77.0806283253549 | etot = -54.4566354589457 +862000 ekin = 7.71251467470176 | erot = 15.5231591806792 | epot = -77.6923093157189 | etot = -54.4566354603379 +863000 ekin = 8.09752575484634 | erot = 15.7236923479157 | epot = -78.2778535645897 | etot = -54.4566354618277 +864000 ekin = 8.47754136486205 | erot = 15.8810831527475 | epot = -78.8152599810381 | etot = -54.4566354634286 +865000 ekin = 8.83903083982985 | erot = 15.9855505169334 | epot = -79.2812168218813 | etot = -54.456635465118 +866000 ekin = 9.16752990645287 | erot = 16.0273731150022 | epot = -79.6515384882752 | etot = -54.4566354668201 +867000 ekin = 9.44819483540946 | erot = 15.997539865398 | epot = -79.9023701692061 | etot = -54.4566354683986 +868000 ekin = 9.66683066873641 | erot = 15.8887400708614 | epot = -80.0122062092691 | etot = -54.4566354696714 +869000 ekin = 9.81140211470355 | erot = 15.6964846394016 | epot = -79.9645222245439 | etot = -54.4566354704387 +870000 ekin = 9.87390363906791 | erot = 15.4200471696184 | epot = -79.7505862792118 | etot = -54.4566354705255 +871000 ekin = 9.8523095259315 | erot = 15.0629113172219 | epot = -79.3718563129752 | etot = -54.4566354698218 +872000 ekin = 9.752187308027 | erot = 14.6325332986052 | epot = -78.841356074952 | etot = -54.4566354683198 +873000 ekin = 9.58749579142185 | erot = 14.1394452329319 | epot = -78.1835764904824 | etot = -54.4566354661287 +874000 ekin = 9.38014472395005 | erot = 13.5959424947095 | epot = -77.4327226821286 | etot = -54.4566354634691 +875000 ekin = 9.15807680471866 | erot = 13.014707802176 | epot = -76.6294200675408 | etot = -54.4566354606461 +876000 ekin = 8.95192933213213 | erot = 12.4076841945948 | epot = -75.816248984735 | etot = -54.4566354580081 +877000 ekin = 8.79071144345444 | erot = 11.7853760071662 | epot = -75.0327229065074 | etot = -54.4566354558868 +878000 ekin = 8.69731943591344 | erot = 11.1566317214223 | epot = -74.3105866118547 | etot = -54.456635454519 +879000 ekin = 8.68495451684523 | erot = 10.5288962872203 | epot = -73.6704862580452 | etot = -54.4566354539797 +880000 ekin = 8.75541640190843 | erot = 9.90888240825742 | epot = -73.1209342643213 | etot = -54.4566354541554 +881000 ekin = 8.8997445293349 | erot = 9.30353954409839 | epot = -72.6599195282146 | etot = -54.4566354547813 +882000 ekin = 9.10092859929824 | erot = 8.72108289024305 | epot = -72.2786469450737 | etot = -54.4566354555324 +883000 ekin = 9.33776725236621 | erot = 8.17174677407215 | epot = -71.9661494825623 | etot = -54.456635456124 +884000 ekin = 9.58873539183595 | erot = 7.66794414586939 | epot = -71.7133149940986 | etot = -54.4566354563932 +885000 ekin = 9.83498174992465 | erot = 7.22368667480856 | epot = -71.5153038810381 | etot = -54.4566354563048 +886000 ekin = 10.0620936934736 | erot = 6.85337791012132 | epot = -71.3721070595231 | etot = -54.4566354559282 +887000 ekin = 10.2607225025527 | erot = 6.57029245231516 | epot = -71.2876504102503 | etot = -54.4566354553824 +888000 ekin = 10.4263755446124 | erot = 6.38509300456668 | epot = -71.2681040039826 | etot = -54.4566354548035 +889000 ekin = 10.5586710814385 | erot = 6.30462943885317 | epot = -71.319935974615 | etot = -54.4566354543233 +890000 ekin = 10.6602540894462 | erot = 6.3311170754918 | epot = -71.4480066190011 | etot = -54.4566354540632 +891000 ekin = 10.7355099946819 | erot = 6.46170576302369 | epot = -71.6538512118289 | etot = -54.4566354541233 +892000 ekin = 10.7892241406154 | erot = 6.68844891426448 | epot = -71.9343085094461 | etot = -54.4566354545662 +893000 ekin = 10.8253819948177 | erot = 6.99871565289404 | epot = -72.280733103109 | etot = -54.4566354553972 +894000 ekin = 10.8463299662712 | erot = 7.37610035056202 | epot = -72.6790657733836 | etot = -54.4566354565504 +895000 ekin = 10.852475486525 | erot = 7.80183940289732 | epot = -73.1109503473091 | etot = -54.4566354578867 +896000 ekin = 10.8425858689659 | erot = 8.25664380954496 | epot = -73.5558651377289 | etot = -54.456635459218 +897000 ekin = 10.8145780999263 | erot = 8.72272211941494 | epot = -73.9939356796854 | etot = -54.4566354603442 +898000 ekin = 10.7665424605736 | erot = 9.18564804398081 | epot = -74.4088259656637 | etot = -54.4566354611092 +899000 ekin = 10.6976805034733 | erot = 9.63567769333504 | epot = -74.7899936582461 | etot = -54.4566354614378 +900000 ekin = 10.6088887087272 | erot = 10.0681851806236 | epot = -75.1337093507081 | etot = -54.4566354613573 +901000 ekin = 10.502853007353 | erot = 10.4830654351765 | epot = -75.4425539035197 | etot = -54.4566354609902 +902000 ekin = 10.3836771774535 | erot = 10.8832063665621 | epot = -75.7235190045351 | etot = -54.4566354605195 +903000 ekin = 10.2561979891383 | erot = 11.2723815658634 | epot = -75.9852150151384 | etot = -54.4566354601367 +904000 ekin = 10.1252127005282 | erot = 11.6530755864755 | epot = -76.2349237469979 | etot = -54.4566354599942 +905000 ekin = 9.99485047044705 | erot = 12.0247708238103 | epot = -76.4762567544226 | etot = -54.4566354601653 +906000 ekin = 9.86826182519167 | erot = 12.3830923597808 | epot = -76.7079896456003 | etot = -54.4566354606279 +907000 ekin = 9.74769326327752 | erot = 12.7199654418464 | epot = -76.9242941664046 | etot = -54.4566354612807 +908000 ekin = 9.63488321935044 | erot = 13.024659583975 | epot = -77.1161782653058 | etot = -54.4566354619803 +909000 ekin = 9.53160068472383 | erot = 13.2853599353513 | epot = -77.2735960826646 | etot = -54.4566354625895 +910000 ekin = 9.44009501998067 | erot = 13.4908067507586 | epot = -77.3875372337547 | etot = -54.4566354630154 +911000 ekin = 9.36326455556512 | erot = 13.6316252373525 | epot = -77.4515252561402 | etot = -54.4566354632226 +912000 ekin = 9.30446941107284 | erot = 13.7011923330111 | epot = -77.4622972073039 | etot = -54.45663546322 +913000 ekin = 9.26705259278318 | erot = 13.6961250397271 | epot = -77.419813095547 | etot = -54.4566354630367 +914000 ekin = 9.25372341949208 | erot = 13.6165806074811 | epot = -77.3269394896719 | etot = -54.4566354626987 +915000 ekin = 9.26596340708621 | erot = 13.4664769842073 | epot = -77.1890758535215 | etot = -54.4566354622281 +916000 ekin = 9.30355576102913 | erot = 13.2535559655594 | epot = -77.0137471882459 | etot = -54.4566354616573 +917000 ekin = 9.36426903858459 | erot = 12.9890809272589 | epot = -76.809985426892 | etot = -54.4566354610485 +918000 ekin = 9.44369101175022 | erot = 12.6869990269965 | epot = -76.587325499227 | etot = -54.4566354604803 +919000 ekin = 9.53522052882113 | erot = 12.3625891360067 | epot = -76.3544451248775 | etot = -54.4566354600497 +920000 ekin = 9.63025415658243 | erot = 12.0308380430302 | epot = -76.1177276594349 | etot = -54.4566354598223 +921000 ekin = 9.71861106511874 | erot = 11.7049052779173 | epot = -75.8801518028705 | etot = -54.4566354598345 +922000 ekin = 9.78920770644036 | erot = 11.3950002816103 | epot = -75.6408434481097 | etot = -54.4566354600591 +923000 ekin = 9.83093885317139 | erot = 11.1078500466024 | epot = -75.3954243602039 | etot = -54.4566354604301 +924000 ekin = 9.83367208378622 | erot = 10.8467682564577 | epot = -75.1370758010956 | etot = -54.4566354608517 +925000 ekin = 9.78923699199639 | erot = 10.6122146417245 | epot = -74.8580870949345 | etot = -54.4566354612136 +926000 ekin = 9.69228799630493 | erot = 10.4026778523962 | epot = -74.5516013101181 | etot = -54.456635461417 +927000 ekin = 9.54094420680802 | erot = 10.2157130838007 | epot = -74.2132927519865 | etot = -54.4566354613778 +928000 ekin = 9.3371459859503 | erot = 10.0489976142885 | epot = -73.8427790612753 | etot = -54.4566354610365 +929000 ekin = 9.08668869599518 | erot = 9.90129105968912 | epot = -73.4446152160518 | etot = -54.4566354603675 +930000 ekin = 8.79893949160058 | erot = 9.77317491044661 | epot = -73.0287498614319 | etot = -54.4566354593847 +931000 ekin = 8.48625276384768 | erot = 9.66741161204924 | epot = -72.6102998340512 | etot = -54.4566354581543 +932000 ekin = 8.16311074513819 | erot = 9.58874585509042 | epot = -72.2084920570281 | etot = -54.4566354567995 +933000 ekin = 7.84503269780539 | erot = 9.54303556689035 | epot = -71.8447037201951 | etot = -54.4566354554993 +934000 ekin = 7.54732721404963 | erot = 9.53576382282306 | epot = -71.5397264913334 | etot = -54.4566354544607 +935000 ekin = 7.28379852832834 | erot = 9.57018935591102 | epot = -71.3106233381242 | etot = -54.4566354538848 +936000 ekin = 7.06554340229853 | erot = 9.64555160732505 | epot = -71.167730463548 | etot = -54.4566354539244 +937000 ekin = 6.89998137838447 | erot = 9.75579580002511 | epot = -71.112412633057 | etot = -54.4566354546474 +938000 ekin = 6.79024863688773 | erot = 9.88921936738739 | epot = -71.1361034602903 | etot = -54.4566354560152 +939000 ekin = 6.73505698751703 | erot = 10.0294464266678 | epot = -71.2211388720031 | etot = -54.4566354578183 +940000 ekin = 6.72907691272921 | erot = 10.1573224430157 | epot = -71.3430348156531 | etot = -54.4566354599082 +941000 ekin = 6.7638392322072 | erot = 10.2535241006084 | epot = -71.473998794711 | etot = -54.4566354618954 +942000 ekin = 6.82912409655559 | erot = 10.3022923171274 | epot = -71.5880518771063 | etot = -54.4566354634233 +943000 ekin = 6.91476596974007 | erot = 10.2946315405203 | epot = -71.6660329744438 | etot = -54.4566354641834 +944000 ekin = 7.01269053560795 | erot = 10.2304790515295 | epot = -71.6998050511278 | etot = -54.4566354639903 +945000 ekin = 7.11873167357596 | erot = 10.1191217606592 | epot = -71.6944888971226 | etot = -54.4566354628875 +946000 ekin = 7.23341535201951 | erot = 9.97742521428816 | epot = -71.6674760275169 | etot = -54.4566354612092 +947000 ekin = 7.36083754475568 | erot = 9.82603454656194 | epot = -71.6435075508528 | etot = -54.4566354595352 +948000 ekin = 7.50549771867048 | erot = 9.68450715332286 | epot = -71.646640330475 | etot = -54.4566354584817 +949000 ekin = 7.66836590288662 | erot = 9.56693750756918 | epot = -71.6919388688627 | etot = -54.4566354584069 +950000 ekin = 7.8444636655597 | erot = 9.47955332201817 | epot = -71.7806524468177 | etot = -54.4566354592398 +951000 ekin = 8.02362258957402 | erot = 9.42089965829233 | epot = -71.9011577084041 | etot = -54.4566354605377 +952000 ekin = 8.19401979343905 | erot = 9.38404388099782 | epot = -72.0346991362141 | etot = -54.4566354617773 +953000 ekin = 8.34627037919898 | erot = 9.35945524415897 | epot = -72.1623610859837 | etot = -54.4566354626257 +954000 ekin = 8.47579105972131 | erot = 9.3373146667663 | epot = -72.2697411895169 | etot = -54.4566354630293 +955000 ekin = 8.58263553139959 | erot = 9.308823031816 | epot = -72.3480940263229 | etot = -54.4566354631073 +956000 ekin = 8.66958271584179 | erot = 9.26689225473929 | epot = -72.393110433665 | etot = -54.4566354630839 +957000 ekin = 8.73983792556415 | erot = 9.20645883858331 | epot = -72.402932227037 | etot = -54.4566354628896 +958000 ekin = 8.79532848877231 | erot = 9.12577516410996 | epot = -72.3777391154678 | etot = -54.4566354625855 +959000 ekin = 8.83590266111342 | erot = 9.02777800336421 | epot = -72.3203161266023 | etot = -54.4566354621246 +960000 ekin = 8.85930075562178 | erot = 8.92058787880297 | epot = -72.2365240958907 | etot = -54.456635461466 +961000 ekin = 8.86161651519074 | erot = 8.8176620297481 | epot = -72.1359140055372 | etot = -54.4566354605984 +962000 ekin = 8.83799666717614 | erot = 8.73718807970271 | epot = -72.0318202064324 | etot = -54.4566354595536 +963000 ekin = 8.7834038645067 | erot = 8.70071313770526 | epot = -71.9407524606206 | etot = -54.4566354584087 +964000 ekin = 8.6933315650967 | erot = 8.73109905622396 | epot = -71.8810660786001 | etot = -54.4566354572794 +965000 ekin = 8.56440365903402 | erot = 8.84996493880067 | epot = -71.8710040541396 | etot = -54.4566354563049 +966000 ekin = 8.39482523796214 | erot = 9.07485296714587 | epot = -71.9263136607553 | etot = -54.4566354556473 +967000 ekin = 8.18467818887415 | erot = 9.41644113229026 | epot = -72.0577547766049 | etot = -54.4566354554405 +968000 ekin = 7.93626974430701 | erot = 9.8761337464021 | epot = -72.2690389465259 | etot = -54.4566354558168 +969000 ekin = 7.65431026894464 | erot = 10.4442911838587 | epot = -72.5552369095504 | etot = -54.4566354567471 +970000 ekin = 7.34450165167553 | erot = 11.1010614724236 | epot = -72.9021985821619 | etot = -54.4566354580628 +971000 ekin = 7.01497831136109 | erot = 11.8180138555475 | epot = -73.2896276264753 | etot = -54.4566354595667 +972000 ekin = 6.67661988307432 | erot = 12.561002201264 | epot = -73.6942575453412 | etot = -54.4566354610029 +973000 ekin = 6.34325563533771 | erot = 13.2935365140162 | epot = -74.093427611541 | etot = -54.4566354621871 +974000 ekin = 6.03126679101612 | erot = 13.9800756161257 | epot = -74.467977870057 | etot = -54.4566354629151 +975000 ekin = 5.75832704440613 | erot = 14.5910245181588 | epot = -74.8059870256856 | etot = -54.4566354631207 +976000 ekin = 5.54248690291485 | erot = 15.1042545810727 | epot = -75.103376946877 | etot = -54.4566354628895 +977000 ekin = 5.4003503184872 | erot = 15.5056612502236 | epot = -75.3626470311159 | etot = -54.4566354624051 +978000 ekin = 5.34501003153766 | erot = 15.7884985247711 | epot = -75.5901440181963 | etot = -54.4566354618875 +979000 ekin = 5.38417633217786 | erot = 15.9518932070818 | epot = -75.7927050007967 | etot = -54.456635461537 +980000 ekin = 5.51889158471155 | erot = 15.999058478668 | epot = -75.9745855248649 | etot = -54.4566354614853 +981000 ekin = 5.74308889432032 | erot = 15.9356762595534 | epot = -76.1354006156442 | etot = -54.4566354617704 +982000 ekin = 6.04407260764492 | erot = 15.7687916692872 | epot = -76.2694997392642 | etot = -54.456635462332 +983000 ekin = 6.4038298993232 | erot = 15.5063975907864 | epot = -76.3668629531362 | etot = -54.4566354630267 +984000 ekin = 6.80095841871057 | erot = 15.1576983609449 | epot = -76.4152922433134 | etot = -54.456635463658 +985000 ekin = 7.21291844142515 | erot = 14.7338425283028 | epot = -76.4033964337531 | etot = -54.4566354640251 +986000 ekin = 7.61828265636069 | erot = 14.2487453064303 | epot = -76.3236634267622 | etot = -54.4566354639712 +987000 ekin = 7.99866441020991 | erot = 13.7195510825214 | epot = -76.17485095616 | etot = -54.4566354634287 +988000 ekin = 8.34006634563207 | erot = 13.1663738041721 | epot = -75.9630756122385 | etot = -54.4566354624343 +989000 ekin = 8.63350862200756 | erot = 12.6111857672338 | epot = -75.7013298503602 | etot = -54.4566354611189 +990000 ekin = 8.87494555503115 | erot = 12.0760163566083 | epot = -75.4075973713094 | etot = -54.45663545967 +991000 ekin = 9.06461955877742 | erot = 11.5808385824354 | epot = -75.1020935994994 | etot = -54.4566354582866 +992000 ekin = 9.20608865934225 | erot = 11.1415830196626 | epot = -74.8043071361417 | etot = -54.4566354571369 +993000 ekin = 9.3051781291951 | erot = 10.7686313368412 | epot = -74.5304449223712 | etot = -54.4566354563349 +994000 ekin = 9.36905574676181 | erot = 10.4659766382208 | epot = -74.2916678409143 | etot = -54.4566354559316 +995000 ekin = 9.4055413677824 | erot = 10.2310751484372 | epot = -74.0932519721414 | etot = -54.4566354559218 +996000 ekin = 9.42266810575618 | erot = 10.055304234773 | epot = -73.934607796785 | etot = -54.4566354562558 +997000 ekin = 9.42843932276535 | erot = 9.92490942423686 | epot = -73.8099842038573 | etot = -54.4566354568551 +998000 ekin = 9.43069348804015 | erot = 9.82234985059454 | epot = -73.7096787962489 | etot = -54.4566354576142 +999000 ekin = 9.43700002885815 | erot = 9.72798019148381 | epot = -73.6216156787693 | etot = -54.4566354584274 +1000000 ekin = 9.45454475437508 | erot = 9.62197027192603 | epot = -73.5331504854538 | etot = -54.4566354591527 + 1000000 352.42265 -75.546285 2.0131342 -64.078606 -0.0098335381 39304000 +Loop time of 9.84056 on 1 procs for 1000000 steps with 10 atoms + +Performance: 149.787 ns/day, 0.160 hours/ns, 101620.202 timesteps/s, 1.016 Matom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.6388 | 7.6388 | 7.6388 | 0.0 | 77.63 +Bond | 0.4116 | 0.4116 | 0.4116 | 0.0 | 4.18 +Neigh | 0.012626 | 0.012626 | 0.012626 | 0.0 | 0.13 +Comm | 0.25713 | 0.25713 | 0.25713 | 0.0 | 2.61 +Output | 0.11932 | 0.11932 | 0.11932 | 0.0 | 1.21 +Modify | 1.1253 | 1.1253 | 1.1253 | 0.0 | 11.44 +Other | | 0.2758 | | | 2.80 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:09 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/log.19May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/log.19May24.duplex1.g++.4 new file mode 100644 index 0000000000..d9917b5143 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/log.19May24.duplex1.g++.4 @@ -0,0 +1,1113 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.008 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna.real with DATE: 2024-04-26 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (stk) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (xstk) file oxdna.real with DATE: 2024-04-26 +Reading oxdna potential (coaxstk) file oxdna.real with DATE: 2024-04-26 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 25.179212 + ghost atom cutoff = 32.4 + binsize = 12.589606, bins = 28 28 28 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 0.01706 +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8452930576479 | etot = -54.4566354061168 +Per MPI rank memory allocation (min/avg/max) = 7.105 | 7.11 | 7.116 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -80.414328 2.5690347 -71.23842 -0.031164648 39304000 +1000 ekin = 6.43820748574481 | erot = 17.3362209220524 | epot = -78.2310638156467 | etot = -54.4566354078494 +2000 ekin = 6.25962687713457 | erot = 17.7614973153004 | epot = -78.4777596014537 | etot = -54.4566354090187 +3000 ekin = 6.07700448778499 | erot = 18.0349390575317 | epot = -78.5685789546716 | etot = -54.4566354093549 +4000 ekin = 5.89744243690135 | erot = 18.1444655563223 | epot = -78.4985434019984 | etot = -54.4566354087747 +5000 ekin = 5.72921495795417 | erot = 18.089813534545 | epot = -78.2756638998997 | etot = -54.4566354074005 +6000 ekin = 5.58102962967702 | erot = 17.8818907378652 | epot = -77.9195557730909 | etot = -54.4566354055487 +7000 ekin = 5.46083564262917 | erot = 17.5394365844243 | epot = -77.4569076305326 | etot = -54.4566354034791 +8000 ekin = 5.37466374419897 | erot = 17.0860544650632 | epot = -76.9173536106637 | etot = -54.4566354014016 +9000 ekin = 5.32595754281565 | erot = 16.5482852541265 | epot = -76.3308781963651 | etot = -54.456635399423 +10000 ekin = 5.31554676342212 | erot = 15.9544138469034 | epot = -75.726596007792 | etot = -54.4566353974665 +11000 ekin = 5.34211698054861 | erot = 15.3332614944564 | epot = -75.1320138708453 | etot = -54.4566353958403 +12000 ekin = 5.40287038471206 | erot = 14.7110834230834 | epot = -74.5705892022623 | etot = -54.4566353944669 +13000 ekin = 5.49411526233303 | erot = 14.1110915850697 | epot = -74.061842240842 | etot = -54.4566353934393 +14000 ekin = 5.61166305682739 | erot = 13.5517399019597 | epot = -73.620038351625 | etot = -54.4566353928379 +15000 ekin = 5.75104953856992 | erot = 13.0453199784602 | epot = -73.2530049096301 | etot = -54.4566353926 +16000 ekin = 5.90767197595969 | erot = 12.5986167018217 | epot = -72.9629240705716 | etot = -54.4566353927902 +17000 ekin = 6.07693584949018 | erot = 12.2121424091129 | epot = -72.7457136520755 | etot = -54.4566353934724 +18000 ekin = 6.25447802454953 | erot = 11.8809715590397 | epot = -72.5920849774633 | etot = -54.456635393874 +19000 ekin = 6.43644156574403 | erot = 11.5970868983705 | epot = -72.4901638588708 | etot = -54.4566353947562 +20000 ekin = 6.61975078718435 | erot = 11.3493268347886 | epot = -72.4257130174612 | etot = -54.4566353954882 +21000 ekin = 6.80231654537102 | erot = 11.1279852357804 | epot = -72.3869371771082 | etot = -54.4566353959567 +22000 ekin = 6.98310666039517 | erot = 10.9264899080746 | epot = -72.3662319645786 | etot = -54.4566353961088 +23000 ekin = 7.16204136914452 | erot = 10.7423471683523 | epot = -72.3610239334526 | etot = -54.4566353959558 +24000 ekin = 7.33971202276069 | erot = 10.5772893708791 | epot = -72.3736367892021 | etot = -54.4566353955622 +25000 ekin = 7.51694389098104 | erot = 10.4366021288186 | epot = -72.4101814148953 | etot = -54.4566353950956 +26000 ekin = 7.69428547961043 | erot = 10.3277743414165 | epot = -72.4786952155958 | etot = -54.4566353945689 +27000 ekin = 7.87150355456855 | erot = 10.2597385959262 | epot = -72.5878775446629 | etot = -54.4566353941681 +28000 ekin = 8.04704621231831 | erot = 10.2410408314319 | epot = -72.7447224377784 | etot = -54.4566353940281 +29000 ekin = 8.21759311371884 | erot = 10.2782069424416 | epot = -72.9524354504283 | etot = -54.4566353942678 +30000 ekin = 8.37773815926537 | erot = 10.3742402092557 | epot = -73.2086137634978 | etot = -54.4566353949767 +31000 ekin = 8.51990636063666 | erot = 10.5273635253436 | epot = -73.5039052821701 | etot = -54.4566353961898 +32000 ekin = 8.63465075758022 | erot = 10.7302372452282 | epot = -73.8215234006611 | etot = -54.4566353978527 +33000 ekin = 8.71148242170772 | erot = 10.9699568578571 | epot = -74.138074679361 | etot = -54.4566353997962 +34000 ekin = 8.74030401673744 | erot = 11.2291118958909 | epot = -74.4260513143626 | etot = -54.4566354017342 +35000 ekin = 8.71331738120349 | erot = 11.4879439611377 | epot = -74.6578967456826 | etot = -54.4566354033414 +36000 ekin = 8.6270076806576 | erot = 11.7272655611852 | epot = -74.8109086460857 | etot = -54.4566354042429 +37000 ekin = 8.48360459165283 | erot = 11.9311379268702 | epot = -74.871377923066 | etot = -54.456635404543 +38000 ekin = 8.29146113848127 | erot = 12.0877506878437 | epot = -74.8358472300847 | etot = -54.4566354037597 +39000 ekin = 8.06413250091585 | erot = 12.193934384732 | epot = -74.7147022878405 | etot = -54.4566354021927 +40000 ekin = 7.81835387769415 | erot = 12.2536662217397 | epot = -74.5286554998775 | etot = -54.4566354004436 +41000 ekin = 7.57154460494732 | erot = 12.2737017000968 | epot = -74.3018817037919 | etot = -54.4566353987478 +42000 ekin = 7.33953370634753 | erot = 12.2616149193731 | epot = -74.0577840229946 | etot = -54.4566353972739 +43000 ekin = 7.13480148719676 | erot = 12.2251511246247 | epot = -73.8165880080337 | etot = -54.4566353962123 +44000 ekin = 6.96550034046782 | erot = 12.1705709864272 | epot = -73.5927067224907 | etot = -54.4566353955957 +45000 ekin = 6.83524619732735 | erot = 12.1023709627633 | epot = -73.3942525554547 | etot = -54.456635395364 +46000 ekin = 6.74354326448681 | erot = 12.0237258448786 | epot = -73.2239045047614 | etot = -54.456635395396 +47000 ekin = 6.68665553239108 | erot = 11.9373578617843 | epot = -73.0806487897224 | etot = -54.456635395547 +48000 ekin = 6.65871606123777 | erot = 11.8463393902399 | epot = -72.9616908473445 | etot = -54.4566353958669 +49000 ekin = 6.65288529209096 | erot = 11.753790570883 | epot = -72.8633112588596 | etot = -54.4566353958856 +50000 ekin = 6.66236602673595 | erot = 11.6656457317317 | epot = -72.7846471541945 | etot = -54.4566353957269 +51000 ekin = 6.6811133846848 | erot = 11.5899588724781 | epot = -72.7277076525686 | etot = -54.4566353954056 +52000 ekin = 6.70418283073775 | erot = 11.5360342718575 | epot = -72.6968524975888 | etot = -54.4566353949935 +53000 ekin = 6.72772596002251 | erot = 11.5133896479184 | epot = -72.6977510025402 | etot = -54.4566353945994 +54000 ekin = 6.74871529529539 | erot = 11.530730873965 | epot = -72.7360815636084 | etot = -54.456635394348 +55000 ekin = 6.76452000506643 | erot = 11.5943437358558 | epot = -72.8154991352808 | etot = -54.4566353943586 +56000 ekin = 6.77244089755618 | erot = 11.7063368897017 | epot = -72.9354131819756 | etot = -54.4566353947177 +57000 ekin = 6.76933125219097 | erot = 11.8641785052097 | epot = -73.0901451528751 | etot = -54.4566353954744 +58000 ekin = 6.75138787630819 | erot = 12.0602581117039 | epot = -73.2682813846355 | etot = -54.4566353966234 +59000 ekin = 6.71417211137197 | erot = 12.2820346405445 | epot = -73.4528421500115 | etot = -54.4566353980951 +60000 ekin = 6.65291138938061 | erot = 12.5128606065817 | epot = -73.6224073957175 | etot = -54.4566353997552 +61000 ekin = 6.56310936736069 | erot = 12.7334757971155 | epot = -73.7532205658834 | etot = -54.4566354014071 +62000 ekin = 6.44146738962339 | erot = 12.924115378406 | epot = -73.8222181708354 | etot = -54.456635402806 +63000 ekin = 6.28706349170159 | erot = 13.0670025811126 | epot = -73.8107014767365 | etot = -54.4566354039223 +64000 ekin = 6.10266894648004 | erot = 13.1477550766289 | epot = -73.707059427161 | etot = -54.4566354040521 +65000 ekin = 5.89591961177657 | erot = 13.159243189225 | epot = -73.5117982043025 | etot = -54.4566354033009 +66000 ekin = 5.67987986272372 | erot = 13.1031941166757 | epot = -73.2397093810282 | etot = -54.4566354016288 +67000 ekin = 5.47247153600082 | erot = 12.9892792342589 | epot = -72.9183861696817 | etot = -54.456635399422 +68000 ekin = 5.29472138366983 | erot = 12.8325717552517 | epot = -72.5839285358207 | etot = -54.4566353968992 +69000 ekin = 5.16838664772562 | erot = 12.6515520795182 | epot = -72.2765741217841 | etot = -54.4566353945403 +70000 ekin = 5.11229587755497 | erot = 12.4645483617666 | epot = -72.0334796321513 | etot = -54.4566353928297 +71000 ekin = 5.13861822273141 | erot = 12.286155039687 | epot = -71.8814086546595 | etot = -54.456635392241 +72000 ekin = 5.24919776269878 | erot = 12.1240996084996 | epot = -71.8299327640232 | etot = -54.4566353928249 +73000 ekin = 5.43492595011674 | erot = 11.9780482590885 | epot = -71.8696096036112 | etot = -54.4566353944059 +74000 ekin = 5.67784516722565 | erot = 11.8411405072579 | epot = -71.9756210710773 | etot = -54.4566353965938 +75000 ekin = 5.95413179780636 | erot = 11.7025554045176 | epot = -72.113322601217 | etot = -54.456635398893 +76000 ekin = 6.23821902238342 | erot = 11.550835238764 | epot = -72.2456896619923 | etot = -54.4566354008449 +77000 ekin = 6.50672473640307 | erot = 11.376950900624 | epot = -72.3403110391609 | etot = -54.4566354021339 +78000 ekin = 6.74134494190868 | erot = 11.176319005782 | epot = -72.3742993503304 | etot = -54.4566354026398 +79000 ekin = 6.93029998725172 | erot = 10.9493831098239 | epot = -72.3363184995026 | etot = -54.456635402427 +80000 ekin = 7.06837455802717 | erot = 10.7008607206271 | epot = -72.2258706803366 | etot = -54.4566354016823 +81000 ekin = 7.1559261286265 | erot = 10.4381578436606 | epot = -72.0507193729194 | etot = -54.4566354006323 +82000 ekin = 7.19737523755975 | erot = 10.169620475243 | epot = -71.8236311122788 | etot = -54.4566353994761 +83000 ekin = 7.19964138072444 | erot = 9.90319185133819 | epot = -71.5594686304058 | etot = -54.4566353983432 +84000 ekin = 7.17082378076146 | erot = 9.64576283606872 | epot = -71.2732220141215 | etot = -54.4566353972913 +85000 ekin = 7.11924100547725 | erot = 9.40319183443934 | epot = -70.9790682362418 | etot = -54.4566353963252 +86000 ekin = 7.05280646949722 | erot = 9.18075710620435 | epot = -70.69019897113 | etot = -54.4566353954284 +87000 ekin = 6.97865213852087 | erot = 8.98373783121296 | epot = -70.4190253643134 | etot = -54.4566353945796 +88000 ekin = 6.90290745250038 | erot = 8.81787505324958 | epot = -70.1774178995224 | etot = -54.4566353937725 +89000 ekin = 6.8305664368472 | erot = 8.68957621789595 | epot = -69.9767780477601 | etot = -54.4566353930169 +90000 ekin = 6.76540803039386 | erot = 8.60583660610408 | epot = -69.8278800288341 | etot = -54.4566353923362 +91000 ekin = 6.70995822419679 | erot = 8.57392290473218 | epot = -69.7405165206908 | etot = -54.4566353917618 +92000 ekin = 6.6654938760643 | erot = 8.6008929317492 | epot = -69.7230221991413 | etot = -54.4566353913278 +93000 ekin = 6.6320939224086 | erot = 8.69302362042084 | epot = -69.7817529338974 | etot = -54.456635391068 +94000 ekin = 6.60873879578613 | erot = 8.85520324232627 | epot = -69.9205774291246 | etot = -54.4566353910122 +95000 ekin = 6.59345542312922 | erot = 9.08998001250007 | epot = -70.1400708268598 | etot = -54.4566353912305 +96000 ekin = 6.5834981640273 | erot = 9.39670336713002 | epot = -70.4368369228347 | etot = -54.4566353916773 +97000 ekin = 6.57557086190908 | erot = 9.77232035429913 | epot = -70.804526608599 | etot = -54.4566353923908 +98000 ekin = 6.56607746070764 | erot = 10.2103280886849 | epot = -71.2330409427607 | etot = -54.4566353933681 +99000 ekin = 6.55139785883052 | erot = 10.7005188751583 | epot = -71.7085521285791 | etot = -54.4566353945903 +100000 ekin = 6.5281974472124 | erot = 11.2290265012449 | epot = -72.2138593444665 | etot = -54.4566353960093 +101000 ekin = 6.49377694354365 | erot = 11.7787444180737 | epot = -72.7291567591601 | etot = -54.4566353975427 +102000 ekin = 6.44645975182853 | erot = 12.3302092947493 | epot = -73.2333044456477 | etot = -54.4566353990699 +103000 ekin = 6.38599188040413 | erot = 12.8629861678438 | epot = -73.7056134486895 | etot = -54.4566354004416 +104000 ekin = 6.31389917689136 | erot = 13.3574827218768 | epot = -74.1280173002666 | etot = -54.4566354014985 +105000 ekin = 6.23372050746358 | erot = 13.796936503081 | epot = -74.487292412784 | etot = -54.4566354022394 +106000 ekin = 6.15161195850888 | erot = 14.1683082609525 | epot = -74.7765556218311 | etot = -54.4566354023697 +107000 ekin = 6.07599644252632 | erot = 14.4651582362854 | epot = -74.997790080969 | etot = -54.4566354021573 +108000 ekin = 6.01224980359702 | erot = 14.6879762973655 | epot = -75.1568615023399 | etot = -54.4566354013773 +109000 ekin = 5.96718055298296 | erot = 14.843530208706 | epot = -75.2673461618521 | etot = -54.4566354001632 +110000 ekin = 5.94906585806687 | erot = 14.943394624523 | epot = -75.3490958813013 | etot = -54.4566353987115 +111000 ekin = 5.96692254396536 | erot = 15.0017732632805 | epot = -75.4253312044823 | etot = -54.4566353972364 +112000 ekin = 6.02963894580617 | erot = 15.0332002745141 | epot = -75.5194746162447 | etot = -54.4566353959245 +113000 ekin = 6.14472749189804 | erot = 15.0506190089294 | epot = -75.6519818961805 | etot = -54.456635395353 +114000 ekin = 6.31294119125814 | erot = 15.0641400294533 | epot = -75.8337166157251 | etot = -54.4566353950137 +115000 ekin = 6.53170723497647 | erot = 15.0810976270009 | epot = -76.0694402570546 | etot = -54.4566353950772 +116000 ekin = 6.79565473868305 | erot = 15.1058873747017 | epot = -76.3581775089261 | etot = -54.4566353955414 +117000 ekin = 7.09589353296846 | erot = 15.1399747310391 | epot = -76.6925036604087 | etot = -54.4566353964011 +118000 ekin = 7.42010913176748 | erot = 15.1818878453232 | epot = -77.0586323747352 | etot = -54.4566353976445 +119000 ekin = 7.75291308545818 | erot = 15.2271156041078 | epot = -77.4366640887991 | etot = -54.4566353992331 +120000 ekin = 8.07655694001048 | erot = 15.2680755527854 | epot = -77.8012678938729 | etot = -54.456635401077 +121000 ekin = 8.3720928345245 | erot = 15.2944252034459 | epot = -78.1231534409883 | etot = -54.4566354030179 +122000 ekin = 8.62097203571297 | erot = 15.2939565964165 | epot = -78.3715640369595 | etot = -54.4566354048301 +123000 ekin = 8.80691805373792 | erot = 15.2541302313797 | epot = -78.5176836913799 | etot = -54.4566354062623 +124000 ekin = 8.91774775140796 | erot = 15.1640393169118 | epot = -78.5384224754126 | etot = -54.4566354070929 +125000 ekin = 8.94673865107553 | erot = 15.0163758445778 | epot = -78.4197499028398 | etot = -54.4566354071866 +126000 ekin = 8.89353504113502 | erot = 14.8103810343866 | epot = -78.1605514820973 | etot = -54.4566354065757 +127000 ekin = 8.76295715660881 | erot = 14.5505246086881 | epot = -77.7701171706755 | etot = -54.4566354053786 +128000 ekin = 8.56412338279188 | erot = 14.2447148868095 | epot = -77.2654736732318 | etot = -54.4566354036303 +129000 ekin = 8.30999977775227 | erot = 13.9056008475451 | epot = -76.6722360268316 | etot = -54.4566354015342 +130000 ekin = 8.01598983357864 | erot = 13.5489784634651 | epot = -76.0216036963415 | etot = -54.4566353992978 +131000 ekin = 7.69860752663272 | erot = 13.1919736282187 | epot = -75.3472165519605 | etot = -54.4566353971091 +132000 ekin = 7.37433696937962 | erot = 12.851299020498 | epot = -74.6822713849979 | etot = -54.4566353951203 +133000 ekin = 7.05872362614942 | erot = 12.5417941515438 | epot = -74.0571531711352 | etot = -54.4566353934419 +134000 ekin = 6.76570888199004 | erot = 12.2753542959287 | epot = -73.4976985700589 | etot = -54.4566353921402 +135000 ekin = 6.50719363731323 | erot = 12.0602549647537 | epot = -73.0240839933238 | etot = -54.4566353912568 +136000 ekin = 6.29279008475048 | erot = 11.9007669358439 | epot = -72.6501924113933 | etot = -54.456635390799 +137000 ekin = 6.12970978276592 | erot = 11.7970576302993 | epot = -72.3834028038277 | etot = -54.4566353907625 +138000 ekin = 6.02274351233308 | erot = 11.7455123962492 | epot = -72.2248912997151 | etot = -54.4566353911327 +139000 ekin = 5.97430404723539 | erot = 11.7390412107208 | epot = -72.169980649849 | etot = -54.4566353918928 +140000 ekin = 5.98449840319435 | erot = 11.766192115145 | epot = -72.2073259113389 | etot = -54.4566353929996 +141000 ekin = 6.05122402382894 | erot = 11.8123445028313 | epot = -72.3202039210585 | etot = -54.4566353943982 +142000 ekin = 6.17031735772885 | erot = 11.8604415111205 | epot = -72.4873942648603 | etot = -54.456635396011 +143000 ekin = 6.33577810129594 | erot = 11.8919671618443 | epot = -72.6843806606496 | etot = -54.4566353975093 +144000 ekin = 6.54009118321911 | erot = 11.8891339130619 | epot = -72.8858604955051 | etot = -54.4566353992241 +145000 ekin = 6.77465866642021 | erot = 11.8352952468168 | epot = -73.0665893139978 | etot = -54.4566354007608 +146000 ekin = 7.03032727827779 | erot = 11.7160091899335 | epot = -73.2029718703312 | etot = -54.4566354021199 +147000 ekin = 7.29660189209746 | erot = 11.5221059419082 | epot = -73.2753432368922 | etot = -54.4566354028866 +148000 ekin = 7.56407690493411 | erot = 11.2503448019254 | epot = -73.271057109966 | etot = -54.4566354031065 +149000 ekin = 7.82544292003312 | erot = 10.9039979828626 | epot = -73.1860763056627 | etot = -54.456635402767 +150000 ekin = 8.07517324147515 | erot = 10.4929858681088 | epot = -73.0247945114901 | etot = -54.4566354019061 +151000 ekin = 8.30975251519315 | erot = 10.0330103746804 | epot = -72.7993982905134 | etot = -54.4566354006398 +152000 ekin = 8.52766332329339 | erot = 9.54393934172104 | epot = -72.5282380641334 | etot = -54.456635399119 +153000 ekin = 8.72913641124975 | erot = 9.04783809539102 | epot = -72.2336099041502 | etot = -54.4566353975094 +154000 ekin = 8.91570927169019 | erot = 8.56693447900203 | epot = -71.9392791466633 | etot = -54.4566353959711 +155000 ekin = 9.08966068414541 | erot = 8.1217860763806 | epot = -71.668082155165 | etot = -54.456635394639 +156000 ekin = 9.25339893961263 | erot = 7.72982624258207 | epot = -71.4398605758096 | etot = -54.4566353936149 +157000 ekin = 9.40888952795367 | erot = 7.4043648312674 | epot = -71.2698897521792 | etot = -54.4566353929582 +158000 ekin = 9.55717923885758 | erot = 7.15403664791629 | epot = -71.1678512794919 | etot = -54.456635392718 +159000 ekin = 9.69792111012121 | erot = 6.98265633604506 | epot = -71.1372128390497 | etot = -54.4566353928835 +160000 ekin = 9.82919776336712 | erot = 6.88943769583961 | epot = -71.1752708526339 | etot = -54.4566353934271 +161000 ekin = 9.94745815557405 | erot = 6.86952397448919 | epot = -71.273617524353 | etot = -54.4566353942898 +162000 ekin = 10.0476105552149 | erot = 6.91481023380469 | epot = -71.419056184406 | etot = -54.4566353953863 +163000 ekin = 10.1232836123725 | erot = 7.01503930069418 | epot = -71.5949583096716 | etot = -54.4566353966049 +164000 ekin = 10.1672576282714 | erot = 7.15913239145027 | epot = -71.7830254175348 | etot = -54.4566353978131 +165000 ekin = 10.1720616886925 | erot = 7.33667115267616 | epot = -71.9653682402332 | etot = -54.4566353988645 +166000 ekin = 10.1307181898823 | erot = 7.53939136045619 | epot = -72.1267449499579 | etot = -54.4566353996194 +167000 ekin = 10.037590674084 | erot = 7.76248640952783 | epot = -72.2567124835707 | etot = -54.4566353999589 +168000 ekin = 9.88925393886035 | erot = 8.00550722627906 | epot = -72.3513965649497 | etot = -54.4566353998102 +169000 ekin = 9.68526445660093 | erot = 8.27264999921073 | epot = -72.4145498549769 | etot = -54.4566353991653 +170000 ekin = 9.42867794112066 | erot = 8.57229328100171 | epot = -72.457606620215 | etot = -54.4566353980927 +171000 ekin = 9.1261691081717 | erot = 8.91577619747958 | epot = -72.4985807023853 | etot = -54.456635396734 +172000 ekin = 8.78767440912551 | erot = 9.3155762089852 | epot = -72.5598860133929 | etot = -54.4566353952822 +173000 ekin = 8.43089026296227 | erot = 9.784044663189 | epot = -72.6715703175853 | etot = -54.456635391434 +174000 ekin = 8.08808636306041 | erot = 10.3303519242776 | epot = -72.8750736787362 | etot = -54.4566353913982 +175000 ekin = 7.76683289792949 | erot = 10.9528766887188 | epot = -73.176344978273 | etot = -54.4566353916247 +176000 ekin = 7.47165533674071 | erot = 11.6455953906595 | epot = -73.5738861195204 | etot = -54.4566353921202 +177000 ekin = 7.20644207982307 | erot = 12.3989755240444 | epot = -74.0620529967119 | etot = -54.4566353928445 +178000 ekin = 6.97426478507405 | erot = 13.2002588275732 | epot = -74.6311590065916 | etot = -54.4566353939443 +179000 ekin = 6.77739061781677 | erot = 14.034248956951 | epot = -75.2682749696775 | etot = -54.4566353949098 +180000 ekin = 6.61743414637963 | erot = 14.8862774181183 | epot = -75.9603469603592 | etot = -54.4566353958613 +181000 ekin = 6.49561144162575 | erot = 15.7407037445534 | epot = -76.6929505832078 | etot = -54.4566353970286 +182000 ekin = 6.41305807096253 | erot = 16.5823414720865 | epot = -77.452034940881 | etot = -54.456635397832 +183000 ekin = 6.37104675400798 | erot = 17.3988622631897 | epot = -78.2265444156999 | etot = -54.4566353985022 +184000 ekin = 6.37106698283396 | erot = 18.1794275278836 | epot = -79.0071299097841 | etot = -54.4566353990665 +185000 ekin = 6.41462378113729 | erot = 18.9143606927311 | epot = -79.7856198734746 | etot = -54.4566353996061 +186000 ekin = 6.50261133383612 | erot = 19.5944597960639 | epot = -80.553706530162 | etot = -54.456635400262 +187000 ekin = 6.63422049770768 | erot = 20.2099561332651 | epot = -81.3008120321887 | etot = -54.456635401216 +188000 ekin = 6.80553106495658 | erot = 20.7492823612688 | epot = -82.011448828868 | etot = -54.4566354026426 +189000 ekin = 7.00817768192241 | erot = 21.1980708186833 | epot = -82.6628839052214 | etot = -54.4566354046157 +190000 ekin = 7.22864796075561 | erot = 21.5390297894763 | epot = -83.2243131572599 | etot = -54.456635407028 +191000 ekin = 7.4476762261859 | erot = 21.7493732842279 | epot = -83.6536849211055 | etot = -54.4566354106917 +192000 ekin = 7.64121438364872 | erot = 21.8048177890289 | epot = -83.9026675850806 | etot = -54.456635412403 +193000 ekin = 7.78824892260277 | erot = 21.6992058928584 | epot = -83.9440902285507 | etot = -54.4566354130896 +194000 ekin = 7.87254337485953 | erot = 21.437602193847 | epot = -83.7667809811829 | etot = -54.4566354124764 +195000 ekin = 7.88497345911802 | erot = 21.0375935324412 | epot = -83.3792024018214 | etot = -54.4566354102622 +196000 ekin = 7.82453658224934 | erot = 20.5298119321333 | epot = -82.8109839217721 | etot = -54.4566354073895 +197000 ekin = 7.69767210841737 | erot = 19.950811734812 | epot = -82.1051192473219 | etot = -54.4566354040925 +198000 ekin = 7.51634139121972 | erot = 19.3371432855416 | epot = -81.3101200775087 | etot = -54.4566354007473 +199000 ekin = 7.29564803023246 | erot = 18.7233240020315 | epot = -80.4756074302738 | etot = -54.4566353980098 +200000 ekin = 7.05166010690275 | erot = 18.1350524779769 | epot = -79.6433479808032 | etot = -54.4566353959236 +201000 ekin = 6.79981173468412 | erot = 17.5880304600566 | epot = -78.8444775892884 | etot = -54.4566353945477 +202000 ekin = 6.55389933641319 | erot = 17.0888778993463 | epot = -78.0994126296062 | etot = -54.4566353938467 +203000 ekin = 6.32553919621424 | erot = 16.6360378263841 | epot = -77.4182124163399 | etot = -54.4566353937415 +204000 ekin = 6.12389632660782 | erot = 16.2211717958518 | epot = -76.8017035165952 | etot = -54.4566353941356 +205000 ekin = 5.95555200640684 | erot = 15.8307416505757 | epot = -76.2429290519083 | etot = -54.4566353949257 +206000 ekin = 5.82446904491528 | erot = 15.4476864597769 | epot = -75.728790900684 | etot = -54.4566353959918 +207000 ekin = 5.73208912867381 | erot = 15.0532400346077 | epot = -75.2419645604683 | etot = -54.4566353971868 +208000 ekin = 5.67762302906544 | erot = 14.6289641823349 | epot = -74.7632226097329 | etot = -54.4566353983326 +209000 ekin = 5.65855387682248 | erot = 14.1589879691241 | epot = -74.2741772451826 | etot = -54.456635399236 +210000 ekin = 5.67127672991778 | erot = 13.6322671582832 | epot = -73.760179287929 | etot = -54.456635399728 +211000 ekin = 5.71170069345543 | erot = 13.0444908839498 | epot = -73.2128269771126 | etot = -54.4566353997073 +212000 ekin = 5.77562712093054 | erot = 12.3991887587355 | epot = -72.6314512788375 | etot = -54.4566353991715 +213000 ekin = 5.85883014811436 | erot = 11.7077170437825 | epot = -72.0231825901079 | etot = -54.4566353982111 +214000 ekin = 5.95693715945814 | erot = 10.9880856586548 | epot = -71.4016582150883 | etot = -54.4566353969753 +215000 ekin = 6.06530009270476 | erot = 10.2628764798238 | epot = -70.7848119681625 | etot = -54.456635395634 +216000 ekin = 6.17899119914079 | erot = 9.5566641239572 | epot = -70.1922907174491 | etot = -54.4566353943512 +217000 ekin = 6.29291855291775 | erot = 8.89336715125394 | epot = -69.6429210974408 | etot = -54.4566353932691 +218000 ekin = 6.40196857726172 | erot = 8.2938959967619 | epot = -69.1524999665194 | etot = -54.4566353924958 +219000 ekin = 6.501101734084 | erot = 7.77437623954234 | epot = -68.73211336572 | etot = -54.4566353920937 +220000 ekin = 6.58540342133204 | erot = 7.34511996776021 | epot = -68.3871587811666 | etot = -54.4566353920744 +221000 ekin = 6.65014690325988 | erot = 7.01039395844519 | epot = -68.1171762541006 | etot = -54.4566353923955 +222000 ekin = 6.69092576193491 | erot = 6.76891043700687 | epot = -67.9164715919178 | etot = -54.456635392976 +223000 ekin = 6.70387621885061 | erot = 6.61487073126159 | epot = -67.7753823438195 | etot = -54.4566353937073 +224000 ekin = 6.6859658221951 | erot = 6.53933741261943 | epot = -67.6819386292903 | etot = -54.4566353944758 +225000 ekin = 6.63529509868586 | erot = 6.53169516027613 | epot = -67.6236256540918 | etot = -54.4566353951298 +226000 ekin = 6.55134622983753 | erot = 6.58124861354915 | epot = -67.5892302390907 | etot = -54.456635395704 +227000 ekin = 6.4351258237356 | erot = 6.67786339098986 | epot = -67.5696246108199 | etot = -54.4566353960945 +228000 ekin = 6.2891982597207 | erot = 6.81242105498861 | epot = -67.5582547110039 | etot = -54.4566353962946 +229000 ekin = 6.11758034387043 | erot = 6.9773732234486 | epot = -67.551588963642 | etot = -54.4566353963229 +230000 ekin = 5.92553219663407 | erot = 7.16667727721339 | epot = -67.5488448700583 | etot = -54.4566353962108 +231000 ekin = 5.71928874368935 | erot = 7.37558258297045 | epot = -67.5515067226471 | etot = -54.4566353959873 +232000 ekin = 5.50576904745257 | erot = 7.60029005185209 | epot = -67.5626944950116 | etot = -54.4566353957069 +233000 ekin = 5.29228522017016 | erot = 7.83763848257012 | epot = -67.5865590981282 | etot = -54.456635395388 +234000 ekin = 5.08626778915252 | erot = 8.08497235755395 | epot = -67.6278755417667 | etot = -54.4566353950602 +235000 ekin = 4.89496149390852 | erot = 8.33993380345567 | epot = -67.6915306921206 | etot = -54.4566353947564 +236000 ekin = 4.72510766288859 | erot = 8.60023942151853 | epot = -67.7819824789156 | etot = -54.4566353945085 +237000 ekin = 4.58266891059355 | erot = 8.86352045028253 | epot = -67.9028247552247 | etot = -54.4566353943486 +238000 ekin = 4.4725435285652 | erot = 9.12714914792106 | epot = -68.0563280707871 | etot = -54.4566353943009 +239000 ekin = 4.39832589608195 | erot = 9.38815494537151 | epot = -68.2431162358287 | etot = -54.4566353943752 +240000 ekin = 4.36214482372901 | erot = 9.64329675760364 | epot = -68.4620769758926 | etot = -54.45663539456 +241000 ekin = 4.36460414736138 | erot = 9.88932905774764 | epot = -68.7105685999319 | etot = -54.4566353948228 +242000 ekin = 4.40483557566148 | erot = 10.1234012790534 | epot = -68.9848722498409 | etot = -54.456635395126 +243000 ekin = 4.4806558711343 | erot = 10.3436288280303 | epot = -69.2809200945631 | etot = -54.4566353953985 +244000 ekin = 4.58880538052901 | erot = 10.5497091929712 | epot = -69.5951499691031 | etot = -54.456635395603 +245000 ekin = 4.72523059106174 | erot = 10.7433050692489 | epot = -69.9251710560126 | etot = -54.4566353957019 +246000 ekin = 4.88536596035982 | erot = 10.9281953102969 | epot = -70.2701966663511 | etot = -54.4566353956944 +247000 ekin = 5.06437032892696 | erot = 11.1100753168562 | epot = -70.631081041388 | etot = -54.4566353956048 +248000 ekin = 5.25728039314947 | erot = 11.295977903806 | epot = -71.0098936924454 | etot = -54.45663539549 +249000 ekin = 5.4590578306862 | erot = 11.493349888506 | epot = -71.4090431146249 | etot = -54.4566353954327 +250000 ekin = 5.66452726893982 | erot = 11.7088807610528 | epot = -71.8300434255207 | etot = -54.4566353955281 +251000 ekin = 5.86822964772049 | erot = 11.9472357725923 | epot = -72.2721008161799 | etot = -54.4566353958671 +252000 ekin = 6.06424926084244 | erot = 12.2098996244403 | epot = -72.7307842817972 | etot = -54.4566353965145 +253000 ekin = 6.24611969949034 | erot = 12.4943889560497 | epot = -73.1971440530269 | etot = -54.4566353974869 +254000 ekin = 6.40686577704143 | erot = 12.7940520504554 | epot = -73.6575532262011 | etot = -54.4566353987043 +255000 ekin = 6.53934545678203 | erot = 13.0988013252464 | epot = -74.094782182033 | etot = -54.4566354000046 +256000 ekin = 6.63702718994409 | erot = 13.3967890648217 | epot = -74.4904516559556 | etot = -54.4566354011898 +257000 ekin = 6.69481406277285 | erot = 13.6763952361342 | epot = -74.8278447009679 | etot = -54.4566354020609 +258000 ekin = 6.70987363015829 | erot = 13.9283274305686 | epot = -75.0948364631864 | etot = -54.4566354024595 +259000 ekin = 6.68224111902752 | erot = 14.1473011903223 | epot = -75.2861777116964 | etot = -54.4566354023465 +260000 ekin = 6.6149121085367 | erot = 14.332625913678 | epot = -75.4041734240278 | etot = -54.4566354018132 +261000 ekin = 6.51341628163392 | erot = 14.487436852557 | epot = -75.4574885351744 | etot = -54.4566354009835 +262000 ekin = 6.38501100285228 | erot = 14.6175606151421 | epot = -75.4592070180357 | etot = -54.4566354000413 +263000 ekin = 6.23771961613781 | erot = 14.7299444235393 | epot = -75.4242994388476 | etot = -54.4566353991704 +264000 ekin = 6.07941608333323 | erot = 14.8311371615553 | epot = -75.3671886433762 | etot = -54.4566353984877 +265000 ekin = 5.91710326790354 | erot = 14.9261997269373 | epot = -75.2999383929177 | etot = -54.4566353980769 +266000 ekin = 5.75646622878376 | erot = 15.0179796909013 | epot = -75.2310813176621 | etot = -54.456635397977 +267000 ekin = 5.60176709254105 | erot = 15.1066567649974 | epot = -75.1650592557177 | etot = -54.4566353981793 +268000 ekin = 5.45614222906157 | erot = 15.1896161580118 | epot = -75.1023937856842 | etot = -54.4566353986109 +269000 ekin = 5.32233940193233 | erot = 15.2616013239948 | epot = -75.0405761254044 | etot = -54.4566353994772 +270000 ekin = 5.20386526321353 | erot = 15.3134126784878 | epot = -74.9739133416008 | etot = -54.4566353998994 +271000 ekin = 5.10636511575788 | erot = 15.3371670926565 | epot = -74.9001676083405 | etot = -54.4566353999261 +272000 ekin = 5.0388326775387 | erot = 15.3275595144047 | epot = -74.8230275914564 | etot = -54.456635399513 +273000 ekin = 5.0140854035876 | erot = 15.2821242951824 | epot = -74.7528450973405 | etot = -54.4566353985705 +274000 ekin = 5.04781979148567 | erot = 15.2024861316973 | epot = -74.706941320485 | etot = -54.4566353973021 +275000 ekin = 5.15587366097644 | erot = 15.0944379866226 | epot = -74.7069470435752 | etot = -54.4566353959761 +276000 ekin = 5.35005421474597 | erot = 14.9659067954337 | epot = -74.7725964054856 | etot = -54.4566353953059 +277000 ekin = 5.63375697520818 | erot = 14.8238362815561 | epot = -74.9142286522922 | etot = -54.4566353955279 +278000 ekin = 5.99906841358956 | erot = 14.6726954109915 | epot = -75.1283992213069 | etot = -54.4566353967258 +279000 ekin = 6.42677541448279 | erot = 14.5136733620326 | epot = -75.3970841751134 | etot = -54.456635398598 +280000 ekin = 6.88949881397129 | erot = 14.345769085061 | epot = -75.6919032996845 | etot = -54.4566354006523 +281000 ekin = 7.35667779023604 | erot = 14.1678579049855 | epot = -75.9811710982522 | etot = -54.4566354030307 +282000 ekin = 7.7988383699336 | erot = 13.978315493388 | epot = -76.2337892675015 | etot = -54.4566354041799 +283000 ekin = 8.19321965983599 | erot = 13.7803017892219 | epot = -76.4301568534981 | etot = -54.4566354044402 +284000 ekin = 8.52580258151957 | erot = 13.5821927274793 | epot = -76.5646307128652 | etot = -54.4566354038664 +285000 ekin = 8.79108509960268 | erot = 13.3960919484868 | epot = -76.6438124507651 | etot = -54.4566354026756 +286000 ekin = 8.99063008546389 | erot = 13.2361528285341 | epot = -76.6834183151734 | etot = -54.4566354011754 +287000 ekin = 9.13077921529927 | erot = 13.1164348721742 | epot = -76.7038494871529 | etot = -54.4566353996795 +288000 ekin = 9.22018153921315 | erot = 13.0487287839825 | epot = -76.7255457216534 | etot = -54.4566353984578 +289000 ekin = 9.26763004982475 | erot = 13.0407273170656 | epot = -76.7649927645839 | etot = -54.4566353976935 +290000 ekin = 9.28050533355268 | erot = 13.0948336925554 | epot = -76.831974423572 | etot = -54.4566353974639 +291000 ekin = 9.26393617617883 | erot = 13.2077741770254 | epot = -76.9283457509546 | etot = -54.4566353977503 +292000 ekin = 9.2206269689545 | erot = 13.3710137562633 | epot = -77.0482761236731 | etot = -54.4566353984553 +293000 ekin = 9.15118773751851 | erot = 13.5717951426576 | epot = -77.1796182796211 | etot = -54.456635399445 +294000 ekin = 9.05474970264902 | erot = 13.7942987417148 | epot = -77.3056838449873 | etot = -54.4566354006235 +295000 ekin = 8.9296668264409 | erot = 14.0208093015791 | epot = -77.4071115298294 | etot = -54.4566354018094 +296000 ekin = 8.77417741279813 | erot = 14.2335710238213 | epot = -77.4643838395581 | etot = -54.4566354029387 +297000 ekin = 8.58698226598745 | erot = 14.4154370340251 | epot = -77.4590547039454 | etot = -54.4566354039329 +298000 ekin = 8.36775865344672 | erot = 14.55062084961 | epot = -77.37501490777 | etot = -54.4566354047133 +299000 ekin = 8.11762616774734 | erot = 14.6254987182077 | epot = -77.199760291155 | etot = -54.4566354051999 +300000 ekin = 7.83954023620377 | erot = 14.6294629242875 | epot = -76.9256385658109 | etot = -54.4566354053197 +301000 ekin = 7.53854212204226 | erot = 14.5557510868017 | epot = -76.550928613871 | etot = -54.456635405027 +302000 ekin = 7.22177736042507 | erot = 14.4020878566535 | epot = -76.0805006213951 | etot = -54.4566354043166 +303000 ekin = 6.89822321248575 | erot = 14.1709638782381 | epot = -75.52582249396 | etot = -54.4566354032361 +304000 ekin = 6.5781308385865 | erot = 13.8694446267246 | epot = -74.9042108671869 | etot = -54.4566354018759 +305000 ekin = 6.27226349854811 | erot = 13.5085175341625 | epot = -74.2374164330635 | etot = -54.4566354003529 +306000 ekin = 5.99106804508657 | erot = 13.1021011111668 | epot = -73.5498045550402 | etot = -54.4566353987867 +307000 ekin = 5.74393176217499 | erot = 12.6659083209208 | epot = -72.8664754803767 | etot = -54.4566353972809 +308000 ekin = 5.53864569893549 | erot = 12.2163535665898 | epot = -72.2116346614312 | etot = -54.4566353959058 +309000 ekin = 5.38113513069954 | erot = 11.7694200620394 | epot = -71.6071905875296 | etot = -54.4566353947906 +310000 ekin = 5.27545873877812 | erot = 11.3397497111531 | epot = -71.071843843725 | etot = -54.4566353937938 +311000 ekin = 5.22395041073517 | erot = 10.9408344797234 | epot = -70.62142028347 | etot = -54.4566353930114 +312000 ekin = 5.22743903848079 | erot = 10.5841016940056 | epot = -70.2681761249511 | etot = -54.4566353924647 +313000 ekin = 5.28546710256986 | erot = 10.2783241765405 | epot = -70.0204266712983 | etot = -54.456635392188 +314000 ekin = 5.39643142780591 | erot = 10.0290048888967 | epot = -69.8820717089291 | etot = -54.4566353922265 +315000 ekin = 5.55762409515217 | erot = 9.83776650485558 | epot = -69.8520259926288 | etot = -54.4566353926211 +316000 ekin = 5.7651953236205 | erot = 9.70186120841432 | epot = -69.9236919254333 | etot = -54.4566353933985 +317000 ekin = 6.01409543293256 | erot = 9.61396213872118 | epot = -70.0846929662035 | etot = -54.4566353945497 +318000 ekin = 6.29807297065279 | erot = 9.56241760985219 | epot = -70.3171259765194 | etot = -54.4566353960145 +319000 ekin = 6.60980622313929 | erot = 9.53213013022109 | epot = -70.5985717510326 | etot = -54.4566353976722 +320000 ekin = 6.94122281959915 | erot = 9.50614507367891 | epot = -70.9040032926207 | etot = -54.4566353993426 +321000 ekin = 7.28401648903199 | erot = 9.46788297195665 | epot = -71.2085348617973 | etot = -54.4566354008087 +322000 ekin = 7.63030660902592 | erot = 9.40373715746107 | epot = -71.4906791683431 | etot = -54.4566354018561 +323000 ekin = 7.97332122461047 | erot = 9.30554772849627 | epot = -71.7355043554335 | etot = -54.4566354023268 +324000 ekin = 8.30794457963584 | erot = 9.17235846963436 | epot = -71.936938451434 | etot = -54.4566354021638 +325000 ekin = 8.63098140949411 | erot = 9.01095664414776 | epot = -72.09857345507 | etot = -54.4566354014281 +326000 ekin = 8.94105719146425 | erot = 8.83498929957085 | epot = -72.2326818913245 | etot = -54.4566354002894 +327000 ekin = 9.23817100548276 | erot = 8.66283136635856 | epot = -72.357637770827 | etot = -54.4566353989857 +328000 ekin = 9.52300348811115 | erot = 8.51468348398446 | epot = -72.4943223698665 | etot = -54.4566353977709 +329000 ekin = 9.79612481313189 | erot = 8.40948710595479 | epot = -72.6622473159623 | etot = -54.4566353968756 +330000 ekin = 10.0572432527148 | erot = 8.3621635183362 | epot = -72.876042167527 | etot = -54.456635396476 +331000 ekin = 10.3046041371606 | erot = 8.38150606119792 | epot = -73.1427455950411 | etot = -54.4566353966826 +332000 ekin = 10.5346182384475 | erot = 8.46889046679882 | epot = -73.4601441027738 | etot = -54.4566353975274 +333000 ekin = 10.7417838215547 | erot = 8.6178796365307 | epot = -73.8162988570423 | etot = -54.456635398957 +334000 ekin = 10.9189661695274 | erot = 8.81478419867182 | epot = -74.1903857690225 | etot = -54.4566354008232 +335000 ekin = 11.0580923139719 | erot = 9.04024450356191 | epot = -74.5549722204147 | etot = -54.4566354028809 +336000 ekin = 11.1512758054888 | erot = 9.27184425622038 | epot = -74.8797554665068 | etot = -54.4566354047977 +337000 ekin = 11.1922834106664 | erot = 9.4875878809539 | epot = -75.1365066978262 | etot = -54.4566354062058 +338000 ekin = 11.1781049966213 | erot = 9.66977867523749 | epot = -75.3045190786353 | etot = -54.4566354067765 +339000 ekin = 11.1102530741368 | erot = 9.80853289682485 | epot = -75.3754213772729 | etot = -54.4566354063113 +340000 ekin = 10.9953916139881 | erot = 9.90404205087346 | epot = -75.3560690696715 | etot = -54.4566354048099 +341000 ekin = 10.8450335653229 | erot = 9.96690251907219 | epot = -75.2685714868729 | etot = -54.4566354024778 +342000 ekin = 10.6743190321432 | erot = 10.0163513348956 | epot = -75.1473057667146 | etot = -54.4566353996758 +343000 ekin = 10.5001667181566 | erot = 10.0768603504166 | epot = -75.0336624653962 | etot = -54.456635396823 +344000 ekin = 10.3392423699684 | erot = 10.1739542078124 | epot = -74.9698319720935 | etot = -54.4566353943128 +345000 ekin = 10.2061520845131 | erot = 10.3301605012967 | epot = -74.9929479782567 | etot = -54.4566353924469 +346000 ekin = 10.112097481436 | erot = 10.5617272299143 | epot = -75.1304601027748 | etot = -54.4566353914245 +347000 ekin = 10.0640336630371 | erot = 10.8763584969724 | epot = -75.3970275513622 | etot = -54.4566353913527 +348000 ekin = 10.0642411405202 | erot = 11.2719278614765 | epot = -75.7928043942647 | etot = -54.456635392268 +349000 ekin = 10.1101933212711 | erot = 11.7360295300931 | epot = -76.3028582455133 | etot = -54.4566353941491 +350000 ekin = 10.1946552474078 | erot = 12.2463088365544 | epot = -76.8975994808607 | etot = -54.4566353968986 +351000 ekin = 10.3060455438612 | erot = 12.7716910290036 | epot = -77.5343719731905 | etot = -54.4566354003258 +352000 ekin = 10.4291816280477 | erot = 13.2747779707961 | epot = -78.160595002948 | etot = -54.4566354041043 +353000 ekin = 10.5465535663563 | erot = 13.7156648337593 | epot = -78.718853807883 | etot = -54.4566354077673 +354000 ekin = 10.6401856668622 | erot = 14.0571283974538 | epot = -79.1539494750778 | etot = -54.4566354107618 +355000 ekin = 10.6939351373338 | erot = 14.270558563148 | epot = -79.4211291130393 | etot = -54.4566354125575 +356000 ekin = 10.6958108467991 | erot = 14.341360446691 | epot = -79.4938067062953 | etot = -54.4566354128053 +357000 ekin = 10.6397218282593 | erot = 14.272243304566 | epot = -79.368600544282 | etot = -54.4566354114567 +358000 ekin = 10.5263737986286 | erot = 14.0832351439846 | epot = -79.0662443502896 | etot = -54.4566354076763 +359000 ekin = 10.3671285162307 | erot = 13.8092183812934 | epot = -78.6329823019441 | etot = -54.45663540442 +360000 ekin = 10.1731657793225 | erot = 13.4915210097263 | epot = -78.1213221900204 | etot = -54.4566354009716 +361000 ekin = 9.95567993139114 | erot = 13.1714056563755 | epot = -77.5837209856629 | etot = -54.4566353978963 +362000 ekin = 9.72639985071578 | erot = 12.8842804433156 | epot = -77.0673156896208 | etot = -54.4566353955895 +363000 ekin = 9.49607796369864 | erot = 12.6551764253562 | epot = -76.6078897832988 | etot = -54.456635394244 +364000 ekin = 9.2736082263338 | erot = 12.4965538445883 | epot = -76.2267974647922 | etot = -54.4566353938701 +365000 ekin = 9.06568784346758 | erot = 12.4083291366491 | epot = -75.9306523744547 | etot = -54.456635394338 +366000 ekin = 8.87683460603723 | erot = 12.379697418538 | epot = -75.7131674200002 | etot = -54.456635395425 +367000 ekin = 8.70961671148385 | erot = 12.392180649522 | epot = -75.5584327578792 | etot = -54.4566353968734 +368000 ekin = 8.56493490850803 | erot = 12.4232160321931 | epot = -75.4447863391433 | etot = -54.4566353984421 +369000 ekin = 8.44226817634411 | erot = 12.4495921416395 | epot = -75.3484957179267 | etot = -54.456635399943 +370000 ekin = 8.33986053924071 | erot = 12.4501922874661 | epot = -75.2466882279597 | etot = -54.4566354012529 +371000 ekin = 8.25489807014507 | erot = 12.4078154254107 | epot = -75.1193488978471 | etot = -54.4566354022914 +372000 ekin = 8.18376802476647 | erot = 12.3101908679608 | epot = -74.9505942957248 | etot = -54.4566354029975 +373000 ekin = 8.1224708952445 | erot = 12.1505028141953 | epot = -74.7296091127495 | etot = -54.4566354033097 +374000 ekin = 8.06687702985228 | erot = 11.9274297055073 | epot = -74.450942138676 | etot = -54.4566354033165 +375000 ekin = 8.01360538997109 | erot = 11.6454303016277 | epot = -74.1156710942663 | etot = -54.4566354026676 +376000 ekin = 7.96102274026872 | erot = 11.3151262124845 | epot = -73.7327843543605 | etot = -54.4566354016074 +377000 ekin = 7.90863816659382 | erot = 10.9518631003588 | epot = -73.3171366672208 | etot = -54.4566354002681 +378000 ekin = 7.85683990183601 | erot = 10.5740091031979 | epot = -72.8874844038688 | etot = -54.4566353988349 +379000 ekin = 7.80642061178984 | erot = 10.2007165018131 | epot = -72.463772511112 | etot = -54.4566353975091 +380000 ekin = 7.7581115274382 | erot = 9.84961398660417 | epot = -72.0643609104773 | etot = -54.4566353964349 +381000 ekin = 7.71654925828585 | erot = 9.53814492421914 | epot = -71.7113295774989 | etot = -54.4566353949939 +382000 ekin = 7.68451239863845 | erot = 9.27843266615522 | epot = -71.4195804598393 | etot = -54.4566353950456 +383000 ekin = 7.65796830191401 | erot = 9.07311806362067 | epot = -71.1877217606715 | etot = -54.4566353951369 +384000 ekin = 7.63469818489975 | erot = 8.92246566923003 | epot = -71.0137992492276 | etot = -54.4566353950979 +385000 ekin = 7.6150389104547 | erot = 8.82614106516781 | epot = -70.8978153704587 | etot = -54.4566353948362 +386000 ekin = 7.60197533239001 | erot = 8.78441775442625 | epot = -70.8430284811969 | etot = -54.4566353943807 +387000 ekin = 7.60049226511034 | erot = 8.79836488560037 | epot = -70.8554925445894 | etot = -54.4566353938787 +388000 ekin = 7.6162903289944 | erot = 8.86890236975378 | epot = -70.9418280923102 | etot = -54.456635393562 +389000 ekin = 7.65416483435022 | erot = 8.99501957468683 | epot = -71.1058198027096 | etot = -54.4566353936725 +390000 ekin = 7.71643785888768 | erot = 9.17173992639764 | epot = -71.3448131796951 | etot = -54.4566353944097 +391000 ekin = 7.80181238366844 | erot = 9.38839302764512 | epot = -71.6468408071612 | etot = -54.4566353958476 +392000 ekin = 7.90489923332377 | erot = 9.62796379831973 | epot = -71.9894984295669 | etot = -54.4566353979234 +393000 ekin = 8.01655002691925 | erot = 9.86772713455431 | epot = -72.3409125619008 | etot = -54.4566354004272 +394000 ekin = 8.12497584792015 | erot = 10.0812703662968 | epot = -72.662881617248 | etot = -54.456635403031 +395000 ekin = 8.21747162081394 | erot = 10.241653382354 | epot = -72.9157604085161 | etot = -54.4566354053482 +396000 ekin = 8.28243832247632 | erot = 10.3253672880888 | epot = -73.0644410175198 | etot = -54.4566354069548 +397000 ekin = 8.31132698802282 | erot = 10.3159962168349 | epot = -73.0839586125433 | etot = -54.4566354076855 +398000 ekin = 8.30014555011308 | erot = 10.206120512034 | epot = -72.9629014694189 | etot = -54.4566354072718 +399000 ekin = 8.25023667086019 | erot = 9.99952429135689 | epot = -72.7063963681449 | etot = -54.4566354059278 +400000 ekin = 8.16818663672813 | erot = 9.70984792288031 | epot = -72.3346699633645 | etot = -54.4566354037561 +401000 ekin = 8.06443767762248 | erot = 9.35851558616598 | epot = -71.8795886650967 | etot = -54.4566354013083 +402000 ekin = 7.95182608081287 | erot = 8.9722073920163 | epot = -71.3806688712303 | etot = -54.4566353984011 +403000 ekin = 7.84544588741245 | erot = 8.57990607062952 | epot = -70.8819873536865 | etot = -54.4566353956445 +404000 ekin = 7.75991092032929 | erot = 8.20916918183379 | epot = -70.4257154955299 | etot = -54.4566353933669 +405000 ekin = 7.70721158903879 | erot = 7.88394698603192 | epot = -70.0477939666144 | etot = -54.4566353915437 +406000 ekin = 7.69666260474535 | erot = 7.62282033660977 | epot = -69.7761183316777 | etot = -54.4566353903226 +407000 ekin = 7.73500402089687 | erot = 7.43821712170657 | epot = -69.6298565323343 | etot = -54.4566353897309 +408000 ekin = 7.82558122096966 | erot = 7.33626935412315 | epot = -69.6184859648506 | etot = -54.4566353897578 +409000 ekin = 7.96830915347866 | erot = 7.31687210469422 | epot = -69.7418166485639 | etot = -54.456635390391 +410000 ekin = 8.15969424373099 | erot = 7.3738695108638 | epot = -69.9901991462061 | etot = -54.4566353916113 +411000 ekin = 8.39287612484498 | erot = 7.49540270153733 | epot = -70.3449142197579 | etot = -54.4566353933756 +412000 ekin = 8.65774455619398 | erot = 7.66457893931641 | epot = -70.7789588911007 | etot = -54.4566353955903 +413000 ekin = 8.94129116530218 | erot = 7.86068273350839 | epot = -71.2586092968941 | etot = -54.4566353980836 +414000 ekin = 9.22842184777127 | erot = 8.06113294632768 | epot = -71.7461901946777 | etot = -54.4566354005787 +415000 ekin = 9.50339868560924 | erot = 8.24420492650335 | epot = -72.2042390148381 | etot = -54.4566354027255 +416000 ekin = 9.75183806738226 | erot = 8.39218393331359 | epot = -72.6006574048759 | etot = -54.45663540418 +417000 ekin = 9.96283208275691 | erot = 8.49422554923971 | epot = -72.9136930367139 | etot = -54.4566354047173 +418000 ekin = 10.130516732358 | erot = 8.54790138251502 | epot = -73.1350535191802 | etot = -54.4566354043071 +419000 ekin = 10.2545191073004 | erot = 8.5593205556536 | epot = -73.2704750660785 | etot = -54.4566354031245 +420000 ekin = 10.3391601305823 | erot = 8.5414769979339 | epot = -73.3372725299922 | etot = -54.456635401476 +421000 ekin = 10.391784764309 | erot = 8.51147867525926 | epot = -73.3598988392523 | etot = -54.456635399684 +422000 ekin = 10.4208099208889 | erot = 8.48775966217129 | epot = -73.365204981078 | etot = -54.4566353980178 +423000 ekin = 10.4339704342051 | erot = 8.48766818013271 | epot = -73.3782740110675 | etot = -54.4566353967297 +424000 ekin = 10.4369827822084 | erot = 8.52566990469808 | epot = -73.4192880827323 | etot = -54.4566353958258 +425000 ekin = 10.4323601115178 | erot = 8.61251346627881 | epot = -73.5015091924256 | etot = -54.456635614629 +426000 ekin = 10.1026717198712 | erot = 8.31096137629846 | epot = -72.8702682878989 | etot = -54.4566351917292 +427000 ekin = 10.5734553943522 | erot = 8.79632347543036 | epot = -73.8264144771538 | etot = -54.4566356073712 +428000 ekin = 10.6072422295352 | erot = 9.02803563914449 | epot = -74.0919131525303 | etot = -54.4566352838506 +429000 ekin = 10.5962603681818 | erot = 9.29488255868299 | epot = -74.347778212505 | etot = -54.4566352856402 +430000 ekin = 10.5389594927114 | erot = 9.58934591829726 | epot = -74.5849406986405 | etot = -54.4566352876318 +431000 ekin = 10.424595394277 | erot = 9.89238704682332 | epot = -74.7736177306447 | etot = -54.4566352895443 +432000 ekin = 10.2456968864566 | erot = 10.1829761184419 | epot = -74.8853082959501 | etot = -54.4566352910516 +433000 ekin = 10.0003056146311 | erot = 10.4407089711168 | epot = -74.8976498775916 | etot = -54.4566352918438 +434000 ekin = 9.69371342949066 | erot = 10.648626947292 | epot = -74.7989756684902 | etot = -54.4566352917075 +435000 ekin = 9.33916315685989 | erot = 10.7956251646138 | epot = -74.5914236120725 | etot = -54.4566352905987 +436000 ekin = 8.95712875743166 | erot = 10.8778397412559 | epot = -74.2916037873533 | etot = -54.4566352886657 +437000 ekin = 8.57313769393628 | erot = 10.8986617406378 | epot = -73.9284347207922 | etot = -54.4566352862182 +438000 ekin = 8.21453260377098 | erot = 10.8674634356788 | epot = -73.5386313230889 | etot = -54.4566352836392 +439000 ekin = 7.90690315351739 | erot = 10.7975428309118 | epot = -73.1610812657131 | etot = -54.4566352812839 +440000 ekin = 7.67099505628251 | erot = 10.7039809990729 | epot = -72.8316113347452 | etot = -54.4566352793899 +441000 ekin = 7.52069557968947 | erot = 10.6019760377327 | epot = -72.5793068954808 | etot = -54.4566352780587 +442000 ekin = 7.46231680922884 | erot = 10.5058607974092 | epot = -72.4248128839175 | etot = -54.4566352772794 +443000 ekin = 7.49502555661017 | erot = 10.4286364553068 | epot = -72.3802972888983 | etot = -54.4566352769813 +444000 ekin = 7.61203666089557 | erot = 10.381643930758 | epot = -72.4503158687433 | etot = -54.4566352770898 +445000 ekin = 7.80213707906935 | erot = 10.374019103461 | epot = -72.6327914600942 | etot = -54.4566352775638 +446000 ekin = 8.05120889605804 | erot = 10.4117932601404 | epot = -72.9196374345776 | etot = -54.4566352783792 +447000 ekin = 8.34362619155747 | erot = 10.4967971423168 | epot = -73.2970586134505 | etot = -54.4566352795762 +448000 ekin = 8.66322518431604 | erot = 10.6255592268189 | epot = -73.7454196922454 | etot = -54.4566352811105 +449000 ekin = 8.99429132590707 | erot = 10.7888572754563 | epot = -74.2397838842746 | etot = -54.4566352829112 +450000 ekin = 9.32243048438082 | erot = 10.9721164674713 | epot = -74.7511822366964 | etot = -54.4566352848442 +451000 ekin = 9.63533692190787 | erot = 11.1567560020506 | epot = -75.2487282106882 | etot = -54.4566352867298 +452000 ekin = 9.92346130382689 | erot = 11.3223196777218 | epot = -75.7024162699088 | etot = -54.4566352883602 +453000 ekin = 10.1805259141588 | erot = 11.449016949531 | epot = -76.0861781532617 | etot = -54.4566352895719 +454000 ekin = 10.4037354723037 | erot = 11.5200589234746 | epot = -76.3804296860463 | etot = -54.456635290268 +455000 ekin = 10.5935831355421 | erot = 11.5233067080478 | epot = -76.5735251340364 | etot = -54.4566352904466 +456000 ekin = 10.753221260939 | erot = 11.4519763299534 | epot = -76.6618328810834 | etot = -54.456635290191 +457000 ekin = 10.8874570866295 | erot = 11.3044410662084 | epot = -76.6485334424738 | etot = -54.456635289636 +458000 ekin = 11.0015355382807 | erot = 11.0834241212083 | epot = -76.5415949484287 | etot = -54.4566352889397 +459000 ekin = 11.0999318012878 | erot = 10.7949138906107 | epot = -76.351480980127 | etot = -54.4566352882285 +460000 ekin = 11.1853777396665 | erot = 10.44712866202 | epot = -76.0891416892873 | etot = -54.4566352876008 +461000 ekin = 11.2582313403146 | erot = 10.0496701056132 | epot = -75.7645367330272 | etot = -54.4566352870993 +462000 ekin = 11.3163274976827 | erot = 9.61299797023314 | epot = -75.3859607546339 | etot = -54.4566352867181 +463000 ekin = 11.3552632497994 | erot = 9.14812026271289 | epot = -74.9600187989476 | etot = -54.4566352864354 +464000 ekin = 11.3690273085602 | erot = 8.66637468807853 | epot = -74.492037282831 | etot = -54.4566352861923 +465000 ekin = 11.3509265610579 | erot = 8.17938417024641 | epot = -73.9869460172111 | etot = -54.4566352859068 +466000 ekin = 11.2946971057464 | erot = 7.69907577472996 | epot = -73.450408166005 | etot = -54.4566352855287 +467000 ekin = 11.1955035374672 | erot = 7.23752069346408 | epot = -72.8896595159555 | etot = -54.4566352850242 +468000 ekin = 11.050822539512 | erot = 6.80654240242868 | epot = -72.3140002263315 | etot = -54.4566352843908 +469000 ekin = 10.8611440667107 | erot = 6.41707429380236 | epot = -71.7348536441621 | etot = -54.456635283649 +470000 ekin = 10.6304433621371 | erot = 6.07835039051434 | epot = -71.1654290354842 | etot = -54.4566352828328 +471000 ekin = 10.3664443931406 | erot = 5.79710085709296 | epot = -70.620180532205 | etot = -54.4566352819714 +472000 ekin = 10.080647886048 | erot = 5.57696288908153 | epot = -70.1142460562208 | etot = -54.4566352810913 +473000 ekin = 9.78800246195762 | erot = 5.41826188422521 | epot = -69.6628996264059 | etot = -54.4566352802231 +474000 ekin = 9.50601286878116 | erot = 5.3182028147351 | epot = -69.2808509629482 | etot = -54.456635279432 +475000 ekin = 9.25312250159501 | erot = 5.27140899121769 | epot = -68.9811667716237 | etot = -54.456635278811 +476000 ekin = 9.04645385403901 | erot = 5.27070679329064 | epot = -68.7737959257915 | etot = -54.4566352784618 +477000 ekin = 8.89934302898377 | erot = 5.3080643166994 | epot = -68.664042624135 | etot = -54.4566352784518 +478000 ekin = 8.81931824252445 | erot = 5.37557918610341 | epot = -68.6515327074218 | etot = -54.4566352787939 +479000 ekin = 8.80699076959969 | erot = 5.46633303731731 | epot = -68.7299590863674 | etot = -54.4566352794504 +480000 ekin = 8.85601818727501 | erot = 5.57490002076168 | epot = -68.8875534883949 | etot = -54.4566352803582 +481000 ekin = 8.95429342118878 | erot = 5.69751011507638 | epot = -69.108438817723 | etot = -54.4566352814579 +482000 ekin = 9.08517946645594 | erot = 5.83167729002342 | epot = -69.3734920391789 | etot = -54.4566352826995 +483000 ekin = 9.2290960727685 | erot = 5.97557873339194 | epot = -69.6613100901891 | etot = -54.4566352840286 +484000 ekin = 9.36521899372712 | erot = 6.127458642182 | epot = -69.949312921278 | etot = -54.4566352853688 +485000 ekin = 9.47322485683908 | erot = 6.28523994694383 | epot = -70.215100090406 | etot = -54.4566352866231 +486000 ekin = 9.53500494319974 | erot = 6.44644593217097 | epot = -70.438086163052 | etot = -54.4566352876813 +487000 ekin = 9.53619997079837 | erot = 6.60840812030681 | epot = -70.6012433795484 | etot = -54.4566352884432 +488000 ekin = 9.4673616575425 | erot = 6.76862588122785 | epot = -70.692622827615 | etot = -54.4566352888446 +489000 ekin = 9.32457274797321 | erot = 6.92507571371342 | epot = -70.7062837505581 | etot = -54.4566352888715 +490000 ekin = 9.10946474824739 | erot = 7.07632195430842 | epot = -70.6424219911187 | etot = -54.4566352885629 +491000 ekin = 8.82888029926593 | erot = 7.22128416903665 | epot = -70.5067997559112 | etot = -54.4566352876086 +492000 ekin = 8.49626753097993 | erot = 7.35784727800451 | epot = -70.3107500960481 | etot = -54.4566352870636 +493000 ekin = 8.12485274299824 | erot = 7.48341898211923 | epot = -70.064907011523 | etot = -54.4566352864055 +494000 ekin = 7.72891988561272 | erot = 7.59489697498567 | epot = -69.7804521462802 | etot = -54.4566352856818 +495000 ekin = 7.32464765068735 | erot = 7.68832902470436 | epot = -69.4696119585145 | etot = -54.4566352831228 +496000 ekin = 6.87909737981739 | erot = 7.73460610288381 | epot = -69.0703390393494 | etot = -54.4566355566482 +497000 ekin = 6.10749796784233 | erot = 7.42289860774637 | epot = -67.9870318122098 | etot = -54.4566352366211 +498000 ekin = 6.82233845536795 | erot = 7.45240806496377 | epot = -68.731382053793 | etot = -54.4566355334613 +499000 ekin = 6.9458581135547 | erot = 7.49819185265288 | epot = -68.900685243359 | etot = -54.4566352771515 +500000 ekin = 6.9687772203723 | erot = 7.49002786304578 | epot = -68.9154403630723 | etot = -54.4566352796543 +501000 ekin = 7.01880112774021 | erot = 7.44438420076566 | epot = -68.9198206071042 | etot = -54.4566352785983 +502000 ekin = 7.10331622209455 | erot = 7.36817394316464 | epot = -68.9281254425226 | etot = -54.4566352772634 +503000 ekin = 7.22893470365061 | erot = 7.2736841510104 | epot = -68.959254130481 | etot = -54.45663527582 +504000 ekin = 7.40053482834885 | erot = 7.17754137262199 | epot = -69.0347114753898 | etot = -54.456635274419 +505000 ekin = 7.62070280613197 | erot = 7.09829571793159 | epot = -69.1756337972853 | etot = -54.4566352732217 +506000 ekin = 7.88915849439799 | erot = 7.05445199996608 | epot = -69.4002457667333 | etot = -54.4566352723693 +507000 ekin = 8.20246554171929 | erot = 7.06247440846451 | epot = -69.7215752221496 | etot = -54.4566352719658 +508000 ekin = 8.55413799383551 | erot = 7.13504955839166 | epot = -70.145822824278 | etot = -54.4566352720509 +509000 ekin = 8.93516686126571 | erot = 7.27981823673993 | epot = -70.6716203706166 | etot = -54.4566352726109 +510000 ekin = 9.33485927283508 | erot = 7.49868525982142 | epot = -71.2901798062416 | etot = -54.4566352735851 +511000 ekin = 9.74175973588398 | erot = 7.78771907260134 | epot = -71.9861140833848 | etot = -54.4566352748994 +512000 ekin = 10.1443557396999 | erot = 8.13756756501622 | epot = -72.738558581206 | etot = -54.4566352764899 +513000 ekin = 10.531312605677 | erot = 8.53426169206068 | epot = -73.5222095760515 | etot = -54.4566352783138 +514000 ekin = 10.8911780109942 | erot = 8.96028799859434 | epot = -74.3081012899268 | etot = -54.4566352803383 +515000 ekin = 11.2118156252243 | erot = 9.39590120046256 | epot = -75.0643521081772 | etot = -54.4566352824903 +516000 ekin = 11.4801179010287 | erot = 9.82075584957822 | epot = -75.7575090352141 | etot = -54.4566352846072 +517000 ekin = 11.6825443563199 | erot = 10.2159440472384 | epot = -76.3551236899899 | etot = -54.4566352864315 +518000 ekin = 11.8066489253425 | erot = 10.5663121117515 | epot = -76.8295963247647 | etot = -54.4566352876706 +519000 ekin = 11.8431629051674 | erot = 10.8625994980219 | epot = -77.1623976912905 | etot = -54.4566352881013 +520000 ekin = 11.787857569085 | erot = 11.102744990217 | epot = -77.3472378469788 | etot = -54.4566352876768 +521000 ekin = 11.6423174236686 | erot = 11.2919310655302 | epot = -77.3908837756977 | etot = -54.456635286499 +522000 ekin = 11.4136719884803 | erot = 11.4412637557252 | epot = -77.3115710290112 | etot = -54.4566352848057 +523000 ekin = 11.113424621935 | erot = 11.5654340582824 | epot = -77.1354939631131 | etot = -54.4566352828957 +524000 ekin = 10.7557913149156 | erot = 11.6798454532669 | epot = -76.8922720492617 | etot = -54.4566352810793 +525000 ekin = 10.3559612263806 | erot = 11.7976117586495 | epot = -76.6102082646709 | etot = -54.4566352796408 +526000 ekin = 9.92854976445471 | erot = 11.9267667903727 | epot = -76.3119518336234 | etot = -54.456635278796 +527000 ekin = 9.48645866347763 | erot = 12.0680840250146 | epot = -76.0111779671512 | etot = -54.456635278659 +528000 ekin = 9.04033350015186 | erot = 12.2139583839329 | epot = -75.7109271632781 | etot = -54.4566352791933 +529000 ekin = 8.5987344363361 | erot = 12.3488338467365 | epot = -75.4042035632657 | etot = -54.4566352801931 +530000 ekin = 8.16898173781198 | erot = 12.4514660033284 | epot = -75.0770830224534 | etot = -54.456635281313 +531000 ekin = 7.75842341267674 | erot = 12.4988592010124 | epot = -74.7139178958321 | etot = -54.4566352821429 +532000 ekin = 7.37569471992756 | erot = 12.4711371154268 | epot = -74.3034671176744 | etot = -54.45663528232 +533000 ekin = 7.03150209880071 | erot = 12.3561420075333 | epot = -73.844279387978 | etot = -54.456635281644 +534000 ekin = 6.7386103799064 | erot = 12.1525081131702 | epot = -73.3477537732032 | etot = -54.4566352801267 +535000 ekin = 6.51098179616902 | erot = 11.8704212665667 | epot = -72.8380383407155 | etot = -54.4566352779798 +536000 ekin = 6.36227279690717 | erot = 11.5300349542156 | epot = -72.3489430266664 | etot = -54.4566352755436 +537000 ekin = 6.30402397010781 | erot = 11.1595690920548 | epot = -71.9202283349053 | etot = -54.4566352727426 +538000 ekin = 6.34384912541234 | erot = 10.7903690893108 | epot = -71.5908534856624 | etot = -54.4566352709393 +539000 ekin = 6.48387052851178 | erot = 10.4493189471733 | epot = -71.3898247456171 | etot = -54.456635269932 +540000 ekin = 6.71957140287839 | erot = 10.1578313306175 | epot = -71.3340380034278 | etot = -54.4566352699319 +541000 ekin = 7.03922441473198 | erot = 9.92917206920642 | epot = -71.4250317549648 | etot = -54.4566352710264 +542000 ekin = 7.42406000056234 | erot = 9.76688711206304 | epot = -71.6475823857816 | etot = -54.4566352731563 +543000 ekin = 7.84930235319357 | erot = 9.66461535275746 | epot = -71.9705529820511 | etot = -54.4566352761 +544000 ekin = 8.28608775690868 | erot = 9.60744188179591 | epot = -72.3501649181961 | etot = -54.4566352794915 +545000 ekin = 8.70408689279382 | erot = 9.57468499689601 | epot = -72.7354071725602 | etot = -54.4566352828704 +546000 ekin = 9.07450055253985 | erot = 9.5437358449094 | epot = -73.0748716832126 | etot = -54.4566352857634 +547000 ekin = 9.3729563042228 | erot = 9.49419334508817 | epot = -73.3237849370942 | etot = -54.4566352877832 +548000 ekin = 9.58182570226172 | erot = 9.4113726281576 | epot = -73.4498336191269 | etot = -54.4566352887075 +549000 ekin = 9.69160120899291 | erot = 9.28840559658494 | epot = -73.4366420940901 | etot = -54.4566352885123 +550000 ekin = 9.70118406829612 | erot = 9.12701779120654 | epot = -73.2848371466999 | etot = -54.4566352871972 +551000 ekin = 9.61716955376783 | erot = 8.93605057966714 | epot = -73.0098554187887 | etot = -54.4566352853538 +552000 ekin = 9.45239020383949 | erot = 8.72803660180396 | epot = -72.6370620887567 | etot = -54.4566352831133 +553000 ekin = 9.2240812648571 | erot = 8.51766004432099 | epot = -72.1983765899246 | etot = -54.4566352807465 +554000 ekin = 8.95200493897852 | erot = 8.31967116937484 | epot = -71.7283113868087 | etot = -54.4566352784553 +555000 ekin = 8.65679189106452 | erot = 8.14750332103372 | epot = -71.2609304884617 | etot = -54.4566352763634 +556000 ekin = 8.35857893218147 | erot = 8.01260395507915 | epot = -70.8278181618014 | etot = -54.4566352745408 +557000 ekin = 8.07596711125517 | erot = 7.92430276672531 | epot = -70.4569051509942 | etot = -54.4566352730137 +558000 ekin = 7.82526545929883 | erot = 7.88998546795632 | epot = -70.1718861990513 | etot = -54.4566352717961 +559000 ekin = 7.61992228152034 | erot = 7.9152795848548 | epot = -69.9918371372886 | etot = -54.4566352709135 +560000 ekin = 7.47007181067657 | erot = 8.0040537978786 | epot = -69.9307608789597 | etot = -54.4566352704045 +561000 ekin = 7.38215855424633 | erot = 8.15814566486797 | epot = -69.9969394894381 | etot = -54.4566352703238 +562000 ekin = 7.35865871745874 | erot = 8.376880609997 | epot = -70.1921745981657 | etot = -54.4566352707099 +563000 ekin = 7.39798626084559 | erot = 8.65660065505618 | epot = -70.5112221874692 | etot = -54.4566352715674 +564000 ekin = 7.49472571183499 | erot = 8.99052373945481 | epot = -70.9418847241114 | etot = -54.4566352728216 +565000 ekin = 7.6403295678358 | erot = 9.36943411106999 | epot = -71.4663989531537 | etot = -54.4566352742479 +566000 ekin = 7.82430710588482 | erot = 9.78260719507037 | epot = -72.0635495767755 | etot = -54.4566352758203 +567000 ekin = 8.03571605972324 | erot = 10.2184542008367 | epot = -72.7108055378515 | etot = -54.4566352772916 +568000 ekin = 8.26456312040914 | erot = 10.6659972236189 | epot = -73.3871956226338 | etot = -54.4566352786058 +569000 ekin = 8.50272301776145 | erot = 11.1149437633325 | epot = -74.0743020608808 | etot = -54.4566352797868 +570000 ekin = 8.74355516146364 | erot = 11.5545029206602 | epot = -74.7546933636264 | etot = -54.4566352815025 +571000 ekin = 8.98090334156988 | erot = 11.972558358418 | epot = -75.4100969833271 | etot = -54.4566352833392 +572000 ekin = 9.20828738370295 | erot = 12.3560364775513 | epot = -76.0209591456352 | etot = -54.4566352843809 +573000 ekin = 9.42081793457053 | erot = 12.6951950119738 | epot = -76.5726482312666 | etot = -54.4566352847223 +574000 ekin = 9.61839098683931 | erot = 12.9876757192449 | epot = -77.0627019900754 | etot = -54.4566352839912 +575000 ekin = 9.80532071145167 | erot = 13.2416249343254 | epot = -77.5035809281439 | etot = -54.4566352823668 +576000 ekin = 9.99002522866369 | erot = 13.4728181323069 | epot = -77.9194786412748 | etot = -54.4566352803041 +577000 ekin = 10.1832012886937 | erot = 13.6997981601557 | epot = -78.3396347273641 | etot = -54.4566352785147 +578000 ekin = 10.3950145220056 | erot = 13.9374358143685 | epot = -78.7890856136979 | etot = -54.4566352773239 +579000 ekin = 10.6321657048142 | erot = 14.1940413546702 | epot = -79.2828423366402 | etot = -54.4566352771559 +580000 ekin = 10.8955063623687 | erot = 14.4691297492109 | epot = -79.8212713897138 | etot = -54.4566352781342 +581000 ekin = 11.1784960139007 | erot = 14.7531280290501 | epot = -80.3882593232073 | etot = -54.4566352802565 +582000 ekin = 11.4666498909183 | erot = 15.0284667683282 | epot = -80.9517519424842 | etot = -54.4566352832377 +583000 ekin = 11.7382109395925 | erot = 15.2729975156575 | epot = -81.4678437419717 | etot = -54.4566352867217 +584000 ekin = 11.9663900039874 | erot = 15.463594812378 | epot = -81.8866201064935 | etot = -54.4566352901281 +585000 ekin = 12.1233421756029 | erot = 15.5804670946814 | epot = -82.1604445630453 | etot = -54.456635292761 +586000 ekin = 12.1853975661852 | erot = 15.611762573636 | epot = -82.2537954338106 | etot = -54.4566352939894 +587000 ekin = 12.1382713602016 | erot = 15.557003831346 | epot = -82.1519104850302 | etot = -54.4566352934825 +588000 ekin = 11.9805642896466 | erot = 15.4278527969129 | epot = -81.8650523779339 | etot = -54.4566352913745 +589000 ekin = 11.7242102225938 | erot = 15.2454372701407 | epot = -81.4262827809785 | etot = -54.456635288244 +590000 ekin = 11.3915725976067 | erot = 15.0348737081526 | epot = -80.8830815906634 | etot = -54.456635284904 +591000 ekin = 11.0102189263661 | erot = 14.8189389013138 | epot = -80.2857931097531 | etot = -54.4566352820732 +592000 ekin = 10.6073918807094 | erot = 14.6132844347391 | epot = -79.6773115955566 | etot = -54.4566352801081 +593000 ekin = 10.2062007298967 | erot = 14.4247656797 | epot = -79.0876016885481 | etot = -54.4566352789514 +594000 ekin = 9.82441079417659 | erot = 14.2527059306663 | epot = -78.5337520031729 | etot = -54.45663527833 +595000 ekin = 9.47516576237465 | erot = 14.091348302824 | epot = -78.0231493432196 | etot = -54.456635278021 +596000 ekin = 9.16820839958766 | erot = 13.9315742319346 | epot = -77.5564179095013 | etot = -54.4566352779791 +597000 ekin = 8.91058714546151 | erot = 13.7613090154786 | epot = -77.1285314391907 | etot = -54.4566352782506 +598000 ekin = 8.70675752393341 | erot = 13.5656177911289 | epot = -76.7290105938819 | etot = -54.4566352788196 +599000 ekin = 8.55850888712236 | erot = 13.3279192983518 | epot = -76.3430634650047 | etot = -54.4566352795306 +600000 ekin = 8.46506040529032 | erot = 13.0357131362493 | epot = -75.9574088199436 | etot = -54.456635278404 +601000 ekin = 8.42304118577515 | erot = 12.686791609959 | epot = -75.566468075024 | etot = -54.4566352792899 +602000 ekin = 8.42687753935408 | erot = 12.2731929910171 | epot = -75.1567058099102 | etot = -54.4566352795389 +603000 ekin = 8.46953848993741 | erot = 11.7970987134719 | epot = -74.7232724825868 | etot = -54.4566352791774 +604000 ekin = 8.54275438846908 | erot = 11.2715335231632 | epot = -74.2709231899985 | etot = -54.4566352783662 +605000 ekin = 8.63734562583461 | erot = 10.7175531247449 | epot = -73.8115340278902 | etot = -54.4566352773107 +606000 ekin = 8.74380130285083 | erot = 10.1605162228269 | epot = -73.3609528018709 | etot = -54.4566352761931 +607000 ekin = 8.85309694756741 | erot = 9.62647077148512 | epot = -72.9362029941922 | etot = -54.4566352751397 +608000 ekin = 8.95762756594859 | erot = 9.13922005194219 | epot = -72.5534828920873 | etot = -54.4566352741965 +609000 ekin = 9.05200869449502 | erot = 8.71853436574554 | epot = -72.2271783337194 | etot = -54.4566352734788 +610000 ekin = 9.13354825725354 | erot = 8.37878256428323 | epot = -71.9689660943716 | etot = -54.4566352728348 +611000 ekin = 9.20214054253083 | erot = 8.12920532171282 | epot = -71.7879811366974 | etot = -54.4566352724537 +612000 ekin = 9.25952066990242 | erot = 7.97330837184469 | epot = -71.6894643141628 | etot = -54.4566352724157 +613000 ekin = 9.30803502781619 | erot = 7.90865833532742 | epot = -71.6733286359666 | etot = -54.456635272823 +614000 ekin = 9.3491671109403 | erot = 7.92697148194727 | epot = -71.7327738666472 | etot = -54.4566352737596 +615000 ekin = 9.38224690749493 | erot = 8.01444322718518 | epot = -71.8533254097698 | etot = -54.4566352750897 +616000 ekin = 9.40371294251254 | erot = 8.15314542839535 | epot = -72.0134936479301 | etot = -54.4566352770223 +617000 ekin = 9.40764668981377 | erot = 8.32057787069446 | epot = -72.184859839695 | etot = -54.4566352791868 +618000 ekin = 9.38714075160097 | erot = 8.49215030182523 | epot = -72.3359263346865 | etot = -54.4566352812603 +619000 ekin = 9.33636921849 | erot = 8.64420325444537 | epot = -72.4372077558095 | etot = -54.4566352828742 +620000 ekin = 9.252854030249 | erot = 8.75716147302693 | epot = -72.4666507869801 | etot = -54.4566352837042 +621000 ekin = 9.13928884697304 | erot = 8.81846717426335 | epot = -72.4143913047831 | etot = -54.4566352835467 +622000 ekin = 9.00442091794753 | erot = 8.82459164772566 | epot = -72.2856478480514 | etot = -54.4566352823782 +623000 ekin = 8.86274189509341 | erot = 8.78159561804225 | epot = -72.1009727932514 | etot = -54.4566352801158 +624000 ekin = 8.73276401802021 | erot = 8.70595407666386 | epot = -71.8953533724934 | etot = -54.4566352778093 +625000 ekin = 8.63399867892453 | erot = 8.6182124697542 | epot = -71.708846423948 | etot = -54.4566352752693 +626000 ekin = 8.58565910356922 | erot = 8.53996947434913 | epot = -71.582263850783 | etot = -54.4566352728646 +627000 ekin = 8.60437912920223 | erot = 8.49303514266094 | epot = -71.5540495428028 | etot = -54.4566352709396 +628000 ekin = 8.70176554881456 | erot = 8.49648522564954 | epot = -71.6548860443321 | etot = -54.456635269868 +629000 ekin = 8.88261620996708 | erot = 8.56350717253297 | epot = -71.9027586522068 | etot = -54.4566352697068 +630000 ekin = 9.14296246576545 | erot = 8.70076359814303 | epot = -72.3003613345765 | etot = -54.456635270668 +631000 ekin = 9.4688770435737 | erot = 8.90689930704519 | epot = -72.8324116238827 | etot = -54.4566352732638 +632000 ekin = 9.8336318583032 | erot = 9.17168072086099 | epot = -73.461947855651 | etot = -54.4566352764868 +633000 ekin = 10.205312415491 | erot = 9.47717112293907 | epot = -74.1391188185627 | etot = -54.4566352801326 +634000 ekin = 10.5495376011183 | erot = 9.8018293365467 | epot = -74.808002221223 | etot = -54.4566352835579 +635000 ekin = 10.8340816739795 | erot = 10.1250818406596 | epot = -75.4157988007439 | etot = -54.4566352861047 +636000 ekin = 11.0341363467081 | erot = 10.4317241828093 | epot = -75.9224958167932 | etot = -54.4566352872758 +637000 ekin = 11.1362536304014 | erot = 10.7150791019197 | epot = -76.3079680193905 | etot = -54.4566352870694 +638000 ekin = 11.1393407346171 | erot = 10.9767172063777 | epot = -76.5726932267179 | etot = -54.4566352857231 +639000 ekin = 11.0528857655821 | erot = 11.2245625296839 | epot = -76.7340835789793 | etot = -54.4566352837134 +640000 ekin = 10.8932833750906 | erot = 11.4701066828092 | epot = -76.8200253394056 | etot = -54.4566352815059 +641000 ekin = 10.6798604052278 | erot = 11.7256640733726 | epot = -76.8621597580235 | etot = -54.4566352794231 +642000 ekin = 10.4319158115311 | erot = 12.0024358075229 | epot = -76.8909868967156 | etot = -54.4566352776616 +643000 ekin = 10.1669531872239 | erot = 12.3092359597637 | epot = -76.9328244231637 | etot = -54.4566352761762 +644000 ekin = 9.90018316848564 | erot = 12.6520525446199 | epot = -77.0088709883572 | etot = -54.4566352752517 +645000 ekin = 9.64412813643985 | erot = 13.0323474006194 | epot = -77.1331108119919 | etot = -54.4566352749326 +646000 ekin = 9.40844464392144 | erot = 13.445899808015 | epot = -77.3109797269448 | etot = -54.4566352750084 +647000 ekin = 9.19998842915914 | erot = 13.8831906422576 | epot = -77.5398143472399 | etot = -54.4566352758232 +648000 ekin = 9.02196759879953 | erot = 14.3279062478315 | epot = -77.8065091239426 | etot = -54.4566352773116 +649000 ekin = 8.87356627778827 | erot = 14.7574673823088 | epot = -78.0876689395587 | etot = -54.4566352794617 +650000 ekin = 8.74956009131858 | erot = 15.1439160026106 | epot = -78.3501113761033 | etot = -54.4566352821742 +651000 ekin = 8.64036637406374 | erot = 15.4556053528513 | epot = -78.5526070121591 | etot = -54.456635285244 +652000 ekin = 8.53277201870133 | erot = 15.6598310256647 | epot = -78.6492383326926 | etot = -54.4566352883265 +653000 ekin = 8.41160402390284 | erot = 15.7264979165423 | epot = -78.5947372313765 | etot = -54.4566352909314 +654000 ekin = 8.26240952717994 | erot = 15.6326986256584 | epot = -78.3517434453699 | etot = -54.4566352925316 +655000 ekin = 8.0747558065804 | erot = 15.3674488766155 | epot = -77.8988399757495 | etot = -54.4566352925536 +656000 ekin = 7.85585683290951 | erot = 14.9355978464948 | epot = -77.2480902330419 | etot = -54.4566355536375 +657000 ekin = 6.26754941231325 | erot = 14.5622178162979 | epot = -75.2864023128906 | etot = -54.4566350842794 +658000 ekin = 6.04146739778998 | erot = 14.8336076396148 | epot = -75.3317103841209 | etot = -54.4566353467161 +659000 ekin = 6.38604373423614 | erot = 14.3792060567669 | epot = -75.2218852651894 | etot = -54.4566354741863 +660000 ekin = 6.51806923667787 | erot = 13.6089213615713 | epot = -74.583626071967 | etot = -54.4566354737179 +661000 ekin = 6.66094978027619 | erot = 12.8243584228189 | epot = -73.9419436733112 | etot = -54.4566354702161 +662000 ekin = 6.81847461883888 | erot = 12.0687190077588 | epot = -73.3438290942572 | etot = -54.4566354676595 +663000 ekin = 6.99157703856281 | erot = 11.3763942501033 | epot = -72.8246067547991 | etot = -54.456635466133 +664000 ekin = 7.17716154109741 | erot = 10.7708280861928 | epot = -72.4046250929277 | etot = -54.4566354656374 +665000 ekin = 7.3675134645839 | erot = 10.2651942829219 | epot = -72.0893432136818 | etot = -54.4566354661759 +666000 ekin = 7.55097379428619 | erot = 9.86605911513289 | epot = -71.8736683769863 | etot = -54.4566354675673 +667000 ekin = 7.71560064025504 | erot = 9.56451333310892 | epot = -71.7367494427 | etot = -54.456635469336 +668000 ekin = 7.84958438766926 | erot = 9.34368947191058 | epot = -71.6499093309775 | etot = -54.4566354713976 +669000 ekin = 7.94295016386841 | erot = 9.18181390482315 | epot = -71.5813995420007 | etot = -54.4566354733091 +670000 ekin = 7.98916842115041 | erot = 9.05573401740469 | epot = -71.5015379133589 | etot = -54.4566354748038 +671000 ekin = 7.98640376802285 | erot = 8.9438936881866 | epot = -71.3869329318896 | etot = -54.4566354756801 +672000 ekin = 7.93814945498434 | erot = 8.82870298531564 | epot = -71.2234879161406 | etot = -54.4566354758406 +673000 ekin = 7.8537861028125 | erot = 8.69868774368351 | epot = -71.0091093212669 | etot = -54.4566354747709 +674000 ekin = 7.74799942745653 | erot = 8.54952007571503 | epot = -70.754154976792 | etot = -54.4566354736204 +675000 ekin = 7.63655278418813 | erot = 8.38180900835833 | epot = -70.4749972647102 | etot = -54.4566354721638 +676000 ekin = 7.53535852002373 | erot = 8.20065006867783 | epot = -70.1926440593739 | etot = -54.4566354706724 +677000 ekin = 7.45814475128924 | erot = 8.01383837145781 | epot = -69.9286185924985 | etot = -54.4566354697515 +678000 ekin = 7.41094295257362 | erot = 7.82760230140571 | epot = -69.6951807230087 | etot = -54.4566354690294 +679000 ekin = 7.39592235494237 | erot = 7.64827405778973 | epot = -69.5008318814476 | etot = -54.4566354687155 +680000 ekin = 7.41177806099165 | erot = 7.48365592355136 | epot = -69.3520694528015 | etot = -54.4566354682585 +681000 ekin = 7.45331527398533 | erot = 7.34392547755159 | epot = -69.2538762205311 | etot = -54.4566354689942 +682000 ekin = 7.50955937699447 | erot = 7.23029783102035 | epot = -69.1964926779924 | etot = -54.4566354699776 +683000 ekin = 7.56739476563308 | erot = 7.14126315258949 | epot = -69.1652933892642 | etot = -54.4566354710416 +684000 ekin = 7.61376409146323 | erot = 7.07385958562239 | epot = -69.1442591490601 | etot = -54.4566354719745 +685000 ekin = 7.63746698434793 | erot = 7.02460383230475 | epot = -69.1187062894122 | etot = -54.4566354727596 +686000 ekin = 7.63051953634283 | erot = 6.98951954533694 | epot = -69.0766745549284 | etot = -54.4566354732486 +687000 ekin = 7.5888614055269 | erot = 6.9642888409131 | epot = -69.0097857199425 | etot = -54.4566354735025 +688000 ekin = 7.51237784441295 | erot = 6.94436871138863 | epot = -68.913382029102 | etot = -54.4566354733004 +689000 ekin = 7.40504576869775 | erot = 6.92768230554917 | epot = -68.7893635471216 | etot = -54.4566354728746 +690000 ekin = 7.2738213082913 | erot = 6.91296338855719 | epot = -68.6434201691413 | etot = -54.4566354722928 +691000 ekin = 7.12767077386446 | erot = 6.8994786138555 | epot = -68.4837848593432 | etot = -54.4566354716233 +692000 ekin = 6.97662396691413 | erot = 6.88703034396566 | epot = -68.3202897818029 | etot = -54.4566354709231 +693000 ekin = 6.83191834521804 | erot = 6.8766124382546 | epot = -68.1651662534375 | etot = -54.4566354699649 +694000 ekin = 6.70652274539129 | erot = 6.87114213827601 | epot = -68.0343003531198 | etot = -54.4566354694525 +695000 ekin = 6.6080964549702 | erot = 6.87168002795425 | epot = -67.9364119519728 | etot = -54.4566354690483 +696000 ekin = 6.54192055188977 | erot = 6.87954258792384 | epot = -67.8780986086002 | etot = -54.4566354687865 +697000 ekin = 6.51083965229348 | erot = 6.89633668057611 | epot = -67.8638118015878 | etot = -54.4566354687182 +698000 ekin = 6.51499125639776 | erot = 6.92351826953845 | epot = -67.8951449951683 | etot = -54.4566354692321 +699000 ekin = 6.55055681857638 | erot = 6.96165096856071 | epot = -67.9688432565943 | etot = -54.4566354694572 +700000 ekin = 6.61234823813492 | erot = 7.01150759223358 | epot = -68.0804913002871 | etot = -54.4566354699186 +701000 ekin = 6.69387980259486 | erot = 7.07317762178765 | epot = -68.2236928948399 | etot = -54.4566354704574 +702000 ekin = 6.78728068984252 | erot = 7.14568383977262 | epot = -68.3896000007052 | etot = -54.4566354710901 +703000 ekin = 6.88400379173301 | erot = 7.22737250161383 | epot = -68.5680117651102 | etot = -54.4566354717634 +704000 ekin = 6.9755683283792 | erot = 7.31572261063307 | epot = -68.7479264114309 | etot = -54.4566354724186 +705000 ekin = 7.05425772044827 | erot = 7.40762548354984 | epot = -68.918518676989 | etot = -54.4566354729909 +706000 ekin = 7.11369388312852 | erot = 7.49985325015459 | epot = -69.0701826067035 | etot = -54.4566354734204 +707000 ekin = 7.14922746291453 | erot = 7.58965466907143 | epot = -69.1955176056455 | etot = -54.4566354736595 +708000 ekin = 7.15811920577057 | erot = 7.6753716118719 | epot = -69.2901262913224 | etot = -54.45663547368 +709000 ekin = 7.13952646260787 | erot = 7.75695073870288 | epot = -69.3531126747875 | etot = -54.4566354734768 +710000 ekin = 7.09433523089743 | erot = 7.83623493467237 | epot = -69.3872056386393 | etot = -54.4566354730695 +711000 ekin = 7.02488197439733 | erot = 7.91695244606741 | epot = -69.3984698929695 | etot = -54.4566354725047 +712000 ekin = 6.93460038930963 | erot = 8.00437692967913 | epot = -69.3956127908343 | etot = -54.4566354718455 +713000 ekin = 6.82762548689843 | erot = 8.10469988090539 | epot = -69.3889608389937 | etot = -54.4566354711898 +714000 ekin = 6.70839192372885 | erot = 8.22401944316087 | epot = -69.3890468375048 | etot = -54.4566354706151 +715000 ekin = 6.58127350483518 | erot = 8.36737765964063 | epot = -69.4052866346802 | etot = -54.4566354702044 +716000 ekin = 6.45031596781454 | erot = 8.53776210682282 | epot = -69.4447135446588 | etot = -54.4566354700214 +717000 ekin = 6.31910573967135 | erot = 8.73523312781141 | epot = -69.5109743375848 | etot = -54.4566354701021 +718000 ekin = 6.19080028787852 | erot = 8.95633319732517 | epot = -69.6037689556476 | etot = -54.4566354704439 +719000 ekin = 6.06832299313999 | erot = 9.19390878350935 | epot = -69.7188672476532 | etot = -54.4566354710038 +720000 ekin = 5.95470075029213 | erot = 9.43744070378272 | epot = -69.848776925771 | etot = -54.4566354716962 +721000 ekin = 5.85349202512794 | erot = 9.67392180067373 | epot = -69.984049298204 | etot = -54.4566354724024 +722000 ekin = 5.7692181161866 | erot = 9.88920295788338 | epot = -70.115056547069 | etot = -54.4566354729991 +723000 ekin = 5.7076753508952 | erot = 10.0695468208552 | epot = -70.2338576451068 | etot = -54.4566354733563 +724000 ekin = 5.67599154890889 | erot = 10.2035425526933 | epot = -70.3361695749994 | etot = -54.4566354733972 +725000 ekin = 5.6823071244365 | erot = 10.2835870142678 | epot = -70.4225296118105 | etot = -54.4566354731061 +726000 ekin = 5.73502013958649 | erot = 10.3068600066592 | epot = -70.4985156187871 | etot = -54.4566354725414 +727000 ekin = 5.84163680643593 | erot = 10.2756197556458 | epot = -70.5738920339005 | etot = -54.4566354718188 +728000 ekin = 6.00741477144206 | erot = 10.1968335781523 | epot = -70.6608838206683 | etot = -54.4566354710739 +729000 ekin = 6.23399006286944 | erot = 10.0813630553867 | epot = -70.7719885887239 | etot = -54.4566354704678 +730000 ekin = 6.51828052766968 | erot = 9.9426735456371 | epot = -70.9175895434409 | etot = -54.4566354701342 +731000 ekin = 6.85187412407457 | erot = 9.79530805493521 | epot = -71.1038176491845 | etot = -54.4566354701747 +732000 ekin = 7.22103408686053 | erot = 9.65327415428921 | epot = -71.3309437117948 | etot = -54.456635470645 +733000 ekin = 7.6073019302977 | erot = 9.5288012152138 | epot = -71.5927386169948 | etot = -54.4566354714833 +734000 ekin = 7.98880332436974 | erot = 9.43074706134312 | epot = -71.8761858584825 | etot = -54.4566354727696 +735000 ekin = 8.34212509376477 | erot = 9.36330983351514 | epot = -72.1620704015887 | etot = -54.4566354743088 +736000 ekin = 8.64442251579602 | erot = 9.3261997193473 | epot = -72.4272577110702 | etot = -54.4566354759269 +737000 ekin = 8.87574972642309 | erot = 9.31509601121895 | epot = -72.6474812150474 | etot = -54.4566354774053 +738000 ekin = 9.0213063017174 | erot = 9.32284410471813 | epot = -72.8007858849472 | etot = -54.4566354785117 +739000 ekin = 9.07331880502731 | erot = 9.34118914838286 | epot = -72.8711434324511 | etot = -54.4566354790409 +740000 ekin = 9.0322576373975 | erot = 9.36274956107302 | epot = -72.8516426773234 | etot = -54.4566354788529 +741000 ekin = 8.90713122013885 | erot = 9.38285576883458 | epot = -72.7466224668824 | etot = -54.4566354779089 +742000 ekin = 8.71472462487314 | erot = 9.40075675434409 | epot = -72.5721168556042 | etot = -54.4566354763869 +743000 ekin = 8.47795966699129 | erot = 9.41969955783427 | epot = -72.3542946989535 | etot = -54.456635474128 +744000 ekin = 8.22400086783694 | erot = 9.44765885711039 | epot = -72.128295196838 | etot = -54.4566354718907 +745000 ekin = 7.97989641728011 | erot = 9.49406284314475 | epot = -71.9305947302623 | etot = -54.4566354698375 +746000 ekin = 7.76957023228948 | erot = 9.56762699730313 | epot = -71.7938326979078 | etot = -54.4566354683152 +747000 ekin = 7.6113281427099 | erot = 9.67405775027494 | epot = -71.7420213607043 | etot = -54.4566354677194 +748000 ekin = 7.51608906093837 | erot = 9.81227809034228 | epot = -71.7850026195292 | etot = -54.4566354682486 +749000 ekin = 7.48509635032519 | erot = 9.97286752414425 | epot = -71.9145993443936 | etot = -54.4566354699242 +750000 ekin = 7.51020628170433 | erot = 10.1380775195597 | epot = -72.1049192737248 | etot = -54.4566354724607 +751000 ekin = 7.57538607459301 | erot = 10.2842078236672 | epot = -72.3162293736845 | etot = -54.4566354754243 +752000 ekin = 7.6598576786284 | erot = 10.3856021559112 | epot = -72.5020953127697 | etot = -54.4566354782301 +753000 ekin = 7.7418988706293 | erot = 10.419001280771 | epot = -72.6175356320473 | etot = -54.456635480647 +754000 ekin = 7.80244855950124 | erot = 10.368071576505 | epot = -72.6271556175909 | etot = -54.4566354815847 +755000 ekin = 7.83000162070187 | erot = 10.2279599096749 | epot = -72.5145970115927 | etot = -54.4566354812159 +756000 ekin = 7.82097337516333 | erot = 10.0059197104044 | epot = -72.2835285652056 | etot = -54.4566354796378 +757000 ekin = 7.77934134709385 | erot = 9.72019517220502 | epot = -71.9561719964632 | etot = -54.4566354771644 +758000 ekin = 7.71519090757765 | erot = 9.39692989176329 | epot = -71.568756273533 | etot = -54.4566354741921 +759000 ekin = 7.64279612361687 | erot = 9.06591672496539 | epot = -71.1653483197966 | etot = -54.4566354712144 +760000 ekin = 7.57755088529913 | erot = 8.75627990045572 | epot = -70.790466254363 | etot = -54.4566354686081 +761000 ekin = 7.53416140037988 | erot = 8.49239651708238 | epot = -70.4831933841097 | etot = -54.4566354666474 +762000 ekin = 7.52513654522363 | erot = 8.29092896402533 | epot = -70.2727009748576 | etot = -54.4566354656086 +763000 ekin = 7.55953487188996 | erot = 8.15857993676166 | epot = -70.1747502740048 | etot = -54.4566354653532 +764000 ekin = 7.64294215278388 | erot = 8.09284507803136 | epot = -70.1924226970296 | etot = -54.4566354662144 +765000 ekin = 7.77642284077532 | erot = 8.08170347279627 | epot = -70.3147617810319 | etot = -54.4566354674603 +766000 ekin = 7.9583426106239 | erot = 8.1071156497746 | epot = -70.5220937294762 | etot = -54.4566354690777 +767000 ekin = 8.18472660663812 | erot = 8.14791972853061 | epot = -70.7892818060129 | etot = -54.4566354708442 +768000 ekin = 8.44981765182505 | erot = 8.18277444598896 | epot = -71.0892275702847 | etot = -54.4566354724707 +769000 ekin = 8.74694394955809 | erot = 8.1934102761401 | epot = -71.3969896994077 | etot = -54.4566354737095 +770000 ekin = 9.06740299947994 | erot = 8.1668925870822 | epot = -71.6909310620033 | etot = -54.4566354754411 +771000 ekin = 9.40024405592185 | erot = 8.0972704268396 | epot = -71.9541499583046 | etot = -54.4566354755431 +772000 ekin = 9.7392466767354 | erot = 7.98875570216604 | epot = -72.1846378540219 | etot = -54.4566354751204 +773000 ekin = 10.0787428377271 | erot = 7.85333550379026 | epot = -72.3887138158951 | etot = -54.4566354743777 +774000 ekin = 10.4126881201152 | erot = 7.7083958703643 | epot = -72.5777194640539 | etot = -54.4566354735744 +775000 ekin = 10.7338614307151 | erot = 7.57363952830843 | epot = -72.7641364319749 | etot = -54.4566354729514 +776000 ekin = 11.0333888249733 | erot = 7.46794248970476 | epot = -72.9579667873444 | etot = -54.4566354726664 +777000 ekin = 11.3009163259239 | erot = 7.4067879580252 | epot = -73.1643397567044 | etot = -54.4566354727553 +778000 ekin = 11.5255306315342 | erot = 7.40073666286383 | epot = -73.3829027675338 | etot = -54.4566354731358 +779000 ekin = 11.6972525421016 | erot = 7.45497855956651 | epot = -73.6088665753392 | etot = -54.4566354736712 +780000 ekin = 11.8087202600939 | erot = 7.56970994296815 | epot = -73.8350656772622 | etot = -54.4566354742001 +781000 ekin = 11.8566181530578 | erot = 7.74100457483039 | epot = -74.0542582025001 | etot = -54.456635474612 +782000 ekin = 11.8424717374629 | erot = 7.96169824312067 | epot = -74.2608054554455 | etot = -54.4566354748619 +783000 ekin = 11.7726960688138 | erot = 8.22211610465601 | epot = -74.451447648427 | etot = -54.4566354749572 +784000 ekin = 11.6588151949644 | erot = 8.51079893970591 | epot = -74.626249609301 | etot = -54.4566354746306 +785000 ekin = 11.5160383797427 | erot = 8.81490190990078 | epot = -74.7875757641929 | etot = -54.4566354745495 +786000 ekin = 11.3604671764187 | erot = 9.12050352622682 | epot = -74.9376061770405 | etot = -54.456635474395 +787000 ekin = 11.2093970331482 | erot = 9.41374363427949 | epot = -75.0797761415915 | etot = -54.4566354741638 +788000 ekin = 11.0803298420515 | erot = 9.68171559586226 | epot = -75.2186809117856 | etot = -54.4566354738718 +789000 ekin = 10.990015347853 | erot = 9.91340849393361 | epot = -75.3600593153028 | etot = -54.4566354735162 +790000 ekin = 10.9532761013188 | erot = 10.1003645461521 | epot = -75.5102761206814 | etot = -54.4566354732105 +791000 ekin = 10.9812861942009 | erot = 10.2367032936414 | epot = -75.6746249609582 | etot = -54.4566354731158 +792000 ekin = 11.07959853459 | erot = 10.3187114954021 | epot = -75.8549455033984 | etot = -54.4566354734063 +793000 ekin = 11.2461815583943 | erot = 10.3441470521576 | epot = -76.04696408486 | etot = -54.4566354743081 +794000 ekin = 11.4700109610192 | erot = 10.3116670234223 | epot = -76.2383134599886 | etot = -54.4566354755471 +795000 ekin = 11.7325834354277 | erot = 10.2211808754199 | epot = -76.4103997878417 | etot = -54.456635476994 +796000 ekin = 12.0100258299308 | erot = 10.0748477065846 | epot = -76.5415090147597 | etot = -54.4566354782444 +797000 ekin = 12.2771250349956 | erot = 9.8787246438661 | epot = -76.6124851577628 | etot = -54.4566354789011 +798000 ekin = 12.5117241722713 | erot = 9.64405687332679 | epot = -76.6124165243526 | etot = -54.4566354787545 +799000 ekin = 12.6978884572411 | erot = 9.38719424491272 | epot = -76.5417181800251 | etot = -54.4566354778713 +800000 ekin = 12.8269839019128 | erot = 9.12779516055864 | epot = -76.4114145390006 | etot = -54.4566354765292 +801000 ekin = 12.8968371081739 | erot = 8.8858893983962 | epot = -76.2393619816496 | etot = -54.4566354750795 +802000 ekin = 12.9098422516567 | erot = 8.67886362135672 | epot = -76.0453413468272 | etot = -54.4566354738138 +803000 ekin = 12.8709437100201 | erot = 8.51925810389878 | epot = -75.8468372868222 | etot = -54.4566354729032 +804000 ekin = 12.7860755415627 | erot = 8.41392281565234 | epot = -75.6566338295777 | etot = -54.4566354723626 +805000 ekin = 12.6610782480597 | erot = 8.36419460868408 | epot = -75.4819083289771 | etot = -54.4566354722333 +806000 ekin = 12.5011884973858 | erot = 8.36563299489813 | epot = -75.3234569648038 | etot = -54.4566354725198 +807000 ekin = 12.3111195445504 | erot = 8.40891169865597 | epot = -75.1766667162171 | etot = -54.4566354730107 +808000 ekin = 12.095121368734 | erot = 8.48285306305284 | epot = -75.0346099055361 | etot = -54.4566354737493 +809000 ekin = 11.8570912953974 | erot = 8.57364419050982 | epot = -74.8873709604715 | etot = -54.4566354745643 +810000 ekin = 11.6008292340201 | erot = 8.66613366753602 | epot = -74.7235983769252 | etot = -54.4566354753691 +811000 ekin = 11.3302304258769 | erot = 8.74588715341365 | epot = -74.5327530553702 | etot = -54.4566354760797 +812000 ekin = 11.0494304355196 | erot = 8.80043497508578 | epot = -74.3065008872132 | etot = -54.4566354766079 +813000 ekin = 10.7661929388064 | erot = 8.82092143844872 | epot = -74.0437498529341 | etot = -54.456635475679 +814000 ekin = 10.4922967616633 | erot = 8.80392368468693 | epot = -73.7528559227946 | etot = -54.4566354764443 +815000 ekin = 10.1508207490589 | erot = 8.72967512609349 | epot = -73.3371313414895 | etot = -54.4566354663372 +816000 ekin = 10.0080919366186 | erot = 8.60822868160767 | epot = -73.0729560943078 | etot = -54.4566354760815 +817000 ekin = 9.94176631885301 | erot = 8.48405485445375 | epot = -72.8824566317337 | etot = -54.4566354584269 +818000 ekin = 9.81594850430121 | erot = 8.3555940593633 | epot = -72.6281780195219 | etot = -54.4566354558574 +819000 ekin = 9.71985113500631 | erot = 8.23701168824747 | epot = -72.4134982795336 | etot = -54.4566354562799 +820000 ekin = 9.65376512613598 | erot = 8.15015673057928 | epot = -72.2605573107521 | etot = -54.4566354540368 +821000 ekin = 9.62982370506 | erot = 8.1144853144284 | epot = -72.2009444716718 | etot = -54.4566354521834 +822000 ekin = 9.66077700454417 | erot = 8.14425821633497 | epot = -72.2616706720654 | etot = -54.4566354511863 +823000 ekin = 9.75392749286654 | erot = 8.24624180246886 | epot = -72.4568047466621 | etot = -54.4566354513267 +824000 ekin = 9.90828878172196 | erot = 8.41865138430695 | epot = -72.7835756186504 | etot = -54.4566354526215 +825000 ekin = 10.1139944761915 | erot = 8.65151311646557 | epot = -73.2221430475064 | etot = -54.4566354548493 +826000 ekin = 10.3538759474141 | erot = 8.92820306631524 | epot = -73.7387144713783 | etot = -54.456635457649 +827000 ekin = 10.6063389826515 | erot = 9.22772390081661 | epot = -74.2906983441037 | etot = -54.4566354606357 +828000 ekin = 10.8484921435448 | erot = 9.52726891661857 | epot = -74.8323965236266 | etot = -54.4566354634633 +829000 ekin = 11.0588299501949 | erot = 9.80476940800405 | epot = -75.3202348240482 | etot = -54.4566354658492 +830000 ekin = 11.2192526327726 | erot = 10.0413124779358 | epot = -75.717200578269 | etot = -54.4566354675605 +831000 ekin = 11.3164768756616 | erot = 10.2234037407987 | epot = -75.996516084876 | etot = -54.4566354684156 +832000 ekin = 11.3429029406333 | erot = 10.3449490492889 | epot = -76.1444874582283 | etot = -54.456635468306 +833000 ekin = 11.2968956967637 | erot = 10.4085990339157 | epot = -76.162130197922 | etot = -54.4566354672427 +834000 ekin = 11.1823662954097 | erot = 10.4259018262208 | epot = -76.0649035870926 | etot = -54.4566354654621 +835000 ekin = 11.0075932321863 | erot = 10.4150642921595 | epot = -75.8792929875085 | etot = -54.4566354631627 +836000 ekin = 10.7833921149651 | erot = 10.3989545533777 | epot = -75.6389821291538 | etot = -54.4566354608111 +837000 ekin = 10.5209501551067 | erot = 10.4011161497741 | epot = -75.3787017636982 | etot = -54.4566354588174 +838000 ekin = 10.2298721897633 | erot = 10.4412405801904 | epot = -75.1277482274284 | etot = -54.4566354574746 +839000 ekin = 9.91696986338476 | erot = 10.5315530525419 | epot = -74.9051583728945 | etot = -54.4566354569678 +840000 ekin = 9.58610156142556 | erot = 10.6755294545447 | epot = -74.7182664730479 | etot = -54.4566354570776 +841000 ekin = 9.23901842928916 | erot = 10.868774358766 | epot = -74.5644282456966 | etot = -54.4566354576414 +842000 ekin = 8.87685056109889 | erot = 11.1001329244443 | epot = -74.4336189441309 | etot = -54.4566354585878 +843000 ekin = 8.50173060237332 | erot = 11.3524188663853 | epot = -74.3107849279809 | etot = -54.4566354592223 +844000 ekin = 8.11795575234117 | erot = 11.6095427521759 | epot = -74.1841339640736 | etot = -54.4566354595565 +845000 ekin = 7.7323636156346 | erot = 11.8578438186145 | epot = -74.0468428937419 | etot = -54.4566354594928 +846000 ekin = 7.35399612877582 | erot = 12.0875238819869 | epot = -73.8981554697915 | etot = -54.4566354590287 +847000 ekin = 6.99323530269368 | erot = 12.2936929402636 | epot = -73.7435637011866 | etot = -54.4566354582293 +848000 ekin = 6.66076569764054 | erot = 12.4765135053587 | epot = -73.5939146602003 | etot = -54.456635457201 +849000 ekin = 6.3666800328782 | erot = 12.6405664290078 | epot = -73.463881917943 | etot = -54.4566354560569 +850000 ekin = 6.11988143346162 | erot = 12.7936422802312 | epot = -73.370159168615 | etot = -54.4566354549222 +851000 ekin = 5.92776024228382 | erot = 12.9452003507133 | epot = -73.3295960469045 | etot = -54.4566354539074 +852000 ekin = 5.7960279636932 | erot = 13.1047455615212 | epot = -73.3574089783272 | etot = -54.4566354531128 +853000 ekin = 5.72859704154505 | erot = 13.2803568756409 | epot = -73.4655893698171 | etot = -54.4566354526311 +854000 ekin = 5.72746205361538 | erot = 13.4775571124567 | epot = -73.6616546185709 | etot = -54.4566354524988 +855000 ekin = 5.79260154211897 | erot = 13.6986462729931 | epot = -73.9478832678393 | etot = -54.4566354527273 +856000 ekin = 5.92195007058806 | erot = 13.9425386772803 | epot = -74.3211242011602 | etot = -54.4566354532919 +857000 ekin = 6.11148060847962 | erot = 14.2050613164675 | epot = -74.7731773790806 | etot = -54.4566354541334 +858000 ekin = 6.35540247730945 | erot = 14.4795962342016 | epot = -75.2916341666887 | etot = -54.4566354551777 +859000 ekin = 6.64643750031564 | erot = 14.7578922330507 | epot = -75.860965189721 | etot = -54.4566354563546 +860000 ekin = 6.97610349831166 | erot = 15.0308449598814 | epot = -76.4635839158042 | etot = -54.4566354576112 +861000 ekin = 7.33492493635959 | erot = 15.289067930086 | epot = -77.0806283253769 | etot = -54.4566354589313 +862000 ekin = 7.71251467471118 | erot = 15.5231591806985 | epot = -77.6923093157332 | etot = -54.4566354603235 +863000 ekin = 8.09752575485436 | erot = 15.7236923479273 | epot = -78.2778535645947 | etot = -54.456635461813 +864000 ekin = 8.47754136486755 | erot = 15.8810831527511 | epot = -78.8152599810321 | etot = -54.4566354634134 +865000 ekin = 8.83903083983137 | erot = 15.9855505169287 | epot = -79.2812168218629 | etot = -54.4566354651028 +866000 ekin = 9.16752990644855 | erot = 16.0273731149892 | epot = -79.6515384882424 | etot = -54.4566354668046 +867000 ekin = 9.4481948353974 | erot = 15.9975398653769 | epot = -79.9023701691577 | etot = -54.4566354683834 +868000 ekin = 9.66683066871462 | erot = 15.8887400708328 | epot = -80.012206209204 | etot = -54.4566354696565 +869000 ekin = 9.8114021146704 | erot = 15.6964846393668 | epot = -79.964522224461 | etot = -54.4566354704238 +870000 ekin = 9.87390363902202 | erot = 15.4200471695787 | epot = -79.7505862791116 | etot = -54.456635470511 +871000 ekin = 9.85230952587241 | erot = 15.0629113171792 | epot = -79.3718563128587 | etot = -54.4566354698071 +872000 ekin = 9.75218730795529 | erot = 14.6325332985615 | epot = -78.8413560748222 | etot = -54.4566354683054 +873000 ekin = 9.58749579133931 | erot = 14.1394452328893 | epot = -78.183576490343 | etot = -54.4566354661144 +874000 ekin = 9.38014472385971 | erot = 13.5959424946698 | epot = -77.4327226819843 | etot = -54.4566354634548 +875000 ekin = 9.15807680462459 | erot = 13.0147078021408 | epot = -76.6294200673967 | etot = -54.4566354606314 +876000 ekin = 8.95192933203906 | erot = 12.4076841945648 | epot = -75.8162489845978 | etot = -54.4566354579939 +877000 ekin = 8.79071144336724 | erot = 11.7853760071416 | epot = -75.0327229063821 | etot = -54.4566354558733 +878000 ekin = 8.69731943583637 | erot = 11.1566317214023 | epot = -74.310586611744 | etot = -54.4566354545054 +879000 ekin = 8.68495451678148 | erot = 10.5288962872035 | epot = -73.6704862579504 | etot = -54.4566354539655 +880000 ekin = 8.75541640185982 | erot = 9.90888240824182 | epot = -73.1209342642439 | etot = -54.4566354541422 +881000 ekin = 8.89974452930202 | erot = 9.30353954408173 | epot = -72.6599195281517 | etot = -54.456635454768 +882000 ekin = 9.10092859928086 | erot = 8.72108289022328 | epot = -72.2786469450228 | etot = -54.4566354555187 +883000 ekin = 9.33776725236377 | erot = 8.1717467740479 | epot = -71.9661494825224 | etot = -54.4566354561108 +884000 ekin = 9.58873539184783 | erot = 7.66794414584009 | epot = -71.7133149940681 | etot = -54.4566354563802 +885000 ekin = 9.83498174995039 | erot = 7.22368667477458 | epot = -71.5153038810174 | etot = -54.4566354562924 +886000 ekin = 10.0620936935129 | erot = 6.85337791008391 | epot = -71.3721070595131 | etot = -54.4566354559163 +887000 ekin = 10.2607225026047 | erot = 6.57029245227609 | epot = -71.287650410252 | etot = -54.4566354553712 +888000 ekin = 10.4263755446762 | erot = 6.3850930045279 | epot = -71.2681040039977 | etot = -54.4566354547936 +889000 ekin = 10.5586710815122 | erot = 6.30462943881654 | epot = -71.3199359746427 | etot = -54.456635454314 +890000 ekin = 10.6602540895274 | erot = 6.33111707545905 | epot = -71.44800661904 | etot = -54.4566354540535 +891000 ekin = 10.7355099947677 | erot = 6.46170576299619 | epot = -71.6538512118778 | etot = -54.4566354541139 +892000 ekin = 10.7892241407025 | erot = 6.68844891424348 | epot = -71.9343085095022 | etot = -54.4566354545561 +893000 ekin = 10.8253819949029 | erot = 6.99871565288043 | epot = -72.2807331031711 | etot = -54.4566354553878 +894000 ekin = 10.8463299663516 | erot = 7.37610035055649 | epot = -72.6790657734492 | etot = -54.4566354565412 +895000 ekin = 10.8524754865981 | erot = 7.80183940290034 | epot = -73.1109503473759 | etot = -54.4566354578775 +896000 ekin = 10.84258586903 | erot = 8.25664380955676 | epot = -73.5558651377955 | etot = -54.4566354592087 +897000 ekin = 10.8145780999804 | erot = 8.72272211943533 | epot = -73.9939356797506 | etot = -54.4566354603349 +898000 ekin = 10.7665424606173 | erot = 9.1856480440094 | epot = -74.408825965727 | etot = -54.4566354611003 +899000 ekin = 10.6976805035067 | erot = 9.63567769337116 | epot = -74.789993658306 | etot = -54.4566354614281 +900000 ekin = 10.6088887087511 | erot = 10.0681851806665 | epot = -75.1337093507649 | etot = -54.4566354613474 +901000 ekin = 10.5028530073684 | erot = 10.4830654352253 | epot = -75.4425539035738 | etot = -54.4566354609801 +902000 ekin = 10.3836771774617 | erot = 10.8832063666161 | epot = -75.7235190045867 | etot = -54.4566354605089 +903000 ekin = 10.2561979891409 | erot = 11.2723815659219 | epot = -75.985215015189 | etot = -54.4566354601263 +904000 ekin = 10.1252127005267 | erot = 11.6530755865379 | epot = -76.2349237470494 | etot = -54.4566354599848 +905000 ekin = 9.99485047044316 | erot = 12.0247708238758 | epot = -76.4762567544754 | etot = -54.4566354601564 +906000 ekin = 9.86826182518682 | erot = 12.3830923598489 | epot = -76.7079896456546 | etot = -54.4566354606189 +907000 ekin = 9.74769326327307 | erot = 12.7199654419163 | epot = -76.924294166461 | etot = -54.4566354612716 +908000 ekin = 9.6348832193475 | erot = 13.024659584046 | epot = -77.1161782653647 | etot = -54.4566354619712 +909000 ekin = 9.53160068472316 | erot = 13.2853599354225 | epot = -77.273596082726 | etot = -54.4566354625803 +910000 ekin = 9.44009501998267 | erot = 13.4908067508291 | epot = -77.3875372338177 | etot = -54.4566354630059 +911000 ekin = 9.36326455556987 | erot = 13.631625237421 | epot = -77.4515252562038 | etot = -54.4566354632128 +912000 ekin = 9.30446941108009 | erot = 13.7011923330762 | epot = -77.4622972073668 | etot = -54.4566354632104 +913000 ekin = 9.26705259279243 | erot = 13.6961250397873 | epot = -77.419813095607 | etot = -54.4566354630273 +914000 ekin = 9.25372341950282 | erot = 13.6165806075345 | epot = -77.3269394897264 | etot = -54.4566354626891 +915000 ekin = 9.26596340709781 | erot = 13.4664769842524 | epot = -77.1890758535679 | etot = -54.4566354622177 +916000 ekin = 9.30355576104106 | erot = 13.2535559655947 | epot = -77.0137471882823 | etot = -54.4566354616466 +917000 ekin = 9.36426903859647 | erot = 12.9890809272832 | epot = -76.8099854269176 | etot = -54.4566354610379 +918000 ekin = 9.4436910117618 | erot = 12.6869990270094 | epot = -76.5873254992422 | etot = -54.456635460471 +919000 ekin = 9.53522052883235 | erot = 12.3625891360082 | epot = -76.3544451248811 | etot = -54.4566354600405 +920000 ekin = 9.63025415659348 | erot = 12.0308380430208 | epot = -76.1177276594267 | etot = -54.4566354598124 +921000 ekin = 9.71861106513001 | erot = 11.7049052778984 | epot = -75.8801518028528 | etot = -54.4566354598243 +922000 ekin = 9.78920770645238 | erot = 11.3950002815838 | epot = -75.6408434480852 | etot = -54.456635460049 +923000 ekin = 9.83093885318482 | erot = 11.1078500465709 | epot = -75.3954243601764 | etot = -54.4566354604207 +924000 ekin = 9.83367208380175 | erot = 10.8467682564238 | epot = -75.1370758010691 | etot = -54.4566354608435 +925000 ekin = 9.78923699201468 | erot = 10.6122146416912 | epot = -74.8580870949111 | etot = -54.4566354612052 +926000 ekin = 9.69228799632639 | erot = 10.4026778523663 | epot = -74.5516013101013 | etot = -54.4566354614087 +927000 ekin = 9.54094420683278 | erot = 10.2157130837765 | epot = -74.2132927519792 | etot = -54.4566354613699 +928000 ekin = 9.33714598597803 | erot = 10.048997614272 | epot = -73.8427790612797 | etot = -54.4566354610296 +929000 ekin = 9.08668869602515 | erot = 9.90129105968178 | epot = -73.4446152160675 | etot = -54.4566354603605 +930000 ekin = 8.79893949163162 | erot = 9.77317491044917 | epot = -73.0287498614586 | etot = -54.4566354593778 +931000 ekin = 8.48625276387823 | erot = 9.66741161206176 | epot = -72.6102998340871 | etot = -54.4566354581471 +932000 ekin = 8.16311074516661 | erot = 9.58874585511257 | epot = -72.2084920570715 | etot = -54.4566354567923 +933000 ekin = 7.84503269783002 | erot = 9.54303556692145 | epot = -71.8447037202439 | etot = -54.4566354554924 +934000 ekin = 7.54732721406884 | erot = 9.53576382286218 | epot = -71.5397264913837 | etot = -54.4566354544527 +935000 ekin = 7.28379852834082 | erot = 9.57018935595719 | epot = -71.3106233381741 | etot = -54.4566354538761 +936000 ekin = 7.06554340230337 | erot = 9.64555160737715 | epot = -71.1677304635952 | etot = -54.4566354539147 +937000 ekin = 6.89998137838108 | erot = 9.75579580008181 | epot = -71.1124126331005 | etot = -54.4566354546376 +938000 ekin = 6.79024863687593 | erot = 9.88921936744704 | epot = -71.1361034603281 | etot = -54.4566354560052 +939000 ekin = 6.735056987497 | erot = 10.0294464267282 | epot = -71.2211388720331 | etot = -54.4566354578079 +940000 ekin = 6.72907691270157 | erot = 10.1573224430746 | epot = -71.3430348156733 | etot = -54.4566354598971 +941000 ekin = 6.76383923217314 | erot = 10.2535241006628 | epot = -71.4739987947202 | etot = -54.4566354618843 +942000 ekin = 6.82912409651702 | erot = 10.3022923171746 | epot = -71.5880518771031 | etot = -54.4566354634114 +943000 ekin = 6.91476596969959 | erot = 10.294631540558 | epot = -71.6660329744293 | etot = -54.4566354641717 +944000 ekin = 7.0126905355688 | erot = 10.2304790515559 | epot = -71.6998050511037 | etot = -54.456635463979 +945000 ekin = 7.11873167354183 | erot = 10.1191217606733 | epot = -71.6944888970905 | etot = -54.4566354628754 +946000 ekin = 7.23341535199415 | erot = 9.97742521428975 | epot = -71.6674760274804 | etot = -54.4566354611965 +947000 ekin = 7.36083754474229 | erot = 9.82603454655117 | epot = -71.6435075508161 | etot = -54.4566354595226 +948000 ekin = 7.50549771867113 | erot = 9.68450715330014 | epot = -71.64664033044 | etot = -54.4566354584687 +949000 ekin = 7.6683659029019 | erot = 9.56693750753481 | epot = -71.6919388688308 | etot = -54.4566354583941 +950000 ekin = 7.84446366558868 | erot = 9.47955332197239 | epot = -71.7806524467887 | etot = -54.4566354592276 +951000 ekin = 8.02362258961447 | erot = 9.42089965823563 | epot = -71.901157708376 | etot = -54.4566354605259 +952000 ekin = 8.19401979348799 | erot = 9.38404388093099 | epot = -72.0346991361836 | etot = -54.4566354617646 +953000 ekin = 8.34627037925309 | erot = 9.35945524408341 | epot = -72.16236108595 | etot = -54.4566354626135 +954000 ekin = 8.47579105977707 | erot = 9.33731466668423 | epot = -72.269741189478 | etot = -54.4566354630167 +955000 ekin = 8.58263553145364 | erot = 9.3088230317301 | epot = -72.3480940262788 | etot = -54.4566354630951 +956000 ekin = 8.66958271589105 | erot = 9.26689225465248 | epot = -72.3931104336158 | etot = -54.4566354630722 +957000 ekin = 8.73983792560592 | erot = 9.20645883849863 | epot = -72.4029322269823 | etot = -54.4566354628778 +958000 ekin = 8.79532848880433 | erot = 9.12577516403045 | epot = -72.3777391154085 | etot = -54.4566354625737 +959000 ekin = 8.835902661134 | erot = 9.02777800329253 | epot = -72.3203161265399 | etot = -54.4566354621134 +960000 ekin = 8.85930075562983 | erot = 8.9205878787414 | epot = -72.2365240958258 | etot = -54.4566354614546 +961000 ekin = 8.86161651518579 | erot = 8.81766202969833 | epot = -72.1359140054711 | etot = -54.4566354605869 +962000 ekin = 8.83799666715819 | erot = 8.73718807966582 | epot = -72.0318202063664 | etot = -54.4566354595424 +963000 ekin = 8.78340386447636 | erot = 8.70071313768174 | epot = -71.9407524605549 | etot = -54.4566354583968 +964000 ekin = 8.69333156505503 | erot = 8.73109905621387 | epot = -71.8810660785369 | etot = -54.456635457268 +965000 ekin = 8.56440365898252 | erot = 8.84996493880353 | epot = -71.8710040540795 | etot = -54.4566354562935 +966000 ekin = 8.39482523790268 | erot = 9.07485296716098 | epot = -71.9263136607 | etot = -54.4566354556363 +967000 ekin = 8.1846781888089 | erot = 9.41644113231655 | epot = -72.0577547765549 | etot = -54.4566354554294 +968000 ekin = 7.93626974423865 | erot = 9.87613374643838 | epot = -72.2690389464832 | etot = -54.4566354558062 +969000 ekin = 7.65431026887565 | erot = 10.4442911839035 | epot = -72.5552369095158 | etot = -54.4566354567367 +970000 ekin = 7.34450165160811 | erot = 11.1010614724754 | epot = -72.9021985821365 | etot = -54.456635458053 +971000 ekin = 7.01497831129744 | erot = 11.8180138556047 | epot = -73.2896276264596 | etot = -54.4566354595575 +972000 ekin = 6.67661988301637 | erot = 12.5610022013245 | epot = -73.6942575453356 | etot = -54.4566354609948 +973000 ekin = 6.34325563528696 | erot = 13.2935365140779 | epot = -74.0934276115446 | etot = -54.4566354621798 +974000 ekin = 6.03126679097362 | erot = 13.9800756161855 | epot = -74.4679778700673 | etot = -54.4566354629081 +975000 ekin = 5.75832704437232 | erot = 14.5910245182133 | epot = -74.8059870256995 | etot = -54.4566354631139 +976000 ekin = 5.54248690288958 | erot = 15.1042545811179 | epot = -75.1033769468906 | etot = -54.4566354628831 +977000 ekin = 5.40035031846992 | erot = 15.5056612502556 | epot = -75.3626470311247 | etot = -54.4566354623992 +978000 ekin = 5.34501003152772 | erot = 15.7884985247861 | epot = -75.5901440181953 | etot = -54.4566354618815 +979000 ekin = 5.38417633217446 | erot = 15.9518932070765 | epot = -75.7927050007827 | etot = -54.4566354615317 +980000 ekin = 5.51889158471417 | erot = 15.9990584786403 | epot = -75.9745855248341 | etot = -54.4566354614796 +981000 ekin = 5.74308889432877 | erot = 15.9356762595028 | epot = -76.1354006155962 | etot = -54.4566354617647 +982000 ekin = 6.04407260765955 | erot = 15.7687916692143 | epot = -76.2694997391999 | etot = -54.4566354623261 +983000 ekin = 6.40382989934479 | erot = 15.5063975906933 | epot = -76.3668629530592 | etot = -54.4566354630211 +984000 ekin = 6.80095841874027 | erot = 15.1576983608347 | epot = -76.4152922432271 | etot = -54.456635463652 +985000 ekin = 7.21291844146417 | erot = 14.7338425281795 | epot = -76.4033964336627 | etot = -54.4566354640191 +986000 ekin = 7.6182826564102 | erot = 14.2487453062978 | epot = -76.3236634266735 | etot = -54.4566354639655 +987000 ekin = 7.99866441027088 | erot = 13.7195510823837 | epot = -76.1748509560775 | etot = -54.4566354634229 +988000 ekin = 8.34006634570511 | erot = 13.1663738040327 | epot = -75.9630756121665 | etot = -54.4566354624287 +989000 ekin = 8.63350862209283 | erot = 12.6111857670953 | epot = -75.7013298503023 | etot = -54.4566354611142 +990000 ekin = 8.87494555512831 | erot = 12.0760163564726 | epot = -75.4075973712662 | etot = -54.4566354596653 +991000 ekin = 9.06461955888563 | erot = 11.5808385823036 | epot = -75.1020935994709 | etot = -54.4566354582817 +992000 ekin = 9.20608865946024 | erot = 11.1415830195349 | epot = -74.8043071361274 | etot = -54.4566354571323 +993000 ekin = 9.30517812932134 | erot = 10.7686313367174 | epot = -74.5304449223696 | etot = -54.4566354563309 +994000 ekin = 9.36905574689451 | erot = 10.4659766381002 | epot = -74.2916678409224 | etot = -54.4566354559277 +995000 ekin = 9.40554136791977 | erot = 10.2310751483189 | epot = -74.0932519721565 | etot = -54.4566354559178 +996000 ekin = 9.42266810589654 | erot = 10.0553042346563 | epot = -73.9346077968042 | etot = -54.4566354562514 +997000 ekin = 9.42843932290709 | erot = 9.92490942412143 | epot = -73.8099842038803 | etot = -54.4566354568518 +998000 ekin = 9.43069348818201 | erot = 9.82234985048033 | epot = -73.7096787962734 | etot = -54.4566354576111 +999000 ekin = 9.43700002899931 | erot = 9.72798019137154 | epot = -73.6216156787951 | etot = -54.4566354584243 +1000000 ekin = 9.45454475451511 | erot = 9.62197027181692 | epot = -73.5331504854816 | etot = -54.4566354591496 + 1000000 352.42265 -75.546285 2.0131342 -64.078606 -0.0098335381 39304000 +Loop time of 10.2487 on 4 procs for 1000000 steps with 10 atoms + +Performance: 143.822 ns/day, 0.167 hours/ns, 97573.589 timesteps/s, 975.736 katom-step/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.464 | 4.1822 | 5.9402 | 50.2 | 40.81 +Bond | 0.13841 | 0.18486 | 0.23656 | 8.9 | 1.80 +Neigh | 0.006895 | 0.006952 | 0.007001 | 0.1 | 0.07 +Comm | 2.2239 | 4.2461 | 5.1692 | 57.6 | 41.43 +Output | 0.059508 | 0.061929 | 0.066381 | 1.1 | 0.60 +Modify | 0.37634 | 0.4606 | 0.52884 | 10.0 | 4.49 +Other | | 1.106 | | | 10.79 + +Nlocal: 2.5 ave 4 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 9 max 6 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25 ave 19 max 5 min +Histogram: 2 1 0 0 0 0 0 0 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:10 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/oxdna_real.cgdna b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/oxdna_real.cgdna new file mode 120000 index 0000000000..8796f00828 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/oxdna_real.cgdna @@ -0,0 +1 @@ +../../../../../../../potentials/oxdna_real.cgdna \ No newline at end of file diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/data.dsring b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/data.dsring new file mode 100644 index 0000000000..33f6115ae5 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/data.dsring @@ -0,0 +1,622 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +148 atoms +4 atom types +148 bonds +1 bond types +148 ellipsoids + +0 851 xlo xhi +0 851 ylo yhi +0 851 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 208.31885120063512 209.07830059400624 213.0216021921939 1 1 1.0016462505133576 0 0 0 +2 4 208.94483576838627 206.4448010919165 216.6882923344523 1 1 1.0016462505133576 0 0 0 +3 3 211.56385346871699 204.30406864289688 220.11920728875927 1 1 1.0016462505133576 0 0 0 +4 2 214.31495335572012 204.35063728809808 223.61677544780568 1 1 1.0016462505133576 0 0 0 +5 1 217.30951997235965 206.16090626093134 225.4674912137906 1 1 1.0016462505133576 0 0 0 +6 2 219.30502197188136 209.00909667501074 227.49674701236893 1 1 1.0016462505133576 0 0 0 +7 3 219.83292281044646 212.19753274141107 230.53026977239148 1 1 1.0016462505133576 0 0 0 +8 2 218.93091557749156 214.31473141418766 234.6931272540053 1 1 1.0016462505133576 0 0 0 +9 4 220.32518751145957 214.85183803522298 239.6469648355356 1 1 1.0016462505133576 0 0 0 +10 2 219.79275827382872 213.3404053532149 243.70006386710043 1 1 1.0016462505133576 0 0 0 +11 3 220.70928151349608 210.21381004200654 247.14815553587854 1 1 1.0016462505133576 0 0 0 +12 2 223.67193733154724 208.04535577836813 249.67978988879284 1 1 1.0016462505133576 0 0 0 +13 2 227.31016552169513 206.16686658451448 251.61597827076264 1 1 1.0016462505133576 0 0 0 +14 1 231.80592101718645 204.9336536048614 251.53105173903185 1 1 1.0016462505133576 0 0 0 +15 2 236.2250804923752 205.47987477011685 250.98539881261863 1 1 1.0016462505133576 0 0 0 +16 3 240.0068773257833 207.77004331975903 249.53594241966383 1 1 1.0016462505133576 0 0 0 +17 1 242.98566065658693 210.5462682234126 249.63496548893542 1 1 1.0016462505133576 0 0 0 +18 4 245.42888445426894 214.27953740691964 250.53493716205472 1 1 1.0016462505133576 0 0 0 +19 2 248.78751685377597 216.90541434653767 253.53160552044426 1 1 1.0016462505133576 0 0 0 +20 4 251.39963359406735 218.16175894319667 257.62870661099066 1 1 1.0016462505133576 0 0 0 +21 2 255.5677235249031 217.61926364274564 260.07819570237643 1 1 1.0016462505133576 0 0 0 +22 3 259.63024332567574 215.18262726567113 260.69715353283686 1 1 1.0016462505133576 0 0 0 +23 1 263.1457867599882 212.6433935962059 258.9487935453862 1 1 1.0016462505133576 0 0 0 +24 1 266.3827446371434 210.87213953618837 256.26055100860737 1 1 1.0016462505133576 0 0 0 +25 2 267.97463902393866 210.20760693366043 251.4251108047254 1 1 1.0016462505133576 0 0 0 +26 3 270.07811694250654 210.90888555541903 247.7392596432837 1 1 1.0016462505133576 0 0 0 +27 1 271.09287437447114 213.11656552311496 244.5712139335691 1 1 1.0016462505133576 0 0 0 +28 4 272.8644901379567 216.09853596389848 242.34668607897146 1 1 1.0016462505133576 0 0 0 +29 3 277.14925724680575 218.15361661850437 241.02448320337692 1 1 1.0016462505133576 0 0 0 +30 2 281.6281862385014 219.54423347807102 240.83577460409623 1 1 1.0016462505133576 0 0 0 +31 4 285.53553117381364 218.07611082158127 239.4456849189117 1 1 1.0016462505133576 0 0 0 +32 2 288.8938226529956 215.3666526766779 237.57548982559325 1 1 1.0016462505133576 0 0 0 +33 1 291.12514756370877 212.98912935663924 233.8324040870632 1 1 1.0016462505133576 0 0 0 +34 4 291.3890795510732 210.45844522291486 230.3986316964525 1 1 1.0016462505133576 0 0 0 +35 2 290.3105820760069 208.74036664050792 226.7042745336879 1 1 1.0016462505133576 0 0 0 +36 4 289.18201447621146 208.91363527052587 222.89820557251684 1 1 1.0016462505133576 0 0 0 +37 2 288.971153902218 209.4805264669763 218.28666756836168 1 1 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9.999999997766462 9.999999997766462 9.999999997766462 -0.2714234139641493 0.5100075547669219 0.7525252671110235 -0.3161128703362045 +141 9.999999997766462 9.999999997766462 9.999999997766462 -0.18623801902606954 0.7425995746707363 0.5393607888180064 -0.35064399531961904 +142 9.999999997766462 9.999999997766462 9.999999997766462 -0.20986530401416495 0.8687694482447833 0.31310815046609125 -0.3211845047308489 +143 9.999999997766462 9.999999997766462 9.999999997766462 -0.1354858154681459 0.9418151150282347 0.014007263864675714 -0.3072973795370049 +144 9.999999997766462 9.999999997766462 9.999999997766462 -0.09121534676964865 0.942226022288734 -0.27543028841845296 -0.16741576884323378 +145 9.999999997766462 9.999999997766462 9.999999997766462 -0.07761809459687324 0.8625267258049417 -0.49537475942792236 -0.06802151413402847 +146 9.999999997766462 9.999999997766462 9.999999997766462 -0.07853628249634757 0.6763776292711046 -0.7295609015799718 -0.06392375019562685 +147 9.999999997766462 9.999999997766462 9.999999997766462 0.18414802295685903 -0.34920401662445405 0.9187682994180332 0.0032973320918147885 +148 9.999999997766462 9.999999997766462 9.999999997766462 0.13019081328575915 -0.1370605858009623 0.9781659097238085 -0.08634929652338917 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/in.dsring b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/in.dsring new file mode 100644 index 0000000000..636af13352 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/in.dsring @@ -0,0 +1,73 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring + +set atom * mass 315.8376 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.1 new file mode 100644 index 0000000000..e605409b1f --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.1 @@ -0,0 +1,286 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring +Reading data file ... + orthogonal box = (0 0 0) to (851 851 851) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 148 atoms + reading velocities ... + 148 velocities + scanning bonds ... + 1 = max bonds/atom + 148 ellipsoids + orthogonal box = (0 0 0) to (851 851 851) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 148 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.012 seconds + +set atom * mass 315.8376 +Setting atom values ... + 148 settings made for mass + +group all type 1 4 +148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 36 36 36 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351 +Per MPI rank memory allocation (min/avg/max) = 7.806 | 7.806 | 7.806 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 278.46107 -1367.7166 42.531022 -1203.1698 -0.0059756093 6.1629505e+08 +1000 ekin = 122.370905858635 | erot = 126.447129514011 | epot = -1326.58529267981 | etot = -1077.76725730717 +2000 ekin = 122.691275133791 | erot = 127.497291822809 | epot = -1327.95582427469 | etot = -1077.76725731809 +3000 ekin = 122.920677842253 | erot = 128.459039892254 | epot = -1329.14697506148 | etot = -1077.76725732698 +4000 ekin = 123.015104309575 | erot = 129.250631266888 | epot = -1330.03299290867 | etot = -1077.76725733221 +5000 ekin = 122.9570060981 | erot = 129.822304188926 | epot = -1330.54656761964 | etot = -1077.76725733262 +6000 ekin = 122.758396503728 | erot = 130.158463496347 | epot = -1330.68411732949 | etot = -1077.76725732941 +7000 ekin = 122.444997038107 | erot = 130.2721351435 | epot = -1330.48438950495 | etot = -1077.76725732334 +8000 ekin = 122.055455926322 | erot = 130.202756105441 | epot = -1330.02546934809 | etot = -1077.76725731633 +9000 ekin = 121.639778047767 | erot = 130.001921534636 | epot = -1329.40895689073 | etot = -1077.76725730833 +10000 ekin = 121.255561480542 | erot = 129.724613334693 | epot = -1328.74743211587 | etot = -1077.76725730064 +11000 ekin = 120.959150047792 | erot = 129.417382591736 | epot = -1328.14378993383 | etot = -1077.7672572943 +12000 ekin = 120.804873255896 | erot = 129.110119861451 | epot = -1327.68225040707 | etot = -1077.76725728973 +13000 ekin = 120.84692312026 | erot = 128.811452781899 | epot = -1327.42563318933 | etot = -1077.76725728717 +14000 ekin = 121.124227416954 | erot = 128.510318857508 | epot = -1327.40180356072 | etot = -1077.76725728626 +15000 ekin = 121.666723735015 | erot = 128.179805529182 | epot = -1327.61378655278 | etot = -1077.76725728858 +16000 ekin = 122.48420413773 | erot = 127.7714101238 | epot = -1328.02287155596 | etot = -1077.76725729443 +17000 ekin = 123.554901437623 | erot = 127.223257664149 | epot = -1328.54541640317 | etot = -1077.7672573014 +18000 ekin = 124.838358543238 | erot = 126.479155255363 | epot = -1329.0847711071 | etot = -1077.7672573085 +19000 ekin = 126.271030938727 | erot = 125.497490625599 | epot = -1329.5357788797 | etot = -1077.76725731537 +20000 ekin = 127.785246119996 | erot = 124.269691231027 | epot = -1329.82219466647 | etot = -1077.76725731544 +21000 ekin = 129.341920134184 | erot = 122.835059904168 | epot = -1329.94423735083 | etot = -1077.76725731248 +22000 ekin = 130.919691006211 | erot = 121.262876727301 | epot = -1329.94982504099 | etot = -1077.76725730747 +23000 ekin = 132.5067055481 | erot = 119.63798200526 | epot = -1329.91194485558 | etot = -1077.76725730222 +24000 ekin = 134.092490326559 | erot = 118.03901918442 | epot = -1329.8987668112 | etot = -1077.76725730022 +25000 ekin = 135.660464836621 | erot = 116.515685186215 | epot = -1329.94340732287 | etot = -1077.76725730004 +26000 ekin = 137.186778726604 | erot = 115.085213344397 | epot = -1330.03924937555 | etot = -1077.76725730455 +27000 ekin = 138.631216641226 | erot = 113.733576310579 | epot = -1330.13205025948 | etot = -1077.76725730768 +28000 ekin = 139.956351860934 | erot = 112.450817889846 | epot = -1330.17442705975 | etot = -1077.76725730897 +29000 ekin = 141.132095730945 | erot = 111.248013058276 | epot = -1330.14736609674 | etot = -1077.76725730752 +30000 ekin = 142.135255524947 | erot = 110.165318126416 | epot = -1330.06783095566 | etot = -1077.7672573043 +31000 ekin = 142.945319498095 | erot = 109.26906345586 | epot = -1329.98164025322 | etot = -1077.76725729927 +32000 ekin = 143.550508334477 | erot = 108.646435343349 | epot = -1329.96420097205 | etot = -1077.76725729422 +33000 ekin = 143.94192379333 | erot = 108.385261854402 | epot = -1330.09444293819 | etot = -1077.76725729046 +34000 ekin = 144.112039801496 | erot = 108.556164698166 | epot = -1330.43546178798 | etot = -1077.76725728832 +35000 ekin = 144.054908300964 | erot = 109.203418763406 | epot = -1331.02558435228 | etot = -1077.76725728791 +36000 ekin = 143.757709793102 | erot = 110.342536293123 | epot = -1331.86750337561 | etot = -1077.76725728938 +37000 ekin = 143.224204313506 | erot = 111.95088434885 | epot = -1332.942345956 | etot = -1077.76725729365 +38000 ekin = 142.457513980673 | erot = 113.968727530034 | epot = -1334.19349881072 | etot = -1077.76725730001 +39000 ekin = 141.463565854942 | erot = 116.29723735485 | epot = -1335.52806051882 | etot = -1077.76725730903 +40000 ekin = 140.250124908962 | erot = 118.793122406283 | epot = -1336.81050463699 | etot = -1077.76725732174 +41000 ekin = 138.820773211814 | erot = 121.268568926308 | epot = -1337.85659947459 | etot = -1077.76725733647 +42000 ekin = 137.182796339923 | erot = 123.506485031842 | epot = -1338.45653872253 | etot = -1077.76725735076 +43000 ekin = 135.367500581476 | erot = 125.29033107441 | epot = -1338.42508901096 | etot = -1077.76725735508 +44000 ekin = 133.337269375167 | erot = 126.415468495777 | epot = -1337.51999529678 | etot = -1077.76725742584 +45000 ekin = 131.439049413892 | erot = 126.724836949372 | epot = -1335.93114371325 | etot = -1077.76725734999 +46000 ekin = 129.845441134595 | erot = 126.391857491267 | epot = -1334.00455608503 | etot = -1077.76725745917 +47000 ekin = 128.256459545521 | erot = 125.565939986762 | epot = -1331.58965689646 | etot = -1077.76725736418 +48000 ekin = 127.882214731217 | erot = 124.234254983921 | epot = -1329.88372728254 | etot = -1077.76725756741 +49000 ekin = 127.351717354214 | erot = 122.498251564086 | epot = -1327.61722629563 | etot = -1077.76725737733 +50000 ekin = 127.042187382637 | erot = 120.712825414822 | epot = -1325.52227015942 | etot = -1077.76725736196 +51000 ekin = 126.939090812203 | erot = 119.088171838498 | epot = -1323.7945200008 | etot = -1077.7672573501 +52000 ekin = 127.052758247807 | erot = 117.797033031223 | epot = -1322.61704861958 | etot = -1077.76725734055 +53000 ekin = 127.367330865571 | erot = 116.951027484839 | epot = -1322.08561579165 | etot = -1077.76725744124 +54000 ekin = 127.699598694243 | erot = 116.588954946935 | epot = -1322.05581098738 | etot = -1077.7672573462 +55000 ekin = 128.765472970124 | erot = 116.722527775949 | epot = -1323.25525818877 | etot = -1077.76725744269 +56000 ekin = 129.745971272492 | erot = 117.329047803033 | epot = -1324.84227644251 | etot = -1077.76725736699 +57000 ekin = 130.68679923891 | erot = 118.336149226794 | epot = -1326.79020584606 | etot = -1077.76725738035 +58000 ekin = 131.547485886187 | erot = 119.658488175854 | epot = -1328.97323145072 | etot = -1077.76725738868 +59000 ekin = 132.288746551762 | erot = 121.192124361468 | epot = -1331.2481283112 | etot = -1077.76725739797 +60000 ekin = 132.889658039575 | erot = 122.813399448196 | epot = -1333.47031489469 | etot = -1077.76725740691 +61000 ekin = 133.34147638721 | erot = 124.387402689362 | epot = -1335.49613649179 | etot = -1077.76725741522 +62000 ekin = 133.649114161524 | erot = 125.778714754977 | epot = -1337.19508633847 | etot = -1077.76725742197 +63000 ekin = 133.82819881192 | erot = 126.867080850077 | epot = -1338.46253708695 | etot = -1077.76725742496 +64000 ekin = 133.906684651824 | erot = 127.563040672905 | epot = -1339.23698275248 | etot = -1077.76725742775 +65000 ekin = 133.909388287634 | erot = 127.810288982225 | epot = -1339.48693469479 | etot = -1077.76725742493 +66000 ekin = 133.86081006735 | erot = 127.603400400037 | epot = -1339.23146788818 | etot = -1077.76725742079 +67000 ekin = 133.775485591323 | erot = 126.989915348575 | epot = -1338.53265835276 | etot = -1077.76725741286 +68000 ekin = 133.656407434476 | erot = 126.056031307506 | epot = -1337.47969615099 | etot = -1077.76725740901 +69000 ekin = 133.498245523806 | erot = 124.901121868324 | epot = -1336.16662479387 | etot = -1077.76725740175 +70000 ekin = 133.29399842671 | erot = 123.635623442427 | epot = -1334.69687926337 | etot = -1077.76725739423 +71000 ekin = 133.029392386924 | erot = 122.365171367186 | epot = -1333.16182114485 | etot = -1077.76725739074 +72000 ekin = 132.685056689193 | erot = 121.171597639892 | epot = -1331.62391171537 | etot = -1077.76725738628 +73000 ekin = 132.251376493387 | erot = 120.116099015078 | epot = -1330.13473289197 | etot = -1077.76725738351 +74000 ekin = 131.726574812548 | erot = 119.247057316129 | epot = -1328.74088951045 | etot = -1077.76725738177 +75000 ekin = 131.110698166934 | erot = 118.598252474103 | epot = -1327.47620801944 | etot = -1077.7672573784 +76000 ekin = 130.422389067205 | erot = 118.195180955537 | epot = -1326.38482739773 | etot = -1077.76725737499 +77000 ekin = 129.697453900293 | erot = 118.05495085627 | epot = -1325.51966212761 | etot = -1077.76725737104 +78000 ekin = 128.983808987508 | erot = 118.189138027539 | epot = -1324.94020438318 | etot = -1077.76725736813 +79000 ekin = 128.33503884882 | erot = 118.595476281743 | epot = -1324.69777249594 | etot = -1077.76725736537 +80000 ekin = 127.800117751073 | erot = 119.26689064397 | epot = -1324.83426576002 | etot = -1077.76725736498 +81000 ekin = 127.407996010304 | erot = 120.178391162382 | epot = -1325.35364454144 | etot = -1077.76725736875 +82000 ekin = 127.161473447285 | erot = 121.280514709077 | epot = -1326.20924553086 | etot = -1077.76725737449 +83000 ekin = 127.04595184901 | erot = 122.504106964497 | epot = -1327.31731619533 | etot = -1077.76725738182 +84000 ekin = 127.034443068044 | erot = 123.770035256801 | epot = -1328.57173571383 | etot = -1077.76725738899 +85000 ekin = 127.100009803031 | erot = 125.002871400657 | epot = -1329.87013859938 | etot = -1077.7672573957 +86000 ekin = 127.209916231691 | erot = 126.126063406782 | epot = -1331.10323704296 | etot = -1077.76725740449 +87000 ekin = 127.33974310822 | erot = 127.079810479666 | epot = -1332.186810994 | etot = -1077.76725740611 +88000 ekin = 127.492851572889 | erot = 127.842496747421 | epot = -1333.1026057236 | etot = -1077.76725740329 +89000 ekin = 127.697668813164 | erot = 128.428193060101 | epot = -1333.89311927022 | etot = -1077.76725739695 +90000 ekin = 128.002367682838 | erot = 128.890624121692 | epot = -1334.66024919208 | etot = -1077.76725738755 +91000 ekin = 128.464258986688 | erot = 129.314890049746 | epot = -1335.54640641371 | etot = -1077.76725737728 +92000 ekin = 129.138404881412 | erot = 129.795965407416 | epot = -1336.70162765837 | etot = -1077.76725736954 +93000 ekin = 130.05988004796 | erot = 130.410441748419 | epot = -1338.23757916353 | etot = -1077.76725736715 +94000 ekin = 131.22652253725 | erot = 131.190635069448 | epot = -1340.18441497914 | etot = -1077.76725737244 +95000 ekin = 132.586213223046 | erot = 132.107679404097 | epot = -1342.46115001118 | etot = -1077.76725738403 +96000 ekin = 134.044080427152 | erot = 133.075735506149 | epot = -1344.8870733339 | etot = -1077.7672574006 +97000 ekin = 135.476028603552 | erot = 133.967715320791 | epot = -1347.21100134248 | etot = -1077.76725741814 +98000 ekin = 136.748227204441 | erot = 134.641388466874 | epot = -1349.15687309791 | etot = -1077.76725742659 +99000 ekin = 137.752624159367 | erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384 +100000 ekin = 138.392477025647 | erot = 134.944608034508 | epot = -1351.10434250636 | etot = -1077.76725744621 + 100000 315.83543 -1390.6819 39.577599 -1212.7119 -0.012722464 6.1629505e+08 +Loop time of 85.2132 on 1 procs for 100000 steps with 148 atoms + +Performance: 1.730 ns/day, 13.875 hours/ns, 1173.528 timesteps/s, 173.682 katom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 81.71 | 81.71 | 81.71 | 0.0 | 95.89 +Bond | 1.103 | 1.103 | 1.103 | 0.0 | 1.29 +Neigh | 0.017589 | 0.017589 | 0.017589 | 0.0 | 0.02 +Comm | 0.055508 | 0.055508 | 0.055508 | 0.0 | 0.07 +Output | 0.1581 | 0.1581 | 0.1581 | 0.0 | 0.19 +Modify | 2.0369 | 2.0369 | 2.0369 | 0.0 | 2.39 +Other | | 0.132 | | | 0.15 + +Nlocal: 148 ave 148 max 148 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4199 ave 4199 max 4199 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4199 +Ave neighs/atom = 28.371622 +Ave special neighs/atom = 6 +Neighbor list builds = 100 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.5.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:01:25 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.4 new file mode 100644 index 0000000000..4701412063 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.4 @@ -0,0 +1,286 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring +Reading data file ... + orthogonal box = (0 0 0) to (851 851 851) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 148 atoms + reading velocities ... + 148 velocities + scanning bonds ... + 1 = max bonds/atom + 148 ellipsoids + orthogonal box = (0 0 0) to (851 851 851) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 148 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.015 seconds + +set atom * mass 315.8376 +Setting atom values ... + 148 settings made for mass + +group all type 1 4 +148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 36 36 36 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351 +Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.668 | 7.742 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 278.46107 -1367.7166 42.531022 -1203.1698 -0.0059756093 6.1629505e+08 +1000 ekin = 122.370905858635 | erot = 126.447129514011 | epot = -1326.58529267981 | etot = -1077.76725730716 +2000 ekin = 122.691275133791 | erot = 127.497291822808 | epot = -1327.95582427469 | etot = -1077.76725731809 +3000 ekin = 122.920677842253 | erot = 128.459039892254 | epot = -1329.14697506148 | etot = -1077.76725732698 +4000 ekin = 123.015104309575 | erot = 129.250631266888 | epot = -1330.03299290867 | etot = -1077.7672573322 +5000 ekin = 122.957006098101 | erot = 129.822304188925 | epot = -1330.54656761964 | etot = -1077.76725733262 +6000 ekin = 122.758396503728 | erot = 130.158463496346 | epot = -1330.68411732949 | etot = -1077.76725732941 +7000 ekin = 122.444997038108 | erot = 130.272135143499 | epot = -1330.48438950495 | etot = -1077.76725732334 +8000 ekin = 122.055455926323 | erot = 130.202756105441 | epot = -1330.02546934809 | etot = -1077.76725731633 +9000 ekin = 121.639778047767 | erot = 130.001921534637 | epot = -1329.40895689073 | etot = -1077.76725730833 +10000 ekin = 121.255561480543 | erot = 129.724613334694 | epot = -1328.74743211587 | etot = -1077.76725730063 +11000 ekin = 120.959150047793 | erot = 129.417382591737 | epot = -1328.14378993382 | etot = -1077.76725729429 +12000 ekin = 120.804873255897 | erot = 129.110119861453 | epot = -1327.68225040707 | etot = -1077.76725728972 +13000 ekin = 120.846923120261 | erot = 128.8114527819 | epot = -1327.42563318933 | etot = -1077.76725728717 +14000 ekin = 121.124227416955 | erot = 128.51031885751 | epot = -1327.40180356072 | etot = -1077.76725728625 +15000 ekin = 121.666723735015 | erot = 128.179805529184 | epot = -1327.61378655278 | etot = -1077.76725728858 +16000 ekin = 122.48420413773 | erot = 127.771410123803 | epot = -1328.02287155596 | etot = -1077.76725729443 +17000 ekin = 123.554901437623 | erot = 127.223257664152 | epot = -1328.54541640317 | etot = -1077.76725730139 +18000 ekin = 124.838358543238 | erot = 126.479155255366 | epot = -1329.0847711071 | etot = -1077.7672573085 +19000 ekin = 126.271030938727 | erot = 125.497490625601 | epot = -1329.53577887969 | etot = -1077.76725731536 +20000 ekin = 127.785246119996 | erot = 124.269691231029 | epot = -1329.82219466646 | etot = -1077.76725731543 +21000 ekin = 129.341920134184 | erot = 122.835059904169 | epot = -1329.94423735083 | etot = -1077.76725731247 +22000 ekin = 130.91969100621 | erot = 121.2628767273 | epot = -1329.94982504098 | etot = -1077.76725730747 +23000 ekin = 132.506705548099 | erot = 119.637982005259 | epot = -1329.91194485557 | etot = -1077.76725730222 +24000 ekin = 134.092490326558 | erot = 118.039019184419 | epot = -1329.89876681119 | etot = -1077.76725730022 +25000 ekin = 135.660464836621 | erot = 116.515685186213 | epot = -1329.94340732286 | etot = -1077.76725730003 +26000 ekin = 137.186778726603 | erot = 115.085213344396 | epot = -1330.03924937554 | etot = -1077.76725730454 +27000 ekin = 138.631216641226 | erot = 113.733576310578 | epot = -1330.13205025948 | etot = -1077.76725730767 +28000 ekin = 139.956351860934 | erot = 112.450817889845 | epot = -1330.17442705975 | etot = -1077.76725730897 +29000 ekin = 141.132095730946 | erot = 111.248013058276 | epot = -1330.14736609673 | etot = -1077.76725730751 +30000 ekin = 142.135255524949 | erot = 110.165318126416 | epot = -1330.06783095566 | etot = -1077.76725730429 +31000 ekin = 142.945319498097 | erot = 109.269063455861 | epot = -1329.98164025322 | etot = -1077.76725729926 +32000 ekin = 143.550508334479 | erot = 108.64643534335 | epot = -1329.96420097205 | etot = -1077.76725729422 +33000 ekin = 143.941923793332 | erot = 108.385261854403 | epot = -1330.09444293819 | etot = -1077.76725729046 +34000 ekin = 144.112039801499 | erot = 108.556164698166 | epot = -1330.43546178798 | etot = -1077.76725728831 +35000 ekin = 144.054908300967 | erot = 109.203418763407 | epot = -1331.02558435228 | etot = -1077.76725728791 +36000 ekin = 143.757709793105 | erot = 110.342536293123 | epot = -1331.8675033756 | etot = -1077.76725728938 +37000 ekin = 143.224204313509 | erot = 111.950884348849 | epot = -1332.942345956 | etot = -1077.76725729364 +38000 ekin = 142.457513980675 | erot = 113.968727530033 | epot = -1334.19349881072 | etot = -1077.76725730001 +39000 ekin = 141.463565854944 | erot = 116.297237354849 | epot = -1335.52806051882 | etot = -1077.76725730903 +40000 ekin = 140.250124908963 | erot = 118.793122406281 | epot = -1336.81050463698 | etot = -1077.76725732174 +41000 ekin = 138.820773211815 | erot = 121.268568926305 | epot = -1337.85659947459 | etot = -1077.76725733647 +42000 ekin = 137.182796339923 | erot = 123.506485031839 | epot = -1338.45653872252 | etot = -1077.76725735076 +43000 ekin = 135.367500581475 | erot = 125.290331074407 | epot = -1338.42508901096 | etot = -1077.76725735507 +44000 ekin = 133.337269375166 | erot = 126.415468495773 | epot = -1337.51999529677 | etot = -1077.76725742583 +45000 ekin = 131.43904941389 | erot = 126.724836949369 | epot = -1335.93114371325 | etot = -1077.76725734999 +46000 ekin = 129.845441134593 | erot = 126.391857491264 | epot = -1334.00455608502 | etot = -1077.76725745916 +47000 ekin = 128.256459545521 | erot = 125.565939986761 | epot = -1331.58965689646 | etot = -1077.76725736417 +48000 ekin = 127.882214731216 | erot = 124.23425498392 | epot = -1329.88372728254 | etot = -1077.7672575674 +49000 ekin = 127.351717354214 | erot = 122.498251564087 | epot = -1327.61722629563 | etot = -1077.76725737733 +50000 ekin = 127.042187382636 | erot = 120.712825414824 | epot = -1325.52227015942 | etot = -1077.76725736196 +51000 ekin = 126.939090812203 | erot = 119.088171838501 | epot = -1323.7945200008 | etot = -1077.76725735009 +52000 ekin = 127.052758247806 | erot = 117.797033031227 | epot = -1322.61704861958 | etot = -1077.76725734055 +53000 ekin = 127.36733086557 | erot = 116.951027484844 | epot = -1322.08561579166 | etot = -1077.76725744124 +54000 ekin = 127.699598694242 | erot = 116.588954946942 | epot = -1322.05581098738 | etot = -1077.7672573462 +55000 ekin = 128.765472970119 | erot = 116.722527775956 | epot = -1323.25525818877 | etot = -1077.76725744269 +56000 ekin = 129.745971272485 | erot = 117.329047803041 | epot = -1324.84227644252 | etot = -1077.76725736699 +57000 ekin = 130.686799238902 | erot = 118.336149226803 | epot = -1326.79020584605 | etot = -1077.76725738035 +58000 ekin = 131.547485886178 | erot = 119.658488175863 | epot = -1328.97323145072 | etot = -1077.76725738868 +59000 ekin = 132.288746551752 | erot = 121.192124361476 | epot = -1331.24812831119 | etot = -1077.76725739797 +60000 ekin = 132.889658039566 | erot = 122.813399448204 | epot = -1333.47031489469 | etot = -1077.76725740692 +61000 ekin = 133.341476387201 | erot = 124.387402689369 | epot = -1335.49613649179 | etot = -1077.76725741522 +62000 ekin = 133.649114161516 | erot = 125.778714754983 | epot = -1337.19508633847 | etot = -1077.76725742197 +63000 ekin = 133.828198811913 | erot = 126.867080850083 | epot = -1338.46253708696 | etot = -1077.76725742496 +64000 ekin = 133.906684651817 | erot = 127.56304067291 | epot = -1339.23698275248 | etot = -1077.76725742776 +65000 ekin = 133.909388287628 | erot = 127.81028898223 | epot = -1339.48693469479 | etot = -1077.76725742493 +66000 ekin = 133.860810067346 | erot = 127.603400400042 | epot = -1339.23146788819 | etot = -1077.7672574208 +67000 ekin = 133.775485591319 | erot = 126.98991534858 | epot = -1338.53265835276 | etot = -1077.76725741286 +68000 ekin = 133.656407434473 | erot = 126.056031307511 | epot = -1337.479696151 | etot = -1077.76725740901 +69000 ekin = 133.498245523803 | erot = 124.901121868328 | epot = -1336.16662479388 | etot = -1077.76725740175 +70000 ekin = 133.293998426708 | erot = 123.635623442431 | epot = -1334.69687926337 | etot = -1077.76725739423 +71000 ekin = 133.029392386922 | erot = 122.36517136719 | epot = -1333.16182114486 | etot = -1077.76725739074 +72000 ekin = 132.685056689192 | erot = 121.171597639896 | epot = -1331.62391171537 | etot = -1077.76725738628 +73000 ekin = 132.251376493386 | erot = 120.116099015081 | epot = -1330.13473289197 | etot = -1077.76725738351 +74000 ekin = 131.726574812547 | erot = 119.247057316132 | epot = -1328.74088951045 | etot = -1077.76725738177 +75000 ekin = 131.110698166933 | erot = 118.598252474106 | epot = -1327.47620801944 | etot = -1077.7672573784 +76000 ekin = 130.422389067204 | erot = 118.195180955539 | epot = -1326.38482739773 | etot = -1077.76725737499 +77000 ekin = 129.697453900292 | erot = 118.054950856271 | epot = -1325.51966212761 | etot = -1077.76725737104 +78000 ekin = 128.983808987507 | erot = 118.18913802754 | epot = -1324.94020438318 | etot = -1077.76725736813 +79000 ekin = 128.33503884882 | erot = 118.595476281743 | epot = -1324.69777249594 | etot = -1077.76725736537 +80000 ekin = 127.800117751073 | erot = 119.266890643969 | epot = -1324.83426576002 | etot = -1077.76725736498 +81000 ekin = 127.407996010304 | erot = 120.178391162381 | epot = -1325.35364454144 | etot = -1077.76725736875 +82000 ekin = 127.161473447286 | erot = 121.280514709075 | epot = -1326.20924553085 | etot = -1077.76725737449 +83000 ekin = 127.045951849011 | erot = 122.504106964495 | epot = -1327.31731619533 | etot = -1077.76725738182 +84000 ekin = 127.034443068046 | erot = 123.770035256799 | epot = -1328.57173571383 | etot = -1077.76725738899 +85000 ekin = 127.100009803033 | erot = 125.002871400656 | epot = -1329.87013859939 | etot = -1077.7672573957 +86000 ekin = 127.209916231694 | erot = 126.12606340678 | epot = -1331.10323704296 | etot = -1077.76725740449 +87000 ekin = 127.339743108223 | erot = 127.079810479664 | epot = -1332.186810994 | etot = -1077.76725740611 +88000 ekin = 127.492851572892 | erot = 127.842496747418 | epot = -1333.1026057236 | etot = -1077.76725740329 +89000 ekin = 127.697668813166 | erot = 128.428193060097 | epot = -1333.89311927021 | etot = -1077.76725739695 +90000 ekin = 128.00236768284 | erot = 128.890624121688 | epot = -1334.66024919208 | etot = -1077.76725738755 +91000 ekin = 128.464258986691 | erot = 129.314890049742 | epot = -1335.54640641371 | etot = -1077.76725737728 +92000 ekin = 129.138404881414 | erot = 129.795965407411 | epot = -1336.70162765836 | etot = -1077.76725736954 +93000 ekin = 130.059880047962 | erot = 130.410441748414 | epot = -1338.23757916353 | etot = -1077.76725736715 +94000 ekin = 131.226522537251 | erot = 131.190635069444 | epot = -1340.18441497913 | etot = -1077.76725737244 +95000 ekin = 132.586213223046 | erot = 132.107679404094 | epot = -1342.46115001117 | etot = -1077.76725738403 +96000 ekin = 134.044080427153 | erot = 133.075735506146 | epot = -1344.88707333389 | etot = -1077.76725740059 +97000 ekin = 135.476028603552 | erot = 133.967715320788 | epot = -1347.21100134248 | etot = -1077.76725741814 +98000 ekin = 136.748227204441 | erot = 134.641388466873 | epot = -1349.15687309791 | etot = -1077.76725742659 +99000 ekin = 137.752624159367 | erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384 +100000 ekin = 138.392477025646 | erot = 134.94460803451 | epot = -1351.10434250636 | etot = -1077.76725744621 + 100000 315.83543 -1390.6819 39.577599 -1212.7119 -0.012722464 6.1629505e+08 +Loop time of 30.2255 on 4 procs for 100000 steps with 148 atoms + +Performance: 4.877 ns/day, 4.921 hours/ns, 3308.461 timesteps/s, 489.652 katom-step/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.766 | 22.691 | 26.962 | 89.3 | 75.07 +Bond | 0.28821 | 0.30757 | 0.32075 | 2.3 | 1.02 +Neigh | 0.008451 | 0.008527 | 0.008607 | 0.1 | 0.03 +Comm | 2.0101 | 6.3007 | 12.277 | 170.6 | 20.85 +Output | 0.051655 | 0.054646 | 0.056776 | 0.9 | 0.18 +Modify | 0.53953 | 0.56983 | 0.63795 | 5.3 | 1.89 +Other | | 0.2934 | | | 0.97 + +Nlocal: 37 ave 38 max 36 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 111 ave 112 max 110 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 1049.75 ave 1288 max 753 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 4199 +Ave neighs/atom = 28.371622 +Ave special neighs/atom = 6 +Neighbor list builds = 100 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.5.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:30 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/data.duplex1 new file mode 100644 index 0000000000..a368cef424 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0 +2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0 +3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0 +4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0 +5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0 +6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0 +7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0 +8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0 +9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0 +10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618 +2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161 +3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145 +4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535 +5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021 +6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764 +7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955 +8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736 +9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246 +10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/in.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/in.duplex1 new file mode 100644 index 0000000000..4936c7e9bd --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/in.duplex1 @@ -0,0 +1,73 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.1 new file mode 100644 index 0000000000..031081bbc4 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.1 @@ -0,0 +1,1186 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.3220946463642 | etot = -49.9334369948331 +Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -79.708623 6.3865285 -66.715222 -0.044062421 39304000 +1000 ekin = 6.41530681673926 | erot = 17.3249659795569 | epot = -73.6737097924625 | etot = -49.9334369961663 +2000 ekin = 6.27960997228419 | erot = 17.8454841526973 | epot = -74.0585311228698 | etot = -49.9334369978883 +3000 ekin = 6.20339572000348 | erot = 18.3141946085155 | epot = -74.4510273282071 | etot = -49.9334369996881 +4000 ekin = 6.18541696870776 | erot = 18.7042662877837 | epot = -74.8231202577462 | etot = -49.9334370012548 +5000 ekin = 6.22079685461299 | erot = 18.9945001618931 | epot = -75.1487340188923 | etot = -49.9334370023862 +6000 ekin = 6.30238619195772 | erot = 19.1711640282348 | epot = -75.4069872232165 | etot = -49.933437003024 +7000 ekin = 6.42181744516985 | erot = 19.2282392613116 | epot = -75.5834937096768 | etot = -49.9334370031954 +8000 ekin = 6.5702083768984 | erot = 19.1666965396848 | epot = -75.670341919563 | etot = -49.9334370029798 +9000 ekin = 6.73869975295017 | erot = 18.9934225090914 | epot = -75.6655592644387 | etot = -49.9334370023971 +10000 ekin = 6.91896362918058 | erot = 18.720482841468 | epot = -75.5728834721419 | etot = -49.9334370014934 +11000 ekin = 7.10364142561688 | erot = 18.3641504994904 | epot = -75.4012289254607 | etot = -49.9334370003534 +12000 ekin = 7.28657388923056 | erot = 17.9433928027825 | epot = -75.1634036911466 | etot = -49.9334369991335 +13000 ekin = 7.46274124826267 | erot = 17.4778556704808 | epot = -74.8740339167287 | etot = -49.9334369979852 +14000 ekin = 7.62796631031633 | erot = 16.985794378233 | epot = -74.5471976856215 | etot = -49.9334369970722 +15000 ekin = 7.77853508999226 | erot = 16.4826987969597 | epot = -74.1946708831607 | etot = -49.9334369962087 +16000 ekin = 7.91091226447414 | erot = 15.9810202779915 | epot = -73.8253695379244 | etot = -49.9334369954588 +17000 ekin = 8.02167864528801 | erot = 15.4888629495771 | epot = -73.4439785905236 | etot = -49.9334369956585 +18000 ekin = 8.10771648329849 | erot = 15.0085330298885 | epot = -73.0496865092416 | etot = -49.9334369960546 +19000 ekin = 8.16663757201098 | erot = 14.5368419756962 | epot = -72.6369165441952 | etot = -49.933436996488 +20000 ekin = 8.19737361822045 | erot = 14.069473517068 | epot = -72.2002841320777 | etot = -49.9334369967892 +21000 ekin = 8.200840326377 | erot = 13.6028244433726 | epot = -71.7371017665554 | etot = -49.9334369968058 +22000 ekin = 8.18058151811635 | erot = 13.1355858369993 | epot = -71.2496043515412 | etot = -49.9334369964255 +23000 ekin = 8.14330066835266 | erot = 12.6698318997777 | epot = -70.7465695637165 | etot = -49.9334369955862 +24000 ekin = 8.09918346860519 | erot = 12.2114790537769 | epot = -70.2440995166709 | etot = -49.9334369942888 +25000 ekin = 8.06188796651942 | erot = 11.7700779899392 | epot = -69.7654029490659 | etot = -49.9334369926073 +26000 ekin = 8.04803038217859 | erot = 11.357977539424 | epot = -69.3394449122889 | etot = -49.9334369906863 +27000 ekin = 8.07613224077752 | erot = 10.9889629668064 | epot = -68.9985321963396 | etot = -49.9334369887557 +28000 ekin = 8.16468286004856 | erot = 10.6764628926903 | epot = -68.7745827398655 | etot = -49.9334369871266 +29000 ekin = 8.32943276357165 | erot = 10.4314466403616 | epot = -68.6943163900859 | etot = -49.9334369861526 +30000 ekin = 8.58019899558303 | erot = 10.260206659823 | epot = -68.7738426415863 | etot = -49.9334369861802 +31000 ekin = 8.91780959359565 | erot = 10.1623429442233 | epot = -69.0135895252605 | etot = -49.9334369874415 +32000 ekin = 9.33207993074479 | erot = 10.1294239012755 | epot = -69.3949408219811 | etot = -49.9334369899608 +33000 ekin = 9.80167373728905 | erot = 10.1460133617213 | epot = -69.8811240921766 | etot = -49.9334369931663 +34000 ekin = 10.296255703772 | erot = 10.1906808991803 | epot = -70.4203736002083 | etot = -49.933436997256 +35000 ekin = 10.7808236403015 | erot = 10.2363285925375 | epot = -70.950589233993 | etot = -49.9334370011539 +36000 ekin = 11.2209991001448 | erot = 10.2573020893315 | epot = -71.4117381937016 | etot = -49.9334370042253 +37000 ekin = 11.5878770725935 | erot = 10.233920295851 | epot = -71.7552343744929 | etot = -49.9334370060484 +38000 ekin = 11.8612836540756 | erot = 10.1555553859583 | epot = -71.9502760465432 | etot = -49.9334370065093 +39000 ekin = 12.0309099424617 | erot = 10.0214706213655 | epot = -71.985817569609 | etot = -49.9334370057818 +40000 ekin = 12.0955556066702 | erot = 9.83943808382945 | epot = -71.8684306947124 | etot = -49.9334370042128 +41000 ekin = 12.0612052446598 | erot = 9.62294084167585 | epot = -71.617583088525 | etot = -49.9334370021893 +42000 ekin = 11.9387239948167 | erot = 9.38805049860224 | epot = -71.2602114934562 | etot = -49.9334370000373 +43000 ekin = 11.7417170850644 | erot = 9.15084162780929 | epot = -70.8259957108611 | etot = -49.9334369979874 +44000 ekin = 11.4847881035009 | erot = 8.92568438359922 | epot = -70.3439094834557 | etot = -49.9334369963556 +45000 ekin = 11.1822274471315 | erot = 8.72337977254416 | epot = -69.8390442145234 | etot = -49.9334369948477 +46000 ekin = 10.8470862022847 | erot = 8.55290687697305 | epot = -69.3334300728894 | etot = -49.9334369936317 +47000 ekin = 10.4905994457614 | erot = 8.42173082249889 | epot = -68.8457672609551 | etot = -49.9334369926948 +48000 ekin = 10.1219833658041 | erot = 8.33574076580856 | epot = -68.3911611235985 | etot = -49.9334369919859 +49000 ekin = 9.74860996204229 | erot = 8.29978137994427 | epot = -67.9818283334164 | etot = -49.9334369914298 +50000 ekin = 9.37652878062106 | erot = 8.3181429829463 | epot = -67.6281087545116 | etot = -49.9334369909443 +51000 ekin = 9.01124628424547 | erot = 8.39494797706923 | epot = -67.3396312517619 | etot = -49.9334369904472 +52000 ekin = 8.65861585992268 | erot = 8.53436345461162 | epot = -67.1264163044102 | etot = -49.9334369898759 +53000 ekin = 8.32565221212492 | erot = 8.74055503681473 | epot = -66.9996442381288 | etot = -49.9334369891891 +54000 ekin = 8.02107164181931 | erot = 9.01735593163919 | epot = -66.9718645619368 | etot = -49.9334369884783 +55000 ekin = 7.75537320775564 | erot = 9.36712982138555 | epot = -67.0559400169756 | etot = -49.9334369878344 +56000 ekin = 7.54033857901023 | erot = 9.78947615586548 | epot = -67.263251722307 | etot = -49.9334369874313 +57000 ekin = 7.38797148977987 | erot = 10.2796726902731 | epot = -67.6010811675105 | etot = -49.9334369874576 +58000 ekin = 7.30907596761463 | erot = 10.8272746456741 | epot = -68.0697876013461 | etot = -49.9334369880574 +59000 ekin = 7.31183154532697 | erot = 11.4154638702662 | epot = -68.6607324048616 | etot = -49.9334369892684 +60000 ekin = 7.40073708729543 | erot = 12.0215350766978 | epot = -69.3557091550092 | etot = -49.933436991016 +61000 ekin = 7.57612697427838 | erot = 12.6184730514599 | epot = -70.1280370189361 | etot = -49.9334369931978 +62000 ekin = 7.83421085835969 | erot = 13.1768169062567 | epot = -70.9444647601164 | etot = -49.9334369955 +63000 ekin = 8.16736345530171 | erot = 13.6689818833254 | epot = -71.7697823361826 | etot = -49.9334369975555 +64000 ekin = 8.56437270810164 | erot = 14.0716865201635 | epot = -72.5694962279815 | etot = -49.9334369997164 +65000 ekin = 9.01149485546105 | erot = 14.3654371918515 | epot = -73.310369048807 | etot = -49.9334370014944 +66000 ekin = 9.49327902442042 | erot = 14.5383989864003 | epot = -73.9651150135785 | etot = -49.9334370027578 +67000 ekin = 9.99325449816094 | erot = 14.5878691516415 | epot = -74.5145606532497 | etot = -49.9334370034473 +68000 ekin = 10.4944771426633 | erot = 14.5206532270625 | epot = -74.9485673733188 | etot = -49.933437003593 +69000 ekin = 10.9798545698929 | erot = 14.3522752904606 | epot = -75.2655668636681 | etot = -49.9334370033147 +70000 ekin = 11.4322492583888 | erot = 14.1050236216679 | epot = -75.4707098828583 | etot = -49.9334370028015 +71000 ekin = 11.8344774050144 | erot = 13.8051158639603 | epot = -75.5730302711275 | etot = -49.9334370021529 +72000 ekin = 12.1694138303341 | erot = 13.4802146493531 | epot = -75.5830654819228 | etot = -49.9334370022356 +73000 ekin = 12.4176450109615 | erot = 13.1540122377618 | epot = -75.5050942510562 | etot = -49.9334370023328 +74000 ekin = 12.5615004066025 | erot = 12.844248053038 | epot = -75.3391854623092 | etot = -49.9334370026687 +75000 ekin = 12.5860719279485 | erot = 12.5626890441996 | epot = -75.0821979751944 | etot = -49.9334370030463 +76000 ekin = 12.4812201739639 | erot = 12.3157495780693 | epot = -74.7304067552152 | etot = -49.933437003182 +77000 ekin = 12.2439814422807 | erot = 12.1061362624702 | epot = -74.2835547075503 | etot = -49.9334370027995 +78000 ekin = 11.8805929734489 | erot = 11.9347890944435 | epot = -73.7488190696168 | etot = -49.9334370017243 +79000 ekin = 11.407513143564 | erot = 11.8023493789743 | epot = -73.1432995224891 | etot = -49.9334369999508 +80000 ekin = 10.8509854812392 | erot = 11.7096658028891 | epot = -72.4940882817776 | etot = -49.9334369976493 +81000 ekin = 10.2450327503611 | erot = 11.6573342346762 | epot = -71.8358039801528 | etot = -49.9334369951155 +82000 ekin = 9.62812700027476 | erot = 11.6446829926405 | epot = -71.2062469856182 | etot = -49.933436992703 +83000 ekin = 9.03903873930662 | erot = 11.6687532921685 | epot = -70.6412290222223 | etot = -49.9334369907472 +84000 ekin = 8.51249186343724 | erot = 11.7236867864198 | epot = -70.1696156393611 | etot = -49.9334369895041 +85000 ekin = 8.07528521987734 | erot = 11.8007513441408 | epot = -69.8094735531451 | etot = -49.933436989127 +86000 ekin = 7.74350481028741 | erot = 11.888905733036 | epot = -69.5658475329518 | etot = -49.9334369896284 +87000 ekin = 7.52120913163795 | erot = 11.9758324996818 | epot = -69.4304786226217 | etot = -49.9334369913019 +88000 ekin = 7.39850764773337 | erot = 12.0479648689118 | epot = -69.3799095098051 | etot = -49.93343699316 +89000 ekin = 7.35699193773618 | erot = 12.0941781544058 | epot = -69.3846070872457 | etot = -49.9334369951037 +90000 ekin = 7.37367999758399 | erot = 12.1080231759532 | epot = -69.4151401703038 | etot = -49.9334369967666 +91000 ekin = 7.42410695857772 | erot = 12.0887796846358 | epot = -69.4463236410925 | etot = -49.9334369978791 +92000 ekin = 7.48574151827147 | erot = 12.042064982234 | epot = -69.4612434988297 | etot = -49.9334369983243 +93000 ekin = 7.5403711898821 | erot = 11.9791807163969 | epot = -69.4529889044436 | etot = -49.9334369981646 +94000 ekin = 7.57533062469026 | erot = 11.9152823419623 | epot = -69.4240499641669 | etot = -49.9334369975144 +95000 ekin = 7.58377941253783 | erot = 11.8670735491572 | epot = -69.3842899582943 | etot = -49.9334369965993 +96000 ekin = 7.56434675210399 | erot = 11.8500107777802 | epot = -69.3477945255051 | etot = -49.9334369956209 +97000 ekin = 7.52038731169875 | erot = 11.8759317072189 | epot = -69.3297560136748 | etot = -49.9334369947572 +98000 ekin = 7.45894830728074 | erot = 11.9513447834672 | epot = -69.3437300849006 | etot = -49.9334369941527 +99000 ekin = 7.3894451101094 | erot = 12.0764734057244 | epot = -69.3993555097599 | etot = -49.9334369939261 +100000 ekin = 7.32205635827605 | erot = 12.2450152227774 | epot = -69.5005085752216 | etot = -49.9334369941681 +101000 ekin = 7.26597138620094 | erot = 12.4445407770089 | epot = -69.6439491581323 | etot = -49.9334369949225 +102000 ekin = 7.22778180819636 | erot = 12.6574945089323 | epot = -69.8187133132872 | etot = -49.9334369961585 +103000 ekin = 7.21040494123207 | erot = 12.8628067179971 | epot = -70.0066486569777 | etot = -49.9334369977485 +104000 ekin = 7.21287832486989 | erot = 13.0381084092498 | epot = -70.1844237335803 | etot = -49.9334369994605 +105000 ekin = 7.23115719659566 | erot = 13.1624311874587 | epot = -70.3270253850435 | etot = -49.9334370009891 +106000 ekin = 7.25975107867426 | erot = 13.2191029175833 | epot = -70.4122909982755 | etot = -49.9334370020179 +107000 ekin = 7.29377758656529 | erot = 13.1984000366873 | epot = -70.4256146255374 | etot = -49.9334370022848 +108000 ekin = 7.33090314151437 | erot = 13.0994774135712 | epot = -70.3638175567295 | etot = -49.933437001644 +109000 ekin = 7.37271454696904 | erot = 12.9312031783767 | epot = -70.2373547254362 | etot = -49.9334370000905 +110000 ekin = 7.42526209058348 | erot = 12.7117380447812 | epot = -70.0704371331194 | etot = -49.9334369977548 +111000 ekin = 7.49872514941575 | erot = 12.4669230054386 | epot = -69.8990851497371 | etot = -49.9334369948828 +112000 ekin = 7.60628796279973 | erot = 12.2276899311231 | epot = -69.7674148857286 | etot = -49.9334369918058 +113000 ekin = 7.76235901185271 | erot = 12.0267610902749 | epot = -69.7225570910432 | etot = -49.9334369889156 +114000 ekin = 7.98027485026653 | erot = 11.8949023522835 | epot = -69.8086141891872 | etot = -49.9334369866372 +115000 ekin = 8.27045851930279 | erot = 11.8569578160189 | epot = -70.0608533199909 | etot = -49.9334369846692 +116000 ekin = 8.64333470390531 | erot = 11.927372525046 | epot = -70.5041442140703 | etot = -49.933436985119 +117000 ekin = 9.09183845377715 | erot = 12.108244816281 | epot = -71.1335202571184 | etot = -49.9334369870603 +118000 ekin = 9.59711279490118 | erot = 12.3880852370698 | epot = -71.9186350224121 | etot = -49.9334369904412 +119000 ekin = 10.1316662415165 | erot = 12.7420777955395 | epot = -72.8071810320392 | etot = -49.9334369949833 +120000 ekin = 10.6612602592498 | erot = 13.1344486371313 | epot = -73.7291458965887 | etot = -49.9334370002077 +121000 ekin = 11.1480057224142 | erot = 13.5226300221742 | epot = -74.6040727500911 | etot = -49.9334370055027 +122000 ekin = 11.5541779480657 | erot = 13.8626563199417 | epot = -75.3502712782362 | etot = -49.9334370102287 +123000 ekin = 11.8461299089274 | erot = 14.1149357811302 | epot = -75.8945027038779 | etot = -49.9334370138204 +124000 ekin = 11.9977139994366 | erot = 14.2494171746183 | epot = -76.1805681899317 | etot = -49.9334370158768 +125000 ekin = 11.9927642881939 | erot = 14.2492577099009 | epot = -76.175459014312 | etot = -49.9334370162172 +126000 ekin = 11.8263836634494 | erot = 14.1123955938888 | epot = -75.8722162722326 | etot = -49.9334370148943 +127000 ekin = 11.5049845403692 | erot = 13.8508742683788 | epot = -75.2892958209089 | etot = -49.9334370121609 +128000 ekin = 11.0452237618988 | erot = 13.48823800404 | epot = -74.4668987743424 | etot = -49.9334370084036 +129000 ekin = 10.4721243932075 | erot = 13.0556836611653 | epot = -73.4612450584324 | etot = -49.9334370040595 +130000 ekin = 9.81675568764214 | erot = 12.5878092612813 | epot = -72.3380019484647 | etot = -49.9334369995413 +131000 ekin = 9.11382601710269 | erot = 12.1187210112526 | epot = -71.165984023543 | etot = -49.9334369951877 +132000 ekin = 8.3994419110073 | erot = 11.6790046180508 | epot = -70.011883520305 | etot = -49.9334369912469 +133000 ekin = 7.70914257803186 | erot = 11.2937451501986 | epot = -68.936324716116 | etot = -49.9334369878856 +134000 ekin = 7.0759988527824 | erot = 10.9811951880483 | epot = -67.9906310260634 | etot = -49.9334369852327 +135000 ekin = 6.52777388754256 | erot = 10.75096079726 | epot = -67.2121716681418 | etot = -49.9334369833392 +136000 ekin = 6.08771006340461 | erot = 10.6081410500038 | epot = -66.6292880956376 | etot = -49.9334369822292 +137000 ekin = 5.77298785581476 | erot = 10.552372604197 | epot = -66.2587974419407 | etot = -49.9334369819289 +138000 ekin = 5.59354954718462 | erot = 10.5779497433281 | epot = -66.1049362729332 | etot = -49.9334369824205 +139000 ekin = 5.55166881072913 | erot = 10.6745917743557 | epot = -66.1596975687036 | etot = -49.9334369836187 +140000 ekin = 5.64223691297485 | erot = 10.8284932797371 | epot = -66.4041671780735 | etot = -49.9334369853615 +141000 ekin = 5.85383891387405 | erot = 11.0237191850704 | epot = -66.8109950863643 | etot = -49.9334369874198 +142000 ekin = 6.17049552359047 | erot = 11.2439004345778 | epot = -67.3478329477023 | etot = -49.9334369895341 +143000 ekin = 6.57375238284704 | erot = 11.4740276162674 | epot = -67.9812169905818 | etot = -49.9334369914673 +144000 ekin = 7.04468895168924 | erot = 11.701994075136 | epot = -68.680120019886 | etot = -49.9334369930608 +145000 ekin = 7.56544773358585 | erot = 11.9199568354569 | epot = -69.4188415632307 | etot = -49.9334369941879 +146000 ekin = 8.1200495304631 | erot = 12.1239691631675 | epot = -70.1774556887215 | etot = -49.933436995091 +147000 ekin = 8.69445128023778 | erot = 12.3121155932595 | epot = -70.9400038693255 | etot = -49.9334369958282 +148000 ekin = 9.27603993874859 | erot = 12.4837480427639 | epot = -71.6932249780922 | etot = -49.9334369965798 +149000 ekin = 9.85285670508252 | erot = 12.6377352950257 | epot = -72.4240289976087 | etot = -49.9334369975005 +150000 ekin = 10.4128357127046 | erot = 12.7710161831569 | epot = -73.1172888945392 | etot = -49.9334369986777 +151000 ekin = 10.9432663251774 | erot = 12.8778265161479 | epot = -73.7545298414573 | etot = -49.933437000132 +152000 ekin = 11.4305853782861 | erot = 12.9496878240708 | epot = -74.3137102041522 | etot = -49.9334370017953 +153000 ekin = 11.8605190183234 | erot = 12.9761831588472 | epot = -74.7701391807206 | etot = -49.9334370035501 +154000 ekin = 12.2185434955891 | erot = 12.9462452354484 | epot = -75.0982257362823 | etot = -49.9334370052448 +155000 ekin = 12.4906128205059 | erot = 12.8496668717377 | epot = -75.2737166989594 | etot = -49.9334370067158 +156000 ekin = 12.6641064725816 | erot = 12.6785919431794 | epot = -75.2761354235628 | etot = -49.9334370078019 +157000 ekin = 12.7289594615905 | erot = 12.4288160114449 | epot = -75.0912124813834 | etot = -49.933437008348 +158000 ekin = 12.6789226204095 | erot = 12.1008375004914 | epot = -74.7131971291116 | etot = -49.9334370082108 +159000 ekin = 12.5128394530715 | erot = 11.7006734245223 | epot = -74.1469498848661 | etot = -49.9334370072723 +160000 ekin = 12.2357211071562 | erot = 11.2404384839248 | epot = -73.4095965965446 | etot = -49.9334370054637 +161000 ekin = 11.8593038686461 | erot = 10.7386616356059 | epot = -72.5314025070534 | etot = -49.9334370028014 +162000 ekin = 11.4017680282997 | erot = 10.2201339236183 | epot = -71.5553389513339 | etot = -49.9334369994158 +163000 ekin = 10.8864473298725 | erot = 9.71510625265767 | epot = -70.5349905780806 | etot = -49.9334369955505 +164000 ekin = 10.339639107013 | erot = 9.25770793160017 | epot = -69.5307840301537 | etot = -49.9334369915405 +165000 ekin = 9.78791680577074 | erot = 8.8835941059149 | epot = -68.60494789944 | etot = -49.9334369877544 +166000 ekin = 9.25550622083803 | erot = 8.62702487817795 | epot = -67.8159680835519 | etot = -49.9334369845359 +167000 ekin = 8.76224456450922 | erot = 8.51776140061236 | epot = -67.2134429472672 | etot = -49.9334369821456 +168000 ekin = 8.32243639262824 | erot = 8.57826893241441 | epot = -66.8341423057718 | etot = -49.9334369807292 +169000 ekin = 7.94465566391787 | erot = 8.82168625048319 | epot = -66.6997788947134 | etot = -49.9334369803124 +170000 ekin = 7.63232945982425 | erot = 9.25084013989436 | epot = -66.8166065805367 | etot = -49.9334369808181 +171000 ekin = 7.38529238380702 | erot = 9.85836147101373 | epot = -67.1770908361287 | etot = -49.9334369813079 +172000 ekin = 7.20610015415374 | erot = 10.627083624393 | epot = -67.766620762232 | etot = -49.9334369836853 +173000 ekin = 7.08749525316584 | erot = 11.5302525574929 | epot = -68.5511847971414 | etot = -49.9334369864827 +174000 ekin = 7.01847526595513 | erot = 12.5352232664751 | epot = -69.4871355219803 | etot = -49.93343698955 +175000 ekin = 6.9877080022007 | erot = 13.6056336792489 | epot = -70.526778674216 | etot = -49.9334369927664 +176000 ekin = 6.98383597858348 | erot = 14.7031290903658 | epot = -71.6204020649724 | etot = -49.9334369960231 +177000 ekin = 6.99559888535589 | erot = 15.7890361276343 | epot = -72.7180720121957 | etot = -49.9334369992054 +178000 ekin = 7.01192097921241 | erot = 16.8261106927661 | epot = -73.7714686741545 | etot = -49.933437002176 +179000 ekin = 7.02209184959173 | erot = 17.7804349003769 | epot = -74.7359637547449 | etot = -49.9334370047763 +180000 ekin = 7.01611155414299 | erot = 18.6234022668396 | epot = -75.572950827824 | etot = -49.9334370068414 +181000 ekin = 6.98519719010984 | erot = 19.333556749081 | epot = -76.2521909474248 | etot = -49.9334370082339 +182000 ekin = 6.92238544527395 | erot = 19.8970971418282 | epot = -76.7529195977555 | etot = -49.9334370106533 +183000 ekin = 6.8222759254291 | erot = 20.2982684170427 | epot = -77.0539813535497 | etot = -49.9334370110779 +184000 ekin = 6.68055376617427 | erot = 20.5336568135041 | epot = -77.1476475904154 | etot = -49.9334370107371 +185000 ekin = 6.49623294826009 | erot = 20.6104471437531 | epot = -77.0401171017118 | etot = -49.9334370096986 +186000 ekin = 6.27250921536155 | erot = 20.5422446873304 | epot = -76.7481909107548 | etot = -49.9334370080628 +187000 ekin = 6.01720154751464 | erot = 20.3471328407271 | epot = -76.2977713941871 | etot = -49.9334370059454 +188000 ekin = 5.74286684715253 | erot = 20.0458090594969 | epot = -75.7221129101206 | etot = -49.9334370034712 +189000 ekin = 5.46641873149874 | erot = 19.6593652976558 | epot = -75.0592210301649 | etot = -49.9334370010103 +190000 ekin = 5.20811212014894 | erot = 19.2080076862205 | epot = -74.3495568046836 | etot = -49.9334369983141 +191000 ekin = 4.98983337888069 | erot = 18.7117448291952 | epot = -73.6350152038308 | etot = -49.9334369957549 +192000 ekin = 4.83291851070295 | erot = 18.1889644778813 | epot = -72.9553199820979 | etot = -49.9334369935137 +193000 ekin = 4.75584764391605 | erot = 17.6560155879572 | epot = -72.3453002236067 | etot = -49.9334369917334 +194000 ekin = 4.77223428975476 | erot = 17.1270435377863 | epot = -71.8327148180403 | etot = -49.9334369904993 +195000 ekin = 4.88948018807988 | erot = 16.6140592370741 | epot = -71.4369764149749 | etot = -49.933436989821 +196000 ekin = 5.10830059790741 | erot = 16.127174742192 | epot = -71.1689123297485 | etot = -49.9334369896491 +197000 ekin = 5.42311350132857 | erot = 15.6748848012688 | epot = -71.0314352924944 | etot = -49.933436989897 +198000 ekin = 5.823101864179 | erot = 15.264261134288 | epot = -71.0207999889323 | etot = -49.9334369904653 +199000 ekin = 6.29365371082596 | erot = 14.9009682646058 | epot = -71.1280589666963 | etot = -49.9334369912645 +200000 ekin = 6.81787606879633 | erot = 14.5890840258131 | epot = -71.3403970868379 | etot = -49.9334369922284 +201000 ekin = 7.37794822150507 | erot = 14.330785798856 | epot = -71.6421710136752 | etot = -49.9334369933141 +202000 ekin = 7.95618720633075 | erot = 14.1260142258945 | epot = -72.0156384267148 | etot = -49.9334369944895 +203000 ekin = 8.53580140319485 | erot = 13.9722340620995 | epot = -72.4414724610252 | etot = -49.9334369957309 +204000 ekin = 9.10137690711189 | erot = 13.8643800543707 | epot = -72.8991939584906 | etot = -49.9334369970081 +205000 ekin = 9.63916729956463 | erot = 13.7950217250094 | epot = -73.3676260228628 | etot = -49.9334369982888 +206000 ekin = 10.1372494437201 | erot = 13.7547335571646 | epot = -73.8254200004191 | etot = -49.9334369995343 +207000 ekin = 10.5855843060113 | erot = 13.7326036344487 | epot = -74.2516249411772 | etot = -49.9334370007172 +208000 ekin = 10.9759973534346 | erot = 13.7167490933405 | epot = -74.6261834485714 | etot = -49.9334370017963 +209000 ekin = 11.3020857284075 | erot = 13.695034284837 | epot = -74.9305570159883 | etot = -49.9334370027438 +210000 ekin = 11.5590623102062 | erot = 13.6557304747736 | epot = -75.1482297885136 | etot = -49.9334370035338 +211000 ekin = 11.7435554570199 | erot = 13.5881804316498 | epot = -75.265172892812 | etot = -49.9334370041423 +212000 ekin = 11.8533937432468 | erot = 13.4834670393969 | epot = -75.2702977872005 | etot = -49.9334370045568 +213000 ekin = 11.887405437966 | erot = 13.3351971168151 | epot = -75.1560395594847 | etot = -49.9334370047037 +214000 ekin = 11.8452570406668 | erot = 13.1395898321962 | epot = -74.918283877557 | etot = -49.9334370046941 +215000 ekin = 11.7273549851562 | erot = 12.8956103790907 | epot = -74.5564023687286 | etot = -49.9334370044816 +216000 ekin = 11.5348514637304 | erot = 12.6051585142611 | epot = -74.073446982084 | etot = -49.9334370040925 +217000 ekin = 11.2698546386903 | erot = 12.2726360414478 | epot = -73.4759276836659 | etot = -49.9334370035278 +218000 ekin = 10.9360036470647 | erot = 11.9044881932643 | epot = -72.773928843055 | etot = -49.933437002726 +219000 ekin = 10.5395729894744 | erot = 11.509107893732 | epot = -71.9821178847383 | etot = -49.9334370015319 +220000 ekin = 10.0911390958416 | erot = 11.0974113407827 | epot = -71.12198743634 | etot = -49.9334369997158 +221000 ekin = 9.60752759203925 | erot = 10.6840231535665 | epot = -70.2249877426727 | etot = -49.9334369970669 +222000 ekin = 9.11332798616989 | erot = 10.2884385364029 | epot = -69.3352035161138 | etot = -49.933436993541 +223000 ekin = 8.64094443085901 | erot = 9.93507521512023 | epot = -68.5094566353819 | etot = -49.9334369894026 +224000 ekin = 8.22827965338114 | erot = 9.65121040808671 | epot = -67.8129270467276 | etot = -49.9334369852597 +225000 ekin = 7.91390905933865 | erot = 9.4625831391754 | epot = -67.3099291804781 | etot = -49.933436981964 +226000 ekin = 7.73074804872823 | erot = 9.38753011757196 | epot = -67.0517151464721 | etot = -49.9334369801719 +227000 ekin = 7.70009206552193 | erot = 9.43243479453588 | epot = -67.0659638403967 | etot = -49.9334369803389 +228000 ekin = 7.82788964264707 | erot = 9.58936456546829 | epot = -67.3506911902218 | etot = -49.9334369821065 +229000 ekin = 8.10285729533807 | erot = 9.8405603901581 | epot = -67.8768546713476 | etot = -49.9334369858514 +230000 ekin = 8.50059317628578 | erot = 10.1544474914862 | epot = -68.5884776580864 | etot = -49.9334369903144 +231000 ekin = 8.98918217097307 | erot = 10.493400619592 | epot = -69.4160197853243 | etot = -49.9334369947592 +232000 ekin = 9.53377851904017 | erot = 10.8217737549011 | epot = -70.2889892725772 | etot = -49.9334369986359 +233000 ekin = 10.1004633099863 | erot = 11.1105033366914 | epot = -71.1444036483326 | etot = -49.9334370016548 +234000 ekin = 10.658612255984 | erot = 11.3394799942009 | epot = -71.9315292539596 | etot = -49.9334370037748 +235000 ekin = 11.1819014328097 | erot = 11.497727774584 | epot = -72.6130662125069 | etot = -49.9334370051133 +236000 ekin = 11.6484473656525 | erot = 11.5820119850608 | epot = -73.1638963565643 | etot = -49.9334370058509 +237000 ekin = 12.0359802131749 | erot = 11.5953554338433 | epot = -73.5647726545056 | etot = -49.9334370074873 +238000 ekin = 12.321983609933 | erot = 11.5429422765501 | epot = -73.7983628944192 | etot = -49.9334370079361 +239000 ekin = 12.4929747866312 | erot = 11.4297860561661 | epot = -73.8561978508111 | etot = -49.9334370080138 +240000 ekin = 12.5412393847429 | erot = 11.2618516717113 | epot = -73.7365280640656 | etot = -49.9334370076113 +241000 ekin = 12.4660778052252 | erot = 11.0462123362422 | epot = -73.4457271480737 | etot = -49.9334370066063 +242000 ekin = 12.2750005609617 | erot = 10.7914527512415 | epot = -72.9998903170961 | etot = -49.9334370048929 +243000 ekin = 11.9845096947868 | erot = 10.5081603107686 | epot = -72.4261070080167 | etot = -49.9334370024614 +244000 ekin = 11.619935904703 | erot = 10.2090471828747 | epot = -71.7624200869649 | etot = -49.9334369993872 +245000 ekin = 11.2141782120078 | erot = 9.90860612972147 | epot = -71.0562213376396 | etot = -49.9334369959104 +246000 ekin = 10.804980066499 | erot = 9.62226262065129 | epot = -70.3606796795521 | etot = -49.9334369924019 +247000 ekin = 10.4306724668814 | erot = 9.36498469828495 | epot = -69.7290941544644 | etot = -49.9334369892981 +248000 ekin = 10.125200565836 | erot = 9.14967551152589 | epot = -69.2083130643903 | etot = -49.9334369870284 +249000 ekin = 9.91424863501087 | erot = 8.98570765839854 | epot = -68.8333932790368 | etot = -49.9334369856274 +250000 ekin = 9.81343088344703 | erot = 8.87752109616444 | epot = -68.6243889655634 | etot = -49.933436985952 +251000 ekin = 9.81990124694966 | erot = 8.82321712561382 | epot = -68.5765553598857 | etot = -49.9334369873223 +252000 ekin = 9.91845576760695 | erot = 8.81663197784401 | epot = -68.6685247348515 | etot = -49.9334369894006 +253000 ekin = 10.0857195322844 | erot = 8.84890482127693 | epot = -68.868061345352 | etot = -49.9334369917907 +254000 ekin = 10.2944154464787 | erot = 8.9101104579529 | epot = -69.1379628985692 | etot = -49.9334369941377 +255000 ekin = 10.5172797771479 | erot = 8.99090198885701 | epot = -69.4416187622177 | etot = -49.9334369962128 +256000 ekin = 10.7298060333095 | erot = 9.08318965779443 | epot = -69.7464326890098 | etot = -49.9334369979058 +257000 ekin = 10.9117548400263 | erot = 9.1804779576833 | epot = -70.025669796896 | etot = -49.9334369991865 +258000 ekin = 11.0477221380872 | erot = 9.27819694071016 | epot = -70.2593560788573 | etot = -49.93343700006 +259000 ekin = 11.1271588600366 | erot = 9.3738110386782 | epot = -70.4344068992479 | etot = -49.9334370005331 +260000 ekin = 11.1442779893458 | erot = 9.4669885218801 | epot = -70.5447035117415 | etot = -49.9334370005156 +261000 ekin = 11.0980856586657 | erot = 9.56016701500807 | epot = -70.5916896739926 | etot = -49.9334370003188 +262000 ekin = 10.9907927218987 | erot = 9.6547424746047 | epot = -70.5789721960225 | etot = -49.9334369995191 +263000 ekin = 10.829537817859 | erot = 9.75638049585076 | epot = -70.5193553118446 | etot = -49.9334369981348 +264000 ekin = 10.6274954670403 | erot = 9.87566396380612 | epot = -70.4365964270687 | etot = -49.9334369962223 +265000 ekin = 10.4029385010147 | erot = 10.0259787584343 | epot = -70.3623542534473 | etot = -49.9334369939982 +266000 ekin = 10.177674265685 | erot = 10.2209385120995 | epot = -70.332049769659 | etot = -49.9334369918746 +267000 ekin = 9.97447897986438 | erot = 10.4715477508096 | epot = -70.3794637208708 | etot = -49.9334369901968 +268000 ekin = 9.81397218089898 | erot = 10.783566213847 | epot = -70.5309753841286 | etot = -49.9334369893826 +269000 ekin = 9.71175762398395 | erot = 11.1545990385867 | epot = -70.7997936521916 | etot = -49.9334369896209 +270000 ekin = 9.67524675614636 | erot = 11.5728282294546 | epot = -71.1815119767635 | etot = -49.9334369911626 +271000 ekin = 9.70205034561283 | erot = 12.0171639615848 | epot = -71.6526513009489 | etot = -49.9334369937513 +272000 ekin = 9.78119590231133 | erot = 12.4591961343094 | epot = -72.1738290335957 | etot = -49.9334369969749 +273000 ekin = 9.89551530292975 | erot = 12.8671360105974 | epot = -72.6960883138096 | etot = -49.9334370002824 +274000 ekin = 10.0251036095154 | erot = 13.2107359457393 | epot = -73.1692765583682 | etot = -49.9334370031136 +275000 ekin = 10.1509497125671 | erot = 13.4661171078288 | epot = -73.5505038254265 | etot = -49.9334370050306 +276000 ekin = 10.2579077802687 | erot = 13.6195042883016 | epot = -73.8108490743552 | etot = -49.9334370057849 +277000 ekin = 10.3365003461945 | erot = 13.6692293787605 | epot = -73.9391667302955 | etot = -49.9334370053404 +278000 ekin = 10.3834483774443 | erot = 13.6258475790822 | epot = -73.9427329603463 | etot = -49.9334370038198 +279000 ekin = 10.4011507785854 | erot = 13.5106897711507 | epot = -73.8452775512667 | etot = -49.9334370015306 +280000 ekin = 10.3964398124889 | erot = 13.3527125117199 | epot = -73.6825893230131 | etot = -49.9334369988043 +281000 ekin = 10.3779527890289 | erot = 13.1828376404639 | epot = -73.4942274264354 | etot = -49.9334369969425 +282000 ekin = 10.353053740349 | erot = 13.0291459793179 | epot = -73.3156367147798 | etot = -49.933436995113 +283000 ekin = 10.3270589211616 | erot = 12.9150697625823 | epot = -73.1755656779524 | etot = -49.9334369942086 +284000 ekin = 10.3012154521609 | erot = 12.8544062464692 | epot = -73.0890586931095 | etot = -49.9334369944795 +285000 ekin = 10.2715544103098 | erot = 12.8490241982299 | epot = -73.0540156044443 | etot = -49.9334369959046 +286000 ekin = 10.2290782152144 | erot = 12.8892797632598 | epot = -73.0517949765399 | etot = -49.9334369980656 +287000 ekin = 10.1619978630747 | erot = 12.9580079590597 | epot = -73.0534428222849 | etot = -49.9334370001504 +288000 ekin = 10.0601300944718 | erot = 13.0376429488846 | epot = -73.0312100445667 | etot = -49.9334370012103 +289000 ekin = 9.9202215965333 | erot = 13.1179600214046 | epot = -72.9716186185634 | etot = -49.9334370006255 +290000 ekin = 9.74965131749658 | erot = 13.2006151946271 | epot = -72.88370351062 | etot = -49.9334369984963 +291000 ekin = 9.56608911179359 | erot = 13.2978259857956 | epot = -72.7973520932151 | etot = -49.9334369956259 +292000 ekin = 9.39289303103483 | erot = 13.4260428295556 | epot = -72.7523728535721 | etot = -49.9334369929817 +293000 ekin = 9.25289876825675 | erot = 13.5983001411125 | epot = -72.7846359009115 | etot = -49.9334369915422 +294000 ekin = 9.16176985520236 | erot = 13.8176522641868 | epot = -72.9128591109228 | etot = -49.9334369915336 +295000 ekin = 9.12570783653474 | erot = 14.0757418165381 | epot = -73.1348866458706 | etot = -49.9334369927977 +296000 ekin = 9.14197328684946 | erot = 14.3545965147092 | epot = -73.4300067964787 | etot = -49.93343699492 +297000 ekin = 9.20093046429169 | erot = 14.6305016956108 | epot = -73.7648691574402 | etot = -49.9334369975377 +298000 ekin = 9.28824464342762 | erot = 14.876884200274 | epot = -74.0985658445748 | etot = -49.9334370008732 +299000 ekin = 9.38785334981351 | erot = 15.06438864853 | epot = -74.3856790018754 | etot = -49.9334370035319 +300000 ekin = 9.48165911896817 | erot = 15.1708080545938 | epot = -74.5859041795344 | etot = -49.9334370059724 +301000 ekin = 9.55009456870998 | erot = 15.1800632839154 | epot = -74.6635948608319 | etot = -49.9334370082066 +302000 ekin = 9.57201526805398 | erot = 15.0823927221944 | epot = -74.5878450007561 | etot = -49.9334370105077 +303000 ekin = 9.52471361885221 | erot = 14.8708920500091 | epot = -74.3290426817247 | etot = -49.9334370128634 +304000 ekin = 9.3848129445937 | erot = 14.5406211738014 | epot = -73.8588711334674 | etot = -49.9334370150724 +305000 ekin = 9.13228587662142 | erot = 14.0911381302414 | epot = -73.1568610219493 | etot = -49.9334370150865 +306000 ekin = 8.75533716881437 | erot = 13.5286285172573 | epot = -72.2174027016023 | etot = -49.9334370155306 +307000 ekin = 8.24994820430533 | erot = 12.8613386577027 | epot = -71.0447238754311 | etot = -49.933437013423 +308000 ekin = 7.64566207604119 | erot = 12.1187367066719 | epot = -69.6978357833361 | etot = -49.9334370006229 +309000 ekin = 6.2156324931436 | erot = 10.8308134934805 | epot = -66.9798826118175 | etot = -49.9334366251935 +310000 ekin = 6.98208788798062 | erot = 9.38517955465197 | epot = -66.3007041395672 | etot = -49.9334366969346 +311000 ekin = 8.46519197710877 | erot = 8.64607863222307 | epot = -67.0447073767795 | etot = -49.9334367674477 +312000 ekin = 8.66431616582106 | erot = 8.18423138032177 | epot = -66.7819843262754 | etot = -49.9334367801326 +313000 ekin = 8.81657453316169 | erot = 7.84806509572883 | epot = -66.5980764070179 | etot = -49.9334367781274 +314000 ekin = 8.92571410839843 | erot = 7.64505956838057 | epot = -66.5042104526831 | etot = -49.9334367759041 +315000 ekin = 9.01908200767406 | erot = 7.5768080611827 | epot = -66.5293268431115 | etot = -49.9334367742548 +316000 ekin = 9.12426361176407 | erot = 7.636994446041 | epot = -66.6946948314336 | etot = -49.9334367736285 +317000 ekin = 9.26338621518957 | erot = 7.81017000722538 | epot = -67.0069929987641 | etot = -49.9334367763492 +318000 ekin = 9.44365313231158 | erot = 8.06449733144152 | epot = -67.4415872427621 | etot = -49.933436779009 +319000 ekin = 9.65799853893101 | erot = 8.35781040128967 | epot = -67.9492457228302 | etot = -49.9334367826095 +320000 ekin = 9.89196359099104 | erot = 8.64893573871685 | epot = -68.4743361164125 | etot = -49.9334367867046 +321000 ekin = 10.1233187755671 | erot = 8.89745069024987 | epot = -68.9542062564504 | etot = -49.9334367906335 +322000 ekin = 10.3265544624694 | erot = 9.06891954454781 | epot = -69.3289108006577 | etot = -49.9334367936406 +323000 ekin = 10.4783638188737 | erot = 9.14041960358909 | epot = -69.5522202175213 | etot = -49.9334367950585 +324000 ekin = 10.5626654861856 | erot = 9.10522153543596 | epot = -69.601323816133 | etot = -49.9334367945114 +325000 ekin = 10.5736671949011 | erot = 8.97511339417776 | epot = -69.4822173812585 | etot = -49.9334367921796 +326000 ekin = 10.5161587200511 | erot = 8.77895419858394 | epot = -69.2285497068497 | etot = -49.9334367882147 +327000 ekin = 10.4032259690655 | erot = 8.56034165158809 | epot = -68.8970044041409 | etot = -49.9334367834874 +328000 ekin = 10.2524292214703 | erot = 8.37036212265312 | epot = -68.5562281228988 | etot = -49.9334367787753 +329000 ekin = 10.0824546438466 | erot = 8.25940958185304 | epot = -68.2753010004092 | etot = -49.9334367747096 +330000 ekin = 9.90858228192529 | erot = 8.27090994172877 | epot = -68.1129289954878 | etot = -49.9334367718337 +331000 ekin = 9.74053523959285 | erot = 8.43704440644498 | epot = -68.111016416305 | etot = -49.9334367702672 +332000 ekin = 9.5832675956993 | erot = 8.77502618163514 | epot = -68.2917305473884 | etot = -49.933436770054 +333000 ekin = 9.43734454313999 | erot = 9.28570909296637 | epot = -68.6564904072819 | etot = -49.9334367711755 +334000 ekin = 9.30005714166466 | erot = 9.95274790624692 | epot = -69.1862418212745 | etot = -49.9334367733629 +335000 ekin = 9.16539195140551 | erot = 10.7463546200975 | epot = -69.8451833478333 | etot = -49.9334367763303 +336000 ekin = 9.02588570624398 | erot = 11.6261652905678 | epot = -70.5854877765507 | etot = -49.9334367797389 +337000 ekin = 8.87412067608633 | erot = 12.5449700956801 | epot = -71.352527555002 | etot = -49.9334367832356 +338000 ekin = 8.70391892935481 | erot = 13.4530941766686 | epot = -72.0904498925114 | etot = -49.933436786488 +339000 ekin = 8.51126560344778 | erot = 14.3027075314279 | epot = -72.7474099241017 | etot = -49.933436789226 +340000 ekin = 8.29488691398144 | erot = 15.0515581550066 | epot = -73.279881860252 | etot = -49.9334367912639 +341000 ekin = 8.05646205380861 | erot = 15.6657657386799 | epot = -73.6556645849945 | etot = -49.9334367925061 +342000 ekin = 7.80050981598768 | erot = 16.1215554932821 | epot = -73.8555021022001 | etot = -49.9334367929303 +343000 ekin = 7.53404165582677 | erot = 16.4060559812044 | epot = -73.8735344295911 | etot = -49.9334367925598 +344000 ekin = 7.26609676908326 | erot = 16.5174328472112 | epot = -73.716966407732 | etot = -49.9334367914375 +345000 ekin = 7.00725922449378 | erot = 16.4646262362322 | epot = -73.4053222503422 | etot = -49.9334367896163 +346000 ekin = 6.76919816417592 | erot = 16.2668142751609 | epot = -72.9694492265047 | etot = -49.9334367871679 +347000 ekin = 6.56418602316429 | erot = 15.9525180661041 | epot = -72.4501408734789 | etot = -49.9334367842106 +348000 ekin = 6.40447863711508 | erot = 15.5581119659908 | epot = -71.8960273840418 | etot = -49.9334367809359 +349000 ekin = 6.30143449814258 | erot = 15.1255022274318 | epot = -71.3603735031937 | etot = -49.9334367776193 +350000 ekin = 6.26433457359998 | erot = 14.6988992514292 | epot = -70.8966705996324 | etot = -49.9334367746033 +351000 ekin = 6.29901365146538 | erot = 14.3208623426265 | epot = -70.5533127663415 | etot = -49.9334367722497 +352000 ekin = 6.40655985354301 | erot = 14.0280287207505 | epot = -70.3680253451799 | etot = -49.9334367708864 +353000 ekin = 6.58240652259401 | erot = 13.8470668708989 | epot = -70.3629101642376 | etot = -49.9334367707447 +354000 ekin = 6.81609810135423 | erot = 13.7914168213438 | epot = -70.5409516946199 | etot = -49.9334367719218 +355000 ekin = 7.09188628775341 | erot = 13.8593469648778 | epot = -70.8846700269776 | etot = -49.9334367743463 +356000 ekin = 7.39015539571547 | erot = 14.033790526784 | epot = -71.3573827002662 | etot = -49.9334367777667 +357000 ekin = 7.68951512332416 | erot = 14.2842611187699 | epot = -71.9072130238669 | etot = -49.9334367817729 +358000 ekin = 7.96924870687132 | erot = 14.5707976474229 | epot = -72.4734831401511 | etot = -49.9334367858569 +359000 ekin = 8.21171431832055 | erot = 14.8493901180684 | epot = -72.9945412258931 | etot = -49.9334367895041 +360000 ekin = 8.40434316521794 | erot = 15.0779079482545 | epot = -73.4156879057477 | etot = -49.9334367922752 +361000 ekin = 8.54093730786224 | erot = 15.223459117279 | epot = -73.6978332181802 | etot = -49.9334367930389 +362000 ekin = 8.62176162458319 | erot = 15.2683190552292 | epot = -73.8235174732548 | etot = -49.9334367934425 +363000 ekin = 8.65376226171469 | erot = 15.2009231864222 | epot = -73.7881222408683 | etot = -49.9334367927313 +364000 ekin = 8.65006194495836 | erot = 15.0202219537552 | epot = -73.6037206897987 | etot = -49.9334367910852 +365000 ekin = 8.62864344793139 | erot = 14.7344841776847 | epot = -73.2965644144207 | etot = -49.9334367888046 +366000 ekin = 8.6102681648128 | erot = 14.358711776373 | epot = -72.9024167274443 | etot = -49.9334367862585 +367000 ekin = 8.61582393192208 | erot = 13.9116488824808 | epot = -72.4609095982182 | etot = -49.9334367838153 +368000 ekin = 8.66349013751643 | erot = 13.4130591643207 | epot = -72.0099860836059 | etot = -49.9334367817688 +369000 ekin = 8.76619052284205 | erot = 12.8818627722083 | epot = -71.5814900753351 | etot = -49.9334367802848 +370000 ekin = 8.9297841248867 | erot = 12.335453757501 | epot = -71.1986746617711 | etot = -49.9334367793833 +371000 ekin = 9.15232413557797 | erot = 11.7901096915281 | epot = -70.8758706060768 | etot = -49.9334367789707 +372000 ekin = 9.42449522042301 | erot = 11.2619930178438 | epot = -70.619925017159 | etot = -49.9334367788923 +373000 ekin = 9.73107815945971 | erot = 10.7680247395864 | epot = -70.4325396780453 | etot = -49.9334367789992 +374000 ekin = 10.0531002399327 | erot = 10.3260325847661 | epot = -70.31256960388 | etot = -49.9334367791812 +375000 ekin = 10.3702930598053 | erot = 9.95400537168857 | epot = -70.2577352108591 | etot = -49.9334367793653 +376000 ekin = 10.6635382209248 | erot = 9.66873204743242 | epot = -70.2657070478751 | etot = -49.9334367795179 +377000 ekin = 10.9144304196578 | erot = 9.48336618941097 | epot = -70.3312333902978 | etot = -49.933436781229 +378000 ekin = 11.1033255489941 | erot = 9.40465442429995 | epot = -70.4414167547152 | etot = -49.9334367814212 +379000 ekin = 11.2228479612869 | erot = 9.43497166219466 | epot = -70.5912564051334 | etot = -49.9334367816518 +380000 ekin = 11.2715765588452 | erot = 9.57046136396965 | epot = -70.775474704902 | etot = -49.9334367820871 +381000 ekin = 11.2520704290781 | erot = 9.80028776495387 | epot = -70.9857949768612 | etot = -49.9334367828293 +382000 ekin = 11.1693057444479 | erot = 10.1070539322048 | epot = -71.2097964605076 | etot = -49.9334367838549 +383000 ekin = 11.0296540359228 | erot = 10.4684110619645 | epot = -71.4315018829166 | etot = -49.9334367850292 +384000 ekin = 10.8406006584011 | erot = 10.8594456848222 | epot = -71.6334831293848 | etot = -49.9334367861616 +385000 ekin = 10.6110745203043 | erot = 11.2550567348661 | epot = -71.7995680421826 | etot = -49.9334367870122 +386000 ekin = 10.3514833909804 | erot = 11.6320380412179 | epot = -71.9169582201447 | etot = -49.9334367879464 +387000 ekin = 10.0722200977276 | erot = 11.9687897481463 | epot = -71.9744466347428 | etot = -49.933436788869 +388000 ekin = 9.78227942381133 | erot = 12.2453759804225 | epot = -71.961092194011 | etot = -49.9334367897772 +389000 ekin = 9.48904126172454 | erot = 12.4455699112058 | epot = -71.8680479631065 | etot = -49.9334367901762 +390000 ekin = 9.1988011058867 | erot = 12.5588554599197 | epot = -71.69109335618 | etot = -49.9334367903736 +391000 ekin = 8.91824243206977 | erot = 12.5805139316136 | epot = -71.4321931531813 | etot = -49.9334367894979 +392000 ekin = 8.6575772689696 | erot = 12.5171399947339 | epot = -71.1081540510193 | etot = -49.9334367873158 +393000 ekin = 8.43231332351752 | erot = 12.3882397426851 | epot = -70.7539898501723 | etot = -49.9334367839697 +394000 ekin = 8.26247251141758 | erot = 12.2242334615178 | epot = -70.4201427530229 | etot = -49.9334367800876 +395000 ekin = 8.16904684405228 | erot = 12.0605939409215 | epot = -70.1630775616218 | etot = -49.9334367766481 +396000 ekin = 8.16818394388909 | erot = 11.9294338996869 | epot = -70.031054618239 | etot = -49.933436774663 +397000 ekin = 8.26509438251318 | erot = 11.8511087055234 | epot = -70.0496398628365 | etot = -49.9334367747999 +398000 ekin = 8.4501402415728 | erot = 11.8286142934125 | epot = -70.2121913121361 | etot = -49.9334367771509 +399000 ekin = 8.6987524085071 | erot = 11.846535735853 | epot = -70.4787249255838 | etot = -49.9334367812237 +400000 ekin = 8.97515584924223 | erot = 11.8745399217494 | epot = -70.7831325571628 | etot = -49.9334367861712 +401000 ekin = 9.23841273736301 | erot = 11.8739232099274 | epot = -71.0457727383469 | etot = -49.9334367910566 +402000 ekin = 9.44890872719654 | erot = 11.8053354457279 | epot = -71.1876809679463 | etot = -49.9334367950219 +403000 ekin = 9.57405438450813 | erot = 11.6363946720643 | epot = -71.1438858539035 | etot = -49.9334367973311 +404000 ekin = 9.59280070366271 | erot = 11.348515161749 | epot = -70.8747526628665 | etot = -49.9334367974547 +405000 ekin = 9.49859029588226 | erot = 10.9420390046576 | epot = -70.3740660957269 | etot = -49.9334367951871 +406000 ekin = 9.30027519156631 | erot = 10.4381532175857 | epot = -69.6718651999802 | etot = -49.9334367908282 +407000 ekin = 9.02027468745294 | erot = 9.87620869145151 | epot = -68.829920164067 | etot = -49.9334367851625 +408000 ekin = 8.69009310249533 | erot = 9.30670442543022 | epot = -67.9302343071319 | etot = -49.9334367792063 +409000 ekin = 8.34449651482889 | erot = 8.78220945751285 | epot = -67.0601427462141 | etot = -49.9334367738723 +410000 ekin = 8.01620286719442 | erot = 8.34920326966272 | epot = -66.2988429065481 | etot = -49.9334367696909 +411000 ekin = 7.53291151045996 | erot = 8.08116831510292 | epot = -65.5475166514788 | etot = -49.9334368259159 +412000 ekin = 6.47552839017785 | erot = 8.45821289457424 | epot = -64.8671779820466 | etot = -49.9334366972945 +413000 ekin = 6.24399442167419 | erot = 8.99561848801201 | epot = -65.1730495934361 | etot = -49.9334366837499 +414000 ekin = 6.18550934222112 | erot = 9.11685651465889 | epot = -65.2358025415366 | etot = -49.9334366846566 +415000 ekin = 6.1970619114856 | erot = 9.37263397423855 | epot = -65.5031325721667 | etot = -49.9334366864426 +416000 ekin = 6.27056156934871 | erot = 9.74301767920604 | epot = -65.9470159374523 | etot = -49.9334366888976 +417000 ekin = 6.39375612507792 | erot = 10.2017877091225 | epot = -66.5289805260413 | etot = -49.9334366918408 +418000 ekin = 6.55151386108778 | erot = 10.718082412043 | epot = -67.2030329682449 | etot = -49.9334366951141 +419000 ekin = 6.72687533385979 | erot = 11.2579372105315 | epot = -67.918249242961 | etot = -49.9334366985696 +420000 ekin = 6.90190857992248 | erot = 11.7859069157866 | epot = -68.6212521977214 | etot = -49.9334367020123 +421000 ekin = 7.05869608070453 | erot = 12.2671743403912 | epot = -69.2593071262431 | etot = -49.9334367051474 +422000 ekin = 7.18084994342412 | erot = 12.6704427611134 | epot = -69.7847294121138 | etot = -49.9334367075762 +423000 ekin = 7.25563872116252 | erot = 12.9714590209572 | epot = -70.1605344510282 | etot = -49.9334367089085 +424000 ekin = 7.27613764929304 | erot = 13.1562785232249 | epot = -70.3658528814317 | etot = -49.9334367089138 +425000 ekin = 7.24240438622737 | erot = 13.2229033437658 | epot = -70.3987444377231 | etot = -49.93343670773 +426000 ekin = 7.16102366031047 | erot = 13.1802284318522 | epot = -70.274688797831 | etot = -49.9334367056683 +427000 ekin = 7.04323569563786 | erot = 13.0453653110875 | epot = -70.0220377098918 | etot = -49.9334367031664 +428000 ekin = 6.90252931709374 | erot = 12.8399447979979 | epot = -69.6759108156912 | etot = -49.9334367005996 +429000 ekin = 6.75380655237967 | erot = 12.5877583897435 | epot = -69.2750016367889 | etot = -49.9334366946657 +430000 ekin = 6.63643931616211 | erot = 12.3309009158442 | epot = -68.9007769264406 | etot = -49.9334366944343 +431000 ekin = 6.56250777539762 | erot = 12.0862249118176 | epot = -68.5821693817337 | etot = -49.9334366945185 +432000 ekin = 6.5277574398518 | erot = 11.8551418290415 | epot = -68.3163359638447 | etot = -49.9334366949515 +433000 ekin = 6.52644586082078 | erot = 11.6363446464993 | epot = -68.0962272029283 | etot = -49.9334366956083 +434000 ekin = 6.54730069025438 | erot = 11.4229959688113 | epot = -67.9037333576921 | etot = -49.9334366986264 +435000 ekin = 6.57899083359961 | erot = 11.2084874067099 | epot = -67.7209149390926 | etot = -49.9334366987831 +436000 ekin = 6.61931202197556 | erot = 10.9928671140558 | epot = -67.5456158350846 | etot = -49.9334366990532 +437000 ekin = 6.66568526291941 | erot = 10.775445555649 | epot = -67.3745675179758 | etot = -49.9334366994074 +438000 ekin = 6.71519766409353 | erot = 10.5550626355899 | epot = -67.2036969994775 | etot = -49.9334366997941 +439000 ekin = 6.76486690072993 | erot = 10.3306264414445 | epot = -67.0289300423136 | etot = -49.9334367001391 +440000 ekin = 6.81204485682425 | erot = 10.1018252021667 | epot = -66.8473067593426 | etot = -49.9334367003517 +441000 ekin = 6.8549402585791 | erot = 9.86991417524556 | epot = -66.6582911341317 | etot = -49.9334367003071 +442000 ekin = 6.89316565875409 | erot = 9.63860472644123 | epot = -66.4652070851976 | etot = -49.9334367000023 +443000 ekin = 6.92830085529117 | erot = 9.41426089210217 | epot = -66.2759984467657 | etot = -49.9334366993723 +444000 ekin = 6.96427254047519 | erot = 9.20573448271171 | epot = -66.1034437216294 | etot = -49.9334366984425 +445000 ekin = 7.00734929586298 | erot = 9.02391831398023 | epot = -65.9647043071521 | etot = -49.9334366973089 +446000 ekin = 7.06567994298367 | erot = 8.88054940607855 | epot = -65.8796660452047 | etot = -49.9334366961425 +447000 ekin = 7.1482693853796 | erot = 8.78650081534135 | epot = -65.868206895892 | etot = -49.933436695171 +448000 ekin = 7.26342746668263 | erot = 8.74982299478608 | epot = -65.9466871561162 | etot = -49.9334366946475 +449000 ekin = 7.41688893788363 | erot = 8.77375650823683 | epot = -66.1240821409159 | etot = -49.9334366947954 +450000 ekin = 7.60996195055461 | erot = 8.85525305879979 | epot = -66.3986517051257 | etot = -49.9334366957713 +451000 ekin = 7.83859627200689 | erot = 8.98479300395988 | epot = -66.7568259731909 | etot = -49.9334366972242 +452000 ekin = 8.0953465489177 | erot = 9.14858392352467 | epot = -67.1773671722438 | etot = -49.9334366998015 +453000 ekin = 8.36501912235157 | erot = 9.32480175710959 | epot = -67.6232575823023 | etot = -49.9334367028412 +454000 ekin = 8.62787482253606 | erot = 9.48861390841596 | epot = -68.0499254368547 | etot = -49.9334367059027 +455000 ekin = 8.86318683153801 | erot = 9.61656796363323 | epot = -68.4131915036411 | etot = -49.9334367084699 +456000 ekin = 9.05301422109849 | erot = 9.6906953996789 | epot = -68.677146330813 | etot = -49.9334367100356 +457000 ekin = 9.18315881760864 | erot = 9.70061032941657 | epot = -68.8172058578391 | etot = -49.9334367108139 +458000 ekin = 9.2473908388488 | erot = 9.64764046615366 | epot = -68.8284680142724 | etot = -49.9334367092699 +459000 ekin = 9.25548953030117 | erot = 9.54869554441728 | epot = -68.7376217810851 | etot = -49.9334367063667 +460000 ekin = 9.22729166752555 | erot = 9.43094677910707 | epot = -68.5916751492618 | etot = -49.9334367026292 +461000 ekin = 9.18866313207529 | erot = 9.32746380432218 | epot = -68.4495636352403 | etot = -49.9334366988429 +462000 ekin = 9.16559319440608 | erot = 9.27112965794425 | epot = -68.3701595482546 | etot = -49.9334366959043 +463000 ekin = 9.17773873091335 | erot = 9.28803491834508 | epot = -68.3992103437155 | etot = -49.9334366944571 +464000 ekin = 9.2334219753185 | erot = 9.39218062503575 | epot = -68.5590392952285 | etot = -49.9334366948742 +465000 ekin = 9.32780582036065 | erot = 9.58246294342806 | epot = -68.8437054607551 | etot = -49.9334366969664 +466000 ekin = 9.44464021675435 | erot = 9.84368987463132 | epot = -69.2217667915085 | etot = -49.9334367001228 +467000 ekin = 9.56120377684457 | erot = 10.1507714878392 | epot = -69.6454119681725 | etot = -49.9334367034887 +468000 ekin = 9.65468489576676 | erot = 10.4750886621804 | epot = -70.0632102642043 | etot = -49.9334367062572 +469000 ekin = 9.70785696604834 | erot = 10.7910978191503 | epot = -70.4323914930665 | etot = -49.9334367078679 +470000 ekin = 9.71262212180167 | erot = 11.0813447197958 | epot = -70.7274035497418 | etot = -49.9334367081443 +471000 ekin = 9.67073883343496 | erot = 11.3387370682914 | epot = -70.9429126090358 | etot = -49.9334367073094 +472000 ekin = 9.59191180300086 | erot = 11.5659397722493 | epot = -71.091288280938 | etot = -49.9334367056878 +473000 ekin = 9.49111612470798 | erot = 11.7727565997472 | epot = -71.1973094282183 | etot = -49.9334367037631 +474000 ekin = 9.38501610880983 | erot = 11.9729251611027 | epot = -71.291377971837 | etot = -49.9334367019244 +475000 ekin = 9.2888723293099 | erot = 12.181090667979 | epot = -71.4033996977682 | etot = -49.9334367004792 +476000 ekin = 9.21413109738119 | erot = 12.4104297276944 | epot = -71.5579975245924 | etot = -49.9334366995168 +477000 ekin = 9.16769186030955 | erot = 12.6713688993763 | epot = -71.7724974587973 | etot = -49.9334366991115 +478000 ekin = 9.15149095806687 | erot = 12.9706692103864 | epot = -72.0555968677338 | etot = -49.9334366992806 +479000 ekin = 9.16265639589747 | erot = 13.3106560519201 | epot = -72.4067491478423 | etot = -49.9334367000247 +480000 ekin = 9.19406563261028 | erot = 13.6885767380482 | epot = -72.8160790719721 | etot = -49.9334367013136 +481000 ekin = 9.2351814536897 | erot = 14.0963491431014 | epot = -73.2649672998307 | etot = -49.9334367030397 +482000 ekin = 9.27324003577829 | erot = 14.5212080502509 | epot = -73.7278847910061 | etot = -49.9334367049769 +483000 ekin = 9.29487863766067 | erot = 14.9475327813956 | epot = -74.1758481259226 | etot = -49.9334367068663 +484000 ekin = 9.28813070974468 | erot = 15.3594466797463 | epot = -74.5810140977087 | etot = -49.9334367082177 +485000 ekin = 9.24449800631886 | erot = 15.7449638956355 | epot = -74.922898610798 | etot = -49.9334367088436 +486000 ekin = 9.16033951363167 | erot = 16.0979673630931 | epot = -75.1917435854299 | etot = -49.9334367087052 +487000 ekin = 9.03726433394301 | erot = 16.4183746409746 | epot = -75.3890756829008 | etot = -49.9334367079832 +488000 ekin = 8.88140769757311 | erot = 16.7103217583947 | epot = -75.5251661629628 | etot = -49.933436706995 +489000 ekin = 8.7019310328288 | erot = 16.9791336192718 | epot = -75.614501358161 | etot = -49.9334367060604 +490000 ekin = 8.50932564387278 | erot = 17.2283334637251 | epot = -75.6710958130029 | etot = -49.933436705405 +491000 ekin = 8.3140279783916 | erot = 17.4577039709126 | epot = -75.7051686544105 | etot = -49.9334367051063 +492000 ekin = 8.12558483923703 | erot = 17.6628124157463 | epot = -75.721833960107 | etot = -49.9334367051237 +493000 ekin = 7.95231204431639 | erot = 17.8358133610015 | epot = -75.7215621106728 | etot = -49.9334367053549 +494000 ekin = 7.80119073598954 | erot = 17.9669524473278 | epot = -75.7015798890239 | etot = -49.9334367057066 +495000 ekin = 7.67769081998003 | erot = 18.0460778615326 | epot = -75.6572053876598 | etot = -49.9334367061471 +496000 ekin = 7.58531059409856 | erot = 18.0636363740809 | epot = -75.5823836748914 | etot = -49.9334367067119 +497000 ekin = 7.52485262514337 | erot = 18.0110549918106 | epot = -75.469344324409 | etot = -49.933436707455 +498000 ekin = 7.49373543820694 | erot = 17.8809293893934 | epot = -75.308101535769 | etot = -49.9334367081687 +499000 ekin = 7.48617782568836 | erot = 17.6689103471237 | epot = -75.0885248818445 | etot = -49.9334367090325 +500000 ekin = 7.49347216210361 | erot = 17.3741777344968 | epot = -74.8010866062347 | etot = -49.9334367096343 +501000 ekin = 7.50537969957539 | erot = 17.0010883509615 | epot = -74.4399047602053 | etot = -49.9334367096683 +502000 ekin = 7.51248513612193 | erot = 16.5621897687607 | epot = -74.0081116138094 | etot = -49.9334367089268 +503000 ekin = 7.50819446611848 | erot = 16.0791838293679 | epot = -73.5208150028627 | etot = -49.9334367073763 +504000 ekin = 7.49011586233679 | erot = 15.5818683068884 | epot = -73.0054208743933 | etot = -49.9334367051681 +505000 ekin = 7.46056991976306 | erot = 15.1049042921301 | epot = -72.4989109145597 | etot = -49.9334367026665 +506000 ekin = 7.426166883467 | erot = 14.6834712564166 | epot = -72.0430748400303 | etot = -49.9334367001468 +507000 ekin = 7.39661274013544 | erot = 14.3486660365891 | epot = -71.6787154748017 | etot = -49.9334366980772 +508000 ekin = 7.38281606554088 | erot = 14.122381305526 | epot = -71.4386340679655 | etot = -49.9334366968986 +509000 ekin = 7.39402992167344 | erot = 14.0119926345969 | epot = -71.3394592535313 | etot = -49.9334366972609 +510000 ekin = 7.4348791744664 | erot = 14.00645497061 | epot = -71.3747708439857 | etot = -49.9334366989093 +511000 ekin = 7.50576717999883 | erot = 14.0784238742641 | epot = -71.5176277562898 | etot = -49.9334367020268 +512000 ekin = 7.60119561215965 | erot = 14.1838211434744 | epot = -71.7184534619007 | etot = -49.9334367062666 +513000 ekin = 7.71044568681027 | erot = 14.2667319445938 | epot = -71.9106143423502 | etot = -49.9334367109461 +514000 ekin = 7.81978747766632 | erot = 14.2680211759095 | epot = -72.0212453686759 | etot = -49.9334367151001 +515000 ekin = 7.91595150928813 | erot = 14.136730975867 | epot = -71.9861192028066 | etot = -49.9334367176515 +516000 ekin = 7.99023839626997 | erot = 13.8421209123312 | epot = -71.765796026329 | etot = -49.9334367177278 +517000 ekin = 8.04205550960352 | erot = 13.3828818541575 | epot = -71.3583740787928 | etot = -49.9334367150318 +518000 ekin = 8.08036426889702 | erot = 12.7898538339902 | epot = -70.8036548129272 | etot = -49.93343671004 +519000 ekin = 8.12206393604817 | erot = 12.1205081667034 | epot = -70.1760088066211 | etot = -49.9334367038696 +520000 ekin = 8.18764894630583 | erot = 11.4468759977119 | epot = -69.5679616418748 | etot = -49.9334366978571 +521000 ekin = 8.29566353773327 | erot = 10.8412363962021 | epot = -69.0703366270684 | etot = -49.933436693133 +522000 ekin = 8.45774428961541 | erot = 10.3639645179526 | epot = -68.7551454979472 | etot = -49.9334366903792 +523000 ekin = 8.6754707032932 | erot = 10.0559571765564 | epot = -68.6648645696558 | etot = -49.9334366898061 +524000 ekin = 8.93944864495669 | erot = 9.93579310878289 | epot = -68.8086784449968 | etot = -49.9334366912572 +525000 ekin = 9.23044472106861 | erot = 10.0004752135613 | epot = -69.1643566289846 | etot = -49.9334366943547 +526000 ekin = 9.52203491653689 | erot = 10.2283307207382 | epot = -69.6838023358922 | etot = -49.9334366986171 +527000 ekin = 9.78409599190119 | erot = 10.5829813010738 | epot = -70.3005139965033 | etot = -49.9334367035283 +528000 ekin = 9.98654469592338 | erot = 11.0178490698024 | epot = -70.937830474285 | etot = -49.9334367085592 +529000 ekin = 10.1029539601439 | erot = 11.4811633033496 | epot = -71.5175539766437 | etot = -49.9334367131502 +530000 ekin = 10.1138818470412 | erot = 11.9216268521526 | epot = -71.9689454159113 | etot = -49.9334367167174 +531000 ekin = 10.009768376633 | erot = 12.2946121702543 | epot = -72.2378172656133 | etot = -49.933436718726 +532000 ekin = 9.79306563777554 | erot = 12.5680717027124 | epot = -72.2945740593142 | etot = -49.9334367188263 +533000 ekin = 9.47905160959907 | erot = 12.7267270062226 | epot = -72.1392153328171 | etot = -49.9334367169954 +534000 ekin = 9.09480598113199 | erot = 12.7731458504705 | epot = -71.8013885451888 | etot = -49.9334367135863 +535000 ekin = 8.67621596356743 | erot = 12.725246773648 | epot = -71.3348994464545 | etot = -49.9334367092391 +536000 ekin = 8.26347380199202 | erot = 12.6111100069009 | epot = -70.808020513579 | etot = -49.9334367046861 +537000 ekin = 7.8959905961062 | erot = 12.4628737027919 | epot = -70.2923009994712 | etot = -49.933436700573 +538000 ekin = 7.60773288315974 | erot = 12.3114435936331 | epot = -69.8526131741348 | etot = -49.933436697342 +539000 ekin = 7.42371159250873 | erot = 12.1829376490021 | epot = -69.5400859367383 | etot = -49.9334366952274 +540000 ekin = 7.35791077724687 | erot = 12.0968490256268 | epot = -69.3881964971777 | etot = -49.933436694304 +541000 ekin = 7.41256804382714 | erot = 12.0653576080474 | epot = -69.4113623464303 | etot = -49.9334366945558 +542000 ekin = 7.57853605040992 | erot = 12.0931906687774 | epot = -69.6051634151016 | etot = -49.9334366959142 +543000 ekin = 7.83646941911308 | erot = 12.1777647790372 | epot = -69.9476708963917 | etot = -49.9334366982414 +544000 ekin = 8.15871763039278 | erot = 12.3097728230818 | epot = -70.4019271547725 | etot = -49.9334367012979 +545000 ekin = 8.51194808021862 | erot = 12.4746658403755 | epot = -70.9200506252934 | etot = -49.9334367046993 +546000 ekin = 8.8605554298828 | erot = 12.6554193667532 | epot = -71.4494115045595 | etot = -49.9334367079235 +547000 ekin = 9.17075161999858 | erot = 12.8364725166206 | epot = -71.9406608470137 | etot = -49.9334367103946 +548000 ekin = 9.41490179012599 | erot = 13.0079503310952 | epot = -72.3562888328661 | etot = -49.9334367116449 +549000 ekin = 9.57534656746483 | erot = 13.1686979374105 | epot = -72.6774812163388 | etot = -49.9334367114634 +550000 ekin = 9.64686209048007 | erot = 13.3267810142535 | epot = -72.9070798147103 | etot = -49.9334367099767 +551000 ekin = 9.63715286761366 | erot = 13.4970109715298 | epot = -73.0676005467461 | etot = -49.9334367076027 +552000 ekin = 9.56521103056892 | erot = 13.6962041250842 | epot = -73.1948518605964 | etot = -49.9334367049433 +553000 ekin = 9.45778037494705 | erot = 13.9376030903696 | epot = -73.328820167963 | etot = -49.9334367026464 +554000 ekin = 9.34444856540419 | erot = 14.2259329985704 | epot = -73.5038182652631 | etot = -49.9334367012885 +555000 ekin = 9.25213586068647 | erot = 14.554187341061 | epot = -73.739759903013 | etot = -49.9334367012655 +556000 ekin = 9.19999740124744 | erot = 14.9027731790121 | epot = -74.0362072829663 | etot = -49.9334367027067 +557000 ekin = 9.19858106847623 | erot = 15.2418626002227 | epot = -74.3738803739402 | etot = -49.9334367052413 +558000 ekin = 9.24425546373156 | erot = 15.533160676273 | epot = -74.7108528491238 | etot = -49.9334367091192 +559000 ekin = 9.31861665860527 | erot = 15.7359099530683 | epot = -74.9879633247355 | etot = -49.9334367130619 +560000 ekin = 9.39695059709786 | erot = 15.8150009569878 | epot = -75.1453882704714 | etot = -49.9334367163857 +561000 ekin = 9.45314011700227 | erot = 15.7467098708858 | epot = -75.1332867063792 | etot = -49.9334367184911 +562000 ekin = 9.46443250758529 | erot = 15.5232568984784 | epot = -74.9211261250191 | etot = -49.9334367189554 +563000 ekin = 9.41516469943674 | erot = 15.1567249816826 | epot = -74.5053263982394 | etot = -49.9334367171201 +564000 ekin = 9.2988962721603 | erot = 14.679911962652 | epot = -73.912244948898 | etot = -49.9334367140856 +565000 ekin = 9.11880310151717 | erot = 14.1400031739803 | epot = -73.1922429852183 | etot = -49.9334367097209 +566000 ekin = 8.88664822048603 | erot = 13.5965040768085 | epot = -72.4165890018559 | etot = -49.9334367045614 +567000 ekin = 8.62095363305963 | erot = 13.1147978259198 | epot = -71.669188158177 | etot = -49.9334366991976 +568000 ekin = 8.34502941995043 | erot = 12.7577046249881 | epot = -71.0361707402981 | etot = -49.9334366953595 +569000 ekin = 8.08308251282 | erot = 12.5716587303351 | epot = -70.5881779352045 | etot = -49.9334366920495 +570000 ekin = 7.85931792269072 | erot = 12.5845592067786 | epot = -70.3773138203158 | etot = -49.9334366908465 +571000 ekin = 7.69515957546865 | erot = 12.7948834197769 | epot = -70.4234796877068 | etot = -49.9334366924613 +572000 ekin = 7.60396111741565 | erot = 13.1643540858181 | epot = -70.7017519004431 | etot = -49.9334366972093 +573000 ekin = 7.58730164850477 | erot = 13.6192730323247 | epot = -71.1400113849128 | etot = -49.9334367040834 +574000 ekin = 7.63520361153434 | erot = 14.0643105452094 | epot = -71.6329508680247 | etot = -49.933436711281 +575000 ekin = 7.73080156106132 | erot = 14.404463219706 | epot = -72.0687014975707 | etot = -49.9334367168034 +576000 ekin = 7.85689248431528 | erot = 14.5664691504383 | epot = -72.3567983545794 | etot = -49.9334367198259 +577000 ekin = 8.00091593729851 | erot = 14.5094673832397 | epot = -72.4438200405807 | etot = -49.9334367200425 +578000 ekin = 8.15665258261498 | erot = 14.2276209559758 | epot = -72.3177102566093 | etot = -49.9334367180185 +579000 ekin = 8.3230672805737 | erot = 13.7443245549161 | epot = -72.0008285501224 | etot = -49.9334367146326 +580000 ekin = 8.50340996044298 | erot = 13.1029754975957 | epot = -71.5398221682012 | etot = -49.9334367101625 +581000 ekin = 8.70208311700319 | erot = 12.3569061227087 | epot = -70.9924259462229 | etot = -49.933436706511 +582000 ekin = 8.91777039447199 | erot = 11.5600287828267 | epot = -70.4112358805434 | etot = -49.9334367032448 +583000 ekin = 9.14731913957018 | erot = 10.7633073833908 | epot = -69.8440632235177 | etot = -49.9334367005567 +584000 ekin = 9.38577210814637 | erot = 10.0114551308019 | epot = -69.3306639375173 | etot = -49.9334366985691 +585000 ekin = 9.62647735599204 | erot = 9.34056459161516 | epot = -68.9004786449768 | etot = -49.9334366973696 +586000 ekin = 9.86132138676436 | erot = 8.77626879101596 | epot = -68.5710268748042 | etot = -49.9334366970239 +587000 ekin = 10.0810752649587 | erot = 8.33235621298659 | epot = -68.3468681754879 | etot = -49.9334366975425 +588000 ekin = 10.2759188426479 | erot = 8.01010405478541 | epot = -68.2194595962795 | etot = -49.9334366988462 +589000 ekin = 10.43624228336 | erot = 7.79886753304834 | epot = -68.168546517119 | etot = -49.9334367007106 +590000 ekin = 10.5537937400067 | erot = 7.67891225367106 | epot = -68.1661426964501 | etot = -49.9334367027724 +591000 ekin = 10.6230840083969 | erot = 7.62453842355608 | epot = -68.1810591364585 | etot = -49.9334367045055 +592000 ekin = 10.6427223551157 | erot = 7.61008622174455 | epot = -68.1862452824154 | etot = -49.9334367055552 +593000 ekin = 10.6162293457351 | erot = 7.61530634627727 | epot = -68.1649723976566 | etot = -49.9334367056442 +594000 ekin = 10.5518689631683 | erot = 7.62911861510402 | epot = -68.1144242830922 | etot = -49.93343670482 +595000 ekin = 10.4613549146823 | erot = 7.650415752318 | epot = -68.0452073703874 | etot = -49.933436703387 +596000 ekin = 10.3577397595494 | erot = 7.68597457794617 | epot = -67.9771510392671 | etot = -49.9334367017716 +597000 ekin = 10.2530110984654 | erot = 7.74702054973694 | epot = -67.9334683485737 | etot = -49.9334367003713 +598000 ekin = 10.1558396073476 | erot = 7.84502642243173 | epot = -67.9343027292742 | etot = -49.9334366994949 +599000 ekin = 10.0716456764075 | erot = 7.98815266721895 | epot = -67.9932350426329 | etot = -49.9334366990064 +600000 ekin = 10.0026338981048 | erot = 8.18253713499505 | epot = -68.1186077321048 | etot = -49.9334366990049 +601000 ekin = 9.9465416303757 | erot = 8.4316149653268 | epot = -68.3115932944627 | etot = -49.9334366987602 +602000 ekin = 9.90213772018176 | erot = 8.73434308375233 | epot = -68.569917503502 | etot = -49.9334366995679 +603000 ekin = 9.86461425681278 | erot = 9.08804689167329 | epot = -68.8860978487964 | etot = -49.9334367003103 +604000 ekin = 9.82582394717072 | erot = 9.49104521651916 | epot = -69.2503058646016 | etot = -49.9334367009117 +605000 ekin = 9.77966552475125 | erot = 9.9415333824285 | epot = -69.6546356086235 | etot = -49.9334367014437 +606000 ekin = 9.72222592517299 | erot = 10.436343641288 | epot = -70.0920062686126 | etot = -49.9334367021516 +607000 ekin = 9.65083110473504 | erot = 10.9682113934829 | epot = -70.5524792017389 | etot = -49.933436703521 +608000 ekin = 9.56210695279333 | erot = 11.5218646669735 | epot = -71.0174083255685 | etot = -49.9334367058017 +609000 ekin = 9.44922522117037 | erot = 12.0704423054806 | epot = -71.4531042366018 | etot = -49.9334367099509 +610000 ekin = 9.30054046556791 | erot = 12.5719096406634 | epot = -71.8058868203983 | etot = -49.9334367141669 +611000 ekin = 9.09998277424836 | erot = 12.9832358346057 | epot = -72.0166553266324 | etot = -49.9334367177783 +612000 ekin = 8.83381798259864 | erot = 13.2691152694793 | epot = -72.0363699714124 | etot = -49.9334367193345 +613000 ekin = 8.49783282731314 | erot = 13.414589684441 | epot = -71.8458592296283 | etot = -49.9334367178742 +614000 ekin = 8.10282385727302 | erot = 13.4329804231671 | epot = -71.4692409939147 | etot = -49.9334367134746 +615000 ekin = 7.67548430528516 | erot = 13.3639670456124 | epot = -70.9728880581183 | etot = -49.9334367072208 +616000 ekin = 7.25407898481442 | erot = 13.262840089535 | epot = -70.4503557749773 | etot = -49.9334367006279 +617000 ekin = 6.88089060447721 | erot = 13.1866181608887 | epot = -70.0009454603655 | etot = -49.9334366949995 +618000 ekin = 6.59435266196333 | erot = 13.1829361442925 | epot = -69.7107254973559 | etot = -49.9334366911 +619000 ekin = 6.42302569827092 | erot = 13.2842954579373 | epot = -69.6407578453999 | etot = -49.9334366891917 +620000 ekin = 6.38233280983342 | erot = 13.5068914944185 | epot = -69.8226609933339 | etot = -49.9334366890821 +621000 ekin = 6.47407410483647 | erot = 13.8532244874395 | epot = -70.2607352827156 | etot = -49.9334366904396 +622000 ekin = 6.68823289727533 | erot = 14.3148945806224 | epot = -70.9365641707564 | etot = -49.9334366928586 +623000 ekin = 7.00613993426487 | erot = 14.8751185926057 | epot = -71.8146952230231 | etot = -49.9334366961525 +624000 ekin = 7.40369975383096 | erot = 15.5093236026734 | epot = -72.8464600565627 | etot = -49.9334367000584 +625000 ekin = 7.85341892223183 | erot = 16.1852180464119 | epot = -73.9720736735381 | etot = -49.9334367048943 +626000 ekin = 8.3247191464959 | erot = 16.8599319289476 | epot = -75.1180877863636 | etot = -49.9334367109201 +627000 ekin = 8.78345982127621 | erot = 17.4776172005326 | epot = -76.1945137397578 | etot = -49.933436717949 +628000 ekin = 9.19295493480404 | erot = 17.9720241171089 | epot = -77.098415776807 | etot = -49.9334367248941 +629000 ekin = 9.51863748532577 | erot = 18.277577695659 | epot = -77.7296519108455 | etot = -49.9334367298608 +630000 ekin = 9.73601789211593 | erot = 18.3475811088937 | epot = -78.0170357280482 | etot = -49.9334367270385 +631000 ekin = 9.84717031281614 | erot = 18.1774007977026 | epot = -77.9580078353464 | etot = -49.9334367248276 +632000 ekin = 9.86514165733081 | erot = 17.7977961670695 | epot = -77.5963745439655 | etot = -49.9334367195651 +633000 ekin = 9.80741211217903 | erot = 17.2626321533498 | epot = -77.0034809786532 | etot = -49.9334367131244 +634000 ekin = 9.69704834103309 | erot = 16.6375206673787 | epot = -76.2680057157435 | etot = -49.9334367073317 +635000 ekin = 9.55480062391363 | erot = 15.9824182747172 | epot = -75.4706556018311 | etot = -49.9334367032003 +636000 ekin = 9.39443376917515 | erot = 15.3418801349166 | epot = -74.6697506049049 | etot = -49.9334367008132 +637000 ekin = 9.22207208580399 | erot = 14.7441119803263 | epot = -73.8996207657959 | etot = -49.9334366996656 +638000 ekin = 9.03836092904166 | erot = 14.2055872728542 | epot = -73.1773849009799 | etot = -49.9334366990841 +639000 ekin = 8.8417163270326 | erot = 13.7372137345686 | epot = -72.5123667601041 | etot = -49.9334366985029 +640000 ekin = 8.63137043882056 | erot = 13.349384650894 | epot = -71.9141917872882 | etot = -49.9334366975736 +641000 ekin = 8.40954916880241 | erot = 13.0548513789787 | epot = -71.3978372439612 | etot = -49.9334366961801 +642000 ekin = 8.18255898209297 | erot = 12.8693803232604 | epot = -70.9853759997537 | etot = -49.9334366944003 +643000 ekin = 7.96078880308601 | erot = 12.8106076124347 | epot = -70.704833107984 | etot = -49.9334366924633 +644000 ekin = 7.75858397891552 | erot = 12.8950460234403 | epot = -70.5870666930887 | etot = -49.933436690733 +645000 ekin = 7.59153605354468 | erot = 13.1346881329385 | epot = -70.6596608761689 | etot = -49.9334366896857 +646000 ekin = 7.47142193123396 | erot = 13.5357483886143 | epot = -70.9406070094471 | etot = -49.9334366895989 +647000 ekin = 7.40688255491842 | erot = 14.0938074621893 | epot = -71.4341267079668 | etot = -49.9334366908591 +648000 ekin = 7.3947726178549 | erot = 14.7853448582563 | epot = -72.1135541745222 | etot = -49.9334366984109 +649000 ekin = 7.4121514857368 | erot = 15.5579695688721 | epot = -72.9035577587517 | etot = -49.9334367041428 +650000 ekin = 7.43748369392265 | erot = 16.3522656883523 | epot = -73.7231860927432 | etot = -49.9334367104683 +651000 ekin = 7.44712966937429 | erot = 17.1032791639312 | epot = -74.483845549307 | etot = -49.9334367160015 +652000 ekin = 7.42218365699006 | erot = 17.7519733432185 | epot = -75.1075937196553 | etot = -49.9334367194467 +653000 ekin = 7.35498154078593 | erot = 18.2566315884541 | epot = -75.5450498494635 | etot = -49.9334367202235 +654000 ekin = 7.25177127174499 | erot = 18.5983433686537 | epot = -75.7835513591201 | etot = -49.9334367187214 +655000 ekin = 7.13014467423054 | erot = 18.7785589482614 | epot = -75.8421403384621 | etot = -49.9334367159702 +656000 ekin = 7.01280585613053 | erot = 18.8114986913181 | epot = -75.7577412604568 | etot = -49.9334367130081 +657000 ekin = 6.92098821820217 | erot = 18.7164621309277 | epot = -75.5708870595781 | etot = -49.9334367104482 +658000 ekin = 6.87020252995195 | erot = 18.5133762497965 | epot = -75.3170154881844 | etot = -49.9334367084359 +659000 ekin = 6.86904868072255 | erot = 18.2216228321915 | epot = -75.024108219778 | etot = -49.9334367068639 +660000 ekin = 6.92024406128872 | erot = 17.8601865758754 | epot = -74.7138673427793 | etot = -49.9334367056152 +661000 ekin = 7.02250789860384 | erot = 17.4471787300407 | epot = -74.403123333353 | etot = -49.9334367047085 +662000 ekin = 7.17216566235826 | erot = 16.997819455819 | epot = -74.1034218225085 | etot = -49.9334367043312 +663000 ekin = 7.36379572139497 | erot = 16.5210347160605 | epot = -73.8182671422448 | etot = -49.9334367047893 +664000 ekin = 7.58974310930137 | erot = 16.0157458208117 | epot = -73.5389256364462 | etot = -49.9334367063331 +665000 ekin = 7.83889852381459 | erot = 15.4688426538688 | epot = -73.2411778865903 | etot = -49.9334367089069 +666000 ekin = 8.0956981591569 | erot = 14.857404004623 | epot = -72.8865388757095 | etot = -49.9334367119296 +667000 ekin = 8.34047460991738 | erot = 14.1568873290818 | epot = -72.430798653333 | etot = -49.9334367143339 +668000 ekin = 8.55167804703958 | erot = 13.35392315052 | epot = -71.8390379125689 | etot = -49.9334367150093 +669000 ekin = 8.70925293287165 | erot = 12.4582854454463 | epot = -71.1009750917497 | etot = -49.9334367134317 +670000 ekin = 8.79758177059105 | erot = 11.507208047482 | epot = -70.2382265280529 | etot = -49.9334367099799 +671000 ekin = 8.80682970149581 | erot = 10.5590297337004 | epot = -69.2992961408452 | etot = -49.933436705649 +672000 ekin = 8.73288275169812 | erot = 9.67972128078157 | epot = -68.3460407339062 | etot = -49.9334367014265 +673000 ekin = 8.57696192208772 | erot = 8.92953158888941 | epot = -67.4399302088216 | etot = -49.9334366978444 +674000 ekin = 8.3456407146255 | erot = 8.35517289124257 | epot = -66.6342503008242 | etot = -49.9334366949561 +675000 ekin = 8.05103177964263 | erot = 7.98833216297783 | epot = -65.9728006352139 | etot = -49.9334366925934 +676000 ekin = 7.71040082008774 | erot = 7.84792602077044 | epot = -65.4917635314901 | etot = -49.933436690632 +677000 ekin = 7.34474807573115 | erot = 7.94294820983828 | epot = -65.2211329746846 | etot = -49.9334366891152 +678000 ekin = 6.97652326979307 | erot = 8.27395942576396 | epot = -65.1839193837997 | etot = -49.9334366882426 +679000 ekin = 6.62703502446414 | erot = 8.8326449184761 | epot = -65.3931166312654 | etot = -49.9334366883252 +680000 ekin = 6.31408234073432 | erot = 9.59961963397869 | epot = -65.847138664448 | etot = -49.933436689735 +681000 ekin = 6.05007024087303 | erot = 10.540924973532 | epot = -66.5244319072614 | etot = -49.9334366928563 +682000 ekin = 5.84069686108073 | erot = 11.6040232365966 | epot = -67.3781567956329 | etot = -49.9334366979556 +683000 ekin = 5.68441215091699 | erot = 12.7150399581897 | epot = -68.3328888140272 | etot = -49.9334367049205 +684000 ekin = 5.57317083684405 | erot = 13.7803400925259 | epot = -69.2869476423183 | etot = -49.9334367129484 +685000 ekin = 5.49512330338869 | erot = 14.6959075813889 | epot = -70.1244676052265 | etot = -49.9334367204489 +686000 ekin = 5.43923671974787 | erot = 15.3654260750172 | epot = -70.738099520247 | etot = -49.9334367254819 +687000 ekin = 5.40037584531758 | erot = 15.7221888729605 | epot = -71.0560014449615 | etot = -49.9334367266834 +688000 ekin = 5.38224990758678 | erot = 15.7449830268383 | epot = -71.0606696584497 | etot = -49.9334367240246 +689000 ekin = 5.39639776098925 | erot = 15.4596385607517 | epot = -70.7894730404996 | etot = -49.9334367187586 +690000 ekin = 5.45787871142683 | erot = 14.9262956798774 | epot = -70.3176111039093 | etot = -49.9334367126051 +691000 ekin = 5.58031564626177 | erot = 14.2204427976204 | epot = -69.7341951507951 | etot = -49.9334367069129 +692000 ekin = 5.77268021073002 | erot = 13.4168709009498 | epot = -69.1229878131825 | etot = -49.9334367015026 +693000 ekin = 6.03848572884837 | erot = 12.5833910058039 | epot = -68.5553134331519 | etot = -49.9334366984996 +694000 ekin = 6.37471136517893 | erot = 11.7714633112457 | epot = -68.0796113729362 | etot = -49.9334366965116 +695000 ekin = 6.77415007784378 | erot = 11.0181330990357 | epot = -67.7257198722643 | etot = -49.9334366953848 +696000 ekin = 7.22672456195984 | erot = 10.3500991256959 | epot = -67.5102603826877 | etot = -49.933436695032 +697000 ekin = 7.71965128594451 | erot = 9.78480932554604 | epot = -67.4378973069032 | etot = -49.9334366954126 +698000 ekin = 8.23736470664202 | erot = 9.33123654406466 | epot = -67.5020379471977 | etot = -49.9334366964911 +699000 ekin = 8.76153382967204 | erot = 8.99061023092158 | epot = -67.6855807587833 | etot = -49.9334366981897 +700000 ekin = 9.27152159730681 | erot = 8.75737705400505 | epot = -67.9623353516544 | etot = -49.9334367003426 +701000 ekin = 9.74214098365044 | erot = 8.61946007697759 | epot = -68.295037764125 | etot = -49.9334367034969 +702000 ekin = 10.1452112686422 | erot = 8.55928312126094 | epot = -68.6379310960345 | etot = -49.9334367061313 +703000 ekin = 10.4587930030187 | erot = 8.55974434423407 | epot = -68.9519740552635 | etot = -49.9334367080107 +704000 ekin = 10.6678411441443 | erot = 8.60820420735217 | epot = -69.2094820602022 | etot = -49.9334367087057 +705000 ekin = 10.7665498375203 | erot = 8.70023426618484 | epot = -69.4002208117645 | etot = -49.9334367080594 +706000 ekin = 10.7588048077098 | erot = 8.84126944079394 | epot = -69.5335109547929 | etot = -49.9334367062891 +707000 ekin = 10.656448369005 | erot = 9.04518277454851 | epot = -69.6350678474683 | etot = -49.9334367039148 +708000 ekin = 10.4759748101243 | erot = 9.33018435435574 | epot = -69.7395958660221 | etot = -49.933436701542 +709000 ekin = 10.2349383724224 | erot = 9.71377701826114 | epot = -69.8821520902998 | etot = -49.9334366996162 +710000 ekin = 9.94939019044299 | erot = 10.2088106033416 | epot = -70.0916374920833 | etot = -49.9334366982987 +711000 ekin = 9.63303801877551 | erot = 10.8217465783871 | epot = -70.3882212946687 | etot = -49.9334366975061 +712000 ekin = 9.29790597030378 | erot = 11.5527669205594 | epot = -70.7841095879538 | etot = -49.9334366970907 +713000 ekin = 8.95557547302581 | erot = 12.396350487225 | epot = -71.2853626572583 | etot = -49.9334366970075 +714000 ekin = 8.61797359535847 | erot = 13.3409900927992 | epot = -71.8924003855459 | etot = -49.9334366973882 +715000 ekin = 8.29712952352225 | erot = 14.3676387565191 | epot = -72.598204978531 | etot = -49.9334366984896 +716000 ekin = 8.00398725897341 | erot = 15.4475133378671 | epot = -73.3849372973991 | etot = -49.9334367005586 +717000 ekin = 7.74683519039089 | erot = 16.540452685342 | epot = -74.2207245793767 | etot = -49.9334367036438 +718000 ekin = 7.52982507895108 | erot = 17.5950557077009 | epot = -75.0583174945533 | etot = -49.9334367079013 +719000 ekin = 7.35243516417203 | erot = 18.5497013193585 | epot = -75.8355731961808 | etot = -49.9334367126502 +720000 ekin = 7.21118318115014 | erot = 19.3392479277128 | epot = -76.4838678260512 | etot = -49.9334367171883 +721000 ekin = 7.10169759019296 | erot = 19.9036057066974 | epot = -76.9387400177134 | etot = -49.9334367208231 +722000 ekin = 7.02044686316244 | erot = 20.1972584111975 | epot = -77.151141996746 | etot = -49.933436722386 +723000 ekin = 6.96887965462612 | erot = 20.1990914032774 | epot = -77.1014077792934 | etot = -49.9334367213898 +724000 ekin = 6.95516719900633 | erot = 19.9185959406872 | epot = -76.8071998576283 | etot = -49.9334367179348 +725000 ekin = 6.99328744827875 | erot = 19.3950419522114 | epot = -76.3217661132555 | etot = -49.9334367127653 +726000 ekin = 7.0998457243209 | erot = 18.6900231618682 | epot = -75.723305593142 | etot = -49.9334367069529 +727000 ekin = 7.28975977543076 | erot = 17.8763690650735 | epot = -75.099565542019 | etot = -49.9334367015148 +728000 ekin = 7.57226569415553 | erot = 17.0272912652274 | epot = -74.5329936565488 | etot = -49.9334366971659 +729000 ekin = 7.94819326092055 | erot = 16.2083660376543 | epot = -74.0899959928354 | etot = -49.9334366942605 +730000 ekin = 8.40885783971974 | erot = 15.4730324367712 | epot = -73.8153269693387 | etot = -49.9334366928478 +731000 ekin = 8.93653983554197 | erot = 14.8609748015031 | epot = -73.730951329818 | etot = -49.9334366927729 +732000 ekin = 9.50625303474118 | erot = 14.3982952548988 | epot = -73.83798498343 | etot = -49.9334366937901 +733000 ekin = 10.0882454135359 | erot = 14.0984617274916 | epot = -74.1201438366822 | etot = -49.9334366956548 +734000 ekin = 10.650584604927 | erot = 13.9633900359381 | epot = -74.5474113390306 | etot = -49.9334366981656 +735000 ekin = 11.1614098846027 | erot = 13.984540795035 | epot = -75.0793873807643 | etot = -49.9334367011267 +736000 ekin = 11.5908641045064 | erot = 14.1443786489916 | epot = -75.668679457787 | etot = -49.933436704289 +737000 ekin = 11.9130267999457 | erot = 14.4186949533298 | epot = -76.2651584605726 | etot = -49.9334367072972 +738000 ekin = 12.1081074328814 | erot = 14.7799937728996 | epot = -76.8215379155122 | etot = -49.9334367097312 +739000 ekin = 12.1647528301869 | erot = 15.2014921459762 | epot = -77.2996816873864 | etot = -49.9334367112233 +740000 ekin = 12.0818547627498 | erot = 15.6606440164826 | epot = -77.6759354908383 | etot = -49.9334367116059 +741000 ekin = 11.8690601673902 | erot = 16.1409035861541 | epot = -77.9434004645535 | etot = -49.9334367110093 +742000 ekin = 11.5454682620885 | erot = 16.6309355138724 | epot = -78.1098404858044 | etot = -49.9334367098434 +743000 ekin = 11.1366225378549 | erot = 17.1214741632573 | epot = -78.1915334097811 | etot = -49.933436708669 +744000 ekin = 10.6705301542887 | erot = 17.6010237792036 | epot = -78.2049906414934 | etot = -49.9334367080012 +745000 ekin = 10.1737520698012 | erot = 18.0520929498985 | epot = -78.1592817278441 | etot = -49.9334367081444 +746000 ekin = 9.66850131293643 | erot = 18.449485732024 | epot = -78.051423754061 | etot = -49.9334367091005 +747000 ekin = 9.17126973094193 | erot = 18.7614465752673 | epot = -77.8661530167956 | etot = -49.9334367105864 +748000 ekin = 8.69297393779132 | erot = 18.9537281304379 | epot = -77.5801387803998 | etot = -49.9334367121705 +749000 ekin = 8.2401685894299 | erot = 18.9943262074662 | epot = -77.1679315102766 | etot = -49.9334367133805 +750000 ekin = 7.81665899721376 | erot = 18.8585564741543 | epot = -76.6086521852683 | etot = -49.9334367139002 +751000 ekin = 7.42490357424127 | erot = 18.5327488586229 | epot = -75.8910891464749 | etot = -49.9334367136107 +752000 ekin = 7.0668899205975 | erot = 18.0154570967688 | epot = -75.0157837299276 | etot = -49.9334367125613 +753000 ekin = 6.74450512428241 | erot = 17.3167499793819 | epot = -73.9946918145492 | etot = -49.9334367108849 +754000 ekin = 6.45964482990575 | erot = 16.4564830608885 | epot = -72.8495645995073 | etot = -49.9334367087131 +755000 ekin = 6.21433593464322 | erot = 15.4623891983789 | epot = -71.6101618391666 | etot = -49.9334367061446 +756000 ekin = 6.01102239393746 | erot = 14.3683296042486 | epot = -70.3127887014469 | etot = -49.9334367032609 +757000 ekin = 5.85298993006189 | erot = 13.2131589079683 | epot = -68.9995855380067 | etot = -49.9334366999765 +758000 ekin = 5.74477587277021 | erot = 12.0391225470957 | epot = -67.7173351165055 | etot = -49.9334366966396 +759000 ekin = 5.6919206485601 | erot = 10.8875839736568 | epot = -66.5129413158661 | etot = -49.9334366936492 +760000 ekin = 5.70117453951192 | erot = 9.79576401873154 | epot = -65.4303752491845 | etot = -49.933436690941 +761000 ekin = 5.78056045501877 | erot = 8.79564789209313 | epot = -64.5096450357696 | etot = -49.9334366886577 +762000 ekin = 5.93878225205486 | erot = 7.91237636476892 | epot = -63.7845953037258 | etot = -49.933436686902 +763000 ekin = 6.184361727704 | erot = 7.1634643452067 | epot = -63.2812627586552 | etot = -49.9334366857445 +764000 ekin = 6.52454675158088 | erot = 6.558765602944 | epot = -63.0167490397578 | etot = -49.9334366852329 +765000 ekin = 6.96404799952946 | erot = 6.10094289765019 | epot = -62.9984275825846 | etot = -49.9334366854049 +766000 ekin = 7.50369090323985 | erot = 5.78618752615102 | epot = -63.2233151156869 | etot = -49.933436686296 +767000 ekin = 8.13911242240163 | erot = 5.60500996902239 | epot = -63.677559079358 | etot = -49.933436687934 +768000 ekin = 8.85968786579912 | erot = 5.54304366995803 | epot = -64.3361682260661 | etot = -49.9334366903089 +769000 ekin = 9.64793234051338 | erot = 5.58192554390406 | epot = -65.1632945777656 | etot = -49.9334366933482 +770000 ekin = 10.4796582496206 | erot = 5.70040197417724 | epot = -66.1134969206841 | etot = -49.9334366968863 +771000 ekin = 11.3236336971393 | erot = 5.87607544107201 | epot = -67.1331458395446 | etot = -49.9334367013334 +772000 ekin = 12.1386957384452 | erot = 6.08706480595257 | epot = -68.1591972497757 | etot = -49.933436705378 +773000 ekin = 12.8870213668035 | erot = 6.3115151369007 | epot = -69.131973212649 | etot = -49.9334367089447 +774000 ekin = 13.5351523878293 | erot = 6.53122680628966 | epot = -69.9998159057768 | etot = -49.9334367116578 +775000 ekin = 14.0571973921013 | erot = 6.73342010745862 | epot = -70.7240542128422 | etot = -49.9334367132823 +776000 ekin = 14.4375527090477 | erot = 6.91134875337371 | epot = -71.2823381762118 | etot = -49.9334367137904 +777000 ekin = 14.6717866848938 | erot = 7.06376577932791 | epot = -71.6689891775945 | etot = -49.9334367133728 +778000 ekin = 14.7653808591766 | erot = 7.19344155381815 | epot = -71.8922591253731 | etot = -49.9334367123783 +779000 ekin = 14.7306938551211 | erot = 7.30529771892011 | epot = -71.9694282852216 | etot = -49.9334367111803 +780000 ekin = 14.5832545303532 | erot = 7.40496111451423 | epot = -71.9216523548738 | etot = -49.9334367100064 +781000 ekin = 14.3388697348004 | erot = 7.49845716253915 | epot = -71.7707636061857 | etot = -49.9334367088461 +782000 ekin = 14.0126322371063 | erot = 7.5932158675189 | epot = -71.5392848121174 | etot = -49.9334367074922 +783000 ekin = 13.6198123291935 | erot = 7.69972925716781 | epot = -71.2529782920828 | etot = -49.9334367057216 +784000 ekin = 13.1775031486146 | erot = 7.83255954697248 | epot = -70.9434993990781 | etot = -49.9334367034911 +785000 ekin = 12.7055342141572 | erot = 8.00936494242475 | epot = -70.6483358576599 | etot = -49.9334367010779 +786000 ekin = 12.2248371391502 | erot = 8.24851507752028 | epot = -70.406788915635 | etot = -49.9334366989645 +787000 ekin = 11.755534291358 | erot = 8.56369046302 | epot = -70.2526614520703 | etot = -49.9334366976922 +788000 ekin = 11.3126236422326 | erot = 8.96026774252352 | epot = -70.2063280823597 | etot = -49.9334366976035 +789000 ekin = 10.9031119971908 | erot = 9.43314525721006 | epot = -70.2696939531076 | etot = -49.9334366987068 +790000 ekin = 10.5250635297227 | erot = 9.96753484561177 | epot = -70.426035076003 | etot = -49.9334367006685 +791000 ekin = 10.169133164058 | erot = 10.5422631474155 | epot = -70.6448330144385 | etot = -49.9334367029649 +792000 ekin = 9.8220583923131 | erot = 11.134119039239 | epot = -70.8896141366244 | etot = -49.9334367050724 +793000 ekin = 9.47084478060325 | erot = 11.7217151485211 | epot = -71.12599663574 | etot = -49.9334367066157 +794000 ekin = 9.10632235967327 | erot = 12.2880425702251 | epot = -71.3278016373417 | etot = -49.9334367074434 +795000 ekin = 8.72525787163131 | erot = 12.8212831281949 | epot = -71.4799777072782 | etot = -49.9334367074519 +796000 ekin = 8.33088740355773 | erot = 13.3158307220539 | epot = -71.5801548323503 | etot = -49.9334367067387 +797000 ekin = 7.93221366074849 | erot = 13.77250193296 | epot = -71.6381522991362 | etot = -49.9334367054277 +798000 ekin = 7.54257513542632 | erot = 14.1976537464586 | epot = -71.6736655855944 | etot = -49.9334367037095 +799000 ekin = 7.1778119415626 | erot = 14.6018729764978 | epot = -71.7131216199232 | etot = -49.9334367018628 +800000 ekin = 6.85418083671326 | erot = 14.9975945326855 | epot = -71.7852120695717 | etot = -49.933436700173 +801000 ekin = 6.5859278756148 | erot = 15.3953862375432 | epot = -71.9147508125563 | etot = -49.9334366993983 +802000 ekin = 6.38182484896285 | erot = 15.7994624724845 | epot = -72.1147240206018 | etot = -49.9334366991545 +803000 ekin = 6.24578962495445 | erot = 16.2061575172355 | epot = -72.3853838428301 | etot = -49.9334367006401 +804000 ekin = 6.17330996107723 | erot = 16.5988082574921 | epot = -72.7055549223796 | etot = -49.9334367038102 +805000 ekin = 6.15098228407021 | erot = 16.9456603305968 | epot = -73.030079322638 | etot = -49.933436707971 +806000 ekin = 6.15947173678508 | erot = 17.2044656438724 | epot = -73.2973740932005 | etot = -49.933436712543 +807000 ekin = 6.17750077533474 | erot = 17.328774957995 | epot = -73.4397124498699 | etot = -49.9334367165402 +808000 ekin = 6.18647751304708 | erot = 17.2774290380561 | epot = -73.3973432700816 | etot = -49.9334367189784 +809000 ekin = 6.17461069457154 | erot = 17.0246492196236 | epot = -73.1326966333926 | etot = -49.9334367191974 +810000 ekin = 6.13919982891883 | erot = 16.5673936174243 | epot = -72.6400301634387 | etot = -49.9334367170956 +811000 ekin = 6.08590405435883 | erot = 15.9262499110281 | epot = -71.9455906786333 | etot = -49.9334367132464 +812000 ekin = 6.02727840092083 | erot = 15.1427857224991 | epot = -71.1035008315788 | etot = -49.9334367081589 +813000 ekin = 5.97994559151117 | erot = 14.2732350595732 | epot = -70.1866173539912 | etot = -49.9334367029068 +814000 ekin = 5.9601940708668 | erot = 13.3776408792751 | epot = -69.2712716483263 | etot = -49.9334366981844 +815000 ekin = 5.98147951154202 | erot = 12.5120766104657 | epot = -68.4269928163856 | etot = -49.9334366943779 +816000 ekin = 6.05315781462583 | erot = 11.723826296871 | epot = -67.7104208031119 | etot = -49.9334366916151 +817000 ekin = 6.18015071653459 | erot = 11.0493436796451 | epot = -67.1629310860532 | etot = -49.9334366898736 +818000 ekin = 6.36343209333698 | erot = 10.5142840565584 | epot = -66.8111528388801 | etot = -49.9334366889847 +819000 ekin = 6.60007567204471 | erot = 10.133823284977 | epot = -66.6673356462673 | etot = -49.9334366892456 +820000 ekin = 6.88150211740216 | erot = 9.91159836418705 | epot = -66.7265371719911 | etot = -49.9334366904018 +821000 ekin = 7.19506666875818 | erot = 9.84129146082237 | epot = -66.9697948219979 | etot = -49.9334366924173 +822000 ekin = 7.52435980169328 | erot = 9.90716288824969 | epot = -67.3649593851487 | etot = -49.9334366952057 +823000 ekin = 7.84992228265532 | erot = 10.08516009644 | epot = -67.8685190769763 | etot = -49.933436697881 +824000 ekin = 8.15279302379501 | erot = 10.3470779177686 | epot = -68.4333076429303 | etot = -49.9334367013667 +825000 ekin = 8.413116660073 | erot = 10.6607446580977 | epot = -69.0072980228678 | etot = -49.9334367046971 +826000 ekin = 8.61249186799867 | erot = 10.9940344467054 | epot = -69.5399630220663 | etot = -49.9334367073623 +827000 ekin = 8.73743000137138 | erot = 11.3203117197338 | epot = -69.9911784300121 | etot = -49.9334367089069 +828000 ekin = 8.78189553863721 | erot = 11.6226054158541 | epot = -70.3379376635552 | etot = -49.9334367090639 +829000 ekin = 8.74900835539536 | erot = 11.8958537704359 | epot = -70.5782988336739 | etot = -49.9334367078426 +830000 ekin = 8.65139592834784 | erot = 12.1464179472968 | epot = -70.7312505811857 | etot = -49.933436705541 +831000 ekin = 8.50494277670857 | erot = 12.3857635079014 | epot = -70.8241429887888 | etot = -49.9334367041789 +832000 ekin = 8.32916055639414 | erot = 12.6288888014105 | epot = -70.891486059017 | etot = -49.9334367012124 +833000 ekin = 8.15183535332413 | erot = 12.893407900769 | epot = -70.9786799529628 | etot = -49.9334366988696 +834000 ekin = 7.99907278376721 | erot = 13.1899071856378 | epot = -71.1224166669729 | etot = -49.9334366975679 +835000 ekin = 7.89187835206051 | erot = 13.518886988671 | epot = -71.3442020382249 | etot = -49.9334366974933 +836000 ekin = 7.843885372326 | erot = 13.8699943192521 | epot = -71.6473163901779 | etot = -49.9334366985998 +837000 ekin = 7.86044932605824 | erot = 14.2233719534942 | epot = -72.0172579801885 | etot = -49.933436700636 +838000 ekin = 7.93910809389695 | erot = 14.5528008610036 | epot = -72.4253456580786 | etot = -49.9334367031781 +839000 ekin = 8.07122306545806 | erot = 14.8302605050907 | epot = -72.8349202762384 | etot = -49.9334367056896 +840000 ekin = 8.24446554245613 | erot = 15.0313446269342 | epot = -73.2092468770139 | etot = -49.9334367076236 +841000 ekin = 8.44565195540588 | erot = 15.1405292661537 | epot = -73.519617930121 | etot = -49.9334367085615 +842000 ekin = 8.66328937917652 | erot = 15.1548179229557 | epot = -73.7515440104965 | etot = -49.9334367083643 +843000 ekin = 8.88920706298556 | erot = 15.0843018301085 | epot = -73.9069456003348 | etot = -49.9334367072407 +844000 ekin = 9.11892160117401 | erot = 14.9490168367877 | epot = -74.0013751436466 | etot = -49.9334367056848 +845000 ekin = 9.35084016251588 | erot = 14.7729101071697 | epot = -74.0571869739696 | etot = -49.933436704284 +846000 ekin = 9.58480624628363 | erot = 14.5769727650674 | epot = -74.0952157148617 | etot = -49.9334367035107 +847000 ekin = 9.8206237614369 | erot = 14.3739562461313 | epot = -74.1280167111316 | etot = -49.9334367035633 +848000 ekin = 10.0570459044803 | erot = 14.1664338893114 | epot = -74.1569164981109 | etot = -49.9334367043192 +849000 ekin = 10.2914310228556 | erot = 13.9486330727968 | epot = -74.173500801075 | etot = -49.9334367054227 +850000 ekin = 10.5200017144501 | erot = 13.7110119884877 | epot = -74.1644504093867 | etot = -49.9334367064489 +851000 ekin = 10.7384803463952 | erot = 13.4455029514379 | epot = -74.1174200049113 | etot = -49.9334367070782 +852000 ekin = 10.9428323035626 | erot = 13.1491363434633 | epot = -74.0254053542589 | etot = -49.933436707233 +853000 ekin = 11.1299150795726 | erot = 12.8245768787165 | epot = -73.8879286653589 | etot = -49.9334367070697 +854000 ekin = 11.2979634934996 | erot = 12.4776173939312 | epot = -73.7090175942955 | etot = -49.9334367068647 +855000 ekin = 11.446963766486 | erot = 12.1131194458193 | epot = -73.4935199191607 | etot = -49.9334367068554 +856000 ekin = 11.5790087135869 | erot = 11.7315500672944 | epot = -73.2439954879912 | etot = -49.9334367071099 +857000 ekin = 11.6987080004869 | erot = 11.3281299265531 | epot = -72.9602746332953 | etot = -49.9334367062553 +858000 ekin = 11.8142530289385 | erot = 10.9010311211914 | epot = -72.6487208568911 | etot = -49.9334367067612 +859000 ekin = 11.9332104305785 | erot = 10.4445616965651 | epot = -72.3112088339654 | etot = -49.9334367068218 +860000 ekin = 12.0636090870968 | erot = 9.95521311091518 | epot = -71.9522589041542 | etot = -49.9334367061422 +861000 ekin = 12.2139179049763 | erot = 9.44036583172 | epot = -71.5877204413513 | etot = -49.933436704655 +862000 ekin = 12.391130281263 | erot = 8.9208765703492 | epot = -71.2454435542372 | etot = -49.933436702625 +863000 ekin = 12.598273363369 | erot = 8.42930400292008 | epot = -70.9610140669502 | etot = -49.9334367006611 +864000 ekin = 12.8318528049167 | erot = 8.00321132292829 | epot = -70.7685008274049 | etot = -49.9334366995598 +865000 ekin = 13.0802810160704 | erot = 7.67501011472909 | epot = -70.6887278307169 | etot = -49.9334366999175 +866000 ekin = 13.3258003937865 | erot = 7.46434239413089 | epot = -70.7235794880246 | etot = -49.9334367001073 +867000 ekin = 13.548377705783 | erot = 7.37573702207222 | epot = -70.8575514307207 | etot = -49.9334367028655 +868000 ekin = 13.7260761155972 | erot = 7.39264351064997 | epot = -71.0521563312952 | etot = -49.9334367050481 +869000 ekin = 13.8458058821776 | erot = 7.49414572990457 | epot = -71.273388318019 | etot = -49.9334367059369 +870000 ekin = 13.9046600884751 | erot = 7.66358743008096 | epot = -71.5016842267386 | etot = -49.9334367081826 +871000 ekin = 13.8960585003033 | erot = 7.88733345656331 | epot = -71.7168286646253 | etot = -49.9334367077587 +872000 ekin = 13.8246751720193 | erot = 8.15489545473567 | epot = -71.9130073339425 | etot = -49.9334367071876 +873000 ekin = 13.70113616587 | erot = 8.45583645754306 | epot = -72.0904093301495 | etot = -49.9334367067364 +874000 ekin = 13.5424081255089 | erot = 8.77750687619779 | epot = -72.2533517069094 | etot = -49.9334367052027 +875000 ekin = 13.364190489811 | erot = 9.10395551733118 | epot = -72.4015827123183 | etot = -49.933436705176 +876000 ekin = 13.1761666319066 | erot = 9.41896925806077 | epot = -72.5285725947969 | etot = -49.9334367048295 +877000 ekin = 12.9897331534367 | erot = 9.70973691408539 | epot = -72.6329067716059 | etot = -49.9334367040838 +878000 ekin = 12.8170836818953 | erot = 9.96795108601403 | epot = -72.7184714714438 | etot = -49.9334367035344 +879000 ekin = 12.6680681077531 | erot = 10.1869039997319 | epot = -72.7884088107404 | etot = -49.9334367032554 +880000 ekin = 12.5485677830274 | erot = 10.3601722386594 | epot = -72.8421767252551 | etot = -49.9334367035683 +881000 ekin = 12.4586640762231 | erot = 10.4797974742248 | epot = -72.8718982550598 | etot = -49.933436704612 +882000 ekin = 12.3916540725039 | erot = 10.5354740122097 | epot = -72.8605647909174 | etot = -49.9334367062038 +883000 ekin = 12.3349006013609 | erot = 10.5163792200971 | epot = -72.7847165294059 | etot = -49.9334367079479 +884000 ekin = 12.2717096495915 | erot = 10.4148307307057 | epot = -72.6199770892637 | etot = -49.9334367089665 +885000 ekin = 12.1859999116201 | erot = 10.2325314578994 | epot = -72.3519680787271 | etot = -49.9334367092076 +886000 ekin = 12.0660600096115 | erot = 9.98113360769406 | epot = -71.980630324473 | etot = -49.9334367071675 +887000 ekin = 11.9066640242377 | erot = 9.6901712661992 | epot = -71.5302719955779 | etot = -49.9334367051409 +888000 ekin = 11.7031668866559 | erot = 9.40001854992544 | epot = -71.0366221380879 | etot = -49.9334367015065 +889000 ekin = 11.4630530596602 | erot = 9.15343792230301 | epot = -70.5499276801541 | etot = -49.9334366981909 +890000 ekin = 11.1987209292475 | erot = 8.98605396726837 | epot = -70.1182115922942 | etot = -49.9334366957783 +891000 ekin = 10.9233111473723 | erot = 8.92029234139208 | epot = -69.7770401832348 | etot = -49.9334366944704 +892000 ekin = 10.6492398279326 | erot = 8.9636967632536 | epot = -69.5463732853673 | etot = -49.9334366941811 +893000 ekin = 10.3877929473946 | erot = 9.11033168293226 | epot = -69.4315613249835 | etot = -49.9334366946567 +894000 ekin = 10.1494275349717 | erot = 9.34401274065503 | epot = -69.4268769711849 | etot = -49.9334366955582 +895000 ekin = 9.94444446382653 | erot = 9.64226259668959 | epot = -69.5201437570929 | etot = -49.9334366965768 +896000 ekin = 9.78365577870636 | erot = 9.98061881069167 | epot = -69.6977112867597 | etot = -49.9334366973616 +897000 ekin = 9.67858194017933 | erot = 10.3366132204216 | epot = -69.9486318584305 | etot = -49.9334366978296 +898000 ekin = 9.6407556754075 | erot = 10.6919016544823 | epot = -70.2660940279635 | etot = -49.9334366980736 +899000 ekin = 9.68004571013824 | erot = 11.0326643700505 | epot = -70.6461467785237 | etot = -49.933436698335 +900000 ekin = 9.8024271898829 | erot = 11.3484734122085 | epot = -71.0843373009746 | etot = -49.9334366988832 +901000 ekin = 10.007986784063 | erot = 11.6305317086353 | epot = -71.5719551925862 | etot = -49.933436699888 +902000 ekin = 10.2899129379698 | erot = 11.8702049217355 | epot = -72.0935545610795 | etot = -49.9334367013742 +903000 ekin = 10.6348280319913 | erot = 12.0586224303205 | epot = -72.6268871654605 | etot = -49.9334367031487 +904000 ekin = 11.0243272478932 | erot = 12.1875535945646 | epot = -73.1453175474375 | etot = -49.9334367049797 +905000 ekin = 11.4372262793892 | erot = 12.2506292974529 | epot = -73.6212922834563 | etot = -49.9334367066141 +906000 ekin = 11.8518934289044 | erot = 12.2446242605752 | epot = -74.0299543973563 | etot = -49.9334367078767 +907000 ekin = 12.2481266389513 | erot = 12.1701657665229 | epot = -74.3517291141781 | etot = -49.9334367087038 +908000 ekin = 12.6082582209791 | erot = 12.0316322967078 | epot = -74.5733272268279 | etot = -49.933436709141 +909000 ekin = 12.9174455820492 | erot = 11.8363878400004 | epot = -74.6872701313401 | etot = -49.9334367092905 +910000 ekin = 13.1633580106047 | erot = 11.5937735119854 | epot = -74.6905682318431 | etot = -49.9334367092529 +911000 ekin = 13.3356415622142 | erot = 11.3143470993626 | epot = -74.5834253706471 | etot = -49.9334367090702 +912000 ekin = 13.4255965683533 | erot = 11.0097178909071 | epot = -74.3687511679624 | etot = -49.9334367087019 +913000 ekin = 13.4301864973424 | erot = 10.6932440964711 | epot = -74.0568672999605 | etot = -49.9334367061471 +914000 ekin = 13.3769940126618 | erot = 10.381150040337 | epot = -73.6915807589639 | etot = -49.9334367059651 +915000 ekin = 13.2641557141759 | erot = 10.0882130478249 | epot = -73.2858054674931 | etot = -49.9334367054924 +916000 ekin = 13.083731249746 | erot = 9.83018237256223 | epot = -72.8473503271071 | etot = -49.9334367047989 +917000 ekin = 12.8312481509851 | erot = 9.62294454968242 | epot = -72.3876294047193 | etot = -49.9334367040518 +918000 ekin = 12.5057291533616 | erot = 9.48024983838272 | epot = -71.9194156951615 | etot = -49.9334367034172 +919000 ekin = 12.1093169179554 | erot = 9.41163285917544 | epot = -71.454386480755 | etot = -49.9334367036241 +920000 ekin = 11.6422865005983 | erot = 9.4228704721618 | epot = -70.9985936755887 | etot = -49.9334367028286 +921000 ekin = 11.1169457294429 | erot = 9.514662295109 | epot = -70.5650447264617 | etot = -49.9334367019098 +922000 ekin = 10.5550472139444 | erot = 9.68352501372713 | epot = -70.1720089283649 | etot = -49.9334367006934 +923000 ekin = 9.9844185002954 | erot = 9.92400943517147 | epot = -69.841864634638 | etot = -49.9334366991712 +924000 ekin = 9.43763475523603 | erot = 10.2296922496116 | epot = -69.6007637024335 | etot = -49.933436697586 +925000 ekin = 8.94863290040244 | erot = 10.5929212895396 | epot = -69.4749908862795 | etot = -49.9334366963374 +926000 ekin = 8.54812299742005 | erot = 11.0037296099244 | epot = -69.4852893031122 | etot = -49.9334366957678 +927000 ekin = 8.25958093088927 | erot = 11.4489178473815 | epot = -69.641935474274 | etot = -49.9334366960032 +928000 ekin = 8.11336972325164 | erot = 11.9118540030811 | epot = -69.9586604228524 | etot = -49.9334366965196 +929000 ekin = 8.06162796660943 | erot = 12.3783092989675 | epot = -70.3733740128366 | etot = -49.9334367472596 +930000 ekin = 8.11332481183543 | erot = 12.8482520257223 | epot = -70.895013541658 | etot = -49.9334367041002 +931000 ekin = 8.66218356996854 | erot = 13.2899790803943 | epot = -71.8855994294646 | etot = -49.9334367791019 +932000 ekin = 9.18948394929502 | erot = 13.6579503933937 | epot = -72.7808710530944 | etot = -49.9334367104058 +933000 ekin = 9.79417016819129 | erot = 13.9483173135533 | epot = -73.6759241999521 | etot = -49.9334367182075 +934000 ekin = 10.4207852551743 | erot = 14.1310962186981 | epot = -74.4853181967703 | etot = -49.9334367228978 +935000 ekin = 10.9969920694641 | erot = 14.1631931276504 | epot = -75.093621923519 | etot = -49.9334367264045 +936000 ekin = 11.4754171702331 | erot = 14.0243625871049 | epot = -75.4332164854376 | etot = -49.9334367280997 +937000 ekin = 11.8281157943456 | erot = 13.7138200009248 | epot = -75.4753725230786 | etot = -49.9334367278082 +938000 ekin = 12.0415685892963 | erot = 13.2461818683037 | epot = -75.2211871836312 | etot = -49.9334367260311 +939000 ekin = 12.1145829475088 | erot = 12.6496470029733 | epot = -74.6976666731298 | etot = -49.9334367226477 +940000 ekin = 12.0589112708443 | erot = 11.9625634903661 | epot = -73.9549114795609 | etot = -49.9334367183504 +941000 ekin = 11.8960551689468 | erot = 11.2288423346464 | epot = -73.0583342172008 | etot = -49.9334367136076 +942000 ekin = 11.6544532360424 | erot = 10.4934965270017 | epot = -72.0813864718405 | etot = -49.9334367087965 +943000 ekin = 11.3669373501322 | erot = 9.79913167085404 | epot = -71.0995057251855 | etot = -49.9334367041992 +944000 ekin = 11.0683221478185 | erot = 9.18351181827745 | epot = -70.1852706661439 | etot = -49.933436700048 +945000 ekin = 10.7929590514068 | erot = 8.67788366901733 | epot = -69.4042794169999 | etot = -49.9334366965758 +946000 ekin = 10.5720940702729 | erot = 8.30555132209777 | epot = -68.8110820864227 | etot = -49.9334366940521 +947000 ekin = 10.4310260783002 | erot = 8.08030170258283 | epot = -68.4447644736504 | etot = -49.9334366927674 +948000 ekin = 10.3863587495399 | erot = 8.00467877120116 | epot = -68.3244742136991 | etot = -49.933436692958 +949000 ekin = 10.4439698322496 | erot = 8.06864252758099 | epot = -68.4460490545133 | etot = -49.9334366946827 +950000 ekin = 10.598452795292 | erot = 8.24950150873035 | epot = -68.7813910017548 | etot = -49.9334366977324 +951000 ekin = 10.8345056212614 | erot = 8.5138596436384 | epot = -69.2818019665296 | etot = -49.9334367016298 +952000 ekin = 11.1300987905274 | erot = 8.8216613045093 | epot = -69.8851968007775 | etot = -49.9334367057407 +953000 ekin = 11.4620681607316 | erot = 9.13289977438979 | epot = -70.5284046438654 | etot = -49.933436708744 +954000 ekin = 11.8086055714806 | erot = 9.4135197269894 | epot = -71.1555620100664 | etot = -49.9334367115964 +955000 ekin = 12.1486594941153 | erot = 9.63629965817728 | epot = -71.7183958656255 | etot = -49.9334367133329 +956000 ekin = 12.4666814283435 | erot = 9.78498285355642 | epot = -72.1851009958388 | etot = -49.9334367139389 +957000 ekin = 12.752812250665 | erot = 9.85475378778989 | epot = -72.5410027520365 | etot = -49.9334367135817 +958000 ekin = 13.0020596902843 | erot = 9.8508529027434 | epot = -72.7863493055655 | etot = -49.9334367125379 +959000 ekin = 13.2129949609978 | erot = 9.78594808492665 | epot = -72.9323797570477 | etot = -49.9334367111232 +960000 ekin = 13.386355352903 | erot = 9.67694964920652 | epot = -72.9967417117402 | etot = -49.9334367096307 +961000 ekin = 13.5237851668172 | erot = 9.54187021018372 | epot = -72.9990920853052 | etot = -49.9334367083043 +962000 ekin = 13.6268083007112 | erot = 9.39714419112168 | epot = -72.9573891991588 | etot = -49.9334367073259 +963000 ekin = 13.6960515852032 | erot = 9.25563590622512 | epot = -72.8851241982366 | etot = -49.9334367068083 +964000 ekin = 13.7307368676617 | erot = 9.12544546212204 | epot = -72.7896190365701 | etot = -49.9334367067864 +965000 ekin = 13.7285055349355 | erot = 9.00957498535981 | epot = -72.6715172275034 | etot = -49.9334367072082 +966000 ekin = 13.6856873973586 | erot = 8.90650288407777 | epot = -72.5256269893647 | etot = -49.9334367079283 +967000 ekin = 13.5981291274025 | erot = 8.81166698277597 | epot = -72.3432328188808 | etot = -49.9334367087023 +968000 ekin = 13.4626202702827 | erot = 8.71972454046795 | epot = -72.1157815199747 | etot = -49.933436709224 +969000 ekin = 13.2787926259635 | erot = 8.6272346515121 | epot = -71.8394639866604 | etot = -49.9334367091848 +970000 ekin = 13.0511641583548 | erot = 8.5351728251111 | epot = -71.5197736918128 | etot = -49.9334367083469 +971000 ekin = 12.790835500682 | erot = 8.45057810222288 | epot = -71.1748503095307 | etot = -49.9334367066258 +972000 ekin = 12.5173507601806 | erot = 8.38683939062077 | epot = -70.8376268546144 | etot = -49.933436703813 +973000 ekin = 12.2569030872258 | erot = 8.36165046190401 | epot = -70.5519902501752 | etot = -49.9334367010454 +974000 ekin = 12.0353982668027 | erot = 8.39463180026175 | epot = -70.3634667673624 | etot = -49.933436700298 +975000 ekin = 11.8648555977054 | erot = 8.50590727188915 | epot = -70.3041995676637 | etot = -49.9334366980691 +976000 ekin = 11.7661195446294 | erot = 8.70975852592755 | epot = -70.4093147672376 | etot = -49.9334366966806 +977000 ekin = 11.7571606517114 | erot = 9.01267063325535 | epot = -70.7032679815678 | etot = -49.933436696601 +978000 ekin = 11.845389677532 | erot = 9.41117900038229 | epot = -71.1900053760384 | etot = -49.9334366981241 +979000 ekin = 12.0246267634795 | erot = 9.89054975636928 | epot = -71.8486132217867 | etot = -49.9334367019379 +980000 ekin = 12.2724364415925 | erot = 10.4232069351304 | epot = -72.6290800834547 | etot = -49.9334367067319 +981000 ekin = 12.5527115600464 | erot = 10.9725890066009 | epot = -73.4587372787754 | etot = -49.9334367121281 +982000 ekin = 12.8238225598972 | erot = 11.4997645673148 | epot = -74.2570238444359 | etot = -49.9334367172239 +983000 ekin = 13.045203571924 | erot = 11.9687211335461 | epot = -74.9473614266356 | etot = -49.9334367211654 +984000 ekin = 13.1839520713158 | erot = 12.3525268370734 | epot = -75.4699156317595 | etot = -49.9334367233703 +985000 ekin = 13.2192870396381 | erot = 12.6377038113229 | epot = -75.7904275746255 | etot = -49.9334367236645 +986000 ekin = 13.1441636152014 | erot = 12.8254874258286 | epot = -75.9030877633242 | etot = -49.9334367222941 +987000 ekin = 12.9766251566426 | erot = 12.9392834379791 | epot = -75.8493453138261 | etot = -49.9334367192044 +988000 ekin = 12.7467127334457 | erot = 13.0092102946402 | epot = -75.689359745868 | etot = -49.9334367177821 +989000 ekin = 12.4647507864812 | erot = 13.0461973424281 | epot = -75.4443848452174 | etot = -49.933436716308 +990000 ekin = 12.1432494339013 | erot = 13.0601008151106 | epot = -75.1367869639831 | etot = -49.9334367149712 +991000 ekin = 11.795493288751 | erot = 13.0588078295985 | epot = -74.7877378321365 | etot = -49.933436713787 +992000 ekin = 11.4345194694535 | erot = 13.0486939332186 | epot = -74.4166501153588 | etot = -49.9334367126867 +993000 ekin = 11.0720454472705 | erot = 13.0357017586968 | epot = -74.0411839179347 | etot = -49.9334367119674 +994000 ekin = 10.7167466984444 | erot = 13.0266560979782 | epot = -73.6768395070751 | etot = -49.9334367106526 +995000 ekin = 10.3805428790882 | erot = 13.0301107637155 | epot = -73.3440903524007 | etot = -49.933436709597 +996000 ekin = 10.0742873843687 | erot = 13.0528189026738 | epot = -73.0605429959124 | etot = -49.9334367088698 +997000 ekin = 9.80713376389113 | erot = 13.0983026561973 | epot = -72.8388731285729 | etot = -49.9334367084844 +998000 ekin = 9.58681345291487 | erot = 13.1663837795911 | epot = -72.68663394091 | etot = -49.9334367084041 +999000 ekin = 9.41957302295624 | erot = 13.2537863500049 | epot = -72.6067960815235 | etot = -49.9334367085624 +1000000 ekin = 9.30950418584537 | erot = 13.3558388696135 | epot = -72.5987797643175 | etot = -49.9334367088586 + 1000000 347.01619 -80.374455 7.7756755 -63.289276 0.11518501 39304000 +Loop time of 19.3079 on 1 procs for 1000000 steps with 10 atoms + +Performance: 76.341 ns/day, 0.314 hours/ns, 51792.277 timesteps/s, 517.923 katom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.904 | 15.904 | 15.904 | 0.0 | 82.37 +Bond | 0.68326 | 0.68326 | 0.68326 | 0.0 | 3.54 +Neigh | 0.011182 | 0.011182 | 0.011182 | 0.0 | 0.06 +Comm | 0.45393 | 0.45393 | 0.45393 | 0.0 | 2.35 +Output | 0.12567 | 0.12567 | 0.12567 | 0.0 | 0.65 +Modify | 1.6705 | 1.6705 | 1.6705 | 0.0 | 8.65 +Other | | 0.459 | | | 2.38 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:19 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.4 new file mode 100644 index 0000000000..36678a7103 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.4 @@ -0,0 +1,1186 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.3220946463646 | etot = -49.9334369948335 +Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -79.708623 6.3865285 -66.715222 -0.044062421 39304000 +1000 ekin = 6.41530681673929 | erot = 17.3249659795569 | epot = -73.6737097924629 | etot = -49.9334369961667 +2000 ekin = 6.27960997228423 | erot = 17.8454841526973 | epot = -74.05853112287 | etot = -49.9334369978885 +3000 ekin = 6.20339572000352 | erot = 18.3141946085155 | epot = -74.4510273282075 | etot = -49.9334369996885 +4000 ekin = 6.18541696870782 | erot = 18.7042662877837 | epot = -74.8231202577463 | etot = -49.9334370012548 +5000 ekin = 6.22079685461306 | erot = 18.9945001618931 | epot = -75.1487340188922 | etot = -49.9334370023861 +6000 ekin = 6.30238619195777 | erot = 19.1711640282347 | epot = -75.4069872232163 | etot = -49.9334370030238 +7000 ekin = 6.42181744516986 | erot = 19.2282392613115 | epot = -75.5834937096766 | etot = -49.9334370031952 +8000 ekin = 6.5702083768984 | erot = 19.1666965396847 | epot = -75.6703419195626 | etot = -49.9334370029795 +9000 ekin = 6.73869975295019 | erot = 18.9934225090913 | epot = -75.6655592644382 | etot = -49.9334370023967 +10000 ekin = 6.91896362918064 | erot = 18.7204828414678 | epot = -75.5728834721416 | etot = -49.9334370014931 +11000 ekin = 7.10364142561699 | erot = 18.3641504994902 | epot = -75.4012289254602 | etot = -49.933437000353 +12000 ekin = 7.28657388923069 | erot = 17.9433928027823 | epot = -75.1634036911464 | etot = -49.9334369991334 +13000 ekin = 7.46274124826284 | erot = 17.4778556704804 | epot = -74.8740339167284 | etot = -49.9334369979851 +14000 ekin = 7.62796631031656 | erot = 16.9857943782326 | epot = -74.5471976856216 | etot = -49.9334369970725 +15000 ekin = 7.77853508999258 | erot = 16.4826987969592 | epot = -74.1946708831611 | etot = -49.9334369962093 +16000 ekin = 7.91091226447451 | erot = 15.981020277991 | epot = -73.8253695379249 | etot = -49.9334369954594 +17000 ekin = 8.02167864528847 | erot = 15.4888629495766 | epot = -73.4439785905244 | etot = -49.9334369956593 +18000 ekin = 8.10771648329903 | erot = 15.008533029888 | epot = -73.0496865092429 | etot = -49.9334369960558 +19000 ekin = 8.16663757201158 | erot = 14.5368419756958 | epot = -72.6369165441965 | etot = -49.9334369964891 +20000 ekin = 8.19737361822104 | erot = 14.0694735170676 | epot = -72.2002841320789 | etot = -49.9334369967902 +21000 ekin = 8.20084032637754 | erot = 13.6028244433723 | epot = -71.7371017665571 | etot = -49.9334369968072 +22000 ekin = 8.1805815181168 | erot = 13.1355858369991 | epot = -71.2496043515424 | etot = -49.9334369964266 +23000 ekin = 8.14330066835297 | erot = 12.6698318997775 | epot = -70.7465695637177 | etot = -49.9334369955872 +24000 ekin = 8.09918346860535 | erot = 12.2114790537767 | epot = -70.2440995166721 | etot = -49.93343699429 +25000 ekin = 8.06188796651938 | erot = 11.7700779899391 | epot = -69.7654029490675 | etot = -49.933436992609 +26000 ekin = 8.04803038217834 | erot = 11.357977539424 | epot = -69.33944491229 | etot = -49.9334369906877 +27000 ekin = 8.07613224077707 | erot = 10.9889629668064 | epot = -68.998532196341 | etot = -49.9334369887575 +28000 ekin = 8.16468286004791 | erot = 10.6764628926904 | epot = -68.7745827398671 | etot = -49.9334369871288 +29000 ekin = 8.32943276357079 | erot = 10.4314466403617 | epot = -68.6943163900876 | etot = -49.9334369861551 +30000 ekin = 8.58019899558199 | erot = 10.260206659823 | epot = -68.7738426415876 | etot = -49.9334369861826 +31000 ekin = 8.91780959359444 | erot = 10.1623429442233 | epot = -69.0135895252616 | etot = -49.9334369874438 +32000 ekin = 9.33207993074349 | erot = 10.1294239012754 | epot = -69.3949408219821 | etot = -49.9334369899632 +33000 ekin = 9.80167373728768 | erot = 10.1460133617211 | epot = -69.8811240921776 | etot = -49.9334369931688 +34000 ekin = 10.2962557037706 | erot = 10.19068089918 | epot = -70.4203736002094 | etot = -49.9334369972588 +35000 ekin = 10.7808236402999 | erot = 10.2363285925372 | epot = -70.9505892339942 | etot = -49.9334370011571 +36000 ekin = 11.2209991001432 | erot = 10.257302089331 | epot = -71.4117381937028 | etot = -49.9334370042287 +37000 ekin = 11.5878770725917 | erot = 10.2339202958504 | epot = -71.7552343744939 | etot = -49.9334370060518 +38000 ekin = 11.8612836540736 | erot = 10.1555553859577 | epot = -71.950276046544 | etot = -49.9334370065127 +39000 ekin = 12.0309099424595 | erot = 10.0214706213648 | epot = -71.9858175696097 | etot = -49.9334370057854 +40000 ekin = 12.0955556066678 | erot = 9.83943808382871 | epot = -71.8684306947129 | etot = -49.9334370042163 +41000 ekin = 12.0612052446572 | erot = 9.62294084167507 | epot = -71.6175830885253 | etot = -49.933437002193 +42000 ekin = 11.9387239948139 | erot = 9.3880504986014 | epot = -71.2602114934566 | etot = -49.9334370000413 +43000 ekin = 11.7417170850614 | erot = 9.15084162780846 | epot = -70.8259957108614 | etot = -49.9334369979915 +44000 ekin = 11.4847881034978 | erot = 8.92568438359842 | epot = -70.3439094834559 | etot = -49.9334369963596 +45000 ekin = 11.1822274471284 | erot = 8.72337977254347 | epot = -69.8390442145235 | etot = -49.9334369948517 +46000 ekin = 10.8470862022816 | erot = 8.55290687697248 | epot = -69.3334300728901 | etot = -49.933436993636 +47000 ekin = 10.4905994457583 | erot = 8.42173082249849 | epot = -68.8457672609562 | etot = -49.9334369926993 +48000 ekin = 10.1219833658012 | erot = 8.33574076580837 | epot = -68.3911611236 | etot = -49.9334369919904 +49000 ekin = 9.74860996203969 | erot = 8.29978137994426 | epot = -67.9818283334184 | etot = -49.9334369914345 +50000 ekin = 9.37652878061875 | erot = 8.31814298294648 | epot = -67.6281087545144 | etot = -49.9334369909492 +51000 ekin = 9.01124628424343 | erot = 8.39494797706957 | epot = -67.3396312517654 | etot = -49.9334369904523 +52000 ekin = 8.65861585992093 | erot = 8.53436345461208 | epot = -67.1264163044142 | etot = -49.9334369898812 +53000 ekin = 8.32565221212344 | erot = 8.74055503681526 | epot = -66.9996442381329 | etot = -49.9334369891942 +54000 ekin = 8.02107164181809 | erot = 9.01735593163973 | epot = -66.9718645619411 | etot = -49.9334369884833 +55000 ekin = 7.75537320775462 | erot = 9.36712982138605 | epot = -67.0559400169796 | etot = -49.9334369878389 +56000 ekin = 7.54033857900942 | erot = 9.78947615586586 | epot = -67.2632517223114 | etot = -49.9334369874361 +57000 ekin = 7.38797148977917 | erot = 10.2796726902733 | epot = -67.6010811675149 | etot = -49.9334369874624 +58000 ekin = 7.30907596761402 | erot = 10.8272746456742 | epot = -68.0697876013507 | etot = -49.9334369880625 +59000 ekin = 7.31183154532636 | erot = 11.4154638702661 | epot = -68.6607324048665 | etot = -49.9334369892741 +60000 ekin = 7.40073708729479 | erot = 12.0215350766975 | epot = -69.3557091550139 | etot = -49.9334369910216 +61000 ekin = 7.57612697427766 | erot = 12.6184730514594 | epot = -70.1280370189406 | etot = -49.9334369932036 +62000 ekin = 7.8342108583589 | erot = 13.1768169062561 | epot = -70.9444647601208 | etot = -49.9334369955058 +63000 ekin = 8.16736345530089 | erot = 13.6689818833246 | epot = -71.7697823361867 | etot = -49.9334369975612 +64000 ekin = 8.56437270810078 | erot = 14.0716865201625 | epot = -72.5694962279854 | etot = -49.9334369997221 +65000 ekin = 9.01149485546011 | erot = 14.3654371918505 | epot = -73.3103690488105 | etot = -49.9334370014999 +66000 ekin = 9.49327902441941 | erot = 14.5383989863992 | epot = -73.9651150135817 | etot = -49.9334370027631 +67000 ekin = 9.99325449815986 | erot = 14.5878691516405 | epot = -74.5145606532531 | etot = -49.9334370034528 +68000 ekin = 10.4944771426622 | erot = 14.5206532270615 | epot = -74.948567373322 | etot = -49.9334370035983 +69000 ekin = 10.9798545698917 | erot = 14.3522752904598 | epot = -75.2655668636716 | etot = -49.9334370033201 +70000 ekin = 11.4322492583878 | erot = 14.1050236216671 | epot = -75.4707098828618 | etot = -49.9334370028069 +71000 ekin = 11.8344774050134 | erot = 13.8051158639594 | epot = -75.5730302711307 | etot = -49.9334370021578 +72000 ekin = 12.1694138303332 | erot = 13.4802146493522 | epot = -75.5830654819262 | etot = -49.9334370022408 +73000 ekin = 12.4176450109607 | erot = 13.1540122377608 | epot = -75.5050942510592 | etot = -49.9334370023378 +74000 ekin = 12.5615004066018 | erot = 12.8442480530367 | epot = -75.3391854623124 | etot = -49.933437002674 +75000 ekin = 12.5860719279478 | erot = 12.562689044198 | epot = -75.0821979751978 | etot = -49.933437003052 +76000 ekin = 12.4812201739633 | erot = 12.3157495780673 | epot = -74.7304067552178 | etot = -49.9334370031873 +77000 ekin = 12.2439814422801 | erot = 12.1061362624676 | epot = -74.2835547075523 | etot = -49.9334370028045 +78000 ekin = 11.8805929734483 | erot = 11.9347890944405 | epot = -73.7488190696183 | etot = -49.9334370017295 +79000 ekin = 11.4075131435635 | erot = 11.8023493789708 | epot = -73.1432995224905 | etot = -49.9334369999562 +80000 ekin = 10.8509854812388 | erot = 11.7096658028851 | epot = -72.4940882817783 | etot = -49.9334369976544 +81000 ekin = 10.2450327503608 | erot = 11.6573342346719 | epot = -71.8358039801533 | etot = -49.9334369951206 +82000 ekin = 9.62812700027457 | erot = 11.644682992636 | epot = -71.2062469856184 | etot = -49.9334369927079 +83000 ekin = 9.03903873930655 | erot = 11.6687532921639 | epot = -70.6412290222223 | etot = -49.9334369907519 +84000 ekin = 8.51249186343722 | erot = 11.7236867864151 | epot = -70.1696156393608 | etot = -49.9334369895085 +85000 ekin = 8.07528521987733 | erot = 11.8007513441363 | epot = -69.8094735531452 | etot = -49.9334369891315 +86000 ekin = 7.74350481028739 | erot = 11.8889057330318 | epot = -69.5658475329519 | etot = -49.9334369896328 +87000 ekin = 7.52120913163793 | erot = 11.975832499678 | epot = -69.430478622622 | etot = -49.9334369913061 +88000 ekin = 7.39850764773335 | erot = 12.0479648689083 | epot = -69.3799095098062 | etot = -49.9334369931645 +89000 ekin = 7.35699193773619 | erot = 12.0941781544029 | epot = -69.3846070872476 | etot = -49.9334369951085 +90000 ekin = 7.37367999758402 | erot = 12.1080231759507 | epot = -69.4151401703062 | etot = -49.9334369967714 +91000 ekin = 7.42410695857778 | erot = 12.0887796846338 | epot = -69.446323641096 | etot = -49.9334369978845 +92000 ekin = 7.48574151827156 | erot = 12.0420649822326 | epot = -69.4612434988335 | etot = -49.9334369983294 +93000 ekin = 7.54037118988228 | erot = 11.9791807163959 | epot = -69.4529889044482 | etot = -49.93343699817 +94000 ekin = 7.57533062469049 | erot = 11.9152823419618 | epot = -69.4240499641718 | etot = -49.9334369975195 +95000 ekin = 7.58377941253808 | erot = 11.8670735491572 | epot = -69.3842899582996 | etot = -49.9334369966043 +96000 ekin = 7.56434675210422 | erot = 11.8500107777805 | epot = -69.3477945255106 | etot = -49.9334369956259 +97000 ekin = 7.52038731169894 | erot = 11.8759317072194 | epot = -69.3297560136805 | etot = -49.9334369947621 +98000 ekin = 7.45894830728087 | erot = 11.9513447834679 | epot = -69.3437300849067 | etot = -49.9334369941579 +99000 ekin = 7.38944511010944 | erot = 12.0764734057251 | epot = -69.3993555097658 | etot = -49.9334369939312 +100000 ekin = 7.322056358276 | erot = 12.2450152227781 | epot = -69.5005085752273 | etot = -49.9334369941732 +101000 ekin = 7.2659713862008 | erot = 12.4445407770094 | epot = -69.6439491581379 | etot = -49.9334369949278 +102000 ekin = 7.22778180819611 | erot = 12.6574945089325 | epot = -69.818713313292 | etot = -49.9334369961634 +103000 ekin = 7.21040494123171 | erot = 12.8628067179968 | epot = -70.006648656982 | etot = -49.9334369977535 +104000 ekin = 7.21287832486941 | erot = 13.0381084092492 | epot = -70.1844237335836 | etot = -49.9334369994651 +105000 ekin = 7.23115719659506 | erot = 13.1624311874576 | epot = -70.3270253850466 | etot = -49.9334370009939 +106000 ekin = 7.25975107867358 | erot = 13.2191029175818 | epot = -70.4122909982778 | etot = -49.9334370020224 +107000 ekin = 7.29377758656457 | erot = 13.1984000366854 | epot = -70.4256146255391 | etot = -49.9334370022891 +108000 ekin = 7.33090314151363 | erot = 13.0994774135691 | epot = -70.3638175567312 | etot = -49.9334370016485 +109000 ekin = 7.37271454696832 | erot = 12.9312031783744 | epot = -70.2373547254377 | etot = -49.9334370000949 +110000 ekin = 7.42526209058281 | erot = 12.711738044779 | epot = -70.0704371331208 | etot = -49.9334369977591 +111000 ekin = 7.49872514941511 | erot = 12.4669230054364 | epot = -69.8990851497386 | etot = -49.933436994887 +112000 ekin = 7.6062879627992 | erot = 12.2276899311212 | epot = -69.7674148857309 | etot = -49.9334369918105 +113000 ekin = 7.76235901185229 | erot = 12.0267610902733 | epot = -69.7225570910465 | etot = -49.9334369889209 +114000 ekin = 7.98027485026616 | erot = 11.8949023522823 | epot = -69.808614189192 | etot = -49.9334369866436 +115000 ekin = 8.2704585193024 | erot = 11.8569578160181 | epot = -70.0608533199963 | etot = -49.9334369846758 +116000 ekin = 8.64333470390486 | erot = 11.9273725250457 | epot = -70.5041442140755 | etot = -49.9334369851249 +117000 ekin = 9.09183845377655 | erot = 12.1082448162811 | epot = -71.1335202571235 | etot = -49.9334369870659 +118000 ekin = 9.59711279490033 | erot = 12.3880852370701 | epot = -71.9186350224172 | etot = -49.9334369904468 +119000 ekin = 10.1316662415153 | erot = 12.74207779554 | epot = -72.8071810320444 | etot = -49.9334369949891 +120000 ekin = 10.6612602592481 | erot = 13.1344486371318 | epot = -73.7291458965934 | etot = -49.9334370002134 +121000 ekin = 11.148005722412 | erot = 13.5226300221746 | epot = -74.6040727500954 | etot = -49.9334370055088 +122000 ekin = 11.5541779480631 | erot = 13.8626563199417 | epot = -75.3502712782397 | etot = -49.9334370102349 +123000 ekin = 11.8461299089241 | erot = 14.1149357811298 | epot = -75.8945027038806 | etot = -49.9334370138267 +124000 ekin = 11.9977139994329 | erot = 14.2494171746175 | epot = -76.1805681899331 | etot = -49.9334370158828 +125000 ekin = 11.9927642881899 | erot = 14.2492577098997 | epot = -76.1754590143128 | etot = -49.9334370162232 +126000 ekin = 11.8263836634452 | erot = 14.1123955938873 | epot = -75.8722162722329 | etot = -49.9334370149003 +127000 ekin = 11.5049845403649 | erot = 13.8508742683772 | epot = -75.2892958209092 | etot = -49.9334370121672 +128000 ekin = 11.0452237618945 | erot = 13.4882380040385 | epot = -74.4668987743425 | etot = -49.9334370084095 +129000 ekin = 10.4721243932035 | erot = 13.055683661164 | epot = -73.4612450584331 | etot = -49.9334370040656 +130000 ekin = 9.81675568763856 | erot = 12.5878092612803 | epot = -72.3380019484663 | etot = -49.9334369995474 +131000 ekin = 9.11382601709968 | erot = 12.1187210112522 | epot = -71.1659840235457 | etot = -49.9334369951938 +132000 ekin = 8.39944191100492 | erot = 11.679004618051 | epot = -70.011883520309 | etot = -49.9334369912532 +133000 ekin = 7.70914257803012 | erot = 11.2937451501993 | epot = -68.9363247161207 | etot = -49.9334369878913 +134000 ekin = 7.07599885278128 | erot = 10.9811951880495 | epot = -67.9906310260697 | etot = -49.9334369852389 +135000 ekin = 6.52777388754206 | erot = 10.7509607972615 | epot = -67.2121716681485 | etot = -49.933436983345 +136000 ekin = 6.08771006340462 | erot = 10.6081410500055 | epot = -66.6292880956454 | etot = -49.9334369822353 +137000 ekin = 5.77298785581516 | erot = 10.5523726041987 | epot = -66.2587974419487 | etot = -49.9334369819349 +138000 ekin = 5.59354954718529 | erot = 10.5779497433295 | epot = -66.1049362729407 | etot = -49.9334369824259 +139000 ekin = 5.55166881072998 | erot = 10.6745917743567 | epot = -66.1596975687106 | etot = -49.9334369836239 +140000 ekin = 5.64223691297579 | erot = 10.8284932797374 | epot = -66.4041671780796 | etot = -49.9334369853664 +141000 ekin = 5.85383891387505 | erot = 11.0237191850698 | epot = -66.8109950863703 | etot = -49.9334369874254 +142000 ekin = 6.17049552359149 | erot = 11.2439004345761 | epot = -67.3478329477066 | etot = -49.933436989539 +143000 ekin = 6.57375238284809 | erot = 11.4740276162647 | epot = -67.9812169905853 | etot = -49.9334369914725 +144000 ekin = 7.04468895169033 | erot = 11.7019940751322 | epot = -68.6801200198881 | etot = -49.9334369930656 +145000 ekin = 7.56544773358706 | erot = 11.9199568354522 | epot = -69.4188415632316 | etot = -49.9334369941924 +146000 ekin = 8.12004953046454 | erot = 12.123969163162 | epot = -70.1774556887221 | etot = -49.9334369950955 +147000 ekin = 8.69445128023948 | erot = 12.3121155932534 | epot = -70.9400038693254 | etot = -49.9334369958325 +148000 ekin = 9.27603993875062 | erot = 12.4837480427576 | epot = -71.6932249780923 | etot = -49.9334369965841 +149000 ekin = 9.85285670508485 | erot = 12.6377352950194 | epot = -72.4240289976089 | etot = -49.9334369975047 +150000 ekin = 10.4128357127072 | erot = 12.7710161831508 | epot = -73.1172888945396 | etot = -49.9334369986815 +151000 ekin = 10.9432663251803 | erot = 12.8778265161423 | epot = -73.7545298414587 | etot = -49.9334370001361 +152000 ekin = 11.4305853782892 | erot = 12.9496878240658 | epot = -74.3137102041548 | etot = -49.9334370017999 +153000 ekin = 11.8605190183265 | erot = 12.9761831588428 | epot = -74.7701391807241 | etot = -49.9334370035548 +154000 ekin = 12.2185434955921 | erot = 12.9462452354448 | epot = -75.0982257362863 | etot = -49.9334370052494 +155000 ekin = 12.4906128205087 | erot = 12.8496668717348 | epot = -75.2737166989638 | etot = -49.9334370067203 +156000 ekin = 12.664106472584 | erot = 12.678591943177 | epot = -75.2761354235672 | etot = -49.9334370078063 +157000 ekin = 12.7289594615924 | erot = 12.428816011443 | epot = -75.0912124813881 | etot = -49.9334370083527 +158000 ekin = 12.6789226204106 | erot = 12.1008375004898 | epot = -74.7131971291158 | etot = -49.9334370082154 +159000 ekin = 12.5128394530718 | erot = 11.7006734245208 | epot = -74.1469498848699 | etot = -49.9334370072773 +160000 ekin = 12.2357211071557 | erot = 11.2404384839233 | epot = -73.4095965965482 | etot = -49.9334370054692 +161000 ekin = 11.8593038686449 | erot = 10.7386616356043 | epot = -72.5314025070556 | etot = -49.9334370028064 +162000 ekin = 11.4017680282977 | erot = 10.2201339236164 | epot = -71.5553389513352 | etot = -49.9334369994211 +163000 ekin = 10.88644732987 | erot = 9.71510625265559 | epot = -70.5349905780812 | etot = -49.9334369955556 +164000 ekin = 10.33963910701 | erot = 9.25770793159798 | epot = -69.5307840301534 | etot = -49.9334369915454 +165000 ekin = 9.78791680576748 | erot = 8.8835941059127 | epot = -68.6049478994392 | etot = -49.933436987759 +166000 ekin = 9.25550622083465 | erot = 8.62702487817599 | epot = -67.8159680835511 | etot = -49.9334369845404 +167000 ekin = 8.76224456450581 | erot = 8.51776140061082 | epot = -67.2134429472669 | etot = -49.9334369821503 +168000 ekin = 8.32243639262484 | erot = 8.57826893241354 | epot = -66.8341423057719 | etot = -49.9334369807335 +169000 ekin = 7.9446556639145 | erot = 8.82168625048316 | epot = -66.699778894715 | etot = -49.9334369803174 +170000 ekin = 7.63232945982093 | erot = 9.25084013989535 | epot = -66.8166065805391 | etot = -49.9334369808228 +171000 ekin = 7.38529238380379 | erot = 9.85836147101584 | epot = -67.1770908361324 | etot = -49.9334369813128 +172000 ekin = 7.20610015415057 | erot = 10.6270836243962 | epot = -67.7666207622371 | etot = -49.9334369836903 +173000 ekin = 7.08749525316268 | erot = 11.5302525574972 | epot = -68.5511847971476 | etot = -49.9334369864877 +174000 ekin = 7.01847526595191 | erot = 12.5352232664804 | epot = -69.4871355219876 | etot = -49.9334369895554 +175000 ekin = 6.98770800219735 | erot = 13.605633679255 | epot = -70.5267786742242 | etot = -49.9334369927719 +176000 ekin = 6.98383597857994 | erot = 14.7031290903724 | epot = -71.6204020649806 | etot = -49.9334369960282 +177000 ekin = 6.99559888535214 | erot = 15.7890361276414 | epot = -72.7180720122036 | etot = -49.9334369992101 +178000 ekin = 7.01192097920841 | erot = 16.8261106927733 | epot = -73.7714686741622 | etot = -49.9334370021805 +179000 ekin = 7.02209184958747 | erot = 17.7804349003838 | epot = -74.7359637547517 | etot = -49.9334370047804 +180000 ekin = 7.01611155413849 | erot = 18.6234022668462 | epot = -75.5729508278298 | etot = -49.9334370068452 +181000 ekin = 6.98519719010516 | erot = 19.3335567490869 | epot = -76.2521909474295 | etot = -49.9334370082374 +182000 ekin = 6.9223854452692 | erot = 19.8970971418332 | epot = -76.7529195977591 | etot = -49.9334370106567 +183000 ekin = 6.82227592542438 | erot = 20.2982684170465 | epot = -77.0539813535525 | etot = -49.9334370110816 +184000 ekin = 6.68055376616976 | erot = 20.5336568135067 | epot = -77.1476475904173 | etot = -49.9334370107408 +185000 ekin = 6.49623294825599 | erot = 20.6104471437544 | epot = -77.0401171017128 | etot = -49.9334370097024 +186000 ekin = 6.27250921535801 | erot = 20.5422446873305 | epot = -76.7481909107551 | etot = -49.9334370080666 +187000 ekin = 6.01720154751183 | erot = 20.3471328407261 | epot = -76.2977713941873 | etot = -49.9334370059494 +188000 ekin = 5.7428668471506 | erot = 20.0458090594948 | epot = -75.7221129101201 | etot = -49.9334370034747 +189000 ekin = 5.46641873149775 | erot = 19.6593652976528 | epot = -75.0592210301642 | etot = -49.9334370010136 +190000 ekin = 5.20811212014886 | erot = 19.2080076862166 | epot = -74.3495568046827 | etot = -49.9334369983173 +191000 ekin = 4.98983337888141 | erot = 18.7117448291905 | epot = -73.6350152038298 | etot = -49.9334369957578 +192000 ekin = 4.83291851070435 | erot = 18.1889644778759 | epot = -72.955319982097 | etot = -49.9334369935167 +193000 ekin = 4.75584764391792 | erot = 17.6560155879512 | epot = -72.3453002236052 | etot = -49.9334369917361 +194000 ekin = 4.77223428975689 | erot = 17.1270435377798 | epot = -71.8327148180384 | etot = -49.9334369905017 +195000 ekin = 4.88948018808209 | erot = 16.6140592370673 | epot = -71.4369764149727 | etot = -49.9334369898233 +196000 ekin = 5.1083005979096 | erot = 16.1271747421851 | epot = -71.1689123297459 | etot = -49.9334369896512 +197000 ekin = 5.42311350133068 | erot = 15.674884801262 | epot = -71.0314352924916 | etot = -49.933436989899 +198000 ekin = 5.82310186418107 | erot = 15.2642611342814 | epot = -71.0207999889298 | etot = -49.9334369904673 +199000 ekin = 6.29365371082805 | erot = 14.9009682645996 | epot = -71.1280589666941 | etot = -49.9334369912664 +200000 ekin = 6.81787606879851 | erot = 14.5890840258075 | epot = -71.3403970868364 | etot = -49.9334369922304 +201000 ekin = 7.37794822150743 | erot = 14.3307857988509 | epot = -71.6421710136744 | etot = -49.933436993316 +202000 ekin = 7.95618720633342 | erot = 14.1260142258902 | epot = -72.0156384267153 | etot = -49.9334369944917 +203000 ekin = 8.53580140319792 | erot = 13.9722340620959 | epot = -72.4414724610271 | etot = -49.9334369957333 +204000 ekin = 9.1013769071154 | erot = 13.8643800543676 | epot = -72.8991939584938 | etot = -49.9334369970108 +205000 ekin = 9.63916729956859 | erot = 13.7950217250069 | epot = -73.3676260228673 | etot = -49.9334369982918 +206000 ekin = 10.1372494437245 | erot = 13.7547335571626 | epot = -73.8254200004241 | etot = -49.9334369995371 +207000 ekin = 10.5855843060159 | erot = 13.732603634447 | epot = -74.2516249411828 | etot = -49.9334370007199 +208000 ekin = 10.9759973534393 | erot = 13.7167490933392 | epot = -74.6261834485772 | etot = -49.9334370017987 +209000 ekin = 11.3020857284123 | erot = 13.6950342848359 | epot = -74.9305570159944 | etot = -49.9334370027462 +210000 ekin = 11.5590623102108 | erot = 13.6557304747726 | epot = -75.1482297885199 | etot = -49.9334370035364 +211000 ekin = 11.743555457024 | erot = 13.5881804316489 | epot = -75.2651728928179 | etot = -49.933437004145 +212000 ekin = 11.8533937432503 | erot = 13.4834670393962 | epot = -75.270297787206 | etot = -49.9334370045595 +213000 ekin = 11.8874054379687 | erot = 13.3351971168144 | epot = -75.1560395594899 | etot = -49.9334370047068 +214000 ekin = 11.8452570406685 | erot = 13.1395898321956 | epot = -74.9182838775613 | etot = -49.9334370046972 +215000 ekin = 11.7273549851568 | erot = 12.8956103790904 | epot = -74.5564023687323 | etot = -49.9334370044851 +216000 ekin = 11.5348514637298 | erot = 12.605158514261 | epot = -74.0734469820868 | etot = -49.9334370040961 +217000 ekin = 11.2698546386884 | erot = 12.2726360414478 | epot = -73.4759276836672 | etot = -49.9334370035311 +218000 ekin = 10.9360036470615 | erot = 11.9044881932645 | epot = -72.7739288430555 | etot = -49.9334370027295 +219000 ekin = 10.5395729894702 | erot = 11.5091078937322 | epot = -71.9821178847381 | etot = -49.9334370015357 +220000 ekin = 10.0911390958365 | erot = 11.097411340783 | epot = -71.1219874363391 | etot = -49.9334369997196 +221000 ekin = 9.60752759203356 | erot = 10.684023153567 | epot = -70.2249877426707 | etot = -49.9334369970702 +222000 ekin = 9.11332798616405 | erot = 10.2884385364035 | epot = -69.3352035161119 | etot = -49.9334369935443 +223000 ekin = 8.64094443085355 | erot = 9.93507521512118 | epot = -68.5094566353803 | etot = -49.9334369894056 +224000 ekin = 8.22827965337653 | erot = 9.65121040808823 | epot = -67.8129270467273 | etot = -49.9334369852625 +225000 ekin = 7.91390905933529 | erot = 9.46258313917753 | epot = -67.3099291804794 | etot = -49.9334369819666 +226000 ekin = 7.73074804872638 | erot = 9.38753011757455 | epot = -67.0517151464751 | etot = -49.9334369801742 +227000 ekin = 7.70009206552171 | erot = 9.4324347945387 | epot = -67.0659638404016 | etot = -49.9334369803412 +228000 ekin = 7.82788964264835 | erot = 9.58936456547093 | epot = -67.3506911902285 | etot = -49.9334369821092 +229000 ekin = 8.10285729534043 | erot = 9.84056039016023 | epot = -67.8768546713549 | etot = -49.9334369858542 +230000 ekin = 8.50059317628882 | erot = 10.1544474914874 | epot = -68.5884776580934 | etot = -49.9334369903171 +231000 ekin = 8.98918217097634 | erot = 10.493400619592 | epot = -69.4160197853296 | etot = -49.9334369947613 +232000 ekin = 9.53377851904336 | erot = 10.8217737548996 | epot = -70.2889892725803 | etot = -49.9334369986374 +233000 ekin = 10.1004633099891 | erot = 11.1105033366884 | epot = -71.1444036483339 | etot = -49.9334370016564 +234000 ekin = 10.6586122559862 | erot = 11.3394799941965 | epot = -71.9315292539587 | etot = -49.933437003776 +235000 ekin = 11.1819014328112 | erot = 11.4977277745786 | epot = -72.6130662125045 | etot = -49.9334370051147 +236000 ekin = 11.6484473656533 | erot = 11.5820119850548 | epot = -73.1638963565605 | etot = -49.9334370058524 +237000 ekin = 12.0359802131753 | erot = 11.595355433837 | epot = -73.5647726545008 | etot = -49.9334370074885 +238000 ekin = 12.321983609933 | erot = 11.5429422765438 | epot = -73.7983628944137 | etot = -49.933437007937 +239000 ekin = 12.492974786631 | erot = 11.42978605616 | epot = -73.8561978508056 | etot = -49.9334370080146 +240000 ekin = 12.5412393847428 | erot = 11.2618516717058 | epot = -73.7365280640612 | etot = -49.9334370076126 +241000 ekin = 12.4660778052252 | erot = 11.0462123362375 | epot = -73.4457271480702 | etot = -49.9334370066076 +242000 ekin = 12.2750005609619 | erot = 10.7914527512376 | epot = -72.9998903170934 | etot = -49.9334370048939 +243000 ekin = 11.9845096947873 | erot = 10.5081603107655 | epot = -72.4261070080154 | etot = -49.9334370024626 +244000 ekin = 11.6199359047039 | erot = 10.2090471828725 | epot = -71.7624200869645 | etot = -49.933436999388 +245000 ekin = 11.2141782120092 | erot = 9.90860612972013 | epot = -71.0562213376399 | etot = -49.9334369959106 +246000 ekin = 10.8049800665009 | erot = 9.62226262065073 | epot = -70.360679679554 | etot = -49.9334369924023 +247000 ekin = 10.4306724668839 | erot = 9.36498469828511 | epot = -69.729094154468 | etot = -49.933436989299 +248000 ekin = 10.1252005658391 | erot = 9.14967551152671 | epot = -69.2083130643951 | etot = -49.9334369870293 +249000 ekin = 9.91424863501444 | erot = 8.9857076584 | epot = -68.8333932790425 | etot = -49.933436985628 +250000 ekin = 9.81343088345104 | erot = 8.87752109616643 | epot = -68.62438896557 | etot = -49.9334369859525 +251000 ekin = 9.81990124695394 | erot = 8.82321712561625 | epot = -68.5765553598928 | etot = -49.9334369873226 +252000 ekin = 9.91845576761142 | erot = 8.81663197784687 | epot = -68.6685247348587 | etot = -49.9334369894004 +253000 ekin = 10.0857195322889 | erot = 8.84890482128012 | epot = -68.8680613453592 | etot = -49.9334369917902 +254000 ekin = 10.2944154464832 | erot = 8.91011045795646 | epot = -69.1379628985768 | etot = -49.9334369941372 +255000 ekin = 10.5172797771523 | erot = 8.99090198886087 | epot = -69.441618762225 | etot = -49.9334369962119 +256000 ekin = 10.7298060333139 | erot = 9.08318965779856 | epot = -69.746432689017 | etot = -49.9334369979045 +257000 ekin = 10.9117548400304 | erot = 9.1804779576876 | epot = -70.0256697969034 | etot = -49.9334369991854 +258000 ekin = 11.0477221380911 | erot = 9.27819694071461 | epot = -70.2593560788645 | etot = -49.9334370000588 +259000 ekin = 11.1271588600402 | erot = 9.37381103868267 | epot = -70.4344068992548 | etot = -49.9334370005319 +260000 ekin = 11.144277989349 | erot = 9.4669885218844 | epot = -70.5447035117475 | etot = -49.9334370005141 +261000 ekin = 11.0980856586685 | erot = 9.56016701501199 | epot = -70.5916896739975 | etot = -49.9334370003171 +262000 ekin = 10.990792721901 | erot = 9.65474247460802 | epot = -70.5789721960267 | etot = -49.9334369995176 +263000 ekin = 10.8295378178608 | erot = 9.75638049585337 | epot = -70.519355311848 | etot = -49.9334369981338 +264000 ekin = 10.6274954670416 | erot = 9.87566396380797 | epot = -70.4365964270709 | etot = -49.9334369962213 +265000 ekin = 10.4029385010157 | erot = 10.0259787584354 | epot = -70.3623542534483 | etot = -49.9334369939972 +266000 ekin = 10.1776742656856 | erot = 10.2209385120998 | epot = -70.332049769659 | etot = -49.9334369918736 +267000 ekin = 9.97447897986485 | erot = 10.4715477508093 | epot = -70.3794637208694 | etot = -49.9334369901952 +268000 ekin = 9.8139721808994 | erot = 10.783566213846 | epot = -70.5309753841262 | etot = -49.9334369893807 +269000 ekin = 9.71175762398456 | erot = 11.1545990385851 | epot = -70.7997936521884 | etot = -49.9334369896187 +270000 ekin = 9.67524675614719 | erot = 11.5728282294524 | epot = -71.1815119767594 | etot = -49.9334369911598 +271000 ekin = 9.70205034561387 | erot = 12.0171639615819 | epot = -71.652651300944 | etot = -49.9334369937482 +272000 ekin = 9.78119590231257 | erot = 12.4591961343061 | epot = -72.1738290335907 | etot = -49.933436996972 +273000 ekin = 9.89551530293124 | erot = 12.8671360105937 | epot = -72.6960883138042 | etot = -49.9334370002793 +274000 ekin = 10.0251036095171 | erot = 13.2107359457352 | epot = -73.1692765583625 | etot = -49.9334370031102 +275000 ekin = 10.150949712569 | erot = 13.4661171078245 | epot = -73.5505038254205 | etot = -49.933437005027 +276000 ekin = 10.2579077802708 | erot = 13.6195042882971 | epot = -73.8108490743491 | etot = -49.9334370057812 +277000 ekin = 10.3365003461967 | erot = 13.6692293787561 | epot = -73.9391667302895 | etot = -49.9334370053367 +278000 ekin = 10.3834483774467 | erot = 13.6258475790782 | epot = -73.9427329603413 | etot = -49.9334370038164 +279000 ekin = 10.4011507785881 | erot = 13.5106897711472 | epot = -73.8452775512625 | etot = -49.9334370015272 +280000 ekin = 10.396439812492 | erot = 13.3527125117171 | epot = -73.6825893230092 | etot = -49.9334369988 +281000 ekin = 10.3779527890325 | erot = 13.1828376404621 | epot = -73.4942274264329 | etot = -49.9334369969383 +282000 ekin = 10.353053740353 | erot = 13.0291459793171 | epot = -73.3156367147788 | etot = -49.9334369951087 +283000 ekin = 10.327058921166 | erot = 12.9150697625826 | epot = -73.1755656779531 | etot = -49.9334369942045 +284000 ekin = 10.3012154521656 | erot = 12.8544062464705 | epot = -73.0890586931117 | etot = -49.9334369944756 +285000 ekin = 10.2715544103146 | erot = 12.8490241982321 | epot = -73.0540156044477 | etot = -49.9334369959009 +286000 ekin = 10.2290782152192 | erot = 12.8892797632625 | epot = -73.0517949765434 | etot = -49.9334369980617 +287000 ekin = 10.1619978630791 | erot = 12.9580079590626 | epot = -73.0534428222875 | etot = -49.9334370001458 +288000 ekin = 10.0601300944757 | erot = 13.0376429488874 | epot = -73.0312100445687 | etot = -49.9334370012057 +289000 ekin = 9.92022159653657 | erot = 13.1179600214074 | epot = -72.9716186185652 | etot = -49.9334370006212 +290000 ekin = 9.74965131749931 | erot = 13.20061519463 | epot = -72.8837035106212 | etot = -49.9334369984919 +291000 ekin = 9.56608911179593 | erot = 13.2978259857988 | epot = -72.7973520932165 | etot = -49.9334369956217 +292000 ekin = 9.39289303103691 | erot = 13.4260428295595 | epot = -72.7523728535736 | etot = -49.9334369929772 +293000 ekin = 9.25289876825867 | erot = 13.5983001411172 | epot = -72.7846359009137 | etot = -49.9334369915379 +294000 ekin = 9.16176985520412 | erot = 13.8176522641924 | epot = -72.9128591109257 | etot = -49.9334369915292 +295000 ekin = 9.12570783653626 | erot = 14.0757418165445 | epot = -73.1348866458741 | etot = -49.9334369927933 +296000 ekin = 9.14197328685053 | erot = 14.3545965147162 | epot = -73.4300067964825 | etot = -49.9334369949157 +297000 ekin = 9.20093046429207 | erot = 14.6305016956182 | epot = -73.7648691574437 | etot = -49.9334369975334 +298000 ekin = 9.2882446434271 | erot = 14.8768842002814 | epot = -74.0985658445776 | etot = -49.9334370008691 +299000 ekin = 9.38785334981196 | erot = 15.064388648537 | epot = -74.3856790018766 | etot = -49.9334370035276 +300000 ekin = 9.4816591189654 | erot = 15.1708080546 | epot = -74.5859041795342 | etot = -49.9334370059688 +301000 ekin = 9.5500945687059 | erot = 15.1800632839206 | epot = -74.6635948608297 | etot = -49.9334370082032 +302000 ekin = 9.57201526804842 | erot = 15.0823927221984 | epot = -74.5878450007517 | etot = -49.9334370105049 +303000 ekin = 9.52471361884508 | erot = 14.8708920500116 | epot = -74.3290426817171 | etot = -49.9334370128604 +304000 ekin = 9.38481294458484 | erot = 14.540621173802 | epot = -73.8588711334567 | etot = -49.9334370150699 +305000 ekin = 9.13228587661077 | erot = 14.09113813024 | epot = -73.156861021935 | etot = -49.9334370150842 +306000 ekin = 8.75533716880198 | erot = 13.5286285172538 | epot = -72.2174027015838 | etot = -49.933437015528 +307000 ekin = 8.24994820429156 | erot = 12.8613386576974 | epot = -71.0447238754095 | etot = -49.9334370134205 +308000 ekin = 7.6456620760276 | erot = 12.1187367066657 | epot = -69.6978357833139 | etot = -49.9334370006206 +309000 ekin = 6.2156324931236 | erot = 10.8308134934624 | epot = -66.9798826117789 | etot = -49.933436625193 +310000 ekin = 6.98208788801171 | erot = 9.38517955464416 | epot = -66.3007041395919 | etot = -49.9334366969361 +311000 ekin = 8.46519197709966 | erot = 8.64607863222292 | epot = -67.0447073767713 | etot = -49.9334367674487 +312000 ekin = 8.66431616581154 | erot = 8.18423138032288 | epot = -66.7819843262681 | etot = -49.9334367801337 +313000 ekin = 8.8165745331513 | erot = 7.84806509573162 | epot = -66.5980764070118 | etot = -49.9334367781288 +314000 ekin = 8.92571410838771 | erot = 7.64505956838544 | epot = -66.5042104526792 | etot = -49.933436775906 +315000 ekin = 9.0190820076634 | erot = 7.57680806118989 | epot = -66.5293268431105 | etot = -49.9334367742572 +316000 ekin = 9.12426361175364 | erot = 7.63699444605061 | epot = -66.6946948314354 | etot = -49.9334367736311 +317000 ekin = 9.26338621517938 | erot = 7.81017000723729 | epot = -67.0069929987678 | etot = -49.9334367763511 +318000 ekin = 9.44365313230142 | erot = 8.06449733145515 | epot = -67.4415872427672 | etot = -49.9334367790106 +319000 ekin = 9.65799853892068 | erot = 8.3578104013044 | epot = -67.9492457228365 | etot = -49.9334367826114 +320000 ekin = 9.89196359098032 | erot = 8.64893573873188 | epot = -68.4743361164189 | etot = -49.9334367867067 +321000 ekin = 10.1233187755557 | erot = 8.89745069026426 | epot = -68.9542062564548 | etot = -49.9334367906348 +322000 ekin = 10.3265544624573 | erot = 9.06891954456067 | epot = -69.3289108006598 | etot = -49.9334367936418 +323000 ekin = 10.4783638188611 | erot = 9.14041960359969 | epot = -69.5522202175209 | etot = -49.9334367950602 +324000 ekin = 10.5626654861724 | erot = 9.10522153544385 | epot = -69.6013238161297 | etot = -49.9334367945135 +325000 ekin = 10.5736671948877 | erot = 8.97511339418284 | epot = -69.4822173812519 | etot = -49.9334367921813 +326000 ekin = 10.5161587200378 | erot = 8.77895419858649 | epot = -69.2285497068407 | etot = -49.9334367882164 +327000 ekin = 10.4032259690527 | erot = 8.56034165158865 | epot = -68.8970044041305 | etot = -49.9334367834891 +328000 ekin = 10.2524292214586 | erot = 8.37036212265245 | epot = -68.5562281228879 | etot = -49.9334367787768 +329000 ekin = 10.0824546438359 | erot = 8.25940958185205 | epot = -68.2753010003991 | etot = -49.9334367747112 +330000 ekin = 9.90858228191592 | erot = 8.27090994172825 | epot = -68.1129289954795 | etot = -49.9334367718353 +331000 ekin = 9.74053523958486 | erot = 8.43704440644557 | epot = -68.1110164162991 | etot = -49.9334367702687 +332000 ekin = 9.58326759569266 | erot = 8.77502618163732 | epot = -68.2917305473855 | etot = -49.9334367700556 +333000 ekin = 9.43734454313463 | erot = 9.28570909297036 | epot = -68.6564904072819 | etot = -49.9334367711769 +334000 ekin = 9.30005714166039 | erot = 9.95274790625269 | epot = -69.1862418212775 | etot = -49.9334367733644 +335000 ekin = 9.16539195140213 | erot = 10.746354620105 | epot = -69.845183347839 | etot = -49.9334367763319 +336000 ekin = 9.02588570624131 | erot = 11.6261652905767 | epot = -70.5854877765583 | etot = -49.9334367797403 +337000 ekin = 8.87412067608417 | erot = 12.5449700956901 | epot = -71.3525275550114 | etot = -49.9334367832371 +338000 ekin = 8.70391892935299 | erot = 13.4530941766793 | epot = -72.0904498925221 | etot = -49.9334367864898 +339000 ekin = 8.51126560344622 | erot = 14.3027075314391 | epot = -72.7474099241128 | etot = -49.9334367892274 +340000 ekin = 8.29488691398008 | erot = 15.051558155018 | epot = -73.2798818602634 | etot = -49.9334367912654 +341000 ekin = 8.05646205380742 | erot = 15.6657657386911 | epot = -73.6556645850059 | etot = -49.9334367925074 +342000 ekin = 7.80050981598662 | erot = 16.1215554932929 | epot = -73.8555021022114 | etot = -49.9334367929319 +343000 ekin = 7.53404165582583 | erot = 16.4060559812146 | epot = -73.8735344296017 | etot = -49.9334367925613 +344000 ekin = 7.26609676908243 | erot = 16.5174328472204 | epot = -73.7169664077419 | etot = -49.9334367914391 +345000 ekin = 7.00725922449314 | erot = 16.4646262362403 | epot = -73.4053222503512 | etot = -49.9334367896178 +346000 ekin = 6.7691981641755 | erot = 16.2668142751678 | epot = -72.9694492265128 | etot = -49.9334367871695 +347000 ekin = 6.56418602316419 | erot = 15.9525180661099 | epot = -72.450140873486 | etot = -49.9334367842119 +348000 ekin = 6.40447863711545 | erot = 15.5581119659957 | epot = -71.8960273840486 | etot = -49.9334367809374 +349000 ekin = 6.30143449814356 | erot = 15.1255022274363 | epot = -71.3603735032007 | etot = -49.9334367776209 +350000 ekin = 6.26433457360178 | erot = 14.6988992514335 | epot = -70.8966705996403 | etot = -49.933436774605 +351000 ekin = 6.29901365146823 | erot = 14.3208623426312 | epot = -70.5533127663506 | etot = -49.9334367722512 +352000 ekin = 6.40655985354709 | erot = 14.028028720756 | epot = -70.3680253451915 | etot = -49.9334367708884 +353000 ekin = 6.58240652259936 | erot = 13.8470668709055 | epot = -70.3629101642515 | etot = -49.9334367707467 +354000 ekin = 6.81609810136072 | erot = 13.7914168213514 | epot = -70.5409516946357 | etot = -49.9334367719236 +355000 ekin = 7.09188628776078 | erot = 13.859346964886 | epot = -70.8846700269952 | etot = -49.9334367743484 +356000 ekin = 7.3901553957234 | erot = 14.0337905267924 | epot = -71.3573827002843 | etot = -49.9334367777685 +357000 ekin = 7.68951512333227 | erot = 14.2842611187776 | epot = -71.9072130238845 | etot = -49.9334367817746 +358000 ekin = 7.96924870687919 | erot = 14.570797647429 | epot = -72.4734831401669 | etot = -49.9334367858587 +359000 ekin = 8.2117143183278 | erot = 14.849390118072 | epot = -72.9945412259058 | etot = -49.933436789506 +360000 ekin = 8.4043431652244 | erot = 15.077907948255 | epot = -73.4156879057563 | etot = -49.9334367922769 +361000 ekin = 8.54093730786782 | erot = 15.2234591172763 | epot = -73.6978332181843 | etot = -49.9334367930402 +362000 ekin = 8.62176162458802 | erot = 15.2683190552232 | epot = -73.8235174732551 | etot = -49.9334367934439 +363000 ekin = 8.65376226171903 | erot = 15.2009231864135 | epot = -73.7881222408649 | etot = -49.9334367927324 +364000 ekin = 8.65006194496262 | erot = 15.0202219537443 | epot = -73.603720689793 | etot = -49.9334367910861 +365000 ekin = 8.62864344793597 | erot = 14.7344841776725 | epot = -73.296564414414 | etot = -49.9334367888055 +366000 ekin = 8.61026816481815 | erot = 14.3587117763602 | epot = -72.9024167274379 | etot = -49.9334367862596 +367000 ekin = 8.61582393192867 | erot = 13.9116488824681 | epot = -72.4609095982132 | etot = -49.9334367838165 +368000 ekin = 8.66349013752459 | erot = 13.4130591643087 | epot = -72.0099860836029 | etot = -49.9334367817696 +369000 ekin = 8.76619052285202 | erot = 12.8818627721973 | epot = -71.5814900753349 | etot = -49.9334367802855 +370000 ekin = 8.92978412489859 | erot = 12.3354537574912 | epot = -71.1986746617739 | etot = -49.9334367793842 +371000 ekin = 9.15232413559173 | erot = 11.7901096915195 | epot = -70.8758706060823 | etot = -49.9334367789711 +372000 ekin = 9.42449522043855 | erot = 11.2619930178364 | epot = -70.6199250171681 | etot = -49.9334367788932 +373000 ekin = 9.73107815947679 | erot = 10.7680247395803 | epot = -70.4325396780573 | etot = -49.9334367790002 +374000 ekin = 10.053100239951 | erot = 10.326032584761 | epot = -70.3125696038944 | etot = -49.9334367791823 +375000 ekin = 10.3702930598245 | erot = 9.95400537168464 | epot = -70.2577352108757 | etot = -49.9334367793666 +376000 ekin = 10.6635382209447 | erot = 9.66873204742958 | epot = -70.2657070478932 | etot = -49.933436779519 +377000 ekin = 10.9144304196776 | erot = 9.48336618940908 | epot = -70.3312333903166 | etot = -49.9334367812299 +378000 ekin = 11.103325549013 | erot = 9.40465442429875 | epot = -70.4414167547338 | etot = -49.933436781422 +379000 ekin = 11.2228479613045 | erot = 9.43497166219392 | epot = -70.5912564051509 | etot = -49.9334367816525 +380000 ekin = 11.271576558861 | erot = 9.5704613639691 | epot = -70.7754747049176 | etot = -49.9334367820875 +381000 ekin = 11.2520704290916 | erot = 9.8002877649533 | epot = -70.9857949768742 | etot = -49.9334367828293 +382000 ekin = 11.1693057444588 | erot = 10.107053932204 | epot = -71.2097964605176 | etot = -49.9334367838548 +383000 ekin = 11.0296540359309 | erot = 10.4684110619634 | epot = -71.4315018829236 | etot = -49.9334367850292 +384000 ekin = 10.8406006584064 | erot = 10.8594456848205 | epot = -71.6334831293883 | etot = -49.9334367861614 +385000 ekin = 10.6110745203069 | erot = 11.2550567348637 | epot = -71.7995680421827 | etot = -49.9334367870121 +386000 ekin = 10.3514833909805 | erot = 11.6320380412151 | epot = -71.9169582201417 | etot = -49.9334367879461 +387000 ekin = 10.0722200977252 | erot = 11.9687897481426 | epot = -71.9744466347363 | etot = -49.9334367888684 +388000 ekin = 9.7822794238066 | erot = 12.2453759804176 | epot = -71.9610921940012 | etot = -49.933436789777 +389000 ekin = 9.48904126171733 | erot = 12.4455699111993 | epot = -71.868047963092 | etot = -49.9334367901753 +390000 ekin = 9.19880110587709 | erot = 12.5588554599113 | epot = -71.6910933561604 | etot = -49.933436790372 +391000 ekin = 8.918242432058 | erot = 12.5805139316032 | epot = -71.4321931531578 | etot = -49.9334367894965 +392000 ekin = 8.65757726895627 | erot = 12.517139994722 | epot = -71.1081540509929 | etot = -49.9334367873146 +393000 ekin = 8.43231332350369 | erot = 12.3882397426725 | epot = -70.7539898501441 | etot = -49.9334367839679 +394000 ekin = 8.2624725114046 | erot = 12.2242334615059 | epot = -70.4201427529966 | etot = -49.9334367800861 +395000 ekin = 8.16904684404172 | erot = 12.0605939409117 | epot = -70.1630775616002 | etot = -49.9334367766468 +396000 ekin = 8.16818394388242 | erot = 11.9294338996806 | epot = -70.0310546182253 | etot = -49.9334367746623 +397000 ekin = 8.26509438251124 | erot = 11.8511087055213 | epot = -70.049639862832 | etot = -49.9334367747995 +398000 ekin = 8.45014024157578 | erot = 11.8286142934143 | epot = -70.2121913121403 | etot = -49.9334367771502 +399000 ekin = 8.6987524085143 | erot = 11.8465357358579 | epot = -70.4787249255957 | etot = -49.9334367812235 +400000 ekin = 8.97515584925231 | erot = 11.8745399217553 | epot = -70.7831325571793 | etot = -49.9334367861717 +401000 ekin = 9.23841273737429 | erot = 11.8739232099322 | epot = -71.0457727383634 | etot = -49.9334367910569 +402000 ekin = 9.44890872720744 | erot = 11.8053354457297 | epot = -71.1876809679593 | etot = -49.9334367950221 +403000 ekin = 9.57405438451724 | erot = 11.6363946720614 | epot = -71.14388585391 | etot = -49.9334367973313 +404000 ekin = 9.5928007036691 | erot = 11.3485151617404 | epot = -70.8747526628644 | etot = -49.9334367974548 +405000 ekin = 9.49859029588566 | erot = 10.9420390046433 | epot = -70.3740660957166 | etot = -49.9334367951877 +406000 ekin = 9.30027519156694 | erot = 10.4381532175666 | epot = -69.6718651999623 | etot = -49.9334367908288 +407000 ekin = 9.02027468745158 | erot = 9.87620869142913 | epot = -68.8299201640438 | etot = -49.9334367851631 +408000 ekin = 8.69009310249299 | erot = 9.30670442540648 | epot = -67.9302343071062 | etot = -49.9334367792067 +409000 ekin = 8.34449651482658 | erot = 8.78220945748962 | epot = -67.0601427461887 | etot = -49.9334367738725 +410000 ekin = 8.01620286719304 | erot = 8.3492032696416 | epot = -66.2988429065259 | etot = -49.9334367696913 +411000 ekin = 7.53291151060122 | erot = 8.0811683150543 | epot = -65.5475166515716 | etot = -49.9334368259161 +412000 ekin = 6.47552839026797 | erot = 8.45821289441942 | epot = -64.8671779819811 | etot = -49.9334366972937 +413000 ekin = 6.24399442168091 | erot = 8.99561848800252 | epot = -65.1730495934321 | etot = -49.9334366837487 +414000 ekin = 6.18550934222995 | erot = 9.11685651465492 | epot = -65.2358025415403 | etot = -49.9334366846554 +415000 ekin = 6.19706191149651 | erot = 9.37263397423959 | epot = -65.5031325721774 | etot = -49.9334366864413 +416000 ekin = 6.27056156936149 | erot = 9.74301767921106 | epot = -65.9470159374681 | etot = -49.9334366888956 +417000 ekin = 6.39375612509216 | erot = 10.2017877091305 | epot = -66.5289805260617 | etot = -49.933436691839 +418000 ekin = 6.55151386110296 | erot = 10.7180824120525 | epot = -67.2030329682677 | etot = -49.9334366951123 +419000 ekin = 6.72687533387526 | erot = 11.2579372105411 | epot = -67.9182492429841 | etot = -49.9334366985678 +420000 ekin = 6.90190857993762 | erot = 11.7859069157948 | epot = -68.6212521977431 | etot = -49.9334367020106 +421000 ekin = 7.05869608071859 | erot = 12.2671743403968 | epot = -69.2593071262608 | etot = -49.9334367051454 +422000 ekin = 7.18084994343646 | erot = 12.6704427611153 | epot = -69.7847294121264 | etot = -49.9334367075746 +423000 ekin = 7.25563872117268 | erot = 12.9714590209547 | epot = -70.1605344510344 | etot = -49.933436708907 +424000 ekin = 7.27613764930075 | erot = 13.156278523218 | epot = -70.365852881431 | etot = -49.9334367089123 +425000 ekin = 7.24240438623258 | erot = 13.2229033437548 | epot = -70.3987444377157 | etot = -49.9334367077283 +426000 ekin = 7.1610236603134 | erot = 13.1802284318378 | epot = -70.274688797818 | etot = -49.9334367056668 +427000 ekin = 7.04323569563879 | erot = 13.0453653110707 | epot = -70.0220377098745 | etot = -49.933436703165 +428000 ekin = 6.90252931709304 | erot = 12.8399447979796 | epot = -69.6759108156707 | etot = -49.9334367005981 +429000 ekin = 6.75380655237798 | erot = 12.5877583897248 | epot = -69.2750016367671 | etot = -49.9334366946643 +430000 ekin = 6.6364393161603 | erot = 12.3309009158262 | epot = -68.9007769264194 | etot = -49.9334366944329 +431000 ekin = 6.56250777539565 | erot = 12.0862249118006 | epot = -68.5821693817131 | etot = -49.9334366945168 +432000 ekin = 6.52775743984955 | erot = 11.8551418290255 | epot = -68.3163359638247 | etot = -49.9334366949496 +433000 ekin = 6.52644586081814 | erot = 11.6363446464843 | epot = -68.0962272029086 | etot = -49.9334366956061 +434000 ekin = 6.54730069025113 | erot = 11.4229959687972 | epot = -67.9037333576728 | etot = -49.9334366986245 +435000 ekin = 6.57899083359573 | erot = 11.2084874066967 | epot = -67.7209149390736 | etot = -49.9334366987812 +436000 ekin = 6.61931202197109 | erot = 10.9928671140437 | epot = -67.5456158350657 | etot = -49.933436699051 +437000 ekin = 6.66568526291443 | erot = 10.7754455556379 | epot = -67.3745675179576 | etot = -49.9334366994052 +438000 ekin = 6.71519766408806 | erot = 10.55506263558 | epot = -67.2036969994596 | etot = -49.9334366997915 +439000 ekin = 6.76486690072405 | erot = 10.3306264414359 | epot = -67.0289300422963 | etot = -49.9334367001363 +440000 ekin = 6.81204485681802 | erot = 10.1018252021595 | epot = -66.8473067593264 | etot = -49.9334367003489 +441000 ekin = 6.85494025857256 | erot = 9.86991417524009 | epot = -66.6582911341172 | etot = -49.9334367003046 +442000 ekin = 6.89316565874743 | erot = 9.63860472643772 | epot = -66.4652070851845 | etot = -49.9334366999993 +443000 ekin = 6.92830085528458 | erot = 9.41426089210094 | epot = -66.2759984467546 | etot = -49.9334366993691 +444000 ekin = 6.96427254046885 | erot = 9.20573448271319 | epot = -66.1034437216215 | etot = -49.9334366984394 +445000 ekin = 7.0073492958572 | erot = 9.02391831398476 | epot = -65.9647043071472 | etot = -49.9334366973052 +446000 ekin = 7.0656799429788 | erot = 8.88054940608633 | epot = -65.879666045204 | etot = -49.9334366961389 +447000 ekin = 7.14826938537586 | erot = 8.78650081535244 | epot = -65.8682068958953 | etot = -49.933436695167 +448000 ekin = 7.26342746668016 | erot = 8.74982299480011 | epot = -65.9466871561239 | etot = -49.9334366946436 +449000 ekin = 7.4168889378824 | erot = 8.77375650825312 | epot = -66.1240821409271 | etot = -49.9334366947916 +450000 ekin = 7.60996195055432 | erot = 8.85525305881733 | epot = -66.3986517051388 | etot = -49.9334366957672 +451000 ekin = 7.83859627200702 | erot = 8.98479300397757 | epot = -66.7568259732047 | etot = -49.9334366972201 +452000 ekin = 8.09534654891772 | erot = 9.14858392354098 | epot = -67.1773671722563 | etot = -49.9334366997976 +453000 ekin = 8.3650191223508 | erot = 9.32480175712275 | epot = -67.6232575823107 | etot = -49.9334367028371 +454000 ekin = 8.62787482253382 | erot = 9.48861390842429 | epot = -68.0499254368569 | etot = -49.9334367058988 +455000 ekin = 8.86318683153382 | erot = 9.61656796363553 | epot = -68.4131915036354 | etot = -49.933436708466 +456000 ekin = 9.0530142210923 | erot = 9.69069539967442 | epot = -68.6771463307981 | etot = -49.9334367100314 +457000 ekin = 9.18315881760057 | erot = 9.70061032940521 | epot = -68.8172058578152 | etot = -49.9334367108094 +458000 ekin = 9.24739083883971 | erot = 9.64764046613612 | epot = -68.8284680142412 | etot = -49.9334367092654 +459000 ekin = 9.25548953029249 | erot = 9.54869554439529 | epot = -68.73762178105 | etot = -49.9334367063622 +460000 ekin = 9.22729166751897 | erot = 9.43094677908273 | epot = -68.5916751492267 | etot = -49.933436702625 +461000 ekin = 9.18866313207254 | erot = 9.32746380429799 | epot = -68.4495636352095 | etot = -49.9334366988389 +462000 ekin = 9.16559319440856 | erot = 9.27112965792235 | epot = -68.3701595482315 | etot = -49.9334366959006 +463000 ekin = 9.17773873092181 | erot = 9.28803491832685 | epot = -68.3992103437024 | etot = -49.9334366944537 +464000 ekin = 9.23342197533264 | erot = 9.39218062502171 | epot = -68.5590392952248 | etot = -49.9334366948705 +465000 ekin = 9.32780582037917 | erot = 9.58246294341779 | epot = -68.8437054607598 | etot = -49.9334366969628 +466000 ekin = 9.44464021677508 | erot = 9.84368987462365 | epot = -69.2217667915182 | etot = -49.9334367001195 +467000 ekin = 9.56120377686489 | erot = 10.1507714878325 | epot = -69.645411968183 | etot = -49.9334367034856 +468000 ekin = 9.65468489578409 | erot = 10.475088662173 | epot = -70.0632102642112 | etot = -49.9334367062541 +469000 ekin = 9.70785696606057 | erot = 10.7910978191412 | epot = -70.4323914930672 | etot = -49.9334367078654 +470000 ekin = 9.71262212180743 | erot = 11.0813447197849 | epot = -70.7274035497351 | etot = -49.9334367081428 +471000 ekin = 9.67073883343365 | erot = 11.3387370682795 | epot = -70.9429126090209 | etot = -49.9334367073077 +472000 ekin = 9.59191180299258 | erot = 11.5659397722382 | epot = -71.0912882809175 | etot = -49.9334367056867 +473000 ekin = 9.49111612469352 | erot = 11.7727565997393 | epot = -71.1973094281946 | etot = -49.9334367037618 +474000 ekin = 9.38501610879041 | erot = 11.9729251611007 | epot = -71.2913779718146 | etot = -49.9334367019235 +475000 ekin = 9.28887232928698 | erot = 12.1810906679857 | epot = -71.4033996977514 | etot = -49.9334367004787 +476000 ekin = 9.2141310973565 | erot = 12.4104297277118 | epot = -71.5579975245851 | etot = -49.9334366995168 +477000 ekin = 9.16769186028445 | erot = 12.6713688994059 | epot = -71.7724974588023 | etot = -49.933436699112 +478000 ekin = 9.15149095804248 | erot = 12.9706692104284 | epot = -72.0555968677513 | etot = -49.9334366992804 +479000 ekin = 9.16265639587432 | erot = 13.3106560519735 | epot = -72.4067491478726 | etot = -49.9334367000247 +480000 ekin = 9.19406563258848 | erot = 13.6885767381103 | epot = -72.816079072012 | etot = -49.9334367013133 +481000 ekin = 9.23518145366876 | erot = 14.0963491431682 | epot = -73.2649672998759 | etot = -49.933436703039 +482000 ekin = 9.27324003575734 | erot = 14.5212080503177 | epot = -73.7278847910509 | etot = -49.9334367049758 +483000 ekin = 9.29487863763872 | erot = 14.9475327814571 | epot = -74.1758481259612 | etot = -49.9334367068654 +484000 ekin = 9.28813070972074 | erot = 15.3594466797976 | epot = -74.5810140977355 | etot = -49.9334367082172 +485000 ekin = 9.24449800629232 | erot = 15.7449638956732 | epot = -74.922898610809 | etot = -49.9334367088435 +486000 ekin = 9.16033951360244 | erot = 16.0979673631151 | epot = -75.1917435854229 | etot = -49.9334367087053 +487000 ekin = 9.03726433391164 | erot = 16.4183746409809 | epot = -75.3890756828753 | etot = -49.9334367079828 +488000 ekin = 8.88140769754063 | erot = 16.7103217583864 | epot = -75.5251661629216 | etot = -49.9334367069945 +489000 ekin = 8.70193103279663 | erot = 16.9791336192514 | epot = -75.6145013581086 | etot = -49.9334367060605 +490000 ekin = 8.50932564384251 | erot = 17.2283334636958 | epot = -75.6710958129435 | etot = -49.9334367054052 +491000 ekin = 8.31402797836484 | erot = 17.4577039708778 | epot = -75.705168654349 | etot = -49.9334367051063 +492000 ekin = 8.12558483921523 | erot = 17.6628124157096 | epot = -75.7218339600475 | etot = -49.9334367051227 +493000 ekin = 7.95231204430058 | erot = 17.835813360966 | epot = -75.72156211062 | etot = -49.9334367053535 +494000 ekin = 7.80119073598032 | erot = 17.9669524472962 | epot = -75.7015798889816 | etot = -49.9334367057051 +495000 ekin = 7.67769081997738 | erot = 18.0460778615069 | epot = -75.6572053876297 | etot = -49.9334367061454 +496000 ekin = 7.58531059410177 | erot = 18.0636363740619 | epot = -75.5823836748741 | etot = -49.9334367067103 +497000 ekin = 7.52485262515086 | erot = 18.0110549917982 | epot = -75.4693443244026 | etot = -49.9334367074536 +498000 ekin = 7.49373543821652 | erot = 17.8809293893866 | epot = -75.3081015357701 | etot = -49.933436708167 +499000 ekin = 7.48617782569716 | erot = 17.6689103471198 | epot = -75.088524881848 | etot = -49.933436709031 +500000 ekin = 7.49347216210887 | erot = 17.3741777344939 | epot = -74.801086606235 | etot = -49.9334367096322 +501000 ekin = 7.5053796995748 | erot = 17.0010883509583 | epot = -74.4399047601992 | etot = -49.9334367096662 +502000 ekin = 7.5124851361138 | erot = 16.5621897687566 | epot = -74.0081116137953 | etot = -49.9334367089248 +503000 ekin = 7.50819446610193 | erot = 16.0791838293638 | epot = -73.5208150028409 | etot = -49.9334367073752 +504000 ekin = 7.49011586231213 | erot = 15.581868306886 | epot = -73.0054208743659 | etot = -49.9334367051677 +505000 ekin = 7.46056991973154 | erot = 15.1049042921319 | epot = -72.4989109145295 | etot = -49.9334367026661 +506000 ekin = 7.42616688343037 | erot = 14.6834712564248 | epot = -72.0430748400018 | etot = -49.9334367001466 +507000 ekin = 7.39661274009595 | erot = 14.3486660366054 | epot = -71.6787154747788 | etot = -49.9334366980775 +508000 ekin = 7.38281606550075 | erot = 14.1223813055505 | epot = -71.4386340679509 | etot = -49.9334366968997 +509000 ekin = 7.39402992163552 | erot = 14.0119926346298 | epot = -71.3394592535268 | etot = -49.9334366972615 +510000 ekin = 7.4348791744325 | erot = 14.0064549706487 | epot = -71.3747708439909 | etot = -49.9334366989097 +511000 ekin = 7.50576717996981 | erot = 14.0784238743036 | epot = -71.5176277563004 | etot = -49.933436702027 +512000 ekin = 7.60119561213566 | erot = 14.1838211435082 | epot = -71.71845346191 | etot = -49.9334367062662 +513000 ekin = 7.71044568679074 | erot = 14.2667319446144 | epot = -71.9106143423507 | etot = -49.9334367109455 +514000 ekin = 7.8197874776503 | erot = 14.2680211759099 | epot = -72.0212453686592 | etot = -49.933436715099 +515000 ekin = 7.9159515092748 | erot = 14.1367309758411 | epot = -71.986119202766 | etot = -49.93343671765 +516000 ekin = 7.99023839625879 | erot = 13.8421209122757 | epot = -71.7657960262611 | etot = -49.9334367177266 +517000 ekin = 8.04205550959456 | erot = 13.3828818540722 | epot = -71.3583740786968 | etot = -49.9334367150301 +518000 ekin = 8.08036426889104 | erot = 12.7898538338779 | epot = -70.8036548128079 | etot = -49.933436710039 +519000 ekin = 8.12206393604654 | erot = 12.1205081665698 | epot = -70.1760088064841 | etot = -49.9334367038678 +520000 ekin = 8.18764894631014 | erot = 11.446875997564 | epot = -69.5679616417302 | etot = -49.9334366978561 +521000 ekin = 8.29566353774508 | erot = 10.8412363960475 | epot = -69.0703366269248 | etot = -49.9334366931322 +522000 ekin = 8.45774428963588 | erot = 10.3639645177985 | epot = -68.7551454978129 | etot = -49.9334366903786 +523000 ekin = 8.675470703323 | erot = 10.0559571764092 | epot = -68.6648645695377 | etot = -49.9334366898055 +524000 ekin = 8.93944864499587 | erot = 9.93579310864772 | epot = -68.8086784449005 | etot = -49.9334366912569 +525000 ekin = 9.23044472111655 | erot = 10.0004752134417 | epot = -69.1643566289133 | etot = -49.9334366943551 +526000 ekin = 9.52203491659237 | erot = 10.228330720636 | epot = -69.683802335846 | etot = -49.9334366986176 +527000 ekin = 9.78409599196242 | erot = 10.5829813009894 | epot = -70.300513996481 | etot = -49.9334367035292 +528000 ekin = 9.98654469598818 | erot = 11.0178490697343 | epot = -70.9378304742832 | etot = -49.9334367085607 +529000 ekin = 10.1029539602098 | erot = 11.4811633032952 | epot = -71.5175539766568 | etot = -49.9334367131518 +530000 ekin = 10.1138818471058 | erot = 11.9216268521084 | epot = -71.9689454159332 | etot = -49.933436716719 +531000 ekin = 10.009768376694 | erot = 12.2946121702168 | epot = -72.2378172656381 | etot = -49.9334367187274 +532000 ekin = 9.79306563783147 | erot = 12.5680717026784 | epot = -72.2945740593373 | etot = -49.9334367188274 +533000 ekin = 9.47905160964921 | erot = 12.7267270061902 | epot = -72.1392153328364 | etot = -49.9334367169971 +534000 ekin = 9.09480598117682 | erot = 12.7731458504392 | epot = -71.8013885452047 | etot = -49.9334367135886 +535000 ekin = 8.67621596360844 | erot = 12.7252467736192 | epot = -71.3348994464689 | etot = -49.9334367092412 +536000 ekin = 8.26347380203143 | erot = 12.611110006877 | epot = -70.8080205135961 | etot = -49.9334367046877 +537000 ekin = 7.8959905961466 | erot = 12.4628737027761 | epot = -70.2923009994975 | etot = -49.9334367005748 +538000 ekin = 7.60773288320374 | erot = 12.3114435936286 | epot = -69.852613174175 | etot = -49.9334366973427 +539000 ekin = 7.42371159255836 | erot = 12.1829376490116 | epot = -69.5400859367976 | etot = -49.9334366952277 +540000 ekin = 7.35791077730336 | erot = 12.0968490256517 | epot = -69.3881964972587 | etot = -49.9334366943036 +541000 ekin = 7.41256804389062 | erot = 12.0653576080878 | epot = -69.4113623465337 | etot = -49.9334366945552 +542000 ekin = 7.57853605047927 | erot = 12.0931906688322 | epot = -69.6051634152252 | etot = -49.9334366959138 +543000 ekin = 7.83646941918601 | erot = 12.1777647791037 | epot = -69.9476708965313 | etot = -49.9334366982416 +544000 ekin = 8.15871763046595 | erot = 12.3097728231561 | epot = -70.4019271549212 | etot = -49.9334367012991 +545000 ekin = 8.51194808028798 | erot = 12.4746658404529 | epot = -70.9200506254413 | etot = -49.9334367047004 +546000 ekin = 8.86055542994395 | erot = 12.6554193668289 | epot = -71.4494115046975 | etot = -49.9334367079246 +547000 ekin = 9.17075162004728 | erot = 12.8364725166905 | epot = -71.9406608471334 | etot = -49.9334367103957 +548000 ekin = 9.41490179015865 | erot = 13.0079503311565 | epot = -72.3562888329616 | etot = -49.9334367116464 +549000 ekin = 9.57534656747892 | erot = 13.1686979374621 | epot = -72.6774812164065 | etot = -49.9334367114655 +550000 ekin = 9.6468620904745 | erot = 13.3267810142959 | epot = -72.9070798147489 | etot = -49.9334367099785 +551000 ekin = 9.6371528675885 | erot = 13.497010971565 | epot = -73.0676005467578 | etot = -49.9334367076043 +552000 ekin = 9.56521103052548 | erot = 13.696204125115 | epot = -73.1948518605858 | etot = -49.9334367049453 +553000 ekin = 9.45778037488728 | erot = 13.9376030903989 | epot = -73.3288201679348 | etot = -49.9334367026486 +554000 ekin = 9.34444856533031 | erot = 14.2259329986005 | epot = -73.5038182652216 | etot = -49.9334367012908 +555000 ekin = 9.25213586060062 | erot = 14.5541873410933 | epot = -73.7397599029621 | etot = -49.9334367012682 +556000 ekin = 9.19999740115139 | erot = 14.902773179047 | epot = -74.0362072829086 | etot = -49.9334367027102 +557000 ekin = 9.19858106837153 | erot = 15.24186260026 | epot = -74.3738803738764 | etot = -49.9334367052449 +558000 ekin = 9.24425546361931 | erot = 15.5331606763114 | epot = -74.710852849054 | etot = -49.9334367091233 +559000 ekin = 9.31861665848668 | erot = 15.7359099531063 | epot = -74.9879633246597 | etot = -49.9334367130667 +560000 ekin = 9.39695059697467 | erot = 15.8150009570236 | epot = -75.1453882703886 | etot = -49.9334367163903 +561000 ekin = 9.45314011687707 | erot = 15.7467098709177 | epot = -75.1332867062887 | etot = -49.9334367184939 +562000 ekin = 9.4644325074614 | erot = 15.5232568985045 | epot = -74.9211261249237 | etot = -49.9334367189578 +563000 ekin = 9.41516469931819 | erot = 15.156724981701 | epot = -74.5053263981417 | etot = -49.9334367171225 +564000 ekin = 9.29889627205163 | erot = 14.6799119626611 | epot = -73.9122449488013 | etot = -49.9334367140885 +565000 ekin = 9.11880310142311 | erot = 14.1400031739786 | epot = -73.1922429851253 | etot = -49.9334367097237 +566000 ekin = 8.88664822041088 | erot = 13.5965040767949 | epot = -72.4165890017699 | etot = -49.9334367045641 +567000 ekin = 8.62095363300708 | erot = 13.1147978258941 | epot = -71.6691881581016 | etot = -49.9334366992005 +568000 ekin = 8.34502941992304 | erot = 12.7577046249506 | epot = -71.0361707402357 | etot = -49.9334366953621 +569000 ekin = 8.08308251281923 | erot = 12.5716587302871 | epot = -70.5881779351587 | etot = -49.9334366920524 +570000 ekin = 7.85931792271714 | erot = 12.5845592067235 | epot = -70.3773138202899 | etot = -49.9334366908492 +571000 ekin = 7.69515957552165 | erot = 12.7948834197191 | epot = -70.4234796877045 | etot = -49.9334366924637 +572000 ekin = 7.60396111749303 | erot = 13.1643540857624 | epot = -70.7017519004665 | etot = -49.9334366972111 +573000 ekin = 7.58730164860276 | erot = 13.6192730322753 | epot = -71.1400113849639 | etot = -49.9334367040858 +574000 ekin = 7.63520361164767 | erot = 14.0643105451696 | epot = -71.6329508681007 | etot = -49.9334367112835 +575000 ekin = 7.7308015611837 | erot = 14.4044632196782 | epot = -72.0687014976682 | etot = -49.9334367168064 +576000 ekin = 7.85689248444025 | erot = 14.5664691504238 | epot = -72.3567983546925 | etot = -49.9334367198285 +577000 ekin = 8.00091593742018 | erot = 14.5094673832396 | epot = -72.4438200407052 | etot = -49.9334367200454 +578000 ekin = 8.15665258272852 | erot = 14.2276209559902 | epot = -72.3177102567398 | etot = -49.9334367180211 +579000 ekin = 8.32306728067564 | erot = 13.7443245549445 | epot = -72.0008285502556 | etot = -49.9334367146355 +580000 ekin = 8.50340996053175 | erot = 13.1029754976368 | epot = -71.5398221683346 | etot = -49.9334367101661 +581000 ekin = 8.70208311707815 | erot = 12.3569061227601 | epot = -70.9924259463535 | etot = -49.9334367065152 +582000 ekin = 8.91777039453314 | erot = 11.5600287828855 | epot = -70.4112358806671 | etot = -49.9334367032485 +583000 ekin = 9.14731913961815 | erot = 10.7633073834542 | epot = -69.8440632236325 | etot = -49.9334367005601 +584000 ekin = 9.3857721081823 | erot = 10.0114551308676 | epot = -69.3306639376224 | etot = -49.9334366985725 +585000 ekin = 9.62647735601733 | erot = 9.34056459168138 | epot = -68.9004786450718 | etot = -49.9334366973731 +586000 ekin = 9.86132138678038 | erot = 8.77626879108137 | epot = -68.5710268748886 | etot = -49.9334366970268 +587000 ekin = 10.0810752649667 | erot = 8.3323562130503 | epot = -68.3468681755626 | etot = -49.9334366975456 +588000 ekin = 10.2759188426488 | erot = 8.01010405484645 | epot = -68.2194595963449 | etot = -49.9334366988497 +589000 ekin = 10.436242283354 | erot = 7.79886753310536 | epot = -68.1685465171737 | etot = -49.9334367007143 +590000 ekin = 10.553793739994 | erot = 7.67891225372246 | epot = -68.1661426964919 | etot = -49.9334367027754 +591000 ekin = 10.6230840083776 | erot = 7.62453842360011 | epot = -68.1810591364858 | etot = -49.9334367045081 +592000 ekin = 10.6427223550897 | erot = 7.61008622177964 | epot = -68.1862452824274 | etot = -49.9334367055581 +593000 ekin = 10.6162293457026 | erot = 7.6153063463023 | epot = -68.1649723976523 | etot = -49.9334367056474 +594000 ekin = 10.5518689631298 | erot = 7.6291186151185 | epot = -68.1144242830721 | etot = -49.9334367048238 +595000 ekin = 10.4613549146384 | erot = 7.65041575232207 | epot = -68.0452073703513 | etot = -49.9334367033908 +596000 ekin = 10.3577397595008 | erot = 7.68597457794039 | epot = -67.9771510392169 | etot = -49.9334367017757 +597000 ekin = 10.2530110984132 | erot = 7.74702054972167 | epot = -67.9334683485101 | etot = -49.9334367003752 +598000 ekin = 10.155839607293 | erot = 7.84502642240808 | epot = -67.9343027291996 | etot = -49.9334366994986 +599000 ekin = 10.071645676352 | erot = 7.98815266718876 | epot = -67.9932350425499 | etot = -49.9334366990092 +600000 ekin = 10.0026338980498 | erot = 8.18253713496056 | epot = -68.1186077320192 | etot = -49.9334366990089 +601000 ekin = 9.94654163032188 | erot = 8.4316149652901 | epot = -68.3115932943765 | etot = -49.9334366987646 +602000 ekin = 9.9021377201314 | erot = 8.7343430837155 | epot = -68.5699175034191 | etot = -49.9334366995722 +603000 ekin = 9.86461425676751 | erot = 9.08804689163901 | epot = -68.8860978487218 | etot = -49.9334367003152 +604000 ekin = 9.82582394713229 | erot = 9.49104521649029 | epot = -69.2503058645391 | etot = -49.9334367009165 +605000 ekin = 9.77966552472142 | erot = 9.94153338240772 | epot = -69.6546356085775 | etot = -49.9334367014483 +606000 ekin = 9.7222259251532 | erot = 10.436343641277 | epot = -70.0920062685874 | etot = -49.9334367021572 +607000 ekin = 9.65083110472607 | erot = 10.9682113934817 | epot = -70.5524792017342 | etot = -49.9334367035264 +608000 ekin = 9.56210695279502 | erot = 11.5218646669798 | epot = -71.0174083255813 | etot = -49.9334367058065 +609000 ekin = 9.44922522118175 | erot = 12.0704423054891 | epot = -71.4531042366253 | etot = -49.9334367099545 +610000 ekin = 9.30054046558592 | erot = 12.5719096406672 | epot = -71.8058868204232 | etot = -49.9334367141701 +611000 ekin = 9.09998277426936 | erot = 12.9832358345976 | epot = -72.0166553266489 | etot = -49.933436717782 +612000 ekin = 8.83381798261941 | erot = 13.2691152694542 | epot = -72.0363699714117 | etot = -49.9334367193381 +613000 ekin = 8.49783282733212 | erot = 13.4145896843968 | epot = -71.8458592296073 | etot = -49.9334367178784 +614000 ekin = 8.10282385729063 | erot = 13.4329804231055 | epot = -71.4692409938747 | etot = -49.9334367134786 +615000 ekin = 7.6754843053033 | erot = 13.3639670455377 | epot = -70.9728880580651 | etot = -49.9334367072241 +616000 ekin = 7.25407898483605 | erot = 13.2628400894521 | epot = -70.4503557749191 | etot = -49.9334367006309 +617000 ekin = 6.88089060450539 | erot = 13.1866181608022 | epot = -70.0009454603096 | etot = -49.9334366950021 +618000 ekin = 6.59435266200065 | erot = 13.1829361442061 | epot = -69.710725497309 | etot = -49.9334366911023 +619000 ekin = 6.42302569831928 | erot = 13.284295457854 | epot = -69.6407578453659 | etot = -49.9334366891927 +620000 ekin = 6.38233280989394 | erot = 13.5068914943409 | epot = -69.8226609933189 | etot = -49.933436689084 +621000 ekin = 6.47407410490947 | erot = 13.8532244873708 | epot = -70.2607352827226 | etot = -49.9334366904423 +622000 ekin = 6.6882328973603 | erot = 14.3148945805657 | epot = -70.9365641707862 | etot = -49.9334366928603 +623000 ekin = 7.00613993436046 | erot = 14.8751185925638 | epot = -71.8146952230787 | etot = -49.9334366961545 +624000 ekin = 7.40369975393462 | erot = 15.5093236026483 | epot = -72.8464600566424 | etot = -49.9334367000594 +625000 ekin = 7.85341892233954 | erot = 16.1852180464027 | epot = -73.9720736736374 | etot = -49.9334367048952 +626000 ekin = 8.324719146602 | erot = 16.8599319289495 | epot = -75.1180877864706 | etot = -49.9334367109191 +627000 ekin = 8.78345982137352 | erot = 17.4776172005369 | epot = -76.1945137398586 | etot = -49.9334367179482 +628000 ekin = 9.19295493488487 | erot = 17.9720241171043 | epot = -77.0984157768825 | etot = -49.9334367248933 +629000 ekin = 9.51863748538358 | erot = 18.2775776956347 | epot = -77.7296519108779 | etot = -49.9334367298596 +630000 ekin = 9.73601789214728 | erot = 18.3475811088435 | epot = -78.0170357280286 | etot = -49.9334367270378 +631000 ekin = 9.84717031282253 | erot = 18.1774007976277 | epot = -77.9580078352772 | etot = -49.933436724827 +632000 ekin = 9.86514165731601 | erot = 17.7977961669757 | epot = -77.5963745438562 | etot = -49.9334367195645 +633000 ekin = 9.80741211214886 | erot = 17.262632153246 | epot = -77.0034809785188 | etot = -49.9334367131239 +634000 ekin = 9.69704834099391 | erot = 16.6375206672738 | epot = -76.2680057155986 | etot = -49.9334367073309 +635000 ekin = 9.55480062387112 | erot = 15.9824182746176 | epot = -75.4706556016888 | etot = -49.9334367032001 +636000 ekin = 9.3944337691337 | erot = 15.3418801348258 | epot = -74.6697506047724 | etot = -49.9334367008129 +637000 ekin = 9.2220720857669 | erot = 14.7441119802455 | epot = -73.8996207656773 | etot = -49.9334366996649 +638000 ekin = 9.03836092901136 | erot = 14.2055872727831 | epot = -73.1773849008786 | etot = -49.9334366990841 +639000 ekin = 8.8417163270111 | erot = 13.7372137345065 | epot = -72.5123667600205 | etot = -49.9334366985029 +640000 ekin = 8.63137043880964 | erot = 13.34938465084 | epot = -71.9141917872224 | etot = -49.9334366975728 +641000 ekin = 8.40954916880358 | erot = 13.0548513789323 | epot = -71.3978372439143 | etot = -49.9334366961784 +642000 ekin = 8.18255898210743 | erot = 12.8693803232219 | epot = -70.9853759997273 | etot = -49.933436694398 +643000 ekin = 7.96078880311479 | erot = 12.8106076124048 | epot = -70.7048331079812 | etot = -49.9334366924617 +644000 ekin = 7.75858397895701 | erot = 12.895046023422 | epot = -70.5870666931113 | etot = -49.9334366907323 +645000 ekin = 7.59153605359928 | erot = 13.1346881329343 | epot = -70.659660876219 | etot = -49.9334366896854 +646000 ekin = 7.4714219313018 | erot = 13.5357483886256 | epot = -70.9406070095256 | etot = -49.9334366895982 +647000 ekin = 7.40688255499808 | erot = 14.093807462216 | epot = -71.434126708072 | etot = -49.9334366908579 +648000 ekin = 7.3947726179394 | erot = 14.7853448582919 | epot = -72.1135541746406 | etot = -49.9334366984093 +649000 ekin = 7.41215148581707 | erot = 15.5579695689084 | epot = -72.9035577588663 | etot = -49.9334367041409 +650000 ekin = 7.43748369398846 | erot = 16.3522656883817 | epot = -73.723186092836 | etot = -49.9334367104659 +651000 ekin = 7.44712966941582 | erot = 17.1032791639477 | epot = -74.4838455493625 | etot = -49.933436715999 +652000 ekin = 7.42218365700039 | erot = 17.7519733432208 | epot = -75.1075937196659 | etot = -49.9334367194447 +653000 ekin = 7.35498154076254 | erot = 18.256631588447 | epot = -75.5450498494313 | etot = -49.9334367202218 +654000 ekin = 7.2517712716901 | erot = 18.598343368647 | epot = -75.7835513590574 | etot = -49.9334367187203 +655000 ekin = 7.13014467414996 | erot = 18.7785589482672 | epot = -75.8421403383857 | etot = -49.9334367159685 +656000 ekin = 7.01280585603195 | erot = 18.811498691348 | epot = -75.7577412603866 | etot = -49.9334367130066 +657000 ekin = 6.92098821809362 | erot = 18.7164621309898 | epot = -75.5708870595303 | etot = -49.933436710447 +658000 ekin = 6.87020252984082 | erot = 18.5133762498954 | epot = -75.3170154881713 | etot = -49.9334367084351 +659000 ekin = 6.86904868061524 | erot = 18.221622832328 | epot = -75.024108219808 | etot = -49.9334367068648 +660000 ekin = 6.9202440611907 | erot = 17.8601865760474 | epot = -74.7138673428541 | etot = -49.933436705616 +661000 ekin = 7.02250789851937 | erot = 17.4471787302428 | epot = -74.4031233334707 | etot = -49.9334367047086 +662000 ekin = 7.1721656622903 | erot = 16.9978194560425 | epot = -74.1034218226649 | etot = -49.9334367043321 +663000 ekin = 7.36379572134484 | erot = 16.5210347162929 | epot = -73.8182671424275 | etot = -49.9334367047897 +664000 ekin = 7.58974310926842 | erot = 16.015745821036 | epot = -73.5389256366374 | etot = -49.933436706333 +665000 ekin = 7.83889852379622 | erot = 15.4688426540646 | epot = -73.2411778867683 | etot = -49.9334367089075 +666000 ekin = 8.09569815914898 | erot = 14.8574040047694 | epot = -72.8865388758488 | etot = -49.9334367119304 +667000 ekin = 8.34047460991551 | erot = 14.1568873291622 | epot = -72.4307986534121 | etot = -49.9334367143344 +668000 ekin = 8.55167804704053 | erot = 13.3539231505273 | epot = -71.8390379125769 | etot = -49.9334367150091 +669000 ekin = 8.70925293287445 | erot = 12.4582854453855 | epot = -71.1009750916909 | etot = -49.933436713431 +670000 ekin = 8.79758177059704 | erot = 11.5072080473696 | epot = -70.2382265279456 | etot = -49.933436709979 +671000 ekin = 8.806829701508 | erot = 10.5590297335602 | epot = -69.2992961407165 | etot = -49.9334367056483 +672000 ekin = 8.73288275171984 | erot = 9.67972128063836 | epot = -68.3460407337836 | etot = -49.9334367014254 +673000 ekin = 8.57696192212147 | erot = 8.92953158876448 | epot = -67.4399302087297 | etot = -49.9334366978437 +674000 ekin = 8.34564071467256 | erot = 8.35517289115185 | epot = -66.6342503007804 | etot = -49.933436694956 +675000 ekin = 8.05103177970298 | erot = 7.98833216293152 | epot = -65.9728006352283 | etot = -49.9334366925938 +676000 ekin = 7.7104008201603 | erot = 7.84792602077389 | epot = -65.4917635315679 | etot = -49.9334366906337 +677000 ekin = 7.34474807581417 | erot = 7.94294820989321 | epot = -65.2211329748236 | etot = -49.9334366891162 +678000 ekin = 6.97652326988432 | erot = 8.273959425869 | epot = -65.1839193839974 | etot = -49.9334366882441 +679000 ekin = 6.62703502456099 | erot = 8.8326449186269 | epot = -65.3931166315143 | etot = -49.9334366883265 +680000 ekin = 6.31408234083374 | erot = 9.59961963416757 | epot = -65.847138664739 | etot = -49.9334366897377 +681000 ekin = 6.05007024097138 | erot = 10.5409249737469 | epot = -66.5244319075782 | etot = -49.9334366928599 +682000 ekin = 5.84069686117359 | erot = 11.6040232368198 | epot = -67.3781567959513 | etot = -49.9334366979579 +683000 ekin = 5.68441215099936 | erot = 12.7150399583984 | epot = -68.3328888143209 | etot = -49.9334367049231 +684000 ekin = 5.57317083691089 | erot = 13.7803400926936 | epot = -69.2869476425548 | etot = -49.9334367129503 +685000 ekin = 5.49512330343633 | erot = 14.6959075814906 | epot = -70.1244676053778 | etot = -49.9334367204509 +686000 ekin = 5.43923671977557 | erot = 15.3654260750359 | epot = -70.7380995202957 | etot = -49.9334367254842 +687000 ekin = 5.4003758453289 | erot = 15.7221888728928 | epot = -71.0560014449076 | etot = -49.9334367266859 +688000 ekin = 5.38224990758936 | erot = 15.744983026696 | epot = -71.0606696583123 | etot = -49.9334367240269 +689000 ekin = 5.39639776099312 | erot = 15.4596385605578 | epot = -70.7894730403118 | etot = -49.9334367187609 +690000 ekin = 5.45787871144207 | erot = 14.9262956796592 | epot = -70.3176111037086 | etot = -49.9334367126074 +691000 ekin = 5.58031564629653 | erot = 14.2204427974029 | epot = -69.7341951506146 | etot = -49.9334367069152 +692000 ekin = 5.77268021078934 | erot = 13.4168709007514 | epot = -69.1229878130452 | etot = -49.9334367015044 +693000 ekin = 6.03848572893413 | erot = 12.5833910056357 | epot = -68.5553134330701 | etot = -49.9334366985003 +694000 ekin = 6.37471136529004 | erot = 11.7714633111127 | epot = -68.0796113729147 | etot = -49.933436696512 +695000 ekin = 6.77415007797664 | erot = 11.0181330989382 | epot = -67.7257198722996 | etot = -49.9334366953848 +696000 ekin = 7.22672456210878 | erot = 10.3500991256303 | epot = -67.5102603827706 | etot = -49.9334366950315 +697000 ekin = 7.71965128610211 | erot = 9.78480932550617 | epot = -67.4378973070206 | etot = -49.9334366954123 +698000 ekin = 8.23736470679943 | erot = 9.33123654404228 | epot = -67.5020379473337 | etot = -49.933436696492 +699000 ekin = 8.76153382981944 | erot = 8.99061023090674 | epot = -67.6855807589161 | etot = -49.9334366981899 +700000 ekin = 9.2715215974341 | erot = 8.75737705398687 | epot = -67.962335351764 | etot = -49.933436700343 +701000 ekin = 9.74214098374746 | erot = 8.61946007694512 | epot = -68.2950377641907 | etot = -49.9334367034981 +702000 ekin = 10.1452112687015 | erot = 8.55928312120505 | epot = -68.6379310960394 | etot = -49.9334367061329 +703000 ekin = 10.4587930030361 | erot = 8.55974434414932 | epot = -68.9519740551977 | etot = -49.9334367080123 +704000 ekin = 10.6678411441203 | erot = 8.60820420723839 | epot = -69.2094820600658 | etot = -49.9334367087071 +705000 ekin = 10.7665498374596 | erot = 8.70023426604803 | epot = -69.4002208115681 | etot = -49.9334367080605 +706000 ekin = 10.7588048076212 | erot = 8.84126944064561 | epot = -69.5335109545564 | etot = -49.9334367062896 +707000 ekin = 10.6564483688995 | erot = 9.04518277440377 | epot = -69.6350678472186 | etot = -49.9334367039153 +708000 ekin = 10.4759748100134 | erot = 9.33018435423022 | epot = -69.7395958657862 | etot = -49.9334367015426 +709000 ekin = 10.2349383723162 | erot = 9.71377701816848 | epot = -69.8821520901019 | etot = -49.9334366996172 +710000 ekin = 9.94939019034938 | erot = 10.2088106032918 | epot = -70.0916374919401 | etot = -49.9334366982989 +711000 ekin = 9.63303801869973 | erot = 10.8217465783858 | epot = -70.388221294592 | etot = -49.9334366975064 +712000 ekin = 9.2979059702487 | erot = 11.5527669206084 | epot = -70.7841095879486 | etot = -49.9334366970915 +713000 ekin = 8.95557547299259 | erot = 12.3963504873229 | epot = -71.2853626573237 | etot = -49.9334366970082 +714000 ekin = 8.617973595347 | erot = 13.3409900929415 | epot = -71.8924003856787 | etot = -49.9334366973902 +715000 ekin = 8.29712952353144 | erot = 14.3676387566984 | epot = -72.5982049787211 | etot = -49.9334366984912 +716000 ekin = 8.00398725900128 | erot = 15.4475133380728 | epot = -73.3849372976347 | etot = -49.9334367005607 +717000 ekin = 7.74683519043469 | erot = 16.5404526855597 | epot = -74.2207245796401 | etot = -49.9334367036457 +718000 ekin = 7.52982507900723 | erot = 17.5950557079123 | epot = -75.0583174948218 | etot = -49.9334367079023 +719000 ekin = 7.35243516423642 | erot = 18.5497013195426 | epot = -75.8355731964305 | etot = -49.9334367126514 +720000 ekin = 7.21118318121855 | erot = 19.3392479278478 | epot = -76.4838678262561 | etot = -49.9334367171898 +721000 ekin = 7.10169759026176 | erot = 19.9036057067636 | epot = -76.9387400178502 | etot = -49.9334367208248 +722000 ekin = 7.02044686322979 | erot = 20.1972584111814 | epot = -77.1511419967982 | etot = -49.933436722387 +723000 ekin = 6.96887965469435 | erot = 20.1990914031759 | epot = -77.1014077792607 | etot = -49.9334367213905 +724000 ekin = 6.95516719908128 | erot = 19.9185959405088 | epot = -76.8071998575259 | etot = -49.9334367179358 +725000 ekin = 6.99328744836862 | erot = 19.3950419519746 | epot = -76.32176611311 | etot = -49.9334367127668 +726000 ekin = 7.09984572443388 | erot = 18.6900231615959 | epot = -75.7233055929846 | etot = -49.9334367069548 +727000 ekin = 7.28975977557264 | erot = 17.8763690647887 | epot = -75.0995655418772 | etot = -49.9334367015159 +728000 ekin = 7.57226569432855 | erot = 17.027291264949 | epot = -74.5329936564447 | etot = -49.9334366971671 +729000 ekin = 7.94819326112271 | erot = 16.2083660373957 | epot = -74.0899959927799 | etot = -49.9334366942615 +730000 ekin = 8.40885783994521 | erot = 15.4730324365404 | epot = -73.8153269693346 | etot = -49.933436692849 +731000 ekin = 8.93653983578192 | erot = 14.8609748013039 | epot = -73.7309513298607 | etot = -49.9334366927749 +732000 ekin = 9.50625303498499 | erot = 14.398295254732 | epot = -73.8379849835087 | etot = -49.9334366937918 +733000 ekin = 10.0882454137722 | erot = 14.0984617273564 | epot = -74.1201438367855 | etot = -49.9334366956568 +734000 ekin = 10.6505846051446 | erot = 13.9633900358324 | epot = -74.5474113391439 | etot = -49.933436698167 +735000 ekin = 11.1614098847907 | erot = 13.9845407949562 | epot = -75.0793873808749 | etot = -49.9334367011279 +736000 ekin = 11.5908641046552 | erot = 14.1443786489366 | epot = -75.668679457882 | etot = -49.9334367042901 +737000 ekin = 11.9130268000472 | erot = 14.4186949532956 | epot = -76.2651584606395 | etot = -49.9334367072967 +738000 ekin = 12.1081074329298 | erot = 14.7799937728837 | epot = -76.8215379155438 | etot = -49.9334367097304 +739000 ekin = 12.1647528301792 | erot = 15.2014921459777 | epot = -77.299681687379 | etot = -49.933436711222 +740000 ekin = 12.0818547626869 | erot = 15.6606440165028 | epot = -77.6759354907942 | etot = -49.9334367116045 +741000 ekin = 11.8690601672769 | erot = 16.1409035861964 | epot = -77.9434004644811 | etot = -49.9334367110078 +742000 ekin = 11.5454682619335 | erot = 16.6309355139422 | epot = -78.109840485719 | etot = -49.9334367098433 +743000 ekin = 11.1366225376696 | erot = 17.1214741633598 | epot = -78.1915334096987 | etot = -49.9334367086694 +744000 ekin = 10.6705301540866 | erot = 17.6010237793427 | epot = -78.2049906414304 | etot = -49.9334367080012 +745000 ekin = 10.1737520695959 | erot = 18.052092950075 | epot = -78.1592817278147 | etot = -49.9334367081438 +746000 ekin = 9.6685013127403 | erot = 18.4494857322339 | epot = -78.0514237540745 | etot = -49.9334367091003 +747000 ekin = 9.17126973076506 | erot = 18.7614465755014 | epot = -77.8661530168527 | etot = -49.9334367105863 +748000 ekin = 8.69297393764094 | erot = 18.953728130683 | epot = -77.5801387804948 | etot = -49.9334367121709 +749000 ekin = 8.24016858931027 | erot = 18.9943262077066 | epot = -77.1679315103983 | etot = -49.9334367133814 +750000 ekin = 7.81665899712657 | erot = 18.8585564743736 | epot = -76.6086521854012 | etot = -49.9334367139011 +751000 ekin = 7.42490357418608 | erot = 18.5327488588056 | epot = -75.891089146604 | etot = -49.9334367136123 +752000 ekin = 7.06688992057231 | erot = 18.0154570969018 | epot = -75.0157837300385 | etot = -49.9334367125643 +753000 ekin = 6.744505124284 | erot = 17.3167499794558 | epot = -73.9946918146284 | etot = -49.9334367108887 +754000 ekin = 6.45964482993023 | erot = 16.456483060898 | epot = -72.8495645995444 | etot = -49.9334367087162 +755000 ekin = 6.21433593468652 | erot = 15.4623891983238 | epot = -71.6101618391579 | etot = -49.9334367061475 +756000 ekin = 6.01102239399577 | erot = 14.3683296041341 | epot = -70.3127887013935 | etot = -49.9334367032637 +757000 ekin = 5.85298993013194 | erot = 13.2131589078038 | epot = -68.999585537915 | etot = -49.9334366999792 +758000 ekin = 5.74477587284935 | erot = 12.0391225468939 | epot = -67.7173351163856 | etot = -49.9334366966423 +759000 ekin = 5.69192064864643 | erot = 10.8875839734322 | epot = -66.5129413157298 | etot = -49.9334366936513 +760000 ekin = 5.7011745396041 | erot = 9.79576401849851 | epot = -65.4303752490455 | etot = -49.9334366909429 +761000 ekin = 5.78056045511594 | erot = 8.79564789186458 | epot = -64.50964503564 | etot = -49.9334366886595 +762000 ekin = 5.93878225215652 | erot = 7.91237636455522 | epot = -63.7845953036168 | etot = -49.9334366869051 +763000 ekin = 6.18436172780979 | erot = 7.16346434501524 | epot = -63.2812627585723 | etot = -49.9334366857473 +764000 ekin = 6.52454675169063 | erot = 6.55876560277926 | epot = -63.0167490397062 | etot = -49.9334366852363 +765000 ekin = 6.96404799964301 | erot = 6.10094289751422 | epot = -62.9984275825647 | etot = -49.9334366854075 +766000 ekin = 7.50369090335682 | erot = 5.78618752604388 | epot = -63.2233151157002 | etot = -49.9334366862995 +767000 ekin = 8.13911242252144 | erot = 5.60500996894259 | epot = -63.6775590794025 | etot = -49.9334366879384 +768000 ekin = 8.85968786592072 | erot = 5.54304366990311 | epot = -64.3361682261375 | etot = -49.9334366903137 +769000 ekin = 9.64793234063518 | erot = 5.58192554387106 | epot = -65.163294577859 | etot = -49.9334366933527 +770000 ekin = 10.4796582497402 | erot = 5.70040197416269 | epot = -66.1134969207945 | etot = -49.9334366968916 +771000 ekin = 11.3236336972485 | erot = 5.87607544107288 | epot = -67.1331458396591 | etot = -49.9334367013377 +772000 ekin = 12.1386957385345 | erot = 6.08706480596381 | epot = -68.1591972498816 | etot = -49.9334367053833 +773000 ekin = 12.8870213668668 | erot = 6.31151513691576 | epot = -69.1319732127323 | etot = -49.9334367089498 +774000 ekin = 13.5351523878613 | erot = 6.53122680630184 | epot = -69.9998159058268 | etot = -49.9334367116636 +775000 ekin = 14.0571973920993 | erot = 6.73342010746164 | epot = -70.7240542128492 | etot = -49.9334367132882 +776000 ekin = 14.4375527090118 | erot = 6.91134875336251 | epot = -71.2823381761708 | etot = -49.9334367137965 +777000 ekin = 14.6717866848274 | erot = 7.06376577929917 | epot = -71.6689891775052 | etot = -49.9334367133787 +778000 ekin = 14.7653808590857 | erot = 7.19344155377075 | epot = -71.8922591252416 | etot = -49.9334367123852 +779000 ekin = 14.730693855013 | erot = 7.30529771885497 | epot = -71.9694282850543 | etot = -49.9334367111863 +780000 ekin = 14.5832545302354 | erot = 7.40496111443451 | epot = -71.9216523546833 | etot = -49.9334367100134 +781000 ekin = 14.3388697346797 | erot = 7.49845716245022 | epot = -71.7707636059834 | etot = -49.9334367088535 +782000 ekin = 14.012632236989 | erot = 7.59321586742884 | epot = -71.5392848119177 | etot = -49.9334367074999 +783000 ekin = 13.6198123290852 | erot = 7.69972925708741 | epot = -71.2529782919019 | etot = -49.9334367057293 +784000 ekin = 13.1775031485212 | erot = 7.83255954691441 | epot = -70.9434993989344 | etot = -49.9334367034988 +785000 ekin = 12.7055342140841 | erot = 8.00936494240152 | epot = -70.648335857571 | etot = -49.9334367010853 +786000 ekin = 12.2248371391007 | erot = 8.24851507754314 | epot = -70.4067889156156 | etot = -49.9334366989718 +787000 ekin = 11.7555342913329 | erot = 8.56369046309548 | epot = -70.2526614521278 | etot = -49.9334366976994 +788000 ekin = 11.3126236422298 | erot = 8.96026774265187 | epot = -70.2063280824941 | etot = -49.9334366976124 +789000 ekin = 10.9031119972051 | erot = 9.43314525738494 | epot = -70.269693953305 | etot = -49.9334366987149 +790000 ekin = 10.5250635297466 | erot = 9.9675348458216 | epot = -70.4260350762463 | etot = -49.9334367006781 +791000 ekin = 10.1691331640835 | erot = 10.5422631476455 | epot = -70.6448330147032 | etot = -49.9334367029742 +792000 ekin = 9.82205839233272 | erot = 11.1341190394736 | epot = -70.889614136888 | etot = -49.9334367050817 +793000 ekin = 9.47084478061163 | erot = 11.7217151487463 | epot = -71.1259966359825 | etot = -49.9334367066245 +794000 ekin = 9.10632235966735 | erot = 12.2880425704295 | epot = -71.3278016375495 | etot = -49.9334367074527 +795000 ekin = 8.72525787161047 | erot = 12.8212831283708 | epot = -71.4799777074429 | etot = -49.9334367074616 +796000 ekin = 8.33088740352323 | erot = 13.3158307221971 | epot = -71.5801548324682 | etot = -49.9334367067479 +797000 ekin = 7.93221366070309 | erot = 13.7725019330702 | epot = -71.6381522992101 | etot = -49.9334367054368 +798000 ekin = 7.54257513537372 | erot = 14.1976537465394 | epot = -71.6736655856302 | etot = -49.9334367037171 +799000 ekin = 7.17781194150715 | erot = 14.6018729765565 | epot = -71.7131216199341 | etot = -49.9334367018705 +800000 ekin = 6.85418083665888 | erot = 14.9975945327312 | epot = -71.7852120695712 | etot = -49.9334367001811 +801000 ekin = 6.58592787556476 | erot = 15.3953862375861 | epot = -71.9147508125572 | etot = -49.9334366994063 +802000 ekin = 6.38182484891886 | erot = 15.7994624725331 | epot = -72.1147240206144 | etot = -49.9334366991624 +803000 ekin = 6.24578962491507 | erot = 16.2061575172937 | epot = -72.3853838428568 | etot = -49.933436700648 +804000 ekin = 6.17330996103834 | erot = 16.5988082575579 | epot = -72.705554922415 | etot = -49.9334367038188 +805000 ekin = 6.15098228402561 | erot = 16.9456603306619 | epot = -73.0300793226669 | etot = -49.9334367079793 +806000 ekin = 6.15947173672835 | erot = 17.204465643924 | epot = -73.2973740932042 | etot = -49.9334367125519 +807000 ekin = 6.17750077526089 | erot = 17.3287749580178 | epot = -73.4397124498275 | etot = -49.9334367165488 +808000 ekin = 6.18647751295405 | erot = 17.2774290380355 | epot = -73.3973432699773 | etot = -49.9334367189878 +809000 ekin = 6.17461069446069 | erot = 17.0246492195491 | epot = -73.1326966332165 | etot = -49.9334367192067 +810000 ekin = 6.13919982879456 | erot = 16.5673936172911 | epot = -72.6400301631896 | etot = -49.933436717104 +811000 ekin = 6.08590405422783 | erot = 15.9262499108383 | epot = -71.9455906783194 | etot = -49.9334367132534 +812000 ekin = 6.02727840079 | erot = 15.1427857222595 | epot = -71.1035008312158 | etot = -49.9334367081663 +813000 ekin = 5.97994559138709 | erot = 14.2732350592946 | epot = -70.1866173535962 | etot = -49.9334367029146 +814000 ekin = 5.96019407075526 | erot = 13.3776408789709 | epot = -69.2712716479184 | etot = -49.9334366981922 +815000 ekin = 5.98147951144783 | erot = 12.5120766101507 | epot = -68.4269928159851 | etot = -49.9334366943865 +816000 ekin = 6.05315781455285 | erot = 11.7238262965607 | epot = -67.710420802737 | etot = -49.9334366916234 +817000 ekin = 6.18015071648599 | erot = 11.0493436793551 | epot = -67.1629310857236 | etot = -49.9334366898825 +818000 ekin = 6.3634320933152 | erot = 10.5142840563038 | epot = -66.8111528386133 | etot = -49.9334366889943 +819000 ekin = 6.60007567205162 | erot = 10.1338232847715 | epot = -66.6673356460786 | etot = -49.9334366892555 +820000 ekin = 6.88150211743858 | erot = 9.91159836404286 | epot = -66.7265371718921 | etot = -49.9334366904106 +821000 ekin = 7.19506666882379 | erot = 9.84129146074887 | epot = -66.969794821999 | etot = -49.9334366924264 +822000 ekin = 7.52435980178613 | erot = 9.90716288825253 | epot = -67.3649593852532 | etot = -49.9334366952145 +823000 ekin = 7.84992228277147 | erot = 10.0851600965204 | epot = -67.8685190771807 | etot = -49.9334366978889 +824000 ekin = 8.15279302392839 | erot = 10.3470779179228 | epot = -68.4333076432256 | etot = -49.9334367013745 +825000 ekin = 8.41311666021598 | erot = 10.6607446583175 | epot = -69.0072980232389 | etot = -49.9334367047055 +826000 ekin = 8.61249186814264 | erot = 10.9940344469789 | epot = -69.5399630224921 | etot = -49.9334367073706 +827000 ekin = 8.73743000150763 | erot = 11.3203117200469 | epot = -69.9911784304707 | etot = -49.9334367089162 +828000 ekin = 8.78189553875811 | erot = 11.6226054161918 | epot = -70.3379376640229 | etot = -49.933436709073 +829000 ekin = 8.7490083554955 | erot = 11.8958537707843 | epot = -70.5782988341314 | etot = -49.9334367078516 +830000 ekin = 8.65139592842453 | erot = 12.1464179476435 | epot = -70.7312505816181 | etot = -49.93343670555 +831000 ekin = 8.5049427767622 | erot = 12.3857635082366 | epot = -70.824142989187 | etot = -49.9334367041882 +832000 ekin = 8.32916055642671 | erot = 12.6288888017249 | epot = -70.8914860593735 | etot = -49.9334367012219 +833000 ekin = 8.15183535333848 | erot = 12.8934079010539 | epot = -70.9786799532708 | etot = -49.9334366988784 +834000 ekin = 7.99907278376575 | erot = 13.1899071858843 | epot = -71.1224166672267 | etot = -49.9334366975767 +835000 ekin = 7.8918783520446 | erot = 13.51888698887 | epot = -71.3442020384175 | etot = -49.9334366975029 +836000 ekin = 7.84388537229555 | erot = 13.8699943193951 | epot = -71.6473163903007 | etot = -49.9334366986101 +837000 ekin = 7.86044932601213 | erot = 14.2233719535747 | epot = -72.0172579802332 | etot = -49.9334367006464 +838000 ekin = 7.93910809383378 | erot = 14.5528008610184 | epot = -72.425345658041 | etot = -49.9334367031888 +839000 ekin = 8.07122306537679 | erot = 14.8302605050415 | epot = -72.8349202761183 | etot = -49.9334367057 +840000 ekin = 8.2444655423568 | erot = 15.0313446268275 | epot = -73.2092468768182 | etot = -49.9334367076339 +841000 ekin = 8.44565195528976 | erot = 15.1405292660009 | epot = -73.5196179298625 | etot = -49.9334367085719 +842000 ekin = 8.66328937904598 | erot = 15.1548179227718 | epot = -73.7515440101925 | etot = -49.9334367083748 +843000 ekin = 8.8892070628438 | erot = 15.0843018299111 | epot = -73.9069456000073 | etot = -49.9334367072525 +844000 ekin = 9.11892160102442 | erot = 14.9490168365956 | epot = -74.0013751433164 | etot = -49.9334367056964 +845000 ekin = 9.35084016236178 | erot = 14.7729101070013 | epot = -74.05718697366 | etot = -49.9334367042969 +846000 ekin = 9.58480624612782 | erot = 14.5769727649397 | epot = -74.0952157145914 | etot = -49.9334367035239 +847000 ekin = 9.82062376128124 | erot = 14.3739562460594 | epot = -74.1280167109161 | etot = -49.9334367035755 +848000 ekin = 10.0570459043257 | erot = 14.1664338893076 | epot = -74.156916497965 | etot = -49.9334367043317 +849000 ekin = 10.2914310227017 | erot = 13.9486330728702 | epot = -74.1735008010071 | etot = -49.9334367054352 +850000 ekin = 10.5200017142957 | erot = 13.7110119886428 | epot = -74.1644504093987 | etot = -49.9334367064603 +851000 ekin = 10.7384803462379 | erot = 13.4455029516737 | epot = -74.1174200050005 | etot = -49.9334367070889 +852000 ekin = 10.9428323033991 | erot = 13.1491363437732 | epot = -74.0254053544163 | etot = -49.933436707244 +853000 ekin = 11.1299150793994 | erot = 12.8245768790877 | epot = -73.8879286655677 | etot = -49.9334367070806 +854000 ekin = 11.2979634933129 | erot = 12.4776173943457 | epot = -73.7090175945331 | etot = -49.9334367068744 +855000 ekin = 11.446963766283 | erot = 12.1131194462544 | epot = -73.4935199194024 | etot = -49.933436706865 +856000 ekin = 11.5790087133663 | erot = 11.7315500677249 | epot = -73.2439954882093 | etot = -49.9334367071181 +857000 ekin = 11.6987080002491 | erot = 11.3281299269516 | epot = -72.9602746334633 | etot = -49.9334367062627 +858000 ekin = 11.8142530286861 | erot = 10.901031121527 | epot = -72.6487208569823 | etot = -49.9334367067692 +859000 ekin = 11.9332104303187 | erot = 10.4445616968173 | epot = -72.3112088339654 | etot = -49.9334367068294 +860000 ekin = 12.0636090868394 | erot = 9.95521311106996 | epot = -71.9522589040587 | etot = -49.9334367061494 +861000 ekin = 12.2139179047323 | erot = 9.44036583177209 | epot = -71.5877204411663 | etot = -49.9334367046619 +862000 ekin = 12.3911302810443 | erot = 8.92087657030383 | epot = -71.2454435539794 | etot = -49.9334367026313 +863000 ekin = 12.5982733631874 | erot = 8.42930400279383 | epot = -70.9610140666498 | etot = -49.9334367006686 +864000 ekin = 12.831852804783 | erot = 8.00321132274768 | epot = -70.768500827096 | etot = -49.9334366995654 +865000 ekin = 13.0802810159932 | erot = 7.67501011452693 | epot = -70.6887278304442 | etot = -49.933436699924 +866000 ekin = 13.3258003937717 | erot = 7.46434239394174 | epot = -70.723579487828 | etot = -49.9334367001145 +867000 ekin = 13.5483777058287 | erot = 7.37573702192118 | epot = -70.8575514306229 | etot = -49.933436702873 +868000 ekin = 13.7260761156947 | erot = 7.39264351054933 | epot = -71.0521563312998 | etot = -49.9334367050558 +869000 ekin = 13.8458058823138 | erot = 7.49414572985504 | epot = -71.2733883181141 | etot = -49.9334367059453 +870000 ekin = 13.9046600886285 | erot = 7.66358743007335 | epot = -71.5016842268922 | etot = -49.9334367081903 +871000 ekin = 13.8960585004465 | erot = 7.88733345658181 | epot = -71.7168286647946 | etot = -49.9334367077664 +872000 ekin = 13.8246751721402 | erot = 8.15489545476625 | epot = -71.9130073341014 | etot = -49.9334367071949 +873000 ekin = 13.7011361659621 | erot = 8.45583645757423 | epot = -72.09040933028 | etot = -49.9334367067436 +874000 ekin = 13.5424081255665 | erot = 8.77750687622158 | epot = -72.2533517069974 | etot = -49.9334367052094 +875000 ekin = 13.3641904898362 | erot = 9.10395551734411 | epot = -72.4015827123631 | etot = -49.9334367051827 +876000 ekin = 13.1761666319033 | erot = 9.4189692580622 | epot = -72.5285725948025 | etot = -49.9334367048371 +877000 ekin = 12.989733153409 | erot = 9.70973691407686 | epot = -72.6329067715772 | etot = -49.9334367040914 +878000 ekin = 12.8170836818463 | erot = 9.96795108599851 | epot = -72.7184714713864 | etot = -49.9334367035416 +879000 ekin = 12.6680681076849 | erot = 10.1869039997134 | epot = -72.7884088106613 | etot = -49.933436703263 +880000 ekin = 12.5485677829416 | erot = 10.360172238643 | epot = -72.8421767251618 | etot = -49.9334367035772 +881000 ekin = 12.4586640761212 | erot = 10.4797974742167 | epot = -72.871898254959 | etot = -49.9334367046212 +882000 ekin = 12.3916540723878 | erot = 10.5354740122172 | epot = -72.8605647908176 | etot = -49.9334367062126 +883000 ekin = 12.3349006012333 | erot = 10.5163792201282 | epot = -72.784716529318 | etot = -49.9334367079565 +884000 ekin = 12.2717096494548 | erot = 10.4148307307664 | epot = -72.6199770891965 | etot = -49.9334367089752 +885000 ekin = 12.1859999114775 | erot = 10.2325314579947 | epot = -72.3519680786886 | etot = -49.9334367092164 +886000 ekin = 12.0660600094667 | erot = 9.98113360782834 | epot = -71.980630324472 | etot = -49.933436707177 +887000 ekin = 11.9066640240886 | erot = 9.69017126637074 | epot = -71.5302719956084 | etot = -49.9334367051491 +888000 ekin = 11.7031668864977 | erot = 9.40001855012972 | epot = -71.0366221381431 | etot = -49.9334367015157 +889000 ekin = 11.4630530594946 | erot = 9.15343792253717 | epot = -70.5499276802314 | etot = -49.9334366981996 +890000 ekin = 11.1987209290775 | erot = 8.98605396753113 | epot = -70.1182115923965 | etot = -49.9334366957879 +891000 ekin = 10.9233111472025 | erot = 8.92029234168423 | epot = -69.7770401833661 | etot = -49.9334366944794 +892000 ekin = 10.6492398277695 | erot = 8.96369676357743 | epot = -69.5463732855374 | etot = -49.9334366941905 +893000 ekin = 10.3877929472456 | erot = 9.11033168329062 | epot = -69.431561325202 | etot = -49.9334366946658 +894000 ekin = 10.1494275348444 | erot = 9.34401274104991 | epot = -69.4268769714607 | etot = -49.9334366955664 +895000 ekin = 9.94444446372759 | erot = 9.64226259712003 | epot = -69.5201437574336 | etot = -49.933436696586 +896000 ekin = 9.78365577864041 | erot = 9.98061881115325 | epot = -69.6977112871638 | etot = -49.9334366973702 +897000 ekin = 9.67858194014779 | erot = 10.3366132209055 | epot = -69.9486318588918 | etot = -49.9334366978385 +898000 ekin = 9.64075567540845 | erot = 10.6919016549755 | epot = -70.2660940284665 | etot = -49.9334366980826 +899000 ekin = 9.68004571016644 | erot = 11.0326643705369 | epot = -70.6461467790468 | etot = -49.9334366983435 +900000 ekin = 9.80242718993076 | erot = 11.3484734126709 | epot = -71.084337301492 | etot = -49.9334366988904 +901000 ekin = 10.0079867841216 | erot = 11.6305317090574 | epot = -71.5719551930728 | etot = -49.9334366998938 +902000 ekin = 10.28991293803 | erot = 11.8702049221031 | epot = -72.0935545615133 | etot = -49.9334367013802 +903000 ekin = 10.6348280320447 | erot = 12.0586224306225 | epot = -72.6268871658226 | etot = -49.9334367031554 +904000 ekin = 11.0243272479324 | erot = 12.1875535947934 | epot = -73.145317547711 | etot = -49.9334367049852 +905000 ekin = 11.4372262794084 | erot = 12.2506292976041 | epot = -73.6212922836315 | etot = -49.933436706619 +906000 ekin = 11.8518934288994 | erot = 12.2446242606477 | epot = -74.0299543974295 | etot = -49.9334367078824 +907000 ekin = 12.2481266389201 | erot = 12.1701657665188 | epot = -74.351729114148 | etot = -49.9334367087091 +908000 ekin = 12.6082582209218 | erot = 12.0316322966321 | epot = -74.5733272267001 | etot = -49.9334367091463 +909000 ekin = 12.917445581968 | erot = 11.8363878398617 | epot = -74.6872701311254 | etot = -49.9334367092957 +910000 ekin = 13.1633580105045 | erot = 11.5937735117952 | epot = -74.6905682315581 | etot = -49.9334367092584 +911000 ekin = 13.3356415621017 | erot = 11.3143470991352 | epot = -74.5834253703139 | etot = -49.933436709077 +912000 ekin = 13.425596568237 | erot = 11.0097178906581 | epot = -74.3687511676035 | etot = -49.9334367087083 +913000 ekin = 13.4301864972375 | erot = 10.6932440962164 | epot = -74.056867299607 | etot = -49.9334367061531 +914000 ekin = 13.3769940125857 | erot = 10.3811500400916 | epot = -73.6915807586478 | etot = -49.9334367059705 +915000 ekin = 13.2641557141347 | erot = 10.0882130475995 | epot = -73.2858054672313 | etot = -49.933436705497 +916000 ekin = 13.0837312497424 | erot = 9.83018237236329 | epot = -72.8473503269087 | etot = -49.9334367048031 +917000 ekin = 12.8312481510179 | erot = 9.62294454951148 | epot = -72.3876294045856 | etot = -49.9334367040562 +918000 ekin = 12.5057291534266 | erot = 9.48024983823758 | epot = -71.9194156950861 | etot = -49.9334367034219 +919000 ekin = 12.1093169180432 | erot = 9.41163285905158 | epot = -71.4543864807244 | etot = -49.9334367036296 +920000 ekin = 11.6422865006934 | erot = 9.42287047205446 | epot = -70.9985936755824 | etot = -49.9334367028345 +921000 ekin = 11.1169457295372 | erot = 9.51466229501161 | epot = -70.5650447264646 | etot = -49.9334367019158 +922000 ekin = 10.5550472140296 | erot = 9.68352501363233 | epot = -70.1720089283617 | etot = -49.9334367006998 +923000 ekin = 9.98441850036398 | erot = 9.92400943507129 | epot = -69.8418646346123 | etot = -49.933436699177 +924000 ekin = 9.43763475528215 | erot = 10.2296922494978 | epot = -69.6007637023709 | etot = -49.933436697591 +925000 ekin = 8.94863290042417 | erot = 10.592921289405 | epot = -69.4749908861711 | etot = -49.9334366963419 +926000 ekin = 8.54812299742105 | erot = 11.003729609764 | epot = -69.4852893029582 | etot = -49.9334366957731 +927000 ekin = 8.25958093087947 | erot = 11.4489178471945 | epot = -69.6419354740825 | etot = -49.9334366960085 +928000 ekin = 8.11336972326081 | erot = 11.9118540028711 | epot = -69.9586604226551 | etot = -49.9334366965232 +929000 ekin = 8.06162796654599 | erot = 12.3783092987422 | epot = -70.3733740125528 | etot = -49.9334367472646 +930000 ekin = 8.11332481200163 | erot = 12.8482520254932 | epot = -70.8950135415971 | etot = -49.9334367041023 +931000 ekin = 8.66218357016193 | erot = 13.2899790801566 | epot = -71.8855994294219 | etot = -49.9334367791033 +932000 ekin = 9.18948394947728 | erot = 13.6579503931781 | epot = -72.7808710530632 | etot = -49.9334367104079 +933000 ekin = 9.79417016839173 | erot = 13.9483173133746 | epot = -73.6759241999747 | etot = -49.9334367182084 +934000 ekin = 10.4207852553787 | erot = 14.1310962185635 | epot = -74.4853181968414 | etot = -49.9334367228992 +935000 ekin = 10.9969920696613 | erot = 14.1631931275595 | epot = -75.0936219236271 | etot = -49.9334367264063 +936000 ekin = 11.4754171704122 | erot = 14.0243625870535 | epot = -75.4332164855681 | etot = -49.9334367281024 +937000 ekin = 11.828115794495 | erot = 13.7138200009053 | epot = -75.4753725232106 | etot = -49.9334367278102 +938000 ekin = 12.0415685894037 | erot = 13.2461818683061 | epot = -75.2211871837423 | etot = -49.9334367260325 +939000 ekin = 12.114582947563 | erot = 12.6496470029865 | epot = -74.6976666731984 | etot = -49.9334367226489 +940000 ekin = 12.0589112708375 | erot = 11.9625634903802 | epot = -73.9549114795693 | etot = -49.9334367183516 +941000 ekin = 11.8960551688751 | erot = 11.228842334653 | epot = -73.0583342171364 | etot = -49.9334367136083 +942000 ekin = 11.6544532359061 | erot = 10.4934965269952 | epot = -72.081386471699 | etot = -49.9334367087977 +943000 ekin = 11.3669373499361 | erot = 9.79913167083184 | epot = -71.0995057249687 | etot = -49.9334367042008 +944000 ekin = 11.0683221475717 | erot = 9.1835118182396 | epot = -70.1852706658605 | etot = -49.9334367000492 +945000 ekin = 10.7929590511223 | erot = 8.67788366896716 | epot = -69.4042794166669 | etot = -49.9334366965775 +946000 ekin = 10.5720940699664 | erot = 8.30555132204176 | epot = -68.8110820860617 | etot = -49.9334366940535 +947000 ekin = 10.431026077989 | erot = 8.08030170253007 | epot = -68.4447644732885 | etot = -49.9334366927694 +948000 ekin = 10.3863587492407 | erot = 8.00467877116281 | epot = -68.324474213363 | etot = -49.9334366929595 +949000 ekin = 10.443969831977 | erot = 8.06864252756914 | epot = -68.4460490542299 | etot = -49.9334366946837 +950000 ekin = 10.5984527950567 | erot = 8.24950150875679 | epot = -68.781391001546 | etot = -49.9334366977325 +951000 ekin = 10.8345056210697 | erot = 8.51385964371356 | epot = -69.2818019664129 | etot = -49.9334367016296 +952000 ekin = 11.1300987903813 | erot = 8.82166130464103 | epot = -69.885196800763 | etot = -49.9334367057407 +953000 ekin = 11.4620681606301 | erot = 9.13289977458331 | epot = -70.5284046439579 | etot = -49.9334367087445 +954000 ekin = 11.8086055714193 | erot = 9.41351972724564 | epot = -71.1555620102617 | etot = -49.9334367115968 +955000 ekin = 12.1486594940869 | erot = 9.63629965849216 | epot = -71.7183958659123 | etot = -49.9334367133333 +956000 ekin = 12.4666814283382 | erot = 9.78498285392056 | epot = -72.1851009961974 | etot = -49.9334367139387 +957000 ekin = 12.752812250671 | erot = 9.85475378818911 | epot = -72.5410027524423 | etot = -49.9334367135821 +958000 ekin = 13.0020596902883 | erot = 9.85085290315995 | epot = -72.7863493059855 | etot = -49.9334367125373 +959000 ekin = 13.2129949609854 | erot = 9.78594808534103 | epot = -72.9323797574491 | etot = -49.9334367111227 +960000 ekin = 13.38635535286 | erot = 9.67694964959962 | epot = -72.9967417120899 | etot = -49.9334367096303 +961000 ekin = 13.5237851667308 | erot = 9.54187021053885 | epot = -72.9990920855742 | etot = -49.9334367083045 +962000 ekin = 13.626808300571 | erot = 9.39714419142608 | epot = -72.9573891993236 | etot = -49.9334367073265 +963000 ekin = 13.6960515850022 | erot = 9.25563590647102 | epot = -72.8851241982819 | etot = -49.9334367068086 +964000 ekin = 13.7307368673975 | erot = 9.12544546230701 | epot = -72.7896190364922 | etot = -49.9334367067877 +965000 ekin = 13.7285055346103 | erot = 9.00957498548651 | epot = -72.6715172273075 | etot = -49.9334367072107 +966000 ekin = 13.6856873969798 | erot = 8.90650288415293 | epot = -72.5256269890622 | etot = -49.9334367079294 +967000 ekin = 13.5981291269817 | erot = 8.81166698280912 | epot = -72.3432328184944 | etot = -49.9334367087035 +968000 ekin = 13.4626202698355 | erot = 8.71972454046941 | epot = -72.1157815195311 | etot = -49.9334367092262 +969000 ekin = 13.2787926255078 | erot = 8.62723465149127 | epot = -71.8394639861855 | etot = -49.9334367091864 +970000 ekin = 13.0511641579098 | erot = 8.53517282507499 | epot = -71.5197736913331 | etot = -49.9334367083484 +971000 ekin = 12.7908355002666 | erot = 8.45057810217557 | epot = -71.174850309069 | etot = -49.9334367066268 +972000 ekin = 12.5173507598131 | erot = 8.38683939056359 | epot = -70.8376268541913 | etot = -49.9334367038146 +973000 ekin = 12.2569030869208 | erot = 8.36165046183605 | epot = -70.5519902498042 | etot = -49.9334367010474 +974000 ekin = 12.0353982665848 | erot = 8.39463180018019 | epot = -70.3634667670655 | etot = -49.9334367003005 +975000 ekin = 11.8648555975993 | erot = 8.50590727179108 | epot = -70.3041995674616 | etot = -49.9334366980712 +976000 ekin = 11.7661195446394 | erot = 8.70975852581276 | epot = -70.4093147671339 | etot = -49.9334366966818 +977000 ekin = 11.7571606518367 | erot = 9.01267063312532 | epot = -70.7032679815637 | etot = -49.9334366966017 +978000 ekin = 11.8453896777667 | erot = 9.41117900024049 | epot = -71.1900053761314 | etot = -49.9334366981242 +979000 ekin = 12.0246267638124 | erot = 9.89054975622095 | epot = -71.8486132219714 | etot = -49.9334367019381 +980000 ekin = 12.2724364420053 | erot = 10.4232069349804 | epot = -72.6290800837174 | etot = -49.9334367067317 +981000 ekin = 12.5527115605182 | erot = 10.972589006457 | epot = -73.4587372791038 | etot = -49.9334367121286 +982000 ekin = 12.8238225604048 | erot = 11.4997645671859 | epot = -74.2570238448159 | etot = -49.9334367172252 +983000 ekin = 13.0452035724442 | erot = 11.9687211334411 | epot = -74.9473614270525 | etot = -49.9334367211672 +984000 ekin = 13.1839520718259 | erot = 12.352526836999 | epot = -75.4699156321967 | etot = -49.9334367233718 +985000 ekin = 13.2192870401165 | erot = 12.6377038112812 | epot = -75.7904275750641 | etot = -49.9334367236663 +986000 ekin = 13.1441636156278 | erot = 12.825487425815 | epot = -75.9030877637388 | etot = -49.933436722296 +987000 ekin = 12.9766251570008 | erot = 12.9392834379828 | epot = -75.8493453141909 | etot = -49.9334367192073 +988000 ekin = 12.7467127337231 | erot = 13.0092102946437 | epot = -75.6893597461514 | etot = -49.9334367177846 +989000 ekin = 12.4647507866674 | erot = 13.046197342409 | epot = -75.4443848453866 | etot = -49.9334367163102 +990000 ekin = 12.1432494339901 | erot = 13.0601008150464 | epot = -75.1367869640102 | etot = -49.9334367149737 +991000 ekin = 11.7954932887414 | erot = 13.0588078294718 | epot = -74.7877378320025 | etot = -49.9334367137893 +992000 ekin = 11.4345194693503 | erot = 13.0486939330205 | epot = -74.4166501150601 | etot = -49.9334367126893 +993000 ekin = 11.0720454470821 | erot = 13.0357017584289 | epot = -74.0411839174814 | etot = -49.9334367119704 +994000 ekin = 10.7167466981842 | erot = 13.0266560976539 | epot = -73.6768395064945 | etot = -49.9334367106565 +995000 ekin = 10.3805428787761 | erot = 13.0301107633585 | epot = -73.3440903517368 | etot = -49.9334367096022 +996000 ekin = 10.0742873840263 | erot = 13.0528189023139 | epot = -73.0605429952154 | etot = -49.9334367088752 +997000 ekin = 9.80713376353975 | erot = 13.0983026558673 | epot = -72.8388731278965 | etot = -49.9334367084895 +998000 ekin = 9.58681345257386 | erot = 13.1663837793229 | epot = -72.686633940305 | etot = -49.9334367084082 +999000 ekin = 9.4195730226422 | erot = 13.2537863498268 | epot = -72.6067960810353 | etot = -49.9334367085663 +1000000 ekin = 9.30950418557169 | erot = 13.3558388695471 | epot = -72.5987797639821 | etot = -49.9334367088633 + 1000000 347.01619 -80.374455 7.7756755 -63.289276 0.11518501 39304000 +Loop time of 17.7764 on 4 procs for 1000000 steps with 10 atoms + +Performance: 82.918 ns/day, 0.289 hours/ns, 56254.421 timesteps/s, 562.544 katom-step/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.0475 | 7.6302 | 10.252 | 57.4 | 42.92 +Bond | 0.22588 | 0.32246 | 0.42602 | 12.9 | 1.81 +Neigh | 0.007601 | 0.007642 | 0.007702 | 0.0 | 0.04 +Comm | 3.9938 | 7.0574 | 8.7017 | 68.2 | 39.70 +Output | 0.07165 | 0.07691 | 0.088092 | 2.4 | 0.43 +Modify | 0.60223 | 0.70805 | 0.84637 | 11.9 | 3.98 +Other | | 1.974 | | | 11.10 + +Nlocal: 2.5 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 8 max 7 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25 ave 15 max 2 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:17 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/data.duplex2 new file mode 100644 index 0000000000..78a6fdd51a --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0 +2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0 +3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0 +4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0 +5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0 +6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0 +7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0 +8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0 +9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0 +10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0 +11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0 +12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0 +13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0 +14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0 +15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0 +16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447 +2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514 +3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762 +4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703 +5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389 +6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085 +7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256 +8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774 +9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824 +10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333 +11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933 +12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927 +13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526 +14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926 +15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399 +16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/in.duplex2 new file mode 100644 index 0000000000..69025d2ae2 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/in.duplex2 @@ -0,0 +1,73 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.1 new file mode 100644 index 0000000000..a0e4dabd93 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.1 @@ -0,0 +1,1188 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -125.483166681887 | etot = -92.6645914514141 +Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -129.82524 4.3420686 -109.36284 0.039706925 39304000 +1000 ekin = 16.1153280108143 | erot = 15.5197830189416 | epot = -124.555012078315 | etot = -92.9199010485588 +2000 ekin = 15.772246419827 | erot = 15.1139636185383 | epot = -123.879088875298 | etot = -92.9928788369323 +3000 ekin = 16.0773390725189 | erot = 15.209959103884 | epot = -123.489559526102 | etot = -92.2022613496986 +4000 ekin = 15.8173041766846 | erot = 14.7611030291702 | epot = -123.285245732656 | etot = -92.7068385268011 +5000 ekin = 15.4977817476135 | erot = 13.136888034624 | epot = -123.146472671991 | etot = -94.511802889753 +6000 ekin = 14.7156620894482 | erot = 14.7421516126936 | epot = -123.022223364177 | etot = -93.5644096620347 +7000 ekin = 14.9944296549912 | erot = 13.783162042227 | epot = -123.190008596649 | etot = -94.4124168994313 +8000 ekin = 15.4784069740882 | erot = 13.849436282597 | epot = -123.501589669336 | etot = -94.1737464126508 +9000 ekin = 14.8187016230064 | erot = 12.4172590954619 | epot = -123.977782239857 | etot = -96.7418215213889 +10000 ekin = 15.0274879557549 | erot = 13.1218082157407 | epot = -124.599335647018 | etot = -96.4500394755227 +11000 ekin = 14.4931845632981 | erot = 14.4826290329821 | epot = -125.349370552054 | etot = -96.3735569557737 +12000 ekin = 14.6238652440025 | erot = 15.0566784473206 | epot = -126.147676000969 | etot = -96.4671323096456 +13000 ekin = 15.137690408925 | erot = 16.3735083921761 | epot = -126.783622343916 | etot = -95.2724235428147 +14000 ekin = 15.0736340167339 | erot = 17.9580151111454 | epot = -127.212455694657 | etot = -94.1808065667773 +15000 ekin = 15.6847409974466 | erot = 16.4414105500024 | epot = -127.359697666437 | etot = -95.2335461189881 +16000 ekin = 15.101909613666 | erot = 17.5942742553051 | epot = -127.202183128007 | etot = -94.5059992590364 +17000 ekin = 15.3727376562683 | erot = 19.1091811430074 | epot = -126.813728712217 | etot = -92.3318099129414 +18000 ekin = 14.8374011694519 | erot = 19.7017705490592 | epot = -126.30449141107 | etot = -91.7653196925591 +19000 ekin = 15.1981564010543 | erot = 18.6439998775122 | epot = -125.672872041634 | etot = -91.830715763067 +20000 ekin = 16.1151841084727 | erot = 20.7585939815706 | epot = -124.972087929324 | etot = -88.0983098392806 +21000 ekin = 16.3338477714416 | erot = 20.8240546257147 | epot = -124.366832858554 | etot = -87.2089304613976 +22000 ekin = 16.1322150698349 | erot = 20.2134381799286 | epot = -123.905804890148 | etot = -87.5601516403842 +23000 ekin = 16.5115128572444 | erot = 17.6994160203144 | epot = -123.55564726802 | etot = -89.3447183904615 +24000 ekin = 16.1352983796458 | erot = 16.3149199437269 | epot = -123.442319677191 | etot = -90.9921013538185 +25000 ekin = 16.022085347148 | erot = 15.583100483768 | epot = -123.449358919593 | etot = -91.8441730886766 +26000 ekin = 16.2893661316802 | erot = 16.2928134270855 | epot = -123.576521595326 | etot = -90.9943420365607 +27000 ekin = 16.7390245507423 | erot = 15.3238654831856 | epot = -123.731718503694 | etot = -91.6688284697663 +28000 ekin = 16.2177081340479 | erot = 14.8307563153175 | epot = -123.99220492136 | etot = -92.9437404719943 +29000 ekin = 16.394983535328 | erot = 14.5241463812386 | epot = -124.513314221131 | etot = -93.5941843045643 +30000 ekin = 16.9754617608551 | erot = 15.2543913785552 | epot = -125.219970033943 | etot = -92.9901168945324 +31000 ekin = 17.5126083496296 | erot = 16.0100732675228 | epot = -126.062415056418 | etot = -92.5397334392652 +32000 ekin = 18.5712292997905 | erot = 16.206627396287 | epot = -126.997383457792 | etot = -92.2195267617144 +33000 ekin = 20.3914733420706 | erot = 17.95620789524 | epot = -127.853083619434 | etot = -89.5054023821237 +34000 ekin = 20.6113627375719 | erot = 19.9540488404715 | epot = -128.630184260389 | etot = -88.0647726823456 +35000 ekin = 20.8360942975504 | erot = 18.7186151968505 | epot = -129.138353151477 | etot = -89.583643657076 +36000 ekin = 20.6985051785528 | erot = 16.975623481333 | epot = -129.307575419352 | etot = -91.6334467594659 +37000 ekin = 20.5167811486514 | erot = 15.2755543486072 | epot = -129.197321856118 | etot = -93.4049863588594 +38000 ekin = 21.1497608417914 | erot = 14.5576638198861 | epot = -128.930481489255 | etot = -93.2230568275779 +39000 ekin = 20.6746026905741 | erot = 14.3039991212366 | epot = -128.401411971525 | etot = -93.4228101597146 +40000 ekin = 20.2458392603998 | erot = 12.3350344432048 | epot = -127.685777608123 | etot = -95.1049039045185 +41000 ekin = 19.9443359632547 | erot = 12.5780453533769 | epot = -127.034234533918 | etot = -94.5118532172866 +42000 ekin = 18.7142138659613 | erot = 15.6025018660211 | epot = -126.430389989682 | etot = -92.1136742577 +43000 ekin = 18.2011859622276 | erot = 12.9029481737254 | epot = -125.805728672502 | etot = -94.7015945365485 +44000 ekin = 17.0231621476026 | erot = 13.3229275319614 | epot = -125.306302559716 | etot = -94.9602128801516 +45000 ekin = 16.152368779228 | erot = 13.1425819599688 | epot = -125.010262919191 | etot = -95.7153121799937 +46000 ekin = 16.7021752482541 | erot = 14.1252164671804 | epot = -124.733270572736 | etot = -93.9058788573016 +47000 ekin = 15.99784829344 | erot = 13.7601120378058 | epot = -124.690287962324 | etot = -94.9323276310783 +48000 ekin = 15.5197793757419 | erot = 12.9242805215039 | epot = -124.828892248156 | etot = -96.3848323509101 +49000 ekin = 16.0883502578865 | erot = 11.6460670991824 | epot = -125.077169952033 | etot = -97.3427525949638 +50000 ekin = 16.5910827451326 | erot = 10.3658274796462 | epot = -125.343780614919 | etot = -98.3868703901406 +51000 ekin = 16.6472854601222 | erot = 10.477376420409 | epot = -125.554004771147 | etot = -98.4293428906161 +52000 ekin = 17.5155585277601 | erot = 12.2350226754088 | epot = -125.797409563523 | etot = -96.0468283603543 +53000 ekin = 17.4722415449292 | erot = 13.1927275265022 | epot = -126.040236812772 | etot = -95.3752677413405 +54000 ekin = 17.6076594913864 | erot = 13.1614957800302 | epot = -126.29136443309 | etot = -95.5222091616737 +55000 ekin = 17.8100170030173 | erot = 14.1252425722699 | epot = -126.659390094792 | etot = -94.7241305195052 +56000 ekin = 17.8387492196087 | erot = 14.0302618957366 | epot = -126.997375569247 | etot = -95.1283644539021 +57000 ekin = 18.1401351862027 | erot = 12.5711347601677 | epot = -127.202256599684 | etot = -96.4909866533135 +58000 ekin = 17.7813245596444 | erot = 12.7191555553695 | epot = -127.338590294723 | etot = -96.8381101797093 +59000 ekin = 17.3503839581068 | erot = 14.1146045471954 | epot = -127.355017342212 | etot = -95.8900288369098 +60000 ekin = 17.7216299019791 | erot = 15.1536630383833 | epot = -127.187386794376 | etot = -94.3120938540139 +61000 ekin = 17.6941198173267 | erot = 14.8383509334028 | epot = -126.818610986476 | etot = -94.2861402357464 +62000 ekin = 17.5641418897184 | erot = 13.0033976525466 | epot = -126.314451969138 | etot = -95.7469124268735 +63000 ekin = 18.0478257135008 | erot = 12.8783262794927 | epot = -125.770715790686 | etot = -94.8445637976929 +64000 ekin = 19.1312112805444 | erot = 12.3333582641774 | epot = -125.534785996931 | etot = -94.0702164522088 +65000 ekin = 19.2188096461596 | erot = 11.534140380085 | epot = -125.40389945946 | etot = -94.6509494332154 +66000 ekin = 18.5078500027816 | erot = 11.5846652158613 | epot = -125.504956118775 | etot = -95.4124409001317 +67000 ekin = 18.638156151796 | erot = 13.7030208647307 | epot = -125.838860350819 | etot = -93.4976833342926 +68000 ekin = 17.8865475786144 | erot = 12.1697153221337 | epot = -126.27822517768 | etot = -96.2219622769318 +69000 ekin = 17.5219063470627 | erot = 12.4929246770787 | epot = -126.717736182271 | etot = -96.7029051581301 +70000 ekin = 17.5814052632097 | erot = 12.0656944954174 | epot = -127.122334765233 | etot = -97.4752350066057 +71000 ekin = 17.6186651902907 | erot = 11.805625199446 | epot = -127.543345427813 | etot = -98.1190550380765 +72000 ekin = 18.0718508623175 | erot = 9.77749946391409 | epot = -127.989924738645 | etot = -100.140574412413 +73000 ekin = 19.0920485574284 | erot = 10.888821079169 | epot = -128.359908178953 | etot = -98.3790385423553 +74000 ekin = 19.2389264009398 | erot = 11.2795143076653 | epot = -128.562954573251 | etot = -98.0445138646455 +75000 ekin = 19.6112927877196 | erot = 11.317568594913 | epot = -128.661300438151 | etot = -97.7324390555186 +76000 ekin = 19.6492516668936 | erot = 11.1717966410452 | epot = -128.559946485653 | etot = -97.7388981777141 +77000 ekin = 21.1068514097441 | erot = 10.4729843548249 | epot = -128.202251226815 | etot = -96.6224154622463 +78000 ekin = 21.1227025352881 | erot = 10.5460147355503 | epot = -127.582218749235 | etot = -95.9135014783966 +79000 ekin = 21.1634476662608 | erot = 11.412795878689 | epot = -126.699422157225 | etot = -94.123178612275 +80000 ekin = 20.5411068465151 | erot = 9.28280579073373 | epot = -125.813611671359 | etot = -95.9896990341104 +81000 ekin = 20.2127188226421 | erot = 8.68741517076759 | epot = -125.052171926345 | etot = -96.1520379329351 +82000 ekin = 19.5639253627065 | erot = 8.24811185652522 | epot = -124.593340202665 | etot = -96.7813029834335 +83000 ekin = 19.5018897695322 | erot = 9.63479707897837 | epot = -124.407709264664 | etot = -95.2710224161539 +84000 ekin = 19.3027647164262 | erot = 9.42639051222035 | epot = -124.334250370385 | etot = -95.6050951417389 +85000 ekin = 19.0487713310452 | erot = 9.79542315457042 | epot = -124.252398919893 | etot = -95.4082044342771 +86000 ekin = 19.3694172993635 | erot = 11.2986506313883 | epot = -124.198542654273 | etot = -93.5304747235215 +87000 ekin = 18.6713589438551 | erot = 11.5853232812429 | epot = -124.290853730472 | etot = -94.0341715053737 +88000 ekin = 18.5500451464139 | erot = 10.655919965597 | epot = -124.63664155045 | etot = -95.4306764384394 +89000 ekin = 18.3872263818112 | erot = 9.75329564920108 | epot = -125.028859357009 | etot = -96.8883373259966 +90000 ekin = 19.0994515181362 | erot = 11.6206668977449 | epot = -125.599576758451 | etot = -94.87945834257 +91000 ekin = 18.762458694279 | erot = 13.4916962121932 | epot = -126.260965836519 | etot = -94.0068109300465 +92000 ekin = 19.2847330458389 | erot = 14.2203422707944 | epot = -127.023086031573 | etot = -93.5180107149399 +93000 ekin = 19.5504808602138 | erot = 13.2606408217758 | epot = -127.650916011537 | etot = -94.839794329547 +94000 ekin = 19.7629848910551 | erot = 12.7340289593159 | epot = -128.193890026322 | etot = -95.6968761759514 +95000 ekin = 19.5164573312404 | erot = 14.1994672700034 | epot = -128.871597081462 | etot = -95.1556724802185 +96000 ekin = 19.2181154642271 | erot = 15.1758927231988 | epot = -129.560918567207 | etot = -95.1669103797815 +97000 ekin = 19.2828087523966 | erot = 15.748540644312 | epot = -130.239899181154 | etot = -95.208549784446 +98000 ekin = 19.130898096078 | erot = 15.9200598142929 | epot = -130.857091082761 | etot = -95.8061331723896 +99000 ekin = 18.5810737782702 | erot = 17.3321684743508 | epot = -131.447004089924 | etot = -95.5337618373029 +100000 ekin = 18.0800633544481 | erot = 17.7023518077182 | epot = -132.024865631774 | etot = -96.2424504696075 +101000 ekin = 17.5896052041272 | erot = 17.1959075049022 | epot = -132.357834696272 | etot = -97.5723219872429 +102000 ekin = 17.0192077298915 | erot = 18.9771880159657 | epot = -132.313152428828 | etot = -96.3167566829707 +103000 ekin = 16.9032784353035 | erot = 18.5152697805926 | epot = -131.919415232451 | etot = -96.500867016555 +104000 ekin = 16.3450502985469 | erot = 16.4796871078877 | epot = -131.372601946296 | etot = -98.5478645398611 +105000 ekin = 16.0157880251461 | erot = 14.5137387234916 | epot = -130.690178340474 | etot = -100.160651591836 +106000 ekin = 15.2781681840949 | erot = 12.2178930878269 | epot = -130.108516100693 | etot = -102.612454828772 +107000 ekin = 14.6195965363415 | erot = 14.0419438496236 | epot = -129.597025617775 | etot = -100.93548523181 +108000 ekin = 15.1311776564956 | erot = 14.392205366199 | epot = -129.226898397379 | etot = -99.703515374684 +109000 ekin = 14.7526348132911 | erot = 13.3877709003095 | epot = -128.961214437226 | etot = -100.820808723625 +110000 ekin = 14.9215683172472 | erot = 11.1115528281189 | epot = -128.900162697442 | etot = -102.867041552076 +111000 ekin = 15.2178285635409 | erot = 11.5265219530728 | epot = -129.02264735669 | etot = -102.278296840076 +112000 ekin = 15.3540615689254 | erot = 11.0854135027605 | epot = -129.156449565022 | etot = -102.716974493336 +113000 ekin = 15.4065622254168 | erot = 9.93115052586711 | epot = -129.264775093603 | etot = -103.927062342319 +114000 ekin = 15.7255993115367 | erot = 11.1268632736623 | epot = -129.296474102219 | etot = -102.44401151702 +115000 ekin = 15.2547531671349 | erot = 11.6530061146701 | epot = -129.424954691359 | etot = -102.517195409554 +116000 ekin = 15.5019695068328 | erot = 11.8342564956936 | epot = -129.611475879022 | etot = -102.275249876496 +117000 ekin = 15.7229455518224 | erot = 12.8683161616472 | epot = -129.846111796993 | etot = -101.254850083523 +118000 ekin = 15.9368151241017 | erot = 12.3779048180477 | epot = -130.050496350427 | etot = -101.735776408277 +119000 ekin = 17.361257323721 | erot = 11.8518613557714 | epot = -130.196521073721 | etot = -100.983402394229 +120000 ekin = 17.5338424127199 | erot = 11.9133772725297 | epot = -130.267749385737 | etot = -100.820529700487 +121000 ekin = 18.1732043783987 | erot = 12.8282861983004 | epot = -130.286986417184 | etot = -99.2854958404852 +122000 ekin = 18.0099423653346 | erot = 12.4654600731294 | epot = -130.383884542817 | etot = -99.9084821043533 +123000 ekin = 17.8506031517267 | erot = 10.5503100490201 | epot = -130.596614601186 | etot = -102.195701400439 +124000 ekin = 17.6710243181817 | erot = 11.7129267154528 | epot = -130.763489485464 | etot = -101.379538451829 +125000 ekin = 17.7891709571639 | erot = 9.81386685043019 | epot = -130.931886974658 | etot = -103.328849167064 +126000 ekin = 17.8350392396833 | erot = 10.4705584397578 | epot = -131.222622366146 | etot = -102.917024686705 +127000 ekin = 18.1416438253932 | erot = 11.0182198075673 | epot = -131.446798072859 | etot = -102.286934439898 +128000 ekin = 18.8582437184471 | erot = 11.8401049533331 | epot = -131.795067249695 | etot = -101.096718577915 +129000 ekin = 18.8650300802711 | erot = 11.7918190138826 | epot = -132.119265989036 | etot = -101.462416894882 +130000 ekin = 18.4257823677809 | erot = 15.0299466324866 | epot = -132.288573044193 | etot = -98.8328440439252 +131000 ekin = 18.1437894207897 | erot = 16.5103668803409 | epot = -132.315884341679 | etot = -97.6617280405481 +132000 ekin = 17.7512583058201 | erot = 15.4247935235789 | epot = -132.043801623743 | etot = -98.8677497943437 +133000 ekin = 18.084680831884 | erot = 14.8524353891271 | epot = -131.387672978511 | etot = -98.4505567574995 +134000 ekin = 17.7192111747964 | erot = 13.5884229143348 | epot = -130.583041739003 | etot = -99.275407649872 +135000 ekin = 17.7536873750666 | erot = 14.0982927325614 | epot = -129.714512834768 | etot = -97.8625327271396 +136000 ekin = 18.2509212913219 | erot = 11.0266206273164 | epot = -128.826275668783 | etot = -99.5487337501442 +137000 ekin = 18.0888537517195 | erot = 10.6764813782231 | epot = -128.070491805314 | etot = -99.3051566753711 +138000 ekin = 17.7812261279265 | erot = 11.6465856631146 | epot = -127.390489385666 | etot = -97.9626775946245 +139000 ekin = 17.9170079781834 | erot = 10.4529474308984 | epot = -126.842446381848 | etot = -98.4724909727663 +140000 ekin = 17.7773492411915 | erot = 9.25494565223195 | epot = -126.432310441117 | etot = -99.4000155476936 +141000 ekin = 17.1244425096873 | erot = 9.65549785466578 | epot = -126.141777730543 | etot = -99.3618373661899 +142000 ekin = 16.5201701593962 | erot = 10.8998964099815 | epot = -125.940729957089 | etot = -98.5206633877113 +143000 ekin = 15.8857666561186 | erot = 10.1784670365893 | epot = -125.90698471032 | etot = -99.8427510176117 +144000 ekin = 15.7565411168065 | erot = 12.047444203328 | epot = -126.125108036528 | etot = -98.321122716393 +145000 ekin = 15.3969621946866 | erot = 13.9459354390538 | epot = -126.373024296495 | etot = -97.030126662755 +146000 ekin = 15.4725607727619 | erot = 14.2570317429904 | epot = -126.498863796023 | etot = -96.7692712802706 +147000 ekin = 15.3450693776366 | erot = 15.6232442146574 | epot = -126.412342603372 | etot = -95.4440290110776 +148000 ekin = 15.8954626715371 | erot = 15.7885966481124 | epot = -126.133296825904 | etot = -94.449237506254 +149000 ekin = 15.5447736469062 | erot = 13.3783461269004 | epot = -125.798608325168 | etot = -96.8754885513612 +150000 ekin = 15.1495805797146 | erot = 13.6429758807529 | epot = -125.407317668973 | etot = -96.6147612085054 +151000 ekin = 15.1616652247071 | erot = 14.0598975281373 | epot = -125.035002166702 | etot = -95.813439413858 +152000 ekin = 15.3091686685073 | erot = 14.4869353531681 | epot = -124.697020998762 | etot = -94.9009169770863 +153000 ekin = 14.9857966418998 | erot = 14.2639845699339 | epot = -124.429194085149 | etot = -95.179412873315 +154000 ekin = 15.2871304577002 | erot = 15.2408560259889 | epot = -124.13138567458 | etot = -93.6033991908905 +155000 ekin = 15.1935902329344 | erot = 16.5332537474993 | epot = -123.717148957551 | etot = -91.9903049771177 +156000 ekin = 14.9318980548606 | erot = 16.9585676917368 | epot = -123.312319455018 | etot = -91.4218537084203 +157000 ekin = 14.9239819478168 | erot = 16.3436933974605 | epot = -122.821468736538 | etot = -91.5537933912602 +158000 ekin = 14.6896340711936 | erot = 16.2520546181314 | epot = -121.560992897385 | etot = -90.6193042080597 +159000 ekin = 14.380371095523 | erot = 17.248314924081 | epot = -121.467420388953 | etot = -89.8387343693487 +160000 ekin = 14.5875486089083 | erot = 17.5905809234816 | epot = -122.699020677454 | etot = -90.5208911450643 +161000 ekin = 14.8276227126018 | erot = 18.3926246794873 | epot = -123.566242857825 | etot = -90.3459954657364 +162000 ekin = 15.6936272173714 | erot = 16.9816508210412 | epot = -124.054848993562 | etot = -91.3795709551497 +163000 ekin = 16.2263820836142 | erot = 17.6245213122907 | epot = -124.736300977309 | etot = -90.8853975814038 +164000 ekin = 17.0093157816188 | erot = 16.6796461814173 | epot = -125.568419886304 | etot = -91.8794579232682 +165000 ekin = 18.009720026184 | erot = 15.3539812192405 | epot = -126.49931452143 | etot = -93.1356132760057 +166000 ekin = 18.8470150492957 | erot = 15.1046721419971 | epot = -127.429741849845 | etot = -93.4780546585521 +167000 ekin = 19.5642890442739 | erot = 15.8598331039342 | epot = -128.291297852841 | etot = -92.8671757046329 +168000 ekin = 19.6862039573375 | erot = 15.8349840859769 | epot = -129.140703889381 | etot = -93.6195158460662 +169000 ekin = 20.6945323087269 | erot = 13.4325872410556 | epot = -129.822388484466 | etot = -95.6952689346837 +170000 ekin = 22.0647526260469 | erot = 12.8942633681097 | epot = -130.419864694263 | etot = -95.4608487001065 +171000 ekin = 22.943639339366 | erot = 11.1816601087484 | epot = -130.898425026419 | etot = -96.7731255783043 +172000 ekin = 23.5487360086972 | erot = 11.709116260819 | epot = -131.153087196089 | etot = -95.8952349265727 +173000 ekin = 23.3892857905513 | erot = 12.7557214142903 | epot = -131.135342861095 | etot = -94.9903356562537 +174000 ekin = 23.35018573525 | erot = 12.8363501231957 | epot = -130.945667676559 | etot = -94.7591318181137 +175000 ekin = 23.3884404339159 | erot = 10.8122258111237 | epot = -130.472641840404 | etot = -96.2719755953642 +176000 ekin = 21.5597457312898 | erot = 10.0374200559152 | epot = -129.874726714678 | etot = -98.2775609274735 +177000 ekin = 20.4815949162203 | erot = 8.99167759948274 | epot = -129.080278974767 | etot = -99.6070064590639 +178000 ekin = 19.6247383858513 | erot = 9.22106961945735 | epot = -128.257986703796 | etot = -99.4121786984872 +179000 ekin = 18.7995820087584 | erot = 10.9357566605628 | epot = -127.480693192329 | etot = -97.7453545230082 +180000 ekin = 18.5383318996741 | erot = 11.695380571584 | epot = -126.758025790561 | etot = -96.5243133193033 +181000 ekin = 17.0447803103657 | erot = 11.8007631437052 | epot = -126.226072012177 | etot = -97.380528558106 +182000 ekin = 16.2894526949276 | erot = 12.416164133038 | epot = -125.887179385862 | etot = -97.1815625578969 +183000 ekin = 16.6080309265792 | erot = 12.8149523345473 | epot = -125.615950231218 | etot = -96.1929669700911 +184000 ekin = 16.3744299525237 | erot = 12.9694537390341 | epot = -125.446432769611 | etot = -96.102549078053 +185000 ekin = 16.1680663279096 | erot = 14.4956894838547 | epot = -125.517482617703 | etot = -94.8537268059389 +186000 ekin = 16.1257587462836 | erot = 15.1875842076049 | epot = -125.659427603794 | etot = -94.3460846499053 +187000 ekin = 16.0397295413223 | erot = 14.4670724430242 | epot = -125.995193074143 | etot = -95.488391089796 +188000 ekin = 15.6899836100949 | erot = 14.7638277675767 | epot = -126.425523467655 | etot = -95.9717120899832 +189000 ekin = 15.0625500409891 | erot = 14.1154735980193 | epot = -126.846152752696 | etot = -97.6681291136872 +190000 ekin = 15.2069054588956 | erot = 14.6859243902427 | epot = -127.433541853514 | etot = -97.5407120043753 +191000 ekin = 15.6740546561506 | erot = 15.9626651851846 | epot = -127.896978550165 | etot = -96.2602587088297 +192000 ekin = 15.4318280527709 | erot = 18.1353702097593 | epot = -128.302111852112 | etot = -94.734913589582 +193000 ekin = 15.3469995573318 | erot = 17.7766470416487 | epot = -128.618975597814 | etot = -95.495328998834 +194000 ekin = 15.2104506233857 | erot = 21.0799824470635 | epot = -128.783338748985 | etot = -92.4929056785358 +195000 ekin = 14.1287522348466 | erot = 23.1619754781382 | epot = -128.29289851349 | etot = -91.0021708005055 +196000 ekin = 13.3885368132018 | erot = 23.1979147136361 | epot = -127.741537167645 | etot = -91.1550856408074 +197000 ekin = 12.4059689641546 | erot = 22.2524136408538 | epot = -127.509097138024 | etot = -92.8507145330151 +198000 ekin = 11.8921374835096 | erot = 19.781728200708 | epot = -127.037889310497 | etot = -95.3640236262798 +199000 ekin = 11.2532240659878 | erot = 18.2188688915955 | epot = -126.340308303153 | etot = -96.8682153455699 +200000 ekin = 11.0987340347435 | erot = 18.60818019739 | epot = -125.85420630367 | etot = -96.1472920715361 +201000 ekin = 11.7489357164156 | erot = 15.281688246823 | epot = -125.682140321791 | etot = -98.6515163585526 +202000 ekin = 11.7145445879392 | erot = 15.0356903466778 | epot = -125.740023875244 | etot = -98.9897889406272 +203000 ekin = 12.0903488366362 | erot = 14.3345717011572 | epot = -126.048866274682 | etot = -99.6239457368885 +204000 ekin = 12.4417683268483 | erot = 14.3229870520558 | epot = -126.529965825482 | etot = -99.7652104465778 +205000 ekin = 13.1698814591864 | erot = 14.6415169346515 | epot = -127.124165984413 | etot = -99.3127675905754 +206000 ekin = 13.8723804085583 | erot = 14.5686570177801 | epot = -127.751024041401 | etot = -99.3099866150631 +207000 ekin = 14.3112273566462 | erot = 13.070167910606 | epot = -128.541344802635 | etot = -101.159949535383 +208000 ekin = 15.16434371668 | erot = 12.0476689292267 | epot = -129.396845246345 | etot = -102.184832600439 +209000 ekin = 15.7182214267953 | erot = 11.9792376393735 | epot = -130.439256642704 | etot = -102.741797576535 +210000 ekin = 16.8116032305538 | erot = 12.8318158803216 | epot = -131.566184333306 | etot = -101.922765222431 +211000 ekin = 17.0286682860339 | erot = 11.9299987181453 | epot = -132.706776286311 | etot = -103.748109282131 +212000 ekin = 17.495092644444 | erot = 13.0542600963912 | epot = -133.734529445312 | etot = -103.185176704477 +213000 ekin = 18.1544022312138 | erot = 12.9214683681872 | epot = -134.668238718993 | etot = -103.592368119592 +214000 ekin = 18.944441841757 | erot = 11.5204669980782 | epot = -135.37166723116 | etot = -104.906758391324 +215000 ekin = 19.2678390020627 | erot = 11.3933718971404 | epot = -135.757866327845 | etot = -105.096655428642 +216000 ekin = 19.2698399527749 | erot = 11.134292164478 | epot = -135.978508576259 | etot = -105.574376459006 +217000 ekin = 19.6693699034603 | erot = 11.8996645917077 | epot = -136.066555103325 | etot = -104.497520608157 +218000 ekin = 19.6558025470516 | erot = 11.6982321377416 | epot = -136.00830488635 | etot = -104.654270201556 +219000 ekin = 19.2866150818585 | erot = 11.5958256376614 | epot = -135.986480868354 | etot = -105.104040148834 +220000 ekin = 19.0299200086328 | erot = 12.7877825940592 | epot = -136.003862431597 | etot = -104.186159828905 +221000 ekin = 18.3887352106328 | erot = 14.0162126644684 | epot = -135.884700146083 | etot = -103.479752270982 +222000 ekin = 17.8182271656908 | erot = 13.3669574260086 | epot = -135.679482053355 | etot = -104.494297461656 +223000 ekin = 17.5268503521898 | erot = 14.6122101838067 | epot = -135.382982684107 | etot = -103.243922148111 +224000 ekin = 17.0683929815185 | erot = 14.6347025849537 | epot = -135.233315947347 | etot = -103.530220380875 +225000 ekin = 17.0633907591624 | erot = 15.7710716167764 | epot = -135.38637693405 | etot = -102.551914558111 +226000 ekin = 16.7787690680764 | erot = 15.7986947056439 | epot = -135.879311388113 | etot = -103.301847614393 +227000 ekin = 16.463912634538 | erot = 15.0990454188237 | epot = -136.352660528608 | etot = -104.789702475246 +228000 ekin = 16.6277811962492 | erot = 14.1044610323435 | epot = -136.763704119537 | etot = -106.031461890944 +229000 ekin = 16.270302581487 | erot = 14.1131098254062 | epot = -136.971116618175 | etot = -106.587704211282 +230000 ekin = 16.2889568947664 | erot = 13.542272603068 | epot = -136.891243624268 | etot = -107.060014126434 +231000 ekin = 16.5868050722652 | erot = 15.2600761973021 | epot = -136.529850670182 | etot = -104.682969400615 +232000 ekin = 16.1288630231825 | erot = 13.1674679001409 | epot = -135.937232830953 | etot = -106.64090190763 +233000 ekin = 15.7857630558791 | erot = 12.5300334624789 | epot = -135.216925627261 | etot = -106.901129108903 +234000 ekin = 15.6125198960089 | erot = 11.2806230486724 | epot = -134.434273419247 | etot = -107.541130474566 +235000 ekin = 15.4569759849517 | erot = 10.8081368630456 | epot = -133.869202645129 | etot = -107.604089797131 +236000 ekin = 14.9820807386331 | erot = 11.1823386784929 | epot = -133.297958923831 | etot = -107.133539506705 +237000 ekin = 14.8216786424466 | erot = 11.2471885188066 | epot = -132.595601448487 | etot = -106.526734287234 +238000 ekin = 14.6706220188174 | erot = 10.1140644021516 | epot = -132.065646431795 | etot = -107.280960010826 +239000 ekin = 14.4348056512931 | erot = 10.1432117067704 | epot = -131.917610583546 | etot = -107.339593225483 +240000 ekin = 14.1316519601016 | erot = 11.8496406962971 | epot = -132.004580752914 | etot = -106.023288096515 +241000 ekin = 14.1719234313466 | erot = 13.8094321611479 | epot = -132.248478579103 | etot = -104.267122986608 +242000 ekin = 14.4067409199113 | erot = 15.2208382789827 | epot = -132.237557462079 | etot = -102.609978263185 +243000 ekin = 13.9001228129608 | erot = 16.4885549233189 | epot = -132.327253958718 | etot = -101.938576222438 +244000 ekin = 14.2124604518254 | erot = 16.3580145393041 | epot = -133.265138084389 | etot = -102.694663093259 +245000 ekin = 13.9391457137868 | erot = 15.7114912432817 | epot = -134.162723777585 | etot = -104.512086820517 +246000 ekin = 13.4634980405893 | erot = 14.8529525187265 | epot = -134.759599084005 | etot = -106.443148524689 +247000 ekin = 13.1394657389663 | erot = 14.9809346189963 | epot = -135.270170814713 | etot = -107.14977045675 +248000 ekin = 12.5974089965367 | erot = 14.1968470998346 | epot = -135.720205164949 | etot = -108.925949068578 +249000 ekin = 13.0079405446737 | erot = 12.6478010567203 | epot = -135.976059745644 | etot = -110.32031814425 +250000 ekin = 11.9665436270665 | erot = 12.7394906885837 | epot = -135.911451138462 | etot = -111.205416822812 +251000 ekin = 11.9761911331982 | erot = 12.8355549179859 | epot = -135.648387424505 | etot = -110.836641373321 +252000 ekin = 12.2240250409318 | erot = 12.5494470999045 | epot = -135.429112694318 | etot = -110.655640553482 +253000 ekin = 11.7586948220616 | erot = 15.2823123339394 | epot = -135.224481555101 | etot = -108.1834743991 +254000 ekin = 11.3311374059083 | erot = 16.4795694427141 | epot = -135.040669148792 | etot = -107.22996230017 +255000 ekin = 11.471231769472 | erot = 16.8299610794708 | epot = -134.929906170188 | etot = -106.628713321245 +256000 ekin = 11.2441754010408 | erot = 14.2749475233363 | epot = -134.76558967984 | etot = -109.246466755463 +257000 ekin = 11.273914355832 | erot = 14.7441264905457 | epot = -134.63597018422 | etot = -108.617929337842 +258000 ekin = 12.128649316714 | erot = 12.3006544166916 | epot = -134.51238338776 | etot = -110.083079654355 +259000 ekin = 12.4162486986459 | erot = 11.8189831631872 | epot = -134.489054265492 | etot = -110.253822403659 +260000 ekin = 12.8516754908381 | erot = 11.497953565895 | epot = -134.553471186685 | etot = -110.203842129952 +261000 ekin = 13.0343910888837 | erot = 10.7691862375377 | epot = -134.729318840158 | etot = -110.925741513736 +262000 ekin = 14.2874948463721 | erot = 10.5582220873925 | epot = -134.990907586225 | etot = -110.145190652461 +263000 ekin = 15.0019927116376 | erot = 10.4048010965419 | epot = -135.379108178799 | etot = -109.972314370619 +264000 ekin = 15.5826861643349 | erot = 10.2546388876574 | epot = -135.848998441352 | etot = -110.01167338936 +265000 ekin = 16.0874701006427 | erot = 10.3511427583311 | epot = -136.380262211566 | etot = -109.941649352592 +266000 ekin = 16.3003073067596 | erot = 11.9373544401253 | epot = -137.009363532579 | etot = -108.771701785694 +267000 ekin = 17.2219404130253 | erot = 12.1424398852432 | epot = -137.561511974844 | etot = -108.197131676575 +268000 ekin = 17.2009756929593 | erot = 14.2660931214315 | epot = -138.134066507026 | etot = -106.666997692635 +269000 ekin = 17.5332603165065 | erot = 14.7566713792615 | epot = -138.587695425486 | etot = -106.297763729718 +270000 ekin = 18.8972170404745 | erot = 14.5838354068123 | epot = -138.68266462674 | etot = -105.201612179454 +271000 ekin = 19.2798632826061 | erot = 13.2959771096333 | epot = -138.517048226924 | etot = -105.941207834685 +272000 ekin = 19.4328171307553 | erot = 13.5758888534677 | epot = -138.17513356012 | etot = -105.166427575897 +273000 ekin = 19.8597451581877 | erot = 13.9959767402809 | epot = -137.648904040346 | etot = -103.793182141877 +274000 ekin = 18.6820893610573 | erot = 13.6482586162615 | epot = -136.938179869851 | etot = -104.607831892532 +275000 ekin = 18.2660791421053 | erot = 12.2609583978932 | epot = -136.164087116334 | etot = -105.637049576335 +276000 ekin = 17.9004867505407 | erot = 14.3974247752901 | epot = -135.325508183154 | etot = -103.027596657323 +277000 ekin = 17.2269955060707 | erot = 15.3022411244147 | epot = -134.486514748267 | etot = -101.957278117782 +278000 ekin = 16.6892354000126 | erot = 14.5893321464561 | epot = -133.733094918947 | etot = -102.454527372478 +279000 ekin = 15.6192008320367 | erot = 13.9737522271236 | epot = -133.065353125456 | etot = -103.472400066296 +280000 ekin = 15.8029815632486 | erot = 14.2001632540758 | epot = -132.421240721495 | etot = -102.41809590417 +281000 ekin = 15.2607705885714 | erot = 12.7607691318965 | epot = -132.022771567729 | etot = -104.001231847261 +282000 ekin = 14.7197627172706 | erot = 12.4260243382723 | epot = -131.782153922758 | etot = -104.636366867215 +283000 ekin = 14.5696242094015 | erot = 11.213371151963 | epot = -131.556720370679 | etot = -105.773725009314 +284000 ekin = 14.2731206049614 | erot = 12.8148966990646 | epot = -131.490239296031 | etot = -104.402221992005 +285000 ekin = 14.2892073777173 | erot = 15.322726695954 | epot = -131.681469234421 | etot = -102.06953516075 +286000 ekin = 14.5295816614891 | erot = 16.9482844272975 | epot = -131.994346482577 | etot = -100.51648039379 +287000 ekin = 13.8119183806608 | erot = 16.9734747395549 | epot = -132.26255120614 | etot = -101.477158085924 +288000 ekin = 13.5104518538994 | erot = 19.15601872209 | epot = -132.571143919699 | etot = -99.9046733437092 +289000 ekin = 13.6879789079896 | erot = 18.5577865527907 | epot = -132.871664328362 | etot = -100.625898867581 +290000 ekin = 13.2976555696433 | erot = 17.1112459528925 | epot = -133.02645983522 | etot = -102.617558312684 +291000 ekin = 13.2211085618527 | erot = 16.1729195781472 | epot = -133.185234708 | etot = -103.791206568 +292000 ekin = 13.1947483461643 | erot = 16.0723910787646 | epot = -133.433270238445 | etot = -104.166130813516 +293000 ekin = 13.2996269037799 | erot = 15.5125592618921 | epot = -133.745707778566 | etot = -104.933521612894 +294000 ekin = 13.4921147160859 | erot = 18.0876895403391 | epot = -133.943082964024 | etot = -102.363278707599 +295000 ekin = 13.6001244303235 | erot = 17.1026862565064 | epot = -134.076076149791 | etot = -103.373265462961 +296000 ekin = 13.4976604407178 | erot = 16.6010516378414 | epot = -134.210092447971 | etot = -104.111380369412 +297000 ekin = 13.9415075561874 | erot = 17.7972728397637 | epot = -134.247712961306 | etot = -102.508932565355 +298000 ekin = 14.1780029375634 | erot = 17.0511963270014 | epot = -134.168924033823 | etot = -102.939724769258 +299000 ekin = 13.8361564139329 | erot = 16.0669521975166 | epot = -134.068492310082 | etot = -104.165383698632 +300000 ekin = 13.7326437681577 | erot = 16.2729547114218 | epot = -133.890944289642 | etot = -103.885345810063 +301000 ekin = 13.7141690556675 | erot = 15.5483729893138 | epot = -133.599370882051 | etot = -104.33682883707 +302000 ekin = 13.8016066958289 | erot = 15.936856523607 | epot = -133.240558832336 | etot = -103.5020956129 +303000 ekin = 14.3450581683325 | erot = 14.3991837835363 | epot = -132.841355292688 | etot = -104.097113340819 +304000 ekin = 14.0432433747207 | erot = 12.2471441381921 | epot = -132.411991934279 | etot = -106.121604421366 +305000 ekin = 13.7451663687168 | erot = 11.8055396154173 | epot = -132.136089702987 | etot = -106.585383718852 +306000 ekin = 13.8602855535103 | erot = 11.2975987457346 | epot = -132.01332305383 | etot = -106.855438754585 +307000 ekin = 14.3933488058418 | erot = 11.4125898833739 | epot = -132.076988534469 | etot = -106.271049845253 +308000 ekin = 14.5877929349634 | erot = 13.7844635852125 | epot = -132.379943681766 | etot = -104.00768716159 +309000 ekin = 14.6468860318721 | erot = 12.8855238046447 | epot = -132.790482577119 | etot = -105.258072740602 +310000 ekin = 15.392372494004 | erot = 14.5395261933749 | epot = -133.139957738231 | etot = -103.208059050852 +311000 ekin = 15.0800623659564 | erot = 16.4619620929048 | epot = -133.366197656559 | etot = -101.824173197698 +312000 ekin = 15.0612640553335 | erot = 17.7716663024468 | epot = -133.463157250145 | etot = -100.630226892364 +313000 ekin = 15.0496012548364 | erot = 16.7171000278227 | epot = -133.572818737683 | etot = -101.806117455024 +314000 ekin = 15.8034899506749 | erot = 16.0925639210479 | epot = -133.470644690524 | etot = -101.574590818801 +315000 ekin = 16.366489345922 | erot = 15.8790190903233 | epot = -133.301536278224 | etot = -101.056027841979 +316000 ekin = 16.8909929849972 | erot = 15.9984636306728 | epot = -132.972647290534 | etot = -100.083190674864 +317000 ekin = 17.785292167189 | erot = 14.9039641317449 | epot = -132.500917675508 | etot = -99.8116613765746 +318000 ekin = 17.5993880908146 | erot = 14.6914071194506 | epot = -132.115571579264 | etot = -99.8247763689988 +319000 ekin = 17.8599367754211 | erot = 14.1353188496931 | epot = -131.708173655537 | etot = -99.712918030423 +320000 ekin = 18.6581032066137 | erot = 13.4331705144337 | epot = -131.273397749098 | etot = -99.1821240280507 +321000 ekin = 19.1474562630728 | erot = 12.1110703081368 | epot = -131.035243134479 | etot = -99.7767165632692 +322000 ekin = 19.8508860282636 | erot = 13.9599076713822 | epot = -131.017079844699 | etot = -97.2062861450529 +323000 ekin = 20.3434128121834 | erot = 14.5284558532583 | epot = -131.242060167605 | etot = -96.370191502163 +324000 ekin = 21.6816363054614 | erot = 11.6094198187815 | epot = -131.687828885057 | etot = -98.3967727608138 +325000 ekin = 21.7556398119963 | erot = 10.9492045533556 | epot = -132.111190356534 | etot = -99.406345991182 +326000 ekin = 22.6473350093869 | erot = 9.57702095551454 | epot = -132.448821068116 | etot = -100.224465103215 +327000 ekin = 22.9547512120162 | erot = 11.0621417409188 | epot = -132.862102217055 | etot = -98.8452092641196 +328000 ekin = 23.5737808038549 | erot = 12.6984438571557 | epot = -133.193143240814 | etot = -96.9209185798029 +329000 ekin = 23.6352335154599 | erot = 12.2956706764736 | epot = -133.395236559297 | etot = -97.4643323673633 +330000 ekin = 23.8391520228329 | erot = 12.0370047788423 | epot = -133.345382913248 | etot = -97.4692261115726 +331000 ekin = 22.8959913619489 | erot = 11.30846430113 | epot = -133.020506291975 | etot = -98.8160506288956 +332000 ekin = 21.8204000909394 | erot = 14.2756313662232 | epot = -132.689351486946 | etot = -96.5933200297831 +333000 ekin = 21.0106478016265 | erot = 13.1455024021325 | epot = -132.253491783917 | etot = -98.0973415801577 +334000 ekin = 19.9217218385571 | erot = 14.091018178305 | epot = -131.971215207996 | etot = -97.9584751911336 +335000 ekin = 19.2873748500285 | erot = 15.3215860418359 | epot = -131.85819529049 | etot = -97.2492343986257 +336000 ekin = 18.7678345301193 | erot = 16.4869510658781 | epot = -131.844352238269 | etot = -96.589566642272 +337000 ekin = 17.6131282411972 | erot = 20.227892880872 | epot = -132.091380721362 | etot = -94.2503595992928 +338000 ekin = 16.5316565058049 | erot = 20.19667842932 | epot = -132.359487287499 | etot = -95.631152352374 +339000 ekin = 15.3093289418818 | erot = 20.0585909980764 | epot = -132.598946045035 | etot = -97.2310261050771 +340000 ekin = 15.1702759209444 | erot = 19.0125223540299 | epot = -132.757880960711 | etot = -98.5750826857363 +341000 ekin = 14.6984201961113 | erot = 19.2973194359688 | epot = -132.768022329401 | etot = -98.7722826973214 +342000 ekin = 14.419185060618 | erot = 18.4871375877433 | epot = -132.715486658902 | etot = -99.8091640105411 +343000 ekin = 14.2510678270355 | erot = 17.8837836084501 | epot = -132.715877324812 | etot = -100.581025889327 +344000 ekin = 14.3088347204905 | erot = 18.3281706547507 | epot = -132.541230881633 | etot = -99.9042255063921 +345000 ekin = 14.7729752840168 | erot = 17.9928124874577 | epot = -132.203322556083 | etot = -99.4375347846084 +346000 ekin = 14.4478987349512 | erot = 14.8603324121466 | epot = -131.791226187862 | etot = -102.482995040764 +347000 ekin = 14.9495411968808 | erot = 15.0531306904129 | epot = -131.581664356582 | etot = -101.578992469288 +348000 ekin = 14.9106344526996 | erot = 16.3222170851953 | epot = -131.315204523293 | etot = -100.082352985399 +349000 ekin = 15.5640705164731 | erot = 16.6567998125757 | epot = -131.03580673161 | etot = -98.8149364025609 +350000 ekin = 15.3525255344555 | erot = 17.1589173845544 | epot = -130.684885383684 | etot = -98.1734424646738 +351000 ekin = 15.5604423853952 | erot = 14.7449001424502 | epot = -130.577479343389 | etot = -100.272136815543 +352000 ekin = 16.0213916155565 | erot = 12.9283234241451 | epot = -130.520782488219 | etot = -101.571067448518 +353000 ekin = 16.2706611268026 | erot = 13.2135527584764 | epot = -130.531272204218 | etot = -101.047058318939 +354000 ekin = 16.7551971771748 | erot = 13.6739898513455 | epot = -130.713465602543 | etot = -100.284278574022 +355000 ekin = 16.8761517885112 | erot = 13.3482375555154 | epot = -131.00169518562 | etot = -100.777305841594 +356000 ekin = 17.6119715794083 | erot = 13.1534547245203 | epot = -131.381977701561 | etot = -100.616551397633 +357000 ekin = 17.9212807392641 | erot = 14.278695302262 | epot = -131.779026398909 | etot = -99.5790503573828 +358000 ekin = 18.7258104781707 | erot = 16.7912517283134 | epot = -132.311439028535 | etot = -96.7943768220511 +359000 ekin = 19.3732736670771 | erot = 17.2739539863543 | epot = -132.879438461778 | etot = -96.2322108083466 +360000 ekin = 19.6464373761355 | erot = 16.0634856117012 | epot = -133.434958740234 | etot = -97.7250357523969 +361000 ekin = 19.7822067135547 | erot = 18.3661629834882 | epot = -133.446226940954 | etot = -95.2978572439108 +362000 ekin = 19.2258029988226 | erot = 17.5528372322332 | epot = -132.301193434443 | etot = -95.5225532033868 +363000 ekin = 19.7930261365336 | erot = 16.9646071251481 | epot = -131.995469208061 | etot = -95.2378359463791 +364000 ekin = 20.6366833282949 | erot = 18.9139523531674 | epot = -132.891077360108 | etot = -93.3404416786456 +365000 ekin = 20.3689030819221 | erot = 17.5903344904057 | epot = -132.578147300574 | etot = -94.6189097282457 +366000 ekin = 19.6055112959891 | erot = 15.9901011051967 | epot = -131.691955629683 | etot = -96.0963432284971 +367000 ekin = 18.6692190631214 | erot = 13.8437371590621 | epot = -130.921138953502 | etot = -98.4081827313182 +368000 ekin = 18.219068783416 | erot = 14.8529187740073 | epot = -130.504389467515 | etot = -97.4324019100922 +369000 ekin = 17.7629678423308 | erot = 12.4989887874946 | epot = -130.274191179522 | etot = -100.012234549696 +370000 ekin = 17.0650223978097 | erot = 13.5821596836016 | epot = -130.335687313643 | etot = -99.6885052322315 +371000 ekin = 16.7913745722517 | erot = 14.9629741940435 | epot = -130.32282870869 | etot = -98.5684799423952 +372000 ekin = 17.2307270306248 | erot = 12.9911617978282 | epot = -130.236933986417 | etot = -100.015045157964 +373000 ekin = 17.0304402846253 | erot = 13.2707537504999 | epot = -130.100796264889 | etot = -99.7996022297637 +374000 ekin = 16.0415595056889 | erot = 15.1803442269075 | epot = -129.972987311626 | etot = -98.7510835790299 +375000 ekin = 15.8176192185438 | erot = 16.9883413755264 | epot = -129.944912466272 | etot = -97.1389518722015 +376000 ekin = 15.2903747494021 | erot = 18.8068775560055 | epot = -129.965681757382 | etot = -95.8684294519739 +377000 ekin = 14.995947034047 | erot = 19.9472899539892 | epot = -129.829932831079 | etot = -94.8866958430433 +378000 ekin = 14.2959318558334 | erot = 18.7668035961228 | epot = -129.592844878311 | etot = -96.5301094263543 +379000 ekin = 13.857355471346 | erot = 17.5724093346652 | epot = -129.233821228828 | etot = -97.8040564228168 +380000 ekin = 12.8275218506783 | erot = 20.5046758847232 | epot = -128.789730014376 | etot = -95.4575322789749 +381000 ekin = 12.735162884832 | erot = 18.5613197500517 | epot = -128.390040910682 | etot = -97.0935582757987 +382000 ekin = 12.2452890160443 | erot = 20.564638156725 | epot = -128.030645015804 | etot = -95.2207178430346 +383000 ekin = 12.1080018787289 | erot = 20.1999409855048 | epot = -127.678397123719 | etot = -95.3704542594853 +384000 ekin = 11.6435047444796 | erot = 20.0195379904968 | epot = -127.335918040772 | etot = -95.6728753057953 +385000 ekin = 11.6405112732186 | erot = 19.0845996443496 | epot = -127.124973960441 | etot = -96.3998630428725 +386000 ekin = 12.1338227535956 | erot = 15.7029155804283 | epot = -127.099493323699 | etot = -99.2627549896752 +387000 ekin = 12.4448216572665 | erot = 15.9527401483909 | epot = -127.113713274559 | etot = -98.716151468902 +388000 ekin = 12.5477526743772 | erot = 15.7264339561621 | epot = -127.302269285959 | etot = -99.0280826554199 +389000 ekin = 12.7365761628926 | erot = 14.8999554020062 | epot = -127.586298095577 | etot = -99.9497665306781 +390000 ekin = 13.2018526541373 | erot = 15.5840879369083 | epot = -127.936145623289 | etot = -99.1502050322436 +391000 ekin = 13.7630478535849 | erot = 14.4376541638023 | epot = -128.303860720027 | etot = -100.103158702639 +392000 ekin = 13.7713771450355 | erot = 13.5356578275445 | epot = -128.58812747767 | etot = -101.28109250509 +393000 ekin = 14.5177182396087 | erot = 13.0863011788344 | epot = -128.867722321476 | etot = -101.263702903033 +394000 ekin = 14.7950835380052 | erot = 11.7665006681664 | epot = -129.02765872441 | etot = -102.466074518239 +395000 ekin = 15.3250550913504 | erot = 11.5930851190037 | epot = -129.381911781199 | etot = -102.463771570845 +396000 ekin = 15.7274830034877 | erot = 12.8428669141979 | epot = -129.670501062476 | etot = -101.100151144791 +397000 ekin = 15.9336057344419 | erot = 12.5423981572936 | epot = -129.882143644775 | etot = -101.40613975304 +398000 ekin = 16.1902642375988 | erot = 13.5464129112161 | epot = -129.92961516752 | etot = -100.192938018705 +399000 ekin = 16.3325461362548 | erot = 11.8125267837203 | epot = -129.86635331385 | etot = -101.721280393875 +400000 ekin = 16.2371759156548 | erot = 10.688472264068 | epot = -129.645266211183 | etot = -102.71961803146 +401000 ekin = 15.9596433115687 | erot = 10.7690637950704 | epot = -129.351599210472 | etot = -102.622892103833 +402000 ekin = 15.8915589358765 | erot = 11.8717442427545 | epot = -128.863730745308 | etot = -101.100427566677 +403000 ekin = 16.1787980975133 | erot = 11.9524066979189 | epot = -128.349870546345 | etot = -100.218665750913 +404000 ekin = 16.2559042324474 | erot = 11.7923315153145 | epot = -127.721941645185 | etot = -99.6737058974226 +405000 ekin = 15.8297631258515 | erot = 11.5147712902976 | epot = -127.044284217556 | etot = -99.6997498014074 +406000 ekin = 15.5346343103188 | erot = 10.5094970219731 | epot = -126.338765848855 | etot = -100.294634516563 +407000 ekin = 14.7958112110859 | erot = 11.3095257330351 | epot = -125.613350484068 | etot = -99.5080135399471 +408000 ekin = 14.8624029878213 | erot = 13.2220079279186 | epot = -124.727782956332 | etot = -96.6433720405917 +409000 ekin = 13.6028613042818 | erot = 13.9313059082655 | epot = -123.943236525651 | etot = -96.4090693131036 +410000 ekin = 12.9391405676151 | erot = 13.9083866084738 | epot = -123.698449973831 | etot = -96.8509227977424 +411000 ekin = 12.9511911958114 | erot = 13.2111133981956 | epot = -123.475848630892 | etot = -97.3135440368848 +412000 ekin = 13.0102946149252 | erot = 11.6293349705262 | epot = -123.312975165786 | etot = -98.6733455803344 +413000 ekin = 13.7672328255849 | erot = 12.3436014571232 | epot = -123.339406487652 | etot = -97.2285722049436 +414000 ekin = 13.9282595375335 | erot = 11.9157312379677 | epot = -123.568171704082 | etot = -97.7241809285804 +415000 ekin = 14.2112002618673 | erot = 12.6165381733728 | epot = -124.074734542967 | etot = -97.2469961077268 +416000 ekin = 14.8471585259496 | erot = 13.9090014073649 | epot = -124.918146496334 | etot = -96.1619865630192 +417000 ekin = 15.1833698247616 | erot = 15.2600269348037 | epot = -125.972782960942 | etot = -95.5293862013764 +418000 ekin = 15.0116385331976 | erot = 16.2202339191643 | epot = -127.001358515785 | etot = -95.7694860634236 +419000 ekin = 15.946640481216 | erot = 16.556706532663 | epot = -127.930826638016 | etot = -95.427479624137 +420000 ekin = 17.0030755122275 | erot = 13.8064387238821 | epot = -128.779917699183 | etot = -97.9704034630734 +421000 ekin = 17.7076999173918 | erot = 15.6607762389099 | epot = -129.712399115792 | etot = -96.3439229594902 +422000 ekin = 19.0288893821844 | erot = 16.9547249541364 | epot = -130.705406615431 | etot = -94.7217922791104 +423000 ekin = 20.0928868467255 | erot = 15.6791978827033 | epot = -131.512201888439 | etot = -95.7401171590101 +424000 ekin = 21.2867782211336 | erot = 14.7249077763209 | epot = -132.144270226839 | etot = -96.1325842293842 +425000 ekin = 22.3046811399301 | erot = 14.0135834881444 | epot = -132.584492965832 | etot = -96.2662283377575 +426000 ekin = 22.6757260607186 | erot = 14.0425771244452 | epot = -132.927022234245 | etot = -96.2087190490815 +427000 ekin = 22.9114920469756 | erot = 13.9187692374731 | epot = -133.17306480712 | etot = -96.3428035226713 +428000 ekin = 22.8833836302245 | erot = 13.3202826174428 | epot = -133.354420414982 | etot = -97.1507541673149 +429000 ekin = 23.1759582261326 | erot = 14.8508769700698 | epot = -133.395233600723 | etot = -95.3683984045205 +430000 ekin = 22.7011135257097 | erot = 14.3323835628523 | epot = -133.281782390496 | etot = -96.2482853019342 +431000 ekin = 22.4860621542188 | erot = 13.5830545588894 | epot = -133.063122899888 | etot = -96.9940061867801 +432000 ekin = 20.9926376577681 | erot = 13.3850499162301 | epot = -132.792306053964 | etot = -98.4146184799654 +433000 ekin = 20.6601187297081 | erot = 13.1353458539732 | epot = -132.632984905955 | etot = -98.8375203222734 +434000 ekin = 19.7772364576386 | erot = 12.5789641824799 | epot = -132.401261608975 | etot = -100.045060968857 +435000 ekin = 18.9180523876104 | erot = 14.9032013087131 | epot = -132.14719170047 | etot = -98.3259380041467 +436000 ekin = 18.0157320272878 | erot = 14.3516355778797 | epot = -131.928263980224 | etot = -99.5608963750566 +437000 ekin = 16.8474929436859 | erot = 12.7767873756002 | epot = -131.753136883159 | etot = -102.128856563873 +438000 ekin = 16.4671541938377 | erot = 14.4213750411729 | epot = -131.725759984879 | etot = -100.837230749868 +439000 ekin = 15.9238388746797 | erot = 15.4702902702385 | epot = -131.833740043839 | etot = -100.43961089892 +440000 ekin = 14.9768489355124 | erot = 17.3584161477327 | epot = -132.010161743274 | etot = -99.6748966600286 +441000 ekin = 14.9478235464867 | erot = 16.2706154773913 | epot = -132.172451698074 | etot = -100.954012674196 +442000 ekin = 14.5971874348284 | erot = 16.3914765923343 | epot = -132.387105996492 | etot = -101.39844196933 +443000 ekin = 14.1938972260854 | erot = 15.7500104224714 | epot = -132.637569125185 | etot = -102.693661476628 +444000 ekin = 14.2106948400759 | erot = 15.9261435937722 | epot = -132.804152949518 | etot = -102.66731451567 +445000 ekin = 14.3504745217208 | erot = 15.4757301980022 | epot = -132.870345661761 | etot = -103.044140942038 +446000 ekin = 14.0762883104816 | erot = 16.2756502679397 | epot = -132.828104290398 | etot = -102.476165711977 +447000 ekin = 14.1069696622209 | erot = 15.3943186838422 | epot = -132.926864854306 | etot = -103.425576508243 +448000 ekin = 13.8424969286477 | erot = 14.0768776395851 | epot = -133.07889196132 | etot = -105.159517393087 +449000 ekin = 14.5602094831078 | erot = 15.6501945950326 | epot = -132.967703020155 | etot = -102.757298942015 +450000 ekin = 14.9711261701579 | erot = 15.7868636107344 | epot = -132.757738590532 | etot = -101.999748809639 +451000 ekin = 14.9520831349878 | erot = 17.6569828498342 | epot = -132.602681277381 | etot = -99.9936152925592 +452000 ekin = 14.9965092624441 | erot = 17.742997702384 | epot = -132.3213447904 | etot = -99.581837825572 +453000 ekin = 14.7863093929959 | erot = 15.3601255964711 | epot = -131.845627968433 | etot = -101.699192978966 +454000 ekin = 15.1253016175455 | erot = 13.835767544551 | epot = -131.226853217639 | etot = -102.265784055542 +455000 ekin = 14.3547689605291 | erot = 15.0536928662401 | epot = -130.646123989566 | etot = -101.237662162797 +456000 ekin = 14.7873663711511 | erot = 14.6097887125708 | epot = -130.159036791418 | etot = -100.761881707696 +457000 ekin = 14.4101192581538 | erot = 14.371400529337 | epot = -129.80422976325 | etot = -101.022709975759 +458000 ekin = 14.7794232424024 | erot = 12.961786275671 | epot = -129.445895613438 | etot = -101.704686095364 +459000 ekin = 14.905480731245 | erot = 12.7036192262007 | epot = -129.120668125581 | etot = -101.511568168135 +460000 ekin = 14.1935048188216 | erot = 11.5773117937114 | epot = -128.824190440567 | etot = -103.053373828034 +461000 ekin = 13.9073192104769 | erot = 11.8465196019207 | epot = -128.567103523397 | etot = -102.813264710999 +462000 ekin = 13.6040511794357 | erot = 10.6529412012384 | epot = -128.498343339882 | etot = -104.241350959208 +463000 ekin = 13.7949695250129 | erot = 10.4405979877883 | epot = -128.633460244471 | etot = -104.39789273167 +464000 ekin = 13.9363536682094 | erot = 11.7923025500535 | epot = -128.950025580843 | etot = -103.22136936258 +465000 ekin = 14.0315715317229 | erot = 11.4183186979088 | epot = -129.399663695114 | etot = -103.949773465483 +466000 ekin = 14.4802887283481 | erot = 10.4358066575657 | epot = -129.863426573792 | etot = -104.947331187878 +467000 ekin = 14.6854676893719 | erot = 10.6584665341399 | epot = -130.272520868508 | etot = -104.928586644996 +468000 ekin = 14.5469456942364 | erot = 10.3055980169457 | epot = -130.575032240544 | etot = -105.722488529361 +469000 ekin = 15.168157151144 | erot = 11.507015709602 | epot = -130.888148525244 | etot = -104.212975664498 +470000 ekin = 15.7011319290239 | erot = 8.977646308534 | epot = -131.052840155166 | etot = -106.374061917608 +471000 ekin = 15.8582623804226 | erot = 10.1529587779977 | epot = -131.152653971397 | etot = -105.141432812977 +472000 ekin = 16.0960791677601 | erot = 10.7379394990764 | epot = -131.176700464405 | etot = -104.342681797569 +473000 ekin = 16.2469673512857 | erot = 12.0638689637426 | epot = -131.178252406718 | etot = -102.86741609169 +474000 ekin = 16.9347610623616 | erot = 13.201470118462 | epot = -131.1257886003 | etot = -100.989557419477 +475000 ekin = 16.7328496952857 | erot = 11.3426592811571 | epot = -131.071794155634 | etot = -102.996285179191 +476000 ekin = 16.2366407965404 | erot = 11.9441332898775 | epot = -131.097072928838 | etot = -102.91629884242 +477000 ekin = 16.9351367402763 | erot = 11.440591798362 | epot = -131.185160242912 | etot = -102.809431704274 +478000 ekin = 16.6616408068105 | erot = 13.9256317118027 | epot = -131.205504523652 | etot = -100.618232005039 +479000 ekin = 16.0008851258034 | erot = 12.9062911465348 | epot = -131.145780442706 | etot = -102.238604170368 +480000 ekin = 16.153051360502 | erot = 13.240187162759 | epot = -131.013990091124 | etot = -101.620751567863 +481000 ekin = 15.6997128899876 | erot = 11.8843332525322 | epot = -130.747154689635 | etot = -103.163108547116 +482000 ekin = 15.461547294599 | erot = 13.2334925131229 | epot = -130.409797459234 | etot = -101.714757651513 +483000 ekin = 14.7289085221475 | erot = 13.8000496019692 | epot = -130.027660388389 | etot = -101.498702264272 +484000 ekin = 15.1136508570559 | erot = 14.7539335670785 | epot = -129.477550930602 | etot = -99.6099665064671 +485000 ekin = 14.9321228859757 | erot = 13.8590042781607 | epot = -128.991380995111 | etot = -100.200253830975 +486000 ekin = 14.7668438833204 | erot = 12.7423551235166 | epot = -128.316975757481 | etot = -100.807776750645 +487000 ekin = 14.1678900372468 | erot = 13.0635828461302 | epot = -127.077452878479 | etot = -99.8459799951017 +488000 ekin = 14.8255095560756 | erot = 11.2316156944368 | epot = -127.051028068959 | etot = -100.993902818447 +489000 ekin = 16.3879092432496 | erot = 11.2815960546274 | epot = -128.026161431286 | etot = -100.356656133409 +490000 ekin = 16.959663291994 | erot = 10.2078247857106 | epot = -128.333865657079 | etot = -101.166377579374 +491000 ekin = 17.0348672433699 | erot = 9.25556052315784 | epot = -128.227912452425 | etot = -101.937484685897 +492000 ekin = 17.3483211459634 | erot = 11.4154185591411 | epot = -128.342672201381 | etot = -99.5789324962765 +493000 ekin = 17.2348576252696 | erot = 12.5648739147125 | epot = -128.479394212831 | etot = -98.6796626728493 +494000 ekin = 17.3038003727757 | erot = 11.5672074462369 | epot = -128.660368070501 | etot = -99.7893602514889 +495000 ekin = 17.1258919991972 | erot = 10.7494061195242 | epot = -128.839810873842 | etot = -100.964512755121 +496000 ekin = 17.318497765135 | erot = 10.2788570970333 | epot = -129.065072827865 | etot = -101.467717965696 +497000 ekin = 16.6874850161065 | erot = 10.4744793096002 | epot = -129.221329775903 | etot = -102.059365450196 +498000 ekin = 16.3405856180467 | erot = 11.3228301656308 | epot = -129.433591069646 | etot = -101.770175285969 +499000 ekin = 16.7128261882854 | erot = 13.7857259990512 | epot = -129.662041831932 | etot = -99.1634896445952 +500000 ekin = 16.9053910911621 | erot = 13.0780218271034 | epot = -129.878668968014 | etot = -99.8952560497487 +501000 ekin = 17.0172390257773 | erot = 14.4629157974909 | epot = -130.073458906796 | etot = -98.5933040835274 +502000 ekin = 17.1282261586988 | erot = 14.9539774859395 | epot = -130.221972157653 | etot = -98.139768513015 +503000 ekin = 17.5546036332384 | erot = 14.0883470413025 | epot = -130.278172755496 | etot = -98.6352220809554 +504000 ekin = 17.7985001597182 | erot = 14.3816843432498 | epot = -130.048618111128 | etot = -97.8684336081601 +505000 ekin = 18.5307913625694 | erot = 12.7305066490212 | epot = -129.690487363962 | etot = -98.4291893523712 +506000 ekin = 18.4661491726515 | erot = 12.0237334573043 | epot = -129.398673769567 | etot = -98.908791139611 +507000 ekin = 18.8565072195484 | erot = 11.6213689291001 | epot = -129.173042833474 | etot = -98.6951666848255 +508000 ekin = 18.3032025118119 | erot = 12.724843938206 | epot = -128.981326874503 | etot = -97.9532804244849 +509000 ekin = 18.6502737002307 | erot = 14.0272268632987 | epot = -128.895304531304 | etot = -96.2178039677745 +510000 ekin = 18.0277632428527 | erot = 13.4299302877474 | epot = -128.922916440059 | etot = -97.4652229094587 +511000 ekin = 17.5260110563993 | erot = 13.8282341255303 | epot = -128.903349958923 | etot = -97.5491047769936 +512000 ekin = 17.5517145472481 | erot = 13.3745126006227 | epot = -128.752491335774 | etot = -97.8262641879036 +513000 ekin = 17.1517712141475 | erot = 14.4018924631723 | epot = -128.640382924002 | etot = -97.0867192466822 +514000 ekin = 17.1581698605642 | erot = 15.1222296324458 | epot = -128.708034248345 | etot = -96.4276347553345 +515000 ekin = 15.8051374112764 | erot = 16.1563790359802 | epot = -128.850754192543 | etot = -96.8892377452867 +516000 ekin = 16.5271623960638 | erot = 18.5505467406792 | epot = -128.839438973065 | etot = -93.7617298363215 +517000 ekin = 16.4868139127013 | erot = 17.8014401654955 | epot = -128.74253830514 | etot = -94.4542842269433 +518000 ekin = 16.1006166424232 | erot = 17.5543821079202 | epot = -128.636126775695 | etot = -94.9811280253518 +519000 ekin = 15.1704632807069 | erot = 15.8604600527579 | epot = -128.481628515987 | etot = -97.4507051825225 +520000 ekin = 14.6622666235346 | erot = 15.5338712986971 | epot = -128.255685868565 | etot = -98.0595479463329 +521000 ekin = 14.3504805791432 | erot = 15.6899297514092 | epot = -128.075540396984 | etot = -98.0351300664311 +522000 ekin = 15.0477672454033 | erot = 15.2642093540337 | epot = -127.956172830119 | etot = -97.6441962306822 +523000 ekin = 14.767767681747 | erot = 13.5814717851208 | epot = -127.539779507626 | etot = -99.1905400407585 +524000 ekin = 14.6069196455603 | erot = 14.0177887916875 | epot = -126.88932478628 | etot = -98.2646163490319 +525000 ekin = 14.081308023724 | erot = 15.3056367474803 | epot = -127.428384894989 | etot = -98.0414401237848 +526000 ekin = 14.3879654378154 | erot = 15.628104596299 | epot = -128.290587621559 | etot = -98.2745175874442 +527000 ekin = 15.0091258995447 | erot = 14.9442651630367 | epot = -128.322770264793 | etot = -98.3693792022119 +528000 ekin = 15.1924000588665 | erot = 15.1405044413986 | epot = -128.275488437959 | etot = -97.9425839376937 +529000 ekin = 14.7608909739065 | erot = 15.3127643348495 | epot = -128.247700144926 | etot = -98.1740448361703 +530000 ekin = 15.3870586818276 | erot = 17.9585974777292 | epot = -128.291764568292 | etot = -94.9461084087352 +531000 ekin = 15.8046429679375 | erot = 16.7231918317401 | epot = -128.52991188429 | etot = -96.0020770846121 +532000 ekin = 15.918762785565 | erot = 16.3467928267805 | epot = -129.051901123749 | etot = -96.7863455114031 +533000 ekin = 16.2642911492058 | erot = 16.5689918544283 | epot = -129.745297141318 | etot = -96.9120141376836 +534000 ekin = 15.7517561484693 | erot = 18.8923343381611 | epot = -130.719587510081 | etot = -96.0754970234509 +535000 ekin = 15.8908651165416 | erot = 19.6077755379398 | epot = -131.691278516183 | etot = -96.1926378617015 +536000 ekin = 15.657422720842 | erot = 19.6944676458463 | epot = -132.625422408951 | etot = -97.2735320422625 +537000 ekin = 16.0881374426079 | erot = 20.4410414617136 | epot = -133.669156764979 | etot = -97.1399778606577 +538000 ekin = 15.9042666213089 | erot = 21.6016620321202 | epot = -134.68322491116 | etot = -97.1772962577309 +539000 ekin = 15.9378287613458 | erot = 21.4872325025689 | epot = -135.446877093373 | etot = -98.0218158294586 +540000 ekin = 15.6112840095225 | erot = 21.4497699911127 | epot = -135.957890823285 | etot = -98.8968368226501 +541000 ekin = 15.9288741786483 | erot = 19.8309966465166 | epot = -136.120934942516 | etot = -100.361064117351 +542000 ekin = 16.1419860736591 | erot = 17.9479523532218 | epot = -135.988037745877 | etot = -101.898099318996 +543000 ekin = 15.1824354162597 | erot = 16.8517890600258 | epot = -135.718162913889 | etot = -103.683938437604 +544000 ekin = 15.1827135168603 | erot = 15.0048696624577 | epot = -135.530755245336 | etot = -105.343172066018 +545000 ekin = 15.2741156854232 | erot = 15.8309704071885 | epot = -135.335682223801 | etot = -104.230596131189 +546000 ekin = 15.3924194729537 | erot = 14.2326619353906 | epot = -135.146089024587 | etot = -105.521007616243 +547000 ekin = 15.5751107564637 | erot = 13.9850378083498 | epot = -134.926334665874 | etot = -105.366186101061 +548000 ekin = 15.6139233872879 | erot = 15.2105492461662 | epot = -134.785867443372 | etot = -103.961394809917 +549000 ekin = 15.9319687156595 | erot = 15.5397222622966 | epot = -134.796303225495 | etot = -103.324612247539 +550000 ekin = 16.234796236126 | erot = 15.7998070510281 | epot = -134.850172284878 | etot = -102.815568997724 +551000 ekin = 16.3550656020587 | erot = 16.6976335106374 | epot = -134.834096493945 | etot = -101.781397381248 +552000 ekin = 16.7982250295082 | erot = 16.4108095890454 | epot = -134.741291181816 | etot = -101.532256563263 +553000 ekin = 16.6471135162259 | erot = 15.2737640610373 | epot = -134.450617410391 | etot = -102.529739833128 +554000 ekin = 16.3112091588779 | erot = 15.8022473729795 | epot = -134.007855613491 | etot = -101.894399081633 +555000 ekin = 15.7348233908133 | erot = 15.5059388504751 | epot = -133.433578685387 | etot = -102.192816444099 +556000 ekin = 15.4281960559873 | erot = 16.9241016935445 | epot = -133.073663452995 | etot = -100.721365703463 +557000 ekin = 14.7744254644961 | erot = 16.8791586531569 | epot = -133.076161177793 | etot = -101.42257706014 +558000 ekin = 14.3343095894577 | erot = 17.4876123230497 | epot = -132.797942898459 | etot = -100.976020985951 +559000 ekin = 14.4150967544258 | erot = 17.0562125021645 | epot = -132.359702332896 | etot = -100.888393076306 +560000 ekin = 14.2886839234454 | erot = 15.3656565141194 | epot = -131.965932895964 | etot = -102.311592458399 +561000 ekin = 14.4055433812606 | erot = 14.49600350596 | epot = -131.509933125069 | etot = -102.608386237849 +562000 ekin = 13.8753316850914 | erot = 16.0129944792554 | epot = -131.36607800742 | etot = -101.477751843073 +563000 ekin = 14.3166497861359 | erot = 15.6497012412811 | epot = -131.389436334525 | etot = -101.423085307108 +564000 ekin = 14.9444351561269 | erot = 14.8671616481941 | epot = -131.509916958159 | etot = -101.698320153838 +565000 ekin = 14.9840128733637 | erot = 14.7409927208675 | epot = -131.690758822109 | etot = -101.965753227878 +566000 ekin = 14.6433599870639 | erot = 13.7649316156739 | epot = -131.839622590928 | etot = -103.43133098819 +567000 ekin = 14.8198853756067 | erot = 12.1213853551919 | epot = -132.041023188438 | etot = -105.099752457639 +568000 ekin = 14.5868002517378 | erot = 12.9304551056786 | epot = -132.179975682384 | etot = -104.662720324968 +569000 ekin = 14.4021331261604 | erot = 12.4240110720475 | epot = -132.286232960564 | etot = -105.460088762356 +570000 ekin = 13.7778229675881 | erot = 11.6082627883511 | epot = -132.33298375932 | etot = -106.94689800338 +571000 ekin = 13.9648715298097 | erot = 11.3524654271521 | epot = -132.363295531801 | etot = -107.045958574839 +572000 ekin = 13.8107293610983 | erot = 13.8613894066824 | epot = -132.331162117028 | etot = -104.659043349247 +573000 ekin = 13.9371184623306 | erot = 12.2414755746739 | epot = -132.193123149789 | etot = -106.014529112784 +574000 ekin = 13.4323120702288 | erot = 12.830383211662 | epot = -132.070898945157 | etot = -105.808203663267 +575000 ekin = 14.2619757827425 | erot = 12.4019752034107 | epot = -131.904315635128 | etot = -105.240364648975 +576000 ekin = 14.3013943500202 | erot = 13.1130761591535 | epot = -131.651722356672 | etot = -104.237251847498 +577000 ekin = 13.8761533925322 | erot = 11.5775193912968 | epot = -131.354888112826 | etot = -105.901215328997 +578000 ekin = 12.9607997314117 | erot = 11.474611691305 | epot = -130.997933169007 | etot = -106.56252174629 +579000 ekin = 12.6094040635563 | erot = 11.503345002677 | epot = -130.579175616204 | etot = -106.466426549971 +580000 ekin = 11.8222758511646 | erot = 11.3314724877752 | epot = -130.044918816031 | etot = -106.891170477091 +581000 ekin = 11.5623099891038 | erot = 11.5204236717994 | epot = -129.459203984987 | etot = -106.376470324083 +582000 ekin = 11.0908793705015 | erot = 10.6909997165271 | epot = -128.99217590891 | etot = -107.210296821882 +583000 ekin = 10.0357308165672 | erot = 10.9504193493993 | epot = -128.761952459723 | etot = -107.775802293756 +584000 ekin = 9.96979580895644 | erot = 9.87641882825156 | epot = -128.739676965292 | etot = -108.893462328084 +585000 ekin = 10.3714607356325 | erot = 10.9356679379603 | epot = -128.965365875863 | etot = -107.65823720227 +586000 ekin = 10.4116016162334 | erot = 10.2113529207472 | epot = -129.368180678409 | etot = -108.745226141428 +587000 ekin = 10.237089300975 | erot = 11.7541762306805 | epot = -129.776818849233 | etot = -107.785553317577 +588000 ekin = 11.1220742099154 | erot = 11.0556200106363 | epot = -130.220508468425 | etot = -108.042814247874 +589000 ekin = 11.0340592312317 | erot = 11.7512538500335 | epot = -130.620979376897 | etot = -107.835666295632 +590000 ekin = 10.9311472445812 | erot = 10.8194747946168 | epot = -130.907016299035 | etot = -109.156394259837 +591000 ekin = 10.8163024481065 | erot = 11.9185941116031 | epot = -130.678625125208 | etot = -107.943728565498 +592000 ekin = 10.2172937646583 | erot = 12.6790802107598 | epot = -130.919975024198 | etot = -108.023601048779 +593000 ekin = 10.2938420054994 | erot = 12.9983490935077 | epot = -131.559728955501 | etot = -108.267537856494 +594000 ekin = 10.461577369823 | erot = 11.856264304853 | epot = -131.741951596953 | etot = -109.424109922277 +595000 ekin = 11.056901905874 | erot = 13.1301785758932 | epot = -131.890307818448 | etot = -107.703227336681 +596000 ekin = 11.0132919720099 | erot = 13.9466596433744 | epot = -132.089150727953 | etot = -107.129199112568 +597000 ekin = 10.8378272336451 | erot = 14.3090562620938 | epot = -132.10967433948 | etot = -106.962790843741 +598000 ekin = 11.1396964341323 | erot = 15.2201613294321 | epot = -132.110967353142 | etot = -105.751109589577 +599000 ekin = 11.4366693174268 | erot = 15.9290474447925 | epot = -132.179576664893 | etot = -104.813859902674 +600000 ekin = 11.853069506235 | erot = 16.6980554217788 | epot = -132.413213746698 | etot = -103.862088818684 +601000 ekin = 11.3731393014526 | erot = 16.8988693116771 | epot = -132.603665782831 | etot = -104.331657169701 +602000 ekin = 11.6288846916753 | erot = 17.3084169077548 | epot = -132.790978516308 | etot = -103.853676916878 +603000 ekin = 11.7283808351674 | erot = 15.8876229233384 | epot = -132.845370173479 | etot = -105.229366414973 +604000 ekin = 11.44401932352 | erot = 16.4551108016216 | epot = -132.758081124222 | etot = -104.858950999081 +605000 ekin = 11.7633043618998 | erot = 15.1811098330878 | epot = -132.421221692429 | etot = -105.476807497441 +606000 ekin = 12.1214438326343 | erot = 13.102235854812 | epot = -131.857167552501 | etot = -106.633487865055 +607000 ekin = 12.2353560435281 | erot = 12.9094585695507 | epot = -131.029223534431 | etot = -105.884408921352 +608000 ekin = 13.0019096138754 | erot = 12.6971647076221 | epot = -130.064319041703 | etot = -104.365244720205 +609000 ekin = 12.8925710430578 | erot = 12.2805351934011 | epot = -129.204447610614 | etot = -104.031341374155 +610000 ekin = 13.0900707944407 | erot = 12.0421993054041 | epot = -128.472375430258 | etot = -103.340105330413 +611000 ekin = 13.1247948731074 | erot = 13.1256764839786 | epot = -127.822619969903 | etot = -101.572148612818 +612000 ekin = 13.3183191664132 | erot = 12.96389541794 | epot = -127.296224301128 | etot = -101.014009716775 +613000 ekin = 13.9769629953256 | erot = 11.2865295624435 | epot = -127.055718105206 | etot = -101.792225547436 +614000 ekin = 14.3890395543953 | erot = 9.9248812934263 | epot = -127.074730201449 | etot = -102.760809353627 +615000 ekin = 14.6567050561459 | erot = 9.95992749791948 | epot = -127.478583088677 | etot = -102.861950534611 +616000 ekin = 15.2016814148893 | erot = 9.73164395406493 | epot = -128.043934938619 | etot = -103.110609569665 +617000 ekin = 16.0807025297027 | erot = 9.98598225137266 | epot = -128.723798364128 | etot = -102.657113583052 +618000 ekin = 17.1570301245589 | erot = 10.7358136674337 | epot = -129.417791581699 | etot = -101.524947789706 +619000 ekin = 18.2645203968826 | erot = 9.8387819670336 | epot = -130.058651014826 | etot = -101.95534865091 +620000 ekin = 18.2329353345973 | erot = 10.6434570665445 | epot = -130.794480704669 | etot = -101.918088303528 +621000 ekin = 19.0631853488392 | erot = 11.0524598837306 | epot = -131.52467427776 | etot = -101.40902904519 +622000 ekin = 19.0814697452848 | erot = 9.78841080836808 | epot = -131.948328552335 | etot = -103.078447998682 +623000 ekin = 19.6689115793648 | erot = 10.1108317760386 | epot = -132.182115057445 | etot = -102.402371702042 +624000 ekin = 20.1424435622364 | erot = 9.65005263120131 | epot = -132.29920261852 | etot = -102.506706425083 +625000 ekin = 20.1789761692576 | erot = 9.23340661934284 | epot = -132.290886616266 | etot = -102.878503827665 +626000 ekin = 19.8331329644991 | erot = 9.3446297079685 | epot = -132.226747350546 | etot = -103.048984678079 +627000 ekin = 19.7699917865906 | erot = 10.2063458557855 | epot = -132.017759980705 | etot = -102.041422338329 +628000 ekin = 18.882283265158 | erot = 11.0882601804713 | epot = -131.239811992474 | etot = -101.269268546845 +629000 ekin = 17.8242062169103 | erot = 11.1109911962111 | epot = -130.767645094112 | etot = -101.832447680991 +630000 ekin = 17.3117221567737 | erot = 12.3442278894691 | epot = -130.769105668562 | etot = -101.113155622319 +631000 ekin = 16.6822887154981 | erot = 12.2752035787203 | epot = -130.265480905641 | etot = -101.307988611422 +632000 ekin = 15.9183023976893 | erot = 12.1344670714203 | epot = -129.709637897154 | etot = -101.656868428045 +633000 ekin = 15.8222932056193 | erot = 12.1446443747701 | epot = -129.264109348895 | etot = -101.297171768506 +634000 ekin = 15.5294990051235 | erot = 12.7487113053321 | epot = -128.880873430724 | etot = -100.602663120268 +635000 ekin = 14.9379626100724 | erot = 10.4365299701931 | epot = -128.516843327075 | etot = -103.14235074681 +636000 ekin = 14.2852533918016 | erot = 11.0630154584387 | epot = -128.345040012588 | etot = -102.996771162348 +637000 ekin = 14.4078244478272 | erot = 11.3085354080839 | epot = -128.340632215988 | etot = -102.624272360077 +638000 ekin = 14.7529412454464 | erot = 14.1213788652934 | epot = -128.390352919974 | etot = -99.5160328092347 +639000 ekin = 14.043316889061 | erot = 14.9971425784089 | epot = -128.430633485756 | etot = -99.3901740182862 +640000 ekin = 14.6298336226098 | erot = 15.9727938774897 | epot = -128.496604272929 | etot = -97.8939767728293 +641000 ekin = 15.3122061230573 | erot = 14.4774681815629 | epot = -128.621986682022 | etot = -98.8323123774021 +642000 ekin = 15.2890375006629 | erot = 14.9559327924486 | epot = -128.670108235029 | etot = -98.4251379419172 +643000 ekin = 15.5837329334813 | erot = 12.7894488254017 | epot = -128.794257348761 | etot = -100.421075589878 +644000 ekin = 15.6301920123022 | erot = 12.7652946748823 | epot = -128.920720014312 | etot = -100.525233327127 +645000 ekin = 16.3030902027485 | erot = 14.0541414816075 | epot = -129.049082733824 | etot = -98.6918510494677 +646000 ekin = 16.387120508912 | erot = 12.9699759961764 | epot = -129.005812913628 | etot = -99.6487164085396 +647000 ekin = 16.7825340632155 | erot = 12.4375474757415 | epot = -128.955788501865 | etot = -99.7357069629082 +648000 ekin = 17.0345267264513 | erot = 11.498688698786 | epot = -129.004379745517 | etot = -100.47116432028 +649000 ekin = 16.9014474492138 | erot = 10.7890889406651 | epot = -129.260191565824 | etot = -101.569655175945 +650000 ekin = 16.8382079727115 | erot = 11.8050330618057 | epot = -129.589908653889 | etot = -100.946667619371 +651000 ekin = 17.4628898229135 | erot = 12.660223006772 | epot = -130.068881730979 | etot = -99.945768901294 +652000 ekin = 17.4703226613751 | erot = 13.5606875051042 | epot = -130.491175025567 | etot = -99.4601648590877 +653000 ekin = 18.1727773843547 | erot = 12.9136750169098 | epot = -130.851123572071 | etot = -99.764671170807 +654000 ekin = 17.6403472545997 | erot = 13.2086323043293 | epot = -131.161919457442 | etot = -100.312939898513 +655000 ekin = 18.0364471374451 | erot = 12.730673315801 | epot = -131.279484009004 | etot = -100.512363555758 +656000 ekin = 17.5019828887948 | erot = 13.0457124380727 | epot = -131.215680922562 | etot = -100.667985595694 +657000 ekin = 16.4993263604709 | erot = 13.8475092591096 | epot = -131.083864393325 | etot = -100.737028773744 +658000 ekin = 16.2103148943266 | erot = 14.4272792701112 | epot = -130.758953393232 | etot = -100.121359228794 +659000 ekin = 15.3155231334765 | erot = 15.300672911428 | epot = -130.299493596426 | etot = -99.6832975515214 +660000 ekin = 14.7775646296185 | erot = 14.318768789963 | epot = -129.835015391247 | etot = -100.738681971665 +661000 ekin = 14.6211939768974 | erot = 14.3018056728567 | epot = -129.467486689383 | etot = -100.544487039629 +662000 ekin = 13.8033290738663 | erot = 14.0167939749792 | epot = -129.088469148259 | etot = -101.268346099414 +663000 ekin = 13.3517604154004 | erot = 12.9953072838245 | epot = -129.00407734233 | etot = -102.657009643105 +664000 ekin = 13.164869401324 | erot = 12.3003668005885 | epot = -129.280833610532 | etot = -103.81559740862 +665000 ekin = 12.7516240761356 | erot = 13.46957828534 | epot = -129.642610115282 | etot = -103.421407753806 +666000 ekin = 12.428601414422 | erot = 15.1092276692713 | epot = -130.152421315356 | etot = -102.614592231662 +667000 ekin = 12.3652219511648 | erot = 15.4128826625787 | epot = -130.799059207917 | etot = -103.020954594173 +668000 ekin = 12.8158537102181 | erot = 14.5582755806601 | epot = -131.364605360156 | etot = -103.990476069278 +669000 ekin = 12.8102296122185 | erot = 14.5120954654184 | epot = -131.945100023905 | etot = -104.622774946268 +670000 ekin = 13.3502521648354 | erot = 15.4295134171481 | epot = -132.394803265261 | etot = -103.615037683278 +671000 ekin = 13.8108076753136 | erot = 16.0688444279687 | epot = -132.838606751597 | etot = -102.958954648315 +672000 ekin = 14.5838232105893 | erot = 15.3125733086222 | epot = -133.30925125661 | etot = -103.412854737399 +673000 ekin = 15.1742132287406 | erot = 16.4381989218504 | epot = -133.906648069242 | etot = -102.294235918651 +674000 ekin = 16.1859219219369 | erot = 15.8377995716349 | epot = -134.49689701807 | etot = -102.473175524498 +675000 ekin = 17.3446680932935 | erot = 13.3475717655493 | epot = -134.852992481676 | etot = -104.160752622833 +676000 ekin = 17.4346563797699 | erot = 12.0386615114386 | epot = -134.994900006578 | etot = -105.521582115369 +677000 ekin = 17.7972067821998 | erot = 11.5890865288702 | epot = -134.955733437646 | etot = -105.569440126576 +678000 ekin = 18.4780404610739 | erot = 10.6707684108267 | epot = -134.706550145781 | etot = -105.55774127388 +679000 ekin = 19.4115608214934 | erot = 11.2357386443761 | epot = -134.337308860919 | etot = -103.69000939505 +680000 ekin = 19.2638935241275 | erot = 10.1305651627585 | epot = -133.928210028253 | etot = -104.533751341367 +681000 ekin = 19.6700539624928 | erot = 10.3454431083984 | epot = -133.521042310882 | etot = -103.505545239991 +682000 ekin = 19.3359998209106 | erot = 9.52465902330683 | epot = -132.975182489739 | etot = -104.114523645522 +683000 ekin = 19.4041793989297 | erot = 10.2693839085273 | epot = -132.357095197692 | etot = -102.683531890235 +684000 ekin = 19.026166211252 | erot = 9.93456762161751 | epot = -131.560535171842 | etot = -102.599801338972 +685000 ekin = 18.6259956808663 | erot = 9.04733455903983 | epot = -130.661849534635 | etot = -102.988519294729 +686000 ekin = 18.3252193809328 | erot = 8.74164773568646 | epot = -129.722434721725 | etot = -102.655567605106 +687000 ekin = 18.2985913889226 | erot = 6.9010094761216 | epot = -128.761264951561 | etot = -103.561664086517 +688000 ekin = 17.1315904753568 | erot = 8.37223490765269 | epot = -127.790766521658 | etot = -102.286941138649 +689000 ekin = 16.0662619762064 | erot = 8.69935614114344 | epot = -126.797769670867 | etot = -102.032151553517 +690000 ekin = 15.5579892808636 | erot = 8.12582832183317 | epot = -125.826625319233 | etot = -102.142807716536 +691000 ekin = 15.1272914825974 | erot = 9.02318757728052 | epot = -125.001806902334 | etot = -100.851327842456 +692000 ekin = 14.6723236215967 | erot = 10.703400172422 | epot = -124.169319486656 | etot = -98.7935956926376 +693000 ekin = 13.8886966370099 | erot = 11.671116130368 | epot = -123.541189168181 | etot = -97.9813764008029 +694000 ekin = 13.1382011026418 | erot = 13.5283479389415 | epot = -123.194036250492 | etot = -96.5274872089086 +695000 ekin = 12.0964926850945 | erot = 13.1995540694749 | epot = -122.915258292391 | etot = -97.6192115378217 +696000 ekin = 11.3281129967711 | erot = 14.9673424290163 | epot = -122.804736868637 | etot = -96.5092814428495 +697000 ekin = 11.0523142434049 | erot = 15.1316462810217 | epot = -122.885904665358 | etot = -96.7019441409312 +698000 ekin = 10.4013795972853 | erot = 16.2296085385526 | epot = -122.998327173131 | etot = -96.3673390372936 +699000 ekin = 10.4403816572152 | erot = 17.0183625907827 | epot = -123.009031610283 | etot = -95.550287362285 +700000 ekin = 9.79780839313734 | erot = 13.9825013046653 | epot = -123.10177535537 | etot = -99.3214656575673 +701000 ekin = 10.0228331203457 | erot = 14.5402014480765 | epot = -123.331702326704 | etot = -98.7686677582819 +702000 ekin = 10.1583370722205 | erot = 14.0156743582463 | epot = -123.641637799928 | etot = -99.467626369461 +703000 ekin = 10.7504295035149 | erot = 13.7545908103613 | epot = -124.16407794377 | etot = -99.6590576298937 +704000 ekin = 11.0555457093456 | erot = 13.5050758987755 | epot = -124.646963748962 | etot = -100.086342140841 +705000 ekin = 11.2294460878403 | erot = 13.0729572110628 | epot = -125.183340489607 | etot = -100.880937190704 +706000 ekin = 11.1960604441277 | erot = 13.6558393018561 | epot = -125.346823029996 | etot = -100.494923284012 +707000 ekin = 11.5224708970186 | erot = 14.2142328387688 | epot = -125.594023659238 | etot = -99.8573199234503 +708000 ekin = 12.4522885138737 | erot = 14.0068393183376 | epot = -126.522280655039 | etot = -100.063152822827 +709000 ekin = 13.1367332092944 | erot = 15.5082067332368 | epot = -127.446760898718 | etot = -98.8018209561866 +710000 ekin = 12.8636357026688 | erot = 16.6255199392494 | epot = -127.91771154272 | etot = -98.4285559008017 +711000 ekin = 12.7984924165004 | erot = 15.2391346521185 | epot = -128.148144543905 | etot = -100.110517475286 +712000 ekin = 13.2202326011118 | erot = 13.6182521364317 | epot = -128.236609333929 | etot = -101.398124596385 +713000 ekin = 13.3090397213361 | erot = 13.981639493869 | epot = -128.200674077415 | etot = -100.90999486221 +714000 ekin = 13.8985073914253 | erot = 13.0863826773607 | epot = -128.10019620519 | etot = -101.115306136404 +715000 ekin = 13.885996905945 | erot = 12.9948094828465 | epot = -127.930101523036 | etot = -101.049295134245 +716000 ekin = 14.106857389279 | erot = 14.0369623093788 | epot = -127.800480905385 | etot = -99.656661206727 +717000 ekin = 14.4540296672478 | erot = 13.4757152487838 | epot = -127.824643226067 | etot = -99.8948983100352 +718000 ekin = 14.1953181204468 | erot = 15.6667330495239 | epot = -128.022904943184 | etot = -98.160853773213 +719000 ekin = 14.4864245735426 | erot = 15.7386323499058 | epot = -128.178727752281 | etot = -97.9536708288325 +720000 ekin = 13.9269939971496 | erot = 15.226043410616 | epot = -128.430679285323 | etot = -99.2776418775573 +721000 ekin = 13.6327433698081 | erot = 15.7080046828304 | epot = -128.900974847994 | etot = -99.5602267953555 +722000 ekin = 13.4788212014213 | erot = 16.9760910626494 | epot = -129.353908351043 | etot = -98.8989960869721 +723000 ekin = 13.3028761637196 | erot = 18.2775912497898 | epot = -129.700083283666 | etot = -98.1196158701566 +724000 ekin = 12.6691752727764 | erot = 16.5973718983537 | epot = -129.830238522371 | etot = -100.563691351241 +725000 ekin = 12.3070413253506 | erot = 15.8887922487905 | epot = -129.840396026009 | etot = -101.644562451868 +726000 ekin = 12.2707495639318 | erot = 15.0780506801526 | epot = -129.667036656087 | etot = -102.318236412003 +727000 ekin = 11.5925214307991 | erot = 15.4249879348656 | epot = -129.370935347703 | etot = -102.353425982038 +728000 ekin = 10.7216103683335 | erot = 15.4824090451025 | epot = -128.927805844505 | etot = -102.723786431069 +729000 ekin = 11.2601188060696 | erot = 14.6107591810147 | epot = -128.387799931657 | etot = -102.516921944572 +730000 ekin = 11.7350431387574 | erot = 14.3631564348304 | epot = -128.11528516637 | etot = -102.017085592782 +731000 ekin = 12.1649383518147 | erot = 12.5709808362469 | epot = -128.259955131528 | etot = -103.524035943466 +732000 ekin = 12.8330950236671 | erot = 13.1957218916743 | epot = -128.591480868645 | etot = -102.562663953304 +733000 ekin = 14.0579021361009 | erot = 12.4721190808736 | epot = -129.01668896584 | etot = -102.486667748865 +734000 ekin = 15.1110844917245 | erot = 14.1564583690187 | epot = -129.658961966441 | etot = -100.391419105698 +735000 ekin = 16.0197435513465 | erot = 15.7506353743269 | epot = -130.095893938393 | etot = -98.3255150127193 +736000 ekin = 16.6945847921112 | erot = 14.0449347923322 | epot = -130.436816706858 | etot = -99.6972971224144 +737000 ekin = 17.3343138190244 | erot = 14.3742554067661 | epot = -130.740810773402 | etot = -99.0322415476119 +738000 ekin = 18.8981484545265 | erot = 12.9357766278087 | epot = -131.007399503818 | etot = -99.1734744214827 +739000 ekin = 19.2988391210311 | erot = 12.1612391227699 | epot = -131.273954699358 | etot = -99.8138764555575 +740000 ekin = 20.2335502456846 | erot = 13.8707762253188 | epot = -131.518858021729 | etot = -97.4145315507254 +741000 ekin = 20.5999936430606 | erot = 13.56045545266 | epot = -131.597958334198 | etot = -97.437509238477 +742000 ekin = 20.2070060967488 | erot = 13.4720713375906 | epot = -131.574160466543 | etot = -97.8950830322039 +743000 ekin = 19.3231984278316 | erot = 13.0245409747774 | epot = -131.570025323295 | etot = -99.2222859206864 +744000 ekin = 19.0692503390929 | erot = 13.3141559483165 | epot = -131.341759093758 | etot = -98.9583528063482 +745000 ekin = 18.7189292498279 | erot = 12.7860415040493 | epot = -130.958428498735 | etot = -99.4534577448577 +746000 ekin = 18.6864477092219 | erot = 13.3388758164248 | epot = -130.47236608065 | etot = -98.4470425550029 +747000 ekin = 18.3173313250173 | erot = 13.5192048925161 | epot = -129.93934086301 | etot = -98.102804645477 +748000 ekin = 17.2338254873791 | erot = 14.3282887100115 | epot = -129.639135690737 | etot = -98.0770214933465 +749000 ekin = 17.217794260759 | erot = 12.2095279173813 | epot = -129.677956076542 | etot = -100.250633898402 +750000 ekin = 17.322354821532 | erot = 12.9101450561862 | epot = -130.009913913551 | etot = -99.7774140358331 +751000 ekin = 17.3874781254986 | erot = 13.6449565123365 | epot = -130.565759755778 | etot = -99.5333251179431 +752000 ekin = 17.7210871961908 | erot = 13.2189598604734 | epot = -131.250107148602 | etot = -100.310060091938 +753000 ekin = 18.6045637166674 | erot = 12.3786799107882 | epot = -132.230628292626 | etot = -101.24738466517 +754000 ekin = 18.5359048037749 | erot = 13.4243859321944 | epot = -133.339419375854 | etot = -101.379128639884 +755000 ekin = 18.9630806091571 | erot = 12.5884391627457 | epot = -134.353323108397 | etot = -102.801803336494 +756000 ekin = 19.1389525652221 | erot = 13.6257967260262 | epot = -135.183874892501 | etot = -102.419125601253 +757000 ekin = 19.2074021502121 | erot = 14.6033526373093 | epot = -135.874252378344 | etot = -102.063497590823 +758000 ekin = 19.1121796439063 | erot = 14.9565159725825 | epot = -136.206305523299 | etot = -102.13760990681 +759000 ekin = 19.1423318788173 | erot = 18.5890624901826 | epot = -136.048218209446 | etot = -98.3168238404462 +760000 ekin = 19.5311507779804 | erot = 16.9319255613276 | epot = -135.196917226891 | etot = -98.7338408875827 +761000 ekin = 18.6147988920608 | erot = 15.6150997729969 | epot = -133.761721489726 | etot = -99.5318228246688 +762000 ekin = 17.8898312713857 | erot = 14.3919784323134 | epot = -132.063295505182 | etot = -99.7814858014828 +763000 ekin = 16.6014084140999 | erot = 13.8632351276383 | epot = -130.323724537176 | etot = -99.8590809954376 +764000 ekin = 15.6584053040862 | erot = 12.9328227142933 | epot = -128.610819336276 | etot = -100.019591317897 +765000 ekin = 14.9788909650146 | erot = 12.5622335735393 | epot = -127.241908830151 | etot = -99.7007842915971 +766000 ekin = 14.5477167314164 | erot = 13.7746272613197 | epot = -126.118360786895 | etot = -97.7960167941586 +767000 ekin = 13.785151386018 | erot = 13.0054724982038 | epot = -124.957942870215 | etot = -98.1673189859932 +768000 ekin = 12.7299307163282 | erot = 14.3330120672192 | epot = -124.073635373819 | etot = -97.0106925902719 +769000 ekin = 12.5663714093458 | erot = 15.7541397725442 | epot = -124.280056400595 | etot = -95.9595452187048 +770000 ekin = 12.6586268245375 | erot = 15.8205064764627 | epot = -124.797338115948 | etot = -96.3182048149479 +771000 ekin = 12.7420905608413 | erot = 15.5161183558408 | epot = -125.41812612012 | etot = -97.1599172034378 +772000 ekin = 13.3752757505982 | erot = 16.3556575181108 | epot = -126.376667550792 | etot = -96.6457342820827 +773000 ekin = 13.9072386557489 | erot = 15.8251712655802 | epot = -127.434400026241 | etot = -97.7019901049119 +774000 ekin = 14.8039326477388 | erot = 16.8286892916392 | epot = -128.483851139656 | etot = -96.8512292002783 +775000 ekin = 15.178405990197 | erot = 17.1855437769234 | epot = -129.533536322552 | etot = -97.1695865554315 +776000 ekin = 16.0355953059781 | erot = 16.2149945035646 | epot = -130.461588087407 | etot = -98.2109982778643 +777000 ekin = 16.5740725735003 | erot = 16.2769620755091 | epot = -131.129471274419 | etot = -98.2784366254093 +778000 ekin = 16.5914878474125 | erot = 16.8822871437972 | epot = -131.582835524617 | etot = -98.1090605334069 +779000 ekin = 16.9585306199765 | erot = 18.1118600069992 | epot = -131.783488421451 | etot = -96.7130977944757 +780000 ekin = 17.1625761703625 | erot = 19.3597953749589 | epot = -131.441337383659 | etot = -94.9189658383374 +781000 ekin = 16.607008799517 | erot = 19.1734052522574 | epot = -130.498972879629 | etot = -94.7185588278549 +782000 ekin = 16.0188029390379 | erot = 18.8814179977964 | epot = -128.92093625018 | etot = -94.0207153133457 +783000 ekin = 16.6590593762785 | erot = 17.6330426248957 | epot = -126.777693594422 | etot = -92.4855915932477 +784000 ekin = 17.1256221009035 | erot = 15.9712513941176 | epot = -125.249818046922 | etot = -92.1529445519011 +785000 ekin = 16.7644697237449 | erot = 14.683021546627 | epot = -124.503071625115 | etot = -93.0555803547427 +786000 ekin = 15.9272514347156 | erot = 13.6983194283386 | epot = -123.974122665387 | etot = -94.3485518023324 +787000 ekin = 15.2518811278669 | erot = 14.4286972189706 | epot = -123.380053055365 | etot = -93.6994747085278 +788000 ekin = 14.7800201067714 | erot = 14.8966905407477 | epot = -123.042883666771 | etot = -93.3661730192519 +789000 ekin = 13.9587924065153 | erot = 15.2858717369538 | epot = -123.076065921558 | etot = -93.8314017780887 +790000 ekin = 13.4997511848366 | erot = 14.9015971901407 | epot = -123.274424885105 | etot = -94.8730765101274 +791000 ekin = 13.1836021896654 | erot = 13.7340704634319 | epot = -123.613115013462 | etot = -96.6954423603651 +792000 ekin = 12.5551146629631 | erot = 14.2671534546052 | epot = -124.072772255755 | etot = -97.2505041381865 +793000 ekin = 12.4465743500408 | erot = 13.941846232668 | epot = -124.610645974427 | etot = -98.222225391718 +794000 ekin = 12.3516116802548 | erot = 13.0393126935391 | epot = -125.229879982672 | etot = -99.8389556088777 +795000 ekin = 12.1834181847055 | erot = 11.5146899143675 | epot = -125.915233228096 | etot = -102.217125129023 +796000 ekin = 12.2469931551647 | erot = 12.1050169300559 | epot = -126.709012662144 | etot = -102.357002576923 +797000 ekin = 12.0691786690398 | erot = 12.2260306613053 | epot = -127.472934929817 | etot = -103.177725599472 +798000 ekin = 12.546533710265 | erot = 11.4457889364443 | epot = -128.179008612303 | etot = -104.186685965594 +799000 ekin = 12.8791491099679 | erot = 10.060246353311 | epot = -128.639424952832 | etot = -105.700029489553 +800000 ekin = 13.2109066844622 | erot = 10.7000400173374 | epot = -128.819221531374 | etot = -104.908274829574 +801000 ekin = 13.2793064836633 | erot = 10.3859354697956 | epot = -129.046956014284 | etot = -105.381714060825 +802000 ekin = 14.5291962548604 | erot = 11.0806161640772 | epot = -129.189781403971 | etot = -103.579968985034 +803000 ekin = 14.9582823531098 | erot = 9.46888824567808 | epot = -129.484049661632 | etot = -105.056879062844 +804000 ekin = 15.1985526581724 | erot = 10.6605068656839 | epot = -130.062154301077 | etot = -104.203094777221 +805000 ekin = 16.7115156945225 | erot = 13.346383471139 | epot = -131.001035992376 | etot = -100.943136826715 +806000 ekin = 17.935509195607 | erot = 15.3128910018764 | epot = -132.157347563542 | etot = -98.9089473660586 +807000 ekin = 18.3821058880095 | erot = 16.14694932317 | epot = -133.465954330989 | etot = -98.9368991198099 +808000 ekin = 18.4586740171017 | erot = 17.4186582435822 | epot = -134.756056842451 | etot = -98.8787245817669 +809000 ekin = 18.7143084542808 | erot = 16.4886282039559 | epot = -135.894878253586 | etot = -100.691941595349 +810000 ekin = 19.0717768833682 | erot = 18.2428020006286 | epot = -136.687610350024 | etot = -99.3730314660267 +811000 ekin = 19.3496015982741 | erot = 16.4166081200059 | epot = -137.087270702521 | etot = -101.321060984241 +812000 ekin = 18.8132921241844 | erot = 15.9355446496578 | epot = -137.109850002122 | etot = -102.361013228279 +813000 ekin = 17.5780403458912 | erot = 16.589165974413 | epot = -136.832999774061 | etot = -102.665793453757 +814000 ekin = 16.9449349535852 | erot = 17.5355957376612 | epot = -136.448934903829 | etot = -101.968404212583 +815000 ekin = 16.4703461010998 | erot = 19.1081842556833 | epot = -136.023652788487 | etot = -100.445122431704 +816000 ekin = 15.4664613390496 | erot = 17.6089822900762 | epot = -135.500704387562 | etot = -102.425260758436 +817000 ekin = 14.8681799821529 | erot = 15.3789825951142 | epot = -135.067114620736 | etot = -104.819952043469 +818000 ekin = 14.05269006138 | erot = 15.7402575489113 | epot = -134.625228894631 | etot = -104.83228128434 +819000 ekin = 13.183800831223 | erot = 13.2388271719912 | epot = -134.209702435244 | etot = -107.78707443203 +820000 ekin = 12.7761038226944 | erot = 13.3080976281738 | epot = -133.968394808085 | etot = -107.884193357216 +821000 ekin = 12.0253186296979 | erot = 13.6405698743307 | epot = -133.760065335415 | etot = -108.094176831387 +822000 ekin = 11.6630918105698 | erot = 12.6998301503219 | epot = -133.53195707022 | etot = -109.169035109328 +823000 ekin = 11.1167413317975 | erot = 14.6011325366125 | epot = -133.461022910971 | etot = -107.743149042562 +824000 ekin = 10.4746391502229 | erot = 12.4758719121113 | epot = -133.511978718426 | etot = -110.561467656092 +825000 ekin = 10.2356976729896 | erot = 12.2904218215826 | epot = -133.700356379562 | etot = -111.17423688499 +826000 ekin = 9.83096239396682 | erot = 11.3745267667888 | epot = -134.123382625473 | etot = -112.917893464718 +827000 ekin = 9.64229733033127 | erot = 12.6419283491478 | epot = -134.603992066152 | etot = -112.319766386673 +828000 ekin = 8.97025933237731 | erot = 11.6048742407818 | epot = -135.011510030303 | etot = -114.436376457144 +829000 ekin = 9.10808626487462 | erot = 13.3671751049059 | epot = -135.176544462071 | etot = -112.701283092291 +830000 ekin = 9.38415183018099 | erot = 13.9027284879972 | epot = -135.380837696259 | etot = -112.093957378081 +831000 ekin = 9.89782748978174 | erot = 14.6473467563042 | epot = -135.550784581084 | etot = -111.005610334998 +832000 ekin = 9.61617429521492 | erot = 14.1142221016976 | epot = -135.565476488835 | etot = -111.835080091923 +833000 ekin = 9.37805099397741 | erot = 14.5448882534449 | epot = -135.557208351876 | etot = -111.634269104454 +834000 ekin = 9.60363615354897 | erot = 13.5658256076977 | epot = -135.503370790537 | etot = -112.33390902929 +835000 ekin = 10.1994042034093 | erot = 13.4310767815474 | epot = -135.486182184481 | etot = -111.855701199524 +836000 ekin = 9.90258198197248 | erot = 14.0997630061159 | epot = -135.415036673347 | etot = -111.412691685258 +837000 ekin = 9.23061363929233 | erot = 13.1013581784861 | epot = -135.377162328567 | etot = -113.045190510789 +838000 ekin = 9.22678257596562 | erot = 11.7950777786698 | epot = -135.309708937396 | etot = -114.287848582761 +839000 ekin = 9.31364044689879 | erot = 9.19117521815819 | epot = -135.224645715934 | etot = -116.719830050877 +840000 ekin = 9.95651666063242 | erot = 10.2562033846855 | epot = -135.050789715828 | etot = -114.83806967051 +841000 ekin = 10.1329136337983 | erot = 11.1215377358375 | epot = -134.844846156174 | etot = -113.590394786538 +842000 ekin = 9.81306935601066 | erot = 11.8450714037862 | epot = -134.621170352062 | etot = -112.963029592265 +843000 ekin = 9.6014172601031 | erot = 11.5647290918967 | epot = -134.324999225728 | etot = -113.158852873729 +844000 ekin = 9.87980157515639 | erot = 12.3554353870616 | epot = -134.065834194652 | etot = -111.830597232434 +845000 ekin = 9.93780379927978 | erot = 12.0090921548411 | epot = -133.814970563149 | etot = -111.868074609028 +846000 ekin = 10.4775554235282 | erot = 12.1654574191588 | epot = -133.472543158636 | etot = -110.829530315949 +847000 ekin = 10.0026611797418 | erot = 11.6213808792176 | epot = -133.066600825389 | etot = -111.44255876643 +848000 ekin = 10.5520984068296 | erot = 11.6099997320351 | epot = -132.780981683409 | etot = -110.618883544544 +849000 ekin = 10.7448279920532 | erot = 11.4890837546211 | epot = -132.676110820266 | etot = -110.442199073591 +850000 ekin = 10.8113038660881 | erot = 10.9488089735479 | epot = -132.895254583106 | etot = -111.13514174347 +851000 ekin = 11.2511239289073 | erot = 11.8929283018388 | epot = -133.389075417486 | etot = -110.24502318674 +852000 ekin = 11.044204555781 | erot = 12.4402386301468 | epot = -134.143640073191 | etot = -110.659196887264 +853000 ekin = 11.7246156001573 | erot = 14.7235683156687 | epot = -135.052215505121 | etot = -108.604031589295 +854000 ekin = 11.8684738498269 | erot = 16.8582257926897 | epot = -136.115564410014 | etot = -107.388864767497 +855000 ekin = 12.0538531934163 | erot = 16.4968100795581 | epot = -137.007305545871 | etot = -108.456642272897 +856000 ekin = 11.8401943131307 | erot = 17.2853860946902 | epot = -137.587232095186 | etot = -108.461651687365 +857000 ekin = 11.599621890787 | erot = 16.4784196407965 | epot = -137.876240736872 | etot = -109.798199205288 +858000 ekin = 10.5710249607862 | erot = 17.774578899555 | epot = -137.72393299091 | etot = -109.378329130569 +859000 ekin = 10.4697302561029 | erot = 17.597107441915 | epot = -137.270423002965 | etot = -109.203585304947 +860000 ekin = 10.1406561107331 | erot = 15.3180480162168 | epot = -136.644343040593 | etot = -111.185638913643 +861000 ekin = 9.65715456935708 | erot = 15.5614532259773 | epot = -135.848542830414 | etot = -110.62993503508 +862000 ekin = 9.85528367938723 | erot = 15.4449729727622 | epot = -134.939823071984 | etot = -109.639566419835 +863000 ekin = 9.69076776402144 | erot = 13.8617702176826 | epot = -134.057449790282 | etot = -110.504911808578 +864000 ekin = 9.83691178944935 | erot = 14.4145092716249 | epot = -133.22233410367 | etot = -108.970913042596 +865000 ekin = 9.70884152940973 | erot = 14.4808352209294 | epot = -132.563697713287 | etot = -108.374020962948 +866000 ekin = 9.11283566820104 | erot = 14.5204631481052 | epot = -131.937901154687 | etot = -108.304602338381 +867000 ekin = 9.2135658001457 | erot = 15.2722616926324 | epot = -131.396165375322 | etot = -106.910337882544 +868000 ekin = 9.07317508153068 | erot = 15.2281990898813 | epot = -131.118523212643 | etot = -106.817149041231 +869000 ekin = 9.56719467261706 | erot = 12.8413524494189 | epot = -131.01323487078 | etot = -108.604687748744 +870000 ekin = 9.72249968111539 | erot = 13.7134538695638 | epot = -131.218120667046 | etot = -107.782167116366 +871000 ekin = 9.85996645893833 | erot = 13.6635792026521 | epot = -131.558103225477 | etot = -108.034557563886 +872000 ekin = 10.4752428180374 | erot = 11.8752328723624 | epot = -131.888428620607 | etot = -109.537952930207 +873000 ekin = 10.8938008841087 | erot = 12.8115939555363 | epot = -132.291734739806 | etot = -108.58633990016 +874000 ekin = 10.8667098405276 | erot = 12.7998561629061 | epot = -132.641951772155 | etot = -108.975385768721 +875000 ekin = 11.5409462432229 | erot = 12.4790882752089 | epot = -132.897239389184 | etot = -108.877204870753 +876000 ekin = 12.2883954932043 | erot = 10.1693017030717 | epot = -133.13826440665 | etot = -110.680567210374 +877000 ekin = 11.9868365460025 | erot = 11.1973354913962 | epot = -133.277164876379 | etot = -110.092992838981 +878000 ekin = 11.7960623014163 | erot = 11.5665973071625 | epot = -133.204556406453 | etot = -109.841896797874 +879000 ekin = 11.3794101440003 | erot = 12.3887904161458 | epot = -133.070672059809 | etot = -109.302471499663 +880000 ekin = 10.7473007273139 | erot = 12.155950661048 | epot = -132.937567335563 | etot = -110.034315947201 +881000 ekin = 11.0382243859572 | erot = 11.3700738104817 | epot = -132.69132443217 | etot = -110.283026235731 +882000 ekin = 11.0268715692644 | erot = 11.2476396846495 | epot = -132.362248590805 | etot = -110.087737336891 +883000 ekin = 11.0960831022765 | erot = 12.1675015631156 | epot = -132.006051221569 | etot = -108.742466556177 +884000 ekin = 10.4356706372254 | erot = 14.3790792419536 | epot = -131.703683205292 | etot = -106.888933326113 +885000 ekin = 10.1809074114291 | erot = 12.6512885344041 | epot = -131.510977940224 | etot = -108.678781994391 +886000 ekin = 9.88536804636765 | erot = 14.3207405049851 | epot = -131.378147411038 | etot = -107.172038859686 +887000 ekin = 9.62079843372949 | erot = 15.0371337320698 | epot = -131.400485267651 | etot = -106.742553101851 +888000 ekin = 9.73389413938928 | erot = 15.1710263384175 | epot = -131.650272106319 | etot = -106.745351628512 +889000 ekin = 9.34497189726216 | erot = 17.4864380141716 | epot = -132.135997200666 | etot = -105.304587289232 +890000 ekin = 9.50892312765913 | erot = 17.8223441845159 | epot = -132.732936870751 | etot = -105.401669558576 +891000 ekin = 9.34170617038541 | erot = 20.6177451138689 | epot = -133.434405161174 | etot = -103.47495387692 +892000 ekin = 9.22652718687059 | erot = 22.2205451959243 | epot = -134.045766158437 | etot = -102.598693775642 +893000 ekin = 9.51353526251288 | erot = 21.3492467917455 | epot = -134.582423327744 | etot = -103.719641273486 +894000 ekin = 9.68540627216124 | erot = 20.7203124322274 | epot = -134.963692741512 | etot = -104.557974037123 +895000 ekin = 9.95671082160135 | erot = 20.8661564008034 | epot = -135.108391715319 | etot = -104.285524492914 +896000 ekin = 9.25648303222798 | erot = 18.4512526441791 | epot = -135.123937491507 | etot = -107.4162018151 +897000 ekin = 9.53459318473638 | erot = 19.0120970545174 | epot = -134.990076473698 | etot = -106.443386234444 +898000 ekin = 9.77485480011757 | erot = 21.0086049051177 | epot = -134.565691552272 | etot = -103.782231847037 +899000 ekin = 10.4975912485659 | erot = 21.3211384106303 | epot = -134.121541482168 | etot = -102.302811822972 +900000 ekin = 10.7040034570073 | erot = 20.7049887334994 | epot = -133.718651895895 | etot = -102.309659705389 +901000 ekin = 11.3149377516008 | erot = 18.3638364663083 | epot = -133.36706652203 | etot = -103.688292304121 +902000 ekin = 11.0832893000046 | erot = 21.0463442003965 | epot = -133.101677545994 | etot = -100.972044045593 +903000 ekin = 10.8652645352773 | erot = 17.5135253954939 | epot = -132.746316141513 | etot = -104.367526210742 +904000 ekin = 10.9199231545732 | erot = 16.5086841323364 | epot = -132.400898639401 | etot = -104.972291352492 +905000 ekin = 11.8265529183729 | erot = 14.2338803732188 | epot = -132.222926764547 | etot = -106.162493472955 +906000 ekin = 12.1112443730427 | erot = 13.9046851351739 | epot = -132.108887856991 | etot = -106.092958348775 +907000 ekin = 12.7249921890105 | erot = 14.8976247467494 | epot = -131.902848545294 | etot = -104.280231609534 +908000 ekin = 13.6491269150615 | erot = 13.1132074135062 | epot = -131.679328194016 | etot = -104.916993865448 +909000 ekin = 13.4654192893617 | erot = 12.4026216006941 | epot = -131.510323746492 | etot = -105.642282856436 +910000 ekin = 13.3669089746771 | erot = 12.2515043108096 | epot = -131.279564850064 | etot = -105.661151564577 +911000 ekin = 13.1803758942232 | erot = 12.3776233805492 | epot = -130.939217067511 | etot = -105.381217792738 +912000 ekin = 13.4936182562076 | erot = 13.0646784895681 | epot = -130.523318371126 | etot = -103.965021625351 +913000 ekin = 13.4654133940855 | erot = 12.7992887229988 | epot = -130.057711790665 | etot = -103.793009673581 +914000 ekin = 13.2424883715306 | erot = 12.5762407989739 | epot = -129.735396069255 | etot = -103.916666898751 +915000 ekin = 13.7568260961906 | erot = 11.979358786625 | epot = -129.408246543188 | etot = -103.672061660372 +916000 ekin = 13.8329970070235 | erot = 13.4868801631182 | epot = -129.017837864616 | etot = -101.697960694474 +917000 ekin = 13.6739342498415 | erot = 14.0172019245937 | epot = -128.74257584105 | etot = -101.051439666615 +918000 ekin = 13.245471595107 | erot = 15.951967354764 | epot = -128.617123842226 | etot = -99.4196848923551 +919000 ekin = 12.9797138485786 | erot = 14.9345708711274 | epot = -128.733889181863 | etot = -100.819604462157 +920000 ekin = 12.2436001260489 | erot = 13.6267663169795 | epot = -128.905668726167 | etot = -103.035302283138 +921000 ekin = 11.6805154863491 | erot = 14.6040007578678 | epot = -129.025116647105 | etot = -102.740600402888 +922000 ekin = 11.2509613017982 | erot = 13.1615261905601 | epot = -129.013398954601 | etot = -104.600911462243 +923000 ekin = 11.0530387912639 | erot = 14.8051452828429 | epot = -128.882878859975 | etot = -103.024694785868 +924000 ekin = 10.864428957365 | erot = 14.5487695471967 | epot = -128.635895835237 | etot = -103.222697330675 +925000 ekin = 10.4368013074651 | erot = 15.9506322379272 | epot = -128.538691204592 | etot = -102.1512576592 +926000 ekin = 10.8708234501058 | erot = 14.499435338498 | epot = -128.530880030449 | etot = -103.160621241845 +927000 ekin = 10.1756205898105 | erot = 14.9151755779541 | epot = -128.657945645067 | etot = -103.567149477302 +928000 ekin = 9.79032376464694 | erot = 15.1711554438299 | epot = -128.994657707943 | etot = -104.033178499466 +929000 ekin = 10.0135841647818 | erot = 13.5327974045767 | epot = -129.564299260408 | etot = -106.01791769105 +930000 ekin = 10.7232337588077 | erot = 14.4150772232789 | epot = -130.372253794754 | etot = -105.233942812668 +931000 ekin = 10.957250201845 | erot = 15.0298851642653 | epot = -131.309548641823 | etot = -105.322413275712 +932000 ekin = 11.3959980921443 | erot = 14.9867277427775 | epot = -132.358040832085 | etot = -105.975314997164 +933000 ekin = 12.4008984499258 | erot = 15.1859215644479 | epot = -133.399347144136 | etot = -105.812527129763 +934000 ekin = 12.8178650688633 | erot = 14.1063647076232 | epot = -134.260016847604 | etot = -107.335787071118 +935000 ekin = 13.4125148241317 | erot = 15.5991487655469 | epot = -135.013664838076 | etot = -106.002001248398 +936000 ekin = 13.5923426534851 | erot = 17.2538639887924 | epot = -135.505358908873 | etot = -104.659152266595 +937000 ekin = 13.4400246720306 | erot = 16.0596443449443 | epot = -135.603355890124 | etot = -106.103686873149 +938000 ekin = 13.6103529372685 | erot = 15.1920952210033 | epot = -135.267026708504 | etot = -106.464578550232 +939000 ekin = 13.2221334283198 | erot = 14.3711020679947 | epot = -134.526020035158 | etot = -106.932784538844 +940000 ekin = 13.0406740143487 | erot = 13.3893112135224 | epot = -133.398922419693 | etot = -106.968937191822 +941000 ekin = 11.7807611095563 | erot = 12.6169081908774 | epot = -132.064733106846 | etot = -107.667063806413 +942000 ekin = 10.8560631703933 | erot = 12.1028950338682 | epot = -130.673314662297 | etot = -107.714356458035 +943000 ekin = 10.5643065816831 | erot = 11.8423377277436 | epot = -129.594814920542 | etot = -107.188170611116 +944000 ekin = 10.370989663475 | erot = 12.0833746672059 | epot = -128.740658913622 | etot = -106.286294582941 +945000 ekin = 10.2962804558076 | erot = 13.1799266129607 | epot = -128.223752772124 | etot = -104.747545703355 +946000 ekin = 11.3534838321474 | erot = 12.7383974360111 | epot = -128.032202727824 | etot = -103.940321459666 +947000 ekin = 12.071576442379 | erot = 13.711541060477 | epot = -128.004967672372 | etot = -102.221850169516 +948000 ekin = 12.1245321275793 | erot = 12.6107396971468 | epot = -128.117296095249 | etot = -103.382024270523 +949000 ekin = 12.90805889959 | erot = 11.8866900148027 | epot = -128.337539014419 | etot = -103.542790100027 +950000 ekin = 13.3527995691362 | erot = 12.6583339419699 | epot = -128.832022322223 | etot = -102.820888811117 +951000 ekin = 14.0353166034226 | erot = 12.4887352237453 | epot = -129.414227058798 | etot = -102.89017523163 +952000 ekin = 14.4539614182342 | erot = 15.5615058449647 | epot = -129.957345323999 | etot = -99.9418780608004 +953000 ekin = 15.3508256645353 | erot = 15.6454407354306 | epot = -130.579053532496 | etot = -99.5827871325296 +954000 ekin = 15.9073052013717 | erot = 14.8907336374863 | epot = -130.944475184772 | etot = -100.146436345914 +955000 ekin = 17.0707787056887 | erot = 16.1503176017207 | epot = -131.120438402122 | etot = -97.8993420947125 +956000 ekin = 18.4222164929532 | erot = 15.6543247459001 | epot = -131.085064350135 | etot = -97.0085231112819 +957000 ekin = 18.2181636890142 | erot = 16.8789809387867 | epot = -130.704563934414 | etot = -95.6074193066135 +958000 ekin = 18.7457849087942 | erot = 15.2649074372207 | epot = -129.893126844032 | etot = -95.882434498017 +959000 ekin = 18.8948326127131 | erot = 14.8187025948101 | epot = -128.827607813188 | etot = -95.1140726056646 +960000 ekin = 17.9232164812531 | erot = 14.5006592659995 | epot = -127.512494075793 | etot = -95.0886183285401 +961000 ekin = 17.5283007778538 | erot = 13.6318013254001 | epot = -125.965759972438 | etot = -94.8056578691841 +962000 ekin = 17.1087856720778 | erot = 13.5209597244085 | epot = -124.308831476352 | etot = -93.6790860798655 +963000 ekin = 16.2294672761422 | erot = 12.0982940138005 | epot = -122.756343433097 | etot = -94.4285821431539 +964000 ekin = 15.217906775052 | erot = 11.3466076337834 | epot = -121.35364013365 | etot = -94.7891257248148 +965000 ekin = 14.4571904869347 | erot = 11.1958015829203 | epot = -120.159287462331 | etot = -94.5062953924763 +966000 ekin = 13.713691048934 | erot = 12.2763392569664 | epot = -119.373509436091 | etot = -93.383479130191 +967000 ekin = 13.0525275313628 | erot = 13.3325378981858 | epot = -118.754627961849 | etot = -92.3695625323 +968000 ekin = 12.6258253330282 | erot = 13.6667960669937 | epot = -118.263761246798 | etot = -91.9711398467763 +969000 ekin = 12.093963793091 | erot = 12.6851784652315 | epot = -118.10172157237 | etot = -93.322579314047 +970000 ekin = 12.2814352863516 | erot = 13.1741722808913 | epot = -118.084891935487 | etot = -92.6292843682446 +971000 ekin = 12.336963793396 | erot = 14.287178261779 | epot = -118.240142548498 | etot = -91.6160004933226 +972000 ekin = 12.7123353326953 | erot = 15.0155999303371 | epot = -118.41298000455 | etot = -90.6850447415176 +973000 ekin = 13.0472009182221 | erot = 16.2295024444777 | epot = -118.471843214116 | etot = -89.1951398514163 +974000 ekin = 12.388354969002 | erot = 17.4722487948746 | epot = -118.364598615294 | etot = -88.5039948514174 +975000 ekin = 11.9685102758026 | erot = 15.3885917283584 | epot = -118.090409410582 | etot = -90.7333074064213 +976000 ekin = 11.3088073476216 | erot = 15.2854132762829 | epot = -117.800271375519 | etot = -91.2060507516144 +977000 ekin = 10.8710842145684 | erot = 15.2909542063552 | epot = -117.349796621949 | etot = -91.1877582010249 +978000 ekin = 10.817860138762 | erot = 13.2276696679694 | epot = -117.117297916081 | etot = -93.0717681093499 +979000 ekin = 11.0709902353881 | erot = 12.5293846344496 | epot = -117.175595959156 | etot = -93.5752210893179 +980000 ekin = 11.2965161569289 | erot = 11.1601040800375 | epot = -117.277906119498 | etot = -94.8212858825316 +981000 ekin = 11.6690570838973 | erot = 10.7736458692936 | epot = -117.768958129291 | etot = -95.3262551760997 +982000 ekin = 12.1575161392224 | erot = 11.9678903157896 | epot = -118.550912187072 | etot = -94.4255057320603 +983000 ekin = 12.4067474872099 | erot = 12.7193186844112 | epot = -119.304867426008 | etot = -94.1788012543873 +984000 ekin = 13.5940880425583 | erot = 13.7165337446016 | epot = -120.273805342163 | etot = -92.9631835550026 +985000 ekin = 13.8874336321484 | erot = 14.1076224004122 | epot = -121.273851753427 | etot = -93.2787957208661 +986000 ekin = 14.1136768141539 | erot = 14.3150637930082 | epot = -122.271363839249 | etot = -93.8426232320867 +987000 ekin = 14.5776610706687 | erot = 15.5141413343671 | epot = -123.255640154049 | etot = -93.1638377490135 +988000 ekin = 14.821884995834 | erot = 15.312967168187 | epot = -124.232918811331 | etot = -94.0980666473104 +989000 ekin = 15.646855689107 | erot = 16.5736195699528 | epot = -125.090514341493 | etot = -92.8700390824336 +990000 ekin = 16.1676158963034 | erot = 18.2046608708844 | epot = -125.736029858856 | etot = -91.3637530916681 +991000 ekin = 16.9467094059315 | erot = 20.3489064269837 | epot = -126.034194682764 | etot = -88.7385788498484 +992000 ekin = 17.1946688955272 | erot = 20.6446832139068 | epot = -126.023723568376 | etot = -88.1843714589421 +993000 ekin = 17.0492861030736 | erot = 20.2357766473302 | epot = -125.775974072184 | etot = -88.4909113217802 +994000 ekin = 17.2852712785184 | erot = 21.9253125145711 | epot = -125.462594884831 | etot = -86.2520110917411 +995000 ekin = 16.9781200706309 | erot = 23.024520231669 | epot = -125.08695964599 | etot = -85.0843193436903 +996000 ekin = 17.1233597247117 | erot = 20.1219478311412 | epot = -124.661238194914 | etot = -87.415930639061 +997000 ekin = 16.9435496098567 | erot = 19.2980117125048 | epot = -124.068366062786 | etot = -87.826804740424 +998000 ekin = 17.0875482949223 | erot = 19.7008126514126 | epot = -123.301709192639 | etot = -86.5133482463046 +999000 ekin = 17.3864595030106 | erot = 19.031153747846 | epot = -122.410040365131 | etot = -85.9924271142742 +1000000 ekin = 17.4266501863313 | erot = 15.93443523795 | epot = -121.571786609929 | etot = -88.2107011856477 + 1000000 389.752 -124.64554 3.0737557 -104.14514 0.13705163 39304000 +Loop time of 40.2662 on 1 procs for 1000000 steps with 16 atoms + +Performance: 36.606 ns/day, 0.656 hours/ns, 24834.718 timesteps/s, 397.355 katom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 33.133 | 33.133 | 33.133 | 0.0 | 82.29 +Bond | 1.0208 | 1.0208 | 1.0208 | 0.0 | 2.54 +Neigh | 0.014956 | 0.014956 | 0.014956 | 0.0 | 0.04 +Comm | 0.45341 | 0.45341 | 0.45341 | 0.0 | 1.13 +Output | 0.19799 | 0.19799 | 0.19799 | 0.0 | 0.49 +Modify | 4.9747 | 4.9747 | 4.9747 | 0.0 | 12.35 +Other | | 0.4711 | | | 1.17 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 107 ave 107 max 107 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:40 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.4 new file mode 100644 index 0000000000..3233f455ba --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.4 @@ -0,0 +1,1188 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -125.483166681887 | etot = -92.6645914514142 +Per MPI rank memory allocation (min/avg/max) = 7.569 | 7.598 | 7.682 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -129.82524 4.3420686 -109.36284 0.039706925 39304000 +1000 ekin = 16.2120472606819 | erot = 18.1599496095378 | epot = -124.47446317797 | etot = -90.1024663077499 +2000 ekin = 16.569523519944 | erot = 14.9387890105384 | epot = -123.413037171619 | etot = -91.9047246411363 +3000 ekin = 16.4908981186509 | erot = 13.6022192081955 | epot = -122.618623142256 | etot = -92.5255058154098 +4000 ekin = 16.1079626485056 | erot = 13.5539684119038 | epot = -122.040001090416 | etot = -92.3780700300069 +5000 ekin = 15.7490458706807 | erot = 13.7529778402768 | epot = -121.760686807838 | etot = -92.2586630968809 +6000 ekin = 15.8428165570837 | erot = 14.2502773311176 | epot = -121.767450145962 | etot = -91.6743562577603 +7000 ekin = 15.9930293388895 | erot = 13.8930009158471 | epot = -122.067912874246 | etot = -92.1818826195096 +8000 ekin = 15.4451133848386 | erot = 12.249209392774 | epot = -122.594420596747 | etot = -94.9000978191339 +9000 ekin = 15.8183735214535 | erot = 12.6133069460231 | epot = -123.340212226912 | etot = -94.9085317594357 +10000 ekin = 16.535439472141 | erot = 15.2936296416421 | epot = -124.081517045064 | etot = -92.2524479312809 +11000 ekin = 15.9395821485727 | erot = 17.2008757458576 | epot = -124.746525377503 | etot = -91.6060674830729 +12000 ekin = 16.0567583424423 | erot = 15.8997870466905 | epot = -125.443598760626 | etot = -93.4870533714936 +13000 ekin = 16.5926769852673 | erot = 15.6504724986658 | epot = -126.226565885733 | etot = -93.9834164017998 +14000 ekin = 16.9649776823382 | erot = 14.5154924112931 | epot = -126.96779874908 | etot = -95.4873286554489 +15000 ekin = 17.2219022906044 | erot = 14.4222207314166 | epot = -127.675598676166 | etot = -96.0314756541453 +16000 ekin = 17.9281730599184 | erot = 15.6859352211796 | epot = -128.337601046979 | etot = -94.7234927658809 +17000 ekin = 18.4043998368515 | erot = 15.0909736720528 | epot = -128.832635802353 | etot = -95.3372622934491 +18000 ekin = 17.7394231189163 | erot = 15.1306161764218 | epot = -129.023891968365 | etot = -96.1538526730274 +19000 ekin = 17.1958950052057 | erot = 15.1680082581212 | epot = -128.898186954897 | etot = -96.5342836915701 +20000 ekin = 15.8516332333669 | erot = 16.7058914738762 | epot = -128.507784811667 | etot = -95.950260104424 +21000 ekin = 15.3509821386759 | erot = 16.3911313534803 | epot = -127.947905478546 | etot = -96.2057919863899 +22000 ekin = 15.1100010513728 | erot = 16.3348681764445 | epot = -127.221649361758 | etot = -95.776780133941 +23000 ekin = 14.3101532123339 | erot = 14.38065004198 | epot = -126.406723576818 | etot = -97.7159203225042 +24000 ekin = 14.0207984762248 | erot = 12.5239038407953 | epot = -125.590087936679 | etot = -99.0453856196591 +25000 ekin = 13.3656192606566 | erot = 13.0304610110196 | epot = -124.906913530424 | etot = -98.5108332587476 +26000 ekin = 12.8395028721761 | erot = 14.6487786191907 | epot = -124.40414059954 | etot = -96.9158591081734 +27000 ekin = 11.5343405898753 | erot = 13.9892144028629 | epot = -124.200412248635 | etot = -98.6768572558971 +28000 ekin = 10.5463186496732 | erot = 14.3895195737251 | epot = -124.136381678731 | etot = -99.2005434553325 +29000 ekin = 10.4413332151611 | erot = 13.1777197784759 | epot = -124.323320612244 | etot = -100.704267618607 +30000 ekin = 10.0863233068856 | erot = 14.5118674812463 | epot = -124.667168249704 | etot = -100.068977461572 +31000 ekin = 10.2842652760412 | erot = 13.8593404324917 | epot = -125.254827370216 | etot = -101.111221661683 +32000 ekin = 11.0369237762493 | erot = 14.1309061312588 | epot = -126.01859175301 | etot = -100.850761845502 +33000 ekin = 11.5007214031922 | erot = 15.2138037514642 | epot = -126.914330568133 | etot = -100.199805413476 +34000 ekin = 11.1182029321626 | erot = 16.1228716001976 | epot = -128.05001788579 | etot = -100.808943353429 +35000 ekin = 10.8779964621956 | erot = 17.1808476098023 | epot = -129.33602603389 | etot = -101.277181961892 +36000 ekin = 11.082269976749 | erot = 16.6476821828852 | epot = -130.561343979461 | etot = -102.831391819827 +37000 ekin = 11.4960912442145 | erot = 17.4508107490648 | epot = -131.749068125386 | etot = -102.802166132107 +38000 ekin = 11.540532301831 | erot = 17.3078054067146 | epot = -132.764750072109 | etot = -103.916412363563 +39000 ekin = 11.985585634338 | erot = 17.5545572023683 | epot = -133.413693734028 | etot = -103.873550897322 +40000 ekin = 11.7470487263253 | erot = 17.4817657014378 | epot = -133.649887617672 | etot = -104.421073189909 +41000 ekin = 12.2634865503825 | erot = 15.9871744208477 | epot = -133.426518105126 | etot = -105.175857133896 +42000 ekin = 12.4634607835446 | erot = 16.072423199732 | epot = -132.888182004717 | etot = -104.35229802144 +43000 ekin = 12.0280103186908 | erot = 17.0183381277729 | epot = -132.109289199579 | etot = -103.062940753116 +44000 ekin = 11.4533011936261 | erot = 16.3340923459992 | epot = -131.295267862326 | etot = -103.5078743227 +45000 ekin = 10.7999971045082 | erot = 13.9453977962157 | epot = -130.566579774554 | etot = -105.82118487383 +46000 ekin = 10.1573148188648 | erot = 14.2465323252113 | epot = -129.933743276335 | etot = -105.529896132259 +47000 ekin = 9.90460787337496 | erot = 14.4980301987449 | epot = -129.32572061471 | etot = -104.92308254259 +48000 ekin = 9.57482091658498 | erot = 13.9987597050574 | epot = -128.711079823658 | etot = -105.137499202016 +49000 ekin = 9.09869677847911 | erot = 11.9262331183526 | epot = -128.201132750429 | etot = -107.176202853598 +50000 ekin = 8.59869176900111 | erot = 12.7238230334899 | epot = -127.833681811867 | etot = -106.511167009376 +51000 ekin = 8.5560087809789 | erot = 13.2937103598389 | epot = -127.458455063941 | etot = -105.608735923124 +52000 ekin = 8.45898358416097 | erot = 13.9183872238093 | epot = -127.22295075507 | etot = -104.8455799471 +53000 ekin = 8.95038819360825 | erot = 15.2829158001115 | epot = -127.176760860616 | etot = -102.943456866896 +54000 ekin = 9.12636274601647 | erot = 16.0621861658105 | epot = -127.241822388736 | etot = -102.053273476909 +55000 ekin = 9.37067262891952 | erot = 13.5370426745154 | epot = -127.353337400326 | etot = -104.445622096891 +56000 ekin = 8.92864226769998 | erot = 13.8952867853169 | epot = -127.52558177761 | etot = -104.701652724593 +57000 ekin = 8.96111715728989 | erot = 13.0396084653198 | epot = -127.808773485405 | etot = -105.808047862795 +58000 ekin = 9.35290907712123 | erot = 12.207612454997 | epot = -128.122352298152 | etot = -106.561830766034 +59000 ekin = 9.80451483320095 | erot = 12.4719934378628 | epot = -128.460109139872 | etot = -106.183600868808 +60000 ekin = 9.63961327714338 | erot = 13.6847336250955 | epot = -128.801154119214 | etot = -105.476807216975 +61000 ekin = 9.88934744800937 | erot = 12.5700101459246 | epot = -129.112108659886 | etot = -106.652751065952 +62000 ekin = 10.2728522782004 | erot = 13.7351395476234 | epot = -129.420335839955 | etot = -105.412344014131 +63000 ekin = 10.065327094074 | erot = 14.5055694779404 | epot = -129.670935318905 | etot = -105.10003874689 +64000 ekin = 10.6077832590941 | erot = 14.5413589291215 | epot = -129.867436868682 | etot = -104.718294680467 +65000 ekin = 10.2070111202922 | erot = 12.2544685960014 | epot = -129.975030414929 | etot = -107.513550698635 +66000 ekin = 10.2705974523514 | erot = 11.2800758761698 | epot = -129.99766952337 | etot = -108.446996194848 +67000 ekin = 10.7977441576603 | erot = 11.7528672948382 | epot = -130.114021659652 | etot = -107.563410207154 +68000 ekin = 11.4530491820265 | erot = 12.1985287417039 | epot = -130.293536175385 | etot = -106.641958251655 +69000 ekin = 11.6726943706713 | erot = 11.9642905500376 | epot = -130.544044272992 | etot = -106.907059352283 +70000 ekin = 12.2017006547911 | erot = 11.903305051201 | epot = -130.797559448952 | etot = -106.69255374296 +71000 ekin = 12.5064639577622 | erot = 11.9877984919706 | epot = -131.038782646501 | etot = -106.544520196768 +72000 ekin = 12.9485830535661 | erot = 13.0020474543087 | epot = -131.254935899906 | etot = -105.304305392031 +73000 ekin = 12.8299582560721 | erot = 14.6117237971354 | epot = -131.393018046916 | etot = -103.951335993709 +74000 ekin = 12.8939000526903 | erot = 12.863379794407 | epot = -131.352988231491 | etot = -105.595708384394 +75000 ekin = 12.7834866734293 | erot = 11.8117510534404 | epot = -131.260283186287 | etot = -106.665045459417 +76000 ekin = 13.3960728764203 | erot = 11.3061825907132 | epot = -131.133000018296 | etot = -106.430744551163 +77000 ekin = 13.3506974256507 | erot = 10.6864897054065 | epot = -130.952178599563 | etot = -106.914991468506 +78000 ekin = 13.422616631272 | erot = 10.809288310476 | epot = -130.758449837676 | etot = -106.526544895928 +79000 ekin = 13.5522973868191 | erot = 10.2030460888822 | epot = -130.503000220167 | etot = -106.747656744465 +80000 ekin = 14.272930353697 | erot = 8.09068479901647 | epot = -130.335854340126 | etot = -107.972239187413 +81000 ekin = 14.7483373328775 | erot = 9.22788595009487 | epot = -130.292625422183 | etot = -106.316402139211 +82000 ekin = 14.7432002071379 | erot = 9.40559435823131 | epot = -130.460105684669 | etot = -106.3113111193 +83000 ekin = 14.8287148416254 | erot = 10.1996443017361 | epot = -130.683921749615 | etot = -105.655562606254 +84000 ekin = 14.5951355381267 | erot = 12.0076426338427 | epot = -130.967249728639 | etot = -104.364471556669 +85000 ekin = 14.2835684903196 | erot = 13.8561283096132 | epot = -131.272994170087 | etot = -103.133297370154 +86000 ekin = 14.8326007867755 | erot = 11.7433108614628 | epot = -131.598596847379 | etot = -105.022685199141 +87000 ekin = 15.377532027873 | erot = 13.4564864072052 | epot = -131.970461301035 | etot = -103.136442865957 +88000 ekin = 16.0704430530011 | erot = 12.7408979774288 | epot = -132.317209652762 | etot = -103.505868622332 +89000 ekin = 16.2384695416373 | erot = 12.6191474341066 | epot = -132.709278600647 | etot = -103.851661624903 +90000 ekin = 16.5589625740267 | erot = 13.7646041545352 | epot = -133.142837994896 | etot = -102.819271266334 +91000 ekin = 16.5798313044953 | erot = 12.2950789135552 | epot = -133.519810794057 | etot = -104.644900576007 +92000 ekin = 16.8149166982992 | erot = 13.5657763083527 | epot = -133.822370527519 | etot = -103.441677520867 +93000 ekin = 16.3468786274472 | erot = 16.2860240192009 | epot = -134.011144678878 | etot = -101.37824203223 +94000 ekin = 16.129418375386 | erot = 16.8197062829578 | epot = -133.975094228095 | etot = -101.025969569751 +95000 ekin = 15.5011453839587 | erot = 17.153924576623 | epot = -133.751136697246 | etot = -101.096066736664 +96000 ekin = 15.652864748389 | erot = 18.7447477546217 | epot = -133.316856446679 | etot = -98.9192439436683 +97000 ekin = 15.1104279096655 | erot = 16.6300340283484 | epot = -132.646862391269 | etot = -100.906400453255 +98000 ekin = 15.7145979364048 | erot = 16.4999837372548 | epot = -132.047118805611 | etot = -99.8325371319517 +99000 ekin = 15.8228787425697 | erot = 16.6038361390489 | epot = -131.431821451522 | etot = -99.0051065699033 +100000 ekin = 15.5866410695988 | erot = 13.1190119540921 | epot = -130.864326580534 | etot = -102.158673556844 +101000 ekin = 15.1760812578527 | erot = 14.1257247435813 | epot = -130.407298723861 | etot = -101.105492722427 +102000 ekin = 14.9747704074343 | erot = 15.55879466272 | epot = -130.093565418176 | etot = -99.5600003480214 +103000 ekin = 14.7283962421382 | erot = 14.7231563764552 | epot = -129.93130638542 | etot = -100.479753766827 +104000 ekin = 14.6842119984616 | erot = 14.8440501791524 | epot = -129.892111822322 | etot = -100.363849644708 +105000 ekin = 14.2242158829698 | erot = 15.6391466981361 | epot = -129.905346426968 | etot = -100.041983845863 +106000 ekin = 13.8024473592344 | erot = 16.4859046142194 | epot = -129.912957387822 | etot = -99.6246054143686 +107000 ekin = 14.0489890701029 | erot = 15.8530920706999 | epot = -129.796538854505 | etot = -99.8944577137018 +108000 ekin = 13.7038910056907 | erot = 15.9635579237138 | epot = -129.555843708098 | etot = -99.8883947786939 +109000 ekin = 13.8779017778047 | erot = 17.5117500859534 | epot = -129.19188012202 | etot = -97.8022282582618 +110000 ekin = 13.5575931419463 | erot = 16.9475088674233 | epot = -128.691334815466 | etot = -98.1862328060965 +111000 ekin = 12.9775620699513 | erot = 14.939714004598 | epot = -127.964290623475 | etot = -100.047014548925 +112000 ekin = 13.0251229242144 | erot = 15.2072508797571 | epot = -126.97429168144 | etot = -98.7419178774685 +113000 ekin = 12.9511649405078 | erot = 13.989248422947 | epot = -125.858806371225 | etot = -98.9183930077706 +114000 ekin = 12.6655947173484 | erot = 14.1639814323438 | epot = -124.757194166389 | etot = -97.9276180166963 +115000 ekin = 12.2870506907596 | erot = 15.4380115846647 | epot = -123.762265142761 | etot = -96.0372028673364 +116000 ekin = 11.9569980647881 | erot = 15.7199780890902 | epot = -122.984476564825 | etot = -95.3075004109468 +117000 ekin = 11.9419697244606 | erot = 15.31088294377 | epot = -122.390478165697 | etot = -95.1376254974661 +118000 ekin = 12.0271503107112 | erot = 14.7200107326366 | epot = -121.920888323926 | etot = -95.1737272805785 +119000 ekin = 11.8399838787179 | erot = 13.5169297141694 | epot = -121.79296629031 | etot = -96.4360526974225 +120000 ekin = 11.5952370535119 | erot = 13.9311166225038 | epot = -121.87490833569 | etot = -96.3485546596742 +121000 ekin = 12.6873846089302 | erot = 14.1262982709265 | epot = -122.214797270773 | etot = -95.4011143909168 +122000 ekin = 12.5508137987138 | erot = 14.8322404188171 | epot = -122.66356039555 | etot = -95.2805061780189 +123000 ekin = 12.9717558281494 | erot = 16.9441051423025 | epot = -123.218059619813 | etot = -93.3021986493609 +124000 ekin = 13.0941543238075 | erot = 16.7664444883521 | epot = -123.78136790574 | etot = -93.9207690935806 +125000 ekin = 13.3545923651314 | erot = 16.9681165575983 | epot = -124.226447493135 | etot = -93.9037385704057 +126000 ekin = 13.707558189241 | erot = 18.6525076646813 | epot = -124.389431605693 | etot = -92.0293657517703 +127000 ekin = 13.9848596504427 | erot = 17.6900678829788 | epot = -124.293801107362 | etot = -92.6188735739405 +128000 ekin = 14.1880153054711 | erot = 14.2986913212233 | epot = -123.895716239617 | etot = -95.4090096129227 +129000 ekin = 14.234396145267 | erot = 12.7929057082143 | epot = -123.45812641228 | etot = -96.4308245587985 +130000 ekin = 13.5490297830189 | erot = 12.3291422436536 | epot = -123.296381301787 | etot = -97.4182092751146 +131000 ekin = 13.625205801969 | erot = 11.5702974231324 | epot = -123.031383858288 | etot = -97.8358806331869 +132000 ekin = 13.5140871505802 | erot = 10.247163811581 | epot = -122.67647424975 | etot = -98.9152232875892 +133000 ekin = 13.6598880155314 | erot = 9.71281275821937 | epot = -122.46511358521 | etot = -99.0924128114592 +134000 ekin = 13.4307752775482 | erot = 10.0356307711687 | epot = -122.323515330483 | etot = -98.8571092817659 +135000 ekin = 12.7746194032244 | erot = 11.0989148526186 | epot = -122.247485302774 | etot = -98.373951046931 +136000 ekin = 12.6978264396143 | erot = 12.1866872670237 | epot = -122.334952758206 | etot = -97.4504390515682 +137000 ekin = 12.3859103295768 | erot = 10.9182734103843 | epot = -122.6462867818 | etot = -99.3421030418394 +138000 ekin = 12.8189864970097 | erot = 11.9822682899718 | epot = -123.216509840159 | etot = -98.4152550531773 +139000 ekin = 13.1473296340096 | erot = 11.606982629379 | epot = -123.964698056414 | etot = -99.2103857930249 +140000 ekin = 13.9352115952455 | erot = 11.6972955590282 | epot = -124.787751042248 | etot = -99.1552438879742 +141000 ekin = 13.3811194780965 | erot = 13.5865824418213 | epot = -125.585833002472 | etot = -98.618131082554 +142000 ekin = 13.0747467175761 | erot = 13.8713107006678 | epot = -126.319406883241 | etot = -99.3733494649974 +143000 ekin = 12.8272953552334 | erot = 14.2382018654909 | epot = -127.071116756404 | etot = -100.00561953568 +144000 ekin = 12.5334679344975 | erot = 14.327823680682 | epot = -127.797657962991 | etot = -100.936366347812 +145000 ekin = 12.2943940063578 | erot = 13.8915509298887 | epot = -128.529313665204 | etot = -102.343368728958 +146000 ekin = 12.8333200360282 | erot = 13.3977934786392 | epot = -129.049828840935 | etot = -102.818715326267 +147000 ekin = 12.7010559531677 | erot = 13.4121259867142 | epot = -129.520646652199 | etot = -103.407464712317 +148000 ekin = 12.7721670089962 | erot = 13.8565791398843 | epot = -130.116749890466 | etot = -103.488003741585 +149000 ekin = 12.6995854093145 | erot = 13.774115319827 | epot = -130.816929745791 | etot = -104.343229016649 +150000 ekin = 12.5910049048873 | erot = 13.5362581130226 | epot = -131.60533209365 | etot = -105.47806907574 +151000 ekin = 12.4308195325608 | erot = 15.131223262504 | epot = -132.258037592352 | etot = -104.695994797287 +152000 ekin = 12.2263570227432 | erot = 16.3567044291132 | epot = -132.779679077057 | etot = -104.1966176252 +153000 ekin = 11.9878029660899 | erot = 15.6767862263482 | epot = -133.177710574428 | etot = -105.51312138199 +154000 ekin = 12.0409493226744 | erot = 14.2476719151489 | epot = -133.549420303725 | etot = -107.260799065902 +155000 ekin = 12.2489628138608 | erot = 14.3648722436256 | epot = -133.789784491732 | etot = -107.175949434245 +156000 ekin = 12.5366959056766 | erot = 13.8065055190009 | epot = -133.518931221763 | etot = -107.175729797085 +157000 ekin = 13.1233683194156 | erot = 13.4715553874451 | epot = -133.321749867141 | etot = -106.72682616028 +158000 ekin = 12.9231372084689 | erot = 12.0286474507292 | epot = -133.418506326403 | etot = -108.466721667204 +159000 ekin = 13.1550032801976 | erot = 12.140848226174 | epot = -133.505005222597 | etot = -108.209153716226 +160000 ekin = 13.6223635027655 | erot = 12.3202375233747 | epot = -133.503234907302 | etot = -107.560633881162 +161000 ekin = 14.0356746314275 | erot = 12.6036824472307 | epot = -133.453141865727 | etot = -106.813784787069 +162000 ekin = 14.5709613441253 | erot = 12.2296759165728 | epot = -133.469813940545 | etot = -106.669176679847 +163000 ekin = 14.2143277130153 | erot = 13.0014485572518 | epot = -133.573164156585 | etot = -106.357387886318 +164000 ekin = 14.0907957992508 | erot = 13.35520362876 | epot = -133.726631699 | etot = -106.280632270989 +165000 ekin = 14.2128485759295 | erot = 13.5077316121454 | epot = -133.999841482384 | etot = -106.279261294309 +166000 ekin = 14.5186142370211 | erot = 16.3543877375713 | epot = -134.25901295015 | etot = -103.386010975557 +167000 ekin = 13.6918258854853 | erot = 16.8454036000666 | epot = -134.419746517248 | etot = -103.882517031696 +168000 ekin = 14.3098776648963 | erot = 14.1755870556485 | epot = -134.43516075271 | etot = -105.949696032165 +169000 ekin = 13.5304488054452 | erot = 14.8109727207072 | epot = -134.270272523649 | etot = -105.928850997496 +170000 ekin = 13.1993881452602 | erot = 16.2742248259377 | epot = -134.136295378236 | etot = -104.662682407038 +171000 ekin = 13.1662666846495 | erot = 17.3853590919123 | epot = -133.896393655866 | etot = -103.344767879304 +172000 ekin = 13.2344724361955 | erot = 16.2957455512213 | epot = -133.530908487908 | etot = -104.000690500491 +173000 ekin = 12.8404298355402 | erot = 15.4795620322766 | epot = -133.036810695805 | etot = -104.716818827988 +174000 ekin = 12.2170050683911 | erot = 17.0999748910801 | epot = -132.490479377943 | etot = -103.173499418472 +175000 ekin = 11.9828009648797 | erot = 17.133145149998 | epot = -132.167689069114 | etot = -103.051742954236 +176000 ekin = 11.26703485225 | erot = 15.851549107765 | epot = -131.994028988287 | etot = -104.875445028272 +177000 ekin = 10.9532619474729 | erot = 17.642067846262 | epot = -132.042511671925 | etot = -103.44718187819 +178000 ekin = 10.6509076271232 | erot = 19.4227764316798 | epot = -132.427928003959 | etot = -102.354243945156 +179000 ekin = 10.7208239698367 | erot = 18.6233655322233 | epot = -133.155790832988 | etot = -103.811601330928 +180000 ekin = 10.3612059999385 | erot = 20.354599815928 | epot = -134.071492664219 | etot = -103.355686848353 +181000 ekin = 10.9272878765522 | erot = 19.3855669963696 | epot = -134.948573396863 | etot = -104.635718523941 +182000 ekin = 11.0949981109546 | erot = 17.7029229528617 | epot = -135.761049961753 | etot = -106.963128897937 +183000 ekin = 11.9475302429042 | erot = 18.6786204586031 | epot = -136.458952174173 | etot = -105.832801472665 +184000 ekin = 11.9692123796945 | erot = 19.3376307966672 | epot = -137.111375615616 | etot = -105.804532439255 +185000 ekin = 12.0887739463894 | erot = 20.9744943691819 | epot = -137.712001992347 | etot = -104.648733676775 +186000 ekin = 13.202054762524 | erot = 21.7329212691712 | epot = -138.252569528231 | etot = -103.317593496536 +187000 ekin = 14.5309082020313 | erot = 23.0892571841143 | epot = -138.562960481472 | etot = -100.942795095327 +188000 ekin = 14.8209433490932 | erot = 23.75343305623 | epot = -138.799089973348 | etot = -100.224713568024 +189000 ekin = 14.8516226045177 | erot = 22.6496900698373 | epot = -138.813459124407 | etot = -101.312146450052 +190000 ekin = 14.8882648654863 | erot = 20.946385270515 | epot = -138.595991071599 | etot = -102.761340935598 +191000 ekin = 14.4852960600141 | erot = 24.3377616270744 | epot = -137.710510436494 | etot = -98.8874527494057 +192000 ekin = 13.9439508660166 | erot = 23.8205912161901 | epot = -137.15563857902 | etot = -99.3910964968136 +193000 ekin = 13.0416663184277 | erot = 22.3479664160949 | epot = -136.749821307025 | etot = -101.360188572502 +194000 ekin = 12.136786835284 | erot = 20.8747662588234 | epot = -136.044702401027 | etot = -103.03314930692 +195000 ekin = 11.7735893875982 | erot = 19.4986101359151 | epot = -135.123514021607 | etot = -103.851314498094 +196000 ekin = 11.8808319913166 | erot = 17.1680950089713 | epot = -134.106716307269 | etot = -105.057789306981 +197000 ekin = 11.7566768590109 | erot = 14.2024644636955 | epot = -133.123489522261 | etot = -107.164348199554 +198000 ekin = 12.1381550502849 | erot = 13.1478608909175 | epot = -132.078377039903 | etot = -106.792361098701 +199000 ekin = 11.9597697644039 | erot = 13.1448027989405 | epot = -131.146235462498 | etot = -106.041662899154 +200000 ekin = 11.8205052250281 | erot = 14.3431211060147 | epot = -130.284658028576 | etot = -104.121031697533 +201000 ekin = 11.8812457901842 | erot = 14.4190696276244 | epot = -129.633912600305 | etot = -103.333597182497 +202000 ekin = 11.1908338617358 | erot = 14.3880198236556 | epot = -129.01607097923 | etot = -103.437217293839 +203000 ekin = 10.6609899095304 | erot = 14.1109959691538 | epot = -128.442280854454 | etot = -103.67029497577 +204000 ekin = 10.0808080300169 | erot = 14.6140545850541 | epot = -128.095060341458 | etot = -103.400197726387 +205000 ekin = 9.85497388226942 | erot = 15.5585210838952 | epot = -127.927122466239 | etot = -102.513627500074 +206000 ekin = 9.44812789479607 | erot = 16.560521312865 | epot = -127.828616126451 | etot = -101.81996691879 +207000 ekin = 9.2705277605019 | erot = 17.5495451600282 | epot = -127.7733931411 | etot = -100.95332022057 +208000 ekin = 9.05667723692406 | erot = 19.1888521647023 | epot = -127.622114295288 | etot = -99.376584893662 +209000 ekin = 9.32667962585868 | erot = 16.4248042387723 | epot = -127.283274007125 | etot = -101.531790142494 +210000 ekin = 9.34011427208157 | erot = 15.3881595231412 | epot = -126.735487311966 | etot = -102.007213516743 +211000 ekin = 9.51343965667034 | erot = 17.6651633952544 | epot = -126.065186083942 | etot = -98.8865830320172 +212000 ekin = 9.26268095198313 | erot = 15.4307754928622 | epot = -125.390904828464 | etot = -100.697448383618 +213000 ekin = 9.90035137711205 | erot = 16.237888309174 | epot = -124.67685918373 | etot = -98.5386194974435 +214000 ekin = 10.0267139039829 | erot = 15.3739472519941 | epot = -124.070465973723 | etot = -98.6698048177462 +215000 ekin = 10.2479120626749 | erot = 15.168771739759 | epot = -123.5900918068 | etot = -98.1734080043657 +216000 ekin = 10.7089047788332 | erot = 14.6064571242228 | epot = -123.264768153567 | etot = -97.9494062505112 +217000 ekin = 11.2868202815268 | erot = 15.3661782864349 | epot = -123.199040854786 | etot = -96.5460422868244 +218000 ekin = 11.3714971690666 | erot = 16.1553589822711 | epot = -123.363179203944 | etot = -95.8363230526061 +219000 ekin = 11.9010741217101 | erot = 15.4153558945661 | epot = -123.502901563405 | etot = -96.1864715471288 +220000 ekin = 12.3176284529673 | erot = 14.9201703957035 | epot = -123.787250097922 | etot = -96.5494512492515 +221000 ekin = 12.1714171931196 | erot = 14.2434404855463 | epot = -124.232136815822 | etot = -97.8172791371565 +222000 ekin = 12.2749120571917 | erot = 15.2768872539485 | epot = -124.823468086325 | etot = -97.2716687751848 +223000 ekin = 11.7897020552869 | erot = 14.2418293066223 | epot = -125.340319541526 | etot = -99.3087881796173 +224000 ekin = 12.5904708265255 | erot = 14.930049355487 | epot = -125.88307315034 | etot = -98.3625529683271 +225000 ekin = 13.2866427416859 | erot = 14.2177414042972 | epot = -126.451944677199 | etot = -98.947560531216 +226000 ekin = 14.0195514204802 | erot = 12.5131492601281 | epot = -126.861509712119 | etot = -100.328809031511 +227000 ekin = 14.5771739053929 | erot = 13.1226878209367 | epot = -127.216548125261 | etot = -99.5166863989319 +228000 ekin = 15.5098492893988 | erot = 13.724631675258 | epot = -127.526961289958 | etot = -98.2924803253013 +229000 ekin = 15.0379991852038 | erot = 15.0421277675249 | epot = -127.746349010415 | etot = -97.6662220576859 +230000 ekin = 14.9655772073185 | erot = 13.2122719576887 | epot = -127.912255072452 | etot = -99.7344059074447 +231000 ekin = 15.149504681299 | erot = 13.2192000733412 | epot = -127.956385488518 | etot = -99.5876807338778 +232000 ekin = 14.9381216821886 | erot = 14.4783826177061 | epot = -127.959401619599 | etot = -98.5428973197041 +233000 ekin = 14.5541213133396 | erot = 13.4137098644268 | epot = -127.978350373815 | etot = -100.010519196048 +234000 ekin = 14.4321853050326 | erot = 13.7604771949198 | epot = -127.932053105819 | etot = -99.7393906058661 +235000 ekin = 14.075998853953 | erot = 13.0397612447523 | epot = -127.801713655073 | etot = -100.685953556368 +236000 ekin = 14.1218487448576 | erot = 11.738392005745 | epot = -127.657366478895 | etot = -101.797125728292 +237000 ekin = 15.0850886197599 | erot = 10.8875373781651 | epot = -127.711659913863 | etot = -101.739033915938 +238000 ekin = 15.1222712066963 | erot = 12.0017200983468 | epot = -127.784954181148 | etot = -100.660962876105 +239000 ekin = 15.513104649803 | erot = 12.9664032026763 | epot = -128.030344605472 | etot = -99.5508367529925 +240000 ekin = 15.6599113206585 | erot = 14.5571933869969 | epot = -128.497592836165 | etot = -98.2804881285095 +241000 ekin = 15.8824211506483 | erot = 15.651281118972 | epot = -129.031608518898 | etot = -97.4979062492773 +242000 ekin = 15.6531568614874 | erot = 17.9847188762554 | epot = -129.475118370063 | etot = -95.8372426323203 +243000 ekin = 16.4286752104464 | erot = 19.5815869009233 | epot = -129.76230861541 | etot = -93.7520465040398 +244000 ekin = 16.3394547967301 | erot = 18.1079320641236 | epot = -129.952517130133 | etot = -95.5051302692797 +245000 ekin = 16.8516652636708 | erot = 21.5084428396106 | epot = -130.042993898219 | etot = -91.682885794938 +246000 ekin = 16.2142794013674 | erot = 20.8328300526537 | epot = -129.969581269428 | etot = -92.9224718154072 +247000 ekin = 15.5351355380904 | erot = 20.3306492075571 | epot = -129.776080373296 | etot = -93.9102956276486 +248000 ekin = 15.5326999292253 | erot = 17.6264238370196 | epot = -129.380780641676 | etot = -96.2216568754307 +249000 ekin = 15.6005286569212 | erot = 14.6372790883696 | epot = -128.991620094036 | etot = -98.7538123487453 +250000 ekin = 15.3019907608705 | erot = 11.5707409659116 | epot = -128.572625786308 | etot = -101.699894059526 +251000 ekin = 14.8424008700845 | erot = 11.5409169047425 | epot = -128.171854875477 | etot = -101.78853710065 +252000 ekin = 14.0881811540469 | erot = 11.935280004933 | epot = -127.786643136826 | etot = -101.763181977847 +253000 ekin = 13.8077466967518 | erot = 11.3150182310599 | epot = -127.466234955236 | etot = -102.343470027424 +254000 ekin = 13.4909914927484 | erot = 11.5319845638397 | epot = -127.362543592254 | etot = -102.339567535666 +255000 ekin = 13.4805976507166 | erot = 11.0955784275857 | epot = -127.397885679708 | etot = -102.821709601406 +256000 ekin = 12.9589283730017 | erot = 12.2379211313913 | epot = -127.489056816356 | etot = -102.292207311963 +257000 ekin = 13.0137415076953 | erot = 11.311393697849 | epot = -127.55538811969 | etot = -103.230252914146 +258000 ekin = 13.5211917161104 | erot = 12.0930034020847 | epot = -127.692253608274 | etot = -102.078058490079 +259000 ekin = 12.6081394987907 | erot = 11.1354151842502 | epot = -127.694681242159 | etot = -103.951126559119 +260000 ekin = 12.0306126643581 | erot = 12.068165825136 | epot = -127.788007862018 | etot = -103.689229372524 +261000 ekin = 11.6712630028346 | erot = 13.0367693142806 | epot = -127.986436961488 | etot = -103.278404644373 +262000 ekin = 11.2413910262091 | erot = 15.7538484940495 | epot = -128.233173068364 | etot = -101.237933548105 +263000 ekin = 11.0950814602042 | erot = 14.7646358718688 | epot = -128.60471709289 | etot = -102.744999760817 +264000 ekin = 10.6119365875484 | erot = 14.4112072406074 | epot = -129.085734723212 | etot = -104.062590895057 +265000 ekin = 10.579570043137 | erot = 16.6560278073956 | epot = -129.542969866575 | etot = -102.307372016042 +266000 ekin = 10.5226588316929 | erot = 18.1113177730103 | epot = -129.974040564248 | etot = -101.340063959545 +267000 ekin = 10.4287003526946 | erot = 16.6877176268463 | epot = -130.344448562148 | etot = -103.228030582607 +268000 ekin = 10.5877901133481 | erot = 15.1656319049267 | epot = -130.637228764668 | etot = -104.883806746393 +269000 ekin = 10.9852811387162 | erot = 16.0320363782053 | epot = -130.794054516044 | etot = -103.776736999123 +270000 ekin = 10.5687078071281 | erot = 16.3743105362243 | epot = -130.736687898519 | etot = -103.793669555167 +271000 ekin = 9.99158423586208 | erot = 15.5228198989367 | epot = -130.512100405461 | etot = -104.997696270662 +272000 ekin = 9.60764690373856 | erot = 14.5365399404247 | epot = -130.052200944354 | etot = -105.908014100191 +273000 ekin = 9.88762102060522 | erot = 13.0362776194251 | epot = -129.564225107536 | etot = -106.640326467505 +274000 ekin = 9.61772274500435 | erot = 13.6398685548783 | epot = -128.999438249703 | etot = -105.74184694982 +275000 ekin = 8.94677992468543 | erot = 12.9556954902446 | epot = -128.332527547958 | etot = -106.430052133028 +276000 ekin = 8.3584335311715 | erot = 13.2017156118579 | epot = -127.585007462439 | etot = -106.02485831941 +277000 ekin = 7.94992551817686 | erot = 12.6842109215291 | epot = -126.918026716016 | etot = -106.28389027631 +278000 ekin = 7.76653215340282 | erot = 12.8531406595677 | epot = -126.484978021444 | etot = -105.865305208474 +279000 ekin = 7.78343352835109 | erot = 14.2332649072589 | epot = -126.253341481669 | etot = -104.236643046059 +280000 ekin = 7.35330887841251 | erot = 14.4673264755642 | epot = -126.163511871335 | etot = -104.342876517359 +281000 ekin = 7.85275326933405 | erot = 14.4133642805592 | epot = -126.259915794876 | etot = -103.993798244983 +282000 ekin = 7.59386790871773 | erot = 16.7968997525039 | epot = -126.548690416207 | etot = -102.157922754985 +283000 ekin = 7.35527594979652 | erot = 16.8857993661909 | epot = -127.193261985613 | etot = -102.952186669625 +284000 ekin = 7.23651097691633 | erot = 17.1029976769801 | epot = -127.931231477133 | etot = -103.591722823237 +285000 ekin = 7.0753360049638 | erot = 17.4467129189669 | epot = -128.607262305958 | etot = -104.085213382028 +286000 ekin = 7.32033319851606 | erot = 17.1633115529782 | epot = -129.218718145393 | etot = -104.735073393899 +287000 ekin = 7.72392787692494 | erot = 16.4914860614417 | epot = -129.660366098165 | etot = -105.444952159798 +288000 ekin = 7.8846803036883 | erot = 14.5346886015918 | epot = -129.959287943351 | etot = -107.539919038071 +289000 ekin = 8.15449180858513 | erot = 13.6497039151859 | epot = -130.191654559662 | etot = -108.387458835891 +290000 ekin = 8.57025733949944 | erot = 11.7337972051479 | epot = -130.427723013256 | etot = -110.123668468609 +291000 ekin = 8.84501371392035 | erot = 11.4464085433319 | epot = -130.776530031292 | etot = -110.48510777404 +292000 ekin = 8.92636761817405 | erot = 11.5339265052695 | epot = -131.116859081799 | etot = -110.656564958356 +293000 ekin = 9.4188092936266 | erot = 10.6139923438188 | epot = -131.543780424308 | etot = -111.510978786863 +294000 ekin = 10.0249117072521 | erot = 11.1467770825211 | epot = -131.989966720275 | etot = -110.818277930502 +295000 ekin = 11.083703631995 | erot = 11.4510452094844 | epot = -132.47789071003 | etot = -109.94314186855 +296000 ekin = 11.6146048856785 | erot = 12.6868535987442 | epot = -132.914414362187 | etot = -108.612955877764 +297000 ekin = 11.8951229320331 | erot = 15.2697825399351 | epot = -133.445892377813 | etot = -106.280986905844 +298000 ekin = 12.4531615126796 | erot = 14.3674160150298 | epot = -133.890492541549 | etot = -107.069915013839 +299000 ekin = 13.196907114984 | erot = 14.7373108470961 | epot = -134.149282525159 | etot = -106.215064563079 +300000 ekin = 13.552623655237 | erot = 13.6896560161013 | epot = -134.199981280003 | etot = -106.957701608665 +301000 ekin = 14.1630542484217 | erot = 10.9749158485264 | epot = -134.19176613126 | etot = -109.053796034312 +302000 ekin = 14.5195459532838 | erot = 12.7065564931488 | epot = -134.217142307031 | etot = -106.991039860598 +303000 ekin = 14.8150523928287 | erot = 10.7628758137702 | epot = -134.250982614669 | etot = -108.67305440807 +304000 ekin = 15.2660168979802 | erot = 10.1752335071963 | epot = -134.244526718419 | etot = -108.803276313243 +305000 ekin = 15.3860602604058 | erot = 9.45759816681305 | epot = -134.133567089515 | etot = -109.289908662296 +306000 ekin = 15.7237397758356 | erot = 9.50282910127752 | epot = -133.94876479662 | etot = -108.722195919507 +307000 ekin = 15.8174557813954 | erot = 11.0016238644609 | epot = -133.697557997488 | etot = -106.878478351632 +308000 ekin = 15.7527451080622 | erot = 12.1931354321227 | epot = -133.444465811955 | etot = -105.49858527177 +309000 ekin = 15.5388064000501 | erot = 12.0318704352104 | epot = -133.232790168995 | etot = -105.662113333734 +310000 ekin = 15.7333675389695 | erot = 14.1342950777931 | epot = -133.029366911719 | etot = -103.161704294957 +311000 ekin = 15.6009535545179 | erot = 13.6526892945678 | epot = -132.838604928597 | etot = -103.584962079511 +312000 ekin = 16.4800347752494 | erot = 13.2349274624762 | epot = -132.817445618549 | etot = -103.102483380823 +313000 ekin = 17.4513785144268 | erot = 14.0129598068591 | epot = -132.753954889153 | etot = -101.289616567867 +314000 ekin = 17.5025641492033 | erot = 11.1600773517397 | epot = -132.721561414482 | etot = -104.058919913539 +315000 ekin = 17.6215931043552 | erot = 11.6530322479369 | epot = -132.83607154178 | etot = -103.561446189488 +316000 ekin = 18.3077509852464 | erot = 11.24428551734 | epot = -132.825110613688 | etot = -103.273074111101 +317000 ekin = 18.6646687475733 | erot = 11.3949578332599 | epot = -132.726178400251 | etot = -102.666551819418 +318000 ekin = 19.0449374377506 | erot = 10.6811792225528 | epot = -132.596843958719 | etot = -102.870727298416 +319000 ekin = 19.4739615661041 | erot = 10.1061598868736 | epot = -132.560298222539 | etot = -102.980176769561 +320000 ekin = 20.0845500729367 | erot = 9.07620734375012 | epot = -132.537630592136 | etot = -103.376873175449 +321000 ekin = 20.3735677110338 | erot = 9.58107527158863 | epot = -132.71350033056 | etot = -102.758857347937 +322000 ekin = 20.6065517684778 | erot = 10.44869872965 | epot = -133.101486382927 | etot = -102.0462358848 +323000 ekin = 20.0755652693402 | erot = 10.5792774360325 | epot = -133.548872422721 | etot = -102.894029717349 +324000 ekin = 19.5470787180692 | erot = 12.2962131053578 | epot = -134.037163912753 | etot = -102.193872089326 +325000 ekin = 19.3574089759549 | erot = 13.9344512333194 | epot = -134.514099492223 | etot = -101.222239282949 +326000 ekin = 18.9578651565007 | erot = 14.0599792857494 | epot = -134.832879117041 | etot = -101.815034674791 +327000 ekin = 18.522430937646 | erot = 15.3237238200694 | epot = -135.011431120887 | etot = -101.165276363172 +328000 ekin = 18.0035567184584 | erot = 14.5279082328483 | epot = -134.974755880337 | etot = -102.44329092903 +329000 ekin = 18.0984071439777 | erot = 15.2396238227656 | epot = -134.609246027312 | etot = -101.271215060568 +330000 ekin = 17.7721143388229 | erot = 13.525941768538 | epot = -134.02382664847 | etot = -102.725770541109 +331000 ekin = 16.9269057974283 | erot = 14.114199498117 | epot = -133.337136919405 | etot = -102.29603162386 +332000 ekin = 16.2137199937952 | erot = 13.5614363871077 | epot = -132.597645626193 | etot = -102.822489245291 +333000 ekin = 15.9975416411886 | erot = 14.1394884933731 | epot = -132.115505382769 | etot = -101.978475248208 +334000 ekin = 15.7346050674188 | erot = 14.4036291079367 | epot = -131.728484776204 | etot = -101.590250600849 +335000 ekin = 14.8435293968564 | erot = 14.34943376694 | epot = -131.346268113982 | etot = -102.153304950185 +336000 ekin = 13.819255551257 | erot = 14.8950079117048 | epot = -131.007488904444 | etot = -102.293225441482 +337000 ekin = 14.256466480469 | erot = 14.0159412985296 | epot = -130.688449631731 | etot = -102.416041852733 +338000 ekin = 14.2560987451645 | erot = 12.7376885355493 | epot = -130.454049417339 | etot = -103.460262136625 +339000 ekin = 14.3621400404064 | erot = 14.439342349414 | epot = -130.394260932836 | etot = -101.592778543015 +340000 ekin = 14.6559878293539 | erot = 14.5595854991738 | epot = -130.334888999638 | etot = -101.11931567111 +341000 ekin = 14.7435791817685 | erot = 15.9322314960963 | epot = -130.388598855483 | etot = -99.7127881776182 +342000 ekin = 15.1053540532649 | erot = 15.5267560594305 | epot = -130.534881968785 | etot = -99.9027718560899 +343000 ekin = 14.8346227466266 | erot = 15.1410476661794 | epot = -130.670876299797 | etot = -100.695205886991 +344000 ekin = 15.3397947857358 | erot = 14.6689121103972 | epot = -130.597244811671 | etot = -100.588537915538 +345000 ekin = 15.5825050885072 | erot = 11.849389855145 | epot = -130.482878783265 | etot = -103.050983839613 +346000 ekin = 15.557081118346 | erot = 12.1818765032741 | epot = -130.483868170778 | etot = -102.744910549158 +347000 ekin = 15.7870950105621 | erot = 12.7946686661666 | epot = -130.422215262255 | etot = -101.840451585527 +348000 ekin = 15.5352792323484 | erot = 13.3447055882308 | epot = -130.353231427955 | etot = -101.473246607375 +349000 ekin = 15.7477186936883 | erot = 14.4233688591029 | epot = -130.329494194302 | etot = -100.158406641511 +350000 ekin = 15.6170178096528 | erot = 14.8151960388694 | epot = -130.17949072562 | etot = -99.747276877098 +351000 ekin = 15.0398392687342 | erot = 15.5254714523236 | epot = -130.080810023417 | etot = -99.5154993023593 +352000 ekin = 14.6968059907976 | erot = 14.4538420025754 | epot = -129.97104832481 | etot = -100.820400331437 +353000 ekin = 14.1112287219651 | erot = 15.2115201534876 | epot = -129.83422590312 | etot = -100.511477027668 +354000 ekin = 13.8771677291463 | erot = 13.4124042697973 | epot = -129.753540110039 | etot = -102.463968111095 +355000 ekin = 13.7170691451417 | erot = 14.3544061195803 | epot = -129.751545876385 | etot = -101.680070611663 +356000 ekin = 13.4694668767048 | erot = 16.133528389581 | epot = -129.824882831913 | etot = -100.221887565627 +357000 ekin = 13.2929931449396 | erot = 16.4038366946648 | epot = -129.876709339247 | etot = -100.179879499643 +358000 ekin = 13.1750980708733 | erot = 17.3241105026107 | epot = -129.989834282264 | etot = -99.4906257087797 +359000 ekin = 13.380329272499 | erot = 19.6824191986732 | epot = -129.988552013529 | etot = -96.9258035423572 +360000 ekin = 13.4193225479689 | erot = 19.2098458345074 | epot = -129.914085935484 | etot = -97.2849175530075 +361000 ekin = 13.1014802992557 | erot = 19.5139031846452 | epot = -129.642748133153 | etot = -97.0273646492518 +362000 ekin = 13.3388646183525 | erot = 17.446873022162 | epot = -129.271499027633 | etot = -98.4857613871179 +363000 ekin = 14.7993334309696 | erot = 17.4970048461568 | epot = -128.636528824995 | etot = -96.3401905478691 +364000 ekin = 15.2510007602818 | erot = 16.7004926087045 | epot = -127.884102298463 | etot = -95.9326089294769 +365000 ekin = 16.0551556298892 | erot = 13.1331682140255 | epot = -127.106944773085 | etot = -97.9186209291702 +366000 ekin = 16.6135251477317 | erot = 10.7882784823258 | epot = -126.481864876555 | etot = -99.0800612464979 +367000 ekin = 17.2397770838844 | erot = 9.07697469116899 | epot = -125.869491600361 | etot = -99.5527398253073 +368000 ekin = 18.2647562627396 | erot = 8.83837372160177 | epot = -125.609398383494 | etot = -98.5062683991522 +369000 ekin = 19.6983956101792 | erot = 9.59177541868033 | epot = -125.74626802455 | etot = -96.4560969956904 +370000 ekin = 19.5709154020794 | erot = 8.91092874647536 | epot = -126.152873219342 | etot = -97.6710290707868 +371000 ekin = 18.8989004192531 | erot = 8.77992407799205 | epot = -126.728037482638 | etot = -99.0492129853924 +372000 ekin = 19.2813162804943 | erot = 10.0479492696922 | epot = -127.425754042496 | etot = -98.096488492309 +373000 ekin = 19.0086401168253 | erot = 10.1075091531877 | epot = -128.182979400039 | etot = -99.0668301300256 +374000 ekin = 19.4563014103425 | erot = 11.7647123799523 | epot = -128.910763698769 | etot = -97.6897499084737 +375000 ekin = 19.6239136950702 | erot = 13.1082491418006 | epot = -129.652938836285 | etot = -96.9207759994137 +376000 ekin = 19.0831811879331 | erot = 13.5410920095561 | epot = -130.604369980802 | etot = -97.9800967833132 +377000 ekin = 18.9430611051657 | erot = 15.4046155861757 | epot = -131.433252086557 | etot = -97.0855753952154 +378000 ekin = 18.4535587013679 | erot = 17.0768375430874 | epot = -132.074544242454 | etot = -96.5441479979988 +379000 ekin = 18.8502578619275 | erot = 17.0886051901337 | epot = -132.576199310533 | etot = -96.6373362584714 +380000 ekin = 19.475671525711 | erot = 17.425300301321 | epot = -132.839195209695 | etot = -95.9382233826627 +381000 ekin = 19.4174760667093 | erot = 16.919974731311 | epot = -132.976364420012 | etot = -96.638913621992 +382000 ekin = 19.1025374334182 | erot = 17.1130645388703 | epot = -132.829331451385 | etot = -96.6137294790962 +383000 ekin = 18.9362566793884 | erot = 17.3266414908685 | epot = -132.614748834884 | etot = -96.3518506646272 +384000 ekin = 18.7506243498791 | erot = 16.6762466864349 | epot = -132.283835208144 | etot = -96.8569641718296 +385000 ekin = 18.0674119365431 | erot = 15.5457529470262 | epot = -131.967883677018 | etot = -98.3547187934491 +386000 ekin = 17.7765715680376 | erot = 15.4653584270643 | epot = -131.931173947405 | etot = -98.689243952303 +387000 ekin = 17.5922997105643 | erot = 15.4866263147305 | epot = -131.962114117862 | etot = -98.8831880925669 +388000 ekin = 17.1354877146972 | erot = 14.6908885713179 | epot = -132.154913188456 | etot = -100.32853690244 +389000 ekin = 17.2978672800278 | erot = 14.3323941781807 | epot = -132.579373908437 | etot = -100.949112450229 +390000 ekin = 16.6548471381054 | erot = 14.4389161904763 | epot = -133.117852071241 | etot = -102.02408874266 +391000 ekin = 16.4991198143141 | erot = 15.6371247388717 | epot = -133.74702014809 | etot = -101.610775594904 +392000 ekin = 16.4281265667573 | erot = 15.2805744092357 | epot = -134.285663015389 | etot = -102.576962039396 +393000 ekin = 16.5088678003344 | erot = 14.6374026351446 | epot = -134.823632354354 | etot = -103.677361918875 +394000 ekin = 16.8667186647237 | erot = 14.4902912223106 | epot = -135.212337585278 | etot = -103.855327698243 +395000 ekin = 17.2109177950877 | erot = 13.0237509296312 | epot = -135.433194422107 | etot = -105.198525697388 +396000 ekin = 17.5831681572179 | erot = 13.0674839764192 | epot = -135.5411310502 | etot = -104.890478916563 +397000 ekin = 18.3467734506846 | erot = 12.3568347780265 | epot = -135.692051757534 | etot = -104.988443528823 +398000 ekin = 18.6260075083868 | erot = 11.5676720862242 | epot = -135.8484417868 | etot = -105.654762192189 +399000 ekin = 18.4927959871705 | erot = 9.61204888160112 | epot = -136.029564032426 | etot = -107.924719163654 +400000 ekin = 18.6435149197571 | erot = 9.559059652791 | epot = -136.063512666361 | etot = -107.860938093813 +401000 ekin = 18.495036639322 | erot = 8.81910426702044 | epot = -135.969397453423 | etot = -108.655256547081 +402000 ekin = 18.0973102085887 | erot = 9.21770434744583 | epot = -135.826258341845 | etot = -108.51124378581 +403000 ekin = 18.0427323472422 | erot = 10.5190252323493 | epot = -135.753331828009 | etot = -107.191574248417 +404000 ekin = 17.5776474210726 | erot = 9.98443155942648 | epot = -135.626108875126 | etot = -108.064029894627 +405000 ekin = 17.708707354373 | erot = 9.34584279346648 | epot = -135.363640656308 | etot = -108.309090508469 +406000 ekin = 17.2396707705326 | erot = 8.90477999440435 | epot = -135.2384727154 | etot = -109.094021950463 +407000 ekin = 17.7583314057474 | erot = 10.2665550367714 | epot = -135.16419443924 | etot = -107.139307996721 +408000 ekin = 16.6497478599537 | erot = 10.611196757942 | epot = -135.101475998093 | etot = -107.840531380197 +409000 ekin = 16.942845841028 | erot = 10.4168945438759 | epot = -135.194509236814 | etot = -107.83476885191 +410000 ekin = 16.4881349577911 | erot = 12.0730971512869 | epot = -135.351255421276 | etot = -106.790023312198 +411000 ekin = 16.1554736030566 | erot = 14.3298422267912 | epot = -135.479919148327 | etot = -104.994603318479 +412000 ekin = 16.5857499566834 | erot = 13.4737312711743 | epot = -135.584889444117 | etot = -105.525408216259 +413000 ekin = 16.9229179279286 | erot = 13.6039157859352 | epot = -135.514436450931 | etot = -104.987602737067 +414000 ekin = 16.5314068368499 | erot = 15.4040344847393 | epot = -135.352428551428 | etot = -103.416987229839 +415000 ekin = 16.1459888084541 | erot = 15.1961034970421 | epot = -135.089001803045 | etot = -103.746909497549 +416000 ekin = 16.0594536949154 | erot = 15.1002331509048 | epot = -134.764864008918 | etot = -103.605177163097 +417000 ekin = 15.6980662646932 | erot = 15.0388392647989 | epot = -134.315494988363 | etot = -103.578589458871 +418000 ekin = 14.8009500438545 | erot = 14.6697393541096 | epot = -133.903967690311 | etot = -104.433278292347 +419000 ekin = 14.6357923304129 | erot = 13.2510064578586 | epot = -133.488837449519 | etot = -105.602038661248 +420000 ekin = 13.7797138062255 | erot = 13.6736426456043 | epot = -133.082126294055 | etot = -105.628769842225 +421000 ekin = 12.919024364293 | erot = 14.4142500849553 | epot = -132.771092930571 | etot = -105.437818481323 +422000 ekin = 12.4606284745775 | erot = 13.6365236121425 | epot = -132.493275384809 | etot = -106.396123298089 +423000 ekin = 12.2948098735175 | erot = 15.893052207907 | epot = -132.380013343043 | etot = -104.192151261619 +424000 ekin = 11.745927681356 | erot = 17.5335098604016 | epot = -132.424796646041 | etot = -103.145359104284 +425000 ekin = 12.0006262659262 | erot = 15.539973283722 | epot = -132.540653755033 | etot = -105.000054205384 +426000 ekin = 11.8843491709195 | erot = 16.7940075159323 | epot = -132.662628106265 | etot = -103.984271419413 +427000 ekin = 11.3591082759808 | erot = 17.0425126325344 | epot = -132.894706769785 | etot = -104.49308586127 +428000 ekin = 10.74405872772 | erot = 18.3249469758695 | epot = -133.166202813839 | etot = -104.097197110249 +429000 ekin = 10.7706487509066 | erot = 17.6551088604746 | epot = -133.358870523568 | etot = -104.933112912187 +430000 ekin = 10.6474001981849 | erot = 18.596041889709 | epot = -133.511953764021 | etot = -104.268511676127 +431000 ekin = 11.1157718416981 | erot = 20.5642690531762 | epot = -133.457724392349 | etot = -101.777683497475 +432000 ekin = 10.9588563257813 | erot = 18.6638268050758 | epot = -133.288845550957 | etot = -103.6661624201 +433000 ekin = 11.6770191364917 | erot = 16.4659565290407 | epot = -133.019945473853 | etot = -104.87696980832 +434000 ekin = 12.1024379349047 | erot = 16.0016819384212 | epot = -132.762722000371 | etot = -104.658602127045 +435000 ekin = 12.349281362769 | erot = 13.3785279839521 | epot = -132.604369715003 | etot = -106.876560368282 +436000 ekin = 13.1471833683191 | erot = 13.9173006161182 | epot = -132.562594724265 | etot = -105.498110739827 +437000 ekin = 13.6350491625079 | erot = 13.1122068961503 | epot = -132.517452891629 | etot = -105.770196832971 +438000 ekin = 13.6930952898924 | erot = 14.2359944827941 | epot = -132.455362578639 | etot = -104.526272805953 +439000 ekin = 13.8605718764543 | erot = 13.5844935351474 | epot = -132.383154183074 | etot = -104.938088771472 +440000 ekin = 13.6442811020083 | erot = 14.4808963859129 | epot = -132.383844089461 | etot = -104.25866660154 +441000 ekin = 13.5515648121245 | erot = 13.0785991097761 | epot = -132.396376591798 | etot = -105.766212669898 +442000 ekin = 14.1256921745767 | erot = 12.4782565032754 | epot = -132.547264323122 | etot = -105.94331564527 +443000 ekin = 14.5691691188627 | erot = 13.8774098742386 | epot = -132.720623905077 | etot = -104.274044911975 +444000 ekin = 14.7351369676478 | erot = 14.3470950238126 | epot = -132.866409443678 | etot = -103.784177452217 +445000 ekin = 14.9644282174562 | erot = 15.6053547547498 | epot = -132.805608746253 | etot = -102.235825774047 +446000 ekin = 15.0045450016756 | erot = 13.6477020624871 | epot = -132.65253892759 | etot = -104.000291863427 +447000 ekin = 14.3245041504183 | erot = 13.6106925210228 | epot = -132.439878435946 | etot = -104.504681764505 +448000 ekin = 14.233916528542 | erot = 12.3909865857314 | epot = -132.243474706559 | etot = -105.618571592286 +449000 ekin = 14.1398313922663 | erot = 12.2685893909668 | epot = -132.06378980736 | etot = -105.655369024127 +450000 ekin = 13.4904273032194 | erot = 12.3330756316191 | epot = -131.830755010798 | etot = -106.00725207596 +451000 ekin = 13.300341297742 | erot = 11.1345212763943 | epot = -131.438716026705 | etot = -107.003853452569 +452000 ekin = 13.1916656544132 | erot = 12.0107960818815 | epot = -131.06562936513 | etot = -105.863167628836 +453000 ekin = 13.6470034210578 | erot = 11.3478854304713 | epot = -130.666197429497 | etot = -105.671308577968 +454000 ekin = 13.7514576509104 | erot = 11.0422941308611 | epot = -130.279471820623 | etot = -105.485720038851 +455000 ekin = 13.6427936386073 | erot = 10.6725549566639 | epot = -130.084596778391 | etot = -105.769248183119 +456000 ekin = 13.0332807830664 | erot = 11.1448945005553 | epot = -130.006108312447 | etot = -105.827933028825 +457000 ekin = 12.6888308068745 | erot = 11.996417916709 | epot = -129.866026242229 | etot = -105.180777518646 +458000 ekin = 12.2236956230155 | erot = 11.9723258535854 | epot = -129.822007447389 | etot = -105.625985970788 +459000 ekin = 12.4187372424446 | erot = 12.2448106818498 | epot = -130.011349416051 | etot = -105.347801491757 +460000 ekin = 12.3181219588596 | erot = 13.6300348406456 | epot = -130.301233711192 | etot = -104.353076911686 +461000 ekin = 13.0224185496646 | erot = 12.4015946976694 | epot = -130.754682803086 | etot = -105.330669555752 +462000 ekin = 13.8272851866575 | erot = 13.7167043927439 | epot = -131.088410073843 | etot = -103.544420494441 +463000 ekin = 14.233581499904 | erot = 12.5329824172969 | epot = -131.331794671857 | etot = -104.565230754656 +464000 ekin = 14.1261800982275 | erot = 13.9303608372166 | epot = -131.548600987817 | etot = -103.492060052373 +465000 ekin = 14.1255464940624 | erot = 13.3900400807099 | epot = -131.630321080862 | etot = -104.114734506089 +466000 ekin = 13.8228140080026 | erot = 12.5884468885677 | epot = -131.60685460129 | etot = -105.195593704719 +467000 ekin = 13.9322919754765 | erot = 13.4312985643275 | epot = -131.680549012765 | etot = -104.316958472961 +468000 ekin = 14.3853651937711 | erot = 12.6461801454634 | epot = -131.625011265765 | etot = -104.59346592653 +469000 ekin = 14.5533304292821 | erot = 16.0723443902969 | epot = -131.418212758337 | etot = -100.792537938758 +470000 ekin = 15.0840954556285 | erot = 16.222522877142 | epot = -131.148990199381 | etot = -99.8423718666102 +471000 ekin = 14.4219777322226 | erot = 15.8873237998424 | epot = -130.678043003916 | etot = -100.368741471851 +472000 ekin = 14.435030670305 | erot = 15.671788565829 | epot = -130.139079955408 | etot = -100.032260719274 +473000 ekin = 13.906204124583 | erot = 15.638897325228 | epot = -129.77698458443 | etot = -100.231883134619 +474000 ekin = 13.6024483079048 | erot = 14.9117660516568 | epot = -129.455404640313 | etot = -100.941190280752 +475000 ekin = 12.824122130844 | erot = 15.5367178310513 | epot = -129.246309588152 | etot = -100.885469626257 +476000 ekin = 12.9055013167445 | erot = 14.6727742202391 | epot = -129.302333908223 | etot = -101.72405837124 +477000 ekin = 12.7196731835606 | erot = 14.3993459723445 | epot = -129.64652145757 | etot = -102.527502301665 +478000 ekin = 13.3386835875674 | erot = 14.5179440867012 | epot = -130.153117698304 | etot = -102.296490024035 +479000 ekin = 13.8396392901302 | erot = 13.6621367485581 | epot = -130.781114095862 | etot = -103.279338057174 +480000 ekin = 14.2724362045435 | erot = 15.784109317918 | epot = -131.413694225648 | etot = -101.357148703186 +481000 ekin = 14.0102282052329 | erot = 16.0578586490324 | epot = -131.929137624341 | etot = -101.861050770076 +482000 ekin = 14.0956208717202 | erot = 15.8675233063324 | epot = -132.167277100212 | etot = -102.204132922159 +483000 ekin = 13.8372321085018 | erot = 14.5340925107821 | epot = -132.001986789449 | etot = -103.630662170165 +484000 ekin = 13.4224547855769 | erot = 11.9661360017051 | epot = -131.683314721398 | etot = -106.294723934116 +485000 ekin = 13.1373330656359 | erot = 11.3254954130182 | epot = -131.289318850469 | etot = -106.826490371815 +486000 ekin = 13.905837100344 | erot = 12.1980994310324 | epot = -130.930010356581 | etot = -104.826073825204 +487000 ekin = 13.2698534777382 | erot = 11.8745698433001 | epot = -130.5624327701 | etot = -105.418009449061 +488000 ekin = 12.9434697199259 | erot = 12.0293958304853 | epot = -130.209265396125 | etot = -105.236399845714 +489000 ekin = 12.5721899198871 | erot = 8.47459617531023 | epot = -129.953831166846 | etot = -108.907045071649 +490000 ekin = 12.3390702542933 | erot = 7.86378661329589 | epot = -129.753215573881 | etot = -109.550358706292 +491000 ekin = 11.9624599841506 | erot = 8.41735013444669 | epot = -129.506172001993 | etot = -109.126361883396 +492000 ekin = 11.7077910623616 | erot = 9.63580876658954 | epot = -129.43578091039 | etot = -108.092181081439 +493000 ekin = 11.1244386116376 | erot = 11.4939505930869 | epot = -129.383239390152 | etot = -106.764850185427 +494000 ekin = 11.0781415353741 | erot = 13.0857204067954 | epot = -129.404483774133 | etot = -105.240621831963 +495000 ekin = 11.4990453516689 | erot = 14.0188122780217 | epot = -129.557836878698 | etot = -104.039979249008 +496000 ekin = 11.5056539707761 | erot = 12.8857921899793 | epot = -129.825905288658 | etot = -105.434459127903 +497000 ekin = 11.33134224258 | erot = 13.2836312713858 | epot = -130.109579120835 | etot = -105.494605606869 +498000 ekin = 11.4981547815264 | erot = 15.3140349034712 | epot = -130.559763793736 | etot = -103.747574108738 +499000 ekin = 11.1599160547319 | erot = 14.6965934583534 | epot = -131.023052476114 | etot = -105.166542963029 +500000 ekin = 10.7780642831738 | erot = 15.7901919369947 | epot = -131.533138574135 | etot = -104.964882353967 +501000 ekin = 10.720403632948 | erot = 14.8758201582326 | epot = -132.030158305869 | etot = -106.433934514688 +502000 ekin = 10.9110010846821 | erot = 16.0790893187808 | epot = -132.428098038251 | etot = -105.438007634788 +503000 ekin = 10.9881321156139 | erot = 18.4086921037074 | epot = -132.690429019574 | etot = -103.293604800253 +504000 ekin = 11.2747688970756 | erot = 18.3069766546834 | epot = -132.868714178775 | etot = -103.286968627016 +505000 ekin = 11.0647415890157 | erot = 16.9097240173448 | epot = -132.895739990367 | etot = -104.921274384007 +506000 ekin = 11.7075716116498 | erot = 15.491840602935 | epot = -132.740532250649 | etot = -105.541120036064 +507000 ekin = 11.3011932151634 | erot = 15.9113427794058 | epot = -132.415188396473 | etot = -105.202652401904 +508000 ekin = 11.6967952061443 | erot = 14.7240977646156 | epot = -131.952406046646 | etot = -105.531513075886 +509000 ekin = 11.6315150466958 | erot = 13.5300219702026 | epot = -131.434217700445 | etot = -106.272680683546 +510000 ekin = 12.2520798346389 | erot = 11.1506231276725 | epot = -130.950401471758 | etot = -107.547698509446 +511000 ekin = 12.5036986807164 | erot = 11.0966142079411 | epot = -130.612066388725 | etot = -107.011753500067 +512000 ekin = 12.3982520931714 | erot = 11.1407951595418 | epot = -130.506298860028 | etot = -106.967251607315 +513000 ekin = 11.8503807436704 | erot = 10.6395006743577 | epot = -130.62994085624 | etot = -108.140059438211 +514000 ekin = 11.6931801130336 | erot = 10.0284485074895 | epot = -131.026141821515 | etot = -109.304513200992 +515000 ekin = 11.7542279720105 | erot = 9.99471209356388 | epot = -131.61924379854 | etot = -109.870303732966 +516000 ekin = 11.4577827917683 | erot = 9.46971305059919 | epot = -132.261609421054 | etot = -111.334113578686 +517000 ekin = 11.2718685099608 | erot = 8.19398630894372 | epot = -132.791968639562 | etot = -113.326113820658 +518000 ekin = 11.3016092575651 | erot = 10.2172039155432 | epot = -133.256960381085 | etot = -111.738147207976 +519000 ekin = 11.3134437464979 | erot = 9.77961157844874 | epot = -133.703814863063 | etot = -112.610759538116 +520000 ekin = 11.9401995794921 | erot = 9.94217963136258 | epot = -134.138670478908 | etot = -112.256291268053 +521000 ekin = 11.6110284291038 | erot = 10.4252254290505 | epot = -134.523960362929 | etot = -112.487706504775 +522000 ekin = 11.7583420057528 | erot = 10.5600256573471 | epot = -134.902954163118 | etot = -112.584586500018 +523000 ekin = 12.2195814890805 | erot = 10.484479844249 | epot = -135.099883008383 | etot = -112.395821675053 +524000 ekin = 12.536206091596 | erot = 10.2464120884985 | epot = -135.197150509169 | etot = -112.414532329075 +525000 ekin = 12.7695180124394 | erot = 12.830924120624 | epot = -135.181443853743 | etot = -109.581001720679 +526000 ekin = 13.4914714182443 | erot = 13.3323995889542 | epot = -134.989013161967 | etot = -108.165142154768 +527000 ekin = 13.6339858533173 | erot = 14.1143226731303 | epot = -134.603919851952 | etot = -106.855611325504 +528000 ekin = 13.9871131035254 | erot = 13.4790195739988 | epot = -134.158105371852 | etot = -106.691972694328 +529000 ekin = 13.6676266211537 | erot = 13.2846277161303 | epot = -133.587001654026 | etot = -106.634747316742 +530000 ekin = 13.8931133897467 | erot = 11.6197807566239 | epot = -132.893711115648 | etot = -107.380816969277 +531000 ekin = 13.1581397494984 | erot = 10.5027113889053 | epot = -132.366500286018 | etot = -108.705649147614 +532000 ekin = 13.0159641084816 | erot = 9.74741653324235 | epot = -132.024821707355 | etot = -109.261441065631 +533000 ekin = 12.7093786848764 | erot = 11.1416896656569 | epot = -131.697717778404 | etot = -107.84664942787 +534000 ekin = 13.1731011809403 | erot = 11.234780019293 | epot = -131.512303718956 | etot = -107.104422518723 +535000 ekin = 12.2968228666283 | erot = 11.4846073479047 | epot = -131.474751059282 | etot = -107.693320844749 +536000 ekin = 11.5423021442201 | erot = 13.2447755418492 | epot = -131.50032350842 | etot = -106.713245822351 +537000 ekin = 11.2051679081485 | erot = 13.3250331992255 | epot = -131.521899174971 | etot = -106.991698067597 +538000 ekin = 10.5294344085608 | erot = 14.7761967332319 | epot = -131.383857857022 | etot = -106.078226715229 +539000 ekin = 10.185806871544 | erot = 15.4028825102826 | epot = -131.074787080495 | etot = -105.486097698668 +540000 ekin = 9.43449944911005 | erot = 16.5592825971122 | epot = -130.579041867527 | etot = -104.585259821305 +541000 ekin = 8.78189284925949 | erot = 16.499053893454 | epot = -129.848069059872 | etot = -104.567122317159 +542000 ekin = 8.57200654572226 | erot = 13.9898084335997 | epot = -128.994341371238 | etot = -106.432526391916 +543000 ekin = 8.48555433974962 | erot = 11.975315234089 | epot = -127.987968360581 | etot = -107.527098786742 +544000 ekin = 7.96647321950487 | erot = 11.2184967506479 | epot = -127.002534367986 | etot = -107.817564397833 +545000 ekin = 7.66004105211321 | erot = 10.7080025987845 | epot = -126.130595958291 | etot = -107.762552307393 +546000 ekin = 7.06613495262288 | erot = 9.6002881909899 | epot = -125.557639605507 | etot = -108.891216461894 +547000 ekin = 7.36411379188746 | erot = 8.5798098555711 | epot = -125.534102025062 | etot = -109.590178377603 +548000 ekin = 7.67836324990163 | erot = 10.4827717354784 | epot = -125.855244036483 | etot = -107.694109051103 +549000 ekin = 7.53512550399845 | erot = 11.187359733996 | epot = -126.364806908004 | etot = -107.64232167001 +550000 ekin = 7.86533308362698 | erot = 12.3828037628687 | epot = -127.001709461581 | etot = -106.753572615086 +551000 ekin = 8.2919003989052 | erot = 14.6756554271348 | epot = -127.700019966059 | etot = -104.732464140019 +552000 ekin = 9.12142958179215 | erot = 15.3500028547346 | epot = -128.331143583993 | etot = -103.859711147467 +553000 ekin = 9.28716397081024 | erot = 14.7937796025153 | epot = -128.943798064185 | etot = -104.862854490859 +554000 ekin = 9.60827102742978 | erot = 14.5542827554277 | epot = -129.315782051341 | etot = -105.153228268484 +555000 ekin = 9.75156872107715 | erot = 13.7256451762815 | epot = -129.402138106003 | etot = -105.924924208644 +556000 ekin = 10.591262420886 | erot = 14.1011153234612 | epot = -129.339658998616 | etot = -104.647281254269 +557000 ekin = 11.0661812655726 | erot = 14.5765059160724 | epot = -129.157158809594 | etot = -103.514471627949 +558000 ekin = 11.9848375025011 | erot = 15.6316594136391 | epot = -128.917135875743 | etot = -101.300638959602 +559000 ekin = 12.4984336945226 | erot = 15.4984434935456 | epot = -128.511580820598 | etot = -100.51470363253 +560000 ekin = 12.7125630744296 | erot = 14.2557121467619 | epot = -128.104959570362 | etot = -101.136684349171 +561000 ekin = 13.0021457709909 | erot = 14.2140861936463 | epot = -127.967258289089 | etot = -100.751026324452 +562000 ekin = 12.9111077378043 | erot = 14.5809064217209 | epot = -127.853767783697 | etot = -100.361753624171 +563000 ekin = 12.8539990412072 | erot = 14.3589235788587 | epot = -127.869234305675 | etot = -100.656311685609 +564000 ekin = 13.6377557966074 | erot = 12.5940313423354 | epot = -128.066659471603 | etot = -101.834872332661 +565000 ekin = 13.7859200073662 | erot = 13.1002138307723 | epot = -128.411125869716 | etot = -101.524992031578 +566000 ekin = 14.3793917966067 | erot = 14.7163468779501 | epot = -128.789096622906 | etot = -99.6933579483494 +567000 ekin = 14.5329135783505 | erot = 15.8458849175852 | epot = -129.174356602354 | etot = -98.7955581064185 +568000 ekin = 15.0126672916507 | erot = 16.3995947000213 | epot = -129.488105101221 | etot = -98.0758431095491 +569000 ekin = 15.4823990471097 | erot = 15.1400173282169 | epot = -129.721190178973 | etot = -99.0987738036465 +570000 ekin = 15.2652432676604 | erot = 14.0400444480291 | epot = -129.663603273428 | etot = -100.358315557738 +571000 ekin = 15.1960180928438 | erot = 15.2333113599558 | epot = -129.285234325386 | etot = -98.8559048725867 +572000 ekin = 14.2244862323778 | erot = 15.3588426722882 | epot = -128.691549749642 | etot = -99.1082208449758 +573000 ekin = 14.3247255314221 | erot = 15.2838217371065 | epot = -127.915895939713 | etot = -98.3073486711846 +574000 ekin = 13.8328485668081 | erot = 16.0911195322339 | epot = -127.259258688926 | etot = -97.3352905898843 +575000 ekin = 12.2894285073784 | erot = 14.0030483890098 | epot = -126.752490227254 | etot = -100.460013330866 +576000 ekin = 12.675092902127 | erot = 13.875494112131 | epot = -126.443913021454 | etot = -99.8933260071956 +577000 ekin = 12.8302006347986 | erot = 13.5566542600766 | epot = -126.229749925447 | etot = -99.8428950305716 +578000 ekin = 12.3973073325353 | erot = 13.367501392846 | epot = -125.944425149808 | etot = -100.179616424427 +579000 ekin = 12.4969856893803 | erot = 13.2211553313989 | epot = -125.639620042896 | etot = -99.9214790221165 +580000 ekin = 12.2171822571891 | erot = 13.6186421452794 | epot = -125.360378762533 | etot = -99.524554360064 +581000 ekin = 12.2252107821838 | erot = 13.688527688114 | epot = -125.066396673108 | etot = -99.15265820281 +582000 ekin = 12.5438750562638 | erot = 14.1768715313422 | epot = -124.698785826033 | etot = -97.9780392384274 +583000 ekin = 12.5380750747106 | erot = 14.5001920749132 | epot = -124.392003106806 | etot = -97.3537359571822 +584000 ekin = 12.3406221559926 | erot = 15.3339504928243 | epot = -124.287586528117 | etot = -96.6130138792997 +585000 ekin = 12.3990757906099 | erot = 15.8020458644105 | epot = -124.119365581542 | etot = -95.9182439265215 +586000 ekin = 12.1190359199953 | erot = 14.1845434930415 | epot = -124.012210724038 | etot = -97.7086313110016 +587000 ekin = 12.3583734147512 | erot = 12.6837508331823 | epot = -124.019651244371 | etot = -98.9775269964375 +588000 ekin = 12.1093370015091 | erot = 12.224929613342 | epot = -124.009485650513 | etot = -99.6752190356617 +589000 ekin = 12.7058628422607 | erot = 12.6755414025477 | epot = -124.146501688458 | etot = -98.7650974436494 +590000 ekin = 13.5724385310838 | erot = 11.6851077070925 | epot = -124.469602180811 | etot = -99.2120559426343 +591000 ekin = 13.9648833175222 | erot = 11.7829550620435 | epot = -124.977098177567 | etot = -99.229259798001 +592000 ekin = 14.4468708943991 | erot = 10.4693339695267 | epot = -125.37966268423 | etot = -100.463457820304 +593000 ekin = 14.2853778011465 | erot = 10.6838640494361 | epot = -125.899049747802 | etot = -100.929807897219 +594000 ekin = 14.2484623315 | erot = 11.3956366286547 | epot = -126.563145974947 | etot = -100.919047014793 +595000 ekin = 14.5432468578032 | erot = 11.5096332395875 | epot = -127.31254003686 | etot = -101.259659939469 +596000 ekin = 15.7004738515543 | erot = 13.9287180268694 | epot = -128.285375863105 | etot = -98.6561839846811 +597000 ekin = 15.9594818135511 | erot = 16.6195679021881 | epot = -129.261139197126 | etot = -96.682089481387 +598000 ekin = 15.688947247649 | erot = 17.7915161364841 | epot = -130.157771281092 | etot = -96.6773078969585 +599000 ekin = 15.3794249114834 | erot = 15.7367004273062 | epot = -130.695250974136 | etot = -99.5791256353462 +600000 ekin = 14.9121548743718 | erot = 17.8944679163932 | epot = -130.884266476227 | etot = -98.0776436854616 +601000 ekin = 14.5733848977638 | erot = 16.7424040931935 | epot = -130.766918234694 | etot = -99.451129243737 +602000 ekin = 14.0065213221307 | erot = 16.001016861689 | epot = -130.525185821509 | etot = -100.517647637689 +603000 ekin = 13.1967928818603 | erot = 16.4154887990088 | epot = -130.236290569545 | etot = -100.624008888676 +604000 ekin = 12.3311914650794 | erot = 15.6969694775336 | epot = -129.841852174415 | etot = -101.813691231802 +605000 ekin = 12.0612301148609 | erot = 19.0702073568416 | epot = -129.265530748919 | etot = -98.1340932772164 +606000 ekin = 11.588475893498 | erot = 18.6236027196818 | epot = -128.561179687128 | etot = -98.349101073948 +607000 ekin = 11.7321101978434 | erot = 16.9146116711412 | epot = -127.723815602833 | etot = -99.0770937338486 +608000 ekin = 11.3658517138785 | erot = 17.8261844157427 | epot = -126.863647516403 | etot = -97.6716113867816 +609000 ekin = 10.6556809697065 | erot = 20.6644350673316 | epot = -125.950421629035 | etot = -94.6303055919974 +610000 ekin = 10.7853361626725 | erot = 21.6050204002385 | epot = -125.00400963072 | etot = -92.6136530678089 +611000 ekin = 11.1706200435126 | erot = 21.0454340328635 | epot = -124.143633036291 | etot = -91.9275789599151 +612000 ekin = 11.7961607726653 | erot = 19.8808360682819 | epot = -123.303763137073 | etot = -91.6267662961261 +613000 ekin = 12.2790441909626 | erot = 18.1523884321779 | epot = -122.55853939467 | etot = -92.1271067715296 +614000 ekin = 12.3418202948158 | erot = 16.0522193746511 | epot = -122.154911138626 | etot = -93.7608714691587 +615000 ekin = 13.0138767109882 | erot = 15.7976520852059 | epot = -122.104539054864 | etot = -93.2930102586696 +616000 ekin = 13.1684757155919 | erot = 14.2607383451312 | epot = -122.282441526308 | etot = -94.8532274655853 +617000 ekin = 13.6404132275008 | erot = 11.794659359218 | epot = -122.517742746132 | etot = -97.0826701594137 +618000 ekin = 13.6659084124786 | erot = 11.759331412587 | epot = -123.061651867184 | etot = -97.6364120421179 +619000 ekin = 14.6065145093282 | erot = 14.7511017433686 | epot = -123.748631170987 | etot = -94.3910149182907 +620000 ekin = 15.50054373939 | erot = 16.0987287820653 | epot = -124.593446193433 | etot = -92.9941736719774 +621000 ekin = 16.3423395899253 | erot = 16.5059806267673 | epot = -125.362014843738 | etot = -92.513694627045 +622000 ekin = 16.5005311105408 | erot = 17.6619817448939 | epot = -126.010027927038 | etot = -91.8475150716028 +623000 ekin = 16.9173697080473 | erot = 16.9196411258518 | epot = -126.526201775063 | etot = -92.6891909411641 +624000 ekin = 16.8630691072179 | erot = 16.4004847277849 | epot = -126.768008337096 | etot = -93.5044545020931 +625000 ekin = 17.4512664612524 | erot = 16.0587940917397 | epot = -126.935422339869 | etot = -93.4253617868772 +626000 ekin = 17.2936665728482 | erot = 15.3128836830613 | epot = -127.037669686934 | etot = -94.4311194310244 +627000 ekin = 17.4654693594244 | erot = 14.8142528789145 | epot = -127.145731848601 | etot = -94.8660096102618 +628000 ekin = 17.5818742341078 | erot = 15.9486246522772 | epot = -127.148364769085 | etot = -93.6178658826997 +629000 ekin = 18.0834611662905 | erot = 14.6756355733634 | epot = -126.952323014996 | etot = -94.1932262753423 +630000 ekin = 17.8840995792684 | erot = 13.401205848584 | epot = -126.678532269084 | etot = -95.3932268412314 +631000 ekin = 18.1935296729536 | erot = 12.4502314489952 | epot = -126.440360181863 | etot = -95.7965990599137 +632000 ekin = 18.9221681447056 | erot = 11.8661552902894 | epot = -126.441308644557 | etot = -95.6529852095616 +633000 ekin = 19.2113067946158 | erot = 13.1594397129498 | epot = -126.706742517594 | etot = -94.3359960100281 +634000 ekin = 20.3301717379256 | erot = 12.4235710364728 | epot = -127.043793535812 | etot = -94.2900507614131 +635000 ekin = 20.7759513247257 | erot = 12.3714841432956 | epot = -127.372941120786 | etot = -94.2255056527646 +636000 ekin = 20.7687696611453 | erot = 12.8074006314596 | epot = -127.520085768786 | etot = -93.9439154761807 +637000 ekin = 21.1093142137652 | erot = 12.4841738790966 | epot = -127.569514049459 | etot = -93.9760259565968 +638000 ekin = 21.1020473669491 | erot = 12.702087177402 | epot = -127.554195141098 | etot = -93.7500605967471 +639000 ekin = 21.0577266467998 | erot = 12.7003005444012 | epot = -127.63753643133 | etot = -93.8795092401288 +640000 ekin = 21.3937406740469 | erot = 12.4472064696826 | epot = -127.682435047445 | etot = -93.8414879037152 +641000 ekin = 21.4216186865483 | erot = 12.3631944402938 | epot = -127.552900136034 | etot = -93.7680870091921 +642000 ekin = 20.4367389932093 | erot = 14.1541808544319 | epot = -127.30152366589 | etot = -92.7106038182489 +643000 ekin = 20.2979377082655 | erot = 15.0024944362832 | epot = -126.889326829062 | etot = -91.5888946845129 +644000 ekin = 20.2058489999334 | erot = 15.491031004524 | epot = -126.334551618194 | etot = -90.6376716137364 +645000 ekin = 18.9169718743869 | erot = 15.6969515425462 | epot = -125.546440489333 | etot = -90.9325170723995 +646000 ekin = 17.4657002730335 | erot = 15.7137371606576 | epot = -124.573135958619 | etot = -91.3936985249283 +647000 ekin = 16.2686752311563 | erot = 16.1291056474252 | epot = -123.636469263527 | etot = -91.2386883849459 +648000 ekin = 14.6234867914952 | erot = 15.1988644086656 | epot = -122.221359701124 | etot = -92.3990085009632 +649000 ekin = 13.9765767464104 | erot = 14.3359749226089 | epot = -122.017908102962 | etot = -93.7053564339431 +650000 ekin = 13.3083593767564 | erot = 13.3294571145747 | epot = -121.878888386605 | etot = -95.2410718952743 +651000 ekin = 13.2481271072517 | erot = 13.6096229918074 | epot = -121.877302511337 | etot = -95.0195524122776 +652000 ekin = 13.358235640095 | erot = 12.2956271119863 | epot = -122.107622041216 | etot = -96.4537592891344 +653000 ekin = 13.2134408727768 | erot = 12.144377852402 | epot = -122.525474643612 | etot = -97.1676559184336 +654000 ekin = 13.6401865133442 | erot = 12.1024105437077 | epot = -123.091177034103 | etot = -97.3485799770511 +655000 ekin = 14.1382388158376 | erot = 11.3185588850676 | epot = -123.754996028194 | etot = -98.2981983272888 +656000 ekin = 15.3589393726188 | erot = 11.7208375803217 | epot = -124.424910472245 | etot = -97.3451335193042 +657000 ekin = 15.985407864231 | erot = 11.40551206666 | epot = -125.026173045199 | etot = -97.6352531143076 +658000 ekin = 15.9208719205986 | erot = 10.5063118388263 | epot = -125.492025652596 | etot = -99.0648418931712 +659000 ekin = 15.4034330423769 | erot = 7.98268499567967 | epot = -125.846077304125 | etot = -102.459959266068 +660000 ekin = 15.8957184486827 | erot = 7.3209534339452 | epot = -126.090355322523 | etot = -102.873683439896 +661000 ekin = 16.0994929831095 | erot = 6.89812040768852 | epot = -126.301291213824 | etot = -103.303677823026 +662000 ekin = 16.037777694708 | erot = 7.39356761966682 | epot = -126.596997952833 | etot = -103.165652638458 +663000 ekin = 16.2514079166258 | erot = 8.77356221161054 | epot = -126.93775348304 | etot = -101.912783354803 +664000 ekin = 16.6901738665476 | erot = 11.4459754779044 | epot = -127.179645052808 | etot = -99.0434957083556 +665000 ekin = 16.5168554988859 | erot = 12.4360899934879 | epot = -127.289193251941 | etot = -98.3362477595674 +666000 ekin = 16.4595059120294 | erot = 12.353053219114 | epot = -127.360757310456 | etot = -98.5481981793122 +667000 ekin = 16.4576302978905 | erot = 10.6184216922781 | epot = -127.296116321961 | etot = -100.220064331792 +668000 ekin = 16.2951279848706 | erot = 11.6399446274125 | epot = -127.06763280924 | etot = -99.1325601969572 +669000 ekin = 15.6309971924969 | erot = 10.9248518784648 | epot = -126.782455817663 | etot = -100.226606746701 +670000 ekin = 14.69938651138 | erot = 10.2971128796956 | epot = -126.574920158785 | etot = -101.57842076771 +671000 ekin = 14.2333953046718 | erot = 10.2958943118339 | epot = -126.494167399866 | etot = -101.96487778336 +672000 ekin = 14.0074824420819 | erot = 12.0298112037107 | epot = -126.517420140033 | etot = -100.48012649424 +673000 ekin = 13.8132378029881 | erot = 13.3257004951971 | epot = -126.699790731221 | etot = -99.5608524330355 +674000 ekin = 14.3310730802634 | erot = 14.2903823669966 | epot = -126.887224692459 | etot = -98.2657692451993 +675000 ekin = 14.094285780631 | erot = 14.2041424258065 | epot = -127.072500358167 | etot = -98.7740721517297 +676000 ekin = 13.8809716162165 | erot = 14.7571704853675 | epot = -127.244568591992 | etot = -98.6064264904077 +677000 ekin = 13.4750319734461 | erot = 15.8989890896798 | epot = -127.406610822491 | etot = -98.0325897593653 +678000 ekin = 13.204536716915 | erot = 17.060711912575 | epot = -127.537901226718 | etot = -97.2726525972281 +679000 ekin = 13.5094667548578 | erot = 15.8485162061999 | epot = -127.492441090116 | etot = -98.1344581290587 +680000 ekin = 13.7317758530289 | erot = 16.6403654355717 | epot = -127.328352212677 | etot = -96.9562109240759 +681000 ekin = 13.7420697940313 | erot = 16.3253050798175 | epot = -127.033355132541 | etot = -96.9659802586922 +682000 ekin = 13.8865876794374 | erot = 14.1705397429866 | epot = -126.713856182991 | etot = -98.6567287605673 +683000 ekin = 14.1539214405653 | erot = 14.3580474340757 | epot = -126.316182701513 | etot = -97.8042138268716 +684000 ekin = 14.9114202003918 | erot = 13.098285055507 | epot = -125.836001617955 | etot = -97.8262963620566 +685000 ekin = 15.6544076621281 | erot = 11.76351824854 | epot = -125.419422292015 | etot = -98.0014963813465 +686000 ekin = 16.1073557341363 | erot = 9.79708868574903 | epot = -125.048475203594 | etot = -99.1440307837083 +687000 ekin = 16.5128176144743 | erot = 9.40698642310967 | epot = -124.806005792176 | etot = -98.8862017545918 +688000 ekin = 15.9944086012455 | erot = 7.89646425166629 | epot = -124.924212239256 | etot = -101.033339386344 +689000 ekin = 16.2230834947296 | erot = 8.55340876385102 | epot = -125.169534908068 | etot = -100.393042649488 +690000 ekin = 16.7878666602026 | erot = 10.2864631449479 | epot = -125.473510294471 | etot = -98.3991804893207 +691000 ekin = 17.8806968640178 | erot = 10.4556964351401 | epot = -125.769184514249 | etot = -97.4327912150911 +692000 ekin = 18.0381729758976 | erot = 11.8035409722969 | epot = -126.182960500285 | etot = -96.3412465520901 +693000 ekin = 18.1893971688534 | erot = 10.8893717674973 | epot = -126.682628911312 | etot = -97.6038599749618 +694000 ekin = 18.0024663245898 | erot = 9.63008190809017 | epot = -127.134149566016 | etot = -99.5016013333359 +695000 ekin = 17.9106177585088 | erot = 9.38908818759556 | epot = -127.458855842113 | etot = -100.159149896008 +696000 ekin = 18.8015538407413 | erot = 11.3106121967171 | epot = -127.951593054122 | etot = -97.8394270166638 +697000 ekin = 19.6151462844322 | erot = 11.749803807872 | epot = -128.248456377438 | etot = -96.883506285134 +698000 ekin = 19.9817732592184 | erot = 11.9234805546314 | epot = -128.37723140647 | etot = -96.4719775926202 +699000 ekin = 20.492332894368 | erot = 10.3463897474668 | epot = -128.344722500898 | etot = -97.5059998590627 +700000 ekin = 20.3061292470497 | erot = 10.4871647814256 | epot = -128.166934219072 | etot = -97.3736401905967 +701000 ekin = 20.435163166204 | erot = 11.9667131012207 | epot = -127.987082299128 | etot = -95.5852060317033 +702000 ekin = 19.6138488562644 | erot = 11.5598664205714 | epot = -127.589391748164 | etot = -96.4156764713278 +703000 ekin = 18.9781269955423 | erot = 11.1471421540445 | epot = -126.963232468615 | etot = -96.8379633190278 +704000 ekin = 18.1895189194246 | erot = 11.7320537727523 | epot = -126.181700585601 | etot = -96.2601278934237 +705000 ekin = 17.3387627788471 | erot = 10.3965571086159 | epot = -125.378399726584 | etot = -97.6430798391206 +706000 ekin = 16.8701199797021 | erot = 9.80258033004247 | epot = -124.55810673811 | etot = -97.8854064283659 +707000 ekin = 16.0344125792805 | erot = 11.7975795061599 | epot = -123.690865123956 | etot = -95.8588730385155 +708000 ekin = 15.1770953189152 | erot = 13.3872681988452 | epot = -122.798269998057 | etot = -94.2339064802965 +709000 ekin = 14.8566591653084 | erot = 14.7625175527179 | epot = -122.05398638328 | etot = -92.4348096652534 +710000 ekin = 14.2446306961825 | erot = 13.499675207948 | epot = -121.547927750292 | etot = -93.8036218461613 +711000 ekin = 13.8799285650757 | erot = 13.7967609326213 | epot = -121.127667714037 | etot = -93.4509782163402 +712000 ekin = 13.6766438887429 | erot = 14.2325414606922 | epot = -120.791432236364 | etot = -92.8822468869287 +713000 ekin = 12.6318627072834 | erot = 15.1001018154683 | epot = -120.505163197108 | etot = -92.7731986743563 +714000 ekin = 12.2169341685705 | erot = 15.7110047543937 | epot = -120.164867442063 | etot = -92.2369285190987 +715000 ekin = 12.0354978004268 | erot = 14.9480388272421 | epot = -119.896822435967 | etot = -92.9132858082978 +716000 ekin = 12.1247018323357 | erot = 15.009272360407 | epot = -119.754186634337 | etot = -92.6202124415946 +717000 ekin = 12.4339332759081 | erot = 14.689545190185 | epot = -119.773695307702 | etot = -92.6502168416085 +718000 ekin = 12.5421685656907 | erot = 15.4913269347027 | epot = -119.995216958968 | etot = -91.9617214585742 +719000 ekin = 12.8745846399692 | erot = 15.8452687118538 | epot = -120.323092184334 | etot = -91.603238832511 +720000 ekin = 13.1266740751758 | erot = 16.314705230934 | epot = -120.747951420241 | etot = -91.3065721141314 +721000 ekin = 13.684105405114 | erot = 17.0704798955969 | epot = -121.389101633572 | etot = -90.6345163328612 +722000 ekin = 14.1310987124484 | erot = 17.0813242672828 | epot = -122.028449574819 | etot = -90.816026595088 +723000 ekin = 14.1807761691476 | erot = 17.6983672283012 | epot = -122.518415688138 | etot = -90.6392722906893 +724000 ekin = 13.9119763497037 | erot = 16.3061756159374 | epot = -122.913742356855 | etot = -92.6955903912141 +725000 ekin = 15.1341788655366 | erot = 16.6282425691433 | epot = -123.267617609515 | etot = -91.5051961748353 +726000 ekin = 15.7434651230328 | erot = 15.6799305516657 | epot = -123.519615991063 | etot = -92.0962203163648 +727000 ekin = 16.5696277513306 | erot = 15.7761828983799 | epot = -123.813517978553 | etot = -91.4677073288423 +728000 ekin = 17.138358866264 | erot = 15.5397944494481 | epot = -124.189446555112 | etot = -91.5112932394 +729000 ekin = 17.8475719432623 | erot = 16.1340960775738 | epot = -124.63939303385 | etot = -90.6577250130135 +730000 ekin = 17.9540212549384 | erot = 16.601310674205 | epot = -125.140051021056 | etot = -90.5847190919131 +731000 ekin = 17.8190386197637 | erot = 17.4167233026914 | epot = -125.555205239652 | etot = -90.319443317197 +732000 ekin = 17.2392386833352 | erot = 15.3434972818983 | epot = -125.913671040018 | etot = -93.3309350747848 +733000 ekin = 17.3863226785689 | erot = 17.3727666834628 | epot = -126.113198330789 | etot = -91.3541089687574 +734000 ekin = 16.9660772739466 | erot = 19.7067074835036 | epot = -126.119820702024 | etot = -89.4470359445737 +735000 ekin = 17.2099696362347 | erot = 19.0860025980318 | epot = -125.998538986046 | etot = -89.7025667517794 +736000 ekin = 16.9363715030583 | erot = 20.5976147990406 | epot = -125.618325716769 | etot = -88.0843394146702 +737000 ekin = 16.2608237238847 | erot = 19.8522799516617 | epot = -125.100604184481 | etot = -88.9875005089344 +738000 ekin = 15.395982158947 | erot = 19.9411959356938 | epot = -124.604460889069 | etot = -89.2672827944282 +739000 ekin = 14.705870676325 | erot = 20.6458397755629 | epot = -124.153094104811 | etot = -88.8013836529227 +740000 ekin = 14.2784412741685 | erot = 20.2601951811175 | epot = -123.677002537444 | etot = -89.1383660821579 +741000 ekin = 13.4955390829594 | erot = 19.3311277036108 | epot = -123.387705919687 | etot = -90.5610391331166 +742000 ekin = 12.8179361413291 | erot = 19.5336860011407 | epot = -123.151449993436 | etot = -90.7998278509665 +743000 ekin = 13.0337014652775 | erot = 17.9841020922867 | epot = -123.012673897736 | etot = -91.9948703401715 +744000 ekin = 12.9813980961597 | erot = 17.726056879389 | epot = -122.916848685485 | etot = -92.2093937099368 +745000 ekin = 13.5311464037343 | erot = 18.1177531188692 | epot = -122.901549018525 | etot = -91.2526494959215 +746000 ekin = 13.5919703939618 | erot = 19.0832740150976 | epot = -123.101419465854 | etot = -90.4261750567945 +747000 ekin = 14.1077674474257 | erot = 17.8226275034512 | epot = -123.58081022616 | etot = -91.650415275283 +748000 ekin = 14.6621453024792 | erot = 17.8312525621379 | epot = -124.112503040582 | etot = -91.6191051759652 +749000 ekin = 15.4518977431962 | erot = 15.7096412244856 | epot = -124.687395203896 | etot = -93.5258562362144 +750000 ekin = 16.1563893654211 | erot = 13.965149665533 | epot = -125.277204558046 | etot = -95.1556655270914 +751000 ekin = 16.2747342933903 | erot = 12.6977317580505 | epot = -125.831806887125 | etot = -96.8593408356843 +752000 ekin = 17.7056563013116 | erot = 13.3824566508439 | epot = -126.411836163195 | etot = -95.3237232110397 +753000 ekin = 17.9854792842255 | erot = 14.8922469505158 | epot = -126.873651180785 | etot = -93.9959249460439 +754000 ekin = 18.5318903204323 | erot = 15.9226115000986 | epot = -127.346494571583 | etot = -92.8919927510522 +755000 ekin = 18.5931261934923 | erot = 13.6718413880936 | epot = -127.742440326195 | etot = -95.4774727446087 +756000 ekin = 18.8286764442108 | erot = 13.0137069564827 | epot = -128.191128040948 | etot = -96.3487446402544 +757000 ekin = 19.4913070071007 | erot = 14.5250853074874 | epot = -128.69789103348 | etot = -94.6814987188918 +758000 ekin = 19.6942603476018 | erot = 14.5104088574756 | epot = -128.979041245958 | etot = -94.7743720408807 +759000 ekin = 18.9325456706996 | erot = 15.1874719906816 | epot = -129.125230915994 | etot = -95.0052132546124 +760000 ekin = 18.9065789818531 | erot = 14.2503021689044 | epot = -129.446059212486 | etot = -96.2891780617282 +761000 ekin = 18.357314022554 | erot = 14.1498937701025 | epot = -129.843841819257 | etot = -97.3366340266 +762000 ekin = 17.9187526439542 | erot = 15.5059590298861 | epot = -130.296359700542 | etot = -96.871648026702 +763000 ekin = 18.7690798800428 | erot = 16.014839272894 | epot = -130.770463803987 | etot = -95.9865446510507 +764000 ekin = 18.8778219119189 | erot = 16.8467266459808 | epot = -131.242851353872 | etot = -95.5183027959724 +765000 ekin = 19.2932441905361 | erot = 18.6166335931794 | epot = -131.514072102331 | etot = -93.6041943186153 +766000 ekin = 19.3126668142697 | erot = 19.7805756720901 | epot = -131.43720495817 | etot = -92.3439624718106 +767000 ekin = 18.8380931693496 | erot = 21.0359980279622 | epot = -131.01637172035 | etot = -91.1422805230381 +768000 ekin = 19.1261539279865 | erot = 20.0058132628391 | epot = -130.383371663231 | etot = -91.2514044724058 +769000 ekin = 18.6658010875798 | erot = 19.8194697215686 | epot = -129.737136131356 | etot = -91.2518653222079 +770000 ekin = 18.6690643877456 | erot = 18.6699378990226 | epot = -129.178488323658 | etot = -91.8394860368895 +771000 ekin = 18.410622704207 | erot = 19.2525778618946 | epot = -128.676630708693 | etot = -91.0134301425919 +772000 ekin = 17.9707250637436 | erot = 17.4114938226956 | epot = -128.261442222035 | etot = -92.8792233355954 +773000 ekin = 17.668312511817 | erot = 17.2569733842433 | epot = -127.87672080999 | etot = -92.9514349139299 +774000 ekin = 17.5550764279839 | erot = 17.4864657435421 | epot = -127.411445006413 | etot = -92.3699028348866 +775000 ekin = 16.8879188430506 | erot = 17.4941622737562 | epot = -127.021017099921 | etot = -92.6389359831145 +776000 ekin = 16.149138831663 | erot = 17.7923322373362 | epot = -126.516975486605 | etot = -92.5755044176057 +777000 ekin = 15.1959987806213 | erot = 16.1719415713515 | epot = -125.8152015468 | etot = -94.4472611948275 +778000 ekin = 14.786810923737 | erot = 12.6586337347389 | epot = -125.146947022063 | etot = -97.7015023635874 +779000 ekin = 14.2187642913764 | erot = 13.6699008100759 | epot = -124.725151042076 | etot = -96.8364859406241 +780000 ekin = 14.1033477025239 | erot = 13.5818589500756 | epot = -124.366246202707 | etot = -96.6810395501076 +781000 ekin = 14.0036276712943 | erot = 13.429175819281 | epot = -124.2212179265 | etot = -96.7884144359251 +782000 ekin = 13.6399725569131 | erot = 12.8638840023592 | epot = -124.177097664268 | etot = -97.6732411049952 +783000 ekin = 13.0983004720875 | erot = 13.566823921084 | epot = -124.330009413018 | etot = -97.6648850198466 +784000 ekin = 12.4232195977069 | erot = 11.7074204511651 | epot = -124.477486844109 | etot = -100.346846795237 +785000 ekin = 12.6954370989424 | erot = 13.3412967612961 | epot = -124.489174891303 | etot = -98.4524410310646 +786000 ekin = 12.2307499602112 | erot = 13.8135463793774 | epot = -124.607122728393 | etot = -98.5628263888048 +787000 ekin = 12.9182869507333 | erot = 13.7218969143707 | epot = -124.82074195056 | etot = -98.1805580854555 +788000 ekin = 13.4238850106927 | erot = 14.1597856773729 | epot = -124.981729531598 | etot = -97.3980588435328 +789000 ekin = 13.2661219147002 | erot = 14.5207070846773 | epot = -125.006998351316 | etot = -97.2201693519387 +790000 ekin = 12.8103412181899 | erot = 17.5755134448426 | epot = -124.942134130136 | etot = -94.5562794671033 +791000 ekin = 12.4503556199692 | erot = 15.5554751941819 | epot = -124.907713394743 | etot = -96.9018825805917 +792000 ekin = 12.6341647652668 | erot = 15.3773249490151 | epot = -125.076595546113 | etot = -97.0651058318309 +793000 ekin = 11.9211100918306 | erot = 16.594091911106 | epot = -125.36944866716 | etot = -96.8542466642231 +794000 ekin = 11.8716704242785 | erot = 14.9353222436754 | epot = -125.573829477738 | etot = -98.7668368097843 +795000 ekin = 12.1403447469577 | erot = 16.5574574396309 | epot = -125.644718200753 | etot = -96.9469160141647 +796000 ekin = 12.0508168262995 | erot = 17.0511498916366 | epot = -125.700608016834 | etot = -96.5986412988983 +797000 ekin = 12.1520050891335 | erot = 16.128920079796 | epot = -125.674769253062 | etot = -97.3938440841321 +798000 ekin = 12.3308917777312 | erot = 15.4742322486099 | epot = -125.711203292271 | etot = -97.9060792659298 +799000 ekin = 12.5178294841378 | erot = 16.3497571956463 | epot = -125.794626964222 | etot = -96.9270402844375 +800000 ekin = 12.6713482903998 | erot = 13.202533976495 | epot = -125.904877500219 | etot = -100.030995233325 +801000 ekin = 12.6154758346025 | erot = 11.5014919425152 | epot = -126.041796456651 | etot = -101.924828679534 +802000 ekin = 12.6238778653705 | erot = 10.2109491974381 | epot = -126.141542234256 | etot = -103.306715171448 +803000 ekin = 12.3228292352108 | erot = 10.6792462756005 | epot = -126.208089431358 | etot = -103.206013920547 +804000 ekin = 12.5796728130751 | erot = 11.4079850056355 | epot = -126.326223101459 | etot = -102.338565282748 +805000 ekin = 12.8287970064896 | erot = 10.5858632741758 | epot = -126.474664523595 | etot = -103.06000424293 +806000 ekin = 13.5426071599717 | erot = 10.3031635227289 | epot = -126.568461827122 | etot = -102.722691144422 +807000 ekin = 13.6641628242498 | erot = 11.894558785332 | epot = -126.710354739398 | etot = -101.151633129816 +808000 ekin = 13.7737479148123 | erot = 12.8123896822599 | epot = -126.952137635789 | etot = -100.366000038717 +809000 ekin = 13.8236121531522 | erot = 13.940446337396 | epot = -127.144137739466 | etot = -99.3800792489183 +810000 ekin = 13.8892027423549 | erot = 13.3573940141124 | epot = -127.193427372693 | etot = -99.9468306162262 +811000 ekin = 13.9170128477122 | erot = 13.7476753490713 | epot = -127.161895550113 | etot = -99.4972073533294 +812000 ekin = 13.1409444391207 | erot = 14.0746090292756 | epot = -127.107311796194 | etot = -99.8917583277978 +813000 ekin = 12.861860574227 | erot = 15.0729933760634 | epot = -127.043075399173 | etot = -99.1082214488824 +814000 ekin = 12.6027576815133 | erot = 15.0392034414281 | epot = -126.907309882891 | etot = -99.26534875995 +815000 ekin = 11.932259654768 | erot = 14.3636897347259 | epot = -126.761432515165 | etot = -100.465483125671 +816000 ekin = 11.35075067959 | erot = 15.5560736114922 | epot = -126.427811274938 | etot = -99.5209869838557 +817000 ekin = 11.2250532397345 | erot = 16.5114599555 | epot = -125.931392843433 | etot = -98.1948796481981 +818000 ekin = 11.0166156367548 | erot = 14.9446469024182 | epot = -125.272330201453 | etot = -99.3110676622805 +819000 ekin = 10.4891738590362 | erot = 16.8855170161758 | epot = -124.371608618457 | etot = -96.9969177432447 +820000 ekin = 10.0266779480879 | erot = 15.7489287908868 | epot = -123.364387874826 | etot = -97.5887811358512 +821000 ekin = 9.90657065780812 | erot = 13.782557974274 | epot = -122.301487334186 | etot = -98.6123587021042 +822000 ekin = 9.87134803404449 | erot = 11.9174872098548 | epot = -121.320354205487 | etot = -99.5315189615877 +823000 ekin = 9.68561032590535 | erot = 9.88574499255545 | epot = -120.422926439408 | etot = -100.851571120948 +824000 ekin = 9.73229013784877 | erot = 10.4633128468899 | epot = -119.699012418505 | etot = -99.5034094337664 +825000 ekin = 9.77876624873007 | erot = 9.68820614527644 | epot = -119.182494546292 | etot = -99.7155221522856 +826000 ekin = 10.1812729286607 | erot = 10.0849550346518 | epot = -118.955325380313 | etot = -98.6890974170011 +827000 ekin = 10.3909867160541 | erot = 11.6016996678967 | epot = -118.985615028296 | etot = -96.9929286443447 +828000 ekin = 10.1585262669409 | erot = 11.3769970039739 | epot = -119.165438228199 | etot = -97.6299149572841 +829000 ekin = 10.5758781643912 | erot = 11.1331031160895 | epot = -119.552009195897 | etot = -97.8430279154163 +830000 ekin = 11.6245431427055 | erot = 11.2796233624081 | epot = -120.103068304228 | etot = -97.1989017991147 +831000 ekin = 12.1645312798119 | erot = 13.0609005527371 | epot = -120.676246029456 | etot = -95.4508141969068 +832000 ekin = 12.0364232066511 | erot = 11.8977492689015 | epot = -121.145022809283 | etot = -97.2108503337307 +833000 ekin = 12.0625993978253 | erot = 12.4878031430518 | epot = -121.624112083074 | etot = -97.0737095421967 +834000 ekin = 11.738654867677 | erot = 12.0283352663614 | epot = -122.076869833623 | etot = -98.309879699585 +835000 ekin = 12.1533002116761 | erot = 10.7471234721626 | epot = -122.470028838848 | etot = -99.5696051550088 +836000 ekin = 12.5678679536299 | erot = 12.5608164431231 | epot = -122.752318094076 | etot = -97.6236336973225 +837000 ekin = 12.677979505358 | erot = 11.9274345095503 | epot = -122.960119628142 | etot = -98.3547056132339 +838000 ekin = 12.5547346979377 | erot = 11.81726541959 | epot = -122.834139956595 | etot = -98.462139839067 +839000 ekin = 12.9964099328755 | erot = 11.5179860497468 | epot = -122.876448848946 | etot = -98.362052866324 +840000 ekin = 13.7833088925338 | erot = 12.8913873957153 | epot = -123.217054126157 | etot = -96.5423578379081 +841000 ekin = 14.4884957751375 | erot = 14.4360444698798 | epot = -123.550011332138 | etot = -94.6254710871206 +842000 ekin = 15.4273410820542 | erot = 15.6028234764419 | epot = -124.140325672202 | etot = -93.1101611137059 +843000 ekin = 15.8829421770905 | erot = 14.8221341991371 | epot = -124.697151795124 | etot = -93.9920754188959 +844000 ekin = 15.6851680737013 | erot = 14.8897161686113 | epot = -125.333544173285 | etot = -94.7586599309723 +845000 ekin = 16.2227462471367 | erot = 14.5146274475107 | epot = -126.136061332131 | etot = -95.3986876374833 +846000 ekin = 16.2721050163556 | erot = 15.9598001647269 | epot = -127.042147653036 | etot = -94.8102424719537 +847000 ekin = 16.4156424253392 | erot = 16.6073118228683 | epot = -127.9555275463 | etot = -94.9325732980929 +848000 ekin = 17.0271849056848 | erot = 16.3052790687785 | epot = -128.925218355557 | etot = -95.5927543810935 +849000 ekin = 17.3479512231277 | erot = 17.7687067215052 | epot = -129.684137598081 | etot = -94.5674796534479 +850000 ekin = 17.0482888853807 | erot = 17.8155859438296 | epot = -130.224252247721 | etot = -95.3603774185109 +851000 ekin = 16.3414840194608 | erot = 18.368119909927 | epot = -130.448061327052 | etot = -95.7384573976638 +852000 ekin = 16.5087616209338 | erot = 17.8733626297512 | epot = -130.233002313213 | etot = -95.8508780625277 +853000 ekin = 16.0022675586976 | erot = 17.3313707856007 | epot = -129.605040671187 | etot = -96.2714023268884 +854000 ekin = 15.8481523640709 | erot = 17.3731469998314 | epot = -128.600740012967 | etot = -95.3794406490646 +855000 ekin = 15.387436296962 | erot = 15.9466424529339 | epot = -127.551417944733 | etot = -96.2173391948372 +856000 ekin = 15.3216011830485 | erot = 14.8576497992235 | epot = -126.542970444436 | etot = -96.3637194621644 +857000 ekin = 15.6611430156851 | erot = 14.2086867473805 | epot = -125.725807505588 | etot = -95.8559777425227 +858000 ekin = 16.3932774116906 | erot = 11.4783454458777 | epot = -125.124867641716 | etot = -97.2532447841477 +859000 ekin = 17.0067307957749 | erot = 9.41761591928337 | epot = -124.765767596223 | etot = -98.3414208811647 +860000 ekin = 17.6921921365598 | erot = 9.88679833635887 | epot = -124.629136018772 | etot = -97.050145545853 +861000 ekin = 18.1187426592769 | erot = 8.73673205883354 | epot = -124.79647020726 | etot = -97.9409954891494 +862000 ekin = 18.8404901657434 | erot = 8.93480913907133 | epot = -125.176719114941 | etot = -97.4014198101266 +863000 ekin = 19.3084808486405 | erot = 8.23780529858733 | epot = -125.665135114142 | etot = -98.1188489669144 +864000 ekin = 20.2764093504144 | erot = 7.93678261423435 | epot = -126.215520017963 | etot = -98.0023280533142 +865000 ekin = 20.4196574350482 | erot = 8.09429532393971 | epot = -126.83410889964 | etot = -98.3201561406524 +866000 ekin = 21.4829378213328 | erot = 7.80836492430302 | epot = -127.512429536164 | etot = -98.2211267905285 +867000 ekin = 21.4887610044054 | erot = 8.80868260679231 | epot = -128.170234943922 | etot = -97.8727913327241 +868000 ekin = 21.7142871399884 | erot = 9.47461659896558 | epot = -128.801589043361 | etot = -97.6126853044068 +869000 ekin = 22.1133192463801 | erot = 10.4861647920119 | epot = -129.339773073194 | etot = -96.7402890348025 +870000 ekin = 21.3481380448441 | erot = 10.9849989949219 | epot = -129.621309896878 | etot = -97.2881728571119 +871000 ekin = 21.9561325516446 | erot = 11.9062217793487 | epot = -129.651390924563 | etot = -95.7890365935695 +872000 ekin = 21.3076494139952 | erot = 13.2463283410523 | epot = -129.542988798125 | etot = -94.9890110430773 +873000 ekin = 21.4299739935353 | erot = 13.6544223896015 | epot = -129.320239107091 | etot = -94.2358427239545 +874000 ekin = 21.0794413188304 | erot = 14.573887219774 | epot = -128.942695133615 | etot = -93.2893665950108 +875000 ekin = 21.0103891922048 | erot = 12.0404980528645 | epot = -128.579828525644 | etot = -95.5289412805743 +876000 ekin = 21.7076508313671 | erot = 11.3031178905217 | epot = -128.188785450586 | etot = -95.178016728697 +877000 ekin = 22.2505358324156 | erot = 10.8996344937665 | epot = -127.77554615513 | etot = -94.6253758289478 +878000 ekin = 22.572764818179 | erot = 11.6318058014138 | epot = -127.562038418745 | etot = -93.3574677991519 +879000 ekin = 22.1079311271033 | erot = 10.4864160952736 | epot = -127.460772833857 | etot = -94.86642561148 +880000 ekin = 21.2718493500246 | erot = 9.70252202565287 | epot = -127.364823607957 | etot = -96.3904522322797 +881000 ekin = 21.0257078575782 | erot = 10.5239361374153 | epot = -127.318073987713 | etot = -95.7684299927199 +882000 ekin = 20.2392286223341 | erot = 10.2655585469409 | epot = -127.115951248162 | etot = -96.6111640788866 +883000 ekin = 19.5926634763368 | erot = 11.4253835216275 | epot = -126.759123154987 | etot = -95.7410761570228 +884000 ekin = 18.6625603965092 | erot = 13.4817805374235 | epot = -126.32853647352 | etot = -94.1841955395878 +885000 ekin = 18.3180772659693 | erot = 12.8339022236605 | epot = -125.76497943843 | etot = -94.6129999488002 +886000 ekin = 18.0055736451768 | erot = 12.7961277363815 | epot = -124.967201184612 | etot = -94.1654998030538 +887000 ekin = 17.2515521488208 | erot = 11.921264571434 | epot = -124.125696183328 | etot = -94.9528794630729 +888000 ekin = 16.669360516195 | erot = 10.2996806839265 | epot = -123.53691035064 | etot = -96.567869150518 +889000 ekin = 15.4931021055659 | erot = 9.82818731105444 | epot = -123.080632734892 | etot = -97.7593433182714 +890000 ekin = 14.9536491761315 | erot = 9.74388242695765 | epot = -122.961194614762 | etot = -98.2636630116728 +891000 ekin = 14.5563310250354 | erot = 9.84917133588156 | epot = -123.201631837732 | etot = -98.7961294768147 +892000 ekin = 13.9709003525822 | erot = 12.5475105338346 | epot = -123.552779811404 | etot = -97.0343689249869 +893000 ekin = 14.1046207703492 | erot = 12.373439335803 | epot = -124.022071734763 | etot = -97.5440116286107 +894000 ekin = 13.981746696699 | erot = 15.8133541008515 | epot = -124.398343032409 | etot = -94.603242234858 +895000 ekin = 14.1143634852376 | erot = 15.1396548037889 | epot = -124.822802398661 | etot = -95.5687841096345 +896000 ekin = 14.0610738017734 | erot = 17.0439053339517 | epot = -125.282135957 | etot = -94.1771568212749 +897000 ekin = 14.554483196482 | erot = 17.6238194381056 | epot = -125.827981585264 | etot = -93.6496789506765 +898000 ekin = 13.8598489512228 | erot = 18.4610583729181 | epot = -126.168315488213 | etot = -93.8474081640722 +899000 ekin = 14.3611073493965 | erot = 19.1793416697318 | epot = -126.303608654933 | etot = -92.7631596358049 +900000 ekin = 14.3464542297122 | erot = 16.2685406955579 | epot = -126.225999898658 | etot = -95.6110049733875 +901000 ekin = 13.7776566976285 | erot = 16.5370114462425 | epot = -125.99255384699 | etot = -95.6778857031195 +902000 ekin = 13.5149469908651 | erot = 15.4305114008538 | epot = -125.750366521606 | etot = -96.8049081298871 +903000 ekin = 13.5498164824643 | erot = 17.5583700285456 | epot = -125.602965520456 | etot = -94.4947790094465 +904000 ekin = 14.1246403611212 | erot = 16.0173961512998 | epot = -125.453101757115 | etot = -95.3110652446938 +905000 ekin = 14.7155252784859 | erot = 17.1334668002383 | epot = -125.318768904924 | etot = -93.4697768261996 +906000 ekin = 13.6449023583548 | erot = 17.2893304116319 | epot = -125.134598551714 | etot = -94.2003657817277 +907000 ekin = 13.258248010078 | erot = 16.5831560416574 | epot = -124.910757681878 | etot = -95.0693536301426 +908000 ekin = 13.0302975650094 | erot = 18.748025713544 | epot = -124.697496883562 | etot = -92.9191736050091 +909000 ekin = 13.1334637854215 | erot = 19.844384931098 | epot = -124.348428326159 | etot = -91.3705796096396 +910000 ekin = 13.5289931510912 | erot = 18.5450660023685 | epot = -123.892710718617 | etot = -91.8186515651572 +911000 ekin = 14.2919545718934 | erot = 17.1538732996284 | epot = -123.389698231818 | etot = -91.9438703602961 +912000 ekin = 13.7316439249099 | erot = 16.1052160616744 | epot = -122.918030498883 | etot = -93.0811705122983 +913000 ekin = 13.9397771675513 | erot = 16.2424107966852 | epot = -122.557278020844 | etot = -92.3750900566078 +914000 ekin = 13.7487442078575 | erot = 13.1532318785282 | epot = -122.329080940675 | etot = -95.4271048542896 +915000 ekin = 13.7308329605517 | erot = 13.5814252587633 | epot = -122.054538980737 | etot = -94.7422807614216 +916000 ekin = 14.5378379517964 | erot = 13.8074853537405 | epot = -121.874760027857 | etot = -93.5294367223197 +917000 ekin = 13.8431749616253 | erot = 13.2096929957287 | epot = -121.812134503636 | etot = -94.7592665462817 +918000 ekin = 13.7991607789687 | erot = 13.9584156708955 | epot = -121.777032791736 | etot = -94.019456341872 +919000 ekin = 13.9743107003906 | erot = 11.376480734218 | epot = -121.787941690802 | etot = -96.4371502561935 +920000 ekin = 14.1537578645617 | erot = 11.8912414462999 | epot = -121.736720902431 | etot = -95.6917215915691 +921000 ekin = 14.5103068743731 | erot = 11.7030743823452 | epot = -121.859562953019 | etot = -95.6461816963007 +922000 ekin = 15.5087906706467 | erot = 11.7650182755899 | epot = -122.052783976836 | etot = -94.7789750305991 +923000 ekin = 15.824540725833 | erot = 11.7429828112815 | epot = -122.321689800206 | etot = -94.7541662630917 +924000 ekin = 16.2118457578851 | erot = 11.4735610997044 | epot = -122.573723642788 | etot = -94.8883167851983 +925000 ekin = 15.7157898733479 | erot = 13.0287931438615 | epot = -122.870813777107 | etot = -94.1262307598975 +926000 ekin = 15.8232662824047 | erot = 12.4206741941128 | epot = -123.323478856275 | etot = -95.0795383797571 +927000 ekin = 16.0403094126387 | erot = 12.0428568481805 | epot = -123.785857340744 | etot = -95.7026910799247 +928000 ekin = 16.7772842109268 | erot = 12.7546635307638 | epot = -124.204094957598 | etot = -94.6721472159076 +929000 ekin = 17.5790100261127 | erot = 16.160558685576 | epot = -124.581498626405 | etot = -90.841929914716 +930000 ekin = 17.5365546397933 | erot = 17.0813652056986 | epot = -124.910877261319 | etot = -90.2929574158269 +931000 ekin = 17.7834886521176 | erot = 17.9815360577043 | epot = -125.205802574187 | etot = -89.440777864365 +932000 ekin = 18.2619260856899 | erot = 16.5368653969913 | epot = -125.376038848337 | etot = -90.5772473656554 +933000 ekin = 18.3152840467822 | erot = 18.5416609167158 | epot = -125.463928469439 | etot = -88.6069835059413 +934000 ekin = 19.2078803403977 | erot = 18.5161844650513 | epot = -125.375129068137 | etot = -87.6510642626877 +935000 ekin = 19.7485108682908 | erot = 19.6156730686703 | epot = -125.07023795911 | etot = -85.7060540221492 +936000 ekin = 20.2957967539069 | erot = 18.9931658332333 | epot = -124.798109430752 | etot = -85.5091468436115 +937000 ekin = 20.7700066695891 | erot = 18.0459227699491 | epot = -124.634102785077 | etot = -85.818173345539 +938000 ekin = 21.2166591879643 | erot = 17.7286136027558 | epot = -124.572231718776 | etot = -85.6269589280562 +939000 ekin = 21.7577967376043 | erot = 18.1536110439922 | epot = -124.632022917129 | etot = -84.7206151355328 +940000 ekin = 21.7563993533876 | erot = 19.1622147401127 | epot = -124.621188398547 | etot = -83.7025743050472 +941000 ekin = 21.6708288051912 | erot = 18.2286801716876 | epot = -124.515208751161 | etot = -84.6156997742824 +942000 ekin = 21.1815139820123 | erot = 16.1097626291255 | epot = -124.287348781255 | etot = -86.9960721701172 +943000 ekin = 20.9151315922865 | erot = 18.7083258209792 | epot = -123.78364783818 | etot = -84.1601904249144 +944000 ekin = 20.6364407090718 | erot = 17.7607975845773 | epot = -122.956797838135 | etot = -84.5595595444854 +945000 ekin = 19.8394382021514 | erot = 15.0995691431346 | epot = -121.94391695222 | etot = -87.0049096069344 +946000 ekin = 18.9174495656799 | erot = 15.948991403541 | epot = -120.81797770207 | etot = -85.9515367328493 +947000 ekin = 17.6519722549426 | erot = 14.4049592033415 | epot = -119.602144541684 | etot = -87.5452130833999 +948000 ekin = 17.150326150994 | erot = 16.4018416217422 | epot = -118.261354993643 | etot = -84.7091872209069 +949000 ekin = 16.4090819032454 | erot = 17.1968654437185 | epot = -116.861399674524 | etot = -83.2554523275598 +950000 ekin = 14.742587969487 | erot = 15.9352061528884 | epot = -115.448063912315 | etot = -84.7702697899391 +951000 ekin = 14.1970965023353 | erot = 12.2798421644794 | epot = -114.107086041751 | etot = -87.6301473749363 +952000 ekin = 14.0927060198374 | erot = 10.3216694625251 | epot = -113.119450769367 | etot = -88.7050752870047 +953000 ekin = 13.5046310501095 | erot = 12.450157023742 | epot = -112.425552892524 | etot = -86.4707648186723 +954000 ekin = 13.468948560794 | erot = 12.6343432244467 | epot = -111.837509178703 | etot = -85.7342173934626 +955000 ekin = 13.6777733496109 | erot = 11.8417648028018 | epot = -111.558902764832 | etot = -86.039364612419 +956000 ekin = 13.574711867833 | erot = 12.6049973337106 | epot = -111.545211737773 | etot = -85.3655025362291 +957000 ekin = 13.6330464633142 | erot = 14.3761738336318 | epot = -112.128030169176 | etot = -84.11880987223 +958000 ekin = 14.0084363389877 | erot = 16.5447727486963 | epot = -113.007910033041 | etot = -82.454700945357 +959000 ekin = 14.2087351825818 | erot = 15.7773301271983 | epot = -114.064087160015 | etot = -84.0780218502353 +960000 ekin = 13.9105457429093 | erot = 17.3230189425809 | epot = -115.173509709766 | etot = -83.9399450242753 +961000 ekin = 13.7232782313952 | erot = 17.1366163828836 | epot = -116.301874390945 | etot = -85.4419797766661 +962000 ekin = 14.1300908335642 | erot = 19.1834424878264 | epot = -117.354152528141 | etot = -84.0406192067499 +963000 ekin = 13.9798760128625 | erot = 18.4550075209063 | epot = -118.206972151129 | etot = -85.7720886173601 +964000 ekin = 13.9181246391495 | erot = 17.8334045791798 | epot = -118.760687299267 | etot = -87.0091580809377 +965000 ekin = 14.4725466154951 | erot = 15.9348125576432 | epot = -119.115139083965 | etot = -88.7077799108268 +966000 ekin = 13.7793869014681 | erot = 16.1858043661218 | epot = -119.263924963707 | etot = -89.2987336961167 +967000 ekin = 13.924823594908 | erot = 15.9375000198072 | epot = -119.240534699135 | etot = -89.3782110844195 +968000 ekin = 13.9419705201903 | erot = 16.1454454067516 | epot = -119.083807794167 | etot = -88.9963918672251 +969000 ekin = 14.3690849278853 | erot = 13.205655023488 | epot = -118.930833582305 | etot = -91.356093630932 +970000 ekin = 14.9185995812819 | erot = 13.2062810807965 | epot = -118.928888853978 | etot = -90.8040081918998 +971000 ekin = 14.184367299462 | erot = 12.0305076598074 | epot = -118.991474962564 | etot = -92.7766000032944 +972000 ekin = 14.188208017276 | erot = 12.0476238940137 | epot = -119.23878461909 | etot = -93.0029527078003 +973000 ekin = 14.5141228505811 | erot = 11.1791903215728 | epot = -119.482959937313 | etot = -93.7896467651595 +974000 ekin = 14.6227825752321 | erot = 10.5615370552088 | epot = -119.797738977139 | etot = -94.6134193466976 +975000 ekin = 14.1818069716479 | erot = 10.6157258452495 | epot = -120.137564506978 | etot = -95.3400316900808 +976000 ekin = 14.266272919117 | erot = 12.5445761157866 | epot = -120.532894837912 | etot = -93.7220458030081 +977000 ekin = 14.1873145651582 | erot = 12.1072472960052 | epot = -120.990453356646 | etot = -94.6958914954822 +978000 ekin = 14.0872157230769 | erot = 13.3166550454898 | epot = -121.488261215249 | etot = -94.0843904466821 +979000 ekin = 14.8429992045431 | erot = 13.7865336818933 | epot = -122.339012921602 | etot = -93.7094800351656 +980000 ekin = 15.2825257184271 | erot = 16.9450933327408 | epot = -123.110230269883 | etot = -90.8826112187148 +981000 ekin = 15.6734301840752 | erot = 16.4399015675571 | epot = -123.956056131479 | etot = -91.8427243798469 +982000 ekin = 15.5561774848902 | erot = 16.6936322487795 | epot = -124.765342820977 | etot = -92.5155330873075 +983000 ekin = 15.5987477396929 | erot = 17.1400159359463 | epot = -125.427460387889 | etot = -92.6886967122494 +984000 ekin = 15.8487635761921 | erot = 17.664888995833 | epot = -125.938030694567 | etot = -92.4243781225422 +985000 ekin = 15.4193899857815 | erot = 19.1714631850008 | epot = -126.275311226509 | etot = -91.6844580557266 +986000 ekin = 15.2507329969684 | erot = 19.661925701056 | epot = -126.459631597701 | etot = -91.5469728996769 +987000 ekin = 15.5016876432465 | erot = 17.6752121438465 | epot = -126.592354148809 | etot = -93.4154543617161 +988000 ekin = 15.1098611004096 | erot = 20.9945187038817 | epot = -126.845591893857 | etot = -90.7412120895656 +989000 ekin = 14.8059038805742 | erot = 24.7484294327106 | epot = -127.090979520225 | etot = -87.5366462069407 +990000 ekin = 15.0487910362319 | erot = 23.0457590429322 | epot = -127.311632746623 | etot = -89.2170826674585 +991000 ekin = 15.3736252894067 | erot = 20.8199208091616 | epot = -127.515655978073 | etot = -91.3221098795049 +992000 ekin = 15.5207083652132 | erot = 19.0611376445553 | epot = -127.784686918491 | etot = -93.2028409087226 +993000 ekin = 15.6031034657673 | erot = 17.8662930030541 | epot = -128.200332799037 | etot = -94.7309363302157 +994000 ekin = 15.6498253251245 | erot = 17.1558885499971 | epot = -128.560961013637 | etot = -95.7552471385152 +995000 ekin = 16.3849621321118 | erot = 16.7571566439574 | epot = -128.927696519966 | etot = -95.7855777438969 +996000 ekin = 15.8638702907294 | erot = 17.4129512678654 | epot = -129.370199240218 | etot = -96.0933776816235 +997000 ekin = 16.7002057380581 | erot = 15.6537424037949 | epot = -129.686247689077 | etot = -97.332299547224 +998000 ekin = 16.6111423570136 | erot = 13.0091456196802 | epot = -129.752845827544 | etot = -100.13255785085 +999000 ekin = 16.492584210326 | erot = 13.0108008173606 | epot = -129.709400513234 | etot = -100.206015485547 +1000000 ekin = 17.097105825142 | erot = 12.6179942372262 | epot = -129.692482442335 | etot = -99.977382379967 + 1000000 382.38165 -132.06191 2.3694293 -112.59538 0.043662828 39304000 +Loop time of 27.2476 on 4 procs for 1000000 steps with 16 atoms + +Performance: 54.096 ns/day, 0.444 hours/ns, 36700.437 timesteps/s, 587.207 katom-step/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.5219 | 13.077 | 17.034 | 78.2 | 47.99 +Bond | 0.38282 | 0.43293 | 0.48144 | 5.8 | 1.59 +Neigh | 0.00956 | 0.0096418 | 0.009729 | 0.1 | 0.04 +Comm | 5.6548 | 9.754 | 12.913 | 88.2 | 35.80 +Output | 0.086221 | 0.091692 | 0.10328 | 2.2 | 0.34 +Modify | 1.4663 | 1.6512 | 1.8474 | 13.1 | 6.06 +Other | | 2.231 | | | 8.19 + +Nlocal: 4 ave 5 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 12 ave 13 max 11 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 26.75 ave 48 max 13 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:27 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/data.duplex3 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/data.duplex3 new file mode 100644 index 0000000000..a5ade0d892 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/data.duplex3 @@ -0,0 +1,68 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 100.0278 +2 100.0278 +3 100.0278 +4 100.0278 + +Atoms # hybrid + +1 1 -0.9600635673395586 -6.697372578532395 11.214288461530149 1 1 0.016231479325760585 0 0 0 +2 2 -1.371418484333729 -8.644426415489871 15.09830243650489 1 1 0.016231479325760585 0 0 0 +3 3 -0.6216529396853785 -10.27130427566052 18.871948109873205 1 1 0.016231479325760585 0 0 0 +4 4 1.779062937600471 -10.807909849707325 23.24831121047697 1 1 0.016231479325760585 0 0 0 +5 1 4.239477379859167 -10.116984578731293 26.59145222824391 1 1 0.016231479325760585 0 0 0 +6 4 -1.9327071764636017 -1.6150385295751968 26.477847842079502 2 1 0.016231479325760585 0 0 0 +7 1 -0.2983880618807194 -0.9579116659377174 23.010952595199885 2 1 0.016231479325760585 0 0 0 +8 2 2.1503419307040095 -0.31467499729662424 19.779605638337472 2 1 0.016231479325760585 0 0 0 +9 3 5.687077844288683 -1.6585607691903788 17.32600745817322 2 1 0.016231479325760585 0 0 0 +10 4 7.960942109870774 -4.424349635235229 15.853866095654556 2 1 0.016231479325760585 0 0 0 + +Velocities + +1 0.003670260004547261 -0.001065537256202598 0.00019820771627082902 2.190783710921869 -2.4582417153465035 1.7715963770507672 +2 0.002291113608335764 0.0007728773438117204 0.002296672286413572 -0.40551125639613556 -0.12256940476096484 0.7114827747471555 +3 -0.0004997750377219465 -0.0006770677373491773 -0.0006775964298166731 2.179995735254803 3.7414175740175044 -1.7280709663891953 +4 -0.00015182185791796758 -4.553427726427798e-05 0.001445301171404135 -0.9443175316300753 1.9770932892489974 -0.3048781148297085 +5 0.00010888231798112065 -0.0017696699496284707 0.002217080679988605 -0.08456353584305179 0.035965271955914695 -0.7051030632137099 +6 0.0002936592731756661 -0.0011965505946877099 0.0004708407813130548 -0.7164699339101465 -1.1698888787077064 2.094408810880699 +7 -2.1364103955982793e-05 5.577692626680783e-05 -0.0005335687118188998 1.5034116933686936 -2.4596844236201743 0.7286296966602159 +8 -0.002835367576168593 -0.00028136761767332186 -0.0006160127733736687 -0.26771671594599533 -2.360332797207871 -1.6798429613010255 +9 0.00037413027551487407 0.001890740851504142 0.0005563994572100851 -1.512871512517161 -1.4691678195901636 -2.245351079807635 +10 -0.0024375187569690418 -0.000550577454043892 0.000971907386756427 0.4399243786321997 1.6207637079017971 1.0900899238856114 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 26.93628110931426 26.93628110931426 26.93628110931426 0.9824438652148015 -0.023183015026523597 -0.18238525095550406 0.031657854475291056 +2 26.93628110931426 26.93628110931426 26.93628110931426 0.9303156820429525 0.02962373336578937 -0.07607439157272995 0.3575581814380256 +3 26.93628110931426 26.93628110931426 26.93628110931426 0.7912072782182723 -0.043679545103099016 -0.05996218100443608 0.6070318583758278 +4 26.93628110931426 26.93628110931426 26.93628110931426 0.6531869542452552 -0.03659000162837596 0.004181596561545229 0.7563005281201641 +5 26.93628110931426 26.93628110931426 26.93628110931426 0.3249781771672557 0.06207197535108856 0.03689277251937633 0.9429608568635791 +6 26.93628110931426 26.93628110931426 26.93628110931426 0.08029535222204207 0.8726095530830543 -0.46831094470633033 -0.11309325067392484 +7 26.93628110931426 26.93628110931426 26.93628110931426 -0.1303991484205687 0.7764383491760718 -0.6081660772848121 0.10135864274905797 +8 26.93628110931426 26.93628110931426 26.93628110931426 -0.14971034142173664 0.5769499085020084 -0.7973230447846137 0.09482393688465168 +9 26.93628110931426 26.93628110931426 26.93628110931426 0.21130729744233523 -0.37917864508185584 0.8946270178621702 -0.10590221939385809 +10 26.93628110931426 26.93628110931426 26.93628110931426 0.34278400171414436 0.15185237372800306 0.9252984668160771 0.05712032974191834 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/in.duplex3 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/in.duplex3 new file mode 100644 index 0000000000..d60a76e9d9 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/in.duplex3 @@ -0,0 +1,73 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 3 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 + +set atom * mass 100.0278 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.1 new file mode 100644 index 0000000000..9db73c4b2d --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.1 @@ -0,0 +1,1186 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 3 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +set atom * mass 100.0278 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.3.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 7.03429942525144 | erot = 12.9873344362494 | epot = -68.5183064451292 | etot = -48.4966725836283 +Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 262.20685 -73.084271 4.565965 -61.484007 -0.0051810598 39304000 +1000 ekin = 6.47818551117441 | erot = 13.3026700489858 | epot = -68.2775281400722 | etot = -48.496672579912 +2000 ekin = 6.03525112997236 | erot = 13.6564943363021 | epot = -68.1884180433538 | etot = -48.4966725770794 +3000 ekin = 5.75105017872919 | erot = 14.0429985067123 | epot = -68.2907212623787 | etot = -48.4966725769372 +4000 ekin = 5.63745048823595 | erot = 14.4525304497378 | epot = -68.5866535170602 | etot = -48.4966725790865 +5000 ekin = 5.67539108471591 | erot = 14.8714892268938 | epot = -69.0435528945028 | etot = -48.4966725828931 +6000 ekin = 5.82255924081694 | erot = 15.2845343223522 | epot = -69.6037661502115 | etot = -48.4966725870424 +7000 ekin = 6.0294913144517 | erot = 15.6780321266846 | epot = -70.2041960313097 | etot = -48.4966725901734 +8000 ekin = 6.25690013504882 | erot = 16.0432406183866 | epot = -70.7968133448984 | etot = -48.496672591463 +9000 ekin = 6.48760823849338 | erot = 16.3777166841148 | epot = -71.3619975139183 | etot = -48.4966725913101 +10000 ekin = 6.722546110018 | erot = 16.6826306715322 | epot = -71.9018493718517 | etot = -48.4966725903016 +11000 ekin = 6.97475226170428 | erot = 16.9603738277431 | epot = -72.431798678795 | etot = -48.4966725893476 +12000 ekin = 7.2596071399058 | erot = 17.2117069445191 | epot = -72.9679866735642 | etot = -48.4966725891392 +13000 ekin = 7.58616001551487 | erot = 17.4338437184062 | epot = -73.5166763239129 | etot = -48.4966725899918 +14000 ekin = 7.95221337497285 | erot = 17.6199690400549 | epot = -74.0688550069353 | etot = -48.4966725919075 +15000 ekin = 8.34290179280008 | erot = 17.7599308757288 | epot = -74.5995052633033 | etot = -48.4966725947744 +16000 ekin = 8.73088347798008 | erot = 17.8412839163863 | epot = -75.0688399931314 | etot = -48.496672598765 +17000 ekin = 9.06872001929353 | erot = 17.8482053032194 | epot = -75.4135979249308 | etot = -48.4966726024179 +18000 ekin = 9.30863890671763 | erot = 17.7686584779302 | epot = -75.5739699900197 | etot = -48.4966726053719 +19000 ekin = 9.41124785647434 | erot = 17.5960512017221 | epot = -75.5039716652992 | etot = -48.4966726071028 +20000 ekin = 9.34910582886757 | erot = 17.3292516593873 | epot = -75.1750300954672 | etot = -48.4966726072124 +21000 ekin = 9.1126689689092 | erot = 16.9731252869532 | epot = -74.5824668613651 | etot = -48.4966726055027 +22000 ekin = 8.71397032422754 | erot = 16.5385032889634 | epot = -73.7491462151204 | etot = -48.4966726019295 +23000 ekin = 8.18690962778233 | erot = 16.0421750929966 | epot = -72.7257573178974 | etot = -48.4966725971185 +24000 ekin = 7.58361736117495 | erot = 15.5032978232031 | epot = -71.5835877759397 | etot = -48.4966725915617 +25000 ekin = 6.96740991674868 | erot = 14.9419969554433 | epot = -70.4060794581741 | etot = -48.4966725859822 +26000 ekin = 6.40397973480484 | erot = 14.3775943404745 | epot = -69.2782466563097 | etot = -48.4966725810304 +27000 ekin = 5.95300264518411 | erot = 13.826953398888 | epot = -68.2766286212089 | etot = -48.4966725771368 +28000 ekin = 5.66210674319994 | erot = 13.3035488276538 | epot = -67.4623281453084 | etot = -48.4966725744547 +29000 ekin = 5.56416292853208 | erot = 12.8173046943285 | epot = -66.8781401957627 | etot = -48.4966725729021 +30000 ekin = 5.67757091398612 | erot = 12.375025427117 | epot = -66.5492689133843 | etot = -48.4966725722812 +31000 ekin = 6.00823180422793 | erot = 11.98136344288 | epot = -66.4862678195145 | etot = -48.4966725724066 +32000 ekin = 6.551664689978 | erot = 11.6395080908376 | epot = -66.6878453540144 | etot = -48.4966725731988 +33000 ekin = 7.29417473532408 | erot = 11.3509752571399 | epot = -67.1418225671842 | etot = -48.4966725747202 +34000 ekin = 8.21244588218592 | erot = 11.116114313427 | epot = -67.8252327728428 | etot = -48.4966725772299 +35000 ekin = 9.27066798181924 | erot = 10.9338272642602 | epot = -68.7011678273399 | etot = -48.4966725812605 +36000 ekin = 10.4137127998433 | erot = 10.8011032352063 | epot = -69.711488622778 | etot = -48.4966725877284 +37000 ekin = 11.5574113355608 | erot = 10.711877433406 | epot = -70.7659613658541 | etot = -48.4966725968872 +38000 ekin = 12.5862131120548 | erot = 10.6570487006396 | epot = -71.7399344196431 | etot = -48.4966726069487 +39000 ekin = 13.3756277697444 | erot = 10.6266661696597 | epot = -72.4989665531961 | etot = -48.496672613792 +40000 ekin = 13.8400144974722 | erot = 10.6149441040862 | epot = -72.9516312154842 | etot = -48.4966726139258 +41000 ekin = 13.9716515751521 | erot = 10.625130322802 | epot = -73.0934545058132 | etot = -48.4966726078591 +42000 ekin = 13.8349966624037 | erot = 10.6693591526026 | epot = -73.0010284144752 | etot = -48.4966725994689 +43000 ekin = 13.486317974579 | erot = 10.7627501491634 | epot = -72.745740917227 | etot = -48.4966727934846 +44000 ekin = 12.8657064139243 | erot = 11.0065042177551 | epot = -72.368883325112 | etot = -48.4966726934325 +45000 ekin = 12.451348070837 | erot = 11.2623687140011 | epot = -72.2103894466182 | etot = -48.4966726617801 +46000 ekin = 11.8973058918006 | erot = 11.5369637549568 | epot = -71.9309423094146 | etot = -48.4966726626572 +47000 ekin = 11.3048691716601 | erot = 11.853410520277 | epot = -71.6549523562342 | etot = -48.4966726642971 +48000 ekin = 10.6681247163118 | erot = 12.1927455857899 | epot = -71.3575429678098 | etot = -48.4966726657081 +49000 ekin = 9.98781452095524 | erot = 12.5337626830794 | epot = -71.0182498702023 | etot = -48.4966726661677 +50000 ekin = 9.27805060546793 | erot = 12.8568502175187 | epot = -70.6315734882952 | etot = -48.4966726653086 +51000 ekin = 8.56816305051923 | erot = 13.1473275670362 | epot = -70.2121632807453 | etot = -48.4966726631899 +52000 ekin = 7.89968625326358 | erot = 13.3972664509232 | epot = -69.7936253644654 | etot = -48.4966726602786 +53000 ekin = 7.31936805861643 | erot = 13.605288301124 | epot = -69.4213290170353 | etot = -48.4966726572949 +54000 ekin = 6.8702643504343 | erot = 13.7746656104191 | epot = -69.1416026158059 | etot = -48.4966726549525 +55000 ekin = 6.58358833130182 | erot = 13.9106626376477 | epot = -68.990923622707 | etot = -48.4966726537575 +56000 ekin = 6.47340776924329 | erot = 14.0180895137411 | epot = -68.9881699369073 | etot = -48.4966726539229 +57000 ekin = 6.5349018939818 | erot = 14.0996443244833 | epot = -69.131218873869 | etot = -48.4966726554039 +58000 ekin = 6.74582948881764 | erot = 14.1551416501596 | epot = -69.397643796883 | etot = -48.4966726579057 +59000 ekin = 7.07026744299398 | erot = 14.1814435236753 | epot = -69.7483836278281 | etot = -48.4966726611589 +60000 ekin = 7.46321119956018 | erot = 14.1729605115927 | epot = -70.1328443758887 | etot = -48.4966726647358 +61000 ekin = 7.8761562094755 | erot = 14.1225980724394 | epot = -70.4954269501747 | etot = -48.4966726682598 +62000 ekin = 8.26246819545866 | erot = 14.0231891838097 | epot = -70.7823300503885 | etot = -48.4966726711202 +63000 ekin = 8.58419585421847 | erot = 13.8690469944667 | epot = -70.9499155215194 | etot = -48.4966726728343 +64000 ekin = 8.81822702695853 | erot = 13.6575496044134 | epot = -70.972449304494 | etot = -48.4966726731221 +65000 ekin = 8.95905321199945 | erot = 13.3902699399848 | epot = -70.8459958240493 | etot = -48.496672672065 +66000 ekin = 9.01708021240078 | erot = 13.0731504494322 | epot = -70.5869033319396 | etot = -48.4966726701066 +67000 ekin = 9.01264024181375 | erot = 12.7157756705984 | epot = -70.2250885803053 | etot = -48.4966726678931 +68000 ekin = 8.96786592552511 | erot = 12.3300108275766 | epot = -69.7945494191634 | etot = -48.4966726660616 +69000 ekin = 8.89809230228762 | erot = 11.9282539830629 | epot = -69.3230189502566 | etot = -48.4966726649061 +70000 ekin = 8.80855518919698 | erot = 11.5224663142642 | epot = -68.8276941678877 | etot = -48.4966726644265 +71000 ekin = 8.69498380037367 | erot = 11.1237231983038 | epot = -68.3153796630099 | etot = -48.4966726643324 +72000 ekin = 8.54784464636703 | erot = 10.7423794346698 | epot = -67.7868967452232 | etot = -48.4966726641863 +73000 ekin = 8.35855300081051 | erot = 10.388582011598 | epot = -67.2438076759785 | etot = -48.4966726635701 +74000 ekin = 8.12576446604041 | erot = 10.0727225309051 | epot = -66.6951596591063 | etot = -48.4966726621608 +75000 ekin = 7.85890437579233 | erot = 9.80548509842777 | epot = -66.1610621343402 | etot = -48.4966726601201 +76000 ekin = 7.57852165402683 | erot = 9.5972708153679 | epot = -65.6724651268119 | etot = -48.4966726574171 +77000 ekin = 7.31582042129772 | erot = 9.45739858079197 | epot = -65.2698916571118 | etot = -48.4966726550221 +78000 ekin = 7.10323229834043 | erot = 9.39173074336844 | epot = -64.9916356947882 | etot = -48.4966726530793 +79000 ekin = 6.96937218054504 | erot = 9.40218099613596 | epot = -64.8682258285428 | etot = -48.4966726518618 +80000 ekin = 6.93674566763505 | erot = 9.48623430706704 | epot = -64.9196526261995 | etot = -48.4966726514974 +81000 ekin = 7.01925680666815 | erot = 9.63726327568291 | epot = -65.1531927343358 | etot = -48.4966726519847 +82000 ekin = 7.22081712459834 | erot = 9.84564997752222 | epot = -65.5631397554121 | etot = -48.4966726532915 +83000 ekin = 7.5341776538645 | erot = 10.1003599019659 | epot = -66.1312102111975 | etot = -48.496672655367 +84000 ekin = 7.94029058934595 | erot = 10.3905229584642 | epot = -66.8274862058439 | etot = -48.4966726580337 +85000 ekin = 8.4098850752269 | erot = 10.7066512628595 | epot = -67.6132089989669 | etot = -48.4966726608805 +86000 ekin = 8.90877838665036 | erot = 11.0413122902596 | epot = -68.4467633402411 | etot = -48.4966726633312 +87000 ekin = 9.40446727185101 | erot = 11.3892123423167 | epot = -69.2903522795809 | etot = -48.4966726654132 +88000 ekin = 9.86641386533863 | erot = 11.7464698262623 | epot = -70.1095563579289 | etot = -48.4966726663279 +89000 ekin = 10.2794449749748 | erot = 12.1093351833934 | epot = -70.8854528250669 | etot = -48.4966726666988 +90000 ekin = 10.6448818632992 | erot = 12.4712192860779 | epot = -71.6127738155188 | etot = -48.4966726661417 +91000 ekin = 10.9592378236983 | erot = 12.8213713070342 | epot = -72.2772817984388 | etot = -48.4966726677064 +92000 ekin = 11.1805024607915 | erot = 13.1782323505896 | epot = -72.8554074847656 | etot = -48.4966726733845 +93000 ekin = 11.3486717558838 | erot = 13.4886662723594 | epot = -73.3340106985081 | etot = -48.4966726702649 +94000 ekin = 11.4194570018415 | erot = 13.7677249757349 | epot = -73.6838546479552 | etot = -48.4966726703788 +95000 ekin = 11.3899765892382 | erot = 14.0119097397866 | epot = -73.8985589999747 | etot = -48.49667267095 +96000 ekin = 11.2605951113208 | erot = 14.2148286413586 | epot = -73.9720964225416 | etot = -48.4966726698623 +97000 ekin = 11.0445904714271 | erot = 14.3764700204598 | epot = -73.9177331597956 | etot = -48.4966726679087 +98000 ekin = 10.7660933774808 | erot = 14.4993108341525 | epot = -73.7620768770611 | etot = -48.4966726654278 +99000 ekin = 10.4555155361515 | erot = 14.5876138558185 | epot = -73.5398020548142 | etot = -48.4966726628441 +100000 ekin = 10.0974774598918 | erot = 14.6249949423901 | epot = -73.2191455720024 | etot = -48.4966731697205 +101000 ekin = 10.0415631096213 | erot = 14.0961872066523 | epot = -72.6344231724585 | etot = -48.4966728561849 +102000 ekin = 10.2892855713186 | erot = 14.0121875104988 | epot = -72.7981457142986 | etot = -48.4966726324812 +103000 ekin = 10.030926337015 | erot = 14.0335683972799 | epot = -72.561167366022 | etot = -48.4966726317272 +104000 ekin = 9.79194699005139 | erot = 14.0507619049252 | epot = -72.3393815271562 | etot = -48.4966726321796 +105000 ekin = 9.56928640949095 | erot = 14.0644676494028 | epot = -72.130426691714 | etot = -48.4966726328202 +106000 ekin = 9.35843270941669 | erot = 14.0738948863193 | epot = -71.9290002289426 | etot = -48.4966726332066 +107000 ekin = 9.15960205394236 | erot = 14.0781570096045 | epot = -71.7344316966944 | etot = -48.4966726331476 +108000 ekin = 8.98058598862026 | erot = 14.075757349537 | epot = -71.5530159707953 | etot = -48.496672632638 +109000 ekin = 8.83500010163816 | erot = 14.0641942059681 | epot = -71.3958669399391 | etot = -48.4966726323328 +110000 ekin = 8.73407156167097 | erot = 14.0396159238031 | epot = -71.2703601184356 | etot = -48.4966726329615 +111000 ekin = 8.6754498316719 | erot = 13.9967358275324 | epot = -71.1688582943783 | etot = -48.496672635174 +112000 ekin = 8.6350044076196 | erot = 13.9293053313389 | epot = -71.0609823775568 | etot = -48.4966726385983 +113000 ekin = 8.57042592578248 | erot = 13.8317248404405 | epot = -70.8988234080958 | etot = -48.4966726418728 +114000 ekin = 8.43989096913481 | erot = 13.7008372464516 | epot = -70.6374008585732 | etot = -48.4966726429868 +115000 ekin = 8.22527688481048 | erot = 13.537458994135 | epot = -70.2594085170045 | etot = -48.4966726380591 +116000 ekin = 7.96055882645525 | erot = 13.3455331436993 | epot = -69.8027646054354 | etot = -48.4966726352808 +117000 ekin = 7.68480617458248 | erot = 13.1328848481101 | epot = -69.314363654913 | etot = -48.4966726322204 +118000 ekin = 7.42978537709923 | erot = 12.9094282247776 | epot = -68.8358862320079 | etot = -48.496672630131 +119000 ekin = 7.21373639393119 | erot = 12.6851208042351 | epot = -68.3955298273807 | etot = -48.4966726292144 +120000 ekin = 7.03803293636593 | erot = 12.469779726339 | epot = -68.0044852916931 | etot = -48.4966726289882 +121000 ekin = 6.89367092643985 | erot = 12.2728949512537 | epot = -67.6632385066874 | etot = -48.4966726289939 +122000 ekin = 6.76879687257078 | erot = 12.1027214693521 | epot = -67.3681909710504 | etot = -48.4966726291276 +123000 ekin = 6.65210407178445 | erot = 11.9648592015088 | epot = -67.1136359029293 | etot = -48.4966726296361 +124000 ekin = 6.53115267708981 | erot = 11.861686116444 | epot = -66.88951142379 | etot = -48.4966726302562 +125000 ekin = 6.39605544212651 | erot = 11.7907254418528 | epot = -66.6834535155169 | etot = -48.4966726315376 +126000 ekin = 6.23766494395307 | erot = 11.7440508510346 | epot = -66.4783884275694 | etot = -48.4966726325818 +127000 ekin = 6.04911470795291 | erot = 11.7111635255669 | epot = -66.2569508666253 | etot = -48.4966726331055 +128000 ekin = 5.83208869215223 | erot = 11.682213880144 | epot = -66.0109752050976 | etot = -48.4966726328014 +129000 ekin = 5.59955533756738 | erot = 11.6485505375866 | epot = -65.7447785065467 | etot = -48.4966726313926 +130000 ekin = 5.37616547346366 | erot = 11.6055192857373 | epot = -65.4783573884606 | etot = -48.4966726292596 +131000 ekin = 5.1962134726015 | erot = 11.5523382042838 | epot = -65.2452243036186 | etot = -48.4966726267333 +132000 ekin = 5.09512855427511 | erot = 11.4915853273363 | epot = -65.0833865066907 | etot = -48.4966726250793 +133000 ekin = 5.09593793196019 | erot = 11.4254654000418 | epot = -65.0180759559348 | etot = -48.4966726239328 +134000 ekin = 5.21315400668809 | erot = 11.3572216289376 | epot = -65.0670482589947 | etot = -48.4966726233689 +135000 ekin = 5.45274887458156 | erot = 11.2905481951996 | epot = -65.239969693084 | etot = -48.4966726233029 +136000 ekin = 5.81359277201749 | erot = 11.229115941649 | epot = -65.5393813373501 | etot = -48.4966726236836 +137000 ekin = 6.28595091475952 | erot = 11.1752215008219 | epot = -65.9578450445961 | etot = -48.4966726290146 +138000 ekin = 6.83489595318488 | erot = 11.1238804126678 | epot = -66.4554489962829 | etot = -48.4966726304302 +139000 ekin = 7.43298982213682 | erot = 11.0759557714597 | epot = -67.0056182256026 | etot = -48.4966726320061 +140000 ekin = 8.05423567523142 | erot = 11.033891553925 | epot = -67.584799863096 | etot = -48.4966726339395 +141000 ekin = 8.66814450976506 | erot = 10.9995435661283 | epot = -68.1643607123595 | etot = -48.4966726364661 +142000 ekin = 9.23299211625349 | erot = 10.9739956101689 | epot = -68.7036603674071 | etot = -48.4966726409846 +143000 ekin = 9.69542810759742 | erot = 10.9568256540431 | epot = -69.1489264066345 | etot = -48.4966726449939 +144000 ekin = 10.0035712730501 | erot = 10.9455251640266 | epot = -69.4457690858237 | etot = -48.4966726487469 +145000 ekin = 10.114017316757 | erot = 10.9367967497652 | epot = -69.5474867174202 | etot = -48.4966726508979 +146000 ekin = 10.0102551934734 | erot = 10.9282120719412 | epot = -69.435139915191 | etot = -48.4966726497764 +147000 ekin = 9.72372844852308 | erot = 10.9204908015183 | epot = -69.1408918943015 | etot = -48.4966726442601 +148000 ekin = 9.3455309212133 | erot = 10.9194622742229 | epot = -68.7616658304618 | etot = -48.4966726350256 +149000 ekin = 9.0130830772134 | erot = 10.9361646162998 | epot = -68.4459203187336 | etot = -48.4966726252203 +150000 ekin = 8.86556491619637 | erot = 10.9838242849002 | epot = -68.3460618203824 | etot = -48.4966726192858 +151000 ekin = 8.98562593113009 | erot = 11.0721207188521 | epot = -68.5544192701787 | etot = -48.4966726201965 +152000 ekin = 9.36317382414577 | erot = 11.2013283048028 | epot = -69.061174756333 | etot = -48.4966726273844 +153000 ekin = 9.90592399926646 | erot = 11.3597169983867 | epot = -69.7623136349275 | etot = -48.4966726372743 +154000 ekin = 10.4876718007886 | erot = 11.5259908274841 | epot = -70.5103352740092 | etot = -48.4966726457364 +155000 ekin = 11.0014546611195 | erot = 11.6755859722277 | epot = -71.1737132837611 | etot = -48.4966726504139 +156000 ekin = 11.3882148349974 | erot = 11.7874454844493 | epot = -71.6723329709537 | etot = -48.4966726515071 +157000 ekin = 11.632971912162 | erot = 11.8481298115866 | epot = -71.9777743743943 | etot = -48.4966726506457 +158000 ekin = 11.7436997816217 | erot = 11.8526024825738 | epot = -72.0929749132284 | etot = -48.496672649033 +159000 ekin = 11.7357219121848 | erot = 11.8034015633386 | epot = -72.035796122215 | etot = -48.4966726466915 +160000 ekin = 11.6305552644559 | erot = 11.7096700273716 | epot = -71.8368979351557 | etot = -48.4966726433281 +161000 ekin = 11.4596686193178 | erot = 11.5857134121766 | epot = -71.5420546707721 | etot = -48.4966726392777 +162000 ekin = 11.2620233891978 | erot = 11.4483738449268 | epot = -71.2070698695269 | etot = -48.4966726354023 +163000 ekin = 11.0755659765699 | erot = 11.3138001976396 | epot = -70.8860388066505 | etot = -48.496672632441 +164000 ekin = 10.9292960811501 | erot = 11.1949564931542 | epot = -70.620925204979 | etot = -48.4966726306746 +165000 ekin = 10.8401906864915 | erot = 11.1006151382438 | epot = -70.4374784546624 | etot = -48.496672629927 +166000 ekin = 10.8146651781023 | erot = 11.0356758462704 | epot = -70.3470136542483 | etot = -48.4966726298757 +167000 ekin = 10.8520567567896 | erot = 11.0022539306514 | epot = -70.3509833175949 | etot = -48.4966726301539 +168000 ekin = 10.9484894336301 | erot = 11.0010183041606 | epot = -70.4461803682589 | etot = -48.4966726304681 +169000 ekin = 11.0998937027407 | erot = 11.0324366339784 | epot = -70.6290029673685 | etot = -48.4966726306495 +170000 ekin = 11.3034839733024 | erot = 11.0977053912593 | epot = -70.8978619952543 | etot = -48.4966726306926 +171000 ekin = 11.5572307267891 | erot = 11.199221278162 | epot = -71.2531246357259 | etot = -48.4966726307748 +172000 ekin = 11.8571464638407 | erot = 11.340530780689 | epot = -71.6943498757674 | etot = -48.4966726312378 +173000 ekin = 12.1927097200966 | erot = 11.5257889190944 | epot = -72.2151712717164 | etot = -48.4966726325253 +174000 ekin = 12.5417902291425 | erot = 11.7588401693295 | epot = -72.7973030335587 | etot = -48.4966726350868 +175000 ekin = 12.8647095032767 | erot = 12.0421936377313 | epot = -73.4035757801763 | etot = -48.4966726391684 +176000 ekin = 13.1024197132893 | erot = 12.3759769580603 | epot = -73.9750693159943 | etot = -48.4966726446447 +177000 ekin = 13.1907180968525 | erot = 12.7566551418159 | epot = -74.4440458869511 | etot = -48.4966726482828 +178000 ekin = 13.0526492219561 | erot = 13.1773711164493 | epot = -74.7266929933906 | etot = -48.4966726549851 +179000 ekin = 12.2089794588716 | erot = 13.583016419723 | epot = -74.2886682061547 | etot = -48.4966723275601 +180000 ekin = 11.9004068675208 | erot = 14.0870661177303 | epot = -74.4841455891948 | etot = -48.4966726039436 +181000 ekin = 10.8654768903664 | erot = 14.5861339869463 | epot = -73.9482834733408 | etot = -48.4966725960281 +182000 ekin = 9.66028270694921 | erot = 15.1104289206582 | epot = -73.2673842110038 | etot = -48.4966725833964 +183000 ekin = 8.48066280387482 | erot = 15.6673690821394 | epot = -72.6447044561298 | etot = -48.4966725701156 +184000 ekin = 7.52630413851928 | erot = 16.2665624203505 | epot = -72.2895391199352 | etot = -48.4966725610654 +185000 ekin = 6.93646433276227 | erot = 16.9124293952408 | epot = -72.3455662872068 | etot = -48.4966725592037 +186000 ekin = 6.75402182356317 | erot = 17.5959531882614 | epot = -72.8466475761013 | etot = -48.4966725642767 +187000 ekin = 6.93176584306308 | erot = 18.290107645954 | epot = -73.7185460628717 | etot = -48.4966725738546 +188000 ekin = 7.36496175936991 | erot = 18.9517169220484 | epot = -74.8133512665755 | etot = -48.4966725851571 +189000 ekin = 7.92587452892086 | erot = 19.5289159490214 | epot = -75.9514630739345 | etot = -48.4966725959922 +190000 ekin = 8.48887345555886 | erot = 19.971100820825 | epot = -76.9566468811641 | etot = -48.4966726047802 +191000 ekin = 8.94279744307508 | erot = 20.2387056809859 | epot = -77.678175735695 | etot = -48.496672611634 +192000 ekin = 9.20220030815946 | erot = 20.3101038067646 | epot = -78.0089767286117 | etot = -48.4966726136877 +193000 ekin = 9.22639739330183 | erot = 20.1841068563642 | epot = -77.907176861092 | etot = -48.496672611426 +194000 ekin = 9.02106352746175 | erot = 19.8798400124544 | epot = -77.3975761450867 | etot = -48.4966726051705 +195000 ekin = 8.63698690389635 | erot = 19.4322506720449 | epot = -76.565910172217 | etot = -48.4966725962758 +196000 ekin = 8.15745599944534 | erot = 18.8847381250325 | epot = -75.5388667111714 | etot = -48.4966725866936 +197000 ekin = 7.67775841891672 | erot = 18.2815207246745 | epot = -74.4559517216667 | etot = -48.4966725780755 +198000 ekin = 7.28589102711731 | erot = 17.6623826120266 | epot = -73.4449462104542 | etot = -48.4966725713103 +199000 ekin = 7.05017610428669 | erot = 17.060606391977 | epot = -72.607455062976 | etot = -48.4966725667124 +200000 ekin = 7.01285264528989 | erot = 16.50301808819 | epot = -72.0125432979108 | etot = -48.4966725644308 +201000 ekin = 7.1862830294852 | erot = 16.010606626529 | epot = -71.6935622206077 | etot = -48.4966725645936 +202000 ekin = 7.55028085659987 | erot = 15.5985035867515 | epot = -71.6454570106413 | etot = -48.4966725672899 +203000 ekin = 8.05261783918064 | erot = 15.2753610695163 | epot = -71.8246514808017 | etot = -48.4966725721048 +204000 ekin = 8.61587119719646 | erot = 15.04304819392 | epot = -72.1555919692024 | etot = -48.4966725780859 +205000 ekin = 9.15150139881729 | erot = 14.8972623538558 | epot = -72.545436336524 | etot = -48.4966725838508 +206000 ekin = 9.57853091802914 | erot = 14.8296218061968 | epot = -72.9048253122554 | etot = -48.4966725880294 +207000 ekin = 9.84110469117199 | erot = 14.8306579376119 | epot = -73.1684352185354 | etot = -48.4966725897515 +208000 ekin = 9.9191538007016 | erot = 14.8924578832503 | epot = -73.3082842728933 | etot = -48.4966725889413 +209000 ekin = 9.82907930165368 | erot = 15.0096951815675 | epot = -73.3354470695323 | etot = -48.4966725863112 +210000 ekin = 9.61485280029705 | erot = 15.178517413709 | epot = -73.2900427971239 | etot = -48.4966725831179 +211000 ekin = 9.33255453637479 | erot = 15.3937274488313 | epot = -73.222954565974 | etot = -48.4966725807679 +212000 ekin = 9.03298062727102 | erot = 15.645385712317 | epot = -73.1750389199413 | etot = -48.4966725803533 +213000 ekin = 8.74801774645632 | erot = 15.916232815536 | epot = -73.1609231441958 | etot = -48.4966725822035 +214000 ekin = 8.48645509186825 | erot = 16.1810372606232 | epot = -73.1641649379145 | etot = -48.4966725854231 +215000 ekin = 8.24361394372392 | erot = 16.4085443498303 | epot = -73.1488308822363 | etot = -48.4966725886821 +216000 ekin = 8.0164414064009 | erot = 16.5671904860397 | epot = -73.0803044821115 | etot = -48.4966725896709 +217000 ekin = 7.82443857147143 | erot = 16.6321169295473 | epot = -72.9532280885849 | etot = -48.4966725875662 +218000 ekin = 7.71607328584953 | erot = 16.5899557796703 | epot = -72.8027016494475 | etot = -48.4966725839277 +219000 ekin = 7.75310717264638 | erot = 16.4350572743174 | epot = -72.6848370278596 | etot = -48.4966725808959 +220000 ekin = 7.98143888037595 | erot = 16.167510735033 | epot = -72.6456221958558 | etot = -48.4966725804469 +221000 ekin = 8.40773648375012 | erot = 15.7897008204118 | epot = -72.6941098869373 | etot = -48.4966725827754 +222000 ekin = 8.99748090378323 | erot = 15.3051579237983 | epot = -72.7993114139574 | etot = -48.4966725863759 +223000 ekin = 9.69291742679225 | erot = 14.7208372414108 | epot = -72.910427257502 | etot = -48.4966725892989 +224000 ekin = 10.4359945859726 | erot = 14.0505863380248 | epot = -72.9832535144505 | etot = -48.496672590453 +225000 ekin = 11.1813440324244 | erot = 13.3180094413839 | epot = -72.9960260640915 | etot = -48.4966725902832 +226000 ekin = 11.889917409358 | erot = 12.555574190437 | epot = -72.9421641905558 | etot = -48.4966725907608 +227000 ekin = 12.5083401208471 | erot = 11.7991557925131 | epot = -72.8041685069158 | etot = -48.4966725935555 +228000 ekin = 12.9540489023972 | erot = 11.0813711809765 | epot = -72.5320926818126 | etot = -48.4966725984389 +229000 ekin = 13.1250482768413 | erot = 10.4265507754551 | epot = -72.0482716553122 | etot = -48.4966726030158 +230000 ekin = 12.935477678669 | erot = 9.84937329189879 | epot = -71.2815235748152 | etot = -48.4966726042475 +231000 ekin = 12.3571979238594 | erot = 9.3566448711741 | epot = -70.2105153953899 | etot = -48.4966726003564 +232000 ekin = 11.441378635523 | erot = 8.95013763085561 | epot = -68.8881888585093 | etot = -48.4966725921307 +233000 ekin = 10.3068608367529 | erot = 8.62874527757124 | epot = -67.4322786963278 | etot = -48.4966725820037 +234000 ekin = 9.10484994366737 | erot = 8.38947611811844 | epot = -65.9909986342478 | etot = -48.496672572462 +235000 ekin = 7.97762335600241 | erot = 8.22796057435479 | epot = -64.7022564960573 | etot = -48.4966725657001 +236000 ekin = 7.03041833666843 | erot = 8.14060898683137 | epot = -63.66769988491 | etot = -48.4966725614102 +237000 ekin = 6.33232778593017 | erot = 8.12400287135145 | epot = -62.9530032163578 | etot = -48.4966725590762 +238000 ekin = 5.92140822284888 | erot = 8.17513077744563 | epot = -62.5932115585206 | etot = -48.4966725582261 +239000 ekin = 5.81123122340323 | erot = 8.29054157425425 | epot = -62.5984453565713 | etot = -48.4966725589138 +240000 ekin = 5.99217826068819 | erot = 8.46489799365566 | epot = -62.9537488157021 | etot = -48.4966725613583 +241000 ekin = 6.43109156575043 | erot = 8.68961368249179 | epot = -63.6173778141177 | etot = -48.4966725658754 +242000 ekin = 7.06756407118994 | erot = 8.9515361448277 | epot = -64.5157727888076 | etot = -48.4966725727899 +243000 ekin = 7.81639319360646 | erot = 9.23207829014518 | epot = -65.5451440641847 | etot = -48.496672580433 +244000 ekin = 8.58044212001563 | erot = 9.5094870156515 | epot = -66.5866017229557 | etot = -48.4966725872886 +245000 ekin = 9.26871916861178 | erot = 9.75990826682403 | epot = -67.5253000301717 | etot = -48.4966725947359 +246000 ekin = 9.78946573665902 | erot = 9.96525866120483 | epot = -68.251396997994 | etot = -48.4966726001302 +247000 ekin = 10.0743388396378 | erot = 10.1147521472207 | epot = -68.6857635892491 | etot = -48.4966726023906 +248000 ekin = 10.0941079494506 | erot = 10.2065328814933 | epot = -68.7973134319809 | etot = -48.496672601037 +249000 ekin = 9.86393967730228 | erot = 10.2475258665297 | epot = -68.608138141035 | etot = -48.496672597203 +250000 ekin = 9.43636984425759 | erot = 10.2506637078715 | epot = -68.1837061428391 | etot = -48.49667259071 +251000 ekin = 8.89229868578272 | erot = 10.2323346091275 | epot = -67.6213058787841 | etot = -48.4966725838739 +252000 ekin = 8.31943898663813 | erot = 10.2075884962971 | epot = -67.0237000610837 | etot = -48.4966725781484 +253000 ekin = 7.79276077495956 | erot = 10.1873587545199 | epot = -66.4767921038581 | etot = -48.4966725743786 +254000 ekin = 7.36152147187708 | erot = 10.1778229232022 | epot = -66.0360169681713 | etot = -48.496672573092 +255000 ekin = 7.04416809514289 | erot = 10.1812481941798 | epot = -65.7220888627795 | etot = -48.4966725734568 +256000 ekin = 6.8353001740143 | erot = 10.1962922388007 | epot = -65.5282649876993 | etot = -48.4966725748843 +257000 ekin = 6.71442148101725 | erot = 10.2200504443727 | epot = -65.4311445018633 | etot = -48.4966725764734 +258000 ekin = 6.65781764565476 | erot = 10.2492124175302 | epot = -65.4037026408489 | etot = -48.496672577664 +259000 ekin = 6.64642051203178 | erot = 10.2806008774778 | epot = -65.4236939679503 | etot = -48.4966725784407 +260000 ekin = 6.66675395817186 | erot = 10.3110375472865 | epot = -65.4744640845822 | etot = -48.4966725791239 +261000 ekin = 6.70841492604912 | erot = 10.3378721255422 | epot = -65.5429596307914 | etot = -48.4966725792001 +262000 ekin = 6.76275619466047 | erot = 10.3595239082574 | epot = -65.618952682714 | etot = -48.4966725797962 +263000 ekin = 6.82191301035398 | erot = 10.3716898912776 | epot = -65.6902754814592 | etot = -48.4966725798277 +264000 ekin = 6.88504914961089 | erot = 10.3708999773049 | epot = -65.7526217059438 | etot = -48.496672579028 +265000 ekin = 6.96089828668844 | erot = 10.3558192629953 | epot = -65.8133901272447 | etot = -48.496672577561 +266000 ekin = 7.06529185642724 | erot = 10.3276065183166 | epot = -65.8895709506602 | etot = -48.4966725759163 +267000 ekin = 7.21505088332344 | erot = 10.2893497391586 | epot = -66.0010731971154 | etot = -48.4966725746334 +268000 ekin = 7.42137725343366 | erot = 10.2450818723121 | epot = -66.1631316998404 | etot = -48.4966725740947 +269000 ekin = 7.6852432971255 | erot = 10.1988935008324 | epot = -66.3808093723997 | etot = -48.4966725744418 +270000 ekin = 7.99580948965905 | erot = 10.1544492652978 | epot = -66.6469313305391 | etot = -48.4966725755823 +271000 ekin = 8.33190485117851 | erot = 10.1151435011289 | epot = -66.9437209293489 | etot = -48.4966725770415 +272000 ekin = 8.66610587589786 | erot = 10.0856409418454 | epot = -67.2484193965687 | etot = -48.4966725788253 +273000 ekin = 8.97042145758361 | erot = 10.0690324252282 | epot = -67.5361264630363 | etot = -48.4966725802245 +274000 ekin = 9.2228768329096 | erot = 10.0690361391114 | epot = -67.7885855527785 | etot = -48.4966725807575 +275000 ekin = 9.41389302940073 | erot = 10.0906946031038 | epot = -68.0012602127282 | etot = -48.4966725802236 +276000 ekin = 9.54942761491813 | erot = 10.1400083113496 | epot = -68.1861085050624 | etot = -48.4966725787947 +277000 ekin = 9.6491359452143 | erot = 10.2229042121058 | epot = -68.3687127343567 | etot = -48.4966725770367 +278000 ekin = 9.73935192456233 | erot = 10.343570015445 | epot = -68.5795945157503 | etot = -48.496672575743 +279000 ekin = 9.84298152731736 | erot = 10.502614040488 | epot = -68.8422681434167 | etot = -48.4966725756113 +280000 ekin = 9.97046187704858 | erot = 10.6957212898423 | epot = -69.1628557437709 | etot = -48.4966725768801 +281000 ekin = 10.1137684706805 | erot = 10.9135096018603 | epot = -69.5239506554908 | etot = -48.49667258295 +282000 ekin = 10.2288689015713 | erot = 11.1422719920843 | epot = -69.8678134801848 | etot = -48.4966725865291 +283000 ekin = 10.2769463822287 | erot = 11.3646568092218 | epot = -70.1382757810685 | etot = -48.496672589618 +284000 ekin = 10.2298350175643 | erot = 11.5634949517897 | epot = -70.2900025609874 | etot = -48.4966725916333 +285000 ekin = 10.0723248849486 | erot = 11.7243250964812 | epot = -70.2933225738249 | etot = -48.4966725923951 +286000 ekin = 9.80394054073949 | erot = 11.8369977519994 | epot = -70.1376108847945 | etot = -48.4966725920556 +287000 ekin = 9.43655233184761 | erot = 11.8964493797707 | epot = -69.8296743025415 | etot = -48.4966725909232 +288000 ekin = 8.99013271756312 | erot = 11.9027405791562 | epot = -69.3895458860358 | etot = -48.4966725893165 +289000 ekin = 8.48857673812088 | erot = 11.8605226371614 | epot = -68.845771962788 | etot = -48.4966725875058 +290000 ekin = 7.9565131170632 | erot = 11.778072078097 | epot = -68.2312577808365 | etot = -48.4966725856763 +291000 ekin = 7.41785902589102 | erot = 11.6660397038366 | epot = -67.5805713135338 | etot = -48.4966725838062 +292000 ekin = 6.89736764547562 | erot = 11.5361414718234 | epot = -66.9301816988922 | etot = -48.4966725815931 +293000 ekin = 6.42572947191785 | erot = 11.400070184943 | epot = -66.3224722354505 | etot = -48.4966725785896 +294000 ekin = 6.04578762671093 | erot = 11.2687731411147 | epot = -65.8112333424662 | etot = -48.4966725746405 +295000 ekin = 5.81372000922306 | erot = 11.1519540391615 | epot = -65.4623466187836 | etot = -48.4966725703991 +296000 ekin = 5.78868895654533 | erot = 11.0574288852216 | epot = -65.3427904091805 | etot = -48.4966725674136 +297000 ekin = 6.01086247217827 | erot = 10.9900621222287 | epot = -65.4975971618208 | etot = -48.4966725674139 +298000 ekin = 6.47793511117819 | erot = 10.9505151838666 | epot = -65.9251228662535 | etot = -48.4966725712087 +299000 ekin = 7.13485226400034 | erot = 10.9343849129914 | epot = -66.5659097550918 | etot = -48.4966725781001 +300000 ekin = 7.88433986354594 | erot = 10.9323127585853 | epot = -67.3133252083742 | etot = -48.496672586243 +301000 ekin = 8.61282845352297 | erot = 10.9313732714636 | epot = -68.0408743185398 | etot = -48.4966725935533 +302000 ekin = 9.21908440274039 | erot = 10.9175582659858 | epot = -68.633315267177 | etot = -48.4966725984508 +303000 ekin = 9.63516616611897 | erot = 10.8787665670557 | epot = -69.0106053333789 | etot = -48.4966726002042 +304000 ekin = 9.83543476974171 | erot = 10.8074962358205 | epot = -69.1396036043407 | etot = -48.4966725987784 +305000 ekin = 9.83532020704072 | erot = 10.7023193346282 | epot = -69.0343121365665 | etot = -48.4966725948976 +306000 ekin = 9.68145093558513 | erot = 10.5677982812262 | epot = -68.7459218064566 | etot = -48.4966725896453 +307000 ekin = 9.43697927068104 | erot = 10.4129945423149 | epot = -68.3466463972406 | etot = -48.4966725842446 +308000 ekin = 9.16617244364725 | erot = 10.2491623578655 | epot = -67.9120073811779 | etot = -48.4966725796651 +309000 ekin = 8.92159986058929 | erot = 10.0874162913126 | epot = -67.5056887285674 | etot = -48.4966725766655 +310000 ekin = 8.73563094099929 | erot = 9.9371510361822 | epot = -67.169454552446 | etot = -48.4966725752645 +311000 ekin = 8.61913259828634 | erot = 9.80527711015154 | epot = -66.9210822838146 | etot = -48.4966725753767 +312000 ekin = 8.56355763426529 | erot = 9.69617071432065 | epot = -66.7564009251108 | etot = -48.4966725765249 +313000 ekin = 8.54744454664532 | erot = 9.61223302160909 | epot = -66.6563501463599 | etot = -48.4966725781055 +314000 ekin = 8.54471031353907 | erot = 9.55468856186606 | epot = -66.5960714549334 | etot = -48.4966725795283 +315000 ekin = 8.53582675036285 | erot = 9.52360081787041 | epot = -66.5561001482904 | etot = -48.4966725800572 +316000 ekin = 8.50947902793441 | erot = 9.51910773892181 | epot = -66.5252593469131 | etot = -48.4966725800569 +317000 ekin = 8.46528361595108 | erot = 9.54310287693593 | epot = -66.5050590717006 | etot = -48.4966725788136 +318000 ekin = 8.42148334748388 | erot = 9.59812356341528 | epot = -66.516279487461 | etot = -48.4966725765619 +319000 ekin = 8.41172051674332 | erot = 9.68666529074796 | epot = -66.5950583814326 | etot = -48.4966725739414 +320000 ekin = 8.47631024940413 | erot = 9.81010411287936 | epot = -66.7830869341493 | etot = -48.4966725718658 +321000 ekin = 8.64981485679785 | erot = 9.96750014912045 | epot = -67.1139875771456 | etot = -48.4966725712273 +322000 ekin = 8.94886501909668 | erot = 10.1545796242721 | epot = -67.6001172159167 | etot = -48.4966725725479 +323000 ekin = 9.36436094198863 | erot = 10.3629464345255 | epot = -68.2239799526584 | etot = -48.4966725761443 +324000 ekin = 9.85762299126876 | erot = 10.5807030497635 | epot = -68.9349986231461 | etot = -48.4966725821139 +325000 ekin = 10.3675336373896 | erot = 10.7915336066481 | epot = -69.6557398310563 | etot = -48.4966725870186 +326000 ekin = 10.8169039905069 | erot = 10.9780749030532 | epot = -70.2916514883353 | etot = -48.4966725947751 +327000 ekin = 11.1080827252351 | erot = 11.1278633890661 | epot = -70.7326187147602 | etot = -48.4966726004589 +328000 ekin = 11.1668072003252 | erot = 11.235581979109 | epot = -70.8990617815916 | etot = -48.4966726021574 +329000 ekin = 10.967403256679 | erot = 11.3047655940184 | epot = -70.768841449617 | etot = -48.4966725989195 +330000 ekin = 10.5471219088133 | erot = 11.3459152750385 | epot = -70.3897097754691 | etot = -48.4966725916173 +331000 ekin = 9.99817977290763 | erot = 11.3709343468917 | epot = -69.8657867027959 | etot = -48.4966725829966 +332000 ekin = 9.43640210782927 | erot = 11.3868472546632 | epot = -69.319921938518 | etot = -48.4966725760255 +333000 ekin = 8.9627531487633 | erot = 11.3930028323085 | epot = -68.8524285534325 | etot = -48.4966725723606 +334000 ekin = 8.63845657354969 | erot = 11.3827647269613 | epot = -68.5178938722226 | etot = -48.4966725717116 +335000 ekin = 8.47696736450443 | erot = 11.3460820193678 | epot = -68.3197219598737 | etot = -48.4966725760015 +336000 ekin = 8.45129453005634 | erot = 11.2716956099987 | epot = -68.2196627183468 | etot = -48.4966725782917 +337000 ekin = 8.52855094860833 | erot = 11.1567863476686 | epot = -68.1820098764218 | etot = -48.4966725801449 +338000 ekin = 8.67667036350951 | erot = 11.0029242666098 | epot = -68.1762672115551 | etot = -48.4966725814358 +339000 ekin = 8.86840718542881 | erot = 10.8141117179184 | epot = -68.1791914857273 | etot = -48.4966725823801 +340000 ekin = 9.08074049345715 | erot = 10.5949858590616 | epot = -68.1723989357497 | etot = -48.4966725832309 +341000 ekin = 9.29280025524277 | erot = 10.3497144840129 | epot = -68.1391873233524 | etot = -48.4966725840967 +342000 ekin = 9.48478364392253 | erot = 10.0817821314002 | epot = -68.0632383602021 | etot = -48.4966725848794 +343000 ekin = 9.63889599726108 | erot = 9.7944839703947 | epot = -67.930052552996 | etot = -48.4966725853402 +344000 ekin = 9.7417975009077 | erot = 9.49171920193303 | epot = -67.7301892880911 | etot = -48.4966725852504 +345000 ekin = 9.78689625544432 | erot = 9.17855510441859 | epot = -67.4621239444743 | etot = -48.4966725846114 +346000 ekin = 9.77487619979532 | erot = 8.86098115604089 | epot = -67.1325299394068 | etot = -48.4966725835706 +347000 ekin = 9.71190434740935 | erot = 8.54542801630241 | epot = -66.7540049461477 | etot = -48.4966725824359 +348000 ekin = 9.60626623887659 | erot = 8.23797752716905 | epot = -66.340916347539 | etot = -48.4966725814934 +349000 ekin = 9.46512205487934 | erot = 7.94382241630924 | epot = -65.9056170520946 | etot = -48.496672580906 +350000 ekin = 9.29263921345274 | erot = 7.66718775573895 | epot = -65.4564995498442 | etot = -48.4966725806525 +351000 ekin = 9.09030704038404 | erot = 7.41172558158068 | epot = -64.9987052024842 | etot = -48.4966725805195 +352000 ekin = 8.85964507189034 | erot = 7.18116708502939 | epot = -64.5374847370686 | etot = -48.4966725801489 +353000 ekin = 8.60706719309285 | erot = 6.97993996553063 | epot = -64.083679737657 | etot = -48.4966725790335 +354000 ekin = 8.35365998674884 | erot = 6.81451510372734 | epot = -63.664847665859 | etot = -48.4966725753828 +355000 ekin = 8.13817060763887 | erot = 6.69316622833436 | epot = -63.3280094087146 | etot = -48.4966725727414 +356000 ekin = 8.00303344814134 | erot = 6.62071403038222 | epot = -63.120420047619 | etot = -48.4966725690954 +357000 ekin = 8.00329594799677 | erot = 6.60119920913289 | epot = -63.101167722592 | etot = -48.4966725654624 +358000 ekin = 8.19390069539973 | erot = 6.6365500519995 | epot = -63.3271233108175 | etot = -48.4966725634183 +359000 ekin = 8.60851483666456 | erot = 6.72479591296309 | epot = -63.8299833140449 | etot = -48.4966725644172 +360000 ekin = 9.24022555642119 | erot = 6.85875874182178 | epot = -64.5956568672064 | etot = -48.4966725689635 +361000 ekin = 10.0343517665272 | erot = 7.02601171013287 | epot = -65.5570360531664 | etot = -48.4966725765063 +362000 ekin = 10.8949623485035 | erot = 7.21007448017166 | epot = -66.6017094133605 | etot = -48.4966725846853 +363000 ekin = 11.7154060071658 | erot = 7.39407842266489 | epot = -67.606157020532 | etot = -48.4966725907012 +364000 ekin = 12.40572233359 | erot = 7.56453665264199 | epot = -68.4669315836044 | etot = -48.4966725973724 +365000 ekin = 12.8900700952231 | erot = 7.71262358053191 | epot = -69.0993662750143 | etot = -48.4966725992593 +366000 ekin = 13.1382701917079 | erot = 7.83636021672802 | epot = -69.4713030061121 | etot = -48.4966725976761 +367000 ekin = 13.1662433494648 | erot = 7.94108342053015 | epot = -69.6039993641331 | etot = -48.4966725941382 +368000 ekin = 13.021625732222 | erot = 8.03746300620857 | epot = -69.5557613271402 | etot = -48.4966725887097 +369000 ekin = 12.7699639205452 | erot = 8.13884083906406 | epot = -69.405477343072 | etot = -48.4966725834627 +370000 ekin = 12.4763633941236 | erot = 8.25852807052614 | epot = -69.2315640445023 | etot = -48.4966725798526 +371000 ekin = 12.1883522141967 | erot = 8.40712894602482 | epot = -69.0921537380662 | etot = -48.4966725778446 +372000 ekin = 11.9337668267027 | erot = 8.59209712214833 | epot = -69.0225365257837 | etot = -48.4966725769327 +373000 ekin = 11.7268114357708 | erot = 8.81820188226925 | epot = -69.0416858944192 | etot = -48.4966725763792 +374000 ekin = 11.5751062922416 | erot = 9.08799140196931 | epot = -69.1597702703733 | etot = -48.4966725761623 +375000 ekin = 11.4816771194464 | erot = 9.40179119698654 | epot = -69.3801408929934 | etot = -48.4966725765605 +376000 ekin = 11.441524446261 | erot = 9.75725267435531 | epot = -69.6954496985913 | etot = -48.4966725779749 +377000 ekin = 11.4364317356708 | erot = 10.1487019288236 | epot = -70.0818062452136 | etot = -48.4966725807192 +378000 ekin = 11.4326847178226 | erot = 10.5666289070243 | epot = -70.4959862088629 | etot = -48.496672584016 +379000 ekin = 11.3879261245005 | erot = 10.9960382478638 | epot = -70.8806369609932 | etot = -48.4966725886289 +380000 ekin = 11.2500883026257 | erot = 11.4211944009614 | epot = -71.1679552963687 | etot = -48.4966725927816 +381000 ekin = 10.972692122943 | erot = 11.826929103362 | epot = -71.2962938220293 | etot = -48.4966725957243 +382000 ekin = 10.52816021539 | erot = 12.1993149200452 | epot = -71.2241477321915 | etot = -48.4966725967563 +383000 ekin = 9.91669157180962 | erot = 12.5275908716532 | epot = -70.9409550387057 | etot = -48.4966725952429 +384000 ekin = 9.1730149286383 | erot = 12.8043890136506 | epot = -70.47407653408 | etot = -48.4966725917911 +385000 ekin = 8.36601181966598 | erot = 13.0251847436255 | epot = -69.8878691486834 | etot = -48.4966725853919 +386000 ekin = 7.59336935509946 | erot = 13.1937587055527 | epot = -69.2838006385302 | etot = -48.496672577878 +387000 ekin = 6.96355937778721 | erot = 13.3174316291766 | epot = -68.7776635784506 | etot = -48.4966725714869 +388000 ekin = 6.56667711261966 | erot = 13.4028350179168 | epot = -68.4661846989115 | etot = -48.4966725683751 +389000 ekin = 6.4452691147135 | erot = 13.4523416306507 | epot = -68.3942833609254 | etot = -48.4966726155612 +390000 ekin = 6.40022004920912 | erot = 13.5413190040259 | epot = -68.4382116193753 | etot = -48.4966725661403 +391000 ekin = 6.74670657784131 | erot = 13.6308036790081 | epot = -68.8741828739401 | etot = -48.4966726170907 +392000 ekin = 7.2705391073813 | erot = 13.5318497226518 | epot = -69.2990614444314 | etot = -48.4966726143983 +393000 ekin = 7.84211066748368 | erot = 13.3471669898704 | epot = -69.685950275308 | etot = -48.4966726179539 +394000 ekin = 8.41137168862949 | erot = 13.0851416289779 | epot = -69.9931859369659 | etot = -48.4966726193585 +395000 ekin = 8.94777378647123 | erot = 12.7509585841161 | epot = -70.1954049894802 | etot = -48.4966726188928 +396000 ekin = 9.44412388892699 | erot = 12.3562529221245 | epot = -70.2970494281421 | etot = -48.4966726170906 +397000 ekin = 9.91050995592809 | erot = 11.9175382863765 | epot = -70.3247208568255 | etot = -48.4966726145209 +398000 ekin = 10.3672265667405 | erot = 11.4545225019134 | epot = -70.3184216802706 | etot = -48.4966726116167 +399000 ekin = 10.8377881060969 | erot = 10.9888166293374 | epot = -70.3232773445268 | etot = -48.4966726090925 +400000 ekin = 11.3412083655784 | erot = 10.5421455765191 | epot = -70.3800265494431 | etot = -48.4966726073456 +401000 ekin = 11.8856989725166 | erot = 10.1353050509382 | epot = -70.5176766301186 | etot = -48.4966726066638 +402000 ekin = 12.4648693384578 | erot = 9.78704273787232 | epot = -70.7485846834432 | etot = -48.4966726071131 +403000 ekin = 13.0574032172325 | erot = 9.5128760737579 | epot = -71.0669518996327 | etot = -48.4966726086423 +404000 ekin = 13.62915634253 | erot = 9.32384163730287 | epot = -71.4496705902163 | etot = -48.4966726103835 +405000 ekin = 14.1398204789976 | erot = 9.22499609598332 | epot = -71.8614891889854 | etot = -48.4966726140045 +406000 ekin = 14.5379075449307 | erot = 9.214739936244 | epot = -72.2493200997808 | etot = -48.4966726186061 +407000 ekin = 14.7678000074139 | erot = 9.28285845908595 | epot = -72.5473310902443 | etot = -48.4966726237445 +408000 ekin = 14.7748392328133 | erot = 9.41288741277312 | epot = -72.6843992736487 | etot = -48.4966726280623 +409000 ekin = 14.5211191200334 | erot = 9.58494933065888 | epot = -72.6027410803731 | etot = -48.4966726296808 +410000 ekin = 14.0080722078323 | erot = 9.780506516484 | epot = -72.2852513516104 | etot = -48.4966726272942 +411000 ekin = 13.2885633490821 | erot = 9.98745844074488 | epot = -71.7726944110176 | etot = -48.4966726211907 +412000 ekin = 12.4602105802628 | erot = 10.2020245096471 | epot = -71.1589077031306 | etot = -48.4966726132206 +413000 ekin = 11.6411968847745 | erot = 10.4265056500176 | epot = -70.5643751405642 | etot = -48.4966726057721 +414000 ekin = 10.9403488034793 | erot = 10.6647067440041 | epot = -70.1017281481897 | etot = -48.4966726007063 +415000 ekin = 10.4337835958954 | erot = 10.9176175688985 | epot = -69.8480737636843 | etot = -48.4966725988903 +416000 ekin = 10.1537726116244 | erot = 11.1808649833009 | epot = -69.8313101952265 | etot = -48.4966726003011 +417000 ekin = 10.0887098231028 | erot = 11.4440532452132 | epot = -70.0294356728343 | etot = -48.4966726045183 +418000 ekin = 10.1900748296408 | erot = 11.6914864860004 | epot = -70.3782339258458 | etot = -48.4966726102046 +419000 ekin = 10.3882021396926 | erot = 11.9042621356366 | epot = -70.7891368916753 | etot = -48.4966726163462 +420000 ekin = 10.6068294649483 | erot = 12.0629207258313 | epot = -71.1664228124895 | etot = -48.4966726217099 +421000 ekin = 10.7783620216856 | erot = 12.1507790873647 | epot = -71.4258137343316 | etot = -48.4966726252813 +422000 ekin = 10.8559244969741 | erot = 12.157227583968 | epot = -71.5098247075273 | etot = -48.4966726265852 +423000 ekin = 10.8187145658756 | erot = 12.0798940410381 | epot = -71.3952812326911 | etot = -48.4966726257774 +424000 ekin = 10.6702271597672 | erot = 11.9248162769271 | epot = -71.0917160600862 | etot = -48.4966726233918 +425000 ekin = 10.432682376079 | erot = 11.7046834731879 | epot = -70.634038469227 | etot = -48.49667261996 +426000 ekin = 10.1418512279923 | erot = 11.4360680199872 | epot = -70.0745918638435 | etot = -48.4966726158641 +427000 ekin = 9.84290131620358 | erot = 11.1364780215289 | epot = -69.4760519492654 | etot = -48.4966726115329 +428000 ekin = 9.58662756132271 | erot = 10.8219607622248 | epot = -68.9052609309321 | etot = -48.4966726073846 +429000 ekin = 9.42385367701729 | erot = 10.5054247282245 | epot = -68.425951009597 | etot = -48.4966726043552 +430000 ekin = 9.39326971066484 | erot = 10.1945970633525 | epot = -68.0845393772879 | etot = -48.4966726032706 +431000 ekin = 9.51026104609048 | erot = 9.89118956778029 | epot = -67.8981232184479 | etot = -48.4966726045772 +432000 ekin = 9.76020464993469 | erot = 9.59158522244582 | epot = -67.8484624803373 | etot = -48.4966726079568 +433000 ekin = 10.1011132166032 | erot = 9.28935747992221 | epot = -67.8871433087259 | etot = -48.4966726122005 +434000 ekin = 10.4772946453592 | erot = 8.97915707057065 | epot = -67.953124331572 | etot = -48.4966726156421 +435000 ekin = 10.8390965471279 | erot = 8.66047090163762 | epot = -67.9962400658339 | etot = -48.4966726170684 +436000 ekin = 11.1581846565891 | erot = 8.3392707492989 | epot = -67.9941280217496 | etot = -48.4966726158617 +437000 ekin = 11.4322684558167 | erot = 8.02673002727517 | epot = -67.9556710974744 | etot = -48.4966726143825 +438000 ekin = 11.667172080674 | erot = 7.73476573347702 | epot = -67.8986104279902 | etot = -48.4966726138391 +439000 ekin = 11.8579368223507 | erot = 7.47155579534428 | epot = -67.8261652326396 | etot = -48.4966726149446 +440000 ekin = 11.9818235336974 | erot = 7.23965689696261 | epot = -67.7181530477202 | etot = -48.4966726170602 +441000 ekin = 12.0063643091956 | erot = 7.03716778990077 | epot = -67.5402047178279 | etot = -48.4966726187316 +442000 ekin = 11.9008309355903 | erot = 6.85995053951222 | epot = -67.2574540950028 | etot = -48.4966726199003 +443000 ekin = 11.6372457710069 | erot = 6.70222774768632 | epot = -66.8361461367792 | etot = -48.496672618086 +444000 ekin = 11.2404935703067 | erot = 6.56274006493714 | epot = -66.2999062491787 | etot = -48.4966726139348 +445000 ekin = 10.7717210496791 | erot = 6.44292159848536 | epot = -65.7113152554569 | etot = -48.4966726072924 +446000 ekin = 10.3146345399971 | erot = 6.34495994126715 | epot = -65.1562670843461 | etot = -48.4966726030818 +447000 ekin = 9.93895886679998 | erot = 6.27103072197052 | epot = -64.7066621875731 | etot = -48.4966725988026 +448000 ekin = 9.70550645608578 | erot = 6.22337425450189 | epot = -64.4255533068205 | etot = -48.4966725962328 +449000 ekin = 9.65303357368844 | erot = 6.20344657438156 | epot = -64.3531527440187 | etot = -48.4966725959487 +450000 ekin = 9.78741215229977 | erot = 6.2110055622371 | epot = -64.4950903141346 | etot = -48.4966725995977 +451000 ekin = 10.0726697695314 | erot = 6.24121610507662 | epot = -64.8105584783937 | etot = -48.4966726037857 +452000 ekin = 10.4498627201613 | erot = 6.28789558017872 | epot = -65.2344309085489 | etot = -48.4966726082089 +453000 ekin = 10.8573529820916 | erot = 6.34427199361566 | epot = -65.6982975880137 | etot = -48.4966726123064 +454000 ekin = 11.2383729595004 | erot = 6.40217211179823 | epot = -66.1372176874595 | etot = -48.4966726161609 +455000 ekin = 11.5411597564324 | erot = 6.45158842061081 | epot = -66.4894207971864 | etot = -48.4966726201432 +456000 ekin = 11.7145965069649 | erot = 6.4809593201101 | epot = -66.6922284512886 | etot = -48.4966726242136 +457000 ekin = 11.7080889257685 | erot = 6.4790494806095 | epot = -66.6838110338662 | etot = -48.4966726274882 +458000 ekin = 11.4817974385095 | erot = 6.43838338687774 | epot = -66.4168534538014 | etot = -48.4966726284142 +459000 ekin = 11.0260461729846 | erot = 6.35890594746662 | epot = -65.8816247459421 | etot = -48.4966726254909 +460000 ekin = 10.3811213891568 | erot = 6.25005112058627 | epot = -65.1278451279094 | etot = -48.4966726181663 +461000 ekin = 9.645004007251 | erot = 6.13001722353708 | epot = -64.2716938384256 | etot = -48.4966726076375 +462000 ekin = 8.96155334211992 | erot = 6.02325653342169 | epot = -63.4814824659819 | etot = -48.4966725904403 +463000 ekin = 8.49356022965856 | erot = 5.96064229272574 | epot = -62.9508751084221 | etot = -48.4966725860378 +464000 ekin = 8.31098322700801 | erot = 5.95399558727495 | epot = -62.7616514011101 | etot = -48.4966725868272 +465000 ekin = 8.41527289817271 | erot = 6.00555163247446 | epot = -62.9174971228056 | etot = -48.4966725921584 +466000 ekin = 8.74071951180857 | erot = 6.10745202461889 | epot = -63.3448441360501 | etot = -48.4966725996226 +467000 ekin = 8.8864065486669 | erot = 6.32601497544667 | epot = -63.7090940528194 | etot = -48.4966725287058 +468000 ekin = 9.07505160348781 | erot = 6.75512448014557 | epot = -64.3268486409024 | etot = -48.496672557269 +469000 ekin = 9.43618930734023 | erot = 6.98018590412308 | epot = -64.9130477258384 | etot = -48.4966725143751 +470000 ekin = 9.53891928920126 | erot = 7.05614003958624 | epot = -65.091731842129 | etot = -48.4966725133415 +471000 ekin = 9.47129866753448 | erot = 7.09012582281433 | epot = -65.0580969997056 | etot = -48.4966725093568 +472000 ekin = 9.2921903929762 | erot = 7.08038845065489 | epot = -64.8692513475735 | etot = -48.4966725039424 +473000 ekin = 9.07859106352921 | erot = 7.03223766268143 | epot = -64.6075012244862 | etot = -48.4966724982756 +474000 ekin = 8.90859119080075 | erot = 6.95657374548138 | epot = -64.3618374293708 | etot = -48.4966724930887 +475000 ekin = 8.85085237799473 | erot = 6.86788557833288 | epot = -64.2154104452115 | etot = -48.4966724888839 +476000 ekin = 8.95844704218284 | erot = 6.78173938273948 | epot = -64.2368589109303 | etot = -48.496672486008 +477000 ekin = 9.2644564286688 | erot = 6.71235576621399 | epot = -64.4734846831893 | etot = -48.4966724883065 +478000 ekin = 9.75673758778777 | erot = 6.67310243752362 | epot = -64.9265125144516 | etot = -48.4966724891402 +479000 ekin = 10.4083719413681 | erot = 6.67104131555415 | epot = -65.5760857487059 | etot = -48.4966724917836 +480000 ekin = 11.178638769262 | erot = 6.70609770630459 | epot = -66.3814089720533 | etot = -48.4966724964866 +481000 ekin = 11.955017983466 | erot = 6.7757371292224 | epot = -67.22742764226 | etot = -48.4966725295717 +482000 ekin = 12.1969877155843 | erot = 6.9718210159753 | epot = -67.665481132394 | etot = -48.4966724008345 +483000 ekin = 12.8315687002499 | erot = 7.27453378452712 | epot = -68.6027750199974 | etot = -48.4966725352203 +484000 ekin = 13.1379089548664 | erot = 7.35121017886252 | epot = -68.9857915492807 | etot = -48.4966724155518 +485000 ekin = 13.1455744815507 | erot = 7.3913203100864 | epot = -69.033567208332 | etot = -48.4966724166949 +486000 ekin = 12.8847677060002 | erot = 7.41820327753848 | epot = -68.7996433974538 | etot = -48.4966724139151 +487000 ekin = 12.3995023295787 | erot = 7.43730294201701 | epot = -68.3334776794578 | etot = -48.4966724078621 +488000 ekin = 11.7801246298361 | erot = 7.45872842910054 | epot = -67.7355254588077 | etot = -48.496672399871 +489000 ekin = 11.1454971167096 | erot = 7.49387389625014 | epot = -67.1360434047318 | etot = -48.4966723917721 +490000 ekin = 10.6174118656957 | erot = 7.55177149144182 | epot = -66.6658557429297 | etot = -48.4966723857921 +491000 ekin = 10.2893788237472 | erot = 7.63548116164754 | epot = -66.421532369588 | etot = -48.4966723841933 +492000 ekin = 10.1956274376079 | erot = 7.73922358370761 | epot = -66.4315234096592 | etot = -48.4966723883437 +493000 ekin = 10.2924671649501 | erot = 7.84793186663804 | epot = -66.6370714291378 | etot = -48.4966723975496 +494000 ekin = 10.4668249564047 | erot = 7.94111684625574 | epot = -66.9046142110857 | etot = -48.4966724084252 +495000 ekin = 10.5791383441902 | erot = 8.00124026343994 | epot = -67.0770510235029 | etot = -48.4966724158728 +496000 ekin = 10.5277635544026 | erot = 8.02342438970481 | epot = -67.0478603599964 | etot = -48.496672415889 +497000 ekin = 10.3008638581338 | erot = 8.02081822152689 | epot = -66.8183544878886 | etot = -48.496672408228 +498000 ekin = 9.98303008285126 | erot = 8.02168645223716 | epot = -66.5013889316258 | etot = -48.4966723965374 +499000 ekin = 9.71342589188279 | erot = 8.05962720415388 | epot = -66.2697254819054 | etot = -48.4966723858687 +500000 ekin = 9.62351689111993 | erot = 8.16244515238151 | epot = -66.2826344234889 | etot = -48.4966723799875 +501000 ekin = 9.78787333396133 | erot = 8.34447303671244 | epot = -66.6290187508761 | etot = -48.4966723802023 +502000 ekin = 10.2050108702547 | erot = 8.6037048525824 | epot = -67.3053881086344 | etot = -48.4966723857973 +503000 ekin = 10.8051989674815 | erot = 8.92246829122841 | epot = -68.2243396539195 | etot = -48.4966723952096 +504000 ekin = 11.4710453970551 | erot = 9.26984220622738 | epot = -69.2375600102568 | etot = -48.4966724069743 +505000 ekin = 12.0583532743051 | erot = 9.60506055563649 | epot = -70.1600862495841 | etot = -48.4966724196425 +506000 ekin = 12.4169616299833 | erot = 9.88273601247277 | epot = -70.796370073167 | etot = -48.4966724307109 +507000 ekin = 12.4225762032897 | erot = 10.0614429671731 | epot = -70.9806916066885 | etot = -48.4966724362257 +508000 ekin = 12.0224546478147 | erot = 10.1150484290289 | epot = -70.634175509719 | etot = -48.4966724328754 +509000 ekin = 11.2713256108322 | erot = 10.0417150355121 | epot = -69.8097130672669 | etot = -48.4966724209226 +510000 ekin = 10.3259224264659 | erot = 9.86440101433983 | epot = -68.6869958452246 | etot = -48.4966724044189 +511000 ekin = 9.39566767794845 | erot = 9.62224126640847 | epot = -67.5145813329448 | etot = -48.4966723885879 +512000 ekin = 8.67739606863532 | erot = 9.3582345202646 | epot = -66.5323029667131 | etot = -48.4966723778132 +513000 ekin = 8.30173505002016 | erot = 9.10874451686367 | epot = -65.907151940734 | etot = -48.4966723738502 +514000 ekin = 8.31133758542276 | erot = 8.90213046048018 | epot = -65.7101404213344 | etot = -48.4966723754314 +515000 ekin = 8.65105183703162 | erot = 8.75142823022383 | epot = -65.8991524514168 | etot = -48.4966723841614 +516000 ekin = 9.19545504802738 | erot = 8.6502059078921 | epot = -66.3423333511625 | etot = -48.496672395243 +517000 ekin = 9.7894801348344 | erot = 8.58459334665713 | epot = -66.8707458886812 | etot = -48.4966724071896 +518000 ekin = 10.2719405203476 | erot = 8.53610767676887 | epot = -67.3047206152534 | etot = -48.496672418137 +519000 ekin = 10.503561904012 | erot = 8.48509741611018 | epot = -67.4853317484724 | etot = -48.4966724283503 +520000 ekin = 10.3837804905294 | erot = 8.41855293461474 | epot = -67.2990058538689 | etot = -48.4966724287248 +521000 ekin = 9.91971480318631 | erot = 8.33012920358482 | epot = -66.7465164260311 | etot = -48.4966724192599 +522000 ekin = 9.25580910208737 | erot = 8.22471517243627 | epot = -65.9771966778249 | etot = -48.4966724033013 +523000 ekin = 8.61677254374638 | erot = 8.11873116214327 | epot = -65.2321760933171 | etot = -48.4966723874275 +524000 ekin = 8.22312599625895 | erot = 8.03533827060582 | epot = -64.7551366426722 | etot = -48.4966723758074 +525000 ekin = 8.23096919100507 | erot = 7.99952905911197 | epot = -64.7271706204061 | etot = -48.4966723702891 +526000 ekin = 8.70541343274283 | erot = 8.03327780735268 | epot = -65.2353636116848 | etot = -48.4966723715893 +527000 ekin = 9.61054447390767 | erot = 8.14859195675917 | epot = -66.2558088113888 | etot = -48.496672380722 +528000 ekin = 10.8064190210713 | erot = 8.34203048709499 | epot = -67.6451219043045 | etot = -48.4966723961382 +529000 ekin = 12.074894702288 | erot = 8.593011410005 | epot = -69.164578526047 | etot = -48.496672413754 +530000 ekin = 13.177289905511 | erot = 8.86731230206088 | epot = -70.5412746358855 | etot = -48.4966724283136 +531000 ekin = 13.9222479331122 | erot = 9.12596646770331 | epot = -71.5448868368323 | etot = -48.4966724360168 +532000 ekin = 14.2109040111186 | erot = 9.33621159855988 | epot = -72.0437880461509 | etot = -48.4966724364724 +533000 ekin = 14.03934960496 | erot = 9.47948522973857 | epot = -72.0155072660371 | etot = -48.4966724313386 +534000 ekin = 13.4765937111696 | erot = 9.55437050364981 | epot = -71.5276366365961 | etot = -48.4966724217767 +535000 ekin = 12.6476855099239 | erot = 9.57521298729339 | epot = -70.719570906088 | etot = -48.4966724088707 +536000 ekin = 11.7187499511252 | erot = 9.56662150347728 | epot = -69.782043849765 | etot = -48.4966723951626 +537000 ekin = 10.8667161280631 | erot = 9.55558575452886 | epot = -68.9189742663218 | etot = -48.4966723837298 +538000 ekin = 10.2407642555984 | erot = 9.56460479407725 | epot = -68.3020414264008 | etot = -48.4966723767251 +539000 ekin = 9.93256310304282 | erot = 9.60813474980997 | epot = -68.0373702277795 | etot = -48.4966723749267 +540000 ekin = 9.96635059453905 | erot = 9.69366995175983 | epot = -68.1566929214946 | etot = -48.4966723751957 +541000 ekin = 10.3033434565407 | erot = 9.8245277345196 | epot = -68.6245435736411 | etot = -48.4966723825808 +542000 ekin = 10.8374546470991 | erot = 9.99210203730023 | epot = -69.3262290764191 | etot = -48.4966723920197 +543000 ekin = 11.4320363085197 | erot = 10.1839460986223 | epot = -70.112654808752 | etot = -48.49667240161 +544000 ekin = 11.9481549487224 | erot = 10.3868550357396 | epot = -70.8316823940766 | etot = -48.4966724096146 +545000 ekin = 12.2696023021453 | erot = 10.5892508891687 | epot = -71.355525606049 | etot = -48.496672414735 +546000 ekin = 12.3217483706317 | erot = 10.7831241362942 | epot = -71.6015449232215 | etot = -48.4966724162956 +547000 ekin = 12.081509089866 | erot = 10.9652333442778 | epot = -71.5434148484535 | etot = -48.4966724143097 +548000 ekin = 11.5772594483449 | erot = 11.1370572249196 | epot = -71.2109890828336 | etot = -48.4966724095691 +549000 ekin = 10.8796146423279 | erot = 11.302741530119 | epot = -70.6790285756037 | etot = -48.4966724031568 +550000 ekin = 10.0861650600912 | erot = 11.4673420616849 | epot = -70.0501795180752 | etot = -48.4966723962991 +551000 ekin = 9.30420856259773 | erot = 11.634606251307 | epot = -69.4354872039898 | etot = -48.496672390085 +552000 ekin = 8.63456852526814 | erot = 11.8051739021451 | epot = -68.9364148128166 | etot = -48.4966723854034 +553000 ekin = 8.15765857157046 | erot = 11.9755314527545 | epot = -68.6298624072797 | etot = -48.4966723829548 +554000 ekin = 7.92204387539979 | erot = 12.1379035109624 | epot = -68.5566197695225 | etot = -48.4966723831603 +555000 ekin = 7.93668594973216 | erot = 12.2813102396174 | epot = -68.7146685753788 | etot = -48.4966723860292 +556000 ekin = 8.16908147835047 | erot = 12.3937793343126 | epot = -69.059533203634 | etot = -48.4966723909709 +557000 ekin = 8.55144497224257 | erot = 12.4654791728174 | epot = -69.5135965419306 | etot = -48.4966723968706 +558000 ekin = 8.99506879129248 | erot = 12.4919043884456 | epot = -69.9836455820569 | etot = -48.4966724023188 +559000 ekin = 9.40988612193456 | erot = 12.4759637500203 | epot = -70.3825222780999 | etot = -48.4966724061451 +560000 ekin = 9.72239125486885 | erot = 12.4279361390898 | epot = -70.6469998019808 | etot = -48.4966724080221 +561000 ekin = 9.88412985930847 | erot = 12.3629252843479 | epot = -70.7437275520998 | etot = -48.4966724084435 +562000 ekin = 9.87014392585068 | erot = 12.2969140239501 | epot = -70.6637303577301 | etot = -48.4966724079293 +563000 ekin = 9.67269052976824 | erot = 12.2435461742289 | epot = -70.4129091123746 | etot = -48.4966724083774 +564000 ekin = 9.29561869654335 | erot = 12.2123745870678 | epot = -70.0046656891709 | etot = -48.4966724055598 +565000 ekin = 8.77967610188736 | erot = 12.2075615848959 | epot = -69.4839100879458 | etot = -48.4966724011626 +566000 ekin = 8.19459477305683 | erot = 12.2284388471579 | epot = -68.9197060161937 | etot = -48.4966723959789 +567000 ekin = 7.62573923576375 | erot = 12.2693533996009 | epot = -68.3917650267332 | etot = -48.4966723913686 +568000 ekin = 7.1540405418275 | erot = 12.3199400383551 | epot = -67.9706529686644 | etot = -48.4966723884818 +569000 ekin = 6.83717313923576 | erot = 12.3666389683348 | epot = -67.7004844953262 | etot = -48.4966723877556 +570000 ekin = 6.69956781471509 | erot = 12.395512588354 | epot = -67.5917527919448 | etot = -48.4966723888758 +571000 ekin = 6.73320809607387 | erot = 12.3955019362998 | epot = -67.6253824234367 | etot = -48.496672391063 +572000 ekin = 6.90669043395716 | erot = 12.3609011894105 | epot = -67.7642640154729 | etot = -48.4966723921052 +573000 ekin = 7.18429647827011 | erot = 12.2951299554893 | epot = -67.976098828917 | etot = -48.4966723951576 +574000 ekin = 7.52006639760762 | erot = 12.2050646486002 | epot = -68.2218034429552 | etot = -48.4966723967474 +575000 ekin = 7.87441000635079 | erot = 12.0985403158716 | epot = -68.4696227188286 | etot = -48.4966723966062 +576000 ekin = 8.23152231491051 | erot = 11.986305371123 | epot = -68.714500081168 | etot = -48.4966723951345 +577000 ekin = 8.59621090785601 | erot = 11.8802945474195 | epot = -68.9731778483469 | etot = -48.4966723930714 +578000 ekin = 8.98550446113749 | erot = 11.7917589254008 | epot = -69.2739357776107 | etot = -48.4966723910724 +579000 ekin = 9.42040764628024 | erot = 11.7296557360612 | epot = -69.6467357718763 | etot = -48.4966723895348 +580000 ekin = 9.92026928431491 | erot = 11.6994636247578 | epot = -70.1164052980429 | etot = -48.4966723889702 +581000 ekin = 10.4812356258575 | erot = 11.703677625259 | epot = -70.6815856415275 | etot = -48.496672390411 +582000 ekin = 11.0803741505447 | erot = 11.7381628956607 | epot = -71.3152094398488 | etot = -48.4966723936434 +583000 ekin = 11.6832905431688 | erot = 11.789805158158 | epot = -71.9697681008392 | etot = -48.4966723995124 +584000 ekin = 12.2265963016612 | erot = 11.8360805991666 | epot = -72.5593493091893 | etot = -48.4966724083615 +585000 ekin = 12.6146924453256 | erot = 11.8453302035176 | epot = -72.9566950678144 | etot = -48.4966724189713 +586000 ekin = 12.7381776542714 | erot = 11.7813880280281 | epot = -73.0162381105139 | etot = -48.4966724282144 +587000 ekin = 12.5064805858531 | erot = 11.6131474320443 | epot = -72.6163004503738 | etot = -48.4966724324764 +588000 ekin = 11.8864734315354 | erot = 11.3251009525692 | epot = -71.7082468122181 | etot = -48.4966724281136 +589000 ekin = 10.9473869135865 | erot = 10.9235098587313 | epot = -70.3675691878643 | etot = -48.4966724155465 +590000 ekin = 9.8603569687158 | erot = 10.4344934450019 | epot = -68.7915228117525 | etot = -48.4966723980348 +591000 ekin = 8.85631509729197 | erot = 9.89621562656566 | epot = -67.2492031047675 | etot = -48.4966723809099 +592000 ekin = 8.15513077390852 | erot = 9.34935781093818 | epot = -66.0011609547222 | etot = -48.4966723698755 +593000 ekin = 7.8886066686561 | erot = 8.82965609782248 | epot = -65.2149351345734 | etot = -48.4966723680948 +594000 ekin = 8.05760926838463 | erot = 8.36349649524626 | epot = -64.9177781380018 | etot = -48.4966723743709 +595000 ekin = 8.55177999820547 | erot = 7.96715997630488 | epot = -65.0156123582395 | etot = -48.4966723837292 +596000 ekin = 9.20240795646935 | erot = 7.64971555626626 | epot = -65.3487959079192 | etot = -48.4966723951836 +597000 ekin = 9.82563991120174 | erot = 7.41365255179059 | epot = -65.7359648663368 | etot = -48.4966724033444 +598000 ekin = 10.2831958981737 | erot = 7.25474571557566 | epot = -66.0346140228186 | etot = -48.4966724090693 +599000 ekin = 10.482354848241 | erot = 7.16384844604204 | epot = -66.1428757065455 | etot = -48.4966724122625 +600000 ekin = 10.3776559577961 | erot = 7.12899314640775 | epot = -66.003321516627 | etot = -48.4966724124232 +601000 ekin = 9.97447570398641 | erot = 7.13881295944498 | epot = -65.609961072411 | etot = -48.4966724089796 +602000 ekin = 9.33239148590697 | erot = 7.18604650079972 | epot = -65.0151103886242 | etot = -48.4966724019175 +603000 ekin = 8.56059728310519 | erot = 7.26939823178089 | epot = -64.3266679073028 | etot = -48.4966723924168 +604000 ekin = 7.79844425920136 | erot = 7.39226229323277 | epot = -63.687378935498 | etot = -48.4966723830639 +605000 ekin = 7.18334355706252 | erot = 7.5587573348131 | epot = -63.2387732679006 | etot = -48.4966723760249 +606000 ekin = 6.82339792277614 | erot = 7.77079572205225 | epot = -63.0908660164404 | etot = -48.496672371612 +607000 ekin = 6.78106761293196 | erot = 8.02640715105649 | epot = -63.304147135455 | etot = -48.4966723714665 +608000 ekin = 7.06650520941636 | erot = 8.31925929522833 | epot = -63.8824368788021 | etot = -48.4966723741574 +609000 ekin = 7.64869014778026 | erot = 8.6406373788116 | epot = -64.7859999055606 | etot = -48.4966723789688 +610000 ekin = 8.45880674199481 | erot = 8.97898134765573 | epot = -65.9344604773792 | etot = -48.4966723877287 +611000 ekin = 9.40012632079646 | erot = 9.32028280858585 | epot = -67.2170815245449 | etot = -48.4966723951626 +612000 ekin = 10.372486444167 | erot = 9.65110388606836 | epot = -68.520262733295 | etot = -48.4966724030596 +613000 ekin = 11.2738822446324 | erot = 9.95564408209938 | epot = -69.7261987373353 | etot = -48.4966724106034 +614000 ekin = 12.0134738011361 | erot = 10.2166935700791 | epot = -70.7268397869989 | etot = -48.4966724157837 +615000 ekin = 12.5325228236193 | erot = 10.4217069667446 | epot = -71.4509022073077 | etot = -48.4966724169438 +616000 ekin = 12.825829471173 | erot = 10.5664745452712 | epot = -71.8889764296329 | etot = -48.4966724131887 +617000 ekin = 12.9484167494881 | erot = 10.6576196900895 | epot = -72.1027088453135 | etot = -48.4966724057359 +618000 ekin = 12.9984754660186 | erot = 10.7112673341617 | epot = -72.2064151974673 | etot = -48.4966723972869 +619000 ekin = 13.0833633892504 | erot = 10.7483523556568 | epot = -72.3283881359066 | etot = -48.4966723909994 +620000 ekin = 13.2805224347085 | erot = 10.7880868966295 | epot = -72.5652817201818 | etot = -48.4966723888438 +621000 ekin = 13.6153158271335 | erot = 10.8424788949131 | epot = -72.954467112884 | etot = -48.4966723908374 +622000 ekin = 14.0617052046194 | erot = 10.9128304449266 | epot = -73.4712080456802 | etot = -48.4966723961342 +623000 ekin = 14.5562524524307 | erot = 10.9888554748175 | epot = -74.0417803306096 | etot = -48.4966724033615 +624000 ekin = 15.0184966480745 | erot = 11.0501520933759 | epot = -74.5653211520102 | etot = -48.4966724105598 +625000 ekin = 15.374006744184 | erot = 11.0719318061442 | epot = -74.9426109654702 | etot = -48.496672415142 +626000 ekin = 15.5799785500752 | erot = 11.0340258807614 | epot = -75.1106768463473 | etot = -48.4966724155108 +627000 ekin = 15.638740686841 | erot = 10.9274345484131 | epot = -75.0628476476207 | etot = -48.4966724123666 +628000 ekin = 15.5850466430001 | erot = 10.7544368612038 | epot = -74.8361559130623 | etot = -48.4966724088584 +629000 ekin = 15.4527585940654 | erot = 10.522207406829 | epot = -74.4716384083982 | etot = -48.4966724075037 +630000 ekin = 15.2487640712961 | erot = 10.2369904052399 | epot = -73.9824268848523 | etot = -48.4966724083164 +631000 ekin = 14.954630859851 | erot = 9.9035059260959 | epot = -73.3548091954574 | etot = -48.4966724095105 +632000 ekin = 14.5471297167831 | erot = 9.52778248753166 | epot = -72.5715846136179 | etot = -48.4966724093032 +633000 ekin = 14.0259983537531 | erot = 9.11935081543026 | epot = -71.6420215736341 | etot = -48.4966724044507 +634000 ekin = 13.434893448857 | erot = 8.69195919080616 | epot = -70.6235250390008 | etot = -48.4966723993376 +635000 ekin = 12.8248958276813 | erot = 8.26734491141948 | epot = -69.5889131330689 | etot = -48.4966723939681 +636000 ekin = 12.2634798859135 | erot = 7.86620866042701 | epot = -68.6263609335985 | etot = -48.496672387258 +637000 ekin = 11.8378305092479 | erot = 7.50870022727772 | epot = -67.8432031169467 | etot = -48.496672380421 +638000 ekin = 11.6379266195945 | erot = 7.21309192660197 | epot = -67.3476909220984 | etot = -48.496672375902 +639000 ekin = 11.7309756692676 | erot = 6.9935850958859 | epot = -67.2212331387219 | etot = -48.4966723735684 +640000 ekin = 12.1483860993111 | erot = 6.85513197124742 | epot = -67.5001904465738 | etot = -48.4966723760153 +641000 ekin = 12.8580389630882 | erot = 6.79197676462279 | epot = -68.1466881105606 | etot = -48.4966723828496 +642000 ekin = 13.767624186513 | erot = 6.78663459553832 | epot = -69.0509311760037 | etot = -48.4966723939524 +643000 ekin = 14.7311148046468 | erot = 6.81269225388644 | epot = -70.0404794653527 | etot = -48.4966724068195 +644000 ekin = 15.5770857379193 | erot = 6.83998967566507 | epot = -70.9137478318837 | etot = -48.4966724182993 +645000 ekin = 16.1508405484789 | erot = 6.84150218311769 | epot = -71.4890151570364 | etot = -48.4966724254398 +646000 ekin = 16.3517339376772 | erot = 6.79972807946899 | epot = -71.6481344439803 | etot = -48.4966724268342 +647000 ekin = 16.1521813974457 | erot = 6.71011075270204 | epot = -71.3589645730051 | etot = -48.4966724228573 +648000 ekin = 15.5941452914098 | erot = 6.58036041645482 | epot = -70.6711781230536 | etot = -48.496672415189 +649000 ekin = 14.7689091850159 | erot = 6.42695236567124 | epot = -69.6925339566958 | etot = -48.4966724060086 +650000 ekin = 13.7897851521548 | erot = 6.27009414201309 | epot = -68.5565516914091 | etot = -48.4966723972413 +651000 ekin = 12.7827854663786 | erot = 6.12965793177462 | epot = -67.409115783844 | etot = -48.4966723856907 +652000 ekin = 11.8480628892552 | erot = 6.02011822002166 | epot = -66.3648534921166 | etot = -48.4966723828397 +653000 ekin = 11.0202985972919 | erot = 5.94865375220468 | epot = -65.465624731493 | etot = -48.4966723819965 +654000 ekin = 10.3091031180503 | erot = 5.91728137261365 | epot = -64.7230568731607 | etot = -48.4966723824968 +655000 ekin = 9.70839056864199 | erot = 5.92392072345228 | epot = -64.1289836756226 | etot = -48.4966723835284 +656000 ekin = 9.20726106546127 | erot = 5.96375787147846 | epot = -63.6676913212765 | etot = -48.4966723843368 +657000 ekin = 8.80019228929313 | erot = 6.03073521932157 | epot = -63.3275998929669 | etot = -48.4966723843521 +658000 ekin = 8.49429330435421 | erot = 6.11901386846824 | epot = -63.1099795561543 | etot = -48.4966723833319 +659000 ekin = 8.31163970837388 | erot = 6.22415392584487 | epot = -63.0324660157173 | etot = -48.4966723814985 +660000 ekin = 8.2857168726607 | erot = 6.34359481939331 | epot = -63.1259840714867 | etot = -48.4966723794327 +661000 ekin = 8.45063623879217 | erot = 6.47625697344822 | epot = -63.4235655907463 | etot = -48.4966723785059 +662000 ekin = 8.82527447336867 | erot = 6.62126989852133 | epot = -63.9432167515224 | etot = -48.4966723796324 +663000 ekin = 9.37687400888537 | erot = 6.77176565493101 | epot = -64.6453120552966 | etot = -48.4966723914803 +664000 ekin = 10.0161883293663 | erot = 6.9167347170585 | epot = -65.4295954441715 | etot = -48.4966723977466 +665000 ekin = 10.6568075639073 | erot = 7.05202630068255 | epot = -66.2055062687951 | etot = -48.4966724042053 +666000 ekin = 11.2095129989439 | erot = 7.17560031612115 | epot = -66.8817857236717 | etot = -48.4966724086066 +667000 ekin = 11.6073208200519 | erot = 7.28956566879928 | epot = -67.3935588983753 | etot = -48.4966724095241 +668000 ekin = 11.8262434819787 | erot = 7.40047545934628 | epot = -67.7233913482482 | etot = -48.4966724069232 +669000 ekin = 11.8877773973786 | erot = 7.51673035650595 | epot = -67.9011801561976 | etot = -48.4966724023131 +670000 ekin = 11.8402449207958 | erot = 7.64485197463754 | epot = -67.9817692948627 | etot = -48.4966723994295 +671000 ekin = 11.7215972610062 | erot = 7.78648852076395 | epot = -68.0047581793401 | etot = -48.49667239757 +672000 ekin = 11.5567362169503 | erot = 7.94128453336362 | epot = -67.9946931468371 | etot = -48.4966723965231 +673000 ekin = 11.3570416456716 | erot = 8.10916533388291 | epot = -67.9628793756527 | etot = -48.4966723960982 +674000 ekin = 11.1259919204572 | erot = 8.29215560394995 | epot = -67.9148199188207 | etot = -48.4966723944136 +675000 ekin = 10.8743945882945 | erot = 8.49470509397004 | epot = -67.8657720761146 | etot = -48.49667239385 +676000 ekin = 10.6087709731309 | erot = 8.72185603056474 | epot = -67.8272993965002 | etot = -48.4966723928045 +677000 ekin = 10.3411925528822 | erot = 8.97814779631624 | epot = -67.8160127410913 | etot = -48.4966723918928 +678000 ekin = 10.0860835583249 | erot = 9.26516881807783 | epot = -67.8479247680228 | etot = -48.4966723916201 +679000 ekin = 9.85460690263328 | erot = 9.57959119584002 | epot = -67.9308704906876 | etot = -48.4966723922143 +680000 ekin = 9.65193484596328 | erot = 9.91222749431411 | epot = -68.0608347338678 | etot = -48.4966723935904 +681000 ekin = 9.4777867402786 | erot = 10.2481668374404 | epot = -68.2226259731627 | etot = -48.4966723954437 +682000 ekin = 9.32915693377952 | erot = 10.5680491155029 | epot = -68.3938784466551 | etot = -48.4966723973727 +683000 ekin = 9.20359209967432 | erot = 10.8502901107227 | epot = -68.5505546094478 | etot = -48.4966723990507 +684000 ekin = 9.10057910407447 | erot = 11.0738485406611 | epot = -68.6711000473925 | etot = -48.4966724026569 +685000 ekin = 9.00949165129753 | erot = 11.2173796936166 | epot = -68.7235437496512 | etot = -48.4966724047371 +686000 ekin = 8.91345829616017 | erot = 11.2659265088162 | epot = -68.6760572116703 | etot = -48.4966724066939 +687000 ekin = 8.79289020081684 | erot = 11.2146418431984 | epot = -68.5042044522316 | etot = -48.4966724082164 +688000 ekin = 8.62699585205897 | erot = 11.0687535113927 | epot = -68.1924217719271 | etot = -48.4966724084754 +689000 ekin = 8.40629613751591 | erot = 10.8436392124157 | epot = -67.7466077562959 | etot = -48.4966724063643 +690000 ekin = 8.14912332610223 | erot = 10.5636669230698 | epot = -67.2094626503497 | etot = -48.4966724011776 +691000 ekin = 7.91246650766668 | erot = 10.2598630021587 | epot = -66.6690019031974 | etot = -48.496672393372 +692000 ekin = 7.7864973239644 | erot = 9.96636747428024 | epot = -66.2495371831641 | etot = -48.4966723849195 +693000 ekin = 7.86849983021928 | erot = 9.7157177975428 | epot = -66.0808900065901 | etot = -48.496672378828 +694000 ekin = 8.22337408804674 | erot = 9.53345750718098 | epot = -66.2535039731099 | etot = -48.4966723778822 +695000 ekin = 8.84810602165013 | erot = 9.43320257958283 | epot = -66.7779809844792 | etot = -48.4966723832463 +696000 ekin = 9.65887172621348 | erot = 9.41372191398151 | epot = -67.5692660339737 | etot = -48.4966723937787 +697000 ekin = 10.5087480397169 | erot = 9.45932512238858 | epot = -68.4647455686608 | etot = -48.4966724065554 +698000 ekin = 11.2285190596257 | erot = 9.54380480099791 | epot = -69.2689962786402 | etot = -48.4966724180166 +699000 ekin = 11.6741833073371 | erot = 9.63725123869461 | epot = -69.8081069711249 | etot = -48.4966724250932 +700000 ekin = 11.7654350678547 | erot = 9.71395728282058 | epot = -69.976064776722 | etot = -48.4966724260467 +701000 ekin = 11.5047049791839 | erot = 9.75894077513181 | epot = -69.7603181752444 | etot = -48.4966724209286 +702000 ekin = 10.9724403691924 | erot = 9.77075075389209 | epot = -69.2398635346446 | etot = -48.4966724115602 +703000 ekin = 10.3024076281298 | erot = 9.75981202354562 | epot = -68.5588920524018 | etot = -48.4966724007264 +704000 ekin = 9.64337665059165 | erot = 9.74344885685364 | epot = -67.8834978991357 | etot = -48.4966723916904 +705000 ekin = 9.11795255237604 | erot = 9.73742730827394 | epot = -67.3520522458547 | etot = -48.4966723852047 +706000 ekin = 8.8126363961415 | erot = 9.75421899371362 | epot = -67.0635277715381 | etot = -48.4966723816829 +707000 ekin = 8.77338019637888 | erot = 9.80175401579289 | epot = -67.0718065928509 | etot = -48.4966723806791 +708000 ekin = 9.01138622873006 | erot = 9.88360177688334 | epot = -67.3916603870485 | etot = -48.4966723814351 +709000 ekin = 9.507479880512 | erot = 9.99905419025802 | epot = -68.0032064567145 | etot = -48.4966723859444 +710000 ekin = 10.2098084036322 | erot = 10.1416258359394 | epot = -68.8481066302707 | etot = -48.4966723906991 +711000 ekin = 11.0523389502551 | erot = 10.2998854259334 | epot = -69.8488967730332 | etot = -48.4966723968448 +712000 ekin = 11.9521069749276 | erot = 10.4562138307596 | epot = -70.9049932107033 | etot = -48.4966724050161 +713000 ekin = 12.815046543433 | erot = 10.5882970355821 | epot = -71.9000159916048 | etot = -48.4966724125897 +714000 ekin = 13.5573027727324 | erot = 10.6741841242495 | epot = -72.728159315078 | etot = -48.4966724180961 +715000 ekin = 14.1179857011503 | erot = 10.6957124390567 | epot = -73.3103705611375 | etot = -48.4966724209306 +716000 ekin = 14.4699787528586 | erot = 10.6432681552738 | epot = -73.6099193281367 | etot = -48.4966724200043 +717000 ekin = 14.6304817623995 | erot = 10.5193699656725 | epot = -73.6465241440422 | etot = -48.4966724159702 +718000 ekin = 14.6433398088089 | erot = 10.3369378985737 | epot = -73.4769501198252 | etot = -48.4966724124426 +719000 ekin = 14.5613025266252 | erot = 10.1163044955734 | epot = -73.1742794291502 | etot = -48.4966724069517 +720000 ekin = 14.4440802768632 | erot = 9.88263320897859 | epot = -72.8233858888948 | etot = -48.496672403053 +721000 ekin = 14.3266924859882 | erot = 9.66028301159175 | epot = -72.4836478992629 | etot = -48.496672401683 +722000 ekin = 14.2082139496557 | erot = 9.46998100592359 | epot = -72.1748673584334 | etot = -48.496672402854 +723000 ekin = 14.0535356857718 | erot = 9.32739231104943 | epot = -71.8776004024297 | etot = -48.4966724056085 +724000 ekin = 13.8083025949352 | erot = 9.2428855238673 | epot = -71.5478605272106 | etot = -48.4966724084081 +725000 ekin = 13.4217406282447 | erot = 9.22217939716601 | epot = -71.1405924351186 | etot = -48.4966724097079 +726000 ekin = 12.8688682438372 | erot = 9.26761054150398 | epot = -70.6331511938425 | etot = -48.4966724085013 +727000 ekin = 12.1644185053382 | erot = 9.37972324051462 | epot = -70.0408141504884 | etot = -48.4966724046356 +728000 ekin = 11.363942609201 | erot = 9.55857934592133 | epot = -69.4191943540498 | etot = -48.4966723989274 +729000 ekin = 10.5512882155693 | erot = 9.80396099287644 | epot = -68.8519216014331 | etot = -48.4966723929874 +730000 ekin = 9.81740771774417 | erot = 10.1147074884202 | epot = -68.4287875945261 | etot = -48.4966723883617 +731000 ekin = 9.23253818728237 | erot = 10.4853428847489 | epot = -68.2145534593311 | etot = -48.4966723872998 +732000 ekin = 8.82544563448641 | erot = 10.9030046167842 | epot = -68.2251226409579 | etot = -48.4966723896873 +733000 ekin = 8.58076650753532 | erot = 11.3480140239965 | epot = -68.4254529263367 | etot = -48.4966723948048 +734000 ekin = 8.44819070663181 | erot = 11.7953928345719 | epot = -68.7402559422253 | etot = -48.4966724010216 +735000 ekin = 8.36308582601686 | erot = 12.2184265333689 | epot = -69.0781847656954 | etot = -48.4966724063097 +736000 ekin = 8.27166179429879 | erot = 12.5931737859848 | epot = -69.3615079892498 | etot = -48.4966724089662 +737000 ekin = 8.15174465756938 | erot = 12.9021375874299 | epot = -69.5505546533663 | etot = -48.4966724083671 +738000 ekin = 8.02032384037336 | erot = 13.1353976436493 | epot = -69.6523938893608 | etot = -48.4966724053382 +739000 ekin = 7.92361863165684 | erot = 13.2888871707161 | epot = -69.7091782040701 | etot = -48.4966724016972 +740000 ekin = 7.9148308910797 | erot = 13.3615962967597 | epot = -69.7730995868771 | etot = -48.4966723990377 +741000 ekin = 8.0330259007673 | erot = 13.3544079573288 | epot = -69.8841062559017 | etot = -48.4966723978055 +742000 ekin = 8.29475492773836 | erot = 13.2712680544976 | epot = -70.062695379681 | etot = -48.4966723974451 +743000 ekin = 8.69783680679613 | erot = 13.1210830215102 | epot = -70.3155922259027 | etot = -48.4966723975964 +744000 ekin = 9.22494090055528 | erot = 12.9171251058713 | epot = -70.6387384052188 | etot = -48.4966723987922 +745000 ekin = 9.83908652683635 | erot = 12.6729415303268 | epot = -71.0087004591722 | etot = -48.4966724020091 +746000 ekin = 10.4767671898614 | erot = 12.3966932528209 | epot = -71.370132850581 | etot = -48.4966724078987 +747000 ekin = 11.0446377698964 | erot = 12.0869928942754 | epot = -71.6283030800949 | etot = -48.4966724159231 +748000 ekin = 11.4295453907525 | erot = 11.7327222579966 | epot = -71.6589400729807 | etot = -48.4966724242316 +749000 ekin = 11.5234364161557 | erot = 11.317448589884 | epot = -71.3375574360207 | etot = -48.496672429981 +750000 ekin = 11.25907985386 | erot = 10.8275036110752 | epot = -70.5832558906309 | etot = -48.4966724256958 +751000 ekin = 10.6566760362235 | erot = 10.2652340949476 | epot = -69.418582551546 | etot = -48.4966724203749 +752000 ekin = 9.81046694514328 | erot = 9.64438866532819 | epot = -67.9515280183084 | etot = -48.4966724078369 +753000 ekin = 8.89134561969272 | erot = 8.99214235499747 | epot = -66.3801603663773 | etot = -48.4966723916871 +754000 ekin = 8.11027945100571 | erot = 8.34642943211771 | epot = -64.9533812595025 | etot = -48.496672376379 +755000 ekin = 7.64805178064424 | erot = 7.74709579287851 | epot = -63.8918199452063 | etot = -48.4966723716836 +756000 ekin = 7.56652741923863 | erot = 7.21880217837636 | epot = -63.2820019731369 | etot = -48.4966723755219 +757000 ekin = 7.80213473501438 | erot = 6.76780334657733 | epot = -63.0666104661334 | etot = -48.4966723845417 +758000 ekin = 8.22136828691586 | erot = 6.38824654020546 | epot = -63.1062872204421 | etot = -48.4966723933208 +759000 ekin = 8.68715060867478 | erot = 6.07044846899398 | epot = -63.254271477475 | etot = -48.4966723998062 +760000 ekin = 9.09933114499266 | erot = 5.80281618237588 | epot = -63.3988197305041 | etot = -48.4966724031356 +761000 ekin = 9.39129570577371 | erot = 5.57472170090487 | epot = -63.4626898092446 | etot = -48.496672402566 +762000 ekin = 9.56563723679221 | erot = 5.38011940085551 | epot = -63.4424290366401 | etot = -48.4966723989924 +763000 ekin = 9.67336099063757 | erot = 5.21718626711669 | epot = -63.3872196518505 | etot = -48.4966723940963 +764000 ekin = 9.78632769692617 | erot = 5.08599588210491 | epot = -63.3689959686529 | etot = -48.4966723896218 +765000 ekin = 9.96960969360812 | erot = 4.9856369884801 | epot = -63.4519190695977 | etot = -48.4966723875095 +766000 ekin = 10.2254800688571 | erot = 4.91845355420055 | epot = -63.6406060068488 | etot = -48.4966723837912 +767000 ekin = 10.5921756589939 | erot = 4.88036713450099 | epot = -63.9692151910276 | etot = -48.4966723975327 +768000 ekin = 11.0286182841544 | erot = 4.84228216956277 | epot = -64.3675728418936 | etot = -48.4966723881764 +769000 ekin = 11.5060819039612 | erot = 4.81203544038845 | epot = -64.8147897343244 | etot = -48.4966723899747 +770000 ekin = 11.9954127335742 | erot = 4.78570420778446 | epot = -65.2777893328501 | etot = -48.4966723914915 +771000 ekin = 12.4710057578583 | erot = 4.76119431130479 | epot = -65.7288724617997 | etot = -48.4966723926366 +772000 ekin = 12.9091287693786 | erot = 4.73689896129648 | epot = -66.1427001248731 | etot = -48.4966723941981 +773000 ekin = 13.2804102672833 | erot = 4.71070995661432 | epot = -66.4877926203597 | etot = -48.4966723964621 +774000 ekin = 13.5460331301913 | erot = 4.67959233332746 | epot = -66.7222978601731 | etot = -48.4966723966543 +775000 ekin = 13.6741516120588 | erot = 4.63765248583542 | epot = -66.8084764977843 | etot = -48.4966723998901 +776000 ekin = 13.6286904224698 | erot = 4.5810340629117 | epot = -66.7063968767974 | etot = -48.4966723914159 +777000 ekin = 13.4182048010108 | erot = 4.51743020935942 | epot = -66.4323074040537 | etot = -48.4966723936834 +778000 ekin = 13.0220035128905 | erot = 4.44948541464092 | epot = -65.9681613216866 | etot = -48.4966723941552 +779000 ekin = 12.4217380617913 | erot = 4.38036222314103 | epot = -65.2987726779784 | etot = -48.496672393046 +780000 ekin = 11.613771531245 | erot = 4.31519453319774 | epot = -64.42563845626 | etot = -48.4966723918173 +781000 ekin = 10.6252323243695 | erot = 4.25886110642314 | epot = -63.380765816722 | etot = -48.4966723859294 +782000 ekin = 9.53385909805364 | erot = 4.22248165795862 | epot = -62.2530131351912 | etot = -48.496672379179 +783000 ekin = 8.43150181423015 | erot = 4.21812348326728 | epot = -61.1462976699004 | etot = -48.496672372403 +784000 ekin = 7.41120665752538 | erot = 4.25753755490016 | epot = -60.1654165788728 | etot = -48.4966723664473 +785000 ekin = 6.55493198849118 | erot = 4.35109016914503 | epot = -59.4026945196836 | etot = -48.4966723620474 +786000 ekin = 5.92286857594027 | erot = 4.50684669643736 | epot = -58.9263876320663 | etot = -48.4966723596887 +787000 ekin = 5.54648098925342 | erot = 4.72991351643046 | epot = -58.7730668651868 | etot = -48.496672359503 +788000 ekin = 5.42684004343809 | erot = 5.02210237708223 | epot = -58.9456147817288 | etot = -48.4966723612085 +789000 ekin = 5.53848888149235 | erot = 5.38186888554717 | epot = -59.417030131357 | etot = -48.4966723643175 +790000 ekin = 5.83681660441396 | erot = 5.80448189900387 | epot = -60.1379708716484 | etot = -48.4966723682306 +791000 ekin = 6.26691431691792 | erot = 6.28226218218035 | epot = -61.0458488715164 | etot = -48.4966723724181 +792000 ekin = 6.77233331545528 | erot = 6.80466729718548 | epot = -62.0736729890538 | etot = -48.4966723764131 +793000 ekin = 7.30112337082801 | erot = 7.3585303753528 | epot = -63.1563261262803 | etot = -48.4966723800995 +794000 ekin = 7.80874279001246 | erot = 7.92855734516373 | epot = -64.2339725184781 | etot = -48.4966723833019 +795000 ekin = 8.16614984086779 | erot = 8.55276407751546 | epot = -65.2155862977053 | etot = -48.496672379322 +796000 ekin = 8.42449679171013 | erot = 9.232341806983 | epot = -66.1535110093845 | etot = -48.4966724106913 +797000 ekin = 8.67431436581401 | erot = 9.7435699527024 | epot = -66.914556725524 | etot = -48.4966724070076 +798000 ekin = 8.8280771563386 | erot = 10.1953217654039 | epot = -67.5200713293495 | etot = -48.4966724076071 +799000 ekin = 8.89463201678151 | erot = 10.5732151310376 | epot = -67.9645195546597 | etot = -48.4966724068406 +800000 ekin = 8.89722969174871 | erot = 10.8667677316358 | epot = -68.2606698285332 | etot = -48.4966724051487 +801000 ekin = 8.87138017727319 | erot = 11.0709907384912 | epot = -68.4390433180044 | etot = -48.49667240224 +802000 ekin = 8.86275607661702 | erot = 11.1875475895059 | epot = -68.5469760649163 | etot = -48.4966723987933 +803000 ekin = 8.91761167485276 | erot = 11.2243264573357 | epot = -68.638610528175 | etot = -48.4966723959866 +804000 ekin = 9.06730079062971 | erot = 11.1932613875641 | epot = -68.7572345732232 | etot = -48.4966723950294 +805000 ekin = 9.31347449976795 | erot = 11.1073163211595 | epot = -68.9174632174952 | etot = -48.4966723965677 +806000 ekin = 9.6271984768999 | erot = 10.9794864721776 | epot = -69.1033573480843 | etot = -48.4966723990068 +807000 ekin = 9.96288601676957 | erot = 10.8230663456226 | epot = -69.2826247658667 | etot = -48.4966724034745 +808000 ekin = 10.2497439836388 | erot = 10.6432283958412 | epot = -69.3896447869791 | etot = -48.4966724074991 +809000 ekin = 10.4243193604973 | erot = 10.4427750451282 | epot = -69.3637668155705 | etot = -48.4966724099449 +810000 ekin = 10.4450308652907 | erot = 10.2230440398756 | epot = -69.1647473164965 | etot = -48.4966724113302 +811000 ekin = 10.272181346896 | erot = 9.97917260820666 | epot = -68.7480263644415 | etot = -48.4966724093388 +812000 ekin = 9.92407619970024 | erot = 9.71416142517266 | epot = -68.134910029841 | etot = -48.4966724049681 +813000 ekin = 9.46374629333194 | erot = 9.43470533288456 | epot = -67.3951240249078 | etot = -48.4966723986913 +814000 ekin = 8.98180729318873 | erot = 9.14902607621865 | epot = -66.6275057608654 | etot = -48.496672391458 +815000 ekin = 8.58163269954382 | erot = 8.8668326192338 | epot = -65.945137703243 | etot = -48.4966723844654 +816000 ekin = 8.36010805240945 | erot = 8.59902958878876 | epot = -65.4558100202893 | etot = -48.4966723790911 +817000 ekin = 8.38734404812207 | erot = 8.35708532043452 | epot = -65.241101745284 | etot = -48.4966723767274 +818000 ekin = 8.68842134779578 | erot = 8.15175683970339 | epot = -65.3368505651542 | etot = -48.496672377655 +819000 ekin = 9.23925212157569 | erot = 7.99221894961925 | epot = -65.7281434524437 | etot = -48.4966723812488 +820000 ekin = 9.85505920608647 | erot = 7.98557734926293 | epot = -66.3373089284081 | etot = -48.4966723730587 +821000 ekin = 10.5581187890191 | erot = 8.08897892780845 | epot = -67.1437700941966 | etot = -48.4966723773691 +822000 ekin = 11.4203555733393 | erot = 8.09820922217477 | epot = -68.0152371766456 | etot = -48.4966723811315 +823000 ekin = 12.2449657838916 | erot = 8.16990204501286 | epot = -68.9115402126078 | etot = -48.4966723837034 +824000 ekin = 12.988754106619 | erot = 8.303289001345 | epot = -69.7887154933773 | etot = -48.4966723854133 +825000 ekin = 13.6250378987267 | erot = 8.49403789382871 | epot = -70.6157481796525 | etot = -48.4966723870971 +826000 ekin = 14.1275801405811 | erot = 8.73182161873989 | epot = -71.3560741518016 | etot = -48.4966723924806 +827000 ekin = 14.4569396382577 | erot = 8.99861686934358 | epot = -71.9522289037119 | etot = -48.4966723961106 +828000 ekin = 14.5801783873678 | erot = 9.27256145493081 | epot = -72.3494122421992 | etot = -48.4966723999006 +829000 ekin = 14.4667887745675 | erot = 9.52899253620437 | epot = -72.4924537134123 | etot = -48.4966724026404 +830000 ekin = 14.1008667936321 | erot = 9.74540563538452 | epot = -72.3429448319433 | etot = -48.4966724029267 +831000 ekin = 13.4937466240961 | erot = 9.90643642504771 | epot = -71.8968554494301 | etot = -48.4966724002863 +832000 ekin = 12.690621379057 | erot = 10.007761953574 | epot = -71.1950557274001 | etot = -48.4966723947691 +833000 ekin = 11.76618490315 | erot = 10.0572478692757 | epot = -70.3201051601282 | etot = -48.4966723877025 +834000 ekin = 10.8109948235413 | erot = 10.0713545045104 | epot = -69.3790217084244 | etot = -48.4966723803727 +835000 ekin = 9.91642597742027 | erot = 10.0705783753312 | epot = -68.4836767280336 | etot = -48.4966723752821 +836000 ekin = 9.14363254517297 | erot = 9.95662954963987 | epot = -67.5969343907267 | etot = -48.4966722959138 +837000 ekin = 8.79163957803918 | erot = 9.91123278077568 | epot = -67.1995446571216 | etot = -48.4966722983067 +838000 ekin = 8.42094145774585 | erot = 9.94835266816688 | epot = -66.8659664253332 | etot = -48.4966722994205 +839000 ekin = 8.20536768127504 | erot = 10.0122432400981 | epot = -66.7142832237513 | etot = -48.4966723023782 +840000 ekin = 8.1093230210224 | erot = 10.100917536094 | epot = -66.7069128624304 | etot = -48.496672305314 +841000 ekin = 8.09432718565605 | erot = 10.2103111783835 | epot = -66.8013106720822 | etot = -48.4966723080426 +842000 ekin = 8.12447284717686 | erot = 10.3366191336996 | epot = -66.9577642910505 | etot = -48.496672310174 +843000 ekin = 8.17242564608534 | erot = 10.4770425710791 | epot = -67.1461405286521 | etot = -48.4966723114877 +844000 ekin = 8.22381294530403 | erot = 10.6297921504136 | epot = -67.3502774076129 | etot = -48.4966723118952 +845000 ekin = 8.27955126793295 | erot = 10.7936569659547 | epot = -67.5698805454519 | etot = -48.4966723115643 +846000 ekin = 8.35455924885402 | erot = 10.967203669213 | epot = -67.8184352290032 | etot = -48.4966723109362 +847000 ekin = 8.47238635239291 | erot = 11.1476305353207 | epot = -68.1166891982393 | etot = -48.4966723105256 +848000 ekin = 8.6581027291424 | erot = 11.3297217896588 | epot = -68.4844968293196 | etot = -48.4966723105184 +849000 ekin = 8.93290208129911 | erot = 11.5057838941209 | epot = -68.9353582864968 | etot = -48.4966723110767 +850000 ekin = 9.30778062392313 | erot = 11.6667367373522 | epot = -69.4711896738413 | etot = -48.4966723125659 +851000 ekin = 9.77385593013607 | erot = 11.8036289171217 | epot = -70.0741571630207 | etot = -48.496672315763 +852000 ekin = 10.2902091190448 | erot = 11.9080163478871 | epot = -70.6948977882805 | etot = -48.4966723213486 +853000 ekin = 10.7774710930233 | erot = 11.9704639293159 | epot = -71.2446073513379 | etot = -48.4966723289987 +854000 ekin = 11.1286098539193 | erot = 11.9790690591239 | epot = -71.6043512495388 | etot = -48.4966723364956 +855000 ekin = 11.2404537272091 | erot = 11.9198426908992 | epot = -71.6569687595576 | etot = -48.4966723414493 +856000 ekin = 11.053327395177 | erot = 11.7779965349299 | epot = -71.3279962710617 | etot = -48.4966723409548 +857000 ekin = 10.584956831702 | erot = 11.5448386364277 | epot = -70.6264678022533 | etot = -48.4966723341237 +858000 ekin = 9.93782549834665 | erot = 11.2226264185437 | epot = -69.6571242394592 | etot = -48.4966723225689 +859000 ekin = 9.27338883945023 | erot = 10.8254282744321 | epot = -68.5954894237091 | etot = -48.4966723098268 +860000 ekin = 8.76267013904095 | erot = 10.3757646971924 | epot = -67.6351071358762 | etot = -48.4966722996429 +861000 ekin = 8.53556496599741 | erot = 9.8992897906932 | epot = -66.9315270509676 | etot = -48.496672294277 +862000 ekin = 8.65070986754626 | erot = 9.42036720175988 | epot = -66.5677493631881 | etot = -48.4966722938819 +863000 ekin = 9.09319445512942 | erot = 8.96001366253682 | epot = -66.5498804148173 | etot = -48.496672297151 +864000 ekin = 9.79331571881421 | erot = 8.53570874460926 | epot = -66.8256967657445 | etot = -48.496672302321 +865000 ekin = 10.6528659431403 | erot = 8.1619337510599 | epot = -67.3114720020424 | etot = -48.4966723078422 +866000 ekin = 11.5706394639051 | erot = 7.85082867751083 | epot = -67.9181404525917 | etot = -48.4966723111758 +867000 ekin = 12.4665855078817 | erot = 7.61306294106123 | epot = -68.5763207633311 | etot = -48.4966723143882 +868000 ekin = 13.2806731160753 | erot = 7.45693596614787 | epot = -69.2342813981118 | etot = -48.4966723158886 +869000 ekin = 13.9812766374186 | erot = 7.38865717396414 | epot = -69.8666061275298 | etot = -48.4966723161471 +870000 ekin = 14.5601728090876 | erot = 7.41145610382319 | epot = -70.4683012292786 | etot = -48.4966723163678 +871000 ekin = 15.0180932071648 | erot = 7.52387391723463 | epot = -71.0386394424244 | etot = -48.496672318025 +872000 ekin = 15.3437544358528 | erot = 7.71754298669858 | epot = -71.5579697448569 | etot = -48.4966723223055 +873000 ekin = 15.4947478869856 | erot = 7.97535948776352 | epot = -71.9667797033426 | etot = -48.4966723285935 +874000 ekin = 15.4072022286222 | erot = 8.27349566903578 | epot = -72.177370232574 | etot = -48.496672334916 +875000 ekin = 15.0202820872088 | erot = 8.58584611982729 | epot = -72.1028005455168 | etot = -48.4966723384808 +876000 ekin = 14.3103753089542 | erot = 8.89001531540942 | epot = -71.6970629614375 | etot = -48.4966723370739 +877000 ekin = 13.3177867571877 | erot = 9.17198109522917 | epot = -70.9864401828287 | etot = -48.4966723304118 +878000 ekin = 12.1489812402072 | erot = 9.42690023133329 | epot = -70.0725537922242 | etot = -48.4966723206837 +879000 ekin = 10.9478679202175 | erot = 9.6557081483768 | epot = -69.1002483801628 | etot = -48.4966723115685 +880000 ekin = 9.84816823723111 | erot = 9.86012585903946 | epot = -68.2049664022824 | etot = -48.4966723060118 +881000 ekin = 8.93418865262183 | erot = 10.0399671445483 | epot = -67.4708281016096 | etot = -48.4966723044394 +882000 ekin = 8.23233878869692 | erot = 10.1944686101309 | epot = -66.9234797039627 | etot = -48.4966723051349 +883000 ekin = 7.7307937415218 | erot = 10.3254556486739 | epot = -66.552921695855 | etot = -48.4966723056593 +884000 ekin = 7.40639355198747 | erot = 10.43895819343 | epot = -66.3420240525079 | etot = -48.4966723070904 +885000 ekin = 7.23012884114594 | erot = 10.5425263248664 | epot = -66.2693274743337 | etot = -48.4966723083214 +886000 ekin = 7.17188160929178 | erot = 10.6423872890754 | epot = -66.3109412080251 | etot = -48.4966723096579 +887000 ekin = 7.20359993877251 | erot = 10.7423767430536 | epot = -66.4426489927797 | etot = -48.4966723109536 +888000 ekin = 7.3008338997157 | erot = 10.8444815138835 | epot = -66.6419877254683 | etot = -48.4966723118691 +889000 ekin = 7.4458466277536 | erot = 10.9502816347756 | epot = -66.8928005748479 | etot = -48.4966723123187 +890000 ekin = 7.62600693804896 | erot = 11.0610746454838 | epot = -67.1837538972842 | etot = -48.4966723137514 +891000 ekin = 7.81873873873223 | erot = 11.1753311187699 | epot = -67.4907421746786 | etot = -48.4966723171765 +892000 ekin = 7.97874968997684 | erot = 11.2859136966781 | epot = -67.7613357091199 | etot = -48.4966723224649 +893000 ekin = 8.03989394874733 | erot = 11.379421430407 | epot = -67.9159877073352 | etot = -48.4966723281809 +894000 ekin = 7.93829359299784 | erot = 11.4397930633308 | epot = -67.8747589881601 | etot = -48.4966723318315 +895000 ekin = 7.64207854906749 | erot = 11.454909658119 | epot = -67.593660529966 | etot = -48.4966723227794 +896000 ekin = 7.25994289813527 | erot = 11.4314794339685 | epot = -67.188094652132 | etot = -48.4966723200283 +897000 ekin = 6.87440345867047 | erot = 11.3807194376691 | epot = -66.7517952114221 | etot = -48.4966723150826 +898000 ekin = 6.54072238253912 | erot = 11.3170504975174 | epot = -66.3544451900592 | etot = -48.4966723100027 +899000 ekin = 6.3149797276302 | erot = 11.2562721805318 | epot = -66.0679242147949 | etot = -48.4966723066329 +900000 ekin = 6.23427080305277 | erot = 11.2089558223275 | epot = -65.9398989312314 | etot = -48.4966723058512 +901000 ekin = 6.30716786580342 | erot = 11.1769913016915 | epot = -65.9808314749347 | etot = -48.4966723074397 +902000 ekin = 6.5160386395389 | erot = 11.1540746008897 | epot = -66.1667855508329 | etot = -48.4966723104043 +903000 ekin = 6.82764115096407 | erot = 11.1292357637691 | epot = -66.4535492282758 | etot = -48.4966723135426 +904000 ekin = 7.20594581556678 | erot = 11.0915307949996 | epot = -66.7941489265111 | etot = -48.4966723159447 +905000 ekin = 7.62139055368882 | erot = 11.0338529955967 | epot = -67.1519158666662 | etot = -48.4966723173806 +906000 ekin = 8.05314401540784 | erot = 10.9545483974327 | epot = -67.5043647309824 | etot = -48.4966723181419 +907000 ekin = 8.48596871213919 | erot = 10.8568809788585 | epot = -67.8395220096489 | etot = -48.4966723186511 +908000 ekin = 8.90584093620398 | erot = 10.747531720664 | epot = -68.1500449760293 | etot = -48.4966723191613 +909000 ekin = 9.29811876751837 | erot = 10.635383593286 | epot = -68.4301746802664 | etot = -48.496672319462 +910000 ekin = 9.64930058056707 | erot = 10.5309201128789 | epot = -68.6768930130078 | etot = -48.4966723195618 +911000 ekin = 9.94798521054174 | erot = 10.4454281278766 | epot = -68.8900856579936 | etot = -48.4966723195752 +912000 ekin = 10.1842847330219 | erot = 10.3896169180644 | epot = -69.0705739710101 | etot = -48.4966723199237 +913000 ekin = 10.3464242506172 | erot = 10.3715034503495 | epot = -69.2146000220349 | etot = -48.4966723210683 +914000 ekin = 10.4159486730007 | erot = 10.3940912362075 | epot = -69.3067122326474 | etot = -48.4966723234391 +915000 ekin = 10.3649219647615 | erot = 10.4538252082086 | epot = -69.3154194996121 | etot = -48.4966723266421 +916000 ekin = 10.161263057762 | erot = 10.5413791276288 | epot = -69.1993145148424 | etot = -48.4966723294517 +917000 ekin = 9.79071146029323 | erot = 10.6444144950114 | epot = -68.9317982858749 | etot = -48.4966723305703 +918000 ekin = 9.26089494942026 | erot = 10.7518360026573 | epot = -68.5094032805132 | etot = -48.4966723284356 +919000 ekin = 8.61736183467543 | erot = 10.8585966350572 | epot = -67.972630791696 | etot = -48.4966723219635 +920000 ekin = 7.96059242024647 | erot = 10.9667865216799 | epot = -67.4240512549228 | etot = -48.4966723129964 +921000 ekin = 7.4206286576543 | erot = 11.0831224393334 | epot = -67.0004234019305 | etot = -48.4966723049428 +922000 ekin = 7.11192603559909 | erot = 11.2138650623263 | epot = -66.8224633994494 | etot = -48.4966723015239 +923000 ekin = 7.08988023753988 | erot = 11.3600862497943 | epot = -66.9466387899774 | etot = -48.4966723026433 +924000 ekin = 7.33691450582434 | erot = 11.5138164853999 | epot = -67.3474033032 | etot = -48.4966723119758 +925000 ekin = 7.75066983511487 | erot = 11.6552585828514 | epot = -67.9026007399031 | etot = -48.4966723219369 +926000 ekin = 8.19653350658662 | erot = 11.7619530785651 | epot = -68.4551589164327 | etot = -48.496672331281 +927000 ekin = 8.5473832953966 | erot = 11.8134968308328 | epot = -68.8575524640472 | etot = -48.4966723378179 +928000 ekin = 8.71145227501004 | erot = 11.7955386634222 | epot = -69.0036632788644 | etot = -48.4966723404322 +929000 ekin = 8.64121811854591 | erot = 11.702544255502 | epot = -68.8404347137197 | etot = -48.4966723396718 +930000 ekin = 8.33447879193368 | erot = 11.5389737739268 | epot = -68.3701249009275 | etot = -48.496672335067 +931000 ekin = 7.84128687140244 | erot = 11.3199153617486 | epot = -67.6578745610736 | etot = -48.4966723279226 +932000 ekin = 7.2443670142799 | erot = 11.0677318793148 | epot = -66.808771213404 | etot = -48.4966723198093 +933000 ekin = 6.63984712932122 | erot = 10.8074687760213 | epot = -65.9439882176745 | etot = -48.496672312332 +934000 ekin = 6.11754592395223 | erot = 10.5621552886432 | epot = -65.1763735193377 | etot = -48.4966723067423 +935000 ekin = 5.74541764855203 | erot = 10.3493855126172 | epot = -64.5914754646948 | etot = -48.4966723035256 +936000 ekin = 5.56181701631155 | erot = 10.1798783920285 | epot = -64.2383677111586 | etot = -48.4966723028186 +937000 ekin = 5.57387639539475 | erot = 10.0571518051793 | epot = -64.1277005048255 | etot = -48.4966723042514 +938000 ekin = 5.7614045533047 | erot = 9.97823911841354 | epot = -64.2363159790546 | etot = -48.4966723073363 +939000 ekin = 6.08318987670676 | erot = 9.93455888295511 | epot = -64.5144210714548 | etot = -48.4966723117929 +940000 ekin = 6.48293884643638 | erot = 9.91175572449271 | epot = -64.8913668882283 | etot = -48.4966723172993 +941000 ekin = 6.89458666429997 | erot = 9.89006577405458 | epot = -65.2813247618071 | etot = -48.4966723234525 +942000 ekin = 7.24869443000576 | erot = 9.84545862012391 | epot = -65.5908253796515 | etot = -48.4966723295218 +943000 ekin = 7.48274007835893 | erot = 9.75224430360331 | epot = -65.7316567161226 | etot = -48.4966723341603 +944000 ekin = 7.55661078091013 | erot = 9.58809869991494 | epot = -65.641381816555 | etot = -48.4966723357299 +945000 ekin = 7.47011756072567 | erot = 9.34043579095589 | epot = -65.3072256847293 | etot = -48.4966723330477 +946000 ekin = 7.27386532071824 | erot = 9.01155536839416 | epot = -64.782093015413 | etot = -48.4966723263006 +947000 ekin = 7.06319369667098 | erot = 8.61969480927007 | epot = -64.1795608235161 | etot = -48.496672317575 +948000 ekin = 6.95249218732834 | erot = 8.19479075043074 | epot = -63.6439552471302 | etot = -48.4966723093711 +949000 ekin = 7.04165184443043 | erot = 7.77196767262919 | epot = -63.3102918214628 | etot = -48.4966723044031 +950000 ekin = 7.3839323473098 | erot = 7.38215863325284 | epot = -63.2627632841868 | etot = -48.4966723036241 +951000 ekin = 7.97686792741366 | erot = 7.04490011727208 | epot = -63.5184403509843 | etot = -48.4966723062986 +952000 ekin = 8.77198923720124 | erot = 6.76886819733595 | epot = -64.0375297458692 | etot = -48.496672311332 +953000 ekin = 9.68951090442199 | erot = 6.55318208634643 | epot = -64.7393653092249 | etot = -48.4966723184564 +954000 ekin = 10.6255451805906 | erot = 6.39139134564297 | epot = -65.5136088525567 | etot = -48.4966723263231 +955000 ekin = 11.4591959855917 | erot = 6.27379827880045 | epot = -66.229666598801 | etot = -48.4966723344089 +956000 ekin = 12.0705908794987 | erot = 6.18965544964755 | epot = -66.7569186705249 | etot = -48.4966723413786 +957000 ekin = 12.3578057603392 | erot = 6.13109120794758 | epot = -66.9855693135646 | etot = -48.4966723452778 +958000 ekin = 12.2639561674295 | erot = 6.09526075790591 | epot = -66.8558892696232 | etot = -48.4966723442878 +959000 ekin = 11.802893283239 | erot = 6.08530913129913 | epot = -66.3848747518536 | etot = -48.4966723373154 +960000 ekin = 11.0657748732924 | erot = 6.10961272567079 | epot = -65.6720599258864 | etot = -48.4966723269232 +961000 ekin = 10.1976851859566 | erot = 6.17940625999531 | epot = -64.8737637613061 | etot = -48.4966723153542 +962000 ekin = 9.36006055931576 | erot = 6.30576434365556 | epot = -64.1624972092091 | etot = -48.4966723062378 +963000 ekin = 8.68052625297112 | erot = 6.49616547099239 | epot = -63.6733640261434 | etot = -48.4966723021798 +964000 ekin = 8.21670813000526 | erot = 6.75219993704958 | epot = -63.465580370563 | etot = -48.4966723035081 +965000 ekin = 7.95112951706077 | erot = 7.06933978142984 | epot = -63.5171416068344 | etot = -48.4966723083438 +966000 ekin = 7.81882046103783 | erot = 7.43840285073269 | epot = -63.7538956254769 | etot = -48.4966723137064 +967000 ekin = 7.74912903354425 | erot = 7.84702228254975 | epot = -64.092823634688 | etot = -48.496672318594 +968000 ekin = 7.67539244952259 | erot = 8.28177833118711 | epot = -64.4538431025099 | etot = -48.4966723218002 +969000 ekin = 7.5599027296028 | erot = 8.72822682089149 | epot = -64.7848018740692 | etot = -48.496672323575 +970000 ekin = 7.38809514858103 | erot = 9.17062532943753 | epot = -65.0553928031058 | etot = -48.4966723250872 +971000 ekin = 7.15239239132996 | erot = 9.59185821972787 | epot = -65.2409229374848 | etot = -48.4966723264269 +972000 ekin = 6.85180496131552 | erot = 9.97461998800994 | epot = -65.323097276516 | etot = -48.4966723271905 +973000 ekin = 6.49404713432455 | erot = 10.3038859967015 | epot = -65.2946054577948 | etot = -48.4966723267688 +974000 ekin = 6.10144997624876 | erot = 10.5696876868507 | epot = -65.1678099874725 | etot = -48.496672324373 +975000 ekin = 5.7182786322542 | erot = 10.7680923498195 | epot = -64.9830433026848 | etot = -48.4966723206111 +976000 ekin = 5.40201312577677 | erot = 10.9003005405809 | epot = -64.7989859829902 | etot = -48.4966723166326 +977000 ekin = 5.20833588400939 | erot = 10.970821414979 | epot = -64.6758296130979 | etot = -48.4966723141095 +978000 ekin = 5.16924582148977 | erot = 10.9846732107755 | epot = -64.6505913465279 | etot = -48.4966723142626 +979000 ekin = 5.27779878029639 | erot = 10.9455170820599 | epot = -64.7199881790626 | etot = -48.4966723167063 +980000 ekin = 5.49322046279538 | erot = 10.8569988040239 | epot = -64.8468915865683 | etot = -48.496672319749 +981000 ekin = 5.76179864599626 | erot = 10.7265177182828 | epot = -64.9849886855903 | etot = -48.4966723213112 +982000 ekin = 6.04348590851364 | erot = 10.5685834926815 | epot = -65.1087417214787 | etot = -48.4966723202835 +983000 ekin = 6.32848466352866 | erot = 10.4050435744172 | epot = -65.2302005549221 | etot = -48.4966723169763 +984000 ekin = 6.63689937855259 | erot = 10.2617391985674 | epot = -65.3953108898229 | etot = -48.4966723127029 +985000 ekin = 7.00519512985904 | erot = 10.1634367406265 | epot = -65.6653041794901 | etot = -48.4966723090046 +986000 ekin = 7.46792965452936 | erot = 10.1293593693436 | epot = -66.0939613309812 | etot = -48.4966723071083 +987000 ekin = 8.04175238535552 | erot = 10.1705679686079 | epot = -66.7089926616745 | etot = -48.4966723077111 +988000 ekin = 8.71523237362382 | erot = 10.2892285282743 | epot = -67.5011332128746 | etot = -48.4966723109765 +989000 ekin = 9.44555554158073 | erot = 10.4792258286134 | epot = -68.4214536898669 | etot = -48.4966723196728 +990000 ekin = 10.1473148545584 | erot = 10.7224786969413 | epot = -69.3664658790832 | etot = -48.4966723275835 +991000 ekin = 10.7156853116756 | erot = 10.9958515472639 | epot = -70.2082091944914 | etot = -48.4966723355518 +992000 ekin = 11.0552138396445 | erot = 11.2781950369919 | epot = -70.8300812183321 | etot = -48.4966723416956 +993000 ekin = 11.0952058505263 | erot = 11.552085152753 | epot = -71.1439633474709 | etot = -48.4966723441916 +994000 ekin = 10.8115610941828 | erot = 11.8083197784902 | epot = -71.116553214722 | etot = -48.496672342049 +995000 ekin = 10.2380910479075 | erot = 12.0483835950987 | epot = -70.783146978687 | etot = -48.4966723356808 +996000 ekin = 9.46083678142998 | erot = 12.2834739173447 | epot = -70.2409830255863 | etot = -48.4966723268117 +997000 ekin = 8.59669860761854 | erot = 12.5302960394062 | epot = -69.6236669647526 | etot = -48.4966723177279 +998000 ekin = 7.76544234454825 | erot = 12.8061283044619 | epot = -69.068242959264 | etot = -48.4966723102538 +999000 ekin = 7.06575293322294 | erot = 13.1250004085097 | epot = -68.6874256472216 | etot = -48.496672305489 +1000000 ekin = 6.56133020088365 | erot = 13.4950386916226 | epot = -68.5530411962168 | etot = -48.4966723037105 + 1000000 244.5767 -69.23317 0.68012891 -61.991711 -0.012778323 39304000 +Loop time of 18.8316 on 1 procs for 1000000 steps with 10 atoms + +Performance: 78.272 ns/day, 0.307 hours/ns, 53102.168 timesteps/s, 531.022 katom-step/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.43 | 15.43 | 15.43 | 0.0 | 81.93 +Bond | 0.69466 | 0.69466 | 0.69466 | 0.0 | 3.69 +Neigh | 0.011044 | 0.011044 | 0.011044 | 0.0 | 0.06 +Comm | 0.4431 | 0.4431 | 0.4431 | 0.0 | 2.35 +Output | 0.12591 | 0.12591 | 0.12591 | 0.0 | 0.67 +Modify | 1.6795 | 1.6795 | 1.6795 | 0.0 | 8.92 +Other | | 0.4478 | | | 2.38 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.3.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:18 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.4 new file mode 100644 index 0000000000..669a86a110 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.4 @@ -0,0 +1,1186 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 3 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +set atom * mass 100.0278 +Setting atom values ... + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.3.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 7.03429942525144 | erot = 12.9873344362494 | epot = -68.5183064451292 | etot = -48.4966725836283 +Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 262.20685 -73.084271 4.565965 -61.484007 -0.0051810598 39304000 +1000 ekin = 6.47818551117441 | erot = 13.3026700489858 | epot = -68.2775281400721 | etot = -48.496672579912 +2000 ekin = 6.03525112997234 | erot = 13.6564943363021 | epot = -68.188418043353 | etot = -48.4966725770786 +3000 ekin = 5.75105017872917 | erot = 14.0429985067123 | epot = -68.2907212623775 | etot = -48.496672576936 +4000 ekin = 5.63745048823597 | erot = 14.4525304497378 | epot = -68.5866535170593 | etot = -48.4966725790856 +5000 ekin = 5.67539108471601 | erot = 14.8714892268938 | epot = -69.0435528945018 | etot = -48.4966725828919 +6000 ekin = 5.8225592408171 | erot = 15.2845343223522 | epot = -69.6037661502108 | etot = -48.4966725870414 +7000 ekin = 6.02949131445188 | erot = 15.6780321266847 | epot = -70.2041960313094 | etot = -48.4966725901728 +8000 ekin = 6.25690013504894 | erot = 16.0432406183867 | epot = -70.796813344898 | etot = -48.4966725914624 +9000 ekin = 6.48760823849336 | erot = 16.3777166841148 | epot = -71.3619975139176 | etot = -48.4966725913094 +10000 ekin = 6.72254611001785 | erot = 16.6826306715322 | epot = -71.9018493718511 | etot = -48.496672590301 +11000 ekin = 6.97475226170405 | erot = 16.9603738277431 | epot = -72.4317986787938 | etot = -48.4966725893467 +12000 ekin = 7.25960713990553 | erot = 17.2117069445192 | epot = -72.9679866735632 | etot = -48.4966725891385 +13000 ekin = 7.5861600155147 | erot = 17.4338437184064 | epot = -73.516676323912 | etot = -48.4966725899909 +14000 ekin = 7.95221337497286 | erot = 17.6199690400551 | epot = -74.0688550069349 | etot = -48.4966725919069 +15000 ekin = 8.34290179280029 | erot = 17.759930875729 | epot = -74.5995052633029 | etot = -48.4966725947736 +16000 ekin = 8.7308834779805 | erot = 17.8412839163866 | epot = -75.0688399931312 | etot = -48.4966725987642 +17000 ekin = 9.06872001929412 | erot = 17.8482053032197 | epot = -75.4135979249309 | etot = -48.4966726024171 +18000 ekin = 9.30863890671833 | erot = 17.7686584779306 | epot = -75.5739699900196 | etot = -48.4966726053707 +19000 ekin = 9.4112478564752 | erot = 17.5960512017225 | epot = -75.5039716652994 | etot = -48.4966726071017 +20000 ekin = 9.34910582886853 | erot = 17.3292516593877 | epot = -75.1750300954674 | etot = -48.4966726072111 +21000 ekin = 9.11266896891016 | erot = 16.9731252869536 | epot = -74.5824668613651 | etot = -48.4966726055014 +22000 ekin = 8.71397032422844 | erot = 16.5385032889637 | epot = -73.7491462151202 | etot = -48.496672601928 +23000 ekin = 8.18690962778313 | erot = 16.0421750929968 | epot = -72.725757317897 | etot = -48.496672597117 +24000 ekin = 7.58361736117564 | erot = 15.5032978232032 | epot = -71.5835877759392 | etot = -48.4966725915604 +25000 ekin = 6.9674099167493 | erot = 14.9419969554433 | epot = -70.4060794581733 | etot = -48.4966725859807 +26000 ekin = 6.40397973480545 | erot = 14.3775943404744 | epot = -69.2782466563088 | etot = -48.4966725810289 +27000 ekin = 5.95300264518483 | erot = 13.8269533988879 | epot = -68.2766286212081 | etot = -48.4966725771354 +28000 ekin = 5.66210674320084 | erot = 13.3035488276536 | epot = -67.462328145308 | etot = -48.4966725744535 +29000 ekin = 5.56416292853322 | erot = 12.8173046943283 | epot = -66.8781401957625 | etot = -48.496672572901 +30000 ekin = 5.67757091398745 | erot = 12.3750254271168 | epot = -66.5492689133851 | etot = -48.4966725722808 +31000 ekin = 6.0082318042294 | erot = 11.9813634428798 | epot = -66.4862678195157 | etot = -48.4966725724065 +32000 ekin = 6.55166468997952 | erot = 11.6395080908375 | epot = -66.6878453540153 | etot = -48.4966725731983 +33000 ekin = 7.29417473532557 | erot = 11.3509752571398 | epot = -67.1418225671851 | etot = -48.4966725747197 +34000 ekin = 8.21244588218725 | erot = 11.1161143134268 | epot = -67.8252327728433 | etot = -48.4966725772293 +35000 ekin = 9.27066798182032 | erot = 10.93382726426 | epot = -68.70116782734 | etot = -48.4966725812597 +36000 ekin = 10.4137127998441 | erot = 10.8011032352061 | epot = -69.711488622778 | etot = -48.4966725877277 +37000 ekin = 11.5574113355614 | erot = 10.7118774334058 | epot = -70.7659613658537 | etot = -48.4966725968865 +38000 ekin = 12.5862131120552 | erot = 10.6570487006394 | epot = -71.7399344196423 | etot = -48.4966726069477 +39000 ekin = 13.3756277697448 | erot = 10.6266661696594 | epot = -72.4989665531952 | etot = -48.496672613791 +40000 ekin = 13.8400144974726 | erot = 10.6149441040859 | epot = -72.9516312154831 | etot = -48.4966726139245 +41000 ekin = 13.9716515751527 | erot = 10.6251303228018 | epot = -73.0934545058123 | etot = -48.4966726078579 +42000 ekin = 13.8349966624045 | erot = 10.6693591526023 | epot = -73.0010284144746 | etot = -48.4966725994678 +43000 ekin = 13.4863179745805 | erot = 10.7627501491632 | epot = -72.7457409172272 | etot = -48.4966727934835 +44000 ekin = 12.8657064139247 | erot = 11.0065042177546 | epot = -72.3688833251111 | etot = -48.4966726934318 +45000 ekin = 12.4513480708381 | erot = 11.2623687140009 | epot = -72.2103894466183 | etot = -48.4966726617792 +46000 ekin = 11.8973058918019 | erot = 11.5369637549566 | epot = -71.9309423094144 | etot = -48.4966726626559 +47000 ekin = 11.3048691716615 | erot = 11.8534105202767 | epot = -71.6549523562343 | etot = -48.4966726642961 +48000 ekin = 10.6681247163132 | erot = 12.1927455857895 | epot = -71.3575429678095 | etot = -48.4966726657067 +49000 ekin = 9.98781452095656 | erot = 12.5337626830789 | epot = -71.0182498702018 | etot = -48.4966726661663 +50000 ekin = 9.27805060546915 | erot = 12.8568502175182 | epot = -70.6315734882951 | etot = -48.4966726653077 +51000 ekin = 8.56816305052028 | erot = 13.1473275670357 | epot = -70.212163280745 | etot = -48.496672663189 +52000 ekin = 7.89968625326438 | erot = 13.3972664509227 | epot = -69.793625364465 | etot = -48.4966726602779 +53000 ekin = 7.31936805861704 | erot = 13.6052883011235 | epot = -69.4213290170347 | etot = -48.4966726572941 +54000 ekin = 6.87026435043475 | erot = 13.7746656104186 | epot = -69.1416026158051 | etot = -48.4966726549518 +55000 ekin = 6.58358833130218 | erot = 13.9106626376473 | epot = -68.9909236227061 | etot = -48.4966726537567 +56000 ekin = 6.47340776924363 | erot = 14.0180895137408 | epot = -68.9881699369064 | etot = -48.496672653922 +57000 ekin = 6.5349018939822 | erot = 14.0996443244831 | epot = -69.1312188738681 | etot = -48.4966726554028 +58000 ekin = 6.74582948881821 | erot = 14.1551416501596 | epot = -69.3976437968824 | etot = -48.4966726579046 +59000 ekin = 7.07026744299479 | erot = 14.1814435236754 | epot = -69.7483836278278 | etot = -48.4966726611576 +60000 ekin = 7.46321119956124 | erot = 14.1729605115931 | epot = -70.1328443758889 | etot = -48.4966726647345 +61000 ekin = 7.87615620947672 | erot = 14.1225980724399 | epot = -70.4954269501755 | etot = -48.4966726682588 +62000 ekin = 8.26246819545997 | erot = 14.0231891838103 | epot = -70.7823300503894 | etot = -48.4966726711191 +63000 ekin = 8.58419585421983 | erot = 13.8690469944675 | epot = -70.9499155215206 | etot = -48.4966726728333 +64000 ekin = 8.81822702695991 | erot = 13.6575496044141 | epot = -70.9724493044953 | etot = -48.4966726731213 +65000 ekin = 8.95905321200092 | erot = 13.3902699399855 | epot = -70.8459958240507 | etot = -48.4966726720642 +66000 ekin = 9.01708021240235 | erot = 13.073150449433 | epot = -70.5869033319405 | etot = -48.4966726701052 +67000 ekin = 9.01264024181533 | erot = 12.7157756705991 | epot = -70.2250885803061 | etot = -48.4966726678916 +68000 ekin = 8.96786592552677 | erot = 12.3300108275772 | epot = -69.7945494191638 | etot = -48.4966726660598 +69000 ekin = 8.89809230228937 | erot = 11.9282539830634 | epot = -69.3230189502575 | etot = -48.4966726649048 +70000 ekin = 8.80855518919879 | erot = 11.5224663142646 | epot = -68.8276941678881 | etot = -48.4966726644248 +71000 ekin = 8.69498380037548 | erot = 11.1237231983041 | epot = -68.3153796630104 | etot = -48.4966726643308 +72000 ekin = 8.54784464636869 | erot = 10.74237943467 | epot = -67.7868967452231 | etot = -48.4966726641844 +73000 ekin = 8.35855300081186 | erot = 10.3885820115981 | epot = -67.2438076759784 | etot = -48.4966726635684 +74000 ekin = 8.12576446604128 | erot = 10.0727225309052 | epot = -66.6951596591059 | etot = -48.4966726621593 +75000 ekin = 7.85890437579262 | erot = 9.80548509842791 | epot = -66.1610621343386 | etot = -48.4966726601181 +76000 ekin = 7.57852165402649 | erot = 9.597270815368 | epot = -65.6724651268096 | etot = -48.4966726574151 +77000 ekin = 7.31582042129685 | erot = 9.45739858079208 | epot = -65.2698916571085 | etot = -48.4966726550196 +78000 ekin = 7.10323229833916 | erot = 9.3917307433686 | epot = -64.9916356947845 | etot = -48.4966726530768 +79000 ekin = 6.9693721805436 | erot = 9.40218099613615 | epot = -64.8682258285396 | etot = -48.4966726518598 +80000 ekin = 6.93674566763362 | erot = 9.48623430706729 | epot = -64.9196526261965 | etot = -48.4966726514956 +81000 ekin = 7.01925680666671 | erot = 9.63726327568322 | epot = -65.1531927343328 | etot = -48.4966726519829 +82000 ekin = 7.22081712459685 | erot = 9.84564997752258 | epot = -65.5631397554092 | etot = -48.4966726532898 +83000 ekin = 7.53417765386279 | erot = 10.1003599019663 | epot = -66.1312102111943 | etot = -48.4966726553652 +84000 ekin = 7.940290589344 | erot = 10.3905229584646 | epot = -66.8274862058405 | etot = -48.4966726580318 +85000 ekin = 8.40988507522461 | erot = 10.7066512628598 | epot = -67.6132089989631 | etot = -48.4966726608787 +86000 ekin = 8.90877838664784 | erot = 11.0413122902599 | epot = -68.4467633402374 | etot = -48.4966726633297 +87000 ekin = 9.40446727184843 | erot = 11.389212342317 | epot = -69.2903522795771 | etot = -48.4966726654117 +88000 ekin = 9.8664138653362 | erot = 11.7464698262625 | epot = -70.109556357925 | etot = -48.4966726663263 +89000 ekin = 10.2794449749729 | erot = 12.1093351833934 | epot = -70.8854528250632 | etot = -48.496672666697 +90000 ekin = 10.644881863298 | erot = 12.4712192860778 | epot = -71.6127738155153 | etot = -48.4966726661396 +91000 ekin = 10.959237823698 | erot = 12.8213713070339 | epot = -72.2772817984363 | etot = -48.4966726677043 +92000 ekin = 11.1805024607923 | erot = 13.1782323505892 | epot = -72.8554074847635 | etot = -48.4966726733821 +93000 ekin = 11.3486717558855 | erot = 13.488666272359 | epot = -73.3340106985069 | etot = -48.4966726702624 +94000 ekin = 11.4194570018441 | erot = 13.7677249757344 | epot = -73.6838546479548 | etot = -48.4966726703763 +95000 ekin = 11.3899765892415 | erot = 14.0119097397859 | epot = -73.8985589999749 | etot = -48.4966726709475 +96000 ekin = 11.2605951113246 | erot = 14.2148286413578 | epot = -73.972096422542 | etot = -48.4966726698596 +97000 ekin = 11.0445904714311 | erot = 14.3764700204589 | epot = -73.9177331597961 | etot = -48.496672667906 +98000 ekin = 10.7660933774849 | erot = 14.4993108341515 | epot = -73.7620768770615 | etot = -48.4966726654252 +99000 ekin = 10.4555155361554 | erot = 14.5876138558175 | epot = -73.5398020548143 | etot = -48.4966726628415 +100000 ekin = 10.0974774598987 | erot = 14.6249949423906 | epot = -73.2191455720071 | etot = -48.4966731697177 +101000 ekin = 10.0415631096137 | erot = 14.0961872066541 | epot = -72.6344231724507 | etot = -48.4966728561828 +102000 ekin = 10.2892855713202 | erot = 14.012187510498 | epot = -72.7981457142972 | etot = -48.4966726324791 +103000 ekin = 10.030926337016 | erot = 14.0335683972792 | epot = -72.5611673660203 | etot = -48.4966726317251 +104000 ekin = 9.79194699005209 | erot = 14.0507619049247 | epot = -72.3393815271541 | etot = -48.4966726321773 +105000 ekin = 9.56928640949136 | erot = 14.0644676494027 | epot = -72.1304266917122 | etot = -48.4966726328182 +106000 ekin = 9.35843270941694 | erot = 14.0738948863194 | epot = -71.9290002289413 | etot = -48.4966726332049 +107000 ekin = 9.15960205394257 | erot = 14.0781570096048 | epot = -71.7344316966933 | etot = -48.496672633146 +108000 ekin = 8.98058598862051 | erot = 14.0757573495376 | epot = -71.5530159707945 | etot = -48.4966726326364 +109000 ekin = 8.83500010163843 | erot = 14.0641942059689 | epot = -71.3958669399389 | etot = -48.4966726323315 +110000 ekin = 8.73407156167122 | erot = 14.0396159238041 | epot = -71.2703601184354 | etot = -48.49667263296 +111000 ekin = 8.67544983167207 | erot = 13.9967358275336 | epot = -71.1688582943783 | etot = -48.4966726351726 +112000 ekin = 8.6350044076198 | erot = 13.9293053313403 | epot = -71.0609823775569 | etot = -48.4966726385968 +113000 ekin = 8.5704259257829 | erot = 13.8317248404421 | epot = -70.898823408096 | etot = -48.496672641871 +114000 ekin = 8.43989096913563 | erot = 13.7008372464532 | epot = -70.6374008585741 | etot = -48.4966726429852 +115000 ekin = 8.22527688481172 | erot = 13.5374589941368 | epot = -70.259408517006 | etot = -48.4966726380575 +116000 ekin = 7.96055882645664 | erot = 13.3455331437012 | epot = -69.8027646054373 | etot = -48.4966726352795 +117000 ekin = 7.68480617458401 | erot = 13.1328848481121 | epot = -69.3143636549154 | etot = -48.4966726322193 +118000 ekin = 7.42978537710071 | erot = 12.9094282247797 | epot = -68.8358862320104 | etot = -48.4966726301299 +119000 ekin = 7.2137363939324 | erot = 12.6851208042373 | epot = -68.3955298273834 | etot = -48.4966726292136 +120000 ekin = 7.03803293636671 | erot = 12.4697797263412 | epot = -68.0044852916952 | etot = -48.4966726289873 +121000 ekin = 6.8936709264401 | erot = 12.272894951256 | epot = -67.6632385066892 | etot = -48.4966726289932 +122000 ekin = 6.76879687257042 | erot = 12.1027214693544 | epot = -67.3681909710515 | etot = -48.4966726291267 +123000 ekin = 6.6521040717835 | erot = 11.9648592015111 | epot = -67.1136359029295 | etot = -48.4966726296349 +124000 ekin = 6.53115267708844 | erot = 11.8616861164462 | epot = -66.8895114237899 | etot = -48.4966726302553 +125000 ekin = 6.39605544212482 | erot = 11.7907254418549 | epot = -66.6834535155165 | etot = -48.4966726315368 +126000 ekin = 6.23766494395132 | erot = 11.7440508510366 | epot = -66.4783884275686 | etot = -48.4966726325807 +127000 ekin = 6.04911470795132 | erot = 11.711163525569 | epot = -66.2569508666246 | etot = -48.4966726331043 +128000 ekin = 5.83208869215098 | erot = 11.682213880146 | epot = -66.0109752050972 | etot = -48.4966726328002 +129000 ekin = 5.59955533756658 | erot = 11.6485505375886 | epot = -65.7447785065467 | etot = -48.4966726313915 +130000 ekin = 5.37616547346342 | erot = 11.6055192857393 | epot = -65.4783573884614 | etot = -48.4966726292587 +131000 ekin = 5.19621347260189 | erot = 11.5523382042858 | epot = -65.2452243036203 | etot = -48.4966726267326 +132000 ekin = 5.09512855427621 | erot = 11.4915853273382 | epot = -65.0833865066928 | etot = -48.4966726250784 +133000 ekin = 5.09593793196195 | erot = 11.4254654000436 | epot = -65.0180759559376 | etot = -48.4966726239321 +134000 ekin = 5.21315400669044 | erot = 11.3572216289393 | epot = -65.0670482589978 | etot = -48.4966726233681 +135000 ekin = 5.45274887458444 | erot = 11.2905481952009 | epot = -65.2399696930873 | etot = -48.4966726233019 +136000 ekin = 5.81359277202082 | erot = 11.2291159416501 | epot = -65.5393813373533 | etot = -48.4966726236824 +137000 ekin = 6.28595091476304 | erot = 11.1752215008227 | epot = -65.9578450445987 | etot = -48.496672629013 +138000 ekin = 6.83489595318816 | erot = 11.123880412668 | epot = -66.4554489962854 | etot = -48.4966726304292 +139000 ekin = 7.43298982213957 | erot = 11.0759557714594 | epot = -67.0056182256037 | etot = -48.4966726320047 +140000 ekin = 8.05423567523354 | erot = 11.0338915539243 | epot = -67.584799863096 | etot = -48.4966726339382 +141000 ekin = 8.66814450976643 | erot = 10.9995435661271 | epot = -68.1643607123582 | etot = -48.4966726364646 +142000 ekin = 9.23299211625417 | erot = 10.9739956101673 | epot = -68.7036603674048 | etot = -48.4966726409833 +143000 ekin = 9.69542810759758 | erot = 10.9568256540412 | epot = -69.148926406631 | etot = -48.4966726449922 +144000 ekin = 10.0035712730501 | erot = 10.9455251640244 | epot = -69.4457690858196 | etot = -48.4966726487451 +145000 ekin = 10.1140173167571 | erot = 10.9367967497628 | epot = -69.5474867174164 | etot = -48.4966726508964 +146000 ekin = 10.010255193474 | erot = 10.9282120719387 | epot = -69.4351399151878 | etot = -48.4966726497751 +147000 ekin = 9.72372844852437 | erot = 10.9204908015157 | epot = -69.1408918942985 | etot = -48.4966726442584 +148000 ekin = 9.34553092121529 | erot = 10.9194622742203 | epot = -68.7616658304598 | etot = -48.4966726350242 +149000 ekin = 9.01308307721587 | erot = 10.9361646162974 | epot = -68.4459203187324 | etot = -48.4966726252192 +150000 ekin = 8.865564916199 | erot = 10.9838242848979 | epot = -68.3460618203819 | etot = -48.496672619285 +151000 ekin = 8.98562593113232 | erot = 11.0721207188499 | epot = -68.5544192701777 | etot = -48.4966726201955 +152000 ekin = 9.36317382414728 | erot = 11.2013283048009 | epot = -69.0611747563319 | etot = -48.4966726273838 +153000 ekin = 9.90592399926709 | erot = 11.3597169983851 | epot = -69.762313634926 | etot = -48.4966726372738 +154000 ekin = 10.4876718007884 | erot = 11.5259908274829 | epot = -70.5103352740072 | etot = -48.4966726457359 +155000 ekin = 11.0014546611185 | erot = 11.6755859722271 | epot = -71.1737132837587 | etot = -48.4966726504131 +156000 ekin = 11.3882148349958 | erot = 11.7874454844493 | epot = -71.6723329709515 | etot = -48.4966726515063 +157000 ekin = 11.6329719121599 | erot = 11.8481298115872 | epot = -71.9777743743921 | etot = -48.496672650645 +158000 ekin = 11.743699781619 | erot = 11.852602482575 | epot = -72.0929749132267 | etot = -48.4966726490327 +159000 ekin = 11.7357219121817 | erot = 11.8034015633403 | epot = -72.035796122213 | etot = -48.4966726466911 +160000 ekin = 11.6305552644523 | erot = 11.7096700273735 | epot = -71.8368979351533 | etot = -48.4966726433274 +161000 ekin = 11.4596686193139 | erot = 11.5857134121787 | epot = -71.5420546707695 | etot = -48.496672639277 +162000 ekin = 11.2620233891936 | erot = 11.448373844929 | epot = -71.2070698695242 | etot = -48.4966726354016 +163000 ekin = 11.0755659765656 | erot = 11.3138001976418 | epot = -70.8860388066474 | etot = -48.49667263244 +164000 ekin = 10.9292960811459 | erot = 11.1949564931563 | epot = -70.6209252049759 | etot = -48.4966726306737 +165000 ekin = 10.8401906864875 | erot = 11.1006151382457 | epot = -70.4374784546595 | etot = -48.4966726299263 +166000 ekin = 10.8146651780986 | erot = 11.035675846272 | epot = -70.3470136542456 | etot = -48.496672629875 +167000 ekin = 10.8520567567864 | erot = 11.0022539306528 | epot = -70.3509833175924 | etot = -48.4966726301532 +168000 ekin = 10.9484894336274 | erot = 11.0010183041617 | epot = -70.4461803682569 | etot = -48.4966726304677 +169000 ekin = 11.0998937027386 | erot = 11.0324366339792 | epot = -70.6290029673671 | etot = -48.4966726306493 +170000 ekin = 11.303483973301 | erot = 11.0977053912599 | epot = -70.8978619952531 | etot = -48.4966726306922 +171000 ekin = 11.5572307267885 | erot = 11.1992212781623 | epot = -71.2531246357255 | etot = -48.4966726307747 +172000 ekin = 11.8571464638408 | erot = 11.340530780689 | epot = -71.6943498757676 | etot = -48.4966726312377 +173000 ekin = 12.1927097200976 | erot = 11.5257889190942 | epot = -72.2151712717163 | etot = -48.4966726325245 +174000 ekin = 12.5417902291443 | erot = 11.758840169329 | epot = -72.7973030335596 | etot = -48.4966726350863 +175000 ekin = 12.8647095032793 | erot = 12.0421936377307 | epot = -73.4035757801782 | etot = -48.4966726391682 +176000 ekin = 13.1024197132925 | erot = 12.3759769580596 | epot = -73.9750693159967 | etot = -48.4966726446446 +177000 ekin = 13.190718096856 | erot = 12.7566551418151 | epot = -74.4440458869535 | etot = -48.4966726482824 +178000 ekin = 13.05264922196 | erot = 13.1773711164485 | epot = -74.7266929933934 | etot = -48.4966726549849 +179000 ekin = 12.2089794588745 | erot = 13.5830164197223 | epot = -74.2886682061569 | etot = -48.4966723275601 +180000 ekin = 11.9004068675239 | erot = 14.0870661177297 | epot = -74.4841455891972 | etot = -48.4966726039435 +181000 ekin = 10.8654768903692 | erot = 14.5861339869459 | epot = -73.9482834733432 | etot = -48.4966725960281 +182000 ekin = 9.66028270695138 | erot = 15.1104289206579 | epot = -73.2673842110059 | etot = -48.4966725833966 +183000 ekin = 8.48066280387605 | erot = 15.6673690821393 | epot = -72.6447044561308 | etot = -48.4966725701155 +184000 ekin = 7.52630413851929 | erot = 16.2665624203507 | epot = -72.2895391199349 | etot = -48.4966725610649 +185000 ekin = 6.93646433276123 | erot = 16.9124293952412 | epot = -72.3455662872057 | etot = -48.4966725592033 +186000 ekin = 6.75402182356136 | erot = 17.5959531882619 | epot = -72.8466475760996 | etot = -48.4966725642764 +187000 ekin = 6.93176584306106 | erot = 18.2901076459546 | epot = -73.7185460628698 | etot = -48.4966725738541 +188000 ekin = 7.36496175936816 | erot = 18.9517169220489 | epot = -74.8133512665733 | etot = -48.4966725851563 +189000 ekin = 7.92587452891987 | erot = 19.5289159490217 | epot = -75.9514630739328 | etot = -48.4966725959912 +190000 ekin = 8.48887345555899 | erot = 19.9711008208249 | epot = -76.9566468811629 | etot = -48.4966726047791 +191000 ekin = 8.94279744307637 | erot = 20.2387056809853 | epot = -77.6781757356946 | etot = -48.4966726116329 +192000 ekin = 9.20220030816187 | erot = 20.3101038067633 | epot = -78.0089767286117 | etot = -48.4966726136866 +193000 ekin = 9.22639739330518 | erot = 20.1841068563623 | epot = -77.9071768610927 | etot = -48.4966726114252 +194000 ekin = 9.02106352746558 | erot = 19.879840012452 | epot = -77.3975761450875 | etot = -48.4966726051699 +195000 ekin = 8.63698690390024 | erot = 19.4322506720419 | epot = -76.5659101722172 | etot = -48.4966725962751 +196000 ekin = 8.15745599944877 | erot = 18.8847381250292 | epot = -75.5388667111713 | etot = -48.4966725866933 +197000 ekin = 7.6777584189192 | erot = 18.2815207246711 | epot = -74.4559517216657 | etot = -48.4966725780754 +198000 ekin = 7.28589102711843 | erot = 17.6623826120232 | epot = -73.4449462104515 | etot = -48.4966725713098 +199000 ekin = 7.05017610428617 | erot = 17.0606063919737 | epot = -72.6074550629725 | etot = -48.4966725667126 +200000 ekin = 7.01285264528771 | erot = 16.5030180881871 | epot = -72.0125432979054 | etot = -48.4966725644306 +201000 ekin = 7.18628302948149 | erot = 16.0106066265263 | epot = -71.6935622206016 | etot = -48.4966725645938 +202000 ekin = 7.55028085659507 | erot = 15.5985035867492 | epot = -71.6454570106341 | etot = -48.4966725672899 +203000 ekin = 8.05261783917546 | erot = 15.2753610695144 | epot = -71.8246514807947 | etot = -48.4966725721048 +204000 ekin = 8.61587119719168 | erot = 15.0430481939185 | epot = -72.1555919691966 | etot = -48.4966725780864 +205000 ekin = 9.15150139881355 | erot = 14.8972623538548 | epot = -72.5454363365197 | etot = -48.4966725838514 +206000 ekin = 9.57853091802685 | erot = 14.8296218061963 | epot = -72.904825312253 | etot = -48.4966725880299 +207000 ekin = 9.84110469117133 | erot = 14.8306579376118 | epot = -73.1684352185348 | etot = -48.4966725897516 +208000 ekin = 9.91915380070236 | erot = 14.8924578832506 | epot = -73.3082842728947 | etot = -48.4966725889417 +209000 ekin = 9.82907930165538 | erot = 15.009695181568 | epot = -73.335447069535 | etot = -48.4966725863117 +210000 ekin = 9.61485280029918 | erot = 15.1785174137095 | epot = -73.2900427971273 | etot = -48.4966725831186 +211000 ekin = 9.33255453637681 | erot = 15.3937274488317 | epot = -73.2229545659769 | etot = -48.4966725807684 +212000 ekin = 9.03298062727245 | erot = 15.645385712317 | epot = -73.1750389199433 | etot = -48.4966725803539 +213000 ekin = 8.74801774645706 | erot = 15.9162328155355 | epot = -73.160923144197 | etot = -48.4966725822045 +214000 ekin = 8.48645509186844 | erot = 16.181037260622 | epot = -73.1641649379154 | etot = -48.4966725854249 +215000 ekin = 8.24361394372388 | erot = 16.4085443498284 | epot = -73.1488308822362 | etot = -48.4966725886839 +216000 ekin = 8.01644140640109 | erot = 16.567190486037 | epot = -73.080304482111 | etot = -48.4966725896729 +217000 ekin = 7.82443857147227 | erot = 16.6321169295439 | epot = -72.9532280885845 | etot = -48.4966725875684 +218000 ekin = 7.71607328585115 | erot = 16.5899557796661 | epot = -72.8027016494467 | etot = -48.4966725839295 +219000 ekin = 7.75310717264871 | erot = 16.4350572743126 | epot = -72.6848370278581 | etot = -48.4966725808969 +220000 ekin = 7.98143888037879 | erot = 16.1675107350278 | epot = -72.6456221958543 | etot = -48.4966725804477 +221000 ekin = 8.40773648375345 | erot = 15.7897008204062 | epot = -72.6941098869361 | etot = -48.4966725827765 +222000 ekin = 8.99748090378716 | erot = 15.3051579237926 | epot = -72.7993114139564 | etot = -48.4966725863767 +223000 ekin = 9.69291742679692 | erot = 14.7208372414052 | epot = -72.9104272575021 | etot = -48.4966725893 +224000 ekin = 10.4359945859782 | erot = 14.0505863380194 | epot = -72.9832535144518 | etot = -48.4966725904542 +225000 ekin = 11.1813440324308 | erot = 13.3180094413787 | epot = -72.996026064094 | etot = -48.4966725902845 +226000 ekin = 11.8899174093651 | erot = 12.5555741904319 | epot = -72.9421641905593 | etot = -48.4966725907622 +227000 ekin = 12.5083401208548 | erot = 11.7991557925081 | epot = -72.8041685069196 | etot = -48.4966725935567 +228000 ekin = 12.9540489024056 | erot = 11.0813711809714 | epot = -72.5320926818165 | etot = -48.4966725984396 +229000 ekin = 13.1250482768505 | erot = 10.4265507754497 | epot = -72.0482716553169 | etot = -48.4966726030167 +230000 ekin = 12.9354776786789 | erot = 9.84937329189316 | epot = -71.2815235748201 | etot = -48.496672604248 +231000 ekin = 12.3571979238697 | erot = 9.35664487116824 | epot = -70.2105153953948 | etot = -48.4966726003569 +232000 ekin = 11.441378635533 | erot = 8.95013763084956 | epot = -68.8881888585135 | etot = -48.4966725921309 +233000 ekin = 10.306860836762 | erot = 8.62874527756515 | epot = -67.4322786963308 | etot = -48.4966725820036 +234000 ekin = 9.10484994367511 | erot = 8.38947611811251 | epot = -65.9909986342493 | etot = -48.4966725724617 +235000 ekin = 7.97762335600863 | erot = 8.2279605743492 | epot = -64.7022564960577 | etot = -48.4966725656998 +236000 ekin = 7.0304183366733 | erot = 8.14060898682625 | epot = -63.6676998849092 | etot = -48.4966725614097 +237000 ekin = 6.3323277859341 | erot = 8.12400287134693 | epot = -62.9530032163567 | etot = -48.4966725590757 +238000 ekin = 5.92140822285225 | erot = 8.17513077744184 | epot = -62.5932115585199 | etot = -48.4966725582258 +239000 ekin = 5.81123122340632 | erot = 8.29054157425132 | epot = -62.5984453565715 | etot = -48.4966725589139 +240000 ekin = 5.99217826069117 | erot = 8.4648979936537 | epot = -62.9537488157034 | etot = -48.4966725613585 +241000 ekin = 6.43109156575349 | erot = 8.68961368249095 | epot = -63.6173778141204 | etot = -48.4966725658759 +242000 ekin = 7.06756407119338 | erot = 8.95153614482818 | epot = -64.5157727888128 | etot = -48.4966725727912 +243000 ekin = 7.81639319361071 | erot = 9.23207829014713 | epot = -65.5451440641925 | etot = -48.4966725804347 +244000 ekin = 8.58044212002104 | erot = 9.50948701565513 | epot = -66.5866017229663 | etot = -48.4966725872901 +245000 ekin = 9.26871916861867 | erot = 9.75990826682941 | epot = -67.5253000301858 | etot = -48.4966725947377 +246000 ekin = 9.78946573666749 | erot = 9.96525866121197 | epot = -68.2513969980116 | etot = -48.4966726001321 +247000 ekin = 10.0743388396476 | erot = 10.1147521472294 | epot = -68.6857635892695 | etot = -48.4966726023925 +248000 ekin = 10.0941079494609 | erot = 10.2065328815033 | epot = -68.7973134320029 | etot = -48.4966726010388 +249000 ekin = 9.86393967731197 | erot = 10.2475258665404 | epot = -68.6081381410575 | etot = -48.4966725972051 +250000 ekin = 9.43636984426512 | erot = 10.2506637078824 | epot = -68.1837061428591 | etot = -48.4966725907116 +251000 ekin = 8.89229868578636 | erot = 10.232334609138 | epot = -67.6213058787997 | etot = -48.4966725838753 +252000 ekin = 8.31943898663656 | erot = 10.2075884963066 | epot = -67.0237000610926 | etot = -48.4966725781494 +253000 ekin = 7.79276077495193 | erot = 10.1873587545281 | epot = -66.4767921038599 | etot = -48.4966725743798 +254000 ekin = 7.36152147186344 | erot = 10.1778229232089 | epot = -66.0360169681652 | etot = -48.4966725730929 +255000 ekin = 7.04416809512428 | erot = 10.181248194185 | epot = -65.7220888627672 | etot = -48.4966725734579 +256000 ekin = 6.83530017399278 | erot = 10.1962922388045 | epot = -65.5282649876823 | etot = -48.496672574885 +257000 ekin = 6.71442148099541 | erot = 10.2200504443756 | epot = -65.4311445018447 | etot = -48.4966725764737 +258000 ekin = 6.65781764563524 | erot = 10.2492124175324 | epot = -65.4037026408317 | etot = -48.4966725776641 +259000 ekin = 6.64642051201687 | erot = 10.2806008774797 | epot = -65.4236939679375 | etot = -48.4966725784409 +260000 ekin = 6.66675395816299 | erot = 10.3110375472883 | epot = -65.4744640845755 | etot = -48.4966725791242 +261000 ekin = 6.70841492604686 | erot = 10.337872125544 | epot = -65.5429596307914 | etot = -48.4966725792006 +262000 ekin = 6.7627561946648 | erot = 10.3595239082592 | epot = -65.618952682721 | etot = -48.496672579797 +263000 ekin = 6.82191301036426 | erot = 10.3716898912795 | epot = -65.690275481472 | etot = -48.4966725798283 +264000 ekin = 6.88504914962626 | erot = 10.3708999773069 | epot = -65.7526217059619 | etot = -48.4966725790287 +265000 ekin = 6.960898286708 | erot = 10.3558192629975 | epot = -65.8133901272671 | etot = -48.4966725775615 +266000 ekin = 7.06529185645044 | erot = 10.3276065183191 | epot = -65.8895709506868 | etot = -48.4966725759173 +267000 ekin = 7.21505088334997 | erot = 10.2893497391616 | epot = -66.0010731971453 | etot = -48.4966725746338 +268000 ekin = 7.42137725346334 | erot = 10.2450818723159 | epot = -66.1631316998746 | etot = -48.4966725740954 +269000 ekin = 7.68524329715843 | erot = 10.1988935008372 | epot = -66.3808093724379 | etot = -48.4966725744423 +270000 ekin = 7.99580948969528 | erot = 10.154449265304 | epot = -66.6469313305823 | etot = -48.496672575583 +271000 ekin = 8.3319048512179 | erot = 10.1151435011367 | epot = -66.9437209293965 | etot = -48.4966725770419 +272000 ekin = 8.66610587594003 | erot = 10.0856409418549 | epot = -67.2484193966209 | etot = -48.4966725788259 +273000 ekin = 8.97042145762764 | erot = 10.0690324252393 | epot = -67.536126463092 | etot = -48.4966725802251 +274000 ekin = 9.22287683295388 | erot = 10.0690361391239 | epot = -67.788585552836 | etot = -48.4966725807582 +275000 ekin = 9.41389302944299 | erot = 10.0906946031174 | epot = -68.0012602127847 | etot = -48.4966725802242 +276000 ekin = 9.54942761495552 | erot = 10.1400083113636 | epot = -68.1861085051145 | etot = -48.4966725787954 +277000 ekin = 9.64913594524363 | erot = 10.2229042121193 | epot = -68.3687127344001 | etot = -48.4966725770371 +278000 ekin = 9.73935192458056 | erot = 10.3435700154574 | epot = -68.5795945157817 | etot = -48.4966725757437 +279000 ekin = 9.84298152732214 | erot = 10.5026140404983 | epot = -68.8422681434335 | etot = -48.496672575613 +280000 ekin = 9.97046187703876 | erot = 10.6957212898499 | epot = -69.1628557437704 | etot = -48.4966725768818 +281000 ekin = 10.1137684706567 | erot = 10.9135096018649 | epot = -69.5239506554729 | etot = -48.4966725829514 +282000 ekin = 10.2288689015359 | erot = 11.142271992086 | epot = -69.8678134801518 | etot = -48.4966725865298 +283000 ekin = 10.2769463821851 | erot = 11.3646568092211 | epot = -70.1382757810248 | etot = -48.4966725896187 +284000 ekin = 10.2298350175167 | erot = 11.5634949517874 | epot = -70.290002560938 | etot = -48.496672591634 +285000 ekin = 10.0723248849016 | erot = 11.7243250964783 | epot = -70.2933225737757 | etot = -48.4966725923958 +286000 ekin = 9.80394054069748 | erot = 11.8369977519972 | epot = -70.137610884751 | etot = -48.4966725920563 +287000 ekin = 9.43655233181395 | erot = 11.8964493797703 | epot = -69.8296743025074 | etot = -48.4966725909231 +288000 ekin = 8.99013271753932 | erot = 11.9027405791585 | epot = -69.3895458860148 | etot = -48.4966725893169 +289000 ekin = 8.48857673810637 | erot = 11.860522637167 | epot = -68.8457719627796 | etot = -48.4966725875062 +290000 ekin = 7.95651311705559 | erot = 11.7780720781063 | epot = -68.2312577808377 | etot = -48.4966725856758 +291000 ekin = 7.41785902588673 | erot = 11.6660397038494 | epot = -67.5805713135416 | etot = -48.4966725838055 +292000 ekin = 6.89736764547106 | erot = 11.5361414718397 | epot = -66.9301816989046 | etot = -48.4966725815939 +293000 ekin = 6.42572947191051 | erot = 11.4000701849624 | epot = -66.322472235463 | etot = -48.4966725785901 +294000 ekin = 6.04578762670029 | erot = 11.268773141137 | epot = -65.811233342478 | etot = -48.4966725746408 +295000 ekin = 5.81372000921063 | erot = 11.1519540391863 | epot = -65.4623466187971 | etot = -48.4966725704001 +296000 ekin = 5.78868895653423 | erot = 11.0574288852487 | epot = -65.3427904091971 | etot = -48.4966725674142 +297000 ekin = 6.01086247217247 | erot = 10.9900621222574 | epot = -65.4975971618444 | etot = -48.4966725674145 +298000 ekin = 6.47793511118133 | erot = 10.9505151838958 | epot = -65.9251228662866 | etot = -48.4966725712095 +299000 ekin = 7.13485226401429 | erot = 10.9343849130194 | epot = -66.5659097551344 | etot = -48.4966725781007 +300000 ekin = 7.88433986357019 | erot = 10.9323127586099 | epot = -67.3133252084237 | etot = -48.4966725862436 +301000 ekin = 8.61282845355444 | erot = 10.9313732714822 | epot = -68.0408743185901 | etot = -48.4966725935534 +302000 ekin = 9.219084402774 | erot = 10.9175582659957 | epot = -68.6333152672212 | etot = -48.4966725984515 +303000 ekin = 9.63516616614934 | erot = 10.8787665670547 | epot = -69.0106053334088 | etot = -48.4966726002047 +304000 ekin = 9.83543476976498 | erot = 10.8074962358075 | epot = -69.1396036043513 | etot = -48.4966725987789 +305000 ekin = 9.83532020705529 | erot = 10.7023193346032 | epot = -69.034312136557 | etot = -48.4966725948985 +306000 ekin = 9.6814509355921 | erot = 10.5677982811905 | epot = -68.7459218064291 | etot = -48.4966725896465 +307000 ekin = 9.43697927068364 | erot = 10.412994542271 | epot = -68.3466463972002 | etot = -48.4966725842456 +308000 ekin = 9.1661724436502 | erot = 10.249162357816 | epot = -67.9120073811322 | etot = -48.496672579666 +309000 ekin = 8.92159986059768 | erot = 10.0874162912603 | epot = -67.5056887285244 | etot = -48.4966725766665 +310000 ekin = 8.73563094101779 | erot = 9.93715103612976 | epot = -67.169454552413 | etot = -48.4966725752654 +311000 ekin = 8.61913259831869 | erot = 9.80527711010105 | epot = -66.9210822837978 | etot = -48.496672575378 +312000 ekin = 8.56355763431388 | erot = 9.69617071427367 | epot = -66.7564009251145 | etot = -48.496672576527 +313000 ekin = 8.54744454671114 | erot = 9.61223302156675 | epot = -66.656350146386 | etot = -48.4966725781081 +314000 ekin = 8.54471031362155 | erot = 9.55468856182909 | epot = -66.5960714549809 | etot = -48.4966725795302 +315000 ekin = 8.53582675046024 | erot = 9.52360081783917 | epot = -66.5561001483586 | etot = -48.4966725800592 +316000 ekin = 8.50947902804238 | erot = 9.51910773889645 | epot = -66.5252593469976 | etot = -48.4966725800588 +317000 ekin = 8.46528361606335 | erot = 9.54310287691632 | epot = -66.5050590717948 | etot = -48.4966725788152 +318000 ekin = 8.42148334759255 | erot = 9.59812356340114 | epot = -66.516279487557 | etot = -48.4966725765634 +319000 ekin = 8.41172051683949 | erot = 9.68666529073887 | epot = -66.5950583815213 | etot = -48.4966725739429 +320000 ekin = 8.47631024947879 | erot = 9.81010411287476 | epot = -66.783086934221 | etot = -48.4966725718674 +321000 ekin = 8.64981485684306 | erot = 9.9675001491197 | epot = -67.1139875771924 | etot = -48.4966725712296 +322000 ekin = 8.94886501910658 | erot = 10.1545796242746 | epot = -67.600117215931 | etot = -48.4966725725498 +323000 ekin = 9.36436094196047 | erot = 10.3629464345309 | epot = -68.2239799526371 | etot = -48.4966725761457 +324000 ekin = 9.85762299120414 | erot = 10.5807030497715 | epot = -68.9349986230914 | etot = -48.4966725821158 +325000 ekin = 10.3675336373 | erot = 10.7915336066581 | epot = -69.6557398309782 | etot = -48.4966725870201 +326000 ekin = 10.8169039904013 | erot = 10.978074903065 | epot = -70.2916514882432 | etot = -48.4966725947768 +327000 ekin = 11.1080827251222 | erot = 11.1278633890798 | epot = -70.7326187146627 | etot = -48.4966726004607 +328000 ekin = 11.1668072002134 | erot = 11.235581979125 | epot = -70.8990617814974 | etot = -48.496672602159 +329000 ekin = 10.967403256575 | erot = 11.3047655940369 | epot = -70.768841449533 | etot = -48.4966725989211 +330000 ekin = 10.5471219087206 | erot = 11.3459152750598 | epot = -70.3897097753988 | etot = -48.4966725916185 +331000 ekin = 9.99817977282685 | erot = 11.3709343469158 | epot = -69.8657867027404 | etot = -48.4966725829977 +332000 ekin = 9.43640210775953 | erot = 11.3868472546905 | epot = -69.319921938477 | etot = -48.496672576027 +333000 ekin = 8.96275314870339 | erot = 11.3930028323391 | epot = -68.8524285534048 | etot = -48.4966725723623 +334000 ekin = 8.63845657349899 | erot = 11.382764726995 | epot = -68.5178938722069 | etot = -48.4966725717129 +335000 ekin = 8.47696736446511 | erot = 11.3460820194054 | epot = -68.319721959873 | etot = -48.4966725760025 +336000 ekin = 8.45129453002892 | erot = 11.2716956100397 | epot = -68.2196627183618 | etot = -48.4966725782932 +337000 ekin = 8.52855094859156 | erot = 11.1567863477114 | epot = -68.1820098764486 | etot = -48.4966725801456 +338000 ekin = 8.67667036350068 | erot = 11.0029242666523 | epot = -68.1762672115904 | etot = -48.4966725814374 +339000 ekin = 8.86840718542409 | erot = 10.8141117179581 | epot = -68.1791914857634 | etot = -48.4966725823812 +340000 ekin = 9.08074049345216 | erot = 10.5949858590956 | epot = -68.17239893578 | etot = -48.4966725832323 +341000 ekin = 9.29280025523327 | erot = 10.3497144840385 | epot = -68.1391873233698 | etot = -48.4966725840981 +342000 ekin = 9.48478364390527 | erot = 10.0817821314149 | epot = -68.0632383602007 | etot = -48.4966725848805 +343000 ekin = 9.6388959972346 | erot = 9.79448397039704 | epot = -67.9300525529737 | etot = -48.4966725853421 +344000 ekin = 9.74179750087265 | erot = 9.49171920192241 | epot = -67.7301892880477 | etot = -48.4966725852527 +345000 ekin = 9.78689625540344 | erot = 9.17855510439542 | epot = -67.462123944412 | etot = -48.4966725846132 +346000 ekin = 9.77487619975293 | erot = 8.86098115600662 | epot = -67.132529939332 | etot = -48.4966725835724 +347000 ekin = 9.71190434737071 | erot = 8.54542801625908 | epot = -66.7540049460671 | etot = -48.4966725824373 +348000 ekin = 9.60626623884699 | erot = 8.23797752711893 | epot = -66.3409163474607 | etot = -48.4966725814948 +349000 ekin = 9.46512205486322 | erot = 7.94382241625456 | epot = -65.9056170520253 | etot = -48.4966725809075 +350000 ekin = 9.29263921345323 | erot = 7.66718775568181 | epot = -65.4564995497893 | etot = -48.4966725806542 +351000 ekin = 9.0903070404026 | erot = 7.41172558152282 | epot = -64.998705202447 | etot = -48.4966725805216 +352000 ekin = 8.85964507192677 | erot = 7.18116708497219 | epot = -64.5374847370494 | etot = -48.4966725801504 +353000 ekin = 8.60706719314483 | erot = 6.97993996547515 | epot = -64.0836797376537 | etot = -48.4966725790337 +354000 ekin = 8.35365998681131 | erot = 6.81451510367391 | epot = -63.6648476658683 | etot = -48.4966725753831 +355000 ekin = 8.13817060770625 | erot = 6.6931662282831 | epot = -63.3280094087312 | etot = -48.4966725727419 +356000 ekin = 8.00303344820868 | erot = 6.62071403033337 | epot = -63.1204200476389 | etot = -48.4966725690968 +357000 ekin = 8.00329594806041 | erot = 6.60119920908672 | epot = -63.1011677226111 | etot = -48.496672565464 +358000 ekin = 8.19390069545826 | erot = 6.63655005195628 | epot = -63.3271233108348 | etot = -48.4966725634203 +359000 ekin = 8.60851483671878 | erot = 6.72479591292301 | epot = -63.8299833140608 | etot = -48.496672564419 +360000 ekin = 9.24022555647312 | erot = 6.85875874178493 | epot = -64.5956568672227 | etot = -48.4966725689646 +361000 ekin = 10.0343517665785 | erot = 7.02601171009903 | epot = -65.5570360531846 | etot = -48.4966725765071 +362000 ekin = 10.8949623485542 | erot = 7.21007448014018 | epot = -66.6017094133803 | etot = -48.496672584686 +363000 ekin = 11.7154060072145 | erot = 7.39407842263496 | epot = -67.6061570205514 | etot = -48.496672590702 +364000 ekin = 12.4057223336305 | erot = 7.56453665261263 | epot = -68.4669315836164 | etot = -48.4966725973732 +365000 ekin = 12.8900700952475 | erot = 7.71262358050216 | epot = -69.0993662750096 | etot = -48.4966725992599 +366000 ekin = 13.1382701917133 | erot = 7.83636021669752 | epot = -69.4713030060874 | etot = -48.4966725976766 +367000 ekin = 13.1662433494503 | erot = 7.94108342049927 | epot = -69.6039993640878 | etot = -48.4966725941383 +368000 ekin = 13.0216257321896 | erot = 8.03746300617804 | epot = -69.5557613270778 | etot = -48.4966725887102 +369000 ekin = 12.769963920499 | erot = 8.13884083903498 | epot = -69.405477342997 | etot = -48.496672583463 +370000 ekin = 12.4763633940696 | erot = 8.2585280704997 | epot = -69.2315640444229 | etot = -48.4966725798536 +371000 ekin = 12.1883522141413 | erot = 8.40712894600212 | epot = -69.0921537379891 | etot = -48.4966725778457 +372000 ekin = 11.9337668266525 | erot = 8.59209712213029 | epot = -69.0225365257159 | etot = -48.4966725769331 +373000 ekin = 11.7268114357317 | erot = 8.81820188225653 | epot = -69.0416858943681 | etot = -48.4966725763799 +374000 ekin = 11.5751062922188 | erot = 9.08799140196232 | epot = -69.1597702703438 | etot = -48.4966725761626 +375000 ekin = 11.4816771194436 | erot = 9.40179119698527 | epot = -69.38014089299 | etot = -48.4966725765611 +376000 ekin = 11.4415244462805 | erot = 9.75725267435965 | epot = -69.6954496986156 | etot = -48.4966725779755 +377000 ekin = 11.4364317357126 | erot = 10.1487019288331 | epot = -70.0818062452646 | etot = -48.496672580719 +378000 ekin = 11.4326847178842 | erot = 10.5666289070383 | epot = -70.495986208938 | etot = -48.4966725840156 +379000 ekin = 11.3879261245754 | erot = 10.9960382478821 | epot = -70.8806369610855 | etot = -48.496672588628 +380000 ekin = 11.2500883027076 | erot = 11.4211944009824 | epot = -71.1679552964707 | etot = -48.4966725927807 +381000 ekin = 10.9726921230238 | erot = 11.8269291033838 | epot = -71.2962938221308 | etot = -48.4966725957232 +382000 ekin = 10.5281602154609 | erot = 12.1993149200657 | epot = -71.2241477322819 | etot = -48.4966725967553 +383000 ekin = 9.91669157186262 | erot = 12.5275908716705 | epot = -70.9409550387754 | etot = -48.4966725952423 +384000 ekin = 9.17301492866742 | erot = 12.8043890136623 | epot = -70.4740765341201 | etot = -48.4966725917904 +385000 ekin = 8.36601181966867 | erot = 13.0251847436305 | epot = -69.88786914869 | etot = -48.4966725853908 +386000 ekin = 7.59336935507729 | erot = 13.1937587055513 | epot = -69.2838006385062 | etot = -48.4966725778776 +387000 ekin = 6.96355937774547 | erot = 13.3174316291699 | epot = -68.7776635784017 | etot = -48.4966725714863 +388000 ekin = 6.56667711256593 | erot = 13.4028350179065 | epot = -68.4661846988466 | etot = -48.4966725683742 +389000 ekin = 6.44526911466385 | erot = 13.452341630637 | epot = -68.3942833608618 | etot = -48.4966726155609 +390000 ekin = 6.40022004919714 | erot = 13.5413190039884 | epot = -68.4382116193256 | etot = -48.49667256614 +391000 ekin = 6.74670657780069 | erot = 13.6308036789756 | epot = -68.8741828738666 | etot = -48.4966726170903 +392000 ekin = 7.27053910735973 | erot = 13.5318497226336 | epot = -69.299061444391 | etot = -48.4966726143977 +393000 ekin = 7.84211066747953 | erot = 13.3471669898581 | epot = -69.6859502752907 | etot = -48.496672617953 +394000 ekin = 8.41137168864405 | erot = 13.0851416289724 | epot = -69.9931859369742 | etot = -48.4966726193577 +395000 ekin = 8.94777378650342 | erot = 12.7509585841179 | epot = -70.1954049895143 | etot = -48.4966726188929 +396000 ekin = 9.44412388897363 | erot = 12.3562529221338 | epot = -70.2970494281978 | etot = -48.4966726170903 +397000 ekin = 9.91050995598383 | erot = 11.9175382863925 | epot = -70.3247208568974 | etot = -48.4966726145211 +398000 ekin = 10.3672265667985 | erot = 11.4545225019349 | epot = -70.3184216803495 | etot = -48.4966726116161 +399000 ekin = 10.8377881061497 | erot = 10.9888166293627 | epot = -70.3232773446045 | etot = -48.4966726090921 +400000 ekin = 11.3412083656195 | erot = 10.5421455765466 | epot = -70.3800265495115 | etot = -48.4966726073453 +401000 ekin = 11.8856989725412 | erot = 10.1353050509662 | epot = -70.5176766301703 | etot = -48.4966726066628 +402000 ekin = 12.4648693384634 | erot = 9.78704273789977 | epot = -70.7485846834754 | etot = -48.4966726071122 +403000 ekin = 13.0574032172191 | erot = 9.51287607378396 | epot = -71.0669518996446 | etot = -48.4966726086415 +404000 ekin = 13.6291563424996 | erot = 9.32384163732728 | epot = -71.4496705902089 | etot = -48.496672610382 +405000 ekin = 14.1398204789533 | erot = 9.2249960960061 | epot = -71.8614891889621 | etot = -48.4966726140027 +406000 ekin = 14.5379075448756 | erot = 9.21473993626553 | epot = -72.2493200997454 | etot = -48.4966726186042 +407000 ekin = 14.7678000073509 | erot = 9.28285845910674 | epot = -72.5473310902002 | etot = -48.4966726237426 +408000 ekin = 14.7748392327449 | erot = 9.4128874127938 | epot = -72.6843992735992 | etot = -48.4966726280605 +409000 ekin = 14.5211191199619 | erot = 9.58494933068023 | epot = -72.6027410803212 | etot = -48.496672629679 +410000 ekin = 14.0080722077603 | erot = 9.78050651650688 | epot = -72.2852513515596 | etot = -48.4966726272924 +411000 ekin = 13.2885633490125 | erot = 9.98745844077018 | epot = -71.7726944109714 | etot = -48.4966726211887 +412000 ekin = 12.4602105801987 | erot = 10.2020245096757 | epot = -71.1589077030933 | etot = -48.4966726132189 +413000 ekin = 11.6411968847183 | erot = 10.4265056500499 | epot = -70.564375140538 | etot = -48.4966726057697 +414000 ekin = 10.9403488034326 | erot = 10.6647067440403 | epot = -70.101728148176 | etot = -48.4966726007031 +415000 ekin = 10.4337835958588 | erot = 10.9176175689382 | epot = -69.8480737636831 | etot = -48.4966725988861 +416000 ekin = 10.1537726115972 | erot = 11.1808649833432 | epot = -69.8313101952366 | etot = -48.4966726002962 +417000 ekin = 10.0887098230839 | erot = 11.4440532452565 | epot = -70.0294356728534 | etot = -48.496672604513 +418000 ekin = 10.1900748296287 | erot = 11.691486486043 | epot = -70.3782339258708 | etot = -48.4966726101992 +419000 ekin = 10.3882021396858 | erot = 11.9042621356762 | epot = -70.7891368917029 | etot = -48.4966726163409 +420000 ekin = 10.6068294649459 | erot = 12.0629207258658 | epot = -71.1664228125149 | etot = -48.4966726217032 +421000 ekin = 10.7783620216873 | erot = 12.1507790873922 | epot = -71.4258137343539 | etot = -48.4966726252744 +422000 ekin = 10.8559244969804 | erot = 12.1572275839872 | epot = -71.5098247075458 | etot = -48.4966726265783 +423000 ekin = 10.8187145658879 | erot = 12.0798940410483 | epot = -71.3952812327063 | etot = -48.4966726257701 +424000 ekin = 10.6702271597875 | erot = 11.9248162769282 | epot = -71.0917160601002 | etot = -48.4966726233845 +425000 ekin = 10.4326823761091 | erot = 11.7046834731806 | epot = -70.6340384692427 | etot = -48.4966726199529 +426000 ekin = 10.1418512280332 | erot = 11.4360680199724 | epot = -70.074591863862 | etot = -48.4966726158564 +427000 ekin = 9.84290131625509 | erot = 11.1364780215079 | epot = -69.4760519492879 | etot = -48.4966726115249 +428000 ekin = 9.58662756138332 | erot = 10.821960762199 | epot = -68.9052609309581 | etot = -48.4966726073758 +429000 ekin = 9.42385367708414 | erot = 10.5054247281949 | epot = -68.4259510096258 | etot = -48.4966726043467 +430000 ekin = 9.3932697107341 | erot = 10.1945970633201 | epot = -68.0845393773157 | etot = -48.4966726032615 +431000 ekin = 9.51026104615778 | erot = 9.89118956774573 | epot = -67.8981232184714 | etot = -48.4966726045679 +432000 ekin = 9.76020464999556 | erot = 9.59158522240952 | epot = -67.8484624803521 | etot = -48.496672607947 +433000 ekin = 10.1011132166541 | erot = 9.28935747988458 | epot = -67.8871433087297 | etot = -48.4966726121911 +434000 ekin = 10.477294645398 | erot = 8.97915707053188 | epot = -67.9531243315628 | etot = -48.4966726156329 +435000 ekin = 10.8390965471541 | erot = 8.66047090159804 | epot = -67.9962400658108 | etot = -48.4966726170586 +436000 ekin = 11.1581846566038 | erot = 8.33927074925892 | epot = -67.9941280217146 | etot = -48.4966726158519 +437000 ekin = 11.4322684558217 | erot = 8.02673002723535 | epot = -67.9556710974297 | etot = -48.4966726143726 +438000 ekin = 11.6671720806722 | erot = 7.73476573343809 | epot = -67.8986104279399 | etot = -48.4966726138296 +439000 ekin = 11.8579368223453 | erot = 7.47155579530697 | epot = -67.8261652325874 | etot = -48.4966726149351 +440000 ekin = 11.9818235336916 | erot = 7.23965689692778 | epot = -67.7181530476712 | etot = -48.4966726170518 +441000 ekin = 12.006364309192 | erot = 7.03716778986921 | epot = -67.5402047177844 | etot = -48.4966726187232 +442000 ekin = 11.9008309355917 | erot = 6.85995053948465 | epot = -67.2574540949691 | etot = -48.4966726198928 +443000 ekin = 11.6372457710143 | erot = 6.7022277476632 | epot = -66.8361461367557 | etot = -48.4966726180783 +444000 ekin = 11.2404935703188 | erot = 6.5627400649185 | epot = -66.2999062491644 | etot = -48.496672613927 +445000 ekin = 10.7717210496939 | erot = 6.44292159847087 | epot = -65.7113152554496 | etot = -48.4966726072849 +446000 ekin = 10.3146345400096 | erot = 6.34495994125589 | epot = -65.1562670843396 | etot = -48.4966726030741 +447000 ekin = 9.93895886680335 | erot = 6.2710307219614 | epot = -64.70666218756 | etot = -48.4966725987952 +448000 ekin = 9.70550645607552 | erot = 6.22337425449395 | epot = -64.4255533067951 | etot = -48.4966725962256 +449000 ekin = 9.65303357366369 | erot = 6.20344657437415 | epot = -64.3531527439794 | etot = -48.4966725959415 +450000 ekin = 9.78741215226451 | erot = 6.21100556223012 | epot = -64.4950903140854 | etot = -48.4966725995908 +451000 ekin = 10.0726697694945 | erot = 6.24121610507066 | epot = -64.8105584783442 | etot = -48.4966726037791 +452000 ekin = 10.4498627201324 | erot = 6.28789558017445 | epot = -65.2344309085094 | etot = -48.4966726082025 +453000 ekin = 10.8573529820792 | erot = 6.3442719936139 | epot = -65.6982975879929 | etot = -48.4966726122998 +454000 ekin = 11.2383729595096 | erot = 6.40217211179981 | epot = -66.1372176874634 | etot = -48.496672616154 +455000 ekin = 11.5411597564631 | erot = 6.45158842061622 | epot = -66.4894207972152 | etot = -48.496672620136 +456000 ekin = 11.7145965070118 | erot = 6.48095932011937 | epot = -66.6922284513372 | etot = -48.496672624206 +457000 ekin = 11.7080889258223 | erot = 6.4790494806222 | epot = -66.6838110339246 | etot = -48.4966726274801 +458000 ekin = 11.4817974385589 | erot = 6.43838338689293 | epot = -66.4168534538574 | etot = -48.4966726284056 +459000 ekin = 11.0260461730192 | erot = 6.35890594748302 | epot = -65.8816247459846 | etot = -48.4966726254824 +460000 ekin = 10.3811213891701 | erot = 6.25005112060255 | epot = -65.1278451279305 | etot = -48.4966726181579 +461000 ekin = 9.64500400724202 | erot = 6.13001722355201 | epot = -64.2716938384229 | etot = -48.4966726076289 +462000 ekin = 8.96155334209401 | erot = 6.0232565334345 | epot = -63.4814824659604 | etot = -48.4966725904319 +463000 ekin = 8.49356022962542 | erot = 5.96064229273601 | epot = -62.950875108391 | etot = -48.4966725860295 +464000 ekin = 8.31098322697756 | erot = 5.95399558728201 | epot = -62.7616514010784 | etot = -48.4966725868188 +465000 ekin = 8.41527289815257 | erot = 6.00555163247755 | epot = -62.9174971227792 | etot = -48.496672592149 +466000 ekin = 8.74071951180125 | erot = 6.107452024617 | epot = -63.3448441360316 | etot = -48.4966725996134 +467000 ekin = 8.88640654813702 | erot = 6.32601497563827 | epot = -63.7090940524723 | etot = -48.496672528697 +468000 ekin = 9.0750516035454 | erot = 6.75512448038786 | epot = -64.326848641194 | etot = -48.4966725572607 +469000 ekin = 9.43618930725295 | erot = 6.98018590406613 | epot = -64.9130477256858 | etot = -48.4966725143667 +470000 ekin = 9.5389192890748 | erot = 7.05614003952522 | epot = -65.0917318419334 | etot = -48.4966725133334 +471000 ekin = 9.47129866737627 | erot = 7.09012582275068 | epot = -65.0580969994753 | etot = -48.4966725093484 +472000 ekin = 9.29219039280112 | erot = 7.08038845059064 | epot = -64.8692513473263 | etot = -48.4966725039346 +473000 ekin = 9.07859106335565 | erot = 7.03223766261859 | epot = -64.6075012242425 | etot = -48.4966724982683 +474000 ekin = 8.90859119064582 | erot = 6.95657374542113 | epot = -64.361837429149 | etot = -48.4966724930821 +475000 ekin = 8.85085237787058 | erot = 6.86788557827541 | epot = -64.2154104450232 | etot = -48.4966724888772 +476000 ekin = 8.95844704209607 | erot = 6.78173938268418 | epot = -64.2368589107825 | etot = -48.4966724860022 +477000 ekin = 9.26445642862314 | erot = 6.71235576615976 | epot = -64.4734846830834 | etot = -48.4966724883005 +478000 ekin = 9.75673758778867 | erot = 6.67310243746892 | epot = -64.9265125143914 | etot = -48.4966724891338 +479000 ekin = 10.4083719414133 | erot = 6.67104131549829 | epot = -65.5760857486891 | etot = -48.4966724917775 +480000 ekin = 11.1786387693468 | erot = 6.70609770624713 | epot = -66.3814089720745 | etot = -48.4966724964806 +481000 ekin = 11.9550179833301 | erot = 6.77573712918461 | epot = -67.2274276420803 | etot = -48.4966725295657 +482000 ekin = 12.1969877154023 | erot = 6.97182101607883 | epot = -67.6654811323096 | etot = -48.4966724008285 +483000 ekin = 12.8315687003902 | erot = 7.27453378457519 | epot = -68.6027750201801 | etot = -48.4966725352147 +484000 ekin = 13.1379089548489 | erot = 7.35121017880495 | epot = -68.9857915491995 | etot = -48.4966724155457 +485000 ekin = 13.1455744815352 | erot = 7.39132031002879 | epot = -69.0335672082532 | etot = -48.4966724166892 +486000 ekin = 12.8847677059838 | erot = 7.41820327748147 | epot = -68.7996433973739 | etot = -48.4966724139086 +487000 ekin = 12.3995023295598 | erot = 7.43730294196129 | epot = -68.3334776793774 | etot = -48.4966724078564 +488000 ekin = 11.7801246298141 | erot = 7.45872842904693 | epot = -67.7355254587262 | etot = -48.4966723998652 +489000 ekin = 11.1454971166853 | erot = 7.49387389619964 | epot = -67.136043404651 | etot = -48.4966723917661 +490000 ekin = 10.6174118656706 | erot = 7.55177149139563 | epot = -66.6658557428531 | etot = -48.4966723857869 +491000 ekin = 10.2893788237227 | erot = 7.63548116160718 | epot = -66.4215323695175 | etot = -48.4966723841876 +492000 ekin = 10.1956274375869 | erot = 7.73922358367483 | epot = -66.4315234095995 | etot = -48.4966723883378 +493000 ekin = 10.2924671649369 | erot = 7.84793186661483 | epot = -66.6370714290956 | etot = -48.4966723975439 +494000 ekin = 10.4668249564063 | erot = 7.94111684624392 | epot = -66.9046142110693 | etot = -48.4966724084191 +495000 ekin = 10.5791383442144 | erot = 8.00124026344057 | epot = -67.0770510235223 | etot = -48.4966724158674 +496000 ekin = 10.5277635544545 | erot = 8.0234243897172 | epot = -67.0478603600559 | etot = -48.4966724158843 +497000 ekin = 10.3008638582113 | erot = 8.02081822154823 | epot = -66.8183544879829 | etot = -48.4966724082233 +498000 ekin = 9.9830300829441 | erot = 8.02168645226284 | epot = -66.501388931739 | etot = -48.496672396532 +499000 ekin = 9.71342589197285 | erot = 8.05962720417813 | epot = -66.2697254820144 | etot = -48.4966723858634 +500000 ekin = 9.6235168911854 | erot = 8.16244515239849 | epot = -66.2826344235657 | etot = -48.4966723799818 +501000 ekin = 9.78787333398157 | erot = 8.3444730367172 | epot = -66.629018750896 | etot = -48.4966723801973 +502000 ekin = 10.2050108702155 | erot = 8.60370485257146 | epot = -67.3053881085791 | etot = -48.4966723857921 +503000 ekin = 10.8051989673788 | erot = 8.92246829120059 | epot = -68.2243396537846 | etot = -48.4966723952051 +504000 ekin = 11.4710453968967 | erot = 9.26984220618396 | epot = -69.2375600100513 | etot = -48.4966724069707 +505000 ekin = 12.0583532741101 | erot = 9.60506055558158 | epot = -70.160086249331 | etot = -48.4966724196392 +506000 ekin = 12.4169616297787 | erot = 9.88273601241314 | epot = -70.7963700728992 | etot = -48.4966724307074 +507000 ekin = 12.4225762031031 | erot = 10.0614429671167 | epot = -70.9806916064419 | etot = -48.496672436222 +508000 ekin = 12.0224546476675 | erot = 10.1150484289833 | epot = -70.6341755095221 | etot = -48.4966724328713 +509000 ekin = 11.2713256107343 | erot = 10.0417150354825 | epot = -69.8097130671352 | etot = -48.4966724209184 +510000 ekin = 10.3259224264145 | erot = 9.86440101432832 | epot = -68.6869958451572 | etot = -48.4966724044144 +511000 ekin = 9.39566767793053 | erot = 9.62224126641417 | epot = -67.5145813329279 | etot = -48.4966723885832 +512000 ekin = 8.67739606863164 | erot = 9.35823452028457 | epot = -66.5323029667235 | etot = -48.4966723778073 +513000 ekin = 8.30173505000993 | erot = 9.10874451689391 | epot = -65.9071519407483 | etot = -48.4966723738445 +514000 ekin = 8.31133758538756 | erot = 8.90213046051507 | epot = -65.710140421329 | etot = -48.4966723754264 +515000 ekin = 8.65105183696316 | erot = 8.7514282302608 | epot = -65.8991524513801 | etot = -48.4966723841561 +516000 ekin = 9.19545504792417 | erot = 8.65020590792967 | epot = -66.3423333510927 | etot = -48.4966723952388 +517000 ekin = 9.78948013470045 | erot = 8.58459334669478 | epot = -66.8707458885787 | etot = -48.4966724071835 +518000 ekin = 10.2719405201907 | erot = 8.53610767680698 | epot = -67.3047206151279 | etot = -48.4966724181302 +519000 ekin = 10.5035619038422 | erot = 8.48509741614985 | epot = -67.4853317483345 | etot = -48.4966724283424 +520000 ekin = 10.3837804903591 | erot = 8.41855293465755 | epot = -67.2990058537329 | etot = -48.4966724287163 +521000 ekin = 9.91971480302427 | erot = 8.33012920363259 | epot = -66.7465164259076 | etot = -48.4966724192507 +522000 ekin = 9.25580910193788 | erot = 8.22471517249033 | epot = -65.9771966777207 | etot = -48.4966724032925 +523000 ekin = 8.61677254360916 | erot = 8.11873116220433 | epot = -65.2321760932319 | etot = -48.4966723874184 +524000 ekin = 8.22312599613015 | erot = 8.03533827067386 | epot = -64.7551366426032 | etot = -48.4966723757992 +525000 ekin = 8.2309691908796 | erot = 7.99952905918643 | epot = -64.7271706203461 | etot = -48.49667237028 +526000 ekin = 8.70541343261598 | erot = 8.03327780743259 | epot = -65.2353636116279 | etot = -48.4966723715793 +527000 ekin = 9.61054447377517 | erot = 8.14859195684391 | epot = -66.2558088113309 | etot = -48.4966723807118 +528000 ekin = 10.8064190209308 | erot = 8.34203048718433 | epot = -67.6451219042434 | etot = -48.4966723961283 +529000 ekin = 12.0748947021392 | erot = 8.59301141009918 | epot = -69.1645785259815 | etot = -48.4966724137432 +530000 ekin = 13.1772899053561 | erot = 8.86731230216095 | epot = -70.5412746358192 | etot = -48.4966724283022 +531000 ekin = 13.9222479329561 | erot = 9.12596646781095 | epot = -71.5448868367725 | etot = -48.4966724360055 +532000 ekin = 14.2109040109712 | erot = 9.33621159867702 | epot = -72.0437880461094 | etot = -48.4966724364612 +533000 ekin = 14.0393496048364 | erot = 9.47948522986669 | epot = -72.0155072660307 | etot = -48.4966724313276 +534000 ekin = 13.4765937110865 | erot = 9.55437050378899 | epot = -71.5276366366405 | etot = -48.496672421765 +535000 ekin = 12.6476855098919 | erot = 9.57521298744177 | epot = -70.719570906192 | etot = -48.4966724088584 +536000 ekin = 11.7187499511448 | erot = 9.56662150363136 | epot = -69.7820438499262 | etot = -48.4966723951501 +537000 ekin = 10.8667161281277 | erot = 9.55558575468458 | epot = -68.9189742665298 | etot = -48.4966723837175 +538000 ekin = 10.2407642556974 | erot = 9.56460479423064 | epot = -68.302041426641 | etot = -48.496672376713 +539000 ekin = 9.93256310316437 | erot = 9.60813474995735 | epot = -68.0373702280363 | etot = -48.4966723749146 +540000 ekin = 9.9663505946704 | erot = 9.69366995189707 | epot = -68.1566929217508 | etot = -48.4966723751834 +541000 ekin = 10.3033434566754 | erot = 9.82452773464469 | epot = -68.6245435738886 | etot = -48.4966723825685 +542000 ekin = 10.8374546472347 | erot = 9.99210203741248 | epot = -69.3262290766553 | etot = -48.4966723920081 +543000 ekin = 11.4320363086548 | erot = 10.1839460987212 | epot = -70.1126548089748 | etot = -48.4966724015988 +544000 ekin = 11.9481549488554 | erot = 10.3868550358245 | epot = -70.8316823942835 | etot = -48.4966724096036 +545000 ekin = 12.2696023022718 | erot = 10.5892508892387 | epot = -71.3555256062342 | etot = -48.4966724147236 +546000 ekin = 12.321748370744 | erot = 10.7831241363479 | epot = -71.601544923376 | etot = -48.4966724162841 +547000 ekin = 12.0815090899527 | erot = 10.9652333443141 | epot = -71.5434148485646 | etot = -48.4966724142979 +548000 ekin = 11.5772594483929 | erot = 11.1370572249374 | epot = -71.2109890828874 | etot = -48.4966724095571 +549000 ekin = 10.8796146423249 | erot = 11.3027415301181 | epot = -70.6790285755882 | etot = -48.4966724031452 +550000 ekin = 10.0861650600294 | erot = 11.4673420616665 | epot = -70.0501795179829 | etot = -48.496672396287 +551000 ekin = 9.30420856247628 | erot = 11.6346062512735 | epot = -69.435487203823 | etot = -48.4966723900733 +552000 ekin = 8.63456852509588 | erot = 11.8051739021005 | epot = -68.9364148125888 | etot = -48.4966723853924 +553000 ekin = 8.15765857136581 | erot = 11.9755314527045 | epot = -68.6298624070135 | etot = -48.4966723829432 +554000 ekin = 7.92204387518784 | erot = 12.1379035109131 | epot = -68.5566197692493 | etot = -48.4966723831483 +555000 ekin = 7.93668594953939 | erot = 12.2813102395747 | epot = -68.7146685751332 | etot = -48.4966723860191 +556000 ekin = 8.16908147819853 | erot = 12.393779334281 | epot = -69.0595332034403 | etot = -48.4966723909608 +557000 ekin = 8.55144497214368 | erot = 12.465479172799 | epot = -69.5135965418038 | etot = -48.4966723968611 +558000 ekin = 8.99506879124846 | erot = 12.4919043884403 | epot = -69.9836455819986 | etot = -48.4966724023098 +559000 ekin = 9.40988612193979 | erot = 12.4759637500258 | epot = -70.3825222781016 | etot = -48.496672406136 +560000 ekin = 9.72239125491496 | erot = 12.4279361391034 | epot = -70.6469998020326 | etot = -48.4966724080143 +561000 ekin = 9.88412985938752 | erot = 12.3629252843669 | epot = -70.7437275521904 | etot = -48.4966724084359 +562000 ekin = 9.87014392595536 | erot = 12.2969140239725 | epot = -70.6637303578499 | etot = -48.496672407922 +563000 ekin = 9.67269052989872 | erot = 12.2435461742526 | epot = -70.4129091125218 | etot = -48.4966724083705 +564000 ekin = 9.29561869669046 | erot = 12.2123745870917 | epot = -70.0046656893348 | etot = -48.4966724055526 +565000 ekin = 8.77967610202421 | erot = 12.2075615849193 | epot = -69.4839100880982 | etot = -48.4966724011548 +566000 ekin = 8.19459477314837 | erot = 12.2284388471803 | epot = -68.9197060163001 | etot = -48.4966723959714 +567000 ekin = 7.62573923577576 | erot = 12.2693533996224 | epot = -68.391765026759 | etot = -48.4966723913608 +568000 ekin = 7.15404054173824 | erot = 12.3199400383766 | epot = -67.9706529685886 | etot = -48.4966723884738 +569000 ekin = 6.83717313904365 | erot = 12.3666389683575 | epot = -67.7004844951495 | etot = -48.4966723877484 +570000 ekin = 6.69956781443878 | erot = 12.3955125883792 | epot = -67.5917527916869 | etot = -48.4966723888689 +571000 ekin = 6.73320809574575 | erot = 12.3955019363285 | epot = -67.6253824231304 | etot = -48.4966723910561 +572000 ekin = 6.90669043361352 | erot = 12.360901189443 | epot = -67.7642640151546 | etot = -48.496672392098 +573000 ekin = 7.18429647793752 | erot = 12.295129955523 | epot = -67.9760988286113 | etot = -48.4966723951508 +574000 ekin = 7.52006639731463 | erot = 12.2050646486354 | epot = -68.2218034426913 | etot = -48.4966723967412 +575000 ekin = 7.87441000611595 | erot = 12.0985403159086 | epot = -68.4696227186239 | etot = -48.4966723965993 +576000 ekin = 8.23152231474211 | erot = 11.9863053711619 | epot = -68.7145000810317 | etot = -48.4966723951277 +577000 ekin = 8.59621090775485 | erot = 11.88029454746 | epot = -68.9731778482791 | etot = -48.4966723930643 +578000 ekin = 8.98550446109966 | erot = 11.7917589254419 | epot = -69.273935777607 | etot = -48.4966723910654 +579000 ekin = 9.42040764629998 | erot = 11.7296557361017 | epot = -69.6467357719303 | etot = -48.4966723895287 +580000 ekin = 9.92026928438504 | erot = 11.6994636247959 | epot = -70.1164052981462 | etot = -48.4966723889653 +581000 ekin = 10.481235625959 | erot = 11.7036776252937 | epot = -70.6815856416595 | etot = -48.4966723904068 +582000 ekin = 11.0803741506679 | erot = 11.7381628956894 | epot = -71.315209439996 | etot = -48.4966723936387 +583000 ekin = 11.6832905433026 | erot = 11.7898051581773 | epot = -71.969768100988 | etot = -48.496672399508 +584000 ekin = 12.2265963017921 | erot = 11.8360805991725 | epot = -72.5593493093226 | etot = -48.4966724083579 +585000 ekin = 12.6146924454376 | erot = 11.8453302035058 | epot = -72.956695067911 | etot = -48.4966724189676 +586000 ekin = 12.7381776543518 | erot = 11.7813880279948 | epot = -73.016238110557 | etot = -48.4966724282105 +587000 ekin = 12.5064805858927 | erot = 11.6131474319877 | epot = -72.6163004503534 | etot = -48.4966724324729 +588000 ekin = 11.8864734315384 | erot = 11.3251009524907 | epot = -71.708246812138 | etot = -48.4966724281089 +589000 ekin = 10.9473869135698 | erot = 10.9235098586354 | epot = -70.3675691877464 | etot = -48.4966724155412 +590000 ekin = 9.86035696870277 | erot = 10.4344934448947 | epot = -68.7915228116269 | etot = -48.4966723980295 +591000 ekin = 8.856315097301 | erot = 9.8962156264538 | epot = -67.24920310466 | etot = -48.4966723809053 +592000 ekin = 8.15513077394364 | erot = 9.34935781082713 | epot = -66.0011609546423 | etot = -48.4966723698715 +593000 ekin = 7.88860666870599 | erot = 8.82965609771594 | epot = -65.2149351345128 | etot = -48.4966723680909 +594000 ekin = 8.05760926843084 | erot = 8.36349649514688 | epot = -64.917778137945 | etot = -48.4966723743673 +595000 ekin = 8.55177999823075 | erot = 7.96715997621382 | epot = -65.0156123581699 | etot = -48.4966723837253 +596000 ekin = 9.20240795646494 | erot = 7.64971555618372 | epot = -65.3487959078275 | etot = -48.4966723951788 +597000 ekin = 9.82563991116664 | erot = 7.41365255171618 | epot = -65.7359648662224 | etot = -48.4966724033396 +598000 ekin = 10.2831958981112 | erot = 7.25474571550897 | epot = -66.0346140226854 | etot = -48.4966724090653 +599000 ekin = 10.4823548481571 | erot = 7.16384844598274 | epot = -66.1428757063982 | etot = -48.4966724122583 +600000 ekin = 10.377655957699 | erot = 7.12899314635559 | epot = -66.0033215164734 | etot = -48.4966724124188 +601000 ekin = 9.97447570388701 | erot = 7.1388129593999 | epot = -65.6099610722624 | etot = -48.4966724089755 +602000 ekin = 9.33239148581919 | erot = 7.18604650076208 | epot = -65.0151103884962 | etot = -48.4966724019149 +603000 ekin = 8.56059728304323 | erot = 7.26939823175125 | epot = -64.3266679072083 | etot = -48.4966723924139 +604000 ekin = 7.7984442591758 | erot = 7.39226229321183 | epot = -63.6873789354487 | etot = -48.4966723830611 +605000 ekin = 7.18334355707592 | erot = 7.55875733480148 | epot = -63.2387732678989 | etot = -48.4966723760215 +606000 ekin = 6.82339792281676 | erot = 7.77079572204939 | epot = -63.0908660164771 | etot = -48.4966723716109 +607000 ekin = 6.78106761298459 | erot = 8.02640715106275 | epot = -63.3041471355128 | etot = -48.4966723714655 +608000 ekin = 7.06650520946426 | erot = 8.31925929524446 | epot = -63.8824368788658 | etot = -48.4966723741571 +609000 ekin = 7.64869014780975 | erot = 8.64063737883881 | epot = -64.7859999056167 | etot = -48.4966723789681 +610000 ekin = 8.45880674200776 | erot = 8.97898134769688 | epot = -65.9344604774328 | etot = -48.4966723877281 +611000 ekin = 9.4001263207956 | erot = 9.32028280864193 | epot = -67.2170815245993 | etot = -48.4966723951617 +612000 ekin = 10.3724864441584 | erot = 9.65110388613771 | epot = -68.5202627333548 | etot = -48.4966724030588 +613000 ekin = 11.273882244626 | erot = 9.9556440821821 | epot = -69.72619873741 | etot = -48.4966724106019 +614000 ekin = 12.0134738011408 | erot = 10.2166935701722 | epot = -70.7268397870958 | etot = -48.4966724157829 +615000 ekin = 12.5325228236381 | erot = 10.4217069668423 | epot = -71.450902207423 | etot = -48.4966724169425 +616000 ekin = 12.8258294711986 | erot = 10.566474545366 | epot = -71.8889764297518 | etot = -48.4966724131872 +617000 ekin = 12.9484167495066 | erot = 10.6576196901733 | epot = -72.1027088454161 | etot = -48.4966724057361 +618000 ekin = 12.998475466013 | erot = 10.7112673342273 | epot = -72.2064151975271 | etot = -48.4966723972868 +619000 ekin = 13.0833633892071 | erot = 10.7483523556986 | epot = -72.3283881359039 | etot = -48.4966723909983 +620000 ekin = 13.2805224346224 | erot = 10.7880868966453 | epot = -72.5652817201107 | etot = -48.496672388843 +621000 ekin = 13.6153158270094 | erot = 10.8424788949038 | epot = -72.9544671127491 | etot = -48.4966723908359 +622000 ekin = 14.0617052044724 | erot = 10.9128304448974 | epot = -73.4712080455024 | etot = -48.4966723961327 +623000 ekin = 14.5562524522845 | erot = 10.9888554747774 | epot = -74.0417803304225 | etot = -48.4966724033606 +624000 ekin = 15.0184966479576 | erot = 11.0501520933367 | epot = -74.5653211518535 | etot = -48.4966724105592 +625000 ekin = 15.3740067441191 | erot = 11.0719318061176 | epot = -74.9426109653785 | etot = -48.4966724151418 +626000 ekin = 15.5799785500671 | erot = 11.0340258807545 | epot = -75.1106768463317 | etot = -48.4966724155101 +627000 ekin = 15.6387406868734 | erot = 10.9274345484273 | epot = -75.0628476476668 | etot = -48.4966724123662 +628000 ekin = 15.5850466430457 | erot = 10.7544368612362 | epot = -74.8361559131403 | etot = -48.4966724088584 +629000 ekin = 15.4527585941032 | erot = 10.5222074068767 | epot = -74.4716384084828 | etot = -48.4966724075029 +630000 ekin = 15.248764071319 | erot = 10.236990405301 | epot = -73.9824268849356 | etot = -48.4966724083155 +631000 ekin = 14.95463085986 | erot = 9.90350592616926 | epot = -73.3548091955386 | etot = -48.4966724095093 +632000 ekin = 14.54712971678 | erot = 9.5277824876148 | epot = -72.571584613696 | etot = -48.4966724093012 +633000 ekin = 14.0259983537383 | erot = 9.11935081551797 | epot = -71.6420215737048 | etot = -48.4966724044485 +634000 ekin = 13.434893448823 | erot = 8.69195919089113 | epot = -70.6235250390489 | etot = -48.4966723993348 +635000 ekin = 12.824895827622 | erot = 8.26734491149425 | epot = -69.588913133081 | etot = -48.4966723939648 +636000 ekin = 12.2634798858286 | erot = 7.86620866048542 | epot = -68.6263609335687 | etot = -48.4966723872547 +637000 ekin = 11.837830509145 | erot = 7.50870022731589 | epot = -67.8432031168793 | etot = -48.4966723804184 +638000 ekin = 11.6379266194863 | erot = 7.21309192661843 | epot = -67.3476909220041 | etot = -48.4966723758993 +639000 ekin = 11.7309756691688 | erot = 6.99358509588195 | epot = -67.2212331386168 | etot = -48.496672373566 +640000 ekin = 12.1483860992341 | erot = 6.85513197122735 | epot = -67.5001904464754 | etot = -48.4966723760139 +641000 ekin = 12.8580389630413 | erot = 6.79197676459362 | epot = -68.1466881104838 | etot = -48.4966723828488 +642000 ekin = 13.7676241865003 | erot = 6.78663459550888 | epot = -69.0509311759616 | etot = -48.4966723939524 +643000 ekin = 14.7311148046696 | erot = 6.81269225386592 | epot = -70.0404794653553 | etot = -48.4966724068198 +644000 ekin = 15.5770857379772 | erot = 6.83998967566151 | epot = -70.9137478319373 | etot = -48.4966724182986 +645000 ekin = 16.1508405485681 | erot = 6.84150218313639 | epot = -71.4890151571444 | etot = -48.4966724254399 +646000 ekin = 16.3517339377883 | erot = 6.79972807951154 | epot = -71.648134444135 | etot = -48.4966724268351 +647000 ekin = 16.1521813975647 | erot = 6.71011075276661 | epot = -71.3589645731898 | etot = -48.4966724228584 +648000 ekin = 15.5941452915208 | erot = 6.58036041653718 | epot = -70.6711781232478 | etot = -48.4966724151898 +649000 ekin = 14.7689091851051 | erot = 6.42695236576629 | epot = -69.6925339568818 | etot = -48.4966724060104 +650000 ekin = 13.7897851522141 | erot = 6.27009414211622 | epot = -68.5565516915737 | etot = -48.4966723972434 +651000 ekin = 12.7827854664051 | erot = 6.12965793188258 | epot = -67.4091157839821 | etot = -48.4966723856945 +652000 ekin = 11.8480628892581 | erot = 6.02011822013316 | epot = -66.3648534922347 | etot = -48.4966723828435 +653000 ekin = 11.0202985972855 | erot = 5.94865375231979 | epot = -65.4656247316048 | etot = -48.4966723819995 +654000 ekin = 10.3091031180511 | erot = 5.91728137273322 | epot = -64.7230568732843 | etot = -48.4966723825 +655000 ekin = 9.70839056866602 | erot = 5.92392072357778 | epot = -64.1289836757749 | etot = -48.4966723835311 +656000 ekin = 9.20726106552158 | erot = 5.96375787161147 | epot = -63.6676913214733 | etot = -48.4966723843402 +657000 ekin = 8.80019228939797 | erot = 6.03073521946339 | epot = -63.3275998932172 | etot = -48.4966723843559 +658000 ekin = 8.49429330450483 | erot = 6.1190138686194 | epot = -63.1099795564599 | etot = -48.4966723833357 +659000 ekin = 8.31163970856305 | erot = 6.22415392600457 | epot = -63.0324660160693 | etot = -48.4966723815017 +660000 ekin = 8.28571687286792 | erot = 6.3435948195595 | epot = -63.1259840718644 | etot = -48.496672379437 +661000 ekin = 8.45063623899349 | erot = 6.47625697361695 | epot = -63.4235655911201 | etot = -48.4966723785096 +662000 ekin = 8.82527447353651 | erot = 6.62126989868729 | epot = -63.94321675186 | etot = -48.4966723796362 +663000 ekin = 9.37687400900737 | erot = 6.77176565509087 | epot = -64.6453120555835 | etot = -48.4966723914853 +664000 ekin = 10.0161883294264 | erot = 6.91673471720662 | epot = -65.4295954443851 | etot = -48.496672397752 +665000 ekin = 10.6568075638947 | erot = 7.05202630081342 | epot = -66.2055062689187 | etot = -48.4966724042105 +666000 ekin = 11.2095129988519 | erot = 7.17560031622941 | epot = -66.8817857236931 | etot = -48.4966724086119 +667000 ekin = 11.6073208198796 | erot = 7.28956566888112 | epot = -67.3935588982907 | etot = -48.4966724095301 +668000 ekin = 11.8262434817302 | erot = 7.40047545940011 | epot = -67.7233913480593 | etot = -48.496672406929 +669000 ekin = 11.8877773970608 | erot = 7.51673035653278 | epot = -67.9011801559119 | etot = -48.4966724023183 +670000 ekin = 11.8402449204143 | erot = 7.64485197464031 | epot = -67.9817692944891 | etot = -48.4966723994345 +671000 ekin = 11.7215972605913 | erot = 7.78648852074884 | epot = -68.0047581789147 | etot = -48.4966723975746 +672000 ekin = 11.5567362165189 | erot = 7.94128453333614 | epot = -67.9946931463828 | etot = -48.4966723965278 +673000 ekin = 11.3570416452435 | erot = 8.10916533384796 | epot = -67.962879375194 | etot = -48.4966723961026 +674000 ekin = 11.1259919200534 | erot = 8.29215560391109 | epot = -67.9148199183824 | etot = -48.4966723944179 +675000 ekin = 10.8743945879396 | erot = 8.49470509392965 | epot = -67.8657720757233 | etot = -48.496672393854 +676000 ekin = 10.6087709728526 | erot = 8.72185603052384 | epot = -67.8272993961854 | etot = -48.4966723928089 +677000 ekin = 10.3411925527036 | erot = 8.97814779627434 | epot = -67.8160127408758 | etot = -48.4966723918979 +678000 ekin = 10.086083558261 | erot = 9.2651688180331 | epot = -67.8479247679199 | etot = -48.4966723916259 +679000 ekin = 9.85460690268808 | erot = 9.57959119578934 | epot = -67.9308704906975 | etot = -48.4966723922201 +680000 ekin = 9.65193484612734 | erot = 9.91222749425356 | epot = -68.0608347339777 | etot = -48.4966723935968 +681000 ekin = 9.47778674052705 | erot = 10.2481668373654 | epot = -68.2226259733431 | etot = -48.4966723954506 +682000 ekin = 9.32915693407332 | erot = 10.5680491154085 | epot = -68.3938784468612 | etot = -48.4966723973794 +683000 ekin = 9.20359209996506 | erot = 10.8502901106042 | epot = -68.5505546096265 | etot = -48.4966723990572 +684000 ekin = 9.10057910431442 | erot = 11.0738485405146 | epot = -68.6711000474925 | etot = -48.4966724026635 +685000 ekin = 9.00949165145505 | erot = 11.2173796934396 | epot = -68.7235437496383 | etot = -48.4966724047436 +686000 ekin = 8.91345829622965 | erot = 11.2659265086073 | epot = -68.6760572115373 | etot = -48.4966724067003 +687000 ekin = 8.79289020082353 | erot = 11.214641842958 | epot = -68.504204452004 | etot = -48.4966724082225 +688000 ekin = 8.6269958520518 | erot = 11.068753511123 | epot = -68.1924217716564 | etot = -48.4966724084816 +689000 ekin = 8.40629613755178 | erot = 10.8436392121208 | epot = -67.7466077560442 | etot = -48.4966724063716 +690000 ekin = 8.14912332622908 | erot = 10.5636669227552 | epot = -67.2094626501689 | etot = -48.4966724011846 +691000 ekin = 7.9124665079121 | erot = 10.2598630018305 | epot = -66.6690019031216 | etot = -48.496672393379 +692000 ekin = 7.78649732433392 | erot = 9.9663674739445 | epot = -66.2495371832041 | etot = -48.4966723849257 +693000 ekin = 7.86849983070142 | erot = 9.71571779720549 | epot = -66.0808900067404 | etot = -48.4966723788335 +694000 ekin = 8.22337408862048 | erot = 9.53345750684774 | epot = -66.2535039733568 | etot = -48.4966723778886 +695000 ekin = 8.84810602229034 | erot = 9.43320257925922 | epot = -66.7779809848027 | etot = -48.4966723832531 +696000 ekin = 9.65887172689219 | erot = 9.41372191367251 | epot = -67.5692660343492 | etot = -48.4966723937845 +697000 ekin = 10.5087480404009 | erot = 9.45932512209752 | epot = -68.4647455690601 | etot = -48.4966724065617 +698000 ekin = 11.2285190602726 | erot = 9.5438048007253 | epot = -69.2689962790206 | etot = -48.4966724180227 +699000 ekin = 11.6741833078953 | erot = 9.63725123843725 | epot = -69.808106971432 | etot = -48.4966724250994 +700000 ekin = 11.7654350682691 | erot = 9.71395728257181 | epot = -69.9760647768934 | etot = -48.4966724260525 +701000 ekin = 11.5047049794079 | erot = 9.75894077488325 | epot = -69.7603181752266 | etot = -48.4966724209354 +702000 ekin = 10.9724403692017 | erot = 9.77075075363618 | epot = -69.2398635344041 | etot = -48.4966724115662 +703000 ekin = 10.3024076279287 | erot = 9.75981202327702 | epot = -68.558892051938 | etot = -48.4966724007323 +704000 ekin = 9.64337665021832 | erot = 9.74344885657128 | epot = -67.883497898486 | etot = -48.4966723916964 +705000 ekin = 9.1179525518903 | erot = 9.73742730798015 | epot = -67.3520522450809 | etot = -48.4966723852105 +706000 ekin = 8.8126363956072 | erot = 9.75421899341161 | epot = -67.063527770709 | etot = -48.4966723816902 +707000 ekin = 8.77338019585092 | erot = 9.80175401548544 | epot = -67.0718065920222 | etot = -48.4966723806858 +708000 ekin = 9.01138622824448 | erot = 9.88360177657119 | epot = -67.3916603862582 | etot = -48.4966723814425 +709000 ekin = 9.50747988008547 | erot = 9.99905418993988 | epot = -68.0032064559779 | etot = -48.4966723859526 +710000 ekin = 10.2098084032625 | erot = 10.1416258356114 | epot = -68.8481066295808 | etot = -48.4966723907069 +711000 ekin = 11.0523389499236 | erot = 10.2998854255891 | epot = -69.8488967723657 | etot = -48.4966723968529 +712000 ekin = 11.9521069746156 | erot = 10.4562138303948 | epot = -70.9049932100343 | etot = -48.4966724050239 +713000 ekin = 12.8150465431179 | erot = 10.5882970351902 | epot = -71.9000159909055 | etot = -48.4966724125975 +714000 ekin = 13.5573027723637 | erot = 10.6741841238219 | epot = -72.72815931429 | etot = -48.4966724181044 +715000 ekin = 14.1179857007345 | erot = 10.6957124385956 | epot = -73.3103705602691 | etot = -48.496672420939 +716000 ekin = 14.4699787524279 | erot = 10.6432681547871 | epot = -73.6099193272276 | etot = -48.4966724200126 +717000 ekin = 14.6304817620082 | erot = 10.5193699651724 | epot = -73.6465241431589 | etot = -48.4966724159783 +718000 ekin = 14.6433398085898 | erot = 10.3369378980817 | epot = -73.4769501191217 | etot = -48.4966724124502 +719000 ekin = 14.5613025266538 | erot = 10.116304495103 | epot = -73.1742794287171 | etot = -48.4966724069602 +720000 ekin = 14.4440802771762 | erot = 9.88263320853942 | epot = -72.8233858887771 | etot = -48.4966724030615 +721000 ekin = 14.32669248658 | erot = 9.66028301118916 | epot = -72.4836478994602 | etot = -48.496672401691 +722000 ekin = 14.208213950476 | erot = 9.46998100555901 | epot = -72.1748673588971 | etot = -48.4966724028621 +723000 ekin = 14.0535356867324 | erot = 9.32739231072085 | epot = -71.8776004030704 | etot = -48.4966724056172 +724000 ekin = 13.8083025959258 | erot = 9.24288552357026 | epot = -71.547860527913 | etot = -48.496672408417 +725000 ekin = 13.4217406291513 | erot = 9.2221793968949 | epot = -71.1405924357641 | etot = -48.4966724097179 +726000 ekin = 12.8688682445621 | erot = 9.26761054125373 | epot = -70.633151194327 | etot = -48.4966724085112 +727000 ekin = 12.164418505818 | erot = 9.3797232402829 | epot = -70.0408141507457 | etot = -48.4966724046448 +728000 ekin = 11.3639426094184 | erot = 9.55857934570968 | epot = -69.4191943540654 | etot = -48.4966723989373 +729000 ekin = 10.5512882155533 | erot = 9.80396099269058 | epot = -68.8519216012415 | etot = -48.4966723929976 +730000 ekin = 9.81740771755529 | erot = 10.1147074882675 | epot = -68.4287875941947 | etot = -48.496672388372 +731000 ekin = 9.23253818700049 | erot = 10.4853428846381 | epot = -68.2145534589486 | etot = -48.4966723873101 +732000 ekin = 8.8254456341921 | erot = 10.9030046167224 | epot = -68.2251226406126 | etot = -48.4966723896981 +733000 ekin = 8.58076650729897 | erot = 11.3480140239877 | epot = -68.4254529261021 | etot = -48.4966723948154 +734000 ekin = 8.44819070650859 | erot = 11.7953928346149 | epot = -68.7402559421549 | etot = -48.4966724010314 +735000 ekin = 8.36308582604301 | erot = 12.2184265334565 | epot = -69.0781847658203 | etot = -48.4966724063208 +736000 ekin = 8.27166179448656 | erot = 12.5931737861028 | epot = -69.3615079895678 | etot = -48.4966724089784 +737000 ekin = 8.15174465790076 | erot = 12.9021375875578 | epot = -69.550554653838 | etot = -48.4966724083795 +738000 ekin = 8.02032384079713 | erot = 13.1353976437632 | epot = -69.6523938899103 | etot = -48.49667240535 +739000 ekin = 7.92361863209752 | erot = 13.288887170794 | epot = -69.7091782046011 | etot = -48.4966724017096 +740000 ekin = 7.91483089146068 | erot = 13.361596296788 | epot = -69.7730995872988 | etot = -48.4966723990502 +741000 ekin = 8.03302590103882 | erot = 13.3544079573073 | epot = -69.8841062561639 | etot = -48.4966723978177 +742000 ekin = 8.29475492789436 | erot = 13.2712680544399 | epot = -70.062695379792 | etot = -48.4966723974577 +743000 ekin = 8.69783680686827 | erot = 13.1210830214386 | epot = -70.3155922259141 | etot = -48.4966723976072 +744000 ekin = 9.22494090059484 | erot = 12.9171251058096 | epot = -70.638738405208 | etot = -48.4966723988036 +745000 ekin = 9.8390865268868 | erot = 12.6729415302935 | epot = -71.008700459201 | etot = -48.4966724020207 +746000 ekin = 10.476767189942 | erot = 12.3966932528263 | epot = -71.3701328506785 | etot = -48.4966724079101 +747000 ekin = 11.0446377699999 | erot = 12.0869928943206 | epot = -71.6283030802541 | etot = -48.4966724159336 +748000 ekin = 11.4295453908524 | erot = 11.7327222580755 | epot = -71.6589400731708 | etot = -48.4966724242429 +749000 ekin = 11.5234364162178 | erot = 11.3174485899859 | epot = -71.3375574361957 | etot = -48.4966724299919 +750000 ekin = 11.259079853854 | erot = 10.8275036111879 | epot = -70.5832558907475 | etot = -48.4966724257056 +751000 ekin = 10.6566760361374 | erot = 10.2652340950593 | epot = -69.418582551581 | etot = -48.4966724203843 +752000 ekin = 9.81046694498496 | erot = 9.64438866543102 | epot = -67.9515280182634 | etot = -48.4966724078474 +753000 ekin = 8.8913456194876 | erot = 8.9921423550876 | epot = -66.3801603662739 | etot = -48.4966723916987 +754000 ekin = 8.11027945078717 | erot = 8.34642943219491 | epot = -64.9533812593719 | etot = -48.4966723763898 +755000 ekin = 7.64805178044942 | erot = 7.74709579294779 | epot = -63.8918199450905 | etot = -48.4966723716933 +756000 ekin = 7.56652741907262 | erot = 7.21880217843953 | epot = -63.2820019730441 | etot = -48.496672375532 +757000 ekin = 7.8021347348581 | erot = 6.76780334663582 | epot = -63.0666104660453 | etot = -48.4966723845514 +758000 ekin = 8.22136828673647 | erot = 6.38824654025972 | epot = -63.1062872203262 | etot = -48.49667239333 +759000 ekin = 8.6871506084408 | erot = 6.07044846904346 | epot = -63.2542714773 | etot = -48.4966723998157 +760000 ekin = 9.09933114469116 | erot = 5.80281618242289 | epot = -63.3988197302598 | etot = -48.4966724031458 +761000 ekin = 9.39129570541632 | erot = 5.57472170095315 | epot = -63.4626898089459 | etot = -48.4966724025765 +762000 ekin = 9.56563723640989 | erot = 5.38011940090967 | epot = -63.4424290363216 | etot = -48.496672399002 +763000 ekin = 9.67336099026896 | erot = 5.21718626718154 | epot = -63.3872196515552 | etot = -48.4966723941047 +764000 ekin = 9.78632769660059 | erot = 5.0859958821846 | epot = -63.3689959684166 | etot = -48.4966723896314 +765000 ekin = 9.96960969337793 | erot = 4.98563698857814 | epot = -63.4519190694749 | etot = -48.4966723875188 +766000 ekin = 10.225480068829 | erot = 4.91845355429151 | epot = -63.6406060069211 | etot = -48.4966723838005 +767000 ekin = 10.5921756590156 | erot = 4.88036713465681 | epot = -63.9692151912139 | etot = -48.4966723975415 +768000 ekin = 11.0286182842439 | erot = 4.84228216973156 | epot = -64.3675728421619 | etot = -48.4966723881864 +769000 ekin = 11.5060819040386 | erot = 4.81203544055977 | epot = -64.8147897345836 | etot = -48.4966723899852 +770000 ekin = 11.9954127335722 | erot = 4.78570420795079 | epot = -65.2777893330256 | etot = -48.4966723915025 +771000 ekin = 12.4710057577347 | erot = 4.76119431146144 | epot = -65.7288724618441 | etot = -48.496672392648 +772000 ekin = 12.9091287691281 | erot = 4.73689896144192 | epot = -66.1427001247808 | etot = -48.4966723942108 +773000 ekin = 13.2804102669379 | erot = 4.71070995674932 | epot = -66.4877926201609 | etot = -48.4966723964737 +774000 ekin = 13.5460331298012 | erot = 4.67959233345448 | epot = -66.722297859922 | etot = -48.4966723966663 +775000 ekin = 13.6741516116327 | erot = 4.63765248596424 | epot = -66.8084764974988 | etot = -48.4966723999019 +776000 ekin = 13.628690422074 | erot = 4.58103406304242 | epot = -66.7063968765447 | etot = -48.4966723914283 +777000 ekin = 13.4182048007198 | erot = 4.51743020949247 | epot = -66.4323074039082 | etot = -48.4966723936959 +778000 ekin = 13.0220035127683 | erot = 4.4494854147762 | epot = -65.9681613217113 | etot = -48.4966723941668 +779000 ekin = 12.4217380619164 | erot = 4.38036222327252 | epot = -65.2987726782465 | etot = -48.4966723930575 +780000 ekin = 11.6137715316259 | erot = 4.31519453332131 | epot = -64.4256384567752 | etot = -48.496672391828 +781000 ekin = 10.6252323249768 | erot = 4.25886110653795 | epot = -63.3807658174541 | etot = -48.4966723859394 +782000 ekin = 9.53385909883344 | erot = 4.2224816580653 | epot = -62.2530131360879 | etot = -48.4966723791891 +783000 ekin = 8.43150181510525 | erot = 4.21812348336708 | epot = -61.1462976708854 | etot = -48.4966723724131 +784000 ekin = 7.41120665840492 | erot = 4.2575375549945 | epot = -60.1654165798559 | etot = -48.4966723664564 +785000 ekin = 6.55493198928447 | erot = 4.35109016923504 | epot = -59.4026945205759 | etot = -48.4966723620564 +786000 ekin = 5.92286857657126 | erot = 4.50684669652378 | epot = -58.9263876327923 | etot = -48.4966723596973 +787000 ekin = 5.54648098967233 | erot = 4.7299135165133 | epot = -58.7730668656963 | etot = -48.4966723595107 +788000 ekin = 5.4268400436267 | erot = 5.02210237716071 | epot = -58.9456147820038 | etot = -48.4966723612164 +789000 ekin = 5.53848888146267 | erot = 5.38186888561947 | epot = -59.417030131408 | etot = -48.4966723643259 +790000 ekin = 5.83681660420195 | erot = 5.80448189906697 | epot = -60.1379708715072 | etot = -48.4966723682383 +791000 ekin = 6.26691431657487 | erot = 6.28226218223002 | epot = -61.0458488712309 | etot = -48.496672372426 +792000 ekin = 6.77233331503648 | erot = 6.80466729721686 | epot = -62.0736729886752 | etot = -48.4966723764219 +793000 ekin = 7.30112337038902 | erot = 7.35853037535933 | epot = -63.1563261258569 | etot = -48.4966723801085 +794000 ekin = 7.80874278960135 | erot = 7.92855734513757 | epot = -64.23397251805 | etot = -48.4966723833111 +795000 ekin = 8.166149843305 | erot = 8.55276407547022 | epot = -65.2155862981077 | etot = -48.4966723793324 +796000 ekin = 8.42449679165107 | erot = 9.23234180670203 | epot = -66.1535110090537 | etot = -48.4966724107006 +797000 ekin = 8.67431436577461 | erot = 9.74356995272924 | epot = -66.9145567255226 | etot = -48.4966724070187 +798000 ekin = 8.82807715634734 | erot = 10.1953217653807 | epot = -67.5200713293466 | etot = -48.4966724076186 +799000 ekin = 8.89463201681582 | erot = 10.5732151309609 | epot = -67.9645195546288 | etot = -48.496672406852 +800000 ekin = 8.89722969177869 | erot = 10.8667677315072 | epot = -68.2606698284465 | etot = -48.4966724051606 +801000 ekin = 8.87138017726285 | erot = 11.0709907383165 | epot = -68.4390433178315 | etot = -48.4966724022522 +802000 ekin = 8.86275607652829 | erot = 11.1875475892946 | epot = -68.5469760646282 | etot = -48.4966723988054 +803000 ekin = 8.9176116746532 | erot = 11.2243264570991 | epot = -68.6386105277505 | etot = -48.4966723959982 +804000 ekin = 9.06730079030281 | erot = 11.193261387315 | epot = -68.7572345726583 | etot = -48.4966723950405 +805000 ekin = 9.31347449932248 | erot = 11.1073163209106 | epot = -68.9174632168106 | etot = -48.4966723965776 +806000 ekin = 9.62719847633812 | erot = 10.9794864719304 | epot = -69.1033573472845 | etot = -48.496672399016 +807000 ekin = 9.96288601612691 | erot = 10.8230663453846 | epot = -69.2826247649949 | etot = -48.4966724034834 +808000 ekin = 10.2497439829731 | erot = 10.6432283956226 | epot = -69.3896447861036 | etot = -48.4966724075079 +809000 ekin = 10.4243193598606 | erot = 10.4427750449352 | epot = -69.3637668147487 | etot = -48.4966724099529 +810000 ekin = 10.4450308647548 | erot = 10.2230440397179 | epot = -69.1647473158114 | etot = -48.4966724113388 +811000 ekin = 10.2721813465492 | erot = 9.97917260809284 | epot = -68.7480263639892 | etot = -48.4966724093471 +812000 ekin = 9.92407619954989 | erot = 9.71416142509092 | epot = -68.1349100296174 | etot = -48.4966724049766 +813000 ekin = 9.46374629336789 | erot = 9.43470533281904 | epot = -67.395124024886 | etot = -48.496672398699 +814000 ekin = 8.98180729338922 | erot = 9.1490260761511 | epot = -66.6275057610053 | etot = -48.4966723914649 +815000 ekin = 8.58163269988549 | erot = 8.8668326191454 | epot = -65.9451377035029 | etot = -48.496672384472 +816000 ekin = 8.36010805287333 | erot = 8.59902958866148 | epot = -65.455810020633 | etot = -48.4966723790982 +817000 ekin = 8.3873440486996 | erot = 8.35708532025249 | epot = -65.2411017456872 | etot = -48.4966723767351 +818000 ekin = 8.68842134848364 | erot = 8.1517568394535 | epot = -65.3368505655993 | etot = -48.4966723776622 +819000 ekin = 9.23925212236388 | erot = 7.99221894929125 | epot = -65.7281434529098 | etot = -48.4966723812547 +820000 ekin = 9.8550592159835 | erot = 7.98557734062691 | epot = -66.3373089296726 | etot = -48.4966723730622 +821000 ekin = 10.558118791073 | erot = 8.08897892641499 | epot = -67.1437700948609 | etot = -48.4966723773729 +822000 ekin = 11.4203555752861 | erot = 8.0982092207411 | epot = -68.0152371771624 | etot = -48.4966723811352 +823000 ekin = 12.244965785656 | erot = 8.16990204354267 | epot = -68.9115402129071 | etot = -48.4966723837084 +824000 ekin = 12.988754108158 | erot = 8.30328899984907 | epot = -69.7887154934266 | etot = -48.4966723854196 +825000 ekin = 13.6250379000391 | erot = 8.49403789232663 | epot = -70.6157481794701 | etot = -48.4966723871044 +826000 ekin = 14.1275801417042 | erot = 8.7318216172602 | epot = -71.3560741514511 | etot = -48.4966723924867 +827000 ekin = 14.4569396392558 | erot = 8.99861686792267 | epot = -71.9522289032949 | etot = -48.4966723961164 +828000 ekin = 14.5801783883225 | erot = 9.2725614536099 | epot = -72.3494122418378 | etot = -48.4966723999054 +829000 ekin = 14.4667887755571 | erot = 9.52899253502381 | epot = -72.4924537132267 | etot = -48.4966724026458 +830000 ekin = 14.1008667947 | erot = 9.74540563437327 | epot = -72.3429448320052 | etot = -48.4966724029319 +831000 ekin = 13.493746625261 | erot = 9.90643642422692 | epot = -71.8968554497801 | etot = -48.4966724002922 +832000 ekin = 12.690621380299 | erot = 10.007761952949 | epot = -71.1950557280236 | etot = -48.4966723947756 +833000 ekin = 11.7661849043984 | erot = 10.0572478688343 | epot = -70.3201051609416 | etot = -48.4966723877089 +834000 ekin = 10.8109948247215 | erot = 10.071354504227 | epot = -69.3790217093276 | etot = -48.496672380379 +835000 ekin = 9.91642597846666 | erot = 10.0705783751749 | epot = -68.483676728931 | etot = -48.4966723752894 +836000 ekin = 9.14363254435414 | erot = 9.95662955052463 | epot = -67.5969343908025 | etot = -48.4966722959237 +837000 ekin = 8.79163957835885 | erot = 9.91123278088581 | epot = -67.1995446575618 | etot = -48.4966722983171 +838000 ekin = 8.42094145797661 | erot = 9.94835266834992 | epot = -66.8659664257576 | etot = -48.4966722994311 +839000 ekin = 8.20536768150395 | erot = 10.012243240367 | epot = -66.7142832242599 | etot = -48.496672302389 +840000 ekin = 8.10932302136739 | erot = 10.1009175364921 | epot = -66.7069128631837 | etot = -48.4966723053242 +841000 ekin = 8.09432718628577 | erot = 10.2103111789734 | epot = -66.8013106733128 | etot = -48.4966723080537 +842000 ekin = 8.12447284830409 | erot = 10.3366191345573 | epot = -66.957764293046 | etot = -48.4966723101846 +843000 ekin = 8.17242564793842 | erot = 10.4770425722838 | epot = -67.1461405317211 | etot = -48.4966723114989 +844000 ekin = 8.22381294807546 | erot = 10.629792152031 | epot = -67.3502774120134 | etot = -48.4966723119069 +845000 ekin = 8.27955127170831 | erot = 10.7936569680123 | epot = -67.5698805512956 | etot = -48.4966723115751 +846000 ekin = 8.35455925353356 | erot = 10.9672036716716 | epot = -67.8184352361507 | etot = -48.4966723109456 +847000 ekin = 8.47238635762968 | erot = 11.1476305380471 | epot = -68.1166892062117 | etot = -48.4966723105349 +848000 ekin = 8.65810273433286 | erot = 11.3297217924147 | epot = -68.4844968372748 | etot = -48.4966723105273 +849000 ekin = 8.9329020856651 | erot = 11.5057838965836 | epot = -68.9353582933334 | etot = -48.4966723110847 +850000 ekin = 9.30778062670253 | erot = 11.6667367391758 | epot = -69.4711896784517 | etot = -48.4966723125733 +851000 ekin = 9.77385593082056 | erot = 11.8036289180235 | epot = -70.074157164614 | etot = -48.4966723157699 +852000 ekin = 10.2902091175593 | erot = 11.9080163477226 | epot = -70.6948977866374 | etot = -48.4966723213555 +853000 ekin = 10.7774710897525 | erot = 11.9704639281082 | epot = -71.2446073468658 | etot = -48.4966723290051 +854000 ekin = 11.1286098495727 | erot = 11.9790690570371 | epot = -71.604351243113 | etot = -48.4966723365032 +855000 ekin = 11.2404537225969 | erot = 11.9198426881727 | epot = -71.6569687522265 | etot = -48.4966723414569 +856000 ekin = 11.0533273910054 | erot = 11.7779965318103 | epot = -71.3279962637786 | etot = -48.4966723409628 +857000 ekin = 10.5849568284532 | erot = 11.5448386331215 | epot = -70.626467795706 | etot = -48.4966723341314 +858000 ekin = 9.93782549625797 | erot = 11.2226264151964 | epot = -69.6571242340316 | etot = -48.4966723225772 +859000 ekin = 9.27338883856784 | erot = 10.8254282711299 | epot = -68.5954894195332 | etot = -48.4966723098354 +860000 ekin = 8.76267013930508 | erot = 10.3757646939758 | epot = -67.6351071329322 | etot = -48.4966722996514 +861000 ekin = 8.53556496732127 | erot = 9.89928978757217 | epot = -66.9315270491791 | etot = -48.4966722942857 +862000 ekin = 8.65070986986339 | erot = 9.42036719872688 | epot = -66.5677493624818 | etot = -48.4966722938915 +863000 ekin = 9.09319445840874 | erot = 8.96001365957565 | epot = -66.5498804151446 | etot = -48.4966722971602 +864000 ekin = 9.79331572305551 | erot = 8.53570874170276 | epot = -66.8256967670887 | etot = -48.4966723023304 +865000 ekin = 10.6528659483603 | erot = 8.1619337481963 | epot = -67.3114720044079 | etot = -48.4966723078513 +866000 ekin = 11.570639470114 | erot = 7.85082867468824 | epot = -67.9181404559871 | etot = -48.4966723111849 +867000 ekin = 12.4665855150464 | erot = 7.61306293828822 | epot = -68.5763207677325 | etot = -48.4966723143979 +868000 ekin = 13.2806731240691 | erot = 7.45693596344013 | epot = -69.2342814034079 | etot = -48.4966723158987 +869000 ekin = 13.9812766459746 | erot = 7.38865717133806 | epot = -69.8666061334702 | etot = -48.4966723161576 +870000 ekin = 14.5601728177746 | erot = 7.41145610128879 | epot = -70.4683012354412 | etot = -48.4966723163778 +871000 ekin = 15.0180932154381 | erot = 7.52387391479662 | epot = -71.0386394482707 | etot = -48.496672318036 +872000 ekin = 15.3437544430603 | erot = 7.71754298435372 | epot = -71.5579697497311 | etot = -48.496672322317 +873000 ekin = 15.4947478924952 | erot = 7.97535948551146 | epot = -71.9667797066116 | etot = -48.496672328605 +874000 ekin = 15.407202231947 | erot = 8.27349566688775 | epot = -72.1773702337631 | etot = -48.4966723349283 +875000 ekin = 15.0202820880963 | erot = 8.58584611780907 | epot = -72.1028005443991 | etot = -48.4966723384937 +876000 ekin = 14.3103753074346 | erot = 8.89001531355927 | epot = -71.6970629580795 | etot = -48.4966723370855 +877000 ekin = 13.3177867535852 | erot = 9.17198109359335 | epot = -70.9864401776007 | etot = -48.4966723304222 +878000 ekin = 12.1489812351109 | erot = 9.42690022996156 | epot = -70.0725537857661 | etot = -48.4966723206936 +879000 ekin = 10.9478679143888 | erot = 9.65570814731649 | epot = -69.1002483732838 | etot = -48.4966723115786 +880000 ekin = 9.84816823143918 | erot = 9.86012585832544 | epot = -68.2049663957869 | etot = -48.4966723060222 +881000 ekin = 8.93418864746356 | erot = 10.0399671441925 | epot = -67.4708280961072 | etot = -48.4966723044512 +882000 ekin = 8.23233878449478 | erot = 10.1944686101195 | epot = -66.9234796997606 | etot = -48.4966723051463 +883000 ekin = 7.73079373835382 | erot = 10.3254556489762 | epot = -66.5529216930004 | etot = -48.4966723056704 +884000 ekin = 7.40639354985591 | erot = 10.4389581940177 | epot = -66.3420240509761 | etot = -48.4966723071025 +885000 ekin = 7.23012883993839 | erot = 10.5425263257092 | epot = -66.2693274739808 | etot = -48.4966723083332 +886000 ekin = 7.17188160896479 | erot = 10.6423872901515 | epot = -66.3109412087852 | etot = -48.4966723096689 +887000 ekin = 7.20359993936233 | erot = 10.7423767443422 | epot = -66.442648994669 | etot = -48.4966723109645 +888000 ekin = 7.30083390128708 | erot = 10.8444815153507 | epot = -66.6419877285173 | etot = -48.4966723118796 +889000 ekin = 7.44584663032084 | erot = 10.9502816363572 | epot = -66.8928005790067 | etot = -48.4966723123287 +890000 ekin = 7.62600694147961 | erot = 11.0610746470698 | epot = -67.1837539023109 | etot = -48.4966723137615 +891000 ekin = 7.81873874270141 | erot = 11.1753311202036 | epot = -67.4907421800912 | etot = -48.4966723171861 +892000 ekin = 7.97874969401364 | erot = 11.2859136977755 | epot = -67.7613357142635 | etot = -48.4966723224743 +893000 ekin = 8.03989395229215 | erot = 11.3794214309858 | epot = -67.9159877114687 | etot = -48.4966723281907 +894000 ekin = 7.93829359555365 | erot = 11.4397930632517 | epot = -67.8747589906465 | etot = -48.4966723318411 +895000 ekin = 7.64207855034557 | erot = 11.4549096573215 | epot = -67.5936605304564 | etot = -48.4966723227894 +896000 ekin = 7.25994289827124 | erot = 11.4314794324918 | epot = -67.1880946508022 | etot = -48.4966723200391 +897000 ekin = 6.87440345797014 | erot = 11.3807194356204 | epot = -66.7517952086825 | etot = -48.496672315092 +898000 ekin = 6.54072238139674 | erot = 11.3170504950422 | epot = -66.354445186451 | etot = -48.496672310012 +899000 ekin = 6.31497972642606 | erot = 11.2562721777788 | epot = -66.0679242108463 | etot = -48.4966723066414 +900000 ekin = 6.23427080209186 | erot = 11.2089558194278 | epot = -65.9398989273792 | etot = -48.4966723058596 +901000 ekin = 6.30716786529804 | erot = 11.1769912987548 | epot = -65.9808314715013 | etot = -48.4966723074485 +902000 ekin = 6.51603863961298 | erot = 11.1540745980084 | epot = -66.166785548034 | etot = -48.4966723104126 +903000 ekin = 6.82764115165212 | erot = 11.1292357610214 | epot = -66.4535492262252 | etot = -48.4966723135516 +904000 ekin = 7.2059458167967 | erot = 11.0915307924457 | epot = -66.7941489251963 | etot = -48.4966723159539 +905000 ekin = 7.62139055525756 | erot = 11.0338529932702 | epot = -67.1519158659189 | etot = -48.4966723173912 +906000 ekin = 8.0531440169716 | erot = 10.9545483953339 | epot = -67.5043647304589 | etot = -48.4966723181534 +907000 ekin = 8.48596871323775 | erot = 10.8568809769567 | epot = -67.839522008857 | etot = -48.4966723186626 +908000 ekin = 8.90584093631453 | erot = 10.7475317189068 | epot = -68.1500449743946 | etot = -48.4966723191733 +909000 ekin = 9.2981187661667 | erot = 10.6353835916215 | epot = -68.4301746772618 | etot = -48.4966723194736 +910000 ekin = 9.64930057745103 | erot = 10.5309201112748 | epot = -68.6768930082989 | etot = -48.4966723195732 +911000 ekin = 9.94798520561604 | erot = 10.445428126332 | epot = -68.8900856515363 | etot = -48.4966723195882 +912000 ekin = 10.1842847265749 | erot = 10.3896169166176 | epot = -69.0705739631292 | etot = -48.4966723199367 +913000 ekin = 10.3464242432486 | erot = 10.371503449062 | epot = -69.2146000133927 | etot = -48.4966723210821 +914000 ekin = 10.4159486656299 | erot = 10.3940912351748 | epot = -69.3067122242574 | etot = -48.4966723234527 +915000 ekin = 10.3649219584732 | erot = 10.4538252075313 | epot = -69.3154194926583 | etot = -48.4966723266538 +916000 ekin = 10.1612630535764 | erot = 10.5413791273757 | epot = -69.1993145104154 | etot = -48.4966723294633 +917000 ekin = 9.79071145878735 | erot = 10.6444144951849 | epot = -68.9317982845541 | etot = -48.4966723305818 +918000 ekin = 9.26089495094651 | erot = 10.7518360031647 | epot = -68.509403282558 | etot = -48.4966723284468 +919000 ekin = 8.61736183915388 | erot = 10.8585966357191 | epot = -67.9726307968488 | etot = -48.4966723219758 +920000 ekin = 7.96059242727767 | erot = 10.9667865222643 | epot = -67.4240512625502 | etot = -48.4966723130081 +921000 ekin = 7.42062866669523 | erot = 11.0831224396019 | epot = -67.0004234112517 | etot = -48.4966723049545 +922000 ekin = 7.11192604620465 | erot = 11.213865062059 | epot = -66.8224634097993 | etot = -48.4966723015356 +923000 ekin = 7.08988024943638 | erot = 11.3600862488331 | epot = -66.9466388009244 | etot = -48.496672302655 +924000 ekin = 7.33691451843237 | erot = 11.5138164836438 | epot = -67.3474033140639 | etot = -48.4966723119878 +925000 ekin = 7.75066984786481 | erot = 11.6552585802304 | epot = -67.9026007500439 | etot = -48.4966723219487 +926000 ekin = 8.19653351914579 | erot = 11.7619530750869 | epot = -68.455158925525 | etot = -48.4966723312923 +927000 ekin = 8.54738330763445 | erot = 11.8134968265722 | epot = -68.8575524720345 | etot = -48.4966723378279 +928000 ekin = 8.71145228710507 | erot = 11.7955386585214 | epot = -69.0036632860693 | etot = -48.4966723404428 +929000 ekin = 8.64121812944182 | erot = 11.702544250028 | epot = -68.8404347191515 | etot = -48.4966723396816 +930000 ekin = 8.33447880146975 | erot = 11.5389737680376 | epot = -68.3701249045833 | etot = -48.4966723350759 +931000 ekin = 7.84128687972334 | erot = 11.3199153556612 | epot = -67.6578745633159 | etot = -48.4966723279314 +932000 ekin = 7.24436702165883 | erot = 11.0677318732717 | epot = -66.808771214749 | etot = -48.4966723198185 +933000 ekin = 6.63984713610501 | erot = 10.8074687702607 | epot = -65.9439882187064 | etot = -48.4966723123406 +934000 ekin = 6.11754593051298 | erot = 10.5621552833725 | epot = -65.1763735206371 | etot = -48.4966723067517 +935000 ekin = 5.74541765521402 | erot = 10.3493855079979 | epot = -64.5914754667476 | etot = -48.4966723035357 +936000 ekin = 5.56181702344705 | erot = 10.1798783881607 | epot = -64.2383677144363 | etot = -48.4966723028286 +937000 ekin = 5.57387640327936 | erot = 10.0571518020917 | epot = -64.1277005096326 | etot = -48.4966723042616 +938000 ekin = 5.76140456209132 | erot = 9.97823911606649 | epot = -64.2363159855043 | etot = -48.4966723073465 +939000 ekin = 6.08318988638494 | erot = 9.93455888124384 | epot = -64.5144210794316 | etot = -48.4966723118029 +940000 ekin = 6.48293885679984 | erot = 9.91175572325734 | epot = -64.8913668973667 | etot = -48.4966723173095 +941000 ekin = 6.89458667494459 | erot = 9.89006577308746 | epot = -65.2813247714941 | etot = -48.4966723234621 +942000 ekin = 7.2486944403872 | erot = 9.84545861919656 | epot = -65.5908253891153 | etot = -48.4966723295315 +943000 ekin = 7.48274008792501 | erot = 9.75224430251525 | epot = -65.73165672461 | etot = -48.4966723341697 +944000 ekin = 7.55661078927992 | erot = 9.58809869855624 | epot = -65.6413818235762 | etot = -48.49667233574 +945000 ekin = 7.47011756783039 | erot = 9.34043578936074 | epot = -65.3072256902498 | etot = -48.4966723330586 +946000 ekin = 7.27386532679615 | erot = 9.01155536675472 | epot = -64.7820930198635 | etot = -48.4966723263126 +947000 ekin = 7.06319370201748 | erot = 8.61969480788043 | epot = -64.179560827485 | etot = -48.4966723175871 +948000 ekin = 6.95249219209068 | erot = 8.19479074961839 | epot = -63.6439552510929 | etot = -48.4966723093838 +949000 ekin = 7.04165184843665 | erot = 7.77196767267864 | epot = -63.3102918255315 | etot = -48.4966723044162 +950000 ekin = 7.38393235005282 | erot = 7.38215863435772 | epot = -63.2627632880478 | etot = -48.4966723036373 +951000 ekin = 7.97686792819456 | erot = 7.04490011949532 | epot = -63.5184403540008 | etot = -48.4966723063109 +952000 ekin = 8.77198923537714 | erot = 6.76886820062407 | epot = -64.0375297473456 | etot = -48.4966723113444 +953000 ekin = 9.68951089962173 | erot = 6.55318209056052 | epot = -64.7393653086516 | etot = -48.4966723184694 +954000 ekin = 10.625545173257 | erot = 6.39139135053334 | epot = -65.5136088501269 | etot = -48.4966723263366 +955000 ekin = 11.459195976534 | erot = 6.27379828419293 | epot = -66.2296665951486 | etot = -48.4966723344217 +956000 ekin = 12.0705908699296 | erot = 6.18965545539867 | epot = -66.7569186667193 | etot = -48.496672341391 +957000 ekin = 12.3578057515742 | erot = 6.13109121395203 | epot = -66.9855693108173 | etot = -48.4966723452911 +958000 ekin = 12.2639561605225 | erot = 6.09526076408633 | epot = -66.8558892689087 | etot = -48.4966723442999 +959000 ekin = 11.8028932787518 | erot = 6.08530913759149 | epot = -66.3848747536715 | etot = -48.4966723373283 +960000 ekin = 11.0657748712033 | erot = 6.10961273201249 | epot = -65.6720599301514 | etot = -48.4966723269356 +961000 ekin = 10.1976851857911 | erot = 6.17940626632498 | epot = -64.8737637674829 | etot = -48.4966723153668 +962000 ekin = 9.36006056033443 | erot = 6.3057643499174 | epot = -64.1624972165041 | etot = -48.4966723062522 +963000 ekin = 8.68052625435703 | erot = 6.49616547714195 | epot = -63.6733640336944 | etot = -48.4966723021954 +964000 ekin = 8.21670813103556 | erot = 6.75219994305738 | epot = -63.4655803776174 | etot = -48.4966723035245 +965000 ekin = 7.95112951723659 | erot = 7.06933978727814 | epot = -63.5171416128752 | etot = -48.4966723083604 +966000 ekin = 7.81882046045959 | erot = 7.43840285638279 | epot = -63.7538956305659 | etot = -48.4966723137236 +967000 ekin = 7.74912903238494 | erot = 7.84702228791584 | epot = -64.0928236389113 | etot = -48.4966723186105 +968000 ekin = 7.67539244782124 | erot = 8.28177833614435 | epot = -64.4538431057827 | etot = -48.4966723218171 +969000 ekin = 7.55990272706149 | erot = 8.72822682525186 | epot = -64.7848018759069 | etot = -48.4966723235936 +970000 ekin = 7.38809514504139 | erot = 9.1706253329465 | epot = -65.0553928030932 | etot = -48.4966723251053 +971000 ekin = 7.15239238646895 | erot = 9.59185822210274 | epot = -65.2409229350178 | etot = -48.4966723264461 +972000 ekin = 6.85180495473256 | erot = 9.97461998900114 | epot = -65.323097270943 | etot = -48.4966723272093 +973000 ekin = 6.49404712572963 | erot = 10.3038859961783 | epot = -65.2946054486949 | etot = -48.4966723267869 +974000 ekin = 6.10144996584987 | erot = 10.5696876848613 | epot = -65.1678099751018 | etot = -48.4966723243906 +975000 ekin = 5.71827862095584 | erot = 10.768092346607 | epot = -64.9830432881918 | etot = -48.4966723206289 +976000 ekin = 5.40201311505247 | erot = 10.9003005365461 | epot = -64.7989859682497 | etot = -48.4966723166511 +977000 ekin = 5.20833587548647 | erot = 10.9708214105959 | epot = -64.6758296002104 | etot = -48.496672314128 +978000 ekin = 5.16924581638857 | erot = 10.9846732064771 | epot = -64.6505913371465 | etot = -48.4966723142808 +979000 ekin = 5.27779877902274 | erot = 10.9455170781611 | epot = -64.7199881739085 | etot = -48.4966723167247 +980000 ekin = 5.49322046495708 | erot = 10.8569988007143 | epot = -64.8468915854391 | etot = -48.4966723197677 +981000 ekin = 5.76179865074904 | erot = 10.726517715687 | epot = -64.9849886877658 | etot = -48.4966723213298 +982000 ekin = 6.0434859150675 | erot = 10.5685834909351 | epot = -65.1087417263039 | etot = -48.4966723203013 +983000 ekin = 6.32848467150841 | erot = 10.4050435737129 | epot = -65.2302005622159 | etot = -48.4966723169946 +984000 ekin = 6.63689938808603 | erot = 10.2617391991563 | epot = -65.3953108999642 | etot = -48.4966723127219 +985000 ekin = 7.00519514142896 | erot = 10.1634367427884 | epot = -65.6653041932412 | etot = -48.4966723090238 +986000 ekin = 7.46792966870151 | erot = 10.1293593733502 | epot = -66.0939613491783 | etot = -48.4966723071267 +987000 ekin = 8.0417524024767 | erot = 10.170567974692 | epot = -66.7089926848975 | etot = -48.4966723077288 +988000 ekin = 8.71523239355653 | erot = 10.2892285366076 | epot = -67.5011332411574 | etot = -48.4966723109932 +989000 ekin = 9.44555556323164 | erot = 10.4792258391849 | epot = -68.4214537221049 | etot = -48.4966723196884 +990000 ekin = 10.147314872708 | erot = 10.722478708467 | epot = -69.3664659087734 | etot = -48.4966723275984 +991000 ekin = 10.7156853232285 | erot = 10.9958515592977 | epot = -70.2082092180937 | etot = -48.4966723355675 +992000 ekin = 11.0552138419303 | erot = 11.2781950491444 | epot = -70.8300812327856 | etot = -48.496672341711 +993000 ekin = 11.0952058420832 | erot = 11.5520851648231 | epot = -71.1439633511133 | etot = -48.496672344207 +994000 ekin = 10.8115610752779 | erot = 11.8083197905567 | epot = -71.1165532078995 | etot = -48.4966723420649 +995000 ekin = 10.2380910205381 | erot = 12.0483836075147 | epot = -70.7831469637494 | etot = -48.4966723356967 +996000 ekin = 9.46083674880266 | erot = 12.2834739306309 | epot = -70.2409830062614 | etot = -48.4966723268278 +997000 ekin = 8.59669857335092 | erot = 12.5302960540965 | epot = -69.6236669451915 | etot = -48.496672317744 +998000 ekin = 7.76544231192214 | erot = 12.806128320963 | epot = -69.0682429431554 | etot = -48.4966723102702 +999000 ekin = 7.06575290471557 | erot = 13.1250004270275 | epot = -68.6874256372488 | etot = -48.4966723055057 +1000000 ekin = 6.56133017801672 | erot = 13.4950387121477 | epot = -68.5530411938935 | etot = -48.4966723037291 + 1000000 244.5767 -69.23317 0.68012891 -61.991711 -0.012778323 39304000 +Loop time of 18.2788 on 4 procs for 1000000 steps with 10 atoms + +Performance: 80.639 ns/day, 0.298 hours/ns, 54708.327 timesteps/s, 547.083 katom-step/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7489 | 7.413 | 10.648 | 77.4 | 40.56 +Bond | 0.2292 | 0.30345 | 0.37909 | 12.0 | 1.66 +Neigh | 0.00759 | 0.0076525 | 0.007698 | 0.0 | 0.04 +Comm | 4.13 | 7.779 | 10.46 | 82.1 | 42.56 +Output | 0.072271 | 0.076746 | 0.085815 | 1.9 | 0.42 +Modify | 0.63917 | 0.69264 | 0.75378 | 6.3 | 3.79 +Other | | 2.006 | | | 10.98 + +Nlocal: 2.5 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 8 max 7 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25 ave 16 max 2 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.3.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:18 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/data.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/data.duplex1 new file mode 100644 index 0000000000..a368cef424 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/data.duplex1 @@ -0,0 +1,68 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +10 atoms +4 atom types +8 bonds +1 bond types +10 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0 +2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0 +3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0 +4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0 +5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0 +6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0 +7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0 +8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0 +9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0 +10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618 +2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161 +3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145 +4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535 +5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021 +6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764 +7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955 +8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736 +9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246 +10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472 +6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199 +8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403 +9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798 +10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/in.duplex1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/in.duplex1 new file mode 100644 index 0000000000..a4df838b14 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/in.duplex1 @@ -0,0 +1,74 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * oxdna2_real.cgdna +special_bonds fene + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv oxdna2_real.cgdna +pair_coeff * * oxdna2/stk seqav 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna +pair_coeff * * oxdna2/hbond seqav oxdna2_real.cgdna +pair_coeff 1 4 oxdna2/hbond seqav oxdna2_real.cgdna +pair_coeff 2 3 oxdna2/hbond seqav oxdna2_real.cgdna +pair_coeff * * oxdna2/xstk oxdna2_real.cgdna +pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna +pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2_real.cgdna + + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/log.19May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/log.19May24.duplex1.g++.1 new file mode 100644 index 0000000000..9408282187 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/log.19May24.duplex1.g++.1 @@ -0,0 +1,1118 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.005 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna2.real with DATE: 2024-04-26 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (stk) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (xstk) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (coaxstk) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (dh) file oxdna2.real with DATE: 2024-04-26 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 36.640032 + ghost atom cutoff = 36.640032 + binsize = 18.320016, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 0.01706 +WARNING: Communication cutoff adjusted to 36.64003240988628 (src/comm.cpp:739) +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.9029330618618 | etot = -50.5142754103307 +Per MPI rank memory allocation (min/avg/max) = 7.467 | 7.467 | 7.467 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -80.289462 6.3865285 -67.29606 -0.044626926 39304000 +1000 ekin = 6.41540831684953 | erot = 17.3249788985168 | epot = -74.2546626270295 | etot = -50.5142754116631 +2000 ekin = 6.27991122577832 | erot = 17.8454504610745 | epot = -74.6396371002362 | etot = -50.5142754133834 +3000 ekin = 6.20398291945338 | erot = 18.314076603922 | epot = -75.0323349385582 | etot = -50.5142754151829 +4000 ekin = 6.1863619976757 | erot = 18.7040547099771 | epot = -75.4046921244017 | etot = -50.5142754167489 +5000 ekin = 6.2221573215847 | erot = 18.9942188143058 | epot = -75.7306515537703 | etot = -50.5142754178798 +6000 ekin = 6.30420734178878 | erot = 19.1708709879921 | epot = -75.9893537482964 | etot = -50.5142754185155 +7000 ekin = 6.42413491039012 | erot = 19.2280244216481 | epot = -76.1664347507277 | etot = -50.5142754186894 +8000 ekin = 6.57305019042843 | erot = 19.1666743693588 | epot = -76.2539999782607 | etot = -50.5142754184734 +9000 ekin = 6.74208660925334 | erot = 18.9937209190127 | epot = -76.2500829461571 | etot = -50.514275417891 +10000 ekin = 6.92290866428275 | erot = 18.721233888504 | epot = -76.1584179697748 | etot = -50.514275416988 +11000 ekin = 7.10814925172427 | erot = 18.3654806858384 | epot = -75.9879053534121 | etot = -50.5142754158494 +12000 ekin = 7.29164020767442 | erot = 17.9454168333363 | epot = -75.7513324556478 | etot = -50.514275414637 +13000 ekin = 7.46835372796839 | erot = 17.4806722087774 | epot = -75.4633013502363 | etot = -50.5142754134906 +14000 ekin = 7.63410684865959 | erot = 16.9894852695683 | epot = -75.1378675308068 | etot = -50.514275412579 +15000 ekin = 7.78518315372064 | erot = 16.4873283506092 | epot = -74.786786916147 | etot = -50.5142754118172 +16000 ekin = 7.91804895618152 | erot = 15.9866370289751 | epot = -74.4189613960958 | etot = -50.5142754109392 +17000 ekin = 8.02929115914049 | erot = 15.4954883395917 | epot = -74.039054909871 | etot = -50.5142754111388 +18000 ekin = 8.11580274929381 | erot = 15.0161795148028 | epot = -73.6462576756318 | etot = -50.5142754115352 +19000 ekin = 8.17521064582063 | erot = 14.545500722027 | epot = -73.2349867798162 | etot = -50.5142754119685 +20000 ekin = 8.2064655331787 | erot = 14.0791106720699 | epot = -72.7998516175188 | etot = -50.5142754122702 +21000 ekin = 8.21050499747768 | erot = 13.6133776866134 | epot = -72.3381580963795 | etot = -50.5142754122884 +22000 ekin = 8.19089628973037 | erot = 13.1469621627645 | epot = -71.8521338644035 | etot = -50.5142754119086 +23000 ekin = 8.154366254026 | erot = 12.6819076192474 | epot = -71.3505492843428 | etot = -50.5142754110693 +24000 ekin = 8.11112226003199 | erot = 12.2241028664328 | epot = -70.8495005362371 | etot = -50.5142754097723 +25000 ekin = 8.07483898562208 | erot = 11.783077489027 | epot = -70.3721918827438 | etot = -50.5142754080948 +26000 ekin = 8.06214574493345 | erot = 11.3711691532402 | epot = -69.9475903043468 | etot = -50.5142754061732 +27000 ekin = 8.09157304392363 | erot = 11.0021655564046 | epot = -69.6080140045702 | etot = -50.5142754042419 +28000 ekin = 8.18160915522528 | erot = 10.6895124998217 | epot = -69.3853970576593 | etot = -50.5142754026123 +29000 ekin = 8.34799192749685 | erot = 10.4442109367339 | epot = -69.3064782658694 | etot = -50.5142754016386 +30000 ekin = 8.6005090155205 | erot = 10.2725968652589 | epot = -69.387381282446 | etot = -50.5142754016666 +31000 ekin = 8.93993736466304 | erot = 10.1743202831904 | epot = -69.628533050782 | etot = -50.5142754029286 +32000 ekin = 9.35601638498844 | erot = 10.140997954843 | epot = -70.0112897452844 | etot = -50.514275405453 +33000 ekin = 9.82730889560453 | erot = 10.157308804684 | epot = -70.4988931092325 | etot = -50.5142754089439 +34000 ekin = 10.3233617248882 | erot = 10.2017701889081 | epot = -71.0394073268383 | etot = -50.5142754130419 +35000 ekin = 10.8090561190438 | erot = 10.247264926477 | epot = -71.5705964624689 | etot = -50.5142754169481 +36000 ekin = 11.249914122839 | erot = 10.2681203532653 | epot = -72.0323098961298 | etot = -50.5142754200254 +37000 ekin = 11.6169651147169 | erot = 10.2446303624725 | epot = -72.3758708990397 | etot = -50.5142754218503 +38000 ekin = 11.8900149081475 | erot = 10.1661461993862 | epot = -72.570436529843 | etot = -50.5142754223094 +39000 ekin = 12.0587831385577 | erot = 10.0319213337583 | epot = -72.6049798938919 | etot = -50.5142754215758 +40000 ekin = 12.122142396546 | erot = 9.84972970547098 | epot = -72.486147522015 | etot = -50.514275419998 +41000 ekin = 12.0861841074656 | erot = 9.63306258024731 | epot = -72.2335221056766 | etot = -50.5142754179636 +42000 ekin = 11.9619003024208 | erot = 9.39799829870687 | epot = -71.87417401693 | etot = -50.5142754158023 +43000 ekin = 11.763028556965 | erot = 9.16060997815283 | epot = -71.437913948862 | etot = -50.5142754137441 +44000 ekin = 11.5042972043492 | erot = 8.9352528014311 | epot = -70.9538254179092 | etot = -50.5142754121289 +45000 ekin = 11.2001042846034 | erot = 8.73270158680084 | epot = -70.4470812820298 | etot = -50.5142754106255 +46000 ekin = 10.8635866168487 | erot = 8.56191440586786 | epot = -69.9397764321241 | etot = -50.5142754094075 +47000 ekin = 10.5060426541438 | erot = 8.43032536515553 | epot = -69.4506434277691 | etot = -50.5142754084698 +48000 ekin = 10.1367333285103 | erot = 8.3437951227817 | epot = -68.9948038590509 | etot = -50.514275407759 +49000 ekin = 9.76306209921957 | erot = 8.30714647396251 | epot = -68.5844839803859 | etot = -50.5142754072038 +50000 ekin = 9.39110096123118 | erot = 8.32465746225203 | epot = -68.2300338302009 | etot = -50.5142754067177 +51000 ekin = 9.02637094808728 | erot = 8.40044977381002 | epot = -67.9410961281177 | etot = -50.5142754062204 +52000 ekin = 8.6747296083158 | erot = 8.53870234353609 | epot = -67.7277073575007 | etot = -50.5142754056488 +53000 ekin = 8.34318047181607 | erot = 8.74362113488868 | epot = -67.6010770116707 | etot = -50.5142754049659 +54000 ekin = 8.04040850085707 | erot = 9.01907630543251 | epot = -67.573760210546 | etot = -50.5142754042564 +55000 ekin = 7.77685567444779 | erot = 9.36744157045986 | epot = -67.6585726485232 | etot = -50.5142754036156 +56000 ekin = 7.56421834771052 | erot = 9.78833936441828 | epot = -67.8668331153473 | etot = -50.5142754032185 +57000 ekin = 7.41438670675999 | erot = 10.2770459211366 | epot = -68.2057080311509 | etot = -50.5142754032544 +58000 ekin = 7.33802624874224 | erot = 10.8230821587553 | epot = -68.6753838113651 | etot = -50.5142754038675 +59000 ekin = 7.34316098271584 | erot = 11.4095663142002 | epot = -69.2670027020093 | etot = -50.5142754050933 +60000 ekin = 7.43413000753824 | erot = 12.0137183042261 | epot = -69.9621237186161 | etot = -50.5142754068517 +61000 ekin = 7.61111888193116 | erot = 12.6084567926324 | epot = -70.7338510836113 | etot = -50.5142754090478 +62000 ekin = 7.870212751877 | erot = 13.1643184159412 | epot = -71.548806579169 | etot = -50.5142754113508 +63000 ekin = 8.20369524488213 | erot = 13.6538505067939 | epot = -72.3718211650923 | etot = -50.5142754134162 +64000 ekin = 8.60031282923883 | erot = 14.0539021280606 | epot = -73.1684903728585 | etot = -50.5142754155591 +65000 ekin = 9.04632694082969 | erot = 14.3452399471043 | epot = -73.9058423052425 | etot = -50.5142754173085 +66000 ekin = 9.52633841545716 | erot = 14.5163977172634 | epot = -74.5570115512596 | etot = -50.5142754185391 +67000 ekin = 10.023966290935 | erot = 14.5650853618126 | epot = -75.1033270719431 | etot = -50.5142754191956 +68000 ekin = 10.5223769651099 | erot = 14.4984989976631 | epot = -75.5351513820878 | etot = -50.5142754193148 +69000 ekin = 11.0045882552174 | erot = 14.3324567229674 | epot = -75.8513203972072 | etot = -50.5142754190223 +70000 ekin = 11.4535533147711 | erot = 14.0893789066284 | epot = -76.057207639911 | etot = -50.5142754185115 +71000 ekin = 11.8521538801903 | erot = 13.79542130906 | epot = -76.1618506069767 | etot = -50.5142754177265 +72000 ekin = 12.1833321321141 | erot = 13.477970603226 | epot = -76.1755781528749 | etot = -50.5142754175347 +73000 ekin = 12.4276815038091 | erot = 13.1602120049099 | epot = -76.1021689263872 | etot = -50.5142754176682 +74000 ekin = 12.5675503165872 | erot = 12.8593249179889 | epot = -75.9411506526185 | etot = -50.5142754180425 +75000 ekin = 12.5880722472041 | erot = 12.5864734132401 | epot = -75.6888210788976 | etot = -50.5142754184534 +76000 ekin = 12.4791879307482 | erot = 12.3474886698871 | epot = -75.3409520192492 | etot = -50.5142754186139 +77000 ekin = 12.2380594263611 | erot = 12.1445664156593 | epot = -74.8969012602668 | etot = -50.5142754182465 +78000 ekin = 11.8710909455366 | erot = 11.9782430722448 | epot = -74.3636094349577 | etot = -50.5142754171763 +79000 ekin = 11.3949317822823 | erot = 11.848879253422 | epot = -73.7580864511041 | etot = -50.5142754153999 +80000 ekin = 10.8360121848366 | erot = 11.7571641077354 | epot = -73.1074517056631 | etot = -50.5142754130911 +81000 ekin = 10.2285029505784 | erot = 11.7036410573988 | epot = -72.4464194185281 | etot = -50.5142754105509 +82000 ekin = 9.61095186500036 | erot = 11.6876732074591 | epot = -71.812900480592 | etot = -50.5142754081325 +83000 ekin = 9.02210953811139 | erot = 11.7064078446989 | epot = -71.2427927889811 | etot = -50.5142754061708 +84000 ekin = 8.49658156956786 | erot = 11.7541576431629 | epot = -70.7650146176588 | etot = -50.514275404928 +85000 ekin = 8.06096889575731 | erot = 11.8223883028496 | epot = -70.3976326031555 | etot = -50.5142754045486 +86000 ekin = 7.73111762512489 | erot = 11.9003213122164 | epot = -70.145714342385 | etot = -50.5142754050437 +87000 ekin = 7.51095945896616 | erot = 11.9760199352984 | epot = -70.0012548008789 | etot = -50.5142754066143 +88000 ekin = 7.39125161739367 | erot = 12.0367692288908 | epot = -69.9422962547361 | etot = -50.5142754084516 +89000 ekin = 7.35291960067763 | erot = 12.0715131146599 | epot = -69.9387081257095 | etot = -50.5142754103719 +90000 ekin = 7.37292152740792 | erot = 12.0742094418178 | epot = -69.9614063812379 | etot = -50.5142754120122 +91000 ekin = 7.42677225769639 | erot = 12.0445134023064 | epot = -69.9855610731053 | etot = -50.5142754131025 +92000 ekin = 7.49195579980711 | erot = 11.9883651963225 | epot = -69.9945964096581 | etot = -50.5142754135285 +93000 ekin = 7.55030810819686 | erot = 11.9173535388133 | epot = -69.9819370603461 | etot = -50.5142754133359 +94000 ekin = 7.58924049100661 | erot = 11.8468330690203 | epot = -69.9503489726995 | etot = -50.5142754126726 +95000 ekin = 7.6020025204481 | erot = 11.7936183338065 | epot = -69.9098962660033 | etot = -50.5142754117487 +96000 ekin = 7.58730388646345 | erot = 11.7732310350296 | epot = -69.8748103322612 | etot = -50.5142754107681 +97000 ekin = 7.54854000456008 | erot = 11.7975124404598 | epot = -69.8603278549292 | etot = -50.5142754099092 +98000 ekin = 7.49272694028245 | erot = 11.8729196687565 | epot = -69.8799220183582 | etot = -50.5142754093192 +99000 ekin = 7.4291494757019 | erot = 11.9995813313698 | epot = -69.9430062161875 | etot = -50.5142754091158 +100000 ekin = 7.36773967938524 | erot = 12.1710710801622 | epot = -70.0530861689363 | etot = -50.5142754093889 +101000 ekin = 7.31732397084039 | erot = 12.3748173436258 | epot = -70.2064167246486 | etot = -50.5142754101824 +102000 ekin = 7.28403638324999 | erot = 12.5931097957223 | epot = -70.3914215904351 | etot = -50.5142754114629 +103000 ekin = 7.27028672218544 | erot = 12.8047065613041 | epot = -70.5892686965879 | etot = -50.5142754130984 +104000 ekin = 7.27461582345194 | erot = 12.9870305824843 | epot = -70.7759218207906 | etot = -50.5142754148544 +105000 ekin = 7.29256428498991 | erot = 13.1188507799813 | epot = -70.9256904813943 | etot = -50.5142754164232 +106000 ekin = 7.31837884124417 | erot = 13.1831707086961 | epot = -71.0158249674225 | etot = -50.5142754174823 +107000 ekin = 7.34712371511234 | erot = 13.1698989274595 | epot = -71.031298060336 | etot = -50.5142754177642 +108000 ekin = 7.37665826766637 | erot = 13.0778272245795 | epot = -70.9687609093631 | etot = -50.5142754171173 +109000 ekin = 7.4090189086913 | erot = 12.9155349189484 | epot = -70.8388292431721 | etot = -50.5142754155324 +110000 ekin = 7.45094132862665 | erot = 12.7010355373242 | epot = -70.6662522790923 | etot = -50.5142754131415 +111000 ekin = 7.51347081219244 | erot = 12.46020149619 | epot = -70.4879477185786 | etot = -50.5142754101962 +112000 ekin = 7.61074849763088 | erot = 12.2241598717144 | epot = -70.3491837763853 | etot = -50.5142754070401 +113000 ekin = 7.75811427376647 | erot = 12.0259242572139 | epot = -70.2983139350605 | etot = -50.5142754040801 +114000 ekin = 7.96968357180601 | erot = 11.8965473949302 | epot = -70.3805063684906 | etot = -50.5142754017543 +115000 ekin = 8.25649742679397 | erot = 11.8610413387427 | epot = -70.6318141648406 | etot = -50.514275399304 +116000 ekin = 8.62901108799767 | erot = 11.9338020389737 | epot = -71.0770885267353 | etot = -50.5142753997639 +117000 ekin = 9.07979306129225 | erot = 12.11683106496 | epot = -71.7108995279875 | etot = -50.5142754017353 +118000 ekin = 9.58966909201972 | erot = 12.3984864178258 | epot = -72.5024309149985 | etot = -50.5142754051531 +119000 ekin = 10.1306989356929 | erot = 12.7538188996439 | epot = -73.3987932450652 | etot = -50.5142754097284 +120000 ekin = 10.6681502559762 | erot = 13.1469968867685 | epot = -74.3294225577253 | etot = -50.5142754149806 +121000 ekin = 11.1636445520073 | erot = 13.5354730446192 | epot = -75.2133930169272 | etot = -50.5142754203007 +122000 ekin = 11.57897975496 | erot = 13.8753321908141 | epot = -75.9685873708298 | etot = -50.5142754250557 +123000 ekin = 11.8800282928193 | erot = 14.1269962436853 | epot = -76.5212999651875 | etot = -50.514275428683 +124000 ekin = 12.0401500514962 | erot = 14.2603474738997 | epot = -76.8147729561754 | etot = -50.5142754307795 +125000 ekin = 12.0426917567921 | erot = 14.2584040043223 | epot = -76.815371192273 | etot = -50.5142754311586 +126000 ekin = 11.8823151169337 | erot = 14.1189492121683 | epot = -76.515539758965 | etot = -50.5142754298629 +127000 ekin = 11.5650853952491 | erot = 13.8539357927793 | epot = -75.9332966151679 | etot = -50.5142754271395 +128000 ekin = 11.1074426377048 | erot = 13.4869506143901 | epot = -75.1086686754654 | etot = -50.5142754233705 +129000 ekin = 10.5343384717472 | erot = 13.0494015453623 | epot = -74.0980154361035 | etot = -50.514275418994 +130000 ekin = 9.87690872398879 | erot = 12.576259576003 | epot = -72.9674437144207 | etot = -50.514275414429 +131000 ekin = 9.17004712474199 | erot = 12.1021279223485 | epot = -71.786450457109 | etot = -50.5142754100185 +132000 ekin = 8.45013853634169 | erot = 11.6581576779292 | epot = -70.6225716202876 | etot = -50.5142754060167 +133000 ekin = 7.75306702335596 | erot = 11.2700074959997 | epot = -69.5373499219504 | etot = -50.5142754025948 +134000 ekin = 7.11230829826017 | erot = 10.9564870021547 | epot = -68.5830707008175 | etot = -50.5142754004026 +135000 ekin = 6.55612439193967 | erot = 10.7277682649122 | epot = -67.7981680553166 | etot = -50.5142753984647 +136000 ekin = 6.10819187150001 | erot = 10.5892176988517 | epot = -67.2116849676778 | etot = -50.5142753973261 +137000 ekin = 5.78608197421734 | erot = 10.540520502847 | epot = -66.8408778740815 | etot = -50.5142753970172 +138000 ekin = 5.60007006615131 | erot = 10.5757913350062 | epot = -66.6901367986762 | etot = -50.5142753975188 +139000 ekin = 5.55268795111527 | erot = 10.6843332994592 | epot = -66.7512966493219 | etot = -50.5142753987475 +140000 ekin = 5.63899580381771 | erot = 10.8516980543445 | epot = -67.0049692587037 | etot = -50.5142754005415 +141000 ekin = 5.84764919447451 | erot = 11.0611136462019 | epot = -67.4230382433434 | etot = -50.514275402667 +142000 ekin = 6.16264005598639 | erot = 11.2952393652934 | epot = -67.972154826137 | etot = -50.5142754048573 +143000 ekin = 6.5653968006486 | erot = 11.5380449116321 | epot = -68.617717119148 | etot = -50.5142754068674 +144000 ekin = 7.03681705533494 | erot = 11.7764583665014 | epot = -69.3275508303656 | etot = -50.5142754085292 +145000 ekin = 7.55883117515757 | erot = 12.0018872087109 | epot = -70.0749937935651 | etot = -50.5142754096967 +146000 ekin = 8.11525467293274 | erot = 12.2097777634812 | epot = -70.8393078470392 | etot = -50.5142754106253 +147000 ekin = 8.69187535303672 | erot = 12.39798317829 | epot = -71.60413394269 | etot = -50.5142754113633 +148000 ekin = 9.27596343937889 | erot = 12.5659623821103 | epot = -72.3562012335808 | etot = -50.5142754120916 +149000 ekin = 9.85549786713737 | erot = 12.7129927814354 | epot = -73.0827660615428 | etot = -50.51427541297 +150000 ekin = 10.4183967686482 | erot = 12.836669784577 | epot = -73.7693419673228 | etot = -50.5142754140976 +151000 ekin = 10.9519669544066 | erot = 12.9320291475734 | epot = -74.3982715174713 | etot = -50.5142754154914 +152000 ekin = 11.442682517049 | erot = 12.9914579844176 | epot = -74.9484159185612 | etot = -50.5142754170946 +153000 ekin = 11.876317648688 | erot = 13.0054164817462 | epot = -75.3960095492277 | etot = -50.5142754187935 +154000 ekin = 12.2384007603464 | erot = 12.9636415213689 | epot = -75.7163177021566 | etot = -50.5142754204413 +155000 ekin = 12.5149348410738 | erot = 12.8565997645015 | epot = -75.8858100274538 | etot = -50.5142754218785 +156000 ekin = 12.6933342582489 | erot = 12.6769330808822 | epot = -75.884542762078 | etot = -50.5142754229468 +157000 ekin = 12.7635394773931 | erot = 12.420726561961 | epot = -75.6985414628473 | etot = -50.5142754234931 +158000 ekin = 12.7192609300237 | erot = 12.0885427176422 | epot = -75.3220790710396 | etot = -50.5142754233736 +159000 ekin = 12.5592455089106 | erot = 11.6862409532775 | epot = -74.7597618846574 | etot = -50.5142754224692 +160000 ekin = 12.2883544579957 | erot = 11.2255943810308 | epot = -74.0282242597327 | etot = -50.5142754207062 +161000 ekin = 11.918138868909 | erot = 10.724624857561 | epot = -73.1570391445678 | etot = -50.5142754180978 +162000 ekin = 11.4665846354855 | erot = 10.2074983581299 | epot = -72.1883584083807 | etot = -50.5142754147653 +163000 ekin = 10.9568419276705 | erot = 9.70380592719131 | epot = -71.174923265813 | etot = -50.5142754109511 +164000 ekin = 10.4150382817266 | erot = 9.24702033764171 | epot = -70.1763340263567 | etot = -50.5142754069884 +165000 ekin = 9.86757905055595 | erot = 8.87218491764885 | epot = -69.2540393714494 | etot = -50.5142754032446 +166000 ekin = 9.33851143761076 | erot = 8.61303477785208 | epot = -68.4658216155234 | etot = -50.5142754000605 +167000 ekin = 8.84748730504149 | erot = 8.49893907243685 | epot = -67.860701775172 | etot = -50.5142753976936 +168000 ekin = 8.40864571542297 | erot = 8.55215074312129 | epot = -67.4750718548273 | etot = -50.514275396283 +169000 ekin = 8.03045700864833 | erot = 8.78581375895565 | epot = -67.3305461634521 | etot = -50.5142753958481 +170000 ekin = 7.71636101684879 | erot = 9.20299038162967 | epot = -67.4336267947965 | etot = -50.514275396318 +171000 ekin = 7.46715080109661 | erot = 9.79683187833261 | epot = -67.7782580760367 | etot = -50.5142753966075 +172000 ekin = 7.28585658179809 | erot = 10.55063278227 | epot = -68.3507647629919 | etot = -50.5142753989238 +173000 ekin = 7.16416011926193 | erot = 11.4382460333909 | epot = -69.1166815542996 | etot = -50.5142754016467 +174000 ekin = 7.09132968419341 | erot = 12.4279054681617 | epot = -70.0335105569871 | etot = -50.514275404632 +175000 ekin = 7.05634491974643 | erot = 13.4842000875635 | epot = -71.0548204150769 | etot = -50.514275407767 +176000 ekin = 7.0481562278597 | erot = 14.5697180479998 | epot = -72.1321496868112 | etot = -50.5142754109517 +177000 ekin = 7.05589089928317 | erot = 15.6465151520291 | epot = -73.2166814653897 | etot = -50.5142754140774 +178000 ekin = 7.06870996384056 | erot = 16.6778391096173 | epot = -74.2608244904867 | etot = -50.5142754170288 +179000 ekin = 7.07565875636382 | erot = 17.6303035880058 | epot = -75.2202377640007 | etot = -50.5142754196311 +180000 ekin = 7.0664071847183 | erot = 18.4755802360983 | epot = -76.0562628425558 | etot = -50.5142754217392 +181000 ekin = 7.03211004009772 | erot = 19.1916515774742 | epot = -76.7380370407757 | etot = -50.5142754232038 +182000 ekin = 6.96555336525017 | erot = 19.7646727182893 | epot = -77.244501509119 | etot = -50.5142754255795 +183000 ekin = 6.86135102663297 | erot = 20.1806311279203 | epot = -77.5562575806605 | etot = -50.5142754261072 +184000 ekin = 6.71513119692767 | erot = 20.4321176363582 | epot = -77.6615242591401 | etot = -50.5142754258542 +185000 ekin = 6.52573507255851 | erot = 20.5251927864042 | epot = -77.5652032838349 | etot = -50.5142754248723 +186000 ekin = 6.29640349453673 | erot = 20.4725850987712 | epot = -77.2832640165617 | etot = -50.5142754232538 +187000 ekin = 6.03524835634356 | erot = 20.2918463237092 | epot = -76.8413701011661 | etot = -50.5142754211133 +188000 ekin = 5.75534624813166 | erot = 20.003513474993 | epot = -76.2731351417078 | etot = -50.5142754185832 +189000 ekin = 5.47428677235272 | erot = 19.6288299760678 | epot = -75.6173921644527 | etot = -50.5142754160321 +190000 ekin = 5.21304528645313 | erot = 19.1884702895166 | epot = -74.9157909892296 | etot = -50.5142754132598 +191000 ekin = 4.99413978963151 | erot = 18.702982729212 | epot = -74.2113979294843 | etot = -50.5142754106408 +192000 ekin = 4.83931815322758 | erot = 18.1912747809759 | epot = -73.5448683425759 | etot = -50.5142754083724 +193000 ekin = 4.76714699157891 | erot = 17.6700691054191 | epot = -72.9514915036064 | etot = -50.5142754066084 +194000 ekin = 4.79094358958821 | erot = 17.1536396953286 | epot = -72.458858690352 | etot = -50.5142754054352 +195000 ekin = 4.91743571189862 | erot = 16.6538363084265 | epot = -72.0855474251817 | etot = -50.5142754048565 +196000 ekin = 5.14635650996878 | erot = 16.1803427452313 | epot = -71.8409746600075 | etot = -50.5142754048074 +197000 ekin = 5.47095769373928 | erot = 15.7410432599948 | epot = -71.7262763589174 | etot = -50.5142754051834 +198000 ekin = 5.87922858421923 | erot = 15.3423400565289 | epot = -71.7358440466121 | etot = -50.514275405864 +199000 ekin = 6.35549663143462 | erot = 14.9892917891109 | epot = -71.8590638272921 | etot = -50.5142754067466 +200000 ekin = 6.88207586328326 | erot = 14.6855189973288 | epot = -72.0818702683696 | etot = -50.5142754077575 +201000 ekin = 7.44070643689874 | erot = 14.4329169816363 | epot = -72.3878988273873 | etot = -50.5142754088523 +202000 ekin = 8.01364908712218 | erot = 14.2312922772059 | epot = -72.7592167743344 | etot = -50.5142754100063 +203000 ekin = 8.58441531263097 | erot = 14.0780678440262 | epot = -73.17675856786 | etot = -50.5142754112029 +204000 ekin = 9.13819316346958 | erot = 13.9681780326739 | epot = -73.6206466085646 | etot = -50.5142754124211 +205000 ekin = 9.66205791777009 | erot = 13.8942152360353 | epot = -74.0705485674259 | etot = -50.5142754136206 +206000 ekin = 10.1450467911539 | erot = 13.8468542669205 | epot = -74.5061764728695 | etot = -50.5142754147951 +207000 ekin = 10.578144322819 | erot = 13.8152589579907 | epot = -74.9076786967 | etot = -50.5142754158903 +208000 ekin = 10.9541942360309 | erot = 13.7878179109834 | epot = -75.2562875638894 | etot = -50.5142754168752 +209000 ekin = 11.267746303547 | erot = 13.7528525924427 | epot = -75.5348743137162 | etot = -50.5142754177265 +210000 ekin = 11.5148381182812 | erot = 13.6992490106689 | epot = -75.7283625473776 | etot = -50.5142754184275 +211000 ekin = 11.6927279463081 | erot = 13.6170543238074 | epot = -75.8240576890816 | etot = -50.514275418966 +212000 ekin = 11.7996107409516 | erot = 13.498093858938 | epot = -75.8119800191621 | etot = -50.5142754192725 +213000 ekin = 11.8343576841801 | erot = 13.3367031669193 | epot = -75.6853362705959 | etot = -50.5142754194966 +214000 ekin = 11.7963237462734 | erot = 13.1291697339434 | epot = -75.4397688997496 | etot = -50.5142754195328 +215000 ekin = 11.6852668694872 | erot = 12.8744302846878 | epot = -75.0739725735764 | etot = -50.5142754194014 +216000 ekin = 11.5014303659807 | erot = 12.5741401329479 | epot = -74.5898459180401 | etot = -50.5142754191115 +217000 ekin = 11.2458820823716 | erot = 12.2323072888257 | epot = -73.9924647898439 | etot = -50.5142754186465 +218000 ekin = 10.9212463786247 | erot = 11.8549524898053 | epot = -73.2904742863556 | etot = -50.5142754179256 +219000 ekin = 10.5329607071043 | erot = 11.4501226259863 | epot = -72.49735874987 | etot = -50.5142754167794 +220000 ekin = 10.0910611337993 | erot = 11.0285507859451 | epot = -71.6338873347152 | etot = -50.5142754149708 +221000 ekin = 9.61219796243707 | erot = 10.6049025440469 | epot = -70.7313759187676 | etot = -50.5142754122836 +222000 ekin = 9.12115937360899 | erot = 10.1989791085947 | epot = -69.8344138908813 | etot = -50.5142754086776 +223000 ekin = 8.65086680646765 | erot = 9.83578310548162 | epot = -69.0009253163756 | etot = -50.5142754044263 +224000 ekin = 8.23994052342008 | erot = 9.54342912562565 | epot = -68.2976450492017 | etot = -50.5142754001559 +225000 ekin = 7.92770828800231 | erot = 9.34870111081527 | epot = -67.790684795513 | etot = -50.5142753966955 +226000 ekin = 7.74769423456926 | erot = 9.27124602945026 | epot = -67.5332156588649 | etot = -50.5142753948454 +227000 ekin = 7.72151333456996 | erot = 9.31824720259745 | epot = -67.5540359321277 | etot = -50.5142753949603 +228000 ekin = 7.85509348312393 | erot = 9.48230636778553 | epot = -67.8516752474347 | etot = -50.5142753965252 +229000 ekin = 8.13704792668027 | erot = 9.74526659084784 | epot = -68.3965899178475 | etot = -50.5142754003194 +230000 ekin = 8.54211975827155 | erot = 10.0762112157464 | epot = -69.1326063789161 | etot = -50.5142754048981 +231000 ekin = 9.03730612207738 | erot = 10.4369573689889 | epot = -69.9885389005795 | etot = -50.5142754095132 +232000 ekin = 9.58655681927075 | erot = 10.7906593081316 | epot = -70.8914915409884 | etot = -50.514275413586 +233000 ekin = 10.1548693407441 | erot = 11.1065562702284 | epot = -71.7757010277629 | etot = -50.5142754167904 +234000 ekin = 10.7108776684931 | erot = 11.3626339427587 | epot = -72.5877870303017 | etot = -50.51427541905 +235000 ekin = 11.2279915296297 | erot = 11.5461467437169 | epot = -73.2884136938096 | etot = -50.514275420463 +236000 ekin = 11.6845296184674 | erot = 11.6525082369784 | epot = -73.8513132774554 | etot = -50.5142754220096 +237000 ekin = 12.0579257921081 | erot = 11.6840457725791 | epot = -74.2562469873985 | etot = -50.5142754227113 +238000 ekin = 12.3279512217302 | erot = 11.6453539329305 | epot = -74.4875805777159 | etot = -50.5142754230552 +239000 ekin = 12.4822356739968 | erot = 11.5417603171812 | epot = -74.5382714141961 | etot = -50.5142754230181 +240000 ekin = 12.5140319304711 | erot = 11.379840095166 | epot = -74.4081474481419 | etot = -50.5142754225049 +241000 ekin = 12.4234383523727 | erot = 11.1674085806407 | epot = -74.1051223544161 | etot = -50.5142754214027 +242000 ekin = 12.2186033883435 | erot = 10.9138071750489 | epot = -73.6466859829951 | etot = -50.5142754196027 +243000 ekin = 11.9165339535856 | erot = 10.6303079140426 | epot = -73.0611172847464 | etot = -50.5142754171182 +244000 ekin = 11.5429037221891 | erot = 10.3301144758701 | epot = -72.3872936120661 | etot = -50.5142754140069 +245000 ekin = 11.1308004491748 | erot = 10.0279651152891 | epot = -71.6730409749943 | etot = -50.5142754105304 +246000 ekin = 10.7178963481097 | erot = 9.73923384809242 | epot = -70.9714056032644 | etot = -50.5142754070622 +247000 ekin = 10.3421796192254 | erot = 9.47853790668963 | epot = -70.3349929299427 | etot = -50.5142754040277 +248000 ekin = 10.0370371760664 | erot = 9.25823648340019 | epot = -69.8095490613036 | etot = -50.5142754018371 +249000 ekin = 9.8280907904655 | erot = 9.08725211026133 | epot = -69.4296183010337 | etot = -50.5142754003068 +250000 ekin = 9.73018117904164 | erot = 8.96958696148835 | epot = -69.2140435411897 | etot = -50.5142754006597 +251000 ekin = 9.73984053867213 | erot = 8.90312708509179 | epot = -69.1572430257806 | etot = -50.5142754020167 +252000 ekin = 9.84186771029289 | erot = 8.88191102821452 | epot = -69.2380541425514 | etot = -50.514275404044 +253000 ekin = 10.0131035686005 | erot = 8.89763848171348 | epot = -69.4250174566707 | etot = -50.5142754063567 +254000 ekin = 10.2265753155491 | erot = 8.94123900968228 | epot = -69.6820897338549 | etot = -50.5142754086236 +255000 ekin = 10.45524859614 | erot = 9.00423312865248 | epot = -69.9737571353842 | etot = -50.5142754105918 +256000 ekin = 10.6747348456415 | erot = 9.07982990112818 | epot = -70.268840158984 | etot = -50.5142754122143 +257000 ekin = 10.8646942922457 | erot = 9.16274367319601 | epot = -70.541713378885 | etot = -50.5142754134433 +258000 ekin = 11.0093996909144 | erot = 9.24945580314721 | epot = -70.7731309083517 | etot = -50.51427541429 +259000 ekin = 11.0977947702397 | erot = 9.33830301516964 | epot = -70.9503732001625 | etot = -50.5142754147531 +260000 ekin = 11.1234502408058 | erot = 9.42959720861292 | epot = -71.0673228642374 | etot = -50.5142754148187 +261000 ekin = 11.084655311668 | erot = 9.52592259400693 | epot = -71.124853320123 | etot = -50.5142754144481 +262000 ekin = 10.9846383161362 | erot = 9.63253179681783 | epot = -71.1314455270271 | etot = -50.5142754140731 +263000 ekin = 10.8299323585372 | erot = 9.7533788602196 | epot = -71.0975866314648 | etot = -50.5142754127079 +264000 ekin = 10.6322589075993 | erot = 9.8966156177294 | epot = -71.0431499363677 | etot = -50.514275411039 +265000 ekin = 10.4088137866296 | erot = 10.0729935919374 | epot = -70.9960827876166 | etot = -50.5142754090497 +266000 ekin = 10.1805628465598 | erot = 10.2939584250803 | epot = -70.9887966787016 | etot = -50.5142754070615 +267000 ekin = 9.96994974150426 | erot = 10.568881698132 | epot = -71.0531068450869 | etot = -50.5142754054507 +268000 ekin = 9.79794557249715 | erot = 10.9022495131646 | epot = -71.2144704902422 | etot = -50.5142754045805 +269000 ekin = 9.68133719081143 | erot = 11.2909602515369 | epot = -71.4865728471577 | etot = -50.5142754048094 +270000 ekin = 9.62864440995344 | erot = 11.7231927403038 | epot = -71.866112556462 | etot = -50.5142754062048 +271000 ekin = 9.63922421060092 | erot = 12.1783004915324 | epot = -72.3318001107773 | etot = -50.5142754086439 +272000 ekin = 9.70377142417774 | erot = 12.6284925682459 | epot = -72.8465394041826 | etot = -50.514275411759 +273000 ekin = 9.80635112697928 | erot = 13.042480366541 | epot = -73.3631069085454 | etot = -50.5142754150251 +274000 ekin = 9.92762957286286 | erot = 13.390209777472 | epot = -73.8321147682227 | etot = -50.5142754178878 +275000 ekin = 10.0484619807291 | erot = 13.6476466829871 | epot = -74.2103840836088 | etot = -50.5142754198926 +276000 ekin = 10.1529836986356 | erot = 13.8005799704974 | epot = -74.4678390899037 | etot = -50.5142754207707 +277000 ekin = 10.2306208739496 | erot = 13.8468297581948 | epot = -74.5917260525737 | etot = -50.5142754204294 +278000 ekin = 10.2768285154718 | erot = 13.7964170571848 | epot = -74.5875209917331 | etot = -50.5142754190766 +279000 ekin = 10.292688733801 | erot = 13.6696245090782 | epot = -74.4765886598123 | etot = -50.5142754169331 +280000 ekin = 10.2837511614466 | erot = 13.4944463812719 | epot = -74.2924729570573 | etot = -50.5142754143388 +281000 ekin = 10.2584490696369 | erot = 13.3029884943441 | epot = -74.0757129756548 | etot = -50.5142754116738 +282000 ekin = 10.2256707145249 | erot = 13.1261764968031 | epot = -73.8661226217354 | etot = -50.5142754104074 +283000 ekin = 10.1905670824301 | erot = 12.9864505984506 | epot = -73.6912930902137 | etot = -50.5142754093331 +284000 ekin = 10.1551014927861 | erot = 12.8990344596004 | epot = -73.5684113617362 | etot = -50.5142754093497 +285000 ekin = 10.1166174221483 | erot = 12.8680165955304 | epot = -73.4989094281415 | etot = -50.5142754104629 +286000 ekin = 10.0677495873413 | erot = 12.8863469806728 | epot = -73.4683719803678 | etot = -50.5142754123536 +287000 ekin = 9.99824250893388 | erot = 12.9388664872157 | epot = -73.4513844104809 | etot = -50.5142754143313 +288000 ekin = 9.89878072361537 | erot = 13.0083713387393 | epot = -73.4214274778763 | etot = -50.5142754155217 +289000 ekin = 9.76588531823529 | erot = 13.0828123958633 | epot = -73.3629731293734 | etot = -50.5142754152748 +290000 ekin = 9.60570842713735 | erot = 13.1602378251772 | epot = -73.2802216658703 | etot = -50.5142754135558 +291000 ekin = 9.43434667886824 | erot = 13.2486965863646 | epot = -73.1973186762419 | etot = -50.5142754110091 +292000 ekin = 9.27394835180399 | erot = 13.3611401460295 | epot = -73.149363906408 | etot = -50.5142754085745 +293000 ekin = 9.14636730713574 | erot = 13.5082961118596 | epot = -73.1689388261818 | etot = -50.5142754071864 +294000 ekin = 9.06768252918411 | erot = 13.6923254511146 | epot = -73.2742833874151 | etot = -50.5142754071164 +295000 ekin = 9.04532028964211 | erot = 13.9047980939001 | epot = -73.4643937919225 | etot = -50.5142754083803 +296000 ekin = 9.0768551421693 | erot = 14.1273095688262 | epot = -73.7184401215824 | etot = -50.5142754105869 +297000 ekin = 9.15243484563929 | erot = 14.3349675764939 | epot = -74.0016778353864 | etot = -50.5142754132531 +298000 ekin = 9.25735642260995 | erot = 14.500914426713 | epot = -74.2725462652362 | etot = -50.5142754159133 +299000 ekin = 9.37408501219885 | erot = 14.6008610261537 | epot = -74.489221456686 | etot = -50.5142754183334 +300000 ekin = 9.48403035595343 | erot = 14.6171008231079 | epot = -74.615406599053 | etot = -50.5142754199917 +301000 ekin = 9.56941047832991 | erot = 14.5422411099636 | epot = -74.6259270092322 | etot = -50.5142754209387 +302000 ekin = 9.61327914963389 | erot = 14.3787237130325 | epot = -74.5062782840224 | etot = -50.5142754213561 +303000 ekin = 9.60019007969739 | erot = 14.1333232517923 | epot = -74.2477887542843 | etot = -50.5142754227947 +304000 ekin = 9.51663443757167 | erot = 13.8077649609075 | epot = -73.838674821887 | etot = -50.5142754234078 +305000 ekin = 9.35052324456253 | erot = 13.4126572581698 | epot = -73.2774559258063 | etot = -50.5142754230739 +306000 ekin = 9.09238614806705 | erot = 12.9580617085539 | epot = -72.5647232811224 | etot = -50.5142754245015 +307000 ekin = 8.73005981827426 | erot = 12.4440345689956 | epot = -71.6883698129583 | etot = -50.5142754256884 +308000 ekin = 8.2566413338506 | erot = 11.8703174730668 | epot = -70.6412342327939 | etot = -50.5142754258766 +309000 ekin = 7.68019887869211 | erot = 11.2440321634468 | epot = -69.4385064478104 | etot = -50.5142754056715 +310000 ekin = 6.10737245369119 | erot = 10.0022284148685 | epot = -66.623875833735 | etot = -50.5142749651753 +311000 ekin = 6.5051663128486 | erot = 8.43886202714501 | epot = -65.4583031837961 | etot = -50.5142748438025 +312000 ekin = 8.70116484242897 | erot = 7.89328716556537 | epot = -67.1087266850311 | etot = -50.5142746770368 +313000 ekin = 8.86124124005507 | erot = 7.60650277386477 | epot = -66.9820187090015 | etot = -50.5142746950817 +314000 ekin = 8.9837585532943 | erot = 7.42590866136506 | epot = -66.9239419073517 | etot = -50.5142746926924 +315000 ekin = 9.08224545795615 | erot = 7.35030056649057 | epot = -66.9468207149345 | etot = -50.5142746904878 +316000 ekin = 9.18875804711078 | erot = 7.37458538818198 | epot = -67.0776181243832 | etot = -50.5142746890904 +317000 ekin = 9.33052371805415 | erot = 7.48774538837777 | epot = -67.3325437958112 | etot = -50.5142746893793 +318000 ekin = 9.51917570867462 | erot = 7.66478668187673 | epot = -67.6982370815964 | etot = -50.514274691045 +319000 ekin = 9.75242332649075 | erot = 7.87397921140501 | epot = -68.1406772315358 | etot = -50.51427469364 +320000 ekin = 10.0191832997552 | erot = 8.08576089652675 | epot = -68.6192188931126 | etot = -50.5142746968307 +321000 ekin = 10.2991596304388 | erot = 8.27181002887634 | epot = -69.0852443594277 | etot = -50.5142747001126 +322000 ekin = 10.5668594668861 | erot = 8.408368577092 | epot = -69.489502746865 | etot = -50.5142747028869 +323000 ekin = 10.796786721459 | erot = 8.47975301095049 | epot = -69.7908144356649 | etot = -50.5142747032554 +324000 ekin = 10.9735635054971 | erot = 8.48122286685502 | epot = -69.9690610761869 | etot = -50.5142747038348 +325000 ekin = 11.0878819432255 | erot = 8.419517756764 | epot = -70.0216744028044 | etot = -50.5142747028149 +326000 ekin = 11.1347107227786 | erot = 8.31335610181585 | epot = -69.9623415249752 | etot = -50.5142747003808 +327000 ekin = 11.1183799650528 | erot = 8.19353318203581 | epot = -69.826187844116 | etot = -50.5142746970274 +328000 ekin = 11.0497327326459 | erot = 8.09852253417839 | epot = -69.6625299601774 | etot = -50.5142746933531 +329000 ekin = 10.9426003402474 | erot = 8.06872590414686 | epot = -69.5256009343292 | etot = -50.5142746899349 +330000 ekin = 10.810605763641 | erot = 8.14099901902899 | epot = -69.4658794698995 | etot = -50.5142746872296 +331000 ekin = 10.6649041616609 | erot = 8.34394296354449 | epot = -69.5231218107328 | etot = -50.5142746855274 +332000 ekin = 10.5130013374362 | erot = 8.69446319291525 | epot = -69.7217392153205 | etot = -50.514274684969 +333000 ekin = 10.3584993437548 | erot = 9.19578452270849 | epot = -70.0685585520209 | etot = -50.5142746855576 +334000 ekin = 10.2015206738985 | erot = 9.83691053813426 | epot = -70.5527058992161 | etot = -50.5142746871833 +335000 ekin = 10.0395335916263 | erot = 10.5934602800294 | epot = -71.147268561303 | etot = -50.5142746896473 +336000 ekin = 9.86837013788818 | erot = 11.4297871185481 | epot = -71.8124319491111 | etot = -50.5142746926749 +337000 ekin = 9.68329052893795 | erot = 12.3021498009575 | epot = -72.4997150262758 | etot = -50.5142746963803 +338000 ekin = 9.47975699830538 | erot = 13.1586156684124 | epot = -73.1526473662277 | etot = -50.51427469951 +339000 ekin = 9.25386163519372 | erot = 13.9501138811508 | epot = -73.7182502184446 | etot = -50.5142747021 +340000 ekin = 9.00411247048268 | erot = 14.6361003739348 | epot = -74.1544875483472 | etot = -50.5142747039298 +341000 ekin = 8.73210815870434 | erot = 15.1850150670287 | epot = -74.4313979306224 | etot = -50.5142747048893 +342000 ekin = 8.44257602319506 | erot = 15.5760933936523 | epot = -74.5329441218175 | etot = -50.5142747049702 +343000 ekin = 8.14306068342756 | erot = 15.7999489751153 | epot = -74.4572843627835 | etot = -50.5142747042406 +344000 ekin = 7.84335230650732 | erot = 15.8582017889364 | epot = -74.2158287982538 | etot = -50.5142747028101 +345000 ekin = 7.5547615812519 | erot = 15.7625218310119 | epot = -73.8315581130675 | etot = -50.5142747008037 +346000 ekin = 7.28933152868289 | erot = 15.533392267927 | epot = -73.3369984949627 | etot = -50.5142746983528 +347000 ekin = 7.05903031454608 | erot = 15.1987186623156 | epot = -72.7720236724633 | etot = -50.5142746956016 +348000 ekin = 6.87492348116728 | erot = 14.7922321909677 | epot = -72.1814303648504 | etot = -50.5142746927155 +349000 ekin = 6.74631360359056 | erot = 14.3515585684899 | epot = -71.6121468619725 | etot = -50.514274689892 +350000 ekin = 6.67986669458013 | erot = 13.915872783233 | epot = -71.1100141651616 | etot = -50.5142746873485 +351000 ekin = 6.67881215223173 | erot = 13.5231979607082 | epot = -70.716284798246 | etot = -50.514274685306 +352000 ekin = 6.7423300232361 | erot = 13.2075061614837 | epot = -70.4641108686885 | etot = -50.5142746839688 +353000 ekin = 6.86523168134182 | erot = 12.9958314200866 | epot = -70.3753377849371 | etot = -50.5142746835087 +354000 ekin = 7.03799439993387 | erot = 12.9056193290539 | epot = -70.4578884130311 | etot = -50.5142746840433 +355000 ekin = 7.24717151817794 | erot = 12.9425723794776 | epot = -70.7040185832753 | etot = -50.5142746856198 +356000 ekin = 7.47618779746083 | erot = 13.0993511153042 | epot = -71.0898136009401 | etot = -50.514274688175 +357000 ekin = 7.70655379467168 | erot = 13.3555627807384 | epot = -71.57639126692 | etot = -50.5142746915099 +358000 ekin = 7.91949851740391 | erot = 13.6794128875227 | epot = -72.1131861002092 | etot = -50.5142746952826 +359000 ekin = 8.09792001679416 | erot = 14.031112267177 | epot = -72.6433069830211 | etot = -50.51427469905 +360000 ekin = 8.22841418972718 | erot = 14.3676693799643 | epot = -73.1103582720313 | etot = -50.5142747023399 +361000 ekin = 8.30307067049243 | erot = 14.6487380645349 | epot = -73.466083439054 | etot = -50.5142747040266 +362000 ekin = 8.32057496602366 | erot = 14.8452541250526 | epot = -73.6801037963561 | etot = -50.5142747052799 +363000 ekin = 8.2859663742638 | erot = 14.9355049198 | epot = -73.7357459994538 | etot = -50.5142747053901 +364000 ekin = 8.21051030664383 | erot = 14.9080133757005 | epot = -73.6327983867829 | etot = -50.5142747044385 +365000 ekin = 8.11062074728132 | erot = 14.762328602042 | epot = -73.3872240519731 | etot = -50.5142747026498 +366000 ekin = 8.00603056267545 | erot = 14.5073568469437 | epot = -73.0276621099691 | etot = -50.5142747003499 +367000 ekin = 7.91744023303304 | erot = 14.1587217212047 | epot = -72.5904366521402 | etot = -50.5142746979025 +368000 ekin = 7.86392049103739 | erot = 13.7358279103936 | epot = -72.1140230970701 | etot = -50.5142746956391 +369000 ekin = 7.86042077698536 | erot = 13.2593035824046 | epot = -71.6339990531952 | etot = -50.5142746938053 +370000 ekin = 7.91575681907929 | erot = 12.7493098978033 | epot = -71.1793414094053 | etot = -50.5142746925228 +371000 ekin = 8.03141765157836 | erot = 12.2248825990312 | epot = -70.7705749423984 | etot = -50.5142746917889 +372000 ekin = 8.20143448680258 | erot = 11.7041154007118 | epot = -70.4198245790145 | etot = -50.5142746915002 +373000 ekin = 8.41338088913735 | erot = 11.2047322599996 | epot = -70.1323878406344 | etot = -50.5142746914974 +374000 ekin = 8.65035651213676 | erot = 10.7445296546632 | epot = -69.9091608584076 | etot = -50.5142746916076 +375000 ekin = 8.89361463866963 | erot = 10.3413213234497 | epot = -69.7492106538015 | etot = -50.5142746916822 +376000 ekin = 9.12537144360732 | erot = 10.0122766242425 | epot = -69.6519227594738 | etot = -50.5142746916241 +377000 ekin = 9.33127044536848 | erot = 9.77273697836932 | epot = -69.6182821151585 | etot = -50.5142746914207 +378000 ekin = 9.50196666765835 | erot = 9.6346566547718 | epot = -69.6508980135944 | etot = -50.5142746911643 +379000 ekin = 9.6334164787518 | erot = 9.60484799639418 | epot = -69.7525391669912 | etot = -50.5142746918452 +380000 ekin = 9.72259425988569 | erot = 9.68264926837071 | epot = -69.9195182203355 | etot = -50.5142746920791 +381000 ekin = 9.76882857108948 | erot = 9.85976932386059 | epot = -70.1428725876802 | etot = -50.5142746927302 +382000 ekin = 9.77534265379327 | erot = 10.121676495812 | epot = -70.4112938433523 | etot = -50.514274693747 +383000 ekin = 9.7455308288081 | erot = 10.4488490599567 | epot = -70.7086545836583 | etot = -50.5142746948936 +384000 ekin = 9.68350130857021 | erot = 10.8197410298628 | epot = -71.0175170342861 | etot = -50.5142746958531 +385000 ekin = 9.59541111931104 | erot = 11.2139279084523 | epot = -71.3236137241633 | etot = -50.5142746963999 +386000 ekin = 9.4905123889625 | erot = 11.6142495069926 | epot = -71.6190365924758 | etot = -50.5142746965207 +387000 ekin = 9.38093820530937 | erot = 12.0071365317809 | epot = -71.9023494335283 | etot = -50.5142746964381 +388000 ekin = 9.27994371661227 | erot = 12.3811396839216 | epot = -72.1753580970413 | etot = -50.5142746965074 +389000 ekin = 9.19914674277392 | erot = 12.7246960950178 | epot = -72.4381175345578 | etot = -50.5142746967661 +390000 ekin = 9.14582012535946 | erot = 13.0260688102897 | epot = -72.6861636335684 | etot = -50.5142746979193 +391000 ekin = 9.12133255591663 | erot = 13.2696465843357 | epot = -72.905253839726 | etot = -50.5142746994737 +392000 ekin = 9.12142280937007 | erot = 13.4389248950419 | epot = -73.0746224054154 | etot = -50.5142747010035 +393000 ekin = 9.13817196413012 | erot = 13.521222955008 | epot = -73.1736696211413 | etot = -50.5142747020031 +394000 ekin = 9.16298117432702 | erot = 13.5118244942667 | epot = -73.1890803706433 | etot = -50.5142747020496 +395000 ekin = 9.18964919962726 | erot = 13.4168358877511 | epot = -73.1207597883378 | etot = -50.5142747009594 +396000 ekin = 9.21646132594054 | erot = 13.2536172301688 | epot = -72.9843532549716 | etot = -50.5142746988622 +397000 ekin = 9.24655582003266 | erot = 13.048360781694 | epot = -72.809191297931 | etot = -50.5142746962043 +398000 ekin = 9.28632448603043 | erot = 12.8312285607695 | epot = -72.6318277404429 | etot = -50.514274693643 +399000 ekin = 9.34221312079044 | erot = 12.6300924932621 | epot = -72.4865803059366 | etot = -50.514274691884 +400000 ekin = 9.41686913721225 | erot = 12.4642777025557 | epot = -72.3954215312665 | etot = -50.5142746914986 +401000 ekin = 9.50589901456697 | erot = 12.339766793681 | epot = -72.359940500998 | etot = -50.51427469275 +402000 ekin = 9.59639944966704 | erot = 12.2470917660162 | epot = -72.3577659111742 | etot = -50.514274695491 +403000 ekin = 9.6679598339413 | erot = 12.1626989619724 | epot = -72.3449334950612 | etot = -50.5142746991475 +404000 ekin = 9.6960891301624 | erot = 12.0539804141974 | epot = -72.2643442471814 | etot = -50.5142747028216 +405000 ekin = 9.65743908961946 | erot = 11.8874299823523 | epot = -72.0591437774177 | etot = -50.5142747054459 +406000 ekin = 9.53561319895846 | erot = 11.6383102531971 | epot = -71.6881981582777 | etot = -50.5142747061221 +407000 ekin = 9.32577307304513 | erot = 11.299022005819 | epot = -71.1390697833186 | etot = -50.5142747044545 +408000 ekin = 9.03640922279408 | erot = 10.8830678024713 | epot = -70.4337517259893 | etot = -50.5142747007238 +409000 ekin = 8.68979508354392 | erot = 10.4228266788975 | epot = -69.6268964554528 | etot = -50.5142746930114 +410000 ekin = 7.95602703558056 | erot = 9.99427140585679 | epot = -68.4645730785575 | etot = -50.5142746371202 +411000 ekin = 6.74655524926026 | erot = 10.0270618219302 | epot = -67.2878915398223 | etot = -50.5142744686318 +412000 ekin = 6.77788460766266 | erot = 10.2313763539033 | epot = -67.5235357279859 | etot = -50.51427476642 +413000 ekin = 6.61781746175654 | erot = 9.98416802498682 | epot = -67.1162600910535 | etot = -50.5142746043101 +414000 ekin = 6.49546599326267 | erot = 9.85785035086806 | epot = -66.8675909468791 | etot = -50.5142746027483 +415000 ekin = 6.41727287248189 | erot = 9.86294960525599 | epot = -66.7944970800185 | etot = -50.5142746022807 +416000 ekin = 6.38652270867731 | erot = 10.0017061049828 | epot = -66.9025034163748 | etot = -50.5142746027147 +417000 ekin = 6.40203155332194 | erot = 10.2671783491659 | epot = -67.1834845063777 | etot = -50.5142746038899 +418000 ekin = 6.45904359291291 | erot = 10.6446827914134 | epot = -67.6180009900212 | etot = -50.5142746056949 +419000 ekin = 6.54999227103668 | erot = 11.1128009050092 | epot = -68.177067784059 | etot = -50.5142746080131 +420000 ekin = 6.66500093977822 | erot = 11.6444776666505 | epot = -68.8237532173566 | etot = -50.5142746109279 +421000 ekin = 6.79216043872236 | erot = 12.2064235895613 | epot = -69.5128586425699 | etot = -50.5142746142862 +422000 ekin = 6.91773851390791 | erot = 12.7612933296126 | epot = -70.1933064611733 | etot = -50.5142746176528 +423000 ekin = 7.02685612353035 | erot = 13.2705085058884 | epot = -70.811639250539 | etot = -50.5142746211202 +424000 ekin = 7.10547271092031 | erot = 13.6958822981223 | epot = -71.3156296329499 | etot = -50.5142746239073 +425000 ekin = 7.14257278346378 | erot = 14.00632169569 | epot = -71.6631691046639 | etot = -50.5142746255101 +426000 ekin = 7.13247824794695 | erot = 14.182567951423 | epot = -71.8293208250291 | etot = -50.5142746256592 +427000 ekin = 7.07609741319096 | erot = 14.2196705903081 | epot = -71.8100426279414 | etot = -50.5142746244424 +428000 ekin = 6.98044576832851 | erot = 14.1262798064217 | epot = -71.6210001969978 | etot = -50.5142746222476 +429000 ekin = 6.85670921306898 | erot = 13.9212692789198 | epot = -71.2922531115578 | etot = -50.514274619569 +430000 ekin = 6.7178161305865 | erot = 13.6292889155649 | epot = -70.8613796631804 | etot = -50.5142746170289 +431000 ekin = 6.58365833328562 | erot = 13.2819652495106 | epot = -70.3798981921713 | etot = -50.5142746093751 +432000 ekin = 6.48411075968897 | erot = 12.9190083014608 | epot = -69.9173936698687 | etot = -50.5142746087189 +433000 ekin = 6.41960617893399 | erot = 12.5531167173917 | epot = -69.4869975047748 | etot = -50.5142746084491 +434000 ekin = 6.38738760765608 | erot = 12.1915446818583 | epot = -69.0932068978254 | etot = -50.514274608311 +435000 ekin = 6.38446518067517 | erot = 11.8388548771081 | epot = -68.737594666638 | etot = -50.5142746088547 +436000 ekin = 6.40158771780273 | erot = 11.4934615671543 | epot = -68.4093238934739 | etot = -50.5142746085169 +437000 ekin = 6.43433296981838 | erot = 11.1572008355194 | epot = -68.105808413647 | etot = -50.5142746083092 +438000 ekin = 6.4825204181187 | erot = 10.8339757935709 | epot = -67.830770819852 | etot = -50.5142746081624 +439000 ekin = 6.545777051164 | erot = 10.5262474658465 | epot = -67.586299125274 | etot = -50.5142746082635 +440000 ekin = 6.62343968576481 | erot = 10.2344360683719 | epot = -67.372150362599 | etot = -50.5142746084622 +441000 ekin = 6.71455901736392 | erot = 9.95770655654166 | epot = -67.186540182668 | etot = -50.5142746087624 +442000 ekin = 6.81814800219619 | erot = 9.69459000556991 | epot = -67.0270126167191 | etot = -50.514274608953 +443000 ekin = 6.93320757980693 | erot = 9.44436660476046 | epot = -66.8918487936045 | etot = -50.5142746090371 +444000 ekin = 7.05887283238864 | erot = 9.20812456867572 | epot = -66.7812720099858 | etot = -50.5142746089214 +445000 ekin = 7.19471792125923 | erot = 8.98907069040902 | epot = -66.6980632207423 | etot = -50.514274609074 +446000 ekin = 7.33895516700839 | erot = 8.79147036186794 | epot = -66.6447001377069 | etot = -50.5142746088306 +447000 ekin = 7.49037827520819 | erot = 8.62086071349769 | epot = -66.6255135972071 | etot = -50.5142746085012 +448000 ekin = 7.64865155422971 | erot = 8.48362573467408 | epot = -66.6465518970615 | etot = -50.5142746081577 +449000 ekin = 7.81370578733081 | erot = 8.38592298858039 | epot = -66.7139033838013 | etot = -50.5142746078901 +450000 ekin = 7.98535597597777 | erot = 8.33253518713107 | epot = -66.8321657709217 | etot = -50.5142746078128 +451000 ekin = 8.16298003842074 | erot = 8.32609814440779 | epot = -67.0033527906226 | etot = -50.514274607794 +452000 ekin = 8.3466507570952 | erot = 8.36815837884311 | epot = -67.2290837442261 | etot = -50.5142746082878 +453000 ekin = 8.53368486477846 | erot = 8.45559889748828 | epot = -67.5035583714211 | etot = -50.5142746091544 +454000 ekin = 8.71876659841696 | erot = 8.58149267466793 | epot = -67.8145338834317 | etot = -50.5142746103468 +455000 ekin = 8.8945819788911 | erot = 8.73616891420663 | epot = -68.1450255048469 | etot = -50.5142746117492 +456000 ekin = 9.05263676519526 | erot = 8.9082562334363 | epot = -68.4751676118086 | etot = -50.514274613177 +457000 ekin = 9.1843646819714 | erot = 9.08589966847123 | epot = -68.7845389652288 | etot = -50.5142746147862 +458000 ekin = 9.27987084845008 | erot = 9.25693683995471 | epot = -69.0510823039163 | etot = -50.5142746155115 +459000 ekin = 9.33585675941296 | erot = 9.41397844083731 | epot = -69.2641098158777 | etot = -50.5142746156275 +460000 ekin = 9.35537570855532 | erot = 9.55424544255629 | epot = -69.4238957661776 | etot = -50.514274615066 +461000 ekin = 9.34708447365392 | erot = 9.67952250490561 | epot = -69.5408815924535 | etot = -50.5142746138939 +462000 ekin = 9.3243802842721 | erot = 9.79582203167512 | epot = -69.6344769282729 | etot = -50.5142746123257 +463000 ekin = 9.30338947377823 | erot = 9.91209761435392 | epot = -69.7297616988258 | etot = -50.5142746106937 +464000 ekin = 9.30012223231539 | erot = 10.0380089094863 | epot = -69.8524057511955 | etot = -50.5142746093938 +465000 ekin = 9.32729383498999 | erot = 10.1814090069829 | epot = -70.0229774507359 | etot = -50.514274608763 +466000 ekin = 9.39154918928888 | erot = 10.3458332464665 | epot = -70.2516570448612 | etot = -50.5142746091058 +467000 ekin = 9.49255088766474 | erot = 10.5268619331796 | epot = -70.533687431223 | etot = -50.5142746103787 +468000 ekin = 9.62305221134184 | erot = 10.7128982306239 | epot = -70.8502250543221 | etot = -50.5142746123563 +469000 ekin = 9.77069488361617 | erot = 10.8867837312521 | epot = -71.1717532295517 | etot = -50.5142746146834 +470000 ekin = 9.92089819251635 | erot = 11.0285784794466 | epot = -71.4637512887688 | etot = -50.5142746168058 +471000 ekin = 10.0595176397096 | erot = 11.1206306062868 | epot = -71.6944228643084 | etot = -50.514274618312 +472000 ekin = 10.1754768606445 | erot = 11.1514441165733 | epot = -71.8411955961169 | etot = -50.5142746188991 +473000 ekin = 10.2623030554399 | erot = 11.1187283838251 | epot = -71.8953060577099 | etot = -50.5142746184449 +474000 ekin = 10.3185312147407 | erot = 11.0305455880016 | epot = -71.863351419831 | etot = -50.5142746170887 +475000 ekin = 10.3471799199443 | erot = 10.9051616574109 | epot = -71.7666161922582 | etot = -50.514274614903 +476000 ekin = 10.3546402104888 | erot = 10.7694904205526 | epot = -71.6384052432813 | etot = -50.5142746122399 +477000 ekin = 10.3491629826105 | erot = 10.6559910559185 | epot = -71.5194286481725 | etot = -50.5142746096436 +478000 ekin = 10.337921781539 | erot = 10.5983211038012 | epot = -71.4505174924961 | etot = -50.5142746071558 +479000 ekin = 10.3280283747164 | erot = 10.627726215543 | epot = -71.4700291953174 | etot = -50.5142746050581 +480000 ekin = 10.3254996650161 | erot = 10.770220178018 | epot = -71.6099944467235 | etot = -50.5142746036895 +481000 ekin = 10.333689005961 | erot = 11.0433446243465 | epot = -71.8913082335923 | etot = -50.5142746032848 +482000 ekin = 10.3524366677706 | erot = 11.4540590314586 | epot = -72.3207703030936 | etot = -50.5142746038644 +483000 ekin = 10.3781084074551 | erot = 11.9979341330605 | epot = -72.8903171458628 | etot = -50.5142746053472 +484000 ekin = 10.4042611097702 | erot = 12.6596244417224 | epot = -73.5781601591086 | etot = -50.5142746076159 +485000 ekin = 10.422130263175 | erot = 13.4142029090766 | epot = -74.3506077826652 | etot = -50.5142746104136 +486000 ekin = 10.4218511022112 | erot = 14.2297763892117 | epot = -75.1659021048436 | etot = -50.5142746134207 +487000 ekin = 10.3939548024778 | erot = 15.0707615261254 | epot = -75.9789909449355 | etot = -50.5142746163324 +488000 ekin = 10.3307490466575 | erot = 15.9010699584849 | epot = -76.7460936240768 | etot = -50.5142746189344 +489000 ekin = 10.2272110328707 | erot = 16.6865229089778 | epot = -77.4280085629796 | etot = -50.5142746211311 +490000 ekin = 10.0812183872014 | erot = 17.3962474873302 | epot = -77.9917404974456 | etot = -50.514274622914 +491000 ekin = 9.89313188199908 | erot = 18.0033313049306 | epot = -78.4107378111931 | etot = -50.5142746242634 +492000 ekin = 9.6654854685475 | erot = 18.4853389017442 | epot = -78.6650989960942 | etot = -50.5142746258026 +493000 ekin = 9.40191070800085 | erot = 18.822957378625 | epot = -78.7391427127391 | etot = -50.5142746261132 +494000 ekin = 9.10904774190992 | erot = 19.0062114320334 | epot = -78.6295337996172 | etot = -50.5142746256739 +495000 ekin = 8.79635273331544 | erot = 19.0345219994561 | epot = -78.3451493571934 | etot = -50.5142746244219 +496000 ekin = 8.47610073021421 | erot = 18.916710534202 | epot = -77.9070858868466 | etot = -50.5142746224304 +497000 ekin = 8.16317181355253 | erot = 18.6700073960972 | epot = -77.3474538295807 | etot = -50.5142746199309 +498000 ekin = 7.87402966204092 | erot = 18.3175884261542 | epot = -76.7058927054729 | etot = -50.5142746172778 +499000 ekin = 7.62493759928334 | erot = 17.8851866271532 | epot = -76.0243988412929 | etot = -50.5142746148563 +500000 ekin = 7.42972946260284 | erot = 17.3977376248947 | epot = -75.3417417004674 | etot = -50.5142746129698 +501000 ekin = 7.29767286843092 | erot = 16.8770499285215 | epot = -74.6889974087191 | etot = -50.5142746117667 +502000 ekin = 7.23199528874835 | erot = 16.3411235838521 | epot = -74.0873934838041 | etot = -50.5142746112037 +503000 ekin = 7.2294568198931 | erot = 15.8051011256293 | epot = -73.5488325566161 | etot = -50.5142746110937 +504000 ekin = 7.28103351461533 | erot = 15.2831943565344 | epot = -73.0785024823396 | etot = -50.5142746111899 +505000 ekin = 7.3734766995099 | erot = 14.7905903684857 | epot = -72.6783416792747 | etot = -50.514274611279 +506000 ekin = 7.49135174829073 | erot = 14.3444485240747 | epot = -72.3500748836015 | etot = -50.514274611236 +507000 ekin = 7.61914293605917 | erot = 13.9635506159553 | epot = -72.0969681630553 | etot = -50.5142746110408 +508000 ekin = 7.74307878353069 | erot = 13.6666853268497 | epot = -71.9240387211432 | etot = -50.5142746107627 +509000 ekin = 7.85243073756074 | erot = 13.4701783615022 | epot = -71.8368837096031 | etot = -50.5142746105402 +510000 ekin = 7.94014182641364 | erot = 13.3851098946224 | epot = -71.8395263315817 | etot = -50.5142746105457 +511000 ekin = 8.00274035613055 | erot = 13.4146098330526 | epot = -71.9316248001711 | etot = -50.5142746109879 +512000 ekin = 8.0395947820545 | erot = 13.5514344935062 | epot = -72.1053038876341 | etot = -50.5142746120734 +513000 ekin = 8.05166756792368 | erot = 13.7761589059528 | epot = -72.3421010878503 | etot = -50.5142746139738 +514000 ekin = 8.04007438030379 | erot = 14.0563762260206 | epot = -72.6107252230582 | etot = -50.5142746167337 +515000 ekin = 8.00493220653697 | erot = 14.3476352397647 | epot = -72.866842066471 | etot = -50.5142746201693 +516000 ekin = 7.94508318888167 | erot = 14.5970448959229 | epot = -73.0564027085865 | etot = -50.5142746237819 +517000 ekin = 7.85912630284244 | erot = 14.7501438289481 | epot = -73.1235447585787 | etot = -50.5142746267882 +518000 ekin = 7.74765591027019 | erot = 14.7604748140602 | epot = -73.0224053526558 | etot = -50.5142746283254 +519000 ekin = 7.61585879290972 | erot = 14.5996265098557 | epot = -72.729759930547 | etot = -50.5142746277817 +520000 ekin = 7.47514959111049 | erot = 14.2643892942165 | epot = -72.2538135103992 | etot = -50.5142746250722 +521000 ekin = 7.3427858954286 | erot = 13.7782408541099 | epot = -71.6353013702292 | etot = -50.5142746206907 +522000 ekin = 7.23932626199338 | erot = 13.186596886737 | epot = -70.9401977642411 | etot = -50.5142746155107 +523000 ekin = 7.18476026651542 | erot = 12.5477212482269 | epot = -70.2467561252271 | etot = -50.5142746104847 +524000 ekin = 7.19456043548838 | erot = 11.9223659335438 | epot = -69.6312009754278 | etot = -50.5142746063956 +525000 ekin = 7.27670076772728 | erot = 11.364776816296 | epot = -69.1557521877544 | etot = -50.5142746037311 +526000 ekin = 7.43017656900148 | erot = 10.916445551457 | epot = -68.8608967231426 | etot = -50.5142746026841 +527000 ekin = 7.64507873199521 | erot = 10.6028306905323 | epot = -68.7621840257271 | etot = -50.5142746031996 +528000 ekin = 7.903968747246 | erot = 10.4326201984723 | epot = -68.8508635507675 | etot = -50.5142746050492 +529000 ekin = 8.18416633903625 | erot = 10.3989120257774 | epot = -69.0973529727054 | etot = -50.5142746078918 +530000 ekin = 8.46054142245487 | erot = 10.4817412712473 | epot = -69.4565573050309 | etot = -50.5142746113288 +531000 ekin = 8.70843705756317 | erot = 10.6515092337968 | epot = -69.8742209062976 | etot = -50.5142746149376 +532000 ekin = 8.90640402473529 | erot = 10.8729770964241 | epot = -70.2936557394646 | etot = -50.5142746183052 +533000 ekin = 9.03848560924205 | erot = 11.1095342988599 | epot = -70.6622945291611 | etot = -50.5142746210592 +534000 ekin = 9.09585660970345 | erot = 11.3274354311236 | epot = -70.9375666637225 | etot = -50.5142746228954 +535000 ekin = 9.07769161963111 | erot = 11.4996353903635 | epot = -71.091601633605 | etot = -50.5142746236104 +536000 ekin = 8.99119538622515 | erot = 11.6087805008686 | epot = -71.1142505102317 | etot = -50.5142746231379 +537000 ekin = 8.85079437598598 | erot = 11.6489142180449 | epot = -71.0139832155935 | etot = -50.5142746215626 +538000 ekin = 8.6765582659833 | erot = 11.6255793580357 | epot = -70.8164122431392 | etot = -50.5142746191202 +539000 ekin = 8.49200375591959 | erot = 11.5542615595909 | epot = -70.5605399316766 | etot = -50.514274616166 +540000 ekin = 8.32364695431123 | erot = 11.4574951670801 | epot = -70.2954167347574 | etot = -50.514274613366 +541000 ekin = 8.19487884818575 | erot = 11.359608827198 | epot = -70.0687622862709 | etot = -50.5142746108871 +542000 ekin = 8.12161273118671 | erot = 11.2840420583372 | epot = -69.9199293984392 | etot = -50.5142746089153 +543000 ekin = 8.11471609564917 | erot = 11.251419263744 | epot = -69.8804099670391 | etot = -50.514274607646 +544000 ekin = 8.17908931153307 | erot = 11.2773707849212 | epot = -69.97073470362 | etot = -50.5142746071658 +545000 ekin = 8.3134477050842 | erot = 11.3713535568191 | epot = -70.19907586937 | etot = -50.5142746074667 +546000 ekin = 8.51069467197093 | erot = 11.5363143613317 | epot = -70.561283641793 | etot = -50.5142746084904 +547000 ekin = 8.75865223741738 | erot = 11.7688547419081 | epot = -71.0417815894908 | etot = -50.5142746101653 +548000 ekin = 9.04082699803126 | erot = 12.0581718441651 | epot = -71.6132734556856 | etot = -50.5142746134893 +549000 ekin = 9.33624649606488 | erot = 12.3823696051936 | epot = -72.2328907177767 | etot = -50.5142746165182 +550000 ekin = 9.62129146822335 | erot = 12.7185500786483 | epot = -72.8541161665286 | etot = -50.514274619657 +551000 ekin = 9.87268266799226 | erot = 13.0427912748185 | epot = -73.4297485653088 | etot = -50.514274622498 +552000 ekin = 10.0704190088569 | erot = 13.3329151351563 | epot = -73.91760876859 | etot = -50.5142746245769 +553000 ekin = 10.2009056939709 | erot = 13.5725638576876 | epot = -74.2877441770597 | etot = -50.5142746254013 +554000 ekin = 10.2593644362673 | erot = 13.753510468764 | epot = -74.5271495300454 | etot = -50.5142746250141 +555000 ekin = 10.2514586319024 | erot = 13.8763528095943 | epot = -74.642086064908 | etot = -50.5142746234113 +556000 ekin = 10.1921106932902 | erot = 13.9500978834556 | epot = -74.6564831978708 | etot = -50.514274621125 +557000 ekin = 10.1015652267051 | erot = 13.9882161029565 | epot = -74.6040559485496 | etot = -50.514274618888 +558000 ekin = 9.99991303231137 | erot = 14.0034286779287 | epot = -74.5176163276028 | etot = -50.5142746173627 +559000 ekin = 9.90202983163985 | erot = 14.0033678523314 | epot = -74.4196722999234 | etot = -50.5142746159522 +560000 ekin = 9.81686282987549 | erot = 13.9898208823654 | epot = -74.3209583290848 | etot = -50.5142746168439 +561000 ekin = 9.74012209780934 | erot = 13.9575380153517 | epot = -74.2119347312478 | etot = -50.5142746180867 +562000 ekin = 9.6620224906263 | erot = 13.8995402247318 | epot = -74.0758373340922 | etot = -50.5142746187341 +563000 ekin = 9.57125126716748 | erot = 13.8130745957307 | epot = -73.8986004819466 | etot = -50.5142746190484 +564000 ekin = 9.45733143833862 | erot = 13.704654695706 | epot = -73.6762607520715 | etot = -50.5142746180269 +565000 ekin = 9.31598070794829 | erot = 13.5911188334432 | epot = -73.4213741578346 | etot = -50.514274616443 +566000 ekin = 9.14991861298779 | erot = 13.4939773072412 | epot = -73.1581705345168 | etot = -50.5142746142878 +567000 ekin = 8.96796855714657 | erot = 13.4373000591331 | epot = -72.9195432283005 | etot = -50.5142746120208 +568000 ekin = 8.7829594372782 | erot = 13.4429949208319 | epot = -72.7402289682284 | etot = -50.5142746101183 +569000 ekin = 8.60911084020179 | erot = 13.5261109884158 | epot = -72.6494964375928 | etot = -50.5142746089752 +570000 ekin = 8.45962137973749 | erot = 13.6911409172854 | epot = -72.6650369058558 | etot = -50.5142746088329 +571000 ekin = 8.34502164172794 | erot = 13.9298996508287 | epot = -72.7891959022988 | etot = -50.5142746097421 +572000 ekin = 8.27150053292934 | erot = 14.2179224508898 | epot = -73.0036975966798 | etot = -50.5142746128607 +573000 ekin = 8.24027906059603 | erot = 14.5163717589467 | epot = -73.2709254351682 | etot = -50.5142746156254 +574000 ekin = 8.25076229272267 | erot = 14.7826990353693 | epot = -73.5477359470996 | etot = -50.5142746190076 +575000 ekin = 8.30023045843066 | erot = 14.9695304974766 | epot = -73.7840355777894 | etot = -50.5142746218821 +576000 ekin = 8.38430166795791 | erot = 15.0355677896539 | epot = -73.9341440816768 | etot = -50.514274624065 +577000 ekin = 8.49786330869482 | erot = 14.9506840672696 | epot = -73.9628220011005 | etot = -50.5142746251361 +578000 ekin = 8.63531193622502 | erot = 14.7010752682888 | epot = -73.850661829671 | etot = -50.5142746251572 +579000 ekin = 8.79067648365993 | erot = 14.2898408975128 | epot = -73.5947920052659 | etot = -50.5142746240931 +580000 ekin = 8.95769742193975 | erot = 13.7363251615306 | epot = -73.2082972056757 | etot = -50.5142746222054 +581000 ekin = 9.12997887069792 | erot = 13.0726035152856 | epot = -72.7168570058288 | etot = -50.5142746198453 +582000 ekin = 9.3013160865459 | erot = 12.33811704705 | epot = -72.1537077509286 | etot = -50.5142746173326 +583000 ekin = 9.46624938717203 | erot = 11.5746138602661 | epot = -71.5551378622606 | etot = -50.5142746148224 +584000 ekin = 9.6207249334283 | erot = 10.8222363956333 | epot = -70.9572359416095 | etot = -50.5142746125479 +585000 ekin = 9.76261487023706 | erot = 10.1164678304031 | epot = -70.3933573111274 | etot = -50.5142746104873 +586000 ekin = 9.89186342302125 | erot = 9.48751958029935 | epot = -69.89365761202 | etot = -50.5142746086994 +587000 ekin = 10.0101586280326 | erot = 8.95961455310412 | epot = -69.4840477884181 | etot = -50.5142746072813 +588000 ekin = 10.1201887301652 | erot = 8.55015736409595 | epot = -69.1846207006327 | etot = -50.5142746063715 +589000 ekin = 10.2246599089045 | erot = 8.26863816357674 | epot = -69.0075726786026 | etot = -50.5142746061214 +590000 ekin = 10.3253143811037 | erot = 8.11543769025587 | epot = -68.9550266780011 | etot = -50.5142746066416 +591000 ekin = 10.4222032216619 | erot = 8.08099811673395 | epot = -69.0174759463446 | etot = -50.5142746079488 +592000 ekin = 10.5134337128834 | erot = 8.14599360018953 | epot = -69.1737019229835 | etot = -50.5142746099106 +593000 ekin = 10.5955057544336 | erot = 8.283064817274 | epot = -69.3928451839437 | etot = -50.5142746122361 +594000 ekin = 10.664166235472 | erot = 8.46027689182427 | epot = -69.6387177418309 | etot = -50.5142746145346 +595000 ekin = 10.7154927999701 | erot = 8.64578434326036 | epot = -69.8755517596524 | etot = -50.5142746164219 +596000 ekin = 10.7467872731101 | erot = 8.81255786150283 | epot = -70.0736197522543 | etot = -50.5142746176414 +597000 ekin = 10.7569302190058 | erot = 8.9418786129938 | epot = -70.2130834501162 | etot = -50.5142746181166 +598000 ekin = 10.7466010847388 | erot = 9.02533979252436 | epot = -70.286215495059 | etot = -50.5142746177959 +599000 ekin = 10.7182887695188 | erot = 9.06507906880464 | epot = -70.2976424556078 | etot = -50.5142746172843 +600000 ekin = 10.672048518945 | erot = 9.06844804973257 | epot = -70.254771185201 | etot = -50.5142746165234 +601000 ekin = 10.6072956941507 | erot = 9.04742526342102 | epot = -70.1689955732011 | etot = -50.5142746156294 +602000 ekin = 10.523317820292 | erot = 9.0169128140318 | epot = -70.0545052489643 | etot = -50.5142746146405 +603000 ekin = 10.4199668052728 | erot = 8.99335643429404 | epot = -69.9275978531109 | etot = -50.5142746135441 +604000 ekin = 10.2985732111555 | erot = 8.99387297244101 | epot = -69.806720795907 | etot = -50.5142746123105 +605000 ekin = 10.1627605691658 | erot = 9.03562879916736 | epot = -69.7126639792936 | etot = -50.5142746109604 +606000 ekin = 10.0187545713334 | erot = 9.13500980542037 | epot = -69.668038986373 | etot = -50.5142746096193 +607000 ekin = 9.87474119403181 | erot = 9.30612986571654 | epot = -69.6951456683299 | etot = -50.5142746085815 +608000 ekin = 9.73894032961195 | erot = 9.55815745315492 | epot = -69.8113723910935 | etot = -50.5142746083266 +609000 ekin = 9.61645131103783 | erot = 9.89160474272124 | epot = -70.0223306631113 | etot = -50.5142746093523 +610000 ekin = 9.5056171781604 | erot = 10.2946039754988 | epot = -70.3144957656481 | etot = -50.5142746119889 +611000 ekin = 9.3954819788822 | erot = 10.7408569963305 | epot = -70.6506135912649 | etot = -50.5142746160522 +612000 ekin = 9.2662925120945 | erot = 11.1926279418144 | epot = -70.973195074468 | etot = -50.5142746205591 +613000 ekin = 9.09415007005058 | erot = 11.6098990355031 | epot = -71.2183237296811 | etot = -50.5142746241274 +614000 ekin = 8.85874044725143 | erot = 11.9622145365451 | epot = -71.3352296093756 | etot = -50.5142746255791 +615000 ekin = 8.55082001881919 | erot = 12.2382561373069 | epot = -71.3033507806173 | etot = -50.5142746244912 +616000 ekin = 8.17588836096349 | erot = 12.4480456866457 | epot = -71.1382086690828 | etot = -50.5142746214735 +617000 ekin = 7.75281434572139 | erot = 12.6167254402989 | epot = -70.8838144036714 | etot = -50.5142746176511 +618000 ekin = 7.30914473380256 | erot = 12.7738647630886 | epot = -70.5972841109796 | etot = -50.5142746140884 +619000 ekin = 6.87603930021606 | erot = 12.9445772325016 | epot = -70.3348911438064 | etot = -50.5142746110888 +620000 ekin = 6.48430188504723 | erot = 13.1463744536982 | epot = -70.1449509480468 | etot = -50.5142746093014 +621000 ekin = 6.15889859795081 | erot = 13.3879128346399 | epot = -70.0610860402008 | etot = -50.5142746076101 +622000 ekin = 5.92489751013321 | erot = 13.6734353594434 | epot = -70.1126074758514 | etot = -50.5142746062747 +623000 ekin = 5.80503635923075 | erot = 14.0046748008182 | epot = -70.3239857654232 | etot = -50.5142746053743 +624000 ekin = 5.81685163240501 | erot = 14.3809730724778 | epot = -70.712099310103 | etot = -50.5142746052201 +625000 ekin = 5.96964537892167 | erot = 14.7975194183874 | epot = -71.2814394036006 | etot = -50.5142746062916 +626000 ekin = 6.26099435194084 | erot = 15.2418617554273 | epot = -72.017130716455 | etot = -50.5142746090868 +627000 ekin = 6.6738932401753 | erot = 15.6898147640126 | epot = -72.8779826180815 | etot = -50.5142746138936 +628000 ekin = 7.17593798620921 | erot = 16.1028362030364 | epot = -73.793048809699 | etot = -50.5142746204534 +629000 ekin = 7.72199923900593 | erot = 16.4299438960732 | epot = -74.6662177627498 | etot = -50.5142746276707 +630000 ekin = 8.26123500942268 | erot = 16.6169483753765 | epot = -75.3924580185318 | etot = -50.5142746337326 +631000 ekin = 8.74754840907595 | erot = 16.6224867206 | epot = -75.8843097661928 | etot = -50.5142746365168 +632000 ekin = 9.15004592009959 | erot = 16.4358276586597 | epot = -76.1001482138241 | etot = -50.5142746350648 +633000 ekin = 9.45937080859952 | erot = 16.0853639088732 | epot = -76.0590093468675 | etot = -50.5142746293948 +634000 ekin = 9.68568488530509 | erot = 15.6315739487035 | epot = -75.8315334570811 | etot = -50.5142746230725 +635000 ekin = 9.84580171437236 | erot = 15.1444204261377 | epot = -75.504496757806 | etot = -50.5142746172959 +636000 ekin = 9.95723404956398 | erot = 14.6860802419334 | epot = -75.1575889048537 | etot = -50.5142746133564 +637000 ekin = 10.0323215960548 | erot = 14.2991433337742 | epot = -74.8457395413136 | etot = -50.5142746114847 +638000 ekin = 10.0765624311321 | erot = 14.0046093482991 | epot = -74.595446390619 | etot = -50.5142746111878 +639000 ekin = 10.0902754260215 | erot = 13.8068600166918 | epot = -74.4114100544242 | etot = -50.514274611711 +640000 ekin = 10.0716366459604 | erot = 13.7011883664072 | epot = -74.2870996247318 | etot = -50.5142746123642 +641000 ekin = 10.0195798551368 | erot = 13.6807153270413 | epot = -74.2145697948544 | etot = -50.5142746126763 +642000 ekin = 9.93575791765933 | erot = 13.7411722988918 | epot = -74.1912048289925 | etot = -50.5142746124414 +643000 ekin = 9.82526205664625 | erot = 13.8830736873739 | epot = -74.2226103557399 | etot = -50.5142746117197 +644000 ekin = 9.69609523854418 | erot = 14.1112875028131 | epot = -74.3216573521581 | etot = -50.5142746108008 +645000 ekin = 9.55761878270953 | erot = 14.4322553940584 | epot = -74.5041487878322 | etot = -50.5142746110643 +646000 ekin = 9.41485510299198 | erot = 14.8475477984815 | epot = -74.776677513142 | etot = -50.5142746116685 +647000 ekin = 9.26709768131387 | erot = 15.3482149652823 | epot = -75.1295872603472 | etot = -50.514274613751 +648000 ekin = 9.1097297858088 | erot = 15.9109204654465 | epot = -75.5349248688731 | etot = -50.5142746176179 +649000 ekin = 8.93158145499244 | erot = 16.4937182185173 | epot = -75.939574296553 | etot = -50.5142746230433 +650000 ekin = 8.71657057992121 | erot = 17.0382000588362 | epot = -76.2690452677801 | etot = -50.5142746290227 +651000 ekin = 8.44844851103753 | erot = 17.4793597702855 | epot = -76.4420829151918 | etot = -50.5142746338688 +652000 ekin = 8.11815479200405 | erot = 17.7619704869967 | epot = -76.3943999148395 | etot = -50.5142746358387 +653000 ekin = 7.73114435531169 | erot = 17.8572650854087 | epot = -76.1026840747697 | etot = -50.5142746340493 +654000 ekin = 7.31085494737133 | erot = 17.7714907196874 | epot = -75.5966202960523 | etot = -50.5142746289936 +655000 ekin = 6.89588215319139 | erot = 17.5418067096241 | epot = -74.951963485066 | etot = -50.5142746222505 +656000 ekin = 6.53171010738367 | erot = 17.2224717011365 | epot = -74.2684564241879 | etot = -50.5142746156678 +657000 ekin = 6.26041816783474 | erot = 16.8689320359789 | epot = -73.643624814452 | etot = -50.5142746106384 +658000 ekin = 6.11203041448849 | erot = 16.5262126841505 | epot = -73.1525177064585 | etot = -50.5142746078195 +659000 ekin = 6.0997254061234 | erot = 16.2236488550371 | epot = -72.8376488683904 | etot = -50.5142746072299 +660000 ekin = 6.21938199685465 | erot = 15.9744887375827 | epot = -72.7081453429338 | etot = -50.5142746084964 +661000 ekin = 6.45261911222383 | erot = 15.777787739745 | epot = -72.7446814630937 | etot = -50.5142746111249 +662000 ekin = 6.77168825556789 | erot = 15.6204850253058 | epot = -72.9064478955754 | etot = -50.5142746147016 +663000 ekin = 7.14435819261658 | erot = 15.4785935640266 | epot = -73.1372263756304 | etot = -50.5142746189873 +664000 ekin = 7.5374031718003 | erot = 15.3176852477657 | epot = -73.3693630433878 | etot = -50.5142746238218 +665000 ekin = 7.91836523033286 | erot = 15.0942309146759 | epot = -73.5268707738858 | etot = -50.5142746288771 +666000 ekin = 8.25643498251185 | erot = 14.7603215859669 | epot = -73.5310312018877 | etot = -50.5142746334089 +667000 ekin = 8.5238576488208 | erot = 14.273632013881 | epot = -73.3117642989558 | etot = -50.514274636254 +668000 ekin = 8.69866667320836 | erot = 13.6113201082106 | epot = -72.8242614177151 | etot = -50.5142746362962 +669000 ekin = 8.76804368923968 | erot = 12.782287305141 | epot = -72.0646056274992 | etot = -50.5142746331185 +670000 ekin = 8.7304670676031 | erot = 11.8307777758175 | epot = -71.0755194707617 | etot = -50.5142746273411 +671000 ekin = 8.59524186893238 | erot = 10.8283334362961 | epot = -69.9378499255365 | etot = -50.514274620308 +672000 ekin = 8.37965784967847 | erot = 9.85799241693729 | epot = -68.7519248800222 | etot = -50.5142746134064 +673000 ekin = 8.10529771610488 | erot = 8.99841190538804 | epot = -67.6179842290275 | etot = -50.5142746075346 +674000 ekin = 7.79494136355158 | erot = 8.31372525731535 | epot = -66.6229412238762 | etot = -50.5142746030093 +675000 ekin = 7.47060107992272 | erot = 7.85026883553715 | epot = -65.8351445152227 | etot = -50.5142745997628 +676000 ekin = 7.15246577752653 | erot = 7.6378972626801 | epot = -65.304637637805 | etot = -50.5142745975984 +677000 ekin = 6.85830618372447 | erot = 7.6928216818834 | epot = -65.065402461981 | etot = -50.5142745963731 +678000 ekin = 6.60298755763437 | erot = 8.01973470911737 | epot = -65.1369968628411 | etot = -50.5142745960894 +679000 ekin = 6.39787215418156 | erot = 8.61208125098986 | epot = -65.5242280021012 | etot = -50.5142745969297 +680000 ekin = 6.2499813420978 | erot = 9.45011609591134 | epot = -66.214372037256 | etot = -50.5142745992468 +681000 ekin = 6.16088982575084 | erot = 10.4969757469227 | epot = -67.1721401761583 | etot = -50.5142746034848 +682000 ekin = 6.12554393407759 | erot = 11.6937893201324 | epot = -68.3336078641875 | etot = -50.5142746099775 +683000 ekin = 6.13157359397284 | erot = 12.9561475536238 | epot = -69.6019957662153 | etot = -50.5142746186187 +684000 ekin = 6.16005916025885 | erot = 14.1756931639 | epot = -70.8500269526455 | etot = -50.5142746284866 +685000 ekin = 6.18869173788201 | erot = 15.2307522948657 | epot = -71.9337186705026 | etot = -50.5142746377548 +686000 ekin = 6.19732878110429 | erot = 16.0068645008467 | epot = -72.7184679261387 | etot = -50.5142746441877 +687000 ekin = 6.17424105601678 | erot = 16.4218469242601 | epot = -73.1103626264033 | etot = -50.5142746461265 +688000 ekin = 6.12017794216041 | erot = 16.444871775218 | epot = -73.0793243606935 | etot = -50.5142746433152 +689000 ekin = 6.04820168734838 | erot = 16.1005193405002 | epot = -72.6629956647693 | etot = -50.5142746369207 +690000 ekin = 5.97970220535046 | erot = 15.4569806258436 | epot = -71.9509574599986 | etot = -50.5142746288046 +691000 ekin = 5.93893719621033 | erot = 14.6057101670997 | epot = -71.058921983986 | etot = -50.514274620676 +692000 ekin = 5.94838842830579 | erot = 13.6417068401798 | epot = -70.1043698821423 | etot = -50.5142746136566 +693000 ekin = 6.02589021174524 | erot = 12.6498891239226 | epot = -69.1900539439234 | etot = -50.5142746082556 +694000 ekin = 6.18463455175186 | erot = 11.7000608799442 | epot = -68.3989700350167 | etot = -50.5142746033207 +695000 ekin = 6.43478432354664 | erot = 10.8472395602264 | epot = -67.7962984855985 | etot = -50.5142746018255 +696000 ekin = 6.77322428392954 | erot = 10.1195064532947 | epot = -67.4070053386816 | etot = -50.5142746014574 +697000 ekin = 7.19141853633608 | erot = 9.53118158814445 | epot = -67.236874726452 | etot = -50.5142746019714 +698000 ekin = 7.67702076753969 | erot = 9.08693839130884 | epot = -67.2782337620451 | etot = -50.5142746031966 +699000 ekin = 8.21429897539183 | erot = 8.78382057636208 | epot = -67.5123941568188 | etot = -50.5142746050649 +700000 ekin = 8.78422716548436 | erot = 8.61224580901898 | epot = -67.91074758211 | etot = -50.5142746076067 +701000 ekin = 9.364239317381 | erot = 8.5560585648262 | epot = -68.4345724931076 | etot = -50.5142746109004 +702000 ekin = 9.92792016716481 | erot = 8.59213538141387 | epot = -69.0343301635188 | etot = -50.5142746149401 +703000 ekin = 10.4452984142738 | erot = 8.69064064747502 | epot = -69.650213681218 | etot = -50.5142746194692 +704000 ekin = 10.8846377327691 | erot = 8.8174132416495 | epot = -70.2163255982631 | etot = -50.5142746238445 +705000 ekin = 11.2162913879776 | erot = 8.93948813627131 | epot = -70.6700541513609 | etot = -50.514274627112 +706000 ekin = 11.4181455722709 | erot = 9.03309347108019 | epot = -70.9655136716858 | etot = -50.5142746283347 +707000 ekin = 11.4809106570109 | erot = 9.09134201924973 | epot = -71.0865273032839 | etot = -50.5142746270233 +708000 ekin = 11.4068982891744 | erot = 9.12200528528136 | epot = -71.0431782001565 | etot = -50.5142746257007 +709000 ekin = 11.2072632913348 | erot = 9.14465465272043 | epot = -70.8661925652315 | etot = -50.5142746211762 +710000 ekin = 10.9083907026857 | erot = 9.19859957945205 | epot = -70.6212648982224 | etot = -50.5142746160846 +711000 ekin = 10.5423746431666 | erot = 9.32614430677755 | epot = -70.3827935613466 | etot = -50.5142746114025 +712000 ekin = 10.1417786131412 | erot = 9.56360239370289 | epot = -70.2196556145968 | etot = -50.5142746077528 +713000 ekin = 9.7360871371676 | erot = 9.93566991054729 | epot = -70.1860316530795 | etot = -50.5142746053646 +714000 ekin = 9.35027943777808 | erot = 10.4538184610759 | epot = -70.3183725027399 | etot = -50.5142746038859 +715000 ekin = 9.00463394824683 | erot = 11.1175080875396 | epot = -70.6364166398399 | etot = -50.5142746040535 +716000 ekin = 8.7124773917152 | erot = 11.9117220716562 | epot = -71.1384740684731 | etot = -50.5142746051017 +717000 ekin = 8.48287816422953 | erot = 12.8114967087969 | epot = -71.8086494800184 | etot = -50.514274606992 +718000 ekin = 8.32091760997486 | erot = 13.7831462397291 | epot = -72.61833845952 | etot = -50.514274609816 +719000 ekin = 8.2270361337422 | erot = 14.7838475725432 | epot = -73.5251583200275 | etot = -50.5142746137421 +720000 ekin = 8.19603263794301 | erot = 15.7606669338436 | epot = -74.4709741906435 | etot = -50.5142746188569 +721000 ekin = 8.21637629745645 | erot = 16.6505227360459 | epot = -75.3811736584475 | etot = -50.5142746249451 +722000 ekin = 8.27076325254595 | erot = 17.3831969889515 | epot = -76.1682348730789 | etot = -50.5142746315814 +723000 ekin = 8.33599195236651 | erot = 17.8873102966889 | epot = -76.7375768863323 | etot = -50.5142746372768 +724000 ekin = 8.38930978725994 | erot = 18.1039114578793 | epot = -77.007495885679 | etot = -50.5142746405398 +725000 ekin = 8.41651864003474 | erot = 18.0027385421696 | epot = -76.9335318225019 | etot = -50.5142746402975 +726000 ekin = 8.41540022325134 | erot = 17.5920134842233 | epot = -76.5216883438459 | etot = -50.5142746363713 +727000 ekin = 8.39679923838451 | erot = 16.9199297230155 | epot = -75.8310035909557 | etot = -50.5142746295557 +728000 ekin = 8.38189420018229 | erot = 16.0663700673842 | epot = -74.9625388888158 | etot = -50.5142746212493 +729000 ekin = 8.39699694302083 | erot = 15.1283483168248 | epot = -74.0396198727756 | etot = -50.51427461293 +730000 ekin = 8.46782543823145 | erot = 14.2043901534046 | epot = -73.1864901974078 | etot = -50.5142746057717 +731000 ekin = 8.61470307561547 | erot = 13.3819120233496 | epot = -72.5108896994624 | etot = -50.5142746004973 +732000 ekin = 8.84928637435931 | erot = 12.7292880230955 | epot = -72.09284899488 | etot = -50.5142745974252 +733000 ekin = 9.1728076670292 | erot = 12.2923211340616 | epot = -71.9794033976681 | etot = -50.5142745965773 +734000 ekin = 9.57560598363367 | erot = 12.0938942191471 | epot = -72.1837748005718 | etot = -50.514274597791 +735000 ekin = 10.0377642396005 | erot = 12.1355113635736 | epot = -72.6875502039631 | etot = -50.5142746007889 +736000 ekin = 10.5307595726466 | erot = 12.3998369838651 | epot = -73.4448711617082 | etot = -50.5142746051965 +737000 ekin = 11.0200914156936 | erot = 12.8538466733553 | epot = -74.3882126996049 | etot = -50.514274610556 +738000 ekin = 11.4687808904929 | erot = 13.4525508838002 | epot = -75.4356063906199 | etot = -50.5142746163267 +739000 ekin = 11.8414287125988 | erot = 14.1433222477412 | epot = -76.4990255822736 | etot = -50.5142746219335 +740000 ekin = 12.1082656211693 | erot = 14.8707107510575 | epot = -77.493250999058 | etot = -50.5142746268312 +741000 ekin = 12.248503233438 | erot = 15.5814643741729 | epot = -78.3442422381644 | etot = -50.5142746305534 +742000 ekin = 12.252426547258 | erot = 16.2294231022188 | epot = -78.9961242822361 | etot = -50.5142746327593 +743000 ekin = 12.1219949949074 | erot = 16.7799163002887 | epot = -79.4161859284567 | etot = -50.5142746332606 +744000 ekin = 11.8700125682075 | erot = 17.2130632823907 | epot = -79.5973504826804 | etot = -50.5142746320822 +745000 ekin = 11.5180572442418 | erot = 17.5250437155279 | epot = -79.5573755892847 | etot = -50.5142746295151 +746000 ekin = 11.0934236280953 | erot = 17.7264433609958 | epot = -79.3341416152003 | etot = -50.5142746261092 +747000 ekin = 10.6254840289969 | erot = 17.8375345490415 | epot = -78.9772932006039 | etot = -50.5142746225655 +748000 ekin = 10.1420744189699 | erot = 17.8814972667785 | epot = -78.5378463053119 | etot = -50.5142746195635 +749000 ekin = 9.66656115774399 | erot = 17.8773814864278 | epot = -78.0582172617743 | etot = -50.5142746176025 +750000 ekin = 9.21603867052602 | erot = 17.8346042171076 | epot = -77.5649175045334 | etot = -50.5142746168998 +751000 ekin = 8.80076552490662 | erot = 17.7502211247384 | epot = -77.0652612670996 | etot = -50.5142746174546 +752000 ekin = 8.42467668904194 | erot = 17.6090413605271 | epot = -76.5479926685053 | etot = -50.5142746189363 +753000 ekin = 8.08670902920299 | erot = 17.3870500518294 | epot = -75.988033701875 | etot = -50.5142746208427 +754000 ekin = 7.78266313548547 | erot = 17.0571798776075 | epot = -75.354117635661 | etot = -50.514274622568 +755000 ekin = 7.50732713163603 | erot = 16.5962021838331 | epot = -74.6178039390137 | etot = -50.5142746235446 +756000 ekin = 7.25656799091011 | erot = 15.9912186969566 | epot = -73.7620613111994 | etot = -50.5142746233326 +757000 ekin = 7.02889011913336 | erot = 15.2437835165739 | epot = -72.7869482577245 | etot = -50.5142746220172 +758000 ekin = 6.82603226742604 | erot = 14.3694235713074 | epot = -71.7097304583781 | etot = -50.5142746196447 +759000 ekin = 6.65556621293785 | erot = 13.4007974874175 | epot = -70.5706383156337 | etot = -50.5142746152784 +760000 ekin = 6.5284061890787 | erot = 12.380862280426 | epot = -69.4235430816228 | etot = -50.5142746121181 +761000 ekin = 6.45348689195663 | erot = 11.3465222562654 | epot = -68.3142837573835 | etot = -50.5142746091615 +762000 ekin = 6.44051607906623 | erot = 10.3317215154602 | epot = -67.2865122011207 | etot = -50.5142746065942 +763000 ekin = 6.49918252432267 | erot = 9.36548217892287 | epot = -66.3789393077251 | etot = -50.5142746044795 +764000 ekin = 6.63833890050988 | erot = 8.47149284054376 | epot = -65.6241063438625 | etot = -50.5142746028089 +765000 ekin = 6.86513419525142 | erot = 7.66877834284249 | epot = -65.0481871396424 | etot = -50.5142746015485 +766000 ekin = 7.1837807709722 | erot = 6.97265281329603 | epot = -64.67070818509 | etot = -50.5142746008218 +767000 ekin = 7.59444235330852 | erot = 6.39557143765804 | epot = -64.5042883914035 | etot = -50.5142746004369 +768000 ekin = 8.09268145324012 | erot = 5.94781682496754 | epot = -64.5547728788043 | etot = -50.5142746005966 +769000 ekin = 8.66808446390167 | erot = 5.63681148450843 | epot = -64.8191705498657 | etot = -50.5142746014556 +770000 ekin = 9.30348521554662 | erot = 5.46582731738535 | epot = -65.283587136076 | etot = -50.5142746031441 +771000 ekin = 9.97431898094657 | erot = 5.43270401328012 | epot = -65.9212975999266 | etot = -50.5142746056999 +772000 ekin = 10.6499862226328 | erot = 5.52827048594237 | epot = -66.6925313175519 | etot = -50.5142746089767 +773000 ekin = 11.2957807948582 | erot = 5.73712650854713 | epot = -67.5471819160367 | etot = -50.5142746126314 +774000 ekin = 11.8763197237593 | erot = 6.03945270148545 | epot = -68.4300470414037 | etot = -50.5142746161589 +775000 ekin = 12.3598322336888 | erot = 6.41425449692265 | epot = -69.2883613496556 | etot = -50.5142746190442 +776000 ekin = 12.7222841193419 | erot = 6.84284553247385 | epot = -70.0794042727422 | etot = -50.5142746209264 +777000 ekin = 12.9503286191155 | erot = 7.31125230206811 | epot = -70.7758555429038 | etot = -50.5142746217202 +778000 ekin = 13.0423382708153 | erot = 7.81051825668182 | epot = -71.3671311491498 | etot = -50.5142746216526 +779000 ekin = 13.0073878068331 | erot = 8.33463285187951 | epot = -71.8562952798855 | etot = -50.5142746211729 +780000 ekin = 12.8626337012878 | erot = 8.87663911987046 | epot = -72.2535474442322 | etot = -50.5142746230739 +781000 ekin = 12.6191311288743 | erot = 9.41238807656042 | epot = -72.5457938291788 | etot = -50.514274623744 +782000 ekin = 12.2922907716842 | erot = 9.90988136283937 | epot = -72.7164467590842 | etot = -50.5142746245607 +783000 ekin = 11.9113538267172 | erot = 10.3385161888649 | epot = -72.7641446399597 | etot = -50.5142746243776 +784000 ekin = 11.5094258764739 | erot = 10.6682447236089 | epot = -72.6919452239908 | etot = -50.514274623908 +785000 ekin = 11.1215244494593 | erot = 10.8798873198842 | epot = -72.5156863910798 | etot = -50.5142746217362 +786000 ekin = 10.7892036478056 | erot = 10.9720367156619 | epot = -72.2755149816011 | etot = -50.5142746181337 +787000 ekin = 10.555029278746 | erot = 10.9621301132836 | epot = -72.0314340061411 | etot = -50.5142746141116 +788000 ekin = 10.4531579062774 | erot = 10.8809781424469 | epot = -71.8484106597301 | etot = -50.5142746110058 +789000 ekin = 10.4992787233554 | erot = 10.7631938893632 | epot = -71.7767472225994 | etot = -50.5142746098808 +790000 ekin = 10.6841251440847 | erot = 10.6378648553805 | epot = -71.8362646105137 | etot = -50.5142746110485 +791000 ekin = 10.9736405231904 | erot = 10.5233964905693 | epot = -72.0113116277152 | etot = -50.5142746139555 +792000 ekin = 11.3161137381175 | erot = 10.4258288161123 | epot = -72.256217172548 | etot = -50.5142746183183 +793000 ekin = 11.6542402037228 | erot = 10.3442073317959 | epot = -72.5127221562072 | etot = -50.5142746206885 +794000 ekin = 11.9411264395415 | erot = 10.2879588172718 | epot = -72.7433598795331 | etot = -50.5142746227198 +795000 ekin = 12.1351044495743 | erot = 10.2641865985143 | epot = -72.9135656717484 | etot = -50.5142746236598 +796000 ekin = 12.2078724557798 | erot = 10.2805672453403 | epot = -73.0027143247989 | etot = -50.5142746236788 +797000 ekin = 12.145259371386 | erot = 10.3450171205794 | epot = -73.0045511149651 | etot = -50.5142746229997 +798000 ekin = 11.9451812221588 | erot = 10.4647770415675 | epot = -72.9242328855249 | etot = -50.5142746217986 +799000 ekin = 11.6151944446074 | erot = 10.6460858263567 | epot = -72.7755548911982 | etot = -50.5142746202341 +800000 ekin = 11.1701119660333 | erot = 10.8937791249724 | epot = -72.5781657095344 | etot = -50.5142746185287 +801000 ekin = 10.6296650136721 | erot = 11.2100289498445 | epot = -72.3539685805623 | etot = -50.5142746170457 +802000 ekin = 10.0162021020414 | erot = 11.5918355781354 | epot = -72.1223122961447 | etot = -50.5142746159679 +803000 ekin = 9.35262484648241 | erot = 12.0292939538292 | epot = -71.8961934158892 | etot = -50.5142746155776 +804000 ekin = 8.66091793166028 | erot = 12.5039909454097 | epot = -71.6791834929645 | etot = -50.5142746158945 +805000 ekin = 7.96269204966567 | erot = 12.990459714855 | epot = -71.4674263808691 | etot = -50.5142746163485 +806000 ekin = 7.28309911913848 | erot = 13.463749946459 | epot = -71.261123682393 | etot = -50.5142746167955 +807000 ekin = 6.64354530302908 | erot = 13.8965012732328 | epot = -71.0543211930859 | etot = -50.514274616824 +808000 ekin = 6.06569426714939 | erot = 14.2665976072253 | epot = -70.8465664904681 | etot = -50.5142746160935 +809000 ekin = 5.57220972267778 | erot = 14.5624309902631 | epot = -70.6489153274786 | etot = -50.5142746145378 +810000 ekin = 5.18560956702226 | erot = 14.7848453683537 | epot = -70.4847295477963 | etot = -50.5142746124203 +811000 ekin = 4.92192373652428 | erot = 14.9394262725461 | epot = -70.375624621343 | etot = -50.5142746122727 +812000 ekin = 4.78454979623265 | erot = 15.0222979446883 | epot = -70.3211223520346 | etot = -50.5142746111137 +813000 ekin = 4.77811513007573 | erot = 15.0438932857333 | epot = -70.3362830266118 | etot = -50.5142746108028 +814000 ekin = 4.89877766102121 | erot = 15.0134686698619 | epot = -70.4265209424707 | etot = -50.5142746115876 +815000 ekin = 5.13224364530848 | erot = 14.9341431305877 | epot = -70.5806613892622 | etot = -50.5142746133661 +816000 ekin = 5.45499511248401 | erot = 14.8029157850397 | epot = -70.7721855132897 | etot = -50.514274615766 +817000 ekin = 5.83730378159657 | erot = 14.6128652259922 | epot = -70.9644436259237 | etot = -50.5142746183349 +818000 ekin = 6.2470507826388 | erot = 14.3559898192088 | epot = -71.1173152225243 | etot = -50.5142746206768 +819000 ekin = 6.6533351986997 | erot = 14.02559371508 | epot = -71.1932035362805 | etot = -50.5142746225008 +820000 ekin = 7.02931213197788 | erot = 13.6180701134041 | epot = -71.1616568689685 | etot = -50.5142746235865 +821000 ekin = 7.35419181513005 | erot = 13.1344275810955 | epot = -71.0028940199835 | etot = -50.5142746237579 +822000 ekin = 7.61452267036041 | erot = 12.5816642165446 | epot = -70.710461509826 | etot = -50.514274622921 +823000 ekin = 7.80457913682541 | erot = 11.9738516457301 | epot = -70.2927054036746 | etot = -50.514274621119 +824000 ekin = 7.92623062485201 | erot = 11.3316465732701 | epot = -69.7721518166521 | etot = -50.51427461853 +825000 ekin = 7.98855124818236 | erot = 10.6800409975003 | epot = -69.1828668611352 | etot = -50.5142746154525 +826000 ekin = 8.00547556716026 | erot = 10.0465644012422 | epot = -68.5663145806636 | etot = -50.5142746122611 +827000 ekin = 7.9933226904963 | erot = 9.45843415914846 | epot = -67.9660314589571 | etot = -50.5142746093124 +828000 ekin = 7.96824966899374 | erot = 8.94000860861965 | epot = -67.4225328845019 | etot = -50.5142746068885 +829000 ekin = 7.94344804464527 | erot = 8.51150826234841 | epot = -66.9692309121181 | etot = -50.5142746051244 +830000 ekin = 7.92872079695388 | erot = 8.18753713456104 | epot = -66.6305325355387 | etot = -50.5142746040238 +831000 ekin = 7.9301544519131 | erot = 7.97742868766256 | epot = -66.4218577430505 | etot = -50.5142746034749 +832000 ekin = 7.95037084501752 | erot = 7.88660237980199 | epot = -66.35124782804 | etot = -50.5142746032205 +833000 ekin = 7.9900087168228 | erot = 7.91841904036411 | epot = -66.42270236042 | etot = -50.5142746032331 +834000 ekin = 8.04830667220734 | erot = 8.07516750501644 | epot = -66.6377487804322 | etot = -50.5142746032084 +835000 ekin = 8.12473779283697 | erot = 8.35958341056793 | epot = -66.9985958064483 | etot = -50.5142746030434 +836000 ekin = 8.22030282864492 | erot = 8.77529455000173 | epot = -67.5098719814205 | etot = -50.5142746027739 +837000 ekin = 8.33787083575325 | erot = 9.32581140976129 | epot = -68.1779568481181 | etot = -50.5142746026035 +838000 ekin = 8.48148351710538 | erot = 10.0120708918826 | epot = -69.0078290118947 | etot = -50.5142746029068 +839000 ekin = 8.6545472339528 | erot = 10.8286339895783 | epot = -69.997455827703 | etot = -50.5142746041719 +840000 ekin = 8.85724897642758 | erot = 11.7591344306047 | epot = -71.1306580138542 | etot = -50.5142746068219 +841000 ekin = 9.08410272398218 | erot = 12.77258772254 | epot = -72.3709650575351 | etot = -50.5142746110129 +842000 ekin = 9.32286445558871 | erot = 13.822272362351 | epot = -73.6594114343907 | etot = -50.514274616451 +843000 ekin = 9.55575186025504 | erot = 14.8485908043933 | epot = -74.9186172870397 | etot = -50.5142746223914 +844000 ekin = 9.76305319172261 | erot = 15.7859703765622 | epot = -76.063298196125 | etot = -50.5142746278402 +845000 ekin = 9.92653283165094 | erot = 16.5722430343869 | epot = -77.0130504982886 | etot = -50.5142746322508 +846000 ekin = 10.0341915121946 | erot = 17.1569368807615 | epot = -77.7054030275234 | etot = -50.5142746345673 +847000 ekin = 10.0842269981591 | erot = 17.5059176317017 | epot = -78.1044192649009 | etot = -50.5142746350401 +848000 ekin = 10.083480736967 | erot = 17.602801490634 | epot = -78.2005568615482 | etot = -50.5142746339472 +849000 ekin = 10.0452569998608 | erot = 17.4478826304392 | epot = -78.0074142619148 | etot = -50.5142746316148 +850000 ekin = 9.98669392840383 | erot = 17.0565884213116 | epot = -77.5575569780125 | etot = -50.5142746282971 +851000 ekin = 9.92663281891543 | erot = 16.4581424380505 | epot = -76.8990498811725 | etot = -50.5142746242065 +852000 ekin = 9.88421071073538 | erot = 15.6937873464926 | epot = -76.0922726768386 | etot = -50.5142746196106 +853000 ekin = 9.87790001921207 | erot = 14.8136202068669 | epot = -75.2057948409522 | etot = -50.5142746148731 +854000 ekin = 9.92462914157822 | erot = 13.8718574790183 | epot = -74.310761231011 | etot = -50.5142746104145 +855000 ekin = 10.0388102442684 | erot = 12.9213545992827 | epot = -73.4744394501745 | etot = -50.5142746066234 +856000 ekin = 10.2313382537762 | erot = 12.0086601024602 | epot = -72.7542729600063 | etot = -50.5142746037699 +857000 ekin = 10.5087335451293 | erot = 11.170590412433 | epot = -72.1935985595479 | etot = -50.5142746019857 +858000 ekin = 10.8725687504192 | erot = 10.4326544037625 | epot = -71.8194977554572 | etot = -50.5142746012754 +859000 ekin = 11.3192383577643 | erot = 9.80910719595831 | epot = -71.642620155266 | etot = -50.5142746015434 +860000 ekin = 11.8400783420205 | erot = 9.30419552787811 | epot = -71.658548472533 | etot = -50.5142746026344 +861000 ekin = 12.4218045286852 | erot = 8.91415835009289 | epot = -71.8502374831343 | etot = -50.5142746043562 +862000 ekin = 13.047159501774 | erot = 8.62956306065923 | epot = -72.1909971689654 | etot = -50.5142746065321 +863000 ekin = 13.6955471607497 | erot = 8.43751332746866 | epot = -72.647335097261 | etot = -50.5142746090426 +864000 ekin = 14.3434008697799 | erot = 8.32326841732247 | epot = -73.1809438989578 | etot = -50.5142746118554 +865000 ekin = 14.9642125533562 | erot = 8.271045708321 | epot = -73.7495328766584 | etot = -50.5142746149813 +866000 ekin = 15.5285589837922 | erot = 8.26427543437267 | epot = -74.3071090365222 | etot = -50.5142746183574 +867000 ekin = 16.004884459812 | erot = 8.28609725289935 | epot = -74.8052563344375 | etot = -50.5142746217262 +868000 ekin = 16.3618698335786 | erot = 8.32099923208314 | epot = -75.1971436902378 | etot = -50.514274624576 +869000 ekin = 16.5726647379719 | erot = 8.35789379698042 | epot = -75.444833161217 | etot = -50.5142746262647 +870000 ekin = 16.6201866860209 | erot = 8.39376845178061 | epot = -75.5282297640759 | etot = -50.5142746262744 +871000 ekin = 16.5016790588097 | erot = 8.43606779494812 | epot = -75.4520214782497 | etot = -50.5142746244918 +872000 ekin = 16.2341552473536 | erot = 8.50234235649182 | epot = -75.2507722227927 | etot = -50.5142746189473 +873000 ekin = 15.8766860459151 | erot = 8.61819397754757 | epot = -75.0091546394492 | etot = -50.5142746159866 +874000 ekin = 15.4649107938791 | erot = 8.80433706336327 | epot = -74.7835224708048 | etot = -50.5142746135625 +875000 ekin = 15.0262874336045 | erot = 9.07115551080233 | epot = -74.6117175567219 | etot = -50.5142746123152 +876000 ekin = 14.5841946134941 | erot = 9.41501293027044 | epot = -74.5134821563096 | etot = -50.5142746125451 +877000 ekin = 14.1547799929574 | erot = 9.81684169519029 | epot = -74.4858963036082 | etot = -50.5142746154604 +878000 ekin = 13.7382136358382 | erot = 10.2440638824515 | epot = -74.4965521349712 | etot = -50.5142746166814 +879000 ekin = 13.3387592431181 | erot = 10.6587148562478 | epot = -74.5117487186855 | etot = -50.5142746193196 +880000 ekin = 12.9616338661233 | erot = 11.0178947403692 | epot = -74.493803227927 | etot = -50.5142746214345 +881000 ekin = 12.6124700510822 | erot = 11.282814649363 | epot = -74.4095593228675 | etot = -50.5142746224222 +882000 ekin = 12.3012191623517 | erot = 11.4261723469453 | epot = -74.2416661314064 | etot = -50.5142746221094 +883000 ekin = 12.0416845184565 | erot = 11.435283897645 | epot = -73.9912430369525 | etot = -50.5142746208509 +884000 ekin = 11.8474220294963 | erot = 11.3115013061744 | epot = -73.6731979550124 | etot = -50.5142746193416 +885000 ekin = 11.7257363966629 | erot = 11.0668464612728 | epot = -73.3068574761389 | etot = -50.5142746182031 +886000 ekin = 11.6731647858944 | erot = 10.7200648867885 | epot = -72.9075042902928 | etot = -50.5142746176099 +887000 ekin = 11.6753437833279 | erot = 10.2941390601762 | epot = -72.4837574607534 | etot = -50.5142746172493 +888000 ekin = 11.7114868674011 | erot = 9.81567994928461 | epot = -72.0414414333127 | etot = -50.5142746166269 +889000 ekin = 11.7608194291219 | erot = 9.31484227783354 | epot = -71.5899363224281 | etot = -50.5142746154726 +890000 ekin = 11.8074394677777 | erot = 8.82394323461783 | epot = -71.1456573163298 | etot = -50.5142746139343 +891000 ekin = 11.8416000935628 | erot = 8.37408459367654 | epot = -70.7299592997222 | etot = -50.5142746124829 +892000 ekin = 11.8578157118592 | erot = 7.99071522456406 | epot = -70.36280554804 | etot = -50.5142746116167 +893000 ekin = 11.8517025878141 | erot = 7.68991980292158 | epot = -70.0558970023627 | etot = -50.514274611627 +894000 ekin = 11.8175069852831 | erot = 7.47687356813375 | epot = -69.8086551659111 | etot = -50.5142746124943 +895000 ekin = 11.7474082014793 | erot = 7.34687884502009 | epot = -69.608561660426 | etot = -50.5142746139266 +896000 ekin = 11.6337519150781 | erot = 7.28921963444749 | epot = -69.4372461644614 | etot = -50.5142746149358 +897000 ekin = 11.472356994567 | erot = 7.29106570298609 | epot = -69.2776973137387 | etot = -50.5142746161856 +898000 ekin = 11.2610645581376 | erot = 7.33791947976118 | epot = -69.1132586561008 | etot = -50.514274618202 +899000 ekin = 10.9996054556735 | erot = 7.41455173571792 | epot = -68.9284318100301 | etot = -50.5142746186387 +900000 ekin = 10.6922844699407 | erot = 7.50755561904315 | epot = -68.7141147070732 | etot = -50.5142746180894 +901000 ekin = 10.35349883072 | erot = 7.60938036319051 | epot = -68.4771538113222 | etot = -50.5142746174117 +902000 ekin = 9.99993129220852 | erot = 7.71616133838586 | epot = -68.230367246768 | etot = -50.5142746161736 +903000 ekin = 9.65023529508671 | erot = 7.82867685331976 | epot = -67.993186763613 | etot = -50.5142746152065 +904000 ekin = 9.31666090716459 | erot = 7.95055248579698 | epot = -67.7814880061039 | etot = -50.5142746131423 +905000 ekin = 9.0151678621596 | erot = 8.09317176469393 | epot = -67.6226142378532 | etot = -50.5142746109997 +906000 ekin = 8.76163371707794 | erot = 8.2719343604388 | epot = -67.5478426867262 | etot = -50.5142746092094 +907000 ekin = 8.56717238120394 | erot = 8.50112591573178 | epot = -67.5825729050883 | etot = -50.5142746081525 +908000 ekin = 8.43684994935758 | erot = 8.78986433043559 | epot = -67.7409888878113 | etot = -50.5142746080181 +909000 ekin = 8.36965149841051 | erot = 9.13947702237007 | epot = -68.023403129548 | etot = -50.5142746087674 +910000 ekin = 8.35959079236633 | erot = 9.54304734377732 | epot = -68.4169127463195 | etot = -50.5142746101759 +911000 ekin = 8.39748118919755 | erot = 9.98695611158263 | epot = -68.8987119127118 | etot = -50.5142746119316 +912000 ekin = 8.47277548197648 | erot = 10.4536385185282 | epot = -69.4406886142433 | etot = -50.5142746137387 +913000 ekin = 8.57499585907974 | erot = 10.9245819662903 | epot = -70.0138524407615 | etot = -50.5142746153915 +914000 ekin = 8.69450482131378 | erot = 11.3827140797361 | epot = -70.5914935178566 | etot = -50.5142746168067 +915000 ekin = 8.82261764862321 | erot = 11.8136624664793 | epot = -71.1505547331184 | etot = -50.5142746180158 +916000 ekin = 8.95125831589976 | erot = 12.2058133556082 | epot = -71.6713462906221 | etot = -50.5142746191141 +917000 ekin = 9.07247170867912 | erot = 12.5495353190533 | epot = -72.1362816479271 | etot = -50.5142746201948 +918000 ekin = 9.17798133023756 | erot = 12.8359656974201 | epot = -72.5282216495854 | etot = -50.5142746219277 +919000 ekin = 9.25795352546051 | erot = 13.0545632678408 | epot = -72.8267914162994 | etot = -50.5142746229981 +920000 ekin = 9.30352764338632 | erot = 13.1980045147827 | epot = -73.0158067819257 | etot = -50.5142746237567 +921000 ekin = 9.30791573962823 | erot = 13.2627586618328 | epot = -73.0849490254401 | etot = -50.514274623979 +922000 ekin = 9.26738318948614 | erot = 13.2504193014238 | epot = -73.032077114381 | etot = -50.5142746234711 +923000 ekin = 9.18225083008032 | erot = 13.1693406239091 | epot = -72.8658660761382 | etot = -50.5142746221487 +924000 ekin = 9.05737763949209 | erot = 13.0352596729487 | epot = -72.6069119325172 | etot = -50.5142746200764 +925000 ekin = 8.9019737971623 | erot = 12.8704449082219 | epot = -72.2866933228554 | etot = -50.5142746174712 +926000 ekin = 8.72875558940198 | erot = 12.7013413967699 | epot = -71.9443716008292 | etot = -50.5142746146573 +927000 ekin = 8.55261219797572 | erot = 12.5551881314088 | epot = -71.6220749413678 | etot = -50.5142746119833 +928000 ekin = 8.38906191378869 | erot = 12.4564414993112 | epot = -71.3597780228518 | etot = -50.5142746097519 +929000 ekin = 8.25278751339911 | erot = 12.4238691104623 | epot = -71.1909312320144 | etot = -50.514274608153 +930000 ekin = 8.15644947625578 | erot = 12.4688675851981 | epot = -71.1395916687183 | etot = -50.5142746072644 +931000 ekin = 8.10980872696185 | erot = 12.5950716572825 | epot = -71.2191549913328 | etot = -50.5142746070885 +932000 ekin = 8.11905369607804 | erot = 12.798887909906 | epot = -71.4322162135849 | etot = -50.5142746076009 +933000 ekin = 8.18618804315994 | erot = 13.0703703777546 | epot = -71.7708330297116 | etot = -50.5142746087971 +934000 ekin = 8.30844961717604 | erot = 13.3939295435153 | epot = -72.2166537713761 | etot = -50.5142746106847 +935000 ekin = 8.47804287614392 | erot = 13.7488706059568 | epot = -72.7411880950829 | etot = -50.5142746129822 +936000 ekin = 8.68285566577444 | erot = 14.1118670755527 | epot = -73.3089973575654 | etot = -50.5142746162383 +937000 ekin = 8.90506344747224 | erot = 14.4532746108157 | epot = -73.8726126780738 | etot = -50.5142746197859 +938000 ekin = 9.12528575776321 | erot = 14.7395572148671 | epot = -74.3791175957916 | etot = -50.5142746231613 +939000 ekin = 9.32644769073843 | erot = 14.9376224441143 | epot = -74.7783447607136 | etot = -50.5142746258609 +940000 ekin = 9.49679607415025 | erot = 15.0191372957794 | epot = -75.0302079974043 | etot = -50.5142746274746 +941000 ekin = 9.63181347023634 | erot = 14.9646422015579 | epot = -75.1107302995734 | etot = -50.5142746277791 +942000 ekin = 9.7345970246142 | erot = 14.7665169184874 | epot = -75.0153885698704 | etot = -50.5142746267687 +943000 ekin = 9.81477003771735 | erot = 14.4302129134903 | epot = -74.7592575758434 | etot = -50.5142746246357 +944000 ekin = 9.88637843640376 | erot = 13.9736039565668 | epot = -74.3742570146764 | etot = -50.5142746217059 +945000 ekin = 9.96538785515584 | erot = 13.4246663205069 | epot = -73.904328794037 | etot = -50.5142746183743 +946000 ekin = 10.0624285977662 | erot = 12.8170998514953 | epot = -73.3938030653477 | etot = -50.5142746160863 +947000 ekin = 10.1824129637518 | erot = 12.1848373687087 | epot = -72.8815249460169 | etot = -50.5142746135564 +948000 ekin = 10.3307952063298 | erot = 11.5602780907907 | epot = -72.4053479087765 | etot = -50.5142746116561 +949000 ekin = 10.5091608692846 | erot = 10.9707033403524 | epot = -71.9941388200363 | etot = -50.5142746103993 +950000 ekin = 10.7157185619705 | erot = 10.436392829731 | epot = -71.6663860014586 | etot = -50.5142746097572 +951000 ekin = 10.9461026016796 | erot = 9.97090696794874 | epot = -71.4312841792187 | etot = -50.5142746095904 +952000 ekin = 11.1944034263847 | erot = 9.58208330477752 | epot = -71.2907613408679 | etot = -50.5142746097057 +953000 ekin = 11.4542745285081 | erot = 9.27371614288968 | epot = -71.2422652813336 | etot = -50.5142746099358 +954000 ekin = 11.7197914421063 | erot = 9.04716566656764 | epot = -71.2812317188749 | etot = -50.5142746102009 +955000 ekin = 11.985807578237 | erot = 8.90221043238509 | epot = -71.4022926211614 | etot = -50.5142746105393 +956000 ekin = 12.2477526012259 | erot = 8.83681504684861 | epot = -71.5988422591496 | etot = -50.5142746110751 +957000 ekin = 12.5001620855863 | erot = 8.84602022701713 | epot = -71.8604569247853 | etot = -50.5142746121818 +958000 ekin = 12.7364419158141 | erot = 8.92025316556045 | epot = -72.1709696949275 | etot = -50.5142746135529 +959000 ekin = 12.9499558171104 | erot = 9.04468571433305 | epot = -72.5089161466905 | etot = -50.514274615247 +960000 ekin = 13.1339945045842 | erot = 9.20006474951547 | epot = -72.8483338711111 | etot = -50.5142746170115 +961000 ekin = 13.2830442059634 | erot = 9.36494740346933 | epot = -73.1622662279336 | etot = -50.5142746185009 +962000 ekin = 13.3943598106719 | erot = 9.51904370684229 | epot = -73.4276781368892 | etot = -50.514274619375 +963000 ekin = 13.4693004785333 | erot = 9.6466908834904 | epot = -73.6302659815043 | etot = -50.5142746194805 +964000 ekin = 13.5138667495702 | erot = 9.73885319426343 | epot = -73.7669945625517 | etot = -50.5142746187181 +965000 ekin = 13.5381869822929 | erot = 9.79431086345277 | epot = -73.8467724630306 | etot = -50.514274617285 +966000 ekin = 13.5561247348925 | erot = 9.81745627086625 | epot = -73.8878556215536 | etot = -50.5142746157949 +967000 ekin = 13.5791884002218 | erot = 9.81700827652725 | epot = -73.9104712911705 | etot = -50.5142746144214 +968000 ekin = 13.6156774161998 | erot = 9.80283527457497 | epot = -73.9327873043165 | etot = -50.5142746135418 +969000 ekin = 13.6696213239404 | erot = 9.78235769607308 | epot = -73.9662536334078 | etot = -50.5142746133943 +970000 ekin = 13.7395769125834 | erot = 9.75809430136155 | epot = -74.0119458280989 | etot = -50.514274614154 +971000 ekin = 13.8188233688189 | erot = 9.72517183373113 | epot = -74.0582698180677 | etot = -50.5142746155177 +972000 ekin = 13.8945737117847 | erot = 9.67630144621188 | epot = -74.0851497751246 | etot = -50.514274617128 +973000 ekin = 13.9510636746107 | erot = 9.60403058377153 | epot = -74.0693688769437 | etot = -50.5142746185615 +974000 ekin = 13.9725505850026 | erot = 9.50361383005942 | epot = -73.990439034536 | etot = -50.514274619474 +975000 ekin = 13.9459468249009 | erot = 9.37533024549605 | epot = -73.8355516900994 | etot = -50.5142746197025 +976000 ekin = 13.8626234187874 | erot = 9.22504260860028 | epot = -73.6019406466906 | etot = -50.514274619303 +977000 ekin = 13.7190808966933 | erot = 9.06288466716476 | epot = -73.2962401823334 | etot = -50.5142746184753 +978000 ekin = 13.5166571665429 | erot = 8.90088911562056 | epot = -72.9318208995972 | etot = -50.5142746174337 +979000 ekin = 13.2607650056573 | erot = 8.75083051915402 | epot = -72.5258701411063 | etot = -50.5142746162949 +980000 ekin = 12.9601438447104 | erot = 8.62327601862834 | epot = -72.0976944783913 | etot = -50.5142746150525 +981000 ekin = 12.6263377401163 | erot = 8.52805592036694 | epot = -71.6686682741084 | etot = -50.5142746136252 +982000 ekin = 12.2732923453016 | erot = 8.47560645870777 | epot = -71.2631734159473 | etot = -50.5142746119379 +983000 ekin = 11.9168085654428 | erot = 8.47829635029741 | epot = -70.9093795257357 | etot = -50.5142746099954 +984000 ekin = 11.5736514704685 | erot = 8.55096975128897 | epot = -70.6388958296694 | etot = -50.5142746079119 +985000 ekin = 11.260336157805 | erot = 8.7102581792731 | epot = -70.4848689429876 | etot = -50.5142746059095 +986000 ekin = 10.9917013457341 | erot = 8.97258068370089 | epot = -70.4785566337324 | etot = -50.5142746042974 +987000 ekin = 10.7795065325224 | erot = 9.35090018037428 | epot = -70.6446813163389 | etot = -50.5142746034422 +988000 ekin = 10.6312152805991 | erot = 9.85057203707997 | epot = -70.9960619213865 | etot = -50.5142746037075 +989000 ekin = 10.5490976147615 | erot = 10.4650086574291 | epot = -71.5283808775621 | etot = -50.5142746053715 +990000 ekin = 10.5298658629642 | erot = 11.172318985671 | epot = -72.216459457117 | etot = -50.5142746084818 +991000 ekin = 10.5651233193796 | erot = 11.9345717218314 | epot = -73.0139696539284 | etot = -50.5142746127174 +992000 ekin = 10.6428905939733 | erot = 12.7012555801191 | epot = -73.8584207914381 | etot = -50.5142746173457 +993000 ekin = 10.7501909020635 | erot = 13.4173760270567 | epot = -74.6818415505024 | etot = -50.5142746213823 +994000 ekin = 10.8760849479378 | erot = 14.034452679583 | epot = -75.4248122514733 | etot = -50.5142746239525 +995000 ekin = 11.014003549658 | erot = 14.5205029285366 | epot = -76.0487811028824 | etot = -50.5142746246879 +996000 ekin = 11.1622832137205 | erot = 14.8647830970565 | epot = -76.5413409346542 | etot = -50.5142746238772 +997000 ekin = 11.3226561298868 | erot = 15.0754558509346 | epot = -76.9123866030921 | etot = -50.5142746222707 +998000 ekin = 11.4975426711617 | erot = 15.1719516024432 | epot = -77.1837688942903 | etot = -50.5142746206854 +999000 ekin = 11.6875167360703 | erot = 15.1760730283588 | epot = -77.3778643840911 | etot = -50.5142746196621 +1000000 ekin = 11.8899772625222 | erot = 15.1055556567953 | epot = -77.5098075386556 | etot = -50.5142746193381 + 1000000 443.20455 -80.663303 3.1534956 -65.61983 -0.0074359672 39304000 +Loop time of 11.0539 on 1 procs for 1000000 steps with 10 atoms + +Performance: 133.346 ns/day, 0.180 hours/ns, 90466.136 timesteps/s, 904.661 katom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.8106 | 8.8106 | 8.8106 | 0.0 | 79.71 +Bond | 0.45112 | 0.45112 | 0.45112 | 0.0 | 4.08 +Neigh | 0.005589 | 0.005589 | 0.005589 | 0.0 | 0.05 +Comm | 0.24664 | 0.24664 | 0.24664 | 0.0 | 2.23 +Output | 0.12442 | 0.12442 | 0.12442 | 0.0 | 1.13 +Modify | 1.1263 | 1.1263 | 1.1263 | 0.0 | 10.19 +Other | | 0.2892 | | | 2.62 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 1.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:11 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/log.19May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/log.19May24.duplex1.g++.4 new file mode 100644 index 0000000000..9a582267b8 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/log.19May24.duplex1.g++.4 @@ -0,0 +1,1118 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + scanning bonds ... + 1 = max bonds/atom + 10 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 8 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.007 seconds +Setting atom values ... + 10 settings made for mass +10 atoms in group all +Reading oxdna potential (fene) file oxdna2.real with DATE: 2024-04-26 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (stk) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (xstk) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (coaxstk) file oxdna2.real with DATE: 2024-04-26 +Reading oxdna potential (dh) file oxdna2.real with DATE: 2024-04-26 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 36.640032 + ghost atom cutoff = 36.640032 + binsize = 18.320016, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 0.01706 +WARNING: Communication cutoff adjusted to 36.64003240988628 (src/comm.cpp:739) +0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.9029330618621 | etot = -50.5142754103311 +Per MPI rank memory allocation (min/avg/max) = 7.451 | 7.452 | 7.453 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 246.27432 -80.289462 6.3865285 -67.29606 -0.044626926 39304000 +1000 ekin = 6.41540831684956 | erot = 17.3249788985168 | epot = -74.2546626270297 | etot = -50.5142754116634 +2000 ekin = 6.27991122577835 | erot = 17.8454504610745 | epot = -74.6396371002369 | etot = -50.514275413384 +3000 ekin = 6.20398291945338 | erot = 18.3140766039219 | epot = -75.0323349385591 | etot = -50.5142754151838 +4000 ekin = 6.18636199767566 | erot = 18.7040547099769 | epot = -75.4046921244024 | etot = -50.5142754167498 +5000 ekin = 6.22215732158458 | erot = 18.9942188143056 | epot = -75.7306515537709 | etot = -50.5142754178807 +6000 ekin = 6.30420734178858 | erot = 19.1708709879918 | epot = -75.9893537482967 | etot = -50.5142754185163 +7000 ekin = 6.4241349103898 | erot = 19.2280244216477 | epot = -76.1664347507275 | etot = -50.51427541869 +8000 ekin = 6.57305019042805 | erot = 19.1666743693583 | epot = -76.2539999782602 | etot = -50.5142754184739 +9000 ekin = 6.74208660925288 | erot = 18.9937209190121 | epot = -76.250082946157 | etot = -50.514275417892 +10000 ekin = 6.92290866428223 | erot = 18.7212338885033 | epot = -76.1584179697745 | etot = -50.514275416989 +11000 ekin = 7.10814925172364 | erot = 18.3654806858375 | epot = -75.9879053534118 | etot = -50.5142754158506 +12000 ekin = 7.29164020767367 | erot = 17.9454168333354 | epot = -75.7513324556475 | etot = -50.5142754146384 +13000 ekin = 7.46835372796753 | erot = 17.4806722087765 | epot = -75.463301350236 | etot = -50.514275413492 +14000 ekin = 7.63410684865866 | erot = 16.9894852695674 | epot = -75.1378675308065 | etot = -50.5142754125804 +15000 ekin = 7.78518315371966 | erot = 16.4873283506083 | epot = -74.7867869161468 | etot = -50.5142754118188 +16000 ekin = 7.9180489561805 | erot = 15.9866370289743 | epot = -74.4189613960958 | etot = -50.514275410941 +17000 ekin = 8.02929115913949 | erot = 15.4954883395909 | epot = -74.0390549098709 | etot = -50.5142754111405 +18000 ekin = 8.11580274929282 | erot = 15.016179514802 | epot = -73.646257675632 | etot = -50.5142754115371 +19000 ekin = 8.17521064581969 | erot = 14.5455007220264 | epot = -73.2349867798163 | etot = -50.5142754119702 +20000 ekin = 8.20646553317788 | erot = 14.0791106720693 | epot = -72.7998516175191 | etot = -50.5142754122719 +21000 ekin = 8.210504997477 | erot = 13.6133776866129 | epot = -72.3381580963801 | etot = -50.5142754122902 +22000 ekin = 8.19089628972989 | erot = 13.1469621627642 | epot = -71.8521338644047 | etot = -50.5142754119106 +23000 ekin = 8.15436625402569 | erot = 12.6819076192472 | epot = -71.3505492843443 | etot = -50.5142754110714 +24000 ekin = 8.11112226003192 | erot = 12.2241028664329 | epot = -70.849500536239 | etot = -50.5142754097742 +25000 ekin = 8.0748389856222 | erot = 11.7830774890271 | epot = -70.3721918827457 | etot = -50.5142754080964 +26000 ekin = 8.06214574493372 | erot = 11.3711691532405 | epot = -69.9475903043491 | etot = -50.5142754061749 +27000 ekin = 8.09157304392403 | erot = 11.0021655564051 | epot = -69.6080140045727 | etot = -50.5142754042436 +28000 ekin = 8.1816091552257 | erot = 10.6895124998223 | epot = -69.3853970576618 | etot = -50.5142754026138 +29000 ekin = 8.34799192749725 | erot = 10.4442109367346 | epot = -69.306478265872 | etot = -50.5142754016401 +30000 ekin = 8.60050901552075 | erot = 10.2725968652597 | epot = -69.3873812824487 | etot = -50.5142754016683 +31000 ekin = 8.93993736466309 | erot = 10.1743202831913 | epot = -69.6285330507847 | etot = -50.5142754029304 +32000 ekin = 9.35601638498826 | erot = 10.1409979548438 | epot = -70.0112897452869 | etot = -50.5142754054548 +33000 ekin = 9.82730889560409 | erot = 10.1573088046849 | epot = -70.4988931092342 | etot = -50.5142754089452 +34000 ekin = 10.3233617248876 | erot = 10.201770188909 | epot = -71.0394073268399 | etot = -50.5142754130433 +35000 ekin = 10.809056119043 | erot = 10.2472649264777 | epot = -71.5705964624701 | etot = -50.5142754169493 +36000 ekin = 11.249914122838 | erot = 10.2681203532659 | epot = -72.0323098961308 | etot = -50.5142754200268 +37000 ekin = 11.6169651147158 | erot = 10.244630362473 | epot = -72.3758708990405 | etot = -50.5142754218516 +38000 ekin = 11.8900149081463 | erot = 10.1661461993865 | epot = -72.5704365298436 | etot = -50.5142754223108 +39000 ekin = 12.0587831385564 | erot = 10.0319213337585 | epot = -72.6049798938924 | etot = -50.5142754215774 +40000 ekin = 12.1221423965446 | erot = 9.84972970547109 | epot = -72.4861475220151 | etot = -50.5142754199994 +41000 ekin = 12.0861841074643 | erot = 9.6330625802473 | epot = -72.2335221056765 | etot = -50.5142754179649 +42000 ekin = 11.9619003024196 | erot = 9.39799829870681 | epot = -71.8741740169304 | etot = -50.514275415804 +43000 ekin = 11.7630285569638 | erot = 9.16060997815271 | epot = -71.4379139488624 | etot = -50.5142754137459 +44000 ekin = 11.5042972043481 | erot = 8.93525280143089 | epot = -70.9538254179095 | etot = -50.5142754121305 +45000 ekin = 11.2001042846024 | erot = 8.73270158680058 | epot = -70.4470812820302 | etot = -50.5142754106272 +46000 ekin = 10.8635866168478 | erot = 8.56191440586752 | epot = -69.9397764321244 | etot = -50.5142754094091 +47000 ekin = 10.506042654143 | erot = 8.43032536515512 | epot = -69.4506434277693 | etot = -50.5142754084712 +48000 ekin = 10.1367333285096 | erot = 8.34379512278126 | epot = -68.9948038590512 | etot = -50.5142754077604 +49000 ekin = 9.76306209921903 | erot = 8.30714647396204 | epot = -68.5844839803861 | etot = -50.5142754072051 +50000 ekin = 9.39110096123079 | erot = 8.32465746225152 | epot = -68.2300338302012 | etot = -50.5142754067189 +51000 ekin = 9.02637094808705 | erot = 8.40044977380951 | epot = -67.9410961281186 | etot = -50.5142754062221 +52000 ekin = 8.67472960831569 | erot = 8.53870234353558 | epot = -67.7277073575016 | etot = -50.5142754056503 +53000 ekin = 8.34318047181608 | erot = 8.74362113488822 | epot = -67.6010770116717 | etot = -50.5142754049674 +54000 ekin = 8.04040850085723 | erot = 9.01907630543207 | epot = -67.5737602105477 | etot = -50.5142754042584 +55000 ekin = 7.77685567444806 | erot = 9.36744157045945 | epot = -67.6585726485249 | etot = -50.5142754036174 +56000 ekin = 7.56421834771092 | erot = 9.78833936441787 | epot = -67.8668331153491 | etot = -50.5142754032203 +57000 ekin = 7.41438670676051 | erot = 10.2770459211361 | epot = -68.2057080311531 | etot = -50.5142754032564 +58000 ekin = 7.33802624874281 | erot = 10.8230821587548 | epot = -68.6753838113668 | etot = -50.5142754038692 +59000 ekin = 7.34316098271645 | erot = 11.4095663141997 | epot = -69.2670027020111 | etot = -50.514275405095 +60000 ekin = 7.4341300075388 | erot = 12.0137183042255 | epot = -69.9621237186179 | etot = -50.5142754068536 +61000 ekin = 7.61111888193163 | erot = 12.6084567926317 | epot = -70.7338510836134 | etot = -50.5142754090501 +62000 ekin = 7.87021275187741 | erot = 13.1643184159405 | epot = -71.5488065791708 | etot = -50.5142754113529 +63000 ekin = 8.20369524488242 | erot = 13.6538505067931 | epot = -72.3718211650938 | etot = -50.5142754134183 +64000 ekin = 8.60031282923891 | erot = 14.0539021280599 | epot = -73.1684903728601 | etot = -50.5142754155613 +65000 ekin = 9.04632694082953 | erot = 14.3452399471035 | epot = -73.9058423052434 | etot = -50.5142754173104 +66000 ekin = 9.52633841545675 | erot = 14.5163977172627 | epot = -74.5570115512606 | etot = -50.5142754185412 +67000 ekin = 10.0239662909343 | erot = 14.5650853618121 | epot = -75.1033270719445 | etot = -50.5142754191981 +68000 ekin = 10.522376965109 | erot = 14.4984989976628 | epot = -75.5351513820892 | etot = -50.5142754193175 +69000 ekin = 11.0045882552163 | erot = 14.3324567229673 | epot = -75.8513203972085 | etot = -50.5142754190249 +70000 ekin = 11.4535533147697 | erot = 14.0893789066283 | epot = -76.0572076399118 | etot = -50.5142754185137 +71000 ekin = 11.8521538801888 | erot = 13.7954213090599 | epot = -76.1618506069774 | etot = -50.5142754177287 +72000 ekin = 12.1833321321126 | erot = 13.477970603226 | epot = -76.1755781528756 | etot = -50.514275417537 +73000 ekin = 12.4276815038076 | erot = 13.1602120049098 | epot = -76.1021689263877 | etot = -50.5142754176703 +74000 ekin = 12.5675503165858 | erot = 12.8593249179885 | epot = -75.9411506526192 | etot = -50.5142754180449 +75000 ekin = 12.5880722472028 | erot = 12.5864734132395 | epot = -75.6888210788983 | etot = -50.514275418456 +76000 ekin = 12.4791879307471 | erot = 12.3474886698862 | epot = -75.34095201925 | etot = -50.5142754186168 +77000 ekin = 12.2380594263604 | erot = 12.144566415658 | epot = -74.8969012602677 | etot = -50.5142754182493 +78000 ekin = 11.8710909455364 | erot = 11.9782430722432 | epot = -74.3636094349585 | etot = -50.5142754171789 +79000 ekin = 11.3949317822826 | erot = 11.84887925342 | epot = -73.7580864511053 | etot = -50.5142754154027 +80000 ekin = 10.8360121848374 | erot = 11.7571641077332 | epot = -73.1074517056643 | etot = -50.5142754130937 +81000 ekin = 10.2285029505798 | erot = 11.7036410573964 | epot = -72.4464194185294 | etot = -50.5142754105532 +82000 ekin = 9.61095186500213 | erot = 11.6876732074566 | epot = -71.8129004805938 | etot = -50.5142754081351 +83000 ekin = 9.02210953811349 | erot = 11.7064078446962 | epot = -71.242792788983 | etot = -50.5142754061733 +84000 ekin = 8.49658156957016 | erot = 11.7541576431601 | epot = -70.7650146176605 | etot = -50.5142754049302 +85000 ekin = 8.06096889575964 | erot = 11.8223883028468 | epot = -70.3976326031568 | etot = -50.5142754045504 +86000 ekin = 7.73111762512716 | erot = 11.9003213122135 | epot = -70.1457143423862 | etot = -50.5142754050455 +87000 ekin = 7.51095945896828 | erot = 11.9760199352957 | epot = -70.0012548008799 | etot = -50.514275406616 +88000 ekin = 7.39125161739554 | erot = 12.0367692288882 | epot = -69.9422962547364 | etot = -50.5142754084527 +89000 ekin = 7.35291960067921 | erot = 12.0715131146574 | epot = -69.9387081257094 | etot = -50.5142754103727 +90000 ekin = 7.3729215274092 | erot = 12.0742094418155 | epot = -69.961406381238 | etot = -50.5142754120133 +91000 ekin = 7.4267722576974 | erot = 12.0445134023044 | epot = -69.9855610731056 | etot = -50.5142754131038 +92000 ekin = 7.49195579980787 | erot = 11.9883651963209 | epot = -69.9945964096583 | etot = -50.5142754135295 +93000 ekin = 7.5503081081974 | erot = 11.9173535388122 | epot = -69.9819370603462 | etot = -50.5142754133367 +94000 ekin = 7.58924049100697 | erot = 11.8468330690197 | epot = -69.9503489726999 | etot = -50.5142754126733 +95000 ekin = 7.60200252044838 | erot = 11.7936183338064 | epot = -69.9098962660036 | etot = -50.5142754117489 +96000 ekin = 7.58730388646369 | erot = 11.77323103503 | epot = -69.8748103322621 | etot = -50.5142754107683 +97000 ekin = 7.54854000456031 | erot = 11.7975124404608 | epot = -69.8603278549306 | etot = -50.5142754099095 +98000 ekin = 7.49272694028264 | erot = 11.872919668758 | epot = -69.87992201836 | etot = -50.5142754093194 +99000 ekin = 7.42914947570204 | erot = 11.9995813313717 | epot = -69.9430062161896 | etot = -50.5142754091159 +100000 ekin = 7.36773967938537 | erot = 12.1710710801644 | epot = -70.053086168939 | etot = -50.5142754093892 +101000 ekin = 7.3173239708405 | erot = 12.3748173436283 | epot = -70.2064167246514 | etot = -50.5142754101825 +102000 ekin = 7.2840363832501 | erot = 12.593109795725 | epot = -70.3914215904381 | etot = -50.514275411463 +103000 ekin = 7.27028672218553 | erot = 12.8047065613068 | epot = -70.5892686965911 | etot = -50.5142754130988 +104000 ekin = 7.27461582345199 | erot = 12.9870305824868 | epot = -70.7759218207938 | etot = -50.5142754148549 +105000 ekin = 7.29256428498991 | erot = 13.1188507799835 | epot = -70.9256904813974 | etot = -50.514275416424 +106000 ekin = 7.31837884124412 | erot = 13.183170708698 | epot = -71.0158249674247 | etot = -50.5142754174826 +107000 ekin = 7.3471237151123 | erot = 13.169898927461 | epot = -71.0312980603379 | etot = -50.5142754177645 +108000 ekin = 7.37665826766646 | erot = 13.0778272245807 | epot = -70.9687609093646 | etot = -50.5142754171175 +109000 ekin = 7.40901890869153 | erot = 12.9155349189492 | epot = -70.8388292431735 | etot = -50.5142754155327 +110000 ekin = 7.45094132862704 | erot = 12.7010355373246 | epot = -70.6662522790932 | etot = -50.5142754131415 +111000 ekin = 7.51347081219303 | erot = 12.4602014961901 | epot = -70.4879477185801 | etot = -50.5142754101971 +112000 ekin = 7.61074849763162 | erot = 12.2241598717142 | epot = -70.3491837763871 | etot = -50.5142754070413 +113000 ekin = 7.75811427376732 | erot = 12.0259242572136 | epot = -70.2983139350622 | etot = -50.5142754040813 +114000 ekin = 7.96968357180692 | erot = 11.8965473949297 | epot = -70.3805063684924 | etot = -50.5142754017558 +115000 ekin = 8.25649742679491 | erot = 11.8610413387419 | epot = -70.6318141648425 | etot = -50.5142753993057 +116000 ekin = 8.62901108799855 | erot = 11.9338020389727 | epot = -71.077088526737 | etot = -50.5142753997658 +117000 ekin = 9.07979306129298 | erot = 12.1168310649588 | epot = -71.7108995279887 | etot = -50.5142754017369 +118000 ekin = 9.58966909202019 | erot = 12.3984864178243 | epot = -72.5024309149993 | etot = -50.5142754051548 +119000 ekin = 10.1306989356931 | erot = 12.7538188996423 | epot = -73.3987932450655 | etot = -50.5142754097302 +120000 ekin = 10.6681502559759 | erot = 13.1469968867666 | epot = -74.3294225577248 | etot = -50.5142754149823 +121000 ekin = 11.1636445520065 | erot = 13.535473044617 | epot = -75.2133930169258 | etot = -50.5142754203023 +122000 ekin = 11.5789797549587 | erot = 13.8753321908118 | epot = -75.9685873708276 | etot = -50.5142754250571 +123000 ekin = 11.8800282928175 | erot = 14.1269962436829 | epot = -76.521299965185 | etot = -50.5142754286847 +124000 ekin = 12.040150051494 | erot = 14.2603474738973 | epot = -76.8147729561726 | etot = -50.5142754307813 +125000 ekin = 12.0426917567894 | erot = 14.2584040043201 | epot = -76.8153711922698 | etot = -50.5142754311602 +126000 ekin = 11.8823151169307 | erot = 14.1189492121665 | epot = -76.5155397589617 | etot = -50.5142754298644 +127000 ekin = 11.5650853952459 | erot = 13.8539357927778 | epot = -75.9332966151645 | etot = -50.5142754271407 +128000 ekin = 11.1074426377014 | erot = 13.4869506143891 | epot = -75.1086686754623 | etot = -50.5142754233718 +129000 ekin = 10.5343384717438 | erot = 13.0494015453618 | epot = -74.0980154361011 | etot = -50.5142754189956 +130000 ekin = 9.87690872398553 | erot = 12.576259576003 | epot = -72.9674437144188 | etot = -50.5142754144302 +131000 ekin = 9.17004712473897 | erot = 12.1021279223491 | epot = -71.7864504571086 | etot = -50.5142754100205 +132000 ekin = 8.45013853633907 | erot = 11.6581576779304 | epot = -70.6225716202886 | etot = -50.5142754060192 +133000 ekin = 7.75306702335383 | erot = 11.2700074960012 | epot = -69.5373499219523 | etot = -50.5142754025972 +134000 ekin = 7.11230829825862 | erot = 10.9564870021566 | epot = -68.5830707008209 | etot = -50.5142754004056 +135000 ekin = 6.55612439193876 | erot = 10.7277682649143 | epot = -67.7981680553211 | etot = -50.5142753984681 +136000 ekin = 6.10819187149973 | erot = 10.5892176988539 | epot = -67.211684967683 | etot = -50.5142753973294 +137000 ekin = 5.78608197421766 | erot = 10.5405205028491 | epot = -66.8408778740874 | etot = -50.5142753970207 +138000 ekin = 5.60007006615214 | erot = 10.575791335008 | epot = -66.6901367986829 | etot = -50.5142753975228 +139000 ekin = 5.55268795111655 | erot = 10.6843332994606 | epot = -66.751296649329 | etot = -50.5142753987518 +140000 ekin = 5.63899580381936 | erot = 10.8516980543454 | epot = -67.00496925871 | etot = -50.5142754005452 +141000 ekin = 5.84764919447641 | erot = 11.0611136462022 | epot = -67.4230382433494 | etot = -50.5142754026708 +142000 ekin = 6.16264005598841 | erot = 11.2952393652931 | epot = -67.9721548261423 | etot = -50.5142754048608 +143000 ekin = 6.56539680065064 | erot = 11.5380449116312 | epot = -68.6177171191527 | etot = -50.5142754068709 +144000 ekin = 7.03681705533687 | erot = 11.7764583665001 | epot = -69.3275508303693 | etot = -50.5142754085323 +145000 ekin = 7.55883117515936 | erot = 12.0018872087092 | epot = -70.074993793568 | etot = -50.5142754096994 +146000 ekin = 8.11525467293437 | erot = 12.2097777634791 | epot = -70.8393078470414 | etot = -50.5142754106279 +147000 ekin = 8.69187535303815 | erot = 12.3979831782877 | epot = -71.604133942692 | etot = -50.5142754113661 +148000 ekin = 9.27596343938009 | erot = 12.5659623821079 | epot = -72.3562012335829 | etot = -50.5142754120949 +149000 ekin = 9.85549786713835 | erot = 12.7129927814329 | epot = -73.0827660615442 | etot = -50.5142754129729 +150000 ekin = 10.418396768649 | erot = 12.8366697845745 | epot = -73.769341967324 | etot = -50.5142754141005 +151000 ekin = 10.9519669544071 | erot = 12.9320291475711 | epot = -74.3982715174723 | etot = -50.5142754154942 +152000 ekin = 11.4426825170492 | erot = 12.9914579844155 | epot = -74.9484159185624 | etot = -50.5142754170976 +153000 ekin = 11.876317648688 | erot = 13.0054164817443 | epot = -75.3960095492288 | etot = -50.5142754187965 +154000 ekin = 12.2384007603461 | erot = 12.9636415213673 | epot = -75.7163177021576 | etot = -50.5142754204442 +155000 ekin = 12.5149348410733 | erot = 12.8565997645001 | epot = -75.8858100274551 | etot = -50.5142754218817 +156000 ekin = 12.6933342582482 | erot = 12.6769330808811 | epot = -75.8845427620791 | etot = -50.5142754229498 +157000 ekin = 12.7635394773922 | erot = 12.4207265619602 | epot = -75.6985414628484 | etot = -50.514275423496 +158000 ekin = 12.7192609300225 | erot = 12.0885427176416 | epot = -75.3220790710407 | etot = -50.5142754233766 +159000 ekin = 12.5592455089091 | erot = 11.6862409532771 | epot = -74.7597618846584 | etot = -50.5142754224722 +160000 ekin = 12.288354457994 | erot = 11.2255943810305 | epot = -74.0282242597334 | etot = -50.5142754207088 +161000 ekin = 11.9181388689072 | erot = 10.7246248575609 | epot = -73.1570391445684 | etot = -50.5142754181004 +162000 ekin = 11.4665846354836 | erot = 10.2074983581298 | epot = -72.1883584083817 | etot = -50.5142754147683 +163000 ekin = 10.9568419276688 | erot = 9.70380592719131 | epot = -71.1749232658142 | etot = -50.5142754109541 +164000 ekin = 10.415038281725 | erot = 9.24702033764179 | epot = -70.1763340263581 | etot = -50.5142754069913 +165000 ekin = 9.86757905055464 | erot = 8.87218491764896 | epot = -69.254039371451 | etot = -50.5142754032474 +166000 ekin = 9.33851143760975 | erot = 8.6130347778522 | epot = -68.4658216155254 | etot = -50.5142754000635 +167000 ekin = 8.84748730504085 | erot = 8.49893907243694 | epot = -67.8607017751746 | etot = -50.5142753976968 +168000 ekin = 8.40864571542269 | erot = 8.55215074312135 | epot = -67.4750718548298 | etot = -50.5142753962858 +169000 ekin = 8.03045700864842 | erot = 8.78581375895569 | epot = -67.3305461634548 | etot = -50.5142753958506 +170000 ekin = 7.71636101684918 | erot = 9.20299038162971 | epot = -67.4336267947997 | etot = -50.5142753963208 +171000 ekin = 7.46715080109723 | erot = 9.79683187833268 | epot = -67.77825807604 | etot = -50.5142753966101 +172000 ekin = 7.28585658179886 | erot = 10.5506327822701 | epot = -68.3507647629954 | etot = -50.5142753989265 +173000 ekin = 7.16416011926273 | erot = 11.4382460333911 | epot = -69.1166815543033 | etot = -50.5142754016495 +174000 ekin = 7.09132968419416 | erot = 12.4279054681619 | epot = -70.0335105569907 | etot = -50.5142754046347 +175000 ekin = 7.05634491974703 | erot = 13.4842000875638 | epot = -71.0548204150808 | etot = -50.51427540777 +176000 ekin = 7.04815622786012 | erot = 14.5697180480002 | epot = -72.1321496868147 | etot = -50.5142754109544 +177000 ekin = 7.05589089928332 | erot = 15.6465151520296 | epot = -73.2166814653926 | etot = -50.5142754140797 +178000 ekin = 7.06870996384048 | erot = 16.6778391096179 | epot = -74.2608244904897 | etot = -50.5142754170313 +179000 ekin = 7.07565875636352 | erot = 17.6303035880064 | epot = -75.2202377640034 | etot = -50.5142754196335 +180000 ekin = 7.06640718471778 | erot = 18.475580236099 | epot = -76.0562628425591 | etot = -50.5142754217424 +181000 ekin = 7.03211004009704 | erot = 19.1916515774748 | epot = -76.7380370407789 | etot = -50.5142754232071 +182000 ekin = 6.96555336524938 | erot = 19.7646727182898 | epot = -77.2445015091219 | etot = -50.5142754255827 +183000 ekin = 6.86135102663214 | erot = 20.1806311279207 | epot = -77.5562575806635 | etot = -50.5142754261107 +184000 ekin = 6.71513119692684 | erot = 20.4321176363584 | epot = -77.6615242591428 | etot = -50.5142754258575 +185000 ekin = 6.52573507255774 | erot = 20.5251927864044 | epot = -77.5652032838376 | etot = -50.5142754248754 +186000 ekin = 6.29640349453609 | erot = 20.4725850987713 | epot = -77.2832640165641 | etot = -50.5142754232567 +187000 ekin = 6.0352483563431 | erot = 20.2918463237094 | epot = -76.8413701011687 | etot = -50.5142754211162 +188000 ekin = 5.75534624813142 | erot = 20.003513474993 | epot = -76.2731351417105 | etot = -50.5142754185861 +189000 ekin = 5.47428677235273 | erot = 19.6288299760677 | epot = -75.6173921644552 | etot = -50.5142754160348 +190000 ekin = 5.21304528645338 | erot = 19.1884702895163 | epot = -74.9157909892313 | etot = -50.5142754132617 +191000 ekin = 4.99413978963197 | erot = 18.7029827292113 | epot = -74.2113979294859 | etot = -50.5142754106427 +192000 ekin = 4.83931815322826 | erot = 18.191274780975 | epot = -73.5448683425773 | etot = -50.5142754083741 +193000 ekin = 4.76714699157977 | erot = 17.6700691054177 | epot = -72.9514915036075 | etot = -50.51427540661 +194000 ekin = 4.79094358958925 | erot = 17.1536396953267 | epot = -72.4588586903521 | etot = -50.5142754054362 +195000 ekin = 4.91743571189986 | erot = 16.6538363084239 | epot = -72.0855474251812 | etot = -50.5142754048574 +196000 ekin = 5.1463565099702 | erot = 16.1803427452281 | epot = -71.8409746600068 | etot = -50.5142754048085 +197000 ekin = 5.4709576937409 | erot = 15.741043259991 | epot = -71.7262763589156 | etot = -50.5142754051837 +198000 ekin = 5.87922858422111 | erot = 15.3423400565245 | epot = -71.7358440466092 | etot = -50.5142754058636 +199000 ekin = 6.35549663143683 | erot = 14.9892917891059 | epot = -71.8590638272886 | etot = -50.5142754067459 +200000 ekin = 6.8820758632859 | erot = 14.6855189973232 | epot = -72.081870268366 | etot = -50.514275407757 +201000 ekin = 7.44070643690184 | erot = 14.4329169816303 | epot = -72.3878988273838 | etot = -50.5142754088517 +202000 ekin = 8.01364908712578 | erot = 14.2312922771998 | epot = -72.7592167743313 | etot = -50.5142754100058 +203000 ekin = 8.58441531263517 | erot = 14.0780678440199 | epot = -73.176758567858 | etot = -50.5142754112029 +204000 ekin = 9.13819316347435 | erot = 13.9681780326677 | epot = -73.6206466085633 | etot = -50.5142754124213 +205000 ekin = 9.66205791777544 | erot = 13.8942152360292 | epot = -74.0705485674246 | etot = -50.5142754136199 +206000 ekin = 10.1450467911598 | erot = 13.8468542669147 | epot = -74.5061764728694 | etot = -50.5142754147949 +207000 ekin = 10.5781443228252 | erot = 13.8152589579854 | epot = -74.9076786967007 | etot = -50.5142754158901 +208000 ekin = 10.9541942360374 | erot = 13.7878179109787 | epot = -75.2562875638908 | etot = -50.5142754168747 +209000 ekin = 11.2677463035536 | erot = 13.7528525924388 | epot = -75.5348743137186 | etot = -50.5142754177263 +210000 ekin = 11.5148381182878 | erot = 13.6992490106657 | epot = -75.7283625473805 | etot = -50.5142754184271 +211000 ekin = 11.6927279463145 | erot = 13.617054323805 | epot = -75.8240576890846 | etot = -50.5142754189651 +212000 ekin = 11.7996107409576 | erot = 13.4980938589365 | epot = -75.8119800191655 | etot = -50.5142754192714 +213000 ekin = 11.8343576841856 | erot = 13.3367031669184 | epot = -75.6853362705999 | etot = -50.5142754194959 +214000 ekin = 11.7963237462782 | erot = 13.1291697339432 | epot = -75.4397688997533 | etot = -50.514275419532 +215000 ekin = 11.6852668694912 | erot = 12.874430284688 | epot = -75.0739725735796 | etot = -50.5142754194004 +216000 ekin = 11.5014303659838 | erot = 12.5741401329483 | epot = -74.5898459180426 | etot = -50.5142754191105 +217000 ekin = 11.2458820823737 | erot = 12.2323072888261 | epot = -73.9924647898455 | etot = -50.5142754186458 +218000 ekin = 10.9212463786256 | erot = 11.8549524898054 | epot = -73.2904742863558 | etot = -50.5142754179248 +219000 ekin = 10.532960707104 | erot = 11.4501226259861 | epot = -72.4973587498683 | etot = -50.5142754167781 +220000 ekin = 10.0910611337979 | erot = 11.0285507859445 | epot = -71.6338873347119 | etot = -50.5142754149696 +221000 ekin = 9.61219796243461 | erot = 10.6049025440457 | epot = -70.7313759187632 | etot = -50.5142754122829 +222000 ekin = 9.12115937360566 | erot = 10.1989791085933 | epot = -69.8344138908757 | etot = -50.5142754086768 +223000 ekin = 8.65086680646373 | erot = 9.83578310548002 | epot = -69.0009253163689 | etot = -50.5142754044252 +224000 ekin = 8.23994052341592 | erot = 9.54342912562408 | epot = -68.2976450491949 | etot = -50.5142754001549 +225000 ekin = 7.92770828799823 | erot = 9.34870111081389 | epot = -67.7906847955069 | etot = -50.5142753966948 +226000 ekin = 7.74769423456563 | erot = 9.27124602944927 | epot = -67.5332156588595 | etot = -50.5142753948446 +227000 ekin = 7.72151333456704 | erot = 9.31824720259694 | epot = -67.5540359321235 | etot = -50.5142753949595 +228000 ekin = 7.8550934831219 | erot = 9.4823063677855 | epot = -67.8516752474312 | etot = -50.5142753965238 +229000 ekin = 8.13704792667924 | erot = 9.74526659084824 | epot = -68.3965899178452 | etot = -50.5142754003177 +230000 ekin = 8.54211975827146 | erot = 10.0762112157472 | epot = -69.1326063789155 | etot = -50.5142754048968 +231000 ekin = 9.03730612207804 | erot = 10.4369573689899 | epot = -69.9885389005796 | etot = -50.5142754095116 +232000 ekin = 9.58655681927191 | erot = 10.7906593081327 | epot = -70.8914915409894 | etot = -50.5142754135848 +233000 ekin = 10.1548693407455 | erot = 11.1065562702293 | epot = -71.7757010277636 | etot = -50.5142754167888 +234000 ekin = 10.7108776684946 | erot = 11.3626339427593 | epot = -72.5877870303025 | etot = -50.5142754190486 +235000 ekin = 11.227991529631 | erot = 11.5461467437172 | epot = -73.2884136938095 | etot = -50.5142754204614 +236000 ekin = 11.6845296184684 | erot = 11.6525082369783 | epot = -73.8513132774546 | etot = -50.5142754220079 +237000 ekin = 12.0579257921087 | erot = 11.6840457725785 | epot = -74.256246987397 | etot = -50.5142754227097 +238000 ekin = 12.3279512217304 | erot = 11.6453539329295 | epot = -74.4875805777133 | etot = -50.5142754230534 +239000 ekin = 12.4822356739966 | erot = 11.5417603171798 | epot = -74.5382714141925 | etot = -50.5142754230161 +240000 ekin = 12.5140319304705 | erot = 11.3798400951642 | epot = -74.4081474481376 | etot = -50.5142754225029 +241000 ekin = 12.4234383523719 | erot = 11.1674085806387 | epot = -74.1051223544116 | etot = -50.514275421401 +242000 ekin = 12.2186033883425 | erot = 10.9138071750467 | epot = -73.6466859829904 | etot = -50.5142754196012 +243000 ekin = 11.9165339535847 | erot = 10.6303079140403 | epot = -73.0611172847419 | etot = -50.5142754171169 +244000 ekin = 11.5429037221883 | erot = 10.3301144758677 | epot = -72.3872936120617 | etot = -50.5142754140058 +245000 ekin = 11.1308004491742 | erot = 10.0279651152867 | epot = -71.6730409749902 | etot = -50.5142754105293 +246000 ekin = 10.7178963481095 | erot = 9.73923384809003 | epot = -70.9714056032603 | etot = -50.5142754070608 +247000 ekin = 10.3421796192255 | erot = 9.47853790668733 | epot = -70.3349929299394 | etot = -50.5142754040265 +248000 ekin = 10.0370371760671 | erot = 9.25823648339794 | epot = -69.8095490613008 | etot = -50.5142754018358 +249000 ekin = 9.82809079046689 | erot = 9.08725211025908 | epot = -69.4296183010316 | etot = -50.5142754003056 +250000 ekin = 9.7301811790438 | erot = 8.96958696148604 | epot = -69.2140435411877 | etot = -50.5142754006578 +251000 ekin = 9.73984053867505 | erot = 8.90312708508932 | epot = -69.1572430257791 | etot = -50.5142754020147 +252000 ekin = 9.84186771029651 | erot = 8.88191102821177 | epot = -69.2380541425503 | etot = -50.5142754040421 +253000 ekin = 10.0131035686047 | erot = 8.89763848171037 | epot = -69.4250174566696 | etot = -50.5142754063545 +254000 ekin = 10.2265753155538 | erot = 8.94123900967878 | epot = -69.6820897338543 | etot = -50.5142754086217 +255000 ekin = 10.4552485961449 | erot = 9.00423312864855 | epot = -69.9737571353835 | etot = -50.5142754105901 +256000 ekin = 10.6747348456466 | erot = 9.07982990112379 | epot = -70.2688401589834 | etot = -50.514275412213 +257000 ekin = 10.8646942922507 | erot = 9.16274367319122 | epot = -70.5417133788841 | etot = -50.5142754134422 +258000 ekin = 11.0093996909192 | erot = 9.24945580314207 | epot = -70.7731309083504 | etot = -50.5142754142891 +259000 ekin = 11.0977947702441 | erot = 9.33830301516425 | epot = -70.9503732001606 | etot = -50.5142754147522 +260000 ekin = 11.1234502408098 | erot = 9.42959720860747 | epot = -71.0673228642354 | etot = -50.5142754148182 +261000 ekin = 11.0846553116714 | erot = 9.52592259400152 | epot = -71.1248533201204 | etot = -50.5142754144474 +262000 ekin = 10.984638316139 | erot = 9.63253179681266 | epot = -71.1314455270241 | etot = -50.5142754140724 +263000 ekin = 10.8299323585395 | erot = 9.75337886021491 | epot = -71.0975866314619 | etot = -50.5142754127075 +264000 ekin = 10.6322589076009 | erot = 9.89661561772529 | epot = -71.043149936365 | etot = -50.5142754110388 +265000 ekin = 10.4088137866306 | erot = 10.0729935919341 | epot = -70.9960827876143 | etot = -50.5142754090497 +266000 ekin = 10.1805628465601 | erot = 10.2939584250778 | epot = -70.9887966786993 | etot = -50.5142754070614 +267000 ekin = 9.96994974150393 | erot = 10.5688816981301 | epot = -71.0531068450853 | etot = -50.5142754054513 +268000 ekin = 9.79794557249612 | erot = 10.9022495131634 | epot = -71.2144704902405 | etot = -50.514275404581 +269000 ekin = 9.68133719080967 | erot = 11.2909602515362 | epot = -71.4865728471559 | etot = -50.51427540481 +270000 ekin = 9.62864440995091 | erot = 11.7231927403034 | epot = -71.8661125564593 | etot = -50.514275406205 +271000 ekin = 9.63922421059774 | erot = 12.1783004915323 | epot = -72.3318001107749 | etot = -50.5142754086448 +272000 ekin = 9.70377142417398 | erot = 12.6284925682459 | epot = -72.8465394041799 | etot = -50.51427541176 +273000 ekin = 9.8063511269751 | erot = 13.0424803665411 | epot = -73.3631069085421 | etot = -50.5142754150259 +274000 ekin = 9.92762957285844 | erot = 13.3902097774721 | epot = -73.8321147682193 | etot = -50.5142754178888 +275000 ekin = 10.0484619807246 | erot = 13.6476466829874 | epot = -74.2103840836058 | etot = -50.5142754198938 +276000 ekin = 10.1529836986312 | erot = 13.8005799704977 | epot = -74.4678390899012 | etot = -50.5142754207723 +277000 ekin = 10.2306208739454 | erot = 13.8468297581951 | epot = -74.5917260525716 | etot = -50.5142754204311 +278000 ekin = 10.2768285154679 | erot = 13.7964170571851 | epot = -74.5875209917308 | etot = -50.5142754190778 +279000 ekin = 10.2926887337975 | erot = 13.6696245090783 | epot = -74.4765886598105 | etot = -50.5142754169347 +280000 ekin = 10.2837511614433 | erot = 13.4944463812718 | epot = -74.2924729570549 | etot = -50.5142754143399 +281000 ekin = 10.2584490696337 | erot = 13.3029884943437 | epot = -74.0757129756518 | etot = -50.5142754116744 +282000 ekin = 10.2256707145218 | erot = 13.1261764968024 | epot = -73.8661226217319 | etot = -50.5142754104077 +283000 ekin = 10.1905670824271 | erot = 12.9864505984498 | epot = -73.6912930902104 | etot = -50.5142754093336 +284000 ekin = 10.1551014927832 | erot = 12.8990344595995 | epot = -73.5684113617333 | etot = -50.5142754093506 +285000 ekin = 10.1166174221453 | erot = 12.8680165955296 | epot = -73.4989094281387 | etot = -50.5142754104637 +286000 ekin = 10.0677495873385 | erot = 12.8863469806722 | epot = -73.4683719803649 | etot = -50.5142754123541 +287000 ekin = 9.99824250893113 | erot = 12.9388664872155 | epot = -73.451384410478 | etot = -50.5142754143313 +288000 ekin = 9.89878072361279 | erot = 13.0083713387396 | epot = -73.4214274778747 | etot = -50.5142754155222 +289000 ekin = 9.76588531823301 | erot = 13.0828123958642 | epot = -73.3629731293727 | etot = -50.5142754152755 +290000 ekin = 9.60570842713546 | erot = 13.1602378251788 | epot = -73.2802216658707 | etot = -50.5142754135565 +291000 ekin = 9.43434667886679 | erot = 13.2486965863666 | epot = -73.1973186762433 | etot = -50.5142754110099 +292000 ekin = 9.27394835180298 | erot = 13.3611401460319 | epot = -73.1493639064103 | etot = -50.5142754085754 +293000 ekin = 9.14636730713516 | erot = 13.508296111862 | epot = -73.1689388261846 | etot = -50.5142754071874 +294000 ekin = 9.06768252918386 | erot = 13.6923254511167 | epot = -73.274283387418 | etot = -50.5142754071174 +295000 ekin = 9.04532028964203 | erot = 13.9047980939014 | epot = -73.4643937919253 | etot = -50.5142754083819 +296000 ekin = 9.07685514216932 | erot = 14.1273095688263 | epot = -73.7184401215834 | etot = -50.5142754105878 +297000 ekin = 9.15243484563929 | erot = 14.3349675764924 | epot = -74.0016778353859 | etot = -50.5142754132543 +298000 ekin = 9.25735642260993 | erot = 14.5009144267095 | epot = -74.272546265234 | etot = -50.5142754159145 +299000 ekin = 9.37408501219885 | erot = 14.6008610261479 | epot = -74.4892214566812 | etot = -50.5142754183345 +300000 ekin = 9.48403035595357 | erot = 14.6171008230997 | epot = -74.6154065990458 | etot = -50.5142754199925 +301000 ekin = 9.56941047833026 | erot = 14.5422411099529 | epot = -74.6259270092226 | etot = -50.5142754209395 +302000 ekin = 9.61327914963467 | erot = 14.378723713019 | epot = -74.5062782840107 | etot = -50.5142754213571 +303000 ekin = 9.60019007969869 | erot = 14.1333232517767 | epot = -74.247788754271 | etot = -50.5142754227957 +304000 ekin = 9.51663443757369 | erot = 13.8077649608907 | epot = -73.8386748218732 | etot = -50.5142754234088 +305000 ekin = 9.35052324456569 | erot = 13.4126572581527 | epot = -73.2774559257932 | etot = -50.5142754230748 +306000 ekin = 9.092386148072 | erot = 12.9580617085375 | epot = -72.5647232811115 | etot = -50.514275424502 +307000 ekin = 8.73005981828168 | erot = 12.4440345689812 | epot = -71.6883698129516 | etot = -50.5142754256887 +308000 ekin = 8.25664133386104 | erot = 11.8703174730556 | epot = -70.6412342327938 | etot = -50.5142754258772 +309000 ekin = 7.68019887870488 | erot = 11.2440321634392 | epot = -69.4385064478165 | etot = -50.5142754056724 +310000 ekin = 6.10737245374142 | erot = 10.002228414897 | epot = -66.6238758338137 | etot = -50.5142749651753 +311000 ekin = 6.50516631276161 | erot = 8.43886202715248 | epot = -65.4583031837191 | etot = -50.514274843805 +312000 ekin = 8.70116484241941 | erot = 7.89328716556354 | epot = -67.1087266850217 | etot = -50.5142746770387 +313000 ekin = 8.86124124004463 | erot = 7.60650277386486 | epot = -66.9820187089931 | etot = -50.5142746950836 +314000 ekin = 8.98375855328481 | erot = 7.42590866136671 | epot = -66.9239419073455 | etot = -50.514274692694 +315000 ekin = 9.08224545794751 | erot = 7.35030056649325 | epot = -66.9468207149303 | etot = -50.5142746904895 +316000 ekin = 9.18875804710271 | erot = 7.3745853881851 | epot = -67.0776181243804 | etot = -50.5142746890926 +317000 ekin = 9.33052371804657 | erot = 7.48774538838077 | epot = -67.3325437958086 | etot = -50.5142746893812 +318000 ekin = 9.51917570866743 | erot = 7.66478668187902 | epot = -67.698237081594 | etot = -50.5142746910475 +319000 ekin = 9.75242332648387 | erot = 7.87397921140609 | epot = -68.1406772315323 | etot = -50.5142746936424 +320000 ekin = 10.0191832997486 | erot = 8.08576089652625 | epot = -68.6192188931081 | etot = -50.5142746968332 +321000 ekin = 10.2991596304326 | erot = 8.27181002887399 | epot = -69.0852443594221 | etot = -50.5142747001155 +322000 ekin = 10.5668594668805 | erot = 8.40836857708763 | epot = -69.4895027468579 | etot = -50.5142747028898 +323000 ekin = 10.7967867214542 | erot = 8.47975301094411 | epot = -69.790814435656 | etot = -50.5142747032577 +324000 ekin = 10.9735635054938 | erot = 8.48122286684698 | epot = -69.9690610761778 | etot = -50.5142747038371 +325000 ekin = 11.0878819432239 | erot = 8.41951775675473 | epot = -70.0216744027954 | etot = -50.5142747028168 +326000 ekin = 11.1347107227788 | erot = 8.31335610180601 | epot = -69.9623415249674 | etot = -50.5142747003826 +327000 ekin = 11.1183799650552 | erot = 8.19353318202614 | epot = -69.8261878441104 | etot = -50.5142746970291 +328000 ekin = 11.0497327326504 | erot = 8.09852253416955 | epot = -69.6625299601751 | etot = -50.5142746933551 +329000 ekin = 10.9426003402541 | erot = 8.06872590413947 | epot = -69.5256009343306 | etot = -50.514274689937 +330000 ekin = 10.8106057636499 | erot = 8.14099901902345 | epot = -69.465879469905 | etot = -50.5142746872316 +331000 ekin = 10.6649041616717 | erot = 8.34394296354098 | epot = -69.5231218107424 | etot = -50.5142746855298 +332000 ekin = 10.5130013374487 | erot = 8.69446319291375 | epot = -69.7217392153338 | etot = -50.5142746849714 +333000 ekin = 10.3584993437686 | erot = 9.19578452270885 | epot = -70.068558552037 | etot = -50.5142746855595 +334000 ekin = 10.2015206739134 | erot = 9.83691053813619 | epot = -70.5527058992349 | etot = -50.5142746871853 +335000 ekin = 10.039533591642 | erot = 10.5934602800325 | epot = -71.1472685613235 | etot = -50.5142746896489 +336000 ekin = 9.86837013790453 | erot = 11.4297871185518 | epot = -71.8124319491329 | etot = -50.5142746926766 +337000 ekin = 9.68329052895473 | erot = 12.3021498009615 | epot = -72.4997150262984 | etot = -50.5142746963822 +338000 ekin = 9.47975699832246 | erot = 13.1586156684166 | epot = -73.1526473662513 | etot = -50.5142746995123 +339000 ekin = 9.25386163521108 | erot = 13.9501138811546 | epot = -73.7182502184674 | etot = -50.5142747021017 +340000 ekin = 9.0041124705003 | erot = 14.6361003739376 | epot = -74.1544875483691 | etot = -50.5142747039313 +341000 ekin = 8.73210815872213 | erot = 15.1850150670298 | epot = -74.431397930643 | etot = -50.5142747048911 +342000 ekin = 8.44257602321301 | erot = 15.5760933936512 | epot = -74.5329441218357 | etot = -50.5142747049715 +343000 ekin = 8.14306068344561 | erot = 15.7999489751116 | epot = -74.457284362799 | etot = -50.5142747042418 +344000 ekin = 7.84335230652546 | erot = 15.85820178893 | epot = -74.2158287982668 | etot = -50.5142747028113 +345000 ekin = 7.55476158127004 | erot = 15.7625218310027 | epot = -73.8315581130777 | etot = -50.514274700805 +346000 ekin = 7.28933152870106 | erot = 15.5333922679153 | epot = -73.3369984949705 | etot = -50.5142746983542 +347000 ekin = 7.05903031456423 | erot = 15.1987186623017 | epot = -72.7720236724687 | etot = -50.5142746956027 +348000 ekin = 6.8749234811854 | erot = 14.7922321909521 | epot = -72.1814303648537 | etot = -50.5142746927162 +349000 ekin = 6.74631360360857 | erot = 14.3515585684733 | epot = -71.612146861975 | etot = -50.5142746898931 +350000 ekin = 6.6798666945979 | erot = 13.9158727832157 | epot = -71.1100141651634 | etot = -50.5142746873498 +351000 ekin = 6.67881215224917 | erot = 13.5231979606908 | epot = -70.7162847982477 | etot = -50.5142746853078 +352000 ekin = 6.74233002325304 | erot = 13.2075061614665 | epot = -70.4641108686907 | etot = -50.5142746839711 +353000 ekin = 6.86523168135804 | erot = 12.99583142007 | epot = -70.3753377849391 | etot = -50.5142746835111 +354000 ekin = 7.03799439994906 | erot = 12.9056193290381 | epot = -70.4578884130328 | etot = -50.5142746840457 +355000 ekin = 7.24717151819179 | erot = 12.9425723794625 | epot = -70.704018583276 | etot = -50.5142746856217 +356000 ekin = 7.4761877974731 | erot = 13.0993511152901 | epot = -71.0898136009402 | etot = -50.514274688177 +357000 ekin = 7.70655379468214 | erot = 13.3555627807251 | epot = -71.576391266919 | etot = -50.5142746915118 +358000 ekin = 7.91949851741237 | erot = 13.6794128875102 | epot = -72.1131861002074 | etot = -50.5142746952848 +359000 ekin = 8.09792001680045 | erot = 14.0311122671652 | epot = -72.643306983018 | etot = -50.5142746990523 +360000 ekin = 8.22841418973107 | erot = 14.3676693799534 | epot = -73.1103582720264 | etot = -50.514274702342 +361000 ekin = 8.30307067049387 | erot = 14.6487380645247 | epot = -73.4660834390475 | etot = -50.5142747040289 +362000 ekin = 8.32057496602261 | erot = 14.8452541250431 | epot = -73.6801037963478 | etot = -50.514274705282 +363000 ekin = 8.28596637426031 | erot = 14.9355049197912 | epot = -73.7357459994441 | etot = -50.5142747053926 +364000 ekin = 8.21051030663795 | erot = 14.9080133756924 | epot = -73.6327983867719 | etot = -50.5142747044415 +365000 ekin = 8.11062074727325 | erot = 14.7623286020347 | epot = -73.3872240519604 | etot = -50.5142747026524 +366000 ekin = 8.00603056266532 | erot = 14.5073568469375 | epot = -73.0276621099553 | etot = -50.5142747003525 +367000 ekin = 7.91744023302101 | erot = 14.1587217211998 | epot = -72.5904366521256 | etot = -50.5142746979048 +368000 ekin = 7.86392049102369 | erot = 13.7358279103901 | epot = -72.114023097055 | etot = -50.5142746956412 +369000 ekin = 7.86042077697011 | erot = 13.2593035824029 | epot = -71.6339990531807 | etot = -50.5142746938077 +370000 ekin = 7.91575681906267 | erot = 12.7493098978033 | epot = -71.1793414093916 | etot = -50.5142746925256 +371000 ekin = 8.0314176515605 | erot = 12.224882599033 | epot = -70.7705749423856 | etot = -50.5142746917921 +372000 ekin = 8.2014344867836 | erot = 11.7041154007154 | epot = -70.4198245790021 | etot = -50.5142746915031 +373000 ekin = 8.41338088911726 | erot = 11.2047322600046 | epot = -70.132387840622 | etot = -50.5142746915001 +374000 ekin = 8.65035651211555 | erot = 10.7445296546692 | epot = -69.9091608583952 | etot = -50.5142746916105 +375000 ekin = 8.8936146386472 | erot = 10.3413213234561 | epot = -69.7492106537874 | etot = -50.5142746916841 +376000 ekin = 9.1253714435836 | erot = 10.0122766242485 | epot = -69.6519227594581 | etot = -50.514274691626 +377000 ekin = 9.33127044534337 | erot = 9.77273697837441 | epot = -69.6182821151407 | etot = -50.5142746914229 +378000 ekin = 9.50196666763184 | erot = 9.63465665477537 | epot = -69.650898013574 | etot = -50.5142746911668 +379000 ekin = 9.63341647872386 | erot = 9.60484799639576 | epot = -69.752539166967 | etot = -50.5142746918473 +380000 ekin = 9.72259425985655 | erot = 9.68264926837001 | epot = -69.9195182203078 | etot = -50.5142746920812 +381000 ekin = 9.76882857105924 | erot = 9.85976932385756 | epot = -70.1428725876487 | etot = -50.5142746927319 +382000 ekin = 9.77534265376213 | erot = 10.1216764958066 | epot = -70.4112938433178 | etot = -50.514274693749 +383000 ekin = 9.74553082877612 | erot = 10.4488490599493 | epot = -70.708654583621 | etot = -50.5142746948956 +384000 ekin = 9.68350130853765 | erot = 10.8197410298538 | epot = -71.0175170342467 | etot = -50.5142746958552 +385000 ekin = 9.5954111192781 | erot = 11.2139279084422 | epot = -71.3236137241221 | etot = -50.5142746964018 +386000 ekin = 9.49051238892938 | erot = 11.614249506982 | epot = -71.6190365924349 | etot = -50.5142746965235 +387000 ekin = 9.38093820527632 | erot = 12.0071365317705 | epot = -71.9023494334877 | etot = -50.5142746964408 +388000 ekin = 9.27994371657981 | erot = 12.3811396839122 | epot = -72.1753580970018 | etot = -50.5142746965098 +389000 ekin = 9.19914674274271 | erot = 12.7246960950101 | epot = -72.4381175345215 | etot = -50.5142746967686 +390000 ekin = 9.14582012533032 | erot = 13.0260688102847 | epot = -72.6861636335371 | etot = -50.5142746979221 +391000 ekin = 9.12133255589048 | erot = 13.2696465843341 | epot = -72.9052538397012 | etot = -50.5142746994766 +392000 ekin = 9.12142280934788 | erot = 13.4389248950445 | epot = -73.0746224053982 | etot = -50.5142747010059 +393000 ekin = 9.1381719641129 | erot = 13.5212229550151 | epot = -73.1736696211337 | etot = -50.5142747020057 +394000 ekin = 9.16298117431549 | erot = 13.5118244942784 | epot = -73.1890803706461 | etot = -50.5142747020522 +395000 ekin = 9.18964919962186 | erot = 13.4168358877668 | epot = -73.1207597883506 | etot = -50.514274700962 +396000 ekin = 9.21646132594111 | erot = 13.2536172301874 | epot = -72.9843532549932 | etot = -50.5142746988646 +397000 ekin = 9.24655582003865 | erot = 13.048360781714 | epot = -72.8091912979599 | etot = -50.5142746962072 +398000 ekin = 9.28632448604099 | erot = 12.8312285607892 | epot = -72.6318277404758 | etot = -50.5142746936456 +399000 ekin = 9.34221312080447 | erot = 12.63009249328 | epot = -72.4865803059712 | etot = -50.5142746918868 +400000 ekin = 9.41686913722861 | erot = 12.4642777025704 | epot = -72.3954215313006 | etot = -50.5142746915016 +401000 ekin = 9.50589901458469 | erot = 12.3397667936919 | epot = -72.3599405010301 | etot = -50.5142746927535 +402000 ekin = 9.59639944968567 | erot = 12.2470917660231 | epot = -72.3577659112033 | etot = -50.5142746954945 +403000 ekin = 9.66795983396075 | erot = 12.1626989619761 | epot = -72.3449334950877 | etot = -50.5142746991509 +404000 ekin = 9.69608913018285 | erot = 12.0539804141988 | epot = -72.2643442472069 | etot = -50.5142747028253 +405000 ekin = 9.65743908964136 | erot = 11.8874299823527 | epot = -72.0591437774434 | etot = -50.5142747054493 +406000 ekin = 9.53561319898212 | erot = 11.6383102531975 | epot = -71.6881981583051 | etot = -50.5142747061255 +407000 ekin = 9.3257730730707 | erot = 11.2990220058201 | epot = -71.1390697833488 | etot = -50.514274704458 +408000 ekin = 9.03640922282147 | erot = 10.8830678024735 | epot = -70.4337517260222 | etot = -50.5142747007272 +409000 ekin = 8.6897950835713 | erot = 10.4228266789006 | epot = -69.6268964554868 | etot = -50.5142746930149 +410000 ekin = 7.9560270357561 | erot = 9.9942714058413 | epot = -68.4645730787207 | etot = -50.5142746371233 +411000 ekin = 6.74655524928412 | erot = 10.0270618218395 | epot = -67.2878915397569 | etot = -50.5142744686333 +412000 ekin = 6.77788460765984 | erot = 10.2313763539054 | epot = -67.5235357279879 | etot = -50.5142747664226 +413000 ekin = 6.6178174617623 | erot = 9.9841680249977 | epot = -67.1162600910728 | etot = -50.5142746043128 +414000 ekin = 6.49546599326978 | erot = 9.85785035087921 | epot = -66.8675909469 | etot = -50.514274602751 +415000 ekin = 6.41727287248962 | erot = 9.86294960526658 | epot = -66.7944970800397 | etot = -50.5142746022835 +416000 ekin = 6.38652270868501 | erot = 10.0017061049924 | epot = -66.9025034163947 | etot = -50.5142746027173 +417000 ekin = 6.4020315533291 | erot = 10.2671783491741 | epot = -67.1834845063956 | etot = -50.5142746038924 +418000 ekin = 6.45904359291919 | erot = 10.6446827914202 | epot = -67.6180009900369 | etot = -50.5142746056975 +419000 ekin = 6.54999227104184 | erot = 11.1128009050149 | epot = -68.1770677840724 | etot = -50.5142746080157 +420000 ekin = 6.66500093978218 | erot = 11.6444776666554 | epot = -68.8237532173681 | etot = -50.5142746109305 +421000 ekin = 6.79216043872518 | erot = 12.2064235895659 | epot = -69.5128586425798 | etot = -50.5142746142886 +422000 ekin = 6.91773851390988 | erot = 12.7612933296174 | epot = -70.1933064611822 | etot = -50.5142746176549 +423000 ekin = 7.02685612353172 | erot = 13.2705085058938 | epot = -70.8116392505478 | etot = -50.5142746211223 +424000 ekin = 7.10547271092138 | erot = 13.6958822981288 | epot = -71.3156296329592 | etot = -50.5142746239091 +425000 ekin = 7.14257278346475 | erot = 14.0063216956977 | epot = -71.6631691046743 | etot = -50.5142746255119 +426000 ekin = 7.13247824794801 | erot = 14.1825679514318 | epot = -71.8293208250407 | etot = -50.5142746256608 +427000 ekin = 7.076097413192 | erot = 14.2196705903179 | epot = -71.8100426279541 | etot = -50.5142746244442 +428000 ekin = 6.98044576832941 | erot = 14.1262798064319 | epot = -71.6210001970106 | etot = -50.5142746222493 +429000 ekin = 6.85670921306948 | erot = 13.9212692789297 | epot = -71.2922531115699 | etot = -50.5142746195707 +430000 ekin = 6.7178161305864 | erot = 13.6292889155741 | epot = -70.8613796631915 | etot = -50.514274617031 +431000 ekin = 6.58365833328427 | erot = 13.2819652495181 | epot = -70.3798981921801 | etot = -50.5142746093777 +432000 ekin = 6.48411075968597 | erot = 12.9190083014664 | epot = -69.9173936698742 | etot = -50.5142746087219 +433000 ekin = 6.41960617892929 | erot = 12.553116717395 | epot = -69.4869975047765 | etot = -50.5142746084522 +434000 ekin = 6.38738760764971 | erot = 12.1915446818595 | epot = -69.093206897824 | etot = -50.5142746083148 +435000 ekin = 6.3844651806673 | erot = 11.8388548771074 | epot = -68.7375946666331 | etot = -50.5142746088584 +436000 ekin = 6.40158771779383 | erot = 11.4934615671522 | epot = -68.4093238934663 | etot = -50.5142746085202 +437000 ekin = 6.43433296980875 | erot = 11.1572008355164 | epot = -68.1058084136378 | etot = -50.5142746083126 +438000 ekin = 6.48252041810872 | erot = 10.8339757935673 | epot = -67.8307708198418 | etot = -50.5142746081658 +439000 ekin = 6.54577705115413 | erot = 10.5262474658429 | epot = -67.5862991252642 | etot = -50.5142746082672 +440000 ekin = 6.6234396857555 | erot = 10.2344360683686 | epot = -67.3721503625897 | etot = -50.5142746084656 +441000 ekin = 6.71455901735561 | erot = 9.95770655653919 | epot = -67.1865401826606 | etot = -50.5142746087658 +442000 ekin = 6.81814800218934 | erot = 9.69459000556867 | epot = -67.0270126167143 | etot = -50.5142746089563 +443000 ekin = 6.93320757980195 | erot = 9.44436660476061 | epot = -66.8918487936025 | etot = -50.51427460904 +444000 ekin = 7.05887283238584 | erot = 9.20812456867728 | epot = -66.7812720099878 | etot = -50.5142746089247 +445000 ekin = 7.19471792125887 | erot = 8.98907069041183 | epot = -66.698063220748 | etot = -50.5142746090773 +446000 ekin = 7.33895516701059 | erot = 8.79147036187154 | epot = -66.6447001377162 | etot = -50.5142746088341 +447000 ekin = 7.49037827521283 | erot = 8.62086071350145 | epot = -66.6255135972191 | etot = -50.5142746085048 +448000 ekin = 7.64865155423642 | erot = 8.4836257346772 | epot = -66.6465518970749 | etot = -50.5142746081613 +449000 ekin = 7.81370578733912 | erot = 8.38592298858194 | epot = -66.7139033838151 | etot = -50.514274607894 +450000 ekin = 7.98535597598701 | erot = 8.33253518713007 | epot = -66.8321657709338 | etot = -50.5142746078167 +451000 ekin = 8.16298003843024 | erot = 8.32609814440351 | epot = -67.0033527906324 | etot = -50.5142746077987 +452000 ekin = 8.34665075710426 | erot = 8.36815837883489 | epot = -67.2290837442314 | etot = -50.5142746082922 +453000 ekin = 8.53368486478645 | erot = 8.45559889747579 | epot = -67.5035583714215 | etot = -50.5142746091592 +454000 ekin = 8.71876659842333 | erot = 8.58149267465122 | epot = -67.814533883426 | etot = -50.5142746103514 +455000 ekin = 8.89458197889553 | erot = 8.73616891418618 | epot = -68.1450255048362 | etot = -50.5142746117544 +456000 ekin = 9.05263676519765 | erot = 8.90825623341302 | epot = -68.475167611793 | etot = -50.5142746131823 +457000 ekin = 9.18436468197176 | erot = 9.08589966844638 | epot = -68.7845389652096 | etot = -50.5142746147915 +458000 ekin = 9.2798708484486 | erot = 9.25693683992989 | epot = -69.0510823038951 | etot = -50.5142746155166 +459000 ekin = 9.33585675940989 | erot = 9.41397844081413 | epot = -69.2641098158563 | etot = -50.5142746156323 +460000 ekin = 9.35537570855096 | erot = 9.55424544253639 | epot = -69.4238957661582 | etot = -50.5142746150708 +461000 ekin = 9.34708447364844 | erot = 9.6795225048903 | epot = -69.5408815924374 | etot = -50.5142746138987 +462000 ekin = 9.32438028426558 | erot = 9.79582203166516 | epot = -69.6344769282607 | etot = -50.5142746123299 +463000 ekin = 9.3033894737706 | erot = 9.91209761434952 | epot = -69.7297616988178 | etot = -50.5142746106976 +464000 ekin = 9.30012223230643 | erot = 10.0380089094871 | epot = -69.8524057511913 | etot = -50.5142746093977 +465000 ekin = 9.32729383497944 | erot = 10.1814090069884 | epot = -70.0229774507351 | etot = -50.5142746087672 +466000 ekin = 9.39154918927656 | erot = 10.3458332464757 | epot = -70.2516570448627 | etot = -50.5142746091105 +467000 ekin = 9.49255088765059 | erot = 10.5268619331915 | epot = -70.5336874312256 | etot = -50.5142746103835 +468000 ekin = 9.62305221132604 | erot = 10.7128982306376 | epot = -70.8502250543247 | etot = -50.514274612361 +469000 ekin = 9.77069488359911 | erot = 10.8867837312668 | epot = -71.1717532295539 | etot = -50.514274614688 +470000 ekin = 9.92089819249867 | erot = 11.0285784794615 | epot = -71.4637512887705 | etot = -50.5142746168103 +471000 ekin = 10.059517639692 | erot = 11.1206306063014 | epot = -71.69442286431 | etot = -50.5142746183166 +472000 ekin = 10.1754768606278 | erot = 11.1514441165871 | epot = -71.8411955961184 | etot = -50.5142746189035 +473000 ekin = 10.2623030554246 | erot = 11.1187283838379 | epot = -71.8953060577122 | etot = -50.5142746184498 +474000 ekin = 10.3185312147273 | erot = 11.030545588013 | epot = -71.8633514198336 | etot = -50.5142746170933 +475000 ekin = 10.3471799199331 | erot = 10.9051616574204 | epot = -71.7666161922609 | etot = -50.5142746149074 +476000 ekin = 10.35464021048 | erot = 10.7694904205599 | epot = -71.638405243284 | etot = -50.5142746122441 +477000 ekin = 10.3491629826044 | erot = 10.6559910559233 | epot = -71.5194286481754 | etot = -50.5142746096478 +478000 ekin = 10.3379217815357 | erot = 10.5983211038034 | epot = -71.4505174924988 | etot = -50.5142746071597 +479000 ekin = 10.328028374716 | erot = 10.6277262155424 | epot = -71.4700291953201 | etot = -50.5142746050617 +480000 ekin = 10.3254996650184 | erot = 10.7702201780147 | epot = -71.6099944467265 | etot = -50.5142746036933 +481000 ekin = 10.333689005966 | erot = 11.0433446243404 | epot = -71.8913082335951 | etot = -50.5142746032886 +482000 ekin = 10.3524366677779 | erot = 11.45405903145 | epot = -72.3207703030967 | etot = -50.5142746038687 +483000 ekin = 10.3781084074647 | erot = 11.9979341330494 | epot = -72.8903171458662 | etot = -50.514274605352 +484000 ekin = 10.4042611097819 | erot = 12.6596244417091 | epot = -73.578160159112 | etot = -50.514274607621 +485000 ekin = 10.4221302631885 | erot = 13.4142029090613 | epot = -74.3506077826684 | etot = -50.5142746104186 +486000 ekin = 10.4218511022266 | erot = 14.2297763891948 | epot = -75.1659021048472 | etot = -50.5142746134258 +487000 ekin = 10.3939548024949 | erot = 15.0707615261073 | epot = -75.9789909449393 | etot = -50.5142746163371 +488000 ekin = 10.3307490466764 | erot = 15.901069958466 | epot = -76.7460936240819 | etot = -50.5142746189395 +489000 ekin = 10.2272110328914 | erot = 16.6865229089584 | epot = -77.4280085629864 | etot = -50.5142746211366 +490000 ekin = 10.0812183872238 | erot = 17.3962474873107 | epot = -77.9917404974535 | etot = -50.5142746229189 +491000 ekin = 9.89313188202311 | erot = 18.0033313049116 | epot = -78.4107378112024 | etot = -50.5142746242677 +492000 ekin = 9.66548546857302 | erot = 18.4853389017258 | epot = -78.6650989961058 | etot = -50.514274625807 +493000 ekin = 9.40191070802767 | erot = 18.8229573786077 | epot = -78.7391427127531 | etot = -50.5142746261177 +494000 ekin = 9.10904774193782 | erot = 19.0062114320175 | epot = -78.6295337996336 | etot = -50.5142746256783 +495000 ekin = 8.79635273334391 | erot = 19.0345219994416 | epot = -78.3451493572118 | etot = -50.5142746244262 +496000 ekin = 8.47610073024254 | erot = 18.9167105341889 | epot = -77.9070858868661 | etot = -50.5142746224347 +497000 ekin = 8.16317181357977 | erot = 18.6700073960851 | epot = -77.3474538295998 | etot = -50.5142746199349 +498000 ekin = 7.87402966206604 | erot = 18.3175884261423 | epot = -76.7058927054906 | etot = -50.5142746172822 +499000 ekin = 7.62493759930534 | erot = 17.8851866271409 | epot = -76.0243988413068 | etot = -50.5142746148606 +500000 ekin = 7.42972946262078 | erot = 17.3977376248812 | epot = -75.3417417004763 | etot = -50.5142746129743 +501000 ekin = 7.2976728684442 | erot = 16.8770499285062 | epot = -74.6889974087211 | etot = -50.5142746117707 +502000 ekin = 7.23199528875678 | erot = 16.3411235838348 | epot = -74.0873934837985 | etot = -50.5142746112069 +503000 ekin = 7.22945681989707 | erot = 15.8051011256099 | epot = -73.5488325566038 | etot = -50.5142746110968 +504000 ekin = 7.28103351461574 | erot = 15.2831943565127 | epot = -73.0785024823216 | etot = -50.5142746111932 +505000 ekin = 7.37347669950783 | erot = 14.7905903684621 | epot = -72.6783416792526 | etot = -50.5142746112827 +506000 ekin = 7.49135174828742 | erot = 14.3444485240495 | epot = -72.3500748835764 | etot = -50.5142746112395 +507000 ekin = 7.61914293605602 | erot = 13.9635506159284 | epot = -72.0969681630287 | etot = -50.5142746110443 +508000 ekin = 7.74307878352891 | erot = 13.6666853268212 | epot = -71.924038721116 | etot = -50.5142746107658 +509000 ekin = 7.85243073756124 | erot = 13.4701783614719 | epot = -71.8368837095767 | etot = -50.5142746105435 +510000 ekin = 7.94014182641694 | erot = 13.38510989459 | epot = -71.8395263315565 | etot = -50.5142746105496 +511000 ekin = 8.00274035613683 | erot = 13.4146098330176 | epot = -71.9316248001467 | etot = -50.5142746109922 +512000 ekin = 8.0395947820636 | erot = 13.5514344934683 | epot = -72.1053038876095 | etot = -50.5142746120776 +513000 ekin = 8.05166756793522 | erot = 13.7761589059122 | epot = -72.3421010878252 | etot = -50.5142746139778 +514000 ekin = 8.0400743803172 | erot = 14.0563762259778 | epot = -72.6107252230327 | etot = -50.5142746167377 +515000 ekin = 8.00493220655174 | erot = 14.3476352397211 | epot = -72.866842066446 | etot = -50.5142746201732 +516000 ekin = 7.94508318889731 | erot = 14.5970448958803 | epot = -73.0564027085642 | etot = -50.5142746237866 +517000 ekin = 7.85912630285855 | erot = 14.7501438289086 | epot = -73.1235447585609 | etot = -50.5142746267938 +518000 ekin = 7.74765591028633 | erot = 14.760474814026 | epot = -73.022405352644 | etot = -50.5142746283317 +519000 ekin = 7.61585879292523 | erot = 14.5996265098283 | epot = -72.7297599305418 | etot = -50.5142746277883 +520000 ekin = 7.47514959112457 | erot = 14.2643892941964 | epot = -72.2538135104003 | etot = -50.5142746250794 +521000 ekin = 7.3427858954402 | erot = 13.7782408540964 | epot = -71.6353013702353 | etot = -50.5142746206986 +522000 ekin = 7.23932626200134 | erot = 13.1865968867284 | epot = -70.9401977642482 | etot = -50.5142746155185 +523000 ekin = 7.18476026651873 | erot = 12.5477212482208 | epot = -70.2467561252324 | etot = -50.5142746104929 +524000 ekin = 7.19456043548625 | erot = 11.9223659335378 | epot = -69.6312009754275 | etot = -50.5142746064035 +525000 ekin = 7.27670076771941 | erot = 11.3647768162878 | epot = -69.1557521877451 | etot = -50.514274603738 +526000 ekin = 7.43017656898807 | erot = 10.9164455514449 | epot = -68.8608967231243 | etot = -50.5142746026914 +527000 ekin = 7.64507873197692 | erot = 10.6028306905154 | epot = -68.7621840256994 | etot = -50.5142746032071 +528000 ekin = 7.90396874722393 | erot = 10.4326201984507 | epot = -68.8508635507307 | etot = -50.5142746050561 +529000 ekin = 8.18416633901187 | erot = 10.3989120257516 | epot = -69.097352972662 | etot = -50.5142746078985 +530000 ekin = 8.46054142242976 | erot = 10.4817412712184 | epot = -69.4565573049844 | etot = -50.5142746113362 +531000 ekin = 8.70843705753887 | erot = 10.6515092337666 | epot = -69.87422090625 | etot = -50.5142746149445 +532000 ekin = 8.90640402471323 | erot = 10.8729770963941 | epot = -70.2936557394195 | etot = -50.5142746183122 +533000 ekin = 9.03848560922355 | erot = 11.1095342988321 | epot = -70.6622945291218 | etot = -50.5142746210661 +534000 ekin = 9.09585660968956 | erot = 11.3274354311 | epot = -70.9375666636919 | etot = -50.5142746229024 +535000 ekin = 9.07769161962254 | erot = 11.4996353903455 | epot = -71.0916016335857 | etot = -50.5142746236176 +536000 ekin = 8.99119538622236 | erot = 11.6087805008578 | epot = -71.1142505102249 | etot = -50.5142746231448 +537000 ekin = 8.85079437598883 | erot = 11.6489142180418 | epot = -71.0139832156003 | etot = -50.5142746215697 +538000 ekin = 8.6765582659912 | erot = 11.6255793580404 | epot = -70.8164122431588 | etot = -50.5142746191272 +539000 ekin = 8.49200375593156 | erot = 11.5542615596027 | epot = -70.5605399317068 | etot = -50.5142746161725 +540000 ekin = 8.32364695432576 | erot = 11.4574951670977 | epot = -70.2954167347966 | etot = -50.5142746133732 +541000 ekin = 8.19487884820117 | erot = 11.3596088272196 | epot = -70.0687622863157 | etot = -50.5142746108949 +542000 ekin = 8.12161273120138 | erot = 11.284042058361 | epot = -69.9199293984864 | etot = -50.5142746089241 +543000 ekin = 8.11471609566151 | erot = 11.2514192637678 | epot = -69.8804099670844 | etot = -50.5142746076551 +544000 ekin = 8.17908931154173 | erot = 11.2773707849429 | epot = -69.9707347036591 | etot = -50.5142746071745 +545000 ekin = 8.31344770508808 | erot = 11.371353556837 | epot = -70.1990758694012 | etot = -50.5142746074761 +546000 ekin = 8.51069467196935 | erot = 11.536314361344 | epot = -70.5612836418126 | etot = -50.5142746084993 +547000 ekin = 8.75865223740997 | erot = 11.7688547419138 | epot = -71.0417815894989 | etot = -50.5142746101751 +548000 ekin = 9.04082699801815 | erot = 12.0581718441636 | epot = -71.6132734556815 | etot = -50.5142746134998 +549000 ekin = 9.33624649604673 | erot = 12.3823696051851 | epot = -72.2328907177602 | etot = -50.5142746165284 +550000 ekin = 9.62129146820136 | erot = 12.7185500786339 | epot = -72.8541161665021 | etot = -50.5142746196668 +551000 ekin = 9.872682667968 | erot = 13.0427912748003 | epot = -73.4297485652762 | etot = -50.5142746225079 +552000 ekin = 10.0704190088322 | erot = 13.3329151351367 | epot = -73.9176087685553 | etot = -50.5142746245863 +553000 ekin = 10.2009056939477 | erot = 13.5725638576694 | epot = -74.2877441770286 | etot = -50.5142746254115 +554000 ekin = 10.2593644362471 | erot = 13.7535104687497 | epot = -74.527149530021 | etot = -50.5142746250242 +555000 ekin = 10.2514586318862 | erot = 13.8763528095856 | epot = -74.6420860648936 | etot = -50.5142746234218 +556000 ekin = 10.1921106932784 | erot = 13.9500978834529 | epot = -74.6564831978669 | etot = -50.5142746211355 +557000 ekin = 10.1015652266976 | erot = 13.9882161029595 | epot = -74.6040559485553 | etot = -50.5142746188982 +558000 ekin = 9.99991303230764 | erot = 14.0034286779365 | epot = -74.5176163276167 | etot = -50.5142746173726 +559000 ekin = 9.90202983163942 | erot = 14.0033678523424 | epot = -74.4196722999438 | etot = -50.514274615962 +560000 ekin = 9.81686282987798 | erot = 13.9898208823782 | epot = -74.3209583291104 | etot = -50.5142746168542 +561000 ekin = 9.74012209781474 | erot = 13.9575380153649 | epot = -74.2119347312768 | etot = -50.5142746180971 +562000 ekin = 9.66202249063476 | erot = 13.8995402247441 | epot = -74.0758373341239 | etot = -50.514274618745 +563000 ekin = 9.57125126717889 | erot = 13.8130745957407 | epot = -73.8986004819793 | etot = -50.5142746190596 +564000 ekin = 9.45733143835268 | erot = 13.7046546957124 | epot = -73.6762607521036 | etot = -50.5142746180385 +565000 ekin = 9.31598070796451 | erot = 13.591118833445 | epot = -73.421374157864 | etot = -50.5142746164544 +566000 ekin = 9.14991861300553 | erot = 13.4939773072373 | epot = -73.1581705345424 | etot = -50.5142746142996 +567000 ekin = 8.96796855716502 | erot = 13.4373000591231 | epot = -72.9195432283204 | etot = -50.5142746120323 +568000 ekin = 8.78295943729665 | erot = 13.4429949208159 | epot = -72.7402289682422 | etot = -50.5142746101297 +569000 ekin = 8.60911084021965 | erot = 13.5261109883945 | epot = -72.6494964376006 | etot = -50.5142746089865 +570000 ekin = 8.45962137975433 | erot = 13.6911409172601 | epot = -72.665036905859 | etot = -50.5142746088445 +571000 ekin = 8.34502164174357 | erot = 13.9298996508014 | epot = -72.789195902299 | etot = -50.5142746097539 +572000 ekin = 8.27150053294362 | erot = 14.2179224508629 | epot = -73.0036975966792 | etot = -50.5142746128727 +573000 ekin = 8.24027906060908 | erot = 14.5163717589229 | epot = -73.2709254351699 | etot = -50.5142746156379 +574000 ekin = 8.25076229273446 | erot = 14.782699035351 | epot = -73.5477359471055 | etot = -50.5142746190201 +575000 ekin = 8.30023045844111 | erot = 14.9695304974658 | epot = -73.7840355778018 | etot = -50.5142746218949 +576000 ekin = 8.38430166796684 | erot = 15.0355677896521 | epot = -73.9341440816966 | etot = -50.5142746240777 +577000 ekin = 8.49786330870201 | erot = 14.9506840672774 | epot = -73.9628220011276 | etot = -50.5142746251482 +578000 ekin = 8.63531193623021 | erot = 14.7010752683058 | epot = -73.8506618297048 | etot = -50.5142746251689 +579000 ekin = 8.79067648366292 | erot = 14.2898408975377 | epot = -73.5947920053057 | etot = -50.514274624105 +580000 ekin = 8.95769742194029 | erot = 13.7363251615615 | epot = -73.208297205719 | etot = -50.5142746222172 +581000 ekin = 9.1299788706959 | erot = 13.0726035153202 | epot = -72.7168570058733 | etot = -50.5142746198572 +582000 ekin = 9.30131608654131 | erot = 12.3381170470857 | epot = -72.1537077509712 | etot = -50.5142746173442 +583000 ekin = 9.46624938716497 | erot = 11.5746138603005 | epot = -71.5551378622994 | etot = -50.514274614834 +584000 ekin = 9.620724933419 | erot = 10.8222363956645 | epot = -70.9572359416422 | etot = -50.5142746125587 +585000 ekin = 9.76261487022584 | erot = 10.1164678304297 | epot = -70.393357311154 | etot = -50.5142746104985 +586000 ekin = 9.89186342300852 | erot = 9.4875195803207 | epot = -69.89365761204 | etot = -50.5142746087107 +587000 ekin = 10.0101586280187 | erot = 8.95961455311989 | epot = -69.4840477884309 | etot = -50.5142746072923 +588000 ekin = 10.1201887301505 | erot = 8.5501573641065 | epot = -69.1846207006391 | etot = -50.514274606382 +589000 ekin = 10.2246599088895 | erot = 8.26863816358287 | epot = -69.0075726786038 | etot = -50.5142746061314 +590000 ekin = 10.3253143810889 | erot = 8.11543769025879 | epot = -68.9550266779995 | etot = -50.5142746066518 +591000 ekin = 10.4222032216477 | erot = 8.0809981167352 | epot = -69.0174759463425 | etot = -50.5142746079596 +592000 ekin = 10.5134337128702 | erot = 8.1459936001908 | epot = -69.173701922983 | etot = -50.514274609922 +593000 ekin = 10.5955057544217 | erot = 8.28306481727704 | epot = -69.3928451839472 | etot = -50.5142746122484 +594000 ekin = 10.6641662354614 | erot = 8.46027689183062 | epot = -69.638717741839 | etot = -50.5142746145469 +595000 ekin = 10.7154927999608 | erot = 8.64578434327109 | epot = -69.875551759666 | etot = -50.5142746164341 +596000 ekin = 10.7467872731018 | erot = 8.81255786151828 | epot = -70.0736197522735 | etot = -50.5142746176534 +597000 ekin = 10.7569302189981 | erot = 8.94187861301369 | epot = -70.2130834501401 | etot = -50.5142746181283 +598000 ekin = 10.7466010847312 | erot = 9.02533979254752 | epot = -70.2862154950865 | etot = -50.5142746178078 +599000 ekin = 10.7182887695106 | erot = 9.0650790688296 | epot = -70.2976424556367 | etot = -50.5142746172965 +600000 ekin = 10.6720485189359 | erot = 9.06844804975761 | epot = -70.254771185229 | etot = -50.5142746165355 +601000 ekin = 10.6072956941404 | erot = 9.04742526344434 | epot = -70.1689955732264 | etot = -50.5142746156417 +602000 ekin = 10.5233178202805 | erot = 9.01691281405176 | epot = -70.0545052489855 | etot = -50.5142746146532 +603000 ekin = 10.4199668052602 | erot = 8.99335643430934 | epot = -69.9275978531261 | etot = -50.5142746135566 +604000 ekin = 10.2985732111422 | erot = 8.99387297245081 | epot = -69.8067207959167 | etot = -50.5142746123237 +605000 ekin = 10.1627605691522 | erot = 9.03562879917117 | epot = -69.7126639792975 | etot = -50.5142746109742 +606000 ekin = 10.0187545713199 | erot = 9.13500980541805 | epot = -69.6680389863702 | etot = -50.5142746096322 +607000 ekin = 9.87474119401897 | erot = 9.30612986570829 | epot = -69.6951456683218 | etot = -50.5142746085945 +608000 ekin = 9.73894032960022 | erot = 9.5581574531413 | epot = -69.8113723910812 | etot = -50.5142746083396 +609000 ekin = 9.61645131102769 | erot = 9.89160474270308 | epot = -70.0223306630962 | etot = -50.5142746093654 +610000 ekin = 9.50561717815242 | erot = 10.2946039754773 | epot = -70.3144957656318 | etot = -50.514274612002 +611000 ekin = 9.39548197887694 | erot = 10.7408569963072 | epot = -70.6506135912498 | etot = -50.5142746160656 +612000 ekin = 9.26629251209254 | erot = 11.1926279417912 | epot = -70.9731950744566 | etot = -50.5142746205729 +613000 ekin = 9.09415007005248 | erot = 11.6098990354819 | epot = -71.2183237296768 | etot = -50.5142746241424 +614000 ekin = 8.85874044725752 | erot = 11.9622145365274 | epot = -71.3352296093783 | etot = -50.5142746255934 +615000 ekin = 8.55082001882929 | erot = 12.2382561372936 | epot = -71.3033507806285 | etot = -50.5142746245056 +616000 ekin = 8.175888360977 | erot = 12.4480456866369 | epot = -71.1382086691017 | etot = -50.5142746214878 +617000 ekin = 7.75281434573713 | erot = 12.6167254402941 | epot = -70.8838144036964 | etot = -50.5142746176652 +618000 ekin = 7.30914473381905 | erot = 12.7738647630868 | epot = -70.5972841110086 | etot = -50.5142746141028 +619000 ekin = 6.87603930023189 | erot = 12.9445772325018 | epot = -70.3348911438367 | etot = -50.514274611103 +620000 ekin = 6.48430188506113 | erot = 13.1463744536997 | epot = -70.1449509480766 | etot = -50.5142746093158 +621000 ekin = 6.15889859796186 | erot = 13.3879128346421 | epot = -70.0610860402284 | etot = -50.5142746076245 +622000 ekin = 5.92489751014034 | erot = 13.6734353594457 | epot = -70.1126074758758 | etot = -50.5142746062898 +623000 ekin = 5.80503635923321 | erot = 14.0046748008201 | epot = -70.323985765443 | etot = -50.5142746053896 +624000 ekin = 5.81685163240234 | erot = 14.3809730724792 | epot = -70.7120993101167 | etot = -50.5142746052353 +625000 ekin = 5.96964537891364 | erot = 14.7975194183877 | epot = -71.2814394036077 | etot = -50.5142746063063 +626000 ekin = 6.26099435192758 | erot = 15.2418617554262 | epot = -72.017130716455 | etot = -50.5142746091012 +627000 ekin = 6.67389324015709 | erot = 15.6898147640095 | epot = -72.8779826180747 | etot = -50.5142746139082 +628000 ekin = 7.17593798618658 | erot = 16.1028362030306 | epot = -73.7930488096841 | etot = -50.5142746204669 +629000 ekin = 7.72199923897968 | erot = 16.4299438960646 | epot = -74.6662177627284 | etot = -50.5142746276842 +630000 ekin = 8.26123500939383 | erot = 16.6169483753651 | epot = -75.3924580185056 | etot = -50.5142746337466 +631000 ekin = 8.74754840904575 | erot = 16.6224867205867 | epot = -75.8843097661632 | etot = -50.5142746365308 +632000 ekin = 9.15004592006942 | erot = 16.4358276586453 | epot = -76.1001482137943 | etot = -50.5142746350796 +633000 ekin = 9.45937080857058 | erot = 16.0853639088586 | epot = -76.0590093468388 | etot = -50.5142746294097 +634000 ekin = 9.68568488527849 | erot = 15.6315739486894 | epot = -75.8315334570553 | etot = -50.5142746230874 +635000 ekin = 9.84580171434891 | erot = 15.1444204261244 | epot = -75.504496757784 | etot = -50.5142746173107 +636000 ekin = 9.95723404954417 | erot = 14.686080241921 | epot = -75.1575889048362 | etot = -50.5142746133711 +637000 ekin = 10.032321596039 | erot = 14.2991433337626 | epot = -74.8457395413004 | etot = -50.5142746114988 +638000 ekin = 10.0765624311206 | erot = 14.0046093482885 | epot = -74.5954463906111 | etot = -50.514274611202 +639000 ekin = 10.0902754260143 | erot = 13.8068600166826 | epot = -74.4114100544216 | etot = -50.5142746117247 +640000 ekin = 10.0716366459578 | erot = 13.7011883664002 | epot = -74.2870996247358 | etot = -50.5142746123778 +641000 ekin = 10.019579855139 | erot = 13.6807153270372 | epot = -74.2145697948658 | etot = -50.5142746126896 +642000 ekin = 9.93575791766622 | erot = 13.7411722988916 | epot = -74.1912048290125 | etot = -50.5142746124548 +643000 ekin = 9.82526205665779 | erot = 13.8830736873786 | epot = -74.222610355769 | etot = -50.5142746117327 +644000 ekin = 9.69609523856024 | erot = 14.1112875028235 | epot = -74.3216573521974 | etot = -50.5142746108136 +645000 ekin = 9.55761878272972 | erot = 14.4322553940752 | epot = -74.5041487878821 | etot = -50.5142746110772 +646000 ekin = 9.41485510301491 | erot = 14.8475477985045 | epot = -74.7766775131998 | etot = -50.5142746116804 +647000 ekin = 9.26709768133843 | erot = 15.3482149653111 | epot = -75.1295872604127 | etot = -50.5142746137632 +648000 ekin = 9.10972978583349 | erot = 15.9109204654798 | epot = -75.5349248689429 | etot = -50.5142746176296 +649000 ekin = 8.9315814550155 | erot = 16.4937182185534 | epot = -75.9395742966243 | etot = -50.5142746230554 +650000 ekin = 8.71657057994074 | erot = 17.0382000588728 | epot = -76.2690452678485 | etot = -50.514274629035 +651000 ekin = 8.44844851105175 | erot = 17.4793597703207 | epot = -76.4420829152532 | etot = -50.5142746338807 +652000 ekin = 8.11815479201172 | erot = 17.7619704870292 | epot = -76.3943999148916 | etot = -50.5142746358506 +653000 ekin = 7.73114435531218 | erot = 17.8572650854382 | epot = -76.1026840748118 | etot = -50.5142746340614 +654000 ekin = 7.31085494736458 | erot = 17.7714907197143 | epot = -75.5966202960844 | etot = -50.5142746290055 +655000 ekin = 6.89588215317778 | erot = 17.5418067096489 | epot = -74.9519634850893 | etot = -50.5142746222626 +656000 ekin = 6.53171010736376 | erot = 17.2224717011596 | epot = -74.2684564242042 | etot = -50.5142746156808 +657000 ekin = 6.26041816780914 | erot = 16.8689320360005 | epot = -73.6436248144601 | etot = -50.5142746106505 +658000 ekin = 6.11203041445794 | erot = 16.5262126841704 | epot = -73.1525177064601 | etot = -50.5142746078318 +659000 ekin = 6.09972540608881 | erot = 16.2236488550554 | epot = -72.837648868387 | etot = -50.5142746072428 +660000 ekin = 6.21938199681726 | erot = 15.9744887375992 | epot = -72.7081453429256 | etot = -50.5142746085091 +661000 ekin = 6.45261911218506 | erot = 15.77778773976 | epot = -72.7446814630817 | etot = -50.5142746111367 +662000 ekin = 6.7716882555292 | erot = 15.6204850253194 | epot = -72.9064478955629 | etot = -50.5142746147143 +663000 ekin = 7.14435819257924 | erot = 15.478593564038 | epot = -73.1372263756168 | etot = -50.5142746189996 +664000 ekin = 7.53740317176545 | erot = 15.3176852477738 | epot = -73.3693630433733 | etot = -50.514274623834 +665000 ekin = 7.91836523030113 | erot = 15.0942309146789 | epot = -73.5268707738693 | etot = -50.5142746288894 +666000 ekin = 8.25643498248337 | erot = 14.7603215859625 | epot = -73.5310312018662 | etot = -50.5142746334204 +667000 ekin = 8.52385764879543 | erot = 14.2736320138678 | epot = -73.3117642989291 | etot = -50.514274636266 +668000 ekin = 8.69866667318591 | erot = 13.6113201081884 | epot = -72.8242614176828 | etot = -50.5142746363085 +669000 ekin = 8.76804368922024 | erot = 12.7822873051114 | epot = -72.0646056274626 | etot = -50.514274633131 +670000 ekin = 8.7304670675869 | erot = 11.8307777757836 | epot = -71.0755194707241 | etot = -50.5142746273536 +671000 ekin = 8.59524186891959 | erot = 10.8283334362616 | epot = -69.937849925502 | etot = -50.5142746203208 +672000 ekin = 8.37965784966922 | erot = 9.85799241690562 | epot = -68.7519248799939 | etot = -50.514274613419 +673000 ekin = 8.10529771609926 | erot = 8.99841190536189 | epot = -67.6179842290081 | etot = -50.5142746075469 +674000 ekin = 7.79494136354955 | erot = 8.31372525729646 | epot = -66.6229412238675 | etot = -50.5142746030214 +675000 ekin = 7.47060107992419 | erot = 7.85026883552638 | epot = -65.8351445152254 | etot = -50.5142745997748 +676000 ekin = 7.15246577753135 | erot = 7.63789726267775 | epot = -65.3046376378203 | etot = -50.5142745976112 +677000 ekin = 6.85830618373252 | erot = 7.69282168188937 | epot = -65.0654024620073 | etot = -50.5142745963854 +678000 ekin = 6.60298755764553 | erot = 8.01973470913126 | epot = -65.1369968628789 | etot = -50.5142745961021 +679000 ekin = 6.39787215419565 | erot = 8.61208125101092 | epot = -65.5242280021487 | etot = -50.5142745969422 +680000 ekin = 6.24998134211449 | erot = 9.45011609593844 | epot = -66.2143720373123 | etot = -50.5142745992594 +681000 ekin = 6.16088982576969 | erot = 10.4969757469541 | epot = -67.1721401762214 | etot = -50.5142746034977 +682000 ekin = 6.12554393409797 | erot = 11.6937893201654 | epot = -68.3336078642541 | etot = -50.5142746099908 +683000 ekin = 6.13157359399397 | erot = 12.9561475536548 | epot = -69.6019957662809 | etot = -50.5142746186321 +684000 ekin = 6.16005916027991 | erot = 14.175693163925 | epot = -70.850026952704 | etot = -50.5142746284992 +685000 ekin = 6.18869173790237 | erot = 15.2307522948807 | epot = -71.9337186705506 | etot = -50.5142746377675 +686000 ekin = 6.19732878112365 | erot = 16.0068645008489 | epot = -72.7184679261729 | etot = -50.5142746442004 +687000 ekin = 6.17424105603543 | erot = 16.4218469242485 | epot = -73.1103626264231 | etot = -50.5142746461392 +688000 ekin = 6.12017794217911 | erot = 16.4448717751939 | epot = -73.0793243607007 | etot = -50.5142746433277 +689000 ekin = 6.04820168736814 | erot = 16.1005193404669 | epot = -72.6629956647682 | etot = -50.5142746369331 +690000 ekin = 5.97970220537207 | erot = 15.4569806258048 | epot = -71.9509574599937 | etot = -50.5142746288169 +691000 ekin = 5.93893719623427 | erot = 14.605710167059 | epot = -71.0589219839816 | etot = -50.5142746206883 +692000 ekin = 5.94838842833223 | erot = 13.6417068401402 | epot = -70.1043698821412 | etot = -50.5142746136687 +693000 ekin = 6.02589021177394 | erot = 12.6498891238861 | epot = -69.1900539439278 | etot = -50.5142746082677 +694000 ekin = 6.18463455178242 | erot = 11.7000608799123 | epot = -68.3989700350278 | etot = -50.514274603333 +695000 ekin = 6.43478432357831 | erot = 10.8472395602001 | epot = -67.7962984856164 | etot = -50.5142746018379 +696000 ekin = 6.77322428396141 | erot = 10.1195064532741 | epot = -67.407005338705 | etot = -50.5142746014695 +697000 ekin = 7.19141853636714 | erot = 9.53118158812937 | epot = -67.2368747264792 | etot = -50.5142746019827 +698000 ekin = 7.67702076756888 | erot = 9.08693839129866 | epot = -67.2782337620764 | etot = -50.5142746032089 +699000 ekin = 8.21429897541807 | erot = 8.78382057635582 | epot = -67.5123941568513 | etot = -50.5142746050775 +700000 ekin = 8.78422716550662 | erot = 8.61224580901528 | epot = -67.9107475821421 | etot = -50.5142746076202 +701000 ekin = 9.36423931739826 | erot = 8.55605856482336 | epot = -68.4345724931355 | etot = -50.5142746109139 +702000 ekin = 9.92792016717606 | erot = 8.59213538140994 | epot = -69.0343301635391 | etot = -50.5142746149531 +703000 ekin = 10.4452984142782 | erot = 8.6906406474678 | epot = -69.650213681228 | etot = -50.5142746194821 +704000 ekin = 10.8846377327658 | erot = 8.817413241637 | epot = -70.21632559826 | etot = -50.5142746238572 +705000 ekin = 11.2162913879666 | erot = 8.93948813625224 | epot = -70.6700541513435 | etot = -50.5142746271246 +706000 ekin = 11.4181455722527 | erot = 9.03309347105436 | epot = -70.9655136716544 | etot = -50.5142746283474 +707000 ekin = 11.4809106569868 | erot = 9.09134201921814 | epot = -71.0865273032402 | etot = -50.5142746270353 +708000 ekin = 11.4068982891467 | erot = 9.12200528524663 | epot = -71.0431782001055 | etot = -50.5142746257122 +709000 ekin = 11.207263291306 | erot = 9.14465465268529 | epot = -70.8661925651784 | etot = -50.5142746211871 +710000 ekin = 10.9083907026581 | erot = 9.19859957941885 | epot = -70.6212648981726 | etot = -50.5142746160956 +711000 ekin = 10.5423746431423 | erot = 9.32614430674808 | epot = -70.3827935613037 | etot = -50.5142746114133 +712000 ekin = 10.1417786131218 | erot = 9.56360239367812 | epot = -70.219655614563 | etot = -50.5142746077631 +713000 ekin = 9.73608713715417 | erot = 9.9356699105274 | epot = -70.1860316530563 | etot = -50.5142746053747 +714000 ekin = 9.35027943777136 | erot = 10.4538184610608 | epot = -70.3183725027277 | etot = -50.5142746038955 +715000 ekin = 9.00463394824735 | erot = 11.1175080875288 | epot = -70.6364166398391 | etot = -50.5142746040629 +716000 ekin = 8.71247739172323 | erot = 11.911722071649 | epot = -71.1384740684836 | etot = -50.5142746051113 +717000 ekin = 8.4828781642453 | erot = 12.8114967087923 | epot = -71.8086494800388 | etot = -50.5142746070012 +718000 ekin = 8.32091760999845 | erot = 13.7831462397263 | epot = -72.6183384595501 | etot = -50.5142746098254 +719000 ekin = 8.22703613377359 | erot = 14.7838475725411 | epot = -73.5251583200662 | etot = -50.5142746137515 +720000 ekin = 8.19603263798189 | erot = 15.7606669338407 | epot = -74.4709741906888 | etot = -50.5142746188662 +721000 ekin = 8.21637629750214 | erot = 16.6505227360403 | epot = -75.3811736584968 | etot = -50.5142746249544 +722000 ekin = 8.27076325259746 | erot = 17.383196988941 | epot = -76.1682348731295 | etot = -50.5142746315911 +723000 ekin = 8.33599195242273 | erot = 17.8873102966714 | epot = -76.7375768863803 | etot = -50.5142746372861 +724000 ekin = 8.38930978731971 | erot = 18.1039114578533 | epot = -77.007495885722 | etot = -50.514274640549 +725000 ekin = 8.4165186400972 | erot = 18.0027385421349 | epot = -76.9335318225387 | etot = -50.5142746403066 +726000 ekin = 8.4154002233162 | erot = 17.5920134841814 | epot = -76.5216883438779 | etot = -50.5142746363804 +727000 ekin = 8.39679923845161 | erot = 16.919929722969 | epot = -75.8310035909851 | etot = -50.5142746295646 +728000 ekin = 8.3818942002517 | erot = 16.0663700673365 | epot = -74.9625388888454 | etot = -50.5142746212571 +729000 ekin = 8.39699694309242 | erot = 15.1283483167792 | epot = -74.0396198728095 | etot = -50.5142746129379 +730000 ekin = 8.4678254383047 | erot = 14.2043901533638 | epot = -73.1864901974477 | etot = -50.5142746057792 +731000 ekin = 8.61470307568928 | erot = 13.3819120233155 | epot = -72.5108896995107 | etot = -50.514274600506 +732000 ekin = 8.84928637443201 | erot = 12.729288023069 | epot = -72.0928489949349 | etot = -50.5142745974338 +733000 ekin = 9.17280766709871 | erot = 12.2923211340428 | epot = -71.9794033977278 | etot = -50.5142745965863 +734000 ekin = 9.57560598369746 | erot = 12.0938942191352 | epot = -72.1837748006325 | etot = -50.5142745977998 +735000 ekin = 10.0377642396558 | erot = 12.1355113635674 | epot = -72.6875502040207 | etot = -50.5142746007974 +736000 ekin = 10.5307595726908 | erot = 12.3998369838626 | epot = -73.4448711617588 | etot = -50.5142746052054 +737000 ekin = 11.020091415724 | erot = 12.8538466733546 | epot = -74.3882126996429 | etot = -50.5142746105643 +738000 ekin = 11.4687808905075 | erot = 13.4525508837993 | epot = -75.4356063906421 | etot = -50.5142746163353 +739000 ekin = 11.8414287125964 | erot = 14.1433222477384 | epot = -76.4990255822779 | etot = -50.5142746219431 +740000 ekin = 12.1082656211499 | erot = 14.8707107510516 | epot = -77.493250999042 | etot = -50.5142746268405 +741000 ekin = 12.2485032334025 | erot = 15.5814643741637 | epot = -78.3442422381294 | etot = -50.5142746305632 +742000 ekin = 12.2524265472084 | erot = 16.2294231022069 | epot = -78.9961242821844 | etot = -50.5142746327691 +743000 ekin = 12.121994994847 | erot = 16.7799163002756 | epot = -79.4161859283928 | etot = -50.5142746332702 +744000 ekin = 11.8700125681399 | erot = 17.2130632823787 | epot = -79.5973504826108 | etot = -50.5142746320923 +745000 ekin = 11.5180572441709 | erot = 17.5250437155193 | epot = -79.5573755892154 | etot = -50.5142746295252 +746000 ekin = 11.0934236280252 | erot = 17.7264433609928 | epot = -79.3341416151374 | etot = -50.5142746261194 +747000 ekin = 10.625484028931 | erot = 17.8375345490455 | epot = -78.9772932005533 | etot = -50.5142746225768 +748000 ekin = 10.1420744189115 | erot = 17.8814972667899 | epot = -78.5378463052758 | etot = -50.5142746195745 +749000 ekin = 9.66656115769509 | erot = 17.8773814864457 | epot = -78.0582172617543 | etot = -50.5142746176135 +750000 ekin = 9.2160386704881 | erot = 17.83460421713 | epot = -77.5649175045286 | etot = -50.5142746169105 +751000 ekin = 8.80076552488041 | erot = 17.7502211247623 | epot = -77.0652612671075 | etot = -50.5142746174648 +752000 ekin = 8.42467668902751 | erot = 17.609041360549 | epot = -76.547992668523 | etot = -50.5142746189465 +753000 ekin = 8.08670902919991 | erot = 17.3870500518455 | epot = -75.9880337018982 | etot = -50.5142746208528 +754000 ekin = 7.78266313549285 | erot = 17.0571798776144 | epot = -75.3541176356852 | etot = -50.514274622578 +755000 ekin = 7.50732713165267 | erot = 16.5962021838286 | epot = -74.6178039390357 | etot = -50.5142746235544 +756000 ekin = 7.25656799093465 | erot = 15.9912186969398 | epot = -73.762061311217 | etot = -50.5142746233426 +757000 ekin = 7.02889011916432 | erot = 15.243783516545 | epot = -72.7869482577366 | etot = -50.5142746220273 +758000 ekin = 6.82603226746188 | erot = 14.3694235712677 | epot = -71.7097304583845 | etot = -50.514274619655 +759000 ekin = 6.65556621297692 | erot = 13.4007974873683 | epot = -70.5706383156341 | etot = -50.5142746152888 +760000 ekin = 6.52840618911949 | erot = 12.3808622803694 | epot = -69.4235430816177 | etot = -50.5142746121288 +761000 ekin = 6.45348689199773 | erot = 11.3465222562028 | epot = -68.3142837573728 | etot = -50.5142746091723 +762000 ekin = 6.44051607910641 | erot = 10.331721515393 | epot = -67.2865122011051 | etot = -50.5142746066057 +763000 ekin = 6.49918252436092 | erot = 9.36548217885221 | epot = -66.3789393077048 | etot = -50.5142746044917 +764000 ekin = 6.63833890054542 | erot = 8.47149284047071 | epot = -65.624106343837 | etot = -50.5142746028209 +765000 ekin = 6.86513419528386 | erot = 7.66877834276847 | epot = -65.0481871396127 | etot = -50.5142746015603 +766000 ekin = 7.18378077100147 | erot = 6.97265281322276 | epot = -64.6707081850581 | etot = -50.5142746008339 +767000 ekin = 7.59444235333481 | erot = 6.3955714375875 | epot = -64.5042883913707 | etot = -50.5142746004484 +768000 ekin = 8.09268145326367 | erot = 5.94781682490191 | epot = -64.5547728787741 | etot = -50.5142746006086 +769000 ekin = 8.66808446392277 | erot = 5.63681148444972 | epot = -64.81917054984 | etot = -50.5142746014675 +770000 ekin = 9.30348521556543 | erot = 5.46582731733528 | epot = -65.2835871360561 | etot = -50.5142746031554 +771000 ekin = 9.97431898096283 | erot = 5.43270401323985 | epot = -65.9212975999135 | etot = -50.5142746057108 +772000 ekin = 10.6499862226458 | erot = 5.5282704859122 | epot = -66.6925313175461 | etot = -50.5142746089881 +773000 ekin = 11.2957807948667 | erot = 5.73712650852638 | epot = -67.5471819160364 | etot = -50.5142746126434 +774000 ekin = 11.8763197237616 | erot = 6.03945270147251 | epot = -68.4300470414055 | etot = -50.5142746161714 +775000 ekin = 12.359832233683 | erot = 6.41425449691518 | epot = -69.2883613496549 | etot = -50.5142746190568 +776000 ekin = 12.7222841193265 | erot = 6.84284553246925 | epot = -70.0794042727346 | etot = -50.5142746209388 +777000 ekin = 12.950328619089 | erot = 7.31125230206383 | epot = -70.7758555428855 | etot = -50.5142746217327 +778000 ekin = 13.0423382707772 | erot = 7.81051825667609 | epot = -71.3671311491184 | etot = -50.5142746216651 +779000 ekin = 13.0073878067837 | erot = 8.33463285187138 | epot = -71.8562952798404 | etot = -50.5142746211853 +780000 ekin = 12.8626337012282 | erot = 8.87663911986012 | epot = -72.2535474441751 | etot = -50.5142746230867 +781000 ekin = 12.6191311288065 | erot = 9.41238807654897 | epot = -72.5457938291128 | etot = -50.5142746237573 +782000 ekin = 12.2922907716106 | erot = 9.90988136282892 | epot = -72.7164467590134 | etot = -50.5142746245739 +783000 ekin = 11.9113538266415 | erot = 10.3385161888582 | epot = -72.76414463989 | etot = -50.5142746243904 +784000 ekin = 11.5094258763993 | erot = 10.6682447236089 | epot = -72.6919452239281 | etot = -50.51427462392 +785000 ekin = 11.1215244493888 | erot = 10.8798873198936 | epot = -72.5156863910302 | etot = -50.5142746217479 +786000 ekin = 10.7892036477414 | erot = 10.9720367156824 | epot = -72.2755149815689 | etot = -50.5142746181451 +787000 ekin = 10.5550292786894 | erot = 10.9621301133158 | epot = -72.0314340061284 | etot = -50.5142746141232 +788000 ekin = 10.4531579062282 | erot = 10.8809781424898 | epot = -71.8484106597352 | etot = -50.5142746110173 +789000 ekin = 10.4992787233121 | erot = 10.7631938894143 | epot = -71.776747222619 | etot = -50.5142746098926 +790000 ekin = 10.6841251440453 | erot = 10.6378648554361 | epot = -71.8362646105419 | etot = -50.5142746110604 +791000 ekin = 10.9736405231527 | erot = 10.5233964906253 | epot = -72.0113116277457 | etot = -50.5142746139677 +792000 ekin = 11.3161137380799 | erot = 10.4258288161654 | epot = -72.2562171725761 | etot = -50.5142746183308 +793000 ekin = 11.6542402036844 | erot = 10.3442073318433 | epot = -72.5127221562285 | etot = -50.5142746207008 +794000 ekin = 11.9411264395025 | erot = 10.2879588173115 | epot = -72.7433598795459 | etot = -50.5142746227319 +795000 ekin = 12.1351044495356 | erot = 10.2641865985452 | epot = -72.9135656717524 | etot = -50.5142746236716 +796000 ekin = 12.2078724557425 | erot = 10.2805672453621 | epot = -73.002714324796 | etot = -50.5142746236914 +797000 ekin = 12.1452593713512 | erot = 10.3450171205922 | epot = -73.0045511149551 | etot = -50.5142746230116 +798000 ekin = 11.9451812221276 | erot = 10.4647770415723 | epot = -72.9242328855099 | etot = -50.5142746218099 +799000 ekin = 11.6151944445807 | erot = 10.6460858263548 | epot = -72.7755548911813 | etot = -50.5142746202458 +800000 ekin = 11.1701119660118 | erot = 10.8937791249656 | epot = -72.5781657095174 | etot = -50.51427461854 +801000 ekin = 10.629665013656 | erot = 11.2100289498347 | epot = -72.3539685805472 | etot = -50.5142746170565 +802000 ekin = 10.0162021020309 | erot = 11.5918355781245 | epot = -72.1223122961343 | etot = -50.5142746159789 +803000 ekin = 9.35262484647737 | erot = 12.0292939538184 | epot = -71.8961934158852 | etot = -50.5142746155894 +804000 ekin = 8.66091793166003 | erot = 12.5039909453998 | epot = -71.6791834929657 | etot = -50.5142746159059 +805000 ekin = 7.96269204966891 | erot = 12.9904597148454 | epot = -71.4674263808736 | etot = -50.5142746163593 +806000 ekin = 7.28309911914363 | erot = 13.4637499464485 | epot = -71.2611236823976 | etot = -50.5142746168054 +807000 ekin = 6.64354530303459 | erot = 13.8965012732196 | epot = -71.0543211930884 | etot = -50.5142746168341 +808000 ekin = 6.06569426715366 | erot = 14.2665976072072 | epot = -70.846566490465 | etot = -50.5142746161041 +809000 ekin = 5.57220972267948 | erot = 14.5624309902382 | epot = -70.6489153274645 | etot = -50.5142746145468 +810000 ekin = 5.18560956702054 | erot = 14.7848453683203 | epot = -70.4847295477707 | etot = -50.5142746124298 +811000 ekin = 4.92192373651933 | erot = 14.9394262725043 | epot = -70.3756246213058 | etot = -50.5142746122821 +812000 ekin = 4.78454979622525 | erot = 15.0222979446393 | epot = -70.3211223519872 | etot = -50.5142746111227 +813000 ekin = 4.77811513006738 | erot = 15.0438932856792 | epot = -70.3362830265582 | etot = -50.5142746108117 +814000 ekin = 4.89877766101389 | erot = 15.0134686698061 | epot = -70.426520942417 | etot = -50.514274611597 +815000 ekin = 5.13224364530435 | erot = 14.9341431305339 | epot = -70.5806613892138 | etot = -50.5142746133756 +816000 ekin = 5.45499511248497 | erot = 14.8029157849916 | epot = -70.772185513252 | etot = -50.5142746157755 +817000 ekin = 5.83730378160397 | erot = 14.6128652259528 | epot = -70.9644436259008 | etot = -50.514274618344 +818000 ekin = 6.24705078265335 | erot = 14.35598981918 | epot = -71.1173152225196 | etot = -50.5142746206862 +819000 ekin = 6.65333519872133 | erot = 14.0255937150625 | epot = -71.1932035362944 | etot = -50.5142746225105 +820000 ekin = 7.02931213200585 | erot = 13.6180701133972 | epot = -71.1616568689995 | etot = -50.5142746235965 +821000 ekin = 7.35419181516296 | erot = 13.1344275810971 | epot = -71.002894020028 | etot = -50.5142746237679 +822000 ekin = 7.61452267039641 | erot = 12.5816642165519 | epot = -70.7104615098789 | etot = -50.5142746229306 +823000 ekin = 7.8045791368625 | erot = 11.9738516457396 | epot = -70.2927054037303 | etot = -50.5142746211282 +824000 ekin = 7.9262306248882 | erot = 11.3316465732783 | epot = -69.7721518167056 | etot = -50.5142746185391 +825000 ekin = 7.98855124821598 | erot = 10.6800409975046 | epot = -69.1828668611821 | etot = -50.5142746154616 +826000 ekin = 8.00547556719018 | erot = 10.0465644012408 | epot = -68.5663145807013 | etot = -50.5142746122704 +827000 ekin = 7.99332269052192 | erot = 9.45843415914092 | epot = -67.9660314589833 | etot = -50.5142746093205 +828000 ekin = 7.96824966901498 | erot = 8.94000860860646 | epot = -67.4225328845179 | etot = -50.5142746068965 +829000 ekin = 7.94344804466234 | erot = 8.51150826233098 | epot = -66.9692309121261 | etot = -50.5142746051328 +830000 ekin = 7.92872079696729 | erot = 8.18753713454097 | epot = -66.6305325355413 | etot = -50.514274604033 +831000 ekin = 7.93015445192337 | erot = 7.97742868764142 | epot = -66.4218577430486 | etot = -50.5142746034839 +832000 ekin = 7.95037084502494 | erot = 7.88660237978092 | epot = -66.3512478280359 | etot = -50.51427460323 +833000 ekin = 7.99000871682723 | erot = 7.91841904034366 | epot = -66.4227023604139 | etot = -50.514274603243 +834000 ekin = 8.04830667220843 | erot = 8.07516750499664 | epot = -66.6377487804233 | etot = -50.5142746032182 +835000 ekin = 8.12473779283404 | erot = 8.35958341054817 | epot = -66.9985958064356 | etot = -50.5142746030534 +836000 ekin = 8.2203028286371 | erot = 8.77529454998099 | epot = -67.5098719814022 | etot = -50.5142746027841 +837000 ekin = 8.33787083573966 | erot = 9.32581140973844 | epot = -68.1779568480919 | etot = -50.5142746026137 +838000 ekin = 8.48148351708533 | erot = 10.0120708918567 | epot = -69.0078290118589 | etot = -50.5142746029169 +839000 ekin = 8.65454723392593 | erot = 10.828633989549 | epot = -69.9974558276565 | etot = -50.5142746041816 +840000 ekin = 8.8572489763941 | erot = 11.7591344305728 | epot = -71.1306580137988 | etot = -50.5142746068319 +841000 ekin = 9.084102723943 | erot = 12.7725877225071 | epot = -72.3709650574723 | etot = -50.5142746110221 +842000 ekin = 9.3228644555453 | erot = 13.8222723623197 | epot = -73.6594114343262 | etot = -50.5142746164612 +843000 ekin = 9.55575186020913 | erot = 14.8485908043665 | epot = -74.9186172869775 | etot = -50.5142746224019 +844000 ekin = 9.76305319167583 | erot = 15.7859703765421 | epot = -76.0632981960683 | etot = -50.5142746278504 +845000 ekin = 9.92653283160569 | erot = 16.5722430343749 | epot = -77.0130504982422 | etot = -50.5142746322615 +846000 ekin = 10.0341915121518 | erot = 17.1569368807579 | epot = -77.705403027488 | etot = -50.5142746345783 +847000 ekin = 10.0842269981193 | erot = 17.5059176317059 | epot = -78.1044192648766 | etot = -50.5142746350513 +848000 ekin = 10.0834807369303 | erot = 17.6028014906451 | epot = -78.2005568615335 | etot = -50.5142746339581 +849000 ekin = 10.0452569998271 | erot = 17.4478826304562 | epot = -78.0074142619096 | etot = -50.5142746316263 +850000 ekin = 9.98669392837276 | erot = 17.0565884213337 | epot = -77.5575569780145 | etot = -50.5142746283081 +851000 ekin = 9.92663281888658 | erot = 16.4581424380771 | epot = -76.8990498811812 | etot = -50.5142746242175 +852000 ekin = 9.88421071070815 | erot = 15.6937873465229 | epot = -76.0922726768526 | etot = -50.5142746196215 +853000 ekin = 9.87790001918571 | erot = 14.8136202069001 | epot = -75.2057948409708 | etot = -50.514274614885 +854000 ekin = 9.92462914155201 | erot = 13.8718574790535 | epot = -74.3107612310318 | etot = -50.5142746104263 +855000 ekin = 10.0388102442415 | erot = 12.9213545993191 | epot = -73.4744394501961 | etot = -50.5142746066355 +856000 ekin = 10.2313382537482 | erot = 12.0086601024974 | epot = -72.7542729600268 | etot = -50.5142746037812 +857000 ekin = 10.5087335451001 | erot = 11.1705904124712 | epot = -72.193598559568 | etot = -50.5142746019967 +858000 ekin = 10.8725687503891 | erot = 10.4326544038022 | epot = -71.8194977554779 | etot = -50.5142746012866 +859000 ekin = 11.3192383577338 | erot = 9.80910719600053 | epot = -71.6426201552897 | etot = -50.5142746015554 +860000 ekin = 11.8400783419905 | erot = 9.30419552792422 | epot = -71.658548472561 | etot = -50.5142746026463 +861000 ekin = 12.4218045286565 | erot = 8.91415835014432 | epot = -71.8502374831694 | etot = -50.5142746043686 +862000 ekin = 13.0471595017477 | erot = 8.62956306071713 | epot = -72.1909971690095 | etot = -50.5142746065447 +863000 ekin = 13.6955471607266 | erot = 8.43751332753371 | epot = -72.6473350973154 | etot = -50.5142746090551 +864000 ekin = 14.3434008697606 | erot = 8.32326841739466 | epot = -73.1809438990228 | etot = -50.5142746118675 +865000 ekin = 14.9642125533412 | erot = 8.27104570839966 | epot = -73.7495328767341 | etot = -50.5142746149933 +866000 ekin = 15.528558983782 | erot = 8.26427543445646 | epot = -74.3071090366081 | etot = -50.5142746183696 +867000 ekin = 16.0048844598068 | erot = 8.28609725298643 | epot = -74.8052563345312 | etot = -50.514274621738 +868000 ekin = 16.3618698335787 | erot = 8.32099923217132 | epot = -75.1971436903374 | etot = -50.5142746245874 +869000 ekin = 16.5726647379777 | erot = 8.35789379706738 | epot = -75.4448331613222 | etot = -50.5142746262771 +870000 ekin = 16.6201866860329 | erot = 8.39376845186404 | epot = -75.5282297641825 | etot = -50.5142746262856 +871000 ekin = 16.5016790588276 | erot = 8.43606779502584 | epot = -75.4520214783566 | etot = -50.5142746245031 +872000 ekin = 16.2341552473781 | erot = 8.50234235656206 | epot = -75.2507722228983 | etot = -50.5142746189581 +873000 ekin = 15.876686045947 | erot = 8.61819397760871 | epot = -75.0091546395533 | etot = -50.5142746159976 +874000 ekin = 15.4649107939159 | erot = 8.80433706341398 | epot = -74.783522470903 | etot = -50.5142746135731 +875000 ekin = 15.0262874336432 | erot = 9.07115551084192 | epot = -74.6117175568101 | etot = -50.5142746123251 +876000 ekin = 14.5841946135315 | erot = 9.41501293029907 | epot = -74.513482156385 | etot = -50.5142746125544 +877000 ekin = 14.1547799929905 | erot = 9.81684169520886 | epot = -74.4858963036691 | etot = -50.5142746154698 +878000 ekin = 13.738213635863 | erot = 10.2440638824616 | epot = -74.496552135016 | etot = -50.5142746166914 +879000 ekin = 13.3387592431327 | erot = 10.6587148562512 | epot = -74.5117487187133 | etot = -50.5142746193294 +880000 ekin = 12.9616338661267 | erot = 11.0178947403681 | epot = -74.4938032279389 | etot = -50.5142746214441 +881000 ekin = 12.6124700510745 | erot = 11.2828146493588 | epot = -74.409559322865 | etot = -50.5142746224317 +882000 ekin = 12.3012191623339 | erot = 11.4261723469392 | epot = -74.2416661313924 | etot = -50.5142746221193 +883000 ekin = 12.041684518431 | erot = 11.4352838976379 | epot = -73.9912430369291 | etot = -50.5142746208602 +884000 ekin = 11.8474220294668 | erot = 11.3115013061668 | epot = -73.6731979549861 | etot = -50.5142746193525 +885000 ekin = 11.7257363966337 | erot = 11.0668464612646 | epot = -73.3068574761126 | etot = -50.5142746182143 +886000 ekin = 11.6731647858694 | erot = 10.7200648867792 | epot = -72.9075042902706 | etot = -50.5142746176219 +887000 ekin = 11.6753437833101 | erot = 10.2941390601645 | epot = -72.483757460736 | etot = -50.5142746172613 +888000 ekin = 11.711486867392 | erot = 9.81567994926898 | epot = -72.0414414333002 | etot = -50.5142746166392 +889000 ekin = 11.7608194291218 | erot = 9.31484227781205 | epot = -71.589936322419 | etot = -50.5142746154851 +890000 ekin = 11.8074394677861 | erot = 8.82394323458894 | epot = -71.1456573163221 | etot = -50.514274613947 +891000 ekin = 11.8416000935789 | erot = 8.37408459363945 | epot = -70.7299592997137 | etot = -50.5142746124953 +892000 ekin = 11.8578157118822 | erot = 7.99071522451893 | epot = -70.3628055480302 | etot = -50.514274611629 +893000 ekin = 11.8517025878437 | erot = 7.68991980286949 | epot = -70.0558970023529 | etot = -50.5142746116397 +894000 ekin = 11.8175069853191 | erot = 7.47687356807654 | epot = -69.8086551659019 | etot = -50.5142746125063 +895000 ekin = 11.7474082015216 | erot = 7.34687884495997 | epot = -69.6085616604206 | etot = -50.5142746139391 +896000 ekin = 11.6337519151265 | erot = 7.2892196343865 | epot = -69.4372461644606 | etot = -50.5142746149475 +897000 ekin = 11.4723569946212 | erot = 7.291065702926 | epot = -69.277697313744 | etot = -50.5142746161968 +898000 ekin = 11.2610645581968 | erot = 7.33791947970324 | epot = -69.1132586561133 | etot = -50.5142746182133 +899000 ekin = 10.9996054557354 | erot = 7.4145517356619 | epot = -68.9284318100476 | etot = -50.5142746186504 +900000 ekin = 10.6922844700029 | erot = 7.50755561898882 | epot = -68.7141147070924 | etot = -50.5142746181007 +901000 ekin = 10.3534988307799 | erot = 7.60938036313742 | epot = -68.477153811341 | etot = -50.5142746174237 +902000 ekin = 9.99993129226381 | erot = 7.71616133833331 | epot = -68.2303672467816 | etot = -50.5142746161845 +903000 ekin = 9.65023529513539 | erot = 7.82867685326672 | epot = -67.9931867636195 | etot = -50.5142746152174 +904000 ekin = 9.31666090720493 | erot = 7.95055248574213 | epot = -67.7814880061006 | etot = -50.5142746131536 +905000 ekin = 9.0151678621896 | erot = 8.0931717646355 | epot = -67.6226142378358 | etot = -50.5142746110107 +906000 ekin = 8.76163371709618 | erot = 8.27193436037489 | epot = -67.5478426866915 | etot = -50.5142746092204 +907000 ekin = 8.5671723812097 | erot = 8.50112591566098 | epot = -67.5825729050348 | etot = -50.5142746081642 +908000 ekin = 8.43684994935096 | erot = 8.78986433035733 | epot = -67.7409888877375 | etot = -50.5142746080292 +909000 ekin = 8.36965149839248 | erot = 9.13947702228474 | epot = -68.0234031294551 | etot = -50.5142746087779 +910000 ekin = 8.35959079233856 | erot = 9.54304734368641 | epot = -68.4169127462108 | etot = -50.5142746101858 +911000 ekin = 8.39748118916213 | erot = 9.98695611148845 | epot = -68.8987119125913 | etot = -50.5142746119407 +912000 ekin = 8.47277548193584 | erot = 10.4536385184336 | epot = -69.440688614117 | etot = -50.5142746137475 +913000 ekin = 8.57499585903622 | erot = 10.9245819661982 | epot = -70.0138524406339 | etot = -50.5142746153994 +914000 ekin = 8.69450482126952 | erot = 11.3827140796491 | epot = -70.5914935177333 | etot = -50.5142746168147 +915000 ekin = 8.82261764858011 | erot = 11.8136624663994 | epot = -71.1505547330035 | etot = -50.514274618024 +916000 ekin = 8.95125831585943 | erot = 12.205813355537 | epot = -71.6713462905192 | etot = -50.5142746191227 +917000 ekin = 9.07247170864295 | erot = 12.5495353189923 | epot = -72.1362816478387 | etot = -50.5142746202035 +918000 ekin = 9.17798133020699 | erot = 12.8359656973712 | epot = -72.5282216495145 | etot = -50.5142746219363 +919000 ekin = 9.25795352543698 | erot = 13.0545632678061 | epot = -72.8267914162506 | etot = -50.5142746230075 +920000 ekin = 9.30352764337116 | erot = 13.1980045147644 | epot = -73.0158067819017 | etot = -50.5142746237662 +921000 ekin = 9.30791573962261 | erot = 13.2627586618327 | epot = -73.0849490254433 | etot = -50.514274623988 +922000 ekin = 9.26738318949092 | erot = 13.2504193014433 | epot = -73.0320771144145 | etot = -50.5142746234803 +923000 ekin = 9.18225083009585 | erot = 13.1693406239485 | epot = -72.8658660762015 | etot = -50.5142746221572 +924000 ekin = 9.05737763951813 | erot = 13.035259673007 | epot = -72.60691193261 | etot = -50.5142746200849 +925000 ekin = 8.90197379719792 | erot = 12.8704449082967 | epot = -72.2866933229743 | etot = -50.5142746174796 +926000 ekin = 8.72875558944565 | erot = 12.7013413968575 | epot = -71.9443716009688 | etot = -50.5142746146656 +927000 ekin = 8.55261219802547 | erot = 12.5551881315045 | epot = -71.6220749415216 | etot = -50.5142746119915 +928000 ekin = 8.3890619138423 | erot = 12.4564414994099 | epot = -71.3597780230131 | etot = -50.5142746097609 +929000 ekin = 8.25278751345445 | erot = 12.4238691105587 | epot = -71.1909312321754 | etot = -50.5142746081623 +930000 ekin = 8.15644947631112 | erot = 12.4688675852871 | epot = -71.1395916688729 | etot = -50.5142746072747 +931000 ekin = 8.10980872701606 | erot = 12.5950716573596 | epot = -71.2191549914745 | etot = -50.5142746070989 +932000 ekin = 8.11905369613075 | erot = 12.7988879099669 | epot = -71.43221621371 | etot = -50.5142746076124 +933000 ekin = 8.18618804321149 | erot = 13.070370377796 | epot = -71.7708330298154 | etot = -50.5142746088079 +934000 ekin = 8.30844961722735 | erot = 13.3939295435348 | epot = -72.2166537714582 | etot = -50.514274610696 +935000 ekin = 8.47804287619654 | erot = 13.7488706059529 | epot = -72.7411880951433 | etot = -50.5142746129938 +936000 ekin = 8.68285566583036 | erot = 14.1118670755257 | epot = -73.3089973576053 | etot = -50.5142746162492 +937000 ekin = 8.90506344753319 | erot = 14.4532746107671 | epot = -73.8726126780966 | etot = -50.5142746197963 +938000 ekin = 9.12528575783064 | erot = 14.7395572147996 | epot = -74.3791175958013 | etot = -50.514274623171 +939000 ekin = 9.32644769081306 | erot = 14.9376224440318 | epot = -74.7783447607167 | etot = -50.5142746258718 +940000 ekin = 9.49679607423193 | erot = 15.0191372956862 | epot = -75.0302079974039 | etot = -50.5142746274858 +941000 ekin = 9.63181347032397 | erot = 14.9646422014584 | epot = -75.1107302995718 | etot = -50.5142746277895 +942000 ekin = 9.73459702470586 | erot = 14.766516918386 | epot = -75.0153885698712 | etot = -50.5142746267793 +943000 ekin = 9.81477003781061 | erot = 14.4302129133908 | epot = -74.7592575758477 | etot = -50.5142746246463 +944000 ekin = 9.88637843649583 | erot = 13.9736039564721 | epot = -74.3742570146845 | etot = -50.5142746217166 +945000 ekin = 9.9653878552439 | erot = 13.4246663204191 | epot = -73.9043287940479 | etot = -50.5142746183849 +946000 ekin = 10.0624285978489 | erot = 12.8170998514157 | epot = -73.3938030653617 | etot = -50.514274616097 +947000 ekin = 10.1824129638269 | erot = 12.1848373686378 | epot = -72.8815249460322 | etot = -50.5142746135675 +948000 ekin = 10.3307952063951 | erot = 11.5602780907278 | epot = -72.4053479087891 | etot = -50.5142746116662 +949000 ekin = 10.509160869338 | erot = 10.9707033402967 | epot = -71.9941388200449 | etot = -50.5142746104101 +950000 ekin = 10.7157185620102 | erot = 10.4363928296814 | epot = -71.6663860014597 | etot = -50.5142746097681 +951000 ekin = 10.946102601704 | erot = 9.97090696790417 | epot = -71.4312841792091 | etot = -50.514274609601 +952000 ekin = 11.1944034263922 | erot = 9.58208330473698 | epot = -71.2907613408455 | etot = -50.5142746097163 +953000 ekin = 11.4542745284974 | erot = 9.27371614285239 | epot = -71.2422652812955 | etot = -50.5142746099457 +954000 ekin = 11.7197914420766 | erot = 9.04716566653344 | epot = -71.2812317188213 | etot = -50.5142746102112 +955000 ekin = 11.9858075781877 | erot = 8.90221043235444 | epot = -71.4022926210912 | etot = -50.5142746105491 +956000 ekin = 12.247752601157 | erot = 8.83681504682281 | epot = -71.5988422590654 | etot = -50.5142746110856 +957000 ekin = 12.5001620854987 | erot = 8.84602022699858 | epot = -71.8604569246898 | etot = -50.5142746121925 +958000 ekin = 12.7364419157096 | erot = 8.9202531655527 | epot = -72.1709696948261 | etot = -50.5142746135637 +959000 ekin = 12.9499558169919 | erot = 9.04468571434051 | epot = -72.5089161465906 | etot = -50.5142746152582 +960000 ekin = 13.1339945044549 | erot = 9.20006474954276 | epot = -72.8483338710208 | etot = -50.5142746170231 +961000 ekin = 13.2830442058268 | erot = 9.36494740352057 | epot = -73.1622662278611 | etot = -50.5142746185137 +962000 ekin = 13.3943598105312 | erot = 9.51904370691999 | epot = -73.4276781368386 | etot = -50.5142746193874 +963000 ekin = 13.4693004783907 | erot = 9.64669088359462 | epot = -73.6302659814776 | etot = -50.5142746194923 +964000 ekin = 13.5138667494266 | erot = 9.73885319439184 | epot = -73.7669945625489 | etot = -50.5142746187304 +965000 ekin = 13.5381869821487 | erot = 9.79431086360019 | epot = -73.8467724630455 | etot = -50.5142746172966 +966000 ekin = 13.5561247347474 | erot = 9.81745627102526 | epot = -73.8878556215787 | etot = -50.514274615806 +967000 ekin = 13.5791884000743 | erot = 9.8170082766903 | epot = -73.9104712911977 | etot = -50.5142746144331 +968000 ekin = 13.6156774160484 | erot = 9.80283527473491 | epot = -73.9327873043372 | etot = -50.5142746135539 +969000 ekin = 13.6696213237842 | erot = 9.782357696224 | epot = -73.9662536334143 | etot = -50.5142746134061 +970000 ekin = 13.7395769124221 | erot = 9.75809430149993 | epot = -74.0119458280882 | etot = -50.5142746141662 +971000 ekin = 13.8188233686534 | erot = 9.72517183385525 | epot = -74.0582698180394 | etot = -50.5142746155307 +972000 ekin = 13.8945737116172 | erot = 9.67630144632062 | epot = -74.0851497750791 | etot = -50.5142746171412 +973000 ekin = 13.9510636744438 | erot = 9.60403058386454 | epot = -74.0693688768831 | etot = -50.5142746185747 +974000 ekin = 13.9725505848395 | erot = 9.50361383013663 | epot = -73.9904390344624 | etot = -50.5142746194863 +975000 ekin = 13.9459468247441 | erot = 9.37533024555715 | epot = -73.8355516900162 | etot = -50.514274619715 +976000 ekin = 13.8626234186394 | erot = 9.22504260864496 | epot = -73.6019406466 | etot = -50.5142746193156 +977000 ekin = 13.7190808965563 | erot = 9.06288466719337 | epot = -73.2962401822375 | etot = -50.5142746184878 +978000 ekin = 13.516657166419 | erot = 8.90088911563463 | epot = -72.9318208994998 | etot = -50.5142746174462 +979000 ekin = 13.2607650055488 | erot = 8.75083051915684 | epot = -72.5258701410125 | etot = -50.5142746163069 +980000 ekin = 12.9601438446192 | erot = 8.62327601862502 | epot = -72.0976944783079 | etot = -50.5142746150637 +981000 ekin = 12.6263377400443 | erot = 8.52805592036366 | epot = -71.6686682740438 | etot = -50.5142746136358 +982000 ekin = 12.2732923452504 | erot = 8.47560645871046 | epot = -71.2631734159094 | etot = -50.5142746119486 +983000 ekin = 11.9168085654132 | erot = 8.47829635031043 | epot = -70.9093795257297 | etot = -50.5142746100061 +984000 ekin = 11.5736514704602 | erot = 8.5509697513139 | epot = -70.6388958296981 | etot = -50.5142746079239 +985000 ekin = 11.2603361578165 | erot = 8.71025817930807 | epot = -70.4848689430464 | etot = -50.5142746059218 +986000 ekin = 10.9917013457631 | erot = 8.97258068374094 | epot = -70.478556633814 | etot = -50.51427460431 +987000 ekin = 10.7795065325659 | erot = 9.35090018041219 | epot = -70.6446813164327 | etot = -50.5142746034546 +988000 ekin = 10.6312152806539 | erot = 9.85057203710816 | epot = -70.9960619214831 | etot = -50.514274603721 +989000 ekin = 10.5490976148249 | erot = 10.4650086574415 | epot = -71.528380877651 | etot = -50.5142746053845 +990000 ekin = 10.5298658630342 | erot = 11.1723189856646 | epot = -72.2164594571936 | etot = -50.5142746084948 +991000 ekin = 10.5651233194553 | erot = 11.9345717218068 | epot = -73.0139696539915 | etot = -50.5142746127294 +992000 ekin = 10.6428905940546 | erot = 12.7012555800802 | epot = -73.8584207914926 | etot = -50.5142746173579 +993000 ekin = 10.7501909021507 | erot = 13.4173760270084 | epot = -74.6818415505524 | etot = -50.5142746213933 +994000 ekin = 10.8760849480312 | erot = 14.0344526795298 | epot = -75.4248122515248 | etot = -50.5142746239637 +995000 ekin = 11.0140035497573 | erot = 14.5205029284807 | epot = -76.0487811029377 | etot = -50.5142746246998 +996000 ekin = 11.1622832138247 | erot = 14.8647830969972 | epot = -76.5413409347103 | etot = -50.5142746238884 +997000 ekin = 11.3226561299946 | erot = 15.0754558508696 | epot = -76.9123866031459 | etot = -50.5142746222818 +998000 ekin = 11.4975426712718 | erot = 15.1719516023698 | epot = -77.1837688943373 | etot = -50.5142746206957 +999000 ekin = 11.6875167361815 | erot = 15.1760730282748 | epot = -77.3778643841292 | etot = -50.5142746196729 +1000000 ekin = 11.8899772626335 | erot = 15.1055556567 | epot = -77.5098075386809 | etot = -50.5142746193474 + 1000000 443.20455 -80.663303 3.1534956 -65.61983 -0.0074359672 39304000 +Loop time of 10.6878 on 4 procs for 1000000 steps with 10 atoms + +Performance: 137.913 ns/day, 0.174 hours/ns, 93564.730 timesteps/s, 935.647 katom-step/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.2507 | 4.5103 | 6.3725 | 53.9 | 42.20 +Bond | 0.14129 | 0.19368 | 0.25474 | 9.5 | 1.81 +Neigh | 0.004024 | 0.0040453 | 0.004073 | 0.0 | 0.04 +Comm | 2.2577 | 4.3405 | 5.6343 | 60.5 | 40.61 +Output | 0.06195 | 0.071184 | 0.095935 | 5.4 | 0.67 +Modify | 0.3976 | 0.46641 | 0.55199 | 10.1 | 4.36 +Other | | 1.102 | | | 10.31 + +Nlocal: 2.5 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 8 max 7 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 9.25 ave 18 max 4 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 37 +Ave neighs/atom = 3.7 +Ave special neighs/atom = 1.6 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:10 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/oxdna2_real.cgdna b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/oxdna2_real.cgdna new file mode 120000 index 0000000000..64eb982c6e --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/oxdna2_real.cgdna @@ -0,0 +1 @@ +../../../../../../../potentials/oxdna2_real.cgdna \ No newline at end of file diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/data.duplex4.4type b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/data.duplex4.4type new file mode 100644 index 0000000000..32b09c9298 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/data.duplex4.4type @@ -0,0 +1,132 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +26 atoms +4 atom types +24 bonds +1 bond types +26 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -5.088903454828145 -4.022006630398617 0.979450832492054 1 1 1.0016462505133576 0 0 0 +2 2 -3.073273348143933 -6.886121795405585 4.2637967191149935 1 1 1.0016462505133576 0 0 0 +3 3 -1.6015249052848957 -7.954971258517993 7.983259491779774 1 1 1.0016462505133576 0 0 0 +4 4 1.6004494372303046 -7.502206000462345 11.142183230976523 1 1 1.0016462505133576 0 0 0 +5 1 3.9762269824284777 -5.378694720128274 14.092706034736517 1 1 1.0016462505133576 0 0 0 +6 2 5.244098183685422 -2.0736999117014334 17.034635513902522 1 1 1.0016462505133576 0 0 0 +7 3 4.66434547759629 0.9057195140116471 20.406471315843888 1 1 1.0016462505133576 0 0 0 +8 4 3.3770131096003007 2.884613516099349 24.32212902640886 1 1 1.0016462505133576 0 0 0 +9 1 0.7795485088930724 2.8596780468864993 27.93316866219941 1 1 1.0016462505133576 0 0 0 +10 2 -2.220644638122167 1.9976911283301424 30.852747566202943 1 1 1.0016462505133576 0 0 0 +11 3 -3.752108563283866 -0.36118973532266224 34.56060757623137 1 1 1.0016462505133576 0 0 0 +12 4 -4.0981351277114095 -3.3336637232155737 38.03472139175804 1 1 1.0016462505133576 0 0 0 +13 1 -2.580860807366316 -5.296690457458744 41.65233354663661 1 1 1.0016462505133576 0 0 0 +14 4 3.11235736590125 3.9787921540654274 41.61858344700847 2 1 1.0016462505133576 0 0 0 +15 1 4.972174868431865 1.22026293032667 39.080053199424356 2 1 1.0016462505133576 0 0 0 +16 2 6.193349083696695 -1.843990009872412 35.70127548826449 2 1 1.0016462505133576 0 0 0 +17 3 4.85045978654294 -5.086115266816092 32.287814957190825 2 1 1.0016462505133576 0 0 0 +18 4 2.7413887948469777 -6.6667612407190076 28.945688671744993 2 1 1.0016462505133576 0 0 0 +19 1 0.23801913694460985 -6.962572452460229 24.638294488589953 2 1 1.0016462505133576 0 0 0 +20 2 -2.929295143505978 -5.793156995357843 22.155368377440084 2 1 1.0016462505133576 0 0 0 +21 3 -4.874287161624311 -2.6868984302083723 19.162406167006097 2 1 1.0016462505133576 0 0 0 +22 4 -4.466038023713098 -0.16009445500929992 14.199167217812603 2 1 1.0016462505133576 0 0 0 +23 1 -3.805032901797115 1.3047989425274054 9.939919176722297 2 1 1.0016462505133576 0 0 0 +24 2 -0.3645313828582167 2.0504253339486334 6.749830838323167 2 1 1.0016462505133576 0 0 0 +25 3 2.8696234661228 1.1843850873648512 3.5779840008575166 2 1 1.0016462505133576 0 0 0 +26 4 4.584052070339748 -2.4162961106383802 0.4178747538604132 2 1 1.0016462505133576 0 0 0 + +Velocities + +1 -0.0007092826233374404 -0.0011683182237858898 0.0009345415878891811 -0.19711297351977997 0.3471662755040702 1.1876949496899232 +2 0.0001692806579311005 0.001454411904318072 -0.0009132068521112497 0.40085230919108755 -0.18887849087800404 0.047091827325408245 +3 0.00026721094548725233 -0.0018474107413693995 -7.33687581476124e-05 0.46267958346439353 1.0098887515959383 0.6393407481151142 +4 0.0005530692647148845 6.276724836348722e-05 0.0011760622369354724 0.485473149019376 -1.016731064060453 0.4763136256195711 +5 0.0010959077967915062 -0.002073578927849095 0.0009200279724368436 1.0623586979165884 1.065939836735458 -1.5037672467577814 +6 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a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/generate_unique.py b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/generate_unique.py new file mode 100644 index 0000000000..330215bd80 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/generate_unique.py @@ -0,0 +1,828 @@ +#!/usr/bin/env python +""" +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ +""" +""" +Creates unique base-pairings to avoid asymmetrical H-bonds. + +Modified to create the bead wall setup. +N_BEADS is the number of beads along one direction, the final system will have N_BEADS^2 beads in the wall. N_BEADS should be set to be odd number. +""" + + +#Define number of base-pairs per turn for B-form DNA +N = 10.5 +#Define distance between the big bead and the centre of mass of the last base-pair +BEAD_OFFSET = 2.0 +WALL_PARTICLE_SIZE = 2.0 +N_BEADS = 11 + +#Number of unique base type groups (1-4) ACGT counts as one group +N_BASE_TYPES = 20 + + +""" +Import basic modules +""" +import sys, os, timeit + +from timeit import default_timer as timer +start_time = timer() +""" +Try to import numpy; if failed, import a local version mynumpy +which needs to be provided +""" +try: + import numpy as np +except: + print("numpy not found. Exiting.", file=sys.stderr) + sys.exit(1) + +""" +Check that the required arguments (box offset and size in simulation units +and the sequence file were provided +""" +try: + box_offset = float(sys.argv[1]) + box_length = float(sys.argv[2]) + infile = sys.argv[3] + if len(sys.argv) == 4: + topo = 'strand' + lk = 0 + elif len(sys.argv) == 5: + topo = 'strand' + lk = int(sys.argv[4]) + +except: + print("Usage: %s <%s> <%s> <%s> <%s> " % (sys.argv[0], \ + "box offset", "box length", "file with sequences", "[Lk]"), file=sys.stderr) + sys.exit(1) +box = np.array ([box_length, box_length, box_length]) + +""" +Try to open the file and fail gracefully if file cannot be opened +""" +try: + inp = open (infile, 'r') + inp.close() +except: + print("Could not open file '%s' for reading. \ + Aborting." % infile, file=sys.stderr) + sys.exit(2) + +# return parts of a string +def partition(s, d): + if d in s: + sp = s.split(d, 1) + return sp[0], d, sp[1] + else: + return s, "", "" + +""" +Define the model constants +""" +# set model constants +PI = np.pi +POS_BASE = 0.4 +POS_BACK = -0.4 +EXCL_RC1 = 0.711879214356 +EXCL_RC2 = 0.335388426126 +EXCL_RC3 = 0.52329943261 + +""" +Define auxiliary variables for the construction of a helix +""" +# center of the double strand +COM_CENTRE_DS = POS_BASE + 0.2 + +# ideal rise between two consecutive nucleotides on the +# same strand which are to be base paired in a duplex +BASE_BASE = 0.3897628551303122 + +# cutoff distance for overlap check +RC2 = 16 + +# squares of the excluded volume distances for overlap check +RC2_BACK = EXCL_RC1**2 +RC2_BASE = EXCL_RC2**2 +RC2_BACK_BASE = EXCL_RC3**2 + +# enumeration to translate from letters to numbers and vice versa +number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'} +base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2, + 'G' : 3, 'g' : 3, 'T' : 4, 't' : 4} + +# auxiliary arrays +positions = [] +a1s = [] +a3s = [] +quaternions = [] + +newpositions = [] +newa1s = [] +newa3s = [] + +basetype = [] +strandnum = [] + +bonds = [] + +""" +Convert local body frame to quaternion DOF +""" +def exyz_to_quat (mya1, mya3): + + mya2 = np.cross(mya3, mya1) + myquat = [1,0,0,0] + + q0sq = 0.25 * (mya1[0] + mya2[1] + mya3[2] + 1.0) + q1sq = q0sq - 0.5 * (mya2[1] + mya3[2]) + q2sq = q0sq - 0.5 * (mya1[0] + mya3[2]) + q3sq = q0sq - 0.5 * (mya1[0] + mya2[1]) + + # some component must be greater than 1/4 since they sum to 1 + # compute other components from it + + if q0sq >= 0.25: + myquat[0] = np.sqrt(q0sq) + myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0]) + myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0]) + myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0]) + elif q1sq >= 0.25: + myquat[1] = np.sqrt(q1sq) + myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1]) + myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1]) + myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1]) + elif q2sq >= 0.25: + myquat[2] = np.sqrt(q2sq) + myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2]) + myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2]) + myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2]) + elif q3sq >= 0.25: + myquat[3] = np.sqrt(q3sq) + myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3]) + myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3]) + myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3]) + + norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \ + myquat[2]*myquat[2] + myquat[3]*myquat[3]) + myquat[0] *= norm + myquat[1] *= norm + myquat[2] *= norm + myquat[3] *= norm + + return np.array([myquat[0],myquat[1],myquat[2],myquat[3]]) + +""" +Adds a strand to the system by appending it to the array of previous strands +""" +def add_strands (mynewpositions, mynewa1s, mynewa3s): + overlap = False + + # This is a simple check for each of the particles where for previously + # placed particles i we check whether it overlaps with any of the + # newly created particles j + + print("## Checking for overlaps", file=sys.stdout) + + for i in range(len(positions)): + + p = positions[i] + pa1 = a1s[i] + + for j in range (len(mynewpositions)): + + q = mynewpositions[j] + qa1 = mynewa1s[j] + + # skip particles that are anyway too far away + dr = p - q + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) > RC2: + continue + + # base site and backbone site of the two particles + p_pos_back = p + pa1 * POS_BACK + p_pos_base = p + pa1 * POS_BASE + q_pos_back = q + qa1 * POS_BACK + q_pos_base = q + qa1 * POS_BASE + + # check for no overlap between the two backbone sites + dr = p_pos_back - q_pos_back + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BACK: + overlap = True + + # check for no overlap between the two base sites + dr = p_pos_base - q_pos_base + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BASE: + overlap = True + + # check for no overlap between backbone site of particle p + # with base site of particle q + dr = p_pos_back - q_pos_base + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BACK_BASE: + overlap = True + + # check for no overlap between base site of particle p and + # backbone site of particle q + dr = p_pos_base - q_pos_back + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BACK_BASE: + overlap = True + + # exit if there is an overlap + if overlap: + return False + + # append to the existing list if no overlap is found + if not overlap: + + for p in mynewpositions: + positions.append(p) + for p in mynewa1s: + a1s.append (p) + for p in mynewa3s: + a3s.append (p) + # calculate quaternion from local body frame and append + for ia in range(len(mynewpositions)): + mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia]) + quaternions.append(mynewquaternions) + + return True + +""" +Calculate angle of rotation site to site +""" +def get_angle(bp): + #n, minimal number of bases per turn + n = 10.5 + found = False + while found == False: + turns = bp/n + diff = abs( turns - round(turns)) + if diff < 0.03: + found = True + turns = round(turns)+lk + angle = (360*turns)/bp + angle = round (angle,2) + #angle =round( 360/n,2) + elif n > 11.5: + angle = 35.9 + found = True + else: + n += 0.02 + return angle + + +def get_angle2(bp): + turns = bp/N + lk + angle = (360*turns)/bp + + return angle + + + +""" +Returns the rotation matrix defined by an axis and angle +""" +def get_rotation_matrix(axis, anglest, nbp=0): + # The argument anglest can be either an angle in radiants + # (accepted types are float, int or np.float64 or np.float64) + # or a tuple [angle, units] where angle is a number and + # units is a string. It tells the routine whether to use degrees, + # radiants (the default) or base pairs turns. + if not isinstance (anglest, (np.float64, np.float32, float, int)): + if len(anglest) > 1: + if anglest[1] in ["degrees", "deg", "o"]: + angle = (np.pi / 180.) * (anglest[0]) + elif anglest[1] in ["bp"]: + if nbp == 0: + angle = int(anglest[0]) * (np.pi / 180.) * (35.9) + else: + ang = get_angle2(nbp) + angle = int(anglest[0]) * (np.pi / 180.) * (ang) + else: + angle = float(anglest[0]) + else: + angle = float(anglest[0]) + else: + angle = float(anglest) # in degrees (?) + + axis = np.array(axis) + axis /= np.sqrt(np.dot(axis, axis)) + + ct = np.cos(angle) + st = np.sin(angle) + olc = 1. - ct + x, y, z = axis + + return np.array([[olc*x*x+ct, olc*x*y-st*z, olc*x*z+st*y], + [olc*x*y+st*z, olc*y*y+ct, olc*y*z-st*x], + [olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]]) + +""" +Generates the position and orientation vectors of a +(single or double) strand from a sequence string +""" +def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \ + dir=np.array([0, 0, 1]), perp=False, double=True, rot=0.): + # generate empty arrays + mynewpositions, mynewa1s, mynewa3s = [], [], [] + + # cast the provided start_pos array into a numpy array + start_pos = np.array(start_pos, dtype=float) + + # overall direction of the helix + dir = np.array(dir, dtype=float) + #if sequence == None: + # sequence = np.random.randint(1, 5, bp) + + # the elseif here is most likely redundant + #elif len(sequence) != bp: + # n = bp - len(sequence) + # sequence += np.random.randint(1, 5, n) + # print("sequence is too short, adding %d random bases" % n, file=sys.stderr) + + # normalize direction + dir_norm = np.sqrt(np.dot(dir,dir)) + if dir_norm < 1e-10: + print("direction must be a valid vector,\ + defaulting to (0, 0, 1)", file=sys.stderr) + dir = np.array([0, 0, 1]) + else: dir /= dir_norm + + # find a vector orthogonal to dir to act as helix direction, + # if not provided switch off random orientation + if perp is None or perp is False: + v1 = np.random.random_sample(3) + # comment in to suppress randomized base vector + v1 = [1,0,0] + v1 -= dir * (np.dot(dir, v1)) + v1 /= np.sqrt(sum(v1*v1)) + else: + v1 = perp; + + # generate rotational matrix representing the overall rotation of the helix + R0 = get_rotation_matrix(dir, rot) + + # rotation matrix corresponding to one step along the helix + R = get_rotation_matrix(dir, [1, "bp"],bp) + + # set the vector a1 (backbone to base) to v1 + a1 = v1 + + # apply the global rotation to a1 + a1 = np.dot(R0, a1) + + # set the position of the fist backbone site to start_pos + rb = np.array(start_pos) + + # set a3 to the direction of the helix + a3 = dir + + for i in range(bp): + # work out the position of the centre of mass of the nucleotide + rcom = rb - COM_CENTRE_DS * a1 + + # append to newpositions + mynewpositions.append(rcom) + mynewa1s.append(a1) + mynewa3s.append(a3) + + # if we are not at the end of the helix, we work out a1 and rb for the + # next nucleotide along the helix + if i != bp - 1: + a1 = np.dot(R, a1) + rb += a3 * BASE_BASE + + # if we are working on a double strand, we do a cycle similar + # to the previous one but backwards + if double == True: + a1 = -a1 + a3 = -dir + R = R.transpose() + for i in range(bp): + rcom = rb - COM_CENTRE_DS * a1 + mynewpositions.append (rcom) + mynewa1s.append (a1) + mynewa3s.append (a3) + a1 = np.dot(R, a1) + rb += a3 * BASE_BASE + + + #Calculate the positions of the bead wall + + last_base1 = mynewpositions[int( len(mynewpositions)/2 - 1) ] + last_base2 = mynewpositions[int( len(mynewpositions)/2) ] + mid_point = (last_base1 + last_base2) / 2 + + NN = N_BEADS**2 + p1 = [mid_point[0] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[1] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[2] + BEAD_OFFSET ] + for i in range(N_BEADS): + for j in range(N_BEADS): + position = [ p1[0] + 2*i*WALL_PARTICLE_SIZE, p1[1] + 2*j*WALL_PARTICLE_SIZE, p1[2]] + mynewa1s.append([1,0,0]) + mynewa3s.append([1,0,0]) + mynewpositions.append(position) + + assert (len (mynewpositions) > 0) + + return [mynewpositions, mynewa1s, mynewa3s] + + + +""" +Main function for this script. +Reads a text file with the following format: +- Each line contains the sequence for a single strand (A,C,G,T) +- Lines beginning with the keyword 'DOUBLE' produce double-stranded DNA + +Ex: Two ssDNA (single stranded DNA) +ATATATA +GCGCGCG + +Ex: Two strands, one double stranded, the other single stranded. +DOUBLE AGGGCT +CCTGTA + +""" + +def read_strands(filename): + try: + infile = open (filename) + except: + print("Could not open file '%s'. Aborting." % filename, file=sys.stderr) + sys.exit(2) + + # This block works out the number of nucleotides and strands by reading + # the number of non-empty lines in the input file and the number of letters, + # taking the possible DOUBLE keyword into account. + nstrands, nnucl, nbonds = 0, 0, 0 + lines = infile.readlines() + for line in lines: + line = line.upper().strip() + if len(line) == 0: + continue + if line[:6] == 'DOUBLE': + line = line.split()[1] + length = len(line) + print("## Found duplex of %i base pairs" % length, file=sys.stdout) + nnucl += 2*length + nstrands += 2 + nbonds+= 2*length + + else: + line = line.split()[0] + length = len(line) + print("## Found single strand of %i bases" % length, file=sys.stdout) + nnucl += length + nstrands += 1 + if topo == 'ring': + nbonds =+ length + else: + nbonds += length+1 + # rewind the sequence input file + infile.seek(0) + + print("## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout) + + # generate the data file in LAMMPS format + try: + out = open ("data.oxdna", "w") + except: + print("Could not open data file for writing. Aborting.", file=sys.stderr) + sys.exit(2) + + lines = infile.readlines() + nlines = len(lines) + i = 1 + myns = 0 + noffset = 1 + + for line in lines: + line = line.upper().strip() + + # skip empty lines + if len(line) == 0: + i += 1 + continue + + # block for duplexes: last argument of the generate function + # is set to 'True' + if line[:6] == 'DOUBLE': + line = line.split()[1] + length = len(line) + seq = [(base_to_number[x]) for x in line] + seq = np.array(seq,dtype=int) + n_a, n_c, n_g, n_t = 0, 0, 0, 0 + for s in range(seq.size): + if seq[s] == 1: + n_a += 1 + elif seq[s] == 2: + n_c += 1 + elif seq[s] ==3: + n_g += 1 + elif seq[s] == 4: + n_t += 1 + smallest_n_bases = n_c + if n_a < n_c: + smallest_n_bases = n_a + if smallest_n_bases > n_t: + smallest_n_bases = n_t + if smallest_n_bases > n_g: + smallest_n_bases = n_g + + if smallest_n_bases < N_BASE_TYPES: + print('## Not enough occurrences of base types in the sequence for ' + str(N_BASE_TYPES)) + print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types') + else: + smallest_n_bases = N_BASE_TYPES + + a, c, g, t = -3, -2, -1, 0 + for s in range(seq.size): + if seq[s] == 1: + if a < (smallest_n_bases*4-3): + a += 4 + else: + a = 1 + seq[s] = a + + elif seq[s] == 2: + if c < (smallest_n_bases*4-2): + c += 4 + else: + c = 2 + seq[s] = c + + elif seq[s] == 3: + if g < (smallest_n_bases*4-1): + g += 4 + else: + g = 3 + seq[s] = g + elif seq[s] == 4: + if t < (smallest_n_bases*4): + t += 4 + else: + t = 4 + seq[s] = t + + + + myns += 1 + + for b in range(length): + basetype.append(seq[b]) + strandnum.append(myns) + + for b in range(length-1): + bondpair = [noffset + b, noffset + b + 1] + bonds.append(bondpair) + + + noffset += length + + # create the sequence of the second strand as made of + # complementary bases + #seq2 = [5-s for s in seq] + seq2 = seq + for s in range(seq2.size): + if seq2[s]%4 == 1: + seq2[s] += 3 + elif seq2[s]%4 == 2: + seq2[s] += 1 + elif seq2[s]%4 == 3: + seq2[s] -= 1 + elif seq2[s]%4 == 0: + seq2[s] -= 3 + + #seq2.reverse() + + myns += 1 + + for b in range(length): + basetype.append(seq2[b]) + strandnum.append(myns) + + for b in range(length-1): + bondpair = [noffset + b, noffset + b + 1] + bonds.append(bondpair) + + + #create wall bead types + bead_type = 4*smallest_n_bases + 1 + for i in range(N_BEADS**2): + + basetype.append(bead_type) + basetype.append(bead_type) + strandnum.append(bead_type) + strandnum.append(bead_type) + #bonds.append([length, noffset + length]) + #bonds.append([length+1, noffset + length]) + + noffset += length + + print("## Created duplex of %i bases" % (2*length), file=sys.stdout) + + # generate random position of the first nucleotide + com = box_offset + np.random.random_sample(3) * box + # comment out to randomize + com = [0,0,0] + + # generate the random direction of the helix + axis = np.random.random_sample(3) + # comment out to randomize + axis = [0,0,1] + axis /= np.sqrt(np.dot(axis, axis)) + + # use the generate function defined above to create + # the position and orientation vector of the strand + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + else: + newpositions, newa1s, newa3s = generate_strand(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + + # generate a new position for the strand until it does not overlap + # with anything already present + start = timer() + while not add_strands(newpositions, newa1s, newa3s): + com = box_offset + np.random.random_sample(3) * box + axis = np.random.random_sample(3) + axis /= np.sqrt(np.dot(axis, axis)) + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + else: + newpositions, newa1s, newa3s = generate_strand(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + print("## Trying %i" % i, file=sys.stdout) + end = timer() + print("## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \ + (2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout) + + # block for single strands: last argument of the generate function + # is set to 'False' + else: + length = len(line) + seq = [(base_to_number[x]) for x in line] + + myns += 1 + for b in range(length): + basetype.append(seq[b]) + strandnum.append(myns) + + for b in range(length-1): + bondpair = [noffset + b, noffset + b + 1] + bonds.append(bondpair) + if topo == 'ring': + bondpair = [noffset, noffset + length-1] + bonds.append(bondpair) + noffset += length + + + # generate random position of the first nucleotide + com = box_offset + np.random.random_sample(3) * box + # comment out to randomize + com = [-30,0,0] + + # generate the random direction of the helix + axis = np.random.random_sample(3) + # comment out to randomize + axis = [0,0,1] + axis /= np.sqrt(np.dot(axis, axis)) + + print("## Created single strand of %i bases" % length, file=sys.stdout) + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + else: + newpositions, newa1s, newa3s = generate_strand(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + start = timer() + while not add_strands(newpositions, newa1s, newa3s): + com = box_offset + np.random.random_sample(3) * box + axis = np.random.random_sample(3) + axis /= np.sqrt(np.dot(axis, axis)) + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + + else: + newpositions, newa1s, newa3s = generate_strand(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + print("## Trying %i" % (i), file=sys.stdout) + end = timer() + print("## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \ + (length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout) + + i += 1 + + # sanity check + #if not len(positions) == nnucl: + # print(len(positions), nnucl) + # raise AssertionError + nnucl = nnucl + (N_BEADS**2) + nbonds -= 4 + + out.write('# LAMMPS data file\n') + out.write('%d atoms\n' % nnucl) + out.write('%d ellipsoids\n' % nnucl) + out.write('%d bonds\n' % nbonds) + out.write('\n') + out.write('%d atom types\n' %bead_type ) + out.write('1 bond types\n') + out.write('\n') + out.write('# System size\n') + out.write('%f %f xlo xhi\n' % (box_offset,box_offset+box_length)) + out.write('%f %f ylo yhi\n' % (box_offset,box_offset+box_length)) + out.write('%f %f zlo zhi\n' % (0,box_length)) + + #out.write('\n') + #out.write('Masses\n') + #out.write('\n') + #out.write('1 3.1575\n') + #out.write('2 3.1575\n') + #out.write('3 3.1575\n') + #out.write('4 3.1575\n') + #out.write('5 3.1575\n') + + # for each nucleotide print a line under the headers + # Atoms, Velocities, Ellipsoids and Bonds + out.write('\n') + out.write(\ + '# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n') + out.write('Atoms\n') + out.write('\n') + + for i in range(nnucl): + out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \ + % (i+1, basetype[i], \ + positions[i][0], positions[i][1], positions[i][2], \ + strandnum[i])) + + out.write('\n') + out.write('# Atom-ID, translational, rotational velocity\n') + out.write('Velocities\n') + out.write('\n') + + for i in range(nnucl): + out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \ + % (i+1,0.0,0.0,0.0,0.0,0.0,0.0)) + + out.write('\n') + out.write('# Atom-ID, shape, quaternion\n') + out.write('Ellipsoids\n') + out.write('\n') + + for i in range(nnucl): + out.write(\ + "%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \ + % (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \ + quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3])) + + out.write('\n') + out.write('# Bond topology\n') + out.write('Bonds\n') + out.write('\n') + + for i in range(nbonds): + if i < nbonds-2: + out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1])) + #else: + + #out.write("%d %d %d %d\n" % (i+1,2,bonds[i][0],bonds[i][1])) + + out.close() + + print("## Wrote data to 'data.oxdna'", file=sys.stdout) + print("## DONE", file=sys.stdout) + +# call the above main() function, which executes the program +read_strands (infile) + +end_time=timer() +runtime = end_time-start_time +hours = runtime/3600 +minutes = (runtime-np.rint(hours)*3600)/60 +seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60 +print("## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout) diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/in.duplex4.4type b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/in.duplex4.4type new file mode 100644 index 0000000000..f88547c423 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/in.duplex4.4type @@ -0,0 +1,87 @@ +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 4 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} + variable basemod equal ${base}%4 + if "${basemod} == 1" then & + "variable comp equal ${base}+3" & + "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then & + "variable comp equal ${base}+1" & + "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/in.duplex4.8type b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/in.duplex4.8type new file mode 100644 index 0000000000..c3bf6ee207 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/in.duplex4.8type @@ -0,0 +1,87 @@ +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 8 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} + variable basemod equal ${base}%4 + if "${basemod} == 1" then & + "variable comp equal ${base}+3" & + "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then & + "variable comp equal ${base}+1" & + "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* \ No newline at end of file diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.1 new file mode 100644 index 0000000000..f454f2d2bf --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.1 @@ -0,0 +1,1234 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 4 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 4 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.4.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 +Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 299.91159 -228.12763 5.3145589 -200.46358 0.037365999 39304000 +1000 ekin = 22.8379863364631 | erot = 20.8727077214658 | epot = -223.40247948455 | etot = -179.691785426621 +2000 ekin = 22.7811305214841 | erot = 22.642319354707 | epot = -224.256117760205 | etot = -178.832667884014 +3000 ekin = 23.3007102476489 | erot = 24.7866780853993 | epot = -225.012681837824 | etot = -176.925293504776 +4000 ekin = 22.7903421051578 | erot = 24.569247173836 | epot = -225.53962239349 | etot = -178.180033114497 +5000 ekin = 22.19925646023 | erot = 25.6289473462429 | epot = -225.721034396187 | etot = -177.892830589714 +6000 ekin = 22.3860723428343 | erot = 25.7078570981677 | epot = -225.520727206183 | etot = -177.426797765181 +7000 ekin = 22.6093903901514 | erot = 24.8279594754098 | epot = -225.139767140542 | etot = -177.702417274981 +8000 ekin = 22.3366506221221 | erot = 25.3490822995746 | epot = -224.659830672346 | etot = -176.97409775065 +9000 ekin = 22.1017491922176 | erot = 23.8561173282126 | epot = -224.102470196007 | etot = -178.144603675577 +10000 ekin = 21.3469487217786 | erot = 23.034985278251 | epot = -223.591750396367 | etot = -179.209816396337 +11000 ekin = 20.5717104541852 | erot = 24.8615565294047 | epot = -223.484019303241 | etot = -178.050752319652 +12000 ekin = 20.411935484151 | erot = 25.1271441409211 | epot = -223.751373801975 | etot = -178.212294176903 +13000 ekin = 20.2798810279148 | erot = 24.281806390477 | epot = -224.390777503839 | etot = -179.829090085447 +14000 ekin = 19.6242363441233 | erot = 26.8542751690783 | epot = -225.215820819941 | etot = -178.73730930674 +15000 ekin = 20.0818097074935 | erot = 29.2937195480841 | epot = -226.167773981604 | etot = -176.792244726026 +16000 ekin = 19.6823418822516 | erot = 30.3811175824271 | epot = -227.408076260742 | etot = -177.344616796063 +17000 ekin = 19.5450698280734 | erot = 32.5391774659612 | epot = -228.808347823448 | etot = -176.724100529413 +18000 ekin = 20.0756319264279 | erot = 33.5672084608192 | epot = -230.110512386278 | etot = -176.467671999031 +19000 ekin = 19.6603874622079 | erot = 32.528542938808 | epot = -231.207417420873 | etot = -179.018487019857 +20000 ekin = 19.5984395633796 | erot = 31.3606067961676 | epot = -232.171981685224 | etot = -181.212935325677 +21000 ekin = 19.8375798064082 | erot = 31.8939937172914 | epot = -232.880097232772 | etot = -181.148523709072 +22000 ekin = 19.9286085655832 | erot = 30.5391742384594 | epot = -233.322303895413 | etot = -182.85452109137 +23000 ekin = 20.1661434732298 | erot = 30.6973170954371 | epot = -233.687536932121 | etot = -182.824076363455 +24000 ekin = 20.5065436368894 | erot = 30.0297091428477 | epot = -233.956998583432 | etot = -183.420745803695 +25000 ekin = 20.529858609709 | erot = 27.1945410830961 | epot = -233.994416252181 | etot = -186.270016559376 +26000 ekin = 20.699035687076 | erot = 29.09174515188 | epot = -233.720969470337 | etot = -183.930188631381 +27000 ekin = 20.7350777764672 | erot = 28.5961324745054 | epot = -233.307821216305 | etot = -183.976610965332 +28000 ekin = 21.1532240716935 | erot = 27.7486079543453 | epot = -232.966688262262 | etot = -184.064856236223 +29000 ekin = 21.3118506902676 | erot = 25.736471201621 | epot = -232.759622611367 | etot = -185.711300719478 +30000 ekin = 20.9513131899827 | erot = 26.876741160358 | epot = -232.673474007172 | etot = -184.845419656831 +31000 ekin = 21.3216486612277 | erot = 26.2777465254033 | epot = -232.609223688159 | etot = -185.009828501528 +32000 ekin = 22.0969166841928 | erot = 24.7959897585166 | epot = -232.612526553891 | etot = -185.719620111181 +33000 ekin = 22.875370966078 | erot = 24.1467590540463 | epot = -232.688992091586 | etot = -185.666862071462 +34000 ekin = 23.5405053823873 | erot = 22.7415684492007 | epot = -232.615611352503 | etot = -186.333537520915 +35000 ekin = 23.7257555349787 | erot = 26.8191624133874 | epot = -232.23498680623 | etot = -181.690068857864 +36000 ekin = 23.2515945340346 | erot = 23.8280794869285 | epot = -231.753024246269 | etot = -184.673350225306 +37000 ekin = 23.8513426401361 | erot = 25.6368246142449 | epot = -231.060980894716 | etot = -181.572813640335 +38000 ekin = 23.8781935722645 | erot = 22.7747736894791 | epot = -230.152104757751 | etot = -183.499137496008 +39000 ekin = 23.3884393320053 | erot = 22.6925700673075 | epot = -229.140534316443 | etot = -183.05952491713 +40000 ekin = 22.7413687353909 | erot = 21.4736378452411 | epot = -228.265631373339 | etot = -184.050624792707 +41000 ekin = 23.2348935054145 | erot = 21.0108525021673 | epot = -227.75573531584 | etot = -183.509989308258 +42000 ekin = 23.3940171890425 | erot = 22.1904243568237 | epot = -227.643506146239 | etot = -182.059064600373 +43000 ekin = 23.2681022018539 | erot = 21.7837756583263 | epot = -227.855518729869 | etot = -182.803640869689 +44000 ekin = 23.5393535337972 | erot = 20.7730908198455 | epot = -228.246566278463 | etot = -183.93412192482 +45000 ekin = 24.1405649747358 | erot = 20.1728652780817 | epot = -228.807425059799 | etot = -184.493994806982 +46000 ekin = 24.585245817982 | erot = 21.0236670642408 | epot = -229.213686304167 | etot = -183.604773421944 +47000 ekin = 24.1560413910622 | erot = 19.6811193727542 | epot = -229.413234324251 | etot = -185.576073560435 +48000 ekin = 23.5246878727431 | erot = 19.721180663017 | epot = -229.434759182691 | etot = -186.188890646931 +49000 ekin = 23.1670415745661 | erot = 22.5501021659482 | epot = -229.177266193688 | etot = -183.460122453174 +50000 ekin = 22.8223612259816 | erot = 22.567605149626 | epot = -228.600859944765 | etot = -183.210893569157 +51000 ekin = 22.9120987888545 | erot = 21.0527888961203 | epot = -227.77037262561 | etot = -183.805484940635 +52000 ekin = 22.187626079843 | erot = 20.5194847365121 | epot = -226.835169897986 | etot = -184.128059081631 +53000 ekin = 21.3650052806676 | erot = 20.2770735131344 | epot = -225.807155710179 | etot = -184.165076916377 +54000 ekin = 20.4303417025859 | erot = 17.9973021512008 | epot = -224.896097666587 | etot = -186.468453812801 +55000 ekin = 19.714913763396 | erot = 18.5590407326034 | epot = -224.06259658443 | etot = -185.788642088431 +56000 ekin = 19.685159503242 | erot = 20.0732971833202 | epot = -223.279023832763 | etot = -183.520567146201 +57000 ekin = 19.060196259904 | erot = 18.256095629202 | epot = -222.84333391372 | etot = -185.527042024614 +58000 ekin = 18.5841091049986 | erot = 19.1515036320309 | epot = -222.696024269362 | etot = -184.960411532333 +59000 ekin = 18.0414625414599 | erot = 18.2275847003703 | epot = -222.821981249891 | etot = -186.55293400806 +60000 ekin = 18.2103913071538 | erot = 18.4755642418172 | epot = -223.234305836724 | etot = -186.548350287753 +61000 ekin = 17.9869947125514 | erot = 22.4458503852164 | epot = -223.797760245785 | etot = -183.364915148017 +62000 ekin = 18.1431070502485 | erot = 21.7652022985207 | epot = -224.318306232552 | etot = -184.409996883783 +63000 ekin = 17.973357520257 | erot = 21.6688824771829 | epot = -224.735623623494 | etot = -185.093383626054 +64000 ekin = 17.8102495654737 | erot = 21.8723940899094 | epot = -225.323991291355 | etot = -185.641347635972 +65000 ekin = 18.0338529130483 | erot = 22.1181740951059 | epot = -225.877150411024 | etot = -185.72512340287 +66000 ekin = 18.1822893834801 | erot = 21.7465005263719 | epot = -226.185684363613 | etot = -186.256894453761 +67000 ekin = 18.5240194292997 | erot = 23.3964917870366 | epot = -226.365163861592 | etot = -184.444652645256 +68000 ekin = 18.5155376828975 | erot = 20.9719183620335 | epot = -226.451473665725 | etot = -186.964017620794 +69000 ekin = 18.6323014683072 | erot = 20.588171070637 | epot = -226.648083130375 | etot = -187.427610591431 +70000 ekin = 19.5343933745558 | erot = 17.5472322005953 | epot = -226.977679956235 | etot = -189.896054381084 +71000 ekin = 20.2276605685904 | erot = 16.3663260398183 | epot = -227.393323574632 | etot = -190.799336966224 +72000 ekin = 20.3130284812279 | erot = 16.4497414610662 | epot = -228.013381961156 | etot = -191.250612018862 +73000 ekin = 21.0477998518383 | erot = 15.4406791831341 | epot = -228.675590564562 | etot = -192.187111529589 +74000 ekin = 21.7371512650598 | erot = 17.5352725761175 | epot = -229.494527276336 | etot = -190.222103435159 +75000 ekin = 22.6680122759915 | erot = 18.5419401178599 | epot = -230.463408123768 | etot = -189.253455729917 +76000 ekin = 23.0346115082234 | erot = 19.8636379382539 | epot = -231.254905942531 | etot = -188.356656496053 +77000 ekin = 23.2797429827865 | erot = 19.7434715156692 | epot = -231.721208677509 | etot = -188.697994179053 +78000 ekin = 23.4106393811464 | erot = 19.4211385461251 | epot = -231.892259154973 | etot = -189.060481227701 +79000 ekin = 23.4632537757978 | erot = 18.8653049537082 | epot = -231.690998177985 | etot = -189.362439448479 +80000 ekin = 23.3884971334889 | erot = 18.1174271773692 | epot = -231.118174876358 | etot = -189.6122505655 +81000 ekin = 23.5022754315906 | erot = 17.1755695884554 | epot = -230.398467043008 | etot = -189.720622022962 +82000 ekin = 23.0472842217945 | erot = 17.2373445724549 | epot = -229.638468243904 | etot = -189.353839449655 +83000 ekin = 21.5042588722365 | erot = 16.786367445308 | epot = -228.921540236372 | etot = -190.630913918827 +84000 ekin = 22.1329940094216 | erot = 16.2632055631471 | epot = -228.335250260719 | etot = -189.93905068815 +85000 ekin = 20.9154057430379 | erot = 16.6557644544218 | epot = -227.803085954943 | etot = -190.231915757484 +86000 ekin = 20.6981517687592 | erot = 18.6120855140407 | epot = -227.283699712715 | etot = -187.973462429915 +87000 ekin = 20.7059776963377 | erot = 18.1357410469598 | epot = -226.805480829165 | etot = -187.963762085867 +88000 ekin = 20.5112535017457 | erot = 17.8809983821762 | epot = -226.459696318129 | etot = -188.067444434207 +89000 ekin = 20.6525596514182 | erot = 20.4133880492623 | epot = -226.205468820861 | etot = -185.139521120181 +90000 ekin = 20.695293192409 | erot = 20.3370512782838 | epot = -225.953852764959 | etot = -184.921508294267 +91000 ekin = 19.7682690703159 | erot = 23.8787808356902 | epot = -225.655385288229 | etot = -182.008335382223 +92000 ekin = 19.6828792607911 | erot = 22.5766537107148 | epot = -225.535582585193 | etot = -183.276049613687 +93000 ekin = 19.3048520995758 | erot = 20.6317228268703 | epot = -225.547774602348 | etot = -185.611199675902 +94000 ekin = 19.028411935034 | erot = 20.0568093447086 | epot = -225.530355910562 | etot = -186.445134630819 +95000 ekin = 18.5452655948058 | erot = 22.9286015621929 | epot = -225.523849045322 | etot = -184.049981888323 +96000 ekin = 18.3728256439782 | erot = 25.039495486179 | epot = -225.537862748503 | etot = -182.125541618346 +97000 ekin = 17.9426894203414 | erot = 28.5848563795549 | epot = -225.638824537989 | etot = -179.111278738092 +98000 ekin = 17.5850264746273 | erot = 26.5739649306284 | epot = -225.648647927869 | etot = -181.489656522613 +99000 ekin = 17.3808762582936 | erot = 24.7289180187015 | epot = -225.594130307751 | etot = -183.484336030756 +100000 ekin = 17.3273680270292 | erot = 22.7273796979409 | epot = -225.299321148282 | etot = -185.244573423312 +101000 ekin = 17.0042319903592 | erot = 20.8052793029198 | epot = -225.102935121042 | etot = -187.293423827763 +102000 ekin = 17.05502613973 | erot = 21.316603586839 | epot = -224.890904735916 | etot = -186.519275009347 +103000 ekin = 17.2263904973081 | erot = 20.3710964353458 | epot = -224.753273552475 | etot = -187.155786619821 +104000 ekin = 16.7943747317823 | erot = 21.7185799033818 | epot = -224.555386740442 | etot = -186.042432105278 +105000 ekin = 16.6865175024786 | erot = 20.0200455556502 | epot = -224.47221260965 | etot = -187.765649551522 +106000 ekin = 16.5925867843767 | erot = 21.7048075291456 | epot = -224.380087441128 | etot = -186.082693127606 +107000 ekin = 17.2054452998434 | erot = 22.6546685111546 | epot = -224.481631442089 | etot = -184.621517631091 +108000 ekin = 16.9267033337673 | erot = 23.5631418034102 | epot = -224.898081411902 | etot = -184.408236274724 +109000 ekin = 17.3821452346864 | erot = 25.9049365088352 | epot = -225.621226955643 | etot = -182.334145212121 +110000 ekin = 17.5124448065073 | erot = 27.8801611895846 | epot = -226.410419972689 | etot = -181.017813976598 +111000 ekin = 18.5487245393564 | erot = 25.6736058140268 | epot = -227.167416210036 | etot = -182.945085856652 +112000 ekin = 19.8365999588111 | erot = 24.2751230291775 | epot = -227.944028021488 | etot = -183.832305033499 +113000 ekin = 20.1722859000849 | erot = 25.3603047130775 | epot = -228.958826647654 | etot = -183.426236034491 +114000 ekin = 20.2870180696113 | erot = 25.6800990417157 | epot = -230.17458939254 | etot = -184.207472281213 +115000 ekin = 21.3318566501428 | erot = 27.1697329853562 | epot = -231.444909631325 | etot = -182.943319995826 +116000 ekin = 22.4210844135644 | erot = 26.004420936002 | epot = -232.710476417833 | etot = -184.284971068267 +117000 ekin = 24.3405871824212 | erot = 25.2077444956265 | epot = -233.933190998453 | etot = -184.384859320406 +118000 ekin = 25.0884094969948 | erot = 26.5527557651617 | epot = -235.048390081924 | etot = -183.407224819767 +119000 ekin = 25.4315051787003 | erot = 26.1546643641889 | epot = -235.858317413788 | etot = -184.272147870899 +120000 ekin = 24.9629495355357 | erot = 25.2895225128999 | epot = -236.253529746916 | etot = -186.00105769848 +121000 ekin = 26.094755391151 | erot = 26.5212744850534 | epot = -236.079647472315 | etot = -183.46361759611 +122000 ekin = 26.1701918491875 | erot = 24.3510759857483 | epot = -235.493876868904 | etot = -184.972609033969 +123000 ekin = 26.4005875446556 | erot = 20.1865632708939 | epot = -234.709375372604 | etot = -188.122224557054 +124000 ekin = 26.3381579249386 | erot = 19.6639335950121 | epot = -233.989222703183 | etot = -187.987131183233 +125000 ekin = 25.4027453417305 | erot = 19.6503648681598 | epot = -233.10224654375 | etot = -188.04913633386 +126000 ekin = 25.3255704653777 | erot = 20.0698371771056 | epot = -232.162556032928 | etot = -186.767148390445 +127000 ekin = 25.0742564529078 | erot = 19.3577482138169 | epot = -231.22010681212 | etot = -186.788102145396 +128000 ekin = 24.1452145463861 | erot = 20.722592883018 | epot = -230.30707206278 | etot = -185.439264633376 +129000 ekin = 24.1836343798902 | erot = 21.1668068192837 | epot = -229.557734556381 | etot = -184.207293357207 +130000 ekin = 23.6272916857115 | erot = 21.0608635320181 | epot = -228.86842777514 | etot = -184.180272557411 +131000 ekin = 23.7733250641655 | erot = 21.7026182128681 | epot = -228.196470483987 | etot = -182.720527206954 +132000 ekin = 22.235523086447 | erot = 22.2423990709498 | epot = -227.377132642704 | etot = -182.899210485307 +133000 ekin = 21.7697258915644 | erot = 21.0688536119307 | epot = -226.678873870809 | etot = -183.840294367314 +134000 ekin = 22.0334013998118 | erot = 23.6876876537064 | epot = -226.110477401204 | etot = -180.389388347686 +135000 ekin = 21.2888725174031 | erot = 23.8731522967533 | epot = -225.586596896472 | etot = -180.424572082316 +136000 ekin = 21.1112833844234 | erot = 23.1441906006998 | epot = -225.02986093909 | etot = -180.774386953966 +137000 ekin = 20.3417544623754 | erot = 19.8373378818128 | epot = -224.306720617089 | etot = -184.127628272901 +138000 ekin = 20.6378655675457 | erot = 20.7041461431297 | epot = -223.935090515208 | etot = -182.593078804533 +139000 ekin = 20.6358768684418 | erot = 19.6349119675149 | epot = -223.695388728766 | etot = -183.42459989281 +140000 ekin = 21.2970180334091 | erot = 20.9859430093584 | epot = -223.44632370732 | etot = -181.163362664552 +141000 ekin = 20.7458666897953 | erot = 22.008168038219 | epot = -223.471675354103 | etot = -180.717640626089 +142000 ekin = 21.6581543402664 | erot = 22.1925330545729 | epot = -223.759999018087 | etot = -179.909311623248 +143000 ekin = 22.137676382598 | erot = 19.8438720355801 | epot = -223.992076444275 | etot = -182.010528026097 +144000 ekin = 21.4512214487569 | erot = 21.2911862274696 | epot = -224.211315350262 | etot = -181.468907674035 +145000 ekin = 21.1677590228455 | erot = 20.1765379829327 | epot = -224.433855912986 | etot = -183.089558907207 +146000 ekin = 21.2954143160548 | erot = 22.315786511802 | epot = -224.708745433142 | etot = -181.097544605285 +147000 ekin = 20.9304440285978 | erot = 24.2948847043021 | epot = -224.826442145057 | etot = -179.601113412157 +148000 ekin = 20.9920002123677 | erot = 25.1867007165295 | epot = -225.027893064869 | etot = -178.849192135972 +149000 ekin = 20.4937916688861 | erot = 25.3412194127539 | epot = -225.235228138764 | etot = -179.400217057124 +150000 ekin = 20.240788496008 | erot = 24.5936585831824 | epot = -225.22294490262 | etot = -180.38849782343 +151000 ekin = 20.1765587397768 | erot = 23.3198992588029 | epot = -224.965480891794 | etot = -181.469022893215 +152000 ekin = 19.9049224846628 | erot = 22.8007918896868 | epot = -224.714024114794 | etot = -182.008309740445 +153000 ekin = 20.2049676657018 | erot = 22.194787629535 | epot = -224.584122527196 | etot = -182.184367231959 +154000 ekin = 20.2787333086907 | erot = 23.5668471416538 | epot = -224.632505362968 | etot = -180.786924912624 +155000 ekin = 20.54327508537 | erot = 21.0208344632846 | epot = -225.11524693997 | etot = -183.551137391316 +156000 ekin = 21.1891534249123 | erot = 21.9641402966851 | epot = -225.922181500193 | etot = -182.768887778596 +157000 ekin = 21.9241933405022 | erot = 22.2820243127273 | epot = -226.791928428935 | etot = -182.585710775706 +158000 ekin = 22.1128564636274 | erot = 21.6071323400673 | epot = -227.681294121914 | etot = -183.961305318219 +159000 ekin = 21.9706527338173 | erot = 23.0889220586676 | epot = -228.293622590392 | etot = -183.234047797907 +160000 ekin = 22.1766068917265 | erot = 24.537009024834 | epot = -228.724261272436 | etot = -182.010645355876 +161000 ekin = 22.2585263955668 | erot = 26.3988206054411 | epot = -229.153198320277 | etot = -180.495851319269 +162000 ekin = 23.9956799056614 | erot = 29.0208643540612 | epot = -229.511788677983 | etot = -176.49524441826 +163000 ekin = 24.0427671853836 | erot = 28.5149092203014 | epot = -229.882700364651 | etot = -177.325023958966 +164000 ekin = 24.6404986309622 | erot = 29.8954353563838 | epot = -230.05653220386 | etot = -175.520598216514 +165000 ekin = 25.37837451169 | erot = 29.3458474374449 | epot = -230.021956695543 | etot = -175.297734746409 +166000 ekin = 24.5018301159861 | erot = 27.0572013521953 | epot = -229.807404132493 | etot = -178.248372664311 +167000 ekin = 24.3635902860623 | erot = 25.1004090825066 | epot = -229.418996399617 | etot = -179.954997031048 +168000 ekin = 24.0782799291434 | erot = 23.6106192667051 | epot = -228.790493183835 | etot = -181.101593987986 +169000 ekin = 23.5408370855421 | erot = 21.779214731184 | epot = -228.096753694582 | etot = -182.776701877856 +170000 ekin = 23.3042056991829 | erot = 22.5887621937051 | epot = -227.644704595797 | etot = -181.751736702909 +171000 ekin = 23.1139069856327 | erot = 25.56161061645 | epot = -227.386750672406 | etot = -178.711233070323 +172000 ekin = 22.4125455911307 | erot = 23.9879390948077 | epot = -227.478440821498 | etot = -181.07795613556 +173000 ekin = 21.1650772689554 | erot = 24.037053824746 | epot = -228.027795739756 | etot = -182.825664646054 +174000 ekin = 21.5377174768009 | erot = 25.6623168386594 | epot = -228.810113267544 | etot = -181.610078952084 +175000 ekin = 21.2673885173618 | erot = 25.3358091366212 | epot = -229.601669873776 | etot = -182.998472219792 +176000 ekin = 22.0549078764628 | erot = 25.1987886573552 | epot = -230.199173516198 | etot = -182.94547698238 +177000 ekin = 22.1952451140842 | erot = 26.2074019384157 | epot = -230.449490408395 | etot = -182.046843355895 +178000 ekin = 22.6474601747908 | erot = 23.8569097796671 | epot = -230.486903876126 | etot = -183.982533921668 +179000 ekin = 22.5332951614051 | erot = 24.1586648743825 | epot = -230.249582873377 | etot = -183.55762283759 +180000 ekin = 22.9130954884035 | erot = 22.1104613694639 | epot = -229.757677624187 | etot = -184.73412076632 +181000 ekin = 22.5830672584554 | erot = 20.450357914035 | epot = -229.205005015184 | etot = -186.171579842693 +182000 ekin = 21.7744390453032 | erot = 20.3565453634741 | epot = -228.578765211469 | etot = -186.447780802691 +183000 ekin = 21.3156414739578 | erot = 21.1055168403748 | epot = -227.936610643158 | etot = -185.515452328825 +184000 ekin = 21.4060237522632 | erot = 20.8540585363569 | epot = -227.278789217958 | etot = -185.018706929338 +185000 ekin = 21.4522029742182 | erot = 19.9268287024307 | epot = -226.747540479433 | etot = -185.368508802785 +186000 ekin = 21.1983246906017 | erot = 21.4683722301386 | epot = -226.354347511139 | etot = -183.687650590399 +187000 ekin = 19.690535005356 | erot = 21.6640179195446 | epot = -225.994223499083 | etot = -184.639670574183 +188000 ekin = 19.3802922890703 | erot = 20.3716521999867 | epot = -225.572007065283 | etot = -185.820062576226 +189000 ekin = 18.4695751736414 | erot = 20.9528614806743 | epot = -225.247637250638 | etot = -185.825200596322 +190000 ekin = 17.4681116945173 | erot = 22.2496740454142 | epot = -224.805249640785 | etot = -185.087463900853 +191000 ekin = 16.6191337946719 | erot = 21.4193312202814 | epot = -224.294610310801 | etot = -186.256145295848 +192000 ekin = 16.0143800470349 | erot = 23.3693680596585 | epot = -223.718710211147 | etot = -184.334962104454 +193000 ekin = 15.7997901257216 | erot = 22.8225508042988 | epot = -223.089938646114 | etot = -184.467597716093 +194000 ekin = 15.2217453118598 | erot = 22.7325306996813 | epot = -222.625275149846 | etot = -184.670999138305 +195000 ekin = 15.1719099531695 | erot = 22.4876618724485 | epot = -222.099560622719 | etot = -184.439988797101 +196000 ekin = 15.3343672188822 | erot = 20.7775889118734 | epot = -221.597631501452 | etot = -185.485675370697 +197000 ekin = 14.766048091889 | erot = 19.7842334059676 | epot = -221.252213948545 | etot = -186.701932450688 +198000 ekin = 14.7770693853773 | erot = 20.3688380244553 | epot = -220.957884756875 | etot = -185.811977347042 +199000 ekin = 14.6937058517326 | erot = 22.6205548299113 | epot = -220.829895321234 | etot = -183.51563463959 +200000 ekin = 15.8653653492245 | erot = 20.8741496651364 | epot = -220.921168840223 | etot = -184.181653825862 +201000 ekin = 16.8728289108128 | erot = 23.0954953178473 | epot = -221.24134564708 | etot = -181.27302141842 +202000 ekin = 17.1574797353138 | erot = 22.285557506037 | epot = -221.513124761678 | etot = -182.070087520327 +203000 ekin = 18.4748883214853 | erot = 21.1472224923989 | epot = -221.731230109427 | etot = -182.109119295543 +204000 ekin = 19.2325496005105 | erot = 20.9923779560698 | epot = -221.821935938326 | etot = -181.597008381746 +205000 ekin = 18.4255902998036 | erot = 21.6289651382083 | epot = -222.10565061528 | etot = -182.051095177268 +206000 ekin = 18.5468871013068 | erot = 22.2892911055978 | epot = -222.480026344849 | etot = -181.643848137944 +207000 ekin = 18.9799810220236 | erot = 25.3769178031176 | epot = -222.656627081049 | etot = -178.299728255907 +208000 ekin = 18.985044800951 | erot = 26.4647809474189 | epot = -222.71751731042 | etot = -177.26769156205 +209000 ekin = 19.7564462509297 | erot = 23.7060464556116 | epot = -222.835034583459 | etot = -179.372541876917 +210000 ekin = 18.930059047627 | erot = 21.9791265973624 | epot = -222.75013900049 | etot = -181.840953355501 +211000 ekin = 19.3637206258675 | erot = 20.2144155977342 | epot = -222.884011041863 | etot = -183.305874818262 +212000 ekin = 18.6127906086045 | erot = 18.7836957734051 | epot = -223.131977986675 | etot = -185.735491604666 +213000 ekin = 18.6207275953171 | erot = 18.079576040676 | epot = -223.568944156785 | etot = -186.868640520792 +214000 ekin = 18.0525593583566 | erot = 20.9785428305194 | epot = -224.281741393784 | etot = -185.250639204908 +215000 ekin = 18.4181697813342 | erot = 21.5844731751551 | epot = -225.36589716156 | etot = -185.363254205071 +216000 ekin = 18.1283838147148 | erot = 26.0258037718262 | epot = -226.609028691632 | etot = -182.454841105091 +217000 ekin = 18.5976564529797 | erot = 25.2672310084213 | epot = -227.604708371557 | etot = -183.739820910156 +218000 ekin = 18.6146376310641 | erot = 23.8235521999893 | epot = -228.575434081834 | etot = -186.13724425078 +219000 ekin = 19.3665245563789 | erot = 24.0423091654174 | epot = -229.487172233029 | etot = -186.078338511233 +220000 ekin = 19.0674806968353 | erot = 24.8437141420456 | epot = -230.380897501689 | etot = -186.469702662808 +221000 ekin = 18.7605746437215 | erot = 26.6882095060636 | epot = -231.213347501054 | etot = -185.764563351269 +222000 ekin = 18.2601086357985 | erot = 26.2872383665376 | epot = -231.899871459307 | etot = -187.352524456971 +223000 ekin = 18.450698620632 | erot = 26.0465542803085 | epot = -232.337267696155 | etot = -187.840014795214 +224000 ekin = 18.9891330599031 | erot = 27.8638375428931 | epot = -232.528415379388 | etot = -185.675444776592 +225000 ekin = 19.4927747283068 | erot = 25.801864264556 | epot = -232.780900379235 | etot = -187.486261386372 +226000 ekin = 19.1531460973279 | erot = 30.4806630263034 | epot = -233.077183634691 | etot = -183.44337451106 +227000 ekin = 18.60714463341 | erot = 30.1777908886287 | epot = -232.964109027209 | etot = -184.179173505171 +228000 ekin = 18.4858074214198 | erot = 31.561135296702 | epot = -232.632194016111 | etot = -182.585251297989 +229000 ekin = 18.121165512591 | erot = 31.2764316650807 | epot = -232.253052683513 | etot = -182.855455505842 +230000 ekin = 17.8908234673042 | erot = 27.5438052529654 | epot = -231.968720310839 | etot = -186.534091590569 +231000 ekin = 17.4046011153877 | erot = 24.8124690524392 | epot = -231.614857480412 | etot = -189.397787312585 +232000 ekin = 16.726949239043 | erot = 25.4479901290198 | epot = -231.298988676823 | etot = -189.12404930876 +233000 ekin = 17.4181301789806 | erot = 25.6698394160172 | epot = -231.284274641405 | etot = -188.196305046407 +234000 ekin = 17.2837229866899 | erot = 24.7490838826286 | epot = -231.292369116174 | etot = -189.259562246856 +235000 ekin = 17.8418429383167 | erot = 21.8691418097328 | epot = -231.251575822849 | etot = -191.5405910748 +236000 ekin = 18.2280444396042 | erot = 22.4776949586945 | epot = -231.507293467971 | etot = -190.801554069672 +237000 ekin = 17.5170325906195 | erot = 23.8831905837694 | epot = -232.09911142057 | etot = -190.698888246182 +238000 ekin = 17.5370495415089 | erot = 23.1397896153992 | epot = -232.813601469978 | etot = -192.13676231307 +239000 ekin = 18.5035461424359 | erot = 23.6314853899781 | epot = -233.424851371331 | etot = -191.289819838917 +240000 ekin = 18.2400558551285 | erot = 25.7782971635906 | epot = -233.735423678076 | etot = -189.717070659357 +241000 ekin = 18.3026727766783 | erot = 24.4472869908134 | epot = -233.913575321003 | etot = -191.163615553511 +242000 ekin = 17.7115212204843 | erot = 24.995729162613 | epot = -234.050352631169 | etot = -191.343102248072 +243000 ekin = 17.2078487224333 | erot = 23.9090981344856 | epot = -234.125136273026 | etot = -193.008189416107 +244000 ekin = 16.2099036691328 | erot = 23.5424124480185 | epot = -234.271072794161 | etot = -194.51875667701 +245000 ekin = 16.2853237680124 | erot = 25.6013260460874 | epot = -234.567326279749 | etot = -192.680676465649 +246000 ekin = 15.9877124738648 | erot = 26.4618528423917 | epot = -234.907254123649 | etot = -192.457688807393 +247000 ekin = 16.278912642661 | erot = 25.6305025080533 | epot = -235.38224025519 | etot = -193.472825104476 +248000 ekin = 16.1891212016019 | erot = 26.7270438066868 | epot = -235.85693800343 | etot = -192.940772995142 +249000 ekin = 16.2464500192795 | erot = 27.0261014884008 | epot = -236.177986894745 | etot = -192.905435387065 +250000 ekin = 15.9341143953265 | erot = 30.8738949363089 | epot = -236.535496633727 | etot = -189.727487302092 +251000 ekin = 15.8028184849003 | erot = 32.1505879831005 | epot = -236.688974719602 | etot = -188.735568251601 +252000 ekin = 16.7909168467857 | erot = 32.8335558099614 | epot = -236.645831434934 | etot = -187.021358778187 +253000 ekin = 16.9139273743643 | erot = 29.2781158099218 | epot = -236.579277646039 | etot = -190.387234461753 +254000 ekin = 16.6934725608083 | erot = 29.105191471631 | epot = -236.457570337498 | etot = -190.658906305059 +255000 ekin = 16.9530894051165 | erot = 28.561900354835 | epot = -236.494291914548 | etot = -190.979302154596 +256000 ekin = 16.8565757743705 | erot = 26.1542309529602 | epot = -236.815950729242 | etot = -193.805144001911 +257000 ekin = 16.585149543856 | erot = 27.2044624689905 | epot = -237.076180448211 | etot = -193.286568435365 +258000 ekin = 16.9649893297413 | erot = 29.5003144318717 | epot = -237.125813775239 | etot = -190.660510013626 +259000 ekin = 16.8759816443281 | erot = 28.8592698754747 | epot = -237.185288834274 | etot = -191.450037314471 +260000 ekin = 16.9796890464332 | erot = 27.618877966906 | epot = -237.312226590128 | etot = -192.713659576789 +261000 ekin = 17.1257291800673 | erot = 26.9320058611979 | epot = -237.262614695238 | etot = -193.204879653972 +262000 ekin = 17.6923394447622 | erot = 27.2700259360803 | epot = -237.143815143362 | etot = -192.18144976252 +263000 ekin = 17.8430352696419 | erot = 25.086676238323 | epot = -236.946345380794 | etot = -194.016633872829 +264000 ekin = 18.0391753861997 | erot = 26.3317958950567 | epot = -236.678672413504 | etot = -192.307701132247 +265000 ekin = 18.013924761071 | erot = 25.5680520302975 | epot = -236.424056901965 | etot = -192.842080110596 +266000 ekin = 17.6154269767062 | erot = 23.675123094962 | epot = -235.997667559883 | etot = -194.707117488214 +267000 ekin = 17.6622486381387 | erot = 26.2267112931792 | epot = -235.553502063923 | etot = -191.664542132605 +268000 ekin = 17.8125223357387 | erot = 27.363444164387 | epot = -235.09406638475 | etot = -189.918099884624 +269000 ekin = 17.4475328870398 | erot = 28.702098419643 | epot = -234.302641461941 | etot = -188.153010155258 +270000 ekin = 17.3046917858623 | erot = 29.7195013929747 | epot = -233.361041913271 | etot = -186.336848734434 +271000 ekin = 17.142474619254 | erot = 29.9663485879831 | epot = -232.456072910032 | etot = -185.347249702795 +272000 ekin = 17.1520876922752 | erot = 28.8349700847661 | epot = -231.55505567112 | etot = -185.567997894079 +273000 ekin = 16.529132536504 | erot = 28.0012512077314 | epot = -230.483093897511 | etot = -185.952710153276 +274000 ekin = 16.0104360170946 | erot = 26.9274909329307 | epot = -229.230529801711 | etot = -186.292602851686 +275000 ekin = 15.5159445897247 | erot = 25.0461733638716 | epot = -227.842923326835 | etot = -187.280805373238 +276000 ekin = 15.3290449735773 | erot = 22.6013849304136 | epot = -226.645721417409 | etot = -188.715291513418 +277000 ekin = 14.8998254086663 | erot = 21.4368139643109 | epot = -225.632942921213 | etot = -189.296303548235 +278000 ekin = 14.6883229783611 | erot = 21.764246814846 | epot = -224.505045285419 | etot = -188.052475492212 +279000 ekin = 14.8047270727149 | erot = 21.9101300703525 | epot = -223.591887497535 | etot = -186.877030354468 +280000 ekin = 15.1052613957242 | erot = 21.2019638470283 | epot = -222.930554266676 | etot = -186.623329023924 +281000 ekin = 15.9185405703085 | erot = 22.7554995785104 | epot = -222.496264131452 | etot = -183.822223982633 +282000 ekin = 15.7118745407237 | erot = 21.6184112020448 | epot = -222.111847398432 | etot = -184.781561655664 +283000 ekin = 15.6333488922702 | erot = 21.465780561396 | epot = -221.697448312628 | etot = -184.598318858962 +284000 ekin = 15.959853189633 | erot = 21.5564118521706 | epot = -221.456027263584 | etot = -183.93976222178 +285000 ekin = 16.1804948749226 | erot = 20.7957823598973 | epot = -221.442032618529 | etot = -184.465755383709 +286000 ekin = 16.2437780433302 | erot = 22.0029966684091 | epot = -221.48947785587 | etot = -183.242703144131 +287000 ekin = 16.5860527634174 | erot = 21.2347797551117 | epot = -221.681437402569 | etot = -183.86060488404 +288000 ekin = 17.4777982920666 | erot = 22.9676186033132 | epot = -222.210097097494 | etot = -181.764680202114 +289000 ekin = 19.2022256495172 | erot = 21.806988434862 | epot = -223.03555219086 | etot = -182.026338106481 +290000 ekin = 20.6029736081834 | erot = 21.6756942552161 | epot = -223.927958525587 | etot = -181.649290662188 +291000 ekin = 21.0325637238795 | erot = 25.0635435951381 | epot = -224.954298339301 | etot = -178.858191020283 +292000 ekin = 21.9992014565845 | erot = 24.5675448811519 | epot = -226.014147345555 | etot = -179.447401007819 +293000 ekin = 22.8449936736823 | erot = 26.0971097085354 | epot = -227.039865181468 | etot = -178.09776179925 +294000 ekin = 24.2424273090434 | erot = 22.3242335931344 | epot = -227.698192270626 | etot = -181.131531368448 +295000 ekin = 25.1430321033927 | erot = 22.81093656589 | epot = -228.272133548427 | etot = -180.318164879144 +296000 ekin = 25.4190616181137 | erot = 23.5935920052844 | epot = -228.827919142591 | etot = -179.815265519193 +297000 ekin = 24.1157580511247 | erot = 24.5278953829289 | epot = -229.421950081214 | etot = -180.77829664716 +298000 ekin = 24.1091297661069 | erot = 24.3527158051324 | epot = -229.912795380237 | etot = -181.450949808998 +299000 ekin = 24.1889413361173 | erot = 28.3512815530446 | epot = -230.356799401626 | etot = -177.816576512464 +300000 ekin = 24.2163939347386 | erot = 26.6122585649448 | epot = -230.754469972665 | etot = -179.925817472982 +301000 ekin = 23.9473801903426 | erot = 27.8600078683744 | epot = -231.048868063292 | etot = -179.241480004575 +302000 ekin = 23.6699655332583 | erot = 27.5610103980966 | epot = -231.2462622361 | etot = -180.015286304745 +303000 ekin = 23.8797875069283 | erot = 29.2034880593161 | epot = -231.3115724611 | etot = -178.228296894856 +304000 ekin = 22.73106672979 | erot = 27.7503022429659 | epot = -231.512470993041 | etot = -181.031102020285 +305000 ekin = 22.1016085656468 | erot = 27.0493993901605 | epot = -231.718355828267 | etot = -182.56734787246 +306000 ekin = 21.3693097984681 | erot = 26.2537086929049 | epot = -231.891297103593 | etot = -184.26827861222 +307000 ekin = 21.0324320589055 | erot = 24.6230768163623 | epot = -232.14138641287 | etot = -186.485877537602 +308000 ekin = 20.1154566391106 | erot = 21.7787557790717 | epot = -232.402656379528 | etot = -190.508443961346 +309000 ekin = 19.6646153697248 | erot = 24.2524356353678 | epot = -232.726752497782 | etot = -188.809701492689 +310000 ekin = 19.506055878272 | erot = 23.0558815582429 | epot = -232.894728269794 | etot = -190.332790833279 +311000 ekin = 19.4366809731017 | erot = 23.3044474838376 | epot = -232.852507372457 | etot = -190.111378915517 +312000 ekin = 18.9851206753984 | erot = 23.3056434770267 | epot = -232.658571091316 | etot = -190.367806938891 +313000 ekin = 18.456476357187 | erot = 22.3541198734799 | epot = -232.226835699179 | etot = -191.416239468512 +314000 ekin = 17.5964963597534 | erot = 24.280152514809 | epot = -231.840379924947 | etot = -189.963731050385 +315000 ekin = 17.4204244485737 | erot = 23.6514203760144 | epot = -231.530486492869 | etot = -190.45864166828 +316000 ekin = 16.1724163728655 | erot = 22.698801275189 | epot = -231.308288231255 | etot = -192.4370705832 +317000 ekin = 16.1754961975214 | erot = 24.7458837009842 | epot = -231.086735374031 | etot = -190.165355475525 +318000 ekin = 15.6276186513821 | erot = 25.4598581999699 | epot = -230.874800576949 | etot = -189.787323725597 +319000 ekin = 15.2218658312374 | erot = 26.310179302591 | epot = -230.890983487464 | etot = -189.358938353635 +320000 ekin = 14.5086838632118 | erot = 25.5779207778604 | epot = -230.835599614339 | etot = -190.748994973267 +321000 ekin = 14.3605129926004 | erot = 24.3299501149204 | epot = -230.738948206952 | etot = -192.048485099431 +322000 ekin = 14.3610877203126 | erot = 22.9310291497487 | epot = -230.65305378356 | etot = -193.360936913499 +323000 ekin = 14.7688305230875 | erot = 22.2970860063464 | epot = -230.465569924266 | etot = -193.399653394832 +324000 ekin = 14.9355157274789 | erot = 21.6250944927411 | epot = -230.284210305093 | etot = -193.723600084873 +325000 ekin = 14.671493713112 | erot = 19.7302049638664 | epot = -230.227419340871 | etot = -195.825720663893 +326000 ekin = 14.9234987156657 | erot = 18.5568938196644 | epot = -230.211337706826 | etot = -196.730945171496 +327000 ekin = 15.4129696630397 | erot = 18.0709384490326 | epot = -230.259317350117 | etot = -196.775409238045 +328000 ekin = 16.3932927560713 | erot = 18.0499060967779 | epot = -230.447119407116 | etot = -196.003920554267 +329000 ekin = 17.4064272548349 | erot = 17.712742044302 | epot = -230.608667384644 | etot = -195.489498085507 +330000 ekin = 17.9751565884689 | erot = 20.51547017577 | epot = -230.944813706002 | etot = -192.454186941763 +331000 ekin = 18.0313803560148 | erot = 22.5739918453344 | epot = -231.277621168628 | etot = -190.672248967279 +332000 ekin = 18.15147843611 | erot = 22.8208528087548 | epot = -231.623777285706 | etot = -190.651446040841 +333000 ekin = 18.0930465656663 | erot = 21.9771411609275 | epot = -231.923848859364 | etot = -191.85366113277 +334000 ekin = 17.7728125353381 | erot = 23.128955301666 | epot = -232.169505006005 | etot = -191.267737169001 +335000 ekin = 19.0031630375606 | erot = 23.3897776040612 | epot = -232.460034619601 | etot = -190.067093977979 +336000 ekin = 19.5591765342243 | erot = 25.3697311547745 | epot = -232.739268822111 | etot = -187.810361133113 +337000 ekin = 19.8563675404798 | erot = 27.3439820813804 | epot = -232.906112080656 | etot = -185.705762458796 +338000 ekin = 19.751099035653 | erot = 24.921360312315 | epot = -232.758554071368 | etot = -188.0860947234 +339000 ekin = 19.9050741791919 | erot = 25.5301605485524 | epot = -232.417171827705 | etot = -186.98193709996 +340000 ekin = 19.8794162185109 | erot = 25.9787598068518 | epot = -231.88072644563 | etot = -186.022550420267 +341000 ekin = 19.9454216521201 | erot = 24.1566390151013 | epot = -231.212127397362 | etot = -187.11006673014 +342000 ekin = 19.9237875292304 | erot = 26.4019287790718 | epot = -230.32153874995 | etot = -183.995822441648 +343000 ekin = 19.1115068720885 | erot = 22.5948467356212 | epot = -229.503208394896 | etot = -187.796854787186 +344000 ekin = 18.3079084943896 | erot = 23.107837537118 | epot = -228.898967466162 | etot = -187.483221434654 +345000 ekin = 18.4650460950013 | erot = 23.8173535141912 | epot = -228.453285301913 | etot = -186.17088569272 +346000 ekin = 18.0304251681423 | erot = 23.3440747631772 | epot = -228.183574545935 | etot = -186.809074614615 +347000 ekin = 17.5483582122927 | erot = 23.0282517992432 | epot = -227.908297752933 | etot = -187.331687741398 +348000 ekin = 17.622359603253 | erot = 22.2176773752137 | epot = -227.687080765617 | etot = -187.847043787151 +349000 ekin = 18.1160269661089 | erot = 23.5048787159375 | epot = -227.62230627499 | etot = -186.001400592943 +350000 ekin = 18.4237634534031 | erot = 23.3245531376522 | epot = -227.749080027053 | etot = -186.000763435998 +351000 ekin = 18.7086532226307 | erot = 23.8443722630501 | epot = -227.802083115351 | etot = -185.24905762967 +352000 ekin = 18.4929053608692 | erot = 23.3879966472946 | epot = -228.059952926951 | etot = -186.179050918787 +353000 ekin = 18.9161069388645 | erot = 23.2227449598892 | epot = -228.455593201501 | etot = -186.316741302748 +354000 ekin = 19.0977071534437 | erot = 26.1711894049523 | epot = -228.863332747988 | etot = -183.594436189592 +355000 ekin = 18.8408988656362 | erot = 25.4820466037911 | epot = -229.149897752163 | etot = -184.826952282736 +356000 ekin = 18.0073291494761 | erot = 26.6233733651629 | epot = -229.30066738625 | etot = -184.669964871611 +357000 ekin = 17.7607082496061 | erot = 25.2859928393404 | epot = -229.131821622954 | etot = -186.085120534008 +358000 ekin = 17.3110477472649 | erot = 23.858172364184 | epot = -228.730492207362 | etot = -187.561272095913 +359000 ekin = 17.2747418765998 | erot = 22.3862089851412 | epot = -228.089331840306 | etot = -188.428380978565 +360000 ekin = 17.2627985134611 | erot = 22.0449155343728 | epot = -227.380056681146 | etot = -188.072342633312 +361000 ekin = 16.7022908865183 | erot = 20.1648887982823 | epot = -226.685841413765 | etot = -189.818661728965 +362000 ekin = 16.5236886103148 | erot = 17.367003581832 | epot = -226.179176639549 | etot = -192.288484447402 +363000 ekin = 16.6039189858822 | erot = 16.0035347935122 | epot = -225.740790574137 | etot = -193.133336794742 +364000 ekin = 15.9788934900066 | erot = 16.6121483003756 | epot = -225.114863846841 | etot = -192.523822056459 +365000 ekin = 15.1431317526968 | erot = 16.9097471834361 | epot = -224.479846480109 | etot = -192.426967543976 +366000 ekin = 14.3990111988618 | erot = 17.0852361664414 | epot = -223.860574415737 | etot = -192.376327050434 +367000 ekin = 14.7093223353035 | erot = 19.9259917527912 | epot = -223.239871274407 | etot = -188.604557186313 +368000 ekin = 14.4767524017819 | erot = 19.8571324274854 | epot = -222.763305586433 | etot = -188.429420757165 +369000 ekin = 14.5295526109511 | erot = 19.4653517852366 | epot = -222.374285556898 | etot = -188.37938116071 +370000 ekin = 14.6624229936735 | erot = 18.4895700260451 | epot = -222.141224908878 | etot = -188.98923188916 +371000 ekin = 14.5457820238232 | erot = 17.1607101368225 | epot = -222.091600781158 | etot = -190.385108620512 +372000 ekin = 14.3765645142415 | erot = 18.3396365891572 | epot = -222.422609627797 | etot = -189.706408524398 +373000 ekin = 14.7873291899404 | erot = 18.9757135731518 | epot = -223.205572088605 | etot = -189.442529325513 +374000 ekin = 15.7125804964135 | erot = 21.4180777064736 | epot = -224.094929147205 | etot = -186.964270944318 +375000 ekin = 15.9971371168641 | erot = 19.8267795606279 | epot = -225.189250395173 | etot = -189.365333717681 +376000 ekin = 16.6671924038023 | erot = 19.2635449216383 | epot = -226.559332642176 | etot = -190.628595316735 +377000 ekin = 17.7603728345199 | erot = 18.779994279654 | epot = -227.963757986198 | etot = -191.423390872024 +378000 ekin = 18.1886050864902 | erot = 20.8441911699424 | epot = -229.547369091145 | etot = -190.514572834712 +379000 ekin = 19.033100220467 | erot = 20.072237741282 | epot = -231.143533498054 | etot = -192.038195536305 +380000 ekin = 19.3958875215032 | erot = 21.4029492342147 | epot = -232.694529537328 | etot = -191.89569278161 +381000 ekin = 19.9083965791013 | erot = 22.0262926736848 | epot = -234.32167171513 | etot = -192.386982462344 +382000 ekin = 20.8309151956209 | erot = 23.0680223560274 | epot = -235.663830319217 | etot = -191.764892767568 +383000 ekin = 21.2110564910967 | erot = 21.0693378226244 | epot = -236.854844845752 | etot = -194.574450532031 +384000 ekin = 22.0271729397392 | erot = 19.5738896898674 | epot = -237.761071028817 | etot = -196.16000839921 +385000 ekin = 21.9888232627756 | erot = 21.9438035828551 | epot = -238.480083243308 | etot = -194.547456397677 +386000 ekin = 22.1638739887246 | erot = 22.6209901962172 | epot = -238.997084576409 | etot = -194.212220391467 +387000 ekin = 22.4704802119025 | erot = 23.1635909564577 | epot = -239.498617670884 | etot = -193.864546502524 +388000 ekin = 22.8360688044956 | erot = 25.0873884717806 | epot = -239.669249619648 | etot = -191.745792343372 +389000 ekin = 23.0584509448569 | erot = 23.7837899729554 | epot = -239.601361166478 | etot = -192.759120248666 +390000 ekin = 23.6960202157352 | erot = 22.2855109641288 | epot = -239.380639976731 | etot = -193.399108796867 +391000 ekin = 23.7991151344636 | erot = 20.6201012177775 | epot = -239.03189252051 | etot = -194.612676168269 +392000 ekin = 23.9591701543348 | erot = 21.9552661146519 | epot = -238.459192052771 | etot = -192.544755783784 +393000 ekin = 23.9801600708864 | erot = 22.869736284692 | epot = -237.591953793527 | etot = -190.742057437948 +394000 ekin = 23.4806447315076 | erot = 23.7894518329385 | epot = -236.673823439361 | etot = -189.403726874915 +395000 ekin = 24.5044542002931 | erot = 22.3496968561238 | epot = -235.743236345989 | etot = -188.889085289572 +396000 ekin = 25.0523490436962 | erot = 21.8742064454878 | epot = -234.847289992152 | etot = -187.920734502968 +397000 ekin = 24.6499536596579 | erot = 21.7645397688862 | epot = -234.02267754065 | etot = -187.608184112106 +398000 ekin = 24.6654129500861 | erot = 22.1514966474267 | epot = -233.052972677734 | etot = -186.236063080221 +399000 ekin = 24.4527034646846 | erot = 22.1387556663723 | epot = -232.022437613541 | etot = -185.430978482484 +400000 ekin = 24.2410273375347 | erot = 20.3962614781508 | epot = -231.005809135405 | etot = -186.36852031972 +401000 ekin = 23.6761212056534 | erot = 22.7225603362526 | epot = -230.115763739954 | etot = -183.717082198048 +402000 ekin = 23.2783312945623 | erot = 21.072405109571 | epot = -229.330217542778 | etot = -184.979481138645 +403000 ekin = 23.3187858415702 | erot = 21.6853668727119 | epot = -228.46646899817 | etot = -183.462316283888 +404000 ekin = 22.6452628627526 | erot = 19.8334541701381 | epot = -227.74020593733 | etot = -185.261488904439 +405000 ekin = 22.8006471912822 | erot = 18.666718374297 | epot = -227.470604446323 | etot = -186.003238880744 +406000 ekin = 22.2794202436027 | erot = 18.3828666900747 | epot = -227.331354672565 | etot = -186.669067738888 +407000 ekin = 22.2172456768627 | erot = 18.4773392588829 | epot = -227.523003290546 | etot = -186.828418354801 +408000 ekin = 22.6521756504711 | erot = 19.4208076833358 | epot = -227.87233388974 | etot = -185.799350555933 +409000 ekin = 23.5573264374349 | erot = 20.5061505842945 | epot = -228.154858179183 | etot = -184.091381157454 +410000 ekin = 24.2750456328492 | erot = 22.8792635845596 | epot = -228.453698162395 | etot = -181.299388944986 +411000 ekin = 25.2420122816034 | erot = 23.7365200565699 | epot = -228.770700580075 | etot = -179.792168241901 +412000 ekin = 25.291356362185 | erot = 23.8310304102202 | epot = -229.010782171434 | etot = -179.888395399029 +413000 ekin = 25.2600396503997 | erot = 22.7169838925796 | epot = -229.062680900308 | etot = -181.085657357328 +414000 ekin = 25.4912045141821 | erot = 23.7306969786591 | epot = -228.998337849082 | etot = -179.77643635624 +415000 ekin = 26.1735887247197 | erot = 22.6674135061758 | epot = -228.693341533324 | etot = -179.852339302428 +416000 ekin = 26.5748108328611 | erot = 21.6439172230018 | epot = -228.361662386621 | etot = -180.142934330759 +417000 ekin = 26.7768070690628 | erot = 21.6230631516283 | epot = -228.087012878216 | etot = -179.687142657525 +418000 ekin = 26.5908575562701 | erot = 22.1239144254595 | epot = -227.62723288751 | etot = -178.912460905781 +419000 ekin = 26.1390688484464 | erot = 19.8809151124988 | epot = -226.977438068285 | etot = -180.95745410734 +420000 ekin = 25.5372021331576 | erot = 18.4693355705533 | epot = -226.169296116375 | etot = -182.162758412664 +421000 ekin = 24.7576070800854 | erot = 21.2379290063398 | epot = -225.177912035829 | etot = -179.182375949404 +422000 ekin = 23.5775097382875 | erot = 20.7150967321225 | epot = -224.071351753226 | etot = -179.778745282816 +423000 ekin = 23.3503211007386 | erot = 20.7766198719257 | epot = -222.934603836064 | etot = -178.807662863399 +424000 ekin = 22.9014106427363 | erot = 21.0323838208275 | epot = -221.865657024477 | etot = -177.931862560913 +425000 ekin = 22.167001043224 | erot = 19.8951057365931 | epot = -221.008759763888 | etot = -178.946652984071 +426000 ekin = 21.7191918731043 | erot = 20.0481315073592 | epot = -220.379164165788 | etot = -178.611840785324 +427000 ekin = 22.3863209159599 | erot = 20.1467365914768 | epot = -219.748771980514 | etot = -177.215714473077 +428000 ekin = 22.3113642728441 | erot = 18.9435836850322 | epot = -219.042454222864 | etot = -177.787506264988 +429000 ekin = 21.8292251452452 | erot = 16.620780664556 | epot = -218.481603976101 | etot = -180.0315981663 +430000 ekin = 21.5787512284699 | erot = 15.9396143193706 | epot = -217.957523577516 | etot = -180.439158029675 +431000 ekin = 21.5476976648958 | erot = 16.0853660094757 | epot = -217.637522182414 | etot = -180.004458508042 +432000 ekin = 20.8305046334209 | erot = 18.3962397210501 | epot = -217.510435589248 | etot = -178.283691234777 +433000 ekin = 21.3366166805747 | erot = 17.1761613375181 | epot = -217.730201210123 | etot = -179.21742319203 +434000 ekin = 21.4473991234971 | erot = 18.3914065237362 | epot = -218.31882890629 | etot = -178.480023259057 +435000 ekin = 21.8938565298032 | erot = 20.4321817028492 | epot = -219.08695235614 | etot = -176.760914123488 +436000 ekin = 22.7745161208294 | erot = 21.7909028890296 | epot = -220.039533912902 | etot = -175.474114903043 +437000 ekin = 23.0603914755853 | erot = 23.5766353307907 | epot = -221.014303297324 | etot = -174.377276490948 +438000 ekin = 24.5047158921013 | erot = 22.5082522761815 | epot = -221.830036253357 | etot = -174.817068085074 +439000 ekin = 24.6143280761287 | erot = 24.2611592034082 | epot = -222.681938930047 | etot = -173.80645165051 +440000 ekin = 24.3817582592681 | erot = 24.7408480502237 | epot = -223.513777238926 | etot = -174.391170929434 +441000 ekin = 24.7073799963697 | erot = 26.0715535157816 | epot = -224.270002709343 | etot = -173.491069197191 +442000 ekin = 24.5768549815013 | erot = 26.1754826601808 | epot = -224.850802162052 | etot = -174.09846452037 +443000 ekin = 25.2420932847023 | erot = 24.7427655137794 | epot = -225.167556551113 | etot = -175.182697752631 +444000 ekin = 25.9747330874369 | erot = 26.9622244259886 | epot = -225.24583879208 | etot = -172.308881278654 +445000 ekin = 26.1721310818258 | erot = 27.8161657482946 | epot = -225.021125061423 | etot = -171.032828231303 +446000 ekin = 26.2042305171885 | erot = 26.6449261740889 | epot = -224.735035228785 | etot = -171.885878537508 +447000 ekin = 25.9445128989677 | erot = 26.4816025199488 | epot = -224.245178179105 | etot = -171.819062760188 +448000 ekin = 25.5372900980307 | erot = 25.0281118333634 | epot = -223.618727357863 | etot = -173.053325426469 +449000 ekin = 25.7322219082413 | erot = 26.9973146922278 | epot = -223.018245220603 | etot = -170.288708620134 +450000 ekin = 25.8738458288472 | erot = 26.4843992391509 | epot = -222.408567465752 | etot = -170.050322397754 +451000 ekin = 25.6858259591492 | erot = 25.2647052575128 | epot = -221.452550893268 | etot = -170.502019676606 +452000 ekin = 25.7815007863341 | erot = 23.0466968711352 | epot = -220.49127053138 | etot = -171.66307287391 +453000 ekin = 25.7970445433776 | erot = 21.1141058412002 | epot = -219.594142395429 | etot = -172.682992010851 +454000 ekin = 25.688804966856 | erot = 22.6294586470315 | epot = -218.915377931307 | etot = -170.59711431742 +455000 ekin = 25.6037732271854 | erot = 22.9697679221883 | epot = -218.493679612878 | etot = -169.920138463504 +456000 ekin = 26.0514762135096 | erot = 23.8916333063363 | epot = -218.316686773003 | etot = -168.373577253157 +457000 ekin = 26.0167886371092 | erot = 22.9916268768507 | epot = -218.187169314675 | etot = -169.178753800715 +458000 ekin = 25.7882597661439 | erot = 20.8748032531609 | epot = -217.987058469246 | etot = -171.323995449942 +459000 ekin = 26.1697981408122 | erot = 21.3086466081266 | epot = -218.026696392449 | etot = -170.54825164351 +460000 ekin = 25.7192439412156 | erot = 24.4214622489547 | epot = -218.347831000891 | etot = -168.207124810721 +461000 ekin = 25.7495969095132 | erot = 26.1294994916656 | epot = -218.822266029574 | etot = -166.943169628395 +462000 ekin = 25.8591234001759 | erot = 26.9103950574254 | epot = -219.538074391763 | etot = -166.768555934162 +463000 ekin = 25.4934778644091 | erot = 28.9857339062074 | epot = -220.244381956634 | etot = -165.765170186017 +464000 ekin = 25.3807989297151 | erot = 28.2636863620641 | epot = -220.82311618793 | etot = -167.178630896151 +465000 ekin = 25.4889304853069 | erot = 26.8232193679972 | epot = -221.238335961676 | etot = -168.926186108372 +466000 ekin = 25.6703409883731 | erot = 25.2637813032743 | epot = -221.475634605288 | etot = -170.54151231364 +467000 ekin = 25.3302831697602 | erot = 24.6072222319647 | epot = -221.607373938226 | etot = -171.669868536501 +468000 ekin = 26.2089173332122 | erot = 22.9661948896766 | epot = -221.830072302435 | etot = -172.654960079546 +469000 ekin = 27.6643804489026 | erot = 22.7018029478283 | epot = -222.234721440326 | etot = -171.868538043595 +470000 ekin = 27.7860331432337 | erot = 23.37749342455 | epot = -222.896428711169 | etot = -171.732902143385 +471000 ekin = 28.3340963939428 | erot = 25.3278577360011 | epot = -223.570564232673 | etot = -169.908610102729 +472000 ekin = 28.5060434759036 | erot = 25.626902389105 | epot = -224.148650689462 | etot = -170.015704824453 +473000 ekin = 28.8298134833811 | erot = 26.1588503986598 | epot = -224.562065916091 | etot = -169.573402034051 +474000 ekin = 28.5479350336082 | erot = 25.8885076622197 | epot = -224.671302893341 | etot = -170.234860197513 +475000 ekin = 28.7950172155165 | erot = 25.1475376581866 | epot = -224.461514143169 | etot = -170.518959269466 +476000 ekin = 28.4606864434488 | erot = 25.2517480986696 | epot = -223.893621964986 | etot = -170.181187422868 +477000 ekin = 28.0142928872112 | erot = 23.5481845275566 | epot = -223.15087114256 | etot = -171.588393727793 +478000 ekin = 27.7552032877925 | erot = 21.0056990914093 | epot = -222.398351737606 | etot = -173.637449358404 +479000 ekin = 26.7537623197156 | erot = 22.040286739641 | epot = -221.556035536971 | etot = -172.761986477614 +480000 ekin = 26.3364213218961 | erot = 21.616270547523 | epot = -220.488389208344 | etot = -172.535697338924 +481000 ekin = 25.5733541062401 | erot = 20.6410322219284 | epot = -219.255993114652 | etot = -173.041606786483 +482000 ekin = 25.3038828266597 | erot = 21.7331282226314 | epot = -218.060917075251 | etot = -171.02390602596 +483000 ekin = 25.4847680481985 | erot = 21.8125494513952 | epot = -217.017386150345 | etot = -169.720068650751 +484000 ekin = 25.4921600059346 | erot = 22.7125552631874 | epot = -216.165477936407 | etot = -167.960762667285 +485000 ekin = 25.1014549873177 | erot = 22.9083083653785 | epot = -215.459368644848 | etot = -167.449605292152 +486000 ekin = 23.7381916279128 | erot = 22.0359551706864 | epot = -214.867401759866 | etot = -169.093254961267 +487000 ekin = 23.1022967247011 | erot = 20.9897368619166 | epot = -214.49309827136 | etot = -170.401064684743 +488000 ekin = 22.3280062343421 | erot = 22.6581977288416 | epot = -214.411928640685 | etot = -169.425724677501 +489000 ekin = 21.5200390992131 | erot = 24.4256444850011 | epot = -214.553046668213 | etot = -168.607363083998 +490000 ekin = 22.1745834778823 | erot = 23.202684442612 | epot = -214.682014948056 | etot = -169.304747027562 +491000 ekin = 22.2155647410761 | erot = 23.9559835315798 | epot = -214.794268468461 | etot = -168.622720195805 +492000 ekin = 21.9074062571785 | erot = 23.0107085417582 | epot = -214.876391213439 | etot = -169.958276414503 +493000 ekin = 21.7673907407181 | erot = 22.3862681939078 | epot = -215.110849414315 | etot = -170.957190479689 +494000 ekin = 20.7745584966346 | erot = 22.7452296264065 | epot = -215.46860879911 | etot = -171.948820676069 +495000 ekin = 19.7536125274935 | erot = 24.534405221311 | epot = -215.973479846197 | etot = -171.685462097392 +496000 ekin = 19.5440096583046 | erot = 23.1762967935367 | epot = -216.627509848901 | etot = -173.90720339706 +497000 ekin = 19.2601107947869 | erot = 27.0129650022824 | epot = -217.496309014045 | etot = -171.223233216976 +498000 ekin = 20.008240149509 | erot = 28.3938360735788 | epot = -218.510580772204 | etot = -170.108504549116 +499000 ekin = 20.2250869378451 | erot = 29.7495194421564 | epot = -219.413536230996 | etot = -169.438929850994 +500000 ekin = 20.5377041017314 | erot = 25.5981483203109 | epot = -220.10250670273 | etot = -173.966654280688 +501000 ekin = 20.7437007868733 | erot = 25.5722254074985 | epot = -220.706620920466 | etot = -174.390694726094 +502000 ekin = 21.3974117388996 | erot = 27.1477040916275 | epot = -221.203987796437 | etot = -172.65887196591 +503000 ekin = 21.9720670171586 | erot = 27.4594748055059 | epot = -221.564705185604 | etot = -172.13316336294 +504000 ekin = 22.0036398241597 | erot = 27.8844566679454 | epot = -221.822730635735 | etot = -171.934634143629 +505000 ekin = 23.1885968423919 | erot = 27.0080739021865 | epot = -222.35778688837 | etot = -172.161116143791 +506000 ekin = 22.722531651873 | erot = 26.6500914123035 | epot = -222.671998920708 | etot = -173.299375856532 +507000 ekin = 22.2628604257524 | erot = 25.1165297319669 | epot = -223.132828338462 | etot = -175.753438180742 +508000 ekin = 22.7028911519561 | erot = 23.4656498814886 | epot = -223.54407467575 | etot = -177.375533642305 +509000 ekin = 22.6654713026151 | erot = 22.3116431994452 | epot = -223.812280936561 | etot = -178.8351664345 +510000 ekin = 23.2444036217202 | erot = 23.7118265646526 | epot = -224.123509542875 | etot = -177.167279356502 +511000 ekin = 22.7352979426128 | erot = 23.8711299722302 | epot = -224.367646933689 | etot = -177.761219018846 +512000 ekin = 22.460433299215 | erot = 25.9025431935021 | epot = -224.625156824351 | etot = -176.262180331634 +513000 ekin = 22.0947651201679 | erot = 24.9904521975554 | epot = -224.816807649759 | etot = -177.731590332036 +514000 ekin = 21.783961391663 | erot = 27.6768125066713 | epot = -224.803176634329 | etot = -175.342402735995 +515000 ekin = 20.8838805084714 | erot = 26.7006493321653 | epot = -224.615071561818 | etot = -177.030541721182 +516000 ekin = 21.4036026624667 | erot = 29.9826472115484 | epot = -224.43203188109 | etot = -173.045782007075 +517000 ekin = 21.0725470625647 | erot = 29.5449947930599 | epot = -224.413593337603 | etot = -173.796051481978 +518000 ekin = 21.1692298808073 | erot = 27.273466345669 | epot = -224.467250578245 | etot = -176.024554351769 +519000 ekin = 21.5445051781035 | erot = 27.4144674038741 | epot = -224.856924566818 | etot = -175.89795198484 +520000 ekin = 21.8088279707338 | erot = 26.9958167714558 | epot = -225.458073506627 | etot = -176.653428764437 +521000 ekin = 21.3359848054427 | erot = 27.3496112855869 | epot = -226.263472854907 | etot = -177.577876763878 +522000 ekin = 21.383381595961 | erot = 28.5594995391198 | epot = -227.177929279517 | etot = -177.235048144436 +523000 ekin = 22.3312177264689 | erot = 28.7548602321851 | epot = -228.039253797182 | etot = -176.953175838528 +524000 ekin = 22.876818128058 | erot = 30.8759050315318 | epot = -228.592215099028 | etot = -174.839491939438 +525000 ekin = 23.6968405729144 | erot = 30.6366736796914 | epot = -229.121694343188 | etot = -174.788180090583 +526000 ekin = 24.0470079695023 | erot = 27.5141010669624 | epot = -229.424175891327 | etot = -177.863066854862 +527000 ekin = 24.7652559941686 | erot = 24.0459690561378 | epot = -229.423371401068 | etot = -180.612146350762 +528000 ekin = 25.8850187683723 | erot = 21.6623200862783 | epot = -229.307228706866 | etot = -181.759889852215 +529000 ekin = 27.0463610704001 | erot = 22.1786800201847 | epot = -229.038404872887 | etot = -179.813363782302 +530000 ekin = 27.7753267980006 | erot = 21.352696690415 | epot = -228.849367136447 | etot = -179.721343648031 +531000 ekin = 27.8126912344675 | erot = 20.3285370027924 | epot = -228.550501942543 | etot = -180.409273705283 +532000 ekin = 28.6172804460881 | erot = 18.3427969924976 | epot = -228.423163122221 | etot = -181.463085683636 +533000 ekin = 28.2068049753172 | erot = 18.2536479974195 | epot = -228.612314526597 | etot = -182.151861553861 +534000 ekin = 28.4495519996443 | erot = 18.0012277086546 | epot = -228.943853455769 | etot = -182.49307374747 +535000 ekin = 28.9497940969891 | erot = 16.8492155357581 | epot = -229.741275998853 | etot = -183.942266366106 +536000 ekin = 28.5652244837817 | erot = 17.3435379345182 | epot = -230.83687671424 | etot = -184.92811429594 +537000 ekin = 29.022362828562 | erot = 17.9527916225231 | epot = -231.95803351984 | etot = -184.982879068755 +538000 ekin = 29.8174105606222 | erot = 16.0379790395698 | epot = -232.791699361863 | etot = -186.936309761671 +539000 ekin = 29.6952792444876 | erot = 17.4273307073527 | epot = -233.496059263026 | etot = -186.373449311186 +540000 ekin = 29.750585937819 | erot = 20.0144365059585 | epot = -234.056270399686 | etot = -184.291247955909 +541000 ekin = 29.368313343467 | erot = 19.579576821786 | epot = -234.349077090936 | etot = -185.401186925683 +542000 ekin = 28.4447550384428 | erot = 19.7945093762075 | epot = -234.236435613877 | etot = -185.997171199227 +543000 ekin = 27.7587268728516 | erot = 21.2328503430547 | epot = -233.528121996461 | etot = -184.536544780555 +544000 ekin = 28.3225695671127 | erot = 17.802768152032 | epot = -232.50551567328 | etot = -186.380177954136 +545000 ekin = 28.0998287685114 | erot = 19.6585770476894 | epot = -231.387898079567 | etot = -183.629492263366 +546000 ekin = 27.3903651306005 | erot = 21.807934581675 | epot = -230.479365576106 | etot = -181.281065863831 +547000 ekin = 26.7970978237519 | erot = 20.9996558932496 | epot = -229.684797062509 | etot = -181.888043345508 +548000 ekin = 26.7983027373764 | erot = 20.8421351684446 | epot = -228.90155588475 | etot = -181.261117978929 +549000 ekin = 26.188169756037 | erot = 21.0585848868904 | epot = -228.206493092338 | etot = -180.95973844941 +550000 ekin = 26.0140312453881 | erot = 22.5801677208772 | epot = -227.777402823687 | etot = -179.183203857422 +551000 ekin = 25.7757664599119 | erot = 23.9110391567262 | epot = -227.517272594077 | etot = -177.830466977439 +552000 ekin = 25.8315344617212 | erot = 23.7338223198244 | epot = -227.474934810832 | etot = -177.909578029286 +553000 ekin = 25.6747033622136 | erot = 22.7253607563637 | epot = -227.635537487589 | etot = -179.235473369012 +554000 ekin = 25.6047324774861 | erot = 22.6670330249201 | epot = -227.987099764937 | etot = -179.715334262531 +555000 ekin = 26.5879549294076 | erot = 24.0685342421982 | epot = -228.529950924382 | etot = -177.873461752776 +556000 ekin = 27.6268706515679 | erot = 22.1109312637994 | epot = -229.425954027825 | etot = -179.688152112458 +557000 ekin = 28.069112907845 | erot = 26.8965683539211 | epot = -230.584971459936 | etot = -175.61929019817 +558000 ekin = 28.0678083112931 | erot = 25.6618030440032 | epot = -231.991530613965 | etot = -178.261919258669 +559000 ekin = 28.9742033607634 | erot = 26.5724591704157 | epot = -233.463994495035 | etot = -177.917331963856 +560000 ekin = 28.9011051536108 | erot = 25.5889025184335 | epot = -234.725653093072 | etot = -180.235645421027 +561000 ekin = 29.4002126238622 | erot = 26.2954345341183 | epot = -235.835285786746 | etot = -180.139638628766 +562000 ekin = 29.975757760105 | erot = 24.4408981516764 | epot = -236.463195408104 | etot = -182.046539496323 +563000 ekin = 29.7752306165208 | erot = 27.2106096805276 | epot = -236.685322677156 | etot = -179.699482380108 +564000 ekin = 29.8813809383381 | erot = 26.6216283857818 | epot = -236.661076407545 | etot = -180.158067083425 +565000 ekin = 29.6774879892468 | erot = 27.2290939876273 | epot = -236.311809225071 | etot = -179.405227248197 +566000 ekin = 28.6346936939147 | erot = 26.8023560052638 | epot = -235.668742898058 | etot = -180.23169319888 +567000 ekin = 27.3954299875009 | erot = 26.5201802334772 | epot = -234.779541480291 | etot = -180.863931259313 +568000 ekin = 27.4071194817491 | erot = 25.1324696708474 | epot = -233.501854955991 | etot = -180.962265803394 +569000 ekin = 26.6231867984125 | erot = 24.6541363875885 | epot = -232.187184366121 | etot = -180.90986118012 +570000 ekin = 27.6093553036065 | erot = 23.6900717393427 | epot = -230.809430752191 | etot = -179.510003709242 +571000 ekin = 26.9083310567801 | erot = 22.528408139646 | epot = -229.566553491015 | etot = -180.129814294588 +572000 ekin = 26.4716627800808 | erot = 22.2845965716381 | epot = -228.619137213519 | etot = -179.8628778618 +573000 ekin = 26.6971389887138 | erot = 21.8798558769198 | epot = -228.034982255581 | etot = -179.457987389947 +574000 ekin = 27.2478685862593 | erot = 21.7451315224891 | epot = -227.459773842304 | etot = -178.466773733556 +575000 ekin = 28.7134212605173 | erot = 21.3522952166471 | epot = -226.994685152085 | etot = -176.928968674921 +576000 ekin = 28.5222344692551 | erot = 18.8986377279701 | epot = -226.85884558054 | etot = -179.437973383315 +577000 ekin = 29.1715076179565 | erot = 20.1101522026671 | epot = -226.880557883166 | etot = -177.598898062543 +578000 ekin = 29.1958211105308 | erot = 20.240027120463 | epot = -226.916258035043 | etot = -177.480409804049 +579000 ekin = 28.7985703505952 | erot = 18.3977325249373 | epot = -226.88304615327 | etot = -179.686743277737 +580000 ekin = 28.4440078780217 | erot = 18.4595801944313 | epot = -226.943317478502 | etot = -180.039729406048 +581000 ekin = 29.6191385878667 | erot = 18.2815372928574 | epot = -227.074832318056 | etot = -179.174156437332 +582000 ekin = 28.8755366565893 | erot = 17.8411251075596 | epot = -227.166122160148 | etot = -180.449460395999 +583000 ekin = 28.6195101128279 | erot = 17.8287187393535 | epot = -227.132715220626 | etot = -180.684486368445 +584000 ekin = 28.2523600687915 | erot = 17.6307832024022 | epot = -227.251691559433 | etot = -181.368548288239 +585000 ekin = 27.5957630773252 | erot = 17.8252193046033 | epot = -227.442847627708 | etot = -182.021865245779 +586000 ekin = 27.7899511430164 | erot = 18.5604184072932 | epot = -227.520178862255 | etot = -181.169809311945 +587000 ekin = 27.3277470399822 | erot = 19.4404091802981 | epot = -227.404442611801 | etot = -180.636286391521 +588000 ekin = 27.3638216941813 | erot = 20.0988247739979 | epot = -227.0932868642 | etot = -179.630640396021 +589000 ekin = 26.9522108357383 | erot = 19.0940445155609 | epot = -226.797323932239 | etot = -180.751068580939 +590000 ekin = 27.0814604422477 | erot = 18.9210809272503 | epot = -226.462739616754 | etot = -180.460198247256 +591000 ekin = 26.6304741560081 | erot = 19.7073249259863 | epot = -226.366593304564 | etot = -180.02879422257 +592000 ekin = 26.6793460171722 | erot = 22.0507306271919 | epot = -226.36463028426 | etot = -177.634553639896 +593000 ekin = 26.4435671908487 | erot = 22.0663123802426 | epot = -226.444524918504 | etot = -177.934645347413 +594000 ekin = 26.051479512619 | erot = 21.4158049135016 | epot = -226.573432513486 | etot = -179.106148087365 +595000 ekin = 25.6800098048177 | erot = 21.489745642643 | epot = -226.861484159439 | etot = -179.691728711979 +596000 ekin = 25.4982303265013 | erot = 22.0961692232522 | epot = -227.19375202979 | etot = -179.599352480036 +597000 ekin = 24.4179219809124 | erot = 21.221622910841 | epot = -227.371569607757 | etot = -181.732024716003 +598000 ekin = 24.2598938247207 | erot = 23.7729295468385 | epot = -227.36641699774 | etot = -179.333593626181 +599000 ekin = 24.2026897211424 | erot = 23.7935607586132 | epot = -227.120360675563 | etot = -179.124110195808 +600000 ekin = 24.6901303608034 | erot = 22.0458619441968 | epot = -226.63280531999 | etot = -179.89681301499 +601000 ekin = 24.7093667383309 | erot = 23.9592983403602 | epot = -225.919718139048 | etot = -177.251053060357 +602000 ekin = 24.9977163593162 | erot = 21.6808979179701 | epot = -225.225550361662 | etot = -178.546936084376 +603000 ekin = 24.909080272873 | erot = 19.8567647026369 | epot = -224.510932501025 | etot = -179.745087525515 +604000 ekin = 25.7672016321128 | erot = 20.1058382913628 | epot = -223.859317715152 | etot = -177.986277791676 +605000 ekin = 26.2854405598537 | erot = 18.6086042172451 | epot = -223.341754324839 | etot = -178.44770954774 +606000 ekin = 26.8878269017605 | erot = 16.8626720456841 | epot = -223.037062471522 | etot = -179.286563524077 +607000 ekin = 27.708630558942 | erot = 16.2639676386698 | epot = -222.903954806076 | etot = -178.931356608464 +608000 ekin = 27.5722592645523 | erot = 16.050800679878 | epot = -222.655822923886 | etot = -179.032762979456 +609000 ekin = 27.3059305453791 | erot = 16.2526674395162 | epot = -222.499289767144 | etot = -178.940691782249 +610000 ekin = 26.0529834115964 | erot = 17.5407293679719 | epot = -222.559467243073 | etot = -178.965754463504 +611000 ekin = 25.6444622853818 | erot = 17.5578356444653 | epot = -222.540154641407 | etot = -179.33785671156 +612000 ekin = 26.1044768868262 | erot = 16.7678551448027 | epot = -222.589366667697 | etot = -179.717034636068 +613000 ekin = 26.778105103681 | erot = 17.5411817669898 | epot = -222.737319173291 | etot = -178.418032302621 +614000 ekin = 27.6064782364792 | erot = 16.8092616077952 | epot = -222.738962051088 | etot = -178.323222206813 +615000 ekin = 27.202348500151 | erot = 18.1300982120248 | epot = -222.580596496295 | etot = -177.248149784119 +616000 ekin = 26.7294242583747 | erot = 17.8023339715893 | epot = -222.270889821123 | etot = -177.739131591159 +617000 ekin = 25.9673127266019 | erot = 19.4938436622423 | epot = -221.855677631762 | etot = -176.394521242918 +618000 ekin = 24.6649274148857 | erot = 19.7556140429642 | epot = -221.395419093589 | etot = -176.974877635739 +619000 ekin = 23.8246156062723 | erot = 22.6932905362597 | epot = -220.85765285395 | etot = -174.339746711418 +620000 ekin = 22.3922506676526 | erot = 23.1856908985781 | epot = -220.581162841993 | etot = -175.003221275762 +621000 ekin = 21.4430140463455 | erot = 20.0877017400879 | epot = -220.316250852764 | etot = -178.785535066331 +622000 ekin = 21.0282015425459 | erot = 21.2952952107454 | epot = -220.469702077462 | etot = -178.146205324171 +623000 ekin = 20.5485493901374 | erot = 21.9686222594177 | epot = -220.884709147042 | etot = -178.367537497487 +624000 ekin = 20.4116762130833 | erot = 24.4448345310671 | epot = -221.506951111473 | etot = -176.650440367323 +625000 ekin = 20.7086024723278 | erot = 24.9980231142946 | epot = -222.442357834988 | etot = -176.735732248366 +626000 ekin = 21.41397100679 | erot = 25.3578069120284 | epot = -223.283385353664 | etot = -176.511607434846 +627000 ekin = 21.8080912412149 | erot = 22.9275444026493 | epot = -223.892792640231 | etot = -179.157156996367 +628000 ekin = 22.0606300305555 | erot = 21.9874550553957 | epot = -224.361440644786 | etot = -180.313355558834 +629000 ekin = 22.2686585302 | erot = 23.3956059048975 | epot = -224.755334667347 | etot = -179.091070232249 +630000 ekin = 22.7261581540143 | erot = 23.599198071745 | epot = -224.949694798805 | etot = -178.624338573046 +631000 ekin = 22.7545989614576 | erot = 18.6693303881336 | epot = -225.170398987567 | etot = -183.746469637976 +632000 ekin = 22.8582899163666 | erot = 18.8600074747406 | epot = -225.453249516017 | etot = -183.734952124909 +633000 ekin = 22.5940364544595 | erot = 19.5865726816331 | epot = -225.675890763231 | etot = -183.495281627138 +634000 ekin = 21.7360344990529 | erot = 21.1386827787326 | epot = -225.807787978514 | etot = -182.933070700728 +635000 ekin = 22.3638048171573 | erot = 20.8651345753279 | epot = -226.017654598281 | etot = -182.788715205795 +636000 ekin = 23.2564468915411 | erot = 20.9568292454768 | epot = -226.474810466865 | etot = -182.261534329847 +637000 ekin = 23.7446282139124 | erot = 20.9649035011187 | epot = -227.255190257715 | etot = -182.545658542684 +638000 ekin = 24.9768211335302 | erot = 20.7684051797868 | epot = -228.339137670731 | etot = -182.593911357414 +639000 ekin = 25.6081152991627 | erot = 20.5394040856467 | epot = -229.535959313578 | etot = -183.388439928768 +640000 ekin = 25.882879312268 | erot = 21.5458521538092 | epot = -230.501601623652 | etot = -183.072870157574 +641000 ekin = 26.7192719153612 | erot = 21.5077808734751 | epot = -231.311086176637 | etot = -183.084033387801 +642000 ekin = 26.7533018509874 | erot = 22.3868483570804 | epot = -231.697126060187 | etot = -182.556975852119 +643000 ekin = 27.227638812425 | erot = 22.7444906941992 | epot = -231.70041423596 | etot = -181.728284729336 +644000 ekin = 28.2340179730461 | erot = 21.2142453447777 | epot = -231.34574674841 | etot = -181.897483430587 +645000 ekin = 27.9813501134116 | erot = 19.5632665182491 | epot = -230.723712640252 | etot = -183.179096008591 +646000 ekin = 27.3510433641092 | erot = 20.3180919491713 | epot = -229.805725426514 | etot = -182.136590113233 +647000 ekin = 27.4763651215188 | erot = 20.1973565201653 | epot = -228.883194713424 | etot = -181.20947307174 +648000 ekin = 26.9203103910451 | erot = 19.3299558126679 | epot = -228.183094649897 | etot = -181.932828446184 +649000 ekin = 27.1584207863441 | erot = 19.7773817590138 | epot = -227.851865720852 | etot = -180.916063175494 +650000 ekin = 27.8558677817717 | erot = 21.5235280981856 | epot = -227.854497907235 | etot = -178.475102027277 +651000 ekin = 27.4752369028502 | erot = 22.4969948370604 | epot = -228.056030460106 | etot = -178.083798720195 +652000 ekin = 27.8926782089265 | erot = 20.2366908977832 | epot = -228.25658268699 | etot = -180.12721358028 +653000 ekin = 27.833217461393 | erot = 22.8857793598376 | epot = -228.476748982019 | etot = -177.757752160788 +654000 ekin = 28.0840949255035 | erot = 20.7706125191501 | epot = -228.683833272169 | etot = -179.829125827515 +655000 ekin = 27.403762673065 | erot = 22.3510763116526 | epot = -229.021084688067 | etot = -179.266245703349 +656000 ekin = 28.3726446615757 | erot = 22.7742600500831 | epot = -229.347089574997 | etot = -178.200184863339 +657000 ekin = 27.7030235167448 | erot = 21.8629223338815 | epot = -229.434356479491 | etot = -179.868410628864 +658000 ekin = 27.1759488980294 | erot = 23.4533512480567 | epot = -229.408283419532 | etot = -178.778983273446 +659000 ekin = 27.1576709282284 | erot = 21.6330760247461 | epot = -229.142943895062 | etot = -180.352196942087 +660000 ekin = 26.3221730814178 | erot = 21.7821345770448 | epot = -228.723364173055 | etot = -180.619056514592 +661000 ekin = 25.779491442224 | erot = 22.2970031395793 | epot = -228.256343213546 | etot = -180.179848631742 +662000 ekin = 25.2646841713566 | erot = 21.3867459046999 | epot = -227.695753928069 | etot = -181.044323852012 +663000 ekin = 25.788599860439 | erot = 22.1358077324136 | epot = -227.095496572601 | etot = -179.171088979748 +664000 ekin = 25.6902100255482 | erot = 21.1754933170497 | epot = -226.605702908437 | etot = -179.739999565839 +665000 ekin = 25.8071177593121 | erot = 20.2980512970803 | epot = -226.316135130784 | etot = -180.210966074392 +666000 ekin = 25.654039027879 | erot = 19.3527959955109 | epot = -226.278718912648 | etot = -181.271883889258 +667000 ekin = 25.259919176648 | erot = 21.3448305524703 | epot = -226.010298820921 | etot = -179.405549091803 +668000 ekin = 24.899938000725 | erot = 20.4509835382855 | epot = -225.592827118275 | etot = -180.241905579265 +669000 ekin = 24.445106638769 | erot = 20.2026559802712 | epot = -225.189465074759 | etot = -180.541702455719 +670000 ekin = 23.6375178330896 | erot = 21.4368740508129 | epot = -224.732122186456 | etot = -179.657730302553 +671000 ekin = 23.6282860496992 | erot = 21.7094329321311 | epot = -224.008580994932 | etot = -178.670862013101 +672000 ekin = 24.0984504997224 | erot = 21.9403750101964 | epot = -223.13895872841 | etot = -177.100133218492 +673000 ekin = 23.7973496489823 | erot = 20.9987265259934 | epot = -222.393285441872 | etot = -177.597209266896 +674000 ekin = 23.7065530280889 | erot = 22.376642799205 | epot = -221.700044416557 | etot = -175.616848589263 +675000 ekin = 23.001776123468 | erot = 23.6694964963629 | epot = -221.420479977735 | etot = -174.749207357904 +676000 ekin = 22.5164066205241 | erot = 22.6402910589994 | epot = -221.322788427074 | etot = -176.16609074755 +677000 ekin = 22.5497630953929 | erot = 23.1877936778892 | epot = -221.402074795503 | etot = -175.664518022221 +678000 ekin = 21.5585311333769 | erot = 22.8702436982297 | epot = -221.697973670764 | etot = -177.269198839157 +679000 ekin = 21.4618959055948 | erot = 23.3865040507615 | epot = -222.015748334195 | etot = -177.167348377838 +680000 ekin = 21.4622800320567 | erot = 21.4127199547269 | epot = -222.429797710664 | etot = -179.55479772388 +681000 ekin = 21.1737975880679 | erot = 21.5846131769088 | epot = -222.953468011023 | etot = -180.195057246046 +682000 ekin = 21.7254656898551 | erot = 21.6540443362751 | epot = -223.45869005669 | etot = -180.07918003056 +683000 ekin = 21.4183563237426 | erot = 23.8796952031651 | epot = -224.031962106781 | etot = -178.733910579873 +684000 ekin = 22.2181785671375 | erot = 26.4163907692242 | epot = -224.556597387323 | etot = -175.922028050961 +685000 ekin = 22.4057534349632 | erot = 26.3514235333686 | epot = -224.764117789834 | etot = -176.006940821502 +686000 ekin = 21.9879963383394 | erot = 25.5983588287999 | epot = -224.837162072601 | etot = -177.250806905461 +687000 ekin = 21.7554417881072 | erot = 27.0115877106503 | epot = -224.825418203926 | etot = -176.058388705169 +688000 ekin = 21.8197561062317 | erot = 25.0081437700991 | epot = -224.863055701397 | etot = -178.035155825067 +689000 ekin = 21.5892200304501 | erot = 29.2491439251534 | epot = -224.907328455093 | etot = -174.068964499489 +690000 ekin = 21.8426769308178 | erot = 27.2293005592937 | epot = -224.943981990783 | etot = -175.872004500672 +691000 ekin = 22.1363752207295 | erot = 25.7931707752218 | epot = -224.746736914525 | etot = -176.817190918574 +692000 ekin = 22.5352297800636 | erot = 25.3446974399755 | epot = -224.434434618052 | etot = -176.554507398013 +693000 ekin = 22.8091228929751 | erot = 26.4872450844796 | epot = -224.047374463991 | etot = -174.751006486536 +694000 ekin = 22.4873583888692 | erot = 25.6513676536721 | epot = -223.737465620132 | etot = -175.598739577591 +695000 ekin = 23.1242633624005 | erot = 21.5570288691547 | epot = -223.550411341546 | etot = -178.869119109991 +696000 ekin = 24.0628961042017 | erot = 18.7702329767746 | epot = -223.663714460872 | etot = -180.830585379896 +697000 ekin = 24.4595165378671 | erot = 16.374437330644 | epot = -224.303732218758 | etot = -183.469778350247 +698000 ekin = 25.8305878390951 | erot = 15.1686612882172 | epot = -225.420465790738 | etot = -184.421216663426 +699000 ekin = 26.583760876588 | erot = 16.914220924162 | epot = -227.004086871952 | etot = -183.506105071201 +700000 ekin = 27.5797608451701 | erot = 19.1004834812402 | epot = -228.733304055557 | etot = -182.053059729146 +701000 ekin = 28.092598661006 | erot = 19.107193423995 | epot = -230.4398691701 | etot = -183.240077085099 +702000 ekin = 28.038659655595 | erot = 20.8470907300003 | epot = -231.921720460127 | etot = -183.035970074532 +703000 ekin = 28.1176122670283 | erot = 20.4831386988919 | epot = -233.089326607717 | etot = -184.488575641797 +704000 ekin = 28.6795532382639 | erot = 21.9842156401384 | epot = -233.886659285723 | etot = -183.222890407321 +705000 ekin = 28.4117756447571 | erot = 25.4648529190999 | epot = -234.312539385659 | etot = -180.435910821802 +706000 ekin = 27.4926471672545 | erot = 26.570396574273 | epot = -234.463545747886 | etot = -180.400502006358 +707000 ekin = 26.4290449605895 | erot = 29.8098318595607 | epot = -234.288422874891 | etot = -178.049546054741 +708000 ekin = 26.785682949808 | erot = 26.5168034780305 | epot = -233.599155373867 | etot = -180.296668946029 +709000 ekin = 26.1152543232575 | erot = 25.8699376167037 | epot = -232.62906889387 | etot = -180.643876953909 +710000 ekin = 25.640992098621 | erot = 24.9444607038658 | epot = -231.31659516414 | etot = -180.731142361653 +711000 ekin = 24.8084490562813 | erot = 22.41486490139 | epot = -230.188845489325 | etot = -182.965531531653 +712000 ekin = 24.0206122957558 | erot = 23.3639832553073 | epot = -229.544707677943 | etot = -182.16011212688 +713000 ekin = 23.3232426911543 | erot = 23.9964282538794 | epot = -229.263722517708 | etot = -181.944051572675 +714000 ekin = 23.3805726450359 | erot = 23.0699795298048 | epot = -229.169110187163 | etot = -182.718558012323 +715000 ekin = 22.6342143618995 | erot = 23.6996306944786 | epot = -229.323793869064 | etot = -182.989948812685 +716000 ekin = 22.7503175950267 | erot = 24.6103793866802 | epot = -229.738719755983 | etot = -182.378022774277 +717000 ekin = 22.7487828419965 | erot = 23.3120643428286 | epot = -230.199311355603 | etot = -184.138464170778 +718000 ekin = 23.7440282855966 | erot = 21.6662565298252 | epot = -230.594844861738 | etot = -185.184560046316 +719000 ekin = 23.0053134398269 | erot = 21.1345728705727 | epot = -230.919025277455 | etot = -186.779138967055 +720000 ekin = 22.7927824705925 | erot = 18.6486137418451 | epot = -231.312571080127 | etot = -189.871174867689 +721000 ekin = 22.9406443866908 | erot = 19.8512244181128 | epot = -231.525388298161 | etot = -188.733519493358 +722000 ekin = 22.6168297832631 | erot = 19.1089757310031 | epot = -231.486078548655 | etot = -189.760273034388 +723000 ekin = 23.2145903286558 | erot = 18.4327411531208 | epot = -231.073654493071 | etot = -189.426323011295 +724000 ekin = 23.1941486606142 | erot = 20.1152704224142 | epot = -230.393344877734 | etot = -187.083925794705 +725000 ekin = 23.2117542270878 | erot = 20.0416524857156 | epot = -229.681975652754 | etot = -186.428568939951 +726000 ekin = 22.4943249505552 | erot = 17.6255689470432 | epot = -229.018602806407 | etot = -188.898708908808 +727000 ekin = 23.0134120388946 | erot = 16.0733087173804 | epot = -228.449610641761 | etot = -189.362889885486 +728000 ekin = 23.6002606897018 | erot = 17.3538640496192 | epot = -227.894896906635 | etot = -186.940772167314 +729000 ekin = 23.2666739347333 | erot = 15.9737775925554 | epot = -227.639499131122 | etot = -188.399047603833 +730000 ekin = 23.6369012496368 | erot = 15.0574600338378 | epot = -227.615876852929 | etot = -188.921515569454 +731000 ekin = 24.2843158588705 | erot = 14.7532999805969 | epot = -227.863610813074 | etot = -188.825994973606 +732000 ekin = 24.5920563697733 | erot = 15.441921529354 | epot = -228.208536089551 | etot = -188.174558190424 +733000 ekin = 24.9542143587772 | erot = 16.2528554884185 | epot = -228.886245906842 | etot = -187.679176059646 +734000 ekin = 25.1975745295967 | erot = 17.5309997011736 | epot = -229.874798122519 | etot = -187.146223891749 +735000 ekin = 26.3384002839214 | erot = 20.2147377764707 | epot = -231.034141807835 | etot = -184.481003747443 +736000 ekin = 26.9977201223223 | erot = 21.4312348250696 | epot = -232.517347753316 | etot = -184.088392805924 +737000 ekin = 27.106843703555 | erot = 21.9213211360194 | epot = -233.962863053087 | etot = -184.934698213512 +738000 ekin = 27.0817280355982 | erot = 23.1086627439609 | epot = -235.308416470173 | etot = -185.118025690614 +739000 ekin = 27.7017346367214 | erot = 23.0670600140734 | epot = -236.434348689915 | etot = -185.66555403912 +740000 ekin = 27.414483533319 | erot = 22.8495946003411 | epot = -237.159045352128 | etot = -186.894967218468 +741000 ekin = 27.1254940524986 | erot = 25.2136677791409 | epot = -237.27567454816 | etot = -184.936512716521 +742000 ekin = 26.1007467617893 | erot = 24.3083714669445 | epot = -237.110037846066 | etot = -186.700919617333 +743000 ekin = 25.9661191503059 | erot = 24.9966890539635 | epot = -236.568563108752 | etot = -185.605754904482 +744000 ekin = 25.9610162148347 | erot = 24.0267364726876 | epot = -235.718093082982 | etot = -185.73034039546 +745000 ekin = 25.1903410925453 | erot = 20.0322158938195 | epot = -234.647323333736 | etot = -189.424766347371 +746000 ekin = 24.5549018272587 | erot = 19.5333934287955 | epot = -233.457073304408 | etot = -189.368778048353 +747000 ekin = 24.6969973760579 | erot = 19.684765269497 | epot = -232.388047096093 | etot = -188.006284450538 +748000 ekin = 23.8661147826955 | erot = 18.7566250549712 | epot = -231.325158225068 | etot = -188.702418387402 +749000 ekin = 22.8905662925953 | erot = 17.616297562066 | epot = -230.516546812681 | etot = -190.009682958019 +750000 ekin = 21.7762308247725 | erot = 18.808565539541 | epot = -229.678177029533 | etot = -189.09338066522 +751000 ekin = 21.470435101573 | erot = 19.3561756327847 | epot = -229.009265480618 | etot = -188.18265474626 +752000 ekin = 21.9146908855108 | erot = 21.6932584373869 | epot = -228.339869446873 | etot = -184.731920123975 +753000 ekin = 21.3126722507014 | erot = 19.4830994613168 | epot = -227.826644686117 | etot = -187.030872974099 +754000 ekin = 21.9973420006405 | erot = 18.3087877257647 | epot = -227.734582363023 | etot = -187.428452636618 +755000 ekin = 22.0630883354931 | erot = 17.7232559029141 | epot = -227.901903373361 | etot = -188.115559134954 +756000 ekin = 22.7885108553802 | erot = 18.9466234012732 | epot = -228.388591706589 | etot = -186.653457449935 +757000 ekin = 23.4273630235623 | erot = 19.3375649643952 | epot = -229.062755020945 | etot = -186.297827032987 +758000 ekin = 23.957213137725 | erot = 17.6511752357222 | epot = -229.883345819876 | etot = -188.274957446429 +759000 ekin = 24.8000463898566 | erot = 19.7556788733861 | epot = -230.860841170257 | etot = -186.305115907015 +760000 ekin = 24.3481865433343 | erot = 19.5845017015682 | epot = -231.819085479179 | etot = -187.886397234276 +761000 ekin = 24.7383964493482 | erot = 19.7052128432058 | epot = -232.446954772443 | etot = -188.003345479889 +762000 ekin = 24.7648359199342 | erot = 19.1678127120839 | epot = -232.719408348113 | etot = -188.786759716095 +763000 ekin = 24.6386313272633 | erot = 20.2072282597132 | epot = -232.892027596087 | etot = -188.046168009111 +764000 ekin = 24.535646123958 | erot = 22.5770425253206 | epot = -232.923754633562 | etot = -185.811065984283 +765000 ekin = 23.5513975921745 | erot = 23.8339377954301 | epot = -232.76312879921 | etot = -185.377793411606 +766000 ekin = 23.3033290453631 | erot = 23.9531600538532 | epot = -232.376570600668 | etot = -185.120081501452 +767000 ekin = 23.3690671647366 | erot = 21.8572954539486 | epot = -231.660452995211 | etot = -186.434090376525 +768000 ekin = 23.2846487005283 | erot = 21.3431585578876 | epot = -230.788764884581 | etot = -186.160957626165 +769000 ekin = 22.639077883555 | erot = 22.2121122667711 | epot = -230.121718934275 | etot = -185.270528783949 +770000 ekin = 22.9570384866444 | erot = 20.3561307423381 | epot = -229.677968740405 | etot = -186.364799511423 +771000 ekin = 23.4805185151499 | erot = 19.2296467559715 | epot = -229.218370670653 | etot = -186.508205399532 +772000 ekin = 23.6763149012215 | erot = 18.7804644565625 | epot = -229.197189562088 | etot = -186.740410204304 +773000 ekin = 23.2744828335044 | erot = 18.3799138508661 | epot = -229.294843443837 | etot = -187.640446759466 +774000 ekin = 24.1615203598158 | erot = 18.900317215458 | epot = -229.618073899692 | etot = -186.556236324418 +775000 ekin = 24.5357529676979 | erot = 22.7624377798731 | epot = -230.089626217906 | etot = -182.791435470335 +776000 ekin = 24.5386633146364 | erot = 21.1855266154048 | epot = -230.582204299442 | etot = -184.8580143694 +777000 ekin = 25.2498386289825 | erot = 21.3517051740902 | epot = -231.095135150134 | etot = -184.493591347061 +778000 ekin = 25.1773810922395 | erot = 21.7257078056424 | epot = -231.571689532577 | etot = -184.668600634695 +779000 ekin = 25.0706221380908 | erot = 23.206106433149 | epot = -231.920098805104 | etot = -183.643370233864 +780000 ekin = 25.0073948183737 | erot = 23.7843076919343 | epot = -231.940828129371 | etot = -183.149125619063 +781000 ekin = 25.862328682591 | erot = 20.6147635245773 | epot = -231.660475043653 | etot = -185.183382836484 +782000 ekin = 26.0106396574312 | erot = 18.4785712250649 | epot = -231.228955508185 | etot = -186.739744625689 +783000 ekin = 26.3548094027823 | erot = 20.3847656672935 | epot = -230.847881341015 | etot = -184.108306270939 +784000 ekin = 26.9941621418946 | erot = 20.6658207449783 | epot = -230.342301897166 | etot = -182.682319010294 +785000 ekin = 27.1272259996373 | erot = 20.0337747206907 | epot = -229.609935110564 | etot = -182.448934390236 +786000 ekin = 26.2875323551626 | erot = 21.2032948699837 | epot = -228.871206104526 | etot = -181.380378879379 +787000 ekin = 27.102289880841 | erot = 22.7511634245655 | epot = -228.229695505568 | etot = -178.376242200162 +788000 ekin = 26.9004033303382 | erot = 23.284460905515 | epot = -227.746200253144 | etot = -177.561336017291 +789000 ekin = 26.296015640084 | erot = 23.9396195703878 | epot = -227.4595974325 | etot = -177.223962222028 +790000 ekin = 26.0014289202783 | erot = 26.1183503632237 | epot = -227.52011756713 | etot = -175.400338283628 +791000 ekin = 26.0417552278906 | erot = 24.4511943151671 | epot = -227.865832903974 | etot = -177.372883360917 +792000 ekin = 24.7829875539951 | erot = 25.7161813251446 | epot = -228.337129921754 | etot = -177.837961042614 +793000 ekin = 24.1365737213691 | erot = 26.6815526928053 | epot = -229.030608073319 | etot = -178.212481659145 +794000 ekin = 24.2497409488624 | erot = 27.0890119453063 | epot = -229.824908003136 | etot = -178.486155108968 +795000 ekin = 24.6407890606403 | erot = 27.889646525042 | epot = -230.805274185753 | etot = -178.27483860007 +796000 ekin = 25.3265228383185 | erot = 27.1393608545888 | epot = -231.693076803536 | etot = -179.227193110629 +797000 ekin = 26.6978206545278 | erot = 26.0659091687928 | epot = -232.555084872404 | etot = -179.791355049083 +798000 ekin = 26.3339851949647 | erot = 24.0430202875505 | epot = -233.536000193098 | etot = -183.158994710583 +799000 ekin = 26.9068087522464 | erot = 22.6750790932831 | epot = -234.458642892057 | etot = -184.876755046527 +800000 ekin = 27.1539987641759 | erot = 23.0521331292966 | epot = -235.226285042255 | etot = -185.020153148783 +801000 ekin = 28.1094335983316 | erot = 25.0050175559563 | epot = -235.765403988368 | etot = -182.65095283408 +802000 ekin = 28.2095765951819 | erot = 27.782893768378 | epot = -236.074276063345 | etot = -180.081805699785 +803000 ekin = 27.5705368050616 | erot = 28.8940855937134 | epot = -236.110252388434 | etot = -179.645629989659 +804000 ekin = 28.2157687187553 | erot = 27.74636434354 | epot = -236.079369382529 | etot = -180.117236320234 +805000 ekin = 28.320866013253 | erot = 29.9910811282246 | epot = -235.90913845068 | etot = -177.597191309203 +806000 ekin = 28.1050825504931 | erot = 26.9917671949644 | epot = -235.67969557003 | etot = -180.582845824572 +807000 ekin = 28.9805100536259 | erot = 27.4290452324766 | epot = -235.492989203125 | etot = -179.083433917023 +808000 ekin = 28.6297117732318 | erot = 26.5808708304162 | epot = -235.318064848412 | etot = -180.107482244764 +809000 ekin = 27.6485930588141 | erot = 26.8549775475233 | epot = -234.976046493401 | etot = -180.472475887064 +810000 ekin = 27.3535576125066 | erot = 27.4159280488332 | epot = -234.674224241899 | etot = -179.90473858056 +811000 ekin = 26.8179323011295 | erot = 23.7813000955385 | epot = -234.075151851674 | etot = -183.475919455006 +812000 ekin = 25.4460426056691 | erot = 22.5673797708771 | epot = -233.183000295958 | etot = -185.169577919411 +813000 ekin = 24.6447760709675 | erot = 21.8823489885933 | epot = -232.313502763387 | etot = -185.786377703826 +814000 ekin = 23.5292099931413 | erot = 23.5195364453851 | epot = -231.540928013004 | etot = -184.492181574478 +815000 ekin = 23.2925196788094 | erot = 24.0874833263439 | epot = -231.037162145188 | etot = -183.657159140034 +816000 ekin = 22.5686853714983 | erot = 23.2614654221577 | epot = -230.69420971902 | etot = -184.864058925364 +817000 ekin = 21.8281820071653 | erot = 23.5211267469624 | epot = -230.271049994022 | etot = -184.921741239894 +818000 ekin = 21.2884404725207 | erot = 24.902381419566 | epot = -229.858747495004 | etot = -183.667925602917 +819000 ekin = 21.0872506325458 | erot = 24.5311269568262 | epot = -229.338784368977 | etot = -183.720406779605 +820000 ekin = 20.8955721018969 | erot = 25.3653144031468 | epot = -228.629666907205 | etot = -182.368780402161 +821000 ekin = 21.0405754334193 | erot = 21.6474705949844 | epot = -227.730299016778 | etot = -185.042252988374 +822000 ekin = 20.9721716781629 | erot = 21.5305117214123 | epot = -226.866605601223 | etot = -184.363922201648 +823000 ekin = 21.3134444479004 | erot = 18.9497629221593 | epot = -225.861340505134 | etot = -185.598133135074 +824000 ekin = 20.9747397211228 | erot = 18.6168738131577 | epot = -225.064270159964 | etot = -185.472656625683 +825000 ekin = 21.3904407523305 | erot = 18.7811321199529 | epot = -224.367454518582 | etot = -184.195881646298 +826000 ekin = 21.8928774215356 | erot = 18.0229901458568 | epot = -223.971578653884 | etot = -184.055711086492 +827000 ekin = 22.7137879274166 | erot = 17.003583367025 | epot = -223.925754778761 | etot = -184.208383484319 +828000 ekin = 23.27710684341 | erot = 16.767643058574 | epot = -223.977166786808 | etot = -183.932416884824 +829000 ekin = 22.9248196274624 | erot = 16.7826748876662 | epot = -224.203173005046 | etot = -184.495678489918 +830000 ekin = 23.4067478420881 | erot = 18.7934665997725 | epot = -224.482791288573 | etot = -182.282576846713 +831000 ekin = 23.4821697156405 | erot = 18.2729392007921 | epot = -224.915819953911 | etot = -183.160711037479 +832000 ekin = 23.6777143333438 | erot = 18.2278960830696 | epot = -225.489645423005 | etot = -183.584035006592 +833000 ekin = 23.472191617002 | erot = 18.0493053174397 | epot = -226.176378068975 | etot = -184.654881134533 +834000 ekin = 23.7368728904259 | erot = 18.0164626266613 | epot = -226.92716915948 | etot = -185.173833642392 +835000 ekin = 24.1489739233553 | erot = 18.9188017440221 | epot = -227.647120026384 | etot = -184.579344359006 +836000 ekin = 24.9827825556416 | erot = 19.495588151043 | epot = -228.34763399319 | etot = -183.869263286505 +837000 ekin = 25.256659406949 | erot = 18.944776639966 | epot = -228.876405841141 | etot = -184.674969794226 +838000 ekin = 25.6241774229268 | erot = 18.8091020128683 | epot = -229.371952192415 | etot = -184.938672756619 +839000 ekin = 24.937654890099 | erot = 19.8676941565057 | epot = -229.858542408147 | etot = -185.053193361542 +840000 ekin = 24.4858927113979 | erot = 20.165387717701 | epot = -230.274829908799 | etot = -185.6235494797 +841000 ekin = 25.2649920297918 | erot = 24.2935866726487 | epot = -230.699551533791 | etot = -181.14097283135 +842000 ekin = 25.1332828225798 | erot = 25.2707888267597 | epot = -231.095538575756 | etot = -180.691466926417 +843000 ekin = 25.1733374952435 | erot = 25.9799311513388 | epot = -231.399217706907 | etot = -180.245949060324 +844000 ekin = 25.6427133855964 | erot = 26.078509916794 | epot = -231.550673355361 | etot = -179.82945005297 +845000 ekin = 25.1297698352677 | erot = 24.7021906095904 | epot = -231.460774324866 | etot = -181.628813880008 +846000 ekin = 23.9774924150437 | erot = 26.9234963124405 | epot = -231.260980839143 | etot = -180.359992111659 +847000 ekin = 23.9502284491091 | erot = 25.3996788275484 | epot = -230.920723601702 | etot = -181.570816325044 +848000 ekin = 23.6157182559703 | erot = 24.5551104055363 | epot = -230.306195126828 | etot = -182.135366465322 +849000 ekin = 22.6955823420992 | erot = 25.5456755652408 | epot = -229.458091789959 | etot = -181.216833882618 +850000 ekin = 22.0235173219512 | erot = 26.2022873474972 | epot = -228.638684453437 | etot = -180.412879783989 +851000 ekin = 20.3765133939015 | erot = 25.395296129778 | epot = -227.4038640863 | etot = -181.632054562621 +852000 ekin = 19.712651245867 | erot = 22.1621130679229 | epot = -226.183276861571 | etot = -184.308512547781 +853000 ekin = 19.9928897638392 | erot = 20.0874368006941 | epot = -225.284467563439 | etot = -185.204140998906 +854000 ekin = 19.488290778963 | erot = 19.9220642414495 | epot = -224.827954241878 | etot = -185.417599221465 +855000 ekin = 19.0625095702531 | erot = 23.1790778413437 | epot = -224.708495395363 | etot = -182.466907983767 +856000 ekin = 18.2834869557216 | erot = 23.7444220411258 | epot = -224.914568249835 | etot = -182.886659252988 +857000 ekin = 18.0511175672903 | erot = 23.2575694040762 | epot = -225.28875879225 | etot = -183.980071820884 +858000 ekin = 17.987864866636 | erot = 22.7427618173349 | epot = -225.735338610943 | etot = -185.004711926972 +859000 ekin = 18.1389416018411 | erot = 21.3928666667423 | epot = -226.037392251567 | etot = -186.505583982984 +860000 ekin = 18.6141725361191 | erot = 20.6939972933922 | epot = -226.430306906883 | etot = -187.122137077371 +861000 ekin = 18.401448708528 | erot = 19.0196700230753 | epot = -226.81711834723 | etot = -189.395999615627 +862000 ekin = 19.1545854076427 | erot = 19.6617033547467 | epot = -227.136988769577 | etot = -188.320700007187 +863000 ekin = 19.7210305410548 | erot = 19.0006017481044 | epot = -227.58643743169 | etot = -188.864805142531 +864000 ekin = 20.4150266073574 | erot = 17.4275270266597 | epot = -227.954722358838 | etot = -190.112168724821 +865000 ekin = 19.9419797685448 | erot = 18.4620038343303 | epot = -228.340343063655 | etot = -189.93635946078 +866000 ekin = 20.0439020993958 | erot = 19.7882082077027 | epot = -228.670054548891 | etot = -188.837944241793 +867000 ekin = 20.4021140966254 | erot = 16.6652764682189 | epot = -228.856375548282 | etot = -191.788984983438 +868000 ekin = 20.0497264126648 | erot = 15.1372589940697 | epot = -228.9464789622 | etot = -193.759493555466 +869000 ekin = 20.3294773849231 | erot = 15.3005394579943 | epot = -228.69433960582 | etot = -193.064322762902 +870000 ekin = 21.0889922536593 | erot = 16.6120429683399 | epot = -228.508354500254 | etot = -190.807319278254 +871000 ekin = 21.4383179744103 | erot = 15.7484322870451 | epot = -228.210620038394 | etot = -191.023869776939 +872000 ekin = 20.9086609371529 | erot = 15.1111364530204 | epot = -227.78534180259 | etot = -191.765544412416 +873000 ekin = 20.8153441906834 | erot = 16.5761474970315 | epot = -227.299271762687 | etot = -189.907780074972 +874000 ekin = 20.9430061532593 | erot = 16.1679775988649 | epot = -226.763117412711 | etot = -189.652133660586 +875000 ekin = 20.8032036636137 | erot = 17.5698273129444 | epot = -226.415697698183 | etot = -188.042666721625 +876000 ekin = 21.2280022982517 | erot = 17.9072946891329 | epot = -226.028708918809 | etot = -186.893411931424 +877000 ekin = 20.7314119673013 | erot = 18.8567759065314 | epot = -225.75544933082 | etot = -186.167261456988 +878000 ekin = 19.6914373366095 | erot = 18.0844279043814 | epot = -225.736073224764 | etot = -187.960207983773 +879000 ekin = 19.3380672635332 | erot = 20.3104617632777 | epot = -225.910509841808 | etot = -186.261980814997 +880000 ekin = 20.1253722733107 | erot = 19.6280011404237 | epot = -226.214189456348 | etot = -186.460816042614 +881000 ekin = 20.260952001898 | erot = 21.2130237420557 | epot = -226.552056767178 | etot = -185.078081023224 +882000 ekin = 21.3999865884411 | erot = 20.028991688965 | epot = -226.705011052036 | etot = -185.27603277463 +883000 ekin = 20.9234278576856 | erot = 17.6868960387749 | epot = -226.60324790835 | etot = -187.992924011889 +884000 ekin = 20.2953614821548 | erot = 19.6437828087785 | epot = -226.531387224454 | etot = -186.59224293352 +885000 ekin = 20.0270746296784 | erot = 18.5836278581865 | epot = -226.609255319515 | etot = -187.99855283165 +886000 ekin = 20.5051703060542 | erot = 18.0664735117856 | epot = -226.96051309001 | etot = -188.38886927217 +887000 ekin = 20.6026175595096 | erot = 18.6797072756244 | epot = -227.547206365853 | etot = -188.264881530719 +888000 ekin = 21.2323390050554 | erot = 20.9767236317906 | epot = -228.222699335688 | etot = -186.013636698842 +889000 ekin = 21.8381850979202 | erot = 25.4926747228943 | epot = -229.035049210771 | etot = -181.704189389957 +890000 ekin = 21.4079820277754 | erot = 27.1125219125164 | epot = -229.846306308658 | etot = -181.325802368367 +891000 ekin = 20.7821773337589 | erot = 28.3638087372895 | epot = -230.472553686443 | etot = -181.326567615394 +892000 ekin = 20.9530226613445 | erot = 29.3670280639872 | epot = -230.939235576405 | etot = -180.619184851073 +893000 ekin = 20.7215793854111 | erot = 31.0978810463376 | epot = -231.283574476306 | etot = -179.464114044558 +894000 ekin = 19.8695855128928 | erot = 31.7444008344117 | epot = -231.206530399661 | etot = -179.592544052357 +895000 ekin = 20.4710472102287 | erot = 32.2571471114376 | epot = -230.935329589533 | etot = -178.207135267867 +896000 ekin = 20.0060219077691 | erot = 31.457482996745 | epot = -230.39059212909 | etot = -178.927087224576 +897000 ekin = 19.5877677637713 | erot = 30.8725368660366 | epot = -229.679299884647 | etot = -179.218995254839 +898000 ekin = 19.5649042545347 | erot = 30.6384498007997 | epot = -228.784507947033 | etot = -178.581153891699 +899000 ekin = 19.552835254318 | erot = 29.951844791116 | epot = -227.835835338061 | etot = -178.331155292627 +900000 ekin = 19.2943713466608 | erot = 28.266076937142 | epot = -226.951949904772 | etot = -179.391501620969 +901000 ekin = 18.7114972173853 | erot = 25.779754104773 | epot = -226.031983135348 | etot = -181.54073181319 +902000 ekin = 18.7187531634708 | erot = 21.6824516537499 | epot = -225.333624072524 | etot = -184.932419255303 +903000 ekin = 18.5839455909793 | erot = 21.3627578096897 | epot = -224.798501909831 | etot = -184.851798509162 +904000 ekin = 18.3200785166187 | erot = 21.0384699999409 | epot = -224.517265654088 | etot = -185.158717137528 +905000 ekin = 18.2865838363112 | erot = 22.5880133859383 | epot = -224.539131448644 | etot = -183.664534226394 +906000 ekin = 18.8425722270119 | erot = 21.9502833403246 | epot = -224.826601919796 | etot = -184.03374635246 +907000 ekin = 18.236662353643 | erot = 21.6508700749443 | epot = -225.411854073913 | etot = -185.524321645325 +908000 ekin = 19.0863284801222 | erot = 21.7256265222381 | epot = -225.925114677336 | etot = -185.113159674975 +909000 ekin = 18.6818812816023 | erot = 20.5599381624967 | epot = -226.282894133629 | etot = -187.04107468953 +910000 ekin = 19.0812656136231 | erot = 20.4145332853015 | epot = -226.698405476378 | etot = -187.202606577453 +911000 ekin = 18.9756818734077 | erot = 19.7026952453737 | epot = -227.201366089943 | etot = -188.522988971161 +912000 ekin = 19.4517334786722 | erot = 19.3460897587287 | epot = -227.803131570748 | etot = -189.005308333347 +913000 ekin = 19.487052846439 | erot = 19.4558063021173 | epot = -228.833499323783 | etot = -189.890640175227 +914000 ekin = 20.0013452620764 | erot = 19.8883578065421 | epot = -230.188717691798 | etot = -190.299014623179 +915000 ekin = 20.9190174527208 | erot = 21.5162066495227 | epot = -231.33235656658 | etot = -188.897132464337 +916000 ekin = 21.0408041290695 | erot = 20.6706622893139 | epot = -232.345019966097 | etot = -190.633553547713 +917000 ekin = 21.4182021320957 | erot = 20.3350739399058 | epot = -233.071031631301 | etot = -191.317755559299 +918000 ekin = 22.0971055055586 | erot = 18.9655185938109 | epot = -233.580798555561 | etot = -192.518174456191 +919000 ekin = 22.5486106562676 | erot = 18.3948377546432 | epot = -234.050312577178 | etot = -193.106864166267 +920000 ekin = 23.3254614038352 | erot = 19.5922944610403 | epot = -234.48534712321 | etot = -191.567591258335 +921000 ekin = 23.5452459126828 | erot = 20.5850080381015 | epot = -234.86333152558 | etot = -190.733077574796 +922000 ekin = 23.548927893765 | erot = 21.8847693351997 | epot = -235.159655748814 | etot = -189.72595851985 +923000 ekin = 23.6264800883718 | erot = 24.823701669703 | epot = -235.319615013714 | etot = -186.869433255639 +924000 ekin = 23.4484029162379 | erot = 25.2387940247724 | epot = -235.348442838844 | etot = -186.661245897834 +925000 ekin = 23.7581201931874 | erot = 26.0564388640377 | epot = -235.235791589113 | etot = -185.421232531888 +926000 ekin = 23.2671712311938 | erot = 27.0589269562523 | epot = -234.804321198793 | etot = -184.478223011347 +927000 ekin = 23.0270381962365 | erot = 29.4095030756175 | epot = -234.307939870163 | etot = -181.871398598309 +928000 ekin = 23.140501344179 | erot = 27.0790502179807 | epot = -233.844847745639 | etot = -183.62529618348 +929000 ekin = 22.2734898741118 | erot = 27.0674755071555 | epot = -233.049914186603 | etot = -183.708948805335 +930000 ekin = 21.6339427121745 | erot = 25.2225644782622 | epot = -232.095625490262 | etot = -185.239118299825 +931000 ekin = 20.9327398893734 | erot = 22.3817305427933 | epot = -231.012404519165 | etot = -187.697934086999 +932000 ekin = 20.4822193525442 | erot = 22.9972350477763 | epot = -230.147455250577 | etot = -186.668000850256 +933000 ekin = 19.9660353920888 | erot = 24.4740543358249 | epot = -229.586577553208 | etot = -185.146487825294 +934000 ekin = 19.3969944972964 | erot = 23.9687951023098 | epot = -229.129558438895 | etot = -185.763768839289 +935000 ekin = 18.8183272744565 | erot = 23.494590376579 | epot = -228.829650383225 | etot = -186.516732732189 +936000 ekin = 17.9161255220784 | erot = 26.3097805675523 | epot = -228.725255966952 | etot = -184.499349877321 +937000 ekin = 17.4090072925044 | erot = 28.2846119714553 | epot = -228.595685952083 | etot = -182.902066688124 +938000 ekin = 17.7095687249429 | erot = 28.4339381503916 | epot = -228.52964518166 | etot = -182.386138306326 +939000 ekin = 17.5520408874173 | erot = 27.0941576154426 | epot = -228.469555611768 | etot = -183.823357108909 +940000 ekin = 17.1798814813059 | erot = 25.8182574439337 | epot = -228.458369765694 | etot = -185.460230840454 +941000 ekin = 18.3127771365279 | erot = 26.1340829522924 | epot = -228.605257427977 | etot = -184.158397339157 +942000 ekin = 18.4394261942677 | erot = 25.2374530821303 | epot = -228.698077294464 | etot = -185.021198018066 +943000 ekin = 18.2926042504087 | erot = 25.6259778525084 | epot = -228.714835650707 | etot = -184.796253547789 +944000 ekin = 18.1985428862211 | erot = 27.2944037574074 | epot = -228.856509809853 | etot = -183.363563166225 +945000 ekin = 18.5074415121775 | erot = 27.6142744599881 | epot = -229.209548154119 | etot = -183.087832181953 +946000 ekin = 19.2233115923275 | erot = 29.6826055408939 | epot = -229.700854946272 | etot = -180.79493781305 +947000 ekin = 19.2209049259883 | erot = 28.9510045058796 | epot = -230.298982034344 | etot = -182.127072602476 +948000 ekin = 19.7441291687864 | erot = 26.2906426684946 | epot = -230.779259933587 | etot = -184.744488096306 +949000 ekin = 19.4506543919674 | erot = 26.8808216821455 | epot = -231.059979079511 | etot = -184.728503005398 +950000 ekin = 20.1645638300332 | erot = 25.6765899295848 | epot = -231.255749555474 | etot = -185.414595795856 +951000 ekin = 20.6156032604793 | erot = 23.3780963018669 | epot = -231.363279926649 | etot = -187.369580364303 +952000 ekin = 20.397762898021 | erot = 21.9317814265749 | epot = -231.413145962119 | etot = -189.083601637523 +953000 ekin = 21.0736084801864 | erot = 21.1438497831439 | epot = -231.535497877041 | etot = -189.318039613711 +954000 ekin = 22.2970457335312 | erot = 21.8052778907762 | epot = -231.61117831621 | etot = -187.508854691902 +955000 ekin = 22.119368227684 | erot = 23.2345496019292 | epot = -231.828383029989 | etot = -186.474465200376 +956000 ekin = 21.4925632863079 | erot = 21.4930515028271 | epot = -232.064300377829 | etot = -189.078685588694 +957000 ekin = 20.8333682688634 | erot = 22.8032486196631 | epot = -232.190793202397 | etot = -188.554176313871 +958000 ekin = 19.8501740638794 | erot = 24.4089530073582 | epot = -232.249982663747 | etot = -187.990855592509 +959000 ekin = 19.2680019449165 | erot = 25.5054723395896 | epot = -232.152549289162 | etot = -187.379075004656 +960000 ekin = 19.7794915155661 | erot = 24.9916198272161 | epot = -231.918033034319 | etot = -187.146921691537 +961000 ekin = 19.2751025937535 | erot = 25.8738975860354 | epot = -231.741716385163 | etot = -186.592716205374 +962000 ekin = 19.5337863893408 | erot = 24.9356255276758 | epot = -231.55739577143 | etot = -187.087983854414 +963000 ekin = 18.9999723551409 | erot = 25.6087844134591 | epot = -231.447506108069 | etot = -186.838749339469 +964000 ekin = 18.8752847703513 | erot = 24.9133910089691 | epot = -231.338447218817 | etot = -187.549771439496 +965000 ekin = 19.291184662028 | erot = 26.9200173912746 | epot = -231.200004911496 | etot = -184.988802858193 +966000 ekin = 19.9923055028309 | erot = 23.6358047261547 | epot = -231.075767261895 | etot = -187.44765703291 +967000 ekin = 20.7057273743393 | erot = 22.5792578588179 | epot = -230.879832297065 | etot = -187.594847063908 +968000 ekin = 20.9571086143562 | erot = 20.068819571795 | epot = -230.940571243941 | etot = -189.914643057789 +969000 ekin = 21.1817427297271 | erot = 21.825570412089 | epot = -231.039838752312 | etot = -188.032525610496 +970000 ekin = 21.6764110888425 | erot = 18.6641228269477 | epot = -231.330833358017 | etot = -190.990299442226 +971000 ekin = 21.6293984081523 | erot = 20.4985343496002 | epot = -231.743853106541 | etot = -189.615920348789 +972000 ekin = 21.8321017334667 | erot = 24.1203627051505 | epot = -232.392520631785 | etot = -186.440056193167 +973000 ekin = 22.2085815332021 | erot = 23.693087815175 | epot = -232.912739470324 | etot = -187.011070121947 +974000 ekin = 23.847360088775 | erot = 24.6762793762862 | epot = -233.368044095902 | etot = -184.844404630841 +975000 ekin = 23.8772760481354 | erot = 23.8186315371493 | epot = -233.675813480515 | etot = -185.979905895231 +976000 ekin = 24.8508847684197 | erot = 25.4916104671426 | epot = -233.730386974331 | etot = -183.387891738769 +977000 ekin = 25.503947524416 | erot = 25.977795351237 | epot = -233.493574624629 | etot = -182.011831748976 +978000 ekin = 25.1301492488327 | erot = 23.6629990089568 | epot = -232.903591402815 | etot = -184.110443145025 +979000 ekin = 24.5159482950054 | erot = 23.0268756855837 | epot = -231.985954800605 | etot = -184.443130820016 +980000 ekin = 24.3566813412311 | erot = 22.1670075667718 | epot = -230.990647999228 | etot = -184.466959091225 +981000 ekin = 23.9671984077651 | erot = 21.1028376661039 | epot = -230.100691904619 | etot = -185.03065583075 +982000 ekin = 24.2014904181518 | erot = 21.766454128543 | epot = -229.357805757613 | etot = -183.389861210918 +983000 ekin = 24.7761393638494 | erot = 21.5867990158502 | epot = -228.528183005968 | etot = -182.165244626269 +984000 ekin = 24.762354593527 | erot = 20.3394309281687 | epot = -227.693626881489 | etot = -182.591841359793 +985000 ekin = 23.1046341904546 | erot = 20.4859555093025 | epot = -226.832364952595 | etot = -183.241775252838 +986000 ekin = 22.9917171657182 | erot = 19.6850542240413 | epot = -225.931729672514 | etot = -183.254958282755 +987000 ekin = 23.0807717247555 | erot = 18.7933780253197 | epot = -225.294914737568 | etot = -183.420764987493 +988000 ekin = 23.4666498858033 | erot = 18.3944401818207 | epot = -224.462201121502 | etot = -182.601111053878 +989000 ekin = 22.8294990773184 | erot = 18.3438283695259 | epot = -223.609265715967 | etot = -182.435938269123 +990000 ekin = 22.7066871299428 | erot = 18.5469186746782 | epot = -222.854303271458 | etot = -181.600697466837 +991000 ekin = 22.1383192479068 | erot = 18.4323256035066 | epot = -222.260388874341 | etot = -181.689744022928 +992000 ekin = 21.6825567231224 | erot = 17.8750037490483 | epot = -221.638206330132 | etot = -182.080645857962 +993000 ekin = 21.6468556176261 | erot = 19.5312645063955 | epot = -221.115778704445 | etot = -179.937658580423 +994000 ekin = 21.4467710605119 | erot = 22.8410951796741 | epot = -220.729552539755 | etot = -176.441686299569 +995000 ekin = 22.4071907674418 | erot = 20.5892070380571 | epot = -220.394740391854 | etot = -177.398342586355 +996000 ekin = 22.1528083326795 | erot = 20.104343598086 | epot = -220.236106067073 | etot = -177.978954136307 +997000 ekin = 21.4854485286746 | erot = 19.7617644517094 | epot = -220.302222594169 | etot = -179.055009613785 +998000 ekin = 22.1449863079611 | erot = 20.4384133517957 | epot = -220.780253661163 | etot = -178.196854001406 +999000 ekin = 22.5781778653751 | erot = 21.7041052467461 | epot = -221.511725171924 | etot = -177.229442059803 +1000000 ekin = 22.8867994582225 | erot = 20.7015166614267 | epot = -222.040127669769 | etot = -178.45181155012 + 1000000 307.12188 -227.88356 5.8434328 -199.15333 0.033370746 39304000 +Loop time of 85.9592 on 1 procs for 1000000 steps with 26 atoms + +Performance: 17.147 ns/day, 1.400 hours/ns, 11633.421 timesteps/s, 302.469 katom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 75.127 | 75.127 | 75.127 | 0.0 | 87.40 +Bond | 1.8597 | 1.8597 | 1.8597 | 0.0 | 2.16 +Neigh | 0.023421 | 0.023421 | 0.023421 | 0.0 | 0.03 +Comm | 0.47775 | 0.47775 | 0.47775 | 0.0 | 0.56 +Output | 0.31455 | 0.31455 | 0.31455 | 0.0 | 0.37 +Modify | 7.8261 | 7.8261 | 7.8261 | 0.0 | 9.10 +Other | | 0.3311 | | | 0.39 + +Nlocal: 26 ave 26 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 301 ave 301 max 301 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.4.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:01:25 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.4 new file mode 100644 index 0000000000..4c158da526 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.4 @@ -0,0 +1,1234 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 4 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 4 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.4.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 +Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 299.91159 -228.12763 5.3145589 -200.46358 0.037365999 39304000 +1000 ekin = 23.3890953137706 | erot = 19.6410994523669 | epot = -223.453852955672 | etot = -180.423658189535 +2000 ekin = 23.1636407259802 | erot = 21.3625588607293 | epot = -224.083184468805 | etot = -179.556984882096 +3000 ekin = 23.2806646382535 | erot = 22.5430917602388 | epot = -224.768803309422 | etot = -178.945046910929 +4000 ekin = 23.9982606831172 | erot = 23.3468002016785 | epot = -225.369139455231 | etot = -178.024078570435 +5000 ekin = 24.165831446691 | erot = 24.309309123119 | epot = -225.647777921139 | etot = -177.172637351329 +6000 ekin = 24.6463592700502 | erot = 24.0743926173796 | epot = -225.506791813463 | etot = -176.786039926033 +7000 ekin = 24.3535569942788 | erot = 23.7545459891526 | epot = -225.024405145301 | etot = -176.91630216187 +8000 ekin = 24.1086868814849 | erot = 22.0830265599649 | epot = -224.271997801092 | etot = -178.080284359642 +9000 ekin = 23.6657562363458 | erot = 23.1988592381777 | epot = -223.434572814547 | etot = -176.569957340023 +10000 ekin = 24.3232494642814 | erot = 24.4646190421148 | epot = -222.599352113837 | etot = -173.811483607441 +11000 ekin = 23.5151408185546 | erot = 24.7247948775442 | epot = -221.829445800186 | etot = -173.589510104087 +12000 ekin = 23.1685925031279 | erot = 24.5168702274895 | epot = -221.283446631497 | etot = -173.597983900879 +13000 ekin = 22.5542770265459 | erot = 23.5479562044803 | epot = -220.966648997482 | etot = -174.864415766456 +14000 ekin = 22.1812934517937 | erot = 22.8843950945786 | epot = -220.909390045146 | etot = -175.843701498774 +15000 ekin = 21.6910740763736 | erot = 20.1250177447006 | epot = -221.050686326242 | etot = -179.234594505167 +16000 ekin = 22.4093549284696 | erot = 20.736944453168 | epot = -221.640495388654 | etot = -178.494196007016 +17000 ekin = 22.679935542291 | erot = 20.1401904659941 | epot = -222.539917467256 | etot = -179.71979145897 +18000 ekin = 22.7533504972992 | erot = 22.7880003534203 | epot = -223.497938845177 | etot = -177.956587994457 +19000 ekin = 22.6910824257598 | erot = 22.6775801630857 | epot = -224.397974314829 | etot = -179.029311725984 +20000 ekin = 22.4764122530343 | erot = 23.7180217709408 | epot = -225.277618576532 | etot = -179.083184552557 +21000 ekin = 22.3910995469036 | erot = 23.2739103814922 | epot = -226.054371546779 | etot = -180.389361618383 +22000 ekin = 22.7568179157572 | erot = 22.0747817368078 | epot = -226.677846442693 | etot = -181.846246790128 +23000 ekin = 23.0388332875658 | erot = 21.0371096765612 | epot = -226.873115293642 | etot = -182.797172329515 +24000 ekin = 22.9280961752663 | erot = 20.7369981826367 | epot = -226.863624686001 | etot = -183.198530328098 +25000 ekin = 23.1552675069494 | erot = 22.7089539602996 | epot = -226.603802406831 | etot = -180.739580939582 +26000 ekin = 23.1603034696877 | erot = 24.1226336440568 | epot = -226.15389780062 | etot = -178.870960686875 +27000 ekin = 22.8639956982148 | erot = 24.9308927260679 | epot = -225.734799028865 | etot = -177.939910604582 +28000 ekin = 22.8686406093792 | erot = 24.6702817199638 | epot = -225.404399605183 | etot = -177.865477275841 +29000 ekin = 22.7329708724114 | erot = 24.8206803603672 | epot = -225.288544762221 | etot = -177.734893529442 +30000 ekin = 23.2224697595134 | erot = 24.1186993911772 | epot = -225.281641810783 | etot = -177.940472660093 +31000 ekin = 23.2116217901824 | erot = 21.2110758669747 | epot = -225.379848736762 | etot = -180.957151079605 +32000 ekin = 22.6705345674289 | erot = 21.1222567836579 | epot = -225.626990597972 | etot = -181.834199246885 +33000 ekin = 22.5742554775595 | erot = 23.8115179286177 | epot = -226.196557922731 | etot = -179.810784516554 +34000 ekin = 22.4811628913946 | erot = 23.1703307206031 | epot = -227.132725939902 | etot = -181.481232327904 +35000 ekin = 22.1305128996843 | erot = 21.7768358380573 | epot = -228.241546350004 | etot = -184.334197612262 +36000 ekin = 22.3064371288266 | erot = 23.6090073902907 | epot = -229.291792709837 | etot = -183.37634819072 +37000 ekin = 22.7954030625747 | erot = 26.5244949994173 | epot = -230.44896109423 | etot = -181.129063032238 +38000 ekin = 22.021936313581 | erot = 28.7809192800672 | epot = -231.527472091849 | etot = -180.724616498201 +39000 ekin = 21.4311061995551 | erot = 30.0076463982257 | epot = -232.292567603581 | etot = -180.8538150058 +40000 ekin = 22.1961102532617 | erot = 28.4384036307401 | epot = -232.768624821777 | etot = -182.134110937775 +41000 ekin = 22.1632663233095 | erot = 27.8241627319402 | epot = -232.914504546317 | etot = -182.927075491067 +42000 ekin = 21.1410868775786 | erot = 26.870218141795 | epot = -232.876921131849 | etot = -184.865616112475 +43000 ekin = 21.3077823999456 | erot = 29.4997981842649 | epot = -232.609490543326 | etot = -181.801909959116 +44000 ekin = 21.0347661835417 | erot = 30.6694367820553 | epot = -232.102541009681 | etot = -180.398338044084 +45000 ekin = 20.0324931780768 | erot = 31.6373084224142 | epot = -231.359075571458 | etot = -179.689273970967 +46000 ekin = 19.8601076626959 | erot = 27.6516450222689 | epot = -230.481472443215 | etot = -182.96971975825 +47000 ekin = 19.9409510348244 | erot = 24.2746077209965 | epot = -229.669745177728 | etot = -185.454186421907 +48000 ekin = 20.2692406564663 | erot = 24.1549347770059 | epot = -228.892944669037 | etot = -184.468769235565 +49000 ekin = 19.7308285932956 | erot = 25.0778897556889 | epot = -228.04425642055 | etot = -183.235538071566 +50000 ekin = 19.5156647106263 | erot = 22.9395420283448 | epot = -227.011157830413 | etot = -184.555951091442 +51000 ekin = 19.6024948282074 | erot = 24.0313890926859 | epot = -226.023373255268 | etot = -182.389489334375 +52000 ekin = 19.8286591378852 | erot = 22.0208354730768 | epot = -225.032119343055 | etot = -183.182624732093 +53000 ekin = 19.3575981919063 | erot = 22.7897166177213 | epot = -224.158699287711 | etot = -182.011384478083 +54000 ekin = 19.597311059818 | erot = 23.0278186836853 | epot = -223.146432587169 | etot = -180.521302843666 +55000 ekin = 19.3207453743081 | erot = 22.0468752508626 | epot = -222.056416747158 | etot = -180.688796121987 +56000 ekin = 18.9770983953914 | erot = 20.6896918925267 | epot = -221.097322814135 | etot = -181.430532526217 +57000 ekin = 19.2291543150894 | erot = 18.2138179116051 | epot = -220.326696880738 | etot = -182.883724654043 +58000 ekin = 19.7989002082911 | erot = 17.8570481045562 | epot = -219.66066516308 | etot = -182.004716850233 +59000 ekin = 20.1354893580566 | erot = 18.0275449356124 | epot = -219.109861890285 | etot = -180.946827596616 +60000 ekin = 20.1400165937336 | erot = 16.7164726976129 | epot = -218.497904222289 | etot = -181.641414930942 +61000 ekin = 20.4228706753348 | erot = 15.3375065644544 | epot = -217.960810097484 | etot = -182.200432857695 +62000 ekin = 20.1686520767929 | erot = 14.8244535971852 | epot = -217.555103496147 | etot = -182.561997822169 +63000 ekin = 19.311066891783 | erot = 16.0064319386931 | epot = -217.355843552053 | etot = -182.038344721576 +64000 ekin = 18.6500742611855 | erot = 16.7733280191606 | epot = -217.424263371911 | etot = -182.000861091564 +65000 ekin = 18.4635153424261 | erot = 17.7526461844363 | epot = -217.607200736113 | etot = -181.391039209251 +66000 ekin = 18.0355770665484 | erot = 17.7854478795887 | epot = -217.893635735966 | etot = -182.072610789828 +67000 ekin = 18.7683164596081 | erot = 19.080252052141 | epot = -218.398035038712 | etot = -180.549466526963 +68000 ekin = 19.5633237463074 | erot = 19.5360521825708 | epot = -219.279673886377 | etot = -180.180297957499 +69000 ekin = 20.2188862219853 | erot = 20.833043152936 | epot = -220.282200151711 | etot = -179.23027077679 +70000 ekin = 20.9970230548361 | erot = 19.0573782912758 | epot = -221.465010968187 | etot = -181.410609622075 +71000 ekin = 22.2151160410886 | erot = 18.5722600954372 | epot = -222.617922299482 | etot = -181.830546162956 +72000 ekin = 23.0812082679138 | erot = 20.9554395379592 | epot = -224.077548221027 | etot = -180.040900415154 +73000 ekin = 24.1112874481562 | erot = 21.3307333887604 | epot = -225.657040151954 | etot = -180.215019315038 +74000 ekin = 25.1420377195353 | erot = 21.9350931527228 | epot = -226.775976258114 | etot = -179.698845385856 +75000 ekin = 25.4905080277013 | erot = 20.8716474966583 | epot = -227.44994158467 | etot = -181.087786060311 +76000 ekin = 26.1889777417351 | erot = 18.9373050893096 | epot = -227.905073960386 | etot = -182.778791129342 +77000 ekin = 26.6309013716286 | erot = 19.5714794491311 | epot = -228.081005377953 | etot = -181.878624557193 +78000 ekin = 27.3057147200393 | erot = 19.5248231586005 | epot = -228.040153322525 | etot = -181.209615443886 +79000 ekin = 28.2640662888057 | erot = 20.2680283946488 | epot = -227.894218120703 | etot = -179.362123437249 +80000 ekin = 28.8799414765843 | erot = 21.2755780503219 | epot = -227.426549194774 | etot = -177.271029667868 +81000 ekin = 28.0858484625652 | erot = 21.7656751298647 | epot = -226.837288216447 | etot = -176.985764624017 +82000 ekin = 27.5576739603813 | erot = 21.5235335244366 | epot = -226.257098694314 | etot = -177.175891209496 +83000 ekin = 27.0556891289388 | erot = 22.6329456874458 | epot = -225.705589513145 | etot = -176.01695469676 +84000 ekin = 26.940061932639 | erot = 22.4076039984471 | epot = -225.381193301861 | etot = -176.033527370774 +85000 ekin = 26.525652465447 | erot = 24.4523763465308 | epot = -225.328349372335 | etot = -174.350320560357 +86000 ekin = 26.2488146649899 | erot = 24.9404486230819 | epot = -225.600551034373 | etot = -174.411287746301 +87000 ekin = 25.8921444638997 | erot = 23.8549898140682 | epot = -225.944879311363 | etot = -176.197745033396 +88000 ekin = 26.2103045690956 | erot = 23.1783147432123 | epot = -226.027774274625 | etot = -176.639154962317 +89000 ekin = 25.9835312219869 | erot = 24.2571523005165 | epot = -225.843728416076 | etot = -175.603044893573 +90000 ekin = 25.0784166533943 | erot = 23.6606895366222 | epot = -225.518913230511 | etot = -176.779807040494 +91000 ekin = 25.1550989963772 | erot = 24.611658714882 | epot = -225.044629759836 | etot = -175.277872048577 +92000 ekin = 24.6322805735348 | erot = 23.0482358024938 | epot = -224.419349930751 | etot = -176.738833554722 +93000 ekin = 24.180459234874 | erot = 20.7592927466895 | epot = -223.586212452689 | etot = -178.646460471126 +94000 ekin = 22.9793960468067 | erot = 20.9605947384726 | epot = -222.799813856714 | etot = -178.859823071435 +95000 ekin = 22.0929244299446 | erot = 22.3265647171473 | epot = -222.029129765178 | etot = -177.609640618086 +96000 ekin = 21.7264489643602 | erot = 21.1719809671405 | epot = -221.221631774717 | etot = -178.323201843216 +97000 ekin = 21.4220036658247 | erot = 21.3543994979149 | epot = -220.52548534737 | etot = -177.74908218363 +98000 ekin = 20.0618032599352 | erot = 22.5876428184093 | epot = -219.923872605452 | etot = -177.274426527108 +99000 ekin = 19.3288174724157 | erot = 23.7511671518151 | epot = -219.367088850842 | etot = -176.287104226611 +100000 ekin = 18.4832594748416 | erot = 23.1505163286733 | epot = -218.93835041027 | etot = -177.304574606755 +101000 ekin = 18.2036045057376 | erot = 23.4110434093513 | epot = -218.810174271335 | etot = -177.195526356247 +102000 ekin = 19.1822681980068 | erot = 24.5380584864956 | epot = -219.20692211123 | etot = -175.486595426727 +103000 ekin = 19.6432797836894 | erot = 24.6590917201035 | epot = -219.897839906815 | etot = -175.595468403022 +104000 ekin = 20.1705942940374 | erot = 24.5511248426482 | epot = -220.691524456858 | etot = -175.969805320173 +105000 ekin = 20.4521236023122 | erot = 24.9947804545851 | epot = -221.484673188626 | etot = -176.037769131728 +106000 ekin = 20.2290985098953 | erot = 27.3725689281464 | epot = -222.355241194015 | etot = -174.753573755973 +107000 ekin = 20.8434847834034 | erot = 26.3604100874063 | epot = -223.150037642897 | etot = -175.946142772087 +108000 ekin = 21.412418363854 | erot = 28.2162878060305 | epot = -223.460424862129 | etot = -173.831718692244 +109000 ekin = 21.4548274110363 | erot = 30.3230159735583 | epot = -223.240254565236 | etot = -171.462411180641 +110000 ekin = 21.0213729404218 | erot = 29.3710550207835 | epot = -222.579286542226 | etot = -172.186858581021 +111000 ekin = 20.9967841720846 | erot = 26.7618200853704 | epot = -221.876250793147 | etot = -174.117646535692 +112000 ekin = 21.7067956747879 | erot = 24.9536304481639 | epot = -221.394505355036 | etot = -174.734079232084 +113000 ekin = 21.4580535818318 | erot = 22.7691051824902 | epot = -221.519820597203 | etot = -177.292661832881 +114000 ekin = 22.2538283177252 | erot = 22.1731381215523 | epot = -221.687750534437 | etot = -177.260784095159 +115000 ekin = 22.7396594344901 | erot = 20.8608644375928 | epot = -222.152243091207 | etot = -178.551719219124 +116000 ekin = 24.1978150545115 | erot = 21.3688456685818 | epot = -222.980866690549 | etot = -177.414205967455 +117000 ekin = 25.4933258533643 | erot = 22.6030027739669 | epot = -224.127289238825 | etot = -176.030960611493 +118000 ekin = 26.5632696276086 | erot = 22.5348729995318 | epot = -225.275605356332 | etot = -176.177462729191 +119000 ekin = 27.3565904118111 | erot = 23.0690511978526 | epot = -226.447636503629 | etot = -176.021994893965 +120000 ekin = 29.3515149477993 | erot = 22.9538643517138 | epot = -227.384133540075 | etot = -175.078754240562 +121000 ekin = 30.5981861627602 | erot = 24.0718786854702 | epot = -228.0863722092 | etot = -173.416307360969 +122000 ekin = 30.8337076451186 | erot = 21.5728983486705 | epot = -228.574513811433 | etot = -176.167907817644 +123000 ekin = 31.5034781314849 | erot = 24.7369743163131 | epot = -228.825132694326 | etot = -172.584680246528 +124000 ekin = 32.5012268554423 | erot = 22.3540490361114 | epot = -229.031726697549 | etot = -174.176450805995 +125000 ekin = 32.7837623568763 | erot = 21.6390695988794 | epot = -229.355357070393 | etot = -174.932525114638 +126000 ekin = 34.6524233539235 | erot = 20.8886638576163 | epot = -229.754016136603 | etot = -174.212928925063 +127000 ekin = 34.0859583483566 | erot = 20.87571356796 | epot = -230.186745529299 | etot = -175.225073612982 +128000 ekin = 33.3654002002854 | erot = 17.8696662885262 | epot = -230.452008826877 | etot = -179.216942338065 +129000 ekin = 32.879700171019 | erot = 20.1227819588362 | epot = -230.66738519366 | etot = -177.664903063805 +130000 ekin = 32.5779755655807 | erot = 22.5079760785794 | epot = -230.755161253226 | etot = -175.669209609066 +131000 ekin = 32.0009253066221 | erot = 23.4002695617563 | epot = -230.587415910688 | etot = -175.186221042309 +132000 ekin = 30.6104507658518 | erot = 23.2152891369288 | epot = -230.187009153994 | etot = -176.361269251214 +133000 ekin = 30.0801055500021 | erot = 24.89872490236 | epot = -229.502463574013 | etot = -174.523633121651 +134000 ekin = 29.5703478432003 | erot = 25.5419443422135 | epot = -228.376328698803 | etot = -173.264036513389 +135000 ekin = 27.8494638285662 | erot = 22.1463271581356 | epot = -226.796614760718 | etot = -176.800823774016 +136000 ekin = 26.7413064146633 | erot = 24.9789465866713 | epot = -225.063840059921 | etot = -173.343587058586 +137000 ekin = 25.6957193105053 | erot = 20.7412156523377 | epot = -223.397630735845 | etot = -176.960695773002 +138000 ekin = 23.6295036307194 | erot = 22.156062146465 | epot = -221.790362287186 | etot = -176.004796510002 +139000 ekin = 21.3906159765428 | erot = 21.7146099871639 | epot = -220.250844850201 | etot = -177.145618886495 +140000 ekin = 20.4985795938428 | erot = 20.8528672558468 | epot = -218.909318457139 | etot = -177.557871607449 +141000 ekin = 20.0359949166403 | erot = 21.2802479225099 | epot = -217.577251694951 | etot = -176.261008855801 +142000 ekin = 18.9631892259955 | erot = 19.8482921778254 | epot = -216.554661187853 | etot = -177.743179784032 +143000 ekin = 18.9783976628076 | erot = 21.2354711831475 | epot = -215.943444643249 | etot = -175.729575797294 +144000 ekin = 18.3622731665631 | erot = 20.8806330220523 | epot = -215.526530561429 | etot = -176.283624372814 +145000 ekin = 18.3633778590725 | erot = 20.9808337178454 | epot = -215.141180064732 | etot = -175.796968487814 +146000 ekin = 18.0030641174453 | erot = 20.1144458830263 | epot = -215.132079230415 | etot = -177.014569229944 +147000 ekin = 18.1301824506837 | erot = 20.0682713533626 | epot = -215.558128457865 | etot = -177.359674653818 +148000 ekin = 18.7692583084233 | erot = 18.7526905862527 | epot = -216.118789082644 | etot = -178.596840187968 +149000 ekin = 18.9701199796348 | erot = 21.3459169858944 | epot = -216.705869035682 | etot = -176.389832070152 +150000 ekin = 19.1460230366766 | erot = 22.9728862104556 | epot = -217.097167008501 | etot = -174.978257761369 +151000 ekin = 19.9232401081762 | erot = 20.8260224389232 | epot = -217.485240320698 | etot = -176.735977773599 +152000 ekin = 20.1824516077178 | erot = 20.0237977742153 | epot = -217.959645068293 | etot = -177.75339568636 +153000 ekin = 21.0207460333017 | erot = 21.268492565156 | epot = -218.612718008189 | etot = -176.323479409731 +154000 ekin = 22.534961994461 | erot = 20.9919099903807 | epot = -219.177409254363 | etot = -175.650537269521 +155000 ekin = 22.8618213684381 | erot = 19.5692643142745 | epot = -219.570021303563 | etot = -177.138935620851 +156000 ekin = 23.1051643701801 | erot = 16.4296764652247 | epot = -219.703156446911 | etot = -180.168315611506 +157000 ekin = 23.2429556198953 | erot = 18.0924487652884 | epot = -219.692327251345 | etot = -178.356922866161 +158000 ekin = 23.0355467188289 | erot = 18.2828932149397 | epot = -219.48465834254 | etot = -178.166218408772 +159000 ekin = 23.1050695121227 | erot = 16.2275027241546 | epot = -219.231547257504 | etot = -179.898975021227 +160000 ekin = 22.7521851912413 | erot = 16.6417481664669 | epot = -219.073812974093 | etot = -179.679879616385 +161000 ekin = 23.2701284387811 | erot = 17.0428745048628 | epot = -218.662884465419 | etot = -178.349881521775 +162000 ekin = 23.4520460412958 | erot = 19.2723698795182 | epot = -218.246057424873 | etot = -175.521641504059 +163000 ekin = 23.689441669341 | erot = 16.1416805717479 | epot = -218.038571722494 | etot = -178.207449481405 +164000 ekin = 23.3619421025109 | erot = 18.22708784978 | epot = -218.093772102733 | etot = -176.504742150442 +165000 ekin = 23.8064702087761 | erot = 19.6627695131554 | epot = -218.432017549968 | etot = -174.962777828037 +166000 ekin = 24.0139008081603 | erot = 20.0731418226024 | epot = -219.005861365541 | etot = -174.918818734778 +167000 ekin = 24.0624950654638 | erot = 20.9748981844942 | epot = -219.683607499488 | etot = -174.64621424953 +168000 ekin = 23.9376600547935 | erot = 20.1285243447132 | epot = -220.420457921599 | etot = -176.354273522093 +169000 ekin = 23.5298927322548 | erot = 20.2068282573737 | epot = -221.313567545343 | etot = -177.576846555714 +170000 ekin = 23.7768907445282 | erot = 21.2771123646888 | epot = -222.337207228985 | etot = -177.283204119768 +171000 ekin = 24.1370595671943 | erot = 23.097407978718 | epot = -223.5506470736 | etot = -176.316179527688 +172000 ekin = 24.4668786543479 | erot = 25.3209673144829 | epot = -224.697775116656 | etot = -174.909929147825 +173000 ekin = 24.6123421907483 | erot = 25.55710330111 | epot = -225.927114756503 | etot = -175.757669264645 +174000 ekin = 24.1184603587473 | erot = 26.344734075088 | epot = -227.192870039681 | etot = -176.729675605846 +175000 ekin = 24.6198790665726 | erot = 26.2179225737243 | epot = -228.430613666214 | etot = -177.592812025917 +176000 ekin = 24.6885745323025 | erot = 25.3760086033795 | epot = -229.590489142521 | etot = -179.525906006839 +177000 ekin = 25.8487289680921 | erot = 27.3473459150405 | epot = -230.512099208118 | etot = -177.316024324985 +178000 ekin = 25.7936599135358 | erot = 26.8557059905942 | epot = -231.146460411413 | etot = -178.497094507283 +179000 ekin = 26.1888961667669 | erot = 29.1002089068839 | epot = -231.411675557269 | etot = -176.122570483618 +180000 ekin = 26.0135600090731 | erot = 27.5817576880658 | epot = -231.273797896987 | etot = -177.678480199848 +181000 ekin = 26.2264624864677 | erot = 25.4290614265803 | epot = -230.913442560937 | etot = -179.257918647889 +182000 ekin = 26.1398552438982 | erot = 24.0809599689769 | epot = -230.511696027826 | etot = -180.290880814951 +183000 ekin = 26.1556145401761 | erot = 24.0766924985731 | epot = -229.818266971064 | etot = -179.585959932315 +184000 ekin = 27.3086871074633 | erot = 24.4288359228746 | epot = -228.839517782805 | etot = -177.101994752467 +185000 ekin = 27.4898787585441 | erot = 24.7938482452323 | epot = -227.666559851805 | etot = -175.382832848029 +186000 ekin = 27.3328782862148 | erot = 22.6658429472471 | epot = -226.350890551421 | etot = -176.352169317959 +187000 ekin = 26.7948174814632 | erot = 22.6470038181953 | epot = -225.081289232844 | etot = -175.639467933186 +188000 ekin = 27.8723845439341 | erot = 23.5234220005291 | epot = -223.908358510605 | etot = -172.512551966142 +189000 ekin = 28.1601880311353 | erot = 23.7261081823951 | epot = -222.800556775815 | etot = -170.914260562285 +190000 ekin = 28.0281791381836 | erot = 22.4495336007974 | epot = -221.746357664621 | etot = -171.26864492564 +191000 ekin = 28.3968994364094 | erot = 24.5513031073085 | epot = -220.887175628872 | etot = -167.938973085154 +192000 ekin = 27.7855852746761 | erot = 25.7678221031458 | epot = -220.147377425492 | etot = -166.59397004767 +193000 ekin = 27.0653969351198 | erot = 26.0797976416142 | epot = -219.448938305435 | etot = -166.303743728701 +194000 ekin = 26.591886956892 | erot = 27.2559987926336 | epot = -218.866818380032 | etot = -165.018932630506 +195000 ekin = 25.3875760139297 | erot = 30.4658402325932 | epot = -218.624921486327 | etot = -162.771505239804 +196000 ekin = 25.2698426080245 | erot = 29.5251795522301 | epot = -218.561614102179 | etot = -163.766591941925 +197000 ekin = 24.2903229144824 | erot = 31.8288244412473 | epot = -218.729796870422 | etot = -162.610649514693 +198000 ekin = 23.7276722827683 | erot = 32.0454149389688 | epot = -218.941804941586 | etot = -163.168717719849 +199000 ekin = 23.8463467560116 | erot = 31.965616978649 | epot = -219.185182684789 | etot = -163.373218950129 +200000 ekin = 23.3466100334222 | erot = 29.1399528434376 | epot = -219.23796368071 | etot = -166.75140080385 +201000 ekin = 22.7487917233094 | erot = 25.7244975420237 | epot = -219.090866114478 | etot = -170.617576849145 +202000 ekin = 22.1721332597989 | erot = 26.1511956277664 | epot = -218.778552074906 | etot = -170.455223187341 +203000 ekin = 21.7181344250325 | erot = 26.0871722320545 | epot = -218.390435495582 | etot = -170.585128838495 +204000 ekin = 21.0376564690026 | erot = 25.6226947809704 | epot = -218.05720217283 | etot = -171.396850922857 +205000 ekin = 20.7302702694838 | erot = 24.1599304176471 | epot = -217.801704730261 | etot = -172.91150404313 +206000 ekin = 21.3382716889647 | erot = 25.5578466968796 | epot = -217.705513220694 | etot = -170.80939483485 +207000 ekin = 21.929943769803 | erot = 24.3043622352602 | epot = -217.500606803152 | etot = -171.266300798088 +208000 ekin = 22.3703602648222 | erot = 23.8138985281345 | epot = -217.448247660947 | etot = -171.263988867991 +209000 ekin = 22.8322135815925 | erot = 24.3154754235774 | epot = -217.780621512497 | etot = -170.632932507327 +210000 ekin = 23.531458296701 | erot = 24.1781224892903 | epot = -218.426497805566 | etot = -170.716917019575 +211000 ekin = 24.3108042780204 | erot = 23.8117896585318 | epot = -219.237721464183 | etot = -171.115127527631 +212000 ekin = 25.5498843003363 | erot = 26.3148102829016 | epot = -220.148368449074 | etot = -168.283673865837 +213000 ekin = 26.7904826379273 | erot = 27.2908991135753 | epot = -221.046804647224 | etot = -166.965422895721 +214000 ekin = 27.9221149858574 | erot = 28.825031948947 | epot = -222.018023522183 | etot = -165.270876587378 +215000 ekin = 29.7060783522062 | erot = 26.6259095075768 | epot = -223.029189042779 | etot = -166.697201182996 +216000 ekin = 30.8166996672947 | erot = 27.4426017797676 | epot = -223.860903452266 | etot = -165.601602005203 +217000 ekin = 32.1062758748256 | erot = 28.480190382591 | epot = -224.420307416779 | etot = -163.833841159362 +218000 ekin = 34.0231354353329 | erot = 28.0396432492363 | epot = -224.762754873132 | etot = -162.699976188563 +219000 ekin = 35.0935147430151 | erot = 27.3420247123898 | epot = -224.844267242182 | etot = -162.408727786777 +220000 ekin = 36.6903483012276 | erot = 26.4046555014058 | epot = -224.674345925857 | etot = -161.579342123224 +221000 ekin = 37.0162358447748 | erot = 27.0644284813825 | epot = -224.294474180674 | etot = -160.213809854517 +222000 ekin = 37.2286352786866 | erot = 29.6452455867393 | epot = -223.646643282534 | etot = -156.772762417109 +223000 ekin = 37.1371706719775 | erot = 29.0338627066246 | epot = -223.02426705627 | etot = -156.853233677668 +224000 ekin = 37.7973687387399 | erot = 29.5349839686757 | epot = -222.452854546985 | etot = -155.120501839569 +225000 ekin = 37.8069973966967 | erot = 29.6422173132561 | epot = -221.948475640134 | etot = -154.499260930181 +226000 ekin = 37.3773991674874 | erot = 28.09605253081 | epot = -221.560990142565 | etot = -156.087538444267 +227000 ekin = 37.527755930331 | erot = 27.6808541221468 | epot = -221.483330512065 | etot = -156.274720459587 +228000 ekin = 38.4470067960778 | erot = 27.8146638288223 | epot = -221.276464510559 | etot = -155.014793885659 +229000 ekin = 39.1836147193506 | erot = 25.70095638706 | epot = -220.76463229751 | etot = -155.880061191099 +230000 ekin = 38.098964797451 | erot = 24.8377609072553 | epot = -219.990046626182 | etot = -157.053320921476 +231000 ekin = 36.1669798709402 | erot = 24.8108260069157 | epot = -219.186001203482 | etot = -158.208195325626 +232000 ekin = 36.2198119684192 | erot = 23.4065079338759 | epot = -218.360141683673 | etot = -158.733821781378 +233000 ekin = 34.9532458569289 | erot = 23.2139515607483 | epot = -217.384236817587 | etot = -159.21703939991 +234000 ekin = 33.7585177506638 | erot = 23.2139271576215 | epot = -216.590184561824 | etot = -159.617739653539 +235000 ekin = 32.5335134532386 | erot = 20.9776329357582 | epot = -215.733671699105 | etot = -162.222525310108 +236000 ekin = 31.2185234875872 | erot = 19.9753628972515 | epot = -214.975828378577 | etot = -163.781941993739 +237000 ekin = 30.4570685291383 | erot = 20.3543664256712 | epot = -214.499912868784 | etot = -163.688477913975 +238000 ekin = 30.2614586325617 | erot = 21.1886832898794 | epot = -214.361693708507 | etot = -162.911551786066 +239000 ekin = 30.4636237840023 | erot = 21.5186095678481 | epot = -214.441235319161 | etot = -162.459001967311 +240000 ekin = 30.1210218817714 | erot = 22.9784100820642 | epot = -214.858237469049 | etot = -161.758805505214 +241000 ekin = 30.3658666076425 | erot = 21.7261951348677 | epot = -215.434563747826 | etot = -163.342502005316 +242000 ekin = 31.3867694338899 | erot = 23.9153977300584 | epot = -216.072635834797 | etot = -160.770468670849 +243000 ekin = 31.1900708118743 | erot = 26.6273701728334 | epot = -216.694600313578 | etot = -158.877159328871 +244000 ekin = 31.1564882281032 | erot = 25.7058049551927 | epot = -217.265423330916 | etot = -160.40313014762 +245000 ekin = 32.4795705887834 | erot = 24.8995064535899 | epot = -217.720460688445 | etot = -160.341383646071 +246000 ekin = 32.872022647284 | erot = 22.333159106545 | epot = -218.061658138483 | etot = -162.856476384654 +247000 ekin = 33.4284260628809 | erot = 24.7591927551794 | epot = -218.263367004162 | etot = -160.075748186102 +248000 ekin = 32.4614988934282 | erot = 23.8539156460749 | epot = -218.302805394426 | etot = -161.987390854923 +249000 ekin = 32.1756176499451 | erot = 23.8767681339002 | epot = -218.304065910381 | etot = -162.251680126536 +250000 ekin = 32.2198888158387 | erot = 22.8375122406138 | epot = -218.144356419904 | etot = -163.086955363451 +251000 ekin = 32.3333741154669 | erot = 22.2973676925259 | epot = -217.820854022814 | etot = -163.190112214821 +252000 ekin = 32.6075392448557 | erot = 23.4769293692233 | epot = -217.429569515478 | etot = -161.345100901399 +253000 ekin = 32.4971688738337 | erot = 24.3030528043931 | epot = -216.984279947662 | etot = -160.184058269435 +254000 ekin = 31.8923138747249 | erot = 24.1415429248736 | epot = -216.529032269096 | etot = -160.495175469498 +255000 ekin = 31.4024206135883 | erot = 23.8129962675095 | epot = -216.108885088425 | etot = -160.893468207327 +256000 ekin = 31.4668964539727 | erot = 25.1555403914743 | epot = -215.777158729505 | etot = -159.154721884058 +257000 ekin = 30.1578271181182 | erot = 25.2224232604804 | epot = -215.398717214095 | etot = -160.018466835496 +258000 ekin = 30.052285311838 | erot = 25.7673281945382 | epot = -215.003795923615 | etot = -159.184182417239 +259000 ekin = 28.790005223663 | erot = 25.9071617879885 | epot = -214.672294871174 | etot = -159.975127859522 +260000 ekin = 28.824260164679 | erot = 25.3762394651934 | epot = -214.438705752551 | etot = -160.238206122679 +261000 ekin = 28.4516249893281 | erot = 24.3935835063456 | epot = -214.056107967132 | etot = -161.210899471458 +262000 ekin = 27.8087703289653 | erot = 22.2360995417882 | epot = -213.52238610892 | etot = -163.477516238166 +263000 ekin = 27.2988805169285 | erot = 22.3316425638774 | epot = -213.209725671803 | etot = -163.579202590997 +264000 ekin = 27.7705600653735 | erot = 23.2743633836993 | epot = -213.047162146333 | etot = -162.00223869726 +265000 ekin = 27.8709800491321 | erot = 23.5211350737156 | epot = -212.86511367636 | etot = -161.472998553512 +266000 ekin = 27.9918135619683 | erot = 23.7232253135648 | epot = -212.641590093523 | etot = -160.92655121799 +267000 ekin = 28.5234357395516 | erot = 24.0561346062967 | epot = -212.474716645669 | etot = -159.895146299821 +268000 ekin = 28.870687215238 | erot = 23.8306167734046 | epot = -212.508203135534 | etot = -159.806899146891 +269000 ekin = 29.2607991052743 | erot = 24.1133194421955 | epot = -212.537028623626 | etot = -159.162910076156 +270000 ekin = 28.5296269979822 | erot = 25.8732554655093 | epot = -212.31029476064 | etot = -157.907412297149 +271000 ekin = 28.9212541346642 | erot = 22.4473820635914 | epot = -212.324230216607 | etot = -160.955594018351 +272000 ekin = 29.6765055230995 | erot = 25.0261431612911 | epot = -212.625998104986 | etot = -157.923349420595 +273000 ekin = 29.7746844908601 | erot = 24.8432699221532 | epot = -212.915298586345 | etot = -158.297344173332 +274000 ekin = 29.9742743190805 | erot = 24.1999136810544 | epot = -213.041688653029 | etot = -158.867500652894 +275000 ekin = 29.5940338177725 | erot = 25.4819616152138 | epot = -213.067492330014 | etot = -157.991496897028 +276000 ekin = 30.2832320515794 | erot = 24.0723230457662 | epot = -213.253118366949 | etot = -158.897563269603 +277000 ekin = 30.4700966177081 | erot = 23.2212292830064 | epot = -213.621019589182 | etot = -159.929693688468 +278000 ekin = 30.67056507496 | erot = 24.4631770981652 | epot = -214.132222700305 | etot = -158.99848052718 +279000 ekin = 30.6357169264609 | erot = 19.8864866789268 | epot = -214.377025145056 | etot = -163.854821539669 +280000 ekin = 30.6259905609972 | erot = 18.665780487499 | epot = -214.4335387873 | etot = -165.141767738804 +281000 ekin = 30.5241190789795 | erot = 17.9408431561163 | epot = -214.446974019773 | etot = -165.982011784677 +282000 ekin = 30.2531856243418 | erot = 16.5789274482122 | epot = -214.432453220479 | etot = -167.600340147925 +283000 ekin = 29.4314819022737 | erot = 14.9978652258759 | epot = -214.684414044695 | etot = -170.255066916545 +284000 ekin = 30.4463102919895 | erot = 13.9713280303416 | epot = -215.084928089016 | etot = -170.667289766685 +285000 ekin = 31.0787017394374 | erot = 14.4465786715638 | epot = -215.631231905545 | etot = -170.105951494544 +286000 ekin = 31.1520316133396 | erot = 14.4930799914547 | epot = -216.300770408183 | etot = -170.655658803388 +287000 ekin = 32.351781766203 | erot = 16.6989745946407 | epot = -216.963878558876 | etot = -167.913122198032 +288000 ekin = 33.005541771032 | erot = 18.134215920469 | epot = -217.673454635531 | etot = -166.53369694403 +289000 ekin = 31.8618589209554 | erot = 18.4772719583004 | epot = -218.379723064086 | etot = -168.04059218483 +290000 ekin = 31.8344575426835 | erot = 19.7422352431296 | epot = -219.065973771903 | etot = -167.48928098609 +291000 ekin = 31.9518185930539 | erot = 20.621627266815 | epot = -219.570480405878 | etot = -166.997034546009 +292000 ekin = 32.6439243188648 | erot = 22.5302835108441 | epot = -219.892967757819 | etot = -164.71875992811 +293000 ekin = 31.4829450686937 | erot = 21.3316743728505 | epot = -219.958047969435 | etot = -167.143428527891 +294000 ekin = 31.6375180782201 | erot = 21.238624328018 | epot = -219.885582904306 | etot = -167.009440498068 +295000 ekin = 31.0253762184145 | erot = 22.4882784169501 | epot = -219.814823672917 | etot = -166.301169037553 +296000 ekin = 30.8124492018732 | erot = 21.713403837488 | epot = -219.710246306785 | etot = -167.184393267424 +297000 ekin = 30.6962957393053 | erot = 21.2387002912486 | epot = -219.446213938046 | etot = -167.511217907492 +298000 ekin = 30.2751045254072 | erot = 21.2588516620972 | epot = -219.069662492538 | etot = -167.535706305033 +299000 ekin = 30.2654549878554 | erot = 19.9050587659481 | epot = -218.83938043646 | etot = -168.668866682656 +300000 ekin = 30.0162960943798 | erot = 22.3467328364631 | epot = -218.595337871123 | etot = -166.232308940281 +301000 ekin = 29.6491535845194 | erot = 19.8418961043971 | epot = -218.642810229095 | etot = -169.151760540178 +302000 ekin = 29.8744151298851 | erot = 18.1734214421702 | epot = -218.872367696606 | etot = -170.824531124551 +303000 ekin = 30.5896376432356 | erot = 18.3628979719825 | epot = -219.385303830194 | etot = -170.432768214976 +304000 ekin = 30.8134874190764 | erot = 19.9151431938305 | epot = -220.085697355968 | etot = -169.357066743061 +305000 ekin = 31.2099214170774 | erot = 20.6624279502763 | epot = -220.87374787482 | etot = -169.001398507466 +306000 ekin = 31.5379241870259 | erot = 21.2324529548628 | epot = -221.686063335012 | etot = -168.915686193123 +307000 ekin = 32.2075616004244 | erot = 23.1042657052719 | epot = -222.42594670972 | etot = -167.114119404023 +308000 ekin = 32.5982898681942 | erot = 23.3642432119933 | epot = -222.922692953037 | etot = -166.96015987285 +309000 ekin = 32.4315134575481 | erot = 23.8633076366207 | epot = -223.184000926484 | etot = -166.889179832315 +310000 ekin = 32.1158150633277 | erot = 23.3576385972236 | epot = -223.437543256612 | etot = -167.964089596061 +311000 ekin = 33.0748530306084 | erot = 23.7247742792265 | epot = -223.800381213498 | etot = -167.000753903663 +312000 ekin = 34.0642489795215 | erot = 24.4005553104056 | epot = -224.015053783926 | etot = -165.550249493999 +313000 ekin = 33.3941820316022 | erot = 22.8657808322912 | epot = -224.224694496321 | etot = -167.964731632427 +314000 ekin = 32.8831430452506 | erot = 22.3521386618945 | epot = -224.328814014534 | etot = -169.093532307389 +315000 ekin = 32.6439304562237 | erot = 24.3395053721963 | epot = -224.403018580942 | etot = -167.419582752522 +316000 ekin = 32.5730201874399 | erot = 25.8715269487792 | epot = -224.429728916574 | etot = -165.985181780355 +317000 ekin = 31.691345936356 | erot = 27.6427411551856 | epot = -224.240735797652 | etot = -164.90664870611 +318000 ekin = 31.1651843502561 | erot = 26.792649242559 | epot = -223.979858021812 | etot = -166.022024428997 +319000 ekin = 31.7256674778549 | erot = 23.8408589889958 | epot = -223.590556061656 | etot = -168.024029594805 +320000 ekin = 31.7060827776545 | erot = 26.4684067579431 | epot = -223.249262306441 | etot = -165.074772770843 +321000 ekin = 31.6031237667453 | erot = 27.4509881705089 | epot = -223.147476089125 | etot = -164.093364151871 +322000 ekin = 30.3481482285902 | erot = 27.7216584811217 | epot = -222.937601855219 | etot = -164.867795145507 +323000 ekin = 29.3228062491828 | erot = 29.7362160481481 | epot = -222.700827695669 | etot = -163.641805398338 +324000 ekin = 30.0900580978278 | erot = 28.3009812560174 | epot = -222.702754485984 | etot = -164.311715132138 +325000 ekin = 28.9724465195176 | erot = 31.4194498954201 | epot = -222.678079364986 | etot = -162.286182950048 +326000 ekin = 29.6807119193739 | erot = 29.8368278955146 | epot = -222.408655317023 | etot = -162.891115502134 +327000 ekin = 30.1649693984999 | erot = 27.5646417986177 | epot = -222.067063198242 | etot = -164.337452001125 +328000 ekin = 30.3408094046572 | erot = 26.5580828070968 | epot = -221.711839024904 | etot = -164.81294681315 +329000 ekin = 29.8995896328213 | erot = 24.6642798907952 | epot = -221.317020601826 | etot = -166.753151078209 +330000 ekin = 29.1001168093683 | erot = 27.3082067727852 | epot = -221.023371065897 | etot = -164.615047483743 +331000 ekin = 29.3349918490581 | erot = 27.5476077161585 | epot = -220.672722242025 | etot = -163.790122676808 +332000 ekin = 29.5801979725688 | erot = 27.2721545786742 | epot = -220.153700211885 | etot = -163.301347660642 +333000 ekin = 28.8256885894683 | erot = 28.4593129139449 | epot = -219.338463478995 | etot = -162.053461975582 +334000 ekin = 29.6068579849397 | erot = 28.2610782505578 | epot = -218.379292922818 | etot = -160.511356687321 +335000 ekin = 29.1933888055502 | erot = 24.4887025724561 | epot = -217.4599543906 | etot = -163.777863012594 +336000 ekin = 30.3071264565402 | erot = 24.6669652156945 | epot = -216.60775546459 | etot = -161.633663792355 +337000 ekin = 30.1138123587914 | erot = 23.8810939282739 | epot = -215.898081222498 | etot = -161.903174935432 +338000 ekin = 30.3467366262656 | erot = 22.5089541109543 | epot = -215.413223769271 | etot = -162.557533032051 +339000 ekin = 29.2241742025094 | erot = 22.9493211875938 | epot = -215.161328851956 | etot = -162.987833461853 +340000 ekin = 30.5171940243424 | erot = 22.1230395830795 | epot = -215.211023569382 | etot = -162.57078996196 +341000 ekin = 30.2990451747942 | erot = 22.0969746780876 | epot = -215.550935218903 | etot = -163.154915366021 +342000 ekin = 30.4576471953255 | erot = 22.8638016940834 | epot = -216.001360002558 | etot = -162.679911113149 +343000 ekin = 30.5621281016439 | erot = 24.4583122950448 | epot = -215.621289056559 | etot = -160.60084865987 +344000 ekin = 32.4519608541283 | erot = 28.5755206655114 | epot = -217.653133425583 | etot = -156.625651905943 +345000 ekin = 31.64186545717 | erot = 32.3842692970166 | epot = -218.708632568144 | etot = -154.682497813957 +346000 ekin = 31.9511111644616 | erot = 30.5483257685665 | epot = -219.014511159579 | etot = -156.515074226551 +347000 ekin = 30.7638178773701 | erot = 27.010357983763 | epot = -218.824845563665 | etot = -161.050669702532 +348000 ekin = 29.6838704731132 | erot = 24.9056867476275 | epot = -218.325871696026 | etot = -163.736314475285 +349000 ekin = 28.9550895574073 | erot = 28.1956349832957 | epot = -217.605556361012 | etot = -160.454831820309 +350000 ekin = 27.8908728899355 | erot = 27.4303776928326 | epot = -216.700972313945 | etot = -161.379721731177 +351000 ekin = 27.2743250159904 | erot = 29.1647807029794 | epot = -215.665223366206 | etot = -159.226117647236 +352000 ekin = 26.9616211386809 | erot = 30.6797251227193 | epot = -214.694539908538 | etot = -157.053193647138 +353000 ekin = 27.348832713772 | erot = 29.6015507795374 | epot = -213.896099461977 | etot = -156.945715968668 +354000 ekin = 26.1507956829831 | erot = 30.7563048879842 | epot = -213.372078199846 | etot = -156.464977628878 +355000 ekin = 25.6190603614018 | erot = 32.5689348009866 | epot = -213.269655859313 | etot = -155.081660696925 +356000 ekin = 25.3669997880113 | erot = 31.0472983763093 | epot = -213.450675449262 | etot = -157.036377284941 +357000 ekin = 25.312758671354 | erot = 31.8479342344932 | epot = -213.695546912804 | etot = -156.534854006956 +358000 ekin = 26.0187679198773 | erot = 31.9758685586405 | epot = -214.009662837489 | etot = -156.015026358971 +359000 ekin = 26.5607225985322 | erot = 29.9396653432688 | epot = -214.192283973959 | etot = -157.691896032158 +360000 ekin = 26.5902994062844 | erot = 25.9943052658055 | epot = -214.124414590833 | etot = -161.539809918743 +361000 ekin = 26.4813018415084 | erot = 24.2616769392684 | epot = -213.85398393885 | etot = -163.111005158073 +362000 ekin = 26.5033314195901 | erot = 26.0990581372781 | epot = -213.545462747037 | etot = -160.943073190169 +363000 ekin = 27.1571133077625 | erot = 25.5067564699878 | epot = -213.334127657296 | etot = -160.670257879545 +364000 ekin = 27.887930595824 | erot = 23.9887993938849 | epot = -212.852508852937 | etot = -160.975778863229 +365000 ekin = 27.967758403039 | erot = 20.854424772872 | epot = -212.290084332197 | etot = -163.467901156286 +366000 ekin = 27.0060927016748 | erot = 20.9170666829011 | epot = -211.843808452849 | etot = -163.920649068273 +367000 ekin = 26.6039768958553 | erot = 23.5699590216425 | epot = -211.557557482102 | etot = -161.383621564604 +368000 ekin = 26.1143377810244 | erot = 24.5362401721805 | epot = -211.384448343648 | etot = -160.733870390443 +369000 ekin = 25.8118104643539 | erot = 22.5391701033533 | epot = -211.406298065096 | etot = -163.055317497389 +370000 ekin = 25.8673504840375 | erot = 22.7731029418705 | epot = -211.64775421813 | etot = -163.007300792222 +371000 ekin = 26.4562588492746 | erot = 23.9905423895665 | epot = -211.815727194594 | etot = -161.368925955753 +372000 ekin = 26.3200791949476 | erot = 22.7189248210943 | epot = -212.040306718402 | etot = -163.00130270236 +373000 ekin = 25.3755530875695 | erot = 25.0380776190232 | epot = -212.072031912698 | etot = -161.658401206106 +374000 ekin = 24.1185712423776 | erot = 25.2038789684849 | epot = -211.935098223519 | etot = -162.612648012656 +375000 ekin = 24.0684595712565 | erot = 23.8499797175989 | epot = -211.793395733322 | etot = -163.874956444466 +376000 ekin = 22.5016871580896 | erot = 25.6118197832101 | epot = -211.409769064352 | etot = -163.296262123053 +377000 ekin = 22.0986939181275 | erot = 24.7100299168742 | epot = -211.045176539028 | etot = -164.236452704026 +378000 ekin = 21.1684841682011 | erot = 25.5492888669468 | epot = -210.660306734319 | etot = -163.942533699171 +379000 ekin = 20.010673971417 | erot = 29.7040277439788 | epot = -210.244603948909 | etot = -160.529902233513 +380000 ekin = 18.6364568547605 | erot = 33.3248766383446 | epot = -210.07312332186 | etot = -158.111789828755 +381000 ekin = 19.1123943604215 | erot = 29.9128186030511 | epot = -210.121981236354 | etot = -161.096768272881 +382000 ekin = 18.488667416097 | erot = 30.6195763742908 | epot = -210.287398668517 | etot = -161.179154878129 +383000 ekin = 17.9867949709769 | erot = 30.4649216268247 | epot = -210.644012249165 | etot = -162.192295651363 +384000 ekin = 18.086653701317 | erot = 30.1682137046886 | epot = -211.454411912153 | etot = -163.199544506147 +385000 ekin = 17.9753010304936 | erot = 30.6444125095994 | epot = -212.324100690826 | etot = -163.704387150733 +386000 ekin = 17.7413668486357 | erot = 30.1012874369922 | epot = -213.259558577419 | etot = -165.416904291791 +387000 ekin = 18.2186784291797 | erot = 28.3029350222839 | epot = -214.13010996286 | etot = -167.608496511396 +388000 ekin = 19.292870919104 | erot = 29.2720917147751 | epot = -214.909679402132 | etot = -166.344716768253 +389000 ekin = 20.4945794932603 | erot = 28.0408016793114 | epot = -215.715111099094 | etot = -167.179729926522 +390000 ekin = 21.4293155611672 | erot = 27.6051655638294 | epot = -216.558290196654 | etot = -167.523809071658 +391000 ekin = 22.3503257992232 | erot = 27.4540127593509 | epot = -217.20378427697 | etot = -167.399445718396 +392000 ekin = 23.5932179843426 | erot = 27.1057144401021 | epot = -217.566275239839 | etot = -166.867342815394 +393000 ekin = 23.7557009876267 | erot = 26.6637680566362 | epot = -217.563756363461 | etot = -167.144287319198 +394000 ekin = 24.4865989987554 | erot = 23.220719991203 | epot = -217.316082883998 | etot = -169.608763894039 +395000 ekin = 24.7595946480364 | erot = 21.8918507069135 | epot = -216.949712698095 | etot = -170.298267343146 +396000 ekin = 24.982464352614 | erot = 22.3354930515494 | epot = -216.416874060901 | etot = -169.098916656738 +397000 ekin = 25.3000376061139 | erot = 18.3060350402966 | epot = -216.050469640324 | etot = -172.444396993914 +398000 ekin = 25.2861319964392 | erot = 20.4058007069709 | epot = -215.762453015488 | etot = -170.070520312078 +399000 ekin = 25.6910756014433 | erot = 17.2458372762693 | epot = -215.449363397805 | etot = -172.512450520093 +400000 ekin = 26.4568923302747 | erot = 20.1388849072962 | epot = -215.187132762528 | etot = -168.591355524957 +401000 ekin = 26.473671301154 | erot = 21.2374664754577 | epot = -215.079189181665 | etot = -167.368051405054 +402000 ekin = 26.9661026532044 | erot = 22.1166726988484 | epot = -215.024717195915 | etot = -165.941941843862 +403000 ekin = 27.3226322136654 | erot = 22.8394489464986 | epot = -214.937632585437 | etot = -164.775551425273 +404000 ekin = 27.8935295461376 | erot = 22.8817369521021 | epot = -214.928408259317 | etot = -164.153141761077 +405000 ekin = 27.9407970657418 | erot = 23.0166667876302 | epot = -215.070859098588 | etot = -164.113395245216 +406000 ekin = 27.8467131583262 | erot = 24.0920158980814 | epot = -215.21564472779 | etot = -163.276915671383 +407000 ekin = 28.1735323456276 | erot = 24.4127070079513 | epot = -215.337654426137 | etot = -162.751415072558 +408000 ekin = 28.0581746931196 | erot = 25.4097057702624 | epot = -215.286666631528 | etot = -161.818786168146 +409000 ekin = 28.4575477087421 | erot = 27.0137932992507 | epot = -215.176589089366 | etot = -159.705248081373 +410000 ekin = 29.085031171955 | erot = 22.9273639101281 | epot = -215.097105269705 | etot = -163.084710187621 +411000 ekin = 28.9671748142217 | erot = 21.8822014832413 | epot = -214.921613402608 | etot = -164.072237105145 +412000 ekin = 29.4064096216751 | erot = 22.5408195016054 | epot = -214.627366977766 | etot = -162.680137854486 +413000 ekin = 29.1673383998257 | erot = 22.321938064771 | epot = -214.45055434655 | etot = -162.961277881953 +414000 ekin = 29.0111563106279 | erot = 18.7948327919326 | epot = -214.508701808542 | etot = -166.702712705981 +415000 ekin = 29.2163525836019 | erot = 18.3535912788607 | epot = -214.674303958464 | etot = -167.104360096002 +416000 ekin = 29.3094098198563 | erot = 17.6709040312385 | epot = -214.87605897502 | etot = -167.895745123926 +417000 ekin = 29.3855401131447 | erot = 16.4805818891855 | epot = -215.210819648773 | etot = -169.344697646443 +418000 ekin = 30.2763385538192 | erot = 20.6340456010144 | epot = -215.816567102338 | etot = -164.906182947505 +419000 ekin = 31.2702871079484 | erot = 21.0558998076069 | epot = -216.353762857211 | etot = -164.027575941656 +420000 ekin = 31.1928990244873 | erot = 23.8599837907919 | epot = -216.890403955335 | etot = -161.837521140056 +421000 ekin = 31.5456444237668 | erot = 23.2548532394917 | epot = -217.344973044312 | etot = -162.544475381054 +422000 ekin = 31.595330248126 | erot = 24.1129799902568 | epot = -217.646733756815 | etot = -161.938423518432 +423000 ekin = 30.3263575817443 | erot = 24.7757808957598 | epot = -217.691567202219 | etot = -162.589428724715 +424000 ekin = 29.6227184353682 | erot = 26.8551354763864 | epot = -217.49353393768 | etot = -161.015680025925 +425000 ekin = 29.5897090928897 | erot = 26.5787069615055 | epot = -217.189735948055 | etot = -161.02131989366 +426000 ekin = 28.3811287852246 | erot = 26.0477945184346 | epot = -216.709754303037 | etot = -162.280830999377 +427000 ekin = 27.7967079006065 | erot = 25.8148017215667 | epot = -215.916318594378 | etot = -162.304808972205 +428000 ekin = 27.0564125148368 | erot = 24.2254396851756 | epot = -214.786030457606 | etot = -163.504178257594 +429000 ekin = 26.4009850387513 | erot = 25.2739282576038 | epot = -213.377238447454 | etot = -161.702325151099 +430000 ekin = 25.8966083026098 | erot = 25.0007234317203 | epot = -211.870124789713 | etot = -160.972793055383 +431000 ekin = 24.7984133581247 | erot = 23.6811925425768 | epot = -210.204391421479 | etot = -161.724785520777 +432000 ekin = 24.5987744680211 | erot = 21.4763884246366 | epot = -208.534970052743 | etot = -162.459807160085 +433000 ekin = 22.9801023558261 | erot = 20.5753920602906 | epot = -207.012668945877 | etot = -163.457174529761 +434000 ekin = 21.7283926559211 | erot = 20.7827792983396 | epot = -205.743779917972 | etot = -163.232607963712 +435000 ekin = 20.6245427682379 | erot = 23.3682934466507 | epot = -204.585339785363 | etot = -160.592503570474 +436000 ekin = 19.7010843166892 | erot = 22.7947216751232 | epot = -203.673192464633 | etot = -161.17738647282 +437000 ekin = 18.8171368139259 | erot = 25.8230091867142 | epot = -202.902988849489 | etot = -158.262842848849 +438000 ekin = 18.5857719223376 | erot = 23.8018783969198 | epot = -202.347858231407 | etot = -159.96020791215 +439000 ekin = 18.4671140963778 | erot = 20.8474712254561 | epot = -202.040176117765 | etot = -162.725590795931 +440000 ekin = 18.7081908968736 | erot = 21.8456146936514 | epot = -202.119006954422 | etot = -161.565201363897 +441000 ekin = 19.1502196807364 | erot = 22.8429897393171 | epot = -202.649140947654 | etot = -160.655931527601 +442000 ekin = 19.6976623491702 | erot = 23.833532038064 | epot = -203.432766723882 | etot = -159.901572336648 +443000 ekin = 20.2692385782964 | erot = 23.174529180215 | epot = -204.244337936897 | etot = -160.800570178386 +444000 ekin = 19.6594548157619 | erot = 25.8570487147508 | epot = -204.964941783042 | etot = -159.448438252529 +445000 ekin = 20.0159531993039 | erot = 25.4583870830884 | epot = -205.887229192997 | etot = -160.412888910605 +446000 ekin = 20.9430057952113 | erot = 27.6789597381082 | epot = -206.884522007063 | etot = -158.262556473743 +447000 ekin = 21.5434157008284 | erot = 26.3367064953282 | epot = -207.875777090658 | etot = -159.995654894502 +448000 ekin = 21.3493130668634 | erot = 28.7124847307391 | epot = -208.826609271652 | etot = -158.76481147405 +449000 ekin = 21.4147217526733 | erot = 30.2712153847118 | epot = -209.889081936843 | etot = -158.203144799458 +450000 ekin = 22.9537180151663 | erot = 30.7913406967762 | epot = -211.045040894093 | etot = -157.29998218215 +451000 ekin = 24.0701784584903 | erot = 33.2662973441661 | epot = -212.037901576699 | etot = -154.701425774043 +452000 ekin = 24.9326594408497 | erot = 33.1807983552873 | epot = -213.020928110261 | etot = -154.907470314124 +453000 ekin = 25.9026870743818 | erot = 29.9694393741095 | epot = -213.918112791264 | etot = -158.045986342772 +454000 ekin = 25.6267674636379 | erot = 30.3094040078412 | epot = -214.751677160517 | etot = -158.815505689038 +455000 ekin = 25.8835420243565 | erot = 31.0348607020646 | epot = -215.515256607227 | etot = -158.596853880806 +456000 ekin = 26.5079598183216 | erot = 31.1273555306477 | epot = -216.246152804127 | etot = -158.610837455158 +457000 ekin = 27.4443036582482 | erot = 29.8343750435819 | epot = -216.811984874468 | etot = -159.533306172638 +458000 ekin = 26.9310118911977 | erot = 27.7201727649044 | epot = -216.756924658081 | etot = -162.105740001979 +459000 ekin = 27.9109641832173 | erot = 25.6787961230286 | epot = -217.297816399931 | etot = -163.708056093685 +460000 ekin = 27.9601360034299 | erot = 25.3252752047677 | epot = -217.967018926065 | etot = -164.681607717868 +461000 ekin = 27.0745859502303 | erot = 25.5847145566425 | epot = -217.810130302685 | etot = -165.150829795813 +462000 ekin = 26.7487951031419 | erot = 24.980711595531 | epot = -217.697766754625 | etot = -165.968260055952 +463000 ekin = 26.0732441338559 | erot = 28.153686894781 | epot = -217.358666684053 | etot = -163.131735655416 +464000 ekin = 26.0396949919171 | erot = 25.8416381117693 | epot = -216.944940451188 | etot = -165.063607347501 +465000 ekin = 25.3226575272321 | erot = 24.0325554854213 | epot = -216.354701601293 | etot = -166.99948858864 +466000 ekin = 24.1231672777327 | erot = 24.4307976004896 | epot = -215.565164328178 | etot = -167.011199449956 +467000 ekin = 23.8540709231575 | erot = 22.124846509072 | epot = -214.920239098285 | etot = -168.941321666055 +468000 ekin = 22.565597367876 | erot = 22.7691054272285 | epot = -214.530469865182 | etot = -169.195767070077 +469000 ekin = 22.2713028791399 | erot = 22.2113409900692 | epot = -214.270807992981 | etot = -169.788164123772 +470000 ekin = 22.4851427578562 | erot = 21.4377178321587 | epot = -214.468076008404 | etot = -170.545215418389 +471000 ekin = 22.1823272554268 | erot = 20.278257170788 | epot = -214.941978893437 | etot = -172.481394467223 +472000 ekin = 21.8731320005381 | erot = 19.0138763043457 | epot = -215.549112362977 | etot = -174.662104058093 +473000 ekin = 20.8777093211568 | erot = 22.4202421701947 | epot = -216.333540945248 | etot = -173.035589453897 +474000 ekin = 21.4845461241046 | erot = 21.5552254985163 | epot = -217.149747427618 | etot = -174.109975804997 +475000 ekin = 21.8424250616637 | erot = 22.343637585153 | epot = -218.003692733599 | etot = -173.817630086783 +476000 ekin = 23.3926359095999 | erot = 23.4769825817391 | epot = -218.918478361235 | etot = -172.048859869896 +477000 ekin = 23.53084242551 | erot = 22.2301883973586 | epot = -219.644035844548 | etot = -173.88300502168 +478000 ekin = 23.6068262804286 | erot = 20.4526014426457 | epot = -220.193888919509 | etot = -176.134461196435 +479000 ekin = 23.4875352763514 | erot = 19.3184155065279 | epot = -220.738674570528 | etot = -177.932723787649 +480000 ekin = 23.0717855202954 | erot = 21.8892004951702 | epot = -221.304242068401 | etot = -176.343256052935 +481000 ekin = 22.3550858352525 | erot = 23.0423486541001 | epot = -221.663877016894 | etot = -176.266442527541 +482000 ekin = 21.9864848364329 | erot = 22.7363916127196 | epot = -221.683762589876 | etot = -176.960886140723 +483000 ekin = 22.6106924731206 | erot = 24.0428223649866 | epot = -221.59708966704 | etot = -174.943574828933 +484000 ekin = 22.5076589696515 | erot = 23.4557074572132 | epot = -221.540386505083 | etot = -175.577020078218 +485000 ekin = 22.6452014843636 | erot = 21.762451203069 | epot = -221.380979387409 | etot = -176.973326699976 +486000 ekin = 22.8884924315959 | erot = 22.3107890975159 | epot = -221.108997132445 | etot = -175.909715603333 +487000 ekin = 22.9971918001234 | erot = 24.3833170218936 | epot = -220.71103827305 | etot = -173.330529451033 +488000 ekin = 22.1533984482818 | erot = 25.7281535841679 | epot = -220.122813937115 | etot = -172.241261904665 +489000 ekin = 22.4515755615887 | erot = 25.0522662107032 | epot = -219.719249535127 | etot = -172.215407762835 +490000 ekin = 22.9547894223432 | erot = 24.517779033553 | epot = -219.418606998125 | etot = -171.946038542229 +491000 ekin = 23.5816418799849 | erot = 22.753839355928 | epot = -218.924118670106 | etot = -172.588637434193 +492000 ekin = 23.8823445747864 | erot = 21.2184779917221 | epot = -218.227735715369 | etot = -173.126913148861 +493000 ekin = 24.3448959898337 | erot = 21.8115598709523 | epot = -217.334509642487 | etot = -171.178053781701 +494000 ekin = 24.4320819054026 | erot = 22.5752180720098 | epot = -216.473641638612 | etot = -169.466341661199 +495000 ekin = 24.3755841384379 | erot = 23.9444067518822 | epot = -215.609878516645 | etot = -167.289887626325 +496000 ekin = 24.8598166549303 | erot = 21.4239924353219 | epot = -214.945231394708 | etot = -168.661422304456 +497000 ekin = 25.2448003736739 | erot = 20.8176798090042 | epot = -214.387561750013 | etot = -168.325081567335 +498000 ekin = 26.5693421635397 | erot = 20.5035803503483 | epot = -214.015978269251 | etot = -166.943055755363 +499000 ekin = 26.7852769961491 | erot = 19.5435940700116 | epot = -213.683959917476 | etot = -167.355088851315 +500000 ekin = 27.535057693355 | erot = 18.705068833847 | epot = -213.607739162636 | etot = -167.367612635434 +501000 ekin = 28.3213060130359 | erot = 17.8116944886089 | epot = -213.67740185523 | etot = -167.544401353585 +502000 ekin = 28.7521713272079 | erot = 18.0095076993248 | epot = -213.852896101639 | etot = -167.091217075106 +503000 ekin = 29.5029581283875 | erot = 18.909099125371 | epot = -214.062334972754 | etot = -165.650277718996 +504000 ekin = 30.3217459607846 | erot = 18.7844890901023 | epot = -214.319342764931 | etot = -165.213107714044 +505000 ekin = 30.1578277397036 | erot = 19.4319341441026 | epot = -214.415908521801 | etot = -164.826146637995 +506000 ekin = 29.209747070706 | erot = 19.026940448028 | epot = -214.633852668846 | etot = -166.397165150112 +507000 ekin = 29.642495894677 | erot = 19.5492883197655 | epot = -214.855190806251 | etot = -165.663406591808 +508000 ekin = 28.5340625040779 | erot = 21.9407235369196 | epot = -215.063369427087 | etot = -164.588583386089 +509000 ekin = 27.8112749390816 | erot = 22.7669227870046 | epot = -215.189489573915 | etot = -164.611291847828 +510000 ekin = 27.8718580299492 | erot = 22.1925267160587 | epot = -215.43076040814 | etot = -165.366375662132 +511000 ekin = 27.5420550600504 | erot = 21.1930166573984 | epot = -215.661435095053 | etot = -166.926363377604 +512000 ekin = 28.0922073127214 | erot = 21.705529509828 | epot = -215.786982318953 | etot = -165.989245496404 +513000 ekin = 28.4464077185633 | erot = 21.5872391817044 | epot = -216.013997388439 | etot = -165.980350488171 +514000 ekin = 28.6738400915053 | erot = 22.761394528105 | epot = -216.375218054325 | etot = -164.939983434714 +515000 ekin = 28.4988335118868 | erot = 21.0723384938813 | epot = -216.772216081264 | etot = -167.201044075496 +516000 ekin = 28.2431215529153 | erot = 22.5108174537502 | epot = -217.625419460918 | etot = -166.871480454252 +517000 ekin = 28.347655310566 | erot = 21.6185847645587 | epot = -218.584116365942 | etot = -168.617876290817 +518000 ekin = 28.7355143896094 | erot = 22.2912135675691 | epot = -219.537764202997 | etot = -168.511036245819 +519000 ekin = 28.0405456500047 | erot = 25.2172553666922 | epot = -220.297953309532 | etot = -167.040152292836 +520000 ekin = 26.9306517754668 | erot = 27.0838156807788 | epot = -220.731765046824 | etot = -166.717297590578 +521000 ekin = 26.1543611134017 | erot = 30.9762120900742 | epot = -221.023845549438 | etot = -163.893272345962 +522000 ekin = 25.2846258443128 | erot = 30.3488474956666 | epot = -221.113718831057 | etot = -165.480245491078 +523000 ekin = 25.3420381973596 | erot = 27.1843281367116 | epot = -221.140536198052 | etot = -168.614169863981 +524000 ekin = 25.7141573378958 | erot = 29.455779249349 | epot = -221.057372075661 | etot = -165.887435488417 +525000 ekin = 25.4838363010697 | erot = 26.3934330170679 | epot = -220.912701137522 | etot = -169.035431819385 +526000 ekin = 26.0079410350116 | erot = 30.2000198054899 | epot = -220.869509193105 | etot = -164.661548352604 +527000 ekin = 26.1588103027025 | erot = 29.7041166536357 | epot = -220.802295317341 | etot = -164.939368361003 +528000 ekin = 26.7938806212106 | erot = 29.1988530061502 | epot = -220.603226285027 | etot = -164.610492657666 +529000 ekin = 26.8945337264061 | erot = 30.8684009418751 | epot = -220.501633795914 | etot = -162.738699127633 +530000 ekin = 26.9078317338313 | erot = 29.6059799090131 | epot = -220.558751011573 | etot = -164.044939368729 +531000 ekin = 27.7935485005803 | erot = 29.2278507025209 | epot = -220.747606613035 | etot = -163.726207409933 +532000 ekin = 27.887349588649 | erot = 27.9662412084584 | epot = -221.046254717572 | etot = -165.192663920465 +533000 ekin = 28.6036302553006 | erot = 30.4080436081815 | epot = -221.390581182077 | etot = -162.378907318595 +534000 ekin = 29.1450459094427 | erot = 29.8984953927896 | epot = -221.618689857672 | etot = -162.57514855544 +535000 ekin = 29.469911033471 | erot = 29.755268847455 | epot = -221.750636117443 | etot = -162.525456236517 +536000 ekin = 29.50494662019 | erot = 30.5743840829575 | epot = -221.629307929619 | etot = -161.549977226472 +537000 ekin = 28.425893453274 | erot = 32.2633658998326 | epot = -221.149883136949 | etot = -160.460623783842 +538000 ekin = 28.0184749761055 | erot = 30.9372043254436 | epot = -220.230421084041 | etot = -161.274741782492 +539000 ekin = 26.9914955024263 | erot = 31.1470532462602 | epot = -218.907897489909 | etot = -160.769348741223 +540000 ekin = 25.8342672805741 | erot = 30.4659839502893 | epot = -217.4023318616 | etot = -161.102080630737 +541000 ekin = 25.026783494083 | erot = 28.6292948272569 | epot = -215.859642568803 | etot = -162.203564247463 +542000 ekin = 24.2196496447266 | erot = 27.1673316851706 | epot = -214.460130991487 | etot = -163.073149661589 +543000 ekin = 23.6870158078332 | erot = 27.3438759386704 | epot = -213.038313075576 | etot = -162.007421329072 +544000 ekin = 23.0676757322196 | erot = 26.7417435047259 | epot = -211.706572811687 | etot = -161.897153574741 +545000 ekin = 21.8293570586022 | erot = 25.2088678150874 | epot = -210.577232175622 | etot = -163.539007301932 +546000 ekin = 21.5224546734963 | erot = 25.7347520792893 | epot = -209.72960555737 | etot = -162.472398804585 +547000 ekin = 20.9968182936697 | erot = 25.5632514150022 | epot = -209.191378920644 | etot = -162.631309211972 +548000 ekin = 19.8988817654073 | erot = 23.2679071410407 | epot = -208.743073804017 | etot = -165.576284897569 +549000 ekin = 19.9727838598321 | erot = 22.3903038756502 | epot = -208.700752574222 | etot = -166.33766483874 +550000 ekin = 19.5901365826176 | erot = 23.3554322669728 | epot = -209.057328163197 | etot = -166.111759313607 +551000 ekin = 19.3625273691881 | erot = 22.3770654995204 | epot = -209.363208919373 | etot = -167.623616050665 +552000 ekin = 19.5151849616975 | erot = 21.2706999045886 | epot = -209.797169625893 | etot = -169.011284759607 +553000 ekin = 19.2265779452039 | erot = 20.4826132865114 | epot = -209.999313263519 | etot = -170.290122031804 +554000 ekin = 19.5496295764989 | erot = 20.8693447741625 | epot = -209.779481348856 | etot = -169.360506998194 +555000 ekin = 19.1735854190619 | erot = 19.9647334065035 | epot = -209.314112705489 | etot = -170.175793879924 +556000 ekin = 18.5478675513136 | erot = 24.137842092091 | epot = -208.401647045382 | etot = -165.715937401977 +557000 ekin = 17.4742761697172 | erot = 24.0319972301999 | epot = -207.527543381088 | etot = -166.021269981171 +558000 ekin = 17.0450293728529 | erot = 25.0431971863445 | epot = -206.756554568577 | etot = -164.66832800938 +559000 ekin = 16.5375595856902 | erot = 23.7766127103862 | epot = -205.999592721795 | etot = -165.685420425718 +560000 ekin = 16.3675553275375 | erot = 22.7274451429466 | epot = -205.532696411942 | etot = -166.437695941458 +561000 ekin = 16.4002686388511 | erot = 23.454222688713 | epot = -205.33653129407 | etot = -165.482039966506 +562000 ekin = 16.8601910320653 | erot = 24.6920222465119 | epot = -205.561599056927 | etot = -164.00938577835 +563000 ekin = 17.4904033581056 | erot = 27.3327302539918 | epot = -206.371449865494 | etot = -161.548316253397 +564000 ekin = 18.2959040777444 | erot = 25.8631538436394 | epot = -207.295829537485 | etot = -163.136771616101 +565000 ekin = 19.1876481491769 | erot = 26.3288155361578 | epot = -208.252583626631 | etot = -162.736119941296 +566000 ekin = 19.3470565924911 | erot = 25.8088677343261 | epot = -209.135375001814 | etot = -163.979450674997 +567000 ekin = 19.3284332398276 | erot = 26.1324360478945 | epot = -210.001092533551 | etot = -164.540223245829 +568000 ekin = 20.2145930912203 | erot = 27.7960775164549 | epot = -210.739375059829 | etot = -162.728704452154 +569000 ekin = 20.7786788494836 | erot = 29.1835546820981 | epot = -211.690043333607 | etot = -161.727809802026 +570000 ekin = 20.4712421095841 | erot = 30.0658782238937 | epot = -212.489990080473 | etot = -161.952869746995 +571000 ekin = 20.1740626295591 | erot = 34.2763104149801 | epot = -212.99657775615 | etot = -158.54620471161 +572000 ekin = 20.2865908439986 | erot = 32.9711037269835 | epot = -213.258049696028 | etot = -160.000355125046 +573000 ekin = 20.2785763047898 | erot = 32.164420996442 | epot = -213.224973233119 | etot = -160.781975931887 +574000 ekin = 20.73420675937 | erot = 33.4121841231608 | epot = -212.911121076823 | etot = -158.764730194292 +575000 ekin = 20.2170533951852 | erot = 31.3247437485476 | epot = -212.546252872734 | etot = -161.004455729001 +576000 ekin = 19.4298111281265 | erot = 32.3261160719177 | epot = -212.142648109265 | etot = -160.386720909221 +577000 ekin = 19.2647608601736 | erot = 34.7383488770083 | epot = -211.774480661784 | etot = -157.771370924603 +578000 ekin = 18.8591531744448 | erot = 34.9578310327361 | epot = -211.41608019627 | etot = -157.599095989089 +579000 ekin = 19.1764535805344 | erot = 34.5315583779688 | epot = -210.953075025527 | etot = -157.245063067024 +580000 ekin = 19.2853428286521 | erot = 34.6365289435264 | epot = -210.25522157758 | etot = -156.333349805402 +581000 ekin = 18.7906308240455 | erot = 33.6526265209018 | epot = -209.637569234705 | etot = -157.194311889758 +582000 ekin = 19.084905315022 | erot = 30.2130120641441 | epot = -209.11867694325 | etot = -159.820759564084 +583000 ekin = 19.7173995337446 | erot = 30.366640119437 | epot = -208.664312052077 | etot = -158.580272398895 +584000 ekin = 20.3909791819401 | erot = 28.9778999219973 | epot = -208.252182490968 | etot = -158.883303387031 +585000 ekin = 20.9470408507438 | erot = 28.5667963345671 | epot = -208.028127454439 | etot = -158.514290269128 +586000 ekin = 21.8171004518006 | erot = 27.8466229838588 | epot = -208.095369306471 | etot = -158.431645870812 +587000 ekin = 23.1615832403556 | erot = 24.9646595929125 | epot = -208.369983933223 | etot = -160.243741099955 +588000 ekin = 23.8959195121688 | erot = 25.24887078156 | epot = -209.101399059693 | etot = -159.956608765964 +589000 ekin = 24.7834285754863 | erot = 26.0497724346551 | epot = -209.871831515904 | etot = -159.038630505763 +590000 ekin = 25.3936432927543 | erot = 23.6572511459096 | epot = -210.480131773127 | etot = -161.429237334463 +591000 ekin = 25.9278610257486 | erot = 23.0115174388733 | epot = -210.978711850373 | etot = -162.039333385751 +592000 ekin = 27.1309273397085 | erot = 23.1610725306481 | epot = -211.238339753623 | etot = -160.946339883266 +593000 ekin = 26.4574056599296 | erot = 23.5297100340712 | epot = -211.398991430669 | etot = -161.411875736668 +594000 ekin = 26.2135133417378 | erot = 24.3682480979618 | epot = -211.629783890836 | etot = -161.048022451137 +595000 ekin = 26.7143131575838 | erot = 25.9581831810466 | epot = -211.492775841309 | etot = -158.820279502679 +596000 ekin = 25.9981237047512 | erot = 24.5874940201996 | epot = -210.994983795865 | etot = -160.409366070915 +597000 ekin = 25.3691803838513 | erot = 25.6177769896042 | epot = -210.235015094311 | etot = -159.248057720855 +598000 ekin = 23.6665857713897 | erot = 26.7002735359816 | epot = -209.31162840973 | etot = -158.944769102359 +599000 ekin = 22.4410822725131 | erot = 24.4123509303077 | epot = -208.296342188806 | etot = -161.442908985985 +600000 ekin = 22.1604509520165 | erot = 23.7403591164762 | epot = -207.435376754137 | etot = -161.534566685645 +601000 ekin = 22.1910498539915 | erot = 25.7876707770135 | epot = -206.80770864539 | etot = -158.828988014385 +602000 ekin = 21.3191775900909 | erot = 24.1816411383452 | epot = -206.419514787599 | etot = -160.918696059162 +603000 ekin = 21.1724174977999 | erot = 23.1636571932934 | epot = -206.285960522692 | etot = -161.949885831599 +604000 ekin = 20.9177152169245 | erot = 23.0600658965548 | epot = -206.401463523596 | etot = -162.423682410117 +605000 ekin = 20.5881838168339 | erot = 23.4945688308947 | epot = -206.783521776426 | etot = -162.700769128698 +606000 ekin = 20.5566050385019 | erot = 24.4436457663487 | epot = -207.302724003666 | etot = -162.302473198816 +607000 ekin = 20.5889650529151 | erot = 24.2601145277504 | epot = -207.849151297373 | etot = -163.000071716707 +608000 ekin = 20.798561595616 | erot = 24.0529914889943 | epot = -208.221016465144 | etot = -163.369463380534 +609000 ekin = 21.3334604629993 | erot = 21.2987977820021 | epot = -208.39362904366 | etot = -165.761370798658 +610000 ekin = 21.0077312853339 | erot = 24.5390976123487 | epot = -208.423455376914 | etot = -162.876626479231 +611000 ekin = 21.2062750244278 | erot = 25.6924763445408 | epot = -208.465273559828 | etot = -161.566522190859 +612000 ekin = 21.1092285061772 | erot = 23.1681846181344 | epot = -208.369973333871 | etot = -164.09256020956 +613000 ekin = 21.3505829699377 | erot = 23.3795515105117 | epot = -208.252217187376 | etot = -163.522082706926 +614000 ekin = 21.9887200992592 | erot = 22.9814942014575 | epot = -208.08425451512 | etot = -163.114040214403 +615000 ekin = 21.9879302481981 | erot = 23.9474635145876 | epot = -208.112157339249 | etot = -162.176763576463 +616000 ekin = 21.6535652813721 | erot = 25.7665709398204 | epot = -208.073996342823 | etot = -160.653860121631 +617000 ekin = 21.5327802980097 | erot = 25.9126271147335 | epot = -208.081562756535 | etot = -160.636155343791 +618000 ekin = 21.6331060335065 | erot = 25.3216229154819 | epot = -208.118612594362 | etot = -161.163883645373 +619000 ekin = 21.5377257980259 | erot = 24.0810842352126 | epot = -208.182453990811 | etot = -162.563643957572 +620000 ekin = 22.2944761843434 | erot = 26.8961911381653 | epot = -208.572090943205 | etot = -159.381423620697 +621000 ekin = 23.2275714627294 | erot = 28.5194568041071 | epot = -209.005121904323 | etot = -157.258093637486 +622000 ekin = 23.8057112362969 | erot = 28.1725382958721 | epot = -209.310919824284 | etot = -157.332670292115 +623000 ekin = 23.836200160347 | erot = 27.2782572535261 | epot = -209.480204064921 | etot = -158.365746651048 +624000 ekin = 23.5225747889065 | erot = 27.5958156421042 | epot = -209.446824879225 | etot = -158.328434448214 +625000 ekin = 23.3180565211004 | erot = 27.7299743553773 | epot = -209.243975503887 | etot = -158.195944627409 +626000 ekin = 23.6186803255339 | erot = 26.3585577647064 | epot = -208.833123041292 | etot = -158.855884951052 +627000 ekin = 23.7020468224909 | erot = 24.8473737782309 | epot = -208.363264541316 | etot = -159.813843940594 +628000 ekin = 23.234214910991 | erot = 23.6981867115843 | epot = -207.745309999887 | etot = -160.812908377311 +629000 ekin = 22.4918100586061 | erot = 24.881640940065 | epot = -207.051343604772 | etot = -159.677892606101 +630000 ekin = 22.1453629035581 | erot = 20.2998733728557 | epot = -206.39001968886 | etot = -163.944783412446 +631000 ekin = 22.7036826399466 | erot = 18.9834012990071 | epot = -205.753133262548 | etot = -164.066049323594 +632000 ekin = 23.0551963097502 | erot = 19.1201804696073 | epot = -205.05968682992 | etot = -162.884310050562 +633000 ekin = 22.747707004055 | erot = 20.2298517397387 | epot = -204.679628820142 | etot = -161.702070076348 +634000 ekin = 22.1372732618932 | erot = 20.0792269586333 | epot = -204.542150052713 | etot = -162.325649832186 +635000 ekin = 21.9900639375166 | erot = 23.0915091625923 | epot = -204.519806168891 | etot = -159.438233068782 +636000 ekin = 22.4343890150495 | erot = 22.7785270631131 | epot = -204.773050210983 | etot = -159.560134132821 +637000 ekin = 22.4930206180041 | erot = 21.8914552071171 | epot = -205.185291613209 | etot = -160.800815788088 +638000 ekin = 22.6067746447143 | erot = 22.2834374488441 | epot = -205.831736530974 | etot = -160.941524437416 +639000 ekin = 22.9634779459864 | erot = 21.0233006007606 | epot = -206.678000527936 | etot = -162.691221981189 +640000 ekin = 23.0006770449898 | erot = 20.1435647319737 | epot = -207.67418045306 | etot = -164.529938676097 +641000 ekin = 22.6796709156744 | erot = 20.1265770944198 | epot = -208.864068916451 | etot = -166.057820906357 +642000 ekin = 23.0426441097264 | erot = 20.3821125283994 | epot = -210.157224630151 | etot = -166.732467992025 +643000 ekin = 23.6886630072442 | erot = 20.9311429904711 | epot = -211.335279277866 | etot = -166.715473280151 +644000 ekin = 23.3501873913686 | erot = 20.2116989369836 | epot = -212.405134347394 | etot = -168.843248019042 +645000 ekin = 24.214183792306 | erot = 19.1997084892897 | epot = -213.275734343161 | etot = -169.861842061566 +646000 ekin = 24.0032353748067 | erot = 18.7366869191874 | epot = -214.020930167623 | etot = -171.281007873629 +647000 ekin = 24.8268141920476 | erot = 20.0966967362663 | epot = -214.740433438135 | etot = -169.816922509822 +648000 ekin = 24.8649186744143 | erot = 20.9050241858578 | epot = -215.442059068409 | etot = -169.672116208136 +649000 ekin = 24.8646057578191 | erot = 21.521791933497 | epot = -216.156866604821 | etot = -169.770468913505 +650000 ekin = 24.0713138258436 | erot = 22.6881112054577 | epot = -216.962642193737 | etot = -170.203217162436 +651000 ekin = 24.0648474956462 | erot = 21.9056553318526 | epot = -217.68682151817 | etot = -171.716318690672 +652000 ekin = 23.7298725103662 | erot = 21.0498830137315 | epot = -218.178357024535 | etot = -173.398601500437 +653000 ekin = 24.2612309905982 | erot = 20.9396425318005 | epot = -218.402996619013 | etot = -173.202123096615 +654000 ekin = 24.5742837739783 | erot = 21.5842057775824 | epot = -218.453825537757 | etot = -172.295335986196 +655000 ekin = 24.8172949648637 | erot = 21.5633790150742 | epot = -218.138128805473 | etot = -171.757454825535 +656000 ekin = 26.1016118595101 | erot = 20.2089399346234 | epot = -217.608120203544 | etot = -171.29756840941 +657000 ekin = 25.5468936086447 | erot = 20.5700758336473 | epot = -216.896383096438 | etot = -170.779413654146 +658000 ekin = 24.8009166899182 | erot = 20.3492391925765 | epot = -215.907642384675 | etot = -170.75748650218 +659000 ekin = 24.2700519127878 | erot = 19.3880786744432 | epot = -214.779591604614 | etot = -171.121461017383 +660000 ekin = 23.7386557662651 | erot = 17.3667145566108 | epot = -213.671617228208 | etot = -172.566246905332 +661000 ekin = 23.101615905894 | erot = 18.0746065237967 | epot = -212.813170220349 | etot = -171.636947790658 +662000 ekin = 23.5132942257758 | erot = 19.3913290878883 | epot = -212.178312398575 | etot = -169.27368908491 +663000 ekin = 22.8490848881554 | erot = 22.3558454667425 | epot = -211.708233502208 | etot = -166.50330314731 +664000 ekin = 22.5371891975751 | erot = 23.8324410238751 | epot = -211.630305812256 | etot = -165.260675590806 +665000 ekin = 22.4828402581824 | erot = 22.1418709319913 | epot = -211.932335178627 | etot = -167.307623988453 +666000 ekin = 21.658575574868 | erot = 23.2685049016563 | epot = -212.34419719029 | etot = -167.417116713765 +667000 ekin = 21.746716005369 | erot = 26.6231378444392 | epot = -212.869195610415 | etot = -164.499341760607 +668000 ekin = 21.8400234731699 | erot = 27.0215900877162 | epot = -213.230575394842 | etot = -164.368961833956 +669000 ekin = 21.5717180264524 | erot = 25.4843097358269 | epot = -213.402729296273 | etot = -166.346701533994 +670000 ekin = 21.2159612264746 | erot = 27.0486352599825 | epot = -213.623541173123 | etot = -165.358944686665 +671000 ekin = 21.0316750378212 | erot = 28.2790369826503 | epot = -213.670944628475 | etot = -164.360232608003 +672000 ekin = 21.0540110477226 | erot = 27.9477049264318 | epot = -213.821833683391 | etot = -164.820117709236 +673000 ekin = 20.622467197854 | erot = 31.8631428606973 | epot = -214.143301465583 | etot = -161.657691407032 +674000 ekin = 19.7399937911566 | erot = 31.3007461152899 | epot = -214.328096065417 | etot = -163.287356158971 +675000 ekin = 19.6812168375245 | erot = 28.9841135234018 | epot = -214.58757301913 | etot = -165.922242658204 +676000 ekin = 20.2683648931208 | erot = 29.0544957444103 | epot = -214.986567261058 | etot = -165.663706623527 +677000 ekin = 20.4847241494001 | erot = 27.1326629448698 | epot = -215.500686522809 | etot = -167.88329942854 +678000 ekin = 21.302019725926 | erot = 26.9440120099185 | epot = -215.97832097774 | etot = -167.732289241896 +679000 ekin = 20.7252183388119 | erot = 27.5800790128446 | epot = -216.242490346929 | etot = -167.937192995272 +680000 ekin = 21.1467020674332 | erot = 27.5476121215625 | epot = -216.37538065002 | etot = -167.681066461025 +681000 ekin = 20.7720273332215 | erot = 27.1624962363794 | epot = -216.426580638711 | etot = -168.49205706911 +682000 ekin = 20.4708699436742 | erot = 26.3358564577069 | epot = -216.448305176171 | etot = -169.64157877479 +683000 ekin = 19.8000088900235 | erot = 27.4272282812591 | epot = -216.207270658414 | etot = -168.980033487131 +684000 ekin = 20.1500542970064 | erot = 26.0761853873505 | epot = -215.864502199571 | etot = -169.638262515214 +685000 ekin = 19.8486865740984 | erot = 26.0238267262043 | epot = -215.500516760578 | etot = -169.628003460275 +686000 ekin = 19.7513338939334 | erot = 25.3757647595747 | epot = -215.210189827277 | etot = -170.083091173769 +687000 ekin = 20.7214918102431 | erot = 24.1072372944022 | epot = -214.967239797801 | etot = -170.138510693156 +688000 ekin = 21.0626981869003 | erot = 23.2762891547382 | epot = -214.979397567732 | etot = -170.640410226093 +689000 ekin = 21.5266424344628 | erot = 20.7174231605385 | epot = -215.094101507179 | etot = -172.850035912178 +690000 ekin = 22.5491523723621 | erot = 20.847571984209 | epot = -214.986970380787 | etot = -171.590246024216 +691000 ekin = 23.8583355308872 | erot = 22.0099769027697 | epot = -214.848454555845 | etot = -168.980142122188 +692000 ekin = 24.96520872453 | erot = 21.4857106199454 | epot = -214.494800129558 | etot = -168.043880785083 +693000 ekin = 26.0051918382276 | erot = 21.3733007404598 | epot = -214.001727781338 | etot = -166.623235202651 +694000 ekin = 26.4392720652869 | erot = 21.3317762759646 | epot = -213.263998412814 | etot = -165.492950071562 +695000 ekin = 27.3615193041949 | erot = 20.6921753134717 | epot = -212.356901954365 | etot = -164.303207336699 +696000 ekin = 27.3093057978157 | erot = 20.0965375265573 | epot = -211.297735908804 | etot = -163.891892584431 +697000 ekin = 26.7453316152447 | erot = 18.7856987042669 | epot = -210.110607673786 | etot = -164.579577354274 +698000 ekin = 25.5722707624857 | erot = 19.6853079921957 | epot = -209.125608153436 | etot = -163.868029398755 +699000 ekin = 24.9916657277841 | erot = 18.4661630806181 | epot = -208.42973768859 | etot = -164.971908880188 +700000 ekin = 24.521058485274 | erot = 16.84944737211 | epot = -207.9193858017 | etot = -166.548879944316 +701000 ekin = 23.7778912460905 | erot = 19.3168143286452 | epot = -207.673622403358 | etot = -164.578916828622 +702000 ekin = 23.4418540405128 | erot = 17.9399262410738 | epot = -207.631679946816 | etot = -166.24989966523 +703000 ekin = 22.5362735605758 | erot = 16.8799469700555 | epot = -207.655410737567 | etot = -168.239190206935 +704000 ekin = 21.6771800595091 | erot = 17.1833672937461 | epot = -207.854126531408 | etot = -168.993579178153 +705000 ekin = 21.4420921851221 | erot = 20.8433776157946 | epot = -208.2214030325 | etot = -165.935933231584 +706000 ekin = 21.2415323522356 | erot = 21.0841388634033 | epot = -208.785212184223 | etot = -166.459540968584 +707000 ekin = 21.1211180279557 | erot = 22.7053094579755 | epot = -209.418467814605 | etot = -165.592040328673 +708000 ekin = 21.4313901815259 | erot = 21.142901789246 | epot = -210.045555019851 | etot = -167.471263049079 +709000 ekin = 21.1002753292038 | erot = 22.8489798007674 | epot = -210.826178475879 | etot = -166.876923345908 +710000 ekin = 21.8422173465255 | erot = 20.0932738292303 | epot = -211.532469955408 | etot = -169.596978779652 +711000 ekin = 22.1026708164741 | erot = 22.4726045475365 | epot = -212.126194080497 | etot = -167.550918716487 +712000 ekin = 22.4258695027194 | erot = 21.442958222841 | epot = -212.558458286709 | etot = -168.689630561149 +713000 ekin = 22.5222749624208 | erot = 20.3898387031543 | epot = -212.978786634482 | etot = -170.066672968907 +714000 ekin = 22.1262254185207 | erot = 21.2706738146545 | epot = -213.406504414377 | etot = -170.009605181201 +715000 ekin = 21.6589564668707 | erot = 22.8713228305269 | epot = -214.103705031576 | etot = -169.573425734178 +716000 ekin = 22.8499377351371 | erot = 22.5811259198023 | epot = -214.886932195704 | etot = -169.455868540765 +717000 ekin = 23.1453273466383 | erot = 22.0823648529859 | epot = -215.752901424345 | etot = -170.52520922472 +718000 ekin = 23.4911204712306 | erot = 21.8266696386258 | epot = -216.797611238792 | etot = -171.479821128935 +719000 ekin = 23.5427559868846 | erot = 20.6352185380146 | epot = -217.868984095443 | etot = -173.691009570544 +720000 ekin = 24.6730711390776 | erot = 21.7437690143765 | epot = -218.925770671597 | etot = -172.508930518143 +721000 ekin = 25.2403931355773 | erot = 19.4577236844891 | epot = -219.945055136347 | etot = -175.246938316281 +722000 ekin = 25.7389977817124 | erot = 21.6950149985872 | epot = -220.731451014357 | etot = -173.297438234057 +723000 ekin = 24.59999507444 | erot = 24.4179337524363 | epot = -221.359631454453 | etot = -172.341702627577 +724000 ekin = 23.8141214256889 | erot = 25.3193356469838 | epot = -221.823580154673 | etot = -172.690123082 +725000 ekin = 23.3651337491413 | erot = 28.7091491551534 | epot = -222.090867886168 | etot = -170.016584981873 +726000 ekin = 23.1307089149661 | erot = 29.7953383527835 | epot = -222.003607909333 | etot = -169.077560641584 +727000 ekin = 22.6496655720656 | erot = 29.2473418500935 | epot = -221.635062275438 | etot = -169.738054853278 +728000 ekin = 21.811364434554 | erot = 31.7331322577198 | epot = -221.154414993919 | etot = -167.609918301645 +729000 ekin = 20.4746743669592 | erot = 32.546576149833 | epot = -220.690887684563 | etot = -167.669637167771 +730000 ekin = 19.8147243806315 | erot = 34.9007244000495 | epot = -220.114078177837 | etot = -165.398629397156 +731000 ekin = 18.6145766929913 | erot = 34.0320241969118 | epot = -219.536330230485 | etot = -166.889729340582 +732000 ekin = 17.8112285881693 | erot = 34.0479803252401 | epot = -218.968869737311 | etot = -167.109660823901 +733000 ekin = 17.6476056471454 | erot = 34.2057929926945 | epot = -218.3294527504 | etot = -166.47605411056 +734000 ekin = 17.7690619853332 | erot = 32.1417337283976 | epot = -217.520065128183 | etot = -167.609269414452 +735000 ekin = 17.0579199291445 | erot = 30.2470102548337 | epot = -216.550373483739 | etot = -169.245443299761 +736000 ekin = 17.5498866135578 | erot = 29.3166528563917 | epot = -215.643405297165 | etot = -168.776865827216 +737000 ekin = 17.6187796043555 | erot = 26.3475349686048 | epot = -214.809218139055 | etot = -170.842903566094 +738000 ekin = 18.2269608592319 | erot = 25.7040359881548 | epot = -214.115591404826 | etot = -170.18459455744 +739000 ekin = 18.7173977512819 | erot = 24.4619685419347 | epot = -213.441484725329 | etot = -170.262118432112 +740000 ekin = 19.0110962436152 | erot = 22.142772803043 | epot = -212.815607635912 | etot = -171.661738589254 +741000 ekin = 18.9267028320974 | erot = 21.3358168112262 | epot = -212.366636079153 | etot = -172.104116435829 +742000 ekin = 19.3549116475726 | erot = 19.5096408469649 | epot = -212.216543882057 | etot = -173.35199138752 +743000 ekin = 20.119013306821 | erot = 18.4104477349336 | epot = -212.288606698492 | etot = -173.759145656738 +744000 ekin = 20.3566526518901 | erot = 19.4246888199086 | epot = -212.75389749051 | etot = -172.972556018711 +745000 ekin = 21.1509415657888 | erot = 20.1659043839807 | epot = -213.418747745429 | etot = -172.10190179566 +746000 ekin = 21.3037423527627 | erot = 20.2172486917649 | epot = -214.157876553476 | etot = -172.636885508949 +747000 ekin = 22.3146611040097 | erot = 21.9871375259789 | epot = -214.88232405197 | etot = -170.580525421981 +748000 ekin = 22.2283253425591 | erot = 22.5065193409822 | epot = -215.506784482801 | etot = -170.77193979926 +749000 ekin = 21.7915806164301 | erot = 22.1396569978617 | epot = -215.707286574207 | etot = -171.776048959915 +750000 ekin = 22.4607758902159 | erot = 23.0482930283985 | epot = -215.651390580345 | etot = -170.142321661731 +751000 ekin = 21.6437369626355 | erot = 20.9291810842114 | epot = -215.338251046595 | etot = -172.765332999748 +752000 ekin = 21.0774801700924 | erot = 19.7791759941412 | epot = -214.933012142375 | etot = -174.076355978141 +753000 ekin = 20.2142777715798 | erot = 19.9156489858756 | epot = -214.515836213762 | etot = -174.385909456307 +754000 ekin = 20.550710880581 | erot = 21.7521689158874 | epot = -214.220858046315 | etot = -171.917978249847 +755000 ekin = 20.4661806652476 | erot = 22.5423956641592 | epot = -214.061716510521 | etot = -171.053140181114 +756000 ekin = 20.9954844614009 | erot = 22.4473939364008 | epot = -213.92503672056 | etot = -170.482158322758 +757000 ekin = 20.6283594838306 | erot = 21.4270437425632 | epot = -213.790125131555 | etot = -171.734721905161 +758000 ekin = 20.5508018897077 | erot = 20.9536901677692 | epot = -213.663158456533 | etot = -172.158666399056 +759000 ekin = 19.6263241751684 | erot = 23.4476640487024 | epot = -213.66383402851 | etot = -170.589845804639 +760000 ekin = 19.9340259748652 | erot = 22.6482020561595 | epot = -213.71724602475 | etot = -171.135017993725 +761000 ekin = 19.6910494084164 | erot = 22.0029116902266 | epot = -213.754878089614 | etot = -172.060916990971 +762000 ekin = 19.7910800016039 | erot = 22.5984804286307 | epot = -213.965250022108 | etot = -171.575689591873 +763000 ekin = 20.5238796096632 | erot = 22.2928877563363 | epot = -214.47551076934 | etot = -171.658743403341 +764000 ekin = 20.6650033448462 | erot = 24.6171910330824 | epot = -214.890202898626 | etot = -169.608008520698 +765000 ekin = 20.4618665382424 | erot = 25.8587140484164 | epot = -215.138274656898 | etot = -168.817694070239 +766000 ekin = 19.6548882123823 | erot = 25.0439293422707 | epot = -215.348875696047 | etot = -170.650058141394 +767000 ekin = 19.3270400363748 | erot = 25.2554744973183 | epot = -215.248876217743 | etot = -170.66636168405 +768000 ekin = 18.5163875301612 | erot = 26.9740801270243 | epot = -214.975549734016 | etot = -169.485082076831 +769000 ekin = 19.2689096458285 | erot = 26.7549801973199 | epot = -214.627183257247 | etot = -168.603293414099 +770000 ekin = 20.3065357099473 | erot = 24.5864981815754 | epot = -214.449155022355 | etot = -169.556121130832 +771000 ekin = 19.8160989352992 | erot = 24.3795653656177 | epot = -214.568609385595 | etot = -170.372945084678 +772000 ekin = 20.0808636272602 | erot = 25.3489458930141 | epot = -214.810149634203 | etot = -169.380340113928 +773000 ekin = 20.4572934790689 | erot = 23.9373155006916 | epot = -215.368798012186 | etot = -170.974189032425 +774000 ekin = 21.4581254177255 | erot = 24.8038079049394 | epot = -216.135566629648 | etot = -169.873633306983 +775000 ekin = 21.56609423293 | erot = 24.7269407163978 | epot = -217.095913678146 | etot = -170.802878728818 +776000 ekin = 21.7139623963331 | erot = 24.678564784346 | epot = -217.949762418936 | etot = -171.557235238257 +777000 ekin = 22.1382470902253 | erot = 26.3515368343078 | epot = -218.812121008321 | etot = -170.322337083788 +778000 ekin = 22.6753074399956 | erot = 26.7132834273965 | epot = -219.665211222619 | etot = -170.276620355226 +779000 ekin = 23.2722008637946 | erot = 25.1496800354838 | epot = -220.353105007404 | etot = -171.931224108126 +780000 ekin = 23.0129926689262 | erot = 23.0916850844916 | epot = -220.994134927724 | etot = -174.889457174306 +781000 ekin = 23.786429669784 | erot = 25.1844301582418 | epot = -221.387914121756 | etot = -172.41705429373 +782000 ekin = 23.5606686383571 | erot = 26.3634060367889 | epot = -221.434267464486 | etot = -171.51019278934 +783000 ekin = 24.0155758037646 | erot = 26.6670282787156 | epot = -221.227091913094 | etot = -170.544487830613 +784000 ekin = 24.0357990642713 | erot = 25.6617687084465 | epot = -220.907876114701 | etot = -171.210308341983 +785000 ekin = 24.5524506997925 | erot = 24.7676360875449 | epot = -220.413360888571 | etot = -171.093274101234 +786000 ekin = 24.4055025806397 | erot = 24.6030636477925 | epot = -219.720284916293 | etot = -170.711718687861 +787000 ekin = 25.0410360300686 | erot = 22.998359933619 | epot = -218.996593162027 | etot = -170.95719719834 +788000 ekin = 24.767877979881 | erot = 21.7923381425487 | epot = -218.352848534383 | etot = -171.792632411953 +789000 ekin = 24.8408040750631 | erot = 24.1208833257935 | epot = -217.830352648894 | etot = -168.868665248037 +790000 ekin = 24.4896562826161 | erot = 23.8855568181502 | epot = -217.476066337486 | etot = -169.10085323672 +791000 ekin = 24.295800420788 | erot = 22.2236025604802 | epot = -217.181373280855 | etot = -170.661970299587 +792000 ekin = 23.8380813001559 | erot = 20.6465905204417 | epot = -216.979132071427 | etot = -172.494460250829 +793000 ekin = 23.4376405312798 | erot = 22.3758695226247 | epot = -217.013967781529 | etot = -171.200457727625 +794000 ekin = 23.6651564360299 | erot = 24.5594365423356 | epot = -217.322425543396 | etot = -169.097832565031 +795000 ekin = 24.2246572084756 | erot = 24.523759714456 | epot = -217.532287869643 | etot = -168.783870946711 +796000 ekin = 24.0060240578042 | erot = 25.0471365078935 | epot = -217.591289135025 | etot = -168.538128569328 +797000 ekin = 24.6806226103091 | erot = 24.5153114750642 | epot = -217.396581247709 | etot = -168.200647162335 +798000 ekin = 23.743570188968 | erot = 26.0446750366824 | epot = -217.042257715778 | etot = -167.254012490128 +799000 ekin = 23.6918256055875 | erot = 25.3998427121517 | epot = -216.430832155802 | etot = -167.339163838063 +800000 ekin = 23.9795390809841 | erot = 26.2050804883332 | epot = -215.909334288757 | etot = -165.724714719439 +801000 ekin = 22.9818713498596 | erot = 26.0822510026421 | epot = -215.192675863883 | etot = -166.128553511382 +802000 ekin = 22.6987202252713 | erot = 24.4605697174941 | epot = -214.288341115587 | etot = -167.129051172822 +803000 ekin = 22.5973595447689 | erot = 25.0746177868642 | epot = -213.399668666611 | etot = -165.727691334978 +804000 ekin = 22.5679051171115 | erot = 23.8929873743116 | epot = -212.445166364649 | etot = -165.984273873226 +805000 ekin = 23.9825063136489 | erot = 23.4605910900564 | epot = -211.763911653385 | etot = -164.32081424968 +806000 ekin = 23.7122851358872 | erot = 24.3242427199374 | epot = -211.391629930493 | etot = -163.355102074668 +807000 ekin = 24.334807708307 | erot = 25.0191489745547 | epot = -211.002022647805 | etot = -161.648065964944 +808000 ekin = 23.5785338219753 | erot = 25.682978373141 | epot = -210.682430009381 | etot = -161.420917814264 +809000 ekin = 23.2672257998437 | erot = 23.7727702775216 | epot = -210.482421836394 | etot = -163.442425759029 +810000 ekin = 23.2973748071818 | erot = 24.561611045747 | epot = -210.255015349723 | etot = -162.396029496794 +811000 ekin = 24.0082703459793 | erot = 24.8986235898251 | epot = -210.100128510354 | etot = -161.19323457455 +812000 ekin = 23.5717850105925 | erot = 22.2118475566537 | epot = -210.079952231166 | etot = -164.29631966392 +813000 ekin = 23.8144414957769 | erot = 23.7648492562902 | epot = -210.006754772319 | etot = -162.427464020252 +814000 ekin = 23.3465977086067 | erot = 23.58039301019 | epot = -210.26830643344 | etot = -163.341315714643 +815000 ekin = 23.7706537845421 | erot = 23.6859516971766 | epot = -210.69986675248 | etot = -163.243261270761 +816000 ekin = 24.4396723738333 | erot = 20.7642731167639 | epot = -211.197880702624 | etot = -165.993935212026 +817000 ekin = 24.5050242640549 | erot = 20.1975149970127 | epot = -211.716456063282 | etot = -167.013916802214 +818000 ekin = 24.6467770699857 | erot = 21.529583415028 | epot = -212.178224182293 | etot = -166.001863697279 +819000 ekin = 23.9362784569689 | erot = 21.885485913296 | epot = -212.7074517228 | etot = -166.885687352535 +820000 ekin = 23.8925161494513 | erot = 21.7993180032808 | epot = -213.102576947411 | etot = -167.410742794679 +821000 ekin = 24.2038142478228 | erot = 22.9479343465945 | epot = -213.713003298829 | etot = -166.561254704412 +822000 ekin = 24.9372292708339 | erot = 23.3111003411094 | epot = -214.446490633768 | etot = -166.198161021825 +823000 ekin = 24.9810184744614 | erot = 19.3880692104392 | epot = -215.313873180455 | etot = -170.944785495554 +824000 ekin = 25.3757196310442 | erot = 19.1383506800577 | epot = -216.195322093276 | etot = -171.681251782174 +825000 ekin = 25.7714493929878 | erot = 20.7852688563227 | epot = -217.289068840725 | etot = -170.732350591415 +826000 ekin = 26.8493153910039 | erot = 21.6412827777179 | epot = -218.435288959846 | etot = -169.944690791124 +827000 ekin = 27.3839801920855 | erot = 21.4692964838888 | epot = -219.392426378877 | etot = -170.539149702903 +828000 ekin = 27.229680724747 | erot = 19.6329742054381 | epot = -220.273927299677 | etot = -173.411272369491 +829000 ekin = 28.1128884812802 | erot = 20.9502927197495 | epot = -221.21471082526 | etot = -172.15152962423 +830000 ekin = 28.8435364019276 | erot = 21.7826449636337 | epot = -222.278080486409 | etot = -171.651899120847 +831000 ekin = 28.382403945525 | erot = 21.9470916756457 | epot = -223.209359588942 | etot = -172.879863967771 +832000 ekin = 29.2687628401495 | erot = 20.5210693984925 | epot = -223.940697765464 | etot = -174.150865526822 +833000 ekin = 29.8001169918452 | erot = 19.1336112091991 | epot = -224.577996191363 | etot = -175.644267990319 +834000 ekin = 29.988952353328 | erot = 18.4370859277507 | epot = -225.027611469757 | etot = -176.601573188678 +835000 ekin = 31.1943711572552 | erot = 19.9395820078326 | epot = -225.505582228924 | etot = -174.371629063836 +836000 ekin = 31.4486064464243 | erot = 18.8230392617263 | epot = -225.897370125356 | etot = -175.625724417205 +837000 ekin = 30.897968105625 | erot = 17.525936203234 | epot = -226.014420243358 | etot = -177.590515934499 +838000 ekin = 30.3278609246781 | erot = 17.8376744101104 | epot = -225.874910017182 | etot = -177.709374682393 +839000 ekin = 28.5705963055734 | erot = 19.0197374605662 | epot = -225.567956855126 | etot = -177.977623088986 +840000 ekin = 27.8420547779393 | erot = 20.3181282989612 | epot = -225.084398799451 | etot = -176.924215722551 +841000 ekin = 26.578531878898 | erot = 18.291693309889 | epot = -224.600684647618 | etot = -179.730459458831 +842000 ekin = 25.021856816298 | erot = 17.0225406378546 | epot = -224.142254239588 | etot = -182.097856785436 +843000 ekin = 23.9095699919698 | erot = 15.4704933701473 | epot = -223.646706047482 | etot = -184.266642685364 +844000 ekin = 22.5803633860571 | erot = 15.9225454375333 | epot = -223.270602971588 | etot = -184.767694147998 +845000 ekin = 22.8380208177356 | erot = 16.9518494619353 | epot = -223.143196252822 | etot = -183.353325973152 +846000 ekin = 22.6092342503318 | erot = 19.1522264883275 | epot = -223.294605543864 | etot = -181.533144805205 +847000 ekin = 22.8438035235789 | erot = 20.5201034436593 | epot = -223.473679851918 | etot = -180.10977288468 +848000 ekin = 24.096705623773 | erot = 23.2844333976006 | epot = -223.639763222442 | etot = -176.258624201068 +849000 ekin = 23.4884021207942 | erot = 25.3929694182074 | epot = -223.896170953652 | etot = -175.01479941465 +850000 ekin = 22.6242009333951 | erot = 26.9404543040126 | epot = -224.252836199893 | etot = -174.688180962486 +851000 ekin = 22.462800324761 | erot = 26.1722746584294 | epot = -224.607456254157 | etot = -175.972381270966 +852000 ekin = 22.9338232909787 | erot = 26.8967348092924 | epot = -224.962026374242 | etot = -175.131468273971 +853000 ekin = 23.5089803042907 | erot = 26.2817254800077 | epot = -225.253808794644 | etot = -175.463103010346 +854000 ekin = 23.4667891668536 | erot = 26.9521294085684 | epot = -225.450940504292 | etot = -175.03202192887 +855000 ekin = 22.8308419775732 | erot = 26.0448263395011 | epot = -225.58818928127 | etot = -176.712520964196 +856000 ekin = 22.8838807708131 | erot = 28.3173269449285 | epot = -225.61075714919 | etot = -174.409549433448 +857000 ekin = 23.1624988447929 | erot = 28.1731020031475 | epot = -225.539880019331 | etot = -174.204279171391 +858000 ekin = 23.010544463387 | erot = 27.4142307819788 | epot = -225.412270604551 | etot = -174.987495359185 +859000 ekin = 22.7753414049503 | erot = 27.6211492713748 | epot = -225.124163927943 | etot = -174.727673251618 +860000 ekin = 23.2703861283527 | erot = 24.9426356523561 | epot = -224.786259608365 | etot = -176.573237827656 +861000 ekin = 23.7729389676944 | erot = 24.8447311566921 | epot = -224.563551923108 | etot = -175.945881798722 +862000 ekin = 23.5340740192712 | erot = 24.4915624205987 | epot = -224.357805969819 | etot = -176.332169529949 +863000 ekin = 23.7375308575266 | erot = 24.2323944373344 | epot = -224.144044493851 | etot = -176.17411919899 +864000 ekin = 23.3716941352973 | erot = 22.3641269665702 | epot = -223.879914649663 | etot = -178.144093547796 +865000 ekin = 23.1186430050472 | erot = 22.7161380633252 | epot = -223.612787576836 | etot = -177.778006508463 +866000 ekin = 22.0842043208688 | erot = 24.9778691380164 | epot = -223.307430080952 | etot = -176.245356622066 +867000 ekin = 21.1657335889336 | erot = 26.0383220824095 | epot = -223.101208746092 | etot = -175.897153074749 +868000 ekin = 20.7974073535693 | erot = 26.8327425921659 | epot = -222.794942007792 | etot = -175.164792062057 +869000 ekin = 20.4042118249737 | erot = 27.1429100482463 | epot = -222.436116261228 | etot = -174.888994388008 +870000 ekin = 20.1957141053955 | erot = 25.7366487329437 | epot = -221.955207275389 | etot = -176.02284443705 +871000 ekin = 20.2123557957261 | erot = 25.1939802920791 | epot = -221.256690821026 | etot = -175.850354733221 +872000 ekin = 20.4032419950175 | erot = 25.4624355027898 | epot = -220.516968111741 | etot = -174.651290613934 +873000 ekin = 19.7555498360178 | erot = 24.5861053407173 | epot = -219.769573418505 | etot = -175.42791824177 +874000 ekin = 18.6683455164676 | erot = 24.6077624002317 | epot = -219.119875205566 | etot = -175.843767288867 +875000 ekin = 18.1744504561662 | erot = 24.6987338548905 | epot = -218.47231102186 | etot = -175.599126710803 +876000 ekin = 18.4401297958598 | erot = 25.8115012454218 | epot = -217.9495809478 | etot = -173.697949906518 +877000 ekin = 17.664381190264 | erot = 26.0938124408268 | epot = -217.613305746208 | etot = -173.855112115117 +878000 ekin = 17.5155425895501 | erot = 26.1251978929977 | epot = -217.353846093228 | etot = -173.71310561068 +879000 ekin = 18.0158870329902 | erot = 22.9229967356032 | epot = -217.142818533763 | etot = -176.20393476517 +880000 ekin = 18.2898091775908 | erot = 21.9678230763756 | epot = -216.947884971478 | etot = -176.690252717512 +881000 ekin = 18.2557212304153 | erot = 20.7986777914948 | epot = -216.867472880906 | etot = -177.813073858995 +882000 ekin = 18.6882799858829 | erot = 22.2873864360058 | epot = -217.05073780239 | etot = -176.075071380501 +883000 ekin = 18.9334632698957 | erot = 21.3254259967097 | epot = -217.335733022766 | etot = -177.076843756161 +884000 ekin = 19.7058560972579 | erot = 20.8095031819962 | epot = -217.759932525085 | etot = -177.244573245831 +885000 ekin = 20.2112631550784 | erot = 19.5575411920434 | epot = -218.268786439491 | etot = -178.49998209237 +886000 ekin = 20.7002616226387 | erot = 19.310776902867 | epot = -218.766008187746 | etot = -178.75496966224 +887000 ekin = 21.556043787289 | erot = 18.6474685520941 | epot = -219.158663992651 | etot = -178.955151653268 +888000 ekin = 21.3334930006689 | erot = 20.4856021155481 | epot = -219.579651710559 | etot = -177.760556594342 +889000 ekin = 22.171697390566 | erot = 20.6166150577233 | epot = -220.153325957315 | etot = -177.365013509026 +890000 ekin = 22.2345451037052 | erot = 21.2895106408631 | epot = -220.540453919156 | etot = -177.016398174588 +891000 ekin = 22.2608122330327 | erot = 20.1682134340203 | epot = -220.830256027334 | etot = -178.401230360281 +892000 ekin = 22.2667041004928 | erot = 21.1835211310339 | epot = -220.974423299556 | etot = -177.52419806803 +893000 ekin = 22.8785998921146 | erot = 22.2656591807102 | epot = -220.854501706686 | etot = -175.710242633862 +894000 ekin = 22.7070083180718 | erot = 20.7443672875634 | epot = -220.57293320363 | etot = -177.121557597995 +895000 ekin = 22.4994314958752 | erot = 20.2750367527769 | epot = -220.21529694266 | etot = -177.440828694008 +896000 ekin = 22.6862504668757 | erot = 21.9474616043293 | epot = -219.676966141549 | etot = -175.043254070344 +897000 ekin = 22.4101657769622 | erot = 20.2849313539379 | epot = -218.954521501181 | etot = -176.259424370281 +898000 ekin = 22.6067604772945 | erot = 22.1361684291271 | epot = -218.088311088299 | etot = -173.345382181877 +899000 ekin = 22.6002362519927 | erot = 22.9443785260411 | epot = -217.224223257415 | etot = -171.679608479382 +900000 ekin = 22.2271969756017 | erot = 21.2795539705332 | epot = -216.378348455151 | etot = -172.871597509016 +901000 ekin = 22.049601241704 | erot = 19.6983125737511 | epot = -215.642075676261 | etot = -173.894161860806 +902000 ekin = 21.5373973946795 | erot = 20.0636413054755 | epot = -215.059151442717 | etot = -173.458112742562 +903000 ekin = 21.3273338630826 | erot = 20.6238147912146 | epot = -214.498710762212 | etot = -172.547562107915 +904000 ekin = 21.0822000097366 | erot = 21.2140090803987 | epot = -214.106117024932 | etot = -171.809907934796 +905000 ekin = 20.688573504515 | erot = 23.6425315011056 | epot = -213.989802974573 | etot = -169.658697968952 +906000 ekin = 20.8777040514165 | erot = 22.1389592583989 | epot = -213.961705252052 | etot = -170.945041942237 +907000 ekin = 21.5380348777401 | erot = 20.2343470856017 | epot = -214.064513257377 | etot = -172.292131294036 +908000 ekin = 20.9274847289174 | erot = 22.9159415344444 | epot = -214.205523604128 | etot = -170.362097340766 +909000 ekin = 20.7056821583171 | erot = 23.1534436178424 | epot = -214.128940350364 | etot = -170.269814574204 +910000 ekin = 20.6850690694788 | erot = 21.783469726861 | epot = -213.91187960968 | etot = -171.44334081334 +911000 ekin = 20.4049026492844 | erot = 24.4277842653814 | epot = -213.485163443353 | etot = -168.652476528687 +912000 ekin = 20.6124368604298 | erot = 25.2278717850118 | epot = -212.994133996415 | etot = -167.153825350974 +913000 ekin = 20.3761012114308 | erot = 24.7723910910313 | epot = -212.657154422535 | etot = -167.508662120073 +914000 ekin = 19.8968997426853 | erot = 25.4410819754834 | epot = -212.497368647685 | etot = -167.159386929516 +915000 ekin = 19.9950171951882 | erot = 25.9419095773569 | epot = -212.507529869006 | etot = -166.570603096461 +916000 ekin = 19.6549262075363 | erot = 24.538237997724 | epot = -212.481735916643 | etot = -168.288571711383 +917000 ekin = 19.1943251031612 | erot = 24.31332627058 | epot = -212.593107757692 | etot = -169.085456383951 +918000 ekin = 18.3242362402623 | erot = 22.0402118609707 | epot = -212.817817515526 | etot = -172.453369414293 +919000 ekin = 18.4622091649616 | erot = 22.0712625398805 | epot = -213.248725483561 | etot = -172.715253778719 +920000 ekin = 19.2487751773886 | erot = 25.3359478866229 | epot = -213.780255594758 | etot = -169.195532530746 +921000 ekin = 19.5018854862383 | erot = 23.5233553159472 | epot = -214.227012786969 | etot = -171.201771984784 +922000 ekin = 20.0460346272463 | erot = 23.3015862848816 | epot = -214.628134308544 | etot = -171.280513396416 +923000 ekin = 19.2900442060425 | erot = 21.7882354465828 | epot = -215.132996794542 | etot = -174.054717141917 +924000 ekin = 19.8084784518446 | erot = 20.6067657458497 | epot = -215.520425153804 | etot = -175.10518095611 +925000 ekin = 19.4297747207056 | erot = 19.7971794451035 | epot = -215.775169090021 | etot = -176.548214924211 +926000 ekin = 19.6579133002046 | erot = 19.0438552077666 | epot = -215.748052097731 | etot = -177.04628358976 +927000 ekin = 20.4195662533946 | erot = 18.9593050109652 | epot = -215.618862876762 | etot = -176.239991612402 +928000 ekin = 20.4817836282247 | erot = 18.9847825923888 | epot = -215.304393191577 | etot = -175.837826970963 +929000 ekin = 20.9504941576429 | erot = 19.7784806309953 | epot = -214.727990541094 | etot = -173.999015752456 +930000 ekin = 21.1315408433683 | erot = 20.6616164444539 | epot = -214.061785502445 | etot = -172.268628214623 +931000 ekin = 21.2634088922109 | erot = 21.9365830714564 | epot = -213.529347543443 | etot = -170.329355579775 +932000 ekin = 21.006213211584 | erot = 21.2825267850011 | epot = -212.999183574852 | etot = -170.710443578267 +933000 ekin = 21.2284411209639 | erot = 20.8232596682586 | epot = -212.371172372981 | etot = -170.319471583758 +934000 ekin = 20.5279385282457 | erot = 20.1701889387579 | epot = -211.858985221721 | etot = -171.160857754718 +935000 ekin = 20.1948548273404 | erot = 19.538371480896 | epot = -211.862647749463 | etot = -172.129421441226 +936000 ekin = 20.1806679134658 | erot = 21.4990281973767 | epot = -212.443949037452 | etot = -170.76425292661 +937000 ekin = 20.0545914091422 | erot = 20.9834617113798 | epot = -213.292670869919 | etot = -172.254617749397 +938000 ekin = 19.8082215701157 | erot = 20.8974589230379 | epot = -214.037804111151 | etot = -173.332123617997 +939000 ekin = 20.3649856793841 | erot = 23.9090631210053 | epot = -214.809663951944 | etot = -170.535615151554 +940000 ekin = 20.9455103352144 | erot = 24.9039051347133 | epot = -215.699887091858 | etot = -169.850471621931 +941000 ekin = 22.0008473383399 | erot = 23.3113935488402 | epot = -216.614986710114 | etot = -171.302745822934 +942000 ekin = 21.6408089485804 | erot = 26.4701413664084 | epot = -217.436072618249 | etot = -169.32512230326 +943000 ekin = 22.0375713327493 | erot = 23.8525644765125 | epot = -218.064504556064 | etot = -172.174368746803 +944000 ekin = 21.3825689791004 | erot = 22.0065856356145 | epot = -218.486120233654 | etot = -175.096965618939 +945000 ekin = 20.850173972681 | erot = 21.1332702356783 | epot = -218.794495873448 | etot = -176.811051665089 +946000 ekin = 20.4139375222148 | erot = 23.6679631776017 | epot = -219.021459743601 | etot = -174.939559043785 +947000 ekin = 20.1906398813672 | erot = 26.5654138598139 | epot = -218.929211499128 | etot = -172.173157757947 +948000 ekin = 20.1586787090284 | erot = 25.3617860657906 | epot = -218.683588417106 | etot = -173.163123642287 +949000 ekin = 20.6015087780768 | erot = 24.0216151369725 | epot = -218.644352518059 | etot = -174.02122860301 +950000 ekin = 20.7471893785302 | erot = 25.3619181001311 | epot = -218.710402012473 | etot = -172.601294533811 +951000 ekin = 20.2569076833938 | erot = 27.0210577095201 | epot = -218.988213515806 | etot = -171.710248122892 +952000 ekin = 20.5584159627657 | erot = 27.2103033079755 | epot = -219.159574869077 | etot = -171.390855598336 +953000 ekin = 21.7412270180337 | erot = 25.7395142553205 | epot = -219.276981606574 | etot = -171.79624033322 +954000 ekin = 22.5769744101438 | erot = 23.3851809606138 | epot = -219.432021398479 | etot = -173.469866027721 +955000 ekin = 22.7540917406293 | erot = 24.0485022563637 | epot = -219.45122924006 | etot = -172.648635243067 +956000 ekin = 23.6959292084454 | erot = 24.2542500120269 | epot = -219.324912206847 | etot = -171.374732986375 +957000 ekin = 24.5172263085672 | erot = 24.1459598029485 | epot = -219.163645858039 | etot = -170.500459746523 +958000 ekin = 25.8225599553336 | erot = 23.6654996104887 | epot = -219.159019217903 | etot = -169.670959652081 +959000 ekin = 26.8068645926446 | erot = 25.0211786091659 | epot = -219.23531458736 | etot = -167.40727138555 +960000 ekin = 26.5999695579089 | erot = 25.6266836486181 | epot = -219.112393893106 | etot = -166.885740686579 +961000 ekin = 27.0539782988757 | erot = 26.1135586378242 | epot = -218.901327623641 | etot = -165.733790686941 +962000 ekin = 27.3128371491059 | erot = 25.6398136135623 | epot = -218.716820658053 | etot = -165.764169895385 +963000 ekin = 27.5776608737564 | erot = 24.2328598021347 | epot = -218.565342926505 | etot = -166.754822250614 +964000 ekin = 28.434847779201 | erot = 23.0688699860552 | epot = -218.32159079768 | etot = -166.817873032424 +965000 ekin = 27.9989611524549 | erot = 21.1729542648574 | epot = -217.935512501719 | etot = -168.763597084407 +966000 ekin = 28.1906276758125 | erot = 19.7596499447264 | epot = -217.551246311047 | etot = -169.600968690508 +967000 ekin = 28.1299488148111 | erot = 19.7764414549918 | epot = -217.022765960343 | etot = -169.11637569054 +968000 ekin = 27.2553372938565 | erot = 18.6432061694697 | epot = -216.345481598031 | etot = -170.446938134704 +969000 ekin = 27.3975194660702 | erot = 16.7046773675797 | epot = -215.471813515321 | etot = -171.369616681671 +970000 ekin = 26.2092304427085 | erot = 16.6741476212952 | epot = -214.618004397777 | etot = -171.734626333774 +971000 ekin = 25.4753520862258 | erot = 16.4961256389214 | epot = -213.774217411075 | etot = -171.802739685927 +972000 ekin = 25.1338150886746 | erot = 17.5885931811208 | epot = -212.941007560394 | etot = -170.218599290598 +973000 ekin = 23.9980459819068 | erot = 19.2413290657419 | epot = -212.209972657659 | etot = -168.97059761001 +974000 ekin = 23.1991915243631 | erot = 20.5621498503079 | epot = -211.643302372093 | etot = -167.881960997422 +975000 ekin = 22.0936708905994 | erot = 23.8925799416044 | epot = -211.258183683576 | etot = -165.271932851372 +976000 ekin = 21.5284614810504 | erot = 24.4823848282085 | epot = -210.871321753255 | etot = -164.860475443996 +977000 ekin = 20.9102492410769 | erot = 21.693728956875 | epot = -210.421620122539 | etot = -167.817641924587 +978000 ekin = 20.5534455754244 | erot = 21.4137671023852 | epot = -210.104378292213 | etot = -168.137165614403 +979000 ekin = 20.4475545334837 | erot = 21.7023482062785 | epot = -209.997680361419 | etot = -167.847777621657 +980000 ekin = 20.0153051482561 | erot = 22.1641624026467 | epot = -209.89453747175 | etot = -167.715069920847 +981000 ekin = 19.2553377922842 | erot = 21.6998257958764 | epot = -209.890607062706 | etot = -168.935443474545 +982000 ekin = 19.3602504755725 | erot = 22.71183002751 | epot = -209.817363885782 | etot = -167.7452833827 +983000 ekin = 19.9918630693289 | erot = 23.202269542363 | epot = -209.824553681854 | etot = -166.630421070162 +984000 ekin = 20.2229931630647 | erot = 22.783376358611 | epot = -209.980959689712 | etot = -166.974590168037 +985000 ekin = 20.1271575518484 | erot = 25.8324951123609 | epot = -210.176274954526 | etot = -164.216622290317 +986000 ekin = 19.8065574143083 | erot = 25.7086232557777 | epot = -210.259482005916 | etot = -164.74430133583 +987000 ekin = 19.8241962308738 | erot = 27.3477557937439 | epot = -210.338061448385 | etot = -163.166109423767 +988000 ekin = 20.5802327460373 | erot = 26.5177798191887 | epot = -210.374636605805 | etot = -163.276624040579 +989000 ekin = 19.8243827036663 | erot = 25.0249543132842 | epot = -210.405555790817 | etot = -165.556218773867 +990000 ekin = 19.6784859521663 | erot = 25.0211614919117 | epot = -210.536148192301 | etot = -165.836500748223 +991000 ekin = 19.8800072497794 | erot = 23.9545983908763 | epot = -210.811356988255 | etot = -166.976751347599 +992000 ekin = 19.9500698690931 | erot = 23.5129947805019 | epot = -211.184932089162 | etot = -167.721867439567 +993000 ekin = 18.937341089784 | erot = 23.1942485295875 | epot = -211.832628892927 | etot = -169.701039273555 +994000 ekin = 19.0566139838972 | erot = 23.5902607657524 | epot = -212.751294519113 | etot = -170.104419769464 +995000 ekin = 19.600538964917 | erot = 24.2017471939332 | epot = -213.671202895863 | etot = -169.868916737012 +996000 ekin = 20.3648160827738 | erot = 24.5056692824139 | epot = -214.567571801734 | etot = -169.697086436546 +997000 ekin = 20.6784197154575 | erot = 22.6383548571427 | epot = -215.397393210187 | etot = -172.080618637587 +998000 ekin = 21.27338897749 | erot = 21.4812766210868 | epot = -216.126312680602 | etot = -173.371647082025 +999000 ekin = 22.1968344281123 | erot = 22.7999859685056 | epot = -216.784980184639 | etot = -171.788159788021 +1000000 ekin = 22.6406306102505 | erot = 22.5936369544571 | epot = -217.43832313152 | etot = -172.204055566812 + 1000000 303.8185 -221.63969 4.201369 -194.79769 -0.0039208577 39304000 +Loop time of 52.1772 on 4 procs for 1000000 steps with 26 atoms + +Performance: 28.250 ns/day, 0.850 hours/ns, 19165.450 timesteps/s, 498.302 katom-step/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.653 | 24.637 | 41.068 | 196.4 | 47.22 +Bond | 0.48356 | 0.63927 | 0.80015 | 17.6 | 1.23 +Neigh | 0.014011 | 0.014287 | 0.01458 | 0.2 | 0.03 +Comm | 6.7344 | 23.772 | 31.096 | 205.7 | 45.56 +Output | 0.12082 | 0.13899 | 0.14687 | 2.8 | 0.27 +Modify | 1.8628 | 2.4412 | 3.0041 | 33.6 | 4.68 +Other | | 0.5347 | | | 1.02 + +Nlocal: 6.5 ave 10 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 19.5 ave 23 max 16 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 75.25 ave 182 max 25 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.4.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:52 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.1 new file mode 100644 index 0000000000..f812593d4d --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.1 @@ -0,0 +1,1276 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 8 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 4 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 7 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.8.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 +Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 299.91159 -228.12763 5.3145589 -200.46358 0.037365999 39304000 +1000 ekin = 22.8379863364631 | erot = 20.8727077214658 | epot = -223.40247948455 | etot = -179.691785426621 +2000 ekin = 22.7811305214841 | erot = 22.642319354707 | epot = -224.256117760205 | etot = -178.832667884014 +3000 ekin = 23.3007102476489 | erot = 24.7866780853993 | epot = -225.012681837824 | etot = -176.925293504776 +4000 ekin = 22.7903421051578 | erot = 24.569247173836 | epot = -225.53962239349 | etot = -178.180033114497 +5000 ekin = 22.19925646023 | erot = 25.6289473462429 | epot = -225.721034396187 | etot = -177.892830589714 +6000 ekin = 22.3860723428343 | erot = 25.7078570981677 | epot = -225.520727206183 | etot = -177.426797765181 +7000 ekin = 22.6093903901514 | erot = 24.8279594754098 | epot = -225.139767140542 | etot = -177.702417274981 +8000 ekin = 22.3366506221221 | erot = 25.3490822995746 | epot = -224.659830672346 | etot = -176.97409775065 +9000 ekin = 22.1017491922176 | erot = 23.8561173282126 | epot = -224.102470196007 | etot = -178.144603675577 +10000 ekin = 21.3469487217786 | erot = 23.034985278251 | epot = -223.591750396367 | etot = -179.209816396337 +11000 ekin = 20.5717104541852 | erot = 24.8615565294047 | epot = -223.484019303241 | etot = -178.050752319652 +12000 ekin = 20.411935484151 | erot = 25.1271441409211 | epot = -223.751373801975 | etot = -178.212294176903 +13000 ekin = 20.2798810279148 | erot = 24.281806390477 | epot = -224.390777503839 | etot = -179.829090085447 +14000 ekin = 19.6242363441233 | erot = 26.8542751690783 | epot = -225.215820819941 | etot = -178.73730930674 +15000 ekin = 20.0818097074935 | erot = 29.2937195480841 | epot = -226.167773981604 | etot = -176.792244726026 +16000 ekin = 19.6823418822516 | erot = 30.3811175824271 | epot = -227.408076260742 | etot = -177.344616796063 +17000 ekin = 19.5450698280734 | erot = 32.5391774659612 | epot = -228.808347823448 | etot = -176.724100529413 +18000 ekin = 20.0756319264279 | erot = 33.5672084608192 | epot = -230.110512386278 | etot = -176.467671999031 +19000 ekin = 19.6603874622079 | erot = 32.528542938808 | epot = -231.207417420873 | etot = -179.018487019857 +20000 ekin = 19.5984395633796 | erot = 31.3606067961676 | epot = -232.171981685224 | etot = -181.212935325677 +21000 ekin = 19.8375798064082 | erot = 31.8939937172914 | epot = -232.880097232772 | etot = -181.148523709072 +22000 ekin = 19.9286085655832 | erot = 30.5391742384594 | epot = -233.322303895413 | etot = -182.85452109137 +23000 ekin = 20.1661434732298 | erot = 30.6973170954371 | epot = -233.687536932121 | etot = -182.824076363455 +24000 ekin = 20.5065436368894 | erot = 30.0297091428477 | epot = -233.956998583432 | etot = -183.420745803695 +25000 ekin = 20.529858609709 | erot = 27.1945410830961 | epot = -233.994416252181 | etot = -186.270016559376 +26000 ekin = 20.699035687076 | erot = 29.09174515188 | epot = -233.720969470337 | etot = -183.930188631381 +27000 ekin = 20.7350777764672 | erot = 28.5961324745054 | epot = -233.307821216305 | etot = -183.976610965332 +28000 ekin = 21.1532240716935 | erot = 27.7486079543453 | epot = -232.966688262262 | etot = -184.064856236223 +29000 ekin = 21.3118506902676 | erot = 25.736471201621 | epot = -232.759622611367 | etot = -185.711300719478 +30000 ekin = 20.9513131899827 | erot = 26.876741160358 | epot = -232.673474007172 | etot = -184.845419656831 +31000 ekin = 21.3216486612277 | erot = 26.2777465254033 | epot = -232.609223688159 | etot = -185.009828501528 +32000 ekin = 22.0969166841928 | erot = 24.7959897585166 | epot = -232.612526553891 | etot = -185.719620111181 +33000 ekin = 22.875370966078 | erot = 24.1467590540463 | epot = -232.688992091586 | etot = -185.666862071462 +34000 ekin = 23.5405053823873 | erot = 22.7415684492007 | epot = -232.615611352503 | etot = -186.333537520915 +35000 ekin = 23.7257555349787 | erot = 26.8191624133874 | epot = -232.23498680623 | etot = -181.690068857864 +36000 ekin = 23.2515945340346 | erot = 23.8280794869285 | epot = -231.753024246269 | etot = -184.673350225306 +37000 ekin = 23.8513426401361 | erot = 25.6368246142449 | epot = -231.060980894716 | etot = -181.572813640335 +38000 ekin = 23.8781935722645 | erot = 22.7747736894791 | epot = -230.152104757751 | etot = -183.499137496008 +39000 ekin = 23.3884393320053 | erot = 22.6925700673075 | epot = -229.140534316443 | etot = -183.05952491713 +40000 ekin = 22.7413687353909 | erot = 21.4736378452411 | epot = -228.265631373339 | etot = -184.050624792707 +41000 ekin = 23.2348935054145 | erot = 21.0108525021673 | epot = -227.75573531584 | etot = -183.509989308258 +42000 ekin = 23.3940171890425 | erot = 22.1904243568237 | epot = -227.643506146239 | etot = -182.059064600373 +43000 ekin = 23.2681022018539 | erot = 21.7837756583263 | epot = -227.855518729869 | etot = -182.803640869689 +44000 ekin = 23.5393535337972 | erot = 20.7730908198455 | epot = -228.246566278463 | etot = -183.93412192482 +45000 ekin = 24.1405649747358 | erot = 20.1728652780817 | epot = -228.807425059799 | etot = -184.493994806982 +46000 ekin = 24.585245817982 | erot = 21.0236670642408 | epot = -229.213686304167 | etot = -183.604773421944 +47000 ekin = 24.1560413910622 | erot = 19.6811193727542 | epot = -229.413234324251 | etot = -185.576073560435 +48000 ekin = 23.5246878727431 | erot = 19.721180663017 | epot = -229.434759182691 | etot = -186.188890646931 +49000 ekin = 23.1670415745661 | erot = 22.5501021659482 | epot = -229.177266193688 | etot = -183.460122453174 +50000 ekin = 22.8223612259816 | erot = 22.567605149626 | epot = -228.600859944765 | etot = -183.210893569157 +51000 ekin = 22.9120987888545 | erot = 21.0527888961203 | epot = -227.77037262561 | etot = -183.805484940635 +52000 ekin = 22.187626079843 | erot = 20.5194847365121 | epot = -226.835169897986 | etot = -184.128059081631 +53000 ekin = 21.3650052806676 | erot = 20.2770735131344 | epot = -225.807155710179 | etot = -184.165076916377 +54000 ekin = 20.4303417025859 | erot = 17.9973021512008 | epot = -224.896097666587 | etot = -186.468453812801 +55000 ekin = 19.714913763396 | erot = 18.5590407326034 | epot = -224.06259658443 | etot = -185.788642088431 +56000 ekin = 19.685159503242 | erot = 20.0732971833202 | epot = -223.279023832763 | etot = -183.520567146201 +57000 ekin = 19.060196259904 | erot = 18.256095629202 | epot = -222.84333391372 | etot = -185.527042024614 +58000 ekin = 18.5841091049986 | erot = 19.1515036320309 | epot = -222.696024269362 | etot = -184.960411532333 +59000 ekin = 18.0414625414599 | erot = 18.2275847003703 | epot = -222.821981249891 | etot = -186.55293400806 +60000 ekin = 18.2103913071538 | erot = 18.4755642418172 | epot = -223.234305836724 | etot = -186.548350287753 +61000 ekin = 17.9869947125514 | erot = 22.4458503852164 | epot = -223.797760245785 | etot = -183.364915148017 +62000 ekin = 18.1431070502485 | erot = 21.7652022985207 | epot = -224.318306232552 | etot = -184.409996883783 +63000 ekin = 17.973357520257 | erot = 21.6688824771829 | epot = -224.735623623494 | etot = -185.093383626054 +64000 ekin = 17.8102495654737 | erot = 21.8723940899094 | epot = -225.323991291355 | etot = -185.641347635972 +65000 ekin = 18.0338529130483 | erot = 22.1181740951059 | epot = -225.877150411024 | etot = -185.72512340287 +66000 ekin = 18.1822893834801 | erot = 21.7465005263719 | epot = -226.185684363613 | etot = -186.256894453761 +67000 ekin = 18.5240194292997 | erot = 23.3964917870366 | epot = -226.365163861592 | etot = -184.444652645256 +68000 ekin = 18.5155376828975 | erot = 20.9719183620335 | epot = -226.451473665725 | etot = -186.964017620794 +69000 ekin = 18.6323014683072 | erot = 20.588171070637 | epot = -226.648083130375 | etot = -187.427610591431 +70000 ekin = 19.5343933745558 | erot = 17.5472322005953 | epot = -226.977679956235 | etot = -189.896054381084 +71000 ekin = 20.2276605685904 | erot = 16.3663260398183 | epot = -227.393323574632 | etot = -190.799336966224 +72000 ekin = 20.3130284812279 | erot = 16.4497414610662 | epot = -228.013381961156 | etot = -191.250612018862 +73000 ekin = 21.0477998518383 | erot = 15.4406791831341 | epot = -228.675590564562 | etot = -192.187111529589 +74000 ekin = 21.7371512650598 | erot = 17.5352725761175 | epot = -229.494527276336 | etot = -190.222103435159 +75000 ekin = 22.6680122759915 | erot = 18.5419401178599 | epot = -230.463408123768 | etot = -189.253455729917 +76000 ekin = 23.0346115082234 | erot = 19.8636379382539 | epot = -231.254905942531 | etot = -188.356656496053 +77000 ekin = 23.2797429827865 | erot = 19.7434715156692 | epot = -231.721208677509 | etot = -188.697994179053 +78000 ekin = 23.4106393811464 | erot = 19.4211385461251 | epot = -231.892259154973 | etot = -189.060481227701 +79000 ekin = 23.4632537757978 | erot = 18.8653049537082 | epot = -231.690998177985 | etot = -189.362439448479 +80000 ekin = 23.3884971334889 | erot = 18.1174271773692 | epot = -231.118174876358 | etot = -189.6122505655 +81000 ekin = 23.5022754315906 | erot = 17.1755695884554 | epot = -230.398467043008 | etot = -189.720622022962 +82000 ekin = 23.0472842217945 | erot = 17.2373445724549 | epot = -229.638468243904 | etot = -189.353839449655 +83000 ekin = 21.5042588722365 | erot = 16.786367445308 | epot = -228.921540236372 | etot = -190.630913918827 +84000 ekin = 22.1329940094216 | erot = 16.2632055631471 | epot = -228.335250260719 | etot = -189.93905068815 +85000 ekin = 20.9154057430379 | erot = 16.6557644544218 | epot = -227.803085954943 | etot = -190.231915757484 +86000 ekin = 20.6981517687592 | erot = 18.6120855140407 | epot = -227.283699712715 | etot = -187.973462429915 +87000 ekin = 20.7059776963377 | erot = 18.1357410469598 | epot = -226.805480829165 | etot = -187.963762085867 +88000 ekin = 20.5112535017457 | erot = 17.8809983821762 | epot = -226.459696318129 | etot = -188.067444434207 +89000 ekin = 20.6525596514182 | erot = 20.4133880492623 | epot = -226.205468820861 | etot = -185.139521120181 +90000 ekin = 20.695293192409 | erot = 20.3370512782838 | epot = -225.953852764959 | etot = -184.921508294267 +91000 ekin = 19.7682690703159 | erot = 23.8787808356902 | epot = -225.655385288229 | etot = -182.008335382223 +92000 ekin = 19.6828792607911 | erot = 22.5766537107148 | epot = -225.535582585193 | etot = -183.276049613687 +93000 ekin = 19.3048520995758 | erot = 20.6317228268703 | epot = -225.547774602348 | etot = -185.611199675902 +94000 ekin = 19.028411935034 | erot = 20.0568093447086 | epot = -225.530355910562 | etot = -186.445134630819 +95000 ekin = 18.5452655948058 | erot = 22.9286015621929 | epot = -225.523849045322 | etot = -184.049981888323 +96000 ekin = 18.3728256439782 | erot = 25.039495486179 | epot = -225.537862748503 | etot = -182.125541618346 +97000 ekin = 17.9426894203414 | erot = 28.5848563795549 | epot = -225.638824537989 | etot = -179.111278738092 +98000 ekin = 17.5850264746273 | erot = 26.5739649306284 | epot = -225.648647927869 | etot = -181.489656522613 +99000 ekin = 17.3808762582936 | erot = 24.7289180187015 | epot = -225.594130307751 | etot = -183.484336030756 +100000 ekin = 17.3273680270292 | erot = 22.7273796979409 | epot = -225.299321148282 | etot = -185.244573423312 +101000 ekin = 17.0042319903592 | erot = 20.8052793029198 | epot = -225.102935121042 | etot = -187.293423827763 +102000 ekin = 17.05502613973 | erot = 21.316603586839 | epot = -224.890904735916 | etot = -186.519275009347 +103000 ekin = 17.2263904973081 | erot = 20.3710964353458 | epot = -224.753273552475 | etot = -187.155786619821 +104000 ekin = 16.7943747317823 | erot = 21.7185799033818 | epot = -224.555386740442 | etot = -186.042432105278 +105000 ekin = 16.6865175024786 | erot = 20.0200455556502 | epot = -224.47221260965 | etot = -187.765649551522 +106000 ekin = 16.5925867843767 | erot = 21.7048075291456 | epot = -224.380087441128 | etot = -186.082693127606 +107000 ekin = 17.2054452998434 | erot = 22.6546685111546 | epot = -224.481631442089 | etot = -184.621517631091 +108000 ekin = 16.9267033337673 | erot = 23.5631418034102 | epot = -224.898081411902 | etot = -184.408236274724 +109000 ekin = 17.3821452346864 | erot = 25.9049365088352 | epot = -225.621226955643 | etot = -182.334145212121 +110000 ekin = 17.5124448065073 | erot = 27.8801611895846 | epot = -226.410419972689 | etot = -181.017813976598 +111000 ekin = 18.5487245393564 | erot = 25.6736058140268 | epot = -227.167416210036 | etot = -182.945085856652 +112000 ekin = 19.8365999588111 | erot = 24.2751230291775 | epot = -227.944028021488 | etot = -183.832305033499 +113000 ekin = 20.1722859000849 | erot = 25.3603047130775 | epot = -228.958826647654 | etot = -183.426236034491 +114000 ekin = 20.2870180696113 | erot = 25.6800990417157 | epot = -230.17458939254 | etot = -184.207472281213 +115000 ekin = 21.3318566501428 | erot = 27.1697329853562 | epot = -231.444909631325 | etot = -182.943319995826 +116000 ekin = 22.4210844135644 | erot = 26.004420936002 | epot = -232.710476417833 | etot = -184.284971068267 +117000 ekin = 24.3405871824212 | erot = 25.2077444956265 | epot = -233.933190998453 | etot = -184.384859320406 +118000 ekin = 25.0884094969948 | erot = 26.5527557651617 | epot = -235.048390081924 | etot = -183.407224819767 +119000 ekin = 25.4315051787003 | erot = 26.1546643641889 | epot = -235.858317413788 | etot = -184.272147870899 +120000 ekin = 24.9629495355357 | erot = 25.2895225128999 | epot = -236.253529746916 | etot = -186.00105769848 +121000 ekin = 26.094755391151 | erot = 26.5212744850534 | epot = -236.079647472315 | etot = -183.46361759611 +122000 ekin = 26.1701918491875 | erot = 24.3510759857483 | epot = -235.493876868904 | etot = -184.972609033969 +123000 ekin = 26.4005875446556 | erot = 20.1865632708939 | epot = -234.709375372604 | etot = -188.122224557054 +124000 ekin = 26.3381579249386 | erot = 19.6639335950121 | epot = -233.989222703183 | etot = -187.987131183233 +125000 ekin = 25.4027453417305 | erot = 19.6503648681598 | epot = -233.10224654375 | etot = -188.04913633386 +126000 ekin = 25.3255704653777 | erot = 20.0698371771056 | epot = -232.162556032928 | etot = -186.767148390445 +127000 ekin = 25.0742564529078 | erot = 19.3577482138169 | epot = -231.22010681212 | etot = -186.788102145396 +128000 ekin = 24.1452145463861 | erot = 20.722592883018 | epot = -230.30707206278 | etot = -185.439264633376 +129000 ekin = 24.1836343798902 | erot = 21.1668068192837 | epot = -229.557734556381 | etot = -184.207293357207 +130000 ekin = 23.6272916857115 | erot = 21.0608635320181 | epot = -228.86842777514 | etot = -184.180272557411 +131000 ekin = 23.7733250641655 | erot = 21.7026182128681 | epot = -228.196470483987 | etot = -182.720527206954 +132000 ekin = 22.235523086447 | erot = 22.2423990709498 | epot = -227.377132642704 | etot = -182.899210485307 +133000 ekin = 21.7697258915644 | erot = 21.0688536119307 | epot = -226.678873870809 | etot = -183.840294367314 +134000 ekin = 22.0334013998118 | erot = 23.6876876537064 | epot = -226.110477401204 | etot = -180.389388347686 +135000 ekin = 21.2888725174031 | erot = 23.8731522967533 | epot = -225.586596896472 | etot = -180.424572082316 +136000 ekin = 21.1112833844234 | erot = 23.1441906006998 | epot = -225.02986093909 | etot = -180.774386953966 +137000 ekin = 20.3417544623754 | erot = 19.8373378818128 | epot = -224.306720617089 | etot = -184.127628272901 +138000 ekin = 20.6378655675457 | erot = 20.7041461431297 | epot = -223.935090515208 | etot = -182.593078804533 +139000 ekin = 20.6358768684418 | erot = 19.6349119675149 | epot = -223.695388728766 | etot = -183.42459989281 +140000 ekin = 21.2970180334091 | erot = 20.9859430093584 | epot = -223.44632370732 | etot = -181.163362664552 +141000 ekin = 20.7458666897953 | erot = 22.008168038219 | epot = -223.471675354103 | etot = -180.717640626089 +142000 ekin = 21.6581543402664 | erot = 22.1925330545729 | epot = -223.759999018087 | etot = -179.909311623248 +143000 ekin = 22.137676382598 | erot = 19.8438720355801 | epot = -223.992076444275 | etot = -182.010528026097 +144000 ekin = 21.4512214487569 | erot = 21.2911862274696 | epot = -224.211315350262 | etot = -181.468907674035 +145000 ekin = 21.1677590228455 | erot = 20.1765379829327 | epot = -224.433855912986 | etot = -183.089558907207 +146000 ekin = 21.2954143160548 | erot = 22.315786511802 | epot = -224.708745433142 | etot = -181.097544605285 +147000 ekin = 20.9304440285978 | erot = 24.2948847043021 | epot = -224.826442145057 | etot = -179.601113412157 +148000 ekin = 20.9920002123677 | erot = 25.1867007165295 | epot = -225.027893064869 | etot = -178.849192135972 +149000 ekin = 20.4937916688861 | erot = 25.3412194127539 | epot = -225.235228138764 | etot = -179.400217057124 +150000 ekin = 20.240788496008 | erot = 24.5936585831824 | epot = -225.22294490262 | etot = -180.38849782343 +151000 ekin = 20.1765587397768 | erot = 23.3198992588029 | epot = -224.965480891794 | etot = -181.469022893215 +152000 ekin = 19.9049224846628 | erot = 22.8007918896868 | epot = -224.714024114794 | etot = -182.008309740445 +153000 ekin = 20.2049676657018 | erot = 22.194787629535 | epot = -224.584122527196 | etot = -182.184367231959 +154000 ekin = 20.2787333086907 | erot = 23.5668471416538 | epot = -224.632505362968 | etot = -180.786924912624 +155000 ekin = 20.54327508537 | erot = 21.0208344632846 | epot = -225.11524693997 | etot = -183.551137391316 +156000 ekin = 21.1891534249123 | erot = 21.9641402966851 | epot = -225.922181500193 | etot = -182.768887778596 +157000 ekin = 21.9241933405022 | erot = 22.2820243127273 | epot = -226.791928428935 | etot = -182.585710775706 +158000 ekin = 22.1128564636274 | erot = 21.6071323400673 | epot = -227.681294121914 | etot = -183.961305318219 +159000 ekin = 21.9706527338173 | erot = 23.0889220586676 | epot = -228.293622590392 | etot = -183.234047797907 +160000 ekin = 22.1766068917265 | erot = 24.537009024834 | epot = -228.724261272436 | etot = -182.010645355876 +161000 ekin = 22.2585263955668 | erot = 26.3988206054411 | epot = -229.153198320277 | etot = -180.495851319269 +162000 ekin = 23.9956799056614 | erot = 29.0208643540612 | epot = -229.511788677983 | etot = -176.49524441826 +163000 ekin = 24.0427671853836 | erot = 28.5149092203014 | epot = -229.882700364651 | etot = -177.325023958966 +164000 ekin = 24.6404986309622 | erot = 29.8954353563838 | epot = -230.05653220386 | etot = -175.520598216514 +165000 ekin = 25.37837451169 | erot = 29.3458474374449 | epot = -230.021956695543 | etot = -175.297734746409 +166000 ekin = 24.5018301159861 | erot = 27.0572013521953 | epot = -229.807404132493 | etot = -178.248372664311 +167000 ekin = 24.3635902860623 | erot = 25.1004090825066 | epot = -229.418996399617 | etot = -179.954997031048 +168000 ekin = 24.0782799291434 | erot = 23.6106192667051 | epot = -228.790493183835 | etot = -181.101593987986 +169000 ekin = 23.5408370855421 | erot = 21.779214731184 | epot = -228.096753694582 | etot = -182.776701877856 +170000 ekin = 23.3042056991829 | erot = 22.5887621937051 | epot = -227.644704595797 | etot = -181.751736702909 +171000 ekin = 23.1139069856327 | erot = 25.56161061645 | epot = -227.386750672406 | etot = -178.711233070323 +172000 ekin = 22.4125455911307 | erot = 23.9879390948077 | epot = -227.478440821498 | etot = -181.07795613556 +173000 ekin = 21.1650772689554 | erot = 24.037053824746 | epot = -228.027795739756 | etot = -182.825664646054 +174000 ekin = 21.5377174768009 | erot = 25.6623168386594 | epot = -228.810113267544 | etot = -181.610078952084 +175000 ekin = 21.2673885173618 | erot = 25.3358091366212 | epot = -229.601669873776 | etot = -182.998472219792 +176000 ekin = 22.0549078764628 | erot = 25.1987886573552 | epot = -230.199173516198 | etot = -182.94547698238 +177000 ekin = 22.1952451140842 | erot = 26.2074019384157 | epot = -230.449490408395 | etot = -182.046843355895 +178000 ekin = 22.6474601747908 | erot = 23.8569097796671 | epot = -230.486903876126 | etot = -183.982533921668 +179000 ekin = 22.5332951614051 | erot = 24.1586648743825 | epot = -230.249582873377 | etot = -183.55762283759 +180000 ekin = 22.9130954884035 | erot = 22.1104613694639 | epot = -229.757677624187 | etot = -184.73412076632 +181000 ekin = 22.5830672584554 | erot = 20.450357914035 | epot = -229.205005015184 | etot = -186.171579842693 +182000 ekin = 21.7744390453032 | erot = 20.3565453634741 | epot = -228.578765211469 | etot = -186.447780802691 +183000 ekin = 21.3156414739578 | erot = 21.1055168403748 | epot = -227.936610643158 | etot = -185.515452328825 +184000 ekin = 21.4060237522632 | erot = 20.8540585363569 | epot = -227.278789217958 | etot = -185.018706929338 +185000 ekin = 21.4522029742182 | erot = 19.9268287024307 | epot = -226.747540479433 | etot = -185.368508802785 +186000 ekin = 21.1983246906017 | erot = 21.4683722301386 | epot = -226.354347511139 | etot = -183.687650590399 +187000 ekin = 19.690535005356 | erot = 21.6640179195446 | epot = -225.994223499083 | etot = -184.639670574183 +188000 ekin = 19.3802922890703 | erot = 20.3716521999867 | epot = -225.572007065283 | etot = -185.820062576226 +189000 ekin = 18.4695751736414 | erot = 20.9528614806743 | epot = -225.247637250638 | etot = -185.825200596322 +190000 ekin = 17.4681116945173 | erot = 22.2496740454142 | epot = -224.805249640785 | etot = -185.087463900853 +191000 ekin = 16.6191337946719 | erot = 21.4193312202814 | epot = -224.294610310801 | etot = -186.256145295848 +192000 ekin = 16.0143800470349 | erot = 23.3693680596585 | epot = -223.718710211147 | etot = -184.334962104454 +193000 ekin = 15.7997901257216 | erot = 22.8225508042988 | epot = -223.089938646114 | etot = -184.467597716093 +194000 ekin = 15.2217453118598 | erot = 22.7325306996813 | epot = -222.625275149846 | etot = -184.670999138305 +195000 ekin = 15.1719099531695 | erot = 22.4876618724485 | epot = -222.099560622719 | etot = -184.439988797101 +196000 ekin = 15.3343672188822 | erot = 20.7775889118734 | epot = -221.597631501452 | etot = -185.485675370697 +197000 ekin = 14.766048091889 | erot = 19.7842334059676 | epot = -221.252213948545 | etot = -186.701932450688 +198000 ekin = 14.7770693853773 | erot = 20.3688380244553 | epot = -220.957884756875 | etot = -185.811977347042 +199000 ekin = 14.6937058517326 | erot = 22.6205548299113 | epot = -220.829895321234 | etot = -183.51563463959 +200000 ekin = 15.8653653492245 | erot = 20.8741496651364 | epot = -220.921168840223 | etot = -184.181653825862 +201000 ekin = 16.8728289108128 | erot = 23.0954953178473 | epot = -221.24134564708 | etot = -181.27302141842 +202000 ekin = 17.1574797353138 | erot = 22.285557506037 | epot = -221.513124761678 | etot = -182.070087520327 +203000 ekin = 18.4748883214853 | erot = 21.1472224923989 | epot = -221.731230109427 | etot = -182.109119295543 +204000 ekin = 19.2325496005105 | erot = 20.9923779560698 | epot = -221.821935938326 | etot = -181.597008381746 +205000 ekin = 18.4255902998036 | erot = 21.6289651382083 | epot = -222.10565061528 | etot = -182.051095177268 +206000 ekin = 18.5468871013068 | erot = 22.2892911055978 | epot = -222.480026344849 | etot = -181.643848137944 +207000 ekin = 18.9799810220236 | erot = 25.3769178031176 | epot = -222.656627081049 | etot = -178.299728255907 +208000 ekin = 18.985044800951 | erot = 26.4647809474189 | epot = -222.71751731042 | etot = -177.26769156205 +209000 ekin = 19.7564462509297 | erot = 23.7060464556116 | epot = -222.835034583459 | etot = -179.372541876917 +210000 ekin = 18.930059047627 | erot = 21.9791265973624 | epot = -222.75013900049 | etot = -181.840953355501 +211000 ekin = 19.3637206258675 | erot = 20.2144155977342 | epot = -222.884011041863 | etot = -183.305874818262 +212000 ekin = 18.6127906086045 | erot = 18.7836957734051 | epot = -223.131977986675 | etot = -185.735491604666 +213000 ekin = 18.6207275953171 | erot = 18.079576040676 | epot = -223.568944156785 | etot = -186.868640520792 +214000 ekin = 18.0525593583566 | erot = 20.9785428305194 | epot = -224.281741393784 | etot = -185.250639204908 +215000 ekin = 18.4181697813342 | erot = 21.5844731751551 | epot = -225.36589716156 | etot = -185.363254205071 +216000 ekin = 18.1283838147148 | erot = 26.0258037718262 | epot = -226.609028691632 | etot = -182.454841105091 +217000 ekin = 18.5976564529797 | erot = 25.2672310084213 | epot = -227.604708371557 | etot = -183.739820910156 +218000 ekin = 18.6146376310641 | erot = 23.8235521999893 | epot = -228.575434081834 | etot = -186.13724425078 +219000 ekin = 19.3665245563789 | erot = 24.0423091654174 | epot = -229.487172233029 | etot = -186.078338511233 +220000 ekin = 19.0674806968353 | erot = 24.8437141420456 | epot = -230.380897501689 | etot = -186.469702662808 +221000 ekin = 18.7605746437215 | erot = 26.6882095060636 | epot = -231.213347501054 | etot = -185.764563351269 +222000 ekin = 18.2601086357985 | erot = 26.2872383665376 | epot = -231.899871459307 | etot = -187.352524456971 +223000 ekin = 18.450698620632 | erot = 26.0465542803085 | epot = -232.337267696155 | etot = -187.840014795214 +224000 ekin = 18.9891330599031 | erot = 27.8638375428931 | epot = -232.528415379388 | etot = -185.675444776592 +225000 ekin = 19.4927747283068 | erot = 25.801864264556 | epot = -232.780900379235 | etot = -187.486261386372 +226000 ekin = 19.1531460973279 | erot = 30.4806630263034 | epot = -233.077183634691 | etot = -183.44337451106 +227000 ekin = 18.60714463341 | erot = 30.1777908886287 | epot = -232.964109027209 | etot = -184.179173505171 +228000 ekin = 18.4858074214198 | erot = 31.561135296702 | epot = -232.632194016111 | etot = -182.585251297989 +229000 ekin = 18.121165512591 | erot = 31.2764316650807 | epot = -232.253052683513 | etot = -182.855455505842 +230000 ekin = 17.8908234673042 | erot = 27.5438052529654 | epot = -231.968720310839 | etot = -186.534091590569 +231000 ekin = 17.4046011153877 | erot = 24.8124690524392 | epot = -231.614857480412 | etot = -189.397787312585 +232000 ekin = 16.726949239043 | erot = 25.4479901290198 | epot = -231.298988676823 | etot = -189.12404930876 +233000 ekin = 17.4181301789806 | erot = 25.6698394160172 | epot = -231.284274641405 | etot = -188.196305046407 +234000 ekin = 17.2837229866899 | erot = 24.7490838826286 | epot = -231.292369116174 | etot = -189.259562246856 +235000 ekin = 17.8418429383167 | erot = 21.8691418097328 | epot = -231.251575822849 | etot = -191.5405910748 +236000 ekin = 18.2280444396042 | erot = 22.4776949586945 | epot = -231.507293467971 | etot = -190.801554069672 +237000 ekin = 17.5170325906195 | erot = 23.8831905837694 | epot = -232.09911142057 | etot = -190.698888246182 +238000 ekin = 17.5370495415089 | erot = 23.1397896153992 | epot = -232.813601469978 | etot = -192.13676231307 +239000 ekin = 18.5035461424359 | erot = 23.6314853899781 | epot = -233.424851371331 | etot = -191.289819838917 +240000 ekin = 18.2400558551285 | erot = 25.7782971635906 | epot = -233.735423678076 | etot = -189.717070659357 +241000 ekin = 18.3026727766783 | erot = 24.4472869908134 | epot = -233.913575321003 | etot = -191.163615553511 +242000 ekin = 17.7115212204843 | erot = 24.995729162613 | epot = -234.050352631169 | etot = -191.343102248072 +243000 ekin = 17.2078487224333 | erot = 23.9090981344856 | epot = -234.125136273026 | etot = -193.008189416107 +244000 ekin = 16.2099036691328 | erot = 23.5424124480185 | epot = -234.271072794161 | etot = -194.51875667701 +245000 ekin = 16.2853237680124 | erot = 25.6013260460874 | epot = -234.567326279749 | etot = -192.680676465649 +246000 ekin = 15.9877124738648 | erot = 26.4618528423917 | epot = -234.907254123649 | etot = -192.457688807393 +247000 ekin = 16.278912642661 | erot = 25.6305025080533 | epot = -235.38224025519 | etot = -193.472825104476 +248000 ekin = 16.1891212016019 | erot = 26.7270438066868 | epot = -235.85693800343 | etot = -192.940772995142 +249000 ekin = 16.2464500192795 | erot = 27.0261014884008 | epot = -236.177986894745 | etot = -192.905435387065 +250000 ekin = 15.9341143953265 | erot = 30.8738949363089 | epot = -236.535496633727 | etot = -189.727487302092 +251000 ekin = 15.8028184849003 | erot = 32.1505879831005 | epot = -236.688974719602 | etot = -188.735568251601 +252000 ekin = 16.7909168467857 | erot = 32.8335558099614 | epot = -236.645831434934 | etot = -187.021358778187 +253000 ekin = 16.9139273743643 | erot = 29.2781158099218 | epot = -236.579277646039 | etot = -190.387234461753 +254000 ekin = 16.6934725608083 | erot = 29.105191471631 | epot = -236.457570337498 | etot = -190.658906305059 +255000 ekin = 16.9530894051165 | erot = 28.561900354835 | epot = -236.494291914548 | etot = -190.979302154596 +256000 ekin = 16.8565757743705 | erot = 26.1542309529602 | epot = -236.815950729242 | etot = -193.805144001911 +257000 ekin = 16.585149543856 | erot = 27.2044624689905 | epot = -237.076180448211 | etot = -193.286568435365 +258000 ekin = 16.9649893297413 | erot = 29.5003144318717 | epot = -237.125813775239 | etot = -190.660510013626 +259000 ekin = 16.8759816443281 | erot = 28.8592698754747 | epot = -237.185288834274 | etot = -191.450037314471 +260000 ekin = 16.9796890464332 | erot = 27.618877966906 | epot = -237.312226590128 | etot = -192.713659576789 +261000 ekin = 17.1257291800673 | erot = 26.9320058611979 | epot = -237.262614695238 | etot = -193.204879653972 +262000 ekin = 17.6923394447622 | erot = 27.2700259360803 | epot = -237.143815143362 | etot = -192.18144976252 +263000 ekin = 17.8430352696419 | erot = 25.086676238323 | epot = -236.946345380794 | etot = -194.016633872829 +264000 ekin = 18.0391753861997 | erot = 26.3317958950567 | epot = -236.678672413504 | etot = -192.307701132247 +265000 ekin = 18.013924761071 | erot = 25.5680520302975 | epot = -236.424056901965 | etot = -192.842080110596 +266000 ekin = 17.6154269767062 | erot = 23.675123094962 | epot = -235.997667559883 | etot = -194.707117488214 +267000 ekin = 17.6622486381387 | erot = 26.2267112931792 | epot = -235.553502063923 | etot = -191.664542132605 +268000 ekin = 17.8125223357387 | erot = 27.363444164387 | epot = -235.09406638475 | etot = -189.918099884624 +269000 ekin = 17.4475328870398 | erot = 28.702098419643 | epot = -234.302641461941 | etot = -188.153010155258 +270000 ekin = 17.3046917858623 | erot = 29.7195013929747 | epot = -233.361041913271 | etot = -186.336848734434 +271000 ekin = 17.142474619254 | erot = 29.9663485879831 | epot = -232.456072910032 | etot = -185.347249702795 +272000 ekin = 17.1520876922752 | erot = 28.8349700847661 | epot = -231.55505567112 | etot = -185.567997894079 +273000 ekin = 16.529132536504 | erot = 28.0012512077314 | epot = -230.483093897511 | etot = -185.952710153276 +274000 ekin = 16.0104360170946 | erot = 26.9274909329307 | epot = -229.230529801711 | etot = -186.292602851686 +275000 ekin = 15.5159445897247 | erot = 25.0461733638716 | epot = -227.842923326835 | etot = -187.280805373238 +276000 ekin = 15.3290449735773 | erot = 22.6013849304136 | epot = -226.645721417409 | etot = -188.715291513418 +277000 ekin = 14.8998254086663 | erot = 21.4368139643109 | epot = -225.632942921213 | etot = -189.296303548235 +278000 ekin = 14.6883229783611 | erot = 21.764246814846 | epot = -224.505045285419 | etot = -188.052475492212 +279000 ekin = 14.8047270727149 | erot = 21.9101300703525 | epot = -223.591887497535 | etot = -186.877030354468 +280000 ekin = 15.1052613957242 | erot = 21.2019638470283 | epot = -222.930554266676 | etot = -186.623329023924 +281000 ekin = 15.9185405703085 | erot = 22.7554995785104 | epot = -222.496264131452 | etot = -183.822223982633 +282000 ekin = 15.7118745407237 | erot = 21.6184112020448 | epot = -222.111847398432 | etot = -184.781561655664 +283000 ekin = 15.6333488922702 | erot = 21.465780561396 | epot = -221.697448312628 | etot = -184.598318858962 +284000 ekin = 15.959853189633 | erot = 21.5564118521706 | epot = -221.456027263584 | etot = -183.93976222178 +285000 ekin = 16.1804948749226 | erot = 20.7957823598973 | epot = -221.442032618529 | etot = -184.465755383709 +286000 ekin = 16.2437780433302 | erot = 22.0029966684091 | epot = -221.48947785587 | etot = -183.242703144131 +287000 ekin = 16.5860527634174 | erot = 21.2347797551117 | epot = -221.681437402569 | etot = -183.86060488404 +288000 ekin = 17.4777982920666 | erot = 22.9676186033132 | epot = -222.210097097494 | etot = -181.764680202114 +289000 ekin = 19.2022256495172 | erot = 21.806988434862 | epot = -223.03555219086 | etot = -182.026338106481 +290000 ekin = 20.6029736081834 | erot = 21.6756942552161 | epot = -223.927958525587 | etot = -181.649290662188 +291000 ekin = 21.0325637238795 | erot = 25.0635435951381 | epot = -224.954298339301 | etot = -178.858191020283 +292000 ekin = 21.9992014565845 | erot = 24.5675448811519 | epot = -226.014147345555 | etot = -179.447401007819 +293000 ekin = 22.8449936736823 | erot = 26.0971097085354 | epot = -227.039865181468 | etot = -178.09776179925 +294000 ekin = 24.2424273090434 | erot = 22.3242335931344 | epot = -227.698192270626 | etot = -181.131531368448 +295000 ekin = 25.1430321033927 | erot = 22.81093656589 | epot = -228.272133548427 | etot = -180.318164879144 +296000 ekin = 25.4190616181137 | erot = 23.5935920052844 | epot = -228.827919142591 | etot = -179.815265519193 +297000 ekin = 24.1157580511247 | erot = 24.5278953829289 | epot = -229.421950081214 | etot = -180.77829664716 +298000 ekin = 24.1091297661069 | erot = 24.3527158051324 | epot = -229.912795380237 | etot = -181.450949808998 +299000 ekin = 24.1889413361173 | erot = 28.3512815530446 | epot = -230.356799401626 | etot = -177.816576512464 +300000 ekin = 24.2163939347386 | erot = 26.6122585649448 | epot = -230.754469972665 | etot = -179.925817472982 +301000 ekin = 23.9473801903426 | erot = 27.8600078683744 | epot = -231.048868063292 | etot = -179.241480004575 +302000 ekin = 23.6699655332583 | erot = 27.5610103980966 | epot = -231.2462622361 | etot = -180.015286304745 +303000 ekin = 23.8797875069283 | erot = 29.2034880593161 | epot = -231.3115724611 | etot = -178.228296894856 +304000 ekin = 22.73106672979 | erot = 27.7503022429659 | epot = -231.512470993041 | etot = -181.031102020285 +305000 ekin = 22.1016085656468 | erot = 27.0493993901605 | epot = -231.718355828267 | etot = -182.56734787246 +306000 ekin = 21.3693097984681 | erot = 26.2537086929049 | epot = -231.891297103593 | etot = -184.26827861222 +307000 ekin = 21.0324320589055 | erot = 24.6230768163623 | epot = -232.14138641287 | etot = -186.485877537602 +308000 ekin = 20.1154566391106 | erot = 21.7787557790717 | epot = -232.402656379528 | etot = -190.508443961346 +309000 ekin = 19.6646153697248 | erot = 24.2524356353678 | epot = -232.726752497782 | etot = -188.809701492689 +310000 ekin = 19.506055878272 | erot = 23.0558815582429 | epot = -232.894728269794 | etot = -190.332790833279 +311000 ekin = 19.4366809731017 | erot = 23.3044474838376 | epot = -232.852507372457 | etot = -190.111378915517 +312000 ekin = 18.9851206753984 | erot = 23.3056434770267 | epot = -232.658571091316 | etot = -190.367806938891 +313000 ekin = 18.456476357187 | erot = 22.3541198734799 | epot = -232.226835699179 | etot = -191.416239468512 +314000 ekin = 17.5964963597534 | erot = 24.280152514809 | epot = -231.840379924947 | etot = -189.963731050385 +315000 ekin = 17.4204244485737 | erot = 23.6514203760144 | epot = -231.530486492869 | etot = -190.45864166828 +316000 ekin = 16.1724163728655 | erot = 22.698801275189 | epot = -231.308288231255 | etot = -192.4370705832 +317000 ekin = 16.1754961975214 | erot = 24.7458837009842 | epot = -231.086735374031 | etot = -190.165355475525 +318000 ekin = 15.6276186513821 | erot = 25.4598581999699 | epot = -230.874800576949 | etot = -189.787323725597 +319000 ekin = 15.2218658312374 | erot = 26.310179302591 | epot = -230.890983487464 | etot = -189.358938353635 +320000 ekin = 14.5086838632118 | erot = 25.5779207778604 | epot = -230.835599614339 | etot = -190.748994973267 +321000 ekin = 14.3605129926004 | erot = 24.3299501149204 | epot = -230.738948206952 | etot = -192.048485099431 +322000 ekin = 14.3610877203126 | erot = 22.9310291497487 | epot = -230.65305378356 | etot = -193.360936913499 +323000 ekin = 14.7688305230875 | erot = 22.2970860063464 | epot = -230.465569924266 | etot = -193.399653394832 +324000 ekin = 14.9355157274789 | erot = 21.6250944927411 | epot = -230.284210305093 | etot = -193.723600084873 +325000 ekin = 14.671493713112 | erot = 19.7302049638664 | epot = -230.227419340871 | etot = -195.825720663893 +326000 ekin = 14.9234987156657 | erot = 18.5568938196644 | epot = -230.211337706826 | etot = -196.730945171496 +327000 ekin = 15.4129696630397 | erot = 18.0709384490326 | epot = -230.259317350117 | etot = -196.775409238045 +328000 ekin = 16.3932927560713 | erot = 18.0499060967779 | epot = -230.447119407116 | etot = -196.003920554267 +329000 ekin = 17.4064272548349 | erot = 17.712742044302 | epot = -230.608667384644 | etot = -195.489498085507 +330000 ekin = 17.9751565884689 | erot = 20.51547017577 | epot = -230.944813706002 | etot = -192.454186941763 +331000 ekin = 18.0313803560148 | erot = 22.5739918453344 | epot = -231.277621168628 | etot = -190.672248967279 +332000 ekin = 18.15147843611 | erot = 22.8208528087548 | epot = -231.623777285706 | etot = -190.651446040841 +333000 ekin = 18.0930465656663 | erot = 21.9771411609275 | epot = -231.923848859364 | etot = -191.85366113277 +334000 ekin = 17.7728125353381 | erot = 23.128955301666 | epot = -232.169505006005 | etot = -191.267737169001 +335000 ekin = 19.0031630375606 | erot = 23.3897776040612 | epot = -232.460034619601 | etot = -190.067093977979 +336000 ekin = 19.5591765342243 | erot = 25.3697311547745 | epot = -232.739268822111 | etot = -187.810361133113 +337000 ekin = 19.8563675404798 | erot = 27.3439820813804 | epot = -232.906112080656 | etot = -185.705762458796 +338000 ekin = 19.751099035653 | erot = 24.921360312315 | epot = -232.758554071368 | etot = -188.0860947234 +339000 ekin = 19.9050741791919 | erot = 25.5301605485524 | epot = -232.417171827705 | etot = -186.98193709996 +340000 ekin = 19.8794162185109 | erot = 25.9787598068518 | epot = -231.88072644563 | etot = -186.022550420267 +341000 ekin = 19.9454216521201 | erot = 24.1566390151013 | epot = -231.212127397362 | etot = -187.11006673014 +342000 ekin = 19.9237875292304 | erot = 26.4019287790718 | epot = -230.32153874995 | etot = -183.995822441648 +343000 ekin = 19.1115068720885 | erot = 22.5948467356212 | epot = -229.503208394896 | etot = -187.796854787186 +344000 ekin = 18.3079084943896 | erot = 23.107837537118 | epot = -228.898967466162 | etot = -187.483221434654 +345000 ekin = 18.4650460950013 | erot = 23.8173535141912 | epot = -228.453285301913 | etot = -186.17088569272 +346000 ekin = 18.0304251681423 | erot = 23.3440747631772 | epot = -228.183574545935 | etot = -186.809074614615 +347000 ekin = 17.5483582122927 | erot = 23.0282517992432 | epot = -227.908297752933 | etot = -187.331687741398 +348000 ekin = 17.622359603253 | erot = 22.2176773752137 | epot = -227.687080765617 | etot = -187.847043787151 +349000 ekin = 18.1160269661089 | erot = 23.5048787159375 | epot = -227.62230627499 | etot = -186.001400592943 +350000 ekin = 18.4237634534031 | erot = 23.3245531376522 | epot = -227.749080027053 | etot = -186.000763435998 +351000 ekin = 18.7086532226307 | erot = 23.8443722630501 | epot = -227.802083115351 | etot = -185.24905762967 +352000 ekin = 18.4929053608692 | erot = 23.3879966472946 | epot = -228.059952926951 | etot = -186.179050918787 +353000 ekin = 18.9161069388645 | erot = 23.2227449598892 | epot = -228.455593201501 | etot = -186.316741302748 +354000 ekin = 19.0977071534437 | erot = 26.1711894049523 | epot = -228.863332747988 | etot = -183.594436189592 +355000 ekin = 18.8408988656362 | erot = 25.4820466037911 | epot = -229.149897752163 | etot = -184.826952282736 +356000 ekin = 18.0073291494761 | erot = 26.6233733651629 | epot = -229.30066738625 | etot = -184.669964871611 +357000 ekin = 17.7607082496061 | erot = 25.2859928393404 | epot = -229.131821622954 | etot = -186.085120534008 +358000 ekin = 17.3110477472649 | erot = 23.858172364184 | epot = -228.730492207362 | etot = -187.561272095913 +359000 ekin = 17.2747418765998 | erot = 22.3862089851412 | epot = -228.089331840306 | etot = -188.428380978565 +360000 ekin = 17.2627985134611 | erot = 22.0449155343728 | epot = -227.380056681146 | etot = -188.072342633312 +361000 ekin = 16.7022908865183 | erot = 20.1648887982823 | epot = -226.685841413765 | etot = -189.818661728965 +362000 ekin = 16.5236886103148 | erot = 17.367003581832 | epot = -226.179176639549 | etot = -192.288484447402 +363000 ekin = 16.6039189858822 | erot = 16.0035347935122 | epot = -225.740790574137 | etot = -193.133336794742 +364000 ekin = 15.9788934900066 | erot = 16.6121483003756 | epot = -225.114863846841 | etot = -192.523822056459 +365000 ekin = 15.1431317526968 | erot = 16.9097471834361 | epot = -224.479846480109 | etot = -192.426967543976 +366000 ekin = 14.3990111988618 | erot = 17.0852361664414 | epot = -223.860574415737 | etot = -192.376327050434 +367000 ekin = 14.7093223353035 | erot = 19.9259917527912 | epot = -223.239871274407 | etot = -188.604557186313 +368000 ekin = 14.4767524017819 | erot = 19.8571324274854 | epot = -222.763305586433 | etot = -188.429420757165 +369000 ekin = 14.5295526109511 | erot = 19.4653517852366 | epot = -222.374285556898 | etot = -188.37938116071 +370000 ekin = 14.6624229936735 | erot = 18.4895700260451 | epot = -222.141224908878 | etot = -188.98923188916 +371000 ekin = 14.5457820238232 | erot = 17.1607101368225 | epot = -222.091600781158 | etot = -190.385108620512 +372000 ekin = 14.3765645142415 | erot = 18.3396365891572 | epot = -222.422609627797 | etot = -189.706408524398 +373000 ekin = 14.7873291899404 | erot = 18.9757135731518 | epot = -223.205572088605 | etot = -189.442529325513 +374000 ekin = 15.7125804964135 | erot = 21.4180777064736 | epot = -224.094929147205 | etot = -186.964270944318 +375000 ekin = 15.9971371168641 | erot = 19.8267795606279 | epot = -225.189250395173 | etot = -189.365333717681 +376000 ekin = 16.6671924038023 | erot = 19.2635449216383 | epot = -226.559332642176 | etot = -190.628595316735 +377000 ekin = 17.7603728345199 | erot = 18.779994279654 | epot = -227.963757986198 | etot = -191.423390872024 +378000 ekin = 18.1886050864902 | erot = 20.8441911699424 | epot = -229.547369091145 | etot = -190.514572834712 +379000 ekin = 19.033100220467 | erot = 20.072237741282 | epot = -231.143533498054 | etot = -192.038195536305 +380000 ekin = 19.3958875215032 | erot = 21.4029492342147 | epot = -232.694529537328 | etot = -191.89569278161 +381000 ekin = 19.9083965791013 | erot = 22.0262926736848 | epot = -234.32167171513 | etot = -192.386982462344 +382000 ekin = 20.8309151956209 | erot = 23.0680223560274 | epot = -235.663830319217 | etot = -191.764892767568 +383000 ekin = 21.2110564910967 | erot = 21.0693378226244 | epot = -236.854844845752 | etot = -194.574450532031 +384000 ekin = 22.0271729397392 | erot = 19.5738896898674 | epot = -237.761071028817 | etot = -196.16000839921 +385000 ekin = 21.9888232627756 | erot = 21.9438035828551 | epot = -238.480083243308 | etot = -194.547456397677 +386000 ekin = 22.1638739887246 | erot = 22.6209901962172 | epot = -238.997084576409 | etot = -194.212220391467 +387000 ekin = 22.4704802119025 | erot = 23.1635909564577 | epot = -239.498617670884 | etot = -193.864546502524 +388000 ekin = 22.8360688044956 | erot = 25.0873884717806 | epot = -239.669249619648 | etot = -191.745792343372 +389000 ekin = 23.0584509448569 | erot = 23.7837899729554 | epot = -239.601361166478 | etot = -192.759120248666 +390000 ekin = 23.6960202157352 | erot = 22.2855109641288 | epot = -239.380639976731 | etot = -193.399108796867 +391000 ekin = 23.7991151344636 | erot = 20.6201012177775 | epot = -239.03189252051 | etot = -194.612676168269 +392000 ekin = 23.9591701543348 | erot = 21.9552661146519 | epot = -238.459192052771 | etot = -192.544755783784 +393000 ekin = 23.9801600708864 | erot = 22.869736284692 | epot = -237.591953793527 | etot = -190.742057437948 +394000 ekin = 23.4806447315076 | erot = 23.7894518329385 | epot = -236.673823439361 | etot = -189.403726874915 +395000 ekin = 24.5044542002931 | erot = 22.3496968561238 | epot = -235.743236345989 | etot = -188.889085289572 +396000 ekin = 25.0523490436962 | erot = 21.8742064454878 | epot = -234.847289992152 | etot = -187.920734502968 +397000 ekin = 24.6499536596579 | erot = 21.7645397688862 | epot = -234.02267754065 | etot = -187.608184112106 +398000 ekin = 24.6654129500861 | erot = 22.1514966474267 | epot = -233.052972677734 | etot = -186.236063080221 +399000 ekin = 24.4527034646846 | erot = 22.1387556663723 | epot = -232.022437613541 | etot = -185.430978482484 +400000 ekin = 24.2410273375347 | erot = 20.3962614781508 | epot = -231.005809135405 | etot = -186.36852031972 +401000 ekin = 23.6761212056534 | erot = 22.7225603362526 | epot = -230.115763739954 | etot = -183.717082198048 +402000 ekin = 23.2783312945623 | erot = 21.072405109571 | epot = -229.330217542778 | etot = -184.979481138645 +403000 ekin = 23.3187858415702 | erot = 21.6853668727119 | epot = -228.46646899817 | etot = -183.462316283888 +404000 ekin = 22.6452628627526 | erot = 19.8334541701381 | epot = -227.74020593733 | etot = -185.261488904439 +405000 ekin = 22.8006471912822 | erot = 18.666718374297 | epot = -227.470604446323 | etot = -186.003238880744 +406000 ekin = 22.2794202436027 | erot = 18.3828666900747 | epot = -227.331354672565 | etot = -186.669067738888 +407000 ekin = 22.2172456768627 | erot = 18.4773392588829 | epot = -227.523003290546 | etot = -186.828418354801 +408000 ekin = 22.6521756504711 | erot = 19.4208076833358 | epot = -227.87233388974 | etot = -185.799350555933 +409000 ekin = 23.5573264374349 | erot = 20.5061505842945 | epot = -228.154858179183 | etot = -184.091381157454 +410000 ekin = 24.2750456328492 | erot = 22.8792635845596 | epot = -228.453698162395 | etot = -181.299388944986 +411000 ekin = 25.2420122816034 | erot = 23.7365200565699 | epot = -228.770700580075 | etot = -179.792168241901 +412000 ekin = 25.291356362185 | erot = 23.8310304102202 | epot = -229.010782171434 | etot = -179.888395399029 +413000 ekin = 25.2600396503997 | erot = 22.7169838925796 | epot = -229.062680900308 | etot = -181.085657357328 +414000 ekin = 25.4912045141821 | erot = 23.7306969786591 | epot = -228.998337849082 | etot = -179.77643635624 +415000 ekin = 26.1735887247197 | erot = 22.6674135061758 | epot = -228.693341533324 | etot = -179.852339302428 +416000 ekin = 26.5748108328611 | erot = 21.6439172230018 | epot = -228.361662386621 | etot = -180.142934330759 +417000 ekin = 26.7768070690628 | erot = 21.6230631516283 | epot = -228.087012878216 | etot = -179.687142657525 +418000 ekin = 26.5908575562701 | erot = 22.1239144254595 | epot = -227.62723288751 | etot = -178.912460905781 +419000 ekin = 26.1390688484464 | erot = 19.8809151124988 | epot = -226.977438068285 | etot = -180.95745410734 +420000 ekin = 25.5372021331576 | erot = 18.4693355705533 | epot = -226.169296116375 | etot = -182.162758412664 +421000 ekin = 24.7576070800854 | erot = 21.2379290063398 | epot = -225.177912035829 | etot = -179.182375949404 +422000 ekin = 23.5775097382875 | erot = 20.7150967321225 | epot = -224.071351753226 | etot = -179.778745282816 +423000 ekin = 23.3503211007386 | erot = 20.7766198719257 | epot = -222.934603836064 | etot = -178.807662863399 +424000 ekin = 22.9014106427363 | erot = 21.0323838208275 | epot = -221.865657024477 | etot = -177.931862560913 +425000 ekin = 22.167001043224 | erot = 19.8951057365931 | epot = -221.008759763888 | etot = -178.946652984071 +426000 ekin = 21.7191918731043 | erot = 20.0481315073592 | epot = -220.379164165788 | etot = -178.611840785324 +427000 ekin = 22.3863209159599 | erot = 20.1467365914768 | epot = -219.748771980514 | etot = -177.215714473077 +428000 ekin = 22.3113642728441 | erot = 18.9435836850322 | epot = -219.042454222864 | etot = -177.787506264988 +429000 ekin = 21.8292251452452 | erot = 16.620780664556 | epot = -218.481603976101 | etot = -180.0315981663 +430000 ekin = 21.5787512284699 | erot = 15.9396143193706 | epot = -217.957523577516 | etot = -180.439158029675 +431000 ekin = 21.5476976648958 | erot = 16.0853660094757 | epot = -217.637522182414 | etot = -180.004458508042 +432000 ekin = 20.8305046334209 | erot = 18.3962397210501 | epot = -217.510435589248 | etot = -178.283691234777 +433000 ekin = 21.3366166805747 | erot = 17.1761613375181 | epot = -217.730201210123 | etot = -179.21742319203 +434000 ekin = 21.4473991234971 | erot = 18.3914065237362 | epot = -218.31882890629 | etot = -178.480023259057 +435000 ekin = 21.8938565298032 | erot = 20.4321817028492 | epot = -219.08695235614 | etot = -176.760914123488 +436000 ekin = 22.7745161208294 | erot = 21.7909028890296 | epot = -220.039533912902 | etot = -175.474114903043 +437000 ekin = 23.0603914755853 | erot = 23.5766353307907 | epot = -221.014303297324 | etot = -174.377276490948 +438000 ekin = 24.5047158921013 | erot = 22.5082522761815 | epot = -221.830036253357 | etot = -174.817068085074 +439000 ekin = 24.6143280761287 | erot = 24.2611592034082 | epot = -222.681938930047 | etot = -173.80645165051 +440000 ekin = 24.3817582592681 | erot = 24.7408480502237 | epot = -223.513777238926 | etot = -174.391170929434 +441000 ekin = 24.7073799963697 | erot = 26.0715535157816 | epot = -224.270002709343 | etot = -173.491069197191 +442000 ekin = 24.5768549815013 | erot = 26.1754826601808 | epot = -224.850802162052 | etot = -174.09846452037 +443000 ekin = 25.2420932847023 | erot = 24.7427655137794 | epot = -225.167556551113 | etot = -175.182697752631 +444000 ekin = 25.9747330874369 | erot = 26.9622244259886 | epot = -225.24583879208 | etot = -172.308881278654 +445000 ekin = 26.1721310818258 | erot = 27.8161657482946 | epot = -225.021125061423 | etot = -171.032828231303 +446000 ekin = 26.2042305171885 | erot = 26.6449261740889 | epot = -224.735035228785 | etot = -171.885878537508 +447000 ekin = 25.9445128989677 | erot = 26.4816025199488 | epot = -224.245178179105 | etot = -171.819062760188 +448000 ekin = 25.5372900980307 | erot = 25.0281118333634 | epot = -223.618727357863 | etot = -173.053325426469 +449000 ekin = 25.7322219082413 | erot = 26.9973146922278 | epot = -223.018245220603 | etot = -170.288708620134 +450000 ekin = 25.8738458288472 | erot = 26.4843992391509 | epot = -222.408567465752 | etot = -170.050322397754 +451000 ekin = 25.6858259591492 | erot = 25.2647052575128 | epot = -221.452550893268 | etot = -170.502019676606 +452000 ekin = 25.7815007863341 | erot = 23.0466968711352 | epot = -220.49127053138 | etot = -171.66307287391 +453000 ekin = 25.7970445433776 | erot = 21.1141058412002 | epot = -219.594142395429 | etot = -172.682992010851 +454000 ekin = 25.688804966856 | erot = 22.6294586470315 | epot = -218.915377931307 | etot = -170.59711431742 +455000 ekin = 25.6037732271854 | erot = 22.9697679221883 | epot = -218.493679612878 | etot = -169.920138463504 +456000 ekin = 26.0514762135096 | erot = 23.8916333063363 | epot = -218.316686773003 | etot = -168.373577253157 +457000 ekin = 26.0167886371092 | erot = 22.9916268768507 | epot = -218.187169314675 | etot = -169.178753800715 +458000 ekin = 25.7882597661439 | erot = 20.8748032531609 | epot = -217.987058469246 | etot = -171.323995449942 +459000 ekin = 26.1697981408122 | erot = 21.3086466081266 | epot = -218.026696392449 | etot = -170.54825164351 +460000 ekin = 25.7192439412156 | erot = 24.4214622489547 | epot = -218.347831000891 | etot = -168.207124810721 +461000 ekin = 25.7495969095132 | erot = 26.1294994916656 | epot = -218.822266029574 | etot = -166.943169628395 +462000 ekin = 25.8591234001759 | erot = 26.9103950574254 | epot = -219.538074391763 | etot = -166.768555934162 +463000 ekin = 25.4934778644091 | erot = 28.9857339062074 | epot = -220.244381956634 | etot = -165.765170186017 +464000 ekin = 25.3807989297151 | erot = 28.2636863620641 | epot = -220.82311618793 | etot = -167.178630896151 +465000 ekin = 25.4889304853069 | erot = 26.8232193679972 | epot = -221.238335961676 | etot = -168.926186108372 +466000 ekin = 25.6703409883731 | erot = 25.2637813032743 | epot = -221.475634605288 | etot = -170.54151231364 +467000 ekin = 25.3302831697602 | erot = 24.6072222319647 | epot = -221.607373938226 | etot = -171.669868536501 +468000 ekin = 26.2089173332122 | erot = 22.9661948896766 | epot = -221.830072302435 | etot = -172.654960079546 +469000 ekin = 27.6643804489026 | erot = 22.7018029478283 | epot = -222.234721440326 | etot = -171.868538043595 +470000 ekin = 27.7860331432337 | erot = 23.37749342455 | epot = -222.896428711169 | etot = -171.732902143385 +471000 ekin = 28.3340963939428 | erot = 25.3278577360011 | epot = -223.570564232673 | etot = -169.908610102729 +472000 ekin = 28.5060434759036 | erot = 25.626902389105 | epot = -224.148650689462 | etot = -170.015704824453 +473000 ekin = 28.8298134833811 | erot = 26.1588503986598 | epot = -224.562065916091 | etot = -169.573402034051 +474000 ekin = 28.5479350336082 | erot = 25.8885076622197 | epot = -224.671302893341 | etot = -170.234860197513 +475000 ekin = 28.7950172155165 | erot = 25.1475376581866 | epot = -224.461514143169 | etot = -170.518959269466 +476000 ekin = 28.4606864434488 | erot = 25.2517480986696 | epot = -223.893621964986 | etot = -170.181187422868 +477000 ekin = 28.0142928872112 | erot = 23.5481845275566 | epot = -223.15087114256 | etot = -171.588393727793 +478000 ekin = 27.7552032877925 | erot = 21.0056990914093 | epot = -222.398351737606 | etot = -173.637449358404 +479000 ekin = 26.7537623197156 | erot = 22.040286739641 | epot = -221.556035536971 | etot = -172.761986477614 +480000 ekin = 26.3364213218961 | erot = 21.616270547523 | epot = -220.488389208344 | etot = -172.535697338924 +481000 ekin = 25.5733541062401 | erot = 20.6410322219284 | epot = -219.255993114652 | etot = -173.041606786483 +482000 ekin = 25.3038828266597 | erot = 21.7331282226314 | epot = -218.060917075251 | etot = -171.02390602596 +483000 ekin = 25.4847680481985 | erot = 21.8125494513952 | epot = -217.017386150345 | etot = -169.720068650751 +484000 ekin = 25.4921600059346 | erot = 22.7125552631874 | epot = -216.165477936407 | etot = -167.960762667285 +485000 ekin = 25.1014549873177 | erot = 22.9083083653785 | epot = -215.459368644848 | etot = -167.449605292152 +486000 ekin = 23.7381916279128 | erot = 22.0359551706864 | epot = -214.867401759866 | etot = -169.093254961267 +487000 ekin = 23.1022967247011 | erot = 20.9897368619166 | epot = -214.49309827136 | etot = -170.401064684743 +488000 ekin = 22.3280062343421 | erot = 22.6581977288416 | epot = -214.411928640685 | etot = -169.425724677501 +489000 ekin = 21.5200390992131 | erot = 24.4256444850011 | epot = -214.553046668213 | etot = -168.607363083998 +490000 ekin = 22.1745834778823 | erot = 23.202684442612 | epot = -214.682014948056 | etot = -169.304747027562 +491000 ekin = 22.2155647410761 | erot = 23.9559835315798 | epot = -214.794268468461 | etot = -168.622720195805 +492000 ekin = 21.9074062571785 | erot = 23.0107085417582 | epot = -214.876391213439 | etot = -169.958276414503 +493000 ekin = 21.7673907407181 | erot = 22.3862681939078 | epot = -215.110849414315 | etot = -170.957190479689 +494000 ekin = 20.7745584966346 | erot = 22.7452296264065 | epot = -215.46860879911 | etot = -171.948820676069 +495000 ekin = 19.7536125274935 | erot = 24.534405221311 | epot = -215.973479846197 | etot = -171.685462097392 +496000 ekin = 19.5440096583046 | erot = 23.1762967935367 | epot = -216.627509848901 | etot = -173.90720339706 +497000 ekin = 19.2601107947869 | erot = 27.0129650022824 | epot = -217.496309014045 | etot = -171.223233216976 +498000 ekin = 20.008240149509 | erot = 28.3938360735788 | epot = -218.510580772204 | etot = -170.108504549116 +499000 ekin = 20.2250869378451 | erot = 29.7495194421564 | epot = -219.413536230996 | etot = -169.438929850994 +500000 ekin = 20.5377041017314 | erot = 25.5981483203109 | epot = -220.10250670273 | etot = -173.966654280688 +501000 ekin = 20.7437007868733 | erot = 25.5722254074985 | epot = -220.706620920466 | etot = -174.390694726094 +502000 ekin = 21.3974117388996 | erot = 27.1477040916275 | epot = -221.203987796437 | etot = -172.65887196591 +503000 ekin = 21.9720670171586 | erot = 27.4594748055059 | epot = -221.564705185604 | etot = -172.13316336294 +504000 ekin = 22.0036398241597 | erot = 27.8844566679454 | epot = -221.822730635735 | etot = -171.934634143629 +505000 ekin = 23.1885968423919 | erot = 27.0080739021865 | epot = -222.35778688837 | etot = -172.161116143791 +506000 ekin = 22.722531651873 | erot = 26.6500914123035 | epot = -222.671998920708 | etot = -173.299375856532 +507000 ekin = 22.2628604257524 | erot = 25.1165297319669 | epot = -223.132828338462 | etot = -175.753438180742 +508000 ekin = 22.7028911519561 | erot = 23.4656498814886 | epot = -223.54407467575 | etot = -177.375533642305 +509000 ekin = 22.6654713026151 | erot = 22.3116431994452 | epot = -223.812280936561 | etot = -178.8351664345 +510000 ekin = 23.2444036217202 | erot = 23.7118265646526 | epot = -224.123509542875 | etot = -177.167279356502 +511000 ekin = 22.7352979426128 | erot = 23.8711299722302 | epot = -224.367646933689 | etot = -177.761219018846 +512000 ekin = 22.460433299215 | erot = 25.9025431935021 | epot = -224.625156824351 | etot = -176.262180331634 +513000 ekin = 22.0947651201679 | erot = 24.9904521975554 | epot = -224.816807649759 | etot = -177.731590332036 +514000 ekin = 21.783961391663 | erot = 27.6768125066713 | epot = -224.803176634329 | etot = -175.342402735995 +515000 ekin = 20.8838805084714 | erot = 26.7006493321653 | epot = -224.615071561818 | etot = -177.030541721182 +516000 ekin = 21.4036026624667 | erot = 29.9826472115484 | epot = -224.43203188109 | etot = -173.045782007075 +517000 ekin = 21.0725470625647 | erot = 29.5449947930599 | epot = -224.413593337603 | etot = -173.796051481978 +518000 ekin = 21.1692298808073 | erot = 27.273466345669 | epot = -224.467250578245 | etot = -176.024554351769 +519000 ekin = 21.5445051781035 | erot = 27.4144674038741 | epot = -224.856924566818 | etot = -175.89795198484 +520000 ekin = 21.8088279707338 | erot = 26.9958167714558 | epot = -225.458073506627 | etot = -176.653428764437 +521000 ekin = 21.3359848054427 | erot = 27.3496112855869 | epot = -226.263472854907 | etot = -177.577876763878 +522000 ekin = 21.383381595961 | erot = 28.5594995391198 | epot = -227.177929279517 | etot = -177.235048144436 +523000 ekin = 22.3312177264689 | erot = 28.7548602321851 | epot = -228.039253797182 | etot = -176.953175838528 +524000 ekin = 22.876818128058 | erot = 30.8759050315318 | epot = -228.592215099028 | etot = -174.839491939438 +525000 ekin = 23.6968405729144 | erot = 30.6366736796914 | epot = -229.121694343188 | etot = -174.788180090583 +526000 ekin = 24.0470079695023 | erot = 27.5141010669624 | epot = -229.424175891327 | etot = -177.863066854862 +527000 ekin = 24.7652559941686 | erot = 24.0459690561378 | epot = -229.423371401068 | etot = -180.612146350762 +528000 ekin = 25.8850187683723 | erot = 21.6623200862783 | epot = -229.307228706866 | etot = -181.759889852215 +529000 ekin = 27.0463610704001 | erot = 22.1786800201847 | epot = -229.038404872887 | etot = -179.813363782302 +530000 ekin = 27.7753267980006 | erot = 21.352696690415 | epot = -228.849367136447 | etot = -179.721343648031 +531000 ekin = 27.8126912344675 | erot = 20.3285370027924 | epot = -228.550501942543 | etot = -180.409273705283 +532000 ekin = 28.6172804460881 | erot = 18.3427969924976 | epot = -228.423163122221 | etot = -181.463085683636 +533000 ekin = 28.2068049753172 | erot = 18.2536479974195 | epot = -228.612314526597 | etot = -182.151861553861 +534000 ekin = 28.4495519996443 | erot = 18.0012277086546 | epot = -228.943853455769 | etot = -182.49307374747 +535000 ekin = 28.9497940969891 | erot = 16.8492155357581 | epot = -229.741275998853 | etot = -183.942266366106 +536000 ekin = 28.5652244837817 | erot = 17.3435379345182 | epot = -230.83687671424 | etot = -184.92811429594 +537000 ekin = 29.022362828562 | erot = 17.9527916225231 | epot = -231.95803351984 | etot = -184.982879068755 +538000 ekin = 29.8174105606222 | erot = 16.0379790395698 | epot = -232.791699361863 | etot = -186.936309761671 +539000 ekin = 29.6952792444876 | erot = 17.4273307073527 | epot = -233.496059263026 | etot = -186.373449311186 +540000 ekin = 29.750585937819 | erot = 20.0144365059585 | epot = -234.056270399686 | etot = -184.291247955909 +541000 ekin = 29.368313343467 | erot = 19.579576821786 | epot = -234.349077090936 | etot = -185.401186925683 +542000 ekin = 28.4447550384428 | erot = 19.7945093762075 | epot = -234.236435613877 | etot = -185.997171199227 +543000 ekin = 27.7587268728516 | erot = 21.2328503430547 | epot = -233.528121996461 | etot = -184.536544780555 +544000 ekin = 28.3225695671127 | erot = 17.802768152032 | epot = -232.50551567328 | etot = -186.380177954136 +545000 ekin = 28.0998287685114 | erot = 19.6585770476894 | epot = -231.387898079567 | etot = -183.629492263366 +546000 ekin = 27.3903651306005 | erot = 21.807934581675 | epot = -230.479365576106 | etot = -181.281065863831 +547000 ekin = 26.7970978237519 | erot = 20.9996558932496 | epot = -229.684797062509 | etot = -181.888043345508 +548000 ekin = 26.7983027373764 | erot = 20.8421351684446 | epot = -228.90155588475 | etot = -181.261117978929 +549000 ekin = 26.188169756037 | erot = 21.0585848868904 | epot = -228.206493092338 | etot = -180.95973844941 +550000 ekin = 26.0140312453881 | erot = 22.5801677208772 | epot = -227.777402823687 | etot = -179.183203857422 +551000 ekin = 25.7757664599119 | erot = 23.9110391567262 | epot = -227.517272594077 | etot = -177.830466977439 +552000 ekin = 25.8315344617212 | erot = 23.7338223198244 | epot = -227.474934810832 | etot = -177.909578029286 +553000 ekin = 25.6747033622136 | erot = 22.7253607563637 | epot = -227.635537487589 | etot = -179.235473369012 +554000 ekin = 25.6047324774861 | erot = 22.6670330249201 | epot = -227.987099764937 | etot = -179.715334262531 +555000 ekin = 26.5879549294076 | erot = 24.0685342421982 | epot = -228.529950924382 | etot = -177.873461752776 +556000 ekin = 27.6268706515679 | erot = 22.1109312637994 | epot = -229.425954027825 | etot = -179.688152112458 +557000 ekin = 28.069112907845 | erot = 26.8965683539211 | epot = -230.584971459936 | etot = -175.61929019817 +558000 ekin = 28.0678083112931 | erot = 25.6618030440032 | epot = -231.991530613965 | etot = -178.261919258669 +559000 ekin = 28.9742033607634 | erot = 26.5724591704157 | epot = -233.463994495035 | etot = -177.917331963856 +560000 ekin = 28.9011051536108 | erot = 25.5889025184335 | epot = -234.725653093072 | etot = -180.235645421027 +561000 ekin = 29.4002126238622 | erot = 26.2954345341183 | epot = -235.835285786746 | etot = -180.139638628766 +562000 ekin = 29.975757760105 | erot = 24.4408981516764 | epot = -236.463195408104 | etot = -182.046539496323 +563000 ekin = 29.7752306165208 | erot = 27.2106096805276 | epot = -236.685322677156 | etot = -179.699482380108 +564000 ekin = 29.8813809383381 | erot = 26.6216283857818 | epot = -236.661076407545 | etot = -180.158067083425 +565000 ekin = 29.6774879892468 | erot = 27.2290939876273 | epot = -236.311809225071 | etot = -179.405227248197 +566000 ekin = 28.6346936939147 | erot = 26.8023560052638 | epot = -235.668742898058 | etot = -180.23169319888 +567000 ekin = 27.3954299875009 | erot = 26.5201802334772 | epot = -234.779541480291 | etot = -180.863931259313 +568000 ekin = 27.4071194817491 | erot = 25.1324696708474 | epot = -233.501854955991 | etot = -180.962265803394 +569000 ekin = 26.6231867984125 | erot = 24.6541363875885 | epot = -232.187184366121 | etot = -180.90986118012 +570000 ekin = 27.6093553036065 | erot = 23.6900717393427 | epot = -230.809430752191 | etot = -179.510003709242 +571000 ekin = 26.9083310567801 | erot = 22.528408139646 | epot = -229.566553491015 | etot = -180.129814294588 +572000 ekin = 26.4716627800808 | erot = 22.2845965716381 | epot = -228.619137213519 | etot = -179.8628778618 +573000 ekin = 26.6971389887138 | erot = 21.8798558769198 | epot = -228.034982255581 | etot = -179.457987389947 +574000 ekin = 27.2478685862593 | erot = 21.7451315224891 | epot = -227.459773842304 | etot = -178.466773733556 +575000 ekin = 28.7134212605173 | erot = 21.3522952166471 | epot = -226.994685152085 | etot = -176.928968674921 +576000 ekin = 28.5222344692551 | erot = 18.8986377279701 | epot = -226.85884558054 | etot = -179.437973383315 +577000 ekin = 29.1715076179565 | erot = 20.1101522026671 | epot = -226.880557883166 | etot = -177.598898062543 +578000 ekin = 29.1958211105308 | erot = 20.240027120463 | epot = -226.916258035043 | etot = -177.480409804049 +579000 ekin = 28.7985703505952 | erot = 18.3977325249373 | epot = -226.88304615327 | etot = -179.686743277737 +580000 ekin = 28.4440078780217 | erot = 18.4595801944313 | epot = -226.943317478502 | etot = -180.039729406048 +581000 ekin = 29.6191385878667 | erot = 18.2815372928574 | epot = -227.074832318056 | etot = -179.174156437332 +582000 ekin = 28.8755366565893 | erot = 17.8411251075596 | epot = -227.166122160148 | etot = -180.449460395999 +583000 ekin = 28.6195101128279 | erot = 17.8287187393535 | epot = -227.132715220626 | etot = -180.684486368445 +584000 ekin = 28.2523600687915 | erot = 17.6307832024022 | epot = -227.251691559433 | etot = -181.368548288239 +585000 ekin = 27.5957630773252 | erot = 17.8252193046033 | epot = -227.442847627708 | etot = -182.021865245779 +586000 ekin = 27.7899511430164 | erot = 18.5604184072932 | epot = -227.520178862255 | etot = -181.169809311945 +587000 ekin = 27.3277470399822 | erot = 19.4404091802981 | epot = -227.404442611801 | etot = -180.636286391521 +588000 ekin = 27.3638216941813 | erot = 20.0988247739979 | epot = -227.0932868642 | etot = -179.630640396021 +589000 ekin = 26.9522108357383 | erot = 19.0940445155609 | epot = -226.797323932239 | etot = -180.751068580939 +590000 ekin = 27.0814604422477 | erot = 18.9210809272503 | epot = -226.462739616754 | etot = -180.460198247256 +591000 ekin = 26.6304741560081 | erot = 19.7073249259863 | epot = -226.366593304564 | etot = -180.02879422257 +592000 ekin = 26.6793460171722 | erot = 22.0507306271919 | epot = -226.36463028426 | etot = -177.634553639896 +593000 ekin = 26.4435671908487 | erot = 22.0663123802426 | epot = -226.444524918504 | etot = -177.934645347413 +594000 ekin = 26.051479512619 | erot = 21.4158049135016 | epot = -226.573432513486 | etot = -179.106148087365 +595000 ekin = 25.6800098048177 | erot = 21.489745642643 | epot = -226.861484159439 | etot = -179.691728711979 +596000 ekin = 25.4982303265013 | erot = 22.0961692232522 | epot = -227.19375202979 | etot = -179.599352480036 +597000 ekin = 24.4179219809124 | erot = 21.221622910841 | epot = -227.371569607757 | etot = -181.732024716003 +598000 ekin = 24.2598938247207 | erot = 23.7729295468385 | epot = -227.36641699774 | etot = -179.333593626181 +599000 ekin = 24.2026897211424 | erot = 23.7935607586132 | epot = -227.120360675563 | etot = -179.124110195808 +600000 ekin = 24.6901303608034 | erot = 22.0458619441968 | epot = -226.63280531999 | etot = -179.89681301499 +601000 ekin = 24.7093667383309 | erot = 23.9592983403602 | epot = -225.919718139048 | etot = -177.251053060357 +602000 ekin = 24.9977163593162 | erot = 21.6808979179701 | epot = -225.225550361662 | etot = -178.546936084376 +603000 ekin = 24.909080272873 | erot = 19.8567647026369 | epot = -224.510932501025 | etot = -179.745087525515 +604000 ekin = 25.7672016321128 | erot = 20.1058382913628 | epot = -223.859317715152 | etot = -177.986277791676 +605000 ekin = 26.2854405598537 | erot = 18.6086042172451 | epot = -223.341754324839 | etot = -178.44770954774 +606000 ekin = 26.8878269017605 | erot = 16.8626720456841 | epot = -223.037062471522 | etot = -179.286563524077 +607000 ekin = 27.708630558942 | erot = 16.2639676386698 | epot = -222.903954806076 | etot = -178.931356608464 +608000 ekin = 27.5722592645523 | erot = 16.050800679878 | epot = -222.655822923886 | etot = -179.032762979456 +609000 ekin = 27.3059305453791 | erot = 16.2526674395162 | epot = -222.499289767144 | etot = -178.940691782249 +610000 ekin = 26.0529834115964 | erot = 17.5407293679719 | epot = -222.559467243073 | etot = -178.965754463504 +611000 ekin = 25.6444622853818 | erot = 17.5578356444653 | epot = -222.540154641407 | etot = -179.33785671156 +612000 ekin = 26.1044768868262 | erot = 16.7678551448027 | epot = -222.589366667697 | etot = -179.717034636068 +613000 ekin = 26.778105103681 | erot = 17.5411817669898 | epot = -222.737319173291 | etot = -178.418032302621 +614000 ekin = 27.6064782364792 | erot = 16.8092616077952 | epot = -222.738962051088 | etot = -178.323222206813 +615000 ekin = 27.202348500151 | erot = 18.1300982120248 | epot = -222.580596496295 | etot = -177.248149784119 +616000 ekin = 26.7294242583747 | erot = 17.8023339715893 | epot = -222.270889821123 | etot = -177.739131591159 +617000 ekin = 25.9673127266019 | erot = 19.4938436622423 | epot = -221.855677631762 | etot = -176.394521242918 +618000 ekin = 24.6649274148857 | erot = 19.7556140429642 | epot = -221.395419093589 | etot = -176.974877635739 +619000 ekin = 23.8246156062723 | erot = 22.6932905362597 | epot = -220.85765285395 | etot = -174.339746711418 +620000 ekin = 22.3922506676526 | erot = 23.1856908985781 | epot = -220.581162841993 | etot = -175.003221275762 +621000 ekin = 21.4430140463455 | erot = 20.0877017400879 | epot = -220.316250852764 | etot = -178.785535066331 +622000 ekin = 21.0282015425459 | erot = 21.2952952107454 | epot = -220.469702077462 | etot = -178.146205324171 +623000 ekin = 20.5485493901374 | erot = 21.9686222594177 | epot = -220.884709147042 | etot = -178.367537497487 +624000 ekin = 20.4116762130833 | erot = 24.4448345310671 | epot = -221.506951111473 | etot = -176.650440367323 +625000 ekin = 20.7086024723278 | erot = 24.9980231142946 | epot = -222.442357834988 | etot = -176.735732248366 +626000 ekin = 21.41397100679 | erot = 25.3578069120284 | epot = -223.283385353664 | etot = -176.511607434846 +627000 ekin = 21.8080912412149 | erot = 22.9275444026493 | epot = -223.892792640231 | etot = -179.157156996367 +628000 ekin = 22.0606300305555 | erot = 21.9874550553957 | epot = -224.361440644786 | etot = -180.313355558834 +629000 ekin = 22.2686585302 | erot = 23.3956059048975 | epot = -224.755334667347 | etot = -179.091070232249 +630000 ekin = 22.7261581540143 | erot = 23.599198071745 | epot = -224.949694798805 | etot = -178.624338573046 +631000 ekin = 22.7545989614576 | erot = 18.6693303881336 | epot = -225.170398987567 | etot = -183.746469637976 +632000 ekin = 22.8582899163666 | erot = 18.8600074747406 | epot = -225.453249516017 | etot = -183.734952124909 +633000 ekin = 22.5940364544595 | erot = 19.5865726816331 | epot = -225.675890763231 | etot = -183.495281627138 +634000 ekin = 21.7360344990529 | erot = 21.1386827787326 | epot = -225.807787978514 | etot = -182.933070700728 +635000 ekin = 22.3638048171573 | erot = 20.8651345753279 | epot = -226.017654598281 | etot = -182.788715205795 +636000 ekin = 23.2564468915411 | erot = 20.9568292454768 | epot = -226.474810466865 | etot = -182.261534329847 +637000 ekin = 23.7446282139124 | erot = 20.9649035011187 | epot = -227.255190257715 | etot = -182.545658542684 +638000 ekin = 24.9768211335302 | erot = 20.7684051797868 | epot = -228.339137670731 | etot = -182.593911357414 +639000 ekin = 25.6081152991627 | erot = 20.5394040856467 | epot = -229.535959313578 | etot = -183.388439928768 +640000 ekin = 25.882879312268 | erot = 21.5458521538092 | epot = -230.501601623652 | etot = -183.072870157574 +641000 ekin = 26.7192719153612 | erot = 21.5077808734751 | epot = -231.311086176637 | etot = -183.084033387801 +642000 ekin = 26.7533018509874 | erot = 22.3868483570804 | epot = -231.697126060187 | etot = -182.556975852119 +643000 ekin = 27.227638812425 | erot = 22.7444906941992 | epot = -231.70041423596 | etot = -181.728284729336 +644000 ekin = 28.2340179730461 | erot = 21.2142453447777 | epot = -231.34574674841 | etot = -181.897483430587 +645000 ekin = 27.9813501134116 | erot = 19.5632665182491 | epot = -230.723712640252 | etot = -183.179096008591 +646000 ekin = 27.3510433641092 | erot = 20.3180919491713 | epot = -229.805725426514 | etot = -182.136590113233 +647000 ekin = 27.4763651215188 | erot = 20.1973565201653 | epot = -228.883194713424 | etot = -181.20947307174 +648000 ekin = 26.9203103910451 | erot = 19.3299558126679 | epot = -228.183094649897 | etot = -181.932828446184 +649000 ekin = 27.1584207863441 | erot = 19.7773817590138 | epot = -227.851865720852 | etot = -180.916063175494 +650000 ekin = 27.8558677817717 | erot = 21.5235280981856 | epot = -227.854497907235 | etot = -178.475102027277 +651000 ekin = 27.4752369028502 | erot = 22.4969948370604 | epot = -228.056030460106 | etot = -178.083798720195 +652000 ekin = 27.8926782089265 | erot = 20.2366908977832 | epot = -228.25658268699 | etot = -180.12721358028 +653000 ekin = 27.833217461393 | erot = 22.8857793598376 | epot = -228.476748982019 | etot = -177.757752160788 +654000 ekin = 28.0840949255035 | erot = 20.7706125191501 | epot = -228.683833272169 | etot = -179.829125827515 +655000 ekin = 27.403762673065 | erot = 22.3510763116526 | epot = -229.021084688067 | etot = -179.266245703349 +656000 ekin = 28.3726446615757 | erot = 22.7742600500831 | epot = -229.347089574997 | etot = -178.200184863339 +657000 ekin = 27.7030235167448 | erot = 21.8629223338815 | epot = -229.434356479491 | etot = -179.868410628864 +658000 ekin = 27.1759488980294 | erot = 23.4533512480567 | epot = -229.408283419532 | etot = -178.778983273446 +659000 ekin = 27.1576709282284 | erot = 21.6330760247461 | epot = -229.142943895062 | etot = -180.352196942087 +660000 ekin = 26.3221730814178 | erot = 21.7821345770448 | epot = -228.723364173055 | etot = -180.619056514592 +661000 ekin = 25.779491442224 | erot = 22.2970031395793 | epot = -228.256343213546 | etot = -180.179848631742 +662000 ekin = 25.2646841713566 | erot = 21.3867459046999 | epot = -227.695753928069 | etot = -181.044323852012 +663000 ekin = 25.788599860439 | erot = 22.1358077324136 | epot = -227.095496572601 | etot = -179.171088979748 +664000 ekin = 25.6902100255482 | erot = 21.1754933170497 | epot = -226.605702908437 | etot = -179.739999565839 +665000 ekin = 25.8071177593121 | erot = 20.2980512970803 | epot = -226.316135130784 | etot = -180.210966074392 +666000 ekin = 25.654039027879 | erot = 19.3527959955109 | epot = -226.278718912648 | etot = -181.271883889258 +667000 ekin = 25.259919176648 | erot = 21.3448305524703 | epot = -226.010298820921 | etot = -179.405549091803 +668000 ekin = 24.899938000725 | erot = 20.4509835382855 | epot = -225.592827118275 | etot = -180.241905579265 +669000 ekin = 24.445106638769 | erot = 20.2026559802712 | epot = -225.189465074759 | etot = -180.541702455719 +670000 ekin = 23.6375178330896 | erot = 21.4368740508129 | epot = -224.732122186456 | etot = -179.657730302553 +671000 ekin = 23.6282860496992 | erot = 21.7094329321311 | epot = -224.008580994932 | etot = -178.670862013101 +672000 ekin = 24.0984504997224 | erot = 21.9403750101964 | epot = -223.13895872841 | etot = -177.100133218492 +673000 ekin = 23.7973496489823 | erot = 20.9987265259934 | epot = -222.393285441872 | etot = -177.597209266896 +674000 ekin = 23.7065530280889 | erot = 22.376642799205 | epot = -221.700044416557 | etot = -175.616848589263 +675000 ekin = 23.001776123468 | erot = 23.6694964963629 | epot = -221.420479977735 | etot = -174.749207357904 +676000 ekin = 22.5164066205241 | erot = 22.6402910589994 | epot = -221.322788427074 | etot = -176.16609074755 +677000 ekin = 22.5497630953929 | erot = 23.1877936778892 | epot = -221.402074795503 | etot = -175.664518022221 +678000 ekin = 21.5585311333769 | erot = 22.8702436982297 | epot = -221.697973670764 | etot = -177.269198839157 +679000 ekin = 21.4618959055948 | erot = 23.3865040507615 | epot = -222.015748334195 | etot = -177.167348377838 +680000 ekin = 21.4622800320567 | erot = 21.4127199547269 | epot = -222.429797710664 | etot = -179.55479772388 +681000 ekin = 21.1737975880679 | erot = 21.5846131769088 | epot = -222.953468011023 | etot = -180.195057246046 +682000 ekin = 21.7254656898551 | erot = 21.6540443362751 | epot = -223.45869005669 | etot = -180.07918003056 +683000 ekin = 21.4183563237426 | erot = 23.8796952031651 | epot = -224.031962106781 | etot = -178.733910579873 +684000 ekin = 22.2181785671375 | erot = 26.4163907692242 | epot = -224.556597387323 | etot = -175.922028050961 +685000 ekin = 22.4057534349632 | erot = 26.3514235333686 | epot = -224.764117789834 | etot = -176.006940821502 +686000 ekin = 21.9879963383394 | erot = 25.5983588287999 | epot = -224.837162072601 | etot = -177.250806905461 +687000 ekin = 21.7554417881072 | erot = 27.0115877106503 | epot = -224.825418203926 | etot = -176.058388705169 +688000 ekin = 21.8197561062317 | erot = 25.0081437700991 | epot = -224.863055701397 | etot = -178.035155825067 +689000 ekin = 21.5892200304501 | erot = 29.2491439251534 | epot = -224.907328455093 | etot = -174.068964499489 +690000 ekin = 21.8426769308178 | erot = 27.2293005592937 | epot = -224.943981990783 | etot = -175.872004500672 +691000 ekin = 22.1363752207295 | erot = 25.7931707752218 | epot = -224.746736914525 | etot = -176.817190918574 +692000 ekin = 22.5352297800636 | erot = 25.3446974399755 | epot = -224.434434618052 | etot = -176.554507398013 +693000 ekin = 22.8091228929751 | erot = 26.4872450844796 | epot = -224.047374463991 | etot = -174.751006486536 +694000 ekin = 22.4873583888692 | erot = 25.6513676536721 | epot = -223.737465620132 | etot = -175.598739577591 +695000 ekin = 23.1242633624005 | erot = 21.5570288691547 | epot = -223.550411341546 | etot = -178.869119109991 +696000 ekin = 24.0628961042017 | erot = 18.7702329767746 | epot = -223.663714460872 | etot = -180.830585379896 +697000 ekin = 24.4595165378671 | erot = 16.374437330644 | epot = -224.303732218758 | etot = -183.469778350247 +698000 ekin = 25.8305878390951 | erot = 15.1686612882172 | epot = -225.420465790738 | etot = -184.421216663426 +699000 ekin = 26.583760876588 | erot = 16.914220924162 | epot = -227.004086871952 | etot = -183.506105071201 +700000 ekin = 27.5797608451701 | erot = 19.1004834812402 | epot = -228.733304055557 | etot = -182.053059729146 +701000 ekin = 28.092598661006 | erot = 19.107193423995 | epot = -230.4398691701 | etot = -183.240077085099 +702000 ekin = 28.038659655595 | erot = 20.8470907300003 | epot = -231.921720460127 | etot = -183.035970074532 +703000 ekin = 28.1176122670283 | erot = 20.4831386988919 | epot = -233.089326607717 | etot = -184.488575641797 +704000 ekin = 28.6795532382639 | erot = 21.9842156401384 | epot = -233.886659285723 | etot = -183.222890407321 +705000 ekin = 28.4117756447571 | erot = 25.4648529190999 | epot = -234.312539385659 | etot = -180.435910821802 +706000 ekin = 27.4926471672545 | erot = 26.570396574273 | epot = -234.463545747886 | etot = -180.400502006358 +707000 ekin = 26.4290449605895 | erot = 29.8098318595607 | epot = -234.288422874891 | etot = -178.049546054741 +708000 ekin = 26.785682949808 | erot = 26.5168034780305 | epot = -233.599155373867 | etot = -180.296668946029 +709000 ekin = 26.1152543232575 | erot = 25.8699376167037 | epot = -232.62906889387 | etot = -180.643876953909 +710000 ekin = 25.640992098621 | erot = 24.9444607038658 | epot = -231.31659516414 | etot = -180.731142361653 +711000 ekin = 24.8084490562813 | erot = 22.41486490139 | epot = -230.188845489325 | etot = -182.965531531653 +712000 ekin = 24.0206122957558 | erot = 23.3639832553073 | epot = -229.544707677943 | etot = -182.16011212688 +713000 ekin = 23.3232426911543 | erot = 23.9964282538794 | epot = -229.263722517708 | etot = -181.944051572675 +714000 ekin = 23.3805726450359 | erot = 23.0699795298048 | epot = -229.169110187163 | etot = -182.718558012323 +715000 ekin = 22.6342143618995 | erot = 23.6996306944786 | epot = -229.323793869064 | etot = -182.989948812685 +716000 ekin = 22.7503175950267 | erot = 24.6103793866802 | epot = -229.738719755983 | etot = -182.378022774277 +717000 ekin = 22.7487828419965 | erot = 23.3120643428286 | epot = -230.199311355603 | etot = -184.138464170778 +718000 ekin = 23.7440282855966 | erot = 21.6662565298252 | epot = -230.594844861738 | etot = -185.184560046316 +719000 ekin = 23.0053134398269 | erot = 21.1345728705727 | epot = -230.919025277455 | etot = -186.779138967055 +720000 ekin = 22.7927824705925 | erot = 18.6486137418451 | epot = -231.312571080127 | etot = -189.871174867689 +721000 ekin = 22.9406443866908 | erot = 19.8512244181128 | epot = -231.525388298161 | etot = -188.733519493358 +722000 ekin = 22.6168297832631 | erot = 19.1089757310031 | epot = -231.486078548655 | etot = -189.760273034388 +723000 ekin = 23.2145903286558 | erot = 18.4327411531208 | epot = -231.073654493071 | etot = -189.426323011295 +724000 ekin = 23.1941486606142 | erot = 20.1152704224142 | epot = -230.393344877734 | etot = -187.083925794705 +725000 ekin = 23.2117542270878 | erot = 20.0416524857156 | epot = -229.681975652754 | etot = -186.428568939951 +726000 ekin = 22.4943249505552 | erot = 17.6255689470432 | epot = -229.018602806407 | etot = -188.898708908808 +727000 ekin = 23.0134120388946 | erot = 16.0733087173804 | epot = -228.449610641761 | etot = -189.362889885486 +728000 ekin = 23.6002606897018 | erot = 17.3538640496192 | epot = -227.894896906635 | etot = -186.940772167314 +729000 ekin = 23.2666739347333 | erot = 15.9737775925554 | epot = -227.639499131122 | etot = -188.399047603833 +730000 ekin = 23.6369012496368 | erot = 15.0574600338378 | epot = -227.615876852929 | etot = -188.921515569454 +731000 ekin = 24.2843158588705 | erot = 14.7532999805969 | epot = -227.863610813074 | etot = -188.825994973606 +732000 ekin = 24.5920563697733 | erot = 15.441921529354 | epot = -228.208536089551 | etot = -188.174558190424 +733000 ekin = 24.9542143587772 | erot = 16.2528554884185 | epot = -228.886245906842 | etot = -187.679176059646 +734000 ekin = 25.1975745295967 | erot = 17.5309997011736 | epot = -229.874798122519 | etot = -187.146223891749 +735000 ekin = 26.3384002839214 | erot = 20.2147377764707 | epot = -231.034141807835 | etot = -184.481003747443 +736000 ekin = 26.9977201223223 | erot = 21.4312348250696 | epot = -232.517347753316 | etot = -184.088392805924 +737000 ekin = 27.106843703555 | erot = 21.9213211360194 | epot = -233.962863053087 | etot = -184.934698213512 +738000 ekin = 27.0817280355982 | erot = 23.1086627439609 | epot = -235.308416470173 | etot = -185.118025690614 +739000 ekin = 27.7017346367214 | erot = 23.0670600140734 | epot = -236.434348689915 | etot = -185.66555403912 +740000 ekin = 27.414483533319 | erot = 22.8495946003411 | epot = -237.159045352128 | etot = -186.894967218468 +741000 ekin = 27.1254940524986 | erot = 25.2136677791409 | epot = -237.27567454816 | etot = -184.936512716521 +742000 ekin = 26.1007467617893 | erot = 24.3083714669445 | epot = -237.110037846066 | etot = -186.700919617333 +743000 ekin = 25.9661191503059 | erot = 24.9966890539635 | epot = -236.568563108752 | etot = -185.605754904482 +744000 ekin = 25.9610162148347 | erot = 24.0267364726876 | epot = -235.718093082982 | etot = -185.73034039546 +745000 ekin = 25.1903410925453 | erot = 20.0322158938195 | epot = -234.647323333736 | etot = -189.424766347371 +746000 ekin = 24.5549018272587 | erot = 19.5333934287955 | epot = -233.457073304408 | etot = -189.368778048353 +747000 ekin = 24.6969973760579 | erot = 19.684765269497 | epot = -232.388047096093 | etot = -188.006284450538 +748000 ekin = 23.8661147826955 | erot = 18.7566250549712 | epot = -231.325158225068 | etot = -188.702418387402 +749000 ekin = 22.8905662925953 | erot = 17.616297562066 | epot = -230.516546812681 | etot = -190.009682958019 +750000 ekin = 21.7762308247725 | erot = 18.808565539541 | epot = -229.678177029533 | etot = -189.09338066522 +751000 ekin = 21.470435101573 | erot = 19.3561756327847 | epot = -229.009265480618 | etot = -188.18265474626 +752000 ekin = 21.9146908855108 | erot = 21.6932584373869 | epot = -228.339869446873 | etot = -184.731920123975 +753000 ekin = 21.3126722507014 | erot = 19.4830994613168 | epot = -227.826644686117 | etot = -187.030872974099 +754000 ekin = 21.9973420006405 | erot = 18.3087877257647 | epot = -227.734582363023 | etot = -187.428452636618 +755000 ekin = 22.0630883354931 | erot = 17.7232559029141 | epot = -227.901903373361 | etot = -188.115559134954 +756000 ekin = 22.7885108553802 | erot = 18.9466234012732 | epot = -228.388591706589 | etot = -186.653457449935 +757000 ekin = 23.4273630235623 | erot = 19.3375649643952 | epot = -229.062755020945 | etot = -186.297827032987 +758000 ekin = 23.957213137725 | erot = 17.6511752357222 | epot = -229.883345819876 | etot = -188.274957446429 +759000 ekin = 24.8000463898566 | erot = 19.7556788733861 | epot = -230.860841170257 | etot = -186.305115907015 +760000 ekin = 24.3481865433343 | erot = 19.5845017015682 | epot = -231.819085479179 | etot = -187.886397234276 +761000 ekin = 24.7383964493482 | erot = 19.7052128432058 | epot = -232.446954772443 | etot = -188.003345479889 +762000 ekin = 24.7648359199342 | erot = 19.1678127120839 | epot = -232.719408348113 | etot = -188.786759716095 +763000 ekin = 24.6386313272633 | erot = 20.2072282597132 | epot = -232.892027596087 | etot = -188.046168009111 +764000 ekin = 24.535646123958 | erot = 22.5770425253206 | epot = -232.923754633562 | etot = -185.811065984283 +765000 ekin = 23.5513975921745 | erot = 23.8339377954301 | epot = -232.76312879921 | etot = -185.377793411606 +766000 ekin = 23.3033290453631 | erot = 23.9531600538532 | epot = -232.376570600668 | etot = -185.120081501452 +767000 ekin = 23.3690671647366 | erot = 21.8572954539486 | epot = -231.660452995211 | etot = -186.434090376525 +768000 ekin = 23.2846487005283 | erot = 21.3431585578876 | epot = -230.788764884581 | etot = -186.160957626165 +769000 ekin = 22.639077883555 | erot = 22.2121122667711 | epot = -230.121718934275 | etot = -185.270528783949 +770000 ekin = 22.9570384866444 | erot = 20.3561307423381 | epot = -229.677968740405 | etot = -186.364799511423 +771000 ekin = 23.4805185151499 | erot = 19.2296467559715 | epot = -229.218370670653 | etot = -186.508205399532 +772000 ekin = 23.6763149012215 | erot = 18.7804644565625 | epot = -229.197189562088 | etot = -186.740410204304 +773000 ekin = 23.2744828335044 | erot = 18.3799138508661 | epot = -229.294843443837 | etot = -187.640446759466 +774000 ekin = 24.1615203598158 | erot = 18.900317215458 | epot = -229.618073899692 | etot = -186.556236324418 +775000 ekin = 24.5357529676979 | erot = 22.7624377798731 | epot = -230.089626217906 | etot = -182.791435470335 +776000 ekin = 24.5386633146364 | erot = 21.1855266154048 | epot = -230.582204299442 | etot = -184.8580143694 +777000 ekin = 25.2498386289825 | erot = 21.3517051740902 | epot = -231.095135150134 | etot = -184.493591347061 +778000 ekin = 25.1773810922395 | erot = 21.7257078056424 | epot = -231.571689532577 | etot = -184.668600634695 +779000 ekin = 25.0706221380908 | erot = 23.206106433149 | epot = -231.920098805104 | etot = -183.643370233864 +780000 ekin = 25.0073948183737 | erot = 23.7843076919343 | epot = -231.940828129371 | etot = -183.149125619063 +781000 ekin = 25.862328682591 | erot = 20.6147635245773 | epot = -231.660475043653 | etot = -185.183382836484 +782000 ekin = 26.0106396574312 | erot = 18.4785712250649 | epot = -231.228955508185 | etot = -186.739744625689 +783000 ekin = 26.3548094027823 | erot = 20.3847656672935 | epot = -230.847881341015 | etot = -184.108306270939 +784000 ekin = 26.9941621418946 | erot = 20.6658207449783 | epot = -230.342301897166 | etot = -182.682319010294 +785000 ekin = 27.1272259996373 | erot = 20.0337747206907 | epot = -229.609935110564 | etot = -182.448934390236 +786000 ekin = 26.2875323551626 | erot = 21.2032948699837 | epot = -228.871206104526 | etot = -181.380378879379 +787000 ekin = 27.102289880841 | erot = 22.7511634245655 | epot = -228.229695505568 | etot = -178.376242200162 +788000 ekin = 26.9004033303382 | erot = 23.284460905515 | epot = -227.746200253144 | etot = -177.561336017291 +789000 ekin = 26.296015640084 | erot = 23.9396195703878 | epot = -227.4595974325 | etot = -177.223962222028 +790000 ekin = 26.0014289202783 | erot = 26.1183503632237 | epot = -227.52011756713 | etot = -175.400338283628 +791000 ekin = 26.0417552278906 | erot = 24.4511943151671 | epot = -227.865832903974 | etot = -177.372883360917 +792000 ekin = 24.7829875539951 | erot = 25.7161813251446 | epot = -228.337129921754 | etot = -177.837961042614 +793000 ekin = 24.1365737213691 | erot = 26.6815526928053 | epot = -229.030608073319 | etot = -178.212481659145 +794000 ekin = 24.2497409488624 | erot = 27.0890119453063 | epot = -229.824908003136 | etot = -178.486155108968 +795000 ekin = 24.6407890606403 | erot = 27.889646525042 | epot = -230.805274185753 | etot = -178.27483860007 +796000 ekin = 25.3265228383185 | erot = 27.1393608545888 | epot = -231.693076803536 | etot = -179.227193110629 +797000 ekin = 26.6978206545278 | erot = 26.0659091687928 | epot = -232.555084872404 | etot = -179.791355049083 +798000 ekin = 26.3339851949647 | erot = 24.0430202875505 | epot = -233.536000193098 | etot = -183.158994710583 +799000 ekin = 26.9068087522464 | erot = 22.6750790932831 | epot = -234.458642892057 | etot = -184.876755046527 +800000 ekin = 27.1539987641759 | erot = 23.0521331292966 | epot = -235.226285042255 | etot = -185.020153148783 +801000 ekin = 28.1094335983316 | erot = 25.0050175559563 | epot = -235.765403988368 | etot = -182.65095283408 +802000 ekin = 28.2095765951819 | erot = 27.782893768378 | epot = -236.074276063345 | etot = -180.081805699785 +803000 ekin = 27.5705368050616 | erot = 28.8940855937134 | epot = -236.110252388434 | etot = -179.645629989659 +804000 ekin = 28.2157687187553 | erot = 27.74636434354 | epot = -236.079369382529 | etot = -180.117236320234 +805000 ekin = 28.320866013253 | erot = 29.9910811282246 | epot = -235.90913845068 | etot = -177.597191309203 +806000 ekin = 28.1050825504931 | erot = 26.9917671949644 | epot = -235.67969557003 | etot = -180.582845824572 +807000 ekin = 28.9805100536259 | erot = 27.4290452324766 | epot = -235.492989203125 | etot = -179.083433917023 +808000 ekin = 28.6297117732318 | erot = 26.5808708304162 | epot = -235.318064848412 | etot = -180.107482244764 +809000 ekin = 27.6485930588141 | erot = 26.8549775475233 | epot = -234.976046493401 | etot = -180.472475887064 +810000 ekin = 27.3535576125066 | erot = 27.4159280488332 | epot = -234.674224241899 | etot = -179.90473858056 +811000 ekin = 26.8179323011295 | erot = 23.7813000955385 | epot = -234.075151851674 | etot = -183.475919455006 +812000 ekin = 25.4460426056691 | erot = 22.5673797708771 | epot = -233.183000295958 | etot = -185.169577919411 +813000 ekin = 24.6447760709675 | erot = 21.8823489885933 | epot = -232.313502763387 | etot = -185.786377703826 +814000 ekin = 23.5292099931413 | erot = 23.5195364453851 | epot = -231.540928013004 | etot = -184.492181574478 +815000 ekin = 23.2925196788094 | erot = 24.0874833263439 | epot = -231.037162145188 | etot = -183.657159140034 +816000 ekin = 22.5686853714983 | erot = 23.2614654221577 | epot = -230.69420971902 | etot = -184.864058925364 +817000 ekin = 21.8281820071653 | erot = 23.5211267469624 | epot = -230.271049994022 | etot = -184.921741239894 +818000 ekin = 21.2884404725207 | erot = 24.902381419566 | epot = -229.858747495004 | etot = -183.667925602917 +819000 ekin = 21.0872506325458 | erot = 24.5311269568262 | epot = -229.338784368977 | etot = -183.720406779605 +820000 ekin = 20.8955721018969 | erot = 25.3653144031468 | epot = -228.629666907205 | etot = -182.368780402161 +821000 ekin = 21.0405754334193 | erot = 21.6474705949844 | epot = -227.730299016778 | etot = -185.042252988374 +822000 ekin = 20.9721716781629 | erot = 21.5305117214123 | epot = -226.866605601223 | etot = -184.363922201648 +823000 ekin = 21.3134444479004 | erot = 18.9497629221593 | epot = -225.861340505134 | etot = -185.598133135074 +824000 ekin = 20.9747397211228 | erot = 18.6168738131577 | epot = -225.064270159964 | etot = -185.472656625683 +825000 ekin = 21.3904407523305 | erot = 18.7811321199529 | epot = -224.367454518582 | etot = -184.195881646298 +826000 ekin = 21.8928774215356 | erot = 18.0229901458568 | epot = -223.971578653884 | etot = -184.055711086492 +827000 ekin = 22.7137879274166 | erot = 17.003583367025 | epot = -223.925754778761 | etot = -184.208383484319 +828000 ekin = 23.27710684341 | erot = 16.767643058574 | epot = -223.977166786808 | etot = -183.932416884824 +829000 ekin = 22.9248196274624 | erot = 16.7826748876662 | epot = -224.203173005046 | etot = -184.495678489918 +830000 ekin = 23.4067478420881 | erot = 18.7934665997725 | epot = -224.482791288573 | etot = -182.282576846713 +831000 ekin = 23.4821697156405 | erot = 18.2729392007921 | epot = -224.915819953911 | etot = -183.160711037479 +832000 ekin = 23.6777143333438 | erot = 18.2278960830696 | epot = -225.489645423005 | etot = -183.584035006592 +833000 ekin = 23.472191617002 | erot = 18.0493053174397 | epot = -226.176378068975 | etot = -184.654881134533 +834000 ekin = 23.7368728904259 | erot = 18.0164626266613 | epot = -226.92716915948 | etot = -185.173833642392 +835000 ekin = 24.1489739233553 | erot = 18.9188017440221 | epot = -227.647120026384 | etot = -184.579344359006 +836000 ekin = 24.9827825556416 | erot = 19.495588151043 | epot = -228.34763399319 | etot = -183.869263286505 +837000 ekin = 25.256659406949 | erot = 18.944776639966 | epot = -228.876405841141 | etot = -184.674969794226 +838000 ekin = 25.6241774229268 | erot = 18.8091020128683 | epot = -229.371952192415 | etot = -184.938672756619 +839000 ekin = 24.937654890099 | erot = 19.8676941565057 | epot = -229.858542408147 | etot = -185.053193361542 +840000 ekin = 24.4858927113979 | erot = 20.165387717701 | epot = -230.274829908799 | etot = -185.6235494797 +841000 ekin = 25.2649920297918 | erot = 24.2935866726487 | epot = -230.699551533791 | etot = -181.14097283135 +842000 ekin = 25.1332828225798 | erot = 25.2707888267597 | epot = -231.095538575756 | etot = -180.691466926417 +843000 ekin = 25.1733374952435 | erot = 25.9799311513388 | epot = -231.399217706907 | etot = -180.245949060324 +844000 ekin = 25.6427133855964 | erot = 26.078509916794 | epot = -231.550673355361 | etot = -179.82945005297 +845000 ekin = 25.1297698352677 | erot = 24.7021906095904 | epot = -231.460774324866 | etot = -181.628813880008 +846000 ekin = 23.9774924150437 | erot = 26.9234963124405 | epot = -231.260980839143 | etot = -180.359992111659 +847000 ekin = 23.9502284491091 | erot = 25.3996788275484 | epot = -230.920723601702 | etot = -181.570816325044 +848000 ekin = 23.6157182559703 | erot = 24.5551104055363 | epot = -230.306195126828 | etot = -182.135366465322 +849000 ekin = 22.6955823420992 | erot = 25.5456755652408 | epot = -229.458091789959 | etot = -181.216833882618 +850000 ekin = 22.0235173219512 | erot = 26.2022873474972 | epot = -228.638684453437 | etot = -180.412879783989 +851000 ekin = 20.3765133939015 | erot = 25.395296129778 | epot = -227.4038640863 | etot = -181.632054562621 +852000 ekin = 19.712651245867 | erot = 22.1621130679229 | epot = -226.183276861571 | etot = -184.308512547781 +853000 ekin = 19.9928897638392 | erot = 20.0874368006941 | epot = -225.284467563439 | etot = -185.204140998906 +854000 ekin = 19.488290778963 | erot = 19.9220642414495 | epot = -224.827954241878 | etot = -185.417599221465 +855000 ekin = 19.0625095702531 | erot = 23.1790778413437 | epot = -224.708495395363 | etot = -182.466907983767 +856000 ekin = 18.2834869557216 | erot = 23.7444220411258 | epot = -224.914568249835 | etot = -182.886659252988 +857000 ekin = 18.0511175672903 | erot = 23.2575694040762 | epot = -225.28875879225 | etot = -183.980071820884 +858000 ekin = 17.987864866636 | erot = 22.7427618173349 | epot = -225.735338610943 | etot = -185.004711926972 +859000 ekin = 18.1389416018411 | erot = 21.3928666667423 | epot = -226.037392251567 | etot = -186.505583982984 +860000 ekin = 18.6141725361191 | erot = 20.6939972933922 | epot = -226.430306906883 | etot = -187.122137077371 +861000 ekin = 18.401448708528 | erot = 19.0196700230753 | epot = -226.81711834723 | etot = -189.395999615627 +862000 ekin = 19.1545854076427 | erot = 19.6617033547467 | epot = -227.136988769577 | etot = -188.320700007187 +863000 ekin = 19.7210305410548 | erot = 19.0006017481044 | epot = -227.58643743169 | etot = -188.864805142531 +864000 ekin = 20.4150266073574 | erot = 17.4275270266597 | epot = -227.954722358838 | etot = -190.112168724821 +865000 ekin = 19.9419797685448 | erot = 18.4620038343303 | epot = -228.340343063655 | etot = -189.93635946078 +866000 ekin = 20.0439020993958 | erot = 19.7882082077027 | epot = -228.670054548891 | etot = -188.837944241793 +867000 ekin = 20.4021140966254 | erot = 16.6652764682189 | epot = -228.856375548282 | etot = -191.788984983438 +868000 ekin = 20.0497264126648 | erot = 15.1372589940697 | epot = -228.9464789622 | etot = -193.759493555466 +869000 ekin = 20.3294773849231 | erot = 15.3005394579943 | epot = -228.69433960582 | etot = -193.064322762902 +870000 ekin = 21.0889922536593 | erot = 16.6120429683399 | epot = -228.508354500254 | etot = -190.807319278254 +871000 ekin = 21.4383179744103 | erot = 15.7484322870451 | epot = -228.210620038394 | etot = -191.023869776939 +872000 ekin = 20.9086609371529 | erot = 15.1111364530204 | epot = -227.78534180259 | etot = -191.765544412416 +873000 ekin = 20.8153441906834 | erot = 16.5761474970315 | epot = -227.299271762687 | etot = -189.907780074972 +874000 ekin = 20.9430061532593 | erot = 16.1679775988649 | epot = -226.763117412711 | etot = -189.652133660586 +875000 ekin = 20.8032036636137 | erot = 17.5698273129444 | epot = -226.415697698183 | etot = -188.042666721625 +876000 ekin = 21.2280022982517 | erot = 17.9072946891329 | epot = -226.028708918809 | etot = -186.893411931424 +877000 ekin = 20.7314119673013 | erot = 18.8567759065314 | epot = -225.75544933082 | etot = -186.167261456988 +878000 ekin = 19.6914373366095 | erot = 18.0844279043814 | epot = -225.736073224764 | etot = -187.960207983773 +879000 ekin = 19.3380672635332 | erot = 20.3104617632777 | epot = -225.910509841808 | etot = -186.261980814997 +880000 ekin = 20.1253722733107 | erot = 19.6280011404237 | epot = -226.214189456348 | etot = -186.460816042614 +881000 ekin = 20.260952001898 | erot = 21.2130237420557 | epot = -226.552056767178 | etot = -185.078081023224 +882000 ekin = 21.3999865884411 | erot = 20.028991688965 | epot = -226.705011052036 | etot = -185.27603277463 +883000 ekin = 20.9234278576856 | erot = 17.6868960387749 | epot = -226.60324790835 | etot = -187.992924011889 +884000 ekin = 20.2953614821548 | erot = 19.6437828087785 | epot = -226.531387224454 | etot = -186.59224293352 +885000 ekin = 20.0270746296784 | erot = 18.5836278581865 | epot = -226.609255319515 | etot = -187.99855283165 +886000 ekin = 20.5051703060542 | erot = 18.0664735117856 | epot = -226.96051309001 | etot = -188.38886927217 +887000 ekin = 20.6026175595096 | erot = 18.6797072756244 | epot = -227.547206365853 | etot = -188.264881530719 +888000 ekin = 21.2323390050554 | erot = 20.9767236317906 | epot = -228.222699335688 | etot = -186.013636698842 +889000 ekin = 21.8381850979202 | erot = 25.4926747228943 | epot = -229.035049210771 | etot = -181.704189389957 +890000 ekin = 21.4079820277754 | erot = 27.1125219125164 | epot = -229.846306308658 | etot = -181.325802368367 +891000 ekin = 20.7821773337589 | erot = 28.3638087372895 | epot = -230.472553686443 | etot = -181.326567615394 +892000 ekin = 20.9530226613445 | erot = 29.3670280639872 | epot = -230.939235576405 | etot = -180.619184851073 +893000 ekin = 20.7215793854111 | erot = 31.0978810463376 | epot = -231.283574476306 | etot = -179.464114044558 +894000 ekin = 19.8695855128928 | erot = 31.7444008344117 | epot = -231.206530399661 | etot = -179.592544052357 +895000 ekin = 20.4710472102287 | erot = 32.2571471114376 | epot = -230.935329589533 | etot = -178.207135267867 +896000 ekin = 20.0060219077691 | erot = 31.457482996745 | epot = -230.39059212909 | etot = -178.927087224576 +897000 ekin = 19.5877677637713 | erot = 30.8725368660366 | epot = -229.679299884647 | etot = -179.218995254839 +898000 ekin = 19.5649042545347 | erot = 30.6384498007997 | epot = -228.784507947033 | etot = -178.581153891699 +899000 ekin = 19.552835254318 | erot = 29.951844791116 | epot = -227.835835338061 | etot = -178.331155292627 +900000 ekin = 19.2943713466608 | erot = 28.266076937142 | epot = -226.951949904772 | etot = -179.391501620969 +901000 ekin = 18.7114972173853 | erot = 25.779754104773 | epot = -226.031983135348 | etot = -181.54073181319 +902000 ekin = 18.7187531634708 | erot = 21.6824516537499 | epot = -225.333624072524 | etot = -184.932419255303 +903000 ekin = 18.5839455909793 | erot = 21.3627578096897 | epot = -224.798501909831 | etot = -184.851798509162 +904000 ekin = 18.3200785166187 | erot = 21.0384699999409 | epot = -224.517265654088 | etot = -185.158717137528 +905000 ekin = 18.2865838363112 | erot = 22.5880133859383 | epot = -224.539131448644 | etot = -183.664534226394 +906000 ekin = 18.8425722270119 | erot = 21.9502833403246 | epot = -224.826601919796 | etot = -184.03374635246 +907000 ekin = 18.236662353643 | erot = 21.6508700749443 | epot = -225.411854073913 | etot = -185.524321645325 +908000 ekin = 19.0863284801222 | erot = 21.7256265222381 | epot = -225.925114677336 | etot = -185.113159674975 +909000 ekin = 18.6818812816023 | erot = 20.5599381624967 | epot = -226.282894133629 | etot = -187.04107468953 +910000 ekin = 19.0812656136231 | erot = 20.4145332853015 | epot = -226.698405476378 | etot = -187.202606577453 +911000 ekin = 18.9756818734077 | erot = 19.7026952453737 | epot = -227.201366089943 | etot = -188.522988971161 +912000 ekin = 19.4517334786722 | erot = 19.3460897587287 | epot = -227.803131570748 | etot = -189.005308333347 +913000 ekin = 19.487052846439 | erot = 19.4558063021173 | epot = -228.833499323783 | etot = -189.890640175227 +914000 ekin = 20.0013452620764 | erot = 19.8883578065421 | epot = -230.188717691798 | etot = -190.299014623179 +915000 ekin = 20.9190174527208 | erot = 21.5162066495227 | epot = -231.33235656658 | etot = -188.897132464337 +916000 ekin = 21.0408041290695 | erot = 20.6706622893139 | epot = -232.345019966097 | etot = -190.633553547713 +917000 ekin = 21.4182021320957 | erot = 20.3350739399058 | epot = -233.071031631301 | etot = -191.317755559299 +918000 ekin = 22.0971055055586 | erot = 18.9655185938109 | epot = -233.580798555561 | etot = -192.518174456191 +919000 ekin = 22.5486106562676 | erot = 18.3948377546432 | epot = -234.050312577178 | etot = -193.106864166267 +920000 ekin = 23.3254614038352 | erot = 19.5922944610403 | epot = -234.48534712321 | etot = -191.567591258335 +921000 ekin = 23.5452459126828 | erot = 20.5850080381015 | epot = -234.86333152558 | etot = -190.733077574796 +922000 ekin = 23.548927893765 | erot = 21.8847693351997 | epot = -235.159655748814 | etot = -189.72595851985 +923000 ekin = 23.6264800883718 | erot = 24.823701669703 | epot = -235.319615013714 | etot = -186.869433255639 +924000 ekin = 23.4484029162379 | erot = 25.2387940247724 | epot = -235.348442838844 | etot = -186.661245897834 +925000 ekin = 23.7581201931874 | erot = 26.0564388640377 | epot = -235.235791589113 | etot = -185.421232531888 +926000 ekin = 23.2671712311938 | erot = 27.0589269562523 | epot = -234.804321198793 | etot = -184.478223011347 +927000 ekin = 23.0270381962365 | erot = 29.4095030756175 | epot = -234.307939870163 | etot = -181.871398598309 +928000 ekin = 23.140501344179 | erot = 27.0790502179807 | epot = -233.844847745639 | etot = -183.62529618348 +929000 ekin = 22.2734898741118 | erot = 27.0674755071555 | epot = -233.049914186603 | etot = -183.708948805335 +930000 ekin = 21.6339427121745 | erot = 25.2225644782622 | epot = -232.095625490262 | etot = -185.239118299825 +931000 ekin = 20.9327398893734 | erot = 22.3817305427933 | epot = -231.012404519165 | etot = -187.697934086999 +932000 ekin = 20.4822193525442 | erot = 22.9972350477763 | epot = -230.147455250577 | etot = -186.668000850256 +933000 ekin = 19.9660353920888 | erot = 24.4740543358249 | epot = -229.586577553208 | etot = -185.146487825294 +934000 ekin = 19.3969944972964 | erot = 23.9687951023098 | epot = -229.129558438895 | etot = -185.763768839289 +935000 ekin = 18.8183272744565 | erot = 23.494590376579 | epot = -228.829650383225 | etot = -186.516732732189 +936000 ekin = 17.9161255220784 | erot = 26.3097805675523 | epot = -228.725255966952 | etot = -184.499349877321 +937000 ekin = 17.4090072925044 | erot = 28.2846119714553 | epot = -228.595685952083 | etot = -182.902066688124 +938000 ekin = 17.7095687249429 | erot = 28.4339381503916 | epot = -228.52964518166 | etot = -182.386138306326 +939000 ekin = 17.5520408874173 | erot = 27.0941576154426 | epot = -228.469555611768 | etot = -183.823357108909 +940000 ekin = 17.1798814813059 | erot = 25.8182574439337 | epot = -228.458369765694 | etot = -185.460230840454 +941000 ekin = 18.3127771365279 | erot = 26.1340829522924 | epot = -228.605257427977 | etot = -184.158397339157 +942000 ekin = 18.4394261942677 | erot = 25.2374530821303 | epot = -228.698077294464 | etot = -185.021198018066 +943000 ekin = 18.2926042504087 | erot = 25.6259778525084 | epot = -228.714835650707 | etot = -184.796253547789 +944000 ekin = 18.1985428862211 | erot = 27.2944037574074 | epot = -228.856509809853 | etot = -183.363563166225 +945000 ekin = 18.5074415121775 | erot = 27.6142744599881 | epot = -229.209548154119 | etot = -183.087832181953 +946000 ekin = 19.2233115923275 | erot = 29.6826055408939 | epot = -229.700854946272 | etot = -180.79493781305 +947000 ekin = 19.2209049259883 | erot = 28.9510045058796 | epot = -230.298982034344 | etot = -182.127072602476 +948000 ekin = 19.7441291687864 | erot = 26.2906426684946 | epot = -230.779259933587 | etot = -184.744488096306 +949000 ekin = 19.4506543919674 | erot = 26.8808216821455 | epot = -231.059979079511 | etot = -184.728503005398 +950000 ekin = 20.1645638300332 | erot = 25.6765899295848 | epot = -231.255749555474 | etot = -185.414595795856 +951000 ekin = 20.6156032604793 | erot = 23.3780963018669 | epot = -231.363279926649 | etot = -187.369580364303 +952000 ekin = 20.397762898021 | erot = 21.9317814265749 | epot = -231.413145962119 | etot = -189.083601637523 +953000 ekin = 21.0736084801864 | erot = 21.1438497831439 | epot = -231.535497877041 | etot = -189.318039613711 +954000 ekin = 22.2970457335312 | erot = 21.8052778907762 | epot = -231.61117831621 | etot = -187.508854691902 +955000 ekin = 22.119368227684 | erot = 23.2345496019292 | epot = -231.828383029989 | etot = -186.474465200376 +956000 ekin = 21.4925632863079 | erot = 21.4930515028271 | epot = -232.064300377829 | etot = -189.078685588694 +957000 ekin = 20.8333682688634 | erot = 22.8032486196631 | epot = -232.190793202397 | etot = -188.554176313871 +958000 ekin = 19.8501740638794 | erot = 24.4089530073582 | epot = -232.249982663747 | etot = -187.990855592509 +959000 ekin = 19.2680019449165 | erot = 25.5054723395896 | epot = -232.152549289162 | etot = -187.379075004656 +960000 ekin = 19.7794915155661 | erot = 24.9916198272161 | epot = -231.918033034319 | etot = -187.146921691537 +961000 ekin = 19.2751025937535 | erot = 25.8738975860354 | epot = -231.741716385163 | etot = -186.592716205374 +962000 ekin = 19.5337863893408 | erot = 24.9356255276758 | epot = -231.55739577143 | etot = -187.087983854414 +963000 ekin = 18.9999723551409 | erot = 25.6087844134591 | epot = -231.447506108069 | etot = -186.838749339469 +964000 ekin = 18.8752847703513 | erot = 24.9133910089691 | epot = -231.338447218817 | etot = -187.549771439496 +965000 ekin = 19.291184662028 | erot = 26.9200173912746 | epot = -231.200004911496 | etot = -184.988802858193 +966000 ekin = 19.9923055028309 | erot = 23.6358047261547 | epot = -231.075767261895 | etot = -187.44765703291 +967000 ekin = 20.7057273743393 | erot = 22.5792578588179 | epot = -230.879832297065 | etot = -187.594847063908 +968000 ekin = 20.9571086143562 | erot = 20.068819571795 | epot = -230.940571243941 | etot = -189.914643057789 +969000 ekin = 21.1817427297271 | erot = 21.825570412089 | epot = -231.039838752312 | etot = -188.032525610496 +970000 ekin = 21.6764110888425 | erot = 18.6641228269477 | epot = -231.330833358017 | etot = -190.990299442226 +971000 ekin = 21.6293984081523 | erot = 20.4985343496002 | epot = -231.743853106541 | etot = -189.615920348789 +972000 ekin = 21.8321017334667 | erot = 24.1203627051505 | epot = -232.392520631785 | etot = -186.440056193167 +973000 ekin = 22.2085815332021 | erot = 23.693087815175 | epot = -232.912739470324 | etot = -187.011070121947 +974000 ekin = 23.847360088775 | erot = 24.6762793762862 | epot = -233.368044095902 | etot = -184.844404630841 +975000 ekin = 23.8772760481354 | erot = 23.8186315371493 | epot = -233.675813480515 | etot = -185.979905895231 +976000 ekin = 24.8508847684197 | erot = 25.4916104671426 | epot = -233.730386974331 | etot = -183.387891738769 +977000 ekin = 25.503947524416 | erot = 25.977795351237 | epot = -233.493574624629 | etot = -182.011831748976 +978000 ekin = 25.1301492488327 | erot = 23.6629990089568 | epot = -232.903591402815 | etot = -184.110443145025 +979000 ekin = 24.5159482950054 | erot = 23.0268756855837 | epot = -231.985954800605 | etot = -184.443130820016 +980000 ekin = 24.3566813412311 | erot = 22.1670075667718 | epot = -230.990647999228 | etot = -184.466959091225 +981000 ekin = 23.9671984077651 | erot = 21.1028376661039 | epot = -230.100691904619 | etot = -185.03065583075 +982000 ekin = 24.2014904181518 | erot = 21.766454128543 | epot = -229.357805757613 | etot = -183.389861210918 +983000 ekin = 24.7761393638494 | erot = 21.5867990158502 | epot = -228.528183005968 | etot = -182.165244626269 +984000 ekin = 24.762354593527 | erot = 20.3394309281687 | epot = -227.693626881489 | etot = -182.591841359793 +985000 ekin = 23.1046341904546 | erot = 20.4859555093025 | epot = -226.832364952595 | etot = -183.241775252838 +986000 ekin = 22.9917171657182 | erot = 19.6850542240413 | epot = -225.931729672514 | etot = -183.254958282755 +987000 ekin = 23.0807717247555 | erot = 18.7933780253197 | epot = -225.294914737568 | etot = -183.420764987493 +988000 ekin = 23.4666498858033 | erot = 18.3944401818207 | epot = -224.462201121502 | etot = -182.601111053878 +989000 ekin = 22.8294990773184 | erot = 18.3438283695259 | epot = -223.609265715967 | etot = -182.435938269123 +990000 ekin = 22.7066871299428 | erot = 18.5469186746782 | epot = -222.854303271458 | etot = -181.600697466837 +991000 ekin = 22.1383192479068 | erot = 18.4323256035066 | epot = -222.260388874341 | etot = -181.689744022928 +992000 ekin = 21.6825567231224 | erot = 17.8750037490483 | epot = -221.638206330132 | etot = -182.080645857962 +993000 ekin = 21.6468556176261 | erot = 19.5312645063955 | epot = -221.115778704445 | etot = -179.937658580423 +994000 ekin = 21.4467710605119 | erot = 22.8410951796741 | epot = -220.729552539755 | etot = -176.441686299569 +995000 ekin = 22.4071907674418 | erot = 20.5892070380571 | epot = -220.394740391854 | etot = -177.398342586355 +996000 ekin = 22.1528083326795 | erot = 20.104343598086 | epot = -220.236106067073 | etot = -177.978954136307 +997000 ekin = 21.4854485286746 | erot = 19.7617644517094 | epot = -220.302222594169 | etot = -179.055009613785 +998000 ekin = 22.1449863079611 | erot = 20.4384133517957 | epot = -220.780253661163 | etot = -178.196854001406 +999000 ekin = 22.5781778653751 | erot = 21.7041052467461 | epot = -221.511725171924 | etot = -177.229442059803 +1000000 ekin = 22.8867994582225 | erot = 20.7015166614267 | epot = -222.040127669769 | etot = -178.45181155012 + 1000000 307.12188 -227.88356 5.8434328 -199.15333 0.033370746 39304000 +Loop time of 85.8602 on 1 procs for 1000000 steps with 26 atoms + +Performance: 17.167 ns/day, 1.398 hours/ns, 11646.839 timesteps/s, 302.818 katom-step/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 75.033 | 75.033 | 75.033 | 0.0 | 87.39 +Bond | 1.7719 | 1.7719 | 1.7719 | 0.0 | 2.06 +Neigh | 0.023059 | 0.023059 | 0.023059 | 0.0 | 0.03 +Comm | 0.51625 | 0.51625 | 0.51625 | 0.0 | 0.60 +Output | 0.31488 | 0.31488 | 0.31488 | 0.0 | 0.37 +Modify | 7.8149 | 7.8149 | 7.8149 | 0.0 | 9.10 +Other | | 0.3861 | | | 0.45 + +Nlocal: 26 ave 26 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 301 ave 301 max 301 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.8.* nocoeff +System init for write_data ... +Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:01:25 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.4 new file mode 100644 index 0000000000..184462d373 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.4 @@ -0,0 +1,1276 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 8 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + scanning bonds ... + 1 = max bonds/atom + 26 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 24 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass +Setting atom values ... + 26 settings made for mass + +group all type 1 4 +26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 7 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.8.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 48.032697 + ghost atom cutoff = 48.032697 + binsize = 24.016348, bins = 15 15 15 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) +0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 +Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 299.91159 -228.12763 5.3145589 -200.46358 0.037365999 39304000 +1000 ekin = 23.3890953137706 | erot = 19.6410994523669 | epot = -223.453852955672 | etot = -180.423658189535 +2000 ekin = 23.1636407259802 | erot = 21.3625588607293 | epot = -224.083184468805 | etot = -179.556984882096 +3000 ekin = 23.2806646382535 | erot = 22.5430917602388 | epot = -224.768803309422 | etot = -178.945046910929 +4000 ekin = 23.9982606831172 | erot = 23.3468002016785 | epot = -225.369139455231 | etot = -178.024078570435 +5000 ekin = 24.165831446691 | erot = 24.309309123119 | epot = -225.647777921139 | etot = -177.172637351329 +6000 ekin = 24.6463592700502 | erot = 24.0743926173796 | epot = -225.506791813463 | etot = -176.786039926033 +7000 ekin = 24.3535569942788 | erot = 23.7545459891526 | epot = -225.024405145301 | etot = -176.91630216187 +8000 ekin = 24.1086868814849 | erot = 22.0830265599649 | epot = -224.271997801092 | etot = -178.080284359642 +9000 ekin = 23.6657562363458 | erot = 23.1988592381777 | epot = -223.434572814547 | etot = -176.569957340023 +10000 ekin = 24.3232494642814 | erot = 24.4646190421148 | epot = -222.599352113837 | etot = -173.811483607441 +11000 ekin = 23.5151408185546 | erot = 24.7247948775442 | epot = -221.829445800186 | etot = -173.589510104087 +12000 ekin = 23.1685925031279 | erot = 24.5168702274895 | epot = -221.283446631497 | etot = -173.597983900879 +13000 ekin = 22.5542770265459 | erot = 23.5479562044803 | epot = -220.966648997482 | etot = -174.864415766456 +14000 ekin = 22.1812934517937 | erot = 22.8843950945786 | epot = -220.909390045146 | etot = -175.843701498774 +15000 ekin = 21.6910740763736 | erot = 20.1250177447006 | epot = -221.050686326242 | etot = -179.234594505167 +16000 ekin = 22.4093549284696 | erot = 20.736944453168 | epot = -221.640495388654 | etot = -178.494196007016 +17000 ekin = 22.679935542291 | erot = 20.1401904659941 | epot = -222.539917467256 | etot = -179.71979145897 +18000 ekin = 22.7533504972992 | erot = 22.7880003534203 | epot = -223.497938845177 | etot = -177.956587994457 +19000 ekin = 22.6910824257598 | erot = 22.6775801630857 | epot = -224.397974314829 | etot = -179.029311725984 +20000 ekin = 22.4764122530343 | erot = 23.7180217709408 | epot = -225.277618576532 | etot = -179.083184552557 +21000 ekin = 22.3910995469036 | erot = 23.2739103814922 | epot = -226.054371546779 | etot = -180.389361618383 +22000 ekin = 22.7568179157572 | erot = 22.0747817368078 | epot = -226.677846442693 | etot = -181.846246790128 +23000 ekin = 23.0388332875658 | erot = 21.0371096765612 | epot = -226.873115293642 | etot = -182.797172329515 +24000 ekin = 22.9280961752663 | erot = 20.7369981826367 | epot = -226.863624686001 | etot = -183.198530328098 +25000 ekin = 23.1552675069494 | erot = 22.7089539602996 | epot = -226.603802406831 | etot = -180.739580939582 +26000 ekin = 23.1603034696877 | erot = 24.1226336440568 | epot = -226.15389780062 | etot = -178.870960686875 +27000 ekin = 22.8639956982148 | erot = 24.9308927260679 | epot = -225.734799028865 | etot = -177.939910604582 +28000 ekin = 22.8686406093792 | erot = 24.6702817199638 | epot = -225.404399605183 | etot = -177.865477275841 +29000 ekin = 22.7329708724114 | erot = 24.8206803603672 | epot = -225.288544762221 | etot = -177.734893529442 +30000 ekin = 23.2224697595134 | erot = 24.1186993911772 | epot = -225.281641810783 | etot = -177.940472660093 +31000 ekin = 23.2116217901824 | erot = 21.2110758669747 | epot = -225.379848736762 | etot = -180.957151079605 +32000 ekin = 22.6705345674289 | erot = 21.1222567836579 | epot = -225.626990597972 | etot = -181.834199246885 +33000 ekin = 22.5742554775595 | erot = 23.8115179286177 | epot = -226.196557922731 | etot = -179.810784516554 +34000 ekin = 22.4811628913946 | erot = 23.1703307206031 | epot = -227.132725939902 | etot = -181.481232327904 +35000 ekin = 22.1305128996843 | erot = 21.7768358380573 | epot = -228.241546350004 | etot = -184.334197612262 +36000 ekin = 22.3064371288266 | erot = 23.6090073902907 | epot = -229.291792709837 | etot = -183.37634819072 +37000 ekin = 22.7954030625747 | erot = 26.5244949994173 | epot = -230.44896109423 | etot = -181.129063032238 +38000 ekin = 22.021936313581 | erot = 28.7809192800672 | epot = -231.527472091849 | etot = -180.724616498201 +39000 ekin = 21.4311061995551 | erot = 30.0076463982257 | epot = -232.292567603581 | etot = -180.8538150058 +40000 ekin = 22.1961102532617 | erot = 28.4384036307401 | epot = -232.768624821777 | etot = -182.134110937775 +41000 ekin = 22.1632663233095 | erot = 27.8241627319402 | epot = -232.914504546317 | etot = -182.927075491067 +42000 ekin = 21.1410868775786 | erot = 26.870218141795 | epot = -232.876921131849 | etot = -184.865616112475 +43000 ekin = 21.3077823999456 | erot = 29.4997981842649 | epot = -232.609490543326 | etot = -181.801909959116 +44000 ekin = 21.0347661835417 | erot = 30.6694367820553 | epot = -232.102541009681 | etot = -180.398338044084 +45000 ekin = 20.0324931780768 | erot = 31.6373084224142 | epot = -231.359075571458 | etot = -179.689273970967 +46000 ekin = 19.8601076626959 | erot = 27.6516450222689 | epot = -230.481472443215 | etot = -182.96971975825 +47000 ekin = 19.9409510348244 | erot = 24.2746077209965 | epot = -229.669745177728 | etot = -185.454186421907 +48000 ekin = 20.2692406564663 | erot = 24.1549347770059 | epot = -228.892944669037 | etot = -184.468769235565 +49000 ekin = 19.7308285932956 | erot = 25.0778897556889 | epot = -228.04425642055 | etot = -183.235538071566 +50000 ekin = 19.5156647106263 | erot = 22.9395420283448 | epot = -227.011157830413 | etot = -184.555951091442 +51000 ekin = 19.6024948282074 | erot = 24.0313890926859 | epot = -226.023373255268 | etot = -182.389489334375 +52000 ekin = 19.8286591378852 | erot = 22.0208354730768 | epot = -225.032119343055 | etot = -183.182624732093 +53000 ekin = 19.3575981919063 | erot = 22.7897166177213 | epot = -224.158699287711 | etot = -182.011384478083 +54000 ekin = 19.597311059818 | erot = 23.0278186836853 | epot = -223.146432587169 | etot = -180.521302843666 +55000 ekin = 19.3207453743081 | erot = 22.0468752508626 | epot = -222.056416747158 | etot = -180.688796121987 +56000 ekin = 18.9770983953914 | erot = 20.6896918925267 | epot = -221.097322814135 | etot = -181.430532526217 +57000 ekin = 19.2291543150894 | erot = 18.2138179116051 | epot = -220.326696880738 | etot = -182.883724654043 +58000 ekin = 19.7989002082911 | erot = 17.8570481045562 | epot = -219.66066516308 | etot = -182.004716850233 +59000 ekin = 20.1354893580566 | erot = 18.0275449356124 | epot = -219.109861890285 | etot = -180.946827596616 +60000 ekin = 20.1400165937336 | erot = 16.7164726976129 | epot = -218.497904222289 | etot = -181.641414930942 +61000 ekin = 20.4228706753348 | erot = 15.3375065644544 | epot = -217.960810097484 | etot = -182.200432857695 +62000 ekin = 20.1686520767929 | erot = 14.8244535971852 | epot = -217.555103496147 | etot = -182.561997822169 +63000 ekin = 19.311066891783 | erot = 16.0064319386931 | epot = -217.355843552053 | etot = -182.038344721576 +64000 ekin = 18.6500742611855 | erot = 16.7733280191606 | epot = -217.424263371911 | etot = -182.000861091564 +65000 ekin = 18.4635153424261 | erot = 17.7526461844363 | epot = -217.607200736113 | etot = -181.391039209251 +66000 ekin = 18.0355770665484 | erot = 17.7854478795887 | epot = -217.893635735966 | etot = -182.072610789828 +67000 ekin = 18.7683164596081 | erot = 19.080252052141 | epot = -218.398035038712 | etot = -180.549466526963 +68000 ekin = 19.5633237463074 | erot = 19.5360521825708 | epot = -219.279673886377 | etot = -180.180297957499 +69000 ekin = 20.2188862219853 | erot = 20.833043152936 | epot = -220.282200151711 | etot = -179.23027077679 +70000 ekin = 20.9970230548361 | erot = 19.0573782912758 | epot = -221.465010968187 | etot = -181.410609622075 +71000 ekin = 22.2151160410886 | erot = 18.5722600954372 | epot = -222.617922299482 | etot = -181.830546162956 +72000 ekin = 23.0812082679138 | erot = 20.9554395379592 | epot = -224.077548221027 | etot = -180.040900415154 +73000 ekin = 24.1112874481562 | erot = 21.3307333887604 | epot = -225.657040151954 | etot = -180.215019315038 +74000 ekin = 25.1420377195353 | erot = 21.9350931527228 | epot = -226.775976258114 | etot = -179.698845385856 +75000 ekin = 25.4905080277013 | erot = 20.8716474966583 | epot = -227.44994158467 | etot = -181.087786060311 +76000 ekin = 26.1889777417351 | erot = 18.9373050893096 | epot = -227.905073960386 | etot = -182.778791129342 +77000 ekin = 26.6309013716286 | erot = 19.5714794491311 | epot = -228.081005377953 | etot = -181.878624557193 +78000 ekin = 27.3057147200393 | erot = 19.5248231586005 | epot = -228.040153322525 | etot = -181.209615443886 +79000 ekin = 28.2640662888057 | erot = 20.2680283946488 | epot = -227.894218120703 | etot = -179.362123437249 +80000 ekin = 28.8799414765843 | erot = 21.2755780503219 | epot = -227.426549194774 | etot = -177.271029667868 +81000 ekin = 28.0858484625652 | erot = 21.7656751298647 | epot = -226.837288216447 | etot = -176.985764624017 +82000 ekin = 27.5576739603813 | erot = 21.5235335244366 | epot = -226.257098694314 | etot = -177.175891209496 +83000 ekin = 27.0556891289388 | erot = 22.6329456874458 | epot = -225.705589513145 | etot = -176.01695469676 +84000 ekin = 26.940061932639 | erot = 22.4076039984471 | epot = -225.381193301861 | etot = -176.033527370774 +85000 ekin = 26.525652465447 | erot = 24.4523763465308 | epot = -225.328349372335 | etot = -174.350320560357 +86000 ekin = 26.2488146649899 | erot = 24.9404486230819 | epot = -225.600551034373 | etot = -174.411287746301 +87000 ekin = 25.8921444638997 | erot = 23.8549898140682 | epot = -225.944879311363 | etot = -176.197745033396 +88000 ekin = 26.2103045690956 | erot = 23.1783147432123 | epot = -226.027774274625 | etot = -176.639154962317 +89000 ekin = 25.9835312219869 | erot = 24.2571523005165 | epot = -225.843728416076 | etot = -175.603044893573 +90000 ekin = 25.0784166533943 | erot = 23.6606895366222 | epot = -225.518913230511 | etot = -176.779807040494 +91000 ekin = 25.1550989963772 | erot = 24.611658714882 | epot = -225.044629759836 | etot = -175.277872048577 +92000 ekin = 24.6322805735348 | erot = 23.0482358024938 | epot = -224.419349930751 | etot = -176.738833554722 +93000 ekin = 24.180459234874 | erot = 20.7592927466895 | epot = -223.586212452689 | etot = -178.646460471126 +94000 ekin = 22.9793960468067 | erot = 20.9605947384726 | epot = -222.799813856714 | etot = -178.859823071435 +95000 ekin = 22.0929244299446 | erot = 22.3265647171473 | epot = -222.029129765178 | etot = -177.609640618086 +96000 ekin = 21.7264489643602 | erot = 21.1719809671405 | epot = -221.221631774717 | etot = -178.323201843216 +97000 ekin = 21.4220036658247 | erot = 21.3543994979149 | epot = -220.52548534737 | etot = -177.74908218363 +98000 ekin = 20.0618032599352 | erot = 22.5876428184093 | epot = -219.923872605452 | etot = -177.274426527108 +99000 ekin = 19.3288174724157 | erot = 23.7511671518151 | epot = -219.367088850842 | etot = -176.287104226611 +100000 ekin = 18.4832594748416 | erot = 23.1505163286733 | epot = -218.93835041027 | etot = -177.304574606755 +101000 ekin = 18.2036045057376 | erot = 23.4110434093513 | epot = -218.810174271335 | etot = -177.195526356247 +102000 ekin = 19.1822681980068 | erot = 24.5380584864956 | epot = -219.20692211123 | etot = -175.486595426727 +103000 ekin = 19.6432797836894 | erot = 24.6590917201035 | epot = -219.897839906815 | etot = -175.595468403022 +104000 ekin = 20.1705942940374 | erot = 24.5511248426482 | epot = -220.691524456858 | etot = -175.969805320173 +105000 ekin = 20.4521236023122 | erot = 24.9947804545851 | epot = -221.484673188626 | etot = -176.037769131728 +106000 ekin = 20.2290985098953 | erot = 27.3725689281464 | epot = -222.355241194015 | etot = -174.753573755973 +107000 ekin = 20.8434847834034 | erot = 26.3604100874063 | epot = -223.150037642897 | etot = -175.946142772087 +108000 ekin = 21.412418363854 | erot = 28.2162878060305 | epot = -223.460424862129 | etot = -173.831718692244 +109000 ekin = 21.4548274110363 | erot = 30.3230159735583 | epot = -223.240254565236 | etot = -171.462411180641 +110000 ekin = 21.0213729404218 | erot = 29.3710550207835 | epot = -222.579286542226 | etot = -172.186858581021 +111000 ekin = 20.9967841720846 | erot = 26.7618200853704 | epot = -221.876250793147 | etot = -174.117646535692 +112000 ekin = 21.7067956747879 | erot = 24.9536304481639 | epot = -221.394505355036 | etot = -174.734079232084 +113000 ekin = 21.4580535818318 | erot = 22.7691051824902 | epot = -221.519820597203 | etot = -177.292661832881 +114000 ekin = 22.2538283177252 | erot = 22.1731381215523 | epot = -221.687750534437 | etot = -177.260784095159 +115000 ekin = 22.7396594344901 | erot = 20.8608644375928 | epot = -222.152243091207 | etot = -178.551719219124 +116000 ekin = 24.1978150545115 | erot = 21.3688456685818 | epot = -222.980866690549 | etot = -177.414205967455 +117000 ekin = 25.4933258533643 | erot = 22.6030027739669 | epot = -224.127289238825 | etot = -176.030960611493 +118000 ekin = 26.5632696276086 | erot = 22.5348729995318 | epot = -225.275605356332 | etot = -176.177462729191 +119000 ekin = 27.3565904118111 | erot = 23.0690511978526 | epot = -226.447636503629 | etot = -176.021994893965 +120000 ekin = 29.3515149477993 | erot = 22.9538643517138 | epot = -227.384133540075 | etot = -175.078754240562 +121000 ekin = 30.5981861627602 | erot = 24.0718786854702 | epot = -228.0863722092 | etot = -173.416307360969 +122000 ekin = 30.8337076451186 | erot = 21.5728983486705 | epot = -228.574513811433 | etot = -176.167907817644 +123000 ekin = 31.5034781314849 | erot = 24.7369743163131 | epot = -228.825132694326 | etot = -172.584680246528 +124000 ekin = 32.5012268554423 | erot = 22.3540490361114 | epot = -229.031726697549 | etot = -174.176450805995 +125000 ekin = 32.7837623568763 | erot = 21.6390695988794 | epot = -229.355357070393 | etot = -174.932525114638 +126000 ekin = 34.6524233539235 | erot = 20.8886638576163 | epot = -229.754016136603 | etot = -174.212928925063 +127000 ekin = 34.0859583483566 | erot = 20.87571356796 | epot = -230.186745529299 | etot = -175.225073612982 +128000 ekin = 33.3654002002854 | erot = 17.8696662885262 | epot = -230.452008826877 | etot = -179.216942338065 +129000 ekin = 32.879700171019 | erot = 20.1227819588362 | epot = -230.66738519366 | etot = -177.664903063805 +130000 ekin = 32.5779755655807 | erot = 22.5079760785794 | epot = -230.755161253226 | etot = -175.669209609066 +131000 ekin = 32.0009253066221 | erot = 23.4002695617563 | epot = -230.587415910688 | etot = -175.186221042309 +132000 ekin = 30.6104507658518 | erot = 23.2152891369288 | epot = -230.187009153994 | etot = -176.361269251214 +133000 ekin = 30.0801055500021 | erot = 24.89872490236 | epot = -229.502463574013 | etot = -174.523633121651 +134000 ekin = 29.5703478432003 | erot = 25.5419443422135 | epot = -228.376328698803 | etot = -173.264036513389 +135000 ekin = 27.8494638285662 | erot = 22.1463271581356 | epot = -226.796614760718 | etot = -176.800823774016 +136000 ekin = 26.7413064146633 | erot = 24.9789465866713 | epot = -225.063840059921 | etot = -173.343587058586 +137000 ekin = 25.6957193105053 | erot = 20.7412156523377 | epot = -223.397630735845 | etot = -176.960695773002 +138000 ekin = 23.6295036307194 | erot = 22.156062146465 | epot = -221.790362287186 | etot = -176.004796510002 +139000 ekin = 21.3906159765428 | erot = 21.7146099871639 | epot = -220.250844850201 | etot = -177.145618886495 +140000 ekin = 20.4985795938428 | erot = 20.8528672558468 | epot = -218.909318457139 | etot = -177.557871607449 +141000 ekin = 20.0359949166403 | erot = 21.2802479225099 | epot = -217.577251694951 | etot = -176.261008855801 +142000 ekin = 18.9631892259955 | erot = 19.8482921778254 | epot = -216.554661187853 | etot = -177.743179784032 +143000 ekin = 18.9783976628076 | erot = 21.2354711831475 | epot = -215.943444643249 | etot = -175.729575797294 +144000 ekin = 18.3622731665631 | erot = 20.8806330220523 | epot = -215.526530561429 | etot = -176.283624372814 +145000 ekin = 18.3633778590725 | erot = 20.9808337178454 | epot = -215.141180064732 | etot = -175.796968487814 +146000 ekin = 18.0030641174453 | erot = 20.1144458830263 | epot = -215.132079230415 | etot = -177.014569229944 +147000 ekin = 18.1301824506837 | erot = 20.0682713533626 | epot = -215.558128457865 | etot = -177.359674653818 +148000 ekin = 18.7692583084233 | erot = 18.7526905862527 | epot = -216.118789082644 | etot = -178.596840187968 +149000 ekin = 18.9701199796348 | erot = 21.3459169858944 | epot = -216.705869035682 | etot = -176.389832070152 +150000 ekin = 19.1460230366766 | erot = 22.9728862104556 | epot = -217.097167008501 | etot = -174.978257761369 +151000 ekin = 19.9232401081762 | erot = 20.8260224389232 | epot = -217.485240320698 | etot = -176.735977773599 +152000 ekin = 20.1824516077178 | erot = 20.0237977742153 | epot = -217.959645068293 | etot = -177.75339568636 +153000 ekin = 21.0207460333017 | erot = 21.268492565156 | epot = -218.612718008189 | etot = -176.323479409731 +154000 ekin = 22.534961994461 | erot = 20.9919099903807 | epot = -219.177409254363 | etot = -175.650537269521 +155000 ekin = 22.8618213684381 | erot = 19.5692643142745 | epot = -219.570021303563 | etot = -177.138935620851 +156000 ekin = 23.1051643701801 | erot = 16.4296764652247 | epot = -219.703156446911 | etot = -180.168315611506 +157000 ekin = 23.2429556198953 | erot = 18.0924487652884 | epot = -219.692327251345 | etot = -178.356922866161 +158000 ekin = 23.0355467188289 | erot = 18.2828932149397 | epot = -219.48465834254 | etot = -178.166218408772 +159000 ekin = 23.1050695121227 | erot = 16.2275027241546 | epot = -219.231547257504 | etot = -179.898975021227 +160000 ekin = 22.7521851912413 | erot = 16.6417481664669 | epot = -219.073812974093 | etot = -179.679879616385 +161000 ekin = 23.2701284387811 | erot = 17.0428745048628 | epot = -218.662884465419 | etot = -178.349881521775 +162000 ekin = 23.4520460412958 | erot = 19.2723698795182 | epot = -218.246057424873 | etot = -175.521641504059 +163000 ekin = 23.689441669341 | erot = 16.1416805717479 | epot = -218.038571722494 | etot = -178.207449481405 +164000 ekin = 23.3619421025109 | erot = 18.22708784978 | epot = -218.093772102733 | etot = -176.504742150442 +165000 ekin = 23.8064702087761 | erot = 19.6627695131554 | epot = -218.432017549968 | etot = -174.962777828037 +166000 ekin = 24.0139008081603 | erot = 20.0731418226024 | epot = -219.005861365541 | etot = -174.918818734778 +167000 ekin = 24.0624950654638 | erot = 20.9748981844942 | epot = -219.683607499488 | etot = -174.64621424953 +168000 ekin = 23.9376600547935 | erot = 20.1285243447132 | epot = -220.420457921599 | etot = -176.354273522093 +169000 ekin = 23.5298927322548 | erot = 20.2068282573737 | epot = -221.313567545343 | etot = -177.576846555714 +170000 ekin = 23.7768907445282 | erot = 21.2771123646888 | epot = -222.337207228985 | etot = -177.283204119768 +171000 ekin = 24.1370595671943 | erot = 23.097407978718 | epot = -223.5506470736 | etot = -176.316179527688 +172000 ekin = 24.4668786543479 | erot = 25.3209673144829 | epot = -224.697775116656 | etot = -174.909929147825 +173000 ekin = 24.6123421907483 | erot = 25.55710330111 | epot = -225.927114756503 | etot = -175.757669264645 +174000 ekin = 24.1184603587473 | erot = 26.344734075088 | epot = -227.192870039681 | etot = -176.729675605846 +175000 ekin = 24.6198790665726 | erot = 26.2179225737243 | epot = -228.430613666214 | etot = -177.592812025917 +176000 ekin = 24.6885745323025 | erot = 25.3760086033795 | epot = -229.590489142521 | etot = -179.525906006839 +177000 ekin = 25.8487289680921 | erot = 27.3473459150405 | epot = -230.512099208118 | etot = -177.316024324985 +178000 ekin = 25.7936599135358 | erot = 26.8557059905942 | epot = -231.146460411413 | etot = -178.497094507283 +179000 ekin = 26.1888961667669 | erot = 29.1002089068839 | epot = -231.411675557269 | etot = -176.122570483618 +180000 ekin = 26.0135600090731 | erot = 27.5817576880658 | epot = -231.273797896987 | etot = -177.678480199848 +181000 ekin = 26.2264624864677 | erot = 25.4290614265803 | epot = -230.913442560937 | etot = -179.257918647889 +182000 ekin = 26.1398552438982 | erot = 24.0809599689769 | epot = -230.511696027826 | etot = -180.290880814951 +183000 ekin = 26.1556145401761 | erot = 24.0766924985731 | epot = -229.818266971064 | etot = -179.585959932315 +184000 ekin = 27.3086871074633 | erot = 24.4288359228746 | epot = -228.839517782805 | etot = -177.101994752467 +185000 ekin = 27.4898787585441 | erot = 24.7938482452323 | epot = -227.666559851805 | etot = -175.382832848029 +186000 ekin = 27.3328782862148 | erot = 22.6658429472471 | epot = -226.350890551421 | etot = -176.352169317959 +187000 ekin = 26.7948174814632 | erot = 22.6470038181953 | epot = -225.081289232844 | etot = -175.639467933186 +188000 ekin = 27.8723845439341 | erot = 23.5234220005291 | epot = -223.908358510605 | etot = -172.512551966142 +189000 ekin = 28.1601880311353 | erot = 23.7261081823951 | epot = -222.800556775815 | etot = -170.914260562285 +190000 ekin = 28.0281791381836 | erot = 22.4495336007974 | epot = -221.746357664621 | etot = -171.26864492564 +191000 ekin = 28.3968994364094 | erot = 24.5513031073085 | epot = -220.887175628872 | etot = -167.938973085154 +192000 ekin = 27.7855852746761 | erot = 25.7678221031458 | epot = -220.147377425492 | etot = -166.59397004767 +193000 ekin = 27.0653969351198 | erot = 26.0797976416142 | epot = -219.448938305435 | etot = -166.303743728701 +194000 ekin = 26.591886956892 | erot = 27.2559987926336 | epot = -218.866818380032 | etot = -165.018932630506 +195000 ekin = 25.3875760139297 | erot = 30.4658402325932 | epot = -218.624921486327 | etot = -162.771505239804 +196000 ekin = 25.2698426080245 | erot = 29.5251795522301 | epot = -218.561614102179 | etot = -163.766591941925 +197000 ekin = 24.2903229144824 | erot = 31.8288244412473 | epot = -218.729796870422 | etot = -162.610649514693 +198000 ekin = 23.7276722827683 | erot = 32.0454149389688 | epot = -218.941804941586 | etot = -163.168717719849 +199000 ekin = 23.8463467560116 | erot = 31.965616978649 | epot = -219.185182684789 | etot = -163.373218950129 +200000 ekin = 23.3466100334222 | erot = 29.1399528434376 | epot = -219.23796368071 | etot = -166.75140080385 +201000 ekin = 22.7487917233094 | erot = 25.7244975420237 | epot = -219.090866114478 | etot = -170.617576849145 +202000 ekin = 22.1721332597989 | erot = 26.1511956277664 | epot = -218.778552074906 | etot = -170.455223187341 +203000 ekin = 21.7181344250325 | erot = 26.0871722320545 | epot = -218.390435495582 | etot = -170.585128838495 +204000 ekin = 21.0376564690026 | erot = 25.6226947809704 | epot = -218.05720217283 | etot = -171.396850922857 +205000 ekin = 20.7302702694838 | erot = 24.1599304176471 | epot = -217.801704730261 | etot = -172.91150404313 +206000 ekin = 21.3382716889647 | erot = 25.5578466968796 | epot = -217.705513220694 | etot = -170.80939483485 +207000 ekin = 21.929943769803 | erot = 24.3043622352602 | epot = -217.500606803152 | etot = -171.266300798088 +208000 ekin = 22.3703602648222 | erot = 23.8138985281345 | epot = -217.448247660947 | etot = -171.263988867991 +209000 ekin = 22.8322135815925 | erot = 24.3154754235774 | epot = -217.780621512497 | etot = -170.632932507327 +210000 ekin = 23.531458296701 | erot = 24.1781224892903 | epot = -218.426497805566 | etot = -170.716917019575 +211000 ekin = 24.3108042780204 | erot = 23.8117896585318 | epot = -219.237721464183 | etot = -171.115127527631 +212000 ekin = 25.5498843003363 | erot = 26.3148102829016 | epot = -220.148368449074 | etot = -168.283673865837 +213000 ekin = 26.7904826379273 | erot = 27.2908991135753 | epot = -221.046804647224 | etot = -166.965422895721 +214000 ekin = 27.9221149858574 | erot = 28.825031948947 | epot = -222.018023522183 | etot = -165.270876587378 +215000 ekin = 29.7060783522062 | erot = 26.6259095075768 | epot = -223.029189042779 | etot = -166.697201182996 +216000 ekin = 30.8166996672947 | erot = 27.4426017797676 | epot = -223.860903452266 | etot = -165.601602005203 +217000 ekin = 32.1062758748256 | erot = 28.480190382591 | epot = -224.420307416779 | etot = -163.833841159362 +218000 ekin = 34.0231354353329 | erot = 28.0396432492363 | epot = -224.762754873132 | etot = -162.699976188563 +219000 ekin = 35.0935147430151 | erot = 27.3420247123898 | epot = -224.844267242182 | etot = -162.408727786777 +220000 ekin = 36.6903483012276 | erot = 26.4046555014058 | epot = -224.674345925857 | etot = -161.579342123224 +221000 ekin = 37.0162358447748 | erot = 27.0644284813825 | epot = -224.294474180674 | etot = -160.213809854517 +222000 ekin = 37.2286352786866 | erot = 29.6452455867393 | epot = -223.646643282534 | etot = -156.772762417109 +223000 ekin = 37.1371706719775 | erot = 29.0338627066246 | epot = -223.02426705627 | etot = -156.853233677668 +224000 ekin = 37.7973687387399 | erot = 29.5349839686757 | epot = -222.452854546985 | etot = -155.120501839569 +225000 ekin = 37.8069973966967 | erot = 29.6422173132561 | epot = -221.948475640134 | etot = -154.499260930181 +226000 ekin = 37.3773991674874 | erot = 28.09605253081 | epot = -221.560990142565 | etot = -156.087538444267 +227000 ekin = 37.527755930331 | erot = 27.6808541221468 | epot = -221.483330512065 | etot = -156.274720459587 +228000 ekin = 38.4470067960778 | erot = 27.8146638288223 | epot = -221.276464510559 | etot = -155.014793885659 +229000 ekin = 39.1836147193506 | erot = 25.70095638706 | epot = -220.76463229751 | etot = -155.880061191099 +230000 ekin = 38.098964797451 | erot = 24.8377609072553 | epot = -219.990046626182 | etot = -157.053320921476 +231000 ekin = 36.1669798709402 | erot = 24.8108260069157 | epot = -219.186001203482 | etot = -158.208195325626 +232000 ekin = 36.2198119684192 | erot = 23.4065079338759 | epot = -218.360141683673 | etot = -158.733821781378 +233000 ekin = 34.9532458569289 | erot = 23.2139515607483 | epot = -217.384236817587 | etot = -159.21703939991 +234000 ekin = 33.7585177506638 | erot = 23.2139271576215 | epot = -216.590184561824 | etot = -159.617739653539 +235000 ekin = 32.5335134532386 | erot = 20.9776329357582 | epot = -215.733671699105 | etot = -162.222525310108 +236000 ekin = 31.2185234875872 | erot = 19.9753628972515 | epot = -214.975828378577 | etot = -163.781941993739 +237000 ekin = 30.4570685291383 | erot = 20.3543664256712 | epot = -214.499912868784 | etot = -163.688477913975 +238000 ekin = 30.2614586325617 | erot = 21.1886832898794 | epot = -214.361693708507 | etot = -162.911551786066 +239000 ekin = 30.4636237840023 | erot = 21.5186095678481 | epot = -214.441235319161 | etot = -162.459001967311 +240000 ekin = 30.1210218817714 | erot = 22.9784100820642 | epot = -214.858237469049 | etot = -161.758805505214 +241000 ekin = 30.3658666076425 | erot = 21.7261951348677 | epot = -215.434563747826 | etot = -163.342502005316 +242000 ekin = 31.3867694338899 | erot = 23.9153977300584 | epot = -216.072635834797 | etot = -160.770468670849 +243000 ekin = 31.1900708118743 | erot = 26.6273701728334 | epot = -216.694600313578 | etot = -158.877159328871 +244000 ekin = 31.1564882281032 | erot = 25.7058049551927 | epot = -217.265423330916 | etot = -160.40313014762 +245000 ekin = 32.4795705887834 | erot = 24.8995064535899 | epot = -217.720460688445 | etot = -160.341383646071 +246000 ekin = 32.872022647284 | erot = 22.333159106545 | epot = -218.061658138483 | etot = -162.856476384654 +247000 ekin = 33.4284260628809 | erot = 24.7591927551794 | epot = -218.263367004162 | etot = -160.075748186102 +248000 ekin = 32.4614988934282 | erot = 23.8539156460749 | epot = -218.302805394426 | etot = -161.987390854923 +249000 ekin = 32.1756176499451 | erot = 23.8767681339002 | epot = -218.304065910381 | etot = -162.251680126536 +250000 ekin = 32.2198888158387 | erot = 22.8375122406138 | epot = -218.144356419904 | etot = -163.086955363451 +251000 ekin = 32.3333741154669 | erot = 22.2973676925259 | epot = -217.820854022814 | etot = -163.190112214821 +252000 ekin = 32.6075392448557 | erot = 23.4769293692233 | epot = -217.429569515478 | etot = -161.345100901399 +253000 ekin = 32.4971688738337 | erot = 24.3030528043931 | epot = -216.984279947662 | etot = -160.184058269435 +254000 ekin = 31.8923138747249 | erot = 24.1415429248736 | epot = -216.529032269096 | etot = -160.495175469498 +255000 ekin = 31.4024206135883 | erot = 23.8129962675095 | epot = -216.108885088425 | etot = -160.893468207327 +256000 ekin = 31.4668964539727 | erot = 25.1555403914743 | epot = -215.777158729505 | etot = -159.154721884058 +257000 ekin = 30.1578271181182 | erot = 25.2224232604804 | epot = -215.398717214095 | etot = -160.018466835496 +258000 ekin = 30.052285311838 | erot = 25.7673281945382 | epot = -215.003795923615 | etot = -159.184182417239 +259000 ekin = 28.790005223663 | erot = 25.9071617879885 | epot = -214.672294871174 | etot = -159.975127859522 +260000 ekin = 28.824260164679 | erot = 25.3762394651934 | epot = -214.438705752551 | etot = -160.238206122679 +261000 ekin = 28.4516249893281 | erot = 24.3935835063456 | epot = -214.056107967132 | etot = -161.210899471458 +262000 ekin = 27.8087703289653 | erot = 22.2360995417882 | epot = -213.52238610892 | etot = -163.477516238166 +263000 ekin = 27.2988805169285 | erot = 22.3316425638774 | epot = -213.209725671803 | etot = -163.579202590997 +264000 ekin = 27.7705600653735 | erot = 23.2743633836993 | epot = -213.047162146333 | etot = -162.00223869726 +265000 ekin = 27.8709800491321 | erot = 23.5211350737156 | epot = -212.86511367636 | etot = -161.472998553512 +266000 ekin = 27.9918135619683 | erot = 23.7232253135648 | epot = -212.641590093523 | etot = -160.92655121799 +267000 ekin = 28.5234357395516 | erot = 24.0561346062967 | epot = -212.474716645669 | etot = -159.895146299821 +268000 ekin = 28.870687215238 | erot = 23.8306167734046 | epot = -212.508203135534 | etot = -159.806899146891 +269000 ekin = 29.2607991052743 | erot = 24.1133194421955 | epot = -212.537028623626 | etot = -159.162910076156 +270000 ekin = 28.5296269979822 | erot = 25.8732554655093 | epot = -212.31029476064 | etot = -157.907412297149 +271000 ekin = 28.9212541346642 | erot = 22.4473820635914 | epot = -212.324230216607 | etot = -160.955594018351 +272000 ekin = 29.6765055230995 | erot = 25.0261431612911 | epot = -212.625998104986 | etot = -157.923349420595 +273000 ekin = 29.7746844908601 | erot = 24.8432699221532 | epot = -212.915298586345 | etot = -158.297344173332 +274000 ekin = 29.9742743190805 | erot = 24.1999136810544 | epot = -213.041688653029 | etot = -158.867500652894 +275000 ekin = 29.5940338177725 | erot = 25.4819616152138 | epot = -213.067492330014 | etot = -157.991496897028 +276000 ekin = 30.2832320515794 | erot = 24.0723230457662 | epot = -213.253118366949 | etot = -158.897563269603 +277000 ekin = 30.4700966177081 | erot = 23.2212292830064 | epot = -213.621019589182 | etot = -159.929693688468 +278000 ekin = 30.67056507496 | erot = 24.4631770981652 | epot = -214.132222700305 | etot = -158.99848052718 +279000 ekin = 30.6357169264609 | erot = 19.8864866789268 | epot = -214.377025145056 | etot = -163.854821539669 +280000 ekin = 30.6259905609972 | erot = 18.665780487499 | epot = -214.4335387873 | etot = -165.141767738804 +281000 ekin = 30.5241190789795 | erot = 17.9408431561163 | epot = -214.446974019773 | etot = -165.982011784677 +282000 ekin = 30.2531856243418 | erot = 16.5789274482122 | epot = -214.432453220479 | etot = -167.600340147925 +283000 ekin = 29.4314819022737 | erot = 14.9978652258759 | epot = -214.684414044695 | etot = -170.255066916545 +284000 ekin = 30.4463102919895 | erot = 13.9713280303416 | epot = -215.084928089016 | etot = -170.667289766685 +285000 ekin = 31.0787017394374 | erot = 14.4465786715638 | epot = -215.631231905545 | etot = -170.105951494544 +286000 ekin = 31.1520316133396 | erot = 14.4930799914547 | epot = -216.300770408183 | etot = -170.655658803388 +287000 ekin = 32.351781766203 | erot = 16.6989745946407 | epot = -216.963878558876 | etot = -167.913122198032 +288000 ekin = 33.005541771032 | erot = 18.134215920469 | epot = -217.673454635531 | etot = -166.53369694403 +289000 ekin = 31.8618589209554 | erot = 18.4772719583004 | epot = -218.379723064086 | etot = -168.04059218483 +290000 ekin = 31.8344575426835 | erot = 19.7422352431296 | epot = -219.065973771903 | etot = -167.48928098609 +291000 ekin = 31.9518185930539 | erot = 20.621627266815 | epot = -219.570480405878 | etot = -166.997034546009 +292000 ekin = 32.6439243188648 | erot = 22.5302835108441 | epot = -219.892967757819 | etot = -164.71875992811 +293000 ekin = 31.4829450686937 | erot = 21.3316743728505 | epot = -219.958047969435 | etot = -167.143428527891 +294000 ekin = 31.6375180782201 | erot = 21.238624328018 | epot = -219.885582904306 | etot = -167.009440498068 +295000 ekin = 31.0253762184145 | erot = 22.4882784169501 | epot = -219.814823672917 | etot = -166.301169037553 +296000 ekin = 30.8124492018732 | erot = 21.713403837488 | epot = -219.710246306785 | etot = -167.184393267424 +297000 ekin = 30.6962957393053 | erot = 21.2387002912486 | epot = -219.446213938046 | etot = -167.511217907492 +298000 ekin = 30.2751045254072 | erot = 21.2588516620972 | epot = -219.069662492538 | etot = -167.535706305033 +299000 ekin = 30.2654549878554 | erot = 19.9050587659481 | epot = -218.83938043646 | etot = -168.668866682656 +300000 ekin = 30.0162960943798 | erot = 22.3467328364631 | epot = -218.595337871123 | etot = -166.232308940281 +301000 ekin = 29.6491535845194 | erot = 19.8418961043971 | epot = -218.642810229095 | etot = -169.151760540178 +302000 ekin = 29.8744151298851 | erot = 18.1734214421702 | epot = -218.872367696606 | etot = -170.824531124551 +303000 ekin = 30.5896376432356 | erot = 18.3628979719825 | epot = -219.385303830194 | etot = -170.432768214976 +304000 ekin = 30.8134874190764 | erot = 19.9151431938305 | epot = -220.085697355968 | etot = -169.357066743061 +305000 ekin = 31.2099214170774 | erot = 20.6624279502763 | epot = -220.87374787482 | etot = -169.001398507466 +306000 ekin = 31.5379241870259 | erot = 21.2324529548628 | epot = -221.686063335012 | etot = -168.915686193123 +307000 ekin = 32.2075616004244 | erot = 23.1042657052719 | epot = -222.42594670972 | etot = -167.114119404023 +308000 ekin = 32.5982898681942 | erot = 23.3642432119933 | epot = -222.922692953037 | etot = -166.96015987285 +309000 ekin = 32.4315134575481 | erot = 23.8633076366207 | epot = -223.184000926484 | etot = -166.889179832315 +310000 ekin = 32.1158150633277 | erot = 23.3576385972236 | epot = -223.437543256612 | etot = -167.964089596061 +311000 ekin = 33.0748530306084 | erot = 23.7247742792265 | epot = -223.800381213498 | etot = -167.000753903663 +312000 ekin = 34.0642489795215 | erot = 24.4005553104056 | epot = -224.015053783926 | etot = -165.550249493999 +313000 ekin = 33.3941820316022 | erot = 22.8657808322912 | epot = -224.224694496321 | etot = -167.964731632427 +314000 ekin = 32.8831430452506 | erot = 22.3521386618945 | epot = -224.328814014534 | etot = -169.093532307389 +315000 ekin = 32.6439304562237 | erot = 24.3395053721963 | epot = -224.403018580942 | etot = -167.419582752522 +316000 ekin = 32.5730201874399 | erot = 25.8715269487792 | epot = -224.429728916574 | etot = -165.985181780355 +317000 ekin = 31.691345936356 | erot = 27.6427411551856 | epot = -224.240735797652 | etot = -164.90664870611 +318000 ekin = 31.1651843502561 | erot = 26.792649242559 | epot = -223.979858021812 | etot = -166.022024428997 +319000 ekin = 31.7256674778549 | erot = 23.8408589889958 | epot = -223.590556061656 | etot = -168.024029594805 +320000 ekin = 31.7060827776545 | erot = 26.4684067579431 | epot = -223.249262306441 | etot = -165.074772770843 +321000 ekin = 31.6031237667453 | erot = 27.4509881705089 | epot = -223.147476089125 | etot = -164.093364151871 +322000 ekin = 30.3481482285902 | erot = 27.7216584811217 | epot = -222.937601855219 | etot = -164.867795145507 +323000 ekin = 29.3228062491828 | erot = 29.7362160481481 | epot = -222.700827695669 | etot = -163.641805398338 +324000 ekin = 30.0900580978278 | erot = 28.3009812560174 | epot = -222.702754485984 | etot = -164.311715132138 +325000 ekin = 28.9724465195176 | erot = 31.4194498954201 | epot = -222.678079364986 | etot = -162.286182950048 +326000 ekin = 29.6807119193739 | erot = 29.8368278955146 | epot = -222.408655317023 | etot = -162.891115502134 +327000 ekin = 30.1649693984999 | erot = 27.5646417986177 | epot = -222.067063198242 | etot = -164.337452001125 +328000 ekin = 30.3408094046572 | erot = 26.5580828070968 | epot = -221.711839024904 | etot = -164.81294681315 +329000 ekin = 29.8995896328213 | erot = 24.6642798907952 | epot = -221.317020601826 | etot = -166.753151078209 +330000 ekin = 29.1001168093683 | erot = 27.3082067727852 | epot = -221.023371065897 | etot = -164.615047483743 +331000 ekin = 29.3349918490581 | erot = 27.5476077161585 | epot = -220.672722242025 | etot = -163.790122676808 +332000 ekin = 29.5801979725688 | erot = 27.2721545786742 | epot = -220.153700211885 | etot = -163.301347660642 +333000 ekin = 28.8256885894683 | erot = 28.4593129139449 | epot = -219.338463478995 | etot = -162.053461975582 +334000 ekin = 29.6068579849397 | erot = 28.2610782505578 | epot = -218.379292922818 | etot = -160.511356687321 +335000 ekin = 29.1933888055502 | erot = 24.4887025724561 | epot = -217.4599543906 | etot = -163.777863012594 +336000 ekin = 30.3071264565402 | erot = 24.6669652156945 | epot = -216.60775546459 | etot = -161.633663792355 +337000 ekin = 30.1138123587914 | erot = 23.8810939282739 | epot = -215.898081222498 | etot = -161.903174935432 +338000 ekin = 30.3467366262656 | erot = 22.5089541109543 | epot = -215.413223769271 | etot = -162.557533032051 +339000 ekin = 29.2241742025094 | erot = 22.9493211875938 | epot = -215.161328851956 | etot = -162.987833461853 +340000 ekin = 30.5171940243424 | erot = 22.1230395830795 | epot = -215.211023569382 | etot = -162.57078996196 +341000 ekin = 30.2990451747942 | erot = 22.0969746780876 | epot = -215.550935218903 | etot = -163.154915366021 +342000 ekin = 30.4576471953255 | erot = 22.8638016940834 | epot = -216.001360002558 | etot = -162.679911113149 +343000 ekin = 30.5621281016439 | erot = 24.4583122950448 | epot = -215.621289056559 | etot = -160.60084865987 +344000 ekin = 32.4519608541283 | erot = 28.5755206655114 | epot = -217.653133425583 | etot = -156.625651905943 +345000 ekin = 31.64186545717 | erot = 32.3842692970166 | epot = -218.708632568144 | etot = -154.682497813957 +346000 ekin = 31.9511111644616 | erot = 30.5483257685665 | epot = -219.014511159579 | etot = -156.515074226551 +347000 ekin = 30.7638178773701 | erot = 27.010357983763 | epot = -218.824845563665 | etot = -161.050669702532 +348000 ekin = 29.6838704731132 | erot = 24.9056867476275 | epot = -218.325871696026 | etot = -163.736314475285 +349000 ekin = 28.9550895574073 | erot = 28.1956349832957 | epot = -217.605556361012 | etot = -160.454831820309 +350000 ekin = 27.8908728899355 | erot = 27.4303776928326 | epot = -216.700972313945 | etot = -161.379721731177 +351000 ekin = 27.2743250159904 | erot = 29.1647807029794 | epot = -215.665223366206 | etot = -159.226117647236 +352000 ekin = 26.9616211386809 | erot = 30.6797251227193 | epot = -214.694539908538 | etot = -157.053193647138 +353000 ekin = 27.348832713772 | erot = 29.6015507795374 | epot = -213.896099461977 | etot = -156.945715968668 +354000 ekin = 26.1507956829831 | erot = 30.7563048879842 | epot = -213.372078199846 | etot = -156.464977628878 +355000 ekin = 25.6190603614018 | erot = 32.5689348009866 | epot = -213.269655859313 | etot = -155.081660696925 +356000 ekin = 25.3669997880113 | erot = 31.0472983763093 | epot = -213.450675449262 | etot = -157.036377284941 +357000 ekin = 25.312758671354 | erot = 31.8479342344932 | epot = -213.695546912804 | etot = -156.534854006956 +358000 ekin = 26.0187679198773 | erot = 31.9758685586405 | epot = -214.009662837489 | etot = -156.015026358971 +359000 ekin = 26.5607225985322 | erot = 29.9396653432688 | epot = -214.192283973959 | etot = -157.691896032158 +360000 ekin = 26.5902994062844 | erot = 25.9943052658055 | epot = -214.124414590833 | etot = -161.539809918743 +361000 ekin = 26.4813018415084 | erot = 24.2616769392684 | epot = -213.85398393885 | etot = -163.111005158073 +362000 ekin = 26.5033314195901 | erot = 26.0990581372781 | epot = -213.545462747037 | etot = -160.943073190169 +363000 ekin = 27.1571133077625 | erot = 25.5067564699878 | epot = -213.334127657296 | etot = -160.670257879545 +364000 ekin = 27.887930595824 | erot = 23.9887993938849 | epot = -212.852508852937 | etot = -160.975778863229 +365000 ekin = 27.967758403039 | erot = 20.854424772872 | epot = -212.290084332197 | etot = -163.467901156286 +366000 ekin = 27.0060927016748 | erot = 20.9170666829011 | epot = -211.843808452849 | etot = -163.920649068273 +367000 ekin = 26.6039768958553 | erot = 23.5699590216425 | epot = -211.557557482102 | etot = -161.383621564604 +368000 ekin = 26.1143377810244 | erot = 24.5362401721805 | epot = -211.384448343648 | etot = -160.733870390443 +369000 ekin = 25.8118104643539 | erot = 22.5391701033533 | epot = -211.406298065096 | etot = -163.055317497389 +370000 ekin = 25.8673504840375 | erot = 22.7731029418705 | epot = -211.64775421813 | etot = -163.007300792222 +371000 ekin = 26.4562588492746 | erot = 23.9905423895665 | epot = -211.815727194594 | etot = -161.368925955753 +372000 ekin = 26.3200791949476 | erot = 22.7189248210943 | epot = -212.040306718402 | etot = -163.00130270236 +373000 ekin = 25.3755530875695 | erot = 25.0380776190232 | epot = -212.072031912698 | etot = -161.658401206106 +374000 ekin = 24.1185712423776 | erot = 25.2038789684849 | epot = -211.935098223519 | etot = -162.612648012656 +375000 ekin = 24.0684595712565 | erot = 23.8499797175989 | epot = -211.793395733322 | etot = -163.874956444466 +376000 ekin = 22.5016871580896 | erot = 25.6118197832101 | epot = -211.409769064352 | etot = -163.296262123053 +377000 ekin = 22.0986939181275 | erot = 24.7100299168742 | epot = -211.045176539028 | etot = -164.236452704026 +378000 ekin = 21.1684841682011 | erot = 25.5492888669468 | epot = -210.660306734319 | etot = -163.942533699171 +379000 ekin = 20.010673971417 | erot = 29.7040277439788 | epot = -210.244603948909 | etot = -160.529902233513 +380000 ekin = 18.6364568547605 | erot = 33.3248766383446 | epot = -210.07312332186 | etot = -158.111789828755 +381000 ekin = 19.1123943604215 | erot = 29.9128186030511 | epot = -210.121981236354 | etot = -161.096768272881 +382000 ekin = 18.488667416097 | erot = 30.6195763742908 | epot = -210.287398668517 | etot = -161.179154878129 +383000 ekin = 17.9867949709769 | erot = 30.4649216268247 | epot = -210.644012249165 | etot = -162.192295651363 +384000 ekin = 18.086653701317 | erot = 30.1682137046886 | epot = -211.454411912153 | etot = -163.199544506147 +385000 ekin = 17.9753010304936 | erot = 30.6444125095994 | epot = -212.324100690826 | etot = -163.704387150733 +386000 ekin = 17.7413668486357 | erot = 30.1012874369922 | epot = -213.259558577419 | etot = -165.416904291791 +387000 ekin = 18.2186784291797 | erot = 28.3029350222839 | epot = -214.13010996286 | etot = -167.608496511396 +388000 ekin = 19.292870919104 | erot = 29.2720917147751 | epot = -214.909679402132 | etot = -166.344716768253 +389000 ekin = 20.4945794932603 | erot = 28.0408016793114 | epot = -215.715111099094 | etot = -167.179729926522 +390000 ekin = 21.4293155611672 | erot = 27.6051655638294 | epot = -216.558290196654 | etot = -167.523809071658 +391000 ekin = 22.3503257992232 | erot = 27.4540127593509 | epot = -217.20378427697 | etot = -167.399445718396 +392000 ekin = 23.5932179843426 | erot = 27.1057144401021 | epot = -217.566275239839 | etot = -166.867342815394 +393000 ekin = 23.7557009876267 | erot = 26.6637680566362 | epot = -217.563756363461 | etot = -167.144287319198 +394000 ekin = 24.4865989987554 | erot = 23.220719991203 | epot = -217.316082883998 | etot = -169.608763894039 +395000 ekin = 24.7595946480364 | erot = 21.8918507069135 | epot = -216.949712698095 | etot = -170.298267343146 +396000 ekin = 24.982464352614 | erot = 22.3354930515494 | epot = -216.416874060901 | etot = -169.098916656738 +397000 ekin = 25.3000376061139 | erot = 18.3060350402966 | epot = -216.050469640324 | etot = -172.444396993914 +398000 ekin = 25.2861319964392 | erot = 20.4058007069709 | epot = -215.762453015488 | etot = -170.070520312078 +399000 ekin = 25.6910756014433 | erot = 17.2458372762693 | epot = -215.449363397805 | etot = -172.512450520093 +400000 ekin = 26.4568923302747 | erot = 20.1388849072962 | epot = -215.187132762528 | etot = -168.591355524957 +401000 ekin = 26.473671301154 | erot = 21.2374664754577 | epot = -215.079189181665 | etot = -167.368051405054 +402000 ekin = 26.9661026532044 | erot = 22.1166726988484 | epot = -215.024717195915 | etot = -165.941941843862 +403000 ekin = 27.3226322136654 | erot = 22.8394489464986 | epot = -214.937632585437 | etot = -164.775551425273 +404000 ekin = 27.8935295461376 | erot = 22.8817369521021 | epot = -214.928408259317 | etot = -164.153141761077 +405000 ekin = 27.9407970657418 | erot = 23.0166667876302 | epot = -215.070859098588 | etot = -164.113395245216 +406000 ekin = 27.8467131583262 | erot = 24.0920158980814 | epot = -215.21564472779 | etot = -163.276915671383 +407000 ekin = 28.1735323456276 | erot = 24.4127070079513 | epot = -215.337654426137 | etot = -162.751415072558 +408000 ekin = 28.0581746931196 | erot = 25.4097057702624 | epot = -215.286666631528 | etot = -161.818786168146 +409000 ekin = 28.4575477087421 | erot = 27.0137932992507 | epot = -215.176589089366 | etot = -159.705248081373 +410000 ekin = 29.085031171955 | erot = 22.9273639101281 | epot = -215.097105269705 | etot = -163.084710187621 +411000 ekin = 28.9671748142217 | erot = 21.8822014832413 | epot = -214.921613402608 | etot = -164.072237105145 +412000 ekin = 29.4064096216751 | erot = 22.5408195016054 | epot = -214.627366977766 | etot = -162.680137854486 +413000 ekin = 29.1673383998257 | erot = 22.321938064771 | epot = -214.45055434655 | etot = -162.961277881953 +414000 ekin = 29.0111563106279 | erot = 18.7948327919326 | epot = -214.508701808542 | etot = -166.702712705981 +415000 ekin = 29.2163525836019 | erot = 18.3535912788607 | epot = -214.674303958464 | etot = -167.104360096002 +416000 ekin = 29.3094098198563 | erot = 17.6709040312385 | epot = -214.87605897502 | etot = -167.895745123926 +417000 ekin = 29.3855401131447 | erot = 16.4805818891855 | epot = -215.210819648773 | etot = -169.344697646443 +418000 ekin = 30.2763385538192 | erot = 20.6340456010144 | epot = -215.816567102338 | etot = -164.906182947505 +419000 ekin = 31.2702871079484 | erot = 21.0558998076069 | epot = -216.353762857211 | etot = -164.027575941656 +420000 ekin = 31.1928990244873 | erot = 23.8599837907919 | epot = -216.890403955335 | etot = -161.837521140056 +421000 ekin = 31.5456444237668 | erot = 23.2548532394917 | epot = -217.344973044312 | etot = -162.544475381054 +422000 ekin = 31.595330248126 | erot = 24.1129799902568 | epot = -217.646733756815 | etot = -161.938423518432 +423000 ekin = 30.3263575817443 | erot = 24.7757808957598 | epot = -217.691567202219 | etot = -162.589428724715 +424000 ekin = 29.6227184353682 | erot = 26.8551354763864 | epot = -217.49353393768 | etot = -161.015680025925 +425000 ekin = 29.5897090928897 | erot = 26.5787069615055 | epot = -217.189735948055 | etot = -161.02131989366 +426000 ekin = 28.3811287852246 | erot = 26.0477945184346 | epot = -216.709754303037 | etot = -162.280830999377 +427000 ekin = 27.7967079006065 | erot = 25.8148017215667 | epot = -215.916318594378 | etot = -162.304808972205 +428000 ekin = 27.0564125148368 | erot = 24.2254396851756 | epot = -214.786030457606 | etot = -163.504178257594 +429000 ekin = 26.4009850387513 | erot = 25.2739282576038 | epot = -213.377238447454 | etot = -161.702325151099 +430000 ekin = 25.8966083026098 | erot = 25.0007234317203 | epot = -211.870124789713 | etot = -160.972793055383 +431000 ekin = 24.7984133581247 | erot = 23.6811925425768 | epot = -210.204391421479 | etot = -161.724785520777 +432000 ekin = 24.5987744680211 | erot = 21.4763884246366 | epot = -208.534970052743 | etot = -162.459807160085 +433000 ekin = 22.9801023558261 | erot = 20.5753920602906 | epot = -207.012668945877 | etot = -163.457174529761 +434000 ekin = 21.7283926559211 | erot = 20.7827792983396 | epot = -205.743779917972 | etot = -163.232607963712 +435000 ekin = 20.6245427682379 | erot = 23.3682934466507 | epot = -204.585339785363 | etot = -160.592503570474 +436000 ekin = 19.7010843166892 | erot = 22.7947216751232 | epot = -203.673192464633 | etot = -161.17738647282 +437000 ekin = 18.8171368139259 | erot = 25.8230091867142 | epot = -202.902988849489 | etot = -158.262842848849 +438000 ekin = 18.5857719223376 | erot = 23.8018783969198 | epot = -202.347858231407 | etot = -159.96020791215 +439000 ekin = 18.4671140963778 | erot = 20.8474712254561 | epot = -202.040176117765 | etot = -162.725590795931 +440000 ekin = 18.7081908968736 | erot = 21.8456146936514 | epot = -202.119006954422 | etot = -161.565201363897 +441000 ekin = 19.1502196807364 | erot = 22.8429897393171 | epot = -202.649140947654 | etot = -160.655931527601 +442000 ekin = 19.6976623491702 | erot = 23.833532038064 | epot = -203.432766723882 | etot = -159.901572336648 +443000 ekin = 20.2692385782964 | erot = 23.174529180215 | epot = -204.244337936897 | etot = -160.800570178386 +444000 ekin = 19.6594548157619 | erot = 25.8570487147508 | epot = -204.964941783042 | etot = -159.448438252529 +445000 ekin = 20.0159531993039 | erot = 25.4583870830884 | epot = -205.887229192997 | etot = -160.412888910605 +446000 ekin = 20.9430057952113 | erot = 27.6789597381082 | epot = -206.884522007063 | etot = -158.262556473743 +447000 ekin = 21.5434157008284 | erot = 26.3367064953282 | epot = -207.875777090658 | etot = -159.995654894502 +448000 ekin = 21.3493130668634 | erot = 28.7124847307391 | epot = -208.826609271652 | etot = -158.76481147405 +449000 ekin = 21.4147217526733 | erot = 30.2712153847118 | epot = -209.889081936843 | etot = -158.203144799458 +450000 ekin = 22.9537180151663 | erot = 30.7913406967762 | epot = -211.045040894093 | etot = -157.29998218215 +451000 ekin = 24.0701784584903 | erot = 33.2662973441661 | epot = -212.037901576699 | etot = -154.701425774043 +452000 ekin = 24.9326594408497 | erot = 33.1807983552873 | epot = -213.020928110261 | etot = -154.907470314124 +453000 ekin = 25.9026870743818 | erot = 29.9694393741095 | epot = -213.918112791264 | etot = -158.045986342772 +454000 ekin = 25.6267674636379 | erot = 30.3094040078412 | epot = -214.751677160517 | etot = -158.815505689038 +455000 ekin = 25.8835420243565 | erot = 31.0348607020646 | epot = -215.515256607227 | etot = -158.596853880806 +456000 ekin = 26.5079598183216 | erot = 31.1273555306477 | epot = -216.246152804127 | etot = -158.610837455158 +457000 ekin = 27.4443036582482 | erot = 29.8343750435819 | epot = -216.811984874468 | etot = -159.533306172638 +458000 ekin = 26.9310118911977 | erot = 27.7201727649044 | epot = -216.756924658081 | etot = -162.105740001979 +459000 ekin = 27.9109641832173 | erot = 25.6787961230286 | epot = -217.297816399931 | etot = -163.708056093685 +460000 ekin = 27.9601360034299 | erot = 25.3252752047677 | epot = -217.967018926065 | etot = -164.681607717868 +461000 ekin = 27.0745859502303 | erot = 25.5847145566425 | epot = -217.810130302685 | etot = -165.150829795813 +462000 ekin = 26.7487951031419 | erot = 24.980711595531 | epot = -217.697766754625 | etot = -165.968260055952 +463000 ekin = 26.0732441338559 | erot = 28.153686894781 | epot = -217.358666684053 | etot = -163.131735655416 +464000 ekin = 26.0396949919171 | erot = 25.8416381117693 | epot = -216.944940451188 | etot = -165.063607347501 +465000 ekin = 25.3226575272321 | erot = 24.0325554854213 | epot = -216.354701601293 | etot = -166.99948858864 +466000 ekin = 24.1231672777327 | erot = 24.4307976004896 | epot = -215.565164328178 | etot = -167.011199449956 +467000 ekin = 23.8540709231575 | erot = 22.124846509072 | epot = -214.920239098285 | etot = -168.941321666055 +468000 ekin = 22.565597367876 | erot = 22.7691054272285 | epot = -214.530469865182 | etot = -169.195767070077 +469000 ekin = 22.2713028791399 | erot = 22.2113409900692 | epot = -214.270807992981 | etot = -169.788164123772 +470000 ekin = 22.4851427578562 | erot = 21.4377178321587 | epot = -214.468076008404 | etot = -170.545215418389 +471000 ekin = 22.1823272554268 | erot = 20.278257170788 | epot = -214.941978893437 | etot = -172.481394467223 +472000 ekin = 21.8731320005381 | erot = 19.0138763043457 | epot = -215.549112362977 | etot = -174.662104058093 +473000 ekin = 20.8777093211568 | erot = 22.4202421701947 | epot = -216.333540945248 | etot = -173.035589453897 +474000 ekin = 21.4845461241046 | erot = 21.5552254985163 | epot = -217.149747427618 | etot = -174.109975804997 +475000 ekin = 21.8424250616637 | erot = 22.343637585153 | epot = -218.003692733599 | etot = -173.817630086783 +476000 ekin = 23.3926359095999 | erot = 23.4769825817391 | epot = -218.918478361235 | etot = -172.048859869896 +477000 ekin = 23.53084242551 | erot = 22.2301883973586 | epot = -219.644035844548 | etot = -173.88300502168 +478000 ekin = 23.6068262804286 | erot = 20.4526014426457 | epot = -220.193888919509 | etot = -176.134461196435 +479000 ekin = 23.4875352763514 | erot = 19.3184155065279 | epot = -220.738674570528 | etot = -177.932723787649 +480000 ekin = 23.0717855202954 | erot = 21.8892004951702 | epot = -221.304242068401 | etot = -176.343256052935 +481000 ekin = 22.3550858352525 | erot = 23.0423486541001 | epot = -221.663877016894 | etot = -176.266442527541 +482000 ekin = 21.9864848364329 | erot = 22.7363916127196 | epot = -221.683762589876 | etot = -176.960886140723 +483000 ekin = 22.6106924731206 | erot = 24.0428223649866 | epot = -221.59708966704 | etot = -174.943574828933 +484000 ekin = 22.5076589696515 | erot = 23.4557074572132 | epot = -221.540386505083 | etot = -175.577020078218 +485000 ekin = 22.6452014843636 | erot = 21.762451203069 | epot = -221.380979387409 | etot = -176.973326699976 +486000 ekin = 22.8884924315959 | erot = 22.3107890975159 | epot = -221.108997132445 | etot = -175.909715603333 +487000 ekin = 22.9971918001234 | erot = 24.3833170218936 | epot = -220.71103827305 | etot = -173.330529451033 +488000 ekin = 22.1533984482818 | erot = 25.7281535841679 | epot = -220.122813937115 | etot = -172.241261904665 +489000 ekin = 22.4515755615887 | erot = 25.0522662107032 | epot = -219.719249535127 | etot = -172.215407762835 +490000 ekin = 22.9547894223432 | erot = 24.517779033553 | epot = -219.418606998125 | etot = -171.946038542229 +491000 ekin = 23.5816418799849 | erot = 22.753839355928 | epot = -218.924118670106 | etot = -172.588637434193 +492000 ekin = 23.8823445747864 | erot = 21.2184779917221 | epot = -218.227735715369 | etot = -173.126913148861 +493000 ekin = 24.3448959898337 | erot = 21.8115598709523 | epot = -217.334509642487 | etot = -171.178053781701 +494000 ekin = 24.4320819054026 | erot = 22.5752180720098 | epot = -216.473641638612 | etot = -169.466341661199 +495000 ekin = 24.3755841384379 | erot = 23.9444067518822 | epot = -215.609878516645 | etot = -167.289887626325 +496000 ekin = 24.8598166549303 | erot = 21.4239924353219 | epot = -214.945231394708 | etot = -168.661422304456 +497000 ekin = 25.2448003736739 | erot = 20.8176798090042 | epot = -214.387561750013 | etot = -168.325081567335 +498000 ekin = 26.5693421635397 | erot = 20.5035803503483 | epot = -214.015978269251 | etot = -166.943055755363 +499000 ekin = 26.7852769961491 | erot = 19.5435940700116 | epot = -213.683959917476 | etot = -167.355088851315 +500000 ekin = 27.535057693355 | erot = 18.705068833847 | epot = -213.607739162636 | etot = -167.367612635434 +501000 ekin = 28.3213060130359 | erot = 17.8116944886089 | epot = -213.67740185523 | etot = -167.544401353585 +502000 ekin = 28.7521713272079 | erot = 18.0095076993248 | epot = -213.852896101639 | etot = -167.091217075106 +503000 ekin = 29.5029581283875 | erot = 18.909099125371 | epot = -214.062334972754 | etot = -165.650277718996 +504000 ekin = 30.3217459607846 | erot = 18.7844890901023 | epot = -214.319342764931 | etot = -165.213107714044 +505000 ekin = 30.1578277397036 | erot = 19.4319341441026 | epot = -214.415908521801 | etot = -164.826146637995 +506000 ekin = 29.209747070706 | erot = 19.026940448028 | epot = -214.633852668846 | etot = -166.397165150112 +507000 ekin = 29.642495894677 | erot = 19.5492883197655 | epot = -214.855190806251 | etot = -165.663406591808 +508000 ekin = 28.5340625040779 | erot = 21.9407235369196 | epot = -215.063369427087 | etot = -164.588583386089 +509000 ekin = 27.8112749390816 | erot = 22.7669227870046 | epot = -215.189489573915 | etot = -164.611291847828 +510000 ekin = 27.8718580299492 | erot = 22.1925267160587 | epot = -215.43076040814 | etot = -165.366375662132 +511000 ekin = 27.5420550600504 | erot = 21.1930166573984 | epot = -215.661435095053 | etot = -166.926363377604 +512000 ekin = 28.0922073127214 | erot = 21.705529509828 | epot = -215.786982318953 | etot = -165.989245496404 +513000 ekin = 28.4464077185633 | erot = 21.5872391817044 | epot = -216.013997388439 | etot = -165.980350488171 +514000 ekin = 28.6738400915053 | erot = 22.761394528105 | epot = -216.375218054325 | etot = -164.939983434714 +515000 ekin = 28.4988335118868 | erot = 21.0723384938813 | epot = -216.772216081264 | etot = -167.201044075496 +516000 ekin = 28.2431215529153 | erot = 22.5108174537502 | epot = -217.625419460918 | etot = -166.871480454252 +517000 ekin = 28.347655310566 | erot = 21.6185847645587 | epot = -218.584116365942 | etot = -168.617876290817 +518000 ekin = 28.7355143896094 | erot = 22.2912135675691 | epot = -219.537764202997 | etot = -168.511036245819 +519000 ekin = 28.0405456500047 | erot = 25.2172553666922 | epot = -220.297953309532 | etot = -167.040152292836 +520000 ekin = 26.9306517754668 | erot = 27.0838156807788 | epot = -220.731765046824 | etot = -166.717297590578 +521000 ekin = 26.1543611134017 | erot = 30.9762120900742 | epot = -221.023845549438 | etot = -163.893272345962 +522000 ekin = 25.2846258443128 | erot = 30.3488474956666 | epot = -221.113718831057 | etot = -165.480245491078 +523000 ekin = 25.3420381973596 | erot = 27.1843281367116 | epot = -221.140536198052 | etot = -168.614169863981 +524000 ekin = 25.7141573378958 | erot = 29.455779249349 | epot = -221.057372075661 | etot = -165.887435488417 +525000 ekin = 25.4838363010697 | erot = 26.3934330170679 | epot = -220.912701137522 | etot = -169.035431819385 +526000 ekin = 26.0079410350116 | erot = 30.2000198054899 | epot = -220.869509193105 | etot = -164.661548352604 +527000 ekin = 26.1588103027025 | erot = 29.7041166536357 | epot = -220.802295317341 | etot = -164.939368361003 +528000 ekin = 26.7938806212106 | erot = 29.1988530061502 | epot = -220.603226285027 | etot = -164.610492657666 +529000 ekin = 26.8945337264061 | erot = 30.8684009418751 | epot = -220.501633795914 | etot = -162.738699127633 +530000 ekin = 26.9078317338313 | erot = 29.6059799090131 | epot = -220.558751011573 | etot = -164.044939368729 +531000 ekin = 27.7935485005803 | erot = 29.2278507025209 | epot = -220.747606613035 | etot = -163.726207409933 +532000 ekin = 27.887349588649 | erot = 27.9662412084584 | epot = -221.046254717572 | etot = -165.192663920465 +533000 ekin = 28.6036302553006 | erot = 30.4080436081815 | epot = -221.390581182077 | etot = -162.378907318595 +534000 ekin = 29.1450459094427 | erot = 29.8984953927896 | epot = -221.618689857672 | etot = -162.57514855544 +535000 ekin = 29.469911033471 | erot = 29.755268847455 | epot = -221.750636117443 | etot = -162.525456236517 +536000 ekin = 29.50494662019 | erot = 30.5743840829575 | epot = -221.629307929619 | etot = -161.549977226472 +537000 ekin = 28.425893453274 | erot = 32.2633658998326 | epot = -221.149883136949 | etot = -160.460623783842 +538000 ekin = 28.0184749761055 | erot = 30.9372043254436 | epot = -220.230421084041 | etot = -161.274741782492 +539000 ekin = 26.9914955024263 | erot = 31.1470532462602 | epot = -218.907897489909 | etot = -160.769348741223 +540000 ekin = 25.8342672805741 | erot = 30.4659839502893 | epot = -217.4023318616 | etot = -161.102080630737 +541000 ekin = 25.026783494083 | erot = 28.6292948272569 | epot = -215.859642568803 | etot = -162.203564247463 +542000 ekin = 24.2196496447266 | erot = 27.1673316851706 | epot = -214.460130991487 | etot = -163.073149661589 +543000 ekin = 23.6870158078332 | erot = 27.3438759386704 | epot = -213.038313075576 | etot = -162.007421329072 +544000 ekin = 23.0676757322196 | erot = 26.7417435047259 | epot = -211.706572811687 | etot = -161.897153574741 +545000 ekin = 21.8293570586022 | erot = 25.2088678150874 | epot = -210.577232175622 | etot = -163.539007301932 +546000 ekin = 21.5224546734963 | erot = 25.7347520792893 | epot = -209.72960555737 | etot = -162.472398804585 +547000 ekin = 20.9968182936697 | erot = 25.5632514150022 | epot = -209.191378920644 | etot = -162.631309211972 +548000 ekin = 19.8988817654073 | erot = 23.2679071410407 | epot = -208.743073804017 | etot = -165.576284897569 +549000 ekin = 19.9727838598321 | erot = 22.3903038756502 | epot = -208.700752574222 | etot = -166.33766483874 +550000 ekin = 19.5901365826176 | erot = 23.3554322669728 | epot = -209.057328163197 | etot = -166.111759313607 +551000 ekin = 19.3625273691881 | erot = 22.3770654995204 | epot = -209.363208919373 | etot = -167.623616050665 +552000 ekin = 19.5151849616975 | erot = 21.2706999045886 | epot = -209.797169625893 | etot = -169.011284759607 +553000 ekin = 19.2265779452039 | erot = 20.4826132865114 | epot = -209.999313263519 | etot = -170.290122031804 +554000 ekin = 19.5496295764989 | erot = 20.8693447741625 | epot = -209.779481348856 | etot = -169.360506998194 +555000 ekin = 19.1735854190619 | erot = 19.9647334065035 | epot = -209.314112705489 | etot = -170.175793879924 +556000 ekin = 18.5478675513136 | erot = 24.137842092091 | epot = -208.401647045382 | etot = -165.715937401977 +557000 ekin = 17.4742761697172 | erot = 24.0319972301999 | epot = -207.527543381088 | etot = -166.021269981171 +558000 ekin = 17.0450293728529 | erot = 25.0431971863445 | epot = -206.756554568577 | etot = -164.66832800938 +559000 ekin = 16.5375595856902 | erot = 23.7766127103862 | epot = -205.999592721795 | etot = -165.685420425718 +560000 ekin = 16.3675553275375 | erot = 22.7274451429466 | epot = -205.532696411942 | etot = -166.437695941458 +561000 ekin = 16.4002686388511 | erot = 23.454222688713 | epot = -205.33653129407 | etot = -165.482039966506 +562000 ekin = 16.8601910320653 | erot = 24.6920222465119 | epot = -205.561599056927 | etot = -164.00938577835 +563000 ekin = 17.4904033581056 | erot = 27.3327302539918 | epot = -206.371449865494 | etot = -161.548316253397 +564000 ekin = 18.2959040777444 | erot = 25.8631538436394 | epot = -207.295829537485 | etot = -163.136771616101 +565000 ekin = 19.1876481491769 | erot = 26.3288155361578 | epot = -208.252583626631 | etot = -162.736119941296 +566000 ekin = 19.3470565924911 | erot = 25.8088677343261 | epot = -209.135375001814 | etot = -163.979450674997 +567000 ekin = 19.3284332398276 | erot = 26.1324360478945 | epot = -210.001092533551 | etot = -164.540223245829 +568000 ekin = 20.2145930912203 | erot = 27.7960775164549 | epot = -210.739375059829 | etot = -162.728704452154 +569000 ekin = 20.7786788494836 | erot = 29.1835546820981 | epot = -211.690043333607 | etot = -161.727809802026 +570000 ekin = 20.4712421095841 | erot = 30.0658782238937 | epot = -212.489990080473 | etot = -161.952869746995 +571000 ekin = 20.1740626295591 | erot = 34.2763104149801 | epot = -212.99657775615 | etot = -158.54620471161 +572000 ekin = 20.2865908439986 | erot = 32.9711037269835 | epot = -213.258049696028 | etot = -160.000355125046 +573000 ekin = 20.2785763047898 | erot = 32.164420996442 | epot = -213.224973233119 | etot = -160.781975931887 +574000 ekin = 20.73420675937 | erot = 33.4121841231608 | epot = -212.911121076823 | etot = -158.764730194292 +575000 ekin = 20.2170533951852 | erot = 31.3247437485476 | epot = -212.546252872734 | etot = -161.004455729001 +576000 ekin = 19.4298111281265 | erot = 32.3261160719177 | epot = -212.142648109265 | etot = -160.386720909221 +577000 ekin = 19.2647608601736 | erot = 34.7383488770083 | epot = -211.774480661784 | etot = -157.771370924603 +578000 ekin = 18.8591531744448 | erot = 34.9578310327361 | epot = -211.41608019627 | etot = -157.599095989089 +579000 ekin = 19.1764535805344 | erot = 34.5315583779688 | epot = -210.953075025527 | etot = -157.245063067024 +580000 ekin = 19.2853428286521 | erot = 34.6365289435264 | epot = -210.25522157758 | etot = -156.333349805402 +581000 ekin = 18.7906308240455 | erot = 33.6526265209018 | epot = -209.637569234705 | etot = -157.194311889758 +582000 ekin = 19.084905315022 | erot = 30.2130120641441 | epot = -209.11867694325 | etot = -159.820759564084 +583000 ekin = 19.7173995337446 | erot = 30.366640119437 | epot = -208.664312052077 | etot = -158.580272398895 +584000 ekin = 20.3909791819401 | erot = 28.9778999219973 | epot = -208.252182490968 | etot = -158.883303387031 +585000 ekin = 20.9470408507438 | erot = 28.5667963345671 | epot = -208.028127454439 | etot = -158.514290269128 +586000 ekin = 21.8171004518006 | erot = 27.8466229838588 | epot = -208.095369306471 | etot = -158.431645870812 +587000 ekin = 23.1615832403556 | erot = 24.9646595929125 | epot = -208.369983933223 | etot = -160.243741099955 +588000 ekin = 23.8959195121688 | erot = 25.24887078156 | epot = -209.101399059693 | etot = -159.956608765964 +589000 ekin = 24.7834285754863 | erot = 26.0497724346551 | epot = -209.871831515904 | etot = -159.038630505763 +590000 ekin = 25.3936432927543 | erot = 23.6572511459096 | epot = -210.480131773127 | etot = -161.429237334463 +591000 ekin = 25.9278610257486 | erot = 23.0115174388733 | epot = -210.978711850373 | etot = -162.039333385751 +592000 ekin = 27.1309273397085 | erot = 23.1610725306481 | epot = -211.238339753623 | etot = -160.946339883266 +593000 ekin = 26.4574056599296 | erot = 23.5297100340712 | epot = -211.398991430669 | etot = -161.411875736668 +594000 ekin = 26.2135133417378 | erot = 24.3682480979618 | epot = -211.629783890836 | etot = -161.048022451137 +595000 ekin = 26.7143131575838 | erot = 25.9581831810466 | epot = -211.492775841309 | etot = -158.820279502679 +596000 ekin = 25.9981237047512 | erot = 24.5874940201996 | epot = -210.994983795865 | etot = -160.409366070915 +597000 ekin = 25.3691803838513 | erot = 25.6177769896042 | epot = -210.235015094311 | etot = -159.248057720855 +598000 ekin = 23.6665857713897 | erot = 26.7002735359816 | epot = -209.31162840973 | etot = -158.944769102359 +599000 ekin = 22.4410822725131 | erot = 24.4123509303077 | epot = -208.296342188806 | etot = -161.442908985985 +600000 ekin = 22.1604509520165 | erot = 23.7403591164762 | epot = -207.435376754137 | etot = -161.534566685645 +601000 ekin = 22.1910498539915 | erot = 25.7876707770135 | epot = -206.80770864539 | etot = -158.828988014385 +602000 ekin = 21.3191775900909 | erot = 24.1816411383452 | epot = -206.419514787599 | etot = -160.918696059162 +603000 ekin = 21.1724174977999 | erot = 23.1636571932934 | epot = -206.285960522692 | etot = -161.949885831599 +604000 ekin = 20.9177152169245 | erot = 23.0600658965548 | epot = -206.401463523596 | etot = -162.423682410117 +605000 ekin = 20.5881838168339 | erot = 23.4945688308947 | epot = -206.783521776426 | etot = -162.700769128698 +606000 ekin = 20.5566050385019 | erot = 24.4436457663487 | epot = -207.302724003666 | etot = -162.302473198816 +607000 ekin = 20.5889650529151 | erot = 24.2601145277504 | epot = -207.849151297373 | etot = -163.000071716707 +608000 ekin = 20.798561595616 | erot = 24.0529914889943 | epot = -208.221016465144 | etot = -163.369463380534 +609000 ekin = 21.3334604629993 | erot = 21.2987977820021 | epot = -208.39362904366 | etot = -165.761370798658 +610000 ekin = 21.0077312853339 | erot = 24.5390976123487 | epot = -208.423455376914 | etot = -162.876626479231 +611000 ekin = 21.2062750244278 | erot = 25.6924763445408 | epot = -208.465273559828 | etot = -161.566522190859 +612000 ekin = 21.1092285061772 | erot = 23.1681846181344 | epot = -208.369973333871 | etot = -164.09256020956 +613000 ekin = 21.3505829699377 | erot = 23.3795515105117 | epot = -208.252217187376 | etot = -163.522082706926 +614000 ekin = 21.9887200992592 | erot = 22.9814942014575 | epot = -208.08425451512 | etot = -163.114040214403 +615000 ekin = 21.9879302481981 | erot = 23.9474635145876 | epot = -208.112157339249 | etot = -162.176763576463 +616000 ekin = 21.6535652813721 | erot = 25.7665709398204 | epot = -208.073996342823 | etot = -160.653860121631 +617000 ekin = 21.5327802980097 | erot = 25.9126271147335 | epot = -208.081562756535 | etot = -160.636155343791 +618000 ekin = 21.6331060335065 | erot = 25.3216229154819 | epot = -208.118612594362 | etot = -161.163883645373 +619000 ekin = 21.5377257980259 | erot = 24.0810842352126 | epot = -208.182453990811 | etot = -162.563643957572 +620000 ekin = 22.2944761843434 | erot = 26.8961911381653 | epot = -208.572090943205 | etot = -159.381423620697 +621000 ekin = 23.2275714627294 | erot = 28.5194568041071 | epot = -209.005121904323 | etot = -157.258093637486 +622000 ekin = 23.8057112362969 | erot = 28.1725382958721 | epot = -209.310919824284 | etot = -157.332670292115 +623000 ekin = 23.836200160347 | erot = 27.2782572535261 | epot = -209.480204064921 | etot = -158.365746651048 +624000 ekin = 23.5225747889065 | erot = 27.5958156421042 | epot = -209.446824879225 | etot = -158.328434448214 +625000 ekin = 23.3180565211004 | erot = 27.7299743553773 | epot = -209.243975503887 | etot = -158.195944627409 +626000 ekin = 23.6186803255339 | erot = 26.3585577647064 | epot = -208.833123041292 | etot = -158.855884951052 +627000 ekin = 23.7020468224909 | erot = 24.8473737782309 | epot = -208.363264541316 | etot = -159.813843940594 +628000 ekin = 23.234214910991 | erot = 23.6981867115843 | epot = -207.745309999887 | etot = -160.812908377311 +629000 ekin = 22.4918100586061 | erot = 24.881640940065 | epot = -207.051343604772 | etot = -159.677892606101 +630000 ekin = 22.1453629035581 | erot = 20.2998733728557 | epot = -206.39001968886 | etot = -163.944783412446 +631000 ekin = 22.7036826399466 | erot = 18.9834012990071 | epot = -205.753133262548 | etot = -164.066049323594 +632000 ekin = 23.0551963097502 | erot = 19.1201804696073 | epot = -205.05968682992 | etot = -162.884310050562 +633000 ekin = 22.747707004055 | erot = 20.2298517397387 | epot = -204.679628820142 | etot = -161.702070076348 +634000 ekin = 22.1372732618932 | erot = 20.0792269586333 | epot = -204.542150052713 | etot = -162.325649832186 +635000 ekin = 21.9900639375166 | erot = 23.0915091625923 | epot = -204.519806168891 | etot = -159.438233068782 +636000 ekin = 22.4343890150495 | erot = 22.7785270631131 | epot = -204.773050210983 | etot = -159.560134132821 +637000 ekin = 22.4930206180041 | erot = 21.8914552071171 | epot = -205.185291613209 | etot = -160.800815788088 +638000 ekin = 22.6067746447143 | erot = 22.2834374488441 | epot = -205.831736530974 | etot = -160.941524437416 +639000 ekin = 22.9634779459864 | erot = 21.0233006007606 | epot = -206.678000527936 | etot = -162.691221981189 +640000 ekin = 23.0006770449898 | erot = 20.1435647319737 | epot = -207.67418045306 | etot = -164.529938676097 +641000 ekin = 22.6796709156744 | erot = 20.1265770944198 | epot = -208.864068916451 | etot = -166.057820906357 +642000 ekin = 23.0426441097264 | erot = 20.3821125283994 | epot = -210.157224630151 | etot = -166.732467992025 +643000 ekin = 23.6886630072442 | erot = 20.9311429904711 | epot = -211.335279277866 | etot = -166.715473280151 +644000 ekin = 23.3501873913686 | erot = 20.2116989369836 | epot = -212.405134347394 | etot = -168.843248019042 +645000 ekin = 24.214183792306 | erot = 19.1997084892897 | epot = -213.275734343161 | etot = -169.861842061566 +646000 ekin = 24.0032353748067 | erot = 18.7366869191874 | epot = -214.020930167623 | etot = -171.281007873629 +647000 ekin = 24.8268141920476 | erot = 20.0966967362663 | epot = -214.740433438135 | etot = -169.816922509822 +648000 ekin = 24.8649186744143 | erot = 20.9050241858578 | epot = -215.442059068409 | etot = -169.672116208136 +649000 ekin = 24.8646057578191 | erot = 21.521791933497 | epot = -216.156866604821 | etot = -169.770468913505 +650000 ekin = 24.0713138258436 | erot = 22.6881112054577 | epot = -216.962642193737 | etot = -170.203217162436 +651000 ekin = 24.0648474956462 | erot = 21.9056553318526 | epot = -217.68682151817 | etot = -171.716318690672 +652000 ekin = 23.7298725103662 | erot = 21.0498830137315 | epot = -218.178357024535 | etot = -173.398601500437 +653000 ekin = 24.2612309905982 | erot = 20.9396425318005 | epot = -218.402996619013 | etot = -173.202123096615 +654000 ekin = 24.5742837739783 | erot = 21.5842057775824 | epot = -218.453825537757 | etot = -172.295335986196 +655000 ekin = 24.8172949648637 | erot = 21.5633790150742 | epot = -218.138128805473 | etot = -171.757454825535 +656000 ekin = 26.1016118595101 | erot = 20.2089399346234 | epot = -217.608120203544 | etot = -171.29756840941 +657000 ekin = 25.5468936086447 | erot = 20.5700758336473 | epot = -216.896383096438 | etot = -170.779413654146 +658000 ekin = 24.8009166899182 | erot = 20.3492391925765 | epot = -215.907642384675 | etot = -170.75748650218 +659000 ekin = 24.2700519127878 | erot = 19.3880786744432 | epot = -214.779591604614 | etot = -171.121461017383 +660000 ekin = 23.7386557662651 | erot = 17.3667145566108 | epot = -213.671617228208 | etot = -172.566246905332 +661000 ekin = 23.101615905894 | erot = 18.0746065237967 | epot = -212.813170220349 | etot = -171.636947790658 +662000 ekin = 23.5132942257758 | erot = 19.3913290878883 | epot = -212.178312398575 | etot = -169.27368908491 +663000 ekin = 22.8490848881554 | erot = 22.3558454667425 | epot = -211.708233502208 | etot = -166.50330314731 +664000 ekin = 22.5371891975751 | erot = 23.8324410238751 | epot = -211.630305812256 | etot = -165.260675590806 +665000 ekin = 22.4828402581824 | erot = 22.1418709319913 | epot = -211.932335178627 | etot = -167.307623988453 +666000 ekin = 21.658575574868 | erot = 23.2685049016563 | epot = -212.34419719029 | etot = -167.417116713765 +667000 ekin = 21.746716005369 | erot = 26.6231378444392 | epot = -212.869195610415 | etot = -164.499341760607 +668000 ekin = 21.8400234731699 | erot = 27.0215900877162 | epot = -213.230575394842 | etot = -164.368961833956 +669000 ekin = 21.5717180264524 | erot = 25.4843097358269 | epot = -213.402729296273 | etot = -166.346701533994 +670000 ekin = 21.2159612264746 | erot = 27.0486352599825 | epot = -213.623541173123 | etot = -165.358944686665 +671000 ekin = 21.0316750378212 | erot = 28.2790369826503 | epot = -213.670944628475 | etot = -164.360232608003 +672000 ekin = 21.0540110477226 | erot = 27.9477049264318 | epot = -213.821833683391 | etot = -164.820117709236 +673000 ekin = 20.622467197854 | erot = 31.8631428606973 | epot = -214.143301465583 | etot = -161.657691407032 +674000 ekin = 19.7399937911566 | erot = 31.3007461152899 | epot = -214.328096065417 | etot = -163.287356158971 +675000 ekin = 19.6812168375245 | erot = 28.9841135234018 | epot = -214.58757301913 | etot = -165.922242658204 +676000 ekin = 20.2683648931208 | erot = 29.0544957444103 | epot = -214.986567261058 | etot = -165.663706623527 +677000 ekin = 20.4847241494001 | erot = 27.1326629448698 | epot = -215.500686522809 | etot = -167.88329942854 +678000 ekin = 21.302019725926 | erot = 26.9440120099185 | epot = -215.97832097774 | etot = -167.732289241896 +679000 ekin = 20.7252183388119 | erot = 27.5800790128446 | epot = -216.242490346929 | etot = -167.937192995272 +680000 ekin = 21.1467020674332 | erot = 27.5476121215625 | epot = -216.37538065002 | etot = -167.681066461025 +681000 ekin = 20.7720273332215 | erot = 27.1624962363794 | epot = -216.426580638711 | etot = -168.49205706911 +682000 ekin = 20.4708699436742 | erot = 26.3358564577069 | epot = -216.448305176171 | etot = -169.64157877479 +683000 ekin = 19.8000088900235 | erot = 27.4272282812591 | epot = -216.207270658414 | etot = -168.980033487131 +684000 ekin = 20.1500542970064 | erot = 26.0761853873505 | epot = -215.864502199571 | etot = -169.638262515214 +685000 ekin = 19.8486865740984 | erot = 26.0238267262043 | epot = -215.500516760578 | etot = -169.628003460275 +686000 ekin = 19.7513338939334 | erot = 25.3757647595747 | epot = -215.210189827277 | etot = -170.083091173769 +687000 ekin = 20.7214918102431 | erot = 24.1072372944022 | epot = -214.967239797801 | etot = -170.138510693156 +688000 ekin = 21.0626981869003 | erot = 23.2762891547382 | epot = -214.979397567732 | etot = -170.640410226093 +689000 ekin = 21.5266424344628 | erot = 20.7174231605385 | epot = -215.094101507179 | etot = -172.850035912178 +690000 ekin = 22.5491523723621 | erot = 20.847571984209 | epot = -214.986970380787 | etot = -171.590246024216 +691000 ekin = 23.8583355308872 | erot = 22.0099769027697 | epot = -214.848454555845 | etot = -168.980142122188 +692000 ekin = 24.96520872453 | erot = 21.4857106199454 | epot = -214.494800129558 | etot = -168.043880785083 +693000 ekin = 26.0051918382276 | erot = 21.3733007404598 | epot = -214.001727781338 | etot = -166.623235202651 +694000 ekin = 26.4392720652869 | erot = 21.3317762759646 | epot = -213.263998412814 | etot = -165.492950071562 +695000 ekin = 27.3615193041949 | erot = 20.6921753134717 | epot = -212.356901954365 | etot = -164.303207336699 +696000 ekin = 27.3093057978157 | erot = 20.0965375265573 | epot = -211.297735908804 | etot = -163.891892584431 +697000 ekin = 26.7453316152447 | erot = 18.7856987042669 | epot = -210.110607673786 | etot = -164.579577354274 +698000 ekin = 25.5722707624857 | erot = 19.6853079921957 | epot = -209.125608153436 | etot = -163.868029398755 +699000 ekin = 24.9916657277841 | erot = 18.4661630806181 | epot = -208.42973768859 | etot = -164.971908880188 +700000 ekin = 24.521058485274 | erot = 16.84944737211 | epot = -207.9193858017 | etot = -166.548879944316 +701000 ekin = 23.7778912460905 | erot = 19.3168143286452 | epot = -207.673622403358 | etot = -164.578916828622 +702000 ekin = 23.4418540405128 | erot = 17.9399262410738 | epot = -207.631679946816 | etot = -166.24989966523 +703000 ekin = 22.5362735605758 | erot = 16.8799469700555 | epot = -207.655410737567 | etot = -168.239190206935 +704000 ekin = 21.6771800595091 | erot = 17.1833672937461 | epot = -207.854126531408 | etot = -168.993579178153 +705000 ekin = 21.4420921851221 | erot = 20.8433776157946 | epot = -208.2214030325 | etot = -165.935933231584 +706000 ekin = 21.2415323522356 | erot = 21.0841388634033 | epot = -208.785212184223 | etot = -166.459540968584 +707000 ekin = 21.1211180279557 | erot = 22.7053094579755 | epot = -209.418467814605 | etot = -165.592040328673 +708000 ekin = 21.4313901815259 | erot = 21.142901789246 | epot = -210.045555019851 | etot = -167.471263049079 +709000 ekin = 21.1002753292038 | erot = 22.8489798007674 | epot = -210.826178475879 | etot = -166.876923345908 +710000 ekin = 21.8422173465255 | erot = 20.0932738292303 | epot = -211.532469955408 | etot = -169.596978779652 +711000 ekin = 22.1026708164741 | erot = 22.4726045475365 | epot = -212.126194080497 | etot = -167.550918716487 +712000 ekin = 22.4258695027194 | erot = 21.442958222841 | epot = -212.558458286709 | etot = -168.689630561149 +713000 ekin = 22.5222749624208 | erot = 20.3898387031543 | epot = -212.978786634482 | etot = -170.066672968907 +714000 ekin = 22.1262254185207 | erot = 21.2706738146545 | epot = -213.406504414377 | etot = -170.009605181201 +715000 ekin = 21.6589564668707 | erot = 22.8713228305269 | epot = -214.103705031576 | etot = -169.573425734178 +716000 ekin = 22.8499377351371 | erot = 22.5811259198023 | epot = -214.886932195704 | etot = -169.455868540765 +717000 ekin = 23.1453273466383 | erot = 22.0823648529859 | epot = -215.752901424345 | etot = -170.52520922472 +718000 ekin = 23.4911204712306 | erot = 21.8266696386258 | epot = -216.797611238792 | etot = -171.479821128935 +719000 ekin = 23.5427559868846 | erot = 20.6352185380146 | epot = -217.868984095443 | etot = -173.691009570544 +720000 ekin = 24.6730711390776 | erot = 21.7437690143765 | epot = -218.925770671597 | etot = -172.508930518143 +721000 ekin = 25.2403931355773 | erot = 19.4577236844891 | epot = -219.945055136347 | etot = -175.246938316281 +722000 ekin = 25.7389977817124 | erot = 21.6950149985872 | epot = -220.731451014357 | etot = -173.297438234057 +723000 ekin = 24.59999507444 | erot = 24.4179337524363 | epot = -221.359631454453 | etot = -172.341702627577 +724000 ekin = 23.8141214256889 | erot = 25.3193356469838 | epot = -221.823580154673 | etot = -172.690123082 +725000 ekin = 23.3651337491413 | erot = 28.7091491551534 | epot = -222.090867886168 | etot = -170.016584981873 +726000 ekin = 23.1307089149661 | erot = 29.7953383527835 | epot = -222.003607909333 | etot = -169.077560641584 +727000 ekin = 22.6496655720656 | erot = 29.2473418500935 | epot = -221.635062275438 | etot = -169.738054853278 +728000 ekin = 21.811364434554 | erot = 31.7331322577198 | epot = -221.154414993919 | etot = -167.609918301645 +729000 ekin = 20.4746743669592 | erot = 32.546576149833 | epot = -220.690887684563 | etot = -167.669637167771 +730000 ekin = 19.8147243806315 | erot = 34.9007244000495 | epot = -220.114078177837 | etot = -165.398629397156 +731000 ekin = 18.6145766929913 | erot = 34.0320241969118 | epot = -219.536330230485 | etot = -166.889729340582 +732000 ekin = 17.8112285881693 | erot = 34.0479803252401 | epot = -218.968869737311 | etot = -167.109660823901 +733000 ekin = 17.6476056471454 | erot = 34.2057929926945 | epot = -218.3294527504 | etot = -166.47605411056 +734000 ekin = 17.7690619853332 | erot = 32.1417337283976 | epot = -217.520065128183 | etot = -167.609269414452 +735000 ekin = 17.0579199291445 | erot = 30.2470102548337 | epot = -216.550373483739 | etot = -169.245443299761 +736000 ekin = 17.5498866135578 | erot = 29.3166528563917 | epot = -215.643405297165 | etot = -168.776865827216 +737000 ekin = 17.6187796043555 | erot = 26.3475349686048 | epot = -214.809218139055 | etot = -170.842903566094 +738000 ekin = 18.2269608592319 | erot = 25.7040359881548 | epot = -214.115591404826 | etot = -170.18459455744 +739000 ekin = 18.7173977512819 | erot = 24.4619685419347 | epot = -213.441484725329 | etot = -170.262118432112 +740000 ekin = 19.0110962436152 | erot = 22.142772803043 | epot = -212.815607635912 | etot = -171.661738589254 +741000 ekin = 18.9267028320974 | erot = 21.3358168112262 | epot = -212.366636079153 | etot = -172.104116435829 +742000 ekin = 19.3549116475726 | erot = 19.5096408469649 | epot = -212.216543882057 | etot = -173.35199138752 +743000 ekin = 20.119013306821 | erot = 18.4104477349336 | epot = -212.288606698492 | etot = -173.759145656738 +744000 ekin = 20.3566526518901 | erot = 19.4246888199086 | epot = -212.75389749051 | etot = -172.972556018711 +745000 ekin = 21.1509415657888 | erot = 20.1659043839807 | epot = -213.418747745429 | etot = -172.10190179566 +746000 ekin = 21.3037423527627 | erot = 20.2172486917649 | epot = -214.157876553476 | etot = -172.636885508949 +747000 ekin = 22.3146611040097 | erot = 21.9871375259789 | epot = -214.88232405197 | etot = -170.580525421981 +748000 ekin = 22.2283253425591 | erot = 22.5065193409822 | epot = -215.506784482801 | etot = -170.77193979926 +749000 ekin = 21.7915806164301 | erot = 22.1396569978617 | epot = -215.707286574207 | etot = -171.776048959915 +750000 ekin = 22.4607758902159 | erot = 23.0482930283985 | epot = -215.651390580345 | etot = -170.142321661731 +751000 ekin = 21.6437369626355 | erot = 20.9291810842114 | epot = -215.338251046595 | etot = -172.765332999748 +752000 ekin = 21.0774801700924 | erot = 19.7791759941412 | epot = -214.933012142375 | etot = -174.076355978141 +753000 ekin = 20.2142777715798 | erot = 19.9156489858756 | epot = -214.515836213762 | etot = -174.385909456307 +754000 ekin = 20.550710880581 | erot = 21.7521689158874 | epot = -214.220858046315 | etot = -171.917978249847 +755000 ekin = 20.4661806652476 | erot = 22.5423956641592 | epot = -214.061716510521 | etot = -171.053140181114 +756000 ekin = 20.9954844614009 | erot = 22.4473939364008 | epot = -213.92503672056 | etot = -170.482158322758 +757000 ekin = 20.6283594838306 | erot = 21.4270437425632 | epot = -213.790125131555 | etot = -171.734721905161 +758000 ekin = 20.5508018897077 | erot = 20.9536901677692 | epot = -213.663158456533 | etot = -172.158666399056 +759000 ekin = 19.6263241751684 | erot = 23.4476640487024 | epot = -213.66383402851 | etot = -170.589845804639 +760000 ekin = 19.9340259748652 | erot = 22.6482020561595 | epot = -213.71724602475 | etot = -171.135017993725 +761000 ekin = 19.6910494084164 | erot = 22.0029116902266 | epot = -213.754878089614 | etot = -172.060916990971 +762000 ekin = 19.7910800016039 | erot = 22.5984804286307 | epot = -213.965250022108 | etot = -171.575689591873 +763000 ekin = 20.5238796096632 | erot = 22.2928877563363 | epot = -214.47551076934 | etot = -171.658743403341 +764000 ekin = 20.6650033448462 | erot = 24.6171910330824 | epot = -214.890202898626 | etot = -169.608008520698 +765000 ekin = 20.4618665382424 | erot = 25.8587140484164 | epot = -215.138274656898 | etot = -168.817694070239 +766000 ekin = 19.6548882123823 | erot = 25.0439293422707 | epot = -215.348875696047 | etot = -170.650058141394 +767000 ekin = 19.3270400363748 | erot = 25.2554744973183 | epot = -215.248876217743 | etot = -170.66636168405 +768000 ekin = 18.5163875301612 | erot = 26.9740801270243 | epot = -214.975549734016 | etot = -169.485082076831 +769000 ekin = 19.2689096458285 | erot = 26.7549801973199 | epot = -214.627183257247 | etot = -168.603293414099 +770000 ekin = 20.3065357099473 | erot = 24.5864981815754 | epot = -214.449155022355 | etot = -169.556121130832 +771000 ekin = 19.8160989352992 | erot = 24.3795653656177 | epot = -214.568609385595 | etot = -170.372945084678 +772000 ekin = 20.0808636272602 | erot = 25.3489458930141 | epot = -214.810149634203 | etot = -169.380340113928 +773000 ekin = 20.4572934790689 | erot = 23.9373155006916 | epot = -215.368798012186 | etot = -170.974189032425 +774000 ekin = 21.4581254177255 | erot = 24.8038079049394 | epot = -216.135566629648 | etot = -169.873633306983 +775000 ekin = 21.56609423293 | erot = 24.7269407163978 | epot = -217.095913678146 | etot = -170.802878728818 +776000 ekin = 21.7139623963331 | erot = 24.678564784346 | epot = -217.949762418936 | etot = -171.557235238257 +777000 ekin = 22.1382470902253 | erot = 26.3515368343078 | epot = -218.812121008321 | etot = -170.322337083788 +778000 ekin = 22.6753074399956 | erot = 26.7132834273965 | epot = -219.665211222619 | etot = -170.276620355226 +779000 ekin = 23.2722008637946 | erot = 25.1496800354838 | epot = -220.353105007404 | etot = -171.931224108126 +780000 ekin = 23.0129926689262 | erot = 23.0916850844916 | epot = -220.994134927724 | etot = -174.889457174306 +781000 ekin = 23.786429669784 | erot = 25.1844301582418 | epot = -221.387914121756 | etot = -172.41705429373 +782000 ekin = 23.5606686383571 | erot = 26.3634060367889 | epot = -221.434267464486 | etot = -171.51019278934 +783000 ekin = 24.0155758037646 | erot = 26.6670282787156 | epot = -221.227091913094 | etot = -170.544487830613 +784000 ekin = 24.0357990642713 | erot = 25.6617687084465 | epot = -220.907876114701 | etot = -171.210308341983 +785000 ekin = 24.5524506997925 | erot = 24.7676360875449 | epot = -220.413360888571 | etot = -171.093274101234 +786000 ekin = 24.4055025806397 | erot = 24.6030636477925 | epot = -219.720284916293 | etot = -170.711718687861 +787000 ekin = 25.0410360300686 | erot = 22.998359933619 | epot = -218.996593162027 | etot = -170.95719719834 +788000 ekin = 24.767877979881 | erot = 21.7923381425487 | epot = -218.352848534383 | etot = -171.792632411953 +789000 ekin = 24.8408040750631 | erot = 24.1208833257935 | epot = -217.830352648894 | etot = -168.868665248037 +790000 ekin = 24.4896562826161 | erot = 23.8855568181502 | epot = -217.476066337486 | etot = -169.10085323672 +791000 ekin = 24.295800420788 | erot = 22.2236025604802 | epot = -217.181373280855 | etot = -170.661970299587 +792000 ekin = 23.8380813001559 | erot = 20.6465905204417 | epot = -216.979132071427 | etot = -172.494460250829 +793000 ekin = 23.4376405312798 | erot = 22.3758695226247 | epot = -217.013967781529 | etot = -171.200457727625 +794000 ekin = 23.6651564360299 | erot = 24.5594365423356 | epot = -217.322425543396 | etot = -169.097832565031 +795000 ekin = 24.2246572084756 | erot = 24.523759714456 | epot = -217.532287869643 | etot = -168.783870946711 +796000 ekin = 24.0060240578042 | erot = 25.0471365078935 | epot = -217.591289135025 | etot = -168.538128569328 +797000 ekin = 24.6806226103091 | erot = 24.5153114750642 | epot = -217.396581247709 | etot = -168.200647162335 +798000 ekin = 23.743570188968 | erot = 26.0446750366824 | epot = -217.042257715778 | etot = -167.254012490128 +799000 ekin = 23.6918256055875 | erot = 25.3998427121517 | epot = -216.430832155802 | etot = -167.339163838063 +800000 ekin = 23.9795390809841 | erot = 26.2050804883332 | epot = -215.909334288757 | etot = -165.724714719439 +801000 ekin = 22.9818713498596 | erot = 26.0822510026421 | epot = -215.192675863883 | etot = -166.128553511382 +802000 ekin = 22.6987202252713 | erot = 24.4605697174941 | epot = -214.288341115587 | etot = -167.129051172822 +803000 ekin = 22.5973595447689 | erot = 25.0746177868642 | epot = -213.399668666611 | etot = -165.727691334978 +804000 ekin = 22.5679051171115 | erot = 23.8929873743116 | epot = -212.445166364649 | etot = -165.984273873226 +805000 ekin = 23.9825063136489 | erot = 23.4605910900564 | epot = -211.763911653385 | etot = -164.32081424968 +806000 ekin = 23.7122851358872 | erot = 24.3242427199374 | epot = -211.391629930493 | etot = -163.355102074668 +807000 ekin = 24.334807708307 | erot = 25.0191489745547 | epot = -211.002022647805 | etot = -161.648065964944 +808000 ekin = 23.5785338219753 | erot = 25.682978373141 | epot = -210.682430009381 | etot = -161.420917814264 +809000 ekin = 23.2672257998437 | erot = 23.7727702775216 | epot = -210.482421836394 | etot = -163.442425759029 +810000 ekin = 23.2973748071818 | erot = 24.561611045747 | epot = -210.255015349723 | etot = -162.396029496794 +811000 ekin = 24.0082703459793 | erot = 24.8986235898251 | epot = -210.100128510354 | etot = -161.19323457455 +812000 ekin = 23.5717850105925 | erot = 22.2118475566537 | epot = -210.079952231166 | etot = -164.29631966392 +813000 ekin = 23.8144414957769 | erot = 23.7648492562902 | epot = -210.006754772319 | etot = -162.427464020252 +814000 ekin = 23.3465977086067 | erot = 23.58039301019 | epot = -210.26830643344 | etot = -163.341315714643 +815000 ekin = 23.7706537845421 | erot = 23.6859516971766 | epot = -210.69986675248 | etot = -163.243261270761 +816000 ekin = 24.4396723738333 | erot = 20.7642731167639 | epot = -211.197880702624 | etot = -165.993935212026 +817000 ekin = 24.5050242640549 | erot = 20.1975149970127 | epot = -211.716456063282 | etot = -167.013916802214 +818000 ekin = 24.6467770699857 | erot = 21.529583415028 | epot = -212.178224182293 | etot = -166.001863697279 +819000 ekin = 23.9362784569689 | erot = 21.885485913296 | epot = -212.7074517228 | etot = -166.885687352535 +820000 ekin = 23.8925161494513 | erot = 21.7993180032808 | epot = -213.102576947411 | etot = -167.410742794679 +821000 ekin = 24.2038142478228 | erot = 22.9479343465945 | epot = -213.713003298829 | etot = -166.561254704412 +822000 ekin = 24.9372292708339 | erot = 23.3111003411094 | epot = -214.446490633768 | etot = -166.198161021825 +823000 ekin = 24.9810184744614 | erot = 19.3880692104392 | epot = -215.313873180455 | etot = -170.944785495554 +824000 ekin = 25.3757196310442 | erot = 19.1383506800577 | epot = -216.195322093276 | etot = -171.681251782174 +825000 ekin = 25.7714493929878 | erot = 20.7852688563227 | epot = -217.289068840725 | etot = -170.732350591415 +826000 ekin = 26.8493153910039 | erot = 21.6412827777179 | epot = -218.435288959846 | etot = -169.944690791124 +827000 ekin = 27.3839801920855 | erot = 21.4692964838888 | epot = -219.392426378877 | etot = -170.539149702903 +828000 ekin = 27.229680724747 | erot = 19.6329742054381 | epot = -220.273927299677 | etot = -173.411272369491 +829000 ekin = 28.1128884812802 | erot = 20.9502927197495 | epot = -221.21471082526 | etot = -172.15152962423 +830000 ekin = 28.8435364019276 | erot = 21.7826449636337 | epot = -222.278080486409 | etot = -171.651899120847 +831000 ekin = 28.382403945525 | erot = 21.9470916756457 | epot = -223.209359588942 | etot = -172.879863967771 +832000 ekin = 29.2687628401495 | erot = 20.5210693984925 | epot = -223.940697765464 | etot = -174.150865526822 +833000 ekin = 29.8001169918452 | erot = 19.1336112091991 | epot = -224.577996191363 | etot = -175.644267990319 +834000 ekin = 29.988952353328 | erot = 18.4370859277507 | epot = -225.027611469757 | etot = -176.601573188678 +835000 ekin = 31.1943711572552 | erot = 19.9395820078326 | epot = -225.505582228924 | etot = -174.371629063836 +836000 ekin = 31.4486064464243 | erot = 18.8230392617263 | epot = -225.897370125356 | etot = -175.625724417205 +837000 ekin = 30.897968105625 | erot = 17.525936203234 | epot = -226.014420243358 | etot = -177.590515934499 +838000 ekin = 30.3278609246781 | erot = 17.8376744101104 | epot = -225.874910017182 | etot = -177.709374682393 +839000 ekin = 28.5705963055734 | erot = 19.0197374605662 | epot = -225.567956855126 | etot = -177.977623088986 +840000 ekin = 27.8420547779393 | erot = 20.3181282989612 | epot = -225.084398799451 | etot = -176.924215722551 +841000 ekin = 26.578531878898 | erot = 18.291693309889 | epot = -224.600684647618 | etot = -179.730459458831 +842000 ekin = 25.021856816298 | erot = 17.0225406378546 | epot = -224.142254239588 | etot = -182.097856785436 +843000 ekin = 23.9095699919698 | erot = 15.4704933701473 | epot = -223.646706047482 | etot = -184.266642685364 +844000 ekin = 22.5803633860571 | erot = 15.9225454375333 | epot = -223.270602971588 | etot = -184.767694147998 +845000 ekin = 22.8380208177356 | erot = 16.9518494619353 | epot = -223.143196252822 | etot = -183.353325973152 +846000 ekin = 22.6092342503318 | erot = 19.1522264883275 | epot = -223.294605543864 | etot = -181.533144805205 +847000 ekin = 22.8438035235789 | erot = 20.5201034436593 | epot = -223.473679851918 | etot = -180.10977288468 +848000 ekin = 24.096705623773 | erot = 23.2844333976006 | epot = -223.639763222442 | etot = -176.258624201068 +849000 ekin = 23.4884021207942 | erot = 25.3929694182074 | epot = -223.896170953652 | etot = -175.01479941465 +850000 ekin = 22.6242009333951 | erot = 26.9404543040126 | epot = -224.252836199893 | etot = -174.688180962486 +851000 ekin = 22.462800324761 | erot = 26.1722746584294 | epot = -224.607456254157 | etot = -175.972381270966 +852000 ekin = 22.9338232909787 | erot = 26.8967348092924 | epot = -224.962026374242 | etot = -175.131468273971 +853000 ekin = 23.5089803042907 | erot = 26.2817254800077 | epot = -225.253808794644 | etot = -175.463103010346 +854000 ekin = 23.4667891668536 | erot = 26.9521294085684 | epot = -225.450940504292 | etot = -175.03202192887 +855000 ekin = 22.8308419775732 | erot = 26.0448263395011 | epot = -225.58818928127 | etot = -176.712520964196 +856000 ekin = 22.8838807708131 | erot = 28.3173269449285 | epot = -225.61075714919 | etot = -174.409549433448 +857000 ekin = 23.1624988447929 | erot = 28.1731020031475 | epot = -225.539880019331 | etot = -174.204279171391 +858000 ekin = 23.010544463387 | erot = 27.4142307819788 | epot = -225.412270604551 | etot = -174.987495359185 +859000 ekin = 22.7753414049503 | erot = 27.6211492713748 | epot = -225.124163927943 | etot = -174.727673251618 +860000 ekin = 23.2703861283527 | erot = 24.9426356523561 | epot = -224.786259608365 | etot = -176.573237827656 +861000 ekin = 23.7729389676944 | erot = 24.8447311566921 | epot = -224.563551923108 | etot = -175.945881798722 +862000 ekin = 23.5340740192712 | erot = 24.4915624205987 | epot = -224.357805969819 | etot = -176.332169529949 +863000 ekin = 23.7375308575266 | erot = 24.2323944373344 | epot = -224.144044493851 | etot = -176.17411919899 +864000 ekin = 23.3716941352973 | erot = 22.3641269665702 | epot = -223.879914649663 | etot = -178.144093547796 +865000 ekin = 23.1186430050472 | erot = 22.7161380633252 | epot = -223.612787576836 | etot = -177.778006508463 +866000 ekin = 22.0842043208688 | erot = 24.9778691380164 | epot = -223.307430080952 | etot = -176.245356622066 +867000 ekin = 21.1657335889336 | erot = 26.0383220824095 | epot = -223.101208746092 | etot = -175.897153074749 +868000 ekin = 20.7974073535693 | erot = 26.8327425921659 | epot = -222.794942007792 | etot = -175.164792062057 +869000 ekin = 20.4042118249737 | erot = 27.1429100482463 | epot = -222.436116261228 | etot = -174.888994388008 +870000 ekin = 20.1957141053955 | erot = 25.7366487329437 | epot = -221.955207275389 | etot = -176.02284443705 +871000 ekin = 20.2123557957261 | erot = 25.1939802920791 | epot = -221.256690821026 | etot = -175.850354733221 +872000 ekin = 20.4032419950175 | erot = 25.4624355027898 | epot = -220.516968111741 | etot = -174.651290613934 +873000 ekin = 19.7555498360178 | erot = 24.5861053407173 | epot = -219.769573418505 | etot = -175.42791824177 +874000 ekin = 18.6683455164676 | erot = 24.6077624002317 | epot = -219.119875205566 | etot = -175.843767288867 +875000 ekin = 18.1744504561662 | erot = 24.6987338548905 | epot = -218.47231102186 | etot = -175.599126710803 +876000 ekin = 18.4401297958598 | erot = 25.8115012454218 | epot = -217.9495809478 | etot = -173.697949906518 +877000 ekin = 17.664381190264 | erot = 26.0938124408268 | epot = -217.613305746208 | etot = -173.855112115117 +878000 ekin = 17.5155425895501 | erot = 26.1251978929977 | epot = -217.353846093228 | etot = -173.71310561068 +879000 ekin = 18.0158870329902 | erot = 22.9229967356032 | epot = -217.142818533763 | etot = -176.20393476517 +880000 ekin = 18.2898091775908 | erot = 21.9678230763756 | epot = -216.947884971478 | etot = -176.690252717512 +881000 ekin = 18.2557212304153 | erot = 20.7986777914948 | epot = -216.867472880906 | etot = -177.813073858995 +882000 ekin = 18.6882799858829 | erot = 22.2873864360058 | epot = -217.05073780239 | etot = -176.075071380501 +883000 ekin = 18.9334632698957 | erot = 21.3254259967097 | epot = -217.335733022766 | etot = -177.076843756161 +884000 ekin = 19.7058560972579 | erot = 20.8095031819962 | epot = -217.759932525085 | etot = -177.244573245831 +885000 ekin = 20.2112631550784 | erot = 19.5575411920434 | epot = -218.268786439491 | etot = -178.49998209237 +886000 ekin = 20.7002616226387 | erot = 19.310776902867 | epot = -218.766008187746 | etot = -178.75496966224 +887000 ekin = 21.556043787289 | erot = 18.6474685520941 | epot = -219.158663992651 | etot = -178.955151653268 +888000 ekin = 21.3334930006689 | erot = 20.4856021155481 | epot = -219.579651710559 | etot = -177.760556594342 +889000 ekin = 22.171697390566 | erot = 20.6166150577233 | epot = -220.153325957315 | etot = -177.365013509026 +890000 ekin = 22.2345451037052 | erot = 21.2895106408631 | epot = -220.540453919156 | etot = -177.016398174588 +891000 ekin = 22.2608122330327 | erot = 20.1682134340203 | epot = -220.830256027334 | etot = -178.401230360281 +892000 ekin = 22.2667041004928 | erot = 21.1835211310339 | epot = -220.974423299556 | etot = -177.52419806803 +893000 ekin = 22.8785998921146 | erot = 22.2656591807102 | epot = -220.854501706686 | etot = -175.710242633862 +894000 ekin = 22.7070083180718 | erot = 20.7443672875634 | epot = -220.57293320363 | etot = -177.121557597995 +895000 ekin = 22.4994314958752 | erot = 20.2750367527769 | epot = -220.21529694266 | etot = -177.440828694008 +896000 ekin = 22.6862504668757 | erot = 21.9474616043293 | epot = -219.676966141549 | etot = -175.043254070344 +897000 ekin = 22.4101657769622 | erot = 20.2849313539379 | epot = -218.954521501181 | etot = -176.259424370281 +898000 ekin = 22.6067604772945 | erot = 22.1361684291271 | epot = -218.088311088299 | etot = -173.345382181877 +899000 ekin = 22.6002362519927 | erot = 22.9443785260411 | epot = -217.224223257415 | etot = -171.679608479382 +900000 ekin = 22.2271969756017 | erot = 21.2795539705332 | epot = -216.378348455151 | etot = -172.871597509016 +901000 ekin = 22.049601241704 | erot = 19.6983125737511 | epot = -215.642075676261 | etot = -173.894161860806 +902000 ekin = 21.5373973946795 | erot = 20.0636413054755 | epot = -215.059151442717 | etot = -173.458112742562 +903000 ekin = 21.3273338630826 | erot = 20.6238147912146 | epot = -214.498710762212 | etot = -172.547562107915 +904000 ekin = 21.0822000097366 | erot = 21.2140090803987 | epot = -214.106117024932 | etot = -171.809907934796 +905000 ekin = 20.688573504515 | erot = 23.6425315011056 | epot = -213.989802974573 | etot = -169.658697968952 +906000 ekin = 20.8777040514165 | erot = 22.1389592583989 | epot = -213.961705252052 | etot = -170.945041942237 +907000 ekin = 21.5380348777401 | erot = 20.2343470856017 | epot = -214.064513257377 | etot = -172.292131294036 +908000 ekin = 20.9274847289174 | erot = 22.9159415344444 | epot = -214.205523604128 | etot = -170.362097340766 +909000 ekin = 20.7056821583171 | erot = 23.1534436178424 | epot = -214.128940350364 | etot = -170.269814574204 +910000 ekin = 20.6850690694788 | erot = 21.783469726861 | epot = -213.91187960968 | etot = -171.44334081334 +911000 ekin = 20.4049026492844 | erot = 24.4277842653814 | epot = -213.485163443353 | etot = -168.652476528687 +912000 ekin = 20.6124368604298 | erot = 25.2278717850118 | epot = -212.994133996415 | etot = -167.153825350974 +913000 ekin = 20.3761012114308 | erot = 24.7723910910313 | epot = -212.657154422535 | etot = -167.508662120073 +914000 ekin = 19.8968997426853 | erot = 25.4410819754834 | epot = -212.497368647685 | etot = -167.159386929516 +915000 ekin = 19.9950171951882 | erot = 25.9419095773569 | epot = -212.507529869006 | etot = -166.570603096461 +916000 ekin = 19.6549262075363 | erot = 24.538237997724 | epot = -212.481735916643 | etot = -168.288571711383 +917000 ekin = 19.1943251031612 | erot = 24.31332627058 | epot = -212.593107757692 | etot = -169.085456383951 +918000 ekin = 18.3242362402623 | erot = 22.0402118609707 | epot = -212.817817515526 | etot = -172.453369414293 +919000 ekin = 18.4622091649616 | erot = 22.0712625398805 | epot = -213.248725483561 | etot = -172.715253778719 +920000 ekin = 19.2487751773886 | erot = 25.3359478866229 | epot = -213.780255594758 | etot = -169.195532530746 +921000 ekin = 19.5018854862383 | erot = 23.5233553159472 | epot = -214.227012786969 | etot = -171.201771984784 +922000 ekin = 20.0460346272463 | erot = 23.3015862848816 | epot = -214.628134308544 | etot = -171.280513396416 +923000 ekin = 19.2900442060425 | erot = 21.7882354465828 | epot = -215.132996794542 | etot = -174.054717141917 +924000 ekin = 19.8084784518446 | erot = 20.6067657458497 | epot = -215.520425153804 | etot = -175.10518095611 +925000 ekin = 19.4297747207056 | erot = 19.7971794451035 | epot = -215.775169090021 | etot = -176.548214924211 +926000 ekin = 19.6579133002046 | erot = 19.0438552077666 | epot = -215.748052097731 | etot = -177.04628358976 +927000 ekin = 20.4195662533946 | erot = 18.9593050109652 | epot = -215.618862876762 | etot = -176.239991612402 +928000 ekin = 20.4817836282247 | erot = 18.9847825923888 | epot = -215.304393191577 | etot = -175.837826970963 +929000 ekin = 20.9504941576429 | erot = 19.7784806309953 | epot = -214.727990541094 | etot = -173.999015752456 +930000 ekin = 21.1315408433683 | erot = 20.6616164444539 | epot = -214.061785502445 | etot = -172.268628214623 +931000 ekin = 21.2634088922109 | erot = 21.9365830714564 | epot = -213.529347543443 | etot = -170.329355579775 +932000 ekin = 21.006213211584 | erot = 21.2825267850011 | epot = -212.999183574852 | etot = -170.710443578267 +933000 ekin = 21.2284411209639 | erot = 20.8232596682586 | epot = -212.371172372981 | etot = -170.319471583758 +934000 ekin = 20.5279385282457 | erot = 20.1701889387579 | epot = -211.858985221721 | etot = -171.160857754718 +935000 ekin = 20.1948548273404 | erot = 19.538371480896 | epot = -211.862647749463 | etot = -172.129421441226 +936000 ekin = 20.1806679134658 | erot = 21.4990281973767 | epot = -212.443949037452 | etot = -170.76425292661 +937000 ekin = 20.0545914091422 | erot = 20.9834617113798 | epot = -213.292670869919 | etot = -172.254617749397 +938000 ekin = 19.8082215701157 | erot = 20.8974589230379 | epot = -214.037804111151 | etot = -173.332123617997 +939000 ekin = 20.3649856793841 | erot = 23.9090631210053 | epot = -214.809663951944 | etot = -170.535615151554 +940000 ekin = 20.9455103352144 | erot = 24.9039051347133 | epot = -215.699887091858 | etot = -169.850471621931 +941000 ekin = 22.0008473383399 | erot = 23.3113935488402 | epot = -216.614986710114 | etot = -171.302745822934 +942000 ekin = 21.6408089485804 | erot = 26.4701413664084 | epot = -217.436072618249 | etot = -169.32512230326 +943000 ekin = 22.0375713327493 | erot = 23.8525644765125 | epot = -218.064504556064 | etot = -172.174368746803 +944000 ekin = 21.3825689791004 | erot = 22.0065856356145 | epot = -218.486120233654 | etot = -175.096965618939 +945000 ekin = 20.850173972681 | erot = 21.1332702356783 | epot = -218.794495873448 | etot = -176.811051665089 +946000 ekin = 20.4139375222148 | erot = 23.6679631776017 | epot = -219.021459743601 | etot = -174.939559043785 +947000 ekin = 20.1906398813672 | erot = 26.5654138598139 | epot = -218.929211499128 | etot = -172.173157757947 +948000 ekin = 20.1586787090284 | erot = 25.3617860657906 | epot = -218.683588417106 | etot = -173.163123642287 +949000 ekin = 20.6015087780768 | erot = 24.0216151369725 | epot = -218.644352518059 | etot = -174.02122860301 +950000 ekin = 20.7471893785302 | erot = 25.3619181001311 | epot = -218.710402012473 | etot = -172.601294533811 +951000 ekin = 20.2569076833938 | erot = 27.0210577095201 | epot = -218.988213515806 | etot = -171.710248122892 +952000 ekin = 20.5584159627657 | erot = 27.2103033079755 | epot = -219.159574869077 | etot = -171.390855598336 +953000 ekin = 21.7412270180337 | erot = 25.7395142553205 | epot = -219.276981606574 | etot = -171.79624033322 +954000 ekin = 22.5769744101438 | erot = 23.3851809606138 | epot = -219.432021398479 | etot = -173.469866027721 +955000 ekin = 22.7540917406293 | erot = 24.0485022563637 | epot = -219.45122924006 | etot = -172.648635243067 +956000 ekin = 23.6959292084454 | erot = 24.2542500120269 | epot = -219.324912206847 | etot = -171.374732986375 +957000 ekin = 24.5172263085672 | erot = 24.1459598029485 | epot = -219.163645858039 | etot = -170.500459746523 +958000 ekin = 25.8225599553336 | erot = 23.6654996104887 | epot = -219.159019217903 | etot = -169.670959652081 +959000 ekin = 26.8068645926446 | erot = 25.0211786091659 | epot = -219.23531458736 | etot = -167.40727138555 +960000 ekin = 26.5999695579089 | erot = 25.6266836486181 | epot = -219.112393893106 | etot = -166.885740686579 +961000 ekin = 27.0539782988757 | erot = 26.1135586378242 | epot = -218.901327623641 | etot = -165.733790686941 +962000 ekin = 27.3128371491059 | erot = 25.6398136135623 | epot = -218.716820658053 | etot = -165.764169895385 +963000 ekin = 27.5776608737564 | erot = 24.2328598021347 | epot = -218.565342926505 | etot = -166.754822250614 +964000 ekin = 28.434847779201 | erot = 23.0688699860552 | epot = -218.32159079768 | etot = -166.817873032424 +965000 ekin = 27.9989611524549 | erot = 21.1729542648574 | epot = -217.935512501719 | etot = -168.763597084407 +966000 ekin = 28.1906276758125 | erot = 19.7596499447264 | epot = -217.551246311047 | etot = -169.600968690508 +967000 ekin = 28.1299488148111 | erot = 19.7764414549918 | epot = -217.022765960343 | etot = -169.11637569054 +968000 ekin = 27.2553372938565 | erot = 18.6432061694697 | epot = -216.345481598031 | etot = -170.446938134704 +969000 ekin = 27.3975194660702 | erot = 16.7046773675797 | epot = -215.471813515321 | etot = -171.369616681671 +970000 ekin = 26.2092304427085 | erot = 16.6741476212952 | epot = -214.618004397777 | etot = -171.734626333774 +971000 ekin = 25.4753520862258 | erot = 16.4961256389214 | epot = -213.774217411075 | etot = -171.802739685927 +972000 ekin = 25.1338150886746 | erot = 17.5885931811208 | epot = -212.941007560394 | etot = -170.218599290598 +973000 ekin = 23.9980459819068 | erot = 19.2413290657419 | epot = -212.209972657659 | etot = -168.97059761001 +974000 ekin = 23.1991915243631 | erot = 20.5621498503079 | epot = -211.643302372093 | etot = -167.881960997422 +975000 ekin = 22.0936708905994 | erot = 23.8925799416044 | epot = -211.258183683576 | etot = -165.271932851372 +976000 ekin = 21.5284614810504 | erot = 24.4823848282085 | epot = -210.871321753255 | etot = -164.860475443996 +977000 ekin = 20.9102492410769 | erot = 21.693728956875 | epot = -210.421620122539 | etot = -167.817641924587 +978000 ekin = 20.5534455754244 | erot = 21.4137671023852 | epot = -210.104378292213 | etot = -168.137165614403 +979000 ekin = 20.4475545334837 | erot = 21.7023482062785 | epot = -209.997680361419 | etot = -167.847777621657 +980000 ekin = 20.0153051482561 | erot = 22.1641624026467 | epot = -209.89453747175 | etot = -167.715069920847 +981000 ekin = 19.2553377922842 | erot = 21.6998257958764 | epot = -209.890607062706 | etot = -168.935443474545 +982000 ekin = 19.3602504755725 | erot = 22.71183002751 | epot = -209.817363885782 | etot = -167.7452833827 +983000 ekin = 19.9918630693289 | erot = 23.202269542363 | epot = -209.824553681854 | etot = -166.630421070162 +984000 ekin = 20.2229931630647 | erot = 22.783376358611 | epot = -209.980959689712 | etot = -166.974590168037 +985000 ekin = 20.1271575518484 | erot = 25.8324951123609 | epot = -210.176274954526 | etot = -164.216622290317 +986000 ekin = 19.8065574143083 | erot = 25.7086232557777 | epot = -210.259482005916 | etot = -164.74430133583 +987000 ekin = 19.8241962308738 | erot = 27.3477557937439 | epot = -210.338061448385 | etot = -163.166109423767 +988000 ekin = 20.5802327460373 | erot = 26.5177798191887 | epot = -210.374636605805 | etot = -163.276624040579 +989000 ekin = 19.8243827036663 | erot = 25.0249543132842 | epot = -210.405555790817 | etot = -165.556218773867 +990000 ekin = 19.6784859521663 | erot = 25.0211614919117 | epot = -210.536148192301 | etot = -165.836500748223 +991000 ekin = 19.8800072497794 | erot = 23.9545983908763 | epot = -210.811356988255 | etot = -166.976751347599 +992000 ekin = 19.9500698690931 | erot = 23.5129947805019 | epot = -211.184932089162 | etot = -167.721867439567 +993000 ekin = 18.937341089784 | erot = 23.1942485295875 | epot = -211.832628892927 | etot = -169.701039273555 +994000 ekin = 19.0566139838972 | erot = 23.5902607657524 | epot = -212.751294519113 | etot = -170.104419769464 +995000 ekin = 19.600538964917 | erot = 24.2017471939332 | epot = -213.671202895863 | etot = -169.868916737012 +996000 ekin = 20.3648160827738 | erot = 24.5056692824139 | epot = -214.567571801734 | etot = -169.697086436546 +997000 ekin = 20.6784197154575 | erot = 22.6383548571427 | epot = -215.397393210187 | etot = -172.080618637587 +998000 ekin = 21.27338897749 | erot = 21.4812766210868 | epot = -216.126312680602 | etot = -173.371647082025 +999000 ekin = 22.1968344281123 | erot = 22.7999859685056 | epot = -216.784980184639 | etot = -171.788159788021 +1000000 ekin = 22.6406306102505 | erot = 22.5936369544571 | epot = -217.43832313152 | etot = -172.204055566812 + 1000000 303.8185 -221.63969 4.201369 -194.79769 -0.0039208577 39304000 +Loop time of 53.157 on 4 procs for 1000000 steps with 26 atoms + +Performance: 27.729 ns/day, 0.866 hours/ns, 18812.191 timesteps/s, 489.117 katom-step/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 17.443 | 25.085 | 41.565 | 193.9 | 47.19 +Bond | 0.47799 | 0.65467 | 0.81319 | 18.1 | 1.23 +Neigh | 0.014771 | 0.014974 | 0.015145 | 0.1 | 0.03 +Comm | 7.0561 | 24.213 | 31.359 | 204.1 | 45.55 +Output | 0.12434 | 0.14455 | 0.15308 | 3.1 | 0.27 +Modify | 1.8662 | 2.4548 | 3.0502 | 36.3 | 4.62 +Other | | 0.5899 | | | 1.11 + +Nlocal: 6.5 ave 10 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 19.5 ave 23 max 16 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 75.25 ave 182 max 25 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 301 +Ave neighs/atom = 11.576923 +Ave special neighs/atom = 5.0769231 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.8.* nocoeff +System init for write_data ... +Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:53 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/data.duplex2 new file mode 100644 index 0000000000..78a6fdd51a --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0 +2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0 +3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0 +4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0 +5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0 +6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0 +7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0 +8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0 +9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0 +10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0 +11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0 +12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0 +13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0 +14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0 +15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0 +16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447 +2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514 +3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762 +4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703 +5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389 +6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085 +7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256 +8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774 +9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824 +10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333 +11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933 +12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927 +13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526 +14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926 +15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399 +16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/in.duplex2 new file mode 100644 index 0000000000..6029ae601d --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/in.duplex2 @@ -0,0 +1,74 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.5 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 11.92337812042065 2.1295 6.482800913 +special_bonds lj 0 1 1 + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxrna2/stk seqdep ${T} 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.1 new file mode 100644 index 0000000000..1368ee307a --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.1 @@ -0,0 +1,1187 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.5 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 11.92337812042065 2.1295 6.482800913 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxrna2/stk seqdep ${T} 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 300 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 0.5 1.02455 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 36.640032 + ghost atom cutoff = 36.640032 + binsize = 18.320016, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 36.640032409886274 (../comm.cpp:739) +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815 +Per MPI rank memory allocation (min/avg/max) = 7.592 | 7.592 | 7.592 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -69.627742 3.2447172 -50.262701 0.034084814 39304000 +1000 ekin = 16.3558183649387 | erot = 16.6323090455317 | epot = -66.5525771041996 | etot = -33.5644496937292 +2000 ekin = 16.6191649168148 | erot = 16.5684372137643 | epot = -66.7520518221218 | etot = -33.5644496915427 +3000 ekin = 16.9230904408655 | erot = 16.5204480451833 | epot = -67.0079881759689 | etot = -33.5644496899201 +4000 ekin = 17.2772162612592 | erot = 16.4986792932201 | epot = -67.3403452437718 | etot = -33.5644496892925 +5000 ekin = 17.6866959075726 | erot = 16.5050138456573 | epot = -67.7561594428213 | etot = -33.5644496895913 +6000 ekin = 18.1531343302965 | erot = 16.5325161302816 | epot = -68.2501001506517 | etot = -33.5644496900737 +7000 ekin = 18.6806534933141 | erot = 16.5738535187237 | epot = -68.818956701435 | etot = -33.5644496893973 +8000 ekin = 19.2766528199697 | erot = 16.626151587963 | epot = -69.4672540969566 | etot = -33.5644496890239 +9000 ekin = 19.946149039732 | erot = 16.690847598574 | epot = -70.2014463262322 | etot = -33.5644496879261 +10000 ekin = 20.6973181248475 | erot = 16.777296043853 | epot = -71.039063854855 | etot = -33.5644496861545 +11000 ekin = 21.5395226247921 | erot = 16.901420997199 | epot = -72.0053933083061 | etot = -33.564449686315 +12000 ekin = 22.4717498465051 | erot = 17.0791755563663 | epot = -73.1153750880499 | etot = -33.5644496851785 +13000 ekin = 23.493621609947 | erot = 17.3228520870333 | epot = -74.3809233816827 | etot = -33.5644496847025 +14000 ekin = 24.6044210071245 | erot = 17.6425688028836 | epot = -75.8114394947882 | etot = -33.56444968478 +15000 ekin = 25.7999389267744 | erot = 18.0453525578632 | epot = -77.4097411694883 | etot = -33.5644496848507 +16000 ekin = 27.0739775537122 | erot = 18.536114233291 | epot = -79.1745414730759 | etot = -33.5644496860726 +17000 ekin = 28.4119581304117 | erot = 19.1137262760957 | epot = -81.0901340949627 | etot = -33.5644496884552 +18000 ekin = 29.7909545183301 | erot = 19.7704759932753 | epot = -83.1258802031779 | etot = -33.5644496915724 +19000 ekin = 31.1831510307731 | erot = 20.4915974540493 | epot = -85.2391981805602 | etot = -33.5644496957377 +20000 ekin = 32.5560965367941 | erot = 21.2528351748732 | epot = -87.373381412572 | etot = -33.5644497009046 +21000 ekin = 33.8683309875658 | erot = 22.0156446407475 | epot = -89.4484253379449 | etot = -33.5644497096315 +22000 ekin = 35.0747510230856 | erot = 22.7306302808711 | epot = -91.3698310187507 | etot = -33.5644497147941 +23000 ekin = 36.1427935644225 | erot = 23.3543658008635 | epot = -93.0616090845418 | etot = -33.5644497192558 +24000 ekin = 37.0484240543208 | erot = 23.8536351256839 | epot = -94.4665089004153 | etot = -33.5644497204106 +25000 ekin = 37.7873483857424 | erot = 24.2156130941778 | epot = -95.567411199049 | etot = -33.5644497191288 +26000 ekin = 38.3695951222895 | erot = 24.4472028227108 | epot = -96.381247661283 | etot = -33.5644497162827 +27000 ekin = 38.814245199114 | erot = 24.569649643868 | epot = -96.948344555808 | etot = -33.564449712826 +28000 ekin = 39.1436511594776 | erot = 24.6108705414912 | epot = -97.318971410458 | etot = -33.5644497094892 +29000 ekin = 39.3799077053085 | erot = 24.5987493007987 | epot = -97.5431067127119 | etot = -33.5644497066047 +30000 ekin = 39.543718776792 | erot = 24.5572061990989 | epot = -97.6653746802846 | etot = -33.5644497043937 +31000 ekin = 39.6556538792218 | erot = 24.5025482878259 | epot = -97.7226518696589 | etot = -33.5644497026113 +32000 ekin = 39.7376908979138 | erot = 24.4447365565301 | epot = -97.7468771552206 | etot = -33.5644497007767 +33000 ekin = 39.8178410436032 | erot = 24.3917276701347 | epot = -97.7740184125893 | etot = -33.5644496988513 +34000 ekin = 39.9276187144877 | erot = 24.3494773308424 | epot = -97.8415457422145 | etot = -33.5644496968845 +35000 ekin = 40.0972017271435 | erot = 24.3220925820239 | epot = -97.9837440042528 | etot = -33.5644496950853 +36000 ekin = 40.3554758289771 | erot = 24.3121132861365 | epot = -98.2320388089549 | etot = -33.5644496938413 +37000 ekin = 40.725317224184 | erot = 24.3194531164605 | epot = -98.609220034252 | etot = -33.5644496936075 +38000 ekin = 41.218461457732 | erot = 24.3399425111004 | epot = -99.1228536635587 | etot = -33.5644496947263 +39000 ekin = 41.8315835745714 | erot = 24.3642621379406 | epot = -99.7602954097942 | etot = -33.5644496972823 +40000 ekin = 42.5444333388251 | erot = 24.3777906096196 | epot = -100.486673649663 | etot = -33.5644497012185 +41000 ekin = 43.3221534386109 | erot = 24.3619359806986 | epot = -101.248539124816 | etot = -33.5644497055066 +42000 ekin = 44.1232219530967 | erot = 24.2968159627003 | epot = -101.984487625365 | etot = -33.5644497095679 +43000 ekin = 44.9043008441337 | erot = 24.1647850477424 | epot = -102.633535604781 | etot = -33.5644497129045 +44000 ekin = 45.6258073685752 | erot = 23.953775477634 | epot = -103.144032561026 | etot = -33.5644497148168 +45000 ekin = 46.2557013508714 | erot = 23.6596129163789 | epot = -103.47976398388 | etot = -33.5644497166297 +46000 ekin = 46.7711396854557 | erot = 23.2746461161514 | epot = -103.610235519167 | etot = -33.5644497175602 +47000 ekin = 47.1576706465411 | erot = 22.7983985986745 | epot = -103.520518961436 | etot = -33.5644497162202 +48000 ekin = 47.4067411848222 | erot = 22.24189270691 | epot = -103.213083606728 | etot = -33.5644497149961 +49000 ekin = 47.5134307536666 | erot = 21.6212608371929 | epot = -102.699141303773 | etot = -33.5644497129138 +50000 ekin = 47.4750496002024 | erot = 20.9637753825411 | epot = -102.003274691403 | etot = -33.5644497086593 +51000 ekin = 47.2893433305646 | erot = 20.3140174296332 | epot = -101.16781046916 | etot = -33.5644497089623 +52000 ekin = 46.9527474071891 | erot = 19.68086855223 | epot = -100.198065668178 | etot = -33.5644497087592 +53000 ekin = 46.4669221029442 | erot = 19.0628634962126 | epot = -99.0942353064246 | etot = -33.5644497072679 +54000 ekin = 45.8347987943733 | erot = 18.4752794596827 | epot = -97.8745279599043 | etot = -33.5644497058483 +55000 ekin = 45.059031662863 | erot = 17.9341671577873 | epot = -96.5576485255764 | etot = -33.5644497049261 +56000 ekin = 44.1409291390452 | erot = 17.4520797326571 | epot = -95.1574585762239 | etot = -33.5644497045216 +57000 ekin = 43.0792908324212 | erot = 17.037334269452 | epot = -93.6810748066111 | etot = -33.5644497047379 +58000 ekin = 41.8704923540597 | erot = 16.6939394056073 | epot = -92.1288814650802 | etot = -33.5644497054133 +59000 ekin = 40.5509408803223 | erot = 16.4316140927959 | epot = -90.5470046657477 | etot = -33.5644496926295 +60000 ekin = 39.1975830612663 | erot = 16.2583411314114 | epot = -89.0203738856257 | etot = -33.5644496929479 +61000 ekin = 35.7114984384222 | erot = 15.7928074869524 | epot = -85.0687559055441 | etot = -33.5644499801694 +62000 ekin = 34.7372517507007 | erot = 15.809440909604 | epot = -84.1111427028021 | etot = -33.5644500424973 +63000 ekin = 35.8178089566977 | erot = 16.1653492511931 | epot = -85.5476088513045 | etot = -33.5644506434137 +64000 ekin = 34.869236370394 | erot = 16.1670101597177 | epot = -84.6006971860832 | etot = -33.5644506559716 +65000 ekin = 33.846449455543 | erot = 16.1402632189656 | epot = -83.5511633293454 | etot = -33.5644506548368 +66000 ekin = 32.7636419796955 | erot = 16.0751240440813 | epot = -82.4032166770506 | etot = -33.5644506532738 +67000 ekin = 31.6420680628872 | erot = 15.9705642956741 | epot = -81.1770830093356 | etot = -33.5644506507743 +68000 ekin = 30.5061166759946 | erot = 15.8342590047122 | epot = -79.9048263284351 | etot = -33.5644506477283 +69000 ekin = 29.3793899831114 | erot = 15.678409289176 | epot = -78.6222499180454 | etot = -33.564450645758 +70000 ekin = 28.284277797061 | erot = 15.5192251789805 | epot = -77.367953618708 | etot = -33.5644506426665 +71000 ekin = 27.2428007223107 | erot = 15.3775924468402 | epot = -76.1848438089708 | etot = -33.5644506398198 +72000 ekin = 26.2738583640461 | erot = 15.2738682128153 | epot = -75.1121772142973 | etot = -33.5644506374359 +73000 ekin = 25.3929266243307 | erot = 15.225238925301 | epot = -74.1826161852592 | etot = -33.5644506356275 +74000 ekin = 24.6118800235875 | erot = 15.2440811522995 | epot = -73.4204118109363 | etot = -33.5644506350493 +75000 ekin = 23.9285421197333 | erot = 15.2937064902868 | epot = -72.7866996078847 | etot = -33.5644509978647 +76000 ekin = 23.6014258497327 | erot = 14.5530249139084 | epot = -71.7189013877706 | etot = -33.5644506241296 +77000 ekin = 24.0021186681933 | erot = 14.66725562535 | epot = -72.2338249119969 | etot = -33.5644506184536 +78000 ekin = 23.7667117018407 | erot = 14.8821032755388 | epot = -72.2132655967916 | etot = -33.5644506194121 +79000 ekin = 23.6362408803388 | erot = 15.1573231058555 | epot = -72.3580146069914 | etot = -33.5644506207971 +80000 ekin = 23.6008292998118 | erot = 15.4801164769236 | epot = -72.6453963992449 | etot = -33.5644506225096 +81000 ekin = 23.6479278988449 | erot = 15.8366782045229 | epot = -73.0490567276759 | etot = -33.5644506243081 +82000 ekin = 23.7631958527379 | erot = 16.2135577483199 | epot = -73.5412042271318 | etot = -33.564450626074 +83000 ekin = 23.9313380513044 | erot = 16.5989137528036 | epot = -74.0947024318235 | etot = -33.5644506277155 +84000 ekin = 24.1405337461447 | erot = 16.9832739889227 | epot = -74.6882583637861 | etot = -33.5644506287187 +85000 ekin = 24.3851366362422 | erot = 17.3594190811811 | epot = -75.3090063475336 | etot = -33.5644506301102 +86000 ekin = 24.6499622429148 | erot = 17.7229731863063 | epot = -75.9373860604631 | etot = -33.5644506312419 +87000 ekin = 24.9195866966142 | erot = 18.0734917202568 | epot = -76.5575290489246 | etot = -33.5644506320536 +88000 ekin = 25.1793742014108 | erot = 18.4146339772126 | epot = -77.158458811171 | etot = -33.5644506325475 +89000 ekin = 25.4156568494618 | erot = 18.7539686693896 | epot = -77.7340761514978 | etot = -33.5644506326463 +90000 ekin = 25.609684003566 | erot = 19.1040901404673 | epot = -78.2782247770974 | etot = -33.564450633064 +91000 ekin = 25.7348417969789 | erot = 19.4865010462251 | epot = -78.7857934757922 | etot = -33.5644506325881 +92000 ekin = 25.7824117490226 | erot = 19.9168308436453 | epot = -79.2636932257737 | etot = -33.5644506331059 +93000 ekin = 25.7436484203098 | erot = 20.4015276208925 | epot = -79.7096266744475 | etot = -33.5644506332451 +94000 ekin = 25.610748739912 | erot = 20.9498819611228 | epot = -80.1250813342097 | etot = -33.564450633175 +95000 ekin = 25.3788454256151 | erot = 21.5718811146967 | epot = -80.5151771730825 | etot = -33.5644506327707 +96000 ekin = 25.0476635684712 | erot = 22.2778886106733 | epot = -80.8900028110714 | etot = -33.5644506319269 +97000 ekin = 24.6228037012614 | erot = 23.0785820232949 | epot = -81.2658363557903 | etot = -33.5644506312341 +98000 ekin = 24.116365030335 | erot = 23.980262455698 | epot = -81.6610781157446 | etot = -33.5644506297116 +99000 ekin = 23.5467601995519 | erot = 24.9897227937723 | epot = -82.1009336213321 | etot = -33.5644506280079 +100000 ekin = 22.9377076830261 | erot = 26.1125444287915 | epot = -82.6147027382494 | etot = -33.5644506264317 +101000 ekin = 22.3162402354139 | erot = 27.3495277986758 | epot = -83.2302186594579 | etot = -33.5644506253682 +102000 ekin = 21.7099673799574 | erot = 28.6941289887295 | epot = -83.9685469938778 | etot = -33.5644506251909 +103000 ekin = 21.1440927333159 | erot = 30.130413105192 | epot = -84.8389564646036 | etot = -33.5644506260957 +104000 ekin = 20.6390360732686 | erot = 31.6318076720637 | epot = -85.8352943737421 | etot = -33.5644506284097 +105000 ekin = 20.2097356178038 | erot = 33.1559511277913 | epot = -86.9301373769589 | etot = -33.5644506313638 +106000 ekin = 19.8659962936248 | erot = 34.6591523175119 | epot = -88.0895992442174 | etot = -33.5644506330807 +107000 ekin = 19.6196926152683 | erot = 36.100338989929 | epot = -89.2844822415662 | etot = -33.5644506363689 +108000 ekin = 19.4737764770476 | erot = 37.4404659123052 | epot = -90.4786930287931 | etot = -33.5644506394402 +109000 ekin = 19.4257211238038 | erot = 38.6395727467607 | epot = -91.629744515762 | etot = -33.5644506451975 +110000 ekin = 19.4643317381238 | erot = 39.6495422786812 | epot = -92.6783246653831 | etot = -33.5644506485781 +111000 ekin = 19.5812097010519 | erot = 40.4340503208693 | epot = -93.5797106732657 | etot = -33.5644506513445 +112000 ekin = 19.7688752467972 | erot = 40.9641614008033 | epot = -94.2974873012517 | etot = -33.5644506536512 +113000 ekin = 20.0199352606492 | erot = 41.223561768641 | epot = -94.8079476827741 | etot = -33.5644506534839 +114000 ekin = 20.3316783135505 | erot = 41.2208106095099 | epot = -95.1169395739246 | etot = -33.5644506508641 +115000 ekin = 20.7092934859859 | erot = 40.9902193450394 | epot = -95.2639634786059 | etot = -33.5644506475807 +116000 ekin = 21.1584070130099 | erot = 40.5711692188944 | epot = -95.2940268781066 | etot = -33.5644506462023 +117000 ekin = 21.6717401642325 | erot = 40.0068194492249 | epot = -95.2430102574753 | etot = -33.5644506440179 +118000 ekin = 22.2304498749719 | erot = 39.3449170917023 | epot = -95.1398176087352 | etot = -33.5644506420609 +119000 ekin = 22.8040322747547 | erot = 38.6279078104798 | epot = -94.9963907285559 | etot = -33.5644506433214 +120000 ekin = 23.3636455910815 | erot = 37.8733163419356 | epot = -94.801412577584 | etot = -33.564450644567 +121000 ekin = 23.888334247959 | erot = 37.0853024873726 | epot = -94.5380873807864 | etot = -33.5644506454549 +122000 ekin = 24.3628295450746 | erot = 36.261752125414 | epot = -94.1890323184781 | etot = -33.5644506479895 +123000 ekin = 24.7728939422985 | erot = 35.3896441641771 | epot = -93.7269887541641 | etot = -33.5644506476884 +124000 ekin = 25.1206142173508 | erot = 34.4655545655651 | epot = -93.1506194284814 | etot = -33.5644506455655 +125000 ekin = 25.4216604350097 | erot = 33.5035163209335 | epot = -92.4896273979244 | etot = -33.5644506419812 +126000 ekin = 25.6927735129491 | erot = 32.5281184075519 | epot = -91.785342561111 | etot = -33.56445064061 +127000 ekin = 25.9460883081172 | erot = 31.5650113724827 | epot = -91.0755503181662 | etot = -33.5644506375663 +128000 ekin = 26.1993872383141 | erot = 30.6366650539223 | epot = -90.4005029275325 | etot = -33.5644506352961 +129000 ekin = 26.4652741313034 | erot = 29.7610339508673 | epot = -89.7907587151 | etot = -33.5644506329293 +130000 ekin = 26.7486727551205 | erot = 28.9506137583613 | epot = -89.2637371464484 | etot = -33.5644506329667 +131000 ekin = 27.0469092029044 | erot = 28.2034442942497 | epot = -88.8148041302872 | etot = -33.5644506331331 +132000 ekin = 27.3542874865317 | erot = 27.5160813886976 | epot = -88.4348195084739 | etot = -33.5644506332445 +133000 ekin = 27.6627378161423 | erot = 26.8888107912285 | epot = -88.115999240573 | etot = -33.5644506332022 +134000 ekin = 27.9672923181963 | erot = 26.3214524159622 | epot = -87.8531953671591 | etot = -33.5644506330005 +135000 ekin = 28.2641150379083 | erot = 25.8141340320102 | epot = -87.6426997025991 | etot = -33.5644506326806 +136000 ekin = 28.5509978141388 | erot = 25.3673179322113 | epot = -87.4827663786189 | etot = -33.5644506322688 +137000 ekin = 28.825915909221 | erot = 24.9801644637638 | epot = -87.3705310053152 | etot = -33.5644506323304 +138000 ekin = 29.0842610649339 | erot = 24.6492546073933 | epot = -87.2979663044158 | etot = -33.5644506320886 +139000 ekin = 29.3272222877258 | erot = 24.3700782380065 | epot = -87.2617511574337 | etot = -33.5644506317014 +140000 ekin = 29.5579798491516 | erot = 24.1376580585779 | epot = -87.2600885391681 | etot = -33.5644506314386 +141000 ekin = 29.7799846346249 | erot = 23.9462429930569 | epot = -87.2906782589382 | etot = -33.5644506312564 +142000 ekin = 29.9959841884915 | erot = 23.7899704636026 | epot = -87.3504052833039 | etot = -33.5644506312098 +143000 ekin = 30.2070349127784 | erot = 23.6632996950641 | epot = -87.4347852391688 | etot = -33.5644506313262 +144000 ekin = 30.4118840029093 | erot = 23.5613798569338 | epot = -87.5377144914396 | etot = -33.5644506315964 +145000 ekin = 30.6068456872279 | erot = 23.4803656669067 | epot = -87.6516619861204 | etot = -33.5644506319858 +146000 ekin = 30.7861230778205 | erot = 23.4176420010718 | epot = -87.7682157113363 | etot = -33.564450632444 +147000 ekin = 30.9424364770385 | erot = 23.3719366394227 | epot = -87.8788237493778 | etot = -33.5644506329166 +148000 ekin = 31.0677916134912 | erot = 23.3433216080134 | epot = -87.9755638548586 | etot = -33.564450633354 +149000 ekin = 31.1542520331539 | erot = 23.3331254537123 | epot = -88.0518281205811 | etot = -33.5644506337149 +150000 ekin = 31.1946418128177 | erot = 23.3437996409507 | epot = -88.1028920877325 | etot = -33.5644506339642 +151000 ekin = 31.1838063839322 | erot = 23.3785936220168 | epot = -88.1268506397958 | etot = -33.5644506338469 +152000 ekin = 31.1202290278299 | erot = 23.4412183836703 | epot = -88.125898045246 | etot = -33.5644506337458 +153000 ekin = 31.0032553217637 | erot = 23.5372189789008 | epot = -88.1049249338467 | etot = -33.5644506331823 +154000 ekin = 30.8354559406746 | erot = 23.6729952126947 | epot = -88.072901786295 | etot = -33.5644506329257 +155000 ekin = 30.6186135870526 | erot = 23.8551009557647 | epot = -88.0381651751689 | etot = -33.5644506323515 +156000 ekin = 30.3571457582588 | erot = 24.0914721103742 | epot = -88.0130685002276 | etot = -33.5644506315946 +157000 ekin = 30.0574108500346 | erot = 24.3907046676056 | epot = -88.0125661484805 | etot = -33.5644506308403 +158000 ekin = 29.725675692331 | erot = 24.7625567196346 | epot = -88.0526830421764 | etot = -33.5644506302108 +159000 ekin = 29.3667041507893 | erot = 25.2124449846207 | epot = -88.1435997656297 | etot = -33.5644506302196 +160000 ekin = 28.9829375848235 | erot = 25.7406189361246 | epot = -88.2880071520098 | etot = -33.5644506310616 +161000 ekin = 28.5708031098605 | erot = 26.3449808633556 | epot = -88.4802346049489 | etot = -33.5644506317328 +162000 ekin = 28.1278607476035 | erot = 27.0188065006218 | epot = -88.7111178809852 | etot = -33.5644506327599 +163000 ekin = 27.6515523776407 | erot = 27.7508923428456 | epot = -88.9668953542076 | etot = -33.5644506337213 +164000 ekin = 27.1398166575402 | erot = 28.5265897115496 | epot = -89.2308570046128 | etot = -33.5644506355231 +165000 ekin = 26.5901801294065 | erot = 29.3236809534458 | epot = -89.478311720126 | etot = -33.5644506372737 +166000 ekin = 26.0027550423919 | erot = 30.1148491025849 | epot = -89.6820547838262 | etot = -33.5644506388494 +167000 ekin = 25.3815734826352 | erot = 30.8714146428653 | epot = -89.8174387656332 | etot = -33.5644506401327 +168000 ekin = 24.7338280126162 | erot = 31.5656853660149 | epot = -89.8639640196475 | etot = -33.5644506410165 +169000 ekin = 24.0691061638267 | erot = 32.1733410341194 | epot = -89.8068978394102 | etot = -33.5644506414641 +170000 ekin = 23.3986380903836 | erot = 32.6761770397884 | epot = -89.6392657713668 | etot = -33.5644506411948 +171000 ekin = 22.7350947047584 | erot = 33.0649339609198 | epot = -89.3644793058835 | etot = -33.5644506402053 +172000 ekin = 22.0927595064379 | erot = 33.3397459263013 | epot = -88.9969560711893 | etot = -33.5644506384501 +173000 ekin = 21.4881436133187 | erot = 33.5098602953101 | epot = -88.5624545444277 | etot = -33.5644506357989 +174000 ekin = 20.9424106184102 | erot = 33.5950638981363 | epot = -88.1019251458272 | etot = -33.5644506292807 +175000 ekin = 20.4887725385275 | erot = 33.6332952588425 | epot = -87.6865184248803 | etot = -33.5644506275103 +176000 ekin = 20.1459992745671 | erot = 33.6413286939806 | epot = -87.3517785947221 | etot = -33.5644506261744 +177000 ekin = 19.9273952403454 | erot = 33.6264319072445 | epot = -87.1182777732156 | etot = -33.5644506256257 +178000 ekin = 19.84052681153 | erot = 33.5862782738547 | epot = -86.9912557125122 | etot = -33.5644506271275 +179000 ekin = 19.8828425829422 | erot = 33.5043404166422 | epot = -86.9516336276486 | etot = -33.5644506280643 +180000 ekin = 20.0524881206256 | erot = 33.3671042345402 | epot = -86.9840429849155 | etot = -33.5644506297498 +181000 ekin = 20.3414841297343 | erot = 33.1581782006442 | epot = -87.0641129622508 | etot = -33.5644506318723 +182000 ekin = 20.7352057198233 | erot = 32.8612622822509 | epot = -87.1609186361483 | etot = -33.5644506340741 +183000 ekin = 21.2137106223656 | erot = 32.4647477949401 | epot = -87.2429090532129 | etot = -33.5644506359073 +184000 ekin = 21.753758772068 | erot = 31.9655803613331 | epot = -87.2837897705988 | etot = -33.5644506371977 +185000 ekin = 22.3286746031905 | erot = 31.370802203917 | epot = -87.2639274448021 | etot = -33.5644506376946 +186000 ekin = 22.9115100132914 | erot = 30.6990331536457 | epot = -87.1749938042645 | etot = -33.5644506373275 +187000 ekin = 23.4775030152646 | erot = 29.9792070479746 | epot = -87.0211606994591 | etot = -33.5644506362199 +188000 ekin = 24.0059463479979 | erot = 29.2469949106376 | epot = -86.8173918933481 | etot = -33.5644506347127 +189000 ekin = 24.4809955944256 | erot = 28.5392131436686 | epot = -86.5846593713985 | etot = -33.5644506333043 +190000 ekin = 24.8911658073154 | erot = 27.8871249849478 | epot = -86.3427414248055 | etot = -33.5644506325423 +191000 ekin = 25.2275609419593 | erot = 27.3101259966561 | epot = -86.1021375715933 | etot = -33.5644506329779 +192000 ekin = 25.4831011426815 | erot = 26.8121375634353 | epot = -85.8596893403699 | etot = -33.564450634253 +193000 ekin = 25.2930335715005 | erot = 26.6410891958414 | epot = -85.4985734034485 | etot = -33.5644506361066 +194000 ekin = 25.0352601614032 | erot = 26.6525265483622 | epot = -85.2522373921937 | etot = -33.5644506824282 +195000 ekin = 25.0363508840855 | erot = 26.2378500699517 | epot = -84.8386516236489 | etot = -33.5644506696116 +196000 ekin = 24.9648942549692 | erot = 25.78683024187 | epot = -84.3161751669041 | etot = -33.5644506700649 +197000 ekin = 24.820085073243 | erot = 25.3002719383723 | epot = -83.684807680623 | etot = -33.5644506690076 +198000 ekin = 24.617288458851 | erot = 24.7762496503728 | epot = -82.9579887758224 | etot = -33.5644506665986 +199000 ekin = 24.377048383026 | erot = 24.2259949153754 | epot = -82.1674939619447 | etot = -33.5644506635433 +200000 ekin = 24.1224360020296 | erot = 23.6691820640811 | epot = -81.3560687261525 | etot = -33.5644506600419 +201000 ekin = 23.8775516468454 | erot = 23.1291743985682 | epot = -80.5711767022417 | etot = -33.5644506568281 +202000 ekin = 23.6646103059715 | erot = 22.6276096876224 | epot = -79.8566706478819 | etot = -33.5644506542881 +203000 ekin = 23.5017139925529 | erot = 22.1809863327317 | epot = -79.2471509779019 | etot = -33.5644506526173 +204000 ekin = 23.4012931943585 | erot = 21.7992926193315 | epot = -78.7650364652111 | etot = -33.5644506515211 +205000 ekin = 23.3698442687714 | erot = 21.4883950765849 | epot = -78.4226899967129 | etot = -33.5644506513567 +206000 ekin = 23.4080277663789 | erot = 21.2503388252137 | epot = -78.2228172433636 | etot = -33.5644506517709 +207000 ekin = 23.510672424487 | erot = 21.0828853352428 | epot = -78.1580084122739 | etot = -33.564450652544 +208000 ekin = 23.6683534180495 | erot = 20.982792192542 | epot = -78.2155962640683 | etot = -33.5644506534769 +209000 ekin = 23.8319531636201 | erot = 20.8686960092813 | epot = -78.2650998050279 | etot = -33.5644506321265 +210000 ekin = 24.1634900876329 | erot = 20.8246815259854 | epot = -78.5526222834702 | etot = -33.5644506698519 +211000 ekin = 24.4545474928994 | erot = 20.8320949387436 | epot = -78.851093093408 | etot = -33.564450661765 +212000 ekin = 24.7210588846791 | erot = 20.8889178093565 | epot = -79.1744273565292 | etot = -33.5644506624935 +213000 ekin = 24.9762555918523 | erot = 20.9956570670851 | epot = -79.5363633251146 | etot = -33.5644506661772 +214000 ekin = 25.205483004635 | erot = 21.1345527593194 | epot = -79.904486430984 | etot = -33.5644506670296 +215000 ekin = 25.4055444850383 | erot = 21.2948000239929 | epot = -80.2647951765804 | etot = -33.5644506675491 +216000 ekin = 25.5773395549964 | erot = 21.4659469017795 | epot = -80.6077371248515 | etot = -33.5644506680756 +217000 ekin = 25.7224226233962 | erot = 21.6383314527683 | epot = -80.925204744665 | etot = -33.5644506685004 +218000 ekin = 25.8456307141035 | erot = 21.7996006617643 | epot = -81.2096820449061 | etot = -33.5644506690382 +219000 ekin = 25.952452354154 | erot = 21.9358336225146 | epot = -81.4527366463123 | etot = -33.5644506696437 +220000 ekin = 26.0480501371105 | erot = 22.0331400323315 | epot = -81.6456408394103 | etot = -33.5644506699683 +221000 ekin = 26.1377559920962 | erot = 22.0801399062532 | epot = -81.7823465685503 | etot = -33.5644506702008 +222000 ekin = 26.2262421156876 | erot = 22.0692633440645 | epot = -81.8599561297652 | etot = -33.5644506700131 +223000 ekin = 26.3184403630104 | erot = 21.9982474658179 | epot = -81.8811384982303 | etot = -33.564450669402 +224000 ekin = 26.4171271373366 | erot = 21.8710288815827 | epot = -81.8526066880995 | etot = -33.5644506691801 +225000 ekin = 26.5225389104573 | erot = 21.6965423523224 | epot = -81.7835319309186 | etot = -33.5644506681389 +226000 ekin = 26.7157923548661 | erot = 21.3119214437974 | epot = -81.5921644821821 | etot = -33.5644506835186 +227000 ekin = 27.2484396437667 | erot = 20.6374955150002 | epot = -81.4503858460625 | etot = -33.5644506872956 +228000 ekin = 27.5078528971351 | erot = 20.2748179574298 | epot = -81.3471215226841 | etot = -33.5644506681192 +229000 ekin = 27.631283055081 | erot = 19.9858964954828 | epot = -81.1816302175522 | etot = -33.5644506669884 +230000 ekin = 27.7676058404106 | erot = 19.7189438600699 | epot = -81.0510003675314 | etot = -33.5644506670509 +231000 ekin = 27.917189899564 | erot = 19.4851196432342 | epot = -80.9667602108556 | etot = -33.5644506680573 +232000 ekin = 28.075807909483 | erot = 19.2892055600532 | epot = -80.9294641380291 | etot = -33.5644506684929 +233000 ekin = 28.2354888581566 | erot = 19.1284398309955 | epot = -80.9283793559269 | etot = -33.5644506667748 +234000 ekin = 28.3953039485291 | erot = 19.0132859353528 | epot = -80.973040551359 | etot = -33.564450667477 +235000 ekin = 28.5569493494324 | erot = 18.9585387746561 | epot = -81.0799387921139 | etot = -33.5644506680254 +236000 ekin = 28.7166448189416 | erot = 18.9671002034007 | epot = -81.2481956904871 | etot = -33.5644506681447 +237000 ekin = 28.872502381955 | erot = 19.0433381874402 | epot = -81.4802912373653 | etot = -33.5644506679701 +238000 ekin = 29.0257746255756 | erot = 19.1916941122086 | epot = -81.7819194053224 | etot = -33.5644506675381 +239000 ekin = 29.1795842186668 | erot = 19.4168064167523 | epot = -82.1608413028715 | etot = -33.5644506674523 +240000 ekin = 29.3337146101792 | erot = 19.7090725309346 | epot = -82.6072378097604 | etot = -33.5644506686467 +241000 ekin = 29.4868078966917 | erot = 20.0596352267871 | epot = -83.1108937927889 | etot = -33.5644506693101 +242000 ekin = 29.6351003169272 | erot = 20.4605457842645 | epot = -83.6600967716849 | etot = -33.5644506704932 +243000 ekin = 29.8921802425096 | erot = 20.6958964400126 | epot = -84.1525273495103 | etot = -33.564450666988 +244000 ekin = 30.2594419587612 | erot = 20.9649617308285 | epot = -84.788854393917 | etot = -33.5644507043273 +245000 ekin = 30.3074620328552 | erot = 21.3089995007004 | epot = -85.1809122847552 | etot = -33.5644507511996 +246000 ekin = 30.6998172933386 | erot = 21.0861202554748 | epot = -85.3503880690327 | etot = -33.5644505202193 +247000 ekin = 31.265212405902 | erot = 21.7433599271637 | epot = -86.5730230769931 | etot = -33.5644507439274 +248000 ekin = 31.2039013197071 | erot = 22.3578318777868 | epot = -87.1261839419724 | etot = -33.5644507444785 +249000 ekin = 31.0628965882674 | erot = 22.9361503364564 | epot = -87.563497668308 | etot = -33.5644507435842 +250000 ekin = 30.8544219835531 | erot = 23.4738999845616 | epot = -87.8927727106375 | etot = -33.5644507425228 +251000 ekin = 30.5979929542296 | erot = 23.9732495372637 | epot = -88.1356932312788 | etot = -33.5644507397854 +252000 ekin = 30.3186084933056 | erot = 24.4470234326924 | epot = -88.3300826628224 | etot = -33.5644507368245 +253000 ekin = 30.041632868323 | erot = 24.9117142614227 | epot = -88.5177978639943 | etot = -33.5644507342486 +254000 ekin = 29.6651322242815 | erot = 25.3352238224839 | epot = -88.5648072260565 | etot = -33.5644511792912 +255000 ekin = 27.9972596305184 | erot = 25.343644566417 | epot = -86.9053550134241 | etot = -33.5644508164887 +256000 ekin = 27.4480536506913 | erot = 26.2038023386853 | epot = -87.216306790649 | etot = -33.5644508012725 +257000 ekin = 28.5107044680624 | erot = 27.5793602337782 | epot = -89.6545158780358 | etot = -33.5644511761952 +258000 ekin = 28.9485040029259 | erot = 27.9141399630899 | epot = -90.4270947739431 | etot = -33.5644508079274 +259000 ekin = 29.1923898091059 | erot = 28.2760336628035 | epot = -91.0328742825817 | etot = -33.5644508106723 +260000 ekin = 29.442065950707 | erot = 28.6795119902558 | epot = -91.6860287570451 | etot = -33.5644508160824 +261000 ekin = 29.6845039883856 | erot = 29.1068404636931 | epot = -92.3557952701953 | etot = -33.5644508181166 +262000 ekin = 29.8834680797666 | erot = 29.5461970802723 | epot = -92.9941159814128 | etot = -33.5644508213739 +263000 ekin = 30.015935190767 | erot = 29.964909738063 | epot = -93.545295753821 | etot = -33.5644508249909 +264000 ekin = 30.0524877647281 | erot = 30.3384906869061 | epot = -93.9554292801698 | etot = -33.5644508285355 +265000 ekin = 29.9659450397407 | erot = 30.6431999052832 | epot = -94.1735957766809 | etot = -33.564450831657 +266000 ekin = 29.7355380957518 | erot = 30.8554934502802 | epot = -94.1554823800682 | etot = -33.5644508340362 +267000 ekin = 29.350217253177 | erot = 30.9531552650149 | epot = -93.8678233536528 | etot = -33.564450835461 +268000 ekin = 28.8109215600445 | erot = 30.9159121160384 | epot = -93.2912845119314 | etot = -33.5644508358484 +269000 ekin = 28.131229902636 | erot = 30.7258800106364 | epot = -92.4215607498827 | etot = -33.5644508366102 +270000 ekin = 27.3365120331628 | erot = 30.3685462542785 | epot = -91.26950914197 | etot = -33.5644508545286 +271000 ekin = 26.4621552466787 | erot = 29.8348321072734 | epot = -89.8614382055512 | etot = -33.5644508515991 +272000 ekin = 25.5514537841055 | erot = 29.123871510934 | epot = -88.2397761425329 | etot = -33.5644508474934 +273000 ekin = 24.6528090193024 | erot = 28.2453291639207 | epot = -86.4625890256565 | etot = -33.5644508424334 +274000 ekin = 23.8212346502742 | erot = 27.2200000603037 | epot = -84.6056855414942 | etot = -33.5644508309163 +275000 ekin = 22.9729777889705 | erot = 26.0804823635512 | epot = -82.6179111121121 | etot = -33.5644509595905 +276000 ekin = 22.0549791971374 | erot = 24.8883860441513 | epot = -80.5078160553758 | etot = -33.5644508140871 +277000 ekin = 22.291845448694 | erot = 23.6844629884807 | epot = -79.540759443928 | etot = -33.5644510067533 +278000 ekin = 22.2933944834771 | erot = 22.3796695906392 | epot = -78.2375149019929 | etot = -33.5644508278766 +279000 ekin = 22.3659748250016 | erot = 21.1183819743967 | epot = -77.0488076287097 | etot = -33.5644508293114 +280000 ekin = 22.5183002078625 | erot = 19.9334324614308 | epot = -76.0161834966431 | etot = -33.5644508273498 +281000 ekin = 22.7529481191411 | erot = 18.8478601493348 | epot = -75.1652590940351 | etot = -33.5644508255591 +282000 ekin = 23.0795879184867 | erot = 17.8776966475211 | epot = -74.5217353872447 | etot = -33.564450821237 +283000 ekin = 23.5210121271307 | erot = 17.0345324476566 | epot = -74.1199953957228 | etot = -33.5644508209355 +284000 ekin = 24.07992475589 | erot = 16.3233784658841 | epot = -73.9677540517476 | etot = -33.5644508299736 +285000 ekin = 24.7785446246423 | erot = 15.7478244913642 | epot = -74.0908199422233 | etot = -33.5644508262167 +286000 ekin = 25.636838734536 | erot = 15.3047487827835 | epot = -74.5060383422483 | etot = -33.5644508249288 +287000 ekin = 26.6214548224706 | erot = 14.9922504829288 | epot = -75.1781561308958 | etot = -33.5644508254964 +288000 ekin = 27.7267158888572 | erot = 14.8012865017013 | epot = -76.0924532218297 | etot = -33.5644508312711 +289000 ekin = 28.8920167227279 | erot = 14.7169892845691 | epot = -77.1734568439386 | etot = -33.5644508366416 +290000 ekin = 30.0553666648387 | erot = 14.7251675417572 | epot = -78.3449850482589 | etot = -33.5644508416631 +291000 ekin = 31.1595769632387 | erot = 14.811929120259 | epot = -79.5359569290839 | etot = -33.5644508455862 +292000 ekin = 32.1608216689813 | erot = 14.9640713088845 | epot = -80.6893438261509 | etot = -33.564450848285 +293000 ekin = 33.0319319380177 | erot = 15.168173905447 | epot = -81.7645566935966 | etot = -33.5644508501319 +294000 ekin = 33.7599421346976 | erot = 15.4088106779812 | epot = -82.7332036642767 | etot = -33.5644508515979 +295000 ekin = 34.3413485939712 | erot = 15.667394334235 | epot = -83.5731937811218 | etot = -33.5644508529156 +296000 ekin = 34.7782829446776 | erot = 15.9229210434175 | epot = -84.26565484209 | etot = -33.5644508539949 +297000 ekin = 35.0767101392392 | erot = 16.1546669536439 | epot = -84.7958279474754 | etot = -33.5644508545923 +298000 ekin = 35.2457989813493 | erot = 16.3457320030339 | epot = -85.1559818389166 | etot = -33.5644508545334 +299000 ekin = 35.2970066855207 | erot = 16.4859983979522 | epot = -85.347455937312 | etot = -33.564450853839 +300000 ekin = 35.2422237261662 | erot = 16.5735941681655 | epot = -85.3802687470049 | etot = -33.5644508526733 +301000 ekin = 35.0916597610801 | erot = 16.6147820199824 | epot = -85.2708926322694 | etot = -33.5644508512069 +302000 ekin = 34.8528128910573 | erot = 16.6227287108408 | epot = -85.0399924514116 | etot = -33.5644508495135 +303000 ekin = 34.5312597670619 | erot = 16.6156181966414 | epot = -84.7113288113064 | etot = -33.5644508476031 +304000 ekin = 34.1313674341479 | erot = 16.6227567332271 | epot = -84.3185750111593 | etot = -33.5644508437843 +305000 ekin = 33.6571822643538 | erot = 16.6720234605616 | epot = -83.8936565670797 | etot = -33.5644508421643 +306000 ekin = 33.1151986332185 | erot = 16.7769746117161 | epot = -83.4566240858681 | etot = -33.5644508409335 +307000 ekin = 32.5134330702932 | erot = 16.9437629167783 | epot = -83.02164682739 | etot = -33.5644508403184 +308000 ekin = 31.8601474906921 | erot = 17.1694637372502 | epot = -82.5940620683754 | etot = -33.564450840433 +309000 ekin = 31.1628016434689 | erot = 17.4420089824522 | epot = -82.169261466886 | etot = -33.564450840965 +310000 ekin = 30.4284939703374 | erot = 17.7430091431839 | epot = -81.7359539560138 | etot = -33.5644508424925 +311000 ekin = 29.6636970637345 | erot = 18.0450727084457 | epot = -81.2732206157263 | etot = -33.5644508435461 +312000 ekin = 28.8763119838581 | erot = 18.3211026916569 | epot = -80.7618655199121 | etot = -33.5644508443971 +313000 ekin = 28.0757317032389 | erot = 18.5482322978723 | epot = -80.18841484566 | etot = -33.5644508445488 +314000 ekin = 27.2754576015478 | erot = 18.7102692133214 | epot = -79.5501776586848 | etot = -33.5644508438156 +315000 ekin = 26.492751287582 | erot = 18.8002978243514 | epot = -78.8574999542526 | etot = -33.5644508423192 +316000 ekin = 25.7476825207451 | erot = 18.8201859998617 | epot = -78.1323193609057 | etot = -33.5644508402989 +317000 ekin = 25.061490505917 | erot = 18.7788964667389 | epot = -77.4048378106934 | etot = -33.5644508380374 +318000 ekin = 24.4546904069621 | erot = 18.6903703700711 | epot = -76.70951161281 | etot = -33.5644508357768 +319000 ekin = 23.9454326767099 | erot = 18.5716676910327 | epot = -76.0815512014053 | etot = -33.5644508336627 +320000 ekin = 23.5484361619436 | erot = 18.4417359442066 | epot = -75.5546229378898 | etot = -33.5644508317396 +321000 ekin = 23.2745454667293 | erot = 18.3209670206422 | epot = -75.1599633173638 | etot = -33.5644508299923 +322000 ekin = 23.1307065451601 | erot = 18.2311244117378 | epot = -74.9262817853413 | etot = -33.5644508284434 +323000 ekin = 23.1199305196705 | erot = 18.1948729379475 | epot = -74.8792542848651 | etot = -33.5644508272471 +324000 ekin = 23.2402241372721 | erot = 18.2346442881315 | epot = -75.0393192521543 | etot = -33.5644508267507 +325000 ekin = 23.4710021373605 | erot = 18.3668956955574 | epot = -75.4023486642627 | etot = -33.5644508313448 +326000 ekin = 23.7795455091373 | erot = 18.5932769387736 | epot = -75.9372732824513 | etot = -33.5644508345405 +327000 ekin = 24.1343713309104 | erot = 18.9009306660405 | epot = -76.5997528364855 | etot = -33.5644508395347 +328000 ekin = 24.4953646019651 | erot = 19.2611055951325 | epot = -77.3209210429526 | etot = -33.564450845855 +329000 ekin = 24.8184483225885 | erot = 19.6309716495633 | epot = -78.0138708245784 | etot = -33.5644508524265 +330000 ekin = 25.064815357625 | erot = 19.9600875040515 | epot = -78.5893537191764 | etot = -33.5644508574999 +331000 ekin = 25.210138372085 | erot = 20.2008919381964 | epot = -78.9754811706065 | etot = -33.5644508603252 +332000 ekin = 25.2457706637465 | erot = 20.3248269292201 | epot = -79.1350484525863 | etot = -33.5644508596197 +333000 ekin = 25.1861890028038 | erot = 20.3296166390246 | epot = -79.0802564973891 | etot = -33.5644508555607 +334000 ekin = 25.0662190978875 | erot = 20.2399843242263 | epot = -78.8706542713047 | etot = -33.5644508491909 +335000 ekin = 24.9333683334916 | erot = 20.10098162188 | epot = -78.5988007973609 | etot = -33.5644508419894 +336000 ekin = 24.838111457398 | erot = 19.9670256543986 | epot = -78.3695879471494 | etot = -33.5644508353528 +337000 ekin = 24.8247545149941 | erot = 19.8908557634947 | epot = -78.2800611092981 | etot = -33.5644508308092 +338000 ekin = 24.9246805340852 | erot = 19.9088859975653 | epot = -78.3980173596517 | etot = -33.5644508280012 +339000 ekin = 25.1522743468773 | erot = 20.043365846553 | epot = -78.7600910207995 | etot = -33.5644508273693 +340000 ekin = 25.5040328013693 | erot = 20.306324357249 | epot = -79.3748079873049 | etot = -33.5644508286866 +341000 ekin = 25.9593882031618 | erot = 20.6972938179444 | epot = -80.2211328525995 | etot = -33.5644508314932 +342000 ekin = 26.4842114254738 | erot = 21.2060406180888 | epot = -81.2547028788679 | etot = -33.5644508353053 +343000 ekin = 27.0356929912357 | erot = 21.815327972342 | epot = -82.4154718031651 | etot = -33.5644508395875 +344000 ekin = 27.5676973344761 | erot = 22.5033872894512 | epot = -83.6355354677601 | etot = -33.5644508438328 +345000 ekin = 28.0359749646807 | erot = 23.2463366467675 | epot = -84.8467624590903 | etot = -33.5644508476421 +346000 ekin = 28.4026013552871 | erot = 24.0201112992161 | epot = -85.9871635052192 | etot = -33.564450850716 +347000 ekin = 28.6398915194528 | erot = 24.8020103746231 | epot = -87.0063527467572 | etot = -33.5644508526813 +348000 ekin = 28.7326075377482 | erot = 25.5714490942921 | epot = -87.8685074860267 | etot = -33.5644508539863 +349000 ekin = 28.6752584344036 | erot = 26.3100180841384 | epot = -88.549727373061 | etot = -33.564450854519 +350000 ekin = 28.4730637357079 | erot = 27.0009502159031 | epot = -89.038464806185 | etot = -33.564450854574 +351000 ekin = 28.1395378484453 | erot = 27.6270646736909 | epot = -89.3310533767997 | etot = -33.5644508546635 +352000 ekin = 27.692958073856 | erot = 28.1676652362281 | epot = -89.4250741653402 | etot = -33.5644508552561 +353000 ekin = 27.1526950366525 | erot = 28.5958100264823 | epot = -89.3129559196985 | etot = -33.5644508565636 +354000 ekin = 26.5365141387121 | erot = 28.8781341171817 | epot = -88.9790991141991 | etot = -33.5644508583052 +355000 ekin = 25.8598799836129 | erot = 28.9793031096872 | epot = -88.4036339528938 | etot = -33.5644508595937 +356000 ekin = 25.1375717946229 | erot = 28.8722956885124 | epot = -87.5743183424417 | etot = -33.5644508593064 +357000 ekin = 24.3868741548633 | erot = 28.5495289601074 | epot = -86.5008539716514 | etot = -33.5644508566807 +358000 ekin = 23.6300778926751 | erot = 28.0297879776407 | epot = -85.2243167221727 | etot = -33.5644508518569 +359000 ekin = 22.8939201469052 | erot = 27.355677035979 | epot = -83.8140480288444 | etot = -33.5644508459602 +360000 ekin = 22.206578007299 | erot = 26.5834479666855 | epot = -82.3544768140201 | etot = -33.5644508400356 +361000 ekin = 21.5986345635157 | erot = 25.7744654426823 | epot = -80.9375508370781 | etot = -33.5644508308802 +362000 ekin = 21.1083260621075 | erot = 24.989507840829 | epot = -79.6622847317925 | etot = -33.564450828856 +363000 ekin = 20.7375100619836 | erot = 24.2576398932737 | epot = -78.5596007834521 | etot = -33.5644508281948 +364000 ekin = 20.476003367975 | erot = 23.5946470163905 | epot = -77.635101212758 | etot = -33.5644508283926 +365000 ekin = 20.3079089893725 | erot = 23.009513896542 | epot = -76.8818737148766 | etot = -33.5644508289621 +366000 ekin = 20.2147979335995 | erot = 22.508371935773 | epot = -76.2876206988782 | etot = -33.5644508295058 +367000 ekin = 20.1786185360397 | erot = 22.0973297018217 | epot = -75.8403990676851 | etot = -33.5644508298237 +368000 ekin = 20.1837486799222 | erot = 21.7835270635243 | epot = -75.5317265733032 | etot = -33.5644508298567 +369000 ekin = 20.2182310118282 | erot = 21.574738818764 | epot = -75.3574206602716 | etot = -33.5644508296795 +370000 ekin = 20.2742556079065 | erot = 21.4781104693876 | epot = -75.3168169068296 | etot = -33.5644508295354 +371000 ekin = 20.3477066126427 | erot = 21.4982876398118 | epot = -75.4104450815928 | etot = -33.5644508291383 +372000 ekin = 20.4391769085492 | erot = 21.6370751258624 | epot = -75.6407028633193 | etot = -33.5644508289077 +373000 ekin = 20.5523906693865 | erot = 21.8921389377599 | epot = -76.0089804360328 | etot = -33.5644508288864 +374000 ekin = 20.6947607298497 | erot = 22.2561865203504 | epot = -76.5153980788613 | etot = -33.5644508286612 +375000 ekin = 20.8734352289465 | erot = 22.7176361068345 | epot = -77.1555221652783 | etot = -33.5644508294973 +376000 ekin = 21.089493504449 | erot = 23.2620769848747 | epot = -77.9160213199094 | etot = -33.5644508305857 +377000 ekin = 21.3446674636834 | erot = 23.8720082855239 | epot = -78.7811265807323 | etot = -33.5644508315251 +378000 ekin = 21.64248542288 | erot = 24.5275644040167 | epot = -79.7345006597438 | etot = -33.5644508328471 +379000 ekin = 21.9906215820674 | erot = 25.2058289791334 | epot = -80.760901395464 | etot = -33.5644508342632 +380000 ekin = 22.3975872844685 | erot = 25.8799316875408 | epot = -81.8419698098752 | etot = -33.5644508378659 +381000 ekin = 22.8474625363943 | erot = 26.5196756829191 | epot = -82.9315890607488 | etot = -33.5644508414354 +382000 ekin = 23.3214968284424 | erot = 27.0935868814443 | epot = -83.9795345552253 | etot = -33.5644508453386 +383000 ekin = 23.7989486472446 | erot = 27.5682880226977 | epot = -84.9316875190629 | etot = -33.5644508491206 +384000 ekin = 24.2602946690265 | erot = 27.9101784190738 | epot = -85.7349239404018 | etot = -33.5644508523015 +385000 ekin = 24.6909701694311 | erot = 28.0892515731128 | epot = -86.3446725966466 | etot = -33.5644508541027 +386000 ekin = 25.0758089633983 | erot = 28.0812872789257 | epot = -86.7215471012156 | etot = -33.5644508588916 +387000 ekin = 25.3886917944075 | erot = 27.8683599140167 | epot = -86.8215025662873 | etot = -33.5644508578631 +388000 ekin = 25.6321888108903 | erot = 27.4567876604955 | epot = -86.6534273266304 | etot = -33.5644508552446 +389000 ekin = 25.8173007945516 | erot = 26.8690369422729 | epot = -86.2507885889323 | etot = -33.5644508521078 +390000 ekin = 25.9562629244357 | erot = 26.1386991559259 | epot = -85.6594129285287 | etot = -33.5644508481671 +391000 ekin = 26.0625510048269 | erot = 25.3050096521924 | epot = -84.9320115015289 | etot = -33.5644508445096 +392000 ekin = 26.1477279258622 | erot = 24.4077754077168 | epot = -84.1199541750021 | etot = -33.5644508414231 +393000 ekin = 26.2207009126332 | erot = 23.4862823971765 | epot = -83.2714341487272 | etot = -33.5644508389175 +394000 ekin = 26.2880235523287 | erot = 22.5776047859249 | epot = -82.4300791763575 | etot = -33.5644508381039 +395000 ekin = 26.3461327830984 | erot = 21.6992206106144 | epot = -81.6098042311068 | etot = -33.564450837394 +396000 ekin = 26.3925769143903 | erot = 20.8648963380663 | epot = -80.8219240890407 | etot = -33.5644508365841 +397000 ekin = 26.428035758933 | erot = 20.0875980485209 | epot = -80.0800846430096 | etot = -33.5644508355556 +398000 ekin = 26.456826416021 | erot = 19.3805747697538 | epot = -79.4018520200386 | etot = -33.5644508342638 +399000 ekin = 26.486391084066 | erot = 18.7576183807505 | epot = -78.8084602983018 | etot = -33.5644508334853 +400000 ekin = 26.5240355653678 | erot = 18.2309165845048 | epot = -78.3194029820227 | etot = -33.5644508321501 +401000 ekin = 26.5785515874793 | erot = 17.8133011772033 | epot = -77.9563035960443 | etot = -33.5644508313617 +402000 ekin = 26.6553316875252 | erot = 17.514632436928 | epot = -77.734414956193 | etot = -33.5644508317398 +403000 ekin = 26.7508441445099 | erot = 17.3369800813554 | epot = -77.652275059838 | etot = -33.5644508339727 +404000 ekin = 26.847889984788 | erot = 17.2703664407998 | epot = -77.6827072638883 | etot = -33.5644508383005 +405000 ekin = 26.913648151536 | erot = 17.2906409832311 | epot = -77.7687399796104 | etot = -33.5644508448433 +406000 ekin = 26.902674398225 | erot = 17.3519919760325 | epot = -77.8191172252429 | etot = -33.5644508509854 +407000 ekin = 26.7697793194821 | erot = 17.4151352557073 | epot = -77.7493654299019 | etot = -33.5644508547125 +408000 ekin = 26.4852107134516 | erot = 17.4599310842078 | epot = -77.5095926523416 | etot = -33.5644508546822 +409000 ekin = 26.0447937750069 | erot = 17.489715636437 | epot = -77.0989602629569 | etot = -33.5644508515129 +410000 ekin = 25.4686689668068 | erot = 17.525308599665 | epot = -76.5584284134685 | etot = -33.5644508469967 +411000 ekin = 24.7901856107123 | erot = 17.5925678630378 | epot = -75.9472043167211 | etot = -33.5644508429709 +412000 ekin = 24.0429450725907 | erot = 17.7112262982761 | epot = -75.3186222112118 | etot = -33.5644508403449 +413000 ekin = 23.2530709445256 | erot = 17.8904894596477 | epot = -74.7080112432066 | etot = -33.5644508390334 +414000 ekin = 22.4380957573478 | erot = 18.1309089877695 | epot = -74.1334555836572 | etot = -33.5644508385398 +415000 ekin = 21.6095002976116 | erot = 18.4284521142751 | epot = -73.602403250255 | etot = -33.5644508383683 +416000 ekin = 20.7759703157875 | erot = 18.7780315269414 | epot = -73.1184526809263 | etot = -33.5644508381974 +417000 ekin = 19.9459219947443 | erot = 19.1754390641456 | epot = -72.6858118967654 | etot = -33.5644508378755 +418000 ekin = 19.1290603146812 | erot = 19.6178812354861 | epot = -72.3113923875162 | etot = -33.5644508373488 +419000 ekin = 18.337241174772 | erot = 20.1037315119174 | epot = -72.0054235233031 | etot = -33.5644508366137 +420000 ekin = 17.5848708568132 | erot = 20.6319495840779 | epot = -71.7812712766011 | etot = -33.56445083571 +421000 ekin = 16.8888669767983 | erot = 21.2012508779721 | epot = -71.654568689522 | etot = -33.5644508347516 +422000 ekin = 16.2680311854784 | erot = 21.8088345390476 | epot = -71.6413165584825 | etot = -33.5644508339565 +423000 ekin = 15.7416423467535 | erot = 22.4484657014465 | epot = -71.7545588818543 | etot = -33.5644508336543 +424000 ekin = 15.3271568811325 | erot = 23.1079611162026 | epot = -71.9995688315969 | etot = -33.5644508342617 +425000 ekin = 15.0370245443348 | erot = 23.7664993128454 | epot = -72.3679746933972 | etot = -33.564450836217 +426000 ekin = 14.8748792453187 | erot = 24.3924933231442 | epot = -72.8318234082976 | etot = -33.5644508398346 +427000 ekin = 14.832039809902 | erot = 24.9432466995696 | epot = -73.3397373544821 | etot = -33.5644508450105 +428000 ekin = 14.8863924965724 | erot = 25.3682827941945 | epot = -73.8191261416202 | etot = -33.5644508508533 +429000 ekin = 15.0062259695096 | erot = 25.6182665544711 | epot = -74.1889433796231 | etot = -33.5644508556425 +430000 ekin = 15.1595389321706 | erot = 25.6590201133014 | epot = -74.3830099029893 | etot = -33.5644508575173 +431000 ekin = 15.3249133699301 | erot = 25.4851984008896 | epot = -74.3745626264541 | etot = -33.5644508556344 +432000 ekin = 15.4974987577291 | erot = 25.1253113466907 | epot = -74.1872609551818 | etot = -33.564450850762 +433000 ekin = 15.6867402477113 | erot = 24.6339851579825 | epot = -73.8851762504141 | etot = -33.5644508447203 +434000 ekin = 15.9084789524794 | erot = 24.0759117528502 | epot = -73.5488415445721 | etot = -33.5644508392426 +435000 ekin = 16.1769022059295 | erot = 23.5103596607615 | epot = -73.2517127019844 | etot = -33.5644508352934 +436000 ekin = 16.4997173059121 | erot = 22.982276516596 | epot = -73.0464446556282 | etot = -33.5644508331201 +437000 ekin = 16.8769806267692 | erot = 22.5199344326914 | epot = -72.9613658918858 | etot = -33.5644508324252 +438000 ekin = 17.3021259571189 | erot = 22.1372453982692 | epot = -73.0038221882045 | etot = -33.5644508328165 +439000 ekin = 17.7637229038904 | erot = 21.8373393625555 | epot = -73.1655131003915 | etot = -33.5644508339456 +440000 ekin = 18.2471223979642 | erot = 21.6157595595105 | epot = -73.4273327930288 | etot = -33.5644508355542 +441000 ekin = 18.7357201395202 | erot = 21.4628710845264 | epot = -73.7630420615274 | etot = -33.5644508374808 +442000 ekin = 19.2118878212758 | erot = 21.3654515420967 | epot = -74.1417902029639 | etot = -33.5644508395913 +443000 ekin = 19.6577318124847 | erot = 21.3079015376766 | epot = -74.53008419193 | etot = -33.5644508417687 +444000 ekin = 20.0558238633514 | erot = 21.2733344148632 | epot = -74.8936091221088 | etot = -33.5644508438943 +445000 ekin = 20.3899893912765 | erot = 21.2445884062657 | epot = -75.1990286433742 | etot = -33.564450845832 +446000 ekin = 20.6461236044623 | erot = 21.2052857367731 | epot = -75.4158601887455 | etot = -33.5644508475101 +447000 ekin = 20.8131102288242 | erot = 21.1405154512163 | epot = -75.5180765281394 | etot = -33.5644508480989 +448000 ekin = 20.8836321566285 | erot = 21.0415726580739 | epot = -75.4896556637134 | etot = -33.564450849011 +449000 ekin = 20.8549766397521 | erot = 20.9006105485552 | epot = -75.3200380377527 | etot = -33.5644508494454 +450000 ekin = 20.7289995990038 | erot = 20.7094982244637 | epot = -75.0029486728388 | etot = -33.5644508493713 +451000 ekin = 20.5121237021944 | erot = 20.4634057687326 | epot = -74.5399803196977 | etot = -33.5644508487708 +452000 ekin = 20.2152499009175 | erot = 20.1611428754593 | epot = -73.9408436240171 | etot = -33.5644508476403 +453000 ekin = 19.8534700766569 | erot = 19.8054562088314 | epot = -73.2233771314871 | etot = -33.5644508459988 +454000 ekin = 19.4456214293028 | erot = 19.4031472753521 | epot = -72.4132195485558 | etot = -33.5644508439009 +455000 ekin = 19.013720522958 | erot = 18.9648723131976 | epot = -71.5430436775731 | etot = -33.5644508414174 +456000 ekin = 18.5823093301098 | erot = 18.5046119868785 | epot = -70.6513721556565 | etot = -33.5644508386682 +457000 ekin = 18.1775784950835 | erot = 18.0385547552667 | epot = -69.78058408621 | etot = -33.5644508358598 +458000 ekin = 17.8262193053526 | erot = 17.5834820270548 | epot = -68.9741521653779 | etot = -33.5644508329705 +459000 ekin = 17.5544328315452 | erot = 17.1574115033618 | epot = -68.2762951652654 | etot = -33.5644508303584 +460000 ekin = 17.3857834994296 | erot = 16.7769882364438 | epot = -67.7272225641225 | etot = -33.5644508282491 +461000 ekin = 17.3389537757626 | erot = 16.455973724737 | epot = -67.3593783273661 | etot = -33.5644508268665 +462000 ekin = 17.4254421541841 | erot = 16.2041333991817 | epot = -67.1940263797602 | etot = -33.5644508263943 +463000 ekin = 17.6475549838229 | erot = 16.0264214063364 | epot = -67.2384272171003 | etot = -33.564450826941 +464000 ekin = 17.9971528391881 | erot = 15.9226257283447 | epot = -67.4842293960243 | etot = -33.5644508284914 +465000 ekin = 18.4555654856042 | erot = 15.8876205732821 | epot = -67.9076368897882 | etot = -33.5644508309019 +466000 ekin = 18.994833816268 | erot = 15.9122553308001 | epot = -68.4715399809881 | etot = -33.56445083392 +467000 ekin = 19.5800987880665 | erot = 15.9847161184822 | epot = -69.1292657437925 | etot = -33.5644508372437 +468000 ekin = 20.1726645576357 | erot = 16.092033474867 | epot = -69.8291488730892 | etot = -33.5644508405865 +469000 ekin = 20.7331520539173 | erot = 16.2213910260308 | epot = -70.5189939236682 | etot = -33.5644508437201 +470000 ekin = 21.2242791251891 | erot = 16.3610502015494 | epot = -71.1497801732201 | etot = -33.5644508464816 +471000 ekin = 21.6130740295016 | erot = 16.5009517692281 | epot = -71.6784766474807 | etot = -33.5644508487511 +472000 ekin = 21.8725913830426 | erot = 16.6332178546314 | epot = -72.0702600880887 | etot = -33.5644508504148 +473000 ekin = 21.9833185471591 | erot = 16.7527436323979 | epot = -72.3005130309141 | etot = -33.5644508513571 +474000 ekin = 21.9344099206197 | erot = 16.8578720765084 | epot = -72.3567328486035 | etot = -33.5644508514753 +475000 ekin = 21.7247480854268 | erot = 16.9509439426178 | epot = -72.2401428787492 | etot = -33.5644508507046 +476000 ekin = 21.3637036554458 | erot = 17.0384540155613 | epot = -71.9666085200589 | etot = -33.5644508490518 +477000 ekin = 20.8713853163245 | erot = 17.1305938642667 | epot = -71.5664300271903 | etot = -33.5644508465991 +478000 ekin = 20.278105615873 | erot = 17.2401904856046 | epot = -71.0827469450555 | etot = -33.5644508435779 +479000 ekin = 19.6228148922665 | erot = 17.3807417056378 | epot = -70.568007438203 | etot = -33.5644508402987 +480000 ekin = 18.9501924820064 | erot = 17.5641098022629 | epot = -70.0787531214702 | etot = -33.5644508372009 +481000 ekin = 18.3063999207717 | erot = 17.7978626898958 | epot = -69.6687134454551 | etot = -33.5644508347876 +482000 ekin = 17.7338800308325 | erot = 18.0826185785594 | epot = -69.3809494429303 | etot = -33.5644508335384 +483000 ekin = 17.2661333869276 | erot = 18.4098565339483 | epot = -69.240440754661 | etot = -33.5644508337851 +484000 ekin = 16.9123469725788 | erot = 18.5839236849874 | epot = -69.0607216152016 | etot = -33.5644509576354 +485000 ekin = 17.2473052114824 | erot = 17.4463141951386 | epot = -68.2580700313457 | etot = -33.5644506247246 +486000 ekin = 18.3155143091698 | erot = 17.1832730976792 | epot = -69.0632384225994 | etot = -33.5644510157505 +487000 ekin = 18.1324826614411 | erot = 17.2801627137661 | epot = -68.97709615336 | etot = -33.5644507781527 +488000 ekin = 18.065066671032 | erot = 17.4264266856946 | epot = -69.0559441347504 | etot = -33.5644507780238 +489000 ekin = 18.1230207571896 | erot = 17.62013699274 | epot = -69.3076085290087 | etot = -33.5644507790791 +490000 ekin = 18.2959502060246 | erot = 17.8551924365762 | epot = -69.7155934233775 | etot = -33.5644507807768 +491000 ekin = 18.5602651979885 | erot = 18.1239992625185 | epot = -70.2487152439638 | etot = -33.5644507834568 +492000 ekin = 18.8855238698909 | erot = 18.4159985147992 | epot = -70.8659731703599 | etot = -33.5644507856698 +493000 ekin = 19.2395352565568 | erot = 18.728264479198 | epot = -71.5322505227183 | etot = -33.5644507869634 +494000 ekin = 19.5921246700955 | erot = 19.0689157919617 | epot = -72.2254912499723 | etot = -33.564450787915 +495000 ekin = 19.0728202093635 | erot = 18.9158482409358 | epot = -71.553118977483 | etot = -33.5644505271837 +496000 ekin = 19.8797920565295 | erot = 18.7380967908333 | epot = -72.1823393794609 | etot = -33.5644505320982 +497000 ekin = 21.3129327566087 | erot = 19.2208596910155 | epot = -74.0982428018017 | etot = -33.5644503541775 +498000 ekin = 21.3264694811286 | erot = 19.7980335585692 | epot = -74.6889533936585 | etot = -33.5644503539607 +499000 ekin = 21.2778907742156 | erot = 20.4793064458065 | epot = -75.3216475743002 | etot = -33.5644503542781 +500000 ekin = 21.1661916282903 | erot = 21.2581781223902 | epot = -75.988820105787 | etot = -33.5644503551065 +501000 ekin = 20.9926825375652 | erot = 22.1178388255783 | epot = -76.6749717195959 | etot = -33.5644503564525 +502000 ekin = 20.7610606941479 | erot = 23.0317414653473 | epot = -77.3572525175607 | etot = -33.5644503580655 +503000 ekin = 20.4798770188399 | erot = 23.9650377707536 | epot = -78.0093651497042 | etot = -33.5644503601106 +504000 ekin = 20.1546807719764 | erot = 24.8789199645846 | epot = -78.5980510989298 | etot = -33.5644503623688 +505000 ekin = 19.7897861052766 | erot = 25.7326258924132 | epot = -79.0868623624994 | etot = -33.5644503648096 +506000 ekin = 19.3875459003549 | erot = 26.4882337371013 | epot = -79.4402300038003 | etot = -33.564450366344 +507000 ekin = 18.9527707503713 | erot = 27.1161379584882 | epot = -79.6333590756734 | etot = -33.5644503668138 +508000 ekin = 18.4930541127617 | erot = 27.6003825990922 | epot = -79.6578870777478 | etot = -33.5644503658939 +509000 ekin = 18.0182547166152 | erot = 27.9414911095304 | epot = -79.5241961902308 | etot = -33.5644503640852 +510000 ekin = 17.5239659446583 | erot = 28.1499521523349 | epot = -79.2383684583427 | etot = -33.5644503613495 +511000 ekin = 17.0202767588224 | erot = 28.2490270330593 | epot = -78.8337541499512 | etot = -33.5644503580695 +512000 ekin = 16.5245718006517 | erot = 28.2698315419544 | epot = -78.3588536974674 | etot = -33.5644503548613 +513000 ekin = 16.0539184296555 | erot = 28.2435719405511 | epot = -77.8619407224233 | etot = -33.5644503522167 +514000 ekin = 15.6229539751463 | erot = 28.1963871950865 | epot = -77.3837915206358 | etot = -33.564450350403 +515000 ekin = 15.2424792420144 | erot = 28.1464443105655 | epot = -76.9533739021307 | etot = -33.5644503495508 +516000 ekin = 14.9188926056263 | erot = 28.102754035252 | epot = -76.5860969902898 | etot = -33.5644503494115 +517000 ekin = 14.6543809151572 | erot = 28.0678237290645 | epot = -76.286654994032 | etot = -33.5644503498102 +518000 ekin = 14.4476572455448 | erot = 28.0395642675265 | epot = -76.0516718635495 | etot = -33.5644503504781 +519000 ekin = 14.2950490439313 | erot = 28.0138489409074 | epot = -75.8733483359815 | etot = -33.5644503511427 +520000 ekin = 14.1917488336712 | erot = 27.9870813583917 | epot = -75.7432805436438 | etot = -33.564450351581 +521000 ekin = 14.1329830510129 | erot = 27.9581295478616 | epot = -75.6555629505529 | etot = -33.5644503516784 +522000 ekin = 14.1002586402904 | erot = 27.7732671764717 | epot = -75.4379761963452 | etot = -33.5644503795831 +523000 ekin = 14.1969588160089 | erot = 27.1027118580652 | epot = -74.8641209749246 | etot = -33.5644503008506 +524000 ekin = 14.7378402614501 | erot = 26.616408914504 | epot = -74.9186994724366 | etot = -33.5644502964825 +525000 ekin = 15.506867285083 | erot = 26.5883544533635 | epot = -75.6596721107952 | etot = -33.5644503723486 +526000 ekin = 15.8574449977295 | erot = 26.6724957238465 | epot = -76.0943910941999 | etot = -33.5644503726239 +527000 ekin = 16.0112069682755 | erot = 26.735509894999 | epot = -76.3111672365705 | etot = -33.5644503732961 +528000 ekin = 16.1641744091399 | erot = 26.794797881151 | epot = -76.5234226642097 | etot = -33.5644503739187 +529000 ekin = 16.3159009762014 | erot = 26.8380825380496 | epot = -76.7184338885631 | etot = -33.564450374312 +530000 ekin = 16.4667477211871 | erot = 26.8553312025443 | epot = -76.8865292981414 | etot = -33.5644503744099 +531000 ekin = 16.6177352356877 | erot = 26.8400251085783 | epot = -77.0222107185202 | etot = -33.5644503742542 +532000 ekin = 16.770215067808 | erot = 26.7891084873303 | epot = -77.1237739290464 | etot = -33.5644503739081 +533000 ekin = 16.9253640369286 | erot = 26.7024973873184 | epot = -77.1923117977069 | etot = -33.5644503734599 +534000 ekin = 17.083644786901 | erot = 26.5822176528864 | epot = -77.2303128128235 | etot = -33.5644503730361 +535000 ekin = 17.2444487917795 | erot = 26.4310079588738 | epot = -77.2399071233944 | etot = -33.5644503727411 +536000 ekin = 17.4060591056372 | erot = 26.2510049056998 | epot = -77.2215143839431 | etot = -33.5644503726061 +537000 ekin = 17.565899198427 | erot = 26.0431264908893 | epot = -77.1734760618753 | etot = -33.5644503725589 +538000 ekin = 17.7209415439151 | erot = 25.807444121848 | epot = -77.0928360383798 | etot = -33.5644503726168 +539000 ekin = 17.8681497081321 | erot = 25.5433035299374 | epot = -76.9759036107203 | etot = -33.5644503726507 +540000 ekin = 18.0048631565718 | erot = 25.2502517038857 | epot = -76.8195652330541 | etot = -33.5644503725966 +541000 ekin = 18.129064827171 | erot = 24.9288645877469 | epot = -76.6223797873357 | etot = -33.5644503724178 +542000 ekin = 18.2395164939016 | erot = 24.5811691615965 | epot = -76.3851360275838 | etot = -33.5644503720856 +543000 ekin = 18.3357700080052 | erot = 24.210846834268 | epot = -76.1110672139389 | etot = -33.5644503716657 +544000 ekin = 18.4180615073977 | erot = 23.8229131244208 | epot = -75.8054250029922 | etot = -33.5644503711738 +545000 ekin = 18.48709013 | erot = 23.4236993423704 | epot = -75.475239842524 | etot = -33.5644503701536 +546000 ekin = 18.5436104708162 | erot = 23.023272620427 | epot = -75.1313334610026 | etot = -33.5644503697594 +547000 ekin = 18.5881260728255 | erot = 22.6282216102247 | epot = -74.780798052539 | etot = -33.5644503694888 +548000 ekin = 18.6206521539779 | erot = 22.2431161969749 | epot = -74.4282187199115 | etot = -33.5644503689587 +549000 ekin = 18.6395328552822 | erot = 21.8731131587291 | epot = -74.0770963833356 | etot = -33.5644503693243 +550000 ekin = 18.6420012526372 | erot = 21.5194517195331 | epot = -73.7259033420982 | etot = -33.5644503699279 +551000 ekin = 18.6249210292856 | erot = 21.1784779028361 | epot = -73.3678493028498 | etot = -33.5644503707282 +552000 ekin = 18.5841928768992 | erot = 20.8452278495212 | epot = -72.9938710980166 | etot = -33.5644503715962 +553000 ekin = 18.515212705724 | erot = 20.5148731368217 | epot = -72.5945362148738 | etot = -33.5644503723281 +554000 ekin = 18.4136816909966 | erot = 20.1848933331084 | epot = -72.1630253967881 | etot = -33.5644503726831 +555000 ekin = 18.2766906401233 | erot = 19.857476932628 | epot = -71.6986179451961 | etot = -33.5644503724447 +556000 ekin = 18.1040115049041 | erot = 19.5406874735951 | epot = -71.20914935019 | etot = -33.5644503716908 +557000 ekin = 17.8992309647499 | erot = 19.2497226287959 | epot = -70.7134039634794 | etot = -33.5644503699335 +558000 ekin = 17.6705778374572 | erot = 19.0080857253366 | epot = -70.2431139302706 | etot = -33.5644503674768 +559000 ekin = 17.4315653927809 | erot = 18.8444628123191 | epot = -69.8404785695829 | etot = -33.5644503644829 +560000 ekin = 17.2006230348878 | erot = 18.7901643782654 | epot = -69.5552377744807 | etot = -33.5644503613275 +561000 ekin = 16.9995569160732 | erot = 18.8749610237664 | epot = -69.438968298262 | etot = -33.5644503584223 +562000 ekin = 16.8505251060201 | erot = 19.1232120100743 | epot = -69.538187472407 | etot = -33.5644503563126 +563000 ekin = 16.7718160200182 | erot = 19.5498137335684 | epot = -69.8860801091477 | etot = -33.5644503555612 +564000 ekin = 16.7730284254869 | erot = 20.1561760612857 | epot = -70.4936548437135 | etot = -33.564450356941 +565000 ekin = 16.8503463818591 | erot = 20.9261148982968 | epot = -71.3409116403028 | etot = -33.5644503601468 +566000 ekin = 16.9881817954648 | erot = 21.8252877510101 | epot = -72.3779199117371 | etot = -33.5644503652621 +567000 ekin = 17.1597730194767 | erot = 22.8021750341433 | epot = -73.5263984254872 | etot = -33.5644503718672 +568000 ekin = 17.3309908966704 | erot = 23.7909429898642 | epot = -74.6863842658269 | etot = -33.5644503792923 +569000 ekin = 17.4658946017947 | erot = 24.7167318453097 | epot = -75.7470768337898 | etot = -33.5644503866854 +570000 ekin = 17.5327796656957 | erot = 25.5030724456584 | epot = -76.6003025044407 | etot = -33.5644503930867 +571000 ekin = 17.5098280200956 | erot = 26.0808668137263 | epot = -77.1551452313793 | etot = -33.5644503975575 +572000 ekin = 17.3896134298641 | erot = 26.3976580231972 | epot = -77.3517218524132 | etot = -33.5644503993519 +573000 ekin = 17.1817696520727 | erot = 26.4252545062395 | epot = -77.1714745564325 | etot = -33.5644503981203 +574000 ekin = 16.9132012155478 | erot = 26.1636856780794 | epot = -76.6413372876784 | etot = -33.5644503940512 +575000 ekin = 16.6253831480204 | erot = 25.6401831359933 | epot = -75.8300166719201 | etot = -33.5644503879064 +576000 ekin = 16.380585448721 | erot = 24.9437607561783 | epot = -74.8887965737009 | etot = -33.5644503688016 +577000 ekin = 16.2309295888517 | erot = 24.1552332190076 | epot = -73.9506131738505 | etot = -33.5644503659912 +578000 ekin = 16.2003426792014 | erot = 23.2996785341935 | epot = -73.0644715774378 | etot = -33.5644503640429 +579000 ekin = 16.2983938260692 | erot = 22.403268564264 | epot = -72.2661127535552 | etot = -33.564450363222 +580000 ekin = 16.5164282817949 | erot = 21.4889399504527 | epot = -71.5698185979652 | etot = -33.5644503657176 +581000 ekin = 16.8294131729517 | erot = 20.5770732253488 | epot = -70.9709367638666 | etot = -33.5644503655661 +582000 ekin = 17.2014342865815 | erot = 19.7085617423075 | epot = -70.4744463947337 | etot = -33.5644503658447 +583000 ekin = 17.5894541379175 | erot = 18.9251667746001 | epot = -70.0790712786264 | etot = -33.5644503661089 +584000 ekin = 17.9521233670864 | erot = 18.2657373645481 | epot = -69.7823110977226 | etot = -33.5644503660881 +585000 ekin = 18.2577014583726 | erot = 17.7627566558239 | epot = -69.5849084798981 | etot = -33.5644503657016 +586000 ekin = 18.4890373219802 | erot = 17.4391816025382 | epot = -69.4926692894764 | etot = -33.564450364958 +587000 ekin = 18.6451700996557 | erot = 17.3070654479175 | epot = -69.5166859114532 | etot = -33.56445036388 +588000 ekin = 18.7400423388426 | erot = 17.3682960794591 | epot = -69.6727887808625 | etot = -33.5644503625608 +589000 ekin = 18.7988289995881 | erot = 17.6163757903826 | epot = -69.9796551512482 | etot = -33.5644503612775 +590000 ekin = 18.8521852512136 | erot = 18.0377077417099 | epot = -70.4543433534176 | etot = -33.5644503604942 +591000 ekin = 18.9335216734591 | erot = 18.6145318738827 | epot = -71.1125039068147 | etot = -33.5644503594728 +592000 ekin = 19.0736372367424 | erot = 19.3273958987853 | epot = -71.9654834959436 | etot = -33.5644503604159 +593000 ekin = 19.2836835998251 | erot = 20.1464047126482 | epot = -72.9945386752994 | etot = -33.5644503628261 +594000 ekin = 19.5596584182911 | erot = 21.034123237702 | epot = -74.1582320224138 | etot = -33.5644503664207 +595000 ekin = 19.8847224289421 | erot = 21.9477887878841 | epot = -75.3969615874945 | etot = -33.5644503706683 +596000 ekin = 20.2229995980596 | erot = 22.8321032481879 | epot = -76.6195532314308 | etot = -33.5644503851833 +597000 ekin = 20.5134057747578 | erot = 23.6125551263639 | epot = -77.690411290674 | etot = -33.5644503895523 +598000 ekin = 20.7238255187825 | erot = 24.2466753991533 | epot = -78.5349513101318 | etot = -33.564450392196 +599000 ekin = 20.8326105241634 | erot = 24.7094660562249 | epot = -79.1065269733091 | etot = -33.5644503929208 +600000 ekin = 20.8281928837872 | erot = 24.9942677730575 | epot = -79.3869110487785 | etot = -33.5644503919338 +601000 ekin = 20.7081769101586 | erot = 25.1108515584272 | epot = -79.3834788582876 | etot = -33.5644503897018 +602000 ekin = 20.4770754644872 | erot = 25.0812117067637 | epot = -79.1227375580319 | etot = -33.564450386781 +603000 ekin = 20.1436196145649 | erot = 24.9343592774281 | epot = -78.642429275663 | etot = -33.5644503836701 +604000 ekin = 19.718418586643 | erot = 24.7015463496202 | epot = -77.9844153169741 | etot = -33.5644503807109 +605000 ekin = 19.2123955084805 | erot = 24.4128183909086 | epot = -77.1896642774627 | etot = -33.5644503780737 +606000 ekin = 18.6360571568103 | erot = 24.0951290270779 | epot = -76.2956365596783 | etot = -33.5644503757901 +607000 ekin = 17.9994317315232 | erot = 23.7717793966555 | epot = -75.3356615019793 | etot = -33.5644503738006 +608000 ekin = 17.3124228754835 | erot = 23.4627525856982 | epot = -74.3396258331827 | etot = -33.5644503720009 +609000 ekin = 16.5853412867126 | erot = 23.1855122482213 | epot = -73.3353039052169 | etot = -33.5644503702829 +610000 ekin = 15.8294285552829 | erot = 22.9559130662675 | epot = -72.349791990107 | etot = -33.5644503685566 +611000 ekin = 15.0572484570073 | erot = 22.7889597209054 | epot = -71.4106585446845 | etot = -33.5644503667718 +612000 ekin = 14.2829782525896 | erot = 22.6991649599953 | epot = -70.5465935774999 | etot = -33.564450364915 +613000 ekin = 13.5233158608979 | erot = 22.7018063034666 | epot = -69.789572526273 | etot = -33.5644503619085 +614000 ekin = 12.7974443554635 | erot = 22.8128628324568 | epot = -69.1747575482518 | etot = -33.5644503603315 +615000 ekin = 12.1222485230176 | erot = 23.0409824260638 | epot = -68.727681308147 | etot = -33.5644503590656 +616000 ekin = 11.5143476716423 | erot = 23.3894333510186 | epot = -68.468231381177 | etot = -33.5644503585161 +617000 ekin = 10.9895105320919 | erot = 23.8529820645469 | epot = -68.4069429553071 | etot = -33.5644503586684 +618000 ekin = 10.562142737904 | erot = 24.4166592385434 | epot = -68.5432523362142 | etot = -33.5644503597668 +619000 ekin = 10.2447233169864 | erot = 25.053936124725 | epot = -68.8631098035728 | etot = -33.5644503618614 +620000 ekin = 10.0473729684105 | erot = 25.7263958146269 | epot = -69.3382191478437 | etot = -33.5644503648063 +621000 ekin = 9.97770919372447 | erot = 26.386029455057 | epot = -69.9281890170002 | etot = -33.5644503682187 +622000 ekin = 10.0410058298604 | erot = 26.9805251344677 | epot = -70.5859813358563 | etot = -33.5644503715282 +623000 ekin = 10.2405907653606 | erot = 27.4608678076243 | epot = -71.265908947125 | etot = -33.5644503741401 +624000 ekin = 10.5781077618222 | erot = 27.789174960281 | epot = -71.9317330977985 | etot = -33.5644503756953 +625000 ekin = 11.0534790507876 | erot = 27.9443540029372 | epot = -72.5622834297716 | etot = -33.5644503760469 +626000 ekin = 11.665023962676 | erot = 27.9236660630966 | epot = -73.153140401212 | etot = -33.5644503754394 +627000 ekin = 12.4090657095855 | erot = 27.7401487506199 | epot = -73.7136648344174 | etot = -33.564450374212 +628000 ekin = 13.2797303352362 | erot = 27.4180442687031 | epot = -74.2622249766746 | etot = -33.5644503727353 +629000 ekin = 14.2227247828091 | erot = 26.9288523650796 | epot = -74.716027794269 | etot = -33.5644506463803 +630000 ekin = 14.6371369670079 | erot = 25.6849986219067 | epot = -73.8865860644015 | etot = -33.5644504754868 +631000 ekin = 15.1932748253831 | erot = 24.8015291116418 | epot = -73.5592542941192 | etot = -33.5644503570943 +632000 ekin = 16.584223183011 | erot = 25.1927867331162 | epot = -75.341460399694 | etot = -33.5644504835668 +633000 ekin = 18.1129981078216 | erot = 25.8399990857076 | epot = -77.5174478439555 | etot = -33.5644506504263 +634000 ekin = 19.1483265856614 | erot = 25.7387528535892 | epot = -78.4515299890265 | etot = -33.564450549776 +635000 ekin = 20.1638306106813 | erot = 25.6154971447985 | epot = -79.3437783094146 | etot = -33.5644505539348 +636000 ekin = 21.1529452215294 | erot = 25.4927802223992 | epot = -80.2101760029174 | etot = -33.5644505589887 +637000 ekin = 22.076840414127 | erot = 25.3376757551748 | epot = -80.9789667330327 | etot = -33.5644505637309 +638000 ekin = 22.8998086513204 | erot = 25.1175243534268 | epot = -81.5817835716912 | etot = -33.564450566944 +639000 ekin = 23.5958452423371 | erot = 24.810324027069 | epot = -81.970619837404 | etot = -33.5644505679979 +640000 ekin = 24.1448393959509 | erot = 24.4104070773779 | epot = -82.1196970414061 | etot = -33.5644505680774 +641000 ekin = 24.5337741528747 | erot = 23.9290519069577 | epot = -82.0272766245586 | etot = -33.5644505647262 +642000 ekin = 24.7698696452211 | erot = 23.3958020412245 | epot = -81.7301222481214 | etot = -33.5644505616758 +643000 ekin = 24.8669267986387 | erot = 22.8392829406438 | epot = -81.270660298016 | etot = -33.5644505587335 +644000 ekin = 24.8431155056926 | erot = 22.2830723080152 | epot = -80.6906383699449 | etot = -33.5644505562371 +645000 ekin = 24.7193046979039 | erot = 21.7428697624476 | epot = -80.0266250145381 | etot = -33.5644505541866 +646000 ekin = 24.5180931827109 | erot = 21.2270132547761 | epot = -79.3095569899392 | etot = -33.5644505524521 +647000 ekin = 24.2628521130092 | erot = 20.7388201342314 | epot = -78.5661227982078 | etot = -33.5644505509672 +648000 ekin = 23.9761808135735 | erot = 20.2787945271196 | epot = -77.8194258904783 | etot = -33.5644505497851 +649000 ekin = 23.67787365498 | erot = 19.8458221792402 | epot = -77.0881463832164 | etot = -33.5644505489962 +650000 ekin = 23.3831896135476 | erot = 19.4375683304372 | epot = -76.3852084925965 | etot = -33.5644505486117 +651000 ekin = 23.1045251387838 | erot = 19.0455994386645 | epot = -75.714575126721 | etot = -33.5644505492727 +652000 ekin = 22.852554089729 | erot = 18.660058243978 | epot = -75.0770628826327 | etot = -33.5644505489257 +653000 ekin = 22.6343633028422 | erot = 18.2797742486811 | epot = -74.4785880997844 | etot = -33.5644505482611 +654000 ekin = 22.457706160496 | erot = 17.9066943677479 | epot = -73.9288510753647 | etot = -33.5644505471209 +655000 ekin = 22.3323244895908 | erot = 17.5466477598824 | epot = -73.4434227950449 | etot = -33.5644505455717 +656000 ekin = 22.2694639392795 | erot = 17.2090068009683 | epot = -73.0429212841433 | etot = -33.5644505438955 +657000 ekin = 22.2796962944035 | erot = 16.9050137475 | epot = -72.7491605844585 | etot = -33.564450542555 +658000 ekin = 22.3696390695847 | erot = 16.644764495761 | epot = -72.578854107433 | etot = -33.5644505420873 +659000 ekin = 22.538589477759 | erot = 16.4332539543396 | epot = -72.5362939750541 | etot = -33.5644505429556 +660000 ekin = 22.7761662587416 | erot = 16.2664693862647 | epot = -72.6070861903694 | etot = -33.5644505453631 +661000 ekin = 23.06230224551 | erot = 16.1290340508052 | epot = -72.7557868430349 | etot = -33.5644505467196 +662000 ekin = 23.3837240385233 | erot = 15.9907831586697 | epot = -72.9389579078995 | etot = -33.5644507107065 +663000 ekin = 23.0541480011267 | erot = 16.1177804885964 | epot = -72.7363790496029 | etot = -33.5644505598799 +664000 ekin = 22.9781515363897 | erot = 16.5698259347579 | epot = -73.1124281192206 | etot = -33.5644506480731 +665000 ekin = 23.374978691534 | erot = 16.4117827405633 | epot = -73.3512120004714 | etot = -33.5644505683742 +666000 ekin = 23.7239501856893 | erot = 16.0357448198421 | epot = -73.3241455722274 | etot = -33.5644505666959 +667000 ekin = 24.0215049450261 | erot = 15.6311856369932 | epot = -73.2171411449521 | etot = -33.5644505629329 +668000 ekin = 24.2720292277934 | erot = 15.2431977237525 | epot = -73.0796775108255 | etot = -33.5644505592796 +669000 ekin = 24.4823401844299 | erot = 14.9164487057863 | epot = -72.9632394465769 | etot = -33.5644505563607 +670000 ekin = 24.6591929169718 | erot = 14.6865199574777 | epot = -72.9101634287588 | etot = -33.5644505543093 +671000 ekin = 24.7891522546301 | erot = 14.5781166473157 | epot = -72.9317194579636 | etot = -33.5644505560177 +672000 ekin = 24.8512867496603 | erot = 14.6015183439962 | epot = -73.0172556489739 | etot = -33.5644505553173 +673000 ekin = 24.8569569355798 | erot = 14.7562217137542 | epot = -73.1776292039339 | etot = -33.5644505545999 +674000 ekin = 24.8222537580567 | erot = 15.0373554087232 | epot = -73.4240597206098 | etot = -33.5644505538298 +675000 ekin = 24.7663204260849 | erot = 15.437295119434 | epot = -73.7680660987755 | etot = -33.5644505532566 +676000 ekin = 24.707973141147 | erot = 15.9453732713287 | epot = -74.2177969658379 | etot = -33.5644505533623 +677000 ekin = 24.660603838739 | erot = 16.5455776357113 | epot = -74.7706320292609 | etot = -33.5644505548106 +678000 ekin = 24.6267378747401 | erot = 17.2129758015017 | epot = -75.4041642342705 | etot = -33.5644505580287 +679000 ekin = 24.5940505550725 | erot = 17.9117017662871 | epot = -76.07020288433 | etot = -33.5644505629703 +680000 ekin = 24.5356055096688 | erot = 18.5957689108381 | epot = -76.6958249893355 | etot = -33.5644505688286 +681000 ekin = 24.4156570895309 | erot = 19.2149559854727 | epot = -77.1950636491504 | etot = -33.5644505741468 +682000 ekin = 24.1989519849675 | erot = 19.7242966838354 | epot = -77.4876992464688 | etot = -33.564450577666 +683000 ekin = 23.8604728477913 | erot = 20.0938581667108 | epot = -77.5187815925336 | etot = -33.5644505780315 +684000 ekin = 23.3975557786275 | erot = 20.3180971806807 | epot = -77.2801035347717 | etot = -33.5644505754635 +685000 ekin = 22.8290459836148 | erot = 20.4129669387004 | epot = -76.80646349322 | etot = -33.5644505709048 +686000 ekin = 22.1833688822011 | erot = 20.3969948279682 | epot = -76.1448143063362 | etot = -33.5644505961669 +687000 ekin = 21.4529188815913 | erot = 20.156733845752 | epot = -75.1741032924797 | etot = -33.5644505651364 +688000 ekin = 20.8420414151281 | erot = 19.8330340922101 | epot = -74.2395260487824 | etot = -33.5644505414442 +689000 ekin = 20.4850454817099 | erot = 19.6177759053663 | epot = -73.6672719440564 | etot = -33.5644505569803 +690000 ekin = 20.2236705266713 | erot = 19.4736760202794 | epot = -73.2617971242667 | etot = -33.564450577316 +691000 ekin = 19.9277329712649 | erot = 19.3525548964651 | epot = -72.8447384060534 | etot = -33.5644505383235 +692000 ekin = 19.7615779525566 | erot = 19.3271485933787 | epot = -72.6531770837385 | etot = -33.5644505378033 +693000 ekin = 19.7317397129722 | erot = 19.4147876345959 | epot = -72.7109778863946 | etot = -33.5644505388264 +694000 ekin = 19.8186070325243 | erot = 19.6208277624943 | epot = -73.0038853362896 | etot = -33.564450541271 +695000 ekin = 19.9894250231729 | erot = 19.9418771486032 | epot = -73.4957527165321 | etot = -33.564450544756 +696000 ekin = 20.2029739946799 | erot = 20.3669312876596 | epot = -74.1343558309875 | etot = -33.564450548648 +697000 ekin = 20.4154400731731 | erot = 20.8809193025054 | epot = -74.8608099281222 | etot = -33.5644505524438 +698000 ekin = 20.586206730696 | erot = 21.4669039267717 | epot = -75.6175612131891 | etot = -33.5644505557214 +699000 ekin = 20.6825995319384 | erot = 22.1076466775274 | epot = -76.3546967677076 | etot = -33.5644505582417 +700000 ekin = 20.6830084845855 | erot = 22.7863311628684 | epot = -77.0337902073835 | etot = -33.5644505599297 +701000 ekin = 20.5781931485901 | erot = 23.4865818275485 | epot = -77.6292255369506 | etot = -33.564450560812 +702000 ekin = 20.371075430213 | erot = 24.1923776502136 | epot = -78.1279036413659 | etot = -33.5644505609394 +703000 ekin = 20.0753347573217 | erot = 24.8884672573789 | epot = -78.5282525750727 | etot = -33.5644505603721 +704000 ekin = 19.7130379606064 | erot = 25.5614200071491 | epot = -78.8389085269638 | etot = -33.5644505592083 +705000 ekin = 19.3114467594506 | erot = 26.2008176331446 | epot = -79.0767149502457 | etot = -33.5644505576504 +706000 ekin = 18.8991937909467 | erot = 26.7996687741907 | epot = -79.2633131211814 | etot = -33.564450556044 +707000 ekin = 18.5022273003166 | erot = 27.3532672615511 | epot = -79.4199451167072 | etot = -33.5644505548395 +708000 ekin = 18.1401729285463 | erot = 27.8564307011234 | epot = -79.5610541841487 | etot = -33.5644505544791 +709000 ekin = 17.8234464183816 | erot = 28.2999901850205 | epot = -79.6878871586751 | etot = -33.564450555273 +710000 ekin = 17.5523632004475 | erot = 28.6678464680811 | epot = -79.7846602257444 | etot = -33.5644505572158 +711000 ekin = 17.3194109792864 | erot = 28.9359249914519 | epot = -79.8197865307446 | etot = -33.5644505600063 +712000 ekin = 17.111217474036 | erot = 29.0741670969728 | epot = -79.7498351340657 | etot = -33.5644505630569 +713000 ekin = 16.9121266187594 | erot = 29.0513180276171 | epot = -79.5278952119951 | etot = -33.5644505656186 +714000 ekin = 16.7079630651497 | erot = 28.8416092702073 | epot = -79.1140229023543 | etot = -33.5644505669974 +715000 ekin = 16.4890214395501 | erot = 28.4313561614791 | epot = -78.4848281678324 | etot = -33.5644505668032 +716000 ekin = 16.2513970064722 | erot = 27.8230898676209 | epot = -77.6389374391847 | etot = -33.5644505650916 +717000 ekin = 15.9963403713229 | erot = 27.0356716306523 | epot = -76.596462564269 | etot = -33.5644505622939 +718000 ekin = 15.736130323464 | erot = 26.1105494903108 | epot = -75.4111303700896 | etot = -33.5644505563148 +719000 ekin = 15.4991442318496 | erot = 25.1078869419086 | epot = -74.1714817285169 | etot = -33.5644505547587 +720000 ekin = 15.2869109972121 | erot = 24.0511182750597 | epot = -72.9024798253532 | etot = -33.5644505530814 +721000 ekin = 15.0983958358413 | erot = 22.9636187898412 | epot = -71.626465177062 | etot = -33.5644505513795 +722000 ekin = 14.9325120649955 | erot = 21.8688846290998 | epot = -70.3658472463797 | etot = -33.5644505522845 +723000 ekin = 14.7807572554272 | erot = 20.7831774063264 | epot = -69.1283852119052 | etot = -33.5644505501515 +724000 ekin = 14.6422909693862 | erot = 19.7295658945069 | epot = -67.9363074121321 | etot = -33.5644505482389 +725000 ekin = 14.5216204989736 | erot = 18.7315290196227 | epot = -66.8176000651018 | etot = -33.5644505465054 +726000 ekin = 14.4243651447115 | erot = 17.809249661836 | epot = -65.7980653514567 | etot = -33.5644505449092 +727000 ekin = 14.3569475468078 | erot = 16.9804196358499 | epot = -64.9018177260886 | etot = -33.5644505434309 +728000 ekin = 14.2536930560822 | erot = 16.2469828256636 | epot = -64.0651265321117 | etot = -33.5644506503659 +729000 ekin = 13.8457257245456 | erot = 15.9222518563763 | epot = -63.3324280816472 | etot = -33.5644505007253 +730000 ekin = 14.0260810346084 | erot = 15.9641149760264 | epot = -63.5546467080333 | etot = -33.5644506973986 +731000 ekin = 14.2598526192304 | erot = 15.8407237762752 | epot = -63.6650270930514 | etot = -33.5644506975458 +732000 ekin = 14.5606957103586 | erot = 15.8547631013359 | epot = -63.9799095104338 | etot = -33.5644506987393 +733000 ekin = 14.9193813445856 | erot = 16.0002143189837 | epot = -64.4840463647582 | etot = -33.5644507011889 +734000 ekin = 15.3191392245689 | erot = 16.2611439993741 | epot = -65.1447339288827 | etot = -33.5644507049397 +735000 ekin = 15.7356019022088 | erot = 16.6113471095831 | epot = -65.911399721546 | etot = -33.5644507097541 +736000 ekin = 16.1415246409903 | erot = 17.0234641329184 | epot = -66.7294394826049 | etot = -33.5644507086962 +737000 ekin = 16.518605610539 | erot = 17.489586803014 | epot = -67.5726431258992 | etot = -33.5644507123462 +738000 ekin = 16.8458492119022 | erot = 17.9860152352149 | epot = -68.396315162061 | etot = -33.5644507149439 +739000 ekin = 17.110149866212 | erot = 18.4929848438385 | epot = -69.1675854260346 | etot = -33.5644507159841 +740000 ekin = 17.3014321683493 | erot = 18.9830167808933 | epot = -69.8488996814749 | etot = -33.5644507322323 +741000 ekin = 17.3865900134394 | erot = 19.3806296464369 | epot = -70.3316703915551 | etot = -33.5644507316788 +742000 ekin = 17.3696644724057 | erot = 19.6766235522529 | epot = -70.6107387544097 | etot = -33.564450729751 +743000 ekin = 17.2668900438488 | erot = 19.8790967510142 | epot = -70.7104375221209 | etot = -33.564450727258 +744000 ekin = 17.0976280300632 | erot = 20.0010316334553 | epot = -70.6631103882319 | etot = -33.5644507247133 +745000 ekin = 16.8806625311108 | erot = 20.0570550573562 | epot = -70.5021683107691 | etot = -33.5644507223021 +746000 ekin = 16.6327129020178 | erot = 20.0624105084052 | epot = -70.2595741304376 | etot = -33.5644507200146 +747000 ekin = 16.3685004966554 | erot = 20.0330168533934 | epot = -69.9659680678506 | etot = -33.5644507178018 +748000 ekin = 16.1014104014477 | erot = 19.9854814624586 | epot = -69.6513425795718 | etot = -33.5644507156654 +749000 ekin = 15.844098014715 | erot = 19.9365592282997 | epot = -69.3451079566726 | etot = -33.5644507136579 +750000 ekin = 15.6090531926207 | erot = 19.9038963443694 | epot = -69.0774002481408 | etot = -33.5644507111507 +751000 ekin = 15.4083916161874 | erot = 19.9047162304915 | epot = -68.8775585564482 | etot = -33.5644507097693 +752000 ekin = 15.2531866593796 | erot = 19.9485427659139 | epot = -68.7661801340112 | etot = -33.5644507087177 +753000 ekin = 15.1543901567613 | erot = 20.0407526950507 | epot = -68.7595935598495 | etot = -33.5644507080375 +754000 ekin = 15.1228286573332 | erot = 20.1821712297509 | epot = -68.8694505948499 | etot = -33.5644507077658 +755000 ekin = 15.1688994243523 | erot = 20.3687544713836 | epot = -69.1021046037276 | etot = -33.5644507079917 +756000 ekin = 15.301499551776 | erot = 20.5913112854955 | epot = -69.4572615461957 | etot = -33.5644507089241 +757000 ekin = 15.5255754913897 | erot = 20.834949244045 | epot = -69.9249754463701 | etot = -33.5644507109354 +758000 ekin = 15.8381446961138 | erot = 21.0780442684797 | epot = -70.4806396790109 | etot = -33.5644507144174 +759000 ekin = 16.2241238953416 | erot = 21.2913511033439 | epot = -71.0799257180851 | etot = -33.5644507193996 +760000 ekin = 16.6551901645912 | erot = 21.4392176773412 | epot = -71.6588585670209 | etot = -33.5644507250884 +761000 ekin = 17.0950183931786 | erot = 21.4853061088372 | epot = -72.1447752318667 | etot = -33.5644507298509 +762000 ekin = 17.5106763998012 | erot = 21.4029539232004 | epot = -72.4780810549596 | etot = -33.564450731958 +763000 ekin = 17.8846255672732 | erot = 21.1859145459706 | epot = -72.6349908439064 | etot = -33.5644507306625 +764000 ekin = 18.2201199376956 | erot = 20.8529192934954 | epot = -72.6374899578081 | etot = -33.5644507266171 +765000 ekin = 18.5372583937382 | erot = 20.4430950169541 | epot = -72.5448041320924 | etot = -33.5644507214001 +766000 ekin = 18.8630996339146 | erot = 20.0050052439806 | epot = -72.4325555942986 | etot = -33.5644507164034 +767000 ekin = 19.2212066800029 | erot = 19.5864803390503 | epot = -72.3721377317783 | etot = -33.5644507127251 +768000 ekin = 19.624511669093 | erot = 19.2265552411511 | epot = -72.4155176211004 | etot = -33.5644507108563 +769000 ekin = 20.0721792333795 | erot = 18.9509745480761 | epot = -72.5876044923609 | etot = -33.5644507109054 +770000 ekin = 20.5498086023516 | erot = 18.7702787047077 | epot = -72.8845380197874 | etot = -33.5644507127281 +771000 ekin = 21.0321028878714 | erot = 18.6794354396568 | epot = -73.2759890434179 | etot = -33.5644507158897 +772000 ekin = 21.4851799442024 | erot = 18.6615620368978 | epot = -73.7111927013751 | etot = -33.564450720275 +773000 ekin = 21.8752230488093 | erot = 18.6848228554718 | epot = -74.1244966289812 | etot = -33.5644507247 +774000 ekin = 22.1763496480937 | erot = 18.7081814115977 | epot = -74.4489817879453 | etot = -33.5644507282539 +775000 ekin = 22.374571784792 | erot = 18.6931201256992 | epot = -74.6321426404729 | etot = -33.5644507299816 +776000 ekin = 22.4709552283027 | erot = 18.6135457380045 | epot = -74.6489516957821 | etot = -33.564450729475 +777000 ekin = 22.4798367644303 | erot = 18.4639882142466 | epot = -74.5082757050196 | etot = -33.5644507263427 +778000 ekin = 22.4355420397867 | erot = 18.2585534576689 | epot = -74.2585462185365 | etot = -33.5644507210809 +779000 ekin = 22.384352941304 | erot = 18.0309205348412 | epot = -73.9797241910754 | etot = -33.5644507149302 +780000 ekin = 22.3744386500498 | erot = 17.8258066858555 | epot = -73.7646960454756 | etot = -33.5644507095703 +781000 ekin = 22.1317599687537 | erot = 17.6891439264797 | epot = -73.385354726192 | etot = -33.5644508309586 +782000 ekin = 21.1592753698204 | erot = 17.9407979475159 | epot = -72.6645240371034 | etot = -33.5644507197671 +783000 ekin = 20.4598020696467 | erot = 19.0285770890208 | epot = -73.0528298813537 | etot = -33.5644507226862 +784000 ekin = 20.520561149809 | erot = 20.4251817114889 | epot = -74.510193700403 | etot = -33.5644508391051 +785000 ekin = 20.9642653603784 | erot = 20.9633174839005 | epot = -75.4920336718239 | etot = -33.564450827545 +786000 ekin = 21.4400765994876 | erot = 21.0615830961954 | epot = -76.0661105274379 | etot = -33.5644508317549 +787000 ekin = 21.883066887488 | erot = 21.057450682238 | epot = -76.5049684031488 | etot = -33.5644508334227 +788000 ekin = 22.267324375569 | erot = 20.946432607028 | epot = -76.7782078151899 | etot = -33.5644508325928 +789000 ekin = 22.5826671479872 | erot = 20.7432248288687 | epot = -76.8903428068424 | etot = -33.5644508299865 +790000 ekin = 22.8323066878114 | erot = 20.4741989858865 | epot = -76.8709565003754 | etot = -33.5644508266776 +791000 ekin = 23.0272356230926 | erot = 20.1684030022638 | epot = -76.7600894489801 | etot = -33.5644508236236 +792000 ekin = 23.1800436946629 | erot = 19.8507212207542 | epot = -76.5952157367535 | etot = -33.5644508213364 +793000 ekin = 23.300603133177 | erot = 19.5391467370145 | epot = -76.4042006900797 | etot = -33.5644508198882 +794000 ekin = 23.3943971219697 | erot = 19.2453890945191 | epot = -76.2042370356008 | etot = -33.564450819112 +795000 ekin = 23.4629811569471 | erot = 18.9772359529009 | epot = -76.0046679285239 | etot = -33.564450818676 +796000 ekin = 23.5050545268219 | erot = 18.7401074069536 | epot = -75.8096127523991 | etot = -33.5644508186236 +797000 ekin = 23.5179235638906 | erot = 18.5376020867796 | epot = -75.6199764693832 | etot = -33.564450818713 +798000 ekin = 23.499309548325 | erot = 18.3721088685451 | epot = -75.4358692357089 | etot = -33.5644508188388 +799000 ekin = 23.448939556091 | erot = 18.2446734452746 | epot = -75.2580638202457 | etot = -33.5644508188801 +800000 ekin = 23.3700597274441 | erot = 18.1549836136211 | epot = -75.0894941597633 | etot = -33.5644508186981 +801000 ekin = 23.2706429278156 | erot = 18.1018392108953 | epot = -74.9369329568679 | etot = -33.564450818157 +802000 ekin = 23.1638659210079 | erot = 18.0841621459371 | epot = -74.8124788841352 | etot = -33.5644508171902 +803000 ekin = 23.0673439612512 | erot = 18.1021655968283 | epot = -74.7339603739616 | etot = -33.564450815882 +804000 ekin = 23.0007989366371 | erot = 18.1579717461939 | epot = -74.7232214973418 | etot = -33.5644508145108 +805000 ekin = 22.9823371343768 | erot = 18.2549251687085 | epot = -74.8017131166306 | etot = -33.5644508135453 +806000 ekin = 23.0241641600763 | erot = 18.3954330803544 | epot = -74.984048053792 | etot = -33.5644508133613 +807000 ekin = 23.128964625391 | erot = 18.5785443285981 | epot = -75.2719597683222 | etot = -33.5644508143331 +808000 ekin = 23.2881607694889 | erot = 18.7969609338812 | epot = -75.649572519887 | etot = -33.5644508165169 +809000 ekin = 23.4826910129567 | erot = 19.0356597598736 | epot = -76.0828015925039 | etot = -33.5644508196735 +810000 ekin = 23.6859311924953 | erot = 19.2727961953261 | epot = -76.5231782111275 | etot = -33.5644508233061 +811000 ekin = 23.8683330202879 | erot = 19.4824424692605 | epot = -76.915226316337 | etot = -33.5644508267886 +812000 ekin = 24.0021280346815 | erot = 19.6390320774525 | epot = -77.2056109410892 | etot = -33.5644508289552 +813000 ekin = 24.0705831557699 | erot = 19.722021914086 | epot = -77.3570559012067 | etot = -33.5644508313508 +814000 ekin = 24.055601152459 | erot = 19.7197957986886 | epot = -77.3398477832757 | etot = -33.5644508321281 +815000 ekin = 23.9426529226646 | erot = 19.6314238617512 | epot = -77.1385276156708 | etot = -33.564450831255 +816000 ekin = 23.7311336934088 | erot = 19.466072034162 | epot = -76.7616565565296 | etot = -33.5644508289587 +817000 ekin = 23.433668535019 | erot = 19.2405112285024 | epot = -76.2386305891648 | etot = -33.5644508256434 +818000 ekin = 23.0739945644854 | erot = 18.9755381767493 | epot = -75.6139835630208 | etot = -33.5644508217861 +819000 ekin = 22.6837324023522 | erot = 18.6923648013821 | epot = -74.940548021756 | etot = -33.5644508180217 +820000 ekin = 22.2835291274414 | erot = 18.4096381970061 | epot = -74.2576181403381 | etot = -33.5644508158905 +821000 ekin = 21.8822278930458 | erot = 18.1412914989096 | epot = -73.5879702064574 | etot = -33.564450814502 +822000 ekin = 21.4884880522555 | erot = 17.8956786284863 | epot = -72.9486174945866 | etot = -33.5644508138448 +823000 ekin = 21.1064787913954 | erot = 17.6755757489858 | epot = -72.3465053541674 | etot = -33.5644508137862 +824000 ekin = 20.7370980684377 | erot = 17.4789023739902 | epot = -71.7804512565368 | etot = -33.5644508141088 +825000 ekin = 20.3797998907961 | erot = 17.3000855971742 | epot = -71.2443363025092 | etot = -33.5644508145388 +826000 ekin = 20.0346218830748 | erot = 17.1319532561702 | epot = -70.7310259540458 | etot = -33.5644508148008 +827000 ekin = 19.7039740634311 | erot = 16.9679189203112 | epot = -70.2363437984045 | etot = -33.5644508146622 +828000 ekin = 19.3938011067031 | erot = 16.8040573698201 | epot = -69.7623092905205 | etot = -33.5644508139974 +829000 ekin = 19.11384865599 | erot = 16.6405709794189 | epot = -69.3188704482339 | etot = -33.564450812825 +830000 ekin = 18.8769326775077 | erot = 16.4822216024693 | epot = -68.9236050912778 | etot = -33.5644508113007 +831000 ekin = 18.6973117703808 | erot = 16.3375582428127 | epot = -68.5993208228909 | etot = -33.5644508096974 +832000 ekin = 18.5884699003301 | erot = 16.2171194687507 | epot = -68.3700401774137 | etot = -33.564450808333 +833000 ekin = 18.560779595016 | erot = 16.1310793366086 | epot = -68.2563097391195 | etot = -33.5644508074948 +834000 ekin = 18.61956558581 | erot = 16.0869173735029 | epot = -68.2709337666952 | etot = -33.5644508073822 +835000 ekin = 18.7639745649932 | erot = 16.0875916865537 | epot = -68.4160170596156 | etot = -33.5644508080686 +836000 ekin = 18.9868442865092 | erot = 16.1305192433203 | epot = -68.6818143393361 | etot = -33.5644508095065 +837000 ekin = 19.2754657671378 | erot = 16.2074384784975 | epot = -69.0473550571903 | etot = -33.564450811555 +838000 ekin = 19.6129197626542 | erot = 16.305100324473 | epot = -69.4824709011417 | etot = -33.5644508140144 +839000 ekin = 19.9795904905589 | erot = 16.4066730035615 | epot = -69.9507143107794 | etot = -33.564450816659 +840000 ekin = 20.3545159446157 | erot = 16.4936833394318 | epot = -70.4126501033158 | etot = -33.5644508192683 +841000 ekin = 20.7164052638984 | erot = 16.548246931381 | epot = -70.8291030169287 | etot = -33.5644508216493 +842000 ekin = 21.0443277172268 | erot = 16.5552492676569 | epot = -71.1640278085398 | etot = -33.5644508236561 +843000 ekin = 21.3182343499603 | erot = 16.5040987153204 | epot = -71.3867838904675 | etot = -33.5644508251868 +844000 ekin = 21.5195641367703 | erot = 16.3898128596529 | epot = -71.4738278225867 | etot = -33.5644508261635 +845000 ekin = 21.6321888565554 | erot = 16.2134452981662 | epot = -71.410084981231 | etot = -33.5644508265094 +846000 ekin = 21.6437998325842 | erot = 15.9820204390976 | epot = -71.1902710978237 | etot = -33.5644508261419 +847000 ekin = 21.5475782493693 | erot = 15.7081282849394 | epot = -70.8201573593162 | etot = -33.5644508250075 +848000 ekin = 21.3436927775388 | erot = 15.4091281501661 | epot = -70.3172717508461 | etot = -33.5644508231412 +849000 ekin = 21.0400180651421 | erot = 15.1057456316713 | epot = -69.7102145175199 | etot = -33.5644508207064 +850000 ekin = 20.651624144221 | erot = 14.819982121726 | epot = -69.0360570839323 | etot = -33.5644508179853 +851000 ekin = 20.1989966727791 | erot = 14.5725796374539 | epot = -68.3360271255451 | etot = -33.5644508153122 +852000 ekin = 19.705405223643 | erot = 14.3805531626584 | epot = -67.650409199298 | etot = -33.5644508129966 +853000 ekin = 19.1940724610505 | erot = 14.25530818557 | epot = -67.0138314578818 | etot = -33.5644508112614 +854000 ekin = 18.6857524015881 | erot = 14.2015962971835 | epot = -66.4517995089979 | etot = -33.5644508102263 +855000 ekin = 18.1970763744836 | erot = 14.2172634276327 | epot = -65.9787906120352 | etot = -33.5644508099189 +856000 ekin = 17.7397499707612 | erot = 14.2936050918535 | epot = -65.5978058729028 | etot = -33.5644508102882 +857000 ekin = 17.3205057782524 | erot = 14.4162007388387 | epot = -65.3011573283104 | etot = -33.5644508112193 +858000 ekin = 16.9416544278078 | erot = 14.5662556875881 | epot = -65.0723609279221 | etot = -33.5644508125262 +859000 ekin = 16.6020780488435 | erot = 14.7225727576944 | epot = -64.8891016204952 | etot = -33.5644508139574 +860000 ekin = 16.2985125162571 | erot = 14.8641879517113 | epot = -64.7271512831937 | etot = -33.5644508152253 +861000 ekin = 16.0269335765221 | erot = 14.9734306263673 | epot = -64.5648150189461 | etot = -33.5644508160567 +862000 ekin = 15.7838145493149 | erot = 15.0388248736918 | epot = -64.3870902392667 | etot = -33.56445081626 +863000 ekin = 15.5670277401482 | erot = 15.0570872004078 | epot = -64.1885657563379 | etot = -33.5644508157819 +864000 ekin = 15.3762443264478 | erot = 15.033644902431 | epot = -63.9743400435875 | etot = -33.5644508147087 +865000 ekin = 15.2131876544491 | erot = 14.9816007278775 | epot = -63.7592391954458 | etot = -33.5644508131193 +866000 ekin = 15.0809818287742 | erot = 14.9194630000228 | epot = -63.5648956402705 | etot = -33.5644508114735 +867000 ekin = 14.9827726501217 | erot = 14.8683323276467 | epot = -63.4155557876376 | etot = -33.5644508098692 +868000 ekin = 14.92180112433 | erot = 14.8493296988562 | epot = -63.3355816316708 | etot = -33.5644508084847 +869000 ekin = 14.9010185116834 | erot = 14.8813223016375 | epot = -63.3467916207947 | etot = -33.5644508074738 +870000 ekin = 14.9227801761236 | erot = 14.9789108660607 | epot = -63.4661418491954 | etot = -33.5644508070111 +871000 ekin = 14.9884139356745 | erot = 15.1503817842349 | epot = -63.7032465271887 | etot = -33.5644508072793 +872000 ekin = 15.0976914319707 | erot = 15.3955923654522 | epot = -64.0577346058697 | etot = -33.5644508084468 +873000 ekin = 15.2480781387988 | erot = 15.7042636439283 | epot = -64.5167925933356 | etot = -33.5644508106085 +874000 ekin = 15.4340038873847 | erot = 16.0553561021191 | epot = -65.053810803158 | etot = -33.5644508136542 +875000 ekin = 15.6465534573556 | erot = 16.4187317070787 | epot = -65.6297359816455 | etot = -33.5644508172112 +876000 ekin = 15.8739222018982 | erot = 16.7595446909201 | epot = -66.1979177135255 | etot = -33.5644508207072 +877000 ekin = 16.1027155795467 | erot = 17.044494341634 | epot = -66.7116607447368 | etot = -33.5644508235561 +878000 ekin = 16.3197910454644 | erot = 17.2478151625915 | epot = -67.1320570334198 | etot = -33.5644508253639 +879000 ekin = 16.5138521394505 | erot = 17.3548092079704 | epot = -67.4331121735215 | etot = -33.5644508261006 +880000 ekin = 16.6772706623824 | erot = 17.3624918569347 | epot = -67.6042133449038 | etot = -33.5644508255867 +881000 ekin = 16.8080553798836 | erot = 17.278452226898 | epot = -67.6509584308199 | etot = -33.5644508240383 +882000 ekin = 16.9100399112771 | erot = 17.119022231693 | epot = -67.5935129646031 | etot = -33.564450821633 +883000 ekin = 16.9925721974834 | erot = 16.9073416506224 | epot = -67.4643646668128 | etot = -33.564450818707 +884000 ekin = 17.0687034065889 | erot = 16.6704808211346 | epot = -67.3036350435126 | etot = -33.5644508157892 +885000 ekin = 17.1519974191521 | erot = 16.4352378677741 | epot = -67.1516861003877 | etot = -33.5644508134615 +886000 ekin = 17.2529390367253 | erot = 16.2234313385346 | epot = -67.040821187416 | etot = -33.564450812156 +887000 ekin = 17.3762921605589 | erot = 16.0482363267111 | epot = -66.9889792992713 | etot = -33.5644508120014 +888000 ekin = 17.5203620939499 | erot = 15.912713009727 | epot = -66.9975259165121 | etot = -33.5644508128352 +889000 ekin = 17.6781644417429 | erot = 15.8105908033725 | epot = -67.0532060594389 | etot = -33.5644508143236 +890000 ekin = 17.8397117311843 | erot = 15.728545074795 | epot = -67.1327076214795 | etot = -33.5644508155002 +891000 ekin = 17.9946822356163 | erot = 15.6526652128514 | epot = -67.2117982661653 | etot = -33.5644508176976 +892000 ekin = 18.1331274108613 | erot = 15.5631846536331 | epot = -67.2607628839469 | etot = -33.5644508194524 +893000 ekin = 18.2472194923555 | erot = 15.4391901233243 | epot = -67.2508604363308 | etot = -33.5644508206509 +894000 ekin = 18.3321686592099 | erot = 15.2648175287635 | epot = -67.1614370091493 | etot = -33.5644508211759 +895000 ekin = 18.3862908731384 | erot = 15.0310128799806 | epot = -66.9817545740828 | etot = -33.5644508209639 +896000 ekin = 18.4109116125628 | erot = 14.7366844064177 | epot = -66.7120468390301 | etot = -33.5644508200496 +897000 ekin = 18.4100489982307 | erot = 14.38859264232 | epot = -66.3630924591407 | etot = -33.56445081859 +898000 ekin = 18.3898281603967 | erot = 13.9998000546359 | epot = -65.954079031856 | etot = -33.5644508168234 +899000 ekin = 18.3577139224559 | erot = 13.5871378078456 | epot = -65.5093025452924 | etot = -33.5644508149909 +900000 ekin = 18.3217786244971 | erot = 13.1685630401998 | epot = -65.0547924779573 | etot = -33.5644508132604 +901000 ekin = 18.2902589888584 | erot = 12.7612484281998 | epot = -64.6159582287385 | etot = -33.5644508116803 +902000 ekin = 18.2715810670069 | erot = 12.3808553817479 | epot = -64.2168872589334 | etot = -33.5644508101785 +903000 ekin = 18.2748902554657 | erot = 12.0419799131758 | epot = -63.8813209772404 | etot = -33.5644508085989 +904000 ekin = 18.310946079998 | erot = 11.759427353884 | epot = -63.6348242406376 | etot = -33.5644508067556 +905000 ekin = 18.3930925503139 | erot = 11.5498594883528 | epot = -63.5074028431725 | etot = -33.5644508045058 +906000 ekin = 18.5347341843358 | erot = 11.429567327747 | epot = -63.5287523170652 | etot = -33.5644508049824 +907000 ekin = 18.7414362451913 | erot = 11.4045037508022 | epot = -63.7103908004036 | etot = -33.5644508044102 +908000 ekin = 19.0194889718029 | erot = 11.4807236813719 | epot = -64.064663457795 | etot = -33.5644508046201 +909000 ekin = 19.3700614262796 | erot = 11.658960594413 | epot = -64.5934728263738 | etot = -33.5644508056812 +910000 ekin = 19.7882105287017 | erot = 11.9333322709223 | epot = -65.2859936069509 | etot = -33.5644508073268 +911000 ekin = 20.2647618472542 | erot = 12.2921701432016 | epot = -66.1213827995986 | etot = -33.5644508091428 +912000 ekin = 20.7894338989449 | erot = 12.7195983435702 | epot = -67.0734830529977 | etot = -33.5644508104826 +913000 ekin = 21.354185735415 | erot = 13.1939380972622 | epot = -68.1125746463993 | etot = -33.564450813722 +914000 ekin = 21.9410171539269 | erot = 13.6876167580563 | epot = -69.1930847298951 | etot = -33.564450817912 +915000 ekin = 22.5188846328755 | erot = 14.1693256791945 | epot = -70.2526611349299 | etot = -33.5644508228598 +916000 ekin = 23.0495496145354 | erot = 14.6035757237462 | epot = -71.2175761670584 | etot = -33.5644508287768 +917000 ekin = 23.4897289759918 | erot = 14.9539952313724 | epot = -72.008175040674 | etot = -33.5644508333098 +918000 ekin = 23.7939185234148 | erot = 15.197647321232 | epot = -72.5560167286604 | etot = -33.5644508840135 +919000 ekin = 23.6168045074412 | erot = 15.3655091430202 | epot = -72.5467644924926 | etot = -33.5644508420312 +920000 ekin = 23.165531585878 | erot = 15.5814764955082 | epot = -72.311458892293 | etot = -33.5644508109067 +921000 ekin = 22.8561009730671 | erot = 15.8041631721062 | epot = -72.2247150051872 | etot = -33.5644508600138 +922000 ekin = 22.440617199678 | erot = 15.7102388661218 | epot = -71.7153069039719 | etot = -33.5644508381722 +923000 ekin = 21.8145072438246 | erot = 15.4204628466349 | epot = -70.7994209206915 | etot = -33.564450830232 +924000 ekin = 21.089710612231 | erot = 15.1252102241701 | epot = -69.7793716556892 | etot = -33.5644508192881 +925000 ekin = 20.3778961082158 | erot = 14.899059611937 | epot = -68.8414065283879 | etot = -33.5644508082351 +926000 ekin = 19.7497733146689 | erot = 14.7841436062358 | epot = -68.0983677263129 | etot = -33.5644508054082 +927000 ekin = 19.2202389452663 | erot = 14.8057849810623 | epot = -67.590474728778 | etot = -33.5644508024493 +928000 ekin = 18.8098178358059 | erot = 14.9862994051908 | epot = -67.3605680408844 | etot = -33.5644507998878 +929000 ekin = 18.5263530322086 | erot = 15.3189513314309 | epot = -67.4097551810462 | etot = -33.5644508174067 +930000 ekin = 18.303158247999 | erot = 15.7144845731335 | epot = -67.5820936492334 | etot = -33.564450828101 +931000 ekin = 18.0528353467031 | erot = 16.092098150507 | epot = -67.7093843340348 | etot = -33.5644508368247 +932000 ekin = 17.7015072493782 | erot = 16.3874716011874 | epot = -67.6534296917457 | etot = -33.5644508411801 +933000 ekin = 17.2115757804696 | erot = 16.5716045694095 | epot = -67.3476311886972 | etot = -33.5644508388181 +934000 ekin = 16.5514003203334 | erot = 16.6395832223659 | epot = -66.755434444527 | etot = -33.5644509018278 +935000 ekin = 15.4338978862408 | erot = 16.4795973505328 | epot = -65.4779460700676 | etot = -33.564450833294 +936000 ekin = 14.2992444275143 | erot = 16.4524645705128 | epot = -64.3161597798994 | etot = -33.5644507818723 +937000 ekin = 13.59487740504 | erot = 16.8307081996587 | epot = -63.9900364163686 | etot = -33.5644508116699 +938000 ekin = 13.1600926964079 | erot = 17.3617572930203 | epot = -64.0863008623788 | etot = -33.5644508729506 +939000 ekin = 12.6302856058614 | erot = 17.6616475284688 | epot = -63.8563839239186 | etot = -33.5644507895884 +940000 ekin = 12.1844103645063 | erot = 17.9750890236239 | epot = -63.7239501782487 | etot = -33.5644507901185 +941000 ekin = 11.8736812756091 | erot = 18.3544207679051 | epot = -63.7925528359821 | etot = -33.5644507924678 +942000 ekin = 11.6856910076193 | erot = 18.7737996767542 | epot = -64.0239414802086 | etot = -33.5644507958351 +943000 ekin = 11.5993719915505 | erot = 19.1997647093009 | epot = -64.3635875002877 | etot = -33.5644507994363 +944000 ekin = 11.591116393097 | erot = 19.5969000254167 | epot = -64.7524672211801 | etot = -33.5644508026663 +945000 ekin = 11.6394594916683 | erot = 19.9326030632592 | epot = -65.1365133600576 | etot = -33.56445080513 +946000 ekin = 11.7278293647869 | erot = 20.1807231613466 | epot = -65.4730033327469 | etot = -33.5644508066135 +947000 ekin = 11.8456010910349 | erot = 20.3241537585671 | epot = -65.7342056566312 | etot = -33.5644508070293 +948000 ekin = 11.9879925905891 | erot = 20.3564922444528 | epot = -65.9089356414658 | etot = -33.564450806424 +949000 ekin = 12.1551997706618 | erot = 20.2822908926568 | epot = -66.0019414683021 | etot = -33.5644508049834 +950000 ekin = 12.3510408582428 | erot = 20.1156595852263 | epot = -66.0311512464897 | etot = -33.5644508030205 +951000 ekin = 12.5812930342184 | erot = 19.8773156458908 | epot = -66.0230594810216 | etot = -33.5644508009124 +952000 ekin = 12.8471183992429 | erot = 19.5848425527081 | epot = -65.9964117535253 | etot = -33.5644508015743 +953000 ekin = 13.1479143766235 | erot = 19.2558560123375 | epot = -65.9682211888452 | etot = -33.5644507998843 +954000 ekin = 13.4859607016749 | erot = 18.9116613752366 | epot = -65.9620728756609 | etot = -33.5644507987494 +955000 ekin = 13.8607396886139 | erot = 18.5688220608356 | epot = -65.9940125476709 | etot = -33.5644507982214 +956000 ekin = 14.2684790839254 | erot = 18.2386766853017 | epot = -66.0716065674655 | etot = -33.5644507982384 +957000 ekin = 14.7022261502645 | erot = 17.9280211817306 | epot = -66.1946981306621 | etot = -33.5644507986669 +958000 ekin = 15.1523557015762 | erot = 17.6404101744164 | epot = -66.3572166753395 | etot = -33.5644507993469 +959000 ekin = 15.6074014601803 | erot = 17.3776018534993 | epot = -66.5494541137976 | etot = -33.5644508001179 +960000 ekin = 16.0551055261351 | erot = 17.1408213325793 | epot = -66.7603776595324 | etot = -33.5644508008181 +961000 ekin = 16.483819511843 | erot = 16.9315994951715 | epot = -66.9798698083909 | etot = -33.5644508013764 +962000 ekin = 16.8831178337395 | erot = 16.7524507837121 | epot = -67.2000194191554 | etot = -33.5644508017038 +963000 ekin = 17.2446402411808 | erot = 16.6070592916238 | epot = -67.4161503345794 | etot = -33.5644508017749 +964000 ekin = 17.5626944186329 | erot = 16.5001400673231 | epot = -67.6272852875597 | etot = -33.5644508016037 +965000 ekin = 17.8343164080137 | erot = 16.4370960223934 | epot = -67.8358632316613 | etot = -33.5644508012542 +966000 ekin = 18.058881794858 | erot = 16.4234839407457 | epot = -68.0468165364294 | etot = -33.5644508008257 +967000 ekin = 18.2373393553309 | erot = 16.4643418581003 | epot = -68.2661320138667 | etot = -33.5644508004355 +968000 ekin = 18.3712253334182 | erot = 16.5634469055311 | epot = -68.4991230391516 | etot = -33.5644508002023 +969000 ekin = 18.4616731642916 | erot = 16.7225928674224 | epot = -68.748716831933 | etot = -33.564450800219 +970000 ekin = 18.508642391898 | erot = 16.9409874226402 | epot = -69.014080615083 | etot = -33.5644508005448 +971000 ekin = 18.5105217351456 | erot = 17.2148322274807 | epot = -69.2898047638157 | etot = -33.5644508011893 +972000 ekin = 18.4641879057989 | erot = 17.5371342370508 | epot = -69.5657729449732 | etot = -33.5644508021236 +973000 ekin = 18.3654967925945 | erot = 17.8977436591339 | epot = -69.8276912550097 | etot = -33.5644508032813 +974000 ekin = 18.2101154179932 | erot = 18.2835968472234 | epot = -70.0581630697874 | etot = -33.5644508045708 +975000 ekin = 17.9945660115437 | erot = 18.6791515809232 | epot = -70.2381683983514 | etot = -33.5644508058845 +976000 ekin = 17.7173305275788 | erot = 19.0670257035496 | epot = -70.3488070382366 | etot = -33.5644508071083 +977000 ekin = 17.3798453157079 | erot = 19.4288693588492 | epot = -70.3731654826817 | etot = -33.5644508081246 +978000 ekin = 16.9872046651528 | erot = 19.7465105308244 | epot = -70.2981660048043 | etot = -33.5644508088271 +979000 ekin = 16.5484156632796 | erot = 20.0033999568713 | epot = -70.1162664292717 | etot = -33.5644508091207 +980000 ekin = 16.0760394561679 | erot = 20.1863036337654 | epot = -69.8267938958194 | etot = -33.5644508058861 +981000 ekin = 15.5958799206067 | erot = 20.2892058118436 | epot = -69.4495365390975 | etot = -33.5644508066472 +982000 ekin = 15.0884229209118 | erot = 20.3042917721005 | epot = -68.9571655433623 | etot = -33.56445085035 +983000 ekin = 14.6278058930741 | erot = 20.1974254363095 | epot = -68.3896821374305 | etot = -33.5644508080469 +984000 ekin = 14.4857180537849 | erot = 20.0570072753869 | epot = -68.1071761999148 | etot = -33.5644508707431 +985000 ekin = 14.2080884745897 | erot = 19.919276344842 | epot = -67.6918156218487 | etot = -33.564450802417 +986000 ekin = 13.9758844712272 | erot = 19.8429645358536 | epot = -67.3832998071099 | etot = -33.5644508000291 +987000 ekin = 13.8444879396752 | erot = 19.8435554330973 | epot = -67.2524941798934 | etot = -33.5644508071209 +988000 ekin = 13.7899575635179 | erot = 19.8765535654025 | epot = -67.2309619340325 | etot = -33.5644508051121 +989000 ekin = 13.7826987510727 | erot = 19.9896359806756 | epot = -67.3367855381806 | etot = -33.5644508064323 +990000 ekin = 13.8064597723693 | erot = 20.1866383120656 | epot = -67.5575488929868 | etot = -33.5644508085519 +991000 ekin = 13.844476200064 | erot = 20.4553568023019 | epot = -67.8642838132361 | etot = -33.5644508108702 +992000 ekin = 13.8831356334462 | erot = 20.7777558499506 | epot = -68.2253422960729 | etot = -33.5644508126761 +993000 ekin = 13.9170731635836 | erot = 21.135407615501 | epot = -68.6169315925055 | etot = -33.564450813421 +994000 ekin = 13.9526839660428 | erot = 21.5142214171928 | epot = -69.0313561961371 | etot = -33.5644508129016 +995000 ekin = 14.0087176813023 | erot = 21.9069609070435 | epot = -69.480129399738 | etot = -33.5644508113922 +996000 ekin = 14.1134296875285 | erot = 22.3130050689718 | epot = -69.9908855656615 | etot = -33.5644508091613 +997000 ekin = 14.3000196822843 | erot = 22.7364207784144 | epot = -70.6008912675636 | etot = -33.5644508068649 +998000 ekin = 14.6010980656079 | erot = 23.1830420844189 | epot = -71.3485909550456 | etot = -33.5644508050188 +999000 ekin = 15.0427312776222 | erot = 23.657392608768 | epot = -72.2645746968681 | etot = -33.5644508104779 +1000000 ekin = 15.613660129969 | erot = 24.1382006023969 | epot = -73.3163115458147 | etot = -33.5644508134487 + 1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160068 39304000 +Loop time of 31.1467 on 1 procs for 1000000 steps with 16 atoms + +Performance: 47.324 ns/day, 0.507 hours/ns, 32106.084 timesteps/s, 513.697 katom-step/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 26.515 | 26.515 | 26.515 | 0.0 | 85.13 +Bond | 1.0244 | 1.0244 | 1.0244 | 0.0 | 3.29 +Neigh | 0.019506 | 0.019506 | 0.019506 | 0.0 | 0.06 +Comm | 0.45429 | 0.45429 | 0.45429 | 0.0 | 1.46 +Output | 0.22043 | 0.22043 | 0.22043 | 0.0 | 0.71 +Modify | 2.4659 | 2.4659 | 2.4659 | 0.0 | 7.92 +Other | | 0.4469 | | | 1.43 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 107 ave 107 max 107 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:31 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.4 new file mode 100644 index 0000000000..81f7f1cafc --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.4 @@ -0,0 +1,1187 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.5 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 +Setting atom values ... + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 11.92337812042065 2.1295 6.482800913 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxrna2/stk seqdep ${T} 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 300 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 0.5 1.02455 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 36.640032 + ghost atom cutoff = 36.640032 + binsize = 18.320016, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 36.640032409886274 (../comm.cpp:739) +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815 +Per MPI rank memory allocation (min/avg/max) = 7.577 | 7.606 | 7.69 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -69.627742 3.2447172 -50.262701 0.034084814 39304000 +1000 ekin = 16.3558183649387 | erot = 16.6323090455317 | epot = -66.5525771041998 | etot = -33.5644496937295 +2000 ekin = 16.6191649168147 | erot = 16.5684372137643 | epot = -66.7520518221219 | etot = -33.5644496915429 +3000 ekin = 16.9230904408654 | erot = 16.5204480451832 | epot = -67.0079881759691 | etot = -33.5644496899204 +4000 ekin = 17.2772162612591 | erot = 16.49867929322 | epot = -67.3403452437715 | etot = -33.5644496892924 +5000 ekin = 17.6866959075726 | erot = 16.5050138456572 | epot = -67.7561594428204 | etot = -33.5644496895906 +6000 ekin = 18.1531343302964 | erot = 16.5325161302815 | epot = -68.2501001506509 | etot = -33.564449690073 +7000 ekin = 18.680653493314 | erot = 16.5738535187235 | epot = -68.8189567014344 | etot = -33.5644496893969 +8000 ekin = 19.2766528199695 | erot = 16.6261515879628 | epot = -69.4672540969553 | etot = -33.564449689023 +9000 ekin = 19.9461490397319 | erot = 16.6908475985738 | epot = -70.201446326231 | etot = -33.5644496879253 +10000 ekin = 20.6973181248474 | erot = 16.7772960438528 | epot = -71.039063854854 | etot = -33.5644496861538 +11000 ekin = 21.539522624792 | erot = 16.9014209971989 | epot = -72.0053933083053 | etot = -33.5644496863144 +12000 ekin = 22.4717498465051 | erot = 17.0791755563662 | epot = -73.1153750880493 | etot = -33.5644496851781 +13000 ekin = 23.493621609947 | erot = 17.3228520870333 | epot = -74.3809233816828 | etot = -33.5644496847026 +14000 ekin = 24.6044210071246 | erot = 17.6425688028838 | epot = -75.8114394947881 | etot = -33.5644496847798 +15000 ekin = 25.7999389267744 | erot = 18.0453525578634 | epot = -77.4097411694886 | etot = -33.5644496848508 +16000 ekin = 27.0739775537123 | erot = 18.5361142332912 | epot = -79.1745414730767 | etot = -33.5644496860731 +17000 ekin = 28.4119581304118 | erot = 19.1137262760959 | epot = -81.0901340949635 | etot = -33.5644496884557 +18000 ekin = 29.7909545183303 | erot = 19.7704759932755 | epot = -83.1258802031785 | etot = -33.5644496915727 +19000 ekin = 31.1831510307732 | erot = 20.4915974540495 | epot = -85.2391981805601 | etot = -33.5644496957374 +20000 ekin = 32.5560965367943 | erot = 21.2528351748734 | epot = -87.3733814125724 | etot = -33.5644497009047 +21000 ekin = 33.868330987566 | erot = 22.0156446407476 | epot = -89.4484253379455 | etot = -33.5644497096318 +22000 ekin = 35.0747510230858 | erot = 22.7306302808711 | epot = -91.3698310187509 | etot = -33.564449714794 +23000 ekin = 36.1427935644227 | erot = 23.3543658008634 | epot = -93.0616090845426 | etot = -33.5644497192564 +24000 ekin = 37.0484240543211 | erot = 23.8536351256838 | epot = -94.4665089004161 | etot = -33.5644497204113 +25000 ekin = 37.7873483857427 | erot = 24.2156130941775 | epot = -95.5674111990494 | etot = -33.5644497191292 +26000 ekin = 38.3695951222899 | erot = 24.4472028227103 | epot = -96.3812476612834 | etot = -33.5644497162832 +27000 ekin = 38.8142451991145 | erot = 24.5696496438673 | epot = -96.9483445558084 | etot = -33.5644497128266 +28000 ekin = 39.1436511594781 | erot = 24.6108705414904 | epot = -97.3189714104584 | etot = -33.5644497094899 +29000 ekin = 39.3799077053091 | erot = 24.5987493007977 | epot = -97.5431067127119 | etot = -33.5644497066052 +30000 ekin = 39.5437187767927 | erot = 24.5572061990977 | epot = -97.6653746802842 | etot = -33.5644497043938 +31000 ekin = 39.6556538792225 | erot = 24.5025482878245 | epot = -97.7226518696582 | etot = -33.5644497026112 +32000 ekin = 39.7376908979144 | erot = 24.4447365565287 | epot = -97.7468771552201 | etot = -33.5644497007771 +33000 ekin = 39.8178410436037 | erot = 24.3917276701332 | epot = -97.7740184125884 | etot = -33.5644496988515 +34000 ekin = 39.927618714488 | erot = 24.3494773308408 | epot = -97.8415457422131 | etot = -33.5644496968843 +35000 ekin = 40.0972017271435 | erot = 24.3220925820223 | epot = -97.9837440042509 | etot = -33.564449695085 +36000 ekin = 40.3554758289768 | erot = 24.3121132861349 | epot = -98.2320388089531 | etot = -33.5644496938414 +37000 ekin = 40.7253172241835 | erot = 24.319453116459 | epot = -98.6092200342501 | etot = -33.5644496936077 +38000 ekin = 41.2184614577313 | erot = 24.3399425110989 | epot = -99.1228536635565 | etot = -33.5644496947263 +39000 ekin = 41.8315835745705 | erot = 24.3642621379391 | epot = -99.7602954097928 | etot = -33.5644496972833 +40000 ekin = 42.5444333388241 | erot = 24.3777906096182 | epot = -100.486673649662 | etot = -33.5644497012195 +41000 ekin = 43.3221534386097 | erot = 24.3619359806971 | epot = -101.248539124814 | etot = -33.5644497055069 +42000 ekin = 44.1232219530953 | erot = 24.2968159626988 | epot = -101.984487625362 | etot = -33.564449709568 +43000 ekin = 44.904300844132 | erot = 24.1647850477408 | epot = -102.633535604778 | etot = -33.5644497129052 +44000 ekin = 45.6258073685734 | erot = 23.9537754776322 | epot = -103.144032561023 | etot = -33.5644497148173 +45000 ekin = 46.2557013508695 | erot = 23.6596129163771 | epot = -103.479763983876 | etot = -33.5644497166297 +46000 ekin = 46.7711396854538 | erot = 23.2746461161496 | epot = -103.610235519163 | etot = -33.5644497175596 +47000 ekin = 47.1576706465393 | erot = 22.7983985986729 | epot = -103.520518961432 | etot = -33.5644497162194 +48000 ekin = 47.4067411848207 | erot = 22.2418927069086 | epot = -103.213083606725 | etot = -33.5644497149953 +49000 ekin = 47.5134307536654 | erot = 21.6212608371917 | epot = -102.69914130377 | etot = -33.564449712913 +50000 ekin = 47.4750496002015 | erot = 20.9637753825402 | epot = -102.0032746914 | etot = -33.5644497086583 +51000 ekin = 47.2893433305643 | erot = 20.3140174296325 | epot = -101.167810469159 | etot = -33.5644497089619 +52000 ekin = 46.9527474071891 | erot = 19.6808685522296 | epot = -100.198065668178 | etot = -33.5644497087591 +53000 ekin = 46.4669221029446 | erot = 19.0628634962124 | epot = -99.0942353064246 | etot = -33.5644497072675 +54000 ekin = 45.8347987943741 | erot = 18.4752794596828 | epot = -97.8745279599047 | etot = -33.5644497058478 +55000 ekin = 45.0590316628642 | erot = 17.9341671577877 | epot = -96.5576485255772 | etot = -33.5644497049254 +56000 ekin = 44.1409291390466 | erot = 17.4520797326575 | epot = -95.1574585762252 | etot = -33.5644497045211 +57000 ekin = 43.0792908324229 | erot = 17.0373342694525 | epot = -93.6810748066133 | etot = -33.5644497047379 +58000 ekin = 41.8704923540616 | erot = 16.6939394056078 | epot = -92.1288814650828 | etot = -33.5644497054134 +59000 ekin = 40.5509408803243 | erot = 16.4316140927963 | epot = -90.5470046657502 | etot = -33.5644496926296 +60000 ekin = 39.1975830612683 | erot = 16.2583411314117 | epot = -89.0203738856281 | etot = -33.564449692948 +61000 ekin = 35.7114984384268 | erot = 15.7928074869535 | epot = -85.0687559055495 | etot = -33.5644499801692 +62000 ekin = 34.7372517506983 | erot = 15.8094409096042 | epot = -84.1111427027985 | etot = -33.564450042496 +63000 ekin = 35.8178089566995 | erot = 16.1653492511937 | epot = -85.5476088513059 | etot = -33.5644506434127 +64000 ekin = 34.8692363703958 | erot = 16.1670101597179 | epot = -84.6006971860838 | etot = -33.5644506559701 +65000 ekin = 33.846449455545 | erot = 16.1402632189654 | epot = -83.5511633293456 | etot = -33.5644506548352 +66000 ekin = 32.7636419796978 | erot = 16.0751240440806 | epot = -82.4032166770508 | etot = -33.5644506532724 +67000 ekin = 31.6420680628897 | erot = 15.970564295673 | epot = -81.1770830093356 | etot = -33.5644506507729 +68000 ekin = 30.5061166759974 | erot = 15.8342590047108 | epot = -79.904826328435 | etot = -33.5644506477268 +69000 ekin = 29.3793899831146 | erot = 15.6784092891742 | epot = -78.6222499180456 | etot = -33.5644506457568 +70000 ekin = 28.2842777970645 | erot = 15.5192251789786 | epot = -77.3679536187083 | etot = -33.5644506426651 +71000 ekin = 27.2428007223146 | erot = 15.3775924468384 | epot = -76.1848438089721 | etot = -33.5644506398192 +72000 ekin = 26.2738583640503 | erot = 15.2738682128135 | epot = -75.1121772142993 | etot = -33.5644506374354 +73000 ekin = 25.3929266243352 | erot = 15.2252389252993 | epot = -74.1826161852624 | etot = -33.5644506356278 +74000 ekin = 24.6118800235924 | erot = 15.2440811522979 | epot = -73.4204118109397 | etot = -33.5644506350493 +75000 ekin = 23.9285421197386 | erot = 15.2937064902862 | epot = -72.7866996078894 | etot = -33.5644509978646 +76000 ekin = 23.6014258497366 | erot = 14.5530249139085 | epot = -71.7189013877723 | etot = -33.5644506241273 +77000 ekin = 24.0021186681998 | erot = 14.6672556253499 | epot = -72.2338249120015 | etot = -33.5644506184517 +78000 ekin = 23.7667117018473 | erot = 14.8821032755388 | epot = -72.2132655967964 | etot = -33.5644506194103 +79000 ekin = 23.6362408803455 | erot = 15.1573231058556 | epot = -72.3580146069965 | etot = -33.5644506207955 +80000 ekin = 23.6008292998183 | erot = 15.4801164769237 | epot = -72.6453963992505 | etot = -33.5644506225085 +81000 ekin = 23.6479278988512 | erot = 15.8366782045229 | epot = -73.0490567276813 | etot = -33.5644506243072 +82000 ekin = 23.763195852744 | erot = 16.2135577483195 | epot = -73.541204227137 | etot = -33.5644506260735 +83000 ekin = 23.93133805131 | erot = 16.5989137528028 | epot = -74.0947024318273 | etot = -33.5644506277145 +84000 ekin = 24.1405337461498 | erot = 16.9832739889214 | epot = -74.6882583637893 | etot = -33.5644506287181 +85000 ekin = 24.3851366362468 | erot = 17.3594190811792 | epot = -75.3090063475356 | etot = -33.5644506301095 +86000 ekin = 24.6499622429188 | erot = 17.7229731863038 | epot = -75.937386060464 | etot = -33.5644506312414 +87000 ekin = 24.9195866966175 | erot = 18.0734917202536 | epot = -76.5575290489239 | etot = -33.5644506320529 +88000 ekin = 25.1793742014134 | erot = 18.4146339772087 | epot = -77.1584588111687 | etot = -33.5644506325466 +89000 ekin = 25.4156568494637 | erot = 18.753968669385 | epot = -77.7340761514942 | etot = -33.5644506326455 +90000 ekin = 25.6096840035671 | erot = 19.1040901404621 | epot = -78.2782247770918 | etot = -33.5644506330626 +91000 ekin = 25.7348417969792 | erot = 19.4865010462193 | epot = -78.7857934757851 | etot = -33.5644506325866 +92000 ekin = 25.7824117490222 | erot = 19.9168308436387 | epot = -79.2636932257648 | etot = -33.5644506331039 +93000 ekin = 25.7436484203088 | erot = 20.4015276208854 | epot = -79.7096266744372 | etot = -33.564450633243 +94000 ekin = 25.6107487399104 | erot = 20.949881961115 | epot = -80.1250813341981 | etot = -33.5644506331727 +95000 ekin = 25.3788454256131 | erot = 21.5718811146881 | epot = -80.5151771730697 | etot = -33.5644506327685 +96000 ekin = 25.0476635684687 | erot = 22.2778886106639 | epot = -80.8900028110571 | etot = -33.5644506319245 +97000 ekin = 24.6228037012584 | erot = 23.0785820232847 | epot = -81.2658363557742 | etot = -33.564450631231 +98000 ekin = 24.1163650303316 | erot = 23.980262455687 | epot = -81.6610781157268 | etot = -33.5644506297082 +99000 ekin = 23.5467601995482 | erot = 24.9897227937605 | epot = -82.1009336213136 | etot = -33.5644506280048 +100000 ekin = 22.9377076830221 | erot = 26.112544428779 | epot = -82.6147027382293 | etot = -33.5644506264282 +101000 ekin = 22.3162402354096 | erot = 27.3495277986626 | epot = -83.2302186594371 | etot = -33.5644506253649 +102000 ekin = 21.7099673799529 | erot = 28.6941289887159 | epot = -83.9685469938564 | etot = -33.5644506251876 +103000 ekin = 21.1440927333112 | erot = 30.1304131051784 | epot = -84.8389564645821 | etot = -33.5644506260925 +104000 ekin = 20.639036073264 | erot = 31.6318076720505 | epot = -85.8352943737208 | etot = -33.5644506284063 +105000 ekin = 20.2097356177992 | erot = 33.155951127779 | epot = -86.9301373769384 | etot = -33.5644506313601 +106000 ekin = 19.8659962936204 | erot = 34.6591523175009 | epot = -88.0895992441982 | etot = -33.5644506330769 +107000 ekin = 19.6196926152642 | erot = 36.1003389899193 | epot = -89.2844822415487 | etot = -33.5644506363652 +108000 ekin = 19.4737764770437 | erot = 37.4404659122968 | epot = -90.4786930287769 | etot = -33.5644506394364 +109000 ekin = 19.4257211237998 | erot = 38.6395727467532 | epot = -91.6297445157463 | etot = -33.5644506451932 +110000 ekin = 19.4643317381198 | erot = 39.6495422786743 | epot = -92.6783246653681 | etot = -33.564450648574 +111000 ekin = 19.5812097010477 | erot = 40.4340503208624 | epot = -93.5797106732505 | etot = -33.5644506513404 +112000 ekin = 19.7688752467926 | erot = 40.9641614007962 | epot = -94.297487301236 | etot = -33.5644506536472 +113000 ekin = 20.0199352606443 | erot = 41.2235617686336 | epot = -94.8079476827577 | etot = -33.5644506534798 +114000 ekin = 20.3316783135453 | erot = 41.2208106095024 | epot = -95.1169395739077 | etot = -33.56445065086 +115000 ekin = 20.7092934859803 | erot = 40.9902193450322 | epot = -95.2639634785888 | etot = -33.5644506475763 +116000 ekin = 21.1584070130043 | erot = 40.5711692188877 | epot = -95.2940268780899 | etot = -33.5644506461979 +117000 ekin = 21.6717401642267 | erot = 40.0068194492192 | epot = -95.2430102574592 | etot = -33.5644506440133 +118000 ekin = 22.2304498749665 | erot = 39.3449170916981 | epot = -95.1398176087205 | etot = -33.5644506420559 +119000 ekin = 22.8040322747498 | erot = 38.6279078104772 | epot = -94.9963907285437 | etot = -33.5644506433167 +120000 ekin = 23.3636455910773 | erot = 37.8733163419346 | epot = -94.8014125775743 | etot = -33.5644506445623 +121000 ekin = 23.8883342479557 | erot = 37.0853024873734 | epot = -94.5380873807793 | etot = -33.5644506454502 +122000 ekin = 24.3628295450724 | erot = 36.2617521254169 | epot = -94.1890323184744 | etot = -33.5644506479851 +123000 ekin = 24.7728939422973 | erot = 35.3896441641822 | epot = -93.7269887541634 | etot = -33.564450647684 +124000 ekin = 25.1206142173503 | erot = 34.4655545655721 | epot = -93.1506194284831 | etot = -33.5644506455608 +125000 ekin = 25.4216604350096 | erot = 33.503516320942 | epot = -92.4896273979272 | etot = -33.5644506419756 +126000 ekin = 25.6927735129487 | erot = 32.5281184075612 | epot = -91.7853425611144 | etot = -33.5644506406046 +127000 ekin = 25.9460883081157 | erot = 31.5650113724921 | epot = -91.0755503181686 | etot = -33.5644506375608 +128000 ekin = 26.1993872383113 | erot = 30.6366650539312 | epot = -90.4005029275328 | etot = -33.5644506352904 +129000 ekin = 26.4652741312988 | erot = 29.761033950875 | epot = -89.790758715097 | etot = -33.5644506329232 +130000 ekin = 26.7486727551143 | erot = 28.9506137583675 | epot = -89.2637371464425 | etot = -33.5644506329608 +131000 ekin = 27.0469092028967 | erot = 28.2034442942545 | epot = -88.8148041302784 | etot = -33.5644506331273 +132000 ekin = 27.354287486523 | erot = 27.516081388701 | epot = -88.4348195084624 | etot = -33.5644506332384 +133000 ekin = 27.6627378161327 | erot = 26.888810791231 | epot = -88.1159992405597 | etot = -33.564450633196 +134000 ekin = 27.967292318186 | erot = 26.3214524159643 | epot = -87.8531953671446 | etot = -33.5644506329943 +135000 ekin = 28.2641150378973 | erot = 25.8141340320123 | epot = -87.6426997025848 | etot = -33.5644506326751 +136000 ekin = 28.5509978141275 | erot = 25.3673179322137 | epot = -87.4827663786045 | etot = -33.5644506322633 +137000 ekin = 28.8259159092095 | erot = 24.9801644637669 | epot = -87.3705310053013 | etot = -33.5644506323249 +138000 ekin = 29.0842610649225 | erot = 24.6492546073972 | epot = -87.2979663044031 | etot = -33.5644506320834 +139000 ekin = 29.3272222877147 | erot = 24.3700782380114 | epot = -87.2617511574221 | etot = -33.5644506316961 +140000 ekin = 29.5579798491409 | erot = 24.1376580585839 | epot = -87.2600885391577 | etot = -33.5644506314329 +141000 ekin = 29.7799846346147 | erot = 23.946242993064 | epot = -87.2906782589293 | etot = -33.5644506312505 +142000 ekin = 29.9959841884821 | erot = 23.7899704636108 | epot = -87.3504052832972 | etot = -33.5644506312043 +143000 ekin = 30.20703491277 | erot = 23.6632996950733 | epot = -87.4347852391637 | etot = -33.5644506313204 +144000 ekin = 30.411884002902 | erot = 23.5613798569439 | epot = -87.537714491437 | etot = -33.564450631591 +145000 ekin = 30.606845687222 | erot = 23.4803656669174 | epot = -87.6516619861197 | etot = -33.5644506319804 +146000 ekin = 30.786123077816 | erot = 23.4176420010831 | epot = -87.7682157113377 | etot = -33.5644506324387 +147000 ekin = 30.9424364770354 | erot = 23.3719366394343 | epot = -87.878823749381 | etot = -33.5644506329113 +148000 ekin = 31.0677916134895 | erot = 23.343321608025 | epot = -87.9755638548643 | etot = -33.5644506333498 +149000 ekin = 31.1542520331538 | erot = 23.3331254537238 | epot = -88.0518281205882 | etot = -33.5644506337106 +150000 ekin = 31.1946418128191 | erot = 23.3437996409618 | epot = -88.1028920877408 | etot = -33.5644506339599 +151000 ekin = 31.183806383935 | erot = 23.3785936220274 | epot = -88.1268506398047 | etot = -33.5644506338423 +152000 ekin = 31.1202290278342 | erot = 23.4412183836801 | epot = -88.1258980452558 | etot = -33.5644506337415 +153000 ekin = 31.0032553217694 | erot = 23.5372189789098 | epot = -88.1049249338573 | etot = -33.5644506331782 +154000 ekin = 30.8354559406818 | erot = 23.6729952127027 | epot = -88.0729017863056 | etot = -33.5644506329211 +155000 ekin = 30.6186135870613 | erot = 23.8551009557717 | epot = -88.0381651751801 | etot = -33.564450632347 +156000 ekin = 30.3571457582689 | erot = 24.0914721103803 | epot = -88.0130685002393 | etot = -33.5644506315902 +157000 ekin = 30.057410850046 | erot = 24.3907046676107 | epot = -88.012566148493 | etot = -33.5644506308362 +158000 ekin = 29.7256756923437 | erot = 24.762556719639 | epot = -88.0526830421884 | etot = -33.5644506302057 +159000 ekin = 29.3667041508031 | erot = 25.2124449846246 | epot = -88.1435997656418 | etot = -33.5644506302141 +160000 ekin = 28.9829375848383 | erot = 25.7406189361283 | epot = -88.2880071520223 | etot = -33.5644506310558 +161000 ekin = 28.5708031098758 | erot = 26.3449808633592 | epot = -88.4802346049617 | etot = -33.5644506317267 +162000 ekin = 28.1278607476191 | erot = 27.0188065006254 | epot = -88.7111178809976 | etot = -33.564450632753 +163000 ekin = 27.6515523776561 | erot = 27.7508923428494 | epot = -88.9668953542198 | etot = -33.5644506337143 +164000 ekin = 27.1398166575548 | erot = 28.5265897115537 | epot = -89.2308570046245 | etot = -33.564450635516 +165000 ekin = 26.59018012942 | erot = 29.3236809534503 | epot = -89.4783117201368 | etot = -33.5644506372666 +166000 ekin = 26.0027550424038 | erot = 30.1148491025895 | epot = -89.6820547838353 | etot = -33.564450638842 +167000 ekin = 25.3815734826451 | erot = 30.8714146428701 | epot = -89.8174387656406 | etot = -33.5644506401255 +168000 ekin = 24.7338280126237 | erot = 31.5656853660197 | epot = -89.8639640196521 | etot = -33.5644506410087 +169000 ekin = 24.0691061638315 | erot = 32.1733410341242 | epot = -89.8068978394117 | etot = -33.564450641456 +170000 ekin = 23.3986380903856 | erot = 32.6761770397929 | epot = -89.6392657713649 | etot = -33.5644506411864 +171000 ekin = 22.7350947047576 | erot = 33.0649339609238 | epot = -89.3644793058787 | etot = -33.5644506401972 +172000 ekin = 22.0927595064345 | erot = 33.3397459263048 | epot = -88.9969560711814 | etot = -33.5644506384421 +173000 ekin = 21.4881436133131 | erot = 33.5098602953131 | epot = -88.5624545444177 | etot = -33.5644506357915 +174000 ekin = 20.9424106184029 | erot = 33.5950638981387 | epot = -88.1019251458152 | etot = -33.5644506292736 +175000 ekin = 20.4887725385188 | erot = 33.6332952588445 | epot = -87.6865184248663 | etot = -33.5644506275031 +176000 ekin = 20.1459992745576 | erot = 33.6413286939825 | epot = -87.351778594707 | etot = -33.564450626167 +177000 ekin = 19.9273952403355 | erot = 33.6264319072463 | epot = -87.1182777732003 | etot = -33.5644506256185 +178000 ekin = 19.8405268115202 | erot = 33.5862782738567 | epot = -86.9912557124967 | etot = -33.5644506271198 +179000 ekin = 19.8828425829329 | erot = 33.5043404166444 | epot = -86.9516336276337 | etot = -33.5644506280564 +180000 ekin = 20.0524881206169 | erot = 33.3671042345424 | epot = -86.9840429849014 | etot = -33.5644506297421 +181000 ekin = 20.3414841297263 | erot = 33.1581782006462 | epot = -87.0641129622371 | etot = -33.5644506318646 +182000 ekin = 20.7352057198159 | erot = 32.8612622822523 | epot = -87.1609186361345 | etot = -33.5644506340663 +183000 ekin = 21.2137106223586 | erot = 32.4647477949406 | epot = -87.2429090531987 | etot = -33.5644506358994 +184000 ekin = 21.7537587720613 | erot = 31.9655803613327 | epot = -87.2837897705835 | etot = -33.5644506371895 +185000 ekin = 22.3286746031838 | erot = 31.3708022039154 | epot = -87.263927444786 | etot = -33.5644506376868 +186000 ekin = 22.9115100132845 | erot = 30.6990331536428 | epot = -87.1749938042474 | etot = -33.5644506373201 +187000 ekin = 23.4775030152572 | erot = 29.9792070479707 | epot = -87.0211606994407 | etot = -33.5644506362127 +188000 ekin = 24.0059463479901 | erot = 29.2469949106332 | epot = -86.8173918933289 | etot = -33.5644506347057 +189000 ekin = 24.4809955944174 | erot = 28.5392131436642 | epot = -86.5846593713795 | etot = -33.5644506332979 +190000 ekin = 24.8911658073071 | erot = 27.8871249849441 | epot = -86.3427414247871 | etot = -33.5644506325359 +191000 ekin = 25.2275609419512 | erot = 27.3101259966536 | epot = -86.1021375715765 | etot = -33.5644506329717 +192000 ekin = 25.4831011426741 | erot = 26.8121375634346 | epot = -85.8596893403555 | etot = -33.5644506342468 +193000 ekin = 25.2930335715097 | erot = 26.641089195829 | epot = -85.4985734034392 | etot = -33.5644506361005 +194000 ekin = 25.0352601614021 | erot = 26.652526548361 | epot = -85.2522373921847 | etot = -33.5644506824216 +195000 ekin = 25.0363508840831 | erot = 26.2378500699574 | epot = -84.838651623646 | etot = -33.5644506696055 +196000 ekin = 24.9648942549683 | erot = 25.7868302418778 | epot = -84.3161751669049 | etot = -33.5644506700588 +197000 ekin = 24.8200850732436 | erot = 25.3002719383815 | epot = -83.684807680627 | etot = -33.5644506690019 +198000 ekin = 24.6172884588533 | erot = 24.7762496503829 | epot = -82.957988775829 | etot = -33.5644506665928 +199000 ekin = 24.3770483830299 | erot = 24.2259949153857 | epot = -82.1674939619529 | etot = -33.5644506635372 +200000 ekin = 24.122436002035 | erot = 23.6691820640912 | epot = -81.3560687261623 | etot = -33.5644506600361 +201000 ekin = 23.8775516468524 | erot = 23.129174398578 | epot = -80.5711767022531 | etot = -33.5644506568227 +202000 ekin = 23.6646103059802 | erot = 22.6276096876317 | epot = -79.856670647895 | etot = -33.5644506542831 +203000 ekin = 23.5017139925634 | erot = 22.1809863327408 | epot = -79.2471509779163 | etot = -33.5644506526121 +204000 ekin = 23.4012931943709 | erot = 21.7992926193403 | epot = -78.7650364652273 | etot = -33.564450651516 +205000 ekin = 23.3698442687857 | erot = 21.4883950765935 | epot = -78.4226899967305 | etot = -33.5644506513513 +206000 ekin = 23.4080277663952 | erot = 21.2503388252223 | epot = -78.222817243383 | etot = -33.5644506517654 +207000 ekin = 23.510672424505 | erot = 21.0828853352514 | epot = -78.1580084122941 | etot = -33.5644506525377 +208000 ekin = 23.668353418069 | erot = 20.9827921925506 | epot = -78.2155962640904 | etot = -33.5644506534708 +209000 ekin = 23.8319531636404 | erot = 20.8686960092894 | epot = -78.2650998050505 | etot = -33.5644506321207 +210000 ekin = 24.1634900876545 | erot = 20.8246815259943 | epot = -78.5526222834943 | etot = -33.5644506698455 +211000 ekin = 24.4545474929207 | erot = 20.8320949387518 | epot = -78.8510930934304 | etot = -33.564450661758 +212000 ekin = 24.7210588847004 | erot = 20.8889178093638 | epot = -79.1744273565512 | etot = -33.564450662487 +213000 ekin = 24.9762555918736 | erot = 20.995657067092 | epot = -79.5363633251364 | etot = -33.5644506661708 +214000 ekin = 25.2054830046564 | erot = 21.1345527593257 | epot = -79.904486431005 | etot = -33.5644506670229 +215000 ekin = 25.4055444850595 | erot = 21.2948000239986 | epot = -80.2647951766001 | etot = -33.564450667542 +216000 ekin = 25.5773395550173 | erot = 21.4659469017842 | epot = -80.6077371248694 | etot = -33.5644506680679 +217000 ekin = 25.7224226234168 | erot = 21.6383314527717 | epot = -80.9252047446809 | etot = -33.5644506684925 +218000 ekin = 25.8456307141236 | erot = 21.7996006617657 | epot = -81.2096820449196 | etot = -33.5644506690303 +219000 ekin = 25.9524523541736 | erot = 21.9358336225136 | epot = -81.4527366463228 | etot = -33.5644506696356 +220000 ekin = 26.0480501371294 | erot = 22.0331400323276 | epot = -81.6456408394172 | etot = -33.5644506699602 +221000 ekin = 26.1377559921142 | erot = 22.0801399062462 | epot = -81.7823465685532 | etot = -33.5644506701928 +222000 ekin = 26.2262421157048 | erot = 22.0692633440543 | epot = -81.859956129764 | etot = -33.564450670005 +223000 ekin = 26.3184403630266 | erot = 21.9982474658049 | epot = -81.8811384982253 | etot = -33.5644506693938 +224000 ekin = 26.4171271373519 | erot = 21.8710288815675 | epot = -81.8526066880913 | etot = -33.5644506691719 +225000 ekin = 26.5225389104719 | erot = 21.6965423523057 | epot = -81.7835319309085 | etot = -33.5644506681309 +226000 ekin = 26.7157923548783 | erot = 21.3119214437842 | epot = -81.5921644821736 | etot = -33.5644506835112 +227000 ekin = 27.2484396437764 | erot = 20.6374955149859 | epot = -81.4503858460509 | etot = -33.5644506872886 +228000 ekin = 27.5078528971482 | erot = 20.2748179574152 | epot = -81.3471215226765 | etot = -33.564450668113 +229000 ekin = 27.6312830550944 | erot = 19.9858964954709 | epot = -81.1816302175473 | etot = -33.564450666982 +230000 ekin = 27.7676058404246 | erot = 19.7189438600613 | epot = -81.0510003675302 | etot = -33.5644506670444 +231000 ekin = 27.9171898995783 | erot = 19.4851196432287 | epot = -80.9667602108582 | etot = -33.5644506680513 +232000 ekin = 28.075807909498 | erot = 19.2892055600519 | epot = -80.9294641380373 | etot = -33.5644506684874 +233000 ekin = 28.2354888581722 | erot = 19.1284398309988 | epot = -80.9283793559407 | etot = -33.5644506667697 +234000 ekin = 28.3953039485459 | erot = 19.0132859353609 | epot = -80.9730405513788 | etot = -33.564450667472 +235000 ekin = 28.5569493494506 | erot = 18.9585387746691 | epot = -81.0799387921407 | etot = -33.564450668021 +236000 ekin = 28.7166448189613 | erot = 18.9671002034186 | epot = -81.2481956905202 | etot = -33.5644506681403 +237000 ekin = 28.8725023819759 | erot = 19.0433381874627 | epot = -81.4802912374047 | etot = -33.5644506679661 +238000 ekin = 29.0257746255977 | erot = 19.1916941122354 | epot = -81.781919405367 | etot = -33.5644506675339 +239000 ekin = 29.1795842186893 | erot = 19.4168064167824 | epot = -82.1608413029194 | etot = -33.5644506674477 +240000 ekin = 29.3337146102013 | erot = 19.7090725309664 | epot = -82.6072378098102 | etot = -33.5644506686425 +241000 ekin = 29.4868078967125 | erot = 20.0596352268188 | epot = -83.1108937928375 | etot = -33.5644506693062 +242000 ekin = 29.6351003169461 | erot = 20.4605457842952 | epot = -83.6600967717312 | etot = -33.5644506704898 +243000 ekin = 29.8921802425375 | erot = 20.6958964400281 | epot = -84.1525273495514 | etot = -33.5644506669859 +244000 ekin = 30.2594419587798 | erot = 20.964961730853 | epot = -84.7888543939581 | etot = -33.5644507043253 +245000 ekin = 30.3074620328625 | erot = 21.308999500704 | epot = -85.1809122847658 | etot = -33.5644507511994 +246000 ekin = 30.6998172933751 | erot = 21.0861202554954 | epot = -85.3503880690886 | etot = -33.5644505202181 +247000 ekin = 31.2652124059134 | erot = 21.7433599271938 | epot = -86.5730230770323 | etot = -33.5644507439251 +248000 ekin = 31.2039013197185 | erot = 22.3578318778188 | epot = -87.1261839420136 | etot = -33.5644507444763 +249000 ekin = 31.0628965882796 | erot = 22.9361503364912 | epot = -87.5634976683527 | etot = -33.5644507435818 +250000 ekin = 30.8544219835667 | erot = 23.4738999845995 | epot = -87.8927727106867 | etot = -33.5644507425205 +251000 ekin = 30.5979929542448 | erot = 23.973249537305 | epot = -88.1356932313339 | etot = -33.5644507397841 +252000 ekin = 30.3186084933224 | erot = 24.447023432737 | epot = -88.3300826628831 | etot = -33.5644507368237 +253000 ekin = 30.0416328683412 | erot = 24.9117142614702 | epot = -88.5177978640591 | etot = -33.5644507342476 +254000 ekin = 29.6651322242409 | erot = 25.3352238225117 | epot = -88.5648072260424 | etot = -33.5644511792898 +255000 ekin = 27.9972596304248 | erot = 25.3436445664535 | epot = -86.9053550133662 | etot = -33.5644508164878 +256000 ekin = 27.4480536507435 | erot = 26.2038023388295 | epot = -87.2163067908443 | etot = -33.5644508012713 +257000 ekin = 28.5107044681316 | erot = 27.5793602338718 | epot = -89.6545158781981 | etot = -33.5644511761947 +258000 ekin = 28.9485040029364 | erot = 27.9141399631527 | epot = -90.4270947740165 | etot = -33.5644508079275 +259000 ekin = 29.1923898090981 | erot = 28.2760336628793 | epot = -91.0328742826499 | etot = -33.5644508106724 +260000 ekin = 29.442065950696 | erot = 28.6795119903338 | epot = -91.6860287571124 | etot = -33.5644508160826 +261000 ekin = 29.6845039883694 | erot = 29.1068404637727 | epot = -92.3557952702589 | etot = -33.5644508181168 +262000 ekin = 29.8834680797453 | erot = 29.5461970803508 | epot = -92.9941159814699 | etot = -33.5644508213738 +263000 ekin = 30.0159351907403 | erot = 29.9649097381375 | epot = -93.5452957538687 | etot = -33.5644508249909 +264000 ekin = 30.0524877646951 | erot = 30.3384906869752 | epot = -93.9554292802054 | etot = -33.5644508285351 +265000 ekin = 29.9659450397006 | erot = 30.6431999053458 | epot = -94.1735957767029 | etot = -33.5644508316564 +266000 ekin = 29.7355380957043 | erot = 30.8554934503359 | epot = -94.1554823800756 | etot = -33.5644508340354 +267000 ekin = 29.350217253122 | erot = 30.9531552650632 | epot = -93.8678233536458 | etot = -33.5644508354606 +268000 ekin = 28.8109215599824 | erot = 30.9159121160793 | epot = -93.2912845119104 | etot = -33.5644508358487 +269000 ekin = 28.1312299025676 | erot = 30.72588001067 | epot = -92.4215607498475 | etot = -33.5644508366099 +270000 ekin = 27.3365120330892 | erot = 30.3685462543054 | epot = -91.2695091419232 | etot = -33.5644508545286 +271000 ekin = 26.4621552466015 | erot = 29.8348321072944 | epot = -89.8614382054951 | etot = -33.5644508515991 +272000 ekin = 25.5514537840266 | erot = 29.1238715109503 | epot = -88.2397761424711 | etot = -33.5644508474942 +273000 ekin = 24.6528090192241 | erot = 28.2453291639337 | epot = -86.4625890255924 | etot = -33.5644508424347 +274000 ekin = 23.821234650199 | erot = 27.2200000603148 | epot = -84.6056855414306 | etot = -33.5644508309167 +275000 ekin = 22.972977788893 | erot = 26.0804823635616 | epot = -82.6179111120453 | etot = -33.5644509595907 +276000 ekin = 22.0549791970788 | erot = 24.8883860441621 | epot = -80.507816055329 | etot = -33.564450814088 +277000 ekin = 22.2918454486476 | erot = 23.6844629884912 | epot = -79.5407594438925 | etot = -33.5644510067537 +278000 ekin = 22.2933944834357 | erot = 22.3796695906513 | epot = -78.237514901963 | etot = -33.5644508278759 +279000 ekin = 22.3659748249692 | erot = 21.1183819744112 | epot = -77.0488076286914 | etot = -33.5644508293109 +280000 ekin = 22.5183002078395 | erot = 19.9334324614475 | epot = -76.0161834966364 | etot = -33.5644508273493 +281000 ekin = 22.7529481191282 | erot = 18.8478601493533 | epot = -75.1652590940401 | etot = -33.5644508255585 +282000 ekin = 23.0795879184844 | erot = 17.877696647541 | epot = -74.5217353872615 | etot = -33.5644508212361 +283000 ekin = 23.5210121271395 | erot = 17.0345324476772 | epot = -74.1199953957519 | etot = -33.5644508209352 +284000 ekin = 24.0799247559117 | erot = 16.3233784659049 | epot = -73.9677540517901 | etot = -33.5644508299735 +285000 ekin = 24.7785446246702 | erot = 15.7478244913859 | epot = -74.0908199422723 | etot = -33.5644508262162 +286000 ekin = 25.6368387345602 | erot = 15.3047487828053 | epot = -74.5060383422943 | etot = -33.5644508249288 +287000 ekin = 26.6214548224918 | erot = 14.9922504829504 | epot = -75.1781561309387 | etot = -33.5644508254965 +288000 ekin = 27.7267158888742 | erot = 14.8012865017222 | epot = -76.092453221868 | etot = -33.5644508312716 +289000 ekin = 28.8920167227402 | erot = 14.7169892845884 | epot = -77.1734568439709 | etot = -33.5644508366423 +290000 ekin = 30.0553666648459 | erot = 14.7251675417739 | epot = -78.3449850482838 | etot = -33.5644508416639 +291000 ekin = 31.1595769632409 | erot = 14.8119291202727 | epot = -79.5359569291001 | etot = -33.5644508455866 +292000 ekin = 32.1608216689788 | erot = 14.9640713088948 | epot = -80.6893438261594 | etot = -33.5644508482858 +293000 ekin = 33.0319319380116 | erot = 15.1681739054538 | epot = -81.7645566935981 | etot = -33.5644508501327 +294000 ekin = 33.7599421346893 | erot = 15.408810677985 | epot = -82.7332036642727 | etot = -33.5644508515984 +295000 ekin = 34.3413485939618 | erot = 15.6673943342359 | epot = -83.5731937811138 | etot = -33.5644508529161 +296000 ekin = 34.7782829446679 | erot = 15.9229210434156 | epot = -84.2656548420787 | etot = -33.5644508539951 +297000 ekin = 35.0767101392297 | erot = 16.1546669536392 | epot = -84.7958279474613 | etot = -33.5644508545924 +298000 ekin = 35.2457989813398 | erot = 16.3457320030263 | epot = -85.1559818388994 | etot = -33.5644508545332 +299000 ekin = 35.2970066855107 | erot = 16.4859983979418 | epot = -85.3474559372914 | etot = -33.5644508538389 +300000 ekin = 35.2422237261552 | erot = 16.573594168153 | epot = -85.380268746981 | etot = -33.5644508526728 +301000 ekin = 35.0916597610679 | erot = 16.6147820199689 | epot = -85.2708926322436 | etot = -33.5644508512068 +302000 ekin = 34.8528128910437 | erot = 16.6227287108284 | epot = -85.0399924513857 | etot = -33.5644508495136 +303000 ekin = 34.5312597670471 | erot = 16.6156181966321 | epot = -84.7113288112829 | etot = -33.5644508476037 +304000 ekin = 34.131367434132 | erot = 16.6227567332235 | epot = -84.3185750111405 | etot = -33.5644508437849 +305000 ekin = 33.6571822643369 | erot = 16.6720234605658 | epot = -83.8936565670678 | etot = -33.5644508421651 +306000 ekin = 33.1151986332002 | erot = 16.7769746117295 | epot = -83.4566240858641 | etot = -33.5644508409344 +307000 ekin = 32.5134330702729 | erot = 16.9437629168019 | epot = -83.0216468273944 | etot = -33.5644508403197 +308000 ekin = 31.8601474906691 | erot = 17.1694637372836 | epot = -82.5940620683869 | etot = -33.5644508404342 +309000 ekin = 31.1628016434418 | erot = 17.4420089824945 | epot = -82.1692614669022 | etot = -33.5644508409659 +310000 ekin = 30.4284939703051 | erot = 17.7430091432334 | epot = -81.7359539560319 | etot = -33.5644508424934 +311000 ekin = 29.6636970636957 | erot = 18.0450727085003 | epot = -81.2732206157428 | etot = -33.5644508435468 +312000 ekin = 28.8763119838117 | erot = 18.3211026917138 | epot = -80.7618655199236 | etot = -33.5644508443981 +313000 ekin = 28.0757317031842 | erot = 18.5482322979291 | epot = -80.1884148456634 | etot = -33.5644508445501 +314000 ekin = 27.2754576014843 | erot = 18.7102692133756 | epot = -79.5501776586764 | etot = -33.5644508438165 +315000 ekin = 26.4927512875096 | erot = 18.8002978244007 | epot = -78.8574999542301 | etot = -33.5644508423198 +316000 ekin = 25.747682520664 | erot = 18.8201859999041 | epot = -78.132319360867 | etot = -33.564450840299 +317000 ekin = 25.0614905058277 | erot = 18.7788964667723 | epot = -77.4048378106377 | etot = -33.5644508380377 +318000 ekin = 24.4546904068649 | erot = 18.6903703700934 | epot = -76.7095116127357 | etot = -33.5644508357774 +319000 ekin = 23.9454326766056 | erot = 18.5716676910418 | epot = -76.0815512013104 | etot = -33.564450833663 +320000 ekin = 23.5484361618332 | erot = 18.4417359442004 | epot = -75.5546229377731 | etot = -33.5644508317395 +321000 ekin = 23.2745454666142 | erot = 18.3209670206188 | epot = -75.159963317225 | etot = -33.5644508299921 +322000 ekin = 23.1307065450427 | erot = 18.2311244116958 | epot = -74.9262817851812 | etot = -33.5644508284427 +323000 ekin = 23.1199305195539 | erot = 18.1948729378857 | epot = -74.8792542846864 | etot = -33.5644508272467 +324000 ekin = 23.2402241371604 | erot = 18.2346442880494 | epot = -75.0393192519605 | etot = -33.5644508267507 +325000 ekin = 23.4710021372648 | erot = 18.3668956954565 | epot = -75.4023486640661 | etot = -33.5644508313448 +326000 ekin = 23.7795455090648 | erot = 18.5932769386575 | epot = -75.9372732822622 | etot = -33.5644508345399 +327000 ekin = 24.1343713308685 | erot = 18.9009306659146 | epot = -76.5997528363167 | etot = -33.5644508395337 +328000 ekin = 24.4953646019599 | erot = 19.2611055950044 | epot = -77.3209210428185 | etot = -33.5644508458542 +329000 ekin = 24.8184483226243 | erot = 19.6309716494425 | epot = -78.0138708244921 | etot = -33.5644508524254 +330000 ekin = 25.0648153577033 | erot = 19.9600875039469 | epot = -78.5893537191492 | etot = -33.564450857499 +331000 ekin = 25.2101383722027 | erot = 20.2008919381154 | epot = -78.9754811706424 | etot = -33.5644508603242 +332000 ekin = 25.2457706638964 | erot = 20.3248269291664 | epot = -79.1350484526804 | etot = -33.5644508596175 +333000 ekin = 25.1861890029755 | erot = 20.3296166389972 | epot = -79.080256497531 | etot = -33.5644508555582 +334000 ekin = 25.06621909807 | erot = 20.2399843242203 | epot = -78.8706542714784 | etot = -33.5644508491881 +335000 ekin = 24.9333683336748 | erot = 20.1009816218885 | epot = -78.5988007975495 | etot = -33.5644508419862 +336000 ekin = 24.8381114575746 | erot = 19.9670256544153 | epot = -78.3695879473404 | etot = -33.5644508353505 +337000 ekin = 24.8247545151604 | erot = 19.8908557635149 | epot = -78.2800611094823 | etot = -33.564450830807 +338000 ekin = 24.9246805342402 | erot = 19.9088859975838 | epot = -78.3980173598233 | etot = -33.5644508279992 +339000 ekin = 25.1522743470225 | erot = 20.043365846569 | epot = -78.7600910209592 | etot = -33.5644508273677 +340000 ekin = 25.5040328015065 | erot = 20.3063243572631 | epot = -79.3748079874543 | etot = -33.5644508286847 +341000 ekin = 25.9593882032928 | erot = 20.6972938179576 | epot = -80.2211328527409 | etot = -33.5644508314906 +342000 ekin = 26.4842114255991 | erot = 21.206040618102 | epot = -81.2547028790046 | etot = -33.5644508353035 +343000 ekin = 27.0356929913546 | erot = 21.8153279723555 | epot = -82.4154718032949 | etot = -33.5644508395848 +344000 ekin = 27.567697334587 | erot = 22.5033872894653 | epot = -83.6355354678824 | etot = -33.5644508438302 +345000 ekin = 28.0359749647809 | erot = 23.2463366467822 | epot = -84.846762459203 | etot = -33.5644508476399 +346000 ekin = 28.4026013553742 | erot = 24.0201112992316 | epot = -85.9871635053201 | etot = -33.5644508507143 +347000 ekin = 28.6398915195253 | erot = 24.8020103746405 | epot = -87.0063527468454 | etot = -33.5644508526796 +348000 ekin = 28.7326075378057 | erot = 25.5714490943132 | epot = -87.8685074861033 | etot = -33.5644508539845 +349000 ekin = 28.6752584344467 | erot = 26.310018084166 | epot = -88.54972737313 | etot = -33.5644508545173 +350000 ekin = 28.4730637357388 | erot = 27.0009502159403 | epot = -89.038464806251 | etot = -33.5644508545719 +351000 ekin = 28.139537848467 | erot = 27.6270646737408 | epot = -89.3310533768684 | etot = -33.5644508546605 +352000 ekin = 27.6929580738718 | erot = 28.1676652362932 | epot = -89.4250741654184 | etot = -33.5644508552534 +353000 ekin = 27.1526950366655 | erot = 28.5958100265632 | epot = -89.3129559197891 | etot = -33.5644508565604 +354000 ekin = 26.5365141387242 | erot = 28.8781341172769 | epot = -88.9790991143028 | etot = -33.5644508583017 +355000 ekin = 25.859879983625 | erot = 28.979303109793 | epot = -88.4036339530082 | etot = -33.5644508595902 +356000 ekin = 25.1375717946349 | erot = 28.8722956886234 | epot = -87.5743183425605 | etot = -33.5644508593022 +357000 ekin = 24.3868741548746 | erot = 28.5495289602174 | epot = -86.5008539717697 | etot = -33.5644508566778 +358000 ekin = 23.6300778926847 | erot = 28.0297879777441 | epot = -85.2243167222827 | etot = -33.5644508518539 +359000 ekin = 22.8939201469121 | erot = 27.3556770360709 | epot = -83.8140480289405 | etot = -33.5644508459575 +360000 ekin = 22.2065780073029 | erot = 26.5834479667625 | epot = -82.3544768140978 | etot = -33.5644508400324 +361000 ekin = 21.5986345635183 | erot = 25.7744654427431 | epot = -80.9375508371388 | etot = -33.5644508308774 +362000 ekin = 21.1083260621098 | erot = 24.989507840873 | epot = -79.6622847318363 | etot = -33.5644508288535 +363000 ekin = 20.7375100619861 | erot = 24.2576398933005 | epot = -78.5596007834792 | etot = -33.5644508281925 +364000 ekin = 20.4760033679782 | erot = 23.5946470164008 | epot = -77.6351012127697 | etot = -33.5644508283907 +365000 ekin = 20.3079089893774 | erot = 23.0095138965374 | epot = -76.8818737148743 | etot = -33.5644508289595 +366000 ekin = 20.2147979336069 | erot = 22.5083719357563 | epot = -76.2876206988662 | etot = -33.564450829503 +367000 ekin = 20.1786185360507 | erot = 22.0973297017962 | epot = -75.8403990676676 | etot = -33.5644508298207 +368000 ekin = 20.1837486799377 | erot = 21.783527063494 | epot = -75.5317265732851 | etot = -33.5644508298534 +369000 ekin = 20.2182310118496 | erot = 21.5747388187329 | epot = -75.3574206602588 | etot = -33.5644508296764 +370000 ekin = 20.2742556079346 | erot = 21.4781104693601 | epot = -75.3168169068273 | etot = -33.5644508295326 +371000 ekin = 20.3477066126786 | erot = 21.4982876397919 | epot = -75.4104450816055 | etot = -33.5644508291351 +372000 ekin = 20.4391769085933 | erot = 21.6370751258538 | epot = -75.6407028633516 | etot = -33.5644508289045 +373000 ekin = 20.5523906694389 | erot = 21.8921389377654 | epot = -76.0089804360871 | etot = -33.5644508288828 +374000 ekin = 20.6947607299073 | erot = 22.2561865203728 | epot = -76.5153980789369 | etot = -33.5644508286568 +375000 ekin = 20.8734352290091 | erot = 22.7176361068752 | epot = -77.1555221653772 | etot = -33.5644508294929 +376000 ekin = 21.0894935045173 | erot = 23.2620769849342 | epot = -77.9160213200335 | etot = -33.564450830582 +377000 ekin = 21.3446674637595 | erot = 23.8720082856019 | epot = -78.7811265808815 | etot = -33.5644508315201 +378000 ekin = 21.6424854229658 | erot = 24.5275644041121 | epot = -79.7345006599212 | etot = -33.5644508328433 +379000 ekin = 21.9906215821683 | erot = 25.2058289792437 | epot = -80.7609013956721 | etot = -33.5644508342601 +380000 ekin = 22.3975872845819 | erot = 25.8799316876613 | epot = -81.8419698101057 | etot = -33.5644508378624 +381000 ekin = 22.8474625365151 | erot = 26.5196756830445 | epot = -82.9315890609908 | etot = -33.5644508414312 +382000 ekin = 23.3214968285656 | erot = 27.0935868815677 | epot = -83.9795345554676 | etot = -33.5644508453342 +383000 ekin = 23.798948647365 | erot = 27.5682880228108 | epot = -84.9316875192928 | etot = -33.564450849117 +384000 ekin = 24.2602946691393 | erot = 27.9101784191673 | epot = -85.7349239406047 | etot = -33.5644508522981 +385000 ekin = 24.6909701695335 | erot = 28.0892515731785 | epot = -86.3446725968127 | etot = -33.5644508541008 +386000 ekin = 25.0758089634755 | erot = 28.0812872789521 | epot = -86.7215471013172 | etot = -33.5644508588896 +387000 ekin = 25.3886917944527 | erot = 27.8683599139988 | epot = -86.8215025663126 | etot = -33.5644508578612 +388000 ekin = 25.6321888109058 | erot = 27.4567876604357 | epot = -86.6534273265843 | etot = -33.5644508552428 +389000 ekin = 25.8173007945418 | erot = 26.8690369421787 | epot = -86.2507885888255 | etot = -33.564450852105 +390000 ekin = 25.9562629244047 | erot = 26.1386991558076 | epot = -85.6594129283773 | etot = -33.5644508481649 +391000 ekin = 26.0625510047816 | erot = 25.3050096520618 | epot = -84.9320115013513 | etot = -33.5644508445078 +392000 ekin = 26.1477279258083 | erot = 24.4077754075857 | epot = -84.1199541748157 | etot = -33.5644508414217 +393000 ekin = 26.2207009125763 | erot = 23.4862823970573 | epot = -83.2714341485498 | etot = -33.5644508389163 +394000 ekin = 26.2880235522712 | erot = 22.5776047858261 | epot = -82.4300791761996 | etot = -33.5644508381023 +395000 ekin = 26.3461327830412 | erot = 21.6992206105417 | epot = -81.6098042309749 | etot = -33.5644508373921 +396000 ekin = 26.3925769143341 | erot = 20.8648963380243 | epot = -80.8219240889404 | etot = -33.564450836582 +397000 ekin = 26.4280357588778 | erot = 20.0875980485136 | epot = -80.0800846429448 | etot = -33.5644508355533 +398000 ekin = 26.4568264159667 | erot = 19.3805747697846 | epot = -79.4018520200129 | etot = -33.5644508342616 +399000 ekin = 26.4863910840118 | erot = 18.7576183808216 | epot = -78.8084602983166 | etot = -33.5644508334833 +400000 ekin = 26.5240355653115 | erot = 18.2309165846171 | epot = -78.3194029820772 | etot = -33.5644508321487 +401000 ekin = 26.5785515874174 | erot = 17.8133011773559 | epot = -77.9563035961333 | etot = -33.56445083136 +402000 ekin = 26.655331687452 | erot = 17.5146324371175 | epot = -77.7344149563074 | etot = -33.564450831738 +403000 ekin = 26.750844144417 | erot = 17.3369800815745 | epot = -77.6522750599618 | etot = -33.5644508339703 +404000 ekin = 26.847889984664 | erot = 17.270366441038 | epot = -77.6827072640007 | etot = -33.5644508382987 +405000 ekin = 26.9136481513682 | erot = 17.290640983477 | epot = -77.7687399796861 | etot = -33.5644508448409 +406000 ekin = 26.9026743980023 | erot = 17.3519919762782 | epot = -77.8191172252627 | etot = -33.5644508509822 +407000 ekin = 26.7697793191984 | erot = 17.4151352559464 | epot = -77.7493654298542 | etot = -33.5644508547094 +408000 ekin = 26.4852107131098 | erot = 17.4599310844412 | epot = -77.50959265223 | etot = -33.564450854679 +409000 ekin = 26.0447937746191 | erot = 17.489715636672 | epot = -77.0989602628005 | etot = -33.5644508515094 +410000 ekin = 25.4686689663916 | erot = 17.525308599911 | epot = -76.5584284132955 | etot = -33.564450846993 +411000 ekin = 24.7901856102895 | erot = 17.5925678633025 | epot = -75.9472043165596 | etot = -33.5644508429676 +412000 ekin = 24.0429450721768 | erot = 17.7112262985626 | epot = -75.3186222110808 | etot = -33.5644508403414 +413000 ekin = 23.2530709441322 | erot = 17.8904894599544 | epot = -74.7080112431157 | etot = -33.5644508390292 +414000 ekin = 22.4380957569814 | erot = 18.1309089880911 | epot = -74.1334555836084 | etot = -33.5644508385359 +415000 ekin = 21.6095002972743 | erot = 18.4284521146042 | epot = -73.6024032502431 | etot = -33.5644508383646 +416000 ekin = 20.7759703154786 | erot = 18.7780315272693 | epot = -73.1184526809416 | etot = -33.5644508381937 +417000 ekin = 19.9459219944617 | erot = 19.1754390644637 | epot = -72.6858118967971 | etot = -33.5644508378717 +418000 ekin = 19.1290603144219 | erot = 19.6178812357862 | epot = -72.3113923875522 | etot = -33.5644508373441 +419000 ekin = 18.337241174533 | erot = 20.1037315121921 | epot = -72.005423523335 | etot = -33.5644508366099 +420000 ekin = 17.5848708565925 | erot = 20.6319495843217 | epot = -71.7812712766207 | etot = -33.5644508357065 +421000 ekin = 16.8888669765948 | erot = 21.2012508781818 | epot = -71.654568689525 | etot = -33.5644508347484 +422000 ekin = 16.2680311852926 | erot = 21.8088345392229 | epot = -71.6413165584697 | etot = -33.5644508339541 +423000 ekin = 15.7416423465874 | erot = 22.4484657015901 | epot = -71.754558881829 | etot = -33.5644508336516 +424000 ekin = 15.3271568809885 | erot = 23.1079611163195 | epot = -71.9995688315673 | etot = -33.5644508342592 +425000 ekin = 15.0370245442154 | erot = 23.7664993129421 | epot = -72.3679746933712 | etot = -33.5644508362137 +426000 ekin = 14.8748792452246 | erot = 24.3924933232269 | epot = -72.8318234082835 | etot = -33.564450839832 +427000 ekin = 14.8320398098318 | erot = 24.9432466996428 | epot = -73.3397373544817 | etot = -33.5644508450071 +428000 ekin = 14.8863924965225 | erot = 25.3682827942598 | epot = -73.8191261416323 | etot = -33.56445085085 +429000 ekin = 15.0062259694751 | erot = 25.6182665545283 | epot = -74.1889433796421 | etot = -33.5644508556387 +430000 ekin = 15.1595389321474 | erot = 25.6590201133498 | epot = -74.3830099030104 | etot = -33.5644508575131 +431000 ekin = 15.3249133699162 | erot = 25.4851984009302 | epot = -74.3745626264769 | etot = -33.5644508556305 +432000 ekin = 15.4974987577243 | erot = 25.1253113467255 | epot = -74.1872609552084 | etot = -33.5644508507585 +433000 ekin = 15.6867402477162 | erot = 24.6339851580146 | epot = -73.8851762504474 | etot = -33.5644508447166 +434000 ekin = 15.908478952494 | erot = 24.0759117528824 | epot = -73.5488415446164 | etot = -33.56445083924 +435000 ekin = 16.1769022059532 | erot = 23.5103596607956 | epot = -73.2517127020391 | etot = -33.5644508352903 +436000 ekin = 16.4997173059431 | erot = 22.9822765166324 | epot = -73.0464446556921 | etot = -33.5644508331166 +437000 ekin = 16.8769806268047 | erot = 22.5199344327298 | epot = -72.9613658919567 | etot = -33.5644508324222 +438000 ekin = 17.3021259571554 | erot = 22.1372453983087 | epot = -73.0038221882772 | etot = -33.5644508328131 +439000 ekin = 17.7637229039241 | erot = 21.8373393625943 | epot = -73.1655131004615 | etot = -33.5644508339431 +440000 ekin = 18.2471223979911 | erot = 21.6157595595468 | epot = -73.4273327930896 | etot = -33.5644508355518 +441000 ekin = 18.7357201395364 | erot = 21.4628710845581 | epot = -73.7630420615727 | etot = -33.5644508374783 +442000 ekin = 19.2118878212778 | erot = 21.365451542122 | epot = -74.1417902029878 | etot = -33.564450839588 +443000 ekin = 19.6577318124694 | erot = 21.3079015376941 | epot = -74.530084191929 | etot = -33.5644508417655 +444000 ekin = 20.0558238633166 | erot = 21.2733344148721 | epot = -74.8936091220801 | etot = -33.5644508438914 +445000 ekin = 20.389989391221 | erot = 21.2445884062662 | epot = -75.1990286433164 | etot = -33.5644508458292 +446000 ekin = 20.6461236043855 | erot = 21.2052857367663 | epot = -75.41586018866 | etot = -33.5644508475082 +447000 ekin = 20.8131102287267 | erot = 21.1405154512044 | epot = -75.5180765280277 | etot = -33.5644508480966 +448000 ekin = 20.8836321565114 | erot = 21.0415726580595 | epot = -75.4896556635799 | etot = -33.5644508490089 +449000 ekin = 20.8549766396171 | erot = 20.9006105485411 | epot = -75.3200380376018 | etot = -33.5644508494435 +450000 ekin = 20.7289995988534 | erot = 20.7094982244521 | epot = -75.0029486726748 | etot = -33.5644508493693 +451000 ekin = 20.5121237020311 | erot = 20.4634057687252 | epot = -74.5399803195251 | etot = -33.5644508487688 +452000 ekin = 20.2152499007445 | erot = 20.1611428754572 | epot = -73.9408436238401 | etot = -33.5644508476384 +453000 ekin = 19.8534700764778 | erot = 19.8054562088345 | epot = -73.2233771313103 | etot = -33.564450845998 +454000 ekin = 19.4456214291213 | erot = 19.4031472753593 | epot = -72.4132195483806 | etot = -33.5644508439 +455000 ekin = 19.0137205227782 | erot = 18.964872313207 | epot = -71.5430436774017 | etot = -33.5644508414165 +456000 ekin = 18.5823093299359 | erot = 18.5046119868878 | epot = -70.6513721554908 | etot = -33.5644508386671 +457000 ekin = 18.1775784949196 | erot = 18.0385547552735 | epot = -69.7805840860522 | etot = -33.5644508358591 +458000 ekin = 17.8262193052027 | erot = 17.5834820270569 | epot = -68.9741521652289 | etot = -33.5644508329693 +459000 ekin = 17.5544328314126 | erot = 17.1574115033566 | epot = -68.2762951651265 | etot = -33.5644508303572 +460000 ekin = 17.3857834993165 | erot = 16.7769882364293 | epot = -67.7272225639932 | etot = -33.5644508282474 +461000 ekin = 17.3389537756698 | erot = 16.4559737247112 | epot = -67.3593783272464 | etot = -33.5644508268654 +462000 ekin = 17.4254421541111 | erot = 16.2041333991429 | epot = -67.1940263796471 | etot = -33.5644508263932 +463000 ekin = 17.6475549837678 | erot = 16.0264214062831 | epot = -67.2384272169901 | etot = -33.5644508269392 +464000 ekin = 17.9971528391479 | erot = 15.9226257282762 | epot = -67.4842293959134 | etot = -33.5644508284893 +465000 ekin = 18.4555654855751 | erot = 15.8876205731988 | epot = -67.9076368896734 | etot = -33.5644508308995 +466000 ekin = 18.9948338162462 | erot = 15.9122553307032 | epot = -68.4715399808675 | etot = -33.5644508339181 +467000 ekin = 19.5800987880483 | erot = 15.9847161183743 | epot = -69.1292657436643 | etot = -33.5644508372418 +468000 ekin = 20.1726645576182 | erot = 16.0920334747517 | epot = -69.8291488729546 | etot = -33.5644508405847 +469000 ekin = 20.7331520538985 | erot = 16.2213910259127 | epot = -70.5189939235296 | etot = -33.5644508437184 +470000 ekin = 21.2242791251678 | erot = 16.3610502014337 | epot = -71.1497801730816 | etot = -33.5644508464802 +471000 ekin = 21.6130740294769 | erot = 16.5009517691198 | epot = -71.6784766473461 | etot = -33.5644508487495 +472000 ekin = 21.8725913830144 | erot = 16.6332178545353 | epot = -72.0702600879624 | etot = -33.5644508504127 +473000 ekin = 21.9833185471274 | erot = 16.7527436323183 | epot = -72.3005130308005 | etot = -33.5644508513548 +474000 ekin = 21.9344099205846 | erot = 16.8578720764489 | epot = -72.3567328485068 | etot = -33.5644508514733 +475000 ekin = 21.7247480853885 | erot = 16.9509439425814 | epot = -72.2401428786726 | etot = -33.5644508507026 +476000 ekin = 21.3637036554054 | erot = 17.0384540155504 | epot = -71.9666085200057 | etot = -33.5644508490499 +477000 ekin = 20.8713853162837 | erot = 17.130593864283 | epot = -71.5664300271643 | etot = -33.5644508465976 +478000 ekin = 20.2781056158348 | erot = 17.2401904856494 | epot = -71.082746945061 | etot = -33.5644508435769 +479000 ekin = 19.6228148922352 | erot = 17.3807417057109 | epot = -70.568007438244 | etot = -33.5644508402978 +480000 ekin = 18.9501924819871 | erot = 17.5641098023629 | epot = -70.078753121549 | etot = -33.5644508371989 +481000 ekin = 18.3063999207698 | erot = 17.7978626900194 | epot = -69.6687134455753 | etot = -33.5644508347861 +482000 ekin = 17.7338800308527 | erot = 18.0826185787009 | epot = -69.3809494430906 | etot = -33.564450833537 +483000 ekin = 17.2661333869729 | erot = 18.4098565340996 | epot = -69.2404407548555 | etot = -33.564450833783 +484000 ekin = 16.9123469726303 | erot = 18.5839236848227 | epot = -69.0607216150868 | etot = -33.5644509576338 +485000 ekin = 17.2473052119872 | erot = 17.4463141948379 | epot = -68.2580700315476 | etot = -33.5644506247225 +486000 ekin = 18.3155143093133 | erot = 17.18327309766 | epot = -69.0632384227249 | etot = -33.5644510157516 +487000 ekin = 18.1324826615341 | erot = 17.2801627137401 | epot = -68.9770961534278 | etot = -33.5644507781536 +488000 ekin = 18.0650666711476 | erot = 17.4264266856646 | epot = -69.0559441348375 | etot = -33.5644507780252 +489000 ekin = 18.1230207573334 | erot = 17.6201369927127 | epot = -69.3076085291276 | etot = -33.5644507790815 +490000 ekin = 18.2959502061969 | erot = 17.8551924365584 | epot = -69.7155934235351 | etot = -33.5644507807797 +491000 ekin = 18.5602651981851 | erot = 18.1239992625136 | epot = -70.2487152441586 | etot = -33.5644507834599 +492000 ekin = 18.8855238701042 | erot = 18.4159985148053 | epot = -70.8659731705823 | etot = -33.5644507856728 +493000 ekin = 19.2395352567771 | erot = 18.728264479211 | epot = -71.5322505229547 | etot = -33.5644507869666 +494000 ekin = 19.5921246703129 | erot = 19.0689157919769 | epot = -72.2254912502075 | etot = -33.5644507879177 +495000 ekin = 19.0728202099565 | erot = 18.9158482412593 | epot = -71.5531189784044 | etot = -33.5644505271886 +496000 ekin = 19.8797920560791 | erot = 18.7380967908761 | epot = -72.1823393790591 | etot = -33.564450532104 +497000 ekin = 21.3129327568523 | erot = 19.22085969099 | epot = -74.0982428020236 | etot = -33.5644503541812 +498000 ekin = 21.3264694813384 | erot = 19.7980335585312 | epot = -74.6889533938341 | etot = -33.5644503539645 +499000 ekin = 21.2778907743885 | erot = 20.4793064457547 | epot = -75.3216475744249 | etot = -33.5644503542817 +500000 ekin = 21.1661916284258 | erot = 21.258178122324 | epot = -75.9888201058597 | etot = -33.5644503551099 +501000 ekin = 20.9926825376647 | erot = 22.1178388254974 | epot = -76.6749717196181 | etot = -33.564450356456 +502000 ekin = 20.7610606942179 | erot = 23.0317414652511 | epot = -77.3572525175369 | etot = -33.5644503580679 +503000 ekin = 20.4798770188891 | erot = 23.9650377706427 | epot = -78.0093651496444 | etot = -33.5644503601125 +504000 ekin = 20.1546807720134 | erot = 24.8789199644612 | epot = -78.5980510988455 | etot = -33.5644503623709 +505000 ekin = 19.7897861053101 | erot = 25.7326258922808 | epot = -79.0868623624028 | etot = -33.5644503648119 +506000 ekin = 19.3875459003948 | erot = 26.488233736964 | epot = -79.4402300037047 | etot = -33.5644503663459 +507000 ekin = 18.9527707504281 | erot = 27.1161379583516 | epot = -79.6333590755957 | etot = -33.564450366816 +508000 ekin = 18.4930541128453 | erot = 27.6003825989619 | epot = -79.6578870777028 | etot = -33.5644503658955 +509000 ekin = 18.0182547167277 | erot = 27.9414911094103 | epot = -79.5241961902249 | etot = -33.5644503640869 +510000 ekin = 17.523965944791 | erot = 28.1499521522236 | epot = -79.2383684583665 | etot = -33.564450361352 +511000 ekin = 17.0202767589766 | erot = 28.2490270329564 | epot = -78.8337541500052 | etot = -33.5644503580722 +512000 ekin = 16.524571800827 | erot = 28.2698315418588 | epot = -78.3588536975498 | etot = -33.564450354864 +513000 ekin = 16.0539184298501 | erot = 28.2435719404605 | epot = -77.8619407225297 | etot = -33.564450352219 +514000 ekin = 15.622953975357 | erot = 28.1963871949976 | epot = -77.3837915207595 | etot = -33.5644503504049 +515000 ekin = 15.2424792422371 | erot = 28.1464443104744 | epot = -76.953373902264 | etot = -33.5644503495525 +516000 ekin = 14.9188926058558 | erot = 28.1027540351543 | epot = -76.5860969904231 | etot = -33.564450349413 +517000 ekin = 14.6543809153874 | erot = 28.0678237289542 | epot = -76.2866549941532 | etot = -33.5644503498116 +518000 ekin = 14.4476572457691 | erot = 28.0395642673969 | epot = -76.0516718636457 | etot = -33.5644503504797 +519000 ekin = 14.2950490441428 | erot = 28.0138489407524 | epot = -75.8733483360399 | etot = -33.5644503511447 +520000 ekin = 14.1917488338634 | erot = 27.9870813582064 | epot = -75.7432805436532 | etot = -33.5644503515833 +521000 ekin = 14.1329830511805 | erot = 27.9581295476446 | epot = -75.6555629505058 | etot = -33.5644503516806 +522000 ekin = 14.1002586404053 | erot = 27.7732671759151 | epot = -75.4379761959062 | etot = -33.5644503795858 +523000 ekin = 14.1969588162511 | erot = 27.1027118573523 | epot = -74.8641209744559 | etot = -33.5644503008525 +524000 ekin = 14.7378402619219 | erot = 26.6164089140764 | epot = -74.9186994724817 | etot = -33.5644502964834 +525000 ekin = 15.5068672854449 | erot = 26.5883544531684 | epot = -75.6596721109621 | etot = -33.5644503723487 +526000 ekin = 15.8574449977267 | erot = 26.6724957236415 | epot = -76.0943910939928 | etot = -33.5644503726246 +527000 ekin = 16.0112069682283 | erot = 26.7355098948156 | epot = -76.311167236341 | etot = -33.5644503732972 +528000 ekin = 16.1641744090515 | erot = 26.7947978809934 | epot = -76.5234226639649 | etot = -33.5644503739199 +529000 ekin = 16.3159009760756 | erot = 26.8380825379191 | epot = -76.7184338883076 | etot = -33.5644503743128 +530000 ekin = 16.466747721028 | erot = 26.8553312024403 | epot = -76.886529297879 | etot = -33.5644503744108 +531000 ekin = 16.6177352354996 | erot = 26.8400251084993 | epot = -77.022210718254 | etot = -33.564450374255 +532000 ekin = 16.7702150675957 | erot = 26.7891084872752 | epot = -77.1237739287798 | etot = -33.5644503739089 +533000 ekin = 16.9253640366974 | erot = 26.7024973872853 | epot = -77.1923117974439 | etot = -33.5644503734612 +534000 ekin = 17.0836447866564 | erot = 26.5822176528732 | epot = -77.230312812567 | etot = -33.5644503730375 +535000 ekin = 17.2444487915268 | erot = 26.4310079588786 | epot = -77.2399071231478 | etot = -33.5644503727425 +536000 ekin = 17.4060591053815 | erot = 26.2510049057206 | epot = -77.2215143837103 | etot = -33.5644503726081 +537000 ekin = 17.5658991981726 | erot = 26.0431264909246 | epot = -77.1734760616575 | etot = -33.5644503725604 +538000 ekin = 17.7209415436652 | erot = 25.8074441218956 | epot = -77.0928360381795 | etot = -33.5644503726186 +539000 ekin = 17.8681497078889 | erot = 25.5433035299955 | epot = -76.9759036105368 | etot = -33.5644503726524 +540000 ekin = 18.004863156336 | erot = 25.2502517039518 | epot = -76.8195652328856 | etot = -33.5644503725978 +541000 ekin = 18.129064826942 | erot = 24.9288645878186 | epot = -76.6223797871797 | etot = -33.564450372419 +542000 ekin = 18.2395164936781 | erot = 24.5811691616713 | epot = -76.3851360274362 | etot = -33.5644503720867 +543000 ekin = 18.335770007785 | erot = 24.2108468343436 | epot = -76.1110672137948 | etot = -33.5644503716662 +544000 ekin = 18.4180615071781 | erot = 23.8229131244954 | epot = -75.805425002847 | etot = -33.5644503711735 +545000 ekin = 18.4870901297785 | erot = 23.4236993424443 | epot = -75.4752398423761 | etot = -33.5644503701532 +546000 ekin = 18.54361047059 | erot = 23.0232726205026 | epot = -75.1313334608523 | etot = -33.5644503697597 +547000 ekin = 18.5881260725922 | erot = 22.6282216103021 | epot = -74.7807980523833 | etot = -33.564450369489 +548000 ekin = 18.6206521537359 | erot = 22.2431161970553 | epot = -74.4282187197494 | etot = -33.5644503689582 +549000 ekin = 18.6395328550285 | erot = 21.8731131588192 | epot = -74.0770963831711 | etot = -33.5644503693234 +550000 ekin = 18.6420012523706 | erot = 21.5194517196355 | epot = -73.7259033419334 | etot = -33.5644503699273 +551000 ekin = 18.624921029005 | erot = 21.1784779029538 | epot = -73.3678493026868 | etot = -33.564450370728 +552000 ekin = 18.5841928766033 | erot = 20.8452278496576 | epot = -72.9938710978566 | etot = -33.5644503715957 +553000 ekin = 18.5152127054113 | erot = 20.5148731369798 | epot = -72.5945362147189 | etot = -33.5644503723278 +554000 ekin = 18.4136816906652 | erot = 20.1848933332903 | epot = -72.1630253966383 | etot = -33.5644503726828 +555000 ekin = 18.2766906397711 | erot = 19.8574769328349 | epot = -71.6986179450508 | etot = -33.5644503724447 +556000 ekin = 18.1040115045293 | erot = 19.5406874738217 | epot = -71.2091493500419 | etot = -33.5644503716909 +557000 ekin = 17.89923096435 | erot = 19.24972262904 | epot = -70.7134039633246 | etot = -33.5644503699346 +558000 ekin = 17.6705778370294 | erot = 19.0080857255953 | epot = -70.2431139301013 | etot = -33.5644503674766 +559000 ekin = 17.4315653923217 | erot = 18.8444628125886 | epot = -69.8404785693936 | etot = -33.5644503644833 +560000 ekin = 17.2006230343926 | erot = 18.7901643785407 | epot = -69.5552377742619 | etot = -33.5644503613287 +561000 ekin = 16.9995569155364 | erot = 18.8749610240394 | epot = -69.4389682979995 | etot = -33.5644503584237 +562000 ekin = 16.8505251054351 | erot = 19.1232120103355 | epot = -69.5381874720851 | etot = -33.5644503563145 +563000 ekin = 16.771816019379 | erot = 19.5498137338075 | epot = -69.8860801087492 | etot = -33.5644503555627 +564000 ekin = 16.7730284247952 | erot = 20.1561760614947 | epot = -70.4936548432322 | etot = -33.5644503569423 +565000 ekin = 16.8503463811215 | erot = 20.9261148984733 | epot = -71.3409116397428 | etot = -33.564450360148 +566000 ekin = 16.9881817946884 | erot = 21.8252877511548 | epot = -72.3779199111064 | etot = -33.5644503652632 +567000 ekin = 17.1597730186738 | erot = 22.8021750342622 | epot = -73.5263984248048 | etot = -33.5644503718688 +568000 ekin = 17.3309908958581 | erot = 23.7909429899681 | epot = -74.6863842651206 | etot = -33.5644503792944 +569000 ekin = 17.4658946009928 | erot = 24.7167318454134 | epot = -75.7470768330927 | etot = -33.5644503866865 +570000 ekin = 17.5327796649247 | erot = 25.503072445778 | epot = -76.60030250379 | etot = -33.5644503930873 +571000 ekin = 17.5098280193733 | erot = 26.0808668138774 | epot = -77.1551452308085 | etot = -33.5644503975578 +572000 ekin = 17.3896134292035 | erot = 26.3976580233915 | epot = -77.3517218519472 | etot = -33.5644503993522 +573000 ekin = 17.1817696514795 | erot = 26.4252545064828 | epot = -77.1714745560827 | etot = -33.5644503981204 +574000 ekin = 16.91320121502 | erot = 26.1636856783704 | epot = -76.6413372874423 | etot = -33.5644503940519 +575000 ekin = 16.6253831475483 | erot = 25.640183136325 | epot = -75.8300166717811 | etot = -33.5644503879079 +576000 ekin = 16.3805854482806 | erot = 24.9437607565116 | epot = -74.8887965735951 | etot = -33.5644503688028 +577000 ekin = 16.23092958843 | erot = 24.1552332193367 | epot = -73.950613173759 | etot = -33.5644503659923 +578000 ekin = 16.2003426787873 | erot = 23.2996785345128 | epot = -73.0644715773449 | etot = -33.5644503640447 +579000 ekin = 16.298393825657 | erot = 22.4032685645682 | epot = -72.2661127534473 | etot = -33.5644503632221 +580000 ekin = 16.5164282813868 | erot = 21.4889399507426 | epot = -71.569818597847 | etot = -33.5644503657176 +581000 ekin = 16.829413172556 | erot = 20.5770732256226 | epot = -70.9709367637454 | etot = -33.5644503655668 +582000 ekin = 17.2014342862117 | erot = 19.7085617425621 | epot = -70.4744463946194 | etot = -33.5644503658456 +583000 ekin = 17.5894541375884 | erot = 18.925166774833 | epot = -70.0790712785306 | etot = -33.5644503661092 +584000 ekin = 17.9521233668095 | erot = 18.2657373647565 | epot = -69.7823110976562 | etot = -33.5644503660902 +585000 ekin = 18.2577014581518 | erot = 17.762756656003 | epot = -69.5849084798605 | etot = -33.5644503657057 +586000 ekin = 18.48903732181 | erot = 17.4391816026807 | epot = -69.4926692894528 | etot = -33.5644503649621 +587000 ekin = 18.6451700995223 | erot = 17.3070654480135 | epot = -69.5166859114209 | etot = -33.5644503638852 +588000 ekin = 18.7400423387256 | erot = 17.3682960794961 | epot = -69.6727887807878 | etot = -33.5644503625662 +589000 ekin = 18.7988289994632 | erot = 17.6163757903472 | epot = -69.9796551510921 | etot = -33.5644503612817 +590000 ekin = 18.8521852510563 | erot = 18.03770774159 | epot = -70.4543433531448 | etot = -33.5644503604985 +591000 ekin = 18.9335216732476 | erot = 18.6145318736687 | epot = -71.1125039063923 | etot = -33.564450359476 +592000 ekin = 19.0736372364623 | erot = 19.3273958984734 | epot = -71.9654834953563 | etot = -33.5644503604206 +593000 ekin = 19.2836835994718 | erot = 20.1464047122411 | epot = -72.9945386745438 | etot = -33.5644503628309 +594000 ekin = 19.5596584178685 | erot = 21.034123237208 | epot = -74.1582320215033 | etot = -33.5644503664268 +595000 ekin = 19.8847224284612 | erot = 21.9477887873151 | epot = -75.3969615864514 | etot = -33.5644503706751 +596000 ekin = 20.2229995975395 | erot = 22.8321032475601 | epot = -76.6195532302897 | etot = -33.56445038519 +597000 ekin = 20.5134057742179 | erot = 23.6125551256778 | epot = -77.6904112894541 | etot = -33.5644503895585 +598000 ekin = 20.7238255182392 | erot = 24.2466753984176 | epot = -78.5349513088604 | etot = -33.5644503922037 +599000 ekin = 20.8326105236303 | erot = 24.7094660554427 | epot = -79.1065269720019 | etot = -33.5644503929288 +600000 ekin = 20.828192883276 | erot = 24.9942677722285 | epot = -79.3869110474472 | etot = -33.5644503919427 +601000 ekin = 20.7081769096798 | erot = 25.11085155755 | epot = -79.3834788569396 | etot = -33.5644503897098 +602000 ekin = 20.4770754640505 | erot = 25.0812117058382 | epot = -79.1227375566785 | etot = -33.5644503867898 +603000 ekin = 20.1436196141802 | erot = 24.9343592764579 | epot = -78.6424292743164 | etot = -33.5644503836784 +604000 ekin = 19.7184185863195 | erot = 24.7015463486128 | epot = -77.9844153156502 | etot = -33.564450380718 +605000 ekin = 19.2123955082262 | erot = 24.4128183898753 | epot = -77.1896642761826 | etot = -33.5644503780811 +606000 ekin = 18.6360571566313 | erot = 24.0951290260324 | epot = -76.2956365584618 | etot = -33.5644503757982 +607000 ekin = 17.9994317314224 | erot = 23.7717793956126 | epot = -75.3356615008433 | etot = -33.5644503738083 +608000 ekin = 17.3124228754604 | erot = 23.4627525846719 | epot = -74.3396258321416 | etot = -33.5644503720093 +609000 ekin = 16.5853412867629 | erot = 23.1855122472229 | epot = -73.3353039042776 | etot = -33.5644503702918 +610000 ekin = 15.8294285553984 | erot = 22.9559130653051 | epot = -72.3497919892683 | etot = -33.5644503685648 +611000 ekin = 15.0572484571768 | erot = 22.7889597199825 | epot = -71.4106585439383 | etot = -33.564450366779 +612000 ekin = 14.2829782528012 | erot = 22.6991649591093 | epot = -70.5465935768327 | etot = -33.5644503649222 +613000 ekin = 13.5233158611292 | erot = 22.7018063026035 | epot = -69.7895725256479 | etot = -33.5644503619153 +614000 ekin = 12.7974443556917 | erot = 22.8128628316047 | epot = -69.1747575476346 | etot = -33.5644503603383 +615000 ekin = 12.1222485232213 | erot = 23.0409824252133 | epot = -68.7276813075076 | etot = -33.564450359073 +616000 ekin = 11.5143476718002 | erot = 23.3894333501644 | epot = -68.4682313804871 | etot = -33.5644503585225 +617000 ekin = 10.9895105321831 | erot = 23.8529820636908 | epot = -68.4069429545483 | etot = -33.5644503586744 +618000 ekin = 10.5621427379082 | erot = 24.4166592376929 | epot = -68.5432523353739 | etot = -33.5644503597728 +619000 ekin = 10.2447233168846 | erot = 25.0539361238965 | epot = -68.8631098026496 | etot = -33.5644503618684 +620000 ekin = 10.0473729681852 | erot = 25.726395813846 | epot = -69.3382191468432 | etot = -33.564450364812 +621000 ekin = 9.97770919335943 | erot = 26.3860294543558 | epot = -69.9281890159394 | etot = -33.5644503682242 +622000 ekin = 10.0410058293406 | erot = 26.9805251338807 | epot = -70.5859813347549 | etot = -33.5644503715336 +623000 ekin = 10.2405907646719 | erot = 27.4608678071822 | epot = -71.2659089459993 | etot = -33.5644503741453 +624000 ekin = 10.5781077609575 | erot = 27.789174960007 | epot = -71.9317330966645 | etot = -33.5644503757 +625000 ekin = 11.0534790497405 | erot = 27.9443540028375 | epot = -72.5622834286287 | etot = -33.5644503760506 +626000 ekin = 11.6650239614417 | erot = 27.9236660631623 | epot = -73.1531404000459 | etot = -33.5644503754418 +627000 ekin = 12.4090657081618 | erot = 27.7401487508296 | epot = -73.713664833205 | etot = -33.5644503742135 +628000 ekin = 13.2797303336247 | erot = 27.4180442690277 | epot = -74.2622249753901 | etot = -33.5644503727378 +629000 ekin = 14.2227247808597 | erot = 26.9288523652634 | epot = -74.7160277925057 | etot = -33.5644506463826 +630000 ekin = 14.6371369646358 | erot = 25.6849986217032 | epot = -73.8865860618273 | etot = -33.5644504754884 +631000 ekin = 15.1932748232492 | erot = 24.8015291118369 | epot = -73.5592542921839 | etot = -33.5644503570978 +632000 ekin = 16.5842231811831 | erot = 25.1927867337753 | epot = -75.3414603985266 | etot = -33.5644504835681 +633000 ekin = 18.1129981057209 | erot = 25.8399990860739 | epot = -77.5174478422231 | etot = -33.5644506504283 +634000 ekin = 19.1483265833795 | erot = 25.7387528538212 | epot = -78.4515299869786 | etot = -33.5644505497779 +635000 ekin = 20.1638306083842 | erot = 25.6154971451023 | epot = -79.3437783074232 | etot = -33.5644505539367 +636000 ekin = 21.1529452192774 | erot = 25.4927802227977 | epot = -80.210176001065 | etot = -33.5644505589899 +637000 ekin = 22.0768404119804 | erot = 25.3376757556836 | epot = -80.9789667313978 | etot = -33.5644505637338 +638000 ekin = 22.8998086493368 | erot = 25.1175243540521 | epot = -81.581783570336 | etot = -33.5644505669471 +639000 ekin = 23.5958452405688 | erot = 24.8103240278057 | epot = -81.9706198363764 | etot = -33.5644505680019 +640000 ekin = 24.1448393944085 | erot = 24.4104070782069 | epot = -82.1196970406963 | etot = -33.5644505680809 +641000 ekin = 24.5337741515846 | erot = 23.9290519078285 | epot = -82.0272766241422 | etot = -33.5644505647291 +642000 ekin = 24.7698696442131 | erot = 23.3958020420911 | epot = -81.7301222479835 | etot = -33.5644505616793 +643000 ekin = 24.8669267979412 | erot = 22.8392829414695 | epot = -81.2706602981471 | etot = -33.5644505587364 +644000 ekin = 24.8431155053321 | erot = 22.2830723087654 | epot = -80.6906383703371 | etot = -33.5644505562396 +645000 ekin = 24.7193046979064 | erot = 21.7428697630937 | epot = -80.0266250151886 | etot = -33.5644505541885 +646000 ekin = 24.5180931831024 | erot = 21.2270132553 | epot = -79.3095569908572 | etot = -33.5644505524548 +647000 ekin = 24.2628521138149 | erot = 20.7388201346271 | epot = -78.5661227994122 | etot = -33.5644505509702 +648000 ekin = 23.9761808148133 | erot = 20.2787945273933 | epot = -77.8194258919934 | etot = -33.5644505497868 +649000 ekin = 23.6778736566609 | erot = 19.8458221794067 | epot = -77.0881463850653 | etot = -33.5644505489977 +650000 ekin = 23.3831896156548 | erot = 19.4375683305137 | epot = -76.3852084947824 | etot = -33.5644505486139 +651000 ekin = 23.1045251412741 | erot = 19.0455994386574 | epot = -75.7145751292058 | etot = -33.5644505492743 +652000 ekin = 22.8525540925228 | erot = 18.6600582438882 | epot = -75.0770628853385 | etot = -33.5644505489275 +653000 ekin = 22.6343633058236 | erot = 18.2797742485017 | epot = -74.4785881025892 | etot = -33.564450548264 +654000 ekin = 22.4577061635195 | erot = 17.9066943674651 | epot = -73.9288510781073 | etot = -33.5644505471227 +655000 ekin = 22.3323244924946 | erot = 17.5466477594773 | epot = -73.4434227975466 | etot = -33.5644505455747 +656000 ekin = 22.2694639419047 | erot = 17.2090068004228 | epot = -73.0429212862265 | etot = -33.5644505438989 +657000 ekin = 22.2796962966157 | erot = 16.9050137467998 | epot = -72.7491605859738 | etot = -33.5644505425584 +658000 ekin = 22.369639071293 | erot = 16.6447644948982 | epot = -72.5788541082823 | etot = -33.5644505420911 +659000 ekin = 22.5385894789304 | erot = 16.4332539533158 | epot = -72.5362939752044 | etot = -33.5644505429582 +660000 ekin = 22.7761662594052 | erot = 16.2664693850933 | epot = -72.6070861898631 | etot = -33.5644505453646 +661000 ekin = 23.0623022457157 | erot = 16.1290340495213 | epot = -72.7557868419576 | etot = -33.5644505467205 +662000 ekin = 23.3837240382632 | erot = 15.9907831573615 | epot = -72.9389579063317 | etot = -33.564450710707 +663000 ekin = 23.054148007274 | erot = 16.1177804827538 | epot = -72.7363790499092 | etot = -33.5644505598814 +664000 ekin = 22.9781515350229 | erot = 16.5698259294712 | epot = -73.112428112566 | etot = -33.5644506480719 +665000 ekin = 23.3749786895457 | erot = 16.411782739857 | epot = -73.3512119977732 | etot = -33.5644505683704 +666000 ekin = 23.723950183745 | erot = 16.0357448193694 | epot = -73.3241455698056 | etot = -33.5644505666911 +667000 ekin = 24.0215049432174 | erot = 15.6311856367398 | epot = -73.2171411428858 | etot = -33.5644505629285 +668000 ekin = 24.2720292261732 | erot = 15.2431977236565 | epot = -73.0796775091056 | etot = -33.5644505592759 +669000 ekin = 24.4823401830215 | erot = 14.9164487057936 | epot = -72.9632394451725 | etot = -33.5644505563574 +670000 ekin = 24.6591929157758 | erot = 14.6865199575477 | epot = -72.9101634276307 | etot = -33.5644505543073 +671000 ekin = 24.7891522537242 | erot = 14.5781166474215 | epot = -72.9317194571598 | etot = -33.5644505560141 +672000 ekin = 24.8512867490322 | erot = 14.6015183441379 | epot = -73.0172556484841 | etot = -33.564450555314 +673000 ekin = 24.8569569351995 | erot = 14.7562217139438 | epot = -73.1776292037397 | etot = -33.5644505545965 +674000 ekin = 24.8222537578926 | erot = 15.0373554089786 | epot = -73.4240597206982 | etot = -33.564450553827 +675000 ekin = 24.7663204261064 | erot = 15.4372951197778 | epot = -73.7680660991378 | etot = -33.5644505532536 +676000 ekin = 24.7079731413268 | erot = 15.9453732717859 | epot = -74.217796966472 | etot = -33.5644505533592 +677000 ekin = 24.6606038390545 | erot = 16.5455776363011 | epot = -74.7706320301637 | etot = -33.5644505548081 +678000 ekin = 24.6267378751708 | erot = 17.2129758022366 | epot = -75.4041642354332 | etot = -33.5644505580258 +679000 ekin = 24.5940505555973 | erot = 17.9117017671719 | epot = -76.0702028857369 | etot = -33.5644505629677 +680000 ekin = 24.5356055102642 | erot = 18.5957689118677 | epot = -76.6958249909574 | etot = -33.5644505688256 +681000 ekin = 24.4156570901708 | erot = 19.2149559866325 | epot = -77.1950636509461 | etot = -33.5644505741429 +682000 ekin = 24.1989519856416 | erot = 19.7242966851149 | epot = -77.487699248418 | etot = -33.5644505776614 +683000 ekin = 23.8604728484841 | erot = 20.0938581680861 | epot = -77.5187815945976 | etot = -33.5644505780274 +684000 ekin = 23.3975557793202 | erot = 20.3180971821174 | epot = -77.2801035368968 | etot = -33.5644505754592 +685000 ekin = 22.8290459842939 | erot = 20.4129669401602 | epot = -76.8064634953545 | etot = -33.5644505709004 +686000 ekin = 22.1833688830902 | erot = 20.3969948298234 | epot = -76.1448143090756 | etot = -33.564450596162 +687000 ekin = 21.4529188825682 | erot = 20.1567338484389 | epot = -75.1741032961385 | etot = -33.5644505651314 +688000 ekin = 20.8420414150976 | erot = 19.8330340944162 | epot = -74.2395260509536 | etot = -33.5644505414398 +689000 ekin = 20.485045480985 | erot = 19.6177759067974 | epot = -73.667271944758 | etot = -33.5644505569757 +690000 ekin = 20.22367052676 | erot = 19.4736760217004 | epot = -73.2617971257719 | etot = -33.5644505773115 +691000 ekin = 19.9277329716986 | erot = 19.3525548976992 | epot = -72.8447384077161 | etot = -33.5644505383183 +692000 ekin = 19.7615779528863 | erot = 19.3271485942255 | epot = -72.6531770849096 | etot = -33.5644505377978 +693000 ekin = 19.7317397131701 | erot = 19.4147876349782 | epot = -72.7109778869691 | etot = -33.5644505388208 +694000 ekin = 19.8186070325659 | erot = 19.6208277623457 | epot = -73.0038853361764 | etot = -33.5644505412647 +695000 ekin = 19.9894250230478 | erot = 19.941877147877 | epot = -73.4957527156739 | etot = -33.5644505447491 +696000 ekin = 20.2029739943976 | erot = 20.3669312863332 | epot = -74.1343558293723 | etot = -33.5644505486415 +697000 ekin = 20.4154400727664 | erot = 20.880919300581 | epot = -74.8608099257857 | etot = -33.5644505524382 +698000 ekin = 20.5862067302191 | erot = 21.4669039242718 | epot = -75.6175612102066 | etot = -33.5644505557157 +699000 ekin = 20.6825995314592 | erot = 22.1076466744899 | epot = -76.3546967641855 | etot = -33.5644505582364 +700000 ekin = 20.6830084841778 | erot = 22.7863311593422 | epot = -77.0337902034447 | etot = -33.5644505599247 +701000 ekin = 20.578193148326 | erot = 23.4865818235912 | epot = -77.629225532724 | etot = -33.5644505608068 +702000 ekin = 20.3710754301549 | erot = 24.1923776458902 | epot = -78.1279036369795 | etot = -33.5644505609343 +703000 ekin = 20.0753347575173 | erot = 24.888467252762 | epot = -78.528252570647 | etot = -33.5644505603677 +704000 ekin = 19.7130379610838 | erot = 25.5614200023189 | epot = -78.838908522607 | etot = -33.5644505592043 +705000 ekin = 19.3114467602167 | erot = 26.2008176281874 | epot = -79.0767149460512 | etot = -33.564450557647 +706000 ekin = 18.8991937919881 | erot = 26.7996687691974 | epot = -79.2633131172258 | etot = -33.5644505560403 +707000 ekin = 18.5022273016031 | erot = 27.3532672566161 | epot = -79.4199451130548 | etot = -33.5644505548355 +708000 ekin = 18.1401729300363 | erot = 27.8564306963449 | epot = -79.5610541808569 | etot = -33.5644505544757 +709000 ekin = 17.8234464200403 | erot = 28.2999901805008 | epot = -79.6878871558114 | etot = -33.5644505552703 +710000 ekin = 17.5523632022352 | erot = 28.66784646393 | epot = -79.7846602233792 | etot = -33.564450557214 +711000 ekin = 17.319410981167 | erot = 28.9359249877842 | epot = -79.8197865289555 | etot = -33.5644505600043 +712000 ekin = 17.1112174759792 | erot = 29.0741670939005 | epot = -79.7498351329345 | etot = -33.5644505630547 +713000 ekin = 16.9121266207384 | erot = 29.0513180252372 | epot = -79.5278952115921 | etot = -33.5644505656165 +714000 ekin = 16.7079630671362 | erot = 28.8416092685853 | epot = -79.1140229027166 | etot = -33.564450566995 +715000 ekin = 16.4890214415111 | erot = 28.4313561606375 | epot = -78.4848281689488 | etot = -33.5644505668002 +716000 ekin = 16.2513970083694 | erot = 27.8230898675347 | epot = -77.6389374409925 | etot = -33.5644505650884 +717000 ekin = 15.9963403731169 | erot = 27.0356716312561 | epot = -76.5964625666635 | etot = -33.5644505622904 +718000 ekin = 15.7361303250895 | erot = 26.1105494914754 | epot = -75.4111303728763 | etot = -33.5644505563113 +719000 ekin = 15.4991442332756 | erot = 25.1078869435359 | epot = -74.1714817315667 | etot = -33.5644505547552 +720000 ekin = 15.2869109984327 | erot = 24.051118277072 | epot = -72.9024798285824 | etot = -33.5644505530778 +721000 ekin = 15.0983958368563 | erot = 22.9636187921636 | epot = -71.6264651803974 | etot = -33.5644505513775 +722000 ekin = 14.9325120658119 | erot = 21.8688846316655 | epot = -70.3658472497603 | etot = -33.5644505522828 +723000 ekin = 14.7807572560571 | erot = 20.783177409075 | epot = -69.1283852152817 | etot = -33.5644505501496 +724000 ekin = 14.6422909698242 | erot = 19.7295658973655 | epot = -67.9363074154255 | etot = -33.5644505482357 +725000 ekin = 14.5216204992091 | erot = 18.7315290225185 | epot = -66.8176000682293 | etot = -33.5644505465018 +726000 ekin = 14.4243651447271 | erot = 17.8092496646936 | epot = -65.7980653543268 | etot = -33.5644505449061 +727000 ekin = 14.3569475465798 | erot = 16.9804196385917 | epot = -64.9018177285995 | etot = -33.564450543428 +728000 ekin = 14.2536930559593 | erot = 16.2469828282715 | epot = -64.0651265345919 | etot = -33.5644506503612 +729000 ekin = 13.8457257235901 | erot = 15.9222518581098 | epot = -63.3324280824188 | etot = -33.5644505007189 +730000 ekin = 14.0260810331572 | erot = 15.9641149780232 | epot = -63.5546467085729 | etot = -33.5644506973925 +731000 ekin = 14.2598526174267 | erot = 15.8407237779026 | epot = -63.6650270928699 | etot = -33.5644506975406 +732000 ekin = 14.5606957082 | erot = 15.8547631025675 | epot = -63.9799095095013 | etot = -33.5644506987338 +733000 ekin = 14.9193813420873 | erot = 16.0002143198209 | epot = -64.4840463630918 | etot = -33.5644507011835 +734000 ekin = 15.3191392217664 | erot = 16.2611439998487 | epot = -65.1447339265492 | etot = -33.5644507049341 +735000 ekin = 15.7356018991576 | erot = 16.6113471097583 | epot = -65.9113997186633 | etot = -33.5644507097475 +736000 ekin = 16.1415246377564 | erot = 17.0234641328674 | epot = -66.7294394793124 | etot = -33.5644507086886 +737000 ekin = 16.5186056071986 | erot = 17.4895868028313 | epot = -67.5726431223686 | etot = -33.5644507123387 +738000 ekin = 16.8458492085384 | erot = 17.9860152350135 | epot = -68.396315158488 | etot = -33.5644507149361 +739000 ekin = 17.1101498629012 | erot = 18.4929848437288 | epot = -69.167585422606 | etot = -33.5644507159759 +740000 ekin = 17.3014321651814 | erot = 18.9830167810243 | epot = -69.8488996784293 | etot = -33.5644507322236 +741000 ekin = 17.386590010487 | erot = 19.3806296469325 | epot = -70.3316703890898 | etot = -33.5644507316703 +742000 ekin = 17.3696644696972 | erot = 19.6766235531722 | epot = -70.6107387526117 | etot = -33.5644507297423 +743000 ekin = 17.2668900413887 | erot = 19.8790967523848 | epot = -70.7104375210217 | etot = -33.5644507272482 +744000 ekin = 17.0976280278394 | erot = 20.0010316352814 | epot = -70.6631103878251 | etot = -33.5644507247043 +745000 ekin = 16.8806625291024 | erot = 20.057055059626 | epot = -70.5021683110215 | etot = -33.5644507222932 +746000 ekin = 16.6327129002015 | erot = 20.0624105110988 | epot = -70.2595741313054 | etot = -33.5644507200051 +747000 ekin = 16.3685004950096 | erot = 20.033016856487 | epot = -69.9659680692887 | etot = -33.5644507177921 +748000 ekin = 16.1014103999543 | erot = 19.9854814659263 | epot = -69.6513425815366 | etot = -33.564450715656 +749000 ekin = 15.8440980133595 | erot = 19.9365592321122 | epot = -69.345107959121 | etot = -33.5644507136493 +750000 ekin = 15.6090531913871 | erot = 19.903896348463 | epot = -69.0774002509923 | etot = -33.5644507111422 +751000 ekin = 15.408391615066 | erot = 19.9047162348154 | epot = -68.8775585596421 | etot = -33.5644507097607 +752000 ekin = 15.2531866583631 | erot = 19.9485427704181 | epot = -68.7661801374899 | etot = -33.5644507087087 +753000 ekin = 15.1543901558436 | erot = 20.0407526996777 | epot = -68.7595935635481 | etot = -33.5644507080268 +754000 ekin = 15.1228286565093 | erot = 20.1821712344388 | epot = -68.8694505987027 | etot = -33.5644507077546 +755000 ekin = 15.1688994236201 | erot = 20.3687544760721 | epot = -69.1021046076738 | etot = -33.5644507079815 +756000 ekin = 15.3014995511365 | erot = 20.5913112901341 | epot = -69.4572615501853 | etot = -33.5644507089146 +757000 ekin = 15.5255754908458 | erot = 20.8349492485987 | epot = -69.9249754503695 | etot = -33.564450710925 +758000 ekin = 15.8381446956662 | erot = 21.0780442729328 | epot = -70.4806396830074 | etot = -33.5644507144084 +759000 ekin = 16.2241238949829 | erot = 21.291351107698 | epot = -71.0799257220707 | etot = -33.5644507193898 +760000 ekin = 16.6551901643007 | erot = 21.4392176816081 | epot = -71.6588585709879 | etot = -33.5644507250792 +761000 ekin = 17.0950183929184 | erot = 21.4853061130269 | epot = -72.1447752357869 | etot = -33.5644507298415 +762000 ekin = 17.5106763995147 | erot = 21.4029539273073 | epot = -72.4780810587706 | etot = -33.5644507319486 +763000 ekin = 17.8846255668858 | erot = 21.185914549962 | epot = -72.6349908475012 | etot = -33.5644507306534 +764000 ekin = 18.2201199371193 | erot = 20.8529192973068 | epot = -72.6374899610343 | etot = -33.5644507266082 +765000 ekin = 18.5372583928787 | erot = 20.4430950204984 | epot = -72.544804134769 | etot = -33.564450721392 +766000 ekin = 18.86309963268 | erot = 20.0050052471612 | epot = -72.4325555962364 | etot = -33.5644507163952 +767000 ekin = 19.2212066783145 | erot = 19.5864803417602 | epot = -72.3721377327923 | etot = -33.5644507127176 +768000 ekin = 19.6245116668901 | erot = 19.2265552432954 | epot = -72.4155176210351 | etot = -33.5644507108497 +769000 ekin = 20.0721792306237 | erot = 18.9509745495803 | epot = -72.5876044911024 | etot = -33.5644507108984 +770000 ekin = 20.5498085990298 | erot = 18.7702787055214 | epot = -72.884538017272 | etot = -33.5644507127209 +771000 ekin = 21.0321028839958 | erot = 18.679435439756 | epot = -73.2759890396338 | etot = -33.5644507158821 +772000 ekin = 21.4851799397904 | erot = 18.6615620363116 | epot = -73.7111926963688 | etot = -33.5644507202668 +773000 ekin = 21.8752230439093 | erot = 18.6848228542269 | epot = -74.1244966228291 | etot = -33.5644507246929 +774000 ekin = 22.1763496427708 | erot = 18.7081814097347 | epot = -74.4489817807521 | etot = -33.5644507282467 +775000 ekin = 22.3745717791238 | erot = 18.6931201232722 | epot = -74.6321426323703 | etot = -33.5644507299744 +776000 ekin = 22.4709552224375 | erot = 18.6135457350496 | epot = -74.648951686955 | etot = -33.564450729468 +777000 ekin = 22.4798367585086 | erot = 18.4639882108411 | epot = -74.5082756956863 | etot = -33.5644507263366 +778000 ekin = 22.4355420339161 | erot = 18.2585534539139 | epot = -74.2585462089044 | etot = -33.5644507210745 +779000 ekin = 22.3843529355789 | erot = 18.0309205308365 | epot = -73.9797241813393 | etot = -33.5644507149239 +780000 ekin = 22.3744386445496 | erot = 17.8258066816941 | epot = -73.7646960358077 | etot = -33.5644507095641 +781000 ekin = 22.1317599829093 | erot = 17.6891439214798 | epot = -73.3853547353444 | etot = -33.5644508309553 +782000 ekin = 21.1592753937775 | erot = 17.9407979297457 | epot = -72.6645240432862 | etot = -33.564450719763 +783000 ekin = 20.4598020812476 | erot = 19.0285770550549 | epot = -73.052829858984 | etot = -33.5644507226814 +784000 ekin = 20.5205611486876 | erot = 20.4251816834892 | epot = -74.5101936712772 | etot = -33.5644508391004 +785000 ekin = 20.9642653572837 | erot = 20.9633174771005 | epot = -75.4920336619114 | etot = -33.5644508275272 +786000 ekin = 21.4400765968759 | erot = 21.061583090539 | epot = -76.0661105191519 | etot = -33.5644508317371 +787000 ekin = 21.8830668853208 | erot = 21.0574506776045 | epot = -76.5049683963306 | etot = -33.5644508334054 +788000 ekin = 22.2673243737814 | erot = 20.9464326031856 | epot = -76.7782078095427 | etot = -33.5644508325756 +789000 ekin = 22.5826671465141 | erot = 20.7432248255376 | epot = -76.8903428020209 | etot = -33.5644508299692 +790000 ekin = 22.8323066866154 | erot = 20.4741989828028 | epot = -76.8709564960782 | etot = -33.56445082666 +791000 ekin = 23.0272356221831 | erot = 20.1684029992233 | epot = -76.7600894450125 | etot = -33.5644508236061 +792000 ekin = 23.1800436940963 | erot = 19.8507212176288 | epot = -76.5952157330443 | etot = -33.5644508213191 +793000 ekin = 23.300603133044 | erot = 19.5391467337423 | epot = -76.404200686658 | etot = -33.5644508198717 +794000 ekin = 23.3943971223733 | erot = 19.2453890910844 | epot = -76.2042370325532 | etot = -33.5644508190955 +795000 ekin = 23.4629811579683 | erot = 18.9772359492812 | epot = -76.0046679259086 | etot = -33.5644508186592 +796000 ekin = 23.5050545285291 | erot = 18.7401074031681 | epot = -75.8096127503046 | etot = -33.5644508186073 +797000 ekin = 23.5179235663088 | erot = 18.5376020828532 | epot = -75.6199764678595 | etot = -33.5644508186975 +798000 ekin = 23.4993095514253 | erot = 18.3721088645044 | epot = -75.4358692347521 | etot = -33.5644508188224 +799000 ekin = 23.4489395597834 | erot = 18.2446734411486 | epot = -75.258063819795 | etot = -33.564450818863 +800000 ekin = 23.3700597315759 | erot = 18.1549836094423 | epot = -75.0894941596996 | etot = -33.5644508186813 +801000 ekin = 23.2706429321765 | erot = 18.1018392066988 | epot = -74.9369329570152 | etot = -33.5644508181399 +802000 ekin = 23.1638659253445 | erot = 18.0841621417591 | epot = -74.8124788842758 | etot = -33.5644508171722 +803000 ekin = 23.0673439652931 | erot = 18.1021655927045 | epot = -74.7339603738614 | etot = -33.5644508158639 +804000 ekin = 23.0007989401313 | erot = 18.1579717421609 | epot = -74.7232214967841 | etot = -33.564450814492 +805000 ekin = 22.9823371371263 | erot = 18.2549251648251 | epot = -74.8017131154778 | etot = -33.5644508135264 +806000 ekin = 23.0241641619703 | erot = 18.3954330766867 | epot = -74.984048052 | etot = -33.5644508133431 +807000 ekin = 23.1289646264206 | erot = 18.5785443252248 | epot = -75.2719597659602 | etot = -33.5644508143147 +808000 ekin = 23.2881607697434 | erot = 18.7969609309069 | epot = -75.6495725171493 | etot = -33.5644508164989 +809000 ekin = 23.4826910126068 | erot = 19.0356597574091 | epot = -76.0828015896723 | etot = -33.5644508196564 +810000 ekin = 23.6859311917307 | erot = 19.2727961935001 | epot = -76.5231782085194 | etot = -33.5644508232885 +811000 ekin = 23.8683330193095 | erot = 19.4824424681752 | epot = -76.9152263142569 | etot = -33.5644508267723 +812000 ekin = 24.0021280336694 | erot = 19.6390320771543 | epot = -77.2056109397628 | etot = -33.5644508289391 +813000 ekin = 24.0705831548813 | erot = 19.7220219145477 | epot = -77.3570559007636 | etot = -33.5644508313346 +814000 ekin = 24.0556011517812 | erot = 19.7197957998033 | epot = -77.3398477836966 | etot = -33.5644508321121 +815000 ekin = 23.9426529222313 | erot = 19.6314238633418 | epot = -77.1385276168128 | etot = -33.5644508312396 +816000 ekin = 23.731133693213 | erot = 19.466072036005 | epot = -76.7616565581624 | etot = -33.5644508289444 +817000 ekin = 23.4336685350294 | erot = 19.2405112303572 | epot = -76.2386305910159 | etot = -33.5644508256293 +818000 ekin = 23.0739945646645 | erot = 18.9755381783867 | epot = -75.6139835648237 | etot = -33.5644508217725 +819000 ekin = 22.6837324026765 | erot = 18.6923648026043 | epot = -74.9405480232895 | etot = -33.5644508180087 +820000 ekin = 22.2835291279714 | erot = 18.4096381976571 | epot = -74.2576181415066 | etot = -33.5644508158781 +821000 ekin = 21.8822278938176 | erot = 18.141291498877 | epot = -73.5879702071845 | etot = -33.5644508144899 +822000 ekin = 21.4884880533111 | erot = 17.8956786276998 | epot = -72.9486174948433 | etot = -33.5644508138324 +823000 ekin = 21.1064787927768 | erot = 17.6755757474125 | epot = -72.3465053539623 | etot = -33.564450813773 +824000 ekin = 20.7370980701816 | erot = 17.4789023716297 | epot = -71.7804512559058 | etot = -33.5644508140945 +825000 ekin = 20.3797998929284 | erot = 17.3000855940531 | epot = -71.2443363015056 | etot = -33.5644508145241 +826000 ekin = 20.0346218856065 | erot = 17.1319532523354 | epot = -70.7310259527282 | etot = -33.5644508147862 +827000 ekin = 19.7039740663547 | erot = 16.9679189158217 | epot = -70.2363437968243 | etot = -33.5644508146479 +828000 ekin = 19.3938011099896 | erot = 16.8040573647366 | epot = -69.7623092887102 | etot = -33.5644508139841 +829000 ekin = 19.1138486595862 | erot = 16.6405709737945 | epot = -69.3188704461918 | etot = -33.5644508128111 +830000 ekin = 18.8769326813353 | erot = 16.4822215963422 | epot = -68.9236050889638 | etot = -33.5644508112863 +831000 ekin = 18.697311774337 | erot = 16.3375582362052 | epot = -68.5993208202243 | etot = -33.5644508096821 +832000 ekin = 18.5884699042913 | erot = 16.2171194616771 | epot = -68.3700401742869 | etot = -33.5644508083185 +833000 ekin = 18.5607795988464 | erot = 16.131079329091 | epot = -68.2563097354189 | etot = -33.5644508074815 +834000 ekin = 18.6195655893721 | erot = 16.0869173655938 | epot = -68.2709337623352 | etot = -33.5644508073693 +835000 ekin = 18.7639745681618 | erot = 16.0875916783619 | epot = -68.4160170545793 | etot = -33.5644508080557 +836000 ekin = 18.9868442891856 | erot = 16.130519235032 | epot = -68.6818143337116 | etot = -33.5644508094941 +837000 ekin = 19.2754657692627 | erot = 16.207438470387 | epot = -69.0473550511925 | etot = -33.5644508115428 +838000 ekin = 19.6129197642166 | erot = 16.3051003168942 | epot = -69.4824708951133 | etot = -33.5644508140025 +839000 ekin = 19.9795904915988 | erot = 16.4066729969167 | epot = -69.9507143051619 | etot = -33.5644508166465 +840000 ekin = 20.3545159452212 | erot = 16.4936833341199 | epot = -70.4126500985958 | etot = -33.5644508192548 +841000 ekin = 20.7164052641964 | erot = 16.548246927735 | epot = -70.829103013567 | etot = -33.5644508216356 +842000 ekin = 21.0443277173709 | erot = 16.5552492658878 | epot = -71.1640278069013 | etot = -33.5644508236425 +843000 ekin = 21.3182343501173 | erot = 16.504098715485 | epot = -71.3867838907757 | etot = -33.5644508251735 +844000 ekin = 21.5195641371082 | erot = 16.3898128616543 | epot = -71.4738278249128 | etot = -33.5644508261503 +845000 ekin = 21.6321888572324 | erot = 16.2134453017857 | epot = -71.4100849855142 | etot = -33.5644508264961 +846000 ekin = 21.6437998337389 | erot = 15.9820204440426 | epot = -71.1902711039102 | etot = -33.5644508261287 +847000 ekin = 21.5475782511098 | erot = 15.7081282908899 | epot = -70.8201573669942 | etot = -33.5644508249945 +848000 ekin = 21.3436927799336 | erot = 15.4091281568063 | epot = -70.3172717598687 | etot = -33.5644508231288 +849000 ekin = 21.040018068204 | erot = 15.1057456387123 | epot = -69.7102145276103 | etot = -33.564450820694 +850000 ekin = 20.6516241479064 | erot = 14.8199821289072 | epot = -69.0360570947859 | etot = -33.5644508179724 +851000 ekin = 20.1989966769928 | erot = 14.5725796445398 | epot = -68.3360271368306 | etot = -33.5644508152979 +852000 ekin = 19.7054052282539 | erot = 14.3805531694316 | epot = -67.6504092106676 | etot = -33.5644508129822 +853000 ekin = 19.1940724659069 | erot = 14.2553081918317 | epot = -67.013831468985 | etot = -33.5644508112464 +854000 ekin = 18.685752406539 | erot = 14.2015963027567 | epot = -66.4517995195066 | etot = -33.5644508102108 +855000 ekin = 18.1970763793973 | erot = 14.217263432367 | epot = -65.9787906216679 | etot = -33.5644508099036 +856000 ekin = 17.7397499755394 | erot = 14.293605095631 | epot = -65.597805881444 | etot = -33.5644508102736 +857000 ekin = 17.3205057828376 | erot = 14.4162007415788 | epot = -65.3011573356223 | etot = -33.5644508112059 +858000 ekin = 16.9416544321828 | erot = 14.5662556892476 | epot = -65.0723609339437 | etot = -33.5644508125133 +859000 ekin = 16.6020780530239 | erot = 14.7225727582617 | epot = -64.8891016252306 | etot = -33.5644508139451 +860000 ekin = 16.2985125202782 | erot = 14.8641879511938 | epot = -64.7271512866837 | etot = -33.5644508152118 +861000 ekin = 16.0269335804234 | erot = 14.9734306247742 | epot = -64.5648150212404 | etot = -33.5644508160429 +862000 ekin = 15.7838145531257 | erot = 15.0388248710163 | epot = -64.3870902403884 | etot = -33.5644508162464 +863000 ekin = 15.5670277438764 | erot = 15.0570871966147 | epot = -64.1885657562588 | etot = -33.5644508157676 +864000 ekin = 15.3762443300744 | erot = 15.0336448974535 | epot = -63.9743400422222 | etot = -33.5644508146943 +865000 ekin = 15.2131876579387 | erot = 14.9816007216251 | epot = -63.7592391926681 | etot = -33.5644508131043 +866000 ekin = 15.0809818320607 | erot = 14.9194629923979 | epot = -63.5648956359166 | etot = -33.5644508114581 +867000 ekin = 14.9827726531226 | erot = 14.8683323185733 | epot = -63.4155557815486 | etot = -33.5644508098527 +868000 ekin = 14.9218011269598 | erot = 14.8493296883198 | epot = -63.3355816237487 | etot = -33.5644508084691 +869000 ekin = 14.9010185138682 | erot = 14.8813222897364 | epot = -63.3467916110622 | etot = -33.5644508074576 +870000 ekin = 14.9227801778206 | erot = 14.9789108530707 | epot = -63.4661418378863 | etot = -33.5644508069951 +871000 ekin = 14.9884139368942 | erot = 15.1503817706812 | epot = -63.703246514838 | etot = -33.5644508072627 +872000 ekin = 15.0976914328012 | erot = 15.3955923521635 | epot = -64.0577345933959 | etot = -33.5644508084312 +873000 ekin = 15.2480781394194 | erot = 15.7042636320403 | epot = -64.5167925820518 | etot = -33.5644508105921 +874000 ekin = 15.4340038880574 | erot = 16.055356092982 | epot = -65.053810794677 | etot = -33.5644508136376 +875000 ekin = 15.6465534583829 | erot = 16.4187317020441 | epot = -65.6297359776216 | etot = -33.5644508171946 +876000 ekin = 15.8739222035519 | erot = 16.7595446910416 | epot = -66.1979177152847 | etot = -33.5644508206912 +877000 ekin = 16.1027155819911 | erot = 17.0444943473801 | epot = -66.7116607529112 | etot = -33.5644508235401 +878000 ekin = 16.319791048708 | erot = 17.2478151737007 | epot = -67.1320570477561 | etot = -33.5644508253474 +879000 ekin = 16.513852143331 | erot = 17.3548092235238 | epot = -67.4331121929392 | etot = -33.5644508260845 +880000 ekin = 16.6772706666643 | erot = 17.3624918756169 | epot = -67.6042133678519 | etot = -33.5644508255706 +881000 ekin = 16.8080553843206 | erot = 17.2784522473064 | epot = -67.6509584556495 | etot = -33.5644508240226 +882000 ekin = 16.9100399156744 | erot = 17.1190222525855 | epot = -67.5935129898763 | etot = -33.5644508216164 +883000 ekin = 16.9925722017344 | erot = 16.9073416710475 | epot = -67.4643646914728 | etot = -33.5644508186909 +884000 ekin = 17.0687034106809 | erot = 16.6704808404549 | epot = -67.3036350669103 | etot = -33.5644508157744 +885000 ekin = 17.1519974231529 | erot = 16.4352378856248 | epot = -67.1516861222243 | etot = -33.5644508134466 +886000 ekin = 17.2529390407585 | erot = 16.2234313547558 | epot = -67.0408212076545 | etot = -33.5644508121402 +887000 ekin = 17.3762921647762 | erot = 16.0482363412789 | epot = -66.9889793180409 | etot = -33.5644508119859 +888000 ekin = 17.520362098505 | erot = 15.9127130226943 | epot = -66.9975259340197 | etot = -33.5644508128205 +889000 ekin = 17.6781644467692 | erot = 15.8105908148255 | epot = -67.053206075905 | etot = -33.5644508143103 +890000 ekin = 17.8397117367786 | erot = 15.7285450848103 | epot = -67.1327076370755 | etot = -33.5644508154865 +891000 ekin = 17.9946822418325 | erot = 15.6526652214473 | epot = -67.2117982809621 | etot = -33.5644508176823 +892000 ekin = 18.1331274177217 | erot = 15.563184660984 | epot = -67.2607628981432 | etot = -33.5644508194375 +893000 ekin = 18.2472194998205 | erot = 15.4391901295465 | epot = -67.2508604500035 | etot = -33.5644508206365 +894000 ekin = 18.3321686671843 | erot = 15.2648175339455 | epot = -67.1614370222908 | etot = -33.564450821161 +895000 ekin = 18.3862908814765 | erot = 15.0310128841995 | epot = -66.9817545866243 | etot = -33.5644508209484 +896000 ekin = 18.4109116210726 | erot = 14.7366844097439 | epot = -66.7120468508501 | etot = -33.5644508200336 +897000 ekin = 18.4100490066795 | erot = 14.3885926448155 | epot = -66.3630924700693 | etot = -33.5644508185744 +898000 ekin = 18.3898281685202 | erot = 13.9998000563491 | epot = -65.9540790416773 | etot = -33.5644508168081 +899000 ekin = 18.3577139299705 | erot = 13.5871378088075 | epot = -65.509302553754 | etot = -33.564450814976 +900000 ekin = 18.3217786311141 | erot = 13.1685630404219 | epot = -65.054792484781 | etot = -33.5644508132449 +901000 ekin = 18.2902589942974 | erot = 12.7612484276711 | epot = -64.6159582336337 | etot = -33.5644508116652 +902000 ekin = 18.2715810710039 | erot = 12.3808553804282 | epot = -64.2168872615955 | etot = -33.5644508101635 +903000 ekin = 18.2748902577742 | erot = 12.04197991098 | epot = -63.8813209773376 | etot = -33.5644508085834 +904000 ekin = 18.3109460803817 | erot = 11.7594273506552 | epot = -63.6348242377774 | etot = -33.5644508067406 +905000 ekin = 18.393092548532 | erot = 11.5498594838196 | epot = -63.507402836842 | etot = -33.5644508044905 +906000 ekin = 18.5347341805732 | erot = 11.4295673220289 | epot = -63.5287523075689 | etot = -33.5644508049669 +907000 ekin = 18.7414362397562 | erot = 11.4045037441698 | epot = -63.7103907883216 | etot = -33.5644508043955 +908000 ekin = 19.01948896505 | erot = 11.4807236741048 | epot = -64.064663443761 | etot = -33.5644508046062 +909000 ekin = 19.370061418707 | erot = 11.6589605869467 | epot = -64.5934728113217 | etot = -33.5644508056681 +910000 ekin = 19.788210520863 | erot = 11.9333322638151 | epot = -65.2859935919935 | etot = -33.5644508073154 +911000 ekin = 20.2647618396155 | erot = 12.2921701370539 | epot = -66.1213827858005 | etot = -33.5644508091311 +912000 ekin = 20.7894338917871 | erot = 12.7195983389508 | epot = -67.0734830412077 | etot = -33.5644508104698 +913000 ekin = 21.3541857291101 | erot = 13.1939380946156 | epot = -68.1125746374356 | etot = -33.5644508137099 +914000 ekin = 21.9410171487178 | erot = 13.6876167577927 | epot = -69.1930847244104 | etot = -33.5644508179 +915000 ekin = 22.518884629029 | erot = 14.1693256816077 | epot = -70.252661133485 | etot = -33.5644508228483 +916000 ekin = 23.0495496122886 | erot = 14.6035757293001 | epot = -71.2175761703539 | etot = -33.5644508287652 +917000 ekin = 23.4897289756407 | erot = 14.9539952399446 | epot = -72.0081750488837 | etot = -33.5644508332984 +918000 ekin = 23.793918530387 | erot = 15.1976473317576 | epot = -72.5560167461632 | etot = -33.5644508840185 +919000 ekin = 23.6168045559219 | erot = 15.3655091451681 | epot = -72.546764543126 | etot = -33.564450842036 +920000 ekin = 23.1655316155466 | erot = 15.5814764778541 | epot = -72.3114589043119 | etot = -33.5644508109111 +921000 ekin = 22.8561009763955 | erot = 15.8041631554327 | epot = -72.2247149918464 | etot = -33.5644508600183 +922000 ekin = 22.4406172099256 | erot = 15.7102388759533 | epot = -71.7153069240717 | etot = -33.5644508381928 +923000 ekin = 21.8145072543786 | erot = 15.4204628569532 | epot = -70.7994209415843 | etot = -33.5644508302526 +924000 ekin = 21.0897106221477 | erot = 15.1252102346463 | epot = -69.7793716761032 | etot = -33.5644508193092 +925000 ekin = 20.3778961154116 | erot = 14.8990596223701 | epot = -68.8414065460385 | etot = -33.5644508082568 +926000 ekin = 19.7497733196884 | erot = 14.7841436172023 | epot = -68.0983677423196 | etot = -33.5644508054289 +927000 ekin = 19.2202389486492 | erot = 14.8057849928954 | epot = -67.5904747440152 | etot = -33.5644508024706 +928000 ekin = 18.8098178378655 | erot = 14.9862994179362 | epot = -67.3605680557094 | etot = -33.5644507999077 +929000 ekin = 18.5263530330417 | erot = 15.3189513447801 | epot = -67.4097551952486 | etot = -33.5644508174268 +930000 ekin = 18.3031582479208 | erot = 15.7144845870462 | epot = -67.5820936630876 | etot = -33.5644508281205 +931000 ekin = 18.0528353461445 | erot = 16.0920981649876 | epot = -67.7093843479757 | etot = -33.5644508368436 +932000 ekin = 17.7015072487275 | erot = 16.3874716161786 | epot = -67.6534297061045 | etot = -33.5644508411985 +933000 ekin = 17.211575779812 | erot = 16.5716045845824 | epot = -67.3476312032304 | etot = -33.5644508388361 +934000 ekin = 16.5514003367762 | erot = 16.6395832467501 | epot = -66.7554344853522 | etot = -33.564450901826 +935000 ekin = 15.4338979248173 | erot = 16.4795973814032 | epot = -65.4779461395113 | etot = -33.5644508332907 +936000 ekin = 14.2992444440305 | erot = 16.4524645769609 | epot = -64.3161598028593 | etot = -33.564450781868 +937000 ekin = 13.594877389297 | erot = 16.8307081817066 | epot = -63.9900363826699 | etot = -33.5644508116663 +938000 ekin = 13.1600926819737 | erot = 17.3617572865251 | epot = -64.0863008414443 | etot = -33.5644508729455 +939000 ekin = 12.6302856042602 | erot = 17.6616475412764 | epot = -63.8563839351059 | etot = -33.5644507895693 +940000 ekin = 12.1844103621837 | erot = 17.9750890379595 | epot = -63.7239501902423 | etot = -33.5644507900991 +941000 ekin = 11.8736812724101 | erot = 18.3544207840917 | epot = -63.79255284895 | etot = -33.5644507924482 +942000 ekin = 11.6856910034444 | erot = 18.7737996951239 | epot = -64.0239414943836 | etot = -33.5644507958152 +943000 ekin = 11.5993719863631 | erot = 19.1997647301752 | epot = -64.3635875159553 | etot = -33.564450799417 +944000 ekin = 11.5911163869142 | erot = 19.5969000490703 | epot = -64.7524672386315 | etot = -33.564450802647 +945000 ekin = 11.639459484541 | erot = 19.9326030898694 | epot = -65.1365133795222 | etot = -33.5644508051117 +946000 ekin = 11.7278293567757 | erot = 20.1807231909362 | epot = -65.4730033543077 | etot = -33.5644508065958 +947000 ekin = 11.8456010821895 | erot = 20.324153790967 | epot = -65.7342056801685 | etot = -33.5644508070121 +948000 ekin = 11.9879925809402 | erot = 20.3564922792948 | epot = -65.9089356666417 | etot = -33.5644508064067 +949000 ekin = 12.1551997602243 | erot = 20.2822909293999 | epot = -66.0019414945905 | etot = -33.5644508049663 +950000 ekin = 12.3510408470325 | erot = 20.115659623218 | epot = -66.0311512732532 | etot = -33.5644508030028 +951000 ekin = 12.5812930222758 | erot = 19.8773156844474 | epot = -66.0230595076182 | etot = -33.5644508008949 +952000 ekin = 12.8471183866925 | erot = 19.5848425912166 | epot = -65.9964117794652 | etot = -33.564450801556 +953000 ekin = 13.1479143636503 | erot = 19.2558560502527 | epot = -65.9682212137687 | etot = -33.5644507998657 +954000 ekin = 13.4859606885364 | erot = 18.9116614121342 | epot = -65.9620728994014 | etot = -33.5644507987308 +955000 ekin = 13.8607396756392 | erot = 18.5688220964155 | epot = -65.994012570258 | etot = -33.5644507982032 +956000 ekin = 14.2684790715045 | erot = 18.23867671937 | epot = -66.0716065890947 | etot = -33.5644507982202 +957000 ekin = 14.7022261388303 | erot = 17.9280212141735 | epot = -66.1946981516521 | etot = -33.5644507986483 +958000 ekin = 15.1523556915809 | erot = 17.6404102051721 | epot = -66.3572166960802 | etot = -33.5644507993272 +959000 ekin = 15.6074014520696 | erot = 17.3776018825342 | epot = -66.5494541347015 | etot = -33.5644508000977 +960000 ekin = 16.055105520303 | erot = 17.1408213598753 | epot = -66.760377680976 | etot = -33.5644508007977 +961000 ekin = 16.4838195085816 | erot = 16.9315995207268 | epot = -66.979869830664 | etot = -33.5644508013556 +962000 ekin = 16.8831178333153 | erot = 16.752450807508 | epot = -67.2000194425075 | etot = -33.5644508016842 +963000 ekin = 17.2446402437768 | erot = 16.6070593136442 | epot = -67.4161503591765 | etot = -33.5644508017555 +964000 ekin = 17.562694424349 | erot = 16.5001400875647 | epot = -67.6272853134984 | etot = -33.5644508015847 +965000 ekin = 17.8343164168747 | erot = 16.437096040881 | epot = -67.8358632589921 | etot = -33.5644508012364 +966000 ekin = 18.0588818068295 | erot = 16.4234839575503 | epot = -68.0468165651874 | etot = -33.5644508008075 +967000 ekin = 18.2373393703384 | erot = 16.4643418733569 | epot = -68.2661320441123 | etot = -33.5644508004171 +968000 ekin = 18.3712253513644 | erot = 16.5634469194537 | epot = -68.4991230710021 | etot = -33.5644508001841 +969000 ekin = 18.4616731850683 | erot = 16.7225928803125 | epot = -68.7487168655807 | etot = -33.5644508001999 +970000 ekin = 18.5086424153895 | erot = 16.9409874348876 | epot = -69.0140806508028 | etot = -33.5644508005257 +971000 ekin = 18.5105217612239 | erot = 17.214832239555 | epot = -69.2898048019491 | etot = -33.5644508011701 +972000 ekin = 18.4641879343137 | erot = 17.5371342494854 | epot = -69.5657729859032 | etot = -33.5644508021041 +973000 ekin = 18.3654968233623 | erot = 17.8977436725043 | epot = -69.8276912991286 | etot = -33.5644508032619 +974000 ekin = 18.2101154507905 | erot = 18.2835968621238 | epot = -70.0581631174661 | etot = -33.5644508045518 +975000 ekin = 17.9945660461061 | erot = 18.679151597941 | epot = -70.2381684499127 | etot = -33.5644508058656 +976000 ekin = 17.717330563609 | erot = 19.0670257232443 | epot = -70.3488070939419 | etot = -33.5644508070885 +977000 ekin = 17.3798453528906 | erot = 19.4288693817331 | epot = -70.3731655427282 | etot = -33.5644508081045 +978000 ekin = 16.9872047031722 | erot = 19.7465105573489 | epot = -70.2981660693277 | etot = -33.5644508088066 +979000 ekin = 16.5484157018381 | erot = 20.0033999874178 | epot = -70.116266498357 | etot = -33.5644508091011 +980000 ekin = 16.0760394950274 | erot = 20.1863036686509 | epot = -69.8267939695453 | etot = -33.5644508058671 +981000 ekin = 15.5958799597593 | erot = 20.2892058513337 | epot = -69.4495366177224 | etot = -33.5644508066295 +982000 ekin = 15.0884229586249 | erot = 20.3042918160036 | epot = -68.9571656249607 | etot = -33.5644508503322 +983000 ekin = 14.6278059338707 | erot = 20.1974254855586 | epot = -68.3896822274588 | etot = -33.5644508080295 +984000 ekin = 14.485718093269 | erot = 20.0570073304459 | epot = -68.1071762944406 | etot = -33.5644508707257 +985000 ekin = 14.2080885116351 | erot = 19.9192764069441 | epot = -67.6918157209786 | etot = -33.5644508023994 +986000 ekin = 13.9758845112991 | erot = 19.8429646049279 | epot = -67.3832999162394 | etot = -33.5644508000123 +987000 ekin = 13.8444879807334 | erot = 19.8435555011179 | epot = -67.2524942889555 | etot = -33.5644508071042 +988000 ekin = 13.7899576039149 | erot = 19.876553633637 | epot = -67.2309620426443 | etot = -33.5644508050923 +989000 ekin = 13.7826987903072 | erot = 19.9896360515821 | epot = -67.3367856483026 | etot = -33.5644508064133 +990000 ekin = 13.8064598100946 | erot = 20.1866383843989 | epot = -67.5575490030266 | etot = -33.5644508085331 +991000 ekin = 13.8444762357552 | erot = 20.455356874306 | epot = -67.8642839209134 | etot = -33.5644508108522 +992000 ekin = 13.8831356664543 | erot = 20.7777559193191 | epot = -68.2253423984327 | etot = -33.5644508126593 +993000 ekin = 13.9170731932667 | erot = 21.1354076794003 | epot = -68.6169316860712 | etot = -33.5644508134042 +994000 ekin = 13.9526839919551 | erot = 21.5142214723578 | epot = -69.0313562771973 | etot = -33.5644508128844 +995000 ekin = 14.0087177033998 | erot = 21.9069609499345 | epot = -69.4801294647094 | etot = -33.5644508113751 +996000 ekin = 14.1134297061039 | erot = 22.3130050958893 | epot = -69.9908856111372 | etot = -33.564450809144 +997000 ekin = 14.3000196986382 | erot = 22.73642078599 | epot = -70.6008912914758 | etot = -33.5644508068476 +998000 ekin = 14.6010980818731 | erot = 23.1830420697638 | epot = -71.3485909566375 | etot = -33.5644508050006 +999000 ekin = 15.04273129669 | erot = 23.6573925697404 | epot = -72.2645746768899 | etot = -33.5644508104595 +1000000 ekin = 15.6136601549948 | erot = 24.1382005377538 | epot = -73.31631150618 | etot = -33.5644508134314 + 1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160018 39304000 +Loop time of 24.0071 on 4 procs for 1000000 steps with 16 atoms + +Performance: 61.398 ns/day, 0.391 hours/ns, 41654.420 timesteps/s, 666.471 katom-step/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.0729 | 11.462 | 13.699 | 68.6 | 47.74 +Bond | 0.30957 | 0.43359 | 0.52757 | 12.0 | 1.81 +Neigh | 0.011335 | 0.011428 | 0.011526 | 0.1 | 0.05 +Comm | 6.994 | 9.2216 | 12.853 | 77.8 | 38.41 +Output | 0.090149 | 0.096079 | 0.10876 | 2.4 | 0.40 +Modify | 0.843 | 0.94516 | 1.0713 | 9.1 | 3.94 +Other | | 1.838 | | | 7.65 + +Nlocal: 4 ave 4 max 4 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 12 ave 12 max 12 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 26.75 ave 47 max 9 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +#write_restart last_config.${number}.* +Total wall time: 0:00:24 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/data.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/data.duplex2 new file mode 100644 index 0000000000..78a6fdd51a --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/data.duplex2 @@ -0,0 +1,91 @@ +LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19 + +16 atoms +4 atom types +13 bonds +1 bond types +16 ellipsoids + +-170 170 xlo xhi +-170 170 ylo yhi +-170 170 zlo zhi + +Masses + +1 315.8376 +2 315.8376 +3 315.8376 +4 315.8376 + +Atoms # hybrid + +1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0 +2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0 +3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0 +4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0 +5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0 +6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0 +7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0 +8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0 +9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0 +10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0 +11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0 +12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0 +13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0 +14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0 +15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0 +16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0 + +Velocities + +1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447 +2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514 +3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762 +4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703 +5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389 +6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085 +7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256 +8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774 +9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824 +10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333 +11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933 +12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927 +13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526 +14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926 +15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399 +16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 + +Ellipsoids + +1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707 +2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305 +3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029 +4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721 +5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086 +6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194 +7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482 +8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644 +9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584 +10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163 +11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784 +12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185 +13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717 +14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799 +15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689 +16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/in.duplex2 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/in.duplex2 new file mode 100644 index 0000000000..74ccf46051 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/in.duplex2 @@ -0,0 +1,74 @@ +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.5 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + +set atom * mass 315.8376 + +group all type 1 4 + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * oxrna2_real.cgdna +special_bonds lj 0 1 1 + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv oxrna2_real.cgdna +pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2_real.cgdna +pair_coeff * * oxrna2/hbond seqdep oxrna2_real.cgdna +pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_real.cgdna +pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_real.cgdna +pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_real.cgdna +pair_coeff * * oxrna2/xstk oxrna2_real.cgdna +pair_coeff * * oxrna2/coaxstk oxrna2_real.cgdna +pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2_real.cgdna + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 + +write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/log.19May24.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/log.19May24.duplex2.g++.1 new file mode 100644 index 0000000000..29558cf7b4 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/log.19May24.duplex2.g++.1 @@ -0,0 +1,1121 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.006 seconds +Setting atom values ... + 16 settings made for mass +16 atoms in group all +Reading oxdna potential (fene) file oxrna2.real with DATE: 2024-04-26 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (stk) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (xstk) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (coaxstk) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (dh) file oxrna2.real with DATE: 2024-04-26 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 36.640032 + ghost atom cutoff = 36.640032 + binsize = 18.320016, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 0.01706 +WARNING: Communication cutoff adjusted to 36.640032409886274 (src/comm.cpp:739) +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815 +Per MPI rank memory allocation (min/avg/max) = 7.592 | 7.592 | 7.592 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -69.627742 3.2447172 -50.262701 0.034084814 39304000 +1000 ekin = 16.3558183649387 | erot = 16.6323090455317 | epot = -66.5525771041996 | etot = -33.5644496937292 +2000 ekin = 16.6191649168148 | erot = 16.5684372137643 | epot = -66.7520518221218 | etot = -33.5644496915427 +3000 ekin = 16.9230904408655 | erot = 16.5204480451833 | epot = -67.0079881759689 | etot = -33.5644496899201 +4000 ekin = 17.2772162612592 | erot = 16.4986792932201 | epot = -67.3403452437718 | etot = -33.5644496892925 +5000 ekin = 17.6866959075726 | erot = 16.5050138456573 | epot = -67.7561594428213 | etot = -33.5644496895913 +6000 ekin = 18.1531343302965 | erot = 16.5325161302816 | epot = -68.2501001506517 | etot = -33.5644496900737 +7000 ekin = 18.6806534933141 | erot = 16.5738535187237 | epot = -68.818956701435 | etot = -33.5644496893973 +8000 ekin = 19.2766528199697 | erot = 16.626151587963 | epot = -69.4672540969566 | etot = -33.5644496890239 +9000 ekin = 19.946149039732 | erot = 16.690847598574 | epot = -70.2014463262322 | etot = -33.5644496879261 +10000 ekin = 20.6973181248475 | erot = 16.777296043853 | epot = -71.039063854855 | etot = -33.5644496861545 +11000 ekin = 21.5395226247921 | erot = 16.901420997199 | epot = -72.0053933083061 | etot = -33.564449686315 +12000 ekin = 22.4717498465051 | erot = 17.0791755563663 | epot = -73.1153750880499 | etot = -33.5644496851785 +13000 ekin = 23.493621609947 | erot = 17.3228520870333 | epot = -74.3809233816827 | etot = -33.5644496847025 +14000 ekin = 24.6044210071245 | erot = 17.6425688028836 | epot = -75.8114394947882 | etot = -33.56444968478 +15000 ekin = 25.7999389267744 | erot = 18.0453525578632 | epot = -77.4097411694883 | etot = -33.5644496848507 +16000 ekin = 27.0739775537122 | erot = 18.536114233291 | epot = -79.1745414730759 | etot = -33.5644496860726 +17000 ekin = 28.4119581304117 | erot = 19.1137262760957 | epot = -81.0901340949627 | etot = -33.5644496884552 +18000 ekin = 29.7909545183301 | erot = 19.7704759932753 | epot = -83.1258802031779 | etot = -33.5644496915724 +19000 ekin = 31.1831510307731 | erot = 20.4915974540493 | epot = -85.2391981805602 | etot = -33.5644496957377 +20000 ekin = 32.5560965367941 | erot = 21.2528351748732 | epot = -87.373381412572 | etot = -33.5644497009046 +21000 ekin = 33.8683309875658 | erot = 22.0156446407475 | epot = -89.4484253379449 | etot = -33.5644497096315 +22000 ekin = 35.0747510230856 | erot = 22.7306302808711 | epot = -91.3698310187507 | etot = -33.5644497147941 +23000 ekin = 36.1427935644225 | erot = 23.3543658008635 | epot = -93.0616090845418 | etot = -33.5644497192558 +24000 ekin = 37.0484240543208 | erot = 23.8536351256839 | epot = -94.4665089004153 | etot = -33.5644497204106 +25000 ekin = 37.7873483857424 | erot = 24.2156130941778 | epot = -95.567411199049 | etot = -33.5644497191288 +26000 ekin = 38.3695951222895 | erot = 24.4472028227108 | epot = -96.381247661283 | etot = -33.5644497162827 +27000 ekin = 38.814245199114 | erot = 24.569649643868 | epot = -96.948344555808 | etot = -33.564449712826 +28000 ekin = 39.1436511594776 | erot = 24.6108705414912 | epot = -97.318971410458 | etot = -33.5644497094892 +29000 ekin = 39.3799077053085 | erot = 24.5987493007987 | epot = -97.5431067127119 | etot = -33.5644497066047 +30000 ekin = 39.543718776792 | erot = 24.5572061990989 | epot = -97.6653746802846 | etot = -33.5644497043937 +31000 ekin = 39.6556538792218 | erot = 24.5025482878259 | epot = -97.7226518696589 | etot = -33.5644497026113 +32000 ekin = 39.7376908979138 | erot = 24.4447365565301 | epot = -97.7468771552206 | etot = -33.5644497007767 +33000 ekin = 39.8178410436032 | erot = 24.3917276701347 | epot = -97.7740184125893 | etot = -33.5644496988513 +34000 ekin = 39.9276187144877 | erot = 24.3494773308424 | epot = -97.8415457422145 | etot = -33.5644496968845 +35000 ekin = 40.0972017271435 | erot = 24.3220925820239 | epot = -97.9837440042528 | etot = -33.5644496950853 +36000 ekin = 40.3554758289771 | erot = 24.3121132861365 | epot = -98.2320388089549 | etot = -33.5644496938413 +37000 ekin = 40.725317224184 | erot = 24.3194531164605 | epot = -98.609220034252 | etot = -33.5644496936075 +38000 ekin = 41.218461457732 | erot = 24.3399425111004 | epot = -99.1228536635587 | etot = -33.5644496947263 +39000 ekin = 41.8315835745714 | erot = 24.3642621379406 | epot = -99.7602954097942 | etot = -33.5644496972823 +40000 ekin = 42.5444333388251 | erot = 24.3777906096196 | epot = -100.486673649663 | etot = -33.5644497012185 +41000 ekin = 43.3221534386109 | erot = 24.3619359806986 | epot = -101.248539124816 | etot = -33.5644497055066 +42000 ekin = 44.1232219530967 | erot = 24.2968159627003 | epot = -101.984487625365 | etot = -33.5644497095679 +43000 ekin = 44.9043008441337 | erot = 24.1647850477424 | epot = -102.633535604781 | etot = -33.5644497129045 +44000 ekin = 45.6258073685752 | erot = 23.953775477634 | epot = -103.144032561026 | etot = -33.5644497148168 +45000 ekin = 46.2557013508714 | erot = 23.6596129163789 | epot = -103.47976398388 | etot = -33.5644497166297 +46000 ekin = 46.7711396854557 | erot = 23.2746461161514 | epot = -103.610235519167 | etot = -33.5644497175602 +47000 ekin = 47.1576706465411 | erot = 22.7983985986745 | epot = -103.520518961436 | etot = -33.5644497162202 +48000 ekin = 47.4067411848222 | erot = 22.24189270691 | epot = -103.213083606728 | etot = -33.5644497149961 +49000 ekin = 47.5134307536666 | erot = 21.6212608371929 | epot = -102.699141303773 | etot = -33.5644497129138 +50000 ekin = 47.4750496002024 | erot = 20.9637753825411 | epot = -102.003274691403 | etot = -33.5644497086593 +51000 ekin = 47.2893433305646 | erot = 20.3140174296332 | epot = -101.16781046916 | etot = -33.5644497089623 +52000 ekin = 46.9527474071891 | erot = 19.68086855223 | epot = -100.198065668178 | etot = -33.5644497087592 +53000 ekin = 46.4669221029442 | erot = 19.0628634962126 | epot = -99.0942353064246 | etot = -33.5644497072679 +54000 ekin = 45.8347987943733 | erot = 18.4752794596827 | epot = -97.8745279599043 | etot = -33.5644497058483 +55000 ekin = 45.059031662863 | erot = 17.9341671577873 | epot = -96.5576485255764 | etot = -33.5644497049261 +56000 ekin = 44.1409291390452 | erot = 17.4520797326571 | epot = -95.1574585762239 | etot = -33.5644497045216 +57000 ekin = 43.0792908324212 | erot = 17.037334269452 | epot = -93.6810748066111 | etot = -33.5644497047379 +58000 ekin = 41.8704923540597 | erot = 16.6939394056073 | epot = -92.1288814650802 | etot = -33.5644497054133 +59000 ekin = 40.5509408803223 | erot = 16.4316140927959 | epot = -90.5470046657477 | etot = -33.5644496926295 +60000 ekin = 39.1975830612663 | erot = 16.2583411314114 | epot = -89.0203738856257 | etot = -33.5644496929479 +61000 ekin = 35.7114984384222 | erot = 15.7928074869524 | epot = -85.0687559055441 | etot = -33.5644499801694 +62000 ekin = 34.7372517507007 | erot = 15.809440909604 | epot = -84.1111427028021 | etot = -33.5644500424973 +63000 ekin = 35.8178089566977 | erot = 16.1653492511931 | epot = -85.5476088513045 | etot = -33.5644506434137 +64000 ekin = 34.869236370394 | erot = 16.1670101597177 | epot = -84.6006971860832 | etot = -33.5644506559716 +65000 ekin = 33.846449455543 | erot = 16.1402632189656 | epot = -83.5511633293454 | etot = -33.5644506548368 +66000 ekin = 32.7636419796955 | erot = 16.0751240440813 | epot = -82.4032166770506 | etot = -33.5644506532738 +67000 ekin = 31.6420680628872 | erot = 15.9705642956741 | epot = -81.1770830093356 | etot = -33.5644506507743 +68000 ekin = 30.5061166759946 | erot = 15.8342590047122 | epot = -79.9048263284351 | etot = -33.5644506477283 +69000 ekin = 29.3793899831114 | erot = 15.678409289176 | epot = -78.6222499180454 | etot = -33.564450645758 +70000 ekin = 28.284277797061 | erot = 15.5192251789805 | epot = -77.367953618708 | etot = -33.5644506426665 +71000 ekin = 27.2428007223107 | erot = 15.3775924468402 | epot = -76.1848438089708 | etot = -33.5644506398198 +72000 ekin = 26.2738583640461 | erot = 15.2738682128153 | epot = -75.1121772142973 | etot = -33.5644506374359 +73000 ekin = 25.3929266243307 | erot = 15.225238925301 | epot = -74.1826161852592 | etot = -33.5644506356275 +74000 ekin = 24.6118800235875 | erot = 15.2440811522995 | epot = -73.4204118109363 | etot = -33.5644506350493 +75000 ekin = 23.9285421197333 | erot = 15.2937064902868 | epot = -72.7866996078847 | etot = -33.5644509978647 +76000 ekin = 23.6014258497327 | erot = 14.5530249139084 | epot = -71.7189013877706 | etot = -33.5644506241296 +77000 ekin = 24.0021186681933 | erot = 14.66725562535 | epot = -72.2338249119969 | etot = -33.5644506184536 +78000 ekin = 23.7667117018407 | erot = 14.8821032755388 | epot = -72.2132655967916 | etot = -33.5644506194121 +79000 ekin = 23.6362408803388 | erot = 15.1573231058555 | epot = -72.3580146069914 | etot = -33.5644506207971 +80000 ekin = 23.6008292998118 | erot = 15.4801164769236 | epot = -72.6453963992449 | etot = -33.5644506225096 +81000 ekin = 23.6479278988449 | erot = 15.8366782045229 | epot = -73.0490567276759 | etot = -33.5644506243081 +82000 ekin = 23.7631958527379 | erot = 16.2135577483199 | epot = -73.5412042271318 | etot = -33.564450626074 +83000 ekin = 23.9313380513044 | erot = 16.5989137528036 | epot = -74.0947024318235 | etot = -33.5644506277155 +84000 ekin = 24.1405337461447 | erot = 16.9832739889227 | epot = -74.6882583637861 | etot = -33.5644506287187 +85000 ekin = 24.3851366362422 | erot = 17.3594190811811 | epot = -75.3090063475336 | etot = -33.5644506301102 +86000 ekin = 24.6499622429148 | erot = 17.7229731863063 | epot = -75.9373860604631 | etot = -33.5644506312419 +87000 ekin = 24.9195866966142 | erot = 18.0734917202568 | epot = -76.5575290489246 | etot = -33.5644506320536 +88000 ekin = 25.1793742014108 | erot = 18.4146339772126 | epot = -77.158458811171 | etot = -33.5644506325475 +89000 ekin = 25.4156568494618 | erot = 18.7539686693896 | epot = -77.7340761514978 | etot = -33.5644506326463 +90000 ekin = 25.609684003566 | erot = 19.1040901404673 | epot = -78.2782247770974 | etot = -33.564450633064 +91000 ekin = 25.7348417969789 | erot = 19.4865010462251 | epot = -78.7857934757922 | etot = -33.5644506325881 +92000 ekin = 25.7824117490226 | erot = 19.9168308436453 | epot = -79.2636932257737 | etot = -33.5644506331059 +93000 ekin = 25.7436484203098 | erot = 20.4015276208925 | epot = -79.7096266744475 | etot = -33.5644506332451 +94000 ekin = 25.610748739912 | erot = 20.9498819611228 | epot = -80.1250813342097 | etot = -33.564450633175 +95000 ekin = 25.3788454256151 | erot = 21.5718811146967 | epot = -80.5151771730825 | etot = -33.5644506327707 +96000 ekin = 25.0476635684712 | erot = 22.2778886106733 | epot = -80.8900028110714 | etot = -33.5644506319269 +97000 ekin = 24.6228037012614 | erot = 23.0785820232949 | epot = -81.2658363557903 | etot = -33.5644506312341 +98000 ekin = 24.116365030335 | erot = 23.980262455698 | epot = -81.6610781157446 | etot = -33.5644506297116 +99000 ekin = 23.5467601995519 | erot = 24.9897227937723 | epot = -82.1009336213321 | etot = -33.5644506280079 +100000 ekin = 22.9377076830261 | erot = 26.1125444287915 | epot = -82.6147027382494 | etot = -33.5644506264317 +101000 ekin = 22.3162402354139 | erot = 27.3495277986758 | epot = -83.2302186594579 | etot = -33.5644506253682 +102000 ekin = 21.7099673799574 | erot = 28.6941289887295 | epot = -83.9685469938778 | etot = -33.5644506251909 +103000 ekin = 21.1440927333159 | erot = 30.130413105192 | epot = -84.8389564646036 | etot = -33.5644506260957 +104000 ekin = 20.6390360732686 | erot = 31.6318076720637 | epot = -85.8352943737421 | etot = -33.5644506284097 +105000 ekin = 20.2097356178038 | erot = 33.1559511277913 | epot = -86.9301373769589 | etot = -33.5644506313638 +106000 ekin = 19.8659962936248 | erot = 34.6591523175119 | epot = -88.0895992442174 | etot = -33.5644506330807 +107000 ekin = 19.6196926152683 | erot = 36.100338989929 | epot = -89.2844822415662 | etot = -33.5644506363689 +108000 ekin = 19.4737764770476 | erot = 37.4404659123052 | epot = -90.4786930287931 | etot = -33.5644506394402 +109000 ekin = 19.4257211238038 | erot = 38.6395727467607 | epot = -91.629744515762 | etot = -33.5644506451975 +110000 ekin = 19.4643317381238 | erot = 39.6495422786812 | epot = -92.6783246653831 | etot = -33.5644506485781 +111000 ekin = 19.5812097010519 | erot = 40.4340503208693 | epot = -93.5797106732657 | etot = -33.5644506513445 +112000 ekin = 19.7688752467972 | erot = 40.9641614008033 | epot = -94.2974873012517 | etot = -33.5644506536512 +113000 ekin = 20.0199352606492 | erot = 41.223561768641 | epot = -94.8079476827741 | etot = -33.5644506534839 +114000 ekin = 20.3316783135505 | erot = 41.2208106095099 | epot = -95.1169395739246 | etot = -33.5644506508641 +115000 ekin = 20.7092934859859 | erot = 40.9902193450394 | epot = -95.2639634786059 | etot = -33.5644506475807 +116000 ekin = 21.1584070130099 | erot = 40.5711692188944 | epot = -95.2940268781066 | etot = -33.5644506462023 +117000 ekin = 21.6717401642325 | erot = 40.0068194492249 | epot = -95.2430102574753 | etot = -33.5644506440179 +118000 ekin = 22.2304498749719 | erot = 39.3449170917023 | epot = -95.1398176087352 | etot = -33.5644506420609 +119000 ekin = 22.8040322747547 | erot = 38.6279078104798 | epot = -94.9963907285559 | etot = -33.5644506433214 +120000 ekin = 23.3636455910815 | erot = 37.8733163419356 | epot = -94.801412577584 | etot = -33.564450644567 +121000 ekin = 23.888334247959 | erot = 37.0853024873726 | epot = -94.5380873807864 | etot = -33.5644506454549 +122000 ekin = 24.3628295450746 | erot = 36.261752125414 | epot = -94.1890323184781 | etot = -33.5644506479895 +123000 ekin = 24.7728939422985 | erot = 35.3896441641771 | epot = -93.7269887541641 | etot = -33.5644506476884 +124000 ekin = 25.1206142173508 | erot = 34.4655545655651 | epot = -93.1506194284814 | etot = -33.5644506455655 +125000 ekin = 25.4216604350097 | erot = 33.5035163209335 | epot = -92.4896273979244 | etot = -33.5644506419812 +126000 ekin = 25.6927735129491 | erot = 32.5281184075519 | epot = -91.785342561111 | etot = -33.56445064061 +127000 ekin = 25.9460883081172 | erot = 31.5650113724827 | epot = -91.0755503181662 | etot = -33.5644506375663 +128000 ekin = 26.1993872383141 | erot = 30.6366650539223 | epot = -90.4005029275325 | etot = -33.5644506352961 +129000 ekin = 26.4652741313034 | erot = 29.7610339508673 | epot = -89.7907587151 | etot = -33.5644506329293 +130000 ekin = 26.7486727551205 | erot = 28.9506137583613 | epot = -89.2637371464484 | etot = -33.5644506329667 +131000 ekin = 27.0469092029044 | erot = 28.2034442942497 | epot = -88.8148041302872 | etot = -33.5644506331331 +132000 ekin = 27.3542874865317 | erot = 27.5160813886976 | epot = -88.4348195084739 | etot = -33.5644506332445 +133000 ekin = 27.6627378161423 | erot = 26.8888107912285 | epot = -88.115999240573 | etot = -33.5644506332022 +134000 ekin = 27.9672923181963 | erot = 26.3214524159622 | epot = -87.8531953671591 | etot = -33.5644506330005 +135000 ekin = 28.2641150379083 | erot = 25.8141340320102 | epot = -87.6426997025991 | etot = -33.5644506326806 +136000 ekin = 28.5509978141388 | erot = 25.3673179322113 | epot = -87.4827663786189 | etot = -33.5644506322688 +137000 ekin = 28.825915909221 | erot = 24.9801644637638 | epot = -87.3705310053152 | etot = -33.5644506323304 +138000 ekin = 29.0842610649339 | erot = 24.6492546073933 | epot = -87.2979663044158 | etot = -33.5644506320886 +139000 ekin = 29.3272222877258 | erot = 24.3700782380065 | epot = -87.2617511574337 | etot = -33.5644506317014 +140000 ekin = 29.5579798491516 | erot = 24.1376580585779 | epot = -87.2600885391681 | etot = -33.5644506314386 +141000 ekin = 29.7799846346249 | erot = 23.9462429930569 | epot = -87.2906782589382 | etot = -33.5644506312564 +142000 ekin = 29.9959841884915 | erot = 23.7899704636026 | epot = -87.3504052833039 | etot = -33.5644506312098 +143000 ekin = 30.2070349127784 | erot = 23.6632996950641 | epot = -87.4347852391688 | etot = -33.5644506313262 +144000 ekin = 30.4118840029093 | erot = 23.5613798569338 | epot = -87.5377144914396 | etot = -33.5644506315964 +145000 ekin = 30.6068456872279 | erot = 23.4803656669067 | epot = -87.6516619861204 | etot = -33.5644506319858 +146000 ekin = 30.7861230778205 | erot = 23.4176420010718 | epot = -87.7682157113363 | etot = -33.564450632444 +147000 ekin = 30.9424364770385 | erot = 23.3719366394227 | epot = -87.8788237493778 | etot = -33.5644506329166 +148000 ekin = 31.0677916134912 | erot = 23.3433216080134 | epot = -87.9755638548586 | etot = -33.564450633354 +149000 ekin = 31.1542520331539 | erot = 23.3331254537123 | epot = -88.0518281205811 | etot = -33.5644506337149 +150000 ekin = 31.1946418128177 | erot = 23.3437996409507 | epot = -88.1028920877325 | etot = -33.5644506339642 +151000 ekin = 31.1838063839322 | erot = 23.3785936220168 | epot = -88.1268506397958 | etot = -33.5644506338469 +152000 ekin = 31.1202290278299 | erot = 23.4412183836703 | epot = -88.125898045246 | etot = -33.5644506337458 +153000 ekin = 31.0032553217637 | erot = 23.5372189789008 | epot = -88.1049249338467 | etot = -33.5644506331823 +154000 ekin = 30.8354559406746 | erot = 23.6729952126947 | epot = -88.072901786295 | etot = -33.5644506329257 +155000 ekin = 30.6186135870526 | erot = 23.8551009557647 | epot = -88.0381651751689 | etot = -33.5644506323515 +156000 ekin = 30.3571457582588 | erot = 24.0914721103742 | epot = -88.0130685002276 | etot = -33.5644506315946 +157000 ekin = 30.0574108500346 | erot = 24.3907046676056 | epot = -88.0125661484805 | etot = -33.5644506308403 +158000 ekin = 29.725675692331 | erot = 24.7625567196346 | epot = -88.0526830421764 | etot = -33.5644506302108 +159000 ekin = 29.3667041507893 | erot = 25.2124449846207 | epot = -88.1435997656297 | etot = -33.5644506302196 +160000 ekin = 28.9829375848235 | erot = 25.7406189361246 | epot = -88.2880071520098 | etot = -33.5644506310616 +161000 ekin = 28.5708031098605 | erot = 26.3449808633556 | epot = -88.4802346049489 | etot = -33.5644506317328 +162000 ekin = 28.1278607476035 | erot = 27.0188065006218 | epot = -88.7111178809852 | etot = -33.5644506327599 +163000 ekin = 27.6515523776407 | erot = 27.7508923428456 | epot = -88.9668953542076 | etot = -33.5644506337213 +164000 ekin = 27.1398166575402 | erot = 28.5265897115496 | epot = -89.2308570046128 | etot = -33.5644506355231 +165000 ekin = 26.5901801294065 | erot = 29.3236809534458 | epot = -89.478311720126 | etot = -33.5644506372737 +166000 ekin = 26.0027550423919 | erot = 30.1148491025849 | epot = -89.6820547838262 | etot = -33.5644506388494 +167000 ekin = 25.3815734826352 | erot = 30.8714146428653 | epot = -89.8174387656332 | etot = -33.5644506401327 +168000 ekin = 24.7338280126162 | erot = 31.5656853660149 | epot = -89.8639640196475 | etot = -33.5644506410165 +169000 ekin = 24.0691061638267 | erot = 32.1733410341194 | epot = -89.8068978394102 | etot = -33.5644506414641 +170000 ekin = 23.3986380903836 | erot = 32.6761770397884 | epot = -89.6392657713668 | etot = -33.5644506411948 +171000 ekin = 22.7350947047584 | erot = 33.0649339609198 | epot = -89.3644793058835 | etot = -33.5644506402053 +172000 ekin = 22.0927595064379 | erot = 33.3397459263013 | epot = -88.9969560711893 | etot = -33.5644506384501 +173000 ekin = 21.4881436133187 | erot = 33.5098602953101 | epot = -88.5624545444277 | etot = -33.5644506357989 +174000 ekin = 20.9424106184102 | erot = 33.5950638981363 | epot = -88.1019251458272 | etot = -33.5644506292807 +175000 ekin = 20.4887725385275 | erot = 33.6332952588425 | epot = -87.6865184248803 | etot = -33.5644506275103 +176000 ekin = 20.1459992745671 | erot = 33.6413286939806 | epot = -87.3517785947221 | etot = -33.5644506261744 +177000 ekin = 19.9273952403454 | erot = 33.6264319072445 | epot = -87.1182777732156 | etot = -33.5644506256257 +178000 ekin = 19.84052681153 | erot = 33.5862782738547 | epot = -86.9912557125122 | etot = -33.5644506271275 +179000 ekin = 19.8828425829422 | erot = 33.5043404166422 | epot = -86.9516336276486 | etot = -33.5644506280643 +180000 ekin = 20.0524881206256 | erot = 33.3671042345402 | epot = -86.9840429849155 | etot = -33.5644506297498 +181000 ekin = 20.3414841297343 | erot = 33.1581782006442 | epot = -87.0641129622508 | etot = -33.5644506318723 +182000 ekin = 20.7352057198233 | erot = 32.8612622822509 | epot = -87.1609186361483 | etot = -33.5644506340741 +183000 ekin = 21.2137106223656 | erot = 32.4647477949401 | epot = -87.2429090532129 | etot = -33.5644506359073 +184000 ekin = 21.753758772068 | erot = 31.9655803613331 | epot = -87.2837897705988 | etot = -33.5644506371977 +185000 ekin = 22.3286746031905 | erot = 31.370802203917 | epot = -87.2639274448021 | etot = -33.5644506376946 +186000 ekin = 22.9115100132914 | erot = 30.6990331536457 | epot = -87.1749938042645 | etot = -33.5644506373275 +187000 ekin = 23.4775030152646 | erot = 29.9792070479746 | epot = -87.0211606994591 | etot = -33.5644506362199 +188000 ekin = 24.0059463479979 | erot = 29.2469949106376 | epot = -86.8173918933481 | etot = -33.5644506347127 +189000 ekin = 24.4809955944256 | erot = 28.5392131436686 | epot = -86.5846593713985 | etot = -33.5644506333043 +190000 ekin = 24.8911658073154 | erot = 27.8871249849478 | epot = -86.3427414248055 | etot = -33.5644506325423 +191000 ekin = 25.2275609419593 | erot = 27.3101259966561 | epot = -86.1021375715933 | etot = -33.5644506329779 +192000 ekin = 25.4831011426815 | erot = 26.8121375634353 | epot = -85.8596893403699 | etot = -33.564450634253 +193000 ekin = 25.2930335715005 | erot = 26.6410891958414 | epot = -85.4985734034485 | etot = -33.5644506361066 +194000 ekin = 25.0352601614032 | erot = 26.6525265483622 | epot = -85.2522373921937 | etot = -33.5644506824282 +195000 ekin = 25.0363508840855 | erot = 26.2378500699517 | epot = -84.8386516236489 | etot = -33.5644506696116 +196000 ekin = 24.9648942549692 | erot = 25.78683024187 | epot = -84.3161751669041 | etot = -33.5644506700649 +197000 ekin = 24.820085073243 | erot = 25.3002719383723 | epot = -83.684807680623 | etot = -33.5644506690076 +198000 ekin = 24.617288458851 | erot = 24.7762496503728 | epot = -82.9579887758224 | etot = -33.5644506665986 +199000 ekin = 24.377048383026 | erot = 24.2259949153754 | epot = -82.1674939619447 | etot = -33.5644506635433 +200000 ekin = 24.1224360020296 | erot = 23.6691820640811 | epot = -81.3560687261525 | etot = -33.5644506600419 +201000 ekin = 23.8775516468454 | erot = 23.1291743985682 | epot = -80.5711767022417 | etot = -33.5644506568281 +202000 ekin = 23.6646103059715 | erot = 22.6276096876224 | epot = -79.8566706478819 | etot = -33.5644506542881 +203000 ekin = 23.5017139925529 | erot = 22.1809863327317 | epot = -79.2471509779019 | etot = -33.5644506526173 +204000 ekin = 23.4012931943585 | erot = 21.7992926193315 | epot = -78.7650364652111 | etot = -33.5644506515211 +205000 ekin = 23.3698442687714 | erot = 21.4883950765849 | epot = -78.4226899967129 | etot = -33.5644506513567 +206000 ekin = 23.4080277663789 | erot = 21.2503388252137 | epot = -78.2228172433636 | etot = -33.5644506517709 +207000 ekin = 23.510672424487 | erot = 21.0828853352428 | epot = -78.1580084122739 | etot = -33.564450652544 +208000 ekin = 23.6683534180495 | erot = 20.982792192542 | epot = -78.2155962640683 | etot = -33.5644506534769 +209000 ekin = 23.8319531636201 | erot = 20.8686960092813 | epot = -78.2650998050279 | etot = -33.5644506321265 +210000 ekin = 24.1634900876329 | erot = 20.8246815259854 | epot = -78.5526222834702 | etot = -33.5644506698519 +211000 ekin = 24.4545474928994 | erot = 20.8320949387436 | epot = -78.851093093408 | etot = -33.564450661765 +212000 ekin = 24.7210588846791 | erot = 20.8889178093565 | epot = -79.1744273565292 | etot = -33.5644506624935 +213000 ekin = 24.9762555918523 | erot = 20.9956570670851 | epot = -79.5363633251146 | etot = -33.5644506661772 +214000 ekin = 25.205483004635 | erot = 21.1345527593194 | epot = -79.904486430984 | etot = -33.5644506670296 +215000 ekin = 25.4055444850383 | erot = 21.2948000239929 | epot = -80.2647951765804 | etot = -33.5644506675491 +216000 ekin = 25.5773395549964 | erot = 21.4659469017795 | epot = -80.6077371248515 | etot = -33.5644506680756 +217000 ekin = 25.7224226233962 | erot = 21.6383314527683 | epot = -80.925204744665 | etot = -33.5644506685004 +218000 ekin = 25.8456307141035 | erot = 21.7996006617643 | epot = -81.2096820449061 | etot = -33.5644506690382 +219000 ekin = 25.952452354154 | erot = 21.9358336225146 | epot = -81.4527366463123 | etot = -33.5644506696437 +220000 ekin = 26.0480501371105 | erot = 22.0331400323315 | epot = -81.6456408394103 | etot = -33.5644506699683 +221000 ekin = 26.1377559920962 | erot = 22.0801399062532 | epot = -81.7823465685503 | etot = -33.5644506702008 +222000 ekin = 26.2262421156876 | erot = 22.0692633440645 | epot = -81.8599561297652 | etot = -33.5644506700131 +223000 ekin = 26.3184403630104 | erot = 21.9982474658179 | epot = -81.8811384982303 | etot = -33.564450669402 +224000 ekin = 26.4171271373366 | erot = 21.8710288815827 | epot = -81.8526066880995 | etot = -33.5644506691801 +225000 ekin = 26.5225389104573 | erot = 21.6965423523224 | epot = -81.7835319309186 | etot = -33.5644506681389 +226000 ekin = 26.7157923548661 | erot = 21.3119214437974 | epot = -81.5921644821821 | etot = -33.5644506835186 +227000 ekin = 27.2484396437667 | erot = 20.6374955150002 | epot = -81.4503858460625 | etot = -33.5644506872956 +228000 ekin = 27.5078528971351 | erot = 20.2748179574298 | epot = -81.3471215226841 | etot = -33.5644506681192 +229000 ekin = 27.631283055081 | erot = 19.9858964954828 | epot = -81.1816302175522 | etot = -33.5644506669884 +230000 ekin = 27.7676058404106 | erot = 19.7189438600699 | epot = -81.0510003675314 | etot = -33.5644506670509 +231000 ekin = 27.917189899564 | erot = 19.4851196432342 | epot = -80.9667602108556 | etot = -33.5644506680573 +232000 ekin = 28.075807909483 | erot = 19.2892055600532 | epot = -80.9294641380291 | etot = -33.5644506684929 +233000 ekin = 28.2354888581566 | erot = 19.1284398309955 | epot = -80.9283793559269 | etot = -33.5644506667748 +234000 ekin = 28.3953039485291 | erot = 19.0132859353528 | epot = -80.973040551359 | etot = -33.564450667477 +235000 ekin = 28.5569493494324 | erot = 18.9585387746561 | epot = -81.0799387921139 | etot = -33.5644506680254 +236000 ekin = 28.7166448189416 | erot = 18.9671002034007 | epot = -81.2481956904871 | etot = -33.5644506681447 +237000 ekin = 28.872502381955 | erot = 19.0433381874402 | epot = -81.4802912373653 | etot = -33.5644506679701 +238000 ekin = 29.0257746255756 | erot = 19.1916941122086 | epot = -81.7819194053224 | etot = -33.5644506675381 +239000 ekin = 29.1795842186668 | erot = 19.4168064167523 | epot = -82.1608413028715 | etot = -33.5644506674523 +240000 ekin = 29.3337146101792 | erot = 19.7090725309346 | epot = -82.6072378097604 | etot = -33.5644506686467 +241000 ekin = 29.4868078966917 | erot = 20.0596352267871 | epot = -83.1108937927889 | etot = -33.5644506693101 +242000 ekin = 29.6351003169272 | erot = 20.4605457842645 | epot = -83.6600967716849 | etot = -33.5644506704932 +243000 ekin = 29.8921802425096 | erot = 20.6958964400126 | epot = -84.1525273495103 | etot = -33.564450666988 +244000 ekin = 30.2594419587612 | erot = 20.9649617308285 | epot = -84.788854393917 | etot = -33.5644507043273 +245000 ekin = 30.3074620328552 | erot = 21.3089995007004 | epot = -85.1809122847552 | etot = -33.5644507511996 +246000 ekin = 30.6998172933386 | erot = 21.0861202554748 | epot = -85.3503880690327 | etot = -33.5644505202193 +247000 ekin = 31.265212405902 | erot = 21.7433599271637 | epot = -86.5730230769931 | etot = -33.5644507439274 +248000 ekin = 31.2039013197071 | erot = 22.3578318777868 | epot = -87.1261839419724 | etot = -33.5644507444785 +249000 ekin = 31.0628965882674 | erot = 22.9361503364564 | epot = -87.563497668308 | etot = -33.5644507435842 +250000 ekin = 30.8544219835531 | erot = 23.4738999845616 | epot = -87.8927727106375 | etot = -33.5644507425228 +251000 ekin = 30.5979929542296 | erot = 23.9732495372637 | epot = -88.1356932312788 | etot = -33.5644507397854 +252000 ekin = 30.3186084933056 | erot = 24.4470234326924 | epot = -88.3300826628224 | etot = -33.5644507368245 +253000 ekin = 30.041632868323 | erot = 24.9117142614227 | epot = -88.5177978639943 | etot = -33.5644507342486 +254000 ekin = 29.6651322242815 | erot = 25.3352238224839 | epot = -88.5648072260565 | etot = -33.5644511792912 +255000 ekin = 27.9972596305184 | erot = 25.343644566417 | epot = -86.9053550134241 | etot = -33.5644508164887 +256000 ekin = 27.4480536506913 | erot = 26.2038023386853 | epot = -87.216306790649 | etot = -33.5644508012725 +257000 ekin = 28.5107044680624 | erot = 27.5793602337782 | epot = -89.6545158780358 | etot = -33.5644511761952 +258000 ekin = 28.9485040029259 | erot = 27.9141399630899 | epot = -90.4270947739431 | etot = -33.5644508079274 +259000 ekin = 29.1923898091059 | erot = 28.2760336628035 | epot = -91.0328742825817 | etot = -33.5644508106723 +260000 ekin = 29.442065950707 | erot = 28.6795119902558 | epot = -91.6860287570451 | etot = -33.5644508160824 +261000 ekin = 29.6845039883856 | erot = 29.1068404636931 | epot = -92.3557952701953 | etot = -33.5644508181166 +262000 ekin = 29.8834680797666 | erot = 29.5461970802723 | epot = -92.9941159814128 | etot = -33.5644508213739 +263000 ekin = 30.015935190767 | erot = 29.964909738063 | epot = -93.545295753821 | etot = -33.5644508249909 +264000 ekin = 30.0524877647281 | erot = 30.3384906869061 | epot = -93.9554292801698 | etot = -33.5644508285355 +265000 ekin = 29.9659450397407 | erot = 30.6431999052832 | epot = -94.1735957766809 | etot = -33.564450831657 +266000 ekin = 29.7355380957518 | erot = 30.8554934502802 | epot = -94.1554823800682 | etot = -33.5644508340362 +267000 ekin = 29.350217253177 | erot = 30.9531552650149 | epot = -93.8678233536528 | etot = -33.564450835461 +268000 ekin = 28.8109215600445 | erot = 30.9159121160384 | epot = -93.2912845119314 | etot = -33.5644508358484 +269000 ekin = 28.131229902636 | erot = 30.7258800106364 | epot = -92.4215607498827 | etot = -33.5644508366102 +270000 ekin = 27.3365120331628 | erot = 30.3685462542785 | epot = -91.26950914197 | etot = -33.5644508545286 +271000 ekin = 26.4621552466787 | erot = 29.8348321072734 | epot = -89.8614382055512 | etot = -33.5644508515991 +272000 ekin = 25.5514537841055 | erot = 29.123871510934 | epot = -88.2397761425329 | etot = -33.5644508474934 +273000 ekin = 24.6528090193024 | erot = 28.2453291639207 | epot = -86.4625890256565 | etot = -33.5644508424334 +274000 ekin = 23.8212346502742 | erot = 27.2200000603037 | epot = -84.6056855414942 | etot = -33.5644508309163 +275000 ekin = 22.9729777889705 | erot = 26.0804823635512 | epot = -82.6179111121121 | etot = -33.5644509595905 +276000 ekin = 22.0549791971374 | erot = 24.8883860441513 | epot = -80.5078160553758 | etot = -33.5644508140871 +277000 ekin = 22.291845448694 | erot = 23.6844629884807 | epot = -79.540759443928 | etot = -33.5644510067533 +278000 ekin = 22.2933944834771 | erot = 22.3796695906392 | epot = -78.2375149019929 | etot = -33.5644508278766 +279000 ekin = 22.3659748250016 | erot = 21.1183819743967 | epot = -77.0488076287097 | etot = -33.5644508293114 +280000 ekin = 22.5183002078625 | erot = 19.9334324614308 | epot = -76.0161834966431 | etot = -33.5644508273498 +281000 ekin = 22.7529481191411 | erot = 18.8478601493348 | epot = -75.1652590940351 | etot = -33.5644508255591 +282000 ekin = 23.0795879184867 | erot = 17.8776966475211 | epot = -74.5217353872447 | etot = -33.564450821237 +283000 ekin = 23.5210121271307 | erot = 17.0345324476566 | epot = -74.1199953957228 | etot = -33.5644508209355 +284000 ekin = 24.07992475589 | erot = 16.3233784658841 | epot = -73.9677540517476 | etot = -33.5644508299736 +285000 ekin = 24.7785446246423 | erot = 15.7478244913642 | epot = -74.0908199422233 | etot = -33.5644508262167 +286000 ekin = 25.636838734536 | erot = 15.3047487827835 | epot = -74.5060383422483 | etot = -33.5644508249288 +287000 ekin = 26.6214548224706 | erot = 14.9922504829288 | epot = -75.1781561308958 | etot = -33.5644508254964 +288000 ekin = 27.7267158888572 | erot = 14.8012865017013 | epot = -76.0924532218297 | etot = -33.5644508312711 +289000 ekin = 28.8920167227279 | erot = 14.7169892845691 | epot = -77.1734568439386 | etot = -33.5644508366416 +290000 ekin = 30.0553666648387 | erot = 14.7251675417572 | epot = -78.3449850482589 | etot = -33.5644508416631 +291000 ekin = 31.1595769632387 | erot = 14.811929120259 | epot = -79.5359569290839 | etot = -33.5644508455862 +292000 ekin = 32.1608216689813 | erot = 14.9640713088845 | epot = -80.6893438261509 | etot = -33.564450848285 +293000 ekin = 33.0319319380177 | erot = 15.168173905447 | epot = -81.7645566935966 | etot = -33.5644508501319 +294000 ekin = 33.7599421346976 | erot = 15.4088106779812 | epot = -82.7332036642767 | etot = -33.5644508515979 +295000 ekin = 34.3413485939712 | erot = 15.667394334235 | epot = -83.5731937811218 | etot = -33.5644508529156 +296000 ekin = 34.7782829446776 | erot = 15.9229210434175 | epot = -84.26565484209 | etot = -33.5644508539949 +297000 ekin = 35.0767101392392 | erot = 16.1546669536439 | epot = -84.7958279474754 | etot = -33.5644508545923 +298000 ekin = 35.2457989813493 | erot = 16.3457320030339 | epot = -85.1559818389166 | etot = -33.5644508545334 +299000 ekin = 35.2970066855207 | erot = 16.4859983979522 | epot = -85.347455937312 | etot = -33.564450853839 +300000 ekin = 35.2422237261662 | erot = 16.5735941681655 | epot = -85.3802687470049 | etot = -33.5644508526733 +301000 ekin = 35.0916597610801 | erot = 16.6147820199824 | epot = -85.2708926322694 | etot = -33.5644508512069 +302000 ekin = 34.8528128910573 | erot = 16.6227287108408 | epot = -85.0399924514116 | etot = -33.5644508495135 +303000 ekin = 34.5312597670619 | erot = 16.6156181966414 | epot = -84.7113288113064 | etot = -33.5644508476031 +304000 ekin = 34.1313674341479 | erot = 16.6227567332271 | epot = -84.3185750111593 | etot = -33.5644508437843 +305000 ekin = 33.6571822643538 | erot = 16.6720234605616 | epot = -83.8936565670797 | etot = -33.5644508421643 +306000 ekin = 33.1151986332185 | erot = 16.7769746117161 | epot = -83.4566240858681 | etot = -33.5644508409335 +307000 ekin = 32.5134330702932 | erot = 16.9437629167783 | epot = -83.02164682739 | etot = -33.5644508403184 +308000 ekin = 31.8601474906921 | erot = 17.1694637372502 | epot = -82.5940620683754 | etot = -33.564450840433 +309000 ekin = 31.1628016434689 | erot = 17.4420089824522 | epot = -82.169261466886 | etot = -33.564450840965 +310000 ekin = 30.4284939703374 | erot = 17.7430091431839 | epot = -81.7359539560138 | etot = -33.5644508424925 +311000 ekin = 29.6636970637345 | erot = 18.0450727084457 | epot = -81.2732206157263 | etot = -33.5644508435461 +312000 ekin = 28.8763119838581 | erot = 18.3211026916569 | epot = -80.7618655199121 | etot = -33.5644508443971 +313000 ekin = 28.0757317032389 | erot = 18.5482322978723 | epot = -80.18841484566 | etot = -33.5644508445488 +314000 ekin = 27.2754576015478 | erot = 18.7102692133214 | epot = -79.5501776586848 | etot = -33.5644508438156 +315000 ekin = 26.492751287582 | erot = 18.8002978243514 | epot = -78.8574999542526 | etot = -33.5644508423192 +316000 ekin = 25.7476825207451 | erot = 18.8201859998617 | epot = -78.1323193609057 | etot = -33.5644508402989 +317000 ekin = 25.061490505917 | erot = 18.7788964667389 | epot = -77.4048378106934 | etot = -33.5644508380374 +318000 ekin = 24.4546904069621 | erot = 18.6903703700711 | epot = -76.70951161281 | etot = -33.5644508357768 +319000 ekin = 23.9454326767099 | erot = 18.5716676910327 | epot = -76.0815512014053 | etot = -33.5644508336627 +320000 ekin = 23.5484361619436 | erot = 18.4417359442066 | epot = -75.5546229378898 | etot = -33.5644508317396 +321000 ekin = 23.2745454667293 | erot = 18.3209670206422 | epot = -75.1599633173638 | etot = -33.5644508299923 +322000 ekin = 23.1307065451601 | erot = 18.2311244117378 | epot = -74.9262817853413 | etot = -33.5644508284434 +323000 ekin = 23.1199305196705 | erot = 18.1948729379475 | epot = -74.8792542848651 | etot = -33.5644508272471 +324000 ekin = 23.2402241372721 | erot = 18.2346442881315 | epot = -75.0393192521543 | etot = -33.5644508267507 +325000 ekin = 23.4710021373605 | erot = 18.3668956955574 | epot = -75.4023486642627 | etot = -33.5644508313448 +326000 ekin = 23.7795455091373 | erot = 18.5932769387736 | epot = -75.9372732824513 | etot = -33.5644508345405 +327000 ekin = 24.1343713309104 | erot = 18.9009306660405 | epot = -76.5997528364855 | etot = -33.5644508395347 +328000 ekin = 24.4953646019651 | erot = 19.2611055951325 | epot = -77.3209210429526 | etot = -33.564450845855 +329000 ekin = 24.8184483225885 | erot = 19.6309716495633 | epot = -78.0138708245784 | etot = -33.5644508524265 +330000 ekin = 25.064815357625 | erot = 19.9600875040515 | epot = -78.5893537191764 | etot = -33.5644508574999 +331000 ekin = 25.210138372085 | erot = 20.2008919381964 | epot = -78.9754811706065 | etot = -33.5644508603252 +332000 ekin = 25.2457706637465 | erot = 20.3248269292201 | epot = -79.1350484525863 | etot = -33.5644508596197 +333000 ekin = 25.1861890028038 | erot = 20.3296166390246 | epot = -79.0802564973891 | etot = -33.5644508555607 +334000 ekin = 25.0662190978875 | erot = 20.2399843242263 | epot = -78.8706542713047 | etot = -33.5644508491909 +335000 ekin = 24.9333683334916 | erot = 20.10098162188 | epot = -78.5988007973609 | etot = -33.5644508419894 +336000 ekin = 24.838111457398 | erot = 19.9670256543986 | epot = -78.3695879471494 | etot = -33.5644508353528 +337000 ekin = 24.8247545149941 | erot = 19.8908557634947 | epot = -78.2800611092981 | etot = -33.5644508308092 +338000 ekin = 24.9246805340852 | erot = 19.9088859975653 | epot = -78.3980173596517 | etot = -33.5644508280012 +339000 ekin = 25.1522743468773 | erot = 20.043365846553 | epot = -78.7600910207995 | etot = -33.5644508273693 +340000 ekin = 25.5040328013693 | erot = 20.306324357249 | epot = -79.3748079873049 | etot = -33.5644508286866 +341000 ekin = 25.9593882031618 | erot = 20.6972938179444 | epot = -80.2211328525995 | etot = -33.5644508314932 +342000 ekin = 26.4842114254738 | erot = 21.2060406180888 | epot = -81.2547028788679 | etot = -33.5644508353053 +343000 ekin = 27.0356929912357 | erot = 21.815327972342 | epot = -82.4154718031651 | etot = -33.5644508395875 +344000 ekin = 27.5676973344761 | erot = 22.5033872894512 | epot = -83.6355354677601 | etot = -33.5644508438328 +345000 ekin = 28.0359749646807 | erot = 23.2463366467675 | epot = -84.8467624590903 | etot = -33.5644508476421 +346000 ekin = 28.4026013552871 | erot = 24.0201112992161 | epot = -85.9871635052192 | etot = -33.564450850716 +347000 ekin = 28.6398915194528 | erot = 24.8020103746231 | epot = -87.0063527467572 | etot = -33.5644508526813 +348000 ekin = 28.7326075377482 | erot = 25.5714490942921 | epot = -87.8685074860267 | etot = -33.5644508539863 +349000 ekin = 28.6752584344036 | erot = 26.3100180841384 | epot = -88.549727373061 | etot = -33.564450854519 +350000 ekin = 28.4730637357079 | erot = 27.0009502159031 | epot = -89.038464806185 | etot = -33.564450854574 +351000 ekin = 28.1395378484453 | erot = 27.6270646736909 | epot = -89.3310533767997 | etot = -33.5644508546635 +352000 ekin = 27.692958073856 | erot = 28.1676652362281 | epot = -89.4250741653402 | etot = -33.5644508552561 +353000 ekin = 27.1526950366525 | erot = 28.5958100264823 | epot = -89.3129559196985 | etot = -33.5644508565636 +354000 ekin = 26.5365141387121 | erot = 28.8781341171817 | epot = -88.9790991141991 | etot = -33.5644508583052 +355000 ekin = 25.8598799836129 | erot = 28.9793031096872 | epot = -88.4036339528938 | etot = -33.5644508595937 +356000 ekin = 25.1375717946229 | erot = 28.8722956885124 | epot = -87.5743183424417 | etot = -33.5644508593064 +357000 ekin = 24.3868741548633 | erot = 28.5495289601074 | epot = -86.5008539716514 | etot = -33.5644508566807 +358000 ekin = 23.6300778926751 | erot = 28.0297879776407 | epot = -85.2243167221727 | etot = -33.5644508518569 +359000 ekin = 22.8939201469052 | erot = 27.355677035979 | epot = -83.8140480288444 | etot = -33.5644508459602 +360000 ekin = 22.206578007299 | erot = 26.5834479666855 | epot = -82.3544768140201 | etot = -33.5644508400356 +361000 ekin = 21.5986345635157 | erot = 25.7744654426823 | epot = -80.9375508370781 | etot = -33.5644508308802 +362000 ekin = 21.1083260621075 | erot = 24.989507840829 | epot = -79.6622847317925 | etot = -33.564450828856 +363000 ekin = 20.7375100619836 | erot = 24.2576398932737 | epot = -78.5596007834521 | etot = -33.5644508281948 +364000 ekin = 20.476003367975 | erot = 23.5946470163905 | epot = -77.635101212758 | etot = -33.5644508283926 +365000 ekin = 20.3079089893725 | erot = 23.009513896542 | epot = -76.8818737148766 | etot = -33.5644508289621 +366000 ekin = 20.2147979335995 | erot = 22.508371935773 | epot = -76.2876206988782 | etot = -33.5644508295058 +367000 ekin = 20.1786185360397 | erot = 22.0973297018217 | epot = -75.8403990676851 | etot = -33.5644508298237 +368000 ekin = 20.1837486799222 | erot = 21.7835270635243 | epot = -75.5317265733032 | etot = -33.5644508298567 +369000 ekin = 20.2182310118282 | erot = 21.574738818764 | epot = -75.3574206602716 | etot = -33.5644508296795 +370000 ekin = 20.2742556079065 | erot = 21.4781104693876 | epot = -75.3168169068296 | etot = -33.5644508295354 +371000 ekin = 20.3477066126427 | erot = 21.4982876398118 | epot = -75.4104450815928 | etot = -33.5644508291383 +372000 ekin = 20.4391769085492 | erot = 21.6370751258624 | epot = -75.6407028633193 | etot = -33.5644508289077 +373000 ekin = 20.5523906693865 | erot = 21.8921389377599 | epot = -76.0089804360328 | etot = -33.5644508288864 +374000 ekin = 20.6947607298497 | erot = 22.2561865203504 | epot = -76.5153980788613 | etot = -33.5644508286612 +375000 ekin = 20.8734352289465 | erot = 22.7176361068345 | epot = -77.1555221652783 | etot = -33.5644508294973 +376000 ekin = 21.089493504449 | erot = 23.2620769848747 | epot = -77.9160213199094 | etot = -33.5644508305857 +377000 ekin = 21.3446674636834 | erot = 23.8720082855239 | epot = -78.7811265807323 | etot = -33.5644508315251 +378000 ekin = 21.64248542288 | erot = 24.5275644040167 | epot = -79.7345006597438 | etot = -33.5644508328471 +379000 ekin = 21.9906215820674 | erot = 25.2058289791334 | epot = -80.760901395464 | etot = -33.5644508342632 +380000 ekin = 22.3975872844685 | erot = 25.8799316875408 | epot = -81.8419698098752 | etot = -33.5644508378659 +381000 ekin = 22.8474625363943 | erot = 26.5196756829191 | epot = -82.9315890607488 | etot = -33.5644508414354 +382000 ekin = 23.3214968284424 | erot = 27.0935868814443 | epot = -83.9795345552253 | etot = -33.5644508453386 +383000 ekin = 23.7989486472446 | erot = 27.5682880226977 | epot = -84.9316875190629 | etot = -33.5644508491206 +384000 ekin = 24.2602946690265 | erot = 27.9101784190738 | epot = -85.7349239404018 | etot = -33.5644508523015 +385000 ekin = 24.6909701694311 | erot = 28.0892515731128 | epot = -86.3446725966466 | etot = -33.5644508541027 +386000 ekin = 25.0758089633983 | erot = 28.0812872789257 | epot = -86.7215471012156 | etot = -33.5644508588916 +387000 ekin = 25.3886917944075 | erot = 27.8683599140167 | epot = -86.8215025662873 | etot = -33.5644508578631 +388000 ekin = 25.6321888108903 | erot = 27.4567876604955 | epot = -86.6534273266304 | etot = -33.5644508552446 +389000 ekin = 25.8173007945516 | erot = 26.8690369422729 | epot = -86.2507885889323 | etot = -33.5644508521078 +390000 ekin = 25.9562629244357 | erot = 26.1386991559259 | epot = -85.6594129285287 | etot = -33.5644508481671 +391000 ekin = 26.0625510048269 | erot = 25.3050096521924 | epot = -84.9320115015289 | etot = -33.5644508445096 +392000 ekin = 26.1477279258622 | erot = 24.4077754077168 | epot = -84.1199541750021 | etot = -33.5644508414231 +393000 ekin = 26.2207009126332 | erot = 23.4862823971765 | epot = -83.2714341487272 | etot = -33.5644508389175 +394000 ekin = 26.2880235523287 | erot = 22.5776047859249 | epot = -82.4300791763575 | etot = -33.5644508381039 +395000 ekin = 26.3461327830984 | erot = 21.6992206106144 | epot = -81.6098042311068 | etot = -33.564450837394 +396000 ekin = 26.3925769143903 | erot = 20.8648963380663 | epot = -80.8219240890407 | etot = -33.5644508365841 +397000 ekin = 26.428035758933 | erot = 20.0875980485209 | epot = -80.0800846430096 | etot = -33.5644508355556 +398000 ekin = 26.456826416021 | erot = 19.3805747697538 | epot = -79.4018520200386 | etot = -33.5644508342638 +399000 ekin = 26.486391084066 | erot = 18.7576183807505 | epot = -78.8084602983018 | etot = -33.5644508334853 +400000 ekin = 26.5240355653678 | erot = 18.2309165845048 | epot = -78.3194029820227 | etot = -33.5644508321501 +401000 ekin = 26.5785515874793 | erot = 17.8133011772033 | epot = -77.9563035960443 | etot = -33.5644508313617 +402000 ekin = 26.6553316875252 | erot = 17.514632436928 | epot = -77.734414956193 | etot = -33.5644508317398 +403000 ekin = 26.7508441445099 | erot = 17.3369800813554 | epot = -77.652275059838 | etot = -33.5644508339727 +404000 ekin = 26.847889984788 | erot = 17.2703664407998 | epot = -77.6827072638883 | etot = -33.5644508383005 +405000 ekin = 26.913648151536 | erot = 17.2906409832311 | epot = -77.7687399796104 | etot = -33.5644508448433 +406000 ekin = 26.902674398225 | erot = 17.3519919760325 | epot = -77.8191172252429 | etot = -33.5644508509854 +407000 ekin = 26.7697793194821 | erot = 17.4151352557073 | epot = -77.7493654299019 | etot = -33.5644508547125 +408000 ekin = 26.4852107134516 | erot = 17.4599310842078 | epot = -77.5095926523416 | etot = -33.5644508546822 +409000 ekin = 26.0447937750069 | erot = 17.489715636437 | epot = -77.0989602629569 | etot = -33.5644508515129 +410000 ekin = 25.4686689668068 | erot = 17.525308599665 | epot = -76.5584284134685 | etot = -33.5644508469967 +411000 ekin = 24.7901856107123 | erot = 17.5925678630378 | epot = -75.9472043167211 | etot = -33.5644508429709 +412000 ekin = 24.0429450725907 | erot = 17.7112262982761 | epot = -75.3186222112118 | etot = -33.5644508403449 +413000 ekin = 23.2530709445256 | erot = 17.8904894596477 | epot = -74.7080112432066 | etot = -33.5644508390334 +414000 ekin = 22.4380957573478 | erot = 18.1309089877695 | epot = -74.1334555836572 | etot = -33.5644508385398 +415000 ekin = 21.6095002976116 | erot = 18.4284521142751 | epot = -73.602403250255 | etot = -33.5644508383683 +416000 ekin = 20.7759703157875 | erot = 18.7780315269414 | epot = -73.1184526809263 | etot = -33.5644508381974 +417000 ekin = 19.9459219947443 | erot = 19.1754390641456 | epot = -72.6858118967654 | etot = -33.5644508378755 +418000 ekin = 19.1290603146812 | erot = 19.6178812354861 | epot = -72.3113923875162 | etot = -33.5644508373488 +419000 ekin = 18.337241174772 | erot = 20.1037315119174 | epot = -72.0054235233031 | etot = -33.5644508366137 +420000 ekin = 17.5848708568132 | erot = 20.6319495840779 | epot = -71.7812712766011 | etot = -33.56445083571 +421000 ekin = 16.8888669767983 | erot = 21.2012508779721 | epot = -71.654568689522 | etot = -33.5644508347516 +422000 ekin = 16.2680311854784 | erot = 21.8088345390476 | epot = -71.6413165584825 | etot = -33.5644508339565 +423000 ekin = 15.7416423467535 | erot = 22.4484657014465 | epot = -71.7545588818543 | etot = -33.5644508336543 +424000 ekin = 15.3271568811325 | erot = 23.1079611162026 | epot = -71.9995688315969 | etot = -33.5644508342617 +425000 ekin = 15.0370245443348 | erot = 23.7664993128454 | epot = -72.3679746933972 | etot = -33.564450836217 +426000 ekin = 14.8748792453187 | erot = 24.3924933231442 | epot = -72.8318234082976 | etot = -33.5644508398346 +427000 ekin = 14.832039809902 | erot = 24.9432466995696 | epot = -73.3397373544821 | etot = -33.5644508450105 +428000 ekin = 14.8863924965724 | erot = 25.3682827941945 | epot = -73.8191261416202 | etot = -33.5644508508533 +429000 ekin = 15.0062259695096 | erot = 25.6182665544711 | epot = -74.1889433796231 | etot = -33.5644508556425 +430000 ekin = 15.1595389321706 | erot = 25.6590201133014 | epot = -74.3830099029893 | etot = -33.5644508575173 +431000 ekin = 15.3249133699301 | erot = 25.4851984008896 | epot = -74.3745626264541 | etot = -33.5644508556344 +432000 ekin = 15.4974987577291 | erot = 25.1253113466907 | epot = -74.1872609551818 | etot = -33.564450850762 +433000 ekin = 15.6867402477113 | erot = 24.6339851579825 | epot = -73.8851762504141 | etot = -33.5644508447203 +434000 ekin = 15.9084789524794 | erot = 24.0759117528502 | epot = -73.5488415445721 | etot = -33.5644508392426 +435000 ekin = 16.1769022059295 | erot = 23.5103596607615 | epot = -73.2517127019844 | etot = -33.5644508352934 +436000 ekin = 16.4997173059121 | erot = 22.982276516596 | epot = -73.0464446556282 | etot = -33.5644508331201 +437000 ekin = 16.8769806267692 | erot = 22.5199344326914 | epot = -72.9613658918858 | etot = -33.5644508324252 +438000 ekin = 17.3021259571189 | erot = 22.1372453982692 | epot = -73.0038221882045 | etot = -33.5644508328165 +439000 ekin = 17.7637229038904 | erot = 21.8373393625555 | epot = -73.1655131003915 | etot = -33.5644508339456 +440000 ekin = 18.2471223979642 | erot = 21.6157595595105 | epot = -73.4273327930288 | etot = -33.5644508355542 +441000 ekin = 18.7357201395202 | erot = 21.4628710845264 | epot = -73.7630420615274 | etot = -33.5644508374808 +442000 ekin = 19.2118878212758 | erot = 21.3654515420967 | epot = -74.1417902029639 | etot = -33.5644508395913 +443000 ekin = 19.6577318124847 | erot = 21.3079015376766 | epot = -74.53008419193 | etot = -33.5644508417687 +444000 ekin = 20.0558238633514 | erot = 21.2733344148632 | epot = -74.8936091221088 | etot = -33.5644508438943 +445000 ekin = 20.3899893912765 | erot = 21.2445884062657 | epot = -75.1990286433742 | etot = -33.564450845832 +446000 ekin = 20.6461236044623 | erot = 21.2052857367731 | epot = -75.4158601887455 | etot = -33.5644508475101 +447000 ekin = 20.8131102288242 | erot = 21.1405154512163 | epot = -75.5180765281394 | etot = -33.5644508480989 +448000 ekin = 20.8836321566285 | erot = 21.0415726580739 | epot = -75.4896556637134 | etot = -33.564450849011 +449000 ekin = 20.8549766397521 | erot = 20.9006105485552 | epot = -75.3200380377527 | etot = -33.5644508494454 +450000 ekin = 20.7289995990038 | erot = 20.7094982244637 | epot = -75.0029486728388 | etot = -33.5644508493713 +451000 ekin = 20.5121237021944 | erot = 20.4634057687326 | epot = -74.5399803196977 | etot = -33.5644508487708 +452000 ekin = 20.2152499009175 | erot = 20.1611428754593 | epot = -73.9408436240171 | etot = -33.5644508476403 +453000 ekin = 19.8534700766569 | erot = 19.8054562088314 | epot = -73.2233771314871 | etot = -33.5644508459988 +454000 ekin = 19.4456214293028 | erot = 19.4031472753521 | epot = -72.4132195485558 | etot = -33.5644508439009 +455000 ekin = 19.013720522958 | erot = 18.9648723131976 | epot = -71.5430436775731 | etot = -33.5644508414174 +456000 ekin = 18.5823093301098 | erot = 18.5046119868785 | epot = -70.6513721556565 | etot = -33.5644508386682 +457000 ekin = 18.1775784950835 | erot = 18.0385547552667 | epot = -69.78058408621 | etot = -33.5644508358598 +458000 ekin = 17.8262193053526 | erot = 17.5834820270548 | epot = -68.9741521653779 | etot = -33.5644508329705 +459000 ekin = 17.5544328315452 | erot = 17.1574115033618 | epot = -68.2762951652654 | etot = -33.5644508303584 +460000 ekin = 17.3857834994296 | erot = 16.7769882364438 | epot = -67.7272225641225 | etot = -33.5644508282491 +461000 ekin = 17.3389537757626 | erot = 16.455973724737 | epot = -67.3593783273661 | etot = -33.5644508268665 +462000 ekin = 17.4254421541841 | erot = 16.2041333991817 | epot = -67.1940263797602 | etot = -33.5644508263943 +463000 ekin = 17.6475549838229 | erot = 16.0264214063364 | epot = -67.2384272171003 | etot = -33.564450826941 +464000 ekin = 17.9971528391881 | erot = 15.9226257283447 | epot = -67.4842293960243 | etot = -33.5644508284914 +465000 ekin = 18.4555654856042 | erot = 15.8876205732821 | epot = -67.9076368897882 | etot = -33.5644508309019 +466000 ekin = 18.994833816268 | erot = 15.9122553308001 | epot = -68.4715399809881 | etot = -33.56445083392 +467000 ekin = 19.5800987880665 | erot = 15.9847161184822 | epot = -69.1292657437925 | etot = -33.5644508372437 +468000 ekin = 20.1726645576357 | erot = 16.092033474867 | epot = -69.8291488730892 | etot = -33.5644508405865 +469000 ekin = 20.7331520539173 | erot = 16.2213910260308 | epot = -70.5189939236682 | etot = -33.5644508437201 +470000 ekin = 21.2242791251891 | erot = 16.3610502015494 | epot = -71.1497801732201 | etot = -33.5644508464816 +471000 ekin = 21.6130740295016 | erot = 16.5009517692281 | epot = -71.6784766474807 | etot = -33.5644508487511 +472000 ekin = 21.8725913830426 | erot = 16.6332178546314 | epot = -72.0702600880887 | etot = -33.5644508504148 +473000 ekin = 21.9833185471591 | erot = 16.7527436323979 | epot = -72.3005130309141 | etot = -33.5644508513571 +474000 ekin = 21.9344099206197 | erot = 16.8578720765084 | epot = -72.3567328486035 | etot = -33.5644508514753 +475000 ekin = 21.7247480854268 | erot = 16.9509439426178 | epot = -72.2401428787492 | etot = -33.5644508507046 +476000 ekin = 21.3637036554458 | erot = 17.0384540155613 | epot = -71.9666085200589 | etot = -33.5644508490518 +477000 ekin = 20.8713853163245 | erot = 17.1305938642667 | epot = -71.5664300271903 | etot = -33.5644508465991 +478000 ekin = 20.278105615873 | erot = 17.2401904856046 | epot = -71.0827469450555 | etot = -33.5644508435779 +479000 ekin = 19.6228148922665 | erot = 17.3807417056378 | epot = -70.568007438203 | etot = -33.5644508402987 +480000 ekin = 18.9501924820064 | erot = 17.5641098022629 | epot = -70.0787531214702 | etot = -33.5644508372009 +481000 ekin = 18.3063999207717 | erot = 17.7978626898958 | epot = -69.6687134454551 | etot = -33.5644508347876 +482000 ekin = 17.7338800308325 | erot = 18.0826185785594 | epot = -69.3809494429303 | etot = -33.5644508335384 +483000 ekin = 17.2661333869276 | erot = 18.4098565339483 | epot = -69.240440754661 | etot = -33.5644508337851 +484000 ekin = 16.9123469725788 | erot = 18.5839236849874 | epot = -69.0607216152016 | etot = -33.5644509576354 +485000 ekin = 17.2473052114824 | erot = 17.4463141951386 | epot = -68.2580700313457 | etot = -33.5644506247246 +486000 ekin = 18.3155143091698 | erot = 17.1832730976792 | epot = -69.0632384225994 | etot = -33.5644510157505 +487000 ekin = 18.1324826614411 | erot = 17.2801627137661 | epot = -68.97709615336 | etot = -33.5644507781527 +488000 ekin = 18.065066671032 | erot = 17.4264266856946 | epot = -69.0559441347504 | etot = -33.5644507780238 +489000 ekin = 18.1230207571896 | erot = 17.62013699274 | epot = -69.3076085290087 | etot = -33.5644507790791 +490000 ekin = 18.2959502060246 | erot = 17.8551924365762 | epot = -69.7155934233775 | etot = -33.5644507807768 +491000 ekin = 18.5602651979885 | erot = 18.1239992625185 | epot = -70.2487152439638 | etot = -33.5644507834568 +492000 ekin = 18.8855238698909 | erot = 18.4159985147992 | epot = -70.8659731703599 | etot = -33.5644507856698 +493000 ekin = 19.2395352565568 | erot = 18.728264479198 | epot = -71.5322505227183 | etot = -33.5644507869634 +494000 ekin = 19.5921246700955 | erot = 19.0689157919617 | epot = -72.2254912499723 | etot = -33.564450787915 +495000 ekin = 19.0728202093635 | erot = 18.9158482409358 | epot = -71.553118977483 | etot = -33.5644505271837 +496000 ekin = 19.8797920565295 | erot = 18.7380967908333 | epot = -72.1823393794609 | etot = -33.5644505320982 +497000 ekin = 21.3129327566087 | erot = 19.2208596910155 | epot = -74.0982428018017 | etot = -33.5644503541775 +498000 ekin = 21.3264694811286 | erot = 19.7980335585692 | epot = -74.6889533936585 | etot = -33.5644503539607 +499000 ekin = 21.2778907742156 | erot = 20.4793064458065 | epot = -75.3216475743002 | etot = -33.5644503542781 +500000 ekin = 21.1661916282903 | erot = 21.2581781223902 | epot = -75.988820105787 | etot = -33.5644503551065 +501000 ekin = 20.9926825375652 | erot = 22.1178388255783 | epot = -76.6749717195959 | etot = -33.5644503564525 +502000 ekin = 20.7610606941479 | erot = 23.0317414653473 | epot = -77.3572525175607 | etot = -33.5644503580655 +503000 ekin = 20.4798770188399 | erot = 23.9650377707536 | epot = -78.0093651497042 | etot = -33.5644503601106 +504000 ekin = 20.1546807719764 | erot = 24.8789199645846 | epot = -78.5980510989298 | etot = -33.5644503623688 +505000 ekin = 19.7897861052766 | erot = 25.7326258924132 | epot = -79.0868623624994 | etot = -33.5644503648096 +506000 ekin = 19.3875459003549 | erot = 26.4882337371013 | epot = -79.4402300038003 | etot = -33.564450366344 +507000 ekin = 18.9527707503713 | erot = 27.1161379584882 | epot = -79.6333590756734 | etot = -33.5644503668138 +508000 ekin = 18.4930541127617 | erot = 27.6003825990922 | epot = -79.6578870777478 | etot = -33.5644503658939 +509000 ekin = 18.0182547166152 | erot = 27.9414911095304 | epot = -79.5241961902308 | etot = -33.5644503640852 +510000 ekin = 17.5239659446583 | erot = 28.1499521523349 | epot = -79.2383684583427 | etot = -33.5644503613495 +511000 ekin = 17.0202767588224 | erot = 28.2490270330593 | epot = -78.8337541499512 | etot = -33.5644503580695 +512000 ekin = 16.5245718006517 | erot = 28.2698315419544 | epot = -78.3588536974674 | etot = -33.5644503548613 +513000 ekin = 16.0539184296555 | erot = 28.2435719405511 | epot = -77.8619407224233 | etot = -33.5644503522167 +514000 ekin = 15.6229539751463 | erot = 28.1963871950865 | epot = -77.3837915206358 | etot = -33.564450350403 +515000 ekin = 15.2424792420144 | erot = 28.1464443105655 | epot = -76.9533739021307 | etot = -33.5644503495508 +516000 ekin = 14.9188926056263 | erot = 28.102754035252 | epot = -76.5860969902898 | etot = -33.5644503494115 +517000 ekin = 14.6543809151572 | erot = 28.0678237290645 | epot = -76.286654994032 | etot = -33.5644503498102 +518000 ekin = 14.4476572455448 | erot = 28.0395642675265 | epot = -76.0516718635495 | etot = -33.5644503504781 +519000 ekin = 14.2950490439313 | erot = 28.0138489409074 | epot = -75.8733483359815 | etot = -33.5644503511427 +520000 ekin = 14.1917488336712 | erot = 27.9870813583917 | epot = -75.7432805436438 | etot = -33.564450351581 +521000 ekin = 14.1329830510129 | erot = 27.9581295478616 | epot = -75.6555629505529 | etot = -33.5644503516784 +522000 ekin = 14.1002586402904 | erot = 27.7732671764717 | epot = -75.4379761963452 | etot = -33.5644503795831 +523000 ekin = 14.1969588160089 | erot = 27.1027118580652 | epot = -74.8641209749246 | etot = -33.5644503008506 +524000 ekin = 14.7378402614501 | erot = 26.616408914504 | epot = -74.9186994724366 | etot = -33.5644502964825 +525000 ekin = 15.506867285083 | erot = 26.5883544533635 | epot = -75.6596721107952 | etot = -33.5644503723486 +526000 ekin = 15.8574449977295 | erot = 26.6724957238465 | epot = -76.0943910941999 | etot = -33.5644503726239 +527000 ekin = 16.0112069682755 | erot = 26.735509894999 | epot = -76.3111672365705 | etot = -33.5644503732961 +528000 ekin = 16.1641744091399 | erot = 26.794797881151 | epot = -76.5234226642097 | etot = -33.5644503739187 +529000 ekin = 16.3159009762014 | erot = 26.8380825380496 | epot = -76.7184338885631 | etot = -33.564450374312 +530000 ekin = 16.4667477211871 | erot = 26.8553312025443 | epot = -76.8865292981414 | etot = -33.5644503744099 +531000 ekin = 16.6177352356877 | erot = 26.8400251085783 | epot = -77.0222107185202 | etot = -33.5644503742542 +532000 ekin = 16.770215067808 | erot = 26.7891084873303 | epot = -77.1237739290464 | etot = -33.5644503739081 +533000 ekin = 16.9253640369286 | erot = 26.7024973873184 | epot = -77.1923117977069 | etot = -33.5644503734599 +534000 ekin = 17.083644786901 | erot = 26.5822176528864 | epot = -77.2303128128235 | etot = -33.5644503730361 +535000 ekin = 17.2444487917795 | erot = 26.4310079588738 | epot = -77.2399071233944 | etot = -33.5644503727411 +536000 ekin = 17.4060591056372 | erot = 26.2510049056998 | epot = -77.2215143839431 | etot = -33.5644503726061 +537000 ekin = 17.565899198427 | erot = 26.0431264908893 | epot = -77.1734760618753 | etot = -33.5644503725589 +538000 ekin = 17.7209415439151 | erot = 25.807444121848 | epot = -77.0928360383798 | etot = -33.5644503726168 +539000 ekin = 17.8681497081321 | erot = 25.5433035299374 | epot = -76.9759036107203 | etot = -33.5644503726507 +540000 ekin = 18.0048631565718 | erot = 25.2502517038857 | epot = -76.8195652330541 | etot = -33.5644503725966 +541000 ekin = 18.129064827171 | erot = 24.9288645877469 | epot = -76.6223797873357 | etot = -33.5644503724178 +542000 ekin = 18.2395164939016 | erot = 24.5811691615965 | epot = -76.3851360275838 | etot = -33.5644503720856 +543000 ekin = 18.3357700080052 | erot = 24.210846834268 | epot = -76.1110672139389 | etot = -33.5644503716657 +544000 ekin = 18.4180615073977 | erot = 23.8229131244208 | epot = -75.8054250029922 | etot = -33.5644503711738 +545000 ekin = 18.48709013 | erot = 23.4236993423704 | epot = -75.475239842524 | etot = -33.5644503701536 +546000 ekin = 18.5436104708162 | erot = 23.023272620427 | epot = -75.1313334610026 | etot = -33.5644503697594 +547000 ekin = 18.5881260728255 | erot = 22.6282216102247 | epot = -74.780798052539 | etot = -33.5644503694888 +548000 ekin = 18.6206521539779 | erot = 22.2431161969749 | epot = -74.4282187199115 | etot = -33.5644503689587 +549000 ekin = 18.6395328552822 | erot = 21.8731131587291 | epot = -74.0770963833356 | etot = -33.5644503693243 +550000 ekin = 18.6420012526372 | erot = 21.5194517195331 | epot = -73.7259033420982 | etot = -33.5644503699279 +551000 ekin = 18.6249210292856 | erot = 21.1784779028361 | epot = -73.3678493028498 | etot = -33.5644503707282 +552000 ekin = 18.5841928768992 | erot = 20.8452278495212 | epot = -72.9938710980166 | etot = -33.5644503715962 +553000 ekin = 18.515212705724 | erot = 20.5148731368217 | epot = -72.5945362148738 | etot = -33.5644503723281 +554000 ekin = 18.4136816909966 | erot = 20.1848933331084 | epot = -72.1630253967881 | etot = -33.5644503726831 +555000 ekin = 18.2766906401233 | erot = 19.857476932628 | epot = -71.6986179451961 | etot = -33.5644503724447 +556000 ekin = 18.1040115049041 | erot = 19.5406874735951 | epot = -71.20914935019 | etot = -33.5644503716908 +557000 ekin = 17.8992309647499 | erot = 19.2497226287959 | epot = -70.7134039634794 | etot = -33.5644503699335 +558000 ekin = 17.6705778374572 | erot = 19.0080857253366 | epot = -70.2431139302706 | etot = -33.5644503674768 +559000 ekin = 17.4315653927809 | erot = 18.8444628123191 | epot = -69.8404785695829 | etot = -33.5644503644829 +560000 ekin = 17.2006230348878 | erot = 18.7901643782654 | epot = -69.5552377744807 | etot = -33.5644503613275 +561000 ekin = 16.9995569160732 | erot = 18.8749610237664 | epot = -69.438968298262 | etot = -33.5644503584223 +562000 ekin = 16.8505251060201 | erot = 19.1232120100743 | epot = -69.538187472407 | etot = -33.5644503563126 +563000 ekin = 16.7718160200182 | erot = 19.5498137335684 | epot = -69.8860801091477 | etot = -33.5644503555612 +564000 ekin = 16.7730284254869 | erot = 20.1561760612857 | epot = -70.4936548437135 | etot = -33.564450356941 +565000 ekin = 16.8503463818591 | erot = 20.9261148982968 | epot = -71.3409116403028 | etot = -33.5644503601468 +566000 ekin = 16.9881817954648 | erot = 21.8252877510101 | epot = -72.3779199117371 | etot = -33.5644503652621 +567000 ekin = 17.1597730194767 | erot = 22.8021750341433 | epot = -73.5263984254872 | etot = -33.5644503718672 +568000 ekin = 17.3309908966704 | erot = 23.7909429898642 | epot = -74.6863842658269 | etot = -33.5644503792923 +569000 ekin = 17.4658946017947 | erot = 24.7167318453097 | epot = -75.7470768337898 | etot = -33.5644503866854 +570000 ekin = 17.5327796656957 | erot = 25.5030724456584 | epot = -76.6003025044407 | etot = -33.5644503930867 +571000 ekin = 17.5098280200956 | erot = 26.0808668137263 | epot = -77.1551452313793 | etot = -33.5644503975575 +572000 ekin = 17.3896134298641 | erot = 26.3976580231972 | epot = -77.3517218524132 | etot = -33.5644503993519 +573000 ekin = 17.1817696520727 | erot = 26.4252545062395 | epot = -77.1714745564325 | etot = -33.5644503981203 +574000 ekin = 16.9132012155478 | erot = 26.1636856780794 | epot = -76.6413372876784 | etot = -33.5644503940512 +575000 ekin = 16.6253831480204 | erot = 25.6401831359933 | epot = -75.8300166719201 | etot = -33.5644503879064 +576000 ekin = 16.380585448721 | erot = 24.9437607561783 | epot = -74.8887965737009 | etot = -33.5644503688016 +577000 ekin = 16.2309295888517 | erot = 24.1552332190076 | epot = -73.9506131738505 | etot = -33.5644503659912 +578000 ekin = 16.2003426792014 | erot = 23.2996785341935 | epot = -73.0644715774378 | etot = -33.5644503640429 +579000 ekin = 16.2983938260692 | erot = 22.403268564264 | epot = -72.2661127535552 | etot = -33.564450363222 +580000 ekin = 16.5164282817949 | erot = 21.4889399504527 | epot = -71.5698185979652 | etot = -33.5644503657176 +581000 ekin = 16.8294131729517 | erot = 20.5770732253488 | epot = -70.9709367638666 | etot = -33.5644503655661 +582000 ekin = 17.2014342865815 | erot = 19.7085617423075 | epot = -70.4744463947337 | etot = -33.5644503658447 +583000 ekin = 17.5894541379175 | erot = 18.9251667746001 | epot = -70.0790712786264 | etot = -33.5644503661089 +584000 ekin = 17.9521233670864 | erot = 18.2657373645481 | epot = -69.7823110977226 | etot = -33.5644503660881 +585000 ekin = 18.2577014583726 | erot = 17.7627566558239 | epot = -69.5849084798981 | etot = -33.5644503657016 +586000 ekin = 18.4890373219802 | erot = 17.4391816025382 | epot = -69.4926692894764 | etot = -33.564450364958 +587000 ekin = 18.6451700996557 | erot = 17.3070654479175 | epot = -69.5166859114532 | etot = -33.56445036388 +588000 ekin = 18.7400423388426 | erot = 17.3682960794591 | epot = -69.6727887808625 | etot = -33.5644503625608 +589000 ekin = 18.7988289995881 | erot = 17.6163757903826 | epot = -69.9796551512482 | etot = -33.5644503612775 +590000 ekin = 18.8521852512136 | erot = 18.0377077417099 | epot = -70.4543433534176 | etot = -33.5644503604942 +591000 ekin = 18.9335216734591 | erot = 18.6145318738827 | epot = -71.1125039068147 | etot = -33.5644503594728 +592000 ekin = 19.0736372367424 | erot = 19.3273958987853 | epot = -71.9654834959436 | etot = -33.5644503604159 +593000 ekin = 19.2836835998251 | erot = 20.1464047126482 | epot = -72.9945386752994 | etot = -33.5644503628261 +594000 ekin = 19.5596584182911 | erot = 21.034123237702 | epot = -74.1582320224138 | etot = -33.5644503664207 +595000 ekin = 19.8847224289421 | erot = 21.9477887878841 | epot = -75.3969615874945 | etot = -33.5644503706683 +596000 ekin = 20.2229995980596 | erot = 22.8321032481879 | epot = -76.6195532314308 | etot = -33.5644503851833 +597000 ekin = 20.5134057747578 | erot = 23.6125551263639 | epot = -77.690411290674 | etot = -33.5644503895523 +598000 ekin = 20.7238255187825 | erot = 24.2466753991533 | epot = -78.5349513101318 | etot = -33.564450392196 +599000 ekin = 20.8326105241634 | erot = 24.7094660562249 | epot = -79.1065269733091 | etot = -33.5644503929208 +600000 ekin = 20.8281928837872 | erot = 24.9942677730575 | epot = -79.3869110487785 | etot = -33.5644503919338 +601000 ekin = 20.7081769101586 | erot = 25.1108515584272 | epot = -79.3834788582876 | etot = -33.5644503897018 +602000 ekin = 20.4770754644872 | erot = 25.0812117067637 | epot = -79.1227375580319 | etot = -33.564450386781 +603000 ekin = 20.1436196145649 | erot = 24.9343592774281 | epot = -78.642429275663 | etot = -33.5644503836701 +604000 ekin = 19.718418586643 | erot = 24.7015463496202 | epot = -77.9844153169741 | etot = -33.5644503807109 +605000 ekin = 19.2123955084805 | erot = 24.4128183909086 | epot = -77.1896642774627 | etot = -33.5644503780737 +606000 ekin = 18.6360571568103 | erot = 24.0951290270779 | epot = -76.2956365596783 | etot = -33.5644503757901 +607000 ekin = 17.9994317315232 | erot = 23.7717793966555 | epot = -75.3356615019793 | etot = -33.5644503738006 +608000 ekin = 17.3124228754835 | erot = 23.4627525856982 | epot = -74.3396258331827 | etot = -33.5644503720009 +609000 ekin = 16.5853412867126 | erot = 23.1855122482213 | epot = -73.3353039052169 | etot = -33.5644503702829 +610000 ekin = 15.8294285552829 | erot = 22.9559130662675 | epot = -72.349791990107 | etot = -33.5644503685566 +611000 ekin = 15.0572484570073 | erot = 22.7889597209054 | epot = -71.4106585446845 | etot = -33.5644503667718 +612000 ekin = 14.2829782525896 | erot = 22.6991649599953 | epot = -70.5465935774999 | etot = -33.564450364915 +613000 ekin = 13.5233158608979 | erot = 22.7018063034666 | epot = -69.789572526273 | etot = -33.5644503619085 +614000 ekin = 12.7974443554635 | erot = 22.8128628324568 | epot = -69.1747575482518 | etot = -33.5644503603315 +615000 ekin = 12.1222485230176 | erot = 23.0409824260638 | epot = -68.727681308147 | etot = -33.5644503590656 +616000 ekin = 11.5143476716423 | erot = 23.3894333510186 | epot = -68.468231381177 | etot = -33.5644503585161 +617000 ekin = 10.9895105320919 | erot = 23.8529820645469 | epot = -68.4069429553071 | etot = -33.5644503586684 +618000 ekin = 10.562142737904 | erot = 24.4166592385434 | epot = -68.5432523362142 | etot = -33.5644503597668 +619000 ekin = 10.2447233169864 | erot = 25.053936124725 | epot = -68.8631098035728 | etot = -33.5644503618614 +620000 ekin = 10.0473729684105 | erot = 25.7263958146269 | epot = -69.3382191478437 | etot = -33.5644503648063 +621000 ekin = 9.97770919372447 | erot = 26.386029455057 | epot = -69.9281890170002 | etot = -33.5644503682187 +622000 ekin = 10.0410058298604 | erot = 26.9805251344677 | epot = -70.5859813358563 | etot = -33.5644503715282 +623000 ekin = 10.2405907653606 | erot = 27.4608678076243 | epot = -71.265908947125 | etot = -33.5644503741401 +624000 ekin = 10.5781077618222 | erot = 27.789174960281 | epot = -71.9317330977985 | etot = -33.5644503756953 +625000 ekin = 11.0534790507876 | erot = 27.9443540029372 | epot = -72.5622834297716 | etot = -33.5644503760469 +626000 ekin = 11.665023962676 | erot = 27.9236660630966 | epot = -73.153140401212 | etot = -33.5644503754394 +627000 ekin = 12.4090657095855 | erot = 27.7401487506199 | epot = -73.7136648344174 | etot = -33.564450374212 +628000 ekin = 13.2797303352362 | erot = 27.4180442687031 | epot = -74.2622249766746 | etot = -33.5644503727353 +629000 ekin = 14.2227247828091 | erot = 26.9288523650796 | epot = -74.716027794269 | etot = -33.5644506463803 +630000 ekin = 14.6371369670079 | erot = 25.6849986219067 | epot = -73.8865860644015 | etot = -33.5644504754868 +631000 ekin = 15.1932748253831 | erot = 24.8015291116418 | epot = -73.5592542941192 | etot = -33.5644503570943 +632000 ekin = 16.584223183011 | erot = 25.1927867331162 | epot = -75.341460399694 | etot = -33.5644504835668 +633000 ekin = 18.1129981078216 | erot = 25.8399990857076 | epot = -77.5174478439555 | etot = -33.5644506504263 +634000 ekin = 19.1483265856614 | erot = 25.7387528535892 | epot = -78.4515299890265 | etot = -33.564450549776 +635000 ekin = 20.1638306106813 | erot = 25.6154971447985 | epot = -79.3437783094146 | etot = -33.5644505539348 +636000 ekin = 21.1529452215294 | erot = 25.4927802223992 | epot = -80.2101760029174 | etot = -33.5644505589887 +637000 ekin = 22.076840414127 | erot = 25.3376757551748 | epot = -80.9789667330327 | etot = -33.5644505637309 +638000 ekin = 22.8998086513204 | erot = 25.1175243534268 | epot = -81.5817835716912 | etot = -33.564450566944 +639000 ekin = 23.5958452423371 | erot = 24.810324027069 | epot = -81.970619837404 | etot = -33.5644505679979 +640000 ekin = 24.1448393959509 | erot = 24.4104070773779 | epot = -82.1196970414061 | etot = -33.5644505680774 +641000 ekin = 24.5337741528747 | erot = 23.9290519069577 | epot = -82.0272766245586 | etot = -33.5644505647262 +642000 ekin = 24.7698696452211 | erot = 23.3958020412245 | epot = -81.7301222481214 | etot = -33.5644505616758 +643000 ekin = 24.8669267986387 | erot = 22.8392829406438 | epot = -81.270660298016 | etot = -33.5644505587335 +644000 ekin = 24.8431155056926 | erot = 22.2830723080152 | epot = -80.6906383699449 | etot = -33.5644505562371 +645000 ekin = 24.7193046979039 | erot = 21.7428697624476 | epot = -80.0266250145381 | etot = -33.5644505541866 +646000 ekin = 24.5180931827109 | erot = 21.2270132547761 | epot = -79.3095569899392 | etot = -33.5644505524521 +647000 ekin = 24.2628521130092 | erot = 20.7388201342314 | epot = -78.5661227982078 | etot = -33.5644505509672 +648000 ekin = 23.9761808135735 | erot = 20.2787945271196 | epot = -77.8194258904783 | etot = -33.5644505497851 +649000 ekin = 23.67787365498 | erot = 19.8458221792402 | epot = -77.0881463832164 | etot = -33.5644505489962 +650000 ekin = 23.3831896135476 | erot = 19.4375683304372 | epot = -76.3852084925965 | etot = -33.5644505486117 +651000 ekin = 23.1045251387838 | erot = 19.0455994386645 | epot = -75.714575126721 | etot = -33.5644505492727 +652000 ekin = 22.852554089729 | erot = 18.660058243978 | epot = -75.0770628826327 | etot = -33.5644505489257 +653000 ekin = 22.6343633028422 | erot = 18.2797742486811 | epot = -74.4785880997844 | etot = -33.5644505482611 +654000 ekin = 22.457706160496 | erot = 17.9066943677479 | epot = -73.9288510753647 | etot = -33.5644505471209 +655000 ekin = 22.3323244895908 | erot = 17.5466477598824 | epot = -73.4434227950449 | etot = -33.5644505455717 +656000 ekin = 22.2694639392795 | erot = 17.2090068009683 | epot = -73.0429212841433 | etot = -33.5644505438955 +657000 ekin = 22.2796962944035 | erot = 16.9050137475 | epot = -72.7491605844585 | etot = -33.564450542555 +658000 ekin = 22.3696390695847 | erot = 16.644764495761 | epot = -72.578854107433 | etot = -33.5644505420873 +659000 ekin = 22.538589477759 | erot = 16.4332539543396 | epot = -72.5362939750541 | etot = -33.5644505429556 +660000 ekin = 22.7761662587416 | erot = 16.2664693862647 | epot = -72.6070861903694 | etot = -33.5644505453631 +661000 ekin = 23.06230224551 | erot = 16.1290340508052 | epot = -72.7557868430349 | etot = -33.5644505467196 +662000 ekin = 23.3837240385233 | erot = 15.9907831586697 | epot = -72.9389579078995 | etot = -33.5644507107065 +663000 ekin = 23.0541480011267 | erot = 16.1177804885964 | epot = -72.7363790496029 | etot = -33.5644505598799 +664000 ekin = 22.9781515363897 | erot = 16.5698259347579 | epot = -73.1124281192206 | etot = -33.5644506480731 +665000 ekin = 23.374978691534 | erot = 16.4117827405633 | epot = -73.3512120004714 | etot = -33.5644505683742 +666000 ekin = 23.7239501856893 | erot = 16.0357448198421 | epot = -73.3241455722274 | etot = -33.5644505666959 +667000 ekin = 24.0215049450261 | erot = 15.6311856369932 | epot = -73.2171411449521 | etot = -33.5644505629329 +668000 ekin = 24.2720292277934 | erot = 15.2431977237525 | epot = -73.0796775108255 | etot = -33.5644505592796 +669000 ekin = 24.4823401844299 | erot = 14.9164487057863 | epot = -72.9632394465769 | etot = -33.5644505563607 +670000 ekin = 24.6591929169718 | erot = 14.6865199574777 | epot = -72.9101634287588 | etot = -33.5644505543093 +671000 ekin = 24.7891522546301 | erot = 14.5781166473157 | epot = -72.9317194579636 | etot = -33.5644505560177 +672000 ekin = 24.8512867496603 | erot = 14.6015183439962 | epot = -73.0172556489739 | etot = -33.5644505553173 +673000 ekin = 24.8569569355798 | erot = 14.7562217137542 | epot = -73.1776292039339 | etot = -33.5644505545999 +674000 ekin = 24.8222537580567 | erot = 15.0373554087232 | epot = -73.4240597206098 | etot = -33.5644505538298 +675000 ekin = 24.7663204260849 | erot = 15.437295119434 | epot = -73.7680660987755 | etot = -33.5644505532566 +676000 ekin = 24.707973141147 | erot = 15.9453732713287 | epot = -74.2177969658379 | etot = -33.5644505533623 +677000 ekin = 24.660603838739 | erot = 16.5455776357113 | epot = -74.7706320292609 | etot = -33.5644505548106 +678000 ekin = 24.6267378747401 | erot = 17.2129758015017 | epot = -75.4041642342705 | etot = -33.5644505580287 +679000 ekin = 24.5940505550725 | erot = 17.9117017662871 | epot = -76.07020288433 | etot = -33.5644505629703 +680000 ekin = 24.5356055096688 | erot = 18.5957689108381 | epot = -76.6958249893355 | etot = -33.5644505688286 +681000 ekin = 24.4156570895309 | erot = 19.2149559854727 | epot = -77.1950636491504 | etot = -33.5644505741468 +682000 ekin = 24.1989519849675 | erot = 19.7242966838354 | epot = -77.4876992464688 | etot = -33.564450577666 +683000 ekin = 23.8604728477913 | erot = 20.0938581667108 | epot = -77.5187815925336 | etot = -33.5644505780315 +684000 ekin = 23.3975557786275 | erot = 20.3180971806807 | epot = -77.2801035347717 | etot = -33.5644505754635 +685000 ekin = 22.8290459836148 | erot = 20.4129669387004 | epot = -76.80646349322 | etot = -33.5644505709048 +686000 ekin = 22.1833688822011 | erot = 20.3969948279682 | epot = -76.1448143063362 | etot = -33.5644505961669 +687000 ekin = 21.4529188815913 | erot = 20.156733845752 | epot = -75.1741032924797 | etot = -33.5644505651364 +688000 ekin = 20.8420414151281 | erot = 19.8330340922101 | epot = -74.2395260487824 | etot = -33.5644505414442 +689000 ekin = 20.4850454817099 | erot = 19.6177759053663 | epot = -73.6672719440564 | etot = -33.5644505569803 +690000 ekin = 20.2236705266713 | erot = 19.4736760202794 | epot = -73.2617971242667 | etot = -33.564450577316 +691000 ekin = 19.9277329712649 | erot = 19.3525548964651 | epot = -72.8447384060534 | etot = -33.5644505383235 +692000 ekin = 19.7615779525566 | erot = 19.3271485933787 | epot = -72.6531770837385 | etot = -33.5644505378033 +693000 ekin = 19.7317397129722 | erot = 19.4147876345959 | epot = -72.7109778863946 | etot = -33.5644505388264 +694000 ekin = 19.8186070325243 | erot = 19.6208277624943 | epot = -73.0038853362896 | etot = -33.564450541271 +695000 ekin = 19.9894250231729 | erot = 19.9418771486032 | epot = -73.4957527165321 | etot = -33.564450544756 +696000 ekin = 20.2029739946799 | erot = 20.3669312876596 | epot = -74.1343558309875 | etot = -33.564450548648 +697000 ekin = 20.4154400731731 | erot = 20.8809193025054 | epot = -74.8608099281222 | etot = -33.5644505524438 +698000 ekin = 20.586206730696 | erot = 21.4669039267717 | epot = -75.6175612131891 | etot = -33.5644505557214 +699000 ekin = 20.6825995319384 | erot = 22.1076466775274 | epot = -76.3546967677076 | etot = -33.5644505582417 +700000 ekin = 20.6830084845855 | erot = 22.7863311628684 | epot = -77.0337902073835 | etot = -33.5644505599297 +701000 ekin = 20.5781931485901 | erot = 23.4865818275485 | epot = -77.6292255369506 | etot = -33.564450560812 +702000 ekin = 20.371075430213 | erot = 24.1923776502136 | epot = -78.1279036413659 | etot = -33.5644505609394 +703000 ekin = 20.0753347573217 | erot = 24.8884672573789 | epot = -78.5282525750727 | etot = -33.5644505603721 +704000 ekin = 19.7130379606064 | erot = 25.5614200071491 | epot = -78.8389085269638 | etot = -33.5644505592083 +705000 ekin = 19.3114467594506 | erot = 26.2008176331446 | epot = -79.0767149502457 | etot = -33.5644505576504 +706000 ekin = 18.8991937909467 | erot = 26.7996687741907 | epot = -79.2633131211814 | etot = -33.564450556044 +707000 ekin = 18.5022273003166 | erot = 27.3532672615511 | epot = -79.4199451167072 | etot = -33.5644505548395 +708000 ekin = 18.1401729285463 | erot = 27.8564307011234 | epot = -79.5610541841487 | etot = -33.5644505544791 +709000 ekin = 17.8234464183816 | erot = 28.2999901850205 | epot = -79.6878871586751 | etot = -33.564450555273 +710000 ekin = 17.5523632004475 | erot = 28.6678464680811 | epot = -79.7846602257444 | etot = -33.5644505572158 +711000 ekin = 17.3194109792864 | erot = 28.9359249914519 | epot = -79.8197865307446 | etot = -33.5644505600063 +712000 ekin = 17.111217474036 | erot = 29.0741670969728 | epot = -79.7498351340657 | etot = -33.5644505630569 +713000 ekin = 16.9121266187594 | erot = 29.0513180276171 | epot = -79.5278952119951 | etot = -33.5644505656186 +714000 ekin = 16.7079630651497 | erot = 28.8416092702073 | epot = -79.1140229023543 | etot = -33.5644505669974 +715000 ekin = 16.4890214395501 | erot = 28.4313561614791 | epot = -78.4848281678324 | etot = -33.5644505668032 +716000 ekin = 16.2513970064722 | erot = 27.8230898676209 | epot = -77.6389374391847 | etot = -33.5644505650916 +717000 ekin = 15.9963403713229 | erot = 27.0356716306523 | epot = -76.596462564269 | etot = -33.5644505622939 +718000 ekin = 15.736130323464 | erot = 26.1105494903108 | epot = -75.4111303700896 | etot = -33.5644505563148 +719000 ekin = 15.4991442318496 | erot = 25.1078869419086 | epot = -74.1714817285169 | etot = -33.5644505547587 +720000 ekin = 15.2869109972121 | erot = 24.0511182750597 | epot = -72.9024798253532 | etot = -33.5644505530814 +721000 ekin = 15.0983958358413 | erot = 22.9636187898412 | epot = -71.626465177062 | etot = -33.5644505513795 +722000 ekin = 14.9325120649955 | erot = 21.8688846290998 | epot = -70.3658472463797 | etot = -33.5644505522845 +723000 ekin = 14.7807572554272 | erot = 20.7831774063264 | epot = -69.1283852119052 | etot = -33.5644505501515 +724000 ekin = 14.6422909693862 | erot = 19.7295658945069 | epot = -67.9363074121321 | etot = -33.5644505482389 +725000 ekin = 14.5216204989736 | erot = 18.7315290196227 | epot = -66.8176000651018 | etot = -33.5644505465054 +726000 ekin = 14.4243651447115 | erot = 17.809249661836 | epot = -65.7980653514567 | etot = -33.5644505449092 +727000 ekin = 14.3569475468078 | erot = 16.9804196358499 | epot = -64.9018177260886 | etot = -33.5644505434309 +728000 ekin = 14.2536930560822 | erot = 16.2469828256636 | epot = -64.0651265321117 | etot = -33.5644506503659 +729000 ekin = 13.8457257245456 | erot = 15.9222518563763 | epot = -63.3324280816472 | etot = -33.5644505007253 +730000 ekin = 14.0260810346084 | erot = 15.9641149760264 | epot = -63.5546467080333 | etot = -33.5644506973986 +731000 ekin = 14.2598526192304 | erot = 15.8407237762752 | epot = -63.6650270930514 | etot = -33.5644506975458 +732000 ekin = 14.5606957103586 | erot = 15.8547631013359 | epot = -63.9799095104338 | etot = -33.5644506987393 +733000 ekin = 14.9193813445856 | erot = 16.0002143189837 | epot = -64.4840463647582 | etot = -33.5644507011889 +734000 ekin = 15.3191392245689 | erot = 16.2611439993741 | epot = -65.1447339288827 | etot = -33.5644507049397 +735000 ekin = 15.7356019022088 | erot = 16.6113471095831 | epot = -65.911399721546 | etot = -33.5644507097541 +736000 ekin = 16.1415246409903 | erot = 17.0234641329184 | epot = -66.7294394826049 | etot = -33.5644507086962 +737000 ekin = 16.518605610539 | erot = 17.489586803014 | epot = -67.5726431258992 | etot = -33.5644507123462 +738000 ekin = 16.8458492119022 | erot = 17.9860152352149 | epot = -68.396315162061 | etot = -33.5644507149439 +739000 ekin = 17.110149866212 | erot = 18.4929848438385 | epot = -69.1675854260346 | etot = -33.5644507159841 +740000 ekin = 17.3014321683493 | erot = 18.9830167808933 | epot = -69.8488996814749 | etot = -33.5644507322323 +741000 ekin = 17.3865900134394 | erot = 19.3806296464369 | epot = -70.3316703915551 | etot = -33.5644507316788 +742000 ekin = 17.3696644724057 | erot = 19.6766235522529 | epot = -70.6107387544097 | etot = -33.564450729751 +743000 ekin = 17.2668900438488 | erot = 19.8790967510142 | epot = -70.7104375221209 | etot = -33.564450727258 +744000 ekin = 17.0976280300632 | erot = 20.0010316334553 | epot = -70.6631103882319 | etot = -33.5644507247133 +745000 ekin = 16.8806625311108 | erot = 20.0570550573562 | epot = -70.5021683107691 | etot = -33.5644507223021 +746000 ekin = 16.6327129020178 | erot = 20.0624105084052 | epot = -70.2595741304376 | etot = -33.5644507200146 +747000 ekin = 16.3685004966554 | erot = 20.0330168533934 | epot = -69.9659680678506 | etot = -33.5644507178018 +748000 ekin = 16.1014104014477 | erot = 19.9854814624586 | epot = -69.6513425795718 | etot = -33.5644507156654 +749000 ekin = 15.844098014715 | erot = 19.9365592282997 | epot = -69.3451079566726 | etot = -33.5644507136579 +750000 ekin = 15.6090531926207 | erot = 19.9038963443694 | epot = -69.0774002481408 | etot = -33.5644507111507 +751000 ekin = 15.4083916161874 | erot = 19.9047162304915 | epot = -68.8775585564482 | etot = -33.5644507097693 +752000 ekin = 15.2531866593796 | erot = 19.9485427659139 | epot = -68.7661801340112 | etot = -33.5644507087177 +753000 ekin = 15.1543901567613 | erot = 20.0407526950507 | epot = -68.7595935598495 | etot = -33.5644507080375 +754000 ekin = 15.1228286573332 | erot = 20.1821712297509 | epot = -68.8694505948499 | etot = -33.5644507077658 +755000 ekin = 15.1688994243523 | erot = 20.3687544713836 | epot = -69.1021046037276 | etot = -33.5644507079917 +756000 ekin = 15.301499551776 | erot = 20.5913112854955 | epot = -69.4572615461957 | etot = -33.5644507089241 +757000 ekin = 15.5255754913897 | erot = 20.834949244045 | epot = -69.9249754463701 | etot = -33.5644507109354 +758000 ekin = 15.8381446961138 | erot = 21.0780442684797 | epot = -70.4806396790109 | etot = -33.5644507144174 +759000 ekin = 16.2241238953416 | erot = 21.2913511033439 | epot = -71.0799257180851 | etot = -33.5644507193996 +760000 ekin = 16.6551901645912 | erot = 21.4392176773412 | epot = -71.6588585670209 | etot = -33.5644507250884 +761000 ekin = 17.0950183931786 | erot = 21.4853061088372 | epot = -72.1447752318667 | etot = -33.5644507298509 +762000 ekin = 17.5106763998012 | erot = 21.4029539232004 | epot = -72.4780810549596 | etot = -33.564450731958 +763000 ekin = 17.8846255672732 | erot = 21.1859145459706 | epot = -72.6349908439064 | etot = -33.5644507306625 +764000 ekin = 18.2201199376956 | erot = 20.8529192934954 | epot = -72.6374899578081 | etot = -33.5644507266171 +765000 ekin = 18.5372583937382 | erot = 20.4430950169541 | epot = -72.5448041320924 | etot = -33.5644507214001 +766000 ekin = 18.8630996339146 | erot = 20.0050052439806 | epot = -72.4325555942986 | etot = -33.5644507164034 +767000 ekin = 19.2212066800029 | erot = 19.5864803390503 | epot = -72.3721377317783 | etot = -33.5644507127251 +768000 ekin = 19.624511669093 | erot = 19.2265552411511 | epot = -72.4155176211004 | etot = -33.5644507108563 +769000 ekin = 20.0721792333795 | erot = 18.9509745480761 | epot = -72.5876044923609 | etot = -33.5644507109054 +770000 ekin = 20.5498086023516 | erot = 18.7702787047077 | epot = -72.8845380197874 | etot = -33.5644507127281 +771000 ekin = 21.0321028878714 | erot = 18.6794354396568 | epot = -73.2759890434179 | etot = -33.5644507158897 +772000 ekin = 21.4851799442024 | erot = 18.6615620368978 | epot = -73.7111927013751 | etot = -33.564450720275 +773000 ekin = 21.8752230488093 | erot = 18.6848228554718 | epot = -74.1244966289812 | etot = -33.5644507247 +774000 ekin = 22.1763496480937 | erot = 18.7081814115977 | epot = -74.4489817879453 | etot = -33.5644507282539 +775000 ekin = 22.374571784792 | erot = 18.6931201256992 | epot = -74.6321426404729 | etot = -33.5644507299816 +776000 ekin = 22.4709552283027 | erot = 18.6135457380045 | epot = -74.6489516957821 | etot = -33.564450729475 +777000 ekin = 22.4798367644303 | erot = 18.4639882142466 | epot = -74.5082757050196 | etot = -33.5644507263427 +778000 ekin = 22.4355420397867 | erot = 18.2585534576689 | epot = -74.2585462185365 | etot = -33.5644507210809 +779000 ekin = 22.384352941304 | erot = 18.0309205348412 | epot = -73.9797241910754 | etot = -33.5644507149302 +780000 ekin = 22.3744386500498 | erot = 17.8258066858555 | epot = -73.7646960454756 | etot = -33.5644507095703 +781000 ekin = 22.1317599687537 | erot = 17.6891439264797 | epot = -73.385354726192 | etot = -33.5644508309586 +782000 ekin = 21.1592753698204 | erot = 17.9407979475159 | epot = -72.6645240371034 | etot = -33.5644507197671 +783000 ekin = 20.4598020696467 | erot = 19.0285770890208 | epot = -73.0528298813537 | etot = -33.5644507226862 +784000 ekin = 20.520561149809 | erot = 20.4251817114889 | epot = -74.510193700403 | etot = -33.5644508391051 +785000 ekin = 20.9642653603784 | erot = 20.9633174839005 | epot = -75.4920336718239 | etot = -33.564450827545 +786000 ekin = 21.4400765994876 | erot = 21.0615830961954 | epot = -76.0661105274379 | etot = -33.5644508317549 +787000 ekin = 21.883066887488 | erot = 21.057450682238 | epot = -76.5049684031488 | etot = -33.5644508334227 +788000 ekin = 22.267324375569 | erot = 20.946432607028 | epot = -76.7782078151899 | etot = -33.5644508325928 +789000 ekin = 22.5826671479872 | erot = 20.7432248288687 | epot = -76.8903428068424 | etot = -33.5644508299865 +790000 ekin = 22.8323066878114 | erot = 20.4741989858865 | epot = -76.8709565003754 | etot = -33.5644508266776 +791000 ekin = 23.0272356230926 | erot = 20.1684030022638 | epot = -76.7600894489801 | etot = -33.5644508236236 +792000 ekin = 23.1800436946629 | erot = 19.8507212207542 | epot = -76.5952157367535 | etot = -33.5644508213364 +793000 ekin = 23.300603133177 | erot = 19.5391467370145 | epot = -76.4042006900797 | etot = -33.5644508198882 +794000 ekin = 23.3943971219697 | erot = 19.2453890945191 | epot = -76.2042370356008 | etot = -33.564450819112 +795000 ekin = 23.4629811569471 | erot = 18.9772359529009 | epot = -76.0046679285239 | etot = -33.564450818676 +796000 ekin = 23.5050545268219 | erot = 18.7401074069536 | epot = -75.8096127523991 | etot = -33.5644508186236 +797000 ekin = 23.5179235638906 | erot = 18.5376020867796 | epot = -75.6199764693832 | etot = -33.564450818713 +798000 ekin = 23.499309548325 | erot = 18.3721088685451 | epot = -75.4358692357089 | etot = -33.5644508188388 +799000 ekin = 23.448939556091 | erot = 18.2446734452746 | epot = -75.2580638202457 | etot = -33.5644508188801 +800000 ekin = 23.3700597274441 | erot = 18.1549836136211 | epot = -75.0894941597633 | etot = -33.5644508186981 +801000 ekin = 23.2706429278156 | erot = 18.1018392108953 | epot = -74.9369329568679 | etot = -33.564450818157 +802000 ekin = 23.1638659210079 | erot = 18.0841621459371 | epot = -74.8124788841352 | etot = -33.5644508171902 +803000 ekin = 23.0673439612512 | erot = 18.1021655968283 | epot = -74.7339603739616 | etot = -33.564450815882 +804000 ekin = 23.0007989366371 | erot = 18.1579717461939 | epot = -74.7232214973418 | etot = -33.5644508145108 +805000 ekin = 22.9823371343768 | erot = 18.2549251687085 | epot = -74.8017131166306 | etot = -33.5644508135453 +806000 ekin = 23.0241641600763 | erot = 18.3954330803544 | epot = -74.984048053792 | etot = -33.5644508133613 +807000 ekin = 23.128964625391 | erot = 18.5785443285981 | epot = -75.2719597683222 | etot = -33.5644508143331 +808000 ekin = 23.2881607694889 | erot = 18.7969609338812 | epot = -75.649572519887 | etot = -33.5644508165169 +809000 ekin = 23.4826910129567 | erot = 19.0356597598736 | epot = -76.0828015925039 | etot = -33.5644508196735 +810000 ekin = 23.6859311924953 | erot = 19.2727961953261 | epot = -76.5231782111275 | etot = -33.5644508233061 +811000 ekin = 23.8683330202879 | erot = 19.4824424692605 | epot = -76.915226316337 | etot = -33.5644508267886 +812000 ekin = 24.0021280346815 | erot = 19.6390320774525 | epot = -77.2056109410892 | etot = -33.5644508289552 +813000 ekin = 24.0705831557699 | erot = 19.722021914086 | epot = -77.3570559012067 | etot = -33.5644508313508 +814000 ekin = 24.055601152459 | erot = 19.7197957986886 | epot = -77.3398477832757 | etot = -33.5644508321281 +815000 ekin = 23.9426529226646 | erot = 19.6314238617512 | epot = -77.1385276156708 | etot = -33.564450831255 +816000 ekin = 23.7311336934088 | erot = 19.466072034162 | epot = -76.7616565565296 | etot = -33.5644508289587 +817000 ekin = 23.433668535019 | erot = 19.2405112285024 | epot = -76.2386305891648 | etot = -33.5644508256434 +818000 ekin = 23.0739945644854 | erot = 18.9755381767493 | epot = -75.6139835630208 | etot = -33.5644508217861 +819000 ekin = 22.6837324023522 | erot = 18.6923648013821 | epot = -74.940548021756 | etot = -33.5644508180217 +820000 ekin = 22.2835291274414 | erot = 18.4096381970061 | epot = -74.2576181403381 | etot = -33.5644508158905 +821000 ekin = 21.8822278930458 | erot = 18.1412914989096 | epot = -73.5879702064574 | etot = -33.564450814502 +822000 ekin = 21.4884880522555 | erot = 17.8956786284863 | epot = -72.9486174945866 | etot = -33.5644508138448 +823000 ekin = 21.1064787913954 | erot = 17.6755757489858 | epot = -72.3465053541674 | etot = -33.5644508137862 +824000 ekin = 20.7370980684377 | erot = 17.4789023739902 | epot = -71.7804512565368 | etot = -33.5644508141088 +825000 ekin = 20.3797998907961 | erot = 17.3000855971742 | epot = -71.2443363025092 | etot = -33.5644508145388 +826000 ekin = 20.0346218830748 | erot = 17.1319532561702 | epot = -70.7310259540458 | etot = -33.5644508148008 +827000 ekin = 19.7039740634311 | erot = 16.9679189203112 | epot = -70.2363437984045 | etot = -33.5644508146622 +828000 ekin = 19.3938011067031 | erot = 16.8040573698201 | epot = -69.7623092905205 | etot = -33.5644508139974 +829000 ekin = 19.11384865599 | erot = 16.6405709794189 | epot = -69.3188704482339 | etot = -33.564450812825 +830000 ekin = 18.8769326775077 | erot = 16.4822216024693 | epot = -68.9236050912778 | etot = -33.5644508113007 +831000 ekin = 18.6973117703808 | erot = 16.3375582428127 | epot = -68.5993208228909 | etot = -33.5644508096974 +832000 ekin = 18.5884699003301 | erot = 16.2171194687507 | epot = -68.3700401774137 | etot = -33.564450808333 +833000 ekin = 18.560779595016 | erot = 16.1310793366086 | epot = -68.2563097391195 | etot = -33.5644508074948 +834000 ekin = 18.61956558581 | erot = 16.0869173735029 | epot = -68.2709337666952 | etot = -33.5644508073822 +835000 ekin = 18.7639745649932 | erot = 16.0875916865537 | epot = -68.4160170596156 | etot = -33.5644508080686 +836000 ekin = 18.9868442865092 | erot = 16.1305192433203 | epot = -68.6818143393361 | etot = -33.5644508095065 +837000 ekin = 19.2754657671378 | erot = 16.2074384784975 | epot = -69.0473550571903 | etot = -33.564450811555 +838000 ekin = 19.6129197626542 | erot = 16.305100324473 | epot = -69.4824709011417 | etot = -33.5644508140144 +839000 ekin = 19.9795904905589 | erot = 16.4066730035615 | epot = -69.9507143107794 | etot = -33.564450816659 +840000 ekin = 20.3545159446157 | erot = 16.4936833394318 | epot = -70.4126501033158 | etot = -33.5644508192683 +841000 ekin = 20.7164052638984 | erot = 16.548246931381 | epot = -70.8291030169287 | etot = -33.5644508216493 +842000 ekin = 21.0443277172268 | erot = 16.5552492676569 | epot = -71.1640278085398 | etot = -33.5644508236561 +843000 ekin = 21.3182343499603 | erot = 16.5040987153204 | epot = -71.3867838904675 | etot = -33.5644508251868 +844000 ekin = 21.5195641367703 | erot = 16.3898128596529 | epot = -71.4738278225867 | etot = -33.5644508261635 +845000 ekin = 21.6321888565554 | erot = 16.2134452981662 | epot = -71.410084981231 | etot = -33.5644508265094 +846000 ekin = 21.6437998325842 | erot = 15.9820204390976 | epot = -71.1902710978237 | etot = -33.5644508261419 +847000 ekin = 21.5475782493693 | erot = 15.7081282849394 | epot = -70.8201573593162 | etot = -33.5644508250075 +848000 ekin = 21.3436927775388 | erot = 15.4091281501661 | epot = -70.3172717508461 | etot = -33.5644508231412 +849000 ekin = 21.0400180651421 | erot = 15.1057456316713 | epot = -69.7102145175199 | etot = -33.5644508207064 +850000 ekin = 20.651624144221 | erot = 14.819982121726 | epot = -69.0360570839323 | etot = -33.5644508179853 +851000 ekin = 20.1989966727791 | erot = 14.5725796374539 | epot = -68.3360271255451 | etot = -33.5644508153122 +852000 ekin = 19.705405223643 | erot = 14.3805531626584 | epot = -67.650409199298 | etot = -33.5644508129966 +853000 ekin = 19.1940724610505 | erot = 14.25530818557 | epot = -67.0138314578818 | etot = -33.5644508112614 +854000 ekin = 18.6857524015881 | erot = 14.2015962971835 | epot = -66.4517995089979 | etot = -33.5644508102263 +855000 ekin = 18.1970763744836 | erot = 14.2172634276327 | epot = -65.9787906120352 | etot = -33.5644508099189 +856000 ekin = 17.7397499707612 | erot = 14.2936050918535 | epot = -65.5978058729028 | etot = -33.5644508102882 +857000 ekin = 17.3205057782524 | erot = 14.4162007388387 | epot = -65.3011573283104 | etot = -33.5644508112193 +858000 ekin = 16.9416544278078 | erot = 14.5662556875881 | epot = -65.0723609279221 | etot = -33.5644508125262 +859000 ekin = 16.6020780488435 | erot = 14.7225727576944 | epot = -64.8891016204952 | etot = -33.5644508139574 +860000 ekin = 16.2985125162571 | erot = 14.8641879517113 | epot = -64.7271512831937 | etot = -33.5644508152253 +861000 ekin = 16.0269335765221 | erot = 14.9734306263673 | epot = -64.5648150189461 | etot = -33.5644508160567 +862000 ekin = 15.7838145493149 | erot = 15.0388248736918 | epot = -64.3870902392667 | etot = -33.56445081626 +863000 ekin = 15.5670277401482 | erot = 15.0570872004078 | epot = -64.1885657563379 | etot = -33.5644508157819 +864000 ekin = 15.3762443264478 | erot = 15.033644902431 | epot = -63.9743400435875 | etot = -33.5644508147087 +865000 ekin = 15.2131876544491 | erot = 14.9816007278775 | epot = -63.7592391954458 | etot = -33.5644508131193 +866000 ekin = 15.0809818287742 | erot = 14.9194630000228 | epot = -63.5648956402705 | etot = -33.5644508114735 +867000 ekin = 14.9827726501217 | erot = 14.8683323276467 | epot = -63.4155557876376 | etot = -33.5644508098692 +868000 ekin = 14.92180112433 | erot = 14.8493296988562 | epot = -63.3355816316708 | etot = -33.5644508084847 +869000 ekin = 14.9010185116834 | erot = 14.8813223016375 | epot = -63.3467916207947 | etot = -33.5644508074738 +870000 ekin = 14.9227801761236 | erot = 14.9789108660607 | epot = -63.4661418491954 | etot = -33.5644508070111 +871000 ekin = 14.9884139356745 | erot = 15.1503817842349 | epot = -63.7032465271887 | etot = -33.5644508072793 +872000 ekin = 15.0976914319707 | erot = 15.3955923654522 | epot = -64.0577346058697 | etot = -33.5644508084468 +873000 ekin = 15.2480781387988 | erot = 15.7042636439283 | epot = -64.5167925933356 | etot = -33.5644508106085 +874000 ekin = 15.4340038873847 | erot = 16.0553561021191 | epot = -65.053810803158 | etot = -33.5644508136542 +875000 ekin = 15.6465534573556 | erot = 16.4187317070787 | epot = -65.6297359816455 | etot = -33.5644508172112 +876000 ekin = 15.8739222018982 | erot = 16.7595446909201 | epot = -66.1979177135255 | etot = -33.5644508207072 +877000 ekin = 16.1027155795467 | erot = 17.044494341634 | epot = -66.7116607447368 | etot = -33.5644508235561 +878000 ekin = 16.3197910454644 | erot = 17.2478151625915 | epot = -67.1320570334198 | etot = -33.5644508253639 +879000 ekin = 16.5138521394505 | erot = 17.3548092079704 | epot = -67.4331121735215 | etot = -33.5644508261006 +880000 ekin = 16.6772706623824 | erot = 17.3624918569347 | epot = -67.6042133449038 | etot = -33.5644508255867 +881000 ekin = 16.8080553798836 | erot = 17.278452226898 | epot = -67.6509584308199 | etot = -33.5644508240383 +882000 ekin = 16.9100399112771 | erot = 17.119022231693 | epot = -67.5935129646031 | etot = -33.564450821633 +883000 ekin = 16.9925721974834 | erot = 16.9073416506224 | epot = -67.4643646668128 | etot = -33.564450818707 +884000 ekin = 17.0687034065889 | erot = 16.6704808211346 | epot = -67.3036350435126 | etot = -33.5644508157892 +885000 ekin = 17.1519974191521 | erot = 16.4352378677741 | epot = -67.1516861003877 | etot = -33.5644508134615 +886000 ekin = 17.2529390367253 | erot = 16.2234313385346 | epot = -67.040821187416 | etot = -33.564450812156 +887000 ekin = 17.3762921605589 | erot = 16.0482363267111 | epot = -66.9889792992713 | etot = -33.5644508120014 +888000 ekin = 17.5203620939499 | erot = 15.912713009727 | epot = -66.9975259165121 | etot = -33.5644508128352 +889000 ekin = 17.6781644417429 | erot = 15.8105908033725 | epot = -67.0532060594389 | etot = -33.5644508143236 +890000 ekin = 17.8397117311843 | erot = 15.728545074795 | epot = -67.1327076214795 | etot = -33.5644508155002 +891000 ekin = 17.9946822356163 | erot = 15.6526652128514 | epot = -67.2117982661653 | etot = -33.5644508176976 +892000 ekin = 18.1331274108613 | erot = 15.5631846536331 | epot = -67.2607628839469 | etot = -33.5644508194524 +893000 ekin = 18.2472194923555 | erot = 15.4391901233243 | epot = -67.2508604363308 | etot = -33.5644508206509 +894000 ekin = 18.3321686592099 | erot = 15.2648175287635 | epot = -67.1614370091493 | etot = -33.5644508211759 +895000 ekin = 18.3862908731384 | erot = 15.0310128799806 | epot = -66.9817545740828 | etot = -33.5644508209639 +896000 ekin = 18.4109116125628 | erot = 14.7366844064177 | epot = -66.7120468390301 | etot = -33.5644508200496 +897000 ekin = 18.4100489982307 | erot = 14.38859264232 | epot = -66.3630924591407 | etot = -33.56445081859 +898000 ekin = 18.3898281603967 | erot = 13.9998000546359 | epot = -65.954079031856 | etot = -33.5644508168234 +899000 ekin = 18.3577139224559 | erot = 13.5871378078456 | epot = -65.5093025452924 | etot = -33.5644508149909 +900000 ekin = 18.3217786244971 | erot = 13.1685630401998 | epot = -65.0547924779573 | etot = -33.5644508132604 +901000 ekin = 18.2902589888584 | erot = 12.7612484281998 | epot = -64.6159582287385 | etot = -33.5644508116803 +902000 ekin = 18.2715810670069 | erot = 12.3808553817479 | epot = -64.2168872589334 | etot = -33.5644508101785 +903000 ekin = 18.2748902554657 | erot = 12.0419799131758 | epot = -63.8813209772404 | etot = -33.5644508085989 +904000 ekin = 18.310946079998 | erot = 11.759427353884 | epot = -63.6348242406376 | etot = -33.5644508067556 +905000 ekin = 18.3930925503139 | erot = 11.5498594883528 | epot = -63.5074028431725 | etot = -33.5644508045058 +906000 ekin = 18.5347341843358 | erot = 11.429567327747 | epot = -63.5287523170652 | etot = -33.5644508049824 +907000 ekin = 18.7414362451913 | erot = 11.4045037508022 | epot = -63.7103908004036 | etot = -33.5644508044102 +908000 ekin = 19.0194889718029 | erot = 11.4807236813719 | epot = -64.064663457795 | etot = -33.5644508046201 +909000 ekin = 19.3700614262796 | erot = 11.658960594413 | epot = -64.5934728263738 | etot = -33.5644508056812 +910000 ekin = 19.7882105287017 | erot = 11.9333322709223 | epot = -65.2859936069509 | etot = -33.5644508073268 +911000 ekin = 20.2647618472542 | erot = 12.2921701432016 | epot = -66.1213827995986 | etot = -33.5644508091428 +912000 ekin = 20.7894338989449 | erot = 12.7195983435702 | epot = -67.0734830529977 | etot = -33.5644508104826 +913000 ekin = 21.354185735415 | erot = 13.1939380972622 | epot = -68.1125746463993 | etot = -33.564450813722 +914000 ekin = 21.9410171539269 | erot = 13.6876167580563 | epot = -69.1930847298951 | etot = -33.564450817912 +915000 ekin = 22.5188846328755 | erot = 14.1693256791945 | epot = -70.2526611349299 | etot = -33.5644508228598 +916000 ekin = 23.0495496145354 | erot = 14.6035757237462 | epot = -71.2175761670584 | etot = -33.5644508287768 +917000 ekin = 23.4897289759918 | erot = 14.9539952313724 | epot = -72.008175040674 | etot = -33.5644508333098 +918000 ekin = 23.7939185234148 | erot = 15.197647321232 | epot = -72.5560167286604 | etot = -33.5644508840135 +919000 ekin = 23.6168045074412 | erot = 15.3655091430202 | epot = -72.5467644924926 | etot = -33.5644508420312 +920000 ekin = 23.165531585878 | erot = 15.5814764955082 | epot = -72.311458892293 | etot = -33.5644508109067 +921000 ekin = 22.8561009730671 | erot = 15.8041631721062 | epot = -72.2247150051872 | etot = -33.5644508600138 +922000 ekin = 22.440617199678 | erot = 15.7102388661218 | epot = -71.7153069039719 | etot = -33.5644508381722 +923000 ekin = 21.8145072438246 | erot = 15.4204628466349 | epot = -70.7994209206915 | etot = -33.564450830232 +924000 ekin = 21.089710612231 | erot = 15.1252102241701 | epot = -69.7793716556892 | etot = -33.5644508192881 +925000 ekin = 20.3778961082158 | erot = 14.899059611937 | epot = -68.8414065283879 | etot = -33.5644508082351 +926000 ekin = 19.7497733146689 | erot = 14.7841436062358 | epot = -68.0983677263129 | etot = -33.5644508054082 +927000 ekin = 19.2202389452663 | erot = 14.8057849810623 | epot = -67.590474728778 | etot = -33.5644508024493 +928000 ekin = 18.8098178358059 | erot = 14.9862994051908 | epot = -67.3605680408844 | etot = -33.5644507998878 +929000 ekin = 18.5263530322086 | erot = 15.3189513314309 | epot = -67.4097551810462 | etot = -33.5644508174067 +930000 ekin = 18.303158247999 | erot = 15.7144845731335 | epot = -67.5820936492334 | etot = -33.564450828101 +931000 ekin = 18.0528353467031 | erot = 16.092098150507 | epot = -67.7093843340348 | etot = -33.5644508368247 +932000 ekin = 17.7015072493782 | erot = 16.3874716011874 | epot = -67.6534296917457 | etot = -33.5644508411801 +933000 ekin = 17.2115757804696 | erot = 16.5716045694095 | epot = -67.3476311886972 | etot = -33.5644508388181 +934000 ekin = 16.5514003203334 | erot = 16.6395832223659 | epot = -66.755434444527 | etot = -33.5644509018278 +935000 ekin = 15.4338978862408 | erot = 16.4795973505328 | epot = -65.4779460700676 | etot = -33.564450833294 +936000 ekin = 14.2992444275143 | erot = 16.4524645705128 | epot = -64.3161597798994 | etot = -33.5644507818723 +937000 ekin = 13.59487740504 | erot = 16.8307081996587 | epot = -63.9900364163686 | etot = -33.5644508116699 +938000 ekin = 13.1600926964079 | erot = 17.3617572930203 | epot = -64.0863008623788 | etot = -33.5644508729506 +939000 ekin = 12.6302856058614 | erot = 17.6616475284688 | epot = -63.8563839239186 | etot = -33.5644507895884 +940000 ekin = 12.1844103645063 | erot = 17.9750890236239 | epot = -63.7239501782487 | etot = -33.5644507901185 +941000 ekin = 11.8736812756091 | erot = 18.3544207679051 | epot = -63.7925528359821 | etot = -33.5644507924678 +942000 ekin = 11.6856910076193 | erot = 18.7737996767542 | epot = -64.0239414802086 | etot = -33.5644507958351 +943000 ekin = 11.5993719915505 | erot = 19.1997647093009 | epot = -64.3635875002877 | etot = -33.5644507994363 +944000 ekin = 11.591116393097 | erot = 19.5969000254167 | epot = -64.7524672211801 | etot = -33.5644508026663 +945000 ekin = 11.6394594916683 | erot = 19.9326030632592 | epot = -65.1365133600576 | etot = -33.56445080513 +946000 ekin = 11.7278293647869 | erot = 20.1807231613466 | epot = -65.4730033327469 | etot = -33.5644508066135 +947000 ekin = 11.8456010910349 | erot = 20.3241537585671 | epot = -65.7342056566312 | etot = -33.5644508070293 +948000 ekin = 11.9879925905891 | erot = 20.3564922444528 | epot = -65.9089356414658 | etot = -33.564450806424 +949000 ekin = 12.1551997706618 | erot = 20.2822908926568 | epot = -66.0019414683021 | etot = -33.5644508049834 +950000 ekin = 12.3510408582428 | erot = 20.1156595852263 | epot = -66.0311512464897 | etot = -33.5644508030205 +951000 ekin = 12.5812930342184 | erot = 19.8773156458908 | epot = -66.0230594810216 | etot = -33.5644508009124 +952000 ekin = 12.8471183992429 | erot = 19.5848425527081 | epot = -65.9964117535253 | etot = -33.5644508015743 +953000 ekin = 13.1479143766235 | erot = 19.2558560123375 | epot = -65.9682211888452 | etot = -33.5644507998843 +954000 ekin = 13.4859607016749 | erot = 18.9116613752366 | epot = -65.9620728756609 | etot = -33.5644507987494 +955000 ekin = 13.8607396886139 | erot = 18.5688220608356 | epot = -65.9940125476709 | etot = -33.5644507982214 +956000 ekin = 14.2684790839254 | erot = 18.2386766853017 | epot = -66.0716065674655 | etot = -33.5644507982384 +957000 ekin = 14.7022261502645 | erot = 17.9280211817306 | epot = -66.1946981306621 | etot = -33.5644507986669 +958000 ekin = 15.1523557015762 | erot = 17.6404101744164 | epot = -66.3572166753395 | etot = -33.5644507993469 +959000 ekin = 15.6074014601803 | erot = 17.3776018534993 | epot = -66.5494541137976 | etot = -33.5644508001179 +960000 ekin = 16.0551055261351 | erot = 17.1408213325793 | epot = -66.7603776595324 | etot = -33.5644508008181 +961000 ekin = 16.483819511843 | erot = 16.9315994951715 | epot = -66.9798698083909 | etot = -33.5644508013764 +962000 ekin = 16.8831178337395 | erot = 16.7524507837121 | epot = -67.2000194191554 | etot = -33.5644508017038 +963000 ekin = 17.2446402411808 | erot = 16.6070592916238 | epot = -67.4161503345794 | etot = -33.5644508017749 +964000 ekin = 17.5626944186329 | erot = 16.5001400673231 | epot = -67.6272852875597 | etot = -33.5644508016037 +965000 ekin = 17.8343164080137 | erot = 16.4370960223934 | epot = -67.8358632316613 | etot = -33.5644508012542 +966000 ekin = 18.058881794858 | erot = 16.4234839407457 | epot = -68.0468165364294 | etot = -33.5644508008257 +967000 ekin = 18.2373393553309 | erot = 16.4643418581003 | epot = -68.2661320138667 | etot = -33.5644508004355 +968000 ekin = 18.3712253334182 | erot = 16.5634469055311 | epot = -68.4991230391516 | etot = -33.5644508002023 +969000 ekin = 18.4616731642916 | erot = 16.7225928674224 | epot = -68.748716831933 | etot = -33.564450800219 +970000 ekin = 18.508642391898 | erot = 16.9409874226402 | epot = -69.014080615083 | etot = -33.5644508005448 +971000 ekin = 18.5105217351456 | erot = 17.2148322274807 | epot = -69.2898047638157 | etot = -33.5644508011893 +972000 ekin = 18.4641879057989 | erot = 17.5371342370508 | epot = -69.5657729449732 | etot = -33.5644508021236 +973000 ekin = 18.3654967925945 | erot = 17.8977436591339 | epot = -69.8276912550097 | etot = -33.5644508032813 +974000 ekin = 18.2101154179932 | erot = 18.2835968472234 | epot = -70.0581630697874 | etot = -33.5644508045708 +975000 ekin = 17.9945660115437 | erot = 18.6791515809232 | epot = -70.2381683983514 | etot = -33.5644508058845 +976000 ekin = 17.7173305275788 | erot = 19.0670257035496 | epot = -70.3488070382366 | etot = -33.5644508071083 +977000 ekin = 17.3798453157079 | erot = 19.4288693588492 | epot = -70.3731654826817 | etot = -33.5644508081246 +978000 ekin = 16.9872046651528 | erot = 19.7465105308244 | epot = -70.2981660048043 | etot = -33.5644508088271 +979000 ekin = 16.5484156632796 | erot = 20.0033999568713 | epot = -70.1162664292717 | etot = -33.5644508091207 +980000 ekin = 16.0760394561679 | erot = 20.1863036337654 | epot = -69.8267938958194 | etot = -33.5644508058861 +981000 ekin = 15.5958799206067 | erot = 20.2892058118436 | epot = -69.4495365390975 | etot = -33.5644508066472 +982000 ekin = 15.0884229209118 | erot = 20.3042917721005 | epot = -68.9571655433623 | etot = -33.56445085035 +983000 ekin = 14.6278058930741 | erot = 20.1974254363095 | epot = -68.3896821374305 | etot = -33.5644508080469 +984000 ekin = 14.4857180537849 | erot = 20.0570072753869 | epot = -68.1071761999148 | etot = -33.5644508707431 +985000 ekin = 14.2080884745897 | erot = 19.919276344842 | epot = -67.6918156218487 | etot = -33.564450802417 +986000 ekin = 13.9758844712272 | erot = 19.8429645358536 | epot = -67.3832998071099 | etot = -33.5644508000291 +987000 ekin = 13.8444879396752 | erot = 19.8435554330973 | epot = -67.2524941798934 | etot = -33.5644508071209 +988000 ekin = 13.7899575635179 | erot = 19.8765535654025 | epot = -67.2309619340325 | etot = -33.5644508051121 +989000 ekin = 13.7826987510727 | erot = 19.9896359806756 | epot = -67.3367855381806 | etot = -33.5644508064323 +990000 ekin = 13.8064597723693 | erot = 20.1866383120656 | epot = -67.5575488929868 | etot = -33.5644508085519 +991000 ekin = 13.844476200064 | erot = 20.4553568023019 | epot = -67.8642838132361 | etot = -33.5644508108702 +992000 ekin = 13.8831356334462 | erot = 20.7777558499506 | epot = -68.2253422960729 | etot = -33.5644508126761 +993000 ekin = 13.9170731635836 | erot = 21.135407615501 | epot = -68.6169315925055 | etot = -33.564450813421 +994000 ekin = 13.9526839660428 | erot = 21.5142214171928 | epot = -69.0313561961371 | etot = -33.5644508129016 +995000 ekin = 14.0087176813023 | erot = 21.9069609070435 | epot = -69.480129399738 | etot = -33.5644508113922 +996000 ekin = 14.1134296875285 | erot = 22.3130050689718 | epot = -69.9908855656615 | etot = -33.5644508091613 +997000 ekin = 14.3000196822843 | erot = 22.7364207784144 | epot = -70.6008912675636 | etot = -33.5644508068649 +998000 ekin = 14.6010980656079 | erot = 23.1830420844189 | epot = -71.3485909550456 | etot = -33.5644508050188 +999000 ekin = 15.0427312776222 | erot = 23.657392608768 | epot = -72.2645746968681 | etot = -33.5644508104779 +1000000 ekin = 15.613660129969 | erot = 24.1382006023969 | epot = -73.3163115458147 | etot = -33.5644508134487 + 1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160068 39304000 +Loop time of 17.9925 on 1 procs for 1000000 steps with 16 atoms + +Performance: 81.922 ns/day, 0.293 hours/ns, 55578.741 timesteps/s, 889.260 katom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.919 | 14.919 | 14.919 | 0.0 | 82.92 +Bond | 0.66748 | 0.66748 | 0.66748 | 0.0 | 3.71 +Neigh | 0.007146 | 0.007146 | 0.007146 | 0.0 | 0.04 +Comm | 0.24907 | 0.24907 | 0.24907 | 0.0 | 1.38 +Output | 0.173 | 0.173 | 0.173 | 0.0 | 0.96 +Modify | 1.6962 | 1.6962 | 1.6962 | 0.0 | 9.43 +Other | | 0.2809 | | | 1.56 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 107 ave 107 max 107 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:18 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/log.19May24.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/log.19May24.duplex2.g++.4 new file mode 100644 index 0000000000..7f5a424467 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/log.19May24.duplex2.g++.4 @@ -0,0 +1,1121 @@ +LAMMPS (17 Apr 2024) + using 1 OpenMP thread(s) per MPI task +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +Reading data file ... + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + scanning bonds ... + 1 = max bonds/atom + 16 ellipsoids + orthogonal box = (-170 -170 -170) to (170 170 170) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 13 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.008 seconds +Setting atom values ... + 16 settings made for mass +16 atoms in group all +Reading oxdna potential (fene) file oxrna2.real with DATE: 2024-04-26 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds +Reading oxdna potential (excv) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (stk) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (hbond) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (xstk) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (coaxstk) file oxrna2.real with DATE: 2024-04-26 +Reading oxdna potential (dh) file oxrna2.real with DATE: 2024-04-26 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 36.640032 + ghost atom cutoff = 36.640032 + binsize = 18.320016, bins = 19 19 19 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 0.01706 +WARNING: Communication cutoff adjusted to 36.640032409886274 (src/comm.cpp:739) +0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815 +Per MPI rank memory allocation (min/avg/max) = 7.577 | 7.606 | 7.69 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 360.53565 -69.627742 3.2447172 -50.262701 0.034084814 39304000 +1000 ekin = 16.3558183649387 | erot = 16.6323090455317 | epot = -66.5525771041998 | etot = -33.5644496937295 +2000 ekin = 16.6191649168147 | erot = 16.5684372137643 | epot = -66.7520518221219 | etot = -33.5644496915429 +3000 ekin = 16.9230904408654 | erot = 16.5204480451832 | epot = -67.0079881759691 | etot = -33.5644496899204 +4000 ekin = 17.2772162612591 | erot = 16.49867929322 | epot = -67.3403452437715 | etot = -33.5644496892924 +5000 ekin = 17.6866959075726 | erot = 16.5050138456572 | epot = -67.7561594428204 | etot = -33.5644496895906 +6000 ekin = 18.1531343302964 | erot = 16.5325161302815 | epot = -68.2501001506509 | etot = -33.564449690073 +7000 ekin = 18.680653493314 | erot = 16.5738535187235 | epot = -68.8189567014344 | etot = -33.5644496893969 +8000 ekin = 19.2766528199695 | erot = 16.6261515879628 | epot = -69.4672540969553 | etot = -33.564449689023 +9000 ekin = 19.9461490397319 | erot = 16.6908475985738 | epot = -70.201446326231 | etot = -33.5644496879253 +10000 ekin = 20.6973181248474 | erot = 16.7772960438528 | epot = -71.039063854854 | etot = -33.5644496861538 +11000 ekin = 21.539522624792 | erot = 16.9014209971989 | epot = -72.0053933083053 | etot = -33.5644496863144 +12000 ekin = 22.4717498465051 | erot = 17.0791755563662 | epot = -73.1153750880493 | etot = -33.5644496851781 +13000 ekin = 23.493621609947 | erot = 17.3228520870333 | epot = -74.3809233816828 | etot = -33.5644496847026 +14000 ekin = 24.6044210071246 | erot = 17.6425688028838 | epot = -75.8114394947881 | etot = -33.5644496847798 +15000 ekin = 25.7999389267744 | erot = 18.0453525578634 | epot = -77.4097411694886 | etot = -33.5644496848508 +16000 ekin = 27.0739775537123 | erot = 18.5361142332912 | epot = -79.1745414730767 | etot = -33.5644496860731 +17000 ekin = 28.4119581304118 | erot = 19.1137262760959 | epot = -81.0901340949635 | etot = -33.5644496884557 +18000 ekin = 29.7909545183303 | erot = 19.7704759932755 | epot = -83.1258802031785 | etot = -33.5644496915727 +19000 ekin = 31.1831510307732 | erot = 20.4915974540495 | epot = -85.2391981805601 | etot = -33.5644496957374 +20000 ekin = 32.5560965367943 | erot = 21.2528351748734 | epot = -87.3733814125724 | etot = -33.5644497009047 +21000 ekin = 33.868330987566 | erot = 22.0156446407476 | epot = -89.4484253379455 | etot = -33.5644497096318 +22000 ekin = 35.0747510230858 | erot = 22.7306302808711 | epot = -91.3698310187509 | etot = -33.564449714794 +23000 ekin = 36.1427935644227 | erot = 23.3543658008634 | epot = -93.0616090845426 | etot = -33.5644497192564 +24000 ekin = 37.0484240543211 | erot = 23.8536351256838 | epot = -94.4665089004161 | etot = -33.5644497204113 +25000 ekin = 37.7873483857427 | erot = 24.2156130941775 | epot = -95.5674111990494 | etot = -33.5644497191292 +26000 ekin = 38.3695951222899 | erot = 24.4472028227103 | epot = -96.3812476612834 | etot = -33.5644497162832 +27000 ekin = 38.8142451991145 | erot = 24.5696496438673 | epot = -96.9483445558084 | etot = -33.5644497128266 +28000 ekin = 39.1436511594781 | erot = 24.6108705414904 | epot = -97.3189714104584 | etot = -33.5644497094899 +29000 ekin = 39.3799077053091 | erot = 24.5987493007977 | epot = -97.5431067127119 | etot = -33.5644497066052 +30000 ekin = 39.5437187767927 | erot = 24.5572061990977 | epot = -97.6653746802842 | etot = -33.5644497043938 +31000 ekin = 39.6556538792225 | erot = 24.5025482878245 | epot = -97.7226518696582 | etot = -33.5644497026112 +32000 ekin = 39.7376908979144 | erot = 24.4447365565287 | epot = -97.7468771552201 | etot = -33.5644497007771 +33000 ekin = 39.8178410436037 | erot = 24.3917276701332 | epot = -97.7740184125884 | etot = -33.5644496988515 +34000 ekin = 39.927618714488 | erot = 24.3494773308408 | epot = -97.8415457422131 | etot = -33.5644496968843 +35000 ekin = 40.0972017271435 | erot = 24.3220925820223 | epot = -97.9837440042509 | etot = -33.564449695085 +36000 ekin = 40.3554758289768 | erot = 24.3121132861349 | epot = -98.2320388089531 | etot = -33.5644496938414 +37000 ekin = 40.7253172241835 | erot = 24.319453116459 | epot = -98.6092200342501 | etot = -33.5644496936077 +38000 ekin = 41.2184614577313 | erot = 24.3399425110989 | epot = -99.1228536635565 | etot = -33.5644496947263 +39000 ekin = 41.8315835745705 | erot = 24.3642621379391 | epot = -99.7602954097928 | etot = -33.5644496972833 +40000 ekin = 42.5444333388241 | erot = 24.3777906096182 | epot = -100.486673649662 | etot = -33.5644497012195 +41000 ekin = 43.3221534386097 | erot = 24.3619359806971 | epot = -101.248539124814 | etot = -33.5644497055069 +42000 ekin = 44.1232219530953 | erot = 24.2968159626988 | epot = -101.984487625362 | etot = -33.564449709568 +43000 ekin = 44.904300844132 | erot = 24.1647850477408 | epot = -102.633535604778 | etot = -33.5644497129052 +44000 ekin = 45.6258073685734 | erot = 23.9537754776322 | epot = -103.144032561023 | etot = -33.5644497148173 +45000 ekin = 46.2557013508695 | erot = 23.6596129163771 | epot = -103.479763983876 | etot = -33.5644497166297 +46000 ekin = 46.7711396854538 | erot = 23.2746461161496 | epot = -103.610235519163 | etot = -33.5644497175596 +47000 ekin = 47.1576706465393 | erot = 22.7983985986729 | epot = -103.520518961432 | etot = -33.5644497162194 +48000 ekin = 47.4067411848207 | erot = 22.2418927069086 | epot = -103.213083606725 | etot = -33.5644497149953 +49000 ekin = 47.5134307536654 | erot = 21.6212608371917 | epot = -102.69914130377 | etot = -33.564449712913 +50000 ekin = 47.4750496002015 | erot = 20.9637753825402 | epot = -102.0032746914 | etot = -33.5644497086583 +51000 ekin = 47.2893433305643 | erot = 20.3140174296325 | epot = -101.167810469159 | etot = -33.5644497089619 +52000 ekin = 46.9527474071891 | erot = 19.6808685522296 | epot = -100.198065668178 | etot = -33.5644497087591 +53000 ekin = 46.4669221029446 | erot = 19.0628634962124 | epot = -99.0942353064246 | etot = -33.5644497072675 +54000 ekin = 45.8347987943741 | erot = 18.4752794596828 | epot = -97.8745279599047 | etot = -33.5644497058478 +55000 ekin = 45.0590316628642 | erot = 17.9341671577877 | epot = -96.5576485255772 | etot = -33.5644497049254 +56000 ekin = 44.1409291390466 | erot = 17.4520797326575 | epot = -95.1574585762252 | etot = -33.5644497045211 +57000 ekin = 43.0792908324229 | erot = 17.0373342694525 | epot = -93.6810748066133 | etot = -33.5644497047379 +58000 ekin = 41.8704923540616 | erot = 16.6939394056078 | epot = -92.1288814650828 | etot = -33.5644497054134 +59000 ekin = 40.5509408803243 | erot = 16.4316140927963 | epot = -90.5470046657502 | etot = -33.5644496926296 +60000 ekin = 39.1975830612683 | erot = 16.2583411314117 | epot = -89.0203738856281 | etot = -33.564449692948 +61000 ekin = 35.7114984384268 | erot = 15.7928074869535 | epot = -85.0687559055495 | etot = -33.5644499801692 +62000 ekin = 34.7372517506983 | erot = 15.8094409096042 | epot = -84.1111427027985 | etot = -33.564450042496 +63000 ekin = 35.8178089566995 | erot = 16.1653492511937 | epot = -85.5476088513059 | etot = -33.5644506434127 +64000 ekin = 34.8692363703958 | erot = 16.1670101597179 | epot = -84.6006971860838 | etot = -33.5644506559701 +65000 ekin = 33.846449455545 | erot = 16.1402632189654 | epot = -83.5511633293456 | etot = -33.5644506548352 +66000 ekin = 32.7636419796978 | erot = 16.0751240440806 | epot = -82.4032166770508 | etot = -33.5644506532724 +67000 ekin = 31.6420680628897 | erot = 15.970564295673 | epot = -81.1770830093356 | etot = -33.5644506507729 +68000 ekin = 30.5061166759974 | erot = 15.8342590047108 | epot = -79.904826328435 | etot = -33.5644506477268 +69000 ekin = 29.3793899831146 | erot = 15.6784092891742 | epot = -78.6222499180456 | etot = -33.5644506457568 +70000 ekin = 28.2842777970645 | erot = 15.5192251789786 | epot = -77.3679536187083 | etot = -33.5644506426651 +71000 ekin = 27.2428007223146 | erot = 15.3775924468384 | epot = -76.1848438089721 | etot = -33.5644506398192 +72000 ekin = 26.2738583640503 | erot = 15.2738682128135 | epot = -75.1121772142993 | etot = -33.5644506374354 +73000 ekin = 25.3929266243352 | erot = 15.2252389252993 | epot = -74.1826161852624 | etot = -33.5644506356278 +74000 ekin = 24.6118800235924 | erot = 15.2440811522979 | epot = -73.4204118109397 | etot = -33.5644506350493 +75000 ekin = 23.9285421197386 | erot = 15.2937064902862 | epot = -72.7866996078894 | etot = -33.5644509978646 +76000 ekin = 23.6014258497366 | erot = 14.5530249139085 | epot = -71.7189013877723 | etot = -33.5644506241273 +77000 ekin = 24.0021186681998 | erot = 14.6672556253499 | epot = -72.2338249120015 | etot = -33.5644506184517 +78000 ekin = 23.7667117018473 | erot = 14.8821032755388 | epot = -72.2132655967964 | etot = -33.5644506194103 +79000 ekin = 23.6362408803455 | erot = 15.1573231058556 | epot = -72.3580146069965 | etot = -33.5644506207955 +80000 ekin = 23.6008292998183 | erot = 15.4801164769237 | epot = -72.6453963992505 | etot = -33.5644506225085 +81000 ekin = 23.6479278988512 | erot = 15.8366782045229 | epot = -73.0490567276813 | etot = -33.5644506243072 +82000 ekin = 23.763195852744 | erot = 16.2135577483195 | epot = -73.541204227137 | etot = -33.5644506260735 +83000 ekin = 23.93133805131 | erot = 16.5989137528028 | epot = -74.0947024318273 | etot = -33.5644506277145 +84000 ekin = 24.1405337461498 | erot = 16.9832739889214 | epot = -74.6882583637893 | etot = -33.5644506287181 +85000 ekin = 24.3851366362468 | erot = 17.3594190811792 | epot = -75.3090063475356 | etot = -33.5644506301095 +86000 ekin = 24.6499622429188 | erot = 17.7229731863038 | epot = -75.937386060464 | etot = -33.5644506312414 +87000 ekin = 24.9195866966175 | erot = 18.0734917202536 | epot = -76.5575290489239 | etot = -33.5644506320529 +88000 ekin = 25.1793742014134 | erot = 18.4146339772087 | epot = -77.1584588111687 | etot = -33.5644506325466 +89000 ekin = 25.4156568494637 | erot = 18.753968669385 | epot = -77.7340761514942 | etot = -33.5644506326455 +90000 ekin = 25.6096840035671 | erot = 19.1040901404621 | epot = -78.2782247770918 | etot = -33.5644506330626 +91000 ekin = 25.7348417969792 | erot = 19.4865010462193 | epot = -78.7857934757851 | etot = -33.5644506325866 +92000 ekin = 25.7824117490222 | erot = 19.9168308436387 | epot = -79.2636932257648 | etot = -33.5644506331039 +93000 ekin = 25.7436484203088 | erot = 20.4015276208854 | epot = -79.7096266744372 | etot = -33.564450633243 +94000 ekin = 25.6107487399104 | erot = 20.949881961115 | epot = -80.1250813341981 | etot = -33.5644506331727 +95000 ekin = 25.3788454256131 | erot = 21.5718811146881 | epot = -80.5151771730697 | etot = -33.5644506327685 +96000 ekin = 25.0476635684687 | erot = 22.2778886106639 | epot = -80.8900028110571 | etot = -33.5644506319245 +97000 ekin = 24.6228037012584 | erot = 23.0785820232847 | epot = -81.2658363557742 | etot = -33.564450631231 +98000 ekin = 24.1163650303316 | erot = 23.980262455687 | epot = -81.6610781157268 | etot = -33.5644506297082 +99000 ekin = 23.5467601995482 | erot = 24.9897227937605 | epot = -82.1009336213136 | etot = -33.5644506280048 +100000 ekin = 22.9377076830221 | erot = 26.112544428779 | epot = -82.6147027382293 | etot = -33.5644506264282 +101000 ekin = 22.3162402354096 | erot = 27.3495277986626 | epot = -83.2302186594371 | etot = -33.5644506253649 +102000 ekin = 21.7099673799529 | erot = 28.6941289887159 | epot = -83.9685469938564 | etot = -33.5644506251876 +103000 ekin = 21.1440927333112 | erot = 30.1304131051784 | epot = -84.8389564645821 | etot = -33.5644506260925 +104000 ekin = 20.639036073264 | erot = 31.6318076720505 | epot = -85.8352943737208 | etot = -33.5644506284063 +105000 ekin = 20.2097356177992 | erot = 33.155951127779 | epot = -86.9301373769384 | etot = -33.5644506313601 +106000 ekin = 19.8659962936204 | erot = 34.6591523175009 | epot = -88.0895992441982 | etot = -33.5644506330769 +107000 ekin = 19.6196926152642 | erot = 36.1003389899193 | epot = -89.2844822415487 | etot = -33.5644506363652 +108000 ekin = 19.4737764770437 | erot = 37.4404659122968 | epot = -90.4786930287769 | etot = -33.5644506394364 +109000 ekin = 19.4257211237998 | erot = 38.6395727467532 | epot = -91.6297445157463 | etot = -33.5644506451932 +110000 ekin = 19.4643317381198 | erot = 39.6495422786743 | epot = -92.6783246653681 | etot = -33.564450648574 +111000 ekin = 19.5812097010477 | erot = 40.4340503208624 | epot = -93.5797106732505 | etot = -33.5644506513404 +112000 ekin = 19.7688752467926 | erot = 40.9641614007962 | epot = -94.297487301236 | etot = -33.5644506536472 +113000 ekin = 20.0199352606443 | erot = 41.2235617686336 | epot = -94.8079476827577 | etot = -33.5644506534798 +114000 ekin = 20.3316783135453 | erot = 41.2208106095024 | epot = -95.1169395739077 | etot = -33.56445065086 +115000 ekin = 20.7092934859803 | erot = 40.9902193450322 | epot = -95.2639634785888 | etot = -33.5644506475763 +116000 ekin = 21.1584070130043 | erot = 40.5711692188877 | epot = -95.2940268780899 | etot = -33.5644506461979 +117000 ekin = 21.6717401642267 | erot = 40.0068194492192 | epot = -95.2430102574592 | etot = -33.5644506440133 +118000 ekin = 22.2304498749665 | erot = 39.3449170916981 | epot = -95.1398176087205 | etot = -33.5644506420559 +119000 ekin = 22.8040322747498 | erot = 38.6279078104772 | epot = -94.9963907285437 | etot = -33.5644506433167 +120000 ekin = 23.3636455910773 | erot = 37.8733163419346 | epot = -94.8014125775743 | etot = -33.5644506445623 +121000 ekin = 23.8883342479557 | erot = 37.0853024873734 | epot = -94.5380873807793 | etot = -33.5644506454502 +122000 ekin = 24.3628295450724 | erot = 36.2617521254169 | epot = -94.1890323184744 | etot = -33.5644506479851 +123000 ekin = 24.7728939422973 | erot = 35.3896441641822 | epot = -93.7269887541634 | etot = -33.564450647684 +124000 ekin = 25.1206142173503 | erot = 34.4655545655721 | epot = -93.1506194284831 | etot = -33.5644506455608 +125000 ekin = 25.4216604350096 | erot = 33.503516320942 | epot = -92.4896273979272 | etot = -33.5644506419756 +126000 ekin = 25.6927735129487 | erot = 32.5281184075612 | epot = -91.7853425611144 | etot = -33.5644506406046 +127000 ekin = 25.9460883081157 | erot = 31.5650113724921 | epot = -91.0755503181686 | etot = -33.5644506375608 +128000 ekin = 26.1993872383113 | erot = 30.6366650539312 | epot = -90.4005029275328 | etot = -33.5644506352904 +129000 ekin = 26.4652741312988 | erot = 29.761033950875 | epot = -89.790758715097 | etot = -33.5644506329232 +130000 ekin = 26.7486727551143 | erot = 28.9506137583675 | epot = -89.2637371464425 | etot = -33.5644506329608 +131000 ekin = 27.0469092028967 | erot = 28.2034442942545 | epot = -88.8148041302784 | etot = -33.5644506331273 +132000 ekin = 27.354287486523 | erot = 27.516081388701 | epot = -88.4348195084624 | etot = -33.5644506332384 +133000 ekin = 27.6627378161327 | erot = 26.888810791231 | epot = -88.1159992405597 | etot = -33.564450633196 +134000 ekin = 27.967292318186 | erot = 26.3214524159643 | epot = -87.8531953671446 | etot = -33.5644506329943 +135000 ekin = 28.2641150378973 | erot = 25.8141340320123 | epot = -87.6426997025848 | etot = -33.5644506326751 +136000 ekin = 28.5509978141275 | erot = 25.3673179322137 | epot = -87.4827663786045 | etot = -33.5644506322633 +137000 ekin = 28.8259159092095 | erot = 24.9801644637669 | epot = -87.3705310053013 | etot = -33.5644506323249 +138000 ekin = 29.0842610649225 | erot = 24.6492546073972 | epot = -87.2979663044031 | etot = -33.5644506320834 +139000 ekin = 29.3272222877147 | erot = 24.3700782380114 | epot = -87.2617511574221 | etot = -33.5644506316961 +140000 ekin = 29.5579798491409 | erot = 24.1376580585839 | epot = -87.2600885391577 | etot = -33.5644506314329 +141000 ekin = 29.7799846346147 | erot = 23.946242993064 | epot = -87.2906782589293 | etot = -33.5644506312505 +142000 ekin = 29.9959841884821 | erot = 23.7899704636108 | epot = -87.3504052832972 | etot = -33.5644506312043 +143000 ekin = 30.20703491277 | erot = 23.6632996950733 | epot = -87.4347852391637 | etot = -33.5644506313204 +144000 ekin = 30.411884002902 | erot = 23.5613798569439 | epot = -87.537714491437 | etot = -33.564450631591 +145000 ekin = 30.606845687222 | erot = 23.4803656669174 | epot = -87.6516619861197 | etot = -33.5644506319804 +146000 ekin = 30.786123077816 | erot = 23.4176420010831 | epot = -87.7682157113377 | etot = -33.5644506324387 +147000 ekin = 30.9424364770354 | erot = 23.3719366394343 | epot = -87.878823749381 | etot = -33.5644506329113 +148000 ekin = 31.0677916134895 | erot = 23.343321608025 | epot = -87.9755638548643 | etot = -33.5644506333498 +149000 ekin = 31.1542520331538 | erot = 23.3331254537238 | epot = -88.0518281205882 | etot = -33.5644506337106 +150000 ekin = 31.1946418128191 | erot = 23.3437996409618 | epot = -88.1028920877408 | etot = -33.5644506339599 +151000 ekin = 31.183806383935 | erot = 23.3785936220274 | epot = -88.1268506398047 | etot = -33.5644506338423 +152000 ekin = 31.1202290278342 | erot = 23.4412183836801 | epot = -88.1258980452558 | etot = -33.5644506337415 +153000 ekin = 31.0032553217694 | erot = 23.5372189789098 | epot = -88.1049249338573 | etot = -33.5644506331782 +154000 ekin = 30.8354559406818 | erot = 23.6729952127027 | epot = -88.0729017863056 | etot = -33.5644506329211 +155000 ekin = 30.6186135870613 | erot = 23.8551009557717 | epot = -88.0381651751801 | etot = -33.564450632347 +156000 ekin = 30.3571457582689 | erot = 24.0914721103803 | epot = -88.0130685002393 | etot = -33.5644506315902 +157000 ekin = 30.057410850046 | erot = 24.3907046676107 | epot = -88.012566148493 | etot = -33.5644506308362 +158000 ekin = 29.7256756923437 | erot = 24.762556719639 | epot = -88.0526830421884 | etot = -33.5644506302057 +159000 ekin = 29.3667041508031 | erot = 25.2124449846246 | epot = -88.1435997656418 | etot = -33.5644506302141 +160000 ekin = 28.9829375848383 | erot = 25.7406189361283 | epot = -88.2880071520223 | etot = -33.5644506310558 +161000 ekin = 28.5708031098758 | erot = 26.3449808633592 | epot = -88.4802346049617 | etot = -33.5644506317267 +162000 ekin = 28.1278607476191 | erot = 27.0188065006254 | epot = -88.7111178809976 | etot = -33.564450632753 +163000 ekin = 27.6515523776561 | erot = 27.7508923428494 | epot = -88.9668953542198 | etot = -33.5644506337143 +164000 ekin = 27.1398166575548 | erot = 28.5265897115537 | epot = -89.2308570046245 | etot = -33.564450635516 +165000 ekin = 26.59018012942 | erot = 29.3236809534503 | epot = -89.4783117201368 | etot = -33.5644506372666 +166000 ekin = 26.0027550424038 | erot = 30.1148491025895 | epot = -89.6820547838353 | etot = -33.564450638842 +167000 ekin = 25.3815734826451 | erot = 30.8714146428701 | epot = -89.8174387656406 | etot = -33.5644506401255 +168000 ekin = 24.7338280126237 | erot = 31.5656853660197 | epot = -89.8639640196521 | etot = -33.5644506410087 +169000 ekin = 24.0691061638315 | erot = 32.1733410341242 | epot = -89.8068978394117 | etot = -33.564450641456 +170000 ekin = 23.3986380903856 | erot = 32.6761770397929 | epot = -89.6392657713649 | etot = -33.5644506411864 +171000 ekin = 22.7350947047576 | erot = 33.0649339609238 | epot = -89.3644793058787 | etot = -33.5644506401972 +172000 ekin = 22.0927595064345 | erot = 33.3397459263048 | epot = -88.9969560711814 | etot = -33.5644506384421 +173000 ekin = 21.4881436133131 | erot = 33.5098602953131 | epot = -88.5624545444177 | etot = -33.5644506357915 +174000 ekin = 20.9424106184029 | erot = 33.5950638981387 | epot = -88.1019251458152 | etot = -33.5644506292736 +175000 ekin = 20.4887725385188 | erot = 33.6332952588445 | epot = -87.6865184248663 | etot = -33.5644506275031 +176000 ekin = 20.1459992745576 | erot = 33.6413286939825 | epot = -87.351778594707 | etot = -33.564450626167 +177000 ekin = 19.9273952403355 | erot = 33.6264319072463 | epot = -87.1182777732003 | etot = -33.5644506256185 +178000 ekin = 19.8405268115202 | erot = 33.5862782738567 | epot = -86.9912557124967 | etot = -33.5644506271198 +179000 ekin = 19.8828425829329 | erot = 33.5043404166444 | epot = -86.9516336276337 | etot = -33.5644506280564 +180000 ekin = 20.0524881206169 | erot = 33.3671042345424 | epot = -86.9840429849014 | etot = -33.5644506297421 +181000 ekin = 20.3414841297263 | erot = 33.1581782006462 | epot = -87.0641129622371 | etot = -33.5644506318646 +182000 ekin = 20.7352057198159 | erot = 32.8612622822523 | epot = -87.1609186361345 | etot = -33.5644506340663 +183000 ekin = 21.2137106223586 | erot = 32.4647477949406 | epot = -87.2429090531987 | etot = -33.5644506358994 +184000 ekin = 21.7537587720613 | erot = 31.9655803613327 | epot = -87.2837897705835 | etot = -33.5644506371895 +185000 ekin = 22.3286746031838 | erot = 31.3708022039154 | epot = -87.263927444786 | etot = -33.5644506376868 +186000 ekin = 22.9115100132845 | erot = 30.6990331536428 | epot = -87.1749938042474 | etot = -33.5644506373201 +187000 ekin = 23.4775030152572 | erot = 29.9792070479707 | epot = -87.0211606994407 | etot = -33.5644506362127 +188000 ekin = 24.0059463479901 | erot = 29.2469949106332 | epot = -86.8173918933289 | etot = -33.5644506347057 +189000 ekin = 24.4809955944174 | erot = 28.5392131436642 | epot = -86.5846593713795 | etot = -33.5644506332979 +190000 ekin = 24.8911658073071 | erot = 27.8871249849441 | epot = -86.3427414247871 | etot = -33.5644506325359 +191000 ekin = 25.2275609419512 | erot = 27.3101259966536 | epot = -86.1021375715765 | etot = -33.5644506329717 +192000 ekin = 25.4831011426741 | erot = 26.8121375634346 | epot = -85.8596893403555 | etot = -33.5644506342468 +193000 ekin = 25.2930335715097 | erot = 26.641089195829 | epot = -85.4985734034392 | etot = -33.5644506361005 +194000 ekin = 25.0352601614021 | erot = 26.652526548361 | epot = -85.2522373921847 | etot = -33.5644506824216 +195000 ekin = 25.0363508840831 | erot = 26.2378500699574 | epot = -84.838651623646 | etot = -33.5644506696055 +196000 ekin = 24.9648942549683 | erot = 25.7868302418778 | epot = -84.3161751669049 | etot = -33.5644506700588 +197000 ekin = 24.8200850732436 | erot = 25.3002719383815 | epot = -83.684807680627 | etot = -33.5644506690019 +198000 ekin = 24.6172884588533 | erot = 24.7762496503829 | epot = -82.957988775829 | etot = -33.5644506665928 +199000 ekin = 24.3770483830299 | erot = 24.2259949153857 | epot = -82.1674939619529 | etot = -33.5644506635372 +200000 ekin = 24.122436002035 | erot = 23.6691820640912 | epot = -81.3560687261623 | etot = -33.5644506600361 +201000 ekin = 23.8775516468524 | erot = 23.129174398578 | epot = -80.5711767022531 | etot = -33.5644506568227 +202000 ekin = 23.6646103059802 | erot = 22.6276096876317 | epot = -79.856670647895 | etot = -33.5644506542831 +203000 ekin = 23.5017139925634 | erot = 22.1809863327408 | epot = -79.2471509779163 | etot = -33.5644506526121 +204000 ekin = 23.4012931943709 | erot = 21.7992926193403 | epot = -78.7650364652273 | etot = -33.564450651516 +205000 ekin = 23.3698442687857 | erot = 21.4883950765935 | epot = -78.4226899967305 | etot = -33.5644506513513 +206000 ekin = 23.4080277663952 | erot = 21.2503388252223 | epot = -78.222817243383 | etot = -33.5644506517654 +207000 ekin = 23.510672424505 | erot = 21.0828853352514 | epot = -78.1580084122941 | etot = -33.5644506525377 +208000 ekin = 23.668353418069 | erot = 20.9827921925506 | epot = -78.2155962640904 | etot = -33.5644506534708 +209000 ekin = 23.8319531636404 | erot = 20.8686960092894 | epot = -78.2650998050505 | etot = -33.5644506321207 +210000 ekin = 24.1634900876545 | erot = 20.8246815259943 | epot = -78.5526222834943 | etot = -33.5644506698455 +211000 ekin = 24.4545474929207 | erot = 20.8320949387518 | epot = -78.8510930934304 | etot = -33.564450661758 +212000 ekin = 24.7210588847004 | erot = 20.8889178093638 | epot = -79.1744273565512 | etot = -33.564450662487 +213000 ekin = 24.9762555918736 | erot = 20.995657067092 | epot = -79.5363633251364 | etot = -33.5644506661708 +214000 ekin = 25.2054830046564 | erot = 21.1345527593257 | epot = -79.904486431005 | etot = -33.5644506670229 +215000 ekin = 25.4055444850595 | erot = 21.2948000239986 | epot = -80.2647951766001 | etot = -33.564450667542 +216000 ekin = 25.5773395550173 | erot = 21.4659469017842 | epot = -80.6077371248694 | etot = -33.5644506680679 +217000 ekin = 25.7224226234168 | erot = 21.6383314527717 | epot = -80.9252047446809 | etot = -33.5644506684925 +218000 ekin = 25.8456307141236 | erot = 21.7996006617657 | epot = -81.2096820449196 | etot = -33.5644506690303 +219000 ekin = 25.9524523541736 | erot = 21.9358336225136 | epot = -81.4527366463228 | etot = -33.5644506696356 +220000 ekin = 26.0480501371294 | erot = 22.0331400323276 | epot = -81.6456408394172 | etot = -33.5644506699602 +221000 ekin = 26.1377559921142 | erot = 22.0801399062462 | epot = -81.7823465685532 | etot = -33.5644506701928 +222000 ekin = 26.2262421157048 | erot = 22.0692633440543 | epot = -81.859956129764 | etot = -33.564450670005 +223000 ekin = 26.3184403630266 | erot = 21.9982474658049 | epot = -81.8811384982253 | etot = -33.5644506693938 +224000 ekin = 26.4171271373519 | erot = 21.8710288815675 | epot = -81.8526066880913 | etot = -33.5644506691719 +225000 ekin = 26.5225389104719 | erot = 21.6965423523057 | epot = -81.7835319309085 | etot = -33.5644506681309 +226000 ekin = 26.7157923548783 | erot = 21.3119214437842 | epot = -81.5921644821736 | etot = -33.5644506835112 +227000 ekin = 27.2484396437764 | erot = 20.6374955149859 | epot = -81.4503858460509 | etot = -33.5644506872886 +228000 ekin = 27.5078528971482 | erot = 20.2748179574152 | epot = -81.3471215226765 | etot = -33.564450668113 +229000 ekin = 27.6312830550944 | erot = 19.9858964954709 | epot = -81.1816302175473 | etot = -33.564450666982 +230000 ekin = 27.7676058404246 | erot = 19.7189438600613 | epot = -81.0510003675302 | etot = -33.5644506670444 +231000 ekin = 27.9171898995783 | erot = 19.4851196432287 | epot = -80.9667602108582 | etot = -33.5644506680513 +232000 ekin = 28.075807909498 | erot = 19.2892055600519 | epot = -80.9294641380373 | etot = -33.5644506684874 +233000 ekin = 28.2354888581722 | erot = 19.1284398309988 | epot = -80.9283793559407 | etot = -33.5644506667697 +234000 ekin = 28.3953039485459 | erot = 19.0132859353609 | epot = -80.9730405513788 | etot = -33.564450667472 +235000 ekin = 28.5569493494506 | erot = 18.9585387746691 | epot = -81.0799387921407 | etot = -33.564450668021 +236000 ekin = 28.7166448189613 | erot = 18.9671002034186 | epot = -81.2481956905202 | etot = -33.5644506681403 +237000 ekin = 28.8725023819759 | erot = 19.0433381874627 | epot = -81.4802912374047 | etot = -33.5644506679661 +238000 ekin = 29.0257746255977 | erot = 19.1916941122354 | epot = -81.781919405367 | etot = -33.5644506675339 +239000 ekin = 29.1795842186893 | erot = 19.4168064167824 | epot = -82.1608413029194 | etot = -33.5644506674477 +240000 ekin = 29.3337146102013 | erot = 19.7090725309664 | epot = -82.6072378098102 | etot = -33.5644506686425 +241000 ekin = 29.4868078967125 | erot = 20.0596352268188 | epot = -83.1108937928375 | etot = -33.5644506693062 +242000 ekin = 29.6351003169461 | erot = 20.4605457842952 | epot = -83.6600967717312 | etot = -33.5644506704898 +243000 ekin = 29.8921802425375 | erot = 20.6958964400281 | epot = -84.1525273495514 | etot = -33.5644506669859 +244000 ekin = 30.2594419587798 | erot = 20.964961730853 | epot = -84.7888543939581 | etot = -33.5644507043253 +245000 ekin = 30.3074620328625 | erot = 21.308999500704 | epot = -85.1809122847658 | etot = -33.5644507511994 +246000 ekin = 30.6998172933751 | erot = 21.0861202554954 | epot = -85.3503880690886 | etot = -33.5644505202181 +247000 ekin = 31.2652124059134 | erot = 21.7433599271938 | epot = -86.5730230770323 | etot = -33.5644507439251 +248000 ekin = 31.2039013197185 | erot = 22.3578318778188 | epot = -87.1261839420136 | etot = -33.5644507444763 +249000 ekin = 31.0628965882796 | erot = 22.9361503364912 | epot = -87.5634976683527 | etot = -33.5644507435818 +250000 ekin = 30.8544219835667 | erot = 23.4738999845995 | epot = -87.8927727106867 | etot = -33.5644507425205 +251000 ekin = 30.5979929542448 | erot = 23.973249537305 | epot = -88.1356932313339 | etot = -33.5644507397841 +252000 ekin = 30.3186084933224 | erot = 24.447023432737 | epot = -88.3300826628831 | etot = -33.5644507368237 +253000 ekin = 30.0416328683412 | erot = 24.9117142614702 | epot = -88.5177978640591 | etot = -33.5644507342476 +254000 ekin = 29.6651322242409 | erot = 25.3352238225117 | epot = -88.5648072260424 | etot = -33.5644511792898 +255000 ekin = 27.9972596304248 | erot = 25.3436445664535 | epot = -86.9053550133662 | etot = -33.5644508164878 +256000 ekin = 27.4480536507435 | erot = 26.2038023388295 | epot = -87.2163067908443 | etot = -33.5644508012713 +257000 ekin = 28.5107044681316 | erot = 27.5793602338718 | epot = -89.6545158781981 | etot = -33.5644511761947 +258000 ekin = 28.9485040029364 | erot = 27.9141399631527 | epot = -90.4270947740165 | etot = -33.5644508079275 +259000 ekin = 29.1923898090981 | erot = 28.2760336628793 | epot = -91.0328742826499 | etot = -33.5644508106724 +260000 ekin = 29.442065950696 | erot = 28.6795119903338 | epot = -91.6860287571124 | etot = -33.5644508160826 +261000 ekin = 29.6845039883694 | erot = 29.1068404637727 | epot = -92.3557952702589 | etot = -33.5644508181168 +262000 ekin = 29.8834680797453 | erot = 29.5461970803508 | epot = -92.9941159814699 | etot = -33.5644508213738 +263000 ekin = 30.0159351907403 | erot = 29.9649097381375 | epot = -93.5452957538687 | etot = -33.5644508249909 +264000 ekin = 30.0524877646951 | erot = 30.3384906869752 | epot = -93.9554292802054 | etot = -33.5644508285351 +265000 ekin = 29.9659450397006 | erot = 30.6431999053458 | epot = -94.1735957767029 | etot = -33.5644508316564 +266000 ekin = 29.7355380957043 | erot = 30.8554934503359 | epot = -94.1554823800756 | etot = -33.5644508340354 +267000 ekin = 29.350217253122 | erot = 30.9531552650632 | epot = -93.8678233536458 | etot = -33.5644508354606 +268000 ekin = 28.8109215599824 | erot = 30.9159121160793 | epot = -93.2912845119104 | etot = -33.5644508358487 +269000 ekin = 28.1312299025676 | erot = 30.72588001067 | epot = -92.4215607498475 | etot = -33.5644508366099 +270000 ekin = 27.3365120330892 | erot = 30.3685462543054 | epot = -91.2695091419232 | etot = -33.5644508545286 +271000 ekin = 26.4621552466015 | erot = 29.8348321072944 | epot = -89.8614382054951 | etot = -33.5644508515991 +272000 ekin = 25.5514537840266 | erot = 29.1238715109503 | epot = -88.2397761424711 | etot = -33.5644508474942 +273000 ekin = 24.6528090192241 | erot = 28.2453291639337 | epot = -86.4625890255924 | etot = -33.5644508424347 +274000 ekin = 23.821234650199 | erot = 27.2200000603148 | epot = -84.6056855414306 | etot = -33.5644508309167 +275000 ekin = 22.972977788893 | erot = 26.0804823635616 | epot = -82.6179111120453 | etot = -33.5644509595907 +276000 ekin = 22.0549791970788 | erot = 24.8883860441621 | epot = -80.507816055329 | etot = -33.564450814088 +277000 ekin = 22.2918454486476 | erot = 23.6844629884912 | epot = -79.5407594438925 | etot = -33.5644510067537 +278000 ekin = 22.2933944834357 | erot = 22.3796695906513 | epot = -78.237514901963 | etot = -33.5644508278759 +279000 ekin = 22.3659748249692 | erot = 21.1183819744112 | epot = -77.0488076286914 | etot = -33.5644508293109 +280000 ekin = 22.5183002078395 | erot = 19.9334324614475 | epot = -76.0161834966364 | etot = -33.5644508273493 +281000 ekin = 22.7529481191282 | erot = 18.8478601493533 | epot = -75.1652590940401 | etot = -33.5644508255585 +282000 ekin = 23.0795879184844 | erot = 17.877696647541 | epot = -74.5217353872615 | etot = -33.5644508212361 +283000 ekin = 23.5210121271395 | erot = 17.0345324476772 | epot = -74.1199953957519 | etot = -33.5644508209352 +284000 ekin = 24.0799247559117 | erot = 16.3233784659049 | epot = -73.9677540517901 | etot = -33.5644508299735 +285000 ekin = 24.7785446246702 | erot = 15.7478244913859 | epot = -74.0908199422723 | etot = -33.5644508262162 +286000 ekin = 25.6368387345602 | erot = 15.3047487828053 | epot = -74.5060383422943 | etot = -33.5644508249288 +287000 ekin = 26.6214548224918 | erot = 14.9922504829504 | epot = -75.1781561309387 | etot = -33.5644508254965 +288000 ekin = 27.7267158888742 | erot = 14.8012865017222 | epot = -76.092453221868 | etot = -33.5644508312716 +289000 ekin = 28.8920167227402 | erot = 14.7169892845884 | epot = -77.1734568439709 | etot = -33.5644508366423 +290000 ekin = 30.0553666648459 | erot = 14.7251675417739 | epot = -78.3449850482838 | etot = -33.5644508416639 +291000 ekin = 31.1595769632409 | erot = 14.8119291202727 | epot = -79.5359569291001 | etot = -33.5644508455866 +292000 ekin = 32.1608216689788 | erot = 14.9640713088948 | epot = -80.6893438261594 | etot = -33.5644508482858 +293000 ekin = 33.0319319380116 | erot = 15.1681739054538 | epot = -81.7645566935981 | etot = -33.5644508501327 +294000 ekin = 33.7599421346893 | erot = 15.408810677985 | epot = -82.7332036642727 | etot = -33.5644508515984 +295000 ekin = 34.3413485939618 | erot = 15.6673943342359 | epot = -83.5731937811138 | etot = -33.5644508529161 +296000 ekin = 34.7782829446679 | erot = 15.9229210434156 | epot = -84.2656548420787 | etot = -33.5644508539951 +297000 ekin = 35.0767101392297 | erot = 16.1546669536392 | epot = -84.7958279474613 | etot = -33.5644508545924 +298000 ekin = 35.2457989813398 | erot = 16.3457320030263 | epot = -85.1559818388994 | etot = -33.5644508545332 +299000 ekin = 35.2970066855107 | erot = 16.4859983979418 | epot = -85.3474559372914 | etot = -33.5644508538389 +300000 ekin = 35.2422237261552 | erot = 16.573594168153 | epot = -85.380268746981 | etot = -33.5644508526728 +301000 ekin = 35.0916597610679 | erot = 16.6147820199689 | epot = -85.2708926322436 | etot = -33.5644508512068 +302000 ekin = 34.8528128910437 | erot = 16.6227287108284 | epot = -85.0399924513857 | etot = -33.5644508495136 +303000 ekin = 34.5312597670471 | erot = 16.6156181966321 | epot = -84.7113288112829 | etot = -33.5644508476037 +304000 ekin = 34.131367434132 | erot = 16.6227567332235 | epot = -84.3185750111405 | etot = -33.5644508437849 +305000 ekin = 33.6571822643369 | erot = 16.6720234605658 | epot = -83.8936565670678 | etot = -33.5644508421651 +306000 ekin = 33.1151986332002 | erot = 16.7769746117295 | epot = -83.4566240858641 | etot = -33.5644508409344 +307000 ekin = 32.5134330702729 | erot = 16.9437629168019 | epot = -83.0216468273944 | etot = -33.5644508403197 +308000 ekin = 31.8601474906691 | erot = 17.1694637372836 | epot = -82.5940620683869 | etot = -33.5644508404342 +309000 ekin = 31.1628016434418 | erot = 17.4420089824945 | epot = -82.1692614669022 | etot = -33.5644508409659 +310000 ekin = 30.4284939703051 | erot = 17.7430091432334 | epot = -81.7359539560319 | etot = -33.5644508424934 +311000 ekin = 29.6636970636957 | erot = 18.0450727085003 | epot = -81.2732206157428 | etot = -33.5644508435468 +312000 ekin = 28.8763119838117 | erot = 18.3211026917138 | epot = -80.7618655199236 | etot = -33.5644508443981 +313000 ekin = 28.0757317031842 | erot = 18.5482322979291 | epot = -80.1884148456634 | etot = -33.5644508445501 +314000 ekin = 27.2754576014843 | erot = 18.7102692133756 | epot = -79.5501776586764 | etot = -33.5644508438165 +315000 ekin = 26.4927512875096 | erot = 18.8002978244007 | epot = -78.8574999542301 | etot = -33.5644508423198 +316000 ekin = 25.747682520664 | erot = 18.8201859999041 | epot = -78.132319360867 | etot = -33.564450840299 +317000 ekin = 25.0614905058277 | erot = 18.7788964667723 | epot = -77.4048378106377 | etot = -33.5644508380377 +318000 ekin = 24.4546904068649 | erot = 18.6903703700934 | epot = -76.7095116127357 | etot = -33.5644508357774 +319000 ekin = 23.9454326766056 | erot = 18.5716676910418 | epot = -76.0815512013104 | etot = -33.564450833663 +320000 ekin = 23.5484361618332 | erot = 18.4417359442004 | epot = -75.5546229377731 | etot = -33.5644508317395 +321000 ekin = 23.2745454666142 | erot = 18.3209670206188 | epot = -75.159963317225 | etot = -33.5644508299921 +322000 ekin = 23.1307065450427 | erot = 18.2311244116958 | epot = -74.9262817851812 | etot = -33.5644508284427 +323000 ekin = 23.1199305195539 | erot = 18.1948729378857 | epot = -74.8792542846864 | etot = -33.5644508272467 +324000 ekin = 23.2402241371604 | erot = 18.2346442880494 | epot = -75.0393192519605 | etot = -33.5644508267507 +325000 ekin = 23.4710021372648 | erot = 18.3668956954565 | epot = -75.4023486640661 | etot = -33.5644508313448 +326000 ekin = 23.7795455090648 | erot = 18.5932769386575 | epot = -75.9372732822622 | etot = -33.5644508345399 +327000 ekin = 24.1343713308685 | erot = 18.9009306659146 | epot = -76.5997528363167 | etot = -33.5644508395337 +328000 ekin = 24.4953646019599 | erot = 19.2611055950044 | epot = -77.3209210428185 | etot = -33.5644508458542 +329000 ekin = 24.8184483226243 | erot = 19.6309716494425 | epot = -78.0138708244921 | etot = -33.5644508524254 +330000 ekin = 25.0648153577033 | erot = 19.9600875039469 | epot = -78.5893537191492 | etot = -33.564450857499 +331000 ekin = 25.2101383722027 | erot = 20.2008919381154 | epot = -78.9754811706424 | etot = -33.5644508603242 +332000 ekin = 25.2457706638964 | erot = 20.3248269291664 | epot = -79.1350484526804 | etot = -33.5644508596175 +333000 ekin = 25.1861890029755 | erot = 20.3296166389972 | epot = -79.080256497531 | etot = -33.5644508555582 +334000 ekin = 25.06621909807 | erot = 20.2399843242203 | epot = -78.8706542714784 | etot = -33.5644508491881 +335000 ekin = 24.9333683336748 | erot = 20.1009816218885 | epot = -78.5988007975495 | etot = -33.5644508419862 +336000 ekin = 24.8381114575746 | erot = 19.9670256544153 | epot = -78.3695879473404 | etot = -33.5644508353505 +337000 ekin = 24.8247545151604 | erot = 19.8908557635149 | epot = -78.2800611094823 | etot = -33.564450830807 +338000 ekin = 24.9246805342402 | erot = 19.9088859975838 | epot = -78.3980173598233 | etot = -33.5644508279992 +339000 ekin = 25.1522743470225 | erot = 20.043365846569 | epot = -78.7600910209592 | etot = -33.5644508273677 +340000 ekin = 25.5040328015065 | erot = 20.3063243572631 | epot = -79.3748079874543 | etot = -33.5644508286847 +341000 ekin = 25.9593882032928 | erot = 20.6972938179576 | epot = -80.2211328527409 | etot = -33.5644508314906 +342000 ekin = 26.4842114255991 | erot = 21.206040618102 | epot = -81.2547028790046 | etot = -33.5644508353035 +343000 ekin = 27.0356929913546 | erot = 21.8153279723555 | epot = -82.4154718032949 | etot = -33.5644508395848 +344000 ekin = 27.567697334587 | erot = 22.5033872894653 | epot = -83.6355354678824 | etot = -33.5644508438302 +345000 ekin = 28.0359749647809 | erot = 23.2463366467822 | epot = -84.846762459203 | etot = -33.5644508476399 +346000 ekin = 28.4026013553742 | erot = 24.0201112992316 | epot = -85.9871635053201 | etot = -33.5644508507143 +347000 ekin = 28.6398915195253 | erot = 24.8020103746405 | epot = -87.0063527468454 | etot = -33.5644508526796 +348000 ekin = 28.7326075378057 | erot = 25.5714490943132 | epot = -87.8685074861033 | etot = -33.5644508539845 +349000 ekin = 28.6752584344467 | erot = 26.310018084166 | epot = -88.54972737313 | etot = -33.5644508545173 +350000 ekin = 28.4730637357388 | erot = 27.0009502159403 | epot = -89.038464806251 | etot = -33.5644508545719 +351000 ekin = 28.139537848467 | erot = 27.6270646737408 | epot = -89.3310533768684 | etot = -33.5644508546605 +352000 ekin = 27.6929580738718 | erot = 28.1676652362932 | epot = -89.4250741654184 | etot = -33.5644508552534 +353000 ekin = 27.1526950366655 | erot = 28.5958100265632 | epot = -89.3129559197891 | etot = -33.5644508565604 +354000 ekin = 26.5365141387242 | erot = 28.8781341172769 | epot = -88.9790991143028 | etot = -33.5644508583017 +355000 ekin = 25.859879983625 | erot = 28.979303109793 | epot = -88.4036339530082 | etot = -33.5644508595902 +356000 ekin = 25.1375717946349 | erot = 28.8722956886234 | epot = -87.5743183425605 | etot = -33.5644508593022 +357000 ekin = 24.3868741548746 | erot = 28.5495289602174 | epot = -86.5008539717697 | etot = -33.5644508566778 +358000 ekin = 23.6300778926847 | erot = 28.0297879777441 | epot = -85.2243167222827 | etot = -33.5644508518539 +359000 ekin = 22.8939201469121 | erot = 27.3556770360709 | epot = -83.8140480289405 | etot = -33.5644508459575 +360000 ekin = 22.2065780073029 | erot = 26.5834479667625 | epot = -82.3544768140978 | etot = -33.5644508400324 +361000 ekin = 21.5986345635183 | erot = 25.7744654427431 | epot = -80.9375508371388 | etot = -33.5644508308774 +362000 ekin = 21.1083260621098 | erot = 24.989507840873 | epot = -79.6622847318363 | etot = -33.5644508288535 +363000 ekin = 20.7375100619861 | erot = 24.2576398933005 | epot = -78.5596007834792 | etot = -33.5644508281925 +364000 ekin = 20.4760033679782 | erot = 23.5946470164008 | epot = -77.6351012127697 | etot = -33.5644508283907 +365000 ekin = 20.3079089893774 | erot = 23.0095138965374 | epot = -76.8818737148743 | etot = -33.5644508289595 +366000 ekin = 20.2147979336069 | erot = 22.5083719357563 | epot = -76.2876206988662 | etot = -33.564450829503 +367000 ekin = 20.1786185360507 | erot = 22.0973297017962 | epot = -75.8403990676676 | etot = -33.5644508298207 +368000 ekin = 20.1837486799377 | erot = 21.783527063494 | epot = -75.5317265732851 | etot = -33.5644508298534 +369000 ekin = 20.2182310118496 | erot = 21.5747388187329 | epot = -75.3574206602588 | etot = -33.5644508296764 +370000 ekin = 20.2742556079346 | erot = 21.4781104693601 | epot = -75.3168169068273 | etot = -33.5644508295326 +371000 ekin = 20.3477066126786 | erot = 21.4982876397919 | epot = -75.4104450816055 | etot = -33.5644508291351 +372000 ekin = 20.4391769085933 | erot = 21.6370751258538 | epot = -75.6407028633516 | etot = -33.5644508289045 +373000 ekin = 20.5523906694389 | erot = 21.8921389377654 | epot = -76.0089804360871 | etot = -33.5644508288828 +374000 ekin = 20.6947607299073 | erot = 22.2561865203728 | epot = -76.5153980789369 | etot = -33.5644508286568 +375000 ekin = 20.8734352290091 | erot = 22.7176361068752 | epot = -77.1555221653772 | etot = -33.5644508294929 +376000 ekin = 21.0894935045173 | erot = 23.2620769849342 | epot = -77.9160213200335 | etot = -33.564450830582 +377000 ekin = 21.3446674637595 | erot = 23.8720082856019 | epot = -78.7811265808815 | etot = -33.5644508315201 +378000 ekin = 21.6424854229658 | erot = 24.5275644041121 | epot = -79.7345006599212 | etot = -33.5644508328433 +379000 ekin = 21.9906215821683 | erot = 25.2058289792437 | epot = -80.7609013956721 | etot = -33.5644508342601 +380000 ekin = 22.3975872845819 | erot = 25.8799316876613 | epot = -81.8419698101057 | etot = -33.5644508378624 +381000 ekin = 22.8474625365151 | erot = 26.5196756830445 | epot = -82.9315890609908 | etot = -33.5644508414312 +382000 ekin = 23.3214968285656 | erot = 27.0935868815677 | epot = -83.9795345554676 | etot = -33.5644508453342 +383000 ekin = 23.798948647365 | erot = 27.5682880228108 | epot = -84.9316875192928 | etot = -33.564450849117 +384000 ekin = 24.2602946691393 | erot = 27.9101784191673 | epot = -85.7349239406047 | etot = -33.5644508522981 +385000 ekin = 24.6909701695335 | erot = 28.0892515731785 | epot = -86.3446725968127 | etot = -33.5644508541008 +386000 ekin = 25.0758089634755 | erot = 28.0812872789521 | epot = -86.7215471013172 | etot = -33.5644508588896 +387000 ekin = 25.3886917944527 | erot = 27.8683599139988 | epot = -86.8215025663126 | etot = -33.5644508578612 +388000 ekin = 25.6321888109058 | erot = 27.4567876604357 | epot = -86.6534273265843 | etot = -33.5644508552428 +389000 ekin = 25.8173007945418 | erot = 26.8690369421787 | epot = -86.2507885888255 | etot = -33.564450852105 +390000 ekin = 25.9562629244047 | erot = 26.1386991558076 | epot = -85.6594129283773 | etot = -33.5644508481649 +391000 ekin = 26.0625510047816 | erot = 25.3050096520618 | epot = -84.9320115013513 | etot = -33.5644508445078 +392000 ekin = 26.1477279258083 | erot = 24.4077754075857 | epot = -84.1199541748157 | etot = -33.5644508414217 +393000 ekin = 26.2207009125763 | erot = 23.4862823970573 | epot = -83.2714341485498 | etot = -33.5644508389163 +394000 ekin = 26.2880235522712 | erot = 22.5776047858261 | epot = -82.4300791761996 | etot = -33.5644508381023 +395000 ekin = 26.3461327830412 | erot = 21.6992206105417 | epot = -81.6098042309749 | etot = -33.5644508373921 +396000 ekin = 26.3925769143341 | erot = 20.8648963380243 | epot = -80.8219240889404 | etot = -33.564450836582 +397000 ekin = 26.4280357588778 | erot = 20.0875980485136 | epot = -80.0800846429448 | etot = -33.5644508355533 +398000 ekin = 26.4568264159667 | erot = 19.3805747697846 | epot = -79.4018520200129 | etot = -33.5644508342616 +399000 ekin = 26.4863910840118 | erot = 18.7576183808216 | epot = -78.8084602983166 | etot = -33.5644508334833 +400000 ekin = 26.5240355653115 | erot = 18.2309165846171 | epot = -78.3194029820772 | etot = -33.5644508321487 +401000 ekin = 26.5785515874174 | erot = 17.8133011773559 | epot = -77.9563035961333 | etot = -33.56445083136 +402000 ekin = 26.655331687452 | erot = 17.5146324371175 | epot = -77.7344149563074 | etot = -33.564450831738 +403000 ekin = 26.750844144417 | erot = 17.3369800815745 | epot = -77.6522750599618 | etot = -33.5644508339703 +404000 ekin = 26.847889984664 | erot = 17.270366441038 | epot = -77.6827072640007 | etot = -33.5644508382987 +405000 ekin = 26.9136481513682 | erot = 17.290640983477 | epot = -77.7687399796861 | etot = -33.5644508448409 +406000 ekin = 26.9026743980023 | erot = 17.3519919762782 | epot = -77.8191172252627 | etot = -33.5644508509822 +407000 ekin = 26.7697793191984 | erot = 17.4151352559464 | epot = -77.7493654298542 | etot = -33.5644508547094 +408000 ekin = 26.4852107131098 | erot = 17.4599310844412 | epot = -77.50959265223 | etot = -33.564450854679 +409000 ekin = 26.0447937746191 | erot = 17.489715636672 | epot = -77.0989602628005 | etot = -33.5644508515094 +410000 ekin = 25.4686689663916 | erot = 17.525308599911 | epot = -76.5584284132955 | etot = -33.564450846993 +411000 ekin = 24.7901856102895 | erot = 17.5925678633025 | epot = -75.9472043165596 | etot = -33.5644508429676 +412000 ekin = 24.0429450721768 | erot = 17.7112262985626 | epot = -75.3186222110808 | etot = -33.5644508403414 +413000 ekin = 23.2530709441322 | erot = 17.8904894599544 | epot = -74.7080112431157 | etot = -33.5644508390292 +414000 ekin = 22.4380957569814 | erot = 18.1309089880911 | epot = -74.1334555836084 | etot = -33.5644508385359 +415000 ekin = 21.6095002972743 | erot = 18.4284521146042 | epot = -73.6024032502431 | etot = -33.5644508383646 +416000 ekin = 20.7759703154786 | erot = 18.7780315272693 | epot = -73.1184526809416 | etot = -33.5644508381937 +417000 ekin = 19.9459219944617 | erot = 19.1754390644637 | epot = -72.6858118967971 | etot = -33.5644508378717 +418000 ekin = 19.1290603144219 | erot = 19.6178812357862 | epot = -72.3113923875522 | etot = -33.5644508373441 +419000 ekin = 18.337241174533 | erot = 20.1037315121921 | epot = -72.005423523335 | etot = -33.5644508366099 +420000 ekin = 17.5848708565925 | erot = 20.6319495843217 | epot = -71.7812712766207 | etot = -33.5644508357065 +421000 ekin = 16.8888669765948 | erot = 21.2012508781818 | epot = -71.654568689525 | etot = -33.5644508347484 +422000 ekin = 16.2680311852926 | erot = 21.8088345392229 | epot = -71.6413165584697 | etot = -33.5644508339541 +423000 ekin = 15.7416423465874 | erot = 22.4484657015901 | epot = -71.754558881829 | etot = -33.5644508336516 +424000 ekin = 15.3271568809885 | erot = 23.1079611163195 | epot = -71.9995688315673 | etot = -33.5644508342592 +425000 ekin = 15.0370245442154 | erot = 23.7664993129421 | epot = -72.3679746933712 | etot = -33.5644508362137 +426000 ekin = 14.8748792452246 | erot = 24.3924933232269 | epot = -72.8318234082835 | etot = -33.564450839832 +427000 ekin = 14.8320398098318 | erot = 24.9432466996428 | epot = -73.3397373544817 | etot = -33.5644508450071 +428000 ekin = 14.8863924965225 | erot = 25.3682827942598 | epot = -73.8191261416323 | etot = -33.56445085085 +429000 ekin = 15.0062259694751 | erot = 25.6182665545283 | epot = -74.1889433796421 | etot = -33.5644508556387 +430000 ekin = 15.1595389321474 | erot = 25.6590201133498 | epot = -74.3830099030104 | etot = -33.5644508575131 +431000 ekin = 15.3249133699162 | erot = 25.4851984009302 | epot = -74.3745626264769 | etot = -33.5644508556305 +432000 ekin = 15.4974987577243 | erot = 25.1253113467255 | epot = -74.1872609552084 | etot = -33.5644508507585 +433000 ekin = 15.6867402477162 | erot = 24.6339851580146 | epot = -73.8851762504474 | etot = -33.5644508447166 +434000 ekin = 15.908478952494 | erot = 24.0759117528824 | epot = -73.5488415446164 | etot = -33.56445083924 +435000 ekin = 16.1769022059532 | erot = 23.5103596607956 | epot = -73.2517127020391 | etot = -33.5644508352903 +436000 ekin = 16.4997173059431 | erot = 22.9822765166324 | epot = -73.0464446556921 | etot = -33.5644508331166 +437000 ekin = 16.8769806268047 | erot = 22.5199344327298 | epot = -72.9613658919567 | etot = -33.5644508324222 +438000 ekin = 17.3021259571554 | erot = 22.1372453983087 | epot = -73.0038221882772 | etot = -33.5644508328131 +439000 ekin = 17.7637229039241 | erot = 21.8373393625943 | epot = -73.1655131004615 | etot = -33.5644508339431 +440000 ekin = 18.2471223979911 | erot = 21.6157595595468 | epot = -73.4273327930896 | etot = -33.5644508355518 +441000 ekin = 18.7357201395364 | erot = 21.4628710845581 | epot = -73.7630420615727 | etot = -33.5644508374783 +442000 ekin = 19.2118878212778 | erot = 21.365451542122 | epot = -74.1417902029878 | etot = -33.564450839588 +443000 ekin = 19.6577318124694 | erot = 21.3079015376941 | epot = -74.530084191929 | etot = -33.5644508417655 +444000 ekin = 20.0558238633166 | erot = 21.2733344148721 | epot = -74.8936091220801 | etot = -33.5644508438914 +445000 ekin = 20.389989391221 | erot = 21.2445884062662 | epot = -75.1990286433164 | etot = -33.5644508458292 +446000 ekin = 20.6461236043855 | erot = 21.2052857367663 | epot = -75.41586018866 | etot = -33.5644508475082 +447000 ekin = 20.8131102287267 | erot = 21.1405154512044 | epot = -75.5180765280277 | etot = -33.5644508480966 +448000 ekin = 20.8836321565114 | erot = 21.0415726580595 | epot = -75.4896556635799 | etot = -33.5644508490089 +449000 ekin = 20.8549766396171 | erot = 20.9006105485411 | epot = -75.3200380376018 | etot = -33.5644508494435 +450000 ekin = 20.7289995988534 | erot = 20.7094982244521 | epot = -75.0029486726748 | etot = -33.5644508493693 +451000 ekin = 20.5121237020311 | erot = 20.4634057687252 | epot = -74.5399803195251 | etot = -33.5644508487688 +452000 ekin = 20.2152499007445 | erot = 20.1611428754572 | epot = -73.9408436238401 | etot = -33.5644508476384 +453000 ekin = 19.8534700764778 | erot = 19.8054562088345 | epot = -73.2233771313103 | etot = -33.564450845998 +454000 ekin = 19.4456214291213 | erot = 19.4031472753593 | epot = -72.4132195483806 | etot = -33.5644508439 +455000 ekin = 19.0137205227782 | erot = 18.964872313207 | epot = -71.5430436774017 | etot = -33.5644508414165 +456000 ekin = 18.5823093299359 | erot = 18.5046119868878 | epot = -70.6513721554908 | etot = -33.5644508386671 +457000 ekin = 18.1775784949196 | erot = 18.0385547552735 | epot = -69.7805840860522 | etot = -33.5644508358591 +458000 ekin = 17.8262193052027 | erot = 17.5834820270569 | epot = -68.9741521652289 | etot = -33.5644508329693 +459000 ekin = 17.5544328314126 | erot = 17.1574115033566 | epot = -68.2762951651265 | etot = -33.5644508303572 +460000 ekin = 17.3857834993165 | erot = 16.7769882364293 | epot = -67.7272225639932 | etot = -33.5644508282474 +461000 ekin = 17.3389537756698 | erot = 16.4559737247112 | epot = -67.3593783272464 | etot = -33.5644508268654 +462000 ekin = 17.4254421541111 | erot = 16.2041333991429 | epot = -67.1940263796471 | etot = -33.5644508263932 +463000 ekin = 17.6475549837678 | erot = 16.0264214062831 | epot = -67.2384272169901 | etot = -33.5644508269392 +464000 ekin = 17.9971528391479 | erot = 15.9226257282762 | epot = -67.4842293959134 | etot = -33.5644508284893 +465000 ekin = 18.4555654855751 | erot = 15.8876205731988 | epot = -67.9076368896734 | etot = -33.5644508308995 +466000 ekin = 18.9948338162462 | erot = 15.9122553307032 | epot = -68.4715399808675 | etot = -33.5644508339181 +467000 ekin = 19.5800987880483 | erot = 15.9847161183743 | epot = -69.1292657436643 | etot = -33.5644508372418 +468000 ekin = 20.1726645576182 | erot = 16.0920334747517 | epot = -69.8291488729546 | etot = -33.5644508405847 +469000 ekin = 20.7331520538985 | erot = 16.2213910259127 | epot = -70.5189939235296 | etot = -33.5644508437184 +470000 ekin = 21.2242791251678 | erot = 16.3610502014337 | epot = -71.1497801730816 | etot = -33.5644508464802 +471000 ekin = 21.6130740294769 | erot = 16.5009517691198 | epot = -71.6784766473461 | etot = -33.5644508487495 +472000 ekin = 21.8725913830144 | erot = 16.6332178545353 | epot = -72.0702600879624 | etot = -33.5644508504127 +473000 ekin = 21.9833185471274 | erot = 16.7527436323183 | epot = -72.3005130308005 | etot = -33.5644508513548 +474000 ekin = 21.9344099205846 | erot = 16.8578720764489 | epot = -72.3567328485068 | etot = -33.5644508514733 +475000 ekin = 21.7247480853885 | erot = 16.9509439425814 | epot = -72.2401428786726 | etot = -33.5644508507026 +476000 ekin = 21.3637036554054 | erot = 17.0384540155504 | epot = -71.9666085200057 | etot = -33.5644508490499 +477000 ekin = 20.8713853162837 | erot = 17.130593864283 | epot = -71.5664300271643 | etot = -33.5644508465976 +478000 ekin = 20.2781056158348 | erot = 17.2401904856494 | epot = -71.082746945061 | etot = -33.5644508435769 +479000 ekin = 19.6228148922352 | erot = 17.3807417057109 | epot = -70.568007438244 | etot = -33.5644508402978 +480000 ekin = 18.9501924819871 | erot = 17.5641098023629 | epot = -70.078753121549 | etot = -33.5644508371989 +481000 ekin = 18.3063999207698 | erot = 17.7978626900194 | epot = -69.6687134455753 | etot = -33.5644508347861 +482000 ekin = 17.7338800308527 | erot = 18.0826185787009 | epot = -69.3809494430906 | etot = -33.564450833537 +483000 ekin = 17.2661333869729 | erot = 18.4098565340996 | epot = -69.2404407548555 | etot = -33.564450833783 +484000 ekin = 16.9123469726303 | erot = 18.5839236848227 | epot = -69.0607216150868 | etot = -33.5644509576338 +485000 ekin = 17.2473052119872 | erot = 17.4463141948379 | epot = -68.2580700315476 | etot = -33.5644506247225 +486000 ekin = 18.3155143093133 | erot = 17.18327309766 | epot = -69.0632384227249 | etot = -33.5644510157516 +487000 ekin = 18.1324826615341 | erot = 17.2801627137401 | epot = -68.9770961534278 | etot = -33.5644507781536 +488000 ekin = 18.0650666711476 | erot = 17.4264266856646 | epot = -69.0559441348375 | etot = -33.5644507780252 +489000 ekin = 18.1230207573334 | erot = 17.6201369927127 | epot = -69.3076085291276 | etot = -33.5644507790815 +490000 ekin = 18.2959502061969 | erot = 17.8551924365584 | epot = -69.7155934235351 | etot = -33.5644507807797 +491000 ekin = 18.5602651981851 | erot = 18.1239992625136 | epot = -70.2487152441586 | etot = -33.5644507834599 +492000 ekin = 18.8855238701042 | erot = 18.4159985148053 | epot = -70.8659731705823 | etot = -33.5644507856728 +493000 ekin = 19.2395352567771 | erot = 18.728264479211 | epot = -71.5322505229547 | etot = -33.5644507869666 +494000 ekin = 19.5921246703129 | erot = 19.0689157919769 | epot = -72.2254912502075 | etot = -33.5644507879177 +495000 ekin = 19.0728202099565 | erot = 18.9158482412593 | epot = -71.5531189784044 | etot = -33.5644505271886 +496000 ekin = 19.8797920560791 | erot = 18.7380967908761 | epot = -72.1823393790591 | etot = -33.564450532104 +497000 ekin = 21.3129327568523 | erot = 19.22085969099 | epot = -74.0982428020236 | etot = -33.5644503541812 +498000 ekin = 21.3264694813384 | erot = 19.7980335585312 | epot = -74.6889533938341 | etot = -33.5644503539645 +499000 ekin = 21.2778907743885 | erot = 20.4793064457547 | epot = -75.3216475744249 | etot = -33.5644503542817 +500000 ekin = 21.1661916284258 | erot = 21.258178122324 | epot = -75.9888201058597 | etot = -33.5644503551099 +501000 ekin = 20.9926825376647 | erot = 22.1178388254974 | epot = -76.6749717196181 | etot = -33.564450356456 +502000 ekin = 20.7610606942179 | erot = 23.0317414652511 | epot = -77.3572525175369 | etot = -33.5644503580679 +503000 ekin = 20.4798770188891 | erot = 23.9650377706427 | epot = -78.0093651496444 | etot = -33.5644503601125 +504000 ekin = 20.1546807720134 | erot = 24.8789199644612 | epot = -78.5980510988455 | etot = -33.5644503623709 +505000 ekin = 19.7897861053101 | erot = 25.7326258922808 | epot = -79.0868623624028 | etot = -33.5644503648119 +506000 ekin = 19.3875459003948 | erot = 26.488233736964 | epot = -79.4402300037047 | etot = -33.5644503663459 +507000 ekin = 18.9527707504281 | erot = 27.1161379583516 | epot = -79.6333590755957 | etot = -33.564450366816 +508000 ekin = 18.4930541128453 | erot = 27.6003825989619 | epot = -79.6578870777028 | etot = -33.5644503658955 +509000 ekin = 18.0182547167277 | erot = 27.9414911094103 | epot = -79.5241961902249 | etot = -33.5644503640869 +510000 ekin = 17.523965944791 | erot = 28.1499521522236 | epot = -79.2383684583665 | etot = -33.564450361352 +511000 ekin = 17.0202767589766 | erot = 28.2490270329564 | epot = -78.8337541500052 | etot = -33.5644503580722 +512000 ekin = 16.524571800827 | erot = 28.2698315418588 | epot = -78.3588536975498 | etot = -33.564450354864 +513000 ekin = 16.0539184298501 | erot = 28.2435719404605 | epot = -77.8619407225297 | etot = -33.564450352219 +514000 ekin = 15.622953975357 | erot = 28.1963871949976 | epot = -77.3837915207595 | etot = -33.5644503504049 +515000 ekin = 15.2424792422371 | erot = 28.1464443104744 | epot = -76.953373902264 | etot = -33.5644503495525 +516000 ekin = 14.9188926058558 | erot = 28.1027540351543 | epot = -76.5860969904231 | etot = -33.564450349413 +517000 ekin = 14.6543809153874 | erot = 28.0678237289542 | epot = -76.2866549941532 | etot = -33.5644503498116 +518000 ekin = 14.4476572457691 | erot = 28.0395642673969 | epot = -76.0516718636457 | etot = -33.5644503504797 +519000 ekin = 14.2950490441428 | erot = 28.0138489407524 | epot = -75.8733483360399 | etot = -33.5644503511447 +520000 ekin = 14.1917488338634 | erot = 27.9870813582064 | epot = -75.7432805436532 | etot = -33.5644503515833 +521000 ekin = 14.1329830511805 | erot = 27.9581295476446 | epot = -75.6555629505058 | etot = -33.5644503516806 +522000 ekin = 14.1002586404053 | erot = 27.7732671759151 | epot = -75.4379761959062 | etot = -33.5644503795858 +523000 ekin = 14.1969588162511 | erot = 27.1027118573523 | epot = -74.8641209744559 | etot = -33.5644503008525 +524000 ekin = 14.7378402619219 | erot = 26.6164089140764 | epot = -74.9186994724817 | etot = -33.5644502964834 +525000 ekin = 15.5068672854449 | erot = 26.5883544531684 | epot = -75.6596721109621 | etot = -33.5644503723487 +526000 ekin = 15.8574449977267 | erot = 26.6724957236415 | epot = -76.0943910939928 | etot = -33.5644503726246 +527000 ekin = 16.0112069682283 | erot = 26.7355098948156 | epot = -76.311167236341 | etot = -33.5644503732972 +528000 ekin = 16.1641744090515 | erot = 26.7947978809934 | epot = -76.5234226639649 | etot = -33.5644503739199 +529000 ekin = 16.3159009760756 | erot = 26.8380825379191 | epot = -76.7184338883076 | etot = -33.5644503743128 +530000 ekin = 16.466747721028 | erot = 26.8553312024403 | epot = -76.886529297879 | etot = -33.5644503744108 +531000 ekin = 16.6177352354996 | erot = 26.8400251084993 | epot = -77.022210718254 | etot = -33.564450374255 +532000 ekin = 16.7702150675957 | erot = 26.7891084872752 | epot = -77.1237739287798 | etot = -33.5644503739089 +533000 ekin = 16.9253640366974 | erot = 26.7024973872853 | epot = -77.1923117974439 | etot = -33.5644503734612 +534000 ekin = 17.0836447866564 | erot = 26.5822176528732 | epot = -77.230312812567 | etot = -33.5644503730375 +535000 ekin = 17.2444487915268 | erot = 26.4310079588786 | epot = -77.2399071231478 | etot = -33.5644503727425 +536000 ekin = 17.4060591053815 | erot = 26.2510049057206 | epot = -77.2215143837103 | etot = -33.5644503726081 +537000 ekin = 17.5658991981726 | erot = 26.0431264909246 | epot = -77.1734760616575 | etot = -33.5644503725604 +538000 ekin = 17.7209415436652 | erot = 25.8074441218956 | epot = -77.0928360381795 | etot = -33.5644503726186 +539000 ekin = 17.8681497078889 | erot = 25.5433035299955 | epot = -76.9759036105368 | etot = -33.5644503726524 +540000 ekin = 18.004863156336 | erot = 25.2502517039518 | epot = -76.8195652328856 | etot = -33.5644503725978 +541000 ekin = 18.129064826942 | erot = 24.9288645878186 | epot = -76.6223797871797 | etot = -33.564450372419 +542000 ekin = 18.2395164936781 | erot = 24.5811691616713 | epot = -76.3851360274362 | etot = -33.5644503720867 +543000 ekin = 18.335770007785 | erot = 24.2108468343436 | epot = -76.1110672137948 | etot = -33.5644503716662 +544000 ekin = 18.4180615071781 | erot = 23.8229131244954 | epot = -75.805425002847 | etot = -33.5644503711735 +545000 ekin = 18.4870901297785 | erot = 23.4236993424443 | epot = -75.4752398423761 | etot = -33.5644503701532 +546000 ekin = 18.54361047059 | erot = 23.0232726205026 | epot = -75.1313334608523 | etot = -33.5644503697597 +547000 ekin = 18.5881260725922 | erot = 22.6282216103021 | epot = -74.7807980523833 | etot = -33.564450369489 +548000 ekin = 18.6206521537359 | erot = 22.2431161970553 | epot = -74.4282187197494 | etot = -33.5644503689582 +549000 ekin = 18.6395328550285 | erot = 21.8731131588192 | epot = -74.0770963831711 | etot = -33.5644503693234 +550000 ekin = 18.6420012523706 | erot = 21.5194517196355 | epot = -73.7259033419334 | etot = -33.5644503699273 +551000 ekin = 18.624921029005 | erot = 21.1784779029538 | epot = -73.3678493026868 | etot = -33.564450370728 +552000 ekin = 18.5841928766033 | erot = 20.8452278496576 | epot = -72.9938710978566 | etot = -33.5644503715957 +553000 ekin = 18.5152127054113 | erot = 20.5148731369798 | epot = -72.5945362147189 | etot = -33.5644503723278 +554000 ekin = 18.4136816906652 | erot = 20.1848933332903 | epot = -72.1630253966383 | etot = -33.5644503726828 +555000 ekin = 18.2766906397711 | erot = 19.8574769328349 | epot = -71.6986179450508 | etot = -33.5644503724447 +556000 ekin = 18.1040115045293 | erot = 19.5406874738217 | epot = -71.2091493500419 | etot = -33.5644503716909 +557000 ekin = 17.89923096435 | erot = 19.24972262904 | epot = -70.7134039633246 | etot = -33.5644503699346 +558000 ekin = 17.6705778370294 | erot = 19.0080857255953 | epot = -70.2431139301013 | etot = -33.5644503674766 +559000 ekin = 17.4315653923217 | erot = 18.8444628125886 | epot = -69.8404785693936 | etot = -33.5644503644833 +560000 ekin = 17.2006230343926 | erot = 18.7901643785407 | epot = -69.5552377742619 | etot = -33.5644503613287 +561000 ekin = 16.9995569155364 | erot = 18.8749610240394 | epot = -69.4389682979995 | etot = -33.5644503584237 +562000 ekin = 16.8505251054351 | erot = 19.1232120103355 | epot = -69.5381874720851 | etot = -33.5644503563145 +563000 ekin = 16.771816019379 | erot = 19.5498137338075 | epot = -69.8860801087492 | etot = -33.5644503555627 +564000 ekin = 16.7730284247952 | erot = 20.1561760614947 | epot = -70.4936548432322 | etot = -33.5644503569423 +565000 ekin = 16.8503463811215 | erot = 20.9261148984733 | epot = -71.3409116397428 | etot = -33.564450360148 +566000 ekin = 16.9881817946884 | erot = 21.8252877511548 | epot = -72.3779199111064 | etot = -33.5644503652632 +567000 ekin = 17.1597730186738 | erot = 22.8021750342622 | epot = -73.5263984248048 | etot = -33.5644503718688 +568000 ekin = 17.3309908958581 | erot = 23.7909429899681 | epot = -74.6863842651206 | etot = -33.5644503792944 +569000 ekin = 17.4658946009928 | erot = 24.7167318454134 | epot = -75.7470768330927 | etot = -33.5644503866865 +570000 ekin = 17.5327796649247 | erot = 25.503072445778 | epot = -76.60030250379 | etot = -33.5644503930873 +571000 ekin = 17.5098280193733 | erot = 26.0808668138774 | epot = -77.1551452308085 | etot = -33.5644503975578 +572000 ekin = 17.3896134292035 | erot = 26.3976580233915 | epot = -77.3517218519472 | etot = -33.5644503993522 +573000 ekin = 17.1817696514795 | erot = 26.4252545064828 | epot = -77.1714745560827 | etot = -33.5644503981204 +574000 ekin = 16.91320121502 | erot = 26.1636856783704 | epot = -76.6413372874423 | etot = -33.5644503940519 +575000 ekin = 16.6253831475483 | erot = 25.640183136325 | epot = -75.8300166717811 | etot = -33.5644503879079 +576000 ekin = 16.3805854482806 | erot = 24.9437607565116 | epot = -74.8887965735951 | etot = -33.5644503688028 +577000 ekin = 16.23092958843 | erot = 24.1552332193367 | epot = -73.950613173759 | etot = -33.5644503659923 +578000 ekin = 16.2003426787873 | erot = 23.2996785345128 | epot = -73.0644715773449 | etot = -33.5644503640447 +579000 ekin = 16.298393825657 | erot = 22.4032685645682 | epot = -72.2661127534473 | etot = -33.5644503632221 +580000 ekin = 16.5164282813868 | erot = 21.4889399507426 | epot = -71.569818597847 | etot = -33.5644503657176 +581000 ekin = 16.829413172556 | erot = 20.5770732256226 | epot = -70.9709367637454 | etot = -33.5644503655668 +582000 ekin = 17.2014342862117 | erot = 19.7085617425621 | epot = -70.4744463946194 | etot = -33.5644503658456 +583000 ekin = 17.5894541375884 | erot = 18.925166774833 | epot = -70.0790712785306 | etot = -33.5644503661092 +584000 ekin = 17.9521233668095 | erot = 18.2657373647565 | epot = -69.7823110976562 | etot = -33.5644503660902 +585000 ekin = 18.2577014581518 | erot = 17.762756656003 | epot = -69.5849084798605 | etot = -33.5644503657057 +586000 ekin = 18.48903732181 | erot = 17.4391816026807 | epot = -69.4926692894528 | etot = -33.5644503649621 +587000 ekin = 18.6451700995223 | erot = 17.3070654480135 | epot = -69.5166859114209 | etot = -33.5644503638852 +588000 ekin = 18.7400423387256 | erot = 17.3682960794961 | epot = -69.6727887807878 | etot = -33.5644503625662 +589000 ekin = 18.7988289994632 | erot = 17.6163757903472 | epot = -69.9796551510921 | etot = -33.5644503612817 +590000 ekin = 18.8521852510563 | erot = 18.03770774159 | epot = -70.4543433531448 | etot = -33.5644503604985 +591000 ekin = 18.9335216732476 | erot = 18.6145318736687 | epot = -71.1125039063923 | etot = -33.564450359476 +592000 ekin = 19.0736372364623 | erot = 19.3273958984734 | epot = -71.9654834953563 | etot = -33.5644503604206 +593000 ekin = 19.2836835994718 | erot = 20.1464047122411 | epot = -72.9945386745438 | etot = -33.5644503628309 +594000 ekin = 19.5596584178685 | erot = 21.034123237208 | epot = -74.1582320215033 | etot = -33.5644503664268 +595000 ekin = 19.8847224284612 | erot = 21.9477887873151 | epot = -75.3969615864514 | etot = -33.5644503706751 +596000 ekin = 20.2229995975395 | erot = 22.8321032475601 | epot = -76.6195532302897 | etot = -33.56445038519 +597000 ekin = 20.5134057742179 | erot = 23.6125551256778 | epot = -77.6904112894541 | etot = -33.5644503895585 +598000 ekin = 20.7238255182392 | erot = 24.2466753984176 | epot = -78.5349513088604 | etot = -33.5644503922037 +599000 ekin = 20.8326105236303 | erot = 24.7094660554427 | epot = -79.1065269720019 | etot = -33.5644503929288 +600000 ekin = 20.828192883276 | erot = 24.9942677722285 | epot = -79.3869110474472 | etot = -33.5644503919427 +601000 ekin = 20.7081769096798 | erot = 25.11085155755 | epot = -79.3834788569396 | etot = -33.5644503897098 +602000 ekin = 20.4770754640505 | erot = 25.0812117058382 | epot = -79.1227375566785 | etot = -33.5644503867898 +603000 ekin = 20.1436196141802 | erot = 24.9343592764579 | epot = -78.6424292743164 | etot = -33.5644503836784 +604000 ekin = 19.7184185863195 | erot = 24.7015463486128 | epot = -77.9844153156502 | etot = -33.564450380718 +605000 ekin = 19.2123955082262 | erot = 24.4128183898753 | epot = -77.1896642761826 | etot = -33.5644503780811 +606000 ekin = 18.6360571566313 | erot = 24.0951290260324 | epot = -76.2956365584618 | etot = -33.5644503757982 +607000 ekin = 17.9994317314224 | erot = 23.7717793956126 | epot = -75.3356615008433 | etot = -33.5644503738083 +608000 ekin = 17.3124228754604 | erot = 23.4627525846719 | epot = -74.3396258321416 | etot = -33.5644503720093 +609000 ekin = 16.5853412867629 | erot = 23.1855122472229 | epot = -73.3353039042776 | etot = -33.5644503702918 +610000 ekin = 15.8294285553984 | erot = 22.9559130653051 | epot = -72.3497919892683 | etot = -33.5644503685648 +611000 ekin = 15.0572484571768 | erot = 22.7889597199825 | epot = -71.4106585439383 | etot = -33.564450366779 +612000 ekin = 14.2829782528012 | erot = 22.6991649591093 | epot = -70.5465935768327 | etot = -33.5644503649222 +613000 ekin = 13.5233158611292 | erot = 22.7018063026035 | epot = -69.7895725256479 | etot = -33.5644503619153 +614000 ekin = 12.7974443556917 | erot = 22.8128628316047 | epot = -69.1747575476346 | etot = -33.5644503603383 +615000 ekin = 12.1222485232213 | erot = 23.0409824252133 | epot = -68.7276813075076 | etot = -33.564450359073 +616000 ekin = 11.5143476718002 | erot = 23.3894333501644 | epot = -68.4682313804871 | etot = -33.5644503585225 +617000 ekin = 10.9895105321831 | erot = 23.8529820636908 | epot = -68.4069429545483 | etot = -33.5644503586744 +618000 ekin = 10.5621427379082 | erot = 24.4166592376929 | epot = -68.5432523353739 | etot = -33.5644503597728 +619000 ekin = 10.2447233168846 | erot = 25.0539361238965 | epot = -68.8631098026496 | etot = -33.5644503618684 +620000 ekin = 10.0473729681852 | erot = 25.726395813846 | epot = -69.3382191468432 | etot = -33.564450364812 +621000 ekin = 9.97770919335943 | erot = 26.3860294543558 | epot = -69.9281890159394 | etot = -33.5644503682242 +622000 ekin = 10.0410058293406 | erot = 26.9805251338807 | epot = -70.5859813347549 | etot = -33.5644503715336 +623000 ekin = 10.2405907646719 | erot = 27.4608678071822 | epot = -71.2659089459993 | etot = -33.5644503741453 +624000 ekin = 10.5781077609575 | erot = 27.789174960007 | epot = -71.9317330966645 | etot = -33.5644503757 +625000 ekin = 11.0534790497405 | erot = 27.9443540028375 | epot = -72.5622834286287 | etot = -33.5644503760506 +626000 ekin = 11.6650239614417 | erot = 27.9236660631623 | epot = -73.1531404000459 | etot = -33.5644503754418 +627000 ekin = 12.4090657081618 | erot = 27.7401487508296 | epot = -73.713664833205 | etot = -33.5644503742135 +628000 ekin = 13.2797303336247 | erot = 27.4180442690277 | epot = -74.2622249753901 | etot = -33.5644503727378 +629000 ekin = 14.2227247808597 | erot = 26.9288523652634 | epot = -74.7160277925057 | etot = -33.5644506463826 +630000 ekin = 14.6371369646358 | erot = 25.6849986217032 | epot = -73.8865860618273 | etot = -33.5644504754884 +631000 ekin = 15.1932748232492 | erot = 24.8015291118369 | epot = -73.5592542921839 | etot = -33.5644503570978 +632000 ekin = 16.5842231811831 | erot = 25.1927867337753 | epot = -75.3414603985266 | etot = -33.5644504835681 +633000 ekin = 18.1129981057209 | erot = 25.8399990860739 | epot = -77.5174478422231 | etot = -33.5644506504283 +634000 ekin = 19.1483265833795 | erot = 25.7387528538212 | epot = -78.4515299869786 | etot = -33.5644505497779 +635000 ekin = 20.1638306083842 | erot = 25.6154971451023 | epot = -79.3437783074232 | etot = -33.5644505539367 +636000 ekin = 21.1529452192774 | erot = 25.4927802227977 | epot = -80.210176001065 | etot = -33.5644505589899 +637000 ekin = 22.0768404119804 | erot = 25.3376757556836 | epot = -80.9789667313978 | etot = -33.5644505637338 +638000 ekin = 22.8998086493368 | erot = 25.1175243540521 | epot = -81.581783570336 | etot = -33.5644505669471 +639000 ekin = 23.5958452405688 | erot = 24.8103240278057 | epot = -81.9706198363764 | etot = -33.5644505680019 +640000 ekin = 24.1448393944085 | erot = 24.4104070782069 | epot = -82.1196970406963 | etot = -33.5644505680809 +641000 ekin = 24.5337741515846 | erot = 23.9290519078285 | epot = -82.0272766241422 | etot = -33.5644505647291 +642000 ekin = 24.7698696442131 | erot = 23.3958020420911 | epot = -81.7301222479835 | etot = -33.5644505616793 +643000 ekin = 24.8669267979412 | erot = 22.8392829414695 | epot = -81.2706602981471 | etot = -33.5644505587364 +644000 ekin = 24.8431155053321 | erot = 22.2830723087654 | epot = -80.6906383703371 | etot = -33.5644505562396 +645000 ekin = 24.7193046979064 | erot = 21.7428697630937 | epot = -80.0266250151886 | etot = -33.5644505541885 +646000 ekin = 24.5180931831024 | erot = 21.2270132553 | epot = -79.3095569908572 | etot = -33.5644505524548 +647000 ekin = 24.2628521138149 | erot = 20.7388201346271 | epot = -78.5661227994122 | etot = -33.5644505509702 +648000 ekin = 23.9761808148133 | erot = 20.2787945273933 | epot = -77.8194258919934 | etot = -33.5644505497868 +649000 ekin = 23.6778736566609 | erot = 19.8458221794067 | epot = -77.0881463850653 | etot = -33.5644505489977 +650000 ekin = 23.3831896156548 | erot = 19.4375683305137 | epot = -76.3852084947824 | etot = -33.5644505486139 +651000 ekin = 23.1045251412741 | erot = 19.0455994386574 | epot = -75.7145751292058 | etot = -33.5644505492743 +652000 ekin = 22.8525540925228 | erot = 18.6600582438882 | epot = -75.0770628853385 | etot = -33.5644505489275 +653000 ekin = 22.6343633058236 | erot = 18.2797742485017 | epot = -74.4785881025892 | etot = -33.564450548264 +654000 ekin = 22.4577061635195 | erot = 17.9066943674651 | epot = -73.9288510781073 | etot = -33.5644505471227 +655000 ekin = 22.3323244924946 | erot = 17.5466477594773 | epot = -73.4434227975466 | etot = -33.5644505455747 +656000 ekin = 22.2694639419047 | erot = 17.2090068004228 | epot = -73.0429212862265 | etot = -33.5644505438989 +657000 ekin = 22.2796962966157 | erot = 16.9050137467998 | epot = -72.7491605859738 | etot = -33.5644505425584 +658000 ekin = 22.369639071293 | erot = 16.6447644948982 | epot = -72.5788541082823 | etot = -33.5644505420911 +659000 ekin = 22.5385894789304 | erot = 16.4332539533158 | epot = -72.5362939752044 | etot = -33.5644505429582 +660000 ekin = 22.7761662594052 | erot = 16.2664693850933 | epot = -72.6070861898631 | etot = -33.5644505453646 +661000 ekin = 23.0623022457157 | erot = 16.1290340495213 | epot = -72.7557868419576 | etot = -33.5644505467205 +662000 ekin = 23.3837240382632 | erot = 15.9907831573615 | epot = -72.9389579063317 | etot = -33.564450710707 +663000 ekin = 23.054148007274 | erot = 16.1177804827538 | epot = -72.7363790499092 | etot = -33.5644505598814 +664000 ekin = 22.9781515350229 | erot = 16.5698259294712 | epot = -73.112428112566 | etot = -33.5644506480719 +665000 ekin = 23.3749786895457 | erot = 16.411782739857 | epot = -73.3512119977732 | etot = -33.5644505683704 +666000 ekin = 23.723950183745 | erot = 16.0357448193694 | epot = -73.3241455698056 | etot = -33.5644505666911 +667000 ekin = 24.0215049432174 | erot = 15.6311856367398 | epot = -73.2171411428858 | etot = -33.5644505629285 +668000 ekin = 24.2720292261732 | erot = 15.2431977236565 | epot = -73.0796775091056 | etot = -33.5644505592759 +669000 ekin = 24.4823401830215 | erot = 14.9164487057936 | epot = -72.9632394451725 | etot = -33.5644505563574 +670000 ekin = 24.6591929157758 | erot = 14.6865199575477 | epot = -72.9101634276307 | etot = -33.5644505543073 +671000 ekin = 24.7891522537242 | erot = 14.5781166474215 | epot = -72.9317194571598 | etot = -33.5644505560141 +672000 ekin = 24.8512867490322 | erot = 14.6015183441379 | epot = -73.0172556484841 | etot = -33.564450555314 +673000 ekin = 24.8569569351995 | erot = 14.7562217139438 | epot = -73.1776292037397 | etot = -33.5644505545965 +674000 ekin = 24.8222537578926 | erot = 15.0373554089786 | epot = -73.4240597206982 | etot = -33.564450553827 +675000 ekin = 24.7663204261064 | erot = 15.4372951197778 | epot = -73.7680660991378 | etot = -33.5644505532536 +676000 ekin = 24.7079731413268 | erot = 15.9453732717859 | epot = -74.217796966472 | etot = -33.5644505533592 +677000 ekin = 24.6606038390545 | erot = 16.5455776363011 | epot = -74.7706320301637 | etot = -33.5644505548081 +678000 ekin = 24.6267378751708 | erot = 17.2129758022366 | epot = -75.4041642354332 | etot = -33.5644505580258 +679000 ekin = 24.5940505555973 | erot = 17.9117017671719 | epot = -76.0702028857369 | etot = -33.5644505629677 +680000 ekin = 24.5356055102642 | erot = 18.5957689118677 | epot = -76.6958249909574 | etot = -33.5644505688256 +681000 ekin = 24.4156570901708 | erot = 19.2149559866325 | epot = -77.1950636509461 | etot = -33.5644505741429 +682000 ekin = 24.1989519856416 | erot = 19.7242966851149 | epot = -77.487699248418 | etot = -33.5644505776614 +683000 ekin = 23.8604728484841 | erot = 20.0938581680861 | epot = -77.5187815945976 | etot = -33.5644505780274 +684000 ekin = 23.3975557793202 | erot = 20.3180971821174 | epot = -77.2801035368968 | etot = -33.5644505754592 +685000 ekin = 22.8290459842939 | erot = 20.4129669401602 | epot = -76.8064634953545 | etot = -33.5644505709004 +686000 ekin = 22.1833688830902 | erot = 20.3969948298234 | epot = -76.1448143090756 | etot = -33.564450596162 +687000 ekin = 21.4529188825682 | erot = 20.1567338484389 | epot = -75.1741032961385 | etot = -33.5644505651314 +688000 ekin = 20.8420414150976 | erot = 19.8330340944162 | epot = -74.2395260509536 | etot = -33.5644505414398 +689000 ekin = 20.485045480985 | erot = 19.6177759067974 | epot = -73.667271944758 | etot = -33.5644505569757 +690000 ekin = 20.22367052676 | erot = 19.4736760217004 | epot = -73.2617971257719 | etot = -33.5644505773115 +691000 ekin = 19.9277329716986 | erot = 19.3525548976992 | epot = -72.8447384077161 | etot = -33.5644505383183 +692000 ekin = 19.7615779528863 | erot = 19.3271485942255 | epot = -72.6531770849096 | etot = -33.5644505377978 +693000 ekin = 19.7317397131701 | erot = 19.4147876349782 | epot = -72.7109778869691 | etot = -33.5644505388208 +694000 ekin = 19.8186070325659 | erot = 19.6208277623457 | epot = -73.0038853361764 | etot = -33.5644505412647 +695000 ekin = 19.9894250230478 | erot = 19.941877147877 | epot = -73.4957527156739 | etot = -33.5644505447491 +696000 ekin = 20.2029739943976 | erot = 20.3669312863332 | epot = -74.1343558293723 | etot = -33.5644505486415 +697000 ekin = 20.4154400727664 | erot = 20.880919300581 | epot = -74.8608099257857 | etot = -33.5644505524382 +698000 ekin = 20.5862067302191 | erot = 21.4669039242718 | epot = -75.6175612102066 | etot = -33.5644505557157 +699000 ekin = 20.6825995314592 | erot = 22.1076466744899 | epot = -76.3546967641855 | etot = -33.5644505582364 +700000 ekin = 20.6830084841778 | erot = 22.7863311593422 | epot = -77.0337902034447 | etot = -33.5644505599247 +701000 ekin = 20.578193148326 | erot = 23.4865818235912 | epot = -77.629225532724 | etot = -33.5644505608068 +702000 ekin = 20.3710754301549 | erot = 24.1923776458902 | epot = -78.1279036369795 | etot = -33.5644505609343 +703000 ekin = 20.0753347575173 | erot = 24.888467252762 | epot = -78.528252570647 | etot = -33.5644505603677 +704000 ekin = 19.7130379610838 | erot = 25.5614200023189 | epot = -78.838908522607 | etot = -33.5644505592043 +705000 ekin = 19.3114467602167 | erot = 26.2008176281874 | epot = -79.0767149460512 | etot = -33.564450557647 +706000 ekin = 18.8991937919881 | erot = 26.7996687691974 | epot = -79.2633131172258 | etot = -33.5644505560403 +707000 ekin = 18.5022273016031 | erot = 27.3532672566161 | epot = -79.4199451130548 | etot = -33.5644505548355 +708000 ekin = 18.1401729300363 | erot = 27.8564306963449 | epot = -79.5610541808569 | etot = -33.5644505544757 +709000 ekin = 17.8234464200403 | erot = 28.2999901805008 | epot = -79.6878871558114 | etot = -33.5644505552703 +710000 ekin = 17.5523632022352 | erot = 28.66784646393 | epot = -79.7846602233792 | etot = -33.564450557214 +711000 ekin = 17.319410981167 | erot = 28.9359249877842 | epot = -79.8197865289555 | etot = -33.5644505600043 +712000 ekin = 17.1112174759792 | erot = 29.0741670939005 | epot = -79.7498351329345 | etot = -33.5644505630547 +713000 ekin = 16.9121266207384 | erot = 29.0513180252372 | epot = -79.5278952115921 | etot = -33.5644505656165 +714000 ekin = 16.7079630671362 | erot = 28.8416092685853 | epot = -79.1140229027166 | etot = -33.564450566995 +715000 ekin = 16.4890214415111 | erot = 28.4313561606375 | epot = -78.4848281689488 | etot = -33.5644505668002 +716000 ekin = 16.2513970083694 | erot = 27.8230898675347 | epot = -77.6389374409925 | etot = -33.5644505650884 +717000 ekin = 15.9963403731169 | erot = 27.0356716312561 | epot = -76.5964625666635 | etot = -33.5644505622904 +718000 ekin = 15.7361303250895 | erot = 26.1105494914754 | epot = -75.4111303728763 | etot = -33.5644505563113 +719000 ekin = 15.4991442332756 | erot = 25.1078869435359 | epot = -74.1714817315667 | etot = -33.5644505547552 +720000 ekin = 15.2869109984327 | erot = 24.051118277072 | epot = -72.9024798285824 | etot = -33.5644505530778 +721000 ekin = 15.0983958368563 | erot = 22.9636187921636 | epot = -71.6264651803974 | etot = -33.5644505513775 +722000 ekin = 14.9325120658119 | erot = 21.8688846316655 | epot = -70.3658472497603 | etot = -33.5644505522828 +723000 ekin = 14.7807572560571 | erot = 20.783177409075 | epot = -69.1283852152817 | etot = -33.5644505501496 +724000 ekin = 14.6422909698242 | erot = 19.7295658973655 | epot = -67.9363074154255 | etot = -33.5644505482357 +725000 ekin = 14.5216204992091 | erot = 18.7315290225185 | epot = -66.8176000682293 | etot = -33.5644505465018 +726000 ekin = 14.4243651447271 | erot = 17.8092496646936 | epot = -65.7980653543268 | etot = -33.5644505449061 +727000 ekin = 14.3569475465798 | erot = 16.9804196385917 | epot = -64.9018177285995 | etot = -33.564450543428 +728000 ekin = 14.2536930559593 | erot = 16.2469828282715 | epot = -64.0651265345919 | etot = -33.5644506503612 +729000 ekin = 13.8457257235901 | erot = 15.9222518581098 | epot = -63.3324280824188 | etot = -33.5644505007189 +730000 ekin = 14.0260810331572 | erot = 15.9641149780232 | epot = -63.5546467085729 | etot = -33.5644506973925 +731000 ekin = 14.2598526174267 | erot = 15.8407237779026 | epot = -63.6650270928699 | etot = -33.5644506975406 +732000 ekin = 14.5606957082 | erot = 15.8547631025675 | epot = -63.9799095095013 | etot = -33.5644506987338 +733000 ekin = 14.9193813420873 | erot = 16.0002143198209 | epot = -64.4840463630918 | etot = -33.5644507011835 +734000 ekin = 15.3191392217664 | erot = 16.2611439998487 | epot = -65.1447339265492 | etot = -33.5644507049341 +735000 ekin = 15.7356018991576 | erot = 16.6113471097583 | epot = -65.9113997186633 | etot = -33.5644507097475 +736000 ekin = 16.1415246377564 | erot = 17.0234641328674 | epot = -66.7294394793124 | etot = -33.5644507086886 +737000 ekin = 16.5186056071986 | erot = 17.4895868028313 | epot = -67.5726431223686 | etot = -33.5644507123387 +738000 ekin = 16.8458492085384 | erot = 17.9860152350135 | epot = -68.396315158488 | etot = -33.5644507149361 +739000 ekin = 17.1101498629012 | erot = 18.4929848437288 | epot = -69.167585422606 | etot = -33.5644507159759 +740000 ekin = 17.3014321651814 | erot = 18.9830167810243 | epot = -69.8488996784293 | etot = -33.5644507322236 +741000 ekin = 17.386590010487 | erot = 19.3806296469325 | epot = -70.3316703890898 | etot = -33.5644507316703 +742000 ekin = 17.3696644696972 | erot = 19.6766235531722 | epot = -70.6107387526117 | etot = -33.5644507297423 +743000 ekin = 17.2668900413887 | erot = 19.8790967523848 | epot = -70.7104375210217 | etot = -33.5644507272482 +744000 ekin = 17.0976280278394 | erot = 20.0010316352814 | epot = -70.6631103878251 | etot = -33.5644507247043 +745000 ekin = 16.8806625291024 | erot = 20.057055059626 | epot = -70.5021683110215 | etot = -33.5644507222932 +746000 ekin = 16.6327129002015 | erot = 20.0624105110988 | epot = -70.2595741313054 | etot = -33.5644507200051 +747000 ekin = 16.3685004950096 | erot = 20.033016856487 | epot = -69.9659680692887 | etot = -33.5644507177921 +748000 ekin = 16.1014103999543 | erot = 19.9854814659263 | epot = -69.6513425815366 | etot = -33.564450715656 +749000 ekin = 15.8440980133595 | erot = 19.9365592321122 | epot = -69.345107959121 | etot = -33.5644507136493 +750000 ekin = 15.6090531913871 | erot = 19.903896348463 | epot = -69.0774002509923 | etot = -33.5644507111422 +751000 ekin = 15.408391615066 | erot = 19.9047162348154 | epot = -68.8775585596421 | etot = -33.5644507097607 +752000 ekin = 15.2531866583631 | erot = 19.9485427704181 | epot = -68.7661801374899 | etot = -33.5644507087087 +753000 ekin = 15.1543901558436 | erot = 20.0407526996777 | epot = -68.7595935635481 | etot = -33.5644507080268 +754000 ekin = 15.1228286565093 | erot = 20.1821712344388 | epot = -68.8694505987027 | etot = -33.5644507077546 +755000 ekin = 15.1688994236201 | erot = 20.3687544760721 | epot = -69.1021046076738 | etot = -33.5644507079815 +756000 ekin = 15.3014995511365 | erot = 20.5913112901341 | epot = -69.4572615501853 | etot = -33.5644507089146 +757000 ekin = 15.5255754908458 | erot = 20.8349492485987 | epot = -69.9249754503695 | etot = -33.564450710925 +758000 ekin = 15.8381446956662 | erot = 21.0780442729328 | epot = -70.4806396830074 | etot = -33.5644507144084 +759000 ekin = 16.2241238949829 | erot = 21.291351107698 | epot = -71.0799257220707 | etot = -33.5644507193898 +760000 ekin = 16.6551901643007 | erot = 21.4392176816081 | epot = -71.6588585709879 | etot = -33.5644507250792 +761000 ekin = 17.0950183929184 | erot = 21.4853061130269 | epot = -72.1447752357869 | etot = -33.5644507298415 +762000 ekin = 17.5106763995147 | erot = 21.4029539273073 | epot = -72.4780810587706 | etot = -33.5644507319486 +763000 ekin = 17.8846255668858 | erot = 21.185914549962 | epot = -72.6349908475012 | etot = -33.5644507306534 +764000 ekin = 18.2201199371193 | erot = 20.8529192973068 | epot = -72.6374899610343 | etot = -33.5644507266082 +765000 ekin = 18.5372583928787 | erot = 20.4430950204984 | epot = -72.544804134769 | etot = -33.564450721392 +766000 ekin = 18.86309963268 | erot = 20.0050052471612 | epot = -72.4325555962364 | etot = -33.5644507163952 +767000 ekin = 19.2212066783145 | erot = 19.5864803417602 | epot = -72.3721377327923 | etot = -33.5644507127176 +768000 ekin = 19.6245116668901 | erot = 19.2265552432954 | epot = -72.4155176210351 | etot = -33.5644507108497 +769000 ekin = 20.0721792306237 | erot = 18.9509745495803 | epot = -72.5876044911024 | etot = -33.5644507108984 +770000 ekin = 20.5498085990298 | erot = 18.7702787055214 | epot = -72.884538017272 | etot = -33.5644507127209 +771000 ekin = 21.0321028839958 | erot = 18.679435439756 | epot = -73.2759890396338 | etot = -33.5644507158821 +772000 ekin = 21.4851799397904 | erot = 18.6615620363116 | epot = -73.7111926963688 | etot = -33.5644507202668 +773000 ekin = 21.8752230439093 | erot = 18.6848228542269 | epot = -74.1244966228291 | etot = -33.5644507246929 +774000 ekin = 22.1763496427708 | erot = 18.7081814097347 | epot = -74.4489817807521 | etot = -33.5644507282467 +775000 ekin = 22.3745717791238 | erot = 18.6931201232722 | epot = -74.6321426323703 | etot = -33.5644507299744 +776000 ekin = 22.4709552224375 | erot = 18.6135457350496 | epot = -74.648951686955 | etot = -33.564450729468 +777000 ekin = 22.4798367585086 | erot = 18.4639882108411 | epot = -74.5082756956863 | etot = -33.5644507263366 +778000 ekin = 22.4355420339161 | erot = 18.2585534539139 | epot = -74.2585462089044 | etot = -33.5644507210745 +779000 ekin = 22.3843529355789 | erot = 18.0309205308365 | epot = -73.9797241813393 | etot = -33.5644507149239 +780000 ekin = 22.3744386445496 | erot = 17.8258066816941 | epot = -73.7646960358077 | etot = -33.5644507095641 +781000 ekin = 22.1317599829093 | erot = 17.6891439214798 | epot = -73.3853547353444 | etot = -33.5644508309553 +782000 ekin = 21.1592753937775 | erot = 17.9407979297457 | epot = -72.6645240432862 | etot = -33.564450719763 +783000 ekin = 20.4598020812476 | erot = 19.0285770550549 | epot = -73.052829858984 | etot = -33.5644507226814 +784000 ekin = 20.5205611486876 | erot = 20.4251816834892 | epot = -74.5101936712772 | etot = -33.5644508391004 +785000 ekin = 20.9642653572837 | erot = 20.9633174771005 | epot = -75.4920336619114 | etot = -33.5644508275272 +786000 ekin = 21.4400765968759 | erot = 21.061583090539 | epot = -76.0661105191519 | etot = -33.5644508317371 +787000 ekin = 21.8830668853208 | erot = 21.0574506776045 | epot = -76.5049683963306 | etot = -33.5644508334054 +788000 ekin = 22.2673243737814 | erot = 20.9464326031856 | epot = -76.7782078095427 | etot = -33.5644508325756 +789000 ekin = 22.5826671465141 | erot = 20.7432248255376 | epot = -76.8903428020209 | etot = -33.5644508299692 +790000 ekin = 22.8323066866154 | erot = 20.4741989828028 | epot = -76.8709564960782 | etot = -33.56445082666 +791000 ekin = 23.0272356221831 | erot = 20.1684029992233 | epot = -76.7600894450125 | etot = -33.5644508236061 +792000 ekin = 23.1800436940963 | erot = 19.8507212176288 | epot = -76.5952157330443 | etot = -33.5644508213191 +793000 ekin = 23.300603133044 | erot = 19.5391467337423 | epot = -76.404200686658 | etot = -33.5644508198717 +794000 ekin = 23.3943971223733 | erot = 19.2453890910844 | epot = -76.2042370325532 | etot = -33.5644508190955 +795000 ekin = 23.4629811579683 | erot = 18.9772359492812 | epot = -76.0046679259086 | etot = -33.5644508186592 +796000 ekin = 23.5050545285291 | erot = 18.7401074031681 | epot = -75.8096127503046 | etot = -33.5644508186073 +797000 ekin = 23.5179235663088 | erot = 18.5376020828532 | epot = -75.6199764678595 | etot = -33.5644508186975 +798000 ekin = 23.4993095514253 | erot = 18.3721088645044 | epot = -75.4358692347521 | etot = -33.5644508188224 +799000 ekin = 23.4489395597834 | erot = 18.2446734411486 | epot = -75.258063819795 | etot = -33.564450818863 +800000 ekin = 23.3700597315759 | erot = 18.1549836094423 | epot = -75.0894941596996 | etot = -33.5644508186813 +801000 ekin = 23.2706429321765 | erot = 18.1018392066988 | epot = -74.9369329570152 | etot = -33.5644508181399 +802000 ekin = 23.1638659253445 | erot = 18.0841621417591 | epot = -74.8124788842758 | etot = -33.5644508171722 +803000 ekin = 23.0673439652931 | erot = 18.1021655927045 | epot = -74.7339603738614 | etot = -33.5644508158639 +804000 ekin = 23.0007989401313 | erot = 18.1579717421609 | epot = -74.7232214967841 | etot = -33.564450814492 +805000 ekin = 22.9823371371263 | erot = 18.2549251648251 | epot = -74.8017131154778 | etot = -33.5644508135264 +806000 ekin = 23.0241641619703 | erot = 18.3954330766867 | epot = -74.984048052 | etot = -33.5644508133431 +807000 ekin = 23.1289646264206 | erot = 18.5785443252248 | epot = -75.2719597659602 | etot = -33.5644508143147 +808000 ekin = 23.2881607697434 | erot = 18.7969609309069 | epot = -75.6495725171493 | etot = -33.5644508164989 +809000 ekin = 23.4826910126068 | erot = 19.0356597574091 | epot = -76.0828015896723 | etot = -33.5644508196564 +810000 ekin = 23.6859311917307 | erot = 19.2727961935001 | epot = -76.5231782085194 | etot = -33.5644508232885 +811000 ekin = 23.8683330193095 | erot = 19.4824424681752 | epot = -76.9152263142569 | etot = -33.5644508267723 +812000 ekin = 24.0021280336694 | erot = 19.6390320771543 | epot = -77.2056109397628 | etot = -33.5644508289391 +813000 ekin = 24.0705831548813 | erot = 19.7220219145477 | epot = -77.3570559007636 | etot = -33.5644508313346 +814000 ekin = 24.0556011517812 | erot = 19.7197957998033 | epot = -77.3398477836966 | etot = -33.5644508321121 +815000 ekin = 23.9426529222313 | erot = 19.6314238633418 | epot = -77.1385276168128 | etot = -33.5644508312396 +816000 ekin = 23.731133693213 | erot = 19.466072036005 | epot = -76.7616565581624 | etot = -33.5644508289444 +817000 ekin = 23.4336685350294 | erot = 19.2405112303572 | epot = -76.2386305910159 | etot = -33.5644508256293 +818000 ekin = 23.0739945646645 | erot = 18.9755381783867 | epot = -75.6139835648237 | etot = -33.5644508217725 +819000 ekin = 22.6837324026765 | erot = 18.6923648026043 | epot = -74.9405480232895 | etot = -33.5644508180087 +820000 ekin = 22.2835291279714 | erot = 18.4096381976571 | epot = -74.2576181415066 | etot = -33.5644508158781 +821000 ekin = 21.8822278938176 | erot = 18.141291498877 | epot = -73.5879702071845 | etot = -33.5644508144899 +822000 ekin = 21.4884880533111 | erot = 17.8956786276998 | epot = -72.9486174948433 | etot = -33.5644508138324 +823000 ekin = 21.1064787927768 | erot = 17.6755757474125 | epot = -72.3465053539623 | etot = -33.564450813773 +824000 ekin = 20.7370980701816 | erot = 17.4789023716297 | epot = -71.7804512559058 | etot = -33.5644508140945 +825000 ekin = 20.3797998929284 | erot = 17.3000855940531 | epot = -71.2443363015056 | etot = -33.5644508145241 +826000 ekin = 20.0346218856065 | erot = 17.1319532523354 | epot = -70.7310259527282 | etot = -33.5644508147862 +827000 ekin = 19.7039740663547 | erot = 16.9679189158217 | epot = -70.2363437968243 | etot = -33.5644508146479 +828000 ekin = 19.3938011099896 | erot = 16.8040573647366 | epot = -69.7623092887102 | etot = -33.5644508139841 +829000 ekin = 19.1138486595862 | erot = 16.6405709737945 | epot = -69.3188704461918 | etot = -33.5644508128111 +830000 ekin = 18.8769326813353 | erot = 16.4822215963422 | epot = -68.9236050889638 | etot = -33.5644508112863 +831000 ekin = 18.697311774337 | erot = 16.3375582362052 | epot = -68.5993208202243 | etot = -33.5644508096821 +832000 ekin = 18.5884699042913 | erot = 16.2171194616771 | epot = -68.3700401742869 | etot = -33.5644508083185 +833000 ekin = 18.5607795988464 | erot = 16.131079329091 | epot = -68.2563097354189 | etot = -33.5644508074815 +834000 ekin = 18.6195655893721 | erot = 16.0869173655938 | epot = -68.2709337623352 | etot = -33.5644508073693 +835000 ekin = 18.7639745681618 | erot = 16.0875916783619 | epot = -68.4160170545793 | etot = -33.5644508080557 +836000 ekin = 18.9868442891856 | erot = 16.130519235032 | epot = -68.6818143337116 | etot = -33.5644508094941 +837000 ekin = 19.2754657692627 | erot = 16.207438470387 | epot = -69.0473550511925 | etot = -33.5644508115428 +838000 ekin = 19.6129197642166 | erot = 16.3051003168942 | epot = -69.4824708951133 | etot = -33.5644508140025 +839000 ekin = 19.9795904915988 | erot = 16.4066729969167 | epot = -69.9507143051619 | etot = -33.5644508166465 +840000 ekin = 20.3545159452212 | erot = 16.4936833341199 | epot = -70.4126500985958 | etot = -33.5644508192548 +841000 ekin = 20.7164052641964 | erot = 16.548246927735 | epot = -70.829103013567 | etot = -33.5644508216356 +842000 ekin = 21.0443277173709 | erot = 16.5552492658878 | epot = -71.1640278069013 | etot = -33.5644508236425 +843000 ekin = 21.3182343501173 | erot = 16.504098715485 | epot = -71.3867838907757 | etot = -33.5644508251735 +844000 ekin = 21.5195641371082 | erot = 16.3898128616543 | epot = -71.4738278249128 | etot = -33.5644508261503 +845000 ekin = 21.6321888572324 | erot = 16.2134453017857 | epot = -71.4100849855142 | etot = -33.5644508264961 +846000 ekin = 21.6437998337389 | erot = 15.9820204440426 | epot = -71.1902711039102 | etot = -33.5644508261287 +847000 ekin = 21.5475782511098 | erot = 15.7081282908899 | epot = -70.8201573669942 | etot = -33.5644508249945 +848000 ekin = 21.3436927799336 | erot = 15.4091281568063 | epot = -70.3172717598687 | etot = -33.5644508231288 +849000 ekin = 21.040018068204 | erot = 15.1057456387123 | epot = -69.7102145276103 | etot = -33.564450820694 +850000 ekin = 20.6516241479064 | erot = 14.8199821289072 | epot = -69.0360570947859 | etot = -33.5644508179724 +851000 ekin = 20.1989966769928 | erot = 14.5725796445398 | epot = -68.3360271368306 | etot = -33.5644508152979 +852000 ekin = 19.7054052282539 | erot = 14.3805531694316 | epot = -67.6504092106676 | etot = -33.5644508129822 +853000 ekin = 19.1940724659069 | erot = 14.2553081918317 | epot = -67.013831468985 | etot = -33.5644508112464 +854000 ekin = 18.685752406539 | erot = 14.2015963027567 | epot = -66.4517995195066 | etot = -33.5644508102108 +855000 ekin = 18.1970763793973 | erot = 14.217263432367 | epot = -65.9787906216679 | etot = -33.5644508099036 +856000 ekin = 17.7397499755394 | erot = 14.293605095631 | epot = -65.597805881444 | etot = -33.5644508102736 +857000 ekin = 17.3205057828376 | erot = 14.4162007415788 | epot = -65.3011573356223 | etot = -33.5644508112059 +858000 ekin = 16.9416544321828 | erot = 14.5662556892476 | epot = -65.0723609339437 | etot = -33.5644508125133 +859000 ekin = 16.6020780530239 | erot = 14.7225727582617 | epot = -64.8891016252306 | etot = -33.5644508139451 +860000 ekin = 16.2985125202782 | erot = 14.8641879511938 | epot = -64.7271512866837 | etot = -33.5644508152118 +861000 ekin = 16.0269335804234 | erot = 14.9734306247742 | epot = -64.5648150212404 | etot = -33.5644508160429 +862000 ekin = 15.7838145531257 | erot = 15.0388248710163 | epot = -64.3870902403884 | etot = -33.5644508162464 +863000 ekin = 15.5670277438764 | erot = 15.0570871966147 | epot = -64.1885657562588 | etot = -33.5644508157676 +864000 ekin = 15.3762443300744 | erot = 15.0336448974535 | epot = -63.9743400422222 | etot = -33.5644508146943 +865000 ekin = 15.2131876579387 | erot = 14.9816007216251 | epot = -63.7592391926681 | etot = -33.5644508131043 +866000 ekin = 15.0809818320607 | erot = 14.9194629923979 | epot = -63.5648956359166 | etot = -33.5644508114581 +867000 ekin = 14.9827726531226 | erot = 14.8683323185733 | epot = -63.4155557815486 | etot = -33.5644508098527 +868000 ekin = 14.9218011269598 | erot = 14.8493296883198 | epot = -63.3355816237487 | etot = -33.5644508084691 +869000 ekin = 14.9010185138682 | erot = 14.8813222897364 | epot = -63.3467916110622 | etot = -33.5644508074576 +870000 ekin = 14.9227801778206 | erot = 14.9789108530707 | epot = -63.4661418378863 | etot = -33.5644508069951 +871000 ekin = 14.9884139368942 | erot = 15.1503817706812 | epot = -63.703246514838 | etot = -33.5644508072627 +872000 ekin = 15.0976914328012 | erot = 15.3955923521635 | epot = -64.0577345933959 | etot = -33.5644508084312 +873000 ekin = 15.2480781394194 | erot = 15.7042636320403 | epot = -64.5167925820518 | etot = -33.5644508105921 +874000 ekin = 15.4340038880574 | erot = 16.055356092982 | epot = -65.053810794677 | etot = -33.5644508136376 +875000 ekin = 15.6465534583829 | erot = 16.4187317020441 | epot = -65.6297359776216 | etot = -33.5644508171946 +876000 ekin = 15.8739222035519 | erot = 16.7595446910416 | epot = -66.1979177152847 | etot = -33.5644508206912 +877000 ekin = 16.1027155819911 | erot = 17.0444943473801 | epot = -66.7116607529112 | etot = -33.5644508235401 +878000 ekin = 16.319791048708 | erot = 17.2478151737007 | epot = -67.1320570477561 | etot = -33.5644508253474 +879000 ekin = 16.513852143331 | erot = 17.3548092235238 | epot = -67.4331121929392 | etot = -33.5644508260845 +880000 ekin = 16.6772706666643 | erot = 17.3624918756169 | epot = -67.6042133678519 | etot = -33.5644508255706 +881000 ekin = 16.8080553843206 | erot = 17.2784522473064 | epot = -67.6509584556495 | etot = -33.5644508240226 +882000 ekin = 16.9100399156744 | erot = 17.1190222525855 | epot = -67.5935129898763 | etot = -33.5644508216164 +883000 ekin = 16.9925722017344 | erot = 16.9073416710475 | epot = -67.4643646914728 | etot = -33.5644508186909 +884000 ekin = 17.0687034106809 | erot = 16.6704808404549 | epot = -67.3036350669103 | etot = -33.5644508157744 +885000 ekin = 17.1519974231529 | erot = 16.4352378856248 | epot = -67.1516861222243 | etot = -33.5644508134466 +886000 ekin = 17.2529390407585 | erot = 16.2234313547558 | epot = -67.0408212076545 | etot = -33.5644508121402 +887000 ekin = 17.3762921647762 | erot = 16.0482363412789 | epot = -66.9889793180409 | etot = -33.5644508119859 +888000 ekin = 17.520362098505 | erot = 15.9127130226943 | epot = -66.9975259340197 | etot = -33.5644508128205 +889000 ekin = 17.6781644467692 | erot = 15.8105908148255 | epot = -67.053206075905 | etot = -33.5644508143103 +890000 ekin = 17.8397117367786 | erot = 15.7285450848103 | epot = -67.1327076370755 | etot = -33.5644508154865 +891000 ekin = 17.9946822418325 | erot = 15.6526652214473 | epot = -67.2117982809621 | etot = -33.5644508176823 +892000 ekin = 18.1331274177217 | erot = 15.563184660984 | epot = -67.2607628981432 | etot = -33.5644508194375 +893000 ekin = 18.2472194998205 | erot = 15.4391901295465 | epot = -67.2508604500035 | etot = -33.5644508206365 +894000 ekin = 18.3321686671843 | erot = 15.2648175339455 | epot = -67.1614370222908 | etot = -33.564450821161 +895000 ekin = 18.3862908814765 | erot = 15.0310128841995 | epot = -66.9817545866243 | etot = -33.5644508209484 +896000 ekin = 18.4109116210726 | erot = 14.7366844097439 | epot = -66.7120468508501 | etot = -33.5644508200336 +897000 ekin = 18.4100490066795 | erot = 14.3885926448155 | epot = -66.3630924700693 | etot = -33.5644508185744 +898000 ekin = 18.3898281685202 | erot = 13.9998000563491 | epot = -65.9540790416773 | etot = -33.5644508168081 +899000 ekin = 18.3577139299705 | erot = 13.5871378088075 | epot = -65.509302553754 | etot = -33.564450814976 +900000 ekin = 18.3217786311141 | erot = 13.1685630404219 | epot = -65.054792484781 | etot = -33.5644508132449 +901000 ekin = 18.2902589942974 | erot = 12.7612484276711 | epot = -64.6159582336337 | etot = -33.5644508116652 +902000 ekin = 18.2715810710039 | erot = 12.3808553804282 | epot = -64.2168872615955 | etot = -33.5644508101635 +903000 ekin = 18.2748902577742 | erot = 12.04197991098 | epot = -63.8813209773376 | etot = -33.5644508085834 +904000 ekin = 18.3109460803817 | erot = 11.7594273506552 | epot = -63.6348242377774 | etot = -33.5644508067406 +905000 ekin = 18.393092548532 | erot = 11.5498594838196 | epot = -63.507402836842 | etot = -33.5644508044905 +906000 ekin = 18.5347341805732 | erot = 11.4295673220289 | epot = -63.5287523075689 | etot = -33.5644508049669 +907000 ekin = 18.7414362397562 | erot = 11.4045037441698 | epot = -63.7103907883216 | etot = -33.5644508043955 +908000 ekin = 19.01948896505 | erot = 11.4807236741048 | epot = -64.064663443761 | etot = -33.5644508046062 +909000 ekin = 19.370061418707 | erot = 11.6589605869467 | epot = -64.5934728113217 | etot = -33.5644508056681 +910000 ekin = 19.788210520863 | erot = 11.9333322638151 | epot = -65.2859935919935 | etot = -33.5644508073154 +911000 ekin = 20.2647618396155 | erot = 12.2921701370539 | epot = -66.1213827858005 | etot = -33.5644508091311 +912000 ekin = 20.7894338917871 | erot = 12.7195983389508 | epot = -67.0734830412077 | etot = -33.5644508104698 +913000 ekin = 21.3541857291101 | erot = 13.1939380946156 | epot = -68.1125746374356 | etot = -33.5644508137099 +914000 ekin = 21.9410171487178 | erot = 13.6876167577927 | epot = -69.1930847244104 | etot = -33.5644508179 +915000 ekin = 22.518884629029 | erot = 14.1693256816077 | epot = -70.252661133485 | etot = -33.5644508228483 +916000 ekin = 23.0495496122886 | erot = 14.6035757293001 | epot = -71.2175761703539 | etot = -33.5644508287652 +917000 ekin = 23.4897289756407 | erot = 14.9539952399446 | epot = -72.0081750488837 | etot = -33.5644508332984 +918000 ekin = 23.793918530387 | erot = 15.1976473317576 | epot = -72.5560167461632 | etot = -33.5644508840185 +919000 ekin = 23.6168045559219 | erot = 15.3655091451681 | epot = -72.546764543126 | etot = -33.564450842036 +920000 ekin = 23.1655316155466 | erot = 15.5814764778541 | epot = -72.3114589043119 | etot = -33.5644508109111 +921000 ekin = 22.8561009763955 | erot = 15.8041631554327 | epot = -72.2247149918464 | etot = -33.5644508600183 +922000 ekin = 22.4406172099256 | erot = 15.7102388759533 | epot = -71.7153069240717 | etot = -33.5644508381928 +923000 ekin = 21.8145072543786 | erot = 15.4204628569532 | epot = -70.7994209415843 | etot = -33.5644508302526 +924000 ekin = 21.0897106221477 | erot = 15.1252102346463 | epot = -69.7793716761032 | etot = -33.5644508193092 +925000 ekin = 20.3778961154116 | erot = 14.8990596223701 | epot = -68.8414065460385 | etot = -33.5644508082568 +926000 ekin = 19.7497733196884 | erot = 14.7841436172023 | epot = -68.0983677423196 | etot = -33.5644508054289 +927000 ekin = 19.2202389486492 | erot = 14.8057849928954 | epot = -67.5904747440152 | etot = -33.5644508024706 +928000 ekin = 18.8098178378655 | erot = 14.9862994179362 | epot = -67.3605680557094 | etot = -33.5644507999077 +929000 ekin = 18.5263530330417 | erot = 15.3189513447801 | epot = -67.4097551952486 | etot = -33.5644508174268 +930000 ekin = 18.3031582479208 | erot = 15.7144845870462 | epot = -67.5820936630876 | etot = -33.5644508281205 +931000 ekin = 18.0528353461445 | erot = 16.0920981649876 | epot = -67.7093843479757 | etot = -33.5644508368436 +932000 ekin = 17.7015072487275 | erot = 16.3874716161786 | epot = -67.6534297061045 | etot = -33.5644508411985 +933000 ekin = 17.211575779812 | erot = 16.5716045845824 | epot = -67.3476312032304 | etot = -33.5644508388361 +934000 ekin = 16.5514003367762 | erot = 16.6395832467501 | epot = -66.7554344853522 | etot = -33.564450901826 +935000 ekin = 15.4338979248173 | erot = 16.4795973814032 | epot = -65.4779461395113 | etot = -33.5644508332907 +936000 ekin = 14.2992444440305 | erot = 16.4524645769609 | epot = -64.3161598028593 | etot = -33.564450781868 +937000 ekin = 13.594877389297 | erot = 16.8307081817066 | epot = -63.9900363826699 | etot = -33.5644508116663 +938000 ekin = 13.1600926819737 | erot = 17.3617572865251 | epot = -64.0863008414443 | etot = -33.5644508729455 +939000 ekin = 12.6302856042602 | erot = 17.6616475412764 | epot = -63.8563839351059 | etot = -33.5644507895693 +940000 ekin = 12.1844103621837 | erot = 17.9750890379595 | epot = -63.7239501902423 | etot = -33.5644507900991 +941000 ekin = 11.8736812724101 | erot = 18.3544207840917 | epot = -63.79255284895 | etot = -33.5644507924482 +942000 ekin = 11.6856910034444 | erot = 18.7737996951239 | epot = -64.0239414943836 | etot = -33.5644507958152 +943000 ekin = 11.5993719863631 | erot = 19.1997647301752 | epot = -64.3635875159553 | etot = -33.564450799417 +944000 ekin = 11.5911163869142 | erot = 19.5969000490703 | epot = -64.7524672386315 | etot = -33.564450802647 +945000 ekin = 11.639459484541 | erot = 19.9326030898694 | epot = -65.1365133795222 | etot = -33.5644508051117 +946000 ekin = 11.7278293567757 | erot = 20.1807231909362 | epot = -65.4730033543077 | etot = -33.5644508065958 +947000 ekin = 11.8456010821895 | erot = 20.324153790967 | epot = -65.7342056801685 | etot = -33.5644508070121 +948000 ekin = 11.9879925809402 | erot = 20.3564922792948 | epot = -65.9089356666417 | etot = -33.5644508064067 +949000 ekin = 12.1551997602243 | erot = 20.2822909293999 | epot = -66.0019414945905 | etot = -33.5644508049663 +950000 ekin = 12.3510408470325 | erot = 20.115659623218 | epot = -66.0311512732532 | etot = -33.5644508030028 +951000 ekin = 12.5812930222758 | erot = 19.8773156844474 | epot = -66.0230595076182 | etot = -33.5644508008949 +952000 ekin = 12.8471183866925 | erot = 19.5848425912166 | epot = -65.9964117794652 | etot = -33.564450801556 +953000 ekin = 13.1479143636503 | erot = 19.2558560502527 | epot = -65.9682212137687 | etot = -33.5644507998657 +954000 ekin = 13.4859606885364 | erot = 18.9116614121342 | epot = -65.9620728994014 | etot = -33.5644507987308 +955000 ekin = 13.8607396756392 | erot = 18.5688220964155 | epot = -65.994012570258 | etot = -33.5644507982032 +956000 ekin = 14.2684790715045 | erot = 18.23867671937 | epot = -66.0716065890947 | etot = -33.5644507982202 +957000 ekin = 14.7022261388303 | erot = 17.9280212141735 | epot = -66.1946981516521 | etot = -33.5644507986483 +958000 ekin = 15.1523556915809 | erot = 17.6404102051721 | epot = -66.3572166960802 | etot = -33.5644507993272 +959000 ekin = 15.6074014520696 | erot = 17.3776018825342 | epot = -66.5494541347015 | etot = -33.5644508000977 +960000 ekin = 16.055105520303 | erot = 17.1408213598753 | epot = -66.760377680976 | etot = -33.5644508007977 +961000 ekin = 16.4838195085816 | erot = 16.9315995207268 | epot = -66.979869830664 | etot = -33.5644508013556 +962000 ekin = 16.8831178333153 | erot = 16.752450807508 | epot = -67.2000194425075 | etot = -33.5644508016842 +963000 ekin = 17.2446402437768 | erot = 16.6070593136442 | epot = -67.4161503591765 | etot = -33.5644508017555 +964000 ekin = 17.562694424349 | erot = 16.5001400875647 | epot = -67.6272853134984 | etot = -33.5644508015847 +965000 ekin = 17.8343164168747 | erot = 16.437096040881 | epot = -67.8358632589921 | etot = -33.5644508012364 +966000 ekin = 18.0588818068295 | erot = 16.4234839575503 | epot = -68.0468165651874 | etot = -33.5644508008075 +967000 ekin = 18.2373393703384 | erot = 16.4643418733569 | epot = -68.2661320441123 | etot = -33.5644508004171 +968000 ekin = 18.3712253513644 | erot = 16.5634469194537 | epot = -68.4991230710021 | etot = -33.5644508001841 +969000 ekin = 18.4616731850683 | erot = 16.7225928803125 | epot = -68.7487168655807 | etot = -33.5644508001999 +970000 ekin = 18.5086424153895 | erot = 16.9409874348876 | epot = -69.0140806508028 | etot = -33.5644508005257 +971000 ekin = 18.5105217612239 | erot = 17.214832239555 | epot = -69.2898048019491 | etot = -33.5644508011701 +972000 ekin = 18.4641879343137 | erot = 17.5371342494854 | epot = -69.5657729859032 | etot = -33.5644508021041 +973000 ekin = 18.3654968233623 | erot = 17.8977436725043 | epot = -69.8276912991286 | etot = -33.5644508032619 +974000 ekin = 18.2101154507905 | erot = 18.2835968621238 | epot = -70.0581631174661 | etot = -33.5644508045518 +975000 ekin = 17.9945660461061 | erot = 18.679151597941 | epot = -70.2381684499127 | etot = -33.5644508058656 +976000 ekin = 17.717330563609 | erot = 19.0670257232443 | epot = -70.3488070939419 | etot = -33.5644508070885 +977000 ekin = 17.3798453528906 | erot = 19.4288693817331 | epot = -70.3731655427282 | etot = -33.5644508081045 +978000 ekin = 16.9872047031722 | erot = 19.7465105573489 | epot = -70.2981660693277 | etot = -33.5644508088066 +979000 ekin = 16.5484157018381 | erot = 20.0033999874178 | epot = -70.116266498357 | etot = -33.5644508091011 +980000 ekin = 16.0760394950274 | erot = 20.1863036686509 | epot = -69.8267939695453 | etot = -33.5644508058671 +981000 ekin = 15.5958799597593 | erot = 20.2892058513337 | epot = -69.4495366177224 | etot = -33.5644508066295 +982000 ekin = 15.0884229586249 | erot = 20.3042918160036 | epot = -68.9571656249607 | etot = -33.5644508503322 +983000 ekin = 14.6278059338707 | erot = 20.1974254855586 | epot = -68.3896822274588 | etot = -33.5644508080295 +984000 ekin = 14.485718093269 | erot = 20.0570073304459 | epot = -68.1071762944406 | etot = -33.5644508707257 +985000 ekin = 14.2080885116351 | erot = 19.9192764069441 | epot = -67.6918157209786 | etot = -33.5644508023994 +986000 ekin = 13.9758845112991 | erot = 19.8429646049279 | epot = -67.3832999162394 | etot = -33.5644508000123 +987000 ekin = 13.8444879807334 | erot = 19.8435555011179 | epot = -67.2524942889555 | etot = -33.5644508071042 +988000 ekin = 13.7899576039149 | erot = 19.876553633637 | epot = -67.2309620426443 | etot = -33.5644508050923 +989000 ekin = 13.7826987903072 | erot = 19.9896360515821 | epot = -67.3367856483026 | etot = -33.5644508064133 +990000 ekin = 13.8064598100946 | erot = 20.1866383843989 | epot = -67.5575490030266 | etot = -33.5644508085331 +991000 ekin = 13.8444762357552 | erot = 20.455356874306 | epot = -67.8642839209134 | etot = -33.5644508108522 +992000 ekin = 13.8831356664543 | erot = 20.7777559193191 | epot = -68.2253423984327 | etot = -33.5644508126593 +993000 ekin = 13.9170731932667 | erot = 21.1354076794003 | epot = -68.6169316860712 | etot = -33.5644508134042 +994000 ekin = 13.9526839919551 | erot = 21.5142214723578 | epot = -69.0313562771973 | etot = -33.5644508128844 +995000 ekin = 14.0087177033998 | erot = 21.9069609499345 | epot = -69.4801294647094 | etot = -33.5644508113751 +996000 ekin = 14.1134297061039 | erot = 22.3130050958893 | epot = -69.9908856111372 | etot = -33.564450809144 +997000 ekin = 14.3000196986382 | erot = 22.73642078599 | epot = -70.6008912914758 | etot = -33.5644508068476 +998000 ekin = 14.6010980818731 | erot = 23.1830420697638 | epot = -71.3485909566375 | etot = -33.5644508050006 +999000 ekin = 15.04273129669 | erot = 23.6573925697404 | epot = -72.2645746768899 | etot = -33.5644508104595 +1000000 ekin = 15.6136601549948 | erot = 24.1382005377538 | epot = -73.31631150618 | etot = -33.5644508134314 + 1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160018 39304000 +Loop time of 15.1991 on 4 procs for 1000000 steps with 16 atoms + +Performance: 96.978 ns/day, 0.247 hours/ns, 65793.330 timesteps/s, 1.053 Matom-step/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5 | 7.3219 | 8.7863 | 57.6 | 48.17 +Bond | 0.16729 | 0.27802 | 0.36232 | 13.4 | 1.83 +Neigh | 0.004996 | 0.0050565 | 0.005082 | 0.0 | 0.03 +Comm | 4.2246 | 5.7942 | 8.2783 | 66.3 | 38.12 +Output | 0.065594 | 0.07006 | 0.079338 | 2.1 | 0.46 +Modify | 0.59597 | 0.6588 | 0.74343 | 7.9 | 4.33 +Other | | 1.071 | | | 7.05 + +Nlocal: 4 ave 4 max 4 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 12 ave 12 max 12 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 26.75 ave 47 max 9 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 107 +Ave neighs/atom = 6.6875 +Ave special neighs/atom = 3.75 +Neighbor list builds = 1000 +Dangerous builds = 0 +System init for write_data ... +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:15 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/oxrna2_real.cgdna b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/oxrna2_real.cgdna new file mode 120000 index 0000000000..014605f135 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/oxrna2_real.cgdna @@ -0,0 +1 @@ +../../../../../../../potentials/oxrna2_real.cgdna \ No newline at end of file diff --git a/examples/PACKAGES/cgdna/examples/test.sh b/examples/PACKAGES/cgdna/examples/test.sh index 152047b94b..11b02ac693 100755 --- a/examples/PACKAGES/cgdna/examples/test.sh +++ b/examples/PACKAGES/cgdna/examples/test.sh @@ -1,11 +1,11 @@ #! /bin/bash -DATE='14Dec21' +DATE='22May24' TOL=1e-8 LMPDIR=/Users/ohenrich/Work/code/lammps SRCDIR=$LMPDIR/src -EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples +EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples/lj_units if [ $# -eq 1 ] && [ $1 = run ]; then echo '# Compiling executable in' $SRCDIR | tee -a $EXDIR/test.log @@ -18,7 +18,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then make -j8 mpi | tee -a $EXDIR/test.log ###################################################### - echo '# Running oxDNA duplex1 test' | tee -a $EXDIR/test.log + printf '\n# Running oxDNA duplex1 test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxDNA/duplex1 mkdir test cd test @@ -26,7 +26,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../in.duplex1 . cp ../data.duplex1 . - mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex1 > /dev/null mv log.lammps log.$DATE.duplex1.g++.1 grep etot log.$DATE.duplex1.g++.1 > e_test.1.dat grep etot ../log*1 > e_old.1.dat @@ -35,10 +35,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex1 > /dev/null mv log.lammps log.$DATE.duplex1.g++.4 grep etot log.$DATE.duplex1.g++.4 > e_test.4.dat grep etot ../log*4 > e_old.4.dat @@ -47,13 +47,13 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks FAILED" | tee -a $EXDIR/test.log fi ###################################################### ###################################################### - echo '# Running oxDNA duplex2 test' | tee -a $EXDIR/test.log + printf '\n# Running oxDNA duplex2 test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxDNA/duplex2 mkdir test cd test @@ -61,7 +61,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../in.duplex2 . cp ../data.duplex2 . - mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex2 > /dev/null mv log.lammps log.$DATE.duplex2.g++.1 grep etot log.$DATE.duplex2.g++.1 > e_test.1.dat grep etot ../log*1 > e_old.1.dat @@ -70,10 +70,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex2 > /dev/null mv log.lammps log.$DATE.duplex2.g++.4 grep etot log.$DATE.duplex2.g++.4 > e_test.4.dat grep etot ../log*4 > e_old.4.dat @@ -82,13 +82,13 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks FAILED" | tee -a $EXDIR/test.log fi ###################################################### ###################################################### - echo '# Running oxDNA2 duplex1 test' | tee -a $EXDIR/test.log + printf '\n# Running oxDNA2 duplex1 test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxDNA2/duplex1 mkdir test cd test @@ -96,7 +96,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../in.duplex1 . cp ../data.duplex1 . - mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex1 > /dev/null mv log.lammps log.$DATE.duplex1.g++.1 grep etot log.$DATE.duplex1.g++.1 > e_test.1.dat grep etot ../log*1 > e_old.1.dat @@ -105,10 +105,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex1 > /dev/null mv log.lammps log.$DATE.duplex1.g++.4 grep etot log.$DATE.duplex1.g++.4 > e_test.4.dat grep etot ../log*4 > e_old.4.dat @@ -117,13 +117,13 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks FAILED" | tee -a $EXDIR/test.log fi ###################################################### ###################################################### - echo '# Running oxDNA2 duplex2 test' | tee -a $EXDIR/test.log + printf '\n# Running oxDNA2 duplex2 test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxDNA2/duplex2 mkdir test cd test @@ -131,7 +131,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../in.duplex2 . cp ../data.duplex2 . - mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex2 > /dev/null mv log.lammps log.$DATE.duplex2.g++.1 grep etot log.$DATE.duplex2.g++.1 > e_test.1.dat grep etot ../log*1 > e_old.1.dat @@ -140,10 +140,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex2 > /dev/null mv log.lammps log.$DATE.duplex2.g++.4 grep etot log.$DATE.duplex2.g++.4 > e_test.4.dat grep etot ../log*4 > e_old.4.dat @@ -152,13 +152,13 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks FAILED" | tee -a $EXDIR/test.log fi ###################################################### ###################################################### - echo '# Running oxDNA2 duplex3 test' | tee -a $EXDIR/test.log + printf '\n# Running oxDNA2 duplex3 test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxDNA2/duplex3 mkdir test cd test @@ -166,7 +166,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../in.duplex3 . cp ../data.duplex3 . - mpirun -np 1 ./lmp_mpi < in.duplex3 > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex3 > /dev/null mv log.lammps log.$DATE.duplex3.g++.1 grep etot log.$DATE.duplex3.g++.1 > e_test.1.dat grep etot ../log*1 > e_old.1.dat @@ -175,10 +175,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex3 > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex3 > /dev/null mv log.lammps log.$DATE.duplex3.g++.4 grep etot log.$DATE.duplex3.g++.4 > e_test.4.dat grep etot ../log*4 > e_old.4.dat @@ -187,13 +187,13 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks FAILED" | tee -a $EXDIR/test.log fi ###################################################### ###################################################### - echo '# Running oxDNA2 unique_bp test' | tee -a $EXDIR/test.log + printf '\n# Running oxDNA2 unique_bp test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxDNA2/unique_bp mkdir test cd test @@ -203,7 +203,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../data.duplex4.4type . cp ../data.duplex4.8type . - mpirun -np 1 ./lmp_mpi < in.duplex4.4type > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex4.4type > /dev/null mv log.lammps log.$DATE.duplex4.4type.g++.1 grep etot log.$DATE.duplex4.4type.g++.1 > e_test.4type.1.dat grep etot ../log*4type*1 > e_old.4type.1.dat @@ -212,10 +212,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task 4 types passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task 4 types unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task 4 types FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex4.4type > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex4.4type > /dev/null mv log.lammps log.$DATE.duplex4.4type.g++.4 grep etot log.$DATE.duplex4.4type.g++.4 > e_test.4type.4.dat grep etot ../log*4type*4 > e_old.4type.4.dat @@ -224,10 +224,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks 4 types passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks 4 types unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks 4 types FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 1 ./lmp_mpi < in.duplex4.8type > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex4.8type > /dev/null mv log.lammps log.$DATE.duplex4.8type.g++.1 grep etot log.$DATE.duplex4.8type.g++.1 > e_test.8type.1.dat grep etot ../log*8type*1 > e_old.8type.1.dat @@ -236,10 +236,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task 8 types passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task 8 types unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task 8 types FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex4.8type > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex4.8type > /dev/null mv log.lammps log.$DATE.duplex4.8type.g++.4 grep etot log.$DATE.duplex4.8type.g++.4 > e_test.8type.4.dat grep etot ../log*8type*4 > e_old.8type.4.dat @@ -248,13 +248,13 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks 8 types passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks 8 types unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks 8 types FAILED" | tee -a $EXDIR/test.log fi ###################################################### ###################################################### - echo '# Running oxDNA2 dsring test' | tee -a $EXDIR/test.log + printf '\n# Running oxDNA2 dsring test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxDNA2/dsring mkdir test cd test @@ -262,7 +262,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../in.dsring . cp ../data.dsring . - mpirun -np 1 ./lmp_mpi < in.dsring > /dev/null + mpirun -np 1 ./lmp_mpi -in in.dsring > /dev/null mv log.lammps log.$DATE.dsring.g++.1 grep etot log.$DATE.dsring.g++.1 > e_test.1.dat grep etot ../log*1 > e_old.1.dat @@ -271,10 +271,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.dsring > /dev/null + mpirun -np 4 ./lmp_mpi -in in.dsring > /dev/null mv log.lammps log.$DATE.dsring.g++.4 grep etot log.$DATE.dsring.g++.4 > e_test.4.dat grep etot ../log*4 > e_old.4.dat @@ -283,13 +283,13 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks FAILED" | tee -a $EXDIR/test.log fi ###################################################### ###################################################### - echo '# Running oxRNA2 duplex2 test' | tee -a $EXDIR/test.log + printf '\n# Running oxRNA2 duplex2 test\n' | tee -a $EXDIR/test.log cd $EXDIR/oxRNA2/duplex2 mkdir test cd test @@ -297,7 +297,7 @@ if [ $# -eq 1 ] && [ $1 = run ]; then cp ../in.duplex2 . cp ../data.duplex2 . - mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null + mpirun -np 1 ./lmp_mpi -in in.duplex2 > /dev/null mv log.lammps log.$DATE.duplex2.g++.1 grep etot log.$DATE.duplex2.g++.1 > e_test.1.dat grep etot ../log*1 > e_old.1.dat @@ -306,10 +306,10 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log else - echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log + echo "# 1 MPI-task FAILED" | tee -a $EXDIR/test.log fi - mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null + mpirun -np 4 ./lmp_mpi -in in.duplex2 > /dev/null mv log.lammps log.$DATE.duplex2.g++.4 grep etot log.$DATE.duplex2.g++.4 > e_test.4.dat grep etot ../log*4 > e_old.4.dat @@ -318,10 +318,11 @@ if [ $# -eq 1 ] && [ $1 = run ]; then then echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log else - echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log + echo "# 4 MPI-tasks FAILED" | tee -a $EXDIR/test.log fi ###################################################### + echo echo '# Done' | tee -a $EXDIR/test.log elif [ $# -eq 1 ] && [ $1 = clean ]; then diff --git a/examples/PACKAGES/cgdna/util/generate.py b/examples/PACKAGES/cgdna/util/generate.py index e85661abb1..0d8630c88b 100644 --- a/examples/PACKAGES/cgdna/util/generate.py +++ b/examples/PACKAGES/cgdna/util/generate.py @@ -1,4 +1,3 @@ -#!/usr/bin/env python """ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator @@ -16,16 +15,23 @@ /* ---------------------------------------------------------------------- Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -""" +Program: generate.py -""" -Import basic modules +Generates a simple initial ssDNA or dsDNA configuration from a given sequence. +For dsDNA the sequence should be preceded by the 'DOUBLE' keyword. + +Usage: +$$ python generate.py box_offset box_length sequence_file """ # for python2/3 compatibility from __future__ import print_function +#!/usr/bin/env python +""" +Import basic modules +""" import sys, os, timeit from timeit import default_timer as timer diff --git a/examples/PACKAGES/cgdna/util/lj2real.py b/examples/PACKAGES/cgdna/util/lj2real.py new file mode 100644 index 0000000000..69076e9b01 --- /dev/null +++ b/examples/PACKAGES/cgdna/util/lj2real.py @@ -0,0 +1,604 @@ +""" +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Kierran Falloon (University of Strathclyde, Glasgow) + Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +Program: + +Usage: +$$ python lj2real.py [-i] +$$ [-i] flag is optional and is used to convert real -> LJ units. + +Requirements: +LAMMPS data file and input file. + +This script assumes a input and data file structure similar to those found in examples/PACKAGES/cgdna/examples/. +""" + +import datetime +import os +import sys + + +class Sections: + """Sections of the data file""" + + def __init__( + self, + bounds: bool, + masses: bool, + atoms: bool, + velocities: bool, + ellipsoids: bool, + ): + self.bounds = bounds # xlo, xhi, ylo, yhi, zlo, zhi + self.masses = masses # Masses + self.atoms = atoms # Atoms + self.velocities = velocities # Velocities + self.ellipsoids = ellipsoids # Ellipsoids + + +# Conversion factors +class ConversionFactors: + """Conversion factors for LJ to real units""" + + def __init__(self, invert: bool = False): + self.inverted = False + self.temp_conv_factor = 3000.038822 + self.energy_conv_factor = 5.961689060210325 + self.kT_conv_factor = 0.001987204155 + self.mass_conv_factor = 100.0277580236 + self.length_conv_factor = 8.518 + self.time_conv_factor = 1706.0 + self.vel_conv_factor = 0.004992966002344666 + self.angular_mom_conv_factor = 4.254188991883894 + self.density_conv_factor = 0.2687551067436886 + + self.oxdna_fene_string = "11.92337812042065 2.1295 6.409795" + self.oxdna_excv_string = "11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576" + self.oxdna_stk_string = "0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65" + self.oxdna_hbond_string = "0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + self.oxdna_hbond_1_4_2_3_string = "6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + self.oxdna_xstk_string = "3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68" + self.oxdna_coaxstk_string = "3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65" + + self.oxdna2_fene_string = "11.92337812042065 2.1295 6.4430152" + self.oxdna2_excv_string = "11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576" + self.oxdna2_stk_string = "0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65" + self.oxdna2_hbond_string = "0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + self.oxdna2_hbond_1_4_2_3_string = "6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + self.oxdna2_xstk_string = "3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68" + self.oxdna2_coaxstk_string = "4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793" + + self.oxrna2_fene_string = "11.92337812042065 2.1295 6.482800913" + self.oxrna2_excv_string = "11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576" + self.oxrna2_stk_string = "0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65" + self.oxrna2_hbond_string = "0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxrna2_hbond_1_4_2_3_3_4_string = "5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxrna2_xstk_string = "4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68" + self.oxrna2_coaxstk_string = "6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65" + + if invert: + self.invert() + + def invert(self): + """Inverts the conversion factors for real -> LJ""" + self.inverted = True + self.temp_conv_factor = 1.0 / self.temp_conv_factor + self.energy_conv_factor = 1.0 / self.energy_conv_factor + self.kT_conv_factor = 1.0 / self.kT_conv_factor + self.mass_conv_factor = 1.0 / self.mass_conv_factor + self.length_conv_factor = 1.0 / self.length_conv_factor + self.time_conv_factor = 1.0 / self.time_conv_factor + self.vel_conv_factor = 1.0 / self.vel_conv_factor + self.angular_mom_conv_factor = 1.0 / self.angular_mom_conv_factor + self.density_conv_factor = 1.0 / self.density_conv_factor + + self.oxdna_fene_string = "2.0 0.25 0.7525" + self.oxdna_excv_string = "2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32" + self.oxdna_stk_string = ( + "6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65" + ) + self.oxdna_hbond_string = "0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxdna_hbond_1_4_2_3_string = "1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxdna_xstk_string = "47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68" + self.oxdna_coaxstk_string = "46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65" + + self.oxdna2_fene_string = "2.0 0.25 0.7564" + self.oxdna2_excv_string = "2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32" + self.oxdna2_stk_string = ( + "6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65" + ) + self.oxdna2_hbond_string = "0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxdna2_hbond_1_4_2_3_string = "1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxdna2_xstk_string = "47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68" + self.oxdna2_coaxstk_string = "58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793" + + self.oxrna2_fene_string = "2.0 0.25 0.761070781051" + self.oxrna2_excv_string = "2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32" + self.oxrna2_stk_string = "6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65" + self.oxrna2_hbond_string = "0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxrna2_hbond_1_4_2_3_3_4_string = "0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + self.oxrna2_xstk_string = "59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68" + self.oxrna2_coaxstk_string = "80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65" + + +def check_datafile_header(line: str, sections: Sections): + """Checks for headers to modify corresponding data, since datafile is split into headers. + Modifies the Sections object to keep track of the current section. + + Args: + line (str): The line to check + masses_section (bool): If the current section is the masses section + atoms_section (bool): If the current section is the atoms section + velocities_section (bool): If the current section is the velocities section + ellipsoids_section (bool): If the current section is the ellipsoids section + """ + + if any(header in line for header in ["xlo", "xhi", "ylo", "yhi", "zlo", "zhi"]): + sections.bounds = True + sections.masses = False + sections.atoms = False + sections.velocities = False + sections.ellipsoids = False + elif "Masses" in line: + sections.bounds = False + sections.masses = True + sections.atoms = False + sections.velocities = False + sections.ellipsoids = False + elif "Atoms" in line: + sections.bounds = False + sections.masses = False + sections.atoms = True + sections.velocities = False + sections.ellipsoids = False + elif "Velocities" in line: + sections.bounds = False + sections.masses = False + sections.atoms = False + sections.velocities = True + sections.ellipsoids = False + elif "Ellipsoids" in line: + sections.bounds = False + sections.masses = False + sections.atoms = False + sections.velocities = False + sections.ellipsoids = True + elif "Bonds" in line: + sections.bounds = False + sections.masses = False + sections.atoms = False + sections.velocities = False + sections.ellipsoids = False + + +def modify_datafile(datafile_path: str, conversion_factors: ConversionFactors): + """Modifies the file by header to use real units. + + Args: + datafile_path (str): The path to the file to modify + """ + lines_changed = 0 + current_section = Sections(False, False, False, False, False) + + with open(datafile_path, "r", encoding="UTF-8") as file: + lines = file.readlines() + if conversion_factors.inverted: + lines[0] = ( + "LAMMPS data file in LJ units via oxdna lj2real.py, date " + + str(datetime.date.today()) + + "\n" + ) + else: + lines[0] = ( + "LAMMPS data file in real units via oxdna lj2real.py, date " + + str(datetime.date.today()) + + "\n" + ) + + for i, line in enumerate(lines): + check_datafile_header(line, current_section) # check for headers + + elements = line.split() + if ( + not elements + or elements[0] == "#" + or any( + header in line + for header in ["Masses", "Atoms", "Velocities", "Ellipsoids", "Bonds"] + ) + ): + continue + + # modify the line based on the current section it is in + if current_section.bounds: + elements[0:2] = [ + str(int(float(x) * conversion_factors.length_conv_factor)) + for x in elements[0:2] + ] + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + if current_section.masses: + elements[1] = str( + round(float(elements[1]) * conversion_factors.mass_conv_factor, 4) + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + elif current_section.atoms: + elements[2:5] = [ + str(float(x) * conversion_factors.length_conv_factor) + for x in elements[2:5] + ] + elements[7] = str( + float(elements[7]) * conversion_factors.density_conv_factor + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + elif current_section.velocities: + elements[1:4] = [ + str(float(x) * conversion_factors.vel_conv_factor) + for x in elements[1:4] + ] + elements[4:7] = [ + str(float(x) * conversion_factors.angular_mom_conv_factor) + for x in elements[4:7] + ] + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + elif current_section.ellipsoids: + elements[1:4] = [ + str(float(x) * conversion_factors.length_conv_factor) + for x in elements[1:4] + ] + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + if conversion_factors.inverted: + new_datafile_path = datafile_path + "_lj" + else: + new_datafile_path = datafile_path + "_real" + + with open(new_datafile_path, "w", encoding="UTF-8") as file: + file.writelines(lines) + if lines_changed == 0: + print( + "Warning: No lines changed in data file. Ensure correct usage: python lj2real.py [-i]" + ) + else: + print(f"Data file lines changed: {lines_changed}") + + return new_datafile_path + + +def modify_inputfile(inputfile_path: str, conversion_factors: ConversionFactors): + """Modifies the input file line by line to use real units. + + Args: + inputfile_path (str): The path to the input file to modify + """ + + lines_changed = 0 + oxdna2_flag, oxrna2_flag = False, False + + with open(inputfile_path, "r", encoding="UTF-8") as file: + lines = file.readlines() + + for i, line in enumerate(lines): + if "oxdna2" in line and not oxdna2_flag: + oxdna2_flag = True + print("Note: oxdna2 found in input file. Using oxdna2 conversion factors.") + if "oxrna2" in line and not oxrna2_flag: + oxrna2_flag = True + print("Note: oxrna2 found in input file. Using oxrna2 conversion factors.") + if oxdna2_flag and oxrna2_flag: + print( + "Warning: Both oxdna2 and oxrna2 found in input file. Output will likely be incorrect." + ) + + if "variable T" in line: + old_value = line.split()[3] + + new_value = str( + round(float(old_value) * conversion_factors.temp_conv_factor, 1) + ) + lines[i] = line.replace(old_value, new_value) + lines_changed += 1 + + elif "units" in line: + if conversion_factors.inverted: + lines[i] = "units lj\n" + else: + lines[i] = "units real\n" + lines_changed += 1 + + elif "atom_modify" in line: + elements = line.split() + elements[3] = str( + round(float(elements[3]) * conversion_factors.length_conv_factor, 3) + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + elif "neighbor" in line: + elements = line.split() + elements[1] = str( + round(float(elements[1]) * conversion_factors.length_conv_factor, 3) + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + elif "read_data" in line: + elements = line.split() + if conversion_factors.inverted: + elements[1] = elements[1] + "_lj" + else: + elements[1] = ( + elements[1] + "_real" + ) # naming convention of datafile after conversion + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + elif "mass" in line: + elements = line.split() + elements[4] = str( + round(float(elements[4]) * conversion_factors.mass_conv_factor, 4) + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + elif "bond_coeff" in line or "pair_coeff" in line: + if ".lj" in line or ".real" in line: + if conversion_factors.inverted: + line = line.replace(".real", ".lj") + else: + line = line.replace(".lj", ".real") + lines[i] = line + lines_changed += 1 + + if "stk" in line and "xstk" not in line and "coaxstk" not in line: + elements = line.split() + elements[6] = str( # convert xi + round( + float(elements[6]) * conversion_factors.energy_conv_factor, + 14, + ) + ) + elements[7] = str( # convert kappa + round(float(elements[7]) * conversion_factors.kT_conv_factor, 9) + ) + lines[i] = " ".join(elements) + "\n" + + else: + elements = line.split() + + if "bond_coeff" in line: + if oxdna2_flag: + elements[2:] = conversion_factors.oxdna2_fene_string.split() + elif oxrna2_flag: + elements[2:] = conversion_factors.oxrna2_fene_string.split() + else: + elements[2:] = conversion_factors.oxdna_fene_string.split() + + elif "excv" in line: + if oxdna2_flag: + elements[4:] = conversion_factors.oxdna2_excv_string.split() + elif oxrna2_flag: + elements[4:] = conversion_factors.oxrna2_excv_string.split() + else: + elements[4:] = conversion_factors.oxdna_excv_string.split() + + elif "stk" in line: + + if "coaxstk" in line: + if oxdna2_flag: + elements[4:] = ( + conversion_factors.oxdna2_coaxstk_string.split() + ) + elif oxrna2_flag: + elements[4:] = ( + conversion_factors.oxrna2_coaxstk_string.split() + ) + else: + elements[4:] = ( + conversion_factors.oxdna_coaxstk_string.split() + ) + + elif "xstk" in line: + if oxdna2_flag: + elements[4:] = conversion_factors.oxdna2_xstk_string.split() + elif oxrna2_flag: + elements[4:] = conversion_factors.oxrna2_xstk_string.split() + else: + elements[4:] = conversion_factors.oxdna_xstk_string.split() + + else: # stk + elements[6] = str( # convert xi + round( + float(elements[6]) + * conversion_factors.energy_conv_factor, + 14, + ) + ) + elements[7] = str( # convert kappa + round( + float(elements[7]) * conversion_factors.kT_conv_factor, + 9, + ) + ) + if oxdna2_flag: + elements[8:] = conversion_factors.oxdna2_stk_string.split() + elif oxrna2_flag: + elements[8:] = conversion_factors.oxrna2_stk_string.split() + else: + elements[8:] = conversion_factors.oxdna_stk_string.split() + + elif "hbond" in line: + if elements[1] == "*" and elements[2] == "*": + if oxdna2_flag: + elements[5:] = ( + conversion_factors.oxdna2_hbond_string.split() + ) + elif oxrna2_flag: + elements[5:] = ( + conversion_factors.oxrna2_hbond_string.split() + ) + else: + elements[5:] = conversion_factors.oxdna_hbond_string.split() + else: + if oxdna2_flag: + elements[5:] = ( + conversion_factors.oxdna2_hbond_1_4_2_3_string.split() + ) + elif oxrna2_flag: + elements[5:] = ( + conversion_factors.oxrna2_hbond_1_4_2_3_3_4_string.split() + ) + else: + elements[5:] = ( + conversion_factors.oxdna_hbond_1_4_2_3_string.split() + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + elif "langevin" in line: + elements = line.split() + elements[6] = str( + round(float(elements[6]) * conversion_factors.time_conv_factor, 2) + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + elif "timestep" in line: + elements = line.split() + elements[1] = str( + round(float(elements[1]) * conversion_factors.time_conv_factor, 5) + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + elif "comm_modify" in line: + elements = line.split() + elements[2] = str( + round(float(elements[2]) * conversion_factors.length_conv_factor, 1) + ) + lines[i] = " ".join(elements) + "\n" + lines_changed += 1 + + else: + continue + + if conversion_factors.inverted: + new_inputfile_path = inputfile_path + "_lj" + else: + new_inputfile_path = inputfile_path + "_real" + + with open(new_inputfile_path, "w", encoding="UTF-8") as file: + if conversion_factors.inverted: + file.write( + "# LAMMPS input file in LJ units via oxdna lj2real.py, date " + + str(datetime.date.today()) + + "\n" + ) + else: + file.write( + "# LAMMPS input file in real units via oxdna lj2real.py, date " + + str(datetime.date.today()) + + "\n" + ) + file.writelines(lines) + if lines_changed == 0: + print( + "Warning: No lines changed in input file. Ensure correct usage: python lj2real.py [-i]" + ) + else: + print(f"Input file lines changed: {lines_changed}") + + return new_inputfile_path + + +def main(): + """Main function""" + + print( + "\nLAMMPS data and input file conversion to real units via oxdna convert_data.py\n" + "Note: This script assumes a input and data file structure similar to those found in examples/PACKAGES/cgdna/examples/.\n" + "Ensure output is checked for correctness." + ) + + if len(sys.argv) > 2: + datafile_path = sys.argv[1] + inputfile_path = sys.argv[2] + invert = False + if len(sys.argv) > 3: + if sys.argv[3] == "-i": + invert = True + print("Performing real -> LJ conversion.") + else: + print( + "Invalid flag. Usage: python lj2real.py [-i]" + ) + sys.exit(1) + + if invert: + conversion_factors = ConversionFactors(invert=True) + print( + "\nUsing conversion factors (real T, m, l, t, v, ρ -> LJ T*, m*, l*, t*, v*, ρ*):" + ) + + else: + conversion_factors = ConversionFactors(invert=False) + print( + "\nUsing conversion factors (LJ T*, m*, l*, t*, v*, ρ* -> real T, m, l, t, v, ρ):" + ) + + else: + print("\nUsage: python lj2real.py [-i]") + print("\t[-i] flag is optional and is used to convert real -> LJ units.\n") + sys.exit(1) + + conversion_factors_string = ( + f"Temperature T\t≈ {round(conversion_factors.temp_conv_factor, 6)} T* (K)\n" + f"Energy ε\t≈ {round(conversion_factors.energy_conv_factor, 6)} ε* (kcal/mol)\n" + f"Mass m\t\t≈ {round(conversion_factors.mass_conv_factor, 6)} m* (g/mol)\n" + f"Length l\t≈ {round(conversion_factors.length_conv_factor, 6)} l* (Å)\n" + f"Time t\t\t≈ {round(conversion_factors.time_conv_factor, 6)} t* (fs)\n" + f"Velocity v\t≈ {round(conversion_factors.vel_conv_factor, 6)} v* (Å/fs)\n" + f"AngMom l\t≈ {round(conversion_factors.angular_mom_conv_factor, 6)} (g/mol Å^2/fs)\n" + f"Density ρ\t≈ {round(conversion_factors.density_conv_factor, 6)} ρ* (g/cm^3)\n" + f"Calculated using Sengar, Ouldridge, Henrich, Rovigatti, & Šulc. Front Mol Biosci 8 (2021). & https://docs.lammps.org/units.html.\n" + f"See examples/PACKAGES/cgdna/util/lj2real.py for exact conversion factors.\n" + ) + print(conversion_factors_string) + + print("Current directory: ", os.getcwd()) + + try: + new_datafile_path = modify_datafile(datafile_path, conversion_factors) + print(f"New data file: {new_datafile_path}") + except Exception as e: + print(f"Error modifying data file: {e}") + + try: + new_inputfile_path = modify_inputfile(inputfile_path, conversion_factors) + print(f"New input file: {new_inputfile_path}\n") + except Exception as e: + print(f"Error modifying input file: {e}") + + +if __name__ == "__main__": + main() diff --git a/examples/PACKAGES/cgdna/util/lmp2vis.py b/examples/PACKAGES/cgdna/util/lmp2vis.py new file mode 100644 index 0000000000..9f55910d6f --- /dev/null +++ b/examples/PACKAGES/cgdna/util/lmp2vis.py @@ -0,0 +1,209 @@ +""" +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +Program: lmp2vis.py + +Produces a simple representation of the oxDNA nucleotide with separate +particles for backbone and base interaction site. The base particle inherits +the atom type, whereas the backbone particle acquires an offset of 10. This +can be changed below. + +Usage: +$$ python lmp2vis.py [visualisation (vmd OR ovito, default=ovito)] input_filename output_filename + +Requirements: +The LAMMPS trajectory input file needs to contain the following data columns: +id mol type x y z vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] +""" + +# for python2/3 compatibility +from __future__ import print_function +#!/usr/bin/env python + +""" +Import basic modules +""" +import sys, math, subprocess + +# converts quaternion DOF into local body reference frame +def q_to_exyz(q1,q2,q3,q4): + + q = [q1, q2, q3, q4] + ex = [0, 0, 0] + ey = [0, 0, 0] + ez = [0, 0, 0] + + ex[0]=q[0]*q[0]+q[1]*q[1]-q[2]*q[2]-q[3]*q[3] + ex[1]=2*(q[1]*q[2]+q[0]*q[3]) + ex[2]=2*(q[1]*q[3]-q[0]*q[2]) + + ey[0]=2*(q[1]*q[2]-q[0]*q[3]) + ey[1]=q[0]*q[0]-q[1]*q[1]+q[2]*q[2]-q[3]*q[3] + ey[2]=2*(q[2]*q[3]+q[0]*q[1]) + + ez[0]=2*(q[1]*q[3]+q[0]*q[2]) + ez[1]=2*(q[2]*q[3]-q[0]*q[1]) + ez[2]=q[0]*q[0]-q[1]*q[1]-q[2]*q[2]+q[3]*q[3] + + return ex,ey,ez + +# processes line by line of LAMMPS trajectory +def transform(line, colind): + + list1 = line.split() + ident, mol, typ = int(list1[colind[0]]), int(list1[colind[1]]), int(list1[colind[2]]) + typb = typ + 10 # defines new backbone types, here offset is 10 from atom (base) type + x, y, z = float(list1[colind[3]]), float(list1[colind[4]]), float(list1[colind[5]]) + vx, vy, vz = float(list1[colind[6]]), float(list1[colind[7]]), float(list1[colind[8]]) + c_quat1, c_quat2, c_quat3, c_quat4 = \ + float(list1[colind[9]]), float(list1[colind[10]]), float(list1[colind[11]]), float(list1[colind[12]]) + + ex, ey, ez = q_to_exyz(c_quat1, c_quat2, c_quat3, c_quat4) + + # position of sugar-phosphate backbone interaction site in oxDNA2 + x1, y1, z1 = x -0.34*ex[0]+0.3408*ey[0],y -0.34*ex[1]+0.3408*ey[1], z-0.34*ex[2]+0.3408*ey[2] + + # position of base interaction site in oxDNA/oxDNA2 + x2, y2, z2 = x +0.4*ex[0], y + 0.4*ex[1], z+0.4*ex[2] + + # compose basic output data: id, molecule id, type, position, velocity quaternion + line1 = '%d'%(2*ident-1) +' '+ '%d'%mol +' '+ '%d'%typb +' '+\ + '%13.6e'%(x1) +' '+ '%13.6e'%(y1) +' '+ '%13.6e'%(z1) +' '+\ + '%13.6e'%(vx) +' '+ '%13.6e'%(vy) +' '+ '%13.6e'%(vz) +' '+\ + '%13.6e'%(c_quat1) +' '+ '%13.6e'%(c_quat2) +' '+ '%13.6e'%(c_quat3) +' '+ '%13.6e'%(c_quat4) + + line2 = '%d'%(2*ident) +' '+ '%d'%mol +' '+ '%d'%typ +' '+\ + '%13.6e'%(x2) +' '+ '%13.6e'%(y2) +' '+ '%13.6e'%(z2) +' '+\ + '%13.6e'%(vx) +' '+ '%13.6e'%(vy) +' '+ '%13.6e'%(vz) +' '+\ + '%13.6e'%(c_quat1) +' '+ '%13.6e'%(c_quat2) +' '+' %13.6e'%(c_quat3) +' '+ '%13.6e'%(c_quat4) + + # use oblate particles for bases in ovito + shape_sphere = ' 0.4 0.4 0.4' + shape_ellipsoid = ' 0.5 0.2 0.1' + if vismethod == 'ovito': + line1 += shape_sphere +' ' + line2 += shape_ellipsoid +' ' + + line1 += '\n' + line2 += '\n' + + line = line1 + line2 + return line + +### main part ### + +# digest command line input +if len(sys.argv)<3: + print("Syntax: $$ python lmp2vis.py [visualisation (vmd OR ovito, default=ovito)] input_filename output_filename") + sys.exit(1) + +if len(sys.argv)==3: + vismethod = 'ovito' # default visualisation method + infilename = sys.argv[1] + outfilename = sys.argv[2] + +if len(sys.argv)==4: + vismethod = sys.argv[1] + if (sys.argv[1]!='vmd' and sys.argv[1]!='ovito'): + vismethod = 'ovito' # default visualisation method + infilename = sys.argv[2] + outfilename = sys.argv[3] + +print('# Converting LAMMPS output for visualisation with %s' % vismethod) + +# count lines to process for progress report +n = 0 +try: + result = subprocess.run(['wc', '-l', '%s'%infilename], stdout=subprocess.PIPE) + reslist=str(result).split() + nlines=float(reslist[5]) +except: + nlines = 100 + +r=open(infilename,'r') +w=open(outfilename,'w+') + +pass1 = 0 + +for line in r: + + sys.stdout.write('# Processed %3d %%\r' % (100*n/nlines)) + + # find number of atoms in timestep + if line.find('ITEM: NUMBER OF ATOMS') != -1: + w.write(line) + N=int(r.readline()) + # write to output file and read next line + w.write('%d'%int(2*N)+'\n') + line=r.readline() + n+=2 + + # find beginning of atom data section + if line.find('ITEM: ATOMS') != -1: + # first pass: extract column number of ID, molecule ID, type, postion, velocity, quaternion in header line + if pass1 == 0: + linestring=line.split() + idindex = linestring.index('id') + molindex = linestring.index('mol') + typeindex = linestring.index('type') + xindex = linestring.index('x') + yindex = linestring.index('y') + zindex = linestring.index('z') + vxindex = linestring.index('vx') + vyindex = linestring.index('vy') + vzindex = linestring.index('vz') + qwindex = linestring.index('c_quat[1]') + qxindex = linestring.index('c_quat[2]') + qyindex = linestring.index('c_quat[3]') + qzindex = linestring.index('c_quat[4]') + + # create header + header = linestring[0] + ' ' + linestring[1] + ' ' + \ + linestring[idindex] + ' ' + linestring[molindex]+ ' ' + linestring[typeindex]+ ' ' + \ + linestring[xindex]+ ' ' + linestring[yindex]+ ' ' + linestring[zindex]+ ' ' + \ + linestring[vxindex]+ ' ' + linestring[vyindex]+ ' ' + linestring[vzindex]+ ' ' + \ + linestring[qwindex]+ ' ' + linestring[qxindex]+ ' ' + linestring[qyindex]+ ' ' + linestring[qzindex] + + # extend header for ovito + if vismethod == 'ovito': + header += ' shape[0] shape[1] shape[2]' + header += '\n' + + # store column number in data line, -2 offset form header line + colind = [idindex-2,molindex-2,typeindex-2,xindex-2,yindex-2,zindex-2,\ + vxindex-2,vyindex-2,vzindex-2,qwindex-2,qxindex-2,qyindex-2,qzindex-2] + pass1 = 1 + + # begin processing atom data in timestep + w.write(header) + # tranform each atom and write to output file + for i in range(N): + line=r.readline() + w.write(transform(line,colind)) + n+=1 + # end processing atom data + + # duplicate all lines that are not in any other section + else: + w.write(line) + n+=1 + +print('# Done ') + +r.close() +w.close() diff --git a/examples/PACKAGES/cgdna/util/nbps.py b/examples/PACKAGES/cgdna/util/nbps.py new file mode 100644 index 0000000000..a067dca1ba --- /dev/null +++ b/examples/PACKAGES/cgdna/util/nbps.py @@ -0,0 +1,167 @@ +""" +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +Program: nbps.py + +Calculates the number of base pairs based on proximity of hydrogen bonding +interaction sites in oxDNA2. + +Usage: +$$ python nbps.py input_filename output_filename + +Requirements: +The LAMMPS trajectory input file needs to contain the following data columns: +id mol type x y z c_quat[1] c_quat[2] c_quat[3] c_quat[4] +""" + +# for python2/3 compatibility +from __future__ import print_function +#!/usr/bin/env python + +import sys, math, subprocess + +# converts quaternion DOF into local body reference frame +def q_to_exyz(q1,q2,q3,q4): + + q = [q1, q2, q3, q4] + ex = [0, 0, 0] + ey = [0, 0, 0] + ez = [0, 0, 0] + + ex[0]=q[0]*q[0]+q[1]*q[1]-q[2]*q[2]-q[3]*q[3] + ex[1]=2*(q[1]*q[2]+q[0]*q[3]) + ex[2]=2*(q[1]*q[3]-q[0]*q[2]) + + ey[0]=2*(q[1]*q[2]-q[0]*q[3]) + ey[1]=q[0]*q[0]-q[1]*q[1]+q[2]*q[2]-q[3]*q[3] + ey[2]=2*(q[2]*q[3]+q[0]*q[1]) + + ez[0]=2*(q[1]*q[3]+q[0]*q[2]) + ez[1]=2*(q[2]*q[3]-q[0]*q[1]) + ez[2]=q[0]*q[0]-q[1]*q[1]-q[2]*q[2]+q[3]*q[3] + + return ex,ey,ez + +# processes line by line of LAMMPS trajectory +def transform(line, colind): + + list1 = line.split() + ident, mol, typ = int(list1[colind[0]]), int(list1[colind[1]]), int(list1[colind[2]]) + x, y, z = float(list1[colind[3]]), float(list1[colind[4]]), float(list1[colind[5]]) + c_quat1, c_quat2, c_quat3, c_quat4 = \ + float(list1[colind[6]]), float(list1[colind[7]]), float(list1[colind[8]]), float(list1[colind[9]]) + + ex, ey, ez = q_to_exyz(c_quat1, c_quat2, c_quat3, c_quat4) + + # position of base interaction site in oxDNA/oxDNA2 + x2, y2, z2 = x +0.4*ex[0], y + 0.4*ex[1], z+0.4*ex[2] + + # compose basic output data: id, molecule id, type, position + line2 = [ident, mol, typ, x2, y2, z2] + + return line2 + +### main part ### + +# digest command line input +if len(sys.argv)<3: + print("Syntax: $$ python nbps.py input_filename output_filename") + sys.exit(1) + +if len(sys.argv)==3: + infilename = sys.argv[1] + outfilename = sys.argv[2] + +print('# Calculating number of base pairs from LAMMPS trajectory output') + +# count lines to process for progress report +n = 0 +try: + result = subprocess.run(['wc', '-l', '%s'%infilename], stdout=subprocess.PIPE) + reslist=str(result).split() + nlines=float(reslist[5]) +except: + nlines = 100 + +r=open(infilename,'r') +w=open(outfilename,'w+') + +pass1 = 0 + +for line in r: + + sys.stdout.write('# Processed %3d %%\r' % (100*n/nlines)) + + # find timestep number + if line.find('ITEM: TIMESTEP') != -1: + t=int(r.readline()) + n+=1 + + # find number of atoms in timestep + if line.find('ITEM: NUMBER OF ATOMS') != -1: + N=int(r.readline()) + n+=1 + + # find beginning of atom data section + if line.find('ITEM: ATOMS') != -1: + # first pass: extract column number of ID, molecule ID, type, postion, velocity, quaternion in header line + if pass1 == 0: + linestring=line.split() + idindex = linestring.index('id') + molindex = linestring.index('mol') + typeindex = linestring.index('type') + xindex = linestring.index('x') + yindex = linestring.index('y') + zindex = linestring.index('z') + qwindex = linestring.index('c_quat[1]') + qxindex = linestring.index('c_quat[2]') + qyindex = linestring.index('c_quat[3]') + qzindex = linestring.index('c_quat[4]') + + # store column number in data line, -2 offset form header line + colind = [idindex-2,molindex-2,typeindex-2,xindex-2,yindex-2,zindex-2,\ + qwindex-2,qxindex-2,qyindex-2,qzindex-2] + pass1 = 1 + + # begin processing atom data + atom = [] + for i in range(N): + line=r.readline() + atom.append(transform(line,colind)) + n +=1 + + rc2 = 0.2 + nbp = 0 + for i in range(N): + for j in range(i+1,N): + if (atom[i][2]+atom[j][2])%4 and atom[i][1]!=atom[j][1]: + r2 = (atom[i][3]-atom[j][3])*(atom[i][3]-atom[j][3]) +\ + (atom[i][4]-atom[j][4])*(atom[i][4]-atom[j][4]) +\ + (atom[i][5]-atom[j][5])*(atom[i][5]-atom[j][5]) + if r2=2.5) version of Python and Numpy, +You should have a relatively recent (>=3.5) version of Python and Numpy, and the public version of i-PI. You can then run i-PI by executing ```bash @@ -33,7 +33,7 @@ and the public version of i-PI. You can then run i-PI by executing ``` In a separate terminal, then, you should run LAMMPS compiled to provide -fix_ipi functionalities. +`fix_ipi` functionalities. ```bash $LAMMPS -in in.graphene @@ -41,6 +41,3 @@ fix_ipi functionalities. You can run multiple instances of LAMMPS if you want to exploit the parallelism over the path integral beads. - - - diff --git a/examples/PACKAGES/ipi/i-pi_input.xml b/examples/PACKAGES/ipi/i-pi_input.xml index 310c909338..7cbf559322 100644 --- a/examples/PACKAGES/ipi/i-pi_input.xml +++ b/examples/PACKAGES/ipi/i-pi_input.xml @@ -1,31 +1,37 @@ - - - i-pi_positions.xyz - [ 51.8,0,0,0, 49.84,0,0,0, 200 ] - 300 - - - [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] + + + [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] [ isotope_tdfep(1.167;C), isotope_scfep(1.167;0) ] - positions{angstrom} - - - 1000 - 128000 - 8417 - - -
graphene
- - - - - - [ 1.124524713863e-3, 1.648702679619e-6, 6.970075857471e-5, -2.202066291263e-4, 1.401342873485e-3, -1.681700567912e-6, 5.197673899653e-10, 4.365423872046e-6, -1.200041116490e-6, 2.564577183580e-6, -8.965478630849e-5, -4.365423872046e-6, 8.218704940997e-6, 3.114246791997e-5, -6.044142906315e-5, -6.272281358913e-5, 1.200041116490e-6, -3.114246791997e-5, 1.612301941566e-4, 6.958958085115e-5, 1.318373360752e-3, -2.564577183580e-6, 6.044142906315e-5, -6.958958085115e-5, 1.872119364197e-3] - - - 1.0 - 300 - True - + [ kinetic_cv{kelvin}(C) ] + positions{angstrom} + kinetic_cv + + + 1000000 + + 31415 + + +
graphene
+ + + + i-pi_positions.xyz + 300 + + + + + + + 1.0 + + 100 + + + + + 300 + + diff --git a/examples/PACKAGES/pedone/in.pedone.melt b/examples/PACKAGES/pedone/in.pedone.melt new file mode 100644 index 0000000000..a2b1c3a71e --- /dev/null +++ b/examples/PACKAGES/pedone/in.pedone.melt @@ -0,0 +1,38 @@ +# Ca-O melt with Pedone potential + +units metal +atom_style charge + +lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations + +region box block 0 4 0 4 0 4 +create_box 2 box +create_atoms 1 box + +lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell +create_atoms 2 box + +mass 1 40.078 +mass 2 15.999 + +set type 1 charge 1.2 +set type 2 charge -1.2 + +timestep 0.002 +neigh_modify delay 5 every 1 check yes + +pair_style hybrid/overlay pedone 15.0 coul/long 15.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 +pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + +velocity all create 6000.0 98347 + +fix 1 all nvt temp 3000.0 3000.0 0.1 + +# dump 1 all atom 500 Ca-O-melt.lammpstrj + +thermo 100 +run 1000 diff --git a/examples/PACKAGES/pedone/in.pedone.relax b/examples/PACKAGES/pedone/in.pedone.relax new file mode 100644 index 0000000000..38ccd651e7 --- /dev/null +++ b/examples/PACKAGES/pedone/in.pedone.relax @@ -0,0 +1,38 @@ +# Ca-O crystal with Pedone potential + +units metal +atom_style charge + +lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations + +region box block 0 4 0 4 0 4 +create_box 2 box +create_atoms 1 box + +lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell +create_atoms 2 box + +mass 1 40.078 +mass 2 15.999 + +displace_atoms all random 0.01 0.01 0.01 9084544 +set type 1 charge 1.2 +set type 2 charge -1.2 + +timestep 0.002 +neigh_modify delay 5 every 1 check yes + +pair_style hybrid/overlay pedone 15.0 coul/long 15.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 +pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + +variable len equal lx*0.25 +thermo_style custom step v_len lx pe press +thermo 100 +fix 1 all box/relax iso 0.0 +minimize 0.0 0.0 1000 10000 + +print "Expected lattice parameter: 4.7748, computed: $(v_len:%6.4f)" diff --git a/examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.1 b/examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.1 new file mode 100644 index 0000000000..dc33289391 --- /dev/null +++ b/examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.1 @@ -0,0 +1,122 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd) + using 1 OpenMP thread(s) per MPI task +# Ca-O melt with Pedone potential + +units metal +atom_style charge + +lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 + +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (19.242 19.242 19.242) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 +create_atoms 2 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +mass 1 40.078 +mass 2 15.999 + +set type 1 charge 1.2 +Setting atom values ... + 256 settings made for charge +set type 2 charge -1.2 +Setting atom values ... + 256 settings made for charge + +timestep 0.002 +neigh_modify delay 5 every 1 check yes + +pair_style hybrid/overlay pedone 15.0 coul/long 15.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 +pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + +velocity all create 6000.0 98347 + +fix 1 all nvt temp 3000.0 3000.0 0.1 + +# dump 1 all atom 500 Ca-O-melt.lammpstrj + +thermo 100 +run 1000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.23676226 + grid = 24 24 24 + stencil order = 5 + estimated absolute RMS force accuracy = 1.3089053e-05 + estimated relative force accuracy = 9.089844e-07 + using double precision FFTW3 + 3d grid and FFT values/proc = 29791 13824 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17 + ghost atom cutoff = 17 + binsize = 8.5, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair pedone, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.239 | 9.239 | 9.239 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 6000 -3771.5568 0 -3375.2452 34213.185 + 100 2894.1756 -3562.491 0 -3371.3251 114640.32 + 200 2980.3531 -3570.2657 0 -3373.4076 123673.56 + 300 2783.0437 -3574.5809 0 -3390.7554 119791.27 + 400 3021.6581 -3568.2149 0 -3368.6285 116032.29 + 500 3112.0438 -3580.0178 0 -3374.4613 114798.18 + 600 2973.4609 -3577.0582 0 -3380.6553 111843.46 + 700 3180.1687 -3568.4542 0 -3358.3979 121008.83 + 800 2923.7803 -3573.3023 0 -3380.181 111459.55 + 900 2940.3133 -3572.1322 0 -3377.9188 118177.36 + 1000 3070.2584 -3575.5655 0 -3372.769 114175.52 +Loop time of 13.683 on 1 procs for 1000 steps with 512 atoms + +Performance: 12.629 ns/day, 1.900 hours/ns, 73.084 timesteps/s, 37.419 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.545 | 11.545 | 11.545 | 0.0 | 84.37 +Kspace | 1.4121 | 1.4121 | 1.4121 | 0.0 | 10.32 +Neigh | 0.65265 | 0.65265 | 0.65265 | 0.0 | 4.77 +Comm | 0.056036 | 0.056036 | 0.056036 | 0.0 | 0.41 +Output | 0.00022945 | 0.00022945 | 0.00022945 | 0.0 | 0.00 +Modify | 0.0090252 | 0.0090252 | 0.0090252 | 0.0 | 0.07 +Other | | 0.00801 | | | 0.06 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10901 ave 10901 max 10901 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 374419 ave 374419 max 374419 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 374419 +Ave neighs/atom = 731.28711 +Neighbor list builds = 71 +Dangerous builds = 0 +Total wall time: 0:00:13 diff --git a/examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.4 b/examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.4 new file mode 100644 index 0000000000..693b8b3050 --- /dev/null +++ b/examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.4 @@ -0,0 +1,122 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd) + using 1 OpenMP thread(s) per MPI task +# Ca-O melt with Pedone potential + +units metal +atom_style charge + +lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 + +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (19.242 19.242 19.242) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 +create_atoms 2 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +mass 1 40.078 +mass 2 15.999 + +set type 1 charge 1.2 +Setting atom values ... + 256 settings made for charge +set type 2 charge -1.2 +Setting atom values ... + 256 settings made for charge + +timestep 0.002 +neigh_modify delay 5 every 1 check yes + +pair_style hybrid/overlay pedone 15.0 coul/long 15.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 +pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + +velocity all create 6000.0 98347 + +fix 1 all nvt temp 3000.0 3000.0 0.1 + +# dump 1 all atom 500 Ca-O-melt.lammpstrj + +thermo 100 +run 1000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.23676226 + grid = 24 24 24 + stencil order = 5 + estimated absolute RMS force accuracy = 1.3089053e-05 + estimated relative force accuracy = 9.089844e-07 + using double precision FFTW3 + 3d grid and FFT values/proc = 11191 3456 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17 + ghost atom cutoff = 17 + binsize = 8.5, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair pedone, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.315 | 5.315 | 5.315 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 6000 -3771.5568 0 -3375.2452 34213.185 + 100 3050.0106 -3571.4712 0 -3370.0121 118480.04 + 200 3100.0073 -3571.2534 0 -3366.492 120618.37 + 300 2959.7127 -3580.0883 0 -3384.5935 109184.72 + 400 2922.7083 -3563.9803 0 -3370.9298 120165.71 + 500 3145.0439 -3571.3828 0 -3363.6465 115057.51 + 600 2741.7439 -3563.5077 0 -3382.4102 115504.31 + 700 2906.3636 -3567.3604 0 -3375.3895 119518.5 + 800 2995.3864 -3567.3838 0 -3369.5327 117975.22 + 900 2965.24 -3565.7983 0 -3369.9385 123362.35 + 1000 2916.6485 -3578.7471 0 -3386.0968 115624.78 +Loop time of 4.50395 on 4 procs for 1000 steps with 512 atoms + +Performance: 38.366 ns/day, 0.626 hours/ns, 222.028 timesteps/s, 113.678 katom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.2703 | 3.2983 | 3.3259 | 1.3 | 73.23 +Kspace | 0.79815 | 0.82633 | 0.85342 | 2.6 | 18.35 +Neigh | 0.18328 | 0.18398 | 0.18472 | 0.1 | 4.08 +Comm | 0.17423 | 0.17508 | 0.17592 | 0.2 | 3.89 +Output | 0.00019336 | 0.0002167 | 0.00028554 | 0.0 | 0.00 +Modify | 0.0089842 | 0.0091093 | 0.0092205 | 0.1 | 0.20 +Other | | 0.01096 | | | 0.24 + +Nlocal: 128 ave 143 max 118 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 7622.75 ave 7651 max 7598 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 93581.8 ave 106456 max 84898 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 374327 +Ave neighs/atom = 731.10742 +Neighbor list builds = 71 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.1 b/examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.1 new file mode 100644 index 0000000000..bf58a8da9b --- /dev/null +++ b/examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.1 @@ -0,0 +1,134 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd) + using 1 OpenMP thread(s) per MPI task +# Ca-O crystal with Pedone potential + +units metal +atom_style charge + +lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 + +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (19.242 19.242 19.242) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 +create_atoms 2 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +mass 1 40.078 +mass 2 15.999 + +displace_atoms all random 0.01 0.01 0.01 9084544 +Displacing atoms ... +set type 1 charge 1.2 +Setting atom values ... + 256 settings made for charge +set type 2 charge -1.2 +Setting atom values ... + 256 settings made for charge + +timestep 0.002 +neigh_modify delay 5 every 1 check yes + +pair_style hybrid/overlay pedone 15.0 coul/long 15.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 +pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + +variable len equal lx*0.25 +thermo_style custom step v_len lx pe press +thermo 100 +fix 1 all box/relax iso 0.0 +minimize 0.0 0.0 1000 10000 +Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.23676226 + grid = 24 24 24 + stencil order = 5 + estimated absolute RMS force accuracy = 1.3089053e-05 + estimated relative force accuracy = 9.089844e-07 + using double precision FFTW3 + 3d grid and FFT values/proc = 29791 13824 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17 + ghost atom cutoff = 17 + binsize = 8.5, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair pedone, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies + (src/min.cpp:219) +Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.33 Mbytes + Step v_len Lx PotEng Press + 0 4.8105 19.242 -3765.9116 -21299.914 + 100 4.7797128 19.118851 -3767.814 -164.13101 + 200 4.7787507 19.115003 -3769.1366 -373.58797 + 300 4.7768265 19.107306 -3770.5634 48.944709 + 400 4.7768265 19.107306 -3770.9879 -258.56116 + 500 4.7758644 19.103458 -3771.3898 173.91894 + 600 4.7758644 19.103458 -3771.7586 -91.813678 + 700 4.7758644 19.103458 -3771.9842 -252.52883 + 800 4.7749023 19.099609 -3772.3526 216.83318 + 857 4.7747927 19.099171 -3772.8223 32.586251 +Loop time of 18.0592 on 1 procs for 857 steps with 512 atoms + +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -3765.91161156884 -3772.82226663623 -3772.82226663623 + Force two-norm initial, final = 284.3967 0.46963871 + Force max component initial, final = 284.14458 0.42827677 + Final line search alpha, max atom move = 2.8580337e-08 1.2240294e-08 + Iterations, force evaluations = 857 894 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.907 | 13.907 | 13.907 | 0.0 | 77.01 +Kspace | 1.3809 | 1.3809 | 1.3809 | 0.0 | 7.65 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.045871 | 0.045871 | 0.045871 | 0.0 | 0.25 +Output | 0.0002809 | 0.0002809 | 0.0002809 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.726 | | | 15.09 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11655 ave 11655 max 11655 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 372155 ave 372155 max 372155 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 372155 +Ave neighs/atom = 726.86523 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "Expected lattice parameter: 4.7748, computed: $(v_len:%6.4f)" +Expected lattice parameter: 4.7748, computed: 4.7748 +Total wall time: 0:00:18 diff --git a/examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.4 b/examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.4 new file mode 100644 index 0000000000..95a84f81e0 --- /dev/null +++ b/examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.4 @@ -0,0 +1,134 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd) + using 1 OpenMP thread(s) per MPI task +# Ca-O crystal with Pedone potential + +units metal +atom_style charge + +lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 + +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (19.242 19.242 19.242) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell +Lattice spacing in x,y,z = 4.8105 4.8105 4.8105 +create_atoms 2 box +Created 256 atoms + using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242) + create_atoms CPU = 0.000 seconds + +mass 1 40.078 +mass 2 15.999 + +displace_atoms all random 0.01 0.01 0.01 9084544 +Displacing atoms ... +set type 1 charge 1.2 +Setting atom values ... + 256 settings made for charge +set type 2 charge -1.2 +Setting atom values ... + 256 settings made for charge + +timestep 0.002 +neigh_modify delay 5 every 1 check yes + +pair_style hybrid/overlay pedone 15.0 coul/long 15.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 +pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + +variable len equal lx*0.25 +thermo_style custom step v_len lx pe press +thermo 100 +fix 1 all box/relax iso 0.0 +minimize 0.0 0.0 1000 10000 +Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.23676226 + grid = 24 24 24 + stencil order = 5 + estimated absolute RMS force accuracy = 1.3089053e-05 + estimated relative force accuracy = 9.089844e-07 + using double precision FFTW3 + 3d grid and FFT values/proc = 11191 3456 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17 + ghost atom cutoff = 17 + binsize = 8.5, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair pedone, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies + (src/min.cpp:219) +Per MPI rank memory allocation (min/avg/max) = 6.44 | 6.44 | 6.44 Mbytes + Step v_len Lx PotEng Press + 0 4.8105 19.242 -3765.9116 -21299.914 + 100 4.7797128 19.118851 -3767.814 -164.13101 + 200 4.7787507 19.115003 -3769.1367 -373.59489 + 300 4.7768265 19.107306 -3770.5868 32.046893 + 400 4.7768265 19.107306 -3771.0322 -290.69703 + 500 4.7758644 19.103458 -3771.4223 150.34606 + 600 4.7758644 19.103458 -3771.7941 -117.26938 + 700 4.7758644 19.103458 -3772.0193 -277.34372 + 800 4.7749023 19.099609 -3772.42 171.95177 + 860 4.7748339 19.099336 -3772.8237 1.0976356 +Loop time of 5.65601 on 4 procs for 860 steps with 512 atoms + +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -3765.91161156888 -3772.82365446552 -3772.82365446552 + Force two-norm initial, final = 284.3967 0.067746634 + Force max component initial, final = 284.14458 0.014426328 + Final line search alpha, max atom move = 1.9073486e-06 2.7516038e-08 + Iterations, force evaluations = 860 922 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.7408 | 3.8442 | 4.0543 | 6.5 | 67.97 +Kspace | 0.60187 | 0.81211 | 0.91543 | 14.1 | 14.36 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.14969 | 0.15017 | 0.15071 | 0.1 | 2.66 +Output | 0.00019203 | 0.00020711 | 0.0002511 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.8494 | | | 15.02 + +Nlocal: 128 ave 135 max 123 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 8175 ave 8180 max 8168 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 93038.8 ave 98164 max 89373 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 372155 +Ave neighs/atom = 726.86523 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "Expected lattice parameter: 4.7748, computed: $(v_len:%6.4f)" +Expected lattice parameter: 4.7748, computed: 4.7748 +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/data.pos b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos index cba35b49c9..3ab4033aee 100644 --- a/examples/PACKAGES/phonon/2-1D-diatomic/data.pos +++ b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos @@ -8,7 +8,7 @@ 0.00000000 64.00000000 xlo xhi 0.00000000 1.00000000 ylo yhi - 0.00000000 1.00000000 zlo zhi + -0.50000000 0.50000000 zlo zhi Atoms diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana index ca49cd50c6..5209adeb4a 100644 --- a/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana +++ b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana @@ -1,4 +1,5 @@ -# 3D simple cubic lattice simulation +# 2D slice of 3D simple cubic lattice simulation + dimension 2 boundary p f p diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 new file mode 100644 index 0000000000..e84bcf8dff --- /dev/null +++ b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 @@ -0,0 +1,20125 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# 3D simple cubic lattice simulation +dimension 2 +boundary p f p + +units lj +atom_style bond +atom_modify sort 0 1. +bond_style harmonic +pair_style none +comm_modify cutoff 2.0 + +# geometry +read_data data.pos +Reading data file ... + orthogonal box = (0 0 -0.5) to (64 1 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 64 atoms + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 64 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.002 seconds + +# +neighbor 1.0 nsq +neigh_modify delay 0 check no + +#Langevin random seed +variable r equal 571101 + +#Langevin Temperature +variable t equal 0.005 + +# Langevin Damping variable +variable d equal 0.5 + +# Create velocities and equilibrate +compute MyTemp all temp/partial 1 0 0 +velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all create 0.005 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all set NULL 0.0 0.0 units box +# +fix 1 all langevin $t $t $d $r +fix 1 all langevin 0.005 $t $d $r +fix 1 all langevin 0.005 0.005 $d $r +fix 1 all langevin 0.005 0.005 0.5 $r +fix 1 all langevin 0.005 0.005 0.5 571101 +fix_modify 1 temp MyTemp +fix 2 all setforce NULL 0. 0. +fix 3 all nve +fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 +fix_modify 4 temp MyTemp + +# 1 2 3 4 +thermo_style custom step temp pe etotal +thermo_modify temp MyTemp +thermo 100 + +# +run 2000000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix phonon command: doi:10.1016/j.cpc.2011.04.019 + +@Article{Kong11, + author = {L. T. Kong}, + title = {Phonon Dispersion Measured Directly from Molecular Dynamics Simulations}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2011, + volume = 182, + pages = {2201--2207} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 3.24 | 3.24 | 3.24 Mbytes + Step Temp PotEng TotEng + 0 0.005 0 0.0024609375 + 100 0.0043574392 0.00069805582 0.0028427329 + 200 0.0050747182 0.001248215 0.0037459279 + 300 0.0042939525 0.0012759486 0.0033893784 + 400 0.0047484976 0.001437393 0.0037745442 + 500 0.004627561 0.0016348645 0.0039124922 + 600 0.0053777922 0.0016710534 0.0043179355 + 700 0.0052695823 0.001835953 0.0044295755 + 800 0.0058609694 0.0019759698 0.0048606657 + 900 0.0041391777 0.0023023409 0.0043395924 + 1000 0.0056759231 0.0025899311 0.0053835496 + 1100 0.0040035566 0.0026989975 0.004669498 + 1200 0.0046087446 0.0024368196 0.004705186 + 1300 0.0044194669 0.0024664612 0.0046416676 + 1400 0.0073096222 0.001870287 0.0054679916 + 1500 0.0051897883 0.0017108961 0.004265245 + 1600 0.0044584884 0.001752323 0.0039467352 + 1700 0.005428529 0.0021271098 0.0047989639 + 1800 0.0051009277 0.0024399413 0.0049505541 + 1900 0.0051964843 0.0024877492 0.0050453939 + 2000 0.0055793788 0.0023282122 0.0050743127 + 2100 0.0056652876 0.0021449654 0.0049333492 + 2200 0.0038066338 0.0021519385 0.004025516 + 2300 0.0057120344 0.0023205208 0.0051319127 + 2400 0.0048840732 0.0021352142 0.004539094 + 2500 0.0046857988 0.0019440455 0.0042503371 + 2600 0.0040103298 0.002513002 0.0044868362 + 2700 0.0057128095 0.002876904 0.0056886774 + 2800 0.0046716608 0.0030252203 0.0053245534 + 2900 0.0051838165 0.0019962325 0.0045476421 + 3000 0.0069632545 0.0012651 0.0046923269 + 3100 0.0048263268 0.0019062765 0.0042817343 + 3200 0.0045447528 0.0022519705 0.004488841 + 3300 0.0046649601 0.0022379997 0.0045340347 + 3400 0.0044544129 0.0019164476 0.0041088539 + 3500 0.0039472772 0.0018036276 0.0037464281 + 3600 0.0046102247 0.0022598943 0.0045289892 + 3700 0.0044370266 0.0024312133 0.0046150624 + 3800 0.0051412618 0.0029112044 0.0054416692 + 3900 0.0061568023 0.0026148329 0.005645134 + 4000 0.006119091 0.0026007629 0.0056125029 + 4100 0.0064752671 0.0026929514 0.0058799969 + 4200 0.0065751558 0.0023915745 0.005627784 + 4300 0.0061381444 0.0022725727 0.0052936906 + 4400 0.0058224538 0.0022860937 0.0051518327 + 4500 0.0061726521 0.0026253408 0.005663443 + 4600 0.0039716434 0.0030400687 0.004994862 + 4700 0.0040469864 0.002831765 0.0048236411 + 4800 0.0048440766 0.0026333078 0.0050175017 + 4900 0.0052442362 0.0023348669 0.0049160145 + 5000 0.0051295286 0.0020219063 0.0045465961 + 5100 0.0057879072 0.0021999673 0.0050487028 + 5200 0.0051142738 0.0018998498 0.0044170315 + 5300 0.0057863143 0.0019625202 0.0048104717 + 5400 0.0058678081 0.0021442684 0.0050323302 + 5500 0.0058645814 0.0023505736 0.0052370472 + 5600 0.0030307183 0.0029662202 0.0044579019 + 5700 0.0055602694 0.0030961043 0.0058327995 + 5800 0.004501128 0.0024716441 0.004687043 + 5900 0.0060587191 0.0021550846 0.0051371104 + 6000 0.007430971 0.0021537443 0.0058111754 + 6100 0.0062865463 0.0024185097 0.0055126692 + 6200 0.0040867151 0.0027590127 0.0047704428 + 6300 0.0052219679 0.0025648111 0.0051349984 + 6400 0.0059641115 0.0027159368 0.005651398 + 6500 0.0055556193 0.0030946318 0.0058290382 + 6600 0.0040555581 0.0033636584 0.0053597534 + 6700 0.0045118142 0.0028218699 0.0050425285 + 6800 0.0058601637 0.0023227311 0.0052070304 + 6900 0.0039481052 0.0023341289 0.004277337 + 7000 0.0042144559 0.0023350045 0.0044093071 + 7100 0.0054929735 0.0020343767 0.0047379496 + 7200 0.0046609622 0.0021430473 0.0044371146 + 7300 0.004585171 0.0021899849 0.0044467487 + 7400 0.0054609862 0.002436333 0.0051241621 + 7500 0.0061609286 0.002218384 0.0052507161 + 7600 0.0069910986 0.0023618412 0.0058027725 + 7700 0.0049048939 0.0028163949 0.0052305224 + 7800 0.0059777828 0.0028555032 0.0057976932 + 7900 0.0056747441 0.0026868768 0.005479915 + 8000 0.0054592173 0.0026213233 0.0053082818 + 8100 0.0060248934 0.0024665402 0.0054319174 + 8200 0.0034740925 0.0022766833 0.0039865882 + 8300 0.0046311032 0.0020748438 0.0043542149 + 8400 0.0055686859 0.0025104548 0.0052512924 + 8500 0.0052091911 0.0031335015 0.0056974002 + 8600 0.0067050757 0.0031081221 0.0064082765 + 8700 0.005609584 0.003129452 0.0058904192 + 8800 0.0062972892 0.0029939671 0.0060934141 + 8900 0.0050003322 0.0033860259 0.0058471269 + 9000 0.0057945805 0.0027651923 0.0056172124 + 9100 0.0050460043 0.0025437242 0.0050273045 + 9200 0.0042363075 0.0024518661 0.0045369237 + 9300 0.0065605566 0.0021761918 0.0054052158 + 9400 0.0046266128 0.0027272818 0.0050044428 + 9500 0.005093908 0.0035739754 0.0060811332 + 9600 0.0056811868 0.0032402711 0.0060364802 + 9700 0.0054339481 0.0027984612 0.0054729825 + 9800 0.0046290197 0.0029933479 0.0052716935 + 9900 0.0040932968 0.0030192789 0.0050339484 + 10000 0.0046184332 0.0027902298 0.0050633649 + 10100 0.0054785105 0.0024845081 0.0051809625 + 10200 0.0036508441 0.0027718363 0.0045687361 + 10300 0.0058397664 0.0024143777 0.0052886377 + 10400 0.0061316511 0.0023004298 0.0053183519 + 10500 0.0063671891 0.002358583 0.0054924339 + 10600 0.0055673068 0.0024652813 0.0052054401 + 10700 0.0044767567 0.0022108097 0.0044142133 + 10800 0.0038516362 0.0021290553 0.0040247825 + 10900 0.0059622925 0.0014383539 0.0043729198 + 11000 0.0047015528 0.0017109579 0.0040250034 + 11100 0.0048324377 0.0022149034 0.0045933689 + 11200 0.0045895327 0.0023331633 0.0045920739 + 11300 0.0057685631 0.0023070843 0.005146299 + 11400 0.0057175293 0.0021263437 0.0049404401 + 11500 0.0042261386 0.0014448706 0.0035249232 + 11600 0.0040073938 0.0016123955 0.0035847846 + 11700 0.0052509295 0.0021014322 0.0046858741 + 11800 0.0046129007 0.0021548504 0.0044252624 + 11900 0.006252411 0.0019672111 0.0050445697 + 12000 0.0042706578 0.0022585261 0.0043604904 + 12100 0.0052386215 0.0021427965 0.0047211805 + 12200 0.0048033303 0.0020771704 0.0044413095 + 12300 0.0054123556 0.0021925501 0.0048564439 + 12400 0.0056958095 0.0024101247 0.005213531 + 12500 0.003936961 0.0025784348 0.0045161578 + 12600 0.005806319 0.0023774483 0.005235246 + 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0.0026460546 0.0057295425 + 1998500 0.0042685253 0.0027045125 0.0048054273 + 1998600 0.0047982195 0.0024999167 0.0048615404 + 1998700 0.0045770619 0.0023965866 0.0046493593 + 1998800 0.006166689 0.0022217336 0.0052569009 + 1998900 0.0060578663 0.0023546222 0.0053362283 + 1999000 0.004238593 0.0024786217 0.0045648042 + 1999100 0.0054266305 0.0028549884 0.0055259081 + 1999200 0.0033827038 0.0027990632 0.0044639877 + 1999300 0.0047584445 0.0023526277 0.0046946746 + 1999400 0.0056181695 0.0020335116 0.0047987044 + 1999500 0.0033374664 0.0023030393 0.0039456986 + 1999600 0.0053943118 0.0023096891 0.004964702 + 1999700 0.0047621637 0.0021943385 0.0045382159 + 1999800 0.0058336388 0.0020055057 0.0048767498 + 1999900 0.0058349189 0.002299977 0.0051718512 + 2000000 0.0046591833 0.0026625608 0.0049557526 +Loop time of 12.6681 on 1 procs for 2000000 steps with 64 atoms + +Performance: 68203007.046 tau/day, 157877.331 timesteps/s, 10.104 Matom-step/s +96.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0.86381 | 0.86381 | 0.86381 | 0.0 | 6.82 +Neigh | 1.2565 | 1.2565 | 1.2565 | 0.0 | 9.92 +Comm | 1.0357 | 1.0357 | 1.0357 | 0.0 | 8.18 +Output | 0.071243 | 0.071243 | 0.071243 | 0.0 | 0.56 +Modify | 7.5928 | 7.5928 | 7.5928 | 0.0 | 59.94 +Other | | 1.848 | | | 14.59 + +Nlocal: 64 ave 64 max 64 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 6 +Neighbor list builds = 2000000 +Dangerous builds not checked +Total wall time: 0:00:12 diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 new file mode 100644 index 0000000000..2bb0c1c972 --- /dev/null +++ b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 @@ -0,0 +1,20125 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# 3D simple cubic lattice simulation +dimension 2 +boundary p f p + +units lj +atom_style bond +atom_modify sort 0 1. +bond_style harmonic +pair_style none +comm_modify cutoff 2.0 + +# geometry +read_data data.pos +Reading data file ... + orthogonal box = (0 0 -0.5) to (64 1 0.5) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 64 atoms + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 64 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# +neighbor 1.0 nsq +neigh_modify delay 0 check no + +#Langevin random seed +variable r equal 571101 + +#Langevin Temperature +variable t equal 0.005 + +# Langevin Damping variable +variable d equal 0.5 + +# Create velocities and equilibrate +compute MyTemp all temp/partial 1 0 0 +velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all create 0.005 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all set NULL 0.0 0.0 units box +# +fix 1 all langevin $t $t $d $r +fix 1 all langevin 0.005 $t $d $r +fix 1 all langevin 0.005 0.005 $d $r +fix 1 all langevin 0.005 0.005 0.5 $r +fix 1 all langevin 0.005 0.005 0.5 571101 +fix_modify 1 temp MyTemp +fix 2 all setforce NULL 0. 0. +fix 3 all nve +fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 +fix_modify 4 temp MyTemp + +# 1 2 3 4 +thermo_style custom step temp pe etotal +thermo_modify temp MyTemp +thermo 100 + +# +run 2000000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix phonon command: doi:10.1016/j.cpc.2011.04.019 + +@Article{Kong11, + author = {L. T. Kong}, + title = {Phonon Dispersion Measured Directly from Molecular Dynamics Simulations}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2011, + volume = 182, + pages = {2201--2207} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. 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0.0022659689 0.0050292709 + 1998200 0.0043151851 0.0025546655 0.0046785456 + 1998300 0.0052712957 0.0024152156 0.0050096815 + 1998400 0.0042348839 0.0024296798 0.0045140367 + 1998500 0.0030287342 0.002623803 0.0041145081 + 1998600 0.0055051309 0.0021173655 0.0048269221 + 1998700 0.0057217041 0.0017686861 0.0045848373 + 1998800 0.0048875419 0.0018746291 0.0042802161 + 1998900 0.007364676 0.0019868413 0.0056116428 + 1999000 0.0053002642 0.0021333448 0.0047420686 + 1999100 0.0044239819 0.0026956169 0.0048730454 + 1999200 0.0037866761 0.0031115123 0.0049752669 + 1999300 0.0045921308 0.0027207583 0.0049809477 + 1999400 0.0052107996 0.0020772636 0.004641954 + 1999500 0.0049143451 0.001868372 0.0042871512 + 1999600 0.0059949807 0.0022728405 0.0052234951 + 1999700 0.0050216233 0.002669087 0.0051406673 + 1999800 0.0049219953 0.0025093587 0.0049319033 + 1999900 0.0045165212 0.0022190108 0.004441986 + 2000000 0.0049904073 0.001955233 0.0044114491 +Loop time of 22.6651 on 4 procs for 2000000 steps with 64 atoms + +Performance: 38120276.772 tau/day, 88241.381 timesteps/s, 5.647 Matom-step/s +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0.37899 | 0.39755 | 0.41982 | 2.3 | 1.75 +Neigh | 2.9184 | 3.0178 | 3.1717 | 5.4 | 13.31 +Comm | 10.429 | 10.694 | 11.003 | 6.2 | 47.18 +Output | 0.12974 | 0.14293 | 0.17878 | 5.5 | 0.63 +Modify | 6.4203 | 6.5794 | 6.7365 | 4.5 | 29.03 +Other | | 1.833 | | | 8.09 + +Nlocal: 16 ave 16 max 16 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4 ave 4 max 4 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 6 +Neighbor list builds = 2000000 +Dangerous builds not checked +Total wall time: 0:00:22 diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps b/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps deleted file mode 100644 index b5867bb658..0000000000 --- a/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps +++ /dev/null @@ -1,20088 +0,0 @@ -LAMMPS (23 Sep 2013) -# 3D simple cubic lattice simulation -dimension 2 -boundary p f p - -units lj -atom_style bond -atom_modify sort 0 1. -bond_style harmonic -pair_style none -communicate single cutoff 2.0 - -# geometry -read_data data.pos - 2 = max bonds/atom - orthogonal box = (0 0 0) to (64 1 1) - 1 by 1 by 1 MPI processor grid - 64 atoms - 64 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -# -neighbor 1.0 nsq -neigh_modify delay 0 check no - -#Langevin random seed -variable r equal 571101 - -#Langevin Temperature -variable t equal 0.005 - -# Langevin Damping variable -variable d equal 0.5 - -# Create velocities and equilibrate -compute MyTemp all temp/partial 1 0 0 -velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp -velocity all create 0.0050000000000000001041 28711 mom yes rot yes dist gaussian temp MyTemp -velocity all set NULL 0.0 0.0 units box -# -fix 1 all langevin $t $t $d $r -fix 1 all langevin 0.0050000000000000001041 $t $d $r -fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 $d $r -fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 $r -fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 571101 -fix_modify 1 temp MyTemp -fix 2 all setforce NULL 0. 0. -fix 3 all nve -fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 -fix_modify 4 temp MyTemp - -# 1 2 3 4 -thermo_style custom step temp pe etotal -thermo_modify temp MyTemp -thermo 100 - -# -run 2000000 -Memory usage per processor = 2.01061 Mbytes -Step Temp PotEng TotEng - 0 0.005 0 0.002421875 - 100 0.0044233185 0.00069227571 0.0028348206 - 200 0.0051557212 0.0012425996 0.003739902 - 300 0.004357315 0.0012750554 0.0033856298 - 400 0.0048269093 0.0014376622 0.0037756964 - 500 0.0047025425 0.0016352541 0.0039130482 - 600 0.0054651713 0.0016709504 0.0043181428 - 700 0.0053552729 0.0018353947 0.0044293551 - 800 0.005954909 0.0019755263 0.0048599354 - 900 0.0042057592 0.0023020508 0.0043392155 - 1000 0.0057669621 0.0025897902 0.0053831625 - 1100 0.0040680049 0.0026989519 0.0046693918 - 1200 0.0046829459 0.0024368094 0.0047051113 - 1300 0.0044905385 0.0024665322 0.0046416368 - 1400 0.0074275036 0.0018704053 0.0054681024 - 1500 0.0052733986 0.0017110596 0.0042653621 - 1600 0.0045302499 0.0017525366 0.0039468764 - 1700 0.0055159362 0.002127395 0.0047991766 - 1800 0.0051833134 0.0024402092 0.0049508766 - 1900 0.0052803653 0.0024879535 0.0050456305 - 2000 0.0056694273 0.0023283837 0.0050745125 - 2100 0.0057566849 0.0021451166 0.0049335108 - 2200 0.00386807 0.0021520647 0.0040256611 - 2300 0.0058041566 0.0023206647 0.0051320531 - 2400 0.0049628786 0.0021353417 0.004539236 - 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4700 0.004112287 0.0028318222 0.0048237112 - 4800 0.0049222174 0.0026333499 0.0050175489 - 4900 0.0053288359 0.0023349026 0.0049160575 - 5000 0.0052122846 0.0020219366 0.0045466369 - 5100 0.0058812614 0.0021999893 0.0050487252 - 5200 0.0051967264 0.0018998782 0.0044170426 - 5300 0.005879625 0.0019625602 0.0048105036 - 5400 0.0059624731 0.0021443126 0.0050323855 - 5500 0.0059591574 0.0023506099 0.0052370768 - 5600 0.003079608 0.0029662562 0.0044579413 - 5700 0.0056499809 0.0030961313 0.0058328408 - 5800 0.004573757 0.0024716554 0.004687069 - 5900 0.0061564453 0.0021550869 0.0051371151 - 6000 0.0075508592 0.0021537409 0.0058111883 - 6100 0.0063879372 0.0024185024 0.0055126595 - 6200 0.0041526115 0.0027590092 0.0047704304 - 6300 0.0053061863 0.0025648127 0.0051349967 - 6400 0.006060304 0.0027159393 0.0056513991 - 6500 0.0056452086 0.0030946398 0.0058290377 - 6600 0.0041209765 0.0033636656 0.0053597636 - 6700 0.0045845779 0.0028218743 0.0050425293 - 6800 0.0059546759 0.0023227413 0.0052070374 - 6900 0.0040117754 0.0023341431 0.0042773468 - 7000 0.0042824332 0.0023350167 0.0044093203 - 7100 0.0055815793 0.0020343862 0.0047379636 - 7200 0.0047361478 0.0021430515 0.0044371231 - 7300 0.0046591248 0.0021899851 0.0044467487 - 7400 0.0055490678 0.0024363348 0.0051241645 - 7500 0.0062602828 0.0022183901 0.0052507145 - 7600 0.0071038558 0.0023618503 0.0058027804 - 7700 0.0049840045 0.0028164024 0.0052305296 - 7800 0.0060742119 0.0028555113 0.0057977076 - 7900 0.0057662888 0.0026868797 0.0054799259 - 8000 0.0055472766 0.0026213197 0.0053082818 - 8100 0.0061220787 0.0024665333 0.0054319151 - 8200 0.0035301258 0.0022766722 0.0039865769 - 8300 0.0047057949 0.0020748339 0.0043542033 - 8400 0.0056584891 0.0025104488 0.0052512795 - 8500 0.0052931944 0.0031335003 0.0056973914 - 8600 0.006813214 0.0031081279 0.0064082784 - 8700 0.0057000798 0.0031294549 0.0058904311 - 8800 0.0063988595 0.0029939656 0.0060934132 - 8900 0.0050809819 0.0033860223 0.0058471229 - 9000 0.0058880586 0.0027651879 0.0056172163 - 9100 0.0051273933 0.0025437215 0.0050273027 - 9200 0.0043046349 0.0024518668 0.0045369243 - 9300 0.006666349 0.0021761986 0.0054052113 - 9400 0.0047012258 0.0027272975 0.0050044538 - 9500 0.0051760716 0.0035739909 0.0060811506 - 9600 0.0057728292 0.0032402839 0.006036498 - 9700 0.0055216035 0.0027984706 0.0054729973 - 9800 0.004703682 0.0029933541 0.0052717001 - 9900 0.0041593147 0.0030192883 0.0050339564 - 10000 0.0046929175 0.0027902403 0.0050633722 - 10100 0.0055668751 0.0024845169 0.005180972 - 10200 0.0037097247 0.0027718476 0.0045687455 - 10300 0.0059339557 0.0024143878 0.0052886476 - 10400 0.0062305492 0.0023004427 0.0053183649 - 10500 0.006469886 0.0023585975 0.0054924485 - 10600 0.005657095 0.0024652988 0.0052054542 - 10700 0.0045489624 0.0022108292 0.0044142329 - 10800 0.0039137671 0.0021290713 0.0040248023 - 10900 0.0060584769 0.0014383624 0.0043729371 - 11000 0.0047773964 0.0017109606 0.0040250119 - 11100 0.0049103899 0.0022149005 0.0045933706 - 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186500 0.004023298 0.0021850719 0.0041338569 - 186600 0.0036155255 0.002280809 0.0040320792 - 186700 0.0038579955 0.0027198323 0.0045885489 - 186800 0.0063677161 0.0025739598 0.0056583222 - 186900 0.0045225785 0.0024861386 0.0046767625 - 187000 0.0049835336 0.0020343537 0.0044482528 - 187100 0.0045320336 0.0021878754 0.0043830792 - 187200 0.0034144141 0.0026306899 0.0042845467 - 187300 0.0039057395 0.002513463 0.0044053056 - 187400 0.0058619531 0.0020707321 0.0049101156 - 187500 0.0064173394 0.0019263661 0.0050347649 - 187600 0.0053520084 0.0019748014 0.0045671805 - 187700 0.0052174347 0.0020493688 0.0045765637 - 187800 0.0046195121 0.0023494084 0.0045869846 - 187900 0.003689577 0.002147859 0.0039349979 - 188000 0.0059961492 0.0017618515 0.0046662363 - 188100 0.0041823325 0.0017718191 0.0037976365 - 188200 0.0043850261 0.00196323 0.004087227 - 188300 0.003635617 0.0019857711 0.0037467731 - 188400 0.0059524417 0.0016029899 0.0044862039 - 188500 0.0056924296 0.0018621911 0.0046194617 - 188600 0.0048042949 0.0024473011 0.0047743814 - 188700 0.0058318226 0.0022984831 0.0051232721 - 188800 0.0052188059 0.0026443254 0.0051721845 - 188900 0.0056113973 0.0025944274 0.0053124479 - 189000 0.0044310254 0.0022104356 0.0043567136 - 189100 0.0047866433 0.0025570562 0.0048755866 - 189200 0.0033139611 0.002889829 0.0044950289 - 189300 0.0038916042 0.0030517495 0.0049367453 - 189400 0.004604689 0.0023109722 0.0045413684 - 189500 0.0062908433 0.0017933712 0.0048404984 - 189600 0.0047164727 0.0021168432 0.0044013847 - 189700 0.0043846343 0.0023526239 0.0044764312 - 189800 0.0062542294 0.0024680157 0.0054974081 - 189900 0.0054322102 0.0028654338 0.0054966607 - 190000 0.0052922781 0.0035149977 0.0060784449 - 190100 0.0048195915 0.0033319567 0.0056664464 - 190200 0.0049659617 0.0031083355 0.0055137232 - 190300 0.0048846338 0.002618541 0.0049845355 - 190400 0.0072407499 0.0025871515 0.0060943898 - 190500 0.0051735903 0.0033501057 0.0058560635 - 190600 0.0040078499 0.0037742335 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0.0025770528 0.0046900019 - 192800 0.0044188753 0.0025913243 0.004731717 - 192900 0.0054753877 0.0025689278 0.0052210687 - 193000 0.0030370073 0.0026801634 0.0041512138 - 193100 0.004409951 0.0022050277 0.0043410977 - 193200 0.0057759185 0.001896822 0.0046945325 - 193300 0.0042752982 0.0025307205 0.0046015681 - 193400 0.0055186183 0.0031917268 0.0058648075 - 193500 0.0060706248 0.0030096467 0.0059501056 - 193600 0.0042938989 0.00264227 0.0047221273 - 193700 0.0055878445 0.0026675461 0.0053741583 - 193800 0.0041577783 0.0032179247 0.0052318486 - 193900 0.0044302076 0.0028307011 0.004976583 - 194000 0.0045536136 0.0026532486 0.0048589052 - 194100 0.0042068026 0.0024913282 0.0045289982 - 194200 0.0037699595 0.0026229049 0.004448979 - 194300 0.0037420602 0.0026526448 0.0044652052 - 194400 0.003878494 0.0026486011 0.0045272466 - 194500 0.0046998411 0.0024972143 0.0047736999 - 194600 0.0074446112 0.0023454877 0.0059514713 - 194700 0.0035616348 0.0025592457 0.0042844125 - 194800 0.004454451 0.0026486558 0.0048062805 - 194900 0.0041375053 0.0031289022 0.0051330063 - 195000 0.0055855352 0.0023818302 0.0050873238 - 195100 0.0049993147 0.0022307876 0.0046523307 - 195200 0.0050902708 0.0024878171 0.004953417 - 195300 0.0052889476 0.0028110914 0.0053729254 - 195400 0.0069216615 0.0026928476 0.0060455273 - 195500 0.0056653594 0.0028165203 0.0055606787 - 195600 0.0068159974 0.0033075535 0.0066090523 - 195700 0.0038892912 0.0033528858 0.0052367612 - 195800 0.0050771126 0.0029442862 0.0054035126 - 195900 0.0049673801 0.0024786018 0.0048846766 - 196000 0.0045366143 0.0023858427 0.0045832652 - 196100 0.0034262945 0.0023407836 0.004000395 - 196200 0.0080690464 0.002105792 0.0060142364 - 196300 0.0055825313 0.0026808195 0.0053848581 - 196400 0.0058569898 0.0025960602 0.0054330397 - 196500 0.0049358445 0.0023874592 0.0047782588 - 196600 0.0057120089 0.0030756087 0.005842363 - 196700 0.0065281028 0.0036266314 0.0067886812 - 196800 0.0083678972 0.002787348 0.0068405482 - 196900 0.0053579919 0.0027321079 0.0053273852 - 197000 0.0051319658 0.0031094842 0.0055952801 - 197100 0.0051893931 0.0026560568 0.0051696691 - 197200 0.0057025248 0.0025227845 0.005284945 - 197300 0.0057190745 0.0021218735 0.0048920502 - 197400 0.0054308536 0.0021085758 0.0047391455 - 197500 0.0061738386 0.0024553693 0.0054458224 - 197600 0.0073637833 0.0034092835 0.006976116 - 197700 0.006880961 0.0038654894 0.0071984549 - 197800 0.0045154568 0.003905548 0.0060927224 - 197900 0.0058546478 0.0034661516 0.0063019967 - 198000 0.006251792 0.0032547858 0.0062829976 - 198100 0.0047231964 0.0027934021 0.0050812004 - 198200 0.0050989071 0.0024584673 0.0049282504 - 198300 0.0066451305 0.0021919512 0.0054106863 - 198400 0.0052993565 0.0027496567 0.0053165324 - 198500 0.0048914502 0.0030021438 0.00537144 - 198600 0.0045970991 0.0028914871 0.005118207 - 198700 0.0046075146 0.0028712859 0.0051030508 - 198800 0.0044019458 0.0030324028 0.0051645953 - 198900 0.0064983384 0.0028781354 0.006025768 - 199000 0.0043115478 0.0026259277 0.0047143336 - 199100 0.0052927869 0.0030187438 0.0055824374 - 199200 0.0046158741 0.0034427209 0.0056785349 - 199300 0.0057827879 0.0033809411 0.0061819789 - 199400 0.0047102404 0.0030595364 0.0053410591 - 199500 0.0065787425 0.0026770398 0.0058636182 - 199600 0.0051927359 0.0026411966 0.005156428 - 199700 0.0045327092 0.0027294203 0.0049249513 - 199800 0.0048496623 0.0025053467 0.0048544019 - 199900 0.0054228679 0.0020631595 0.0046898612 - 200000 0.0055794195 0.0018362356 0.0045387669 - 200100 0.0046262225 0.0020656778 0.0043065043 - 200200 0.003627737 0.002270457 0.0040276421 - 200300 0.0038479801 0.0021699958 0.0040338612 - 200400 0.0050120202 0.002216547 0.0046442443 - 200500 0.0049172792 0.0023821287 0.0047639358 - 200600 0.0036694163 0.0025848857 0.0043622592 - 200700 0.0041600694 0.0027527852 0.0047678188 - 200800 0.004511666 0.0024639128 0.004649251 - 200900 0.0066329627 0.0025066272 0.0057194686 - 201000 0.0050300515 0.0032750403 0.0057114715 - 201100 0.0059981294 0.0034641684 0.0063695123 - 201200 0.0053221902 0.0032550253 0.0058329612 - 201300 0.004780854 0.0027813602 0.0050970863 - 201400 0.0047724553 0.0027331203 0.0050447783 - 201500 0.0083500719 0.0026781623 0.0067227284 - 201600 0.0057064719 0.0026443441 0.0054084164 - 201700 0.0053270485 0.0031907506 0.0057710397 - 201800 0.0056772678 0.0027345683 0.0054844949 - 201900 0.0051556952 0.0026502128 0.0051475027 - 202000 0.0054386571 0.0024793145 0.0051136641 - 202100 0.0060716989 0.002756279 0.0056972581 - 202200 0.0040641357 0.0033367206 0.0053052863 - 202300 0.0046033751 0.0032435963 0.0054733561 - 202400 0.004246771 0.0028810152 0.0049380449 - 202500 0.0058791109 0.002499567 0.0053472613 - 202600 0.0044302003 0.0030500904 0.0051959687 - 202700 0.0045842744 0.0028628921 0.0050834 - 202800 0.0056273109 0.0031744904 0.0059002191 - 202900 0.0066554885 0.0030585302 0.0062822825 - 203000 0.0059381392 0.0028487683 0.0057250544 - 203100 0.0051322804 0.0031226977 0.005608646 - 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0.0036500107 - 1964500 0.0056158655 0.0022641806 0.0049843654 - 1964600 0.0041059066 0.0023263417 0.0043151402 - 1964700 0.0038937764 0.0024393851 0.004325433 - 1964800 0.0069307578 0.0025497371 0.0059068229 - 1964900 0.0053878812 0.0027493608 0.0053591157 - 1965000 0.0064602479 0.0025418261 0.0056710086 - 1965100 0.0050866897 0.002606692 0.0050705573 - 1965200 0.0055577587 0.0026632069 0.0053552462 - 1965300 0.0053032321 0.0027575158 0.0053262688 - 1965400 0.0054482398 0.0025362095 0.0051752007 - 1965500 0.0058227454 0.0020405503 0.0048609426 - 1965600 0.0068704891 0.0024043677 0.0057322609 - 1965700 0.0068144301 0.0027667175 0.0060674571 - 1965800 0.0040656864 0.0024551339 0.0044244507 - 1965900 0.0063331825 0.0021690624 0.0052366976 - 1966000 0.0059347292 0.0022528503 0.0051274848 - 1966100 0.0038014443 0.002395169 0.0042364936 - 1966200 0.0051626019 0.002402328 0.0049029633 - 1966300 0.0055720666 0.0024380918 0.0051370616 - 1966400 0.0045167335 0.0020777425 0.0042655352 - 1966500 0.0051957139 0.0018010772 0.0043177511 - 1966600 0.0037150002 0.0020400365 0.0038394897 - 1966700 0.0041872098 0.0021180504 0.0041462302 - 1966800 0.00465358 0.0021848257 0.0044389035 - 1966900 0.0062002548 0.0027371496 0.0057403981 - 1967000 0.0057532758 0.0025965471 0.0053832901 - 1967100 0.0061909045 0.0026552122 0.0056539315 - 1967200 0.0058882778 0.0021289476 0.0049810822 - 1967300 0.0048178375 0.0021041628 0.0044378028 - 1967400 0.0047987529 0.0023754572 0.0046998532 - 1967500 0.0047794899 0.0022176643 0.0045327297 - 1967600 0.0044560078 0.0025284402 0.004686819 - 1967700 0.0046207226 0.0029978622 0.0052360248 - 1967800 0.0045441823 0.0027242031 0.0049252913 - 1967900 0.0042010496 0.0025077714 0.0045426548 - 1968000 0.0051831559 0.0015424749 0.0040530661 - 1968100 0.0044980132 0.0015126516 0.0036913768 - 1968200 0.0052936774 0.0019109596 0.0044750846 - 1968300 0.0054982661 0.0023438293 0.0050070519 - 1968400 0.0052859491 0.0022122354 0.004772617 - 1968500 0.0063679749 0.0020335453 0.0051180331 - 1968600 0.0059179053 0.0020508671 0.0049173525 - 1968700 0.0061646476 0.0020515531 0.0050375543 - 1968800 0.0055456491 0.002212246 0.0048984198 - 1968900 0.0036189282 0.0026052277 0.004358146 - 1969000 0.0055062192 0.002573247 0.0052403219 - 1969100 0.0043925083 0.0021020917 0.0042297129 - 1969200 0.0051957778 0.0021091525 0.0046258573 - 1969300 0.0059397662 0.0019518892 0.0048289634 - 1969400 0.0042516611 0.0019568573 0.0040162556 - 1969500 0.0056378026 0.0019161023 0.004646913 - 1969600 0.0056264339 0.0022012944 0.0049265983 - 1969700 0.0045997285 0.0025249533 0.0047529468 - 1969800 0.0062267986 0.002665873 0.0056819786 - 1969900 0.0049730875 0.0029549784 0.0053638176 - 1970000 0.0064854485 0.0030570939 0.0061984831 - 1970100 0.0080774649 0.0027469063 0.0066594283 - 1970200 0.0043251534 0.0025904999 0.0046854961 - 1970300 0.0062825382 0.0027827784 0.0058258829 - 1970400 0.004528342 0.0031298734 0.0053232891 - 1970500 0.0056682583 0.0029247608 0.0056703235 - 1970600 0.0057537252 0.0027874039 0.0055743646 - 1970700 0.0047225525 0.0025042377 0.0047917241 - 1970800 0.0053366631 0.0023905823 0.0049755285 - 1970900 0.0089082225 0.0027393317 0.007054252 - 1971000 0.0049441819 0.003062321 0.0054571591 - 1971100 0.0054766257 0.0032058845 0.005858625 - 1971200 0.0042832485 0.0030911895 0.005165888 - 1971300 0.0042925749 0.0027016 0.0047808159 - 1971400 0.0042251995 0.0026380988 0.0046846798 - 1971500 0.0057608068 0.0023601876 0.0051505784 - 1971600 0.0048267975 0.0021694997 0.0045074797 - 1971700 0.0036845697 0.002277363 0.0040620765 - 1971800 0.0040564366 0.0025434426 0.0045082791 - 1971900 0.0053801013 0.0030542676 0.0056602542 - 1972000 0.0049635061 0.0031348497 0.005539048 - 1972100 0.0052640529 0.0029293056 0.0054790813 - 1972200 0.0044742313 0.0026739334 0.0048411392 - 1972300 0.0056218147 0.0023577961 0.0050808626 - 1972400 0.0037431127 0.0024419225 0.0042549927 - 1972500 0.005060015 0.0025287977 0.0049797425 - 1972600 0.004866404 0.0028103724 0.0051675368 - 1972700 0.0040923386 0.0028180666 0.0048002931 - 1972800 0.0052979951 0.0026281261 0.0051943425 - 1972900 0.0046227859 0.0026969517 0.0049361136 - 1973000 0.0043350752 0.0023557858 0.0044555878 - 1973100 0.0039664036 0.0028230566 0.0047442833 - 1973200 0.0053598809 0.0029705491 0.0055667414 - 1973300 0.0052497984 0.0029784724 0.0055213435 - 1973400 0.0047805678 0.0027277293 0.0050433169 - 1973500 0.0054698797 0.002779874 0.0054293469 - 1973600 0.0067283504 0.0023810291 0.0056400738 - 1973700 0.0041397623 0.0026570758 0.0046622731 - 1973800 0.0036262128 0.0029934372 0.0047498841 - 1973900 0.006031899 0.003181333 0.0061030341 - 1974000 0.0063327192 0.0033460501 0.006413461 - 1974100 0.0052555677 0.0031859296 0.0057315952 - 1974200 0.005185452 0.0031881479 0.0056998512 - 1974300 0.0061520968 0.0032340787 0.0062140006 - 1974400 0.0060844363 0.0031463562 0.006093505 - 1974500 0.0054164261 0.0030716635 0.0056952449 - 1974600 0.0054331191 0.0029142453 0.0055459123 - 1974700 0.0074740317 0.0022399864 0.0058602206 - 1974800 0.0060482682 0.0025337519 0.0054633817 - 1974900 0.0050154909 0.0027719504 0.0052013288 - 1975000 0.0045335664 0.0030395025 0.0052354487 - 1975100 0.0046638217 0.0028020992 0.0050611378 - 1975200 0.004873034 0.002848826 0.0052092018 - 1975300 0.0042910303 0.002913311 0.0049917787 - 1975400 0.0051556367 0.0031093931 0.0056066547 - 1975500 0.0040694394 0.0030316112 0.0050027459 - 1975600 0.0058378983 0.002423874 0.005251606 - 1975700 0.0053371129 0.0021502419 0.004735406 - 1975800 0.0070446923 0.0021047481 0.0055170209 - 1975900 0.006559973 0.0023314058 0.0055088927 - 1976000 0.0052979827 0.0023618796 0.00492809 - 1976100 0.0045817236 0.0026409467 0.0048602191 - 1976200 0.004473997 0.0024717308 0.0046388231 - 1976300 0.0037308915 0.0021052169 0.0039123675 - 1976400 0.0050736595 0.0021350389 0.0045925927 - 1976500 0.0047211873 0.0026576123 0.0049444374 - 1976600 0.0051823742 0.002915772 0.0054259845 - 1976700 0.0055667224 0.0029714565 0.0056678377 - 1976800 0.0038088425 0.0026669281 0.0045118362 - 1976900 0.0052066277 0.0022477273 0.0047696876 - 1977000 0.0042668185 0.0028161513 0.0048828915 - 1977100 0.0040233428 0.0032010428 0.0051498494 - 1977200 0.0059016387 0.0025410678 0.0053996741 - 1977300 0.0060788044 0.0025806854 0.0055251063 - 1977400 0.0062889813 0.0028776728 0.0059238981 - 1977500 0.0032107879 0.003219768 0.0047749934 - 1977600 0.0048271814 0.0031008448 0.0054390108 - 1977700 0.0039721478 0.0031140292 0.0050380383 - 1977800 0.0049130448 0.0027406432 0.0051203993 - 1977900 0.0039220526 0.0026374838 0.004537228 - 1978000 0.0049530761 0.0026458429 0.0050449892 - 1978100 0.0058477313 0.0027040842 0.0055365791 - 1978200 0.0046354224 0.0029584259 0.0052037086 - 1978300 0.005457118 0.0031401241 0.0057834156 - 1978400 0.0043750854 0.0035560459 0.0056752279 - 1978500 0.0050376813 0.0029973742 0.0054375011 - 1978600 0.0055113232 0.0025874049 0.005256952 - 1978700 0.0048874684 0.0028211325 0.0051885 - 1978800 0.004561218 0.0030247895 0.0052341295 - 1978900 0.004649609 0.0029502179 0.0052023723 - 1979000 0.0061386174 0.0029548338 0.0059282266 - 1979100 0.0043850939 0.0030199504 0.0051439803 - 1979200 0.0059819611 0.0027335317 0.0056310441 - 1979300 0.0048187475 0.0027734638 0.0051075446 - 1979400 0.0045799377 0.0029437671 0.0051621745 - 1979500 0.005523774 0.0024135131 0.0050890911 - 1979600 0.0040420342 0.0019942777 0.003952138 - 1979700 0.0057359773 0.0017813829 0.0045597469 - 1979800 0.0042200444 0.0023567126 0.0044007966 - 1979900 0.0051318171 0.0028423141 0.005328038 - 1980000 0.0064015161 0.0024439437 0.0055446781 - 1980100 0.0053352823 0.0025956758 0.0051799532 - 1980200 0.0050231942 0.002769345 0.0052024547 - 1980300 0.006619252 0.0020366298 0.00524283 - 1980400 0.0062049134 0.0018875618 0.0048930668 - 1980500 0.0051416895 0.0021138048 0.0046043107 - 1980600 0.0052995442 0.0028344629 0.0054014297 - 1980700 0.0056324243 0.0026775714 0.0054057769 - 1980800 0.0070507367 0.0029468265 0.0063620271 - 1980900 0.0048590894 0.0028670738 0.0052206952 - 1981000 0.0043643056 0.0030986563 0.0052126168 - 1981100 0.0059884883 0.0028801275 0.0057808015 - 1981200 0.0052383865 0.0025165771 0.0050539206 - 1981300 0.0042253591 0.0024423829 0.0044890413 - 1981400 0.0041889244 0.0027406088 0.0047696191 - 1981500 0.0042360903 0.003124121 0.0051759772 - 1981600 0.0055854364 0.0025034131 0.0052088588 - 1981700 0.0060298884 0.0023962616 0.0053169888 - 1981800 0.0051099318 0.0029115977 0.0053867209 - 1981900 0.007432557 0.0031682516 0.0067683964 - 1982000 0.0051651015 0.0027414071 0.0052432531 - 1982100 0.0031482323 0.0023919215 0.0039168466 - 1982200 0.0050324706 0.0019992191 0.004436822 - 1982300 0.0045776837 0.0022314753 0.0044487909 - 1982400 0.0050757808 0.0025842099 0.0050427912 - 1982500 0.0038937605 0.0025762614 0.0044623017 - 1982600 0.0048099064 0.0020768117 0.0044066102 - 1982700 0.0048078708 0.0020836694 0.0044124818 - 1982800 0.0038340538 0.0027345713 0.0045916911 - 1982900 0.0046449049 0.0026494406 0.0048993164 - 1983000 0.0055783579 0.0021691463 0.0048711634 - 1983100 0.0047203041 0.0019030225 0.0041894198 - 1983200 0.0055060166 0.0022998265 0.0049668032 - 1983300 0.0055737916 0.0024850769 0.0051848822 - 1983400 0.0050966465 0.0024651767 0.0049338649 - 1983500 0.0034818344 0.0028266297 0.0045131432 - 1983600 0.0059945363 0.0026177563 0.0055213598 - 1983700 0.004267897 0.0022676125 0.0043348751 - 1983800 0.0056603714 0.0022174523 0.0049591946 - 1983900 0.0051517181 0.0022974572 0.0047928206 - 1984000 0.0051474378 0.0025681994 0.0050614896 - 1984100 0.005460167 0.0024815444 0.0051263129 - 1984200 0.0054376744 0.0018492774 0.0044831509 - 1984300 0.0055410768 0.0018767829 0.004560742 - 1984400 0.0050647983 0.0021000771 0.0045533388 - 1984500 0.0043126595 0.0030772223 0.0051661667 - 1984600 0.0037685928 0.0029275743 0.0047529864 - 1984700 0.0081352754 0.0023483682 0.0062888923 - 1984800 0.0057769913 0.0024488912 0.0052471214 - 1984900 0.004978804 0.001879708 0.0042913162 - 1985000 0.0048145303 0.0016232973 0.0039553354 - 1985100 0.0051224975 0.0016960054 0.0041772151 - 1985200 0.0069831704 0.0019689625 0.0053514357 - 1985300 0.0060294024 0.002259717 0.0051802088 - 1985400 0.0057887876 0.0023596115 0.0051635555 - 1985500 0.005588287 0.0019500888 0.0046569153 - 1985600 0.0056547797 0.0018248935 0.0045639275 - 1985700 0.0033519597 0.0015875152 0.0032111206 - 1985800 0.0047733698 0.0019011104 0.0042132115 - 1985900 0.0049710853 0.0020709354 0.0044788048 - 1986000 0.0051061302 0.0020213273 0.0044946091 - 1986100 0.0054134899 0.0021487742 0.0047709334 - 1986200 0.0040267681 0.002647106 0.0045975718 - 1986300 0.0043519756 0.0028408882 0.0049488764 - 1986400 0.0067032628 0.0024620465 0.0057089395 - 1986500 0.005056597 0.0022323524 0.0046816416 - 1986600 0.0051228808 0.0019012453 0.0043826406 - 1986700 0.0058110347 0.0019400205 0.0047547404 - 1986800 0.0050110146 0.002240595 0.0046678052 - 1986900 0.005864026 0.0020852965 0.0049256841 - 1987000 0.0056545357 0.0017174938 0.0044564095 - 1987100 0.0056803806 0.0017661794 0.0045176137 - 1987200 0.0062633742 0.0024604312 0.0054942531 - 1987300 0.0054471498 0.0024218447 0.0050603078 - 1987400 0.0044758873 0.0021148092 0.0042828171 - 1987500 0.0051304638 0.0026949514 0.0051800198 - 1987600 0.0033567354 0.0028827272 0.0045086459 - 1987700 0.0057063021 0.0026394497 0.0054034398 - 1987800 0.0046798921 0.0024753942 0.004742217 - 1987900 0.0054774371 0.0019866846 0.0046398182 - 1988000 0.0050890975 0.0021466774 0.004611709 - 1988100 0.0038729382 0.0023440655 0.0042200199 - 1988200 0.0055760036 0.0018172397 0.0045181165 - 1988300 0.0047048483 0.0017158983 0.0039948092 - 1988400 0.0046541239 0.0018986344 0.0041529757 - 1988500 0.0042934389 0.0021489599 0.0042285943 - 1988600 0.0047159057 0.0027011784 0.0049854453 - 1988700 0.005847541 0.0027889251 0.0056213278 - 1988800 0.004829912 0.0025011755 0.0048406641 - 1988900 0.0056956836 0.0020999981 0.0048588448 - 1989000 0.0047076006 0.0022881468 0.0045683908 - 1989100 0.005091665 0.0021371748 0.0046034501 - 1989200 0.004117067 0.0018519146 0.0038461189 - 1989300 0.0060880931 0.0015364795 0.0044853996 - 1989400 0.0035161215 0.0018072419 0.0035103633 - 1989500 0.0043151298 0.0020787266 0.0041688676 - 1989600 0.0052430814 0.002514277 0.0050538946 - 1989700 0.0043809065 0.0025939534 0.0047159549 - 1989800 0.0041960335 0.0025453096 0.0045777634 - 1989900 0.0039563302 0.0026856849 0.0046020323 - 1990000 0.0057348699 0.0022228385 0.0050006661 - 1990100 0.0047898563 0.0022843105 0.0046043972 - 1990200 0.0051976815 0.0025090598 0.0050266868 - 1990300 0.0050077625 0.0023855288 0.0048111637 - 1990400 0.0053204764 0.0023640181 0.0049411239 - 1990500 0.0052841198 0.0020073376 0.0045668331 - 1990600 0.0053451514 0.0018676685 0.0044567262 - 1990700 0.0033328477 0.0019433734 0.0035577215 - 1990800 0.0044006934 0.0019865754 0.0041181613 - 1990900 0.0050452301 0.0020408853 0.0044846686 - 1991000 0.0065300025 0.0023365408 0.0054995107 - 1991100 0.0051928278 0.0024265468 0.0049418228 - 1991200 0.0053469544 0.0028286653 0.0054185964 - 1991300 0.0034592909 0.0029405703 0.0046161643 - 1991400 0.0057569225 0.002730733 0.0055192423 - 1991500 0.0057598209 0.002308152 0.0050980653 - 1991600 0.005152249 0.0025708244 0.005066445 - 1991700 0.0044006429 0.0029145105 0.0050460719 - 1991800 0.0053758242 0.0030241416 0.0056280565 - 1991900 0.0049695684 0.0032815402 0.0056886749 - 1992000 0.0055769618 0.0034554958 0.0061568366 - 1992100 0.0059583852 0.0032399942 0.006126087 - 1992200 0.0046716994 0.002824056 0.0050869104 - 1992300 0.0048192819 0.0025829998 0.0049173394 - 1992400 0.0038993345 0.002542284 0.0044310241 - 1992500 0.0058376134 0.0024547601 0.0052823541 - 1992600 0.0060848393 0.0020066323 0.0049539764 - 1992700 0.0052477907 0.0020321311 0.0045740297 - 1992800 0.005249679 0.0025529926 0.0050958058 - 1992900 0.0053727672 0.0029005984 0.0055030325 - 1993000 0.0052625154 0.002932028 0.0054810588 - 1993100 0.0047142363 0.0029994144 0.0052828727 - 1993200 0.0053191154 0.0028774698 0.0054539163 - 1993300 0.0048289049 0.0025951217 0.0049341224 - 1993400 0.0076168859 0.0025009687 0.0061903978 - 1993500 0.0039761104 0.0032317131 0.0051576416 - 1993600 0.0044341498 0.0032938349 0.0054416262 - 1993700 0.0044275168 0.0031057684 0.0052503469 - 1993800 0.0075731693 0.0026348982 0.0063031521 - 1993900 0.0038286962 0.0026274942 0.0044820189 - 1994000 0.0050633462 0.0021650901 0.0046176484 - 1994100 0.0056199345 0.0020324649 0.0047546207 - 1994200 0.0048056788 0.0024693387 0.0047970894 - 1994300 0.006459677 0.0024678261 0.0055967322 - 1994400 0.0053801503 0.0024082668 0.0050142771 - 1994500 0.0048374889 0.0022730389 0.0046161976 - 1994600 0.0071441213 0.0018187729 0.0052792067 - 1994700 0.0064209046 0.0015227998 0.0046329255 - 1994800 0.0059406221 0.0016856726 0.0045631614 - 1994900 0.0045269071 0.0019621556 0.0041548762 - 1995000 0.0052455402 0.0020446714 0.0045854799 - 1995100 0.0042616975 0.00222956 0.0042938197 - 1995200 0.0039930582 0.0022136127 0.0041477503 - 1995300 0.0041277274 0.0018235115 0.0038228795 - 1995400 0.0050126134 0.0016191577 0.0040471423 - 1995500 0.0051791589 0.0019933343 0.0045019894 - 1995600 0.0063261234 0.0020172697 0.0050814857 - 1995700 0.0040529898 0.0017794217 0.0037425886 - 1995800 0.004570197 0.0017709365 0.0039846257 - 1995900 0.0054443845 0.0021039712 0.0047410949 - 1996000 0.0065881402 0.0020022043 0.0051933347 - 1996100 0.0047293703 0.0021049099 0.0043956986 - 1996200 0.0058157538 0.002259823 0.0050768287 - 1996300 0.0040998142 0.0023433742 0.0043292217 - 1996400 0.0052792745 0.0026857358 0.0052428843 - 1996500 0.0044951832 0.0025509056 0.00472826 - 1996600 0.0066010422 0.0021231854 0.0053205652 - 1996700 0.0038160025 0.0020482724 0.0038966486 - 1996800 0.0039766657 0.0021095955 0.0040357929 - 1996900 0.0044950258 0.002243618 0.0044208961 - 1997000 0.0045608723 0.0024545671 0.0046637396 - 1997100 0.005528286 0.0025390388 0.0052168023 - 1997200 0.0045379632 0.0023606972 0.0045587731 - 1997300 0.004636872 0.0025142273 0.0047602122 - 1997400 0.0053189046 0.0027464507 0.0053227951 - 1997500 0.0048530074 0.002783892 0.0051345675 - 1997600 0.0057274054 0.0021685357 0.0049427477 - 1997700 0.0038524705 0.0019583496 0.00382439 - 1997800 0.0051296654 0.0022335132 0.0047181949 - 1997900 0.0051018744 0.0027812269 0.0052524473 - 1998000 0.0047275885 0.0028043102 0.0050942359 - 1998100 0.0070847667 0.0019055429 0.0053372267 - 1998200 0.0065207742 0.0018082562 0.0049667562 - 1998300 0.0061191428 0.0020378316 0.0050017913 - 1998400 0.0063659105 0.0026460546 0.0057295425 - 1998500 0.0043373725 0.0027045125 0.0048054273 - 1998600 0.0048756101 0.0024999167 0.0048615404 - 1998700 0.0046508855 0.0023965866 0.0046493593 - 1998800 0.0062661518 0.0022217336 0.0052569009 - 1998900 0.0061555738 0.0023546222 0.0053362283 - 1999000 0.0043069574 0.0024786217 0.0045648042 - 1999100 0.0055141568 0.0028549884 0.0055259081 - 1999200 0.0034372635 0.0027990632 0.0044639877 - 1999300 0.0048351937 0.0023526277 0.0046946746 - 1999400 0.0057087851 0.0020335116 0.0047987044 - 1999500 0.0033912965 0.0023030393 0.0039456986 - 1999600 0.0054813169 0.0023096891 0.004964702 - 1999700 0.0048389727 0.0021943385 0.0045382159 - 1999800 0.0059277298 0.0020055057 0.0048767498 - 1999900 0.0059290305 0.002299977 0.0051718512 - 2000000 0.0047343315 0.0026625608 0.0049557526 -Loop time of 36.7413 on 1 procs for 2000000 steps with 64 atoms - -Pair time (%) = 0 (0) -Bond time (%) = 6.21948 (16.9278) -Neigh time (%) = 3.63757 (9.9005) -Comm time (%) = 3.27223 (8.90612) -Outpt time (%) = 2.95884 (8.05317) -Other time (%) = 20.6532 (56.2125) - -Nlocal: 64 ave 64 max 64 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4 ave 4 max 4 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 6 -Neighbor list builds = 2000000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 deleted file mode 100644 index e68a1d56d4..0000000000 Binary files a/examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 and /dev/null differ diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log deleted file mode 100644 index 86c0a385ce..0000000000 --- a/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log +++ /dev/null @@ -1,206 +0,0 @@ -############################################################ -# group name of the atoms under study : all -# total number of atoms in the group : 64 -# dimension of the system : 1 D -# number of atoms per unit cell : 2 -# dimension of the FFT mesh : 32 x 1 x 1 -# number of wait steps before measurement : 500000 -# frequency of the measurement : 10 -# output result after this many measurement: 50000 -# number of processors used by this run : 1 -############################################################ -# mapping information between lattice index and atom id -# nx ny nz nucell -32 1 1 2 -# l1 l2 l3 k atom_id -0 0 0 0 1 -0 0 0 1 2 -1 0 0 0 3 -1 0 0 1 4 -2 0 0 0 5 -2 0 0 1 6 -3 0 0 0 7 -3 0 0 1 8 -4 0 0 0 9 -4 0 0 1 10 -5 0 0 0 11 -5 0 0 1 12 -6 0 0 0 13 -6 0 0 1 14 -7 0 0 0 15 -7 0 0 1 16 -8 0 0 0 17 -8 0 0 1 18 -9 0 0 0 19 -9 0 0 1 20 -10 0 0 0 21 -10 0 0 1 22 -11 0 0 0 23 -11 0 0 1 24 -12 0 0 0 25 -12 0 0 1 26 -13 0 0 0 27 -13 0 0 1 28 -14 0 0 0 29 -14 0 0 1 30 -15 0 0 0 31 -15 0 0 1 32 -16 0 0 0 33 -16 0 0 1 34 -17 0 0 0 35 -17 0 0 1 36 -18 0 0 0 37 -18 0 0 1 38 -19 0 0 0 39 -19 0 0 1 40 -20 0 0 0 41 -20 0 0 1 42 -21 0 0 0 43 -21 0 0 1 44 -22 0 0 0 45 -22 0 0 1 46 -23 0 0 0 47 -23 0 0 1 48 -24 0 0 0 49 -24 0 0 1 50 -25 0 0 0 51 -25 0 0 1 52 -26 0 0 0 53 -26 0 0 1 54 -27 0 0 0 55 -27 0 0 1 56 -28 0 0 0 57 -28 0 0 1 58 -29 0 0 0 59 -29 0 0 1 60 -30 0 0 0 61 -30 0 0 1 62 -31 0 0 0 63 -31 0 0 1 64 -############################################################ -############################################################ -# Current time step : 1000000 -# Total number of measurements : 50000 -# Average temperature of the measurement : 0.00499889 -# Boltzmann constant under current units : 1 -# basis vector A1 = [2 0 0] -# basis vector A2 = [0 1 0] -# basis vector A3 = [0 0 1] -############################################################ -# qx qy qz Phi(q) -0 0 0 2.0269 0 -1.43323 0 -1.43323 0 1.01345 0 -0.03125 0 0 2.06958 0 -1.44367 0.144297 -1.44367 -0.144297 1.03745 0 -0.0625 0 0 2.00734 -7.10386e-17 -1.36818 0.273607 -1.36818 -0.273607 1.02097 0 -0.09375 0 0 2.06033 7.36546e-16 -1.32894 0.389454 -1.32894 -0.389454 1.00889 3.19674e-16 -0.125 0 0 2.04516 7.25738e-16 -1.20961 0.516478 -1.20961 -0.516478 1.0073 2.84154e-16 -0.15625 0 0 2.05756 0 -1.12954 0.615757 -1.12954 -0.615757 1.02862 0 -0.1875 0 0 2.01319 0 -0.970491 0.627631 -0.970491 -0.627631 0.998014 0 -0.21875 0 0 1.92269 1.42077e-16 -0.863486 0.66779 -0.863486 -0.66779 1.00343 8.73509e-17 -0.25 0 0 1.99044 1.71855e-16 -0.671658 0.661397 -0.671658 -0.661397 0.956893 7.10386e-17 -0.28125 0 0 1.96341 -7.10386e-17 -0.556809 0.66713 -0.556809 -0.66713 0.987126 4.2268e-17 -0.3125 0 0 2.04354 0 -0.442943 0.661601 -0.442943 -0.661601 0.961726 1.77596e-17 -0.34375 0 0 1.98412 0 -0.313464 0.632666 -0.313464 -0.632666 1.01134 -2.21836e-17 -0.375 0 0 2.00509 2.17993e-17 -0.187554 0.499349 -0.187554 -0.499349 0.953607 -8.87982e-18 -0.40625 0 0 1.91679 0 -0.0962947 0.408121 -0.0962947 -0.408121 1.02919 0 -0.4375 0 0 1.98963 0 -0.0137565 0.277826 -0.0137565 -0.277826 1.01624 0 -0.46875 0 0 2.08228 0 -0.0312083 0.0872272 -0.0312083 -0.0872272 0.991567 0 -0.5 0 0 1.95481 0 0.0542224 0 0.0542224 0 1.00583 0 -0.53125 0 0 2.08228 0 -0.0312083 -0.0872272 -0.0312083 0.0872272 0.991567 0 -0.5625 0 0 1.98963 0 -0.0137565 -0.277826 -0.0137565 0.277826 1.01624 0 -0.59375 0 0 1.91679 0 -0.0962947 -0.408121 -0.0962947 0.408121 1.02919 0 -0.625 0 0 2.00509 -2.17993e-17 -0.187554 -0.499349 -0.187554 0.499349 0.953607 8.87982e-18 -0.65625 0 0 1.98412 0 -0.313464 -0.632666 -0.313464 0.632666 1.01134 2.21836e-17 -0.6875 0 0 2.04354 0 -0.442943 -0.661601 -0.442943 0.661601 0.961726 -1.77596e-17 -0.71875 0 0 1.96341 7.10386e-17 -0.556809 -0.66713 -0.556809 0.66713 0.987126 -4.2268e-17 -0.75 0 0 1.99044 -1.71855e-16 -0.671658 -0.661397 -0.671658 0.661397 0.956893 -7.10386e-17 -0.78125 0 0 1.92269 -1.42077e-16 -0.863486 -0.66779 -0.863486 0.66779 1.00343 -8.73509e-17 -0.8125 0 0 2.01319 0 -0.970491 -0.627631 -0.970491 0.627631 0.998014 0 -0.84375 0 0 2.05756 0 -1.12954 -0.615757 -1.12954 0.615757 1.02862 0 -0.875 0 0 2.04516 -7.25738e-16 -1.20961 -0.516478 -1.20961 0.516478 1.0073 -2.84154e-16 -0.90625 0 0 2.06033 -7.36546e-16 -1.32894 -0.389454 -1.32894 0.389454 1.00889 -3.19674e-16 -0.9375 0 0 2.00734 7.10386e-17 -1.36818 -0.273607 -1.36818 0.273607 1.02097 0 -0.96875 0 0 2.06958 0 -1.44367 -0.144297 -1.44367 0.144297 1.03745 0 -############################################################ -# Current time step : 1500000 -# Total number of measurements : 100000 -# Average temperature of the measurement : 0.00499969 -# Boltzmann constant under current units : 1 -# basis vector A1 = [2 0 0] -# basis vector A2 = [0 1 0] -# basis vector A3 = [0 0 1] -############################################################ -# qx qy qz Phi(q) -0 0 0 2.00227 0 -1.41582 0 -1.41582 0 1.00114 0 -0.03125 0 0 2.06839 -2.94857e-15 -1.44775 0.141336 -1.44775 -0.141336 1.03568 -1.48867e-15 -0.0625 0 0 1.99449 0 -1.35985 0.267438 -1.35985 -0.267438 0.997747 0 -0.09375 0 0 2.01906 7.07225e-16 -1.30258 0.390432 -1.30258 -0.390432 1.00279 3.55249e-16 -0.125 0 0 2.0047 0 -1.19787 0.503497 -1.19787 -0.503497 1.00067 -3.55249e-17 -0.15625 0 0 2.05042 4.26299e-16 -1.12849 0.613659 -1.12849 -0.613659 1.03457 1.85685e-16 -0.1875 0 0 1.99151 0 -0.971684 0.625667 -0.971684 -0.625667 0.990665 0 -0.21875 0 0 1.96519 -7.10498e-17 -0.861495 0.687109 -0.861495 -0.687109 1.0008 0 -0.25 0 0 2.01865 0 -0.687312 0.684014 -0.687312 -0.684014 0.977055 0 -0.28125 0 0 1.9933 0 -0.560168 0.698726 -0.560168 -0.698726 1.00805 -4.40715e-17 -0.3125 0 0 2.01323 0 -0.446505 0.648764 -0.446505 -0.648764 1.00283 -1.77625e-17 -0.34375 0 0 2.00398 0 -0.313827 0.630741 -0.313827 -0.630741 0.996834 0 -0.375 0 0 2.0191 0 -0.216211 0.499651 -0.216211 -0.499651 0.978322 0 -0.40625 0 0 1.97734 -4.44061e-18 -0.102328 0.398954 -0.102328 -0.398954 1.03793 0 -0.4375 0 0 1.99332 -2.22031e-18 -0.0639782 0.238226 -0.0639782 -0.238226 1.00811 -1.3774e-18 -0.46875 0 0 2.02854 0 -0.0151203 0.0911116 -0.0151203 -0.0911116 1.00593 0 -0.5 0 0 1.99466 0 0.0671755 0 0.0671755 0 0.967275 0 -0.53125 0 0 2.02854 0 -0.0151203 -0.0911116 -0.0151203 0.0911116 1.00593 0 -0.5625 0 0 1.99332 2.22031e-18 -0.0639782 -0.238226 -0.0639782 0.238226 1.00811 1.3774e-18 -0.59375 0 0 1.97734 4.44061e-18 -0.102328 -0.398954 -0.102328 0.398954 1.03793 0 -0.625 0 0 2.0191 0 -0.216211 -0.499651 -0.216211 0.499651 0.978322 0 -0.65625 0 0 2.00398 0 -0.313827 -0.630741 -0.313827 0.630741 0.996834 0 -0.6875 0 0 2.01323 0 -0.446505 -0.648764 -0.446505 0.648764 1.00283 1.77625e-17 -0.71875 0 0 1.9933 0 -0.560168 -0.698726 -0.560168 0.698726 1.00805 4.40715e-17 -0.75 0 0 2.01865 0 -0.687312 -0.684014 -0.687312 0.684014 0.977055 0 -0.78125 0 0 1.96519 7.10498e-17 -0.861495 -0.687109 -0.861495 0.687109 1.0008 0 -0.8125 0 0 1.99151 0 -0.971684 -0.625667 -0.971684 0.625667 0.990665 0 -0.84375 0 0 2.05042 -4.26299e-16 -1.12849 -0.613659 -1.12849 0.613659 1.03457 -1.85685e-16 -0.875 0 0 2.0047 0 -1.19787 -0.503497 -1.19787 0.503497 1.00067 3.55249e-17 -0.90625 0 0 2.01906 -7.07225e-16 -1.30258 -0.390432 -1.30258 0.390432 1.00279 -3.55249e-16 -0.9375 0 0 1.99449 0 -1.35985 -0.267438 -1.35985 0.267438 0.997747 0 -0.96875 0 0 2.06839 2.94857e-15 -1.44775 -0.141336 -1.44775 0.141336 1.03568 1.48867e-15 -############################################################ -# Current time step : 2000000 -# Total number of measurements : 150000 -# Average temperature of the measurement : 0.00499897 -# Boltzmann constant under current units : 1 -# basis vector A1 = [2 0 0] -# basis vector A2 = [0 1 0] -# basis vector A3 = [0 0 1] -############################################################ -# qx qy qz Phi(q) -0 0 0 1.99479 0 -1.41053 0 -1.41053 0 0.997396 0 -0.03125 0 0 2.03068 0 -1.41965 0.138345 -1.41965 -0.138345 1.0155 0 -0.0625 0 0 1.99892 7.10396e-17 -1.36162 0.269053 -1.36162 -0.269053 1.00066 0 -0.09375 0 0 2.00599 0 -1.29893 0.389829 -1.29893 -0.389829 0.995323 0 -0.125 0 0 1.991 6.87803e-16 -1.20232 0.495552 -1.20232 -0.495552 0.991252 2.84159e-16 -0.15625 0 0 2.05187 1.42079e-16 -1.12612 0.617447 -1.12612 -0.617447 1.02736 0 -0.1875 0 0 1.97476 7.10396e-17 -0.972012 0.630423 -0.972012 -0.630423 0.996946 0 -0.21875 0 0 2.00314 0 -0.862555 0.695244 -0.862555 -0.695244 0.999215 0 -0.25 0 0 1.9755 0 -0.69573 0.680591 -0.69573 -0.680591 0.988546 0 -0.28125 0 0 1.99393 0 -0.560979 0.692292 -0.560979 -0.692292 0.995507 -3.55198e-17 -0.3125 0 0 2.00817 0 -0.436753 0.642127 -0.436753 -0.642127 0.989051 0 -0.34375 0 0 2.02348 0 -0.310766 0.620888 -0.310766 -0.620888 1.01631 0 -0.375 0 0 2.01177 0 -0.213987 0.483325 -0.213987 -0.483325 0.98933 0 -0.40625 0 0 1.97394 0 -0.116509 0.382146 -0.116509 -0.382146 1.03672 0 -0.4375 0 0 1.98656 0 -0.0609164 0.250798 -0.0609164 -0.250798 1.01266 1.39007e-18 -0.46875 0 0 2.03013 0 -0.0242785 0.120597 -0.0242785 -0.120597 1.02741 1.78858e-19 -0.5 0 0 1.98872 0 0.0648313 0 0.0648313 0 0.973791 0 -0.53125 0 0 2.03013 0 -0.0242785 -0.120597 -0.0242785 0.120597 1.02741 -1.78858e-19 -0.5625 0 0 1.98656 0 -0.0609164 -0.250798 -0.0609164 0.250798 1.01266 -1.39007e-18 -0.59375 0 0 1.97394 0 -0.116509 -0.382146 -0.116509 0.382146 1.03672 0 -0.625 0 0 2.01177 0 -0.213987 -0.483325 -0.213987 0.483325 0.98933 0 -0.65625 0 0 2.02348 0 -0.310766 -0.620888 -0.310766 0.620888 1.01631 0 -0.6875 0 0 2.00817 0 -0.436753 -0.642127 -0.436753 0.642127 0.989051 0 -0.71875 0 0 1.99393 0 -0.560979 -0.692292 -0.560979 0.692292 0.995507 3.55198e-17 -0.75 0 0 1.9755 0 -0.69573 -0.680591 -0.69573 0.680591 0.988546 0 -0.78125 0 0 2.00314 0 -0.862555 -0.695244 -0.862555 0.695244 0.999215 0 -0.8125 0 0 1.97476 -7.10396e-17 -0.972012 -0.630423 -0.972012 0.630423 0.996946 0 -0.84375 0 0 2.05187 -1.42079e-16 -1.12612 -0.617447 -1.12612 0.617447 1.02736 0 -0.875 0 0 1.991 -6.87803e-16 -1.20232 -0.495552 -1.20232 0.495552 0.991252 -2.84159e-16 -0.90625 0 0 2.00599 0 -1.29893 -0.389829 -1.29893 0.389829 0.995323 0 -0.9375 0 0 1.99892 -7.10396e-17 -1.36162 -0.269053 -1.36162 0.269053 1.00066 0 -0.96875 0 0 2.03068 0 -1.41965 -0.138345 -1.41965 0.138345 1.0155 0 diff --git a/examples/PACKAGES/pod/InP/InP_coefficients.pod b/examples/PACKAGES/pod/InP/InP_coefficients.pod new file mode 100644 index 0000000000..faccfa072d --- /dev/null +++ b/examples/PACKAGES/pod/InP/InP_coefficients.pod @@ -0,0 +1,305 @@ +model_coefficients: 304 0 0 +-3.756301 +914.674801 +-370.747265 +-141.227291 +97.101196 +-59.216907 +9.975284 +87.329406 +-10.969150 +14.411744 +-2.270453 +0.798817 +-0.121719 +114.805574 +-2631.563672 +-869.027988 +-1038.286258 +2431.480027 +31.972558 +139.437898 +29.230520 +39.179879 +-189.998549 +-16.358691 +18.699184 +13.386293 +12.847911 +7.310155 +1.677341 +-9.237073 +-2.228285 +0.137303 +6.446888 +-0.385837 +0.272000 +0.111052 +-1.264342 +-0.711451 +450.463638 +-499.339551 +550.704146 +-1638.278950 +-1311.408792 +-24.811632 +-14.000684 +-39.928838 +44.690659 +35.934791 +-0.425535 +16.810067 +-1.951262 +26.118670 +28.549237 +-1.779991 +-1.907896 +4.278671 +-5.852529 +-11.518503 +0.285252 +0.210939 +-1.153276 +0.744801 +2.765281 +-365.425648 +892.154409 +616.198109 +-808.930752 +-241.494545 +60.329248 +-50.220263 +-89.366098 +47.692144 +12.376825 +-11.304060 +-0.465577 +20.908593 +0.768057 +-0.296966 +-1.434787 +0.089423 +-3.273582 +1.085951 +1.627005 +0.063449 +0.501713 +-0.025247 +-1.127277 +-0.619276 +-950.742997 +11175.508296 +1041.077100 +-8713.542159 +11.024588 +-193.368092 +-17.871650 +193.000879 +-1.221800 +0.201038 +-0.297456 +10.197177 +0.118306 +-2.486775 +0.340362 +0.179573 +2064.315112 +11898.567992 +-7130.614814 +-2965.017905 +-36.665484 +-156.646217 +112.838247 +64.147104 +-0.187677 +8.822337 +-2.516814 +0.833110 +-0.808597 +-3.112898 +2.172317 +1.684634 +-5.757502 +4129.051881 +-2191.420379 +-5640.863432 +2.123836 +-34.024960 +35.525113 +106.884920 +0.406772 +6.365527 +-0.015093 +2.711538 +-0.263692 +-0.604293 +0.790243 +1.092726 +593.864089 +-2785.368577 +-1100.723468 +4424.744171 +-20.023164 +47.252092 +34.797296 +-101.504738 +-1.911711 +-0.110737 +3.998625 +-2.768303 +-0.189524 +0.793288 +-0.405026 +-1.116385 +4.808874 +86.919761 +-10.887316 +14.382398 +-2.271034 +0.710124 +-0.114050 +170.975102 +-54.119757 +-23.638119 +28.153323 +-15.183264 +2.919447 +-185.866164 +-1165.581453 +-1256.610349 +1133.815010 +814.761739 +9.901474 +31.315227 +40.389531 +-39.201068 +-50.871475 +3.268994 +19.578821 +12.684861 +-13.440885 +2.022633 +1.483279 +-4.388229 +0.944679 +3.110080 +-2.163427 +0.160512 +-0.197641 +-1.121333 +1.023995 +2.077494 +-78.649494 +15.740666 +1379.998028 +-267.931116 +-631.685867 +0.779724 +-28.384680 +-104.334909 +40.727192 +54.977623 +4.534376 +13.738711 +2.994157 +-10.950852 +-4.057951 +1.099589 +-1.782453 +3.174200 +2.605193 +-1.835511 +0.063386 +0.124447 +-0.881517 +-0.703873 +0.712785 +-567.114384 +363.884433 +-300.309621 +-1421.591050 +-1083.371637 +45.559123 +-7.797512 +24.330267 +71.829748 +60.799510 +-2.099976 +-9.821055 +-6.488823 +9.426431 +6.385231 +-0.836215 +3.533300 +2.741734 +-3.602311 +-3.863372 +-0.122980 +-0.147120 +-0.378902 +-0.232987 +0.445875 +-237.448044 +442.663085 +2103.157345 +-2382.920549 +0.583996 +-6.353184 +-17.798247 +72.320744 +-0.422216 +1.198193 +3.257409 +6.944903 +0.255190 +-0.887514 +-0.316214 +0.345565 +-242.443134 +4329.522091 +534.487792 +-4571.367114 +-9.591790 +-62.990215 +20.323544 +169.640829 +-2.788146 +2.114659 +7.272737 +21.210166 +0.904969 +-1.154060 +-1.376235 +-1.148246 +129.689234 +5953.209838 +667.823321 +-83.797221 +3.417016 +-126.968016 +-14.909772 +41.785404 +1.415997 +-5.278588 +-0.463605 +8.009232 +0.030211 +-0.765006 +-0.826223 +0.103515 +147.565462 +4404.556538 +3774.833555 +-2327.923578 +-5.422196 +-107.433002 +-70.175719 +74.887031 +-0.424490 +-6.620110 +-2.179770 +5.588150 +-0.222514 +-0.435209 +0.034179 +0.388588 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod b/examples/PACKAGES/pod/InP/InP_data.pod similarity index 58% rename from examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod rename to examples/PACKAGES/pod/InP/InP_data.pod index 2aed5d60dd..7dfc09fd38 100644 --- a/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod +++ b/examples/PACKAGES/pod/InP/InP_data.pod @@ -1,20 +1,21 @@ file_format extxyz file_extension xyz -path_to_training_data_set "../Ta/XYZ" -path_to_test_data_set "../Ta/XYZ" +path_to_training_data_set "XYZ" +path_to_test_data_set "XYZ" +path_to_environment_configuration_set "XYZ" fitting_weight_energy 100.0 fitting_weight_force 1.0 -fitting_regularization_parameter 1e-10 +fitting_regularization_parameter 1e-12 error_analysis_for_training_data_set 1 error_analysis_for_test_data_set 0 # Add the following basename to the name of output files -basename_for_output_files Ta +basename_for_output_files InP # number of digits after the decimal point for pod coefficients -precision_for_pod_coefficients 5 +precision_for_pod_coefficients 6 diff --git a/examples/PACKAGES/pod/InP/InP_param.pod b/examples/PACKAGES/pod/InP/InP_param.pod new file mode 100644 index 0000000000..08d3cbd412 --- /dev/null +++ b/examples/PACKAGES/pod/InP/InP_param.pod @@ -0,0 +1,48 @@ +# chemical element symbols +species In P + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 0.8 + +# outer cut-off radius +rcut 5.0 + +# use only for enviroment-adaptive potentials +number_of_environment_clusters 1 + +# principal_components of local descriptors +number_of_principal_components 2 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 4 +inverse_polynomial_degree 8 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_angular_degree 4 + +# four-body linear POD potential +fourbody_number_radial_basis_functions 4 +fourbody_angular_degree 2 + +# five-body linear POD potential +fivebody_number_radial_basis_functions 0 +fivebody_angular_degree 0 + +# six-body linear POD potential +sixbody_number_radial_basis_functions 0 +sixbody_angular_degree 0 + +# seven-body linear POD potential +sevenbody_number_radial_basis_functions 0 +sevenbody_angular_degree 0 + diff --git a/examples/PACKAGES/pod/InP/InP_training_analysis.pod b/examples/PACKAGES/pod/InP/InP_training_analysis.pod new file mode 100644 index 0000000000..c5978b4f41 --- /dev/null +++ b/examples/PACKAGES/pod/InP/InP_training_analysis.pod @@ -0,0 +1,1932 @@ +# Bulk.xyz + config # atoms volume energy DFT energy energy error force DFT force force error + 1 8 198.155287 -38.7142527 -38.72767843 0.001678216549 6.295437039e-14 0 1.001296846e-14 +# EOS.xyz + config # atoms volume energy DFT energy energy error force DFT force force error + 2 4 100.2503986 -19.34119279 -19.33946215 0.0004326611879 0.06711672157 0.004696 0.01040891634 + 3 4 87.78666244 -18.97507078 -18.99216114 0.004272590246 0.0921948579 0.015096 0.01790247305 + 4 4 84.97085209 -18.74485578 -18.75980296 0.003736795403 0.1445652479 0.026416 0.0285296792 + 5 4 82.52133779 -18.48336398 -18.49408247 0.002679621564 0.204459569 0.036914 0.04029250893 + 6 4 80.35345611 -18.19667652 -18.20222587 0.001387336859 0.2609967925 0.055734 0.05282608186 + 7 4 78.40832856 -17.88702363 -17.88899513 0.0004928743307 0.3331404351 0.063452 0.06612221232 + 8 4 76.64099144 -17.5584741 -17.55730043 0.0002934176408 0.4032831914 0.080334 0.08066051764 + 9 4 75.04528905 -17.21835854 -17.2153404 0.0007545342183 0.5044230229 0.087346 0.09875170581 + 10 4 73.54481067 -16.85564361 -16.85354169 0.0005254799895 0.6206833374 0.104282 0.1209082138 + 11 4 95.10547773 -19.29849191 -19.30657301 0.002020274276 0.01107877122 0.007376 0.0006388833987 + 12 4 91.0912603 -19.16490969 -19.18005062 0.003785233211 0.04261952943 0.009042 0.008630599736 + 13 4 133.5525685 -17.87016662 -17.83772988 0.00810918539 0.06023506826 0.00984 0.01168970277 + 14 4 103.4647206 -19.30816075 -19.30159325 0.001641875814 0.08325884021 0.004756 0.01308430812 + 15 4 107.3699915 -19.20438939 -19.20780056 0.0008527912821 0.05045401328 0.000514 0.008330624503 + 16 4 112.3942784 -19.0449568 -19.02621709 0.004684928181 0.06542263844 0.00049 0.01083729791 + 17 4 119.5073443 -18.7116458 -18.68388388 0.00694047906 0.03149028764 0.005468 0.006171255461 + 18 8 125 -24.90402469 -24.90732287 0.0004122725924 2.120052354e-13 0 3.533631721e-14 + 19 8 125.751501 -25.32593152 -25.33111609 0.000648070627 1.855681908e-13 0 2.977248078e-14 + 20 8 125 -34.1306733 -34.11351114 0.00214526983 2.107129136e-14 0 3.234263281e-15 + 21 8 126.506008 -25.73866893 -25.74566406 0.0008743906955 3.068919123e-13 0 5.246728977e-14 + 22 8 127.263527 -26.14241366 -26.1510292 0.001076942689 4.443348898e-13 0 7.630007737e-14 + 23 8 128.024064 -26.53733606 -26.54747446 0.001267300611 3.650160727e-13 0 6.500355809e-14 + 24 8 128.787625 -26.92360021 -26.93512423 0.001440502614 2.360835421e-13 0 3.975523614e-14 + 25 8 129.554216 -27.30136406 -27.3140736 0.001588692672 3.658450198e-13 0 6.010007307e-14 + 26 8 130.323843 -27.67077954 -27.68445805 0.001709813913 1.712785934e-13 0 2.999452538e-14 + 27 8 131.096512 -28.03199274 -28.04644254 0.001806225048 1.533791492e-13 0 2.552587771e-14 + 28 8 131.872229 -28.38514408 -28.400158 0.001876739913 1.164238116e-13 0 2.002102188e-14 + 29 8 132.651 -28.7303685 -28.74572124 0.001919092806 2.893581151e-13 0 4.934941344e-14 + 30 8 133.432831 -29.06779564 -29.0832711 0.001934432199 1.391778701e-13 0 2.377727644e-14 + 31 8 132.651 -35.59602814 -35.60415475 0.001015826139 1.122420132e-13 0 1.753298217e-14 + 32 8 134.217728 -29.3975501 -29.41294262 0.001924065454 3.038656689e-13 0 4.987676938e-14 + 33 8 135.005697 -29.71975159 -29.73481243 0.001882604646 1.515014749e-13 0 2.575717417e-14 + 34 8 135.796744 -30.03451525 -30.04902687 0.001813952399 2.876096334e-13 0 4.718910448e-14 + 35 8 136.590875 -30.34195182 -30.35573414 0.001722790348 3.38400877e-13 0 5.85411349e-14 + 36 8 137.388096 -30.64216792 -30.65504269 0.001609346582 4.726965504e-13 0 8.307706375e-14 + 37 8 138.188413 -30.93526631 -30.94704781 0.001472687261 4.109208686e-13 0 6.826483823e-14 + 38 8 138.991832 -31.22134616 -31.23186179 0.001314453749 1.218514658e-13 0 2.031245542e-14 + 39 8 139.798359 -31.50050329 -31.50962505 0.001140220421 2.015321164e-13 0 3.149332647e-14 + 40 8 140.608 -31.77283045 -31.78044211 0.0009514570428 2.106780929e-13 0 3.373227623e-14 + 41 8 141.420761 -32.03841763 -32.04448224 0.0007580758701 3.291275771e-13 0 5.363764988e-14 + 42 8 140.608 -36.55772971 -36.57876366 0.002629243454 9.469273174e-14 0 1.522483356e-14 + 43 8 142.236648 -32.29735228 -32.30180778 0.0005569373789 2.195289666e-13 0 3.634130034e-14 + 44 8 143.055667 -32.54971961 -32.55240718 0.0003359460022 2.564620474e-13 0 4.091171846e-14 + 45 8 143.877824 -32.79560287 -32.79646907 0.0001082748383 1.388261422e-13 0 2.455905849e-14 + 46 8 144.703125 -33.0350836 -33.0341342 0.000118675575 8.878230772e-14 0 1.40350694e-14 + 47 8 145.531576 -33.26824192 -33.26546078 0.0003476429419 1.107578655e-13 0 1.813364274e-14 + 48 8 146.363183 -33.49515677 -33.4905808 0.0005719957242 1.124750174e-13 0 1.83973207e-14 + 49 8 147.197952 -33.71590615 -33.70959217 0.0007892472898 1.581120916e-13 0 2.577105196e-14 + 50 8 148.035889 -33.93056741 -33.92253789 0.001003690304 1.601498541e-13 0 2.389292468e-14 + 51 8 148.877 -34.13921746 -34.12960189 0.001201946146 1.299656777e-13 0 2.102484853e-14 + 52 8 149.721291 -34.34193297 -34.3308093 0.001390459219 2.114973405e-13 0 3.46759658e-14 + 53 8 148.877 -37.11337019 -37.12608044 0.001588781299 4.438547723e-14 0 6.519942956e-15 + 54 8 150.568768 -34.53879064 -34.52629014 0.001562562212 3.57767505e-13 0 5.77038417e-14 + 55 8 151.419437 -34.72986733 -34.71610965 0.001719709628 1.129431907e-13 0 1.711131237e-14 + 56 8 152.273304 -34.9152403 -34.90038699 0.001856663168 9.209632916e-14 0 1.458092906e-14 + 57 8 153.130375 -35.09498734 -35.07920914 0.001972275052 1.651847707e-13 0 2.654358215e-14 + 58 8 153.990656 -35.26918695 -35.25266839 0.002064820348 2.178540205e-13 0 3.863113533e-14 + 59 8 154.854153 -35.43791845 -35.42083938 0.002134883141 2.275918207e-13 0 3.872827984e-14 + 60 8 155.720872 -35.60126206 -35.58377308 0.002186122667 2.013056315e-13 0 3.199292683e-14 + 61 8 156.590819 -35.75929906 -35.74165769 0.002205171711 3.270916194e-13 0 5.238864897e-14 + 62 8 157.464 -35.9121118 -35.89454795 0.002195480918 1.566843717e-13 0 2.638630055e-14 + 63 8 158.340421 -36.05978373 -36.04247856 0.002163146364 1.471988685e-13 0 2.336556874e-14 + 64 8 157.464 -37.32735447 -37.32262953 0.0005906170637 3.985130574e-14 0 5.104321388e-15 + 65 8 159.220088 -36.20239947 -36.18557035 0.00210364029 1.763124698e-13 0 2.87964097e-14 + 66 8 160.103007 -36.34004476 -36.32389911 0.002018206127 5.697726866e-14 0 9.344377124e-15 + 67 8 160.989184 -36.47280642 -36.45752485 0.001910196485 1.975928454e-13 0 2.924975077e-14 + 68 8 161.878625 -36.60077232 -36.58655803 0.001776786564 1.555190252e-13 0 2.624289674e-14 + 69 8 162.771336 -36.72403126 -36.71102998 0.00162516042 1.412460708e-13 0 2.504940699e-14 + 70 8 163.667323 -36.84267287 -36.83107858 0.00144928636 2.003522571e-13 0 3.272844958e-14 + 71 8 164.566592 -36.95678745 -36.94671248 0.001259371456 2.802794912e-13 0 4.816517555e-14 + 72 8 165.469149 -37.06646582 -37.05803876 0.001053382772 1.501596136e-13 0 2.396925251e-14 + 73 8 166.375 -37.17179911 -37.16514204 0.0008321341323 5.511762558e-14 0 8.525587643e-15 + 74 8 167.284151 -37.27287855 -37.26803657 0.0006052473145 9.834232472e-14 0 1.762479052e-14 + 75 8 166.375 -37.24337005 -37.23643929 0.0008663449821 7.193383609e-14 0 9.097007751e-15 + 76 8 168.196608 -37.3697952 -37.36679872 0.0003745603949 1.247370278e-13 0 2.163547119e-14 + 77 8 169.112377 -37.46263974 -37.46157771 0.0001327534529 1.644603556e-13 0 2.518124598e-14 + 78 8 170.031464 -37.55150212 -37.55237754 0.0001094280476 1.000876217e-13 0 1.617918762e-14 + 79 8 170.953875 -37.63647131 -37.6392704 0.0003498868469 1.237283914e-13 0 2.00719071e-14 + 80 8 171.879616 -37.71763497 -37.72232209 0.0005858902543 1.1589855e-13 0 1.841351146e-14 + 81 8 172.808693 -37.79507914 -37.80157766 0.0008123150872 1.562897313e-13 0 2.502165142e-14 + 82 8 173.741112 -37.86888791 -37.87745843 0.001071315566 9.890270877e-14 0 1.448378454e-14 + 83 8 174.676879 -37.93914308 -37.94934999 0.001275863594 4.971171589e-14 0 7.433868336e-15 + 84 8 175.616 -38.00592389 -38.01765923 0.001466916916 2.357725957e-13 0 4.002816597e-14 + 85 8 176.558481 -38.06930668 -38.08244214 0.001641931917 9.399919782e-14 0 1.53233907e-14 + 86 8 175.616 -36.91159044 -36.92303918 0.0014310923 1.339836444e-13 0 2.427135868e-14 + 87 8 177.504328 -38.12936462 -38.14373382 0.001796150207 8.346269116e-14 0 1.405126016e-14 + 88 8 178.453547 -38.18616744 -38.20162048 0.001931630609 7.090560403e-14 0 1.097039126e-14 + 89 8 179.406144 -38.23978123 -38.25614712 0.00204573683 2.0462588e-13 0 3.108624469e-14 + 90 8 180.362125 -38.29026825 -38.30736293 0.002136834871 1.332582387e-13 0 2.197316403e-14 + 91 8 181.321496 -38.33768682 -38.35533434 0.002205940396 2.138344018e-13 0 3.67298784e-14 + 92 8 182.284263 -38.3820912 -38.40014053 0.002256166343 9.767720229e-14 0 1.706389659e-14 + 93 8 183.250432 -38.42353164 -38.44178079 0.002281143553 5.579154461e-14 0 9.012466699e-15 + 94 8 184.220009 -38.46205442 -38.48039501 0.002292573571 1.271642832e-13 0 2.144118216e-14 + 95 8 185.193 -38.497702 -38.51595497 0.002281621574 9.534022447e-14 0 1.486658019e-14 + 96 8 186.169411 -38.53051324 -38.54855587 0.00225532886 1.343761993e-13 0 2.300705922e-14 + 97 8 185.193 -36.40728171 -36.42582461 0.002317863018 3.728109844e-14 0 5.238184183e-15 + 98 8 187.149248 -38.56052374 -38.57822204 0.002212287058 1.210326629e-13 0 2.001177002e-14 + 99 8 188.132517 -38.58776624 -38.60507996 0.002164215247 1.827469955e-13 0 2.709002004e-14 + 100 8 189.119224 -38.61227107 -38.62911702 0.002105744085 1.11818836e-13 0 1.864538616e-14 + 101 8 190.109375 -38.63406676 -38.65037737 0.002038826527 4.734898438e-14 0 8.10983225e-15 + 102 8 191.102976 -38.65318065 -38.66895988 0.00197240398 4.766169611e-13 0 7.396340485e-14 + 103 8 192.100033 -38.66963957 -38.68491445 0.001909359901 3.949754638e-14 0 6.445365075e-15 + 104 8 193.100552 -38.68347056 -38.69826028 0.0018487148 6.030624548e-14 0 9.948928255e-15 + 105 8 194.104539 -38.69470157 -38.70903762 0.001792006038 9.213473725e-14 0 1.528927448e-14 + 106 8 195.112 -38.70336215 -38.71735037 0.001748527793 1.109561733e-13 0 1.686310235e-14 + 107 8 196.122941 -38.70948404 -38.72316577 0.001710215895 6.429045107e-14 0 1.149239847e-14 + 108 8 195.112 -35.7778757 -35.78277343 0.00061221655 2.431616332e-14 0 3.581646775e-15 + 109 8 197.137368 -38.71310172 -38.72661844 0.001689590126 5.158256025e-14 0 8.690964615e-15 + 110 8 198.155287 -38.7142527 -38.72767843 0.001678216549 6.295437039e-14 0 1.001296846e-14 + 111 8 199.176704 -38.71297772 -38.72640441 0.001678335766 1.486959607e-13 0 2.249314739e-14 + 112 8 200.201625 -38.70932072 -38.72284809 0.001690921727 7.483452632e-14 0 1.283796564e-14 + 113 8 201.230056 -38.70332849 -38.71708504 0.001719568745 7.139256276e-14 0 1.011472084e-14 + 114 8 202.262003 -38.69505027 -38.70909826 0.001755998973 6.964302642e-14 0 1.121769778e-14 + 115 8 203.297472 -38.68453702 -38.69896441 0.001803424077 1.020500203e-13 0 1.557006477e-14 + 116 8 204.336469 -38.67184068 -38.68669915 0.001857308565 9.935211667e-14 0 1.716416722e-14 + 117 8 205.379 -38.65701341 -38.67236985 0.001919555536 8.333501328e-14 0 1.49671038e-14 + 118 8 206.425071 -38.64010685 -38.65601166 0.001988100659 3.510246123e-14 0 6.352462501e-15 + 119 8 205.379 -35.04118028 -35.02683676 0.001792939447 5.615527816e-15 0 6.958062516e-16 + 120 8 207.474688 -38.62117171 -38.63763952 0.002058475908 6.191049403e-14 0 9.797560927e-15 + 121 8 208.527857 -38.60025741 -38.61729887 0.002130182498 4.810564452e-14 0 6.746513099e-15 + 122 8 209.584584 -38.57741206 -38.59504202 0.002203745201 3.945529953e-14 0 6.402572273e-15 + 123 8 210.644875 -38.55268252 -38.57091757 0.002279381049 3.772859434e-14 0 6.467852489e-15 + 124 8 211.708736 -38.52611453 -38.54483207 0.002339693042 8.68311853e-14 0 1.290685828e-14 + 125 8 212.776173 -38.49775274 -38.51692278 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0.4641675188 0.10066527 0.02146506191 + 1687 65 1604.70183 -312.7824096 -312.8661537 0.001288371058 0.4593230578 0.1160045485 0.02140721242 + 1688 65 1604.70183 -312.7827097 -312.8670765 0.001297951341 0.4517517795 0.07223430571 0.02117155404 + 1689 65 1604.70183 -312.7827062 -312.867388 0.001302795928 0.449515524 0.09349027471 0.02138303966 + 1690 65 1604.70183 -312.782481 -312.8681361 0.001317770758 0.4484735522 0.06209768045 0.02071424159 + 1691 65 1604.70183 -312.7820984 -312.8684286 0.001328157453 0.4503763125 0.08406537966 0.02040153776 + 1692 65 1604.70183 -312.7821998 -312.8690162 0.001335637848 0.4443115411 0.06841735028 0.01988575967 + 1693 65 1604.70183 -312.7821284 -312.8690893 0.001337859188 0.4443389193 0.09535145 0.01972203653 + 1694 65 1604.70183 -312.7823322 -312.8694314 0.001339986902 0.4430941658 0.06817042813 0.01978224298 + 1695 65 1604.70183 -312.7823842 -312.8695849 0.001341548832 0.4457852869 0.08261573572 0.01996550908 + 1696 65 1604.70183 -312.7473949 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1604.70183 -312.780274 -312.8644088 0.001294382113 0.4775291363 0.1553162351 0.0219119218 +# s_vIn.xyz + config # atoms volume energy DFT energy energy error force DFT force force error + 1707 63 1604.70183 -302.4723613 -301.963864 0.00807138611 0.7503228209 1.255303072 0.0411580261 + 1708 63 1604.70183 -302.5717986 -302.0639546 0.008061015576 0.6187164138 0.1439802587 0.02075486367 + 1709 63 1604.70183 -302.5825981 -302.0650808 0.008214560288 0.6244236845 0.1518789276 0.02150426704 + 1710 63 1604.70183 -302.5901442 -302.0666063 0.008310125706 0.6198998723 0.06759786497 0.02257459914 + 1711 63 1604.70183 -302.593363 -302.066815 0.008357905249 0.6199076487 0.07299485635 0.02333115775 + 1712 63 1604.70183 -302.5945672 -302.0672434 0.008370219359 0.630274001 0.03153428306 0.02339946701 + 1713 63 1604.70183 -302.5950709 -302.0673202 0.008376994643 0.6357040225 0.03175548866 0.02354731292 + 1714 63 1604.70183 -302.5957252 -302.0673961 0.008386175162 0.637111431 0.0141777282 0.02371649196 + 1715 63 1604.70183 -302.5957163 -302.067397 0.008386021098 0.6370587111 0.01392129466 0.02371037802 + 1716 63 1604.70183 -302.4988 -302.0161101 0.007661744499 0.4741019735 0.5230398817 0.02392615243 + 1717 63 1604.70183 -302.503196 -302.0242245 0.007602723414 0.4439845687 0.3934456449 0.01954618673 + 1718 63 1604.70183 -302.5080162 -302.0319351 0.007556843796 0.4343436784 0.3097762997 0.01835533205 + 1719 63 1604.70183 -302.5166858 -302.041557 0.007541726152 0.4729170245 0.3339746283 0.022282543 + 1720 63 1604.70183 -302.5184911 -302.0422479 0.007559415992 0.4963638653 0.3907744969 0.02355220095 + 1721 63 1604.70183 -302.5264677 -302.0489124 0.007580244183 0.5171429359 0.3084001845 0.0223657876 + 1722 63 1604.70183 -302.5511078 -302.0592399 0.007807428146 0.6003753884 0.2324725691 0.02006992626 + 1723 63 1604.70183 -302.556945 -302.0598006 0.007891181519 0.6221745869 0.264032255 0.02043094953 +# s_vP.xyz + config # atoms volume energy DFT energy energy error force DFT force force error 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0.1256294185 0.01463001989 + 1763 63 1604.70183 -300.9142963 -300.9048357 0.0001501672728 0.2662175163 0.1107049978 0.01404799852 + 1764 63 1604.70183 -300.8440167 -300.8676537 0.0003751906939 0.5188260296 0.4282552364 0.02256107812 + 1765 63 1604.70183 -300.8533013 -300.8785697 0.0004010870151 0.5278911297 0.4623712699 0.02278426515 + 1766 63 1604.70183 -300.8631711 -300.8902517 0.0004298512535 0.4598639491 0.2758713346 0.019775999 + 1767 63 1604.70183 -300.868526 -300.8946842 0.0004152100696 0.4364336409 0.2591136678 0.01977322923 + 1768 63 1604.70183 -300.8732182 -300.8986431 0.0004035700916 0.3865654608 0.1411599181 0.01802163002 + 1769 63 1604.70183 -300.8747167 -300.8991785 0.0003882834203 0.3761269693 0.1663823221 0.0180423025 + 1770 63 1604.70183 -300.761731 -300.7360143 0.0004082013901 1.088711264 1.699764745 0.04991863474 + 1771 63 1604.70183 -300.8774963 -300.9010154 0.0003733197156 0.3607214994 0.09504134909 0.01755173421 + 1772 63 1604.70183 -300.8786136 -300.9012712 0.0003596452757 0.3589639067 0.119374214 0.01804353093 + 1773 63 1604.70183 -300.880973 -300.9024223 0.0003404644159 0.3485633579 0.07390057041 0.01757646984 + 1774 63 1604.70183 -300.8826168 -300.9027788 0.000320032806 0.3445418235 0.08547472507 0.01764048595 + 1775 63 1604.70183 -300.8843564 -300.9033786 0.0003019393787 0.340641137 0.06234713001 0.01751041824 + 1776 63 1604.70183 -300.8848447 -300.9034138 0.0002947492049 0.3409421669 0.08066884258 0.01765797968 + 1777 63 1604.70183 -300.8866912 -300.903892 0.0002730290476 0.3352449255 0.06653314188 0.01747264198 + 1778 63 1604.70183 -300.8900552 -300.9042326 0.0002250376891 0.3295433142 0.1065524981 0.01776518759 + 1779 63 1604.70183 -300.8914458 -300.9046115 0.0002089783543 0.323406022 0.08556001491 0.0175519089 + 1780 63 1604.70183 -300.895163 -300.9051837 0.0001590574148 0.309224247 0.0656817627 0.01711876094 + 1781 63 1604.70183 -300.8187471 -300.8329203 0.0002249710683 0.66864894 0.7696926803 0.02893295017 + 1782 63 1604.70183 -300.9006657 -300.9039288 5.179512331e-05 0.3015549559 0.1959501679 0.01784227538 + 1783 63 1604.70183 -300.8971273 -300.9051255 0.0001269544058 0.3038211379 0.0951464456 0.01720447875 + 1784 63 1604.70183 -300.8988964 -300.9054262 0.0001036472504 0.2994103378 0.06599897376 0.01645634222 + 1785 63 1604.70183 -300.9012511 -300.9053614 6.524274878e-05 0.2989152142 0.08283985757 0.01600751186 + 1786 63 1604.70183 -300.9028834 -300.9055698 4.264202282e-05 0.2962186456 0.06327067003 0.01571353764 + 1787 63 1604.70183 -300.9045357 -300.9054704 1.483672216e-05 0.2973243048 0.09085590033 0.01575272449 + 1788 63 1604.70183 -300.9063552 -300.9057429 9.71799273e-06 0.2884807401 0.06941819226 0.01542035128 + 1789 63 1604.70183 -300.9088724 -300.9057308 4.986613893e-05 0.2793016715 0.08288516362 0.01507898621 + 1790 63 1604.70183 -300.9124503 -300.9040208 0.0001338020263 0.2812060245 0.1928511178 0.01489387029 + 1791 63 1604.70183 -300.9109141 -300.9051512 9.147555261e-05 0.2768512385 0.1334998331 0.01491976915 + 1792 63 1604.70183 -300.8321213 -300.8505367 0.0002923070174 0.5785146021 0.6213955083 0.02714672019 + 1793 63 1604.70183 -300.9118449 -300.9051298 0.0001065894855 0.2734464626 0.1256294185 0.01463001989 + 1794 63 1604.70183 -300.9142963 -300.9048357 0.0001501672728 0.2662175163 0.1107049978 0.01404799852 + 1795 63 1604.70183 -300.8440167 -300.8676537 0.0003751906939 0.5188260296 0.4282552364 0.02256107812 + 1796 63 1604.70183 -300.8533013 -300.8785697 0.0004010870151 0.5278911297 0.4623712699 0.02278426515 + 1797 63 1604.70183 -300.8631711 -300.8902517 0.0004298512535 0.4598639491 0.2758713346 0.019775999 + 1798 63 1604.70183 -300.868526 -300.8946842 0.0004152100696 0.4364336409 0.2591136678 0.01977322923 + 1799 63 1604.70183 -300.8732182 -300.8986431 0.0004035700916 0.3865654608 0.1411599181 0.01802163002 + 1800 63 1604.70183 -300.8747167 -300.8991785 0.0003882834203 0.3761269693 0.1663823221 0.0180423025 +# s_vv.xyz + config # atoms volume energy DFT energy energy error force DFT force force error + 1801 62 1604.70183 -294.9672599 -294.8464567 0.001948438254 1.218592891 1.936865193 0.07017898882 + 1802 62 1604.70183 -295.0806403 -295.0536882 0.0004347107556 0.4790988623 0.08041896133 0.02586848956 + 1803 62 1604.70183 -295.0802893 -295.0537321 0.0004283418966 0.4769065652 0.07305595364 0.02581295717 + 1804 62 1604.70183 -295.082277 -295.0540018 0.0004560523149 0.4827633663 0.04177577511 0.0261722975 + 1805 62 1604.70183 -295.0831119 -295.0539914 0.0004696866105 0.4862810393 0.04851777377 0.0263634702 + 1806 62 1604.70183 -295.084722 -295.0539856 0.0004957492172 0.4859169347 0.02910152903 0.02721708228 + 1807 62 1604.70183 -295.0851873 -295.053941 0.0005039725832 0.4862267386 0.03746575669 0.02747371134 + 1808 62 1604.70183 -295.0865698 -295.053892 0.0005270617212 0.491291173 0.0277012169 0.02755786861 + 1809 62 1604.70183 -295.087454 -295.0538036 0.0005427479138 0.4947408414 0.03202675709 0.02758035141 + 1810 62 1604.70183 -295.0882799 -295.0537477 0.0005569707518 0.4985048115 0.02262651179 0.02774193499 + 1811 62 1604.70183 -295.0881928 -295.0537638 0.0005553056396 0.4980384905 0.01969124237 0.02772529649 + 1812 62 1604.70183 -295.0299407 -294.970757 0.0009545770193 0.7396456888 0.805841392 0.04335219622 + 1813 62 1604.70183 -295.0386565 -294.9904052 0.0007782470124 0.6635399904 0.5736876726 0.03643190175 + 1814 62 1604.70183 -295.0444726 -295.005392 0.0006303314528 0.5735987201 0.4288010958 0.03344109746 + 1815 62 1604.70183 -295.0497423 -295.0199643 0.0004802911362 0.4468853577 0.4788589248 0.03319399744 + 1816 62 1604.70183 -295.0511289 -295.0334233 0.0002855751486 0.412914223 0.3523211178 0.02798643806 + 1817 62 1604.70183 -295.0579787 -295.0457463 0.0001972962478 0.4728593576 0.364632667 0.02225997414 + 1818 62 1604.70183 -295.0715407 -295.0529039 0.0003005931017 0.4519887681 0.1424499642 0.02461639629 + 1819 62 1604.70183 -295.075468 -295.0528367 0.0003650211985 0.4598058593 0.1613427988 0.02601893431 + 1820 62 1604.70183 -295.6437402 -295.7667974 0.001984794478 1.101951383 1.241933429 0.07065064344 + 1821 62 1604.70183 -295.6584317 -295.8428527 0.002974532108 0.9059245159 0.06042308731 0.05397637275 + 1822 62 1604.70183 -295.6569539 -295.8430049 0.003000823493 0.9094440307 0.06690064222 0.05432239756 + 1823 62 1604.70183 -295.6564417 -295.8432599 0.003013196244 0.9085919464 0.03776811079 0.0541815139 + 1824 62 1604.70183 -295.6563667 -295.8432638 0.003014469616 0.9086613285 0.04101536582 0.0541603965 + 1825 62 1604.70183 -295.6563009 -295.8433898 0.003017563205 0.9083144105 0.02632908316 0.05437937781 + 1826 62 1604.70183 -295.6561776 -295.8434206 0.003020049312 0.9084065836 0.03543869754 0.05456180745 + 1827 62 1604.70183 -295.6557963 -295.8435125 0.003027680833 0.9083240905 0.02411023484 0.05431494177 + 1828 62 1604.70183 -295.6555947 -295.8435306 0.00303122537 0.9083567026 0.03077112026 0.05419333611 + 1829 62 1604.70183 -295.6552005 -295.8436004 0.003038707443 0.9077274908 0.01562662785 0.05419756291 + 1830 62 1604.70183 -295.6550681 -295.8436057 0.003040928899 0.9075878917 0.01708384052 0.05421249554 + 1831 62 1604.70183 -295.6648112 -295.8167845 0.002451182587 0.9539499354 0.4894330363 0.05675946661 + 1832 62 1604.70183 -295.6653242 -295.8230259 0.002543575659 0.9619624781 0.3758007258 0.05332120959 + 1833 62 1604.70183 -295.669588 -295.8292232 0.002574759832 0.9252453911 0.2702858705 0.0539704111 + 1834 62 1604.70183 -295.6742885 -295.83394 0.002575022934 0.8769729734 0.3148796555 0.05736904735 + 1835 62 1604.70183 -295.6707998 -295.8386637 0.002707482523 0.8782946659 0.1730625895 0.0560009008 + 1836 62 1604.70183 -295.6665416 -295.8399442 0.002796816345 0.8904229731 0.1749793019 0.05515358217 + 1837 62 1604.70183 -295.6633037 -295.8416248 0.002876145486 0.8955998748 0.1010047833 0.05420821043 + 1838 62 1604.70183 -295.6604964 -295.8420227 0.00292784398 0.9024681482 0.1152879517 0.05365567368 + 1839 62 1604.70183 -295.0461481 -294.8382597 0.003353038484 1.376007463 2.058118771 0.07224160463 + 1840 62 1604.70183 -295.1913814 -295.0875434 0.001674805691 0.5384196148 0.1272566374 0.02884710964 + 1841 62 1604.70183 -295.1933389 -295.0877404 0.001703201426 0.5410283372 0.1535920653 0.02886210343 + 1842 62 1604.70183 -295.1981877 -295.0897485 0.00174901827 0.5321510958 0.0919085924 0.02901561245 + 1843 62 1604.70183 -295.200779 -295.0902028 0.001783487411 0.5323027483 0.1148826245 0.0291975135 + 1844 62 1604.70183 -295.2038752 -295.0912372 0.001816742655 0.5270744721 0.07476920569 0.03063740088 + 1845 62 1604.70183 -295.2039072 -295.091241 0.001817196234 0.5270243274 0.07566021039 0.03064624634 + 1846 62 1604.70183 -295.204807 -295.0919271 0.001820643746 0.5297843394 0.05720549079 0.03055348833 + 1847 62 1604.70183 -295.2056422 -295.0923212 0.001827758618 0.5355035428 0.08758261141 0.03054338637 + 1848 62 1604.70183 -295.2059626 -295.0928299 0.001824721919 0.5401130703 0.05949483075 0.03049009024 + 1849 62 1604.70183 -295.2062009 -295.0932507 0.001821776549 0.5493673198 0.05423584132 0.03047836645 + 1850 62 1604.70183 -295.1209612 -294.981282 0.002252891456 0.8897996853 0.9234967041 0.04631741112 + 1851 62 1604.70183 -295.2065108 -295.0935197 0.001822437283 0.54608975 0.03621646964 0.03069436061 + 1852 62 1604.70183 -295.2068164 -295.0937106 0.001824287496 0.5427350597 0.04645181891 0.03111035478 + 1853 62 1604.70183 -295.206795 -295.0938805 0.001821201387 0.542289608 0.03076074258 0.03089061049 + 1854 62 1604.70183 -295.2067584 -295.093914 0.001820072237 0.5423513532 0.03399974318 0.03080694168 + 1855 62 1604.70183 -295.2065054 -295.0939969 0.001814654016 0.5431894835 0.02214248645 0.03079316353 + 1856 62 1604.70183 -295.2062055 -295.0940078 0.001809639985 0.5444393002 0.03072664822 0.03075298998 + 1857 62 1604.70183 -295.205989 -295.0940237 0.001805892068 0.5439592622 0.01965117363 0.03070060288 + 1858 62 1604.70183 -295.2058644 -295.0940064 0.001804160999 0.5438513129 0.02250610148 0.03064219726 + 1859 62 1604.70183 -295.13325 -295.0077715 0.002023846035 0.8068358492 0.6723254144 0.04044178823 + 1860 62 1604.70183 -295.1436331 -295.0284846 0.001857234389 0.7267919929 0.4990357282 0.03730438599 + 1861 62 1604.70183 -295.1525145 -295.0474413 0.001694729171 0.6685615954 0.5617965412 0.03668174015 + 1862 62 1604.70183 -295.1609362 -295.0650615 0.001546366017 0.6192067901 0.3763318358 0.03169583822 + 1863 62 1604.70183 -295.1686429 -295.0746943 0.00151529915 0.6225145556 0.4005004763 0.02822416942 + 1864 62 1604.70183 -295.1809286 -295.083709 0.001568057798 0.5558429155 0.1971474907 0.02853862703 + 1865 62 1604.70183 -295.1849742 -295.0842832 0.001624048373 0.5478533467 0.2301211223 0.02973137408 +# vP.xyz + config # atoms volume energy DFT energy energy error force DFT force force error + 1866 215 5415.868678 -1036.385715 -1036.518623 0.0006181733332 0.2431233829 0.1455333724 0.005585521055 + 1867 215 5415.868678 -1036.384949 -1036.524675 0.0006498895246 0.2141173893 0.04865629092 0.00529898731 + 1868 215 5415.868678 -1036.385733 -1036.519724 0.0006232139374 0.235014552 0.1182395714 0.00558028699 + 1869 215 5415.868678 -1036.385495 -1036.521456 0.0006323721406 0.2251511787 0.1204748543 0.005807924957 + 1870 215 5415.868678 -1036.385246 -1036.521815 0.0006352031266 0.225887845 0.1537923189 0.006003361061 + 1871 215 5415.868678 -1036.385015 -1036.522616 0.0006400020199 0.2255660556 0.1181713349 0.005730052687 + 1872 215 5415.868678 -1036.384202 -1036.523741 0.0006490150934 0.2372088591 0.09590202083 0.005383730036 + 1873 215 5415.868678 -1036.38431 -1036.524159 0.0006504598813 0.2337842778 0.06651800554 0.005128186479 + 1874 215 5415.868678 -1036.384343 -1036.524443 0.0006516260193 0.2332451848 0.06506700127 0.004942329637 + 1875 215 5415.868678 -1036.384694 -1036.524643 0.0006509222256 0.2225473259 0.03789590619 0.005057838722 +# vv.xyz + config # atoms volume energy DFT energy energy error force DFT force force error + 1876 214 5415.868678 -1030.597339 -1030.827092 0.00107361233 0.6568010127 0.3690492999 0.0163065602 + 1877 214 5415.868678 -1030.594629 -1030.831236 0.0011056399 0.6357552261 0.206246824 0.01610434446 + 1878 214 5415.868678 -1030.590721 -1030.832172 0.001128277401 0.6329388724 0.1753841469 0.01617119335 + 1879 214 5415.868678 -1030.586604 -1030.833731 0.001154798659 0.622831011 0.1305811393 0.01575711862 + 1880 214 5415.868678 -1030.574281 -1030.835231 0.001219390099 0.6058441093 0.1712622619 0.01462296559 + 1881 214 5415.868678 -1030.577119 -1030.835309 0.001206496713 0.6078344155 0.1384739781 0.0149084475 + 1882 214 5415.868678 -1030.573021 -1030.836422 0.001230843439 0.5944631515 0.08661607918 0.01427931238 + 1883 214 5415.868678 -1031.088359 -1031.461821 0.001745151303 1.034421614 0.2826455022 0.02606357092 + 1884 214 5415.868678 -1031.091064 -1031.465067 0.001747677127 0.9999048413 0.2065295166 0.02710925733 + 1885 214 5415.868678 -1031.094371 -1031.4678 0.00174499978 0.9485372815 0.2160317144 0.02943944547 + 1886 214 5415.868678 -1031.088638 -1031.470432 0.001784087942 0.9757776537 0.1228543654 0.02787463064 + 1887 214 5415.868678 -1031.081777 -1031.471654 0.001821852033 1.009792825 0.1258656337 0.026410081 + 1888 214 5415.868678 -1031.080586 -1031.472689 0.001832259675 0.9991562544 0.07554789307 0.02736556898 + 1889 214 5415.868678 -1031.078938 -1031.473011 0.00184146258 0.9907336313 0.110225689 0.02845759869 + 1890 214 5415.868678 -1031.07504 -1031.4736 0.001862430081 1.000961382 0.07186162854 0.02803213684 + 1891 214 5415.868678 -1030.690689 -1030.838186 0.0006892363267 0.7780571869 0.4067819182 0.01689825621 + 1892 214 5415.868678 -1030.690244 -1030.843044 0.0007140167877 0.7445713294 0.2451309087 0.01688677179 + 1893 214 5415.868678 -1030.687684 -1030.844175 0.0007312652947 0.7279686394 0.2296418926 0.01780386462 + 1894 214 5415.868678 -1030.684559 -1030.846722 0.00075777015 0.7177620911 0.1735900426 0.01718475276 diff --git a/examples/PACKAGES/pod/InP/InP_training_errors.pod b/examples/PACKAGES/pod/InP/InP_training_errors.pod new file mode 100644 index 0000000000..475faf24e0 --- /dev/null +++ b/examples/PACKAGES/pod/InP/InP_training_errors.pod @@ -0,0 +1,27 @@ +**************** Begin of Error Analysis for the Training Data Set **************** +-------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +-------------------------------------------------------------------------------------------- +Bulk.xyz 1 8 0.001678 0.001678 0.000000 0.000000 +EOS.xyz 268 2080 0.001463 0.001817 0.001107 0.015463 +Shear.xyz 346 2768 0.000415 0.000640 0.008336 0.012865 +Strain.xyz 163 1304 0.001129 0.001374 0.000021 0.000036 +aIn.xyz 54 11664 0.000737 0.000796 0.007969 0.016112 +aP.xyz 21 4536 0.001396 0.001407 0.019599 0.054174 +aa.xyz 20 4320 0.001991 0.001991 0.016735 0.027955 +iIn.xyz 41 8897 0.001548 0.001687 0.013910 0.025462 +iP.xyz 100 21700 0.001090 0.001203 0.009692 0.018549 +s_aIn.xyz 121 7744 0.000856 0.000889 0.011041 0.017399 +s_aP.xyz 72 4608 0.002255 0.003587 0.032425 0.045878 +s_aa.xyz 18 1152 0.001198 0.001200 0.037169 0.047713 +s_iIn.xyz 144 9360 0.002014 0.002255 0.035374 0.050726 +s_iP.xyz 337 21905 0.001655 0.002178 0.025130 0.038368 +s_vIn.xyz 17 1071 0.007984 0.007992 0.023190 0.039575 +s_vP.xyz 77 4851 0.000245 0.000281 0.018303 0.025819 +s_vv.xyz 65 4030 0.001759 0.001986 0.039037 0.052667 +vP.xyz 10 2150 0.000640 0.000640 0.005452 0.009834 +vv.xyz 19 4066 0.001336 0.001403 0.020930 0.034386 +-------------------------------------------------------------------------------------------- +All files 1894 118214 0.001288 0.001855 0.018109 0.032649 +-------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/InP/README.md b/examples/PACKAGES/pod/InP/README.md new file mode 100644 index 0000000000..9555fa2123 --- /dev/null +++ b/examples/PACKAGES/pod/InP/README.md @@ -0,0 +1,16 @@ +### POD example for InP + +We will fit a potential to the `InP` training data in the `XYZ` directory, which houses `.xyz` files + +Please download the training data from [the repo](https://github.com/cesmix-mit/pod-examples/tree/main/JCP2023_InP/XYZ) + +Fit POD with + + lmp -in in.fitpod + +This creates `InP_coefficients.pod` for the linear model, which we can use to run MD with + + lmp -in in.pod + + + diff --git a/examples/PACKAGES/pod/InP/in.fitpod b/examples/PACKAGES/pod/InP/in.fitpod new file mode 100644 index 0000000000..cfb230c7d6 --- /dev/null +++ b/examples/PACKAGES/pod/InP/in.fitpod @@ -0,0 +1 @@ +fitpod InP_param.pod InP_data.pod \ No newline at end of file diff --git a/examples/PACKAGES/pod/Ta_Quadratic/in.pod b/examples/PACKAGES/pod/InP/in.pod similarity index 63% rename from examples/PACKAGES/pod/Ta_Quadratic/in.pod rename to examples/PACKAGES/pod/InP/in.pod index bde2df00a1..81a0998971 100644 --- a/examples/PACKAGES/pod/Ta_Quadratic/in.pod +++ b/examples/PACKAGES/pod/InP/in.pod @@ -1,13 +1,13 @@ -# Demonstrate POD Ta potential +# Demonstrate POD potential for InP # Initialize simulation variable nsteps index 100 variable nrep equal 4 -variable a equal 3.316 +variable a equal 5.83 units metal -# generate the box and atom positions using a BCC lattice +# generate the box and atom positions using a FCC lattice variable nx equal ${nrep} variable ny equal ${nrep} @@ -15,17 +15,17 @@ variable nz equal ${nrep} boundary p p p -lattice bcc $a +lattice diamond $a region box block 0 ${nx} 0 ${ny} 0 ${nz} -create_box 1 box -create_atoms 1 box - -mass 1 180.88 +create_box 2 box +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 +mass 1 114.76 +mass 2 30.98 # POD potential pair_style pod -pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta +pair_coeff * * InP_param.pod InP_coefficients.pod In P # Setup output @@ -44,4 +44,3 @@ velocity all create 300.0 4928459 loop geom fix 1 all nve run ${nsteps} - diff --git a/examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.1 b/examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.1 new file mode 100644 index 0000000000..c5bd10bac8 --- /dev/null +++ b/examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.1 @@ -0,0 +1,163 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +fitpod InP_param.pod InP_data.pod +**************** Begin of POD Potentials **************** +species: In P +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 0.8 +outer cut-off radius: 5 +bessel polynomial degree: 4 +inverse polynomial degree: 8 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 4 +four-body angular degree: 2 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 12 +number of local descriptors per element for three-body potential: 75 +number of local descriptors per element for four-body potential: 64 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 152 +number of global descriptors: 304 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: XYZ +path to test data set: XYZ +path to environment configuration set: XYZ +basename for output files: InP +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +save pod descriptors: 0 +compute pod descriptors: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +-------------------------------------------------------- + data file | number of configurations | number of atoms +-------------------------------------------------------- + Bulk.xyz | 1 | 8 + EOS.xyz | 268 | 2080 + Shear.xyz | 346 | 2768 + Strain.xyz | 163 | 1304 + aIn.xyz | 54 | 11664 + aP.xyz | 21 | 4536 + aa.xyz | 20 | 4320 + iIn.xyz | 41 | 8897 + iP.xyz | 100 | 21700 + s_aIn.xyz | 121 | 7744 + s_aP.xyz | 72 | 4608 + s_aa.xyz | 18 | 1152 + s_iIn.xyz | 144 | 9360 + s_iP.xyz | 337 | 21905 + s_vIn.xyz | 17 | 1071 + s_vP.xyz | 77 | 4851 + s_vv.xyz | 65 | 4030 + vP.xyz | 10 | 2150 + vv.xyz | 19 | 4066 +-------------------------------------------------------- +number of files: 19 +number of configurations in all files: 1894 +number of atoms in all files: 118214 +minimum number of atoms: 4 +maximum number of atoms: 217 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 217 +maximum number of atoms in extended domain: 5859 +maximum number of neighbors in extended domain: 1271403 +size of double memory: 5555904 +size of descriptor matrix: 304 x 304 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +Configuration: # 401 +Configuration: # 501 +Configuration: # 601 +Configuration: # 701 +Configuration: # 801 +Configuration: # 901 +Configuration: # 1001 +Configuration: # 1101 +Configuration: # 1201 +Configuration: # 1301 +Configuration: # 1401 +Configuration: # 1501 +Configuration: # 1601 +Configuration: # 1701 +Configuration: # 1801 +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +Configuration: # 401 +Configuration: # 501 +Configuration: # 601 +Configuration: # 701 +Configuration: # 801 +Configuration: # 901 +Configuration: # 1001 +Configuration: # 1101 +Configuration: # 1201 +Configuration: # 1301 +Configuration: # 1401 +Configuration: # 1501 +Configuration: # 1601 +Configuration: # 1701 +Configuration: # 1801 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +-------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +-------------------------------------------------------------------------------------------- +Bulk.xyz 1 8 0.001678 0.001678 0.000000 0.000000 +EOS.xyz 268 2080 0.001463 0.001817 0.001107 0.015464 +Shear.xyz 346 2768 0.000415 0.000640 0.008335 0.012863 +Strain.xyz 163 1304 0.001129 0.001374 0.000021 0.000036 +aIn.xyz 54 11664 0.000737 0.000796 0.007969 0.016112 +aP.xyz 21 4536 0.001396 0.001407 0.019599 0.054174 +aa.xyz 20 4320 0.001991 0.001991 0.016735 0.027955 +iIn.xyz 41 8897 0.001548 0.001687 0.013910 0.025462 +iP.xyz 100 21700 0.001090 0.001203 0.009692 0.018549 +s_aIn.xyz 121 7744 0.000856 0.000889 0.011041 0.017399 +s_aP.xyz 72 4608 0.002255 0.003587 0.032425 0.045878 +s_aa.xyz 18 1152 0.001198 0.001200 0.037169 0.047713 +s_iIn.xyz 144 9360 0.002014 0.002255 0.035374 0.050726 +s_iP.xyz 337 21905 0.001655 0.002178 0.025130 0.038368 +s_vIn.xyz 17 1071 0.007984 0.007992 0.023190 0.039575 +s_vP.xyz 77 4851 0.000245 0.000281 0.018303 0.025818 +s_vv.xyz 65 4030 0.001759 0.001986 0.039037 0.052667 +vP.xyz 10 2150 0.000640 0.000640 0.005452 0.009834 +vv.xyz 19 4066 0.001336 0.001403 0.020930 0.034386 +-------------------------------------------------------------------------------------------- +All files 1894 118214 0.001288 0.001855 0.018109 0.032648 +-------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** +Total wall time: 0:00:27 diff --git a/examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.4 b/examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.4 new file mode 100644 index 0000000000..928591cbcf --- /dev/null +++ b/examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.4 @@ -0,0 +1,163 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +fitpod InP_param.pod InP_data.pod +**************** Begin of POD Potentials **************** +species: In P +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 0.8 +outer cut-off radius: 5 +bessel polynomial degree: 4 +inverse polynomial degree: 8 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 4 +four-body angular degree: 2 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 12 +number of local descriptors per element for three-body potential: 75 +number of local descriptors per element for four-body potential: 64 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 152 +number of global descriptors: 304 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: XYZ +path to test data set: XYZ +path to environment configuration set: XYZ +basename for output files: InP +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +save pod descriptors: 0 +compute pod descriptors: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +-------------------------------------------------------- + data file | number of configurations | number of atoms +-------------------------------------------------------- + Bulk.xyz | 1 | 8 + EOS.xyz | 268 | 2080 + Shear.xyz | 346 | 2768 + Strain.xyz | 163 | 1304 + aIn.xyz | 54 | 11664 + aP.xyz | 21 | 4536 + aa.xyz | 20 | 4320 + iIn.xyz | 41 | 8897 + iP.xyz | 100 | 21700 + s_aIn.xyz | 121 | 7744 + s_aP.xyz | 72 | 4608 + s_aa.xyz | 18 | 1152 + s_iIn.xyz | 144 | 9360 + s_iP.xyz | 337 | 21905 + s_vIn.xyz | 17 | 1071 + s_vP.xyz | 77 | 4851 + s_vv.xyz | 65 | 4030 + vP.xyz | 10 | 2150 + vv.xyz | 19 | 4066 +-------------------------------------------------------- +number of files: 19 +number of configurations in all files: 1894 +number of atoms in all files: 118214 +minimum number of atoms: 4 +maximum number of atoms: 217 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 217 +maximum number of atoms in extended domain: 5859 +maximum number of neighbors in extended domain: 1271403 +size of double memory: 5555904 +size of descriptor matrix: 304 x 304 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +Configuration: # 401 +Configuration: # 501 +Configuration: # 601 +Configuration: # 701 +Configuration: # 801 +Configuration: # 901 +Configuration: # 1001 +Configuration: # 1101 +Configuration: # 1201 +Configuration: # 1301 +Configuration: # 1401 +Configuration: # 1501 +Configuration: # 1601 +Configuration: # 1701 +Configuration: # 1801 +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +Configuration: # 401 +Configuration: # 501 +Configuration: # 601 +Configuration: # 701 +Configuration: # 801 +Configuration: # 901 +Configuration: # 1001 +Configuration: # 1101 +Configuration: # 1201 +Configuration: # 1301 +Configuration: # 1401 +Configuration: # 1501 +Configuration: # 1601 +Configuration: # 1701 +Configuration: # 1801 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +-------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +-------------------------------------------------------------------------------------------- +Bulk.xyz 1 8 0.001678 0.001678 0.000000 0.000000 +EOS.xyz 268 2080 0.001463 0.001817 0.001107 0.015463 +Shear.xyz 346 2768 0.000415 0.000640 0.008336 0.012865 +Strain.xyz 163 1304 0.001129 0.001374 0.000021 0.000036 +aIn.xyz 54 11664 0.000737 0.000796 0.007969 0.016112 +aP.xyz 21 4536 0.001396 0.001407 0.019599 0.054174 +aa.xyz 20 4320 0.001991 0.001991 0.016735 0.027955 +iIn.xyz 41 8897 0.001548 0.001687 0.013910 0.025462 +iP.xyz 100 21700 0.001090 0.001203 0.009692 0.018549 +s_aIn.xyz 121 7744 0.000856 0.000889 0.011041 0.017399 +s_aP.xyz 72 4608 0.002255 0.003587 0.032425 0.045878 +s_aa.xyz 18 1152 0.001198 0.001200 0.037169 0.047713 +s_iIn.xyz 144 9360 0.002014 0.002255 0.035374 0.050726 +s_iP.xyz 337 21905 0.001655 0.002178 0.025130 0.038368 +s_vIn.xyz 17 1071 0.007984 0.007992 0.023190 0.039575 +s_vP.xyz 77 4851 0.000245 0.000281 0.018303 0.025819 +s_vv.xyz 65 4030 0.001759 0.001986 0.039037 0.052667 +vP.xyz 10 2150 0.000640 0.000640 0.005452 0.009834 +vv.xyz 19 4066 0.001336 0.001403 0.020930 0.034386 +-------------------------------------------------------------------------------------------- +All files 1894 118214 0.001288 0.001855 0.018109 0.032649 +-------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** +Total wall time: 0:00:10 diff --git a/examples/PACKAGES/pod/InP/log.22May24.pod.g++.1 b/examples/PACKAGES/pod/InP/log.22May24.pod.g++.1 new file mode 100644 index 0000000000..99ee0b90b0 --- /dev/null +++ b/examples/PACKAGES/pod/InP/log.22May24.pod.g++.1 @@ -0,0 +1,155 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD potential for InP + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 5.83 +units metal + +# generate the box and atom positions using a FCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice diamond $a +lattice diamond 5.83 +Lattice spacing in x,y,z = 5.83 5.83 5.83 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (23.32 23.32 23.32) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 +Created 512 atoms + using lattice units in orthogonal box = (0 0 0) to (23.32 23.32 23.32) + create_atoms CPU = 0.001 seconds + +mass 1 114.76 +mass 2 30.98 + +# POD potential +pair_style pod +pair_coeff * * InP_param.pod InP_coefficients.pod In P +**************** Begin of POD Potentials **************** +species: In P +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 0.8 +outer cut-off radius: 5 +bessel polynomial degree: 4 +inverse polynomial degree: 8 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 4 +four-body angular degree: 2 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 12 +number of local descriptors per element for three-body potential: 75 +number of local descriptors per element for four-body potential: 64 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 152 +number of global descriptors: 304 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 304 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.244 | 3.244 | 3.244 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4.8392777 0 -4.8005754 1561.0654 + 10 291.27079 -4.8381515 0 -4.8005753 1709.509 + 20 266.69372 -4.8349805 0 -4.8005749 2126.86 + 30 230.86163 -4.8303573 0 -4.8005744 2735.6894 + 40 190.64668 -4.8251686 0 -4.8005738 3416.9247 + 50 153.9516 -4.8204341 0 -4.8005732 4022.2533 + 60 127.93805 -4.8170778 0 -4.8005728 4405.9763 + 70 117.12501 -4.8156828 0 -4.8005727 4475.6131 + 80 122.09497 -4.8163242 0 -4.800573 4231.7934 + 90 139.42686 -4.8185607 0 -4.8005735 3766.8505 + 100 162.84813 -4.8215828 0 -4.8005741 3221.8605 +Loop time of 2.18542 on 1 procs for 100 steps with 512 atoms + +Performance: 1.977 ns/day, 12.141 hours/ns, 45.758 timesteps/s, 23.428 katom-step/s +97.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1829 | 2.1829 | 2.1829 | 0.0 | 99.88 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00080748 | 0.00080748 | 0.00080748 | 0.0 | 0.04 +Output | 0.00033584 | 0.00033584 | 0.00033584 | 0.0 | 0.02 +Modify | 0.00071224 | 0.00071224 | 0.00071224 | 0.0 | 0.03 +Other | | 0.000686 | | | 0.03 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1451 ave 1451 max 1451 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 17408 ave 17408 max 17408 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 17408 +Ave neighs/atom = 34 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/pod/InP/log.22May24.pod.g++.4 b/examples/PACKAGES/pod/InP/log.22May24.pod.g++.4 new file mode 100644 index 0000000000..67f8575cf5 --- /dev/null +++ b/examples/PACKAGES/pod/InP/log.22May24.pod.g++.4 @@ -0,0 +1,155 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD potential for InP + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 5.83 +units metal + +# generate the box and atom positions using a FCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice diamond $a +lattice diamond 5.83 +Lattice spacing in x,y,z = 5.83 5.83 5.83 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (23.32 23.32 23.32) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 +Created 512 atoms + using lattice units in orthogonal box = (0 0 0) to (23.32 23.32 23.32) + create_atoms CPU = 0.001 seconds + +mass 1 114.76 +mass 2 30.98 + +# POD potential +pair_style pod +pair_coeff * * InP_param.pod InP_coefficients.pod In P +**************** Begin of POD Potentials **************** +species: In P +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 0.8 +outer cut-off radius: 5 +bessel polynomial degree: 4 +inverse polynomial degree: 8 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 4 +four-body angular degree: 2 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 12 +number of local descriptors per element for three-body potential: 75 +number of local descriptors per element for four-body potential: 64 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 152 +number of global descriptors: 304 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 304 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.215 | 3.215 | 3.215 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4.8392777 0 -4.8005754 1561.0654 + 10 291.27079 -4.8381515 0 -4.8005753 1709.509 + 20 266.69372 -4.8349805 0 -4.8005749 2126.86 + 30 230.86163 -4.8303573 0 -4.8005744 2735.6894 + 40 190.64668 -4.8251686 0 -4.8005738 3416.9247 + 50 153.9516 -4.8204341 0 -4.8005732 4022.2533 + 60 127.93805 -4.8170778 0 -4.8005728 4405.9763 + 70 117.12501 -4.8156828 0 -4.8005727 4475.6131 + 80 122.09497 -4.8163242 0 -4.800573 4231.7934 + 90 139.42686 -4.8185607 0 -4.8005735 3766.8505 + 100 162.84813 -4.8215828 0 -4.8005741 3221.8605 +Loop time of 0.818141 on 4 procs for 100 steps with 512 atoms + +Performance: 5.280 ns/day, 4.545 hours/ns, 122.228 timesteps/s, 62.581 katom-step/s +94.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.70717 | 0.7255 | 0.75748 | 2.2 | 88.68 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.05765 | 0.088203 | 0.10797 | 6.3 | 10.78 +Output | 0.00030107 | 0.00039215 | 0.00055987 | 0.0 | 0.05 +Modify | 0.00051915 | 0.00059064 | 0.00069306 | 0.0 | 0.07 +Other | | 0.003452 | | | 0.42 + +Nlocal: 128 ave 128 max 128 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 783 ave 783 max 783 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 4352 ave 4352 max 4352 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 17408 +Ave neighs/atom = 34 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/README.md b/examples/PACKAGES/pod/README.md index 2c6db69200..1f7714d4db 100644 --- a/examples/PACKAGES/pod/README.md +++ b/examples/PACKAGES/pod/README.md @@ -3,19 +3,36 @@ Go to `lammps` directory and build with the POD package: cd path/to/lammps - mkdir build-pod - cd build-pod + mkdir build + cd build cmake -C ../cmake/presets/basic.cmake -D PKG_ML-POD=on ../cmake cmake --build . -### Fit a POD potential for tantalum +### Compile LAMMPS/POD with Kokkos + + cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake -D PKG_ML-POD=on ../cmake + +### Fit a POD potential for Tantalum Go to `lammps/examples/PACKAGES/pod/Ta` directory and run - lmp -in in.podfit + lmp -in Ta_fit.pod -See the README in `lammps/examples/PACKAGES/pod/Ta` for instructions on how to run MD with the potential. +This creates `Ta_coefficients.pod` for the linear model, which we can use to run MD with + + lmp -in Ta_mdrun.pod + +### Fit a POD potential for Indium Phosphide + +Go to `lammps/examples/PACKAGES/pod/InP` directory and run + + lmp -in InP_fit.pod + +This creates `InP_coefficients.pod` for the linear model, which we can use to run MD with + + lmp -in InP_mdrun.pod ### Examples for other materials See [https://github.com/cesmix-mit/pod-examples](https://github.com/cesmix-mit/pod-examples) + diff --git a/examples/PACKAGES/pod/Ta/Ta_coeff.pod b/examples/PACKAGES/pod/Ta/Ta_coeff.pod deleted file mode 120000 index ddf9c1426d..0000000000 --- a/examples/PACKAGES/pod/Ta/Ta_coeff.pod +++ /dev/null @@ -1 +0,0 @@ -../../../../potentials/Ta_coeff.pod \ No newline at end of file diff --git a/examples/PACKAGES/pod/Ta/Ta_coeff.pod b/examples/PACKAGES/pod/Ta/Ta_coeff.pod new file mode 100644 index 0000000000..ab5e5fd43a --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_coeff.pod @@ -0,0 +1,33 @@ +model_coefficients: 32 0 0 +-4.45745 +29.40034 +-13.69439 +-0.32907 +-0.14786 +-1.35221 +-0.59315 +-26.30409 +-33.37233 +162.42473 +144.67248 +-149.50021 +1.78603 +2.49026 +-11.04768 +-11.14333 +12.40537 +0.48284 +0.39345 +-2.25812 +-1.38908 +1.31551 +0.02974 +-0.05094 +-0.21177 +0.12127 +0.23170 +0.02426 +-0.15305 +-0.10803 +0.25628 +0.01291 diff --git a/examples/PACKAGES/pod/Ta/Ta_coefficients.pod b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod index 5222e9e600..ab5e5fd43a 100644 --- a/examples/PACKAGES/pod/Ta/Ta_coefficients.pod +++ b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod @@ -1,33 +1,33 @@ -POD_coefficients: 32 --4.44242 -4.10219 -2.36987 -3.92184 --0.83796 --0.79457 --0.26230 --21.24294 --15.38460 --38.44056 -8.29872 --42.54514 -2.79976 -3.76109 -5.23499 -0.04878 -2.96006 -0.09101 --0.19257 --0.24326 --0.16735 -0.53738 -0.02236 --0.00154 -0.02488 --0.00565 -0.07672 --0.05894 --0.05604 --0.12664 -0.11723 -0.00262 +model_coefficients: 32 0 0 +-4.45745 +29.40034 +-13.69439 +-0.32907 +-0.14786 +-1.35221 +-0.59315 +-26.30409 +-33.37233 +162.42473 +144.67248 +-149.50021 +1.78603 +2.49026 +-11.04768 +-11.14333 +12.40537 +0.48284 +0.39345 +-2.25812 +-1.38908 +1.31551 +0.02974 +-0.05094 +-0.21177 +0.12127 +0.23170 +0.02426 +-0.15305 +-0.10803 +0.25628 +0.01291 diff --git a/examples/PACKAGES/pod/Ta/Ta_data.pod b/examples/PACKAGES/pod/Ta/Ta_data.pod index 0933f3e79a..477d27dfed 100644 --- a/examples/PACKAGES/pod/Ta/Ta_data.pod +++ b/examples/PACKAGES/pod/Ta/Ta_data.pod @@ -3,10 +3,11 @@ file_extension xyz path_to_training_data_set "XYZ" path_to_test_data_set "XYZ" +path_to_environment_configuration_set "XYZ" fitting_weight_energy 100.0 fitting_weight_force 1.0 -fitting_regularization_parameter 1e-10 +fitting_regularization_parameter 1e-12 error_analysis_for_training_data_set 1 error_analysis_for_test_data_set 0 @@ -17,4 +18,3 @@ basename_for_output_files Ta # number of digits after the decimal point for pod coefficients precision_for_pod_coefficients 5 - diff --git a/examples/PACKAGES/pod/Ta/Ta_param.pod b/examples/PACKAGES/pod/Ta/Ta_param.pod index 00c01b01a6..f5dbaf9254 100644 --- a/examples/PACKAGES/pod/Ta/Ta_param.pod +++ b/examples/PACKAGES/pod/Ta/Ta_param.pod @@ -1,4 +1,3 @@ -# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 # chemical element symbols species Ta @@ -11,22 +10,37 @@ rin 1.0 # outer cut-off radius rcut 5.0 +# use only for enviroment-adaptive potentials +number_of_environment_clusters 1 + +# principal_components of local descriptors +number_of_principal_components 2 + # polynomial degrees for radial basis functions bessel_polynomial_degree 3 inverse_polynomial_degree 6 -# one-body potential -onebody 1 - # two-body linear POD potential twobody_number_radial_basis_functions 6 # three-body linear POD potential threebody_number_radial_basis_functions 5 -threebody_number_angular_basis_functions 5 +threebody_angular_degree 4 + +# four-body linear POD potential +fourbody_number_radial_basis_functions 0 +fourbody_angular_degree 0 + +# five-body linear POD potential +fivebody_number_radial_basis_functions 0 +fivebody_angular_degree 0 + +# six-body linear POD potential +sixbody_number_radial_basis_functions 0 +sixbody_angular_degree 0 + +# seven-body linear POD potential +sevenbody_number_radial_basis_functions 0 +sevenbody_angular_degree 0 -# four-body linear SNAP potential -fourbody_snap_twojmax 0 -# quadratic POD potential -quadratic_pod_potential 0 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod index ff9704ce8a..c1910e232d 100644 --- a/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod +++ b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod @@ -1,387 +1,387 @@ # Displaced_A15.xyz - config # atoms energy DFT energy energy error force DFT force force error - 1 64 -753.4412087 -754.220443 0.01217553565 7.734608752 8.398670477 0.1147177501 - 2 64 -752.99206 -753.865255 0.01364367179 8.845831302 9.134430545 0.128875643 - 3 64 -753.3230789 -754.0221 0.01092220404 8.320493902 9.017261102 0.1155421197 - 4 64 -753.5972757 -754.279613 0.01066151964 7.709417684 8.381725092 0.1058659753 - 5 64 -753.0554721 -753.777209 0.01127713895 8.89827564 9.478314477 0.1191609049 - 6 64 -753.3515905 -754.048643 0.01089144564 7.808950564 8.465317938 0.1128142237 - 7 64 -753.6515992 -754.317603 0.01040630929 7.441773668 8.127690491 0.1024025645 - 8 64 -753.3305668 -753.969161 0.009978033993 8.524333384 9.425464952 0.1066300011 - 9 64 -753.3982699 -754.141988 0.01162059588 8.165654685 8.821346913 0.1141641875 + config # atoms volume energy DFT energy energy error force DFT force force error + 1 64 1191.016129 -753.1698421 -754.220443 0.01641563835 7.40295037 8.398670477 0.1439758999 + 2 64 1191.016129 -752.7395784 -753.865255 0.01758869658 8.280515739 9.134430545 0.1607787343 + 3 64 1191.016129 -753.08785 -754.0221 0.01459765574 7.697535492 9.017261102 0.1420603113 + 4 64 1191.016129 -753.3517402 -754.279613 0.01449801277 7.132364917 8.381725092 0.1340575727 + 5 64 1191.016129 -752.7757043 -753.777209 0.01564851147 8.360253864 9.478314477 0.1513006151 + 6 64 1191.016129 -753.0381763 -754.048643 0.01578854208 7.591838888 8.465317938 0.1285134018 + 7 64 1191.016129 -753.3574797 -754.317603 0.01500192578 7.082010429 8.127690491 0.1223953112 + 8 64 1191.016129 -753.1004299 -753.969161 0.01357392266 7.903578432 9.425464952 0.1365521197 + 9 64 1191.016129 -753.1947122 -754.141988 0.01480118465 7.516622986 8.821346913 0.1457127007 # Displaced_BCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 10 54 -631.72742 -631.019667 0.01310653789 15.42892812 16.625876 0.264811012 - 11 54 -632.2725892 -631.719595 0.01024063328 14.51788198 15.58666626 0.2236637006 - 12 54 -631.9431698 -631.386255 0.01031323642 15.21539049 15.92378883 0.2259171686 - 13 54 -633.0728554 -632.575826 0.00920424781 13.38472946 14.55977162 0.2050161952 - 14 54 -630.8933737 -630.450212 0.008206698429 16.5539163 16.96340726 0.2366453149 - 15 54 -632.0739208 -631.669379 0.007491515672 15.23887638 16.05757315 0.2280333831 - 16 54 -632.8030856 -632.431277 0.006885343815 14.21127984 14.69810718 0.2026063598 - 17 54 -631.6814096 -630.960068 0.01335817778 14.70924474 15.99073148 0.2283605143 - 18 54 -625.0410285 -623.378198 0.03079315656 23.39224423 24.67640432 0.3504654115 + config # atoms volume energy DFT energy energy error force DFT force force error + 10 54 988.0479474 -631.5404329 -631.019667 0.009643812587 15.64136862 16.625876 0.2725503749 + 11 54 988.0479474 -632.1993857 -631.719595 0.008885012437 14.51345042 15.58666626 0.2369926956 + 12 54 988.0479474 -631.7954039 -631.386255 0.007576831115 15.20757603 15.92378883 0.2310810758 + 13 54 988.0479474 -633.0131535 -632.575826 0.00809865759 13.46782392 14.55977162 0.2185066317 + 14 54 988.0479474 -630.6309514 -630.450212 0.003347025529 17.00218411 16.96340726 0.2580441627 + 15 54 988.0479474 -631.9637644 -631.669379 0.00545158078 15.32548025 16.05757315 0.2336752679 + 16 54 988.0479474 -632.6507522 -632.431277 0.004064355464 14.35795151 14.69810718 0.2158812969 + 17 54 988.0479474 -631.5521869 -630.960068 0.0109651643 14.75319251 15.99073148 0.2285673047 + 18 54 988.0479474 -624.854495 -623.378198 0.02733883252 23.58927768 24.67640432 0.3545478911 # Displaced_FCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 19 48 -555.9696753 -555.899463 0.001462755232 6.079460735 6.084617063 0.07083484607 - 20 48 -555.9506355 -555.922478 0.0005866147697 6.28112122 6.297071211 0.09285822038 - 21 48 -555.8344979 -555.800269 0.000713101184 6.153574445 6.021098636 0.08137696888 - 22 48 -556.2639568 -556.196151 0.00141262046 5.066504178 5.127955094 0.08649299664 - 23 48 -555.6269121 -555.488929 0.002874647697 6.848109843 7.050223459 0.08116202322 - 24 48 -556.1089332 -556.027926 0.001687649405 5.662035842 5.611881174 0.07953916326 - 25 48 -556.0580873 -555.968399 0.001868505799 5.879931332 5.979217189 0.07470196865 - 26 48 -556.0083267 -556.047132 0.0008084440258 5.752828608 5.544452585 0.08224848502 - 27 48 -555.82441 -555.747848 0.001595040721 6.367423657 6.47892568 0.09497869851 + config # atoms volume energy DFT energy energy error force DFT force force error + 19 48 889.0559462 -555.8989975 -555.899463 9.69792269e-06 6.387988875 6.084617063 0.07805905013 + 20 48 889.0559462 -555.8789297 -555.922478 0.000907256654 6.632232564 6.297071211 0.1040918647 + 21 48 889.0559462 -555.7628778 -555.800269 0.0007789836645 6.45057814 6.021098636 0.09471102034 + 22 48 889.0559462 -556.2253041 -556.196151 0.0006073561042 5.301350042 5.127955094 0.09123176401 + 23 48 889.0559462 -555.5406596 -555.488929 0.001077721414 7.195160551 7.050223459 0.08747135986 + 24 48 889.0559462 -556.0330633 -556.027926 0.0001070272218 6.009103539 5.611881174 0.08935441647 + 25 48 889.0559462 -555.9945281 -555.968399 0.0005443553218 6.212902066 5.979217189 0.081244274 + 26 48 889.0559462 -555.9554151 -556.047132 0.001910769529 6.012019145 5.544452585 0.09545132709 + 27 48 889.0559462 -555.7366233 -555.747848 0.0002338482448 6.764939057 6.47892568 0.1011665243 # Elastic_BCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 28 2 -23.68353253 -23.689367 0.002917237243 0.0006486347527 0.0006222748589 7.696560647e-06 - 29 2 -23.68281295 -23.689888 0.003537526523 0.0006442481331 0.0006166052222 7.353613433e-06 - 30 2 -23.68293438 -23.689996 0.00353080996 0.0009115876426 0.0008810425642 1.183334558e-05 - 31 2 -23.68108003 -23.690957 0.004938485589 1.044193543e-06 0 4.166082999e-07 - 32 2 -23.67919793 -23.690521 0.005661535829 0.0006261455712 0.0005982273815 7.573309962e-06 - 33 2 -23.67785535 -23.69038 0.006262326378 0.0006219476538 0.0005925723585 8.098703345e-06 - 34 2 -23.68415292 -23.689202 0.00252453823 0.0006520193214 0.0006279363025 7.128171197e-06 - 35 2 -23.68169552 -23.690482 0.004393238412 0.0009021557258 0.0008640138888 1.329061297e-05 - 36 2 -23.68301023 -23.689902 0.003445886213 0.0006432418939 0.0006152154094 8.589463686e-06 - 37 2 -23.68063814 -23.690563 0.004962429905 0.0006318669831 0.0006038725031 7.463726891e-06 - 38 2 -23.68337588 -23.690207 0.003415557958 0.001118071502 0.00107369735 1.811741272e-05 - 39 2 -23.68369233 -23.689285 0.00279633424 0.0009215683923 0.000890013483 1.127366011e-05 - 40 2 -23.68344234 -23.689768 0.003162828655 0.001120158205 0.001080249045 1.630224161e-05 - 41 2 -23.68224173 -23.68968 0.003719136062 0.0009070521506 0.0008680034562 1.339908745e-05 - 42 2 -23.68259685 -23.690074 0.003738573623 0.00143649564 0.001373818765 2.432187597e-05 - 43 2 -23.68469428 -23.688108 0.001706858485 0.0006587619148 0.0006336134468 7.932733888e-06 - 44 2 -23.68405177 -23.689241 0.002594615211 0.0009223784492 0.0008880101351 1.189350098e-05 - 45 2 -23.68384626 -23.68952 0.002836868987 0.0009181252225 0.0008860011287 1.116431522e-05 - 46 2 -23.68524763 -23.686278 0.0005151850613 0.0006668258323 0.0006406777661 8.58562287e-06 - 47 2 -23.67629396 -23.690097 0.006901518594 0.0008737523828 0.0008410160522 1.125104926e-05 - 48 2 -23.67835169 -23.690811 0.006229654604 0.0008814028122 0.0008500070588 1.103963422e-05 - 49 2 -23.67981574 -23.690266 0.005225130991 0.001091936388 0.001044322747 1.944706281e-05 - 50 2 -23.68209703 -23.690597 0.004249983197 0.001105769275 0.001050833003 2.242828165e-05 - 51 2 -23.68050418 -23.690673 0.005084408246 0.000631172526 0.0006038907186 7.85857762e-06 - 52 2 -23.68185505 -23.690551 0.00434797299 0.0009022813915 0.0008590064028 1.486707593e-05 - 53 2 -23.68191508 -23.690693 0.004388958442 0.0009013677777 0.0008590110593 1.516503239e-05 - 54 2 -23.68097184 -23.69021 0.004619081961 0.0009000307855 0.0008730051546 9.670733045e-06 - 55 2 -23.68426495 -23.688943 0.002339025274 0.0009232115961 0.0008800306813 1.619629586e-05 - 56 2 -23.67842316 -23.690136 0.005856419419 0.0006239138245 0.000593996633 8.394193459e-06 - 57 2 -23.6849427 -23.687444 0.001250651312 0.0009347957747 0.000903059245 1.290489522e-05 - 58 2 -23.6836322 -23.689801 0.003084401813 0.0009160470298 0.0008740011442 1.424271291e-05 - 59 2 -23.6814842 -23.690408 0.00446190038 8.690218902e-07 0 3.245696976e-07 - 60 2 -23.68115817 -23.690362 0.004601914896 0.0006345480975 0.0006067503605 9.377221838e-06 - 61 2 -23.67229452 -23.688881 0.008293240443 0.0008566684404 0.0008250054545 1.108928728e-05 - 62 2 -23.6791352 -23.690515 0.005689901939 0.001534883496 0.001475779794 2.124695951e-05 - 63 2 -23.67786743 -23.690551 0.006341785918 0.0006228264143 0.0005996599036 7.295416678e-06 - 64 2 -23.68316372 -23.689487 0.003161641446 0.0006469755816 0.0006194384554 7.530154689e-06 - 65 2 -23.6834063 -23.68986 0.003226849907 0.0009142334935 0.0008860124153 1.052672488e-05 - 66 2 -23.68377813 -23.689288 0.002754934411 0.00145229412 0.001396479144 1.702826801e-05 - 67 2 -23.67700773 -23.690457 0.006724637324 0.0006187196638 0.0005939831647 7.080762895e-06 - 68 2 -23.67552804 -23.689792 0.007131981721 0.0008698720997 0.0008340587509 1.418233126e-05 - 69 2 -23.67583966 -23.690006 0.007083167888 0.0006146073806 0.0005897694465 8.07065747e-06 - 70 2 -23.6777397 -23.690571 0.006415648131 0.0006207500925 0.0005939781141 7.401996527e-06 - 71 2 -23.68270064 -23.690213 0.003756180649 0.001112284016 0.001084315452 1.142137177e-05 - 72 2 -23.67870666 -23.690617 0.005955171449 0.0006250314539 0.0006024682564 6.623275772e-06 - 73 2 -23.68231586 -23.689761 0.00372256923 0.0009095463313 0.0008790688255 1.222939687e-05 - 74 2 -23.67673328 -23.69027 0.006768359835 7.188704983e-07 0 2.129270726e-07 - 75 2 -23.68164707 -23.690599 0.004475963334 0.0006376044826 0.0006137752031 6.574310078e-06 - 76 2 -23.67997815 -23.69061 0.00531592353 9.698202031e-07 0 3.95870452e-07 - 77 2 -23.68008634 -23.690603 0.005258328411 0.0008923489326 0.0008590331775 1.256831367e-05 - 78 2 -23.68488966 -23.687908 0.001509170978 0.0009340324028 0.0009010105438 1.204104822e-05 - 79 2 -23.6795094 -23.690688 0.005589299031 0.0008890828456 0.0008470064935 1.419626566e-05 - 80 2 -23.68316126 -23.689988 0.003413372454 0.0006451612224 0.0006194465272 7.422528505e-06 - 81 2 -23.68321956 -23.689613 0.003196718897 0.000912899593 0.0008740732235 1.539555522e-05 - 82 2 -23.68181374 -23.690678 0.004432127652 0.0006373963006 0.0006123757017 7.454253265e-06 - 83 2 -23.68196226 -23.69017 0.004103870298 0.0009041773842 0.0008750051428 9.854119736e-06 - 84 2 -23.68483517 -23.687892 0.001528413806 0.001142179928 0.001112070142 1.229243027e-05 - 85 2 -23.68271169 -23.690132 0.003710155487 0.0009085291666 0.000868018433 1.49999647e-05 - 86 2 -23.68018066 -23.690843 0.005331170668 0.0006305009468 0.0006081134763 5.90881572e-06 - 87 2 -23.67957976 -23.690598 0.005509118787 0.001259431767 0.001217674833 1.243374729e-05 - 88 2 -23.67869549 -23.690656 0.005980257091 0.0006251939788 0.0006024765556 7.13023928e-06 - 89 2 -23.67884961 -23.690254 0.005702197143 0.001084797449 0.001043496047 1.68662339e-05 - 90 2 -23.67961701 -23.690694 0.005538492834 0.0006273834422 0.0006010740387 8.134278748e-06 - 91 2 -23.68202458 -23.690097 0.004036211359 0.0009041492449 0.0008730234819 1.169617364e-05 - 92 2 -23.68476212 -23.688402 0.001819942156 0.0006575509652 0.000632180354 7.7469499e-06 - 93 2 -23.68425036 -23.688669 0.002209320265 0.001133553123 0.001092474256 1.677033392e-05 - 94 2 -23.68017683 -23.690538 0.005180583191 0.0008923392716 0.0008610145179 1.053989885e-05 - 95 2 -23.68290142 -23.689722 0.003410287964 0.0006465597037 0.0006251287867 7.275875006e-06 - 96 2 -23.6789537 -23.690581 0.005813649829 7.452601432e-07 0 2.355432868e-07 - 97 2 -23.6840847 -23.688755 0.002335150427 0.0006519723076 0.0006251143895 8.25078808e-06 - 98 2 -23.67367881 -23.689312 0.007816596299 0.0008618264365 0.0008290597083 1.323477647e-05 - 99 2 -23.68489152 -23.687388 0.001248238956 0.001145929445 0.001120237475 1.049029355e-05 - 100 2 -23.68174648 -23.690664 0.004458761579 0.0006367386055 0.0006109402589 6.270984336e-06 - 101 2 -23.67450636 -23.68941 0.007451817634 0.0006119997091 0.0005883553348 7.715800125e-06 - 102 2 -23.68321442 -23.690035 0.003410290658 0.0009128748923 0.0008810062429 1.106310227e-05 - 103 2 -23.67584952 -23.690015 0.007082738579 0.0008706222251 0.0008450195264 9.898495893e-06 - 104 2 -23.67856154 -23.690752 0.006095232174 0.0006245583967 0.0005996415596 7.033875201e-06 - 105 2 -23.68297614 -23.689825 0.00342442945 0.0009134966073 0.0008800215906 1.147892484e-05 - 106 2 -23.67876135 -23.690562 0.00590032283 0.0008849512172 0.0008560011682 1.005528708e-05 - 107 2 -23.67874342 -23.690622 0.005939288687 0.0008835043772 0.0008390017878 1.530603189e-05 - 108 2 -23.6843441 -23.688764 0.002209950672 0.0009250850126 0.0008910185183 1.254407066e-05 - 109 2 -23.68340608 -23.690011 0.003302460748 0.0006464901241 0.0006194287691 7.216590251e-06 - 110 2 -23.68476306 -23.687696 0.001466471271 0.001143422035 0.001087589996 2.279977174e-05 - 111 2 -23.67977853 -23.691019 0.005620235289 0.000888876189 0.0008540035129 1.1779733e-05 - 112 2 -23.68440001 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-23.690561 0.006065426647 0.0006235069318 0.0005982273815 6.816496585e-06 - 124 2 -23.67292129 -23.689107 0.00809285397 0.0008589766346 0.0008180073349 1.439377155e-05 - 125 2 -23.68123551 -23.690145 0.004454742608 0.0009009679944 0.0008740766557 1.132072203e-05 - 126 2 -23.67777646 -23.690482 0.006352769316 0.0006215821083 0.0005939983165 8.362048689e-06 - 127 2 -23.68318209 -23.689864 0.003340952886 0.0009142894487 0.0008860124153 1.044271435e-05 + config # atoms volume energy DFT energy energy error force DFT force force error + 28 2 36.40799882 -23.68590704 -23.689367 0.001729981765 0.0005857469375 0.0006222748589 9.806537327e-06 + 29 2 36.47727251 -23.68481169 -23.689888 0.00253815708 0.0005821264542 0.0006166052222 8.797319207e-06 + 30 2 36.47184897 -23.68494784 -23.689996 0.002524078869 0.0008240616654 0.0008810425642 2.037428468e-05 + 31 2 36.62078348 -23.68225087 -23.690957 0.004353065844 9.422546395e-07 0 3.770200667e-07 + 32 2 36.71197042 -23.67989944 -23.690521 0.005310779451 0.000566950477 0.0005982273815 8.158760804e-06 + 33 2 36.77593928 -23.67819051 -23.69038 0.00609474427 0.0005635032259 0.0005925723585 7.849374173e-06 + 34 2 36.36547558 -23.68676383 -23.689202 0.001219083545 0.0005885128327 0.0006279363025 1.053580541e-05 + 35 2 36.55974375 -23.68319963 -23.690482 0.003641183354 0.000815464884 0.0008640138888 1.662920456e-05 + 36 2 36.46414346 -23.68507116 -23.689902 0.002415420054 0.0005812774047 0.0006152154094 9.669302107e-06 + 37 2 36.63368821 -23.6817672 -23.690563 0.004397900334 0.0005717456253 0.0006038725031 8.311567538e-06 + 38 2 36.45345189 -23.68547117 -23.690207 0.002367914312 0.001009744333 0.00107369735 2.610693709e-05 + 39 2 36.38484847 -23.68616091 -23.689285 0.001562044483 0.0008322058899 0.000890013483 1.991679691e-05 + 40 2 36.43347895 -23.68567207 -23.689768 0.002047966899 0.001012061035 0.001080249045 2.782864008e-05 + 41 2 36.50220719 -23.68411383 -23.68968 0.002783085738 0.0008199315614 0.0008680034562 1.637343483e-05 + 42 2 36.50719109 -23.68445604 -23.690074 0.002808981302 0.001296718439 0.001373818765 2.64147971e-05 + 43 2 36.28428565 -23.68777598 -23.688108 0.0001660085343 0.000594221946 0.0006336134468 1.099939509e-05 + 44 2 36.3642236 -23.68663754 -23.689241 0.001301727662 0.0008329159633 0.0008880101351 1.874593476e-05 + 45 2 36.40397469 -23.68626116 -23.68952 0.001629419996 0.0008297070704 0.0008860011287 1.917842744e-05 + 46 2 36.15958616 -23.68901859 -23.686278 0.001370293226 0.0006010646632 0.0006406777661 1.138305654e-05 + 47 2 36.85012426 -23.6762264 -23.690097 0.006935298115 0.0007925625457 0.0008410160522 1.643998947e-05 + 48 2 36.76983294 -23.67871264 -23.690811 0.006049181932 0.0007984019479 0.0008500070588 1.765059262e-05 + 49 2 36.6630398 -23.68078335 -23.690266 0.004741323226 0.0009871892379 0.001044322747 2.331514572e-05 + 50 2 36.55357619 -23.68366573 -23.690597 0.003465633435 0.0009975988347 0.001050833003 2.173210926e-05 + 51 2 36.65271066 -23.68154759 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1.009250412e-05 + 61 2 37.02589653 -23.67131384 -23.688881 0.008783582181 0.0007776878254 0.0008250054545 1.619373008e-05 + 62 2 36.71189602 -23.67982686 -23.690515 0.005344069182 0.001390387166 0.001475779794 3.436613175e-05 + 63 2 36.78962367 -23.67814275 -23.690551 0.006204123773 0.0005637977551 0.0005996599036 1.001095778e-05 + 64 2 36.42642467 -23.68541088 -23.689487 0.002038057601 0.0005844344049 0.0006194384554 9.105178613e-06 + 65 2 36.4423543 -23.68559418 -23.68986 0.002132908295 0.0008266682194 0.0008860124153 2.074533254e-05 + 66 2 36.39164409 -23.68624726 -23.689288 0.001520371922 0.001312283722 0.001396479144 2.724122629e-05 + 67 2 36.83059874 -23.67704953 -23.690457 0.006703736699 0.0005605067938 0.0005939831647 8.903855256e-06 + 68 2 36.8936692 -23.67527599 -23.689792 0.007258002565 0.000787658236 0.0008340587509 1.727027889e-05 + 69 2 36.88495742 -23.67562381 -23.690006 0.007191094218 0.0005570824127 0.0005897694465 9.526352044e-06 + 70 2 36.7928657 -23.67798232 -23.690571 0.00629434147 0.0005623157716 0.0005939781141 8.388724073e-06 + 71 2 36.50844234 -23.6845524 -23.690213 0.002830300186 0.001007417856 0.001084315452 3.13901245e-05 + 72 2 36.74419477 -23.67922697 -23.690617 0.005695015742 0.0005656413796 0.0006024682564 9.800558604e-06 + 73 2 36.49448266 -23.68420852 -23.689761 0.002776239615 0.0008225588858 0.0008790688255 2.057348461e-05 + 74 2 36.83933705 -23.67673911 -23.69027 0.006765442668 6.51984476e-07 0 1.932645324e-07 + 75 2 36.5709148 -23.68309624 -23.690599 0.003751378046 0.0005763054751 0.0006137752031 9.640531893e-06 + 76 2 36.67683082 -23.68088394 -23.69061 0.004863030461 8.763722169e-07 0 3.577227741e-07 + 77 2 36.66115635 -23.68104805 -23.690603 0.004777472809 0.0008071491031 0.0008590331775 1.853779451e-05 + 78 2 36.25583797 -23.68810086 -23.687908 9.643173451e-05 0.0008433322094 0.0009010105438 2.010525612e-05 + 79 2 36.69315685 -23.68027964 -23.690688 0.005204178753 0.0008040458508 0.0008470064935 1.442630316e-05 + 80 2 36.46769977 -23.68522986 -23.689988 0.002379071717 0.0005827976437 0.0006194465272 9.763878015e-06 + 81 2 36.44434113 -23.68541392 -23.689613 0.00209953858 0.0008243238033 0.0008740732235 1.862099135e-05 + 82 2 36.57453003 -23.68327227 -23.690678 0.003702863528 0.0005762034709 0.0006123757017 9.833686501e-06 + 83 2 36.54218785 -23.68361157 -23.69017 0.003279215566 0.0008176791029 0.0008750051428 1.921467316e-05 + 84 2 36.26350252 -23.68802292 -23.687892 6.545993121e-05 0.001032253376 0.001112070142 3.258468659e-05 + 85 2 36.49725495 -23.68460293 -23.690132 0.002764534398 0.0008196684225 0.000868018433 1.73736591e-05 + 86 2 36.66468316 -23.68110857 -23.690843 0.004867214139 0.0005702307406 0.0006081134763 9.414220345e-06 + 87 2 36.69098146 -23.68038294 -23.690598 0.005107529327 0.001139059342 0.001217674833 2.06566425e-05 + 88 2 36.7498524 -23.67919254 -23.690656 0.005731731866 0.0005658199144 0.0006024765556 1.012824587e-05 + 89 2 36.72620595 -23.67950048 -23.690254 0.005376762214 0.0009822281627 0.001043496047 2.500732518e-05 + 90 2 36.7046344 -23.68037755 -23.690694 0.00515822503 0.0005678245812 0.0006010740387 9.481625137e-06 + 91 2 36.53215524 -23.6837194 -23.690097 0.00318880242 0.0008183268201 0.0008730234819 1.936710758e-05 + 92 2 36.28988463 -23.68778953 -23.688402 0.000306233365 0.0005932101303 0.000632180354 1.068318322e-05 + 93 2 36.330155 -23.68704981 -23.688669 0.0008095957127 0.001023514967 0.001092474256 2.815195409e-05 + 94 2 36.65451876 -23.68118381 -23.690538 0.004677093696 0.0008073441427 0.0008610145179 1.797964322e-05 + 95 2 36.46623662 -23.68497164 -23.689722 0.002375180903 0.0005838510966 0.0006251287867 1.162407198e-05 + 96 2 36.73431174 -23.67954699 -23.690581 0.005517005254 6.747207861e-07 0 2.132659501e-07 + 97 2 36.34544239 -23.68680631 -23.688755 0.0009743455055 0.0005885973278 0.0006251143895 1.022234556e-05 + 98 2 36.9736935 -23.67299367 -23.689312 0.008159162687 0.0007819742447 0.0008290597083 1.76069415e-05 + 99 2 36.24487417 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0.0008354959994 0.0008910185183 1.950545073e-05 + 109 2 36.44122368 -23.68556667 -23.690011 0.002222166915 0.0005839138329 0.0006194287691 9.095263256e-06 + 110 2 36.25348342 -23.68799518 -23.687696 0.0001495917205 0.001029561919 0.001087589996 2.368346819e-05 + 111 2 36.69693588 -23.68052902 -23.691019 0.005244990763 0.0008045111684 0.0008540035129 1.660792245e-05 + 112 2 36.3425194 -23.68713615 -23.689025 0.0009444242204 6.048393422e-07 0 2.391864739e-07 + 113 2 36.51656499 -23.68385666 -23.689952 0.003047669619 6.637963301e-07 0 2.603475835e-07 + 114 2 36.71447816 -23.68006157 -23.69061 0.005274216197 0.0008035446124 0.0008580011655 1.851139775e-05 + 115 2 36.62519495 -23.68220128 -23.690595 0.004196860391 0.0008113491541 0.0008680069124 1.944419979e-05 + 116 2 36.80154127 -23.67766382 -23.690231 0.006283590712 0.0005612910408 0.0005925892338 9.235122707e-06 + 117 2 36.77742539 -23.67845523 -23.690469 0.006006884644 0.0007980880228 0.0008500294113 1.88002833e-05 + 118 2 36.50183296 -23.68462479 -23.690482 0.002928604258 0.0008206653147 0.0008740102974 1.862862483e-05 + 119 2 36.93568763 -23.67391526 -23.689613 0.007848867984 0.0007836859568 0.0008320192305 1.723468539e-05 + 120 2 36.23289183 -23.68838681 -23.687426 0.0004804048231 0.001032041797 0.00109577735 2.600453853e-05 + 121 2 36.44295904 -23.68519521 -23.689562 0.002183395162 0.0005844757167 0.0006265237426 1.128889659e-05 + 122 2 36.59751671 -23.68271637 -23.6904 0.003841815485 3.610825174e-07 0 1.4665868e-07 + 123 2 36.76766724 -23.67885647 -23.690561 0.005852264977 0.0005645533896 0.0005982273815 8.625051998e-06 + 124 2 37.00025894 -23.67207453 -23.689107 0.008516233835 0.0007781106616 0.0008180073349 1.390580399e-05 + 125 2 36.58722353 -23.68265657 -23.690145 0.00374421628 0.0008159137665 0.0008740766557 2.136045675e-05 + 126 2 36.79405605 -23.67803714 -23.690482 0.006222430293 0.0005630702013 0.0005939983165 8.85354297e-06 + 127 2 36.45320348 -23.68530353 -23.689864 0.002280236365 0.0008267100988 0.0008860124153 2.061923922e-05 # Elastic_FCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 128 4 -46.449456 -46.437936 0.002880000611 0.0007088173441 0.001265949446 0.0001573706237 - 129 4 -46.45317307 -46.438504 0.003667267825 0.0007210982328 0.001492549497 0.0002032393675 - 130 4 -46.44686167 -46.436378 0.002620918523 0.0004870837365 0.000810592376 0.0001107544174 - 131 4 -46.45357979 -46.441551 0.003007196305 0.0008634182131 0.001283675193 0.0001231453909 - 132 4 -46.42409677 -46.416957 0.001784942313 0.0007481922079 0.001186145859 0.0001205918882 - 133 4 -46.45078882 -46.440495 0.002573455911 0.0007289008721 0.001212440514 0.0001119490174 - 134 4 -46.4501363 -46.437972 0.003041076136 0.001116532125 0.002358226452 0.0003166808771 - 135 4 -46.46241981 -46.44586 0.004139951294 0.001077737689 0.002033949852 0.0002702964015 - 136 4 -46.44743429 -46.435744 0.002922571394 0.0008383971706 0.001690849491 0.0002711013554 - 137 4 -46.45237555 -46.438209 0.003541637787 0.0007039962535 0.001160049999 0.0001096430557 - 138 4 -46.43645451 -46.42629 0.002541127472 0.0004839683449 0.0005297018029 1.480491546e-05 - 139 4 -46.45466199 -46.443301 0.002840247268 0.0008590849412 0.001818421568 0.0002395191538 - 140 4 -46.4513559 -46.439002 0.003088474484 0.000980675092 0.001416973535 0.0001142710898 - 141 4 -46.44224357 -46.432438 0.00245139227 0.0008958100898 0.001010469198 5.862303988e-05 - 142 4 -46.41846428 -46.412654 0.001452568802 0.001104791425 0.001801959766 0.0001900084105 - 143 4 -46.45594552 -46.443231 0.003178629143 0.0006959928784 0.001691590967 0.0002104366356 - 144 4 -46.44141177 -46.431513 0.00247469212 0.001149659372 0.001680544852 0.0001329997121 - 145 4 -46.44458344 -46.435608 0.00224385943 0.000711021509 0.0009593039143 5.831382606e-05 - 146 4 -46.45129649 -46.437689 0.003401871689 0.0007271142738 0.001217708504 0.0001414871092 - 147 4 -46.43755262 -46.428447 0.002276404472 0.0008708378565 0.002060081552 0.0003082033743 - 148 4 -46.44295113 -46.432255 0.00267403188 0.0005315813764 0.0006274201144 5.596270268e-05 - 149 4 -46.45482154 -46.442315 0.003126635324 0.0008653689406 0.002424436842 0.0004107290683 - 150 4 -46.44918467 -46.436613 0.003142918309 0.0004839663128 0.0005321240457 3.890880543e-05 - 151 4 -46.44094809 -46.430825 0.002530772174 0.0007559646277 0.001399987143 0.0001669802678 - 152 4 -46.44335614 -46.43312 0.002559035587 0.0004859700309 0.0007272771136 6.315695513e-05 - 153 4 -46.44518607 -46.434347 0.002709767129 0.0007148497795 0.001284451634 0.0001580665901 - 154 4 -46.43969219 -46.430573 0.002279798333 0.00072875179 0.001315746176 0.000142372977 - 155 4 -46.46201856 -46.445665 0.004088390852 0.0008369246217 0.00180789159 0.0002715757049 - 156 4 -46.44738266 -46.435898 0.002871166201 0.0007118215897 0.001869300939 0.0002650888178 - 157 4 -46.45279209 -46.442107 0.002671271631 0.0005099355574 0.0006020930161 3.155335447e-05 - 158 4 -46.44687446 -46.434432 0.003110615714 0.0008364031703 0.001092982159 9.484366005e-05 - 159 4 -46.45033825 -46.436308 0.003507562522 0.0009954281391 0.001839150891 0.0002479613631 - 160 4 -46.43248168 -46.423938 0.002135919949 0.0007772193879 0.001463463016 0.0001986681069 - 161 4 -46.43702199 -46.428115 0.002226747981 0.0005418219957 0.0008584497656 9.283863381e-05 - 162 4 -46.43553597 -46.4269 0.002158992752 0.001008467413 0.001845719914 0.00024455962 - 163 4 -46.43191737 -46.421142 0.00269384137 0.0009169914298 0.001309150106 9.335100097e-05 - 164 4 -46.44107961 -46.432233 0.002211651338 0.0006944670911 0.0007253109678 2.446203898e-05 - 165 4 -46.44097784 -46.429408 0.002892459649 0.0007189999753 0.001068327665 9.331287519e-05 - 166 4 -46.45970672 -46.445145 0.003640430606 0.0008323398895 0.001776038288 0.000241778013 - 167 4 -46.44583143 -46.435868 0.002490857628 0.001007239475 0.002376074704 0.0003893124404 - 168 4 -46.4515773 -46.439663 0.002978574612 0.0004764710524 0.001119403413 0.0001156692402 - 169 4 -46.43612447 -46.428287 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0.0009534044263 0.0001064495091 - 223 4 -46.45000759 -46.43773 0.003069396495 0.0006831478015 0.000926180328 7.390298375e-05 - 224 4 -46.42538863 -46.416525 0.002215907169 0.0005605993692 0.0007573664899 5.946405938e-05 - 225 4 -46.45386072 -46.440293 0.003391930454 0.0006980795454 0.0007725386722 1.86450807e-05 - 226 4 -46.4527969 -46.43839 0.003601726069 0.0005103417187 0.0005612022808 1.656002337e-05 - 227 4 -46.45374294 -46.438916 0.00370673382 0.0006956794369 0.001650878554 0.0002154167998 + config # atoms volume energy DFT energy energy error force DFT force force error + 128 4 74.14589882 -46.45131085 -46.437936 0.003343711499 0.0008256456522 0.001265949446 0.0001479290162 + 129 4 74.26852111 -46.45483689 -46.438504 0.00408322283 0.0008748833702 0.001492549497 0.0001669960806 + 130 4 74.05957274 -46.44875622 -46.436378 0.00309455485 0.0005424811735 0.000810592376 0.0001015808542 + 131 4 74.30647158 -46.45520791 -46.441551 0.003414228451 0.001024641 0.001283675193 8.610021967e-05 + 132 4 73.40902276 -46.4265266 -46.416957 0.002392400067 0.0008639837782 0.001186145859 9.385948781e-05 + 133 4 74.1804881 -46.45258342 -46.440495 0.003022104862 0.0008837693055 0.001212440514 7.54705377e-05 + 134 4 74.17596744 -46.45191353 -46.437972 0.00348538317 0.001290912634 0.002358226452 0.0002715207448 + 135 4 74.73528136 -46.46363987 -46.44586 0.004444967559 0.001259032014 0.002033949852 0.0002223899959 + 136 4 74.0787509 -46.44925412 -46.435744 0.003377531217 0.0009337469328 0.001690849491 0.0002527015084 + 137 4 74.24609528 -46.45412062 -46.438209 0.003977905441 0.0008183472184 0.001160049999 8.303212282e-05 + 138 4 73.73005434 -46.43863377 -46.42629 0.003085943173 0.0005398665308 0.0005297018029 9.433755819e-06 + 139 4 74.33993289 -46.45634184 -46.443301 0.003260209859 0.001019667847 0.001818421568 0.0002031714008 + 140 4 74.20715045 -46.45310823 -46.439002 0.003526557791 0.001120917878 0.001416973535 8.385490094e-05 + 141 4 73.89686848 -46.44426829 -46.432438 0.002957572572 0.001055104669 0.001010469198 5.761635655e-05 + 142 4 73.27773838 -46.42097352 -46.412654 0.002079881174 0.001288759108 0.001801959766 0.0001651013922 + 143 4 74.40027968 -46.45756841 -46.443231 0.003584351835 0.0008139750432 0.001691590967 0.0002012572515 + 144 4 73.86123747 -46.44349423 -46.431513 0.002995306686 0.00134586635 0.001680544852 8.973225319e-05 + 145 4 73.96908649 -46.4465827 -46.435608 0.002743674619 0.0008335711035 0.0009593039143 3.003885348e-05 + 146 4 74.18717232 -46.45311791 -46.437689 0.003857228017 0.0008866862425 0.001217708504 0.0001038986229 + 147 4 73.76897316 -46.43964365 -46.428447 0.002799161691 0.0009977338004 0.002060081552 0.0002905770514 + 148 4 73.9161373 -46.44497446 -46.432255 0.003179865353 0.0006398887096 0.0006274201144 6.119155431e-05 + 149 4 74.36502962 -46.45637695 -46.442315 0.003515486518 0.001024758209 0.002424436842 0.0003681838217 + 150 4 74.11860796 -46.45104156 -46.436613 0.003607139707 0.000542307804 0.0005321240457 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0.00113392416 9.087921501e-05 + 208 4 74.19814905 -46.45309789 -46.439106 0.003497972207 0.001159709328 0.001830731002 0.0002004464824 + 209 4 74.51720313 -46.45968457 -46.443073 0.004152892794 0.0005327789399 0.0005766870902 1.911195046e-05 + 210 4 74.29924604 -46.45529068 -46.4397 0.003897668752 0.0008203202583 0.001204174406 8.707934353e-05 + 211 4 74.09425795 -46.45003681 -46.436374 0.003415701915 0.0008937039936 0.001461656594 0.0001906816478 + 212 4 73.73717548 -46.43887502 -46.426557 0.003079503833 0.0008473432438 0.001359624213 0.0001078467328 + 213 4 73.99983876 -46.44675075 -46.434009 0.00318543858 0.0009993979373 0.001391131194 0.000126864771 + 214 4 74.07916779 -46.4492147 -46.436262 0.003238173905 0.0012911873 0.002503347159 0.0002946038716 + 215 4 73.94744484 -46.44611874 -46.434505 0.0029034362 0.0009930846846 0.001041637173 1.44560542e-05 + 216 4 74.2021224 -46.45267242 -46.438768 0.003476105557 0.0009790325482 0.001098285027 5.900684038e-05 + 217 4 74.20389194 -46.45287404 -46.440254 0.003155011025 0.0005440222637 0.0006069892915 4.917760806e-05 + 218 4 73.66782167 -46.43682196 -46.42286 0.003490490208 0.0005521691303 0.0007365242698 6.657586723e-05 + 219 4 73.46349993 -46.42843317 -46.418078 0.002588792975 0.001215695483 0.002028412187 0.0002117690174 + 220 4 74.30307454 -46.45509879 -46.440513 0.003646448628 0.0008205757569 0.001158189967 0.000110036346 + 221 4 73.21819832 -46.41838058 -46.409824 0.002139145869 0.000869266353 0.001759573812 0.0002125030952 + 222 4 74.35772636 -46.45658501 -46.440329 0.004064003047 0.0006179175264 0.0009534044263 8.737057714e-05 + 223 4 74.17615527 -46.45177345 -46.43773 0.003510862689 0.0007631781991 0.000926180328 6.446679043e-05 + 224 4 73.43860935 -46.4277585 -46.416525 0.002808375906 0.0006623119965 0.0007573664899 4.251239635e-05 + 225 4 74.31356506 -46.45553467 -46.440293 0.003810416894 0.0008201864367 0.0007725386722 1.244767351e-05 + 226 4 74.25452523 -46.45450406 -46.43839 0.004028515986 0.000624431309 0.0005612022808 1.898088401e-05 + 227 4 74.27331932 -46.45546024 -46.438916 0.004136060657 0.0008098609869 0.001650878554 0.0001889274693 # GSF_110.xyz - config # atoms energy DFT energy energy error force DFT force force error - 228 24 -278.7403996 -279.068761 0.01368172569 2.282668754 1.756353161 0.0474563559 - 229 24 -279.902595 -279.784296 0.004929123882 0.9479314831 0.9057668891 0.02403120774 - 230 24 -279.9942014 -279.901657 0.003856015841 0.2795933118 0.001565946359 0.01120665859 - 231 24 -279.6335344 -279.584238 0.002054016531 1.573004204 1.035572248 0.05514377891 - 232 24 -279.9025974 -279.784283 0.004929767703 0.947921084 0.9056396189 0.02406018404 - 233 24 -279.1817177 -279.302158 0.005018345952 2.388096516 1.771965137 0.06275542538 - 234 24 -279.5900705 -279.55564 0.001434605813 1.950503627 1.405626506 0.05370441115 - 235 24 -279.0106063 -279.246939 0.00984719392 1.577003357 0.4813964151 0.08190583543 - 236 24 -279.1817217 -279.302157 0.005018138375 2.388094324 1.771953347 0.06275588675 - 237 24 -279.0107548 -279.246935 0.009840841347 1.576191869 0.4809484798 0.0819682416 - 238 24 -279.9941671 -279.896025 0.004089255845 0.2809227604 0.01060549839 0.01118927817 - 239 24 -279.6337951 -279.584237 0.002064919631 1.571895405 1.035836121 0.05510997377 - 240 24 -278.8616595 -279.124427 0.0109486445 2.383512182 1.809545887 0.06232801199 - 241 24 -279.2927133 -279.379366 0.003610531084 1.779238829 0.8982692706 0.07658702105 - 242 24 -279.292656 -279.37937 0.003613082676 1.779203263 0.898081355 0.0765940488 - 243 24 -278.8616573 -279.124427 0.01094873842 2.383511745 1.809523374 0.06232387507 - 244 24 -279.9942014 -279.901657 0.003856015842 0.27959331 0.001570374478 0.01120603916 - 245 24 -279.9072278 -279.79264 0.004774491325 0.8361247356 0.8392614852 0.02418251879 - 246 24 -279.9941671 -279.896025 0.004089255843 0.2809227622 0.01060243293 0.01118973247 - 247 24 -278.8973689 -279.206496 0.01288029691 1.390234609 0.005326518563 0.06648378416 - 248 24 -279.590075 -279.55564 0.001434791018 1.950495712 1.4056319 0.05370353355 - 249 24 -279.9072386 -279.79264 0.004774943229 0.8361385582 0.8392625708 0.02418484015 + config # atoms volume energy DFT energy energy error force DFT force force error + 228 24 828.0362386 -278.8410589 -279.068761 0.009487586046 2.726148177 1.756353161 0.06344241374 + 229 24 828.0362386 -280.0438878 -279.784296 0.01081632552 1.025836691 0.9057668891 0.03431923408 + 230 24 828.0362386 -280.1389453 -279.901657 0.009887011104 0.3820870056 0.001565946359 0.02063932212 + 231 24 828.0362386 -279.7578636 -279.584238 0.007234400289 1.646483877 1.035572248 0.06317254006 + 232 24 828.0362386 -280.0438905 -279.784283 0.01081698125 1.025825697 0.9056396189 0.03433377902 + 233 24 828.0362386 -279.2779929 -279.302158 0.001006879708 2.597392642 1.771965137 0.07498219236 + 234 24 828.0362386 -279.7119341 -279.55564 0.006512252548 2.085996302 1.405626506 0.06414553539 + 235 24 828.0362386 -279.1342144 -279.246939 0.004696857796 1.7145726 0.4813964151 0.09091186796 + 236 24 828.0362386 -279.2779974 -279.302157 0.001006650079 2.59739139 1.771953347 0.07498197018 + 237 24 828.0362386 -279.1342234 -279.246935 0.004696316576 1.714140427 0.4809484798 0.09087969403 + 238 24 828.0362386 -280.1388645 -279.896025 0.01011831143 0.3833172699 0.01060549839 0.0205724723 + 239 24 828.0362386 -279.7581378 -279.584237 0.007245866604 1.645952103 1.035836121 0.06318595533 + 240 24 828.0362386 -278.9562357 -279.124427 0.007007972259 2.699607205 1.809545887 0.07438804482 + 241 24 828.0362386 -279.4052861 -279.379366 0.00108000439 1.874556392 0.8982692706 0.08646596743 + 242 24 828.0362386 -279.4051598 -279.37937 0.001074574944 1.874858028 0.898081355 0.08649971418 + 243 24 828.0362386 -278.9562334 -279.124427 0.007008065732 2.699608673 1.809523374 0.07438947193 + 244 24 828.0362386 -280.1389453 -279.901657 0.009887011104 0.382087008 0.001570374478 0.02063718463 + 245 24 828.0362386 -280.0482205 -279.79264 0.01064918897 0.9069086057 0.8392614852 0.03243659951 + 246 24 828.0362386 -280.1388645 -279.896025 0.01011831143 0.3833172675 0.01060243293 0.02057250032 + 247 24 828.0362386 -279.0366628 -279.206496 0.007076382361 1.638514407 0.005326518563 0.08048168704 + 248 24 828.0362386 -279.7119391 -279.55564 0.006512460902 2.085987992 1.4056319 0.06414586851 + 249 24 828.0362386 -280.0482407 -279.79264 0.01065002958 0.9067922986 0.8392625708 0.03242814224 # GSF_112.xyz - config # atoms energy DFT energy energy error force DFT force force error - 250 30 -345.1428414 -345.175835 0.001099787279 2.717783384 1.057395322 0.1393371019 - 251 30 -346.8213325 -346.361714 0.01532061701 1.6320981 1.220284939 0.1010819808 - 252 30 -346.3061373 -345.795524 0.01702044399 2.435031121 2.112860875 0.1171529224 - 253 30 -344.8834516 -345.164602 0.009371679668 3.314987489 1.765832199 0.1576958872 - 254 30 -346.9668291 -346.593523 0.01244353764 1.327935537 0.01148867129 0.08670065177 - 255 30 -346.7938009 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267 30 -346.9664062 -346.582565 0.0127947081 1.328695393 0.01254743735 0.08670444025 - 268 30 -344.5284456 -344.91356 0.012837147 4.30679737 3.441834403 0.1293440404 - 269 30 -346.3471173 -345.836703 0.01701381162 2.177883948 1.608769148 0.1178087924 - 270 30 -344.9135302 -344.984307 0.002359225816 3.517317775 2.542628782 0.122092966 - 271 30 -346.7846048 -346.393931 0.01302245877 1.941770224 1.211680725 0.09898842713 + config # atoms volume energy DFT energy energy error force DFT force force error + 250 30 1075.650827 -344.9605863 -345.175835 0.007174958242 2.758670703 1.057395322 0.1516335449 + 251 30 1075.650827 -346.7372372 -346.361714 0.01251744041 1.674795336 1.220284939 0.09596889278 + 252 30 1075.650827 -346.1686186 -345.795524 0.0124364868 2.551456187 2.112860875 0.1075528655 + 253 30 1075.650827 -344.7305027 -345.164602 0.01446997708 3.364761651 1.765832199 0.1653996104 + 254 30 1075.650827 -346.8954513 -346.593523 0.01006427628 1.339499001 0.01148867129 0.08728299447 + 255 30 1075.650827 -346.7069529 -346.396186 0.01035889705 1.846653887 0.9954683928 0.09979294451 + 256 30 1075.650827 -344.9126927 -345.319406 0.01355711006 3.783666815 1.772040852 0.1835364962 + 257 30 1075.650827 -345.4584504 -345.594794 0.004544785139 3.694055398 1.516014157 0.1747792869 + 258 30 1075.650827 -346.1486771 -345.98566 0.005433903845 2.934925394 1.406252265 0.1397537934 + 259 30 1075.650827 -345.5181007 -345.383994 0.00447022439 2.558293398 0.963574308 0.1353120293 + 260 30 1075.650827 -346.8950741 -346.582564 0.01041700207 1.340303074 0.0126740587 0.08735503715 + 261 30 1075.650827 -345.1232455 -345.452139 0.01096311715 4.843836394 2.787719406 0.158731815 + 262 30 1075.650827 -346.8954617 -346.593523 0.01006462208 1.339471584 0.01148834 0.08728175252 + 263 30 1075.650827 -345.3878123 -345.281949 0.003528777779 3.04388336 1.873142686 0.1266226401 + 264 30 1075.650827 -346.0211337 -345.928661 0.003082422836 3.704012447 2.100874472 0.1385926656 + 265 30 1075.650827 -344.4666474 -345.111657 0.0215003205 5.060940978 3.358068319 0.1556709723 + 266 30 1075.650827 -346.731384 -346.367123 0.01214203185 1.743704774 1.335797131 0.0964003512 + 267 30 1075.650827 -346.8950084 -346.582565 0.0104147809 1.34025766 0.01254743735 0.08735400875 + 268 30 1075.650827 -344.3283906 -344.91356 0.01950564575 4.516603649 3.441834403 0.1385132929 + 269 30 1075.650827 -346.2085633 -345.836703 0.01239534254 2.265804409 1.608769148 0.108126121 + 270 30 1075.650827 -344.700705 -344.984307 0.009453398382 3.625655349 2.542628782 0.1276641348 + 271 30 1075.650827 -346.7005545 -346.393931 0.01022078221 2.065166442 1.211680725 0.1018842071 # Liquid.xyz - config # atoms energy DFT energy energy error force DFT force force error - 272 100 -1104.74829 -1105.601723 0.008534329546 31.13590643 31.39853886 0.5826598142 - 273 100 -1099.007356 -1099.673012 0.006656557481 34.30763539 32.03167218 0.6355970492 - 274 100 -1123.744375 -1121.31506 0.0242931528 23.69463257 20.81076453 0.4843518851 + config # atoms volume energy DFT energy energy error force DFT force force error + 272 100 2002.996789 -1105.503318 -1105.601723 0.0009840495195 33.67286942 31.39853886 0.5196524511 + 273 100 2002.996789 -1100.916702 -1099.673012 0.01243689799 34.89745034 32.03167218 0.569788481 + 274 100 2002.996789 -1125.248108 -1121.31506 0.03933048075 23.1042808 20.81076453 0.4236223924 # Surface.xyz - config # atoms energy DFT energy energy error force DFT force force error - 275 24 -279.9941674 -279.911828 0.003430809358 0.2809230274 0.002753093533 0.01155715982 - 276 48 -551.0953781 -555.359452 0.08883487284 6.541312712 0.003020630398 0.1949601982 - 277 40 -458.209131 -459.216162 0.02517577443 5.605061426 5.0461364 0.1098503638 - 278 40 -459.8554229 -461.144076 0.03221632783 2.691145822 0.005582740008 0.0817493 - 279 24 -279.8970746 -279.635146 0.01091369091 1.238573481 1.288799837 0.008644383713 - 280 30 -346.9668295 -346.592525 0.01247681774 1.32793475 0.008446203407 0.08664452133 - 281 30 -345.8871537 -345.744506 0.004754921864 3.992236552 3.124961367 0.08594721633 + config # atoms volume energy DFT energy energy error force DFT force force error + 275 24 828.0362197 -280.1388649 -279.911828 0.009459870394 0.3833165637 0.002753093533 0.0209958793 + 276 48 1756.536679 -551.9765065 -555.359452 0.07047803038 5.695770431 0.003020630398 0.1710474815 + 277 40 1394.433693 -457.8965908 -459.216162 0.03298927919 6.47605009 5.0461364 0.1141155284 + 278 40 1394.433693 -459.4317427 -461.144076 0.04280833158 2.948762022 0.005582740008 0.1122771088 + 279 24 828.0362197 -279.9357878 -279.635146 0.01252674323 2.282528363 1.288799837 0.0489285834 + 280 30 1075.65076 -346.8954518 -346.592525 0.01009756105 1.339498529 0.008446203407 0.08713647389 + 281 30 1075.65076 -345.7511061 -345.744506 0.0002200037964 4.894457614 3.124961367 0.1246204459 # Volume_A15.xyz - config # atoms energy DFT energy energy error force DFT force force error - 282 8 -66.46788051 -66.990732 0.06535643627 8.928342366e-15 0 1.501728429e-15 - 283 8 -72.67646146 -72.957807 0.03516819273 3.04869178e-14 0 5.1001593e-15 - 284 8 -94.20621366 -94.145745 0.00755858243 1.880283026e-14 0 2.444387059e-15 - 285 8 -94.43981933 -94.554682 0.01435783313 5.684495802e-15 0 8.992080697e-16 - 286 8 -79.39814886 -79.438363 0.005026767696 1.186991025e-14 0 1.998979685e-15 - 287 8 -69.38946962 -69.627817 0.02979342197 5.582708452e-15 0 9.058870552e-16 - 288 8 -83.05531805 -82.604907 0.05630138147 5.067400154e-15 0 8.060681752e-16 - 289 8 14.36690687 14.89048 0.0654466408 7.096605716e-14 0 9.778491674e-15 - 290 8 -94.13472519 -94.367599 0.02910922586 1.767991013e-14 0 2.1395518e-15 - 291 8 -89.38757156 -89.248227 0.01741807051 8.884610804e-15 0 1.30769238e-15 - 292 8 -87.49741165 -87.211997 0.03567683079 8.006170389e-15 0 1.152290069e-15 - 293 8 -93.42285179 -93.66897 0.03076477666 2.280172604e-15 0 3.891032311e-16 - 294 8 -8.05187323 -7.989166 0.007838403785 7.482512497e-14 0 1.195728177e-14 - 295 8 -85.3779751 -84.982834 0.04939263793 3.220622406e-15 0 4.863008144e-16 - 296 8 -92.37490481 -92.536373 0.0201835236 1.673164165e-14 0 2.290124109e-15 - 297 8 -26.56925158 -26.77612 0.02585855302 4.751528484e-14 0 7.423756449e-15 - 298 8 -77.90929192 -77.544107 0.04564811452 4.617032687e-15 0 7.294873617e-16 - 299 8 -80.55632181 -80.114217 0.05526310126 8.324980615e-15 0 1.201946528e-15 - 300 8 -41.83202596 -42.143041 0.03887688062 3.384606082e-14 0 5.356279237e-15 - 301 8 -91.02235339 -91.040671 0.002289700675 3.337550263e-15 0 5.490399801e-16 - 302 8 -84.76781055 -84.499231 0.03357244376 3.246108052e-14 0 5.927694678e-15 - 303 8 -60.71236154 -61.825173 0.1391014324 7.918599116e-15 0 1.30776466e-15 - 304 8 -91.5794594 -91.156873 0.05282330009 3.642169681e-15 0 5.988997276e-16 - 305 8 -54.28408457 -54.658744 0.04683242815 8.878350559e-14 0 1.511496461e-14 - 306 8 -72.29317827 -72.277255 0.00199040924 2.467731222e-15 0 3.339523392e-16 - 307 8 -75.14428628 -74.923334 0.02761903549 3.575872549e-15 0 5.510457542e-16 - 308 8 -64.41647714 -64.798066 0.04769860741 1.525236831e-14 0 2.48556962e-15 - 309 8 -93.29905733 -93.048342 0.03133941583 1.463792794e-14 0 2.408158856e-15 - 310 8 -63.56375833 -64.38702 0.1029077093 2.897725758e-15 0 5.108399236e-16 - 311 8 -88.81067445 -88.352871 0.05722543104 1.077500255e-14 0 1.707889472e-15 + config # atoms volume energy DFT energy energy error force DFT force force error + 282 8 300.763 -66.50302875 -66.990732 0.06096290674 1.941277332e-14 0 3.37325783e-15 + 283 8 97.336 -72.75000964 -72.957807 0.0259746695 1.351006698e-13 0 2.177344384e-14 + 284 8 140.608 -94.15533163 -94.145745 0.001198328985 4.044529328e-14 0 6.693247629e-15 + 285 8 148.877 -94.40707977 -94.554682 0.01845027858 6.513916874e-14 0 1.052717644e-14 + 286 8 103.823 -79.45083178 -79.438363 0.001558598047 1.722214314e-13 0 2.77785865e-14 + 287 8 287.496 -69.43914664 -69.627817 0.02358379473 1.869801108e-14 0 2.486725909e-15 + 288 8 226.981 -83.07759076 -82.604907 0.05908546939 1.580586786e-14 0 2.506150792e-15 + 289 8 64 14.38834339 14.89048 0.06276707625 3.142551462e-13 0 4.611672661e-14 + 290 8 157.464 -94.121065 -94.367599 0.03081674996 4.627906691e-14 0 7.060581015e-15 + 291 8 195.112 -89.39236133 -89.248227 0.01801679107 2.992297744e-14 0 4.401789389e-15 + 292 8 205.379 -87.50415023 -87.211997 0.03651915426 2.29993221e-14 0 3.752044138e-15 + 293 8 166.375 -93.42125038 -93.66897 0.03096495278 2.907694533e-14 0 4.724788551e-15 + 294 8 68.921 -8.019333034 -7.989166 0.003770879216 3.356694228e-13 0 6.09434176e-14 + 295 8 216 -85.39060668 -84.982834 0.0509715856 9.263122354e-15 0 1.424782104e-15 + 296 8 175.616 -92.37850178 -92.536373 0.01973390211 3.567976799e-14 0 6.038472675e-15 + 297 8 74.088 -26.52314912 -26.77612 0.03162135966 2.830510779e-13 0 4.116147259e-14 + 298 8 250.047 -77.95455874 -77.544107 0.05130646772 1.722828231e-14 0 2.531351199e-15 + 299 8 238.328 -80.59031991 -80.114217 0.05951286389 1.790178605e-14 0 2.961270842e-15 + 300 8 79.507 -41.81723354 -42.143041 0.04072593188 2.017987815e-13 0 3.254206583e-14 + 301 8 185.193 -91.02736742 -91.040671 0.001662947812 2.413722535e-14 0 4.098218376e-15 + 302 8 110.592 -84.77992099 -84.499231 0.035086249 6.257383276e-14 0 9.730565054e-15 + 303 8 328.509 -60.69292469 -61.825173 0.1415310384 2.336487667e-14 0 4.192320181e-15 + 304 8 125 -91.53133052 -91.156873 0.04680718995 4.580314378e-14 0 7.417918736e-15 + 305 8 85.184 -54.31160005 -54.658744 0.04339299436 2.081820808e-13 0 3.494754179e-14 + 306 8 274.625 -72.34854762 -72.277255 0.008911577286 3.722472678e-15 0 6.21411631e-16 + 307 8 262.144 -75.19753913 -74.923334 0.03427564069 1.368884593e-14 0 2.258168709e-15 + 308 8 91.125 -64.47776048 -64.798066 0.04003818964 1.208370656e-13 0 1.995060684e-14 + 309 8 132.651 -93.2347704 -93.048342 0.02330355033 5.798970328e-14 0 9.670321353e-15 + 310 8 314.432 -63.5755377 -64.38702 0.1014352879 7.556804155e-15 0 1.29652209e-15 + 311 8 117.649 -88.79067694 -88.352871 0.05472574302 7.470145864e-14 0 1.29226998e-14 # Volume_BCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 312 2 -16.38936242 -16.763625 0.1871312901 5.164700352e-16 0 1.827242061e-16 - 313 2 16.19675433 16.314145 0.05869533666 6.530646709e-14 0 1.921032777e-14 - 314 2 -21.24238574 -21.209071 0.01665736942 1.908874745e-15 0 7.170229344e-16 - 315 2 -15.80560502 -15.780524 0.01254051029 3.122816732e-14 0 1.231252513e-14 - 316 2 -19.05526774 -19.002205 0.02653137194 7.555287577e-15 0 2.037557095e-15 - 317 2 -22.67434567 -22.620568 0.02688883674 1.349360652e-15 0 4.857225733e-16 - 318 2 4.04311049 4.096885 0.02688725502 1.772872048e-14 0 6.601201067e-15 - 319 2 56.2105911 56.26276 0.02608445186 1.377801077e-13 0 4.795418557e-14 - 320 2 -22.55797904 -22.585113 0.01356697915 3.380715703e-15 0 1.276756478e-15 - 321 2 -21.75972417 -21.795501 0.0178884163 1.168374574e-15 0 4.533410684e-16 - 322 2 33.30678917 33.110078 0.09835558332 3.387360342e-14 0 9.173217741e-15 - 323 2 -20.82125169 -20.885998 0.0323731563 9.918492908e-16 0 3.654484123e-16 - 324 2 -23.55239721 -23.601336 0.02446939304 2.356479148e-15 0 7.090682208e-16 - 325 2 -23.17147126 -23.207313 0.01792086946 1.448170847e-15 0 4.901445524e-16 - 326 2 -19.78146338 -19.898089 0.05831281177 7.349099448e-15 0 2.984880861e-15 - 327 2 -23.45038238 -23.405474 0.02245418985 2.124472575e-15 0 7.6356745e-16 - 328 2 -4.653232293 -4.781324 0.06404585371 1.121589994e-14 0 3.980033895e-15 - 329 2 -18.67517238 -18.864936 0.09488180756 4.972820174e-16 0 1.896631e-16 - 330 2 -17.53439276 -17.813086 0.1393466189 8.350923499e-16 0 3.215020842e-16 - 331 2 -11.04889659 -11.197201 0.07415220345 1.822150476e-14 0 6.092637968e-15 - 332 2 -23.68489671 -23.696705 0.00590414498 1.240124986e-15 0 4.153217122e-16 + config # atoms volume energy DFT energy energy error force DFT force force error + 312 2 74.088 -16.41904746 -16.763625 0.172288768 8.881784197e-16 0 2.960594732e-16 + 313 2 13.824 16.2292442 16.314145 0.04245040205 6.132313711e-13 0 2.290852693e-13 + 314 2 27 -21.2109771 -21.209071 0.0009530502432 1.123466673e-14 0 3.552712694e-15 + 315 2 21.952 -15.82599793 -15.780524 0.02273696393 2.538428743e-13 0 1.020665034e-13 + 316 2 24.389 -19.01309058 -19.002205 0.005442789013 7.306210466e-15 0 2.50031477e-15 + 317 2 29.791 -22.67048776 -22.620568 0.02495988117 2.031435111e-14 0 8.215650382e-15 + 318 2 15.625 4.095802366 4.096885 0.0005413171271 6.359497134e-14 0 2.069640755e-14 + 319 2 10.648 56.21520101 56.26276 0.0237794968 6.137452342e-13 0 2.262703913e-13 + 320 2 46.656 -22.54194179 -22.585113 0.02158560454 1.006819876e-14 0 3.996802889e-15 + 321 2 50.653 -21.73865048 -21.795501 0.0284252602 1.776356839e-15 0 5.921189465e-16 + 322 2 12.167 33.26085588 33.110078 0.0753889407 1.720476052e-13 0 4.707345624e-14 + 323 2 54.872 -20.80030783 -20.885998 0.04284508708 1.538370149e-15 0 5.921189465e-16 + 324 2 39.304 -23.54386901 -23.601336 0.02873349282 4.528839094e-15 0 1.480297366e-15 + 325 2 42.875 -23.16144784 -23.207313 0.02293258231 2.082963029e-15 0 7.401486831e-16 + 326 2 59.319 -19.76694674 -19.898089 0.06557112796 4.389974022e-14 0 1.776356839e-14 + 327 2 32.768 -23.46365391 -23.405474 0.0290899572 1.331156944e-14 0 5.403085387e-15 + 328 2 17.576 -4.6700202 -4.781324 0.05565189983 4.987657631e-14 0 1.465494393e-14 + 329 2 64 -18.67254286 -18.864936 0.09619657243 8.881784197e-16 0 2.960594732e-16 + 330 2 68.921 -17.54726713 -17.813086 0.1329094363 1.371024298e-15 0 4.440892099e-16 + 331 2 19.683 -11.12327165 -11.197201 0.03696467615 4.343228798e-14 0 1.539509261e-14 + 332 2 35.937 -23.68985458 -23.696705 0.003425208911 8.588276581e-15 0 2.812564996e-15 # Volume_FCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 333 4 -19.13390887 -19.075994 0.01447871809 1.022152812e-14 0 2.293587909e-15 - 334 4 -35.26038882 -34.873619 0.0966924543 1.299038035e-15 0 3.09937261e-16 - 335 4 -43.93272346 -43.950003 0.004319884816 1.839067075e-15 0 3.483902981e-16 - 336 4 -41.03733831 -40.991909 0.01135732773 4.481141716e-15 0 9.930207698e-16 - 337 4 -43.4228254 -43.453929 0.007775899668 3.563251054e-14 0 1.025252039e-14 - 338 4 -42.67289278 -42.686077 0.003296053998 3.08362874e-15 0 8.245357522e-16 - 339 4 -33.58842759 -33.224653 0.09094364633 7.806891681e-16 0 2.054201716e-16 - 340 4 -27.01189372 -26.862709 0.03729618105 6.429823751e-15 0 1.469359846e-15 - 341 4 -25.59030438 -25.519883 0.01760534598 1.262126674e-15 0 3.031429274e-16 - 342 4 3.441093749 3.463071 0.005494312714 2.222300041e-14 0 5.686075706e-15 - 343 4 -31.9073245 -31.59595 0.07784362479 8.772505365e-16 0 2.178523565e-16 - 344 4 -45.06068744 -45.100466 0.009944641012 2.844345405e-15 0 6.141228113e-16 - 345 4 -46.03981427 -46.052258 0.0031109323 3.085311895e-15 0 7.534482297e-16 - 346 4 -30.24326213 -30.001189 0.06051828302 1.033301257e-15 0 2.648344507e-16 - 347 4 -22.957351 -22.8504 0.02673775024 1.649470508e-15 0 4.625206468e-16 - 348 4 -9.130654755 -9.164691 0.008509061334 1.441769296e-14 0 2.967949237e-15 - 349 4 -24.21746226 -24.150343 0.01677981454 9.080179666e-16 0 2.344767898e-16 - 350 4 -46.44761241 -46.426795 0.005204351765 1.356833237e-15 0 3.249715312e-16 - 351 4 -28.62111495 -28.451145 0.04249248833 8.73448718e-15 0 2.511662753e-15 - 352 4 40.31615798 40.341566 0.006352005142 4.072809775e-14 0 8.11641299e-15 - 353 4 19.51151427 19.617912 0.02659943252 2.395447746e-14 0 5.536534686e-15 - 354 4 -27.06356399 -26.954384 0.02729499736 7.989451601e-16 0 1.662443331e-16 - 355 4 -46.3678929 -46.323696 0.01104922394 3.225354336e-15 0 8.604228441e-16 - 356 4 -45.87221055 -45.828947 0.01081588677 3.654195723e-15 0 9.691321819e-16 - 357 4 -38.47076405 -38.16029 0.0776185126 1.743572283e-15 0 4.628820475e-16 - 358 4 -33.06813795 -32.919741 0.03709923634 1.476523661e-14 0 4.182418301e-15 - 359 4 -41.34431995 -41.272675 0.01791123821 3.354385367e-15 0 9.014870014e-16 - 360 4 -39.95757678 -39.753322 0.05106369446 1.803308855e-15 0 4.257287097e-16 - 361 4 -37.66252943 -37.547435 0.02877360828 4.901403086e-15 0 1.0480621e-15 - 362 4 -36.89659259 -36.52595 0.09266064636 2.659569984e-15 0 6.744460314e-16 - 363 4 -45.03250721 -45.016087 0.004105053075 1.580168365e-15 0 3.385601984e-16 + config # atoms volume energy DFT energy energy error force DFT force force error + 333 4 39.304 -19.04121551 -19.075994 0.008694621404 9.324046941e-14 0 2.550216982e-14 + 334 4 140.608 -35.2532829 -34.873619 0.09491597439 7.957989483e-17 0 1.134599845e-17 + 335 4 97.336 -43.90903851 -43.950003 0.01024112333 9.677895068e-15 0 2.24135791e-15 + 336 4 54.872 -41.05446227 -40.991909 0.01563831765 1.98280496e-14 0 4.875440329e-15 + 337 4 59.319 -43.40999789 -43.453929 0.01098277702 9.570074295e-14 0 2.719164593e-14 + 338 4 103.823 -42.63532355 -42.686077 0.01268836179 2.539930576e-15 0 4.806204543e-16 + 339 4 148.877 -33.58964546 -33.224653 0.09124811554 2.796923066e-17 0 3.296205444e-18 + 340 4 42.875 -26.8499756 -26.862709 0.003183350784 4.824942051e-14 0 1.148213469e-14 + 341 4 195.112 -25.5782856 -25.519883 0.01460065124 2.683808864e-16 0 5.477307421e-17 + 342 4 32.768 3.274215348 3.463071 0.04721391298 1.751484723e-13 0 4.608697683e-14 + 343 4 157.464 -31.91218763 -31.59595 0.07905940659 3.590442267e-17 0 4.231376791e-18 + 344 4 64 -45.05473725 -45.100466 0.01143218825 7.235555613e-15 0 1.620123306e-15 + 345 4 68.921 -46.04331302 -46.052258 0.002236244179 5.893206675e-15 0 1.299708229e-15 + 346 4 166.375 -30.2468098 -30.001189 0.06140519937 2.820758891e-16 0 5.580616674e-17 + 347 4 216 -22.95485577 -22.8504 0.02611394167 1.164554524e-16 0 2.312964635e-17 + 348 4 35.937 -9.215415964 -9.164691 0.01268124103 4.893101434e-14 0 1.156092005e-14 + 349 4 205.379 -24.20645978 -24.150343 0.01402919404 2.781506505e-18 0 3.278036852e-19 + 350 4 74.088 -46.44951294 -46.426795 0.005679484598 2.411816735e-15 0 4.763070257e-16 + 351 4 175.616 -28.61960857 -28.451145 0.04211589328 1.078338842e-14 0 3.09506759e-15 + 352 4 27 40.45415396 40.341566 0.02814698887 1.556900619e-13 0 3.789568123e-14 + 353 4 29.791 19.42166568 19.617912 0.04906157941 1.398773649e-13 0 3.335786504e-14 + 354 4 185.193 -27.05578105 -26.954384 0.02534926276 2.758936733e-16 0 5.630535877e-17 + 355 4 79.507 -46.36425384 -46.323696 0.01013945879 2.152124725e-15 0 4.437884935e-16 + 356 4 85.184 -45.86352273 -45.828947 0.008643933117 3.448840532e-14 0 9.539924949e-15 + 357 4 125 -38.44027502 -38.16029 0.06999625463 1.884407826e-15 0 4.44194105e-16 + 358 4 46.656 -32.97168631 -32.919741 0.01298632653 1.142146022e-13 0 2.894877625e-14 + 359 4 110.592 -41.29864314 -41.272675 0.006492033936 3.342024128e-14 0 9.358862094e-15 + 360 4 117.649 -39.91686354 -39.753322 0.04088538603 7.303704341e-15 0 1.704201263e-15 + 361 4 50.653 -37.65718147 -37.547435 0.02743661628 2.105764443e-14 0 5.292352205e-15 + 362 4 132.651 -36.87810682 -36.52595 0.08803920465 3.379802923e-17 0 3.983135944e-18 + 363 4 91.125 -45.01844387 -45.016087 0.0005892174087 1.081458604e-14 0 2.513809578e-15 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_errors.pod b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod index 39b7af3723..02d9f823fc 100644 --- a/examples/PACKAGES/pod/Ta/Ta_training_errors.pod +++ b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod @@ -2,19 +2,19 @@ --------------------------------------------------------------------------------------------------- File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force --------------------------------------------------------------------------------------------------- -Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 -Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 -Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 -Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 -Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 -GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 -GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 -Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 -Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 -Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +Displaced_A15.xyz 9 576 0.015324 0.015365 0.140594 0.184797 +Displaced_BCC.xyz 9 486 0.009486 0.011643 0.249983 0.320375 +Displaced_FCC.xyz 9 432 0.000686 0.000880 0.091420 0.113585 +Elastic_BCC.xyz 100 200 0.003796 0.004379 0.000015 0.000020 +Elastic_FCC.xyz 100 400 0.003332 0.003372 0.000122 0.000178 +GSF_110.xyz 22 528 0.007027 0.007797 0.057637 0.115638 +GSF_112.xyz 22 660 0.010396 0.011347 0.125237 0.198553 +Liquid.xyz 3 300 0.017584 0.023822 0.504354 0.660300 +Surface.xyz 7 236 0.025511 0.034302 0.107190 0.285034 +Volume_A15.xyz 30 240 0.038624 0.048355 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.044423 0.061685 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030062 0.041271 0.000000 0.000000 --------------------------------------------------------------------------------------------------- -All files 363 4224 0.012917 0.025797 0.122473 0.260052 +All files 363 4224 0.012618 0.024806 0.125879 0.247229 --------------------------------------------------------------------------------------------------- **************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/Ta/in.fitpod b/examples/PACKAGES/pod/Ta/in.fitpod index 7b932558ea..2c2a5e57bb 100644 --- a/examples/PACKAGES/pod/Ta/in.fitpod +++ b/examples/PACKAGES/pod/Ta/in.fitpod @@ -1,5 +1 @@ -# Demonstrate fitpod for POD potential - -units metal -fitpod Ta_param.pod Ta_data.pod - +fitpod Ta_param.pod Ta_data.pod \ No newline at end of file diff --git a/examples/PACKAGES/pod/Ta/in.pod b/examples/PACKAGES/pod/Ta/in.pod index 866ee40549..5d2d646835 100644 --- a/examples/PACKAGES/pod/Ta/in.pod +++ b/examples/PACKAGES/pod/Ta/in.pod @@ -44,4 +44,3 @@ velocity all create 300.0 4928459 loop geom fix 1 all nve run ${nsteps} - diff --git a/examples/PACKAGES/pod/Ta/in.pod.compute b/examples/PACKAGES/pod/Ta/in.pod.compute new file mode 100644 index 0000000000..609c794e7f --- /dev/null +++ b/examples/PACKAGES/pod/Ta/in.pod.compute @@ -0,0 +1,52 @@ +# Demonstrate bispectrum computes + +# initialize simulation + +variable nsteps index 0 +variable nrep equal 2 +variable a equal 2.0 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +atom_modify map hash +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 2 box +create_atoms 2 box + +mass * 180.88 + +displace_atoms all random 0.1 0.1 0.1 123456 + +# set up dummy potential to satisfy cutoff +variable rcutfac equal 6.0 +pair_style zero ${rcutfac} +pair_coeff * * + +# set up per-atom computes + +compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta +compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta + +# set up compute snap generating global array + +compute gdd all pod/global Ta_param.pod Ta_coefficients.pod Ta Ta +#fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector + +compute ldd all pod/local Ta_param.pod Ta_coefficients.pod Ta Ta +#fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector + +#dump mydump_ld all custom 1000 dump_ld id c_ld[*] +#dump mydump_dd all custom 1000 dump_dd id c_dd[*] + +variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor +fix ldprint all print 1 "${sample_ld1}" + +run ${nsteps} diff --git a/examples/PACKAGES/pod/Ta/log.4Jan23.fitpod.g++.4 b/examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.1 similarity index 57% rename from examples/PACKAGES/pod/Ta/log.4Jan23.fitpod.g++.4 rename to examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.1 index 18c7775bd7..2b9c569949 100644 --- a/examples/PACKAGES/pod/Ta/log.4Jan23.fitpod.g++.4 +++ b/examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.1 @@ -1,32 +1,37 @@ -LAMMPS (22 Dec 2022) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-177-g86abf4f680-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task -# Demonstrate fitpod for POD potential - -units metal fitpod Ta_param.pod Ta_data.pod -Reading potential file Ta_param.pod with DATE: 2022-11-30 **************** Begin of POD Potentials **************** species: Ta periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 inner cut-off radius: 1 outer cut-off radius: 5 bessel polynomial degree: 3 inverse polynomial degree: 6 one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 32 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 **************** End of POD Potentials **************** **************** Begin of Data File **************** @@ -34,6 +39,8 @@ file format: extxyz file extension: xyz path to training data set: XYZ path to test data set: XYZ +path to environment configuration set: XYZ +basename for output files: Ta training fraction: 1 test fraction: 1 randomize training data set: 1 @@ -45,7 +52,8 @@ energy/force calculation for test data set: 0 fitting weight for energy: 100 fitting weight for force: 1 fitting weight for stress: 0 -fitting regularization parameter: 1e-10 +save pod descriptors: 0 +compute pod descriptors: 0 **************** End of Data File **************** **************** Begin of Training Data Set **************** --------------------------------------------------------------- @@ -74,8 +82,7 @@ maximum number of atoms: 100 maximum number of atoms in periodic domain: 100 maximum number of atoms in extended domain: 2700 maximum number of neighbors in extended domain: 270000 -size of double memory: 223201 -size of int memory: 14709 +size of double memory: 232128 size of descriptor matrix: 32 x 32 **************** End of Memory Allocation **************** **************** Begin of Least-Squares Fitting **************** @@ -83,7 +90,6 @@ Configuration: # 1 Configuration: # 101 Configuration: # 201 Configuration: # 301 -**************** End of Least-Squares Fitting **************** **************** Begin of Error Calculation **************** Configuration: # 1 Configuration: # 101 @@ -94,21 +100,20 @@ Configuration: # 301 --------------------------------------------------------------------------------------------------- File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force --------------------------------------------------------------------------------------------------- -Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 -Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 -Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 -Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 -Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 -GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 -GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 -Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 -Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 -Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +Displaced_A15.xyz 9 576 0.015324 0.015365 0.140594 0.184797 +Displaced_BCC.xyz 9 486 0.009486 0.011643 0.249983 0.320375 +Displaced_FCC.xyz 9 432 0.000686 0.000880 0.091420 0.113585 +Elastic_BCC.xyz 100 200 0.003796 0.004379 0.000015 0.000020 +Elastic_FCC.xyz 100 400 0.003332 0.003372 0.000122 0.000178 +GSF_110.xyz 22 528 0.007027 0.007797 0.057637 0.115638 +GSF_112.xyz 22 660 0.010396 0.011347 0.125237 0.198553 +Liquid.xyz 3 300 0.017584 0.023822 0.504354 0.660300 +Surface.xyz 7 236 0.025511 0.034302 0.107190 0.285034 +Volume_A15.xyz 30 240 0.038624 0.048355 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.044423 0.061685 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030062 0.041271 0.000000 0.000000 --------------------------------------------------------------------------------------------------- -All files 363 4224 0.012917 0.025797 0.122473 0.260052 +All files 363 4224 0.012618 0.024806 0.125879 0.247229 --------------------------------------------------------------------------------------------------- **************** End of Error Analysis for the Training Data Set **************** - Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.4Jan23.fitpod.g++.1 b/examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.4 similarity index 57% rename from examples/PACKAGES/pod/Ta/log.4Jan23.fitpod.g++.1 rename to examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.4 index fa625116f3..2b9c569949 100644 --- a/examples/PACKAGES/pod/Ta/log.4Jan23.fitpod.g++.1 +++ b/examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.4 @@ -1,32 +1,37 @@ -LAMMPS (22 Dec 2022) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-177-g86abf4f680-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task -# Demonstrate fitpod for POD potential - -units metal fitpod Ta_param.pod Ta_data.pod -Reading potential file Ta_param.pod with DATE: 2022-11-30 **************** Begin of POD Potentials **************** species: Ta periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 inner cut-off radius: 1 outer cut-off radius: 5 bessel polynomial degree: 3 inverse polynomial degree: 6 one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 32 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 **************** End of POD Potentials **************** **************** Begin of Data File **************** @@ -34,6 +39,8 @@ file format: extxyz file extension: xyz path to training data set: XYZ path to test data set: XYZ +path to environment configuration set: XYZ +basename for output files: Ta training fraction: 1 test fraction: 1 randomize training data set: 1 @@ -45,7 +52,8 @@ energy/force calculation for test data set: 0 fitting weight for energy: 100 fitting weight for force: 1 fitting weight for stress: 0 -fitting regularization parameter: 1e-10 +save pod descriptors: 0 +compute pod descriptors: 0 **************** End of Data File **************** **************** Begin of Training Data Set **************** --------------------------------------------------------------- @@ -74,8 +82,7 @@ maximum number of atoms: 100 maximum number of atoms in periodic domain: 100 maximum number of atoms in extended domain: 2700 maximum number of neighbors in extended domain: 270000 -size of double memory: 223201 -size of int memory: 14709 +size of double memory: 232128 size of descriptor matrix: 32 x 32 **************** End of Memory Allocation **************** **************** Begin of Least-Squares Fitting **************** @@ -83,7 +90,6 @@ Configuration: # 1 Configuration: # 101 Configuration: # 201 Configuration: # 301 -**************** End of Least-Squares Fitting **************** **************** Begin of Error Calculation **************** Configuration: # 1 Configuration: # 101 @@ -94,21 +100,20 @@ Configuration: # 301 --------------------------------------------------------------------------------------------------- File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force --------------------------------------------------------------------------------------------------- -Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 -Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 -Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 -Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 -Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 -GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 -GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 -Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 -Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 -Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +Displaced_A15.xyz 9 576 0.015324 0.015365 0.140594 0.184797 +Displaced_BCC.xyz 9 486 0.009486 0.011643 0.249983 0.320375 +Displaced_FCC.xyz 9 432 0.000686 0.000880 0.091420 0.113585 +Elastic_BCC.xyz 100 200 0.003796 0.004379 0.000015 0.000020 +Elastic_FCC.xyz 100 400 0.003332 0.003372 0.000122 0.000178 +GSF_110.xyz 22 528 0.007027 0.007797 0.057637 0.115638 +GSF_112.xyz 22 660 0.010396 0.011347 0.125237 0.198553 +Liquid.xyz 3 300 0.017584 0.023822 0.504354 0.660300 +Surface.xyz 7 236 0.025511 0.034302 0.107190 0.285034 +Volume_A15.xyz 30 240 0.038624 0.048355 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.044423 0.061685 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030062 0.041271 0.000000 0.000000 --------------------------------------------------------------------------------------------------- -All files 363 4224 0.012917 0.025797 0.122473 0.260052 +All files 363 4224 0.012618 0.024806 0.125879 0.247229 --------------------------------------------------------------------------------------------------- **************** End of Error Analysis for the Training Data Set **************** - -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.22May24.pod.compute.g++.1 b/examples/PACKAGES/pod/Ta/log.22May24.pod.compute.g++.1 new file mode 100644 index 0000000000..b32649c492 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.22May24.pod.compute.g++.1 @@ -0,0 +1,293 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-177-g86abf4f680-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate bispectrum computes + +# initialize simulation + +variable nsteps index 0 +variable nrep equal 2 +variable a equal 2.0 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 2 +variable ny equal ${nrep} +variable ny equal 2 +variable nz equal ${nrep} +variable nz equal 2 + +boundary p p p + +atom_modify map hash +lattice bcc $a +lattice bcc 2 +Lattice spacing in x,y,z = 2 2 2 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 2 0 ${ny} 0 ${nz} +region box block 0 2 0 2 0 ${nz} +region box block 0 2 0 2 0 2 +create_box 2 box +Created orthogonal box = (0 0 0) to (4 4 4) + 1 by 1 by 1 MPI processor grid +create_atoms 2 box +Created 16 atoms + using lattice units in orthogonal box = (0 0 0) to (4 4 4) + create_atoms CPU = 0.001 seconds + +mass * 180.88 + +displace_atoms all random 0.1 0.1 0.1 123456 +Displacing atoms ... + +# set up dummy potential to satisfy cutoff +variable rcutfac equal 6.0 +pair_style zero ${rcutfac} +pair_style zero 6 +pair_coeff * * + +# set up per-atom computes + +compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + + +# set up compute snap generating global array + +compute gdd all pod/gdd Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +#fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector + +compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +#fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector + +#dump mydump_ld all custom 1000 dump_ld id c_ld[*] +#dump mydump_dd all custom 1000 dump_dd id c_dd[*] + +variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor +fix ldprint all print 1 "${sample_ld1}" + +run ${nsteps} +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +WARNING: More than one compute pod (src/ML-POD/compute_pod_atom.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_podd_atom.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_pod_global.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_pod_local.cpp:89) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8 + ghost atom cutoff = 8 + binsize = 4, bins = 1 1 1 + 5 neighbor lists, perpetual/occasional/extra = 1 4 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pod/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) compute podd/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (4) compute pod/gdd, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (5) compute pod/ldd, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +0.344594831165384 +Per MPI rank memory allocation (min/avg/max) = 6.326 | 6.326 | 6.326 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 1.207e-06 on 1 procs for 0 steps with 16 atoms + +165.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.207e-06 | | |100.00 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1984 ave 1984 max 1984 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4311 ave 4311 max 4311 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 8623 ave 8623 max 8623 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8623 +Ave neighs/atom = 538.9375 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.22May24.pod.g++.1 b/examples/PACKAGES/pod/Ta/log.22May24.pod.g++.1 new file mode 100644 index 0000000000..f72962432d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.22May24.pod.g++.1 @@ -0,0 +1,155 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-177-g86abf4f680-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.001 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.207 | 3.207 | 3.207 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.842971 0 -11.804496 -24843.054 + 10 296.87227 -11.84257 0 -11.804496 -24609.859 + 20 287.65971 -11.841388 0 -11.804496 -23926.722 + 30 272.87511 -11.839492 0 -11.804496 -22841.672 + 40 253.34724 -11.836988 0 -11.804496 -21429.268 + 50 230.17169 -11.834015 0 -11.804496 -19782.77 + 60 204.64408 -11.830741 0 -11.804496 -18004.755 + 70 178.17888 -11.827347 0 -11.804495 -16197.482 + 80 152.21769 -11.824017 0 -11.804495 -14454.425 + 90 128.13189 -11.820928 0 -11.804495 -12854.075 + 100 107.12666 -11.818234 0 -11.804495 -11456.437 +Loop time of 0.394952 on 1 procs for 100 steps with 128 atoms + +Performance: 10.938 ns/day, 2.194 hours/ns, 253.196 timesteps/s, 32.409 katom-step/s +97.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.39249 | 0.39249 | 0.39249 | 0.0 | 99.38 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00087496 | 0.00087496 | 0.00087496 | 0.0 | 0.22 +Output | 0.00030885 | 0.00030885 | 0.00030885 | 0.0 | 0.08 +Modify | 0.00053218 | 0.00053218 | 0.00053218 | 0.0 | 0.13 +Other | | 0.0007481 | | | 0.19 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.22May24.pod.g++.4 b/examples/PACKAGES/pod/Ta/log.22May24.pod.g++.4 new file mode 100644 index 0000000000..3b66d3969f --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.22May24.pod.g++.4 @@ -0,0 +1,155 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-177-g86abf4f680-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.001 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.187 | 3.187 | 3.187 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.842971 0 -11.804496 -24843.054 + 10 296.87227 -11.84257 0 -11.804496 -24609.859 + 20 287.65971 -11.841388 0 -11.804496 -23926.722 + 30 272.87511 -11.839492 0 -11.804496 -22841.672 + 40 253.34724 -11.836988 0 -11.804496 -21429.268 + 50 230.17169 -11.834015 0 -11.804496 -19782.77 + 60 204.64408 -11.830741 0 -11.804496 -18004.755 + 70 178.17888 -11.827347 0 -11.804495 -16197.482 + 80 152.21769 -11.824017 0 -11.804495 -14454.425 + 90 128.13189 -11.820928 0 -11.804495 -12854.075 + 100 107.12666 -11.818234 0 -11.804495 -11456.437 +Loop time of 0.153961 on 4 procs for 100 steps with 128 atoms + +Performance: 28.059 ns/day, 0.855 hours/ns, 649.516 timesteps/s, 83.138 katom-step/s +96.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.1281 | 0.12977 | 0.1312 | 0.3 | 84.29 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.01967 | 0.021169 | 0.022796 | 0.8 | 13.75 +Output | 0.00045049 | 0.00053796 | 0.00078459 | 0.0 | 0.35 +Modify | 0.00039544 | 0.0004393 | 0.00048043 | 0.0 | 0.29 +Other | | 0.002049 | | | 1.33 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.fitpod.g++.4 b/examples/PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 similarity index 55% rename from examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.fitpod.g++.4 rename to examples/PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 index 6de2055d56..6dd2ab946c 100644 --- a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.fitpod.g++.4 +++ b/examples/PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 @@ -1,39 +1,46 @@ -LAMMPS (22 Dec 2022) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-179-g353121c942-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task -# Demonstrate fitpod for POD potential - -units metal fitpod Ta_param.pod Ta_data.pod -Reading potential file Ta_param.pod with DATE: 2022-11-30 **************** Begin of POD Potentials **************** species: Ta periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 inner cut-off radius: 1 outer cut-off radius: 5 bessel polynomial degree: 3 inverse polynomial degree: 6 one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 1 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 150 -total number of descriptors for all potentials: 182 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 **************** End of POD Potentials **************** **************** Begin of Data File **************** file format: extxyz file extension: xyz -path to training data set: ../Ta/XYZ -path to test data set: ../Ta/XYZ +path to training data set: XYZ +path to test data set: XYZ +path to environment configuration set: XYZ +basename for output files: Ta training fraction: 1 test fraction: 1 randomize training data set: 1 @@ -45,7 +52,8 @@ energy/force calculation for test data set: 0 fitting weight for energy: 100 fitting weight for force: 1 fitting weight for stress: 0 -fitting regularization parameter: 1e-10 +save pod descriptors: 0 +compute pod descriptors: 0 **************** End of Data File **************** **************** Begin of Training Data Set **************** --------------------------------------------------------------- @@ -74,16 +82,14 @@ maximum number of atoms: 100 maximum number of atoms in periodic domain: 100 maximum number of atoms in extended domain: 2700 maximum number of neighbors in extended domain: 270000 -size of double memory: 223201 -size of int memory: 14709 -size of descriptor matrix: 182 x 182 +size of double memory: 232128 +size of descriptor matrix: 32 x 32 **************** End of Memory Allocation **************** **************** Begin of Least-Squares Fitting **************** Configuration: # 1 Configuration: # 101 Configuration: # 201 Configuration: # 301 -**************** End of Least-Squares Fitting **************** **************** Begin of Error Calculation **************** Configuration: # 1 Configuration: # 101 @@ -94,21 +100,20 @@ Configuration: # 301 --------------------------------------------------------------------------------------------------- File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force --------------------------------------------------------------------------------------------------- -Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 -Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 -Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 -Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 -Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 -GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765 -GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 -Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 -Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 -Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 +Displaced_A15.xyz 9 576 0.015324 0.015365 0.140594 0.184797 +Displaced_BCC.xyz 9 486 0.009486 0.011643 0.249983 0.320375 +Displaced_FCC.xyz 9 432 0.000686 0.000880 0.091420 0.113585 +Elastic_BCC.xyz 100 200 0.003796 0.004379 0.000015 0.000020 +Elastic_FCC.xyz 100 400 0.003332 0.003372 0.000122 0.000178 +GSF_110.xyz 22 528 0.007027 0.007797 0.057637 0.115638 +GSF_112.xyz 22 660 0.010396 0.011347 0.125237 0.198553 +Liquid.xyz 3 300 0.017584 0.023822 0.504354 0.660300 +Surface.xyz 7 236 0.025511 0.034302 0.107190 0.285034 +Volume_A15.xyz 30 240 0.038624 0.048355 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.044423 0.061685 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030062 0.041271 0.000000 0.000000 --------------------------------------------------------------------------------------------------- -All files 363 4224 0.001053 0.002171 0.059051 0.106960 +All files 363 4224 0.012618 0.024806 0.125879 0.247229 --------------------------------------------------------------------------------------------------- **************** End of Error Analysis for the Training Data Set **************** - Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.24June24.pod.compute.g++.1 b/examples/PACKAGES/pod/Ta/log.24June24.pod.compute.g++.1 new file mode 100644 index 0000000000..f120ddd5e5 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.24June24.pod.compute.g++.1 @@ -0,0 +1,293 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-179-g353121c942-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate bispectrum computes + +# initialize simulation + +variable nsteps index 0 +variable nrep equal 2 +variable a equal 2.0 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 2 +variable ny equal ${nrep} +variable ny equal 2 +variable nz equal ${nrep} +variable nz equal 2 + +boundary p p p + +atom_modify map hash +lattice bcc $a +lattice bcc 2 +Lattice spacing in x,y,z = 2 2 2 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 2 0 ${ny} 0 ${nz} +region box block 0 2 0 2 0 ${nz} +region box block 0 2 0 2 0 2 +create_box 2 box +Created orthogonal box = (0 0 0) to (4 4 4) + 1 by 1 by 1 MPI processor grid +create_atoms 2 box +Created 16 atoms + using lattice units in orthogonal box = (0 0 0) to (4 4 4) + create_atoms CPU = 0.001 seconds + +mass * 180.88 + +displace_atoms all random 0.1 0.1 0.1 123456 +Displacing atoms ... + +# set up dummy potential to satisfy cutoff +variable rcutfac equal 6.0 +pair_style zero ${rcutfac} +pair_style zero 6 +pair_coeff * * + +# set up per-atom computes + +compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + + +# set up compute snap generating global array + +compute gdd all pod/global Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +#fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector + +compute ldd all pod/local Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +#fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector + +#dump mydump_ld all custom 1000 dump_ld id c_ld[*] +#dump mydump_dd all custom 1000 dump_dd id c_dd[*] + +variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor +fix ldprint all print 1 "${sample_ld1}" + +run ${nsteps} +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +WARNING: More than one compute pod (src/ML-POD/compute_pod_atom.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_podd_atom.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_pod_global.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_pod_local.cpp:89) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8 + ghost atom cutoff = 8 + binsize = 4, bins = 1 1 1 + 5 neighbor lists, perpetual/occasional/extra = 1 4 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pod/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) compute podd/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (4) compute pod/global, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (5) compute pod/local, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +0.344594831165384 +Per MPI rank memory allocation (min/avg/max) = 6.326 | 6.326 | 6.326 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 1.23e-06 on 1 procs for 0 steps with 16 atoms + +243.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.23e-06 | | |100.00 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1984 ave 1984 max 1984 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4311 ave 4311 max 4311 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 8623 ave 8623 max 8623 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8623 +Ave neighs/atom = 538.9375 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.4Jan23.pod.g++.1 b/examples/PACKAGES/pod/Ta/log.4Jan23.pod.g++.1 deleted file mode 100644 index e7c52bfd13..0000000000 --- a/examples/PACKAGES/pod/Ta/log.4Jan23.pod.g++.1 +++ /dev/null @@ -1,142 +0,0 @@ -LAMMPS (22 Dec 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate POD Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 128 atoms - using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) - create_atoms CPU = 0.000 seconds - -mass 1 180.88 - - -# POD potential -pair_style pod -pair_coeff * * Ta_param.pod Ta_coeff.pod Ta -Reading potential file Ta_param.pod with DATE: 2022-11-30 -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 32 -**************** End of POD Potentials **************** - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 loop geom -fix 1 all nve -run ${nsteps} -run 100 -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair pod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 300 -11.841512 0 -11.803037 -15933.622 - 10 296.91721 -11.841117 0 -11.803037 -15691.904 - 20 287.83555 -11.839952 0 -11.803037 -14982.977 - 30 273.25574 -11.838082 0 -11.803037 -13853.44 - 40 253.98821 -11.835611 0 -11.803037 -12375.459 - 50 231.10664 -11.832676 0 -11.803037 -10639.774 - 60 205.8844 -11.829441 0 -11.803037 -8747.2222 - 70 179.71599 -11.826085 0 -11.803037 -6799.8371 - 80 154.02711 -11.822791 0 -11.803037 -4892.7805 - 90 130.17821 -11.819732 0 -11.803036 -3108.1226 - 100 109.36842 -11.817063 0 -11.803036 -1510.9592 -Loop time of 1.51641 on 1 procs for 100 steps with 128 atoms - -Performance: 2.849 ns/day, 8.425 hours/ns, 65.945 timesteps/s, 8.441 katom-step/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5158 | 1.5158 | 1.5158 | 0.0 | 99.96 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00023616 | 0.00023616 | 0.00023616 | 0.0 | 0.02 -Output | 0.00010779 | 0.00010779 | 0.00010779 | 0.0 | 0.01 -Modify | 9.7284e-05 | 9.7284e-05 | 9.7284e-05 | 0.0 | 0.01 -Other | | 0.0001254 | | | 0.01 - -Nlocal: 128 ave 128 max 128 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 727 ave 727 max 727 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 7424 ave 7424 max 7424 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - - -Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta/log.4Jan23.pod.g++.4 b/examples/PACKAGES/pod/Ta/log.4Jan23.pod.g++.4 deleted file mode 100644 index 8d3496f563..0000000000 --- a/examples/PACKAGES/pod/Ta/log.4Jan23.pod.g++.4 +++ /dev/null @@ -1,142 +0,0 @@ -LAMMPS (22 Dec 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate POD Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 128 atoms - using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) - create_atoms CPU = 0.000 seconds - -mass 1 180.88 - - -# POD potential -pair_style pod -pair_coeff * * Ta_param.pod Ta_coeff.pod Ta -Reading potential file Ta_param.pod with DATE: 2022-11-30 -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 32 -**************** End of POD Potentials **************** - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 loop geom -fix 1 all nve -run ${nsteps} -run 100 -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair pod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 300 -11.841512 0 -11.803037 -15933.622 - 10 296.91721 -11.841117 0 -11.803037 -15691.904 - 20 287.83555 -11.839952 0 -11.803037 -14982.977 - 30 273.25574 -11.838082 0 -11.803037 -13853.44 - 40 253.98821 -11.835611 0 -11.803037 -12375.459 - 50 231.10664 -11.832676 0 -11.803037 -10639.774 - 60 205.8844 -11.829441 0 -11.803037 -8747.2222 - 70 179.71599 -11.826085 0 -11.803037 -6799.8371 - 80 154.02711 -11.822791 0 -11.803037 -4892.7805 - 90 130.17821 -11.819732 0 -11.803036 -3108.1226 - 100 109.36842 -11.817063 0 -11.803036 -1510.9592 -Loop time of 0.437423 on 4 procs for 100 steps with 128 atoms - -Performance: 9.876 ns/day, 2.430 hours/ns, 228.612 timesteps/s, 29.262 katom-step/s -98.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.41133 | 0.41882 | 0.42464 | 0.7 | 95.75 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.011279 | 0.017302 | 0.024975 | 3.7 | 3.96 -Output | 0.00012956 | 0.00029493 | 0.00077991 | 0.0 | 0.07 -Modify | 4.2093e-05 | 4.7838e-05 | 5.3039e-05 | 0.0 | 0.01 -Other | | 0.0009598 | | | 0.22 - -Nlocal: 32 ave 32 max 32 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 431 ave 431 max 431 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1856 ave 1856 max 1856 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod deleted file mode 100644 index de76b2e90e..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod +++ /dev/null @@ -1,183 +0,0 @@ -POD_coefficients: 182 --4.35182 -3.57837 -2.25497 -4.84612 --2.06319 --1.17070 --0.23842 -9.17160 -36.02366 -16.65304 --141.18403 -37.17722 -0.46028 --9.76148 --0.03681 -15.64520 -2.29791 -0.02143 -2.69735 --0.35336 -0.51108 --2.36290 -0.18617 --0.13079 -1.02666 -0.21514 -0.08075 --0.28347 --0.45059 --0.24762 --1.13671 --0.30577 -0.60504 -0.31285 --0.10639 --0.06957 -0.21961 --0.10426 -0.80318 --11.41460 --10.26102 --0.03887 --18.86071 --4.47372 --1.76858 --0.92503 -0.42654 -0.35849 -0.56611 --0.79354 -5.65136 -8.75283 --6.22283 --4.34623 -10.20031 -6.53360 -7.16688 -2.19236 -5.90789 -3.52173 -7.97264 -0.21104 --0.01015 -0.01023 -0.03088 -0.10222 -0.05366 --0.08037 --3.17612 --3.45669 --0.79282 --2.38323 --0.69797 --1.44780 --0.03351 --0.05645 -0.01901 --0.01923 -0.05401 --0.02095 -1.45651 -1.58812 -1.41188 -2.18122 -3.04893 -1.09294 -3.03781 -1.07249 -0.50262 -0.81150 -0.35997 -0.64602 --0.04245 -0.00113 --0.02894 -0.04382 --0.06556 -0.00052 -4.67541 -0.11812 -1.52428 --0.17075 -0.20231 -0.36857 -0.61744 -0.20190 --0.00816 -0.16194 --0.12948 --0.02136 --2.19271 -0.62510 -0.20030 --0.27621 --0.58116 --0.21792 --1.82295 --0.32166 --0.64550 --0.11580 --0.02438 --0.08057 -0.19538 -0.04119 -0.00323 -0.06530 --0.02547 --0.01404 -0.22336 --0.48191 --0.10715 --0.25685 --0.65069 --0.31428 --0.06947 -0.11924 -0.05467 -0.12105 --0.03980 --0.00295 --2.14413 -0.82345 -0.23083 --0.24925 --0.36678 --0.16709 -1.20410 --0.47756 --0.11104 -0.09587 -0.03722 -0.00309 --0.29879 --0.06463 --0.10236 --0.02276 --0.06012 --0.02985 -12.06876 --3.39995 -0.85590 --0.77481 --1.13392 --0.40511 --0.08005 --0.07162 --0.05978 --0.02407 --0.06031 --0.02307 --10.24105 -2.49356 --1.14052 -0.70453 -0.99988 -0.33862 -2.43469 --1.16557 --0.23708 -0.03482 --0.05280 --0.02735 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod deleted file mode 100644 index adfe772d10..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod +++ /dev/null @@ -1,33 +0,0 @@ -# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 -# chemical element symbols -species Ta - -# periodic boundary conditions -pbc 1 1 1 - -# inner cut-off radius -rin 1.0 - -# outer cut-off radius -rcut 5.0 - -# polynomial degrees for radial basis functions -bessel_polynomial_degree 3 -inverse_polynomial_degree 6 - -# one-body potential -onebody 1 - -# two-body linear POD potential -twobody_number_radial_basis_functions 6 - -# three-body linear POD potential -threebody_number_radial_basis_functions 5 -threebody_number_angular_basis_functions 5 - -# four-body linear SNAP potential -fourbody_snap_twojmax 0 - -# quadratic POD potential -quadratic_pod_potential 1 - diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod deleted file mode 100644 index b87f585e66..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod +++ /dev/null @@ -1,387 +0,0 @@ -# Displaced_A15.xyz - config # atoms energy DFT energy energy error force DFT force force error - 1 64 -754.2481469 -754.220443 0.0004328739544 8.011514562 8.398670477 0.06376624845 - 2 64 -753.8045629 -753.865255 0.0009483144042 9.036674821 9.134430545 0.07283326238 - 3 64 -754.1013214 -754.0221 0.001237834258 8.637024088 9.017261102 0.06364800593 - 4 64 -754.2847414 -754.279613 8.013173542e-05 8.107730622 8.381725092 0.06510174353 - 5 64 -753.8382044 -753.777209 0.0009530527364 9.104258904 9.478314477 0.07200164536 - 6 64 -754.0793448 -754.048643 0.0004797149286 8.152198894 8.465317938 0.06707941365 - 7 64 -754.3310528 -754.317603 0.0002101531052 7.9440922 8.127690491 0.05987172107 - 8 64 -754.0070856 -753.969161 0.0005925720361 9.179443805 9.425464952 0.06695320222 - 9 64 -754.1450602 -754.141988 4.800358611e-05 8.574170786 8.821346913 0.06628506232 -# Displaced_BCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 10 54 -630.8081935 -631.019667 0.003916175555 15.97497534 16.625876 0.1021118679 - 11 54 -631.4580134 -631.719595 0.004844103559 15.24068949 15.58666626 0.1043856792 - 12 54 -631.1667566 -631.386255 0.004064785931 15.46091788 15.92378883 0.1062824093 - 13 54 -632.3004944 -632.575826 0.005098733346 14.4261974 14.55977162 0.0983914465 - 14 54 -630.089475 -630.450212 0.006680315456 16.78432947 16.96340726 0.1085102316 - 15 54 -631.3402507 -631.669379 0.006094968558 15.8289421 16.05757315 0.1000888617 - 16 54 -632.0447348 -632.431277 0.007158189539 14.73098416 14.69810718 0.09621569386 - 17 54 -630.7186536 -630.960068 0.004470636457 15.62236511 15.99073148 0.1063789621 - 18 54 -623.3884977 -623.378198 0.0001907343232 23.9739298 24.67640432 0.1519105596 -# Displaced_FCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 19 48 -556.0112403 -555.899463 0.002328692864 5.300795546 6.084617063 0.07215982294 - 20 48 -555.9884377 -555.922478 0.001374159425 5.509767245 6.297071211 0.08438730171 - 21 48 -555.8765558 -555.800269 0.001589309295 5.420812146 6.021098636 0.07404418561 - 22 48 -556.2511475 -556.196151 0.001145760427 4.541854917 5.127955094 0.06609455537 - 23 48 -555.6590668 -555.488929 0.003544536845 6.087063152 7.050223459 0.09107542897 - 24 48 -556.1020655 -556.027926 0.001544573067 5.048523277 5.611881174 0.06751584111 - 25 48 -556.0607474 -555.968399 0.001923924855 5.209756732 5.979217189 0.08024047849 - 26 48 -556.0598015 -556.047132 0.0002639485133 4.995519804 5.544452585 0.07745361595 - 27 48 -555.8256424 -555.747848 0.00162071731 5.762702675 6.47892568 0.08480576837 -# Elastic_BCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 28 2 -23.69025375 -23.689367 0.0004433751768 0.0006229111456 0.0006222748589 9.850534294e-07 - 29 2 -23.690768 -23.689888 0.0004399996606 0.0006181832344 0.0006166052222 1.005063831e-06 - 30 2 -23.69082186 -23.689996 0.0004129292199 0.0008798076914 0.0008810425642 1.748431771e-06 - 31 2 -23.69166748 -23.690957 0.0003552395228 1.000599546e-06 0 4.011214433e-07 - 32 2 -23.69137648 -23.690521 0.0004277406839 0.0005992884516 0.0005982273815 7.219402767e-07 - 33 2 -23.69120607 -23.69038 0.000413036746 0.000594795449 0.0005925723585 9.949794864e-07 - 34 2 -23.6900782 -23.689202 0.000438099978 0.0006263336007 0.0006279363025 1.111474332e-06 - 35 2 -23.69121642 -23.690482 0.0003672088475 0.00086350893 0.0008640138888 1.400551425e-06 - 36 2 -23.69074792 -23.689902 0.0004229601404 0.0006176589245 0.0006152154094 9.894995842e-07 - 37 2 -23.6914111 -23.690563 0.0004240514006 0.0006052368582 0.0006038725031 4.148713688e-07 - 38 2 -23.69095105 -23.690207 0.0003720253444 0.001071999394 0.00107369735 7.195087511e-07 - 39 2 -23.69007856 -23.689285 0.0003967806815 0.0008875291033 0.000890013483 1.187797446e-06 - 40 2 -23.69061639 -23.689768 0.0004241940528 0.00107874486 0.001080249045 1.09850755e-06 - 41 2 -23.69064479 -23.68968 0.0004823957182 0.0008702114429 0.0008680034562 8.482668094e-07 - 42 2 -23.6910243 -23.690074 0.0004751495365 0.001368926593 0.001373818765 2.351835771e-06 - 43 2 -23.68910107 -23.688108 0.0004965341502 0.0006334704764 0.0006336134468 5.990110163e-07 - 44 2 -23.69003986 -23.689241 0.0003994287496 0.0008886654529 0.0008880101351 1.319380731e-06 - 45 2 -23.69042994 -23.68952 0.0004549677771 0.0008868888968 0.0008860011287 4.688590432e-07 - 46 2 -23.68738487 -23.686278 0.0005534329248 0.0006426681164 0.0006406777661 9.718938063e-07 - 47 2 -23.69095089 -23.690097 0.0004269463837 0.0008409065407 0.0008410160522 1.331153983e-06 - 48 2 -23.69158161 -23.690811 0.0003853032969 0.0008464480591 0.0008500070588 1.611890257e-06 - 49 2 -23.69114597 -23.690266 0.0004399838162 0.001039354626 0.001044322747 3.354760892e-06 - 50 2 -23.6914223 -23.690597 0.0004126524984 0.001045529019 0.001050833003 2.164890519e-06 - 51 2 -23.69157045 -23.690673 0.000448723371 0.0006045419676 0.0006038907186 7.138092253e-07 - 52 2 -23.69135377 -23.690551 0.0004013838132 0.0008554941993 0.0008590064028 1.199818147e-06 - 53 2 -23.6914855 -23.690693 0.0003962481391 0.0008561040807 0.0008590110593 1.062310127e-06 - 54 2 -23.69110782 -23.69021 0.0004489100066 0.0008699576152 0.0008730051546 1.100920756e-06 - 55 2 -23.68987142 -23.688943 0.0004642105928 0.0008789741194 0.0008800306813 8.92018913e-07 - 56 2 -23.69108099 -23.690136 0.0004724937378 0.0005971006713 0.000593996633 9.809423198e-07 - 57 2 -23.6884849 -23.687444 0.0005204491042 0.000904649919 0.000903059245 1.159812589e-06 - 58 2 -23.69061659 -23.689801 0.0004077963743 0.0008734822906 0.0008740011442 2.825876968e-07 - 59 2 -23.69129673 -23.690408 0.0004443659273 8.294238722e-07 0 3.094976672e-07 - 60 2 -23.69128183 -23.690362 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2 -23.69101815 -23.690015 0.0005015766298 0.0008420116739 0.0008450195264 1.339928081e-06 - 104 2 -23.6915919 -23.690752 0.0004199497676 0.0005974770628 0.0005996415596 9.70808844e-07 - 105 2 -23.69060481 -23.689825 0.0003899065755 0.0008774617579 0.0008800215906 1.681761199e-06 - 106 2 -23.69149834 -23.690562 0.0004681676 0.0008527074936 0.0008560011682 1.11226924e-06 - 107 2 -23.69145561 -23.690622 0.0004168050595 0.0008363624298 0.0008390017878 8.930611273e-07 - 108 2 -23.68965306 -23.688764 0.0004445297309 0.0008936263738 0.0008910185183 1.309339573e-06 - 109 2 -23.69077552 -23.690011 0.0003822592712 0.0006203793746 0.0006194287691 3.133550229e-07 - 110 2 -23.68867102 -23.687696 0.0004875100015 0.001086068328 0.001087589996 1.327020171e-06 - 111 2 -23.69172933 -23.691019 0.0003551646935 0.000852013148 0.0008540035129 9.847230007e-07 - 112 2 -23.68991099 -23.689025 0.000442996005 6.46227386e-07 0 2.557212911e-07 - 113 2 -23.69080506 -23.689952 0.0004265318142 7.012777671e-07 0 2.758977769e-07 - 114 2 -23.69152793 -23.69061 0.0004589654148 0.0008542966264 0.0008580011655 1.338482046e-06 - 115 2 -23.69153556 -23.690595 0.0004702783823 0.000867974804 0.0008680069124 6.687384672e-07 - 116 2 -23.69117399 -23.690231 0.000471493636 0.0005924023762 0.0005925892338 1.259776007e-07 - 117 2 -23.69139497 -23.690469 0.0004629856458 0.0008486906688 0.0008500294113 6.344879116e-07 - 118 2 -23.69122801 -23.690482 0.0003730070077 0.0008734801582 0.0008740102974 2.172190141e-07 - 119 2 -23.69055118 -23.689613 0.0004690919274 0.0008237358825 0.0008320192305 2.927942421e-06 - 120 2 -23.68847553 -23.687426 0.0005247657372 0.001093739709 0.00109577735 8.307823424e-07 - 121 2 -23.69041353 -23.689562 0.000425762889 0.0006210724415 0.0006265237426 1.574752432e-06 - 122 2 -23.69137916 -23.6904 0.0004895814578 3.712921801e-07 0 1.509058252e-07 - 123 2 -23.69152029 -23.690561 0.0004796427403 0.0005964911748 0.0005982273815 1.201511775e-06 - 124 2 -23.69012377 -23.689107 0.0005083837539 0.0008124995989 0.0008180073349 1.97846325e-06 - 125 2 -23.69112303 -23.690145 0.000489014125 0.0008742245309 0.0008740766557 1.981010569e-06 - 126 2 -23.6913827 -23.690482 0.00045035056 0.0005944563316 0.0005939983165 2.227151791e-07 - 127 2 -23.69071568 -23.689864 0.0004258388591 0.0008855411376 0.0008860124153 7.974985004e-07 -# Elastic_FCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 128 4 -46.43709855 -46.437936 0.0002093617328 0.0008950059332 0.001265949446 0.0001464529791 - 129 4 -46.4407039 -46.438504 0.0005499744469 0.0009975948265 0.001492549497 0.0001384062515 - 130 4 -46.43497365 -46.436378 0.0003510867184 0.0005521282525 0.000810592376 9.989141969e-05 - 131 4 -46.44077415 -46.441551 0.0001942123898 0.001132197907 0.001283675193 6.296966657e-05 - 132 4 -46.41517164 -46.416957 0.0004463408133 0.000917990147 0.001186145859 8.226324971e-05 - 133 4 -46.43849879 -46.440495 0.0004990529713 0.001000780113 0.001212440514 6.935590465e-05 - 134 4 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0.0006588778339 5.645487424e-05 - 198 4 -46.44980864 -46.449806 6.606823266e-07 0.001232826529 0.002135055034 0.0002384857832 - 199 4 -46.42466674 -46.427189 0.0006305654832 0.001011828255 0.001050788276 2.797047454e-05 - 200 4 -46.42588993 -46.427857 0.000491766418 0.001010915484 0.001487666629 0.0001398462887 - 201 4 -46.44273693 -46.44004 0.0006742317456 0.0007050795233 0.000757202747 2.506458135e-05 - 202 4 -46.43659247 -46.437214 0.0001553829854 0.0008924045914 0.001505586265 0.0001475571029 - 203 4 -46.42189527 -46.422628 0.0001831835233 0.0009120248848 0.001601713458 0.0002207350143 - 204 4 -46.44387014 -46.443535 8.378431277e-05 0.001253187495 0.001590304373 0.0001006147174 - 205 4 -46.4386991 -46.439922 0.0003057254875 0.001138308324 0.001530493385 0.0001018467819 - 206 4 -46.43732669 -46.437675 8.707637653e-05 0.00144833639 0.002440246094 0.0003149341193 - 207 4 -46.44459348 -46.445558 0.0002411303465 0.0008716893522 0.00113392416 7.56134454e-05 - 208 4 -46.43888136 -46.439106 5.615896373e-05 0.001259801268 0.001830731002 0.0001709222499 - 209 4 -46.44452218 -46.443073 0.000362294488 0.0005355233492 0.0005766870902 1.79131844e-05 - 210 4 -46.44072829 -46.4397 0.0002570727366 0.0008912594074 0.001204174406 7.190949652e-05 - 211 4 -46.43632905 -46.436374 1.123701302e-05 0.00100454144 0.001461656594 0.0001640759619 - 212 4 -46.42622449 -46.426557 8.312836801e-05 0.0009090508417 0.001359624213 9.618645017e-05 - 213 4 -46.43334095 -46.434009 0.0001670117853 0.001064727099 0.001391131194 0.0001118380718 - 214 4 -46.43528491 -46.436262 0.0002442735765 0.001381671175 0.002503347159 0.0002862586192 - 215 4 -46.43302209 -46.434505 0.0003707286996 0.001050895795 0.001041637173 1.894959196e-05 - 216 4 -46.43866543 -46.438768 2.564354619e-05 0.001038218613 0.001098285027 4.514351427e-05 - 217 4 -46.43867092 -46.440254 0.000395771139 0.0005510961745 0.0006069892915 4.783705107e-05 - 218 4 -46.42481603 -46.42286 0.0004890086715 0.0005673661918 0.0007365242698 6.506184883e-05 - 219 4 -46.41707211 -46.418078 0.0002514715464 0.001292943265 0.002028412187 0.0002017017408 - 220 4 -46.44058128 -46.440513 1.706961588e-05 0.0008917162415 0.001158189967 9.459271337e-05 - 221 4 -46.40786735 -46.409824 0.000489161666 0.000915995593 0.001759573812 0.0002027400318 - 222 4 -46.44176165 -46.440329 0.0003581615225 0.0007050784001 0.0009534044263 7.330945846e-05 - 223 4 -46.43764613 -46.43773 2.096761683e-05 0.000774718051 0.000926180328 6.358620287e-05 - 224 4 -46.41646676 -46.416525 1.456068592e-05 0.0007183862165 0.0007573664899 3.367541267e-05 - 225 4 -46.44086814 -46.440293 0.0001437843048 0.0008909024924 0.0007725386722 2.803785114e-05 - 226 4 -46.44027213 -46.43839 0.0004705337314 0.000707862011 0.0005612022808 3.305821092e-05 - 227 4 -46.44117428 -46.438916 0.0005645706045 0.0008843758872 0.001650878554 0.0001728226219 -# GSF_110.xyz - config # atoms energy DFT energy energy error force DFT force force error - 228 24 -278.9717069 -279.068761 0.004043919984 1.716820818 1.756353161 0.02195804808 - 229 24 -279.8354387 -279.784296 0.002130947227 0.8360148085 0.9057668891 0.02306494198 - 230 24 -279.920921 -279.901657 0.0008026661363 0.2958425997 0.001565946359 0.01411644584 - 231 24 -279.6113309 -279.584238 0.001128870276 1.136927478 1.035572248 0.0268109436 - 232 24 -279.8354404 -279.784283 0.002131557004 0.8360112083 0.9056396189 0.02305363685 - 233 24 -279.302435 -279.302158 1.154096848e-05 1.736732738 1.771965137 0.03376130194 - 234 24 -279.5958843 -279.55564 0.001676844981 1.457718936 1.405626506 0.02601748107 - 235 24 -279.1575825 -279.246939 0.003723187357 0.7701803397 0.4813964151 0.04047323625 - 236 24 -279.3024375 -279.302157 1.168852836e-05 1.736736025 1.771953347 0.03376039536 - 237 24 -279.1575946 -279.246935 0.003722518226 0.7692677843 0.4809484798 0.04044520421 - 238 24 -279.9208868 -279.896025 0.001035907873 0.2963184571 0.01060549839 0.01410249844 - 239 24 -279.6115695 -279.584237 0.001138852664 1.13770573 1.035836121 0.02686761528 - 240 24 -279.064529 -279.124427 0.002495750967 1.76375665 1.809545887 0.03536482035 - 241 24 -279.3562359 -279.379366 0.000963755899 1.070359933 0.8982692706 0.03586365384 - 242 24 -279.3561337 -279.37937 0.0009681791432 1.070187041 0.898081355 0.03582334182 - 243 24 -279.0645273 -279.124427 0.002495818902 1.763753116 1.809523374 0.03536507377 - 244 24 -279.920921 -279.901657 0.0008026661364 0.295842601 0.001570374478 0.01411415473 - 245 24 -279.835369 -279.79264 0.001780376182 0.7694168746 0.8392614852 0.02365583077 - 246 24 -279.9208868 -279.896025 0.001035907873 0.2963184557 0.01060243293 0.01410273421 - 247 24 -279.0819585 -279.206496 0.005189061107 0.548788431 0.005326518563 0.03225764062 - 248 24 -279.5958869 -279.55564 0.001676956181 1.457719116 1.4056319 0.02601845486 - 249 24 -279.8353874 -279.79264 0.001781141415 0.7694021079 0.8392625708 0.0236575616 -# GSF_112.xyz - config # atoms energy DFT energy energy error force DFT force force error - 250 30 -345.1958147 -345.175835 0.0006659888828 1.417827685 1.057395322 0.04924259711 - 251 30 -346.4091654 -346.361714 0.001581712645 1.014644886 1.220284939 0.04659093523 - 252 30 -345.9623042 -345.795524 0.005559340233 1.678459906 2.112860875 0.06265040874 - 253 30 -345.1047773 -345.164602 0.001994157897 1.817583015 1.765832199 0.05258058387 - 254 30 -346.5687925 -346.593523 0.0008243492414 0.5266160053 0.01148867129 0.03755504848 - 255 30 -346.4165137 -346.396186 0.0006775885975 1.101956458 0.9954683928 0.04399110332 - 256 30 -345.2521553 -345.319406 0.00224168982 2.024011434 1.772040852 0.05936118376 - 257 30 -345.5898528 -345.594794 0.0001647082757 2.048144835 1.516014157 0.06040121307 - 258 30 -346.0297765 -345.98566 0.001470549283 1.767327791 1.406252265 0.05243702855 - 259 30 -345.5053828 -345.383994 0.004046292585 1.336428571 0.963574308 0.05104895348 - 260 30 -346.5686342 -346.582564 0.0004643258311 0.5264214865 0.0126740587 0.03760971825 - 261 30 -345.4208872 -345.452139 0.001041727499 3.011665478 2.787719406 0.06345649484 - 262 30 -346.5687922 -346.593523 0.000824358736 0.5266293188 0.01148834 0.03755660424 - 263 30 -345.4303122 -345.281949 0.004945440141 1.947208063 1.873142686 0.05337069289 - 264 30 -345.95932 -345.928661 0.001021967701 2.362723976 2.100874472 0.05002108374 - 265 30 -345.0137677 -345.111657 0.003262976998 3.19378163 3.358068319 0.06536423133 - 266 30 -346.4078756 -346.367123 0.001358420679 1.085591236 1.335797131 0.04639235845 - 267 30 -346.5685864 -346.582565 0.0004659529893 0.5264879505 0.01254743735 0.03760890253 - 268 30 -344.8663405 -344.91356 0.001573984549 2.930408919 3.441834403 0.06926998065 - 269 30 -345.9709087 -345.836703 0.004473521714 1.391835251 1.608769148 0.0557054003 - 270 30 -345.0229891 -344.984307 0.001289401895 2.372016819 2.542628782 0.05571749983 - 271 30 -346.4089445 -346.393931 0.0005004501598 1.297845976 1.211680725 0.04319349672 -# Liquid.xyz - config # atoms energy DFT energy energy error force DFT force force error - 272 100 -1105.559726 -1105.601723 0.0004199683753 30.70196346 31.39853886 0.2273901869 - 273 100 -1099.629534 -1099.673012 0.0004347802829 31.98646736 32.03167218 0.2226202775 - 274 100 -1121.43168 -1121.31506 0.001166195007 21.23863202 20.81076453 0.2037539309 -# Surface.xyz - config # atoms energy DFT energy energy error force DFT force force error - 275 24 -279.9208871 -279.911828 0.0003774634676 0.2963192975 0.002753093533 0.01433131958 - 276 48 -554.241479 -555.359452 0.02329110353 1.363109446 0.003020630398 0.0573825018 - 277 40 -459.5808398 -459.216162 0.009116945293 3.33149843 5.0461364 0.07877996461 - 278 40 -460.5932467 -461.144076 0.01377073163 0.8854479197 0.005582740008 0.03813349763 - 279 24 -279.8214986 -279.635146 0.007764693427 0.982012045 1.288799837 0.01857540863 - 280 30 -346.5687933 -346.592525 0.000791056775 0.5266154723 0.008446203407 0.03726637101 - 281 30 -346.0051971 -345.744506 0.008689702509 2.266739618 3.124961367 0.06591070739 -# Volume_A15.xyz - config # atoms energy DFT energy energy error force DFT force force error - 282 8 -67.00264003 -66.990732 0.001488503243 8.978495355e-15 0 1.554167674e-15 - 283 8 -72.95775645 -72.957807 6.318335608e-06 6.173563626e-14 0 9.086337007e-15 - 284 8 -94.15079079 -94.145745 0.0006307242955 1.257001279e-14 0 1.651353601e-15 - 285 8 -94.55576971 -94.554682 0.0001359640227 7.864226848e-15 0 1.351609702e-15 - 286 8 -79.41650989 -79.438363 0.002731638712 2.922311383e-14 0 4.6112564e-15 - 287 8 -69.6319055 -69.627817 0.0005110626381 3.131450246e-15 0 5.512083845e-16 - 288 8 -82.6140242 -82.604907 0.001139650038 1.015341342e-14 0 1.573105072e-15 - 289 8 14.8871533 14.89048 0.0004158371788 2.179622647e-13 0 3.718594804e-14 - 290 8 -94.35602701 -94.367599 0.001446498413 1.681327296e-14 0 2.430951383e-15 - 291 8 -89.2494361 -89.248227 0.0001511372198 1.602695388e-14 0 2.27566808e-15 - 292 8 -87.22359357 -87.211997 0.001449571359 5.891018761e-15 0 1.023486851e-15 - 293 8 -93.64917633 -93.66897 0.002474209194 1.737070481e-15 0 2.726891929e-16 - 294 8 -7.974970896 -7.989166 0.001774387948 5.346466786e-13 0 7.317740119e-14 - 295 8 -84.99735697 -84.982834 0.001815371577 1.628985705e-15 0 2.68014777e-16 - 296 8 -92.51696442 -92.536373 0.002426072159 3.702813287e-14 0 5.965135793e-15 - 297 8 -26.79883523 -26.77612 0.002839403163 2.314654929e-13 0 3.768467838e-14 - 298 8 -77.53738473 -77.544107 0.0008402842141 2.975839122e-15 0 5.1405639e-16 - 299 8 -80.11476757 -80.114217 6.882064461e-05 9.414427891e-15 0 1.325473296e-15 - 300 8 -42.12903262 -42.143041 0.001751047533 2.610061598e-13 0 3.565304919e-14 - 301 8 -91.02990946 -91.040671 0.001345192241 8.368513177e-15 0 1.310872707e-15 - 302 8 -84.50933121 -84.499231 0.001262526145 5.714110441e-14 0 1.066782658e-14 - 303 8 -61.79844789 -61.825173 0.003340638518 6.62953849e-15 0 1.015391475e-15 - 304 8 -91.13057644 -91.156873 0.003287069749 4.719369293e-15 0 6.76336609e-16 - 305 8 -54.64916677 -54.658744 0.001197153514 1.464956394e-13 0 2.113576767e-14 - 306 8 -72.27319255 -72.277255 0.0005078062019 8.658199332e-16 0 1.410908427e-16 - 307 8 -74.9147183 -74.923334 0.001076962465 4.434219242e-15 0 6.615078855e-16 - 308 8 -64.81833247 -64.798066 0.002533308735 3.748412002e-14 0 5.576268614e-15 - 309 8 -93.03489726 -93.048342 0.001680592822 1.857310674e-14 0 2.604235054e-15 - 310 8 -64.39098013 -64.38702 0.0004950167019 5.001001166e-15 0 5.722057666e-16 - 311 8 -88.36401125 -88.352871 0.001392531574 1.47982807e-14 0 2.645507511e-15 -# Volume_BCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 312 2 -16.76594323 -16.763625 0.0011591154 3.058627912e-16 0 7.979727989e-17 - 313 2 16.31372699 16.314145 0.0002090027274 8.186542193e-13 0 2.624717573e-13 - 314 2 -21.21034402 -21.209071 0.000636508568 6.029606478e-15 0 1.688464572e-15 - 315 2 -15.7845968 -15.780524 0.002036397536 5.051396178e-14 0 1.863971217e-14 - 316 2 -18.99841038 -19.002205 0.001897311189 3.70201696e-14 0 1.247006253e-14 - 317 2 -22.6245193 -22.620568 0.001975650815 3.866866338e-15 0 1.424786215e-15 - 318 2 4.098164527 4.096885 0.0006397634862 6.334293648e-14 0 2.151519703e-14 - 319 2 56.26275599 56.26276 2.005221472e-06 2.247995559e-12 0 7.580021273e-13 - 320 2 -22.58944012 -22.585113 0.002163562406 1.113168148e-15 0 3.747002708e-16 - 321 2 -21.79724015 -21.795501 0.0008695760695 1.09344287e-15 0 3.700743415e-16 - 322 2 33.11015633 33.110078 3.916354612e-05 4.904232742e-13 0 1.492139745e-13 - 323 2 -20.88315873 -20.885998 0.001419634185 1.859416424e-15 0 7.401486831e-16 - 324 2 -23.59568898 -23.601336 0.002823509954 1.486164289e-15 0 4.916167932e-16 - 325 2 -23.20858071 -23.207313 0.0006338528204 8.900302643e-16 0 3.147520853e-16 - 326 2 -19.89310507 -19.898089 0.002491965758 8.784897284e-16 0 3.064678141e-16 - 327 2 -23.40543384 -23.405474 2.007854096e-05 9.04864091e-16 0 2.55004351e-16 - 328 2 -4.783890314 -4.781324 0.00128315718 1.026901322e-13 0 2.670433319e-14 - 329 2 -18.86311291 -18.864936 0.0009115426716 2.305551267e-16 0 7.864079758e-17 - 330 2 -17.81642588 -17.813086 0.001669937839 1.716587549e-16 0 6.245004514e-17 - 331 2 -11.19369732 -11.197201 0.001751842379 6.247077482e-14 0 2.245483891e-14 - 332 2 -23.6830862 -23.696705 0.006809399945 1.843658888e-15 0 7.087971703e-16 -# Volume_FCC.xyz - config # atoms energy DFT energy energy error force DFT force force error - 333 4 -19.07363592 -19.075994 0.0005895202867 4.838977351e-14 0 1.162785146e-14 - 334 4 -34.87911157 -34.873619 0.001373142448 2.834773835e-16 0 5.955883934e-17 - 335 4 -43.95312208 -43.950003 0.0007797711561 2.246784353e-15 0 4.928060275e-16 - 336 4 -40.99484531 -40.991909 0.0007340763059 8.408019466e-15 0 2.017013582e-15 - 337 4 -43.44688587 -43.453929 0.001760782795 1.105978561e-14 0 2.960654589e-15 - 338 4 -42.69057259 -42.686077 0.001123896575 2.15077979e-15 0 5.053466326e-16 - 339 4 -33.22567657 -33.224653 0.0002558935333 6.71927174e-16 0 1.601728009e-16 - 340 4 -26.86518979 -26.862709 0.0006201969912 3.31529179e-14 0 7.652202346e-15 - 341 4 -25.52095377 -25.519883 0.0002676922193 3.655453829e-16 0 7.199102425e-17 - 342 4 3.462101367 3.463071 0.0002424081278 1.816025861e-13 0 4.023864575e-14 - 343 4 -31.5932268 -31.59595 0.0006807997919 3.628185658e-16 0 8.557969148e-17 - 344 4 -45.10086835 -45.100466 0.0001005873411 2.465692424e-15 0 5.323999453e-16 - 345 4 -46.05341345 -46.052258 0.0002888629271 8.511696107e-16 0 1.9963776e-16 - 346 4 -29.99832749 -30.001189 0.0007153784531 3.847020655e-16 0 1.014813233e-16 - 347 4 -22.85257327 -22.8504 0.0005433170403 7.603433695e-16 0 2.026735261e-16 - 348 4 -9.165925377 -9.164691 0.0003085942037 6.355991568e-14 0 1.496321874e-14 - 349 4 -24.14844545 -24.150343 0.0004743875843 4.762376771e-16 0 9.887923813e-17 - 350 4 -46.43546878 -46.426795 0.002168445654 2.389854689e-15 0 6.508104241e-16 - 351 4 -28.45126723 -28.451145 3.055783253e-05 7.811231556e-15 0 2.246466901e-15 - 352 4 40.34134283 40.341566 5.579164045e-05 4.392900751e-13 0 1.047052708e-13 - 353 4 19.618876 19.617912 0.0002409995917 2.653013854e-13 0 4.82657932e-14 - 354 4 -26.95747287 -26.954384 0.0007722170381 5.063966549e-16 0 1.225871256e-16 - 355 4 -46.33491981 -46.323696 0.002805953551 3.211950954e-15 0 8.731441496e-16 - 356 4 -45.83316791 -45.828947 0.001055227438 1.228572267e-14 0 3.512236798e-15 - 357 4 -38.16058675 -38.16029 7.418651586e-05 1.457184241e-15 0 3.625572065e-16 - 358 4 -32.91257363 -32.919741 0.001791843199 5.73065335e-14 0 1.529158744e-14 - 359 4 -41.2675262 -41.272675 0.001287199354 7.138843467e-15 0 2.027950471e-15 - 360 4 -39.74460494 -39.753322 0.002179265661 7.861049173e-16 0 1.651275908e-16 - 361 4 -37.55548161 -37.547435 0.002011652753 1.155947671e-14 0 2.497062164e-15 - 362 4 -36.53186908 -36.52595 0.001479769423 3.660718685e-16 0 9.51206706e-17 - 363 4 -45.01550153 -45.016087 0.0001463673621 1.766214736e-15 0 4.760370339e-16 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod deleted file mode 100644 index b375be15d6..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod +++ /dev/null @@ -1,20 +0,0 @@ -**************** Begin of Error Analysis for the Training Data Set **************** ---------------------------------------------------------------------------------------------------- - File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force ---------------------------------------------------------------------------------------------------- -Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 -Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 -Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 -Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 -Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 -GSF_110.xyz 22 528 0.001852 0.002260 0.027303 0.044765 -GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 -Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 -Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 -Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 ---------------------------------------------------------------------------------------------------- -All files 363 4224 0.001053 0.002171 0.059051 0.106960 ---------------------------------------------------------------------------------------------------- -**************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod b/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod deleted file mode 100644 index 7b932558ea..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod +++ /dev/null @@ -1,5 +0,0 @@ -# Demonstrate fitpod for POD potential - -units metal -fitpod Ta_param.pod Ta_data.pod - diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.fitpod.g++.1 b/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.fitpod.g++.1 deleted file mode 100644 index 751bb0ffd8..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.fitpod.g++.1 +++ /dev/null @@ -1,114 +0,0 @@ -LAMMPS (22 Dec 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate fitpod for POD potential - -units metal -fitpod Ta_param.pod Ta_data.pod -Reading potential file Ta_param.pod with DATE: 2022-11-30 -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 1 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 150 -total number of descriptors for all potentials: 182 -**************** End of POD Potentials **************** - -**************** Begin of Data File **************** -file format: extxyz -file extension: xyz -path to training data set: ../Ta/XYZ -path to test data set: ../Ta/XYZ -training fraction: 1 -test fraction: 1 -randomize training data set: 1 -randomize test data set: 1 -error analysis for training data set: 1 -error analysis for test data set: 0 -energy/force calculation for training data set: 0 -energy/force calculation for test data set: 0 -fitting weight for energy: 100 -fitting weight for force: 1 -fitting weight for stress: 0 -fitting regularization parameter: 1e-10 -**************** End of Data File **************** -**************** Begin of Training Data Set **************** ---------------------------------------------------------------- - data file | number of configurations | number of atoms ---------------------------------------------------------------- - Displaced_A15.xyz | 9 | 576 - Displaced_BCC.xyz | 9 | 486 - Displaced_FCC.xyz | 9 | 432 - Elastic_BCC.xyz | 100 | 200 - Elastic_FCC.xyz | 100 | 400 - GSF_110.xyz | 22 | 528 - GSF_112.xyz | 22 | 660 - Liquid.xyz | 3 | 300 - Surface.xyz | 7 | 236 - Volume_A15.xyz | 30 | 240 - Volume_BCC.xyz | 21 | 42 - Volume_FCC.xyz | 31 | 124 ---------------------------------------------------------------- -number of files: 12 -number of configurations in all files: 363 -number of atoms in all files: 4224 -minimum number of atoms: 2 -maximum number of atoms: 100 -**************** End of Training Data Set **************** -**************** Begin of Memory Allocation **************** -maximum number of atoms in periodic domain: 100 -maximum number of atoms in extended domain: 2700 -maximum number of neighbors in extended domain: 270000 -size of double memory: 223201 -size of int memory: 14709 -size of descriptor matrix: 182 x 182 -**************** End of Memory Allocation **************** -**************** Begin of Least-Squares Fitting **************** -Configuration: # 1 -Configuration: # 101 -Configuration: # 201 -Configuration: # 301 -**************** End of Least-Squares Fitting **************** -**************** Begin of Error Calculation **************** -Configuration: # 1 -Configuration: # 101 -Configuration: # 201 -Configuration: # 301 -**************** End of Error Calculation **************** -**************** Begin of Error Analysis for the Training Data Set **************** ---------------------------------------------------------------------------------------------------- - File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force ---------------------------------------------------------------------------------------------------- -Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 -Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 -Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 -Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 -Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 -GSF_110.xyz 22 528 0.001852 0.002260 0.027303 0.044765 -GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 -Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 -Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 -Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 ---------------------------------------------------------------------------------------------------- -All files 363 4224 0.001053 0.002171 0.059051 0.106960 ---------------------------------------------------------------------------------------------------- -**************** End of Error Analysis for the Training Data Set **************** - -Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.pod.g++.1 b/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.pod.g++.1 deleted file mode 100644 index 08b43e2262..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.pod.g++.1 +++ /dev/null @@ -1,142 +0,0 @@ -LAMMPS (22 Dec 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate POD Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 128 atoms - using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) - create_atoms CPU = 0.000 seconds - -mass 1 180.88 - - -# POD potential -pair_style pod -pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta -Reading potential file Ta_param.pod with DATE: 2022-11-30 -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 1 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 150 -total number of descriptors for all potentials: 182 -**************** End of POD Potentials **************** - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 loop geom -fix 1 all nve -run ${nsteps} -run 100 -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair pod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 300 -11.847697 0 -11.809222 13502.169 - 10 296.47494 -11.847245 0 -11.809222 13529.584 - 20 286.0918 -11.845913 0 -11.809222 13613.884 - 30 269.42275 -11.843776 0 -11.809222 13759.746 - 40 247.39423 -11.84095 0 -11.809222 13972.073 - 50 221.23976 -11.837596 0 -11.809222 14253.202 - 60 192.43252 -11.833901 0 -11.809222 14600.367 - 70 162.59874 -11.830075 0 -11.809221 15004.156 - 80 133.41531 -11.826332 0 -11.809221 15448.418 - 90 106.49785 -11.82288 0 -11.809221 15911.638 - 100 83.288219 -11.819903 0 -11.809221 16369.373 -Loop time of 1.51781 on 1 procs for 100 steps with 128 atoms - -Performance: 2.846 ns/day, 8.432 hours/ns, 65.884 timesteps/s, 8.433 katom-step/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5172 | 1.5172 | 1.5172 | 0.0 | 99.96 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0002542 | 0.0002542 | 0.0002542 | 0.0 | 0.02 -Output | 0.00013308 | 0.00013308 | 0.00013308 | 0.0 | 0.01 -Modify | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.01 -Other | | 0.0001446 | | | 0.01 - -Nlocal: 128 ave 128 max 128 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 727 ave 727 max 727 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 7424 ave 7424 max 7424 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - - -Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.pod.g++.4 b/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.pod.g++.4 deleted file mode 100644 index d94755ed0e..0000000000 --- a/examples/PACKAGES/pod/Ta_Quadratic/log.4Jan23.pod.g++.4 +++ /dev/null @@ -1,142 +0,0 @@ -LAMMPS (22 Dec 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate POD Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 128 atoms - using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) - create_atoms CPU = 0.000 seconds - -mass 1 180.88 - - -# POD potential -pair_style pod -pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta -Reading potential file Ta_param.pod with DATE: 2022-11-30 -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 1 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 150 -total number of descriptors for all potentials: 182 -**************** End of POD Potentials **************** - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 loop geom -fix 1 all nve -run ${nsteps} -run 100 -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair pod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 300 -11.847697 0 -11.809222 13502.169 - 10 296.47494 -11.847245 0 -11.809222 13529.584 - 20 286.0918 -11.845913 0 -11.809222 13613.884 - 30 269.42275 -11.843776 0 -11.809222 13759.746 - 40 247.39423 -11.84095 0 -11.809222 13972.073 - 50 221.23976 -11.837596 0 -11.809222 14253.202 - 60 192.43252 -11.833901 0 -11.809222 14600.367 - 70 162.59874 -11.830075 0 -11.809221 15004.156 - 80 133.41531 -11.826332 0 -11.809221 15448.418 - 90 106.49785 -11.82288 0 -11.809221 15911.638 - 100 83.288219 -11.819903 0 -11.809221 16369.373 -Loop time of 0.427448 on 4 procs for 100 steps with 128 atoms - -Performance: 10.106 ns/day, 2.375 hours/ns, 233.947 timesteps/s, 29.945 katom-step/s -97.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40622 | 0.40946 | 0.419 | 0.9 | 95.79 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0071192 | 0.016995 | 0.020439 | 4.4 | 3.98 -Output | 0.00012904 | 0.0002071 | 0.00043132 | 0.0 | 0.05 -Modify | 3.905e-05 | 4.8089e-05 | 5.5714e-05 | 0.0 | 0.01 -Other | | 0.0007341 | | | 0.17 - -Nlocal: 32 ave 32 max 32 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 431 ave 431 max 431 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1856 ave 1856 max 1856 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt index 635b2c9750..fb0324cabe 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt @@ -38,6 +38,7 @@ molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 # dump 1 all xyz 100 test_vis.xyz +# dump_modify 1 types labels fix myrxns all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & diff --git a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized index 7e0350cdb0..4c23143474 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized +++ b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized @@ -35,6 +35,7 @@ molecule mol6 rxn2_stp2_post.molecule_template thermo 50 # dump 1 all xyz 1 test_vis.xyz +# dump_modify 1 types labels fix rxns all bond/react stabilization yes statted_grp .03 & react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map & diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized index 853bc45f1e..60d33aa351 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized @@ -39,6 +39,7 @@ molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 # dump 1 all xyz 1 test_vis.xyz +# dump_modify 1 types labels fix myrxns all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability index f3c32f3cbd..770f4fc3b1 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability @@ -43,6 +43,7 @@ molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 # dump 1 all xyz 1 test_vis.xyz +# dump_modify 1 types labels fix myrxns all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 & diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized index e5cbaaaf86..4ade3f8b99 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized @@ -40,6 +40,7 @@ molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 # dump 1 all xyz 1 test_vis.xyz +# dump_modify 1 types labels fix myrxns all bond/react stabilization no & react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized index 230998fcd3..34346d9ef7 100644 --- a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized +++ b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized @@ -41,6 +41,7 @@ molecule mol6 chain_chain_reacted.molecule_template thermo 100 # dump 1 all xyz 5 test_vis.xyz +# dump_modify 1 types labels fix rxn1 all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 & diff --git a/examples/PACKAGES/uf3/Nb.uf3 b/examples/PACKAGES/uf3/Nb.uf3 new file mode 120000 index 0000000000..cb0fdd480d --- /dev/null +++ b/examples/PACKAGES/uf3/Nb.uf3 @@ -0,0 +1 @@ +../../../potentials/Nb.uf3 \ No newline at end of file diff --git a/examples/PACKAGES/uf3/in.uf3.Nb b/examples/PACKAGES/uf3/in.uf3.Nb new file mode 100644 index 0000000000..19b37ccc0b --- /dev/null +++ b/examples/PACKAGES/uf3/in.uf3.Nb @@ -0,0 +1,46 @@ +# Demonstrate UF3 W potential + +# # ============= Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.3005 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 92.906 + +# # ============= set pair style + +pair_style uf3 3 +pair_coeff * * Nb.uf3 Nb + + +# # ============= Setup output + +thermo 10 +thermo_modify norm yes + +# # ============= Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# # ============= Run MD + +velocity all create 300.0 2367804 loop geom +fix 1 all nve +run ${nsteps} diff --git a/examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1 b/examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1 new file mode 100644 index 0000000000..0c9c0bffa2 --- /dev/null +++ b/examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1 @@ -0,0 +1,118 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate UF3 W potential + +# # ============= Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.3005 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.3005 +Lattice spacing in x,y,z = 3.3005 3.3005 3.3005 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.202 13.202 13.202) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202) + create_atoms CPU = 0.000 seconds + +mass 1 92.906 + +# # ============= set pair style + +pair_style uf3 3 +pair_coeff * * Nb.uf3 Nb +Reading potential file Nb.uf3 with DATE: 2024-04-02 + + +# # ============= Setup output + +thermo 10 +thermo_modify norm yes + +# # ============= Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# # ============= Run MD + +velocity all create 300.0 2367804 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9 + ghost atom cutoff = 9 + binsize = 4.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair uf3, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.376 | 3.376 | 3.376 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4.4256832 0 -4.3872081 90756.437 + 10 294.36659 -4.4249607 0 -4.3872081 91006.427 + 20 277.9021 -4.422849 0 -4.387208 91716.126 + 30 251.88303 -4.4195119 0 -4.3872078 92789.12 + 40 218.42803 -4.4152211 0 -4.3872076 94118.45 + 50 180.40641 -4.4103445 0 -4.3872073 95579.009 + 60 141.2326 -4.4053202 0 -4.3872071 97031.816 + 70 104.54429 -4.4006146 0 -4.3872068 98332.882 + 80 73.787889 -4.3966699 0 -4.3872066 99351.332 + 90 51.759956 -4.3938446 0 -4.3872064 99992.934 + 100 40.209821 -4.3923633 0 -4.3872064 100211.98 +Loop time of 0.385575 on 1 procs for 100 steps with 128 atoms + +Performance: 11.204 ns/day, 2.142 hours/ns, 259.353 timesteps/s, 33.197 katom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.38403 | 0.38403 | 0.38403 | 0.0 | 99.60 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00090609 | 0.00090609 | 0.00090609 | 0.0 | 0.23 +Output | 0.00017626 | 0.00017626 | 0.00017626 | 0.0 | 0.05 +Modify | 0.00018204 | 0.00018204 | 0.00018204 | 0.0 | 0.05 +Other | | 0.0002795 | | | 0.07 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1601 ave 1601 max 1601 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 21504 ave 21504 max 21504 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 21504 +Ave neighs/atom = 168 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4 b/examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4 new file mode 100644 index 0000000000..cd46d8da14 --- /dev/null +++ b/examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4 @@ -0,0 +1,118 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate UF3 W potential + +# # ============= Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.3005 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.3005 +Lattice spacing in x,y,z = 3.3005 3.3005 3.3005 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.202 13.202 13.202) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202) + create_atoms CPU = 0.001 seconds + +mass 1 92.906 + +# # ============= set pair style + +pair_style uf3 3 +pair_coeff * * Nb.uf3 Nb +Reading potential file Nb.uf3 with DATE: 2024-04-02 + + +# # ============= Setup output + +thermo 10 +thermo_modify norm yes + +# # ============= Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# # ============= Run MD + +velocity all create 300.0 2367804 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9 + ghost atom cutoff = 9 + binsize = 4.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair uf3, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.351 | 3.351 | 3.351 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4.4256832 0 -4.3872081 90756.437 + 10 294.36659 -4.4249607 0 -4.3872081 91006.427 + 20 277.9021 -4.422849 0 -4.387208 91716.126 + 30 251.88303 -4.4195119 0 -4.3872078 92789.12 + 40 218.42803 -4.4152211 0 -4.3872076 94118.45 + 50 180.40641 -4.4103445 0 -4.3872073 95579.009 + 60 141.2326 -4.4053202 0 -4.3872071 97031.816 + 70 104.54429 -4.4006146 0 -4.3872068 98332.882 + 80 73.787889 -4.3966699 0 -4.3872066 99351.332 + 90 51.759956 -4.3938446 0 -4.3872064 99992.934 + 100 40.209821 -4.3923633 0 -4.3872064 100211.98 +Loop time of 0.11881 on 4 procs for 100 steps with 128 atoms + +Performance: 36.361 ns/day, 0.660 hours/ns, 841.679 timesteps/s, 107.735 katom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.10673 | 0.10875 | 0.11236 | 0.7 | 91.53 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0057324 | 0.0093477 | 0.011375 | 2.4 | 7.87 +Output | 0.00016629 | 0.00018236 | 0.00022483 | 0.0 | 0.15 +Modify | 9.4948e-05 | 0.00010621 | 0.00012066 | 0.0 | 0.09 +Other | | 0.0004263 | | | 0.36 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1049 ave 1049 max 1049 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 5376 ave 5376 max 5376 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 21504 +Ave neighs/atom = 168 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/README b/examples/README index 62a09f654d..90831b49f0 100644 --- a/examples/README +++ b/examples/README @@ -104,6 +104,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script qeq: use of QEQ package for charge equilibration reaxff: RDX and TATB and several other models using ReaxFF +replicate: use of replicate command rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void @@ -115,6 +116,7 @@ tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si template: examples for using atom_style template and comparing to atom style molecular tersoff: regression test input for Tersoff variants threebody: regression test input for a variety of threebody potentials +triclinic: general triclinic simulation boxes versus orthogonal boxes ttm: two-temeperature model examples vashishta: models using the Vashishta potential voronoi: Voronoi tesselation via compute voronoi/atom command diff --git a/examples/granular/data.particles b/examples/granular/data.particles new file mode 100644 index 0000000000..c9f3bd7a9c --- /dev/null +++ b/examples/granular/data.particles @@ -0,0 +1,18 @@ +Python generated LAMMPS data file + +2 atoms +1 atom types + +0 0.08 xlo xhi +0 0.04 ylo yhi +0 0.08 zlo zhi + +Atoms # sphere + +1 1 0.004 2500 0.04 0.02 0.04 0 0 0 +2 1 0.004 2500 0.04 0.02 0.04416 0 0 0 + +Velocities + +1 0.0 0.0 1 0 0 0 +2 0.0 0.0 -1 0 0 0 diff --git a/examples/granular/in.restitution b/examples/granular/in.restitution new file mode 100644 index 0000000000..e441ed67a7 --- /dev/null +++ b/examples/granular/in.restitution @@ -0,0 +1,24 @@ +units si +atom_style sphere + +boundary p p f +region box block 0 80e-3 0 40e-3 0 80e-3 open 3 open 4 +create_box 2 box + +read_data data.particles add append +group mb type 1 + +pair_style granular +pair_coeff * * hertz/material 1e6 0.8 0.4 tangential mindlin NULL 0.0 0.5 damping coeff_restitution +# pair_coeff * * hooke 1e6 0.5 tangential mindlin 1 1.0 0.0 damping coeff_restitution +comm_modify vel yes + +timestep 1e-9 +fix 1 all nve/sphere +compute s all stress/atom NULL pair + +#dump 1 all custom 2000000 op.dump id x y z vx vy vz +#dump_modify 1 pad 8 +thermo_style custom step ke +run_style verlet +run 10000000 diff --git a/examples/granular/log.13May23.restitution.g++.1 b/examples/granular/log.13May23.restitution.g++.1 new file mode 100644 index 0000000000..e51709d10d --- /dev/null +++ b/examples/granular/log.13May23.restitution.g++.1 @@ -0,0 +1,80 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-93-g4e7bddaa0b) + using 1 OpenMP thread(s) per MPI task +units si +atom_style sphere + +boundary p p f +region box block 0 80e-3 0 40e-3 0 80e-3 open 3 open 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (0.08 0.04 0.08) + 1 by 1 by 1 MPI processor grid + +read_data data.particles add append +Reading data file ... + orthogonal box = (0 0 0) to (0.08 0.04 0.08) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + reading velocities ... + 2 velocities + read_data CPU = 0.002 seconds +group mb type 1 +2 atoms in group mb + +pair_style granular +pair_coeff * * hertz/material 1e6 0.8 0.4 tangential mindlin NULL 0.0 0.5 damping coeff_restitution +# pair_coeff * * hooke 1e6 0.5 tangential mindlin 1 1.0 0.0 damping coeff_restitution +comm_modify vel yes + +timestep 1e-9 +fix 1 all nve/sphere +compute s all stress/atom NULL pair + +#dump 1 all custom 2000000 op.dump id x y z vx vy vz +#dump_modify 1 pad 8 +thermo_style custom step ke +run_style verlet +run 10000000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.005 + ghost atom cutoff = 0.005 + binsize = 0.0025, bins = 32 16 32 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.1 | 10.1 | 10.1 Mbytes + Step KinEng + 0 8.3775804e-05 + 10000000 5.3616513e-05 +Loop time of 5.99782 on 1 procs for 10000000 steps with 2 atoms + +77.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.60235 | 0.60235 | 0.60235 | 0.0 | 10.04 +Neigh | 0.00021965 | 0.00021965 | 0.00021965 | 0.0 | 0.00 +Comm | 1.7939 | 1.7939 | 1.7939 | 0.0 | 29.91 +Output | 2.5955e-05 | 2.5955e-05 | 2.5955e-05 | 0.0 | 0.00 +Modify | 1.7622 | 1.7622 | 1.7622 | 0.0 | 29.38 +Other | | 1.839 | | | 30.66 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 14 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/meam/msmeam/HGa.meam b/examples/meam/msmeam/HGa.meam deleted file mode 100644 index 9f01501c16..0000000000 --- a/examples/meam/msmeam/HGa.meam +++ /dev/null @@ -1,30 +0,0 @@ -bkgd_dyn = 1 -emb_lin_neg = 1 -augt1=0 -ialloy=1 -rc = 5.9 -#H -attrac(1,1)=0.460 -repuls(1,1)=0.460 -Cmin(1,1,1)=1.3 # PuMS -Cmax(1,1,1)= 2.80 -nn2(1,1)=1 -#Ga -rho0(2) = 0.6 -attrac(2,2)=0.097 -repuls(2,2)=0.097 -nn2(2,2)=1 -#HGa -attrac(1,2)=0.300 -repuls(1,2)=0.300 -lattce(1,2)=l12 -re(1,2)=3.19 -delta(1,2)=-0.48 -alpha(1,2)=6.6 -Cmin(1,1,2)=2.0 -Cmin(2,1,2)= 2.0 -Cmin(1,2,1)=2.0 -Cmin(2,2,1) = 1.4 -Cmin(1,2,2) = 1.4 -Cmin(1,1,2) = 1.4 -nn2(1,2)=1 diff --git a/examples/meam/msmeam/HGa.msmeam b/examples/meam/msmeam/HGa.msmeam new file mode 120000 index 0000000000..5629006d1d --- /dev/null +++ b/examples/meam/msmeam/HGa.msmeam @@ -0,0 +1 @@ +../../../potentials/HGa.msmeam \ No newline at end of file diff --git a/examples/meam/msmeam/data.msmeam.bu b/examples/meam/msmeam/data.msmeam.bu deleted file mode 100644 index 576a3c50de..0000000000 --- a/examples/meam/msmeam/data.msmeam.bu +++ /dev/null @@ -1,25 +0,0 @@ -LAMMPS data file via write_data, version 16 Feb 2016, timestep = 1 - -3 atoms -2 atom types - --4.0000000000000000e+00 4.0000000000000000e+00 xlo xhi --4.0000000000000000e+00 4.0000000000000000e+00 ylo yhi --4.0000000000000000e+00 4.0000000000000000e+00 zlo zhi - -Masses - -1 1.0079 -2 69.723 - -Atoms # atomic - -1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 -2 2 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 -3 2 2.9999999999999999e-01 2.2999999999999998e+00 0.0000000000000000e+00 0 0 0 - -Velocities - -1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 diff --git a/examples/meam/msmeam/in.msmeam b/examples/meam/msmeam/in.msmeam index 82ffb89a13..e8d13f8682 100644 --- a/examples/meam/msmeam/in.msmeam +++ b/examples/meam/msmeam/in.msmeam @@ -1,5 +1,3 @@ -echo both -log log.msmeam # Test of MEAM potential for HGa # ------------------------ INITIALIZATION ---------------------------- @@ -21,11 +19,11 @@ create_atoms 1 single 0 0 0 units box create_atoms 2 single 2.2 0 0 units box create_atoms 2 single 0.3 2.3 0 units box # ---------- Define Settings --------------------- -variable teng equal "c_eatoms" +variable teng equal "c_eatoms" compute pot_energy all pe/atom compute stress all stress/atom NULL dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] -run 1 -write_data data.msmeam +run 1 +#write_data data.msmeam print "All done!" diff --git a/examples/meam/msmeam/library.msmeam b/examples/meam/msmeam/library.msmeam deleted file mode 100644 index 9937eaee08..0000000000 --- a/examples/meam/msmeam/library.msmeam +++ /dev/null @@ -1,14 +0,0 @@ -# DATE: 2018-09-22 UNITS: metal CONTRIBUTOR: Steve Valone, smv@lanl.gov CITATION: Baskes, PRB 1992; smv, sr, mib, JNM 2010 -# ms-meam data format May 2010 -# elt lat z ielement atwt -# alpha b0 b1 b2 b3 b1m b2m b3m alat esub asub -# - t0 t1 t2 t3 t1m t2m t3m rozero ibar -# NOTE: leading character cannot be a space - -'H' 'dim' 1.0 1 1.0079 -2.960 2.960 3.0 1.0 1.0 1.0 3.0 1.0 0.741 2.235 2.50 -1.0 0.44721 0.0 0.00 0.0 0.31623 0 6.70 0 - -'Ga4' 'fcc' 12.0 31 69.723 -4.42 4.80 3.10 6.00 0.00 0.0 0.0 0.5 4.247 2.897 0.97 -1.0 1.649 1.435 0.00 0.0 0.0 2.0 0.70 0 diff --git a/examples/meam/msmeam/library.msmeam b/examples/meam/msmeam/library.msmeam new file mode 120000 index 0000000000..2226ef99da --- /dev/null +++ b/examples/meam/msmeam/library.msmeam @@ -0,0 +1 @@ +../../../potentials/library.msmeam \ No newline at end of file diff --git a/examples/meam/msmeam/log.1Mar2024.msmeam.g++.1 b/examples/meam/msmeam/log.1Mar2024.msmeam.g++.1 new file mode 100644 index 0000000000..70fbbdd89c --- /dev/null +++ b/examples/meam/msmeam/log.1Mar2024.msmeam.g++.1 @@ -0,0 +1,126 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Test of MEAM potential for HGa + +# ------------------------ INITIALIZATION ---------------------------- +units metal +dimension 3 +boundary p p p +atom_style atomic +variable latparam equal 4.646 +variable ncell equal 3 + +# ----------------------- ATOM DEFINITION ---------------------------- +region box block -4 4 -4 4 -4 4 +create_box 2 box +Created orthogonal box = (-4 -4 -4) to (4 4 4) + 1 by 1 by 1 MPI processor grid + +# + +include potential.mod +# NOTE: This script can be modified for different pair styles +# See in.elastic for more info. + +variable Pu string H +print "potential chosen ${Pu}" +potential chosen H +# Choose potential +pair_style meam/ms +print "we just executed" +we just executed + +pair_coeff * * library.msmeam ${Pu} Ga4 HGa.msmeam ${Pu} Ga4 +pair_coeff * * library.msmeam H Ga4 HGa.msmeam ${Pu} Ga4 +pair_coeff * * library.msmeam H Ga4 HGa.msmeam H Ga4 +Reading MEAM library file library.msmeam with DATE: 2018-09-22 +# Setup neighbor style +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Setup minimization style +variable dmax equal 1.0e-2 +min_style cg +min_modify dmax ${dmax} line quadratic +min_modify dmax 0.01 line quadratic +compute eng all pe/atom +compute eatoms all reduce sum c_eng + +# Setup output +thermo 100 +thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms +thermo_modify norm yes +create_atoms 1 single 0 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-4 -4 -4) to (4 4 4) + create_atoms CPU = 0.000 seconds +create_atoms 2 single 2.2 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-4 -4 -4) to (4 4 4) + create_atoms CPU = 0.000 seconds +create_atoms 2 single 0.3 2.3 0 units box +Created 1 atoms + using box units in orthogonal box = (-4 -4 -4) to (4 4 4) + create_atoms CPU = 0.000 seconds +# ---------- Define Settings --------------------- +variable teng equal "c_eatoms" +compute pot_energy all pe/atom +compute stress all stress/atom NULL +# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +run 1 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.9 + ghost atom cutoff = 6.9 + binsize = 3.45, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/ms, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/ms, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.587 | 8.587 | 8.587 Mbytes + Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms + 0 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079 + 1 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079 +Loop time of 4.4446e-05 on 1 procs for 1 steps with 3 atoms + +Performance: 1943.932 ns/day, 0.012 hours/ns, 22499.213 timesteps/s, 67.498 katom-step/s +31.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.9908e-05 | 2.9908e-05 | 2.9908e-05 | 0.0 | 67.29 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.033e-06 | 1.033e-06 | 1.033e-06 | 0.0 | 2.32 +Output | 9.347e-06 | 9.347e-06 | 9.347e-06 | 0.0 | 21.03 +Modify | 2.02e-07 | 2.02e-07 | 2.02e-07 | 0.0 | 0.45 +Other | | 3.956e-06 | | | 8.90 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 78 ave 78 max 78 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7 ave 7 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 14 ave 14 max 14 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14 +Ave neighs/atom = 4.6666667 +Neighbor list builds = 0 +Dangerous builds = 0 +#write_data data.msmeam + +print "All done!" +All done! +Total wall time: 0:00:00 diff --git a/examples/meam/msmeam/log.1Mar2024.msmeam.g++.4 b/examples/meam/msmeam/log.1Mar2024.msmeam.g++.4 new file mode 100644 index 0000000000..6951a64945 --- /dev/null +++ b/examples/meam/msmeam/log.1Mar2024.msmeam.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Test of MEAM potential for HGa + +# ------------------------ INITIALIZATION ---------------------------- +units metal +dimension 3 +boundary p p p +atom_style atomic +variable latparam equal 4.646 +variable ncell equal 3 + +# ----------------------- ATOM DEFINITION ---------------------------- +region box block -4 4 -4 4 -4 4 +create_box 2 box +Created orthogonal box = (-4 -4 -4) to (4 4 4) + 1 by 2 by 2 MPI processor grid + +# + +include potential.mod +# NOTE: This script can be modified for different pair styles +# See in.elastic for more info. + +variable Pu string H +print "potential chosen ${Pu}" +potential chosen H +# Choose potential +pair_style meam/ms +print "we just executed" +we just executed + +pair_coeff * * library.msmeam ${Pu} Ga4 HGa.msmeam ${Pu} Ga4 +pair_coeff * * library.msmeam H Ga4 HGa.msmeam ${Pu} Ga4 +pair_coeff * * library.msmeam H Ga4 HGa.msmeam H Ga4 +Reading MEAM library file library.msmeam with DATE: 2018-09-22 +# Setup neighbor style +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Setup minimization style +variable dmax equal 1.0e-2 +min_style cg +min_modify dmax ${dmax} line quadratic +min_modify dmax 0.01 line quadratic +compute eng all pe/atom +compute eatoms all reduce sum c_eng + +# Setup output +thermo 100 +thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms +thermo_modify norm yes +create_atoms 1 single 0 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-4 -4 -4) to (4 4 4) + create_atoms CPU = 0.000 seconds +create_atoms 2 single 2.2 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-4 -4 -4) to (4 4 4) + create_atoms CPU = 0.000 seconds +create_atoms 2 single 0.3 2.3 0 units box +Created 1 atoms + using box units in orthogonal box = (-4 -4 -4) to (4 4 4) + create_atoms CPU = 0.000 seconds +# ---------- Define Settings --------------------- +variable teng equal "c_eatoms" +compute pot_energy all pe/atom +compute stress all stress/atom NULL +# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +run 1 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.9 + ghost atom cutoff = 6.9 + binsize = 3.45, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/ms, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/ms, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.965 | 8.123 | 8.594 Mbytes + Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms + 0 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079 + 1 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079 +Loop time of 8.70645e-05 on 4 procs for 1 steps with 3 atoms + +Performance: 992.368 ns/day, 0.024 hours/ns, 11485.738 timesteps/s, 34.457 katom-step/s +29.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3957e-05 | 4.67e-05 | 5.1056e-05 | 0.0 | 53.64 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.105e-05 | 1.3822e-05 | 1.7033e-05 | 0.0 | 15.88 +Output | 1.5765e-05 | 1.9045e-05 | 2.5216e-05 | 0.0 | 21.87 +Modify | 2.58e-07 | 3.465e-07 | 3.81e-07 | 0.0 | 0.40 +Other | | 7.151e-06 | | | 8.21 + +Nlocal: 0.75 ave 3 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 38.25 ave 42 max 36 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 1.75 ave 7 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +FullNghs: 3.5 ave 14 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 14 +Ave neighs/atom = 4.6666667 +Neighbor list builds = 0 +Dangerous builds = 0 +#write_data data.msmeam + +print "All done!" +All done! +Total wall time: 0:00:00 diff --git a/examples/meam/msmeam/log.msmeam.bu b/examples/meam/msmeam/log.msmeam.bu deleted file mode 100644 index 8eac453c1e..0000000000 --- a/examples/meam/msmeam/log.msmeam.bu +++ /dev/null @@ -1,107 +0,0 @@ -# Test of MEAM potential for HGa - -# ------------------------ INITIALIZATION ---------------------------- -units metal -dimension 3 -boundary p p p -atom_style atomic -variable latparam equal 4.646 -variable ncell equal 3 - -# ----------------------- ATOM DEFINITION ---------------------------- -region box block -4 4 -4 4 -4 4 -create_box 2 box -Created orthogonal box = (-4 -4 -4) to (4 4 4) - 1 by 1 by 1 MPI processor grid - -# - -include potential.mod -# NOTE: This script can be modified for different pair styles -# See in.elastic for more info. - -variable Pu string H -print "potential chosen ${Pu}" -potential chosen H -# Choose potential -pair_style MSmeam -print "we just executed" -we just executed - -pair_coeff * * library.MSmeam ${Pu} Ga4 HGaMS.meam ${Pu} Ga4 -pair_coeff * * library.MSmeam H Ga4 HGaMS.meam ${Pu} Ga4 -pair_coeff * * library.MSmeam H Ga4 HGaMS.meam H Ga4 -Reading potential file library.MSmeam with DATE: 2018-09-22 -# Setup neighbor style -neighbor 1.0 nsq -neigh_modify once no every 1 delay 0 check yes - -# Setup minimization style -variable dmax equal 1.0e-2 -min_style cg -min_modify dmax ${dmax} line quadratic -min_modify dmax 0.01 line quadratic -compute eng all pe/atom -compute eatoms all reduce sum c_eng - -# Setup output -thermo 100 -thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms -thermo_modify norm yes -create_atoms 1 single 0 0 0 units box -Created 1 atoms -create_atoms 2 single 2.2 0 0 units box -Created 1 atoms -create_atoms 2 single 0.3 2.3 0 units box -Created 1 atoms -# ---------- Define Settings --------------------- -variable teng equal "c_eatoms" -compute pot_energy all pe/atom -compute stress all stress/atom NULL -dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] -run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6.9 - ghost atom cutoff = 6.9 -Memory usage per processor = 12.9295 Mbytes -Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume eatoms - 0 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079 - 1 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079 -Loop time of 0.000172138 on 1 procs for 1 steps with 3 atoms - -Performance: 501.922 ns/day, 0.048 hours/ns, 5809.285 timesteps/s -81.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 38.92 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 1.11 -Output | 9.7036e-05 | 9.7036e-05 | 9.7036e-05 | 0.0 | 56.37 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 6.199e-06 | | | 3.60 - -Nlocal: 3 ave 3 max 3 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 78 ave 78 max 78 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 7 ave 7 max 7 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 14 ave 14 max 14 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 14 -Ave neighs/atom = 4.66667 -Neighbor list builds = 0 -Dangerous builds = 0 -write_data data.msmeam - -print "All done!" -All done! -Total wall time: 0:00:00 - diff --git a/examples/meam/msmeam/msmeam.dump.bu b/examples/meam/msmeam/msmeam.dump.bu deleted file mode 100644 index 039f630073..0000000000 --- a/examples/meam/msmeam/msmeam.dump.bu +++ /dev/null @@ -1,24 +0,0 @@ -ITEM: TIMESTEP -0 -ITEM: NUMBER OF ATOMS -3 -ITEM: BOX BOUNDS pp pp pp --4 4 --4 4 --4 4 -ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] -1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 -2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 -3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 -ITEM: TIMESTEP -1 -ITEM: NUMBER OF ATOMS -3 -ITEM: BOX BOUNDS pp pp pp --4 4 --4 4 --4 4 -ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] -1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 -2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 -3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 diff --git a/examples/meam/msmeam/potential.mod b/examples/meam/msmeam/potential.mod index 760cc93503..117736743b 100644 --- a/examples/meam/msmeam/potential.mod +++ b/examples/meam/msmeam/potential.mod @@ -7,7 +7,7 @@ print "potential chosen ${Pu}" pair_style meam/ms print "we just executed" -pair_coeff * * library.msmeam ${Pu} Ga4 HGa.meam ${Pu} Ga4 +pair_coeff * * library.msmeam ${Pu} Ga4 HGa.msmeam ${Pu} Ga4 # Setup neighbor style neighbor 1.0 bin neigh_modify once no every 1 delay 0 check yes diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 deleted file mode 100644 index f1001e6cea..0000000000 --- a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000473022 secs - read_data CPU = 0.0024147 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00022316 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms - -Performance: 2093802.885 tau/day, 4846.766 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21 -Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11 -Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64 -Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86 -Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17 -Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37 -Other | | 0.002726 | | | 2.64 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 197 ave 197 max 197 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3094 ave 3094 max 3094 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3094 -Ave neighs/atom = 2.57833 -Ave special neighs/atom = 0.5 -Neighbor list builds = 52 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 - 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 - 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 - 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 - 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 - 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 - 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 - 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 - 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 -Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms - -Performance: 1208012.705 tau/day, 2796.326 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17 -Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38 -Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92 -Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45 -Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10 -Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34 -Other | | 0.00293 | | | 1.64 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 416 ave 416 max 416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8769 ave 8769 max 8769 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8769 -Ave neighs/atom = 7.3075 -Ave special neighs/atom = 0.5 -Neighbor list builds = 47 -Dangerous builds = 2 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 0.00015378 secs -150 rigid bodies with 450 atoms - 1.30435 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes -Step Temp E_pair E_mol TotEng Press - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 - 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 - 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 - 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 - 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 - 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 - 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 - 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 - 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 - 950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332 - 1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141 -Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms - -Performance: 1297278.008 tau/day, 3002.958 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51 -Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56 -Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83 -Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44 -Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11 -Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66 -Other | | 0.003141 | | | 1.89 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 415 ave 415 max 415 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8743 ave 8743 max 8743 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8743 -Ave neighs/atom = 7.28583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 40 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 deleted file mode 100644 index e65f67a527..0000000000 --- a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000422001 secs - read_data CPU = 0.00473404 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000183344 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms - -Performance: 5066547.720 tau/day, 11728.120 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 -Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 -Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 -Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 -Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 -Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 -Other | | 0.002669 | | | 6.26 - -Nlocal: 300 ave 304 max 292 min -Histogram: 1 0 0 0 0 0 0 0 2 1 -Nghost: 103.5 ave 108 max 98 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 773.5 ave 792 max 735 min -Histogram: 1 0 0 0 0 0 0 0 2 1 - -Total # of neighbors = 3094 -Ave neighs/atom = 2.57833 -Ave special neighs/atom = 0.5 -Neighbor list builds = 52 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 - 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 - 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 - 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 - 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 - 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 - 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 - 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 - 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 -Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms - -Performance: 2434100.210 tau/day, 5634.491 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 -Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 -Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 -Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 -Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 -Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 -Other | | 0.002938 | | | 3.31 - -Nlocal: 300 ave 309 max 291 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 218.75 ave 223 max 216 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Neighs: 2192.25 ave 2251 max 2113 min -Histogram: 1 0 0 1 0 0 0 0 0 2 - -Total # of neighbors = 8769 -Ave neighs/atom = 7.3075 -Ave special neighs/atom = 0.5 -Neighbor list builds = 47 -Dangerous builds = 2 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 7.70092e-05 secs -150 rigid bodies with 450 atoms - 1.30435 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes -Step Temp E_pair E_mol TotEng Press - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 - 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 - 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 - 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 - 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 - 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 - 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 - 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 - 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 - 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 - 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 -Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms - -Performance: 3671840.233 tau/day, 8499.630 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 -Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 -Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 -Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 -Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 -Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 -Other | | 0.00224 | | | 3.81 - -Nlocal: 300 ave 303 max 295 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 219 ave 224 max 215 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Neighs: 2185.75 ave 2244 max 2143 min -Histogram: 1 1 0 0 0 1 0 0 0 1 - -Total # of neighbors = 8743 -Ave neighs/atom = 7.28583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 40 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.4Apr2024.micelle-rigid.g++.1 b/examples/micelle/log.4Apr2024.micelle-rigid.g++.1 new file mode 100644 index 0000000000..d3cb98940d --- /dev/null +++ b/examples/micelle/log.4Apr2024.micelle-rigid.g++.1 @@ -0,0 +1,271 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified) +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.005 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0365221 on 1 procs for 500 steps with 1200 atoms + +Performance: 5914221.123 tau/day, 13690.327 timesteps/s, 16.428 Matom-step/s +89.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022939 | 0.022939 | 0.022939 | 0.0 | 62.81 +Bond | 0.00073851 | 0.00073851 | 0.00073851 | 0.0 | 2.02 +Neigh | 0.0078339 | 0.0078339 | 0.0078339 | 0.0 | 21.45 +Comm | 0.00072134 | 0.00072134 | 0.00072134 | 0.0 | 1.98 +Output | 7.1419e-05 | 7.1419e-05 | 7.1419e-05 | 0.0 | 0.20 +Modify | 0.0034868 | 0.0034868 | 0.0034868 | 0.0 | 9.55 +Other | | 0.0007314 | | | 2.00 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 197 ave 197 max 197 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3094 ave 3094 max 3094 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.5783333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 + 150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 + 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 + 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 + 200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262 + 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 + 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 + 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 + 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 + 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 +Loop time of 0.0650638 on 1 procs for 500 steps with 1200 atoms + +Performance: 3319817.322 tau/day, 7684.762 timesteps/s, 9.222 Matom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.027565 | 0.027565 | 0.027565 | 0.0 | 42.37 +Bond | 0.0007043 | 0.0007043 | 0.0007043 | 0.0 | 1.08 +Neigh | 0.012724 | 0.012724 | 0.012724 | 0.0 | 19.56 +Comm | 0.00091442 | 0.00091442 | 0.00091442 | 0.0 | 1.41 +Output | 6.004e-05 | 6.004e-05 | 6.004e-05 | 0.0 | 0.09 +Modify | 0.022329 | 0.022329 | 0.022329 | 0.0 | 34.32 +Other | | 0.0007666 | | | 1.18 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 411 ave 411 max 411 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8759 ave 8759 max 8759 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8759 +Ave neighs/atom = 7.2991667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 46 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.000 seconds + 150 rigid bodies with 450 atoms + 1.3043524 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 9.306 | 9.306 | 9.306 Mbytes + Step Temp E_pair E_mol TotEng Press + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 + 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 + 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 + 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 + 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 + 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 + 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 + 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 + 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 + 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 + 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630988 +Loop time of 0.0592806 on 1 procs for 500 steps with 1200 atoms + +Performance: 3643690.276 tau/day, 8434.468 timesteps/s, 10.121 Matom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.026866 | 0.026866 | 0.026866 | 0.0 | 45.32 +Bond | 0.00071863 | 0.00071863 | 0.00071863 | 0.0 | 1.21 +Neigh | 0.010927 | 0.010927 | 0.010927 | 0.0 | 18.43 +Comm | 0.00084187 | 0.00084187 | 0.00084187 | 0.0 | 1.42 +Output | 6.8106e-05 | 6.8106e-05 | 6.8106e-05 | 0.0 | 0.11 +Modify | 0.019075 | 0.019075 | 0.019075 | 0.0 | 32.18 +Other | | 0.000783 | | | 1.32 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 417 ave 417 max 417 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8654 ave 8654 max 8654 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8654 +Ave neighs/atom = 7.2116667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 39 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.4Apr2024.micelle-rigid.g++.4 b/examples/micelle/log.4Apr2024.micelle-rigid.g++.4 new file mode 100644 index 0000000000..ce15cfec21 --- /dev/null +++ b/examples/micelle/log.4Apr2024.micelle-rigid.g++.4 @@ -0,0 +1,272 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0138659 on 4 procs for 500 steps with 1200 atoms + +Performance: 15577811.312 tau/day, 36059.748 timesteps/s, 43.272 Matom-step/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0053896 | 0.0057144 | 0.0060899 | 0.4 | 41.21 +Bond | 0.00020074 | 0.00021422 | 0.00022291 | 0.0 | 1.54 +Neigh | 0.0025301 | 0.0025401 | 0.0025501 | 0.0 | 18.32 +Comm | 0.0031194 | 0.0035074 | 0.0038196 | 0.4 | 25.30 +Output | 6.4137e-05 | 6.7743e-05 | 7.7909e-05 | 0.0 | 0.49 +Modify | 0.0013391 | 0.0013582 | 0.0013972 | 0.1 | 9.80 +Other | | 0.0004638 | | | 3.34 + +Nlocal: 300 ave 304 max 292 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Nghost: 103.5 ave 108 max 98 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 773.5 ave 792 max 735 min +Histogram: 1 0 0 0 0 0 0 0 2 1 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.5783333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 + 150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 + 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 + 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 + 200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262 + 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 + 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 + 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 + 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 + 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 +Loop time of 0.0381773 on 4 procs for 500 steps with 1200 atoms + +Performance: 5657810.772 tau/day, 13096.784 timesteps/s, 15.716 Matom-step/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0059651 | 0.0062314 | 0.0066404 | 0.3 | 16.32 +Bond | 0.00021057 | 0.00022477 | 0.0002333 | 0.0 | 0.59 +Neigh | 0.0041424 | 0.0041487 | 0.0041512 | 0.0 | 10.87 +Comm | 0.004264 | 0.0047244 | 0.0050297 | 0.4 | 12.37 +Output | 8.2396e-05 | 8.6559e-05 | 9.6749e-05 | 0.0 | 0.23 +Modify | 0.021833 | 0.021946 | 0.022094 | 0.1 | 57.48 +Other | | 0.0008157 | | | 2.14 + +Nlocal: 300 ave 303 max 296 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 216.25 ave 219 max 214 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 2189.75 ave 2205 max 2173 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 8759 +Ave neighs/atom = 7.2991667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 46 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.000 seconds + 150 rigid bodies with 450 atoms + 1.3043524 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes + Step Temp E_pair E_mol TotEng Press + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 + 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 + 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 + 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 + 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 + 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 + 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 + 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 + 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 + 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 + 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987 +Loop time of 0.0236819 on 4 procs for 500 steps with 1200 atoms + +Performance: 9120883.727 tau/day, 21113.157 timesteps/s, 25.336 Matom-step/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0058656 | 0.0059718 | 0.0061355 | 0.1 | 25.22 +Bond | 0.0002083 | 0.00022447 | 0.00023485 | 0.0 | 0.95 +Neigh | 0.0035477 | 0.0035644 | 0.0035824 | 0.0 | 15.05 +Comm | 0.0041037 | 0.0042227 | 0.0043024 | 0.1 | 17.83 +Output | 7.4355e-05 | 7.8273e-05 | 8.7777e-05 | 0.0 | 0.33 +Modify | 0.008976 | 0.0090549 | 0.0091663 | 0.1 | 38.24 +Other | | 0.0005654 | | | 2.39 + +Nlocal: 300 ave 306 max 295 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Nghost: 221 ave 226 max 217 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 2163.5 ave 2271 max 2100 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 8654 +Ave neighs/atom = 7.2116667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 39 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mliap/ACE_NN_Pytorch.pt b/examples/mliap/ACE_NN_Pytorch.pt new file mode 100644 index 0000000000..c8fa74f6e0 Binary files /dev/null and b/examples/mliap/ACE_NN_Pytorch.pt differ diff --git a/examples/mliap/Cu_ACE.mliap.pytorch.model.pt b/examples/mliap/Cu_ACE.mliap.pytorch.model.pt new file mode 100644 index 0000000000..cdcff59f44 Binary files /dev/null and b/examples/mliap/Cu_ACE.mliap.pytorch.model.pt differ diff --git a/examples/mliap/H_N_O_ccs.yace b/examples/mliap/H_N_O_ccs.yace new file mode 100644 index 0000000000..2953222216 --- /dev/null +++ b/examples/mliap/H_N_O_ccs.yace @@ -0,0 +1,294 @@ +elements: [H, N, O] +E0: [0.000000, 0.000000, 0.000000] +deltaSplineBins: 0.001000 +embeddings: + 0: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250} + 1: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250} + 2: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250} +bonds: + [0, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.0, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [0, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [0, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [1, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [1, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 4.4, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [1, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [2, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [2, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} + [2, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance} +functions: + 0: + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, 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0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 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0.4472135954999579]} + - {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 1], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 1, 2], ns: [1, 1, 1], ls: [1, 2, 1], ms_combs: [-1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 1, 2], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 2], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 2, 2], ns: [1, 1, 1], ls: [2, 1, 1], ms_combs: [-2, 1, 1, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 2, -1, -1], ctildes: [0.25819888974716115, -0.18257418583505536, -0.18257418583505536, 0.10540925533894599, 0.21081851067789198, 0.10540925533894599, -0.18257418583505536, -0.18257418583505536, 0.25819888974716115]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 1], ns: [1, 1, 1], ls: [2, 1, 1], ms_combs: [-2, 1, 1, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 2, -1, -1], ctildes: [0.25819888974716115, -0.18257418583505536, -0.18257418583505536, 0.10540925533894599, 0.21081851067789198, 0.10540925533894599, -0.18257418583505536, -0.18257418583505536, 0.25819888974716115]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 2], ns: [1, 1, 1], ls: [2, 1, 1], ms_combs: [-2, 1, 1, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 2, -1, -1], ctildes: [0.25819888974716115, -0.18257418583505536, -0.18257418583505536, 0.10540925533894599, 0.21081851067789198, 0.10540925533894599, -0.18257418583505536, -0.18257418583505536, 0.25819888974716115]} + - {mu0: 1, rank: 3, ndensity: 1, 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1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]} + - {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 1], ns: [1, 1, 1], ls: [2, 1, 1], ms_combs: [-2, 1, 1, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 2, -1, -1], ctildes: [0.25819888974716115, -0.18257418583505536, -0.18257418583505536, 0.10540925533894599, 0.21081851067789198, 0.10540925533894599, -0.18257418583505536, -0.18257418583505536, 0.25819888974716115]} + - {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 2], ns: [1, 1, 1], ls: [2, 1, 1], ms_combs: [-2, 1, 1, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 2, -1, -1], ctildes: [0.25819888974716115, -0.18257418583505536, -0.18257418583505536, 0.10540925533894599, 0.21081851067789198, 0.10540925533894599, -0.18257418583505536, 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ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]} + - {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [2, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]} diff --git a/examples/mliap/README b/examples/mliap/README index 070ce86bfd..26d4640946 100644 --- a/examples/mliap/README +++ b/examples/mliap/README @@ -160,3 +160,44 @@ in.mliap.so3.nn.Si ------------------ Example of NN model with SO3 descriptors for Si + +NOTE: The use of ACE within mliap requires the generalized Glebsch-Gordan +coefficients (a.k.a. coupling coefficients, ccs, etc.) are defined within +a ctilde file. These are used to construct the ACE descriptors for both +linear models and non-linear models within mliap. These define the size +of the ACE basis used as well as hyperparameters for the basis functions +for descriptors in mliap. These files may be generated with various +software for fitting ACE models must follow the format for ACE C-Tilde +potential files in `../PACKAGES/pace/*.ace` or the convenient yaml-based +`.yace` format. For the ACE mliap interface, the coupling coefficient file +should NOT include linear model coefficients. If the linear model coefficients +are included in the coupling coefficient file, mliap will evaluate ACE +contributions to a linear model rather than ACE descriptors. + +One convenient feature of mliap/ace, is that it enables the user to +decouple the linear model coefficients and the ace descriptors. Both are +typically included in ACE potentials with C-Tilde format. This is +demonstrated in the first example for ACE: linear model coefficients are +provided separately (in `linear_ACE_coeff.acecoeff`) from coupling +coefficients (in `linear_ACE_ccs.yace`). They are combined in a linear +pytorch model using `convert_mliap_lin_ACE.py`. + +in.mliap.pytorch.ace +------------------ + +Example of linear model with ACE descriptors for minimal Ta dataset + +in.mliap.ace.compute +------------------ + +Example for calculating multi-element ACE descriptors through ML-IAP + +in.mliap.pytorch.ace.NN +------------------ + +Example of NN model with ACE descriptors for minimal Ta dataset + +mliap_pytorch_ACE.py +------------------ + +Example of NN model with ACE descriptors for minimal Ta dataset through mliappy diff --git a/examples/mliap/Ta06A.mliap.pytorch.model.pt b/examples/mliap/Ta06A.mliap.pytorch.model.pt new file mode 100644 index 0000000000..bbce9a2249 Binary files /dev/null and b/examples/mliap/Ta06A.mliap.pytorch.model.pt differ diff --git a/examples/mliap/Ta_ACE.mliap.pytorch.model.pt b/examples/mliap/Ta_ACE.mliap.pytorch.model.pt new file mode 100644 index 0000000000..905ef37086 Binary files /dev/null and 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+ 161 1 4.2956948500000003 4.7644888099999996 6.3801669700000003 diff --git a/examples/mliap/ccs_single_element.yace b/examples/mliap/ccs_single_element.yace new file mode 100644 index 0000000000..b51ee1320f --- /dev/null +++ b/examples/mliap/ccs_single_element.yace @@ -0,0 +1,46 @@ +elements: [Ta] +E0: [0.000000] +deltaSplineBins: 0.001000 +embeddings: + 0: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250} +bonds: + [0, 0]: {nradmax: 8, lmax: 2, nradbasemax: 8, radbasename: ChebExpCos, radparameters: [0.5723], radcoefficients: [[[1, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0]], [[0, 1, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0]], [[0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0]], [[0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0]], [[0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0]], [[0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0]], [[0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 1, 0]], [[0, 0, 0, 0, 0, 0, 0, 1], [0, 0, 0, 0, 0, 0, 0, 1], [0, 0, 0, 0, 0, 0, 0, 1]]], prehc: 0, lambdahc: 0.5723, rcut: 4.842, dcut: 0.01, rcut_in: 0.595, dcut_in: 0.01, inner_cutoff_type: distance} +functions: + 0: + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [3], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [4], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [5], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [6], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [7], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [8], ls: [0], ms_combs: [0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 1, mus: [0, 0], ns: [1, 1], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 1, mus: [0, 0], ns: [1, 2], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 1, mus: [0, 0], ns: [1, 3], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 1, mus: [0, 0], ns: [2, 2], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 1, mus: [0, 0], ns: [2, 3], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 1, mus: [0, 0], ns: [3, 3], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 3], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [2, 3], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [3, 3], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 3], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [2, 3], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [3, 3], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [1, 1, 2], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [1, 2, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [1, 2, 2], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [2, 2, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [2, 2, 2], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [1, 1, 2], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [1, 2, 2], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [2, 2, 2], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 0], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]} diff --git a/examples/mliap/convert_mliap_lin_ACE.py b/examples/mliap/convert_mliap_lin_ACE.py new file mode 100644 index 0000000000..a9925989e5 --- /dev/null +++ b/examples/mliap/convert_mliap_lin_ACE.py @@ -0,0 +1,32 @@ +import sys +import numpy as np +import torch + +# torch.nn.modules useful for defining a MLIAPPY model. +from lammps.mliap.pytorch import TorchWrapper, IgnoreElems + +# Read coefficients +coeffs = np.genfromtxt("linear_ACE_coeff.acecoeff",skip_header=4) +# If using the "linear_ACE_pot.yace" instead of just the clebsch-gordan coefficients in "linear_ACE_ccs.yace", +# uncomment below + +#B_coeffs = np.genfromtxt("linear_ACE_coeff.acecoeff",skip_header=4) +#coeffs = np.append(np.zeros(1),np.ones(len(B_coeffs)-1)) + +# Write coefficients to a pytorch linear model +bias = coeffs[0] +weights = coeffs[1:] +lin = torch.nn.Linear(weights.shape[0],1) +lin.to(torch.float64) +with torch.autograd.no_grad(): + lin.weight.set_(torch.from_numpy(weights).unsqueeze(0)) + lin.bias.set_(torch.as_tensor(bias,dtype=torch.float64).unsqueeze(0)) + +# Wrap the pytorch model for usage with mliappy coupling. +model = IgnoreElems(lin) # The linear module does not use the types. +n_descriptors = lin.weight.shape[1] +print ('ndescriptors',n_descriptors) +n_elements = 1 +linked_model = TorchWrapper(model,n_descriptors=n_descriptors,n_elements=n_elements) + +torch.save(linked_model,"Ta_ACE.mliap.pytorch.model.pt") diff --git a/examples/mliap/dat_out.03Mar24.mliap.ace.compute.g++.1 b/examples/mliap/dat_out.03Mar24.mliap.ace.compute.g++.1 new file mode 100644 index 0000000000..d416269aec --- /dev/null +++ b/examples/mliap/dat_out.03Mar24.mliap.ace.compute.g++.1 @@ -0,0 +1,494 @@ +# Time-averaged data for fix ace +# TimeStep Number-of-rows +# Row c_ace[1] c_ace[2] c_ace[3] c_ace[4] c_ace[5] c_ace[6] c_ace[7] c_ace[8] c_ace[9] c_ace[10] c_ace[11] c_ace[12] c_ace[13] c_ace[14] c_ace[15] c_ace[16] c_ace[17] c_ace[18] c_ace[19] c_ace[20] c_ace[21] c_ace[22] c_ace[23] c_ace[24] c_ace[25] c_ace[26] c_ace[27] c_ace[28] c_ace[29] c_ace[30] c_ace[31] c_ace[32] c_ace[33] c_ace[34] c_ace[35] c_ace[36] c_ace[37] c_ace[38] c_ace[39] c_ace[40] c_ace[41] c_ace[42] c_ace[43] c_ace[44] c_ace[45] c_ace[46] c_ace[47] c_ace[48] c_ace[49] c_ace[50] c_ace[51] c_ace[52] c_ace[53] c_ace[54] c_ace[55] c_ace[56] c_ace[57] c_ace[58] c_ace[59] c_ace[60] c_ace[61] c_ace[62] c_ace[63] c_ace[64] c_ace[65] c_ace[66] c_ace[67] c_ace[68] c_ace[69] c_ace[70] c_ace[71] c_ace[72] c_ace[73] c_ace[74] c_ace[75] c_ace[76] c_ace[77] c_ace[78] c_ace[79] c_ace[80] c_ace[81] c_ace[82] c_ace[83] c_ace[84] c_ace[85] c_ace[86] c_ace[87] c_ace[88] c_ace[89] c_ace[90] c_ace[91] c_ace[92] c_ace[93] c_ace[94] c_ace[95] c_ace[96] c_ace[97] c_ace[98] c_ace[99] c_ace[100] c_ace[101] c_ace[102] c_ace[103] c_ace[104] c_ace[105] c_ace[106] c_ace[107] c_ace[108] c_ace[109] c_ace[110] c_ace[111] c_ace[112] c_ace[113] c_ace[114] c_ace[115] c_ace[116] c_ace[117] c_ace[118] c_ace[119] c_ace[120] c_ace[121] c_ace[122] c_ace[123] c_ace[124] c_ace[125] c_ace[126] c_ace[127] c_ace[128] c_ace[129] c_ace[130] c_ace[131] c_ace[132] c_ace[133] c_ace[134] c_ace[135] c_ace[136] c_ace[137] c_ace[138] c_ace[139] c_ace[140] c_ace[141] c_ace[142] c_ace[143] c_ace[144] c_ace[145] c_ace[146] c_ace[147] c_ace[148] c_ace[149] c_ace[150] c_ace[151] c_ace[152] c_ace[153] c_ace[154] c_ace[155] c_ace[156] c_ace[157] c_ace[158] c_ace[159] c_ace[160] c_ace[161] c_ace[162] c_ace[163] c_ace[164] c_ace[165] c_ace[166] c_ace[167] c_ace[168] c_ace[169] c_ace[170] c_ace[171] c_ace[172] c_ace[173] c_ace[174] c_ace[175] c_ace[176] c_ace[177] c_ace[178] c_ace[179] c_ace[180] c_ace[181] c_ace[182] c_ace[183] c_ace[184] c_ace[185] c_ace[186] c_ace[187] c_ace[188] c_ace[189] c_ace[190] c_ace[191] c_ace[192] c_ace[193] c_ace[194] c_ace[195] c_ace[196] c_ace[197] c_ace[198] c_ace[199] c_ace[200] c_ace[201] c_ace[202] c_ace[203] c_ace[204] c_ace[205] c_ace[206] c_ace[207] c_ace[208] c_ace[209] c_ace[210] c_ace[211] c_ace[212] c_ace[213] c_ace[214] c_ace[215] c_ace[216] c_ace[217] c_ace[218] c_ace[219] c_ace[220] c_ace[221] c_ace[222] c_ace[223] c_ace[224] c_ace[225] c_ace[226] c_ace[227] c_ace[228] c_ace[229] c_ace[230] c_ace[231] c_ace[232] c_ace[233] c_ace[234] c_ace[235] c_ace[236] c_ace[237] c_ace[238] c_ace[239] c_ace[240] c_ace[241] c_ace[242] c_ace[243] c_ace[244] c_ace[245] c_ace[246] c_ace[247] c_ace[248] c_ace[249] c_ace[250] c_ace[251] c_ace[252] c_ace[253] c_ace[254] c_ace[255] c_ace[256] c_ace[257] c_ace[258] c_ace[259] c_ace[260] c_ace[261] c_ace[262] c_ace[263] c_ace[264] c_ace[265] c_ace[266] c_ace[267] c_ace[268] c_ace[269] c_ace[270] c_ace[271] c_ace[272] c_ace[273] c_ace[274] c_ace[275] c_ace[276] c_ace[277] +0 490 +1 110 633.523 94.3568 17.1047 76.4593 415.72 84.4227 -10.3669 -22.6058 87.5916 -41.6713 14.2935 27.1643 -8.83449 45.539 0.0366547 86.1936 355.524 -9.24098 -4.62886 253.597 -3.89066 -13.051 12.2233 -13.4372 -10.3377 26.0544 5.90582 -29.6058 -123.735 14.1872 28.3718 -2.68723 -36.2963 17.3347 -7.52363 4.01093 21.5542 -150.176 49.1667 106.382 -20.5777 75.3918 12.7539 111.763 -61.6208 56.1044 -51.3912 -31.1257 -21.8452 31.6135 -16.4593 -46.7547 8.4484 -2.80826 -1.50179 2.5356 12.6505 -3.37075 15.4133 24.4245 -17.8721 -68.7976 3.20778 -20.9546 -24.8015 -0.708063 16.8285 25.2232 -31.5949 10.7568 -4.07798 17.5517 -24.71 -27.9933 19.8963 -19.4328 298.998 84.3421 43.4922 99.149 -70.3035 176.822 52.3432 -31.6464 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-0.474851 -0.42294 1.55577 0.571317 4.25915 4.09073 -2.17707 3.82838 0.341378 -4.74905 -0.203726 -2.66634 -0.0775865 -48.0281 -0.310203 5.37433 1.96399 -0.0659725 -13.7711 7.40565 0.515475 -0.0249172 -0.65564 -0.0308012 -2.0487 -1.43116 -0.0158888 -6.92515 -5.95796 -0.0357136 -0.194234 -0.767528 0.0118209 0.0780052 3.91601 -19.6127 1.30233 0.671868 20.8764 -0.296887 7.78508 -1.46411 0.61173 -6.38478 1.2373 3.18546 -8.01273 1.61338 11.0295 76.3328 -0.0272367 2.79981 -0.125313 0.996112 3.05001 -2.54373 0.515527 -0.715533 -0.0253005 -0.0908025 1.54838 -96.8991 -29.6753 25.7231 -7.83316 1.05908 3.90979 -3.21038 1.51359 -2.72086 8.64121 -0.735253 -0.303906 -0.082213 -0.461399 3.78221 0 diff --git a/examples/mliap/dat_out.03Mar24.mliap.ace.compute.g++.4 b/examples/mliap/dat_out.03Mar24.mliap.ace.compute.g++.4 new file mode 100644 index 0000000000..d416269aec --- /dev/null +++ b/examples/mliap/dat_out.03Mar24.mliap.ace.compute.g++.4 @@ -0,0 +1,494 @@ +# Time-averaged data for fix ace +# TimeStep Number-of-rows +# Row c_ace[1] c_ace[2] c_ace[3] c_ace[4] c_ace[5] c_ace[6] c_ace[7] c_ace[8] c_ace[9] c_ace[10] c_ace[11] c_ace[12] c_ace[13] c_ace[14] c_ace[15] c_ace[16] c_ace[17] c_ace[18] c_ace[19] c_ace[20] c_ace[21] c_ace[22] c_ace[23] c_ace[24] c_ace[25] c_ace[26] c_ace[27] c_ace[28] c_ace[29] c_ace[30] c_ace[31] c_ace[32] c_ace[33] c_ace[34] c_ace[35] c_ace[36] c_ace[37] c_ace[38] c_ace[39] c_ace[40] c_ace[41] c_ace[42] c_ace[43] c_ace[44] c_ace[45] c_ace[46] c_ace[47] c_ace[48] c_ace[49] c_ace[50] c_ace[51] c_ace[52] c_ace[53] c_ace[54] c_ace[55] c_ace[56] c_ace[57] c_ace[58] c_ace[59] c_ace[60] c_ace[61] c_ace[62] c_ace[63] c_ace[64] c_ace[65] c_ace[66] c_ace[67] c_ace[68] c_ace[69] c_ace[70] c_ace[71] c_ace[72] c_ace[73] c_ace[74] c_ace[75] c_ace[76] c_ace[77] c_ace[78] c_ace[79] c_ace[80] c_ace[81] c_ace[82] c_ace[83] c_ace[84] c_ace[85] c_ace[86] c_ace[87] c_ace[88] c_ace[89] c_ace[90] c_ace[91] c_ace[92] c_ace[93] c_ace[94] c_ace[95] c_ace[96] c_ace[97] c_ace[98] c_ace[99] c_ace[100] c_ace[101] c_ace[102] c_ace[103] c_ace[104] c_ace[105] c_ace[106] c_ace[107] c_ace[108] c_ace[109] c_ace[110] c_ace[111] c_ace[112] c_ace[113] c_ace[114] c_ace[115] c_ace[116] c_ace[117] c_ace[118] c_ace[119] c_ace[120] c_ace[121] c_ace[122] c_ace[123] c_ace[124] c_ace[125] c_ace[126] c_ace[127] c_ace[128] c_ace[129] c_ace[130] c_ace[131] c_ace[132] c_ace[133] c_ace[134] c_ace[135] c_ace[136] c_ace[137] c_ace[138] c_ace[139] c_ace[140] c_ace[141] c_ace[142] c_ace[143] c_ace[144] c_ace[145] c_ace[146] c_ace[147] c_ace[148] c_ace[149] c_ace[150] c_ace[151] c_ace[152] c_ace[153] c_ace[154] c_ace[155] c_ace[156] c_ace[157] c_ace[158] c_ace[159] c_ace[160] c_ace[161] c_ace[162] c_ace[163] c_ace[164] c_ace[165] c_ace[166] c_ace[167] c_ace[168] c_ace[169] c_ace[170] c_ace[171] c_ace[172] c_ace[173] c_ace[174] c_ace[175] c_ace[176] c_ace[177] c_ace[178] c_ace[179] c_ace[180] c_ace[181] c_ace[182] c_ace[183] c_ace[184] c_ace[185] c_ace[186] c_ace[187] c_ace[188] c_ace[189] c_ace[190] c_ace[191] c_ace[192] c_ace[193] c_ace[194] c_ace[195] c_ace[196] c_ace[197] c_ace[198] c_ace[199] c_ace[200] c_ace[201] c_ace[202] c_ace[203] c_ace[204] c_ace[205] c_ace[206] c_ace[207] c_ace[208] c_ace[209] c_ace[210] c_ace[211] c_ace[212] c_ace[213] c_ace[214] c_ace[215] c_ace[216] c_ace[217] c_ace[218] c_ace[219] c_ace[220] c_ace[221] c_ace[222] c_ace[223] c_ace[224] c_ace[225] c_ace[226] c_ace[227] c_ace[228] c_ace[229] c_ace[230] c_ace[231] c_ace[232] c_ace[233] c_ace[234] c_ace[235] c_ace[236] c_ace[237] c_ace[238] c_ace[239] c_ace[240] c_ace[241] c_ace[242] c_ace[243] c_ace[244] c_ace[245] c_ace[246] c_ace[247] c_ace[248] c_ace[249] c_ace[250] c_ace[251] c_ace[252] c_ace[253] c_ace[254] c_ace[255] c_ace[256] c_ace[257] c_ace[258] c_ace[259] c_ace[260] c_ace[261] c_ace[262] c_ace[263] c_ace[264] c_ace[265] c_ace[266] c_ace[267] c_ace[268] c_ace[269] c_ace[270] c_ace[271] c_ace[272] c_ace[273] c_ace[274] c_ace[275] c_ace[276] c_ace[277] +0 490 +1 110 633.523 94.3568 17.1047 76.4593 415.72 84.4227 -10.3669 -22.6058 87.5916 -41.6713 14.2935 27.1643 -8.83449 45.539 0.0366547 86.1936 355.524 -9.24098 -4.62886 253.597 -3.89066 -13.051 12.2233 -13.4372 -10.3377 26.0544 5.90582 -29.6058 -123.735 14.1872 28.3718 -2.68723 -36.2963 17.3347 -7.52363 4.01093 21.5542 -150.176 49.1667 106.382 -20.5777 75.3918 12.7539 111.763 -61.6208 56.1044 -51.3912 -31.1257 -21.8452 31.6135 -16.4593 -46.7547 8.4484 -2.80826 -1.50179 2.5356 12.6505 -3.37075 15.4133 24.4245 -17.8721 -68.7976 3.20778 -20.9546 -24.8015 -0.708063 16.8285 25.2232 -31.5949 10.7568 -4.07798 17.5517 -24.71 -27.9933 19.8963 -19.4328 298.998 84.3421 43.4922 99.149 -70.3035 176.822 52.3432 -31.6464 42.3741 32.5112 80.4142 -51.6128 67.8793 -73.6841 197.193 8 1.52077 0.095878 25.0149 2.59269 17.1047 76.4593 0.0761166 0.811713 -1.30106 -0.00129584 0.111902 -0.0021799 0.0422313 -0.251236 0.0584668 -0.0193025 -0.01626 0.0327912 -0.206827 0.9039 -0.0332059 3.01698 -1.13334 0.00387133 6.40468 4.05506 0.00624923 -0.0527616 -2.82349 22.795 -2.42196 0.0251087 0.553167 6.5214 -0.15104 -5.49453 -0.0802715 0.913327 -0.334148 0.371537 0.101263 -0.293913 0.00293122 -14.9572 -0.0221277 -0.438643 -0.00945227 1.15262 0.325325 -0.0479565 -0.0576038 -2.21483 0.0504201 0.051311 -2.85708 -0.252836 -0.147617 0.195349 0.0168697 -0.173079 -0.290278 -0.122316 0.657922 -0.00989331 -3.23063 -0.0649301 -0.0401127 -0.245247 0.0816411 -0.366203 2.08759 -0.808832 -1.27672 0.0275694 0.976563 0.0311902 44.7557 2.54472 4.6908 0.618434 -0.591044 6.06674 0.00299428 0.0388937 0.216562 0.685479 0.0208758 -0.0286578 0.0927639 -0.175599 1.58264 43 415.72 25.0149 84.4227 2.59269 112.55 11.2771 19.2603 -1.22032 27.1819 -1.40836 -1.25201 -13.3198 -0.183368 -1.72716 2.25056 0.669987 -1.28528 -11.5485 4.82046 32.6867 -23.7778 -1.32993 -3.13072 0.649938 -11.5006 -2.62278 5.10788 0.548024 219.188 10.0932 -110.928 30.4814 0.276871 -8.57081 -42.4809 -0.452488 0.144132 -0.275055 1.20694 -20.9224 3.34223 -0.36309 69.1926 28.1069 -0.140381 1.18327 3.75663 4.05765 -1.06858 -3.14327 -1.12221 0.910422 2.88772 10.5331 -4.93061 -11.8662 3.67678 -3.34633 -0.0501799 0.46571 -1.69755 6.2103 -3.44241 -3.91512 26.2264 -1.55167 1.4658 -0.808121 0.272213 6.48859 2.32689 -2.05316 2.03777 1.25839 0.0492927 -7.12287 381.036 52.2256 27.4835 34.5144 -28.0414 61.287 8.66705 -6.46335 7.84842 5.0521 6.94067 -5.54313 6.83136 -6.70729 14.1039 0 +2 0 0 0 0 0 0.019982 -0.390456 1.12581 1.89207 0 0 -0.857617 -2.61627 0 -6.01795 -0.158418 0 0 0 -0.324065 -7.22232 0 0 0 0 0.667987 0 0 1.00017 8.66857 -1.52916 0 -0.312051 0 0 0.506707 -0.143287 0 0 -2.56201 -2.77154 0 0 -0.537342 -11.0941 0 -1.29022 2.76894 -0.277586 0.796272 0.890361 0.341017 0 0.787035 -0.300377 -0.356484 -0.855919 0.32443 -1.06247 0 0 -0.397307 5.54335 0 -0.407508 -0.911793 -1.37427 0 0 0 0 0.867341 -0.994681 0 2.84811 -0.402481 0 0 0 -3.22735 0 2.45634 -10.0229 0 0.16544 -1.18401 -5.69172 0 1.26917 -4.56391 7.1909 -20.1025 0 0 0 0.241195 0.0639042 0 0 0 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3.18546 -8.01273 1.61338 11.0295 76.3328 -0.0272367 2.79981 -0.125313 0.996112 3.05001 -2.54373 0.515527 -0.715533 -0.0253005 -0.0908025 1.54838 -96.8991 -29.6753 25.7231 -7.83316 1.05908 3.90979 -3.21038 1.51359 -2.72086 8.64121 -0.735253 -0.303906 -0.082213 -0.461399 3.78221 0 diff --git a/examples/mliap/in.mliap.ace.compute b/examples/mliap/in.mliap.ace.compute new file mode 100644 index 0000000000..fa9a35da96 --- /dev/null +++ b/examples/mliap/in.mliap.ace.compute @@ -0,0 +1,25 @@ +#info all out log +units metal +atom_style atomic +boundary p p p +atom_modify map hash +read_data ace_compute_struct.data +mass 1 1.00 +mass 2 14.00 +mass 3 15.999 + +pair_style zero 5.7 +pair_coeff * * + + +compute ace all mliap descriptor ace H_N_O_ccs.yace model linear gradgradflag 1 +fix ace all ave/time 1 1 1 c_ace[*] file desc_out.dat mode vector + +thermo 1 +thermo_style custom & + pe pxy c_ace[1][1] c_ace[1][2] +thermo_modify norm no +run 0 + +uncompute ace +unfix ace diff --git a/examples/mliap/in.mliap.pytorch.ace b/examples/mliap/in.mliap.pytorch.ace new file mode 100644 index 0000000000..cc4363498f --- /dev/null +++ b/examples/mliap/in.mliap.pytorch.ace @@ -0,0 +1,54 @@ +# Demonstrate MLIAP/PyTorch interface to linear SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + +# choose potential + +pair_style mliap model mliappy Ta_ACE.mliap.pytorch.model.pt descriptor ace linear_ACE_ccs.yace +pair_coeff * * Ta + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} + diff --git a/examples/mliap/in.mliap.pytorch.ace.NN b/examples/mliap/in.mliap.pytorch.ace.NN new file mode 100644 index 0000000000..e99f7a4969 --- /dev/null +++ b/examples/mliap/in.mliap.pytorch.ace.NN @@ -0,0 +1,60 @@ +# Demonstrate MLIAP/PyTorch interface to linear ACE potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + +# choose potential + +pair_style mliap model mliappy ACE_NN_Pytorch.pt descriptor ace ccs_single_element.yace +pair_coeff * * Ta + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +# Uncomment dumps commands for visualization +#dump 0 all cfg 10 min.*.cfg mass type xs ys zs +#dump_modify 0 element Ta + +run ${nsteps} + diff --git a/examples/mliap/linear_ACE_ccs.yace b/examples/mliap/linear_ACE_ccs.yace new file mode 100644 index 0000000000..ca6043c8cd --- /dev/null +++ b/examples/mliap/linear_ACE_ccs.yace @@ -0,0 +1,150 @@ +elements: [Ta] +E0: [0.000000] +deltaSplineBins: 0.001000 +embeddings: + 0: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250} +bonds: + [0, 0]: {nradmax: 22, lmax: 5, nradbasemax: 22, radbasename: ChebExpCos, radparameters: [1.275], radcoefficients: [[[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0]], [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0]], [[0, 0, 0, 0, 0, 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2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [1, 3, 3], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [2, 2, 2], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [2, 2, 3], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [2, 3, 3], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [3, 3, 3], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]} + - {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 0], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]} diff --git a/examples/mliap/linear_ACE_coeff.acecoeff b/examples/mliap/linear_ACE_coeff.acecoeff new file mode 100644 index 0000000000..7d03528ea8 --- /dev/null +++ b/examples/mliap/linear_ACE_coeff.acecoeff @@ -0,0 +1,148 @@ +# FitSNAP generated on 2024-02-14 14:25:57.119062 with Hash: 25830dc0b45aefc59d0d17c55647440f + +1 142 +Ta + 0.0 # B[0] + -22.5771067833568999 # B[1, 0, 0, 1, 0] + -0.0226270954591753157 # B[2, 0, 0, 2, 0] + 21.0023473528220208 # B[3, 0, 0, 3, 0] + 1.7434645625400198 # B[4, 0, 0, 4, 0] + 0.113236864432865389 # B[5, 0, 0, 5, 0] + 5.43628451822269376 # B[6, 0, 0, 6, 0] + -2.36555723449260613 # B[7, 0, 0, 7, 0] + 0.0 # B[8, 0, 0, 8, 0] + 0.0 # B[9, 0, 0, 9, 0] + 0.0 # B[10, 0, 0, 10, 0] + 0.0 # B[11, 0, 0, 11, 0] + 0.0 # B[12, 0, 0, 12, 0] + 0.0 # B[13, 0, 0, 13, 0] + 0.0 # B[14, 0, 0, 14, 0] + 0.0 # B[15, 0, 0, 15, 0] + 0.0 # B[16, 0, 0, 16, 0] + 0.0 # B[17, 0, 0, 17, 0] + 0.0 # B[18, 0, 0, 18, 0] + 0.0 # B[19, 0, 0, 19, 0] + 0.0 # B[20, 0, 0, 20, 0] + 0.0 # B[21, 0, 0, 21, 0] + 0.0 # B[22, 0, 0, 22, 0] + 10.170453688417453 # B[23, 0, 0, 0, 1, 1, 0, 0] + -1044.76281713462254 # B[24, 0, 0, 0, 1, 2, 0, 0] + 572.709651057556016 # B[25, 0, 0, 0, 1, 3, 0, 0] + -207.396680818678306 # B[26, 0, 0, 0, 1, 4, 0, 0] + 32.7288559698408079 # B[27, 0, 0, 0, 1, 5, 0, 0] + 0.00305266310444371686 # B[28, 0, 0, 0, 2, 2, 0, 0] + 400.569893681083443 # B[29, 0, 0, 0, 2, 3, 0, 0] + 778.880194276356406 # B[30, 0, 0, 0, 2, 4, 0, 0] + 170.855019855882375 # B[31, 0, 0, 0, 2, 5, 0, 0] + -205.570286473228464 # B[32, 0, 0, 0, 3, 3, 0, 0] + -398.963313160853545 # B[33, 0, 0, 0, 3, 4, 0, 0] + -83.81056240085789 # B[34, 0, 0, 0, 3, 5, 0, 0] + 180.0562397293142 # B[35, 0, 0, 0, 4, 4, 0, 0] + -20.5002365523065428 # B[36, 0, 0, 0, 4, 5, 0, 0] + 0.0 # B[37, 0, 0, 0, 5, 5, 0, 0] + -24.8835644197873833 # B[38, 0, 0, 0, 1, 1, 1, 1] + 147.129769901050679 # B[39, 0, 0, 0, 1, 2, 1, 1] + 0.0713620917875858463 # B[40, 0, 0, 0, 1, 3, 1, 1] + -17.3833330953580933 # B[41, 0, 0, 0, 1, 4, 1, 1] + 37.5505432848029557 # B[42, 0, 0, 0, 1, 5, 1, 1] + 0.0191804654757119011 # B[43, 0, 0, 0, 2, 2, 1, 1] + -96.7487163459104664 # B[44, 0, 0, 0, 2, 3, 1, 1] + -0.00658154694809357909 # B[45, 0, 0, 0, 2, 4, 1, 1] + -208.124342352098012 # B[46, 0, 0, 0, 2, 5, 1, 1] + -0.0268971567040146194 # B[47, 0, 0, 0, 3, 3, 1, 1] + 8.21287123634444605 # B[48, 0, 0, 0, 3, 4, 1, 1] + 71.6589883121345395 # B[49, 0, 0, 0, 3, 5, 1, 1] + 17.6098825203311371 # B[50, 0, 0, 0, 4, 4, 1, 1] + -39.1469526467952562 # B[51, 0, 0, 0, 4, 5, 1, 1] + 0.0 # B[52, 0, 0, 0, 5, 5, 1, 1] + 2.81218558029911136 # B[53, 0, 0, 0, 1, 1, 2, 2] + -80.6108937358992534 # B[54, 0, 0, 0, 1, 2, 2, 2] + 25.3006460556791914 # B[55, 0, 0, 0, 1, 3, 2, 2] + -0.116123733569896734 # B[56, 0, 0, 0, 1, 4, 2, 2] + -8.10435957901752779 # B[57, 0, 0, 0, 1, 5, 2, 2] + 0.00593831884284745735 # B[58, 0, 0, 0, 2, 2, 2, 2] + 0.0206072280264136751 # B[59, 0, 0, 0, 2, 3, 2, 2] + 112.907541723710054 # B[60, 0, 0, 0, 2, 4, 2, 2] + -25.3781020910149273 # B[61, 0, 0, 0, 2, 5, 2, 2] + 15.4580129414526724 # B[62, 0, 0, 0, 3, 3, 2, 2] + -58.4875833673028822 # B[63, 0, 0, 0, 3, 4, 2, 2] + 27.8541236484384527 # B[64, 0, 0, 0, 3, 5, 2, 2] + 0.0 # B[65, 0, 0, 0, 4, 4, 2, 2] + 0.0 # B[66, 0, 0, 0, 4, 5, 2, 2] + 0.0 # B[67, 0, 0, 0, 5, 5, 2, 2] + 9.58210832281941371 # B[68, 0, 0, 0, 1, 1, 3, 3] + -33.4771846186537587 # B[69, 0, 0, 0, 1, 2, 3, 3] + -0.147879214073858095 # B[70, 0, 0, 0, 1, 3, 3, 3] + -0.983689688855974187 # B[71, 0, 0, 0, 1, 4, 3, 3] + -11.2679823588990811 # B[72, 0, 0, 0, 1, 5, 3, 3] + 189.312912024886742 # B[73, 0, 0, 0, 2, 2, 3, 3] + -0.0774443286916917523 # B[74, 0, 0, 0, 2, 3, 3, 3] + -0.102873783395946994 # B[75, 0, 0, 0, 2, 4, 3, 3] + -0.0756462323598340036 # B[76, 0, 0, 0, 2, 5, 3, 3] + -53.7511259632733953 # B[77, 0, 0, 0, 3, 3, 3, 3] + 33.9879339807403227 # B[78, 0, 0, 0, 3, 4, 3, 3] + 0.0 # B[79, 0, 0, 0, 3, 5, 3, 3] + -0.00814999871185459988 # B[80, 0, 0, 0, 4, 4, 3, 3] + 0.0 # B[81, 0, 0, 0, 4, 5, 3, 3] + 3.05035839717992552 # B[82, 0, 0, 0, 5, 5, 3, 3] + 1.76189504052993939 # B[83, 0, 0, 0, 1, 1, 4, 4] + -0.0109697500983353419 # B[84, 0, 0, 0, 1, 2, 4, 4] + -5.99440757040523309 # B[85, 0, 0, 0, 1, 3, 4, 4] + 0.116301402805795331 # B[86, 0, 0, 0, 1, 4, 4, 4] + 0.0 # B[87, 0, 0, 0, 1, 5, 4, 4] + 0.0172995235996694294 # B[88, 0, 0, 0, 2, 2, 4, 4] + -0.00135295336403791727 # B[89, 0, 0, 0, 2, 3, 4, 4] + -31.9743471589821553 # B[90, 0, 0, 0, 2, 4, 4, 4] + 11.6375525926016525 # B[91, 0, 0, 0, 2, 5, 4, 4] + 7.1785297948853044 # B[92, 0, 0, 0, 3, 3, 4, 4] + 12.9049178783604273 # B[93, 0, 0, 0, 3, 4, 4, 4] + 0.0173960354063151836 # B[94, 0, 0, 0, 3, 5, 4, 4] + -5.44937275307428326 # B[95, 0, 0, 0, 4, 4, 4, 4] + 0.0 # B[96, 0, 0, 0, 4, 5, 4, 4] + 0.0 # B[97, 0, 0, 0, 5, 5, 4, 4] + 0.0 # B[98, 0, 0, 0, 1, 1, 5, 5] + 10.7017857691284473 # B[99, 0, 0, 0, 1, 2, 5, 5] + 0.0 # B[100, 0, 0, 0, 1, 3, 5, 5] + -2.64659600238826176 # B[101, 0, 0, 0, 1, 4, 5, 5] + 0.0 # B[102, 0, 0, 0, 1, 5, 5, 5] + -360.963728954691078 # B[103, 0, 0, 0, 2, 2, 5, 5] + 180.302930506343245 # B[104, 0, 0, 0, 2, 3, 5, 5] + -0.0927167842886253007 # B[105, 0, 0, 0, 2, 4, 5, 5] + -54.9792205296734906 # B[106, 0, 0, 0, 2, 5, 5, 5] + 0.0622968474897991967 # B[107, 0, 0, 0, 3, 3, 5, 5] + -19.0759694688697401 # B[108, 0, 0, 0, 3, 4, 5, 5] + 26.6639152270046758 # B[109, 0, 0, 0, 3, 5, 5, 5] + 0.0 # B[110, 0, 0, 0, 4, 4, 5, 5] + -2.17726871628644325 # B[111, 0, 0, 0, 4, 5, 5, 5] + 0.0 # B[112, 0, 0, 0, 5, 5, 5, 5] + 4.41210696714003525 # B[113, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2] + 0.0497159733881680083 # B[114, 0, 0, 0, 0, 1, 1, 2, 1, 1, 2, 2] + 3.50516630159326947 # B[115, 0, 0, 0, 0, 1, 1, 3, 1, 1, 2, 2] + 14.6179669221722417 # B[116, 0, 0, 0, 0, 1, 2, 1, 1, 1, 2, 2] + 755.058663506306175 # B[117, 0, 0, 0, 0, 1, 2, 2, 1, 1, 2, 2] + -240.568322578754731 # B[118, 0, 0, 0, 0, 1, 2, 3, 1, 1, 2, 2] + 0.0488714570610267046 # B[119, 0, 0, 0, 0, 1, 3, 1, 1, 1, 2, 2] + -187.841135117587072 # B[120, 0, 0, 0, 0, 1, 3, 2, 1, 1, 2, 2] + 32.3758624271038684 # B[121, 0, 0, 0, 0, 1, 3, 3, 1, 1, 2, 2] + 118.101507848151186 # B[122, 0, 0, 0, 0, 2, 2, 1, 1, 1, 2, 2] + -0.0136264036603733017 # B[123, 0, 0, 0, 0, 2, 2, 2, 1, 1, 2, 2] + -226.591848522424016 # B[124, 0, 0, 0, 0, 2, 2, 3, 1, 1, 2, 2] + 0.0333288835492624586 # B[125, 0, 0, 0, 0, 2, 3, 1, 1, 1, 2, 2] + -0.0087547361274342983 # B[126, 0, 0, 0, 0, 2, 3, 2, 1, 1, 2, 2] + 0.0104057653307802946 # B[127, 0, 0, 0, 0, 2, 3, 3, 1, 1, 2, 2] + -25.2394489573255107 # B[128, 0, 0, 0, 0, 3, 3, 1, 1, 1, 2, 2] + -83.6076290271592057 # B[129, 0, 0, 0, 0, 3, 3, 2, 1, 1, 2, 2] + 80.3884647598460305 # B[130, 0, 0, 0, 0, 3, 3, 3, 1, 1, 2, 2] + -0.669731707137959487 # B[131, 0, 0, 0, 0, 1, 1, 1, 2, 2, 2, 2] + 0.0358960112501990058 # B[132, 0, 0, 0, 0, 1, 1, 2, 2, 2, 2, 2] + 0.613904373803016767 # B[133, 0, 0, 0, 0, 1, 1, 3, 2, 2, 2, 2] + 0.00183254800152801494 # B[134, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2] + 0.0722024283268215966 # B[135, 0, 0, 0, 0, 1, 2, 3, 2, 2, 2, 2] + 0.0 # B[136, 0, 0, 0, 0, 1, 3, 3, 2, 2, 2, 2] + -0.0365564305694157377 # B[137, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2] + 0.0114527487193957864 # B[138, 0, 0, 0, 0, 2, 2, 3, 2, 2, 2, 2] + 0.0 # B[139, 0, 0, 0, 0, 2, 3, 3, 2, 2, 2, 2] + 0.0 # B[140, 0, 0, 0, 0, 3, 3, 3, 2, 2, 2, 2] + 0.0 # B[141, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0] + +# End of potential \ No newline at end of file diff --git a/examples/mliap/log.03Mar24.mliap.ace.compute.g++.1 b/examples/mliap/log.03Mar24.mliap.ace.compute.g++.1 new file mode 100644 index 0000000000..9e5df53111 --- /dev/null +++ b/examples/mliap/log.03Mar24.mliap.ace.compute.g++.1 @@ -0,0 +1,83 @@ +LAMMPS (21 Nov 2023 - Development - e94d89ee3c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +#info all out log +units metal +atom_style atomic +boundary p p p +atom_modify map hash +read_data ace_compute_struct.data +Reading data file ... + orthogonal box = (0 0 0) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 161 atoms + read_data CPU = 0.010 seconds +mass 1 1.00 +mass 2 14.00 +mass 3 15.999 + +pair_style zero 5.7 +pair_coeff * * + + +compute ace all mliap descriptor ace H_N_O_ccs.yace model linear gradgradflag 1 +fix ace all ave/time 1 1 1 c_ace[*] file desc_out.dat mode vector + +thermo 1 +thermo_style custom pe pxy c_ace[1][1] c_ace[1][2] +thermo_modify norm no +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute mliap, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 128.7 | 128.7 | 128.7 Mbytes + PotEng Pxy c_ace[1][1] c_ace[1][2] + 0 0 110 633.5226 +Loop time of 1.931e-06 on 1 procs for 0 steps with 161 atoms + +155.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.931e-06 | | |100.00 + +Nlocal: 161 ave 161 max 161 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1754 ave 1754 max 1754 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 14230 ave 14230 max 14230 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 28460 ave 28460 max 28460 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 28460 +Ave neighs/atom = 176.77019 +Neighbor list builds = 0 +Dangerous builds = 0 + +uncompute ace +unfix ace +Total wall time: 0:00:00 diff --git a/examples/mliap/log.03Mar24.mliap.ace.compute.g++.4 b/examples/mliap/log.03Mar24.mliap.ace.compute.g++.4 new file mode 100644 index 0000000000..27341450cd --- /dev/null +++ b/examples/mliap/log.03Mar24.mliap.ace.compute.g++.4 @@ -0,0 +1,83 @@ +LAMMPS (21 Nov 2023 - Development - e94d89ee3c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +#info all out log +units metal +atom_style atomic +boundary p p p +atom_modify map hash +read_data ace_compute_struct.data +Reading data file ... + orthogonal box = (0 0 0) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 161 atoms + read_data CPU = 0.002 seconds +mass 1 1.00 +mass 2 14.00 +mass 3 15.999 + +pair_style zero 5.7 +pair_coeff * * + + +compute ace all mliap descriptor ace H_N_O_ccs.yace model linear gradgradflag 1 +fix ace all ave/time 1 1 1 c_ace[*] file desc_out.dat mode vector + +thermo 1 +thermo_style custom pe pxy c_ace[1][1] c_ace[1][2] +thermo_modify norm no +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute mliap, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 111 | 111.3 | 111.6 Mbytes + PotEng Pxy c_ace[1][1] c_ace[1][2] + 0 0 110 633.5226 +Loop time of 5.06375e-06 on 4 procs for 0 steps with 161 atoms + +64.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 5.064e-06 | | |100.00 + +Nlocal: 40.25 ave 44 max 35 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 1134.5 ave 1159 max 1117 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Neighs: 3557.5 ave 4115 max 3189 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +FullNghs: 7115 ave 7755 max 6158 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 28460 +Ave neighs/atom = 176.77019 +Neighbor list builds = 0 +Dangerous builds = 0 + +uncompute ace +unfix ace +Total wall time: 0:00:00 diff --git a/examples/mliap/log.03Mar24.mliap.pytorch.ace.NN.g++.1 b/examples/mliap/log.03Mar24.mliap.pytorch.ace.NN.g++.1 new file mode 100644 index 0000000000..1c72671b81 --- /dev/null +++ b/examples/mliap/log.03Mar24.mliap.pytorch.ace.NN.g++.1 @@ -0,0 +1,132 @@ +LAMMPS (21 Nov 2023 - Development - e94d89ee3c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate MLIAP/PyTorch interface to linear ACE potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# choose potential + +pair_style mliap model mliappy ACE_NN_Pytorch.pt descriptor ace ccs_single_element.yace +Loading python model complete. +pair_coeff * * Ta + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +# Uncomment dumps commands for visualization +#dump 0 all cfg 10 min.*.cfg mass type xs ys zs +#dump_modify 0 element Ta + +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.684 + ghost atom cutoff = 10.684 + binsize = 5.3419999, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3040 | 3040 | 3040 Mbytes + Step Temp E_pair c_energy TotEng Press v_press + 0 300 -10.799771 -10.799771 -10.761296 -124096.28 124096.28 + 10 297.05593 -10.799394 -10.799394 -10.761296 -124021.81 124021.81 + 20 293.90126 -10.798989 -10.798989 -10.761296 -123931.98 123931.98 + 30 290.75573 -10.798586 -10.798586 -10.761296 -123830.65 123830.65 + 40 287.87299 -10.798216 -10.798216 -10.761296 -123723.2 123723.2 + 50 285.52822 -10.797915 -10.797915 -10.761296 -123616.33 123616.33 + 60 283.89424 -10.806252 -10.806252 -10.769843 -123186.35 123186.35 + 70 283.0133 -10.814468 -10.814468 -10.778171 -122622.74 122622.74 + 80 283.82159 -10.850734 -10.850734 -10.814333 -121100.05 121100.05 + 90 285.70388 -10.87694 -10.87694 -10.840299 -119481.05 119481.05 + 100 289.39 -10.889368 -10.889368 -10.852253 -118417.49 118417.49 +Loop time of 5.22636 on 1 procs for 100 steps with 128 atoms + +Performance: 0.827 ns/day, 29.035 hours/ns, 19.134 timesteps/s, 2.449 katom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.2238 | 5.2238 | 5.2238 | 0.0 | 99.95 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00091245 | 0.00091245 | 0.00091245 | 0.0 | 0.02 +Output | 0.0010643 | 0.0010643 | 0.0010643 | 0.0 | 0.02 +Modify | 0.00019072 | 0.00019072 | 0.00019072 | 0.0 | 0.00 +Other | | 0.0003712 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2203 ave 2203 max 2203 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 36096 ave 36096 max 36096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36096 +Ave neighs/atom = 282 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:06 diff --git a/examples/mliap/log.03Mar24.mliap.pytorch.ace.NN.g++.4 b/examples/mliap/log.03Mar24.mliap.pytorch.ace.NN.g++.4 new file mode 100644 index 0000000000..4d9f41d34a --- /dev/null +++ b/examples/mliap/log.03Mar24.mliap.pytorch.ace.NN.g++.4 @@ -0,0 +1,132 @@ +LAMMPS (21 Nov 2023 - Development - e94d89ee3c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate MLIAP/PyTorch interface to linear ACE potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# choose potential + +pair_style mliap model mliappy ACE_NN_Pytorch.pt descriptor ace ccs_single_element.yace +Loading python model complete. +pair_coeff * * Ta + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +# Uncomment dumps commands for visualization +#dump 0 all cfg 10 min.*.cfg mass type xs ys zs +#dump_modify 0 element Ta + +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.684 + ghost atom cutoff = 10.684 + binsize = 5.3419999, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3029 | 3029 | 3029 Mbytes + Step Temp E_pair c_energy TotEng Press v_press + 0 300 -10.799771 -10.799771 -10.761296 -124096.28 124096.28 + 10 297.05593 -10.799394 -10.799394 -10.761296 -124021.81 124021.81 + 20 293.90126 -10.798989 -10.798989 -10.761296 -123931.98 123931.98 + 30 290.75573 -10.798586 -10.798586 -10.761296 -123830.65 123830.65 + 40 287.87299 -10.798216 -10.798216 -10.761296 -123723.2 123723.2 + 50 285.52822 -10.797915 -10.797915 -10.761296 -123616.33 123616.33 + 60 283.89424 -10.806252 -10.806252 -10.769843 -123186.35 123186.35 + 70 283.0133 -10.814468 -10.814468 -10.778171 -122622.74 122622.74 + 80 283.82159 -10.850734 -10.850734 -10.814333 -121100.05 121100.05 + 90 285.70388 -10.87694 -10.87694 -10.840299 -119481.05 119481.05 + 100 289.39 -10.889368 -10.889368 -10.852253 -118417.49 118417.49 +Loop time of 1.42477 on 4 procs for 100 steps with 128 atoms + +Performance: 3.032 ns/day, 7.915 hours/ns, 70.187 timesteps/s, 8.984 katom-step/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3575 | 1.3845 | 1.4057 | 1.7 | 97.17 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.016517 | 0.03758 | 0.064384 | 10.0 | 2.64 +Output | 0.0016464 | 0.0016915 | 0.0017802 | 0.1 | 0.12 +Modify | 0.00010363 | 0.00011648 | 0.00012936 | 0.0 | 0.01 +Other | | 0.0008911 | | | 0.06 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1499 ave 1499 max 1499 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 9024 ave 9024 max 9024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36096 +Ave neighs/atom = 282 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/mliap/log.03Mar24.mliap.pytorch.ace.g++.1 b/examples/mliap/log.03Mar24.mliap.pytorch.ace.g++.1 new file mode 100644 index 0000000000..83461ddad4 --- /dev/null +++ b/examples/mliap/log.03Mar24.mliap.pytorch.ace.g++.1 @@ -0,0 +1,126 @@ +LAMMPS (21 Nov 2023 - Development - e94d89ee3c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate MLIAP/PyTorch interface to linear SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# choose potential + +pair_style mliap model mliappy Ta_ACE.mliap.pytorch.model.pt descriptor ace linear_ACE_ccs.yace +Loading python model complete. +pair_coeff * * Ta + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.62 + ghost atom cutoff = 10.62 + binsize = 5.3099999, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 69.54 | 69.54 | 69.54 Mbytes + Step Temp E_pair c_energy TotEng Press v_press + 0 300 -10.649822 -10.649822 -10.611347 -149369.7 149369.7 + 10 301.54363 -10.65002 -10.65002 -10.611347 -149189.04 149189.04 + 20 310.2497 -10.651137 -10.651137 -10.611347 -148663.85 148663.85 + 30 325.56462 -10.653101 -10.653101 -10.611347 -147792.6 147792.6 + 40 346.54011 -10.655791 -10.655791 -10.611347 -146568.54 146568.54 + 50 371.896 -10.659043 -10.659043 -10.611348 -144972.13 144972.13 + 60 400.11547 -10.662663 -10.662663 -10.611348 -143011.4 143011.4 + 70 429.4367 -10.666423 -10.666423 -10.611348 -140773.79 140773.79 + 80 457.62121 -10.685721 -10.685721 -10.627031 -137496.07 137496.07 + 90 481.87191 -10.697719 -10.697719 -10.635919 -133888.57 133888.57 + 100 500.38073 -10.708101 -10.708101 -10.643927 -130768.99 130768.99 +Loop time of 94.0137 on 1 procs for 100 steps with 128 atoms + +Performance: 0.046 ns/day, 522.299 hours/ns, 1.064 timesteps/s, 136.150 atom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 94.01 | 94.01 | 94.01 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0011604 | 0.0011604 | 0.0011604 | 0.0 | 0.00 +Output | 0.0011648 | 0.0011648 | 0.0011648 | 0.0 | 0.00 +Modify | 0.00031951 | 0.00031951 | 0.00031951 | 0.0 | 0.00 +Other | | 0.0007277 | | | 0.00 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2203 ave 2203 max 2203 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 36096 ave 36096 max 36096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36096 +Ave neighs/atom = 282 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:01:36 diff --git a/examples/mliap/log.03Mar24.mliap.pytorch.ace.g++.4 b/examples/mliap/log.03Mar24.mliap.pytorch.ace.g++.4 new file mode 100644 index 0000000000..b50f4e79bf --- /dev/null +++ b/examples/mliap/log.03Mar24.mliap.pytorch.ace.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (21 Nov 2023 - Development - e94d89ee3c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate MLIAP/PyTorch interface to linear SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# choose potential + +pair_style mliap model mliappy Ta_ACE.mliap.pytorch.model.pt descriptor ace linear_ACE_ccs.yace +Loading python model complete. +pair_coeff * * Ta + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.62 + ghost atom cutoff = 10.62 + binsize = 5.3099999, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 58.24 | 58.24 | 58.24 Mbytes + Step Temp E_pair c_energy TotEng Press v_press + 0 300 -10.649822 -10.649822 -10.611347 -149369.7 149369.7 + 10 301.54363 -10.65002 -10.65002 -10.611347 -149189.04 149189.04 + 20 310.2497 -10.651137 -10.651137 -10.611347 -148663.85 148663.85 + 30 325.56462 -10.653101 -10.653101 -10.611347 -147792.6 147792.6 + 40 346.54011 -10.655791 -10.655791 -10.611347 -146568.54 146568.54 + 50 371.896 -10.659043 -10.659043 -10.611348 -144972.13 144972.13 + 60 400.11547 -10.662663 -10.662663 -10.611348 -143011.4 143011.4 + 70 429.4367 -10.666423 -10.666423 -10.611348 -140773.79 140773.79 + 80 457.62121 -10.685721 -10.685721 -10.627031 -137496.07 137496.07 + 90 481.87191 -10.697719 -10.697719 -10.635919 -133888.57 133888.57 + 100 500.38073 -10.708101 -10.708101 -10.643927 -130768.99 130768.99 +Loop time of 24.6242 on 4 procs for 100 steps with 128 atoms + +Performance: 0.175 ns/day, 136.801 hours/ns, 4.061 timesteps/s, 519.813 atom-step/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 23.421 | 24.105 | 24.588 | 8.7 | 97.89 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.032393 | 0.51582 | 1.1996 | 59.7 | 2.09 +Output | 0.0020103 | 0.0020589 | 0.0021633 | 0.1 | 0.01 +Modify | 0.00021557 | 0.00023585 | 0.00025912 | 0.0 | 0.00 +Other | | 0.001166 | | | 0.00 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1499 ave 1499 max 1499 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 9024 ave 9024 max 9024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36096 +Ave neighs/atom = 282 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:26 diff --git a/examples/mliap/mliap_pytorch_ACE.py b/examples/mliap/mliap_pytorch_ACE.py new file mode 100644 index 0000000000..7c98b90054 --- /dev/null +++ b/examples/mliap/mliap_pytorch_ACE.py @@ -0,0 +1,97 @@ +# Demonstrate how to load a model from the python side. +# This is essentially the same as in.mliap.pytorch.MOF +# except that python is the driving program, and lammps +# is in library mode. +before_loading =\ +"""# Demonstrate MLIAP/PyTorch interface to torch model + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + +# define potential with LATER mliappy + + +pair_style mliap model mliappy LATER descriptor ace ccs_single_element.yace +pair_coeff * * Ta + +""" +after_loading =\ +""" + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run +dump 1 all cfg 10 ats.*.cfg mass type xs ys zs +dump_modify 1 element Ta + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +""" +import lammps + +lmp = lammps.lammps(cmdargs=['-echo','both']) + +# Before defining the pair style, one must do the following: +import lammps.mliap +lammps.mliap.activate_mliappy(lmp) +# Otherwise, when running lammps in library mode, +# you will get an error: +# "ERROR: Loading MLIAPPY coupling module failure." + +# Setup the simulation and declare an empty model +# by specifying model filename as "LATER" +lmp.commands_string(before_loading) + +# Define the model however you like. In this example +# we load it from disk: +import os +import torch +torch_model = 'ACE_NN_Pytorch.pt' +if not os.path.exists(torch_model): + raise FileNotFoundError(f"Generate {torch_model} first") +model = torch.load(torch_model) + +# Connect the PyTorch model to the mliap pair style. +lammps.mliap.load_model(model) + +# run the simulation with the mliap pair style +lmp.commands_string(after_loading) +lmp.close() +lmp.finalize() diff --git a/examples/rdf-adf/in.spce b/examples/rdf-adf/in.spce index 9a9d99fd42..6627924adc 100644 --- a/examples/rdf-adf/in.spce +++ b/examples/rdf-adf/in.spce @@ -1,22 +1,22 @@ # Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom) -units real -atom_style full +units real +atom_style full -read_data data.spce +read_data data.spce pair_style lj/cut/coul/long 12.0 12.0 pair_coeff * * 0.0 1.0 pair_coeff 1 1 0.15535 3.166 -kspace_style pppm 1.0e-6 +kspace_style pppm 1.0e-6 -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 # need to set bond/angle inclusion to > 0.0 # so that intramolecular pairs are included in neighbor lists (required for second ADF) @@ -26,8 +26,8 @@ neighbor 2.0 bin timestep 2.0 neigh_modify every 1 delay 2 check yes -fix 1 all shake 0.0001 20 0 b 1 a 1 -fix 2 all nvt temp 300.0 300.0 100.0 +fix 1 all shake 0.0001 20 0 b 1 a 1 +fix 2 all nvt temp 300.0 300.0 100.0 velocity all create 300.0 6244325 diff --git a/examples/replicate/README b/examples/replicate/README new file mode 100644 index 0000000000..e33739672c --- /dev/null +++ b/examples/replicate/README @@ -0,0 +1,32 @@ +This directory has input scripts which demonstrate how to use the +replicate command both for systems with and without periodic bond +loops. A periodic bond loop is where a chain of bonds spans a +periodic dimension of the box and includes one or more bonds which +cross the periodic boundary to close the loop. + +To run these scripts, LAMMPS should be built with the MOLECULE and +CLASS2 packages. The latter is only needed for the CNT example. + +-------- + +These scripts are tiny examples which illustrate both kinds of +systems. Each produces a series of images which can be visualized. +If the 3 lines for a dump movie command are uncommented, a MPG movie +is produced, assuming LAMMPS is build with FFMPEG support. + +in.replicate.bond.x # linear chains in x direction, bond loop in x +in.replcate.bond.x.y # 2d grid of bonded atoms, bond loops in x and y +in.replicate.bond.xy # linear chains in diagonal direction, bond loop in x and y +in.replicate.bond.noloop # linear chains in x direction, no bond loop + +If you do not use the bond/periodic keyword with the replicate command +in the first 3 of these scripts (which have periodic bond loops), and +visualize the dynamics of hee simulation, you will see how the +replication creates a bogus system. + +-------- + +This script is for a complex system of 3 orthogonal CNTs which has +periodic bond loops in all 3 dimensions xyz. + +in.replicate.cnt diff --git a/examples/replicate/data.bond.x b/examples/replicate/data.bond.x new file mode 100644 index 0000000000..b5f4d49f2d --- /dev/null +++ b/examples/replicate/data.bond.x @@ -0,0 +1,22 @@ +# system with periodic bonds in x + +3 atoms +3 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 1 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 +2 1 1 1.5 0.5 0 +3 1 1 2.5 0.5 0 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 1 diff --git a/examples/replicate/data.bond.x.noloop b/examples/replicate/data.bond.x.noloop new file mode 100644 index 0000000000..4c096724be --- /dev/null +++ b/examples/replicate/data.bond.x.noloop @@ -0,0 +1,21 @@ +# system with non-periodic bonds in x + +3 atoms +2 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 1 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 0 0 0 +2 1 1 1.5 0.5 0 0 0 0 +3 1 1 2.5 0.5 0 -1 0 0 + +Bonds + +1 1 1 2 +2 1 3 1 diff --git a/examples/replicate/data.bond.x.y b/examples/replicate/data.bond.x.y new file mode 100644 index 0000000000..7eaf19a2ae --- /dev/null +++ b/examples/replicate/data.bond.x.y @@ -0,0 +1,43 @@ +# system with periodic bonds in both x and y + +9 atoms +18 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 3 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 +2 1 1 1.5 0.5 0 +3 1 1 2.5 0.5 0 +4 1 1 0.5 1.5 0 +5 1 1 1.5 1.5 0 +6 1 1 2.5 1.5 0 +7 1 1 0.5 2.5 0 +8 1 1 1.5 2.5 0 +9 1 1 2.5 2.5 0 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 1 +4 1 4 5 +5 1 5 6 +6 1 6 4 +7 1 7 8 +8 1 8 9 +9 1 9 7 +10 1 1 4 +11 1 4 7 +12 1 7 1 +13 1 2 5 +14 1 5 8 +15 1 8 2 +16 1 3 6 +17 1 6 9 +18 1 9 3 diff --git a/examples/replicate/data.bond.xy b/examples/replicate/data.bond.xy new file mode 100644 index 0000000000..31e9d8785a --- /dev/null +++ b/examples/replicate/data.bond.xy @@ -0,0 +1,22 @@ +# system with periodic bonds in xy direction + +3 atoms +3 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 3 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 +2 1 1 1.5 1.5 0 +3 1 1 2.5 2.5 0 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 1 diff --git a/examples/replicate/in.replicate.bond.x b/examples/replicate/in.replicate.bond.x new file mode 100644 index 0000000000..868e05f177 --- /dev/null +++ b/examples/replicate/in.replicate.bond.x @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.x + +dump 1 all image 100 tmp.image.x.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate.bond.x.noloop b/examples/replicate/in.replicate.bond.x.noloop new file mode 100644 index 0000000000..b9862f844d --- /dev/null +++ b/examples/replicate/in.replicate.bond.x.noloop @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x.noloop + +replicate 3 3 1 +#replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.001 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.x.non + +dump 1 all image 100 tmp.image.x.non.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.non.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate.bond.x.y b/examples/replicate/in.replicate.bond.x.y new file mode 100644 index 0000000000..100350dc18 --- /dev/null +++ b/examples/replicate/in.replicate.bond.x.y @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in both x and y + +dimension 2 +atom_style molecular + +read_data data.bond.x.y + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.x.y + +dump 1 all image 100 tmp.image.x.y.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.y.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate.bond.xy b/examples/replicate/in.replicate.bond.xy new file mode 100644 index 0000000000..52ca79ace7 --- /dev/null +++ b/examples/replicate/in.replicate.bond.xy @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in xy diagonal direction + +dimension 2 +atom_style molecular + +read_data data.bond.xy + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.5 + +bond_style harmonic +bond_coeff 1 50.0 1.414 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.xy + +dump 1 all image 100 tmp.image.xy.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.xy.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate.cnt b/examples/replicate/in.replicate.cnt new file mode 100644 index 0000000000..0b8b384bbb --- /dev/null +++ b/examples/replicate/in.replicate.cnt @@ -0,0 +1,32 @@ +# three orthogonal periodic CNTs +# demo for replicating triply looped system +# infinite loops in x, y, z +# includes bonded interactions across box corners +# includes bonds, angles, dihedrals, impropers (class2) + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 10 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data three_periodic_CNTs.data.gz + +replicate 2 2 2 bond/periodic + +fix 1 all nve + +run 100 + +# write_restart replicate.restart +# write_data replicate.data diff --git a/examples/replicate/log.6May24.replicate.bond.x.g++.1 b/examples/replicate/log.6May24.replicate.bond.x.g++.1 new file mode 100644 index 0000000000..3f65d11c15 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 1 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 9.00 out of 9 (100.00%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.302 | 6.302 | 6.302 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1057636 9.028122 + 5000 0.54111971 -1.9054641 0.29066874 -1.0937172 3.4346743 +Loop time of 0.0764878 on 1 procs for 5000 steps with 27 atoms + +Performance: 28239805.842 tau/day, 65369.921 timesteps/s, 1.765 Matom-step/s +66.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0048837 | 0.0048837 | 0.0048837 | 0.0 | 6.38 +Bond | 0.00065879 | 0.00065879 | 0.00065879 | 0.0 | 0.86 +Neigh | 0.0019897 | 0.0019897 | 0.0019897 | 0.0 | 2.60 +Comm | 0.0012815 | 0.0012815 | 0.0012815 | 0.0 | 1.68 +Output | 0.066351 | 0.066351 | 0.066351 | 0.0 | 86.75 +Modify | 0.00069789 | 0.00069789 | 0.00069789 | 0.0 | 0.91 +Other | | 0.0006247 | | | 0.82 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 108 ave 108 max 108 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 284 ave 284 max 284 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 284 +Ave neighs/atom = 10.518519 +Ave special neighs/atom = 2 +Neighbor list builds = 287 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.g++.4 b/examples/replicate/log.6May24.replicate.bond.x.g++.4 new file mode 100644 index 0000000000..9e4423d5f6 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 4 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 5.25 out of 9 (58.33%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.002 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1057636 9.028122 + 5000 0.50911963 -1.7968226 0.21209852 -1.0944607 4.1676488 +Loop time of 0.21682 on 4 procs for 5000 steps with 27 atoms + +Performance: 9962160.612 tau/day, 23060.557 timesteps/s, 622.635 katom-step/s +93.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.001787 | 0.0021247 | 0.0028772 | 1.0 | 0.98 +Bond | 0.00039682 | 0.00045617 | 0.00059887 | 0.0 | 0.21 +Neigh | 0.0013626 | 0.0014006 | 0.0014798 | 0.1 | 0.65 +Comm | 0.017009 | 0.01791 | 0.018656 | 0.5 | 8.26 +Output | 0.06892 | 0.12188 | 0.18918 | 13.7 | 56.21 +Modify | 0.00060336 | 0.00072159 | 0.00088047 | 0.0 | 0.33 +Other | | 0.07233 | | | 33.36 + +Nlocal: 6.75 ave 7 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 64.5 ave 65 max 63 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 70.25 ave 77 max 60 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 281 +Ave neighs/atom = 10.407407 +Ave special neighs/atom = 2 +Neighbor list builds = 287 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 new file mode 100644 index 0000000000..54893b449a --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 @@ -0,0 +1,121 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x.non +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +replicate 3 3 1 +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 1 by 1 by 1 MPI processor grid + 27 atoms + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds +#replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.001 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.non +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.non.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.non.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 6.052 | 6.052 | 6.052 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.001 -1.1250229 0 -1.1240599 13.009826 + 5000 0.62003692 -2.0147214 0.30861545 -1.1090334 8.0279226 +Loop time of 0.0734456 on 1 procs for 5000 steps with 27 atoms + +Performance: 29409520.548 tau/day, 68077.594 timesteps/s, 1.838 Matom-step/s +94.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0051444 | 0.0051444 | 0.0051444 | 0.0 | 7.00 +Bond | 0.00048789 | 0.00048789 | 0.00048789 | 0.0 | 0.66 +Neigh | 0.0019333 | 0.0019333 | 0.0019333 | 0.0 | 2.63 +Comm | 0.001332 | 0.001332 | 0.001332 | 0.0 | 1.81 +Output | 0.063139 | 0.063139 | 0.063139 | 0.0 | 85.97 +Modify | 0.00077014 | 0.00077014 | 0.00077014 | 0.0 | 1.05 +Other | | 0.0006387 | | | 0.87 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 101 ave 101 max 101 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 288 ave 288 max 288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 288 +Ave neighs/atom = 10.666667 +Ave special neighs/atom = 1.3333333 +Neighbor list builds = 322 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.4 b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.4 new file mode 100644 index 0000000000..54d9741781 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.4 @@ -0,0 +1,122 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x.non +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading bonds ... + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +replicate 3 3 1 +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 4 by 1 by 1 MPI processor grid + 27 atoms + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.002 seconds +#replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.001 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.non +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.non.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.non.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 6.059 | 6.059 | 6.059 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.001 -1.1250229 0 -1.1240599 13.009826 + 5000 0.74931971 -2.233724 0.40158766 -1.1105692 5.6354701 +Loop time of 0.197835 on 4 procs for 5000 steps with 27 atoms + +Performance: 10918214.594 tau/day, 25273.645 timesteps/s, 682.388 katom-step/s +88.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0018771 | 0.0021131 | 0.0027188 | 0.8 | 1.07 +Bond | 0.00032659 | 0.00038248 | 0.00049555 | 0.0 | 0.19 +Neigh | 0.001385 | 0.0014211 | 0.0014704 | 0.1 | 0.72 +Comm | 0.017163 | 0.017405 | 0.017805 | 0.2 | 8.80 +Output | 0.070971 | 0.11052 | 0.17112 | 12.1 | 55.87 +Modify | 0.00058993 | 0.00067708 | 0.00075608 | 0.0 | 0.34 +Other | | 0.06532 | | | 33.02 + +Nlocal: 6.75 ave 7 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 59.75 ave 60 max 59 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 72 ave 79 max 63 min +Histogram: 1 0 0 0 0 0 2 0 0 1 + +Total # of neighbors = 288 +Ave neighs/atom = 10.666667 +Ave special neighs/atom = 1.3333333 +Neighbor list builds = 323 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.y.g++.1 b/examples/replicate/log.6May24.replicate.bond.x.y.g++.1 new file mode 100644 index 0000000000..45308d9a90 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.y.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in both x and y + +dimension 2 +atom_style molecular + +read_data data.bond.x.y +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 9 atoms + scanning bonds ... + 2 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 8 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 1 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 9.00 out of 9 (100.00%) + 81 atoms + 162 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 4 = max # of 1-2 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.y +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.y.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.y.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 7.555 | 7.555 | 7.555 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1052698 -2.9713842 + 5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897 +Loop time of 0.212344 on 1 procs for 5000 steps with 81 atoms + +Performance: 10172161.526 tau/day, 23546.670 timesteps/s, 1.907 Matom-step/s +93.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.01283 | 0.01283 | 0.01283 | 0.0 | 6.04 +Bond | 0.0032785 | 0.0032785 | 0.0032785 | 0.0 | 1.54 +Neigh | 0.0018379 | 0.0018379 | 0.0018379 | 0.0 | 0.87 +Comm | 0.0016247 | 0.0016247 | 0.0016247 | 0.0 | 0.77 +Output | 0.18991 | 0.18991 | 0.18991 | 0.0 | 89.44 +Modify | 0.0018198 | 0.0018198 | 0.0018198 | 0.0 | 0.86 +Other | | 0.001039 | | | 0.49 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 144 ave 144 max 144 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 714 ave 714 max 714 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 714 +Ave neighs/atom = 8.8148148 +Ave special neighs/atom = 4 +Neighbor list builds = 72 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.y.g++.4 b/examples/replicate/log.6May24.replicate.bond.x.y.g++.4 new file mode 100644 index 0000000000..f232a4e428 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.y.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in both x and y + +dimension 2 +atom_style molecular + +read_data data.bond.x.y +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 9 atoms + scanning bonds ... + 2 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading bonds ... + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 8 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 2 by 2 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 6.25 out of 9 (69.44%) + 81 atoms + 162 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 4 = max # of 1-2 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.y +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.y.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.y.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.552 | 7.552 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1052698 -2.9713842 + 5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897 +Loop time of 0.273847 on 4 procs for 5000 steps with 81 atoms + +Performance: 7887622.810 tau/day, 18258.386 timesteps/s, 1.479 Matom-step/s +92.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0039465 | 0.0042593 | 0.0046129 | 0.4 | 1.56 +Bond | 0.0011489 | 0.001207 | 0.0012757 | 0.2 | 0.44 +Neigh | 0.00079819 | 0.0008044 | 0.00081324 | 0.0 | 0.29 +Comm | 0.024107 | 0.024703 | 0.025269 | 0.3 | 9.02 +Output | 0.14406 | 0.18123 | 0.23779 | 8.7 | 66.18 +Modify | 0.00089401 | 0.00095321 | 0.0010422 | 0.0 | 0.35 +Other | | 0.06069 | | | 22.16 + +Nlocal: 20.25 ave 22 max 19 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 81.5 ave 82 max 80 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 178.5 ave 195 max 165 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 714 +Ave neighs/atom = 8.8148148 +Ave special neighs/atom = 4 +Neighbor list builds = 72 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.xy.g++.1 b/examples/replicate/log.6May24.replicate.bond.xy.g++.1 new file mode 100644 index 0000000000..207b65ef9b --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.xy.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in xy diagonal direction + +dimension 2 +atom_style molecular + +read_data data.bond.xy +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 1 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 9.00 out of 9 (100.00%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.5 + +bond_style harmonic +bond_coeff 1 50.0 1.414 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.xy +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.xy.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.xy.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.302 | 6.302 | 6.302 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -0.66256987 2.2804444e-06 -0.64330834 -0.59475371 + 5000 0.43110862 -1.1484506 0.16888799 -0.56442095 -0.3683968 +Loop time of 0.124095 on 1 procs for 5000 steps with 27 atoms + +Performance: 17406010.885 tau/day, 40291.692 timesteps/s, 1.088 Matom-step/s +82.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0013734 | 0.0013734 | 0.0013734 | 0.0 | 1.11 +Bond | 0.00064058 | 0.00064058 | 0.00064058 | 0.0 | 0.52 +Neigh | 0.00090424 | 0.00090424 | 0.00090424 | 0.0 | 0.73 +Comm | 0.00081732 | 0.00081732 | 0.00081732 | 0.0 | 0.66 +Output | 0.11905 | 0.11905 | 0.11905 | 0.0 | 95.93 +Modify | 0.0007252 | 0.0007252 | 0.0007252 | 0.0 | 0.58 +Other | | 0.0005888 | | | 0.47 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 66 ave 66 max 66 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 66 +Ave neighs/atom = 2.4444444 +Ave special neighs/atom = 2 +Neighbor list builds = 244 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.xy.g++.4 b/examples/replicate/log.6May24.replicate.bond.xy.g++.4 new file mode 100644 index 0000000000..a8ef944ec7 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.xy.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in xy diagonal direction + +dimension 2 +atom_style molecular + +read_data data.bond.xy +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 2 by 2 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 6.25 out of 9 (69.44%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.5 + +bond_style harmonic +bond_coeff 1 50.0 1.414 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.xy +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.xy.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.xy.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.301 | 6.301 | 6.301 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -0.66256988 2.2804444e-06 -0.64330834 -0.59475371 + 5000 0.43110877 -1.1484507 0.168888 -0.56442093 -0.36839692 +Loop time of 0.286423 on 4 procs for 5000 steps with 27 atoms + +Performance: 7541285.935 tau/day, 17456.680 timesteps/s, 471.330 katom-step/s +92.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00054941 | 0.00084836 | 0.0013689 | 0.0 | 0.30 +Bond | 0.00034068 | 0.00045816 | 0.00068461 | 0.0 | 0.16 +Neigh | 0.00092076 | 0.00098494 | 0.0010463 | 0.0 | 0.34 +Comm | 0.018151 | 0.018737 | 0.019531 | 0.4 | 6.54 +Output | 0.13261 | 0.19363 | 0.2596 | 10.7 | 67.60 +Modify | 0.00053153 | 0.00071381 | 0.0010268 | 0.0 | 0.25 +Other | | 0.07105 | | | 24.81 + +Nlocal: 6.75 ave 9 max 5 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 26.25 ave 28 max 25 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 16.5 ave 23 max 10 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 66 +Ave neighs/atom = 2.4444444 +Ave special neighs/atom = 2 +Neighbor list builds = 244 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.cnt.g++.1 b/examples/replicate/log.6May24.replicate.cnt.g++.1 new file mode 100644 index 0000000000..f44032e723 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.cnt.g++.1 @@ -0,0 +1,134 @@ +LAMMPS (17 Apr 2024) +# three orthogonal periodic CNTs +# demo for replicating triply looped system +# infinite loops in x, y, z +# includes bonded interactions across box corners +# includes bonds, angles, dihedrals, impropers (class2) + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 10 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data three_periodic_CNTs.data.gz +Reading data file ... + orthogonal box = (0 0 0) to (80.96 80.96 80.96) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3168 atoms + reading velocities ... + 3168 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 3 = max angles/atom + scanning dihedrals ... + 12 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + orthogonal box = (0 0 0) to (80.96 80.96 80.96) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 4752 bonds + reading angles ... + 9504 angles + reading dihedrals ... + 19008 dihedrals + reading impropers ... + 3168 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 18 = max # of 1-4 neighbors + 18 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.056 seconds + +replicate 2 2 2 bond/periodic +Replication is creating a 2x2x2 = 8 times larger system... + orthogonal box = (0 0 0) to (161.92 161.92 161.92) + 1 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 1.62 MB + average # of replicas added to proc = 8.00 out of 8 (100.00%) + 25344 atoms + 38016 bonds + 76032 angles + 152064 dihedrals + 25344 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 18 = max # of 1-4 neighbors + 18 = max # of special neighbors + special bonds CPU = 0.012 seconds + replicate CPU = 0.027 seconds + +fix 1 all nve + +run 100 +Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 27 27 27 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/class2, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 51.87 | 51.87 | 51.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -14266.189 1466925.5 1452659.3 -29908.753 + 100 2155.9128 -17224.188 1306769.8 1452409 1985.2082 +Loop time of 5.0155 on 1 procs for 100 steps with 25344 atoms + +Performance: 1.723 ns/day, 13.932 hours/ns, 19.938 timesteps/s, 505.314 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6557 | 1.6557 | 1.6557 | 0.0 | 33.01 +Bond | 3.2813 | 3.2813 | 3.2813 | 0.0 | 65.42 +Neigh | 0.047025 | 0.047025 | 0.047025 | 0.0 | 0.94 +Comm | 0.0085317 | 0.0085317 | 0.0085317 | 0.0 | 0.17 +Output | 7.8551e-05 | 7.8551e-05 | 7.8551e-05 | 0.0 | 0.00 +Modify | 0.014635 | 0.014635 | 0.014635 | 0.0 | 0.29 +Other | | 0.008159 | | | 0.16 + +Nlocal: 25344 ave 25344 max 25344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 22737 ave 22737 max 22737 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.89358e+06 ave 2.89358e+06 max 2.89358e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2893576 +Ave neighs/atom = 114.17203 +Ave special neighs/atom = 18 +Neighbor list builds = 1 +Dangerous builds = 0 + +# write_restart replicate.restart +# write_data replicate.data +Total wall time: 0:00:05 diff --git a/examples/replicate/log.6May24.replicate.cnt.g++.4 b/examples/replicate/log.6May24.replicate.cnt.g++.4 new file mode 100644 index 0000000000..57abdf767d --- /dev/null +++ b/examples/replicate/log.6May24.replicate.cnt.g++.4 @@ -0,0 +1,135 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# three orthogonal periodic CNTs +# demo for replicating triply looped system +# infinite loops in x, y, z +# includes bonded interactions across box corners +# includes bonds, angles, dihedrals, impropers (class2) + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 10 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data three_periodic_CNTs.data.gz +Reading data file ... + orthogonal box = (0 0 0) to (80.96 80.96 80.96) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3168 atoms + reading velocities ... + 3168 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 3 = max angles/atom + scanning dihedrals ... + 12 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + orthogonal box = (0 0 0) to (80.96 80.96 80.96) + 1 by 2 by 2 MPI processor grid + reading bonds ... + 4752 bonds + reading angles ... + 9504 angles + reading dihedrals ... + 19008 dihedrals + reading impropers ... + 3168 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 18 = max # of 1-4 neighbors + 18 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.064 seconds + +replicate 2 2 2 bond/periodic +Replication is creating a 2x2x2 = 8 times larger system... + orthogonal box = (0 0 0) to (161.92 161.92 161.92) + 1 by 2 by 2 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 1.62 MB + average # of replicas added to proc = 4.50 out of 8 (56.25%) + 25344 atoms + 38016 bonds + 76032 angles + 152064 dihedrals + 25344 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 18 = max # of 1-4 neighbors + 18 = max # of special neighbors + special bonds CPU = 0.004 seconds + replicate CPU = 0.012 seconds + +fix 1 all nve + +run 100 +Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 27 27 27 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/class2, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 28.69 | 28.69 | 28.69 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -14266.189 1466925.5 1452659.3 -29908.753 + 100 2155.9128 -17224.188 1306769.8 1452409 1985.2082 +Loop time of 1.3667 on 4 procs for 100 steps with 25344 atoms + +Performance: 6.322 ns/day, 3.796 hours/ns, 73.169 timesteps/s, 1.854 Matom-step/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.43424 | 0.43539 | 0.43741 | 0.2 | 31.86 +Bond | 0.88613 | 0.89013 | 0.90094 | 0.7 | 65.13 +Neigh | 0.013198 | 0.013199 | 0.013201 | 0.0 | 0.97 +Comm | 0.010742 | 0.020522 | 0.02546 | 4.1 | 1.50 +Output | 3.2788e-05 | 3.6302e-05 | 4.4556e-05 | 0.0 | 0.00 +Modify | 0.0042029 | 0.0042366 | 0.004267 | 0.0 | 0.31 +Other | | 0.003188 | | | 0.23 + +Nlocal: 6336 ave 6336 max 6336 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 10558 ave 10558 max 10558 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 723394 ave 723394 max 723394 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2893576 +Ave neighs/atom = 114.17203 +Ave special neighs/atom = 18 +Neighbor list builds = 1 +Dangerous builds = 0 + +# write_restart replicate.restart +# write_data replicate.data +Total wall time: 0:00:01 diff --git a/examples/replicate/three_periodic_CNTs.data.gz b/examples/replicate/three_periodic_CNTs.data.gz new file mode 100644 index 0000000000..718c91896a Binary files /dev/null and b/examples/replicate/three_periodic_CNTs.data.gz differ diff --git a/examples/triclinic/README b/examples/triclinic/README new file mode 100644 index 0000000000..c68bd709ac --- /dev/null +++ b/examples/triclinic/README @@ -0,0 +1,110 @@ +* Various input scripts for systems with general triclinic boxes + versus orthogonal boxes + +in.bcc.primitive = 1 atom for bcc lattice with primitive unit cell +in.fcc.primitive = 1 atom for fcc lattice with primitive unit cell +in.hex.primitive = 1 atom for 2d hex lattice with primitive unit cell +in.sq2.primitive = 1 atom for 2d sq2 lattice with primitive unit cell + +in.bcc.orthog = 2 atoms for bcc lattice with orthogonal unit cell +in.fcc.orthog = 4 atoms for fcc lattice with orthogonal unit cell +in.hex.orthog = 2 atoms for 2d hex ;attice with orthogonal unit cell +in.sq2.orthog = 2 atoms for 2d sq2 lattice with orthogonal unit cell + +energy and pressure should be same for primitive and orthogonal unit cells + +in.data.general = read a data file in general triclinic format + +* Run all the scripts on 1 proc + +lmp_mpi < in.bcc.primitive +mv log.lammps log.compare.bcc.primitive.g++.1 +mv tmp.data.bcc.primitive data.compare.bcc.primitive.g++.1 +mv tmp.dump.bcc.primitive dump.compare.bcc.primitive.g++.1 + +lmp_mpi < in.fcc.primitive +mv log.lammps log.compare.fcc.primitive.g++.1 +mv tmp.data.fcc.primitive data.compare.fcc.primitive.g++.1 +mv tmp.dump.fcc.primitive dump.compare.fcc.primitive.g++.1 + +lmp_mpi < in.hex.primitive +mv log.lammps log.compare.hex.primitive.g++.1 +mv tmp.data.hex.primitive data.compare.hex.primitive.g++.1 +mv tmp.dump.hex.primitive dump.compare.hex.primitive.g++.1 + +lmp_mpi < in.sq2.primitive +mv log.lammps log.compare.sq2.primitive.g++.1 +mv tmp.data.sq2.primitive data.compare.sq2.primitive.g++.1 +mv tmp.dump.sq2.primitive dump.compare.sq2.primitive.g++.1 + +lmp_mpi < in.bcc.orthog +mv log.lammps log.compare.bcc.orthog.g++.1 +mv tmp.data.bcc.orthog data.compare.bcc.orthog.g++.1 +mv tmp.dump.bcc.orthog dump.compare.bcc.orthog.g++.1 + +lmp_mpi < in.fcc.orthog +mv log.lammps log.compare.fcc.orthog.g++.1 +mv tmp.data.fcc.orthog data.compare.fcc.orthog.g++.1 +mv tmp.dump.fcc.orthog dump.compare.fcc.orthog.g++.1 + +lmp_mpi < in.hex.orthog +mv log.lammps log.compare.hex.orthog.g++.1 +mv tmp.data.hex.orthog data.compare.hex.orthog.g++.1 +mv tmp.dump.hex.orthog dump.compare.hex.orthog.g++.1 + +lmp_mpi < in.sq2.orthog +mv log.lammps log.compare.sq2.orthog.g++.1 +mv tmp.data.sq2.orthog data.compare.sq2.orthog.g++.1 +mv tmp.dump.sq2.orthog dump.compare.sq2.orthog.g++.1 + +lmp_mpi < in.data.general +mv log.lammps log.compare.data.general.g++.1 +mv tmp.data.general data.compare.general.g++.1 +mv tmp.dump.general dump.compare.general.g++.1 + +* Run all the scripts on 4 procs + +mpirun -np 4 lmp_mpi < in.bcc.primitive +mv log.lammps log.compare.bcc.primitive.g++.4 +mv tmp.data.bcc.primitive data.compare.bcc.primitive.g++.4 +mv tmp.dump.bcc.primitive dump.compare.bcc.primitive.g++.4 + +mpirun -np 4 lmp_mpi < in.fcc.primitive +mv log.lammps log.compare.fcc.primitive.g++.4 +mv tmp.data.fcc.primitive data.compare.fcc.primitive.g++.4 +mv tmp.dump.fcc.primitive dump.compare.fcc.primitive.g++.4 + +mpirun -np 4 lmp_mpi < in.hex.primitive +mv log.lammps log.compare.hex.primitive.g++.4 +mv tmp.data.hex.primitive data.compare.hex.primitive.g++.4 +mv tmp.dump.hex.primitive dump.compare.hex.primitive.g++.4 + +mpirun -np 4 lmp_mpi < in.sq2.primitive +mv log.lammps log.compare.sq2.primitive.g++.4 +mv tmp.data.sq2.primitive data.compare.sq2.primitive.g++.4 +mv tmp.dump.sq2.primitive dump.compare.sq2.primitive.g++.4 + +mpirun -np 4 lmp_mpi < in.bcc.orthog +mv log.lammps log.compare.bcc.orthog.g++.4 +mv tmp.data.bcc.orthog data.compare.bcc.orthog.g++.4 +mv tmp.dump.bcc.orthog dump.compare.bcc.orthog.g++.4 + +mpirun -np 4 lmp_mpi < in.fcc.orthog +mv log.lammps log.compare.fcc.orthog.g++.4 +mv tmp.data.fcc.orthog data.compare.fcc.orthog.g++.4 +mv tmp.dump.fcc.orthog dump.compare.fcc.orthog.g++.4 + +mpirun -np 4 lmp_mpi < in.hex.orthog +mv log.lammps log.compare.hex.orthog.g++.4 +mv tmp.data.hex.orthog data.compare.hex.orthog.g++.4 +mv tmp.dump.hex.orthog dump.compare.hex.orthog.g++.4 + +mpirun -np 4 lmp_mpi < in.sq2.orthog +mv log.lammps log.compare.sq2.orthog.g++.4 +mv tmp.data.sq2.orthog data.compare.sq2.orthog.g++.4 +mv tmp.dump.sq2.orthog dump.compare.sq2.orthog.g++.4 + +mpirun -np 4 lmp_mpi < in.data.general +mv log.lammps log.compare.data.general.g++.4 +mv tmp.data.general data.compare.general.g++.4 +mv tmp.dump.general dump.compare.general.g++.4 diff --git a/examples/triclinic/data.8Apr24.bcc.orthog.g++.1 b/examples/triclinic/data.8Apr24.bcc.orthog.g++.1 new file mode 100644 index 0000000000..d785b97148 --- /dev/null +++ b/examples/triclinic/data.8Apr24.bcc.orthog.g++.1 @@ -0,0 +1,22 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0 1.2599210498948732 xlo xhi +0 1.2599210498948732 ylo yhi +0 1.2599210498948732 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.6299605249474366 0.6299605249474366 0.6299605249474366 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.bcc.orthog.g++.4 b/examples/triclinic/data.8Apr24.bcc.orthog.g++.4 new file mode 100644 index 0000000000..d785b97148 --- /dev/null +++ b/examples/triclinic/data.8Apr24.bcc.orthog.g++.4 @@ -0,0 +1,22 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0 1.2599210498948732 xlo xhi +0 1.2599210498948732 ylo yhi +0 1.2599210498948732 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.6299605249474366 0.6299605249474366 0.6299605249474366 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.bcc.primitive.g++.1 b/examples/triclinic/data.8Apr24.bcc.primitive.g++.1 new file mode 100644 index 0000000000..d2f30610d4 --- /dev/null +++ b/examples/triclinic/data.8Apr24.bcc.primitive.g++.1 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +-0.6299605249474365 0.6299605249474365 0.6299605249474364 avec +0.6299605249474367 -0.6299605249474365 0.6299605249474365 bvec +0.6299605249474363 0.6299605249474365 -0.6299605249474363 cvec +0 0 0 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.8Apr24.bcc.primitive.g++.4 b/examples/triclinic/data.8Apr24.bcc.primitive.g++.4 new file mode 100644 index 0000000000..d2f30610d4 --- /dev/null +++ b/examples/triclinic/data.8Apr24.bcc.primitive.g++.4 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +-0.6299605249474365 0.6299605249474365 0.6299605249474364 avec +0.6299605249474367 -0.6299605249474365 0.6299605249474365 bvec +0.6299605249474363 0.6299605249474365 -0.6299605249474363 cvec +0 0 0 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.8Apr24.fcc.orthog.g++.1 b/examples/triclinic/data.8Apr24.fcc.orthog.g++.1 new file mode 100644 index 0000000000..4e1a9e286f --- /dev/null +++ b/examples/triclinic/data.8Apr24.fcc.orthog.g++.1 @@ -0,0 +1,26 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +4 atoms +1 atom types + +0 1.5377619196572583 xlo xhi +0 1.5377619196572583 ylo yhi +0 1.5377619196572583 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.7688809598286291 0.7688809598286291 0 0 0 0 +3 1 0.7688809598286291 0 0.7688809598286291 0 0 0 +4 1 0 0.7688809598286291 0.7688809598286291 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 diff --git a/examples/triclinic/data.8Apr24.fcc.orthog.g++.4 b/examples/triclinic/data.8Apr24.fcc.orthog.g++.4 new file mode 100644 index 0000000000..dbcdc3ddaa --- /dev/null +++ b/examples/triclinic/data.8Apr24.fcc.orthog.g++.4 @@ -0,0 +1,26 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +4 atoms +1 atom types + +0 1.5377619196572583 xlo xhi +0 1.5377619196572583 ylo yhi +0 1.5377619196572583 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0 0.7688809598286291 0.7688809598286291 0 0 0 +3 1 0.7688809598286291 0.7688809598286291 0 0 0 0 +4 1 0.7688809598286291 0 0.7688809598286291 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 diff --git a/examples/triclinic/data.8Apr24.fcc.primitive.g++.1 b/examples/triclinic/data.8Apr24.fcc.primitive.g++.1 new file mode 100644 index 0000000000..99c74fb188 --- /dev/null +++ b/examples/triclinic/data.8Apr24.fcc.primitive.g++.1 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +0.7688809598286291 0.7688809598286293 -6.036070983262366e-17 avec +-5.551115123125783e-17 0.7688809598286293 0.7688809598286293 bvec +0.768880959828629 0 0.768880959828629 cvec +0 0 0 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.8Apr24.fcc.primitive.g++.4 b/examples/triclinic/data.8Apr24.fcc.primitive.g++.4 new file mode 100644 index 0000000000..99c74fb188 --- /dev/null +++ b/examples/triclinic/data.8Apr24.fcc.primitive.g++.4 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +0.7688809598286291 0.7688809598286293 -6.036070983262366e-17 avec +-5.551115123125783e-17 0.7688809598286293 0.7688809598286293 bvec +0.768880959828629 0 0.768880959828629 cvec +0 0 0 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.8Apr24.general.g++.1 b/examples/triclinic/data.8Apr24.general.g++.1 new file mode 100644 index 0000000000..1de194fb1c --- /dev/null +++ b/examples/triclinic/data.8Apr24.general.g++.1 @@ -0,0 +1,23 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0.9999999999999998 -1 0 avec +0.9999999999999999 0.9999999999999999 0 bvec +0.9999999999999999 0.9999999999999999 1 cvec +0 0 0 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0.2 -1.3877787807814457e-17 0.1 0 0 0 +2 1 0.8 -1.1102230246251565e-16 0.3 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.general.g++.4 b/examples/triclinic/data.8Apr24.general.g++.4 new file mode 100644 index 0000000000..1de194fb1c --- /dev/null +++ b/examples/triclinic/data.8Apr24.general.g++.4 @@ -0,0 +1,23 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0.9999999999999998 -1 0 avec +0.9999999999999999 0.9999999999999999 0 bvec +0.9999999999999999 0.9999999999999999 1 cvec +0 0 0 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0.2 -1.3877787807814457e-17 0.1 0 0 0 +2 1 0.8 -1.1102230246251565e-16 0.3 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.hex.orthog.g++.1 b/examples/triclinic/data.8Apr24.hex.orthog.g++.1 new file mode 100644 index 0000000000..503f636a88 --- /dev/null +++ b/examples/triclinic/data.8Apr24.hex.orthog.g++.1 @@ -0,0 +1,22 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0 1.074569931823542 xlo xhi +0 1.8612097182041991 ylo yhi +-0.537284965911771 0.537284965911771 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.537284965911771 0.9306048591020996 0 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.hex.orthog.g++.4 b/examples/triclinic/data.8Apr24.hex.orthog.g++.4 new file mode 100644 index 0000000000..503f636a88 --- /dev/null +++ b/examples/triclinic/data.8Apr24.hex.orthog.g++.4 @@ -0,0 +1,22 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0 1.074569931823542 xlo xhi +0 1.8612097182041991 ylo yhi +-0.537284965911771 0.537284965911771 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.537284965911771 0.9306048591020996 0 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.hex.primitive.g++.1 b/examples/triclinic/data.8Apr24.hex.primitive.g++.1 new file mode 100644 index 0000000000..5c1ee38bac --- /dev/null +++ b/examples/triclinic/data.8Apr24.hex.primitive.g++.1 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +1.0745699318262956 0 0 avec +0.5372849659131478 0.9306048590997147 0 bvec +0 0 1.0745699318262956 cvec +0 0 -0.5372849659131478 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.8Apr24.hex.primitive.g++.4 b/examples/triclinic/data.8Apr24.hex.primitive.g++.4 new file mode 100644 index 0000000000..5c1ee38bac --- /dev/null +++ b/examples/triclinic/data.8Apr24.hex.primitive.g++.4 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +1.0745699318262956 0 0 avec +0.5372849659131478 0.9306048590997147 0 bvec +0 0 1.0745699318262956 cvec +0 0 -0.5372849659131478 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.8Apr24.sq2.orthog.g++.1 b/examples/triclinic/data.8Apr24.sq2.orthog.g++.1 new file mode 100644 index 0000000000..732e6ed77f --- /dev/null +++ b/examples/triclinic/data.8Apr24.sq2.orthog.g++.1 @@ -0,0 +1,22 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0 1.348399724926484 xlo xhi +0 1.348399724926484 ylo yhi +-0.674199862463242 0.674199862463242 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.674199862463242 0.674199862463242 0 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.sq2.orthog.g++.4 b/examples/triclinic/data.8Apr24.sq2.orthog.g++.4 new file mode 100644 index 0000000000..732e6ed77f --- /dev/null +++ b/examples/triclinic/data.8Apr24.sq2.orthog.g++.4 @@ -0,0 +1,22 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +2 atoms +1 atom types + +0 1.348399724926484 xlo xhi +0 1.348399724926484 ylo yhi +-0.674199862463242 0.674199862463242 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.674199862463242 0.674199862463242 0 0 0 0 + +Velocities + +1 0 0 0 +2 0 0 0 diff --git a/examples/triclinic/data.8Apr24.sq2.primitive.g++.1 b/examples/triclinic/data.8Apr24.sq2.primitive.g++.1 new file mode 100644 index 0000000000..5a679f612c --- /dev/null +++ b/examples/triclinic/data.8Apr24.sq2.primitive.g++.1 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +0.6741998624632419 -0.674199862463242 0 avec +0.6741998624632419 0.674199862463242 0 bvec +0 0 1.348399724926484 cvec +0 0 -0.674199862463242 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.8Apr24.sq2.primitive.g++.4 b/examples/triclinic/data.8Apr24.sq2.primitive.g++.4 new file mode 100644 index 0000000000..5a679f612c --- /dev/null +++ b/examples/triclinic/data.8Apr24.sq2.primitive.g++.4 @@ -0,0 +1,21 @@ +LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj + +1 atoms +1 atom types + +0.6741998624632419 -0.674199862463242 0 avec +0.6741998624632419 0.674199862463242 0 bvec +0 0 1.348399724926484 cvec +0 0 -0.674199862463242 abc origin + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 + +Velocities + +1 0 0 0 diff --git a/examples/triclinic/data.general b/examples/triclinic/data.general new file mode 100644 index 0000000000..3ae6cdd0b5 --- /dev/null +++ b/examples/triclinic/data.general @@ -0,0 +1,13 @@ +# simple general triclinic simulation box with 2 atoms + +2 atoms +1 atom types +1 -1 0 avec +1 1 0 bvec +1 1 1 cvec +0 0 0 abc origin + +Atoms + +1 1 0.2 0.0 0.1 +2 1 0.8 0.0 0.3 diff --git a/examples/triclinic/dump.8Apr24.bcc.orthog.g++.1 b/examples/triclinic/dump.8Apr24.bcc.orthog.g++.1 new file mode 100644 index 0000000000..3023d4f393 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.bcc.orthog.g++.1 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.2599210498948732e+00 +0.0000000000000000e+00 1.2599210498948732e+00 +0.0000000000000000e+00 1.2599210498948732e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0.629961 0.629961 0.629961 diff --git a/examples/triclinic/dump.8Apr24.bcc.orthog.g++.4 b/examples/triclinic/dump.8Apr24.bcc.orthog.g++.4 new file mode 100644 index 0000000000..3023d4f393 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.bcc.orthog.g++.4 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.2599210498948732e+00 +0.0000000000000000e+00 1.2599210498948732e+00 +0.0000000000000000e+00 1.2599210498948732e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0.629961 0.629961 0.629961 diff --git a/examples/triclinic/dump.8Apr24.bcc.primitive.g++.1 b/examples/triclinic/dump.8Apr24.bcc.primitive.g++.1 new file mode 100644 index 0000000000..f987a77a35 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.bcc.primitive.g++.1 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +-6.2996052494743648e-01 6.2996052494743648e-01 6.2996052494743637e-01 0.0000000000000000e+00 +6.2996052494743671e-01 -6.2996052494743648e-01 6.2996052494743648e-01 0.0000000000000000e+00 +6.2996052494743626e-01 6.2996052494743648e-01 -6.2996052494743626e-01 0.0000000000000000e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/dump.8Apr24.bcc.primitive.g++.4 b/examples/triclinic/dump.8Apr24.bcc.primitive.g++.4 new file mode 100644 index 0000000000..f987a77a35 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.bcc.primitive.g++.4 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +-6.2996052494743648e-01 6.2996052494743648e-01 6.2996052494743637e-01 0.0000000000000000e+00 +6.2996052494743671e-01 -6.2996052494743648e-01 6.2996052494743648e-01 0.0000000000000000e+00 +6.2996052494743626e-01 6.2996052494743648e-01 -6.2996052494743626e-01 0.0000000000000000e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/dump.8Apr24.fcc.orthog.g++.1 b/examples/triclinic/dump.8Apr24.fcc.orthog.g++.1 new file mode 100644 index 0000000000..9f5f64f547 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.fcc.orthog.g++.1 @@ -0,0 +1,13 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +4 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.5377619196572583e+00 +0.0000000000000000e+00 1.5377619196572583e+00 +0.0000000000000000e+00 1.5377619196572583e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0.768881 0.768881 0 +3 1 0.768881 0 0.768881 +4 1 0 0.768881 0.768881 diff --git a/examples/triclinic/dump.8Apr24.fcc.orthog.g++.4 b/examples/triclinic/dump.8Apr24.fcc.orthog.g++.4 new file mode 100644 index 0000000000..0952b45b15 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.fcc.orthog.g++.4 @@ -0,0 +1,13 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +4 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.5377619196572583e+00 +0.0000000000000000e+00 1.5377619196572583e+00 +0.0000000000000000e+00 1.5377619196572583e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0 0.768881 0.768881 +3 1 0.768881 0.768881 0 +4 1 0.768881 0 0.768881 diff --git a/examples/triclinic/dump.8Apr24.fcc.primitive.g++.1 b/examples/triclinic/dump.8Apr24.fcc.primitive.g++.1 new file mode 100644 index 0000000000..7ec2c11e1b --- /dev/null +++ b/examples/triclinic/dump.8Apr24.fcc.primitive.g++.1 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +7.6888095982862914e-01 7.6888095982862925e-01 -6.0360709832623663e-17 0.0000000000000000e+00 +-5.5511151231257827e-17 7.6888095982862925e-01 7.6888095982862925e-01 0.0000000000000000e+00 +7.6888095982862903e-01 0.0000000000000000e+00 7.6888095982862903e-01 0.0000000000000000e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/dump.8Apr24.fcc.primitive.g++.4 b/examples/triclinic/dump.8Apr24.fcc.primitive.g++.4 new file mode 100644 index 0000000000..7ec2c11e1b --- /dev/null +++ b/examples/triclinic/dump.8Apr24.fcc.primitive.g++.4 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +7.6888095982862914e-01 7.6888095982862925e-01 -6.0360709832623663e-17 0.0000000000000000e+00 +-5.5511151231257827e-17 7.6888095982862925e-01 7.6888095982862925e-01 0.0000000000000000e+00 +7.6888095982862903e-01 0.0000000000000000e+00 7.6888095982862903e-01 0.0000000000000000e+00 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/dump.8Apr24.general.g++.1 b/examples/triclinic/dump.8Apr24.general.g++.1 new file mode 100644 index 0000000000..2452b17086 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.general.g++.1 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS abc origin pp pp pp +9.9999999999999978e-01 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +9.9999999999999989e-01 9.9999999999999989e-01 0.0000000000000000e+00 0.0000000000000000e+00 +9.9999999999999989e-01 9.9999999999999989e-01 1.0000000000000000e+00 0.0000000000000000e+00 +ITEM: ATOMS id type x y z +1 1 0.2 -1.38778e-17 0.1 +2 1 0.8 -1.11022e-16 0.3 diff --git a/examples/triclinic/dump.8Apr24.general.g++.4 b/examples/triclinic/dump.8Apr24.general.g++.4 new file mode 100644 index 0000000000..2452b17086 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.general.g++.4 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS abc origin pp pp pp +9.9999999999999978e-01 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +9.9999999999999989e-01 9.9999999999999989e-01 0.0000000000000000e+00 0.0000000000000000e+00 +9.9999999999999989e-01 9.9999999999999989e-01 1.0000000000000000e+00 0.0000000000000000e+00 +ITEM: ATOMS id type x y z +1 1 0.2 -1.38778e-17 0.1 +2 1 0.8 -1.11022e-16 0.3 diff --git a/examples/triclinic/dump.8Apr24.hex.orthog.g++.1 b/examples/triclinic/dump.8Apr24.hex.orthog.g++.1 new file mode 100644 index 0000000000..498573a753 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.hex.orthog.g++.1 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.0745699318235420e+00 +0.0000000000000000e+00 1.8612097182041991e+00 +-5.3728496591177100e-01 5.3728496591177100e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0.537285 0.930605 0 diff --git a/examples/triclinic/dump.8Apr24.hex.orthog.g++.4 b/examples/triclinic/dump.8Apr24.hex.orthog.g++.4 new file mode 100644 index 0000000000..498573a753 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.hex.orthog.g++.4 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.0745699318235420e+00 +0.0000000000000000e+00 1.8612097182041991e+00 +-5.3728496591177100e-01 5.3728496591177100e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0.537285 0.930605 0 diff --git a/examples/triclinic/dump.8Apr24.hex.primitive.g++.1 b/examples/triclinic/dump.8Apr24.hex.primitive.g++.1 new file mode 100644 index 0000000000..e4e1e88430 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.hex.primitive.g++.1 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +1.0745699318262956e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +5.3728496591314778e-01 9.3060485909971469e-01 0.0000000000000000e+00 0.0000000000000000e+00 +0.0000000000000000e+00 0.0000000000000000e+00 1.0745699318262956e+00 -5.3728496591314778e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/dump.8Apr24.hex.primitive.g++.4 b/examples/triclinic/dump.8Apr24.hex.primitive.g++.4 new file mode 100644 index 0000000000..e4e1e88430 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.hex.primitive.g++.4 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +1.0745699318262956e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +5.3728496591314778e-01 9.3060485909971469e-01 0.0000000000000000e+00 0.0000000000000000e+00 +0.0000000000000000e+00 0.0000000000000000e+00 1.0745699318262956e+00 -5.3728496591314778e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/dump.8Apr24.sq2.orthog.g++.1 b/examples/triclinic/dump.8Apr24.sq2.orthog.g++.1 new file mode 100644 index 0000000000..9735deffb2 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.sq2.orthog.g++.1 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.3483997249264841e+00 +0.0000000000000000e+00 1.3483997249264841e+00 +-6.7419986246324204e-01 6.7419986246324204e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0.6742 0.6742 0 diff --git a/examples/triclinic/dump.8Apr24.sq2.orthog.g++.4 b/examples/triclinic/dump.8Apr24.sq2.orthog.g++.4 new file mode 100644 index 0000000000..9735deffb2 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.sq2.orthog.g++.4 @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 1.3483997249264841e+00 +0.0000000000000000e+00 1.3483997249264841e+00 +-6.7419986246324204e-01 6.7419986246324204e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 +2 1 0.6742 0.6742 0 diff --git a/examples/triclinic/dump.8Apr24.sq2.primitive.g++.1 b/examples/triclinic/dump.8Apr24.sq2.primitive.g++.1 new file mode 100644 index 0000000000..8f8487e237 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.sq2.primitive.g++.1 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +6.7419986246324193e-01 -6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00 +6.7419986246324193e-01 6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00 +0.0000000000000000e+00 0.0000000000000000e+00 1.3483997249264841e+00 -6.7419986246324204e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/dump.8Apr24.sq2.primitive.g++.4 b/examples/triclinic/dump.8Apr24.sq2.primitive.g++.4 new file mode 100644 index 0000000000..8f8487e237 --- /dev/null +++ b/examples/triclinic/dump.8Apr24.sq2.primitive.g++.4 @@ -0,0 +1,10 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +1 +ITEM: BOX BOUNDS abc origin pp pp pp +6.7419986246324193e-01 -6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00 +6.7419986246324193e-01 6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00 +0.0000000000000000e+00 0.0000000000000000e+00 1.3483997249264841e+00 -6.7419986246324204e-01 +ITEM: ATOMS id type x y z +1 1 0 0 0 diff --git a/examples/triclinic/in.bcc.orthog b/examples/triclinic/in.bcc.orthog new file mode 100644 index 0000000000..b25241c700 --- /dev/null +++ b/examples/triclinic/in.bcc.orthog @@ -0,0 +1,23 @@ +# orthogonal box for bcc lattice unit cell + +lattice bcc 1.0 + +region mybox block 0 1 0 1 0 1 +create_box 1 mybox +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.bcc.orthog + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz & + cvecx cvecy cvecz pxx pyy pzz vol + +dump 1 all custom 100 tmp.dump.bcc.orthog id type x y z + +run 0 diff --git a/examples/triclinic/in.bcc.primitive b/examples/triclinic/in.bcc.primitive new file mode 100644 index 0000000000..2c1a1f9b6f --- /dev/null +++ b/examples/triclinic/in.bcc.primitive @@ -0,0 +1,25 @@ +# general triclinic box for bcc lattice primitive cell + +lattice custom 1.0 a1 -0.5 0.5 0.5 a2 0.5 -0.5 0.5 a3 0.5 0.5 -0.5 & + basis 0.0 0.0 0.0 triclinic/general + +create_box 1 NULL 0 1 0 1 0 1 +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.bcc.primitive triclinic/general + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz & + cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.bcc.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 diff --git a/examples/triclinic/in.data.general b/examples/triclinic/in.data.general new file mode 100644 index 0000000000..8e3d7bc287 --- /dev/null +++ b/examples/triclinic/in.data.general @@ -0,0 +1,21 @@ +# read a general triclinic data file + +read_data data.general + +mass * 1.0 + +write_data tmp.data.general triclinic/general + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz & + cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.general id type x y z +dump_modify 1 triclinic/general yes + +run 0 diff --git a/examples/triclinic/in.fcc.orthog b/examples/triclinic/in.fcc.orthog new file mode 100644 index 0000000000..a33b6c4a81 --- /dev/null +++ b/examples/triclinic/in.fcc.orthog @@ -0,0 +1,23 @@ +# orthogonal box for fcc lattice unit cell + +lattice fcc 1.1 + +region mybox block 0 1 0 1 0 1 +create_box 1 mybox +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.fcc.orthog + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz & + cvecx cvecy cvecz pxx pyy pzz vol + +dump 1 all custom 100 tmp.dump.fcc.orthog id type x y z + +run 0 diff --git a/examples/triclinic/in.fcc.primitive b/examples/triclinic/in.fcc.primitive new file mode 100644 index 0000000000..2836d39eea --- /dev/null +++ b/examples/triclinic/in.fcc.primitive @@ -0,0 +1,25 @@ +# general triclinic box for fcc lattice primitive cell + +lattice custom 1.1 a2 0.0 0.5 0.5 a3 0.5 0.0 0.5 a1 0.5 0.5 0.0 & + basis 0.0 0.0 0.0 triclinic/general + +create_box 1 NULL 0 1 0 1 0 1 +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.fcc.primitive triclinic/general + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz & + cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.fcc.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 diff --git a/examples/triclinic/in.hex.orthog b/examples/triclinic/in.hex.orthog new file mode 100644 index 0000000000..41d70916d1 --- /dev/null +++ b/examples/triclinic/in.hex.orthog @@ -0,0 +1,24 @@ +# orthogonal box for 2d hex lattice unit cell + +dimension 2 + +lattice hex 1.0 + +region mybox block 0 1 0 1 -0.5 0.5 +create_box 1 mybox +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.hex.orthog + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol + +dump 1 all custom 100 tmp.dump.hex.orthog id type x y z + +run 0 diff --git a/examples/triclinic/in.hex.primitive b/examples/triclinic/in.hex.primitive new file mode 100644 index 0000000000..f76ccbbdf2 --- /dev/null +++ b/examples/triclinic/in.hex.primitive @@ -0,0 +1,26 @@ +# general triclinic box for 2d hex lattice primitive cell + +dimension 2 + +lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 & + a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general + +create_box 1 NULL 0 1 0 1 -0.5 0.5 +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.hex.primitive triclinic/general + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.hex.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 diff --git a/examples/triclinic/in.sq2.orthog b/examples/triclinic/in.sq2.orthog new file mode 100644 index 0000000000..366703a6ee --- /dev/null +++ b/examples/triclinic/in.sq2.orthog @@ -0,0 +1,24 @@ +# orthogonal box for 2d sq2 lattice unit cell + +dimension 2 + +lattice sq2 1.1 + +region mybox block 0 1 0 1 -0.5 0.5 +create_box 1 mybox +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.sq2.orthog + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol + +dump 1 all custom 100 tmp.dump.sq2.orthog id type x y z + +run 0 diff --git a/examples/triclinic/in.sq2.primitive b/examples/triclinic/in.sq2.primitive new file mode 100644 index 0000000000..5333fd2b99 --- /dev/null +++ b/examples/triclinic/in.sq2.primitive @@ -0,0 +1,26 @@ +# general triclinic box for 2d sq2 lattice primitive cell + +dimension 2 + +lattice custom 1.1 a1 0.5 -0.5 0.0 a2 0.5 0.5 0.0 a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 triclinic/general + +create_box 1 NULL 0 1 0 1 -0.5 0.5 +create_atoms 1 box + +mass * 1.0 + +write_data tmp.data.sq2.primitive triclinic/general + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.sq2.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 diff --git a/examples/triclinic/log.8Apr24.bcc.orthog.g++.1 b/examples/triclinic/log.8Apr24.bcc.orthog.g++.1 new file mode 100644 index 0000000000..72bbc4505c --- /dev/null +++ b/examples/triclinic/log.8Apr24.bcc.orthog.g++.1 @@ -0,0 +1,74 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# orthogonal box for bcc lattice unit cell + +lattice bcc 1.0 +Lattice spacing in x,y,z = 1.259921 1.259921 1.259921 + +region mybox block 0 1 0 1 0 1 +create_box 1 mybox +Created orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.bcc.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol + +dump 1 all custom 100 tmp.dump.bcc.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -3.8628258 1.259921 0 0 0 1.259921 0 0 0 1.259921 3.5116598 3.5116598 3.5116598 2 +Loop time of 8.27e-07 on 1 procs for 0 steps with 2 atoms + +120.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.27e-07 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 33 ave 33 max 33 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8 +Ave neighs/atom = 4 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.bcc.orthog.g++.4 b/examples/triclinic/log.8Apr24.bcc.orthog.g++.4 new file mode 100644 index 0000000000..389d66f413 --- /dev/null +++ b/examples/triclinic/log.8Apr24.bcc.orthog.g++.4 @@ -0,0 +1,75 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# orthogonal box for bcc lattice unit cell + +lattice bcc 1.0 +Lattice spacing in x,y,z = 1.259921 1.259921 1.259921 + +region mybox block 0 1 0 1 0 1 +create_box 1 mybox +Created orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.bcc.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol + +dump 1 all custom 100 tmp.dump.bcc.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.948 | 3.011 | 3.073 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -3.8628258 1.259921 0 0 0 1.259921 0 0 0 1.259921 3.5116598 3.5116598 3.5116598 2 +Loop time of 1.3815e-06 on 4 procs for 0 steps with 2 atoms + +54.3% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.382e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 19.5 ave 20 max 19 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 2 ave 4 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 8 +Ave neighs/atom = 4 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.bcc.primitive.g++.1 b/examples/triclinic/log.8Apr24.bcc.primitive.g++.1 new file mode 100644 index 0000000000..d1c8cca311 --- /dev/null +++ b/examples/triclinic/log.8Apr24.bcc.primitive.g++.1 @@ -0,0 +1,76 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# general triclinic box for bcc lattice primitive cell + +lattice custom 1.0 a1 -0.5 0.5 0.5 a2 0.5 -0.5 0.5 a3 0.5 0.5 -0.5 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 1.8185394 1.5430818 0.89089872 + +create_box 1 NULL 0 1 0 1 0 1 +Created triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.bcc.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.bcc.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 4 3 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.084 | 3.084 | 3.084 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -3.8628258 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 3.5116598 3.5116598 3.5116598 1 +Loop time of 6.86e-07 on 1 procs for 0 steps with 1 atoms + +145.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 6.86e-07 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 63 ave 63 max 63 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4 +Ave neighs/atom = 4 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.bcc.primitive.g++.4 b/examples/triclinic/log.8Apr24.bcc.primitive.g++.4 new file mode 100644 index 0000000000..f8e979976f --- /dev/null +++ b/examples/triclinic/log.8Apr24.bcc.primitive.g++.4 @@ -0,0 +1,77 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# general triclinic box for bcc lattice primitive cell + +lattice custom 1.0 a1 -0.5 0.5 0.5 a2 0.5 -0.5 0.5 a3 0.5 0.5 -0.5 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 1.8185394 1.5430818 0.89089872 + +create_box 1 NULL 0 1 0 1 0 1 +Created triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 2 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.bcc.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.bcc.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 4 3 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.973 | 3.005 | 3.098 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -3.8628258 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 3.5116598 3.5116598 3.5116598 1 +Loop time of 2.1275e-06 on 4 procs for 0 steps with 1 atoms + +70.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.127e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 35.75 ave 36 max 35 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 1 ave 4 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 4 +Ave neighs/atom = 4 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.data.general.g++.1 b/examples/triclinic/log.8Apr24.data.general.g++.1 new file mode 100644 index 0000000000..3874a8c77e --- /dev/null +++ b/examples/triclinic/log.8Apr24.data.general.g++.1 @@ -0,0 +1,73 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# read a general triclinic data file + +read_data data.general +Reading data file ... + triclinic box = (0 0 0) to (1.4142136 1.4142136 1) with tilt (-1.110223e-16 -1.110223e-16 1.4142136) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + read_data CPU = 0.001 seconds + +mass * 1.0 + +write_data tmp.data.general triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.general id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 3 5 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.076 | 3.076 | 3.076 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 456.05603 1 -1 0 1 1 0 1 1 1 2555.5604 2555.5604 598.94037 2 +Loop time of 7.31e-07 on 1 procs for 0 steps with 2 atoms + +136.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.31e-07 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 66 ave 66 max 66 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6 +Ave neighs/atom = 3 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.data.general.g++.4 b/examples/triclinic/log.8Apr24.data.general.g++.4 new file mode 100644 index 0000000000..f03d1ffb58 --- /dev/null +++ b/examples/triclinic/log.8Apr24.data.general.g++.4 @@ -0,0 +1,74 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# read a general triclinic data file + +read_data data.general +Reading data file ... + triclinic box = (0 0 0) to (1.4142136 1.4142136 1) with tilt (-1.110223e-16 -1.110223e-16 1.4142136) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 2 atoms + read_data CPU = 0.001 seconds + +mass * 1.0 + +write_data tmp.data.general triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.general id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 3 5 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.966 | 2.997 | 3.091 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 456.05603 1 -1 0 1 1 0 1 1 1 2555.5604 2555.5604 598.94037 2 +Loop time of 2.13e-06 on 4 procs for 0 steps with 2 atoms + +70.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.13e-06 | | |100.00 + +Nlocal: 0.5 ave 2 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 47.5 ave 48 max 46 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 1.5 ave 6 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 6 +Ave neighs/atom = 3 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.fcc.orthog.g++.1 b/examples/triclinic/log.8Apr24.fcc.orthog.g++.1 new file mode 100644 index 0000000000..fc608c042a --- /dev/null +++ b/examples/triclinic/log.8Apr24.fcc.orthog.g++.1 @@ -0,0 +1,74 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# orthogonal box for fcc lattice unit cell + +lattice fcc 1.1 +Lattice spacing in x,y,z = 1.5377619 1.5377619 1.5377619 + +region mybox block 0 1 0 1 0 1 +create_box 1 mybox +Created orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.fcc.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol + +dump 1 all custom 100 tmp.dump.fcc.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.059 | 3.059 | 3.059 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -5.7354 1.5377619 0 0 0 1.5377619 0 0 0 1.5377619 6.70824 6.70824 6.70824 3.6363636 +Loop time of 8.53e-07 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.53e-07 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 58 ave 58 max 58 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 24 +Ave neighs/atom = 6 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.fcc.orthog.g++.4 b/examples/triclinic/log.8Apr24.fcc.orthog.g++.4 new file mode 100644 index 0000000000..f5464d238d --- /dev/null +++ b/examples/triclinic/log.8Apr24.fcc.orthog.g++.4 @@ -0,0 +1,75 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# orthogonal box for fcc lattice unit cell + +lattice fcc 1.1 +Lattice spacing in x,y,z = 1.5377619 1.5377619 1.5377619 + +region mybox block 0 1 0 1 0 1 +create_box 1 mybox +Created orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619) + 2 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.fcc.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol + +dump 1 all custom 100 tmp.dump.fcc.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.074 | 3.074 | 3.074 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -5.7354 1.5377619 0 0 0 1.5377619 0 0 0 1.5377619 6.70824 6.70824 6.70824 3.6363636 +Loop time of 3.291e-06 on 4 procs for 0 steps with 4 atoms + +76.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.291e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 39 ave 39 max 39 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 6 ave 6 max 6 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 24 +Ave neighs/atom = 6 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.fcc.primitive.g++.1 b/examples/triclinic/log.8Apr24.fcc.primitive.g++.1 new file mode 100644 index 0000000000..21fccdca1f --- /dev/null +++ b/examples/triclinic/log.8Apr24.fcc.primitive.g++.1 @@ -0,0 +1,76 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# general triclinic box for fcc lattice primitive cell + +lattice custom 1.1 a2 0.0 0.5 0.5 a3 0.5 0.0 0.5 a1 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 2.1747238 1.2555773 0.88782726 + +create_box 1 NULL 0 1 0 1 0 1 +Created triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.fcc.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.fcc.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 4 3 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.084 | 3.084 | 3.084 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -5.7354 0.76888096 0.76888096 -6.036071e-17 -5.5511151e-17 0.76888096 0.76888096 0.76888096 0 0.76888096 6.70824 6.70824 6.70824 0.90909091 +Loop time of 8.83e-07 on 1 procs for 0 steps with 1 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.83e-07 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 63 ave 63 max 63 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6 +Ave neighs/atom = 6 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.fcc.primitive.g++.4 b/examples/triclinic/log.8Apr24.fcc.primitive.g++.4 new file mode 100644 index 0000000000..651da16e79 --- /dev/null +++ b/examples/triclinic/log.8Apr24.fcc.primitive.g++.4 @@ -0,0 +1,77 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# general triclinic box for fcc lattice primitive cell + +lattice custom 1.1 a2 0.0 0.5 0.5 a3 0.5 0.0 0.5 a1 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 2.1747238 1.2555773 0.88782726 + +create_box 1 NULL 0 1 0 1 0 1 +Created triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.fcc.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.2 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.fcc.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 4 3 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.973 | 3.005 | 3.098 Mbytes + Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume + 0 -5.7354 0.76888096 0.76888096 -6.036071e-17 -5.5511151e-17 0.76888096 0.76888096 0.76888096 0 0.76888096 6.70824 6.70824 6.70824 0.90909091 +Loop time of 1.7905e-06 on 4 procs for 0 steps with 1 atoms + +55.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.791e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 35.75 ave 36 max 35 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 1.5 ave 6 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 6 +Ave neighs/atom = 6 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.hex.orthog.g++.1 b/examples/triclinic/log.8Apr24.hex.orthog.g++.1 new file mode 100644 index 0000000000..001f2300e4 --- /dev/null +++ b/examples/triclinic/log.8Apr24.hex.orthog.g++.1 @@ -0,0 +1,76 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# orthogonal box for 2d hex lattice unit cell + +dimension 2 + +lattice hex 1.0 +Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699 + +region mybox block 0 1 0 1 -0.5 0.5 +create_box 1 mybox +Created orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.hex.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol + +dump 1 all custom 100 tmp.dump.hex.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 2 4 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.054 | 3.054 | 3.054 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 -2.7317286 1.0745699 0 0 1.8612097 6.9923141 6.9923141 2 +Loop time of 9.26e-07 on 1 procs for 0 steps with 2 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.26e-07 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 15 ave 15 max 15 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6 +Ave neighs/atom = 3 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.hex.orthog.g++.4 b/examples/triclinic/log.8Apr24.hex.orthog.g++.4 new file mode 100644 index 0000000000..880d532957 --- /dev/null +++ b/examples/triclinic/log.8Apr24.hex.orthog.g++.4 @@ -0,0 +1,77 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# orthogonal box for 2d hex lattice unit cell + +dimension 2 + +lattice hex 1.0 +Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699 + +region mybox block 0 1 0 1 -0.5 0.5 +create_box 1 mybox +Created orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.hex.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol + +dump 1 all custom 100 tmp.dump.hex.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 2 4 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.945 | 2.945 | 2.945 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 -2.7317286 1.0745699 0 0 1.8612097 6.9923141 6.9923141 2 +Loop time of 1.9155e-06 on 4 procs for 0 steps with 2 atoms + +52.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.915e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 11.5 ave 12 max 11 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 1.5 ave 3 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 6 +Ave neighs/atom = 3 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.hex.primitive.g++.1 b/examples/triclinic/log.8Apr24.hex.primitive.g++.1 new file mode 100644 index 0000000000..71f3fc6d13 --- /dev/null +++ b/examples/triclinic/log.8Apr24.hex.primitive.g++.1 @@ -0,0 +1,78 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# general triclinic box for 2d hex lattice primitive cell + +dimension 2 + +lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 1.6118549 0.93060486 1.0745699 + +create_box 1 NULL 0 1 0 1 -0.5 0.5 +Created triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.hex.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.hex.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 3 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 -2.7317286 1.0745699 0 0.53728497 0.93060486 6.9923141 6.9923141 1 +Loop time of 1.03e-06 on 1 procs for 0 steps with 1 atoms + +97.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.03e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 15 ave 15 max 15 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3 +Ave neighs/atom = 3 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.hex.primitive.g++.4 b/examples/triclinic/log.8Apr24.hex.primitive.g++.4 new file mode 100644 index 0000000000..b7703b2678 --- /dev/null +++ b/examples/triclinic/log.8Apr24.hex.primitive.g++.4 @@ -0,0 +1,79 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# general triclinic box for 2d hex lattice primitive cell + +dimension 2 + +lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 1.6118549 0.93060486 1.0745699 + +create_box 1 NULL 0 1 0 1 -0.5 0.5 +Created triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0) +WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.hex.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.hex.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 3 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.953 | 2.953 | 2.953 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 -2.7317286 1.0745699 0 0.53728497 0.93060486 6.9923141 6.9923141 1 +Loop time of 2.45225e-06 on 4 procs for 0 steps with 1 atoms + +61.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.452e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 8.75 ave 9 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0.75 ave 3 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 3 +Ave neighs/atom = 3 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.sq2.orthog.g++.1 b/examples/triclinic/log.8Apr24.sq2.orthog.g++.1 new file mode 100644 index 0000000000..bae7c7eae1 --- /dev/null +++ b/examples/triclinic/log.8Apr24.sq2.orthog.g++.1 @@ -0,0 +1,76 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# orthogonal box for 2d sq2 lattice unit cell + +dimension 2 + +lattice sq2 1.1 +Lattice spacing in x,y,z = 1.3483997 1.3483997 1.3483997 + +region mybox block 0 1 0 1 -0.5 0.5 +create_box 1 mybox +Created orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.sq2.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol + +dump 1 all custom 100 tmp.dump.sq2.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.046 | 3.046 | 3.046 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 3.524488 1.3483997 0 0 1.3483997 58.400021 58.400021 1.8181818 +Loop time of 9.37e-07 on 1 procs for 0 steps with 2 atoms + +106.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.37e-07 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11 ave 11 max 11 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4 +Ave neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.sq2.orthog.g++.4 b/examples/triclinic/log.8Apr24.sq2.orthog.g++.4 new file mode 100644 index 0000000000..c54078ae97 --- /dev/null +++ b/examples/triclinic/log.8Apr24.sq2.orthog.g++.4 @@ -0,0 +1,77 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# orthogonal box for 2d sq2 lattice unit cell + +dimension 2 + +lattice sq2 1.1 +Lattice spacing in x,y,z = 1.3483997 1.3483997 1.3483997 + +region mybox block 0 1 0 1 -0.5 0.5 +create_box 1 mybox +Created orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.sq2.orthog +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol + +dump 1 all custom 100 tmp.dump.sq2.orthog id type x y z + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.937 | 2.937 | 2.937 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 3.524488 1.3483997 0 0 1.3483997 58.400021 58.400021 1.8181818 +Loop time of 1.703e-06 on 4 procs for 0 steps with 2 atoms + +29.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.703e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 7.5 ave 8 max 7 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 1 ave 2 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 4 +Ave neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.sq2.primitive.g++.1 b/examples/triclinic/log.8Apr24.sq2.primitive.g++.1 new file mode 100644 index 0000000000..07195085ae --- /dev/null +++ b/examples/triclinic/log.8Apr24.sq2.primitive.g++.1 @@ -0,0 +1,77 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +# general triclinic box for 2d sq2 lattice primitive cell + +dimension 2 + +lattice custom 1.1 a1 0.5 -0.5 0.0 a2 0.5 0.5 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 0.95346259 0.95346259 1.3483997 + +create_box 1 NULL 0 1 0 1 -0.5 0.5 +Created triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.sq2.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.sq2.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 2 2 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.937 | 2.937 | 2.937 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 3.524488 0.67419986 -0.67419986 0.67419986 0.67419986 58.400021 58.400021 0.90909091 +Loop time of 8.38e-07 on 1 procs for 0 steps with 1 atoms + +119.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.38e-07 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 15 ave 15 max 15 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2 +Ave neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/triclinic/log.8Apr24.sq2.primitive.g++.4 b/examples/triclinic/log.8Apr24.sq2.primitive.g++.4 new file mode 100644 index 0000000000..1f2c758d65 --- /dev/null +++ b/examples/triclinic/log.8Apr24.sq2.primitive.g++.4 @@ -0,0 +1,78 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# general triclinic box for 2d sq2 lattice primitive cell + +dimension 2 + +lattice custom 1.1 a1 0.5 -0.5 0.0 a2 0.5 0.5 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general +Lattice spacing in x,y,z = 0.95346259 0.95346259 1.3483997 + +create_box 1 NULL 0 1 0 1 -0.5 0.5 +Created triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0) + create_atoms CPU = 0.000 seconds + +mass * 1.0 + +write_data tmp.data.sq2.primitive triclinic/general +System init for write_data ... +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) + +pair_style lj/cut 1.1 +pair_coeff * * 1.0 1.0 + +neighbor 0.0 bin + +thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol +thermo_modify triclinic/general yes + +dump 1 all custom 100 tmp.dump.sq2.primitive id type x y z +dump_modify 1 triclinic/general yes + +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55, bins = 2 2 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.953 | 2.953 | 2.953 Mbytes + Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume + 0 3.524488 0.67419986 -0.67419986 0.67419986 0.67419986 58.400021 58.400021 0.90909091 +Loop time of 1.91525e-06 on 4 procs for 0 steps with 1 atoms + +52.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.915e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 8.75 ave 9 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0.5 ave 2 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2 +Ave neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/ttm/Si.ttm_mod b/examples/ttm/Si.ttm_mod index 6e047857ff..ad407352e7 100644 --- a/examples/ttm/Si.ttm_mod +++ b/examples/ttm/Si.ttm_mod @@ -17,9 +17,9 @@ rho_e, electrons/volume units D_e, length^2/time units 20000 gamma_p, mass/time units -39.235 -gamma_s, mass/time units 24.443 +gamma_s, mass/time units +39.235 v_0, length/time units 79.76 I_0, energy/(time*length^2) units diff --git a/examples/ttm/log.18May23.ttm.mod.g++.1 b/examples/ttm/log.15Apr24.ttm.mod.g++.1 similarity index 66% rename from examples/ttm/log.18May23.ttm.mod.g++.1 rename to examples/ttm/log.15Apr24.ttm.mod.g++.1 index b97e8ab0ea..4b4f88b2a2 100644 --- a/examples/ttm/log.18May23.ttm.mod.g++.1 +++ b/examples/ttm/log.15Apr24.ttm.mod.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (28 Mar 2023 - Development) +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-394-g03ab36a37d) + using 1 OpenMP thread(s) per MPI task units metal atom_style atomic boundary p p p @@ -13,7 +14,7 @@ mass 1 28.0855 create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1 Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309) - create_atoms CPU = 0.002 seconds + create_atoms CPU = 0.001 seconds pair_style sw pair_coeff * * Si.sw Si @@ -79,30 +80,30 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes Step Temp TotEng f_twotemp[1] f_twotemp[2] 0 0 -34692.79996100604 -52.79390940511979 0 - 100 2.004897156140836 -34690.27961013186 -55.3499730543189 0.01301140393178352 - 200 2.837118035232607 -34687.74741132015 -57.93445748841876 0.02696025968760173 - 300 4.263087164947482 -34684.98084093686 -60.75945453846793 0.02175636603841567 - 400 5.568003854939066 -34682.25271040963 -63.56896518300499 0.03000618483472749 - 500 6.225602451570786 -34679.49948952029 -66.40897551884574 0.02768827702656703 - 600 7.608847536264781 -34676.69728436362 -69.32060611557282 0.05579466731854091 - 700 9.049471241531297 -34674.00093206036 -72.10055094219462 0.004335980559879032 - 800 9.826796099683211 -34671.27720242751 -74.95010610862134 0.02371649678091515 - 900 11.8609224958918 -34668.35091308811 -77.98544170794545 0.004658649791374908 - 1000 13.88037467640968 -34665.35025858006 -81.16445160194111 0.07684078334464743 -Loop time of 2.48942 on 1 procs for 1000 steps with 8000 atoms + 100 1.255921182965094 -34691.22889627319 -54.38067722556279 0.004868249873095404 + 200 1.858362347834853 -34689.5405389424 -56.09419523244324 0.01649190747838086 + 300 2.581575104085017 -34687.9650112138 -57.69350558275053 0.01683584513983131 + 400 3.47533128765632 -34686.2796683925 -59.40465113478642 0.005727647825729662 + 500 4.080137293185865 -34684.25857873315 -61.46449138661911 0.005828121949923951 + 600 4.816104423494803 -34682.51412688349 -63.25804498666959 0.02397283419020746 + 700 5.937291156573137 -34680.64941595491 -65.17152689673857 0.02604017750117964 + 800 6.487028971399661 -34678.87151939966 -66.99420300650799 0.009720189851817886 + 900 7.461479797687167 -34677.29259652842 -68.63442522233655 0.02576822683306545 + 1000 8.696444335455215 -34675.39247806347 -70.59264558122587 0.0147252863003017 +Loop time of 5.11497 on 1 procs for 1000 steps with 8000 atoms -Performance: 3.471 ns/day, 6.915 hours/ns, 401.700 timesteps/s, 3.214 Matom-step/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.689 ns/day, 14.208 hours/ns, 195.505 timesteps/s, 1.564 Matom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.126 | 2.126 | 2.126 | 0.0 | 85.40 +Pair | 4.3498 | 4.3498 | 4.3498 | 0.0 | 85.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.016147 | 0.016147 | 0.016147 | 0.0 | 0.65 -Output | 0.0013116 | 0.0013116 | 0.0013116 | 0.0 | 0.05 -Modify | 0.33864 | 0.33864 | 0.33864 | 0.0 | 13.60 -Other | | 0.007318 | | | 0.29 +Comm | 0.037981 | 0.037981 | 0.037981 | 0.0 | 0.74 +Output | 0.0025641 | 0.0025641 | 0.0025641 | 0.0 | 0.05 +Modify | 0.71279 | 0.71279 | 0.71279 | 0.0 | 13.94 +Other | | 0.01179 | | | 0.23 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -117,4 +118,4 @@ Total # of neighbors = 272000 Ave neighs/atom = 34 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:05 diff --git a/examples/ttm/log.18May23.ttm.mod.g++.4 b/examples/ttm/log.15Apr24.ttm.mod.g++.4 similarity index 65% rename from examples/ttm/log.18May23.ttm.mod.g++.4 rename to examples/ttm/log.15Apr24.ttm.mod.g++.4 index ea675c8594..231a9af2c9 100644 --- a/examples/ttm/log.18May23.ttm.mod.g++.4 +++ b/examples/ttm/log.15Apr24.ttm.mod.g++.4 @@ -1,5 +1,5 @@ -LAMMPS (28 Mar 2023 - Development) -WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:531) +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-394-g03ab36a37d) + using 1 OpenMP thread(s) per MPI task units metal atom_style atomic boundary p p p @@ -14,7 +14,7 @@ mass 1 28.0855 create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1 Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309) - create_atoms CPU = 0.001 seconds + create_atoms CPU = 0.002 seconds pair_style sw pair_coeff * * Si.sw Si @@ -80,30 +80,30 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.436 | 3.436 | 3.436 Mbytes Step Temp TotEng f_twotemp[1] f_twotemp[2] 0 0 -34692.79996100361 -52.79390940511979 0 - 100 1.852689977101411 -34690.49204900486 -55.14271612882064 0.02726188676577098 - 200 2.735750477179192 -34688.11139028054 -57.57110998717798 0.03387986355513584 - 300 3.931848271449558 -34685.54667417785 -60.18684521127231 0.02261256315262403 - 400 5.462009198576365 -34682.74455105668 -63.05420336037233 0.002402241637719578 - 500 6.267811692893873 -34679.96493887379 -65.93304222280051 0.02448378880218699 - 600 7.21148216150661 -34677.41455784726 -68.58391420045926 0.04114045759945374 - 700 8.84660534187052 -34674.40610468235 -71.68798344296859 0.02372984027434538 - 800 10.1748456457686 -34671.08749605772 -75.11943618276216 0.007538225788030307 - 900 11.27479036162859 -34668.4118066423 -77.92921692176756 0.02537529314475071 - 1000 13.26881394868076 -34665.56617589539 -80.91544540266317 0.03112665440209921 -Loop time of 0.995347 on 4 procs for 1000 steps with 8000 atoms + 100 1.20337355884597 -34691.30677367127 -54.30747356568817 0.01557346850238741 + 200 1.709631732825883 -34689.83859944795 -55.7982356998371 0.02508386983502213 + 300 2.488524478071323 -34688.26307995134 -57.3977272154369 0.02664346353990833 + 400 3.38535890366476 -34686.51395648598 -59.17547816947624 0.02164200191836632 + 500 3.838163353802383 -34684.79466673204 -60.92228950760077 0.005860499116196545 + 600 4.675913079756001 -34683.03448988724 -62.72423959707044 0.0106700119158327 + 700 5.637185532827328 -34681.25888274477 -64.5491928842093 0.01568536325219336 + 800 6.316986413957468 -34679.29231578312 -66.57005328290739 0.02035373879569394 + 900 7.211479047111087 -34677.61236020172 -68.30976417874265 0.03239086895076279 + 1000 8.431725106300505 -34675.81097854214 -70.161139196977 0.01219385884660358 +Loop time of 1.73439 on 4 procs for 1000 steps with 8000 atoms -Performance: 8.680 ns/day, 2.765 hours/ns, 1004.675 timesteps/s, 8.037 Matom-step/s -97.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 4.982 ns/day, 4.818 hours/ns, 576.572 timesteps/s, 4.613 Matom-step/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.65351 | 0.6616 | 0.66783 | 0.8 | 66.47 +Pair | 1.127 | 1.1392 | 1.1511 | 1.0 | 65.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.041606 | 0.048314 | 0.056589 | 2.9 | 4.85 -Output | 0.0014609 | 0.0014742 | 0.0014968 | 0.0 | 0.15 -Modify | 0.27934 | 0.28016 | 0.28089 | 0.1 | 28.15 -Other | | 0.003798 | | | 0.38 +Comm | 0.068488 | 0.082304 | 0.094797 | 4.1 | 4.75 +Output | 0.0024745 | 0.0025221 | 0.0025705 | 0.1 | 0.15 +Modify | 0.50194 | 0.50329 | 0.50522 | 0.2 | 29.02 +Other | | 0.007117 | | | 0.41 Nlocal: 2000 ave 2000 max 2000 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/voronoi/in.voronoi.2d b/examples/voronoi/in.voronoi.2d index 74bde73f1b..25628bd19a 100644 --- a/examples/voronoi/in.voronoi.2d +++ b/examples/voronoi/in.voronoi.2d @@ -7,46 +7,46 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary p p p +units metal +boundary p p p #lattice sq 1.0 origin 0.5 0.5 0.0 lattice hex 1.0 origin 0.5 0.5 0.0 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} +region box block 0 ${len} 0 ${len} -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 create_box 1 box create_atoms 1 region atoms -mass 1 1.0 +mass 1 1.0 pair_style lj/cut ${rcut} pair_coeff 1 1 0.0 1.0 -neighbor ${rskin} nsq +neighbor ${rskin} nsq # set the minimum communication cut-off comm_modify cutoff ${rcomm} -compute v1 all voronoi/atom neighbors yes -compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys -thermo_style custom c_volvor v_volsys vol v_err -thermo 1 +compute v1 all voronoi/atom neighbors yes +compute volvor all reduce sum c_v1[1] +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys +thermo_style custom c_volvor v_volsys vol v_err +thermo 1 # # TEST 1: Volume check for 2d bulk system # -run 0 +run 0 # # TEST 2: Volume check for 2d finite system # add margins in x and y directions # -change_box all boundary f f p -run 0 +change_box all boundary f f p +run 0 diff --git a/examples/voronoi/in.voronoi.data b/examples/voronoi/in.voronoi.data index e5d925c498..cbcc530649 100644 --- a/examples/voronoi/in.voronoi.data +++ b/examples/voronoi/in.voronoi.data @@ -4,24 +4,24 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary f f p +units metal +boundary f f p lattice hex 1.0 origin 0.25 0.25 0.0 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} +region box block 0 ${len} 0 ${len} -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 create_box 1 box create_atoms 1 region atoms -mass 1 1.0 +mass 1 1.0 pair_style lj/cut 2.5 pair_coeff 1 1 0.0 1.0 -neighbor 1.0 nsq +neighbor 1.0 nsq # # TEST 1: @@ -30,11 +30,11 @@ neighbor 1.0 nsq # This compute voronoi generates all three # types of quantity: per-atom, local, and global -compute v1 all voronoi/atom neighbors yes edge_histo 6 +compute v1 all voronoi/atom neighbors yes edge_histo 6 # write voronoi per-atom quantities to a file -dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] +dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] # writing voronoi local quantities to a file @@ -42,17 +42,17 @@ dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] # sum up a voronoi per-atom quantity -compute volvor all reduce sum c_v1[1] +compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys # output voronoi global quantities -thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] -thermo 1 +thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +thermo 1 -run 0 +run 0 uncompute v1 uncompute volvor @@ -65,7 +65,7 @@ undump dlocal # This compute voronoi generates peratom and local and global quantities -compute v2 all voronoi/atom neighbors yes edge_histo 6 +compute v2 all voronoi/atom neighbors yes edge_histo 6 # write voronoi local quantities to a file @@ -73,11 +73,11 @@ dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] # sum up a voronoi local quantity -compute sumarea all reduce sum c_v2[3] inputs local +compute sumarea all reduce sum c_v2[3] inputs local # output voronoi global quantities -thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] -thermo 1 +thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] +thermo 1 -run 0 +run 0 diff --git a/examples/voronoi/log.27Nov18.voronoi.data.g++.1 b/examples/voronoi/log.27Nov18.voronoi.data.g++.1 deleted file mode 100644 index 04bc629d87..0000000000 --- a/examples/voronoi/log.27Nov18.voronoi.data.g++.1 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Exercise different output data options - -variable len equal 4.0 -variable lenz equal 10.0 - -dimension 2 -units metal -boundary f f p - -lattice hex 1.0 origin 0.25 0.25 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 - -atom_style atomic - -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 -region atoms block 0 ${len} 0 ${len} 0.0 0.0 -region atoms block 0 4 0 ${len} 0.0 0.0 -region atoms block 0 4 0 4 0.0 0.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) - 1 by 1 by 1 MPI processor grid -create_atoms 1 region atoms -Created 32 atoms - Time spent = 0.000315666 secs - -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 0.0 1.0 - -neighbor 1.0 nsq - -# -# TEST 1: -# - -# This compute voronoi generates all three -# types of quantity: per-atom, local, and global - -compute v1 all voronoi/atom neighbors yes edge_histo 6 - -# write voronoi per-atom quantities to a file - -dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] - -# writing voronoi local quantities to a file - -dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] - -# sum up a voronoi per-atom quantity - -compute volvor all reduce sum c_v1[1] - -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys - -# output voronoi global quantities - -thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.5 - ghost atom cutoff = 3.5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/nsq/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 10.04 | 10.04 | 10.04 Mbytes -c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] - 277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0 -Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms - -0.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 7.153e-07 | | |100.00 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 325 ave 325 max 325 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - -uncompute v1 -uncompute volvor -undump dperatom -undump dlocal - -# -# TEST 2: -# - -# This compute voronoi generates -# local and global quantities, but -# not per-atom quantities - -compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no - -# write voronoi local quantities to a file - -dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] - -# sum up a voronoi local quantity - -compute sumarea all reduce sum c_v2[3] - -# output voronoi global quantities - -thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Per MPI rank memory allocation (min/avg/max) = 8.787 | 8.787 | 8.787 Mbytes -c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] - 1215.0706 0 186 12 36 0 -Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms - -139.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 7.153e-07 | | |100.00 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 325 ave 325 max 325 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - - - -Total wall time: 0:00:00 diff --git a/examples/voronoi/log.27Nov18.voronoi.data.g++.4 b/examples/voronoi/log.27Nov18.voronoi.data.g++.4 deleted file mode 100644 index be028e4d2f..0000000000 --- a/examples/voronoi/log.27Nov18.voronoi.data.g++.4 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Exercise different output data options - -variable len equal 4.0 -variable lenz equal 10.0 - -dimension 2 -units metal -boundary f f p - -lattice hex 1.0 origin 0.25 0.25 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 - -atom_style atomic - -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 -region atoms block 0 ${len} 0 ${len} 0.0 0.0 -region atoms block 0 4 0 ${len} 0.0 0.0 -region atoms block 0 4 0 4 0.0 0.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) - 2 by 2 by 1 MPI processor grid -create_atoms 1 region atoms -Created 32 atoms - Time spent = 0.000311136 secs - -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 0.0 1.0 - -neighbor 1.0 nsq - -# -# TEST 1: -# - -# This compute voronoi generates all three -# types of quantity: per-atom, local, and global - -compute v1 all voronoi/atom neighbors yes edge_histo 6 - -# write voronoi per-atom quantities to a file - -dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] - -# writing voronoi local quantities to a file - -dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] - -# sum up a voronoi per-atom quantity - -compute volvor all reduce sum c_v1[1] - -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys - -# output voronoi global quantities - -thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.5 - ghost atom cutoff = 3.5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/nsq/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 9.922 | 9.922 | 9.922 Mbytes -c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] - 277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0 -Loop time of 1.40667e-05 on 4 procs for 0 steps with 32 atoms - -46.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.407e-05 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 24 ave 24 max 24 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 81.25 ave 84 max 77 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - -uncompute v1 -uncompute volvor -undump dperatom -undump dlocal - -# -# TEST 2: -# - -# This compute voronoi generates -# local and global quantities, but -# not per-atom quantities - -compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no - -# write voronoi local quantities to a file - -dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] - -# sum up a voronoi local quantity - -compute sumarea all reduce sum c_v2[3] - -# output voronoi global quantities - -thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Per MPI rank memory allocation (min/avg/max) = 8.671 | 8.671 | 8.671 Mbytes -c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] - 1215.0706 0 186 12 36 0 -Loop time of 2.71797e-05 on 4 procs for 0 steps with 32 atoms - -57.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.718e-05 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 24 ave 24 max 24 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 81.25 ave 84 max 77 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - - - -Total wall time: 0:00:00 diff --git a/examples/voronoi/log.27Nov18.voronoi.2d.g++.1 b/examples/voronoi/log.6Dec23.voronoi.2d.g++.1 similarity index 53% rename from examples/voronoi/log.27Nov18.voronoi.2d.g++.1 rename to examples/voronoi/log.6Dec23.voronoi.2d.g++.1 index a591db8b4f..0f1bc89bb9 100644 --- a/examples/voronoi/log.27Nov18.voronoi.2d.g++.1 +++ b/examples/voronoi/log.6Dec23.voronoi.2d.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (27 Nov 2018) +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Test volume definitions for 2d and finite systems @@ -9,57 +10,58 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary p p p +units metal +boundary p p p #lattice sq 1.0 origin 0.5 0.5 0.0 lattice hex 1.0 origin 0.5 0.5 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 +Lattice spacing in x,y,z = 1 1.7320508 1 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 region atoms block 0 4 0 ${len} 0.0 0.0 region atoms block 0 4 0 4 0.0 0.0 create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) 1 by 1 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms - Time spent = 0.000315905 secs + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds -mass 1 1.0 +mass 1 1.0 pair_style lj/cut ${rcut} pair_style lj/cut 10 pair_coeff 1 1 0.0 1.0 -neighbor ${rskin} nsq -neighbor 2 nsq +neighbor ${rskin} nsq +neighbor 2 nsq # set the minimum communication cut-off comm_modify cutoff ${rcomm} comm_modify cutoff 20 -compute v1 all voronoi/atom neighbors yes -compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys -thermo_style custom c_volvor v_volsys vol v_err -thermo 1 +compute v1 all voronoi/atom neighbors yes +compute volvor all reduce sum c_v1[1] +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys +thermo_style custom c_volvor v_volsys vol v_err +thermo 1 # # TEST 1: Volume check for 2d bulk system # -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 20 @@ -69,12 +71,12 @@ Neighbor list info ... pair build: half/nsq/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 3.007 | 3.007 | 3.007 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 5.6843419e-14 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms +Per MPI rank memory allocation (min/avg/max) = 3.008 | 3.008 | 3.008 Mbytes + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 -3.5527137e-15 +Loop time of 6.33e-07 on 1 procs for 0 steps with 32 atoms -209.7% CPU use with 1 MPI tasks x 1 OpenMP threads +316.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -84,13 +86,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 6.33e-07 | | |100.00 -Nlocal: 32 ave 32 max 32 min +Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2415 ave 2415 max 2415 min +Nghost: 2415 ave 2415 max 2415 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8256 ave 8256 max 8256 min +Neighs: 8256 ave 8256 max 8256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8256 @@ -103,15 +105,17 @@ Dangerous builds = 0 # add margins in x and y directions # -change_box all boundary f f p -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +change_box all boundary f f p +Changing box ... +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 7.688 | 7.688 | 7.688 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 3.4106051e-13 -Loop time of 4.76837e-07 on 1 procs for 0 steps with 32 atoms + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 3.5527137e-14 +Loop time of 3.93e-07 on 1 procs for 0 steps with 32 atoms -209.7% CPU use with 1 MPI tasks x 1 OpenMP threads +254.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -121,13 +125,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 4.768e-07 | | |100.00 +Other | | 3.93e-07 | | |100.00 -Nlocal: 32 ave 32 max 32 min +Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min +Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 496 ave 496 max 496 min +Neighs: 496 ave 496 max 496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496 diff --git a/examples/voronoi/log.27Nov18.voronoi.2d.g++.4 b/examples/voronoi/log.6Dec23.voronoi.2d.g++.4 similarity index 51% rename from examples/voronoi/log.27Nov18.voronoi.2d.g++.4 rename to examples/voronoi/log.6Dec23.voronoi.2d.g++.4 index 841f8dcb81..f5a5052c4f 100644 --- a/examples/voronoi/log.27Nov18.voronoi.2d.g++.4 +++ b/examples/voronoi/log.6Dec23.voronoi.2d.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (27 Nov 2018) +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Test volume definitions for 2d and finite systems @@ -9,57 +10,58 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary p p p +units metal +boundary p p p #lattice sq 1.0 origin 0.5 0.5 0.0 lattice hex 1.0 origin 0.5 0.5 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 +Lattice spacing in x,y,z = 1 1.7320508 1 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 region atoms block 0 4 0 ${len} 0.0 0.0 region atoms block 0 4 0 4 0.0 0.0 create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) 2 by 2 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms - Time spent = 0.000319481 secs + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds -mass 1 1.0 +mass 1 1.0 pair_style lj/cut ${rcut} pair_style lj/cut 10 pair_coeff 1 1 0.0 1.0 -neighbor ${rskin} nsq -neighbor 2 nsq +neighbor ${rskin} nsq +neighbor 2 nsq # set the minimum communication cut-off comm_modify cutoff ${rcomm} comm_modify cutoff 20 -compute v1 all voronoi/atom neighbors yes -compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys -thermo_style custom c_volvor v_volsys vol v_err -thermo 1 +compute v1 all voronoi/atom neighbors yes +compute volvor all reduce sum c_v1[1] +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys +thermo_style custom c_volvor v_volsys vol v_err +thermo 1 # # TEST 1: Volume check for 2d bulk system # -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 20 @@ -69,12 +71,12 @@ Neighbor list info ... pair build: half/nsq/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 3.042 | 3.042 | 3.042 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 5.1159077e-13 -Loop time of 2.79546e-05 on 4 procs for 0 steps with 32 atoms +Per MPI rank memory allocation (min/avg/max) = 3.038 | 3.038 | 3.038 Mbytes + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 2.1316282e-14 +Loop time of 2.18725e-06 on 4 procs for 0 steps with 32 atoms -51.9% CPU use with 4 MPI tasks x 1 OpenMP threads +45.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -84,13 +86,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.795e-05 | | |100.00 +Other | | 2.187e-06 | | |100.00 -Nlocal: 8 ave 8 max 8 min +Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 2159 ave 2159 max 2159 min +Nghost: 2159 ave 2159 max 2159 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 2064 ave 2077 max 2051 min +Neighs: 2064 ave 2077 max 2051 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 8256 @@ -103,15 +105,17 @@ Dangerous builds = 0 # add margins in x and y directions # -change_box all boundary f f p -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Per MPI rank memory allocation (min/avg/max) = 7.678 | 7.678 | 7.678 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 3.4106051e-13 -Loop time of 1.88947e-05 on 4 procs for 0 steps with 32 atoms +change_box all boundary f f p +Changing box ... +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.671 | 7.671 | 7.671 Mbytes + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 3.907985e-14 +Loop time of 2.22e-06 on 4 procs for 0 steps with 32 atoms -47.6% CPU use with 4 MPI tasks x 1 OpenMP threads +112.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -121,13 +125,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.889e-05 | | |100.00 +Other | | 2.22e-06 | | |100.00 -Nlocal: 8 ave 8 max 8 min +Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 24 ave 24 max 24 min +Nghost: 24 ave 24 max 24 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 124 ave 124 max 124 min +Neighs: 124 ave 124 max 124 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496 diff --git a/examples/voronoi/log.6Dec23.voronoi.data.g++.1 b/examples/voronoi/log.6Dec23.voronoi.data.g++.1 new file mode 100644 index 0000000000..b598b251dc --- /dev/null +++ b/examples/voronoi/log.6Dec23.voronoi.data.g++.1 @@ -0,0 +1,168 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Exercise different output data options + +variable len equal 4.0 +variable lenz equal 10.0 + +dimension 2 +units metal +boundary f f p + +lattice hex 1.0 origin 0.25 0.25 0.0 +Lattice spacing in x,y,z = 1 1.7320508 1 + +atom_style atomic + +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 +region atoms block 0 ${len} 0 ${len} 0.0 0.0 +region atoms block 0 4 0 ${len} 0.0 0.0 +region atoms block 0 4 0 4 0.0 0.0 +create_box 1 box +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region atoms +Created 32 atoms + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds + +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 0.0 1.0 + +neighbor 1.0 nsq + +# +# TEST 1: +# + +# This compute voronoi generates all three +# types of quantity: per-atom, local, and global + +compute v1 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi per-atom quantities to a file + +dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] + +# writing voronoi local quantities to a file + +dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] + +# sum up a voronoi per-atom quantity + +compute volvor all reduce sum c_v1[1] + +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys + +# output voronoi global quantities + +thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.5 + ghost atom cutoff = 3.5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes + c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] + 27.712813 27.712813 27.712813 3.1974423e-14 0 186 12 36 0 +Loop time of 7.96e-07 on 1 procs for 0 steps with 32 atoms + +125.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.96e-07 | | |100.00 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 325 ave 325 max 325 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 + +uncompute v1 +uncompute volvor +undump dperatom +undump dlocal + +# +# TEST 2: +# + +# This compute voronoi generates peratom and local and global quantities + +compute v2 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi local quantities to a file + +dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] + +# sum up a voronoi local quantity + +compute sumarea all reduce sum c_v2[3] inputs local + +# output voronoi global quantities + +thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes + c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] + 171.39013 0 186 12 36 0 +Loop time of 3.74e-07 on 1 procs for 0 steps with 32 atoms + +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.74e-07 | | |100.00 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 325 ave 325 max 325 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/voronoi/log.6Dec23.voronoi.data.g++.4 b/examples/voronoi/log.6Dec23.voronoi.data.g++.4 new file mode 100644 index 0000000000..dc0855c2c7 --- /dev/null +++ b/examples/voronoi/log.6Dec23.voronoi.data.g++.4 @@ -0,0 +1,168 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Exercise different output data options + +variable len equal 4.0 +variable lenz equal 10.0 + +dimension 2 +units metal +boundary f f p + +lattice hex 1.0 origin 0.25 0.25 0.0 +Lattice spacing in x,y,z = 1 1.7320508 1 + +atom_style atomic + +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 +region atoms block 0 ${len} 0 ${len} 0.0 0.0 +region atoms block 0 4 0 ${len} 0.0 0.0 +region atoms block 0 4 0 4 0.0 0.0 +create_box 1 box +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region atoms +Created 32 atoms + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds + +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 0.0 1.0 + +neighbor 1.0 nsq + +# +# TEST 1: +# + +# This compute voronoi generates all three +# types of quantity: per-atom, local, and global + +compute v1 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi per-atom quantities to a file + +dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] + +# writing voronoi local quantities to a file + +dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] + +# sum up a voronoi per-atom quantity + +compute volvor all reduce sum c_v1[1] + +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys + +# output voronoi global quantities + +thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.5 + ghost atom cutoff = 3.5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes + c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] + 27.712813 27.712813 27.712813 3.907985e-14 0 186 12 36 0 +Loop time of 2.21425e-06 on 4 procs for 0 steps with 32 atoms + +45.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.214e-06 | | |100.00 + +Nlocal: 8 ave 8 max 8 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 24 ave 24 max 24 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 81.25 ave 84 max 77 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 + +uncompute v1 +uncompute volvor +undump dperatom +undump dlocal + +# +# TEST 2: +# + +# This compute voronoi generates peratom and local and global quantities + +compute v2 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi local quantities to a file + +dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] + +# sum up a voronoi local quantity + +compute sumarea all reduce sum c_v2[3] inputs local + +# output voronoi global quantities + +thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes + c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] + 171.39013 0 186 12 36 0 +Loop time of 1.82375e-06 on 4 procs for 0 steps with 32 atoms + +82.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.824e-06 | | |100.00 + +Nlocal: 8 ave 8 max 8 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 24 ave 24 max 24 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 81.25 ave 84 max 77 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/fortran/lammps.f90 b/fortran/lammps.f90 index d0133f075c..083fcbe948 100644 --- a/fortran/lammps.f90 +++ b/fortran/lammps.f90 @@ -113,6 +113,9 @@ MODULE LIBLAMMPS PROCEDURE :: get_mpi_comm => lmp_get_mpi_comm PROCEDURE :: extract_setting => lmp_extract_setting PROCEDURE :: extract_global => lmp_extract_global + PROCEDURE, PRIVATE :: lmp_map_atom_int + PROCEDURE, PRIVATE :: lmp_map_atom_big + GENERIC :: map_atom => lmp_map_atom_int, lmp_map_atom_big PROCEDURE :: extract_atom => lmp_extract_atom PROCEDURE :: extract_compute => lmp_extract_compute PROCEDURE :: extract_fix => lmp_extract_fix @@ -508,6 +511,13 @@ MODULE LIBLAMMPS TYPE(c_ptr) :: lammps_extract_global END FUNCTION lammps_extract_global + FUNCTION lammps_map_atom(handle, tag) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), INTENT(IN), VALUE :: handle, tag + INTEGER(c_int) :: lammps_map_atom + END FUNCTION lammps_map_atom + FUNCTION lammps_extract_atom_datatype(handle, name) BIND(C) IMPORT :: c_ptr, c_int IMPLICIT NONE @@ -1323,6 +1333,38 @@ CONTAINS END SELECT END FUNCTION + ! equivalent function to lammps_map_atom (for 32-bit integer tags) + INTEGER FUNCTION lmp_map_atom_int(self, id) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int), INTENT(IN), TARGET :: id + INTEGER(c_int64_t), TARGET :: id64 + TYPE(c_ptr) :: Cptr + + IF (SIZE_TAGINT == 8) THEN + id64 = id + Cptr = C_LOC(id64) + ELSE + Cptr = C_LOC(id) + END IF + lmp_map_atom_int = lammps_map_atom(self%handle, Cptr) + 1 + END FUNCTION lmp_map_atom_int + + ! equivalent function to lammps_map_atom (for 64-bit integer tags) + INTEGER FUNCTION lmp_map_atom_big(self, id) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int64_t), INTENT(IN), TARGET :: id + INTEGER(c_int), TARGET :: id32 + TYPE(c_ptr) :: Cptr + + IF (SIZE_TAGINT == 8) THEN + Cptr = C_LOC(id) + ELSE + id32 = id + Cptr = C_LOC(id32) + END IF + lmp_map_atom_big = lammps_map_atom(self%handle, Cptr) + 1 + END FUNCTION lmp_map_atom_big + ! equivalent function to lammps_extract_atom ! the assignment is actually overloaded so as to bind the pointers to ! lammps data based on the information available from LAMMPS @@ -3687,7 +3729,7 @@ CONTAINS n = LEN_TRIM(f_string) ptr = lammps_malloc(n+1) - CALL C_F_POINTER(ptr, c_string, [1]) + CALL C_F_POINTER(ptr, c_string, [n+1]) DO i=1, n c_string(i) = f_string(i:i) END DO diff --git a/lib/gpu/lal_base_amoeba.h b/lib/gpu/lal_base_amoeba.h index f415b30334..7255b8770f 100644 --- a/lib/gpu/lal_base_amoeba.h +++ b/lib/gpu/lal_base_amoeba.h @@ -33,6 +33,7 @@ //#define ASYNC_DEVICE_COPY +#if 0 #if !defined(USE_OPENCL) && !defined(USE_HIP) // temporary workaround for int2 also defined in cufft #ifdef int2 @@ -40,6 +41,7 @@ #endif #include "cufft.h" #endif +#endif namespace LAMMPS_AL { @@ -313,10 +315,11 @@ class BaseAmoeba { virtual int fphi_mpole(); virtual int polar_real(const int eflag, const int vflag) = 0; - +#if 0 #if !defined(USE_OPENCL) && !defined(USE_HIP) cufftHandle plan; #endif +#endif bool fft_plan_created; }; diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp index 0ddd24d21e..dfeaf24ce9 100644 --- a/lib/gpu/lal_base_dpd.cpp +++ b/lib/gpu/lal_base_dpd.cpp @@ -57,7 +57,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall, const double cell_size, const double gpu_split, FILE *_screen, const void *pair_program, const char *k_name, const int onetype, - const int extra_fields) { + const int extra_fields, bool need_charges) { screen=_screen; int gpu_nbor=0; @@ -73,7 +73,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall, _threads_per_atom=device->threads_per_atom(); - bool charge = false; + bool charge = need_charges; bool rot = false; bool vel = true; _extra_fields = extra_fields; diff --git a/lib/gpu/lal_base_dpd.h b/lib/gpu/lal_base_dpd.h index 64ec725d95..658147419d 100644 --- a/lib/gpu/lal_base_dpd.h +++ b/lib/gpu/lal_base_dpd.h @@ -53,7 +53,8 @@ class BaseDPD { const int maxspecial, const double cell_size, const double gpu_split, FILE *screen, const void *pair_program, const char *k_name, - const int onetype=0, const int extra_fields=0); + const int onetype=0, const int extra_fields=0, + bool need_charges=false); /// Estimate the overhead for GPU context changes and CPU driver void estimate_gpu_overhead(); diff --git a/lib/gpu/lal_dpd_coul_slater_long.cpp b/lib/gpu/lal_dpd_coul_slater_long.cpp new file mode 100644 index 0000000000..aa2b73566c --- /dev/null +++ b/lib/gpu/lal_dpd_coul_slater_long.cpp @@ -0,0 +1,238 @@ +/*************************************************************************** + lal_dpd_coul_slater_long.cpp + ------------------- + Eddy BARRAUD (IFPEN/Sorbonne) + + Class for acceleration of the dpd/coul/slater/long pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : May 28, 2024 + email : eddy.barraud@outlook.fr + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "dpd_coul_slater_long_cl.h" +#elif defined(USE_CUDART) +const char *dpd_coul_slater_long=0; +#else +#include "dpd_coul_slater_long_cubin.h" +#endif + +#include "lal_dpd_coul_slater_long.h" +#include +namespace LAMMPS_AL { +#define DPDCoulSlaterLongT DPDCoulSlaterLong + +extern Device device; + +template +DPDCoulSlaterLongT::DPDCoulSlaterLong() : BaseDPD(), _allocated(false) { +} + +template +DPDCoulSlaterLongT::~DPDCoulSlaterLong() { + clear(); +} + +template +int DPDCoulSlaterLongT::bytes_per_atom(const int max_nbors) const { + return this->bytes_per_atom_atomic(max_nbors); +} + +template +int DPDCoulSlaterLongT::init(const int ntypes, + double **host_cutsq, double **host_a0, + double **host_gamma, double **host_sigma, + double **host_cut_dpd, double **host_cut_dpdsq, + double **host_cut_slatersq, double *host_special_lj, + const bool tstat_only, + const int nlocal, const int nall, + const int max_nbors, const int maxspecial, + const double cell_size, + const double gpu_split, FILE *_screen, double *host_special_coul, + const double qqrd2e, const double g_ewald, double lamda) { + const int max_shared_types=this->device->max_shared_types(); + + int onetype=0; + #ifdef USE_OPENCL + if (maxspecial==0) + for (int i=1; i0) { + if (onetype>0) + onetype=-1; + else if (onetype==0) + onetype=i*max_shared_types+j; + } + if (onetype<0) onetype=0; + #endif + int extra_fields = 4; // round up to accomodate quadruples of numtyp values + // q + int success; + bool need_charges = true; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size, + gpu_split,_screen,dpd_coul_slater_long,"k_dpd_coul_slater_long",onetype, extra_fields, need_charges); + + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + shared_types=false; + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + shared_types=true; + } + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write_coul(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write_coul[i]=host_special_coul[i]; + } + ucl_copy(sp_cl,host_write_coul,4,false); + + _lj_types=lj_types; + _qqrd2e=qqrd2e; + _g_ewald=g_ewald; + _lamda=lamda; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_a0,host_gamma, + host_sigma,host_cut_dpd); + + cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,cutsq,host_write,host_cutsq, + host_cut_dpdsq,host_cut_slatersq); + + double special_sqrt[4]; + special_sqrt[0] = sqrt(host_special_lj[0]); + special_sqrt[1] = sqrt(host_special_lj[1]); + special_sqrt[2] = sqrt(host_special_lj[2]); + special_sqrt[3] = sqrt(host_special_lj[3]); + + UCL_H_Vec dview; + sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY); + dview.view(host_special_lj,4,*(this->ucl_device)); + ucl_copy(sp_lj,dview,false); + sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY); + dview.view(special_sqrt,4,*(this->ucl_device)); + ucl_copy(sp_sqrt,dview,false); + + _tstat_only = 0; + if (tstat_only) _tstat_only=1; + + _allocated=true; + this->_max_bytes=coeff.row_bytes()+cutsq.row_bytes()+sp_lj.row_bytes()+sp_sqrt.row_bytes(); + return 0; +} + +template +void DPDCoulSlaterLongT::clear() { + if (!_allocated) + return; + _allocated=false; + + coeff.clear(); + cutsq.clear(); + sp_lj.clear(); + sp_sqrt.clear(); + this->clear_atomic(); +} + +template +double DPDCoulSlaterLongT::host_memory_usage() const { + return this->host_memory_usage_atomic()+sizeof(DPDCoulSlaterLong); +} + +// --------------------------------------------------------------------------- +// Calculate energies, forces, and torques +// --------------------------------------------------------------------------- +template +int DPDCoulSlaterLongT::loop(const int eflag, const int vflag) { + + int nall = this->atom->nall(); + // signal that we need to transfer extra data from the host + + this->atom->extra_data_unavail(); + + numtyp4 *pextra=reinterpret_cast(&(this->atom->extra[0])); + + int n = 0; + int nstride = 1; + for (int i = 0; i < nall; i++) { + int idx = n+i*nstride; + numtyp4 v; + v.x = q[i]; + v.y = 0; + v.z = 0; + v.w = 0; + pextra[idx] = v; + } + this->atom->add_extra_data(); + + // Compute the block size and grid size to keep all cores busy + const int BX=this->block_size(); + int GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/this->_threads_per_atom))); + + int ainum=this->ans->inum(); + int nbor_pitch=this->nbor->nbor_pitch(); + this->time_pair.start(); + if (shared_types) { + this->k_pair_sel->set_size(GX,BX); + this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &sp_lj, &sp_cl, &sp_sqrt, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, + &vflag, &ainum, &nbor_pitch, &this->atom->v, &cutsq, + &this->_dtinvsqrt, &this->_seed, &this->_timestep, + &_qqrd2e, &_g_ewald, &_lamda, + &this->_tstat_only, &this->_threads_per_atom); + } else { + this->k_pair.set_size(GX,BX); + this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &_lj_types, &sp_lj, &sp_cl, &sp_sqrt, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, &vflag, + &ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt, + &this->_seed, &this->_timestep, + &_qqrd2e, &_g_ewald, &_lamda, + &this->_tstat_only, &this->_threads_per_atom); + } + this->time_pair.stop(); + return GX; +} + +template +void DPDCoulSlaterLongT::update_coeff(int ntypes, double **host_a0, double **host_gamma, + double **host_sigma, double **host_cut_dpd) +{ + UCL_H_Vec host_write(_lj_types*_lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + this->atom->type_pack4(ntypes,_lj_types,coeff,host_write,host_a0,host_gamma, + host_sigma,host_cut_dpd); +} + +// --------------------------------------------------------------------------- +// Get the extra data pointers from host +// --------------------------------------------------------------------------- + +template +void DPDCoulSlaterLongT::get_extra_data(double *host_q) { + q = host_q; +} + +template class DPDCoulSlaterLong; +} + + diff --git a/lib/gpu/lal_dpd_coul_slater_long.cu b/lib/gpu/lal_dpd_coul_slater_long.cu new file mode 100644 index 0000000000..d9679ccdfd --- /dev/null +++ b/lib/gpu/lal_dpd_coul_slater_long.cu @@ -0,0 +1,523 @@ +// ************************************************************************** +// dpd.cu +// ------------------- +// Eddy BARRAUD (IFPEN/Sorbonne) +// Trung Dac Nguyen (U Chicago) +// +// Device code for acceleration of the dpd/coul/slater/long pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : May 28, 2024 +// email : eddy.barraud@outlook.fr +// *************************************************************************** + +#if defined(NV_KERNEL) || defined(USE_HIP) +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +_texture( pos_tex,float4); +_texture( vel_tex,float4); +#else +_texture_2d( pos_tex,int4); +_texture_2d( vel_tex,int4); +#endif +#else +#define pos_tex x_ +#define vel_tex v_ +#endif + +#define EPSILON (numtyp)1.0e-10 + +//#define _USE_UNIFORM_SARU_LCG +//#define _USE_UNIFORM_SARU_TEA8 +//#define _USE_GAUSSIAN_SARU_LCG + +#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG) +#define _USE_UNIFORM_SARU_LCG +#endif + +// References: +// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128. +// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201. +// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19 + +#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */ +#define LCGC 0x2600e1f7 +#define oWeylPeriod 0xda879add /* Prime period 3666320093 */ +#define oWeylOffset 0x8009d14b +#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */ + +// specifically implemented for steps = 1; high = 1.0; low = -1.0 +// returns uniformly distributed random numbers u in [-1.0;1.0] +// using the inherent LCG, then multiply u with sqrt(3) to "match" +// with a normal random distribution. +// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12) +// Curly brackets to make variables local to the scope. +#ifdef _USE_UNIFORM_SARU_LCG +#define SQRT3 (numtyp)1.7320508075688772935274463 +#define saru(seed1, seed2, seed, timestep, randnum) { \ + unsigned int seed3 = seed + timestep; \ + seed3^=(seed1<<7)^(seed2>>6); \ + seed2+=(seed1>>4)^(seed3>>15); \ + seed1^=(seed2<<9)+(seed3<<8); \ + seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \ + seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \ + seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \ + seed2+=seed1*seed3; \ + seed1+=seed3 ^ (seed2>>2); \ + seed2^=((signed int)seed2)>>17; \ + unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \ + unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \ + state = state + (wstate*(wstate^0xdddf97f5)); \ + wstate = 0xABCB96F7 + (wstate>>1); \ + state = LCGA*state + LCGC; \ + wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \ + unsigned int v = (state ^ (state>>26)) + wstate; \ + unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \ + randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \ +} +#endif + +// specifically implemented for steps = 1; high = 1.0; low = -1.0 +// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8 +// then multiply u with sqrt(3) to "match" with a normal random distribution +// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12) +#ifdef _USE_UNIFORM_SARU_TEA8 +#define SQRT3 (numtyp)1.7320508075688772935274463 +#define k0 0xA341316C +#define k1 0xC8013EA4 +#define k2 0xAD90777D +#define k3 0x7E95761E +#define delta 0x9e3779b9 +#define rounds 8 +#define saru(seed1, seed2, seed, timestep, randnum) { \ + unsigned int seed3 = seed + timestep; \ + seed3^=(seed1<<7)^(seed2>>6); \ + seed2+=(seed1>>4)^(seed3>>15); \ + seed1^=(seed2<<9)+(seed3<<8); \ + seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \ + seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \ + seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \ + seed2+=seed1*seed3; \ + seed1+=seed3 ^ (seed2>>2); \ + seed2^=((signed int)seed2)>>17; \ + unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \ + unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \ + state = state + (wstate*(wstate^0xdddf97f5)); \ + wstate = 0xABCB96F7 + (wstate>>1); \ + unsigned int sum = 0; \ + for (int i=0; i < rounds; i++) { \ + sum += delta; \ + state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \ + wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \ + } \ + unsigned int v = (state ^ (state>>26)) + wstate; \ + unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \ + randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \ +} +#endif + +// specifically implemented for steps = 1; high = 1.0; low = -1.0 +// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0], +// and uses the polar method (Marsaglia's) to transform to a normal random value +// This is used to compared with CPU DPD using RandMars::gaussian() +#ifdef _USE_GAUSSIAN_SARU_LCG +#define saru(seed1, seed2, seed, timestep, randnum) { \ + unsigned int seed3 = seed + timestep; \ + seed3^=(seed1<<7)^(seed2>>6); \ + seed2+=(seed1>>4)^(seed3>>15); \ + seed1^=(seed2<<9)+(seed3<<8); \ + seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \ + seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \ + seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \ + seed2+=seed1*seed3; \ + seed1+=seed3 ^ (seed2>>2); \ + seed2^=((signed int)seed2)>>17; \ + unsigned int state=0x12345678; \ + unsigned int wstate=12345678; \ + state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \ + wstate = (state + seed2) ^ (((signed int)state)>>8); \ + state = state + (wstate*(wstate^0xdddf97f5)); \ + wstate = 0xABCB96F7 + (wstate>>1); \ + unsigned int v, s; \ + numtyp r1, r2, rsq; \ + while (1) { \ + state = LCGA*state + LCGC; \ + wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \ + v = (state ^ (state>>26)) + wstate; \ + s = (signed int)((v^(v>>20))*0x6957f5a7); \ + r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \ + state = LCGA*state + LCGC; \ + wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \ + v = (state ^ (state>>26)) + wstate; \ + s = (signed int)((v^(v>>20))*0x6957f5a7); \ + r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \ + rsq = r1 * r1 + r2 * r2; \ + if (rsq < (numtyp)1.0) break; \ + } \ + numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq); \ + randnum = r2*fac; \ +} +#endif + +__kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict extra, + const __global numtyp4 *restrict coeff, + const int lj_types, + const __global numtyp *restrict sp_lj, + const __global numtyp *restrict sp_cl_in, + const __global numtyp *restrict sp_sqrt, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp3 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp4 *restrict v_, + const __global numtyp4 *restrict cutsq, + const numtyp dtinvsqrt, const int seed, + const int timestep, const numtyp qqrd2e, + const numtyp g_ewald, const numtyp lamda, + const int tstat_only, + const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_cl[4]; + ///local_allocate_store_charge(); + + sp_cl[0]=sp_cl_in[0]; + sp_cl[1]=sp_cl_in[1]; + sp_cl[2]=sp_cl_in[2]; + sp_cl[3]=sp_cl_in[3]; + + int n_stride; + local_allocate_store_pair(); + + acctyp3 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp e_coul, energy, virial[6]; + if (EVFLAG) { + energy=(acctyp)0; + e_coul=(acctyp)0; + for (int i=0; i<6; i++) virial[i]=(acctyp)0; + } + + if (ii global squared cutoff + if (rsq DPD squared cutoff + if (rsq < cutsq[mtype].y && r > EPSILON) { + + numtyp rinv=ucl_recip(r); + numtyp delvx = iv.x - jv.x; + numtyp delvy = iv.y - jv.y; + numtyp delvz = iv.z - jv.z; + numtyp dot = delx*delvx + dely*delvy + delz*delvz; + numtyp wd = (numtyp)1.0 - r/coeff[mtype].w; + + unsigned int tag1=itag, tag2=jtag; + if (tag1 > tag2) { + tag1 = jtag; tag2 = itag; + } + + numtyp randnum = (numtyp)0.0; + saru(tag1, tag2, seed, timestep, randnum); + + // conservative force = a0 * wd, or 0 if tstat only + // drag force = -gamma * wd^2 * (delx dot delv) / r + // random force = sigma * wd * rnd * dtinvsqrt; + + if (!tstat_only) force_dpd = coeff[mtype].x*wd; + force_dpd -= coeff[mtype].y*wd*wd*dot*rinv; + force_dpd *= factor_dpd; + force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt; + force_dpd *=rinv; + + if (EVFLAG && eflag) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd; + energy += factor_dpd*e; + } + + }// if cut_dpdsq + + // apply Slater electrostatic force if distance below Slater cutoff + // and the two species have a slater coeff + // cutsq[mtype].z -> Coulombic squared cutoff + if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){ + numtyp r2inv=ucl_recip(rsq); + numtyp _erfc; + numtyp grij = g_ewald * r; + numtyp expm2 = ucl_exp(-grij*grij); + numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); + _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + numtyp prefactor = extra[j].x; + prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r; + numtyp rlamdainv = r * lamdainv; + numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv); + numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv))); + force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term); + if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term); + force_coul *= r2inv; + + if (EVFLAG && eflag) { + numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv; + numtyp e = prefactor*(_erfc-e_slater); + if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater); + e_coul += e; + } + } // if cut_coulsq + + numtyp force = force_coul + force_dpd; + f.x += delx*force; + f.y += dely*force; + f.z += delz*force; + + if (EVFLAG && vflag) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + + } // if cutsq + + } // for nbor + } // if ii + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, + ans,engv); +} + +__kernel void k_dpd_coul_slater_long_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict extra, + const __global numtyp4 *restrict coeff_in, + const __global numtyp *restrict sp_lj_in, + const __global numtyp *restrict sp_cl_in, + const __global numtyp *restrict sp_sqrt_in, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp3 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp4 *restrict v_, + const __global numtyp4 *restrict cutsq_in, + const numtyp dtinvsqrt, const int seed, + const int timestep, const numtyp qqrd2e, + const numtyp g_ewald, const numtyp lamda, + const int tstat_only, + const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[4]; + __local numtyp sp_sqrt[4]; + /// COUL Init + __local numtyp sp_cl[4]; + if (tid<4) { + sp_lj[tid]=sp_lj_in[tid]; + sp_sqrt[tid]=sp_sqrt_in[tid]; + sp_cl[tid]=sp_cl_in[tid]; + } + if (tid DPD squared cutoff + if (rsq < cutsq[mtype].y && r > EPSILON) { + + numtyp rinv=ucl_recip(r); + numtyp delvx = iv.x - jv.x; + numtyp delvy = iv.y - jv.y; + numtyp delvz = iv.z - jv.z; + numtyp dot = delx*delvx + dely*delvy + delz*delvz; + numtyp wd = (numtyp)1.0 - r/coeff[mtype].w; + + unsigned int tag1=itag, tag2=jtag; + if (tag1 > tag2) { + tag1 = jtag; tag2 = itag; + } + + numtyp randnum = (numtyp)0.0; + saru(tag1, tag2, seed, timestep, randnum); + + // conservative force = a0 * wd, or 0 if tstat only + // drag force = -gamma * wd^2 * (delx dot delv) / r + // random force = sigma * wd * rnd * dtinvsqrt; + /// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd + + if (!tstat_only) force_dpd = coeff[mtype].x*wd; + force_dpd -= coeff[mtype].y*wd*wd*dot*rinv; + force_dpd *= factor_dpd; + force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt; + force_dpd *=rinv; + + if (EVFLAG && eflag) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd; + energy += factor_dpd*e; + } + + }// if cut_dpdsq + + // apply Slater electrostatic force if distance below Slater cutoff + // and the two species have a slater coeff + // cutsq[mtype].z -> Coulombic squared cutoff + if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){ + numtyp r2inv=ucl_recip(rsq); + numtyp _erfc; + numtyp grij = g_ewald * r; + numtyp expm2 = ucl_exp(-grij*grij); + numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); + _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + numtyp prefactor = extra[j].x; + prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r; + numtyp rlamdainv = r * lamdainv; + numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv); + numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv))); + force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term); + if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term); + force_coul *= r2inv; + + if (EVFLAG && eflag) { + numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv; + numtyp e_sf = prefactor*(_erfc-e_slater); + if (factor_coul > (numtyp)0) e_sf -= factor_coul*prefactor*((numtyp)1.0 - e_slater); + e_coul += e_sf; + } + } // if cut_coulsq + + numtyp force = force_coul + force_dpd; + f.x += delx*force; + f.y += dely*force; + f.z += delz*force; + + if (EVFLAG && vflag) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + + } // if cutsq + + } // for nbor + } // if ii + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, + ans,engv); +} + diff --git a/lib/gpu/lal_dpd_coul_slater_long.h b/lib/gpu/lal_dpd_coul_slater_long.h new file mode 100644 index 0000000000..1870255998 --- /dev/null +++ b/lib/gpu/lal_dpd_coul_slater_long.h @@ -0,0 +1,100 @@ +/*************************************************************************** + lal_dpd_coul_slater_long.h + ------------------- + Eddy BARRAUD (IFPEN/Sorbonne) + + Class for acceleration of the dpd/coul/slater/long pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : May 28, 2024 + email : eddy.barraud@outlook.fr + ***************************************************************************/ + +#ifndef LAL_DPD_CHARGED_H +#define LAL_DPD_CHARGED_H + +#include "lal_base_dpd.h" + +namespace LAMMPS_AL { + +template +class DPDCoulSlaterLong : public BaseDPD { + public: + DPDCoulSlaterLong(); + ~DPDCoulSlaterLong(); + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successful + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, double **host_a0, double **host_gamma, + double **host_sigma, double **host_cut_dpd, double **host_cut_dpdsq, + double **host_cut_slatersq, double *host_special_lj, bool tstat_only, const int nlocal, + const int nall, const int max_nbors, const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, double *host_special_coul, const double qqrd2e, + const double g_ewald, const double lamda); + + /// Clear all host and device data + /** \note This is called at the beginning of the init() routine **/ + void clear(); + + /// Returns memory usage on device per atom + int bytes_per_atom(const int max_nbors) const; + + /// Total host memory used by library for pair style + double host_memory_usage() const; + + /// Update coeff if needed (tstat only) + void update_coeff(int ntypes, double **host_a0, double **host_gamma, + double **host_sigma, double **host_cut_dpd ); + + void get_extra_data(double *host_q); + + // --------------------------- TYPE DATA -------------------------- + + /// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd + UCL_D_Vec coeff; + + /// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.w = cut_slatersq + UCL_D_Vec cutsq; + + /// Special LJ values + UCL_D_Vec sp_lj, sp_sqrt; + + /// Special Coul values [0-3] + UCL_D_Vec sp_cl; + + + /// If atom type constants fit in shared memory, use fast kernels + bool shared_types; + + /// Number of atom types + int _lj_types; + + /// Only used for thermostat + int _tstat_only; + + /// Coulombic terms + numtyp _qqrd2e, _g_ewald, _lamda; + + /// pointer to host data for atom charge + double *q; + + private: + bool _allocated; + int loop(const int eflag, const int vflag); +}; + +} + +#endif diff --git a/lib/gpu/lal_dpd_coul_slater_long_ext.cpp b/lib/gpu/lal_dpd_coul_slater_long_ext.cpp new file mode 100644 index 0000000000..ceed1b85be --- /dev/null +++ b/lib/gpu/lal_dpd_coul_slater_long_ext.cpp @@ -0,0 +1,142 @@ +/*************************************************************************** + lal_dpd_coul_slater_long_ext.cpp + ------------------- + Eddy BARRAUD (IFPEN/Sorbonne) + + Functions for LAMMPS access to dpd/coul/slater/long acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : May 28, 2024 + email : eddy.barraud@outlook.fr + ***************************************************************************/ + +#include +#include +#include + +#include "lal_dpd_coul_slater_long.h" + +using namespace std; +using namespace LAMMPS_AL; + +static DPDCoulSlaterLong DPDCMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int dpd_coul_slater_long_gpu_init(const int ntypes, double **host_cutsq, double **host_a0, + double **host_gamma, double **host_sigma, double **host_cut_dpd, + double **host_cut_dpdsq, double **host_cut_slatersq, + double *special_lj, const int inum, const int nall, + const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double *host_special_coul, const double qqrd2e, + const double g_ewald, const double lamda) { + DPDCMF.clear(); + gpu_mode=DPDCMF.device->gpu_mode(); + double gpu_split=DPDCMF.device->particle_split(); + int first_gpu=DPDCMF.device->first_device(); + int last_gpu=DPDCMF.device->last_device(); + int world_me=DPDCMF.device->world_me(); + int gpu_rank=DPDCMF.device->gpu_rank(); + int procs_per_gpu=DPDCMF.device->procs_per_gpu(); + + DPDCMF.device->init_message(screen,"dpd",first_gpu,last_gpu); + + bool message=false; + if (DPDCMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=DPDCMF.init(ntypes, host_cutsq, host_a0, host_gamma, host_sigma, host_cut_dpd, + host_cut_dpdsq, host_cut_slatersq, special_lj, false, inum, nall, + max_nbors, maxspecial, cell_size, gpu_split, screen, host_special_coul, + qqrd2e, g_ewald, lamda); + + DPDCMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; iserialize_init(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + DPDCMF.estimate_gpu_overhead(); + return init_ok; +} + +void dpd_coul_slater_long_gpu_clear() { + DPDCMF.clear(); +} + +int ** dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, double *sublo, + double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, bool &success, + double **host_v, const double dtinvsqrt, + const int seed, const int timestep, + double *boxlo, double *prd) { + return DPDCMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_v, dtinvsqrt, seed, timestep, boxlo, prd); +} + +void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, tagint *tag, + double **host_v, const double dtinvsqrt, + const int seed, const int timestep, + const int nlocal, double *boxlo, double *prd) { + DPDCMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj, + firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success, + tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd); +} + +void dpd_coul_slater_long_gpu_update_coeff(int ntypes, double **host_a0, double **host_gamma, + double **host_sigma, double **host_cut_dpd) +{ + DPDCMF.update_coeff(ntypes,host_a0,host_gamma,host_sigma, host_cut_dpd); +} + +void dpd_coul_slater_long_gpu_get_extra_data(double *host_q) { + DPDCMF.get_extra_data(host_q); +} + +double dpd_coul_slater_long_gpu_bytes() { + return DPDCMF.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_sph_heatconduction.cu b/lib/gpu/lal_sph_heatconduction.cu index e2ba40db0c..8e4ec6ff19 100644 --- a/lib/gpu/lal_sph_heatconduction.cu +++ b/lib/gpu/lal_sph_heatconduction.cu @@ -29,23 +29,23 @@ _texture_2d( vel_tex,int4); #if (SHUFFLE_AVAIL == 0) -#define store_dE(dEacc, ii, inum, tid, t_per_atom, offset, dE) \ +#define store_dE(dEacc, ii, inum, tid, t_per_atom, offset, i, dE) \ if (t_per_atom>1) { \ simdsync(); \ simd_reduce_add1(t_per_atom, red_acc, offset, tid, dEacc); \ } \ if (offset==0 && ii1) { \ for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ dEacc += shfl_down(dEacc, s, t_per_atom); \ } \ } \ if (offset==0 && ii1) { \ - simdsync(); \ - simd_reduce_add2(t_per_atom, red_acc, offset, tid, \ - drhoEacc.x, drhoEacc.y); \ - } \ - if (offset==0 && ii1) { \ + simdsync(); \ + simd_reduce_add2(t_per_atom, red_acc, offset, tid, \ + drhoEacc.x, drhoEacc.y); \ + } \ + if (offset==0 && ii1) { \ for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ drhoEacc.x += shfl_down(drhoEacc.x, s, t_per_atom); \ @@ -47,7 +48,8 @@ _texture_2d( vel_tex,int4); } \ } \ if (offset==0 && ii1) { \ - simdsync(); \ - simd_reduce_add2(t_per_atom, red_acc, offset, tid, \ - drhoEacc.x, drhoEacc.y); \ - } \ - if (offset==0 && ii1) { \ + simdsync(); \ + simd_reduce_add2(t_per_atom, red_acc, offset, tid, \ + drhoEacc.x, drhoEacc.y); \ + } \ + if (offset==0 && ii1) { \ for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ drhoEacc.x += shfl_down(drhoEacc.x, s, t_per_atom); \ @@ -47,7 +48,8 @@ _texture_2d( vel_tex,int4); } \ } \ if (offset==0 && ii= 5.7) and RDC [\#6857](https://github.com/kokkos/kokkos/pull/6857) + * Use rocthrust for sorting, when available [\#6793](https://github.com/kokkos/kokkos/pull/6793) + +#### SYCL: +* We only support OneAPI SYCL implementation: add check during initialization + * Error out on initialization if the backend is different from `ext_oneapi_*` [\#6784](https://github.com/kokkos/kokkos/pull/6784) + * Filter GPU devices for `ext_onapi_*` GPU devices [\#6758](https://github.com/kokkos/kokkos/pull/6784) +* Performance Improvements + * Avoid unnecessary zero-memset of the scratch flags in SYCL [\#6739](https://github.com/kokkos/kokkos/pull/6739) + * Use host-pinned memory to copy reduction/scan result [\#6500](https://github.com/kokkos/kokkos/pull/6500) +* Address deprecations after oneAPI 2023.2.0 [\#6577](https://github.com/kokkos/kokkos/pull/6739) +* Make sure to call find_dependency for oneDPL if necessary [\#6870](https://github.com/kokkos/kokkos/pull/6870) + +#### OpenMPTarget: +* Use LLVM extensions for dynamic shared memory [\#6380](https://github.com/kokkos/kokkos/pull/6380) +* Guard scratch memory usage in ParallelReduce [\#6585 ](https://github.com/kokkos/kokkos/pull/6585) +* Update linker flags for Intel GPUs update [\#6735](https://github.com/kokkos/kokkos/pull/6735) +* Improve handling of printf on Intel GPUs [\#6652](https://github.com/kokkos/kokkos/pull/6652) + +#### OpenACC: +* Add atomics support [\#6446](https://github.com/kokkos/kokkos/pull/6446) +* Make the OpenACC backend asynchronous [\#6772](https://github.com/kokkos/kokkos/pull/6772) + +#### Threads: +* Add missing broadcast to TeamThreadRange parallel_scan [\#6601](https://github.com/kokkos/kokkos/pull/6601) + +#### OpenMP: +* Improve performance of view initializations and filling with zeros [\#6573](https://github.com/kokkos/kokkos/pull/6573) + +### General Enhancements + +* Improve performance of random number generation when using a normal distribution on GPUs [\#6556](https://github.com/kokkos/kokkos/pull/6556) +* Allocate temporary view with the user-provided execution space instance and do not initialize in `unique` algorithm [\#6598](https://github.com/kokkos/kokkos/pull/6598) +* Add deduction guide for `Kokkos::Array` [\#6373](https://github.com/kokkos/kokkos/pull/6373) +* Provide new public headers `` and `` [\#6687](https://github.com/kokkos/kokkos/pull/6687) +* Fix/improvement to `remove_if` parallel algorithm: use the provided execution space instance for temporary allocations and drop unnecessaryinitialization + avoid evaluating twice the predicate during final pass [\#6747](https://github.com/kokkos/kokkos/pull/6747) +* Add runtime function to query the number of devices and make device ID consistent with `KOKKOS_VISIBLE_DEVICES` [\#6713](https://github.com/kokkos/kokkos/pull/6713) +* simd: support `vector_aligned_tag` [\#6243](https://github.com/kokkos/kokkos/pull/6243) +* Avoid unnecessary allocation when default constructing Bitset [\#6524](https://github.com/kokkos/kokkos/pull/6524) +* Fix constness for views in std algorithms [\#6813](https://github.com/kokkos/kokkos/pull/6813) +* Improve error message on unsafe implicit conversion in MDRangePolicy [\#6855](https://github.com/kokkos/kokkos/pull/6855) +* CTAD (deduction guides) for RangePolicy [\#6850](https://github.com/kokkos/kokkos/pull/6850) +* CTAD (deduction guides) for MDRangePolicy [\#5516](https://github.com/kokkos/kokkos/pull/5516) + +### Build System Changes +* Require `Kokkos_ENABLE_ATOMICS_BYPASS` option to bypass atomic operation for Serial backend only builds [\#6692](https://github.com/kokkos/kokkos/pull/6692) +* Add support for RISCV and the Milk-V's Pioneer [\#6773](https://github.com/kokkos/kokkos/pull/6773) +* Add C++26 standard to CMake setup [\#6733](https://github.com/kokkos/kokkos/pull/6733) +* Fix Makefile when using gnu_generate_makefile.sh and make >= 4.3 [\#6606](https://github.com/kokkos/kokkos/pull/6606) +* Cuda: Fix configuring with CMake >= 3.28.4 - temporary fallback to internal CudaToolkit.cmake [\#6898](https://github.com/kokkos/kokkos/pull/6898) + +### Incompatibilities (i.e. breaking changes) +* Remove all `DEPRECATED_CODE_3` option and all code that was guarded by it [\#6523](https://github.com/kokkos/kokkos/pull/6523) +* Drop guards to accommodate external code defining `KOKKOS_ASSERT` [\#6665](https://github.com/kokkos/kokkos/pull/6665) +* `Profiling::ProfilingSection(std::string)` constructor marked explicit and nodiscard [\#6690](https://github.com/kokkos/kokkos/pull/6690) +* Add bound check preconditions for `RangePolicy` and `MDRangePolicy` [\#6617](https://github.com/kokkos/kokkos/pull/6617) [\#6726](https://github.com/kokkos/kokkos/pull/6726) +* Add checks for unsafe implicit conversions in RangePolicy [\#6754](https://github.com/kokkos/kokkos/pull/6754) +* Remove Kokkos::[b]half_t volatile overloads [\#6579](https://github.com/kokkos/kokkos/pull/6579) +* Remove KOKKOS_IMPL_DO_NOT_USE_PRINTF [\#6593](https://github.com/kokkos/kokkos/pull/6593) +* Check matching static extents in View constructor [\#5190 ](https://github.com/kokkos/kokkos/pull/5190) +* Tools(profiling): fix typo Kokkos_Tools_Optim[i]zationGoal [\#6642](https://github.com/kokkos/kokkos/pull/6642) +* Remove variadic range policy constructor (disallow passing multiple trailing chunk size arguments) [\#6845](https://github.com/kokkos/kokkos/pull/6845) +* Improve message on view out of bounds access and always abort [\#6861](https://github.com/kokkos/kokkos/pull/6861) +* Drop `KOKKOS_ENABLE_INTEL_MM_ALLOC` macro [\#6797](https://github.com/kokkos/kokkos/pull/6797) +* Remove `Kokkos::Experimental::LogicalMemorySpace` (without going through deprecation) [\#6557](https://github.com/kokkos/kokkos/pull/6557) +* Remove `Experimental::HBWSpace` and support for linking against memkind [\#6791](https://github.com/kokkos/kokkos/pull/6791) +* Drop librt TPL and associated `KOKKOS_ENABLE_LIBRT` macro [\#6798](https://github.com/kokkos/kokkos/pull/6798) +* Drop support for old CPU architectures (`ARCH_BGQ`, `ARCH_POWER7`, `ARCH_WSM` and associated `ARCH_SSE4` macro) [\#6806](https://github.com/kokkos/kokkos/pull/6806) +* Drop support for deprecated command-line arguments and environment variables [\#6744](https://github.com/kokkos/kokkos/pull/6744) + +### Deprecations +* Provide kokkos_swap as part of Core and deprecate Experimental::swap in Algorithms [\#6697](https://github.com/kokkos/kokkos/pull/6697) +* Deprecate {Cuda,HIP}::detect_device_count() and Cuda::[detect_]device_arch() [\#6710](https://github.com/kokkos/kokkos/pull/6710) +* Deprecate `ExecutionSpace::in_parallel()` [\#6582](https://github.com/kokkos/kokkos/pull/6582) + +### Bug Fixes +* Fix team-level MDRange reductions: [\#6511](https://github.com/kokkos/kokkos/pull/6511) +* Fix CUDA and SYCL small value type (16-bit) team reductions [\#5334](https://github.com/kokkos/kokkos/pull/5334) +* Enable `{transform_}exclusive_scan` in place [\#6667](https://github.com/kokkos/kokkos/pull/6667) +* `fill_random` overload that do not take an execution space instance argument should fence [\#6658](https://github.com/kokkos/kokkos/pull/6658) +* HIP,Cuda,OpenMPTarget: Fixup use provided execution space when copying host inaccessible reduction result [\#6777](https://github.com/kokkos/kokkos/pull/6777) +* Fix typo in `cuda_func_set_attribute[s]_wrapper` preventing proper setting of desired occupancy [\#6786](https://github.com/kokkos/kokkos/pull/6786) +* Avoid undefined behavior due to conversion between signed and unsigned integers in shift_{right, left}_team_impl [\#6821](https://github.com/kokkos/kokkos/pull/6821) +* Fix a bug in Makefile.kokkos when using AMD GPU architectures as `AMD_GFXYYY` [\#6892](https://github.com/kokkos/kokkos/pull/6892) + +## [4.2.01](https://github.com/kokkos/kokkos/tree/4.2.01) (2023-12-07) +[Full Changelog](https://github.com/kokkos/kokkos/compare/4.2.00...4.2.01) + +### Backend and Architecture Enhancements: + +#### CUDA: +- Add warp sync for `parallel_reduce` to avoid race condition [\#6630](https://github.com/kokkos/kokkos/pull/6630), [\#6746](https://github.com/kokkos/kokkos/pull/6746) + +#### HIP: +- Fix Graph "multiple definition of" linking error (missing `inline` specifier) [\#6624](https://github.com/kokkos/kokkos/pull/6624) +- Add support for gfx940 (AMD Instinct MI300 GPU) [\#6671](https://github.com/kokkos/kokkos/pull/6671) + +### Build System +- CMake: Don't let Kokkos set `CMAKE_CXX_FLAGS` for Trilinos builds [\#6742](https://github.com/kokkos/kokkos/pull/6742) + +### Bug Fixes +- Remove deprecation warning for `AllocationMechanism` for GCC <11.0 [\#6653](https://github.com/kokkos/kokkos/pull/6653) +- Fix bug early tools finalize with non-default host execution instances [\#6635](https://github.com/kokkos/kokkos/pull/6635) +- Fix various issues for MSVC CUDA builds [\#6659](https://github.com/kokkos/kokkos/pull/6659) +- Fix "extra `;`" warning with `-pedantic` flag in `` [\#6510](https://github.com/kokkos/kokkos/pull/6510) + ## [4.2.00](https://github.com/kokkos/kokkos/tree/4.2.00) (2023-11-06) [Full Changelog](https://github.com/kokkos/kokkos/compare/4.1.00...4.2.00) @@ -43,7 +177,7 @@ #### SYCL: - Enforce external `sycl::queues` to be in-order [\#6246](https://github.com/kokkos/kokkos/pull/6246) -- Improve reduction performance: [\#6272](https://github.com/kokkos/kokkos/pull/6272) [\#6271](https://github.com/kokkos/kokkos/pull/6271) [\#6270](https://github.com/kokkos/kokkos/pull/6270) [\#6264](https://github.com/kokkos/kokkos/pull/6264) +- Improve reduction performance: [\#6272](https://github.com/kokkos/kokkos/pull/6272) [\#6271](https://github.com/kokkos/kokkos/pull/6271) [\#6270](https://github.com/kokkos/kokkos/pull/6270) [\#6264](https://github.com/kokkos/kokkos/pull/6264) - Allow using the SYCL execution space on AMD GPUs [\#6321](https://github.com/kokkos/kokkos/pull/6321) - Allow sorting via native oneDPL to support Views with stride=1 [\#6322](https://github.com/kokkos/kokkos/pull/6322) - Make in-order queues the default via macro [\#6189](https://github.com/kokkos/kokkos/pull/6189) @@ -64,7 +198,7 @@ - Add converting assignment to `DualView`: [\#6474](https://github.com/kokkos/kokkos/pull/6474) -### Build System Changes +### Build System Changes - Export `Kokkos_CXX_COMPILER_VERSION` [\#6282](https://github.com/kokkos/kokkos/pull/6282) - Disable default oneDPL support in Trilinos [\#6342](https://github.com/kokkos/kokkos/pull/6342) @@ -978,95 +1112,95 @@ - Major update for OpenMPTarget: many capabilities now work. For details contact us. - Added DPC++/SYCL backend: primary capabilites are working. - Added Kokkos Graph API analogous to CUDA Graphs. -- Added parallel_scan support with TeamThreadRange [\#3536](https://github.com/kokkos/kokkos/pull/#3536) -- Added Logical Memory Spaces [\#3546](https://github.com/kokkos/kokkos/pull/#3546) -- Added initial half precision support [\#3439](https://github.com/kokkos/kokkos/pull/#3439) -- Experimental feature: control cuda occupancy [\#3379](https://github.com/kokkos/kokkos/pull/#3379) +- Added parallel_scan support with TeamThreadRange [\#3536](https://github.com/kokkos/kokkos/pull/3536) +- Added Logical Memory Spaces [\#3546](https://github.com/kokkos/kokkos/pull/3546) +- Added initial half precision support [\#3439](https://github.com/kokkos/kokkos/pull/3439) +- Experimental feature: control cuda occupancy [\#3379](https://github.com/kokkos/kokkos/pull/3379) **Implemented enhancements Backends and Archs:** -- Add a64fx and fujitsu Compiler support [\#3614](https://github.com/kokkos/kokkos/pull/#3614) -- Adding support for AMD gfx908 archictecture [\#3375](https://github.com/kokkos/kokkos/pull/#3375) -- SYCL parallel\_for MDRangePolicy [\#3583](https://github.com/kokkos/kokkos/pull/#3583) -- SYCL add parallel\_scan [\#3577](https://github.com/kokkos/kokkos/pull/#3577) -- SYCL custom reductions [\#3544](https://github.com/kokkos/kokkos/pull/#3544) -- SYCL Enable container unit tests [\#3550](https://github.com/kokkos/kokkos/pull/#3550) -- SYCL feature level 5 [\#3480](https://github.com/kokkos/kokkos/pull/#3480) -- SYCL Feature level 4 (parallel\_for) [\#3474](https://github.com/kokkos/kokkos/pull/#3474) -- SYCL feature level 3 [\#3451](https://github.com/kokkos/kokkos/pull/#3451) -- SYCL feature level 2 [\#3447](https://github.com/kokkos/kokkos/pull/#3447) -- OpenMPTarget: Hierarchial reduction for + operator on scalars [\#3504](https://github.com/kokkos/kokkos/pull/#3504) -- OpenMPTarget hierarchical [\#3411](https://github.com/kokkos/kokkos/pull/#3411) -- HIP Add Impl::atomic\_[store,load] [\#3440](https://github.com/kokkos/kokkos/pull/#3440) -- HIP enable global lock arrays [\#3418](https://github.com/kokkos/kokkos/pull/#3418) -- HIP Implement multiple occupancy paths for various HIP kernel launchers [\#3366](https://github.com/kokkos/kokkos/pull/#3366) +- Add a64fx and fujitsu Compiler support [\#3614](https://github.com/kokkos/kokkos/pull/3614) +- Adding support for AMD gfx908 archictecture [\#3375](https://github.com/kokkos/kokkos/pull/3375) +- SYCL parallel\_for MDRangePolicy [\#3583](https://github.com/kokkos/kokkos/pull/3583) +- SYCL add parallel\_scan [\#3577](https://github.com/kokkos/kokkos/pull/3577) +- SYCL custom reductions [\#3544](https://github.com/kokkos/kokkos/pull/3544) +- SYCL Enable container unit tests [\#3550](https://github.com/kokkos/kokkos/pull/3550) +- SYCL feature level 5 [\#3480](https://github.com/kokkos/kokkos/pull/3480) +- SYCL Feature level 4 (parallel\_for) [\#3474](https://github.com/kokkos/kokkos/pull/3474) +- SYCL feature level 3 [\#3451](https://github.com/kokkos/kokkos/pull/3451) +- SYCL feature level 2 [\#3447](https://github.com/kokkos/kokkos/pull/3447) +- OpenMPTarget: Hierarchial reduction for + operator on scalars [\#3504](https://github.com/kokkos/kokkos/pull/3504) +- OpenMPTarget hierarchical [\#3411](https://github.com/kokkos/kokkos/pull/3411) +- HIP Add Impl::atomic\_[store,load] [\#3440](https://github.com/kokkos/kokkos/pull/3440) +- HIP enable global lock arrays [\#3418](https://github.com/kokkos/kokkos/pull/3418) +- HIP Implement multiple occupancy paths for various HIP kernel launchers [\#3366](https://github.com/kokkos/kokkos/pull/3366) **Implemented enhancements Policies:** -- MDRangePolicy: Let it be semiregular [\#3494](https://github.com/kokkos/kokkos/pull/#3494) -- MDRangePolicy: Check narrowing conversion in construction [\#3527](https://github.com/kokkos/kokkos/pull/#3527) -- MDRangePolicy: CombinedReducers support [\#3395](https://github.com/kokkos/kokkos/pull/#3395) -- Kokkos Graph: Interface and Default Implementation [\#3362](https://github.com/kokkos/kokkos/pull/#3362) -- Kokkos Graph: add Cuda Graph implementation [\#3369](https://github.com/kokkos/kokkos/pull/#3369) -- TeamPolicy: implemented autotuning of team sizes and vector lengths [\#3206](https://github.com/kokkos/kokkos/pull/#3206) -- RangePolicy: Initialize all data members in default constructor [\#3509](https://github.com/kokkos/kokkos/pull/#3509) +- MDRangePolicy: Let it be semiregular [\#3494](https://github.com/kokkos/kokkos/pull/3494) +- MDRangePolicy: Check narrowing conversion in construction [\#3527](https://github.com/kokkos/kokkos/pull/3527) +- MDRangePolicy: CombinedReducers support [\#3395](https://github.com/kokkos/kokkos/pull/3395) +- Kokkos Graph: Interface and Default Implementation [\#3362](https://github.com/kokkos/kokkos/pull/3362) +- Kokkos Graph: add Cuda Graph implementation [\#3369](https://github.com/kokkos/kokkos/pull/3369) +- TeamPolicy: implemented autotuning of team sizes and vector lengths [\#3206](https://github.com/kokkos/kokkos/pull/3206) +- RangePolicy: Initialize all data members in default constructor [\#3509](https://github.com/kokkos/kokkos/pull/3509) **Implemented enhancements BuildSystem:** -- Auto-generate core test files for all backends [\#3488](https://github.com/kokkos/kokkos/pull/#3488) -- Avoid rewriting test files when calling cmake [\#3548](https://github.com/kokkos/kokkos/pull/#3548) -- RULE\_LAUNCH\_COMPILE and RULE\_LAUNCH\_LINK system for nvcc\_wrapper [\#3136](https://github.com/kokkos/kokkos/pull/#3136) -- Adding -include as a known argument to nvcc\_wrapper [\#3434](https://github.com/kokkos/kokkos/pull/#3434) -- Install hpcbind script [\#3402](https://github.com/kokkos/kokkos/pull/#3402) -- cmake/kokkos\_tribits.cmake: add parsing for args [\#3457](https://github.com/kokkos/kokkos/pull/#3457) +- Auto-generate core test files for all backends [\#3488](https://github.com/kokkos/kokkos/pull/3488) +- Avoid rewriting test files when calling cmake [\#3548](https://github.com/kokkos/kokkos/pull/3548) +- RULE\_LAUNCH\_COMPILE and RULE\_LAUNCH\_LINK system for nvcc\_wrapper [\#3136](https://github.com/kokkos/kokkos/pull/3136) +- Adding -include as a known argument to nvcc\_wrapper [\#3434](https://github.com/kokkos/kokkos/pull/3434) +- Install hpcbind script [\#3402](https://github.com/kokkos/kokkos/pull/3402) +- cmake/kokkos\_tribits.cmake: add parsing for args [\#3457](https://github.com/kokkos/kokkos/pull/3457) **Implemented enhancements Tools:** -- Changed namespacing of Kokkos::Tools::Impl::Impl::tune\_policy [\#3455](https://github.com/kokkos/kokkos/pull/#3455) -- Delegate to an impl allocate/deallocate method to allow specifying a SpaceHandle for MemorySpaces [\#3530](https://github.com/kokkos/kokkos/pull/#3530) -- Use the Kokkos Profiling interface rather than the Impl interface [\#3518](https://github.com/kokkos/kokkos/pull/#3518) -- Runtime option for tuning [\#3459](https://github.com/kokkos/kokkos/pull/#3459) -- Dual View Tool Events [\#3326](https://github.com/kokkos/kokkos/pull/#3326) +- Changed namespacing of Kokkos::Tools::Impl::Impl::tune\_policy [\#3455](https://github.com/kokkos/kokkos/pull/3455) +- Delegate to an impl allocate/deallocate method to allow specifying a SpaceHandle for MemorySpaces [\#3530](https://github.com/kokkos/kokkos/pull/3530) +- Use the Kokkos Profiling interface rather than the Impl interface [\#3518](https://github.com/kokkos/kokkos/pull/3518) +- Runtime option for tuning [\#3459](https://github.com/kokkos/kokkos/pull/3459) +- Dual View Tool Events [\#3326](https://github.com/kokkos/kokkos/pull/3326) **Implemented enhancements Other:** -- Abort on errors instead of just printing [\#3528](https://github.com/kokkos/kokkos/pull/#3528) -- Enable C++14 macros unconditionally [\#3449](https://github.com/kokkos/kokkos/pull/#3449) -- Make ViewMapping trivially copyable [\#3436](https://github.com/kokkos/kokkos/pull/#3436) -- Rename struct ViewMapping to class [\#3435](https://github.com/kokkos/kokkos/pull/#3435) -- Replace enums in Kokkos\_ViewMapping.hpp (removes -Wextra) [\#3422](https://github.com/kokkos/kokkos/pull/#3422) -- Use bool for enums representing bools [\#3416](https://github.com/kokkos/kokkos/pull/#3416) -- Fence active instead of default execution space instances [\#3388](https://github.com/kokkos/kokkos/pull/#3388) -- Refactor parallel\_reduce fence usage [\#3359](https://github.com/kokkos/kokkos/pull/#3359) -- Moved Space EBO helpers to Kokkos\_EBO [\#3357](https://github.com/kokkos/kokkos/pull/#3357) -- Add remove\_cvref type trait [\#3340](https://github.com/kokkos/kokkos/pull/#3340) -- Adding identity type traits and update definition of identity\_t alias [\#3339](https://github.com/kokkos/kokkos/pull/#3339) -- Add is\_specialization\_of type trait [\#3338](https://github.com/kokkos/kokkos/pull/#3338) -- Make ScratchMemorySpace semi-regular [\#3309](https://github.com/kokkos/kokkos/pull/#3309) -- Optimize min/max atomics with early exit on no-op case [\#3265](https://github.com/kokkos/kokkos/pull/#3265) -- Refactor Backend Development [\#2941](https://github.com/kokkos/kokkos/pull/#2941) +- Abort on errors instead of just printing [\#3528](https://github.com/kokkos/kokkos/pull/3528) +- Enable C++14 macros unconditionally [\#3449](https://github.com/kokkos/kokkos/pull/3449) +- Make ViewMapping trivially copyable [\#3436](https://github.com/kokkos/kokkos/pull/3436) +- Rename struct ViewMapping to class [\#3435](https://github.com/kokkos/kokkos/pull/3435) +- Replace enums in Kokkos\_ViewMapping.hpp (removes -Wextra) [\#3422](https://github.com/kokkos/kokkos/pull/3422) +- Use bool for enums representing bools [\#3416](https://github.com/kokkos/kokkos/pull/3416) +- Fence active instead of default execution space instances [\#3388](https://github.com/kokkos/kokkos/pull/3388) +- Refactor parallel\_reduce fence usage [\#3359](https://github.com/kokkos/kokkos/pull/3359) +- Moved Space EBO helpers to Kokkos\_EBO [\#3357](https://github.com/kokkos/kokkos/pull/3357) +- Add remove\_cvref type trait [\#3340](https://github.com/kokkos/kokkos/pull/3340) +- Adding identity type traits and update definition of identity\_t alias [\#3339](https://github.com/kokkos/kokkos/pull/3339) +- Add is\_specialization\_of type trait [\#3338](https://github.com/kokkos/kokkos/pull/3338) +- Make ScratchMemorySpace semi-regular [\#3309](https://github.com/kokkos/kokkos/pull/3309) +- Optimize min/max atomics with early exit on no-op case [\#3265](https://github.com/kokkos/kokkos/pull/3265) +- Refactor Backend Development [\#2941](https://github.com/kokkos/kokkos/pull/2941) **Fixed bugs:** -- Fixup MDRangePolicy construction from Kokkos arrays [\#3591](https://github.com/kokkos/kokkos/pull/#3591) -- Add atomic functions for unsigned long long using gcc built-in [\#3588](https://github.com/kokkos/kokkos/pull/#3588) -- Fixup silent pointless comparison with zero in checked\_narrow\_cast (compiler workaround) [\#3566](https://github.com/kokkos/kokkos/pull/#3566) -- Fixes for ROCm 3.9 [\#3565](https://github.com/kokkos/kokkos/pull/#3565) -- Fix windows build issues which crept in for the CUDA build [\#3532](https://github.com/kokkos/kokkos/pull/#3532) -- HIP Fix atomics of large data types and clean up lock arrays [\#3529](https://github.com/kokkos/kokkos/pull/#3529) -- Pthreads fix exception resulting from 0 grain size [\#3510](https://github.com/kokkos/kokkos/pull/#3510) -- Fixup do not require atomic operation to be default constructible [\#3503](https://github.com/kokkos/kokkos/pull/#3503) -- Fix race condition in HIP backend [\#3467](https://github.com/kokkos/kokkos/pull/#3467) -- Replace KOKKOS\_DEBUG with KOKKOS\_ENABLE\_DEBUG [\#3458](https://github.com/kokkos/kokkos/pull/#3458) -- Fix multi-stream team scratch space definition for HIP [\#3398](https://github.com/kokkos/kokkos/pull/#3398) -- HIP fix template deduction [\#3393](https://github.com/kokkos/kokkos/pull/#3393) -- Fix compiling with HIP and C++17 [\#3390](https://github.com/kokkos/kokkos/pull/#3390) -- Fix sigFPE in HIP blocksize deduction [\#3378](https://github.com/kokkos/kokkos/pull/#3378) -- Type alias change: replace CS with CTS to avoid conflicts with NVSHMEM [\#3348](https://github.com/kokkos/kokkos/pull/#3348) -- Clang compilation of CUDA backend on Windows [\#3345](https://github.com/kokkos/kokkos/pull/#3345) -- Fix HBW support [\#3343](https://github.com/kokkos/kokkos/pull/#3343) -- Added missing fences to unique token [\#3260](https://github.com/kokkos/kokkos/pull/#3260) +- Fixup MDRangePolicy construction from Kokkos arrays [\#3591](https://github.com/kokkos/kokkos/pull/3591) +- Add atomic functions for unsigned long long using gcc built-in [\#3588](https://github.com/kokkos/kokkos/pull/3588) +- Fixup silent pointless comparison with zero in checked\_narrow\_cast (compiler workaround) [\#3566](https://github.com/kokkos/kokkos/pull/3566) +- Fixes for ROCm 3.9 [\#3565](https://github.com/kokkos/kokkos/pull/3565) +- Fix windows build issues which crept in for the CUDA build [\#3532](https://github.com/kokkos/kokkos/pull/3532) +- HIP Fix atomics of large data types and clean up lock arrays [\#3529](https://github.com/kokkos/kokkos/pull/3529) +- Pthreads fix exception resulting from 0 grain size [\#3510](https://github.com/kokkos/kokkos/pull/3510) +- Fixup do not require atomic operation to be default constructible [\#3503](https://github.com/kokkos/kokkos/pull/3503) +- Fix race condition in HIP backend [\#3467](https://github.com/kokkos/kokkos/pull/3467) +- Replace KOKKOS\_DEBUG with KOKKOS\_ENABLE\_DEBUG [\#3458](https://github.com/kokkos/kokkos/pull/3458) +- Fix multi-stream team scratch space definition for HIP [\#3398](https://github.com/kokkos/kokkos/pull/3398) +- HIP fix template deduction [\#3393](https://github.com/kokkos/kokkos/pull/3393) +- Fix compiling with HIP and C++17 [\#3390](https://github.com/kokkos/kokkos/pull/3390) +- Fix sigFPE in HIP blocksize deduction [\#3378](https://github.com/kokkos/kokkos/pull/3378) +- Type alias change: replace CS with CTS to avoid conflicts with NVSHMEM [\#3348](https://github.com/kokkos/kokkos/pull/3348) +- Clang compilation of CUDA backend on Windows [\#3345](https://github.com/kokkos/kokkos/pull/3345) +- Fix HBW support [\#3343](https://github.com/kokkos/kokkos/pull/3343) +- Added missing fences to unique token [\#3260](https://github.com/kokkos/kokkos/pull/3260) **Incompatibilities:** -- Remove unused utilities (forward, move, and expand\_variadic) from Kokkos::Impl [\#3535](https://github.com/kokkos/kokkos/pull/#3535) -- Remove unused traits [\#3534](https://github.com/kokkos/kokkos/pull/#3534) -- HIP: Remove old HCC code [\#3301](https://github.com/kokkos/kokkos/pull/#3301) -- Prepare for deprecation of ViewAllocateWithoutInitializing [\#3264](https://github.com/kokkos/kokkos/pull/#3264) -- Remove ROCm backend [\#3148](https://github.com/kokkos/kokkos/pull/#3148) +- Remove unused utilities (forward, move, and expand\_variadic) from Kokkos::Impl [\#3535](https://github.com/kokkos/kokkos/pull/3535) +- Remove unused traits [\#3534](https://github.com/kokkos/kokkos/pull/3534) +- HIP: Remove old HCC code [\#3301](https://github.com/kokkos/kokkos/pull/3301) +- Prepare for deprecation of ViewAllocateWithoutInitializing [\#3264](https://github.com/kokkos/kokkos/pull/3264) +- Remove ROCm backend [\#3148](https://github.com/kokkos/kokkos/pull/3148) ## [3.2.01](https://github.com/kokkos/kokkos/tree/3.2.01) (2020-11-17) [Full Changelog](https://github.com/kokkos/kokkos/compare/3.2.00...3.2.01) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index f6bd81058e..76f2183db8 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -150,8 +150,8 @@ ENDIF() set(Kokkos_VERSION_MAJOR 4) -set(Kokkos_VERSION_MINOR 2) -set(Kokkos_VERSION_PATCH 0) +set(Kokkos_VERSION_MINOR 3) +set(Kokkos_VERSION_PATCH 1) set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}") message(STATUS "Kokkos version: ${Kokkos_VERSION}") math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}") @@ -252,7 +252,6 @@ ENDIF() # subpackages ## This restores the old behavior of ProjectCompilerPostConfig.cmake -# It sets the CMAKE_CXX_FLAGS globally to those used by Kokkos # We must do this before KOKKOS_PACKAGE_DECL IF (KOKKOS_HAS_TRILINOS) # Overwrite the old flags at the top-level @@ -280,21 +279,13 @@ IF (KOKKOS_HAS_TRILINOS) SET(KOKKOSCORE_XCOMPILER_OPTIONS "${KOKKOSCORE_XCOMPILER_OPTIONS} -Xcompiler ${XCOMP_FLAG}") LIST(APPEND KOKKOS_ALL_COMPILE_OPTIONS -Xcompiler ${XCOMP_FLAG}) ENDFOREACH() - SET(KOKKOSCORE_CXX_FLAGS "${KOKKOSCORE_COMPILE_OPTIONS} ${KOKKOSCORE_XCOMPILER_OPTIONS}") IF (KOKKOS_ENABLE_CUDA) STRING(REPLACE ";" " " KOKKOSCORE_CUDA_OPTIONS "${KOKKOS_CUDA_OPTIONS}") FOREACH(CUDAFE_FLAG ${KOKKOS_CUDAFE_OPTIONS}) SET(KOKKOSCORE_CUDAFE_OPTIONS "${KOKKOSCORE_CUDAFE_OPTIONS} -Xcudafe ${CUDAFE_FLAG}") LIST(APPEND KOKKOS_ALL_COMPILE_OPTIONS -Xcudafe ${CUDAFE_FLAG}) ENDFOREACH() - SET(KOKKOSCORE_CXX_FLAGS "${KOKKOSCORE_CXX_FLAGS} ${KOKKOSCORE_CUDA_OPTIONS} ${KOKKOSCORE_CUDAFE_OPTIONS}") ENDIF() - # Both parent scope and this package - # In ProjectCompilerPostConfig.cmake, we capture the "global" flags Trilinos wants in - # TRILINOS_TOPLEVEL_CXX_FLAGS - SET(CMAKE_CXX_FLAGS "${TRILINOS_TOPLEVEL_CXX_FLAGS} ${KOKKOSCORE_CXX_FLAGS}" PARENT_SCOPE) - SET(CMAKE_CXX_FLAGS "${TRILINOS_TOPLEVEL_CXX_FLAGS} ${KOKKOSCORE_CXX_FLAGS}") - #CMAKE_CXX_FLAGS will get added to Kokkos and Kokkos dependencies automatically here #These flags get set up in KOKKOS_PACKAGE_DECL, which means they #must be configured before KOKKOS_PACKAGE_DECL SET(KOKKOS_ALL_COMPILE_OPTIONS diff --git a/lib/kokkos/Copyright.txt b/lib/kokkos/Copyright.txt index 5e2f8d8647..cbba3efc7b 100644 --- a/lib/kokkos/Copyright.txt +++ b/lib/kokkos/Copyright.txt @@ -1,41 +1,8 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER +************************************************************************ + + Kokkos v. 4.0 + Copyright (2022) National Technology & Engineering + Solutions of Sandia, LLC (NTESS). + +Under the terms of Contract DE-NA0003525 with NTESS, +the U.S. Government retains certain rights in this software. diff --git a/lib/kokkos/LICENSE b/lib/kokkos/LICENSE index 6572cc2db0..4d9d69d7c4 100644 --- a/lib/kokkos/LICENSE +++ b/lib/kokkos/LICENSE @@ -1,13 +1,3 @@ - ************************************************************************ - - Kokkos v. 4.0 - Copyright (2022) National Technology & Engineering - Solutions of Sandia, LLC (NTESS). - - Under the terms of Contract DE-NA0003525 with NTESS, - the U.S. Government retains certain rights in this software. - - ============================================================================== Kokkos is under the Apache License v2.0 with LLVM Exceptions: ============================================================================== diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index c970f72755..14a417b532 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -11,8 +11,8 @@ CXXFLAGS += $(SHFLAGS) endif KOKKOS_VERSION_MAJOR = 4 -KOKKOS_VERSION_MINOR = 2 -KOKKOS_VERSION_PATCH = 0 +KOKKOS_VERSION_MINOR = 3 +KOKKOS_VERSION_PATCH = 1 KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc) # Options: Cuda,HIP,SYCL,OpenMPTarget,OpenMP,Threads,Serial @@ -22,14 +22,14 @@ KOKKOS_DEVICES ?= "OpenMP" # Intel: KNC,KNL,SNB,HSW,BDW,SKL,SKX,ICL,ICX,SPR # NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80,Ampere86,Ada89,Hopper90 # ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX -# IBM: BGQ,Power7,Power8,Power9 -# AMD-GPUS: GFX906,GFX908,GFX90A,GFX942,GFX1030,GFX1100 +# IBM: Power8,Power9 +# AMD-GPUS: AMD_GFX906,AMD_GFX908,AMD_GFX90A,AMD_GFX940,AMD_GFX942,AMD_GFX1030,AMD_GFX1100 # AMD-CPUS: AMDAVX,Zen,Zen2,Zen3 # Intel-GPUs: Gen9,Gen11,Gen12LP,DG1,XeHP,PVC KOKKOS_ARCH ?= "" # Options: yes,no KOKKOS_DEBUG ?= "no" -# Options: hwloc,librt,experimental_memkind +# Options: hwloc KOKKOS_USE_TPLS ?= "" # Options: c++17,c++1z,c++20,c++2a,c++23,c++2b KOKKOS_CXX_STANDARD ?= "c++17" @@ -56,7 +56,7 @@ uppercase_internal=$(if $1,$$(subst $(firstword $1),$(call uppercase_internal,$( uppercase=$(eval uppercase_RESULT:=$(call uppercase_internal,$(uppercase_TABLE),$1))$(uppercase_RESULT) # Return a 1 if a string contains a substring and 0 if not # Note the search string should be without '"' -# Example: $(call kokkos_has_string,"hwloc,librt",hwloc) +# Example: $(call kokkos_has_string,"hwloc,libdl",hwloc) # Will return a 1 kokkos_has_string=$(if $(findstring $(call uppercase,$2),$(call uppercase,$1)),1,0) # Returns 1 if the path exists, 0 otherwise @@ -73,11 +73,11 @@ KOKKOS_INTERNAL_ENABLE_CXX20 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD), KOKKOS_INTERNAL_ENABLE_CXX2A := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++2a) KOKKOS_INTERNAL_ENABLE_CXX23 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++23) KOKKOS_INTERNAL_ENABLE_CXX2B := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++2b) +KOKKOS_INTERNAL_ENABLE_CXX26 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++26) +KOKKOS_INTERNAL_ENABLE_CXX2C := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++2c) # Check for external libraries. KOKKOS_INTERNAL_USE_HWLOC := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),hwloc) -KOKKOS_INTERNAL_USE_LIBRT := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),librt) -KOKKOS_INTERNAL_USE_MEMKIND := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),experimental_memkind) # Check for advanced settings. KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),compiler_warnings) @@ -318,7 +318,6 @@ endif # Intel based. KOKKOS_INTERNAL_USE_ARCH_KNC := $(call kokkos_has_string,$(KOKKOS_ARCH),KNC) -KOKKOS_INTERNAL_USE_ARCH_WSM := $(call kokkos_has_string,$(KOKKOS_ARCH),WSM) KOKKOS_INTERNAL_USE_ARCH_SNB := $(call kokkos_has_string,$(KOKKOS_ARCH),SNB) KOKKOS_INTERNAL_USE_ARCH_HSW := $(call kokkos_has_string,$(KOKKOS_ARCH),HSW) KOKKOS_INTERNAL_USE_ARCH_BDW := $(call kokkos_has_string,$(KOKKOS_ARCH),BDW) @@ -398,11 +397,9 @@ KOKKOS_INTERNAL_USE_ARCH_A64FX := $(call kokkos_has_string,$(KOKKOS_ARCH),A64FX) KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2)+$(KOKKOS_INTERNAL_USE_ARCH_A64FX) | bc)) # IBM based. -KOKKOS_INTERNAL_USE_ARCH_BGQ := $(call kokkos_has_string,$(KOKKOS_ARCH),BGQ) -KOKKOS_INTERNAL_USE_ARCH_POWER7 := $(call kokkos_has_string,$(KOKKOS_ARCH),Power7) KOKKOS_INTERNAL_USE_ARCH_POWER8 := $(call kokkos_has_string,$(KOKKOS_ARCH),Power8) KOKKOS_INTERNAL_USE_ARCH_POWER9 := $(call kokkos_has_string,$(KOKKOS_ARCH),Power9) -KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_BGQ)+$(KOKKOS_INTERNAL_USE_ARCH_POWER7)+$(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc)) +KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc)) # AMD based. KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX) @@ -413,20 +410,37 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN3), 0) KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen) endif endif -KOKKOS_INTERNAL_USE_ARCH_AMD_GFX906 := $(or $(call kokkos_has_string,$(KOKKOS_ARCH),VEGA906),$(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX906)) -KOKKOS_INTERNAL_USE_ARCH_AMD_GFX908 := $(or $(call kokkos_has_string,$(KOKKOS_ARCH),VEGA908),$(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX908)) -KOKKOS_INTERNAL_USE_ARCH_AMD_GFX90A := $(or $(call kokkos_has_string,$(KOKKOS_ARCH),VEGA90A),$(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX90A)) -KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1030 := $(or $(call kokkos_has_string,$(KOKKOS_ARCH),NAVI1030),$(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX1030)) -KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100 := $(or $(call kokkos_has_string,$(KOKKOS_ARCH),NAVI1100),$(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX1100)) + +KOKKOS_INTERNAL_USE_ARCH_AMD_GFX906 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX906) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX906), 0) + KOKKOS_INTERNAL_USE_ARCH_AMD_GFX906 := $(call kokkos_has_string,$(KOKKOS_ARCH),VEGA906) +endif +KOKKOS_INTERNAL_USE_ARCH_AMD_GFX908 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX908) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX908), 0) + KOKKOS_INTERNAL_USE_ARCH_AMD_GFX908 := $(call kokkos_has_string,$(KOKKOS_ARCH),VEGA908) +endif +KOKKOS_INTERNAL_USE_ARCH_AMD_GFX90A := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX90A) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX90A), 0) + KOKKOS_INTERNAL_USE_ARCH_AMD_GFX90A := $(call kokkos_has_string,$(KOKKOS_ARCH),VEGA90A) +endif +KOKKOS_INTERNAL_USE_ARCH_AMD_GFX940 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX940) +KOKKOS_INTERNAL_USE_ARCH_AMD_GFX942 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX942) +KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1030 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX1030) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1030), 0) + KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1030 := $(call kokkos_has_string,$(KOKKOS_ARCH),NAVI1030) +endif +KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX1100) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100), 0) + KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100 := $(call kokkos_has_string,$(KOKKOS_ARCH),NAVI1100) +endif # Any AVX? -KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM)) KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX)) KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3)) KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL)) # Incompatible flags? -KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_SSE42)+$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_SKL)+$(KOKKOS_INTERNAL_USE_ARCH_SKX)+$(KOKKOS_INTERNAL_USE_ARCH_ICL)+$(KOKKOS_INTERNAL_USE_ARCH_ICX)+$(KOKKOS_INTERNAL_USE_ARCH_SPR)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1") | bc) +KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_SKL)+$(KOKKOS_INTERNAL_USE_ARCH_SKX)+$(KOKKOS_INTERNAL_USE_ARCH_ICL)+$(KOKKOS_INTERNAL_USE_ARCH_ICX)+$(KOKKOS_INTERNAL_USE_ARCH_SPR)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1") | bc) KOKKOS_INTERNAL_USE_ARCH_MULTIGPU := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_NVIDIA)>1") | bc) ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MULTIHOST), 1) @@ -571,6 +585,16 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX2B), 1) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX2B_FLAG) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX23") endif +ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX26), 1) + #I cannot make CMake add this in a good way - so add it here + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX26_FLAG) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX26") +endif +ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX2C), 1) + #I cannot make CMake add this in a good way - so add it here + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX2C_FLAG) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX26") +endif ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1) ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) @@ -610,27 +634,6 @@ ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_HWLOC") endif -ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1) - tmp := $(call kokkos_append_header,"$H""define KOKKOS_USE_LIBRT") - KOKKOS_LIBS += -lrt - KOKKOS_TPL_LIBRARY_NAMES += rt -endif - -ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) - ifneq ($(KOKKOS_CMAKE), yes) - ifneq ($(MEMKIND_PATH),) - KOKKOS_CPPFLAGS += -I$(MEMKIND_PATH)/include - KOKKOS_LIBDIRS += -L$(MEMKIND_PATH)/lib - KOKKOS_CXXLDFLAGS += -L$(MEMKIND_PATH)/lib - KOKKOS_TPL_INCLUDE_DIRS += $(MEMKIND_PATH)/include - KOKKOS_TPL_LIBRARY_DIRS += $(MEMKIND_PATH)/lib - endif - KOKKOS_LIBS += -lmemkind -lnuma - KOKKOS_TPL_LIBRARY_NAMES += memkind numa - endif - tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_HBWSPACE") -endif - ifeq ($(KOKKOS_INTERNAL_ENABLE_LARGE_MEM_TESTS), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_LARGE_MEM_TESTS") endif @@ -697,10 +700,6 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) endif endif - ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - tmp := $(call kokkos_append_header,"$H""define KOKKOS_IMPL_CUDA_CLANG_WORKAROUND") - endif - ifeq ($(KOKKOS_INTERNAL_CUDA_DISABLE_MALLOC_ASYNC), 0) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_IMPL_CUDA_MALLOC_ASYNC") else @@ -825,20 +824,6 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2), 1) endif endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_SSE42), 1) - tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_SSE42") - - ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) - KOKKOS_CXXFLAGS += -xSSE4.2 - KOKKOS_LDFLAGS += -xSSE4.2 - else ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) - else - # Assume that this is a really a GNU compiler. - KOKKOS_CXXFLAGS += -msse4.2 - KOKKOS_LDFLAGS += -msse4.2 - endif -endif - ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX") @@ -1113,6 +1098,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX90A), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GPU") KOKKOS_INTERNAL_HIP_ARCH_FLAG := --offload-arch=gfx90a endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX940), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GFX940") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GPU") + KOKKOS_INTERNAL_HIP_ARCH_FLAG := --offload-arch=gfx940 +endif ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX942), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GFX942") tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GPU") @@ -1242,7 +1232,22 @@ ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0) tmp := $(call kokkos_update_config_header, KOKKOS_FWD_HPP_, "KokkosCore_Config_FwdBackend.tmp", "KokkosCore_Config_FwdBackend.hpp") tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config_SetupBackend.tmp", "KokkosCore_Config_SetupBackend.hpp") tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp") - tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp") + ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_THREADS), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif + ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + endif ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") @@ -1262,30 +1267,10 @@ ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0) tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") endif - ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") - endif ifeq ($(KOKKOS_INTERNAL_USE_OPENACC), 1) tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif - ifeq ($(KOKKOS_INTERNAL_USE_THREADS), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") - endif - ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") - endif - ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") - endif - ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") - endif endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/*.hpp) @@ -1396,11 +1381,6 @@ ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1) KOKKOS_TPL_LIBRARY_NAMES += hpx endif -# Don't include Kokkos_HBWSpace.cpp if not using MEMKIND to avoid a link warning. -ifneq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) - KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp,$(KOKKOS_SRC)) -endif - # With Cygwin functions such as fdopen and fileno are not defined # when strict ansi is enabled. strict ansi gets enabled with -std=c++14 # though. So we hard undefine it here. Not sure if that has any bad side effects @@ -1454,6 +1434,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) else tmp := $(call desul_append_header,"/* $H""undef DESUL_ATOMICS_ENABLE_OPENMP */") endif + +ifeq ($(KOKKOS_INTERNAL_USE_OPENACC), 1) + tmp := $(call desul_append_header,"$H""define DESUL_ATOMICS_ENABLE_OPENACC") +else + tmp := $(call desul_append_header,"/* $H""undef DESUL_ATOMICS_ENABLE_OPENACC */") +endif tmp := $(call desul_append_header, "") tmp := $(call desul_append_header, "$H""endif") @@ -1486,7 +1472,7 @@ include $(KOKKOS_PATH)/Makefile.targets kokkos-clean: rm -f $(KOKKOS_OBJ_LINK) $(DESUL_CONFIG_HEADER) $(DESUL_INTERNAL_CONFIG_TMP) KokkosCore_config.h KokkosCore_config.tmp libkokkos.a KokkosCore_Config_SetupBackend.hpp \ KokkosCore_Config_FwdBackend.hpp KokkosCore_Config_DeclareBackend.hpp KokkosCore_Config_DeclareBackend.tmp \ - KokkosCore_Config_FwdBackend.tmp KokkosCore_Config_PostInclude.hpp KokkosCore_Config_PostInclude.tmp KokkosCore_Config_SetupBackend.tmp + KokkosCore_Config_FwdBackend.tmp KokkosCore_Config_SetupBackend.tmp libkokkos.a: $(KOKKOS_OBJ_LINK) $(KOKKOS_SRC) $(KOKKOS_HEADERS) ar cr libkokkos.a $(KOKKOS_OBJ_LINK) diff --git a/lib/kokkos/Makefile.targets b/lib/kokkos/Makefile.targets index ec8770dd7d..e6900a822a 100644 --- a/lib/kokkos/Makefile.targets +++ b/lib/kokkos/Makefile.targets @@ -20,8 +20,6 @@ Kokkos_TaskQueue.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Ta $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_TaskQueue.cpp Kokkos_HostThreadTeam.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostThreadTeam.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostThreadTeam.cpp -Kokkos_Spinwait.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Spinwait.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Spinwait.cpp Kokkos_HostBarrier.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp Kokkos_Profiling.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling.cpp @@ -30,8 +28,6 @@ Kokkos_SharedAlloc.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_ $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_SharedAlloc.cpp Kokkos_MemoryPool.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp -Kokkos_MemorySpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_MemorySpace.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemorySpace.cpp Kokkos_HostSpace_deepcopy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp Kokkos_NumericTraits.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_NumericTraits.cpp @@ -82,8 +78,10 @@ Lock_Array_HIP.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/tpls/desul/src/Lock_Array endif ifeq ($(KOKKOS_INTERNAL_USE_THREADS), 1) -Kokkos_ThreadsExec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp +Kokkos_Threads_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_Threads_Instance.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_Threads_Instance.cpp +Kokkos_Threads_Spinwait.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_Threads_Spinwait.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_Spinwait.cpp endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) @@ -123,6 +121,3 @@ Kokkos_OpenACC_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenACC Kokkos_OpenACC_SharedAllocationRecord.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp endif - -Kokkos_HBWSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp diff --git a/lib/kokkos/README.md b/lib/kokkos/README.md index 033346e956..19793bb82d 100644 --- a/lib/kokkos/README.md +++ b/lib/kokkos/README.md @@ -28,7 +28,7 @@ To start learning about Kokkos: - [Use cases and Examples](https://kokkos.github.io/kokkos-core-wiki/usecases.html): a series of examples ranging from how to use Kokkos with MPI to Fortran interoperability. -For questions find us on Slack: https://kokkosteam.slack.com or open a github issue. +For questions find us on Slack: https://kokkosteam.slack.com or open a GitHub issue. For non-public questions send an email to: *crtrott(at)sandia.gov* @@ -48,10 +48,10 @@ Please see the [following page](https://kokkos.github.io/kokkos-core-wiki/citati # License -[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) +[![License](https://img.shields.io/badge/License-Apache--2.0_WITH_LLVM--exception-blue)](https://spdx.org/licenses/LLVM-exception.html) Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software. -The full license statement used in all headers is available [here](https://kokkos.github.io/kokkos-core-wiki/license.html) or -[here](https://github.com/kokkos/kokkos/blob/master/LICENSE). +The full license statement used in all headers is available [here](https://kokkos.org/kokkos-core-wiki/license.html) or +[here](https://github.com/kokkos/kokkos/blob/develop/LICENSE). diff --git a/lib/kokkos/SECURITY.md b/lib/kokkos/SECURITY.md new file mode 100644 index 0000000000..93cf6e3663 --- /dev/null +++ b/lib/kokkos/SECURITY.md @@ -0,0 +1,12 @@ +# Reporting Security Issues + +To report a security issue, please email +[lebrungrandt@ornl.gov](mailto:lebrungrandt@ornl.gov) +and [crtrott@sandia.gov](mailto:crtrott@sandia.gov) +with a description of the issue, the steps you took to create the issue, +affected versions, and, if known, mitigations for the issue. + +Our vulnerability management team will respond within 5 working days of your +email. If the issue is confirmed as a vulnerability, we will open a +Security Advisory and acknowledge your contributions as part of it. This project +follows a 90 day disclosure timeline. diff --git a/lib/kokkos/Spack.md b/lib/kokkos/Spack.md index 79606c259d..06c763a64e 100644 --- a/lib/kokkos/Spack.md +++ b/lib/kokkos/Spack.md @@ -159,7 +159,6 @@ If you don't specify a CUDA build variant in a `packages.yaml` and you build you > spack install superscience ```` you may end up just getting the default Kokkos (i.e. Serial). -Some examples are included in the `config/yaml` folder for common platforms. Before running `spack install ` we recommend running `spack spec ` to confirm your dependency tree is correct. For example, with Kokkos Kernels: ````bash diff --git a/lib/kokkos/algorithms/src/CMakeLists.txt b/lib/kokkos/algorithms/src/CMakeLists.txt index 1695778947..b490caca62 100644 --- a/lib/kokkos/algorithms/src/CMakeLists.txt +++ b/lib/kokkos/algorithms/src/CMakeLists.txt @@ -30,5 +30,5 @@ KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkosalgorithms ${CMAKE_CURRENT_SOURCE_DIR} ) - - +KOKKOS_LINK_TPL(kokkoscontainers PUBLIC ROCTHRUST) +KOKKOS_LINK_TPL(kokkoscore PUBLIC ONEDPL) diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index 2d7d236d2f..7df12b8518 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -849,18 +849,17 @@ class Random_XorShift64 { return drand(end - start) + start; } - // Marsaglia polar method for drawing a standard normal distributed random + // Box-muller method for drawing a standard normal distributed random // number KOKKOS_INLINE_FUNCTION double normal() { - double S = 2.0; - double U; - while (S >= 1.0) { - U = 2.0 * drand() - 1.0; - const double V = 2.0 * drand() - 1.0; - S = U * U + V * V; - } - return U * std::sqrt(-2.0 * std::log(S) / S); + constexpr auto two_pi = 2 * Kokkos::numbers::pi_v; + + const double u = drand(); + const double v = drand(); + const double r = Kokkos::sqrt(-2.0 * Kokkos::log(u)); + const double theta = v * two_pi; + return r * Kokkos::cos(theta); } KOKKOS_INLINE_FUNCTION @@ -1094,18 +1093,17 @@ class Random_XorShift1024 { return drand(end - start) + start; } - // Marsaglia polar method for drawing a standard normal distributed random + // Box-muller method for drawing a standard normal distributed random // number KOKKOS_INLINE_FUNCTION double normal() { - double S = 2.0; - double U; - while (S >= 1.0) { - U = 2.0 * drand() - 1.0; - const double V = 2.0 * drand() - 1.0; - S = U * U + V * V; - } - return U * std::sqrt(-2.0 * std::log(S) / S); + constexpr auto two_pi = 2 * Kokkos::numbers::pi_v; + + const double u = drand(); + const double v = drand(); + const double r = Kokkos::sqrt(-2.0 * Kokkos::log(u)); + const double theta = v * two_pi; + return r * Kokkos::cos(theta); } KOKKOS_INLINE_FUNCTION @@ -1545,13 +1543,23 @@ template void fill_random(ViewType a, RandomPool g, typename ViewType::const_value_type begin, typename ViewType::const_value_type end) { - fill_random(typename ViewType::execution_space{}, a, g, begin, end); + Kokkos::fence( + "fill_random: fence before since no execution space instance provided"); + typename ViewType::execution_space exec; + fill_random(exec, a, g, begin, end); + exec.fence( + "fill_random: fence after since no execution space instance provided"); } template void fill_random(ViewType a, RandomPool g, typename ViewType::const_value_type range) { - fill_random(typename ViewType::execution_space{}, a, g, 0, range); + Kokkos::fence( + "fill_random: fence before since no execution space instance provided"); + typename ViewType::execution_space exec; + fill_random(exec, a, g, 0, range); + exec.fence( + "fill_random: fence after since no execution space instance provided"); } } // namespace Kokkos diff --git a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp index f77484cc55..136b4ec82d 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp @@ -23,6 +23,7 @@ #include "sorting/Kokkos_BinSortPublicAPI.hpp" #include "sorting/Kokkos_SortPublicAPI.hpp" +#include "sorting/Kokkos_SortByKeyPublicAPI.hpp" #include "sorting/Kokkos_NestedSortPublicAPI.hpp" #ifdef KOKKOS_IMPL_PUBLIC_INCLUDE_NOTDEFINED_SORT diff --git a/lib/kokkos/algorithms/src/Kokkos_StdAlgorithms.hpp b/lib/kokkos/algorithms/src/Kokkos_StdAlgorithms.hpp index 436ae0d10b..b532a774e1 100644 --- a/lib/kokkos/algorithms/src/Kokkos_StdAlgorithms.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_StdAlgorithms.hpp @@ -35,7 +35,6 @@ // following the std classification. // modifying ops -#include "std_algorithms/Kokkos_Swap.hpp" #include "std_algorithms/Kokkos_IterSwap.hpp" // non-modifying sequence diff --git a/lib/kokkos/algorithms/src/sorting/Kokkos_SortByKeyPublicAPI.hpp b/lib/kokkos/algorithms/src/sorting/Kokkos_SortByKeyPublicAPI.hpp new file mode 100644 index 0000000000..fc73eccad6 --- /dev/null +++ b/lib/kokkos/algorithms/src/sorting/Kokkos_SortByKeyPublicAPI.hpp @@ -0,0 +1,117 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_SORT_BY_KEY_PUBLIC_API_HPP_ +#define KOKKOS_SORT_BY_KEY_PUBLIC_API_HPP_ + +#include "./impl/Kokkos_SortByKeyImpl.hpp" +#include +#include + +namespace Kokkos::Experimental { + +// --------------------------------------------------------------- +// basic overloads +// --------------------------------------------------------------- + +template +void sort_by_key( + const ExecutionSpace& exec, + const Kokkos::View& keys, + const Kokkos::View& values) { + // constraints + using KeysType = Kokkos::View; + using ValuesType = Kokkos::View; + ::Kokkos::Impl::static_assert_is_admissible_to_kokkos_sort_by_key(keys); + ::Kokkos::Impl::static_assert_is_admissible_to_kokkos_sort_by_key(values); + + static_assert(SpaceAccessibility::accessible, + "Kokkos::sort: execution space instance is not able to access " + "the memory space of the keys View argument!"); + static_assert( + SpaceAccessibility::accessible, + "Kokkos::sort: execution space instance is not able to access " + "the memory space of the values View argument!"); + + static_assert(KeysType::static_extent(0) == 0 || + ValuesType::static_extent(0) == 0 || + KeysType::static_extent(0) == ValuesType::static_extent(0)); + if (values.size() != keys.size()) + Kokkos::abort((std::string("values and keys extents must be the same. The " + "values extent is ") + + std::to_string(values.size()) + ", and the keys extent is " + + std::to_string(keys.size()) + ".") + .c_str()); + + if (keys.extent(0) <= 1) { + return; + } + + ::Kokkos::Impl::sort_by_key_device_view_without_comparator(exec, keys, + values); +} + +// --------------------------------------------------------------- +// overloads supporting a custom comparator +// --------------------------------------------------------------- + +template +void sort_by_key( + const ExecutionSpace& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + const ComparatorType& comparator) { + // constraints + using KeysType = Kokkos::View; + using ValuesType = Kokkos::View; + ::Kokkos::Impl::static_assert_is_admissible_to_kokkos_sort_by_key(keys); + ::Kokkos::Impl::static_assert_is_admissible_to_kokkos_sort_by_key(values); + + static_assert(SpaceAccessibility::accessible, + "Kokkos::sort: execution space instance is not able to access " + "the memory space of the keys View argument!"); + static_assert( + SpaceAccessibility::accessible, + "Kokkos::sort: execution space instance is not able to access " + "the memory space of the values View argument!"); + + static_assert(KeysType::static_extent(0) == 0 || + ValuesType::static_extent(0) == 0 || + KeysType::static_extent(0) == ValuesType::static_extent(0)); + if (values.size() != keys.size()) + Kokkos::abort((std::string("values and keys extents must be the same. The " + "values extent is ") + + std::to_string(values.size()) + ", and the keys extent is " + + std::to_string(keys.size()) + ".") + .c_str()); + + if (keys.extent(0) <= 1) { + return; + } + + ::Kokkos::Impl::sort_by_key_device_view_with_comparator(exec, keys, values, + comparator); +} + +} // namespace Kokkos::Experimental +#endif diff --git a/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp b/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp index a763c41e58..308e9e3a00 100644 --- a/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp +++ b/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp @@ -29,7 +29,7 @@ namespace Kokkos { // --------------------------------------------------------------- template -void sort([[maybe_unused]] const ExecutionSpace& exec, +void sort(const ExecutionSpace& exec, const Kokkos::View& view) { // constraints using ViewType = Kokkos::View; @@ -52,6 +52,7 @@ void sort([[maybe_unused]] const ExecutionSpace& exec, } if constexpr (Impl::better_off_calling_std_sort_v) { + exec.fence("Kokkos::sort without comparator use std::sort"); auto first = ::Kokkos::Experimental::begin(view); auto last = ::Kokkos::Experimental::end(view); std::sort(first, last); @@ -82,7 +83,7 @@ void sort(const Kokkos::View& view) { // --------------------------------------------------------------- template -void sort([[maybe_unused]] const ExecutionSpace& exec, +void sort(const ExecutionSpace& exec, const Kokkos::View& view, const ComparatorType& comparator) { // constraints @@ -105,6 +106,7 @@ void sort([[maybe_unused]] const ExecutionSpace& exec, } if constexpr (Impl::better_off_calling_std_sort_v) { + exec.fence("Kokkos::sort with comparator use std::sort"); auto first = ::Kokkos::Experimental::begin(view); auto last = ::Kokkos::Experimental::end(view); std::sort(first, last, comparator); diff --git a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_NestedSortImpl.hpp b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_NestedSortImpl.hpp index 50ac823319..2fe58272d9 100644 --- a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_NestedSortImpl.hpp +++ b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_NestedSortImpl.hpp @@ -18,7 +18,6 @@ #define KOKKOS_NESTED_SORT_IMPL_HPP_ #include -#include namespace Kokkos { namespace Experimental { @@ -99,7 +98,7 @@ KOKKOS_INLINE_FUNCTION void sort_nested_impl( keyView(elem1) = key2; keyView(elem2) = key1; if constexpr (!std::is_same_v) { - Kokkos::Experimental::swap(valueView(elem1), valueView(elem2)); + Kokkos::kokkos_swap(valueView(elem1), valueView(elem2)); } } } diff --git a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp new file mode 100644 index 0000000000..36deccdfb1 --- /dev/null +++ b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp @@ -0,0 +1,401 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_SORT_BY_KEY_FREE_FUNCS_IMPL_HPP_ +#define KOKKOS_SORT_BY_KEY_FREE_FUNCS_IMPL_HPP_ + +#include + +#if defined(KOKKOS_ENABLE_CUDA) + +// Workaround for `Instruction 'shfl' without '.sync' is not supported on +// .target sm_70 and higher from PTX ISA version 6.4`. +// Also see https://github.com/NVIDIA/cub/pull/170. +#if !defined(CUB_USE_COOPERATIVE_GROUPS) +#define CUB_USE_COOPERATIVE_GROUPS +#endif + +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" + +#if defined(KOKKOS_COMPILER_CLANG) +// Some versions of Clang fail to compile Thrust, failing with errors like +// this: +// /thrust/system/cuda/detail/core/agent_launcher.h:557:11: +// error: use of undeclared identifier 'va_printf' +// The exact combination of versions for Clang and Thrust (or CUDA) for this +// failure was not investigated, however even very recent version combination +// (Clang 10.0.0 and Cuda 10.0) demonstrated failure. +// +// Defining _CubLog here locally allows us to avoid that code path, however +// disabling some debugging diagnostics +#pragma push_macro("_CubLog") +#ifdef _CubLog +#undef _CubLog +#endif +#define _CubLog +#include +#include +#pragma pop_macro("_CubLog") +#else +#include +#include +#endif + +#pragma GCC diagnostic pop + +#endif + +#if defined(KOKKOS_ENABLE_ROCTHRUST) +#include +#include +#endif + +#if defined(KOKKOS_ENABLE_ONEDPL) && \ + (ONEDPL_VERSION_MAJOR > 2022 || \ + (ONEDPL_VERSION_MAJOR == 2022 && ONEDPL_VERSION_MINOR >= 2)) +#define KOKKOS_ONEDPL_HAS_SORT_BY_KEY +#include +#include +#endif + +namespace Kokkos::Impl { + +template +constexpr inline bool is_admissible_to_kokkos_sort_by_key = + ::Kokkos::is_view::value&& T::rank() == 1 && + (std::is_same::value || + std::is_same::value || + std::is_same::value); + +template +KOKKOS_INLINE_FUNCTION constexpr void +static_assert_is_admissible_to_kokkos_sort_by_key(const ViewType& /* view */) { + static_assert(is_admissible_to_kokkos_sort_by_key, + "Kokkos::sort_by_key only accepts 1D values View with " + "LayoutRight, LayoutLeft or LayoutStride."); +} + +// For the fallback implementation for sort_by_key using Kokkos::sort, we need +// to consider if Kokkos::sort defers to the fallback implementation that copies +// the array to the host and uses std::sort, see +// copy_to_host_run_stdsort_copy_back() in impl/Kokkos_SortImpl.hpp. If +// sort_on_device_v is true, we assume that std::sort doesn't copy data. +// Otherwise, we manually copy all data to the host and provide Kokkos::sort +// with a host execution space. +template +inline constexpr bool sort_on_device_v = false; + +#if defined(KOKKOS_ENABLE_CUDA) +template +inline constexpr bool sort_on_device_v = true; + +template +void sort_by_key_cudathrust( + const Kokkos::Cuda& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + MaybeComparator&&... maybeComparator) { + const auto policy = thrust::cuda::par.on(exec.cuda_stream()); + auto keys_first = ::Kokkos::Experimental::begin(keys); + auto keys_last = ::Kokkos::Experimental::end(keys); + auto values_first = ::Kokkos::Experimental::begin(values); + thrust::sort_by_key(policy, keys_first, keys_last, values_first, + std::forward(maybeComparator)...); +} +#endif + +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +inline constexpr bool sort_on_device_v = true; + +template +void sort_by_key_rocthrust( + const Kokkos::HIP& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + MaybeComparator&&... maybeComparator) { + const auto policy = thrust::hip::par.on(exec.hip_stream()); + auto keys_first = ::Kokkos::Experimental::begin(keys); + auto keys_last = ::Kokkos::Experimental::end(keys); + auto values_first = ::Kokkos::Experimental::begin(values); + thrust::sort_by_key(policy, keys_first, keys_last, values_first, + std::forward(maybeComparator)...); +} +#endif + +#if defined(KOKKOS_ENABLE_ONEDPL) +template +inline constexpr bool sort_on_device_v = + std::is_same_v || + std::is_same_v; + +#ifdef KOKKOS_ONEDPL_HAS_SORT_BY_KEY +template +void sort_by_key_onedpl( + const Kokkos::Experimental::SYCL& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + MaybeComparator&&... maybeComparator) { + if (keys.stride(0) != 1 && values.stride(0) != 1) { + Kokkos::abort( + "SYCL sort_by_key only supports rank-1 Views with stride(0) = 1."); + } + + // Can't use Experimental::begin/end here since the oneDPL then assumes that + // the data is on the host. + auto queue = exec.sycl_queue(); + auto policy = oneapi::dpl::execution::make_device_policy(queue); + const int n = keys.extent(0); + oneapi::dpl::sort_by_key(policy, keys.data(), keys.data() + n, values.data(), + std::forward(maybeComparator)...); +} +#endif +#endif + +template +void applyPermutation(const ExecutionSpace& space, + const PermutationView& permutation, + const ViewType& view) { + static_assert(std::is_integral::value); + + auto view_copy = Kokkos::create_mirror( + Kokkos::view_alloc(space, typename ExecutionSpace::memory_space{}, + Kokkos::WithoutInitializing), + view); + Kokkos::deep_copy(space, view_copy, view); + Kokkos::parallel_for( + "Kokkos::sort_by_key_via_sort::permute_" + view.label(), + Kokkos::RangePolicy(space, 0, view.extent(0)), + KOKKOS_LAMBDA(int i) { view(i) = view_copy(permutation(i)); }); +} + +template +void sort_by_key_via_sort( + const ExecutionSpace& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + MaybeComparator&&... maybeComparator) { + static_assert(sizeof...(MaybeComparator) <= 1); + + auto const n = keys.size(); + + Kokkos::View permute( + Kokkos::view_alloc(exec, Kokkos::WithoutInitializing, + "Kokkos::sort_by_key_via_sort::permute"), + n); + + // iota + Kokkos::parallel_for( + "Kokkos::sort_by_key_via_sort::iota", + Kokkos::RangePolicy(exec, 0, n), + KOKKOS_LAMBDA(int i) { permute(i) = i; }); + + using Layout = + typename Kokkos::View::array_layout; + if constexpr (!sort_on_device_v) { + auto host_keys = Kokkos::create_mirror_view( + Kokkos::view_alloc(Kokkos::HostSpace{}, Kokkos::WithoutInitializing), + keys); + auto host_permute = Kokkos::create_mirror_view( + Kokkos::view_alloc(Kokkos::HostSpace{}, Kokkos::WithoutInitializing), + permute); + Kokkos::deep_copy(exec, host_keys, keys); + Kokkos::deep_copy(exec, host_permute, permute); + + exec.fence("Kokkos::Impl::sort_by_key_via_sort: before host sort"); + Kokkos::DefaultHostExecutionSpace host_exec; + + if constexpr (sizeof...(MaybeComparator) == 0) { + Kokkos::sort( + host_exec, host_permute, + KOKKOS_LAMBDA(int i, int j) { return host_keys(i) < host_keys(j); }); + } else { + auto keys_comparator = + std::get<0>(std::tuple(maybeComparator...)); + Kokkos::sort( + host_exec, host_permute, KOKKOS_LAMBDA(int i, int j) { + return keys_comparator(host_keys(i), host_keys(j)); + }); + } + host_exec.fence("Kokkos::Impl::sort_by_key_via_sort: after host sort"); + Kokkos::deep_copy(exec, permute, host_permute); + } else { +#ifdef KOKKOS_ENABLE_SYCL + auto* raw_keys_in_comparator = keys.data(); + auto stride = keys.stride(0); + if constexpr (sizeof...(MaybeComparator) == 0) { + Kokkos::sort( + exec, permute, KOKKOS_LAMBDA(int i, int j) { + return raw_keys_in_comparator[i * stride] < + raw_keys_in_comparator[j * stride]; + }); + } else { + auto keys_comparator = + std::get<0>(std::tuple(maybeComparator...)); + Kokkos::sort( + exec, permute, KOKKOS_LAMBDA(int i, int j) { + return keys_comparator(raw_keys_in_comparator[i * stride], + raw_keys_in_comparator[j * stride]); + }); + } +#else + if constexpr (sizeof...(MaybeComparator) == 0) { + Kokkos::sort( + exec, permute, + KOKKOS_LAMBDA(int i, int j) { return keys(i) < keys(j); }); + } else { + auto keys_comparator = + std::get<0>(std::tuple(maybeComparator...)); + Kokkos::sort( + exec, permute, KOKKOS_LAMBDA(int i, int j) { + return keys_comparator(keys(i), keys(j)); + }); + } +#endif + } + + applyPermutation(exec, permute, keys); + applyPermutation(exec, permute, values); +} + +// ------------------------------------------------------ +// +// specialize cases for sorting by key without comparator +// +// ------------------------------------------------------ + +#if defined(KOKKOS_ENABLE_CUDA) +template +void sort_by_key_device_view_without_comparator( + const Kokkos::Cuda& exec, + const Kokkos::View& keys, + const Kokkos::View& values) { + sort_by_key_cudathrust(exec, keys, values); +} +#endif + +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +void sort_by_key_device_view_without_comparator( + const Kokkos::HIP& exec, + const Kokkos::View& keys, + const Kokkos::View& values) { + sort_by_key_rocthrust(exec, keys, values); +} +#endif + +#if defined(KOKKOS_ENABLE_ONEDPL) +template +void sort_by_key_device_view_without_comparator( + const Kokkos::Experimental::SYCL& exec, + const Kokkos::View& keys, + const Kokkos::View& values) { +#ifdef KOKKOS_ONEDPL_HAS_SORT_BY_KEY + if (keys.stride(0) == 1 && values.stride(0) == 1) + sort_by_key_onedpl(exec, keys, values); + else +#endif + sort_by_key_via_sort(exec, keys, values); +} +#endif + +// fallback case +template +std::enable_if_t::value> +sort_by_key_device_view_without_comparator( + const ExecutionSpace& exec, + const Kokkos::View& keys, + const Kokkos::View& values) { + sort_by_key_via_sort(exec, keys, values); +} + +// --------------------------------------------------- +// +// specialize cases for sorting by key with comparator +// +// --------------------------------------------------- + +#if defined(KOKKOS_ENABLE_CUDA) +template +void sort_by_key_device_view_with_comparator( + const Kokkos::Cuda& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + const ComparatorType& comparator) { + sort_by_key_cudathrust(exec, keys, values, comparator); +} +#endif + +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +void sort_by_key_device_view_with_comparator( + const Kokkos::HIP& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + const ComparatorType& comparator) { + sort_by_key_rocthrust(exec, keys, values, comparator); +} +#endif + +#if defined(KOKKOS_ENABLE_ONEDPL) +template +void sort_by_key_device_view_with_comparator( + const Kokkos::Experimental::SYCL& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + const ComparatorType& comparator) { +#ifdef KOKKOS_ONEDPL_HAS_SORT_BY_KEY + if (keys.stride(0) == 1 && values.stride(0) == 1) + sort_by_key_onedpl(exec, keys, values, comparator); + else +#endif + sort_by_key_via_sort(exec, keys, values, comparator); +} +#endif + +// fallback case +template +std::enable_if_t::value> +sort_by_key_device_view_with_comparator( + const ExecutionSpace& exec, + const Kokkos::View& keys, + const Kokkos::View& values, + const ComparatorType& comparator) { + sort_by_key_via_sort(exec, keys, values, comparator); +} + +#undef KOKKOS_ONEDPL_HAS_SORT_BY_KEY + +} // namespace Kokkos::Impl +#endif diff --git a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp index d87ab09e77..0894622891 100644 --- a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp +++ b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp @@ -63,6 +63,11 @@ #endif +#if defined(KOKKOS_ENABLE_ROCTHRUST) +#include +#include +#endif + #if defined(KOKKOS_ENABLE_ONEDPL) #include #include @@ -184,6 +189,26 @@ void sort_cudathrust(const Cuda& space, } #endif +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +void sort_rocthrust(const HIP& space, + const Kokkos::View& view, + MaybeComparator&&... maybeComparator) { + using ViewType = Kokkos::View; + static_assert(ViewType::rank == 1, + "Kokkos::sort: currently only supports rank-1 Views."); + + if (view.extent(0) <= 1) { + return; + } + const auto exec = thrust::hip::par.on(space.hip_stream()); + auto first = ::Kokkos::Experimental::begin(view); + auto last = ::Kokkos::Experimental::end(view); + thrust::sort(exec, first, last, + std::forward(maybeComparator)...); +} +#endif + #if defined(KOKKOS_ENABLE_ONEDPL) template void sort_onedpl(const Kokkos::Experimental::SYCL& space, @@ -274,6 +299,14 @@ void sort_device_view_without_comparator( } #endif +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +void sort_device_view_without_comparator( + const HIP& exec, const Kokkos::View& view) { + sort_rocthrust(exec, view); +} +#endif + #if defined(KOKKOS_ENABLE_ONEDPL) template void sort_device_view_without_comparator( @@ -320,6 +353,15 @@ void sort_device_view_with_comparator( } #endif +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +void sort_device_view_with_comparator( + const HIP& exec, const Kokkos::View& view, + const ComparatorType& comparator) { + sort_rocthrust(exec, view, comparator); +} +#endif + #if defined(KOKKOS_ENABLE_ONEDPL) template void sort_device_view_with_comparator( @@ -357,9 +399,14 @@ sort_device_view_with_comparator( using ViewType = Kokkos::View; using MemSpace = typename ViewType::memory_space; +// Note with HIP unified memory this code path is still the right thing to do +// if we end up here when RocThrust is not enabled. +// The create_mirror_view_and_copy will do the right thing (no copy). +#ifndef KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY static_assert(!SpaceAccessibility::accessible, "Impl::sort_device_view_with_comparator: should not be called " "on a view that is already accessible on the host"); +#endif copy_to_host_run_stdsort_copy_back(exec, view, comparator); } diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Copy.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Copy.hpp index b7ce1ba5ed..c5406c72b0 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Copy.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Copy.hpp @@ -50,7 +50,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -66,7 +66,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -93,7 +93,7 @@ template & source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyBackward.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyBackward.hpp index 8f9e0f19b8..82071a9362 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyBackward.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyBackward.hpp @@ -50,7 +50,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy_backward(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -65,7 +65,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy_backward(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -92,7 +92,7 @@ template & source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyIf.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyIf.hpp index ba18bc76b9..599fde5737 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyIf.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyIf.hpp @@ -54,7 +54,8 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy_if(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest, Predicate pred) { + const ::Kokkos::View& dest, + Predicate pred) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -69,7 +70,8 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy_if(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest, Predicate pred) { + const ::Kokkos::View& dest, + Predicate pred) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -96,7 +98,7 @@ template & source, - ::Kokkos::View& dest, Predicate pred) { + const ::Kokkos::View& dest, Predicate pred) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyN.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyN.hpp index 43c9120483..637d8d4cbc 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyN.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyN.hpp @@ -51,7 +51,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy_n(const ExecutionSpace& ex, const ::Kokkos::View& source, Size count, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -66,7 +66,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto copy_n(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, Size count, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -93,7 +93,7 @@ template & source, Size count, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Equal.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Equal.hpp index a72a49cc22..593c42f87e 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Equal.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Equal.hpp @@ -80,7 +80,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> bool equal(const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2) { + const ::Kokkos::View& view2) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -96,7 +96,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> bool equal(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2) { + const ::Kokkos::View& view2) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -111,7 +111,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> bool equal(const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2, + const ::Kokkos::View& view2, BinaryPredicateType predicate) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -128,7 +128,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> bool equal(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2, + const ::Kokkos::View& view2, BinaryPredicateType predicate) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -227,7 +227,7 @@ template & view1, - ::Kokkos::View& view2) { + const ::Kokkos::View& view2) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -243,7 +243,7 @@ template & view1, - ::Kokkos::View& view2, + const ::Kokkos::View& view2, BinaryPredicateType predicate) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_IterSwap.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_IterSwap.hpp index a796a306dd..5bb2d1039d 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_IterSwap.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_IterSwap.hpp @@ -19,7 +19,6 @@ #include #include "impl/Kokkos_Constraints.hpp" -#include "Kokkos_Swap.hpp" namespace Kokkos { namespace Experimental { @@ -33,7 +32,7 @@ struct StdIterSwapFunctor { KOKKOS_FUNCTION void operator()(int i) const { (void)i; - ::Kokkos::Experimental::swap(*m_a, *m_b); + ::Kokkos::kokkos_swap(*m_a, *m_b); } KOKKOS_FUNCTION @@ -58,6 +57,16 @@ void iter_swap(IteratorType1 a, IteratorType2 b) { Impl::iter_swap_impl(a, b); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 +template +KOKKOS_DEPRECATED_WITH_COMMENT("Use Kokkos::kokkos_swap instead!") +KOKKOS_FUNCTION + void swap(T& a, T& b) noexcept(::Kokkos::kokkos_swap(std::declval(), + std::declval())) { + ::Kokkos::kokkos_swap(a, b); +} +#endif + } // namespace Experimental } // namespace Kokkos diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_LexicographicalCompare.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_LexicographicalCompare.hpp index 4b5c69df45..e13479c370 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_LexicographicalCompare.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_LexicographicalCompare.hpp @@ -54,7 +54,7 @@ template < bool lexicographical_compare( const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2) { + const ::Kokkos::View& view2) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -71,7 +71,7 @@ template < bool lexicographical_compare( const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2) { + const ::Kokkos::View& view2) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -112,7 +112,8 @@ template < bool lexicographical_compare( const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2, ComparatorType comp) { + const ::Kokkos::View& view2, + ComparatorType comp) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -129,7 +130,8 @@ template < bool lexicographical_compare( const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& view1, - ::Kokkos::View& view2, ComparatorType comp) { + const ::Kokkos::View& view2, + ComparatorType comp) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -161,7 +163,7 @@ template & view1, - ::Kokkos::View& view2) { + const ::Kokkos::View& view2) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); @@ -187,7 +189,8 @@ template & view1, - ::Kokkos::View& view2, ComparatorType comp) { + const ::Kokkos::View& view2, + ComparatorType comp) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(view2); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Move.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Move.hpp index f04ea12ba8..ac308ea184 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Move.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Move.hpp @@ -50,7 +50,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto move(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -64,7 +64,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto move(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -92,7 +92,7 @@ template & source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_MoveBackward.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_MoveBackward.hpp index 375474ca57..2789ab2179 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_MoveBackward.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_MoveBackward.hpp @@ -41,7 +41,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto move_backward(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -65,7 +65,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto move_backward(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -94,7 +94,7 @@ template & source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_ReverseCopy.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_ReverseCopy.hpp index 37336c983a..66f39c4eaa 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_ReverseCopy.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_ReverseCopy.hpp @@ -50,7 +50,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto reverse_copy(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -65,7 +65,7 @@ template < std::enable_if_t<::Kokkos::is_execution_space_v, int> = 0> auto reverse_copy(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -94,7 +94,7 @@ template & source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_SwapRanges.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_SwapRanges.hpp index 39f33b6487..d66763d304 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_SwapRanges.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_SwapRanges.hpp @@ -40,7 +40,7 @@ template , int> = 0> auto swap_ranges(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -64,7 +64,7 @@ template , int> = 0> auto swap_ranges(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -94,7 +94,7 @@ template & source, - ::Kokkos::View& dest) { + const ::Kokkos::View& dest) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Transform.hpp b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Transform.hpp index 838c9169e2..84cbed524d 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Transform.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Transform.hpp @@ -58,7 +58,7 @@ template , int> = 0> auto transform(const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest, + const ::Kokkos::View& dest, UnaryOperation unary_op) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -73,7 +73,7 @@ template , int> = 0> auto transform(const std::string& label, const ExecutionSpace& ex, const ::Kokkos::View& source, - ::Kokkos::View& dest, + const ::Kokkos::View& dest, UnaryOperation unary_op) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -119,7 +119,7 @@ template & source1, const ::Kokkos::View& source2, - ::Kokkos::View& dest, + const ::Kokkos::View& dest, BinaryOperation binary_op) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source2); @@ -137,7 +137,7 @@ template & source1, const ::Kokkos::View& source2, - ::Kokkos::View& dest, + const ::Kokkos::View& dest, BinaryOperation binary_op) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source2); @@ -174,7 +174,8 @@ template & source, - ::Kokkos::View& dest, UnaryOperation unary_op) { + const ::Kokkos::View& dest, + UnaryOperation unary_op) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(dest); @@ -207,7 +208,7 @@ KOKKOS_FUNCTION auto transform( const TeamHandleType& teamHandle, const ::Kokkos::View& source1, const ::Kokkos::View& source2, - ::Kokkos::View& dest, + const ::Kokkos::View& dest, BinaryOperation binary_op) { Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source1); Impl::static_assert_is_admissible_to_kokkos_std_algorithms(source2); diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_FunctorsForExclusiveScan.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_FunctorsForExclusiveScan.hpp index 8151ee3495..5a7fe16984 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_FunctorsForExclusiveScan.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_FunctorsForExclusiveScan.hpp @@ -47,8 +47,9 @@ struct ExclusiveScanDefaultFunctorForKnownNeutralElement { KOKKOS_FUNCTION void operator()(const IndexType i, ValueType& update, const bool final_pass) const { + const auto tmp = m_first_from[i]; if (final_pass) m_first_dest[i] = update + m_init_value; - update += m_first_from[i]; + update += tmp; } }; @@ -73,6 +74,7 @@ struct ExclusiveScanDefaultFunctorWithValueWrapper { KOKKOS_FUNCTION void operator()(const IndexType i, value_type& update, const bool final_pass) const { + const auto tmp = value_type{m_first_from[i], false}; if (final_pass) { if (i == 0) { m_first_dest[i] = m_init_value; @@ -81,7 +83,6 @@ struct ExclusiveScanDefaultFunctorWithValueWrapper { } } - const auto tmp = value_type{m_first_from[i], false}; this->join(update, tmp); } @@ -132,6 +133,7 @@ struct TransformExclusiveScanFunctorWithValueWrapper { KOKKOS_FUNCTION void operator()(const IndexType i, value_type& update, const bool final_pass) const { + const auto tmp = value_type{m_unary_op(m_first_from[i]), false}; if (final_pass) { if (i == 0) { // for both ExclusiveScan and TransformExclusiveScan, @@ -142,7 +144,6 @@ struct TransformExclusiveScanFunctorWithValueWrapper { } } - const auto tmp = value_type{m_unary_op(m_first_from[i]), false}; this->join(update, tmp); } @@ -190,6 +191,7 @@ struct TransformExclusiveScanFunctorWithoutValueWrapper { KOKKOS_FUNCTION void operator()(const IndexType i, ValueType& update, const bool final_pass) const { + const auto tmp = ValueType{m_unary_op(m_first_from[i])}; if (final_pass) { if (i == 0) { // for both ExclusiveScan and TransformExclusiveScan, @@ -200,7 +202,6 @@ struct TransformExclusiveScanFunctorWithoutValueWrapper { } } - const auto tmp = ValueType{m_unary_op(m_first_from[i])}; this->join(update, tmp); } diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RemoveAllVariants.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RemoveAllVariants.hpp index 50224c8874..456df43aed 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RemoveAllVariants.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RemoveAllVariants.hpp @@ -46,15 +46,14 @@ struct StdRemoveIfStage1Functor { void operator()(const IndexType i, IndexType& update, const bool final_pass) const { auto& myval = m_first_from[i]; - if (final_pass) { - if (!m_must_remove(myval)) { + + if (!m_must_remove(myval)) { + if (final_pass) { // calling move here is ok because we are inside final pass // we are calling move assign as specified by the std m_first_dest[update] = std::move(myval); } - } - if (!m_must_remove(myval)) { update += 1; } } @@ -108,7 +107,9 @@ IteratorType remove_if_exespace_impl(const std::string& label, // create helper tmp view using value_type = typename IteratorType::value_type; using tmp_view_type = Kokkos::View; - tmp_view_type tmp_view("std_remove_if_tmp_view", keep_count); + tmp_view_type tmp_view(Kokkos::view_alloc(Kokkos::WithoutInitializing, ex, + "std_remove_if_tmp_view"), + keep_count); using tmp_readwrite_iterator_type = decltype(begin(tmp_view)); // in stage 1, *move* all elements to keep from original range to tmp diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Reverse.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Reverse.hpp index 428dc0d744..b4046c7645 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Reverse.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Reverse.hpp @@ -21,7 +21,6 @@ #include "Kokkos_Constraints.hpp" #include "Kokkos_HelperPredicates.hpp" #include -#include #include namespace Kokkos { @@ -39,7 +38,7 @@ struct StdReverseFunctor { KOKKOS_FUNCTION void operator()(index_type i) const { - ::Kokkos::Experimental::swap(m_first[i], m_last[-i - 1]); + ::Kokkos::kokkos_swap(m_first[i], m_last[-i - 1]); } KOKKOS_FUNCTION diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftLeft.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftLeft.hpp index 50bc7c8d61..9414748507 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftLeft.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftLeft.hpp @@ -126,10 +126,11 @@ KOKKOS_FUNCTION IteratorType shift_left_team_impl( // execution space impl because for this team impl we are // within a parallel region, so for now we solve serially - const std::size_t numElementsToMove = + using difference_type = typename IteratorType::difference_type; + const difference_type numElementsToMove = ::Kokkos::Experimental::distance(first + n, last); Kokkos::single(Kokkos::PerTeam(teamHandle), [=]() { - for (std::size_t i = 0; i < numElementsToMove; ++i) { + for (difference_type i = 0; i < numElementsToMove; ++i) { first[i] = std::move(first[i + n]); } }); diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftRight.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftRight.hpp index cac20bfbba..0414e6f1c2 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftRight.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ShiftRight.hpp @@ -103,26 +103,6 @@ IteratorType shift_right_exespace_impl( return first + n; } -template -struct StdShiftRightTeamSingleFunctor { - Iterator m_first; - Iterator m_last; - std::size_t m_shift; - - KOKKOS_FUNCTION - void operator()() const { - // the impl function calling this functor guarantees that - // - m_shift is non-negative - // - m_first, m_last identify a valid range with m_last > m_first - // - m_shift is less than m_last - m_first - // so I can safely use std::size_t here - } - - KOKKOS_FUNCTION - StdShiftRightTeamSingleFunctor(Iterator _first, Iterator _last, std::size_t n) - : m_first(std::move(_first)), m_last(std::move(_last)), m_shift(n) {} -}; - template KOKKOS_FUNCTION IteratorType shift_right_team_impl( const TeamHandleType& teamHandle, IteratorType first, IteratorType last, @@ -145,10 +125,11 @@ KOKKOS_FUNCTION IteratorType shift_right_team_impl( // execution space impl because for this team impl we are // within a parallel region, so for now we solve serially - const std::size_t numElementsToMove = + using difference_type = typename IteratorType::difference_type; + const difference_type numElementsToMove = ::Kokkos::Experimental::distance(first, last - n); Kokkos::single(Kokkos::PerTeam(teamHandle), [=]() { - for (std::size_t i = 0; i < numElementsToMove; ++i) { + for (difference_type i = 0; i < numElementsToMove; ++i) { last[-i - 1] = std::move(last[-n - i - 1]); } }); diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_SwapRanges.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_SwapRanges.hpp index 5bc77ed7dd..930a14ac48 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_SwapRanges.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_SwapRanges.hpp @@ -21,7 +21,6 @@ #include "Kokkos_Constraints.hpp" #include "Kokkos_HelperPredicates.hpp" #include -#include #include namespace Kokkos { @@ -36,7 +35,7 @@ struct StdSwapRangesFunctor { KOKKOS_FUNCTION void operator()(index_type i) const { - ::Kokkos::Experimental::swap(m_first1[i], m_first2[i]); + ::Kokkos::kokkos_swap(m_first1[i], m_first2[i]); } KOKKOS_FUNCTION diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp index 11afa8ed6e..2863582458 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp @@ -105,7 +105,9 @@ IteratorType unique_exespace_impl(const std::string& label, // using the same algorithm used for unique_copy but we now move things using value_type = typename IteratorType::value_type; using tmp_view_type = Kokkos::View; - tmp_view_type tmp_view("std_unique_tmp_view", num_elements_to_explore); + tmp_view_type tmp_view(Kokkos::view_alloc(ex, Kokkos::WithoutInitializing, + "std_unique_tmp_view"), + num_elements_to_explore); // scan extent is: num_elements_to_explore - 1 // for same reason as the one explained in unique_copy diff --git a/lib/kokkos/algorithms/unit_tests/CMakeLists.txt b/lib/kokkos/algorithms/unit_tests/CMakeLists.txt index 419f5ec1d1..db184bc8a9 100644 --- a/lib/kokkos/algorithms/unit_tests/CMakeLists.txt +++ b/lib/kokkos/algorithms/unit_tests/CMakeLists.txt @@ -25,6 +25,7 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) set(ALGO_SORT_SOURCES) foreach(SOURCE_Input TestSort + TestSortByKey TestSortCustomComp TestBinSortA TestBinSortB @@ -57,35 +58,37 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) configure_file(${dir}/dummy.cpp ${file}) list(APPEND ALGO_RANDOM_SOURCES ${file}) endforeach() + endif() +endforeach() - # ------------------------------------------ - # std set A - # ------------------------------------------ - set(STDALGO_SOURCES_A) - foreach(Name +# ------------------------------------------ +# std set A +# ------------------------------------------ +set(STDALGO_SOURCES_A) +foreach(Name StdReducers StdAlgorithmsConstraints RandomAccessIterator - ) - list(APPEND STDALGO_SOURCES_A Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_SOURCES_A Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std set B - # ------------------------------------------ - set(STDALGO_SOURCES_B) - foreach(Name +# ------------------------------------------ +# std set B +# ------------------------------------------ +set(STDALGO_SOURCES_B) +foreach(Name StdAlgorithmsCommon StdAlgorithmsMinMaxElementOps - ) - list(APPEND STDALGO_SOURCES_B Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_SOURCES_B Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std set C - # ------------------------------------------ - set(STDALGO_SOURCES_C) - foreach(Name +# ------------------------------------------ +# std set C +# ------------------------------------------ +set(STDALGO_SOURCES_C) +foreach(Name StdAlgorithmsCommon StdAlgorithmsLexicographicalCompare StdAlgorithmsForEach @@ -100,15 +103,15 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) StdAlgorithmsSearch_n StdAlgorithmsMismatch StdAlgorithmsMoveBackward - ) - list(APPEND STDALGO_SOURCES_C Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_SOURCES_C Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std set D - # ------------------------------------------ - set(STDALGO_SOURCES_D) - foreach(Name +# ------------------------------------------ +# std set D +# ------------------------------------------ +set(STDALGO_SOURCES_D) +foreach(Name StdAlgorithmsCommon StdAlgorithmsModOps StdAlgorithmsModSeqOps @@ -128,15 +131,15 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) StdAlgorithmsReverse StdAlgorithmsShiftLeft StdAlgorithmsShiftRight - ) - list(APPEND STDALGO_SOURCES_D Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_SOURCES_D Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std set E - # ------------------------------------------ - set(STDALGO_SOURCES_E) - foreach(Name +# ------------------------------------------ +# std set E +# ------------------------------------------ +set(STDALGO_SOURCES_E) +foreach(Name StdAlgorithmsCommon StdAlgorithmsIsSorted StdAlgorithmsIsSortedUntil @@ -149,83 +152,83 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) StdAlgorithmsTransformUnaryOp StdAlgorithmsTransformExclusiveScan StdAlgorithmsTransformInclusiveScan - ) - list(APPEND STDALGO_SOURCES_E Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_SOURCES_E Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team Q - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_Q) - foreach(Name +# ------------------------------------------ +# std team Q +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_Q) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamInclusiveScan StdAlgorithmsTeamTransformInclusiveScan - ) - list(APPEND STDALGO_TEAM_SOURCES_Q Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_Q Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team P - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_P) - foreach(Name +# ------------------------------------------ +# std team P +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_P) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamExclusiveScan StdAlgorithmsTeamTransformExclusiveScan - ) - list(APPEND STDALGO_TEAM_SOURCES_P Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_P Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team M - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_M) - foreach(Name +# ------------------------------------------ +# std team M +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_M) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamTransformUnaryOp StdAlgorithmsTeamTransformBinaryOp StdAlgorithmsTeamGenerate StdAlgorithmsTeamGenerate_n StdAlgorithmsTeamSwapRanges - ) - list(APPEND STDALGO_TEAM_SOURCES_M Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_M Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team L - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_L) - foreach(Name +# ------------------------------------------ +# std team L +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_L) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamIsSorted StdAlgorithmsTeamIsSortedUntil StdAlgorithmsTeamIsPartitioned StdAlgorithmsTeamPartitionCopy StdAlgorithmsTeamPartitionPoint - ) - list(APPEND STDALGO_TEAM_SOURCES_L Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_L Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team I - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_I) - foreach(Name +# ------------------------------------------ +# std team I +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_I) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamUnique StdAlgorithmsTeamAdjacentDifference StdAlgorithmsTeamReduce StdAlgorithmsTeamTransformReduce - ) - list(APPEND STDALGO_TEAM_SOURCES_I Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_I Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team H - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_H) - foreach(Name +# ------------------------------------------ +# std team H +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_H) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamCopy StdAlgorithmsTeamCopy_n @@ -236,43 +239,43 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) StdAlgorithmsTeamRemoveIf StdAlgorithmsTeamRemoveCopy StdAlgorithmsTeamRemoveCopyIf - ) - list(APPEND STDALGO_TEAM_SOURCES_H Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_H Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team G - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_G) - foreach(Name +# ------------------------------------------ +# std team G +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_G) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamMove StdAlgorithmsTeamMoveBackward StdAlgorithmsTeamShiftLeft StdAlgorithmsTeamShiftRight - ) - list(APPEND STDALGO_TEAM_SOURCES_G Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_G Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team F - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_F) - foreach(Name +# ------------------------------------------ +# std team F +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_F) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamReverse StdAlgorithmsTeamReverseCopy StdAlgorithmsTeamRotate StdAlgorithmsTeamRotateCopy - ) - list(APPEND STDALGO_TEAM_SOURCES_F Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_F Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team E - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_E) - foreach(Name +# ------------------------------------------ +# std team E +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_E) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamFill StdAlgorithmsTeamFill_n @@ -280,28 +283,28 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) StdAlgorithmsTeamReplaceIf StdAlgorithmsTeamReplaceCopy StdAlgorithmsTeamReplaceCopyIf - ) - list(APPEND STDALGO_TEAM_SOURCES_E Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_E Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team D - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_D) - foreach(Name +# ------------------------------------------ +# std team D +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_D) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamMinElement StdAlgorithmsTeamMaxElement StdAlgorithmsTeamMinMaxElement - ) - list(APPEND STDALGO_TEAM_SOURCES_D Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_D Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team C - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_C) - foreach(Name +# ------------------------------------------ +# std team C +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_C) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamFind StdAlgorithmsTeamFindIf @@ -310,29 +313,29 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) StdAlgorithmsTeamAnyOf StdAlgorithmsTeamNoneOf StdAlgorithmsTeamSearchN - ) - list(APPEND STDALGO_TEAM_SOURCES_C Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_C Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team B - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_B) - foreach(Name +# ------------------------------------------ +# std team B +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_B) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamEqual StdAlgorithmsTeamSearch StdAlgorithmsTeamFindEnd StdAlgorithmsTeamFindFirstOf - ) - list(APPEND STDALGO_TEAM_SOURCES_B Test${Name}.cpp) - endforeach() + ) + list(APPEND STDALGO_TEAM_SOURCES_B Test${Name}.cpp) +endforeach() - # ------------------------------------------ - # std team A - # ------------------------------------------ - set(STDALGO_TEAM_SOURCES_A) - foreach(Name +# ------------------------------------------ +# std team A +# ------------------------------------------ +set(STDALGO_TEAM_SOURCES_A) +foreach(Name StdAlgorithmsCommon StdAlgorithmsTeamAdjacentFind StdAlgorithmsTeamCount @@ -341,11 +344,8 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) StdAlgorithmsTeamForEachN StdAlgorithmsTeamLexicographicalCompare StdAlgorithmsTeamMismatch - ) - list(APPEND STDALGO_TEAM_SOURCES_A Test${Name}.cpp) - endforeach() - - endif() + ) + list(APPEND STDALGO_TEAM_SOURCES_A Test${Name}.cpp) endforeach() # FIXME_OPENMPTARGET - remove sort test as it leads to ICE with clang/16 and above at compile time. diff --git a/lib/kokkos/algorithms/unit_tests/Makefile b/lib/kokkos/algorithms/unit_tests/Makefile index 601217799a..d3946c149b 100644 --- a/lib/kokkos/algorithms/unit_tests/Makefile +++ b/lib/kokkos/algorithms/unit_tests/Makefile @@ -27,13 +27,13 @@ TARGETS = tmp := $(foreach device, $(KOKKOS_DEVICELIST), \ $(if $(filter Test$(device).cpp, $(shell ls Test$(device).cpp 2>/dev/null)),,\ - $(shell echo "\#include " > Test$(device).cpp); \ - $(shell echo "\#include " >> Test$(device).cpp); \ - $(shell echo "\#include " >> Test$(device).cpp); \ - $(shell echo "\#include " >> Test$(device).cpp); \ - $(shell echo "\#include " >> Test$(device).cpp); \ - $(shell echo "\#include " >> Test$(device).cpp); \ - $(shell echo "\#include " >> Test$(device).cpp); \ + $(shell echo "$(H)include " > Test$(device).cpp); \ + $(shell echo "$(H)include " >> Test$(device).cpp); \ + $(shell echo "$(H)include " >> Test$(device).cpp); \ + $(shell echo "$(H)include " >> Test$(device).cpp); \ + $(shell echo "$(H)include " >> Test$(device).cpp); \ + $(shell echo "$(H)include " >> Test$(device).cpp); \ + $(shell echo "$(H)include " >> Test$(device).cpp); \ ) \ ) diff --git a/lib/kokkos/algorithms/unit_tests/TestSortByKey.hpp b/lib/kokkos/algorithms/unit_tests/TestSortByKey.hpp new file mode 100644 index 0000000000..16f68eaaf2 --- /dev/null +++ b/lib/kokkos/algorithms/unit_tests/TestSortByKey.hpp @@ -0,0 +1,241 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_ALGORITHMS_UNITTESTS_TEST_SORT_BY_KEY_HPP +#define KOKKOS_ALGORITHMS_UNITTESTS_TEST_SORT_BY_KEY_HPP + +#include +#include +#include +#include + +#include // pair + +namespace Test { +namespace SortImpl { + +struct Less { + template + KOKKOS_INLINE_FUNCTION bool operator()(const ValueType &lhs, + const ValueType &rhs) const { + return lhs < rhs; + } +}; + +struct Greater { + template + KOKKOS_INLINE_FUNCTION bool operator()(const ValueType &lhs, + const ValueType &rhs) const { + return lhs > rhs; + } +}; + +template +struct is_sorted_by_key_struct { + Keys keys; + Keys keys_orig; + Permute permute; + Comparator comparator; + + is_sorted_by_key_struct(Keys keys_, Keys keys_orig_, Permute permute_, + Comparator comparator_ = Comparator{}) + : keys(keys_), + keys_orig(keys_orig_), + permute(permute_), + comparator(comparator_) {} + KOKKOS_INLINE_FUNCTION + void operator()(int i, unsigned int &count) const { + if (i < keys.extent_int(0) - 1 && comparator(keys(i + 1), keys(i))) ++count; + if (keys(i) != keys_orig(permute(i))) ++count; + } +}; + +template +void iota(ExecutionSpace const &space, ViewType const &v, + typename ViewType::value_type value = 0) { + using ValueType = typename ViewType::value_type; + Kokkos::parallel_for( + "ArborX::Algorithms::iota", + Kokkos::RangePolicy(space, 0, v.extent(0)), + KOKKOS_LAMBDA(int i) { v(i) = value + (ValueType)i; }); +} + +} // namespace SortImpl + +TEST(TEST_CATEGORY, SortByKeyEmptyView) { + using ExecutionSpace = TEST_EXECSPACE; + + // does not matter if we use int or something else + Kokkos::View keys("keys", 0); + Kokkos::View values("values", 0); + + ASSERT_NO_THROW( + Kokkos::Experimental::sort_by_key(ExecutionSpace(), keys, values)); +} + +TEST(TEST_CATEGORY, SortByKey) { + using ExecutionSpace = TEST_EXECSPACE; + using MemorySpace = typename ExecutionSpace::memory_space; + + ExecutionSpace space{}; + + for (auto keys_vector : {std::vector{36, 19, 25, 17, 3, 7, 1, 2, 9}, + std::vector{36, 19, 25, 17, 3, 9, 1, 2, 7}, + std::vector{100, 19, 36, 17, 3, 25, 1, 2, 7}, + std::vector{15, 5, 11, 3, 4, 8}}) { + auto const n = keys_vector.size(); + + auto keys = Kokkos::create_mirror_view_and_copy( + MemorySpace{}, + Kokkos::View( + keys_vector.data(), n)); + + auto keys_orig = Kokkos::create_mirror(space, keys); + Kokkos::deep_copy(space, keys_orig, keys); + + Kokkos::View permute("permute", n); + SortImpl::iota(space, permute); + + Kokkos::Experimental::sort_by_key(space, keys, permute); + + unsigned int sort_fails = 0; + Kokkos::parallel_reduce( + Kokkos::RangePolicy(space, 0, n), + SortImpl::is_sorted_by_key_struct(keys, keys_orig, + permute), + sort_fails); + + ASSERT_EQ(sort_fails, 0u); + } +} + +TEST(TEST_CATEGORY, SortByKeyWithComparator) { + using ExecutionSpace = TEST_EXECSPACE; + using MemorySpace = typename ExecutionSpace::memory_space; + + ExecutionSpace space{}; + + SortImpl::Greater comparator; + + for (auto keys_vector : {std::vector{36, 19, 25, 17, 3, 7, 1, 2, 9}, + std::vector{36, 19, 25, 17, 3, 9, 1, 2, 7}, + std::vector{100, 19, 36, 17, 3, 25, 1, 2, 7}, + std::vector{15, 5, 11, 3, 4, 8}}) { + auto const n = keys_vector.size(); + + auto keys = Kokkos::create_mirror_view_and_copy( + MemorySpace{}, + Kokkos::View( + keys_vector.data(), n)); + + auto keys_orig = Kokkos::create_mirror(space, keys); + Kokkos::deep_copy(space, keys_orig, keys); + + Kokkos::View permute("permute", n); + SortImpl::iota(space, permute); + + Kokkos::Experimental::sort_by_key(space, keys, permute, comparator); + + unsigned int sort_fails = 0; + Kokkos::parallel_reduce( + Kokkos::RangePolicy(space, 0, n), + SortImpl::is_sorted_by_key_struct( + keys, keys_orig, permute, comparator), + sort_fails); + + ASSERT_EQ(sort_fails, 0u); + } +} + +TEST(TEST_CATEGORY, SortByKeyStaticExtents) { + using ExecutionSpace = TEST_EXECSPACE; + + ExecutionSpace space{}; + + Kokkos::View keys("keys"); + + Kokkos::View values_static("values_static"); + ASSERT_NO_THROW( + Kokkos::Experimental::sort_by_key(space, keys, values_static)); + + Kokkos::View values_dynamic("values_dynamic", 10); + ASSERT_NO_THROW( + Kokkos::Experimental::sort_by_key(space, keys, values_dynamic)); +} + +template +void buildViewsForStrided(ExecutionSpace const &space, int n, Keys &keys, + Values &values) { + Kokkos::parallel_for( + "create_data", + Kokkos::MDRangePolicy, ExecutionSpace>(space, {0, 0, 0}, + {n, n, n}), + KOKKOS_LAMBDA(int i, int j, int k) { + keys(i, j, k) = n - i; + values(i, j, k) = j; + }); +} + +TEST(TEST_CATEGORY, SortByKeyWithStrides) { + using ExecutionSpace = TEST_EXECSPACE; + + ExecutionSpace space{}; + + auto const n = 10; + + Kokkos::View keys("keys", n, n, n); + Kokkos::View values("values", n, n, n); + buildViewsForStrided(space, n, keys, values); + + auto keys_sub = Kokkos::subview(keys, Kokkos::ALL(), 1, 2); + auto values_sub = Kokkos::subview(values, 4, Kokkos::ALL(), 6); + + auto keys_orig = Kokkos::create_mirror(space, keys_sub); + Kokkos::deep_copy(space, keys_orig, keys_sub); + + Kokkos::Experimental::sort_by_key(space, keys_sub, values_sub); + + unsigned int sort_fails = 0; + Kokkos::parallel_reduce( + Kokkos::RangePolicy(space, 0, n), + SortImpl::is_sorted_by_key_struct( + keys_sub, keys_orig, values_sub), + sort_fails); + + ASSERT_EQ(sort_fails, 0u); +} + +TEST(TEST_CATEGORY, SortByKeyKeysLargerThanValues) { + using ExecutionSpace = TEST_EXECSPACE; + + // does not matter if we use int or something else + Kokkos::View keys("keys", 3); + Kokkos::View values("values", 1); + + ASSERT_DEATH( + Kokkos::Experimental::sort_by_key(ExecutionSpace(), keys, values), + "values and keys extents must be the same"); + ASSERT_DEATH(Kokkos::Experimental::sort_by_key(ExecutionSpace(), keys, values, + SortImpl::Greater{}), + "values and keys extents must be the same"); +} + +} // namespace Test +#endif diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp index b962218b5f..67052e2f9d 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp @@ -198,8 +198,9 @@ auto create_deep_copyable_compatible_view_with_same_extent(ViewType view) { // this is needed for intel to avoid // error #1011: missing return statement at end of non-void function -#if defined KOKKOS_COMPILER_INTEL || \ - (defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130) +#if defined KOKKOS_COMPILER_INTEL || \ + (defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ + !defined(KOKKOS_COMPILER_MSVC)) __builtin_unreachable(); #endif } @@ -238,16 +239,8 @@ KOKKOS_FUNCTION bool team_members_have_matching_result( // set accum to 1 if a mismach is found const bool mismatch = memberValue != target; int accum = static_cast(mismatch); - // FIXME_OPENMPTARGET: team API does not meet the TeamHandle concept and - // ignores the reducer passed -#if defined KOKKOS_ENABLE_OPENMPTARGET - Kokkos::Sum dummyReducer(accum); - const auto result = teamHandle.team_reduce(accum, dummyReducer); - return (result == 0); -#else teamHandle.team_reduce(Kokkos::Sum(accum)); return (accum == 0); -#endif } template diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp index 6ab68a1987..b364c53a88 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp @@ -16,6 +16,7 @@ #include #include +#include namespace Test { namespace stdalgos { @@ -132,47 +133,6 @@ void my_host_exclusive_scan(it1 first, it1 last, it2 dest, ValType init, } } -template -void verify_data(ViewType1 data_view, // contains data - ViewType2 test_view, // the view to test - ValueType init_value, BinaryOp bop) { - //! always careful because views might not be deep copyable - - auto data_view_dc = create_deep_copyable_compatible_clone(data_view); - auto data_view_h = - create_mirror_view_and_copy(Kokkos::HostSpace(), data_view_dc); - - using gold_view_value_type = typename ViewType2::value_type; - Kokkos::View gold_h( - "goldh", data_view.extent(0)); - my_host_exclusive_scan(KE::cbegin(data_view_h), KE::cend(data_view_h), - KE::begin(gold_h), init_value, bop); - - auto test_view_dc = create_deep_copyable_compatible_clone(test_view); - auto test_view_h = - create_mirror_view_and_copy(Kokkos::HostSpace(), test_view_dc); - if (test_view_h.extent(0) > 0) { - for (std::size_t i = 0; i < test_view_h.extent(0); ++i) { - // std::cout << i << " " << std::setprecision(15) << data_view_h(i) << " " - // << gold_h(i) << " " << test_view_h(i) << " " - // << std::abs(gold_h(i) - test_view_h(i)) << std::endl; - if (std::is_same::value) { - ASSERT_EQ(gold_h(i), test_view_h(i)); - } else { - const auto error = - std::abs(static_cast(gold_h(i) - test_view_h(i))); - if (error > 1e-10) { - std::cout << i << " " << std::setprecision(15) << data_view_h(i) - << " " << gold_h(i) << " " << test_view_h(i) << " " - << std::abs(static_cast(gold_h(i) - test_view_h(i))) - << std::endl; - } - EXPECT_LT(error, 1e-10); - } - } - } -} - template struct MultiplyFunctor { KOKKOS_INLINE_FUNCTION @@ -189,107 +149,153 @@ struct SumFunctor { } }; +struct VerifyData { + template + void operator()(ViewType1 data_view, // contains data + ViewType2 test_view, // the view to test + ValueType init_value, BinaryOp bop) { + //! always careful because views might not be deep copyable + + auto data_view_dc = create_deep_copyable_compatible_clone(data_view); + auto data_view_h = + create_mirror_view_and_copy(Kokkos::HostSpace(), data_view_dc); + + using gold_view_value_type = typename ViewType2::value_type; + Kokkos::View gold_h( + "goldh", data_view.extent(0)); + my_host_exclusive_scan(KE::cbegin(data_view_h), KE::cend(data_view_h), + KE::begin(gold_h), init_value, bop); + + auto test_view_dc = create_deep_copyable_compatible_clone(test_view); + auto test_view_h = + create_mirror_view_and_copy(Kokkos::HostSpace(), test_view_dc); + if (test_view_h.extent(0) > 0) { + for (std::size_t i = 0; i < test_view_h.extent(0); ++i) { + if (std::is_same::value) { + ASSERT_EQ(gold_h(i), test_view_h(i)); + } else { + const auto error = + std::abs(static_cast(gold_h(i) - test_view_h(i))); + ASSERT_LT(error, 1e-10) << i << " " << std::setprecision(15) << error + << static_cast(test_view_h(i)) << " " + << static_cast(gold_h(i)); + } + } + } + } + + template + void operator()(ViewType1 data_view, // contains data + ViewType2 test_view, // the view to test + ValueType init_value) { + (*this)(data_view, test_view, init_value, SumFunctor()); + } +}; + std::string value_type_to_string(int) { return "int"; } std::string value_type_to_string(double) { return "double"; } -template -void run_single_scenario_default_op(const InfoType& scenario_info, - ValueType init_value) { - using default_op = SumFunctor; +template +void run_single_scenario(const InfoType& scenario_info, ValueType init_value, + OpOrEmpty... empty_or_op) { const auto name = std::get<0>(scenario_info); const std::size_t view_ext = std::get<1>(scenario_info); - // std::cout << "exclusive_scan default op: " << name << ", " - // << view_tag_to_string(Tag{}) << ", " - // << value_type_to_string(ValueType()) << ", " - // << "init = " << init_value << std::endl; auto view_dest = create_view(Tag{}, view_ext, "exclusive_scan"); auto view_from = create_view(Tag{}, view_ext, "exclusive_scan"); fill_view(view_from, name); + // view_dest is filled with zeros before calling the algorithm everytime to + // ensure the algorithm does something meaningful { fill_zero(view_dest); auto r = KE::exclusive_scan(exespace(), KE::cbegin(view_from), KE::cend(view_from), KE::begin(view_dest), - init_value); + init_value, empty_or_op...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, default_op()); + VerifyData()(view_from, view_dest, init_value, empty_or_op...); } { fill_zero(view_dest); auto r = KE::exclusive_scan("label", exespace(), KE::cbegin(view_from), KE::cend(view_from), KE::begin(view_dest), - init_value); + init_value, empty_or_op...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, default_op()); + VerifyData()(view_from, view_dest, init_value, empty_or_op...); } { fill_zero(view_dest); - auto r = KE::exclusive_scan(exespace(), view_from, view_dest, init_value); + auto r = KE::exclusive_scan(exespace(), view_from, view_dest, init_value, + empty_or_op...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, default_op()); + VerifyData()(view_from, view_dest, init_value, empty_or_op...); } { fill_zero(view_dest); auto r = KE::exclusive_scan("label", exespace(), view_from, view_dest, - init_value); + init_value, empty_or_op...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, default_op()); + VerifyData()(view_from, view_dest, init_value, empty_or_op...); } Kokkos::fence(); } -template -void run_single_scenario_custom_op(const InfoType& scenario_info, - ValueType init_value, BinaryOp bop) { +template +void run_single_scenario_inplace(const InfoType& scenario_info, + ValueType init_value, + OpOrEmpty... empty_or_op) { const auto name = std::get<0>(scenario_info); const std::size_t view_ext = std::get<1>(scenario_info); - // std::cout << "exclusive_scan custom op: " << name << ", " - // << view_tag_to_string(Tag{}) << ", " - // << value_type_to_string(ValueType()) << ", " - // << "init = " << init_value << std::endl; - auto view_dest = create_view(Tag{}, view_ext, "exclusive_scan"); - auto view_from = create_view(Tag{}, view_ext, "exclusive_scan"); - fill_view(view_from, name); + // since here we call the in-place operation, we need to use two views: + // view1: filled according to what the scenario asks for and is not modified + // view2: filled according to what the scenario asks for and used for the + // in-place op Therefore, after the op is done, view2 should contain the + // result of doing exclusive scan NOTE: view2 is filled below every time + // because the algorithm acts in place + auto view1 = + create_view(Tag{}, view_ext, "exclusive_scan_inplace_view1"); + fill_view(view1, name); + + auto view2 = + create_view(Tag{}, view_ext, "exclusive_scan_inplace_view2"); { - fill_zero(view_dest); - auto r = KE::exclusive_scan(exespace(), KE::cbegin(view_from), - KE::cend(view_from), KE::begin(view_dest), - init_value, bop); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, bop); + fill_view(view2, name); + auto r = KE::exclusive_scan(exespace(), KE::cbegin(view2), KE::cend(view2), + KE::begin(view2), init_value, empty_or_op...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, init_value, empty_or_op...); } { - fill_zero(view_dest); - auto r = KE::exclusive_scan("label", exespace(), KE::cbegin(view_from), - KE::cend(view_from), KE::begin(view_dest), - init_value, bop); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, bop); + fill_view(view2, name); + auto r = KE::exclusive_scan("label", exespace(), KE::cbegin(view2), + KE::cend(view2), KE::begin(view2), init_value, + empty_or_op...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, init_value, empty_or_op...); } { - fill_zero(view_dest); - auto r = - KE::exclusive_scan(exespace(), view_from, view_dest, init_value, bop); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, bop); + fill_view(view2, name); + auto r = KE::exclusive_scan(exespace(), view2, view2, init_value, + empty_or_op...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, init_value, empty_or_op...); } { - fill_zero(view_dest); - auto r = KE::exclusive_scan("label", exespace(), view_from, view_dest, - init_value, bop); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, init_value, bop); + fill_view(view2, name); + auto r = KE::exclusive_scan("label", exespace(), view2, view2, init_value, + empty_or_op...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, init_value, empty_or_op...); } Kokkos::fence(); @@ -303,34 +309,39 @@ void run_exclusive_scan_all_scenarios() { {"medium", 1103}, {"large", 10513}}; for (const auto& it : scenarios) { - run_single_scenario_default_op(it, ValueType{0}); - run_single_scenario_default_op(it, ValueType{1}); - run_single_scenario_default_op(it, ValueType{-2}); - run_single_scenario_default_op(it, ValueType{3}); + run_single_scenario(it, ValueType{0}); + run_single_scenario(it, ValueType{1}); + run_single_scenario(it, ValueType{-2}); + run_single_scenario(it, ValueType{3}); + + run_single_scenario_inplace(it, ValueType{0}); + run_single_scenario_inplace(it, ValueType{-2}); #if !defined KOKKOS_ENABLE_OPENMPTARGET // custom multiply op is only run for small views otherwise it overflows if (it.first == "small-a" || it.first == "small-b") { using custom_bop_t = MultiplyFunctor; - run_single_scenario_custom_op(it, ValueType{0}, - custom_bop_t()); - run_single_scenario_custom_op(it, ValueType{1}, - custom_bop_t()); - run_single_scenario_custom_op(it, ValueType{-2}, - custom_bop_t()); - run_single_scenario_custom_op(it, ValueType{3}, - custom_bop_t()); + run_single_scenario(it, ValueType{0}, custom_bop_t()); + run_single_scenario(it, ValueType{1}, custom_bop_t()); + run_single_scenario(it, ValueType{-2}, custom_bop_t()); + run_single_scenario(it, ValueType{3}, custom_bop_t()); + + run_single_scenario_inplace(it, ValueType{0}, + custom_bop_t()); + run_single_scenario_inplace(it, ValueType{-2}, + custom_bop_t()); } using custom_bop_t = SumFunctor; - run_single_scenario_custom_op(it, ValueType{0}, - custom_bop_t()); - run_single_scenario_custom_op(it, ValueType{1}, - custom_bop_t()); - run_single_scenario_custom_op(it, ValueType{-2}, - custom_bop_t()); - run_single_scenario_custom_op(it, ValueType{3}, - custom_bop_t()); + run_single_scenario(it, ValueType{0}, custom_bop_t()); + run_single_scenario(it, ValueType{1}, custom_bop_t()); + run_single_scenario(it, ValueType{-2}, custom_bop_t()); + run_single_scenario(it, ValueType{3}, custom_bop_t()); + + run_single_scenario_inplace(it, ValueType{0}, + custom_bop_t()); + run_single_scenario_inplace(it, ValueType{-2}, + custom_bop_t()); #endif } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp index 8e60a43e5f..a08a737210 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp @@ -16,6 +16,7 @@ #include #include +#include namespace Test { namespace stdalgos { @@ -143,51 +144,6 @@ void my_host_inclusive_scan(it1 first, it1 last, it2 dest, BinOp bop, } } -template -void verify_data(ViewType1 data_view, // contains data - ViewType2 test_view, // the view to test - BinaryOp bop, Args... args /* copy on purpose */) { - //! always careful because views might not be deep copyable - - auto data_view_dc = create_deep_copyable_compatible_clone(data_view); - auto data_view_h = - create_mirror_view_and_copy(Kokkos::HostSpace(), data_view_dc); - - using gold_view_value_type = typename ViewType2::value_type; - Kokkos::View gold_h( - "goldh", data_view.extent(0)); - my_host_inclusive_scan(KE::cbegin(data_view_h), KE::cend(data_view_h), - KE::begin(gold_h), bop, args...); - - auto test_view_dc = create_deep_copyable_compatible_clone(test_view); - auto test_view_h = - create_mirror_view_and_copy(Kokkos::HostSpace(), test_view_dc); - - const auto ext = test_view_h.extent(0); - if (ext > 0) { - for (std::size_t i = 0; i < ext; ++i) { - // std::cout << i << " " << std::setprecision(15) << data_view_h(i) << " " - // << gold_h(i) << " " << test_view_h(i) << " " - // << std::abs(gold_h(i) - test_view_h(i)) << std::endl; - - if (std::is_same::value) { - ASSERT_EQ(gold_h(i), test_view_h(i)); - } else { - const auto error = - std::abs(static_cast(gold_h(i) - test_view_h(i))); - if (error > 1e-10) { - std::cout << i << " " << std::setprecision(15) << data_view_h(i) - << " " << gold_h(i) << " " << test_view_h(i) << " " - << std::abs(static_cast(gold_h(i) - test_view_h(i))) - << std::endl; - } - EXPECT_LT(error, 1e-10); - } - } - // std::cout << " last el: " << test_view_h(ext-1) << std::endl; - } -} - template struct MultiplyFunctor { KOKKOS_INLINE_FUNCTION @@ -204,107 +160,151 @@ struct SumFunctor { } }; +struct VerifyData { + template + void operator()(ViewType1 data_view, // contains data + ViewType2 test_view, // the view to test + BinaryOp bop, Args... args /* copy on purpose */) { + //! always careful because views might not be deep copyable + + auto data_view_dc = create_deep_copyable_compatible_clone(data_view); + auto data_view_h = + create_mirror_view_and_copy(Kokkos::HostSpace(), data_view_dc); + + using gold_view_value_type = typename ViewType2::value_type; + Kokkos::View gold_h( + "goldh", data_view.extent(0)); + my_host_inclusive_scan(KE::cbegin(data_view_h), KE::cend(data_view_h), + KE::begin(gold_h), bop, args...); + + auto test_view_dc = create_deep_copyable_compatible_clone(test_view); + auto test_view_h = + create_mirror_view_and_copy(Kokkos::HostSpace(), test_view_dc); + + const auto ext = test_view_h.extent(0); + if (ext > 0) { + for (std::size_t i = 0; i < ext; ++i) { + if (std::is_same::value) { + ASSERT_EQ(gold_h(i), test_view_h(i)); + } else { + const auto error = + std::abs(static_cast(gold_h(i) - test_view_h(i))); + ASSERT_LT(error, 1e-10) << i << " " << std::setprecision(15) << error + << static_cast(test_view_h(i)) << " " + << static_cast(gold_h(i)); + } + } + } + } + + template + void operator()(ViewType1 data_view, // contains data + ViewType2 test_view) // the view to test + { + using value_type = typename ViewType1::non_const_value_type; + (*this)(data_view, test_view, SumFunctor()); + } +}; + std::string value_type_to_string(int) { return "int"; } std::string value_type_to_string(double) { return "double"; } -template -void run_single_scenario_default_op(const InfoType& scenario_info) { - using default_op = SumFunctor; +template +void run_single_scenario(const InfoType& scenario_info, + Args... args /* copy on purpose */) { const auto name = std::get<0>(scenario_info); const std::size_t view_ext = std::get<1>(scenario_info); - // std::cout << "inclusive_scan default op: " << name << ", " - // << view_tag_to_string(Tag{}) << ", " - // << value_type_to_string(ValueType()) << std::endl; auto view_dest = create_view(Tag{}, view_ext, "inclusive_scan"); auto view_from = create_view(Tag{}, view_ext, "inclusive_scan"); fill_view(view_from, name); + // view_dest is filled with zeros before calling the algorithm everytime to + // ensure the algorithm does something meaningful { fill_zero(view_dest); - auto r = KE::inclusive_scan(exespace(), KE::cbegin(view_from), - KE::cend(view_from), KE::begin(view_dest)); + auto r = + KE::inclusive_scan(exespace(), KE::cbegin(view_from), + KE::cend(view_from), KE::begin(view_dest), args...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, default_op()); + VerifyData()(view_from, view_dest, args...); } { fill_zero(view_dest); - auto r = KE::inclusive_scan("label", exespace(), KE::cbegin(view_from), - KE::cend(view_from), KE::begin(view_dest)); + auto r = + KE::inclusive_scan("label", exespace(), KE::cbegin(view_from), + KE::cend(view_from), KE::begin(view_dest), args...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, default_op()); + VerifyData()(view_from, view_dest, args...); } { fill_zero(view_dest); - auto r = KE::inclusive_scan(exespace(), view_from, view_dest); + auto r = KE::inclusive_scan(exespace(), view_from, view_dest, args...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, default_op()); + VerifyData()(view_from, view_dest, args...); } { fill_zero(view_dest); - auto r = KE::inclusive_scan("label", exespace(), view_from, view_dest); + auto r = + KE::inclusive_scan("label", exespace(), view_from, view_dest, args...); ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, default_op()); + VerifyData()(view_from, view_dest, args...); } Kokkos::fence(); } -template -void run_single_scenario_custom_op(const InfoType& scenario_info, BinaryOp bop, - Args... args /* copy on purpose */) { +template +void run_single_scenario_inplace(const InfoType& scenario_info, + Args... args /* copy on purpose */) { const auto name = std::get<0>(scenario_info); const std::size_t view_ext = std::get<1>(scenario_info); - // if (1 == sizeof...(Args)) { - // std::cout << "inclusive_scan custom op and init value: " << name << ", " - // << view_tag_to_string(Tag{}) << ", " - // << value_type_to_string(ValueType()) << ", " << std::endl; - // } else { - // std::cout << "inclusive_scan custom op: " << name << ", " - // << view_tag_to_string(Tag{}) << ", " - // << value_type_to_string(ValueType()) << ", " << std::endl; - // } + // since here we call the in-place operation, we need to use two views: + // view1: filled according to what the scenario asks for and is not modified + // view2: filled according to what the scenario asks for and used for the + // in-place op Therefore, after the op is done, view_2 should contain the + // result of doing exclusive scan NOTE: view2 is filled below every time + // because the algorithm acts in place - auto view_dest = create_view(Tag{}, view_ext, "inclusive_scan"); - auto view_from = create_view(Tag{}, view_ext, "inclusive_scan"); - fill_view(view_from, name); + auto view1 = + create_view(Tag{}, view_ext, "inclusive_scan_inplace_view1"); + fill_view(view1, name); + + auto view2 = + create_view(Tag{}, view_ext, "inclusive_scan_inplace_view2"); { - fill_zero(view_dest); - auto r = KE::inclusive_scan(exespace(), KE::cbegin(view_from), - KE::cend(view_from), KE::begin(view_dest), bop, - args...); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, bop, args...); + fill_view(view2, name); + auto r = KE::inclusive_scan(exespace(), KE::cbegin(view2), KE::cend(view2), + KE::begin(view2), args...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, args...); } { - fill_zero(view_dest); - auto r = KE::inclusive_scan("label", exespace(), KE::cbegin(view_from), - KE::cend(view_from), KE::begin(view_dest), bop, - args...); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, bop, args...); + fill_view(view2, name); + auto r = KE::inclusive_scan("label", exespace(), KE::cbegin(view2), + KE::cend(view2), KE::begin(view2), args...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, args...); } { - fill_zero(view_dest); - auto r = KE::inclusive_scan(exespace(), view_from, view_dest, bop, args...); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, bop, args...); + fill_view(view2, name); + auto r = KE::inclusive_scan(exespace(), view2, view2, args...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, args...); } { - fill_zero(view_dest); - auto r = KE::inclusive_scan("label", exespace(), view_from, view_dest, bop, - args...); - ASSERT_EQ(r, KE::end(view_dest)); - verify_data(view_from, view_dest, bop, args...); + fill_view(view2, name); + auto r = KE::inclusive_scan("label", exespace(), view2, view2, args...); + ASSERT_EQ(r, KE::end(view2)); + VerifyData()(view1, view2, args...); } Kokkos::fence(); @@ -318,27 +318,35 @@ void run_inclusive_scan_all_scenarios() { {"medium-a", 313}, {"medium-b", 1103}, {"large", 10513}}; for (const auto& it : scenarios) { - run_single_scenario_default_op(it); + run_single_scenario(it); + run_single_scenario_inplace(it); #if !defined KOKKOS_ENABLE_OPENMPTARGET // the sum custom op is always run using sum_binary_op = SumFunctor; sum_binary_op sbop; - run_single_scenario_custom_op(it, sbop); - run_single_scenario_custom_op(it, sbop, ValueType{0}); - run_single_scenario_custom_op(it, sbop, ValueType{1}); - run_single_scenario_custom_op(it, sbop, ValueType{-2}); - run_single_scenario_custom_op(it, sbop, ValueType{3}); + run_single_scenario(it, sbop); + run_single_scenario(it, sbop, ValueType{0}); + run_single_scenario(it, sbop, ValueType{1}); + run_single_scenario(it, sbop, ValueType{-2}); + run_single_scenario(it, sbop, ValueType{3}); + + run_single_scenario_inplace(it, sbop, ValueType{0}); + run_single_scenario_inplace(it, sbop, ValueType{-2}); // custom multiply only for small views to avoid overflows if (it.first == "small-a" || it.first == "small-b") { using mult_binary_op = MultiplyFunctor; mult_binary_op mbop; - run_single_scenario_custom_op(it, mbop); - run_single_scenario_custom_op(it, mbop, ValueType{0}); - run_single_scenario_custom_op(it, mbop, ValueType{1}); - run_single_scenario_custom_op(it, mbop, ValueType{-2}); - run_single_scenario_custom_op(it, mbop, ValueType{3}); + run_single_scenario(it, mbop); + run_single_scenario(it, mbop, ValueType{0}); + run_single_scenario(it, mbop, ValueType{1}); + run_single_scenario(it, mbop, ValueType{-2}); + run_single_scenario(it, mbop, ValueType{3}); + + run_single_scenario_inplace(it, mbop); + run_single_scenario_inplace(it, mbop, ValueType{0}); + run_single_scenario_inplace(it, mbop, ValueType{-2}); } #endif } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSorted.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSorted.cpp index f31d49e06b..75d4f0afeb 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSorted.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSorted.cpp @@ -146,7 +146,7 @@ void run_single_scenario(const InfoType& scenario_info) { resultsA[3] = KE::is_sorted("label", exespace(), view); const auto allA = std::all_of(resultsA.cbegin(), resultsA.cend(), [=](bool v) { return v == gold; }); - EXPECT_TRUE(allA); + EXPECT_TRUE(allA) << name << ", " << view_tag_to_string(Tag{}); #if !defined KOKKOS_ENABLE_OPENMPTARGET CustomLessThanComparator comp; @@ -159,7 +159,7 @@ void run_single_scenario(const InfoType& scenario_info) { resultsB[3] = KE::is_sorted("label", exespace(), view, comp); const auto allB = std::all_of(resultsB.cbegin(), resultsB.cend(), [=](bool v) { return v == gold; }); - EXPECT_TRUE(allB); + EXPECT_TRUE(allB) << name << ", " << view_tag_to_string(Tag{}); #endif Kokkos::fence(); @@ -173,9 +173,6 @@ void run_is_sorted_all_scenarios() { {"medium-a", 1003}, {"medium-b", 1003}, {"large-a", 101513}, {"large-b", 101513}}; - std::cout << "is_sorted: " << view_tag_to_string(Tag{}) - << ", all overloads \n"; - for (const auto& it : scenarios) { run_single_scenario(it); } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp index dcfe8ad67e..29ac7cc9bc 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp @@ -145,10 +145,10 @@ void run_single_scenario(const InfoType& scenario_info) { KE::is_sorted_until("label", exespace(), KE::begin(view), KE::end(view)); auto r3 = KE::is_sorted_until(exespace(), view); auto r4 = KE::is_sorted_until("label", exespace(), view); - ASSERT_EQ(r1, gold); - ASSERT_EQ(r2, gold); - ASSERT_EQ(r3, gold); - ASSERT_EQ(r4, gold); + ASSERT_EQ(r1, gold) << name << ", " << view_tag_to_string(Tag{}); + ASSERT_EQ(r2, gold) << name << ", " << view_tag_to_string(Tag{}); + ASSERT_EQ(r3, gold) << name << ", " << view_tag_to_string(Tag{}); + ASSERT_EQ(r4, gold) << name << ", " << view_tag_to_string(Tag{}); #if !defined KOKKOS_ENABLE_OPENMPTARGET CustomLessThanComparator comp; @@ -160,10 +160,10 @@ void run_single_scenario(const InfoType& scenario_info) { auto r8 = KE::is_sorted_until("label", exespace(), view, comp); #endif - ASSERT_EQ(r1, gold); - ASSERT_EQ(r2, gold); - ASSERT_EQ(r3, gold); - ASSERT_EQ(r4, gold); + ASSERT_EQ(r1, gold) << name << ", " << view_tag_to_string(Tag{}); + ASSERT_EQ(r2, gold) << name << ", " << view_tag_to_string(Tag{}); + ASSERT_EQ(r3, gold) << name << ", " << view_tag_to_string(Tag{}); + ASSERT_EQ(r4, gold) << name << ", " << view_tag_to_string(Tag{}); Kokkos::fence(); } @@ -176,9 +176,6 @@ void run_is_sorted_until_all_scenarios() { {"medium-a", 1003}, {"medium-b", 1003}, {"large-a", 101513}, {"large-b", 101513}}; - std::cout << "is_sorted_until: " << view_tag_to_string(Tag{}) - << ", all overloads \n"; - for (const auto& it : scenarios) { run_single_scenario(it); } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp index 4604764097..1b1a02f39c 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp @@ -48,7 +48,7 @@ struct MyMovableType { TEST(std_algorithms_mod_ops_test, move) { MyMovableType a; using move_t = decltype(std::move(a)); - static_assert(std::is_rvalue_reference::value, ""); + static_assert(std::is_rvalue_reference::value); // move constr MyMovableType b(std::move(a)); @@ -70,7 +70,7 @@ struct StdAlgoModSeqOpsTestMove { void operator()(const int index) const { typename ViewType::value_type a{11}; using move_t = decltype(std::move(a)); - static_assert(std::is_rvalue_reference::value, ""); + static_assert(std::is_rvalue_reference::value); m_view(index) = std::move(a); } @@ -89,50 +89,6 @@ TEST(std_algorithms_mod_ops_test, move_within_parfor) { } } -// ------------ -// swap -// ------------ -TEST(std_algorithms_mod_ops_test, swap) { - { - int a = 1; - int b = 2; - KE::swap(a, b); - ASSERT_EQ(a, 2); - ASSERT_EQ(b, 1); - } - - { - double a = 3.; - double b = 1.; - KE::swap(a, b); - EXPECT_DOUBLE_EQ(a, 1.); - EXPECT_DOUBLE_EQ(b, 3.); - } -} - -template -struct StdAlgoModSeqOpsTestSwap { - ViewType m_view; - - KOKKOS_INLINE_FUNCTION - void operator()(const int index) const { - typename ViewType::value_type newval{11}; - KE::swap(m_view(index), newval); - } - - StdAlgoModSeqOpsTestSwap(ViewType aIn) : m_view(aIn) {} -}; - -TEST(std_algorithms_mod_ops_test, swap_within_parfor) { - auto a = create_view(stdalgos::DynamicTag{}, 10, "a"); - StdAlgoModSeqOpsTestSwap fnc(a); - Kokkos::parallel_for(a.extent(0), fnc); - auto a_h = Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), a); - for (std::size_t i = 0; i < a.extent(0); ++i) { - EXPECT_DOUBLE_EQ(a_h(0), 11.); - } -} - // ------------ // iter_swap // ------------ diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsPartitionCopy.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsPartitionCopy.cpp index f169fd9ce8..a36c9db2b9 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsPartitionCopy.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsPartitionCopy.cpp @@ -110,11 +110,9 @@ void verify_data(const std::string& name, ResultType my_result, ViewTypeDestFalse view_dest_false, PredType pred) { using value_type = typename ViewTypeFrom::value_type; static_assert( - std::is_same::value, - ""); + std::is_same::value); static_assert( - std::is_same::value, - ""); + std::is_same::value); const std::size_t ext = view_from.extent(0); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamCopyIf.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamCopyIf.cpp index b32a9be3a1..7c3c465dc8 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamCopyIf.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamCopyIf.cpp @@ -139,7 +139,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { auto intraTeamSentinelView_h = create_host_space_copy(intraTeamSentinelView); Kokkos::View stdDestView("stdDestView", numTeams, numCols); - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); for (std::size_t i = 0; i < sourceView.extent(0); ++i) { auto rowFrom = Kokkos::subview(sourceViewBeforeOp_h, i, Kokkos::ALL()); auto rowDest = Kokkos::subview(stdDestView, i, Kokkos::ALL()); @@ -166,6 +166,10 @@ void run_all_scenarios() { } TEST(std_algorithms_copy_if_team_test, test) { +// FIXME_OPENMPTARGET +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + GTEST_SKIP() << "the test is known to fail with OpenMPTarget on Intel GPUs"; +#endif run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp index c6b2566c6c..2c8fee02f4 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp @@ -121,7 +121,9 @@ struct TestFunctorA { } }; -template +struct InPlace {}; + +template void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { /* description: use a rank-2 view randomly filled with values, @@ -147,9 +149,6 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { using space_t = Kokkos::DefaultExecutionSpace; Kokkos::TeamPolicy policy(numTeams, Kokkos::AUTO()); - // create the destination view - Kokkos::View destView("destView", numTeams, numCols); - // exclusive_scan returns an iterator so to verify that it is correct // each team stores the distance of the returned iterator from the beginning // of the interval that team operates on and then we check that these @@ -168,12 +167,19 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { rand_pool pool(lowerBound * upperBound); Kokkos::fill_random(initValuesView_h, pool, lowerBound, upperBound); - // use CTAD for functor auto initValuesView = Kokkos::create_mirror_view_and_copy(space_t(), initValuesView_h); - TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, - initValuesView, binaryOp, apiId); - Kokkos::parallel_for(policy, fnc); + + Kokkos::View destView("destView", numTeams, numCols); + if constexpr (std::is_same_v) { + TestFunctorA fnc(sourceView, sourceView, distancesView, + intraTeamSentinelView, initValuesView, binaryOp, apiId); + Kokkos::parallel_for(policy, fnc); + } else { + TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, + initValuesView, binaryOp, apiId); + Kokkos::parallel_for(policy, fnc); + } // ----------------------------------------------- // run cpp-std kernel and check @@ -223,11 +229,16 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { #undef exclusive_scan } - auto dataViewAfterOp_h = create_host_space_copy(destView); - expect_equal_host_views(stdDestView, dataViewAfterOp_h); + if constexpr (std::is_same_v) { + auto dataViewAfterOp_h = create_host_space_copy(sourceView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } else { + auto dataViewAfterOp_h = create_host_space_copy(destView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } } -template +template void run_all_scenarios() { for (int numTeams : teamSizesToTest) { for (const auto& numCols : {0, 1, 2, 13, 101, 1444, 8153}) { @@ -236,16 +247,24 @@ void run_all_scenarios() { #else for (int apiId : {0, 1}) { #endif - test_A(numTeams, numCols, apiId); + test_A(numTeams, numCols, apiId); } } } } TEST(std_algorithms_exclusive_scan_team_test, test) { +// FIXME_OPENMPTARGET +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + GTEST_SKIP() << "the test is known to fail with OpenMPTarget on Intel GPUs"; +#endif run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); + + run_all_scenarios(); + run_all_scenarios(); + run_all_scenarios(); } } // namespace TeamExclusiveScan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp index 0daf9dbfe8..b5f4cdd612 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp @@ -139,7 +139,9 @@ struct TestFunctorA { } }; -template +struct InPlace {}; + +template void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { /* description: use a rank-2 view randomly filled with values, @@ -165,9 +167,6 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { using space_t = Kokkos::DefaultExecutionSpace; Kokkos::TeamPolicy policy(numTeams, Kokkos::AUTO()); - // create the destination view - Kokkos::View destView("destView", numTeams, numCols); - // inclusive_scan returns an iterator so to verify that it is correct // each team stores the distance of the returned iterator from the beginning // of the interval that team operates on and then we check that these @@ -186,12 +185,20 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { rand_pool pool(lowerBound * upperBound); Kokkos::fill_random(initValuesView_h, pool, lowerBound, upperBound); - // use CTAD for functor auto initValuesView = Kokkos::create_mirror_view_and_copy(space_t(), initValuesView_h); - TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, - initValuesView, binaryOp, apiId); - Kokkos::parallel_for(policy, fnc); + + // create the destination view + Kokkos::View destView("destView", numTeams, numCols); + if constexpr (std::is_same_v) { + TestFunctorA fnc(sourceView, sourceView, distancesView, + intraTeamSentinelView, initValuesView, binaryOp, apiId); + Kokkos::parallel_for(policy, fnc); + } else { + TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, + initValuesView, binaryOp, apiId); + Kokkos::parallel_for(policy, fnc); + } // ----------------------------------------------- // run cpp-std kernel and check @@ -251,25 +258,38 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { #undef inclusive_scan } - auto dataViewAfterOp_h = create_host_space_copy(destView); - expect_equal_host_views(stdDestView, dataViewAfterOp_h); + if constexpr (std::is_same_v) { + auto dataViewAfterOp_h = create_host_space_copy(sourceView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } else { + auto dataViewAfterOp_h = create_host_space_copy(destView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } } -template +template void run_all_scenarios() { for (int numTeams : teamSizesToTest) { for (const auto& numCols : {0, 1, 2, 13, 101, 1444, 8153}) { for (int apiId : {0, 1, 2, 3, 4, 5}) { - test_A(numTeams, numCols, apiId); + test_A(numTeams, numCols, apiId); } } } } TEST(std_algorithms_inclusive_scan_team_test, test) { +// FIXME_OPENMPTARGET +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + GTEST_SKIP() << "the test is known to fail with OpenMPTarget on Intel GPUs"; +#endif run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); + + run_all_scenarios(); + run_all_scenarios(); + run_all_scenarios(); } } // namespace TeamInclusiveScan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamIsPartitioned.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamIsPartitioned.cpp index 1928f95588..21da333e75 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamIsPartitioned.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamIsPartitioned.cpp @@ -191,7 +191,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId, // ----------------------------------------------- auto returnView_h = create_host_space_copy(returnView); auto intraTeamSentinelView_h = create_host_space_copy(intraTeamSentinelView); - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); for (std::size_t i = 0; i < dataView_dc_h.extent(0); ++i) { auto myRow = Kokkos::subview(dataView_dc_h, i, Kokkos::ALL()); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionCopy.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionCopy.cpp index c0bbdfa390..78ab6bf1f8 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionCopy.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionCopy.cpp @@ -240,7 +240,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId, "stdDestTrueView", numTeams, numCols); Kokkos::View stdDestFalseView( "stdDestFalseView", numTeams, numCols); - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); for (std::size_t i = 0; i < sourceView_dc_h.extent(0); ++i) { auto myRowSource = Kokkos::subview(sourceView_dc_h, i, Kokkos::ALL()); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionPoint.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionPoint.cpp index 954d461246..370e91cc1f 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionPoint.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamPartitionPoint.cpp @@ -197,7 +197,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId, auto distancesView_h = create_host_space_copy(distancesView); auto dataViewAfterOp_h = create_host_space_copy(dataView); auto intraTeamSentinelView_h = create_host_space_copy(intraTeamSentinelView); - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); for (std::size_t i = 0; i < dataView_dc_h.extent(0); ++i) { auto myRow = Kokkos::subview(dataView_dc_h, i, Kokkos::ALL()); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopy.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopy.cpp index 24b840154b..6bb0d24998 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopy.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopy.cpp @@ -212,6 +212,10 @@ void run_all_scenarios() { } TEST(std_algorithms_remove_copy_team_test, test) { +// FIXME_OPENMPTARGET +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + GTEST_SKIP() << "the test is known to fail with OpenMPTarget on Intel GPUs"; +#endif run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopyIf.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopyIf.cpp index 2082fa9728..cff9aa178a 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopyIf.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveCopyIf.cpp @@ -138,7 +138,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { auto intraTeamSentinelView_h = create_host_space_copy(intraTeamSentinelView); Kokkos::View stdDestView("stdDestView", numTeams, numCols); - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); for (std::size_t i = 0; i < destViewAfterOp_h.extent(0); ++i) { auto rowFrom = Kokkos::subview(cloneOfSourceViewBeforeOp_h, i, Kokkos::ALL()); @@ -168,6 +168,10 @@ void run_all_scenarios() { } TEST(std_algorithms_remove_copy_if_team_test, test) { +// FIXME_OPENMPTARGET +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + GTEST_SKIP() << "the test is known to fail with OpenMPTarget on Intel GPUs"; +#endif run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveIf.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveIf.cpp index 3315f281da..3dd7cb764c 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveIf.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamRemoveIf.cpp @@ -127,7 +127,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { // ----------------------------------------------- // check against std // ----------------------------------------------- - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); auto dataViewAfterOp_h = create_host_space_copy(dataView); auto distancesView_h = create_host_space_copy(distancesView); auto intraTeamSentinelView_h = create_host_space_copy(intraTeamSentinelView); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceCopyIf.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceCopyIf.cpp index ae43a2a426..d0217aed7a 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceCopyIf.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceCopyIf.cpp @@ -145,7 +145,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { auto intraTeamSentinelView_h = create_host_space_copy(intraTeamSentinelView); Kokkos::View stdDestView("stdDestView", numTeams, numCols); - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); for (std::size_t i = 0; i < sourceView.extent(0); ++i) { auto rowFrom = Kokkos::subview(cloneOfSourceViewBeforeOp_h, i, Kokkos::ALL()); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceIf.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceIf.cpp index 1d5d9578f9..d79b53d355 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceIf.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReplaceIf.cpp @@ -103,7 +103,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { stdDataView(i, j) = cloneOfDataViewBeforeOp_h(i, j); } } - GreaterThanValueFunctor predicate(threshold); + GreaterThanValueFunctor predicate(threshold); for (std::size_t i = 0; i < dataView.extent(0); ++i) { auto thisRow = Kokkos::subview(stdDataView, i, Kokkos::ALL()); std::replace_if(KE::begin(thisRow), KE::end(thisRow), predicate, newVal); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp index 9f30812d8e..60fa369af1 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp @@ -108,7 +108,9 @@ struct TestFunctorA { } }; -template +struct InPlace {}; + +template void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { /* description: use a rank-2 view randomly filled with values, @@ -134,9 +136,6 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { using space_t = Kokkos::DefaultExecutionSpace; Kokkos::TeamPolicy policy(numTeams, Kokkos::AUTO()); - // create the destination view - Kokkos::View destView("destView", numTeams, numCols); - // tranform_exclusive_scan returns an iterator so to verify that it is correct // each team stores the distance of the returned iterator from the beginning // of the interval that team operates on and then we check that these @@ -156,12 +155,21 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { rand_pool pool(lowerBound * upperBound); Kokkos::fill_random(initValuesView_h, pool, lowerBound, upperBound); - // use CTAD for functor auto initValuesView = Kokkos::create_mirror_view_and_copy(space_t(), initValuesView_h); - TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, - initValuesView, binaryOp, unaryOp, apiId); - Kokkos::parallel_for(policy, fnc); + + // create the destination view + Kokkos::View destView("destView", numTeams, numCols); + if constexpr (std::is_same_v) { + TestFunctorA fnc(sourceView, sourceView, distancesView, + intraTeamSentinelView, initValuesView, binaryOp, unaryOp, + apiId); + Kokkos::parallel_for(policy, fnc); + } else { + TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, + initValuesView, binaryOp, unaryOp, apiId); + Kokkos::parallel_for(policy, fnc); + } // ----------------------------------------------- // run cpp-std kernel and check @@ -200,16 +208,21 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { #undef transform_exclusive_scan } - auto dataViewAfterOp_h = create_host_space_copy(destView); - expect_equal_host_views(stdDestView, dataViewAfterOp_h); + if constexpr (std::is_same_v) { + auto dataViewAfterOp_h = create_host_space_copy(sourceView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } else { + auto dataViewAfterOp_h = create_host_space_copy(destView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } } -template +template void run_all_scenarios() { for (int numTeams : teamSizesToTest) { for (const auto& numCols : {0, 1, 2, 13, 101, 1444, 8153}) { for (int apiId : {0, 1}) { - test_A(numTeams, numCols, apiId); + test_A(numTeams, numCols, apiId); } } } @@ -219,6 +232,10 @@ TEST(std_algorithms_transform_exclusive_scan_team_test, test) { run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); + + run_all_scenarios(); + run_all_scenarios(); + run_all_scenarios(); } } // namespace TeamTransformExclusiveScan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp index 4b31660232..10454d6551 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp @@ -131,7 +131,9 @@ struct TestFunctorA { } }; -template +struct InPlace {}; + +template void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { /* description: use a rank-2 view randomly filled with values, @@ -157,9 +159,6 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { using space_t = Kokkos::DefaultExecutionSpace; Kokkos::TeamPolicy policy(numTeams, Kokkos::AUTO()); - // create the destination view - Kokkos::View destView("destView", numTeams, numCols); - // tranform_inclusive_scan returns an iterator so to verify that it is correct // each team stores the distance of the returned iterator from the beginning // of the interval that team operates on and then we check that these @@ -179,12 +178,21 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { rand_pool pool(lowerBound * upperBound); Kokkos::fill_random(initValuesView_h, pool, lowerBound, upperBound); - // use CTAD for functor auto initValuesView = Kokkos::create_mirror_view_and_copy(space_t(), initValuesView_h); - TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, - initValuesView, binaryOp, unaryOp, apiId); - Kokkos::parallel_for(policy, fnc); + + // create the destination view + Kokkos::View destView("destView", numTeams, numCols); + if constexpr (std::is_same_v) { + TestFunctorA fnc(sourceView, sourceView, distancesView, + intraTeamSentinelView, initValuesView, binaryOp, unaryOp, + apiId); + Kokkos::parallel_for(policy, fnc); + } else { + TestFunctorA fnc(sourceView, destView, distancesView, intraTeamSentinelView, + initValuesView, binaryOp, unaryOp, apiId); + Kokkos::parallel_for(policy, fnc); + } // ----------------------------------------------- // run cpp-std kernel and check @@ -236,16 +244,21 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { } #undef transform_inclusive_scan - auto dataViewAfterOp_h = create_host_space_copy(destView); - expect_equal_host_views(stdDestView, dataViewAfterOp_h); + if constexpr (std::is_same_v) { + auto dataViewAfterOp_h = create_host_space_copy(sourceView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } else { + auto dataViewAfterOp_h = create_host_space_copy(destView); + expect_equal_host_views(stdDestView, dataViewAfterOp_h); + } } -template +template void run_all_scenarios() { for (int numTeams : teamSizesToTest) { for (const auto& numCols : {0, 1, 2, 13, 101, 1444, 8153}) { for (int apiId : {0, 1, 2, 3}) { - test_A(numTeams, numCols, apiId); + test_A(numTeams, numCols, apiId); } } } @@ -255,6 +268,10 @@ TEST(std_algorithms_transform_inclusive_scan_team_test, test) { run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); + + run_all_scenarios(); + run_all_scenarios(); + run_all_scenarios(); } } // namespace TeamTransformInclusiveScan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamUniqueCopy.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamUniqueCopy.cpp index 87687b60a1..0d3289e196 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamUniqueCopy.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamUniqueCopy.cpp @@ -186,6 +186,10 @@ void run_all_scenarios() { } TEST(std_algorithms_unique_copy_team_test, test) { + // FIXME_OPENMPTARGET +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + GTEST_SKIP() << "the test is known to fail with OpenMPTarget on Intel GPUs"; +#endif run_all_scenarios(); run_all_scenarios(); run_all_scenarios(); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp index 9dac3ce75f..fa2804256a 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp @@ -16,6 +16,7 @@ #include #include +#include namespace Test { namespace stdalgos { @@ -160,24 +161,15 @@ void verify_data(ViewType1 data_view, // contains data create_mirror_view_and_copy(Kokkos::HostSpace(), test_view_dc); if (test_view_h.extent(0) > 0) { for (std::size_t i = 0; i < test_view_h.extent(0); ++i) { - // std::cout << i << " " << std::setprecision(15) << data_view_h(i) << " " - // << gold_h(i) << " " << test_view_h(i) << " " - // << std::abs(gold_h(i) - test_view_h(i)) << std::endl; - if (std::is_same::value) { ASSERT_EQ(gold_h(i), test_view_h(i)); } else { const auto error = std::abs(gold_h(i) - test_view_h(i)); - if (error > 1e-10) { - std::cout << i << " " << std::setprecision(15) << data_view_h(i) - << " " << gold_h(i) << " " << test_view_h(i) << " " - << std::abs(gold_h(i) - test_view_h(i)) << std::endl; - } - EXPECT_LT(error, 1e-10); + ASSERT_LT(error, 1e-10) << i << " " << std::setprecision(15) << error + << static_cast(test_view_h(i)) << " " + << static_cast(gold_h(i)); } } - // std::cout << " last el: " << test_view_h(test_view_h.extent(0)-1) << - // std::endl; } } @@ -205,17 +197,13 @@ void run_single_scenario(const InfoType& scenario_info, ValueType init_value, BinaryOp bop, UnaryOp uop) { const auto name = std::get<0>(scenario_info); const std::size_t view_ext = std::get<1>(scenario_info); - // std::cout << "transform_exclusive_scan custom op: " << name << ", " - // << view_tag_to_string(Tag{}) << ", " - // << value_type_to_string(ValueType()) << ", " - // << "init = " << init_value << std::endl; - auto view_dest = - create_view(Tag{}, view_ext, "transform_exclusive_scan"); - auto view_from = - create_view(Tag{}, view_ext, "transform_exclusive_scan"); + auto view_from = create_view(Tag{}, view_ext, + "transform_exclusive_scan_view_from"); fill_view(view_from, name); + auto view_dest = create_view(Tag{}, view_ext, + "transform_exclusive_scan_view_dest"); { fill_zero(view_dest); auto r = KE::transform_exclusive_scan( @@ -253,6 +241,65 @@ void run_single_scenario(const InfoType& scenario_info, ValueType init_value, Kokkos::fence(); } +template +void run_single_scenario_inplace(const InfoType& scenario_info, + ValueType init_value, BinaryOp bop, + UnaryOp uop) { + const auto name = std::get<0>(scenario_info); + const std::size_t view_ext = std::get<1>(scenario_info); + + // since here we call the in-place operation, we need to use two views: + // view1: filled according to what the scenario asks for and is not modified + // view2: filled according to what the scenario asks for and used for the + // in-place op Therefore, after the op is done, view2 should contain the + // result of doing exclusive scan NOTE: view2 is filled below every time + // because the algorithm acts in place + + auto view1 = + create_view(Tag{}, view_ext, "transform_exclusive_scan_view1"); + fill_view(view1, name); + + auto view2 = + create_view(Tag{}, view_ext, "transform_exclusive_scan_view2"); + + { + fill_view(view2, name); + auto r = KE::transform_exclusive_scan(exespace(), KE::cbegin(view2), + KE::cend(view2), KE::begin(view2), + init_value, bop, uop); + ASSERT_EQ(r, KE::end(view2)); + verify_data(view1, view2, init_value, bop, uop); + } + + { + fill_view(view2, name); + auto r = KE::transform_exclusive_scan( + "label", exespace(), KE::cbegin(view2), KE::cend(view2), + KE::begin(view2), init_value, bop, uop); + ASSERT_EQ(r, KE::end(view2)); + verify_data(view1, view2, init_value, bop, uop); + } + + { + fill_view(view2, name); + auto r = KE::transform_exclusive_scan(exespace(), view2, view2, init_value, + bop, uop); + ASSERT_EQ(r, KE::end(view2)); + verify_data(view1, view2, init_value, bop, uop); + } + + { + fill_view(view2, name); + auto r = KE::transform_exclusive_scan("label", exespace(), view2, view2, + init_value, bop, uop); + ASSERT_EQ(r, KE::end(view2)); + verify_data(view1, view2, init_value, bop, uop); + } + + Kokkos::fence(); +} + template void run_all_scenarios() { const std::map scenarios = { @@ -267,6 +314,11 @@ void run_all_scenarios() { run_single_scenario(it, ValueType{1}, bop_t(), uop_t()); run_single_scenario(it, ValueType{-2}, bop_t(), uop_t()); run_single_scenario(it, ValueType{3}, bop_t(), uop_t()); + + run_single_scenario_inplace(it, ValueType{0}, bop_t(), + uop_t()); + run_single_scenario_inplace(it, ValueType{-2}, bop_t(), + uop_t()); } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp index a90a68ca1d..fb81ae91b0 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp @@ -16,6 +16,7 @@ #include #include +#include namespace Test { namespace stdalgos { @@ -172,24 +173,15 @@ void verify_data(ViewType1 data_view, // contains data create_mirror_view_and_copy(Kokkos::HostSpace(), test_view_dc); if (test_view_h.extent(0) > 0) { for (std::size_t i = 0; i < test_view_h.extent(0); ++i) { - // std::cout << i << " " << std::setprecision(15) << data_view_h(i) << " " - // << gold_h(i) << " " << test_view_h(i) << " " - // << std::abs(gold_h(i) - test_view_h(i)) << std::endl; - if (std::is_same::value) { ASSERT_EQ(gold_h(i), test_view_h(i)); } else { const auto error = std::abs(gold_h(i) - test_view_h(i)); - if (error > 1e-10) { - std::cout << i << " " << std::setprecision(15) << data_view_h(i) - << " " << gold_h(i) << " " << test_view_h(i) << " " - << std::abs(gold_h(i) - test_view_h(i)) << std::endl; - } - EXPECT_LT(error, 1e-10); + ASSERT_LT(error, 1e-10) << i << " " << std::setprecision(15) << error + << static_cast(test_view_h(i)) << " " + << static_cast(gold_h(i)); } } - // std::cout << " last el: " << test_view_h(test_view_h.extent(0)-1) << - // std::endl; } } @@ -210,30 +202,11 @@ struct SumBinaryFunctor { std::string value_type_to_string(int) { return "int"; } std::string value_type_to_string(double) { return "double"; } -template -void print_scenario_details(const std::string& name, BopT bop, UopT uop) { - (void)bop; - (void)uop; - std::cout << "transform_inclusive_scan: " << name << ", " - << view_tag_to_string(Tag{}) << std::endl; -} - -template -void print_scenario_details(const std::string& name, BopT bop, UopT uop, - ValueType init_value) { - (void)bop; - (void)uop; - std::cout << "transform_inclusive_scan: " << name << ", " - << view_tag_to_string(Tag{}) << ", " - << "init = " << init_value << std::endl; -} - template void run_single_scenario(const InfoType& scenario_info, Args... args /* by value on purpose*/) { const auto name = std::get<0>(scenario_info); const std::size_t view_ext = std::get<1>(scenario_info); - // print_scenario_details(name, args...); auto view_dest = create_view(Tag{}, view_ext, "transform_inclusive_scan"); @@ -278,6 +251,63 @@ void run_single_scenario(const InfoType& scenario_info, Kokkos::fence(); } +template +void run_single_scenario_inplace(const InfoType& scenario_info, + Args... args /* by value on purpose*/) { + const auto name = std::get<0>(scenario_info); + const std::size_t view_ext = std::get<1>(scenario_info); + + // since here we call the in-place operation, we need to use two views: + // view1: filled according to scenario and is not modified + // view2: filled according scenario and used for the in-place op + // Therefore, after the op is done, view_2 should contain the + // result of doing exclusive scan. + // NOTE: view2 must be filled before every call to the algorithm + // because the algorithm acts in place + + auto view_1 = create_view(Tag{}, view_ext, + "transform_inclusive_scan_view_1"); + fill_view(view_1, name); + + auto view_2 = create_view(Tag{}, view_ext, + "transform_inclusive_scan_view_2"); + + { + fill_view(view_2, name); + auto r = KE::transform_inclusive_scan(exespace(), KE::cbegin(view_2), + KE::cend(view_2), KE::begin(view_2), + args...); + ASSERT_EQ(r, KE::end(view_2)); + verify_data(view_1, view_2, args...); + } + + { + fill_view(view_2, name); + auto r = KE::transform_inclusive_scan("label", exespace(), + KE::cbegin(view_2), KE::cend(view_2), + KE::begin(view_2), args...); + ASSERT_EQ(r, KE::end(view_2)); + verify_data(view_1, view_2, args...); + } + + { + fill_view(view_2, name); + auto r = KE::transform_inclusive_scan(exespace(), view_2, view_2, args...); + ASSERT_EQ(r, KE::end(view_2)); + verify_data(view_1, view_2, args...); + } + + { + fill_view(view_2, name); + auto r = KE::transform_inclusive_scan("label", exespace(), view_2, view_2, + args...); + ASSERT_EQ(r, KE::end(view_2)); + verify_data(view_1, view_2, args...); + } + + Kokkos::fence(); +} + template void run_all_scenarios() { const std::map scenarios = { @@ -294,15 +324,23 @@ void run_all_scenarios() { run_single_scenario(it, bop_t(), uop_t(), ValueType{2}); run_single_scenario(it, bop_t(), uop_t(), ValueType{-1}); run_single_scenario(it, bop_t(), uop_t(), ValueType{-2}); + + run_single_scenario_inplace(it, bop_t(), uop_t()); + run_single_scenario_inplace(it, bop_t(), uop_t(), + ValueType{0}); + run_single_scenario_inplace(it, bop_t(), uop_t(), + ValueType{2}); + run_single_scenario_inplace(it, bop_t(), uop_t(), + ValueType{-2}); } } #if !defined KOKKOS_ENABLE_OPENMPTARGET TEST(std_algorithms_numeric_ops_test, transform_inclusive_scan) { run_all_scenarios(); - // run_all_scenarios(); - // run_all_scenarios(); - // run_all_scenarios(); + run_all_scenarios(); + run_all_scenarios(); + run_all_scenarios(); } #endif diff --git a/lib/kokkos/algorithms/unit_tests/TestStdReducers.cpp b/lib/kokkos/algorithms/unit_tests/TestStdReducers.cpp index 3847e1e6a3..c05006a161 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdReducers.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdReducers.cpp @@ -83,9 +83,6 @@ auto run_min_or_max_test(ViewType view, StdReducersTestEnumOrder enValue) { static_assert(std::is_same::value, "test is only enabled for HostSpace"); - std::cout << "checking reduction with order: " << order_to_string(enValue) - << "\n"; - using view_value_type = typename ViewType::value_type; using reducer_type = std::conditional_t< (flag == 0), Kokkos::MaxFirstLoc, @@ -132,18 +129,24 @@ TEST(std_algorithms_reducers, max_first_loc) { const auto pair1 = run_min_or_max_test<0, hostspace, index_type>( view_h, StdReducersTestEnumOrder::LeftToRight); - ASSERT_EQ(pair1.first, gold_value); - ASSERT_EQ(pair1.second, gold_location); + ASSERT_EQ(pair1.first, gold_value) + << order_to_string(StdReducersTestEnumOrder::LeftToRight); + ASSERT_EQ(pair1.second, gold_location) + << order_to_string(StdReducersTestEnumOrder::LeftToRight); const auto pair2 = run_min_or_max_test<0, hostspace, index_type>( view_h, StdReducersTestEnumOrder::RightToLeft); - ASSERT_EQ(pair2.first, gold_value); - ASSERT_EQ(pair2.second, gold_location); + ASSERT_EQ(pair2.first, gold_value) + << order_to_string(StdReducersTestEnumOrder::RightToLeft); + ASSERT_EQ(pair2.second, gold_location) + << order_to_string(StdReducersTestEnumOrder::RightToLeft); const auto pair3 = run_min_or_max_test<0, hostspace, index_type>( view_h, StdReducersTestEnumOrder::Random); - ASSERT_EQ(pair3.first, gold_value); - ASSERT_EQ(pair3.second, gold_location); + ASSERT_EQ(pair3.first, gold_value) + << order_to_string(StdReducersTestEnumOrder::Random); + ASSERT_EQ(pair3.second, gold_location) + << order_to_string(StdReducersTestEnumOrder::Random); } TEST(std_algorithms_reducers, min_first_loc) { @@ -191,9 +194,6 @@ void run_min_max_test(ViewType view, StdReducersTestEnumOrder enValue, static_assert(std::is_same::value, "test is only enabled for HostSpace"); - std::cout << "checking reduction with order: " << order_to_string(enValue) - << "\n"; - using view_value_type = typename ViewType::value_type; using reducer_type = Kokkos::MinMaxFirstLastLoc; @@ -212,10 +212,10 @@ void run_min_max_test(ViewType view, StdReducersTestEnumOrder enValue, reduction_value_type{view(index), view(index), index, index}); } - ASSERT_EQ(red_result.min_val, gold_values.first); - ASSERT_EQ(red_result.max_val, gold_values.second); - ASSERT_EQ(red_result.min_loc, gold_locs.first); - ASSERT_EQ(red_result.max_loc, gold_locs.second); + ASSERT_EQ(red_result.min_val, gold_values.first) << order_to_string(enValue); + ASSERT_EQ(red_result.max_val, gold_values.second) << order_to_string(enValue); + ASSERT_EQ(red_result.min_loc, gold_locs.first) << order_to_string(enValue); + ASSERT_EQ(red_result.max_loc, gold_locs.second) << order_to_string(enValue); } TEST(std_algorithms_reducers, min_max_first_last_loc) { diff --git a/lib/kokkos/benchmarks/CMakeLists.txt b/lib/kokkos/benchmarks/CMakeLists.txt index 42279bf55d..abf5028359 100644 --- a/lib/kokkos/benchmarks/CMakeLists.txt +++ b/lib/kokkos/benchmarks/CMakeLists.txt @@ -1 +1,12 @@ +#FIXME_OPENMPTARGET - compiling in debug mode causes ICE. +KOKKOS_ADD_BENCHMARK_DIRECTORIES(atomic) +KOKKOS_ADD_BENCHMARK_DIRECTORIES(gather) KOKKOS_ADD_BENCHMARK_DIRECTORIES(gups) +KOKKOS_ADD_BENCHMARK_DIRECTORIES(launch_latency) +KOKKOS_ADD_BENCHMARK_DIRECTORIES(stream) + +#FIXME_OPENMPTARGET - These two benchmarks cause ICE. Commenting them for now but a deeper analysis on the cause and a possible fix will follow. +IF(NOT Kokkos_ENABLE_OPENMPTARGET) + KOKKOS_ADD_BENCHMARK_DIRECTORIES(policy_performance) + KOKKOS_ADD_BENCHMARK_DIRECTORIES(bytes_and_flops) +ENDIF() diff --git a/lib/kokkos/benchmarks/atomic/CMakeLists.txt b/lib/kokkos/benchmarks/atomic/CMakeLists.txt new file mode 100644 index 0000000000..85f7412f49 --- /dev/null +++ b/lib/kokkos/benchmarks/atomic/CMakeLists.txt @@ -0,0 +1,4 @@ +KOKKOS_ADD_EXECUTABLE( + atomic + SOURCES main.cpp +) diff --git a/lib/kokkos/benchmarks/bytes_and_flops/CMakeLists.txt b/lib/kokkos/benchmarks/bytes_and_flops/CMakeLists.txt new file mode 100644 index 0000000000..0ce44a6f1a --- /dev/null +++ b/lib/kokkos/benchmarks/bytes_and_flops/CMakeLists.txt @@ -0,0 +1,4 @@ +KOKKOS_ADD_EXECUTABLE( + bytes_and_flops + SOURCES bench_double.cpp bench_float.cpp bench_int32_t.cpp bench_int64_t.cpp main.cpp +) diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp b/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp index 2589fd7309..88830af624 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp @@ -37,22 +37,22 @@ struct RunStride { }; #define STRIDE 1 -#include +#include "bench_stride.hpp" #undef STRIDE #define STRIDE 2 -#include +#include "bench_stride.hpp" #undef STRIDE #define STRIDE 4 -#include +#include "bench_stride.hpp" #undef STRIDE #define STRIDE 8 -#include +#include "bench_stride.hpp" #undef STRIDE #define STRIDE 16 -#include +#include "bench_stride.hpp" #undef STRIDE #define STRIDE 32 -#include +#include "bench_stride.hpp" #undef STRIDE template diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_double.cpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_double.cpp index f955c99666..2fda1ae3d4 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_double.cpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_double.cpp @@ -14,7 +14,7 @@ // //@HEADER -#include +#include "bench.hpp" template void run_stride_unroll(int N, int K, int R, int D, int U, int F, int T, int S, int B, int I); diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_float.cpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_float.cpp index 137ff67d40..3210116a9e 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_float.cpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_float.cpp @@ -14,7 +14,7 @@ // //@HEADER -#include +#include "bench.hpp" template void run_stride_unroll(int N, int K, int R, int D, int U, int F, int T, int S, int B, int I); diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_int32_t.cpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_int32_t.cpp index 29ccec0141..24a5dcd389 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_int32_t.cpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_int32_t.cpp @@ -14,7 +14,7 @@ // //@HEADER -#include +#include "bench.hpp" template void run_stride_unroll(int N, int K, int R, int D, int U, int F, int T, int S, int B, int I); diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_int64_t.cpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_int64_t.cpp index c153d5eff3..0634700c31 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_int64_t.cpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_int64_t.cpp @@ -14,7 +14,7 @@ // //@HEADER -#include +#include "bench.hpp" template void run_stride_unroll(int N, int K, int R, int D, int U, int F, int T, int S, int B, int I); diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp index b63d486fc9..80f017fbe8 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp @@ -15,28 +15,28 @@ //@HEADER #define UNROLL 1 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL #define UNROLL 2 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL #define UNROLL 3 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL #define UNROLL 4 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL #define UNROLL 5 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL #define UNROLL 6 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL #define UNROLL 7 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL #define UNROLL 8 -#include +#include "bench_unroll_stride.hpp" #undef UNROLL template diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp index 0f7a298c1b..78cfd48eff 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp @@ -26,7 +26,7 @@ struct Run { Kokkos::deep_copy(C, Scalar(3.5)); Kokkos::Timer timer; - for (int i = 0; i < I; ++i) { + for (int iter = 0; iter < I; ++iter) { Kokkos::parallel_for( "BenchmarkKernel", Kokkos::TeamPolicy<>(N, T).set_scratch_size(0, Kokkos::PerTeam(S)), diff --git a/lib/kokkos/benchmarks/bytes_and_flops/main.cpp b/lib/kokkos/benchmarks/bytes_and_flops/main.cpp index 20077757d1..fdfcc4ea64 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/main.cpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/main.cpp @@ -16,7 +16,7 @@ #include #include -#include +#include "bench.hpp" #include extern template void run_stride_unroll(int, int, int, int, int, int, int, @@ -86,7 +86,7 @@ int main(int argc, char* argv[]) { printf("D must be one of 1,2,4,8,16,32\n"); return 0; } - if ((P < 1) && (P > 2)) { + if ((P < 1) || (P > 4)) { printf("P must be one of 1,2,3,4\n"); return 0; } diff --git a/lib/kokkos/benchmarks/gather/CMakeLists.txt b/lib/kokkos/benchmarks/gather/CMakeLists.txt new file mode 100644 index 0000000000..24c7062772 --- /dev/null +++ b/lib/kokkos/benchmarks/gather/CMakeLists.txt @@ -0,0 +1,4 @@ +KOKKOS_ADD_EXECUTABLE( + gather + SOURCES main.cpp +) diff --git a/lib/kokkos/benchmarks/gather/gather.hpp b/lib/kokkos/benchmarks/gather/gather.hpp index d83461702c..90b1101c1d 100644 --- a/lib/kokkos/benchmarks/gather/gather.hpp +++ b/lib/kokkos/benchmarks/gather/gather.hpp @@ -20,28 +20,28 @@ struct RunGather { }; #define UNROLL 1 -#include +#include "gather_unroll.hpp" #undef UNROLL #define UNROLL 2 -#include +#include "gather_unroll.hpp" #undef UNROLL #define UNROLL 3 -#include +#include "gather_unroll.hpp" #undef UNROLL #define UNROLL 4 -#include +#include "gather_unroll.hpp" #undef UNROLL #define UNROLL 5 -#include +#include "gather_unroll.hpp" #undef UNROLL #define UNROLL 6 -#include +#include "gather_unroll.hpp" #undef UNROLL #define UNROLL 7 -#include +#include "gather_unroll.hpp" #undef UNROLL #define UNROLL 8 -#include +#include "gather_unroll.hpp" #undef UNROLL template diff --git a/lib/kokkos/benchmarks/gather/gather_unroll.hpp b/lib/kokkos/benchmarks/gather/gather_unroll.hpp index 5ee5742a3f..1aa73091bc 100644 --- a/lib/kokkos/benchmarks/gather/gather_unroll.hpp +++ b/lib/kokkos/benchmarks/gather/gather_unroll.hpp @@ -138,7 +138,7 @@ struct RunGather { printf( "SNKDRUF: %i %i %i %i %i %i %i Time: %lfs Bandwidth: %lfGiB/s GFlop/s: " "%lf GGather/s: %lf\n", - sizeof(Scalar) / 4, N, K, D, R, UNROLL, F, seconds, + static_cast(sizeof(Scalar) / 4), N, K, D, R, UNROLL, F, seconds, 1.0 * bytes / seconds / 1024 / 1024 / 1024, 1.e-9 * flops / seconds, 1.e-9 * gather_ops / seconds); } diff --git a/lib/kokkos/benchmarks/gather/main.cpp b/lib/kokkos/benchmarks/gather/main.cpp index 7f4fc9ede6..07fca9fdc6 100644 --- a/lib/kokkos/benchmarks/gather/main.cpp +++ b/lib/kokkos/benchmarks/gather/main.cpp @@ -16,7 +16,7 @@ #include #include -#include +#include "gather.hpp" #include int main(int argc, char* argv[]) { diff --git a/lib/kokkos/benchmarks/launch_latency/CMakeLists.txt b/lib/kokkos/benchmarks/launch_latency/CMakeLists.txt new file mode 100644 index 0000000000..bb14da749d --- /dev/null +++ b/lib/kokkos/benchmarks/launch_latency/CMakeLists.txt @@ -0,0 +1,4 @@ +KOKKOS_ADD_EXECUTABLE( + launch_latency + SOURCES launch_latency.cpp +) diff --git a/lib/kokkos/benchmarks/launch_latency/launch_latency.cpp b/lib/kokkos/benchmarks/launch_latency/launch_latency.cpp new file mode 100644 index 0000000000..73b176ab8d --- /dev/null +++ b/lib/kokkos/benchmarks/launch_latency/launch_latency.cpp @@ -0,0 +1,283 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +/*! \file launch_latency.cpp + + Tests of parallel_for and parallel_reduce latency for different + circumstances. + + Three launch kinds are tested: parallel_for, parallel_reduce into scalar, + and parallel_reduce into view + + N controls how large the parallel loops is + V controls how large the functor is + M controls across how many launches the latency is averaged + K controls how larege the nested loop is (no larger than V) + + For each launch kind, + 1. Avg functor dispatch latency: (time to do M launches) / M + 2. Avg functor completion throughput: (M launches + sync) / M + 3. Avg functor completion latency: (M (launch + sync)) / M +*/ + +#include + +template +struct TestFunctor { + double values[V]; + Kokkos::View a; + int K; + TestFunctor(Kokkos::View a_, int K_) : a(a_), K(K_) {} + + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + for (int j = 0; j < K; j++) a(i) += 1.0 * i * values[j]; + } +}; + +template +struct TestRFunctor { + double values[V]; + Kokkos::View a; + int K; + TestRFunctor(Kokkos::View a_, int K_) : a(a_), K(K_) {} + + KOKKOS_INLINE_FUNCTION + void operator()(const int i, double& lsum) const { + for (int j = 0; j < K; j++) a(i) += 1.0 * i * values[j]; + lsum += a(i); + } +}; + +struct Opts { + bool par_for = true; + bool par_reduce = true; + bool par_reduce_view = true; +}; + +template +void run(int N, int M, int K, const Opts& opts) { + std::string l_no_fence, l_fence, l_red_no_fence, l_red_fence, + l_red_view_no_fence, l_red_view_fence; + { + std::ostringstream ostream; + ostream << "RunNoFence_" << N << "_" << K << std::endl; + l_no_fence = ostream.str(); + } + { + std::ostringstream ostream; + ostream << "RunFence_" << N << "_" << K << std::endl; + l_fence = ostream.str(); + } + { + std::ostringstream ostream; + ostream << "RunReduceNoFence_" << N << "_" << K << std::endl; + l_red_no_fence = ostream.str(); + } + { + std::ostringstream ostream; + ostream << "RunReduceFence_" << N << "_" << K << std::endl; + l_red_fence = ostream.str(); + } + { + std::ostringstream ostream; + ostream << "RunReduceViewNoFence_" << N << "_" << K << std::endl; + l_red_view_no_fence = ostream.str(); + } + { + std::ostringstream ostream; + ostream << "RunReduceViewFence_" << N << "_" << K << std::endl; + l_red_view_fence = ostream.str(); + } + + double result; + Kokkos::View a("A", N); + Kokkos::View v_result("result"); + TestFunctor f(a, K); + TestRFunctor rf(a, K); + Kokkos::Timer timer; + + // initialize to an obviously wrong value + double time_no_fence = -1; // launch loop + double time_no_fence_fenced = -1; // launch loop then fence + double time_fence = -1; // launch&fence loop + + double time_red_no_fence = -1; + double time_red_no_fence_fenced = -1; + double time_red_fence = -1; + + double time_red_view_no_fence = -1; + double time_red_view_no_fence_fenced = -1; + double time_red_view_fence = -1; + + if (opts.par_for) { + // warmup + for (int i = 0; i < 4; ++i) { + Kokkos::parallel_for(l_no_fence, N, f); + } + Kokkos::fence(); + + timer.reset(); + for (int i = 0; i < M; i++) { + Kokkos::parallel_for(l_no_fence, N, f); + } + time_no_fence = timer.seconds(); + Kokkos::fence(); + time_no_fence_fenced = timer.seconds(); + + timer.reset(); + for (int i = 0; i < M; i++) { + Kokkos::parallel_for(l_fence, N, f); + Kokkos::fence(); + } + time_fence = timer.seconds(); + } + + if (opts.par_reduce) { + // warmup + for (int i = 0; i < 4; ++i) { + Kokkos::parallel_reduce(l_red_no_fence, N, rf, result); + } + Kokkos::fence(); + + timer.reset(); + for (int i = 0; i < M; i++) { + Kokkos::parallel_reduce(l_red_no_fence, N, rf, result); + } + time_red_no_fence = timer.seconds(); + Kokkos::fence(); + time_red_no_fence_fenced = timer.seconds(); + + timer.reset(); + for (int i = 0; i < M; i++) { + Kokkos::parallel_reduce(l_red_fence, N, rf, result); + Kokkos::fence(); + } + time_red_fence = timer.seconds(); + Kokkos::fence(); + } + + if (opts.par_reduce_view) { + // warmup + for (int i = 0; i < 4; ++i) { + Kokkos::parallel_reduce(l_red_view_no_fence, N, rf, v_result); + } + Kokkos::fence(); + + timer.reset(); + for (int i = 0; i < M; i++) { + Kokkos::parallel_reduce(l_red_view_no_fence, N, rf, v_result); + } + time_red_view_no_fence = timer.seconds(); + Kokkos::fence(); + time_red_view_no_fence_fenced = timer.seconds(); + + timer.reset(); + for (int i = 0; i < M; i++) { + Kokkos::parallel_reduce(l_red_view_fence, N, rf, v_result); + Kokkos::fence(); + } + time_red_view_fence = timer.seconds(); + Kokkos::fence(); + timer.reset(); + } + + const double x = 1.e6 / M; + printf("%i %i %i %i", N, V, K, M); + if (opts.par_for) { + printf(" parallel_for: %lf %lf ( %lf )", x * time_no_fence, x * time_fence, + x * time_no_fence_fenced); + } + if (opts.par_reduce) { + printf(" parallel_reduce: %lf %lf ( %lf )", x * time_red_no_fence, + x * time_red_fence, x * time_red_no_fence_fenced); + } + if (opts.par_reduce_view) { + printf(" parallel_reduce(view): %lf %lf ( %lf )", + x * time_red_view_no_fence, x * time_red_view_fence, + x * time_red_view_no_fence_fenced); + } + printf("\n"); +} +int main(int argc, char* argv[]) { + Kokkos::initialize(argc, argv); + { + int N = 10000; + int M = 20; + int K = 1; + + Opts opts; + + printf("==========================\n"); + printf("Kokkos Launch Latency Test\n"); + printf("==========================\n"); + printf("\n"); + printf("Usage: %s ARGUMENTS [OPTIONS...]\n\n", argv[0]); + printf("Arguments: N M K\n"); + printf(" N: loop length\n"); + printf(" M: how many kernels to dispatch\n"); + printf( + " K: nested loop length (capped by size of functor member array\n\n"); + printf("Options:\n"); + printf(" --no-parallel-for: skip parallel_for benchmark\n"); + printf(" --no-parallel-reduce: skip parallel_reduce benchmark\n"); + printf( + " --no-parallel-reduce-view: skip parallel_reduce into view " + "benchmark\n"); + printf("\n\n"); + printf(" Output V is the size of the functor member array\n"); + printf("\n\n"); + + for (int i = 1; i < argc; ++i) { + const std::string_view arg(argv[i]); + + // anything that doesn't start with -- + if (arg.size() < 2 || + (arg.size() >= 2 && arg[0] != '-' && arg[1] != '-')) { + if (i == 1) + N = atoi(arg.data()); + else if (i == 2) + M = atoi(arg.data()); + else if (i == 3) + K = atoi(arg.data()); + else { + throw std::runtime_error("unexpected argument!"); + } + } else if (arg == "--no-parallel-for") { + opts.par_for = false; + } else if (arg == "--no-parallel-reduce") { + opts.par_reduce = false; + } else if (arg == "--no-parallel-reduce-view") { + opts.par_reduce_view = false; + } else { + std::stringstream ss; + ss << "unexpected argument \"" << arg << "\" at position " << i; + throw std::runtime_error(ss.str()); + } + } + + printf("N V K M time_no_fence time_fence (time_no_fence_fenced)\n"); + + /* A backend may have different launch strategies for functors of different + * sizes: test a variety of functor sizes.*/ + run<1>(N, M, K <= 1 ? K : 1, opts); + run<16>(N, M, K <= 16 ? K : 16, opts); + run<200>(N, M, K <= 200 ? K : 200, opts); + run<3000>(N, M, K <= 3000 ? K : 3000, opts); + run<30000>(N, M, K <= 30000 ? K : 30000, opts); + } + Kokkos::finalize(); +} diff --git a/lib/kokkos/benchmarks/policy_performance/CMakeLists.txt b/lib/kokkos/benchmarks/policy_performance/CMakeLists.txt new file mode 100644 index 0000000000..929b9c9702 --- /dev/null +++ b/lib/kokkos/benchmarks/policy_performance/CMakeLists.txt @@ -0,0 +1,4 @@ +KOKKOS_ADD_EXECUTABLE( + policy_performance + SOURCES main.cpp +) diff --git a/lib/kokkos/benchmarks/policy_performance/main.cpp b/lib/kokkos/benchmarks/policy_performance/main.cpp index 28cfde552a..0983a3d535 100644 --- a/lib/kokkos/benchmarks/policy_performance/main.cpp +++ b/lib/kokkos/benchmarks/policy_performance/main.cpp @@ -106,8 +106,9 @@ int main(int argc, char* argv[]) { Kokkos::parallel_reduce( "parallel_reduce warmup", Kokkos::TeamPolicy<>(10, 1), - KOKKOS_LAMBDA(const Kokkos::TeamPolicy<>::member_type team, - double& lval) { lval += 1; }, + KOKKOS_LAMBDA(const Kokkos::TeamPolicy<>::member_type&, double& lval) { + lval += 1; + }, result); using view_type_1d = Kokkos::View; diff --git a/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp b/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp index cc2cc40257..0e23d221f6 100644 --- a/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp +++ b/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp @@ -21,13 +21,13 @@ struct ParallelScanFunctor { using value_type = double; ViewType v; - ParallelScanFunctor(const ViewType& v_) : v(v_) {} + explicit ParallelScanFunctor(const ViewType& v_) : v(v_) {} KOKKOS_INLINE_FUNCTION - void operator()(const int idx, value_type& val, const bool& final) const { + void operator()(const int idx, value_type& val, const bool& is_final) const { // inclusive scan val += v(idx); - if (final) { + if (is_final) { v(idx) = val; } } @@ -109,7 +109,7 @@ void test_policy(int team_range, int thread_range, int vector_range, vector_result = 0.0; Kokkos::parallel_reduce( Kokkos::ThreadVectorRange(team, vector_range), - [&](const int vi, double& vval) { vval += 1; }, + [&](const int, double& vval) { vval += 1; }, vector_result); } v2(idx, t) = vector_result; @@ -128,7 +128,7 @@ void test_policy(int team_range, int thread_range, int vector_range, team_result = 0.0; Kokkos::parallel_reduce( Kokkos::TeamThreadRange(team, thread_range), - [&](const int t, double& lval) { lval += 1; }, team_result); + [&](const int, double& lval) { lval += 1; }, team_result); } v1(idx) = team_result; // prevent compiler optimizing loop away @@ -170,13 +170,13 @@ void test_policy(int team_range, int thread_range, int vector_range, for (int tr = 0; tr < thread_repeat; ++tr) { Kokkos::parallel_reduce( Kokkos::TeamThreadRange(team, thread_range), - [&](const int t, double& lval) { + [&](const int, double& lval) { double vector_result = 0.0; for (int vr = 0; vr < inner_repeat; ++vr) { vector_result = 0.0; Kokkos::parallel_reduce( Kokkos::ThreadVectorRange(team, vector_range), - [&](const int vi, double& vval) { vval += 1; }, + [&](const int, double& vval) { vval += 1; }, vector_result); lval += vector_result; } diff --git a/lib/kokkos/benchmarks/stream/CMakeLists.txt b/lib/kokkos/benchmarks/stream/CMakeLists.txt new file mode 100644 index 0000000000..0dded6e3a5 --- /dev/null +++ b/lib/kokkos/benchmarks/stream/CMakeLists.txt @@ -0,0 +1,4 @@ +KOKKOS_ADD_EXECUTABLE( + stream + SOURCES stream-kokkos.cpp +) diff --git a/lib/kokkos/bin/nvcc_wrapper b/lib/kokkos/bin/nvcc_wrapper index c140087240..dbfef2267f 100755 --- a/lib/kokkos/bin/nvcc_wrapper +++ b/lib/kokkos/bin/nvcc_wrapper @@ -229,7 +229,7 @@ do fi ;; #Handle known nvcc args - --dryrun|--verbose|--keep|--source-in-ptx|-src-in-ptx|--keep-dir*|-G|-lineinfo|-extended-lambda|-expt-extended-lambda|-expt-relaxed-constexpr|--resource-usage|--fmad=*|--use_fast_math|--Wext-lambda-captures-this|-Wext-lambda-captures-this) + --dryrun|-dryrun|--verbose|--keep|-keep|--source-in-ptx|-src-in-ptx|--keep-dir*|-keep-dir*|-G|-lineinfo|--generate-line-info|-extended-lambda|-expt-extended-lambda|-expt-relaxed-constexpr|--resource-usage|-res-usage|--fmad=*|-fmad=*|--use_fast_math|-use_fast_math|--Wext-lambda-captures-this|-Wext-lambda-captures-this) cuda_args="$cuda_args $1" ;; #Handle more known nvcc args diff --git a/lib/kokkos/cmake/KokkosConfig.cmake.in b/lib/kokkos/cmake/KokkosConfig.cmake.in index e26c75b312..1b6d1b66ff 100644 --- a/lib/kokkos/cmake/KokkosConfig.cmake.in +++ b/lib/kokkos/cmake/KokkosConfig.cmake.in @@ -39,10 +39,12 @@ IF("launch_compiler" IN_LIST Kokkos_FIND_COMPONENTS) GLOBAL CHECK_CUDA_COMPILES) -ELSEIF(@Kokkos_ENABLE_CUDA@ AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) +ELSEIF(@Kokkos_ENABLE_CUDA@ + AND NOT @KOKKOS_COMPILE_LANGUAGE@ STREQUAL CUDA + AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) # - # if CUDA was enabled, separable compilation was not specified, and current compiler - # cannot compile CUDA, then set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK globally and + # if CUDA was enabled, the compilation language was not set to CUDA, and separable compilation was not + # specified, then set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK globally and # kokkos_launch_compiler will re-direct to the compiler used to compile CUDA code during installation. # kokkos_launch_compiler will re-direct if ${CMAKE_CXX_COMPILER} and -DKOKKOS_DEPENDENCE is present, # otherwise, the original command will be executed diff --git a/lib/kokkos/cmake/KokkosCore_config.h.in b/lib/kokkos/cmake/KokkosCore_config.h.in index bec59ebd03..3ab39cd6ab 100644 --- a/lib/kokkos/cmake/KokkosCore_config.h.in +++ b/lib/kokkos/cmake/KokkosCore_config.h.in @@ -23,8 +23,6 @@ #cmakedefine KOKKOS_ENABLE_CUDA #cmakedefine KOKKOS_ENABLE_HIP #cmakedefine KOKKOS_ENABLE_HPX -#cmakedefine KOKKOS_ENABLE_MEMKIND -#cmakedefine KOKKOS_ENABLE_LIBRT #cmakedefine KOKKOS_ENABLE_SYCL #cmakedefine KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED @@ -32,6 +30,7 @@ #cmakedefine KOKKOS_ENABLE_CXX17 #cmakedefine KOKKOS_ENABLE_CXX20 #cmakedefine KOKKOS_ENABLE_CXX23 +#cmakedefine KOKKOS_ENABLE_CXX26 #cmakedefine KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE #cmakedefine KOKKOS_ENABLE_CUDA_UVM @@ -40,12 +39,12 @@ #cmakedefine KOKKOS_ENABLE_IMPL_CUDA_MALLOC_ASYNC #cmakedefine KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE #cmakedefine KOKKOS_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS +#cmakedefine KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY #cmakedefine KOKKOS_ENABLE_IMPL_HPX_ASYNC_DISPATCH #cmakedefine KOKKOS_ENABLE_DEBUG #cmakedefine KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK #cmakedefine KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK #cmakedefine KOKKOS_ENABLE_TUNING -#cmakedefine KOKKOS_ENABLE_DEPRECATED_CODE_3 #cmakedefine KOKKOS_ENABLE_DEPRECATED_CODE_4 #cmakedefine KOKKOS_ENABLE_DEPRECATION_WARNINGS #cmakedefine KOKKOS_ENABLE_LARGE_MEM_TESTS @@ -53,17 +52,15 @@ #cmakedefine KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION // deprecated #cmakedefine KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION #cmakedefine KOKKOS_ENABLE_IMPL_MDSPAN +#cmakedefine KOKKOS_ENABLE_ATOMICS_BYPASS /* TPL Settings */ #cmakedefine KOKKOS_ENABLE_HWLOC -#cmakedefine KOKKOS_USE_LIBRT -#cmakedefine KOKKOS_ENABLE_HBWSPACE #cmakedefine KOKKOS_ENABLE_LIBDL #cmakedefine KOKKOS_ENABLE_LIBQUADMATH -#cmakedefine KOKKOS_IMPL_CUDA_CLANG_WORKAROUND #cmakedefine KOKKOS_ENABLE_ONEDPL +#cmakedefine KOKKOS_ENABLE_ROCTHRUST -#cmakedefine KOKKOS_ARCH_SSE42 #cmakedefine KOKKOS_ARCH_ARMV80 #cmakedefine KOKKOS_ARCH_ARMV8_THUNDERX #cmakedefine KOKKOS_ARCH_ARMV81 @@ -78,6 +75,7 @@ #cmakedefine KOKKOS_ARCH_POWER7 #cmakedefine KOKKOS_ARCH_POWER8 #cmakedefine KOKKOS_ARCH_POWER9 +#cmakedefine KOKKOS_ARCH_RISCV_SG2042 #cmakedefine KOKKOS_ARCH_INTEL_GEN #cmakedefine KOKKOS_ARCH_INTEL_DG1 #cmakedefine KOKKOS_ARCH_INTEL_GEN9 @@ -114,6 +112,7 @@ #cmakedefine KOKKOS_ARCH_AMD_GFX906 #cmakedefine KOKKOS_ARCH_AMD_GFX908 #cmakedefine KOKKOS_ARCH_AMD_GFX90A +#cmakedefine KOKKOS_ARCH_AMD_GFX940 #cmakedefine KOKKOS_ARCH_AMD_GFX942 #cmakedefine KOKKOS_ARCH_AMD_GFX1030 #cmakedefine KOKKOS_ARCH_AMD_GFX1100 diff --git a/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake b/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake index 792c92c07e..5a62c530fc 100644 --- a/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake +++ b/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake @@ -7,7 +7,8 @@ IF (NOT CUDAToolkit_ROOT) ENDIF() ENDIF() -IF(CMAKE_VERSION VERSION_GREATER_EQUAL "3.17.0") +# FIXME CMake 3.28.4 creates more targets than we export +IF(CMAKE_VERSION VERSION_GREATER_EQUAL "3.17.0" AND CMAKE_VERSION VERSION_LESS "3.28.4") find_package(CUDAToolkit) ELSE() include(${CMAKE_CURRENT_LIST_DIR}/CudaToolkit.cmake) diff --git a/lib/kokkos/cmake/Modules/FindTPLLIBRT.cmake b/lib/kokkos/cmake/Modules/FindTPLLIBRT.cmake deleted file mode 100644 index e75da56b5b..0000000000 --- a/lib/kokkos/cmake/Modules/FindTPLLIBRT.cmake +++ /dev/null @@ -1 +0,0 @@ -KOKKOS_FIND_IMPORTED(LIBRT HEADER time.h LIBRARY rt) diff --git a/lib/kokkos/cmake/Modules/FindTPLMEMKIND.cmake b/lib/kokkos/cmake/Modules/FindTPLMEMKIND.cmake deleted file mode 100644 index 20aaff2295..0000000000 --- a/lib/kokkos/cmake/Modules/FindTPLMEMKIND.cmake +++ /dev/null @@ -1 +0,0 @@ -KOKKOS_FIND_IMPORTED(MEMKIND HEADER memkind.h LIBRARY memkind) diff --git a/lib/kokkos/cmake/Modules/FindTPLONEDPL.cmake b/lib/kokkos/cmake/Modules/FindTPLONEDPL.cmake index 01791cff44..603510c315 100644 --- a/lib/kokkos/cmake/Modules/FindTPLONEDPL.cmake +++ b/lib/kokkos/cmake/Modules/FindTPLONEDPL.cmake @@ -43,4 +43,7 @@ ELSE() COMPILE_DEFINITIONS PSTL_USE_PARALLEL_POLICIES=0 _GLIBCXX_USE_TBB_PAR_BACKEND=0 ) ENDIF() + + # Export oneDPL as a Kokkos dependency + KOKKOS_EXPORT_CMAKE_TPL(oneDPL) ENDIF() diff --git a/lib/kokkos/cmake/Modules/FindTPLROCTHRUST.cmake b/lib/kokkos/cmake/Modules/FindTPLROCTHRUST.cmake new file mode 100644 index 0000000000..dae7dc3c95 --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindTPLROCTHRUST.cmake @@ -0,0 +1,15 @@ +# ROCm 5.6 and earlier set AMDGPU_TARGETS and GPU_TARGETS to all the supported +# architectures. Therefore, we end up compiling Kokkos for all the supported +# architecture. Starting with ROCm 5.7 AMDGPU_TARGETS and GPU_TARGETS are empty. +# It is the user's job to set the variables. Since we are injecting the +# architecture flag ourselves, we can let the variables empty. To replicate the +# behavior of ROCm 5.7 and later for earlier version of ROCm we set +# AMDGPU_TARGETS and GPU_TARGETS to empty and set the values in the cache. If +# the values are not cached, FIND_PACKAGE(rocthrust) will overwrite them. +SET(AMDGPU_TARGETS "" CACHE STRING "AMD GPU targets to compile for") +SET(GPU_TARGETS "" CACHE STRING "GPU targets to compile for") +FIND_PACKAGE(rocthrust REQUIRED) +KOKKOS_CREATE_IMPORTED_TPL(ROCTHRUST INTERFACE LINK_LIBRARIES roc::rocthrust) + +# Export ROCTHRUST as a Kokkos dependency +KOKKOS_EXPORT_CMAKE_TPL(rocthrust) diff --git a/lib/kokkos/cmake/kokkos_arch.cmake b/lib/kokkos/cmake/kokkos_arch.cmake index bccf674d76..34e9f05986 100644 --- a/lib/kokkos/cmake/kokkos_arch.cmake +++ b/lib/kokkos/cmake/kokkos_arch.cmake @@ -49,7 +49,6 @@ DECLARE_AND_CHECK_HOST_ARCH(ARMV81 "ARMv8.1 Compatible CPU") DECLARE_AND_CHECK_HOST_ARCH(ARMV8_THUNDERX "ARMv8 Cavium ThunderX CPU") DECLARE_AND_CHECK_HOST_ARCH(ARMV8_THUNDERX2 "ARMv8 Cavium ThunderX2 CPU") DECLARE_AND_CHECK_HOST_ARCH(A64FX "ARMv8.2 with SVE Support") -DECLARE_AND_CHECK_HOST_ARCH(WSM "Intel Westmere CPU") DECLARE_AND_CHECK_HOST_ARCH(SNB "Intel Sandy/Ivy Bridge CPUs") DECLARE_AND_CHECK_HOST_ARCH(HSW "Intel Haswell CPUs") DECLARE_AND_CHECK_HOST_ARCH(BDW "Intel Broadwell Xeon E-class CPUs") @@ -60,13 +59,12 @@ DECLARE_AND_CHECK_HOST_ARCH(SKX "Intel Skylake Xeon Server CPUs (A DECLARE_AND_CHECK_HOST_ARCH(KNC "Intel Knights Corner Xeon Phi") DECLARE_AND_CHECK_HOST_ARCH(KNL "Intel Knights Landing Xeon Phi") DECLARE_AND_CHECK_HOST_ARCH(SPR "Intel Sapphire Rapids Xeon Server CPUs (AVX512)") -DECLARE_AND_CHECK_HOST_ARCH(BGQ "IBM Blue Gene Q") -DECLARE_AND_CHECK_HOST_ARCH(POWER7 "IBM POWER7 CPUs") DECLARE_AND_CHECK_HOST_ARCH(POWER8 "IBM POWER8 CPUs") DECLARE_AND_CHECK_HOST_ARCH(POWER9 "IBM POWER9 CPUs") DECLARE_AND_CHECK_HOST_ARCH(ZEN "AMD Zen architecture") DECLARE_AND_CHECK_HOST_ARCH(ZEN2 "AMD Zen2 architecture") DECLARE_AND_CHECK_HOST_ARCH(ZEN3 "AMD Zen3 architecture") +DECLARE_AND_CHECK_HOST_ARCH(RISCV_SG2042 "SG2042 (RISC-V) CPUs") IF(Kokkos_ENABLE_CUDA OR Kokkos_ENABLE_OPENMPTARGET OR Kokkos_ENABLE_OPENACC OR Kokkos_ENABLE_SYCL) SET(KOKKOS_SHOW_CUDA_ARCHS ON) @@ -94,9 +92,9 @@ IF(Kokkos_ENABLE_HIP OR Kokkos_ENABLE_OPENMPTARGET OR Kokkos_ENABLE_OPENACC OR K ENDIF() # AMD archs ordered in decreasing priority of autodetection -LIST(APPEND SUPPORTED_AMD_GPUS MI300) -LIST(APPEND SUPPORTED_AMD_ARCHS AMD_GFX942) -LIST(APPEND CORRESPONDING_AMD_FLAGS gfx942) +LIST(APPEND SUPPORTED_AMD_GPUS MI300 MI300) +LIST(APPEND SUPPORTED_AMD_ARCHS AMD_GFX942 AMD_GFX940) +LIST(APPEND CORRESPONDING_AMD_FLAGS gfx942 gfx940) LIST(APPEND SUPPORTED_AMD_GPUS MI200 MI200 MI100 MI100) LIST(APPEND SUPPORTED_AMD_ARCHS VEGA90A AMD_GFX90A VEGA908 AMD_GFX908) LIST(APPEND CORRESPONDING_AMD_FLAGS gfx90a gfx90a gfx908 gfx908) @@ -191,9 +189,6 @@ IF (KOKKOS_CXX_COMPILER_ID STREQUAL Clang) ELSEIF(CUDAToolkit_BIN_DIR) GLOBAL_APPEND(KOKKOS_CUDA_OPTIONS --cuda-path=${CUDAToolkit_BIN_DIR}/..) ENDIF() - IF (KOKKOS_ENABLE_CUDA) - SET(KOKKOS_IMPL_CUDA_CLANG_WORKAROUND ON CACHE BOOL "enable CUDA Clang workarounds" FORCE) - ENDIF() ELSEIF (KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC) SET(CUDA_ARCH_FLAG "-gpu") GLOBAL_APPEND(KOKKOS_CUDA_OPTIONS -cuda) @@ -342,18 +337,6 @@ IF (KOKKOS_ARCH_ZEN3) SET(KOKKOS_ARCH_AVX2 ON) ENDIF() -IF (KOKKOS_ARCH_WSM) - COMPILER_SPECIFIC_FLAGS( - COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID - Cray NO-VALUE-SPECIFIED - Intel -xSSE4.2 - MSVC NO-VALUE-SPECIFIED - NVHPC -tp=px - DEFAULT -msse4.2 - ) - SET(KOKKOS_ARCH_SSE42 ON) -ENDIF() - IF (KOKKOS_ARCH_SNB OR KOKKOS_ARCH_AMDAVX) SET(KOKKOS_ARCH_AVX ON) COMPILER_SPECIFIC_FLAGS( @@ -378,6 +361,23 @@ IF (KOKKOS_ARCH_HSW) ) ENDIF() +IF (KOKKOS_ARCH_RISCV_SG2042) + IF(NOT + (KOKKOS_CXX_COMPILER_ID STREQUAL GNU + AND KOKKOS_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12) + OR + (KOKKOS_CXX_COMPILER_ID STREQUAL Clang + AND KOKKOS_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 14) + ) + MESSAGE(SEND_ERROR "Only gcc >= 12 and clang >= 14 support RISC-V.") + ENDIF() + COMPILER_SPECIFIC_FLAGS( + COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID + DEFAULT -march=rv64imafdcv + ) +ENDIF() + + IF (KOKKOS_ARCH_BDW) SET(KOKKOS_ARCH_AVX2 ON) COMPILER_SPECIFIC_FLAGS( @@ -571,6 +571,11 @@ IF (KOKKOS_ENABLE_HIP) COMPILER_SPECIFIC_FLAGS( DEFAULT -fgpu-rdc ) + IF (NOT KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) + COMPILER_SPECIFIC_LINK_OPTIONS( + DEFAULT --hip-link + ) + ENDIF() ELSE() COMPILER_SPECIFIC_FLAGS( DEFAULT -fno-gpu-rdc @@ -588,32 +593,44 @@ IF (KOKKOS_ENABLE_SYCL) ENDIF() # Check support for device_global variables -# FIXME_SYCL Once the feature test macro SYCL_EXT_ONEAPI_DEVICE_GLOBAL is -# available, use that instead. -IF(KOKKOS_ENABLE_SYCL AND NOT BUILD_SHARED_LIBS) - INCLUDE(CheckCXXSourceCompiles) +# FIXME_SYCL If SYCL_EXT_ONEAPI_DEVICE_GLOBAL is defined, we can use device +# global variables with shared libraries using the "non-separable compilation" +# implementation. Otherwise, the feature is not supported when building shared +# libraries. Thus, we don't even check for support if shared libraries are +# requested and SYCL_EXT_ONEAPI_DEVICE_GLOBAL is not defined. +IF(KOKKOS_ENABLE_SYCL) STRING(REPLACE ";" " " CMAKE_REQUIRED_FLAGS "${KOKKOS_COMPILE_OPTIONS}") - CHECK_CXX_SOURCE_COMPILES(" - #include - using namespace sycl::ext::oneapi::experimental; - using namespace sycl; + INCLUDE(CheckCXXSymbolExists) + CHECK_CXX_SYMBOL_EXISTS(SYCL_EXT_ONEAPI_DEVICE_GLOBAL "sycl/sycl.hpp" KOKKOS_IMPL_HAVE_SYCL_EXT_ONEAPI_DEVICE_GLOBAL) + IF (KOKKOS_IMPL_HAVE_SYCL_EXT_ONEAPI_DEVICE_GLOBAL) + SET(KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED ON) + # Use the non-separable compilation implementation to support shared libraries as well. + COMPILER_SPECIFIC_FLAGS(DEFAULT -DDESUL_SYCL_DEVICE_GLOBAL_SUPPORTED) + ELSEIF(NOT BUILD_SHARED_LIBS) + INCLUDE(CheckCXXSourceCompiles) + CHECK_CXX_SOURCE_COMPILES(" + #include + using namespace sycl::ext::oneapi::experimental; + using namespace sycl; - SYCL_EXTERNAL device_global Foo; + SYCL_EXTERNAL device_global Foo; - void bar(queue q) { - q.single_task([=] { - Foo = 42; - }); - } + void bar(queue q) { + q.single_task([=] { + Foo = 42; + }); + } - int main(){ return 0; } - " - KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED) + int main(){ return 0; } + " + KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED) - IF(KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED) - COMPILER_SPECIFIC_FLAGS( - DEFAULT -fsycl-device-code-split=off -DDESUL_SYCL_DEVICE_GLOBAL_SUPPORTED - ) + IF(KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED) + # Only the separable compilation implementation is supported. + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-device-code-split=off -DDESUL_SYCL_DEVICE_GLOBAL_SUPPORTED + ) + ENDIF() ENDIF() ENDIF() @@ -767,30 +784,35 @@ IF (KOKKOS_ENABLE_OPENMPTARGET) COMPILER_SPECIFIC_FLAGS( IntelLLVM -fopenmp-targets=spir64 -D__STRICT_ANSI__ ) - ELSEIF(KOKKOS_ARCH_INTEL_GEN9) - COMPILER_SPECIFIC_FLAGS( - IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device gen9" -D__STRICT_ANSI__ + ELSE() + COMPILER_SPECIFIC_OPTIONS( + IntelLLVM -fopenmp-targets=spir64_gen -D__STRICT_ANSI__ ) - ELSEIF(KOKKOS_ARCH_INTEL_GEN11) - COMPILER_SPECIFIC_FLAGS( - IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device gen11" -D__STRICT_ANSI__ - ) - ELSEIF(KOKKOS_ARCH_INTEL_GEN12LP) - COMPILER_SPECIFIC_FLAGS( - IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device gen12lp" -D__STRICT_ANSI__ - ) - ELSEIF(KOKKOS_ARCH_INTEL_DG1) - COMPILER_SPECIFIC_FLAGS( - IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device dg1" -D__STRICT_ANSI__ - ) - ELSEIF(KOKKOS_ARCH_INTEL_XEHP) - COMPILER_SPECIFIC_FLAGS( - IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device 12.50.4" -D__STRICT_ANSI__ - ) - ELSEIF(KOKKOS_ARCH_INTEL_PVC) - COMPILER_SPECIFIC_FLAGS( - IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device 12.60.7" -D__STRICT_ANSI__ + IF(KOKKOS_ARCH_INTEL_GEN9) + COMPILER_SPECIFIC_LINK_OPTIONS( + IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device gen9" + ) + ELSEIF(KOKKOS_ARCH_INTEL_GEN11) + COMPILER_SPECIFIC_LINK_OPTIONS( + IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device gen11" + ) + ELSEIF(KOKKOS_ARCH_INTEL_GEN12LP) + COMPILER_SPECIFIC_LINK_OPTIONS( + IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device gen12lp" + ) + ELSEIF(KOKKOS_ARCH_INTEL_DG1) + COMPILER_SPECIFIC_LINK_OPTIONS( + IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device dg1" + ) + ELSEIF(KOKKOS_ARCH_INTEL_XEHP) + COMPILER_SPECIFIC_LINK_OPTIONS( + IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device 12.50.4" + ) + ELSEIF(KOKKOS_ARCH_INTEL_PVC) + COMPILER_SPECIFIC_LINK_OPTIONS( + IntelLLVM -fopenmp-targets=spir64_gen -Xopenmp-target-backend "-device 12.60.7" ) + ENDIF() ENDIF() ENDIF() @@ -1130,3 +1152,14 @@ MESSAGE(STATUS "Architectures:") FOREACH(Arch ${KOKKOS_ENABLED_ARCH_LIST}) MESSAGE(STATUS " ${Arch}") ENDFOREACH() + + +IF(KOKKOS_ENABLE_ATOMICS_BYPASS) + IF(NOT _HOST_PARALLEL STREQUAL "NoTypeDefined" OR NOT _DEVICE_PARALLEL STREQUAL "NoTypeDefined") + MESSAGE(FATAL_ERROR "Not allowed to disable atomics (via -DKokkos_ENABLE_AROMICS_BYPASS=ON) if neither a host parallel nor a device backend is enabled!") + ENDIF() + IF(NOT KOKKOS_ENABLE_SERIAL) + MESSAGE(FATAL_ERROR "Implementation bug") # safeguard + ENDIF() + MESSAGE(STATUS "Atomics: **DISABLED**") +ENDIF() diff --git a/lib/kokkos/cmake/kokkos_compiler_id.cmake b/lib/kokkos/cmake/kokkos_compiler_id.cmake index 04589befc3..9135ca2b41 100644 --- a/lib/kokkos/cmake/kokkos_compiler_id.cmake +++ b/lib/kokkos/cmake/kokkos_compiler_id.cmake @@ -152,6 +152,7 @@ ENDIF() SET(KOKKOS_MESSAGE_TEXT "Compiler not supported by Kokkos. Required compiler versions:") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang(CPU) 8.0.0 or higher") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang(CUDA) 10.0.0 or higher") +SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang(OpenMPTarget) 15.0.0 or higher") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n GCC 8.2.0 or higher") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Intel 19.0.5 or higher") SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n IntelLLVM(CPU) 2021.1.1 or higher") @@ -210,6 +211,10 @@ ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL "MSVC") ENDIF() ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL XL OR KOKKOS_CXX_COMPILER_ID STREQUAL XLClang) MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang AND Kokkos_ENABLE_OPENMPTARGET) + IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 15.0.0) + MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + ENDIF() ENDIF() IF(NOT DEFINED KOKKOS_CXX_HOST_COMPILER_ID) diff --git a/lib/kokkos/cmake/kokkos_enable_devices.cmake b/lib/kokkos/cmake/kokkos_enable_devices.cmake index 9a977520a3..c7d189285c 100644 --- a/lib/kokkos/cmake/kokkos_enable_devices.cmake +++ b/lib/kokkos/cmake/kokkos_enable_devices.cmake @@ -40,6 +40,26 @@ ELSE() ENDIF() KOKKOS_DEVICE_OPTION(OPENMP ${OMP_DEFAULT} HOST "Whether to build OpenMP backend") + +# We want this to default to OFF for cache reasons, but if no +# host space is given, then activate serial +IF (KOKKOS_HAS_TRILINOS) + #However, Trilinos always wants Serial ON + SET(SERIAL_DEFAULT ON) +ELSEIF (KOKKOS_HAS_HOST) + SET(SERIAL_DEFAULT OFF) +ELSE() + SET(SERIAL_DEFAULT ON) + IF (NOT DEFINED Kokkos_ENABLE_SERIAL) + MESSAGE(STATUS "SERIAL backend is being turned on to ensure there is at least one Host space. To change this, you must enable another host execution space and configure with -DKokkos_ENABLE_SERIAL=OFF or change CMakeCache.txt") + ENDIF() +ENDIF() +KOKKOS_DEVICE_OPTION(SERIAL ${SERIAL_DEFAULT} HOST "Whether to build serial backend") + +KOKKOS_DEVICE_OPTION(HPX OFF HOST "Whether to build HPX backend (experimental)") + +# Device backends have to come after host backends for header include order reasons +# Without this we can't make e.g. CudaSpace accessible by HostSpace KOKKOS_DEVICE_OPTION(OPENACC OFF DEVICE "Whether to build the OpenACC backend") IF (KOKKOS_ENABLE_OPENACC) COMPILER_SPECIFIC_FLAGS( @@ -90,23 +110,6 @@ IF (KOKKOS_ENABLE_CUDA) LIST(APPEND DEVICE_SETUP_LIST Cuda) ENDIF() -# We want this to default to OFF for cache reasons, but if no -# host space is given, then activate serial -IF (KOKKOS_HAS_TRILINOS) - #However, Trilinos always wants Serial ON - SET(SERIAL_DEFAULT ON) -ELSEIF (KOKKOS_HAS_HOST) - SET(SERIAL_DEFAULT OFF) -ELSE() - SET(SERIAL_DEFAULT ON) - IF (NOT DEFINED Kokkos_ENABLE_SERIAL) - MESSAGE(STATUS "SERIAL backend is being turned on to ensure there is at least one Host space. To change this, you must enable another host execution space and configure with -DKokkos_ENABLE_SERIAL=OFF or change CMakeCache.txt") - ENDIF() -ENDIF() -KOKKOS_DEVICE_OPTION(SERIAL ${SERIAL_DEFAULT} HOST "Whether to build serial backend") - -KOKKOS_DEVICE_OPTION(HPX OFF HOST "Whether to build HPX backend (experimental)") - KOKKOS_DEVICE_OPTION(HIP OFF DEVICE "Whether to build HIP backend") ## HIP has extra setup requirements, turn on Kokkos_Setup_HIP.hpp in macros diff --git a/lib/kokkos/cmake/kokkos_enable_options.cmake b/lib/kokkos/cmake/kokkos_enable_options.cmake index 89e23b019b..32788e7aa0 100644 --- a/lib/kokkos/cmake/kokkos_enable_options.cmake +++ b/lib/kokkos/cmake/kokkos_enable_options.cmake @@ -48,7 +48,6 @@ KOKKOS_ENABLE_OPTION(CUDA_LAMBDA ${CUDA_LAMBDA_DEFAULT} "Whether to allow lambda # resolved but we keep the option around a bit longer to be safe. KOKKOS_ENABLE_OPTION(IMPL_CUDA_MALLOC_ASYNC ON "Whether to enable CudaMallocAsync (requires CUDA Toolkit 11.2)") KOKKOS_ENABLE_OPTION(IMPL_NVHPC_AS_DEVICE_COMPILER OFF "Whether to allow nvc++ as Cuda device compiler") -KOKKOS_ENABLE_OPTION(DEPRECATED_CODE_3 OFF "Whether code deprecated in major release 3 is available" ) KOKKOS_ENABLE_OPTION(DEPRECATED_CODE_4 ON "Whether code deprecated in major release 4 is available" ) KOKKOS_ENABLE_OPTION(DEPRECATION_WARNINGS ON "Whether to emit deprecation warnings" ) KOKKOS_ENABLE_OPTION(HIP_RELOCATABLE_DEVICE_CODE OFF "Whether to enable relocatable device code (RDC) for HIP") @@ -71,9 +70,11 @@ KOKKOS_ENABLE_OPTION(TUNING OFF "Whether to create bindings for tu KOKKOS_ENABLE_OPTION(AGGRESSIVE_VECTORIZATION OFF "Whether to aggressively vectorize loops") KOKKOS_ENABLE_OPTION(COMPILE_AS_CMAKE_LANGUAGE OFF "Whether to use native cmake language support") KOKKOS_ENABLE_OPTION(HIP_MULTIPLE_KERNEL_INSTANTIATIONS OFF "Whether multiple kernels are instantiated at compile time - improve performance but increase compile time") +KOKKOS_ENABLE_OPTION(IMPL_HIP_UNIFIED_MEMORY OFF "Whether to leverage unified memory architectures for HIP") # This option will go away eventually, but allows fallback to old implementation when needed. KOKKOS_ENABLE_OPTION(DESUL_ATOMICS_EXTERNAL OFF "Whether to use an external desul installation") +KOKKOS_ENABLE_OPTION(ATOMICS_BYPASS OFF "**NOT RECOMMENDED** Whether to make atomics non-atomic for non-threaded MPI-only use cases") KOKKOS_ENABLE_OPTION(IMPL_MDSPAN OFF "Whether to enable experimental mdspan support") KOKKOS_ENABLE_OPTION(MDSPAN_EXTERNAL OFF BOOL "Whether to use an external version of mdspan") diff --git a/lib/kokkos/cmake/kokkos_pick_cxx_std.cmake b/lib/kokkos/cmake/kokkos_pick_cxx_std.cmake index d4eca651d4..ae14a10d53 100644 --- a/lib/kokkos/cmake/kokkos_pick_cxx_std.cmake +++ b/lib/kokkos/cmake/kokkos_pick_cxx_std.cmake @@ -7,6 +7,7 @@ KOKKOS_OPTION(CXX_STANDARD "" STRING "[[DEPRECATED - USE CMAKE_CXX_STANDARD INST SET(KOKKOS_ENABLE_CXX17 OFF) SET(KOKKOS_ENABLE_CXX20 OFF) SET(KOKKOS_ENABLE_CXX23 OFF) +SET(KOKKOS_ENABLE_CXX26 OFF) IF (KOKKOS_CXX_STANDARD) MESSAGE(FATAL_ERROR "Setting the variable Kokkos_CXX_STANDARD in configuration is deprecated - set CMAKE_CXX_STANDARD directly instead") ENDIF() diff --git a/lib/kokkos/cmake/kokkos_test_cxx_std.cmake b/lib/kokkos/cmake/kokkos_test_cxx_std.cmake index 7ad49fdd2d..b075a3e36b 100644 --- a/lib/kokkos/cmake/kokkos_test_cxx_std.cmake +++ b/lib/kokkos/cmake/kokkos_test_cxx_std.cmake @@ -74,6 +74,10 @@ ELSEIF(KOKKOS_CXX_STANDARD STREQUAL "23") kokkos_set_cxx_standard_feature(23) SET(KOKKOS_CXX_INTERMEDIATE_STANDARD "2B") SET(KOKKOS_ENABLE_CXX23 ON) +ELSEIF(KOKKOS_CXX_STANDARD STREQUAL "26") + kokkos_set_cxx_standard_feature(26) + SET(KOKKOS_CXX_INTERMEDIATE_STANDARD "2C") + SET(KOKKOS_ENABLE_CXX26 ON) ELSE() MESSAGE(FATAL_ERROR "Kokkos requires C++17 or newer but requested ${KOKKOS_CXX_STANDARD}!") ENDIF() diff --git a/lib/kokkos/cmake/kokkos_tpls.cmake b/lib/kokkos/cmake/kokkos_tpls.cmake index f124596a84..6ef3b79bde 100644 --- a/lib/kokkos/cmake/kokkos_tpls.cmake +++ b/lib/kokkos/cmake/kokkos_tpls.cmake @@ -32,19 +32,21 @@ FUNCTION(KOKKOS_TPL_OPTION PKG DEFAULT) ENDFUNCTION() KOKKOS_TPL_OPTION(HWLOC Off TRIBITS HWLOC) -KOKKOS_TPL_OPTION(MEMKIND Off) -IF(KOKKOS_ENABLE_MEMKIND) - SET(KOKKOS_ENABLE_HBWSPACE ON) -ENDIF() KOKKOS_TPL_OPTION(CUDA ${Kokkos_ENABLE_CUDA} TRIBITS CUDA) -KOKKOS_TPL_OPTION(LIBRT Off) IF(KOKKOS_ENABLE_HIP AND NOT KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC AND NOT KOKKOS_HAS_TRILINOS) SET(ROCM_DEFAULT ON) ELSE() SET(ROCM_DEFAULT OFF) ENDIF() +IF(KOKKOS_ENABLE_HIP AND NOT KOKKOS_HAS_TRILINOS) + SET(ROCTHRUST_DEFAULT ON) +ELSE() + SET(ROCTHRUST_DEFAULT OFF) +ENDIF() KOKKOS_TPL_OPTION(ROCM ${ROCM_DEFAULT}) +KOKKOS_TPL_OPTION(ROCTHRUST ${ROCTHRUST_DEFAULT}) + IF(KOKKOS_ENABLE_SYCL AND NOT KOKKOS_HAS_TRILINOS) SET(ONEDPL_DEFAULT ON) ELSE() @@ -77,21 +79,18 @@ KOKKOS_TPL_OPTION(LIBQUADMATH ${LIBQUADMATH_DEFAULT} TRIBITS quadmath) #Make sure we use our local FindKokkosCuda.cmake KOKKOS_IMPORT_TPL(HPX INTERFACE) -IF (NOT KOKKOS_ENABLE_COMPILE_AS_CMAKE_LANGUAGE) - KOKKOS_IMPORT_TPL(CUDA INTERFACE) -ENDIF() +KOKKOS_IMPORT_TPL(CUDA INTERFACE) KOKKOS_IMPORT_TPL(HWLOC) -KOKKOS_IMPORT_TPL(LIBRT) KOKKOS_IMPORT_TPL(LIBDL) -KOKKOS_IMPORT_TPL(MEMKIND) IF (NOT WIN32) KOKKOS_IMPORT_TPL(THREADS INTERFACE) ENDIF() IF (NOT KOKKOS_ENABLE_COMPILE_AS_CMAKE_LANGUAGE) KOKKOS_IMPORT_TPL(ROCM INTERFACE) - KOKKOS_IMPORT_TPL(ONEDPL INTERFACE) ENDIF() +KOKKOS_IMPORT_TPL(ONEDPL INTERFACE) KOKKOS_IMPORT_TPL(LIBQUADMATH) +KOKKOS_IMPORT_TPL(ROCTHRUST) IF (Kokkos_ENABLE_DESUL_ATOMICS_EXTERNAL) find_package(desul REQUIRED COMPONENTS atomics) @@ -119,7 +118,3 @@ STRING(REPLACE ";" "\n" KOKKOS_TPL_EXPORT_TEMP "${KOKKOS_TPL_EXPORTS}") #Convert to a regular variable UNSET(KOKKOS_TPL_EXPORTS CACHE) SET(KOKKOS_TPL_EXPORTS ${KOKKOS_TPL_EXPORT_TEMP}) -IF (KOKKOS_ENABLE_MEMKIND) - SET(KOKKOS_ENABLE_HBWSPACE) - LIST(APPEND KOKKOS_MEMSPACE_LIST HBWSpace) -ENDIF() diff --git a/lib/kokkos/cmake/kokkos_tribits.cmake b/lib/kokkos/cmake/kokkos_tribits.cmake index b30ca70ab9..060a7a8472 100644 --- a/lib/kokkos/cmake/kokkos_tribits.cmake +++ b/lib/kokkos/cmake/kokkos_tribits.cmake @@ -237,18 +237,10 @@ ENDMACRO() ## KOKKOS_DECLARE is the declaration set ## KOKKOS_POST_INCLUDE is included at the end of Kokkos_Core.hpp MACRO(KOKKOS_CONFIGURE_CORE) - SET(FWD_BACKEND_LIST) - FOREACH(MEMSPACE ${KOKKOS_MEMSPACE_LIST}) - LIST(APPEND FWD_BACKEND_LIST ${MEMSPACE}) - ENDFOREACH() - FOREACH(BACKEND_ ${KOKKOS_ENABLED_DEVICES}) - LIST(APPEND FWD_BACKEND_LIST ${BACKEND_}) - ENDFOREACH() - MESSAGE(STATUS "Kokkos Devices: ${KOKKOS_ENABLED_DEVICES}, Kokkos Backends: ${FWD_BACKEND_LIST}") - KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_FwdBackend.hpp "KOKKOS_FWD" "fwd/Kokkos_Fwd" "${FWD_BACKEND_LIST}") + MESSAGE(STATUS "Kokkos Backends: ${KOKKOS_ENABLED_DEVICES}") + KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_FwdBackend.hpp "KOKKOS_FWD" "fwd/Kokkos_Fwd" "${KOKKOS_ENABLED_DEVICES}") KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_SetupBackend.hpp "KOKKOS_SETUP" "setup/Kokkos_Setup" "${DEVICE_SETUP_LIST}") - KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_DeclareBackend.hpp "KOKKOS_DECLARE" "decl/Kokkos_Declare" "${FWD_BACKEND_LIST}") - KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_PostInclude.hpp "KOKKOS_POST_INCLUDE" "Kokkos_Post_Include" "${KOKKOS_BACKEND_POST_INCLUDE_LIST}") + KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_DeclareBackend.hpp "KOKKOS_DECLARE" "decl/Kokkos_Declare" "${KOKKOS_ENABLED_DEVICES}") SET(_DEFAULT_HOST_MEMSPACE "::Kokkos::HostSpace") KOKKOS_OPTION(DEFAULT_DEVICE_MEMORY_SPACE "" STRING "Override default device memory space") KOKKOS_OPTION(DEFAULT_HOST_MEMORY_SPACE "" STRING "Override default host memory space") @@ -309,7 +301,6 @@ MACRO(KOKKOS_INSTALL_ADDITIONAL_FILES) "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_FwdBackend.hpp" "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_SetupBackend.hpp" "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_DeclareBackend.hpp" - "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_PostInclude.hpp" DESTINATION ${KOKKOS_HEADER_DIR}) ENDMACRO() diff --git a/lib/kokkos/config/test_all_sandia b/lib/kokkos/config/test_all_sandia deleted file mode 100755 index 193a162a4e..0000000000 --- a/lib/kokkos/config/test_all_sandia +++ /dev/null @@ -1,773 +0,0 @@ -#!/bin/bash -e - -# -# Global config -# - -set -o pipefail - -# Determine current machine. - -MACHINE="" -HOSTNAME=$(hostname) -PROCESSOR=`uname -p` - -if [[ "$HOSTNAME" =~ (white|ride).* ]]; then - MACHINE=white - module load git -fi - -if [[ "$HOSTNAME" =~ .*bowman.* ]]; then - MACHINE=bowman - module load git -fi - -if [[ "$HOSTNAME" == n* ]]; then # Warning: very generic name - if [[ "$PROCESSOR" = "aarch64" ]]; then - MACHINE=sullivan - module load git - fi -fi - -if [[ "$HOSTNAME" == node* ]]; then # Warning: very generic name - if [[ "$MACHINE" = "" ]]; then - MACHINE=shepard - module load git - fi -fi - -if [[ "$HOSTNAME" == apollo\.* ]]; then - MACHINE=apollo - module load git -fi - -if [[ "$HOSTNAME" == sullivan ]]; then - MACHINE=sullivan - module load git -fi - -if [[ "$HOSTNAME" == mayer\.* ]]; then - MACHINE=mayer -# module load git -fi -if [[ "$HOSTNAME" == cn* ]]; then # Warning: very generic name - MACHINE=mayer -fi - -if [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then - if [[ "$MACHINE" = "" ]]; then - MACHINE=sems - module load sems-git - fi -fi - -if [[ "$MACHINE" = "" ]]; then - echo "Unrecognized machine" >&2 - exit 1 -fi - -echo "Running on machine: $MACHINE" - -GCC_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial" -IBM_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" -ARM_GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" -INTEL_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial" -CLANG_BUILD_LIST="Pthread,Serial,Pthread_Serial" -CUDA_BUILD_LIST="Cuda_OpenMP,Cuda_Pthread,Cuda_Serial" -CUDA_IBM_BUILD_LIST="Cuda_OpenMP,Cuda_Serial" - -GCC_WARNING_FLAGS="-Wall,-Wunused-parameter,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wignored-qualifiers,-Wempty-body,-Wclobbered,-Wuninitialized" -IBM_WARNING_FLAGS="-Wall,-Wunused-parameter,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" -CLANG_WARNING_FLAGS="-Wall,-Wunused-parameter,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" -INTEL_WARNING_FLAGS="-Wall,-Wunused-parameter,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" -#CUDA_WARNING_FLAGS="-Wall,-Wunused-parameter,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" -CUDA_WARNING_FLAGS="-Wall,-Wunused-parameter,-Wshadow,-pedantic,-Wsign-compare,-Wtype-limits,-Wuninitialized" -PGI_WARNING_FLAGS="" - -# Default. Machine specific can override. -DEBUG=False -ARGS="" -CUSTOM_BUILD_LIST="" -DRYRUN=False -BUILD_ONLY=False -declare -i NUM_JOBS_TO_RUN_IN_PARALLEL=1 -TEST_SCRIPT=False -SKIP_HWLOC=False -SPOT_CHECK=False - -PRINT_HELP=False -OPT_FLAG="" -CXX_FLAGS_EXTRA="" -LD_FLAGS_EXTRA="" -KOKKOS_OPTIONS="" - -# -# Handle arguments. -# - -while [[ $# > 0 ]] -do - key="$1" - - case $key in - --kokkos-path*) - KOKKOS_PATH="${key#*=}" - ;; - --build-list*) - CUSTOM_BUILD_LIST="${key#*=}" - ;; - --debug*) - DEBUG=True - ;; - --build-only*) - BUILD_ONLY=True - ;; - --test-script*) - TEST_SCRIPT=True - ;; - --skip-hwloc*) - SKIP_HWLOC=True - ;; - --num*) - NUM_JOBS_TO_RUN_IN_PARALLEL="${key#*=}" - ;; - --dry-run*) - DRYRUN=True - ;; - --spot-check*) - SPOT_CHECK=True - ;; - --arch*) - ARCH_FLAG="--arch=${key#*=}" - ;; - --opt-flag*) - OPT_FLAG="${key#*=}" - ;; - --with-cuda-options*) - KOKKOS_CUDA_OPTIONS="--with-cuda-options=${key#*=}" - ;; - --with-options*) - KOKKOS_OPTIONS="--with-options=enable_large_mem_tests,${key#*=}" - ;; - --cxxflags-extra*) - CXX_FLAGS_EXTRA="${key#*=}" - ;; - --ldflags-extra*) - LD_FLAGS_EXTRA="${key#*=}" - ;; - --help*) - PRINT_HELP=True - ;; - *) - # args, just append - ARGS="$ARGS $1" - ;; - esac - - shift -done - -SCRIPT_KOKKOS_ROOT=$( cd "$( dirname "$0" )" && cd .. && pwd ) - -# Set kokkos path. -if [ -z "$KOKKOS_PATH" ]; then - KOKKOS_PATH=$SCRIPT_KOKKOS_ROOT -else - # Ensure KOKKOS_PATH is abs path. - KOKKOS_PATH=$( cd $KOKKOS_PATH && pwd ) -fi - -UNCOMMITTED=`cd ${KOKKOS_PATH}; git status --porcelain 2>/dev/null` -if ! [ -z "$UNCOMMITTED" ]; then - echo "WARNING!! THE FOLLOWING CHANGES ARE UNCOMMITTED!! :" - echo "$UNCOMMITTED" - echo "" -fi - -GITSTATUS=`cd ${KOKKOS_PATH}; git log -n 1 --format=oneline` -echo "Repository Status: " ${GITSTATUS} -echo "" -echo "" - -# -# Machine specific config. -# - -if [ "$MACHINE" = "sems" ]; then - source /projects/sems/modulefiles/utils/sems-modules-init.sh - - BASE_MODULE_LIST="sems-env,kokkos-env,kokkos-hwloc/1.10.1/base,sems-/" - CUDA_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/4.8.4,kokkos-hwloc/1.10.1/base" - CUDA8_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/5.3.0,kokkos-hwloc/1.10.1/base" - - if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="" - fi - - if [ "$SPOT_CHECK" = "True" ]; then - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/5.3.0 $BASE_MODULE_LIST "OpenMP" g++ $GCC_WARNING_FLAGS" - "gcc/6.1.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" - "intel/17.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" - "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" - "cuda/8.0.44 $CUDA8_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - ) - else - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/4.8.4 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "gcc/4.9.3 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "gcc/5.3.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "gcc/6.1.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "intel/15.0.2 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "intel/16.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "intel/16.0.3 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "clang/3.7.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "clang/3.8.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "clang/3.9.0 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/8.0.44 $CUDA8_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - ) - fi -elif [ "$MACHINE" = "white" ]; then - source /etc/profile.d/modules.sh - SKIP_HWLOC=True - export SLURM_TASKS_PER_NODE=32 - - BASE_MODULE_LIST="/" - IBM_MODULE_LIST="/xl/" - CUDA_MODULE_LIST="/,gcc/6.4.0,ibm/xl/16.1.0" - - # Don't do pthread on white. - GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" - - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/5.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "gcc/6.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "ibm/16.1.0 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" - "cuda/9.0.103 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - ) - - if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="--arch=Power8,Kepler37" - fi - - NUM_JOBS_TO_RUN_IN_PARALLEL=1 - -elif [ "$MACHINE" = "bowman" ]; then - source /etc/profile.d/modules.sh - SKIP_HWLOC=True - export SLURM_TASKS_PER_NODE=32 - - BASE_MODULE_LIST="/compilers/" - - OLD_INTEL_BUILD_LIST="Pthread,Serial,Pthread_Serial" - - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("intel/16.4.258 $BASE_MODULE_LIST $OLD_INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "intel/17.2.174 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "intel/18.0.128 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - ) - - if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="--arch=KNL" - fi - - NUM_JOBS_TO_RUN_IN_PARALLEL=1 - -elif [ "$MACHINE" = "sullivan" ]; then - source /etc/profile.d/modules.sh - SKIP_HWLOC=True - export SLURM_TASKS_PER_NODE=96 - - BASE_MODULE_LIST="/" - - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/6.1.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS") - - if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="--arch=ARMv8-ThunderX" - fi - - NUM_JOBS_TO_RUN_IN_PARALLEL=1 - -elif [ "$MACHINE" = "mayer" ]; then - SKIP_HWLOC=True - export SLURM_TASKS_PER_NODE=96 - - BASE_MODULE_LIST="/" - ARM_MODULE_LIST="/" - - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/7.2.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "arm/1.4.0 $ARM_MODULE_LIST $ARM_GCC_BUILD_LIST armclang++ $CLANG_WARNING_FLAGS") - - if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="--arch=ARMv8-TX2" - fi - - NUM_JOBS_TO_RUN_IN_PARALLEL=1 - -elif [ "$MACHINE" = "shepard" ]; then - source /etc/profile.d/modules.sh - SKIP_HWLOC=True - export SLURM_TASKS_PER_NODE=32 - - BASE_MODULE_LIST="/" - BASE_MODULE_LIST_INTEL="/compilers/" - - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("intel/17.4.196 $BASE_MODULE_LIST_INTEL $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "intel/18.0.128 $BASE_MODULE_LIST_INTEL $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "pgi/17.10.0 $BASE_MODULE_LIST $GCC_BUILD_LIST pgc++ $PGI_WARNING_FLAGS" - ) - - if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="--arch=HSW" - fi - NUM_JOBS_TO_RUN_IN_PARALLEL=1 - -elif [ "$MACHINE" = "apollo" ]; then - source /projects/sems/modulefiles/utils/sems-modules-init.sh - module use /home/projects/modulefiles/local/x86-64 - module load kokkos-env - - module load sems-git - module load sems-tex - module load sems-cmake/3.5.2 - module load sems-gdb - - SKIP_HWLOC=True - - BASE_MODULE_LIST="sems-env,kokkos-env,sems-/,kokkos-hwloc/1.10.1/base" - CUDA_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/4.8.4,kokkos-hwloc/1.10.1/base" - CUDA8_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/5.3.0,kokkos-hwloc/1.10.1/base" - - CLANG_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,cuda/9.0.69" - NVCC_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,sems-gcc/5.3.0" - - BUILD_LIST_CUDA_NVCC="Cuda_Serial,Cuda_OpenMP" - BUILD_LIST_CUDA_CLANG="Cuda_Serial,Cuda_Pthread" - BUILD_LIST_CLANG="Serial,Pthread,OpenMP" - - if [ "$SPOT_CHECK" = "True" ]; then - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/4.8.4 $BASE_MODULE_LIST "OpenMP,Pthread" g++ $GCC_WARNING_FLAGS" - "gcc/5.3.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" - "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" - "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" - "clang/6.0 $CLANG_MODULE_LIST "Cuda_Pthread,OpenMP" clang++ $CUDA_WARNING_FLAGS" - "cuda/9.1 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - ) - else - # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("cuda/9.1 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - "clang/6.0 $CLANG_MODULE_LIST $BUILD_LIST_CUDA_CLANG clang++ $CUDA_WARNING_FLAGS" - "clang/3.9.0 $CLANG_MODULE_LIST $BUILD_LIST_CLANG clang++ $CLANG_WARNING_FLAGS" - "gcc/4.8.4 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "gcc/4.9.3 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "gcc/5.3.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "gcc/6.1.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "intel/15.0.2 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "intel/16.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "intel/17.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" - "clang/3.5.2 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - ) - fi - - if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="--arch=SNB,Volta70" - fi - - NUM_JOBS_TO_RUN_IN_PARALLEL=1 - -else - echo "Unhandled machine $MACHINE" >&2 - exit 1 -fi - -export OMP_NUM_THREADS=4 - -declare -i NUM_RESULTS_TO_KEEP=7 - -RESULT_ROOT_PREFIX=TestAll - -if [ "$PRINT_HELP" = "True" ]; then - echo "test_all_sandia :" - echo "--kokkos-path=/Path/To/Kokkos: Path to the Kokkos root directory" - echo " Defaults to root repo containing this script" - echo "--debug: Run tests in debug. Defaults to False" - echo "--test-script: Test this script, not Kokkos" - echo "--skip-hwloc: Do not do hwloc tests" - echo "--num=N: Number of jobs to run in parallel" - echo "--spot-check: Minimal test set to issue pull request" - echo "--dry-run: Just print what would be executed" - echo "--build-only: Just do builds, don't run anything" - echo "--opt-flag=FLAG: Optimization flag (default: -O3)" - echo "--cxxflags-extra=FLAGS: Extra flags to be added to CXX_FLAGS" - echo "--ldflags-extra=FLAGS: Extra flags to be added to LD_FLAGS" - echo "--arch=ARCHITECTURE: overwrite architecture flags" - echo "--with-cuda-options=OPT: set KOKKOS_CUDA_OPTIONS" - echo "--build-list=BUILD,BUILD,BUILD..." - echo " Provide a comma-separated list of builds instead of running all builds" - echo " Valid items:" - echo " OpenMP, Pthread, Serial, OpenMP_Serial, Pthread_Serial" - echo " Cuda_OpenMP, Cuda_Pthread, Cuda_Serial" - echo "" - - echo "ARGS: list of expressions matching compilers to test" - echo " supported compilers sems" - for COMPILER_DATA in "${COMPILERS[@]}"; do - ARR=($COMPILER_DATA) - COMPILER=${ARR[0]} - echo " $COMPILER" - done - echo "" - - echo "Examples:" - echo " Run all tests" - echo " % test_all_sandia" - echo "" - echo " Run all gcc tests" - echo " % test_all_sandia gcc" - echo "" - echo " Run all gcc/4.8.4 and all intel tests" - echo " % test_all_sandia gcc/4.8.4 intel" - echo "" - echo " Run all tests in debug" - echo " % test_all_sandia --debug" - echo "" - echo " Run gcc/4.8.4 and only do OpenMP and OpenMP_Serial builds" - echo " % test_all_sandia gcc/4.8.4 --build-list=OpenMP,OpenMP_Serial" - echo "" - echo "If you want to kill the tests, do:" - echo " hit ctrl-z" - echo " % kill -9 %1" - echo - exit 0 -fi - -# Set build type. -if [ "$DEBUG" = "True" ]; then - BUILD_TYPE=debug -else - BUILD_TYPE=release -fi - -# If no args provided, do all compilers. -if [ -z "$ARGS" ]; then - ARGS='?' -fi - -# Process args to figure out which compilers to test. -COMPILERS_TO_TEST="" - -for ARG in $ARGS; do - for COMPILER_DATA in "${COMPILERS[@]}"; do - ARR=($COMPILER_DATA) - COMPILER=${ARR[0]} - - if [[ "$COMPILER" = $ARG* ]]; then - if [[ "$COMPILERS_TO_TEST" != *${COMPILER}* ]]; then - COMPILERS_TO_TEST="$COMPILERS_TO_TEST $COMPILER" - else - echo "Tried to add $COMPILER twice" - fi - fi - done -done - -# -# Functions. -# - -# get_compiler_name -get_compiler_name() { - echo $1 | cut -d/ -f1 -} - -# get_compiler_version -get_compiler_version() { - echo $1 | cut -d/ -f2 -} - -# Do not call directly. -get_compiler_data() { - local compiler=$1 - local item=$2 - local compiler_name=$(get_compiler_name $compiler) - local compiler_vers=$(get_compiler_version $compiler) - - local compiler_data - for compiler_data in "${COMPILERS[@]}" ; do - local arr=($compiler_data) - - if [ "$compiler" = "${arr[0]}" ]; then - echo "${arr[$item]}" | tr , ' ' | sed -e "s//$compiler_name/g" -e "s//$compiler_vers/g" - return 0 - fi - done - - # Not found. - echo "Unreconized compiler $compiler" >&2 - exit 1 -} - -# -# For all getters, usage: -# - -get_compiler_modules() { - get_compiler_data $1 1 -} - -get_compiler_build_list() { - get_compiler_data $1 2 -} - -get_compiler_exe_name() { - get_compiler_data $1 3 -} - -get_compiler_warning_flags() { - get_compiler_data $1 4 -} - -run_cmd() { - echo "RUNNING: $*" - if [ "$DRYRUN" != "True" ]; then - eval "$* 2>&1" - fi -} - -# report_and_log_test_results -report_and_log_test_result() { - # Use sane var names. - local success=$1; local desc=$2; local comment=$3; - - if [ "$success" = "0" ]; then - echo " PASSED $desc" - echo $comment > $PASSED_DIR/$desc - else - # For failures, comment should be the name of the phase that failed. - echo " FAILED $desc" >&2 - echo $comment > $FAILED_DIR/$desc - cat ${desc}.${comment}.log - fi -} - -setup_env() { - local compiler=$1 - local compiler_modules=$(get_compiler_modules $compiler) - - module purge - - local mod - for mod in $compiler_modules; do - echo "Loading module $mod" - module load $mod 2>&1 - # It is ridiculously hard to check for the success of a loaded - # module. Module does not return error codes and piping to grep - # causes module to run in a subshell. - module list 2>&1 | grep "$mod" >& /dev/null || return 1 - done - - return 0 -} - -# single_build_and_test -single_build_and_test() { - # Use sane var names. - local compiler=$1; local build=$2; local build_type=$3; - - # Set up env. - mkdir -p $ROOT_DIR/$compiler/"${build}-$build_type" - cd $ROOT_DIR/$compiler/"${build}-$build_type" - local desc=$(echo "${compiler}-${build}-${build_type}" | sed 's:/:-:g') - setup_env $compiler >& ${desc}.configure.log || { report_and_log_test_result 1 ${desc} configure && return 0; } - - # Set up flags. - local compiler_warning_flags=$(get_compiler_warning_flags $compiler) - local compiler_exe=$(get_compiler_exe_name $compiler) - - if [[ "$build_type" = hwloc* ]]; then - local extra_args=--with-hwloc=$(dirname $(dirname $(which hwloc-info))) - fi - - if [[ "$OPT_FLAG" = "" ]]; then - OPT_FLAG="-O3" - fi - - if [[ "$build_type" = *debug* ]]; then - local extra_args="$extra_args --debug" - local cxxflags="-g $compiler_warning_flags" - local ldflags="-g" - else - local cxxflags="$OPT_FLAG $compiler_warning_flags" - local ldflags="${OPT_FLAG}" - fi - - local cxxflags="${cxxflags} ${CXX_FLAGS_EXTRA}" - local ldflags="${ldflags} ${LD_FLAGS_EXTRA}" - - if [[ "$KOKKOS_CUDA_OPTIONS" != "" ]]; then - local extra_args="$extra_args $KOKKOS_CUDA_OPTIONS" - fi - if [[ "$KOKKOS_OPTIONS" != "" ]]; then - local extra_args="$extra_args $KOKKOS_OPTIONS" - else - local extra_args="$extra_args --with-options=enable_large_mem_tests" - fi - - echo " Starting job $desc" - - local comment="no_comment" - - if [ "$TEST_SCRIPT" = "True" ]; then - local rand=$[ 1 + $[ RANDOM % 10 ]] - sleep $rand - - if [ $rand -gt 5 ]; then - run_cmd ls fake_problem >& ${desc}.configure.log || { report_and_log_test_result 1 $desc configure && return 0; } - fi - else - run_cmd ${KOKKOS_PATH}/generate_makefile.bash --with-devices=$build $ARCH_FLAG --compiler=$(which $compiler_exe) --cxxflags=\"$cxxflags\" --ldflags=\"$ldflags\" $extra_args &>> ${desc}.configure.log || { report_and_log_test_result 1 ${desc} configure && return 0; } - local -i build_start_time=$(date +%s) - run_cmd make -j 48 build-test >& ${desc}.build.log || { report_and_log_test_result 1 ${desc} build && return 0; } - local -i build_end_time=$(date +%s) - comment="build_time=$(($build_end_time-$build_start_time))" - - if [[ "$BUILD_ONLY" == False ]]; then - run_cmd make test >& ${desc}.test.log || { report_and_log_test_result 1 ${desc} test && return 0; } - local -i run_end_time=$(date +%s) - comment="$comment run_time=$(($run_end_time-$build_end_time))" - fi - fi - - report_and_log_test_result 0 $desc "$comment" - - return 0 -} - -# wait_for_jobs -wait_for_jobs() { - local -i max_jobs=$1 - local -i num_active_jobs=$(jobs | wc -l) - while [ $num_active_jobs -ge $max_jobs ] - do - sleep 1 - num_active_jobs=$(jobs | wc -l) - jobs >& /dev/null - done -} - -# run_in_background -run_in_background() { - local compiler=$1 - - local -i num_jobs=$NUM_JOBS_TO_RUN_IN_PARALLEL - # Don't override command line input. - # if [[ "$BUILD_ONLY" == True ]]; then - # num_jobs=8 - # else - if [[ "$compiler" == cuda* ]]; then - num_jobs=1 - fi - if [[ "$compiler" == clang ]]; then - num_jobs=1 - fi - # fi - wait_for_jobs $num_jobs - - single_build_and_test $* & -} - -# build_and_test_all -build_and_test_all() { - # Get compiler data. - local compiler=$1 - if [ -z "$CUSTOM_BUILD_LIST" ]; then - local compiler_build_list=$(get_compiler_build_list $compiler) - else - local compiler_build_list=$(echo "$CUSTOM_BUILD_LIST" | tr , ' ') - fi - - # Do builds. - local build - for build in $compiler_build_list - do - run_in_background $compiler $build $BUILD_TYPE - - # If not cuda, do a hwloc test too. - if [[ "$compiler" != cuda* && "$SKIP_HWLOC" == False ]]; then - run_in_background $compiler $build "hwloc-$BUILD_TYPE" - fi - done - - return 0 -} - -get_test_root_dir() { - local existing_results=$(find . -maxdepth 1 -name "$RESULT_ROOT_PREFIX*" | sort) - local -i num_existing_results=$(echo $existing_results | tr ' ' '\n' | wc -l) - local -i num_to_delete=${num_existing_results}-${NUM_RESULTS_TO_KEEP} - - if [ $num_to_delete -gt 0 ]; then - /bin/rm -rf $(echo $existing_results | tr ' ' '\n' | head -n $num_to_delete) - fi - - echo $(pwd)/${RESULT_ROOT_PREFIX}_$(date +"%Y-%m-%d_%H.%M.%S") -} - -wait_summarize_and_exit() { - wait_for_jobs 1 - - echo "#######################################################" - echo "PASSED TESTS" - echo "#######################################################" - - local passed_test - for passed_test in $(\ls -1 $PASSED_DIR | sort) - do - echo $passed_test $(cat $PASSED_DIR/$passed_test) - done - - local -i rv=0 - if [ "$(ls -A $FAILED_DIR)" ]; then - echo "#######################################################" - echo "FAILED TESTS" - echo "#######################################################" - - local failed_test - for failed_test in $(\ls -1 $FAILED_DIR | sort) - do - echo $failed_test "("$(cat $FAILED_DIR/$failed_test)" failed)" - rv=$rv+1 - done - fi - - exit $rv -} - -# -# Main. -# - -ROOT_DIR=$(get_test_root_dir) -mkdir -p $ROOT_DIR -cd $ROOT_DIR - -PASSED_DIR=$ROOT_DIR/results/passed -FAILED_DIR=$ROOT_DIR/results/failed -mkdir -p $PASSED_DIR -mkdir -p $FAILED_DIR - -echo "Going to test compilers: " $COMPILERS_TO_TEST -for COMPILER in $COMPILERS_TO_TEST; do - echo "Testing compiler $COMPILER" - build_and_test_all $COMPILER -done - -wait_summarize_and_exit diff --git a/lib/kokkos/config/yaml/volta.yaml b/lib/kokkos/config/yaml/volta.yaml deleted file mode 100644 index f67af9c2a4..0000000000 --- a/lib/kokkos/config/yaml/volta.yaml +++ /dev/null @@ -1,4 +0,0 @@ -packages: - kokkos: - variants: +cuda +openmp +volta70 +cuda_lambda +wrapper ^cuda@10.1 - compiler: [gcc@7.2.0] diff --git a/lib/kokkos/containers/src/Kokkos_Bitset.hpp b/lib/kokkos/containers/src/Kokkos_Bitset.hpp index cd5ca4ea51..f50ab0a0f7 100644 --- a/lib/kokkos/containers/src/Kokkos_Bitset.hpp +++ b/lib/kokkos/containers/src/Kokkos_Bitset.hpp @@ -28,24 +28,6 @@ namespace Kokkos { -namespace Impl { -//! Either append to the label if the property already exists, or set it. -template -auto with_updated_label(const ViewCtorProp& view_ctor_prop, - const std::string& label) { - using vcp_t = ViewCtorProp; - //! If the label property is already set, append. Otherwise, set label. - if constexpr (vcp_t::has_label) { - vcp_t new_ctor_props(view_ctor_prop); - static_cast&>(new_ctor_props) - .value.append(label); - return new_ctor_props; - } else { - return Impl::with_properties_if_unset(view_ctor_prop, label); - } -} -} // namespace Impl - template class Bitset; @@ -92,9 +74,10 @@ class Bitset { using block_view_type = View>; public: - /// constructor + Bitset() = default; + /// arg_size := number of bit in set - Bitset(unsigned arg_size = 0u) : Bitset(Kokkos::view_alloc(), arg_size) {} + Bitset(unsigned arg_size) : Bitset(Kokkos::view_alloc(), arg_size) {} template Bitset(const Impl::ViewCtorProp& arg_prop, unsigned arg_size) @@ -108,9 +91,8 @@ class Bitset { "Allocation properties should not contain the 'pointer' property."); //! Update 'label' property and allocate. - const auto prop_copy = Kokkos::Impl::with_updated_label( - Impl::with_properties_if_unset(arg_prop, std::string("Bitset")), - " - blocks"); + const auto prop_copy = + Impl::with_properties_if_unset(arg_prop, std::string("Bitset")); m_blocks = block_view_type(prop_copy, ((m_size + block_mask) >> block_shift)); @@ -310,8 +292,8 @@ class Bitset { } private: - unsigned m_size; - unsigned m_last_block_mask; + unsigned m_size = 0; + unsigned m_last_block_mask = 0; block_view_type m_blocks; private: diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 84bced2cc4..e821570a8d 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -292,15 +292,6 @@ class DualView : public ViewTraits { d_view(src.d_view), h_view(src.h_view) {} - //! Copy assignment operator (shallow copy assignment) - template - DualView& operator=(const DualView& src) { - modified_flags = src.modified_flags; - d_view = src.d_view; - h_view = src.h_view; - return *this; - } - //! Subview constructor template DualView(const DualView& src, const Arg0& arg0, Args... args) diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index 52aa86d8ee..5fa59f1b7c 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -1340,7 +1340,7 @@ class ViewMapping< template struct apply { - static_assert(Kokkos::is_memory_traits::value, ""); + static_assert(Kokkos::is_memory_traits::value); using traits_type = Kokkos::ViewTraits::type, Args...>( - v.data(), v.impl_map().layout()); + auto layout = v.impl_map().layout(); + + if constexpr (std::is_same_v || + std::is_same_v || + std::is_same_v || + is_layouttiled::value) { + for (int i = N; i < 7; ++i) + layout.dimension[i] = KOKKOS_IMPL_CTOR_DEFAULT_ARG; + } + + return View::type, Args...>(v.data(), layout); } template diff --git a/lib/kokkos/containers/src/Kokkos_OffsetView.hpp b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp index 92aead2878..91a7e4a927 100644 --- a/lib/kokkos/containers/src/Kokkos_OffsetView.hpp +++ b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp @@ -124,15 +124,8 @@ KOKKOS_INLINE_FUNCTION void offsetview_verify_operator_bounds( args...); Kokkos::Impl::throw_runtime_exception(std::string(buffer));)) - KOKKOS_IF_ON_DEVICE(( - /* Check #1: is there a SharedAllocationRecord? - (we won't use it, but if it is not there then there isn't - a corresponding SharedAllocationHeader containing a label). - This check should cover the case of Views that don't - have the Unmanaged trait but were initialized by pointer. */ - if (tracker.has_record()) { - Kokkos::Impl::operator_bounds_error_on_device(map); - } else { Kokkos::abort("OffsetView bounds error"); })) + KOKKOS_IF_ON_DEVICE( + (Kokkos::abort("OffsetView bounds error"); (void)tracker;)) } } diff --git a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp index e001c062de..78a6a238ec 100644 --- a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp +++ b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp @@ -243,16 +243,16 @@ class UnorderedMap { using const_map_type = UnorderedMap; - static const bool is_set = std::is_void::value; - static const bool has_const_key = - std::is_same::value; - static const bool has_const_value = - is_set || std::is_same::value; + static constexpr bool is_set = std::is_void_v; + static constexpr bool has_const_key = + std::is_same_v; + static constexpr bool has_const_value = + is_set || std::is_same_v; - static const bool is_insertable_map = + static constexpr bool is_insertable_map = !has_const_key && (is_set || !has_const_value); - static const bool is_modifiable_map = has_const_key && !has_const_value; - static const bool is_const_map = has_const_key && has_const_value; + static constexpr bool is_modifiable_map = has_const_key && !has_const_value; + static constexpr bool is_const_map = has_const_key && has_const_value; using insert_result = UnorderedMapInsertResult; @@ -337,27 +337,27 @@ class UnorderedMap { Impl::get_property(prop_copy) + " - size")); m_available_indexes = - bitset_type(Kokkos::Impl::with_updated_label(prop_copy, " - bitset"), + bitset_type(Kokkos::Impl::append_to_label(prop_copy, " - bitset"), calculate_capacity(capacity_hint)); m_hash_lists = size_type_view( - Kokkos::Impl::with_updated_label(prop_copy_noinit, " - hash list"), + Kokkos::Impl::append_to_label(prop_copy_noinit, " - hash list"), Impl::find_hash_size(capacity())); m_next_index = size_type_view( - Kokkos::Impl::with_updated_label(prop_copy_noinit, " - next index"), + Kokkos::Impl::append_to_label(prop_copy_noinit, " - next index"), capacity() + 1); // +1 so that the *_at functions can always return a // valid reference - m_keys = key_type_view( - Kokkos::Impl::with_updated_label(prop_copy, " - keys"), capacity()); + m_keys = key_type_view(Kokkos::Impl::append_to_label(prop_copy, " - keys"), + capacity()); - m_values = value_type_view( - Kokkos::Impl::with_updated_label(prop_copy, " - values"), - is_set ? 0 : capacity()); + m_values = + value_type_view(Kokkos::Impl::append_to_label(prop_copy, " - values"), + is_set ? 0 : capacity()); m_scalars = - scalars_view(Kokkos::Impl::with_updated_label(prop_copy, " - scalars")); + scalars_view(Kokkos::Impl::append_to_label(prop_copy, " - scalars")); /** * Deep copies should also be done using the space instance if given. diff --git a/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp b/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp index 8f8cd9523b..a979ee40d8 100644 --- a/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp +++ b/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp @@ -27,6 +27,18 @@ namespace Kokkos { namespace Impl { +//! Append to the label contained in view_ctor_prop. +template +auto append_to_label(const ViewCtorProp& view_ctor_prop, + const std::string& label) { + using vcp_t = ViewCtorProp; + static_assert(vcp_t::has_label); + vcp_t new_ctor_props(view_ctor_prop); + static_cast&>(new_ctor_props) + .value.append(label); + return new_ctor_props; +} + uint32_t find_hash_size(uint32_t size); template diff --git a/lib/kokkos/containers/unit_tests/Makefile b/lib/kokkos/containers/unit_tests/Makefile index 2e35832cc8..18410882bc 100644 --- a/lib/kokkos/containers/unit_tests/Makefile +++ b/lib/kokkos/containers/unit_tests/Makefile @@ -35,8 +35,8 @@ TESTS = Bitset DualView DynamicView DynViewAPI_generic DynViewAPI_rank12345 DynV tmp := $(foreach device, $(KOKKOS_DEVICELIST), \ tmp2 := $(foreach test, $(TESTS), \ $(if $(filter Test$(device)_$(test).cpp, $(shell ls Test$(device)_$(test).cpp 2>/dev/null)),,\ - $(shell echo "\#include" > Test$(device)_$(test).cpp); \ - $(shell echo "\#include" >> Test$(device)_$(test).cpp); \ + $(shell echo "$(H)include" > Test$(device)_$(test).cpp); \ + $(shell echo "$(H)include" >> Test$(device)_$(test).cpp); \ )\ ) \ ) diff --git a/lib/kokkos/containers/unit_tests/TestBitset.hpp b/lib/kokkos/containers/unit_tests/TestBitset.hpp index 3ad0d2bf57..9923453f72 100644 --- a/lib/kokkos/containers/unit_tests/TestBitset.hpp +++ b/lib/kokkos/containers/unit_tests/TestBitset.hpp @@ -23,6 +23,8 @@ #include #include +#include <../../core/unit_test/tools/include/ToolTestingUtilities.hpp> + namespace Test { namespace Impl { @@ -155,7 +157,7 @@ void test_bitset() { { unsigned ts = 100u; - bitset_type b1; + bitset_type b1(Kokkos::view_alloc("MyBitset"), 0); ASSERT_TRUE(b1.is_allocated()); b1 = bitset_type(ts); @@ -165,6 +167,9 @@ void test_bitset() { ASSERT_TRUE(b1.is_allocated()); ASSERT_TRUE(b2.is_allocated()); ASSERT_TRUE(b3.is_allocated()); + + bitset_type b4; + ASSERT_FALSE(b4.is_allocated()); } std::array test_sizes = { @@ -237,6 +242,24 @@ void test_bitset() { } TEST(TEST_CATEGORY, bitset) { test_bitset(); } + +TEST(TEST_CATEGORY, bitset_default_constructor_no_alloc) { + using namespace Kokkos::Test::Tools; + listen_tool_events(Config::DisableAll(), Config::EnableAllocs()); + + auto success = validate_absence( + [&]() { + Kokkos::Bitset bs; + EXPECT_FALSE(bs.is_allocated()); + }, + [&](AllocateDataEvent) { + return MatchDiagnostic{true, {"Found alloc event"}}; + }); + ASSERT_TRUE(success); + + listen_tool_events(Config::DisableAll()); +} + } // namespace Test #endif // KOKKOS_TEST_BITSET_HPP diff --git a/lib/kokkos/core/perf_test/CMakeLists.txt b/lib/kokkos/core/perf_test/CMakeLists.txt index 7f3916da31..e0dba03e1e 100644 --- a/lib/kokkos/core/perf_test/CMakeLists.txt +++ b/lib/kokkos/core/perf_test/CMakeLists.txt @@ -50,8 +50,8 @@ ELSE() FetchContent_Declare( googlebenchmark DOWNLOAD_EXTRACT_TIMESTAMP FALSE - URL https://github.com/google/benchmark/archive/refs/tags/v1.6.2.tar.gz - URL_HASH MD5=14d14849e075af116143a161bc3b927b + URL https://github.com/google/benchmark/archive/refs/tags/v1.7.1.tar.gz + URL_HASH MD5=0459a6c530df9851bee6504c3e37c2e7 ) FetchContent_MakeAvailable(googlebenchmark) list(POP_BACK CMAKE_MESSAGE_INDENT) diff --git a/lib/kokkos/core/src/CMakeLists.txt b/lib/kokkos/core/src/CMakeLists.txt index 012af0a7d0..b84677e61b 100644 --- a/lib/kokkos/core/src/CMakeLists.txt +++ b/lib/kokkos/core/src/CMakeLists.txt @@ -18,10 +18,16 @@ IF (NOT desul_FOUND) ENDIF() IF(KOKKOS_ENABLE_SYCL) SET(DESUL_ATOMICS_ENABLE_SYCL ON) + IF(KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED AND NOT KOKKOS_IMPL_HAVE_SYCL_EXT_ONEAPI_DEVICE_GLOBAL) + SET(DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION ON) + ENDIF() ENDIF() IF(KOKKOS_ENABLE_OPENMPTARGET) SET(DESUL_ATOMICS_ENABLE_OPENMP ON) # not a typo Kokkos OpenMPTarget -> Desul OpenMP ENDIF() + IF(KOKKOS_ENABLE_OPENACC) + SET(DESUL_ATOMICS_ENABLE_OPENACC ON) + ENDIF() CONFIGURE_FILE( ${CMAKE_CURRENT_SOURCE_DIR}/../../tpls/desul/Config.hpp.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/desul/atomics/Config.hpp @@ -80,10 +86,6 @@ IF (KOKKOS_ENABLE_HPX) APPEND_GLOB(KOKKOS_CORE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/HPX/*.hpp) ENDIF() -IF (NOT KOKKOS_ENABLE_MEMKIND) - LIST(REMOVE_ITEM KOKKOS_CORE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/impl/Kokkos_HBWSpace.cpp) -ENDIF() - IF (KOKKOS_ENABLE_SERIAL) APPEND_GLOB(KOKKOS_CORE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/Serial/*.cpp) APPEND_GLOB(KOKKOS_CORE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/Serial/*.hpp) @@ -180,20 +182,15 @@ IF (Kokkos_ENABLE_IMPL_MDSPAN) ENDIF() KOKKOS_LINK_TPL(kokkoscore PUBLIC HWLOC) -KOKKOS_LINK_TPL(kokkoscore PUBLIC MEMKIND) -IF (NOT KOKKOS_ENABLE_COMPILE_AS_CMAKE_LANGUAGE) - KOKKOS_LINK_TPL(kokkoscore PUBLIC CUDA) -ENDIF() +KOKKOS_LINK_TPL(kokkoscore PUBLIC CUDA) KOKKOS_LINK_TPL(kokkoscore PUBLIC HPX) KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBDL) -KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBRT) # On *nix-like systems (Linux, macOS) we need pthread for C++ std::thread IF (NOT WIN32) KOKKOS_LINK_TPL(kokkoscore PUBLIC THREADS) ENDIF() IF (NOT KOKKOS_ENABLE_COMPILE_AS_CMAKE_LANGUAGE) KOKKOS_LINK_TPL(kokkoscore PUBLIC ROCM) - KOKKOS_LINK_TPL(kokkoscore PUBLIC ONEDPL) ENDIF() # FIXME: We need a proper solution to figure out whether to enable diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda.hpp index 8bfaf8317b..276d03da26 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda.hpp @@ -46,7 +46,6 @@ static_assert(false, namespace Kokkos { namespace Impl { -class CudaExec; class CudaInternal; } // namespace Impl } // namespace Kokkos @@ -129,33 +128,16 @@ class Cuda { /// \brief True if and only if this method is being called in a /// thread-parallel function. - KOKKOS_INLINE_FUNCTION static int in_parallel() { + +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED KOKKOS_INLINE_FUNCTION static int in_parallel() { #if defined(__CUDA_ARCH__) return true; #else return false; #endif } - - /** \brief Set the device in a "sleep" state. - * - * This function sets the device in a "sleep" state in which it is - * not ready for work. This may consume less resources than if the - * device were in an "awake" state, but it may also take time to - * bring the device from a sleep state to be ready for work. - * - * \return True if the device is in the "sleep" state, else false if - * the device is actively working and could not enter the "sleep" - * state. - */ - static bool sleep(); - - /// \brief Wake the device from the 'sleep' state so it is ready for work. - /// - /// \return True if the device is in the "ready" state, else "false" - /// if the device is actively working (which also means that it's - /// awake). - static bool wake(); +#endif /// \brief Wait until all dispatched functors complete. /// @@ -199,18 +181,37 @@ class Cuda { //! Initialize, telling the CUDA run-time library which device to use. static void impl_initialize(InitializationSettings const&); +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 /// \brief Cuda device architecture of the selected device. /// /// This matches the __CUDA_ARCH__ specification. - static size_type device_arch(); + KOKKOS_DEPRECATED static size_type device_arch() { + const cudaDeviceProp& cudaProp = Cuda().cuda_device_prop(); + return cudaProp.major * 100 + cudaProp.minor; + } //! Query device count. - static size_type detect_device_count(); + KOKKOS_DEPRECATED static size_type detect_device_count() { + int count; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceCount(&count)); + return count; + } /** \brief Detect the available devices and their architecture * as defined by the __CUDA_ARCH__ specification. */ - static std::vector detect_device_arch(); + KOKKOS_DEPRECATED static std::vector detect_device_arch() { + int count; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceCount(&count)); + std::vector out; + for (int i = 0; i < count; ++i) { + cudaDeviceProp prop; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceProperties(&prop, i)); + out.push_back(prop.major * 100 + prop.minor); + } + return out; + } +#endif cudaStream_t cuda_stream() const; int cuda_device() const; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp index c6512f44da..0944937e1b 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp @@ -33,7 +33,6 @@ //#include #include -#include #include @@ -83,11 +82,11 @@ void DeepCopyAsyncCuda(void *dst, const void *src, size_t n) { KOKKOS_IMPL_CUDA_SAFE_CALL( (CudaInternal::singleton().cuda_memcpy_async_wrapper( dst, src, n, cudaMemcpyDefault, s))); - Impl::cuda_stream_synchronize( - s, + Kokkos::Tools::Experimental::Impl::profile_fence_event( + "Kokkos::Impl::DeepCopyAsyncCuda: Deep Copy Stream Sync", Kokkos::Tools::Experimental::SpecialSynchronizationCases:: DeepCopyResourceSynchronization, - "Kokkos::Impl::DeepCopyAsyncCuda: Deep Copy Stream Sync"); + [&]() { KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamSynchronize(s)); }); } } // namespace Impl @@ -135,11 +134,23 @@ void kokkos_impl_cuda_set_pin_uvm_to_host(bool val) { namespace Kokkos { -CudaSpace::CudaSpace() : m_device(Kokkos::Cuda().cuda_device()) {} +CudaSpace::CudaSpace() + : m_device(Kokkos::Cuda().cuda_device()), + m_stream(Kokkos::Cuda().cuda_stream()) {} +CudaSpace::CudaSpace(int device_id, cudaStream_t stream) + : m_device(device_id), m_stream(stream) {} -CudaUVMSpace::CudaUVMSpace() : m_device(Kokkos::Cuda().cuda_device()) {} +CudaUVMSpace::CudaUVMSpace() + : m_device(Kokkos::Cuda().cuda_device()), + m_stream(Kokkos::Cuda().cuda_stream()) {} +CudaUVMSpace::CudaUVMSpace(int device_id, cudaStream_t stream) + : m_device(device_id), m_stream(stream) {} -CudaHostPinnedSpace::CudaHostPinnedSpace() {} +CudaHostPinnedSpace::CudaHostPinnedSpace() + : m_device(Kokkos::Cuda().cuda_device()), + m_stream(Kokkos::Cuda().cuda_stream()) {} +CudaHostPinnedSpace::CudaHostPinnedSpace(int device_id, cudaStream_t stream) + : m_device(device_id), m_stream(stream) {} size_t memory_threshold_g = 40000; // 40 kB @@ -161,52 +172,38 @@ void *CudaSpace::allocate(const char *arg_label, const size_t arg_alloc_size, } namespace { -void *impl_allocate_common(const Cuda &exec_space, const char *arg_label, - const size_t arg_alloc_size, +void *impl_allocate_common(const int device_id, + [[maybe_unused]] const cudaStream_t stream, + const char *arg_label, const size_t arg_alloc_size, const size_t arg_logical_size, const Kokkos::Tools::SpaceHandle arg_handle, - bool exec_space_provided) { + [[maybe_unused]] bool stream_sync_only) { void *ptr = nullptr; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(device_id)); + cudaError_t error_code = cudaSuccess; #ifndef CUDART_VERSION #error CUDART_VERSION undefined! #elif (defined(KOKKOS_ENABLE_IMPL_CUDA_MALLOC_ASYNC) && CUDART_VERSION >= 11020) - cudaError_t error_code; if (arg_alloc_size >= memory_threshold_g) { - if (exec_space_provided) { - error_code = - exec_space.impl_internal_space_instance()->cuda_malloc_async_wrapper( - &ptr, arg_alloc_size); - exec_space.fence("Kokkos::Cuda: backend fence after async malloc"); - } else { - error_code = Impl::CudaInternal::singleton().cuda_malloc_async_wrapper( - &ptr, arg_alloc_size); - Impl::cuda_device_synchronize( - "Kokkos::Cuda: backend fence after async malloc"); + error_code = cudaMallocAsync(&ptr, arg_alloc_size, stream); + + if (error_code == cudaSuccess) { + if (stream_sync_only) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamSynchronize(stream)); + } else { + Impl::cuda_device_synchronize( + "Kokkos::Cuda: backend fence after async malloc"); + } } - } else { - error_code = - (exec_space_provided - ? exec_space.impl_internal_space_instance()->cuda_malloc_wrapper( - &ptr, arg_alloc_size) - : Impl::CudaInternal::singleton().cuda_malloc_wrapper( - &ptr, arg_alloc_size)); - } -#else - cudaError_t error_code; - if (exec_space_provided) { - error_code = exec_space.impl_internal_space_instance()->cuda_malloc_wrapper( - &ptr, arg_alloc_size); - } else { - error_code = Impl::CudaInternal::singleton().cuda_malloc_wrapper( - &ptr, arg_alloc_size); - } + } else #endif + { error_code = cudaMalloc(&ptr, arg_alloc_size); } if (error_code != cudaSuccess) { // TODO tag as unlikely branch // This is the only way to clear the last error, which // we should do here since we're turning it into an // exception here - exec_space.impl_internal_space_instance()->cuda_get_last_error_wrapper(); + cudaGetLastError(); throw Experimental::CudaRawMemoryAllocationFailure( arg_alloc_size, error_code, Experimental::RawMemoryAllocationFailure::AllocationMechanism:: @@ -226,7 +223,7 @@ void *CudaSpace::impl_allocate( const char *arg_label, const size_t arg_alloc_size, const size_t arg_logical_size, const Kokkos::Tools::SpaceHandle arg_handle) const { - return impl_allocate_common(Kokkos::Cuda{}, arg_label, arg_alloc_size, + return impl_allocate_common(m_device, m_stream, arg_label, arg_alloc_size, arg_logical_size, arg_handle, false); } @@ -234,8 +231,9 @@ void *CudaSpace::impl_allocate( const Cuda &exec_space, const char *arg_label, const size_t arg_alloc_size, const size_t arg_logical_size, const Kokkos::Tools::SpaceHandle arg_handle) const { - return impl_allocate_common(exec_space, arg_label, arg_alloc_size, - arg_logical_size, arg_handle, true); + return impl_allocate_common( + exec_space.cuda_device(), exec_space.cuda_stream(), arg_label, + arg_alloc_size, arg_logical_size, arg_handle, true); } void *CudaUVMSpace::allocate(const size_t arg_alloc_size) const { @@ -256,28 +254,27 @@ void *CudaUVMSpace::impl_allocate( if (arg_alloc_size > 0) { Kokkos::Impl::num_uvm_allocations++; - auto error_code = - Impl::CudaInternal::singleton().cuda_malloc_managed_wrapper( - &ptr, arg_alloc_size, cudaMemAttachGlobal); - -#ifdef KOKKOS_IMPL_DEBUG_CUDA_PIN_UVM_TO_HOST - if (Kokkos::CudaUVMSpace::cuda_pin_uvm_to_host()) - KOKKOS_IMPL_CUDA_SAFE_CALL( - (Impl::CudaInternal::singleton().cuda_mem_advise_wrapper( - ptr, arg_alloc_size, cudaMemAdviseSetPreferredLocation, - cudaCpuDeviceId))); -#endif + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_device)); + cudaError_t error_code = + cudaMallocManaged(&ptr, arg_alloc_size, cudaMemAttachGlobal); if (error_code != cudaSuccess) { // TODO tag as unlikely branch // This is the only way to clear the last error, which // we should do here since we're turning it into an // exception here - Impl::CudaInternal::singleton().cuda_get_last_error_wrapper(); + cudaGetLastError(); throw Experimental::CudaRawMemoryAllocationFailure( arg_alloc_size, error_code, Experimental::RawMemoryAllocationFailure::AllocationMechanism:: CudaMallocManaged); } + +#ifdef KOKKOS_IMPL_DEBUG_CUDA_PIN_UVM_TO_HOST + if (Kokkos::CudaUVMSpace::cuda_pin_uvm_to_host()) + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMemAdvise(ptr, arg_alloc_size, cudaMemAdviseSetPreferredLocation, + cudaCpuDeviceId)); +#endif } Cuda::impl_static_fence( "Kokkos::CudaUVMSpace::impl_allocate: Post UVM Allocation"); @@ -302,13 +299,14 @@ void *CudaHostPinnedSpace::impl_allocate( const Kokkos::Tools::SpaceHandle arg_handle) const { void *ptr = nullptr; - auto error_code = Impl::CudaInternal::singleton().cuda_host_alloc_wrapper( - &ptr, arg_alloc_size, cudaHostAllocDefault); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_device)); + cudaError_t error_code = + cudaHostAlloc(&ptr, arg_alloc_size, cudaHostAllocDefault); if (error_code != cudaSuccess) { // TODO tag as unlikely branch // This is the only way to clear the last error, which // we should do here since we're turning it into an // exception here - Impl::CudaInternal::singleton().cuda_get_last_error_wrapper(); + cudaGetLastError(); throw Experimental::CudaRawMemoryAllocationFailure( arg_alloc_size, error_code, Experimental::RawMemoryAllocationFailure::AllocationMechanism:: @@ -350,18 +348,17 @@ void CudaSpace::impl_deallocate( if (arg_alloc_size >= memory_threshold_g) { Impl::cuda_device_synchronize( "Kokkos::Cuda: backend fence before async free"); - KOKKOS_IMPL_CUDA_SAFE_CALL( - (Impl::CudaInternal::singleton().cuda_free_async_wrapper( - arg_alloc_ptr))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFreeAsync(arg_alloc_ptr, m_stream)); Impl::cuda_device_synchronize( "Kokkos::Cuda: backend fence after async free"); } else { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (Impl::CudaInternal::singleton().cuda_free_wrapper(arg_alloc_ptr))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); } #else - KOKKOS_IMPL_CUDA_SAFE_CALL( - (Impl::CudaInternal::singleton().cuda_free_wrapper(arg_alloc_ptr))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); #endif } catch (...) { } @@ -393,8 +390,8 @@ void CudaUVMSpace::impl_deallocate( try { if (arg_alloc_ptr != nullptr) { Kokkos::Impl::num_uvm_allocations--; - KOKKOS_IMPL_CUDA_SAFE_CALL( - (Impl::CudaInternal::singleton().cuda_free_wrapper(arg_alloc_ptr))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(arg_alloc_ptr)); } } catch (...) { } @@ -424,8 +421,8 @@ void CudaHostPinnedSpace::impl_deallocate( reported_size); } try { - KOKKOS_IMPL_CUDA_SAFE_CALL(( - Impl::CudaInternal::singleton().cuda_free_host_wrapper(arg_alloc_ptr))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFreeHost(arg_alloc_ptr)); } catch (...) { } } @@ -438,160 +435,6 @@ void CudaHostPinnedSpace::impl_deallocate( namespace Kokkos { namespace Impl { -#ifdef KOKKOS_ENABLE_DEBUG -SharedAllocationRecord - SharedAllocationRecord::s_root_record; - -SharedAllocationRecord - SharedAllocationRecord::s_root_record; - -SharedAllocationRecord - SharedAllocationRecord::s_root_record; -#endif - -//============================================================================== -// {{{1 - -SharedAllocationRecord::~SharedAllocationRecord() { - auto alloc_size = SharedAllocationRecord::m_alloc_size; - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - alloc_size, (alloc_size - sizeof(SharedAllocationHeader))); -} - -void SharedAllocationRecord::deep_copy_header_no_exec( - void *ptr, const void *header) { - Kokkos::Cuda exec; - Kokkos::Impl::DeepCopy(exec, ptr, header, - sizeof(SharedAllocationHeader)); - exec.fence( - "SharedAllocationRecord::SharedAllocationRecord(): fence after copying header from " - "HostSpace"); -} - -SharedAllocationRecord::~SharedAllocationRecord() { - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - SharedAllocationRecord::m_alloc_size, - (SharedAllocationRecord::m_alloc_size - - sizeof(SharedAllocationHeader))); -} - -SharedAllocationRecord::~SharedAllocationRecord() { - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - SharedAllocationRecord::m_alloc_size, - (SharedAllocationRecord::m_alloc_size - - sizeof(SharedAllocationHeader))); -} - -// end SharedAllocationRecord destructors }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -SharedAllocationRecord::SharedAllocationRecord( - const Kokkos::CudaSpace &arg_space, const std::string &arg_label, - const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - // Copy to device memory - Kokkos::Cuda exec; - Kokkos::Impl::DeepCopy( - exec, RecordBase::m_alloc_ptr, &header, sizeof(SharedAllocationHeader)); - exec.fence( - "SharedAllocationRecord::SharedAllocationRecord(): fence after copying header from " - "HostSpace"); -} - -SharedAllocationRecord::SharedAllocationRecord( - const Kokkos::Cuda &arg_exec_space, const Kokkos::CudaSpace &arg_space, - const std::string &arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_exec_space, arg_space, - arg_label, arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - // Copy to device memory - Kokkos::Impl::DeepCopy(arg_exec_space, - RecordBase::m_alloc_ptr, &header, - sizeof(SharedAllocationHeader)); -} - -SharedAllocationRecord::SharedAllocationRecord( - const Kokkos::CudaUVMSpace &arg_space, const std::string &arg_label, - const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::CudaHostPinnedSpace &arg_space, - const std::string &arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); -} - -// end SharedAllocationRecord constructors }}}1 -//============================================================================== - void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, bool to_device) { if ((ptr == nullptr) || (bytes == 0)) return; @@ -620,19 +463,12 @@ void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, #include -namespace Kokkos { -namespace Impl { - -// To avoid additional compilation cost for something that's (mostly?) not -// performance sensitive, we explicity instantiate these CRTP base classes here, -// where we have access to the associated *_timpl.hpp header files. -template class SharedAllocationRecordCommon; -template class HostInaccessibleSharedAllocationRecordCommon; -template class SharedAllocationRecordCommon; -template class SharedAllocationRecordCommon; - -} // end namespace Impl -} // end namespace Kokkos +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::CudaSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::CudaUVMSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::CudaHostPinnedSpace); // end Explicit instantiations of CRTP Base classes }}}1 //============================================================================== diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.hpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.hpp index b8fa335cd3..0e20193e8b 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.hpp @@ -68,6 +68,11 @@ class CudaSpace { /*--------------------------------*/ CudaSpace(); + + private: + CudaSpace(int device_id, cudaStream_t stream); + + public: CudaSpace(CudaSpace&& rhs) = default; CudaSpace(const CudaSpace& rhs) = default; CudaSpace& operator=(CudaSpace&& rhs) = default; @@ -89,9 +94,11 @@ class CudaSpace { const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; + static CudaSpace impl_create(int device_id, cudaStream_t stream) { + return CudaSpace(device_id, stream); + } + private: - template - friend class Kokkos::Experimental::LogicalMemorySpace; void* impl_allocate(const Cuda& exec_space, const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0, @@ -112,10 +119,10 @@ class CudaSpace { static constexpr const char* name() { return m_name; } private: - int m_device; ///< Which Cuda device + int m_device; + cudaStream_t m_stream; static constexpr const char* m_name = "Cuda"; - friend class Kokkos::Impl::SharedAllocationRecord; }; template <> @@ -149,6 +156,11 @@ class CudaUVMSpace { /*--------------------------------*/ CudaUVMSpace(); + + private: + CudaUVMSpace(int device_id, cudaStream_t stream); + + public: CudaUVMSpace(CudaUVMSpace&& rhs) = default; CudaUVMSpace(const CudaUVMSpace& rhs) = default; CudaUVMSpace& operator=(CudaUVMSpace&& rhs) = default; @@ -156,6 +168,16 @@ class CudaUVMSpace { ~CudaUVMSpace() = default; /**\brief Allocate untracked memory in the cuda space */ + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const size_t arg_alloc_size) const; void* allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; @@ -167,8 +189,6 @@ class CudaUVMSpace { const size_t arg_logical_size = 0) const; private: - template - friend class Kokkos::Experimental::LogicalMemorySpace; void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0, const Kokkos::Tools::SpaceHandle = @@ -189,8 +209,13 @@ class CudaUVMSpace { #endif /*--------------------------------*/ + static CudaUVMSpace impl_create(int device_id, cudaStream_t stream) { + return CudaUVMSpace(device_id, stream); + } + private: - int m_device; ///< Which Cuda device + int m_device; + cudaStream_t m_stream; #ifdef KOKKOS_IMPL_DEBUG_CUDA_PIN_UVM_TO_HOST static bool kokkos_impl_cuda_pin_uvm_to_host_v; @@ -223,6 +248,11 @@ class CudaHostPinnedSpace { /*--------------------------------*/ CudaHostPinnedSpace(); + + private: + CudaHostPinnedSpace(int device_id, cudaStream_t stream); + + public: CudaHostPinnedSpace(CudaHostPinnedSpace&& rhs) = default; CudaHostPinnedSpace(const CudaHostPinnedSpace& rhs) = default; CudaHostPinnedSpace& operator=(CudaHostPinnedSpace&& rhs) = default; @@ -230,6 +260,16 @@ class CudaHostPinnedSpace { ~CudaHostPinnedSpace() = default; /**\brief Allocate untracked memory in the space */ + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const size_t arg_alloc_size) const; void* allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; @@ -240,9 +280,11 @@ class CudaHostPinnedSpace { const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; + static CudaHostPinnedSpace impl_create(int device_id, cudaStream_t stream) { + return CudaHostPinnedSpace(device_id, stream); + } + private: - template - friend class Kokkos::Experimental::LogicalMemorySpace; void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0, const Kokkos::Tools::SpaceHandle = @@ -258,6 +300,9 @@ class CudaHostPinnedSpace { static constexpr const char* name() { return m_name; } private: + int m_device; + cudaStream_t m_stream; + static constexpr const char* m_name = "CudaHostPinned"; /*--------------------------------*/ @@ -280,15 +325,12 @@ const std::unique_ptr& cuda_get_deep_copy_space( bool initialize = true); static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); -static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::CudaSpace>::assignable); +static_assert(Kokkos::Impl::MemorySpaceAccess< + Kokkos::CudaUVMSpace, Kokkos::CudaUVMSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::CudaHostPinnedSpace>::assignable); //---------------------------------------- @@ -516,179 +558,10 @@ struct DeepCopy -class SharedAllocationRecord - : public HostInaccessibleSharedAllocationRecordCommon { - private: - friend class SharedAllocationRecord; - friend class SharedAllocationRecordCommon; - friend class HostInaccessibleSharedAllocationRecordCommon; - - using RecordBase = SharedAllocationRecord; - using base_t = - HostInaccessibleSharedAllocationRecordCommon; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - -#ifdef KOKKOS_ENABLE_DEBUG - static RecordBase s_root_record; -#endif - - const Kokkos::CudaSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - // This constructor does not forward to the one without exec_space arg - // in order to work around https://github.com/kokkos/kokkos/issues/5258 - // This constructor is templated so I can't just put it into the cpp file - // like the other constructor. - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, const Kokkos::CudaSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - // Copy to device memory - // workaround for issue with NVCC and MSVC - // https://github.com/kokkos/kokkos/issues/5258 - deep_copy_header_no_exec(RecordBase::m_alloc_ptr, &header); - } - - SharedAllocationRecord( - const Kokkos::Cuda& exec_space, const Kokkos::CudaSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); - - SharedAllocationRecord( - const Kokkos::CudaSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); - - // helper function to work around MSVC+NVCC issue - // https://github.com/kokkos/kokkos/issues/5258 - static void deep_copy_header_no_exec(void*, const void*); -}; - -template <> -class SharedAllocationRecord - : public SharedAllocationRecordCommon { - private: - friend class SharedAllocationRecordCommon; - - using base_t = SharedAllocationRecordCommon; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - - static RecordBase s_root_record; - - const Kokkos::CudaUVMSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - // This constructor does not forward to the one without exec_space arg - // in order to work around https://github.com/kokkos/kokkos/issues/5258 - // This constructor is templated so I can't just put it into the cpp file - // like the other constructor. - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, - const Kokkos::CudaUVMSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); - } - - SharedAllocationRecord( - const Kokkos::CudaUVMSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; - -template <> -class SharedAllocationRecord - : public SharedAllocationRecordCommon { - private: - friend class SharedAllocationRecordCommon; - - using RecordBase = SharedAllocationRecord; - using base_t = SharedAllocationRecordCommon; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - - static RecordBase s_root_record; - - const Kokkos::CudaHostPinnedSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - // This constructor does not forward to the one without exec_space arg - // in order to work around https://github.com/kokkos/kokkos/issues/5258 - // This constructor is templated so I can't just put it into the cpp file - // like the other constructor. - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, - const Kokkos::CudaHostPinnedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); - } - - SharedAllocationRecord( - const Kokkos::CudaHostPinnedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; - -} // namespace Impl -} // namespace Kokkos +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_SPECIALIZATION( + Kokkos::CudaSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION(Kokkos::CudaUVMSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION(Kokkos::CudaHostPinnedSpace); //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp index f68e05f780..c4458c910c 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp @@ -27,10 +27,6 @@ namespace Kokkos { namespace Impl { -void cuda_stream_synchronize( - const cudaStream_t stream, - Kokkos::Tools::Experimental::SpecialSynchronizationCases reason, - const std::string& name); void cuda_device_synchronize(const std::string& name); void cuda_stream_synchronize(const cudaStream_t stream, const std::string& name); diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_GraphNodeKernel.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_GraphNodeKernel.hpp index a4d064e544..5a821ab64a 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_GraphNodeKernel.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_GraphNodeKernel.hpp @@ -23,8 +23,7 @@ #include -#include // GraphAccess needs to be complete -#include // SharedAllocationRecord +#include // GraphAccess needs to be complete #include #include @@ -50,10 +49,6 @@ class GraphNodeKernelImpl m_graph_ptr = nullptr; Kokkos::ObservingRawPtr m_graph_node_ptr = nullptr; - // Note: owned pointer to CudaSpace memory (used for global memory launches), - // which we're responsible for deallocating, but not responsible for calling - // its destructor. - using Record = Kokkos::Impl::SharedAllocationRecord; // Basically, we have to make this mutable for the same reasons that the // global kernel buffers in the Cuda instance are mutable... mutable Kokkos::OwningRawPtr m_driver_storage = nullptr; @@ -82,9 +77,7 @@ class GraphNodeKernelImpl allocate_driver_memory_buffer() const { KOKKOS_EXPECTS(m_driver_storage == nullptr) - - auto* record = Record::allocate( - Kokkos::CudaSpace{}, "GraphNodeKernel global memory functor storage", - sizeof(base_t)); - - Record::increment(record); - m_driver_storage = reinterpret_cast(record->data()); + m_driver_storage = static_cast(Kokkos::CudaSpace().allocate( + "GraphNodeKernel global memory functor storage", sizeof(base_t))); KOKKOS_ENSURES(m_driver_storage != nullptr) return m_driver_storage; } diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp index d7f853d991..849e8b3b30 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp @@ -26,10 +26,10 @@ #include -#include -#include -#include -#include +//#include +//#include +//#include +//#include #include #include #include @@ -97,21 +97,21 @@ __global__ void query_cuda_kernel_arch(int *d_arch) { } /** Query what compute capability is actually launched to the device: */ -int cuda_kernel_arch() { +int cuda_kernel_arch(int device_id) { int arch = 0; int *d_arch = nullptr; - KOKKOS_IMPL_CUDA_SAFE_CALL((CudaInternal::singleton().cuda_malloc_wrapper( - reinterpret_cast(&d_arch), sizeof(int)))); - KOKKOS_IMPL_CUDA_SAFE_CALL((CudaInternal::singleton().cuda_memcpy_wrapper( - d_arch, &arch, sizeof(int), cudaMemcpyDefault))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(device_id)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMalloc(reinterpret_cast(&d_arch), sizeof(int))); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMemcpy(d_arch, &arch, sizeof(int), cudaMemcpyDefault)); query_cuda_kernel_arch<<<1, 1>>>(d_arch); - KOKKOS_IMPL_CUDA_SAFE_CALL((CudaInternal::singleton().cuda_memcpy_wrapper( - &arch, d_arch, sizeof(int), cudaMemcpyDefault))); KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_free_wrapper(d_arch))); + cudaMemcpy(&arch, d_arch, sizeof(int), cudaMemcpyDefault)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(d_arch)); return arch; } @@ -135,7 +135,6 @@ Kokkos::View cuda_global_unique_token_locks( return locks; } -// FIXME_CUDA_MULTIPLE_DEVICES void cuda_device_synchronize(const std::string &name) { Kokkos::Tools::Experimental::Impl::profile_fence_event( name, @@ -144,16 +143,16 @@ void cuda_device_synchronize(const std::string &name) { #if defined(KOKKOS_COMPILER_CLANG) // annotate with __host__ silence a clang warning about using // cudaDeviceSynchronize in device code - [] __host__() { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_synchronize_wrapper())); - }); + [] __host__() #else - []() { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_synchronize_wrapper())); - }); + []() #endif + { + for (int cuda_device : Kokkos::Impl::CudaInternal::cuda_devices) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(cuda_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaDeviceSynchronize()); + } + }); } void cuda_stream_synchronize(const cudaStream_t stream, const CudaInternal *ptr, @@ -168,25 +167,11 @@ void cuda_stream_synchronize(const cudaStream_t stream, const CudaInternal *ptr, }); } -void cuda_stream_synchronize( - const cudaStream_t stream, - Kokkos::Tools::Experimental::SpecialSynchronizationCases reason, - const std::string &name) { - Kokkos::Tools::Experimental::Impl::profile_fence_event( - name, reason, [&]() { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (Impl::CudaInternal::singleton().cuda_stream_synchronize_wrapper( - stream))); - }); -} - void cuda_internal_error_throw(cudaError e, const char *name, const char *file, const int line) { std::ostringstream out; - out << name << " error( " - << CudaInternal::singleton().cuda_get_error_name_wrapper(e) - << "): " - << CudaInternal::singleton().cuda_get_error_string_wrapper(e); + out << name << " error( " << cudaGetErrorName(e) + << "): " << cudaGetErrorString(e); if (file) { out << " " << file << ":" << line; } @@ -196,10 +181,8 @@ void cuda_internal_error_throw(cudaError e, const char *name, const char *file, void cuda_internal_error_abort(cudaError e, const char *name, const char *file, const int line) { std::ostringstream out; - out << name << " error( " - << CudaInternal::singleton().cuda_get_error_name_wrapper(e) - << "): " - << CudaInternal::singleton().cuda_get_error_string_wrapper(e); + out << name << " error( " << cudaGetErrorName(e) + << "): " << cudaGetErrorString(e); if (file) { out << " " << file << ":" << line; } @@ -208,96 +191,6 @@ void cuda_internal_error_abort(cudaError e, const char *name, const char *file, host_abort(out.str().c_str()); } -//---------------------------------------------------------------------------- -// Some significant cuda device properties: -// -// cudaDeviceProp::name : Text label for device -// cudaDeviceProp::major : Device major number -// cudaDeviceProp::minor : Device minor number -// cudaDeviceProp::warpSize : number of threads per warp -// cudaDeviceProp::multiProcessorCount : number of multiprocessors -// cudaDeviceProp::sharedMemPerBlock : capacity of shared memory per block -// cudaDeviceProp::totalConstMem : capacity of constant memory -// cudaDeviceProp::totalGlobalMem : capacity of global memory -// cudaDeviceProp::maxGridSize[3] : maximum grid size - -// -// Section 4.4.2.4 of the CUDA Toolkit Reference Manual -// -// struct cudaDeviceProp { -// char name[256]; -// size_t totalGlobalMem; -// size_t sharedMemPerBlock; -// int regsPerBlock; -// int warpSize; -// size_t memPitch; -// int maxThreadsPerBlock; -// int maxThreadsDim[3]; -// int maxGridSize[3]; -// size_t totalConstMem; -// int major; -// int minor; -// int clockRate; -// size_t textureAlignment; -// int deviceOverlap; -// int multiProcessorCount; -// int kernelExecTimeoutEnabled; -// int integrated; -// int canMapHostMemory; -// int computeMode; -// int concurrentKernels; -// int ECCEnabled; -// int pciBusID; -// int pciDeviceID; -// int tccDriver; -// int asyncEngineCount; -// int unifiedAddressing; -// int memoryClockRate; -// int memoryBusWidth; -// int l2CacheSize; -// int maxThreadsPerMultiProcessor; -// }; - -namespace { - -class CudaInternalDevices { - public: - enum { MAXIMUM_DEVICE_COUNT = 64 }; - struct cudaDeviceProp m_cudaProp[MAXIMUM_DEVICE_COUNT]; - int m_cudaDevCount; - - CudaInternalDevices(); - - static const CudaInternalDevices &singleton(); -}; - -CudaInternalDevices::CudaInternalDevices() { - // See 'cudaSetDeviceFlags' for host-device thread interaction - // Section 4.4.2.6 of the CUDA Toolkit Reference Manual - - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_get_device_count_wrapper( - &m_cudaDevCount))); - - if (m_cudaDevCount > MAXIMUM_DEVICE_COUNT) { - Kokkos::abort( - "Sorry, you have more GPUs per node than we thought anybody would ever " - "have. Please report this to github.com/kokkos/kokkos."); - } - for (int i = 0; i < m_cudaDevCount; ++i) { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_get_device_properties_wrapper( - m_cudaProp + i, i))); - } -} - -const CudaInternalDevices &CudaInternalDevices::singleton() { - static CudaInternalDevices self; - return self; -} - -} // namespace - //---------------------------------------------------------------------------- int Impl::CudaInternal::concurrency() { @@ -307,8 +200,6 @@ int Impl::CudaInternal::concurrency() { } void CudaInternal::print_configuration(std::ostream &s) const { - const CudaInternalDevices &dev_info = CudaInternalDevices::singleton(); - #if defined(KOKKOS_ENABLE_CUDA) s << "macro KOKKOS_ENABLE_CUDA : defined\n"; #endif @@ -317,22 +208,23 @@ void CudaInternal::print_configuration(std::ostream &s) const { << CUDA_VERSION / 1000 << "." << (CUDA_VERSION % 1000) / 10 << '\n'; #endif - for (int i = 0; i < dev_info.m_cudaDevCount; ++i) { - s << "Kokkos::Cuda[ " << i << " ] " << dev_info.m_cudaProp[i].name - << " capability " << dev_info.m_cudaProp[i].major << "." - << dev_info.m_cudaProp[i].minor << ", Total Global Memory: " - << human_memory_size(dev_info.m_cudaProp[i].totalGlobalMem) + for (int i : get_visible_devices()) { + cudaDeviceProp prop; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceProperties(&prop, i)); + s << "Kokkos::Cuda[ " << i << " ] " << prop.name << " capability " + << prop.major << "." << prop.minor + << ", Total Global Memory: " << human_memory_size(prop.totalGlobalMem) << ", Shared Memory per Block: " - << human_memory_size(dev_info.m_cudaProp[i].sharedMemPerBlock); + << human_memory_size(prop.sharedMemPerBlock); if (m_cudaDev == i) s << " : Selected"; - s << std::endl; + s << '\n'; } } //---------------------------------------------------------------------------- CudaInternal::~CudaInternal() { - if (m_stream || m_scratchSpace || m_scratchFlags || m_scratchUnified) { + if (m_scratchSpace || m_scratchFlags || m_scratchUnified) { std::cerr << "Kokkos::Cuda ERROR: Failed to call Kokkos::Cuda::finalize()" << std::endl; } @@ -370,45 +262,53 @@ void CudaInternal::fence() const { fence("Kokkos::CudaInternal::fence(): Unnamed Instance Fence"); } -void CudaInternal::initialize(cudaStream_t stream, bool manage_stream) { +void CudaInternal::initialize(cudaStream_t stream) { KOKKOS_EXPECTS(!is_initialized()); if (was_finalized) Kokkos::abort("Calling Cuda::initialize after Cuda::finalize is illegal\n"); was_initialized = true; + // Check that the device associated with the stream matches cuda_device + CUcontext context; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaError_t(cuStreamGetCtx(stream, &context))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaError_t(cuCtxPushCurrent(context))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaError_t(cuCtxGetDevice(&m_cudaDev))); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(m_cudaDev)); + + m_stream = stream; + CudaInternal::cuda_devices.insert(m_cudaDev); + + // Allocate a staging buffer for constant mem in pinned host memory + // and an event to avoid overwriting driver for previous kernel launches + if (!constantMemHostStagingPerDevice[m_cudaDev]) + KOKKOS_IMPL_CUDA_SAFE_CALL((cuda_malloc_host_wrapper( + reinterpret_cast(&constantMemHostStagingPerDevice[m_cudaDev]), + CudaTraits::ConstantMemoryUsage))); + + if (!constantMemReusablePerDevice[m_cudaDev]) + KOKKOS_IMPL_CUDA_SAFE_CALL( + (cuda_event_create_wrapper(&constantMemReusablePerDevice[m_cudaDev]))); + //---------------------------------- // Multiblock reduction uses scratch flags for counters // and scratch space for partial reduction values. // Allocate some initial space. This will grow as needed. { - const unsigned reduce_block_count = - m_maxWarpCount * Impl::CudaTraits::WarpSize; + // Maximum number of warps, + // at most one warp per thread in a warp for reduction. + auto const maxWarpCount = std::min( + m_deviceProp.maxThreadsPerBlock / CudaTraits::WarpSize, + CudaTraits::WarpSize); + unsigned const reduce_block_count = + maxWarpCount * Impl::CudaTraits::WarpSize; (void)scratch_unified(16 * sizeof(size_type)); (void)scratch_flags(reduce_block_count * 2 * sizeof(size_type)); (void)scratch_space(reduce_block_count * 16 * sizeof(size_type)); } - // Init the array for used for arbitrarily sized atomics - if (this == &singleton()) { - desul::Impl::init_lock_arrays(); // FIXME - } - - // Allocate a staging buffer for constant mem in pinned host memory - // and an event to avoid overwriting driver for previous kernel launches - if (this == &singleton()) { - KOKKOS_IMPL_CUDA_SAFE_CALL((cuda_malloc_host_wrapper( - reinterpret_cast(&constantMemHostStaging), - CudaTraits::ConstantMemoryUsage))); - - KOKKOS_IMPL_CUDA_SAFE_CALL( - (cuda_event_create_wrapper(&constantMemReusable))); - } - - m_stream = stream; - m_manage_stream = manage_stream; for (int i = 0; i < m_n_team_scratch; ++i) { m_team_scratch_current_size[i] = 0; m_team_scratch_ptr[i] = nullptr; @@ -427,22 +327,23 @@ void CudaInternal::initialize(cudaStream_t stream, bool manage_stream) { Cuda::size_type *CudaInternal::scratch_flags(const std::size_t size) const { if (verify_is_initialized("scratch_flags") && m_scratchFlagsCount < scratch_count(size)) { + auto mem_space = Kokkos::CudaSpace::impl_create(m_cudaDev, m_stream); + + if (m_scratchFlags) { + mem_space.deallocate(m_scratchFlags, + m_scratchFlagsCount * sizeScratchGrain); + } + m_scratchFlagsCount = scratch_count(size); - using Record = - Kokkos::Impl::SharedAllocationRecord; - - if (m_scratchFlags) Record::decrement(Record::get_record(m_scratchFlags)); - std::size_t alloc_size = multiply_overflow_abort(m_scratchFlagsCount, sizeScratchGrain); - Record *const r = Record::allocate( - Kokkos::CudaSpace(), "Kokkos::InternalScratchFlags", alloc_size); - - Record::increment(r); - - m_scratchFlags = reinterpret_cast(r->data()); + m_scratchFlags = static_cast( + mem_space.allocate("Kokkos::InternalScratchFlags", alloc_size)); + // We only zero-initialize the allocation when we actually allocate. + // It's the responsibility of the features using scratch_flags, + // namely parallel_reduce and parallel_scan, to reset the used values to 0. KOKKOS_IMPL_CUDA_SAFE_CALL( (cuda_memset_wrapper(m_scratchFlags, 0, alloc_size))); } @@ -453,21 +354,19 @@ Cuda::size_type *CudaInternal::scratch_flags(const std::size_t size) const { Cuda::size_type *CudaInternal::scratch_space(const std::size_t size) const { if (verify_is_initialized("scratch_space") && m_scratchSpaceCount < scratch_count(size)) { + auto mem_space = Kokkos::CudaSpace::impl_create(m_cudaDev, m_stream); + + if (m_scratchSpace) { + mem_space.deallocate(m_scratchSpace, + m_scratchSpaceCount * sizeScratchGrain); + } + m_scratchSpaceCount = scratch_count(size); - using Record = - Kokkos::Impl::SharedAllocationRecord; - - if (m_scratchSpace) Record::decrement(Record::get_record(m_scratchSpace)); - std::size_t alloc_size = multiply_overflow_abort(m_scratchSpaceCount, sizeScratchGrain); - Record *const r = Record::allocate( - Kokkos::CudaSpace(), "Kokkos::InternalScratchSpace", alloc_size); - - Record::increment(r); - - m_scratchSpace = reinterpret_cast(r->data()); + m_scratchSpace = static_cast( + mem_space.allocate("Kokkos::InternalScratchSpace", alloc_size)); } return m_scratchSpace; @@ -476,23 +375,20 @@ Cuda::size_type *CudaInternal::scratch_space(const std::size_t size) const { Cuda::size_type *CudaInternal::scratch_unified(const std::size_t size) const { if (verify_is_initialized("scratch_unified") && m_scratchUnifiedCount < scratch_count(size)) { + auto mem_space = + Kokkos::CudaHostPinnedSpace::impl_create(m_cudaDev, m_stream); + + if (m_scratchUnified) { + mem_space.deallocate(m_scratchUnified, + m_scratchUnifiedCount * sizeScratchGrain); + } + m_scratchUnifiedCount = scratch_count(size); - using Record = - Kokkos::Impl::SharedAllocationRecord; - - if (m_scratchUnified) - Record::decrement(Record::get_record(m_scratchUnified)); - std::size_t alloc_size = multiply_overflow_abort(m_scratchUnifiedCount, sizeScratchGrain); - Record *const r = - Record::allocate(Kokkos::CudaHostPinnedSpace(), - "Kokkos::InternalScratchUnified", alloc_size); - - Record::increment(r); - - m_scratchUnified = reinterpret_cast(r->data()); + m_scratchUnified = static_cast( + mem_space.allocate("Kokkos::InternalScratchUnified", alloc_size)); } return m_scratchUnified; @@ -500,21 +396,16 @@ Cuda::size_type *CudaInternal::scratch_unified(const std::size_t size) const { Cuda::size_type *CudaInternal::scratch_functor(const std::size_t size) const { if (verify_is_initialized("scratch_functor") && m_scratchFunctorSize < size) { + auto mem_space = Kokkos::CudaSpace::impl_create(m_cudaDev, m_stream); + + if (m_scratchFunctor) { + mem_space.deallocate(m_scratchFunctor, m_scratchFunctorSize); + } + m_scratchFunctorSize = size; - using Record = - Kokkos::Impl::SharedAllocationRecord; - - if (m_scratchFunctor) - Record::decrement(Record::get_record(m_scratchFunctor)); - - Record *const r = - Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchFunctor", - m_scratchFunctorSize); - - Record::increment(r); - - m_scratchFunctor = reinterpret_cast(r->data()); + m_scratchFunctor = static_cast(mem_space.allocate( + "Kokkos::InternalScratchFunctor", m_scratchFunctorSize)); } return m_scratchFunctor; @@ -537,21 +428,21 @@ void *CudaInternal::resize_team_scratch_space(int scratch_pool_id, // Multiple ParallelFor/Reduce Teams can call this function at the same time // and invalidate the m_team_scratch_ptr. We use a pool to avoid any race // condition. + auto mem_space = Kokkos::CudaSpace::impl_create(m_cudaDev, m_stream); if (m_team_scratch_current_size[scratch_pool_id] == 0) { m_team_scratch_current_size[scratch_pool_id] = bytes; m_team_scratch_ptr[scratch_pool_id] = - Kokkos::kokkos_malloc( - "Kokkos::CudaSpace::TeamScratchMemory", - m_team_scratch_current_size[scratch_pool_id]); + mem_space.allocate("Kokkos::CudaSpace::TeamScratchMemory", + m_team_scratch_current_size[scratch_pool_id]); } if ((bytes > m_team_scratch_current_size[scratch_pool_id]) || ((bytes < m_team_scratch_current_size[scratch_pool_id]) && (force_shrink))) { + mem_space.deallocate(m_team_scratch_ptr[scratch_pool_id], + m_team_scratch_current_size[scratch_pool_id]); m_team_scratch_current_size[scratch_pool_id] = bytes; m_team_scratch_ptr[scratch_pool_id] = - Kokkos::kokkos_realloc( - m_team_scratch_ptr[scratch_pool_id], - m_team_scratch_current_size[scratch_pool_id]); + mem_space.allocate("Kokkos::CudaSpace::TeamScratchMemory", bytes); } return m_team_scratch_ptr[scratch_pool_id]; } @@ -568,50 +459,33 @@ void CudaInternal::finalize() { was_finalized = true; - // Only finalize this if we're the singleton - if (this == &singleton()) { - (void)Impl::cuda_global_unique_token_locks(true); - desul::Impl::finalize_lock_arrays(); // FIXME - - KOKKOS_IMPL_CUDA_SAFE_CALL( - (cuda_free_host_wrapper(constantMemHostStaging))); - KOKKOS_IMPL_CUDA_SAFE_CALL( - (cuda_event_destroy_wrapper(constantMemReusable))); - auto &deep_copy_space = - Kokkos::Impl::cuda_get_deep_copy_space(/*initialize*/ false); - if (deep_copy_space) - deep_copy_space->impl_internal_space_instance()->finalize(); - KOKKOS_IMPL_CUDA_SAFE_CALL( - (cuda_stream_destroy_wrapper(cuda_get_deep_copy_stream()))); - } - + auto cuda_mem_space = Kokkos::CudaSpace::impl_create(m_cudaDev, m_stream); if (nullptr != m_scratchSpace || nullptr != m_scratchFlags) { - using RecordCuda = Kokkos::Impl::SharedAllocationRecord; - using RecordHost = - Kokkos::Impl::SharedAllocationRecord; - - RecordCuda::decrement(RecordCuda::get_record(m_scratchFlags)); - RecordCuda::decrement(RecordCuda::get_record(m_scratchSpace)); - RecordHost::decrement(RecordHost::get_record(m_scratchUnified)); - if (m_scratchFunctorSize > 0) - RecordCuda::decrement(RecordCuda::get_record(m_scratchFunctor)); + auto host_mem_space = + Kokkos::CudaHostPinnedSpace::impl_create(m_cudaDev, m_stream); + cuda_mem_space.deallocate(m_scratchFlags, + m_scratchFlagsCount * sizeScratchGrain); + cuda_mem_space.deallocate(m_scratchSpace, + m_scratchSpaceCount * sizeScratchGrain); + host_mem_space.deallocate(m_scratchUnified, + m_scratchUnifiedCount * sizeScratchGrain); + if (m_scratchFunctorSize > 0) { + cuda_mem_space.deallocate(m_scratchFunctor, m_scratchFunctorSize); + } } for (int i = 0; i < m_n_team_scratch; ++i) { if (m_team_scratch_current_size[i] > 0) - Kokkos::kokkos_free(m_team_scratch_ptr[i]); + cuda_mem_space.deallocate(m_team_scratch_ptr[i], + m_team_scratch_current_size[i]); } - if (m_manage_stream && get_stream() != nullptr) - KOKKOS_IMPL_CUDA_SAFE_CALL((cuda_stream_destroy_wrapper(m_stream))); - m_scratchSpaceCount = 0; m_scratchFlagsCount = 0; m_scratchUnifiedCount = 0; m_scratchSpace = nullptr; m_scratchFlags = nullptr; m_scratchUnified = nullptr; - m_stream = nullptr; for (int i = 0; i < m_n_team_scratch; ++i) { m_team_scratch_current_size[i] = 0; m_team_scratch_ptr[i] = nullptr; @@ -624,30 +498,6 @@ void CudaInternal::finalize() { //---------------------------------------------------------------------------- -Cuda::size_type cuda_internal_multiprocessor_count() { - return CudaInternal::singleton().m_multiProcCount; -} - -CudaSpace::size_type cuda_internal_maximum_concurrent_block_count() { -#if defined(KOKKOS_ARCH_KEPLER) - // Compute capability 3.0 through 3.7 - enum : int { max_resident_blocks_per_multiprocessor = 16 }; -#else - // Compute capability 5.0 through 6.2 - enum : int { max_resident_blocks_per_multiprocessor = 32 }; -#endif - return CudaInternal::singleton().m_multiProcCount * - max_resident_blocks_per_multiprocessor; -}; - -Cuda::size_type cuda_internal_maximum_warp_count() { - return CudaInternal::singleton().m_maxWarpCount; -} - -std::array cuda_internal_maximum_grid_count() { - return CudaInternal::singleton().m_maxBlock; -} - Cuda::size_type *cuda_internal_scratch_space(const Cuda &instance, const std::size_t size) { return instance.impl_internal_space_instance()->scratch_space(size); @@ -670,10 +520,6 @@ Cuda::size_type *cuda_internal_scratch_unified(const Cuda &instance, namespace Kokkos { -Cuda::size_type Cuda::detect_device_count() { - return Impl::CudaInternalDevices::singleton().m_cudaDevCount; -} - #ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 int Cuda::concurrency() { #else @@ -687,25 +533,23 @@ int Cuda::impl_is_initialized() { } void Cuda::impl_initialize(InitializationSettings const &settings) { - const int cuda_device_id = Impl::get_gpu(settings); - const auto &dev_info = Impl::CudaInternalDevices::singleton(); + const std::vector &visible_devices = Impl::get_visible_devices(); + const int cuda_device_id = + Impl::get_gpu(settings).value_or(visible_devices[0]); - const struct cudaDeviceProp &cudaProp = dev_info.m_cudaProp[cuda_device_id]; - - Impl::CudaInternal::m_cudaDev = cuda_device_id; + cudaDeviceProp cudaProp; + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaGetDeviceProperties(&cudaProp, cuda_device_id)); Impl::CudaInternal::m_deviceProp = cudaProp; - - Kokkos::Impl::cuda_device_synchronize( - "Kokkos::CudaInternal::initialize: Fence on space initialization"); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(cuda_device_id)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaDeviceSynchronize()); // Query what compute capability architecture a kernel executes: - Impl::CudaInternal::m_cudaArch = Impl::cuda_kernel_arch(); + Impl::CudaInternal::m_cudaArch = Impl::cuda_kernel_arch(cuda_device_id); if (Impl::CudaInternal::m_cudaArch == 0) { - std::stringstream ss; - ss << "Kokkos::Cuda::initialize ERROR: likely mismatch of architecture\n"; - std::string msg = ss.str(); - Kokkos::abort(msg.c_str()); + Kokkos::abort( + "Kokkos::Cuda::initialize ERROR: likely mismatch of architecture\n"); } int compiled_major = Impl::CudaInternal::m_cudaArch / 100; @@ -761,78 +605,42 @@ Kokkos::Cuda::initialize WARNING: Cuda is allocating into UVMSpace by default } #endif - //---------------------------------- - // number of multiprocessors - Impl::CudaInternal::m_multiProcCount = cudaProp.multiProcessorCount; - - //---------------------------------- - // Maximum number of warps, - // at most one warp per thread in a warp for reduction. - Impl::CudaInternal::m_maxWarpCount = - cudaProp.maxThreadsPerBlock / Impl::CudaTraits::WarpSize; - - if (Impl::CudaTraits::WarpSize < Impl::CudaInternal::m_maxWarpCount) { - Impl::CudaInternal::m_maxWarpCount = Impl::CudaTraits::WarpSize; - } - - //---------------------------------- - // Maximum number of blocks: - - Impl::CudaInternal::m_maxBlock[0] = cudaProp.maxGridSize[0]; - Impl::CudaInternal::m_maxBlock[1] = cudaProp.maxGridSize[1]; - Impl::CudaInternal::m_maxBlock[2] = cudaProp.maxGridSize[2]; - - Impl::CudaInternal::m_shmemPerSM = cudaProp.sharedMemPerMultiprocessor; - Impl::CudaInternal::m_maxShmemPerBlock = cudaProp.sharedMemPerBlock; - Impl::CudaInternal::m_maxBlocksPerSM = - Impl::CudaInternal::m_cudaArch < 500 - ? 16 - : (Impl::CudaInternal::m_cudaArch < 750 - ? 32 - : (Impl::CudaInternal::m_cudaArch == 750 ? 16 : 32)); - Impl::CudaInternal::m_maxThreadsPerSM = cudaProp.maxThreadsPerMultiProcessor; - Impl::CudaInternal::m_maxThreadsPerBlock = cudaProp.maxThreadsPerBlock; - //---------------------------------- cudaStream_t singleton_stream; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(cuda_device_id)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamCreate(&singleton_stream)); + + // Init the array for used for arbitrarily sized atomics + desul::Impl::init_lock_arrays(); // FIXME + + Impl::CudaInternal::singleton().initialize(singleton_stream); +} + +void Cuda::impl_finalize() { + (void)Impl::cuda_global_unique_token_locks(true); + desul::Impl::finalize_lock_arrays(); // FIXME + + for (const auto cuda_device : Kokkos::Impl::CudaInternal::cuda_devices) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(cuda_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaFreeHost(Kokkos::Impl::CudaInternal::constantMemHostStagingPerDevice + [cuda_device])); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaEventDestroy( + Kokkos::Impl::CudaInternal::constantMemReusablePerDevice[cuda_device])); + } + + auto &deep_copy_space = Impl::cuda_get_deep_copy_space(/*initialize*/ false); + if (deep_copy_space) + deep_copy_space->impl_internal_space_instance()->finalize(); KOKKOS_IMPL_CUDA_SAFE_CALL( - (Impl::CudaInternal::singleton().cuda_stream_create_wrapper( - &singleton_stream))); + cudaStreamDestroy(Impl::cuda_get_deep_copy_stream())); - auto &cuda_singleton = Impl::CudaInternal::singleton(); - cuda_singleton.initialize(singleton_stream, /*manage*/ true); + Impl::CudaInternal::singleton().finalize(); + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaStreamDestroy(Impl::CudaInternal::singleton().m_stream)); } -std::vector Cuda::detect_device_arch() { - const Impl::CudaInternalDevices &s = Impl::CudaInternalDevices::singleton(); - - std::vector output(s.m_cudaDevCount); - - for (int i = 0; i < s.m_cudaDevCount; ++i) { - output[i] = s.m_cudaProp[i].major * 100 + s.m_cudaProp[i].minor; - } - - return output; -} - -Cuda::size_type Cuda::device_arch() { - const int dev_id = Impl::CudaInternal::singleton().m_cudaDev; - - int dev_arch = 0; - - if (0 <= dev_id) { - const struct cudaDeviceProp &cudaProp = - Impl::CudaInternalDevices::singleton().m_cudaProp[dev_id]; - - dev_arch = cudaProp.major * 100 + cudaProp.minor; - } - - return dev_arch; -} - -void Cuda::impl_finalize() { Impl::CudaInternal::singleton().finalize(); } - Cuda::Cuda() : m_space_instance(&Impl::CudaInternal::singleton(), [](Impl::CudaInternal *) {}) { @@ -845,13 +653,17 @@ KOKKOS_DEPRECATED Cuda::Cuda(cudaStream_t stream, bool manage_stream) manage_stream ? Impl::ManageStream::yes : Impl::ManageStream::no) {} Cuda::Cuda(cudaStream_t stream, Impl::ManageStream manage_stream) - : m_space_instance(new Impl::CudaInternal, [](Impl::CudaInternal *ptr) { - ptr->finalize(); - delete ptr; - }) { + : m_space_instance( + new Impl::CudaInternal, [manage_stream](Impl::CudaInternal *ptr) { + ptr->finalize(); + if (static_cast(manage_stream)) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamDestroy(ptr->m_stream)); + } + delete ptr; + }) { Impl::CudaInternal::singleton().verify_is_initialized( "Cuda instance constructor"); - m_space_instance->initialize(stream, static_cast(manage_stream)); + m_space_instance->initialize(stream); } void Cuda::print_configuration(std::ostream &os, bool /*verbose*/) const { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp index a324adecfe..24f4af3101 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp @@ -22,6 +22,10 @@ #include #include #include +#include "Kokkos_CudaSpace.hpp" + +#include +#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -55,27 +59,10 @@ struct CudaTraits { unsigned long[ConstantMemoryUsage / sizeof(unsigned long)]; static constexpr int ConstantMemoryUseThreshold = 0x000200 /* 512 bytes */; - - KOKKOS_INLINE_FUNCTION static CudaSpace::size_type warp_count( - CudaSpace::size_type i) { - return (i + WarpIndexMask) >> WarpIndexShift; - } - - KOKKOS_INLINE_FUNCTION static CudaSpace::size_type warp_align( - CudaSpace::size_type i) { - constexpr CudaSpace::size_type Mask = ~WarpIndexMask; - return (i + WarpIndexMask) & Mask; - } }; //---------------------------------------------------------------------------- -CudaSpace::size_type cuda_internal_multiprocessor_count(); -CudaSpace::size_type cuda_internal_maximum_warp_count(); -std::array cuda_internal_maximum_grid_count(); - -CudaSpace::size_type cuda_internal_maximum_concurrent_block_count(); - CudaSpace::size_type* cuda_internal_scratch_flags(const Cuda&, const std::size_t size); CudaSpace::size_type* cuda_internal_scratch_space(const Cuda&, @@ -101,18 +88,10 @@ class CudaInternal { public: using size_type = Cuda::size_type; - inline static int m_cudaDev = -1; + int m_cudaDev = -1; // Device Properties - inline static int m_cudaArch = -1; - inline static unsigned m_multiProcCount = 0; - inline static unsigned m_maxWarpCount = 0; - inline static std::array m_maxBlock = {0, 0, 0}; - inline static int m_shmemPerSM = 0; - inline static int m_maxShmemPerBlock = 0; - inline static int m_maxBlocksPerSM = 0; - inline static int m_maxThreadsPerSM = 0; - inline static int m_maxThreadsPerBlock = 0; + inline static int m_cudaArch = -1; static int concurrency(); inline static cudaDeviceProp m_deviceProp; @@ -129,7 +108,6 @@ class CudaInternal { mutable size_type* m_scratchFunctor; cudaStream_t m_stream; uint32_t m_instance_id; - bool m_manage_stream; // Team Scratch Level 1 Space int m_n_team_scratch = 10; @@ -142,11 +120,11 @@ class CudaInternal { bool was_initialized = false; bool was_finalized = false; - // FIXME_CUDA: these want to be per-device, not per-stream... use of 'static' - // here will break once there are multiple devices though - inline static unsigned long* constantMemHostStaging = nullptr; - inline static cudaEvent_t constantMemReusable = nullptr; - inline static std::mutex constantMemMutex; + inline static std::set cuda_devices = {}; + inline static std::map constantMemHostStagingPerDevice = + {}; + inline static std::map constantMemReusablePerDevice = {}; + inline static std::map constantMemMutexPerDevice = {}; static CudaInternal& singleton(); @@ -156,7 +134,7 @@ class CudaInternal { return nullptr != m_scratchSpace && nullptr != m_scratchFlags; } - void initialize(cudaStream_t stream, bool manage_stream); + void initialize(cudaStream_t stream); void finalize(); void print_configuration(std::ostream&) const; @@ -247,12 +225,6 @@ class CudaInternal { return cudaDeviceSetLimit(limit, value); } - template - cudaError_t cuda_device_synchronize_wrapper() const { - if constexpr (setCudaDevice) set_cuda_device(); - return cudaDeviceSynchronize(); - } - template cudaError_t cuda_event_create_wrapper(cudaEvent_t* event) const { if constexpr (setCudaDevice) set_cuda_device(); @@ -290,37 +262,6 @@ class CudaInternal { return cudaFreeHost(ptr); } - template - cudaError_t cuda_get_device_count_wrapper(int* count) const { - if constexpr (setCudaDevice) set_cuda_device(); - return cudaGetDeviceCount(count); - } - - template - cudaError_t cuda_get_device_properties_wrapper(cudaDeviceProp* prop, - int device) const { - if constexpr (setCudaDevice) set_cuda_device(); - return cudaGetDeviceProperties(prop, device); - } - - template - const char* cuda_get_error_name_wrapper(cudaError_t error) const { - if constexpr (setCudaDevice) set_cuda_device(); - return cudaGetErrorName(error); - } - - template - const char* cuda_get_error_string_wrapper(cudaError_t error) const { - if constexpr (setCudaDevice) set_cuda_device(); - return cudaGetErrorString(error); - } - - template - cudaError_t cuda_get_last_error_wrapper() const { - if constexpr (setCudaDevice) set_cuda_device(); - return cudaGetLastError(); - } - template cudaError_t cuda_graph_add_dependencies_wrapper( cudaGraph_t graph, const cudaGraphNode_t* from, const cudaGraphNode_t* to, @@ -506,10 +447,10 @@ class CudaInternal { } template - cudaError_t cuda_func_set_attributes_wrapper(T* entry, cudaFuncAttribute attr, - int value) const { + cudaError_t cuda_func_set_attribute_wrapper(T* entry, cudaFuncAttribute attr, + int value) const { if constexpr (setCudaDevice) set_cuda_device(); - return cudaFuncSetAttributes(entry, attr, value); + return cudaFuncSetAttribute(entry, attr, value); } template diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp index 82a72b6902..b0dadb45f7 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp @@ -21,7 +21,6 @@ #ifdef KOKKOS_ENABLE_CUDA #include -#include #include #include #include @@ -118,42 +117,43 @@ inline bool is_empty_launch(dim3 const& grid, dim3 const& block) { } inline void check_shmem_request(CudaInternal const* cuda_instance, int shmem) { - if (cuda_instance->m_maxShmemPerBlock < shmem) { + int const maxShmemPerBlock = cuda_instance->m_deviceProp.sharedMemPerBlock; + if (maxShmemPerBlock < shmem) { Kokkos::Impl::throw_runtime_exception( - std::string("CudaParallelLaunch (or graph node creation) FAILED: shared" - " memory request is too large")); + "CudaParallelLaunch (or graph node creation) FAILED: shared memory " + "request is too large"); } } // These functions need to be templated on DriverType and LaunchBounds // so that the static bool is unique for each type combo // KernelFuncPtr does not necessarily contain that type information. -// FIXME_CUDA_MULTIPLE_DEVICES template const cudaFuncAttributes& get_cuda_kernel_func_attributes( - const KernelFuncPtr& func) { + int cuda_device, const KernelFuncPtr& func) { // Only call cudaFuncGetAttributes once for each unique kernel // by leveraging static variable initialization rules - auto wrap_get_attributes = [&]() -> cudaFuncAttributes { + static std::map func_attr; + if (func_attr.find(cuda_device) == func_attr.end()) { cudaFuncAttributes attr; - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_func_get_attributes_wrapper(&attr, - func))); - return attr; - }; - static cudaFuncAttributes func_attr = wrap_get_attributes(); - return func_attr; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(cuda_device)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFuncGetAttributes(&attr, func)); + func_attr.emplace(cuda_device, attr); + } + return func_attr[cuda_device]; } template -inline void configure_shmem_preference(const KernelFuncPtr& func, +inline void configure_shmem_preference(const int cuda_device, + const KernelFuncPtr& func, const cudaDeviceProp& device_props, const size_t block_size, int& shmem, const size_t occupancy) { #ifndef KOKKOS_ARCH_KEPLER const auto& func_attr = - get_cuda_kernel_func_attributes(func); + get_cuda_kernel_func_attributes(cuda_device, + func); // Compute limits for number of blocks due to registers/SM const size_t regs_per_sm = device_props.regsPerMultiprocessor; @@ -222,7 +222,7 @@ inline void configure_shmem_preference(const KernelFuncPtr& func, // FIXME_CUDA_MULTIPLE_DEVICES auto set_cache_config = [&] { KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_func_set_attributes_wrapper( + (CudaInternal::singleton().cuda_func_set_attribute_wrapper( func, cudaFuncAttributePreferredSharedMemoryCarveout, carveout))); return carveout; }; @@ -387,8 +387,8 @@ struct CudaParallelLaunchKernelInvoker< driver.get_policy().impl_get_desired_occupancy().value(); size_t block_size = block.x * block.y * block.z; Impl::configure_shmem_preference( - base_t::get_kernel_func(), cuda_instance->m_deviceProp, block_size, - shmem, desired_occupancy); + cuda_instance->m_cudaDev, base_t::get_kernel_func(), + cuda_instance->m_deviceProp, block_size, shmem, desired_occupancy); } void const* args[] = {&driver}; @@ -487,8 +487,8 @@ struct CudaParallelLaunchKernelInvoker< driver.get_policy().impl_get_desired_occupancy().value(); size_t block_size = block.x * block.y * block.z; Impl::configure_shmem_preference( - base_t::get_kernel_func(), cuda_instance->m_deviceProp, block_size, - shmem, desired_occupancy); + cuda_instance->m_cudaDev, base_t::get_kernel_func(), + cuda_instance->m_deviceProp, block_size, shmem, desired_occupancy); } auto* driver_ptr = Impl::allocate_driver_storage_for_kernel(driver); @@ -576,13 +576,16 @@ struct CudaParallelLaunchKernelInvoker< static void invoke_kernel(DriverType const& driver, dim3 const& grid, dim3 const& block, int shmem, CudaInternal const* cuda_instance) { + int cuda_device = cuda_instance->m_cudaDev; // Wait until the previous kernel that uses the constant buffer is done - std::lock_guard lock(CudaInternal::constantMemMutex); + std::lock_guard lock( + CudaInternal::constantMemMutexPerDevice[cuda_device]); KOKKOS_IMPL_CUDA_SAFE_CALL((cuda_instance->cuda_event_synchronize_wrapper( - CudaInternal::constantMemReusable))); + CudaInternal::constantMemReusablePerDevice[cuda_device]))); // Copy functor (synchronously) to staging buffer in pinned host memory - unsigned long* staging = cuda_instance->constantMemHostStaging; + unsigned long* staging = + cuda_instance->constantMemHostStagingPerDevice[cuda_device]; memcpy(staging, &driver, sizeof(DriverType)); // Copy functor asynchronously from there to constant memory on the device @@ -597,7 +600,7 @@ struct CudaParallelLaunchKernelInvoker< // Record an event that says when the constant buffer can be reused KOKKOS_IMPL_CUDA_SAFE_CALL((cuda_instance->cuda_event_record_wrapper( - CudaInternal::constantMemReusable))); + CudaInternal::constantMemReusablePerDevice[cuda_device]))); } inline static void create_parallel_launch_graph_node( @@ -665,8 +668,8 @@ struct CudaParallelLaunchImpl< Impl::configure_shmem_preference< DriverType, Kokkos::LaunchBounds>( - base_t::get_kernel_func(), cuda_instance->m_deviceProp, block_size, - shmem, desired_occupancy); + cuda_instance->m_cudaDev, base_t::get_kernel_func(), + cuda_instance->m_deviceProp, block_size, shmem, desired_occupancy); } desul::ensure_cuda_lock_arrays_on_device(); @@ -675,18 +678,17 @@ struct CudaParallelLaunchImpl< base_t::invoke_kernel(driver, grid, block, shmem, cuda_instance); #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) - KOKKOS_IMPL_CUDA_SAFE_CALL( - (cuda_instance->cuda_get_last_error_wrapper())); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); cuda_instance->fence( "Kokkos::Impl::launch_kernel: Debug Only Check for Execution Error"); #endif } } - static cudaFuncAttributes get_cuda_func_attributes() { + static cudaFuncAttributes get_cuda_func_attributes(int cuda_device) { return get_cuda_kernel_func_attributes< DriverType, Kokkos::LaunchBounds>( - base_t::get_kernel_func()); + cuda_device, base_t::get_kernel_func()); } }; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp index 7492ab49e5..2c7eba7a18 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp @@ -40,8 +40,8 @@ template <> inline TileSizeProperties get_tile_size_properties( const Kokkos::Cuda& space) { TileSizeProperties properties; - properties.max_threads = - space.impl_internal_space_instance()->m_maxThreadsPerSM; + properties.max_threads = space.impl_internal_space_instance() + ->m_deviceProp.maxThreadsPerMultiProcessor; properties.default_largest_tile_size = 16; properties.default_tile_size = 2; properties.max_total_tile_size = 512; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_MDRange.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_MDRange.hpp index 8aae27d091..6303898400 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_MDRange.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_MDRange.hpp @@ -28,7 +28,6 @@ #include #include #include -#include #include #include @@ -42,8 +41,8 @@ namespace Impl { template int max_tile_size_product_helper(const Policy& pol, const LaunchBounds&) { cudaFuncAttributes attr = - CudaParallelLaunch::get_cuda_func_attributes(); + CudaParallelLaunch::get_cuda_func_attributes( + pol.space().cuda_device()); auto const& prop = pol.space().cuda_device_prop(); // Limits due to registers/SM, MDRange doesn't have @@ -96,7 +95,7 @@ class ParallelFor, Kokkos::Cuda> { inline void execute() const { if (m_rp.m_num_tiles == 0) return; - const auto maxblocks = cuda_internal_maximum_grid_count(); + const auto maxblocks = m_rp.space().cuda_device_prop().maxGridSize; if (RP::rank == 2) { const dim3 block(m_rp.m_tile[0], m_rp.m_tile[1], 1); KOKKOS_ASSERT(block.x > 0); @@ -309,6 +308,11 @@ class ParallelReduce( f, n); using closure_type = Impl::ParallelReduce, Policy, Kokkos::Cuda>; - cudaFuncAttributes attr = - CudaParallelLaunch::get_cuda_func_attributes(); + cudaFuncAttributes attr = CudaParallelLaunch:: + get_cuda_func_attributes(m_policy.space().cuda_device()); while ( - (n && - (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < - shmem_size)) || + (n && (maxShmemPerBlock < shmem_size)) || (n > static_cast( Kokkos::Impl::cuda_get_max_block_size( diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Range.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Range.hpp index 5226c48bd9..334834938a 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Range.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Range.hpp @@ -28,7 +28,6 @@ #include #include #include -#include #include #include @@ -86,18 +85,18 @@ class ParallelFor, Kokkos::Cuda> { const typename Policy::index_type nwork = m_policy.end() - m_policy.begin(); cudaFuncAttributes attr = - CudaParallelLaunch::get_cuda_func_attributes(); + CudaParallelLaunch::get_cuda_func_attributes( + m_policy.space().cuda_device()); const int block_size = Kokkos::Impl::cuda_get_opt_block_size( m_policy.space().impl_internal_space_instance(), attr, m_functor, 1, 0, 0); KOKKOS_ASSERT(block_size > 0); dim3 block(1, block_size, 1); + const int maxGridSizeX = m_policy.space().cuda_device_prop().maxGridSize[0]; dim3 grid( - std::min( - typename Policy::index_type((nwork + block.y - 1) / block.y), - typename Policy::index_type(cuda_internal_maximum_grid_count()[0])), + std::min(typename Policy::index_type((nwork + block.y - 1) / block.y), + typename Policy::index_type(maxGridSizeX)), 1, 1); #ifdef KOKKOS_IMPL_DEBUG_CUDA_SERIAL_EXECUTION if (Kokkos::Impl::CudaInternal::cuda_use_serial_execution()) { @@ -243,6 +242,12 @@ class ParallelReduce, if (CudaTraits::WarpSize < word_count.value) { __syncthreads(); + } else if (word_count.value > 1) { + // Inside cuda_single_inter_block_reduce_scan() and final() above, + // shared[i] below might have been updated by a single thread within a + // warp without synchronization afterwards. Synchronize threads within + // warp to avoid potential race condition. + __syncwarp(0xffffffff); } for (unsigned i = threadIdx.y; i < word_count.value; i += blockDim.y) { @@ -254,19 +259,18 @@ class ParallelReduce, // Determine block size constrained by shared memory: inline unsigned local_block_size(const FunctorType& f) { unsigned n = CudaTraits::WarpSize * 8; + const int maxShmemPerBlock = + m_policy.space().cuda_device_prop().sharedMemPerBlock; int shmem_size = cuda_single_inter_block_reduce_scan_shmem( f, n); using closure_type = Impl::ParallelReduce, Policy, Kokkos::Cuda>; - cudaFuncAttributes attr = - CudaParallelLaunch::get_cuda_func_attributes(); + cudaFuncAttributes attr = CudaParallelLaunch:: + get_cuda_func_attributes(m_policy.space().cuda_device()); while ( - (n && - (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < - shmem_size)) || + (n && (maxShmemPerBlock < shmem_size)) || (n > static_cast( Kokkos::Impl::cuda_get_max_block_size( @@ -308,8 +312,9 @@ class ParallelReduce, // REQUIRED ( 1 , N , 1 ) dim3 block(1, block_size, 1); // Required grid.x <= block.y - dim3 grid(std::min(int(block.y), int((nwork + block.y - 1) / block.y)), 1, - 1); + dim3 grid(std::min(index_type(block.y), + index_type((nwork + block.y - 1) / block.y)), + 1, 1); // TODO @graph We need to effectively insert this in to the graph const int shmem = @@ -609,11 +614,11 @@ class ParallelScan, Kokkos::Cuda> { // 4 warps was 10% faster than 8 warps and 20% faster than 16 warps in unit // testing + const int maxShmemPerBlock = + m_policy.space().cuda_device_prop().sharedMemPerBlock; unsigned n = CudaTraits::WarpSize * 4; while (n && - unsigned(m_policy.space() - .impl_internal_space_instance() - ->m_maxShmemPerBlock) < + unsigned(maxShmemPerBlock) < cuda_single_inter_block_reduce_scan_shmem(f, n)) { n >>= 1; @@ -933,11 +938,11 @@ class ParallelScanWithTotal, // 4 warps was 10% faster than 8 warps and 20% faster than 16 warps in unit // testing + const int maxShmemPerBlock = + m_policy.space().cuda_device_prop().sharedMemPerBlock; unsigned n = CudaTraits::WarpSize * 4; while (n && - unsigned(m_policy.space() - .impl_internal_space_instance() - ->m_maxShmemPerBlock) < + unsigned(maxShmemPerBlock) < cuda_single_inter_block_reduce_scan_shmem(f, n)) { n >>= 1; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Team.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Team.hpp index 498e57f94a..9f7be45c83 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Team.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel_Team.hpp @@ -32,7 +32,7 @@ #include #include #include -#include +#include #include #include @@ -98,7 +98,7 @@ class TeamPolicyInternal Impl::ParallelFor>; cudaFuncAttributes attr = CudaParallelLaunch:: - get_cuda_func_attributes(); + get_cuda_func_attributes(space().cuda_device()); int block_size = Kokkos::Impl::cuda_get_max_block_size( @@ -137,7 +137,7 @@ class TeamPolicyInternal Impl::ParallelFor>; cudaFuncAttributes attr = CudaParallelLaunch:: - get_cuda_func_attributes(); + get_cuda_func_attributes(space().cuda_device()); const int block_size = Kokkos::Impl::cuda_get_opt_block_size( @@ -262,7 +262,8 @@ class TeamPolicyInternal m_tune_team(bool(team_size_request <= 0)), m_tune_vector(bool(vector_length_request <= 0)) { // Make sure league size is permissible - if (league_size_ >= int(Impl::cuda_internal_maximum_grid_count()[0])) + const int maxGridSizeX = m_space.cuda_device_prop().maxGridSize[0]; + if (league_size_ >= maxGridSizeX) Impl::throw_runtime_exception( "Requested too large league_size for TeamPolicy on Cuda execution " "space."); @@ -369,7 +370,7 @@ class TeamPolicyInternal cudaFuncAttributes attr = CudaParallelLaunch:: - get_cuda_func_attributes(); + get_cuda_func_attributes(space().cuda_device()); const int block_size = std::forward(block_size_callable)( space().impl_internal_space_instance(), attr, f, (size_t)impl_vector_length(), @@ -539,8 +540,8 @@ class ParallelFor, auto internal_space_instance = m_policy.space().impl_internal_space_instance(); cudaFuncAttributes attr = - CudaParallelLaunch::get_cuda_func_attributes(); + CudaParallelLaunch::get_cuda_func_attributes( + internal_space_instance->m_cudaDev); m_team_size = m_team_size >= 0 ? m_team_size @@ -575,10 +576,11 @@ class ParallelFor, static_cast(m_league_size)))); } + const int maxShmemPerBlock = + m_policy.space().cuda_device_prop().sharedMemPerBlock; const int shmem_size_total = m_shmem_begin + m_shmem_size; - if (internal_space_instance->m_maxShmemPerBlock < shmem_size_total) { - printf("%i %i\n", internal_space_instance->m_maxShmemPerBlock, - shmem_size_total); + if (maxShmemPerBlock < shmem_size_total) { + printf("%i %i\n", maxShmemPerBlock, shmem_size_total); Kokkos::Impl::throw_runtime_exception(std::string( "Kokkos::Impl::ParallelFor< Cuda > insufficient shared memory")); } @@ -623,6 +625,22 @@ class ParallelReduce 4 bytes in size, indexing into shared/global memory relies + // on the block and grid dimensions to ensure that we index at the correct + // offset rather than at every 4 byte word; such that, when the join is + // performed, we have the correct data that was copied over in chunks of 4 + // bytes. + using word_size_type = std::conditional_t< + sizeof(value_type) < sizeof(Kokkos::Cuda::size_type), + std::conditional_t, + Kokkos::Cuda::size_type>; using size_type = Cuda::size_type; using reducer_type = ReducerType; @@ -646,9 +664,11 @@ class ParallelReduce + const integral_nonzero_constant word_count(m_functor_reducer.get_reducer().value_size() / - sizeof(size_type)); + sizeof(word_size_type)); reference_type value = m_functor_reducer.get_reducer().init( - kokkos_impl_cuda_shared_memory() + + kokkos_impl_cuda_shared_memory() + threadIdx.y * word_count.value); // Iterate this block through the league @@ -721,18 +742,19 @@ class ParallelReduce( m_functor_reducer.get_reducer(), blockIdx.x, gridDim.x, - kokkos_impl_cuda_shared_memory(), m_scratch_space, + kokkos_impl_cuda_shared_memory(), m_scratch_space, m_scratch_flags); if (do_final_reduction) { // This is the final block with the final result at the final threads' // location - size_type* const shared = kokkos_impl_cuda_shared_memory() + - (blockDim.y - 1) * word_count.value; + word_size_type* const shared = + kokkos_impl_cuda_shared_memory() + + (blockDim.y - 1) * word_count.value; size_type* const global = m_result_ptr_device_accessible - ? reinterpret_cast(m_result_ptr) + ? reinterpret_cast(m_result_ptr) : (m_unified_space ? m_unified_space : m_scratch_space); if (threadIdx.y == 0) { @@ -742,6 +764,11 @@ class ParallelReduce(m_scratch_space), result, + m_scratch_flags, blockDim.y)) { const unsigned id = threadIdx.y * blockDim.x + threadIdx.x; if (id == 0) { m_functor_reducer.get_reducer().final(&value); @@ -803,13 +831,15 @@ class ParallelReduce(cuda_internal_scratch_space( + m_policy.space(), + m_functor_reducer.get_reducer().value_size() * block_count)); m_scratch_flags = cuda_internal_scratch_flags(m_policy.space(), sizeof(size_type)); - m_unified_space = cuda_internal_scratch_unified( - m_policy.space(), m_functor_reducer.get_reducer().value_size()); + m_unified_space = + reinterpret_cast(cuda_internal_scratch_unified( + m_policy.space(), m_functor_reducer.get_reducer().value_size())); dim3 block(m_vector_size, m_team_size, 1); dim3 grid(block_count, 1, 1); @@ -842,7 +872,8 @@ class ParallelReduce(m_result_ptr, m_scratch_space, size); + DeepCopy(m_policy.space(), m_result_ptr, + m_scratch_space, size); } } } @@ -878,9 +909,8 @@ class ParallelReduce::get_cuda_func_attributes(); + cudaFuncAttributes attr = CudaParallelLaunch:: + get_cuda_func_attributes(internal_space_instance->m_cudaDev); m_team_size = m_team_size >= 0 ? m_team_size @@ -935,6 +965,8 @@ class ParallelReduce bad team size")); } - if (internal_space_instance->m_maxShmemPerBlock < shmem_size_total) { + if (maxShmemPerBlock < shmem_size_total) { Kokkos::Impl::throw_runtime_exception( std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too much " "L0 scratch memory")); diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp index 7ccedbfe28..3037c4ab54 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp @@ -103,7 +103,7 @@ template __device__ bool cuda_inter_block_reduction( typename FunctorType::reference_type value, typename FunctorType::reference_type neutral, const FunctorType& reducer, - Cuda::size_type* const m_scratch_space, + typename FunctorType::pointer_type const m_scratch_space, typename FunctorType::pointer_type const /*result*/, Cuda::size_type* const m_scratch_flags, const int max_active_thread = blockDim.y) { @@ -117,7 +117,7 @@ __device__ bool cuda_inter_block_reduction( // One thread in the block writes block result to global scratch_memory if (id == 0) { - pointer_type global = ((pointer_type)m_scratch_space) + blockIdx.x; + pointer_type global = m_scratch_space + blockIdx.x; *global = value; } @@ -140,7 +140,7 @@ __device__ bool cuda_inter_block_reduction( last_block = true; value = neutral; - pointer_type const volatile global = (pointer_type)m_scratch_space; + pointer_type const volatile global = m_scratch_space; // Reduce all global values with splitting work over threads in one warp const int step_size = @@ -702,8 +702,7 @@ inline void check_reduced_view_shmem_size(const Policy& policy, unsigned reqShmemSize = cuda_single_inter_block_reduce_scan_shmem( functor, minBlockSize); - size_t maxShmemPerBlock = - policy.space().impl_internal_space_instance()->m_maxShmemPerBlock; + size_t maxShmemPerBlock = policy.space().cuda_device_prop().sharedMemPerBlock; if (reqShmemSize > maxShmemPerBlock) { Kokkos::Impl::throw_runtime_exception( diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp index baff7ef3f5..86d6d91bbe 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp @@ -84,8 +84,8 @@ class TaskQueueSpecialization> { KOKKOS_INLINE_FUNCTION static void iff_single_thread_recursive_execute(scheduler_type const&) {} - static int get_max_team_count(execution_space const&) { - return Kokkos::Impl::cuda_internal_multiprocessor_count() * warps_per_block; + static int get_max_team_count(execution_space const& space) { + return space.cuda_device_prop().multiProcessorCount * warps_per_block; } __device__ static void driver(scheduler_type scheduler, @@ -225,7 +225,11 @@ class TaskQueueSpecialization> { // FIXME_CUDA_MULTIPLE_DEVICES static void execute(scheduler_type const& scheduler) { const int shared_per_warp = 2048; - const dim3 grid(Kokkos::Impl::cuda_internal_multiprocessor_count(), 1, 1); + const Kokkos::Cuda& exec = scheduler.get_execution_space(); + const auto& impl_instance = exec.impl_internal_space_instance(); + const int multi_processor_count = + exec.cuda_device_prop().multiProcessorCount; + const dim3 grid(multi_processor_count, 1, 1); const dim3 block(1, Kokkos::Impl::CudaTraits::WarpSize, warps_per_block); const int shared_total = shared_per_warp * warps_per_block; const cudaStream_t stream = nullptr; @@ -245,34 +249,30 @@ class TaskQueueSpecialization> { // Query the stack size, in bytes: size_t previous_stack_size = 0; - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_get_limit_wrapper( - &previous_stack_size, cudaLimitStackSize))); + KOKKOS_IMPL_CUDA_SAFE_CALL(impl_instance->cuda_device_get_limit_wrapper( + &previous_stack_size, cudaLimitStackSize)); // If not large enough then set the stack size, in bytes: const size_t larger_stack_size = 1 << 11; if (previous_stack_size < larger_stack_size) { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_set_limit_wrapper( - cudaLimitStackSize, larger_stack_size))); + KOKKOS_IMPL_CUDA_SAFE_CALL(impl_instance->cuda_device_set_limit_wrapper( + cudaLimitStackSize, larger_stack_size)); } cuda_task_queue_execute<<>>( scheduler, shared_per_warp); - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_get_last_error_wrapper())); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); Impl::cuda_device_synchronize( "Kokkos::Impl::TaskQueueSpecialization::execute: Post Task Execution"); if (previous_stack_size < larger_stack_size) { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_set_limit_wrapper( - cudaLimitStackSize, previous_stack_size))); + KOKKOS_IMPL_CUDA_SAFE_CALL(impl_instance->cuda_device_set_limit_wrapper( + cudaLimitStackSize, previous_stack_size)); } } @@ -300,8 +300,8 @@ class TaskQueueSpecialization> { set_cuda_task_base_apply_function_pointer <<<1, 1>>>(ptr_ptr, dtor_ptr); - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_get_last_error_wrapper())); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); + Impl::cuda_device_synchronize( "Kokkos::Impl::TaskQueueSpecialization::execute: Post Get Function Pointer for Tasks"); @@ -466,7 +466,13 @@ class TaskQueueSpecializationConstrained< static void execute(scheduler_type const& scheduler) { const int shared_per_warp = 2048; const int warps_per_block = 4; - const dim3 grid(Kokkos::Impl::cuda_internal_multiprocessor_count(), 1, 1); + const Kokkos::Cuda exec = Cuda(); // FIXME_CUDA_MULTIPLE_DEVICES + const auto& impl_instance = exec.impl_internal_space_instance(); + const int multi_processor_count = + // FIXME not sure why this didn't work + // exec.cuda_device_prop().multiProcessorCount; + impl_instance->m_deviceProp.multiProcessorCount; + const dim3 grid(multi_processor_count, 1, 1); // const dim3 grid( 1 , 1 , 1 ); const dim3 block(1, Kokkos::Impl::CudaTraits::WarpSize, warps_per_block); const int shared_total = shared_per_warp * warps_per_block; @@ -482,34 +488,30 @@ class TaskQueueSpecializationConstrained< // Query the stack size, in bytes: size_t previous_stack_size = 0; - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_get_limit_wrapper( - &previous_stack_size, cudaLimitStackSize))); + KOKKOS_IMPL_CUDA_SAFE_CALL(impl_instance->cuda_device_get_limit_wrapper( + &previous_stack_size, cudaLimitStackSize)); // If not large enough then set the stack size, in bytes: const size_t larger_stack_size = 2048; if (previous_stack_size < larger_stack_size) { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_set_limit_wrapper( - cudaLimitStackSize, larger_stack_size))); + KOKKOS_IMPL_CUDA_SAFE_CALL(impl_instance->cuda_device_set_limit_wrapper( + cudaLimitStackSize, larger_stack_size)); } cuda_task_queue_execute<<>>( scheduler, shared_per_warp); - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_get_last_error_wrapper())); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); Impl::cuda_device_synchronize( "Kokkos::Impl::TaskQueueSpecializationConstrained::execute: Post Execute Task"); if (previous_stack_size < larger_stack_size) { - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_device_set_limit_wrapper( - cudaLimitStackSize, previous_stack_size))); + KOKKOS_IMPL_CUDA_SAFE_CALL(impl_instance->cuda_device_set_limit_wrapper( + cudaLimitStackSize, previous_stack_size)); } } @@ -532,8 +534,7 @@ class TaskQueueSpecializationConstrained< set_cuda_task_base_apply_function_pointer <<<1, 1>>>(ptr_ptr, dtor_ptr); - KOKKOS_IMPL_CUDA_SAFE_CALL( - (CudaInternal::singleton().cuda_get_last_error_wrapper())); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetLastError()); Impl::cuda_device_synchronize( "Kokkos::Impl::TaskQueueSpecializationConstrained::get_function_pointer: Post Get Function Pointer"); diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_UniqueToken.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_UniqueToken.hpp index abb747e39a..94a428493f 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_UniqueToken.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_UniqueToken.hpp @@ -22,7 +22,6 @@ #include #include -#include namespace Kokkos { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp index a945a716bc..c7ea6988a5 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp @@ -77,7 +77,9 @@ class ParallelFor, inline void execute() { const int warps_per_block = 4; - const dim3 grid(Kokkos::Impl::cuda_internal_multiprocessor_count(), 1, 1); + const int multi_processor_count = + m_policy.space().cuda_device_prop().multiProcessorCount; + const dim3 grid(multi_processor_count, 1, 1); const dim3 block(1, Kokkos::Impl::CudaTraits::WarpSize, warps_per_block); const int shared = 0; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ZeroMemset.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ZeroMemset.hpp index c7f0d12d91..517c592af7 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ZeroMemset.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ZeroMemset.hpp @@ -25,23 +25,14 @@ namespace Impl { template struct ZeroMemset> { - ZeroMemset(const Kokkos::Cuda& exec_space_instance, const View& dst, - typename View::const_value_type&) { + ZeroMemset(const Kokkos::Cuda& exec_space_instance, + const View& dst) { KOKKOS_IMPL_CUDA_SAFE_CALL( (exec_space_instance.impl_internal_space_instance() ->cuda_memset_async_wrapper( dst.data(), 0, dst.size() * sizeof(typename View::value_type)))); } - - ZeroMemset(const View& dst, - typename View::const_value_type&) { - // FIXME_CUDA_MULTIPLE_DEVICES - KOKKOS_IMPL_CUDA_SAFE_CALL( - (Kokkos::Impl::CudaInternal::singleton().cuda_memset_wrapper( - dst.data(), 0, - dst.size() * sizeof(typename View::value_type)))); - } }; } // namespace Impl diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP.cpp index f78bfd28b2..aced2083ff 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP.cpp @@ -18,6 +18,7 @@ #define KOKKOS_IMPL_PUBLIC_INCLUDE #endif +#include #include #include @@ -41,7 +42,9 @@ int HIP::impl_is_initialized() { } void HIP::impl_initialize(InitializationSettings const& settings) { - const int hip_device_id = Impl::get_gpu(settings); + const std::vector& visible_devices = Impl::get_visible_devices(); + const int hip_device_id = + Impl::get_gpu(settings).value_or(visible_devices[0]); Impl::HIPInternal::m_hipDev = hip_device_id; KOKKOS_IMPL_HIP_SAFE_CALL( @@ -89,10 +92,23 @@ void HIP::impl_initialize(InitializationSettings const& settings) { hipStream_t singleton_stream; KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamCreate(&singleton_stream)); - Impl::HIPInternal::singleton().initialize(singleton_stream, /*manage*/ true); + Impl::HIPInternal::singleton().initialize(singleton_stream); } -void HIP::impl_finalize() { Impl::HIPInternal::singleton().finalize(); } +void HIP::impl_finalize() { + (void)Impl::hip_global_unique_token_locks(true); + + desul::Impl::finalize_lock_arrays(); // FIXME + + KOKKOS_IMPL_HIP_SAFE_CALL( + hipEventDestroy(Impl::HIPInternal::constantMemReusable)); + KOKKOS_IMPL_HIP_SAFE_CALL( + hipHostFree(Impl::HIPInternal::constantMemHostStaging)); + + Impl::HIPInternal::singleton().finalize(); + KOKKOS_IMPL_HIP_SAFE_CALL( + hipStreamDestroy(Impl::HIPInternal::singleton().m_stream)); +} HIP::HIP() : m_space_instance(&Impl::HIPInternal::singleton(), @@ -102,13 +118,17 @@ HIP::HIP() } HIP::HIP(hipStream_t const stream, Impl::ManageStream manage_stream) - : m_space_instance(new Impl::HIPInternal, [](Impl::HIPInternal* ptr) { - ptr->finalize(); - delete ptr; - }) { + : m_space_instance( + new Impl::HIPInternal, [manage_stream](Impl::HIPInternal* ptr) { + ptr->finalize(); + if (static_cast(manage_stream)) { + KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamDestroy(ptr->m_stream)); + } + delete ptr; + }) { Impl::HIPInternal::singleton().verify_is_initialized( "HIP instance constructor"); - m_space_instance->initialize(stream, static_cast(manage_stream)); + m_space_instance->initialize(stream); } KOKKOS_DEPRECATED HIP::HIP(hipStream_t const stream, bool manage_stream) @@ -126,6 +146,10 @@ void HIP::print_configuration(std::ostream& os, bool /*verbose*/) const { #else os << "no\n"; #endif +#ifdef KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY + os << " KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY: "; + os << "yes\n"; +#endif os << "\nRuntime Configuration:\n"; diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP.hpp index 61ed346b21..3a88e97ee3 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP.hpp @@ -57,13 +57,15 @@ class HIP { //! \name Functions that all Kokkos devices must implement. //@{ - KOKKOS_INLINE_FUNCTION static int in_parallel() { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED KOKKOS_INLINE_FUNCTION static int in_parallel() { #if defined(__HIP_DEVICE_COMPILE__) return true; #else return false; #endif } +#endif /** \brief Wait until all dispatched functors complete. * @@ -94,9 +96,13 @@ class HIP { static int impl_is_initialized(); - // static size_type device_arch(); - - static size_type detect_device_count(); +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED static size_type detect_device_count() { + int count; + KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceCount(&count)); + return count; + } +#endif #ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 static int concurrency(); diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_GraphNodeKernel.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_GraphNodeKernel.hpp index 576c53426b..5f0df72df1 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_GraphNodeKernel.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_GraphNodeKernel.hpp @@ -20,13 +20,11 @@ #include #include -#include #include #include #include -#include #include namespace Kokkos { @@ -43,7 +41,6 @@ class GraphNodeKernelImpl using base_t = typename PatternImplSpecializationFromTag::type; - using Record = Kokkos::Impl::SharedAllocationRecord; // TODO use the name and executionspace template @@ -60,7 +57,7 @@ class GraphNodeKernelImpl ~GraphNodeKernelImpl() { if (m_driver_storage) { - Record::decrement(Record::get_record(m_driver_storage)); + Kokkos::HIPSpace().deallocate(m_driver_storage, sizeof(base_t)); } } @@ -78,15 +75,9 @@ class GraphNodeKernelImpl Kokkos::ObservingRawPtr allocate_driver_memory_buffer() const { KOKKOS_EXPECTS(m_driver_storage == nullptr); - - auto* record = Record::allocate( - Kokkos::HIPSpace{}, "GraphNodeKernel global memory functor storage", - sizeof(base_t)); - - Record::increment(record); - m_driver_storage = reinterpret_cast(record->data()); + m_driver_storage = static_cast(Kokkos::HIPSpace().allocate( + "GraphNodeKernel global memory functor storage", sizeof(base_t))); KOKKOS_ENSURES(m_driver_storage != nullptr); - return m_driver_storage; } diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Graph_Impl.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Graph_Impl.hpp index 3bde15444c..7cc06d02fb 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Graph_Impl.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Graph_Impl.hpp @@ -83,7 +83,7 @@ class GraphImpl { hipGraphExec_t m_graph_exec = nullptr; }; -GraphImpl::~GraphImpl() { +inline GraphImpl::~GraphImpl() { m_execution_space.fence("Kokkos::GraphImpl::~GraphImpl: Graph Destruction"); KOKKOS_EXPECTS(m_graph); if (m_graph_exec) { @@ -92,12 +92,12 @@ GraphImpl::~GraphImpl() { KOKKOS_IMPL_HIP_SAFE_CALL(hipGraphDestroy(m_graph)); } -GraphImpl::GraphImpl(Kokkos::HIP instance) +inline GraphImpl::GraphImpl(Kokkos::HIP instance) : m_execution_space(std::move(instance)) { KOKKOS_IMPL_HIP_SAFE_CALL(hipGraphCreate(&m_graph, 0)); } -void GraphImpl::add_node( +inline void GraphImpl::add_node( std::shared_ptr const& arg_node_ptr) { // All of the predecessors are just added as normal, so all we need to // do here is add an empty node @@ -110,7 +110,7 @@ void GraphImpl::add_node( // Requires NodeImplPtr is a shared_ptr to specialization of GraphNodeImpl // Also requires that the kernel has the graph node tag in it's policy template -void GraphImpl::add_node( +inline void GraphImpl::add_node( std::shared_ptr const& arg_node_ptr) { static_assert(NodeImpl::kernel_type::Policy::is_graph_kernel::value); KOKKOS_EXPECTS(arg_node_ptr); @@ -129,8 +129,8 @@ void GraphImpl::add_node( // already been added to this graph and NodeImpl is a specialization of // GraphNodeImpl that has already been added to this graph. template -void GraphImpl::add_predecessor(NodeImplPtr arg_node_ptr, - PredecessorRef arg_pred_ref) { +inline void GraphImpl::add_predecessor( + NodeImplPtr arg_node_ptr, PredecessorRef arg_pred_ref) { KOKKOS_EXPECTS(arg_node_ptr); auto pred_ptr = GraphAccess::get_node_ptr(arg_pred_ref); KOKKOS_EXPECTS(pred_ptr); @@ -145,7 +145,7 @@ void GraphImpl::add_predecessor(NodeImplPtr arg_node_ptr, hipGraphAddDependencies(m_graph, &pred_node, &node, 1)); } -void GraphImpl::submit() { +inline void GraphImpl::submit() { if (!m_graph_exec) { instantiate_graph(); } @@ -153,12 +153,12 @@ void GraphImpl::submit() { hipGraphLaunch(m_graph_exec, m_execution_space.hip_stream())); } -Kokkos::HIP const& GraphImpl::get_execution_space() const +inline Kokkos::HIP const& GraphImpl::get_execution_space() const noexcept { return m_execution_space; } -auto GraphImpl::create_root_node_ptr() { +inline auto GraphImpl::create_root_node_ptr() { KOKKOS_EXPECTS(m_graph); KOKKOS_EXPECTS(!m_graph_exec); auto rv = std::make_shared(get_execution_space(), @@ -172,7 +172,7 @@ auto GraphImpl::create_root_node_ptr() { } template -auto GraphImpl::create_aggregate_ptr(PredecessorRefs&&...) { +inline auto GraphImpl::create_aggregate_ptr(PredecessorRefs&&...) { // The attachment to predecessors, which is all we really need, happens // in the generic layer, which calls through to add_predecessor for // each predecessor ref, so all we need to do here is create the (trivial) diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp index 7f04eb721c..22c0db047f 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp @@ -27,6 +27,7 @@ #include #include #include +#include #include /*--------------------------------------------------------------------------*/ @@ -89,10 +90,14 @@ void HIPInternal::print_configuration(std::ostream &s) const { << '\n'; #endif - int hipDevCount; - KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceCount(&hipDevCount)); + s << "macro KOKKOS_ENABLE_ROCTHRUST : " +#if defined(KOKKOS_ENABLE_ROCTHRUST) + << "defined\n"; +#else + << "undefined\n"; +#endif - for (int i = 0; i < hipDevCount; ++i) { + for (int i : get_visible_devices()) { hipDeviceProp_t hipProp; KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceProperties(&hipProp, i)); std::string gpu_type = hipProp.integrated == 1 ? "APU" : "dGPU"; @@ -159,14 +164,13 @@ void HIPInternal::fence(const std::string &name) const { [&]() { KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamSynchronize(m_stream)); }); } -void HIPInternal::initialize(hipStream_t stream, bool manage_stream) { +void HIPInternal::initialize(hipStream_t stream) { KOKKOS_EXPECTS(!is_initialized()); if (was_finalized) Kokkos::abort("Calling HIP::initialize after HIP::finalize is illegal\n"); - m_stream = stream; - m_manage_stream = manage_stream; + m_stream = stream; //---------------------------------- // Multiblock reduction uses scratch flags for counters @@ -192,20 +196,19 @@ void HIPInternal::initialize(hipStream_t stream, bool manage_stream) { Kokkos::HIP::size_type *HIPInternal::scratch_space(const std::size_t size) { if (verify_is_initialized("scratch_space") && m_scratchSpaceCount < scratch_count(size)) { + Kokkos::HIPSpace mem_space; + + if (m_scratchSpace) { + mem_space.deallocate(m_scratchSpace, + m_scratchSpaceCount * sizeScratchGrain); + } + m_scratchSpaceCount = scratch_count(size); - using Record = Kokkos::Impl::SharedAllocationRecord; - - if (m_scratchSpace) Record::decrement(Record::get_record(m_scratchSpace)); - std::size_t alloc_size = multiply_overflow_abort(m_scratchSpaceCount, sizeScratchGrain); - Record *const r = Record::allocate( - Kokkos::HIPSpace(), "Kokkos::InternalScratchSpace", alloc_size); - - Record::increment(r); - - m_scratchSpace = reinterpret_cast(r->data()); + m_scratchSpace = static_cast( + mem_space.allocate("Kokkos::InternalScratchSpace", alloc_size)); } return m_scratchSpace; @@ -214,21 +217,23 @@ Kokkos::HIP::size_type *HIPInternal::scratch_space(const std::size_t size) { Kokkos::HIP::size_type *HIPInternal::scratch_flags(const std::size_t size) { if (verify_is_initialized("scratch_flags") && m_scratchFlagsCount < scratch_count(size)) { + Kokkos::HIPSpace mem_space; + + if (m_scratchFlags) { + mem_space.deallocate(m_scratchFlags, + m_scratchFlagsCount * sizeScratchGrain); + } + m_scratchFlagsCount = scratch_count(size); - using Record = Kokkos::Impl::SharedAllocationRecord; - - if (m_scratchFlags) Record::decrement(Record::get_record(m_scratchFlags)); - std::size_t alloc_size = multiply_overflow_abort(m_scratchFlagsCount, sizeScratchGrain); - Record *const r = Record::allocate( - Kokkos::HIPSpace(), "Kokkos::InternalScratchFlags", alloc_size); - - Record::increment(r); - - m_scratchFlags = reinterpret_cast(r->data()); + m_scratchFlags = static_cast( + mem_space.allocate("Kokkos::InternalScratchFlags", alloc_size)); + // We only zero-initialize the allocation when we actually allocate. + // It's the responsibility of the features using scratch_flags, + // namely parallel_reduce and parallel_scan, to reset the used values to 0. KOKKOS_IMPL_HIP_SAFE_CALL(hipMemset(m_scratchFlags, 0, alloc_size)); } @@ -238,29 +243,20 @@ Kokkos::HIP::size_type *HIPInternal::scratch_flags(const std::size_t size) { Kokkos::HIP::size_type *HIPInternal::stage_functor_for_execution( void const *driver, std::size_t const size) const { if (verify_is_initialized("scratch_functor") && m_scratchFunctorSize < size) { - m_scratchFunctorSize = size; - - using Record = Kokkos::Impl::SharedAllocationRecord; - using RecordHost = - Kokkos::Impl::SharedAllocationRecord; + Kokkos::HIPSpace device_mem_space; + Kokkos::HIPHostPinnedSpace host_mem_space; if (m_scratchFunctor) { - Record::decrement(Record::get_record(m_scratchFunctor)); - RecordHost::decrement(RecordHost::get_record(m_scratchFunctorHost)); + device_mem_space.deallocate(m_scratchFunctor, m_scratchFunctorSize); + host_mem_space.deallocate(m_scratchFunctorHost, m_scratchFunctorSize); } - Record *const r = - Record::allocate(Kokkos::HIPSpace(), "Kokkos::InternalScratchFunctor", - m_scratchFunctorSize); - RecordHost *const r_host = RecordHost::allocate( - Kokkos::HIPHostPinnedSpace(), "Kokkos::InternalScratchFunctorHost", - m_scratchFunctorSize); + m_scratchFunctorSize = size; - Record::increment(r); - RecordHost::increment(r_host); - - m_scratchFunctor = reinterpret_cast(r->data()); - m_scratchFunctorHost = reinterpret_cast(r_host->data()); + m_scratchFunctor = static_cast(device_mem_space.allocate( + "Kokkos::InternalScratchFunctor", m_scratchFunctorSize)); + m_scratchFunctorHost = static_cast(host_mem_space.allocate( + "Kokkos::InternalScratchFunctorHost", m_scratchFunctorSize)); } // When using HSA_XNACK=1, it is necessary to copy the driver to the host to @@ -323,23 +319,18 @@ void HIPInternal::finalize() { this->fence("Kokkos::HIPInternal::finalize: fence on finalization"); was_finalized = true; - if (this == &singleton()) { - (void)Kokkos::Impl::hip_global_unique_token_locks(true); - desul::Impl::finalize_lock_arrays(); // FIXME - - KOKKOS_IMPL_HIP_SAFE_CALL(hipHostFree(constantMemHostStaging)); - KOKKOS_IMPL_HIP_SAFE_CALL(hipEventDestroy(constantMemReusable)); - } - if (nullptr != m_scratchSpace || nullptr != m_scratchFlags) { - using RecordHIP = Kokkos::Impl::SharedAllocationRecord; + Kokkos::HIPSpace device_mem_space; - RecordHIP::decrement(RecordHIP::get_record(m_scratchFlags)); - RecordHIP::decrement(RecordHIP::get_record(m_scratchSpace)); + device_mem_space.deallocate(m_scratchFlags, + m_scratchSpaceCount * sizeScratchGrain); + device_mem_space.deallocate(m_scratchSpace, + m_scratchFlagsCount * sizeScratchGrain); if (m_scratchFunctorSize > 0) { - RecordHIP::decrement(RecordHIP::get_record(m_scratchFunctor)); - RecordHIP::decrement(RecordHIP::get_record(m_scratchFunctorHost)); + device_mem_space.deallocate(m_scratchFunctor, m_scratchFunctorSize); + Kokkos::HIPHostPinnedSpace host_mem_space; + host_mem_space.deallocate(m_scratchFunctorHost, m_scratchFunctorSize); } } @@ -348,14 +339,10 @@ void HIPInternal::finalize() { Kokkos::kokkos_free(m_team_scratch_ptr[i]); } - if (m_manage_stream && m_stream != nullptr) - KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamDestroy(m_stream)); - m_scratchSpaceCount = 0; m_scratchFlagsCount = 0; m_scratchSpace = nullptr; m_scratchFlags = nullptr; - m_stream = nullptr; for (int i = 0; i < m_n_team_scratch; ++i) { m_team_scratch_current_size[i] = 0; m_team_scratch_ptr[i] = nullptr; @@ -419,13 +406,3 @@ void Kokkos::Impl::create_HIP_instances(std::vector &instances) { instances[s] = HIP(stream, ManageStream::yes); } } - -//---------------------------------------------------------------------------- - -namespace Kokkos { -HIP::size_type HIP::detect_device_count() { - int hipDevCount; - KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceCount(&hipDevCount)); - return hipDevCount; -} -} // namespace Kokkos diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp index ef140ec46c..142008124a 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp @@ -30,7 +30,8 @@ namespace Impl { struct HIPTraits { #if defined(KOKKOS_ARCH_AMD_GFX906) || defined(KOKKOS_ARCH_AMD_GFX908) || \ - defined(KOKKOS_ARCH_AMD_GFX90A) || defined(KOKKOS_ARCH_AMD_GFX942) + defined(KOKKOS_ARCH_AMD_GFX90A) || defined(KOKKOS_ARCH_AMD_GFX940) || \ + defined(KOKKOS_ARCH_AMD_GFX942) static constexpr int WarpSize = 64; static constexpr int WarpIndexMask = 0x003f; /* hexadecimal for 63 */ static constexpr int WarpIndexShift = 6; /* WarpSize == 1 << WarpShift*/ @@ -97,7 +98,6 @@ class HIPInternal { uint32_t m_instance_id = Kokkos::Tools::Experimental::Impl::idForInstance( reinterpret_cast(this)); - bool m_manage_stream = false; // Team Scratch Level 1 Space int m_n_team_scratch = 10; @@ -123,7 +123,7 @@ class HIPInternal { return nullptr != m_scratchSpace && nullptr != m_scratchFlags; } - void initialize(hipStream_t stream, bool manage_stream); + void initialize(hipStream_t stream); void finalize(); void print_configuration(std::ostream &) const; diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_MDRange.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_MDRange.hpp new file mode 100644 index 0000000000..db07c360b5 --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_MDRange.hpp @@ -0,0 +1,173 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_HIP_PARALLEL_FOR_MDRANGE_HPP +#define KOKKOS_HIP_PARALLEL_FOR_MDRANGE_HPP + +#include + +#include +#include +#include +#include + +namespace Kokkos { +namespace Impl { + +// ParallelFor +template +class ParallelFor, HIP> { + public: + using Policy = Kokkos::MDRangePolicy; + using functor_type = FunctorType; + + private: + using array_index_type = typename Policy::array_index_type; + using index_type = typename Policy::index_type; + using LaunchBounds = typename Policy::launch_bounds; + + const FunctorType m_functor; + const Policy m_policy; + + public: + ParallelFor() = delete; + ParallelFor(ParallelFor const&) = default; + ParallelFor& operator=(ParallelFor const&) = delete; + + inline __device__ void operator()() const { + Kokkos::Impl::DeviceIterateTile(m_policy, + m_functor) + .exec_range(); + } + + inline void execute() const { + using ClosureType = ParallelFor; + if (m_policy.m_num_tiles == 0) return; + auto const maxblocks = hip_internal_maximum_grid_count(); + if (Policy::rank == 2) { + dim3 const block(m_policy.m_tile[0], m_policy.m_tile[1], 1); + dim3 const grid( + std::min( + (m_policy.m_upper[0] - m_policy.m_lower[0] + block.x - 1) / + block.x, + maxblocks[0]), + std::min( + (m_policy.m_upper[1] - m_policy.m_lower[1] + block.y - 1) / + block.y, + maxblocks[1]), + 1); + hip_parallel_launch( + *this, grid, block, 0, + m_policy.space().impl_internal_space_instance(), false); + } else if (Policy::rank == 3) { + dim3 const block(m_policy.m_tile[0], m_policy.m_tile[1], + m_policy.m_tile[2]); + dim3 const grid( + std::min( + (m_policy.m_upper[0] - m_policy.m_lower[0] + block.x - 1) / + block.x, + maxblocks[0]), + std::min( + (m_policy.m_upper[1] - m_policy.m_lower[1] + block.y - 1) / + block.y, + maxblocks[1]), + std::min( + (m_policy.m_upper[2] - m_policy.m_lower[2] + block.z - 1) / + block.z, + maxblocks[2])); + hip_parallel_launch( + *this, grid, block, 0, + m_policy.space().impl_internal_space_instance(), false); + } else if (Policy::rank == 4) { + // id0,id1 encoded within threadIdx.x; id2 to threadIdx.y; id3 to + // threadIdx.z + dim3 const block(m_policy.m_tile[0] * m_policy.m_tile[1], + m_policy.m_tile[2], m_policy.m_tile[3]); + dim3 const grid( + std::min( + m_policy.m_tile_end[0] * m_policy.m_tile_end[1], maxblocks[0]), + std::min( + (m_policy.m_upper[2] - m_policy.m_lower[2] + block.y - 1) / + block.y, + maxblocks[1]), + std::min( + (m_policy.m_upper[3] - m_policy.m_lower[3] + block.z - 1) / + block.z, + maxblocks[2])); + hip_parallel_launch( + *this, grid, block, 0, + m_policy.space().impl_internal_space_instance(), false); + } else if (Policy::rank == 5) { + // id0,id1 encoded within threadIdx.x; id2,id3 to threadIdx.y; id4 + // to threadIdx.z + dim3 const block(m_policy.m_tile[0] * m_policy.m_tile[1], + m_policy.m_tile[2] * m_policy.m_tile[3], + m_policy.m_tile[4]); + dim3 const grid( + std::min( + m_policy.m_tile_end[0] * m_policy.m_tile_end[1], maxblocks[0]), + std::min( + m_policy.m_tile_end[2] * m_policy.m_tile_end[3], maxblocks[1]), + std::min( + (m_policy.m_upper[4] - m_policy.m_lower[4] + block.z - 1) / + block.z, + maxblocks[2])); + hip_parallel_launch( + *this, grid, block, 0, + m_policy.space().impl_internal_space_instance(), false); + } else if (Policy::rank == 6) { + // id0,id1 encoded within threadIdx.x; id2,id3 to threadIdx.y; + // id4,id5 to threadIdx.z + dim3 const block(m_policy.m_tile[0] * m_policy.m_tile[1], + m_policy.m_tile[2] * m_policy.m_tile[3], + m_policy.m_tile[4] * m_policy.m_tile[5]); + dim3 const grid( + std::min( + m_policy.m_tile_end[0] * m_policy.m_tile_end[1], maxblocks[0]), + std::min( + m_policy.m_tile_end[2] * m_policy.m_tile_end[3], maxblocks[1]), + std::min( + m_policy.m_tile_end[4] * m_policy.m_tile_end[5], maxblocks[2])); + hip_parallel_launch( + *this, grid, block, 0, + m_policy.space().impl_internal_space_instance(), false); + } else { + Kokkos::abort("Kokkos::MDRange Error: Exceeded rank bounds with HIP\n"); + } + + } // end execute + + ParallelFor(FunctorType const& arg_functor, Policy const& arg_policy) + : m_functor(arg_functor), m_policy(arg_policy) {} + + template + static int max_tile_size_product(const Policy&, const Functor&) { + using closure_type = + ParallelFor, HIP>; + unsigned block_size = hip_get_max_blocksize(); + if (block_size == 0) + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelFor< HIP > could not find a valid " + "tile size.")); + return block_size; + } +}; + +} // namespace Impl +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_Range.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_Range.hpp new file mode 100644 index 0000000000..9355c1c75f --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_Range.hpp @@ -0,0 +1,100 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_HIP_PARALLEL_FOR_RANGE_HPP +#define KOKKOS_HIP_PARALLEL_FOR_RANGE_HPP + +#include + +#include +#include + +namespace Kokkos { +namespace Impl { + +template +class ParallelFor, Kokkos::HIP> { + public: + using Policy = Kokkos::RangePolicy; + + private: + using Member = typename Policy::member_type; + using WorkTag = typename Policy::work_tag; + using LaunchBounds = typename Policy::launch_bounds; + + const FunctorType m_functor; + const Policy m_policy; + + template + inline __device__ std::enable_if_t::value> exec_range( + const Member i) const { + m_functor(i); + } + + template + inline __device__ std::enable_if_t::value> exec_range( + const Member i) const { + m_functor(TagType(), i); + } + + public: + using functor_type = FunctorType; + + ParallelFor() = delete; + ParallelFor(ParallelFor const&) = default; + ParallelFor& operator=(ParallelFor const&) = delete; + + inline __device__ void operator()() const { + const Member work_stride = blockDim.y * gridDim.x; + const Member work_end = m_policy.end(); + + for (Member iwork = + m_policy.begin() + threadIdx.y + blockDim.y * blockIdx.x; + iwork < work_end; + iwork = iwork < work_end - work_stride ? iwork + work_stride + : work_end) { + this->template exec_range(iwork); + } + } + + inline void execute() const { + const typename Policy::index_type nwork = m_policy.end() - m_policy.begin(); + + using DriverType = ParallelFor; + const int block_size = + Kokkos::Impl::hip_get_preferred_blocksize(); + const dim3 block(1, block_size, 1); + const dim3 grid( + typename Policy::index_type((nwork + block.y - 1) / block.y), 1, 1); + + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelFor< HIP > could not find a " + "valid execution configuration.")); + } + Kokkos::Impl::hip_parallel_launch( + *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), + false); + } + + ParallelFor(const FunctorType& arg_functor, const Policy& arg_policy) + : m_functor(arg_functor), m_policy(arg_policy) {} +}; + +} // namespace Impl +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_Team.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_Team.hpp new file mode 100644 index 0000000000..bf0c219338 --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelFor_Team.hpp @@ -0,0 +1,177 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_HIP_PARALLEL_FOR_TEAM_HPP +#define KOKKOS_HIP_PARALLEL_FOR_TEAM_HPP + +#include + +#include +#include +#include +#include + +namespace Kokkos { +namespace Impl { + +template +class ParallelFor, HIP> { + public: + using Policy = TeamPolicy; + using functor_type = FunctorType; + using size_type = HIP::size_type; + + private: + using member_type = typename Policy::member_type; + using work_tag = typename Policy::work_tag; + using launch_bounds = typename Policy::launch_bounds; + + // Algorithmic constraints: blockDim.y is a power of two AND + // blockDim.y == blockDim.z == 1 shared memory utilization: + // + // [ team reduce space ] + // [ team shared space ] + + FunctorType const m_functor; + Policy const m_policy; + size_type const m_league_size; + int m_team_size; + size_type const m_vector_size; + int m_shmem_begin; + int m_shmem_size; + void* m_scratch_ptr[2]; + size_t m_scratch_size[2]; + int m_scratch_pool_id = -1; + int32_t* m_scratch_locks; + size_t m_num_scratch_locks; + + template + __device__ inline std::enable_if_t::value> exec_team( + const member_type& member) const { + m_functor(member); + } + + template + __device__ inline std::enable_if_t::value> exec_team( + const member_type& member) const { + m_functor(TagType(), member); + } + + public: + ParallelFor() = delete; + ParallelFor(ParallelFor const&) = default; + ParallelFor& operator=(ParallelFor const&) = delete; + + __device__ inline void operator()() const { + // Iterate this block through the league + int64_t threadid = 0; + if (m_scratch_size[1] > 0) { + threadid = hip_get_scratch_index(m_league_size, m_scratch_locks, + m_num_scratch_locks); + } + + int const int_league_size = static_cast(m_league_size); + for (int league_rank = blockIdx.x; league_rank < int_league_size; + league_rank += gridDim.x) { + this->template exec_team(typename Policy::member_type( + kokkos_impl_hip_shared_memory(), m_shmem_begin, m_shmem_size, + static_cast(static_cast(m_scratch_ptr[1]) + + ptrdiff_t(threadid / (blockDim.x * blockDim.y)) * + m_scratch_size[1]), + m_scratch_size[1], league_rank, m_league_size)); + } + if (m_scratch_size[1] > 0) { + hip_release_scratch_index(m_scratch_locks, threadid); + } + } + + inline void execute() const { + int64_t const shmem_size_total = m_shmem_begin + m_shmem_size; + dim3 const grid(static_cast(m_league_size), 1, 1); + dim3 const block(static_cast(m_vector_size), + static_cast(m_team_size), 1); + + using closure_type = + ParallelFor, HIP>; + Impl::hip_parallel_launch( + *this, grid, block, shmem_size_total, + m_policy.space().impl_internal_space_instance(), + true); // copy to device and execute + } + + ParallelFor(FunctorType const& arg_functor, Policy const& arg_policy) + : m_functor(arg_functor), + m_policy(arg_policy), + m_league_size(arg_policy.league_size()), + m_team_size(arg_policy.team_size()), + m_vector_size(arg_policy.impl_vector_length()) { + auto internal_space_instance = + m_policy.space().impl_internal_space_instance(); + m_team_size = m_team_size >= 0 ? m_team_size + : arg_policy.team_size_recommended( + arg_functor, ParallelForTag()); + + m_shmem_begin = (sizeof(double) * (m_team_size + 2)); + m_shmem_size = + (m_policy.scratch_size(0, m_team_size) + + FunctorTeamShmemSize::value(m_functor, m_team_size)); + m_scratch_size[0] = m_policy.scratch_size(0, m_team_size); + m_scratch_size[1] = m_policy.scratch_size(1, m_team_size); + m_scratch_locks = internal_space_instance->m_scratch_locks; + m_num_scratch_locks = internal_space_instance->m_num_scratch_locks; + + // Functor's reduce memory, team scan memory, and team shared memory depend + // upon team size. + m_scratch_ptr[0] = nullptr; + if (m_team_size <= 0) { + m_scratch_ptr[1] = nullptr; + } else { + m_scratch_pool_id = internal_space_instance->acquire_team_scratch_space(); + m_scratch_ptr[1] = internal_space_instance->resize_team_scratch_space( + m_scratch_pool_id, + static_cast(m_scratch_size[1]) * + (std::min( + static_cast(HIP().concurrency() / + (m_team_size * m_vector_size)), + static_cast(m_league_size)))); + } + + int const shmem_size_total = m_shmem_begin + m_shmem_size; + if (internal_space_instance->m_maxShmemPerBlock < shmem_size_total) { + Kokkos::Impl::throw_runtime_exception(std::string( + "Kokkos::Impl::ParallelFor< HIP > insufficient shared memory")); + } + + size_t max_size = arg_policy.team_size_max(arg_functor, ParallelForTag()); + if (static_cast(m_team_size) > static_cast(max_size)) { + Kokkos::Impl::throw_runtime_exception(std::string( + "Kokkos::Impl::ParallelFor< HIP > requested too large team size.")); + } + } + + ~ParallelFor() { + if (m_scratch_pool_id >= 0) { + m_policy.space() + .impl_internal_space_instance() + ->release_team_scratch_space(m_scratch_pool_id); + } + } +}; + +} // namespace Impl +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_MDRange.hpp similarity index 61% rename from lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp rename to lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_MDRange.hpp index 0fa325cb12..55b6218d1c 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_MDRange.hpp @@ -14,157 +14,19 @@ // //@HEADER -#ifndef KOKKOS_HIP_PARALLEL_MDRANGE_HPP -#define KOKKOS_HIP_PARALLEL_MDRANGE_HPP +#ifndef KOKKOS_HIP_PARALLEL_REDUCE_MDRANGE_HPP +#define KOKKOS_HIP_PARALLEL_REDUCE_MDRANGE_HPP + +#include #include #include #include #include #include -#include namespace Kokkos { namespace Impl { -// ParallelFor -template -class ParallelFor, HIP> { - public: - using Policy = Kokkos::MDRangePolicy; - using functor_type = FunctorType; - - private: - using array_index_type = typename Policy::array_index_type; - using index_type = typename Policy::index_type; - using LaunchBounds = typename Policy::launch_bounds; - - const FunctorType m_functor; - const Policy m_policy; - - public: - ParallelFor() = delete; - ParallelFor(ParallelFor const&) = default; - ParallelFor& operator=(ParallelFor const&) = delete; - - inline __device__ void operator()() const { - Kokkos::Impl::DeviceIterateTile(m_policy, - m_functor) - .exec_range(); - } - - inline void execute() const { - using ClosureType = ParallelFor; - if (m_policy.m_num_tiles == 0) return; - auto const maxblocks = hip_internal_maximum_grid_count(); - if (Policy::rank == 2) { - dim3 const block(m_policy.m_tile[0], m_policy.m_tile[1], 1); - dim3 const grid( - std::min( - (m_policy.m_upper[0] - m_policy.m_lower[0] + block.x - 1) / - block.x, - maxblocks[0]), - std::min( - (m_policy.m_upper[1] - m_policy.m_lower[1] + block.y - 1) / - block.y, - maxblocks[1]), - 1); - hip_parallel_launch( - *this, grid, block, 0, - m_policy.space().impl_internal_space_instance(), false); - } else if (Policy::rank == 3) { - dim3 const block(m_policy.m_tile[0], m_policy.m_tile[1], - m_policy.m_tile[2]); - dim3 const grid( - std::min( - (m_policy.m_upper[0] - m_policy.m_lower[0] + block.x - 1) / - block.x, - maxblocks[0]), - std::min( - (m_policy.m_upper[1] - m_policy.m_lower[1] + block.y - 1) / - block.y, - maxblocks[1]), - std::min( - (m_policy.m_upper[2] - m_policy.m_lower[2] + block.z - 1) / - block.z, - maxblocks[2])); - hip_parallel_launch( - *this, grid, block, 0, - m_policy.space().impl_internal_space_instance(), false); - } else if (Policy::rank == 4) { - // id0,id1 encoded within threadIdx.x; id2 to threadIdx.y; id3 to - // threadIdx.z - dim3 const block(m_policy.m_tile[0] * m_policy.m_tile[1], - m_policy.m_tile[2], m_policy.m_tile[3]); - dim3 const grid( - std::min( - m_policy.m_tile_end[0] * m_policy.m_tile_end[1], maxblocks[0]), - std::min( - (m_policy.m_upper[2] - m_policy.m_lower[2] + block.y - 1) / - block.y, - maxblocks[1]), - std::min( - (m_policy.m_upper[3] - m_policy.m_lower[3] + block.z - 1) / - block.z, - maxblocks[2])); - hip_parallel_launch( - *this, grid, block, 0, - m_policy.space().impl_internal_space_instance(), false); - } else if (Policy::rank == 5) { - // id0,id1 encoded within threadIdx.x; id2,id3 to threadIdx.y; id4 - // to threadIdx.z - dim3 const block(m_policy.m_tile[0] * m_policy.m_tile[1], - m_policy.m_tile[2] * m_policy.m_tile[3], - m_policy.m_tile[4]); - dim3 const grid( - std::min( - m_policy.m_tile_end[0] * m_policy.m_tile_end[1], maxblocks[0]), - std::min( - m_policy.m_tile_end[2] * m_policy.m_tile_end[3], maxblocks[1]), - std::min( - (m_policy.m_upper[4] - m_policy.m_lower[4] + block.z - 1) / - block.z, - maxblocks[2])); - hip_parallel_launch( - *this, grid, block, 0, - m_policy.space().impl_internal_space_instance(), false); - } else if (Policy::rank == 6) { - // id0,id1 encoded within threadIdx.x; id2,id3 to threadIdx.y; - // id4,id5 to threadIdx.z - dim3 const block(m_policy.m_tile[0] * m_policy.m_tile[1], - m_policy.m_tile[2] * m_policy.m_tile[3], - m_policy.m_tile[4] * m_policy.m_tile[5]); - dim3 const grid( - std::min( - m_policy.m_tile_end[0] * m_policy.m_tile_end[1], maxblocks[0]), - std::min( - m_policy.m_tile_end[2] * m_policy.m_tile_end[3], maxblocks[1]), - std::min( - m_policy.m_tile_end[4] * m_policy.m_tile_end[5], maxblocks[2])); - hip_parallel_launch( - *this, grid, block, 0, - m_policy.space().impl_internal_space_instance(), false); - } else { - Kokkos::abort("Kokkos::MDRange Error: Exceeded rank bounds with HIP\n"); - } - - } // end execute - - ParallelFor(FunctorType const& arg_functor, Policy const& arg_policy) - : m_functor(arg_functor), m_policy(arg_policy) {} - - template - static int max_tile_size_product(const Policy&, const Functor&) { - using closure_type = - ParallelFor, HIP>; - unsigned block_size = hip_get_max_blocksize(); - if (block_size == 0) - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::ParallelFor< HIP > could not find a valid " - "tile size.")); - return block_size; - } -}; // ParallelReduce template diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_Range.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_Range.hpp new file mode 100644 index 0000000000..c8981866e8 --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_Range.hpp @@ -0,0 +1,329 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_HIP_PARALLEL_REDUCE_RANGE_HPP +#define KOKKOS_HIP_PARALLEL_REDUCE_RANGE_HPP + +#include + +#include +#include +#include +#include + +namespace Kokkos { +namespace Impl { + +template +class ParallelReduce, + Kokkos::HIP> { + public: + using Policy = Kokkos::RangePolicy; + using FunctorType = typename CombinedFunctorReducerType::functor_type; + using ReducerType = typename CombinedFunctorReducerType::reducer_type; + + private: + using WorkRange = typename Policy::WorkRange; + using WorkTag = typename Policy::work_tag; + using Member = typename Policy::member_type; + using LaunchBounds = typename Policy::launch_bounds; + + public: + using pointer_type = typename ReducerType::pointer_type; + using value_type = typename ReducerType::value_type; + using reference_type = typename ReducerType::reference_type; + using functor_type = FunctorType; + using reducer_type = ReducerType; + using size_type = Kokkos::HIP::size_type; + using index_type = typename Policy::index_type; + // Conditionally set word_size_type to int16_t or int8_t if value_type is + // smaller than int32_t (Kokkos::HIP::size_type) + // word_size_type is used to determine the word count, shared memory buffer + // size, and global memory buffer size before the scan is performed. + // Within the scan, the word count is recomputed based on word_size_type + // and when calculating indexes into the shared/global memory buffers for + // performing the scan, word_size_type is used again. + // For scalars > 4 bytes in size, indexing into shared/global memory relies + // on the block and grid dimensions to ensure that we index at the correct + // offset rather than at every 4 byte word; such that, when the join is + // performed, we have the correct data that was copied over in chunks of 4 + // bytes. + using word_size_type = std::conditional_t< + sizeof(value_type) < sizeof(size_type), + std::conditional_t, size_type>; + + // Algorithmic constraints: blockSize is a power of two AND blockDim.y == + // blockDim.z == 1 + + const CombinedFunctorReducerType m_functor_reducer; + const Policy m_policy; + const pointer_type m_result_ptr; + const bool m_result_ptr_device_accessible; + const bool m_result_ptr_host_accessible; + word_size_type* m_scratch_space = nullptr; + size_type* m_scratch_flags = nullptr; + + static constexpr bool UseShflReduction = false; + + private: + struct ShflReductionTag {}; + struct SHMEMReductionTag {}; + + // Make the exec_range calls call to Reduce::DeviceIterateTile + template + __device__ inline std::enable_if_t::value> exec_range( + const Member& i, reference_type update) const { + m_functor_reducer.get_functor()(i, update); + } + + template + __device__ inline std::enable_if_t::value> exec_range( + const Member& i, reference_type update) const { + m_functor_reducer.get_functor()(TagType(), i, update); + } + + public: + __device__ inline void operator()() const { + using ReductionTag = std::conditional_t; + run(ReductionTag{}); + } + + __device__ inline void run(SHMEMReductionTag) const { + const ReducerType& reducer = m_functor_reducer.get_reducer(); + const integral_nonzero_constant + word_count(reducer.value_size() / sizeof(word_size_type)); + + { + reference_type value = reducer.init(reinterpret_cast( + ::Kokkos::kokkos_impl_hip_shared_memory() + + threadIdx.y * word_count.value)); + + // Number of blocks is bounded so that the reduction can be limited to two + // passes. Each thread block is given an approximately equal amount of + // work to perform. Accumulate the values for this block. The accumulation + // ordering does not match the final pass, but is arithmetically + // equivalent. + + const WorkRange range(m_policy, blockIdx.x, gridDim.x); + + for (Member iwork = range.begin() + threadIdx.y, iwork_end = range.end(); + iwork < iwork_end; iwork += blockDim.y) { + this->template exec_range(iwork, value); + } + } + + // Reduce with final value at blockDim.y - 1 location. + // Shortcut for length zero reduction + bool do_final_reduction = m_policy.begin() == m_policy.end(); + if (!do_final_reduction) + do_final_reduction = hip_single_inter_block_reduce_scan( + reducer, blockIdx.x, gridDim.x, + ::Kokkos::kokkos_impl_hip_shared_memory(), + m_scratch_space, m_scratch_flags); + if (do_final_reduction) { + // This is the final block with the final result at the final threads' + // location + + word_size_type* const shared = + ::Kokkos::kokkos_impl_hip_shared_memory() + + (blockDim.y - 1) * word_count.value; + word_size_type* const global = + m_result_ptr_device_accessible + ? reinterpret_cast(m_result_ptr) + : m_scratch_space; + + if (threadIdx.y == 0) { + reducer.final(reinterpret_cast(shared)); + } + + if (::Kokkos::Impl::HIPTraits::WarpSize < word_count.value) { + __syncthreads(); + } + + for (unsigned i = threadIdx.y; i < word_count.value; i += blockDim.y) { + global[i] = shared[i]; + } + } + } + + __device__ inline void run(ShflReductionTag) const { + const ReducerType& reducer = m_functor_reducer.get_reducer(); + + value_type value; + reducer.init(&value); + // Number of blocks is bounded so that the reduction can be limited to two + // passes. Each thread block is given an approximately equal amount of work + // to perform. Accumulate the values for this block. The accumulation + // ordering does not match the final pass, but is arithmetically equivalent. + + WorkRange const range(m_policy, blockIdx.x, gridDim.x); + + for (Member iwork = range.begin() + threadIdx.y, iwork_end = range.end(); + iwork < iwork_end; iwork += blockDim.y) { + this->template exec_range(iwork, value); + } + + pointer_type const result = reinterpret_cast(m_scratch_space); + + int max_active_thread = static_cast(range.end() - range.begin()) < + static_cast(blockDim.y) + ? range.end() - range.begin() + : blockDim.y; + + max_active_thread = + (max_active_thread == 0) ? blockDim.y : max_active_thread; + + value_type init; + reducer.init(&init); + if (m_policy.begin() == m_policy.end()) { + reducer.final(&value); + pointer_type const final_result = + m_result_ptr_device_accessible ? m_result_ptr : result; + *final_result = value; + } else if (Impl::hip_inter_block_shuffle_reduction<>( + value, init, reducer, m_scratch_space, result, + m_scratch_flags, max_active_thread)) { + unsigned int const id = threadIdx.y * blockDim.x + threadIdx.x; + if (id == 0) { + reducer.final(&value); + pointer_type const final_result = + m_result_ptr_device_accessible ? m_result_ptr : result; + *final_result = value; + } + } + } + + // Determine block size constrained by shared memory: + inline unsigned local_block_size(const FunctorType& f) { + const auto& instance = m_policy.space().impl_internal_space_instance(); + auto shmem_functor = [&f](unsigned n) { + return hip_single_inter_block_reduce_scan_shmem(f, n); + }; + return Kokkos::Impl::hip_get_preferred_blocksize( + instance, shmem_functor); + } + + inline void execute() { + const ReducerType& reducer = m_functor_reducer.get_reducer(); + + const index_type nwork = m_policy.end() - m_policy.begin(); + const bool need_device_set = ReducerType::has_init_member_function() || + ReducerType::has_final_member_function() || + !m_result_ptr_host_accessible || + !std::is_same::value; + if ((nwork > 0) || need_device_set) { + const int block_size = local_block_size(m_functor_reducer.get_functor()); + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > could not find a " + "valid execution configuration.")); + } + + // REQUIRED ( 1 , N , 1 ) + dim3 block(1, block_size, 1); + // use a slightly less constrained, but still well bounded limit for + // scratch + int nblocks = (nwork + block.y - 1) / block.y; + // Heuristic deciding the value of nblocks. + // The general idea here is we want to: + // 1. Not undersubscribe the device (i.e., we want at least + // preferred_block_min blocks) + // 2. Have each thread reduce > 1 value to minimize overheads + // 3. Limit the total # of blocks, to avoid unbounded scratch space + constexpr int block_max = 4096; + constexpr int preferred_block_min = 1024; + + if (nblocks < preferred_block_min) { + // keep blocks as is, already have low parallelism + } else if (nblocks > block_max) { + // "large dispatch" -> already have lots of parallelism + nblocks = block_max; + } else { + // in the intermediate range, try to have each thread process multiple + // items to offset the cost of the reduction (with not enough + // parallelism to hide it) + int items_per_thread = + (nwork + nblocks * block_size - 1) / (nblocks * block_size); + if (items_per_thread < 4) { + int ratio = std::min( + (nblocks + preferred_block_min - 1) / preferred_block_min, + (4 + items_per_thread - 1) / items_per_thread); + nblocks /= ratio; + } + } + + // TODO: down casting these uses more space than required? + m_scratch_space = + (word_size_type*)::Kokkos::Impl::hip_internal_scratch_space( + m_policy.space(), reducer.value_size() * nblocks); + // Intentionally do not downcast to word_size_type since we use HIP + // atomics in Kokkos_HIP_ReduceScan.hpp + m_scratch_flags = ::Kokkos::Impl::hip_internal_scratch_flags( + m_policy.space(), sizeof(size_type)); + // Required grid.x <= block.y + dim3 grid(nblocks, 1, 1); + + if (nwork == 0) { + block = dim3(1, 1, 1); + grid = dim3(1, 1, 1); + } + const int shmem = + UseShflReduction + ? 0 + : hip_single_inter_block_reduce_scan_shmem( + m_functor_reducer.get_functor(), block.y); + + Kokkos::Impl::hip_parallel_launch( + *this, grid, block, shmem, + m_policy.space().impl_internal_space_instance(), + false); // copy to device and execute + + if (!m_result_ptr_device_accessible && m_result_ptr) { + const int size = reducer.value_size(); + DeepCopy(m_policy.space(), m_result_ptr, + m_scratch_space, size); + } + } else { + if (m_result_ptr) { + reducer.init(m_result_ptr); + } + } + } + + template + ParallelReduce(const CombinedFunctorReducerType& arg_functor_reducer, + const Policy& arg_policy, const ViewType& arg_result) + : m_functor_reducer(arg_functor_reducer), + m_policy(arg_policy), + m_result_ptr(arg_result.data()), + m_result_ptr_device_accessible( + MemorySpaceAccess::accessible), + m_result_ptr_host_accessible( + MemorySpaceAccess::accessible) {} +}; + +} // namespace Impl +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_Team.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_Team.hpp new file mode 100644 index 0000000000..609ba28b86 --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelReduce_Team.hpp @@ -0,0 +1,394 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_HIP_PARALLEL_REDUCE_TEAM_HPP +#define KOKKOS_HIP_PARALLEL_REDUCE_TEAM_HPP + +#include + +#include +#include +#include +#include + +namespace Kokkos { +namespace Impl { + +template +class ParallelReduce, HIP> { + public: + using Policy = TeamPolicyInternal; + using FunctorType = typename CombinedFunctorReducerType::functor_type; + using ReducerType = typename CombinedFunctorReducerType::reducer_type; + + private: + using member_type = typename Policy::member_type; + using work_tag = typename Policy::work_tag; + using launch_bounds = typename Policy::launch_bounds; + + using pointer_type = typename ReducerType::pointer_type; + using reference_type = typename ReducerType::reference_type; + using value_type = typename ReducerType::value_type; + + public: + using functor_type = FunctorType; + using size_type = HIP::size_type; + + // static int constexpr UseShflReduction = false; + // FIXME_HIP This should be disabled unconditionally for best performance, but + // it currently causes tests to fail. + static constexpr int UseShflReduction = + (ReducerType::static_value_size() != 0); + + private: + struct ShflReductionTag {}; + struct SHMEMReductionTag {}; + + // Algorithmic constraints: blockDim.y is a power of two AND + // blockDim.y == blockDim.z == 1 shared memory utilization: + // + // [ global reduce space ] + // [ team reduce space ] + // [ team shared space ] + // + + const CombinedFunctorReducerType m_functor_reducer; + const Policy m_policy; + const pointer_type m_result_ptr; + const bool m_result_ptr_device_accessible; + const bool m_result_ptr_host_accessible; + size_type* m_scratch_space; + size_type* m_scratch_flags; + size_type m_team_begin; + size_type m_shmem_begin; + size_type m_shmem_size; + void* m_scratch_ptr[2]; + size_t m_scratch_size[2]; + int m_scratch_pool_id = -1; + int32_t* m_scratch_locks; + size_t m_num_scratch_locks; + const size_type m_league_size; + int m_team_size; + const size_type m_vector_size; + + template + __device__ inline std::enable_if_t::value> exec_team( + member_type const& member, reference_type update) const { + m_functor_reducer.get_functor()(member, update); + } + + template + __device__ inline std::enable_if_t::value> exec_team( + member_type const& member, reference_type update) const { + m_functor_reducer.get_functor()(TagType(), member, update); + } + + __device__ inline void iterate_through_league(int const threadid, + reference_type value) const { + int const int_league_size = static_cast(m_league_size); + for (int league_rank = blockIdx.x; league_rank < int_league_size; + league_rank += gridDim.x) { + this->template exec_team( + member_type( + kokkos_impl_hip_shared_memory() + m_team_begin, + m_shmem_begin, m_shmem_size, + reinterpret_cast( + reinterpret_cast(m_scratch_ptr[1]) + + static_cast(threadid / (blockDim.x * blockDim.y)) * + m_scratch_size[1]), + m_scratch_size[1], league_rank, m_league_size), + value); + } + } + + int compute_block_count() const { + constexpr auto light_weight = + Kokkos::Experimental::WorkItemProperty::HintLightWeight; + constexpr typename Policy::work_item_property property; + // Numbers were tuned on MI210 using dot product and yAx benchmarks + constexpr int block_max = + (property & light_weight) == light_weight ? 2097152 : 65536; + constexpr int preferred_block_min = 1024; + int block_count = m_league_size; + if (block_count < preferred_block_min) { + // keep blocks as is, already low parallelism + } else if (block_count >= block_max) { + block_count = block_max; + + } else { + int nwork = m_league_size * m_team_size; + int items_per_thread = + (nwork + block_count * m_team_size - 1) / (block_count * m_team_size); + if (items_per_thread < 4) { + int ratio = std::min( + (block_count + preferred_block_min - 1) / preferred_block_min, + (4 + items_per_thread - 1) / items_per_thread); + block_count /= ratio; + } + } + + return block_count; + } + + public: + __device__ inline void operator()() const { + int64_t threadid = 0; + if (m_scratch_size[1] > 0) { + threadid = hip_get_scratch_index(m_league_size, m_scratch_locks, + m_num_scratch_locks); + } + + using ReductionTag = std::conditional_t; + run(ReductionTag{}, threadid); + + if (m_scratch_size[1] > 0) { + hip_release_scratch_index(m_scratch_locks, threadid); + } + } + + __device__ inline void run(SHMEMReductionTag, int const threadid) const { + const ReducerType& reducer = m_functor_reducer.get_reducer(); + + integral_nonzero_constant const + word_count(reducer.value_size() / sizeof(size_type)); + + reference_type value = + reducer.init(kokkos_impl_hip_shared_memory() + + threadIdx.y * word_count.value); + // Iterate this block through the league + iterate_through_league(threadid, value); + + // Reduce with final value at blockDim.y - 1 location. + bool do_final_reduce = (m_league_size == 0); + if (!do_final_reduce) + do_final_reduce = + hip_single_inter_block_reduce_scan( + reducer, blockIdx.x, gridDim.x, + kokkos_impl_hip_shared_memory(), m_scratch_space, + m_scratch_flags); + if (do_final_reduce) { + // This is the final block with the final result at the final threads' + // location + + size_type* const shared = kokkos_impl_hip_shared_memory() + + (blockDim.y - 1) * word_count.value; + size_type* const global = m_result_ptr_device_accessible + ? reinterpret_cast(m_result_ptr) + : m_scratch_space; + + if (threadIdx.y == 0) { + reducer.final(reinterpret_cast(shared)); + } + + if (HIPTraits::WarpSize < word_count.value) { + __syncthreads(); + } + + for (unsigned i = threadIdx.y; i < word_count.value; i += blockDim.y) { + global[i] = shared[i]; + } + } + } + + __device__ inline void run(ShflReductionTag, int const threadid) const { + const ReducerType& reducer = m_functor_reducer.get_reducer(); + + value_type value; + reducer.init(&value); + + // Iterate this block through the league + iterate_through_league(threadid, value); + + pointer_type const result = + m_result_ptr_device_accessible + ? m_result_ptr + : reinterpret_cast(m_scratch_space); + + value_type init; + reducer.init(&init); + if (m_league_size == 0) { + reducer.final(&value); + *result = value; + } else if (Impl::hip_inter_block_shuffle_reduction( + value, init, reducer, m_scratch_space, result, + m_scratch_flags, blockDim.y)) { + unsigned int const id = threadIdx.y * blockDim.x + threadIdx.x; + if (id == 0) { + reducer.final(&value); + *result = value; + } + } + } + + inline void execute() { + const ReducerType& reducer = m_functor_reducer.get_reducer(); + + const bool is_empty_range = m_league_size == 0 || m_team_size == 0; + const bool need_device_set = ReducerType::has_init_member_function() || + ReducerType::has_final_member_function() || + !m_result_ptr_host_accessible || + Policy::is_graph_kernel::value || + !std::is_same::value; + if (!is_empty_range || need_device_set) { + int const block_count = compute_block_count(); + + m_scratch_space = hip_internal_scratch_space( + m_policy.space(), reducer.value_size() * block_count); + m_scratch_flags = + hip_internal_scratch_flags(m_policy.space(), sizeof(size_type)); + + dim3 block(m_vector_size, m_team_size, 1); + dim3 grid(block_count, 1, 1); + if (is_empty_range) { + block = dim3(1, 1, 1); + grid = dim3(1, 1, 1); + } + const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size; + + Impl::hip_parallel_launch( + *this, grid, block, shmem_size_total, + m_policy.space().impl_internal_space_instance(), + true); // copy to device and execute + + if (!m_result_ptr_device_accessible) { + m_policy.space().impl_internal_space_instance()->fence(); + + if (m_result_ptr) { + const int size = reducer.value_size(); + DeepCopy(m_policy.space(), m_result_ptr, + m_scratch_space, size); + } + } + } else { + if (m_result_ptr) { + reducer.init(m_result_ptr); + } + } + } + + template + ParallelReduce(CombinedFunctorReducerType const& arg_functor_reducer, + Policy const& arg_policy, ViewType const& arg_result) + : m_functor_reducer(arg_functor_reducer), + m_policy(arg_policy), + m_result_ptr(arg_result.data()), + m_result_ptr_device_accessible( + MemorySpaceAccess::accessible), + m_result_ptr_host_accessible( + MemorySpaceAccess::accessible), + m_scratch_space(nullptr), + m_scratch_flags(nullptr), + m_team_begin(0), + m_shmem_begin(0), + m_shmem_size(0), + m_scratch_ptr{nullptr, nullptr}, + m_league_size(arg_policy.league_size()), + m_team_size(arg_policy.team_size()), + m_vector_size(arg_policy.impl_vector_length()) { + auto internal_space_instance = + m_policy.space().impl_internal_space_instance(); + m_team_size = m_team_size >= 0 ? m_team_size + : arg_policy.team_size_recommended( + arg_functor_reducer.get_functor(), + arg_functor_reducer.get_reducer(), + ParallelReduceTag()); + + m_team_begin = + UseShflReduction + ? 0 + : hip_single_inter_block_reduce_scan_shmem( + arg_functor_reducer.get_functor(), m_team_size); + m_shmem_begin = sizeof(double) * (m_team_size + 2); + m_shmem_size = m_policy.scratch_size(0, m_team_size) + + FunctorTeamShmemSize::value( + arg_functor_reducer.get_functor(), m_team_size); + m_scratch_size[0] = m_shmem_size; + m_scratch_size[1] = m_policy.scratch_size(1, m_team_size); + m_scratch_locks = internal_space_instance->m_scratch_locks; + m_num_scratch_locks = internal_space_instance->m_num_scratch_locks; + if (m_team_size <= 0) { + m_scratch_ptr[1] = nullptr; + } else { + m_scratch_pool_id = internal_space_instance->acquire_team_scratch_space(); + m_scratch_ptr[1] = internal_space_instance->resize_team_scratch_space( + m_scratch_pool_id, + static_cast(m_scratch_size[1]) * + (std::min( + static_cast(HIP().concurrency() / + (m_team_size * m_vector_size)), + static_cast(m_league_size)))); + } + + // The global parallel_reduce does not support vector_length other than 1 at + // the moment + if ((arg_policy.impl_vector_length() > 1) && !UseShflReduction) + Impl::throw_runtime_exception( + "Kokkos::parallel_reduce with a TeamPolicy using a vector length of " + "greater than 1 is not currently supported for HIP for dynamic " + "sized reduction types."); + + if ((m_team_size < HIPTraits::WarpSize) && !UseShflReduction) + Impl::throw_runtime_exception( + "Kokkos::parallel_reduce with a TeamPolicy using a team_size smaller " + "than 64 is not currently supported with HIP for dynamic sized " + "reduction types."); + + // Functor's reduce memory, team scan memory, and team shared memory depend + // upon team size. + + const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size; + + if (!Kokkos::Impl::is_integral_power_of_two(m_team_size) && + !UseShflReduction) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > bad team size")); + } + + if (internal_space_instance->m_maxShmemPerBlock < shmem_size_total) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > requested too much " + "L0 scratch memory")); + } + + size_t max_size = arg_policy.team_size_max( + arg_functor_reducer.get_functor(), arg_functor_reducer.get_reducer(), + ParallelReduceTag()); + if (static_cast(m_team_size) > static_cast(max_size)) { + Kokkos::Impl::throw_runtime_exception( + std::string("Kokkos::Impl::ParallelReduce< HIP > requested too " + "large team size.")); + } + } + + ~ParallelReduce() { + if (m_scratch_pool_id >= 0) { + m_policy.space() + .impl_internal_space_instance() + ->release_team_scratch_space(m_scratch_pool_id); + } + } +}; + +} // namespace Impl +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelScan_Range.hpp similarity index 50% rename from lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp rename to lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelScan_Range.hpp index 26e8be4698..41692a3291 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ParallelScan_Range.hpp @@ -14,390 +14,18 @@ // //@HEADER -#ifndef KOKKO_HIP_PARALLEL_RANGE_HPP -#define KOKKO_HIP_PARALLEL_RANGE_HPP +#ifndef KOKKOS_HIP_PARALLEL_SCAN_RANGE_HPP +#define KOKKOS_HIP_PARALLEL_SCAN_RANGE_HPP #include -#if defined(__HIPCC__) - #include #include #include -#include -#include namespace Kokkos { namespace Impl { -template -class ParallelFor, Kokkos::HIP> { - public: - using Policy = Kokkos::RangePolicy; - - private: - using Member = typename Policy::member_type; - using WorkTag = typename Policy::work_tag; - using LaunchBounds = typename Policy::launch_bounds; - - const FunctorType m_functor; - const Policy m_policy; - - template - inline __device__ std::enable_if_t::value> exec_range( - const Member i) const { - m_functor(i); - } - - template - inline __device__ std::enable_if_t::value> exec_range( - const Member i) const { - m_functor(TagType(), i); - } - - public: - using functor_type = FunctorType; - - ParallelFor() = delete; - ParallelFor(ParallelFor const&) = default; - ParallelFor& operator=(ParallelFor const&) = delete; - - inline __device__ void operator()() const { - const Member work_stride = blockDim.y * gridDim.x; - const Member work_end = m_policy.end(); - - for (Member iwork = - m_policy.begin() + threadIdx.y + blockDim.y * blockIdx.x; - iwork < work_end; - iwork = iwork < work_end - work_stride ? iwork + work_stride - : work_end) { - this->template exec_range(iwork); - } - } - - inline void execute() const { - const typename Policy::index_type nwork = m_policy.end() - m_policy.begin(); - - using DriverType = ParallelFor; - const int block_size = - Kokkos::Impl::hip_get_preferred_blocksize(); - const dim3 block(1, block_size, 1); - const dim3 grid( - typename Policy::index_type((nwork + block.y - 1) / block.y), 1, 1); - - if (block_size == 0) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::ParallelFor< HIP > could not find a " - "valid execution configuration.")); - } - Kokkos::Impl::hip_parallel_launch( - *this, grid, block, 0, m_policy.space().impl_internal_space_instance(), - false); - } - - ParallelFor(const FunctorType& arg_functor, const Policy& arg_policy) - : m_functor(arg_functor), m_policy(arg_policy) {} -}; - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -template -class ParallelReduce, - Kokkos::HIP> { - public: - using Policy = Kokkos::RangePolicy; - using FunctorType = typename CombinedFunctorReducerType::functor_type; - using ReducerType = typename CombinedFunctorReducerType::reducer_type; - - private: - using WorkRange = typename Policy::WorkRange; - using WorkTag = typename Policy::work_tag; - using Member = typename Policy::member_type; - using LaunchBounds = typename Policy::launch_bounds; - - public: - using pointer_type = typename ReducerType::pointer_type; - using value_type = typename ReducerType::value_type; - using reference_type = typename ReducerType::reference_type; - using functor_type = FunctorType; - using reducer_type = ReducerType; - using size_type = Kokkos::HIP::size_type; - using index_type = typename Policy::index_type; - // Conditionally set word_size_type to int16_t or int8_t if value_type is - // smaller than int32_t (Kokkos::HIP::size_type) - // word_size_type is used to determine the word count, shared memory buffer - // size, and global memory buffer size before the scan is performed. - // Within the scan, the word count is recomputed based on word_size_type - // and when calculating indexes into the shared/global memory buffers for - // performing the scan, word_size_type is used again. - // For scalars > 4 bytes in size, indexing into shared/global memory relies - // on the block and grid dimensions to ensure that we index at the correct - // offset rather than at every 4 byte word; such that, when the join is - // performed, we have the correct data that was copied over in chunks of 4 - // bytes. - using word_size_type = std::conditional_t< - sizeof(value_type) < sizeof(size_type), - std::conditional_t, size_type>; - - // Algorithmic constraints: blockSize is a power of two AND blockDim.y == - // blockDim.z == 1 - - const CombinedFunctorReducerType m_functor_reducer; - const Policy m_policy; - const pointer_type m_result_ptr; - const bool m_result_ptr_device_accessible; - const bool m_result_ptr_host_accessible; - word_size_type* m_scratch_space = nullptr; - size_type* m_scratch_flags = nullptr; - - static constexpr bool UseShflReduction = false; - - private: - struct ShflReductionTag {}; - struct SHMEMReductionTag {}; - - // Make the exec_range calls call to Reduce::DeviceIterateTile - template - __device__ inline std::enable_if_t::value> exec_range( - const Member& i, reference_type update) const { - m_functor_reducer.get_functor()(i, update); - } - - template - __device__ inline std::enable_if_t::value> exec_range( - const Member& i, reference_type update) const { - m_functor_reducer.get_functor()(TagType(), i, update); - } - - public: - __device__ inline void operator()() const { - using ReductionTag = std::conditional_t; - run(ReductionTag{}); - } - - __device__ inline void run(SHMEMReductionTag) const { - const ReducerType& reducer = m_functor_reducer.get_reducer(); - const integral_nonzero_constant - word_count(reducer.value_size() / sizeof(word_size_type)); - - { - reference_type value = reducer.init(reinterpret_cast( - ::Kokkos::kokkos_impl_hip_shared_memory() + - threadIdx.y * word_count.value)); - - // Number of blocks is bounded so that the reduction can be limited to two - // passes. Each thread block is given an approximately equal amount of - // work to perform. Accumulate the values for this block. The accumulation - // ordering does not match the final pass, but is arithmetically - // equivalent. - - const WorkRange range(m_policy, blockIdx.x, gridDim.x); - - for (Member iwork = range.begin() + threadIdx.y, iwork_end = range.end(); - iwork < iwork_end; iwork += blockDim.y) { - this->template exec_range(iwork, value); - } - } - - // Reduce with final value at blockDim.y - 1 location. - // Shortcut for length zero reduction - bool do_final_reduction = m_policy.begin() == m_policy.end(); - if (!do_final_reduction) - do_final_reduction = hip_single_inter_block_reduce_scan( - reducer, blockIdx.x, gridDim.x, - ::Kokkos::kokkos_impl_hip_shared_memory(), - m_scratch_space, m_scratch_flags); - if (do_final_reduction) { - // This is the final block with the final result at the final threads' - // location - - word_size_type* const shared = - ::Kokkos::kokkos_impl_hip_shared_memory() + - (blockDim.y - 1) * word_count.value; - word_size_type* const global = - m_result_ptr_device_accessible - ? reinterpret_cast(m_result_ptr) - : m_scratch_space; - - if (threadIdx.y == 0) { - reducer.final(reinterpret_cast(shared)); - } - - if (::Kokkos::Impl::HIPTraits::WarpSize < word_count.value) { - __syncthreads(); - } - - for (unsigned i = threadIdx.y; i < word_count.value; i += blockDim.y) { - global[i] = shared[i]; - } - } - } - - __device__ inline void run(ShflReductionTag) const { - const ReducerType& reducer = m_functor_reducer.get_reducer(); - - value_type value; - reducer.init(&value); - // Number of blocks is bounded so that the reduction can be limited to two - // passes. Each thread block is given an approximately equal amount of work - // to perform. Accumulate the values for this block. The accumulation - // ordering does not match the final pass, but is arithmetically equivalent. - - WorkRange const range(m_policy, blockIdx.x, gridDim.x); - - for (Member iwork = range.begin() + threadIdx.y, iwork_end = range.end(); - iwork < iwork_end; iwork += blockDim.y) { - this->template exec_range(iwork, value); - } - - pointer_type const result = reinterpret_cast(m_scratch_space); - - int max_active_thread = static_cast(range.end() - range.begin()) < - static_cast(blockDim.y) - ? range.end() - range.begin() - : blockDim.y; - - max_active_thread = - (max_active_thread == 0) ? blockDim.y : max_active_thread; - - value_type init; - reducer.init(&init); - if (m_policy.begin() == m_policy.end()) { - reducer.final(&value); - pointer_type const final_result = - m_result_ptr_device_accessible ? m_result_ptr : result; - *final_result = value; - } else if (Impl::hip_inter_block_shuffle_reduction<>( - value, init, reducer, m_scratch_space, result, - m_scratch_flags, max_active_thread)) { - unsigned int const id = threadIdx.y * blockDim.x + threadIdx.x; - if (id == 0) { - reducer.final(&value); - pointer_type const final_result = - m_result_ptr_device_accessible ? m_result_ptr : result; - *final_result = value; - } - } - } - - // Determine block size constrained by shared memory: - inline unsigned local_block_size(const FunctorType& f) { - const auto& instance = m_policy.space().impl_internal_space_instance(); - auto shmem_functor = [&f](unsigned n) { - return hip_single_inter_block_reduce_scan_shmem(f, n); - }; - return Kokkos::Impl::hip_get_preferred_blocksize( - instance, shmem_functor); - } - - inline void execute() { - const ReducerType& reducer = m_functor_reducer.get_reducer(); - - const index_type nwork = m_policy.end() - m_policy.begin(); - const bool need_device_set = ReducerType::has_init_member_function() || - ReducerType::has_final_member_function() || - !m_result_ptr_host_accessible || - !std::is_same::value; - if ((nwork > 0) || need_device_set) { - const int block_size = local_block_size(m_functor_reducer.get_functor()); - if (block_size == 0) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::ParallelReduce< HIP > could not find a " - "valid execution configuration.")); - } - - // REQUIRED ( 1 , N , 1 ) - dim3 block(1, block_size, 1); - // use a slightly less constrained, but still well bounded limit for - // scratch - int nblocks = (nwork + block.y - 1) / block.y; - // Heuristic deciding the value of nblocks. - // The general idea here is we want to: - // 1. Not undersubscribe the device (i.e., we want at least - // preferred_block_min blocks) - // 2. Have each thread reduce > 1 value to minimize overheads - // 3. Limit the total # of blocks, to avoid unbounded scratch space - constexpr int block_max = 4096; - constexpr int preferred_block_min = 1024; - - if (nblocks < preferred_block_min) { - // keep blocks as is, already have low parallelism - } else if (nblocks > block_max) { - // "large dispatch" -> already have lots of parallelism - nblocks = block_max; - } else { - // in the intermediate range, try to have each thread process multiple - // items to offset the cost of the reduction (with not enough - // parallelism to hide it) - int items_per_thread = - (nwork + nblocks * block_size - 1) / (nblocks * block_size); - if (items_per_thread < 4) { - int ratio = std::min( - (nblocks + preferred_block_min - 1) / preferred_block_min, - (4 + items_per_thread - 1) / items_per_thread); - nblocks /= ratio; - } - } - - // TODO: down casting these uses more space than required? - m_scratch_space = - (word_size_type*)::Kokkos::Impl::hip_internal_scratch_space( - m_policy.space(), reducer.value_size() * nblocks); - // Intentionally do not downcast to word_size_type since we use HIP - // atomics in Kokkos_HIP_ReduceScan.hpp - m_scratch_flags = ::Kokkos::Impl::hip_internal_scratch_flags( - m_policy.space(), sizeof(size_type)); - // Required grid.x <= block.y - dim3 grid(nblocks, 1, 1); - - if (nwork == 0) { - block = dim3(1, 1, 1); - grid = dim3(1, 1, 1); - } - const int shmem = - UseShflReduction - ? 0 - : hip_single_inter_block_reduce_scan_shmem( - m_functor_reducer.get_functor(), block.y); - - Kokkos::Impl::hip_parallel_launch( - *this, grid, block, shmem, - m_policy.space().impl_internal_space_instance(), - false); // copy to device and execute - - if (!m_result_ptr_device_accessible && m_result_ptr) { - const int size = reducer.value_size(); - DeepCopy(m_policy.space(), m_result_ptr, - m_scratch_space, size); - } - } else { - if (m_result_ptr) { - reducer.init(m_result_ptr); - } - } - } - - template - ParallelReduce(const CombinedFunctorReducerType& arg_functor_reducer, - const Policy& arg_policy, const ViewType& arg_result) - : m_functor_reducer(arg_functor_reducer), - m_policy(arg_policy), - m_result_ptr(arg_result.data()), - m_result_ptr_device_accessible( - MemorySpaceAccess::accessible), - m_result_ptr_host_accessible( - MemorySpaceAccess::accessible) {} -}; - template class ParallelScanHIPBase { public: @@ -763,5 +391,3 @@ class ParallelScanWithTotal, } // namespace Kokkos #endif - -#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp deleted file mode 100644 index 3fe568ac36..0000000000 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp +++ /dev/null @@ -1,936 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#ifndef KOKKO_HIP_PARALLEL_TEAM_HPP -#define KOKKO_HIP_PARALLEL_TEAM_HPP - -#include - -#if defined(__HIPCC__) - -#include -#include -#include -#include - -namespace Kokkos { -namespace Impl { - -template -class TeamPolicyInternal - : public PolicyTraits { - public: - using execution_policy = TeamPolicyInternal; - - using traits = PolicyTraits; - - template - friend class TeamPolicyInternal; - - private: - typename traits::execution_space m_space; - int m_league_size; - int m_team_size; - int m_vector_length; - size_t m_team_scratch_size[2]; - size_t m_thread_scratch_size[2]; - int m_chunk_size; - bool m_tune_team_size; - bool m_tune_vector_length; - - public: - using execution_space = HIP; - - template - TeamPolicyInternal(TeamPolicyInternal const& p) { - m_league_size = p.m_league_size; - m_team_size = p.m_team_size; - m_vector_length = p.m_vector_length; - m_team_scratch_size[0] = p.m_team_scratch_size[0]; - m_team_scratch_size[1] = p.m_team_scratch_size[1]; - m_thread_scratch_size[0] = p.m_thread_scratch_size[0]; - m_thread_scratch_size[1] = p.m_thread_scratch_size[1]; - m_chunk_size = p.m_chunk_size; - m_space = p.m_space; - m_tune_team_size = p.m_tune_team_size; - m_tune_vector_length = p.m_tune_vector_length; - } - - template - int team_size_max(FunctorType const& f, ParallelForTag const&) const { - using closure_type = - Impl::ParallelFor>; - - return internal_team_size_common(f); - } - - template - inline int team_size_max(const FunctorType& f, - const ParallelReduceTag&) const { - using functor_analysis_type = - Impl::FunctorAnalysis; - using closure_type = Impl::ParallelReduce< - CombinedFunctorReducer, - TeamPolicy, Kokkos::HIP>; - return internal_team_size_common< - BlockType::Max, closure_type, - typename functor_analysis_type::value_type>(f); - } - - template - inline int team_size_max(const FunctorType& f, const ReducerType&, - const ParallelReduceTag&) const { - using closure_type = - Impl::ParallelReduce, - TeamPolicy, Kokkos::HIP>; - return internal_team_size_common(f); - } - - template - int team_size_recommended(FunctorType const& f, ParallelForTag const&) const { - using closure_type = - Impl::ParallelFor>; - - return internal_team_size_common( - f); - } - - template - inline int team_size_recommended(FunctorType const& f, - ParallelReduceTag const&) const { - using functor_analysis_type = - Impl::FunctorAnalysis; - using closure_type = Impl::ParallelReduce< - CombinedFunctorReducer, - TeamPolicy, Kokkos::HIP>; - return internal_team_size_common< - BlockType::Preferred, closure_type, - typename functor_analysis_type::value_type>(f); - } - - template - int team_size_recommended(FunctorType const& f, ReducerType const&, - ParallelReduceTag const&) const { - using closure_type = - Impl::ParallelReduce, - TeamPolicy, Kokkos::HIP>; - return internal_team_size_common(f); - } - - inline bool impl_auto_vector_length() const { return m_tune_vector_length; } - inline bool impl_auto_team_size() const { return m_tune_team_size; } - static int vector_length_max() { return HIPTraits::WarpSize; } - - static int verify_requested_vector_length(int requested_vector_length) { - int test_vector_length = - std::min(requested_vector_length, vector_length_max()); - - // Allow only power-of-two vector_length - if (!(is_integral_power_of_two(test_vector_length))) { - int test_pow2 = 1; - constexpr int warp_size = HIPTraits::WarpSize; - while (test_pow2 < warp_size) { - test_pow2 <<= 1; - if (test_pow2 > test_vector_length) { - break; - } - } - test_vector_length = test_pow2 >> 1; - } - - return test_vector_length; - } - - inline static int scratch_size_max(int level) { - // HIP Teams use (team_size + 2)*sizeof(double) shared memory for team - // reductions. They also use one int64_t in static shared memory for a - // shared ID. Furthermore, they use additional scratch memory in some - // reduction scenarios, which depend on the size of the value_type and is - // NOT captured here - constexpr size_t max_possible_team_size = 1024; - constexpr size_t max_reserved_shared_mem_per_team = - (max_possible_team_size + 2) * sizeof(double) + sizeof(int64_t); - // arbitrarily setting level 1 scratch limit to 20MB, for a - // MI250 that would give us about 4.4GB for 2 teams per CU - constexpr size_t max_l1_scratch_size = 20 * 1024 * 1024; - - size_t max_shmem = HIP().hip_device_prop().sharedMemPerBlock; - return (level == 0 ? max_shmem - max_reserved_shared_mem_per_team - : max_l1_scratch_size); - } - - inline void impl_set_vector_length(size_t size) { m_vector_length = size; } - inline void impl_set_team_size(size_t size) { m_team_size = size; } - int impl_vector_length() const { return m_vector_length; } - - int team_size() const { return m_team_size; } - - int league_size() const { return m_league_size; } - - size_t scratch_size(int level, int team_size_ = -1) const { - if (team_size_ < 0) team_size_ = m_team_size; - return m_team_scratch_size[level] + - team_size_ * m_thread_scratch_size[level]; - } - - size_t team_scratch_size(int level) const { - return m_team_scratch_size[level]; - } - - size_t thread_scratch_size(int level) const { - return m_thread_scratch_size[level]; - } - - typename traits::execution_space space() const { return m_space; } - - TeamPolicyInternal() - : m_space(typename traits::execution_space()), - m_league_size(0), - m_team_size(-1), - m_vector_length(0), - m_team_scratch_size{0, 0}, - m_thread_scratch_size{0, 0}, - m_chunk_size(HIPTraits::WarpSize), - m_tune_team_size(false), - m_tune_vector_length(false) {} - - /** \brief Specify league size, request team size */ - TeamPolicyInternal(const execution_space space_, int league_size_, - int team_size_request, int vector_length_request = 1) - : m_space(space_), - m_league_size(league_size_), - m_team_size(team_size_request), - m_vector_length( - (vector_length_request > 0) - ? verify_requested_vector_length(vector_length_request) - : (verify_requested_vector_length(1))), - m_team_scratch_size{0, 0}, - m_thread_scratch_size{0, 0}, - m_chunk_size(HIPTraits::WarpSize), - m_tune_team_size(bool(team_size_request <= 0)), - m_tune_vector_length(bool(vector_length_request <= 0)) { - // Make sure league size is permissible - if (league_size_ >= static_cast(hip_internal_maximum_grid_count()[0])) - Impl::throw_runtime_exception( - "Requested too large league_size for TeamPolicy on HIP execution " - "space."); - - // Make sure total block size is permissible - if (m_team_size * m_vector_length > HIPTraits::MaxThreadsPerBlock) { - Impl::throw_runtime_exception( - std::string("Kokkos::TeamPolicy< HIP > the team size is too large. " - "Team size x vector length must be smaller than 1024.")); - } - } - - /** \brief Specify league size, request team size */ - TeamPolicyInternal(const execution_space space_, int league_size_, - const Kokkos::AUTO_t& /* team_size_request */, - int vector_length_request = 1) - : TeamPolicyInternal(space_, league_size_, -1, vector_length_request) {} - // FLAG - /** \brief Specify league size and team size, request vector length*/ - TeamPolicyInternal(const execution_space space_, int league_size_, - int team_size_request, - const Kokkos::AUTO_t& /* vector_length_request */ - ) - : TeamPolicyInternal(space_, league_size_, team_size_request, -1) - - {} - - /** \brief Specify league size, request team size and vector length*/ - TeamPolicyInternal(const execution_space space_, int league_size_, - const Kokkos::AUTO_t& /* team_size_request */, - const Kokkos::AUTO_t& /* vector_length_request */ - - ) - : TeamPolicyInternal(space_, league_size_, -1, -1) - - {} - - TeamPolicyInternal(int league_size_, int team_size_request, - int vector_length_request = 1) - : TeamPolicyInternal(typename traits::execution_space(), league_size_, - team_size_request, vector_length_request) {} - - TeamPolicyInternal(int league_size_, - const Kokkos::AUTO_t& /* team_size_request */, - int vector_length_request = 1) - : TeamPolicyInternal(typename traits::execution_space(), league_size_, -1, - vector_length_request) {} - - /** \brief Specify league size and team size, request vector length*/ - TeamPolicyInternal(int league_size_, int team_size_request, - const Kokkos::AUTO_t& /* vector_length_request */ - - ) - : TeamPolicyInternal(typename traits::execution_space(), league_size_, - team_size_request, -1) - - {} - - /** \brief Specify league size, request team size and vector length*/ - TeamPolicyInternal(int league_size_, - const Kokkos::AUTO_t& /* team_size_request */, - const Kokkos::AUTO_t& /* vector_length_request */ - - ) - : TeamPolicyInternal(typename traits::execution_space(), league_size_, -1, - -1) {} - - int chunk_size() const { return m_chunk_size; } - - TeamPolicyInternal& set_chunk_size(typename traits::index_type chunk_size_) { - m_chunk_size = chunk_size_; - return *this; - } - - /** \brief set per team scratch size for a specific level of the scratch - * hierarchy */ - TeamPolicyInternal& set_scratch_size(int level, - PerTeamValue const& per_team) { - m_team_scratch_size[level] = per_team.value; - return *this; - } - - /** \brief set per thread scratch size for a specific level of the scratch - * hierarchy */ - TeamPolicyInternal& set_scratch_size(int level, - PerThreadValue const& per_thread) { - m_thread_scratch_size[level] = per_thread.value; - return *this; - } - - /** \brief set per thread and per team scratch size for a specific level of - * the scratch hierarchy */ - TeamPolicyInternal& set_scratch_size(int level, PerTeamValue const& per_team, - PerThreadValue const& per_thread) { - m_team_scratch_size[level] = per_team.value; - m_thread_scratch_size[level] = per_thread.value; - return *this; - } - - using member_type = Kokkos::Impl::HIPTeamMember; - - protected: - template - int internal_team_size_common(FunctorType const& f) const { - const unsigned shmem_block = team_scratch_size(0) + 2 * sizeof(double); - unsigned shmem_thread = thread_scratch_size(0) + sizeof(double); - using Tag = typename PatternTagFromImplSpecialization::type; - if constexpr (std::is_same_v) { - using Interface = - typename Impl::DeduceFunctorPatternInterface::type; - using Analysis = - Impl::FunctorAnalysis; - shmem_thread += - ((Analysis::StaticValueSize != 0) ? 0 : Analysis::value_size(f)); - } - const int vector_length = impl_vector_length(); - - const auto functor = [&f, shmem_block, shmem_thread, vector_length]( - const hipFuncAttributes& attr, int block_size) { - int functor_shmem = - ::Kokkos::Impl::FunctorTeamShmemSize::value( - f, block_size / vector_length); - return shmem_block + shmem_thread * (block_size / vector_length) + - functor_shmem + attr.sharedSizeBytes; - }; - int block_size; - if constexpr (BlockSize == BlockType::Max) { - block_size = hip_get_max_team_blocksize( - space().impl_internal_space_instance(), functor); - } else { - block_size = - hip_get_preferred_team_blocksize( - space().impl_internal_space_instance(), functor); - } - - if (block_size == 0) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::ParallelFor/Reduce< HIP > could not find a valid " - "team size.")); - } - if constexpr (std::is_same_v) { - return block_size / impl_vector_length(); - } else { - // Currently we require Power-of-2 team size for reductions. - int p2 = 1; - while (p2 <= block_size) p2 *= 2; - p2 /= 2; - return p2 / impl_vector_length(); - } - } -}; - -__device__ inline int64_t hip_get_scratch_index(HIP::size_type league_size, - int32_t* scratch_locks, - size_t num_scratch_locks) { - int64_t threadid = 0; - __shared__ int64_t base_thread_id; - if (threadIdx.x == 0 && threadIdx.y == 0) { - int64_t const wraparound_len = - Kokkos::min(int64_t(league_size), - int64_t(num_scratch_locks) / (blockDim.x * blockDim.y)); - threadid = (blockIdx.x * blockDim.z + threadIdx.z) % wraparound_len; - threadid *= blockDim.x * blockDim.y; - int done = 0; - while (!done) { - done = (0 == atomicCAS(&scratch_locks[threadid], 0, 1)); - if (!done) { - threadid += blockDim.x * blockDim.y; - if (int64_t(threadid + blockDim.x * blockDim.y) >= - wraparound_len * blockDim.x * blockDim.y) - threadid = 0; - } - } - base_thread_id = threadid; - } - __syncthreads(); - threadid = base_thread_id; - return threadid; -} - -__device__ inline void hip_release_scratch_index(int32_t* scratch_locks, - int64_t threadid) { - __syncthreads(); - if (threadIdx.x == 0 && threadIdx.y == 0) { - scratch_locks[threadid] = 0; - } -} - -template -class ParallelFor, HIP> { - public: - using Policy = TeamPolicy; - using functor_type = FunctorType; - using size_type = HIP::size_type; - - private: - using member_type = typename Policy::member_type; - using work_tag = typename Policy::work_tag; - using launch_bounds = typename Policy::launch_bounds; - - // Algorithmic constraints: blockDim.y is a power of two AND - // blockDim.y == blockDim.z == 1 shared memory utilization: - // - // [ team reduce space ] - // [ team shared space ] - - FunctorType const m_functor; - Policy const m_policy; - size_type const m_league_size; - int m_team_size; - size_type const m_vector_size; - int m_shmem_begin; - int m_shmem_size; - void* m_scratch_ptr[2]; - size_t m_scratch_size[2]; - int m_scratch_pool_id = -1; - int32_t* m_scratch_locks; - size_t m_num_scratch_locks; - - template - __device__ inline std::enable_if_t::value> exec_team( - const member_type& member) const { - m_functor(member); - } - - template - __device__ inline std::enable_if_t::value> exec_team( - const member_type& member) const { - m_functor(TagType(), member); - } - - public: - ParallelFor() = delete; - ParallelFor(ParallelFor const&) = default; - ParallelFor& operator=(ParallelFor const&) = delete; - - __device__ inline void operator()() const { - // Iterate this block through the league - int64_t threadid = 0; - if (m_scratch_size[1] > 0) { - threadid = hip_get_scratch_index(m_league_size, m_scratch_locks, - m_num_scratch_locks); - } - - int const int_league_size = static_cast(m_league_size); - for (int league_rank = blockIdx.x; league_rank < int_league_size; - league_rank += gridDim.x) { - this->template exec_team(typename Policy::member_type( - kokkos_impl_hip_shared_memory(), m_shmem_begin, m_shmem_size, - static_cast(static_cast(m_scratch_ptr[1]) + - ptrdiff_t(threadid / (blockDim.x * blockDim.y)) * - m_scratch_size[1]), - m_scratch_size[1], league_rank, m_league_size)); - } - if (m_scratch_size[1] > 0) { - hip_release_scratch_index(m_scratch_locks, threadid); - } - } - - inline void execute() const { - int64_t const shmem_size_total = m_shmem_begin + m_shmem_size; - dim3 const grid(static_cast(m_league_size), 1, 1); - dim3 const block(static_cast(m_vector_size), - static_cast(m_team_size), 1); - - using closure_type = - ParallelFor, HIP>; - Impl::hip_parallel_launch( - *this, grid, block, shmem_size_total, - m_policy.space().impl_internal_space_instance(), - true); // copy to device and execute - } - - ParallelFor(FunctorType const& arg_functor, Policy const& arg_policy) - : m_functor(arg_functor), - m_policy(arg_policy), - m_league_size(arg_policy.league_size()), - m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { - auto internal_space_instance = - m_policy.space().impl_internal_space_instance(); - m_team_size = m_team_size >= 0 ? m_team_size - : arg_policy.team_size_recommended( - arg_functor, ParallelForTag()); - - m_shmem_begin = (sizeof(double) * (m_team_size + 2)); - m_shmem_size = - (m_policy.scratch_size(0, m_team_size) + - FunctorTeamShmemSize::value(m_functor, m_team_size)); - m_scratch_size[0] = m_policy.scratch_size(0, m_team_size); - m_scratch_size[1] = m_policy.scratch_size(1, m_team_size); - m_scratch_locks = internal_space_instance->m_scratch_locks; - m_num_scratch_locks = internal_space_instance->m_num_scratch_locks; - - // Functor's reduce memory, team scan memory, and team shared memory depend - // upon team size. - m_scratch_ptr[0] = nullptr; - if (m_team_size <= 0) { - m_scratch_ptr[1] = nullptr; - } else { - m_scratch_pool_id = internal_space_instance->acquire_team_scratch_space(); - m_scratch_ptr[1] = internal_space_instance->resize_team_scratch_space( - m_scratch_pool_id, - static_cast(m_scratch_size[1]) * - (std::min( - static_cast(HIP().concurrency() / - (m_team_size * m_vector_size)), - static_cast(m_league_size)))); - } - - int const shmem_size_total = m_shmem_begin + m_shmem_size; - if (internal_space_instance->m_maxShmemPerBlock < shmem_size_total) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::ParallelFor< HIP > insufficient shared memory")); - } - - size_t max_size = arg_policy.team_size_max(arg_functor, ParallelForTag()); - if (static_cast(m_team_size) > static_cast(max_size)) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::ParallelFor< HIP > requested too large team size.")); - } - } - - ~ParallelFor() { - if (m_scratch_pool_id >= 0) { - m_policy.space() - .impl_internal_space_instance() - ->release_team_scratch_space(m_scratch_pool_id); - } - } -}; - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -template -class ParallelReduce, HIP> { - public: - using Policy = TeamPolicyInternal; - using FunctorType = typename CombinedFunctorReducerType::functor_type; - using ReducerType = typename CombinedFunctorReducerType::reducer_type; - - private: - using member_type = typename Policy::member_type; - using work_tag = typename Policy::work_tag; - using launch_bounds = typename Policy::launch_bounds; - - using pointer_type = typename ReducerType::pointer_type; - using reference_type = typename ReducerType::reference_type; - using value_type = typename ReducerType::value_type; - - public: - using functor_type = FunctorType; - using size_type = HIP::size_type; - - // static int constexpr UseShflReduction = false; - // FIXME_HIP This should be disabled unconditionally for best performance, but - // it currently causes tests to fail. - static constexpr int UseShflReduction = - (ReducerType::static_value_size() != 0); - - private: - struct ShflReductionTag {}; - struct SHMEMReductionTag {}; - - // Algorithmic constraints: blockDim.y is a power of two AND - // blockDim.y == blockDim.z == 1 shared memory utilization: - // - // [ global reduce space ] - // [ team reduce space ] - // [ team shared space ] - // - - const CombinedFunctorReducerType m_functor_reducer; - const Policy m_policy; - const pointer_type m_result_ptr; - const bool m_result_ptr_device_accessible; - const bool m_result_ptr_host_accessible; - size_type* m_scratch_space; - size_type* m_scratch_flags; - size_type m_team_begin; - size_type m_shmem_begin; - size_type m_shmem_size; - void* m_scratch_ptr[2]; - size_t m_scratch_size[2]; - int m_scratch_pool_id = -1; - int32_t* m_scratch_locks; - size_t m_num_scratch_locks; - const size_type m_league_size; - int m_team_size; - const size_type m_vector_size; - - template - __device__ inline std::enable_if_t::value> exec_team( - member_type const& member, reference_type update) const { - m_functor_reducer.get_functor()(member, update); - } - - template - __device__ inline std::enable_if_t::value> exec_team( - member_type const& member, reference_type update) const { - m_functor_reducer.get_functor()(TagType(), member, update); - } - - __device__ inline void iterate_through_league(int const threadid, - reference_type value) const { - int const int_league_size = static_cast(m_league_size); - for (int league_rank = blockIdx.x; league_rank < int_league_size; - league_rank += gridDim.x) { - this->template exec_team( - member_type( - kokkos_impl_hip_shared_memory() + m_team_begin, - m_shmem_begin, m_shmem_size, - reinterpret_cast( - reinterpret_cast(m_scratch_ptr[1]) + - static_cast(threadid / (blockDim.x * blockDim.y)) * - m_scratch_size[1]), - m_scratch_size[1], league_rank, m_league_size), - value); - } - } - - int compute_block_count() const { - constexpr auto light_weight = - Kokkos::Experimental::WorkItemProperty::HintLightWeight; - constexpr typename Policy::work_item_property property; - // Numbers were tuned on MI210 using dot product and yAx benchmarks - constexpr int block_max = - (property & light_weight) == light_weight ? 2097152 : 65536; - constexpr int preferred_block_min = 1024; - int block_count = m_league_size; - if (block_count < preferred_block_min) { - // keep blocks as is, already low parallelism - } else if (block_count >= block_max) { - block_count = block_max; - - } else { - int nwork = m_league_size * m_team_size; - int items_per_thread = - (nwork + block_count * m_team_size - 1) / (block_count * m_team_size); - if (items_per_thread < 4) { - int ratio = std::min( - (block_count + preferred_block_min - 1) / preferred_block_min, - (4 + items_per_thread - 1) / items_per_thread); - block_count /= ratio; - } - } - - return block_count; - } - - public: - __device__ inline void operator()() const { - int64_t threadid = 0; - if (m_scratch_size[1] > 0) { - threadid = hip_get_scratch_index(m_league_size, m_scratch_locks, - m_num_scratch_locks); - } - - using ReductionTag = std::conditional_t; - run(ReductionTag{}, threadid); - - if (m_scratch_size[1] > 0) { - hip_release_scratch_index(m_scratch_locks, threadid); - } - } - - __device__ inline void run(SHMEMReductionTag, int const threadid) const { - const ReducerType& reducer = m_functor_reducer.get_reducer(); - - integral_nonzero_constant const - word_count(reducer.value_size() / sizeof(size_type)); - - reference_type value = - reducer.init(kokkos_impl_hip_shared_memory() + - threadIdx.y * word_count.value); - // Iterate this block through the league - iterate_through_league(threadid, value); - - // Reduce with final value at blockDim.y - 1 location. - bool do_final_reduce = (m_league_size == 0); - if (!do_final_reduce) - do_final_reduce = - hip_single_inter_block_reduce_scan( - reducer, blockIdx.x, gridDim.x, - kokkos_impl_hip_shared_memory(), m_scratch_space, - m_scratch_flags); - if (do_final_reduce) { - // This is the final block with the final result at the final threads' - // location - - size_type* const shared = kokkos_impl_hip_shared_memory() + - (blockDim.y - 1) * word_count.value; - size_type* const global = m_result_ptr_device_accessible - ? reinterpret_cast(m_result_ptr) - : m_scratch_space; - - if (threadIdx.y == 0) { - reducer.final(reinterpret_cast(shared)); - } - - if (HIPTraits::WarpSize < word_count.value) { - __syncthreads(); - } - - for (unsigned i = threadIdx.y; i < word_count.value; i += blockDim.y) { - global[i] = shared[i]; - } - } - } - - __device__ inline void run(ShflReductionTag, int const threadid) const { - const ReducerType& reducer = m_functor_reducer.get_reducer(); - - value_type value; - reducer.init(&value); - - // Iterate this block through the league - iterate_through_league(threadid, value); - - pointer_type const result = - m_result_ptr_device_accessible - ? m_result_ptr - : reinterpret_cast(m_scratch_space); - - value_type init; - reducer.init(&init); - if (m_league_size == 0) { - reducer.final(&value); - *result = value; - } else if (Impl::hip_inter_block_shuffle_reduction( - value, init, reducer, m_scratch_space, result, - m_scratch_flags, blockDim.y)) { - unsigned int const id = threadIdx.y * blockDim.x + threadIdx.x; - if (id == 0) { - reducer.final(&value); - *result = value; - } - } - } - - inline void execute() { - const ReducerType& reducer = m_functor_reducer.get_reducer(); - - const bool is_empty_range = m_league_size == 0 || m_team_size == 0; - const bool need_device_set = ReducerType::has_init_member_function() || - ReducerType::has_final_member_function() || - !m_result_ptr_host_accessible || - Policy::is_graph_kernel::value || - !std::is_same::value; - if (!is_empty_range || need_device_set) { - int const block_count = compute_block_count(); - - m_scratch_space = hip_internal_scratch_space( - m_policy.space(), reducer.value_size() * block_count); - m_scratch_flags = - hip_internal_scratch_flags(m_policy.space(), sizeof(size_type)); - - dim3 block(m_vector_size, m_team_size, 1); - dim3 grid(block_count, 1, 1); - if (is_empty_range) { - block = dim3(1, 1, 1); - grid = dim3(1, 1, 1); - } - const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size; - - Impl::hip_parallel_launch( - *this, grid, block, shmem_size_total, - m_policy.space().impl_internal_space_instance(), - true); // copy to device and execute - - if (!m_result_ptr_device_accessible) { - m_policy.space().impl_internal_space_instance()->fence(); - - if (m_result_ptr) { - const int size = reducer.value_size(); - DeepCopy(m_result_ptr, m_scratch_space, size); - } - } - } else { - if (m_result_ptr) { - reducer.init(m_result_ptr); - } - } - } - - template - ParallelReduce(CombinedFunctorReducerType const& arg_functor_reducer, - Policy const& arg_policy, ViewType const& arg_result) - : m_functor_reducer(arg_functor_reducer), - m_policy(arg_policy), - m_result_ptr(arg_result.data()), - m_result_ptr_device_accessible( - MemorySpaceAccess::accessible), - m_result_ptr_host_accessible( - MemorySpaceAccess::accessible), - m_scratch_space(nullptr), - m_scratch_flags(nullptr), - m_team_begin(0), - m_shmem_begin(0), - m_shmem_size(0), - m_scratch_ptr{nullptr, nullptr}, - m_league_size(arg_policy.league_size()), - m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { - auto internal_space_instance = - m_policy.space().impl_internal_space_instance(); - m_team_size = m_team_size >= 0 ? m_team_size - : arg_policy.team_size_recommended( - arg_functor_reducer.get_functor(), - arg_functor_reducer.get_reducer(), - ParallelReduceTag()); - - m_team_begin = - UseShflReduction - ? 0 - : hip_single_inter_block_reduce_scan_shmem( - arg_functor_reducer.get_functor(), m_team_size); - m_shmem_begin = sizeof(double) * (m_team_size + 2); - m_shmem_size = m_policy.scratch_size(0, m_team_size) + - FunctorTeamShmemSize::value( - arg_functor_reducer.get_functor(), m_team_size); - m_scratch_size[0] = m_shmem_size; - m_scratch_size[1] = m_policy.scratch_size(1, m_team_size); - m_scratch_locks = internal_space_instance->m_scratch_locks; - m_num_scratch_locks = internal_space_instance->m_num_scratch_locks; - if (m_team_size <= 0) { - m_scratch_ptr[1] = nullptr; - } else { - m_scratch_pool_id = internal_space_instance->acquire_team_scratch_space(); - m_scratch_ptr[1] = internal_space_instance->resize_team_scratch_space( - m_scratch_pool_id, - static_cast(m_scratch_size[1]) * - (std::min( - static_cast(HIP().concurrency() / - (m_team_size * m_vector_size)), - static_cast(m_league_size)))); - } - - // The global parallel_reduce does not support vector_length other than 1 at - // the moment - if ((arg_policy.impl_vector_length() > 1) && !UseShflReduction) - Impl::throw_runtime_exception( - "Kokkos::parallel_reduce with a TeamPolicy using a vector length of " - "greater than 1 is not currently supported for HIP for dynamic " - "sized reduction types."); - - if ((m_team_size < HIPTraits::WarpSize) && !UseShflReduction) - Impl::throw_runtime_exception( - "Kokkos::parallel_reduce with a TeamPolicy using a team_size smaller " - "than 64 is not currently supported with HIP for dynamic sized " - "reduction types."); - - // Functor's reduce memory, team scan memory, and team shared memory depend - // upon team size. - - const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size; - - if (!Kokkos::Impl::is_integral_power_of_two(m_team_size) && - !UseShflReduction) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::ParallelReduce< HIP > bad team size")); - } - - if (internal_space_instance->m_maxShmemPerBlock < shmem_size_total) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::ParallelReduce< HIP > requested too much " - "L0 scratch memory")); - } - - size_t max_size = arg_policy.team_size_max( - arg_functor_reducer.get_functor(), arg_functor_reducer.get_reducer(), - ParallelReduceTag()); - if (static_cast(m_team_size) > static_cast(max_size)) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::ParallelReduce< HIP > requested too " - "large team size.")); - } - } - - ~ParallelReduce() { - if (m_scratch_pool_id >= 0) { - m_policy.space() - .impl_internal_space_instance() - ->release_team_scratch_space(m_scratch_pool_id); - } - } -}; -} // namespace Impl -} // namespace Kokkos - -#endif - -#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.cpp index ea599989e7..83f829fdda 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.cpp @@ -18,138 +18,18 @@ #define KOKKOS_IMPL_PUBLIC_INCLUDE #endif -#include -#include #include +#include +#include +#include -namespace Kokkos { -namespace Impl { - -#ifdef KOKKOS_ENABLE_DEBUG -SharedAllocationRecord - SharedAllocationRecord::s_root_record; - -SharedAllocationRecord - SharedAllocationRecord::s_root_record; - -SharedAllocationRecord - SharedAllocationRecord::s_root_record; +#ifndef KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::HIPSpace); +#else +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION(Kokkos::HIPSpace); #endif - -SharedAllocationRecord::~SharedAllocationRecord() { - auto alloc_size = SharedAllocationRecord::m_alloc_size; - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - alloc_size, (alloc_size - sizeof(SharedAllocationHeader))); -} - -SharedAllocationRecord::~SharedAllocationRecord() { - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - SharedAllocationRecord::m_alloc_size); -} - -SharedAllocationRecord::~SharedAllocationRecord() { - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - SharedAllocationRecord::m_alloc_size); -} - -SharedAllocationRecord::SharedAllocationRecord( - const HIPSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Kokkos::Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - // Copy to device memory - HIP exec; - Kokkos::Impl::DeepCopy( - exec, RecordBase::m_alloc_ptr, &header, sizeof(SharedAllocationHeader)); - exec.fence( - "SharedAllocationRecord::SharedAllocationRecord(): fence after copying header from " - "HostSpace"); -} - -SharedAllocationRecord::SharedAllocationRecord( - const HIP& arg_exec_space, const HIPSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Kokkos::Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - // Copy to device memory - Kokkos::Impl::DeepCopy(arg_exec_space, - RecordBase::m_alloc_ptr, &header, - sizeof(SharedAllocationHeader)); -} - -SharedAllocationRecord::SharedAllocationRecord( - const HIPHostPinnedSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Kokkos::Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - // Fill in the Header information, directly accessible via host pinned memory - this->base_t::_fill_host_accessible_header_info(*RecordBase::m_alloc_ptr, - arg_label); -} - -SharedAllocationRecord::SharedAllocationRecord( - const HIPManagedSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Kokkos::Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - // Fill in the Header information, directly accessible via managed memory - this->base_t::_fill_host_accessible_header_info(*RecordBase::m_alloc_ptr, - arg_label); -} - -} // namespace Impl -} // namespace Kokkos +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::HIPHostPinnedSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::HIPManagedSpace); diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.hpp index e68bad9723..1ca7bd5cd0 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.hpp @@ -18,120 +18,15 @@ #define KOKKOS_HIP_SHARED_ALLOCATION_RECORD_HPP #include +#include -namespace Kokkos { -namespace Impl { - -template <> -class SharedAllocationRecord - : public HostInaccessibleSharedAllocationRecordCommon { - private: - friend class SharedAllocationRecordCommon; - friend class HostInaccessibleSharedAllocationRecordCommon; - using base_t = HostInaccessibleSharedAllocationRecordCommon; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - -#ifdef KOKKOS_ENABLE_DEBUG - static RecordBase s_root_record; +#if defined(KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY) +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION(Kokkos::HIPSpace); +#else +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_SPECIALIZATION( + Kokkos::HIPSpace); #endif - - const HIPSpace m_space; - - protected: - ~SharedAllocationRecord(); - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec*/, const HIPSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const HIP& exec_space, const HIPSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); - - SharedAllocationRecord( - const HIPSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; - -template <> -class SharedAllocationRecord - : public SharedAllocationRecordCommon { - private: - friend class SharedAllocationRecordCommon; - using base_t = SharedAllocationRecordCommon; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - -#ifdef KOKKOS_ENABLE_DEBUG - static RecordBase s_root_record; -#endif - - const HIPHostPinnedSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, const HIPHostPinnedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const HIPHostPinnedSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; - -template <> -class SharedAllocationRecord - : public SharedAllocationRecordCommon { - private: - friend class SharedAllocationRecordCommon; - using base_t = SharedAllocationRecordCommon; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - -#ifdef KOKKOS_ENABLE_DEBUG - static RecordBase s_root_record; -#endif - - const HIPManagedSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, const HIPManagedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const HIPManagedSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; -} // namespace Impl -} // namespace Kokkos +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION(Kokkos::HIPHostPinnedSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION(Kokkos::HIPManagedSpace); #endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp index 7f6aa0d8e8..e8bdfca66f 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp @@ -24,10 +24,8 @@ #include #include -#include #include -#include #include #include @@ -287,22 +285,3 @@ void HIPManagedSpace::impl_deallocate( } } // namespace Kokkos - -/*--------------------------------------------------------------------------*/ -/*--------------------------------------------------------------------------*/ - -#include - -namespace Kokkos { -namespace Impl { - -// To avoid additional compilation cost for something that's (mostly?) not -// performance sensitive, we explicity instantiate these CRTP base classes here, -// where we have access to the associated *_timpl.hpp header files. -template class HostInaccessibleSharedAllocationRecordCommon; -template class SharedAllocationRecordCommon; -template class SharedAllocationRecordCommon; -template class SharedAllocationRecordCommon; - -} // end namespace Impl -} // end namespace Kokkos diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.hpp index f3e5adf87e..e1b4768b87 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.hpp @@ -65,6 +65,28 @@ class HIPSpace { ~HIPSpace() = default; /**\brief Allocate untracked memory in the hip space */ +#ifdef KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } +#else + // FIXME_HIP Use execution space instance + void* allocate(const HIP&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + // FIXME_HIP Use execution space instance + void* allocate(const HIP&, const char* arg_label, const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } +#endif void* allocate(const size_t arg_alloc_size) const; void* allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; @@ -76,8 +98,6 @@ class HIPSpace { const size_t arg_logical_size = 0) const; private: - template - friend class LogicalMemorySpace; void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0, const Kokkos::Tools::SpaceHandle = @@ -94,8 +114,6 @@ class HIPSpace { private: int m_device; ///< Which HIP device - - friend class Kokkos::Impl::SharedAllocationRecord; }; template <> @@ -129,6 +147,16 @@ class HIPHostPinnedSpace { ~HIPHostPinnedSpace() = default; /**\brief Allocate untracked memory in the space */ + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const size_t arg_alloc_size) const; void* allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; @@ -140,8 +168,6 @@ class HIPHostPinnedSpace { const size_t arg_logical_size = 0) const; private: - template - friend class LogicalMemorySpace; void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0, const Kokkos::Tools::SpaceHandle = @@ -194,6 +220,16 @@ class HIPManagedSpace { ~HIPManagedSpace() = default; /**\brief Allocate untracked memory in the space */ + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const size_t arg_alloc_size) const; void* allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; @@ -209,8 +245,6 @@ class HIPManagedSpace { private: int m_device; ///< Which HIP device - template - friend class LogicalMemorySpace; void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0, const Kokkos::Tools::SpaceHandle = @@ -239,15 +273,18 @@ struct Impl::is_hip_type_space : public std::true_type {}; namespace Kokkos { namespace Impl { -static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); +static_assert(Kokkos::Impl::MemorySpaceAccess::assignable); //---------------------------------------- template <> struct MemorySpaceAccess { enum : bool { assignable = false }; - enum : bool { accessible = false }; +#if !defined(KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY) + enum : bool{accessible = false}; +#else + enum : bool { accessible = true }; +#endif enum : bool { deepcopy = true }; }; diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_TeamPolicyInternal.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_TeamPolicyInternal.hpp new file mode 100644 index 0000000000..67e1181125 --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_TeamPolicyInternal.hpp @@ -0,0 +1,421 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_HIP_TEAM_POLICY_INTERNAL_HPP +#define KOKKOS_HIP_TEAM_POLICY_INTERNAL_HPP + +#include + +namespace Kokkos { +namespace Impl { + +template +class TeamPolicyInternal + : public PolicyTraits { + public: + using execution_policy = TeamPolicyInternal; + + using traits = PolicyTraits; + + template + friend class TeamPolicyInternal; + + private: + typename traits::execution_space m_space; + int m_league_size; + int m_team_size; + int m_vector_length; + size_t m_team_scratch_size[2]; + size_t m_thread_scratch_size[2]; + int m_chunk_size; + bool m_tune_team_size; + bool m_tune_vector_length; + + public: + using execution_space = HIP; + + template + TeamPolicyInternal(TeamPolicyInternal const& p) { + m_league_size = p.m_league_size; + m_team_size = p.m_team_size; + m_vector_length = p.m_vector_length; + m_team_scratch_size[0] = p.m_team_scratch_size[0]; + m_team_scratch_size[1] = p.m_team_scratch_size[1]; + m_thread_scratch_size[0] = p.m_thread_scratch_size[0]; + m_thread_scratch_size[1] = p.m_thread_scratch_size[1]; + m_chunk_size = p.m_chunk_size; + m_space = p.m_space; + m_tune_team_size = p.m_tune_team_size; + m_tune_vector_length = p.m_tune_vector_length; + } + + template + int team_size_max(FunctorType const& f, ParallelForTag const&) const { + using closure_type = + Impl::ParallelFor>; + + return internal_team_size_common(f); + } + + template + inline int team_size_max(const FunctorType& f, + const ParallelReduceTag&) const { + using functor_analysis_type = + Impl::FunctorAnalysis; + using closure_type = Impl::ParallelReduce< + CombinedFunctorReducer, + TeamPolicy, Kokkos::HIP>; + return internal_team_size_common< + BlockType::Max, closure_type, + typename functor_analysis_type::value_type>(f); + } + + template + inline int team_size_max(const FunctorType& f, const ReducerType&, + const ParallelReduceTag&) const { + using closure_type = + Impl::ParallelReduce, + TeamPolicy, Kokkos::HIP>; + return internal_team_size_common(f); + } + + template + int team_size_recommended(FunctorType const& f, ParallelForTag const&) const { + using closure_type = + Impl::ParallelFor>; + + return internal_team_size_common( + f); + } + + template + inline int team_size_recommended(FunctorType const& f, + ParallelReduceTag const&) const { + using functor_analysis_type = + Impl::FunctorAnalysis; + using closure_type = Impl::ParallelReduce< + CombinedFunctorReducer, + TeamPolicy, Kokkos::HIP>; + return internal_team_size_common< + BlockType::Preferred, closure_type, + typename functor_analysis_type::value_type>(f); + } + + template + int team_size_recommended(FunctorType const& f, ReducerType const&, + ParallelReduceTag const&) const { + using closure_type = + Impl::ParallelReduce, + TeamPolicy, Kokkos::HIP>; + return internal_team_size_common(f); + } + + inline bool impl_auto_vector_length() const { return m_tune_vector_length; } + inline bool impl_auto_team_size() const { return m_tune_team_size; } + static int vector_length_max() { return HIPTraits::WarpSize; } + + static int verify_requested_vector_length(int requested_vector_length) { + int test_vector_length = + std::min(requested_vector_length, vector_length_max()); + + // Allow only power-of-two vector_length + if (!(is_integral_power_of_two(test_vector_length))) { + int test_pow2 = 1; + constexpr int warp_size = HIPTraits::WarpSize; + while (test_pow2 < warp_size) { + test_pow2 <<= 1; + if (test_pow2 > test_vector_length) { + break; + } + } + test_vector_length = test_pow2 >> 1; + } + + return test_vector_length; + } + + inline static int scratch_size_max(int level) { + // HIP Teams use (team_size + 2)*sizeof(double) shared memory for team + // reductions. They also use one int64_t in static shared memory for a + // shared ID. Furthermore, they use additional scratch memory in some + // reduction scenarios, which depend on the size of the value_type and is + // NOT captured here + constexpr size_t max_possible_team_size = 1024; + constexpr size_t max_reserved_shared_mem_per_team = + (max_possible_team_size + 2) * sizeof(double) + sizeof(int64_t); + // arbitrarily setting level 1 scratch limit to 20MB, for a + // MI250 that would give us about 4.4GB for 2 teams per CU + constexpr size_t max_l1_scratch_size = 20 * 1024 * 1024; + + size_t max_shmem = HIP().hip_device_prop().sharedMemPerBlock; + return (level == 0 ? max_shmem - max_reserved_shared_mem_per_team + : max_l1_scratch_size); + } + + inline void impl_set_vector_length(size_t size) { m_vector_length = size; } + inline void impl_set_team_size(size_t size) { m_team_size = size; } + int impl_vector_length() const { return m_vector_length; } + + int team_size() const { return m_team_size; } + + int league_size() const { return m_league_size; } + + size_t scratch_size(int level, int team_size_ = -1) const { + if (team_size_ < 0) team_size_ = m_team_size; + return m_team_scratch_size[level] + + team_size_ * m_thread_scratch_size[level]; + } + + size_t team_scratch_size(int level) const { + return m_team_scratch_size[level]; + } + + size_t thread_scratch_size(int level) const { + return m_thread_scratch_size[level]; + } + + typename traits::execution_space space() const { return m_space; } + + TeamPolicyInternal() + : m_space(typename traits::execution_space()), + m_league_size(0), + m_team_size(-1), + m_vector_length(0), + m_team_scratch_size{0, 0}, + m_thread_scratch_size{0, 0}, + m_chunk_size(HIPTraits::WarpSize), + m_tune_team_size(false), + m_tune_vector_length(false) {} + + /** \brief Specify league size, request team size */ + TeamPolicyInternal(const execution_space space_, int league_size_, + int team_size_request, int vector_length_request = 1) + : m_space(space_), + m_league_size(league_size_), + m_team_size(team_size_request), + m_vector_length( + (vector_length_request > 0) + ? verify_requested_vector_length(vector_length_request) + : (verify_requested_vector_length(1))), + m_team_scratch_size{0, 0}, + m_thread_scratch_size{0, 0}, + m_chunk_size(HIPTraits::WarpSize), + m_tune_team_size(bool(team_size_request <= 0)), + m_tune_vector_length(bool(vector_length_request <= 0)) { + // Make sure league size is permissible + if (league_size_ >= static_cast(hip_internal_maximum_grid_count()[0])) + Impl::throw_runtime_exception( + "Requested too large league_size for TeamPolicy on HIP execution " + "space."); + + // Make sure total block size is permissible + if (m_team_size * m_vector_length > HIPTraits::MaxThreadsPerBlock) { + Impl::throw_runtime_exception( + std::string("Kokkos::TeamPolicy< HIP > the team size is too large. " + "Team size x vector length must be smaller than 1024.")); + } + } + + /** \brief Specify league size, request team size */ + TeamPolicyInternal(const execution_space space_, int league_size_, + const Kokkos::AUTO_t& /* team_size_request */, + int vector_length_request = 1) + : TeamPolicyInternal(space_, league_size_, -1, vector_length_request) {} + // FLAG + /** \brief Specify league size and team size, request vector length*/ + TeamPolicyInternal(const execution_space space_, int league_size_, + int team_size_request, + const Kokkos::AUTO_t& /* vector_length_request */ + ) + : TeamPolicyInternal(space_, league_size_, team_size_request, -1) + + {} + + /** \brief Specify league size, request team size and vector length*/ + TeamPolicyInternal(const execution_space space_, int league_size_, + const Kokkos::AUTO_t& /* team_size_request */, + const Kokkos::AUTO_t& /* vector_length_request */ + + ) + : TeamPolicyInternal(space_, league_size_, -1, -1) + + {} + + TeamPolicyInternal(int league_size_, int team_size_request, + int vector_length_request = 1) + : TeamPolicyInternal(typename traits::execution_space(), league_size_, + team_size_request, vector_length_request) {} + + TeamPolicyInternal(int league_size_, + const Kokkos::AUTO_t& /* team_size_request */, + int vector_length_request = 1) + : TeamPolicyInternal(typename traits::execution_space(), league_size_, -1, + vector_length_request) {} + + /** \brief Specify league size and team size, request vector length*/ + TeamPolicyInternal(int league_size_, int team_size_request, + const Kokkos::AUTO_t& /* vector_length_request */ + + ) + : TeamPolicyInternal(typename traits::execution_space(), league_size_, + team_size_request, -1) + + {} + + /** \brief Specify league size, request team size and vector length*/ + TeamPolicyInternal(int league_size_, + const Kokkos::AUTO_t& /* team_size_request */, + const Kokkos::AUTO_t& /* vector_length_request */ + + ) + : TeamPolicyInternal(typename traits::execution_space(), league_size_, -1, + -1) {} + + int chunk_size() const { return m_chunk_size; } + + TeamPolicyInternal& set_chunk_size(typename traits::index_type chunk_size_) { + m_chunk_size = chunk_size_; + return *this; + } + + /** \brief set per team scratch size for a specific level of the scratch + * hierarchy */ + TeamPolicyInternal& set_scratch_size(int level, + PerTeamValue const& per_team) { + m_team_scratch_size[level] = per_team.value; + return *this; + } + + /** \brief set per thread scratch size for a specific level of the scratch + * hierarchy */ + TeamPolicyInternal& set_scratch_size(int level, + PerThreadValue const& per_thread) { + m_thread_scratch_size[level] = per_thread.value; + return *this; + } + + /** \brief set per thread and per team scratch size for a specific level of + * the scratch hierarchy */ + TeamPolicyInternal& set_scratch_size(int level, PerTeamValue const& per_team, + PerThreadValue const& per_thread) { + m_team_scratch_size[level] = per_team.value; + m_thread_scratch_size[level] = per_thread.value; + return *this; + } + + using member_type = Kokkos::Impl::HIPTeamMember; + + protected: + template + int internal_team_size_common(FunctorType const& f) const { + const unsigned shmem_block = team_scratch_size(0) + 2 * sizeof(double); + unsigned shmem_thread = thread_scratch_size(0) + sizeof(double); + using Tag = typename PatternTagFromImplSpecialization::type; + if constexpr (std::is_same_v) { + using Interface = + typename Impl::DeduceFunctorPatternInterface::type; + using Analysis = + Impl::FunctorAnalysis; + shmem_thread += + ((Analysis::StaticValueSize != 0) ? 0 : Analysis::value_size(f)); + } + const int vector_length = impl_vector_length(); + + const auto functor = [&f, shmem_block, shmem_thread, vector_length]( + const hipFuncAttributes& attr, int block_size) { + int functor_shmem = + ::Kokkos::Impl::FunctorTeamShmemSize::value( + f, block_size / vector_length); + return shmem_block + shmem_thread * (block_size / vector_length) + + functor_shmem + attr.sharedSizeBytes; + }; + int block_size; + if constexpr (BlockSize == BlockType::Max) { + block_size = hip_get_max_team_blocksize( + space().impl_internal_space_instance(), functor); + } else { + block_size = + hip_get_preferred_team_blocksize( + space().impl_internal_space_instance(), functor); + } + + if (block_size == 0) { + Kokkos::Impl::throw_runtime_exception(std::string( + "Kokkos::Impl::ParallelFor/Reduce< HIP > could not find a valid " + "team size.")); + } + if constexpr (std::is_same_v) { + return block_size / impl_vector_length(); + } else { + // Currently we require Power-of-2 team size for reductions. + int p2 = 1; + while (p2 <= block_size) p2 *= 2; + p2 /= 2; + return p2 / impl_vector_length(); + } + } +}; + +__device__ inline int64_t hip_get_scratch_index(HIP::size_type league_size, + int32_t* scratch_locks, + size_t num_scratch_locks) { + int64_t threadid = 0; + __shared__ int64_t base_thread_id; + if (threadIdx.x == 0 && threadIdx.y == 0) { + int64_t const wraparound_len = + Kokkos::min(int64_t(league_size), + int64_t(num_scratch_locks) / (blockDim.x * blockDim.y)); + threadid = (blockIdx.x * blockDim.z + threadIdx.z) % wraparound_len; + threadid *= blockDim.x * blockDim.y; + int done = 0; + while (!done) { + done = (0 == atomicCAS(&scratch_locks[threadid], 0, 1)); + if (!done) { + threadid += blockDim.x * blockDim.y; + if (int64_t(threadid + blockDim.x * blockDim.y) >= + wraparound_len * blockDim.x * blockDim.y) + threadid = 0; + } + } + base_thread_id = threadid; + } + __syncthreads(); + threadid = base_thread_id; + return threadid; +} + +__device__ inline void hip_release_scratch_index(int32_t* scratch_locks, + int64_t threadid) { + __syncthreads(); + if (threadIdx.x == 0 && threadIdx.y == 0) { + scratch_locks[threadid] = 0; + } +} + +} // namespace Impl +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_UniqueToken.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_UniqueToken.hpp index 313e5f5217..3d70b59646 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_UniqueToken.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_UniqueToken.hpp @@ -19,7 +19,6 @@ #include #include -#include namespace Kokkos { diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_ZeroMemset.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_ZeroMemset.hpp index 5c40d0fbc8..4bca29868f 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_ZeroMemset.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_ZeroMemset.hpp @@ -25,19 +25,11 @@ namespace Impl { template struct ZeroMemset> { - ZeroMemset(const HIP& exec_space, const View& dst, - typename View::const_value_type&) { + ZeroMemset(const HIP& exec_space, const View& dst) { KOKKOS_IMPL_HIP_SAFE_CALL(hipMemsetAsync( dst.data(), 0, dst.size() * sizeof(typename View::value_type), exec_space.hip_stream())); } - - ZeroMemset(const View& dst, - typename View::const_value_type&) { - KOKKOS_IMPL_HIP_SAFE_CALL( - hipMemset(dst.data(), 0, - dst.size() * sizeof(typename View::value_type))); - } }; } // namespace Impl diff --git a/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp b/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp index 4a40ffcaa4..6d541a6414 100644 --- a/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp +++ b/lib/kokkos/core/src/HPX/Kokkos_HPX.cpp @@ -103,6 +103,7 @@ void HPX::print_configuration(std::ostream &os, const bool) const { os << hpx::configuration_string() << '\n'; } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 bool &HPX::impl_get_in_parallel() noexcept { static thread_local bool in_parallel = false; return in_parallel; @@ -127,6 +128,7 @@ HPX::impl_not_in_parallel_scope::~impl_not_in_parallel_scope() noexcept { KOKKOS_EXPECTS(!impl_get_in_parallel()); impl_get_in_parallel() = true; } +#endif void HPX::impl_decrement_active_parallel_region_count() { std::unique_lock l(m_active_parallel_region_count_mutex); diff --git a/lib/kokkos/core/src/HPX/Kokkos_HPX.hpp b/lib/kokkos/core/src/HPX/Kokkos_HPX.hpp index 1dfc5b4064..26181a7c05 100644 --- a/lib/kokkos/core/src/HPX/Kokkos_HPX.hpp +++ b/lib/kokkos/core/src/HPX/Kokkos_HPX.hpp @@ -27,14 +27,6 @@ static_assert(false, #include -#include -#include -#include - -#ifdef KOKKOS_ENABLE_HBWSPACE -#include -#endif - #include #include #include @@ -59,6 +51,7 @@ static_assert(false, #include +#include #include #include #include @@ -201,6 +194,7 @@ class HPX { return impl_get_instance_data().m_instance_id; } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 static bool &impl_get_in_parallel() noexcept; struct impl_in_parallel_scope { @@ -223,9 +217,10 @@ class HPX { delete; }; - static bool in_parallel(HPX const & = HPX()) noexcept { + KOKKOS_DEPRECATED static bool in_parallel(HPX const & = HPX()) noexcept { return impl_get_in_parallel(); } +#endif static void impl_decrement_active_parallel_region_count(); static void impl_increment_active_parallel_region_count(); @@ -248,18 +243,6 @@ class HPX { #endif } -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - template - KOKKOS_DEPRECATED static void partition_master( - F const &, int requested_num_partitions = 0, int = 0) { - if (requested_num_partitions > 1) { - Kokkos::abort( - "Kokkos::Experimental::HPX::partition_master: can't partition an " - "HPX instance\n"); - } - } -#endif - #ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 static int concurrency(); #else @@ -355,7 +338,9 @@ class HPX { hpx::threads::thread_stacksize::default_) const { impl_bulk_plain_erased(force_synchronous, is_light_weight_policy, {[functor](Index i) { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 impl_in_parallel_scope p; +#endif functor.execute_range(i); }}, n, stacksize); @@ -417,15 +402,21 @@ class HPX { hpx::threads::thread_stacksize::default_) const { impl_bulk_setup_finalize_erased(force_synchronous, is_light_weight_policy, {[functor](Index i) { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 impl_in_parallel_scope p; +#endif functor.execute_range(i); }}, {[functor]() { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 impl_in_parallel_scope p; +#endif functor.setup(); }}, {[functor]() { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 impl_in_parallel_scope p; +#endif functor.finalize(); }}, n, stacksize); @@ -1292,6 +1283,7 @@ class ParallelScan, const WorkRange range(m_policy, t, num_worker_threads); execute_chunk(range.begin(), range.end(), update_sum, false); +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 { // Since arrive_and_wait may yield and resume on another worker thread we // set in_parallel = false on the current thread before suspending and set @@ -1299,6 +1291,9 @@ class ParallelScan, Kokkos::Experimental::HPX::impl_not_in_parallel_scope p; barrier.arrive_and_wait(); } +#else + barrier.arrive_and_wait(); +#endif if (t == 0) { final_reducer.init(reinterpret_cast( @@ -1320,6 +1315,7 @@ class ParallelScan, } } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 { // Since arrive_and_wait may yield and resume on another worker thread we // set in_parallel = false on the current thread before suspending and set @@ -1327,6 +1323,9 @@ class ParallelScan, Kokkos::Experimental::HPX::impl_not_in_parallel_scope p; barrier.arrive_and_wait(); } +#else + barrier.arrive_and_wait(); +#endif reference_type update_base = Analysis::Reducer::reference(reinterpret_cast( @@ -1407,6 +1406,7 @@ class ParallelScanWithTotal, const WorkRange range(m_policy, t, num_worker_threads); execute_chunk(range.begin(), range.end(), update_sum, false); +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 { // Since arrive_and_wait may yield and resume on another worker thread we // set in_parallel = false on the current thread before suspending and set @@ -1414,6 +1414,9 @@ class ParallelScanWithTotal, Kokkos::Experimental::HPX::impl_not_in_parallel_scope p; barrier.arrive_and_wait(); } +#else + barrier.arrive_and_wait(); +#endif if (t == 0) { final_reducer.init(reinterpret_cast( @@ -1435,6 +1438,7 @@ class ParallelScanWithTotal, } } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 { // Since arrive_and_wait may yield and resume on another worker thread we // set in_parallel = false on the current thread before suspending and set @@ -1442,6 +1446,9 @@ class ParallelScanWithTotal, Kokkos::Experimental::HPX::impl_not_in_parallel_scope p; barrier.arrive_and_wait(); } +#else + barrier.arrive_and_wait(); +#endif reference_type update_base = Analysis::Reducer::reference(reinterpret_cast( diff --git a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp index c9080db01c..297b1fadee 100644 --- a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp +++ b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp @@ -73,7 +73,7 @@ is_less_than_value_initialized_variable(T arg) { // Checked narrowing conversion that calls abort if the cast changes the value template -constexpr To checked_narrow_cast(From arg) { +constexpr To checked_narrow_cast(From arg, std::size_t idx) { constexpr const bool is_different_signedness = (std::is_signed::value != std::is_signed::value); auto const ret = static_cast(arg); @@ -81,7 +81,12 @@ constexpr To checked_narrow_cast(From arg) { (is_different_signedness && is_less_than_value_initialized_variable(arg) != is_less_than_value_initialized_variable(ret))) { - Kokkos::abort("unsafe narrowing conversion"); + auto msg = + "Kokkos::MDRangePolicy bound type error: an unsafe implicit conversion " + "is performed on a bound (" + + std::to_string(arg) + ") in dimension (" + std::to_string(idx) + + "), which may not preserve its original value.\n"; + Kokkos::abort(msg.c_str()); } return ret; } @@ -96,15 +101,15 @@ constexpr Array to_array_potentially_narrowing(const U (&init)[M]) { using T = typename Array::value_type; Array a{}; constexpr std::size_t N = a.size(); - static_assert(M <= N, ""); + static_assert(M <= N); auto* ptr = a.data(); // NOTE equivalent to // std::transform(std::begin(init), std::end(init), a.data(), // [](U x) { return static_cast(x); }); // except that std::transform is not constexpr. - for (auto x : init) { - *ptr++ = checked_narrow_cast(x); - (void)checked_narrow_cast(x); // see note above + for (std::size_t i = 0; i < M; ++i) { + *ptr++ = checked_narrow_cast(init[i], i); + (void)checked_narrow_cast(init[i], i); // see note above } return a; } @@ -120,10 +125,10 @@ constexpr NVCC_WONT_LET_ME_CALL_YOU_Array to_array_potentially_narrowing( using T = typename NVCC_WONT_LET_ME_CALL_YOU_Array::value_type; NVCC_WONT_LET_ME_CALL_YOU_Array a{}; constexpr std::size_t N = a.size(); - static_assert(M <= N, ""); + static_assert(M <= N); for (std::size_t i = 0; i < M; ++i) { - a[i] = checked_narrow_cast(other[i]); - (void)checked_narrow_cast(other[i]); // see note above + a[i] = checked_narrow_cast(other[i], i); + (void)checked_narrow_cast(other[i], i); // see note above } return a; } @@ -150,9 +155,20 @@ TileSizeProperties get_tile_size_properties(const ExecutionSpace&) { // multi-dimensional iteration pattern template -struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { - using traits = Kokkos::Impl::PolicyTraits; - using range_policy = RangePolicy; +struct MDRangePolicy; + +// Note: If MDRangePolicy has a primary template, implicit CTAD (deduction +// guides) are generated -> MDRangePolicy<> by some compilers, which is +// incorrect. By making it a template specialization instead, no implicit CTAD +// is generated. This works because there has to be at least one property +// specified (which is Rank<...>); otherwise, we'd get the static_assert +// "Kokkos::Error: MD iteration pattern not defined". This template +// specialization uses in all places for correctness. +template +struct MDRangePolicy + : public Kokkos::Impl::PolicyTraits { + using traits = Kokkos::Impl::PolicyTraits; + using range_policy = RangePolicy; typename traits::execution_space m_space; @@ -161,8 +177,8 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { typename traits::schedule_type, typename traits::index_type>; using execution_policy = - MDRangePolicy; // needed for is_execution_space - // interrogation + MDRangePolicy; // needed for is_execution_policy + // interrogation template friend struct MDRangePolicy; @@ -327,6 +343,20 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { } for (int i = rank_start; i != rank_end; i += increment) { const index_type length = m_upper[i] - m_lower[i]; + + if (m_upper[i] < m_lower[i]) { + std::string msg = + "Kokkos::MDRangePolicy bounds error: The lower bound (" + + std::to_string(m_lower[i]) + ") is greater than its upper bound (" + + std::to_string(m_upper[i]) + ") in dimension " + std::to_string(i) + + ".\n"; +#if !defined(KOKKOS_ENABLE_DEPRECATED_CODE_4) + Kokkos::abort(msg.c_str()); +#elif defined(KOKKOS_ENABLE_DEPRECATION_WARNINGS) + Kokkos::Impl::log_warning(msg); +#endif + } + if (m_tile[i] <= 0) { m_tune_tile_size = true; if ((inner_direction == Iterate::Right && (i < rank - 1)) || @@ -358,6 +388,60 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { } }; +template +MDRangePolicy(const LT (&)[N], const UT (&)[N])->MDRangePolicy>; + +template +MDRangePolicy(const LT (&)[N], const UT (&)[N], const TT (&)[TN]) + ->MDRangePolicy>; + +template +MDRangePolicy(DefaultExecutionSpace const&, const LT (&)[N], const UT (&)[N]) + ->MDRangePolicy>; + +template +MDRangePolicy(DefaultExecutionSpace const&, const LT (&)[N], const UT (&)[N], + const TT (&)[TN]) + ->MDRangePolicy>; + +template >> +MDRangePolicy(ES const&, const LT (&)[N], const UT (&)[N]) + ->MDRangePolicy>; + +template >> +MDRangePolicy(ES const&, const LT (&)[N], const UT (&)[N], const TT (&)[TN]) + ->MDRangePolicy>; + +template +MDRangePolicy(Array const&, Array const&)->MDRangePolicy>; + +template +MDRangePolicy(Array const&, Array const&, Array const&) + ->MDRangePolicy>; + +template +MDRangePolicy(DefaultExecutionSpace const&, Array const&, + Array const&) + ->MDRangePolicy>; + +template +MDRangePolicy(DefaultExecutionSpace const&, Array const&, + Array const&, Array const&) + ->MDRangePolicy>; + +template >> +MDRangePolicy(ES const&, Array const&, Array const&) + ->MDRangePolicy>; + +template >> +MDRangePolicy(ES const&, Array const&, Array const&, + Array const&) + ->MDRangePolicy>; + } // namespace Kokkos #endif // KOKKOS_CORE_EXP_MD_RANGE_POLICY_HPP diff --git a/lib/kokkos/core/src/Kokkos_Array.hpp b/lib/kokkos/core/src/Kokkos_Array.hpp index 82ceaaec21..ba1626bb72 100644 --- a/lib/kokkos/core/src/Kokkos_Array.hpp +++ b/lib/kokkos/core/src/Kokkos_Array.hpp @@ -22,6 +22,7 @@ #endif #include +#include #include #include @@ -320,6 +321,9 @@ struct Array::strided> { : m_elem(arg_ptr), m_size(arg_size), m_stride(arg_stride) {} }; +template +Array(T, Us...)->Array; + } // namespace Kokkos // diff --git a/lib/kokkos/core/src/Kokkos_Assert.hpp b/lib/kokkos/core/src/Kokkos_Assert.hpp index c3b9004734..6fea286005 100644 --- a/lib/kokkos/core/src/Kokkos_Assert.hpp +++ b/lib/kokkos/core/src/Kokkos_Assert.hpp @@ -44,9 +44,6 @@ __LINE__) " \n"); \ } \ } -// some projects already define this for themselves, so don't mess -// them up -#ifndef KOKKOS_ASSERT #define KOKKOS_ASSERT(...) \ { \ if (!bool(__VA_ARGS__)) { \ @@ -58,8 +55,7 @@ __LINE__) " \n"); \ } \ } -#endif // ifndef KOKKOS_ASSERT -#else // not debug mode +#else // not debug mode #define KOKKOS_EXPECTS(...) #define KOKKOS_ENSURES(...) #ifndef KOKKOS_ASSERT diff --git a/lib/kokkos/core/src/Kokkos_Atomics_Desul_Volatile_Wrapper.hpp b/lib/kokkos/core/src/Kokkos_Atomics_Desul_Volatile_Wrapper.hpp index 1c43474632..9acacef901 100644 --- a/lib/kokkos/core/src/Kokkos_Atomics_Desul_Volatile_Wrapper.hpp +++ b/lib/kokkos/core/src/Kokkos_Atomics_Desul_Volatile_Wrapper.hpp @@ -25,7 +25,7 @@ static_assert(false, #include #include -#ifdef KOKKOS_INTERNAL_NOT_PARALLEL +#ifdef KOKKOS_ENABLE_ATOMICS_BYPASS #define KOKKOS_DESUL_MEM_SCOPE desul::MemoryScopeCaller() #else #define KOKKOS_DESUL_MEM_SCOPE desul::MemoryScopeDevice() diff --git a/lib/kokkos/core/src/Kokkos_Atomics_Desul_Wrapper.hpp b/lib/kokkos/core/src/Kokkos_Atomics_Desul_Wrapper.hpp index bda3783980..eebdd20f15 100644 --- a/lib/kokkos/core/src/Kokkos_Atomics_Desul_Wrapper.hpp +++ b/lib/kokkos/core/src/Kokkos_Atomics_Desul_Wrapper.hpp @@ -49,7 +49,7 @@ inline const char* atomic_query_version() { return "KOKKOS_DESUL_ATOMICS"; } #endif // ============================================================ -#ifdef KOKKOS_INTERNAL_NOT_PARALLEL +#ifdef KOKKOS_ENABLE_ATOMICS_BYPASS #define KOKKOS_DESUL_MEM_SCOPE desul::MemoryScopeCaller() #else #define KOKKOS_DESUL_MEM_SCOPE desul::MemoryScopeDevice() diff --git a/lib/kokkos/core/src/Kokkos_Clamp.hpp b/lib/kokkos/core/src/Kokkos_Clamp.hpp new file mode 100644 index 0000000000..033cde9ab8 --- /dev/null +++ b/lib/kokkos/core/src/Kokkos_Clamp.hpp @@ -0,0 +1,41 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_CLAMP_HPP +#define KOKKOS_CLAMP_HPP + +#include + +namespace Kokkos { + +template +constexpr KOKKOS_INLINE_FUNCTION const T& clamp(const T& value, const T& lo, + const T& hi) { + KOKKOS_EXPECTS(!(hi < lo)); + return (value < lo) ? lo : (hi < value) ? hi : value; +} + +template +constexpr KOKKOS_INLINE_FUNCTION const T& clamp(const T& value, const T& lo, + const T& hi, + ComparatorType comp) { + KOKKOS_EXPECTS(!comp(hi, lo)); + return comp(value, lo) ? lo : comp(hi, value) ? hi : value; +} + +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/Kokkos_CopyViews.hpp b/lib/kokkos/core/src/Kokkos_CopyViews.hpp index a0ca55be70..08f6ba8d69 100644 --- a/lib/kokkos/core/src/Kokkos_CopyViews.hpp +++ b/lib/kokkos/core/src/Kokkos_CopyViews.hpp @@ -22,6 +22,7 @@ static_assert(false, #ifndef KOKKOS_COPYVIEWS_HPP_ #define KOKKOS_COPYVIEWS_HPP_ #include +#include #include #include #include @@ -612,12 +613,17 @@ void view_copy(const DstType& dst, const SrcType& src) { }; if (!DstExecCanAccessSrc && !SrcExecCanAccessDst) { - std::string message( - "Error: Kokkos::deep_copy with no available copy mechanism: "); - message += src.label(); - message += " to "; - message += dst.label(); - Kokkos::Impl::throw_runtime_exception(message); + std::ostringstream ss; + ss << "Error: Kokkos::deep_copy with no available copy mechanism: " + << "from source view (\"" << src.label() << "\") to destination view (\"" + << dst.label() << "\").\n" + << "There is no common execution space that can access both source's " + "space\n" + << "(" << src_memory_space().name() << ") and destination's space (" + << dst_memory_space().name() << "), " + << "so source and destination\n" + << "must be contiguous and have the same layout.\n"; + Kokkos::Impl::throw_runtime_exception(ss.str()); } // Figure out iteration order in case we need it @@ -1330,13 +1336,12 @@ inline void contiguous_fill( // Default implementation for execution spaces that don't provide a definition template struct ZeroMemset { - ZeroMemset(const ExecutionSpace& exec_space, const ViewType& dst, - typename ViewType::const_value_type& value) { - contiguous_fill(exec_space, dst, value); - } - - ZeroMemset(const ViewType& dst, typename ViewType::const_value_type& value) { - contiguous_fill(ExecutionSpace(), dst, value); + ZeroMemset(const ExecutionSpace& exec_space, const ViewType& dst) { + using ValueType = typename ViewType::value_type; + alignas(alignof(ValueType)) unsigned char + zero_initialized_storage[sizeof(ValueType)] = {}; + contiguous_fill(exec_space, dst, + *reinterpret_cast(zero_initialized_storage)); } }; @@ -1348,13 +1353,18 @@ inline std::enable_if_t< contiguous_fill_or_memset( const ExecutionSpace& exec_space, const View& dst, typename ViewTraits::const_value_type& value) { -// On A64FX memset seems to do the wrong thing with regards to first touch -// leading to the significant performance issues -#ifndef KOKKOS_ARCH_A64FX - if (Impl::is_zero_byte(value)) - ZeroMemset>(exec_space, dst, value); - else + // With OpenMP, using memset has significant performance issues. + if (Impl::is_zero_byte(value) +#ifdef KOKKOS_ENABLE_OPENMP + && !std::is_same_v #endif + ) + // FIXME intel/19 icpc fails to deduce template parameters here, + // resulting in compilation errors; explicitly passing the template + // parameters to ZeroMemset helps workaround the issue + // See https://github.com/kokkos/kokkos/issues/6775 + ZeroMemset>(exec_space, dst); + else contiguous_fill(exec_space, dst, value); } @@ -1379,15 +1389,20 @@ contiguous_fill_or_memset( typename ViewTraits::const_value_type& value) { using ViewType = View; using exec_space_type = typename ViewType::execution_space; + exec_space_type exec; // On A64FX memset seems to do the wrong thing with regards to first touch // leading to the significant performance issues #ifndef KOKKOS_ARCH_A64FX if (Impl::is_zero_byte(value)) - ZeroMemset>(dst, value); + // FIXME intel/19 icpc fails to deduce template parameters here, + // resulting in compilation errors; explicitly passing the template + // parameters to ZeroMemset helps workaround the issue + // See https://github.com/kokkos/kokkos/issues/6775 + ZeroMemset(exec, dst); else #endif - contiguous_fill(exec_space_type(), dst, value); + contiguous_fill(exec, dst, value); } template diff --git a/lib/kokkos/core/src/Kokkos_Core.hpp b/lib/kokkos/core/src/Kokkos_Core.hpp index 805411a699..1f146563be 100644 --- a/lib/kokkos/core/src/Kokkos_Core.hpp +++ b/lib/kokkos/core/src/Kokkos_Core.hpp @@ -46,14 +46,15 @@ #include #include -#include #include -#include +#include +#include #include #include #include #include #include +#include #include #include #include @@ -101,6 +102,7 @@ void declare_configuration_metadata(const std::string& category, [[nodiscard]] bool is_finalized() noexcept; [[nodiscard]] int device_id() noexcept; +[[nodiscard]] int num_devices() noexcept; [[nodiscard]] int num_threads() noexcept; bool show_warnings() noexcept; @@ -300,9 +302,6 @@ std::vector partition_space(ExecSpace const& space, // implementation of the RAII wrapper is using Kokkos::single. #include -// Specializations required after core definitions -#include - //---------------------------------------------------------------------------- // Redefinition of the macros min and max if we pushed them at entry of // Kokkos_Core.hpp diff --git a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp index 44f1c5b42f..7edb35f00e 100644 --- a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp +++ b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp @@ -30,10 +30,6 @@ #include #include -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -#include -#endif - //---------------------------------------------------------------------------- // Have assumed a 64-bit build (8-byte pointers) throughout the code base. // 32-bit build allowed but unsupported. @@ -75,9 +71,6 @@ template struct Device; // forward declare here so that backend initializer calls can use it. -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -struct InitArguments; -#endif class InitializationSettings; } // namespace Kokkos @@ -262,12 +255,6 @@ KOKKOS_FUNCTION void runtime_check_memory_access_violation( } } // namespace Impl - -namespace Experimental { -template -class LogicalMemorySpace; -} - } // namespace Kokkos //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp index ae1585a498..5f251eeb26 100644 --- a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp +++ b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp @@ -28,6 +28,7 @@ static_assert(false, #include #include #include +#include //---------------------------------------------------------------------------- @@ -114,62 +115,67 @@ class RangePolicy : public Impl::PolicyTraits { m_granularity_mask(0) {} /** \brief Total range */ + template && + std::is_convertible_v), + bool> = false> + inline RangePolicy(const IndexType1 work_begin, const IndexType2 work_end) + : RangePolicy(typename traits::execution_space(), work_begin, work_end) {} + + /** \brief Total range */ + template && + std::is_convertible_v), + bool> = false> inline RangePolicy(const typename traits::execution_space& work_space, - const member_type work_begin, const member_type work_end) + const IndexType1 work_begin, const IndexType2 work_end) : m_space(work_space), - m_begin(work_begin < work_end ? work_begin : 0), - m_end(work_begin < work_end ? work_end : 0), + m_begin(work_begin), + m_end(work_end), m_granularity(0), m_granularity_mask(0) { + check_conversion_safety(work_begin); + check_conversion_safety(work_end); + check_bounds_validity(); set_auto_chunk_size(); } - /** \brief Total range */ - inline RangePolicy(const member_type work_begin, const member_type work_end) - : RangePolicy(typename traits::execution_space(), work_begin, work_end) { - set_auto_chunk_size(); - } - - /** \brief Total range */ - template - inline RangePolicy(const typename traits::execution_space& work_space, - const member_type work_begin, const member_type work_end, - Args... args) + template && + std::is_convertible_v), + bool> = false> + RangePolicy(const typename traits::execution_space& work_space, + const IndexType1 work_begin, const IndexType2 work_end, + const ChunkSize chunk_size) : m_space(work_space), - m_begin(work_begin < work_end ? work_begin : 0), - m_end(work_begin < work_end ? work_end : 0), + m_begin(work_begin), + m_end(work_end), m_granularity(0), m_granularity_mask(0) { - set_auto_chunk_size(); - set(args...); + check_conversion_safety(work_begin); + check_conversion_safety(work_end); + check_bounds_validity(); + set_chunk_size(chunk_size.value); } /** \brief Total range */ - template - inline RangePolicy(const member_type work_begin, const member_type work_end, - Args... args) - : RangePolicy(typename traits::execution_space(), work_begin, work_end) { - set_auto_chunk_size(); - set(args...); - } - - private: - inline void set() {} + template && + std::is_convertible_v), + bool> = false> + RangePolicy(const IndexType1 work_begin, const IndexType2 work_end, + const ChunkSize chunk_size) + : RangePolicy(typename traits::execution_space(), work_begin, work_end, + chunk_size) {} public: - template - inline void set(Args...) { - static_assert( - 0 == sizeof...(Args), - "Kokkos::RangePolicy: unhandled constructor arguments encountered."); - } - - template - inline void set(const ChunkSize& chunksize, Args... args) { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED_WITH_COMMENT("Use set_chunk_size instead") + inline void set(ChunkSize chunksize) { m_granularity = chunksize.value; m_granularity_mask = m_granularity - 1; - set(args...); } +#endif public: /** \brief return chunk_size */ @@ -218,6 +224,67 @@ class RangePolicy : public Impl::PolicyTraits { m_granularity_mask = m_granularity - 1; } + void check_bounds_validity() { + if (m_end < m_begin) { + std::string msg = "Kokkos::RangePolicy bounds error: The lower bound (" + + std::to_string(m_begin) + + ") is greater than the upper bound (" + + std::to_string(m_end) + ").\n"; +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE_4 + Kokkos::abort(msg.c_str()); +#endif + m_begin = 0; + m_end = 0; +#ifdef KOKKOS_ENABLE_DEPRECATION_WARNINGS + Kokkos::Impl::log_warning(msg); +#endif + } + } + + // To be replaced with std::in_range (c++20) + template + static void check_conversion_safety(const IndexType bound) { +#if !defined(KOKKOS_ENABLE_DEPRECATED_CODE_4) || \ + defined(KOKKOS_ENABLE_DEPRECATION_WARNINGS) + + std::string msg = + "Kokkos::RangePolicy bound type error: an unsafe implicit conversion " + "is performed on a bound (" + + std::to_string(bound) + + "), which may " + "not preserve its original value.\n"; + bool warn = false; + + if constexpr (std::is_signed_v != + std::is_signed_v) { + // check signed to unsigned + if constexpr (std::is_signed_v) + warn |= (bound < static_cast( + std::numeric_limits::min())); + + // check unsigned to signed + if constexpr (std::is_signed_v) + warn |= (bound > static_cast( + std::numeric_limits::max())); + } + + // check narrowing + warn |= (static_cast(static_cast(bound)) != bound); + + if (warn) { +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE_4 + Kokkos::abort(msg.c_str()); +#endif + +#ifdef KOKKOS_ENABLE_DEPRECATION_WARNINGS + Kokkos::Impl::log_warning(msg); +#endif + } +#else + (void)bound; +#endif + } + public: /** \brief Subrange for a partition's rank and size. * @@ -261,6 +328,21 @@ class RangePolicy : public Impl::PolicyTraits { }; }; +RangePolicy()->RangePolicy<>; + +RangePolicy(int64_t, int64_t)->RangePolicy<>; +RangePolicy(int64_t, int64_t, ChunkSize const&)->RangePolicy<>; + +RangePolicy(DefaultExecutionSpace const&, int64_t, int64_t)->RangePolicy<>; +RangePolicy(DefaultExecutionSpace const&, int64_t, int64_t, ChunkSize const&) + ->RangePolicy<>; + +template >> +RangePolicy(ES const&, int64_t, int64_t)->RangePolicy; + +template >> +RangePolicy(ES const&, int64_t, int64_t, ChunkSize const&)->RangePolicy; + } // namespace Kokkos //---------------------------------------------------------------------------- @@ -983,7 +1065,16 @@ template const& policy, Lambda const& lambda, ReducerValueType& val) { + static_assert(/*!Kokkos::is_view_v &&*/ + !std::is_array_v && + !std::is_pointer_v && + !Kokkos::is_reducer_v, + "Only scalar return types are allowed!"); + + val = ReducerValueType{}; Impl::md_parallel_impl(policy, lambda, val); + policy.team.team_reduce( + Kokkos::Sum{val}); } template @@ -997,7 +1088,29 @@ template const& policy, Lambda const& lambda, ReducerValueType& val) { + static_assert(/*!Kokkos::is_view_v &&*/ + !std::is_array_v && + !std::is_pointer_v && + !Kokkos::is_reducer_v, + "Only a scalar return types are allowed!"); + + val = ReducerValueType{}; Impl::md_parallel_impl(policy, lambda, val); + if constexpr (false +#ifdef KOKKOS_ENABLE_CUDA + || std::is_same_v +#elif defined(KOKKOS_ENABLE_HIP) + || std::is_same_v +#elif defined(KOKKOS_ENABLE_SYCL) + || std::is_same_v +#endif + ) + policy.team.vector_reduce( + Kokkos::Sum{ + val}); } template @@ -1011,7 +1124,31 @@ template const& policy, Lambda const& lambda, ReducerValueType& val) { + static_assert(/*!Kokkos::is_view_v &&*/ + !std::is_array_v && + !std::is_pointer_v && + !Kokkos::is_reducer_v, + "Only a scalar return types are allowed!"); + + val = ReducerValueType{}; Impl::md_parallel_impl(policy, lambda, val); + if constexpr (false +#ifdef KOKKOS_ENABLE_CUDA + || std::is_same_v +#elif defined(KOKKOS_ENABLE_HIP) + || std::is_same_v +#elif defined(KOKKOS_ENABLE_SYCL) + || std::is_same_v +#endif + ) + policy.team.vector_reduce( + Kokkos::Sum{ + val}); + policy.team.team_reduce( + Kokkos::Sum{val}); } template diff --git a/lib/kokkos/core/src/Kokkos_HBWSpace.hpp b/lib/kokkos/core/src/Kokkos_HBWSpace.hpp deleted file mode 100644 index 369b7bafb7..0000000000 --- a/lib/kokkos/core/src/Kokkos_HBWSpace.hpp +++ /dev/null @@ -1,308 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#ifndef KOKKOS_IMPL_PUBLIC_INCLUDE -#include -static_assert(false, - "Including non-public Kokkos header files is not allowed."); -#endif -#ifndef KOKKOS_HBWSPACE_HPP -#define KOKKOS_HBWSPACE_HPP - -#include -#ifdef KOKKOS_ENABLE_HBWSPACE - -#include - -namespace Kokkos { - -namespace Experimental { - -/// \class HBWSpace -/// \brief Memory management for host memory. -/// -/// HBWSpace is a memory space that governs host memory. "Host" -/// memory means the usual CPU-accessible memory. -class HBWSpace { - public: - //! Tag this class as a kokkos memory space - using memory_space = HBWSpace; - using size_type = size_t; - - /// \typedef execution_space - /// \brief Default execution space for this memory space. - /// - /// Every memory space has a default execution space. This is - /// useful for things like initializing a View (which happens in - /// parallel using the View's default execution space). - using execution_space = Kokkos::DefaultHostExecutionSpace; - - //! This memory space preferred device_type - using device_type = Kokkos::Device; - - /**\brief Default memory space instance */ - HBWSpace(); - HBWSpace(const HBWSpace& rhs) = default; - HBWSpace& operator=(const HBWSpace&) = default; - ~HBWSpace() = default; - - /**\brief Non-default memory space instance to choose allocation mechansim, - * if available */ - - enum AllocationMechanism { - STD_MALLOC, - POSIX_MEMALIGN, - POSIX_MMAP, - INTEL_MM_ALLOC - }; - - explicit HBWSpace(const AllocationMechanism&); - - /**\brief Allocate untracked memory in the space */ - void* allocate(const size_t arg_alloc_size) const; - void* allocate(const char* arg_label, const size_t arg_alloc_size, - const size_t arg_logical_size = 0) const; - - /**\brief Deallocate untracked memory in the space */ - void deallocate(void* const arg_alloc_ptr, const size_t arg_alloc_size) const; - void deallocate(const char* arg_label, void* const arg_alloc_ptr, - const size_t arg_alloc_size, - const size_t arg_logical_size = 0) const; - - private: - template - friend class LogicalMemorySpace; - - void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, - const size_t arg_logical_size = 0, - const Kokkos::Tools::SpaceHandle = - Kokkos::Tools::make_space_handle(name())) const; - void impl_deallocate(const char* arg_label, void* const arg_alloc_ptr, - const size_t arg_alloc_size, - const size_t arg_logical_size = 0, - const Kokkos::Tools::SpaceHandle = - Kokkos::Tools::make_space_handle(name())) const; - - public: - /**\brief Return Name of the MemorySpace */ - static constexpr const char* name() { return "HBW"; } - - private: - AllocationMechanism m_alloc_mech; - friend class Kokkos::Impl::SharedAllocationRecord< - Kokkos::Experimental::HBWSpace, void>; -}; - -} // namespace Experimental - -} // namespace Kokkos - -//---------------------------------------------------------------------------- - -namespace Kokkos { - -namespace Impl { - -template <> -class SharedAllocationRecord - : public SharedAllocationRecord { - private: - friend Kokkos::Experimental::HBWSpace; - - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - - static void deallocate(RecordBase*); - -#ifdef KOKKOS_ENABLE_DEBUG - /**\brief Root record for tracked allocations from this HBWSpace instance */ - static RecordBase s_root_record; -#endif - - const Kokkos::Experimental::HBWSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - SharedAllocationRecord( - const Kokkos::Experimental::HBWSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); - - public: - inline std::string get_label() const { - return std::string(RecordBase::head()->m_label); - } - - KOKKOS_INLINE_FUNCTION static SharedAllocationRecord* allocate( - const Kokkos::Experimental::HBWSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size) { - KOKKOS_IF_ON_HOST((return new SharedAllocationRecord(arg_space, arg_label, - arg_alloc_size);)) - KOKKOS_IF_ON_DEVICE(((void)arg_space; (void)arg_label; (void)arg_alloc_size; - return nullptr;)) - } - - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const Kokkos::Experimental::HBWSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size); - - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr); - - static SharedAllocationRecord* get_record(void* arg_alloc_ptr); - - static void print_records(std::ostream&, - const Kokkos::Experimental::HBWSpace&, - bool detail = false); -}; - -} // namespace Impl - -} // namespace Kokkos - -//---------------------------------------------------------------------------- - -namespace Kokkos { - -namespace Impl { - -static_assert( - Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - -template <> -struct MemorySpaceAccess { - enum : bool { assignable = true }; - enum : bool { accessible = true }; - enum : bool { deepcopy = true }; -}; - -template <> -struct MemorySpaceAccess { - enum : bool { assignable = false }; - enum : bool { accessible = true }; - enum : bool { deepcopy = true }; -}; - -} // namespace Impl - -} // namespace Kokkos - -//---------------------------------------------------------------------------- - -namespace Kokkos { - -namespace Impl { - -template <> -struct DeepCopy { - DeepCopy(void* dst, const void* src, size_t n) { - hostspace_parallel_deepcopy(dst, src, n); - } - - DeepCopy(const DefaultHostExecutionSpace& exec, void* dst, const void* src, - size_t n) { - hostspace_parallel_deepcopy(exec, dst, src, n); - } -}; - -template -struct DeepCopy { - DeepCopy(void* dst, const void* src, size_t n) { - hostspace_parallel_deepcopy(dst, src, n); - } - - DeepCopy(const ExecutionSpace& exec, void* dst, const void* src, size_t n) { - exec.fence( - "Kokkos::Impl::DeepCopy -struct DeepCopy { - DeepCopy(void* dst, const void* src, size_t n) { - hostspace_parallel_deepcopy(dst, src, n); - } - - DeepCopy(const DefaultHostExecutionSpace& exec, void* dst, const void* src, - size_t n) { - hostspace_parallel_deepcopy(exec, dst, src, n); - } -}; - -template -struct DeepCopy { - DeepCopy(void* dst, const void* src, size_t n) { - hostspace_parallel_deepcopy(dst, src, n); - } - - DeepCopy(const ExecutionSpace& exec, void* dst, const void* src, size_t n) { - exec.fence( - "Kokkos::Impl::DeepCopy::DeepCopy: fence before copy"); - hostspace_parallel_deepcopy_async(copy_space, dst, src, n); - } -}; - -template <> -struct DeepCopy { - DeepCopy(void* dst, const void* src, size_t n) { - hostspace_parallel_deepcopy(dst, src, n); - } - - DeepCopy(const DefaultHostExecutionSpace& exec, void* dst, const void* src, - size_t n) { - hostspace_parallel_deepcopy(exec, dst, src, n); - } -}; - -template -struct DeepCopy { - DeepCopy(void* dst, const void* src, size_t n) { - hostspace_parallel_deepcopy(dst, src, n); - } - - DeepCopy(const ExecutionSpace& exec, void* dst, const void* src, size_t n) { - exec.fence( - "Kokkos::Impl::DeepCopy::DeepCopy: fence before copy"); - hostspace_parallel_deepcopy_async(dst, src, n); - } -}; - -} // namespace Impl - -} // namespace Kokkos - -#endif -#endif // #define KOKKOS_HBWSPACE_HPP diff --git a/lib/kokkos/core/src/Kokkos_HostSpace.hpp b/lib/kokkos/core/src/Kokkos_HostSpace.hpp index 90d1404063..a1fb0f5a67 100644 --- a/lib/kokkos/core/src/Kokkos_HostSpace.hpp +++ b/lib/kokkos/core/src/Kokkos_HostSpace.hpp @@ -37,7 +37,6 @@ static_assert(false, #include #include "impl/Kokkos_HostSpace_deepcopy.hpp" -#include /*--------------------------------------------------------------------------*/ @@ -75,18 +74,35 @@ class HostSpace { /**\brief Non-default memory space instance to choose allocation mechansim, * if available */ - enum KOKKOS_DEPRECATED AllocationMechanism { - STD_MALLOC, - POSIX_MEMALIGN, - POSIX_MMAP, - INTEL_MM_ALLOC - }; +#if defined(KOKKOS_COMPILER_GNU) && KOKKOS_COMPILER_GNU < 1100 + // We see deprecation warnings even when not using the deprecated + // HostSpace constructor below when using gcc before release 11. + enum +#else + enum KOKKOS_DEPRECATED +#endif + AllocationMechanism { + STD_MALLOC, + POSIX_MEMALIGN, + POSIX_MMAP, + INTEL_MM_ALLOC + }; KOKKOS_DEPRECATED explicit HostSpace(const AllocationMechanism&); #endif /**\brief Allocate untracked memory in the space */ + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const size_t arg_alloc_size) const; void* allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; @@ -98,9 +114,6 @@ class HostSpace { const size_t arg_logical_size = 0) const; private: - template - friend class Kokkos::Experimental::LogicalMemorySpace; - void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0, const Kokkos::Tools::SpaceHandle = @@ -117,7 +130,6 @@ class HostSpace { private: static constexpr const char* m_name = "Host"; - friend class Kokkos::Impl::SharedAllocationRecord; }; } // namespace Kokkos @@ -129,8 +141,7 @@ namespace Kokkos { namespace Impl { static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); template struct HostMirror { @@ -166,75 +177,7 @@ struct HostMirror { //---------------------------------------------------------------------------- -namespace Kokkos { - -namespace Impl { - -template <> -class SharedAllocationRecord - : public SharedAllocationRecordCommon { - private: - friend Kokkos::HostSpace; - friend class SharedAllocationRecordCommon; - - using base_t = SharedAllocationRecordCommon; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - -#ifdef KOKKOS_ENABLE_DEBUG - /**\brief Root record for tracked allocations from this HostSpace instance */ - static RecordBase s_root_record; -#endif - - Kokkos::HostSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - // This constructor does not forward to the one without exec_space arg - // in order to work around https://github.com/kokkos/kokkos/issues/5258 - // This constructor is templated so I can't just put it into the cpp file - // like the other constructor. - template - SharedAllocationRecord( - const ExecutionSpace& /* exec_space*/, const Kokkos::HostSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate) - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - this->base_t::_fill_host_accessible_header_info(*RecordBase::m_alloc_ptr, - arg_label); - } - - SharedAllocationRecord( - const Kokkos::HostSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); - - public: - KOKKOS_INLINE_FUNCTION static SharedAllocationRecord* allocate( - const Kokkos::HostSpace& arg_space, const std::string& arg_label, - const size_t arg_alloc_size) { - KOKKOS_IF_ON_HOST((return new SharedAllocationRecord(arg_space, arg_label, - arg_alloc_size);)) - KOKKOS_IF_ON_DEVICE(((void)arg_space; (void)arg_label; (void)arg_alloc_size; - return nullptr;)) - } -}; - -} // namespace Impl - -} // namespace Kokkos +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION(Kokkos::HostSpace); //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/Kokkos_LogicalSpaces.hpp b/lib/kokkos/core/src/Kokkos_LogicalSpaces.hpp deleted file mode 100644 index 1ee1d2c81f..0000000000 --- a/lib/kokkos/core/src/Kokkos_LogicalSpaces.hpp +++ /dev/null @@ -1,413 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#ifndef KOKKOS_IMPL_PUBLIC_INCLUDE -#include -static_assert(false, - "Including non-public Kokkos header files is not allowed."); -#endif -#ifndef KOKKOS_LOGICALSPACES_HPP -#define KOKKOS_LOGICALSPACES_HPP - -#include -#include -#include -#include -#include -#include -#include -#include -namespace Kokkos { -namespace Experimental { -struct DefaultMemorySpaceNamer { - static constexpr const char* get_name() { - return "DefaultLogicalMemorySpaceName"; - } -}; - -struct LogicalSpaceSharesAccess { - struct shared_access {}; - struct no_shared_access {}; -}; - -/// \class LogicalMemorySpace -/// \brief -/// -/// LogicalMemorySpace is a space that is identical to another space, -/// but differentiable by name and template argument -template -class LogicalMemorySpace { -#ifdef KOKKOS_ENABLE_OPENMPTARGET - // [DZP] For some reason I don't yet know, using LogicalMemorySpaces - // inside an OpenMPTarget build causes errors in the - // SharedAllocationRecords of other types. This is my way of erroring - // a build if we instantiate a LogicalMemSpace in an OMPTarget build - static_assert(!std::is_same::value, - "Can't use LogicalMemorySpaces in an OpenMPTarget build, we're " - "debugging memory issues"); -#endif - public: - //! Tag this class as a kokkos memory space - using memory_space = LogicalMemorySpace; - using size_type = typename BaseSpace::size_type; - - /// \typedef execution_space - /// \brief Default execution space for this memory space. - /// - /// Every memory space has a default execution space. This is - /// useful for things like initializing a View (which happens in - /// parallel using the View's default execution space). - - using execution_space = - std::conditional_t::value, - typename BaseSpace::execution_space, - DefaultBaseExecutionSpace>; - - using device_type = Kokkos::Device; - - LogicalMemorySpace() = default; - - template - LogicalMemorySpace(Args&&... args) : underlying_space((Args &&) args...) {} - - /**\brief Allocate untracked memory in the space */ - void* allocate(const size_t arg_alloc_size) const { - return allocate("[unlabeled]", arg_alloc_size); - } - void* allocate(const char* arg_label, const size_t arg_alloc_size, - const size_t arg_logical_size = 0) const { - return impl_allocate(arg_label, arg_alloc_size, arg_logical_size); - } - - /**\brief Deallocate untracked memory in the space */ - void deallocate(void* const arg_alloc_ptr, - const size_t arg_alloc_size) const { - deallocate("[unlabeled]", arg_alloc_ptr, arg_alloc_size); - } - void deallocate(const char* arg_label, void* const arg_alloc_ptr, - const size_t arg_alloc_size, - const size_t arg_logical_size = 0) const { - impl_deallocate(arg_label, arg_alloc_ptr, arg_alloc_size, arg_logical_size); - } - - /**\brief Return Name of the MemorySpace */ - constexpr static const char* name() { return Namer::get_name(); } - - private: - BaseSpace underlying_space; - template - friend class LogicalMemorySpace; - friend class Kokkos::Impl::SharedAllocationRecord; - - void* impl_allocate(const char* arg_label, const size_t arg_alloc_size, - const size_t arg_logical_size = 0, - Kokkos::Tools::SpaceHandle arg_handle = - Kokkos::Tools::make_space_handle(name())) const { - return underlying_space.impl_allocate(arg_label, arg_alloc_size, - arg_logical_size, arg_handle); - } - void impl_deallocate(const char* arg_label, void* const arg_alloc_ptr, - const size_t arg_alloc_size, - const size_t arg_logical_size = 0, - const Kokkos::Tools::SpaceHandle arg_handle = - Kokkos::Tools::make_space_handle(name())) const { - underlying_space.impl_deallocate(arg_label, arg_alloc_ptr, arg_alloc_size, - arg_logical_size, arg_handle); - } -}; -} // namespace Experimental -} // namespace Kokkos - -//---------------------------------------------------------------------------- - -namespace Kokkos { - -namespace Impl { - -template -struct MemorySpaceAccess< - Kokkos::Experimental::LogicalMemorySpace< - BaseSpace, DefaultBaseExecutionSpace, Namer, - Kokkos::Experimental::LogicalSpaceSharesAccess::shared_access>, - OtherSpace> { - enum { assignable = MemorySpaceAccess::assignable }; - enum { accessible = MemorySpaceAccess::accessible }; - enum { deepcopy = MemorySpaceAccess::deepcopy }; -}; - -template -struct MemorySpaceAccess< - OtherSpace, - Kokkos::Experimental::LogicalMemorySpace< - BaseSpace, DefaultBaseExecutionSpace, Namer, - Kokkos::Experimental::LogicalSpaceSharesAccess::shared_access>> { - enum { assignable = MemorySpaceAccess::assignable }; - enum { accessible = MemorySpaceAccess::accessible }; - enum { deepcopy = MemorySpaceAccess::deepcopy }; -}; - -template -struct MemorySpaceAccess< - Kokkos::Experimental::LogicalMemorySpace< - BaseSpace, DefaultBaseExecutionSpace, Namer, - Kokkos::Experimental::LogicalSpaceSharesAccess::shared_access>, - Kokkos::Experimental::LogicalMemorySpace< - BaseSpace, DefaultBaseExecutionSpace, Namer, - Kokkos::Experimental::LogicalSpaceSharesAccess::shared_access>> { - enum { assignable = true }; - enum { accessible = true }; - enum { deepcopy = true }; -}; - -} // namespace Impl - -} // namespace Kokkos - -//---------------------------------------------------------------------------- - -namespace Kokkos { - -namespace Impl { -template -class SharedAllocationRecord, - void> : public SharedAllocationRecord { - private: - using SpaceType = - Kokkos::Experimental::LogicalMemorySpace; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - - static void deallocate(RecordBase* arg_rec) { - delete static_cast(arg_rec); - } - -#ifdef KOKKOS_ENABLE_DEBUG - /**\brief Root record for tracked allocations from this - * LogicalMemorySpace instance */ - static RecordBase s_root_record; -#endif - - const SpaceType m_space; - - protected: - ~SharedAllocationRecord() { - m_space.deallocate(RecordBase::m_alloc_ptr->m_label, - SharedAllocationRecord::m_alloc_ptr, - SharedAllocationRecord::m_alloc_size, - (SharedAllocationRecord::m_alloc_size - - sizeof(SharedAllocationHeader))); - } - SharedAllocationRecord() = default; - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, const SpaceType& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const SpaceType& arg_space, const std::string& arg_label, - const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate) - : SharedAllocationRecord( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - // Fill in the Header information - RecordBase::m_alloc_ptr->m_record = - static_cast*>(this); - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length - 1); - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = '\0'; - } - - public: - inline std::string get_label() const { - return std::string(RecordBase::head()->m_label); - } - KOKKOS_INLINE_FUNCTION static SharedAllocationRecord* allocate( - const SpaceType& arg_space, const std::string& arg_label, - const size_t arg_alloc_size) { - KOKKOS_IF_ON_HOST((return new SharedAllocationRecord(arg_space, arg_label, - arg_alloc_size);)) - KOKKOS_IF_ON_DEVICE(((void)arg_space; (void)arg_label; (void)arg_alloc_size; - return nullptr;)) - } - - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const SpaceType& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return (void*)nullptr; - - SharedAllocationRecord* const r = - allocate(arg_space, arg_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); - } - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size) { - SharedAllocationRecord* const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord* const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - Kokkos::fence( - "SharedAllocationRecord::reallocate_tracked: fence after copying data"); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); - } - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord* const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } - } - - static SharedAllocationRecord* get_record(void* alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordHost = SharedAllocationRecord; - - SharedAllocationHeader const* const head = - alloc_ptr ? Header::get_header(alloc_ptr) - : (SharedAllocationHeader*)nullptr; - RecordHost* const record = - head ? static_cast(head->m_record) : (RecordHost*)nullptr; - - if (!alloc_ptr || record->m_alloc_ptr != head) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::SharedAllocationRecord< LogicalMemorySpace<> , " - "void >::get_record ERROR")); - } - - return record; - } -#ifdef KOKKOS_ENABLE_DEBUG - static void print_records(std::ostream& s, const SpaceType&, - bool detail = false) { - SharedAllocationRecord::print_host_accessible_records( - s, "HostSpace", &s_root_record, detail); - } -#else - static void print_records(std::ostream&, const SpaceType&, - bool detail = false) { - (void)detail; - throw_runtime_exception( - "SharedAllocationRecord::print_records only works " - "with KOKKOS_ENABLE_DEBUG enabled"); - } -#endif -}; -#ifdef KOKKOS_ENABLE_DEBUG -/**\brief Root record for tracked allocations from this LogicalSpace - * instance */ -template -SharedAllocationRecord - SharedAllocationRecord, - void>::s_root_record; -#endif - -} // namespace Impl - -} // namespace Kokkos - -//---------------------------------------------------------------------------- - -namespace Kokkos { - -namespace Impl { - -template -struct DeepCopy, - Kokkos::Experimental::LogicalMemorySpace< - BaseSpace, DefaultBaseExecutionSpace, Namer, SharesAccess>, - ExecutionSpace> { - DeepCopy(void* dst, void* src, size_t n) { - DeepCopy(dst, src, n); - } - DeepCopy(const ExecutionSpace& exec, void* dst, void* src, size_t n) { - DeepCopy(exec, dst, src, n); - } -}; - -template -struct DeepCopy, - ExecutionSpace> { - DeepCopy(void* dst, void* src, size_t n) { - DeepCopy(dst, src, n); - } - DeepCopy(const ExecutionSpace& exec, void* dst, void* src, size_t n) { - DeepCopy(exec, dst, src, n); - } -}; - -template -struct DeepCopy, - DestinationSpace, ExecutionSpace> { - DeepCopy(void* dst, void* src, size_t n) { - DeepCopy(dst, src, n); - } - DeepCopy(const ExecutionSpace& exec, void* dst, void* src, size_t n) { - DeepCopy(exec, dst, src, n); - } -}; -} // namespace Impl - -} // namespace Kokkos -#endif // KOKKOS_LOGICALSPACES_HPP diff --git a/lib/kokkos/core/src/Kokkos_Macros.hpp b/lib/kokkos/core/src/Kokkos_Macros.hpp index 3cf7ac4fa2..b255d2a519 100644 --- a/lib/kokkos/core/src/Kokkos_Macros.hpp +++ b/lib/kokkos/core/src/Kokkos_Macros.hpp @@ -84,11 +84,12 @@ //---------------------------------------------------------------------------- -#if !defined(KOKKOS_ENABLE_THREADS) && !defined(KOKKOS_ENABLE_CUDA) && \ - !defined(KOKKOS_ENABLE_OPENMP) && !defined(KOKKOS_ENABLE_HPX) && \ - !defined(KOKKOS_ENABLE_OPENMPTARGET) && !defined(KOKKOS_ENABLE_HIP) && \ - !defined(KOKKOS_ENABLE_SYCL) -#define KOKKOS_INTERNAL_NOT_PARALLEL +#if defined(KOKKOS_ENABLE_ATOMICS_BYPASS) && \ + (defined(KOKKOS_ENABLE_THREADS) || defined(KOKKOS_ENABLE_CUDA) || \ + defined(KOKKOS_ENABLE_OPENMP) || defined(KOKKOS_ENABLE_HPX) || \ + defined(KOKKOS_ENABLE_OPENMPTARGET) || defined(KOKKOS_ENABLE_HIP) || \ + defined(KOKKOS_ENABLE_SYCL) || defined(KOKKOS_ENABLE_OPENACC)) +#error Atomics may only be disabled if neither a host parallel nor a device backend is enabled #endif #define KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA @@ -339,12 +340,6 @@ #define KOKKOS_IMPL_DEVICE_FUNCTION #endif -// Temporary solution for SYCL not supporting printf in kernels. -// Might disappear at any point once we have found another solution. -#if !defined(KOKKOS_IMPL_DO_NOT_USE_PRINTF) -#define KOKKOS_IMPL_DO_NOT_USE_PRINTF(...) ::printf(__VA_ARGS__) -#endif - //---------------------------------------------------------------------------- // Define final version of functions. This is so that clang tidy can find these // macros more easily @@ -433,22 +428,6 @@ #define KOKKOS_ENABLE_DEFAULT_DEVICE_TYPE_SERIAL #endif -//---------------------------------------------------------------------------- -// Determine for what space the code is being compiled: -#if defined(KOKKOS_ENABLE_DEPRECATED_CODE_3) - -#if defined(__CUDACC__) && defined(__CUDA_ARCH__) && defined(KOKKOS_ENABLE_CUDA) -#define KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA -#elif defined(__SYCL_DEVICE_ONLY__) && defined(KOKKOS_ENABLE_SYCL) -#define KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL -#elif defined(__HIPCC__) && defined(__HIP_DEVICE_COMPILE__) && \ - defined(KOKKOS_ENABLE_HIP) -#define KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HIP_GPU -#else -#define KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST -#endif - -#endif //---------------------------------------------------------------------------- // Remove surrounding parentheses if present diff --git a/lib/kokkos/core/src/Kokkos_MasterLock.hpp b/lib/kokkos/core/src/Kokkos_MasterLock.hpp deleted file mode 100644 index 1d09617371..0000000000 --- a/lib/kokkos/core/src/Kokkos_MasterLock.hpp +++ /dev/null @@ -1,56 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#ifndef KOKKOS_IMPL_PUBLIC_INCLUDE -#include -static_assert(false, - "Including non-public Kokkos header files is not allowed."); -#endif -#ifndef KOKKOS_MASTER_LOCK_HPP -#define KOKKOS_MASTER_LOCK_HPP - -#include - -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - -namespace Kokkos { -namespace Experimental { - -// my be used to coordinate work between master instances -// SHOULD NOT be used within a parallel algorithm -// -// This lock should be used with with a scoped lock guard -// i.e. std::unique_lock, std::lock_guard -// -// cannot be copied or moved -// has the following functions available -// -// Lock() -// ~Lock() -// -// void lock() -// void unlock() -// bool try_lock() -// -template -class MasterLock; - -} // namespace Experimental -} // namespace Kokkos - -#endif - -#endif // KOKKOS_MASTER_LOCK_HPP diff --git a/lib/kokkos/core/src/Kokkos_MathematicalConstants.hpp b/lib/kokkos/core/src/Kokkos_MathematicalConstants.hpp index 51a50d347d..1a77f373fd 100644 --- a/lib/kokkos/core/src/Kokkos_MathematicalConstants.hpp +++ b/lib/kokkos/core/src/Kokkos_MathematicalConstants.hpp @@ -51,24 +51,6 @@ KOKKOS_IMPL_MATH_CONSTANT(phi, 1.618033988749894848204586834365638118L); } // namespace Kokkos::numbers -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -namespace Kokkos::Experimental { -using Kokkos::numbers::e_v; -using Kokkos::numbers::egamma_v; -using Kokkos::numbers::inv_pi_v; -using Kokkos::numbers::inv_sqrt3_v; -using Kokkos::numbers::inv_sqrtpi_v; -using Kokkos::numbers::ln10_v; -using Kokkos::numbers::ln2_v; -using Kokkos::numbers::log10e_v; -using Kokkos::numbers::log2e_v; -using Kokkos::numbers::phi_v; -using Kokkos::numbers::pi_v; -using Kokkos::numbers::sqrt2_v; -using Kokkos::numbers::sqrt3_v; -} // namespace Kokkos::Experimental -#endif - #ifdef KOKKOS_IMPL_PUBLIC_INCLUDE_NOTDEFINED_MATHCONSTANTS #undef KOKKOS_IMPL_PUBLIC_INCLUDE #undef KOKKOS_IMPL_PUBLIC_INCLUDE_NOTDEFINED_MATHCONSTANTS diff --git a/lib/kokkos/core/src/Kokkos_MathematicalFunctions.hpp b/lib/kokkos/core/src/Kokkos_MathematicalFunctions.hpp index ee64c67b93..3fead8dd29 100644 --- a/lib/kokkos/core/src/Kokkos_MathematicalFunctions.hpp +++ b/lib/kokkos/core/src/Kokkos_MathematicalFunctions.hpp @@ -92,16 +92,6 @@ using promote_3_t = typename promote_3::type; #endif #endif -#if defined(KOKKOS_ENABLE_DEPRECATED_CODE_3) -#define KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( \ - USING_DECLARATIONS_IN_EXPERIMENTAL_NAMESPACE) \ - USING_DECLARATIONS_IN_EXPERIMENTAL_NAMESPACE -#else -#define KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( \ - USING_DECLARATIONS_IN_EXPERIMENTAL_NAMESPACE) \ - /* nothing */ -#endif - #define KOKKOS_IMPL_MATH_UNARY_FUNCTION(FUNC) \ KOKKOS_INLINE_FUNCTION float FUNC(float x) { \ using KOKKOS_IMPL_MATH_FUNCTIONS_NAMESPACE::FUNC; \ @@ -128,13 +118,7 @@ using promote_3_t = typename promote_3::type; T x) { \ using KOKKOS_IMPL_MATH_FUNCTIONS_NAMESPACE::FUNC; \ return FUNC(static_cast(x)); \ - } \ - KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( \ - namespace Experimental { \ - using ::Kokkos::FUNC; \ - using ::Kokkos::FUNC##f; \ - using ::Kokkos::FUNC##l; \ - }) + } // isinf, isnan, and isinfinite do not work on Windows with CUDA with std:: // getting warnings about calling host function in device function then @@ -151,9 +135,7 @@ using promote_3_t = typename promote_3::type; KOKKOS_INLINE_FUNCTION std::enable_if_t, bool> FUNC( \ T x) { \ return ::FUNC(static_cast(x)); \ - } \ - KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( \ - namespace Experimental { using ::Kokkos::FUNC; }) + } #else #define KOKKOS_IMPL_MATH_UNARY_PREDICATE(FUNC) \ KOKKOS_INLINE_FUNCTION bool FUNC(float x) { \ @@ -173,9 +155,7 @@ using promote_3_t = typename promote_3::type; T x) { \ using KOKKOS_IMPL_MATH_FUNCTIONS_NAMESPACE::FUNC; \ return FUNC(static_cast(x)); \ - } \ - KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( \ - namespace Experimental { using ::Kokkos::FUNC; }) + } #endif #define KOKKOS_IMPL_MATH_BINARY_FUNCTION(FUNC) \ @@ -218,16 +198,10 @@ using promote_3_t = typename promote_3::type; long double> \ FUNC(T1 x, T2 y) { \ using Promoted = Kokkos::Impl::promote_2_t; \ - static_assert(std::is_same_v, ""); \ + static_assert(std::is_same_v); \ using std::FUNC; \ return FUNC(static_cast(x), static_cast(y)); \ - } \ - KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( \ - namespace Experimental { \ - using ::Kokkos::FUNC; \ - using ::Kokkos::FUNC##f; \ - using ::Kokkos::FUNC##l; \ - }) + } #define KOKKOS_IMPL_MATH_TERNARY_FUNCTION(FUNC) \ KOKKOS_INLINE_FUNCTION float FUNC(float x, float y, float z) { \ @@ -314,8 +288,6 @@ inline long double abs(long double x) { using std::abs; return abs(x); } -KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( - namespace Experimental { using ::Kokkos::abs; }) KOKKOS_IMPL_MATH_UNARY_FUNCTION(fabs) KOKKOS_IMPL_MATH_BINARY_FUNCTION(fmod) KOKKOS_IMPL_MATH_BINARY_FUNCTION(remainder) @@ -336,12 +308,6 @@ KOKKOS_INLINE_FUNCTION float nanf(char const*) { return sycl::nan(0u); } KOKKOS_INLINE_FUNCTION double nan(char const*) { return sycl::nan(0ul); } #endif inline long double nanl(char const* arg) { return ::nanl(arg); } -KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED( - namespace Experimental { - using ::Kokkos::nan; - using ::Kokkos::nanf; - using ::Kokkos::nanl; - }) // Exponential functions KOKKOS_IMPL_MATH_UNARY_FUNCTION(exp) // FIXME_NVHPC nvc++ has issues with exp2 @@ -478,7 +444,6 @@ KOKKOS_IMPL_MATH_UNARY_PREDICATE(signbit) // islessgreater // isunordered -#undef KOKKOS_IMPL_MATH_FUNCTIONS_DEFINED_IF_DEPRECATED_CODE_ENABLED #undef KOKKOS_IMPL_MATH_FUNCTIONS_NAMESPACE #undef KOKKOS_IMPL_MATH_UNARY_FUNCTION #undef KOKKOS_IMPL_MATH_UNARY_PREDICATE diff --git a/lib/kokkos/core/src/Kokkos_MinMaxClamp.hpp b/lib/kokkos/core/src/Kokkos_MinMax.hpp similarity index 83% rename from lib/kokkos/core/src/Kokkos_MinMaxClamp.hpp rename to lib/kokkos/core/src/Kokkos_MinMax.hpp index 37a28a80b6..5c60a88bfb 100644 --- a/lib/kokkos/core/src/Kokkos_MinMaxClamp.hpp +++ b/lib/kokkos/core/src/Kokkos_MinMax.hpp @@ -14,13 +14,8 @@ // //@HEADER -#ifndef KOKKOS_IMPL_PUBLIC_INCLUDE -#include -static_assert(false, - "Including non-public Kokkos header files is not allowed."); -#endif -#ifndef KOKKOS_MIN_MAX_CLAMP_HPP -#define KOKKOS_MIN_MAX_CLAMP_HPP +#ifndef KOKKOS_MIN_MAX_HPP +#define KOKKOS_MIN_MAX_HPP #include #include @@ -29,22 +24,6 @@ static_assert(false, namespace Kokkos { -// clamp -template -constexpr KOKKOS_INLINE_FUNCTION const T& clamp(const T& value, const T& lo, - const T& hi) { - KOKKOS_EXPECTS(!(hi < lo)); - return (value < lo) ? lo : (hi < value) ? hi : value; -} - -template -constexpr KOKKOS_INLINE_FUNCTION const T& clamp(const T& value, const T& lo, - const T& hi, - ComparatorType comp) { - KOKKOS_EXPECTS(!comp(hi, lo)); - return comp(value, lo) ? lo : comp(hi, value) ? hi : value; -} - // max template constexpr KOKKOS_INLINE_FUNCTION const T& max(const T& a, const T& b) { @@ -199,15 +178,6 @@ KOKKOS_INLINE_FUNCTION constexpr Kokkos::pair minmax( return result; } -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -namespace Experimental { -using ::Kokkos::clamp; -using ::Kokkos::max; -using ::Kokkos::min; -using ::Kokkos::minmax; -} // namespace Experimental -#endif - } // namespace Kokkos #endif diff --git a/lib/kokkos/core/src/Kokkos_Pair.hpp b/lib/kokkos/core/src/Kokkos_Pair.hpp index 7127c78280..9be8d8d7aa 100644 --- a/lib/kokkos/core/src/Kokkos_Pair.hpp +++ b/lib/kokkos/core/src/Kokkos_Pair.hpp @@ -28,6 +28,7 @@ #endif #include +#include #include namespace Kokkos { @@ -484,7 +485,6 @@ KOKKOS_FORCEINLINE_FUNCTION constexpr bool operator>=( } namespace Impl { - template struct is_pair_like : std::false_type {}; template diff --git a/lib/kokkos/core/src/Kokkos_Printf.hpp b/lib/kokkos/core/src/Kokkos_Printf.hpp index af20221a5a..63a4cce2ae 100644 --- a/lib/kokkos/core/src/Kokkos_Printf.hpp +++ b/lib/kokkos/core/src/Kokkos_Printf.hpp @@ -30,6 +30,9 @@ namespace Kokkos { // In contrast to std::printf, return void to get a consistent behavior across // backends. The GPU backends always return 1 and NVHPC only compiles if we // don't ask for the return value. +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) +using ::printf; +#else template KOKKOS_FORCEINLINE_FUNCTION void printf(const char* format, Args... args) { #ifdef KOKKOS_ENABLE_SYCL @@ -39,15 +42,13 @@ KOKKOS_FORCEINLINE_FUNCTION void printf(const char* format, Args... args) { else sycl::ext::oneapi::experimental::printf(format, args...); #else - if constexpr (sizeof...(Args) == 0) ::printf("%s", format); - // FIXME_OPENMPTARGET non-string-literal argument used in printf is not - // supported for spir64 -#if !(defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU)) + if constexpr (sizeof...(Args) == 0) + ::printf("%s", format); else ::printf(format, args...); #endif -#endif } +#endif } // namespace Kokkos diff --git a/lib/kokkos/core/src/Kokkos_Profiling_ProfileSection.hpp b/lib/kokkos/core/src/Kokkos_Profiling_ProfileSection.hpp index 29a04ac3b0..e7a9ba0c7e 100644 --- a/lib/kokkos/core/src/Kokkos_Profiling_ProfileSection.hpp +++ b/lib/kokkos/core/src/Kokkos_Profiling_ProfileSection.hpp @@ -22,49 +22,34 @@ #endif #include -#include #include #include -namespace Kokkos { -namespace Profiling { +namespace Kokkos::Profiling { + +class [[nodiscard]] ProfilingSection { + uint32_t sectionID; -class ProfilingSection { public: ProfilingSection(ProfilingSection const&) = delete; ProfilingSection& operator=(ProfilingSection const&) = delete; - ProfilingSection(const std::string& sectionName) { - if (Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::createProfileSection(sectionName, &secID); - } +#if defined(__has_cpp_attribute) && __has_cpp_attribute(nodiscard) >= 201907 + [[nodiscard]] +#endif + explicit ProfilingSection(const std::string& sectionName) { + Kokkos::Profiling::createProfileSection(sectionName, §ionID); } - void start() { - if (Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::startSection(secID); - } - } + void start() { Kokkos::Profiling::startSection(sectionID); } - void stop() { - if (Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::stopSection(secID); - } - } + void stop() { Kokkos::Profiling::stopSection(sectionID); } - ~ProfilingSection() { - if (Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::destroyProfileSection(secID); - } - } - - protected: - uint32_t secID; + ~ProfilingSection() { Kokkos::Profiling::destroyProfileSection(sectionID); } }; -} // namespace Profiling -} // namespace Kokkos +} // namespace Kokkos::Profiling #ifdef KOKKOS_IMPL_PUBLIC_INCLUDE_NOTDEFINED_CORE #undef KOKKOS_IMPL_PUBLIC_INCLUDE diff --git a/lib/kokkos/core/src/Kokkos_Swap.hpp b/lib/kokkos/core/src/Kokkos_Swap.hpp new file mode 100644 index 0000000000..2f849a13ab --- /dev/null +++ b/lib/kokkos/core/src/Kokkos_Swap.hpp @@ -0,0 +1,68 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_SWAP_HPP +#define KOKKOS_SWAP_HPP + +#include + +#include +#include +#include + +namespace Kokkos { + +template +KOKKOS_FUNCTION constexpr std::enable_if_t && + std::is_move_assignable_v> +kokkos_swap(T& a, T& b) noexcept(std::is_nothrow_move_constructible_v&& + std::is_nothrow_move_assignable_v) { + T t(std::move(a)); + a = std::move(b); + b = std::move(t); +} + +namespace Impl { + +template +struct is_swappable { + template + static decltype(kokkos_swap(std::declval(), std::declval())) + test_swap(int); + struct Nope; + template + static Nope test_swap(long); + static constexpr bool value = + !std::is_same_v(0)), Nope>; +}; + +template +inline constexpr bool is_nothrow_swappable_v = + noexcept(kokkos_swap(std::declval(), std::declval())); + +} // namespace Impl + +template +KOKKOS_FUNCTION constexpr std::enable_if_t::value> +kokkos_swap(T (&a)[N], T (&b)[N]) noexcept(Impl::is_nothrow_swappable_v) { + for (std::size_t i = 0; i < N; ++i) { + kokkos_swap(a[i], b[i]); + } +} + +} // namespace Kokkos + +#endif diff --git a/lib/kokkos/core/src/Kokkos_Tuners.hpp b/lib/kokkos/core/src/Kokkos_Tuners.hpp index 618401654e..f5ffc66af5 100644 --- a/lib/kokkos/core/src/Kokkos_Tuners.hpp +++ b/lib/kokkos/core/src/Kokkos_Tuners.hpp @@ -256,13 +256,14 @@ auto get_point_helper(const PointType& in, const ArrayType& indices, template struct GetPoint; -template -struct GetPoint> { +template +struct GetPoint< + PointType, + std::array> { using index_set_type = - std::array; + std::array; static auto build(const PointType& in, const index_set_type& indices) { - return get_point_helper(in, indices, std::make_index_sequence{}); + return get_point_helper(in, indices, std::make_index_sequence{}); } }; diff --git a/lib/kokkos/core/src/Kokkos_View.hpp b/lib/kokkos/core/src/Kokkos_View.hpp index bcbb28014c..484a0e6f62 100644 --- a/lib/kokkos/core/src/Kokkos_View.hpp +++ b/lib/kokkos/core/src/Kokkos_View.hpp @@ -39,7 +39,7 @@ static_assert(false, #ifdef KOKKOS_ENABLE_IMPL_MDSPAN #include #endif -#include +#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -75,25 +75,59 @@ constexpr KOKKOS_INLINE_FUNCTION std::size_t count_valid_integers( (i6 != KOKKOS_INVALID_INDEX) + (i7 != KOKKOS_INVALID_INDEX); } -KOKKOS_INLINE_FUNCTION -void runtime_check_rank(const size_t rank, const size_t dyn_rank, - const bool is_void_spec, const size_t i0, - const size_t i1, const size_t i2, const size_t i3, - const size_t i4, const size_t i5, const size_t i6, - const size_t i7, const std::string& label) { +// FIXME Ideally, we would not instantiate this function for every possible View +// type. We should be able to only pass "extent" when we use mdspan. +template +KOKKOS_INLINE_FUNCTION void runtime_check_rank( + const View&, const bool is_void_spec, const size_t i0, const size_t i1, + const size_t i2, const size_t i3, const size_t i4, const size_t i5, + const size_t i6, const size_t i7, const char* label) { (void)(label); if (is_void_spec) { const size_t num_passed_args = count_valid_integers(i0, i1, i2, i3, i4, i5, i6, i7); + // We either allow to pass as many extents as the dynamic rank is, or + // as many extents as the total rank is. In the latter case, the given + // extents for the static dimensions must match the + // compile-time extents. + constexpr int rank = View::rank(); + constexpr int dyn_rank = View::rank_dynamic(); + const bool n_args_is_dyn_rank = num_passed_args == dyn_rank; + const bool n_args_is_rank = num_passed_args == rank; - if (num_passed_args != dyn_rank && num_passed_args != rank) { + if constexpr (rank != dyn_rank) { + if (n_args_is_rank) { + size_t new_extents[8] = {i0, i1, i2, i3, i4, i5, i6, i7}; + for (int i = dyn_rank; i < rank; ++i) + if (new_extents[i] != View::static_extent(i)) { + KOKKOS_IF_ON_HOST( + const std::string message = + "The specified run-time extent for Kokkos::View '" + + std::string(label) + + "' does not match the compile-time extent in dimension " + + std::to_string(i) + ". The given extent is " + + std::to_string(new_extents[i]) + " but should be " + + std::to_string(View::static_extent(i)) + ".\n"; + Kokkos::abort(message.c_str());) + KOKKOS_IF_ON_DEVICE( + Kokkos::abort( + "The specified run-time extents for a Kokkos::View " + "do not match the compile-time extents.");) + } + } + } + + if (!n_args_is_dyn_rank && !n_args_is_rank) { KOKKOS_IF_ON_HOST( const std::string message = - "Constructor for Kokkos View '" + label + - "' has mismatched number of arguments. Number of arguments = " + + "Constructor for Kokkos::View '" + std::string(label) + + "' has mismatched number of arguments. The number " + "of arguments = " + std::to_string(num_passed_args) + - " but dynamic rank = " + std::to_string(dyn_rank) + " \n"; + " neither matches the dynamic rank = " + + std::to_string(dyn_rank) + + " nor the total rank = " + std::to_string(rank) + "\n"; Kokkos::abort(message.c_str());) KOKKOS_IF_ON_DEVICE(Kokkos::abort("Constructor for Kokkos View has " "mismatched number of arguments.");) @@ -814,15 +848,15 @@ class View : public ViewTraits { template static KOKKOS_FUNCTION void check_access_member_function_valid_args(Is...) { - static_assert(rank <= sizeof...(Is), ""); - static_assert(sizeof...(Is) <= 8, ""); - static_assert(Kokkos::Impl::are_integral::value, ""); + static_assert(rank <= sizeof...(Is)); + static_assert(sizeof...(Is) <= 8); + static_assert(Kokkos::Impl::are_integral::value); } template static KOKKOS_FUNCTION void check_operator_parens_valid_args(Is...) { - static_assert(rank == sizeof...(Is), ""); - static_assert(Kokkos::Impl::are_integral::value, ""); + static_assert(rank == sizeof...(Is)); + static_assert(Kokkos::Impl::are_integral::value); } public: @@ -1402,21 +1436,30 @@ class View : public ViewTraits { "execution space"); } - size_t i0 = arg_layout.dimension[0]; - size_t i1 = arg_layout.dimension[1]; - size_t i2 = arg_layout.dimension[2]; - size_t i3 = arg_layout.dimension[3]; - size_t i4 = arg_layout.dimension[4]; - size_t i5 = arg_layout.dimension[5]; - size_t i6 = arg_layout.dimension[6]; - size_t i7 = arg_layout.dimension[7]; +#ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK + if constexpr (std::is_same_v || + std::is_same_v || + std::is_same_v || + is_layouttiled::value) { + size_t i0 = arg_layout.dimension[0]; + size_t i1 = arg_layout.dimension[1]; + size_t i2 = arg_layout.dimension[2]; + size_t i3 = arg_layout.dimension[3]; + size_t i4 = arg_layout.dimension[4]; + size_t i5 = arg_layout.dimension[5]; + size_t i6 = arg_layout.dimension[6]; + size_t i7 = arg_layout.dimension[7]; - const std::string& alloc_name = - Impl::get_property(prop_copy); - Impl::runtime_check_rank( - rank, rank_dynamic, - std::is_same::value, i0, i1, i2, i3, - i4, i5, i6, i7, alloc_name); + const std::string& alloc_name = + Impl::get_property(prop_copy); + Impl::runtime_check_rank( + *this, std::is_same::value, i0, i1, + i2, i3, i4, i5, i6, i7, alloc_name.c_str()); + } +#endif Kokkos::Impl::SharedAllocationRecord<>* record = m_map.allocate_shared( prop_copy, arg_layout, Impl::ViewCtorProp::has_execution_space); @@ -1445,6 +1488,29 @@ class View : public ViewTraits { typename Impl::ViewCtorProp::pointer_type>::value, "Constructing View to wrap user memory must supply matching pointer " "type"); + +#ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK + if constexpr (std::is_same_v || + std::is_same_v || + std::is_same_v || + is_layouttiled::value) { + size_t i0 = arg_layout.dimension[0]; + size_t i1 = arg_layout.dimension[1]; + size_t i2 = arg_layout.dimension[2]; + size_t i3 = arg_layout.dimension[3]; + size_t i4 = arg_layout.dimension[4]; + size_t i5 = arg_layout.dimension[5]; + size_t i6 = arg_layout.dimension[6]; + size_t i7 = arg_layout.dimension[7]; + + Impl::runtime_check_rank( + *this, std::is_same::value, i0, i1, + i2, i3, i4, i5, i6, i7, "UNMANAGED"); + } +#endif } // Simple dimension-only layout diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.cpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.cpp index f54c44d66f..99daf379b6 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.cpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.cpp @@ -58,8 +58,10 @@ void Kokkos::Experimental::OpenACC::impl_initialize( Impl::OpenACCInternal::m_acc_device_num = acc_get_device_num(acc_device_host); } else { + using Kokkos::Impl::get_visible_devices; + std::vector const& visible_devices = get_visible_devices(); using Kokkos::Impl::get_gpu; - int const dev_num = get_gpu(settings); + int const dev_num = get_gpu(settings).value_or(visible_devices[0]); acc_set_device_num(dev_num, Impl::OpenACC_Traits::dev_type); Impl::OpenACCInternal::m_acc_device_num = dev_num; } diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.hpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.hpp index b012f6a42a..5155bee33d 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.hpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC.hpp @@ -91,7 +91,11 @@ class OpenACC { #else int concurrency() const { return 256000; } // FIXME_OPENACC #endif - static bool in_parallel() { return acc_on_device(acc_device_not_host); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED static bool in_parallel() { + return acc_on_device(acc_device_not_host); + } +#endif uint32_t impl_instance_id() const noexcept; Impl::OpenACCInternal* impl_internal_space_instance() const { return m_space_instance.get(); diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACCSpace.cpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACCSpace.cpp index 141ec77fd1..acc0dcd3c6 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACCSpace.cpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACCSpace.cpp @@ -19,8 +19,8 @@ #include #include #include -#include #include +#include #include @@ -66,6 +66,19 @@ void *Kokkos::Experimental::OpenACCSpace::impl_allocate( ptr = acc_malloc(arg_alloc_size); + if (!ptr) { + size_t alignment = 1; // OpenACC does not handle alignment + using Kokkos::Experimental::RawMemoryAllocationFailure; + auto failure_mode = + arg_alloc_size > 0 + ? RawMemoryAllocationFailure::FailureMode::OutOfMemoryError + : RawMemoryAllocationFailure::FailureMode::InvalidAllocationSize; + auto alloc_mechanism = + RawMemoryAllocationFailure::AllocationMechanism::OpenACCMalloc; + throw RawMemoryAllocationFailure(arg_alloc_size, alignment, failure_mode, + alloc_mechanism); + } + if (Kokkos::Profiling::profileLibraryLoaded()) { const size_t reported_size = (arg_logical_size > 0) ? arg_logical_size : arg_alloc_size; diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_DeepCopy.hpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_DeepCopy.hpp index 4aed7e00f7..ca022192b0 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_DeepCopy.hpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_DeepCopy.hpp @@ -34,7 +34,7 @@ struct Kokkos::Impl::DeepCopy 0) { - acc_memcpy_device(dst, const_cast(src), n); + acc_memcpy_device_async(dst, const_cast(src), n, acc_async_noval); } } DeepCopy(const Kokkos::Experimental::OpenACC& exec, void* dst, @@ -52,7 +52,7 @@ struct Kokkos::Impl::DeepCopy { DeepCopy(void* dst, const void* src, size_t n) { if (n > 0) { - acc_memcpy_device(dst, const_cast(src), n); + acc_memcpy_device_async(dst, const_cast(src), n, acc_async_noval); } } DeepCopy(const ExecutionSpace& exec, void* dst, const void* src, size_t n) { @@ -60,7 +60,7 @@ struct Kokkos::Impl::DeepCopy::DeepCopy: fence before copy"); if (n > 0) { - acc_memcpy_device(dst, const_cast(src), n); + acc_memcpy_device_async(dst, const_cast(src), n, acc_async_noval); } } }; @@ -70,7 +70,9 @@ struct Kokkos::Impl::DeepCopy { DeepCopy(void* dst, const void* src, size_t n) { - if (n > 0) acc_memcpy_to_device(dst, const_cast(src), n); + if (n > 0) + acc_memcpy_to_device_async(dst, const_cast(src), n, + acc_async_noval); } DeepCopy(const Kokkos::Experimental::OpenACC& exec, void* dst, const void* src, size_t n) { @@ -85,7 +87,8 @@ struct Kokkos::Impl::DeepCopy { DeepCopy(void* dst, const void* src, size_t n) { if (n > 0) { - acc_memcpy_to_device(dst, const_cast(src), n); + acc_memcpy_to_device_async(dst, const_cast(src), n, + acc_async_noval); } } DeepCopy(const ExecutionSpace& exec, void* dst, const void* src, size_t n) { @@ -93,7 +96,8 @@ struct Kokkos::Impl::DeepCopy::DeepCopy: fence before copy"); if (n > 0) { - acc_memcpy_to_device(dst, const_cast(src), n); + acc_memcpy_to_device_async(dst, const_cast(src), n, + acc_async_noval); } } }; @@ -104,7 +108,8 @@ struct Kokkos::Impl::DeepCopy { DeepCopy(void* dst, const void* src, size_t n) { if (n > 0) { - acc_memcpy_from_device(dst, const_cast(src), n); + acc_memcpy_from_device_async(dst, const_cast(src), n, + acc_async_noval); } } DeepCopy(const Kokkos::Experimental::OpenACC& exec, void* dst, @@ -120,14 +125,17 @@ template struct Kokkos::Impl::DeepCopy< Kokkos::HostSpace, Kokkos::Experimental::OpenACCSpace, ExecutionSpace> { DeepCopy(void* dst, const void* src, size_t n) { - if (n > 0) acc_memcpy_from_device(dst, const_cast(src), n); + if (n > 0) + acc_memcpy_from_device_async(dst, const_cast(src), n, + acc_async_noval); } DeepCopy(const ExecutionSpace& exec, void* dst, const void* src, size_t n) { exec.fence( "Kokkos::Impl::DeepCopy::DeepCopy: fence before copy"); if (n > 0) { - acc_memcpy_from_device(dst, const_cast(src), n); + acc_memcpy_from_device_async(dst, const_cast(src), n, + acc_async_noval); } } }; diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Instance.hpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Instance.hpp index 6645616ba5..c3d7236872 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Instance.hpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Instance.hpp @@ -35,7 +35,7 @@ class OpenACCInternal { public: static int m_acc_device_num; - int m_async_arg = acc_async_sync; + int m_async_arg = acc_async_noval; OpenACCInternal() = default; @@ -43,7 +43,7 @@ class OpenACCInternal { bool verify_is_initialized(const char* const label) const; - void initialize(int async_arg = acc_async_sync); + void initialize(int async_arg = acc_async_noval); void finalize(); bool is_initialized() const; diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_ParallelReduce_MDRange.hpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_ParallelReduce_MDRange.hpp index 2c7793dc11..5afb5e75d3 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_ParallelReduce_MDRange.hpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_ParallelReduce_MDRange.hpp @@ -31,7 +31,7 @@ template ::value, + static_assert(Kokkos::Impl::always_false::value, "not implemented"); } }; @@ -136,6 +136,7 @@ class Kokkos::Impl::ParallelReduce> struct OpenACCParallelReduceHelper { OpenACCParallelReduceHelper(Functor const&, Reducer const&, Policy const&) { - static_assert(!Kokkos::Impl::always_true::value, + static_assert(Kokkos::Impl::always_false::value, "not implemented"); } }; @@ -140,6 +140,7 @@ class Kokkos::Impl::ParallelReduce::value, + static_assert(Kokkos::Impl::always_false::value, "not implemented"); } }; @@ -129,7 +129,7 @@ KOKKOS_INLINE_FUNCTION void parallel_reduce( const Impl::TeamThreadRangeBoundariesStruct& loop_boundaries, const Lambda& lambda, const JoinType& join, ValueType& init_result) { - static_assert(!Kokkos::Impl::always_true::value, + static_assert(Kokkos::Impl::always_false::value, "custom reduction is not implemented"); } @@ -140,7 +140,7 @@ KOKKOS_INLINE_FUNCTION void parallel_reduce( const Impl::ThreadVectorRangeBoundariesStruct< iType, Impl::OpenACCTeamMember>& loop_boundaries, const Lambda& lambda, const JoinType& join, ValueType& init_result) { - static_assert(!Kokkos::Impl::always_true::value, + static_assert(Kokkos::Impl::always_false::value, "custom reduction is not implemented"); } @@ -394,6 +394,7 @@ KOKKOS_INLINE_FUNCTION void parallel_reduce( vector_length); \ functor(team, val); \ } \ + acc_wait(async_arg); \ aval = val; \ } \ } // namespace Kokkos::Experimental::Impl diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp index 91faa64f73..76e1514476 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp @@ -16,92 +16,11 @@ #define KOKKOS_IMPL_PUBLIC_INCLUDE -#include +#include #include -#include -#include - -#ifdef KOKKOS_ENABLE_DEBUG -Kokkos::Impl::SharedAllocationRecord SharedAllocationRecord< - Kokkos::Experimental::OpenACCSpace, void>::s_root_record; -#endif - -Kokkos::Impl::SharedAllocationRecord::~SharedAllocationRecord() { - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - (SharedAllocationRecord::m_alloc_size - - sizeof(SharedAllocationHeader))); -} - -Kokkos::Impl::SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::OpenACCSpace &arg_space, - const std::string &arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - Kokkos::Impl::DeepCopy( - RecordBase::m_alloc_ptr, &header, sizeof(SharedAllocationHeader)); - Kokkos::fence( - "SharedAllocationRecord::SharedAllocationRecord(): fence after copying header from " - "HostSpace"); -} - -Kokkos::Impl::SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::OpenACC &arg_exec_space, - const Kokkos::Experimental::OpenACCSpace &arg_space, - const std::string &arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_exec_space, arg_space, - arg_label, arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - Kokkos::Impl::DeepCopy( - arg_exec_space, RecordBase::m_alloc_ptr, &header, - sizeof(SharedAllocationHeader)); -} - -//============================================================================== -// {{{1 +#include #include -// To avoid additional compilation cost for something that's (mostly?) not -// performance sensitive, we explicitly instantiate these CRTP base classes -// here, where we have access to the associated *_timpl.hpp header files. -template class Kokkos::Impl::HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenACCSpace>; -template class Kokkos::Impl::SharedAllocationRecordCommon< - Kokkos::Experimental::OpenACCSpace>; - -// end Explicit instantiations of CRTP Base classes }}}1 -//============================================================================== +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::Experimental::OpenACCSpace); diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.hpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.hpp index cf83a5b27b..cde5ecdcb7 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.hpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.hpp @@ -20,55 +20,7 @@ #include #include -#include - -template <> -class Kokkos::Impl::SharedAllocationRecord - : public HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenACCSpace> { - private: - friend class HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenACCSpace>; - friend class SharedAllocationRecordCommon; - friend Kokkos::Experimental::OpenACCSpace; - - using base_t = HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenACCSpace>; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - - /**\brief Root record for tracked allocations from this OpenACCSpace - * instance */ - static RecordBase s_root_record; - - const Kokkos::Experimental::OpenACCSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, - const Kokkos::Experimental::OpenACCSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const Kokkos::Experimental::OpenACC& exec_space, - const Kokkos::Experimental::OpenACCSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); - - SharedAllocationRecord( - const Kokkos::Experimental::OpenACCSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); -}; +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_SPECIALIZATION( + Kokkos::Experimental::OpenACCSpace); #endif diff --git a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Team.hpp b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Team.hpp index 4ec71f56ef..20ea392452 100644 --- a/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Team.hpp +++ b/lib/kokkos/core/src/OpenACC/Kokkos_OpenACC_Team.hpp @@ -82,7 +82,7 @@ class OpenACCTeamMember { // FIXME_OPENACC: team_broadcast() is not implemented. template KOKKOS_FUNCTION void team_broadcast(ValueType& value, int thread_id) const { - static_assert(!Kokkos::Impl::always_true::value, + static_assert(Kokkos::Impl::always_false::value, "Kokkos Error: team_broadcast() is not implemented for the " "OpenACC backend"); return ValueType(); @@ -99,7 +99,7 @@ class OpenACCTeamMember { template KOKKOS_FUNCTION ValueType team_reduce(const ValueType& value, const JoinOp& op_in) const { - static_assert(!Kokkos::Impl::always_true::value, + static_assert(Kokkos::Impl::always_false::value, "Kokkos Error: team_reduce() is not implemented for the " "OpenACC backend"); return ValueType(); @@ -110,7 +110,7 @@ class OpenACCTeamMember { KOKKOS_FUNCTION ArgType team_scan(const ArgType& /*value*/, ArgType* const /*global_accum*/) const { static_assert( - !Kokkos::Impl::always_true::value, + Kokkos::Impl::always_false::value, "Kokkos Error: team_scan() is not implemented for the OpenACC backend"); return ArgType(); } diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.cpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.cpp index 9a169a435c..81f2c5c305 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.cpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.cpp @@ -81,29 +81,16 @@ bool OpenMP::impl_is_initialized() noexcept { return Impl::OpenMPInternal::singleton().is_initialized(); } -bool OpenMP::in_parallel(OpenMP const &exec_space) noexcept { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - return ( - (exec_space.impl_internal_space_instance()->m_level < omp_get_level()) && - (!Impl::t_openmp_instance || - Impl::t_openmp_instance->m_level < omp_get_level())); -#else +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 +KOKKOS_DEPRECATED bool OpenMP::in_parallel(OpenMP const &exec_space) noexcept { return exec_space.impl_internal_space_instance()->m_level < omp_get_level(); -#endif } +#endif int OpenMP::impl_thread_pool_size() const noexcept { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - return OpenMP::in_parallel(*this) - ? omp_get_num_threads() - : (Impl::t_openmp_instance - ? Impl::t_openmp_instance->m_pool_size - : impl_internal_space_instance()->m_pool_size); -#else - return OpenMP::in_parallel(*this) + return (impl_internal_space_instance()->get_level() < omp_get_level()) ? omp_get_num_threads() : impl_internal_space_instance()->m_pool_size; -#endif } int OpenMP::impl_max_hardware_threads() noexcept { diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.hpp index 594f40d524..11292af84a 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.hpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP.hpp @@ -27,14 +27,7 @@ static_assert(false, #include -#include -#include #include - -#ifdef KOKKOS_ENABLE_HBWSPACE -#include -#endif - #include #include #include @@ -45,6 +38,8 @@ static_assert(false, #include +#include +#include #include /*--------------------------------------------------------------------------*/ @@ -53,11 +48,6 @@ namespace Kokkos { namespace Impl { class OpenMPInternal; - -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -// FIXME_OPENMP we can remove this after we remove partition_master -inline thread_local OpenMPInternal* t_openmp_instance = nullptr; -#endif } // namespace Impl /// \class OpenMP @@ -67,12 +57,7 @@ class OpenMP { //! Tag this class as a kokkos execution space using execution_space = OpenMP; - using memory_space = -#ifdef KOKKOS_ENABLE_HBWSPACE - Experimental::HBWSpace; -#else - HostSpace; -#endif + using memory_space = HostSpace; //! This execution space preferred device_type using device_type = Kokkos::Device; @@ -87,8 +72,10 @@ class OpenMP { /// \brief Print configuration information to the given output stream. void print_configuration(std::ostream& os, bool verbose = false) const; +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 /// \brief is the instance running a parallel algorithm - static bool in_parallel(OpenMP const& = OpenMP()) noexcept; + KOKKOS_DEPRECATED static bool in_parallel(OpenMP const& = OpenMP()) noexcept; +#endif /// \brief Wait until all dispatched functors complete on the given instance /// @@ -104,18 +91,6 @@ class OpenMP { /// This always returns false on OpenMP inline static bool is_asynchronous(OpenMP const& = OpenMP()) noexcept; -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - /// \brief Partition the default instance and call 'f' on each new 'master' - /// thread - /// - /// Func is a functor with the following signiture - /// void( int partition_id, int num_partitions ) - template - KOKKOS_DEPRECATED static void partition_master( - F const& f, int requested_num_partitions = 0, - int requested_partition_size = 0); -#endif - #ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 static int concurrency(OpenMP const& = OpenMP()); #else @@ -166,14 +141,7 @@ class OpenMP { }; inline int OpenMP::impl_thread_pool_rank() noexcept { - // FIXME_OPENMP Can we remove this when removing partition_master? It's only - // used in one partition_master test -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - KOKKOS_IF_ON_HOST( - (return Impl::t_openmp_instance ? 0 : omp_get_thread_num();)) -#else KOKKOS_IF_ON_HOST((return omp_get_thread_num();)) -#endif KOKKOS_IF_ON_DEVICE((return -1;)) } diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.cpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.cpp index 44f0fbc180..32172fbc6c 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.cpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.cpp @@ -47,61 +47,6 @@ void OpenMPInternal::release_lock() { desul::MemoryScopeDevice()); } -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -void OpenMPInternal::validate_partition_impl(const int nthreads, - int &num_partitions, - int &partition_size) { - if (nthreads == 1) { - num_partitions = 1; - partition_size = 1; - } else if (num_partitions < 1 && partition_size < 1) { - int idle = nthreads; - for (int np = 2; np <= nthreads; ++np) { - for (int ps = 1; ps <= nthreads / np; ++ps) { - if (nthreads - np * ps < idle) { - idle = nthreads - np * ps; - num_partitions = np; - partition_size = ps; - } - if (idle == 0) { - break; - } - } - } - } else if (num_partitions < 1 && partition_size > 0) { - if (partition_size <= nthreads) { - num_partitions = nthreads / partition_size; - } else { - num_partitions = 1; - partition_size = nthreads; - } - } else if (num_partitions > 0 && partition_size < 1) { - if (num_partitions <= nthreads) { - partition_size = nthreads / num_partitions; - } else { - num_partitions = nthreads; - partition_size = 1; - } - } else if (num_partitions * partition_size > nthreads) { - int idle = nthreads; - const int NP = num_partitions; - const int PS = partition_size; - for (int np = NP; np > 0; --np) { - for (int ps = PS; ps > 0; --ps) { - if ((np * ps <= nthreads) && (nthreads - np * ps < idle)) { - idle = nthreads - np * ps; - num_partitions = np; - partition_size = ps; - } - if (idle == 0) { - break; - } - } - } - } -} -#endif - void OpenMPInternal::clear_thread_data() { const size_t member_bytes = sizeof(int64_t) * @@ -359,8 +304,6 @@ void OpenMPInternal::finalize() { } m_initialized = false; - - Kokkos::Profiling::finalize(); } void OpenMPInternal::print_configuration(std::ostream &s) const { diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.hpp index 4586406e16..35b9aa93ba 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.hpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.hpp @@ -41,16 +41,6 @@ #include /*--------------------------------------------------------------------------*/ -namespace Kokkos { -namespace Impl { - -inline bool execute_in_serial(OpenMP const& space = OpenMP()) { - return (OpenMP::in_parallel(space) && - !(omp_get_nested() && (omp_get_level() == 1))); -} - -} // namespace Impl -} // namespace Kokkos namespace Kokkos { namespace Impl { @@ -99,11 +89,6 @@ class OpenMPInternal { // Release lock used to protect access to m_pool void release_lock(); -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - static void validate_partition_impl(const int nthreads, int& num_partitions, - int& partition_size); -#endif - void resize_thread_data(size_t pool_reduce_bytes, size_t team_reduce_bytes, size_t team_shared_bytes, size_t thread_local_bytes); @@ -115,6 +100,8 @@ class OpenMPInternal { return m_pool[i]; } + int get_level() const { return m_level; } + bool is_initialized() const { return m_initialized; } bool verify_is_initialized(const char* const label) const; @@ -122,32 +109,20 @@ class OpenMPInternal { void print_configuration(std::ostream& s) const; }; -} // namespace Impl - -namespace Experimental { - -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -template <> -class MasterLock { - public: - void lock() { omp_set_lock(&m_lock); } - void unlock() { omp_unset_lock(&m_lock); } - bool try_lock() { return static_cast(omp_test_lock(&m_lock)); } - - KOKKOS_DEPRECATED MasterLock() { omp_init_lock(&m_lock); } - ~MasterLock() { omp_destroy_lock(&m_lock); } - - MasterLock(MasterLock const&) = delete; - MasterLock(MasterLock&&) = delete; - MasterLock& operator=(MasterLock const&) = delete; - MasterLock& operator=(MasterLock&&) = delete; - - private: - omp_lock_t m_lock; -}; +inline bool execute_in_serial(OpenMP const& space = OpenMP()) { +// The default value returned by `omp_get_max_active_levels` with gcc version +// lower than 11.1.0 is 2147483647 instead of 1. +#if (!defined(KOKKOS_COMPILER_GNU) || KOKKOS_COMPILER_GNU >= 1110) && \ + _OPENMP >= 201511 + bool is_nested = omp_get_max_active_levels() > 1; +#else + bool is_nested = static_cast(omp_get_nested()); #endif + return (space.impl_internal_space_instance()->get_level() < omp_get_level() && + !(is_nested && (omp_get_level() == 1))); +} -} // namespace Experimental +} // namespace Impl namespace Experimental { namespace Impl { @@ -202,48 +177,6 @@ std::vector partition_space(OpenMP const& main_instance, return Impl::create_OpenMP_instances(main_instance, weights); } } // namespace Experimental - -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -template -KOKKOS_DEPRECATED void OpenMP::partition_master(F const& f, int num_partitions, - int partition_size) { -#if _OPENMP >= 201511 - if (omp_get_max_active_levels() > 1) { -#else - if (omp_get_nested()) { -#endif - using Exec = Impl::OpenMPInternal; - - Exec* prev_instance = &Impl::OpenMPInternal::singleton(); - - Exec::validate_partition_impl(prev_instance->m_pool_size, num_partitions, - partition_size); - -#pragma omp parallel num_threads(num_partitions) - { - Exec thread_local_instance(partition_size); - Impl::t_openmp_instance = &thread_local_instance; - - size_t pool_reduce_bytes = 32 * partition_size; - size_t team_reduce_bytes = 32 * partition_size; - size_t team_shared_bytes = 1024 * partition_size; - size_t thread_local_bytes = 1024; - - thread_local_instance.resize_thread_data( - pool_reduce_bytes, team_reduce_bytes, team_shared_bytes, - thread_local_bytes); - - omp_set_num_threads(partition_size); - f(omp_get_thread_num(), omp_get_num_threads()); - Impl::t_openmp_instance = nullptr; - } - } else { - // nested openmp not enabled - f(0, 1); - } -} -#endif - } // namespace Kokkos #endif diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_For.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_For.hpp index 96dc664eb7..823a7e668e 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_For.hpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_For.hpp @@ -147,15 +147,7 @@ class ParallelFor, Kokkos::OpenMP> { inline ParallelFor(const FunctorType& arg_functor, Policy arg_policy) : m_instance(nullptr), m_functor(arg_functor), m_policy(arg_policy) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - if (t_openmp_instance) { - m_instance = t_openmp_instance; - } else { - m_instance = arg_policy.space().impl_internal_space_instance(); - } -#else m_instance = arg_policy.space().impl_internal_space_instance(); -#endif } }; @@ -251,16 +243,9 @@ class ParallelFor, inline ParallelFor(const FunctorType& arg_functor, MDRangePolicy arg_policy) : m_instance(nullptr), m_iter(arg_policy, arg_functor) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - if (t_openmp_instance) { - m_instance = t_openmp_instance; - } else { - m_instance = arg_policy.space().impl_internal_space_instance(); - } -#else m_instance = arg_policy.space().impl_internal_space_instance(); -#endif } + template static int max_tile_size_product(const Policy&, const Functor&) { /** @@ -409,15 +394,7 @@ class ParallelFor, m_shmem_size(arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize::value( arg_functor, arg_policy.team_size())) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - if (t_openmp_instance) { - m_instance = t_openmp_instance; - } else { - m_instance = arg_policy.space().impl_internal_space_instance(); - } -#else m_instance = arg_policy.space().impl_internal_space_instance(); -#endif } }; diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_Reduce.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_Reduce.hpp index 52cdef18e6..05fd1c9dce 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_Reduce.hpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel_Reduce.hpp @@ -170,15 +170,7 @@ class ParallelReduce, m_functor_reducer(arg_functor_reducer), m_policy(arg_policy), m_result_ptr(arg_view.data()) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - if (t_openmp_instance) { - m_instance = t_openmp_instance; - } else { - m_instance = arg_policy.space().impl_internal_space_instance(); - } -#else m_instance = arg_policy.space().impl_internal_space_instance(); -#endif static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, @@ -319,15 +311,7 @@ class ParallelReduce::accessible, @@ -543,15 +527,7 @@ class ParallelReduce::value( arg_functor_reducer.get_functor(), arg_policy.team_size())) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - if (t_openmp_instance) { - m_instance = t_openmp_instance; - } else { - m_instance = arg_policy.space().impl_internal_space_instance(); - } -#else m_instance = arg_policy.space().impl_internal_space_instance(); -#endif static_assert( Kokkos::Impl::MemorySpaceAccess, inline ParallelScan(const FunctorType& arg_functor, const Policy& arg_policy) : m_instance(nullptr), m_functor(arg_functor), m_policy(arg_policy) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - if (t_openmp_instance) { - m_instance = t_openmp_instance; - } else { - m_instance = arg_policy.space().impl_internal_space_instance(); - } -#else m_instance = arg_policy.space().impl_internal_space_instance(); -#endif } }; @@ -292,15 +284,7 @@ class ParallelScanWithTotal, Kokkos::Impl::MemorySpaceAccess::accessible, "Kokkos::OpenMP parallel_scan result must be host-accessible!"); -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - if (t_openmp_instance) { - m_instance = t_openmp_instance; - } else { - m_instance = arg_policy.space().impl_internal_space_instance(); - } -#else m_instance = arg_policy.space().impl_internal_space_instance(); -#endif } //---------------------------------------- diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget.hpp index adf972dd08..ea4e7f6bab 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget.hpp @@ -65,7 +65,11 @@ class OpenMPTarget { using scratch_memory_space = ScratchMemorySpace; - inline static bool in_parallel() { return omp_in_parallel(); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED inline static bool in_parallel() { + return omp_in_parallel(); + } +#endif static void fence(const std::string& name = "Kokkos::OpenMPTarget::fence: Unnamed Instance Fence"); diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp index 81fbc56de0..a414b34d7c 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp @@ -37,7 +37,6 @@ #include #include #include -#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -110,79 +109,13 @@ void OpenMPTargetSpace::deallocate(const char* arg_label, } // namespace Experimental } // namespace Kokkos -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - -#ifdef KOKKOS_ENABLE_DEBUG -SharedAllocationRecord SharedAllocationRecord< - Kokkos::Experimental::OpenMPTargetSpace, void>::s_root_record; -#endif - -SharedAllocationRecord::~SharedAllocationRecord() { - auto alloc_size = SharedAllocationRecord::m_alloc_size; - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - alloc_size, (alloc_size - sizeof(SharedAllocationHeader))); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::OpenMPTargetSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Kokkos::Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, arg_label); - - // TODO DeepCopy - // DeepCopy - Kokkos::Impl::DeepCopy( - RecordBase::m_alloc_ptr, &header, sizeof(SharedAllocationHeader)); - Kokkos::fence( - "SharedAllocationRecord::SharedAllocationRecord(): fence after copying header from " - "HostSpace"); -} - -//---------------------------------------------------------------------------- - -} // namespace Impl -} // namespace Kokkos - //============================================================================== // {{{1 #include -namespace Kokkos { -namespace Impl { - -// To avoid additional compilation cost for something that's (mostly?) not -// performance sensitive, we explicity instantiate these CRTP base classes here, -// where we have access to the associated *_timpl.hpp header files. -template class HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenMPTargetSpace>; -template class SharedAllocationRecordCommon< - Kokkos::Experimental::OpenMPTargetSpace>; - -} // end namespace Impl -} // end namespace Kokkos +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::Experimental::OpenMPTargetSpace); // end Explicit instantiations of CRTP Base classes }}}1 //============================================================================== diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.hpp index e5b33d0982..ed625cfcc8 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.hpp @@ -98,6 +98,16 @@ class OpenMPTargetSpace { ~OpenMPTargetSpace() = default; /**\brief Allocate untracked memory in the space */ + // FIXME_OPENMPTARGET Use execution space instance + void* allocate(const OpenMPTarget&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + // FIXME_OPENMPTARGET Use execution space instance + void* allocate(const OpenMPTarget&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const size_t arg_alloc_size) const; void* allocate(const char* arg_label, const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; @@ -121,9 +131,6 @@ class OpenMPTargetSpace { const size_t arg_logical_size = 0, const Kokkos::Tools::SpaceHandle = Kokkos::Tools::make_space_handle(name())) const; - - friend class Kokkos::Impl::SharedAllocationRecord< - Kokkos::Experimental::OpenMPTargetSpace, void>; }; } // namespace Experimental } // namespace Kokkos @@ -131,64 +138,8 @@ class OpenMPTargetSpace { //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- -namespace Kokkos { -namespace Impl { - -template <> -class SharedAllocationRecord - : public HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenMPTargetSpace> { - private: - friend class HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenMPTargetSpace>; - friend class SharedAllocationRecordCommon< - Kokkos::Experimental::OpenMPTargetSpace>; - friend Kokkos::Experimental::OpenMPTargetSpace; - - using base_t = HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::OpenMPTargetSpace>; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - - /**\brief Root record for tracked allocations from this OpenMPTargetSpace - * instance */ - static RecordBase s_root_record; - - const Kokkos::Experimental::OpenMPTargetSpace m_space; - - protected: - ~SharedAllocationRecord(); - SharedAllocationRecord() = default; - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, - const Kokkos::Experimental::OpenMPTargetSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const Kokkos::Experimental::OpenMPTargetSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); - - public: - KOKKOS_INLINE_FUNCTION static SharedAllocationRecord* allocate( - const Kokkos::Experimental::OpenMPTargetSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc) { - KOKKOS_IF_ON_HOST( - (return new SharedAllocationRecord(arg_space, arg_label, arg_alloc);)) - KOKKOS_IF_ON_DEVICE( - ((void)arg_space; (void)arg_label; (void)arg_alloc; return nullptr;)) - } -}; - -} // namespace Impl -} // namespace Kokkos +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_SPECIALIZATION( + Kokkos::Experimental::OpenMPTargetSpace); //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp index 1902c38409..b39f5aca35 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp @@ -75,6 +75,7 @@ int* OpenMPTargetExec::m_lock_array = nullptr; uint64_t OpenMPTargetExec::m_lock_size = 0; uint32_t* OpenMPTargetExec::m_uniquetoken_ptr = nullptr; int OpenMPTargetExec::MAX_ACTIVE_THREADS = 0; +std::mutex OpenMPTargetExec::m_mutex_scratch_ptr; void OpenMPTargetExec::clear_scratch() { Kokkos::Experimental::OpenMPTargetSpace space; @@ -98,6 +99,11 @@ void OpenMPTargetExec::resize_scratch(int64_t team_size, int64_t shmem_size_L0, int64_t shmem_size_L1, int64_t league_size) { Kokkos::Experimental::OpenMPTargetSpace space; + // Level-0 scratch when using clang/17 and higher comes from their OpenMP + // extension, `ompx_dyn_cgroup_mem`. +#if defined(KOKKOS_IMPL_OPENMPTARGET_LLVM_EXTENSIONS) + shmem_size_L0 = 0; +#endif const int64_t shmem_size = shmem_size_L0 + shmem_size_L1; // L0 + L1 scratch memory per team. const int64_t padding = shmem_size * 10 / 100; // Padding per team. diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Instance.cpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Instance.cpp index 9e8844a6f2..3387108da3 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Instance.cpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Instance.cpp @@ -178,8 +178,10 @@ void OpenMPTarget::impl_static_fence(const std::string& name) { } void OpenMPTarget::impl_initialize(InitializationSettings const& settings) { + using Kokkos::Impl::get_visible_devices; + std::vector const& visible_devices = get_visible_devices(); using Kokkos::Impl::get_gpu; - const int device_num = get_gpu(settings); + const int device_num = get_gpu(settings).value_or(visible_devices[0]); omp_set_default_device(device_num); Impl::OpenMPTargetInternal::impl_singleton()->impl_initialize(); diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Macros.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Macros.hpp new file mode 100644 index 0000000000..2bd672f4d0 --- /dev/null +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Macros.hpp @@ -0,0 +1,46 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_OPENMPTARGET_MACROS_HPP +#define KOKKOS_OPENMPTARGET_MACROS_HPP + +// Intel architectures prefer the classical hierarchical parallelism that relies +// on OpenMP. +#if defined(KOKKOS_ARCH_INTEL_GPU) +#define KOKKOS_IMPL_OPENMPTARGET_HIERARCHICAL_INTEL_GPU +#endif + +// Define a macro for llvm compiler greater than version 17 and on NVIDIA and +// AMD GPUs. This would be useful in cases where non-OpenMP standard llvm +// extensions can be used. +#if defined(KOKKOS_COMPILER_CLANG) && (KOKKOS_COMPILER_CLANG >= 1700) && \ + (defined(KOKKOS_ARCH_AMD_GPU) || defined(KOKKOS_IMPL_ARCH_NVIDIA_GPU)) +#define KOKKOS_IMPL_OPENMPTARGET_LLVM_EXTENSIONS +#endif + +#define KOKKOS_IMPL_OPENMPTARGET_PRAGMA_HELPER(x) _Pragma(#x) +#define KOKKOS_IMPL_OMPTARGET_PRAGMA(x) \ + KOKKOS_IMPL_OPENMPTARGET_PRAGMA_HELPER(omp target x) + +// Use scratch memory extensions to request dynamic shared memory for the +// right compiler/architecture combination. +#ifdef KOKKOS_IMPL_OPENMPTARGET_LLVM_EXTENSIONS +#define KOKKOS_IMPL_OMPX_DYN_CGROUP_MEM(N) ompx_dyn_cgroup_mem(N) +#else +#define KOKKOS_IMPL_OMPX_DYN_CGROUP_MEM(N) +#endif + +#endif // KOKKOS_OPENMPTARGET_MACROS_HPP diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel.hpp index 9767d8e53e..dcc509d2fa 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel.hpp @@ -21,16 +21,10 @@ #include #include #include -#include #include #include "Kokkos_OpenMPTarget_Abort.hpp" - -// Intel architectures prefer the classical hierarchical parallelism that relies -// on OpenMP. -#if defined(KOKKOS_ARCH_INTEL_GPU) -#define KOKKOS_IMPL_OPENMPTARGET_HIERARCHICAL_INTEL_GPU -#endif +#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -113,14 +107,20 @@ class OpenMPTargetExecTeamMember { team_broadcast(value, thread_id); } - // FIXME_OPENMPTARGET this function has the wrong interface and currently - // ignores the reducer passed. - template - KOKKOS_INLINE_FUNCTION ValueType team_reduce(const ValueType& value, - const JoinOp&) const { + template + KOKKOS_INLINE_FUNCTION std::enable_if_t::value> + team_reduce(ReducerType const& reducer) const noexcept { + team_reduce(reducer, reducer.reference()); + } + + // FIXME_OPENMPTARGET this function currently ignores the reducer passed. + template + KOKKOS_INLINE_FUNCTION std::enable_if_t::value> + team_reduce(ReducerType const&, typename ReducerType::value_type& value) const + noexcept { #pragma omp barrier - using value_type = ValueType; + using value_type = typename ReducerType::value_type; // const JoinLambdaAdapter op(op_in); // Make sure there is enough scratch space: @@ -149,8 +149,9 @@ class OpenMPTargetExecTeamMember { } #pragma omp barrier } - return team_scratch[0]; + value = team_scratch[0]; } + /** \brief Intra-team exclusive prefix sum with team_rank() ordering * with intra-team non-deterministic ordering accumulation. * @@ -249,15 +250,37 @@ class OpenMPTargetExecTeamMember { // and L1 shmem size. TEAM_REDUCE_SIZE = 512 bytes saved per team for // hierarchical reduction. There is an additional 10% of the requested // scratch memory allocated per team as padding. Hence the product with 0.1. + // + // Use llvm extensions for dynamic shared memory with compilers/architecture + // combinations where it is supported. + // + // Size allocated in HBM will now change based on whether we use llvm + // extensions. +#if defined(KOKKOS_IMPL_OPENMPTARGET_LLVM_EXTENSIONS) + const int total_shmem = shmem_size_L1 + shmem_size_L1 * 0.1; +#else + const int total_shmem = + shmem_size_L0 + shmem_size_L1 + (shmem_size_L0 + shmem_size_L1) * 0.1; +#endif + + // Per team offset for buffer in HBM. const int reduce_offset = - m_shmem_block_index * - (shmem_size_L0 + shmem_size_L1 + - ((shmem_size_L0 + shmem_size_L1) * 0.1) + TEAM_REDUCE_SIZE); + m_shmem_block_index * (total_shmem + TEAM_REDUCE_SIZE); + +#if defined(KOKKOS_IMPL_OPENMPTARGET_LLVM_EXTENSIONS) + const int l1_offset = reduce_offset + TEAM_REDUCE_SIZE; + char* l0_scratch = + static_cast(llvm_omp_target_dynamic_shared_alloc()); + m_team_shared = scratch_memory_space( + l0_scratch, shmem_size_L0, static_cast(glb_scratch) + l1_offset, + shmem_size_L1); +#else const int l0_offset = reduce_offset + TEAM_REDUCE_SIZE; const int l1_offset = l0_offset + shmem_size_L0; m_team_shared = scratch_memory_space( (static_cast(glb_scratch) + l0_offset), shmem_size_L0, static_cast(glb_scratch) + l1_offset, shmem_size_L1); +#endif m_reduce_scratch = static_cast(glb_scratch) + reduce_offset; m_league_rank = league_rank; m_team_rank = omp_tid; @@ -751,6 +774,7 @@ class OpenMPTargetExec { int64_t thread_local_bytes, int64_t league_size); static void* m_scratch_ptr; + static std::mutex m_mutex_scratch_ptr; static int64_t m_scratch_size; static int* m_lock_array; static uint64_t m_lock_size; diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelFor_Team.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelFor_Team.hpp index 1abc925cae..26085f1140 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelFor_Team.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelFor_Team.hpp @@ -19,6 +19,7 @@ #include #include +#include #include #include @@ -140,8 +141,10 @@ class ParallelFor, // guarantees that the number of teams specified in the `num_teams` clause is // always less than or equal to the maximum concurrently running teams. #if !defined(KOKKOS_IMPL_OPENMPTARGET_HIERARCHICAL_INTEL_GPU) -#pragma omp target teams thread_limit(team_size) firstprivate(a_functor) \ - num_teams(max_active_teams) is_device_ptr(scratch_ptr) + KOKKOS_IMPL_OMPTARGET_PRAGMA( + teams thread_limit(team_size) firstprivate(a_functor) + num_teams(max_active_teams) is_device_ptr(scratch_ptr) + KOKKOS_IMPL_OMPX_DYN_CGROUP_MEM(shmem_size_L0)) #pragma omp parallel { if (omp_get_num_teams() > max_active_teams) diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Range.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Range.hpp index 4452af3846..caa568a892 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Range.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Range.hpp @@ -55,6 +55,9 @@ class ParallelReduce, const pointer_type m_result_ptr; bool m_result_ptr_on_device; const int m_result_ptr_num_elems; + // Only let one ParallelReduce instance at a time use the scratch memory. + // The constructor acquires the mutex which is released in the destructor. + std::scoped_lock m_scratch_memory_lock; using TagType = typename Policy::work_tag; public: @@ -105,7 +108,8 @@ class ParallelReduce, m_result_ptr_on_device( MemorySpaceAccess::accessible), - m_result_ptr_num_elems(arg_result_view.size()) {} + m_result_ptr_num_elems(arg_result_view.size()), + m_scratch_memory_lock(OpenMPTargetExec::m_mutex_scratch_ptr) {} }; } // namespace Impl diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Team.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Team.hpp index a302fa7151..8abffa47a4 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Team.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelReduce_Team.hpp @@ -470,6 +470,10 @@ class ParallelReduce m_scratch_memory_lock; + public: void execute() const { const FunctorType& functor = m_functor_reducer.get_functor(); @@ -517,7 +521,8 @@ class ParallelReduce::value( - arg_functor_reducer.get_functor(), arg_policy.team_size())) {} + arg_functor_reducer.get_functor(), arg_policy.team_size())), + m_scratch_memory_lock(OpenMPTargetExec::m_mutex_scratch_ptr) {} }; } // namespace Impl diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelScan_Range.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelScan_Range.hpp index 1d6677a1df..c1f7851f41 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelScan_Range.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelScan_Range.hpp @@ -238,8 +238,10 @@ class ParallelScanWithTotal, if (!base_t::m_result_ptr_device_accessible) { const int size = base_t::m_functor_reducer.get_reducer().value_size(); - DeepCopy( - base_t::m_result_ptr, chunk_values.data() + (n_chunks - 1), size); + DeepCopy( + base_t::m_policy.space(), base_t::m_result_ptr, + chunk_values.data() + (n_chunks - 1), size); } } else if (!base_t::m_result_ptr_device_accessible) { base_t::m_functor_reducer.get_reducer().init(base_t::m_result_ptr); diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_Common.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_Common.hpp index fb75f05f27..eb3dc3773c 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_Common.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_Common.hpp @@ -21,6 +21,7 @@ #include #include #include +#include namespace Kokkos { namespace Impl { @@ -394,9 +395,11 @@ struct ParallelReduceSpecialize, initializer(OpenMPTargetReducerWrapper ::init(omp_priv)) #if !defined(KOKKOS_IMPL_OPENMPTARGET_HIERARCHICAL_INTEL_GPU) -#pragma omp target teams num_teams(max_active_teams) thread_limit(team_size) \ - firstprivate(f) is_device_ptr(scratch_ptr) reduction(custom \ - : result) + KOKKOS_IMPL_OMPTARGET_PRAGMA( + teams num_teams(max_active_teams) thread_limit(team_size) + firstprivate(f) is_device_ptr(scratch_ptr) reduction(custom + : result) + KOKKOS_IMPL_OMPX_DYN_CGROUP_MEM(shmem_size_L0)) #pragma omp parallel reduction(custom : result) { if (omp_get_num_teams() > max_active_teams) @@ -482,9 +485,11 @@ struct ParallelReduceSpecialize, // Case where reduction is on a native data type. if constexpr (std::is_arithmetic::value) { -#pragma omp target teams num_teams(max_active_teams) thread_limit(team_size) map(to \ - : f) \ - is_device_ptr(scratch_ptr) reduction(+: result) + // Use scratch memory extensions to request dynamic shared memory for + // the right compiler/architecture combination. + KOKKOS_IMPL_OMPTARGET_PRAGMA(teams num_teams(max_active_teams) thread_limit(team_size) map(to: f) \ + is_device_ptr(scratch_ptr) reduction(+: result) \ + KOKKOS_IMPL_OMPX_DYN_CGROUP_MEM(shmem_size_L0)) #pragma omp parallel reduction(+ : result) { if (omp_get_num_teams() > max_active_teams) @@ -636,11 +641,13 @@ struct ParallelReduceSpecialize, return; } - -#pragma omp target teams num_teams(nteams) thread_limit(team_size) map(to \ - : f) \ - is_device_ptr(scratch_ptr) - { + // Use scratch memory extensions to request dynamic shared memory for the + // right compiler/architecture combination. + KOKKOS_IMPL_OMPTARGET_PRAGMA( + teams num_teams(nteams) thread_limit(team_size) map(to + : f) + is_device_ptr(scratch_ptr) + KOKKOS_IMPL_OMPX_DYN_CGROUP_MEM(shmem_size_L0)) { #pragma omp parallel { const int team_num = omp_get_team_num(); @@ -665,9 +672,8 @@ struct ParallelReduceSpecialize, int tree_neighbor_offset = 1; do { -#pragma omp target teams distribute parallel for simd map(to \ - : final_reducer) \ - is_device_ptr(scratch_ptr) +#pragma omp target teams distribute parallel for simd firstprivate( \ + final_reducer) is_device_ptr(scratch_ptr) for (int i = 0; i < nteams - tree_neighbor_offset; i += 2 * tree_neighbor_offset) { ValueType* team_scratch = static_cast(scratch_ptr); diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_MDRange.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_MDRange.hpp index 41e62ce6e6..6878531730 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_MDRange.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Parallel_MDRange.hpp @@ -438,6 +438,10 @@ class ParallelReduce m_scratch_memory_lock; + public: inline void execute() const { execute_tile( @@ -452,7 +456,8 @@ class ParallelReduce::accessible) {} + typename ViewType::memory_space>::accessible), + m_scratch_memory_lock(OpenMPTargetExec::m_mutex_scratch_ptr) {} template inline std::enable_if_t execute_tile(const FunctorType& functor, diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Reducer.hpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Reducer.hpp index 672271ed6b..9b578aca11 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Reducer.hpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Reducer.hpp @@ -18,7 +18,6 @@ #define KOKKOS_OPENMPTARGETREDUCER_HPP #include -#include #include #include "Kokkos_OpenMPTarget_Abort.hpp" diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL.cpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL.cpp index 7fa935f693..9a246f7642 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL.cpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL.cpp @@ -88,26 +88,57 @@ bool SYCL::impl_is_initialized() { void SYCL::impl_finalize() { Impl::SYCLInternal::singleton().finalize(); } void SYCL::print_configuration(std::ostream& os, bool verbose) const { - os << "Devices:\n"; - os << " KOKKOS_ENABLE_SYCL: yes\n"; - os << "\nRuntime Configuration:\n"; - os << "macro KOKKOS_ENABLE_SYCL : defined\n"; +#ifdef KOKKOS_ENABLE_ONEDPL + os << "macro KOKKOS_ENABLE_ONEDPL : defined\n"; +#else + os << "macro KOKKOS_ENABLE_ONEDPL : undefined\n"; +#endif #ifdef KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED os << "macro KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED : defined\n"; #else os << "macro KOKKOS_IMPL_SYCL_DEVICE_GLOBAL_SUPPORTED : undefined\n"; #endif - +#ifdef SYCL_EXT_ONEAPI_DEVICE_GLOBAL + os << "macro SYCL_EXT_ONEAPI_DEVICE_GLOBAL : defined\n"; +#else + os << "macro SYCL_EXT_ONEAPI_DEVICE_GLOBAL : undefined\n"; +#endif #ifdef KOKKOS_IMPL_SYCL_USE_IN_ORDER_QUEUES os << "macro KOKKOS_IMPL_SYCL_USE_IN_ORDER_QUEUES : defined\n"; #else os << "macro KOKKOS_IMPL_SYCL_USE_IN_ORDER_QUEUES : undefined\n"; #endif - if (verbose) + int counter = 0; + int active_device = Kokkos::device_id(); + std::cout << "\nAvailable devices: \n"; + std::vector devices = Impl::get_sycl_devices(); + for (const auto& device : devices) { + std::string device_type; + switch (device.get_info()) { + case sycl::info::device_type::cpu: device_type = "cpu"; break; + case sycl::info::device_type::gpu: device_type = "gpu"; break; + case sycl::info::device_type::accelerator: + device_type = "accelerator"; + break; + case sycl::info::device_type::custom: device_type = "custom"; break; + case sycl::info::device_type::automatic: device_type = "automatic"; break; + case sycl::info::device_type::host: device_type = "host"; break; + case sycl::info::device_type::all: device_type = "all"; break; + } + os << "[" << device.get_backend() << "]:" << device_type << ':' << counter + << "] " << device.get_info(); + if (counter == active_device) os << " : Selected"; + os << '\n'; + ++counter; + } + + if (verbose) { + os << '\n'; SYCL::impl_sycl_info(os, m_space_instance->m_queue->get_device()); + } } void SYCL::fence(const std::string& name) const { @@ -137,20 +168,11 @@ void SYCL::impl_static_fence(const std::string& name) { } void SYCL::impl_initialize(InitializationSettings const& settings) { - std::vector gpu_devices = - sycl::device::get_devices(sycl::info::device_type::gpu); - // If the device id is not specified and there are no GPUs, sidestep Kokkos - // device selection and use whatever is available (if no GPU architecture is - // specified). -#if !defined(KOKKOS_ARCH_INTEL_GPU) && !defined(KOKKOS_IMPL_ARCH_NVIDIA_GPU) - if (!settings.has_device_id() && gpu_devices.empty()) { - Impl::SYCLInternal::singleton().initialize(sycl::device()); - Impl::SYCLInternal::m_syclDev = 0; - return; - } -#endif - const auto id = ::Kokkos::Impl::get_gpu(settings); - Impl::SYCLInternal::singleton().initialize(gpu_devices[id]); + const auto& visible_devices = ::Kokkos::Impl::get_visible_devices(); + const auto id = + ::Kokkos::Impl::get_gpu(settings).value_or(visible_devices[0]); + std::vector sycl_devices = Impl::get_sycl_devices(); + Impl::SYCLInternal::singleton().initialize(sycl_devices[id]); Impl::SYCLInternal::m_syclDev = id; } @@ -243,9 +265,32 @@ std::ostream& SYCL::impl_sycl_info(std::ostream& os, namespace Impl { +std::vector get_sycl_devices() { +#if defined(KOKKOS_ARCH_INTEL_GPU) || defined(KOKKOS_IMPL_ARCH_NVIDIA_GPU) || \ + defined(KOKKOS_ARCH_AMD_GPU) + std::vector devices = + sycl::device::get_devices(sycl::info::device_type::gpu); +#if defined(KOKKOS_ARCH_INTEL_GPU) + sycl::backend backend = sycl::backend::ext_oneapi_level_zero; +#elif defined(KOKKOS_IMPL_ARCH_NVIDIA_GPU) + sycl::backend backend = sycl::backend::ext_oneapi_cuda; +#elif defined(KOKKOS_ARCH_AMD_GPU) + sycl::backend backend = sycl::backend::ext_oneapi_hip; +#endif + devices.erase(std::remove_if(devices.begin(), devices.end(), + [backend](const sycl::device& d) { + return d.get_backend() != backend; + }), + devices.end()); +#else + std::vector devices = sycl::device::get_devices(); +#endif + return devices; +} + int g_sycl_space_factory_initialized = Kokkos::Impl::initialize_space_factory("170_SYCL"); -} +} // namespace Impl } // namespace Experimental } // namespace Kokkos diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL.hpp index be6b4b8930..0f3d1f0994 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL.hpp @@ -78,19 +78,15 @@ class SYCL { //! \name Functions that all Kokkos devices must implement. //@{ - KOKKOS_INLINE_FUNCTION static int in_parallel() { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED KOKKOS_INLINE_FUNCTION static int in_parallel() { #if defined(__SYCL_DEVICE_ONLY__) return true; #else return false; #endif } - - /** \brief Set the device in a "sleep" state. */ - static bool sleep(); - - /** \brief Wake the device from the 'sleep' state. A noop for OpenMP. */ - static bool wake(); +#endif /** \brief Wait until all dispatched functors complete. A noop for OpenMP. */ static void impl_static_fence(const std::string& name); @@ -188,6 +184,10 @@ std::vector partition_space(const SYCL& sycl_space, sycl::queue(context, device, sycl::property::queue::in_order())); return instances; } + +namespace Impl { +std::vector get_sycl_devices(); +} // namespace Impl } // namespace Experimental } // namespace Kokkos diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.cpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.cpp index 080369770d..0e67adb578 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.cpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.cpp @@ -54,7 +54,7 @@ Kokkos::View sycl_global_unique_token_locks( } SYCLInternal::~SYCLInternal() { - if (!was_finalized || m_scratchSpace || m_scratchFlags) { + if (!was_finalized || m_scratchSpace || m_scratchHost || m_scratchFlags) { std::cerr << "Kokkos::Experimental::SYCL ERROR: Failed to call " "Kokkos::Experimental::SYCL::finalize()" << std::endl; @@ -102,6 +102,23 @@ void SYCLInternal::initialize(const sycl::device& d) { void SYCLInternal::initialize(const sycl::queue& q) { KOKKOS_EXPECTS(!is_initialized()); +#define KOKKOS_IMPL_CHECK_SYCL_BACKEND_SUPPORT(BACKEND, REQUIRED) \ + if (BACKEND != REQUIRED) \ + Kokkos::abort( \ + "The SYCL execution space instance was initialized with an " \ + "unsupported backend type! For this GPU architecture, only " #REQUIRED \ + " is supported.") +#if defined(KOKKOS_ARCH_INTEL_GPU) + KOKKOS_IMPL_CHECK_SYCL_BACKEND_SUPPORT(q.get_backend(), + sycl::backend::ext_oneapi_level_zero); +#elif defined(KOKKOS_IMPL_ARCH_NVIDIA_GPU) + KOKKOS_IMPL_CHECK_SYCL_BACKEND_SUPPORT(q.get_backend(), + sycl::backend::ext_oneapi_cuda); +#elif defined(KOKKOS_ARCH_AMD_GPU) + KOKKOS_IMPL_CHECK_SYCL_BACKEND_SUPPORT(q.get_backend(), + sycl::backend::ext_oneapi_hip); +#endif + if (was_finalized) Kokkos::abort("Calling SYCL::initialize after SYCL::finalize is illegal\n"); @@ -196,14 +213,22 @@ void SYCLInternal::finalize() { #endif } - using RecordSYCL = Kokkos::Impl::SharedAllocationRecord; + auto device_mem_space = SYCLDeviceUSMSpace(*m_queue); + auto host_mem_space = SYCLHostUSMSpace(*m_queue); if (nullptr != m_scratchSpace) - RecordSYCL::decrement(RecordSYCL::get_record(m_scratchSpace)); + device_mem_space.deallocate(m_scratchSpace, + m_scratchSpaceCount * sizeScratchGrain); + if (nullptr != m_scratchHost) + host_mem_space.deallocate(m_scratchHost, + m_scratchHostCount * sizeScratchGrain); if (nullptr != m_scratchFlags) - RecordSYCL::decrement(RecordSYCL::get_record(m_scratchFlags)); + device_mem_space.deallocate(m_scratchFlags, + m_scratchFlagsCount * sizeScratchGrain); m_syclDev = -1; m_scratchSpaceCount = 0; m_scratchSpace = nullptr; + m_scratchHostCount = 0; + m_scratchHost = nullptr; m_scratchFlagsCount = 0; m_scratchFlags = nullptr; @@ -228,54 +253,68 @@ void SYCLInternal::finalize() { sycl::device_ptr SYCLInternal::scratch_space(const std::size_t size) { if (verify_is_initialized("scratch_space") && m_scratchSpaceCount < scratch_count(size)) { - m_scratchSpaceCount = scratch_count(size); - - using Record = Kokkos::Impl::SharedAllocationRecord< - Kokkos::Experimental::SYCLDeviceUSMSpace, void>; + auto mem_space = Kokkos::Experimental::SYCLDeviceUSMSpace(*m_queue); if (nullptr != m_scratchSpace) - Record::decrement(Record::get_record(m_scratchSpace)); + mem_space.deallocate(m_scratchSpace, + m_scratchSpaceCount * sizeScratchGrain); + + m_scratchSpaceCount = scratch_count(size); std::size_t alloc_size = Kokkos::Impl::multiply_overflow_abort( m_scratchSpaceCount, sizeScratchGrain); - Record* const r = Record::allocate( - Kokkos::Experimental::SYCLDeviceUSMSpace(*m_queue), - "Kokkos::Experimental::SYCL::InternalScratchSpace", alloc_size); - - Record::increment(r); - - m_scratchSpace = reinterpret_cast(r->data()); + m_scratchSpace = static_cast(mem_space.allocate( + "Kokkos::Experimental::SYCL::InternalScratchSpace", alloc_size)); } return m_scratchSpace; } +sycl::host_ptr SYCLInternal::scratch_host(const std::size_t size) { + if (verify_is_initialized("scratch_unified") && + m_scratchHostCount < scratch_count(size)) { + auto mem_space = Kokkos::Experimental::SYCLHostUSMSpace(*m_queue); + + if (nullptr != m_scratchHost) + mem_space.deallocate(m_scratchHost, + m_scratchHostCount * sizeScratchGrain); + + m_scratchHostCount = scratch_count(size); + + std::size_t alloc_size = Kokkos::Impl::multiply_overflow_abort( + m_scratchHostCount, sizeScratchGrain); + m_scratchHost = static_cast(mem_space.allocate( + "Kokkos::Experimental::SYCL::InternalScratchHost", alloc_size)); + } + + return m_scratchHost; +} + sycl::device_ptr SYCLInternal::scratch_flags(const std::size_t size) { if (verify_is_initialized("scratch_flags") && m_scratchFlagsCount < scratch_count(size)) { - m_scratchFlagsCount = scratch_count(size); - - using Record = Kokkos::Impl::SharedAllocationRecord< - Kokkos::Experimental::SYCLDeviceUSMSpace, void>; + auto mem_space = Kokkos::Experimental::SYCLDeviceUSMSpace(*m_queue); if (nullptr != m_scratchFlags) - Record::decrement(Record::get_record(m_scratchFlags)); + mem_space.deallocate(m_scratchFlags, + m_scratchFlagsCount * sizeScratchGrain); + + m_scratchFlagsCount = scratch_count(size); std::size_t alloc_size = Kokkos::Impl::multiply_overflow_abort( m_scratchFlagsCount, sizeScratchGrain); - Record* const r = Record::allocate( - Kokkos::Experimental::SYCLDeviceUSMSpace(*m_queue), - "Kokkos::Experimental::SYCL::InternalScratchFlags", alloc_size); + m_scratchFlags = static_cast(mem_space.allocate( + "Kokkos::Experimental::SYCL::InternalScratchFlags", alloc_size)); - Record::increment(r); - - m_scratchFlags = reinterpret_cast(r->data()); - } - auto memset_event = m_queue->memset(m_scratchFlags, 0, - m_scratchFlagsCount * sizeScratchGrain); + // We only zero-initialize the allocation when we actually allocate. + // It's the responsibility of the features using scratch_flags, + // namely parallel_reduce and parallel_scan, to reset the used values to 0. + auto memset_event = m_queue->memset(m_scratchFlags, 0, + m_scratchFlagsCount * sizeScratchGrain); #ifndef KOKKOS_IMPL_SYCL_USE_IN_ORDER_QUEUES - m_queue->ext_oneapi_submit_barrier(std::vector{memset_event}); + m_queue->ext_oneapi_submit_barrier(std::vector{memset_event}); #endif + } return m_scratchFlags; } @@ -318,15 +357,12 @@ size_t SYCLInternal::USMObjectMem::reserve(size_t n) { assert(m_q); if (m_capacity < n) { - using Record = Kokkos::Impl::SharedAllocationRecord; - // First free what we have (in case malloc can reuse it) - if (m_data) Record::decrement(Record::get_record(m_data)); + AllocationSpace alloc_space(*m_q); + if (m_data) alloc_space.deallocate(m_data, m_capacity); - Record* const r = Record::allocate( - AllocationSpace(*m_q), "Kokkos::Experimental::SYCL::USMObjectMem", n); - Record::increment(r); + m_data = + alloc_space.allocate("Kokkos::Experimental::SYCL::USMObjectMem", n); - m_data = r->data(); if constexpr (sycl::usm::alloc::device == Kind) m_staging.reset(new char[n]); m_capacity = n; @@ -340,8 +376,8 @@ void SYCLInternal::USMObjectMem::reset() { if (m_data) { // This implies a fence since this class is not copyable // and deallocating implies a fence across all registered queues. - using Record = Kokkos::Impl::SharedAllocationRecord; - Record::decrement(Record::get_record(m_data)); + AllocationSpace alloc_space(*m_q); + alloc_space.deallocate(m_data, m_capacity); m_capacity = 0; m_data = nullptr; diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp index 51a617054d..ab7e8ce71e 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Instance.hpp @@ -45,6 +45,7 @@ class SYCLInternal { sycl::device_ptr scratch_space(const std::size_t size); sycl::device_ptr scratch_flags(const std::size_t size); + sycl::host_ptr scratch_host(const std::size_t size); int acquire_team_scratch_space(); sycl::device_ptr resize_team_scratch_space(int scratch_pool_id, std::int64_t bytes, @@ -60,6 +61,8 @@ class SYCLInternal { std::size_t m_scratchSpaceCount = 0; sycl::device_ptr m_scratchSpace = nullptr; + std::size_t m_scratchHostCount = 0; + sycl::host_ptr m_scratchHost = nullptr; std::size_t m_scratchFlagsCount = 0; sycl::device_ptr m_scratchFlags = nullptr; // mutex to access shared memory @@ -330,8 +333,8 @@ struct sycl::is_device_copyable< Kokkos::Experimental::Impl::SYCLFunctionWrapper> : std::true_type {}; -// FIXME_SYCL Remove when this specialization when specializations for -// sycl::device_copyable also apply to const-qualified types. +#if (defined(__INTEL_LLVM_COMPILER) && __INTEL_LLVM_COMPILER < 20240000) || \ + (defined(__LIBSYCL_MAJOR_VERSION) && __LIBSYCL_MAJOR_VERSION < 7) template struct NonTriviallyCopyableAndDeviceCopyable { NonTriviallyCopyableAndDeviceCopyable( @@ -356,3 +359,4 @@ struct sycl::is_device_copyable< : std::true_type {}; #endif #endif +#endif diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_MDRange.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_MDRange.hpp index f4fada570b..7fbf5420f8 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_MDRange.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_MDRange.hpp @@ -118,6 +118,8 @@ class Kokkos::Impl::ParallelFor, const BarePolicy bare_policy(m_policy); + desul::ensure_sycl_lock_arrays_on_device(q); + auto parallel_for_event = q.submit([&](sycl::handler& cgh) { const auto range = compute_ranges(); const sycl::range<3> global_range = range.get_global_range(); diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Range.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Range.hpp index 9c5767d209..b4de7eb89f 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Range.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Range.hpp @@ -81,6 +81,8 @@ class Kokkos::Impl::ParallelFor, const Kokkos::Experimental::SYCL& space = policy.space(); sycl::queue& q = space.sycl_queue(); + desul::ensure_sycl_lock_arrays_on_device(q); + auto parallel_for_event = q.submit([&](sycl::handler& cgh) { #ifndef KOKKOS_IMPL_SYCL_USE_IN_ORDER_QUEUES cgh.depends_on(memcpy_event); diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Team.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Team.hpp index 4fc5818ce9..ecb4a863da 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Team.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelFor_Team.hpp @@ -46,9 +46,9 @@ class Kokkos::Impl::ParallelFor, int m_shmem_size; sycl::device_ptr m_global_scratch_ptr; size_t m_scratch_size[2]; - // Only let one ParallelFor/Reduce modify the team scratch memory. The - // constructor acquires the mutex which is released in the destructor. - std::scoped_lock m_scratch_lock; + // Only let one ParallelFor instance at a time use the team scratch memory. + // The constructor acquires the mutex which is released in the destructor. + std::scoped_lock m_scratch_buffers_lock; int m_scratch_pool_id = -1; template @@ -59,6 +59,8 @@ class Kokkos::Impl::ParallelFor, const Kokkos::Experimental::SYCL& space = policy.space(); sycl::queue& q = space.sycl_queue(); + desul::ensure_sycl_lock_arrays_on_device(q); + auto parallel_for_event = q.submit([&](sycl::handler& cgh) { // FIXME_SYCL accessors seem to need a size greater than zero at least for // host queues @@ -74,7 +76,8 @@ class Kokkos::Impl::ParallelFor, auto lambda = [=](sycl::nd_item<2> item) { const member_type team_member( - team_scratch_memory_L0.get_pointer(), shmem_begin, scratch_size[0], + KOKKOS_IMPL_SYCL_GET_MULTI_PTR(team_scratch_memory_L0), shmem_begin, + scratch_size[0], global_scratch_ptr + item.get_group(1) * scratch_size[1], scratch_size[1], item, item.get_group_linear_id(), item.get_group_range(1)); @@ -141,9 +144,9 @@ class Kokkos::Impl::ParallelFor, m_league_size(arg_policy.league_size()), m_team_size(arg_policy.team_size()), m_vector_size(arg_policy.impl_vector_length()), - m_scratch_lock(arg_policy.space() - .impl_internal_space_instance() - ->m_team_scratch_mutex) { + m_scratch_buffers_lock(arg_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { // FIXME_SYCL optimize if (m_team_size < 0) m_team_size = diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_MDRange.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_MDRange.hpp index 6964c2dbcf..f55280e22e 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_MDRange.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_MDRange.hpp @@ -78,7 +78,7 @@ class Kokkos::Impl::ParallelReduce::accessible), - m_shared_memory_lock( + m_scratch_buffers_lock( m_space.impl_internal_space_instance()->m_mutexScratchSpace) {} private: @@ -95,9 +95,16 @@ class Kokkos::Impl::ParallelReduce results_ptr; + auto host_result_ptr = + (m_result_ptr && !m_result_ptr_device_accessible) + ? static_cast>( + instance.scratch_host(sizeof(value_type) * value_count)) + : nullptr; sycl::event last_reduction_event; + desul::ensure_sycl_lock_arrays_on_device(q); + // If n_tiles==0 we only call init() and final() working with the global // scratch memory but don't copy back to m_result_ptr yet. if (n_tiles == 0) { @@ -109,8 +116,10 @@ class Kokkos::Impl::ParallelReduce>( instance.scratch_space(sizeof(value_type) * value_count)); - sycl::global_ptr device_accessible_result_ptr = - m_result_ptr_device_accessible ? m_result_ptr : nullptr; + auto device_accessible_result_ptr = + m_result_ptr_device_accessible + ? static_cast>(m_result_ptr) + : static_cast>(host_result_ptr); cgh.single_task([=]() { const CombinedFunctorReducerType& functor_reducer = functor_reducer_wrapper.get_functor(); @@ -148,8 +157,10 @@ class Kokkos::Impl::ParallelReduce>( instance.scratch_space(sizeof(value_type) * value_count * n_wgroups)); - sycl::global_ptr device_accessible_result_ptr = - m_result_ptr_device_accessible ? m_result_ptr : nullptr; + auto device_accessible_result_ptr = + m_result_ptr_device_accessible + ? static_cast>(m_result_ptr) + : static_cast>(host_result_ptr); auto scratch_flags = static_cast>( instance.scratch_flags(sizeof(unsigned int))); @@ -223,6 +234,7 @@ class Kokkos::Impl::ParallelReduce= static_cast(n_wgroups)) reducer.init(&local_mem[local_id * value_count]); else { @@ -268,6 +280,7 @@ class Kokkos::Impl::ParallelReduce= static_cast(n_wgroups)) reducer.init(&local_value); else { @@ -296,11 +309,13 @@ class Kokkos::Impl::ParallelReduce( - m_space, m_result_ptr, results_ptr, - sizeof(*m_result_ptr) * value_count); + // Using DeepCopy instead of fence+memcpy turned out to be up to 2x slower. + if (host_result_ptr) { + m_space.fence( + "Kokkos::Impl::ParallelReduce::execute: result " + "not device-accessible"); + std::memcpy(m_result_ptr, host_result_ptr, + sizeof(value_type) * value_count); } return last_reduction_event; @@ -335,9 +350,9 @@ class Kokkos::Impl::ParallelReduce m_shared_memory_lock; + // Only let one ParallelReduce instance at a time use the host scratch memory. + // The constructor acquires the mutex which is released in the destructor. + std::scoped_lock m_scratch_buffers_lock; }; #endif /* KOKKOS_SYCL_PARALLEL_REDUCE_MDRANGE_HPP */ diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Range.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Range.hpp index 8c900cfa42..5333e3c8a8 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Range.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Range.hpp @@ -51,7 +51,7 @@ class Kokkos::Impl::ParallelReduce::accessible), - m_shared_memory_lock( + m_scratch_buffers_lock( p.space().impl_internal_space_instance()->m_mutexScratchSpace) {} private: @@ -70,11 +70,20 @@ class Kokkos::Impl::ParallelReduce results_ptr = nullptr; - sycl::global_ptr device_accessible_result_ptr = - m_result_ptr_device_accessible ? m_result_ptr : nullptr; + auto host_result_ptr = + (m_result_ptr && !m_result_ptr_device_accessible) + ? static_cast>( + instance.scratch_host(sizeof(value_type) * value_count)) + : nullptr; + auto device_accessible_result_ptr = + m_result_ptr_device_accessible + ? static_cast>(m_result_ptr) + : static_cast>(host_result_ptr); sycl::event last_reduction_event; + desul::ensure_sycl_lock_arrays_on_device(q); + // If size<=1 we only call init(), the functor and possibly final once // working with the global scratch memory but don't copy back to // m_result_ptr yet. @@ -168,6 +177,7 @@ class Kokkos::Impl::ParallelReduce= n_wgroups) reducer.init(&local_mem[local_id * value_count]); else { @@ -210,6 +220,7 @@ class Kokkos::Impl::ParallelReduce= n_wgroups) reducer.init(&local_value); else { @@ -320,11 +331,13 @@ class Kokkos::Impl::ParallelReduce( - space, m_result_ptr, results_ptr, - sizeof(*m_result_ptr) * value_count); + // Using DeepCopy instead of fence+memcpy turned out to be up to 2x slower. + if (host_result_ptr) { + space.fence( + "Kokkos::Impl::ParallelReduce::execute: result " + "not device-accessible"); + std::memcpy(m_result_ptr, host_result_ptr, + sizeof(*m_result_ptr) * value_count); } return last_reduction_event; @@ -354,9 +367,9 @@ class Kokkos::Impl::ParallelReduce m_shared_memory_lock; + // Only let one ParallelReduce instance at a time use the host scratch memory. + // The constructor acquires the mutex which is released in the destructor. + std::scoped_lock m_scratch_buffers_lock; }; #endif /* KOKKOS_SYCL_PARALLEL_REDUCE_RANGE_HPP */ diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Team.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Team.hpp index 07145b0fb9..27165c59e3 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Team.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelReduce_Team.hpp @@ -59,9 +59,10 @@ class Kokkos::Impl::ParallelReduce m_scratch_lock; + // Only let one ParallelReduce instance at a time use the team scratch memory + // and the host scratch memory. The constructor acquires the mutex which is + // released in the destructor. + std::scoped_lock m_scratch_buffers_lock; int m_scratch_pool_id = -1; template @@ -79,9 +80,16 @@ class Kokkos::Impl::ParallelReduce>( + instance.scratch_host(sizeof(value_type) * value_count)) + : nullptr; sycl::event last_reduction_event; + desul::ensure_sycl_lock_arrays_on_device(q); + // If size<=1 we only call init(), the functor and possibly final once // working with the global scratch memory but don't copy back to // m_result_ptr yet. @@ -89,8 +97,10 @@ class Kokkos::Impl::ParallelReduce>(instance.scratch_space( sizeof(value_type) * std::max(value_count, 1u))); - sycl::global_ptr device_accessible_result_ptr = - m_result_ptr_device_accessible ? m_result_ptr : nullptr; + auto device_accessible_result_ptr = + m_result_ptr_device_accessible + ? static_cast>(m_result_ptr) + : static_cast>(host_result_ptr); auto parallel_reduce_event = q.submit([&](sycl::handler& cgh) { // FIXME_SYCL accessors seem to need a size greater than zero at least @@ -121,9 +131,10 @@ class Kokkos::Impl::ParallelReduce) functor(team_member, update); else @@ -160,12 +171,16 @@ class Kokkos::Impl::ParallelReduce const global_scratch_ptr = m_global_scratch_ptr; + sycl::local_accessor num_teams_done(1, cgh); auto team_reduction_factory = [&](sycl::local_accessor local_mem, sycl::device_ptr results_ptr) { - sycl::global_ptr device_accessible_result_ptr = - m_result_ptr_device_accessible ? m_result_ptr : nullptr; + auto device_accessible_result_ptr = + m_result_ptr_device_accessible + ? static_cast>(m_result_ptr) + : static_cast>( + host_result_ptr); auto lambda = [=](sycl::nd_item<2> item) { auto n_wgroups = item.get_group_range()[1]; int wgroup_size = @@ -173,8 +188,6 @@ class Kokkos::Impl::ParallelReduce( - local_mem[wgroup_size * std::max(value_count, 1u)]); const auto local_id = item.get_local_linear_id(); const CombinedFunctorReducerType& functor_reducer = functor_reducer_wrapper.get_functor(); @@ -188,8 +201,8 @@ class Kokkos::Impl::ParallelReduce scratch_flags_ref(*scratch_flags); - num_teams_done = ++scratch_flags_ref; + num_teams_done[0] = ++scratch_flags_ref; } sycl::group_barrier(item.get_group()); - if (num_teams_done == n_wgroups) { + if (num_teams_done[0] == n_wgroups) { + if (local_id == 0) *scratch_flags = 0; if (local_id >= n_wgroups) reducer.init(&local_mem[local_id * value_count]); else { @@ -241,8 +255,8 @@ class Kokkos::Impl::ParallelReduce scratch_flags_ref(*scratch_flags); - num_teams_done = ++scratch_flags_ref; + num_teams_done[0] = ++scratch_flags_ref; } item.barrier(sycl::access::fence_space::local_space); - if (num_teams_done == n_wgroups) { + if (num_teams_done[0] == n_wgroups) { + if (local_id == 0) *scratch_flags = 0; if (local_id >= n_wgroups) reducer.init(&local_value); else { @@ -311,10 +326,7 @@ class Kokkos::Impl::ParallelReduce local_mem( - sycl::range<1>(wgroup_size) * std::max(value_count, 1u) + - (sizeof(unsigned int) + sizeof(value_type) - 1) / - sizeof(value_type), - cgh); + sycl::range<1>(wgroup_size) * std::max(value_count, 1u), cgh); const auto init_size = std::max((size + wgroup_size - 1) / wgroup_size, 1); @@ -358,11 +370,13 @@ class Kokkos::Impl::ParallelReduce( - space, m_result_ptr, results_ptr, - sizeof(*m_result_ptr) * value_count); + // Using DeepCopy instead of fence+memcpy turned out to be up to 2x slower. + if (host_result_ptr) { + space.fence( + "Kokkos::Impl::ParallelReduce::execute: result not " + "device-accessible"); + std::memcpy(m_result_ptr, host_result_ptr, + sizeof(*m_result_ptr) * value_count); } return last_reduction_event; @@ -448,9 +462,9 @@ class Kokkos::Impl::ParallelReducem_team_scratch_mutex) { + m_scratch_buffers_lock(arg_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { initialize(); } }; diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelScan_Range.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelScan_Range.hpp index 04425723e1..977b69bc9e 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelScan_Range.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ParallelScan_Range.hpp @@ -14,8 +14,8 @@ // //@HEADER -#ifndef KOKKO_SYCL_PARALLEL_SCAN_RANGE_HPP -#define KOKKO_SYCL_PARALLEL_SCAN_RANGE_HPP +#ifndef KOKKOS_SYCL_PARALLEL_SCAN_RANGE_HPP +#define KOKKOS_SYCL_PARALLEL_SCAN_RANGE_HPP #include #include @@ -111,13 +111,13 @@ class ParallelScanSYCLBase { const CombinedFunctorReducer m_functor_reducer; const Policy m_policy; - pointer_type m_scratch_space = nullptr; - const pointer_type m_result_ptr; + sycl::host_ptr m_scratch_host = nullptr; + pointer_type m_result_ptr; const bool m_result_ptr_device_accessible; - // Only let one Parallel/Scan modify the shared memory. The - // constructor acquires the mutex which is released in the destructor. - std::scoped_lock m_shared_memory_lock; + // Only let one ParallelScan instance at a time use the host scratch memory. + // The constructor acquires the mutex which is released in the destructor. + std::scoped_lock m_scratch_buffers_lock; private: template @@ -187,6 +187,7 @@ class ParallelScanSYCLBase { } item.barrier(sycl::access::fence_space::global_space); if (num_teams_done[0] == n_wgroups) { + if (local_id == 0) *scratch_flags = 0; value_type total; reducer.init(&total); @@ -220,6 +221,8 @@ class ParallelScanSYCLBase { sycl::device_ptr global_mem; sycl::device_ptr group_results; + desul::ensure_sycl_lock_arrays_on_device(q); + auto perform_work_group_scans = q.submit([&](sycl::handler& cgh) { sycl::local_accessor num_teams_done(1, cgh); @@ -253,7 +256,8 @@ class ParallelScanSYCLBase { global_mem = static_cast>(instance.scratch_space( n_wgroups * (wgroup_size + 1) * sizeof(value_type))); - m_scratch_space = global_mem; + m_scratch_host = static_cast>( + instance.scratch_host(sizeof(value_type))); group_results = global_mem + n_wgroups * wgroup_size; @@ -281,10 +285,11 @@ class ParallelScanSYCLBase { // Write results to global memory auto update_global_results = q.submit([&](sycl::handler& cgh) { - auto result_ptr_device_accessible = m_result_ptr_device_accessible; // The compiler failed with CL_INVALID_ARG_VALUE if using m_result_ptr // directly. - auto result_ptr = m_result_ptr_device_accessible ? m_result_ptr : nullptr; + pointer_type result_ptr = m_result_ptr_device_accessible + ? m_result_ptr + : static_cast(m_scratch_host); #ifndef KOKKOS_IMPL_SYCL_USE_IN_ORDER_QUEUES cgh.depends_on(perform_work_group_scans); @@ -293,7 +298,6 @@ class ParallelScanSYCLBase { cgh.parallel_for( sycl::nd_range<1>(n_wgroups * wgroup_size, wgroup_size), [=](sycl::nd_item<1> item) { - auto global_mem_copy = global_mem; const index_type global_id = item.get_global_linear_id(); const CombinedFunctorReducer< FunctorType, typename Analysis::Reducer>& functor_reducer = @@ -312,9 +316,7 @@ class ParallelScanSYCLBase { else functor(WorkTag(), global_id + begin, update, true); - global_mem_copy[global_id] = update; - if (global_id == size - 1 && result_ptr_device_accessible) - *result_ptr = update; + if (global_id == size - 1) *result_ptr = update; } }); }); @@ -351,9 +353,9 @@ class ParallelScanSYCLBase { m_policy(arg_policy), m_result_ptr(arg_result_ptr), m_result_ptr_device_accessible(arg_result_ptr_device_accessible), - m_shared_memory_lock(m_policy.space() - .impl_internal_space_instance() - ->m_mutexScratchSpace) {} + m_scratch_buffers_lock(m_policy.space() + .impl_internal_space_instance() + ->m_mutexScratchSpace) {} }; } // namespace Kokkos::Impl @@ -390,11 +392,13 @@ class Kokkos::Impl::ParallelScanWithTotal< Base::impl_execute([&]() { const long long nwork = Base::m_policy.end() - Base::m_policy.begin(); if (nwork > 0 && !Base::m_result_ptr_device_accessible) { + // Using DeepCopy instead of fence+memcpy turned out to be up to 2x + // slower. + m_exec.fence( + "Kokkos::Impl::ParallelReduce::execute: " + "result not device-accessible"); const int size = Base::m_functor_reducer.get_reducer().value_size(); - DeepCopy(m_exec, Base::m_result_ptr, - Base::m_scratch_space + nwork - 1, - size); + std::memcpy(Base::m_result_ptr, Base::m_scratch_host, size); } }); } diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.cpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.cpp index 64b7f56796..9cc8008cdf 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.cpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.cpp @@ -25,7 +25,6 @@ #include #include #include -#include #include /*--------------------------------------------------------------------------*/ @@ -243,226 +242,17 @@ void SYCLHostUSMSpace::deallocate(const char* arg_label, } // namespace Experimental } // namespace Kokkos -namespace Kokkos { -namespace Impl { - -#ifdef KOKKOS_ENABLE_DEBUG -SharedAllocationRecord SharedAllocationRecord< - Kokkos::Experimental::SYCLDeviceUSMSpace, void>::s_root_record; - -SharedAllocationRecord SharedAllocationRecord< - Kokkos::Experimental::SYCLSharedUSMSpace, void>::s_root_record; - -SharedAllocationRecord SharedAllocationRecord< - Kokkos::Experimental::SYCLHostUSMSpace, void>::s_root_record; -#endif - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::SYCLDeviceUSMSpace& space, - const std::string& label, const size_t size, - const SharedAllocationRecord::function_type dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Kokkos::Impl::checked_allocation_with_header(space, label, size), - sizeof(SharedAllocationHeader) + size, dealloc, label), - m_space(space) { - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, label); - - // Copy to device memory - Kokkos::Experimental::SYCL exec; - Kokkos::Impl::DeepCopy( - exec, RecordBase::m_alloc_ptr, &header, sizeof(SharedAllocationHeader)); - exec.fence( - "SharedAllocationRecord::SharedAllocationRecord(): fence after copying header from " - "HostSpace"); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::SYCL& arg_exec_space, - const Kokkos::Experimental::SYCLDeviceUSMSpace& space, - const std::string& label, const size_t size, - const SharedAllocationRecord::function_type dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Kokkos::Impl::checked_allocation_with_header(arg_exec_space, space, - label, size), - sizeof(SharedAllocationHeader) + size, dealloc, label), - m_space(space) { - SharedAllocationHeader header; - - this->base_t::_fill_host_accessible_header_info(header, label); - - // Copy to device memory - Kokkos::Impl::DeepCopy( - arg_exec_space, RecordBase::m_alloc_ptr, &header, - sizeof(SharedAllocationHeader)); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::SYCL& exec_space, - const Kokkos::Experimental::SYCLSharedUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(exec_space, arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::SYCLSharedUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::SYCL& exec_space, - const Kokkos::Experimental::SYCLHostUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(exec_space, arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::SYCLHostUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - - this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, - arg_label); -} - -} // namespace Impl -} // namespace Kokkos - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - -SharedAllocationRecord::~SharedAllocationRecord() { - const auto alloc_size = SharedAllocationRecord::m_alloc_size; - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - alloc_size, alloc_size - sizeof(SharedAllocationHeader)); -} - -SharedAllocationRecord::~SharedAllocationRecord() { - const auto alloc_size = SharedAllocationRecord::m_alloc_size; - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - alloc_size, alloc_size - sizeof(SharedAllocationHeader)); -} - -SharedAllocationRecord::~SharedAllocationRecord() { - const auto alloc_size = SharedAllocationRecord::m_alloc_size; - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - alloc_size, alloc_size - sizeof(SharedAllocationHeader)); -} - -//---------------------------------------------------------------------------- - -} // namespace Impl -} // namespace Kokkos - //============================================================================== // {{{1 #include -namespace Kokkos { -namespace Impl { - -// To avoid additional compilation cost for something that's (mostly?) not -// performance sensitive, we explicity instantiate these CRTP base classes here, -// where we have access to the associated *_timpl.hpp header files. -template class HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::SYCLDeviceUSMSpace>; -template class SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLDeviceUSMSpace>; -template class SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLSharedUSMSpace>; -template class SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLHostUSMSpace>; - -} // namespace Impl -} // namespace Kokkos +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::Experimental::SYCLDeviceUSMSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::Experimental::SYCLSharedUSMSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( + Kokkos::Experimental::SYCLHostUSMSpace); // end Explicit instantiations of CRTP Base classes }}}1 //============================================================================== diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.hpp index 239c6e3ce0..b86cfca413 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Space.hpp @@ -66,11 +66,6 @@ class SYCLDeviceUSMSpace { const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; - private: - template - friend class LogicalMemorySpace; - - public: static constexpr const char* name() { return "SYCLDeviceUSM"; }; private: @@ -87,6 +82,16 @@ class SYCLSharedUSMSpace { SYCLSharedUSMSpace(); explicit SYCLSharedUSMSpace(sycl::queue queue); + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const SYCL& exec_space, const std::size_t arg_alloc_size) const; void* allocate(const SYCL& exec_space, const char* arg_label, @@ -102,11 +107,6 @@ class SYCLSharedUSMSpace { const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; - private: - template - friend class LogicalMemorySpace; - - public: static constexpr const char* name() { return "SYCLSharedUSM"; }; private: @@ -123,6 +123,16 @@ class SYCLHostUSMSpace { SYCLHostUSMSpace(); explicit SYCLHostUSMSpace(sycl::queue queue); + template + void* allocate(const ExecutionSpace&, const size_t arg_alloc_size) const { + return allocate(arg_alloc_size); + } + template + void* allocate(const ExecutionSpace&, const char* arg_label, + const size_t arg_alloc_size, + const size_t arg_logical_size = 0) const { + return allocate(arg_label, arg_alloc_size, arg_logical_size); + } void* allocate(const SYCL& exec_space, const std::size_t arg_alloc_size) const; void* allocate(const SYCL& exec_space, const char* arg_label, @@ -138,11 +148,6 @@ class SYCLHostUSMSpace { const size_t arg_alloc_size, const size_t arg_logical_size = 0) const; - private: - template - friend class LogicalMemorySpace; - - public: static constexpr const char* name() { return "SYCLHostUSM"; }; private: @@ -166,19 +171,16 @@ struct is_sycl_type_space : public std::true_type {}; static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLDeviceUSMSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLDeviceUSMSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLSharedUSMSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLDeviceUSMSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLDeviceUSMSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable); template <> struct MemorySpaceAccess -class SharedAllocationRecord - : public HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::SYCLDeviceUSMSpace> { - private: - friend class SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLDeviceUSMSpace>; - friend class HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::SYCLDeviceUSMSpace>; - using base_t = HostInaccessibleSharedAllocationRecordCommon< - Kokkos::Experimental::SYCLDeviceUSMSpace>; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord(SharedAllocationRecord&&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(SharedAllocationRecord&&) = delete; - -#ifdef KOKKOS_ENABLE_DEBUG - static RecordBase s_root_record; -#endif - - const Kokkos::Experimental::SYCLDeviceUSMSpace m_space; - - protected: - ~SharedAllocationRecord(); - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, - const Kokkos::Experimental::SYCLDeviceUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const Kokkos::Experimental::SYCL& exec_space, - const Kokkos::Experimental::SYCLDeviceUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); - - SharedAllocationRecord( - const Kokkos::Experimental::SYCLDeviceUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; - -template <> -class SharedAllocationRecord - : public SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLSharedUSMSpace> { - private: - friend class SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLSharedUSMSpace>; - using base_t = - SharedAllocationRecordCommon; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord(SharedAllocationRecord&&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(SharedAllocationRecord&&) = delete; - - static RecordBase s_root_record; - - const Kokkos::Experimental::SYCLSharedUSMSpace m_space; - - protected: - ~SharedAllocationRecord(); - - SharedAllocationRecord() = default; - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, - const Kokkos::Experimental::SYCLSharedUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const Kokkos::Experimental::SYCL& exec_space, - const Kokkos::Experimental::SYCLSharedUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); - - SharedAllocationRecord( - const Kokkos::Experimental::SYCLSharedUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; - -template <> -class SharedAllocationRecord - : public SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLHostUSMSpace> { - private: - friend class SharedAllocationRecordCommon< - Kokkos::Experimental::SYCLHostUSMSpace>; - using base_t = - SharedAllocationRecordCommon; - using RecordBase = SharedAllocationRecord; - - SharedAllocationRecord(const SharedAllocationRecord&) = delete; - SharedAllocationRecord(SharedAllocationRecord&&) = delete; - SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - SharedAllocationRecord& operator=(SharedAllocationRecord&&) = delete; - - static RecordBase s_root_record; - - const Kokkos::Experimental::SYCLHostUSMSpace m_space; - - protected: - ~SharedAllocationRecord(); - - SharedAllocationRecord() = default; - - template - SharedAllocationRecord( - const ExecutionSpace& /*exec_space*/, - const Kokkos::Experimental::SYCLHostUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate) - : SharedAllocationRecord(arg_space, arg_label, arg_alloc_size, - arg_dealloc) {} - - SharedAllocationRecord( - const Kokkos::Experimental::SYCL& exec_space, - const Kokkos::Experimental::SYCLHostUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); - - SharedAllocationRecord( - const Kokkos::Experimental::SYCLHostUSMSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &base_t::deallocate); -}; - -} // namespace Impl - } // namespace Kokkos +KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_SPECIALIZATION( + Kokkos::Experimental::SYCLDeviceUSMSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION( + Kokkos::Experimental::SYCLSharedUSMSpace); +KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION( + Kokkos::Experimental::SYCLHostUSMSpace); + #endif #endif diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Team.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Team.hpp index 89c09c3195..dbba382758 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Team.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_Team.hpp @@ -140,9 +140,14 @@ class SYCLTeamMember { } value = sg.shuffle(value, 0); + const auto n_subgroups = sg.get_group_range()[0]; + if (n_subgroups == 1) { + reducer.reference() = value; + return; + } + // We need to chunk up the whole reduction because we might not have // allocated enough memory. - const auto n_subgroups = sg.get_group_range()[0]; const unsigned int maximum_work_range = std::min(m_team_reduce_size / sizeof(value_type), n_subgroups); diff --git a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ZeroMemset.hpp b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ZeroMemset.hpp index 9548f211d9..61db6b34aa 100644 --- a/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ZeroMemset.hpp +++ b/lib/kokkos/core/src/SYCL/Kokkos_SYCL_ZeroMemset.hpp @@ -26,8 +26,7 @@ namespace Impl { template struct ZeroMemset> { ZeroMemset(const Kokkos::Experimental::SYCL& exec_space, - const View& dst, - typename View::const_value_type&) { + const View& dst) { auto event = exec_space.impl_internal_space_instance()->m_queue->memset( dst.data(), 0, dst.size() * sizeof(typename View::value_type)); #ifndef KOKKOS_IMPL_SYCL_USE_IN_ORDER_QUEUES @@ -35,12 +34,6 @@ struct ZeroMemset> { ->m_queue->ext_oneapi_submit_barrier(std::vector{event}); #endif } - - ZeroMemset(const View& dst, - typename View::const_value_type&) { - Experimental::Impl::SYCLInternal::singleton().m_queue->memset( - dst.data(), 0, dst.size() * sizeof(typename View::value_type)); - } }; } // namespace Impl diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp b/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp index e81e834939..39b201976b 100644 --- a/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp +++ b/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp @@ -58,8 +58,6 @@ void SerialInternal::finalize() { m_thread_team_data.scratch_assign(nullptr, 0, 0, 0, 0, 0); } - Kokkos::Profiling::finalize(); - m_is_initialized = false; } @@ -155,7 +153,7 @@ void Serial::print_configuration(std::ostream& os, bool /*verbose*/) const { os << "Host Serial Execution Space:\n"; os << " KOKKOS_ENABLE_SERIAL: yes\n"; -#ifdef KOKKOS_INTERNAL_NOT_PARALLEL +#ifdef KOKKOS_ENABLE_ATOMICS_BYPASS os << "Kokkos atomics disabled\n"; #endif diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial.hpp b/lib/kokkos/core/src/Serial/Kokkos_Serial.hpp index db1567610b..43eb4992ed 100644 --- a/lib/kokkos/core/src/Serial/Kokkos_Serial.hpp +++ b/lib/kokkos/core/src/Serial/Kokkos_Serial.hpp @@ -30,6 +30,7 @@ static_assert(false, #include #include +#include #include #include #include @@ -120,7 +121,10 @@ class Serial { /// For the Serial device, this method always returns false, /// because parallel_for or parallel_reduce with the Serial device /// always execute sequentially. - inline static int in_parallel() { return false; } + +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED inline static int in_parallel() { return false; } +#endif /// \brief Wait until all dispatched functors complete. /// diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp index 69787aa500..67978aa3e9 100644 --- a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp +++ b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp @@ -14,8 +14,8 @@ // //@HEADER -#ifndef KOKKO_SERIAL_PARALLEL_MDRANGE_HPP -#define KOKKO_SERIAL_PARALLEL_MDRANGE_HPP +#ifndef KOKKOS_SERIAL_PARALLEL_MDRANGE_HPP +#define KOKKOS_SERIAL_PARALLEL_MDRANGE_HPP #include #include diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Range.hpp b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Range.hpp index 56894716db..91b4c56711 100644 --- a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Range.hpp +++ b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Range.hpp @@ -14,8 +14,8 @@ // //@HEADER -#ifndef KOKKO_SERIAL_PARALLEL_RANGE_HPP -#define KOKKO_SERIAL_PARALLEL_RANGE_HPP +#ifndef KOKKOS_SERIAL_PARALLEL_RANGE_HPP +#define KOKKOS_SERIAL_PARALLEL_RANGE_HPP #include diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Team.hpp b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Team.hpp index 0876f1af22..a25b51496e 100644 --- a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Team.hpp +++ b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Team.hpp @@ -14,8 +14,8 @@ // //@HEADER -#ifndef KOKKO_SERIAL_PARALLEL_TEAM_HPP -#define KOKKO_SERIAL_PARALLEL_TEAM_HPP +#ifndef KOKKOS_SERIAL_PARALLEL_TEAM_HPP +#define KOKKOS_SERIAL_PARALLEL_TEAM_HPP #include @@ -37,6 +37,8 @@ class TeamPolicyInternal int m_league_size; int m_chunk_size; + Kokkos::Serial m_space; + public: //! Tag this class as a kokkos execution policy using execution_policy = TeamPolicyInternal; @@ -46,10 +48,7 @@ class TeamPolicyInternal //! Execution space of this execution policy: using execution_space = Kokkos::Serial; - const typename traits::execution_space& space() const { - static typename traits::execution_space m_space; - return m_space; - } + const typename traits::execution_space& space() const { return m_space; } template friend class TeamPolicyInternal; @@ -116,12 +115,13 @@ class TeamPolicyInternal return (level == 0 ? 1024 * 32 : 20 * 1024 * 1024); } /** \brief Specify league size, request team size */ - TeamPolicyInternal(const execution_space&, int league_size_request, + TeamPolicyInternal(const execution_space& space, int league_size_request, int team_size_request, int /* vector_length_request */ = 1) : m_team_scratch_size{0, 0}, m_thread_scratch_size{0, 0}, m_league_size(league_size_request), - m_chunk_size(32) { + m_chunk_size(32), + m_space(space) { if (team_size_request > 1) Kokkos::abort("Kokkos::abort: Requested Team Size is too large!"); } diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial_Task.hpp b/lib/kokkos/core/src/Serial/Kokkos_Serial_Task.hpp index f9c86f55ce..5905d6d32e 100644 --- a/lib/kokkos/core/src/Serial/Kokkos_Serial_Task.hpp +++ b/lib/kokkos/core/src/Serial/Kokkos_Serial_Task.hpp @@ -121,7 +121,7 @@ class TaskQueueSpecializationConstrained< using task_base_type = TaskBase; using queue_type = typename scheduler_type::queue_type; - task_base_type* const end = (task_base_type*)task_base_type::EndTag; + auto* const end = reinterpret_cast(task_base_type::EndTag); execution_space serial_execution_space; auto& data = serial_execution_space.impl_internal_space_instance() @@ -157,7 +157,7 @@ class TaskQueueSpecializationConstrained< using task_base_type = TaskBase; using queue_type = typename scheduler_type::queue_type; - task_base_type* const end = (task_base_type*)task_base_type::EndTag; + auto* const end = reinterpret_cast(task_base_type::EndTag); execution_space serial_execution_space; diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial_ZeroMemset.hpp b/lib/kokkos/core/src/Serial/Kokkos_Serial_ZeroMemset.hpp index 3ec2dfbcfa..6ad6aabc5a 100644 --- a/lib/kokkos/core/src/Serial/Kokkos_Serial_ZeroMemset.hpp +++ b/lib/kokkos/core/src/Serial/Kokkos_Serial_ZeroMemset.hpp @@ -22,6 +22,7 @@ #include #include +#include namespace Kokkos { namespace Impl { @@ -34,14 +35,11 @@ template struct ZeroMemset< std::conditional_t::value, Serial, DummyExecutionSpace>, - View> - : public ZeroMemset> { - using Base = ZeroMemset>; - using Base::Base; - - ZeroMemset(const Serial&, const View& dst, - typename View::const_value_type& value) - : Base(dst, value) {} + View> { + ZeroMemset(const Serial&, const View& dst) { + using ValueType = typename View::value_type; + std::memset(dst.data(), 0, sizeof(ValueType) * dst.size()); + } }; } // namespace Impl diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads.hpp index c0d70c03ec..31653c46ca 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads.hpp @@ -38,15 +38,6 @@ static_assert(false, /*--------------------------------------------------------------------------*/ -namespace Kokkos { -namespace Impl { -class ThreadsExec; -enum class fence_is_static { yes, no }; -} // namespace Impl -} // namespace Kokkos - -/*--------------------------------------------------------------------------*/ - namespace Kokkos { /** \brief Execution space for a pool of C++11 threads on a CPU. */ @@ -73,7 +64,9 @@ class Threads { /// \brief True if and only if this method is being called in a /// thread-parallel function. - static int in_parallel(); +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED static int in_parallel(); +#endif /// \brief Print configuration information to the given output stream. void print_configuration(std::ostream& os, bool verbose = false) const; diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_Instance.cpp similarity index 56% rename from lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp rename to lib/kokkos/core/src/Threads/Kokkos_Threads_Instance.cpp index c754091e87..3842966cd7 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_Instance.cpp @@ -16,17 +16,15 @@ #ifndef KOKKOS_IMPL_PUBLIC_INCLUDE #define KOKKOS_IMPL_PUBLIC_INCLUDE +#include "Threads/Kokkos_Threads_Instance.hpp" #endif #include -#include -#include #include #include #include #include -#include #include @@ -41,7 +39,6 @@ namespace Kokkos { namespace Impl { namespace { -std::mutex host_internal_cppthread_mutex; // std::thread compatible driver. // Recovery from an exception would require constant intra-thread health @@ -49,7 +46,7 @@ std::mutex host_internal_cppthread_mutex; // abort the process. void internal_cppthread_driver() { try { - ThreadsExec::driver(); + ThreadsInternal::driver(); } catch (const std::exception &x) { std::cerr << "Exception thrown from worker thread: " << x.what() << std::endl; @@ -62,32 +59,17 @@ void internal_cppthread_driver() { } } -ThreadsExec s_threads_process; -ThreadsExec *s_threads_exec[ThreadsExec::MAX_THREAD_COUNT] = {nullptr}; -std::thread::id s_threads_pid[ThreadsExec::MAX_THREAD_COUNT]; -std::pair s_threads_coord[ThreadsExec::MAX_THREAD_COUNT]; +ThreadsInternal s_threads_process; +ThreadsInternal *s_threads_exec[ThreadsInternal::MAX_THREAD_COUNT] = {nullptr}; +std::thread::id s_threads_pid[ThreadsInternal::MAX_THREAD_COUNT]; +std::pair + s_threads_coord[ThreadsInternal::MAX_THREAD_COUNT]; int s_thread_pool_size[3] = {0, 0, 0}; -unsigned s_current_reduce_size = 0; -unsigned s_current_shared_size = 0; - -void (*volatile s_current_function)(ThreadsExec &, const void *); +void (*volatile s_current_function)(ThreadsInternal &, const void *); const void *volatile s_current_function_arg = nullptr; -struct Sentinel { - ~Sentinel() { - if (s_thread_pool_size[0] || s_thread_pool_size[1] || - s_thread_pool_size[2] || s_current_reduce_size || - s_current_shared_size || s_current_function || s_current_function_arg || - s_threads_exec[0]) { - std::cerr << "ERROR : Process exiting while Kokkos::Threads is still " - "initialized" - << std::endl; - } - } -}; - inline unsigned fan_size(const unsigned rank, const unsigned size) { const unsigned rank_rev = size - (rank + 1); unsigned count = 0; @@ -97,6 +79,12 @@ inline unsigned fan_size(const unsigned rank, const unsigned size) { return count; } +void wait_yield(volatile ThreadState &flag, const ThreadState value) { + while (value == flag) { + std::this_thread::yield(); + } +} + } // namespace } // namespace Impl } // namespace Kokkos @@ -107,66 +95,44 @@ inline unsigned fan_size(const unsigned rank, const unsigned size) { namespace Kokkos { namespace Impl { -//---------------------------------------------------------------------------- -// Spawn a thread - -void ThreadsExec::spawn() { - std::thread t(internal_cppthread_driver); - t.detach(); -} - -//---------------------------------------------------------------------------- - -bool ThreadsExec::is_process() { +bool ThreadsInternal::is_process() { static const std::thread::id master_pid = std::this_thread::get_id(); return master_pid == std::this_thread::get_id(); } -void ThreadsExec::global_lock() { host_internal_cppthread_mutex.lock(); } - -void ThreadsExec::global_unlock() { host_internal_cppthread_mutex.unlock(); } - //---------------------------------------------------------------------------- -void ThreadsExec::wait_yield(volatile int &flag, const int value) { - while (value == flag) { - std::this_thread::yield(); - } -} +void execute_function_noop(ThreadsInternal &, const void *) {} -void execute_function_noop(ThreadsExec &, const void *) {} - -void ThreadsExec::driver() { +void ThreadsInternal::driver() { SharedAllocationRecord::tracking_enable(); - ThreadsExec this_thread; + ThreadsInternal this_thread; - while (ThreadsExec::Active == this_thread.m_pool_state) { + while (this_thread.m_pool_state == ThreadState::Active) { (*s_current_function)(this_thread, s_current_function_arg); // Deactivate thread and wait for reactivation - this_thread.m_pool_state = ThreadsExec::Inactive; + this_thread.m_pool_state = ThreadState::Inactive; - wait_yield(this_thread.m_pool_state, ThreadsExec::Inactive); + wait_yield(this_thread.m_pool_state, ThreadState::Inactive); } } -ThreadsExec::ThreadsExec() +ThreadsInternal::ThreadsInternal() : m_pool_base(nullptr), m_scratch(nullptr), m_scratch_reduce_end(0), m_scratch_thread_end(0), - m_numa_rank(0), - m_numa_core_rank(0), m_pool_rank(0), m_pool_size(0), m_pool_fan_size(0), - m_pool_state(ThreadsExec::Terminating) { + m_pool_state(ThreadState::Terminating) { if (&s_threads_process != this) { - // A spawned thread - - ThreadsExec *const nil = nullptr; + // The code in the if is executed by a spawned thread not by the root + // thread + ThreadsInternal *const nil = nullptr; // Which entry in 's_threads_exec', possibly determined from hwloc binding const int entry = reinterpret_cast(s_current_function_arg) < @@ -178,80 +144,66 @@ ThreadsExec::ThreadsExec() // Given a good entry set this thread in the 's_threads_exec' array if (entry < s_thread_pool_size[0] && nil == atomic_compare_exchange(s_threads_exec + entry, nil, this)) { - const std::pair coord = - Kokkos::hwloc::get_this_thread_coordinate(); - - m_numa_rank = coord.first; - m_numa_core_rank = coord.second; - m_pool_base = s_threads_exec; - m_pool_rank = s_thread_pool_size[0] - (entry + 1); - m_pool_rank_rev = s_thread_pool_size[0] - (pool_rank() + 1); - m_pool_size = s_thread_pool_size[0]; - m_pool_fan_size = fan_size(m_pool_rank, m_pool_size); - m_pool_state = ThreadsExec::Active; + m_pool_base = s_threads_exec; + m_pool_rank = s_thread_pool_size[0] - (entry + 1); + m_pool_rank_rev = s_thread_pool_size[0] - (pool_rank() + 1); + m_pool_size = s_thread_pool_size[0]; + m_pool_fan_size = fan_size(m_pool_rank, m_pool_size); + m_pool_state = ThreadState::Active; s_threads_pid[m_pool_rank] = std::this_thread::get_id(); // Inform spawning process that the threads_exec entry has been set. - s_threads_process.m_pool_state = ThreadsExec::Active; + s_threads_process.m_pool_state = ThreadState::Active; } else { // Inform spawning process that the threads_exec entry could not be set. - s_threads_process.m_pool_state = ThreadsExec::Terminating; + s_threads_process.m_pool_state = ThreadState::Terminating; } } else { // Enables 'parallel_for' to execute on unitialized Threads device m_pool_rank = 0; m_pool_size = 1; - m_pool_state = ThreadsExec::Inactive; + m_pool_state = ThreadState::Inactive; s_threads_pid[m_pool_rank] = std::this_thread::get_id(); } } -ThreadsExec::~ThreadsExec() { +ThreadsInternal::~ThreadsInternal() { const unsigned entry = m_pool_size - (m_pool_rank + 1); - using Record = Kokkos::Impl::SharedAllocationRecord; - if (m_scratch) { - Record *const r = Record::get_record(m_scratch); - + Kokkos::kokkos_free(m_scratch); m_scratch = nullptr; - - Record::decrement(r); } m_pool_base = nullptr; m_scratch_reduce_end = 0; m_scratch_thread_end = 0; - m_numa_rank = 0; - m_numa_core_rank = 0; m_pool_rank = 0; m_pool_size = 0; m_pool_fan_size = 0; - m_pool_state = ThreadsExec::Terminating; + m_pool_state = ThreadState::Terminating; if (&s_threads_process != this && entry < MAX_THREAD_COUNT) { - ThreadsExec *const nil = nullptr; + ThreadsInternal *const nil = nullptr; atomic_compare_exchange(s_threads_exec + entry, this, nil); - s_threads_process.m_pool_state = ThreadsExec::Terminating; + s_threads_process.m_pool_state = ThreadState::Terminating; } } -int ThreadsExec::get_thread_count() { return s_thread_pool_size[0]; } - -ThreadsExec *ThreadsExec::get_thread(const int init_thread_rank) { - ThreadsExec *const th = +ThreadsInternal *ThreadsInternal::get_thread(const int init_thread_rank) { + ThreadsInternal *const th = init_thread_rank < s_thread_pool_size[0] ? s_threads_exec[s_thread_pool_size[0] - (init_thread_rank + 1)] : nullptr; if (nullptr == th || th->m_pool_rank != init_thread_rank) { std::ostringstream msg; - msg << "Kokkos::Impl::ThreadsExec::get_thread ERROR : " + msg << "Kokkos::Impl::ThreadsInternal::get_thread ERROR : " << "thread " << init_thread_rank << " of " << s_thread_pool_size[0]; if (nullptr == th) { msg << " does not exist"; @@ -264,24 +216,6 @@ ThreadsExec *ThreadsExec::get_thread(const int init_thread_rank) { return th; } -//---------------------------------------------------------------------------- - -void ThreadsExec::execute_sleep(ThreadsExec &exec, const void *) { - ThreadsExec::global_lock(); - ThreadsExec::global_unlock(); - - const int n = exec.m_pool_fan_size; - const int rank_rev = exec.m_pool_size - (exec.m_pool_rank + 1); - - for (int i = 0; i < n; ++i) { - Impl::spinwait_while_equal( - exec.m_pool_base[rank_rev + (1 << i)]->m_pool_state, - ThreadsExec::Active); - } - - exec.m_pool_state = ThreadsExec::Inactive; -} - } // namespace Impl } // namespace Kokkos @@ -290,8 +224,8 @@ void ThreadsExec::execute_sleep(ThreadsExec &exec, const void *) { namespace Kokkos { namespace Impl { -void ThreadsExec::verify_is_process(const std::string &name, - const bool initialized) { +void ThreadsInternal::verify_is_process(const std::string &name, + const bool initialized) { if (!is_process()) { std::string msg(name); msg.append( @@ -307,63 +241,48 @@ void ThreadsExec::verify_is_process(const std::string &name, } } -int ThreadsExec::in_parallel() { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 +KOKKOS_DEPRECATED int ThreadsInternal::in_parallel() { // A thread function is in execution and // the function argument is not the special threads process argument and // the master process is a worker or is not the master process. return s_current_function && (&s_threads_process != s_current_function_arg) && (s_threads_process.m_pool_base || !is_process()); } -void ThreadsExec::fence() { internal_fence(Impl::fence_is_static::yes); } -void ThreadsExec::fence(const std::string &name) { - internal_fence(name, Impl::fence_is_static::yes); +#endif +void ThreadsInternal::fence() { + fence("Kokkos::ThreadsInternal::fence: Unnamed Instance Fence"); } - -void ThreadsExec::internal_fence(Impl::fence_is_static is_static) { - internal_fence((is_static == Impl::fence_is_static::no) - ? "Kokkos::ThreadsExec::fence: Unnamed Instance Fence" - : "Kokkos::ThreadsExec::fence: Unnamed Static Fence", - is_static); +void ThreadsInternal::fence(const std::string &name) { + Kokkos::Tools::Experimental::Impl::profile_fence_event( + name, Kokkos::Tools::Experimental::Impl::DirectFenceIDHandle{1}, + internal_fence); } // Wait for root thread to become inactive -void ThreadsExec::internal_fence(const std::string &name, - Impl::fence_is_static is_static) { - const auto &fence_lam = [&]() { - if (s_thread_pool_size[0]) { - // Wait for the root thread to complete: - Impl::spinwait_while_equal(s_threads_exec[0]->m_pool_state, - ThreadsExec::Active); - } - - s_current_function = nullptr; - s_current_function_arg = nullptr; - - // Make sure function and arguments are cleared before - // potentially re-activating threads with a subsequent launch. - memory_fence(); - }; - if (is_static == Impl::fence_is_static::yes) { - Kokkos::Tools::Experimental::Impl::profile_fence_event( - name, - Kokkos::Tools::Experimental::SpecialSynchronizationCases:: - GlobalDeviceSynchronization, - fence_lam); - } else { - Kokkos::Tools::Experimental::Impl::profile_fence_event( - name, Kokkos::Tools::Experimental::Impl::DirectFenceIDHandle{1}, - fence_lam); +void ThreadsInternal::internal_fence() { + if (s_thread_pool_size[0]) { + // Wait for the root thread to complete: + Impl::spinwait_while_equal(s_threads_exec[0]->m_pool_state, + ThreadState::Active); } + + s_current_function = nullptr; + s_current_function_arg = nullptr; + + // Make sure function and arguments are cleared before + // potentially re-activating threads with a subsequent launch. + memory_fence(); } /** \brief Begin execution of the asynchronous functor */ -void ThreadsExec::start(void (*func)(ThreadsExec &, const void *), - const void *arg) { - verify_is_process("ThreadsExec::start", true); +void ThreadsInternal::start(void (*func)(ThreadsInternal &, const void *), + const void *arg) { + verify_is_process("ThreadsInternal::start", true); if (s_current_function || s_current_function_arg) { Kokkos::Impl::throw_runtime_exception( - std::string("ThreadsExec::start() FAILED : already executing")); + std::string("ThreadsInternal::start() FAILED : already executing")); } s_current_function = func; @@ -372,68 +291,29 @@ void ThreadsExec::start(void (*func)(ThreadsExec &, const void *), // Make sure function and arguments are written before activating threads. memory_fence(); - // Activate threads: + // Activate threads. The spawned threads will start working on + // s_current_function. The root thread is only set to active, we still need to + // call s_current_function. for (int i = s_thread_pool_size[0]; 0 < i--;) { - s_threads_exec[i]->m_pool_state = ThreadsExec::Active; + s_threads_exec[i]->m_pool_state = ThreadState::Active; } if (s_threads_process.m_pool_size) { // Master process is the root thread, run it: (*func)(s_threads_process, arg); - s_threads_process.m_pool_state = ThreadsExec::Inactive; + s_threads_process.m_pool_state = ThreadState::Inactive; } } //---------------------------------------------------------------------------- -bool ThreadsExec::sleep() { - verify_is_process("ThreadsExec::sleep", true); - - if (&execute_sleep == s_current_function) return false; - - fence(); - - ThreadsExec::global_lock(); - - s_current_function = &execute_sleep; - - // Activate threads: - for (unsigned i = s_thread_pool_size[0]; 0 < i;) { - s_threads_exec[--i]->m_pool_state = ThreadsExec::Active; - } - - return true; -} - -bool ThreadsExec::wake() { - verify_is_process("ThreadsExec::wake", true); - - if (&execute_sleep != s_current_function) return false; - - ThreadsExec::global_unlock(); - - if (s_threads_process.m_pool_base) { - execute_sleep(s_threads_process, nullptr); - s_threads_process.m_pool_state = ThreadsExec::Inactive; - } - - fence(); - - return true; -} - -//---------------------------------------------------------------------------- - -void ThreadsExec::execute_resize_scratch_in_serial() { +void ThreadsInternal::execute_resize_scratch_in_serial() { const unsigned begin = s_threads_process.m_pool_base ? 1 : 0; - auto deallocate_scratch_memory = [](ThreadsExec &exec) { + auto deallocate_scratch_memory = [](ThreadsInternal &exec) { if (exec.m_scratch) { - using Record = - Kokkos::Impl::SharedAllocationRecord; - Record *const r = Record::get_record(exec.m_scratch); - exec.m_scratch = nullptr; - Record::decrement(r); + Kokkos::kokkos_free(exec.m_scratch); + exec.m_scratch = nullptr; } }; if (s_threads_process.m_pool_base) { @@ -449,18 +329,18 @@ void ThreadsExec::execute_resize_scratch_in_serial() { memory_fence(); for (unsigned i = s_thread_pool_size[0]; begin < i;) { - ThreadsExec &th = *s_threads_exec[--i]; + ThreadsInternal &th = *s_threads_exec[--i]; - th.m_pool_state = ThreadsExec::Active; + th.m_pool_state = ThreadState::Active; - wait_yield(th.m_pool_state, ThreadsExec::Active); + wait_yield(th.m_pool_state, ThreadState::Active); } if (s_threads_process.m_pool_base) { deallocate_scratch_memory(s_threads_process); - s_threads_process.m_pool_state = ThreadsExec::Active; + s_threads_process.m_pool_state = ThreadState::Active; first_touch_allocate_thread_private_scratch(s_threads_process, nullptr); - s_threads_process.m_pool_state = ThreadsExec::Inactive; + s_threads_process.m_pool_state = ThreadState::Inactive; } s_current_function_arg = nullptr; @@ -472,27 +352,20 @@ void ThreadsExec::execute_resize_scratch_in_serial() { //---------------------------------------------------------------------------- -void *ThreadsExec::root_reduce_scratch() { +void *ThreadsInternal::root_reduce_scratch() { return s_threads_process.reduce_memory(); } -void ThreadsExec::first_touch_allocate_thread_private_scratch(ThreadsExec &exec, - const void *) { +void ThreadsInternal::first_touch_allocate_thread_private_scratch( + ThreadsInternal &exec, const void *) { exec.m_scratch_reduce_end = s_threads_process.m_scratch_reduce_end; exec.m_scratch_thread_end = s_threads_process.m_scratch_thread_end; if (s_threads_process.m_scratch_thread_end) { // Allocate tracked memory: { - using Record = - Kokkos::Impl::SharedAllocationRecord; - Record *const r = - Record::allocate(Kokkos::HostSpace(), "Kokkos::thread_scratch", - s_threads_process.m_scratch_thread_end); - - Record::increment(r); - - exec.m_scratch = r->data(); + exec.m_scratch = Kokkos::kokkos_malloc( + "Kokkos::thread_scratch", s_threads_process.m_scratch_thread_end); } unsigned *ptr = reinterpret_cast(exec.m_scratch); @@ -505,7 +378,7 @@ void ThreadsExec::first_touch_allocate_thread_private_scratch(ThreadsExec &exec, } } -void *ThreadsExec::resize_scratch(size_t reduce_size, size_t thread_size) { +void *ThreadsInternal::resize_scratch(size_t reduce_size, size_t thread_size) { enum { ALIGN_MASK = Kokkos::Impl::MEMORY_ALIGNMENT - 1 }; fence(); @@ -522,7 +395,7 @@ void *ThreadsExec::resize_scratch(size_t reduce_size, size_t thread_size) { if ((old_reduce_size < reduce_size) || (old_thread_size < thread_size) || ((reduce_size == 0 && thread_size == 0) && (old_reduce_size != 0 || old_thread_size != 0))) { - verify_is_process("ThreadsExec::resize_scratch", true); + verify_is_process("ThreadsInternal::resize_scratch", true); s_threads_process.m_scratch_reduce_end = reduce_size; s_threads_process.m_scratch_thread_end = reduce_size + thread_size; @@ -537,27 +410,22 @@ void *ThreadsExec::resize_scratch(size_t reduce_size, size_t thread_size) { //---------------------------------------------------------------------------- -void ThreadsExec::print_configuration(std::ostream &s, const bool detail) { - verify_is_process("ThreadsExec::print_configuration", false); +void ThreadsInternal::print_configuration(std::ostream &s, const bool detail) { + verify_is_process("ThreadsInternal::print_configuration", false); fence(); - const unsigned numa_count = Kokkos::hwloc::get_available_numa_count(); - const unsigned cores_per_numa = Kokkos::hwloc::get_available_cores_per_numa(); - const unsigned threads_per_core = - Kokkos::hwloc::get_available_threads_per_core(); - - // Forestall compiler warnings for unused variables. - (void)numa_count; - (void)cores_per_numa; - (void)threads_per_core; - s << "Kokkos::Threads"; #if defined(KOKKOS_ENABLE_THREADS) s << " KOKKOS_ENABLE_THREADS"; #endif #if defined(KOKKOS_ENABLE_HWLOC) + const unsigned numa_count = Kokkos::hwloc::get_available_numa_count(); + const unsigned cores_per_numa = Kokkos::hwloc::get_available_cores_per_numa(); + const unsigned threads_per_core = + Kokkos::hwloc::get_available_threads_per_core(); + s << " hwloc[" << numa_count << "x" << cores_per_numa << "x" << threads_per_core << "]"; #endif @@ -569,25 +437,21 @@ void ThreadsExec::print_configuration(std::ostream &s, const bool detail) { if (nullptr == s_threads_process.m_pool_base) { s << " Asynchronous"; } - s << " ReduceScratch[" << s_current_reduce_size << "]" - << " SharedScratch[" << s_current_shared_size << "]"; s << std::endl; if (detail) { for (int i = 0; i < s_thread_pool_size[0]; ++i) { - ThreadsExec *const th = s_threads_exec[i]; + ThreadsInternal *const th = s_threads_exec[i]; if (th) { const int rank_rev = th->m_pool_size - (th->m_pool_rank + 1); - s << " Thread[ " << th->m_pool_rank << " : " << th->m_numa_rank << "." - << th->m_numa_core_rank << " ]"; + s << " Thread[ " << th->m_pool_rank << " ]"; s << " Fan{"; for (int j = 0; j < th->m_pool_fan_size; ++j) { - ThreadsExec *const thfan = th->m_pool_base[rank_rev + (1 << j)]; - s << " [ " << thfan->m_pool_rank << " : " << thfan->m_numa_rank - << "." << thfan->m_numa_core_rank << " ]"; + ThreadsInternal *const thfan = th->m_pool_base[rank_rev + (1 << j)]; + s << " [ " << thfan->m_pool_rank << " ]"; } s << " }"; @@ -605,29 +469,21 @@ void ThreadsExec::print_configuration(std::ostream &s, const bool detail) { //---------------------------------------------------------------------------- -int ThreadsExec::is_initialized() { return nullptr != s_threads_exec[0]; } +int ThreadsInternal::is_initialized() { return nullptr != s_threads_exec[0]; } -void ThreadsExec::initialize(int thread_count_arg) { - // legacy arguments - unsigned thread_count = thread_count_arg == -1 ? 0 : thread_count_arg; - unsigned use_numa_count = 0; - unsigned use_cores_per_numa = 0; - bool allow_asynchronous_threadpool = false; - // need to provide an initializer for Intel compilers - static const Sentinel sentinel = {}; +void ThreadsInternal::initialize(int thread_count_arg) { + unsigned thread_count = thread_count_arg == -1 ? 0 : thread_count_arg; const bool is_initialized = 0 != s_thread_pool_size[0]; unsigned thread_spawn_failed = 0; - for (int i = 0; i < ThreadsExec::MAX_THREAD_COUNT; i++) + for (int i = 0; i < ThreadsInternal::MAX_THREAD_COUNT; i++) s_threads_exec[i] = nullptr; if (!is_initialized) { - // If thread_count, use_numa_count, or use_cores_per_numa are zero - // then they will be given default values based upon hwloc detection - // and allowed asynchronous execution. - + // If thread_count is zero then it will be given default values based upon + // hwloc detection. const bool hwloc_avail = Kokkos::hwloc::available(); const bool hwloc_can_bind = hwloc_avail && Kokkos::hwloc::can_bind_threads(); @@ -640,17 +496,18 @@ void ThreadsExec::initialize(int thread_count_arg) { : 1; } - const unsigned thread_spawn_begin = hwloc::thread_mapping( - "Kokkos::Threads::initialize", allow_asynchronous_threadpool, - thread_count, use_numa_count, use_cores_per_numa, s_threads_coord); + const bool allow_asynchronous_threadpool = false; + unsigned use_numa_count = 0; + unsigned use_cores_per_numa = 0; + hwloc::thread_mapping("Kokkos::Threads::initialize", + allow_asynchronous_threadpool, thread_count, + use_numa_count, use_cores_per_numa, s_threads_coord); const std::pair proc_coord = s_threads_coord[0]; - if (thread_spawn_begin) { - // Synchronous with s_threads_coord[0] as the process core - // Claim entry #0 for binding the process core. - s_threads_coord[0] = std::pair(~0u, ~0u); - } + // Synchronous with s_threads_coord[0] as the process core + // Claim entry #0 for binding the process core. + s_threads_coord[0] = std::pair(~0u, ~0u); s_thread_pool_size[0] = thread_count; s_thread_pool_size[1] = s_thread_pool_size[0] / use_numa_count; @@ -658,8 +515,8 @@ void ThreadsExec::initialize(int thread_count_arg) { s_current_function = &execute_function_noop; // Initialization work function - for (unsigned ith = thread_spawn_begin; ith < thread_count; ++ith) { - s_threads_process.m_pool_state = ThreadsExec::Inactive; + for (unsigned ith = 1; ith < thread_count; ++ith) { + s_threads_process.m_pool_state = ThreadState::Inactive; // If hwloc available then spawned thread will // choose its own entry in 's_threads_coord' @@ -675,18 +532,20 @@ void ThreadsExec::initialize(int thread_count_arg) { // Wait until spawned thread has attempted to initialize. // If spawning and initialization is successful then // an entry in 's_threads_exec' will be assigned. - ThreadsExec::spawn(); - wait_yield(s_threads_process.m_pool_state, ThreadsExec::Inactive); - if (s_threads_process.m_pool_state == ThreadsExec::Terminating) break; + std::thread t(internal_cppthread_driver); + t.detach(); + wait_yield(s_threads_process.m_pool_state, ThreadState::Inactive); + if (s_threads_process.m_pool_state == ThreadState::Terminating) break; } // Wait for all spawned threads to deactivate before zeroing the function. - for (unsigned ith = thread_spawn_begin; ith < thread_count; ++ith) { + for (unsigned ith = 1; ith < thread_count; ++ith) { // Try to protect against cache coherency failure by casting to volatile. - ThreadsExec *const th = ((ThreadsExec * volatile *)s_threads_exec)[ith]; + ThreadsInternal *const th = + ((ThreadsInternal * volatile *)s_threads_exec)[ith]; if (th) { - wait_yield(th->m_pool_state, ThreadsExec::Active); + wait_yield(th->m_pool_state, ThreadState::Active); } else { ++thread_spawn_failed; } @@ -694,7 +553,7 @@ void ThreadsExec::initialize(int thread_count_arg) { s_current_function = nullptr; s_current_function_arg = nullptr; - s_threads_process.m_pool_state = ThreadsExec::Inactive; + s_threads_process.m_pool_state = ThreadState::Inactive; memory_fence(); @@ -705,30 +564,17 @@ void ThreadsExec::initialize(int thread_count_arg) { Kokkos::hwloc::bind_this_thread(proc_coord); } - if (thread_spawn_begin) { // Include process in pool. - const std::pair coord = - Kokkos::hwloc::get_this_thread_coordinate(); - - s_threads_exec[0] = &s_threads_process; - s_threads_process.m_numa_rank = coord.first; - s_threads_process.m_numa_core_rank = coord.second; - s_threads_process.m_pool_base = s_threads_exec; - s_threads_process.m_pool_rank = - thread_count - 1; // Reversed for scan-compatible reductions - s_threads_process.m_pool_size = thread_count; - s_threads_process.m_pool_fan_size = fan_size( - s_threads_process.m_pool_rank, s_threads_process.m_pool_size); - s_threads_pid[s_threads_process.m_pool_rank] = - std::this_thread::get_id(); - } else { - s_threads_process.m_pool_base = nullptr; - s_threads_process.m_pool_rank = 0; - s_threads_process.m_pool_size = 0; - s_threads_process.m_pool_fan_size = 0; - } + s_threads_exec[0] = &s_threads_process; + s_threads_process.m_pool_base = s_threads_exec; + s_threads_process.m_pool_rank = + thread_count - 1; // Reversed for scan-compatible reductions + s_threads_process.m_pool_size = thread_count; + s_threads_process.m_pool_fan_size = fan_size( + s_threads_process.m_pool_rank, s_threads_process.m_pool_size); + s_threads_pid[s_threads_process.m_pool_rank] = std::this_thread::get_id(); // Initial allocations: - ThreadsExec::resize_scratch(1024, 1024); + ThreadsInternal::resize_scratch(1024, 1024); } else { s_thread_pool_size[0] = 0; s_thread_pool_size[1] = 0; @@ -773,8 +619,8 @@ void ThreadsExec::initialize(int thread_count_arg) { //---------------------------------------------------------------------------- -void ThreadsExec::finalize() { - verify_is_process("ThreadsExec::finalize", false); +void ThreadsInternal::finalize() { + verify_is_process("ThreadsInternal::finalize", false); fence(); @@ -784,18 +630,18 @@ void ThreadsExec::finalize() { for (unsigned i = s_thread_pool_size[0]; begin < i--;) { if (s_threads_exec[i]) { - s_threads_exec[i]->m_pool_state = ThreadsExec::Terminating; + s_threads_exec[i]->m_pool_state = ThreadState::Terminating; - wait_yield(s_threads_process.m_pool_state, ThreadsExec::Inactive); + wait_yield(s_threads_process.m_pool_state, ThreadState::Inactive); - s_threads_process.m_pool_state = ThreadsExec::Inactive; + s_threads_process.m_pool_state = ThreadState::Inactive; } s_threads_pid[i] = std::thread::id(); } if (s_threads_process.m_pool_base) { - (&s_threads_process)->~ThreadsExec(); + (&s_threads_process)->~ThreadsInternal(); s_threads_exec[0] = nullptr; } @@ -808,15 +654,11 @@ void ThreadsExec::finalize() { s_thread_pool_size[2] = 0; // Reset master thread to run solo. - s_threads_process.m_numa_rank = 0; - s_threads_process.m_numa_core_rank = 0; - s_threads_process.m_pool_base = nullptr; - s_threads_process.m_pool_rank = 0; - s_threads_process.m_pool_size = 1; - s_threads_process.m_pool_fan_size = 0; - s_threads_process.m_pool_state = ThreadsExec::Inactive; - - Kokkos::Profiling::finalize(); + s_threads_process.m_pool_base = nullptr; + s_threads_process.m_pool_rank = 0; + s_threads_process.m_pool_size = 1; + s_threads_process.m_pool_fan_size = 0; + s_threads_process.m_pool_state = ThreadState::Inactive; } //---------------------------------------------------------------------------- @@ -836,7 +678,7 @@ int Threads::concurrency() const { return impl_thread_pool_size(0); } #endif void Threads::fence(const std::string &name) const { - Impl::ThreadsExec::internal_fence(name, Impl::fence_is_static::no); + Impl::ThreadsInternal::fence(name); } Threads &Threads::impl_instance(int) { diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_Instance.hpp similarity index 76% rename from lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp rename to lib/kokkos/core/src/Threads/Kokkos_Threads_Instance.hpp index 377e096bfb..a5eb231cb0 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_Instance.hpp @@ -14,8 +14,8 @@ // //@HEADER -#ifndef KOKKOS_THREADSEXEC_HPP -#define KOKKOS_THREADSEXEC_HPP +#ifndef KOKKOS_THREADS_INSTANCE_HPP +#define KOKKOS_THREADS_INSTANCE_HPP #include @@ -23,41 +23,25 @@ #include #include -#include - #include #include #include #include +#include +#include //---------------------------------------------------------------------------- namespace Kokkos { namespace Impl { -class ThreadsExec { +class ThreadsInternal { public: // Fan array has log_2(NT) reduction threads plus 2 scan threads // Currently limited to 16k threads. - enum { MAX_FAN_COUNT = 16 }; - enum { MAX_THREAD_COUNT = 1 << (MAX_FAN_COUNT - 2) }; - enum { VECTOR_LENGTH = 8 }; - - /** \brief States of a worker thread */ - enum { - Terminating ///< Termination in progress - , - Inactive ///< Exists, waiting for work - , - Active ///< Exists, performing work - , - Rendezvous ///< Exists, waiting in a barrier or reduce - - , - ScanCompleted, - ScanAvailable, - ReductionAvailable - }; + static constexpr int MAX_FAN_COUNT = 16; + static constexpr int MAX_THREAD_COUNT = 1 << (MAX_FAN_COUNT - 2); + static constexpr int VECTOR_LENGTH = 8; private: friend class Kokkos::Threads; @@ -67,18 +51,16 @@ class ThreadsExec { // the threads that need them. // For a simple reduction the thread location is arbitrary. - ThreadsExec *const *m_pool_base; ///< Base for pool fan-in + ThreadsInternal *const *m_pool_base; ///< Base for pool fan-in void *m_scratch; int m_scratch_reduce_end; size_t m_scratch_thread_end; - int m_numa_rank; - int m_numa_core_rank; int m_pool_rank; int m_pool_rank_rev; int m_pool_size; int m_pool_fan_size; - int volatile m_pool_state; ///< State for global synchronizations + ThreadState volatile m_pool_state; ///< State for global synchronizations // Members for dynamic scheduling // Which thread am I stealing from currently @@ -93,41 +75,36 @@ class ThreadsExec { static void global_lock(); static void global_unlock(); - static void spawn(); - static void first_touch_allocate_thread_private_scratch(ThreadsExec &, + static void first_touch_allocate_thread_private_scratch(ThreadsInternal &, const void *); - static void execute_sleep(ThreadsExec &, const void *); - ThreadsExec(const ThreadsExec &); - ThreadsExec &operator=(const ThreadsExec &); + ThreadsInternal(const ThreadsInternal &); + ThreadsInternal &operator=(const ThreadsInternal &); static void execute_resize_scratch_in_serial(); public: KOKKOS_INLINE_FUNCTION int pool_size() const { return m_pool_size; } KOKKOS_INLINE_FUNCTION int pool_rank() const { return m_pool_rank; } - KOKKOS_INLINE_FUNCTION int numa_rank() const { return m_numa_rank; } - KOKKOS_INLINE_FUNCTION int numa_core_rank() const { return m_numa_core_rank; } inline long team_work_index() const { return m_team_work_index; } - static int get_thread_count(); - static ThreadsExec *get_thread(const int init_thread_rank); + static ThreadsInternal *get_thread(const int init_thread_rank); inline void *reduce_memory() const { return m_scratch; } KOKKOS_INLINE_FUNCTION void *scratch_memory() const { return reinterpret_cast(m_scratch) + m_scratch_reduce_end; } - KOKKOS_INLINE_FUNCTION int volatile &state() { return m_pool_state; } - KOKKOS_INLINE_FUNCTION ThreadsExec *const *pool_base() const { + KOKKOS_INLINE_FUNCTION ThreadState volatile &state() { return m_pool_state; } + KOKKOS_INLINE_FUNCTION ThreadsInternal *const *pool_base() const { return m_pool_base; } static void driver(void); - ~ThreadsExec(); - ThreadsExec(); + ~ThreadsInternal(); + ThreadsInternal(); static void *resize_scratch(size_t reduce_size, size_t thread_size); @@ -143,15 +120,8 @@ class ThreadsExec { static void finalize(); - /* Given a requested team size, return valid team size */ - static unsigned team_size_valid(unsigned); - static void print_configuration(std::ostream &, const bool detail = false); - //------------------------------------ - - static void wait_yield(volatile int &, const int); - //------------------------------------ // All-thread functions: @@ -166,14 +136,14 @@ class ThreadsExec { // Fan-in reduction with highest ranking thread as the root for (int i = 0; i < m_pool_fan_size; ++i) { // Wait: Active -> Rendezvous - Impl::spinwait_while_equal( - m_pool_base[rev_rank + (1 << i)]->m_pool_state, ThreadsExec::Active); + spinwait_while_equal(m_pool_base[rev_rank + (1 << i)]->m_pool_state, + ThreadState::Active); } if (rev_rank) { - m_pool_state = ThreadsExec::Rendezvous; + m_pool_state = ThreadState::Rendezvous; // Wait: Rendezvous -> Active - Impl::spinwait_while_equal(m_pool_state, ThreadsExec::Rendezvous); + spinwait_while_equal(m_pool_state, ThreadState::Rendezvous); } else { // Root thread does the reduction and broadcast @@ -191,7 +161,7 @@ class ThreadsExec { memory_fence(); for (int rank = 0; rank < m_pool_size; ++rank) { - get_thread(rank)->m_pool_state = ThreadsExec::Active; + get_thread(rank)->m_pool_state = ThreadState::Active; } } @@ -207,21 +177,21 @@ class ThreadsExec { // Fan-in reduction with highest ranking thread as the root for (int i = 0; i < m_pool_fan_size; ++i) { // Wait: Active -> Rendezvous - Impl::spinwait_while_equal( - m_pool_base[rev_rank + (1 << i)]->m_pool_state, ThreadsExec::Active); + spinwait_while_equal(m_pool_base[rev_rank + (1 << i)]->m_pool_state, + ThreadState::Active); } if (rev_rank) { - m_pool_state = ThreadsExec::Rendezvous; + m_pool_state = ThreadState::Rendezvous; // Wait: Rendezvous -> Active - Impl::spinwait_while_equal(m_pool_state, ThreadsExec::Rendezvous); + spinwait_while_equal(m_pool_state, ThreadState::Rendezvous); } else { // Root thread does the reduction and broadcast memory_fence(); for (int rank = 0; rank < m_pool_size; ++rank) { - get_thread(rank)->m_pool_state = ThreadsExec::Active; + get_thread(rank)->m_pool_state = ThreadState::Active; } } } @@ -234,9 +204,9 @@ class ThreadsExec { const int rev_rank = m_pool_size - (m_pool_rank + 1); for (int i = 0; i < m_pool_fan_size; ++i) { - ThreadsExec &fan = *m_pool_base[rev_rank + (1 << i)]; + ThreadsInternal &fan = *m_pool_base[rev_rank + (1 << i)]; - Impl::spinwait_while_equal(fan.m_pool_state, ThreadsExec::Active); + spinwait_while_equal(fan.m_pool_state, ThreadState::Active); f.join( reinterpret_cast(reduce_memory()), @@ -265,8 +235,8 @@ class ThreadsExec { const int rev_rank = m_pool_size - (m_pool_rank + 1); for (int i = 0; i < m_pool_fan_size; ++i) { - Impl::spinwait_while_equal( - m_pool_base[rev_rank + (1 << i)]->m_pool_state, ThreadsExec::Active); + spinwait_while_equal(m_pool_base[rev_rank + (1 << i)]->m_pool_state, + ThreadState::Active); } } @@ -289,10 +259,10 @@ class ThreadsExec { //-------------------------------- // Fan-in reduction with highest ranking thread as the root for (int i = 0; i < m_pool_fan_size; ++i) { - ThreadsExec &fan = *m_pool_base[rev_rank + (1 << i)]; + ThreadsInternal &fan = *m_pool_base[rev_rank + (1 << i)]; // Wait: Active -> ReductionAvailable (or ScanAvailable) - Impl::spinwait_while_equal(fan.m_pool_state, ThreadsExec::Active); + spinwait_while_equal(fan.m_pool_state, ThreadState::Active); f.join(work_value, fan.reduce_memory()); } @@ -303,39 +273,37 @@ class ThreadsExec { if (rev_rank) { // Set: Active -> ReductionAvailable - m_pool_state = ThreadsExec::ReductionAvailable; + m_pool_state = ThreadState::ReductionAvailable; // Wait for contributing threads' scan value to be available. if ((1 << m_pool_fan_size) < (m_pool_rank + 1)) { - ThreadsExec &th = *m_pool_base[rev_rank + (1 << m_pool_fan_size)]; + ThreadsInternal &th = *m_pool_base[rev_rank + (1 << m_pool_fan_size)]; // Wait: Active -> ReductionAvailable // Wait: ReductionAvailable -> ScanAvailable - Impl::spinwait_while_equal(th.m_pool_state, ThreadsExec::Active); - Impl::spinwait_while_equal(th.m_pool_state, - ThreadsExec::ReductionAvailable); + spinwait_while_equal(th.m_pool_state, ThreadState::Active); + spinwait_while_equal(th.m_pool_state, ThreadState::ReductionAvailable); f.join(work_value + count, ((scalar_type *)th.reduce_memory()) + count); } // This thread has completed inclusive scan // Set: ReductionAvailable -> ScanAvailable - m_pool_state = ThreadsExec::ScanAvailable; + m_pool_state = ThreadState::ScanAvailable; // Wait for all threads to complete inclusive scan // Wait: ScanAvailable -> Rendezvous - Impl::spinwait_while_equal(m_pool_state, ThreadsExec::ScanAvailable); + spinwait_while_equal(m_pool_state, ThreadState::ScanAvailable); } //-------------------------------- for (int i = 0; i < m_pool_fan_size; ++i) { - ThreadsExec &fan = *m_pool_base[rev_rank + (1 << i)]; + ThreadsInternal &fan = *m_pool_base[rev_rank + (1 << i)]; // Wait: ReductionAvailable -> ScanAvailable - Impl::spinwait_while_equal(fan.m_pool_state, - ThreadsExec::ReductionAvailable); + spinwait_while_equal(fan.m_pool_state, ThreadState::ReductionAvailable); // Set: ScanAvailable -> Rendezvous - fan.m_pool_state = ThreadsExec::Rendezvous; + fan.m_pool_state = ThreadState::Rendezvous; } // All threads have completed the inclusive scan. @@ -346,7 +314,7 @@ class ThreadsExec { if ((rev_rank + 1) < m_pool_size) { // Exclusive scan: copy the previous thread's inclusive scan value - ThreadsExec &th = *m_pool_base[rev_rank + 1]; // Not the root thread + ThreadsInternal &th = *m_pool_base[rev_rank + 1]; // Not the root thread const scalar_type *const src_value = ((scalar_type *)th.reduce_memory()) + count; @@ -362,19 +330,18 @@ class ThreadsExec { // Wait for all threads to copy previous thread's inclusive scan value // Wait for all threads: Rendezvous -> ScanCompleted for (int i = 0; i < m_pool_fan_size; ++i) { - Impl::spinwait_while_equal( - m_pool_base[rev_rank + (1 << i)]->m_pool_state, - ThreadsExec::Rendezvous); + spinwait_while_equal(m_pool_base[rev_rank + (1 << i)]->m_pool_state, + ThreadState::Rendezvous); } if (rev_rank) { // Set: ScanAvailable -> ScanCompleted - m_pool_state = ThreadsExec::ScanCompleted; + m_pool_state = ThreadState::ScanCompleted; // Wait: ScanCompleted -> Active - Impl::spinwait_while_equal(m_pool_state, ThreadsExec::ScanCompleted); + spinwait_while_equal(m_pool_state, ThreadState::ScanCompleted); } // Set: ScanCompleted -> Active for (int i = 0; i < m_pool_fan_size; ++i) { - m_pool_base[rev_rank + (1 << i)]->m_pool_state = ThreadsExec::Active; + m_pool_base[rev_rank + (1 << i)]->m_pool_state = ThreadState::Active; } } @@ -391,8 +358,8 @@ class ThreadsExec { // Fan-in reduction with highest ranking thread as the root for (int i = 0; i < m_pool_fan_size; ++i) { // Wait: Active -> Rendezvous - Impl::spinwait_while_equal( - m_pool_base[rev_rank + (1 << i)]->m_pool_state, ThreadsExec::Active); + spinwait_while_equal(m_pool_base[rev_rank + (1 << i)]->m_pool_state, + ThreadState::Active); } for (unsigned i = 0; i < count; ++i) { @@ -400,9 +367,9 @@ class ThreadsExec { } if (rev_rank) { - m_pool_state = ThreadsExec::Rendezvous; + m_pool_state = ThreadState::Rendezvous; // Wait: Rendezvous -> Active - Impl::spinwait_while_equal(m_pool_state, ThreadsExec::Rendezvous); + spinwait_while_equal(m_pool_state, ThreadState::Rendezvous); } else { // Root thread does the thread-scan before releasing threads @@ -424,7 +391,7 @@ class ThreadsExec { } for (int i = 0; i < m_pool_fan_size; ++i) { - m_pool_base[rev_rank + (1 << i)]->m_pool_state = ThreadsExec::Active; + m_pool_base[rev_rank + (1 << i)]->m_pool_state = ThreadState::Active; } } @@ -433,18 +400,14 @@ class ThreadsExec { * complete and release the Threads device. * Acquire the Threads device and start this functor. */ - static void start(void (*)(ThreadsExec &, const void *), const void *); + static void start(void (*)(ThreadsInternal &, const void *), const void *); - static int in_parallel(); +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 + KOKKOS_DEPRECATED static int in_parallel(); +#endif static void fence(); static void fence(const std::string &); - static void internal_fence( - Impl::fence_is_static is_static = Impl::fence_is_static::yes); - static void internal_fence( - const std::string &, - Impl::fence_is_static is_static = Impl::fence_is_static::yes); - static bool sleep(); - static bool wake(); + static void internal_fence(); /* Dynamic Scheduling related functionality */ // Initialize the work range for this thread @@ -583,30 +546,38 @@ class ThreadsExec { namespace Kokkos { -inline int Threads::in_parallel() { return Impl::ThreadsExec::in_parallel(); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 +KOKKOS_DEPRECATED inline int Threads::in_parallel() { + return Impl::ThreadsInternal::in_parallel(); +} +#endif inline int Threads::impl_is_initialized() { - return Impl::ThreadsExec::is_initialized(); + return Impl::ThreadsInternal::is_initialized(); } inline void Threads::impl_initialize(InitializationSettings const &settings) { - Impl::ThreadsExec::initialize( + Impl::ThreadsInternal::initialize( settings.has_num_threads() ? settings.get_num_threads() : -1); } -inline void Threads::impl_finalize() { Impl::ThreadsExec::finalize(); } +inline void Threads::impl_finalize() { Impl::ThreadsInternal::finalize(); } inline void Threads::print_configuration(std::ostream &os, bool verbose) const { os << "Host Parallel Execution Space:\n"; os << " KOKKOS_ENABLE_THREADS: yes\n"; os << "\nThreads Runtime Configuration:\n"; - Impl::ThreadsExec::print_configuration(os, verbose); + Impl::ThreadsInternal::print_configuration(os, verbose); } inline void Threads::impl_static_fence(const std::string &name) { - Impl::ThreadsExec::internal_fence(name, Impl::fence_is_static::yes); + Kokkos::Tools::Experimental::Impl::profile_fence_event( + name, + Kokkos::Tools::Experimental::SpecialSynchronizationCases:: + GlobalDeviceSynchronization, + Impl::ThreadsInternal::internal_fence); } } /* namespace Kokkos */ -#endif /* #define KOKKOS_THREADSEXEC_HPP */ +#endif diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_MDRange.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_MDRange.hpp index 0828f26299..59577609ab 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_MDRange.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_MDRange.hpp @@ -46,54 +46,54 @@ class ParallelFor, } } - static void exec(ThreadsExec &exec, const void *arg) { - exec_schedule(exec, arg); + static void exec(ThreadsInternal &instance, const void *arg) { + exec_schedule(instance, arg); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelFor &self = *((const ParallelFor *)arg); auto const num_tiles = self.m_iter.m_rp.m_num_tiles; - WorkRange range(Policy(0, num_tiles).set_chunk_size(1), exec.pool_rank(), - exec.pool_size()); + WorkRange range(Policy(0, num_tiles).set_chunk_size(1), + instance.pool_rank(), instance.pool_size()); self.exec_range(range.begin(), range.end()); - exec.fan_in(); + instance.fan_in(); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelFor &self = *((const ParallelFor *)arg); auto const num_tiles = self.m_iter.m_rp.m_num_tiles; - WorkRange range(Policy(0, num_tiles).set_chunk_size(1), exec.pool_rank(), - exec.pool_size()); + WorkRange range(Policy(0, num_tiles).set_chunk_size(1), + instance.pool_rank(), instance.pool_size()); - exec.set_work_range(range.begin(), range.end(), 1); - exec.reset_steal_target(); - exec.barrier(); + instance.set_work_range(range.begin(), range.end(), 1); + instance.reset_steal_target(); + instance.barrier(); - long work_index = exec.get_work_index(); + long work_index = instance.get_work_index(); while (work_index != -1) { const Member begin = static_cast(work_index); const Member end = begin + 1 < num_tiles ? begin + 1 : num_tiles; self.exec_range(begin, end); - work_index = exec.get_work_index(); + work_index = instance.get_work_index(); } - exec.fan_in(); + instance.fan_in(); } public: inline void execute() const { - ThreadsExec::start(&ParallelFor::exec, this); - ThreadsExec::fence(); + ThreadsInternal::start(&ParallelFor::exec, this); + ThreadsInternal::fence(); } ParallelFor(const FunctorType &arg_functor, const MDRangePolicy &arg_policy) diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Range.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Range.hpp index 3698416ef1..4a89c4fad8 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Range.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Range.hpp @@ -59,37 +59,37 @@ class ParallelFor, } } - static void exec(ThreadsExec &exec, const void *arg) { - exec_schedule(exec, arg); + static void exec(ThreadsInternal &instance, const void *arg) { + exec_schedule(instance, arg); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelFor &self = *((const ParallelFor *)arg); - WorkRange range(self.m_policy, exec.pool_rank(), exec.pool_size()); + WorkRange range(self.m_policy, instance.pool_rank(), instance.pool_size()); ParallelFor::template exec_range(self.m_functor, range.begin(), range.end()); - exec.fan_in(); + instance.fan_in(); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelFor &self = *((const ParallelFor *)arg); - WorkRange range(self.m_policy, exec.pool_rank(), exec.pool_size()); + WorkRange range(self.m_policy, instance.pool_rank(), instance.pool_size()); - exec.set_work_range(range.begin() - self.m_policy.begin(), - range.end() - self.m_policy.begin(), - self.m_policy.chunk_size()); - exec.reset_steal_target(); - exec.barrier(); + instance.set_work_range(range.begin() - self.m_policy.begin(), + range.end() - self.m_policy.begin(), + self.m_policy.chunk_size()); + instance.reset_steal_target(); + instance.barrier(); - long work_index = exec.get_work_index(); + long work_index = instance.get_work_index(); while (work_index != -1) { const Member begin = @@ -100,16 +100,16 @@ class ParallelFor, ? begin + self.m_policy.chunk_size() : self.m_policy.end(); ParallelFor::template exec_range(self.m_functor, begin, end); - work_index = exec.get_work_index(); + work_index = instance.get_work_index(); } - exec.fan_in(); + instance.fan_in(); } public: inline void execute() const { - ThreadsExec::start(&ParallelFor::exec, this); - ThreadsExec::fence(); + ThreadsInternal::start(&ParallelFor::exec, this); + ThreadsInternal::fence(); } ParallelFor(const FunctorType &arg_functor, const Policy &arg_policy) diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Team.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Team.hpp index 36404857a2..f927d7c6a6 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Team.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelFor_Team.hpp @@ -73,14 +73,14 @@ class ParallelFor, } } - static void exec(ThreadsExec &exec, const void *arg) { + static void exec(ThreadsInternal &instance, const void *arg) { const ParallelFor &self = *((const ParallelFor *)arg); ParallelFor::exec_team( - self.m_functor, Member(&exec, self.m_policy, self.m_shared)); + self.m_functor, Member(&instance, self.m_policy, self.m_shared)); - exec.barrier(); - exec.fan_in(); + instance.barrier(); + instance.fan_in(); } template Policy fix_policy(Policy policy) { @@ -96,12 +96,12 @@ class ParallelFor, public: inline void execute() const { - ThreadsExec::resize_scratch( + ThreadsInternal::resize_scratch( 0, Policy::member_type::team_reduce_size() + m_shared); - ThreadsExec::start(&ParallelFor::exec, this); + ThreadsInternal::start(&ParallelFor::exec, this); - ThreadsExec::fence(); + ThreadsInternal::fence(); } ParallelFor(const FunctorType &arg_functor, const Policy &arg_policy) diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_MDRange.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_MDRange.hpp index 3d06379480..fa63215a9e 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_MDRange.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_MDRange.hpp @@ -54,67 +54,67 @@ class ParallelReduce(exec, arg); + static void exec(ThreadsInternal &instance, const void *arg) { + exec_schedule(instance, arg); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelReduce &self = *((const ParallelReduce *)arg); const auto num_tiles = self.m_iter.m_rp.m_num_tiles; const WorkRange range(Policy(0, num_tiles).set_chunk_size(1), - exec.pool_rank(), exec.pool_size()); + instance.pool_rank(), instance.pool_size()); const ReducerType &reducer = self.m_iter.m_func.get_reducer(); self.exec_range( range.begin(), range.end(), - reducer.init(static_cast(exec.reduce_memory()))); + reducer.init(static_cast(instance.reduce_memory()))); - exec.fan_in_reduce(reducer); + instance.fan_in_reduce(reducer); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelReduce &self = *((const ParallelReduce *)arg); const auto num_tiles = self.m_iter.m_rp.m_num_tiles; const WorkRange range(Policy(0, num_tiles).set_chunk_size(1), - exec.pool_rank(), exec.pool_size()); + instance.pool_rank(), instance.pool_size()); - exec.set_work_range(range.begin(), range.end(), 1); - exec.reset_steal_target(); - exec.barrier(); + instance.set_work_range(range.begin(), range.end(), 1); + instance.reset_steal_target(); + instance.barrier(); - long work_index = exec.get_work_index(); + long work_index = instance.get_work_index(); const ReducerType &reducer = self.m_iter.m_func.get_reducer(); - reference_type update = - self.m_reducer.init(static_cast(exec.reduce_memory())); + reference_type update = self.m_reducer.init( + static_cast(instance.reduce_memory())); while (work_index != -1) { const Member begin = static_cast(work_index); const Member end = begin + 1 < num_tiles ? begin + 1 : num_tiles; self.exec_range(begin, end, update); - work_index = exec.get_work_index(); + work_index = instance.get_work_index(); } - exec.fan_in_reduce(self.m_reducer); + instance.fan_in_reduce(self.m_reducer); } public: inline void execute() const { const ReducerType &reducer = m_iter.m_func.get_reducer(); - ThreadsExec::resize_scratch(reducer.value_size(), 0); + ThreadsInternal::resize_scratch(reducer.value_size(), 0); - ThreadsExec::start(&ParallelReduce::exec, this); + ThreadsInternal::start(&ParallelReduce::exec, this); - ThreadsExec::fence(); + ThreadsInternal::fence(); if (m_result_ptr) { const pointer_type data = - (pointer_type)ThreadsExec::root_reduce_scratch(); + (pointer_type)ThreadsInternal::root_reduce_scratch(); const unsigned n = reducer.value_count(); for (unsigned i = 0; i < n; ++i) { diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Range.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Range.hpp index 5fa97b403c..bf4c2a532a 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Range.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Range.hpp @@ -68,42 +68,44 @@ class ParallelReduce, } } - static void exec(ThreadsExec &exec, const void *arg) { - exec_schedule(exec, arg); + static void exec(ThreadsInternal &instance, const void *arg) { + exec_schedule(instance, arg); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelReduce &self = *((const ParallelReduce *)arg); - const WorkRange range(self.m_policy, exec.pool_rank(), exec.pool_size()); + const WorkRange range(self.m_policy, instance.pool_rank(), + instance.pool_size()); const ReducerType &reducer = self.m_functor_reducer.get_reducer(); ParallelReduce::template exec_range( self.m_functor_reducer.get_functor(), range.begin(), range.end(), - reducer.init(static_cast(exec.reduce_memory()))); + reducer.init(static_cast(instance.reduce_memory()))); - exec.fan_in_reduce(reducer); + instance.fan_in_reduce(reducer); } template static std::enable_if_t::value> - exec_schedule(ThreadsExec &exec, const void *arg) { + exec_schedule(ThreadsInternal &instance, const void *arg) { const ParallelReduce &self = *((const ParallelReduce *)arg); - const WorkRange range(self.m_policy, exec.pool_rank(), exec.pool_size()); + const WorkRange range(self.m_policy, instance.pool_rank(), + instance.pool_size()); - exec.set_work_range(range.begin() - self.m_policy.begin(), - range.end() - self.m_policy.begin(), - self.m_policy.chunk_size()); - exec.reset_steal_target(); - exec.barrier(); + instance.set_work_range(range.begin() - self.m_policy.begin(), + range.end() - self.m_policy.begin(), + self.m_policy.chunk_size()); + instance.reset_steal_target(); + instance.barrier(); - long work_index = exec.get_work_index(); + long work_index = instance.get_work_index(); const ReducerType &reducer = self.m_functor_reducer.get_reducer(); reference_type update = - reducer.init(static_cast(exec.reduce_memory())); + reducer.init(static_cast(instance.reduce_memory())); while (work_index != -1) { const Member begin = static_cast(work_index) * self.m_policy.chunk_size() + @@ -114,10 +116,10 @@ class ParallelReduce, : self.m_policy.end(); ParallelReduce::template exec_range( self.m_functor_reducer.get_functor(), begin, end, update); - work_index = exec.get_work_index(); + work_index = instance.get_work_index(); } - exec.fan_in_reduce(reducer); + instance.fan_in_reduce(reducer); } public: @@ -130,15 +132,15 @@ class ParallelReduce, reducer.final(m_result_ptr); } } else { - ThreadsExec::resize_scratch(reducer.value_size(), 0); + ThreadsInternal::resize_scratch(reducer.value_size(), 0); - ThreadsExec::start(&ParallelReduce::exec, this); + ThreadsInternal::start(&ParallelReduce::exec, this); - ThreadsExec::fence(); + ThreadsInternal::fence(); if (m_result_ptr) { const pointer_type data = - (pointer_type)ThreadsExec::root_reduce_scratch(); + (pointer_type)ThreadsInternal::root_reduce_scratch(); const unsigned n = reducer.value_count(); for (unsigned i = 0; i < n; ++i) { diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Team.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Team.hpp index c4b6100a9d..4db310701f 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Team.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_ParallelReduce_Team.hpp @@ -58,16 +58,16 @@ class ParallelReduce( self.m_functor_reducer.get_functor(), - Member(&exec, self.m_policy, self.m_shared), + Member(&instance, self.m_policy, self.m_shared), self.m_functor_reducer.get_reducer().init( - static_cast(exec.reduce_memory()))); + static_cast(instance.reduce_memory()))); - exec.fan_in_reduce(self.m_functor_reducer.get_reducer()); + instance.fan_in_reduce(self.m_functor_reducer.get_reducer()); } public: @@ -80,17 +80,17 @@ class ParallelReduce, } } - static void exec(ThreadsExec &exec, const void *arg) { + static void exec(ThreadsInternal &instance, const void *arg) { const ParallelScan &self = *((const ParallelScan *)arg); - const WorkRange range(self.m_policy, exec.pool_rank(), exec.pool_size()); + const WorkRange range(self.m_policy, instance.pool_rank(), + instance.pool_size()); typename Analysis::Reducer final_reducer(self.m_functor); reference_type update = - final_reducer.init(static_cast(exec.reduce_memory())); + final_reducer.init(static_cast(instance.reduce_memory())); ParallelScan::template exec_range(self.m_functor, range.begin(), range.end(), update, false); - // exec.template scan_large( final_reducer ); - exec.scan_small(final_reducer); + instance.scan_small(final_reducer); ParallelScan::template exec_range(self.m_functor, range.begin(), range.end(), update, true); - exec.fan_in(); + instance.fan_in(); } public: inline void execute() const { - ThreadsExec::resize_scratch(2 * Analysis::value_size(m_functor), 0); - ThreadsExec::start(&ParallelScan::exec, this); - ThreadsExec::fence(); + ThreadsInternal::resize_scratch(2 * Analysis::value_size(m_functor), 0); + ThreadsInternal::start(&ParallelScan::exec, this); + ThreadsInternal::fence(); } ParallelScan(const FunctorType &arg_functor, const Policy &arg_policy) @@ -145,37 +145,37 @@ class ParallelScanWithTotal, } } - static void exec(ThreadsExec &exec, const void *arg) { + static void exec(ThreadsInternal &instance, const void *arg) { const ParallelScanWithTotal &self = *((const ParallelScanWithTotal *)arg); - const WorkRange range(self.m_policy, exec.pool_rank(), exec.pool_size()); + const WorkRange range(self.m_policy, instance.pool_rank(), + instance.pool_size()); typename Analysis::Reducer final_reducer(self.m_functor); reference_type update = - final_reducer.init(static_cast(exec.reduce_memory())); + final_reducer.init(static_cast(instance.reduce_memory())); ParallelScanWithTotal::template exec_range( self.m_functor, range.begin(), range.end(), update, false); - // exec.template scan_large(final_reducer); - exec.scan_small(final_reducer); + instance.scan_small(final_reducer); ParallelScanWithTotal::template exec_range( self.m_functor, range.begin(), range.end(), update, true); - exec.fan_in(); + instance.fan_in(); - if (exec.pool_rank() == exec.pool_size() - 1) { + if (instance.pool_rank() == instance.pool_size() - 1) { *self.m_result_ptr = update; } } public: inline void execute() const { - ThreadsExec::resize_scratch(2 * Analysis::value_size(m_functor), 0); - ThreadsExec::start(&ParallelScanWithTotal::exec, this); - ThreadsExec::fence(); + ThreadsInternal::resize_scratch(2 * Analysis::value_size(m_functor), 0); + ThreadsInternal::start(&ParallelScanWithTotal::exec, this); + ThreadsInternal::fence(); } template diff --git a/lib/kokkos/core/src/impl/Kokkos_Spinwait.cpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_Spinwait.cpp similarity index 90% rename from lib/kokkos/core/src/impl/Kokkos_Spinwait.cpp rename to lib/kokkos/core/src/Threads/Kokkos_Threads_Spinwait.cpp index 0a7eda29bc..3df9dc07bf 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Spinwait.cpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_Spinwait.cpp @@ -21,7 +21,7 @@ #include #include -#include +#include #include #include @@ -108,5 +108,15 @@ void host_thread_yield(const uint32_t i, const WaitMode mode) { #endif /* defined( KOKKOS_ENABLE_ASM ) */ } +void spinwait_while_equal(ThreadState const volatile& flag, + ThreadState const value) { + Kokkos::store_fence(); + uint32_t i = 0; + while (value == flag) { + host_thread_yield(++i, WaitMode::ACTIVE); + } + Kokkos::load_fence(); +} + } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Swap.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_Spinwait.hpp similarity index 52% rename from lib/kokkos/algorithms/src/std_algorithms/Kokkos_Swap.hpp rename to lib/kokkos/core/src/Threads/Kokkos_Threads_Spinwait.hpp index acd2a572c8..b98b6dbb73 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/Kokkos_Swap.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_Spinwait.hpp @@ -14,28 +14,30 @@ // //@HEADER -#ifndef KOKKOS_STD_ALGORITHMS_SWAP_HPP -#define KOKKOS_STD_ALGORITHMS_SWAP_HPP +#ifndef KOKKOS_THREADS_SPINWAIT_HPP +#define KOKKOS_THREADS_SPINWAIT_HPP -#include +#include + +#include namespace Kokkos { -namespace Experimental { +namespace Impl { -// swap -template -KOKKOS_INLINE_FUNCTION void swap(T& a, T& b) noexcept { - static_assert( - std::is_move_assignable::value && std::is_move_constructible::value, - "Kokkos::Experimental::swap arguments must be move assignable " - "and move constructible"); +enum class WaitMode : int { + ACTIVE // Used for tight loops to keep threads active longest + , + PASSIVE // Used to quickly yield the thread to quite down the system + , + ROOT // Never sleep or yield the root thread +}; - T tmp = std::move(a); - a = std::move(b); - b = std::move(tmp); -} +void host_thread_yield(const uint32_t i, const WaitMode mode); -} // namespace Experimental +void spinwait_while_equal(ThreadState const volatile& flag, + ThreadState const value); + +} // namespace Impl } // namespace Kokkos #endif diff --git a/lib/kokkos/core/src/fwd/Kokkos_Fwd_HBWSpace.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_State.hpp similarity index 59% rename from lib/kokkos/core/src/fwd/Kokkos_Fwd_HBWSpace.hpp rename to lib/kokkos/core/src/Threads/Kokkos_Threads_State.hpp index 21ba7fad01..148e9aa4e0 100644 --- a/lib/kokkos/core/src/fwd/Kokkos_Fwd_HBWSpace.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_State.hpp @@ -14,16 +14,26 @@ // //@HEADER -#ifndef KOKKOS_HBWSPACE_FWD_HPP_ -#define KOKKOS_HBWSPACE_FWD_HPP_ +#ifndef KOKKOS_THREADS_STATE_HPP +#define KOKKOS_THREADS_STATE_HPP -#ifdef KOKKOS_ENABLE_HBWSPACE namespace Kokkos { - -namespace Experimental { -class HBWSpace; /// Memory space for hbw_malloc from memkind (e.g. for KNL - /// processor) -} // namespace Experimental +namespace Impl { +/** \brief States of a worker thread */ +enum class ThreadState { + Terminating ///< Termination in progress + , + Inactive ///< Exists, waiting for work + , + Active ///< Exists, performing work + , + Rendezvous ///< Exists, waiting in a barrier or reduce + , + ScanCompleted, + ScanAvailable, + ReductionAvailable +}; +} // namespace Impl } // namespace Kokkos -#endif + #endif diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_Team.hpp similarity index 95% rename from lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp rename to lib/kokkos/core/src/Threads/Kokkos_Threads_Team.hpp index b1cadc7c48..fd0f221365 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_Team.hpp @@ -22,10 +22,11 @@ #include #include -#include #include #include +#include +#include //---------------------------------------------------------------------------- @@ -50,8 +51,8 @@ class ThreadsExecTeamMember { private: using space = execution_space::scratch_memory_space; - ThreadsExec* const m_exec; - ThreadsExec* const* m_team_base; ///< Base for team fan-in + ThreadsInternal* const m_instance; + ThreadsInternal* const* m_team_base; ///< Base for team fan-in space m_team_shared; size_t m_team_shared_size; int m_team_size; @@ -84,14 +85,13 @@ class ThreadsExecTeamMember { for (n = 1; (!(m_team_rank_rev & n)) && ((j = m_team_rank_rev + n) < m_team_size); n <<= 1) { - Impl::spinwait_while_equal(m_team_base[j]->state(), - ThreadsExec::Active); + spinwait_while_equal(m_team_base[j]->state(), ThreadState::Active); } // If not root then wait for release if (m_team_rank_rev) { - m_exec->state() = ThreadsExec::Rendezvous; - Impl::spinwait_while_equal(m_exec->state(), ThreadsExec::Rendezvous); + m_instance->state() = ThreadState::Rendezvous; + spinwait_while_equal(m_instance->state(), ThreadState::Rendezvous); } return !m_team_rank_rev; @@ -102,7 +102,7 @@ class ThreadsExecTeamMember { for (n = 1; (!(m_team_rank_rev & n)) && ((j = m_team_rank_rev + n) < m_team_size); n <<= 1) { - m_team_base[j]->state() = ThreadsExec::Active; + m_team_base[j]->state() = ThreadState::Active; } } @@ -188,10 +188,10 @@ class ThreadsExecTeamMember { using type = typename if_c::type; - if (nullptr == m_exec) return value; + if (m_instance == nullptr) return value; if (team_rank() != team_size() - 1) * - ((volatile type*)m_exec->scratch_memory()) = value; + ((volatile type*)m_instance->scratch_memory()) = value; memory_fence(); @@ -229,9 +229,9 @@ class ThreadsExecTeamMember { using type = typename if_c::type; - if (nullptr == m_exec) return; + if (m_instance == nullptr) return; - type* const local_value = ((type*)m_exec->scratch_memory()); + type* const local_value = ((type*)m_instance->scratch_memory()); // Set this thread's contribution if (team_rank() != team_size() - 1) { *local_value = contribution; } @@ -285,9 +285,9 @@ class ThreadsExecTeamMember { using type = typename if_c::type; - if (nullptr == m_exec) return type(0); + if (m_instance == nullptr) return type(0); - volatile type* const work_value = ((type*)m_exec->scratch_memory()); + volatile type* const work_value = ((type*)m_instance->scratch_memory()); *work_value = value; @@ -342,10 +342,10 @@ class ThreadsExecTeamMember { template ThreadsExecTeamMember( - Impl::ThreadsExec* exec, + Impl::ThreadsInternal* instance, const TeamPolicyInternal& team, const size_t shared_size) - : m_exec(exec), + : m_instance(instance), m_team_base(nullptr), m_team_shared(nullptr, 0), m_team_shared_size(shared_size), @@ -361,9 +361,11 @@ class ThreadsExecTeamMember { if (team.league_size()) { // Execution is using device-team interface: - const int pool_rank_rev = m_exec->pool_size() - (m_exec->pool_rank() + 1); + const int pool_rank_rev = + m_instance->pool_size() - (m_instance->pool_rank() + 1); const int team_rank_rev = pool_rank_rev % team.team_alloc(); - const size_t pool_league_size = m_exec->pool_size() / team.team_alloc(); + const size_t pool_league_size = + m_instance->pool_size() / team.team_alloc(); const size_t pool_league_rank_rev = pool_rank_rev / team.team_alloc(); if (pool_league_rank_rev >= pool_league_size) { m_invalid_thread = 1; @@ -372,7 +374,7 @@ class ThreadsExecTeamMember { const size_t pool_league_rank = pool_league_size - (pool_league_rank_rev + 1); - const int pool_num_teams = m_exec->pool_size() / team.team_alloc(); + const int pool_num_teams = m_instance->pool_size() / team.team_alloc(); const int chunk_size = team.chunk_size() > 0 ? team.chunk_size() : team.team_iter(); const int chunks_per_team = @@ -387,8 +389,8 @@ class ThreadsExecTeamMember { if ((team.team_alloc() > size_t(m_team_size)) ? (team_rank_rev >= m_team_size) - : (m_exec->pool_size() - pool_num_teams * m_team_size > - m_exec->pool_rank())) + : (m_instance->pool_size() - pool_num_teams * m_team_size > + m_instance->pool_rank())) m_invalid_thread = 1; else m_invalid_thread = 0; @@ -398,7 +400,7 @@ class ThreadsExecTeamMember { if (team_rank_rev < team.team_size() && !m_invalid_thread) { m_team_base = - m_exec->pool_base() + team.team_alloc() * pool_league_rank_rev; + m_instance->pool_base() + team.team_alloc() * pool_league_rank_rev; m_team_size = team.team_size(); m_team_rank = team.team_size() - (team_rank_rev + 1); m_team_rank_rev = team_rank_rev; @@ -413,13 +415,13 @@ class ThreadsExecTeamMember { } if ((m_team_rank_rev == 0) && (m_invalid_thread == 0)) { - m_exec->set_work_range(m_league_rank, m_league_end, m_chunk_size); - m_exec->reset_steal_target(m_team_size); + m_instance->set_work_range(m_league_rank, m_league_end, m_chunk_size); + m_instance->reset_steal_target(m_team_size); } if (std::is_same::schedule_type::type, Kokkos::Dynamic>::value) { - m_exec->barrier(); + m_instance->barrier(); } } else { m_invalid_thread = 1; @@ -427,7 +429,7 @@ class ThreadsExecTeamMember { } ThreadsExecTeamMember() - : m_exec(nullptr), + : m_instance(nullptr), m_team_base(nullptr), m_team_shared(nullptr, 0), m_team_shared_size(0), @@ -442,8 +444,8 @@ class ThreadsExecTeamMember { m_invalid_thread(0), m_team_alloc(0) {} - inline ThreadsExec& threads_exec_team_base() const { - return m_team_base ? **m_team_base : *m_exec; + inline ThreadsInternal& threads_exec_team_base() const { + return m_team_base ? **m_team_base : *m_instance; } bool valid_static() const { return m_league_rank < m_league_end; } @@ -999,8 +1001,10 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( lambda(i, scan_val, false); } + auto& team_member = loop_bounds.thread; + // 'scan_val' output is the exclusive prefix sum - scan_val = loop_bounds.thread.team_scan(scan_val); + scan_val = team_member.team_scan(scan_val); #ifdef KOKKOS_ENABLE_PRAGMA_IVDEP #pragma ivdep @@ -1010,6 +1014,8 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( lambda(i, scan_val, true); } + team_member.team_broadcast(scan_val, team_member.team_size() - 1); + return_val = scan_val; } diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_WorkGraphPolicy.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_WorkGraphPolicy.hpp index d4ce697548..c88d66db5f 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_WorkGraphPolicy.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_WorkGraphPolicy.hpp @@ -18,7 +18,7 @@ #define KOKKOS_THREADS_WORKGRAPHPOLICY_HPP #include -#include +#include namespace Kokkos { namespace Impl { @@ -61,16 +61,17 @@ class ParallelFor, } } - static inline void thread_main(ThreadsExec& exec, const void* arg) noexcept { + static inline void thread_main(ThreadsInternal& instance, + const void* arg) noexcept { const Self& self = *(static_cast(arg)); self.exec_one_thread(); - exec.fan_in(); + instance.fan_in(); } public: inline void execute() { - ThreadsExec::start(&Self::thread_main, this); - ThreadsExec::fence(); + ThreadsInternal::start(&Self::thread_main, this); + ThreadsInternal::fence(); } inline ParallelFor(const FunctorType& arg_functor, const Policy& arg_policy) diff --git a/lib/kokkos/core/src/decl/Kokkos_Declare_HBWSpace.hpp b/lib/kokkos/core/src/decl/Kokkos_Declare_HBWSpace.hpp deleted file mode 100644 index 1328c93135..0000000000 --- a/lib/kokkos/core/src/decl/Kokkos_Declare_HBWSpace.hpp +++ /dev/null @@ -1,24 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#ifndef KOKKOS_DECLARE_HBWSPACE_HPP -#define KOKKOS_DECLARE_HBWSPACE_HPP - -#ifdef KOKKOS_ENABLE_HBWSPACE -#include -#endif - -#endif diff --git a/lib/kokkos/core/src/decl/Kokkos_Declare_HIP.hpp b/lib/kokkos/core/src/decl/Kokkos_Declare_HIP.hpp index e115f7051f..cf405e57b8 100644 --- a/lib/kokkos/core/src/decl/Kokkos_Declare_HIP.hpp +++ b/lib/kokkos/core/src/decl/Kokkos_Declare_HIP.hpp @@ -25,9 +25,13 @@ #include #include #include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include #include #include #include diff --git a/lib/kokkos/core/src/decl/Kokkos_Declare_THREADS.hpp b/lib/kokkos/core/src/decl/Kokkos_Declare_THREADS.hpp index f5cbc0c1d1..4d7caec6f5 100644 --- a/lib/kokkos/core/src/decl/Kokkos_Declare_THREADS.hpp +++ b/lib/kokkos/core/src/decl/Kokkos_Declare_THREADS.hpp @@ -19,7 +19,7 @@ #if defined(KOKKOS_ENABLE_THREADS) #include -#include +#include #include #include #include @@ -28,7 +28,7 @@ #include #include #include -#include +#include #include #endif diff --git a/lib/kokkos/core/src/impl/Kokkos_Core.cpp b/lib/kokkos/core/src/impl/Kokkos_Core.cpp index 5c182db566..4a69652616 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Core.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_Core.cpp @@ -90,8 +90,6 @@ void combine(Kokkos::InitializationSettings& out, KOKKOS_IMPL_COMBINE_SETTING(num_threads); KOKKOS_IMPL_COMBINE_SETTING(map_device_id_by); KOKKOS_IMPL_COMBINE_SETTING(device_id); - KOKKOS_IMPL_COMBINE_SETTING(num_devices); - KOKKOS_IMPL_COMBINE_SETTING(skip_device); KOKKOS_IMPL_COMBINE_SETTING(disable_warnings); KOKKOS_IMPL_COMBINE_SETTING(tune_internals); KOKKOS_IMPL_COMBINE_SETTING(tools_help); @@ -131,11 +129,15 @@ void combine(Kokkos::Tools::InitArguments& out, int get_device_count() { #if defined(KOKKOS_ENABLE_CUDA) - return Kokkos::Cuda::detect_device_count(); + int count; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceCount(&count)); + return count; #elif defined(KOKKOS_ENABLE_HIP) - return Kokkos::HIP::detect_device_count(); + int count; + KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceCount(&count)); + return count; #elif defined(KOKKOS_ENABLE_SYCL) - return sycl::device::get_devices(sycl::info::device_type::gpu).size(); + return Kokkos::Experimental::Impl::get_sycl_devices().size(); #elif defined(KOKKOS_ENABLE_OPENACC) return acc_get_num_devices( Kokkos::Experimental::Impl::OpenACC_Traits::dev_type); @@ -165,20 +167,43 @@ bool is_valid_map_device_id_by(std::string const& x) { } // namespace +std::vector const& Kokkos::Impl::get_visible_devices() { + static auto devices = get_visible_devices(get_device_count()); + return devices; +} + [[nodiscard]] int Kokkos::device_id() noexcept { #if defined(KOKKOS_ENABLE_CUDA) - return Cuda().cuda_device(); + int device = Cuda().cuda_device(); #elif defined(KOKKOS_ENABLE_HIP) - return HIP().hip_device(); + int device = HIP().hip_device(); #elif defined(KOKKOS_ENABLE_OPENACC) - return Experimental::OpenACC().acc_device_number(); + int device = Experimental::OpenACC().acc_device_number(); #elif defined(KOKKOS_ENABLE_OPENMPTARGET) - return omp_get_default_device(); // FIXME_OPENMPTARGET + int device = omp_get_default_device(); // FIXME_OPENMPTARGET #elif defined(KOKKOS_ENABLE_SYCL) - return Experimental::Impl::SYCLInternal::m_syclDev; + int device = Experimental::Impl::SYCLInternal::m_syclDev; #else - return -1; + int device = -1; + return device; #endif + auto const& visible_devices = Impl::get_visible_devices(); + for (std::size_t i = 0; i < visible_devices.size(); ++i) { + if (visible_devices[i] == device) { + return i; + } + } + Kokkos::abort("Unexpected error: cannot determine device id"); + return -1; +} + +[[nodiscard]] int Kokkos::num_devices() noexcept { + if constexpr (std::is_same_v) { + return -1; // no GPU backend enabled + } else { + return Impl::get_visible_devices().size(); + } } [[nodiscard]] int Kokkos::num_threads() noexcept { @@ -313,8 +338,7 @@ int Kokkos::Impl::get_ctest_gpu(int local_rank) { return std::stoi(id.c_str()); } -std::vector Kokkos::Impl::get_visible_devices( - Kokkos::InitializationSettings const& settings, int device_count) { +std::vector Kokkos::Impl::get_visible_devices(int device_count) { std::vector visible_devices; char* env_visible_devices = std::getenv("KOKKOS_VISIBLE_DEVICES"); if (env_visible_devices) { @@ -341,30 +365,9 @@ std::vector Kokkos::Impl::get_visible_devices( } } } else { - int num_devices = - settings.has_num_devices() ? settings.get_num_devices() : device_count; - if (num_devices > device_count) { - std::stringstream ss; - ss << "Error: Specified number of devices '" << num_devices - << "' exceeds the actual number of GPUs available for execution '" - << device_count << "'." - << " Raised by Kokkos::initialize().\n"; - Kokkos::abort(ss.str().c_str()); - } - for (int i = 0; i < num_devices; ++i) { + for (int i = 0; i < device_count; ++i) { visible_devices.push_back(i); } - if (settings.has_skip_device()) { - if (visible_devices.size() == 1 && settings.get_skip_device() == 0) { - Kokkos::abort( - "Error: skipping the only GPU available for execution.\n" - " Raised by Kokkos::initialize().\n"); - } - visible_devices.erase( - std::remove(visible_devices.begin(), visible_devices.end(), - settings.get_skip_device()), - visible_devices.end()); - } } if (visible_devices.empty()) { Kokkos::abort( @@ -374,10 +377,10 @@ std::vector Kokkos::Impl::get_visible_devices( return visible_devices; } -int Kokkos::Impl::get_gpu(const InitializationSettings& settings) { - std::vector visible_devices = - get_visible_devices(settings, get_device_count()); - int const num_devices = visible_devices.size(); +std::optional Kokkos::Impl::get_gpu( + const InitializationSettings& settings) { + std::vector visible_devices = get_visible_devices(get_device_count()); + int const num_devices = visible_devices.size(); // device_id is provided if (settings.has_device_id()) { int const id = settings.get_device_id(); @@ -423,14 +426,15 @@ int Kokkos::Impl::get_gpu(const InitializationSettings& settings) { int const mpi_local_rank = mpi_local_rank_on_node(); - // use first GPU available for execution if unable to detect local MPI rank + // if unable to detect local MPI rank return nullopt to delegate device + // selection to the backend if (mpi_local_rank < 0) { if (settings.has_map_device_id_by()) { std::cerr << "Warning: unable to detect local MPI rank." << " Falling back to the first GPU available for execution." << " Raised by Kokkos::initialize()." << std::endl; } - return visible_devices[0]; + return std::nullopt; } // use device assigned by CTest when resource allocation is activated @@ -445,13 +449,6 @@ int Kokkos::Impl::get_gpu(const InitializationSettings& settings) { namespace { void initialize_backends(const Kokkos::InitializationSettings& settings) { -// This is an experimental setting -// For KNL in Flat mode this variable should be set, so that -// memkind allocates high bandwidth memory correctly. -#ifdef KOKKOS_ENABLE_HBWSPACE - setenv("MEMKIND_HBW_NODES", "1", 0); -#endif - Kokkos::Impl::ExecSpaceManager::get_instance().initialize_spaces(settings); } @@ -571,19 +568,6 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { "no"); #endif -#ifdef KOKKOS_ENABLE_HBWSPACE - declare_configuration_metadata("memory", "KOKKOS_ENABLE_HBWSPACE", "yes"); -#else - declare_configuration_metadata("memory", "KOKKOS_ENABLE_HBWSPACE", "no"); -#endif -#ifdef KOKKOS_ENABLE_INTEL_MM_ALLOC - declare_configuration_metadata("memory", "KOKKOS_ENABLE_INTEL_MM_ALLOC", - "yes"); -#else - declare_configuration_metadata("memory", "KOKKOS_ENABLE_INTEL_MM_ALLOC", - "no"); -#endif - #ifdef KOKKOS_ENABLE_ASM declare_configuration_metadata("options", "KOKKOS_ENABLE_ASM", "yes"); #else @@ -604,6 +588,11 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { #else declare_configuration_metadata("options", "KOKKOS_ENABLE_CXX23", "no"); #endif +#ifdef KOKKOS_ENABLE_CXX26 + declare_configuration_metadata("options", "KOKKOS_ENABLE_CXX26", "yes"); +#else + declare_configuration_metadata("options", "KOKKOS_ENABLE_CXX26", "no"); +#endif #ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK declare_configuration_metadata("options", "KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK", "yes"); @@ -616,11 +605,6 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { #else declare_configuration_metadata("options", "KOKKOS_ENABLE_HWLOC", "no"); #endif -#ifdef KOKKOS_ENABLE_LIBRT - declare_configuration_metadata("options", "KOKKOS_ENABLE_LIBRT", "yes"); -#else - declare_configuration_metadata("options", "KOKKOS_ENABLE_LIBRT", "no"); -#endif #ifdef KOKKOS_ENABLE_LIBDL declare_configuration_metadata("options", "KOKKOS_ENABLE_LIBDL", "yes"); #else @@ -645,8 +629,6 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { "ARMV8_THUNDERX2"); #elif defined(KOKKOS_ARCH_BDW) declare_configuration_metadata("architecture", "CPU architecture", "BDW"); -#elif defined(KOKKOS_ARCH_BGQ) - declare_configuration_metadata("architecture", "CPU architecture", "BGQ"); #elif defined(KOKKOS_ARCH_HSW) declare_configuration_metadata("architecture", "CPU architecture", "HSW"); #elif defined(KOKKOS_ARCH_ICL) @@ -659,8 +641,6 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { declare_configuration_metadata("architecture", "CPU architecture", "KNL"); #elif defined(KOKKOS_ARCH_NATIVE) declare_configuration_metadata("architecture", "CPU architecture", "NATIVE"); -#elif defined(KOKKOS_ARCH_POWER7) - declare_configuration_metadata("architecture", "CPU architecture", "POWER7"); #elif defined(KOKKOS_ARCH_POWER8) declare_configuration_metadata("architecture", "CPU architecture", "POWER8"); #elif defined(KOKKOS_ARCH_POWER9) @@ -673,8 +653,6 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { declare_configuration_metadata("architecture", "CPU architecture", "SNB"); #elif defined(KOKKOS_ARCH_SPR) declare_configuration_metadata("architecture", "CPU architecture", "SPR"); -#elif defined(KOKKOS_ARCH_WSM) - declare_configuration_metadata("architecture", "CPU architecture", "WSM"); #elif defined(KOKKOS_ARCH_AMD_ZEN) declare_configuration_metadata("architecture", "CPU architecture", "AMD_ZEN"); #elif defined(KOKKOS_ARCH_AMD_ZEN2) @@ -683,6 +661,9 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { #elif defined(KOKKOS_ARCH_AMD_ZEN3) declare_configuration_metadata("architecture", "CPU architecture", "AMD_ZEN3"); +#elif defined(KOKKOS_ARCH_RISCV_SG2042) + declare_configuration_metadata("architecture", "CPU architecture", + "SG2042 (RISC-V)") #else declare_configuration_metadata("architecture", "CPU architecture", "none"); #endif @@ -752,8 +733,8 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) { #elif defined(KOKKOS_ARCH_ADA89) declare_configuration_metadata("architecture", "GPU architecture", "ADA89"); #elif defined(KOKKOS_ARCH_HOPPER90) - declare_configuration_metadata("architecture", "GPU architecture", - "HOPPER90"); + declare_configuration_metadata("architecture", "GPU architecture", + "HOPPER90"); #elif defined(KOKKOS_ARCH_AMD_GFX906) declare_configuration_metadata("architecture", "GPU architecture", "AMD_GFX906"); @@ -911,36 +892,18 @@ void Kokkos::Impl::parse_command_line_arguments( int num_threads; int device_id; - int num_devices; // deprecated - int skip_device; // deprecated std::string map_device_id_by; bool disable_warnings; bool print_configuration; bool tune_internals; - auto get_flag = [](std::string s) -> std::string { - return s.erase(s.find('=')); - }; - bool help_flag = false; int iarg = 0; while (iarg < argc) { bool remove_flag = false; - if (check_arg(argv[iarg], "--kokkos-numa") || - check_arg(argv[iarg], "--numa")) { - warn_deprecated_command_line_argument(get_flag(argv[iarg])); - // remove flag if prefixed with '--kokkos-' - remove_flag = std::string(argv[iarg]).find("--kokkos-") == 0; - } else if (check_arg_int(argv[iarg], "--kokkos-num-threads", num_threads) || - check_arg_int(argv[iarg], "--num-threads", num_threads) || - check_arg_int(argv[iarg], "--kokkos-threads", num_threads) || - check_arg_int(argv[iarg], "--threads", num_threads)) { - if (get_flag(argv[iarg]) != "--kokkos-num-threads") { - warn_deprecated_command_line_argument(get_flag(argv[iarg]), - "--kokkos-num-threads"); - } + if (check_arg_int(argv[iarg], "--kokkos-num-threads", num_threads)) { if (!is_valid_num_threads(num_threads)) { std::stringstream ss; ss << "Error: command line argument '" << argv[iarg] << "' is invalid." @@ -949,15 +912,8 @@ void Kokkos::Impl::parse_command_line_arguments( Kokkos::abort(ss.str().c_str()); } settings.set_num_threads(num_threads); - remove_flag = std::string(argv[iarg]).find("--kokkos-") == 0; - } else if (check_arg_int(argv[iarg], "--kokkos-device-id", device_id) || - check_arg_int(argv[iarg], "--device-id", device_id) || - check_arg_int(argv[iarg], "--kokkos-device", device_id) || - check_arg_int(argv[iarg], "--device", device_id)) { - if (get_flag(argv[iarg]) != "--kokkos-device-id") { - warn_deprecated_command_line_argument(get_flag(argv[iarg]), - "--kokkos-device-id"); - } + remove_flag = true; + } else if (check_arg_int(argv[iarg], "--kokkos-device-id", device_id)) { if (!is_valid_device_id(device_id)) { std::stringstream ss; ss << "Error: command line argument '" << argv[iarg] << "' is invalid." @@ -966,70 +922,7 @@ void Kokkos::Impl::parse_command_line_arguments( Kokkos::abort(ss.str().c_str()); } settings.set_device_id(device_id); - remove_flag = std::string(argv[iarg]).find("--kokkos-") == 0; - } else if (check_arg(argv[iarg], "--kokkos-num-devices") || - check_arg(argv[iarg], "--num-devices") || - check_arg(argv[iarg], "--kokkos-ndevices") || - check_arg(argv[iarg], "--ndevices")) { - if (check_arg(argv[iarg], "--num-devices")) { - warn_deprecated_command_line_argument("--num-devices", - "--kokkos-num-devices"); - } - if (check_arg(argv[iarg], "--ndevices")) { - warn_deprecated_command_line_argument("--ndevices", - "--kokkos-num-devices"); - } - if (check_arg(argv[iarg], "--kokkos-ndevices")) { - warn_deprecated_command_line_argument("--kokkos-ndevices", - "--kokkos-num-devices"); - } - warn_deprecated_command_line_argument( - "--kokkos-num-devices", "--kokkos-map-device-id-by=mpi_rank"); - // Find the number of device (expecting --device=XX) - if (!((strncmp(argv[iarg], "--kokkos-num-devices=", 21) == 0) || - (strncmp(argv[iarg], "--num-devices=", 14) == 0) || - (strncmp(argv[iarg], "--kokkos-ndevices=", 18) == 0) || - (strncmp(argv[iarg], "--ndevices=", 11) == 0))) - throw_runtime_exception( - "Error: expecting an '=INT[,INT]' after command line argument " - "'--kokkos-num-devices'." - " Raised by Kokkos::initialize()."); - - char* num1 = strchr(argv[iarg], '=') + 1; - char* num2 = strpbrk(num1, ","); - int num1_len = num2 == nullptr ? strlen(num1) : num2 - num1; - char* num1_only = new char[num1_len + 1]; - strncpy(num1_only, num1, num1_len); - num1_only[num1_len] = '\0'; - - if (!is_unsigned_int(num1_only) || (strlen(num1_only) == 0)) { - throw_runtime_exception( - "Error: expecting an integer number after command line argument " - "'--kokkos-num-devices'." - " Raised by Kokkos::initialize()."); - } - if (check_arg(argv[iarg], "--kokkos-num-devices") || - check_arg(argv[iarg], "--kokkos-ndevices")) { - num_devices = std::stoi(num1_only); - settings.set_num_devices(num_devices); - settings.set_map_device_id_by("mpi_rank"); - } - delete[] num1_only; - - if (num2 != nullptr) { - if ((!is_unsigned_int(num2 + 1)) || (strlen(num2) == 1)) - throw_runtime_exception( - "Error: expecting an integer number after command line argument " - "'--kokkos-num-devices=XX,'." - " Raised by Kokkos::initialize()."); - - if (check_arg(argv[iarg], "--kokkos-num-devices") || - check_arg(argv[iarg], "--kokkos-ndevices")) { - skip_device = std::stoi(num2 + 1); - settings.set_skip_device(skip_device); - } - } - remove_flag = std::string(argv[iarg]).find("--kokkos-") == 0; + remove_flag = true; } else if (check_arg_bool(argv[iarg], "--kokkos-disable-warnings", disable_warnings)) { settings.set_disable_warnings(disable_warnings); @@ -1098,9 +991,6 @@ void Kokkos::Impl::parse_environment_variables( } combine(settings, tools_init_arguments); - if (std::getenv("KOKKOS_NUMA")) { - warn_deprecated_environment_variable("KOKKOS_NUMA"); - } int num_threads; if (check_env_int("KOKKOS_NUM_THREADS", num_threads)) { if (!is_valid_num_threads(num_threads)) { @@ -1125,34 +1015,6 @@ void Kokkos::Impl::parse_environment_variables( } settings.set_device_id(device_id); } - int num_devices; - int rand_devices; - bool has_num_devices = check_env_int("KOKKOS_NUM_DEVICES", num_devices); - bool has_rand_devices = check_env_int("KOKKOS_RAND_DEVICES", rand_devices); - if (has_rand_devices && has_num_devices) { - Impl::throw_runtime_exception( - "Error: cannot specify both KOKKOS_NUM_DEVICES and " - "KOKKOS_RAND_DEVICES." - " Raised by Kokkos::initialize()."); - } - if (has_num_devices) { - warn_deprecated_environment_variable("KOKKOS_NUM_DEVICES", - "KOKKOS_MAP_DEVICE_ID_BY=mpi_rank"); - settings.set_map_device_id_by("mpi_rank"); - settings.set_num_devices(num_devices); - } - if (has_rand_devices) { - warn_deprecated_environment_variable("KOKKOS_RAND_DEVICES", - "KOKKOS_MAP_DEVICE_ID_BY=random"); - settings.set_map_device_id_by("random"); - settings.set_num_devices(rand_devices); - } - if (has_num_devices || has_rand_devices) { - int skip_device; - if (check_env_int("KOKKOS_SKIP_DEVICE", skip_device)) { - settings.set_skip_device(skip_device); - } - } bool disable_warnings; if (check_env_bool("KOKKOS_DISABLE_WARNINGS", disable_warnings)) { settings.set_disable_warnings(disable_warnings); diff --git a/lib/kokkos/core/src/impl/Kokkos_DeviceManagement.hpp b/lib/kokkos/core/src/impl/Kokkos_DeviceManagement.hpp index bd89c8b19c..70dca5d8fa 100644 --- a/lib/kokkos/core/src/impl/Kokkos_DeviceManagement.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_DeviceManagement.hpp @@ -17,17 +17,17 @@ #ifndef KOKKOS_DEVICE_MANAGEMENT_HPP #define KOKKOS_DEVICE_MANAGEMENT_HPP +#include #include namespace Kokkos { class InitializationSettings; namespace Impl { -int get_gpu(const Kokkos::InitializationSettings& settings); +std::optional get_gpu(const Kokkos::InitializationSettings& settings); // This declaration is provided for testing purposes only int get_ctest_gpu(int local_rank); -// ditto -std::vector get_visible_devices( - Kokkos::InitializationSettings const& settings, int device_count); +std::vector get_visible_devices(int device_count); // test-only +std::vector const& get_visible_devices(); // use this instead } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/core/src/impl/Kokkos_Error.cpp b/lib/kokkos/core/src/impl/Kokkos_Error.cpp index 4babe2d72b..de6e83ed1f 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Error.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_Error.cpp @@ -21,10 +21,11 @@ #include #include -#include +#include #include #include #include +#include // show_warnings #include #include @@ -38,6 +39,12 @@ void throw_runtime_exception(const std::string &msg) { throw std::runtime_error(msg); } +void log_warning(const std::string &msg) { + if (show_warnings()) { + std::cerr << msg << std::flush; + } +} + std::string human_memory_size(size_t arg_bytes) { double bytes = arg_bytes; const double K = 1024; @@ -64,7 +71,8 @@ std::string human_memory_size(size_t arg_bytes) { void Experimental::RawMemoryAllocationFailure::print_error_message( std::ostream &o) const { - o << "Allocation of size " << Impl::human_memory_size(m_attempted_size); + o << "Allocation of size " + << ::Kokkos::Impl::human_memory_size(m_attempted_size); o << " failed"; switch (m_failure_mode) { case FailureMode::OutOfMemoryError: diff --git a/lib/kokkos/core/src/impl/Kokkos_Error.hpp b/lib/kokkos/core/src/impl/Kokkos_Error.hpp index 3d0b1d3274..1058fd98db 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Error.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Error.hpp @@ -28,6 +28,8 @@ namespace Impl { [[noreturn]] void throw_runtime_exception(const std::string &msg); +void log_warning(const std::string &msg); + std::string human_memory_size(size_t arg_bytes); } // namespace Impl @@ -58,7 +60,8 @@ class RawMemoryAllocationFailure : public std::bad_alloc { HIPMallocManaged, SYCLMallocDevice, SYCLMallocShared, - SYCLMallocHost + SYCLMallocHost, + OpenACCMalloc, }; private: diff --git a/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp b/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp deleted file mode 100644 index cd640b88cb..0000000000 --- a/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp +++ /dev/null @@ -1,313 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#ifndef KOKKOS_IMPL_PUBLIC_INCLUDE -#define KOKKOS_IMPL_PUBLIC_INCLUDE -#endif - -#include - -#include -#include -#include -#include - -#include -#include -#include -#include - -#include -#include -#include -#include -#ifdef KOKKOS_ENABLE_HBWSPACE -#include -#endif - -#include - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- -#ifdef KOKKOS_ENABLE_HBWSPACE -#define MEMKIND_TYPE MEMKIND_HBW // hbw_get_kind(HBW_PAGESIZE_4KB) - -/*--------------------------------------------------------------------------*/ - -namespace Kokkos { -namespace Experimental { - -/* Default allocation mechanism */ -HBWSpace::HBWSpace() : m_alloc_mech(HBWSpace::STD_MALLOC) { - printf("Init\n"); - setenv("MEMKIND_HBW_NODES", "1", 0); -} - -/* Default allocation mechanism */ -HBWSpace::HBWSpace(const HBWSpace::AllocationMechanism &arg_alloc_mech) - : m_alloc_mech(HBWSpace::STD_MALLOC) { - printf("Init2\n"); - setenv("MEMKIND_HBW_NODES", "1", 0); - if (arg_alloc_mech == STD_MALLOC) { - m_alloc_mech = HBWSpace::STD_MALLOC; - } -} - -void *HBWSpace::allocate(const size_t arg_alloc_size) const { - return allocate("[unlabeled]", arg_alloc_size); -} -void *HBWSpace::allocate(const char *arg_label, const size_t arg_alloc_size, - const size_t arg_logical_size) const { - return impl_allocate(arg_label, arg_alloc_size, arg_logical_size); -} -void *HBWSpace::impl_allocate( - const char *arg_label, const size_t arg_alloc_size, - const size_t arg_logical_size, - const Kokkos::Tools::SpaceHandle arg_handle) const { - static_assert(sizeof(void *) == sizeof(uintptr_t), - "Error sizeof(void*) != sizeof(uintptr_t)"); - - static_assert( - Kokkos::Impl::power_of_two::value, - "Memory alignment must be power of two"); - - constexpr uintptr_t alignment = Kokkos::Impl::MEMORY_ALIGNMENT; - constexpr uintptr_t alignment_mask = alignment - 1; - - void *ptr = nullptr; - - if (arg_alloc_size) { - if (m_alloc_mech == STD_MALLOC) { - // Over-allocate to and round up to guarantee proper alignment. - size_t size_padded = arg_alloc_size + sizeof(void *) + alignment; - - void *alloc_ptr = memkind_malloc(MEMKIND_TYPE, size_padded); - - if (alloc_ptr) { - uintptr_t address = reinterpret_cast(alloc_ptr); - - // offset enough to record the alloc_ptr - address += sizeof(void *); - uintptr_t rem = address % alignment; - uintptr_t offset = rem ? (alignment - rem) : 0u; - address += offset; - ptr = reinterpret_cast(address); - // record the alloc'd pointer - address -= sizeof(void *); - *reinterpret_cast(address) = alloc_ptr; - } - } - } - - if ((ptr == nullptr) || (reinterpret_cast(ptr) == ~uintptr_t(0)) || - (reinterpret_cast(ptr) & alignment_mask)) { - std::ostringstream msg; - msg << "Kokkos::Experimental::HBWSpace::allocate[ "; - switch (m_alloc_mech) { - case STD_MALLOC: msg << "STD_MALLOC"; break; - case POSIX_MEMALIGN: msg << "POSIX_MEMALIGN"; break; - case POSIX_MMAP: msg << "POSIX_MMAP"; break; - case INTEL_MM_ALLOC: msg << "INTEL_MM_ALLOC"; break; - } - msg << " ]( " << arg_alloc_size << " ) FAILED"; - if (ptr == nullptr) { - msg << " nullptr"; - } else { - msg << " NOT ALIGNED " << ptr; - } - - std::cerr << msg.str() << std::endl; - std::cerr.flush(); - - Kokkos::Impl::throw_runtime_exception(msg.str()); - } - if (Kokkos::Profiling::profileLibraryLoaded()) { - const size_t reported_size = - (arg_logical_size > 0) ? arg_logical_size : arg_alloc_size; - Kokkos::Profiling::allocateData(arg_handle, arg_label, ptr, reported_size); - } - - return ptr; -} - -void HBWSpace::deallocate(void *const arg_alloc_ptr, - const size_t arg_alloc_size) const { - deallocate("[unlabeled]", arg_alloc_ptr, arg_alloc_size); -} -void HBWSpace::deallocate(const char *arg_label, void *const arg_alloc_ptr, - const size_t arg_alloc_size, - const size_t arg_logical_size) const { - impl_deallocate(arg_label, arg_alloc_ptr, arg_alloc_size, arg_logical_size); -} -void HBWSpace::impl_deallocate( - const char *arg_label, void *const arg_alloc_ptr, - const size_t arg_alloc_size, const size_t arg_logical_size, - const Kokkos::Tools::SpaceHandle arg_handle) const { - if (arg_alloc_ptr) { - if (Kokkos::Profiling::profileLibraryLoaded()) { - const size_t reported_size = - (arg_logical_size > 0) ? arg_logical_size : arg_alloc_size; - Kokkos::Profiling::deallocateData(arg_handle, arg_label, arg_alloc_ptr, - reported_size); - } - - if (m_alloc_mech == STD_MALLOC) { - void *alloc_ptr = *(reinterpret_cast(arg_alloc_ptr) - 1); - memkind_free(MEMKIND_TYPE, alloc_ptr); - } - } -} - -} // namespace Experimental -} // namespace Kokkos - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - -#ifdef KOKKOS_ENABLE_DEBUG -SharedAllocationRecord - SharedAllocationRecord::s_root_record; -#endif - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord *arg_rec) { - delete static_cast(arg_rec); -} - -SharedAllocationRecord::~SharedAllocationRecord() { - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - SharedAllocationRecord::m_alloc_size, - (SharedAllocationRecord::m_alloc_size - - sizeof(SharedAllocationHeader))); -} - -SharedAllocationRecord:: - SharedAllocationRecord( - const Kokkos::Experimental::HBWSpace &arg_space, - const std::string &arg_label, const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : SharedAllocationRecord( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - // Fill in the Header information - RecordBase::m_alloc_ptr->m_record = - static_cast *>(this); - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length - 1); - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = '\0'; -} - -//---------------------------------------------------------------------------- - -void * -SharedAllocationRecord::allocate_tracked( - const Kokkos::Experimental::HBWSpace &arg_space, - const std::string &arg_alloc_label, const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord *const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked(void *const - arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord *const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void *SharedAllocationRecord:: - reallocate_tracked(void *const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord *const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord *const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - Kokkos::fence( - "SharedAllocationRecord::reallocate_tracked(): fence after copying data"); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -SharedAllocationRecord - *SharedAllocationRecord::get_record( - void *alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordHost = - SharedAllocationRecord; - - SharedAllocationHeader const *const head = - alloc_ptr ? Header::get_header(alloc_ptr) : nullptr; - RecordHost *const record = - head ? static_cast(head->m_record) : nullptr; - - if (!alloc_ptr || record->m_alloc_ptr != head) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::SharedAllocationRecord< Kokkos::Experimental::HBWSpace " - ", void >::get_record ERROR")); - } - - return record; -} - -// Iterate records to print orphaned memory ... -void SharedAllocationRecord:: - print_records(std::ostream &s, const Kokkos::Experimental::HBWSpace &space, - bool detail) { -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord::print_host_accessible_records( - s, "HBWSpace", &s_root_record, detail); -#else - throw_runtime_exception( - "SharedAllocationRecord::print_records" - " only works with KOKKOS_ENABLE_DEBUG enabled"); -#endif -} - -} // namespace Impl -} // namespace Kokkos - -#endif diff --git a/lib/kokkos/core/src/impl/Kokkos_Half_FloatingPointWrapper.hpp b/lib/kokkos/core/src/impl/Kokkos_Half_FloatingPointWrapper.hpp index 4a22898d16..bcce013b00 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Half_FloatingPointWrapper.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Half_FloatingPointWrapper.hpp @@ -196,12 +196,12 @@ KOKKOS_INLINE_FUNCTION template static KOKKOS_INLINE_FUNCTION Kokkos::Experimental::half_t cast_to_wrapper( - T x, const volatile Kokkos::Impl::half_impl_t::type&); + T x, const Kokkos::Impl::half_impl_t::type&); #ifdef KOKKOS_IMPL_BHALF_TYPE_DEFINED template static KOKKOS_INLINE_FUNCTION Kokkos::Experimental::bhalf_t cast_to_wrapper( - T x, const volatile Kokkos::Impl::bhalf_impl_t::type&); + T x, const Kokkos::Impl::bhalf_impl_t::type&); #endif // KOKKOS_IMPL_BHALF_TYPE_DEFINED template @@ -283,13 +283,6 @@ class alignas(FloatType) floating_point_wrapper { private: impl_type val; - using fixed_width_integer_type = std::conditional_t< - sizeof(impl_type) == 2, uint16_t, - std::conditional_t< - sizeof(impl_type) == 4, uint32_t, - std::conditional_t>>; - static_assert(!std::is_void::value, - "Invalid impl_type"); public: // In-class initialization and defaulted default constructors not used @@ -318,18 +311,6 @@ class alignas(FloatType) floating_point_wrapper { default; #endif - KOKKOS_INLINE_FUNCTION - floating_point_wrapper(const volatile floating_point_wrapper& rhs) { -#if defined(KOKKOS_HALF_IS_FULL_TYPE_ON_ARCH) && !defined(KOKKOS_ENABLE_SYCL) - val = rhs.val; -#else - const volatile fixed_width_integer_type* rv_ptr = - reinterpret_cast(&rhs.val); - const fixed_width_integer_type rv_val = *rv_ptr; - val = reinterpret_cast(rv_val); -#endif // KOKKOS_HALF_IS_FULL_TYPE_ON_ARCH - } - KOKKOS_FUNCTION floating_point_wrapper(bit_comparison_type rhs) { val = Kokkos::bit_cast(rhs); @@ -492,15 +473,6 @@ class alignas(FloatType) floating_point_wrapper { return *this; } - template - KOKKOS_FUNCTION void operator=(T rhs) volatile { - impl_type new_val = cast_to_wrapper(rhs, val).val; - volatile fixed_width_integer_type* val_ptr = - reinterpret_cast( - const_cast(&val)); - *val_ptr = reinterpret_cast(new_val); - } - // Compound operators KOKKOS_FUNCTION floating_point_wrapper& operator+=(floating_point_wrapper rhs) { @@ -515,15 +487,6 @@ class alignas(FloatType) floating_point_wrapper { return *this; } - KOKKOS_FUNCTION - void operator+=(const volatile floating_point_wrapper& rhs) volatile { - floating_point_wrapper tmp_rhs = rhs; - floating_point_wrapper tmp_lhs = *this; - - tmp_lhs += tmp_rhs; - *this = tmp_lhs; - } - // Compound operators: upcast overloads for += template KOKKOS_FUNCTION friend std::enable_if_t< @@ -560,15 +523,6 @@ class alignas(FloatType) floating_point_wrapper { return *this; } - KOKKOS_FUNCTION - void operator-=(const volatile floating_point_wrapper& rhs) volatile { - floating_point_wrapper tmp_rhs = rhs; - floating_point_wrapper tmp_lhs = *this; - - tmp_lhs -= tmp_rhs; - *this = tmp_lhs; - } - // Compund operators: upcast overloads for -= template KOKKOS_FUNCTION friend std::enable_if_t< @@ -605,15 +559,6 @@ class alignas(FloatType) floating_point_wrapper { return *this; } - KOKKOS_FUNCTION - void operator*=(const volatile floating_point_wrapper& rhs) volatile { - floating_point_wrapper tmp_rhs = rhs; - floating_point_wrapper tmp_lhs = *this; - - tmp_lhs *= tmp_rhs; - *this = tmp_lhs; - } - // Compund operators: upcast overloads for *= template KOKKOS_FUNCTION friend std::enable_if_t< @@ -650,15 +595,6 @@ class alignas(FloatType) floating_point_wrapper { return *this; } - KOKKOS_FUNCTION - void operator/=(const volatile floating_point_wrapper& rhs) volatile { - floating_point_wrapper tmp_rhs = rhs; - floating_point_wrapper tmp_lhs = *this; - - tmp_lhs /= tmp_rhs; - *this = tmp_lhs; - } - // Compund operators: upcast overloads for /= template KOKKOS_FUNCTION friend std::enable_if_t< @@ -884,27 +820,6 @@ class alignas(FloatType) floating_point_wrapper { #endif } - KOKKOS_FUNCTION - friend bool operator==(const volatile floating_point_wrapper& lhs, - const volatile floating_point_wrapper& rhs) { - floating_point_wrapper tmp_lhs = lhs, tmp_rhs = rhs; - return tmp_lhs == tmp_rhs; - } - - KOKKOS_FUNCTION - friend bool operator!=(const volatile floating_point_wrapper& lhs, - const volatile floating_point_wrapper& rhs) { - floating_point_wrapper tmp_lhs = lhs, tmp_rhs = rhs; - return tmp_lhs != tmp_rhs; - } - - KOKKOS_FUNCTION - friend bool operator<(const volatile floating_point_wrapper& lhs, - const volatile floating_point_wrapper& rhs) { - floating_point_wrapper tmp_lhs = lhs, tmp_rhs = rhs; - return tmp_lhs < tmp_rhs; - } - template KOKKOS_FUNCTION friend std::enable_if_t && (std::is_same_v || @@ -923,13 +838,6 @@ class alignas(FloatType) floating_point_wrapper { return lhs < static_cast(rhs); } - KOKKOS_FUNCTION - friend bool operator>(const volatile floating_point_wrapper& lhs, - const volatile floating_point_wrapper& rhs) { - floating_point_wrapper tmp_lhs = lhs, tmp_rhs = rhs; - return tmp_lhs > tmp_rhs; - } - template KOKKOS_FUNCTION friend std::enable_if_t && (std::is_same_v || @@ -948,13 +856,6 @@ class alignas(FloatType) floating_point_wrapper { return lhs > static_cast(rhs); } - KOKKOS_FUNCTION - friend bool operator<=(const volatile floating_point_wrapper& lhs, - const volatile floating_point_wrapper& rhs) { - floating_point_wrapper tmp_lhs = lhs, tmp_rhs = rhs; - return tmp_lhs <= tmp_rhs; - } - template KOKKOS_FUNCTION friend std::enable_if_t && (std::is_same_v || @@ -973,13 +874,6 @@ class alignas(FloatType) floating_point_wrapper { return lhs <= static_cast(rhs); } - KOKKOS_FUNCTION - friend bool operator>=(const volatile floating_point_wrapper& lhs, - const volatile floating_point_wrapper& rhs) { - floating_point_wrapper tmp_lhs = lhs, tmp_rhs = rhs; - return tmp_lhs >= tmp_rhs; - } - template KOKKOS_FUNCTION friend std::enable_if_t && (std::is_same_v || @@ -1018,14 +912,14 @@ class alignas(FloatType) floating_point_wrapper { // Declare wrapper overloads now that floating_point_wrapper is declared template static KOKKOS_INLINE_FUNCTION Kokkos::Experimental::half_t cast_to_wrapper( - T x, const volatile Kokkos::Impl::half_impl_t::type&) { + T x, const Kokkos::Impl::half_impl_t::type&) { return Kokkos::Experimental::cast_to_half(x); } #ifdef KOKKOS_IMPL_BHALF_TYPE_DEFINED template static KOKKOS_INLINE_FUNCTION Kokkos::Experimental::bhalf_t cast_to_wrapper( - T x, const volatile Kokkos::Impl::bhalf_impl_t::type&) { + T x, const Kokkos::Impl::bhalf_impl_t::type&) { return Kokkos::Experimental::cast_to_bhalf(x); } #endif // KOKKOS_IMPL_BHALF_TYPE_DEFINED diff --git a/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp b/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp index a9d7216059..1047b773d7 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp @@ -20,23 +20,11 @@ #include +#include +#include #include -#include #include -/*--------------------------------------------------------------------------*/ - -#if (defined(KOKKOS_COMPILER_INTEL) || defined(KOKKOS_COMPILER_INTEL_LLVM)) && \ - !defined(KOKKOS_ENABLE_CUDA) - -// Intel specialized allocator does not interoperate with CUDA memory allocation - -#define KOKKOS_ENABLE_INTEL_MM_ALLOC - -#endif - -/*--------------------------------------------------------------------------*/ - #include #include #include @@ -50,10 +38,6 @@ #include #endif -#include -#include -#include - //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -150,84 +134,6 @@ void HostSpace::impl_deallocate( } // namespace Kokkos -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - -#ifdef KOKKOS_ENABLE_DEBUG -SharedAllocationRecord - SharedAllocationRecord::s_root_record; -#endif - -SharedAllocationRecord::~SharedAllocationRecord() { - m_space.deallocate(m_label.c_str(), - SharedAllocationRecord::m_alloc_ptr, - SharedAllocationRecord::m_alloc_size, - (SharedAllocationRecord::m_alloc_size - - sizeof(SharedAllocationHeader))); -} - -SharedAllocationHeader *_do_allocation(Kokkos::HostSpace const &space, - std::string const &label, - size_t alloc_size) { - try { - return reinterpret_cast( - space.allocate(alloc_size)); - } catch (Experimental::RawMemoryAllocationFailure const &failure) { - if (failure.failure_mode() == Experimental::RawMemoryAllocationFailure:: - FailureMode::AllocationNotAligned) { - // TODO: delete the misaligned memory - } - - std::cerr << "Kokkos failed to allocate memory for label \"" << label - << "\". Allocation using MemorySpace named \"" << space.name() - << " failed with the following error: "; - failure.print_error_message(std::cerr); - std::cerr.flush(); - Kokkos::Impl::throw_runtime_exception("Memory allocation failure"); - } - return nullptr; // unreachable -} - -SharedAllocationRecord::SharedAllocationRecord( - const Kokkos::HostSpace &arg_space, const std::string &arg_label, - const size_t arg_alloc_size, - const SharedAllocationRecord::function_type arg_dealloc) - // Pass through allocated [ SharedAllocationHeader , user_memory ] - // Pass through deallocation function - : base_t( -#ifdef KOKKOS_ENABLE_DEBUG - &SharedAllocationRecord::s_root_record, -#endif - Impl::checked_allocation_with_header(arg_space, arg_label, - arg_alloc_size), - sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc, - arg_label), - m_space(arg_space) { - this->base_t::_fill_host_accessible_header_info(*RecordBase::m_alloc_ptr, - arg_label); -} - -} // namespace Impl -} // namespace Kokkos - -//============================================================================== -// {{{1 - #include -namespace Kokkos { -namespace Impl { - -// To avoid additional compilation cost for something that's (mostly?) not -// performance sensitive, we explicity instantiate these CRTP base classes here, -// where we have access to the associated *_timpl.hpp header files. -template class SharedAllocationRecordCommon; - -} // end namespace Impl -} // end namespace Kokkos - -// end Explicit instantiations of CRTP Base classes }}}1 -//============================================================================== +KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION(Kokkos::HostSpace); diff --git a/lib/kokkos/core/src/impl/Kokkos_HostSpace_ZeroMemset.hpp b/lib/kokkos/core/src/impl/Kokkos_HostSpace_ZeroMemset.hpp index f740c408fb..3072e2ce82 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostSpace_ZeroMemset.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostSpace_ZeroMemset.hpp @@ -26,8 +26,7 @@ namespace Impl { template struct ZeroMemset> { - ZeroMemset(const HostSpace::execution_space& exec, const View& dst, - typename View::const_value_type&) { + ZeroMemset(const HostSpace::execution_space& exec, const View& dst) { // Host spaces, except for HPX, are synchronous and we need to fence for HPX // since we can't properly enqueue a std::memset otherwise. // We can't use exec.fence() directly since we don't have a full definition @@ -36,12 +35,6 @@ struct ZeroMemset> { using ValueType = typename View::value_type; std::memset(dst.data(), 0, sizeof(ValueType) * dst.size()); } - - ZeroMemset(const View& dst, - typename View::const_value_type&) { - using ValueType = typename View::value_type; - std::memset(dst.data(), 0, sizeof(ValueType) * dst.size()); - } }; } // end namespace Impl diff --git a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp index bfe5902bf7..11bf701b57 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp @@ -22,7 +22,6 @@ #include #include #include -#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp index 51f25a8b60..25f09b8286 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp @@ -885,7 +885,7 @@ KOKKOS_INLINE_FUNCTION closure(i, accum, false); } - auto team_member = loop_boundaries.thread; + auto& team_member = loop_boundaries.thread; // 'accum' output is the exclusive prefix sum accum = team_member.team_scan(accum); diff --git a/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp b/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp index ab4350f3a7..11a93c6bb5 100644 --- a/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp @@ -24,32 +24,6 @@ namespace Kokkos { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -struct InitArguments { - int num_threads; - int num_numa; - int device_id; - int ndevices; - int skip_device; - bool disable_warnings; - bool tune_internals; - bool tool_help = false; - std::string tool_lib = {}; - std::string tool_args = {}; - - KOKKOS_DEPRECATED_WITH_COMMENT("Use InitializationSettings instead!") - InitArguments(int nt = -1, int nn = -1, int dv = -1, bool dw = false, - bool ti = false) - : num_threads{nt}, - num_numa{nn}, - device_id{dv}, - ndevices{-1}, - skip_device{9999}, - disable_warnings{dw}, - tune_internals{ti} {} -}; -#endif - class InitializationSettings { #define KOKKOS_IMPL_DECLARE(TYPE, NAME) \ private: \ @@ -64,12 +38,32 @@ class InitializationSettings { TYPE get_##NAME() const noexcept { return *m_##NAME; } \ static_assert(true, "no-op to require trailing semicolon") +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 +#define KOKKOS_IMPL_DECLARE_DEPRECATED(TYPE, NAME) \ + private: \ + std::optional m_##NAME; \ + \ + public: \ + KOKKOS_DEPRECATED InitializationSettings& set_##NAME(TYPE NAME) { \ + m_##NAME = NAME; \ + return *this; \ + } \ + KOKKOS_DEPRECATED bool has_##NAME() const noexcept { \ + return static_cast(m_##NAME); \ + } \ + KOKKOS_DEPRECATED TYPE get_##NAME() const noexcept { return *m_##NAME; } \ + static_assert(true, "no-op to require trailing semicolon") +#else +#define KOKKOS_IMPL_DECLARE_DEPRECATED(TYPE, NAME) \ + static_assert(true, "no-op to require trailing semicolon") +#endif + public: KOKKOS_IMPL_DECLARE(int, num_threads); KOKKOS_IMPL_DECLARE(int, device_id); KOKKOS_IMPL_DECLARE(std::string, map_device_id_by); - KOKKOS_IMPL_DECLARE(int, num_devices); // deprecated - KOKKOS_IMPL_DECLARE(int, skip_device); // deprecated + KOKKOS_IMPL_DECLARE_DEPRECATED(int, num_devices); + KOKKOS_IMPL_DECLARE_DEPRECATED(int, skip_device); KOKKOS_IMPL_DECLARE(bool, disable_warnings); KOKKOS_IMPL_DECLARE(bool, print_configuration); KOKKOS_IMPL_DECLARE(bool, tune_internals); @@ -80,41 +74,6 @@ class InitializationSettings { #undef KOKKOS_IMPL_INIT_ARGS_DATA_MEMBER_TYPE #undef KOKKOS_IMPL_INIT_ARGS_DATA_MEMBER #undef KOKKOS_IMPL_DECLARE - -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 - public: - InitializationSettings() = default; - - InitializationSettings(InitArguments const& old) { - if (old.num_threads != -1) { - set_num_threads(old.num_threads); - } - if (old.device_id != -1) { - set_device_id(old.device_id); - } - if (old.ndevices != -1) { - set_num_devices(old.ndevices); - } - if (old.skip_device != 9999) { - set_skip_device(old.skip_device); - } - if (old.disable_warnings) { - set_disable_warnings(true); - } - if (old.tune_internals) { - set_tune_internals(true); - } - if (old.tool_help) { - set_tools_help(true); - } - if (!old.tool_lib.empty()) { - set_tools_libs(old.tool_lib); - } - if (!old.tool_args.empty()) { - set_tools_args(old.tool_args); - } - } -#endif }; } // namespace Kokkos diff --git a/lib/kokkos/core/src/impl/Kokkos_MemorySpace.cpp b/lib/kokkos/core/src/impl/Kokkos_MemorySpace.cpp deleted file mode 100644 index 2f0e01c5b2..0000000000 --- a/lib/kokkos/core/src/impl/Kokkos_MemorySpace.cpp +++ /dev/null @@ -1,72 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -/** @file Kokkos_MemorySpace.cpp - * - * Operations common to memory space instances, or at least default - * implementations thereof. - */ - -#ifndef KOKKOS_IMPL_PUBLIC_INCLUDE -#define KOKKOS_IMPL_PUBLIC_INCLUDE -#endif - -#include - -#include -#include -#include - -namespace Kokkos { -namespace Impl { - -void safe_throw_allocation_with_header_failure( - std::string const& space_name, std::string const& label, - Kokkos::Experimental::RawMemoryAllocationFailure const& failure) { - auto generate_failure_message = [&](std::ostream& o) { - o << "Kokkos failed to allocate memory for label \"" << label - << "\". Allocation using MemorySpace named \"" << space_name - << "\" failed with the following error: "; - failure.print_error_message(o); - if (failure.failure_mode() == - Kokkos::Experimental::RawMemoryAllocationFailure::FailureMode:: - AllocationNotAligned) { - // TODO: delete the misaligned memory? - o << "Warning: Allocation failed due to misalignment; memory may " - "be leaked.\n"; - } - o.flush(); - }; - try { - std::ostringstream sstr; - generate_failure_message(sstr); - Kokkos::Impl::throw_runtime_exception(sstr.str()); - } catch (std::bad_alloc const&) { - // Probably failed to allocate the string because we're so close to out - // of memory. Try printing to std::cerr instead - try { - generate_failure_message(std::cerr); - } catch (std::bad_alloc const&) { - // oh well, we tried... - } - Kokkos::Impl::throw_runtime_exception( - "Kokkos encountered an allocation failure, then another allocation " - "failure while trying to create the error message."); - } -} - -} // end namespace Impl -} // end namespace Kokkos diff --git a/lib/kokkos/core/src/impl/Kokkos_MemorySpace.hpp b/lib/kokkos/core/src/impl/Kokkos_MemorySpace.hpp deleted file mode 100644 index 44956dd7c5..0000000000 --- a/lib/kokkos/core/src/impl/Kokkos_MemorySpace.hpp +++ /dev/null @@ -1,71 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -/** @file Kokkos_MemorySpace.hpp - * - * Operations common to memory space instances, or at least default - * implementations thereof. - */ - -#ifndef KOKKOS_IMPL_MEMORYSPACE_HPP -#define KOKKOS_IMPL_MEMORYSPACE_HPP - -#include -#include -#include - -#include - -namespace Kokkos { -namespace Impl { - -// Defined in implementation file to avoid having to include iostream -void safe_throw_allocation_with_header_failure( - std::string const &space_name, std::string const &label, - Kokkos::Experimental::RawMemoryAllocationFailure const &failure); - -template -SharedAllocationHeader *checked_allocation_with_header(MemorySpace const &space, - std::string const &label, - size_t alloc_size) { - try { - return reinterpret_cast(space.allocate( - label.c_str(), alloc_size + sizeof(SharedAllocationHeader), - alloc_size)); - } catch (Kokkos::Experimental::RawMemoryAllocationFailure const &failure) { - safe_throw_allocation_with_header_failure(space.name(), label, failure); - } - return nullptr; // unreachable -} - -template -SharedAllocationHeader *checked_allocation_with_header( - ExecutionSpace const &exec_space, MemorySpace const &space, - std::string const &label, size_t alloc_size) { - try { - return reinterpret_cast(space.allocate( - exec_space, label.c_str(), alloc_size + sizeof(SharedAllocationHeader), - alloc_size)); - } catch (Kokkos::Experimental::RawMemoryAllocationFailure const &failure) { - safe_throw_allocation_with_header_failure(space.name(), label, failure); - } - return nullptr; // unreachable -} - -} // end namespace Impl -} // end namespace Kokkos - -#endif // KOKKOS_IMPL_MEMORYSPACE_HPP diff --git a/lib/kokkos/core/src/impl/Kokkos_Memory_Fence.hpp b/lib/kokkos/core/src/impl/Kokkos_Memory_Fence.hpp deleted file mode 100644 index 42a53b04fb..0000000000 --- a/lib/kokkos/core/src/impl/Kokkos_Memory_Fence.hpp +++ /dev/null @@ -1,54 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#include -#if defined(KOKKOS_ATOMIC_HPP) && !defined(KOKKOS_MEMORY_FENCE_HPP) -#define KOKKOS_MEMORY_FENCE_HPP -namespace Kokkos { - -////////////////////////////////////////////////////// -// store_fence() -// -// If possible use a store fence on the architecture, if not run a full memory -// fence - -KOKKOS_FORCEINLINE_FUNCTION -void store_fence() { -#if defined(KOKKOS_ENABLE_ASM) && defined(KOKKOS_ENABLE_ISA_X86_64) - asm volatile("sfence" ::: "memory"); -#else - memory_fence(); -#endif -} - -////////////////////////////////////////////////////// -// load_fence() -// -// If possible use a load fence on the architecture, if not run a full memory -// fence - -KOKKOS_FORCEINLINE_FUNCTION -void load_fence() { -#if defined(KOKKOS_ENABLE_ASM) && defined(KOKKOS_ENABLE_ISA_X86_64) - asm volatile("lfence" ::: "memory"); -#else - memory_fence(); -#endif -} - -} // namespace Kokkos - -#endif diff --git a/lib/kokkos/core/src/impl/Kokkos_Profiling_C_Interface.h b/lib/kokkos/core/src/impl/Kokkos_Profiling_C_Interface.h index 731a11e917..15c466b27e 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Profiling_C_Interface.h +++ b/lib/kokkos/core/src/impl/Kokkos_Profiling_C_Interface.h @@ -154,7 +154,7 @@ enum Kokkos_Tools_OptimizationType { Kokkos_Tools_Maximize }; -struct Kokkos_Tools_OptimzationGoal { +struct Kokkos_Tools_OptimizationGoal { size_t type_id; enum Kokkos_Tools_OptimizationType goal; }; @@ -220,7 +220,7 @@ typedef void (*Kokkos_Tools_contextBeginFunction)(const size_t); typedef void (*Kokkos_Tools_contextEndFunction)( const size_t, struct Kokkos_Tools_VariableValue); typedef void (*Kokkos_Tools_optimizationGoalDeclarationFunction)( - const size_t, const struct Kokkos_Tools_OptimzationGoal goal); + const size_t, const struct Kokkos_Tools_OptimizationGoal goal); struct Kokkos_Profiling_EventSet { Kokkos_Profiling_initFunction init; diff --git a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp index af71932e47..b66886d9f7 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp @@ -226,7 +226,7 @@ using ValueType = Kokkos_Tools_VariableInfo_ValueType; using CandidateValueType = Kokkos_Tools_VariableInfo_CandidateValueType; using SetOrRange = Kokkos_Tools_VariableInfo_SetOrRange; using VariableInfo = Kokkos_Tools_VariableInfo; -using OptimizationGoal = Kokkos_Tools_OptimzationGoal; +using OptimizationGoal = Kokkos_Tools_OptimizationGoal; using TuningString = Kokkos_Tools_Tuning_String; using VariableValue = Kokkos_Tools_VariableValue; diff --git a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.cpp b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.cpp index 255f5125f4..0bc3814b3a 100644 --- a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.cpp @@ -20,6 +20,8 @@ #include #include +#include +#include namespace Kokkos { namespace Impl { @@ -321,5 +323,53 @@ void SharedAllocationRecord::print_host_accessible_records( } #endif +void safe_throw_allocation_with_header_failure( + std::string const& space_name, std::string const& label, + Kokkos::Experimental::RawMemoryAllocationFailure const& failure) { + auto generate_failure_message = [&](std::ostream& o) { + o << "Kokkos failed to allocate memory for label \"" << label + << "\". Allocation using MemorySpace named \"" << space_name + << "\" failed with the following error: "; + failure.print_error_message(o); + if (failure.failure_mode() == + Kokkos::Experimental::RawMemoryAllocationFailure::FailureMode:: + AllocationNotAligned) { + // TODO: delete the misaligned memory? + o << "Warning: Allocation failed due to misalignment; memory may " + "be leaked.\n"; + } + o.flush(); + }; + try { + std::ostringstream sstr; + generate_failure_message(sstr); + Kokkos::Impl::throw_runtime_exception(sstr.str()); + } catch (std::bad_alloc const&) { + // Probably failed to allocate the string because we're so close to out + // of memory. Try printing to std::cerr instead + try { + generate_failure_message(std::cerr); + } catch (std::bad_alloc const&) { + // oh well, we tried... + } + Kokkos::Impl::throw_runtime_exception( + "Kokkos encountered an allocation failure, then another allocation " + "failure while trying to create the error message."); + } +} + +void fill_host_accessible_header_info( + SharedAllocationRecord* arg_record, + SharedAllocationHeader& arg_header, std::string const& arg_label) { + // Fill in the Header information, directly accessible on the host + + arg_header.m_record = arg_record; + + strncpy(arg_header.m_label, arg_label.c_str(), + SharedAllocationHeader::maximum_label_length); + // Set last element zero, in case c_str is too long + arg_header.m_label[SharedAllocationHeader::maximum_label_length - 1] = '\0'; +} + } /* namespace Impl */ } /* namespace Kokkos */ diff --git a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp index 043505a158..99ab660213 100644 --- a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp @@ -51,6 +51,9 @@ class SharedAllocationHeader { friend class SharedAllocationRecordCommon; template friend class HostInaccessibleSharedAllocationRecordCommon; + friend void fill_host_accessible_header_info( + SharedAllocationRecord*, SharedAllocationHeader&, + std::string const&); Record* m_record; char m_label[maximum_label_length]; @@ -145,25 +148,23 @@ class SharedAllocationRecord { SharedAllocationRecord() : m_alloc_ptr(nullptr), m_alloc_size(0), - m_dealloc(nullptr) + m_dealloc(nullptr), #ifdef KOKKOS_ENABLE_DEBUG - , m_root(this), m_prev(this), - m_next(this) + m_next(this), #endif - , m_count(0) { } static constexpr unsigned maximum_label_length = SharedAllocationHeader::maximum_label_length; - KOKKOS_INLINE_FUNCTION + KOKKOS_FUNCTION const SharedAllocationHeader* head() const { return m_alloc_ptr; } /* User's memory begins at the end of the header */ - KOKKOS_INLINE_FUNCTION + KOKKOS_FUNCTION void* data() const { return static_cast(m_alloc_ptr + 1); } /* User's memory begins at the end of the header */ @@ -195,23 +196,79 @@ class SharedAllocationRecord { const SharedAllocationRecord* const root, const bool detail); }; +void safe_throw_allocation_with_header_failure( + std::string const& space_name, std::string const& label, + Kokkos::Experimental::RawMemoryAllocationFailure const& failure); + +template +SharedAllocationHeader* checked_allocation_with_header(MemorySpace const& space, + std::string const& label, + size_t alloc_size) { + try { + return reinterpret_cast(space.allocate( + label.c_str(), alloc_size + sizeof(SharedAllocationHeader), + alloc_size)); + } catch (Kokkos::Experimental::RawMemoryAllocationFailure const& failure) { + safe_throw_allocation_with_header_failure(space.name(), label, failure); + } + return nullptr; // unreachable +} + +template +SharedAllocationHeader* checked_allocation_with_header( + ExecutionSpace const& exec_space, MemorySpace const& space, + std::string const& label, size_t alloc_size) { + try { + return reinterpret_cast(space.allocate( + exec_space, label.c_str(), alloc_size + sizeof(SharedAllocationHeader), + alloc_size)); + } catch (Kokkos::Experimental::RawMemoryAllocationFailure const& failure) { + safe_throw_allocation_with_header_failure(space.name(), label, failure); + } + return nullptr; // unreachable +} + +void fill_host_accessible_header_info(SharedAllocationHeader& arg_header, + std::string const& arg_label); + template class SharedAllocationRecordCommon : public SharedAllocationRecord { private: using derived_t = SharedAllocationRecord; using record_base_t = SharedAllocationRecord; - derived_t& self() { return *static_cast(this); } - derived_t const& self() const { return *static_cast(this); } protected: using record_base_t::record_base_t; - void _fill_host_accessible_header_info(SharedAllocationHeader& arg_header, - std::string const& arg_label); + MemorySpace m_space; + +#ifdef KOKKOS_ENABLE_DEBUG + static record_base_t s_root_record; +#endif static void deallocate(record_base_t* arg_rec); public: + ~SharedAllocationRecordCommon(); + template + SharedAllocationRecordCommon( + ExecutionSpace const& exec, MemorySpace const& space, + std::string const& label, std::size_t alloc_size, + record_base_t::function_type dealloc = &deallocate) + : SharedAllocationRecord( +#ifdef KOKKOS_ENABLE_DEBUG + &s_root_record, +#endif + checked_allocation_with_header(exec, space, label, alloc_size), + sizeof(SharedAllocationHeader) + alloc_size, dealloc, label), + m_space(space) { + auto& header = *SharedAllocationRecord::m_alloc_ptr; + fill_host_accessible_header_info(this, header, label); + } + SharedAllocationRecordCommon( + MemorySpace const& space, std::string const& label, std::size_t size, + record_base_t::function_type dealloc = &deallocate); + static auto allocate(MemorySpace const& arg_space, std::string const& arg_label, size_t arg_alloc_size) -> derived_t*; @@ -231,22 +288,103 @@ class SharedAllocationRecordCommon : public SharedAllocationRecord { template class HostInaccessibleSharedAllocationRecordCommon - : public SharedAllocationRecordCommon { + : public SharedAllocationRecord { private: - using base_t = SharedAllocationRecordCommon; using derived_t = SharedAllocationRecord; using record_base_t = SharedAllocationRecord; protected: - using base_t::base_t; + using record_base_t::record_base_t; + + MemorySpace m_space; + +#ifdef KOKKOS_ENABLE_DEBUG + static record_base_t s_root_record; +#endif + + static void deallocate(record_base_t* arg_rec); public: + ~HostInaccessibleSharedAllocationRecordCommon(); + template + HostInaccessibleSharedAllocationRecordCommon( + ExecutionSpace const& exec, MemorySpace const& space, + std::string const& label, std::size_t alloc_size, + record_base_t::function_type dealloc = &deallocate) + : SharedAllocationRecord( +#ifdef KOKKOS_ENABLE_DEBUG + &s_root_record, +#endif + checked_allocation_with_header(exec, space, label, alloc_size), + sizeof(SharedAllocationHeader) + alloc_size, dealloc, label), + m_space(space) { + SharedAllocationHeader header; + + fill_host_accessible_header_info(this, header, label); + + Kokkos::Impl::DeepCopy( + exec, SharedAllocationRecord::m_alloc_ptr, &header, + sizeof(SharedAllocationHeader)); + } + HostInaccessibleSharedAllocationRecordCommon( + MemorySpace const& space, std::string const& label, std::size_t size, + record_base_t::function_type dealloc = &deallocate); + + static auto allocate(MemorySpace const& arg_space, + std::string const& arg_label, size_t arg_alloc_size) + -> derived_t*; + /**\brief Allocate tracked memory in the space */ + static void* allocate_tracked(MemorySpace const& arg_space, + std::string const& arg_alloc_label, + size_t arg_alloc_size); + /**\brief Reallocate tracked memory in the space */ + static void deallocate_tracked(void* arg_alloc_ptr); + /**\brief Deallocate tracked memory in the space */ + static void* reallocate_tracked(void* arg_alloc_ptr, size_t arg_alloc_size); + static void print_records(std::ostream& s, MemorySpace const&, bool detail = false); static auto get_record(void* alloc_ptr) -> derived_t*; std::string get_label() const; }; +#ifdef KOKKOS_ENABLE_DEBUG +template +SharedAllocationRecord + SharedAllocationRecordCommon::s_root_record; + +template +SharedAllocationRecord + HostInaccessibleSharedAllocationRecordCommon::s_root_record; +#endif + +#define KOKKOS_IMPL_SHARED_ALLOCATION_SPECIALIZATION(MEMORY_SPACE) \ + template <> \ + class Kokkos::Impl::SharedAllocationRecord \ + : public Kokkos::Impl::SharedAllocationRecordCommon { \ + using SharedAllocationRecordCommon< \ + MEMORY_SPACE>::SharedAllocationRecordCommon; \ + } + +#define KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_SPECIALIZATION( \ + MEMORY_SPACE) \ + template <> \ + class Kokkos::Impl::SharedAllocationRecord \ + : public Kokkos::Impl::HostInaccessibleSharedAllocationRecordCommon< \ + MEMORY_SPACE> { \ + using HostInaccessibleSharedAllocationRecordCommon< \ + MEMORY_SPACE>::HostInaccessibleSharedAllocationRecordCommon; \ + } + +#define KOKKOS_IMPL_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( \ + MEMORY_SPACE) \ + template class Kokkos::Impl::SharedAllocationRecordCommon + +#define KOKKOS_IMPL_HOST_INACCESSIBLE_SHARED_ALLOCATION_RECORD_EXPLICIT_INSTANTIATION( \ + MEMORY_SPACE) \ + template class Kokkos::Impl::HostInaccessibleSharedAllocationRecordCommon< \ + MEMORY_SPACE> + namespace { /* Taking the address of this function so make sure it is unique */ diff --git a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc_timpl.hpp b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc_timpl.hpp index d403ef9db0..41036ab067 100644 --- a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc_timpl.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc_timpl.hpp @@ -31,6 +31,66 @@ namespace Kokkos { namespace Impl { +template +SharedAllocationRecordCommon::~SharedAllocationRecordCommon() { + auto alloc_ptr = SharedAllocationRecord::m_alloc_ptr; + auto alloc_size = SharedAllocationRecord::m_alloc_size; + auto label = SharedAllocationRecord::m_label; + m_space.deallocate(label.c_str(), alloc_ptr, alloc_size, + alloc_size - sizeof(SharedAllocationHeader)); +} +template +HostInaccessibleSharedAllocationRecordCommon< + MemorySpace>::~HostInaccessibleSharedAllocationRecordCommon() { + auto alloc_ptr = SharedAllocationRecord::m_alloc_ptr; + auto alloc_size = SharedAllocationRecord::m_alloc_size; + auto label = SharedAllocationRecord::m_label; + m_space.deallocate(label.c_str(), alloc_ptr, alloc_size, + alloc_size - sizeof(SharedAllocationHeader)); +} + +template +SharedAllocationRecordCommon::SharedAllocationRecordCommon( + MemorySpace const& space, std::string const& label, std::size_t alloc_size, + SharedAllocationRecord::function_type dealloc) + : SharedAllocationRecord( +#ifdef KOKKOS_ENABLE_DEBUG + &s_root_record, +#endif + checked_allocation_with_header(space, label, alloc_size), + sizeof(SharedAllocationHeader) + alloc_size, dealloc, label), + m_space(space) { + auto& header = *SharedAllocationRecord::m_alloc_ptr; + fill_host_accessible_header_info(this, header, label); +} + +template +HostInaccessibleSharedAllocationRecordCommon:: + HostInaccessibleSharedAllocationRecordCommon( + MemorySpace const& space, std::string const& label, + std::size_t alloc_size, + SharedAllocationRecord::function_type dealloc) + : SharedAllocationRecord( +#ifdef KOKKOS_ENABLE_DEBUG + &s_root_record, +#endif + checked_allocation_with_header(space, label, alloc_size), + sizeof(SharedAllocationHeader) + alloc_size, dealloc, label), + m_space(space) { + SharedAllocationHeader header; + + fill_host_accessible_header_info(this, header, label); + + typename MemorySpace::execution_space exec; + Kokkos::Impl::DeepCopy( + exec, SharedAllocationRecord::m_alloc_ptr, &header, + sizeof(SharedAllocationHeader)); + exec.fence(std::string("SharedAllocationRecord::SharedAllocationRecord(): " + "fence after copying header from HostSpace"); +} + template auto SharedAllocationRecordCommon::allocate( MemorySpace const& arg_space, std::string const& arg_label, @@ -76,9 +136,64 @@ void* SharedAllocationRecordCommon::reallocate_tracked( Kokkos::Impl::DeepCopy( r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - Kokkos::fence( - "SharedAllocationRecord::reallocate_tracked(): fence after copying data"); + Kokkos::fence(std::string("SharedAllocationRecord<") + MemorySpace::name() + + ", void>::reallocate_tracked(): fence after copying data"); + + record_base_t::increment(r_new); + record_base_t::decrement(r_old); + + return r_new->data(); +} + +template +auto HostInaccessibleSharedAllocationRecordCommon::allocate( + MemorySpace const& arg_space, std::string const& arg_label, + size_t arg_alloc_size) -> derived_t* { + return new derived_t(arg_space, arg_label, arg_alloc_size); +} + +template +void* HostInaccessibleSharedAllocationRecordCommon< + MemorySpace>::allocate_tracked(const MemorySpace& arg_space, + const std::string& arg_alloc_label, + size_t arg_alloc_size) { + if (!arg_alloc_size) return nullptr; + + SharedAllocationRecord* const r = + allocate(arg_space, arg_alloc_label, arg_alloc_size); + + record_base_t::increment(r); + + return r->data(); +} + +template +void HostInaccessibleSharedAllocationRecordCommon::deallocate( + HostInaccessibleSharedAllocationRecordCommon::record_base_t* arg_rec) { + delete static_cast(arg_rec); +} + +template +void HostInaccessibleSharedAllocationRecordCommon< + MemorySpace>::deallocate_tracked(void* arg_alloc_ptr) { + if (arg_alloc_ptr != nullptr) { + SharedAllocationRecord* const r = derived_t::get_record(arg_alloc_ptr); + record_base_t::decrement(r); + } +} + +template +void* HostInaccessibleSharedAllocationRecordCommon< + MemorySpace>::reallocate_tracked(void* arg_alloc_ptr, + size_t arg_alloc_size) { + derived_t* const r_old = derived_t::get_record(arg_alloc_ptr); + derived_t* const r_new = + allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); + + Kokkos::Impl::DeepCopy( + r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); + Kokkos::fence(std::string("SharedAllocationRecord<") + MemorySpace::name() + + ", void>::reallocate_tracked(): fence after copying data"); record_base_t::increment(r_new); record_base_t::decrement(r_old); @@ -108,20 +223,6 @@ std::string SharedAllocationRecordCommon::get_label() const { return record_base_t::m_label; } -template -void SharedAllocationRecordCommon:: - _fill_host_accessible_header_info(SharedAllocationHeader& arg_header, - std::string const& arg_label) { - // Fill in the Header information, directly accessible on the host - - arg_header.m_record = &self(); - - strncpy(arg_header.m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - arg_header.m_label[SharedAllocationHeader::maximum_label_length - 1] = '\0'; -} - template void SharedAllocationRecordCommon::print_records( std::ostream& s, const MemorySpace&, bool detail) { diff --git a/lib/kokkos/core/src/impl/Kokkos_Spinwait.hpp b/lib/kokkos/core/src/impl/Kokkos_Spinwait.hpp deleted file mode 100644 index c57b17d646..0000000000 --- a/lib/kokkos/core/src/impl/Kokkos_Spinwait.hpp +++ /dev/null @@ -1,109 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#ifndef KOKKOS_SPINWAIT_HPP -#define KOKKOS_SPINWAIT_HPP - -#include -#include - -#include - -#include - -namespace Kokkos { -namespace Impl { - -enum class WaitMode : int { - ACTIVE // Used for tight loops to keep threads active longest - , - PASSIVE // Used to quickly yield the thread to quite down the system - , - ROOT // Never sleep or yield the root thread -}; - -void host_thread_yield(const uint32_t i, const WaitMode mode); - -template -std::enable_if_t::value, void> root_spinwait_while_equal( - T const volatile& flag, const T value) { - Kokkos::store_fence(); - uint32_t i = 0; - while (value == flag) { - host_thread_yield(++i, WaitMode::ROOT); - } - Kokkos::load_fence(); -} - -template -std::enable_if_t::value, void> root_spinwait_until_equal( - T const volatile& flag, const T value) { - Kokkos::store_fence(); - uint32_t i = 0; - while (value != flag) { - host_thread_yield(++i, WaitMode::ROOT); - } - Kokkos::load_fence(); -} - -template -std::enable_if_t::value, void> spinwait_while_equal( - T const volatile& flag, const T value) { - Kokkos::store_fence(); - uint32_t i = 0; - while (value == flag) { - host_thread_yield(++i, WaitMode::ACTIVE); - } - Kokkos::load_fence(); -} - -template -std::enable_if_t::value, void> yield_while_equal( - T const volatile& flag, const T value) { - Kokkos::store_fence(); - uint32_t i = 0; - while (value == flag) { - host_thread_yield(++i, WaitMode::PASSIVE); - } - Kokkos::load_fence(); -} - -template -std::enable_if_t::value, void> spinwait_until_equal( - T const volatile& flag, const T value) { - Kokkos::store_fence(); - uint32_t i = 0; - while (value != flag) { - host_thread_yield(++i, WaitMode::ACTIVE); - } - Kokkos::load_fence(); -} - -template -std::enable_if_t::value, void> yield_until_equal( - T const volatile& flag, const T value) { - Kokkos::store_fence(); - uint32_t i = 0; - while (value != flag) { - host_thread_yield(++i, WaitMode::PASSIVE); - } - Kokkos::load_fence(); -} - -} /* namespace Impl */ -} /* namespace Kokkos */ - -#endif /* #ifndef KOKKOS_SPINWAIT_HPP */ diff --git a/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp b/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp index 7e2f130564..cadeed1a6d 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp @@ -49,6 +49,11 @@ struct integral_constant { template struct always_true : std::true_type {}; +// type-dependent expression that is always false intended for use in +// static_assert to check "we should never get there" +template +struct always_false : std::false_type {}; + //============================================================================== #if defined(__cpp_lib_type_identity) diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp index 725ba5de09..fe43b63018 100644 --- a/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp @@ -27,10 +27,9 @@ struct ViewDataAnalysis> { private: using array_analysis = ViewArrayAnalysis; - static_assert(std::is_void

::value, ""); + static_assert(std::is_void

::value); static_assert(std::is_same>::value, - ""); + Kokkos::Array>::value); static_assert(std::is_scalar::value, "View of Array type must be of a scalar type"); @@ -130,6 +129,12 @@ class ViewMapping> { return m_impl_offset.m_dim.extent(r); } + static KOKKOS_INLINE_FUNCTION constexpr size_t static_extent( + const unsigned r) noexcept { + using dim_type = typename offset_type::dimension_type; + return dim_type::static_extent(r); + } + KOKKOS_INLINE_FUNCTION constexpr typename Traits::array_layout layout() const { return m_impl_offset.layout(); @@ -507,7 +512,7 @@ class ViewMapping< Kokkos::LayoutStride>::value))>, SrcTraits, Args...> { private: - static_assert(SrcTraits::rank == sizeof...(Args), ""); + static_assert(SrcTraits::rank == sizeof...(Args)); enum : bool { R0 = is_integral_extent<0, Args...>::value, diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewDataAnalysis.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewDataAnalysis.hpp new file mode 100644 index 0000000000..04c0c9aeed --- /dev/null +++ b/lib/kokkos/core/src/impl/Kokkos_ViewDataAnalysis.hpp @@ -0,0 +1,402 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_IMPL_PUBLIC_INCLUDE +static_assert(false, + "Including non-public Kokkos header files is not allowed."); +#endif + +#ifndef KOKKOS_VIEW_DATA_ANALYSIS_HPP +#define KOKKOS_VIEW_DATA_ANALYSIS_HPP + +#include + +namespace Kokkos::Impl { + +template +struct variadic_size_t { + enum : size_t { value = KOKKOS_INVALID_INDEX }; +}; + +template +struct variadic_size_t<0, Val, Args...> { + enum : size_t { value = Val }; +}; + +template +struct variadic_size_t { + enum : size_t { value = variadic_size_t::value }; +}; + +template +struct rank_dynamic; + +template <> +struct rank_dynamic<> { + enum : unsigned { value = 0 }; +}; + +template +struct rank_dynamic { + enum : unsigned { value = (Val == 0 ? 1 : 0) + rank_dynamic::value }; +}; + +#define KOKKOS_IMPL_VIEW_DIMENSION(R) \ + template \ + struct ViewDimension##R { \ + static constexpr size_t ArgN##R = (V != KOKKOS_INVALID_INDEX ? V : 1); \ + static constexpr size_t N##R = (V != KOKKOS_INVALID_INDEX ? V : 1); \ + KOKKOS_INLINE_FUNCTION explicit ViewDimension##R(size_t) {} \ + ViewDimension##R() = default; \ + ViewDimension##R(const ViewDimension##R&) = default; \ + ViewDimension##R& operator=(const ViewDimension##R&) = default; \ + }; \ + template \ + constexpr size_t ViewDimension##R::ArgN##R; \ + template \ + constexpr size_t ViewDimension##R::N##R; \ + template \ + struct ViewDimension##R<0u, RD> { \ + static constexpr size_t ArgN##R = 0; \ + std::conditional_t<(RD < 3), size_t, unsigned> N##R; \ + ViewDimension##R() = default; \ + ViewDimension##R(const ViewDimension##R&) = default; \ + ViewDimension##R& operator=(const ViewDimension##R&) = default; \ + KOKKOS_INLINE_FUNCTION explicit ViewDimension##R(size_t V) : N##R(V) {} \ + }; \ + template \ + constexpr size_t ViewDimension##R<0u, RD>::ArgN##R; + +KOKKOS_IMPL_VIEW_DIMENSION(0) +KOKKOS_IMPL_VIEW_DIMENSION(1) +KOKKOS_IMPL_VIEW_DIMENSION(2) +KOKKOS_IMPL_VIEW_DIMENSION(3) +KOKKOS_IMPL_VIEW_DIMENSION(4) +KOKKOS_IMPL_VIEW_DIMENSION(5) +KOKKOS_IMPL_VIEW_DIMENSION(6) +KOKKOS_IMPL_VIEW_DIMENSION(7) + +#undef KOKKOS_IMPL_VIEW_DIMENSION + +// MSVC does not do empty base class optimization by default. +// Per standard it is required for standard layout types +template +struct KOKKOS_IMPL_ENFORCE_EMPTY_BASE_OPTIMIZATION ViewDimension + : public ViewDimension0::value, + rank_dynamic::value>, + public ViewDimension1::value, + rank_dynamic::value>, + public ViewDimension2::value, + rank_dynamic::value>, + public ViewDimension3::value, + rank_dynamic::value>, + public ViewDimension4::value, + rank_dynamic::value>, + public ViewDimension5::value, + rank_dynamic::value>, + public ViewDimension6::value, + rank_dynamic::value>, + public ViewDimension7::value, + rank_dynamic::value> { + using D0 = ViewDimension0::value, + rank_dynamic::value>; + using D1 = ViewDimension1::value, + rank_dynamic::value>; + using D2 = ViewDimension2::value, + rank_dynamic::value>; + using D3 = ViewDimension3::value, + rank_dynamic::value>; + using D4 = ViewDimension4::value, + rank_dynamic::value>; + using D5 = ViewDimension5::value, + rank_dynamic::value>; + using D6 = ViewDimension6::value, + rank_dynamic::value>; + using D7 = ViewDimension7::value, + rank_dynamic::value>; + + using D0::ArgN0; + using D1::ArgN1; + using D2::ArgN2; + using D3::ArgN3; + using D4::ArgN4; + using D5::ArgN5; + using D6::ArgN6; + using D7::ArgN7; + + using D0::N0; + using D1::N1; + using D2::N2; + using D3::N3; + using D4::N4; + using D5::N5; + using D6::N6; + using D7::N7; + + static constexpr unsigned rank = sizeof...(Vals); + static constexpr unsigned rank_dynamic = Impl::rank_dynamic::value; + + ViewDimension() = default; + ViewDimension(const ViewDimension&) = default; + ViewDimension& operator=(const ViewDimension&) = default; + + KOKKOS_INLINE_FUNCTION + constexpr ViewDimension(size_t n0, size_t n1, size_t n2, size_t n3, size_t n4, + size_t n5, size_t n6, size_t n7) + : D0(n0 == KOKKOS_INVALID_INDEX ? 1 : n0), + D1(n1 == KOKKOS_INVALID_INDEX ? 1 : n1), + D2(n2 == KOKKOS_INVALID_INDEX ? 1 : n2), + D3(n3 == KOKKOS_INVALID_INDEX ? 1 : n3), + D4(n4 == KOKKOS_INVALID_INDEX ? 1 : n4), + D5(n5 == KOKKOS_INVALID_INDEX ? 1 : n5), + D6(n6 == KOKKOS_INVALID_INDEX ? 1 : n6), + D7(n7 == KOKKOS_INVALID_INDEX ? 1 : n7) {} + + KOKKOS_INLINE_FUNCTION + constexpr size_t extent(const unsigned r) const noexcept { + return r == 0 + ? N0 + : (r == 1 + ? N1 + : (r == 2 + ? N2 + : (r == 3 + ? N3 + : (r == 4 + ? N4 + : (r == 5 + ? N5 + : (r == 6 + ? N6 + : (r == 7 ? N7 + : 0))))))); + } + + static KOKKOS_INLINE_FUNCTION constexpr size_t static_extent( + const unsigned r) noexcept { + return r == 0 + ? ArgN0 + : (r == 1 + ? ArgN1 + : (r == 2 + ? ArgN2 + : (r == 3 + ? ArgN3 + : (r == 4 + ? ArgN4 + : (r == 5 + ? ArgN5 + : (r == 6 + ? ArgN6 + : (r == 7 ? ArgN7 + : 0))))))); + } + + template + struct prepend { + using type = ViewDimension; + }; + + template + struct append { + using type = ViewDimension; + }; +}; + +template +struct ViewDimensionJoin; + +template +struct ViewDimensionJoin, ViewDimension> { + using type = ViewDimension; +}; + +//---------------------------------------------------------------------------- + +template +struct ViewDimensionAssignable; + +template +struct ViewDimensionAssignable, + ViewDimension> { + using dst = ViewDimension; + using src = ViewDimension; + + enum { + value = unsigned(dst::rank) == unsigned(src::rank) && + ( + // Compile time check that potential static dimensions match + ((1 > dst::rank_dynamic && 1 > src::rank_dynamic) + ? (size_t(dst::ArgN0) == size_t(src::ArgN0)) + : true) && + ((2 > dst::rank_dynamic && 2 > src::rank_dynamic) + ? (size_t(dst::ArgN1) == size_t(src::ArgN1)) + : true) && + ((3 > dst::rank_dynamic && 3 > src::rank_dynamic) + ? (size_t(dst::ArgN2) == size_t(src::ArgN2)) + : true) && + ((4 > dst::rank_dynamic && 4 > src::rank_dynamic) + ? (size_t(dst::ArgN3) == size_t(src::ArgN3)) + : true) && + ((5 > dst::rank_dynamic && 5 > src::rank_dynamic) + ? (size_t(dst::ArgN4) == size_t(src::ArgN4)) + : true) && + ((6 > dst::rank_dynamic && 6 > src::rank_dynamic) + ? (size_t(dst::ArgN5) == size_t(src::ArgN5)) + : true) && + ((7 > dst::rank_dynamic && 7 > src::rank_dynamic) + ? (size_t(dst::ArgN6) == size_t(src::ArgN6)) + : true) && + ((8 > dst::rank_dynamic && 8 > src::rank_dynamic) + ? (size_t(dst::ArgN7) == size_t(src::ArgN7)) + : true)) + }; +}; + +/** \brief Given a value type and dimension generate the View data type */ +template +struct ViewDataType; + +template +struct ViewDataType> { + using type = T; +}; + +template +struct ViewDataType> { + using type = typename ViewDataType>::type; +}; + +template +struct ViewDataType> { + using type = typename ViewDataType>::type[N]; +}; + +/**\brief Analysis of View data type. + * + * Data type conforms to one of the following patterns : + * {const} value_type [][#][#][#] + * {const} value_type ***[#][#][#] + * Where the sum of counts of '*' and '[#]' is at most ten. + * + * Provide alias for ViewDimension<...> and value_type. + */ +template +struct ViewArrayAnalysis { + using value_type = T; + using const_value_type = std::add_const_t; + using non_const_value_type = std::remove_const_t; + using static_dimension = ViewDimension<>; + using dynamic_dimension = ViewDimension<>; + using dimension = ViewDimension<>; +}; + +template +struct ViewArrayAnalysis { + private: + using nested = ViewArrayAnalysis; + + public: + using value_type = typename nested::value_type; + using const_value_type = typename nested::const_value_type; + using non_const_value_type = typename nested::non_const_value_type; + + using static_dimension = + typename nested::static_dimension::template prepend::type; + + using dynamic_dimension = typename nested::dynamic_dimension; + + using dimension = + typename ViewDimensionJoin::type; +}; + +template +struct ViewArrayAnalysis { + private: + using nested = ViewArrayAnalysis; + using nested_dimension = typename nested::dimension; + + public: + using value_type = typename nested::value_type; + using const_value_type = typename nested::const_value_type; + using non_const_value_type = typename nested::non_const_value_type; + + using dynamic_dimension = + typename nested::dynamic_dimension::template prepend<0>::type; + + using static_dimension = typename nested::static_dimension; + + using dimension = + typename ViewDimensionJoin::type; +}; + +template +struct ViewArrayAnalysis { + private: + using nested = ViewArrayAnalysis; + + public: + using value_type = typename nested::value_type; + using const_value_type = typename nested::const_value_type; + using non_const_value_type = typename nested::non_const_value_type; + + using dynamic_dimension = + typename nested::dynamic_dimension::template prepend<0>::type; + + using static_dimension = typename nested::static_dimension; + + using dimension = + typename ViewDimensionJoin::type; +}; + +template +struct ViewDataAnalysis { + private: + using array_analysis = ViewArrayAnalysis; + + // ValueType is opportunity for partial specialization. + // Must match array analysis when this default template is used. + static_assert( + std::is_same::value); + + public: + using specialize = void; // No specialization + + using dimension = typename array_analysis::dimension; + using value_type = typename array_analysis::value_type; + using const_value_type = typename array_analysis::const_value_type; + using non_const_value_type = typename array_analysis::non_const_value_type; + + // Generate analogous multidimensional array specification type. + using type = typename ViewDataType::type; + using const_type = typename ViewDataType::type; + using non_const_type = + typename ViewDataType::type; + + // Generate "flattened" multidimensional array specification type. + using scalar_array_type = type; + using const_scalar_array_type = const_type; + using non_const_scalar_array_type = non_const_type; +}; + +template +struct ViewOffset { + using is_mapping_plugin = std::false_type; +}; +} // namespace Kokkos::Impl + +#endif // KOKKOS_VIEW_DATA_ANALYSIS_HPP diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp index 01d0dc4f68..3217c76e38 100644 --- a/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_ViewMapping.hpp @@ -33,255 +33,7 @@ #include #include #include - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - -template -struct variadic_size_t { - enum : size_t { value = KOKKOS_INVALID_INDEX }; -}; - -template -struct variadic_size_t<0, Val, Args...> { - enum : size_t { value = Val }; -}; - -template -struct variadic_size_t { - enum : size_t { value = variadic_size_t::value }; -}; - -template -struct rank_dynamic; - -template <> -struct rank_dynamic<> { - enum : unsigned { value = 0 }; -}; - -template -struct rank_dynamic { - enum : unsigned { value = (Val == 0 ? 1 : 0) + rank_dynamic::value }; -}; - -#define KOKKOS_IMPL_VIEW_DIMENSION(R) \ - template \ - struct ViewDimension##R { \ - static constexpr size_t ArgN##R = (V != KOKKOS_INVALID_INDEX ? V : 1); \ - static constexpr size_t N##R = (V != KOKKOS_INVALID_INDEX ? V : 1); \ - KOKKOS_INLINE_FUNCTION explicit ViewDimension##R(size_t) {} \ - ViewDimension##R() = default; \ - ViewDimension##R(const ViewDimension##R&) = default; \ - ViewDimension##R& operator=(const ViewDimension##R&) = default; \ - }; \ - template \ - constexpr size_t ViewDimension##R::ArgN##R; \ - template \ - constexpr size_t ViewDimension##R::N##R; \ - template \ - struct ViewDimension##R<0u, RD> { \ - static constexpr size_t ArgN##R = 0; \ - std::conditional_t<(RD < 3), size_t, unsigned> N##R; \ - ViewDimension##R() = default; \ - ViewDimension##R(const ViewDimension##R&) = default; \ - ViewDimension##R& operator=(const ViewDimension##R&) = default; \ - KOKKOS_INLINE_FUNCTION explicit ViewDimension##R(size_t V) : N##R(V) {} \ - }; \ - template \ - constexpr size_t ViewDimension##R<0u, RD>::ArgN##R; - -KOKKOS_IMPL_VIEW_DIMENSION(0) -KOKKOS_IMPL_VIEW_DIMENSION(1) -KOKKOS_IMPL_VIEW_DIMENSION(2) -KOKKOS_IMPL_VIEW_DIMENSION(3) -KOKKOS_IMPL_VIEW_DIMENSION(4) -KOKKOS_IMPL_VIEW_DIMENSION(5) -KOKKOS_IMPL_VIEW_DIMENSION(6) -KOKKOS_IMPL_VIEW_DIMENSION(7) - -#undef KOKKOS_IMPL_VIEW_DIMENSION - -// MSVC does not do empty base class optimization by default. -// Per standard it is required for standard layout types -template -struct KOKKOS_IMPL_ENFORCE_EMPTY_BASE_OPTIMIZATION ViewDimension - : public ViewDimension0::value, - rank_dynamic::value>, - public ViewDimension1::value, - rank_dynamic::value>, - public ViewDimension2::value, - rank_dynamic::value>, - public ViewDimension3::value, - rank_dynamic::value>, - public ViewDimension4::value, - rank_dynamic::value>, - public ViewDimension5::value, - rank_dynamic::value>, - public ViewDimension6::value, - rank_dynamic::value>, - public ViewDimension7::value, - rank_dynamic::value> { - using D0 = ViewDimension0::value, - rank_dynamic::value>; - using D1 = ViewDimension1::value, - rank_dynamic::value>; - using D2 = ViewDimension2::value, - rank_dynamic::value>; - using D3 = ViewDimension3::value, - rank_dynamic::value>; - using D4 = ViewDimension4::value, - rank_dynamic::value>; - using D5 = ViewDimension5::value, - rank_dynamic::value>; - using D6 = ViewDimension6::value, - rank_dynamic::value>; - using D7 = ViewDimension7::value, - rank_dynamic::value>; - - using D0::ArgN0; - using D1::ArgN1; - using D2::ArgN2; - using D3::ArgN3; - using D4::ArgN4; - using D5::ArgN5; - using D6::ArgN6; - using D7::ArgN7; - - using D0::N0; - using D1::N1; - using D2::N2; - using D3::N3; - using D4::N4; - using D5::N5; - using D6::N6; - using D7::N7; - - static constexpr unsigned rank = sizeof...(Vals); - static constexpr unsigned rank_dynamic = Impl::rank_dynamic::value; - - ViewDimension() = default; - ViewDimension(const ViewDimension&) = default; - ViewDimension& operator=(const ViewDimension&) = default; - - KOKKOS_INLINE_FUNCTION - constexpr ViewDimension(size_t n0, size_t n1, size_t n2, size_t n3, size_t n4, - size_t n5, size_t n6, size_t n7) - : D0(n0 == KOKKOS_INVALID_INDEX ? 1 : n0), - D1(n1 == KOKKOS_INVALID_INDEX ? 1 : n1), - D2(n2 == KOKKOS_INVALID_INDEX ? 1 : n2), - D3(n3 == KOKKOS_INVALID_INDEX ? 1 : n3), - D4(n4 == KOKKOS_INVALID_INDEX ? 1 : n4), - D5(n5 == KOKKOS_INVALID_INDEX ? 1 : n5), - D6(n6 == KOKKOS_INVALID_INDEX ? 1 : n6), - D7(n7 == KOKKOS_INVALID_INDEX ? 1 : n7) {} - - KOKKOS_INLINE_FUNCTION - constexpr size_t extent(const unsigned r) const noexcept { - return r == 0 - ? N0 - : (r == 1 - ? N1 - : (r == 2 - ? N2 - : (r == 3 - ? N3 - : (r == 4 - ? N4 - : (r == 5 - ? N5 - : (r == 6 - ? N6 - : (r == 7 ? N7 - : 0))))))); - } - - static KOKKOS_INLINE_FUNCTION constexpr size_t static_extent( - const unsigned r) noexcept { - return r == 0 - ? ArgN0 - : (r == 1 - ? ArgN1 - : (r == 2 - ? ArgN2 - : (r == 3 - ? ArgN3 - : (r == 4 - ? ArgN4 - : (r == 5 - ? ArgN5 - : (r == 6 - ? ArgN6 - : (r == 7 ? ArgN7 - : 0))))))); - } - - template - struct prepend { - using type = ViewDimension; - }; - - template - struct append { - using type = ViewDimension; - }; -}; - -template -struct ViewDimensionJoin; - -template -struct ViewDimensionJoin, ViewDimension> { - using type = ViewDimension; -}; - -//---------------------------------------------------------------------------- - -template -struct ViewDimensionAssignable; - -template -struct ViewDimensionAssignable, - ViewDimension> { - using dst = ViewDimension; - using src = ViewDimension; - - enum { - value = unsigned(dst::rank) == unsigned(src::rank) && - ( - // Compile time check that potential static dimensions match - ((1 > dst::rank_dynamic && 1 > src::rank_dynamic) - ? (size_t(dst::ArgN0) == size_t(src::ArgN0)) - : true) && - ((2 > dst::rank_dynamic && 2 > src::rank_dynamic) - ? (size_t(dst::ArgN1) == size_t(src::ArgN1)) - : true) && - ((3 > dst::rank_dynamic && 3 > src::rank_dynamic) - ? (size_t(dst::ArgN2) == size_t(src::ArgN2)) - : true) && - ((4 > dst::rank_dynamic && 4 > src::rank_dynamic) - ? (size_t(dst::ArgN3) == size_t(src::ArgN3)) - : true) && - ((5 > dst::rank_dynamic && 5 > src::rank_dynamic) - ? (size_t(dst::ArgN4) == size_t(src::ArgN4)) - : true) && - ((6 > dst::rank_dynamic && 6 > src::rank_dynamic) - ? (size_t(dst::ArgN5) == size_t(src::ArgN5)) - : true) && - ((7 > dst::rank_dynamic && 7 > src::rank_dynamic) - ? (size_t(dst::ArgN6) == size_t(src::ArgN6)) - : true) && - ((8 > dst::rank_dynamic && 8 > src::rank_dynamic) - ? (size_t(dst::ArgN7) == size_t(src::ArgN7)) - : true)) - }; -}; - -} // namespace Impl -} // namespace Kokkos +#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -657,21 +409,20 @@ struct SubviewExtents { template KOKKOS_INLINE_FUNCTION SubviewExtents(const ViewDimension& dim, Args... args) { - static_assert(DomainRank == sizeof...(DimArgs), ""); - static_assert(DomainRank == sizeof...(Args), ""); + static_assert(DomainRank == sizeof...(DimArgs)); + static_assert(DomainRank == sizeof...(Args)); // Verifies that all arguments, up to 8, are integral types, // integral extents, or don't exist. - static_assert( - RangeRank == unsigned(is_integral_extent<0, Args...>::value) + - unsigned(is_integral_extent<1, Args...>::value) + - unsigned(is_integral_extent<2, Args...>::value) + - unsigned(is_integral_extent<3, Args...>::value) + - unsigned(is_integral_extent<4, Args...>::value) + - unsigned(is_integral_extent<5, Args...>::value) + - unsigned(is_integral_extent<6, Args...>::value) + - unsigned(is_integral_extent<7, Args...>::value), - ""); + static_assert(RangeRank == + unsigned(is_integral_extent<0, Args...>::value) + + unsigned(is_integral_extent<1, Args...>::value) + + unsigned(is_integral_extent<2, Args...>::value) + + unsigned(is_integral_extent<3, Args...>::value) + + unsigned(is_integral_extent<4, Args...>::value) + + unsigned(is_integral_extent<5, Args...>::value) + + unsigned(is_integral_extent<6, Args...>::value) + + unsigned(is_integral_extent<7, Args...>::value)); if (RangeRank == 0) { m_length[0] = 0; @@ -708,149 +459,6 @@ struct SubviewExtents { namespace Kokkos { namespace Impl { - -/** \brief Given a value type and dimension generate the View data type */ -template -struct ViewDataType; - -template -struct ViewDataType> { - using type = T; -}; - -template -struct ViewDataType> { - using type = typename ViewDataType>::type; -}; - -template -struct ViewDataType> { - using type = typename ViewDataType>::type[N]; -}; - -/**\brief Analysis of View data type. - * - * Data type conforms to one of the following patterns : - * {const} value_type [][#][#][#] - * {const} value_type ***[#][#][#] - * Where the sum of counts of '*' and '[#]' is at most ten. - * - * Provide alias for ViewDimension<...> and value_type. - */ -template -struct ViewArrayAnalysis { - using value_type = T; - using const_value_type = std::add_const_t; - using non_const_value_type = std::remove_const_t; - using static_dimension = ViewDimension<>; - using dynamic_dimension = ViewDimension<>; - using dimension = ViewDimension<>; -}; - -template -struct ViewArrayAnalysis { - private: - using nested = ViewArrayAnalysis; - - public: - using value_type = typename nested::value_type; - using const_value_type = typename nested::const_value_type; - using non_const_value_type = typename nested::non_const_value_type; - - using static_dimension = - typename nested::static_dimension::template prepend::type; - - using dynamic_dimension = typename nested::dynamic_dimension; - - using dimension = - typename ViewDimensionJoin::type; -}; - -template -struct ViewArrayAnalysis { - private: - using nested = ViewArrayAnalysis; - using nested_dimension = typename nested::dimension; - - public: - using value_type = typename nested::value_type; - using const_value_type = typename nested::const_value_type; - using non_const_value_type = typename nested::non_const_value_type; - - using dynamic_dimension = - typename nested::dynamic_dimension::template prepend<0>::type; - - using static_dimension = typename nested::static_dimension; - - using dimension = - typename ViewDimensionJoin::type; -}; - -template -struct ViewArrayAnalysis { - private: - using nested = ViewArrayAnalysis; - - public: - using value_type = typename nested::value_type; - using const_value_type = typename nested::const_value_type; - using non_const_value_type = typename nested::non_const_value_type; - - using dynamic_dimension = - typename nested::dynamic_dimension::template prepend<0>::type; - - using static_dimension = typename nested::static_dimension; - - using dimension = - typename ViewDimensionJoin::type; -}; - -template -struct ViewDataAnalysis { - private: - using array_analysis = ViewArrayAnalysis; - - // ValueType is opportunity for partial specialization. - // Must match array analysis when this default template is used. - static_assert( - std::is_same::value, - ""); - - public: - using specialize = void; // No specialization - - using dimension = typename array_analysis::dimension; - using value_type = typename array_analysis::value_type; - using const_value_type = typename array_analysis::const_value_type; - using non_const_value_type = typename array_analysis::non_const_value_type; - - // Generate analogous multidimensional array specification type. - using type = typename ViewDataType::type; - using const_type = typename ViewDataType::type; - using non_const_type = - typename ViewDataType::type; - - // Generate "flattened" multidimensional array specification type. - using scalar_array_type = type; - using const_scalar_array_type = const_type; - using non_const_scalar_array_type = non_const_type; -}; - -} // namespace Impl -} // namespace Kokkos - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - -template -struct ViewOffset { - using is_mapping_plugin = std::false_type; -}; - //---------------------------------------------------------------------------- // LayoutLeft AND ( 1 >= rank OR 0 == rank_dynamic ) : no padding / striding template @@ -2919,13 +2527,9 @@ struct ViewValueFunctor { "Kokkos::View::initialization [" + name + "] via memset", Kokkos::Profiling::Experimental::device_id(space), &kpID); } - (void)ZeroMemset< - ExecSpace, Kokkos::View>>( - space, - Kokkos::View>(ptr, n), - value); + (void)ZeroMemset( + space, Kokkos::View>(ptr, n)); if (Kokkos::Profiling::profileLibraryLoaded()) { Kokkos::Profiling::endParallelFor(kpID); @@ -2949,37 +2553,33 @@ struct ViewValueFunctor { template void parallel_for_implementation() { - if (!space.in_parallel()) { - using PolicyType = - Kokkos::RangePolicy, Tag>; - PolicyType policy(space, 0, n); - uint64_t kpID = 0; - if (Kokkos::Profiling::profileLibraryLoaded()) { - const std::string functor_name = - (std::is_same_v - ? "Kokkos::View::destruction [" + name + "]" - : "Kokkos::View::initialization [" + name + "]"); - Kokkos::Profiling::beginParallelFor( - functor_name, Kokkos::Profiling::Experimental::device_id(space), - &kpID); - } + using PolicyType = + Kokkos::RangePolicy, Tag>; + PolicyType policy(space, 0, n); + uint64_t kpID = 0; + if (Kokkos::Profiling::profileLibraryLoaded()) { + const std::string functor_name = + (std::is_same_v + ? "Kokkos::View::destruction [" + name + "]" + : "Kokkos::View::initialization [" + name + "]"); + Kokkos::Profiling::beginParallelFor( + functor_name, Kokkos::Profiling::Experimental::device_id(space), + &kpID); + } #ifdef KOKKOS_ENABLE_CUDA - if (std::is_same::value) { - Kokkos::Impl::cuda_prefetch_pointer(space, ptr, sizeof(ValueType) * n, - true); - } + if (std::is_same::value) { + Kokkos::Impl::cuda_prefetch_pointer(space, ptr, sizeof(ValueType) * n, + true); + } #endif - const Kokkos::Impl::ParallelFor closure( - *this, policy); - closure.execute(); - if (default_exec_space || std::is_same_v) - space.fence("Kokkos::Impl::ViewValueFunctor: View init/destroy fence"); - if (Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::endParallelFor(kpID); - } - } else { - for (size_t i = 0; i < n; ++i) operator()(Tag{}, i); + const Kokkos::Impl::ParallelFor closure( + *this, policy); + closure.execute(); + if (default_exec_space || std::is_same_v) + space.fence("Kokkos::Impl::ViewValueFunctor: View init/destroy fence"); + if (Kokkos::Profiling::profileLibraryLoaded()) { + Kokkos::Profiling::endParallelFor(kpID); } } @@ -3057,13 +2657,9 @@ struct ViewValueFunctor { Kokkos::Profiling::Experimental::device_id(space), &kpID); } - (void)ZeroMemset< - ExecSpace, Kokkos::View>>( - space, - Kokkos::View>(ptr, n), - value); + (void)ZeroMemset( + space, Kokkos::View>(ptr, n)); if (Kokkos::Profiling::profileLibraryLoaded()) { Kokkos::Profiling::endParallelFor(kpID); @@ -3086,32 +2682,28 @@ struct ViewValueFunctor { } void parallel_for_implementation() { - if (!space.in_parallel()) { - PolicyType policy(0, n); - uint64_t kpID = 0; - if (Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::beginParallelFor( - "Kokkos::View::initialization [" + name + "]", - Kokkos::Profiling::Experimental::device_id(space), &kpID); - } + PolicyType policy(0, n); + uint64_t kpID = 0; + if (Kokkos::Profiling::profileLibraryLoaded()) { + Kokkos::Profiling::beginParallelFor( + "Kokkos::View::initialization [" + name + "]", + Kokkos::Profiling::Experimental::device_id(space), &kpID); + } #ifdef KOKKOS_ENABLE_CUDA - if (std::is_same::value) { - Kokkos::Impl::cuda_prefetch_pointer(space, ptr, sizeof(ValueType) * n, - true); - } + if (std::is_same::value) { + Kokkos::Impl::cuda_prefetch_pointer(space, ptr, sizeof(ValueType) * n, + true); + } #endif - const Kokkos::Impl::ParallelFor closure( - *this, PolicyType(0, n)); - closure.execute(); - if (default_exec_space) - space.fence( - "Kokkos::Impl::ViewValueFunctor: Fence after setting values in " - "view"); - if (Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::endParallelFor(kpID); - } - } else { - for (size_t i = 0; i < n; ++i) operator()(i); + const Kokkos::Impl::ParallelFor closure( + *this, PolicyType(0, n)); + closure.execute(); + if (default_exec_space) + space.fence( + "Kokkos::Impl::ViewValueFunctor: Fence after setting values in " + "view"); + if (Kokkos::Profiling::profileLibraryLoaded()) { + Kokkos::Profiling::endParallelFor(kpID); } } @@ -3896,7 +3488,7 @@ class ViewMapping< template struct apply { - static_assert(Kokkos::is_memory_traits::value, ""); + static_assert(Kokkos::is_memory_traits::value); using traits_type = Kokkos::ViewTraits -KOKKOS_INLINE_FUNCTION bool view_verify_operator_bounds(const MapType&) { - return true; +template +KOKKOS_FUNCTION bool within_range(Map const& map, + std::index_sequence, + Indices... indices) { + return (((std::size_t)indices < map.extent(Enumerate)) && ...); } -template -KOKKOS_INLINE_FUNCTION bool view_verify_operator_bounds(const MapType& map, - const iType& i, - Args... args) { - return (size_t(i) < map.extent(R)) && - view_verify_operator_bounds(map, args...); +template +KOKKOS_FUNCTION constexpr char* append_formatted_multidimensional_index( + char* dest, Indices... indices) { + char* d = dest; + strcat(d, "["); + ( + [&] { + d += strlen(d); + to_chars_i(d, + d + 20, // 20 digits ought to be enough + indices); + strcat(d, ","); + }(), + ...); + d[strlen(d) - 1] = ']'; // overwrite trailing comma + return dest; } -template -inline void view_error_operator_bounds(char*, int, const MapType&) {} - -template -inline void view_error_operator_bounds(char* buf, int len, const MapType& map, - const iType& i, Args... args) { - const int n = snprintf( - buf, len, " %ld < %ld %c", static_cast(i), - static_cast(map.extent(R)), (sizeof...(Args) ? ',' : ')')); - view_error_operator_bounds(buf + n, len - n, map, args...); +template +KOKKOS_FUNCTION void print_extents(char* dest, Map const& map, + std::index_sequence) { + append_formatted_multidimensional_index(dest, map.extent(Enumerate)...); } -/* Check #3: is the View managed as determined by the MemoryTraits? */ -template -struct OperatorBoundsErrorOnDevice; - -template -struct OperatorBoundsErrorOnDevice { - KOKKOS_INLINE_FUNCTION - static void run(MapType const&) { Kokkos::abort("View bounds error"); } -}; - -template -struct OperatorBoundsErrorOnDevice { - KOKKOS_INLINE_FUNCTION - static void run(MapType const& map) { - SharedAllocationHeader const* const header = - SharedAllocationHeader::get_header( - static_cast(map.data())); - char const* const label = header->label(); - enum { LEN = 128 }; - char msg[LEN]; - char const* const first_part = "View bounds error of view "; - char* p = msg; - char* const end = msg + LEN - 1; - for (char const* p2 = first_part; (*p2 != '\0') && (p < end); ++p, ++p2) { - *p = *p2; - } - for (char const* p2 = label; (*p2 != '\0') && (p < end); ++p, ++p2) { - *p = *p2; - } - *p = '\0'; - Kokkos::abort(msg); - } -}; - -/* Check #2: does the ViewMapping have the printable_label_typedef defined? - See above that only the non-specialized standard-layout ViewMapping has - this defined by default. - The existence of this alias indicates the existence of MapType::is_managed - */ template using printable_label_typedef_t = typename T::printable_label_typedef; -template -KOKKOS_FUNCTION - std::enable_if_t::value> - operator_bounds_error_on_device(Map const&) { - Kokkos::abort("View bounds error"); -} - -template -KOKKOS_FUNCTION - std::enable_if_t::value> - operator_bounds_error_on_device(Map const& map) { - OperatorBoundsErrorOnDevice::run(map); -} - template KOKKOS_INLINE_FUNCTION void view_verify_operator_bounds( Kokkos::Impl::ViewTracker const& tracker, const MapType& map, Args... args) { - if (!view_verify_operator_bounds<0>(map, args...)) { + if (!within_range(map, std::make_index_sequence(), + args...)) { + char err[256] = ""; + strcat(err, "Kokkos::View ERROR: out of bounds access"); + strcat(err, " label=(\""); KOKKOS_IF_ON_HOST( - (enum {LEN = 1024}; char buffer[LEN]; - const std::string label = - tracker.m_tracker.template get_label(); - int n = snprintf(buffer, LEN, "View bounds error of view %s (", - label.c_str()); - view_error_operator_bounds<0>(buffer + n, LEN - n, map, args...); - Kokkos::Impl::throw_runtime_exception(std::string(buffer));)) - - KOKKOS_IF_ON_DEVICE(( - /* Check #1: is there a SharedAllocationRecord? - (we won't use it, but if its not there then there isn't - a corresponding SharedAllocationHeader containing a label). - This check should cover the case of Views that don't - have the Unmanaged trait but were initialized by pointer. */ if (tracker.m_tracker.has_record()) { - operator_bounds_error_on_device(map); - } else { Kokkos::abort("View bounds error"); })) + strncat(err, tracker.m_tracker.template get_label().c_str(), + 128); + } else { strcat(err, "**UNMANAGED**"); }) + KOKKOS_IF_ON_DEVICE([&] { + // Check #1: is there a SharedAllocationRecord? (we won't use it, but + // if its not there then there isn't a corresponding + // SharedAllocationHeader containing a label). This check should cover + // the case of Views that don't have the Unmanaged trait but were + // initialized by pointer. + if (!tracker.m_tracker.has_record()) { + strcat(err, "**UNMANAGED**"); + return; + } + // Check #2: does the ViewMapping have the printable_label_typedef + // defined? See above that only the non-specialized standard-layout + // ViewMapping has this defined by default. The existence of this + // alias indicates the existence of MapType::is_managed + if constexpr (is_detected_v) { + // Check #3: is the View managed as determined by the MemoryTraits? + if constexpr (MapType::is_managed != 0) { + SharedAllocationHeader const* const header = + SharedAllocationHeader::get_header( + static_cast(map.data())); + char const* const label = header->label(); + strcat(err, label); + return; + } + strcat(err, "**UNAVAILABLE**"); + } + }();) + strcat(err, "\") with indices "); + append_formatted_multidimensional_index(err, args...); + strcat(err, " but extents "); + print_extents(err, map, std::make_index_sequence()); + Kokkos::abort(err); } } diff --git a/lib/kokkos/core/src/setup/Kokkos_Setup_SYCL.hpp b/lib/kokkos/core/src/setup/Kokkos_Setup_SYCL.hpp index 7f7957bc61..30f6fa2ad2 100644 --- a/lib/kokkos/core/src/setup/Kokkos_Setup_SYCL.hpp +++ b/lib/kokkos/core/src/setup/Kokkos_Setup_SYCL.hpp @@ -38,12 +38,11 @@ #include #endif -#ifdef __SYCL_DEVICE_ONLY__ -#define KOKKOS_IMPL_DO_NOT_USE_PRINTF(format, ...) \ - do { \ - const __attribute__((opencl_constant)) char fmt[] = (format); \ - sycl::ext::oneapi::experimental::printf(fmt, ##__VA_ARGS__); \ - } while (0) +#if defined(__INTEL_LLVM_COMPILER) && __INTEL_LLVM_COMPILER >= 20230200 +#define KOKKOS_IMPL_SYCL_GET_MULTI_PTR(accessor) \ + accessor.get_multi_ptr() +#else +#define KOKKOS_IMPL_SYCL_GET_MULTI_PTR(accessor) accessor.get_pointer() #endif #endif diff --git a/lib/kokkos/core/src/traits/Kokkos_IndexTypeTrait.hpp b/lib/kokkos/core/src/traits/Kokkos_IndexTypeTrait.hpp index 91820fbcca..e43535451c 100644 --- a/lib/kokkos/core/src/traits/Kokkos_IndexTypeTrait.hpp +++ b/lib/kokkos/core/src/traits/Kokkos_IndexTypeTrait.hpp @@ -83,7 +83,7 @@ struct IndexTypePolicyMixin : AnalyzeNextTrait { "Kokkos Error: More than one index type given. Search " "compiler output for 'show_extra_index_type' to see the " "type of the errant tag."); - static_assert(std::is_integral::value, ""); + static_assert(std::is_integral::value); static constexpr bool index_type_is_defaulted = false; using index_type = Kokkos::IndexType; }; diff --git a/lib/kokkos/core/src/traits/Kokkos_OccupancyControlTrait.hpp b/lib/kokkos/core/src/traits/Kokkos_OccupancyControlTrait.hpp index dadf582c37..c2ca5a341f 100644 --- a/lib/kokkos/core/src/traits/Kokkos_OccupancyControlTrait.hpp +++ b/lib/kokkos/core/src/traits/Kokkos_OccupancyControlTrait.hpp @@ -163,7 +163,7 @@ auto prefer(Policy const& p, DesiredOccupancy occ) { template constexpr auto prefer(Policy const& p, MaximizeOccupancy) { - static_assert(Kokkos::is_execution_policy::value, ""); + static_assert(Kokkos::is_execution_policy::value); using new_policy_t = Kokkos::Impl::OccupancyControlTrait::policy_with_trait; diff --git a/lib/kokkos/core/src/traits/Kokkos_PolicyTraitAdaptor.hpp b/lib/kokkos/core/src/traits/Kokkos_PolicyTraitAdaptor.hpp index 578e9e762a..98ad1d7ebb 100644 --- a/lib/kokkos/core/src/traits/Kokkos_PolicyTraitAdaptor.hpp +++ b/lib/kokkos/core/src/traits/Kokkos_PolicyTraitAdaptor.hpp @@ -68,7 +68,7 @@ struct PolicyTraitAdaptorImpl< TraitSpec, PolicyTemplate, type_list, type_list, NewTrait, std::enable_if_t::value>> { - static_assert(PolicyTraitMatcher::value, ""); + static_assert(PolicyTraitMatcher::value); using type = PolicyTemplate; }; @@ -92,7 +92,7 @@ template class PolicyTemplate, struct PolicyTraitAdaptorImpl, type_list<>, NewTrait> { - static_assert(PolicyTraitMatcher::value, ""); + static_assert(PolicyTraitMatcher::value); using type = PolicyTemplate; }; diff --git a/lib/kokkos/core/src/traits/Kokkos_ScheduleTrait.hpp b/lib/kokkos/core/src/traits/Kokkos_ScheduleTrait.hpp index 8613002553..4e91d89f0f 100644 --- a/lib/kokkos/core/src/traits/Kokkos_ScheduleTrait.hpp +++ b/lib/kokkos/core/src/traits/Kokkos_ScheduleTrait.hpp @@ -78,7 +78,7 @@ namespace Experimental { template constexpr auto require(Policy const& p, Kokkos::Schedule) { - static_assert(Kokkos::is_execution_policy::value, ""); + static_assert(Kokkos::is_execution_policy::value); using new_policy_t = Kokkos::Impl::ScheduleTrait::policy_with_trait< Policy, Kokkos::Schedule>; return new_policy_t{p}; diff --git a/lib/kokkos/core/src/traits/Kokkos_WorkItemPropertyTrait.hpp b/lib/kokkos/core/src/traits/Kokkos_WorkItemPropertyTrait.hpp index 8f95385c85..ae7aa6e534 100644 --- a/lib/kokkos/core/src/traits/Kokkos_WorkItemPropertyTrait.hpp +++ b/lib/kokkos/core/src/traits/Kokkos_WorkItemPropertyTrait.hpp @@ -57,7 +57,7 @@ namespace Experimental { template constexpr auto require(const Policy p, WorkItemProperty::ImplWorkItemProperty) { - static_assert(Kokkos::is_execution_policy::value, ""); + static_assert(Kokkos::is_execution_policy::value); using new_policy_t = Kokkos::Impl::WorkItemPropertyTrait::policy_with_trait< Policy, WorkItemProperty::ImplWorkItemProperty>; return new_policy_t{p}; diff --git a/lib/kokkos/core/unit_test/CMakeLists.txt b/lib/kokkos/core/unit_test/CMakeLists.txt index b71c72c3c9..6dfb7505c5 100644 --- a/lib/kokkos/core/unit_test/CMakeLists.txt +++ b/lib/kokkos/core/unit_test/CMakeLists.txt @@ -65,7 +65,7 @@ SET(KOKKOS_THREADS_NAME Threads) IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) SET(KOKKOS_OPENACC_FEATURE_LEVEL 9) ELSE() - SET(KOKKOS_OPENACC_FEATURE_LEVEL 16) + SET(KOKKOS_OPENACC_FEATURE_LEVEL 17) ENDIF() SET(KOKKOS_OPENACC_NAME Experimental::OpenACC) @@ -86,11 +86,13 @@ SET(COMPILE_ONLY_SOURCES TestDetectionIdiom.cpp TestBitManipulation.cpp TestInterOp.cpp + TestRangePolicyCTAD.cpp TestStringManipulation.cpp TestVersionMacros.cpp TestViewRank.cpp TestViewTypeTraits.cpp TestTypeList.cpp + TestMDRangePolicyCTAD.cpp view/TestExtentsDatatypeConversion.cpp ) @@ -184,6 +186,7 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;OpenMPTarget;OpenACC;HIP;SYCL) MDSpan MinMaxClamp NumericTraits + OccupancyControlTrait Other ParallelScanRangePolicy Printf @@ -200,6 +203,7 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;OpenMPTarget;OpenACC;HIP;SYCL) Reductions Reductions_DeviceView SharedAlloc + Swap ) set(file ${dir}/Test${Tag}_${Name}.cpp) # Write to a temporary intermediate file and call configure_file to avoid @@ -233,6 +237,7 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;OpenMPTarget;OpenACC;HIP;SYCL) ViewCopy_a ViewCopy_b ViewCtorDimMatch + ViewEmptyRuntimeUnmanaged ViewHooks ViewLayoutStrideAssignment ViewMapping_a @@ -240,6 +245,7 @@ foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;OpenMPTarget;OpenACC;HIP;SYCL) ViewMapping_subview ViewMemoryAccessViolation ViewOfClass + ViewOutOfBoundsAccess ViewResize WorkGraph WithoutInitializing @@ -372,20 +378,21 @@ if(Kokkos_ENABLE_OPENMPTARGET) ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_TeamCombinedReducers.cpp ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_TeamReductionScan.cpp ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_WorkGraph.cpp - IF (KOKKOS_CXX_COMPILER_ID STREQUAL "Clang" AND KOKKOS_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 16.0.0) - ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_SubView_c01.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_SubView_c02.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_SubView_c03.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_Reducers_d.cpp - endif() IF (KOKKOS_CXX_COMPILER_ID STREQUAL "Clang" AND KOKKOS_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 16.0.0) ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_AtomicOperations_shared.cpp ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_MinMaxClamp.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_TeamVectorRange.cpp ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_LocalDeepCopy.cpp + ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_Reducers_d.cpp + ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_TeamVectorRange.cpp + ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_ViewAPI_e.cpp ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_TeamScan.cpp ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_TeamBasic.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_ViewAPI_e.cpp + IF (KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 17.0.3) + ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_SubView_c01.cpp + ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_SubView_c02.cpp + ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_SubView_c03.cpp + ${CMAKE_CURRENT_BINARY_DIR}/openmptarget/TestOpenMPTarget_Reducers_d.cpp + endif() endif() # FIXME_OPENMPTARGET_CRAY: The following tests fail at compile time when the OpenMPTarget backend is enabled with the Cray compiler. # Atomic compare/exchange is used in these tests which can be one of the reasons for the compilation failures. @@ -522,17 +529,7 @@ IF(KOKKOS_ENABLE_OPENACC AND KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC) list(REMOVE_ITEM OpenACC_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/default/TestDefaultDeviceType_a1.cpp ${CMAKE_CURRENT_SOURCE_DIR}/default/TestDefaultDeviceType_b1.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_double.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_float.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_int.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_longint.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_longlongint.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_shared.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_unsignedint.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicOperations_unsignedlongint.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_Atomics.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_AtomicViews.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_BlockSizeDeduction.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_DeepCopyAlignment.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_HostSharedPtr.cpp @@ -549,17 +546,10 @@ IF(KOKKOS_ENABLE_OPENACC AND KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC) ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_Reducers_d.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_Reductions.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_Reductions_DeviceView.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_SubView_b.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_SubView_c02.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_SubView_c03.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_SubView_c05.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_SubView_c08.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_SubView_c11.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_TeamBasic.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_TeamScratch.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_TeamTeamSize.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_UniqueToken.cpp - ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_ViewMapping_b.cpp ${CMAKE_CURRENT_BINARY_DIR}/openacc/TestOpenACC_ViewResize.cpp ) endif() @@ -677,7 +667,6 @@ endif() if (Kokkos_ENABLE_OPENMP) set(OpenMP_EXTRA_SOURCES openmp/TestOpenMP_Task.cpp - openmp/TestOpenMP_PartitionMaster.cpp ) KOKKOS_ADD_EXECUTABLE_AND_TEST( CoreUnitTest_OpenMP @@ -724,12 +713,14 @@ if(Kokkos_ENABLE_HPX) hpx/TestHPX_IndependentInstancesRefCounting.cpp hpx/TestHPX_IndependentInstancesSynchronization.cpp ) +if(Kokkos_ENABLE_DEPRECATED_CODE_4) KOKKOS_ADD_EXECUTABLE_AND_TEST( CoreUnitTest_HPX_InParallel SOURCES UnitTestMainInit.cpp hpx/TestHPX_InParallel.cpp ) + endif() endif() if(Kokkos_ENABLE_OPENMPTARGET) @@ -797,6 +788,12 @@ if(Kokkos_ENABLE_CUDA) UnitTestMain.cpp cuda/TestCuda_InterOp_Streams.cpp ) + KOKKOS_ADD_EXECUTABLE_AND_TEST( + CoreUnitTest_CudaInterOpStreamsMultiGPU + SOURCES + UnitTestMainInit.cpp + cuda/TestCuda_InterOp_StreamsMultiGPU.cpp + ) KOKKOS_ADD_EXECUTABLE_AND_TEST( CoreUnitTest_CudaGraph SOURCES @@ -1039,13 +1036,7 @@ KOKKOS_ADD_ADVANCED_TEST( CoreUnitTest_PushFinalizeHook_terminate tools/TestCategoricalTuner.cpp ) endif() - if((NOT Kokkos_ENABLE_OPENMPTARGET) AND (NOT Kokkos_ENABLE_OPENACC)) - KOKKOS_ADD_EXECUTABLE_AND_TEST( - CoreUnitTest_LogicalSpaces - SOURCES - tools/TestLogicalSpaces.cpp - ) - endif() + SET(KOKKOSP_SOURCES UnitTestMainInit.cpp tools/TestEventCorrectness.cpp @@ -1167,15 +1158,6 @@ KOKKOS_ADD_TEST( NAME CoreUnitTest_StackTraceTest ) endif() -if(Kokkos_ENABLE_DEPRECATED_CODE_3) - foreach(INITTESTS_NUM RANGE 1 18) - KOKKOS_ADD_EXECUTABLE_AND_TEST( - CoreUnitTest_DefaultInit_${INITTESTS_NUM} - SOURCES UnitTestMain.cpp default/TestDefaultDeviceTypeInit_${INITTESTS_NUM}.cpp - ) - endforeach(INITTESTS_NUM) -endif() - if (KOKKOS_ENABLE_HWLOC) KOKKOS_ADD_EXECUTABLE_AND_TEST( CoreUnitTest_HWLOC @@ -1259,12 +1241,10 @@ if (NOT KOKKOS_HAS_TRILINOS) INPUT TestDeviceAndThreads.py ${USE_SOURCE_PERMISSIONS_WHEN_SUPPORTED} ) - if(NOT Kokkos_ENABLE_OPENMPTARGET) # FIXME_OPENMPTARGET does not select the right device - add_test( - NAME Kokkos_CoreUnitTest_DeviceAndThreads - COMMAND ${Python3_EXECUTABLE} -m unittest -v $/TestDeviceAndThreads.py - ) - endif() + add_test( + NAME Kokkos_CoreUnitTest_DeviceAndThreads + COMMAND ${Python3_EXECUTABLE} -m unittest -v $/TestDeviceAndThreads.py + ) endif() endif() diff --git a/lib/kokkos/core/unit_test/Makefile b/lib/kokkos/core/unit_test/Makefile index 33a84b61f9..202809d3fc 100644 --- a/lib/kokkos/core/unit_test/Makefile +++ b/lib/kokkos/core/unit_test/Makefile @@ -67,8 +67,8 @@ TESTS = AtomicOperations_int AtomicOperations_unsignedint AtomicOperations_longi tmp := $(foreach device, $(KOKKOS_DEVICELIST), \ tmp2 := $(foreach test, $(TESTS), \ $(if $(filter Test$(device)_$(test).cpp, $(shell ls Test$(device)_$(test).cpp 2>/dev/null)),,\ - $(shell echo "\#include " > Test$(device)_$(test).cpp); \ - $(shell echo "\#include " >> Test$(device)_$(test).cpp); \ + $(shell echo "$(H)include " > Test$(device)_$(test).cpp); \ + $(shell echo "$(H)include " >> Test$(device)_$(test).cpp); \ ) \ ) \ ) @@ -82,8 +82,8 @@ KOKKOS_SUBVIEW_DEVICELIST := $(filter-out Cuda, $(KOKKOS_DEVICELIST)) tmp := $(foreach device, $(KOKKOS_SUBVIEW_DEVICELIST), \ tmp2 := $(foreach test, $(SUBVIEW_TESTS), \ $(if $(filter Test$(device)_$(test).cpp, $(shell ls Test$(device)_$(test).cpp 2>/dev/null)),, \ - $(shell echo "\#include " > Test$(device)_$(test).cpp); \ - $(shell echo "\#include " >> Test$(device)_$(test).cpp); \ + $(shell echo "$(H)include " > Test$(device)_$(test).cpp); \ + $(shell echo "$(H)include " >> Test$(device)_$(test).cpp); \ ) \ )\ ) @@ -91,8 +91,8 @@ tmp := $(foreach device, $(KOKKOS_SUBVIEW_DEVICELIST), \ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp2 := $(foreach test, $(SUBVIEW_TESTS), \ $(if $(filter TestCuda_$(test).cpp, $(shell ls TestCuda_$(test).cpp 2>/dev/null)),,\ - $(shell echo "\#include " > TestCuda_$(test).cpp); \ - $(shell echo "\#include " >> TestCuda_$(test).cpp); \ + $(shell echo "$(H)include " > TestCuda_$(test).cpp); \ + $(shell echo "$(H)include " >> TestCuda_$(test).cpp); \ )\ ) @@ -100,8 +100,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp := $(foreach space, $(GPU_SPACES), \ tmp2 := $(foreach test, $(GPU_SPACE_TESTS), \ $(if $(filter Test$(space)_$(test).cpp, $(shell ls Test$(space)_$(test).cpp 2>/dev/null)),,\ - $(shell echo "\#include " > Test$(space)_$(test).cpp); \ - $(shell echo "\#include " >> Test$(space)_$(test).cpp); \ + $(shell echo "$(H)include " > Test$(space)_$(test).cpp); \ + $(shell echo "$(H)include " >> Test$(space)_$(test).cpp); \ )\ )\ ) @@ -277,8 +277,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) tmp := $(foreach space, $(GPU_SPACES), \ tmp2 := $(foreach test, $(GPU_SPACE_TESTS), \ $(if $(filter Test$(space)_$(test).cpp, $(shell ls Test$(space)_$(test).cpp 2>/dev/null)),,\ - $(shell echo "\#include " > Test$(space)_$(test).cpp); \ - $(shell echo "\#include " >> Test$(space)_$(test).cpp); \ + $(shell echo "$(H)include " > Test$(space)_$(test).cpp); \ + $(shell echo "$(H)include " >> Test$(space)_$(test).cpp); \ )\ )\ ) diff --git a/lib/kokkos/core/unit_test/TestAggregate.hpp b/lib/kokkos/core/unit_test/TestAggregate.hpp index 4f67b2eddc..f1316a7426 100644 --- a/lib/kokkos/core/unit_test/TestAggregate.hpp +++ b/lib/kokkos/core/unit_test/TestAggregate.hpp @@ -29,35 +29,31 @@ void TestViewAggregate() { value_type>; static_assert( - std::is_same >::value, - ""); + std::is_same >::value); using a32_traits = Kokkos::ViewTraits; using flat_traits = Kokkos::ViewTraits; static_assert( - std::is_same >::value, - ""); + std::is_same >::value); static_assert( - std::is_same::value, ""); - static_assert(a32_traits::rank == 2, ""); - static_assert(a32_traits::rank_dynamic == 2, ""); + std::is_same::value); + static_assert(a32_traits::rank == 2); + static_assert(a32_traits::rank_dynamic == 2); - static_assert(std::is_void::value, ""); - static_assert(flat_traits::rank == 3, ""); - static_assert(flat_traits::rank_dynamic == 2, ""); - static_assert(flat_traits::dimension::N2 == 32, ""); + static_assert(std::is_void::value); + static_assert(flat_traits::rank == 3); + static_assert(flat_traits::rank_dynamic == 2); + static_assert(flat_traits::dimension::N2 == 32); using a32_type = Kokkos::View **, DeviceType>; using a32_flat_type = typename a32_type::array_type; - static_assert(std::is_same::value, - ""); - static_assert(std::is_same::value, - ""); - static_assert(a32_type::rank == 2, ""); - static_assert(a32_flat_type::rank == 3, ""); + static_assert(std::is_same::value); + static_assert(std::is_same::value); + static_assert(a32_type::rank == 2); + static_assert(a32_flat_type::rank == 3); a32_type x("test", 4, 5); a32_flat_type y(x); diff --git a/lib/kokkos/core/unit_test/TestArray.cpp b/lib/kokkos/core/unit_test/TestArray.cpp index d3bdc4f93f..673d0036b7 100644 --- a/lib/kokkos/core/unit_test/TestArray.cpp +++ b/lib/kokkos/core/unit_test/TestArray.cpp @@ -49,4 +49,28 @@ KOKKOS_FUNCTION constexpr bool test_array_structured_binding_support() { static_assert(test_array_structured_binding_support()); +template +KOKKOS_FUNCTION constexpr bool is_equal(L const& l, R const& r) { + if (std::size(l) != std::size(r)) return false; + + for (size_t i = 0; i != std::size(l); ++i) { + if (l[i] != r[i]) return false; + } + + return true; +} + +// Disable ctad test for intel versions < 2021, see issue #6702 +#if !defined(KOKKOS_COMPILER_INTEL) || KOKKOS_COMPILER_INTEL >= 2021 +KOKKOS_FUNCTION constexpr bool test_array_ctad() { + constexpr int x = 10; + constexpr Kokkos::Array a{1, 2, 3, 5, x}; + constexpr Kokkos::Array b{1, 2, 3, 5, x}; + + return std::is_same_v && is_equal(a, b); +} + +static_assert(test_array_ctad()); +#endif + } // namespace diff --git a/lib/kokkos/core/unit_test/TestAtomicOperations.hpp b/lib/kokkos/core/unit_test/TestAtomicOperations.hpp index a5aebed413..cd7ba47aa1 100644 --- a/lib/kokkos/core/unit_test/TestAtomicOperations.hpp +++ b/lib/kokkos/core/unit_test/TestAtomicOperations.hpp @@ -368,6 +368,63 @@ bool atomic_op_test(T old_val, T update) { return result == 0; } +template +constexpr T relative_error_threshold = T(1.0e-15); + +template +bool atomic_op_test_rel(T old_val, T update) { + Kokkos::View op_data("op_data"); + Kokkos::deep_copy(op_data, old_val); + int result = 0; + Kokkos::parallel_reduce( + Kokkos::RangePolicy(0, 1), + KOKKOS_LAMBDA(int, int& local_result) { + auto fetch_result = + Op::atomic_op(&op_data(0), &op_data(1), &op_data(2), update); + T expected_val = Op::op(old_val, update); + Kokkos::memory_fence(); + if (expected_val == T(0)) { + if (fabs(op_data(0)) > relative_error_threshold) local_result += 1; + if (fabs(op_data(1)) > relative_error_threshold) local_result += 2; + if (fabs(op_data(2)) > relative_error_threshold) local_result += 4; + if (fetch_result.first != old_val) local_result += 8; + if (fabs(fetch_result.second) > relative_error_threshold) + local_result += 16; + } else { + if (fabs((op_data(0) - expected_val) / expected_val) > + relative_error_threshold) + local_result += 1; + if (fabs((op_data(1) - expected_val) / expected_val) > + relative_error_threshold) + local_result += 2; + if (fabs((op_data(2) - expected_val) / expected_val) > + relative_error_threshold) + local_result += 4; + if (fetch_result.first != old_val) local_result += 8; + if (fabs((fetch_result.second - expected_val) / expected_val) > + relative_error_threshold) + local_result += 16; + } + }, + result); + if ((result & 1) != 0) + printf("atomic_%s failed with type %s\n", Op::name(), typeid(T).name()); + if ((result & 2) != 0) + printf("atomic_fetch_%s failed with type %s\n", Op::name(), + typeid(T).name()); + if ((result & 4) != 0) + printf("atomic_%s_fetch failed with type %s\n", Op::name(), + typeid(T).name()); + if ((result & 8) != 0) + printf("atomic_fetch_%s did not return old value with type %s\n", + Op::name(), typeid(T).name()); + if ((result & 16) != 0) + printf("atomic_%s_fetch did not return updated value with type %s\n", + Op::name(), typeid(T).name()); + + return result == 0; +} + //--------------------------------------------------- //--------------atomic_test_control------------------ //--------------------------------------------------- @@ -395,6 +452,12 @@ bool AtomicOperationsTestIntegralType(int old_val_in, int update_in, int test) { case 9: return atomic_op_test(old_val, update); case 10: return atomic_op_test(old_val, update); +#if defined(KOKKOS_ENABLE_OPENACC) && defined(KOKKOS_COMPILER_NVHPC) + // FIXME_NVHPC: atomic-fetch-shift operation fails due to NVHPC OpenACC + // compiler bugs, which are reported to NVIDIA. + case 11: return true; + case 12: return true; +#else case 11: return update_in >= 0 ? atomic_op_test( old_val, update) @@ -403,6 +466,7 @@ bool AtomicOperationsTestIntegralType(int old_val_in, int update_in, int test) { return update_in >= 0 ? atomic_op_test( old_val, update) : true; +#endif case 13: return atomic_op_test(old_val, update); case 14: @@ -440,10 +504,20 @@ bool AtomicOperationsTestNonIntegralType(int old_val_in, int update_in, case 2: return atomic_op_test(old_val, update); case 3: return atomic_op_test(old_val, update); case 4: return atomic_op_test(old_val, update); +#if defined(KOKKOS_ENABLE_OPENACC) && defined(KOKKOS_COMPILER_NVHPC) + // NVHPC may use different internal precisions for the device and host + // atomic operations. Therefore, relative errors are used to compare the + // host results and device results. + case 5: + return update != 0 ? atomic_op_test_rel( + old_val, update) + : true; +#else case 5: return update != 0 ? atomic_op_test(old_val, update) : true; +#endif case 6: return atomic_op_test(old_val, update); } diff --git a/lib/kokkos/core/unit_test/TestAtomics.hpp b/lib/kokkos/core/unit_test/TestAtomics.hpp index 2b40f12d0a..5f48e8c974 100644 --- a/lib/kokkos/core/unit_test/TestAtomics.hpp +++ b/lib/kokkos/core/unit_test/TestAtomics.hpp @@ -498,7 +498,9 @@ TEST(TEST_CATEGORY, atomics) { ASSERT_TRUE((TestAtomic::Loop(100, 2))); ASSERT_TRUE((TestAtomic::Loop(100, 3))); -#ifndef KOKKOS_ENABLE_OPENMPTARGET + // FIXME_OPENMPTARGET + // FIXME_OPENACC: atomic operations on composite types are not supported. +#if !defined(KOKKOS_ENABLE_OPENMPTARGET) && !defined(KOKKOS_ENABLE_OPENACC) ASSERT_TRUE((TestAtomic::Loop, TEST_EXECSPACE>(1, 1))); ASSERT_TRUE((TestAtomic::Loop, TEST_EXECSPACE>(1, 2))); ASSERT_TRUE((TestAtomic::Loop, TEST_EXECSPACE>(1, 3))); diff --git a/lib/kokkos/core/unit_test/TestBitManipulationBuiltins.hpp b/lib/kokkos/core/unit_test/TestBitManipulationBuiltins.hpp index 092e7cff61..2f3bcfe817 100644 --- a/lib/kokkos/core/unit_test/TestBitManipulationBuiltins.hpp +++ b/lib/kokkos/core/unit_test/TestBitManipulationBuiltins.hpp @@ -804,26 +804,26 @@ struct TestBitCastFunction { using Kokkos::bit_cast; if (bit_cast(123) != 123) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed check #1\n"); + Kokkos::printf("failed check #1\n"); } if (bit_cast(123u) != 123) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed check #2\n"); + Kokkos::printf("failed check #2\n"); } if (bit_cast(~0u) != ~0) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed check #3\n"); + Kokkos::printf("failed check #3\n"); } if constexpr (sizeof(int) == sizeof(float)) { if (!check(12.34f)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed check #4\n"); + Kokkos::printf("failed check #4\n"); } } if constexpr (sizeof(unsigned long long) == sizeof(double)) { if (!check(123.456)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed check #5\n"); + Kokkos::printf("failed check #5\n"); } } @@ -848,11 +848,11 @@ struct TestBitCastFunction { } if (!(bit_cast(arr) == arr)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed check #6\n"); + Kokkos::printf("failed check #6\n"); } if (!(bit_cast(arr2) == arr2)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed check #7\n"); + Kokkos::printf("failed check #7\n"); } } }; diff --git a/lib/kokkos/core/unit_test/TestComplex.hpp b/lib/kokkos/core/unit_test/TestComplex.hpp index bcae2e1d81..5501a35b7f 100644 --- a/lib/kokkos/core/unit_test/TestComplex.hpp +++ b/lib/kokkos/core/unit_test/TestComplex.hpp @@ -451,17 +451,15 @@ TEST(TEST_CATEGORY, complex_issue_3867) { ASSERT_FLOAT_EQ(x.real(), y.real()); ASSERT_FLOAT_EQ(x.imag(), y.imag()); -#define CHECK_POW_COMPLEX_PROMOTION(ARGTYPE1, ARGTYPE2, RETURNTYPE) \ - static_assert( \ - std::is_same(), \ - std::declval()))>::value, \ - ""); \ - static_assert( \ - std::is_same(), \ - std::declval()))>::value, \ - ""); +#define CHECK_POW_COMPLEX_PROMOTION(ARGTYPE1, ARGTYPE2, RETURNTYPE) \ + static_assert( \ + std::is_same(), \ + std::declval()))>::value); \ + static_assert( \ + std::is_same(), \ + std::declval()))>::value); CHECK_POW_COMPLEX_PROMOTION(Kokkos::complex, long double, Kokkos::complex); diff --git a/lib/kokkos/core/unit_test/TestConcepts.hpp b/lib/kokkos/core/unit_test/TestConcepts.hpp index 476a884832..b85867bf63 100644 --- a/lib/kokkos/core/unit_test/TestConcepts.hpp +++ b/lib/kokkos/core/unit_test/TestConcepts.hpp @@ -22,42 +22,42 @@ using ExecutionSpace = TEST_EXECSPACE; using MemorySpace = typename ExecutionSpace::memory_space; using DeviceType = typename ExecutionSpace::device_type; -static_assert(Kokkos::is_execution_space{}, ""); -static_assert(Kokkos::is_execution_space{}, ""); -static_assert(!Kokkos::is_execution_space{}, ""); -static_assert(!Kokkos::is_execution_space{}, ""); +static_assert(Kokkos::is_execution_space{}); +static_assert(Kokkos::is_execution_space{}); +static_assert(!Kokkos::is_execution_space{}); +static_assert(!Kokkos::is_execution_space{}); -static_assert(Kokkos::is_memory_space{}, ""); -static_assert(Kokkos::is_memory_space{}, ""); -static_assert(!Kokkos::is_memory_space{}, ""); -static_assert(!Kokkos::is_memory_space{}, ""); +static_assert(Kokkos::is_memory_space{}); +static_assert(Kokkos::is_memory_space{}); +static_assert(!Kokkos::is_memory_space{}); +static_assert(!Kokkos::is_memory_space{}); -static_assert(Kokkos::is_device{}, ""); -static_assert(Kokkos::is_device{}, ""); -static_assert(!Kokkos::is_device{}, ""); -static_assert(!Kokkos::is_device{}, ""); +static_assert(Kokkos::is_device{}); +static_assert(Kokkos::is_device{}); +static_assert(!Kokkos::is_device{}); +static_assert(!Kokkos::is_device{}); -static_assert(!Kokkos::is_device{}, ""); -static_assert(!Kokkos::is_device{}, ""); +static_assert(!Kokkos::is_device{}); +static_assert(!Kokkos::is_device{}); -static_assert(Kokkos::is_space{}, ""); -static_assert(Kokkos::is_space{}, ""); -static_assert(Kokkos::is_space{}, ""); -static_assert(Kokkos::is_space{}, ""); -static_assert(Kokkos::is_space{}, ""); -static_assert(Kokkos::is_space{}, ""); -static_assert(!Kokkos::is_space{}, ""); -static_assert(!Kokkos::is_space{}, ""); -static_assert(!Kokkos::is_space{}, ""); +static_assert(Kokkos::is_space{}); +static_assert(Kokkos::is_space{}); +static_assert(Kokkos::is_space{}); +static_assert(Kokkos::is_space{}); +static_assert(Kokkos::is_space{}); +static_assert(Kokkos::is_space{}); +static_assert(!Kokkos::is_space{}); +static_assert(!Kokkos::is_space{}); +static_assert(!Kokkos::is_space{}); -static_assert(Kokkos::is_execution_space_v, ""); -static_assert(!Kokkos::is_execution_space_v, ""); +static_assert(Kokkos::is_execution_space_v); +static_assert(!Kokkos::is_execution_space_v); static_assert( - std::is_same>{}, ""); -static_assert(std::is_same>{}, ""); -static_assert(std::is_same>{}, ""); -static_assert(std::is_same>{}, ""); + std::is_same>{}); +static_assert(std::is_same>{}); +static_assert(std::is_same>{}); +static_assert(std::is_same>{}); /*------------------------------------------------- begin test for team_handle concept diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp deleted file mode 100644 index 929c91db4e..0000000000 --- a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp +++ /dev/null @@ -1,491 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#include - -#include - -#ifdef KOKKOS_ENABLE_OPENMP -#include -#endif -#include -#if !defined(KOKKOS_ENABLE_CUDA) || defined(__CUDACC__) - -namespace Test { - -namespace Impl { - -std::set delete_these; -void cleanup_memory() { - for (auto x : delete_these) { - delete[] x; - } -} - -char** init_kokkos_args(bool do_threads, bool do_numa, bool do_device, - bool do_other, bool do_tune, int& nargs, - Kokkos::InitArguments& init_args) { - nargs = (do_threads ? 1 : 0) + (do_numa ? 1 : 0) + (do_device ? 1 : 0) + - (do_other ? 4 : 0) + (do_tune ? 1 : 0); - - char** args_kokkos = new char*[nargs]; - const int max_args_size = 45; - for (int i = 0; i < nargs; i++) { - args_kokkos[i] = new char[max_args_size]; - delete_these.insert(args_kokkos[i]); - } - - int threads_idx = do_other ? 1 : 0; - int numa_idx = (do_other ? 3 : 0) + (do_threads ? 1 : 0); - int device_idx = - (do_other ? 3 : 0) + (do_threads ? 1 : 0) + (do_numa ? 1 : 0); - int tune_idx = (do_other ? 4 : 0) + (do_threads ? 1 : 0) + (do_numa ? 1 : 0) + - (do_device ? 1 : 0); - - if (do_threads) { - int nthreads = 3; - -#ifdef KOKKOS_ENABLE_OPENMP - if (omp_get_max_threads() < nthreads) { - nthreads = omp_get_max_threads(); - } -#elif defined(KOKKOS_ENABLE_HPX) - const int concurrency = std::thread::hardware_concurrency(); - if (concurrency < nthreads) { - nthreads = concurrency; - } -#endif - - if (Kokkos::hwloc::available()) { - if (Kokkos::hwloc::get_available_threads_per_core() < - static_cast(nthreads)) - nthreads = Kokkos::hwloc::get_available_threads_per_core() * - Kokkos::hwloc::get_available_numa_count(); - } - -#ifdef KOKKOS_ENABLE_SERIAL - if (std::is_same::value || - std::is_same::value) { - nthreads = 1; - } -#endif - - init_args.num_threads = nthreads; - snprintf(args_kokkos[threads_idx], max_args_size, "--threads=%i", nthreads); - } - - if (do_numa) { - int numa = 1; - if (Kokkos::hwloc::available()) { - numa = Kokkos::hwloc::get_available_numa_count(); - } - -#ifdef KOKKOS_ENABLE_SERIAL - if (std::is_same::value || - std::is_same::value) { - numa = 1; - } -#endif - - init_args.num_numa = numa; - snprintf(args_kokkos[numa_idx], max_args_size, "--numa=%i", numa); - } - - if (do_device) { - init_args.device_id = 0; - snprintf(args_kokkos[device_idx], max_args_size, "--device-id=%i", 0); - } - - if (do_other) { - snprintf(args_kokkos[0], max_args_size, "--dummyarg=1"); - snprintf(args_kokkos[threads_idx + (do_threads ? 1 : 0)], max_args_size, - "--dummy2arg"); - snprintf(args_kokkos[threads_idx + (do_threads ? 1 : 0) + 1], max_args_size, - "dummy3arg"); - snprintf(args_kokkos[device_idx + (do_device ? 1 : 0)], max_args_size, - "dummy4arg=1"); - } - - if (do_tune) { - init_args.tune_internals = true; - snprintf(args_kokkos[tune_idx], max_args_size, "--kokkos-tune-internals"); - } - - return args_kokkos; -} - -Kokkos::InitArguments init_initstruct(bool do_threads, bool do_numa, - bool do_device, bool do_tune) { - Kokkos::InitArguments args; - - if (do_threads) { - int nthreads = 3; - -#ifdef KOKKOS_ENABLE_OPENMP - if (omp_get_max_threads() < nthreads) { - nthreads = omp_get_max_threads(); - } -#elif defined(KOKKOS_ENABLE_HPX) - const int concurrency = std::thread::hardware_concurrency(); - if (concurrency < nthreads) { - nthreads = concurrency; - } -#endif - - if (Kokkos::hwloc::available()) { - if (Kokkos::hwloc::get_available_threads_per_core() < - static_cast(nthreads)) { - nthreads = Kokkos::hwloc::get_available_threads_per_core() * - Kokkos::hwloc::get_available_numa_count(); - } - } - -#ifdef KOKKOS_ENABLE_SERIAL - if (std::is_same::value || - std::is_same::value) { - nthreads = 1; - } -#endif - - args.num_threads = nthreads; - } - - if (do_numa) { - int numa = 1; - if (Kokkos::hwloc::available()) { - numa = Kokkos::hwloc::get_available_numa_count(); - } - -#ifdef KOKKOS_ENABLE_SERIAL - if (std::is_same::value || - std::is_same::value) { - numa = 1; - } -#endif - - args.num_numa = numa; - } - - if (do_device) { - args.device_id = 0; - } - - if (do_tune) { - args.tune_internals = true; - } - - return args; -} - -void check_correct_initialization(const Kokkos::InitArguments& argstruct) { - ASSERT_EQ(Kokkos::DefaultExecutionSpace::impl_is_initialized(), 1); - ASSERT_EQ(Kokkos::HostSpace::execution_space::impl_is_initialized(), 1); - - // Figure out the number of threads the HostSpace ExecutionSpace should have - // initialized to. - int expected_nthreads = argstruct.num_threads; - -#ifdef KOKKOS_ENABLE_OPENMP - if (std::is_same::value) { - // use openmp default num threads - if (expected_nthreads < 0 || - (expected_nthreads == 0 && !Kokkos::hwloc::available())) { - expected_nthreads = omp_get_max_threads(); - } - // use hwloc if available - else if (expected_nthreads == 0 && Kokkos::hwloc::available()) { - expected_nthreads = Kokkos::hwloc::get_available_numa_count() * - Kokkos::hwloc::get_available_cores_per_numa() * - Kokkos::hwloc::get_available_threads_per_core(); - } - } -#endif - - if (expected_nthreads < 1) { - if (Kokkos::hwloc::available()) { - expected_nthreads = Kokkos::hwloc::get_available_numa_count() * - Kokkos::hwloc::get_available_cores_per_numa() * - Kokkos::hwloc::get_available_threads_per_core(); - } else { - expected_nthreads = 1; - } - -#ifdef KOKKOS_ENABLE_SERIAL - if (std::is_same::value || - std::is_same::value) { - expected_nthreads = 1; - } -#endif - -#ifdef KOKKOS_ENABLE_HPX - // HPX uses all cores on machine by default. Skip this test. - if (std::is_same::value || - std::is_same::value) { - return; - } -#endif - } - - int expected_numa = argstruct.num_numa; - - if (expected_numa < 1) { - if (Kokkos::hwloc::available()) { - expected_numa = Kokkos::hwloc::get_available_numa_count(); - } else { - expected_numa = 1; - } - -#ifdef KOKKOS_ENABLE_SERIAL - if (std::is_same::value || - std::is_same::value) - expected_numa = 1; -#endif - } - - ASSERT_EQ(Kokkos::HostSpace::execution_space().impl_thread_pool_size(), - expected_nthreads); - -#ifdef KOKKOS_ENABLE_CUDA - if (std::is_same::value) { - int device; - cudaGetDevice(&device); - - int expected_device = argstruct.device_id; - if (argstruct.device_id < 0) { - expected_device = Kokkos::Cuda().cuda_device(); - } - - ASSERT_EQ(expected_device, device); - } -#endif - ASSERT_EQ(argstruct.tune_internals, Kokkos::tune_internals()); -} - -// TODO: Add check whether correct number of threads are actually started. -void test_no_arguments() { - Kokkos::initialize(); - check_correct_initialization(Kokkos::InitArguments()); - Kokkos::finalize(); -} - -void test_commandline_args(int nargs, char** args, - const Kokkos::InitArguments& argstruct) { - Kokkos::initialize(nargs, args); - check_correct_initialization(argstruct); - Kokkos::finalize(); -} - -void test_initstruct_args(const Kokkos::InitArguments& args) { - Kokkos::initialize(args); - check_correct_initialization(args); - Kokkos::finalize(); -} - -} // namespace Impl - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_01 -TEST(defaultdevicetypeinit, no_args) { Impl::test_no_arguments(); } -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_02 -TEST(defaultdevicetypeinit, commandline_args_empty) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = Impl::init_kokkos_args(false, false, false, false, false, nargs, - argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_03 -TEST(defaultdevicetypeinit, commandline_args_other) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = Impl::init_kokkos_args(false, false, false, true, false, nargs, - argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_04 -TEST(defaultdevicetypeinit, commandline_args_nthreads) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = Impl::init_kokkos_args(true, false, false, false, false, nargs, - argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_05 -TEST(defaultdevicetypeinit, commandline_args_nthreads_numa) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = - Impl::init_kokkos_args(true, true, false, false, false, nargs, argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_06 -TEST(defaultdevicetypeinit, commandline_args_nthreads_numa_device) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = - Impl::init_kokkos_args(true, true, true, false, false, nargs, argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_07 -TEST(defaultdevicetypeinit, commandline_args_nthreads_device) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = - Impl::init_kokkos_args(true, false, true, false, false, nargs, argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_08 -TEST(defaultdevicetypeinit, commandline_args_numa_device) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = - Impl::init_kokkos_args(false, true, true, false, false, nargs, argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_09 -TEST(defaultdevicetypeinit, commandline_args_device) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = Impl::init_kokkos_args(false, false, true, false, false, nargs, - argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_10 -TEST(defaultdevicetypeinit, commandline_args_nthreads_numa_device_other) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = - Impl::init_kokkos_args(true, true, true, true, false, nargs, argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_11 -TEST(defaultdevicetypeinit, commandline_args_nthreads_numa_device_other_tune) { - Kokkos::InitArguments argstruct; - int nargs = 0; - char** args = - Impl::init_kokkos_args(true, true, true, true, true, nargs, argstruct); - Impl::test_commandline_args(nargs, args, argstruct); - Impl::cleanup_memory(); - delete[] args; -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_12 -TEST(defaultdevicetypeinit, initstruct_default) { - Kokkos::InitArguments args; - Impl::test_initstruct_args(args); -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_13 -TEST(defaultdevicetypeinit, initstruct_nthreads) { - Kokkos::InitArguments args = Impl::init_initstruct(true, false, false, false); - Impl::test_initstruct_args(args); -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_14 -TEST(defaultdevicetypeinit, initstruct_nthreads_numa) { - Kokkos::InitArguments args = Impl::init_initstruct(true, true, false, false); - Impl::test_initstruct_args(args); -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_15 -TEST(defaultdevicetypeinit, initstruct_device) { - Kokkos::InitArguments args = Impl::init_initstruct(false, false, true, false); - Impl::test_initstruct_args(args); -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_16 -TEST(defaultdevicetypeinit, initstruct_nthreads_device) { - Kokkos::InitArguments args = Impl::init_initstruct(true, false, true, false); - Impl::test_initstruct_args(args); -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_17 -TEST(defaultdevicetypeinit, initstruct_nthreads_numa_device) { - Kokkos::InitArguments args = Impl::init_initstruct(true, true, true, false); - Impl::test_initstruct_args(args); -} -#endif - -#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_18 -TEST(defaultdevicetypeinit, initstruct_nthreads_numa_device_tune) { - Kokkos::InitArguments args = Impl::init_initstruct(true, true, true, true); - Impl::test_initstruct_args(args); -} -#endif - -} // namespace Test - -#endif diff --git a/lib/kokkos/core/unit_test/TestDeviceAndThreads.py b/lib/kokkos/core/unit_test/TestDeviceAndThreads.py index 1d3ff8eea7..63d26ad41a 100644 --- a/lib/kokkos/core/unit_test/TestDeviceAndThreads.py +++ b/lib/kokkos/core/unit_test/TestDeviceAndThreads.py @@ -17,6 +17,8 @@ import unittest import subprocess +import platform +import os PREFIX = "$" EXECUTABLE = "$" @@ -30,7 +32,22 @@ def GetFlag(flag, *extra_args): return int(p.stdout) def GetNumThreads(max_threads): - for x in [1, 2, 3, 5, 7]: + args = [] + name = platform.system() + if name == 'Darwin': + args = ['sysctl', '-n', 'hw.physicalcpu_max'] + elif name == 'Linux': + args = ['nproc', '--all'] + else: + args = ['wmic', 'cpu', 'get', 'NumberOfCores'] + + result = subprocess.run(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + output = result.stdout.decode('utf-8') + phys_cores_count = int(output) + looplist = [1] + [i*phys_cores_count for i in [1,2,3,4,5,6,7]] \ + if GetFlag("hwloc_enabled") else [1,2,3,4,5] + + for x in looplist: if x >= max_threads: break yield x @@ -48,13 +65,25 @@ class KokkosInitializationTestCase(unittest.TestCase): "num_threads", "--kokkos-num-threads={}".format(num_threads))) + def test_num_devices(self): + if "KOKKOS_VISIBLE_DEVICES" in os.environ: + self.skipTest("KOKKOS_VISIBLE_DEVICES environment variable is set") + num_devices = GetFlag("num_devices") + self.assertNotEqual(num_devices, 0) + if num_devices == -1: + self.skipTest("no device backend enabled") + self.assertGreaterEqual(num_devices, 1) + def test_device_id(self): - device_count = GetFlag("device_count") - if device_count == 0: - self.skipTest("no device detected") + if "KOKKOS_VISIBLE_DEVICES" in os.environ: + self.skipTest("KOKKOS_VISIBLE_DEVICES environment variable is set") + num_devices = GetFlag("num_devices") + if num_devices == -1: + self.assertEqual(-1, GetFlag("device_id")) + self.skipTest("no device backend enabled") # by default use the first GPU available for execution self.assertEqual(0, GetFlag("device_id")) - for device_id in range(device_count): + for device_id in range(num_devices): self.assertEqual( device_id, GetFlag( diff --git a/lib/kokkos/core/unit_test/TestExecSpacePartitioning.hpp b/lib/kokkos/core/unit_test/TestExecSpacePartitioning.hpp index 65314d6be7..f8b570ab64 100644 --- a/lib/kokkos/core/unit_test/TestExecSpacePartitioning.hpp +++ b/lib/kokkos/core/unit_test/TestExecSpacePartitioning.hpp @@ -28,6 +28,17 @@ struct SumFunctor { void operator()(int i, int& lsum) const { lsum += i; } }; +template +void check_space_member_for_policies(const ExecSpace& exec) { + Kokkos::RangePolicy range_policy(exec, 0, 1); + ASSERT_EQ(range_policy.space(), exec); + Kokkos::MDRangePolicy> mdrange_policy(exec, {0, 0}, + {1, 1}); + ASSERT_EQ(mdrange_policy.space(), exec); + Kokkos::TeamPolicy team_policy(exec, 1, Kokkos::AUTO); + ASSERT_EQ(team_policy.space(), exec); +} + template void check_distinctive([[maybe_unused]] ExecSpace exec1, [[maybe_unused]] ExecSpace exec2) { @@ -89,6 +100,9 @@ void run_threaded_test(const Lambda1 l1, const Lambda2 l2) { void test_partitioning(std::vector& instances) { check_distinctive(instances[0], instances[1]); + check_space_member_for_policies(instances[0]); + check_space_member_for_policies(instances[1]); + int sum1, sum2; int N = 3910; run_threaded_test( diff --git a/lib/kokkos/core/unit_test/TestExecutionSpace.hpp b/lib/kokkos/core/unit_test/TestExecutionSpace.hpp index 6f0f159c17..983a5975af 100644 --- a/lib/kokkos/core/unit_test/TestExecutionSpace.hpp +++ b/lib/kokkos/core/unit_test/TestExecutionSpace.hpp @@ -25,13 +25,7 @@ struct CheckClassWithExecutionSpaceAsDataMemberIsCopyable { Kokkos::DefaultExecutionSpace device; Kokkos::DefaultHostExecutionSpace host; - KOKKOS_FUNCTION void operator()(int, int& e) const { - // not actually doing anything useful, mostly checking that - // ExecutionSpace::in_parallel() is callable - if (static_cast(device.in_parallel()) < 0) { - ++e; - } - } + KOKKOS_FUNCTION void operator()(int i, int& e) const { e += i; } CheckClassWithExecutionSpaceAsDataMemberIsCopyable() { int errors; diff --git a/lib/kokkos/core/unit_test/TestFunctorAnalysis.hpp b/lib/kokkos/core/unit_test/TestFunctorAnalysis.hpp index c024526111..e58324144e 100644 --- a/lib/kokkos/core/unit_test/TestFunctorAnalysis.hpp +++ b/lib/kokkos/core/unit_test/TestFunctorAnalysis.hpp @@ -59,16 +59,15 @@ void test_functor_analysis() { using R01 = typename A01::Reducer; - static_assert(std::is_void::value, ""); - static_assert(std::is_void::value, ""); - static_assert(std::is_void::value, ""); - static_assert(std::is_same::value, - ""); + static_assert(std::is_void::value); + static_assert(std::is_void::value); + static_assert(std::is_void::value); + static_assert(std::is_same::value); - static_assert(!A01::has_join_member_function, ""); - static_assert(!A01::has_init_member_function, ""); - static_assert(!A01::has_final_member_function, ""); - static_assert(A01::StaticValueSize == 0, ""); + static_assert(!A01::has_join_member_function); + static_assert(!A01::has_init_member_function); + static_assert(!A01::has_final_member_function); + static_assert(A01::StaticValueSize == 0); ASSERT_EQ(R01(c01).length(), 0); //------------------------------ @@ -78,16 +77,15 @@ void test_functor_analysis() { Kokkos::RangePolicy, decltype(c02), void>; using R02 = typename A02::Reducer; - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, - ""); + static_assert(std::is_same::value); + static_assert(std::is_same::value); + static_assert(std::is_same::value); + static_assert(std::is_same::value); - static_assert(!A02::has_join_member_function, ""); - static_assert(!A02::has_init_member_function, ""); - static_assert(!A02::has_final_member_function, ""); - static_assert(A02::StaticValueSize == sizeof(double), ""); + static_assert(!A02::has_join_member_function); + static_assert(!A02::has_init_member_function); + static_assert(!A02::has_final_member_function); + static_assert(A02::StaticValueSize == sizeof(double)); ASSERT_EQ(R02(c02).length(), 1); //------------------------------ @@ -99,23 +97,19 @@ void test_functor_analysis() { using R03 = typename A03::Reducer; static_assert(std::is_same::value, - ""); + TestFunctorAnalysis_03::value_type>::value); static_assert(std::is_same::value, - ""); + TestFunctorAnalysis_03::value_type*>::value); static_assert(std::is_same::value, - ""); + TestFunctorAnalysis_03::value_type&>::value); static_assert( - std::is_same::value, - ""); + std::is_same::value); - static_assert(A03::has_join_member_function, ""); - static_assert(A03::has_init_member_function, ""); - static_assert(!A03::has_final_member_function, ""); - static_assert( - A03::StaticValueSize == sizeof(TestFunctorAnalysis_03::value_type), ""); + static_assert(A03::has_join_member_function); + static_assert(A03::has_init_member_function); + static_assert(!A03::has_final_member_function); + static_assert(A03::StaticValueSize == + sizeof(TestFunctorAnalysis_03::value_type)); ASSERT_EQ(R03(c03).length(), 1); //------------------------------ diff --git a/lib/kokkos/core/unit_test/TestHalfOperators.hpp b/lib/kokkos/core/unit_test/TestHalfOperators.hpp index 752e3b5081..c69cdd5703 100644 --- a/lib/kokkos/core/unit_test/TestHalfOperators.hpp +++ b/lib/kokkos/core/unit_test/TestHalfOperators.hpp @@ -268,96 +268,6 @@ enum OP_TESTS { N_OP_TESTS }; -// volatile-qualified parameter type 'volatile half_type' is deprecated -#if !defined(KOKKOS_ENABLE_CXX20) && !defined(KOKKOS_ENABLE_CXX23) -template -struct Functor_TestHalfVolatileOperators { - volatile half_type h_lhs, h_rhs; - view_type actual_lhs, expected_lhs; - double d_lhs, d_rhs; - Functor_TestHalfVolatileOperators(volatile half_type lhs = half_type(0), - volatile half_type rhs = half_type(0)) - : h_lhs(lhs), h_rhs(rhs) { - actual_lhs = view_type("actual_lhs", N_OP_TESTS); - expected_lhs = view_type("expected_lhs", N_OP_TESTS); - half_type nv_tmp; - nv_tmp = h_lhs; - d_lhs = static_cast(nv_tmp); - nv_tmp = h_rhs; - d_rhs = static_cast(nv_tmp); - if (std::is_same::value) { - auto run_on_host = *this; - run_on_host(0); - } else { - Kokkos::parallel_for("Test::Functor_TestHalfVolatileOperators", - Kokkos::RangePolicy(0, 1), *this); - } - } - - KOKKOS_FUNCTION - void operator()(int) const { - volatile half_type tmp_lhs; - half_type nv_tmp; - - // Initialze output views to catch missing test invocations - for (int i = 0; i < N_OP_TESTS; ++i) { - actual_lhs(i) = 1; - expected_lhs(i) = -1; - } - - nv_tmp = h_lhs; - actual_lhs(ASSIGN) = static_cast(nv_tmp); - expected_lhs(ASSIGN) = d_lhs; - - actual_lhs(LT_H_H) = h_lhs < h_rhs; - expected_lhs(LT_H_H) = d_lhs < d_rhs; - - actual_lhs(LE_H_H) = h_lhs <= h_rhs; - expected_lhs(LE_H_H) = d_lhs <= d_rhs; - - actual_lhs(NEQ) = h_lhs != h_rhs; - expected_lhs(NEQ) = d_lhs != d_rhs; - - actual_lhs(GT_H_H) = h_lhs > h_rhs; - expected_lhs(GT_H_H) = d_lhs > d_rhs; - - actual_lhs(GE_H_H) = h_lhs >= h_rhs; - expected_lhs(GE_H_H) = d_lhs >= d_rhs; - - actual_lhs(EQ) = h_lhs == h_rhs; - expected_lhs(EQ) = d_lhs == d_rhs; - - tmp_lhs = h_lhs; - tmp_lhs += h_rhs; - nv_tmp = tmp_lhs; - actual_lhs(CADD_H_H) = static_cast(nv_tmp); - expected_lhs(CADD_H_H) = d_lhs; - expected_lhs(CADD_H_H) += d_rhs; - - tmp_lhs = h_lhs; - tmp_lhs -= h_rhs; - nv_tmp = tmp_lhs; - actual_lhs(CSUB_H_H) = static_cast(nv_tmp); - expected_lhs(CSUB_H_H) = d_lhs; - expected_lhs(CSUB_H_H) -= d_rhs; - - tmp_lhs = h_lhs; - tmp_lhs *= h_rhs; - nv_tmp = tmp_lhs; - actual_lhs(CMUL_H_H) = static_cast(nv_tmp); - expected_lhs(CMUL_H_H) = d_lhs; - expected_lhs(CMUL_H_H) *= d_rhs; - - tmp_lhs = h_lhs; - tmp_lhs /= h_rhs; - nv_tmp = tmp_lhs; - actual_lhs(CDIV_H_H) = static_cast(nv_tmp); - expected_lhs(CDIV_H_H) = d_lhs; - expected_lhs(CDIV_H_H) /= d_rhs; - } -}; -#endif - template struct Functor_TestHalfOperators { half_type h_lhs, h_rhs; @@ -995,33 +905,6 @@ void __test_half_operators(half_type h_lhs, half_type h_rhs) { static_cast(epsilon)); } -// volatile-qualified parameter type 'volatile half_type' is deprecated -#if !defined(KOKKOS_ENABLE_CXX20) && !defined(KOKKOS_ENABLE_CXX23) - // Test partial volatile support - volatile half_type _h_lhs = h_lhs; - volatile half_type _h_rhs = h_rhs; - Functor_TestHalfVolatileOperators f_volatile_device( - _h_lhs, _h_rhs); - Functor_TestHalfVolatileOperators f_volatile_host( - _h_lhs, _h_rhs); - - ExecutionSpace().fence(); - Kokkos::deep_copy(f_device_actual_lhs, f_device.actual_lhs); - Kokkos::deep_copy(f_device_expected_lhs, f_device.expected_lhs); - for (int op_test = 0; op_test < N_OP_TESTS; op_test++) { - // printf("op_test = %d\n", op_test); - if (op_test == ASSIGN || op_test == LT_H_H || op_test == LE_H_H || - op_test == NEQ || op_test == EQ || op_test == GT_H_H || - op_test == GE_H_H || op_test == CADD_H_H || op_test == CSUB_H_H || - op_test == CMUL_H_H || op_test == CDIV_H_H) { - ASSERT_NEAR(f_device_actual_lhs(op_test), f_device_expected_lhs(op_test), - static_cast(epsilon)); - ASSERT_NEAR(f_host.actual_lhs(op_test), f_host.expected_lhs(op_test), - static_cast(epsilon)); - } - } -#endif - // is_trivially_copyable is false with the addition of explicit // copy constructors that are required for supporting reductions // ASSERT_TRUE(std::is_trivially_copyable::value); diff --git a/lib/kokkos/core/unit_test/TestHostSharedPtrAccessOnDevice.hpp b/lib/kokkos/core/unit_test/TestHostSharedPtrAccessOnDevice.hpp index 3ee2ff5205..467b9ad157 100644 --- a/lib/kokkos/core/unit_test/TestHostSharedPtrAccessOnDevice.hpp +++ b/lib/kokkos/core/unit_test/TestHostSharedPtrAccessOnDevice.hpp @@ -37,7 +37,7 @@ template struct CheckAccessStoredPointerAndDereferenceOnDevice { SmartPtr m_device_ptr; using ElementType = typename SmartPtr::element_type; - static_assert(std::is_same::value, ""); + static_assert(std::is_same::value); CheckAccessStoredPointerAndDereferenceOnDevice(SmartPtr device_ptr) : m_device_ptr(device_ptr) { diff --git a/lib/kokkos/core/unit_test/TestInitializationSettings.cpp b/lib/kokkos/core/unit_test/TestInitializationSettings.cpp index f5be0e47aa..40dc3f11df 100644 --- a/lib/kokkos/core/unit_test/TestInitializationSettings.cpp +++ b/lib/kokkos/core/unit_test/TestInitializationSettings.cpp @@ -20,30 +20,6 @@ namespace { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -void take_initialization_settings(Kokkos::InitializationSettings const&) {} - -TEST(defaultdevicetype, - init_arguments_implicit_conversion_to_initialization_settings) { - Kokkos::InitArguments arguments; - take_initialization_settings(arguments); // check that conversion is implicit - arguments.device_id = 1; - arguments.tune_internals = true; - Kokkos::InitializationSettings settings{arguments}; - EXPECT_FALSE(settings.has_num_threads()); - EXPECT_TRUE(settings.has_device_id()); - EXPECT_EQ(settings.get_device_id(), 1); - EXPECT_FALSE(settings.has_num_devices()); - EXPECT_FALSE(settings.has_skip_device()); - EXPECT_FALSE(settings.has_disable_warnings()); - EXPECT_TRUE(settings.has_tune_internals()); - EXPECT_TRUE(settings.get_tune_internals()); - EXPECT_FALSE(settings.has_tools_help()); - EXPECT_FALSE(settings.has_tools_libs()); - EXPECT_FALSE(settings.has_tools_args()); -} -#endif - TEST(defaultdevicetype, initialization_settings) { auto const settings = Kokkos::InitializationSettings() .set_num_threads(255) @@ -52,8 +28,6 @@ TEST(defaultdevicetype, initialization_settings) { EXPECT_TRUE(settings.has_num_threads()); EXPECT_EQ(settings.get_num_threads(), 255); EXPECT_FALSE(settings.has_device_id()); - EXPECT_FALSE(settings.has_num_devices()); - EXPECT_FALSE(settings.has_skip_device()); EXPECT_TRUE(settings.has_disable_warnings()); EXPECT_FALSE(settings.get_disable_warnings()); EXPECT_FALSE(settings.has_tune_internals()); @@ -75,8 +49,6 @@ constexpr bool test_initialization_settings_getter() { TYPE>::value); CHECK_INITIALIZATION_SETTINGS_GETTER_RETURN_TYPE(num_threads, int); CHECK_INITIALIZATION_SETTINGS_GETTER_RETURN_TYPE(device_id, int); - CHECK_INITIALIZATION_SETTINGS_GETTER_RETURN_TYPE(num_devices, int); - CHECK_INITIALIZATION_SETTINGS_GETTER_RETURN_TYPE(skip_device, int); CHECK_INITIALIZATION_SETTINGS_GETTER_RETURN_TYPE(disable_warnings, bool); CHECK_INITIALIZATION_SETTINGS_GETTER_RETURN_TYPE(tune_internals, bool); CHECK_INITIALIZATION_SETTINGS_GETTER_RETURN_TYPE(tools_help, bool); diff --git a/lib/kokkos/core/unit_test/TestJoinBackwardCompatibility.hpp b/lib/kokkos/core/unit_test/TestJoinBackwardCompatibility.hpp index 24cf52aa70..efe4a2307a 100644 --- a/lib/kokkos/core/unit_test/TestJoinBackwardCompatibility.hpp +++ b/lib/kokkos/core/unit_test/TestJoinBackwardCompatibility.hpp @@ -36,9 +36,8 @@ KOKKOS_FUNCTION constexpr MyErrorCode operator|(MyErrorCode lhs, } static_assert((no_error | error_operator_plus_equal_volatile) == - error_operator_plus_equal_volatile, - ""); -static_assert((error_join_volatile | error_operator_plus_equal) == 0b101, ""); + error_operator_plus_equal_volatile); +static_assert((error_join_volatile | error_operator_plus_equal) == 0b101); struct MyJoinBackCompatValueType { MyErrorCode err = no_error; diff --git a/lib/kokkos/core/unit_test/TestMDRangePolicyCTAD.cpp b/lib/kokkos/core/unit_test/TestMDRangePolicyCTAD.cpp new file mode 100644 index 0000000000..b2c3d021c3 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestMDRangePolicyCTAD.cpp @@ -0,0 +1,138 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include + +namespace { + +struct TestMDRangePolicyCTAD { + template + static void maybe_unused(Ts&&...) {} + + struct SomeExecutionSpace { + using execution_space = SomeExecutionSpace; + using size_type = size_t; + }; + static_assert(Kokkos::is_execution_space_v); + + struct ImplicitlyConvertibleToDefaultExecutionSpace { + [[maybe_unused]] operator Kokkos::DefaultExecutionSpace() const { + return Kokkos::DefaultExecutionSpace(); + } + }; + static_assert(!Kokkos::is_execution_space_v< + ImplicitlyConvertibleToDefaultExecutionSpace>); + + [[maybe_unused]] static inline Kokkos::DefaultExecutionSpace des; + [[maybe_unused]] static inline ImplicitlyConvertibleToDefaultExecutionSpace + notEs; + [[maybe_unused]] static inline SomeExecutionSpace ses; + + [[maybe_unused]] static inline int t[5]; + [[maybe_unused]] static inline int64_t tt[5]; + [[maybe_unused]] static inline Kokkos::Array a; + [[maybe_unused]] static inline Kokkos::Array aa; + [[maybe_unused]] static inline int64_t i64; + + // Workaround for nvc++ (CUDA-11.7-NVHPC) ignoring [[maybe_unused]] on + // ImplicitlyConvertibleToDefaultExecutionSpace::operator + // Kokkos::DefaultExecutionSpace() const + [[maybe_unused]] static inline Kokkos::DefaultExecutionSpace notEsToDes = + notEs; + + // Workaround for HIP-ROCm-5.2 "declared but never referenced" + TestMDRangePolicyCTAD() { + maybe_unused(des, notEs, ses, t, tt, a, aa, notEsToDes, i64); + } + + // MDRangePolicy with C array parameters + + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(t, t))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(t, t, tt))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(des, t, tt))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(notEs, t, t))>); + + static_assert( + std::is_same_v< + Kokkos::MDRangePolicy>, + decltype(Kokkos::MDRangePolicy(ses, t, t))>); + + // MDRangePolicy with Kokkos::initializer_list parameters + + static_assert(std::is_same_v>, + decltype(Kokkos::MDRangePolicy( + {1, 2, 3, 4, 5, 6}, {1, 2, 3, 4, 5, 6}))>); + + static_assert(std::is_same_v>, + decltype(Kokkos::MDRangePolicy( + {1, 2, 3, 4, 5, 6}, {1, 2, 3, 4, 5, 6}, + {i64, i64, i64, i64, i64, i64}))>); + + static_assert(std::is_same_v>, + decltype(Kokkos::MDRangePolicy( + des, {1, 2, 3, 4, 5, 6}, + {i64, i64, i64, i64, i64, i64}))>); + + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(notEs, {1, 2, 3, 4, 5, 6}, + {1, 2, 3, 4, 5, 6}))>); + + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(ses, {1, 2, 3, 4, 5, 6}, + {1, 2, 3, 4, 5, 6}))>); + + // MDRangePolicy with Kokkos::Array parameters + + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(a, a))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(a, a, aa))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(des, a, a))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(notEs, a, a))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(des, a, a, aa))>); + static_assert( + std::is_same_v>, + decltype(Kokkos::MDRangePolicy(notEs, a, a, aa))>); + + static_assert( + std::is_same_v< + Kokkos::MDRangePolicy>, + decltype(Kokkos::MDRangePolicy(ses, a, a))>); + static_assert( + std::is_same_v< + Kokkos::MDRangePolicy>, + decltype(Kokkos::MDRangePolicy(ses, a, a, aa))>); +}; + +} // namespace diff --git a/lib/kokkos/core/unit_test/TestMDRangePolicyConstructors.hpp b/lib/kokkos/core/unit_test/TestMDRangePolicyConstructors.hpp index f577f415e7..6f241b45d4 100644 --- a/lib/kokkos/core/unit_test/TestMDRangePolicyConstructors.hpp +++ b/lib/kokkos/core/unit_test/TestMDRangePolicyConstructors.hpp @@ -18,6 +18,8 @@ #include +#include + namespace { template @@ -86,12 +88,56 @@ TEST(TEST_CATEGORY_DEATH, policy_bounds_unsafe_narrowing_conversions) { using Policy = Kokkos::MDRangePolicy, Kokkos::IndexType>; + std::string msg = + "Kokkos::MDRangePolicy bound type error: an unsafe implicit conversion " + "is " + "performed on a bound (-1) in dimension (0), which may not preserve its " + "original value.\n"; + std::string expected = std::regex_replace(msg, std::regex("\\(|\\)"), "\\$&"); + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; - ASSERT_DEATH( - { - (void)Policy({-1, 0}, {2, 3}); - }, - "unsafe narrowing conversion"); + ASSERT_DEATH({ (void)Policy({-1, 0}, {2, 3}); }, expected); +} + +TEST(TEST_CATEGORY_DEATH, policy_invalid_bounds) { + using Policy = Kokkos::MDRangePolicy>; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + + auto [dim0, dim1] = (Policy::inner_direction == Kokkos::Iterate::Right) + ? std::make_pair(1, 0) + : std::make_pair(0, 1); + std::string msg1 = + "Kokkos::MDRangePolicy bounds error: The lower bound (100) is greater " + "than its upper bound (90) in dimension " + + std::to_string(dim0) + ".\n"; + + std::string msg2 = + "Kokkos::MDRangePolicy bounds error: The lower bound (100) is greater " + "than its upper bound (90) in dimension " + + std::to_string(dim1) + ".\n"; + +#if !defined(KOKKOS_ENABLE_DEPRECATED_CODE_4) + // escape the parentheses in the regex to match the error message + msg1 = std::regex_replace(msg1, std::regex("\\(|\\)"), "\\$&"); + (void)msg2; + ASSERT_DEATH({ (void)Policy({100, 100}, {90, 90}); }, msg1); +#else + if (!Kokkos::show_warnings()) { + GTEST_SKIP() << "Kokkos warning messages are disabled"; + } + + ::testing::internal::CaptureStderr(); + (void)Policy({100, 100}, {90, 90}); +#ifdef KOKKOS_ENABLE_DEPRECATION_WARNINGS + ASSERT_EQ(::testing::internal::GetCapturedStderr(), msg1 + msg2); +#else + ASSERT_TRUE(::testing::internal::GetCapturedStderr().empty()); + (void)msg1; + (void)msg2; +#endif + +#endif } #endif diff --git a/lib/kokkos/core/unit_test/TestMathematicalFunctions.hpp b/lib/kokkos/core/unit_test/TestMathematicalFunctions.hpp index d32ef4ca23..ad035d4e4b 100644 --- a/lib/kokkos/core/unit_test/TestMathematicalFunctions.hpp +++ b/lib/kokkos/core/unit_test/TestMathematicalFunctions.hpp @@ -30,8 +30,9 @@ #define MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS #endif -#if defined KOKKOS_COMPILER_INTEL || \ - (defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130) +#if defined KOKKOS_COMPILER_INTEL || \ + (defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ + !defined(KOKKOS_COMPILER_MSVC)) #define MATHEMATICAL_FUNCTIONS_TEST_UNREACHABLE __builtin_unreachable(); #else #define MATHEMATICAL_FUNCTIONS_TEST_UNREACHABLE @@ -286,21 +287,20 @@ struct FloatingPointComparison { public: template - KOKKOS_FUNCTION bool compare_near_zero(FPT const& fpv, double ulp) const { + KOKKOS_FUNCTION bool compare_near_zero(FPT const& fpv, int ulp) const { auto abs_tol = eps(fpv) * ulp; bool ar = absolute(fpv) < abs_tol; if (!ar) { Kokkos::printf("absolute value exceeds tolerance [|%e| > %e]\n", - (double)fpv, abs_tol); + (double)fpv, (double)abs_tol); } return ar; } template - KOKKOS_FUNCTION bool compare(Lhs const& lhs, Rhs const& rhs, - double ulp) const { + KOKKOS_FUNCTION bool compare(Lhs const& lhs, Rhs const& rhs, int ulp) const { if (lhs == 0) { return compare_near_zero(rhs, ulp); } else if (rhs == 0) { @@ -314,7 +314,7 @@ struct FloatingPointComparison { bool ar = abs_diff == 0 || rel_diff < rel_tol; if (!ar) { Kokkos::printf("relative difference exceeds tolerance [%e > %e]\n", - (double)rel_diff, rel_tol); + (double)rel_diff, (double)rel_tol); } return ar; @@ -347,7 +347,7 @@ struct math_function_name; } \ MATHEMATICAL_FUNCTIONS_TEST_UNREACHABLE \ } \ - static KOKKOS_FUNCTION double ulp_factor() { return ULP_FACTOR; } \ + static KOKKOS_FUNCTION int ulp_factor() { return ULP_FACTOR; } \ }; \ using kk_##FUNC = MathUnaryFunction_##FUNC; \ template <> \ @@ -372,7 +372,7 @@ struct math_function_name; math_unary_function_return_type_t>::value); \ return REF_FUNC; \ } \ - static KOKKOS_FUNCTION double ulp_factor() { return ULP_FACTOR; } \ + static KOKKOS_FUNCTION int ulp_factor() { return ULP_FACTOR; } \ }; \ using kk_##FUNC = MathUnaryFunction_##FUNC; \ template <> \ @@ -394,10 +394,12 @@ DEFINE_UNARY_FUNCTION_EVAL(log2, 2); DEFINE_UNARY_FUNCTION_EVAL(log1p, 2); #endif -#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_1 +#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_2 DEFINE_UNARY_FUNCTION_EVAL(sqrt, 2); DEFINE_UNARY_FUNCTION_EVAL(cbrt, 2); +#endif +#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_1 DEFINE_UNARY_FUNCTION_EVAL(sin, 2); DEFINE_UNARY_FUNCTION_EVAL(cos, 2); DEFINE_UNARY_FUNCTION_EVAL(tan, 2); @@ -474,7 +476,7 @@ DEFINE_UNARY_FUNCTION_EVAL(logb, 2); } \ MATHEMATICAL_FUNCTIONS_TEST_UNREACHABLE \ } \ - static KOKKOS_FUNCTION double ulp_factor() { return ULP_FACTOR; } \ + static KOKKOS_FUNCTION int ulp_factor() { return ULP_FACTOR; } \ }; \ using kk_##FUNC = MathBinaryFunction_##FUNC; \ template <> \ @@ -483,11 +485,9 @@ DEFINE_UNARY_FUNCTION_EVAL(logb, 2); }; \ constexpr char math_function_name::name[] -#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_1 +#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_2 DEFINE_BINARY_FUNCTION_EVAL(pow, 2); DEFINE_BINARY_FUNCTION_EVAL(hypot, 2); -#endif -#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_2 DEFINE_BINARY_FUNCTION_EVAL(nextafter, 1); DEFINE_BINARY_FUNCTION_EVAL(copysign, 1); #endif @@ -510,7 +510,7 @@ DEFINE_BINARY_FUNCTION_EVAL(copysign, 1); math_ternary_function_return_type_t>::value); \ return std::FUNC(x, y, z); \ } \ - static KOKKOS_FUNCTION double ulp_factor() { return ULP_FACTOR; } \ + static KOKKOS_FUNCTION int ulp_factor() { return ULP_FACTOR; } \ }; \ using kk3_##FUNC = MathTernaryFunction_##FUNC; \ template <> \ @@ -519,7 +519,7 @@ DEFINE_BINARY_FUNCTION_EVAL(copysign, 1); }; \ constexpr char math_function_name::name[] -#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_1 +#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_2 DEFINE_TERNARY_FUNCTION_EVAL(hypot, 2); DEFINE_TERNARY_FUNCTION_EVAL(fma, 2); #endif @@ -787,7 +787,9 @@ TEST(TEST_CATEGORY, mathematical_functions_trigonometric_functions) { // TODO atan2 } +#endif +#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_2 TEST(TEST_CATEGORY, mathematical_functions_power_functions) { TEST_MATH_FUNCTION(sqrt)({0, 1, 2, 3, 5, 7, 11}); TEST_MATH_FUNCTION(sqrt)({0l, 1l, 2l, 3l, 5l, 7l, 11l}); @@ -1304,12 +1306,12 @@ struct TestAbsoluteValueFunction { if (abs(static_cast(4.f)) != static_cast(4.f) || abs(static_cast(-4.f)) != static_cast(4.f)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed abs(KE::half_t)\n"); + Kokkos::printf("failed abs(KE::half_t)\n"); } if (abs(static_cast(4.f)) != static_cast(4.f) || abs(static_cast(-4.f)) != static_cast(4.f)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed abs(KE::bhalf_t)\n"); + Kokkos::printf("failed abs(KE::bhalf_t)\n"); } if (abs(5.) != 5. || abs(-5.) != 5.) { ++e; @@ -1329,19 +1331,17 @@ struct TestAbsoluteValueFunction { Kokkos::printf("failed abs(floating_point) special values\n"); } - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); + static_assert(std::is_same::value); + static_assert(std::is_same::value); + static_assert(std::is_same::value); static_assert(std::is_same(4.f))), - KE::half_t>::value, - ""); + KE::half_t>::value); static_assert(std::is_same(4.f))), - KE::bhalf_t>::value, - ""); - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); + KE::bhalf_t>::value); + static_assert(std::is_same::value); + static_assert(std::is_same::value); #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS - static_assert(std::is_same::value, ""); + static_assert(std::is_same::value); #endif } }; @@ -1362,26 +1362,26 @@ struct TestFloatingPointAbsoluteValueFunction { using Kokkos::fabs; if (fabs(4.f) != 4.f || fabs(-4.f) != 4.f) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fabs(float)\n"); + Kokkos::printf("failed fabs(float)\n"); } if (fabs(static_cast(4.f)) != static_cast(4.f) || fabs(static_cast(-4.f)) != static_cast(4.f)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fabs(KE::half_t)\n"); + Kokkos::printf("failed fabs(KE::half_t)\n"); } if (fabs(static_cast(4.f)) != static_cast(4.f) || fabs(static_cast(-4.f)) != static_cast(4.f)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fabs(KE::bhalf_t)\n"); + Kokkos::printf("failed fabs(KE::bhalf_t)\n"); } if (fabs(5.) != 5. || fabs(-5.) != 5.) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fabs(double)\n"); + Kokkos::printf("failed fabs(double)\n"); } #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS if (fabs(6.l) != 6.l || fabs(-6.l) != 6.l) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fabs(long double)\n"); + Kokkos::printf("failed fabs(long double)\n"); } #endif // special values @@ -1389,8 +1389,7 @@ struct TestFloatingPointAbsoluteValueFunction { using Kokkos::isnan; if (fabs(-0.) != 0. || !isinf(fabs(-INFINITY)) || !isnan(fabs(-NAN))) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF( - "failed fabs(floating_point) special values\n"); + Kokkos::printf("failed fabs(floating_point) special values\n"); } static_assert(std::is_same(4.f))), @@ -1422,7 +1421,7 @@ struct TestFloatingPointRemainderFunction : FloatingPointComparison { if (!compare(fmod(6.2f, 4.f), 2.2f, 1) && !compare(fmod(-6.2f, 4.f), -2.2f, 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fmod(float)\n"); + Kokkos::printf("failed fmod(float)\n"); } if (!compare( fmod(static_cast(6.2f), static_cast(4.f)), @@ -1431,7 +1430,7 @@ struct TestFloatingPointRemainderFunction : FloatingPointComparison { fmod(static_cast(-6.2f), static_cast(4.f)), -static_cast(2.2f), 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fmod(KE::half_t)\n"); + Kokkos::printf("failed fmod(KE::half_t)\n"); } if (!compare( fmod(static_cast(6.2f), static_cast(4.f)), @@ -1440,17 +1439,17 @@ struct TestFloatingPointRemainderFunction : FloatingPointComparison { static_cast(4.f)), -static_cast(2.2f), 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fmod(KE::bhalf_t)\n"); + Kokkos::printf("failed fmod(KE::bhalf_t)\n"); } if (!compare(fmod(6.2, 4.), 2.2, 1) && !compare(fmod(-6.2, 4.), -2.2, 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fmod(double)\n"); + Kokkos::printf("failed fmod(double)\n"); } #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS if (!compare(fmod(6.2l, 4.l), 2.2l, 1) && !compare(fmod(-6.2l, 4.l), -2.2l, 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed fmod(long double)\n"); + Kokkos::printf("failed fmod(long double)\n"); } #endif // special values @@ -1459,23 +1458,19 @@ struct TestFloatingPointRemainderFunction : FloatingPointComparison { if (!isinf(fmod(-KE::infinity::value, 1.f)) && !isnan(fmod(-KE::quiet_NaN::value, 1.f))) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF( - "failed fmod(floating_point) special values\n"); + Kokkos::printf("failed fmod(floating_point) special values\n"); } static_assert(std::is_same(4.f), static_cast(4.f))), - KE::half_t>::value, - ""); + KE::half_t>::value); static_assert(std::is_same(4.f), static_cast(4.f))), - KE::bhalf_t>::value, - ""); - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); + KE::bhalf_t>::value); + static_assert(std::is_same::value); + static_assert(std::is_same::value); #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS - static_assert(std::is_same::value, - ""); + static_assert(std::is_same::value); #endif } }; @@ -1499,7 +1494,7 @@ struct TestIEEEFloatingPointRemainderFunction : FloatingPointComparison { if (!compare(remainder(6.2f, 4.f), 2.2f, 2) && !compare(remainder(-6.2f, 4.f), 2.2f, 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed remainder(float)\n"); + Kokkos::printf("failed remainder(float)\n"); } if (!compare(remainder(static_cast(6.2f), static_cast(4.f)), @@ -1508,7 +1503,7 @@ struct TestIEEEFloatingPointRemainderFunction : FloatingPointComparison { static_cast(4.f)), -static_cast(2.2f), 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed remainder(KE::half_t)\n"); + Kokkos::printf("failed remainder(KE::half_t)\n"); } if (!compare(remainder(static_cast(6.2f), static_cast(4.f)), @@ -1517,18 +1512,18 @@ struct TestIEEEFloatingPointRemainderFunction : FloatingPointComparison { static_cast(4.f)), -static_cast(2.2f), 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed remainder(KE::bhalf_t)\n"); + Kokkos::printf("failed remainder(KE::bhalf_t)\n"); } if (!compare(remainder(6.2, 4.), 2.2, 2) && !compare(remainder(-6.2, 4.), 2.2, 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed remainder(double)\n"); + Kokkos::printf("failed remainder(double)\n"); } #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS if (!compare(remainder(6.2l, 4.l), 2.2l, 1) && !compare(remainder(-6.2l, 4.l), -2.2l, 1)) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed remainder(long double)\n"); + Kokkos::printf("failed remainder(long double)\n"); } #endif // special values @@ -1537,26 +1532,23 @@ struct TestIEEEFloatingPointRemainderFunction : FloatingPointComparison { if (!isinf(remainder(-KE::infinity::value, 1.f)) && !isnan(remainder(-KE::quiet_NaN::value, 1.f))) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF( + Kokkos::printf( "failed remainder(floating_point) special values\n"); } static_assert( std::is_same(4.f), static_cast(4.f))), - KE::half_t>::value, - ""); + KE::half_t>::value); static_assert( std::is_same(4.f), static_cast(4.f))), - KE::bhalf_t>::value, - ""); - static_assert(std::is_same::value, - ""); - static_assert(std::is_same::value, ""); + KE::bhalf_t>::value); + static_assert(std::is_same::value); + static_assert(std::is_same::value); #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS static_assert( - std::is_same::value, ""); + std::is_same::value); #endif } }; @@ -1568,6 +1560,7 @@ TEST(TEST_CATEGORY, mathematical_functions_ieee_remainder_function) { // TODO: TestFpClassify, see https://github.com/kokkos/kokkos/issues/6279 +#ifndef KOKKOS_MATHEMATICAL_FUNCTIONS_SKIP_2 template struct TestIsFinite { TestIsFinite() { run(); } @@ -1591,6 +1584,7 @@ struct TestIsFinite { ++e; Kokkos::printf("failed isfinite(float)\n"); } +#if !(defined(KOKKOS_ENABLE_CUDA) && defined(KOKKOS_COMPILER_MSVC)) if (!isfinite(static_cast(2.f)) #ifndef KOKKOS_COMPILER_NVHPC // FIXME_NVHPC 23.7 || isfinite(quiet_NaN::value) || @@ -1611,6 +1605,7 @@ struct TestIsFinite { ++e; Kokkos::printf("failed isfinite(KE::bhalf_t)\n"); } +#endif if (!isfinite(3.) #ifndef KOKKOS_COMPILER_NVHPC // FIXME_NVHPC 23.7 || isfinite(quiet_NaN::value) || @@ -1670,6 +1665,7 @@ struct TestIsInf { ++e; Kokkos::printf("failed isinf(float)\n"); } +#if !(defined(KOKKOS_ENABLE_CUDA) && defined(KOKKOS_COMPILER_MSVC)) if (isinf(static_cast(2.f)) #ifndef KOKKOS_COMPILER_NVHPC // FIXME_NVHPC 23.7 || isinf(quiet_NaN::value) || @@ -1690,6 +1686,7 @@ struct TestIsInf { ++e; Kokkos::printf("failed isinf(KE::bhalf_t)\n"); } +#endif if (isinf(3.) #ifndef KOKKOS_COMPILER_NVHPC // FIXME_NVHPC 23.7 || isinf(quiet_NaN::value) || @@ -1748,6 +1745,7 @@ struct TestIsNaN { ++e; Kokkos::printf("failed isnan(float)\n"); } +#if !(defined(KOKKOS_ENABLE_CUDA) && defined(KOKKOS_COMPILER_MSVC)) if (isnan(static_cast(2.f)) #ifndef KOKKOS_COMPILER_NVHPC // FIXME_NVHPC 23.7 || !isnan(quiet_NaN::value) || @@ -1756,7 +1754,7 @@ struct TestIsNaN { #endif ) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed isnan(KE::half_t)\n"); + Kokkos::printf("failed isnan(KE::half_t)\n"); } if (isnan(static_cast(2.f)) #ifndef KOKKOS_COMPILER_NVHPC // FIXME_NVHPC 23.7 @@ -1766,7 +1764,7 @@ struct TestIsNaN { #endif ) { ++e; - KOKKOS_IMPL_DO_NOT_USE_PRINTF("failed isnan(KE::bhalf_t)\n"); + Kokkos::printf("failed isnan(KE::bhalf_t)\n"); } if (isnan(3.) #ifndef KOKKOS_COMPILER_NVHPC // FIXME_NVHPC 23.7 @@ -1777,6 +1775,7 @@ struct TestIsNaN { ++e; Kokkos::printf("failed isnan(double)\n"); } +#endif #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS if (isnan(4.l) || !isnan(quiet_NaN::value) || !isnan(signaling_NaN::value) || @@ -1791,11 +1790,11 @@ struct TestIsNaN { Kokkos::printf("failed isnan(floating_point) special values\n"); } - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); - static_assert(std::is_same::value, ""); + static_assert(std::is_same::value); + static_assert(std::is_same::value); + static_assert(std::is_same::value); #ifdef MATHEMATICAL_FUNCTIONS_HAVE_LONG_DOUBLE_OVERLOADS - static_assert(std::is_same::value, ""); + static_assert(std::is_same::value); #endif } }; @@ -1803,6 +1802,7 @@ struct TestIsNaN { TEST(TEST_CATEGORY, mathematical_functions_isnan) { TestIsNaN(); } +#endif // TODO: TestSignBit, see https://github.com/kokkos/kokkos/issues/6279 #endif diff --git a/lib/kokkos/core/unit_test/TestMathematicalSpecialFunctions.hpp b/lib/kokkos/core/unit_test/TestMathematicalSpecialFunctions.hpp index 06c84c7513..7969dc8686 100644 --- a/lib/kokkos/core/unit_test/TestMathematicalSpecialFunctions.hpp +++ b/lib/kokkos/core/unit_test/TestMathematicalSpecialFunctions.hpp @@ -1213,13 +1213,13 @@ struct TestComplexBesselI0K0Function { } EXPECT_EQ(h_ref_cbk0(0), h_cbk0(0)); - int upper_limit = N; + int upper_limit_0 = N; // FIXME_SYCL Failing for Intel GPUs, 19 is the first failing test case #if defined(KOKKOS_ENABLE_SYCL) && defined(KOKKOS_ARCH_INTEL_GPU) if (std::is_same_v) - upper_limit = 19; + upper_limit_0 = 19; #endif - for (int i = 1; i < upper_limit; i++) { + for (int i = 1; i < upper_limit_0; i++) { EXPECT_LE(Kokkos::abs(h_cbk0(i) - h_ref_cbk0(i)), Kokkos::abs(h_ref_cbk0(i)) * 1e-13) << "at index " << i; @@ -1462,13 +1462,13 @@ struct TestComplexBesselI1K1Function { } EXPECT_EQ(h_ref_cbk1(0), h_cbk1(0)); - int upper_limit = N; + int upper_limit_1 = N; // FIXME_SYCL Failing for Intel GPUs, 8 is the first failing test case #if defined(KOKKOS_ENABLE_SYCL) && defined(KOKKOS_ARCH_INTEL_GPU) if (std::is_same_v) - upper_limit = 8; + upper_limit_1 = 8; #endif - for (int i = 1; i < upper_limit; i++) { + for (int i = 1; i < upper_limit_1; i++) { EXPECT_LE(Kokkos::abs(h_cbk1(i) - h_ref_cbk1(i)), Kokkos::abs(h_ref_cbk1(i)) * 1e-13) << "at index " << i; @@ -1718,20 +1718,26 @@ struct TestComplexBesselH1Function { ((HIP_VERSION_MAJOR == 5) && \ !((HIP_VERSION_MINOR == 5) || (HIP_VERSION_MINOR == 6))) EXPECT_EQ(h_ref_ch10(0), h_ch10(0)); - for (int i = 1; i < N; i++) { + int upper_limit_10 = N; +// FIXME_SYCL Failing for Intel GPUs, 17 is the first failing test case +#if defined(KOKKOS_ENABLE_SYCL) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + upper_limit_10 = 17; +#endif + for (int i = 1; i < upper_limit_10; i++) { EXPECT_LE(Kokkos::abs(h_ch10(i) - h_ref_ch10(i)), Kokkos::abs(h_ref_ch10(i)) * 1e-13) << "at index " << i; } EXPECT_EQ(h_ref_ch11(0), h_ch11(0)); - int upper_limit = N; - // FIXME_SYCL Failing for Intel GPUs, 16 is the first failing test case + int upper_limit_11 = N; + // FIXME_SYCL Failing for Intel GPUs, 2 is the first failing test case #if defined(KOKKOS_ENABLE_SYCL) && defined(KOKKOS_ARCH_INTEL_GPU) if (std::is_same_v) - upper_limit = 16; + upper_limit_11 = 2; #endif - for (int i = 1; i < upper_limit; i++) { + for (int i = 1; i < upper_limit_11; i++) { EXPECT_LE(Kokkos::abs(h_ch11(i) - h_ref_ch11(i)), Kokkos::abs(h_ref_ch11(i)) * 1e-13) << "at index " << i; @@ -1912,19 +1918,26 @@ struct TestComplexBesselH2Function { ((HIP_VERSION_MAJOR == 5) && \ !((HIP_VERSION_MINOR == 5) || (HIP_VERSION_MINOR == 6))) EXPECT_EQ(h_ref_ch20(0), h_ch20(0)); - for (int i = 1; i < N; i++) { + int upper_limit_20 = N; +// FIXME_SYCL Failing for Intel GPUs, 16 is the first failing test case +#if defined(KOKKOS_ENABLE_SYCL) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + upper_limit_20 = 16; +#endif + for (int i = 1; i < upper_limit_20; i++) { EXPECT_LE(Kokkos::abs(h_ch20(i) - h_ref_ch20(i)), - Kokkos::abs(h_ref_ch20(i)) * 1e-13); + Kokkos::abs(h_ref_ch20(i)) * 1e-13) + << "at index " << i; } EXPECT_EQ(h_ref_ch21(0), h_ch21(0)); - int upper_limit = N; - // FIXME_SYCL Failing for Intel GPUs, 17 is the first failing test case + int upper_limit_21 = N; + // FIXME_SYCL Failing for Intel GPUs, 1 is the first failing test case #if defined(KOKKOS_ENABLE_SYCL) && defined(KOKKOS_ARCH_INTEL_GPU) if (std::is_same_v) - upper_limit = 17; + upper_limit_21 = 1; #endif - for (int i = 1; i < upper_limit; i++) { + for (int i = 1; i < upper_limit_21; i++) { EXPECT_LE(Kokkos::abs(h_ch21(i) - h_ref_ch21(i)), Kokkos::abs(h_ref_ch21(i)) * 1e-13) << "at index " << i; @@ -1954,31 +1967,61 @@ TEST(TEST_CATEGORY, mathspecialfunc_errorfunc) { #endif TEST(TEST_CATEGORY, mathspecialfunc_cbesselj0y0) { +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + GTEST_SKIP() << "skipping since test is known to fail with OpenMPTarget on " + "Intel GPUs"; // FIXME_OPENMPTARGET +#endif TestComplexBesselJ0Y0Function test; test.testit(); } TEST(TEST_CATEGORY, mathspecialfunc_cbesselj1y1) { +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + GTEST_SKIP() << "skipping since test is known to fail with OpenMPTarget on " + "Intel GPUs"; // FIXME_OPENMPTARGET +#endif TestComplexBesselJ1Y1Function test; test.testit(); } TEST(TEST_CATEGORY, mathspecialfunc_cbesseli0k0) { +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + GTEST_SKIP() << "skipping since test is known to fail with OpenMPTarget on " + "Intel GPUs"; // FIXME_OPENMPTARGET +#endif TestComplexBesselI0K0Function test; test.testit(); } TEST(TEST_CATEGORY, mathspecialfunc_cbesseli1k1) { +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + GTEST_SKIP() << "skipping since test is known to fail with OpenMPTarget on " + "Intel GPUs"; // FIXME_OPENMPTARGET +#endif TestComplexBesselI1K1Function test; test.testit(); } TEST(TEST_CATEGORY, mathspecialfunc_cbesselh1stkind) { +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + GTEST_SKIP() << "skipping since test is known to fail with OpenMPTarget on " + "Intel GPUs"; // FIXME_OPENMPTARGET +#endif TestComplexBesselH1Function test; test.testit(); } TEST(TEST_CATEGORY, mathspecialfunc_cbesselh2ndkind) { +#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_ARCH_INTEL_GPU) + if (std::is_same_v) + GTEST_SKIP() << "skipping since test is known to fail with OpenMPTarget on " + "Intel GPUs"; // FIXME_OPENMPTARGET +#endif TestComplexBesselH2Function test; test.testit(); } diff --git a/lib/kokkos/core/unit_test/TestNonTrivialScalarTypes.hpp b/lib/kokkos/core/unit_test/TestNonTrivialScalarTypes.hpp index eaf7a4125c..116ac58c39 100644 --- a/lib/kokkos/core/unit_test/TestNonTrivialScalarTypes.hpp +++ b/lib/kokkos/core/unit_test/TestNonTrivialScalarTypes.hpp @@ -214,7 +214,7 @@ struct point_t { uint8_t x, y, z; KOKKOS_FUNCTION - point_t() : x(1), y(1), z(1){}; + point_t() : x(0), y(0), z(0){}; KOKKOS_FUNCTION point_t(const point_t &val) : x(val.x), y(val.y), z(val.z){}; diff --git a/lib/kokkos/core/unit_test/TestNumericTraits.hpp b/lib/kokkos/core/unit_test/TestNumericTraits.hpp index 2b5531f29a..81a9d0a5e0 100644 --- a/lib/kokkos/core/unit_test/TestNumericTraits.hpp +++ b/lib/kokkos/core/unit_test/TestNumericTraits.hpp @@ -110,8 +110,8 @@ struct TestNumericTraits { KOKKOS_FUNCTION void operator()(Epsilon, int, int& e) const { using Kokkos::Experimental::epsilon; - auto const eps = epsilon::value; - auto const one = T(1); + T const eps = epsilon::value; + T const one = 1; // Avoid higher precision intermediate representation compare() = one + eps; e += (int)!(compare() != one); @@ -210,9 +210,10 @@ TEST(TEST_CATEGORY, numeric_traits_infinity) { #endif TestNumericTraits(); TestNumericTraits(); - // FIXME_NVHPC long double not supported -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -224,9 +225,9 @@ TEST(TEST_CATEGORY, numeric_traits_epsilon) { #endif TestNumericTraits(); TestNumericTraits(); - // FIXME_NVHPC long double not supported -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -239,9 +240,9 @@ TEST(TEST_CATEGORY, numeric_traits_round_error) { #endif TestNumericTraits(); TestNumericTraits(); - // FIXME_NVHPC long double not supported -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -253,9 +254,9 @@ TEST(TEST_CATEGORY, numeric_traits_norm_min) { #endif TestNumericTraits(); TestNumericTraits(); - // FIXME_NVHPC long double not supported -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -263,9 +264,9 @@ TEST(TEST_CATEGORY, numeric_traits_norm_min) { TEST(TEST_CATEGORY, numeric_traits_denorm_min) { TestNumericTraits(); TestNumericTraits(); - // FIXME_NVHPC long double not supported -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -302,8 +303,10 @@ TEST(TEST_CATEGORY, numeric_traits_finite_min_max) { TestNumericTraits(); TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); TestNumericTraits(); #endif @@ -326,8 +329,10 @@ TEST(TEST_CATEGORY, numeric_traits_digits) { TestNumericTraits(); TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -349,8 +354,10 @@ TEST(TEST_CATEGORY, numeric_traits_digits10) { TestNumericTraits(); TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -358,8 +365,10 @@ TEST(TEST_CATEGORY, numeric_traits_digits10) { TEST(TEST_CATEGORY, numeric_traits_max_digits10) { TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -380,8 +389,10 @@ TEST(TEST_CATEGORY, numeric_traits_radix) { TestNumericTraits(); TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); #endif } @@ -395,8 +406,10 @@ TEST(TEST_CATEGORY, numeric_traits_min_max_exponent) { TestNumericTraits(); TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); TestNumericTraits(); #endif @@ -407,8 +420,10 @@ TEST(TEST_CATEGORY, numeric_traits_min_max_exponent10) { TestNumericTraits(); TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); TestNumericTraits(); #endif @@ -426,8 +441,10 @@ TEST(TEST_CATEGORY, numeric_traits_quiet_and_signaling_nan) { TestNumericTraits(); TestNumericTraits(); TestNumericTraits(); -#if !defined(KOKKOS_ENABLE_CUDA) || \ - !defined(KOKKOS_COMPILER_NVHPC) // 23.7 long double: + // FIXME_NVHPC 23.7 long double + // FIXME_OPENMPTARGET long double on Intel GPUs +#if (!defined(KOKKOS_ENABLE_CUDA) || !defined(KOKKOS_COMPILER_NVHPC)) && \ + (!defined(KOKKOS_ENABLE_OPENMPTARGET) || !defined(KOKKOS_ARCH_INTEL_GPU)) TestNumericTraits(); TestNumericTraits(); #endif @@ -442,7 +459,7 @@ struct HasNoSpecialization {}; using TRAIT##_value_t = decltype(Kokkos::Experimental::TRAIT::value); \ template \ using has_##TRAIT = Kokkos::is_detected; \ - static_assert(!has_##TRAIT::value, ""); + static_assert(!has_##TRAIT::value); CHECK_TRAIT_IS_SFINAE_FRIENDLY(infinity) CHECK_TRAIT_IS_SFINAE_FRIENDLY(finite_min) @@ -524,39 +541,39 @@ CHECK_SAME_AS_NUMERIC_LIMITS_MEMBER_FUNCTION(long double, denorm_min); #endif // clang-format off -static_assert(Kokkos::Experimental::norm_min::value == std::numeric_limits< float>::min(), ""); -static_assert(Kokkos::Experimental::norm_min::value == std::numeric_limits< double>::min(), ""); -static_assert(Kokkos::Experimental::norm_min::value == std::numeric_limits::min(), ""); +static_assert(Kokkos::Experimental::norm_min::value == std::numeric_limits< float>::min()); +static_assert(Kokkos::Experimental::norm_min::value == std::numeric_limits< double>::min()); +static_assert(Kokkos::Experimental::norm_min::value == std::numeric_limits::min()); // integer types -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< char>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< signed char>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned char>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< short>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned short>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< int>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned int>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< long int>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned long int>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< long long int>::min(), ""); -static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits::min(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< char>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< signed char>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned char>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< short>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned short>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< int>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned int>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< long int>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned long int>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< long long int>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits::max(), ""); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< char>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< signed char>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned char>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< short>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned short>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< int>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned int>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< long int>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< unsigned long int>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits< long long int>::min()); +static_assert(Kokkos::Experimental::finite_min::value == std::numeric_limits::min()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< char>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< signed char>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned char>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< short>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned short>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< int>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned int>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< long int>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< unsigned long int>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< long long int>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits::max()); // floating point types -static_assert(Kokkos::Experimental::finite_min::value == -std::numeric_limits< float>::max(), ""); -static_assert(Kokkos::Experimental::finite_min::value == -std::numeric_limits< double>::max(), ""); -static_assert(Kokkos::Experimental::finite_min::value == -std::numeric_limits::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< float>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< double>::max(), ""); -static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits::max(), ""); +static_assert(Kokkos::Experimental::finite_min::value == -std::numeric_limits< float>::max()); +static_assert(Kokkos::Experimental::finite_min::value == -std::numeric_limits< double>::max()); +static_assert(Kokkos::Experimental::finite_min::value == -std::numeric_limits::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< float>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits< double>::max()); +static_assert(Kokkos::Experimental::finite_max::value == std::numeric_limits::max()); // clang-format on CHECK_SAME_AS_NUMERIC_LIMITS_MEMBER_CONSTANT(bool, digits); @@ -623,15 +640,13 @@ CHECK_SAME_AS_NUMERIC_LIMITS_MEMBER_CONSTANT(long double, max_exponent10); #undef CHECK_SAME_AS_NUMERIC_LIMITS_MEMBER_FUNCTION #undef CHECK_SAME_AS_NUMERIC_LIMITS_MEMBER_CONSTANT -#define CHECK_NAN_SAME_AS_NUMERIC_LIMITS_MEMBER_FUNCTION(T, TRAIT) \ - static_assert(Kokkos::Experimental::TRAIT::value != \ - Kokkos::Experimental::TRAIT::value, \ - ""); \ - static_assert( \ - std::numeric_limits::TRAIT() != std::numeric_limits::TRAIT(), ""); \ - static_assert(Kokkos::Experimental::TRAIT::value != \ - std::numeric_limits::TRAIT(), \ - "") +#define CHECK_NAN_SAME_AS_NUMERIC_LIMITS_MEMBER_FUNCTION(T, TRAIT) \ + static_assert(Kokkos::Experimental::TRAIT::value != \ + Kokkos::Experimental::TRAIT::value); \ + static_assert(std::numeric_limits::TRAIT() != \ + std::numeric_limits::TRAIT()); \ + static_assert(Kokkos::Experimental::TRAIT::value != \ + std::numeric_limits::TRAIT()) // Workaround compiler issue error: expression must have a constant value // See kokkos/kokkos#4574 @@ -651,14 +666,11 @@ CHECK_NAN_SAME_AS_NUMERIC_LIMITS_MEMBER_FUNCTION(long double, signaling_NaN); #define CHECK_INSTANTIATED_ON_CV_QUALIFIED_TYPES(T, TRAIT) \ static_assert(Kokkos::Experimental::TRAIT::value == \ - Kokkos::Experimental::TRAIT::value, \ - ""); \ + Kokkos::Experimental::TRAIT::value); \ static_assert(Kokkos::Experimental::TRAIT::value == \ - Kokkos::Experimental::TRAIT::value, \ - ""); \ + Kokkos::Experimental::TRAIT::value); \ static_assert(Kokkos::Experimental::TRAIT::value == \ - Kokkos::Experimental::TRAIT::value, \ - "") + Kokkos::Experimental::TRAIT::value) #define CHECK_INSTANTIATED_ON_CV_QUALIFIED_TYPES_FLOATING_POINT(TRAIT) \ CHECK_INSTANTIATED_ON_CV_QUALIFIED_TYPES(float, TRAIT); \ @@ -706,17 +718,13 @@ CHECK_INSTANTIATED_ON_CV_QUALIFIED_TYPES_FLOATING_POINT(max_exponent10); #define CHECK_NAN_INSTANTIATED_ON_CV_QUALIFIED_TYPES(T, TRAIT) \ static_assert(Kokkos::Experimental::TRAIT::value != \ - Kokkos::Experimental::TRAIT::value, \ - ""); \ + Kokkos::Experimental::TRAIT::value); \ static_assert(Kokkos::Experimental::TRAIT::value != \ - Kokkos::Experimental::TRAIT::value, \ - ""); \ + Kokkos::Experimental::TRAIT::value); \ static_assert(Kokkos::Experimental::TRAIT::value != \ - Kokkos::Experimental::TRAIT::value, \ - ""); \ + Kokkos::Experimental::TRAIT::value); \ static_assert(Kokkos::Experimental::TRAIT::value != \ - Kokkos::Experimental::TRAIT::value, \ - "") + Kokkos::Experimental::TRAIT::value) #define CHECK_NAN_INSTANTIATED_ON_CV_QUALIFIED_TYPES_FLOATING_POINT(TRAIT) \ CHECK_NAN_INSTANTIATED_ON_CV_QUALIFIED_TYPES(float, TRAIT); \ diff --git a/lib/kokkos/core/unit_test/TestOccupancyControlTrait.hpp b/lib/kokkos/core/unit_test/TestOccupancyControlTrait.hpp new file mode 100644 index 0000000000..345a906d66 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestOccupancyControlTrait.hpp @@ -0,0 +1,80 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include + +namespace { + +template +void test_policy_execution(const Kokkos::RangePolicy& policy) { + Kokkos::parallel_for(policy, KOKKOS_LAMBDA(int){}); +} +template +void test_policy_execution(const Kokkos::TeamPolicy& policy) { + Kokkos::parallel_for( + policy, + KOKKOS_LAMBDA( + const typename Kokkos::TeamPolicy::member_type&){}); +} +template +void test_policy_execution(const Kokkos::MDRangePolicy& policy) { + Kokkos::parallel_for(policy, KOKKOS_LAMBDA(int, int){}); +} + +template +void test_prefer_desired_occupancy(Policy policy) { + using Kokkos::Experimental::DesiredOccupancy; + using Kokkos::Experimental::MaximizeOccupancy; + using Kokkos::Experimental::prefer; + using Kokkos::Experimental::WorkItemProperty; + + // MaximizeOccupancy -> MaximizeOccupancy + auto const policy_still_no_occ = prefer(policy, MaximizeOccupancy{}); + test_policy_execution(policy_still_no_occ); + + // MaximizeOccupancy -> DesiredOccupancy + auto const policy_with_occ = + prefer(policy_still_no_occ, DesiredOccupancy{33}); + test_policy_execution(policy_with_occ); + + // DesiredOccupancy -> DesiredOccupancy + auto const policy_change_occ = prefer(policy_with_occ, DesiredOccupancy{24}); + test_policy_execution(policy_change_occ); + + // DesiredOccupancy -> DesiredOccupancy w/ hint + auto policy_with_occ_and_hint = Kokkos::Experimental::require( + policy_change_occ, + Kokkos::Experimental::WorkItemProperty::HintLightWeight); + test_policy_execution(policy_with_occ_and_hint); + + // DesiredOccupancy -> MaximizeOccupancy + auto const policy_drop_occ = + prefer(policy_with_occ_and_hint, MaximizeOccupancy{}); + test_policy_execution(policy_drop_occ); +} + +// FIXME_MSVC_WITH_CUDA +// This test doesn't compile with CUDA on Windows +#if !(defined(_WIN32) && defined(KOKKOS_ENABLE_CUDA)) +TEST(TEST_CATEGORY, occupancy_control) { + test_prefer_desired_occupancy(Kokkos::RangePolicy(0, 1)); + test_prefer_desired_occupancy( + Kokkos::TeamPolicy{1, Kokkos::AUTO}); + test_prefer_desired_occupancy( + Kokkos::MDRangePolicy>{{0, 0}, {1, 1}}); +} +#endif +} // namespace diff --git a/lib/kokkos/core/unit_test/TestParseCmdLineArgsAndEnvVars.cpp b/lib/kokkos/core/unit_test/TestParseCmdLineArgsAndEnvVars.cpp index 176ce9b5fe..a56dfd9efc 100644 --- a/lib/kokkos/core/unit_test/TestParseCmdLineArgsAndEnvVars.cpp +++ b/lib/kokkos/core/unit_test/TestParseCmdLineArgsAndEnvVars.cpp @@ -166,22 +166,6 @@ TEST(defaultdevicetype, cmd_line_args_device_id) { EXPECT_REMAINING_COMMAND_LINE_ARGUMENTS(cla, {"--dummy"}); } -TEST(defaultdevicetype, cmd_line_args_num_devices) { - CmdLineArgsHelper cla = {{ - "--kokkos-num-devices=5,6", - "--kokkos-num-devices=7", - "-v", - }}; - Kokkos::InitializationSettings settings; - Kokkos::Impl::parse_command_line_arguments(cla.argc(), cla.argv(), settings); - EXPECT_TRUE(settings.has_num_devices()); - EXPECT_EQ(settings.get_num_devices(), 7); - // this is the current behavior, not suggesting this cannot be revisited - EXPECT_TRUE(settings.has_skip_device()) << "behavior changed see comment"; - EXPECT_EQ(settings.get_skip_device(), 6) << "behavior changed see comment"; - EXPECT_REMAINING_COMMAND_LINE_ARGUMENTS(cla, {"-v"}); -} - TEST(defaultdevicetype, cmd_line_args_disable_warning) { CmdLineArgsHelper cla = {{ "--kokkos-disable-warnings=1", @@ -351,20 +335,6 @@ TEST(defaultdevicetype, env_vars_device_id) { EXPECT_EQ(settings.get_device_id(), 33); } -TEST(defaultdevicetype, env_vars_num_devices) { - EnvVarsHelper ev = {{ - {"KOKKOS_NUM_DEVICES", "4"}, - {"KOKKOS_SKIP_DEVICE", "1"}, - }}; - SKIP_IF_ENVIRONMENT_VARIABLE_ALREADY_SET(ev); - Kokkos::InitializationSettings settings; - Kokkos::Impl::parse_environment_variables(settings); - EXPECT_TRUE(settings.has_num_devices()); - EXPECT_EQ(settings.get_num_devices(), 4); - EXPECT_TRUE(settings.has_skip_device()); - EXPECT_EQ(settings.get_skip_device(), 1); -} - TEST(defaultdevicetype, env_vars_disable_warnings) { for (auto const& value_true : {"1", "true", "TRUE", "yEs"}) { EnvVarsHelper ev = {{ @@ -420,22 +390,20 @@ TEST(defaultdevicetype, env_vars_tune_internals) { } TEST(defaultdevicetype, visible_devices) { -#define KOKKOS_TEST_VISIBLE_DEVICES(ENV, CNT, DEV) \ - do { \ - EnvVarsHelper ev{ENV}; \ - SKIP_IF_ENVIRONMENT_VARIABLE_ALREADY_SET(ev); \ - Kokkos::InitializationSettings settings; \ - Kokkos::Impl::parse_environment_variables(settings); \ - auto computed = Kokkos::Impl::get_visible_devices(settings, CNT); \ - std::vector expected = DEV; \ - EXPECT_EQ(expected.size(), computed.size()) \ - << ev << "device count: " << CNT; \ - auto n = std::min(expected.size(), computed.size()); \ - for (int i = 0; i < n; ++i) { \ - EXPECT_EQ(expected[i], computed[i]) \ - << "devices differ at index " << i << '\n' \ - << ev << "device count: " << CNT; \ - } \ +#define KOKKOS_TEST_VISIBLE_DEVICES(ENV, CNT, DEV) \ + do { \ + EnvVarsHelper ev{ENV}; \ + SKIP_IF_ENVIRONMENT_VARIABLE_ALREADY_SET(ev); \ + auto computed = Kokkos::Impl::get_visible_devices(CNT); \ + std::vector expected = DEV; \ + EXPECT_EQ(expected.size(), computed.size()) \ + << ev << "device count: " << CNT; \ + auto n = std::min(expected.size(), computed.size()); \ + for (int i = 0; i < n; ++i) { \ + EXPECT_EQ(expected[i], computed[i]) \ + << "devices differ at index " << i << '\n' \ + << ev << "device count: " << CNT; \ + } \ } while (false) #define DEV(...) \ @@ -444,6 +412,8 @@ TEST(defaultdevicetype, visible_devices) { // first test with all environment variables that are involved in determining // the visible devices so user set var do not mess up the logic below. + // KOKKOS_NUM_DEVICES and KOKKOS_SKIP_DEVICE are deprecated since 3.7 and are + // not taken into account anymore. KOKKOS_TEST_VISIBLE_DEVICES( ENV({"KOKKOS_VISIBLE_DEVICES", "2,1"}, {"KOKKOS_NUM_DEVICES", "8"}, {"KOKKOS_SKIP_DEVICE", "1"}), @@ -452,10 +422,10 @@ TEST(defaultdevicetype, visible_devices) { ENV({"KOKKOS_VISIBLE_DEVICES", "2,1"}, {"KOKKOS_NUM_DEVICES", "8"}, ), 6, DEV(2, 1)); KOKKOS_TEST_VISIBLE_DEVICES(ENV({"KOKKOS_NUM_DEVICES", "3"}), 6, - DEV(0, 1, 2)); + DEV(0, 1, 2, 3, 4, 5)); KOKKOS_TEST_VISIBLE_DEVICES( ENV({"KOKKOS_NUM_DEVICES", "4"}, {"KOKKOS_SKIP_DEVICE", "1"}, ), 6, - DEV(0, 2, 3)); + DEV(0, 1, 2, 3, 4, 5)); KOKKOS_TEST_VISIBLE_DEVICES(ENV({"KOKKOS_VISIBLE_DEVICES", "1,3,4"}), 6, DEV(1, 3, 4)); KOKKOS_TEST_VISIBLE_DEVICES( diff --git a/lib/kokkos/core/unit_test/TestRangePolicyCTAD.cpp b/lib/kokkos/core/unit_test/TestRangePolicyCTAD.cpp new file mode 100644 index 0000000000..20288e2b40 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestRangePolicyCTAD.cpp @@ -0,0 +1,150 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include +#include "Kokkos_Core_fwd.hpp" + +namespace { + +struct TestRangePolicyCTAD { + struct SomeExecutionSpace { + using execution_space = SomeExecutionSpace; + using size_type = size_t; + + [[maybe_unused]] static int concurrency() { return 0; } + }; + static_assert(Kokkos::is_execution_space_v); + + struct ImplicitlyConvertibleToDefaultExecutionSpace { + [[maybe_unused]] operator Kokkos::DefaultExecutionSpace() const { + return Kokkos::DefaultExecutionSpace(); + } + }; + static_assert(!Kokkos::is_execution_space_v< + ImplicitlyConvertibleToDefaultExecutionSpace>); + + [[maybe_unused]] static inline auto i64 = int64_t(); + [[maybe_unused]] static inline auto i32 = int32_t(); + [[maybe_unused]] static inline auto cs = Kokkos::ChunkSize(0); + [[maybe_unused]] static inline auto des = Kokkos::DefaultExecutionSpace(); + [[maybe_unused]] static inline auto nes = + ImplicitlyConvertibleToDefaultExecutionSpace(); + [[maybe_unused]] static inline auto ses = SomeExecutionSpace(); + + // RangePolicy() + + [[maybe_unused]] static inline auto rp = Kokkos::RangePolicy{}; + static_assert(std::is_same_v, decltype(rp)>); + + // RangePolicy(index_type, index_type) + + [[maybe_unused]] static inline auto rpi64i64 = Kokkos::RangePolicy(i64, i64); + static_assert(std::is_same_v, decltype(rpi64i64)>); + + [[maybe_unused]] static inline auto rpi64i32 = Kokkos::RangePolicy(i64, i32); + static_assert(std::is_same_v, decltype(rpi64i32)>); + + [[maybe_unused]] static inline auto rpi32i64 = Kokkos::RangePolicy(i32, i64); + static_assert(std::is_same_v, decltype(rpi32i64)>); + + [[maybe_unused]] static inline auto rpi32i32 = Kokkos::RangePolicy(i32, i32); + static_assert(std::is_same_v, decltype(rpi32i32)>); + + // RangePolicy(index_type, index_type, ChunkSize) + + [[maybe_unused]] static inline auto rpi64i64cs = + Kokkos::RangePolicy(i64, i64, cs); + static_assert(std::is_same_v, decltype(rpi64i64cs)>); + + [[maybe_unused]] static inline auto rpi64i32cs = + Kokkos::RangePolicy(i64, i32, cs); + static_assert(std::is_same_v, decltype(rpi64i32cs)>); + + [[maybe_unused]] static inline auto rpi32i64cs = + Kokkos::RangePolicy(i32, i64, cs); + static_assert(std::is_same_v, decltype(rpi32i64cs)>); + + [[maybe_unused]] static inline auto rpi32i32cs = + Kokkos::RangePolicy(i32, i32, cs); + static_assert(std::is_same_v, decltype(rpi32i32cs)>); + + // RangePolicy(execution_space, index_type, index_type) + + [[maybe_unused]] static inline auto rpdesi64i64 = + Kokkos::RangePolicy(des, i64, i64); + static_assert(std::is_same_v, decltype(rpdesi64i64)>); + + [[maybe_unused]] static inline auto rpdesi32i32 = + Kokkos::RangePolicy(des, i32, i32); + static_assert(std::is_same_v, decltype(rpdesi32i32)>); + + [[maybe_unused]] static inline auto rpnesi64i64 = + Kokkos::RangePolicy(nes, i64, i64); + static_assert(std::is_same_v, decltype(rpnesi64i64)>); + + [[maybe_unused]] static inline auto rpnesi32i32 = + Kokkos::RangePolicy(nes, i32, i32); + static_assert(std::is_same_v, decltype(rpnesi32i32)>); + + [[maybe_unused]] static inline auto rpsesi64i64 = + Kokkos::RangePolicy(ses, i64, i64); + static_assert(std::is_same_v, + decltype(rpsesi64i64)>); + + [[maybe_unused]] static inline auto rpsesi32i32 = + Kokkos::RangePolicy(ses, i32, i32); + static_assert(std::is_same_v, + decltype(rpsesi32i32)>); + + // RangePolicy(execution_space, index_type, index_type, ChunkSize) + + [[maybe_unused]] static inline auto rpdesi64i64cs = + Kokkos::RangePolicy(des, i64, i64, cs); + static_assert(std::is_same_v, decltype(rpdesi64i64cs)>); + + [[maybe_unused]] static inline auto rpdesi32i32cs = + Kokkos::RangePolicy(des, i32, i32, cs); + static_assert(std::is_same_v, decltype(rpdesi32i32cs)>); + + [[maybe_unused]] static inline auto rpnesi64i64cs = + Kokkos::RangePolicy(nes, i64, i64, cs); + static_assert(std::is_same_v, decltype(rpnesi64i64cs)>); + + [[maybe_unused]] static inline auto rpnesi32i32cs = + Kokkos::RangePolicy(nes, i32, i32, cs); + static_assert(std::is_same_v, decltype(rpnesi32i32cs)>); + + [[maybe_unused]] static inline auto rpsesi64i64cs = + Kokkos::RangePolicy(ses, i64, i64, cs); + static_assert(std::is_same_v, + decltype(rpsesi64i64cs)>); + + [[maybe_unused]] static inline auto rpsesi32i32cs = + Kokkos::RangePolicy(ses, i32, i32, cs); + static_assert(std::is_same_v, + decltype(rpsesi32i32cs)>); + +}; // TestRangePolicyCTAD struct + +// To eliminate maybe_unused warning on some compilers + +[[maybe_unused]] const Kokkos::DefaultExecutionSpace nestodes = + TestRangePolicyCTAD::ImplicitlyConvertibleToDefaultExecutionSpace(); + +[[maybe_unused]] const auto sesconcurrency = + TestRangePolicyCTAD::ses.concurrency(); + +} // namespace diff --git a/lib/kokkos/core/unit_test/TestRangePolicyConstructors.hpp b/lib/kokkos/core/unit_test/TestRangePolicyConstructors.hpp index 0a7e59ed98..c8c1542af1 100644 --- a/lib/kokkos/core/unit_test/TestRangePolicyConstructors.hpp +++ b/lib/kokkos/core/unit_test/TestRangePolicyConstructors.hpp @@ -18,6 +18,9 @@ #include +#include +#include + namespace { TEST(TEST_CATEGORY, range_policy_runtime_parameters) { @@ -70,4 +73,127 @@ TEST(TEST_CATEGORY, range_policy_runtime_parameters) { } } +TEST(TEST_CATEGORY_DEATH, range_policy_invalid_bounds) { + using Policy = Kokkos::RangePolicy; + using ChunkSize = Kokkos::ChunkSize; + + std::string msg = + "Kokkos::RangePolicy bounds error: The lower bound (100) is greater than " + "the upper bound (90).\n"; +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE_4 + // escape the parentheses in the regex to match the error message + msg = std::regex_replace(msg, std::regex("\\(|\\)"), "\\$&"); + ASSERT_DEATH({ (void)Policy(100, 90); }, msg); + + ASSERT_DEATH({ (void)Policy(TEST_EXECSPACE(), 100, 90, ChunkSize(10)); }, + msg); +#else + + if (!Kokkos::show_warnings()) { + GTEST_SKIP() << "Kokkos warning messages are disabled"; + } + + { + ::testing::internal::CaptureStderr(); + Policy policy(100, 90); + ASSERT_EQ((int)policy.begin(), 0); + ASSERT_EQ((int)policy.end(), 0); +#ifdef KOKKOS_ENABLE_DEPRECATION_WARNINGS + ASSERT_EQ(::testing::internal::GetCapturedStderr(), msg); +#else + ASSERT_TRUE(::testing::internal::GetCapturedStderr().empty()); + (void)msg; +#endif + } + + { + ::testing::internal::CaptureStderr(); + Policy policy(TEST_EXECSPACE(), 100, 90, ChunkSize(10)); + ASSERT_EQ((int)policy.begin(), 0); + ASSERT_EQ((int)policy.end(), 0); +#ifdef KOKKOS_ENABLE_DEPRECATION_WARNINGS + ASSERT_EQ(::testing::internal::GetCapturedStderr(), msg); +#else + ASSERT_TRUE(::testing::internal::GetCapturedStderr().empty()); + (void)msg; +#endif + } + +#endif +} + +TEST(TEST_CATEGORY_DEATH, range_policy_implicitly_converted_bounds) { + using UIntIndexType = Kokkos::IndexType; + using IntIndexType = Kokkos::IndexType; + using UIntPolicy = Kokkos::RangePolicy; + using IntPolicy = Kokkos::RangePolicy; + + std::string msg = + "Kokkos::RangePolicy bound type error: an unsafe implicit conversion is " + "performed on a bound (), which may not preserve its original value.\n"; + + auto get_error_msg = [](auto str, auto val) { + return str.insert(str.find("(") + 1, std::to_string(val).c_str()); + }; +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE_4 + std::string expected = std::regex_replace(msg, std::regex("\\(|\\)"), "\\$&"); + { + int test_val = -1; + ASSERT_DEATH({ (void)UIntPolicy(test_val, 10); }, + get_error_msg(expected, test_val)); + } + { + unsigned test_val = std::numeric_limits::max(); + ASSERT_DEATH({ (void)IntPolicy(0u, test_val); }, + get_error_msg(expected, test_val)); + } + { + long long test_val = std::numeric_limits::max(); + ASSERT_DEATH({ (void)IntPolicy(0LL, test_val); }, + get_error_msg(expected, test_val)); + } + { + int test_val = -1; + ASSERT_DEATH({ (void)UIntPolicy(test_val, 10, Kokkos::ChunkSize(2)); }, + get_error_msg(expected, test_val)); + } + +#else + { + ::testing::internal::CaptureStderr(); + int test_val = -1; + UIntPolicy policy(test_val, 10); + ASSERT_EQ(policy.begin(), 0u); + ASSERT_EQ(policy.end(), 0u); +#ifdef KOKKOS_ENABLE_DEPRECATION_WARNINGS + if (Kokkos::show_warnings()) { + auto s = std::string(::testing::internal::GetCapturedStderr()); + ASSERT_EQ(s.substr(0, s.find("\n") + 1), get_error_msg(msg, test_val)); + } +#else + ASSERT_TRUE(::testing::internal::GetCapturedStderr().empty()); + (void)msg; + (void)get_error_msg; +#endif + } + { + ::testing::internal::CaptureStderr(); + unsigned test_val = std::numeric_limits::max(); + IntPolicy policy(0u, test_val); + ASSERT_EQ(policy.begin(), 0); + ASSERT_EQ(policy.end(), 0); +#ifdef KOKKOS_ENABLE_DEPRECATION_WARNINGS + if (Kokkos::show_warnings()) { + auto s = std::string(::testing::internal::GetCapturedStderr()); + ASSERT_EQ(s.substr(0, s.find("\n") + 1), get_error_msg(msg, test_val)); + } +#else + ASSERT_TRUE(::testing::internal::GetCapturedStderr().empty()); + (void)msg; + (void)get_error_msg; +#endif + } +#endif +} + } // namespace diff --git a/lib/kokkos/core/unit_test/TestReduce.hpp b/lib/kokkos/core/unit_test/TestReduce.hpp index e1aa851f10..61b2bfb150 100644 --- a/lib/kokkos/core/unit_test/TestReduce.hpp +++ b/lib/kokkos/core/unit_test/TestReduce.hpp @@ -625,4 +625,30 @@ TEST(TEST_CATEGORY, int_combined_reduce_mixed) { } #endif #endif + +#if defined(NDEBUG) +// the following test was made for: +// https://github.com/kokkos/kokkos/issues/6517 + +struct FunctorReductionWithLargeIterationCount { + KOKKOS_FUNCTION void operator()(const int64_t /*i*/, double& update) const { + update += 1.0; + } +}; + +TEST(TEST_CATEGORY, reduction_with_large_iteration_count) { + if constexpr (std::is_same_v) { + GTEST_SKIP() << "Disabling for host backends"; + } + + const int64_t N = pow(2LL, 39LL) - pow(2LL, 8LL) + 1; + Kokkos::RangePolicy> p(0, N); + double nu = 0; + EXPECT_NO_THROW(Kokkos::parallel_reduce( + "sample reduction", p, FunctorReductionWithLargeIterationCount(), nu)); + ASSERT_DOUBLE_EQ(nu, double(N)); +} +#endif + } // namespace Test diff --git a/lib/kokkos/core/unit_test/TestReducers.hpp b/lib/kokkos/core/unit_test/TestReducers.hpp index 957b9a0ca1..fbcb9629af 100644 --- a/lib/kokkos/core/unit_test/TestReducers.hpp +++ b/lib/kokkos/core/unit_test/TestReducers.hpp @@ -19,6 +19,7 @@ #include #include +#include //-------------------------------------------------------------------------- @@ -46,6 +47,37 @@ struct TestReducers { void operator()(const int& i, Scalar& value) const { value += values(i); } }; + struct TeamSumFunctor { + using member_type = typename Kokkos::TeamPolicy::member_type; + + KOKKOS_INLINE_FUNCTION + void operator()(const member_type& m, Scalar& value) const { + if (m.team_rank() == m.team_size() - 1) value += Scalar(1); + } + }; + + struct TeamSumNestedFunctor { + using member_type = typename Kokkos::TeamPolicy::member_type; + + SumFunctor f; + int M, N; + Kokkos::View result; + + TeamSumNestedFunctor(SumFunctor& f_, const int M_, const int N_, + Kokkos::View result_) + : f(f_), M(M_), N(N_), result(result_) {} + + KOKKOS_INLINE_FUNCTION + void operator()(const member_type& m) const { + const int i = m.league_rank(); + Scalar local_scalar; + Kokkos::Sum reducer_scalar( + local_scalar); + Kokkos::parallel_reduce(Kokkos::TeamThreadRange(m, N), f, reducer_scalar); + result(i) = local_scalar; + } + }; + struct ProdFunctor { Kokkos::View values; @@ -319,6 +351,102 @@ struct TestReducers { value = value || values(i); } }; + + // get number of teams for TeamPolicy depending on the tested type + constexpr static int get_num_teams() { + if constexpr (sizeof(Scalar) == 1) { + return 126; + } else if constexpr (std::is_same_v) { + return 256; + } + + return 1024; + } + + static void test_sum_team_policy(int N, SumFunctor f, Scalar reference_sum) { +#ifdef KOKKOS_ENABLE_OPENACC + if constexpr (std::is_same_v && + (std::is_same_v || + std::is_same_v)) { + return; // FIXME_OPENACC + } +#endif + + Scalar sum_scalar; + Kokkos::View sum_view("result"); + Kokkos::deep_copy(sum_view, Scalar(1)); + + // Test team policy reduction + { + constexpr int num_teams = get_num_teams(); + TeamSumFunctor tf; + // FIXME_OPENMPTARGET temporary restriction for team size to be at least + // 32 +#ifdef KOKKOS_ENABLE_OPENMPTARGET + int team_size = + std::is_same::value + ? 32 + : 1; +#else + int team_size = 1; +#endif + auto team_pol = Kokkos::TeamPolicy(num_teams, team_size); + Kokkos::parallel_reduce(team_pol, tf, sum_view); + Kokkos::deep_copy(sum_scalar, sum_view); + ASSERT_EQ(sum_scalar, Scalar{num_teams}) << "num_teams: " << num_teams; + } + + // Test TeamThreadRange level reduction with 0 work produces 0 result + { + const int league_size = 1; + Kokkos::View result("result", league_size); + TeamSumNestedFunctor tnf(f, league_size, 0, result); + // FIXME_OPENMPTARGET temporary restriction for team size to be at least + // 32 +#ifdef KOKKOS_ENABLE_OPENMPTARGET + int team_size = + std::is_same::value + ? 32 + : 1; +#else + int team_size = 1; +#endif + auto team_pol = Kokkos::TeamPolicy(1, team_size); + Kokkos::parallel_for(team_pol, tnf); + auto result_h = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), result); + ASSERT_EQ(result_h(0), Scalar{0}) << "N: " << N; + } + + // Same test as above, but with inner reduction over N, and league_size=10 + { + const int league_size = 10; + Kokkos::View result("result", league_size); + TeamSumNestedFunctor tnf(f, league_size, N, result); + // FIXME_OPENMPTARGET temporary restriction for team size to be at least + // 32 +#ifdef KOKKOS_ENABLE_OPENMPTARGET + int initial_team_size = + std::is_same_v ? 32 + : 1; +#else + int initial_team_size = 1; +#endif + auto team_size_max = + Kokkos::TeamPolicy(league_size, initial_team_size) + .team_size_max(tnf, Kokkos::ParallelForTag()); + auto team_size = std::min(team_size_max, TEST_EXECSPACE().concurrency()); + auto team_pol = Kokkos::TeamPolicy(league_size, team_size); + Kokkos::parallel_for(team_pol, tnf); + auto result_h = + Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), result); + for (int i = 0; i < result_h.extent_int(0); ++i) { + ASSERT_EQ(result_h(i), reference_sum) << "N: " << N; + } + } + } + static void test_sum(int N) { Kokkos::View values("Values", N); auto h_values = Kokkos::create_mirror_view(values); @@ -374,6 +502,8 @@ struct TestReducers { ASSERT_EQ(sum_scalar_view, reference_sum) << "N: " << N; } + test_sum_team_policy(N, f, reference_sum); + { Kokkos::View sum_view("View"); sum_view() = Scalar(1); diff --git a/lib/kokkos/core/unit_test/TestReducers_d.hpp b/lib/kokkos/core/unit_test/TestReducers_d.hpp index 19eaa6d700..ecf851aa10 100644 --- a/lib/kokkos/core/unit_test/TestReducers_d.hpp +++ b/lib/kokkos/core/unit_test/TestReducers_d.hpp @@ -80,6 +80,20 @@ TEST(TEST_CATEGORY, reducers_int8_t) { TestReducers::test_prod(4); } +TEST(TEST_CATEGORY, reducers_int16_t) { + using ThisTestType = int16_t; + + TestReducers::test_sum(1); + TestReducers::test_sum(2); + TestReducers::test_sum(3); + TestReducers::test_sum(4); + + TestReducers::test_prod(1); + TestReducers::test_prod(2); + TestReducers::test_prod(3); + TestReducers::test_prod(4); +} + #if !defined(KOKKOS_ENABLE_HIP) && !defined(KOKKOS_ENABLE_OPENMPTARGET) // TODO - resolve: "Kokkos_HIP_Vectorization.hpp:80:15: error: call to // implicitly-deleted default constructor of 'conv_type' diff --git a/lib/kokkos/core/unit_test/TestSwap.hpp b/lib/kokkos/core/unit_test/TestSwap.hpp new file mode 100644 index 0000000000..4e98351cf1 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestSwap.hpp @@ -0,0 +1,68 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include + +#include +#include +#include + +namespace { + +template +struct TestSwap { + KOKKOS_FUNCTION void operator()(int, int& err) const { + { + int a = 1; + int b = 2; + Kokkos::kokkos_swap(a, b); + if (!(a == 2 && b == 1)) { + Kokkos::printf("Failed Kokkos::kokkos_swap(int, int)\n"); + ++err; + } + } + { + float a = 1; + float b = 2; + Kokkos::kokkos_swap(a, b); + if (!(a == 2 && b == 1)) { + Kokkos::printf("Failed Kokkos::kokkos_swap(float, float)\n"); + ++err; + } + } + { + int a[3] = {1, 2, 3}; + int b[3] = {4, 5, 6}; + Kokkos::kokkos_swap(a, b); + if (!(a[0] == 4 && a[1] == 5 && a[2] == 6 && b[0] == 1 && b[1] == 2 && + b[2] == 3)) { + Kokkos::printf("Failed Kokkos::kokkos_swap(int[3], int[3])\n"); + ++err; + } + } + } + + TestSwap() { + int errors; + Kokkos::parallel_reduce( + "TestSwap", Kokkos::RangePolicy(0, 1), *this, errors); + EXPECT_EQ(errors, 0); + } +}; + +TEST(TEST_CATEGORY, kokkos_swap) { TestSwap(); } + +} // namespace diff --git a/lib/kokkos/core/unit_test/TestTeamBasic.hpp b/lib/kokkos/core/unit_test/TestTeamBasic.hpp index c395bc0837..a3d84c5e16 100644 --- a/lib/kokkos/core/unit_test/TestTeamBasic.hpp +++ b/lib/kokkos/core/unit_test/TestTeamBasic.hpp @@ -280,7 +280,7 @@ namespace Test { // Test for non-arithmetic type TEST(TEST_CATEGORY, team_broadcast_long_wrapper) { - static_assert(!std::is_arithmetic::value, ""); + static_assert(!std::is_arithmetic::value); TestTeamBroadcast, long_wrapper>::test_teambroadcast(0, 1); diff --git a/lib/kokkos/core/unit_test/TestTeamMDRange.hpp b/lib/kokkos/core/unit_test/TestTeamMDRange.hpp index 6e65cde0cf..81931467c5 100644 --- a/lib/kokkos/core/unit_test/TestTeamMDRange.hpp +++ b/lib/kokkos/core/unit_test/TestTeamMDRange.hpp @@ -169,7 +169,14 @@ struct TestTeamThreadMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -202,7 +209,14 @@ struct TestTeamThreadMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -236,7 +250,14 @@ struct TestTeamThreadMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -272,7 +293,14 @@ struct TestTeamThreadMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3, n4); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -310,7 +338,14 @@ struct TestTeamThreadMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3, n4, n5); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -350,7 +385,14 @@ struct TestTeamThreadMDRangeParallelFor : public TestTeamMDParallelFor { n6); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -420,7 +462,14 @@ struct TestThreadVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -457,7 +506,14 @@ struct TestThreadVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -496,7 +552,14 @@ struct TestThreadVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3, n4); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -536,7 +599,14 @@ struct TestThreadVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3, n4, n5); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -579,7 +649,14 @@ struct TestThreadVectorMDRangeParallelFor : public TestTeamMDParallelFor { n6); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -620,7 +697,14 @@ struct TestTeamVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -653,7 +737,14 @@ struct TestTeamVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -687,7 +778,14 @@ struct TestTeamVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -723,7 +821,14 @@ struct TestTeamVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3, n4); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -761,7 +866,14 @@ struct TestTeamVectorMDRangeParallelFor : public TestTeamMDParallelFor { FillFlattenedIndex fillFlattenedIndex(leagueSize, n0, n1, n2, n3, n4, n5); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -801,7 +913,14 @@ struct TestTeamVectorMDRangeParallelFor : public TestTeamMDParallelFor { n6); Kokkos::parallel_for( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(const TeamType& team) { int leagueRank = team.league_rank(); @@ -908,13 +1027,20 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k) = fillFlattenedIndex(i, j, k); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; Kokkos::parallel_reduce( Kokkos::TeamThreadMDRange, TeamType>( @@ -923,7 +1049,13 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { threadSum += v(leagueRank, i, j); }, teamSum); - leagueSum += teamSum; + // FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -952,13 +1084,20 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l) = fillFlattenedIndex(i, j, k, l); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; Kokkos::parallel_reduce( Kokkos::TeamThreadMDRange, TeamType>( @@ -966,7 +1105,13 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { [=](const int& i, const int& j, const int& k, DataType& threadSum) { threadSum += v(leagueRank, i, j, k); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -997,13 +1142,20 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l, m) = fillFlattenedIndex(i, j, k, l, m); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; Kokkos::parallel_reduce( Kokkos::TeamThreadMDRange, TeamType>( @@ -1013,7 +1165,13 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { threadSum += v(leagueRank, i, j, k, l); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1045,13 +1203,20 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l, m, n) = fillFlattenedIndex(i, j, k, l, m, n); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; Kokkos::parallel_reduce( Kokkos::TeamThreadMDRange, TeamType>( @@ -1061,7 +1226,13 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { threadSum += v(leagueRank, i, j, k, l, m); }, teamSum); - leagueSum += teamSum; + // FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1100,13 +1271,20 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { } }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; Kokkos::parallel_reduce( Kokkos::TeamThreadMDRange, TeamType>( @@ -1116,7 +1294,13 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { threadSum += v(leagueRank, i, j, k, l, m, n); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1157,13 +1341,20 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { } }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; Kokkos::parallel_reduce( Kokkos::TeamThreadMDRange, TeamType>( @@ -1174,7 +1365,13 @@ struct TestTeamThreadMDRangeParallelReduce : public TestTeamMDParallelReduce { threadSum += v(leagueRank, i, j, k, l, m, n, o); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1207,20 +1404,26 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l) = fillFlattenedIndex(i, j, k, l); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); auto teamThreadRange = Kokkos::TeamThreadRange(team, n0); auto threadVectorRange = Kokkos::ThreadVectorMDRange, TeamType>( team, n1, n2); - Kokkos::parallel_for(teamThreadRange, [=, &teamSum](const int& i) { + Kokkos::parallel_for(teamThreadRange, [=, &leagueSum](const int& i) { DataType threadSum = 0; Kokkos::parallel_reduce( threadVectorRange, @@ -1228,11 +1431,9 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { vectorSum += v(leagueRank, i, j, k); }, threadSum); - - teamSum += threadSum; + Kokkos::single(Kokkos::PerThread(team), + [&]() { leagueSum += threadSum; }); }); - - leagueSum += teamSum; }, finalSum); @@ -1263,20 +1464,26 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l, m) = fillFlattenedIndex(i, j, k, l, m); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); auto teamThreadRange = Kokkos::TeamThreadRange(team, n0); auto threadVectorRange = Kokkos::ThreadVectorMDRange, TeamType>( team, n1, n2, n3); - Kokkos::parallel_for(teamThreadRange, [=, &teamSum](const int& i) { + Kokkos::parallel_for(teamThreadRange, [=, &leagueSum](const int& i) { DataType threadSum = 0; Kokkos::parallel_reduce( threadVectorRange, @@ -1286,10 +1493,9 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { }, threadSum); - teamSum += threadSum; + Kokkos::single(Kokkos::PerThread(team), + [&]() { leagueSum += threadSum; }); }); - - leagueSum += teamSum; }, finalSum); @@ -1321,20 +1527,26 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l, m, n) = fillFlattenedIndex(i, j, k, l, m, n); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); auto teamThreadRange = Kokkos::TeamThreadRange(team, n0); auto threadVectorRange = Kokkos::ThreadVectorMDRange, TeamType>( team, n1, n2, n3, n4); - Kokkos::parallel_for(teamThreadRange, [=, &teamSum](const int& i) { + Kokkos::parallel_for(teamThreadRange, [=, &leagueSum](const int& i) { DataType threadSum = 0; Kokkos::parallel_reduce( threadVectorRange, @@ -1344,10 +1556,9 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { }, threadSum); - teamSum += threadSum; + Kokkos::single(Kokkos::PerThread(team), + [&]() { leagueSum += threadSum; }); }); - - leagueSum += teamSum; }, finalSum); @@ -1384,20 +1595,26 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { } }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); auto teamThreadRange = Kokkos::TeamThreadRange(team, n0); auto threadVectorRange = Kokkos::ThreadVectorMDRange, TeamType>( team, n1, n2, n3, n4, n5); - Kokkos::parallel_for(teamThreadRange, [=, &teamSum](const int& i) { + Kokkos::parallel_for(teamThreadRange, [=, &leagueSum](const int& i) { DataType threadSum = 0; Kokkos::parallel_reduce( threadVectorRange, @@ -1407,10 +1624,9 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { }, threadSum); - teamSum += threadSum; + Kokkos::single(Kokkos::PerThread(team), + [&]() { leagueSum += threadSum; }); }); - - leagueSum += teamSum; }, finalSum); @@ -1451,20 +1667,26 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { } }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); auto teamThreadRange = Kokkos::TeamThreadRange(team, n0); auto threadVectorRange = Kokkos::ThreadVectorMDRange, TeamType>( team, n1, n2, n3, n4, n5, n6); - Kokkos::parallel_for(teamThreadRange, [=, &teamSum](const int& i) { + Kokkos::parallel_for(teamThreadRange, [=, &leagueSum](const int& i) { DataType threadSum = 0; Kokkos::parallel_reduce( threadVectorRange, @@ -1474,10 +1696,9 @@ struct TestThreadVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { }, threadSum); - teamSum += threadSum; + Kokkos::single(Kokkos::PerThread(team), + [&]() { leagueSum += threadSum; }); }); - - leagueSum += teamSum; }, finalSum); @@ -1510,13 +1731,20 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l) = fillFlattenedIndex(i, j, k, l); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; auto teamVectorRange = Kokkos::TeamVectorMDRange, TeamType>( @@ -1527,7 +1755,13 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { [=](const int& i, const int& j, const int& k, DataType& vectorSum) { vectorSum += v(leagueRank, i, j, k); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1558,13 +1792,20 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l, m) = fillFlattenedIndex(i, j, k, l, m); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; auto teamVectorRange = Kokkos::TeamVectorMDRange, TeamType>( @@ -1577,7 +1818,13 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { vectorSum += v(leagueRank, i, j, k, l); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1609,13 +1856,20 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { v(i, j, k, l, m, n) = fillFlattenedIndex(i, j, k, l, m, n); }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; auto teamVectorRange = Kokkos::TeamVectorMDRange, TeamType>( @@ -1628,7 +1882,13 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { vectorSum += v(leagueRank, i, j, k, l, m); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1665,13 +1925,20 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { } }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; auto teamVectorRange = Kokkos::TeamVectorMDRange, TeamType>( @@ -1684,7 +1951,13 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { vectorSum += v(leagueRank, i, j, k, l, m, n); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1725,13 +1998,20 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { } }); - DataType finalSum = 0; + DataType finalSum; Kokkos::parallel_reduce( - Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO), + Kokkos::TeamPolicy(leagueSize, Kokkos::AUTO, +#ifdef KOKKOS_ENABLE_OPENMPTARGET + 2 +#else + Kokkos::TeamPolicy< + ExecSpace>::vector_length_max() +#endif + ), KOKKOS_LAMBDA(TeamType const& team, DataType& leagueSum) { - auto leagueRank = team.league_rank(); - DataType teamSum = 0; + auto leagueRank = team.league_rank(); + DataType teamSum; auto teamVectorRange = Kokkos::TeamVectorMDRange, TeamType>( @@ -1745,7 +2025,13 @@ struct TestTeamVectorMDRangeParallelReduce : public TestTeamMDParallelReduce { vectorSum += v(leagueRank, i, j, k, l, m, n, o); }, teamSum); - leagueSum += teamSum; +// FIXME_OPENMPTARGET +#ifdef KOKKOS_ENABLE_OPENMPTARGET + if (team.team_rank() == 0) leagueSum += teamSum; +#else + Kokkos::single(Kokkos::PerTeam(team), + [&]() { leagueSum += teamSum; }); +#endif }, finalSum); @@ -1904,13 +2190,6 @@ TEST(TEST_CATEGORY, ThreadVectorMDRangeParallelReduce) { GTEST_SKIP() << "skipping because of bug in group_barrier implementation"; #endif -// FIXME_OPENMPTARGET_CRAY: The unit tests fails correctness. -#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_COMPILER_CRAYCLANG) - if (std::is_same_v) - GTEST_SKIP() << "Cray compiler fails correctness at runtime with the " - "OpenMPTarget backend."; -#endif - TestThreadVectorMDRangeParallelReduce:: test_parallel_reduce_for_4D_ThreadVectorMDRange(dims); TestThreadVectorMDRangeParallelReduce:: @@ -1944,13 +2223,6 @@ TEST(TEST_CATEGORY, TeamVectorMDRangeParallelReduce) { GTEST_SKIP() << "skipping because of bug in group_barrier implementation"; #endif -// FIXME_OPENMPTARGET_CRAY: The unit tests fails correctness. -#if defined(KOKKOS_ENABLE_OPENMPTARGET) && defined(KOKKOS_COMPILER_CRAYCLANG) - if (std::is_same_v) - GTEST_SKIP() << "Cray compiler fails correctness at runtime with the " - "OpenMPTarget backend."; -#endif - TestTeamVectorMDRangeParallelReduce:: test_parallel_reduce_for_4D_TeamVectorMDRange(dims); TestTeamVectorMDRangeParallelReduce:: diff --git a/lib/kokkos/core/unit_test/TestTeamPolicyConstructors.hpp b/lib/kokkos/core/unit_test/TestTeamPolicyConstructors.hpp index 5b0bfdb175..9d89f75708 100644 --- a/lib/kokkos/core/unit_test/TestTeamPolicyConstructors.hpp +++ b/lib/kokkos/core/unit_test/TestTeamPolicyConstructors.hpp @@ -20,11 +20,24 @@ namespace { +struct SomeTag {}; + +struct FunctorFor { + KOKKOS_FUNCTION + void operator()( + Kokkos::TeamPolicy::member_type const&) const {} + + KOKKOS_FUNCTION + void operator()( + SomeTag, Kokkos::TeamPolicy::member_type const&) const {} +}; + template void test_run_time_parameters() { int league_size = 131; using ExecutionSpace = typename Policy::execution_space; + using ParallelTag = Kokkos::ParallelForTag; int team_size = 4 < ExecutionSpace().concurrency() ? 4 : ExecutionSpace().concurrency(); #ifdef KOKKOS_ENABLE_HPX @@ -44,6 +57,8 @@ void test_run_time_parameters() { ASSERT_EQ(p1.team_size(), team_size); ASSERT_GT(p1.chunk_size(), 0); ASSERT_EQ(p1.scratch_size(0), 0u); + ASSERT_GT(p1.team_size_max(FunctorFor(), ParallelTag()), 0); + ASSERT_GT(p1.team_size_recommended(FunctorFor(), ParallelTag()), 0); Policy p2 = p1.set_chunk_size(chunk_size); ASSERT_EQ(p1.league_size(), league_size); @@ -112,6 +127,8 @@ void test_run_time_parameters() { Policy p8; // default constructed ASSERT_EQ(p8.league_size(), 0); ASSERT_EQ(p8.scratch_size(0), 0u); + ASSERT_GT(p8.team_size_max(FunctorFor(), ParallelTag()), 0); + ASSERT_GT(p8.team_size_recommended(FunctorFor(), ParallelTag()), 0); p8 = p3; // call assignment operator ASSERT_EQ(p3.league_size(), league_size); ASSERT_EQ(p3.team_size(), team_size); @@ -121,11 +138,25 @@ void test_run_time_parameters() { ASSERT_EQ(p8.team_size(), team_size); ASSERT_EQ(p8.chunk_size(), chunk_size); ASSERT_EQ(p8.scratch_size(0), size_t(scratch_size)); + + Policy p9(league_size, Kokkos::AUTO); + ASSERT_EQ(p9.league_size(), league_size); + ASSERT_GT(p9.team_size_max(FunctorFor(), ParallelTag()), 0); + ASSERT_GT(p9.team_size_recommended(FunctorFor(), ParallelTag()), 0); + + Policy p10(league_size, team_size, Kokkos::AUTO); + ASSERT_EQ(p10.league_size(), league_size); + ASSERT_EQ(p10.team_size(), team_size); + ASSERT_GT(p10.team_size_max(FunctorFor(), ParallelTag()), 0); + ASSERT_GT(p10.team_size_recommended(FunctorFor(), ParallelTag()), 0); + + Policy p11(league_size, Kokkos::AUTO, Kokkos::AUTO); + ASSERT_EQ(p11.league_size(), league_size); + ASSERT_GT(p11.team_size_max(FunctorFor(), ParallelTag()), 0); + ASSERT_GT(p11.team_size_recommended(FunctorFor(), ParallelTag()), 0); } TEST(TEST_CATEGORY, team_policy_runtime_parameters) { - struct SomeTag {}; - using TestExecSpace = TEST_EXECSPACE; using DynamicSchedule = Kokkos::Schedule; using LongIndex = Kokkos::IndexType; diff --git a/lib/kokkos/core/unit_test/TestTeamVector.hpp b/lib/kokkos/core/unit_test/TestTeamVector.hpp index 39122736ed..5e16539d65 100644 --- a/lib/kokkos/core/unit_test/TestTeamVector.hpp +++ b/lib/kokkos/core/unit_test/TestTeamVector.hpp @@ -1012,7 +1012,6 @@ struct checkScan { }; } // namespace VectorScanReducer -#if !defined(KOKKOS_IMPL_CUDA_CLANG_WORKAROUND) TEST(TEST_CATEGORY, team_vector) { ASSERT_TRUE((TestTeamVector::Test(0))); ASSERT_TRUE((TestTeamVector::Test(1))); @@ -1028,9 +1027,7 @@ TEST(TEST_CATEGORY, team_vector) { ASSERT_TRUE((TestTeamVector::Test(11))); ASSERT_TRUE((TestTeamVector::Test(12))); } -#endif -#if !defined(KOKKOS_IMPL_CUDA_CLANG_WORKAROUND) TEST(TEST_CATEGORY, triple_nested_parallelism) { // With KOKKOS_ENABLE_DEBUG enabled, the functor uses too many registers to run // with a team size of 32 on GPUs, 16 is the max possible (at least on a K80 @@ -1055,7 +1052,6 @@ TEST(TEST_CATEGORY, triple_nested_parallelism) { TestTripleNestedReduce(8192, 2048, 16, 16); TestTripleNestedReduce(8192, 2048, 7, 16); } -#endif TEST(TEST_CATEGORY, parallel_scan_with_reducers) { using T = double; diff --git a/lib/kokkos/core/unit_test/TestUtilities.hpp b/lib/kokkos/core/unit_test/TestUtilities.hpp index b1f9d30c1f..ad5a0df92d 100644 --- a/lib/kokkos/core/unit_test/TestUtilities.hpp +++ b/lib/kokkos/core/unit_test/TestUtilities.hpp @@ -25,20 +25,18 @@ namespace Test { void test_is_specialization_of() { using Kokkos::Impl::is_specialization_of; - static_assert(is_specialization_of, Kokkos::pair>{}, - ""); - static_assert(!is_specialization_of, Kokkos::pair>{}, ""); - static_assert(is_specialization_of, Kokkos::View>{}, ""); + static_assert(is_specialization_of, Kokkos::pair>{}); + static_assert(!is_specialization_of, Kokkos::pair>{}); + static_assert(is_specialization_of, Kokkos::View>{}); // NOTE Not removing cv-qualifiers - static_assert(!is_specialization_of const, Kokkos::View>{}, - ""); + static_assert( + !is_specialization_of const, Kokkos::View>{}); // NOTE Would not compile because Kokkos::Array takes a non-type template // parameter - // static_assert(is_specialization_of, Kokkos::Array>{}, - // ""); + // static_assert(is_specialization_of, + // Kokkos::Array>{}); // But this is fine of course - static_assert(!is_specialization_of, Kokkos::pair>{}, - ""); + static_assert(!is_specialization_of, Kokkos::pair>{}); } namespace { diff --git a/lib/kokkos/core/unit_test/TestViewAPI.hpp b/lib/kokkos/core/unit_test/TestViewAPI.hpp index ffc500e4a9..ca098dbc24 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI.hpp @@ -958,8 +958,7 @@ class TestViewAPI { using mirror_type = typename view_type::HostMirror; static_assert(std::is_same::value, - ""); + typename mirror_type::memory_space>::value); view_type a("a"); mirror_type am = Kokkos::create_mirror_view(a); @@ -1005,25 +1004,25 @@ class TestViewAPI { hView3 hv_3("dView3::HostMirror", N0); hView4 hv_4("dView4::HostMirror", N0); - dView0 dv_0_1(nullptr, 0); + dView0 dv_0_1(nullptr); dView0 dv_0_2(hv_0.label(), hv_0.layout()); - dView1 dv_1_1(nullptr, 0); + dView1 dv_1_1(nullptr, N0); dView1 dv_1_2(hv_1.label(), hv_1.layout()); - dView2 dv_2_1(nullptr, 0); + dView2 dv_2_1(nullptr, N0); dView2 dv_2_2(hv_2.label(), hv_2.layout()); - dView3 dv_3_1(nullptr, 0); + dView3 dv_3_1(nullptr, N0); dView3 dv_3_2(hv_3.label(), hv_3.layout()); - dView4 dv_4_1(nullptr, 0); + dView4 dv_4_1(nullptr, N0); dView4 dv_4_2(hv_4.label(), hv_4.layout()); } static void run_test_contruction_from_layout_2() { using dView3_0 = Kokkos::View; - using dView3_1 = Kokkos::View; + using dView3_1 = Kokkos::View; using dView3_2 = Kokkos::View; using dView3_3 = Kokkos::View; @@ -1554,6 +1553,7 @@ class TestViewAPI { Kokkos::CudaUVMSpace>::value) return; #endif + bool did_throw = false; auto alloc_size = std::numeric_limits::max() - 42; try { auto should_always_fail = dView1("hello_world_failure", alloc_size); @@ -1585,7 +1585,9 @@ class TestViewAPI { "because of an unknown error.", msg); } #endif + did_throw = true; } + ASSERT_TRUE(did_throw); } }; diff --git a/lib/kokkos/core/unit_test/TestViewAPI_d.hpp b/lib/kokkos/core/unit_test/TestViewAPI_d.hpp index 08d21f5449..b0d759ffcc 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI_d.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI_d.hpp @@ -27,8 +27,19 @@ TEST(TEST_CATEGORY, view_api_d) { } TEST(TEST_CATEGORY, view_allocation_error) { +#if defined(__has_feature) +#if __has_feature(address_sanitizer) + GTEST_SKIP() << "AddressSanitzer detects allocating too much memory " + "preventing our checks to run"; +#endif +#endif #if ((HIP_VERSION_MAJOR == 5) && (HIP_VERSION_MINOR == 3)) GTEST_SKIP() << "ROCm 5.3 segfaults when trying to allocate too much memory"; +#endif +#if defined(KOKKOS_ENABLE_OPENACC) // FIXME_OPENACC + if (std::is_same_v) { + GTEST_SKIP() << "acc_malloc() not properly returning nullptr"; + } #endif TestViewAPI::run_test_error(); } diff --git a/lib/kokkos/core/unit_test/TestViewCopy_a.hpp b/lib/kokkos/core/unit_test/TestViewCopy_a.hpp index 3bfc93aada..a4735b2998 100644 --- a/lib/kokkos/core/unit_test/TestViewCopy_a.hpp +++ b/lib/kokkos/core/unit_test/TestViewCopy_a.hpp @@ -147,6 +147,40 @@ TEST(TEST_CATEGORY, view_copy_tests) { Kokkos::deep_copy(s_a, hs_a); ASSERT_TRUE(run_check(s_a, 6)); } + } else { + // These copies won't succeed, but they should each throw + // an exception whose message contains the view labels, + // and the names of the views' memory spaces. + // + // Note: original a,b both have the same device type, + // and their mirrors have the same device type. + using memory_space = typename decltype(a)::memory_space; + using mirror_memory_space = typename decltype(h_a)::memory_space; + bool threw = false; + std::string msg; + try { + Kokkos::deep_copy(hs_b, s_b); + } catch (std::exception& e) { + threw = true; + msg = e.what(); + } + ASSERT_TRUE(threw); + ASSERT_NE(msg.find(hs_b.label()), std::string::npos); + ASSERT_NE(msg.find(s_b.label()), std::string::npos); + ASSERT_NE(msg.find(memory_space().name()), std::string::npos); + ASSERT_NE(msg.find(mirror_memory_space().name()), std::string::npos); + threw = false; + try { + Kokkos::deep_copy(s_a, hs_a); + } catch (std::exception& e) { + threw = true; + msg = e.what(); + } + ASSERT_TRUE(threw); + ASSERT_NE(msg.find(s_a.label()), std::string::npos); + ASSERT_NE(msg.find(hs_a.label()), std::string::npos); + ASSERT_NE(msg.find(memory_space().name()), std::string::npos); + ASSERT_NE(msg.find(mirror_memory_space().name()), std::string::npos); } // Contiguous copies diff --git a/lib/kokkos/core/unit_test/TestViewCtorDimMatch.hpp b/lib/kokkos/core/unit_test/TestViewCtorDimMatch.hpp index d71841eef8..40b7737f2e 100644 --- a/lib/kokkos/core/unit_test/TestViewCtorDimMatch.hpp +++ b/lib/kokkos/core/unit_test/TestViewCtorDimMatch.hpp @@ -19,33 +19,72 @@ namespace Test { -#define LIVE(EXPR, ARGS, DYNRANK) EXPECT_NO_THROW(EXPR) -#define DIE(EXPR, ARGS, DYNRANK) \ - ASSERT_DEATH( \ - EXPR, \ - "Constructor for Kokkos View 'v_" #ARGS \ - "' has mismatched number of arguments. Number of arguments = " #ARGS \ - " but dynamic rank = " #DYNRANK) +template +void test_matching_arguments_rank_helper(std::index_sequence) { + constexpr int nargs = sizeof...(Is); + using view_type = Kokkos::View; + if (nargs == rank || nargs == dynrank) { + EXPECT_NO_THROW({ view_type v("v", ((Is * 0) + 1)...); }); + EXPECT_NO_THROW({ view_type v(nullptr, ((Is * 0) + 1)...); }); + } else { + ASSERT_DEATH( + { view_type v("v", ((Is * 0) + 1)...); }, + "Constructor for Kokkos::View 'v' has mismatched number of arguments. " + "The number of arguments = " + + std::to_string(nargs) + + " neither matches the dynamic rank = " + std::to_string(dynrank) + + " nor the total rank = " + std::to_string(rank)); + ASSERT_DEATH( + { view_type v(nullptr, ((Is * 0) + 1)...); }, + "Constructor for Kokkos::View 'UNMANAGED' has mismatched number of " + "arguments. " + "The number of arguments = " + + std::to_string(nargs) + + " neither matches the dynamic rank = " + std::to_string(dynrank) + + " nor the total rank = " + std::to_string(rank)); + } +} -#define PARAM_0 -#define PARAM_1 1 -#define PARAM_2 1, 1 -#define PARAM_3 1, 1, 1 -#define PARAM_4 1, 1, 1, 1 -#define PARAM_5 1, 1, 1, 1, 1 -#define PARAM_6 1, 1, 1, 1, 1, 1 -#define PARAM_7 1, 1, 1, 1, 1, 1, 1 +template class RankType> +void test_matching_arguments_rank() { + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<0>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<1>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<2>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<3>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<4>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<5>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<6>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<7>()); + test_matching_arguments_rank_helper::type>( + std::make_index_sequence<8>()); +} -#define PARAM_0_RANK 0 -#define PARAM_1_RANK 1 -#define PARAM_2_RANK 2 -#define PARAM_3_RANK 3 -#define PARAM_4_RANK 4 -#define PARAM_5_RANK 5 -#define PARAM_6_RANK 6 -#define PARAM_7_RANK 7 +template +struct DynamicRank { + using type = typename DynamicRank::type*; +}; -using DType = int; +template <> +struct DynamicRank<0> { + using type = int; +}; // Skip test execution when KOKKOS_ENABLE_OPENMPTARGET is enabled until // Kokkos::abort() aborts properly on that backend @@ -53,348 +92,110 @@ using DType = int; TEST(TEST_CATEGORY_DEATH, view_construction_with_wrong_params_dyn) { ::testing::FLAGS_gtest_death_test_style = "threadsafe"; - using DType_0 = DType; - using DType_1 = DType *; - using DType_2 = DType **; - using DType_3 = DType ***; - using DType_4 = DType ****; - using DType_5 = DType *****; - using DType_6 = DType ******; - using DType_7 = DType *******; - { - // test View parameters for View dim = 0, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 1, dynamic = 1 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 1); - LIVE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 1); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 1); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 1); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 1); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 1); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 1); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 1); - } - - { - // test View parameters for View dim = 2, dynamic = 2 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 2); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 2); - LIVE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 2); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 2); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 2); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 2); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 2); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 2); - } - - { - // test View parameters for View dim = 3, dynamic = 3 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 3); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 3); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 3); - LIVE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 3); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 3); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 3); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 3); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 3); - } - - { - // test View parameters for View dim = 4, dynamic = 4 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 4); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 4); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 4); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 4); - LIVE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 4); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 4); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 4); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 4); - } - - { - // test View parameters for View dim = 5, dynamic = 5 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 5); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 5); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 5); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 5); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 5); - LIVE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 5); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 5); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 5); - } - - { - // test View parameters for View dim = 6, dynamic = 6 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 6); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 6); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 6); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 6); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 6); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 6); - LIVE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 6); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 6); - } - - { - // test View parameters for View dim = 7, dynamic = 7 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 7); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 7); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 7); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 7); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 7); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 7); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 7); - LIVE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 7); - } +#ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECKS + test_matching_arguments_rank<0, 0, DynamicRank>(); // dim = 0, dynamic = 0 + test_matching_arguments_rank<1, 1, DynamicRank>(); // dim = 1, dynamic = 1 + test_matching_arguments_rank<2, 2, DynamicRank>(); // dim = 2, dynamic = 2 + test_matching_arguments_rank<3, 3, DynamicRank>(); // dim = 3, dynamic = 3 + test_matching_arguments_rank<4, 4, DynamicRank>(); // dim = 4, dynamic = 4 + test_matching_arguments_rank<5, 5, DynamicRank>(); // dim = 5, dynamic = 5 + test_matching_arguments_rank<6, 6, DynamicRank>(); // dim = 6, dynamic = 6 + test_matching_arguments_rank<7, 7, DynamicRank>(); // dim = 7, dynamic = 7 + test_matching_arguments_rank<8, 8, DynamicRank>(); // dim = 8, dynamic = 8 +#endif } +template +struct StaticRank { + using type = typename StaticRank::type[1]; +}; + +template <> +struct StaticRank<0> { + using type = int; +}; + TEST(TEST_CATEGORY_DEATH, view_construction_with_wrong_params_stat) { ::testing::FLAGS_gtest_death_test_style = "threadsafe"; - using DType_0 = DType; - using DType_1 = DType[1]; - using DType_2 = DType[1][1]; - using DType_3 = DType[1][1][1]; - using DType_4 = DType[1][1][1][1]; - using DType_5 = DType[1][1][1][1][1]; - using DType_6 = DType[1][1][1][1][1][1]; - using DType_7 = DType[1][1][1][1][1][1][1]; - { - // test View parameters for View dim = 0, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 1, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - LIVE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 2, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - LIVE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 3, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - LIVE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 4, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - LIVE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 5, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - LIVE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 6, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - LIVE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 7, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - LIVE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } +#ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECKS + test_matching_arguments_rank<0, 0, StaticRank>(); // dim = 0, dynamic = 0 + test_matching_arguments_rank<1, 0, StaticRank>(); // dim = 1, dynamic = 0 + test_matching_arguments_rank<2, 0, StaticRank>(); // dim = 2, dynamic = 0 + test_matching_arguments_rank<3, 0, StaticRank>(); // dim = 3, dynamic = 0 + test_matching_arguments_rank<4, 0, StaticRank>(); // dim = 4, dynamic = 0 + test_matching_arguments_rank<5, 0, StaticRank>(); // dim = 5, dynamic = 0 + test_matching_arguments_rank<6, 0, StaticRank>(); // dim = 6, dynamic = 0 + test_matching_arguments_rank<7, 0, StaticRank>(); // dim = 7, dynamic = 0 + test_matching_arguments_rank<8, 0, StaticRank>(); // dim = 8, dynamic = 0 +#endif } +template +struct MixedRank { + using type = typename DynamicRank::type[1]; +}; + +template <> +struct MixedRank<0> { + using type = int; +}; + TEST(TEST_CATEGORY_DEATH, view_construction_with_wrong_params_mix) { ::testing::FLAGS_gtest_death_test_style = "threadsafe"; - using DType_0 = DType; - using DType_1 = DType[1]; - using DType_2 = DType * [1]; - using DType_3 = DType * * [1]; - using DType_4 = DType ** * [1]; - using DType_5 = DType *** * [1]; - using DType_6 = DType **** * [1]; - using DType_7 = DType ***** * [1]; - { - // test View parameters for View dim = 0, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 1, dynamic = 0 - LIVE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 0); - LIVE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 0); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 0); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 0); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 0); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 0); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 0); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 0); - } - - { - // test View parameters for View dim = 2, dynamic = 1 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 1); - LIVE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 1); - LIVE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 1); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 1); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 1); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 1); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 1); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 1); - } - - { - // test View parameters for View dim = 3, dynamic = 2 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 2); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 2); - LIVE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 2); - LIVE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 2); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 2); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 2); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 2); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 2); - } - - { - // test View parameters for View dim = 4, dynamic = 3 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 3); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 3); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 3); - LIVE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 3); - LIVE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 3); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 3); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 3); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 3); - } - - { - // test View parameters for View dim = 5, dynamic = 4 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 4); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 4); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 4); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 4); - LIVE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 4); - LIVE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 4); - DIE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 4); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 4); - } - - { - // test View parameters for View dim = 6, dynamic = 5 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 5); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 5); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 5); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 5); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 5); - LIVE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 5); - LIVE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 5); - DIE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 5); - } - - { - // test View parameters for View dim = 7, dynamic = 6 - DIE({ Kokkos::View v_0("v_0" PARAM_0); }, 0, 6); - DIE({ Kokkos::View v_1("v_1", PARAM_1); }, 1, 6); - DIE({ Kokkos::View v_2("v_2", PARAM_2); }, 2, 6); - DIE({ Kokkos::View v_3("v_3", PARAM_3); }, 3, 6); - DIE({ Kokkos::View v_4("v_4", PARAM_4); }, 4, 6); - DIE({ Kokkos::View v_5("v_5", PARAM_5); }, 5, 6); - LIVE({ Kokkos::View v_6("v_6", PARAM_6); }, 6, 6); - LIVE({ Kokkos::View v_7("v_7", PARAM_7); }, 7, 6); - } +#ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECKS + test_matching_arguments_rank<0, 0, MixedRank>(); // dim = 0, dynamic = 0 + test_matching_arguments_rank<1, 0, MixedRank>(); // dim = 1, dynamic = 0 + test_matching_arguments_rank<2, 1, MixedRank>(); // dim = 2, dynamic = 1 + test_matching_arguments_rank<3, 2, MixedRank>(); // dim = 3, dynamic = 2 + test_matching_arguments_rank<4, 3, MixedRank>(); // dim = 4, dynamic = 3 + test_matching_arguments_rank<5, 4, MixedRank>(); // dim = 5, dynamic = 4 + test_matching_arguments_rank<6, 5, MixedRank>(); // dim = 6, dynamic = 5 + test_matching_arguments_rank<7, 6, MixedRank>(); // dim = 7, dynamic = 6 + test_matching_arguments_rank<8, 7, MixedRank>(); // dim = 8, dynamic = 7 +#endif } + +#define CHECK_DEATH(EXPR) \ + ASSERT_DEATH(EXPR, \ + "The specified run-time extent for Kokkos::View 'v' does not " \ + "match the compile-time extent in dimension 0. The given " \ + "extent is 2 but should be 1.") + +#define CHECK_DEATH_UNMANAGED(EXPR) \ + ASSERT_DEATH( \ + EXPR, \ + "The specified run-time extent for Kokkos::View 'UNMANAGED' does not " \ + "match the compile-time extent in dimension 0. The given " \ + "extent is 2 but should be 1.") + +TEST(TEST_CATEGORY_DEATH, view_construction_with_wrong_static_extents) { + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + +#ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECKS + // clang-format off + CHECK_DEATH({ Kokkos::View v("v", 2); }); + CHECK_DEATH({ Kokkos::View v("v", 2, 1); }); + CHECK_DEATH({ Kokkos::View v("v", 2, 1, 1); }); + CHECK_DEATH({ Kokkos::View v("v", 2, 1, 1, 1); }); + CHECK_DEATH({ Kokkos::View v("v", 2, 1, 1, 1, 1); }); + CHECK_DEATH({ Kokkos::View v("v", 2, 1, 1, 1, 1, 1); }); + CHECK_DEATH({ Kokkos::View v("v", 2, 1, 1, 1, 1, 1, 1); }); + CHECK_DEATH({ Kokkos::View v("v", 2, 1, 1, 1, 1, 1, 1, 1); }); + + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2); }); + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2, 1); }); + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2, 1, 1); }); + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2, 1, 1, 1); }); + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2, 1, 1, 1, 1); }); + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2, 1, 1, 1, 1, 1); }); + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2, 1, 1, 1, 1, 1, 1); }); + CHECK_DEATH_UNMANAGED({ Kokkos::View v(nullptr, 2, 1, 1, 1, 1, 1, 1, 1); }); + // clang-format on +#endif +} + +#undef CHECK_DEATH #endif // KOKKOS_ENABLE_OPENMPTARGET - -#undef PARAM_0 -#undef PARAM_1 -#undef PARAM_2 -#undef PARAM_3 -#undef PARAM_4 -#undef PARAM_5 -#undef PARAM_6 -#undef PARAM_7 - -#undef PARAM_0_RANK -#undef PARAM_1_RANK -#undef PARAM_2_RANK -#undef PARAM_3_RANK -#undef PARAM_4_RANK -#undef PARAM_5_RANK -#undef PARAM_6_RANK -#undef PARAM_7_RANK - -#undef DType - -#undef LIVE -#undef DIE } // namespace Test diff --git a/lib/kokkos/core/unit_test/TestViewEmptyRuntimeUnmanaged.hpp b/lib/kokkos/core/unit_test/TestViewEmptyRuntimeUnmanaged.hpp new file mode 100644 index 0000000000..b156b72860 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestViewEmptyRuntimeUnmanaged.hpp @@ -0,0 +1,55 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include + +#include + +namespace { + +template +void test_empty_view_runtime_unmanaged() { + T d{}; + auto* p = reinterpret_cast(0xABADBABE); + + (void)Kokkos::View(p); + (void)Kokkos::View(&d); + (void)Kokkos::View(nullptr); + (void)Kokkos::View(NULL); // NOLINT(modernize-use-nullptr) + (void)Kokkos::View(0); // NOLINT(modernize-use-nullptr) + + (void)Kokkos::View(p, 0); + (void)Kokkos::View(&d, 0); + (void)Kokkos::View(nullptr, 0); + (void)Kokkos::View(NULL, 0); // NOLINT(modernize-use-nullptr) + (void)Kokkos::View(0, 0); // NOLINT(modernize-use-nullptr) + + (void)Kokkos::View(p, 0, 0); + (void)Kokkos::View(&d, 0, 0); + (void)Kokkos::View(nullptr, 0, 0); + (void)Kokkos::View(NULL, 0, 0); // NOLINT(modernize-use-nullptr) + (void)Kokkos::View(0, 0, 0); // NOLINT(modernize-use-nullptr) +} + +TEST(TEST_CATEGORY, view_empty_runtime_unmanaged) { + test_empty_view_runtime_unmanaged(); + test_empty_view_runtime_unmanaged(); + test_empty_view_runtime_unmanaged(); + test_empty_view_runtime_unmanaged(); + test_empty_view_runtime_unmanaged(); +} + +} // namespace diff --git a/lib/kokkos/core/unit_test/TestViewMapping_a.hpp b/lib/kokkos/core/unit_test/TestViewMapping_a.hpp index 9173f0d431..a4dfdb26e3 100644 --- a/lib/kokkos/core/unit_test/TestViewMapping_a.hpp +++ b/lib/kokkos/core/unit_test/TestViewMapping_a.hpp @@ -73,67 +73,67 @@ void test_view_mapping() { ASSERT_LE(sizeof(dim_s0_s0_s0_s0_s0_s0_s0), 8 * sizeof(unsigned)); ASSERT_EQ(sizeof(dim_s0_s0_s0_s0_s0_s0_s0_s0), 8 * sizeof(unsigned)); #endif - static_assert(int(dim_0::rank) == int(0), ""); - static_assert(int(dim_0::rank_dynamic) == int(0), ""); - static_assert(int(dim_0::ArgN0) == 1, ""); - static_assert(int(dim_0::ArgN1) == 1, ""); - static_assert(int(dim_0::ArgN2) == 1, ""); + static_assert(int(dim_0::rank) == int(0)); + static_assert(int(dim_0::rank_dynamic) == int(0)); + static_assert(int(dim_0::ArgN0) == 1); + static_assert(int(dim_0::ArgN1) == 1); + static_assert(int(dim_0::ArgN2) == 1); - static_assert(int(dim_s2::rank) == int(1), ""); - static_assert(int(dim_s2::rank_dynamic) == int(0), ""); - static_assert(int(dim_s2::ArgN0) == 2, ""); - static_assert(int(dim_s2::ArgN1) == 1, ""); + static_assert(int(dim_s2::rank) == int(1)); + static_assert(int(dim_s2::rank_dynamic) == int(0)); + static_assert(int(dim_s2::ArgN0) == 2); + static_assert(int(dim_s2::ArgN1) == 1); - static_assert(int(dim_s2_s3::rank) == int(2), ""); - static_assert(int(dim_s2_s3::rank_dynamic) == int(0), ""); - static_assert(int(dim_s2_s3::ArgN0) == 2, ""); - static_assert(int(dim_s2_s3::ArgN1) == 3, ""); - static_assert(int(dim_s2_s3::ArgN2) == 1, ""); + static_assert(int(dim_s2_s3::rank) == int(2)); + static_assert(int(dim_s2_s3::rank_dynamic) == int(0)); + static_assert(int(dim_s2_s3::ArgN0) == 2); + static_assert(int(dim_s2_s3::ArgN1) == 3); + static_assert(int(dim_s2_s3::ArgN2) == 1); - static_assert(int(dim_s2_s3_s4::rank) == int(3), ""); - static_assert(int(dim_s2_s3_s4::rank_dynamic) == int(0), ""); - static_assert(int(dim_s2_s3_s4::ArgN0) == 2, ""); - static_assert(int(dim_s2_s3_s4::ArgN1) == 3, ""); - static_assert(int(dim_s2_s3_s4::ArgN2) == 4, ""); - static_assert(int(dim_s2_s3_s4::ArgN3) == 1, ""); + static_assert(int(dim_s2_s3_s4::rank) == int(3)); + static_assert(int(dim_s2_s3_s4::rank_dynamic) == int(0)); + static_assert(int(dim_s2_s3_s4::ArgN0) == 2); + static_assert(int(dim_s2_s3_s4::ArgN1) == 3); + static_assert(int(dim_s2_s3_s4::ArgN2) == 4); + static_assert(int(dim_s2_s3_s4::ArgN3) == 1); - static_assert(int(dim_s0::rank) == int(1), ""); - static_assert(int(dim_s0::rank_dynamic) == int(1), ""); + static_assert(int(dim_s0::rank) == int(1)); + static_assert(int(dim_s0::rank_dynamic) == int(1)); - static_assert(int(dim_s0_s3::rank) == int(2), ""); - static_assert(int(dim_s0_s3::rank_dynamic) == int(1), ""); - static_assert(int(dim_s0_s3::ArgN0) == 0, ""); - static_assert(int(dim_s0_s3::ArgN1) == 3, ""); + static_assert(int(dim_s0_s3::rank) == int(2)); + static_assert(int(dim_s0_s3::rank_dynamic) == int(1)); + static_assert(int(dim_s0_s3::ArgN0) == 0); + static_assert(int(dim_s0_s3::ArgN1) == 3); - static_assert(int(dim_s0_s3_s4::rank) == int(3), ""); - static_assert(int(dim_s0_s3_s4::rank_dynamic) == int(1), ""); - static_assert(int(dim_s0_s3_s4::ArgN0) == 0, ""); - static_assert(int(dim_s0_s3_s4::ArgN1) == 3, ""); - static_assert(int(dim_s0_s3_s4::ArgN2) == 4, ""); + static_assert(int(dim_s0_s3_s4::rank) == int(3)); + static_assert(int(dim_s0_s3_s4::rank_dynamic) == int(1)); + static_assert(int(dim_s0_s3_s4::ArgN0) == 0); + static_assert(int(dim_s0_s3_s4::ArgN1) == 3); + static_assert(int(dim_s0_s3_s4::ArgN2) == 4); - static_assert(int(dim_s0_s0_s4::rank) == int(3), ""); - static_assert(int(dim_s0_s0_s4::rank_dynamic) == int(2), ""); - static_assert(int(dim_s0_s0_s4::ArgN0) == 0, ""); - static_assert(int(dim_s0_s0_s4::ArgN1) == 0, ""); - static_assert(int(dim_s0_s0_s4::ArgN2) == 4, ""); + static_assert(int(dim_s0_s0_s4::rank) == int(3)); + static_assert(int(dim_s0_s0_s4::rank_dynamic) == int(2)); + static_assert(int(dim_s0_s0_s4::ArgN0) == 0); + static_assert(int(dim_s0_s0_s4::ArgN1) == 0); + static_assert(int(dim_s0_s0_s4::ArgN2) == 4); - static_assert(int(dim_s0_s0_s0::rank) == int(3), ""); - static_assert(int(dim_s0_s0_s0::rank_dynamic) == int(3), ""); + static_assert(int(dim_s0_s0_s0::rank) == int(3)); + static_assert(int(dim_s0_s0_s0::rank_dynamic) == int(3)); - static_assert(int(dim_s0_s0_s0_s0::rank) == int(4), ""); - static_assert(int(dim_s0_s0_s0_s0::rank_dynamic) == int(4), ""); + static_assert(int(dim_s0_s0_s0_s0::rank) == int(4)); + static_assert(int(dim_s0_s0_s0_s0::rank_dynamic) == int(4)); - static_assert(int(dim_s0_s0_s0_s0_s0::rank) == int(5), ""); - static_assert(int(dim_s0_s0_s0_s0_s0::rank_dynamic) == int(5), ""); + static_assert(int(dim_s0_s0_s0_s0_s0::rank) == int(5)); + static_assert(int(dim_s0_s0_s0_s0_s0::rank_dynamic) == int(5)); - static_assert(int(dim_s0_s0_s0_s0_s0_s0::rank) == int(6), ""); - static_assert(int(dim_s0_s0_s0_s0_s0_s0::rank_dynamic) == int(6), ""); + static_assert(int(dim_s0_s0_s0_s0_s0_s0::rank) == int(6)); + static_assert(int(dim_s0_s0_s0_s0_s0_s0::rank_dynamic) == int(6)); - static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0::rank) == int(7), ""); - static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0::rank_dynamic) == int(7), ""); + static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0::rank) == int(7)); + static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0::rank_dynamic) == int(7)); - static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0_s0::rank) == int(8), ""); - static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0_s0::rank_dynamic) == int(8), ""); + static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0_s0::rank) == int(8)); + static_assert(int(dim_s0_s0_s0_s0_s0_s0_s0_s0::rank_dynamic) == int(8)); dim_s0 d1(2, 3, 4, 5, 6, 7, 8, 9); dim_s0_s0 d2(2, 3, 4, 5, 6, 7, 8, 9); @@ -514,11 +514,11 @@ void test_view_mapping() { { using namespace Kokkos::Impl; - static_assert(rank_dynamic<>::value == 0, ""); - static_assert(rank_dynamic<1>::value == 0, ""); - static_assert(rank_dynamic<0>::value == 1, ""); - static_assert(rank_dynamic<0, 1>::value == 1, ""); - static_assert(rank_dynamic<0, 0, 1>::value == 2, ""); + static_assert(rank_dynamic<>::value == 0); + static_assert(rank_dynamic<1>::value == 0); + static_assert(rank_dynamic<0>::value == 1); + static_assert(rank_dynamic<0, 1>::value == 1); + static_assert(rank_dynamic<0, 0, 1>::value == 2); } { @@ -529,54 +529,48 @@ void test_view_mapping() { using a_const_int_r1 = ViewArrayAnalysis; using a_const_int_r5 = ViewArrayAnalysis; - static_assert(a_int_r1::dimension::rank == 1, ""); - static_assert(a_int_r1::dimension::rank_dynamic == 1, ""); - static_assert(a_int_r5::dimension::ArgN0 == 0, ""); - static_assert(a_int_r5::dimension::ArgN1 == 0, ""); - static_assert(a_int_r5::dimension::ArgN2 == 4, ""); - static_assert(a_int_r5::dimension::ArgN3 == 5, ""); - static_assert(a_int_r5::dimension::ArgN4 == 6, ""); - static_assert(a_int_r5::dimension::ArgN5 == 1, ""); + static_assert(a_int_r1::dimension::rank == 1); + static_assert(a_int_r1::dimension::rank_dynamic == 1); + static_assert(a_int_r5::dimension::ArgN0 == 0); + static_assert(a_int_r5::dimension::ArgN1 == 0); + static_assert(a_int_r5::dimension::ArgN2 == 4); + static_assert(a_int_r5::dimension::ArgN3 == 5); + static_assert(a_int_r5::dimension::ArgN4 == 6); + static_assert(a_int_r5::dimension::ArgN5 == 1); static_assert( - std::is_same >::value, - ""); + std::is_same >::value); static_assert( - std::is_same::value, ""); + std::is_same::value); - static_assert(a_const_int_r1::dimension::rank == 1, ""); - static_assert(a_const_int_r1::dimension::rank_dynamic == 1, ""); + static_assert(a_const_int_r1::dimension::rank == 1); + static_assert(a_const_int_r1::dimension::rank_dynamic == 1); static_assert(std::is_same >::value, - ""); - static_assert( - std::is_same::value, - ""); + ViewDimension<0> >::value); + static_assert(std::is_same::value); - static_assert(a_const_int_r5::dimension::rank == 5, ""); - static_assert(a_const_int_r5::dimension::rank_dynamic == 2, ""); + static_assert(a_const_int_r5::dimension::rank == 5); + static_assert(a_const_int_r5::dimension::rank_dynamic == 2); - static_assert(a_const_int_r5::dimension::ArgN0 == 0, ""); - static_assert(a_const_int_r5::dimension::ArgN1 == 0, ""); - static_assert(a_const_int_r5::dimension::ArgN2 == 4, ""); - static_assert(a_const_int_r5::dimension::ArgN3 == 5, ""); - static_assert(a_const_int_r5::dimension::ArgN4 == 6, ""); - static_assert(a_const_int_r5::dimension::ArgN5 == 1, ""); + static_assert(a_const_int_r5::dimension::ArgN0 == 0); + static_assert(a_const_int_r5::dimension::ArgN1 == 0); + static_assert(a_const_int_r5::dimension::ArgN2 == 4); + static_assert(a_const_int_r5::dimension::ArgN3 == 5); + static_assert(a_const_int_r5::dimension::ArgN4 == 6); + static_assert(a_const_int_r5::dimension::ArgN5 == 1); static_assert(std::is_same >::value, - ""); - static_assert( - std::is_same::value, - ""); + ViewDimension<0, 0, 4, 5, 6> >::value); + static_assert(std::is_same::value); - static_assert(a_int_r5::dimension::rank == 5, ""); - static_assert(a_int_r5::dimension::rank_dynamic == 2, ""); + static_assert(a_int_r5::dimension::rank == 5); + static_assert(a_int_r5::dimension::rank_dynamic == 2); static_assert(std::is_same >::value, - ""); + ViewDimension<0, 0, 4, 5, 6> >::value); static_assert( - std::is_same::value, ""); + std::is_same::value); } { @@ -587,15 +581,15 @@ void test_view_mapping() { // Dimensions of t_i4 are appended to the multdimensional array. using a_int_r5 = ViewArrayAnalysis; - static_assert(a_int_r5::dimension::rank == 5, ""); - static_assert(a_int_r5::dimension::rank_dynamic == 3, ""); - static_assert(a_int_r5::dimension::ArgN0 == 0, ""); - static_assert(a_int_r5::dimension::ArgN1 == 0, ""); - static_assert(a_int_r5::dimension::ArgN2 == 0, ""); - static_assert(a_int_r5::dimension::ArgN3 == 3, ""); - static_assert(a_int_r5::dimension::ArgN4 == 4, ""); + static_assert(a_int_r5::dimension::rank == 5); + static_assert(a_int_r5::dimension::rank_dynamic == 3); + static_assert(a_int_r5::dimension::ArgN0 == 0); + static_assert(a_int_r5::dimension::ArgN1 == 0); + static_assert(a_int_r5::dimension::ArgN2 == 0); + static_assert(a_int_r5::dimension::ArgN3 == 3); + static_assert(a_int_r5::dimension::ArgN4 == 4); static_assert( - std::is_same::value, ""); + std::is_same::value); } { @@ -603,71 +597,54 @@ void test_view_mapping() { using a_const_int_r1 = ViewDataAnalysis; - static_assert(std::is_void::value, ""); + static_assert(std::is_void::value); static_assert(std::is_same >::value, - ""); + Kokkos::Impl::ViewDimension<0> >::value); static_assert( - std::is_same::value, ""); + std::is_same::value); static_assert( - std::is_same::value, - ""); + std::is_same::value); static_assert(std::is_same::value, - ""); + const int*>::value); static_assert( - std::is_same::value, - ""); + std::is_same::value); static_assert(std::is_same::value, - ""); + const int>::value); static_assert(std::is_same::value, - ""); + const int*>::value); static_assert( - std::is_same::value, ""); - static_assert( - std::is_same::value, - ""); + std::is_same::value); + static_assert(std::is_same::value); using a_const_int_r3 = ViewDataAnalysis; - static_assert(std::is_void::value, ""); + static_assert(std::is_void::value); static_assert(std::is_same >::value, - ""); + Kokkos::Impl::ViewDimension<0, 0, 4> >::value); static_assert( - std::is_same::value, - ""); + std::is_same::value); static_assert( - std::is_same::value, - ""); + std::is_same::value); static_assert(std::is_same::value, - ""); + const int* * [4]>::value); static_assert(std::is_same::value, - ""); + const int* * [4]>::value); static_assert(std::is_same::value, - ""); + const int>::value); static_assert(std::is_same::value, - ""); + const int* * [4]>::value); static_assert(std::is_same::value, - ""); - static_assert( - std::is_same::value, - ""); + int* * [4]>::value); + static_assert(std::is_same::value); static_assert( std::is_same::value, - ""); + int* * [4]>::value); // std::cout << "typeid( const int**[4] ).name() = " << typeid( const // int**[4] ).name() << std::endl; diff --git a/lib/kokkos/core/unit_test/TestViewMapping_b.hpp b/lib/kokkos/core/unit_test/TestViewMapping_b.hpp index 9ac4e7da84..4aee035d17 100644 --- a/lib/kokkos/core/unit_test/TestViewMapping_b.hpp +++ b/lib/kokkos/core/unit_test/TestViewMapping_b.hpp @@ -156,7 +156,7 @@ TEST(TEST_CATEGORY, view_mapping_assignable) { using dst_traits = Kokkos::ViewTraits; using src_traits = Kokkos::ViewTraits; using mapping = Kokkos::Impl::ViewMapping; - static_assert(mapping::is_assignable, ""); + static_assert(mapping::is_assignable); Kokkos::View src; Kokkos::View dst(src); @@ -167,7 +167,7 @@ TEST(TEST_CATEGORY, view_mapping_assignable) { using dst_traits = Kokkos::ViewTraits; using src_traits = Kokkos::ViewTraits; using mapping = Kokkos::Impl::ViewMapping; - static_assert(mapping::is_assignable, ""); + static_assert(mapping::is_assignable); Kokkos::View src; Kokkos::View dst(src); @@ -180,7 +180,7 @@ TEST(TEST_CATEGORY, view_mapping_assignable) { using src_traits = Kokkos::ViewTraits; using mapping = Kokkos::Impl::ViewMapping; - static_assert(mapping::is_assignable, ""); + static_assert(mapping::is_assignable); Kokkos::View src; Kokkos::View dst(src); @@ -193,7 +193,7 @@ TEST(TEST_CATEGORY, view_mapping_assignable) { using src_traits = Kokkos::ViewTraits; using mapping = Kokkos::Impl::ViewMapping; - static_assert(mapping::is_assignable, ""); + static_assert(mapping::is_assignable); Kokkos::View src; Kokkos::View dst(src); @@ -206,7 +206,7 @@ TEST(TEST_CATEGORY, view_mapping_assignable) { using src_traits = Kokkos::ViewTraits; using mapping = Kokkos::Impl::ViewMapping; - static_assert(!mapping::is_assignable, ""); + static_assert(!mapping::is_assignable); } { // Assignment of rank-2 Right = Left @@ -215,7 +215,7 @@ TEST(TEST_CATEGORY, view_mapping_assignable) { using src_traits = Kokkos::ViewTraits; using mapping = Kokkos::Impl::ViewMapping; - static_assert(!mapping::is_assignable, ""); + static_assert(!mapping::is_assignable); } } @@ -226,7 +226,7 @@ TEST(TEST_CATEGORY, view_mapping_trivially_copyable) { using src_traits = dst_traits; using mapping = Kokkos::Impl::ViewMapping; - static_assert(std::is_trivially_copyable{}, ""); + static_assert(std::is_trivially_copyable{}); } } // namespace Test diff --git a/lib/kokkos/core/unit_test/TestViewOutOfBoundsAccess.hpp b/lib/kokkos/core/unit_test/TestViewOutOfBoundsAccess.hpp new file mode 100644 index 0000000000..2716856c1f --- /dev/null +++ b/lib/kokkos/core/unit_test/TestViewOutOfBoundsAccess.hpp @@ -0,0 +1,175 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include +#include + +#include + +namespace { + +TEST(TEST_CATEGORY, append_formatted_multidimensional_index) { + using Kokkos::Impl::append_formatted_multidimensional_index; + { + char buffer[64] = "my prefix "; + append_formatted_multidimensional_index(buffer, 1); + EXPECT_STREQ(buffer, "my prefix [1]"); + } + { + char buffer[64] = "I was here"; + append_formatted_multidimensional_index(buffer, 1, 2, 3); + EXPECT_STREQ(buffer, "I was here[1,2,3]"); + } + { + char buffer[64] = "with mixed integer types "; + append_formatted_multidimensional_index(buffer, 1u, -2); + EXPECT_STREQ(buffer, "with mixed integer types [1,-2]"); + } +} + +#ifdef KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK + +template +struct TestViewOutOfBoundAccess { + View v; + static constexpr auto rank = View::rank; + + template + KOKKOS_FUNCTION decltype(auto) bad_access(std::index_sequence) const { + return v((Is * 1 + Is == 0 ? v.extent(Is) + 3 : 0)...); + } + + KOKKOS_FUNCTION void operator()(int) const { + ++bad_access(std::make_index_sequence{}); + } + + template + std::string get_details(std::index_sequence) { + std::stringstream ss; + ss << "with indices \\["; + ((ss << (Is == 0 ? v.extent(Is) + 3 : 0) + << (Is == View::rank() - 1 ? "\\]" : ",")), + ...); + ss << " but extents \\["; + ((ss << v.extent(Is) << (Is == View::rank() - 1 ? "\\]" : ",")), ...); + return ss.str(); + } + + auto get_details() { + return get_details(std::make_index_sequence()); + } + + TestViewOutOfBoundAccess(View w, ExecutionSpace const& s, std::string matcher) + : v(std::move(w)) { + constexpr bool view_accessible_from_execution_space = + Kokkos::SpaceAccessibility< + /*AccessSpace=*/ExecutionSpace, + /*MemorySpace=*/typename View::memory_space>::accessible; + EXPECT_TRUE(view_accessible_from_execution_space); + + matcher += ".*" + get_details(); + + EXPECT_DEATH( + { + Kokkos::parallel_for(Kokkos::RangePolicy(s, 0, 1), + *this); + Kokkos::fence(); + }, + matcher); + } +}; + +template +auto make_view_impl(LblOrPtr x, std::index_sequence) { + return View(x, (Is + 1)...); +} + +template +auto make_view(LblOrPtr x) { + return make_view_impl(std::move(x), + std::make_index_sequence()); +} + +template +void test_view_out_of_bounds_access() { + ExecutionSpace const exec_space{}; + // clang-format off + using V1 = Kokkos::View; + using V2 = Kokkos::View; + using V3 = Kokkos::View; + using V4 = Kokkos::View; + using V5 = Kokkos::View; + using V6 = Kokkos::View; + using V7 = Kokkos::View; + using V8 = Kokkos::View; + std::string const prefix = "Kokkos::View ERROR: out of bounds access"; + std::string const lbl = "my_label"; + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + TestViewOutOfBoundAccess(make_view(lbl), exec_space, prefix + ".*" + lbl); + int* const ptr = nullptr; + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + TestViewOutOfBoundAccess(make_view(ptr), exec_space, prefix + ".*UNMANAGED"); + // clang-format on +} + +TEST(TEST_CATEGORY_DEATH, view_out_of_bounds_access) { + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + + using ExecutionSpace = TEST_EXECSPACE; + + if (false && Kokkos::SpaceAccessibility< + /*AccessSpace=*/ExecutionSpace, + /*MemorySpace=*/Kokkos::HostSpace>::accessible) { + GTEST_SKIP() << "skipping since no memory access violation would occur"; + } + +#if defined(KOKKOS_ENABLE_SYCL) && defined(NDEBUG) // FIXME_SYCL + if (std::is_same_v) { + GTEST_SKIP() << "skipping SYCL device-side abort does not work when NDEBUG " + "is defined"; + } +#endif +#if defined(KOKKOS_ENABLE_OPENMPTARGET) // FIXME_OPENMPTARGET + if (std::is_same_v) { + GTEST_SKIP() << "skipping because OpenMPTarget backend is currently not " + "able to abort from the device"; + } +#endif +#if defined(KOKKOS_ENABLE_OPENACC) // FIXME_OPENACC + if (std::is_same::value) { + GTEST_SKIP() << "skipping because OpenACC backend is currently not " + "able to abort from the device"; + } +#endif + + test_view_out_of_bounds_access(); +} + +#endif + +} // namespace diff --git a/lib/kokkos/core/unit_test/UnitTest_DeviceAndThreads.cpp b/lib/kokkos/core/unit_test/UnitTest_DeviceAndThreads.cpp index b522ac3e69..25442146fb 100644 --- a/lib/kokkos/core/unit_test/UnitTest_DeviceAndThreads.cpp +++ b/lib/kokkos/core/unit_test/UnitTest_DeviceAndThreads.cpp @@ -19,22 +19,23 @@ #include #include -int get_device_count() { +int get_num_devices() { + int num_devices; #if defined(KOKKOS_ENABLE_CUDA) - int count; - KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceCount(&count)); - return count; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceCount(&num_devices)); #elif defined(KOKKOS_ENABLE_HIP) - int count; - KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDevice(&count)); - return count; + KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDeviceCount(&num_devices)); #elif defined(KOKKOS_ENABLE_OPENMPTARGET) - return omp_get_num_devices(); + num_devices = omp_get_num_devices(); #elif defined(KOKKOS_ENABLE_OPENACC) - return acc_get_num_devices(acc_get_device_type()); + num_devices = acc_get_num_devices(acc_get_device_type()); +#elif defined(KOKKOS_ENABLE_SYCL) + num_devices = sycl::device::get_devices(sycl::info::device_type::gpu).size(); #else - return 0; + num_devices = -1; #endif + assert(num_devices == Kokkos::num_devices()); + return num_devices; } int get_device_id() { @@ -44,15 +45,17 @@ int get_device_id() { #elif defined(KOKKOS_ENABLE_HIP) KOKKOS_IMPL_HIP_SAFE_CALL(hipGetDevice(&device_id)); #elif defined(KOKKOS_ENABLE_OPENMPTARGET) - device_id = omp_get_device_num(); + device_id = omp_get_default_device(); #elif defined(KOKKOS_ENABLE_OPENACC) - device_id = acc_get_device_num(acc_get_device_type()); + device_id = acc_get_device_num(acc_get_device_type()); #elif defined(KOKKOS_ENABLE_SYCL) - // FIXME_SYCL ? - assert(false); - return -2; + // Not able to query the underlying runtime because there is no such thing as + // device currently being used with SYCL. We go through the Kokkos runtime + // which makes the assert below pointless but it still let us check that + // Kokkos selected the device we asked for from the Python tests. + device_id = Kokkos::device_id(); #else - device_id = -1; + device_id = -1; #endif assert(device_id == Kokkos::device_id()); return device_id; @@ -68,6 +71,14 @@ int get_max_threads() { #endif } +int get_hwloc_enabled() { +#ifdef KOKKOS_ENABLE_HWLOC + return 1; +#else + return 0; +#endif +} + int get_num_threads() { int const num_threads = Kokkos::DefaultHostExecutionSpace().concurrency(); assert(num_threads == Kokkos::num_threads()); @@ -90,9 +101,10 @@ int print_flag(std::string const& flag) { KOKKOS_TEST_PRINT_FLAG(num_threads); KOKKOS_TEST_PRINT_FLAG(max_threads); KOKKOS_TEST_PRINT_FLAG(device_id); - KOKKOS_TEST_PRINT_FLAG(device_count); + KOKKOS_TEST_PRINT_FLAG(num_devices); KOKKOS_TEST_PRINT_FLAG(disable_warnings); KOKKOS_TEST_PRINT_FLAG(tune_internals); + KOKKOS_TEST_PRINT_FLAG(hwloc_enabled); #undef KOKKOS_TEST_PRINT_FLAG diff --git a/lib/kokkos/core/unit_test/configuration/test-code/test_config_arch_list.bash b/lib/kokkos/core/unit_test/configuration/test-code/test_config_arch_list.bash index 8fe8e2b5ec..8bc8ef21cd 100755 --- a/lib/kokkos/core/unit_test/configuration/test-code/test_config_arch_list.bash +++ b/lib/kokkos/core/unit_test/configuration/test-code/test_config_arch_list.bash @@ -4,7 +4,7 @@ HostArch=(SNB HSW SKX KNL) DeviceArch=(Kepler35 Kepler37 Pascal60 Pascal61 Volta70) if [ ! -z "$KOKKOS_HOST_ARCH_TEST" ]; then export KOKKOS_ARCH_TEST=1 - HostArch=(WSM SNB HSW SKX WSM AMDAVX ARMv80 ARMv81 BDW KNC KNL BGQ Power7 Power8 Power9 Zen Zen2 Zen3 ARMv8_ThunderX ARMv8_ThunderX2) + HostArch=(SNB HSW SKX AMDAVX ARMv80 ARMv81 BDW KNC KNL Power8 Power9 Zen Zen2 Zen3 ARMv8_ThunderX ARMv8_ThunderX2) DeviceArch=() fi diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_StreamsMultiGPU.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_StreamsMultiGPU.cpp new file mode 100644 index 0000000000..d94735ceb2 --- /dev/null +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_StreamsMultiGPU.cpp @@ -0,0 +1,268 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include +#include + +namespace { + +struct StreamsAndDevices { + std::array streams; + std::array devices; + + StreamsAndDevices() { + int n_devices; + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaGetDeviceCount(&n_devices)); + + devices = {0, n_devices - 1}; + for (int i = 0; i < 2; ++i) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(devices[i])); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamCreate(&streams[i])); + } + } + StreamsAndDevices(const StreamsAndDevices &) = delete; + StreamsAndDevices &operator=(const StreamsAndDevices &) = delete; + ~StreamsAndDevices() { + for (int i = 0; i < 2; ++i) { + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(devices[i])); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaStreamDestroy(streams[i])); + } + } +}; + +std::array get_execution_spaces( + const StreamsAndDevices &streams_and_devices) { + TEST_EXECSPACE exec0(streams_and_devices.streams[0]); + TEST_EXECSPACE exec1(streams_and_devices.streams[1]); + + // Must return void to use ASSERT_EQ + [&]() { + ASSERT_EQ(exec0.cuda_device(), streams_and_devices.devices[0]); + ASSERT_EQ(exec1.cuda_device(), streams_and_devices.devices[1]); + }(); + + return {exec0, exec1}; +} + +// Test Interoperability with Cuda Streams +void test_policies(TEST_EXECSPACE exec0, Kokkos::View v0, + TEST_EXECSPACE exec, Kokkos::View v) { + using MemorySpace = typename TEST_EXECSPACE::memory_space; + + Kokkos::deep_copy(exec, v, 5); + Kokkos::deep_copy(exec0, v0, 5); + + Kokkos::deep_copy(v, v0); + + int sum; + int sum0; + + Kokkos::parallel_for("Test::cuda::raw_cuda_stream::Range_0", + Kokkos::RangePolicy(exec0, 0, 100), + Test::FunctorRange(v0)); + Kokkos::parallel_for("Test::cuda::raw_cuda_stream::Range", + Kokkos::RangePolicy(exec, 0, 100), + Test::FunctorRange(v)); + Kokkos::parallel_reduce( + "Test::cuda::raw_cuda_stream::RangeReduce_0", + Kokkos::RangePolicy>(exec0, + 0, 100), + Test::FunctorRangeReduce(v0), sum0); + Kokkos::parallel_reduce( + "Test::cuda::raw_cuda_stream::RangeReduce", + Kokkos::RangePolicy>(exec, 0, + 100), + Test::FunctorRangeReduce(v), sum); + ASSERT_EQ(600, sum0); + ASSERT_EQ(600, sum); + + Kokkos::parallel_for("Test::cuda::raw_cuda_stream::MDRange_0", + Kokkos::MDRangePolicy>( + exec0, {0, 0}, {10, 10}), + Test::FunctorMDRange(v0)); + Kokkos::parallel_for("Test::cuda::raw_cuda_stream::MDRange", + Kokkos::MDRangePolicy>( + exec, {0, 0}, {10, 10}), + Test::FunctorMDRange(v)); + Kokkos::parallel_reduce("Test::cuda::raw_cuda_stream::MDRangeReduce_0", + Kokkos::MDRangePolicy, + Kokkos::LaunchBounds<128, 2>>( + exec0, {0, 0}, {10, 10}), + Test::FunctorMDRangeReduce(v0), sum0); + Kokkos::parallel_reduce("Test::cuda::raw_cuda_stream::MDRangeReduce", + Kokkos::MDRangePolicy, + Kokkos::LaunchBounds<128, 2>>( + exec, {0, 0}, {10, 10}), + Test::FunctorMDRangeReduce(v), sum); + ASSERT_EQ(700, sum0); + ASSERT_EQ(700, sum); + + Kokkos::parallel_for("Test::cuda::raw_cuda_stream::Team_0", + Kokkos::TeamPolicy(exec0, 10, 10), + Test::FunctorTeam(v0)); + Kokkos::parallel_for("Test::cuda::raw_cuda_stream::Team", + Kokkos::TeamPolicy(exec, 10, 10), + Test::FunctorTeam(v)); + Kokkos::parallel_reduce( + "Test::cuda::raw_cuda_stream::Team_0", + Kokkos::TeamPolicy>(exec0, + 10, 10), + Test::FunctorTeamReduce(v0), sum0); + Kokkos::parallel_reduce( + "Test::cuda::raw_cuda_stream::Team", + Kokkos::TeamPolicy>(exec, 10, + 10), + Test::FunctorTeamReduce(v), sum); + ASSERT_EQ(800, sum0); + ASSERT_EQ(800, sum); +} + +TEST(cuda_multi_gpu, managed_views) { + StreamsAndDevices streams_and_devices; + { + std::array execs = + get_execution_spaces(streams_and_devices); + + Kokkos::View view0( + Kokkos::view_alloc("v0", execs[0]), 100); + Kokkos::View view(Kokkos::view_alloc("v", execs[1]), + 100); + + test_policies(execs[0], view0, execs[1], view); + } +} + +TEST(cuda_multi_gpu, unmanaged_views) { + StreamsAndDevices streams_and_devices; + { + std::array execs = + get_execution_spaces(streams_and_devices); + + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(execs[0].cuda_device())); + int *p0; + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMalloc(reinterpret_cast(&p0), sizeof(int) * 100)); + Kokkos::View view0(p0, 100); + + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaSetDevice(execs[1].cuda_device())); + int *p; + KOKKOS_IMPL_CUDA_SAFE_CALL( + cudaMalloc(reinterpret_cast(&p), sizeof(int) * 100)); + Kokkos::View view(p, 100); + + test_policies(execs[0], view0, execs[1], view); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(p0)); + KOKKOS_IMPL_CUDA_SAFE_CALL(cudaFree(p)); + } +} + +struct ScratchFunctor { + int scratch_size; + int R; + + ScratchFunctor(int scratch_size_, int R_) + : scratch_size(scratch_size_), R(R_) {} + + KOKKOS_FUNCTION + void operator()(const Kokkos::TeamPolicy::member_type &team, + int &error_accum) const { + Kokkos::View scratch_mem( + team.team_scratch(1), scratch_size); + + // Initialize scratch memory + Kokkos::parallel_for(Kokkos::TeamVectorRange(team, 0, scratch_size), + [&](int i) { scratch_mem(i) = 0; }); + team.team_barrier(); + + // Increment each entry in scratch memory R times + for (int r = 0; r < R; ++r) { + Kokkos::parallel_for(Kokkos::TeamVectorRange(team, 0, scratch_size), + [&](int i) { scratch_mem(i) += 1; }); + } + team.team_barrier(); + + // Check that each scratch entry has been incremented exactly R times + int team_error_accum; + auto R_loc = R; // avoid implicit capture of this + Kokkos::parallel_reduce( + Kokkos::TeamVectorRange(team, 0, scratch_size), + [&](int i, int &tsum) { + if (scratch_mem(i) != R_loc) { + tsum += 1; + } + }, + team_error_accum); + Kokkos::single(Kokkos::PerTeam(team), + [&]() { error_accum += team_error_accum; }); + } +}; + +void test_scratch(TEST_EXECSPACE exec0, TEST_EXECSPACE exec1) { + constexpr int N = 10; + constexpr int R = 1000; + constexpr int scratch_size = 100; + using ScratchType = Kokkos::View; + + // Test allocating and using scratch space + ScratchFunctor f(scratch_size, R); + + auto policy0 = + Kokkos::TeamPolicy(exec0, N, 10) + .set_scratch_size( + 1, Kokkos::PerTeam(ScratchType::shmem_size(scratch_size))); + auto policy1 = + Kokkos::TeamPolicy(exec1, N, 10) + .set_scratch_size( + 1, Kokkos::PerTeam(ScratchType::shmem_size(scratch_size))); + + int error0, error1; + + Kokkos::parallel_reduce("test_scratch_device_0", policy0, f, error0); + Kokkos::parallel_reduce("test_scratch_device_1", policy1, f, error1); + ASSERT_EQ(error0, 0); + ASSERT_EQ(error1, 0); + + // Request larger scratch size to trigger a realloc and test + const auto new_scratch_size = scratch_size + 10; + ScratchFunctor f_more_scratch(new_scratch_size, R); + + auto policy0_more_scratch = + Kokkos::TeamPolicy(exec0, N, 10) + .set_scratch_size( + 1, Kokkos::PerTeam(ScratchType::shmem_size(new_scratch_size))); + auto policy1_more_scratch = + Kokkos::TeamPolicy(exec1, N, 10) + .set_scratch_size( + 1, Kokkos::PerTeam(ScratchType::shmem_size(new_scratch_size))); + + Kokkos::parallel_reduce("test_realloc_scratch_device_0", policy0_more_scratch, + f_more_scratch, error0); + Kokkos::parallel_reduce("test_realloc_scratch_device_1", policy1_more_scratch, + f_more_scratch, error1); + ASSERT_EQ(error0, 0); + ASSERT_EQ(error1, 0); +} + +TEST(cuda_multi_gpu, scratch_space) { + StreamsAndDevices streams_and_devices; + { + std::array execs = + get_execution_spaces(streams_and_devices); + + test_scratch(execs[0], execs[1]); + } +} +} // namespace diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp index ae603101ab..11fe6b8555 100644 --- a/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp @@ -29,200 +29,166 @@ __global__ void test_cuda_spaces_int_value(int *ptr) { TEST(cuda, space_access) { static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::CudaHostPinnedSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::CudaSpace>::assignable); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::CudaUVMSpace>::accessible); //-------------------------------------- static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::CudaSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::CudaUVMSpace>::assignable); + + static_assert(!Kokkos::Impl::MemorySpaceAccess< + Kokkos::CudaSpace, Kokkos::CudaHostPinnedSpace>::assignable); + + static_assert( + Kokkos::Impl::MemorySpaceAccess::accessible); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); static_assert( - Kokkos::Impl::MemorySpaceAccess::accessible, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + !Kokkos::Impl::MemorySpaceAccess::accessible); //-------------------------------------- static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(Kokkos::Impl::MemorySpaceAccess::accessible, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::CudaUVMSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::CudaSpace>::assignable); + + static_assert(Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::assignable); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert(!Kokkos::Impl::MemorySpaceAccess< + Kokkos::CudaUVMSpace, Kokkos::CudaHostPinnedSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::CudaHostPinnedSpace>::accessible); //-------------------------------------- static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(Kokkos::Impl::MemorySpaceAccess::accessible, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::CudaHostPinnedSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); + + static_assert(Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::assignable); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::CudaUVMSpace>::accessible); //-------------------------------------- static_assert( - !Kokkos::SpaceAccessibility::accessible, - ""); + !Kokkos::SpaceAccessibility::accessible); static_assert( - Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::SpaceAccessibility::accessible); static_assert(Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::CudaUVMSpace>::accessible); static_assert( Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::CudaHostPinnedSpace>::accessible); static_assert(!Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::CudaSpace>::accessible); static_assert(Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::CudaUVMSpace>::accessible); static_assert( Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::CudaHostPinnedSpace>::accessible); static_assert(std::is_same::Space, - Kokkos::HostSpace>::value, - ""); + Kokkos::HostSpace>::value); static_assert( std::is_same::Space, Kokkos::Device>::value, - ""); + Kokkos::CudaUVMSpace>>::value); static_assert( std::is_same::Space, - Kokkos::CudaHostPinnedSpace>::value, - ""); + Kokkos::CudaHostPinnedSpace>::value); static_assert(std::is_same, Kokkos::Device>::value, - ""); + Kokkos::CudaUVMSpace>>::value); static_assert( Kokkos::SpaceAccessibility::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror::Space, + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror::Space, + Kokkos::HostSpace>::accessible); - static_assert( - Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror::Space, - Kokkos::HostSpace>::accessible, - ""); + static_assert(Kokkos::SpaceAccessibility< + Kokkos::Impl::HostMirror::Space, + Kokkos::HostSpace>::accessible); #ifdef KOKKOS_ENABLE_CUDA_UVM using uvm_view = Kokkos::View; static_assert(std::is_same::Space; static_assert(Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::HostSpace>::accessible); static_assert( - Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::SpaceAccessibility::accessible); static_assert( - Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::SpaceAccessibility::accessible); } } // namespace Test diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_1.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_1.cpp deleted file mode 100644 index 348b9feeab..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_1.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_01 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_10.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_10.cpp deleted file mode 100644 index a77a55ea65..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_10.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_10 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_11.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_11.cpp deleted file mode 100644 index 1b6a140920..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_11.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_11 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_12.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_12.cpp deleted file mode 100644 index 316bc85526..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_12.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_12 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_13.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_13.cpp deleted file mode 100644 index 6344960a1c..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_13.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_13 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_14.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_14.cpp deleted file mode 100644 index 4515174b82..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_14.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_14 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_15.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_15.cpp deleted file mode 100644 index 7ead50f094..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_15.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_15 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_16.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_16.cpp deleted file mode 100644 index e12b9b3894..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_16.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_16 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_17.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_17.cpp deleted file mode 100644 index 959d0ab750..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_17.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_17 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_18.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_18.cpp deleted file mode 100644 index 07d841519d..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_18.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_18 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_2.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_2.cpp deleted file mode 100644 index 042a515b16..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_2.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_02 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_3.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_3.cpp deleted file mode 100644 index dba401e5bc..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_3.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_03 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_4.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_4.cpp deleted file mode 100644 index a44c58bdb5..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_4.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_04 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_5.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_5.cpp deleted file mode 100644 index cac0841dd8..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_5.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_05 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_6.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_6.cpp deleted file mode 100644 index bafe3b3fd2..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_6.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_06 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_7.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_7.cpp deleted file mode 100644 index 3a4dd9d253..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_7.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_07 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_8.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_8.cpp deleted file mode 100644 index 4e92aae565..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_8.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_08 -#include diff --git a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_9.cpp b/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_9.cpp deleted file mode 100644 index 44b8f3428d..0000000000 --- a/lib/kokkos/core/unit_test/default/TestDefaultDeviceTypeInit_9.cpp +++ /dev/null @@ -1,18 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_09 -#include diff --git a/lib/kokkos/core/unit_test/hip/TestHIP_Memory_Requirements.cpp b/lib/kokkos/core/unit_test/hip/TestHIP_Memory_Requirements.cpp index 8c72e9f297..a213453ea1 100644 --- a/lib/kokkos/core/unit_test/hip/TestHIP_Memory_Requirements.cpp +++ b/lib/kokkos/core/unit_test/hip/TestHIP_Memory_Requirements.cpp @@ -48,6 +48,9 @@ TEST(hip, memory_requirements) { // we want all user-facing memory in hip to be coarse grained. As of // today(07.01.22) the documentation is not reliable/correct, we test the // memory on the device and host + // FIXME_HIP + GTEST_SKIP() << "skipping the test because the CI on MI100 returns: error( " + "hipErrorInvalidValue)"; KOKKOS_TEST_MEMORY_COARSEGRAINEDNESS(Kokkos::HIPSpace, int, 10); KOKKOS_TEST_MEMORY_COARSEGRAINEDNESS(Kokkos::HIPHostPinnedSpace, int, 10); KOKKOS_TEST_MEMORY_COARSEGRAINEDNESS(Kokkos::HIPManagedSpace, int, 10); diff --git a/lib/kokkos/core/unit_test/hip/TestHIP_Spaces.cpp b/lib/kokkos/core/unit_test/hip/TestHIP_Spaces.cpp index 14fd4e2883..673c0f0fff 100644 --- a/lib/kokkos/core/unit_test/hip/TestHIP_Spaces.cpp +++ b/lib/kokkos/core/unit_test/hip/TestHIP_Spaces.cpp @@ -29,198 +29,180 @@ __global__ void test_hip_spaces_int_value(int *ptr) { TEST(hip, space_access) { static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HIPHostPinnedSpace>::assignable); static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HIPSpace>::assignable); +#if !defined(KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY) static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPSpace>::accessible); +#else + static_assert(Kokkos::Impl::MemorySpaceAccess::accessible); +#endif static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HIPManagedSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPManagedSpace>::accessible); //-------------------------------------- static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HIPSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HIPHostPinnedSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPHostPinnedSpace>::accessible); - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + static_assert( + !Kokkos::Impl::MemorySpaceAccess::assignable); - static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + static_assert( + !Kokkos::Impl::MemorySpaceAccess::accessible); static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HIPManagedSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPManagedSpace>::accessible); //-------------------------------------- static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(Kokkos::Impl::MemorySpaceAccess::accessible, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPHostPinnedSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); + + static_assert(Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable); + + static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPManagedSpace>::accessible); //-------------------------------------- static_assert( Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::accessible, - ""); - - static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable, - ""); - - static_assert(Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPManagedSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert(!Kokkos::Impl::MemorySpaceAccess::assignable); + + static_assert(Kokkos::Impl::MemorySpaceAccess::accessible); + + static_assert( + !Kokkos::Impl::MemorySpaceAccess::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HIPHostPinnedSpace>::accessible); //-------------------------------------- static_assert( - !Kokkos::SpaceAccessibility::accessible, - ""); + !Kokkos::SpaceAccessibility::accessible); static_assert( - Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::SpaceAccessibility::accessible); static_assert( Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::HIPHostPinnedSpace>::accessible); - static_assert(Kokkos::SpaceAccessibility::accessible, - ""); + static_assert( + Kokkos::SpaceAccessibility::accessible); +#if !defined(KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY) static_assert(!Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::HIPSpace>::accessible); +#else + static_assert(Kokkos::SpaceAccessibility::accessible); +#endif static_assert( Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::HIPHostPinnedSpace>::accessible); - static_assert(Kokkos::SpaceAccessibility::accessible, - ""); + static_assert( + Kokkos::SpaceAccessibility::accessible); +#if !defined(KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY) static_assert(std::is_same::Space, - Kokkos::HostSpace>::value, - ""); + Kokkos::HostSpace>::value); +#else + static_assert(std::is_same::Space, + Kokkos::Device>::value); +#endif static_assert( std::is_same::Space, - Kokkos::HIPHostPinnedSpace>::value, - ""); + Kokkos::HIPHostPinnedSpace>::value); static_assert( std::is_same::Space, Kokkos::Device>::value, - ""); + Kokkos::HIPManagedSpace>>::value); static_assert( Kokkos::SpaceAccessibility::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror::Space, + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror::Space, + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror::Space, + Kokkos::HostSpace>::accessible); } template diff --git a/lib/kokkos/core/unit_test/incremental/Test01_execspace.hpp b/lib/kokkos/core/unit_test/incremental/Test01_execspace.hpp index 25c7138ed3..d7b2a57b44 100644 --- a/lib/kokkos/core/unit_test/incremental/Test01_execspace.hpp +++ b/lib/kokkos/core/unit_test/incremental/Test01_execspace.hpp @@ -62,8 +62,10 @@ struct TestIncrExecSpace { auto concurrency = ExecSpace().concurrency(); ASSERT_GT(concurrency, 0); +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4 int in_parallel = ExecSpace::in_parallel(); ASSERT_FALSE(in_parallel); +#endif const char* name = ExecSpace::name(); std::cout << name << std::endl; diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_PartitionMaster.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_PartitionMaster.cpp deleted file mode 100644 index 92b8032bf0..0000000000 --- a/lib/kokkos/core/unit_test/openmp/TestOpenMP_PartitionMaster.cpp +++ /dev/null @@ -1,105 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER - -#include -#include - -#include - -namespace Test { - -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3 -TEST(openmp, partition_master) { - using Mutex = Kokkos::Experimental::MasterLock; - - Mutex mtx; - int errors = 0; - - auto master = [&errors, &mtx](int /*partition_id*/, int /*num_partitions*/) { - const int pool_size = Kokkos::OpenMP().impl_thread_pool_size(); - - { - std::unique_lock lock(mtx); - if (Kokkos::OpenMP::in_parallel()) { - ++errors; - } - if (Kokkos::OpenMP::impl_thread_pool_rank() != 0) { - ++errors; - } - } - - { - int local_errors = 0; - Kokkos::parallel_reduce( - Kokkos::RangePolicy(0, 1000), - [pool_size](const int, int& errs) { - if (Kokkos::OpenMP().impl_thread_pool_size() != pool_size) { - ++errs; - } - }, - local_errors); - Kokkos::atomic_add(&errors, local_errors); - } - - Kokkos::Experimental::UniqueToken token; - - Kokkos::View count("", token.size()); - - Kokkos::parallel_for(Kokkos::RangePolicy(0, 1000), - [=](const int) { - int i = token.acquire(); - ++count[i]; - token.release(i); - }); - - Kokkos::View sum(""); - Kokkos::parallel_for( - Kokkos::RangePolicy(0, token.size()), - [=](const int i) { Kokkos::atomic_add(sum.data(), count[i]); }); - - if (sum() != 1000) { - Kokkos::atomic_add(&errors, 1); - } - }; - - master(0, 1); - - ASSERT_EQ(errors, 0); - - Kokkos::OpenMP::partition_master(master); - ASSERT_EQ(errors, 0); - - Kokkos::OpenMP::partition_master(master, 4, 0); - ASSERT_EQ(errors, 0); - - Kokkos::OpenMP::partition_master(master, 0, 4); - ASSERT_EQ(errors, 0); - - Kokkos::OpenMP::partition_master(master, 2, 2); - ASSERT_EQ(errors, 0); - - Kokkos::OpenMP::partition_master(master, 8, 0); - ASSERT_EQ(errors, 0); - - Kokkos::OpenMP::partition_master(master, 0, 8); - ASSERT_EQ(errors, 0); - - Kokkos::OpenMP::partition_master(master, 8, 8); - ASSERT_EQ(errors, 0); -} -#endif - -} // namespace Test diff --git a/lib/kokkos/core/unit_test/sycl/TestSYCL_Spaces.cpp b/lib/kokkos/core/unit_test/sycl/TestSYCL_Spaces.cpp index 914f843248..a4fd053e83 100644 --- a/lib/kokkos/core/unit_test/sycl/TestSYCL_Spaces.cpp +++ b/lib/kokkos/core/unit_test/sycl/TestSYCL_Spaces.cpp @@ -21,235 +21,192 @@ namespace Test { TEST(sycl, space_access) { static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::assignable, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::assignable); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::assignable, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::accessible, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::accessible); //-------------------------------------- static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLDeviceUSMSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLDeviceUSMSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLDeviceUSMSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLDeviceUSMSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::assignable); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLDeviceUSMSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLDeviceUSMSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLDeviceUSMSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCLDeviceUSMSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::accessible); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HostSpace>::accessible); //-------------------------------------- static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLSharedUSMSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::assignable); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLSharedUSMSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLSharedUSMSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HostSpace>::accessible); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLSharedUSMSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLSharedUSMSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::accessible); //-------------------------------------- static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLHostUSMSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLHostUSMSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::assignable); static_assert( !Kokkos::Impl::MemorySpaceAccess::assignable, - ""); + Kokkos::HostSpace>::assignable); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HostSpace>::accessible); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLHostUSMSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLHostUSMSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::assignable); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLHostUSMSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCLHostUSMSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible); static_assert(!Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLHostUSMSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::assignable, - ""); + Kokkos::Experimental::SYCLHostUSMSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::assignable); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::Experimental::SYCLHostUSMSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCLHostUSMSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::accessible); //-------------------------------------- static_assert(!Kokkos::SpaceAccessibility::accessible, - ""); + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Experimental::SYCL, - Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCL, + Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Experimental::SYCL, - Kokkos::Experimental::SYCLSharedUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCL, + Kokkos::Experimental::SYCLSharedUSMSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Experimental::SYCL, - Kokkos::Experimental::SYCLHostUSMSpace>::accessible, - ""); + Kokkos::Experimental::SYCL, + Kokkos::Experimental::SYCLHostUSMSpace>::accessible); static_assert(!Kokkos::SpaceAccessibility< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLDeviceUSMSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLSharedUSMSpace>::accessible, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLSharedUSMSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::accessible, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::accessible); static_assert( std::is_same::Space, - Kokkos::HostSpace>::value, - ""); + Kokkos::HostSpace>::value); static_assert( std::is_same< Kokkos::Impl::HostMirror< Kokkos::Experimental::SYCLSharedUSMSpace>::Space, Kokkos::Device>::value, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace>>::value); static_assert( Kokkos::Impl::MemorySpaceAccess::accessible, - ""); + Kokkos::HostSpace>::accessible); static_assert(Kokkos::Impl::MemorySpaceAccess< - Kokkos::HostSpace, - Kokkos::Experimental::SYCLHostUSMSpace>::accessible, - ""); + Kokkos::HostSpace, + Kokkos::Experimental::SYCLHostUSMSpace>::accessible); static_assert(std::is_same::Space, - Kokkos::Experimental::SYCLHostUSMSpace>::value, - ""); + Kokkos::Experimental::SYCLHostUSMSpace>::value); static_assert( std::is_same< Kokkos::Device, Kokkos::Device>::value, - ""); + Kokkos::Experimental::SYCLSharedUSMSpace>>::value); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror::Space, + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror< - Kokkos::Experimental::SYCLDeviceUSMSpace>::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror< + Kokkos::Experimental::SYCLDeviceUSMSpace>::Space, + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror< - Kokkos::Experimental::SYCLSharedUSMSpace>::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror< + Kokkos::Experimental::SYCLSharedUSMSpace>::Space, + Kokkos::HostSpace>::accessible); static_assert(Kokkos::SpaceAccessibility< - Kokkos::Impl::HostMirror< - Kokkos::Experimental::SYCLHostUSMSpace>::Space, - Kokkos::HostSpace>::accessible, - ""); + Kokkos::Impl::HostMirror< + Kokkos::Experimental::SYCLHostUSMSpace>::Space, + Kokkos::HostSpace>::accessible); } TEST(sycl, uvm) { diff --git a/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp b/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp index 3c85f661aa..946169a786 100644 --- a/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp +++ b/lib/kokkos/core/unit_test/tools/TestEventCorrectness.hpp @@ -409,14 +409,19 @@ TEST(kokkosp, parallel_scan_no_fence) { << "skipping since the OpenMPTarget backend has unexpected fences"; #endif + // Execute the parallel_scan first without looking for fence events. + // Depending on the backend implementation and the order of tests, + // it might be that the first call to parallel_scan is reallocating scratch + // memory which implies a fence when deallocating. We are not interested in + // detecting this event. + TestScanFunctor tf; + Kokkos::parallel_scan("dogs", Kokkos::RangePolicy<>(0, 1), tf); + using namespace Kokkos::Test::Tools; listen_tool_events(Config::DisableAll(), Config::EnableKernels(), Config::EnableFences()); auto success = validate_absence( - [=]() { - TestScanFunctor tf; - Kokkos::parallel_scan("dogs", Kokkos::RangePolicy<>(0, 1), tf); - }, + [=]() { Kokkos::parallel_scan("dogs", Kokkos::RangePolicy<>(0, 1), tf); }, [=](BeginFenceEvent begin_event) { if (begin_event.name.find("Debug Only Check for Execution Error") != std::string::npos || @@ -450,13 +455,20 @@ TEST(kokkosp, parallel_scan_no_fence_view) { << "skipping since the OpenMPTarget backend has unexpected fences"; #endif + // Execute the parallel_scan first without looking for fence events. + // Depending on the backend implementation and the order of tests, + // it might be that the first call to parallel_scan is reallocating scratch + // memory which implies a fence when deallocating. We are not interested in + // detecting this event. + TestScanFunctor tf; + Kokkos::View v("scan_result"); + Kokkos::parallel_scan("dogs", Kokkos::RangePolicy<>(0, 1), tf, v); + using namespace Kokkos::Test::Tools; listen_tool_events(Config::DisableAll(), Config::EnableKernels(), Config::EnableFences()); - Kokkos::View v("scan_result"); auto success = validate_absence( [=]() { - TestScanFunctor tf; Kokkos::parallel_scan("dogs", Kokkos::RangePolicy<>(0, 1), tf, v); }, [=](BeginFenceEvent begin_event) { diff --git a/lib/kokkos/core/unit_test/tools/TestLogicalSpaces.hpp b/lib/kokkos/core/unit_test/tools/TestLogicalSpaces.hpp deleted file mode 100644 index 4e56f8996a..0000000000 --- a/lib/kokkos/core/unit_test/tools/TestLogicalSpaces.hpp +++ /dev/null @@ -1,177 +0,0 @@ -//@HEADER -// ************************************************************************ -// -// Kokkos v. 4.0 -// Copyright (2022) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. -// See https://kokkos.org/LICENSE for license information. -// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception -// -//@HEADER -#include -#include -#include "Kokkos_Core.hpp" - -#include - -namespace Test { - -void debug_print(const Kokkos_Profiling_SpaceHandle hand, const char* name, - const void* ptr, const size_t size) { - std::cout << "Alloc: " << hand.name << ", [" << name << "," << ptr << "] " - << size << std::endl; -} -void debug_dealloc(const Kokkos_Profiling_SpaceHandle hand, const char* name, - const void* ptr, const size_t size) { - std::cout << "Dealloc: " << hand.name << ", [" << name << "," << ptr << "] " - << size << std::endl; -} - -void fail_on_event(const Kokkos::Profiling::SpaceHandle, const char*, - const void*, const uint64_t) { - ASSERT_TRUE(false) << "Unexpected memory event"; -} - -void expect_no_events() { - Kokkos::Tools::Experimental::set_allocate_data_callback(&fail_on_event); - Kokkos::Tools::Experimental::set_deallocate_data_callback(&fail_on_event); -} - -std::string expected_view_name; -std::string expected_space_name; -std::string error_message; -void expect_allocation_event(const std::string evn, const std::string esn, - const std::string em) { - expected_view_name = evn; - expected_space_name = esn; - error_message = em; - Kokkos::Tools::Experimental::set_allocate_data_callback( - [](const Kokkos_Profiling_SpaceHandle hand, const char* name, const void*, - const uint64_t) { - ASSERT_EQ(std::string(hand.name), expected_space_name) - << error_message << " (bad handle)"; - ASSERT_EQ(std::string(name), expected_view_name) - << error_message << " (bad view name)"; - expect_no_events(); - }); -} -void expect_deallocation_event(const std::string& evn, const std::string& esn, - const std::string em) { - expected_view_name = evn; - expected_space_name = esn; - error_message = em; - Kokkos::Tools::Experimental::set_deallocate_data_callback( - [](const Kokkos_Profiling_SpaceHandle hand, const char* name, const void*, - const uint64_t) { - ASSERT_EQ(std::string(hand.name), expected_space_name) - << error_message << " (bad handle)"; - ASSERT_EQ(std::string(name), expected_view_name) - << error_message << " (bad view name)"; - expect_no_events(); - }); -} - -struct TestSpaceNamer { - static constexpr const char* get_name() { return "TestSpace"; } -}; -struct TestSpaceNamerTwo { - static constexpr const char* get_name() { return "YoDawg"; } -}; -struct TestSpaceNamerThree { - static constexpr const char* get_name() { return "CustomAccessSpace"; } -}; -using fake_memory_space = Kokkos::Experimental::LogicalMemorySpace< - Kokkos::HostSpace, Kokkos::DefaultHostExecutionSpace, TestSpaceNamer, - Kokkos::Experimental::LogicalSpaceSharesAccess::shared_access>; - -void test_view_construct() { - { - expect_allocation_event("puppy_view", "TestSpace", "View allocation"); - Kokkos::View pup_view("puppy_view", 1000); - expect_deallocation_event("puppy_view", "TestSpace", "View free"); - } - Kokkos::Tools::Experimental::pause_tools(); -} -void test_malloc_free() { - expect_allocation_event("does_malloc_work", "TestSpace", - "Error in malloc event"); - auto* temp = - Kokkos::kokkos_malloc("does_malloc_work", 1000); - expect_deallocation_event("does_malloc_work", "TestSpace", "Error in free"); - Kokkos::kokkos_free(temp); - Kokkos::Tools::Experimental::pause_tools(); -} -void test_chained_spaces() { - using doubly_fake_memory_space = Kokkos::Experimental::LogicalMemorySpace< - fake_memory_space, Kokkos::DefaultHostExecutionSpace, TestSpaceNamerTwo, - Kokkos::Experimental::LogicalSpaceSharesAccess::shared_access>; - { - expect_allocation_event("xzibit_dot_jpeg", "YoDawg", - "Chained space view allocation"); - Kokkos::View pup_view("xzibit_dot_jpeg", - 1000); - expect_deallocation_event("xzibit_dot_jpeg", "YoDawg", - "Chained space free"); - } - Kokkos::Tools::Experimental::pause_tools(); -} -void test_space_allocations() { - fake_memory_space debug_space; - expect_allocation_event("allocation_from_space", "TestSpace", - "Space allocation"); - auto* temp = debug_space.allocate("allocation_from_space", 1000); - expect_deallocation_event("allocation_from_space", "TestSpace", - "Space deallocation"); - debug_space.deallocate("allocation_from_space", temp, 1000); - Kokkos::Tools::Experimental::pause_tools(); -} -template -struct AccessCheckKernel { - Kokkos::View data; - KOKKOS_FUNCTION void operator()(const int i) const { data[i] = i; } -}; - -template -void test_allowed_access() { - constexpr const int data_size = 1000; - // We use an unmananged View here since we want to detect a memory access - // violation in the parallel_for and not in the initialization of the View. - std::vector test_data(data_size); - Kokkos::View test_view(test_data.data(), data_size); - AccessCheckKernel functor{test_view}; - Kokkos::parallel_for( - "access_allowed", - Kokkos::RangePolicy(0, data_size), - functor); - Kokkos::fence(); -} - -using semantically_independent_logical_space = - Kokkos::Experimental::LogicalMemorySpace< - Kokkos::HostSpace, Kokkos::DefaultHostExecutionSpace, - TestSpaceNamerThree, - Kokkos::Experimental::LogicalSpaceSharesAccess::no_shared_access>; - -TEST(defaultdevicetype, logical_space_views) { test_view_construct(); } -TEST(defaultdevicetype, logical_space_malloc) { test_malloc_free(); } -TEST(defaultdevicetype, logical_space_alloc) { test_space_allocations(); } -TEST(defaultdevicetype, chained_logical_spaces) { test_chained_spaces(); } -TEST(defaultdevicetype, access_allowed) { - test_allowed_access(); -} -// FIXME_SYCL -#if !(defined(KOKKOS_COMPILER_INTEL_LLVM) && defined(KOKKOS_ENABLE_SYCL)) -TEST(defaultdevicetype_DeathTest, access_forbidden) { - ::testing::FLAGS_gtest_death_test_style = "threadsafe"; - ASSERT_DEATH( - { test_allowed_access(); }, - "Kokkos::View ERROR: attempt to access inaccessible memory space"); -} -#endif - -} // namespace Test diff --git a/lib/kokkos/core/unit_test/tools/TestProfilingSection.cpp b/lib/kokkos/core/unit_test/tools/TestProfilingSection.cpp index 318766ac45..9d35d67feb 100644 --- a/lib/kokkos/core/unit_test/tools/TestProfilingSection.cpp +++ b/lib/kokkos/core/unit_test/tools/TestProfilingSection.cpp @@ -108,8 +108,8 @@ TEST(defaultdevicetype, profiling_section) { } using Kokkos::Profiling::ProfilingSection; -static_assert(!std::is_default_constructible::value, ""); -static_assert(!std::is_copy_constructible::value, ""); -static_assert(!std::is_move_constructible::value, ""); -static_assert(!std::is_copy_assignable::value, ""); -static_assert(!std::is_move_assignable::value, ""); +static_assert(!std::is_default_constructible::value); +static_assert(!std::is_copy_constructible::value); +static_assert(!std::is_move_constructible::value); +static_assert(!std::is_copy_assignable::value); +static_assert(!std::is_move_assignable::value); diff --git a/lib/kokkos/example/tutorial/01_hello_world/hello_world.cpp b/lib/kokkos/example/tutorial/01_hello_world/hello_world.cpp index 5b8a21af83..22b8b6d63c 100644 --- a/lib/kokkos/example/tutorial/01_hello_world/hello_world.cpp +++ b/lib/kokkos/example/tutorial/01_hello_world/hello_world.cpp @@ -58,12 +58,7 @@ struct hello_world { // is unnecessary but harmless. KOKKOS_INLINE_FUNCTION void operator()(const int i) const { - // FIXME_SYCL needs workaround for printf -#ifndef __SYCL_DEVICE_ONLY__ - printf("Hello from i = %i\n", i); -#else - (void)i; -#endif + Kokkos::printf("Hello from i = %i\n", i); } }; diff --git a/lib/kokkos/example/tutorial/01_hello_world_lambda/hello_world_lambda.cpp b/lib/kokkos/example/tutorial/01_hello_world_lambda/hello_world_lambda.cpp index c78f307636..909765e1fc 100644 --- a/lib/kokkos/example/tutorial/01_hello_world_lambda/hello_world_lambda.cpp +++ b/lib/kokkos/example/tutorial/01_hello_world_lambda/hello_world_lambda.cpp @@ -76,13 +76,9 @@ int main(int argc, char* argv[]) { #if defined(KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA) Kokkos::parallel_for( 15, KOKKOS_LAMBDA(const int i) { - // FIXME_SYCL needs workaround for printf -#ifndef __SYCL_DEVICE_ONLY__ - // printf works in a CUDA parallel kernel; std::ostream does not. - printf("Hello from i = %i\n", i); -#else - (void)i; -#endif + // Kokko::printf works for all backends in a parallel kernel; + // std::ostream does not. + Kokkos::printf("Hello from i = %i\n", i); }); #endif // You must call finalize() after you are done using Kokkos. diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp index b041f8d435..ee3f4721d9 100644 --- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp +++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp @@ -47,13 +47,9 @@ struct hello_world { // The TeamPolicy<>::member_type provides functions to query the multi // dimensional index of a thread as well as the number of thread-teams and // the size of each team. -#ifndef __SYCL_DEVICE_ONLY__ - // FIXME_SYCL needs printf workaround - printf("Hello World: %i %i // %i %i\n", thread.league_rank(), - thread.team_rank(), thread.league_size(), thread.team_size()); -#else - (void)thread; -#endif + Kokkos::printf("Hello World: %i %i // %i %i\n", thread.league_rank(), + thread.team_rank(), thread.league_size(), + thread.team_size()); } }; diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp index 933b254f7c..1e6812adea 100644 --- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp +++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp @@ -57,16 +57,12 @@ int main(int narg, char* args[]) { policy, KOKKOS_LAMBDA(const team_member& thread, int& lsum) { lsum += 1; - // TeamPolicy<>::member_type provides functions to query the - // multidimensional index of a thread, as well as the number of - // thread teams and the size of each team. -#ifndef __SYCL_DEVICE_ONLY__ - // FIXME_SYCL needs workaround for printf - printf("Hello World: %i %i // %i %i\n", thread.league_rank(), - thread.team_rank(), thread.league_size(), thread.team_size()); -#else - (void)thread; -#endif + // TeamPolicy<>::member_type provides functions to query the + // multidimensional index of a thread, as well as the number of + // thread teams and the size of each team. + Kokkos::printf("Hello World: %i %i // %i %i\n", thread.league_rank(), + thread.team_rank(), thread.league_size(), + thread.team_size()); }, sum); #endif diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp index 398810d133..75d6089e9a 100644 --- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp +++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp @@ -43,16 +43,11 @@ struct hello_world { // the operator using a team_policy acts like a parallel region for the // team. That means that everything outside of the nested parallel_for is // also executed by all threads of the team. - Kokkos::parallel_for(Kokkos::TeamThreadRange(thread, 31), - [&](const int& i) { -#ifndef __SYCL_DEVICE_ONLY__ - // FIXME_SYCL needs printf workaround - printf("Hello World: (%i , %i) executed loop %i \n", - thread.league_rank(), thread.team_rank(), i); -#else - (void) i; -#endif - }); + Kokkos::parallel_for( + Kokkos::TeamThreadRange(thread, 31), [&](const int& i) { + Kokkos::printf("Hello World: (%i , %i) executed loop %i \n", + thread.league_rank(), thread.team_rank(), i); + }); } }; diff --git a/lib/kokkos/generate_makefile.bash b/lib/kokkos/generate_makefile.bash index 1b216d9fe3..25370daa3f 100755 --- a/lib/kokkos/generate_makefile.bash +++ b/lib/kokkos/generate_makefile.bash @@ -160,6 +160,7 @@ display_help_text() { echo " AMD_GFX906 = AMD GPU MI50/MI60 GFX906" echo " AMD_GFX908 = AMD GPU MI100 GFX908" echo " AMD_GFX90A = AMD GPU MI200 GFX90A" + echo " AMD_GFX940 = AMD GPU MI300 GFX940" echo " AMD_GFX942 = AMD GPU MI300 GFX942" echo " AMD_GFX1030 = AMD GPU V620/W6800 GFX1030" echo " AMD_GFX1100 = AMD GPU RX 7900 XT(X) GFX1100" @@ -169,12 +170,9 @@ display_help_text() { echo " ARMV8_THUNDERX = ARMv8 Cavium ThunderX CPU" echo " ARMV8_THUNDERX2 = ARMv8 Cavium ThunderX2 CPU" echo " [IBM]" - echo " BGQ = IBM Blue Gene Q" - echo " Power7 = IBM POWER7 and POWER7+ CPUs" echo " Power8 = IBM POWER8 CPUs" echo " Power9 = IBM POWER9 CPUs" echo " [Intel]" - echo " WSM = Intel Westmere CPUs" echo " SNB = Intel Sandy/Ivy Bridge CPUs" echo " HSW = Intel Haswell CPUs" echo " BDW = Intel Broadwell Xeon E-class CPUs" @@ -225,7 +223,6 @@ display_help_text() { echo "--with-gtest=/Path/To/Gtest: Set path to gtest. (Used in unit and performance" echo " tests.)" echo "--with-hwloc=/Path/To/Hwloc: Set path to hwloc library." - echo "--with-memkind=/Path/To/MemKind: Set path to memkind library." echo "--with-options=[OPT]: Additional options to Kokkos:" echo " compiler_warnings" echo " aggressive_vectorization = add ivdep on loops" @@ -341,10 +338,6 @@ do KOKKOS_HWLOC=ON HWLOC_PATH="${key#*=}" ;; - --with-memkind*) - KOKKOS_MEMKIND=ON - MEMKIND_PATH="${key#*=}" - ;; --arch*) KOKKOS_ARCH="${key#*=}" ;; @@ -451,15 +444,6 @@ else KOKKOS_HWLOC_CMD= fi -if [ "$KOKKOS_MEMKIND" == "ON" ]; then - KOKKOS_MEMKIND_CMD=-DKokkos_ENABLE_MEMKIND=ON - if [ "$MEMKIND_PATH" != "" ]; then - KOKKOS_MEMKIND_PATH_CMD=-DMEMKIND_ROOT=$MEMKIND_PATH - fi -else - KOKKOS_MEMKIND_CMD= -fi - if [ ! -e ${KOKKOS_PATH}/CMakeLists.txt ]; then if [ "${KOKKOS_PATH}" == "" ]; then CM_SCRIPT=$0 @@ -505,5 +489,5 @@ if [[ ${COMPILER} == *clang* ]]; then fi fi -echo cmake $COMPILER_CMD -DCMAKE_CXX_FLAGS="${KOKKOS_CXXFLAGS}" -DCMAKE_EXE_LINKER_FLAGS="${KOKKOS_LDFLAGS}" -DCMAKE_INSTALL_PREFIX=${PREFIX} ${KOKKOS_DEVICE_CMD} ${KOKKOS_ARCH_CMD} -DKokkos_ENABLE_TESTS=${KOKKOS_DO_TESTS} -DKokkos_ENABLE_EXAMPLES=${KOKKOS_DO_EXAMPLES} ${KOKKOS_OPTION_CMD} ${KOKKOS_CUDA_OPTION_CMD} ${KOKKOS_HIP_OPTION_CMD} -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_CXX_EXTENSIONS=OFF ${STANDARD_CMD} ${KOKKOS_DEBUG_CMD} ${KOKKOS_BC_CMD} ${KOKKOS_HWLOC_CMD} ${KOKKOS_HWLOC_PATH_CMD} ${KOKKOS_MEMKIND_CMD} ${KOKKOS_MEMKIND_PATH_CMD} -DKokkos_ENABLE_DEPRECATION_WARNINGS=${KOKKOS_DEPRECATED_CODE_WARNINGS} -DKokkos_ENABLE_DEPRECATED_CODE_4=${KOKKOS_DEPRECATED_CODE} ${KOKKOS_PATH} -cmake $COMPILER_CMD -DCMAKE_CXX_FLAGS="${KOKKOS_CXXFLAGS//\"}" -DCMAKE_EXE_LINKER_FLAGS="${KOKKOS_LDFLAGS//\"}" -DCMAKE_INSTALL_PREFIX=${PREFIX} ${KOKKOS_DEVICE_CMD} ${KOKKOS_ARCH_CMD} -DKokkos_ENABLE_TESTS=${KOKKOS_DO_TESTS} -DKokkos_ENABLE_EXAMPLES=${KOKKOS_DO_EXAMPLES} ${KOKKOS_OPTION_CMD} ${KOKKOS_CUDA_OPTION_CMD} ${KOKKOS_HIP_OPTION_CMD} -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_CXX_EXTENSIONS=OFF ${STANDARD_CMD} ${KOKKOS_DEBUG_CMD} ${KOKKOS_BC_CMD} ${KOKKOS_HWLOC_CMD} ${KOKKOS_HWLOC_PATH_CMD} ${KOKKOS_MEMKIND_CMD} ${KOKKOS_MEMKIND_PATH_CMD} ${PASSTHRU_CMAKE_FLAGS} -DKokkos_ENABLE_DEPRECATION_WARNINGS=${KOKKOS_DEPRECATED_CODE_WARNINGS} -DKokkos_ENABLE_DEPRECATED_CODE_4=${KOKKOS_DEPRECATED_CODE} ${KOKKOS_PATH} +echo cmake $COMPILER_CMD -DCMAKE_CXX_FLAGS="${KOKKOS_CXXFLAGS}" -DCMAKE_EXE_LINKER_FLAGS="${KOKKOS_LDFLAGS}" -DCMAKE_INSTALL_PREFIX=${PREFIX} ${KOKKOS_DEVICE_CMD} ${KOKKOS_ARCH_CMD} -DKokkos_ENABLE_TESTS=${KOKKOS_DO_TESTS} -DKokkos_ENABLE_EXAMPLES=${KOKKOS_DO_EXAMPLES} ${KOKKOS_OPTION_CMD} ${KOKKOS_CUDA_OPTION_CMD} ${KOKKOS_HIP_OPTION_CMD} -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_CXX_EXTENSIONS=OFF ${STANDARD_CMD} ${KOKKOS_DEBUG_CMD} ${KOKKOS_BC_CMD} ${KOKKOS_HWLOC_CMD} ${KOKKOS_HWLOC_PATH_CMD} -DKokkos_ENABLE_DEPRECATION_WARNINGS=${KOKKOS_DEPRECATED_CODE_WARNINGS} -DKokkos_ENABLE_DEPRECATED_CODE_4=${KOKKOS_DEPRECATED_CODE} ${KOKKOS_PATH} +cmake $COMPILER_CMD -DCMAKE_CXX_FLAGS="${KOKKOS_CXXFLAGS//\"}" -DCMAKE_EXE_LINKER_FLAGS="${KOKKOS_LDFLAGS//\"}" -DCMAKE_INSTALL_PREFIX=${PREFIX} ${KOKKOS_DEVICE_CMD} ${KOKKOS_ARCH_CMD} -DKokkos_ENABLE_TESTS=${KOKKOS_DO_TESTS} -DKokkos_ENABLE_EXAMPLES=${KOKKOS_DO_EXAMPLES} ${KOKKOS_OPTION_CMD} ${KOKKOS_CUDA_OPTION_CMD} ${KOKKOS_HIP_OPTION_CMD} -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_CXX_EXTENSIONS=OFF ${STANDARD_CMD} ${KOKKOS_DEBUG_CMD} ${KOKKOS_BC_CMD} ${KOKKOS_HWLOC_CMD} ${KOKKOS_HWLOC_PATH_CMD} ${PASSTHRU_CMAKE_FLAGS} -DKokkos_ENABLE_DEPRECATION_WARNINGS=${KOKKOS_DEPRECATED_CODE_WARNINGS} -DKokkos_ENABLE_DEPRECATED_CODE_4=${KOKKOS_DEPRECATED_CODE} ${KOKKOS_PATH} diff --git a/lib/kokkos/gnu_generate_makefile.bash b/lib/kokkos/gnu_generate_makefile.bash index 5ea159cdd4..7a197bb71d 100755 --- a/lib/kokkos/gnu_generate_makefile.bash +++ b/lib/kokkos/gnu_generate_makefile.bash @@ -74,9 +74,6 @@ do --with-hwloc*) HWLOC_PATH="${key#*=}" ;; - --with-memkind*) - MEMKIND_PATH="${key#*=}" - ;; --arch*) KOKKOS_ARCH="${key#*=}" ;; @@ -148,12 +145,9 @@ do echo " ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU" echo " ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU" echo " [IBM]" - echo " BGQ = IBM Blue Gene Q" - echo " Power7 = IBM POWER7 and POWER7+ CPUs" echo " Power8 = IBM POWER8 CPUs" echo " Power9 = IBM POWER9 CPUs" echo " [Intel]" - echo " WSM = Intel Westmere CPUs" echo " SNB = Intel Sandy/Ivy Bridge CPUs" echo " HSW = Intel Haswell CPUs" echo " BDW = Intel Broadwell Xeon E-class CPUs" @@ -198,7 +192,6 @@ do echo "--with-gtest=/Path/To/Gtest: Set path to gtest. (Used in unit and performance" echo " tests.)" echo "--with-hwloc=/Path/To/Hwloc: Set path to hwloc library." - echo "--with-memkind=/Path/To/MemKind: Set path to memkind library." echo "--with-options=[OPT]: Additional options to Kokkos:" echo " compiler_warnings" echo " aggressive_vectorization = add ivdep on loops" @@ -298,11 +291,6 @@ if [ ${#HWLOC_PATH} -gt 0 ]; then KOKKOS_USE_TPLS="${KOKKOS_USE_TPLS},hwloc" fi -if [ ${#MEMKIND_PATH} -gt 0 ]; then - KOKKOS_SETTINGS="${KOKKOS_SETTINGS} MEMKIND_PATH=${MEMKIND_PATH}" - KOKKOS_USE_TPLS="${KOKKOS_USE_TPLS},experimental_memkind" -fi - if [ ${#KOKKOS_USE_TPLS} -gt 0 ]; then KOKKOS_SETTINGS="${KOKKOS_SETTINGS} KOKKOS_USE_TPLS=${KOKKOS_USE_TPLS}" fi diff --git a/lib/kokkos/master_history.txt b/lib/kokkos/master_history.txt index fd0020b8d5..31be925325 100644 --- a/lib/kokkos/master_history.txt +++ b/lib/kokkos/master_history.txt @@ -34,3 +34,6 @@ tag: 4.0.00 date: 02:23:2023 master: 5ad60966 release: 52ea2953 tag: 4.0.01 date: 04:26:2023 master: aa1f48f3 release: 5893754f tag: 4.1.00 date: 06:20:2023 master: 62d2b6c8 release: adde1e6a tag: 4.2.00 date: 11:09:2023 master: 1a3ea28f release: abe01c88 +tag: 4.2.01 date: 01:30:2024 master: 71a9bcae release: 221e5f7a +tag: 4.3.00 date: 04:03:2024 master: e0dc0128 release: f08217a4 +tag: 4.3.01 date: 05:07:2024 master: 486cc745 release: 262d2d6e diff --git a/lib/kokkos/simd/src/Kokkos_SIMD_AVX2.hpp b/lib/kokkos/simd/src/Kokkos_SIMD_AVX2.hpp index 521160b76f..6d0956f383 100644 --- a/lib/kokkos/simd/src/Kokkos_SIMD_AVX2.hpp +++ b/lib/kokkos/simd/src/Kokkos_SIMD_AVX2.hpp @@ -30,9 +30,11 @@ "Kokkos_SIMD_AVX2.hpp must be included before Kokkos_SIMD_Common_Math.hpp!" #endif -// FIXME_HIP ROCm 5.6 and 5.7 can't compile with the intrinsic used here. -#if defined(__HIPCC__) && (HIP_VERSION_MAJOR == 5) && \ - ((HIP_VERSION_MINOR == 6) || (HIP_VERSION_MINOR == 7)) +// FIXME_HIP ROCm 5.6, 5.7, and 6.0 can't compile with the intrinsic used here. +#if defined(__HIPCC__) && \ + (((HIP_VERSION_MAJOR == 5) && \ + ((HIP_VERSION_MINOR == 6) || (HIP_VERSION_MINOR == 7))) || \ + ((HIP_VERSION_MAJOR == 6) && ((HIP_VERSION_MINOR == 0)))) #define KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE #endif @@ -563,10 +565,18 @@ class simd> { element_aligned_tag) { m_value = _mm256_loadu_pd(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm256_load_pd(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm256_storeu_pd(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm256_store_pd(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m256d() const { return m_value; @@ -818,10 +828,18 @@ class simd> { element_aligned_tag) { m_value = _mm_loadu_ps(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm_load_ps(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm_storeu_ps(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm_store_ps(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m128() const { return m_value; @@ -1059,17 +1077,31 @@ class simd> { } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, element_aligned_tag) { - // FIXME_HIP ROCm 5.6 can't compile with the intrinsic used here. + // FIXME_HIP ROCm 5.6, 5.7, and 6.0 can't compile with the intrinsic used + // here. #ifdef KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE m_value = _mm_loadu_si128(reinterpret_cast<__m128i const*>(ptr)); #else m_value = _mm_maskload_epi32(ptr, static_cast<__m128i>(mask_type(true))); +#endif + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + // FIXME_HIP ROCm 5.6 can't compile with the intrinsic used here. +#ifdef KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE + m_value = _mm_load_si128(reinterpret_cast<__m128i const*>(ptr)); +#else + m_value = _mm_maskload_epi32(ptr, static_cast<__m128i>(mask_type(true))); #endif } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm_maskstore_epi32(ptr, static_cast<__m128i>(mask_type(true)), m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm_maskstore_epi32(ptr, static_cast<__m128i>(mask_type(true)), m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m128i() const { return m_value; @@ -1111,6 +1143,11 @@ class simd> { return simd( _mm_add_epi32(static_cast<__m128i>(lhs), static_cast<__m128i>(rhs))); } + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator*( + simd const& lhs, simd const& rhs) noexcept { + return simd( + _mm_mullo_epi32(static_cast<__m128i>(lhs), static_cast<__m128i>(rhs))); + } [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator>>( simd const& lhs, int rhs) noexcept { @@ -1249,6 +1286,15 @@ class simd> { #else m_value = _mm256_maskload_epi64(reinterpret_cast(ptr), static_cast<__m256i>(mask_type(true))); +#endif + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { +#ifdef KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE + m_value = _mm256_load_si256(reinterpret_cast<__m256i const*>(ptr)); +#else + m_value = _mm256_maskload_epi64(reinterpret_cast(ptr), + static_cast<__m256i>(mask_type(true))); #endif } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( @@ -1256,6 +1302,11 @@ class simd> { _mm256_maskstore_epi64(reinterpret_cast(ptr), static_cast<__m256i>(mask_type(true)), m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm256_maskstore_epi64(reinterpret_cast(ptr), + static_cast<__m256i>(mask_type(true)), m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m256i() const { return m_value; @@ -1278,6 +1329,13 @@ class simd> { _mm256_add_epi64(static_cast<__m256i>(lhs), static_cast<__m256i>(rhs))); } + // fallback simd multiplication using generator constructor + // multiplying vectors of 64-bit signed integers is not available in AVX2 + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator*( + simd const& lhs, simd const& rhs) noexcept { + return simd([&](std::size_t i) { return lhs[i] * rhs[i]; }); + } + // AVX2 only has eq and gt comparisons for int64 [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend mask_type operator==(simd const& lhs, simd const& rhs) noexcept { @@ -1306,17 +1364,19 @@ class simd> { return !(lhs == rhs); } + // fallback simd shift right arithmetic using generator constructor // Shift right arithmetic for 64bit packed ints is not availalbe in AVX2 - // [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd( - // simd const& lhs, int rhs) noexcept { - // return simd(_mm256_srai_epi64(static_cast<__m256i>(lhs), rhs)); - // } + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator>>( + simd const& lhs, int rhs) noexcept { + return simd([&](std::size_t i) { return lhs[i] >> rhs; }); + } - // [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd( - // simd const& lhs, simd const& rhs) noexcept { - // return simd(_mm256_srav_epi64(static_cast<__m256i>(lhs), - // static_cast<__m256i>(rhs)))); - // } + // fallback simd shift right arithmetic using generator constructor + // Shift right arithmetic for 64bit packed ints is not availalbe in AVX2 + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator>>( + simd const& lhs, simd const& rhs) noexcept { + return simd([&](std::size_t i) { return lhs[i] >> rhs[i]; }); + } [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator<<( simd const& lhs, int rhs) noexcept { @@ -1444,6 +1504,15 @@ class simd> { #else m_value = _mm256_maskload_epi64(reinterpret_cast(ptr), static_cast<__m256i>(mask_type(true))); +#endif + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { +#ifdef KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE + m_value = _mm256_load_si256(reinterpret_cast<__m256i const*>(ptr)); +#else + m_value = _mm256_maskload_epi64(reinterpret_cast(ptr), + static_cast<__m256i>(mask_type(true))); #endif } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m256i() @@ -1460,6 +1529,14 @@ class simd> { return simd( _mm256_sub_epi64(static_cast<__m256i>(lhs), static_cast<__m256i>(rhs))); } + + // fallback simd multiplication using generator constructor + // multiplying vectors of 64-bit unsigned integers is not available in AVX2 + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator*( + simd const& lhs, simd const& rhs) noexcept { + return simd([&](std::size_t i) { return lhs[i] * rhs[i]; }); + } + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator>>( simd const& lhs, int rhs) noexcept { return _mm256_srli_epi64(static_cast<__m256i>(lhs), rhs); @@ -1588,6 +1665,11 @@ class const_where_expression>, static_cast<__m256d>(m_value)); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(double* mem, vector_aligned_tag) const { + _mm256_maskstore_pd(mem, _mm256_castpd_si256(static_cast<__m256d>(m_mask)), + static_cast<__m256d>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( double* mem, simd> const& index) const { @@ -1624,6 +1706,11 @@ class where_expression>, mem, _mm256_castpd_si256(static_cast<__m256d>(m_mask)))); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(double const* mem, vector_aligned_tag) { + m_value = value_type(_mm256_maskload_pd( + mem, _mm256_castpd_si256(static_cast<__m256d>(m_mask)))); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( double const* mem, simd> const& index) { @@ -1667,6 +1754,11 @@ class const_where_expression>, static_cast<__m128>(m_value)); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(float* mem, vector_aligned_tag) const { + _mm_maskstore_ps(mem, _mm_castps_si128(static_cast<__m128>(m_mask)), + static_cast<__m128>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( float* mem, simd> const& index) const { @@ -1703,6 +1795,11 @@ class where_expression>, _mm_maskload_ps(mem, _mm_castps_si128(static_cast<__m128>(m_mask)))); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(float const* mem, vector_aligned_tag) { + m_value = value_type( + _mm_maskload_ps(mem, _mm_castps_si128(static_cast<__m128>(m_mask)))); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( float const* mem, simd> const& index) { @@ -1746,6 +1843,12 @@ class const_where_expression< _mm_maskstore_epi32(mem, static_cast<__m128i>(m_mask), static_cast<__m128i>(m_value)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(std::int32_t* mem, vector_aligned_tag) const { + _mm_maskstore_epi32(mem, static_cast<__m128i>(m_mask), + static_cast<__m128i>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::int32_t* mem, @@ -1786,6 +1889,16 @@ class where_expression>, m_value = value_type(_mm_maskload_epi32(mem, static_cast<__m128i>(m_mask))); #endif } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(std::int32_t const* mem, vector_aligned_tag) { +#ifdef KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE + __m128i tmp = _mm_load_si128(reinterpret_cast<__m128i const*>(mem)); + m_value = value_type(_mm_and_si128(tmp, static_cast<__m128i>(m_mask))); +#else + m_value = value_type(_mm_maskload_epi32(mem, static_cast<__m128i>(m_mask))); +#endif + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::int32_t const* mem, @@ -1833,6 +1946,13 @@ class const_where_expression< static_cast<__m256i>(m_mask), static_cast<__m256i>(m_value)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(std::int64_t* mem, + vector_aligned_tag) const { + _mm256_maskstore_epi64(reinterpret_cast(mem), + static_cast<__m256i>(m_mask), + static_cast<__m256i>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::int64_t* mem, @@ -1874,6 +1994,17 @@ class where_expression>, reinterpret_cast(mem), static_cast<__m256i>(m_mask))); #endif } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(std::int64_t const* mem, + vector_aligned_tag) { +#ifdef KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE + __m256i tmp = _mm256_load_si256(reinterpret_cast<__m256i const*>(mem)); + m_value = value_type(_mm256_and_si256(tmp, static_cast<__m256i>(m_mask))); +#else + m_value = value_type(_mm256_maskload_epi64( + reinterpret_cast(mem), static_cast<__m256i>(m_mask))); +#endif + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::int64_t const* mem, @@ -1922,6 +2053,13 @@ class const_where_expression< static_cast<__m256i>(m_mask), static_cast<__m256i>(m_value)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(std::uint64_t* mem, + vector_aligned_tag) const { + _mm256_maskstore_epi64(reinterpret_cast(mem), + static_cast<__m256i>(m_mask), + static_cast<__m256i>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::uint64_t* mem, @@ -1963,6 +2101,17 @@ class where_expression>, reinterpret_cast(mem), static_cast<__m256i>(m_mask))); #endif } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(std::uint64_t const* mem, + vector_aligned_tag) { +#ifdef KOKKOS_IMPL_WORKAROUND_ROCM_AVX2_ISSUE + __m256i tmp = _mm256_load_si256(reinterpret_cast<__m256i const*>(mem)); + m_value = value_type(_mm256_and_si256(tmp, static_cast<__m256i>(m_mask))); +#else + m_value = value_type(_mm256_maskload_epi64( + reinterpret_cast(mem), static_cast<__m256i>(m_mask))); +#endif + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::uint64_t const* mem, diff --git a/lib/kokkos/simd/src/Kokkos_SIMD_AVX512.hpp b/lib/kokkos/simd/src/Kokkos_SIMD_AVX512.hpp index c5d1717ad4..7fa35c204a 100644 --- a/lib/kokkos/simd/src/Kokkos_SIMD_AVX512.hpp +++ b/lib/kokkos/simd/src/Kokkos_SIMD_AVX512.hpp @@ -193,10 +193,18 @@ class simd> { element_aligned_tag) { m_value = _mm512_loadu_pd(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm512_load_pd(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm512_storeu_pd(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm512_store_pd(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m512d() const { return m_value; @@ -475,10 +483,18 @@ class simd> { element_aligned_tag) { m_value = _mm256_loadu_ps(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm256_load_ps(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm256_storeu_ps(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm256_store_ps(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m256() const { return m_value; @@ -735,15 +751,25 @@ class simd> { operator[](std::size_t i) const { return reinterpret_cast(&m_value)[i]; } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + element_aligned_tag) { + m_value = _mm256_mask_loadu_epi32( + _mm256_set1_epi32(0), static_cast<__mmask8>(mask_type(true)), ptr); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm256_mask_load_epi32( + _mm256_set1_epi32(0), static_cast<__mmask8>(mask_type(true)), ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm256_mask_storeu_epi32(ptr, static_cast<__mmask8>(mask_type(true)), m_value); } - KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, - element_aligned_tag) { - m_value = _mm256_mask_loadu_epi32( - _mm256_set1_epi32(0), static_cast<__mmask8>(mask_type(true)), ptr); + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm256_mask_store_epi32(ptr, static_cast<__mmask8>(mask_type(true)), + m_value); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m256i() const { @@ -934,21 +960,30 @@ class simd> { operator[](std::size_t i) const { return reinterpret_cast(&m_value)[i]; } - KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( - value_type* ptr, element_aligned_tag) const { - _mm256_mask_storeu_epi32(ptr, static_cast<__mmask8>(mask_type(true)), - m_value); - } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, element_aligned_tag) { m_value = _mm256_mask_loadu_epi32( _mm256_set1_epi32(0), static_cast<__mmask8>(mask_type(true)), ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm256_mask_load_epi32( + _mm256_set1_epi32(0), static_cast<__mmask8>(mask_type(true)), ptr); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( + value_type* ptr, element_aligned_tag) const { + _mm256_mask_storeu_epi32(ptr, static_cast<__mmask8>(mask_type(true)), + m_value); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm256_mask_store_epi32(ptr, static_cast<__mmask8>(mask_type(true)), + m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m256i() const { return m_value; } - [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator*( simd const& lhs, simd const& rhs) noexcept { return simd(_mm256_mullo_epi32(static_cast<__m256i>(lhs), @@ -1130,10 +1165,19 @@ class simd> { element_aligned_tag) { m_value = _mm512_loadu_si512(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm512_load_si512(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm512_storeu_si512(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm512_store_si512(ptr, m_value); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m512i() const { return m_value; @@ -1331,10 +1375,19 @@ class simd> { element_aligned_tag) { m_value = _mm512_loadu_si512(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = _mm512_load_si512(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { _mm512_storeu_si512(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + _mm512_store_si512(ptr, m_value); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator __m512i() const { return m_value; @@ -1505,6 +1558,11 @@ class const_where_expression>, static_cast<__m512d>(m_value)); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(double* mem, vector_aligned_tag) const { + _mm512_mask_store_pd(mem, static_cast<__mmask8>(m_mask), + static_cast<__m512d>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( double* mem, simd> const& index) const { @@ -1541,6 +1599,11 @@ class where_expression>, _mm512_set1_pd(0.0), static_cast<__mmask8>(m_mask), mem)); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(double const* mem, vector_aligned_tag) { + m_value = value_type(_mm512_mask_load_pd( + _mm512_set1_pd(0.0), static_cast<__mmask8>(m_mask), mem)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( double const* mem, simd> const& index) { @@ -1584,6 +1647,11 @@ class const_where_expression>, static_cast<__m256>(m_value)); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(float* mem, vector_aligned_tag) const { + _mm256_mask_store_ps(mem, static_cast<__mmask8>(m_mask), + static_cast<__m256>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( float* mem, simd> const& index) const { @@ -1619,6 +1687,10 @@ class where_expression>, m_value = value_type(_mm256_mask_loadu_ps( _mm256_set1_ps(0.0), static_cast<__mmask8>(m_mask), mem)); } + void copy_from(float const* mem, vector_aligned_tag) { + m_value = value_type(_mm256_mask_load_ps( + _mm256_set1_ps(0.0), static_cast<__mmask8>(m_mask), mem)); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( float const* mem, @@ -1666,6 +1738,12 @@ class const_where_expression< _mm256_mask_storeu_epi32(mem, static_cast<__mmask8>(m_mask), static_cast<__m256i>(m_value)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(std::int32_t* mem, vector_aligned_tag) const { + _mm256_mask_store_epi32(mem, static_cast<__mmask8>(m_mask), + static_cast<__m256i>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::int32_t* mem, @@ -1702,6 +1780,11 @@ class where_expression>, m_value = value_type(_mm256_mask_loadu_epi32( _mm256_set1_epi32(0), static_cast<__mmask8>(m_mask), mem)); } + void copy_from(std::int32_t const* mem, vector_aligned_tag) { + m_value = value_type(_mm256_mask_load_epi32( + _mm256_set1_epi32(0), static_cast<__mmask8>(m_mask), mem)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::int32_t const* mem, @@ -1710,6 +1793,7 @@ class where_expression>, static_cast<__m256i>(m_value), static_cast<__mmask8>(m_mask), static_cast<__m256i>(index), mem, 4)); } + template (m_mask), static_cast<__m256i>(m_value)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(std::uint32_t* mem, vector_aligned_tag) const { + _mm256_mask_store_epi32(mem, static_cast<__mmask8>(m_mask), + static_cast<__m256i>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::uint32_t* mem, @@ -1784,6 +1874,12 @@ class where_expression>, m_value = value_type(_mm256_mask_loadu_epi32( _mm256_set1_epi32(0), static_cast<__mmask8>(m_mask), mem)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(std::uint32_t const* mem, vector_aligned_tag) { + m_value = value_type(_mm256_mask_load_epi32( + _mm256_set1_epi32(0), static_cast<__mmask8>(m_mask), mem)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::uint32_t const* mem, @@ -1792,6 +1888,7 @@ class where_expression>, static_cast<__m256i>(m_value), static_cast<__mmask8>(m_mask), static_cast<__m256i>(index), mem, 4)); } + template (m_mask), static_cast<__m512i>(m_value)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(std::int64_t* mem, vector_aligned_tag) const { + _mm512_mask_store_epi64(mem, static_cast<__mmask8>(m_mask), + static_cast<__m512i>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::int64_t* mem, @@ -1866,6 +1969,12 @@ class where_expression>, m_value = value_type(_mm512_mask_loadu_epi64( _mm512_set1_epi64(0.0), static_cast<__mmask8>(m_mask), mem)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(std::int64_t const* mem, vector_aligned_tag) { + m_value = value_type(_mm512_mask_load_epi64( + _mm512_set1_epi64(0.0), static_cast<__mmask8>(m_mask), mem)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::int64_t const* mem, @@ -1874,6 +1983,7 @@ class where_expression>, static_cast<__m512i>(m_value), static_cast<__mmask8>(m_mask), static_cast<__m256i>(index), mem, 8)); } + template (m_mask), static_cast<__m512i>(m_value)); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(std::uint64_t* mem, vector_aligned_tag) const { + _mm512_mask_store_epi64(mem, static_cast<__mmask8>(m_mask), + static_cast<__m512i>(m_value)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::uint64_t* mem, @@ -1949,6 +2065,11 @@ class where_expression>, _mm512_set1_epi64(0.0), static_cast<__mmask8>(m_mask), mem)); } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(std::uint64_t const* mem, vector_aligned_tag) { + m_value = value_type(_mm512_mask_load_epi64( + _mm512_set1_epi64(0.0), static_cast<__mmask8>(m_mask), mem)); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::uint64_t const* mem, simd> const& index) { @@ -1956,6 +2077,7 @@ class where_expression>, static_cast<__m512i>(m_value), static_cast<__mmask8>(m_mask), static_cast<__m256i>(index), mem, 8)); } + template class simd_mask; -struct element_aligned_tag {}; +class simd_alignment_vector_aligned {}; + +template +struct simd_flags {}; + +inline constexpr simd_flags<> simd_flag_default{}; +inline constexpr simd_flags simd_flag_aligned{}; + +using element_aligned_tag = simd_flags<>; +using vector_aligned_tag = simd_flags; // class template declarations for const_where_expression and where_expression @@ -117,48 +126,6 @@ template return const_where_expression(mask, value); } -// fallback simd multiplication using generator constructor -// At the time of this writing, this fallback is only used -// to multiply vectors of 64-bit signed integers for the AVX2 backend - -template -[[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION simd operator*( - simd const& lhs, simd const& rhs) { - return simd([&](std::size_t i) { return lhs[i] * rhs[i]; }); -} - -// fallback simd shift using generator constructor -// At the time of this edit, only the fallback for shift vectors of -// 64-bit signed integers for the AVX2 backend is used - -template >> -[[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION simd operator>>( - simd const& lhs, int rhs) { - return simd([&](std::size_t i) { return lhs[i] >> rhs; }); -} - -template >> -[[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION simd operator<<( - simd const& lhs, int rhs) { - return simd([&](std::size_t i) { return lhs[i] << rhs; }); -} - -template >> -[[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION simd operator>>( - simd const& lhs, simd const& rhs) { - return simd([&](std::size_t i) { return lhs[i] >> rhs[i]; }); -} - -template >> -[[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION simd operator<<( - simd const& lhs, simd const& rhs) { - return simd([&](std::size_t i) { return lhs[i] << rhs[i]; }); -} - // The code below provides: // operator@(simd, Arithmetic) // operator@(Arithmetic, simd) diff --git a/lib/kokkos/simd/src/Kokkos_SIMD_NEON.hpp b/lib/kokkos/simd/src/Kokkos_SIMD_NEON.hpp index 43ece20389..efc81135d1 100644 --- a/lib/kokkos/simd/src/Kokkos_SIMD_NEON.hpp +++ b/lib/kokkos/simd/src/Kokkos_SIMD_NEON.hpp @@ -363,10 +363,18 @@ class simd> { element_aligned_tag) { m_value = vld1q_f64(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = vld1q_f64(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { vst1q_f64(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + vst1q_f64(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator float64x2_t() const { return m_value; @@ -607,10 +615,18 @@ class simd> { element_aligned_tag) { m_value = vld1_f32(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = vld1_f32(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { vst1_f32(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + vst1_f32(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator float32x2_t() const { return m_value; @@ -844,10 +860,18 @@ class simd> { element_aligned_tag) { m_value = vld1_s32(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = vld1_s32(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { vst1_s32(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + vst1_s32(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator int32x2_t() const { return m_value; @@ -868,7 +892,11 @@ class simd> { return simd( vadd_s32(static_cast(lhs), static_cast(rhs))); } - + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator*( + simd const& lhs, simd const& rhs) noexcept { + return simd( + vmul_s32(static_cast(lhs), static_cast(rhs))); + } [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend mask_type operator==(simd const& lhs, simd const& rhs) noexcept { return mask_type( @@ -1044,10 +1072,18 @@ class simd> { element_aligned_tag) { m_value = vld1q_s64(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = vld1q_s64(ptr); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( value_type* ptr, element_aligned_tag) const { vst1q_s64(ptr, m_value); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + vst1q_s64(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator int64x2_t() const { return m_value; @@ -1068,7 +1104,10 @@ class simd> { return simd( vaddq_s64(static_cast(lhs), static_cast(rhs))); } - + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator*( + simd const& lhs, simd const& rhs) noexcept { + return simd([&](std::size_t i) { return lhs[i] * rhs[i]; }); + } [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend mask_type operator==(simd const& lhs, simd const& rhs) noexcept { return mask_type( @@ -1246,6 +1285,18 @@ class simd> { element_aligned_tag) { m_value = vld1q_u64(ptr); } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_from(value_type const* ptr, + vector_aligned_tag) { + m_value = vld1q_u64(ptr); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to( + value_type* ptr, element_aligned_tag) const { + vst1q_u64(ptr, m_value); + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void copy_to(value_type* ptr, + vector_aligned_tag) const { + vst1q_u64(ptr, m_value); + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION constexpr explicit operator uint64x2_t() const { return m_value; @@ -1261,7 +1312,10 @@ class simd> { return simd( vaddq_u64(static_cast(lhs), static_cast(rhs))); } - + [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator*( + simd const& lhs, simd const& rhs) noexcept { + return simd([&](std::size_t i) { return lhs[i] * rhs[i]; }); + } [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION friend simd operator&( simd const& lhs, simd const& rhs) noexcept { return simd( @@ -1386,6 +1440,11 @@ class const_where_expression>, if (m_mask[1]) mem[1] = m_value[1]; } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(double* mem, vector_aligned_tag) const { + if (m_mask[0]) mem[0] = m_value[0]; + if (m_mask[1]) mem[1] = m_value[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( double* mem, simd> const& index) const { @@ -1421,6 +1480,11 @@ class where_expression>, if (m_mask[1]) m_value[1] = mem[1]; } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(double const* mem, vector_aligned_tag) { + if (m_mask[0]) m_value[0] = mem[0]; + if (m_mask[1]) m_value[1] = mem[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( double const* mem, simd> const& index) { @@ -1464,6 +1528,11 @@ class const_where_expression>, if (m_mask[1]) mem[1] = m_value[1]; } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(float* mem, vector_aligned_tag) const { + if (m_mask[0]) mem[0] = m_value[0]; + if (m_mask[1]) mem[1] = m_value[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( float* mem, simd> const& index) const { @@ -1498,6 +1567,10 @@ class where_expression>, if (m_mask[0]) m_value[0] = mem[0]; if (m_mask[1]) m_value[1] = mem[1]; } + void copy_from(float const* mem, vector_aligned_tag) { + if (m_mask[0]) m_value[0] = mem[0]; + if (m_mask[1]) m_value[1] = mem[1]; + } KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( float const* mem, @@ -1542,6 +1615,12 @@ class const_where_expression< if (m_mask[0]) mem[0] = m_value[0]; if (m_mask[1]) mem[1] = m_value[1]; } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(std::int32_t* mem, vector_aligned_tag) const { + if (m_mask[0]) mem[0] = m_value[0]; + if (m_mask[1]) mem[1] = m_value[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::int32_t* mem, @@ -1577,6 +1656,12 @@ class where_expression>, if (m_mask[0]) m_value[0] = mem[0]; if (m_mask[1]) m_value[1] = mem[1]; } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(std::int32_t const* mem, vector_aligned_tag) { + if (m_mask[0]) m_value[0] = mem[0]; + if (m_mask[1]) m_value[1] = mem[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::int32_t const* mem, @@ -1584,6 +1669,7 @@ class where_expression>, if (m_mask[0]) m_value[0] = mem[index[0]]; if (m_mask[1]) m_value[1] = mem[index[1]]; } + template < class U, std::enable_if_t< @@ -1622,6 +1708,12 @@ class const_where_expression< if (m_mask[0]) mem[0] = m_value[0]; if (m_mask[1]) mem[1] = m_value[1]; } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_to(std::int64_t* mem, vector_aligned_tag) const { + if (m_mask[0]) mem[0] = m_value[0]; + if (m_mask[1]) mem[1] = m_value[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void scatter_to( std::int64_t* mem, @@ -1657,6 +1749,12 @@ class where_expression>, if (m_mask[0]) m_value[0] = mem[0]; if (m_mask[1]) m_value[1] = mem[1]; } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(std::int64_t const* mem, vector_aligned_tag) { + if (m_mask[0]) m_value[0] = mem[0]; + if (m_mask[1]) m_value[1] = mem[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::int64_t const* mem, @@ -1664,6 +1762,7 @@ class where_expression>, if (m_mask[0]) m_value[0] = mem[index[0]]; if (m_mask[1]) m_value[1] = mem[index[1]]; } + template < class U, std::enable_if_t>, if (m_mask[0]) m_value[0] = mem[0]; if (m_mask[1]) m_value[1] = mem[1]; } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION + void copy_from(std::uint64_t const* mem, vector_aligned_tag) { + if (m_mask[0]) m_value[0] = mem[0]; + if (m_mask[1]) m_value[1] = mem[1]; + } + KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION void gather_from( std::uint64_t const* mem, @@ -1744,6 +1855,7 @@ class where_expression>, if (m_mask[0]) m_value[0] = mem[index[0]]; if (m_mask[1]) m_value[1] = mem[index[1]]; } + template { element_aligned_tag) { m_value = *ptr; } + KOKKOS_FORCEINLINE_FUNCTION void copy_from(T const* ptr, vector_aligned_tag) { + m_value = *ptr; + } KOKKOS_FORCEINLINE_FUNCTION void copy_to(T* ptr, element_aligned_tag) const { *ptr = m_value; } + KOKKOS_FORCEINLINE_FUNCTION void copy_to(T* ptr, vector_aligned_tag) const { + *ptr = m_value; + } + KOKKOS_FORCEINLINE_FUNCTION reference operator[](std::size_t) { return m_value; } @@ -224,7 +231,7 @@ template using data_type = std::conditional_t, T, double>; return Experimental::simd( Kokkos::floor(static_cast(a[0]))); -}; +} template [[nodiscard]] KOKKOS_FORCEINLINE_FUNCTION auto ceil( @@ -232,7 +239,7 @@ template using data_type = std::conditional_t, T, double>; return Experimental::simd( Kokkos::ceil(static_cast(a[0]))); -}; +} template [[nodiscard]] KOKKOS_FORCEINLINE_FUNCTION auto round( @@ -240,7 +247,7 @@ template using data_type = std::conditional_t, T, double>; return Experimental::simd( Experimental::round_half_to_nearest_even(static_cast(a[0]))); -}; +} template [[nodiscard]] KOKKOS_FORCEINLINE_FUNCTION auto trunc( @@ -248,7 +255,7 @@ template using data_type = std::conditional_t, T, double>; return Experimental::simd( Kokkos::trunc(static_cast(a[0]))); -}; +} template [[nodiscard]] KOKKOS_FORCEINLINE_FUNCTION @@ -308,6 +315,10 @@ class const_where_expression, void copy_to(T* mem, element_aligned_tag) const { if (static_cast(m_mask)) *mem = static_cast(m_value); } + KOKKOS_FORCEINLINE_FUNCTION + void copy_to(T* mem, vector_aligned_tag) const { + if (static_cast(m_mask)) *mem = static_cast(m_value); + } template KOKKOS_FORCEINLINE_FUNCTION std::enable_if_t> scatter_to(T* mem, simd const& index) const { @@ -315,13 +326,13 @@ class const_where_expression, mem[static_cast(index)] = static_cast(m_value); } - [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION value_type const& - impl_get_value() const { + [[nodiscard]] KOKKOS_FORCEINLINE_FUNCTION value_type const& impl_get_value() + const { return m_value; } - [[nodiscard]] KOKKOS_IMPL_HOST_FORCEINLINE_FUNCTION mask_type const& - impl_get_mask() const { + [[nodiscard]] KOKKOS_FORCEINLINE_FUNCTION mask_type const& impl_get_mask() + const { return m_mask; } }; @@ -344,6 +355,10 @@ class where_expression, void copy_from(T const* mem, element_aligned_tag) { if (static_cast(this->m_mask)) this->m_value = *mem; } + KOKKOS_FORCEINLINE_FUNCTION + void copy_from(T const* mem, vector_aligned_tag) { + if (static_cast(this->m_mask)) this->m_value = *mem; + } template KOKKOS_FORCEINLINE_FUNCTION std::enable_if_t> gather_from(T const* mem, simd const& index) { diff --git a/lib/kokkos/simd/unit_tests/TestSIMD.cpp b/lib/kokkos/simd/unit_tests/TestSIMD.cpp index 61c076e824..7a1f9be2a0 100644 --- a/lib/kokkos/simd/unit_tests/TestSIMD.cpp +++ b/lib/kokkos/simd/unit_tests/TestSIMD.cpp @@ -21,3 +21,4 @@ #include #include #include +#include diff --git a/lib/kokkos/simd/unit_tests/include/SIMDTesting_Ops.hpp b/lib/kokkos/simd/unit_tests/include/SIMDTesting_Ops.hpp index 6529f20e66..c587ccf304 100644 --- a/lib/kokkos/simd/unit_tests/include/SIMDTesting_Ops.hpp +++ b/lib/kokkos/simd/unit_tests/include/SIMDTesting_Ops.hpp @@ -209,4 +209,165 @@ class shift_left { } }; +class cbrt_op { + public: + template + auto on_host(T const& a) const { +#if defined(KOKKOS_ENABLE_DEPRECATED_CODE_4) + return Kokkos::Experimental::cbrt(a); +#else + return Kokkos::cbrt(a); +#endif + } + template + auto on_host_serial(T const& a) const { + return Kokkos::cbrt(a); + } +}; + +class exp_op { + public: + template + auto on_host(T const& a) const { +#if defined(KOKKOS_ENABLE_DEPRECATED_CODE_4) + return Kokkos::Experimental::exp(a); +#else + return Kokkos::exp(a); +#endif + } + template + auto on_host_serial(T const& a) const { + return Kokkos::exp(a); + } +}; + +class log_op { + public: + template + auto on_host(T const& a) const { +#if defined(KOKKOS_ENABLE_DEPRECATED_CODE_4) + return Kokkos::Experimental::log(a); +#else + return Kokkos::log(a); +#endif + } + template + auto on_host_serial(T const& a) const { + return Kokkos::log(a); + } +}; + +class hmin { + public: + template + auto on_host(T const& a) const { + return Kokkos::Experimental::hmin(a); + } + template + auto on_host_serial(T const& a) const { + using DataType = typename T::value_type::value_type; + + auto const& v = a.impl_get_value(); + auto const& m = a.impl_get_mask(); + auto result = Kokkos::reduction_identity::min(); + for (std::size_t i = 0; i < v.size(); ++i) { + if (m[i]) result = Kokkos::min(result, v[i]); + } + return result; + } + + template + KOKKOS_INLINE_FUNCTION auto on_device(T const& a) const { + return Kokkos::Experimental::hmin(a); + } + template + KOKKOS_INLINE_FUNCTION auto on_device_serial(T const& a) const { + using DataType = typename T::value_type::value_type; + + auto const& v = a.impl_get_value(); + auto const& m = a.impl_get_mask(); + auto result = Kokkos::reduction_identity::min(); + for (std::size_t i = 0; i < v.size(); ++i) { + if (m[i]) result = Kokkos::min(result, v[i]); + } + return result; + } +}; + +class hmax { + public: + template + auto on_host(T const& a) const { + return Kokkos::Experimental::hmax(a); + } + template + auto on_host_serial(T const& a) const { + using DataType = typename T::value_type::value_type; + + auto const& v = a.impl_get_value(); + auto const& m = a.impl_get_mask(); + auto result = Kokkos::reduction_identity::max(); + for (std::size_t i = 0; i < v.size(); ++i) { + if (m[i]) result = Kokkos::max(result, v[i]); + } + return result; + } + + template + KOKKOS_INLINE_FUNCTION auto on_device(T const& a) const { + return Kokkos::Experimental::hmax(a); + } + template + KOKKOS_INLINE_FUNCTION auto on_device_serial(T const& a) const { + using DataType = typename T::value_type::value_type; + + auto const& v = a.impl_get_value(); + auto const& m = a.impl_get_mask(); + auto result = Kokkos::reduction_identity::max(); + for (std::size_t i = 0; i < v.size(); ++i) { + if (m[i]) result = Kokkos::max(result, v[i]); + } + return result; + } +}; + +class reduce { + public: + template + auto on_host(T const& a) const { + using DataType = typename T::value_type::value_type; + return Kokkos::Experimental::reduce(a, DataType(0), std::plus<>()); + } + template + auto on_host_serial(T const& a) const { + using DataType = typename T::value_type::value_type; + + auto const& v = a.impl_get_value(); + auto const& m = a.impl_get_mask(); + auto result = Kokkos::reduction_identity::sum(); + for (std::size_t i = 0; i < v.size(); ++i) { + if (m[i]) result += v[i]; + } + return result; + } + + template + KOKKOS_INLINE_FUNCTION auto on_device(T const& a) const { + using DataType = typename T::value_type::value_type; + return Kokkos::Experimental::reduce(a, DataType(0), std::plus<>()); + } + template + KOKKOS_INLINE_FUNCTION auto on_device_serial(T const& a) const { + using DataType = typename T::value_type::value_type; + + auto const& v = a.impl_get_value(); + auto const& m = a.impl_get_mask(); + auto result = Kokkos::reduction_identity::sum(); + for (std::size_t i = 0; i < v.size(); ++i) { + if (m[i]) result += v[i]; + } + return result; + } +}; + #endif diff --git a/lib/kokkos/simd/unit_tests/include/SIMDTesting_Utilities.hpp b/lib/kokkos/simd/unit_tests/include/SIMDTesting_Utilities.hpp index ae2ab2c697..d36e1e5afc 100644 --- a/lib/kokkos/simd/unit_tests/include/SIMDTesting_Utilities.hpp +++ b/lib/kokkos/simd/unit_tests/include/SIMDTesting_Utilities.hpp @@ -93,7 +93,7 @@ class load_element_aligned { bool host_load(T const* mem, std::size_t n, Kokkos::Experimental::simd& result) const { if (n < result.size()) return false; - result.copy_from(mem, Kokkos::Experimental::element_aligned_tag()); + result.copy_from(mem, Kokkos::Experimental::simd_flag_default); return true; } template @@ -101,7 +101,26 @@ class load_element_aligned { T const* mem, std::size_t n, Kokkos::Experimental::simd& result) const { if (n < result.size()) return false; - result.copy_from(mem, Kokkos::Experimental::element_aligned_tag()); + result.copy_from(mem, Kokkos::Experimental::simd_flag_default); + return true; + } +}; + +class load_vector_aligned { + public: + template + bool host_load(T const* mem, std::size_t n, + Kokkos::Experimental::simd& result) const { + if (n < result.size()) return false; + result.copy_from(mem, Kokkos::Experimental::simd_flag_aligned); + return true; + } + template + KOKKOS_INLINE_FUNCTION bool device_load( + T const* mem, std::size_t n, + Kokkos::Experimental::simd& result) const { + if (n < result.size()) return false; + result.copy_from(mem, Kokkos::Experimental::simd_flag_aligned); return true; } }; @@ -116,8 +135,7 @@ class load_masked { for (std::size_t i = 0; i < n; ++i) { mask[i] = true; } - where(mask, result) - .copy_from(mem, Kokkos::Experimental::element_aligned_tag()); + where(mask, result).copy_from(mem, Kokkos::Experimental::simd_flag_default); where(!mask, result) = 0; return true; } @@ -130,8 +148,7 @@ class load_masked { for (std::size_t i = 0; i < n; ++i) { mask[i] = true; } - where(mask, result) - .copy_from(mem, Kokkos::Experimental::element_aligned_tag()); + where(mask, result).copy_from(mem, Kokkos::Experimental::simd_flag_default); where(!mask, result) = T(0); return true; } diff --git a/lib/kokkos/simd/unit_tests/include/TestSIMD_GeneratorCtors.hpp b/lib/kokkos/simd/unit_tests/include/TestSIMD_GeneratorCtors.hpp index 4feff3a89d..23e3826c75 100644 --- a/lib/kokkos/simd/unit_tests/include/TestSIMD_GeneratorCtors.hpp +++ b/lib/kokkos/simd/unit_tests/include/TestSIMD_GeneratorCtors.hpp @@ -37,11 +37,12 @@ inline void host_check_gen_ctor() { } simd_type rhs; - rhs.copy_from(init, Kokkos::Experimental::element_aligned_tag()); + rhs.copy_from(init, Kokkos::Experimental::simd_flag_default); simd_type blend; - blend.copy_from(expected, Kokkos::Experimental::element_aligned_tag()); + blend.copy_from(expected, Kokkos::Experimental::simd_flag_default); +#if !(defined(KOKKOS_ENABLE_CUDA) && defined(KOKKOS_COMPILER_MSVC)) if constexpr (std::is_same_v) { simd_type basic(KOKKOS_LAMBDA(std::size_t i) { return init[i]; }); host_check_equality(basic, rhs, lanes); @@ -63,6 +64,7 @@ inline void host_check_gen_ctor() { host_check_equality(blend, result, lanes); } +#endif } template @@ -96,7 +98,7 @@ KOKKOS_INLINE_FUNCTION void device_check_gen_ctor() { simd_type basic(KOKKOS_LAMBDA(std::size_t i) { return init[i]; }); simd_type rhs; - rhs.copy_from(init, Kokkos::Experimental::element_aligned_tag()); + rhs.copy_from(init, Kokkos::Experimental::simd_flag_default); device_check_equality(basic, rhs, lanes); simd_type lhs(KOKKOS_LAMBDA(std::size_t i) { return init[i] * 9; }); @@ -104,7 +106,7 @@ KOKKOS_INLINE_FUNCTION void device_check_gen_ctor() { KOKKOS_LAMBDA(std::size_t i) { return (mask[i]) ? lhs[i] : rhs[i]; }); simd_type blend; - blend.copy_from(expected, Kokkos::Experimental::element_aligned_tag()); + blend.copy_from(expected, Kokkos::Experimental::simd_flag_default); device_check_equality(result, blend, lanes); } diff --git a/lib/kokkos/simd/unit_tests/include/TestSIMD_MathOps.hpp b/lib/kokkos/simd/unit_tests/include/TestSIMD_MathOps.hpp index 802e41efe5..59f2f6c18f 100644 --- a/lib/kokkos/simd/unit_tests/include/TestSIMD_MathOps.hpp +++ b/lib/kokkos/simd/unit_tests/include/TestSIMD_MathOps.hpp @@ -61,13 +61,18 @@ void host_check_math_op_one_loader(UnaryOp unary_op, std::size_t n, simd_type arg; bool const loaded_arg = loader.host_load(args + i, nlanes, arg); if (!loaded_arg) continue; - auto computed_result = unary_op.on_host(arg); - decltype(computed_result) expected_result; + decltype(unary_op.on_host(arg)) expected_result; for (std::size_t lane = 0; lane < simd_type::size(); ++lane) { - if (lane < nlanes) + if (lane < nlanes) { + if constexpr (std::is_same_v || + std::is_same_v || + std::is_same_v) + arg[lane] = Kokkos::abs(arg[lane]); expected_result[lane] = unary_op.on_host_serial(T(arg[lane])); + } } + auto computed_result = unary_op.on_host(arg); host_check_equality(expected_result, computed_result, nlanes); } } @@ -78,6 +83,7 @@ inline void host_check_math_op_all_loaders(Op op, std::size_t n, host_check_math_op_one_loader(op, n, args...); host_check_math_op_one_loader(op, n, args...); host_check_math_op_one_loader(op, n, args...); + host_check_math_op_one_loader(op, n, args...); } template @@ -96,6 +102,13 @@ inline void host_check_all_math_ops(const DataType (&first_args)[n], // TODO: Place fallback implementations for all simd integer types if constexpr (std::is_floating_point_v) { host_check_math_op_all_loaders(divides(), n, first_args, second_args); + +#if defined(__INTEL_COMPILER) && \ + (defined(KOKKOS_ARCH_AVX2) || defined(KOKKOS_ARCH_AVX512XEON)) + host_check_math_op_all_loaders(cbrt_op(), n, first_args); + host_check_math_op_all_loaders(exp_op(), n, first_args); + host_check_math_op_all_loaders(log_op(), n, first_args); +#endif } } @@ -109,23 +122,29 @@ inline void host_check_abi_size() { template inline void host_check_math_ops() { constexpr size_t n = 11; + constexpr size_t alignment = + Kokkos::Experimental::simd::size() * sizeof(DataType); host_check_abi_size(); if constexpr (!std::is_integral_v) { - DataType const first_args[n] = {0.1, 0.4, 0.5, 0.7, 1.0, 1.5, - -2.0, 10.0, 0.0, 1.2, -2.8}; - DataType const second_args[n] = {1.0, 0.2, 1.1, 1.8, -0.1, -3.0, - -2.4, 1.0, 13.0, -3.2, -2.1}; + alignas(alignment) DataType const first_args[n] = { + 0.1, 0.4, 0.5, 0.7, 1.0, 1.5, -2.0, 10.0, 0.0, 1.2, -2.8}; + alignas(alignment) DataType const second_args[n] = { + 1.0, 0.2, 1.1, 1.8, -0.1, -3.0, -2.4, 1.0, 13.0, -3.2, -2.1}; host_check_all_math_ops(first_args, second_args); } else { if constexpr (std::is_signed_v) { - DataType const first_args[n] = {1, 2, -1, 10, 0, 1, -2, 10, 0, 1, -2}; - DataType const second_args[n] = {1, 2, 1, 1, 1, -3, -2, 1, 13, -3, -2}; + alignas(alignment) + DataType const first_args[n] = {1, 2, -1, 10, 0, 1, -2, 10, 0, 1, -2}; + alignas(alignment) DataType const second_args[n] = {1, 2, 1, 1, 1, -3, + -2, 1, 13, -3, -2}; host_check_all_math_ops(first_args, second_args); } else { - DataType const first_args[n] = {1, 2, 1, 10, 0, 1, 2, 10, 0, 1, 2}; - DataType const second_args[n] = {1, 2, 1, 1, 1, 3, 2, 1, 13, 3, 2}; + alignas(alignment) + DataType const first_args[n] = {1, 2, 1, 10, 0, 1, 2, 10, 0, 1, 2}; + alignas(alignment) + DataType const second_args[n] = {1, 2, 1, 1, 1, 3, 2, 1, 13, 3, 2}; host_check_all_math_ops(first_args, second_args); } } @@ -202,6 +221,7 @@ KOKKOS_INLINE_FUNCTION void device_check_math_op_all_loaders(Op op, device_check_math_op_one_loader(op, n, args...); device_check_math_op_one_loader(op, n, args...); device_check_math_op_one_loader(op, n, args...); + device_check_math_op_one_loader(op, n, args...); } template @@ -282,8 +302,13 @@ TEST(simd, host_math_ops) { } TEST(simd, device_math_ops) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0, 1), - simd_device_math_ops_functor()); +#ifdef KOKKOS_ENABLE_OPENMPTARGET // FIXME_OPENMPTARGET + GTEST_SKIP() + << "skipping because of a non-deterministic failure reporting: " + "Failure to synchronize stream (nil): Error in " + "cuStreamSynchronize: an illegal memory access was encountered"; +#endif + Kokkos::parallel_for(1, simd_device_math_ops_functor()); } #endif diff --git a/lib/kokkos/simd/unit_tests/include/TestSIMD_Reductions.hpp b/lib/kokkos/simd/unit_tests/include/TestSIMD_Reductions.hpp new file mode 100644 index 0000000000..b3c7ac9a01 --- /dev/null +++ b/lib/kokkos/simd/unit_tests/include/TestSIMD_Reductions.hpp @@ -0,0 +1,184 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#ifndef KOKKOS_TEST_SIMD_REDUCTIONS_HPP +#define KOKKOS_TEST_SIMD_REDUCTIONS_HPP + +#include +#include + +template +inline void host_check_reduction_one_loader(ReductionOp reduce_op, + std::size_t n, T const* args) { + Loader loader; + using simd_type = Kokkos::Experimental::simd; + using mask_type = typename Kokkos::Experimental::simd::mask_type; + constexpr std::size_t width = simd_type::size(); + + for (std::size_t i = 0; i < n; i += width) { + std::size_t const nremaining = n - i; + std::size_t const nlanes = Kokkos::min(nremaining, width); + simd_type arg; + bool const loaded_arg = loader.host_load(args + i, nlanes, arg); + if (!loaded_arg) continue; + + mask_type mask(false); + for (std::size_t j = 0; j < n; ++j) { + mask[j] = true; + } + auto value = where(mask, arg); + auto expected = reduce_op.on_host_serial(value); + auto computed = reduce_op.on_host(value); + + gtest_checker().equality(expected, computed); + } +} + +template +inline void host_check_reduction_all_loaders(ReductionOp reduce_op, + std::size_t n, T const* args) { + host_check_reduction_one_loader(reduce_op, n, + args); + host_check_reduction_one_loader(reduce_op, n, args); + host_check_reduction_one_loader(reduce_op, n, args); +} + +template +inline void host_check_all_reductions(const DataType (&args)[n]) { + host_check_reduction_all_loaders(hmin(), n, args); + host_check_reduction_all_loaders(hmax(), n, args); + host_check_reduction_all_loaders(reduce(), n, args); +} + +template +inline void host_check_reductions() { + constexpr size_t n = 11; + + if constexpr (std::is_signed_v) { + DataType const args[n] = {1, 2, -1, 10, 0, 1, -2, 10, 0, 1, -2}; + host_check_all_reductions(args); + } else { + DataType const args[n] = {1, 2, 1, 10, 0, 1, 2, 10, 0, 1, 2}; + host_check_all_reductions(args); + } +} + +template +inline void host_check_reductions_all_types( + Kokkos::Experimental::Impl::data_types) { + (host_check_reductions(), ...); +} + +template +inline void host_check_reductions_all_abis( + Kokkos::Experimental::Impl::abi_set) { + using DataTypes = Kokkos::Experimental::Impl::data_type_set; + (host_check_reductions_all_types(DataTypes()), ...); +} + +template +KOKKOS_INLINE_FUNCTION void device_check_reduction_one_loader( + ReductionOp reduce_op, std::size_t n, T const* args) { + Loader loader; + using simd_type = Kokkos::Experimental::simd; + using mask_type = typename Kokkos::Experimental::simd::mask_type; + constexpr std::size_t width = simd_type::size(); + + for (std::size_t i = 0; i < n; i += width) { + std::size_t const nremaining = n - i; + std::size_t const nlanes = Kokkos::min(nremaining, width); + simd_type arg; + bool const loaded_arg = loader.device_load(args + i, nlanes, arg); + if (!loaded_arg) continue; + + mask_type mask(false); + for (std::size_t j = 0; j < n; ++j) { + mask[j] = true; + } + auto value = where(mask, arg); + auto expected = reduce_op.on_device_serial(value); + auto computed = reduce_op.on_device(value); + + kokkos_checker().equality(expected, computed); + } +} + +template +KOKKOS_INLINE_FUNCTION void device_check_reduction_all_loaders( + ReductionOp reduce_op, std::size_t n, T const* args) { + device_check_reduction_one_loader(reduce_op, n, + args); + device_check_reduction_one_loader(reduce_op, n, args); + device_check_reduction_one_loader(reduce_op, n, args); +} + +template +KOKKOS_INLINE_FUNCTION void device_check_all_reductions( + const DataType (&args)[n]) { + device_check_reduction_all_loaders(hmin(), n, args); + device_check_reduction_all_loaders(hmax(), n, args); + device_check_reduction_all_loaders(reduce(), n, args); +} + +template +KOKKOS_INLINE_FUNCTION void device_check_reductions() { + constexpr size_t n = 11; + + if constexpr (std::is_signed_v) { + DataType const args[n] = {1, 2, -1, 10, 0, 1, -2, 10, 0, 1, -2}; + device_check_all_reductions(args); + } else { + DataType const args[n] = {1, 2, 1, 10, 0, 1, 2, 10, 0, 1, 2}; + device_check_all_reductions(args); + } +} + +template +KOKKOS_INLINE_FUNCTION void device_check_reductions_all_types( + Kokkos::Experimental::Impl::data_types) { + (device_check_reductions(), ...); +} + +template +KOKKOS_INLINE_FUNCTION void device_check_reductions_all_abis( + Kokkos::Experimental::Impl::abi_set) { + using DataTypes = Kokkos::Experimental::Impl::data_type_set; + (device_check_reductions_all_types(DataTypes()), ...); +} + +class simd_device_reduction_functor { + public: + KOKKOS_INLINE_FUNCTION void operator()(int) const { + device_check_reductions_all_abis( + Kokkos::Experimental::Impl::device_abi_set()); + } +}; + +TEST(simd, host_reductions) { + host_check_reductions_all_abis(Kokkos::Experimental::Impl::host_abi_set()); +} + +TEST(simd, device_reductions) { +#ifdef KOKKOS_ENABLE_OPENMPTARGET // FIXME_OPENMPTARGET + GTEST_SKIP() + << "skipping because of a non-deterministic failure reporting: " + "Failure to synchronize stream (nil): Error in " + "cuStreamSynchronize: an illegal memory access was encountered"; +#endif + Kokkos::parallel_for(1, simd_device_reduction_functor()); +} + +#endif diff --git a/lib/kokkos/simd/unit_tests/include/TestSIMD_ShiftOps.hpp b/lib/kokkos/simd/unit_tests/include/TestSIMD_ShiftOps.hpp index f6fdcb920e..ffdd2cba4a 100644 --- a/lib/kokkos/simd/unit_tests/include/TestSIMD_ShiftOps.hpp +++ b/lib/kokkos/simd/unit_tests/include/TestSIMD_ShiftOps.hpp @@ -85,10 +85,11 @@ inline void host_check_shift_op_all_loaders(ShiftOp shift_op, shift_by, n); host_check_shift_on_one_loader(shift_op, test_vals, shift_by, n); + host_check_shift_on_one_loader(shift_op, test_vals, + shift_by, n); Kokkos::Experimental::simd shift_by_lanes; - shift_by_lanes.copy_from(shift_by, - Kokkos::Experimental::element_aligned_tag()); + shift_by_lanes.copy_from(shift_by, Kokkos::Experimental::simd_flag_default); host_check_shift_by_lanes_on_one_loader( shift_op, test_vals, shift_by_lanes); @@ -96,6 +97,8 @@ inline void host_check_shift_op_all_loaders(ShiftOp shift_op, shift_by_lanes); host_check_shift_by_lanes_on_one_loader( shift_op, test_vals, shift_by_lanes); + host_check_shift_by_lanes_on_one_loader( + shift_op, test_vals, shift_by_lanes); } template @@ -104,12 +107,14 @@ inline void host_check_shift_ops() { using simd_type = Kokkos::Experimental::simd; constexpr std::size_t width = simd_type::size(); constexpr std::size_t num_cases = 8; + constexpr size_t alignment = + Kokkos::Experimental::simd::size() * sizeof(DataType); DataType max = std::numeric_limits::max(); - DataType shift_by[num_cases] = { + alignas(alignment) DataType shift_by[num_cases] = { 0, 1, 3, width / 2, width / 2 + 1, width - 1, width, width + 1}; - DataType test_vals[width]; + alignas(alignment) DataType test_vals[width]; for (std::size_t i = 0; i < width; ++i) { DataType inc = max / width; test_vals[i] = i * inc + 1; @@ -201,10 +206,11 @@ KOKKOS_INLINE_FUNCTION void device_check_shift_op_all_loaders( shift_by, n); device_check_shift_on_one_loader(shift_op, test_vals, shift_by, n); + device_check_shift_on_one_loader( + shift_op, test_vals, shift_by, n); Kokkos::Experimental::simd shift_by_lanes; - shift_by_lanes.copy_from(shift_by, - Kokkos::Experimental::element_aligned_tag()); + shift_by_lanes.copy_from(shift_by, Kokkos::Experimental::simd_flag_default); device_check_shift_by_lanes_on_one_loader( shift_op, test_vals, shift_by_lanes); @@ -212,6 +218,8 @@ KOKKOS_INLINE_FUNCTION void device_check_shift_op_all_loaders( shift_op, test_vals, shift_by_lanes); device_check_shift_by_lanes_on_one_loader( shift_op, test_vals, shift_by_lanes); + device_check_shift_by_lanes_on_one_loader( + shift_op, test_vals, shift_by_lanes); } template diff --git a/lib/kokkos/simd/unit_tests/include/TestSIMD_WhereExpressions.hpp b/lib/kokkos/simd/unit_tests/include/TestSIMD_WhereExpressions.hpp index 129f2b0d5c..152fd9e984 100644 --- a/lib/kokkos/simd/unit_tests/include/TestSIMD_WhereExpressions.hpp +++ b/lib/kokkos/simd/unit_tests/include/TestSIMD_WhereExpressions.hpp @@ -29,7 +29,7 @@ inline void host_check_where_expr_scatter_to() { std::size_t nlanes = simd_type::size(); DataType init[] = {11, 13, 17, 19, 23, 29, 31, 37}; simd_type src; - src.copy_from(init, Kokkos::Experimental::element_aligned_tag()); + src.copy_from(init, Kokkos::Experimental::simd_flag_default); for (std::size_t idx = 0; idx < nlanes; ++idx) { mask_type mask(true); @@ -46,7 +46,7 @@ inline void host_check_where_expr_scatter_to() { where(mask, src).scatter_to(dst, index); simd_type dst_simd; - dst_simd.copy_from(dst, Kokkos::Experimental::element_aligned_tag()); + dst_simd.copy_from(dst, Kokkos::Experimental::simd_flag_default); host_check_equality(expected_result, dst_simd, nlanes); } @@ -107,7 +107,7 @@ KOKKOS_INLINE_FUNCTION void device_check_where_expr_scatter_to() { std::size_t nlanes = simd_type::size(); DataType init[] = {11, 13, 17, 19, 23, 29, 31, 37}; simd_type src; - src.copy_from(init, Kokkos::Experimental::element_aligned_tag()); + src.copy_from(init, Kokkos::Experimental::simd_flag_default); for (std::size_t idx = 0; idx < nlanes; ++idx) { mask_type mask(true); @@ -124,7 +124,7 @@ KOKKOS_INLINE_FUNCTION void device_check_where_expr_scatter_to() { where(mask, src).scatter_to(dst, index); simd_type dst_simd; - dst_simd.copy_from(dst, Kokkos::Experimental::element_aligned_tag()); + dst_simd.copy_from(dst, Kokkos::Experimental::simd_flag_default); device_check_equality(expected_result, dst_simd, nlanes); } diff --git a/lib/kokkos/tpls/desul/Config.hpp.cmake.in b/lib/kokkos/tpls/desul/Config.hpp.cmake.in index a7bc738191..aed7ecfabc 100644 --- a/lib/kokkos/tpls/desul/Config.hpp.cmake.in +++ b/lib/kokkos/tpls/desul/Config.hpp.cmake.in @@ -14,6 +14,8 @@ SPDX-License-Identifier: (BSD-3-Clause) #cmakedefine DESUL_ATOMICS_ENABLE_HIP #cmakedefine DESUL_ATOMICS_ENABLE_HIP_SEPARABLE_COMPILATION #cmakedefine DESUL_ATOMICS_ENABLE_SYCL +#cmakedefine DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION #cmakedefine DESUL_ATOMICS_ENABLE_OPENMP +#cmakedefine DESUL_ATOMICS_ENABLE_OPENACC #endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Adapt_SYCL.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Adapt_SYCL.hpp index 082fc132de..15c6d78d94 100644 --- a/lib/kokkos/tpls/desul/include/desul/atomics/Adapt_SYCL.hpp +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Adapt_SYCL.hpp @@ -88,15 +88,18 @@ using sycl_atomic_ref = sycl::atomic_ref; #endif -// FIXME_SYCL Use SYCL_EXT_ONEAPI_DEVICE_GLOBAL when available instead #ifdef DESUL_SYCL_DEVICE_GLOBAL_SUPPORTED -// FIXME_SYCL The compiler forces us to use device_image_scope. Drop this when possible. +#ifdef SYCL_EXT_ONEAPI_DEVICE_GLOBAL +template +using sycl_device_global = sycl::ext::oneapi::experimental::device_global; +#else template using sycl_device_global = sycl::ext::oneapi::experimental::device_global< T, decltype(sycl::ext::oneapi::experimental::properties( sycl::ext::oneapi::experimental::device_image_scope))>; #endif +#endif } // namespace Impl } // namespace desul diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Compare_Exchange.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Compare_Exchange.hpp index e91569e1de..72639fc493 100644 --- a/lib/kokkos/tpls/desul/include/desul/atomics/Compare_Exchange.hpp +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Compare_Exchange.hpp @@ -26,6 +26,9 @@ SPDX-License-Identifier: (BSD-3-Clause) #ifdef DESUL_HAVE_OPENMP_ATOMICS #include #endif +#ifdef DESUL_HAVE_OPENACC_ATOMICS +#include +#endif #ifdef DESUL_HAVE_SYCL_ATOMICS #include #endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Compare_Exchange_OpenACC.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Compare_Exchange_OpenACC.hpp new file mode 100644 index 0000000000..77149bd474 --- /dev/null +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Compare_Exchange_OpenACC.hpp @@ -0,0 +1,153 @@ +/* +Copyright (c) 2019, Lawrence Livermore National Security, LLC +and DESUL project contributors. See the COPYRIGHT file for details. +Source: https://github.com/desul/desul + +SPDX-License-Identifier: (BSD-3-Clause) +*/ + +#ifndef DESUL_ATOMICS_COMPARE_EXCHANGE_OPENACC_HPP_ +#define DESUL_ATOMICS_COMPARE_EXCHANGE_OPENACC_HPP_ + +#include + +#include +#include +#include + +namespace desul { +namespace Impl { + +#ifdef __NVCOMPILER + +#pragma acc routine seq +template +T device_atomic_exchange(T* dest, T value, MemoryOrder, MemoryScope /*scope*/) { + if constexpr (std::is_arithmetic_v && ((sizeof(T) == 4) || (sizeof(T) == 8))) { + T return_val; +#pragma acc atomic capture + { + return_val = *dest; + *dest = value; + } + return return_val; + } else { + // FIXME_OPENACC + if (acc_on_device(acc_device_not_host)) { + printf( + "DESUL error in device_atomic_exchange(): Not supported atomic operation in " + "the OpenACC backend\n"); + } + // Acquire a lock for the address + // while (!lock_address_openacc((void*)dest, scope)) { + // } + // device_atomic_thread_fence(MemoryOrderAcquire(), scope); + T return_val = *dest; + *dest = value; + // device_atomic_thread_fence(MemoryOrderRelease(), scope); + // unlock_address_openacc((void*)dest, scope); + return return_val; + } +} + +#pragma acc routine seq +template +T device_atomic_compare_exchange( + T* dest, T compare, T value, MemoryOrder, MemoryScope scope) { + // Floating point types treated separetely to work around compiler errors + // "parse invalid cast opcode for cast from 'i32' to 'float'". + // Also not just "forwarding" arguments to atomicCAS because it does not have an + // overload that takes int64_t + if constexpr (std::is_integral_v && ((sizeof(T) == 4) || (sizeof(T) == 8))) { + static_assert(sizeof(unsigned int) == 4); + static_assert(sizeof(unsigned long long int) == 8); + using cas_t = + std::conditional_t<(sizeof(T) == 4), unsigned int, unsigned long long int>; + cas_t return_val = atomicCAS(reinterpret_cast(dest), + reinterpret_cast(compare), + reinterpret_cast(value)); + return reinterpret_cast(return_val); +#ifdef DESUL_CUDA_ARCH_IS_PRE_PASCAL + } else if constexpr (std::is_same_v) { +#else + } else if constexpr (std::is_same_v || std::is_same_v) { +#endif + return atomicCAS(dest, compare, value); + } else { + // FIXME_OPENACC + if (acc_on_device(acc_device_not_host)) { + printf( + "DESUL error in device_atomic_compare_exchange(): Not supported atomic " + "operation in the OpenACC backend\n"); + } + T current_val = *dest; + // Acquire a lock for the address + // while (!lock_address_openacc((void*)dest, scope)) { + //} + // device_atomic_thread_fence(MemoryOrderAcquire(), scope); + if (current_val == compare) { + *dest = value; + // device_atomic_thread_fence(MemoryOrderRelease(), scope); + } + // unlock_address_openacc((void*)dest, scope); + return current_val; + } +} + +#else // not NVHPC + +#pragma acc routine seq +template +T device_atomic_exchange(T* dest, T value, MemoryOrder, MemoryScope) { + if constexpr (std::is_arithmetic_v) { + T return_val; +#pragma acc atomic capture + { + return_val = *dest; + *dest = value; + } + return return_val; + } else { + // FIXME_OPENACC + printf( + "DESUL error in device_atomic_exchange(): Not supported atomic operation in " + "the OpenACC backend\n"); + // Acquire a lock for the address + // while (!lock_address_openacc((void*)dest, scope)) { + // } + // device_atomic_thread_fence(MemoryOrderAcquire(), scope); + T return_val = *dest; + *dest = value; + // device_atomic_thread_fence(MemoryOrderRelease(), scope); + // unlock_address_openacc((void*)dest, scope); + return return_val; + } +} + +#pragma acc routine seq +template +T device_atomic_compare_exchange( + T* dest, T compare, T value, MemoryOrder, MemoryScope scope) { + // FIXME_OPENACC + printf( + "DESUL error in device_atomic_compare_exchange(): Not supported atomic operation " + "in the OpenACC backend\n"); + T current_val = *dest; + // Acquire a lock for the address + // while (!lock_address_openacc((void*)dest, scope)) { + //} + // device_atomic_thread_fence(MemoryOrderAcquire(), scope); + if (current_val == compare) { + *dest = value; + // device_atomic_thread_fence(MemoryOrderRelease(), scope); + } + // unlock_address_openacc((void*)dest, scope); + return current_val; +} + +#endif + +} // namespace Impl +} // namespace desul + +#endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Fetch_Op.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Fetch_Op.hpp index adf75c5743..1b161397c7 100644 --- a/lib/kokkos/tpls/desul/include/desul/atomics/Fetch_Op.hpp +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Fetch_Op.hpp @@ -23,6 +23,9 @@ SPDX-License-Identifier: (BSD-3-Clause) #ifdef DESUL_HAVE_OPENMP_ATOMICS #include #endif +#ifdef DESUL_HAVE_OPENACC_ATOMICS +#include +#endif #ifdef DESUL_HAVE_SYCL_ATOMICS #include #endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Fetch_Op_OpenACC.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Fetch_Op_OpenACC.hpp new file mode 100644 index 0000000000..ab570ac578 --- /dev/null +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Fetch_Op_OpenACC.hpp @@ -0,0 +1,431 @@ +/* +Copyright (c) 2019, Lawrence Livermore National Security, LLC +and DESUL project contributors. See the COPYRIGHT file for details. +Source: https://github.com/desul/desul + +SPDX-License-Identifier: (BSD-3-Clause) +*/ +#ifndef DESUL_ATOMICS_FETCH_OP_OPENACC_HPP_ +#define DESUL_ATOMICS_FETCH_OP_OPENACC_HPP_ + +#include // min, max +#include +#include + +namespace desul { +namespace Impl { + +#ifdef __NVCOMPILER + +template +inline constexpr bool is_openacc_integral_type_v = + std::is_same_v || std::is_same_v || + std::is_same_v; + +template +inline constexpr bool is_openacc_arithmetic_type_v = std::is_same_v || +#ifndef DESUL_CUDA_ARCH_IS_PRE_PASCAL + std::is_same_v || +#endif + is_openacc_integral_type_v; + +#else + +template +inline constexpr bool is_openacc_integral_type_v = std::is_integral_v; + +template +inline constexpr bool is_openacc_arithmetic_type_v = std::is_arithmetic_v; + +#endif + +// +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_add( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr += val; + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_inc( + T* ptr, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr += T(1); + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_sub( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr -= val; + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_dec( + T* ptr, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr -= T(1); + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_mul( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr *= val; + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_div( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr /= val; + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_lshift( + T* ptr, const unsigned int val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr = *ptr << val; + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_rshift( + T* ptr, const unsigned int val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr = *ptr >> val; + } + return old; +} + +#ifdef __NVCOMPILER +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_max( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; + old = atomicMax(ptr, val); + return old; +} +#endif + +#ifdef __NVCOMPILER +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_min( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + int old; + old = atomicMin(ptr, val); + return old; +} +#endif + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_and( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr &= val; + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_or( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr |= val; + } + return old; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_fetch_xor( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T old; +#pragma acc atomic capture + { + old = *ptr; + *ptr ^= val; + } + return old; +} +// + +// +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_add_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr += val; + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_inc_fetch( + T* ptr, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr += T(1); + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_sub_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr -= val; + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_dec_fetch( + T* ptr, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr -= T(1); + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_mul_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr *= val; + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_div_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr /= val; + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_lshift_fetch( + T* ptr, const unsigned int val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr = *ptr << val; + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_rshift_fetch( + T* ptr, const unsigned int val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr = *ptr >> val; + tmp = *ptr; + } + return tmp; +} + +#ifdef __NVCOMPILER +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_max_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; + tmp = atomicMax(ptr, val); + tmp = std::max(tmp, val); + return tmp; +} +#endif + +#ifdef __NVCOMPILER +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_min_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; + tmp = atomicMin(ptr, val); + tmp = std::min(tmp, val); + return tmp; +} +#endif + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_and_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr &= val; + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_or_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr |= val; + tmp = *ptr; + } + return tmp; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_xor_fetch( + T* ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { + T tmp; +#pragma acc atomic capture + { + *ptr ^= val; + tmp = *ptr; + } + return tmp; +} +// + +// +#pragma acc routine seq +template +std::enable_if_t, void> device_atomic_store( + T* const ptr, const T val, MemoryOrderRelaxed, MemoryScopeDevice) { +#pragma acc atomic write + *ptr = val; +} + +#pragma acc routine seq +template +std::enable_if_t, void> device_atomic_store( + T* const ptr, const T val, MemoryOrderRelease, MemoryScopeDevice) { + if (acc_on_device(acc_device_not_host)) { + printf( + "DESUL error in device_atomic_store(MemoryOrderRelease): Not supported atomic " + "operation in the OpenACC backend\n"); + } +#pragma acc atomic write + *ptr = val; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_load( + const T* const ptr, MemoryOrderRelaxed, MemoryScopeDevice) { + T retval; +#pragma acc atomic read + retval = *ptr; + return retval; +} + +#pragma acc routine seq +template +std::enable_if_t, T> device_atomic_load( + const T* const ptr, MemoryOrderAcquire, MemoryScopeDevice) { + if (acc_on_device(acc_device_not_host)) { + printf( + "DESUL error in device_atomic_load(MemoryOrderAcquire): Not supported atomic " + "operation in the OpenACC backend\n"); + } + T retval; +#pragma acc atomic read + retval = *ptr; + return retval; +} +// + +} // namespace Impl +} // namespace desul + +#endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Generic.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Generic.hpp index fef10222e3..fa71477c29 100644 --- a/lib/kokkos/tpls/desul/include/desul/atomics/Generic.hpp +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Generic.hpp @@ -18,11 +18,14 @@ SPDX-License-Identifier: (BSD-3-Clause) namespace desul { +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_thread_fence(MemoryOrder order, MemoryScope scope) { DESUL_IF_ON_DEVICE(return Impl::device_atomic_thread_fence(order, scope);) DESUL_IF_ON_HOST(return Impl::host_atomic_thread_fence(order, scope);) } + +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_exchange(T* dest, T val, MemoryOrder order, MemoryScope scope) { @@ -30,6 +33,7 @@ atomic_exchange(T* dest, T val, MemoryOrder order, MemoryScope scope) { DESUL_IF_ON_HOST(return Impl::host_atomic_exchange(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_compare_exchange(T* dest, T cmp, T val, MemoryOrder order, MemoryScope scope) { @@ -40,6 +44,7 @@ atomic_compare_exchange(T* dest, T cmp, T val, MemoryOrder order, MemoryScope sc } // Fetch_Oper atomics: return value before operation +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_add(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -47,6 +52,7 @@ atomic_fetch_add(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_add(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_sub(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -54,6 +60,7 @@ atomic_fetch_sub(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_sub(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_max(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -61,6 +68,7 @@ atomic_fetch_max(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_max(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_min(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -68,6 +76,7 @@ atomic_fetch_min(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_min(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_mul(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -75,6 +84,7 @@ atomic_fetch_mul(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_mul(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_div(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -82,6 +92,7 @@ atomic_fetch_div(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_div(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_mod(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -89,6 +100,7 @@ atomic_fetch_mod(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_mod(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_and(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -96,6 +108,7 @@ atomic_fetch_and(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_and(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_or(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -103,6 +116,7 @@ atomic_fetch_or(T* const dest, const T val, MemoryOrder order, MemoryScope scope DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_or(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_xor(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -110,6 +124,7 @@ atomic_fetch_xor(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_xor(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_nand(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -117,6 +132,7 @@ atomic_fetch_nand(T* const dest, const T val, MemoryOrder order, MemoryScope sco DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_nand(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_lshift(T* const dest, const unsigned int val, @@ -126,6 +142,7 @@ DESUL_INLINE_FUNCTION T atomic_fetch_lshift(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_lshift(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_rshift(T* const dest, const unsigned int val, @@ -136,6 +153,7 @@ DESUL_INLINE_FUNCTION T atomic_fetch_rshift(T* const dest, } // Oper Fetch atomics: return value after operation +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_add_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -143,6 +161,7 @@ atomic_add_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_add_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_sub_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -150,6 +169,7 @@ atomic_sub_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_sub_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_max_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -157,6 +177,7 @@ atomic_max_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_max_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_min_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -164,6 +185,7 @@ atomic_min_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_min_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_mul_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -171,6 +193,7 @@ atomic_mul_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_mul_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_div_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -178,6 +201,7 @@ atomic_div_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_div_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_mod_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -185,6 +209,7 @@ atomic_mod_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_mod_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_and_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -192,6 +217,7 @@ atomic_and_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_and_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_or_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -199,6 +225,7 @@ atomic_or_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope DESUL_IF_ON_HOST(return Impl::host_atomic_or_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_xor_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -206,6 +233,7 @@ atomic_xor_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scop DESUL_IF_ON_HOST(return Impl::host_atomic_xor_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_nand_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope scope) { @@ -213,6 +241,7 @@ atomic_nand_fetch(T* const dest, const T val, MemoryOrder order, MemoryScope sco DESUL_IF_ON_HOST(return Impl::host_atomic_nand_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_lshift_fetch(T* const dest, const unsigned int val, @@ -222,6 +251,7 @@ DESUL_INLINE_FUNCTION T atomic_lshift_fetch(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_lshift_fetch(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_rshift_fetch(T* const dest, const unsigned int val, @@ -233,6 +263,7 @@ DESUL_INLINE_FUNCTION T atomic_rshift_fetch(T* const dest, // Other atomics +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_load(const T* const dest, MemoryOrder order, @@ -241,6 +272,7 @@ DESUL_INLINE_FUNCTION T atomic_load(const T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_load(dest, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_store(T* const dest, const T val, @@ -250,6 +282,7 @@ DESUL_INLINE_FUNCTION void atomic_store(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_store(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_add(T* const dest, const T val, @@ -259,6 +292,7 @@ DESUL_INLINE_FUNCTION void atomic_add(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_add(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_sub(T* const dest, const T val, @@ -268,6 +302,7 @@ DESUL_INLINE_FUNCTION void atomic_sub(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_sub(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_mul(T* const dest, const T val, @@ -277,6 +312,7 @@ DESUL_INLINE_FUNCTION void atomic_mul(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_mul(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_div(T* const dest, const T val, @@ -286,6 +322,7 @@ DESUL_INLINE_FUNCTION void atomic_div(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_div(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_min(T* const dest, const T val, @@ -295,6 +332,7 @@ DESUL_INLINE_FUNCTION void atomic_min(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_min(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_max(T* const dest, const T val, @@ -304,6 +342,7 @@ DESUL_INLINE_FUNCTION void atomic_max(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_max(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_inc_fetch(T* const dest, MemoryOrder order, @@ -312,6 +351,7 @@ DESUL_INLINE_FUNCTION T atomic_inc_fetch(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_inc_fetch(dest, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_dec_fetch(T* const dest, MemoryOrder order, @@ -320,6 +360,7 @@ DESUL_INLINE_FUNCTION T atomic_dec_fetch(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_dec_fetch(dest, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_inc(T* const dest, MemoryOrder order, @@ -328,6 +369,7 @@ DESUL_INLINE_FUNCTION T atomic_fetch_inc(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_inc(dest, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_inc_mod(T* const dest, T val, MemoryOrder order, MemoryScope scope) { @@ -335,6 +377,7 @@ atomic_fetch_inc_mod(T* const dest, T val, MemoryOrder order, MemoryScope scope) DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_inc_mod(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_dec(T* const dest, MemoryOrder order, @@ -343,6 +386,7 @@ DESUL_INLINE_FUNCTION T atomic_fetch_dec(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_dec(dest, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION T atomic_fetch_dec_mod(T* const dest, T val, MemoryOrder order, MemoryScope scope) { @@ -350,6 +394,7 @@ atomic_fetch_dec_mod(T* const dest, T val, MemoryOrder order, MemoryScope scope) DESUL_IF_ON_HOST(return Impl::host_atomic_fetch_dec_mod(dest, val, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_inc(T* const dest, MemoryOrder order, @@ -358,6 +403,7 @@ DESUL_INLINE_FUNCTION void atomic_inc(T* const dest, DESUL_IF_ON_HOST(return Impl::host_atomic_inc(dest, order, scope);) } +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template DESUL_INLINE_FUNCTION void atomic_dec(T* const dest, MemoryOrder order, @@ -367,6 +413,7 @@ DESUL_INLINE_FUNCTION void atomic_dec(T* const dest, } // FIXME +DESUL_IMPL_ACC_ROUTINE_DIRECTIVE template SYCL_SPACE_ATOMIC_LOCKS_DEVICE; +#ifdef DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION +SYCL_EXTERNAL extern +#else +static +#endif + sycl_device_global + SYCL_SPACE_ATOMIC_LOCKS_DEVICE; -SYCL_EXTERNAL extern sycl_device_global SYCL_SPACE_ATOMIC_LOCKS_NODE; +#ifdef DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION +SYCL_EXTERNAL extern +#else +static +#endif + sycl_device_global + SYCL_SPACE_ATOMIC_LOCKS_NODE; #define SYCL_SPACE_ATOMIC_MASK 0x1FFFF @@ -128,6 +149,34 @@ inline void unlock_address_sycl(void* ptr, MemoryScopeNode) { lock_node_ref.exchange(0); } +#ifdef DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION +inline +#else +inline static +#endif + void + copy_sycl_lock_arrays_to_device(sycl::queue q) { + static bool once = [&q]() { +#ifdef SYCL_EXT_ONEAPI_DEVICE_GLOBAL + q.memcpy(SYCL_SPACE_ATOMIC_LOCKS_DEVICE, + &SYCL_SPACE_ATOMIC_LOCKS_DEVICE_h, + sizeof(int32_t*)); + q.memcpy(SYCL_SPACE_ATOMIC_LOCKS_NODE, + &SYCL_SPACE_ATOMIC_LOCKS_NODE_h, + sizeof(int32_t*)); +#else + auto device_ptr = SYCL_SPACE_ATOMIC_LOCKS_DEVICE_h; + auto node_ptr = SYCL_SPACE_ATOMIC_LOCKS_NODE_h; + q.single_task([=] { + SYCL_SPACE_ATOMIC_LOCKS_DEVICE.get() = device_ptr; + SYCL_SPACE_ATOMIC_LOCKS_NODE.get() = node_ptr; + }); +#endif + return true; + }(); + (void)once; +} + #else // not supported template @@ -155,7 +204,26 @@ inline bool lock_address_sycl(void*, MemoryScopeNode) { inline void unlock_address_sycl(void*, MemoryScopeDevice) { assert(false); } inline void unlock_address_sycl(void*, MemoryScopeNode) { assert(false); } + +#ifdef DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION +inline +#else +inline static +#endif + void + copy_sycl_lock_arrays_to_device(sycl::queue) { +} + #endif } // namespace Impl + +#ifdef DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION +inline void ensure_sycl_lock_arrays_on_device(sycl::queue) {} +#else +static inline void ensure_sycl_lock_arrays_on_device(sycl::queue q) { + Impl::copy_sycl_lock_arrays_to_device(q); +} +#endif + } // namespace desul #endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Based_Fetch_Op.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Based_Fetch_Op.hpp index cb97f4a906..b6a399100b 100644 --- a/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Based_Fetch_Op.hpp +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Based_Fetch_Op.hpp @@ -17,6 +17,9 @@ SPDX-License-Identifier: (BSD-3-Clause) #ifdef DESUL_HAVE_HIP_ATOMICS #include #endif +#ifdef DESUL_HAVE_OPENACC_ATOMICS +#include +#endif #ifdef DESUL_HAVE_SYCL_ATOMICS #include #endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Based_Fetch_Op_OpenACC.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Based_Fetch_Op_OpenACC.hpp new file mode 100644 index 0000000000..d4dd74588b --- /dev/null +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Based_Fetch_Op_OpenACC.hpp @@ -0,0 +1,81 @@ +/* +Copyright (c) 2019, Lawrence Livermore National Security, LLC +and DESUL project contributors. See the COPYRIGHT file for details. +Source: https://github.com/desul/desul + +SPDX-License-Identifier: (BSD-3-Clause) +*/ + +#ifndef DESUL_ATOMICS_LOCK_BASED_FETCH_OP_OPENACC_HPP_ +#define DESUL_ATOMICS_LOCK_BASED_FETCH_OP_OPENACC_HPP_ + +#include +#include +#include +#include + +namespace desul { +namespace Impl { + +template = 0> +inline T device_atomic_fetch_oper(const Oper& op, + T* const dest, + dont_deduce_this_parameter_t val, + MemoryOrder /*order*/, + MemoryScope scope) { + if (acc_on_device(acc_device_not_host)) { + printf( + "DESUL error in device_atomic_fetch_oper(): Not supported atomic operation in " + "the OpenACC backend\n"); + } + // Acquire a lock for the address + while (!lock_address((void*)dest, scope)) { + } + + device_atomic_thread_fence(MemoryOrderAcquire(), scope); + T return_val = *dest; + *dest = op.apply(return_val, val); + device_atomic_thread_fence(MemoryOrderRelease(), scope); + unlock_address((void*)dest, scope); + return return_val; +} + +template = 0> +inline T device_atomic_oper_fetch(const Oper& op, + T* const dest, + dont_deduce_this_parameter_t val, + MemoryOrder /*order*/, + MemoryScope scope) { + if (acc_on_device(acc_device_not_host)) { + printf( + "DESUL error in device_atomic_oper_fetch(): Not supported atomic operation in " + "the OpenACC backend\n"); + } + // Acquire a lock for the address + while (!lock_address((void*)dest, scope)) { + } + + device_atomic_thread_fence(MemoryOrderAcquire(), scope); + T return_val = op.apply(*dest, val); + *dest = return_val; + device_atomic_thread_fence(MemoryOrderRelease(), scope); + unlock_address((void*)dest, scope); + return return_val; +} + +} // namespace Impl +} // namespace desul + +#endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Macros.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Macros.hpp index 3a14b93d32..d11beb0c80 100644 --- a/lib/kokkos/tpls/desul/include/desul/atomics/Macros.hpp +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Macros.hpp @@ -57,6 +57,10 @@ SPDX-License-Identifier: (BSD-3-Clause) #define DESUL_HAVE_OPENMP_ATOMICS #endif +#if defined(DESUL_ATOMICS_ENABLE_OPENACC) +#define DESUL_HAVE_OPENACC_ATOMICS +#endif + // ONLY use GNUC atomics if not explicitly say to use OpenMP atomics #if !defined(DESUL_HAVE_OPENMP_ATOMICS) && defined(__GNUC__) #define DESUL_HAVE_GCC_ATOMICS @@ -123,6 +127,30 @@ static constexpr bool desul_impl_omp_on_host() { return false; } #endif #endif +#if defined(DESUL_HAVE_OPENACC_ATOMICS) +#include +#ifdef __NVCOMPILER +// FIXME_OPENACC We cannot determine in a constant expresion whether we are on host or +// on device with NVHPC. We use the device implementation on both sides. +#define DESUL_IF_ON_DEVICE(CODE) \ + { DESUL_IMPL_STRIP_PARENS(CODE) } +#define DESUL_IF_ON_HOST(CODE) \ + {} +#else +#define DESUL_IF_ON_DEVICE(CODE) \ + if constexpr (acc_on_device(acc_device_not_host)) { \ + DESUL_IMPL_STRIP_PARENS(CODE) \ + } +#define DESUL_IF_ON_HOST(CODE) \ + if constexpr (acc_on_device(acc_device_host)) { \ + DESUL_IMPL_STRIP_PARENS(CODE) \ + } +#endif +#define DESUL_IMPL_ACC_ROUTINE_DIRECTIVE _Pragma("acc routine seq") +#else +#define DESUL_IMPL_ACC_ROUTINE_DIRECTIVE +#endif + #if !defined(DESUL_IF_ON_HOST) && !defined(DESUL_IF_ON_DEVICE) #if (defined(DESUL_ATOMICS_ENABLE_CUDA) && defined(__CUDA_ARCH__)) || \ (defined(DESUL_ATOMICS_ENABLE_HIP) && defined(__HIP_DEVICE_COMPILE__)) || \ diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Thread_Fence.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Thread_Fence.hpp index 24078aae07..6a741f6d47 100644 --- a/lib/kokkos/tpls/desul/include/desul/atomics/Thread_Fence.hpp +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Thread_Fence.hpp @@ -26,6 +26,9 @@ SPDX-License-Identifier: (BSD-3-Clause) #ifdef DESUL_HAVE_OPENMP_ATOMICS #include #endif +#ifdef DESUL_HAVE_OPENACC_ATOMICS +#include +#endif #ifdef DESUL_HAVE_SYCL_ATOMICS #include #endif diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Thread_Fence_OpenACC.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Thread_Fence_OpenACC.hpp new file mode 100644 index 0000000000..a5c8aa1c8a --- /dev/null +++ b/lib/kokkos/tpls/desul/include/desul/atomics/Thread_Fence_OpenACC.hpp @@ -0,0 +1,25 @@ +/* +Copyright (c) 2019, Lawrence Livermore National Security, LLC +and DESUL project contributors. See the COPYRIGHT file for details. +Source: https://github.com/desul/desul + +SPDX-License-Identifier: (BSD-3-Clause) +*/ + +#ifndef DESUL_ATOMICS_THREAD_FENCE_OPENACC_HPP_ +#define DESUL_ATOMICS_THREAD_FENCE_OPENACC_HPP_ + +namespace desul { +namespace Impl { + +#pragma acc routine seq +template +void device_atomic_thread_fence(MemoryOrder, MemoryScope) { + // FIXME_OPENACC: The current OpenACC standard does not support explicit thread fence + // operations. +} + +} // namespace Impl +} // namespace desul + +#endif diff --git a/lib/kokkos/tpls/desul/src/Lock_Array_SYCL.cpp b/lib/kokkos/tpls/desul/src/Lock_Array_SYCL.cpp index 9e84c60e41..6660c76e11 100644 --- a/lib/kokkos/tpls/desul/src/Lock_Array_SYCL.cpp +++ b/lib/kokkos/tpls/desul/src/Lock_Array_SYCL.cpp @@ -14,10 +14,12 @@ SPDX-License-Identifier: (BSD-3-Clause) namespace desul::Impl { +#ifdef DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION SYCL_EXTERNAL sycl_device_global SYCL_SPACE_ATOMIC_LOCKS_DEVICE; SYCL_EXTERNAL sycl_device_global SYCL_SPACE_ATOMIC_LOCKS_NODE; +#endif int32_t* SYCL_SPACE_ATOMIC_LOCKS_DEVICE_h = nullptr; int32_t* SYCL_SPACE_ATOMIC_LOCKS_NODE_h = nullptr; @@ -31,19 +33,7 @@ void init_lock_arrays_sycl(sycl::queue q) { SYCL_SPACE_ATOMIC_LOCKS_NODE_h = sycl::malloc_host(SYCL_SPACE_ATOMIC_MASK + 1, q); - // FIXME_SYCL Once supported, the following should be replaced by - // q.memcpy(SYCL_SPACE_ATOMIC_LOCKS_DEVICE, - // &SYCL_SPACE_ATOMIC_LOCKS_DEVICE_h, - // sizeof(int32_t*)); - // q.memcpy(SYCL_SPACE_ATOMIC_LOCKS_NODE, - // &SYCL_SPACE_ATOMIC_LOCKS_NODE_h, - // sizeof(int32_t*)); - auto device_ptr = SYCL_SPACE_ATOMIC_LOCKS_DEVICE_h; - auto node_ptr = SYCL_SPACE_ATOMIC_LOCKS_NODE_h; - q.single_task([=] { - SYCL_SPACE_ATOMIC_LOCKS_DEVICE.get() = device_ptr; - SYCL_SPACE_ATOMIC_LOCKS_NODE.get() = node_ptr; - }); + copy_sycl_lock_arrays_to_device(q); q.memset(SYCL_SPACE_ATOMIC_LOCKS_DEVICE_h, 0, @@ -63,7 +53,10 @@ void finalize_lock_arrays_sycl(sycl::queue q) { sycl::free(SYCL_SPACE_ATOMIC_LOCKS_NODE_h, q); SYCL_SPACE_ATOMIC_LOCKS_DEVICE_h = nullptr; SYCL_SPACE_ATOMIC_LOCKS_NODE_h = nullptr; +#ifdef DESUL_ATOMICS_ENABLE_SYCL_SEPARABLE_COMPILATION + copy_sycl_lock_arrays_to_device(q); +#endif } -} // namespace desul::Impl +} // namespace desul::Impl #endif diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/compressed_pair.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/compressed_pair.hpp index ab1561bd47..25389a2fa5 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/compressed_pair.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/compressed_pair.hpp @@ -27,165 +27,165 @@ namespace detail { // For no unique address emulation, this is the case taken when neither are empty. // For real `[[no_unique_address]]`, this case is always taken. -template struct __compressed_pair { - _MDSPAN_NO_UNIQUE_ADDRESS _T __t_val; - _MDSPAN_NO_UNIQUE_ADDRESS _U __u_val; - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T &__first() noexcept { return __t_val; } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _T const &__first() const noexcept { - return __t_val; +template struct __compressed_pair { + _MDSPAN_NO_UNIQUE_ADDRESS _T1 __t1_val{}; + _MDSPAN_NO_UNIQUE_ADDRESS _T2 __t2_val{}; + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T1 &__first() noexcept { return __t1_val; } + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T1 const &__first() const noexcept { + return __t1_val; } - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _U &__second() noexcept { return __u_val; } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _U const &__second() const noexcept { - return __u_val; + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T2 &__second() noexcept { return __t2_val; } + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T2 const &__second() const noexcept { + return __t2_val; } MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair() noexcept = default; + constexpr __compressed_pair() = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair const &) noexcept = default; + constexpr __compressed_pair(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair &&) noexcept = default; + constexpr __compressed_pair(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair const &) noexcept = default; + operator=(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair &&) noexcept = default; + operator=(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - ~__compressed_pair() noexcept = default; - template - MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_TLike &&__t, _ULike &&__u) - : __t_val((_TLike &&) __t), __u_val((_ULike &&) __u) {} + ~__compressed_pair() = default; + template + MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_T1Like &&__t1, _T2Like &&__t2) + : __t1_val((_T1Like &&) __t1), __t2_val((_T2Like &&) __t2) {} }; #if !defined(_MDSPAN_USE_ATTRIBUTE_NO_UNIQUE_ADDRESS) // First empty. -template +template struct __compressed_pair< - _T, _U, - std::enable_if_t<_MDSPAN_TRAIT(std::is_empty, _T) && !_MDSPAN_TRAIT(std::is_empty, _U)>> - : private _T { - _U __u_val; - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T &__first() noexcept { - return *static_cast<_T *>(this); + _T1, _T2, + std::enable_if_t<_MDSPAN_TRAIT(std::is_empty, _T1) && !_MDSPAN_TRAIT(std::is_empty, _T2)>> + : private _T1 { + _T2 __t2_val{}; + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T1 &__first() noexcept { + return *static_cast<_T1 *>(this); } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _T const &__first() const noexcept { - return *static_cast<_T const *>(this); + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T1 const &__first() const noexcept { + return *static_cast<_T1 const *>(this); } - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _U &__second() noexcept { return __u_val; } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _U const &__second() const noexcept { - return __u_val; + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T2 &__second() noexcept { return __t2_val; } + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T2 const &__second() const noexcept { + return __t2_val; } MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair() noexcept = default; + constexpr __compressed_pair() = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair const &) noexcept = default; + constexpr __compressed_pair(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair &&) noexcept = default; + constexpr __compressed_pair(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair const &) noexcept = default; + operator=(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair &&) noexcept = default; + operator=(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - ~__compressed_pair() noexcept = default; - template - MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_TLike &&__t, _ULike &&__u) - : _T((_TLike &&) __t), __u_val((_ULike &&) __u) {} + ~__compressed_pair() = default; + template + MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_T1Like &&__t1, _T2Like &&__t2) + : _T1((_T1Like &&) __t1), __t2_val((_T2Like &&) __t2) {} }; // Second empty. -template +template struct __compressed_pair< - _T, _U, - std::enable_if_t> - : private _U { - _T __t_val; - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T &__first() noexcept { return __t_val; } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _T const &__first() const noexcept { - return __t_val; + _T1, _T2, + std::enable_if_t> + : private _T2 { + _T1 __t1_val{}; + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T1 &__first() noexcept { return __t1_val; } + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T1 const &__first() const noexcept { + return __t1_val; } - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _U &__second() noexcept { - return *static_cast<_U *>(this); + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T2 &__second() noexcept { + return *static_cast<_T2 *>(this); } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _U const &__second() const noexcept { - return *static_cast<_U const *>(this); + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T2 const &__second() const noexcept { + return *static_cast<_T2 const *>(this); } MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair() noexcept = default; + constexpr __compressed_pair() = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair const &) noexcept = default; + constexpr __compressed_pair(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair &&) noexcept = default; + constexpr __compressed_pair(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair const &) noexcept = default; + operator=(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair &&) noexcept = default; + operator=(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - ~__compressed_pair() noexcept = default; + ~__compressed_pair() = default; - template - MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_TLike &&__t, _ULike &&__u) - : _U((_ULike &&) __u), __t_val((_TLike &&) __t) {} + template + MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_T1Like &&__t1, _T2Like &&__t2) + : _T2((_T2Like &&) __t2), __t1_val((_T1Like &&) __t1) {} }; // Both empty. -template +template struct __compressed_pair< - _T, _U, - std::enable_if_t<_MDSPAN_TRAIT(std::is_empty, _T) && _MDSPAN_TRAIT(std::is_empty, _U)>> + _T1, _T2, + std::enable_if_t<_MDSPAN_TRAIT(std::is_empty, _T1) && _MDSPAN_TRAIT(std::is_empty, _T2)>> // We need to use the __no_unique_address_emulation wrapper here to avoid // base class ambiguities. #ifdef _MDSPAN_COMPILER_MSVC // MSVC doesn't allow you to access public static member functions of a type // when you *happen* to privately inherit from that type. - : protected __no_unique_address_emulation<_T, 0>, - protected __no_unique_address_emulation<_U, 1> + : protected __no_unique_address_emulation<_T1, 0>, + protected __no_unique_address_emulation<_T2, 1> #else - : private __no_unique_address_emulation<_T, 0>, - private __no_unique_address_emulation<_U, 1> + : private __no_unique_address_emulation<_T1, 0>, + private __no_unique_address_emulation<_T2, 1> #endif { - using __first_base_t = __no_unique_address_emulation<_T, 0>; - using __second_base_t = __no_unique_address_emulation<_U, 1>; + using __first_base_t = __no_unique_address_emulation<_T1, 0>; + using __second_base_t = __no_unique_address_emulation<_T2, 1>; - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T &__first() noexcept { + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T1 &__first() noexcept { return this->__first_base_t::__ref(); } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _T const &__first() const noexcept { + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T1 const &__first() const noexcept { return this->__first_base_t::__ref(); } - MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _U &__second() noexcept { + MDSPAN_FORCE_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 _T2 &__second() noexcept { return this->__second_base_t::__ref(); } - MDSPAN_FORCE_INLINE_FUNCTION constexpr _U const &__second() const noexcept { + MDSPAN_FORCE_INLINE_FUNCTION constexpr _T2 const &__second() const noexcept { return this->__second_base_t::__ref(); } MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair() noexcept = default; + constexpr __compressed_pair() = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair const &) noexcept = default; + constexpr __compressed_pair(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - constexpr __compressed_pair(__compressed_pair &&) noexcept = default; + constexpr __compressed_pair(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair const &) noexcept = default; + operator=(__compressed_pair const &) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED _MDSPAN_CONSTEXPR_14_DEFAULTED __compressed_pair & - operator=(__compressed_pair &&) noexcept = default; + operator=(__compressed_pair &&) = default; MDSPAN_INLINE_FUNCTION_DEFAULTED - ~__compressed_pair() noexcept = default; - template - MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_TLike &&__t, _ULike &&__u) noexcept - : __first_base_t(_T((_TLike &&) __t)), - __second_base_t(_U((_ULike &&) __u)) + ~__compressed_pair() = default; + template + MDSPAN_INLINE_FUNCTION constexpr __compressed_pair(_T1Like &&__t1, _T2Like &&__t2) noexcept + : __first_base_t(_T1((_T1Like &&) __t1)), + __second_base_t(_T2((_T2Like &&) __t2)) { } }; diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/config.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/config.hpp index d35e201ceb..8e42a37ba7 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/config.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/config.hpp @@ -35,10 +35,17 @@ #define MDSPAN_CXX_STD_14 201402L #define MDSPAN_CXX_STD_17 201703L #define MDSPAN_CXX_STD_20 202002L +// Note GCC has not updated this in version 13 +#ifdef __clang__ +#define MDSPAN_CXX_STD_23 202302L +#else +#define MDSPAN_CXX_STD_23 202100L +#endif #define MDSPAN_HAS_CXX_14 (_MDSPAN_CPLUSPLUS >= MDSPAN_CXX_STD_14) #define MDSPAN_HAS_CXX_17 (_MDSPAN_CPLUSPLUS >= MDSPAN_CXX_STD_17) #define MDSPAN_HAS_CXX_20 (_MDSPAN_CPLUSPLUS >= MDSPAN_CXX_STD_20) +#define MDSPAN_HAS_CXX_23 (_MDSPAN_CPLUSPLUS >= MDSPAN_CXX_STD_23) static_assert(_MDSPAN_CPLUSPLUS >= MDSPAN_CXX_STD_14, "mdspan requires C++14 or later."); @@ -224,7 +231,7 @@ static_assert(_MDSPAN_CPLUSPLUS >= MDSPAN_CXX_STD_14, "mdspan requires C++14 or #endif #ifndef MDSPAN_CONDITIONAL_EXPLICIT -# if MDSPAN_HAS_CXX_20 && !defined(_MDSPAN_COMPILER_MSVC) +# if MDSPAN_HAS_CXX_20 # define MDSPAN_CONDITIONAL_EXPLICIT(COND) explicit(COND) # else # define MDSPAN_CONDITIONAL_EXPLICIT(COND) diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/extents.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/extents.hpp index 0dd31c4cd0..9a28c3ed5c 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/extents.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/extents.hpp @@ -55,6 +55,14 @@ __check_compatible_extents( return {}; } +template +MDSPAN_INLINE_FUNCTION +static constexpr bool are_valid_indices() { + return + (std::is_convertible::value && ... && true) && + (std::is_nothrow_constructible::value && ... && true); +} + // ------------------------------------------------------------------ // ------------ static_array ---------------------------------------- // ------------------------------------------------------------------ @@ -140,7 +148,8 @@ struct index_sequence_scan_impl { template struct index_sequence_scan_impl { -#if defined(__NVCC__) || defined(__NVCOMPILER) +#if defined(__NVCC__) || defined(__NVCOMPILER) || \ + defined(_MDSPAN_COMPILER_INTEL) // NVCC warns about pointless comparison with 0 for R==0 and r being const // evaluatable and also 0. MDSPAN_INLINE_FUNCTION @@ -167,7 +176,7 @@ template <> struct index_sequence_scan_impl<0> { // all static values. template struct possibly_empty_array { - T vals[N]; + T vals[N]{}; MDSPAN_INLINE_FUNCTION constexpr T &operator[](size_t r) { return vals[r]; } MDSPAN_INLINE_FUNCTION @@ -251,12 +260,17 @@ public: #ifdef __cpp_lib_span MDSPAN_TEMPLATE_REQUIRES(class T, size_t N, - /* requires */ (N == m_size_dynamic)) + /* requires */ (N == m_size_dynamic && N > 0)) MDSPAN_INLINE_FUNCTION constexpr maybe_static_array(const std::span &vals) { for (size_t r = 0; r < N; r++) m_dyn_vals[r] = static_cast(vals[r]); } + + MDSPAN_TEMPLATE_REQUIRES(class T, size_t N, + /* requires */ (N == m_size_dynamic && N == 0)) + MDSPAN_INLINE_FUNCTION + constexpr maybe_static_array(const std::span &) : m_dyn_vals{} {} #endif // constructors from all values @@ -423,9 +437,9 @@ public: class OtherIndexType, size_t N, /* requires */ ( - _MDSPAN_TRAIT(std::is_convertible, OtherIndexType, index_type) && + _MDSPAN_TRAIT(std::is_convertible, const OtherIndexType&, index_type) && _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, - OtherIndexType) && + const OtherIndexType&) && (N == m_rank || N == m_rank_dynamic))) MDSPAN_INLINE_FUNCTION MDSPAN_CONDITIONAL_EXPLICIT(N != m_rank_dynamic) @@ -436,8 +450,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class OtherIndexType, size_t N, /* requires */ - (_MDSPAN_TRAIT(std::is_convertible, OtherIndexType, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, OtherIndexType) && + (_MDSPAN_TRAIT(std::is_convertible, const OtherIndexType&, index_type) && + _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, const OtherIndexType&) && (N == m_rank || N == m_rank_dynamic))) MDSPAN_INLINE_FUNCTION MDSPAN_CONDITIONAL_EXPLICIT(N != m_rank_dynamic) @@ -454,6 +468,7 @@ private: size_t DynCount, size_t R, class OtherExtents, class... DynamicValues, /* requires */ ((R < m_rank) && (static_extent(R) == dynamic_extent))) MDSPAN_INLINE_FUNCTION + constexpr vals_t __construct_vals_from_extents(std::integral_constant, std::integral_constant, const OtherExtents &exts, @@ -468,6 +483,7 @@ private: size_t DynCount, size_t R, class OtherExtents, class... DynamicValues, /* requires */ ((R < m_rank) && (static_extent(R) != dynamic_extent))) MDSPAN_INLINE_FUNCTION + constexpr vals_t __construct_vals_from_extents(std::integral_constant, std::integral_constant, const OtherExtents &exts, @@ -481,6 +497,7 @@ private: size_t DynCount, size_t R, class OtherExtents, class... DynamicValues, /* requires */ ((R == m_rank) && (DynCount == m_rank_dynamic))) MDSPAN_INLINE_FUNCTION + constexpr vals_t __construct_vals_from_extents(std::integral_constant, std::integral_constant, const OtherExtents &, @@ -491,17 +508,20 @@ private: public: // Converting constructor from other extents specializations - MDSPAN_TEMPLATE_REQUIRES( - class OtherIndexType, size_t... OtherExtents, - /* requires */ - ( - /* multi-stage check to protect from invalid pack expansion when sizes - don't match? */ - decltype(detail::__check_compatible_extents( - std::integral_constant{}, + MDSPAN_TEMPLATE_REQUIRES( + class OtherIndexType, size_t... OtherExtents, + /* requires */ + ( + /* multi-stage check to protect from invalid pack expansion when sizes + don't match? */ + decltype(detail::__check_compatible_extents( + // using: sizeof...(Extents) == sizeof...(OtherExtents) as the second argument fails with MSVC+NVCC with some obscure expansion error + // MSVC: 19.38.33133 NVCC: 12.0 + std::integral_constant::rank() == extents::rank()>{}, std::integer_sequence{}, - std::integer_sequence{}))::value)) + std::integer_sequence{}))::value + ) + ) MDSPAN_INLINE_FUNCTION MDSPAN_CONDITIONAL_EXPLICIT((((Extents != dynamic_extent) && (OtherExtents == dynamic_extent)) || @@ -518,10 +538,14 @@ public: MDSPAN_INLINE_FUNCTION friend constexpr bool operator==(const extents &lhs, const extents &rhs) noexcept { - bool value = true; - for (size_type r = 0; r < m_rank; r++) - value &= rhs.extent(r) == lhs.extent(r); - return value; + if constexpr (rank() != extents::rank()) { + return false; + } else { + using common_t = std::common_type_t; + for (size_type r = 0; r < m_rank; r++) + if(static_cast(rhs.extent(r)) != static_cast(lhs.extent(r))) return false; + } + return true; } #if !(MDSPAN_HAS_CXX_20) @@ -570,7 +594,7 @@ using dextents = typename detail::__make_dextents::type; template extents(IndexTypes...) -> extents; + ((void) sizeof(IndexTypes), ::MDSPAN_IMPL_STANDARD_NAMESPACE::dynamic_extent)...>; #endif // Helper type traits for identifying a class as extents. diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_left.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_left.hpp index af44494a98..83ed9ef7fe 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_left.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_left.hpp @@ -18,6 +18,9 @@ #include "macros.hpp" #include "trait_backports.hpp" #include "extents.hpp" +#include "../__p2642_bits/layout_padded_fwd.hpp" +#include +#include namespace MDSPAN_IMPL_STANDARD_NAMESPACE { @@ -108,6 +111,36 @@ class layout_left::mapping { */ } +#if MDSPAN_HAS_CXX_17 + /** + * Converting constructor from `layout_left_padded::mapping`. + * + * This overload participates in overload resolution only if _Mapping is a layout_left_padded mapping and + * extents_type is constructible from _Mapping::extents_type. + * + * \note There is currently a difference from p2642r2, where this function is specified as taking + * `layout_left_padded< padding_value >::mapping< Extents>`. However, this makes `padding_value` non-deducible. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + MDSPAN_IMPL_PROPOSED_NAMESPACE::detail::is_layout_left_padded_mapping<_Mapping>::value + && std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((!std::is_convertible_v)) + mapping(const _Mapping& __other) noexcept + : __extents(__other.extents()) + { + MDSPAN_IMPL_PROPOSED_NAMESPACE::detail:: + check_padded_layout_converting_constructor_mandates(); + MDSPAN_IMPL_PROPOSED_NAMESPACE::detail:: + check_padded_layout_converting_constructor_preconditions< + extents_type>(__other); + } +#endif + MDSPAN_TEMPLATE_REQUIRES( class OtherExtents, /* requires */ ( @@ -124,13 +157,14 @@ class layout_left::mapping { * other.required_span_size() is a representable value of type index_type */ #if !defined(_MDSPAN_HAS_CUDA) && !defined(_MDSPAN_HAS_HIP) && !defined(NDEBUG) - index_type stride = 1; - for(rank_type r=0; r<__extents.rank(); r++) { - if(stride != static_cast(other.stride(r))) { - // Note this throw will lead to a terminate if triggered since this function is marked noexcept - throw std::runtime_error("Assigning layout_stride to layout_left with invalid strides."); + if constexpr (extents_type::rank() > 0) { + index_type stride = 1; + using common_t = std::common_type_t; + for(rank_type r=0; r<__extents.rank(); r++) { + if(static_cast(stride) != static_cast(other.stride(r))) + std::abort(); // ("Assigning layout_stride to layout_left with invalid strides."); + stride *= __extents.extent(r); } - stride *= __extents.extent(r); } #endif } @@ -155,10 +189,7 @@ class layout_left::mapping { class... Indices, /* requires */ ( (sizeof...(Indices) == extents_type::rank()) && - _MDSPAN_FOLD_AND( - (_MDSPAN_TRAIT(std::is_convertible, Indices, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, Indices)) - ) + (detail::are_valid_indices()) ) ) _MDSPAN_HOST_DEVICE @@ -172,9 +203,9 @@ class layout_left::mapping { MDSPAN_INLINE_FUNCTION static constexpr bool is_always_exhaustive() noexcept { return true; } MDSPAN_INLINE_FUNCTION static constexpr bool is_always_strided() noexcept { return true; } - MDSPAN_INLINE_FUNCTION constexpr bool is_unique() const noexcept { return true; } - MDSPAN_INLINE_FUNCTION constexpr bool is_exhaustive() const noexcept { return true; } - MDSPAN_INLINE_FUNCTION constexpr bool is_strided() const noexcept { return true; } + MDSPAN_INLINE_FUNCTION static constexpr bool is_unique() noexcept { return true; } + MDSPAN_INLINE_FUNCTION static constexpr bool is_exhaustive() noexcept { return true; } + MDSPAN_INLINE_FUNCTION static constexpr bool is_strided() noexcept { return true; } MDSPAN_INLINE_FUNCTION constexpr index_type stride(rank_type i) const noexcept @@ -187,7 +218,10 @@ class layout_left::mapping { return value; } - template + MDSPAN_TEMPLATE_REQUIRES( + class OtherExtents, + /* requires */ ( Extents::rank() == OtherExtents::rank()) + ) MDSPAN_INLINE_FUNCTION friend constexpr bool operator==(mapping const& lhs, mapping const& rhs) noexcept { return lhs.extents() == rhs.extents(); @@ -195,7 +229,10 @@ class layout_left::mapping { // In C++ 20 the not equal exists if equal is found #if !(MDSPAN_HAS_CXX_20) - template + MDSPAN_TEMPLATE_REQUIRES( + class OtherExtents, + /* requires */ ( Extents::rank() == OtherExtents::rank()) + ) MDSPAN_INLINE_FUNCTION friend constexpr bool operator!=(mapping const& lhs, mapping const& rhs) noexcept { return lhs.extents() != rhs.extents(); @@ -215,6 +252,17 @@ class layout_left::mapping { private: _MDSPAN_NO_UNIQUE_ADDRESS extents_type __extents{}; + // [mdspan.submdspan.mapping], submdspan mapping specialization + template + MDSPAN_INLINE_FUNCTION + constexpr auto submdspan_mapping_impl( + SliceSpecifiers... slices) const; + + template + friend constexpr auto submdspan_mapping( + const mapping& src, SliceSpecifiers... slices) { + return src.submdspan_mapping_impl(slices...); + } }; diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_right.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_right.hpp index a058648420..3d3927df7b 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_right.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_right.hpp @@ -20,6 +20,7 @@ #include "extents.hpp" #include #include "layout_stride.hpp" +#include "../__p2642_bits/layout_padded_fwd.hpp" namespace MDSPAN_IMPL_STANDARD_NAMESPACE { @@ -113,6 +114,34 @@ class layout_right::mapping { */ } + /** + * Converting constructor from `layout_right_padded::mapping`. + * + * This overload participates in overload resolution only if _Mapping is a layout_right_padded mapping and + * extents_type is constructible from _Mapping::extents_type. + * + * \note There is currently a difference from p2642r2, where this function is specified as taking + * `layout_right_padded< padding_value >::mapping< Extents>`. However, this makes `padding_value` non-deducible. + */ +#if MDSPAN_HAS_CXX_17 + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + MDSPAN_IMPL_PROPOSED_NAMESPACE::detail::is_layout_right_padded_mapping<_Mapping>::value + && std::is_constructible_v)) + MDSPAN_CONDITIONAL_EXPLICIT((!std::is_convertible_v)) + mapping(const _Mapping &__other) noexcept + : __extents(__other.extents()) + { + MDSPAN_IMPL_PROPOSED_NAMESPACE::detail:: + check_padded_layout_converting_constructor_mandates(); + MDSPAN_IMPL_PROPOSED_NAMESPACE::detail:: + check_padded_layout_converting_constructor_preconditions< + extents_type>(__other); + } +#endif + MDSPAN_TEMPLATE_REQUIRES( class OtherExtents, /* requires */ ( @@ -129,13 +158,14 @@ class layout_right::mapping { * other.required_span_size() is a representable value of type index_type */ #if !defined(_MDSPAN_HAS_CUDA) && !defined(_MDSPAN_HAS_HIP) && !defined(NDEBUG) - index_type stride = 1; - for(rank_type r=__extents.rank(); r>0; r--) { - if(stride != static_cast(other.stride(r-1))) { - // Note this throw will lead to a terminate if triggered since this function is marked noexcept - throw std::runtime_error("Assigning layout_stride to layout_right with invalid strides."); + if constexpr (extents_type::rank() > 0) { + index_type stride = 1; + using common_t = std::common_type_t; + for(rank_type r=__extents.rank(); r>0; r--) { + if(static_cast(stride) != static_cast(other.stride(r-1))) + std::abort(); // ("Assigning layout_stride to layout_right with invalid strides."); + stride *= __extents.extent(r-1); } - stride *= __extents.extent(r-1); } #endif } @@ -157,13 +187,10 @@ class layout_right::mapping { //-------------------------------------------------------------------------------- MDSPAN_TEMPLATE_REQUIRES( - class... Indices, + class ... Indices, /* requires */ ( - (sizeof...(Indices) == extents_type::rank()) && - _MDSPAN_FOLD_AND( - (_MDSPAN_TRAIT(std::is_convertible, Indices, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, Indices)) - ) + (sizeof...(Indices) == extents_type::rank()) && + (detail::are_valid_indices()) ) ) _MDSPAN_HOST_DEVICE @@ -174,9 +201,9 @@ class layout_right::mapping { MDSPAN_INLINE_FUNCTION static constexpr bool is_always_unique() noexcept { return true; } MDSPAN_INLINE_FUNCTION static constexpr bool is_always_exhaustive() noexcept { return true; } MDSPAN_INLINE_FUNCTION static constexpr bool is_always_strided() noexcept { return true; } - MDSPAN_INLINE_FUNCTION constexpr bool is_unique() const noexcept { return true; } - MDSPAN_INLINE_FUNCTION constexpr bool is_exhaustive() const noexcept { return true; } - MDSPAN_INLINE_FUNCTION constexpr bool is_strided() const noexcept { return true; } + MDSPAN_INLINE_FUNCTION static constexpr bool is_unique() noexcept { return true; } + MDSPAN_INLINE_FUNCTION static constexpr bool is_exhaustive() noexcept { return true; } + MDSPAN_INLINE_FUNCTION static constexpr bool is_strided() noexcept { return true; } MDSPAN_INLINE_FUNCTION constexpr index_type stride(rank_type i) const noexcept @@ -189,7 +216,10 @@ class layout_right::mapping { return value; } - template + MDSPAN_TEMPLATE_REQUIRES( + class OtherExtents, + /* requires */ ( Extents::rank() == OtherExtents::rank()) + ) MDSPAN_INLINE_FUNCTION friend constexpr bool operator==(mapping const& lhs, mapping const& rhs) noexcept { return lhs.extents() == rhs.extents(); @@ -197,7 +227,10 @@ class layout_right::mapping { // In C++ 20 the not equal exists if equal is found #if !(MDSPAN_HAS_CXX_20) - template + MDSPAN_TEMPLATE_REQUIRES( + class OtherExtents, + /* requires */ (Extents::rank() == OtherExtents::rank()) + ) MDSPAN_INLINE_FUNCTION friend constexpr bool operator!=(mapping const& lhs, mapping const& rhs) noexcept { return lhs.extents() != rhs.extents(); @@ -217,6 +250,17 @@ class layout_right::mapping { private: _MDSPAN_NO_UNIQUE_ADDRESS extents_type __extents{}; + // [mdspan.submdspan.mapping], submdspan mapping specialization + template + MDSPAN_INLINE_FUNCTION + constexpr auto submdspan_mapping_impl( + SliceSpecifiers... slices) const; + + template + friend constexpr auto submdspan_mapping( + const mapping& src, SliceSpecifiers... slices) { + return src.submdspan_mapping_impl(slices...); + } }; } // end namespace MDSPAN_IMPL_STANDARD_NAMESPACE diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_stride.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_stride.hpp index 030a494529..15ad577d14 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_stride.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/layout_stride.hpp @@ -88,7 +88,7 @@ struct layout_stride { : private detail::__no_unique_address_emulation< detail::__compressed_pair< Extents, - std::array + detail::possibly_empty_array > > #endif @@ -109,7 +109,7 @@ struct layout_stride { //---------------------------------------------------------------------------- - using __strides_storage_t = std::array; + using __strides_storage_t = detail::possibly_empty_array; using __member_pair_t = detail::__compressed_pair; #if defined(_MDSPAN_USE_ATTRIBUTE_NO_UNIQUE_ADDRESS) @@ -158,14 +158,16 @@ struct layout_stride { template MDSPAN_INLINE_FUNCTION static constexpr bool _eq_impl(mapping const& self, mapping const& other) noexcept { - return _MDSPAN_FOLD_AND((self.stride(Idxs) == other.stride(Idxs)) /* && ... */) - && _MDSPAN_FOLD_AND((self.extents().extent(Idxs) == other.extents().extent(Idxs)) /* || ... */); + using common_t = std::common_type_t; + return _MDSPAN_FOLD_AND((static_cast(self.stride(Idxs)) == static_cast(other.stride(Idxs))) /* && ... */) + && _MDSPAN_FOLD_AND((static_cast(self.extents().extent(Idxs)) == static_cast(other.extents().extent(Idxs))) /* || ... */); } template MDSPAN_INLINE_FUNCTION static constexpr bool _not_eq_impl(mapping const& self, mapping const& other) noexcept { - return _MDSPAN_FOLD_OR((self.stride(Idxs) != other.stride(Idxs)) /* || ... */) - || _MDSPAN_FOLD_OR((self.extents().extent(Idxs) != other.extents().extent(Idxs)) /* || ... */); + using common_t = std::common_type_t; + return _MDSPAN_FOLD_OR((static_cast(self.stride(Idxs)) != static_cast(other.stride(Idxs))) /* || ... */) + || _MDSPAN_FOLD_OR((static_cast(self.extents().extent(Idxs)) != static_cast(other.extents().extent(Idxs))) /* || ... */); } template @@ -205,6 +207,11 @@ struct layout_stride { } #endif + MDSPAN_INLINE_FUNCTION + static constexpr std::array return_strides(const __strides_storage_t& s) { + return std::array{s[Idxs]...}; + } + template MDSPAN_INLINE_FUNCTION static constexpr size_t __return_zero() { return 0; } @@ -218,6 +225,21 @@ struct layout_stride { // Can't use defaulted parameter in the __deduction_workaround template because of a bug in MSVC warning C4348. using __impl = __deduction_workaround>; + static constexpr __strides_storage_t strides_storage(std::true_type) { + __strides_storage_t s{}; + + extents_type e; + index_type stride = 1; + for(int r = static_cast(extents_type::rank() - 1); r >= 0; r--) { + s[r] = stride; + stride *= e.extent(r); + } + + return s; + } + static constexpr __strides_storage_t strides_storage(std::false_type) { + return {}; + } //---------------------------------------------------------------------------- @@ -233,7 +255,21 @@ struct layout_stride { //-------------------------------------------------------------------------------- - MDSPAN_INLINE_FUNCTION_DEFAULTED constexpr mapping() noexcept = default; + MDSPAN_INLINE_FUNCTION_DEFAULTED constexpr mapping() noexcept +#if defined(_MDSPAN_USE_ATTRIBUTE_NO_UNIQUE_ADDRESS) + : __members{ +#else + : __base_t(__base_t{__member_pair_t( +#endif + extents_type(), + __strides_storage_t(strides_storage(std::integral_constant 0)>{})) +#if defined(_MDSPAN_USE_ATTRIBUTE_NO_UNIQUE_ADDRESS) + } +#else + )}) +#endif + {} + MDSPAN_INLINE_FUNCTION_DEFAULTED constexpr mapping(mapping const&) noexcept = default; MDSPAN_TEMPLATE_REQUIRES( @@ -332,10 +368,10 @@ struct layout_stride { ) #endif MDSPAN_CONDITIONAL_EXPLICIT( - (!std::is_convertible::value) && - (detail::__is_mapping_of || - detail::__is_mapping_of || - detail::__is_mapping_of) + !(std::is_convertible::value && + (detail::__is_mapping_of || + detail::__is_mapping_of || + detail::__is_mapping_of)) ) // needs two () due to comma MDSPAN_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 mapping(StridedLayoutMapping const& other) noexcept // NOLINT(google-explicit-constructor) @@ -374,7 +410,7 @@ struct layout_stride { MDSPAN_INLINE_FUNCTION constexpr std::array< index_type, extents_type::rank() > strides() const noexcept { - return __strides_storage(); + return __impl::return_strides(__strides_storage()); } MDSPAN_INLINE_FUNCTION @@ -393,8 +429,7 @@ struct layout_stride { class... Indices, /* requires */ ( sizeof...(Indices) == Extents::rank() && - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_convertible, Indices, index_type) /*&& ...*/ ) && - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, Indices) /*&& ...*/) + (detail::are_valid_indices()) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -410,17 +445,37 @@ struct layout_stride { MDSPAN_INLINE_FUNCTION static constexpr bool is_unique() noexcept { return true; } MDSPAN_INLINE_FUNCTION _MDSPAN_CONSTEXPR_14 bool is_exhaustive() const noexcept { - return required_span_size() == __get_size(extents(), std::make_index_sequence()); + if constexpr (extents_type::rank() == 0) + return true; + else { + index_type span_size = required_span_size(); + if (span_size == static_cast(0)) { + if constexpr (extents_type::rank() == 1) { + return stride(0) == 1; + } else { + rank_type r_largest = 0; + for (rank_type r = 1; r < extents_type::rank(); r++) { + if (stride(r) > stride(r_largest)) { + r_largest = r; + } + } + for (rank_type r = 0; r < extents_type::rank(); r++) { + if (extents().extent(r) == 0 && r != r_largest) { + return false; + } + } + return true; + } + } else { + return required_span_size() == __get_size(extents(), std::make_index_sequence()); + } + } } MDSPAN_INLINE_FUNCTION static constexpr bool is_strided() noexcept { return true; } MDSPAN_INLINE_FUNCTION - constexpr index_type stride(rank_type r) const noexcept -#if MDSPAN_HAS_CXX_20 - requires ( Extents::rank() > 0 ) -#endif - { + constexpr index_type stride(rank_type r) const noexcept { return __strides_storage()[r]; } @@ -444,10 +499,13 @@ struct layout_stride { MDSPAN_INLINE_FUNCTION friend constexpr bool operator==(const mapping& x, const StridedLayoutMapping& y) noexcept { bool strides_match = true; - for(rank_type r = 0; r < extents_type::rank(); r++) - strides_match = strides_match && (x.stride(r) == y.stride(r)); + if constexpr (extents_type::rank() > 0) { + using common_t = std::common_type_t; + for(rank_type r = 0; r < extents_type::rank(); r++) + strides_match = strides_match && (static_cast(x.stride(r)) == static_cast(y.stride(r))); + } return (x.extents() == y.extents()) && - (__impl::__OFFSET(y)== static_cast(0)) && + (__impl::__OFFSET(y) == static_cast(0)) && strides_match; } @@ -489,6 +547,17 @@ struct layout_stride { } #endif + // [mdspan.submdspan.mapping], submdspan mapping specialization + template + MDSPAN_INLINE_FUNCTION + constexpr auto submdspan_mapping_impl( + SliceSpecifiers... slices) const; + + template + friend constexpr auto submdspan_mapping( + const mapping& src, SliceSpecifiers... slices) { + return src.submdspan_mapping_impl(slices...); + } }; }; diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/mdspan.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/mdspan.hpp index 6febe30021..d6ec49e65b 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/mdspan.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p0009_bits/mdspan.hpp @@ -55,6 +55,13 @@ private: ReferenceType __callop(mdspan const& __self, const std::array& indices) noexcept { return __self.__accessor_ref().access(__self.__ptr_ref(), __self.__mapping_ref()(indices[Idxs]...)); } +#ifdef __cpp_lib_span + template + MDSPAN_FORCE_INLINE_FUNCTION static constexpr + ReferenceType __callop(mdspan const& __self, const std::span& indices) noexcept { + return __self.__accessor_ref().access(__self.__ptr_ref(), __self.__mapping_ref()(indices[Idxs]...)); + } +#endif }; public: @@ -109,9 +116,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class... SizeTypes, /* requires */ ( - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_convertible, SizeTypes, index_type) /* && ... */) && - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeTypes) /* && ... */) && ((sizeof...(SizeTypes) == rank()) || (sizeof...(SizeTypes) == rank_dynamic())) && + (detail::are_valid_indices()) && _MDSPAN_TRAIT(std::is_constructible, mapping_type, extents_type) && _MDSPAN_TRAIT(std::is_default_constructible, accessor_type) ) @@ -125,8 +131,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class SizeType, size_t N, /* requires */ ( - _MDSPAN_TRAIT(std::is_convertible, SizeType, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeType) && + _MDSPAN_TRAIT(std::is_convertible, const SizeType&, index_type) && + _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, const SizeType&) && ((N == rank()) || (N == rank_dynamic())) && _MDSPAN_TRAIT(std::is_constructible, mapping_type, extents_type) && _MDSPAN_TRAIT(std::is_default_constructible, accessor_type) @@ -142,8 +148,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class SizeType, size_t N, /* requires */ ( - _MDSPAN_TRAIT(std::is_convertible, SizeType, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeType) && + _MDSPAN_TRAIT(std::is_convertible, const SizeType&, index_type) && + _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, const SizeType&) && ((N == rank()) || (N == rank_dynamic())) && _MDSPAN_TRAIT(std::is_constructible, mapping_type, extents_type) && _MDSPAN_TRAIT(std::is_default_constructible, accessor_type) @@ -160,7 +166,7 @@ public: (MDSPAN_INLINE_FUNCTION constexpr), mdspan, (data_handle_type p, const extents_type& exts), , /* requires */ (_MDSPAN_TRAIT(std::is_default_constructible, accessor_type) && - _MDSPAN_TRAIT(std::is_constructible, mapping_type, extents_type)) + _MDSPAN_TRAIT(std::is_constructible, mapping_type, const extents_type&)) ) : __members(std::move(p), __map_acc_pair_t(mapping_type(exts), accessor_type())) { } @@ -179,10 +185,14 @@ public: MDSPAN_TEMPLATE_REQUIRES( class OtherElementType, class OtherExtents, class OtherLayoutPolicy, class OtherAccessor, /* requires */ ( - _MDSPAN_TRAIT(std::is_constructible, mapping_type, typename OtherLayoutPolicy::template mapping) && - _MDSPAN_TRAIT(std::is_constructible, accessor_type, OtherAccessor) + _MDSPAN_TRAIT(std::is_constructible, mapping_type, const typename OtherLayoutPolicy::template mapping&) && + _MDSPAN_TRAIT(std::is_constructible, accessor_type, const OtherAccessor&) ) ) + MDSPAN_CONDITIONAL_EXPLICIT( + !_MDSPAN_TRAIT(std::is_convertible, const typename OtherLayoutPolicy::template mapping&, mapping_type) || + !_MDSPAN_TRAIT(std::is_convertible, const OtherAccessor&, accessor_type) + ) MDSPAN_INLINE_FUNCTION constexpr mdspan(const mdspan& other) : __members(other.__ptr_ref(), __map_acc_pair_t(other.__mapping_ref(), other.__accessor_ref())) @@ -226,8 +236,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class SizeType, /* requires */ ( - _MDSPAN_TRAIT(std::is_convertible, SizeType, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeType) + _MDSPAN_TRAIT(std::is_convertible, const SizeType&, index_type) && + _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, const SizeType&) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -240,8 +250,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class SizeType, /* requires */ ( - _MDSPAN_TRAIT(std::is_convertible, SizeType, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeType) + _MDSPAN_TRAIT(std::is_convertible, const SizeType&, index_type) && + _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, const SizeType&) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -271,9 +281,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class... SizeTypes, /* requires */ ( - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_convertible, SizeTypes, index_type) /* && ... */) && - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeTypes) /* && ... */) && - extents_type::rank() == sizeof...(SizeTypes) + extents_type::rank() == sizeof...(SizeTypes) && + (detail::are_valid_indices()) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -285,8 +294,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class SizeType, /* requires */ ( - _MDSPAN_TRAIT(std::is_convertible, SizeType, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeType) + _MDSPAN_TRAIT(std::is_convertible, const SizeType&, index_type) && + _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, const SizeType&) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -299,8 +308,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class SizeType, /* requires */ ( - _MDSPAN_TRAIT(std::is_convertible, SizeType, index_type) && - _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, SizeType) + _MDSPAN_TRAIT(std::is_convertible, const SizeType&, index_type) && + _MDSPAN_TRAIT(std::is_nothrow_constructible, index_type, const SizeType&) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -311,7 +320,7 @@ public: #endif // __cpp_lib_span #endif // MDSPAN_USE_PAREN_OPERATOR - MDSPAN_INLINE_FUNCTION constexpr size_t size() const noexcept { + MDSPAN_INLINE_FUNCTION constexpr size_type size() const noexcept { return __impl::__size(*this); }; @@ -346,13 +355,13 @@ public: //-------------------------------------------------------------------------------- // [mdspan.basic.obs], mdspan observers of the mapping - MDSPAN_INLINE_FUNCTION static constexpr bool is_always_unique() noexcept { return mapping_type::is_always_unique(); }; - MDSPAN_INLINE_FUNCTION static constexpr bool is_always_exhaustive() noexcept { return mapping_type::is_always_exhaustive(); }; - MDSPAN_INLINE_FUNCTION static constexpr bool is_always_strided() noexcept { return mapping_type::is_always_strided(); }; + MDSPAN_INLINE_FUNCTION static constexpr bool is_always_unique() { return mapping_type::is_always_unique(); }; + MDSPAN_INLINE_FUNCTION static constexpr bool is_always_exhaustive() { return mapping_type::is_always_exhaustive(); }; + MDSPAN_INLINE_FUNCTION static constexpr bool is_always_strided() { return mapping_type::is_always_strided(); }; - MDSPAN_INLINE_FUNCTION constexpr bool is_unique() const noexcept { return __mapping_ref().is_unique(); }; - MDSPAN_INLINE_FUNCTION constexpr bool is_exhaustive() const noexcept { return __mapping_ref().is_exhaustive(); }; - MDSPAN_INLINE_FUNCTION constexpr bool is_strided() const noexcept { return __mapping_ref().is_strided(); }; + MDSPAN_INLINE_FUNCTION constexpr bool is_unique() const { return __mapping_ref().is_unique(); }; + MDSPAN_INLINE_FUNCTION constexpr bool is_exhaustive() const { return __mapping_ref().is_exhaustive(); }; + MDSPAN_INLINE_FUNCTION constexpr bool is_strided() const { return __mapping_ref().is_strided(); }; MDSPAN_INLINE_FUNCTION constexpr index_type stride(size_t r) const { return __mapping_ref().stride(r); }; private: @@ -374,7 +383,7 @@ private: #if defined(_MDSPAN_USE_CLASS_TEMPLATE_ARGUMENT_DEDUCTION) MDSPAN_TEMPLATE_REQUIRES( class ElementType, class... SizeTypes, - /* requires */ _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_integral, SizeTypes) /* && ... */) && + /* requires */ _MDSPAN_FOLD_AND(_MDSPAN_TRAIT(std::is_convertible, SizeTypes, size_t) /* && ... */) && (sizeof...(SizeTypes) > 0) ) MDSPAN_DEDUCTION_GUIDE explicit mdspan(ElementType*, SizeTypes...) diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p1684_bits/mdarray.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p1684_bits/mdarray.hpp index 3950273a83..bdc5925f71 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p1684_bits/mdarray.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p1684_bits/mdarray.hpp @@ -103,8 +103,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class... SizeTypes, /* requires */ ( - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT( std::is_convertible, SizeTypes, index_type) /* && ... */) && - _MDSPAN_TRAIT( std::is_constructible, extents_type, SizeTypes...) && + (::MDSPAN_IMPL_STANDARD_NAMESPACE::detail::are_valid_indices()) && + _MDSPAN_TRAIT( std::is_constructible, extents_type, SizeTypes...) && _MDSPAN_TRAIT( std::is_constructible, mapping_type, extents_type) && (_MDSPAN_TRAIT( std::is_constructible, container_type, size_t) || container_is_array::value) && @@ -133,61 +133,29 @@ public: ) : map_(m), ctr_(container_is_array::construct(map_)) { } - // Constructors from container - MDSPAN_TEMPLATE_REQUIRES( - class... SizeTypes, - /* requires */ ( - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT( std::is_convertible, SizeTypes, index_type) /* && ... */) && - _MDSPAN_TRAIT( std::is_constructible, extents_type, SizeTypes...) && - _MDSPAN_TRAIT( std::is_constructible, mapping_type, extents_type) - ) - ) - MDSPAN_INLINE_FUNCTION - explicit constexpr mdarray(const container_type& ctr, SizeTypes... dynamic_extents) - : map_(extents_type(dynamic_extents...)), ctr_(ctr) - { assert(ctr.size() >= static_cast(map_.required_span_size())); } - - MDSPAN_FUNCTION_REQUIRES( (MDSPAN_INLINE_FUNCTION constexpr), - mdarray, (const container_type& ctr, const extents_type& exts), , + mdarray, (const extents_type& exts, const container_type& ctr), , /* requires */ (_MDSPAN_TRAIT( std::is_constructible, mapping_type, extents_type)) ) : map_(exts), ctr_(ctr) { assert(ctr.size() >= static_cast(map_.required_span_size())); } - constexpr mdarray(const container_type& ctr, const mapping_type& m) + constexpr mdarray(const mapping_type& m, const container_type& ctr) : map_(m), ctr_(ctr) { assert(ctr.size() >= static_cast(map_.required_span_size())); } - - // Constructors from container - MDSPAN_TEMPLATE_REQUIRES( - class... SizeTypes, - /* requires */ ( - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT( std::is_convertible, SizeTypes, index_type) /* && ... */) && - _MDSPAN_TRAIT( std::is_constructible, extents_type, SizeTypes...) && - _MDSPAN_TRAIT( std::is_constructible, mapping_type, extents_type) - ) - ) - MDSPAN_INLINE_FUNCTION - explicit constexpr mdarray(container_type&& ctr, SizeTypes... dynamic_extents) - : map_(extents_type(dynamic_extents...)), ctr_(std::move(ctr)) - { assert(ctr_.size() >= static_cast(map_.required_span_size())); } - - MDSPAN_FUNCTION_REQUIRES( (MDSPAN_INLINE_FUNCTION constexpr), - mdarray, (container_type&& ctr, const extents_type& exts), , + mdarray, (const extents_type& exts, container_type&& ctr), , /* requires */ (_MDSPAN_TRAIT( std::is_constructible, mapping_type, extents_type)) ) : map_(exts), ctr_(std::move(ctr)) { assert(ctr_.size() >= static_cast(map_.required_span_size())); } - constexpr mdarray(container_type&& ctr, const mapping_type& m) + constexpr mdarray(const mapping_type& m, container_type&& ctr) : map_(m), ctr_(std::move(ctr)) { assert(ctr_.size() >= static_cast(map_.required_span_size())); } - MDSPAN_TEMPLATE_REQUIRES( class OtherElementType, class OtherExtents, class OtherLayoutPolicy, class OtherContainer, /* requires */ ( @@ -229,7 +197,7 @@ public: _MDSPAN_TRAIT( std::is_constructible, mapping_type, extents_type)) ) MDSPAN_INLINE_FUNCTION - constexpr mdarray(const container_type& ctr, const extents_type& exts, const Alloc& a) + constexpr mdarray(const extents_type& exts, const container_type& ctr, const Alloc& a) : map_(exts), ctr_(ctr, a) { assert(ctr_.size() >= static_cast(map_.required_span_size())); } @@ -238,7 +206,7 @@ public: /* requires */ (_MDSPAN_TRAIT( std::is_constructible, container_type, size_t, Alloc)) ) MDSPAN_INLINE_FUNCTION - constexpr mdarray(const container_type& ctr, const mapping_type& map, const Alloc& a) + constexpr mdarray(const mapping_type& map, const container_type& ctr, const Alloc& a) : map_(map), ctr_(ctr, a) { assert(ctr_.size() >= static_cast(map_.required_span_size())); } @@ -248,7 +216,7 @@ public: _MDSPAN_TRAIT( std::is_constructible, mapping_type, extents_type)) ) MDSPAN_INLINE_FUNCTION - constexpr mdarray(container_type&& ctr, const extents_type& exts, const Alloc& a) + constexpr mdarray(const extents_type& exts, container_type&& ctr, const Alloc& a) : map_(exts), ctr_(std::move(ctr), a) { assert(ctr_.size() >= static_cast(map_.required_span_size())); } @@ -257,7 +225,7 @@ public: /* requires */ (_MDSPAN_TRAIT( std::is_constructible, container_type, size_t, Alloc)) ) MDSPAN_INLINE_FUNCTION - constexpr mdarray(container_type&& ctr, const mapping_type& map, const Alloc& a) + constexpr mdarray(const mapping_type& map, container_type&& ctr, const Alloc& a) : map_(map), ctr_(std::move(ctr), a) { assert(ctr_.size() >= map_.required_span_size()); } @@ -344,8 +312,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class... SizeTypes, /* requires */ ( - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT( std::is_convertible, SizeTypes, index_type) /* && ... */) && - extents_type::rank() == sizeof...(SizeTypes) + (::MDSPAN_IMPL_STANDARD_NAMESPACE::detail::are_valid_indices()) && + extents_type::rank() == sizeof...(SizeTypes) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -356,8 +324,8 @@ public: MDSPAN_TEMPLATE_REQUIRES( class... SizeTypes, /* requires */ ( - _MDSPAN_FOLD_AND(_MDSPAN_TRAIT( std::is_convertible, SizeTypes, index_type) /* && ... */) && - extents_type::rank() == sizeof...(SizeTypes) + (::MDSPAN_IMPL_STANDARD_NAMESPACE::detail::are_valid_indices()) && + extents_type::rank() == sizeof...(SizeTypes) ) ) MDSPAN_FORCE_INLINE_FUNCTION @@ -433,8 +401,9 @@ public: class OtherElementType, class OtherExtents, class OtherLayoutType, class OtherAccessorType, /* requires */ ( - _MDSPAN_TRAIT(std::is_assignable, mdspan_type, - mdspan) + _MDSPAN_TRAIT(std::is_assignable, + mdspan, + mdspan_type) ) ) constexpr operator mdspan () { @@ -445,8 +414,9 @@ public: class OtherElementType, class OtherExtents, class OtherLayoutType, class OtherAccessorType, /* requires */ ( - _MDSPAN_TRAIT(std::is_assignable, const_mdspan_type, - mdspan) + _MDSPAN_TRAIT(std::is_assignable, + mdspan, + const_mdspan_type) ) ) constexpr operator mdspan () const { diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/strided_slice.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/strided_slice.hpp index 58f38620ba..89ba8202fb 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/strided_slice.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/strided_slice.hpp @@ -20,7 +20,6 @@ #include namespace MDSPAN_IMPL_STANDARD_NAMESPACE { -namespace MDSPAN_IMPL_PROPOSED_NAMESPACE { namespace { template @@ -29,6 +28,7 @@ namespace { template struct __mdspan_is_integral_constant>: std::true_type {}; } + // Slice Specifier allowing for strides and compile time extent template struct strided_slice { @@ -36,14 +36,13 @@ struct strided_slice { using extent_type = ExtentType; using stride_type = StrideType; - OffsetType offset; - ExtentType extent; - StrideType stride; + _MDSPAN_NO_UNIQUE_ADDRESS OffsetType offset{}; + _MDSPAN_NO_UNIQUE_ADDRESS ExtentType extent{}; + _MDSPAN_NO_UNIQUE_ADDRESS StrideType stride{}; static_assert(std::is_integral_v || __mdspan_is_integral_constant::value); static_assert(std::is_integral_v || __mdspan_is_integral_constant::value); static_assert(std::is_integral_v || __mdspan_is_integral_constant::value); }; -} // MDSPAN_IMPL_PROPOSED_NAMESPACE } // MDSPAN_IMPL_STANDARD_NAMESPACE diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan.hpp index b9672b7f9a..abddd0b59d 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan.hpp @@ -20,23 +20,21 @@ #include "submdspan_mapping.hpp" namespace MDSPAN_IMPL_STANDARD_NAMESPACE { -namespace MDSPAN_IMPL_PROPOSED_NAMESPACE { template MDSPAN_INLINE_FUNCTION constexpr auto submdspan(const mdspan &src, SliceSpecifiers... slices) { - const auto sub_mapping_offset = submdspan_mapping(src.mapping(), slices...); + const auto sub_submdspan_mapping_result = submdspan_mapping(src.mapping(), slices...); // NVCC has a problem with the deduction so lets figure out the type - using sub_mapping_t = std::remove_cv_t; + using sub_mapping_t = std::remove_cv_t; using sub_extents_t = typename sub_mapping_t::extents_type; using sub_layout_t = typename sub_mapping_t::layout_type; using sub_accessor_t = typename AccessorPolicy::offset_policy; return mdspan( - src.accessor().offset(src.data_handle(), sub_mapping_offset.offset), - sub_mapping_offset.mapping, + src.accessor().offset(src.data_handle(), sub_submdspan_mapping_result.offset), + sub_submdspan_mapping_result.mapping, sub_accessor_t(src.accessor())); } -} // namespace MDSPAN_IMPL_PROPOSED_NAMESPACE } // namespace MDSPAN_IMPL_STANDARD_NAMESPACE diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_extents.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_extents.hpp index f56ce023f1..c3b2f78fb9 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_extents.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_extents.hpp @@ -20,7 +20,6 @@ #include "strided_slice.hpp" namespace MDSPAN_IMPL_STANDARD_NAMESPACE { -namespace MDSPAN_IMPL_PROPOSED_NAMESPACE { namespace detail { // Mapping from submapping ranks to srcmapping ranks @@ -319,5 +318,4 @@ constexpr auto submdspan_extents(const extents &src_exts, return detail::extents_constructor::next_extent( src_exts, slices...); } -} // namespace MDSPAN_IMPL_PROPOSED_NAMESPACE } // namespace MDSPAN_IMPL_STANDARD_NAMESPACE diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_mapping.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_mapping.hpp index 48778d57e7..ca6948c9a9 100644 --- a/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_mapping.hpp +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p2630_bits/submdspan_mapping.hpp @@ -22,21 +22,15 @@ #include // index_sequence namespace MDSPAN_IMPL_STANDARD_NAMESPACE { -namespace MDSPAN_IMPL_PROPOSED_NAMESPACE { //****************************************** // Return type of submdspan_mapping overloads //****************************************** -template struct mapping_offset { - Mapping mapping; +template struct submdspan_mapping_result { + _MDSPAN_NO_UNIQUE_ADDRESS LayoutMapping mapping{}; size_t offset; }; -} // namespace MDSPAN_IMPL_PROPOSED_NAMESPACE namespace detail { -using MDSPAN_IMPL_PROPOSED_NAMESPACE::detail::first_of; -using MDSPAN_IMPL_PROPOSED_NAMESPACE::detail::stride_of; -using MDSPAN_IMPL_PROPOSED_NAMESPACE::detail::inv_map_rank; - // constructs sub strides template MDSPAN_INLINE_FUNCTION @@ -98,17 +92,15 @@ struct preserve_layout_left_mapping, SubRank, #pragma diag_suppress = implicit_return_from_non_void_function #endif // Actual submdspan mapping call -template +template +template MDSPAN_INLINE_FUNCTION constexpr auto -submdspan_mapping(const layout_left::mapping &src_mapping, - SliceSpecifiers... slices) { - using MDSPAN_IMPL_PROPOSED_NAMESPACE::submdspan_extents; - using MDSPAN_IMPL_PROPOSED_NAMESPACE::mapping_offset; +layout_left::mapping::submdspan_mapping_impl(SliceSpecifiers... slices) const { // compute sub extents using src_ext_t = Extents; - auto dst_ext = submdspan_extents(src_mapping.extents(), slices...); + auto dst_ext = submdspan_extents(extents(), slices...); using dst_ext_t = decltype(dst_ext); // figure out sub layout type @@ -121,18 +113,18 @@ submdspan_mapping(const layout_left::mapping &src_mapping, if constexpr (std::is_same_v) { // layout_left case - return mapping_offset{ + return submdspan_mapping_result{ dst_mapping_t(dst_ext), - static_cast(src_mapping(detail::first_of(slices)...))}; + static_cast(this->operator()(detail::first_of(slices)...))}; } else { // layout_stride case auto inv_map = detail::inv_map_rank( std::integral_constant(), std::index_sequence<>(), slices...); - return mapping_offset{ + return submdspan_mapping_result{ dst_mapping_t(dst_ext, detail::construct_sub_strides( - src_mapping, inv_map, + *this, inv_map, // HIP needs deduction guides to have markups so we need to be explicit // NVCC 11.0 has a bug with deduction guide here, tested that 11.2 does not have the issue #if defined(_MDSPAN_HAS_HIP) || (defined(__NVCC__) && (__CUDACC_VER_MAJOR__ * 100 + __CUDACC_VER_MINOR__ * 10) < 1120) @@ -140,7 +132,7 @@ submdspan_mapping(const layout_left::mapping &src_mapping, #else std::tuple{detail::stride_of(slices)...})), #endif - static_cast(src_mapping(detail::first_of(slices)...))}; + static_cast(this->operator()(detail::first_of(slices)...))}; } #if defined(__NVCC__) && !defined(__CUDA_ARCH__) && defined(__GNUC__) __builtin_unreachable(); @@ -207,17 +199,15 @@ struct preserve_layout_right_mapping, SubRank, #pragma diagnostic push #pragma diag_suppress = implicit_return_from_non_void_function #endif -template +template +template MDSPAN_INLINE_FUNCTION constexpr auto -submdspan_mapping(const layout_right::mapping &src_mapping, - SliceSpecifiers... slices) { - using MDSPAN_IMPL_PROPOSED_NAMESPACE::submdspan_extents; - using MDSPAN_IMPL_PROPOSED_NAMESPACE::mapping_offset; - +layout_right::mapping::submdspan_mapping_impl( + SliceSpecifiers... slices) const { // get sub extents using src_ext_t = Extents; - auto dst_ext = submdspan_extents(src_mapping.extents(), slices...); + auto dst_ext = submdspan_extents(extents(), slices...); using dst_ext_t = decltype(dst_ext); // determine new layout type @@ -230,18 +220,18 @@ submdspan_mapping(const layout_right::mapping &src_mapping, if constexpr (std::is_same_v) { // layout_right case - return mapping_offset{ + return submdspan_mapping_result{ dst_mapping_t(dst_ext), - static_cast(src_mapping(detail::first_of(slices)...))}; + static_cast(this->operator()(detail::first_of(slices)...))}; } else { // layout_stride case auto inv_map = detail::inv_map_rank( std::integral_constant(), std::index_sequence<>(), slices...); - return mapping_offset{ + return submdspan_mapping_result{ dst_mapping_t(dst_ext, detail::construct_sub_strides( - src_mapping, inv_map, + *this, inv_map, // HIP needs deduction guides to have markups so we need to be explicit // NVCC 11.0 has a bug with deduction guide here, tested that 11.2 does not have the issue #if defined(_MDSPAN_HAS_HIP) || (defined(__NVCC__) && (__CUDACC_VER_MAJOR__ * 100 + __CUDACC_VER_MINOR__ * 10) < 1120) @@ -249,7 +239,7 @@ submdspan_mapping(const layout_right::mapping &src_mapping, #else std::tuple{detail::stride_of(slices)...})), #endif - static_cast(src_mapping(detail::first_of(slices)...))}; + static_cast(this->operator()(detail::first_of(slices)...))}; } #if defined(__NVCC__) && !defined(__CUDA_ARCH__) && defined(__GNUC__) __builtin_unreachable(); @@ -270,23 +260,22 @@ submdspan_mapping(const layout_right::mapping &src_mapping, //********************************** // layout_stride submdspan_mapping //********************************* -template +template +template MDSPAN_INLINE_FUNCTION constexpr auto -submdspan_mapping(const layout_stride::mapping &src_mapping, - SliceSpecifiers... slices) { - using MDSPAN_IMPL_PROPOSED_NAMESPACE::submdspan_extents; - using MDSPAN_IMPL_PROPOSED_NAMESPACE::mapping_offset; - auto dst_ext = submdspan_extents(src_mapping.extents(), slices...); +layout_stride::mapping::submdspan_mapping_impl( + SliceSpecifiers... slices) const { + auto dst_ext = submdspan_extents(extents(), slices...); using dst_ext_t = decltype(dst_ext); auto inv_map = detail::inv_map_rank( std::integral_constant(), std::index_sequence<>(), slices...); using dst_mapping_t = typename layout_stride::template mapping; - return mapping_offset{ + return submdspan_mapping_result{ dst_mapping_t(dst_ext, detail::construct_sub_strides( - src_mapping, inv_map, + *this, inv_map, // HIP needs deduction guides to have markups so we need to be explicit // NVCC 11.0 has a bug with deduction guide here, tested that 11.2 does not have the issue #if defined(_MDSPAN_HAS_HIP) || (defined(__NVCC__) && (__CUDACC_VER_MAJOR__ * 100 + __CUDACC_VER_MINOR__ * 10) < 1120) @@ -294,6 +283,7 @@ submdspan_mapping(const layout_stride::mapping &src_mapping, #else std::tuple(detail::stride_of(slices)...))), #endif - static_cast(src_mapping(detail::first_of(slices)...))}; + static_cast(this->operator()(detail::first_of(slices)...))}; } + } // namespace MDSPAN_IMPL_STANDARD_NAMESPACE diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p2642_bits/layout_padded.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p2642_bits/layout_padded.hpp new file mode 100644 index 0000000000..a801486792 --- /dev/null +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p2642_bits/layout_padded.hpp @@ -0,0 +1,793 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER +#pragma once + +#include +#include "layout_padded_fwd.hpp" +#include "../__p0009_bits/dynamic_extent.hpp" +#include "../__p0009_bits/extents.hpp" +#include "../__p0009_bits/mdspan.hpp" +#include "../__p0009_bits/layout_left.hpp" +#include "../__p0009_bits/layout_right.hpp" +#include "../__p0009_bits/layout_stride.hpp" + +namespace MDSPAN_IMPL_STANDARD_NAMESPACE { +namespace MDSPAN_IMPL_PROPOSED_NAMESPACE { + +namespace detail { +template +MDSPAN_INLINE_FUNCTION +constexpr _T +find_next_multiple(_T alignment, _T offset) +{ + if ( alignment == 0 ) { + return _T(0); + } else { + return ( ( offset + alignment - 1 ) / alignment) * alignment; + } +} + +template +MDSPAN_INLINE_FUNCTION constexpr size_t get_actual_static_padding_value() { + constexpr auto rank = _ExtentsType::rank(); + + if constexpr (rank <= typename _ExtentsType::rank_type(1)) { + return 0; + } else if constexpr (_PaddingValue != dynamic_extent && + _ExtentsType::static_extent(_ExtentToPadIdx) != + dynamic_extent) { + static_assert( + (_PaddingValue != 0) || + (_ExtentsType::static_extent(_ExtentToPadIdx) == 0), + "padding stride can be 0 only if " + "extents_type::static_extent(extent-to-pad) is 0 or dynamic_extent"); + return find_next_multiple(_PaddingValue, + _ExtentsType::static_extent(_ExtentToPadIdx)); + } else { + return dynamic_extent; + } +} + +template +struct static_array_type_for_padded_extent +{ + static constexpr size_t padding_value = _PaddingValue; + using index_type = typename _Extents::index_type; + using extents_type = _Extents; + using type = ::MDSPAN_IMPL_STANDARD_NAMESPACE::detail::maybe_static_array< + index_type, size_t, dynamic_extent, + detail::get_actual_static_padding_value()>; +}; + +template +struct static_array_type_for_padded_extent<_PaddingValue, _Extents, + _ExtentToPadIdx, Rank, std::enable_if_t> { + using index_type = typename _Extents::index_type; + using extents_type = _Extents; + using type = + ::MDSPAN_IMPL_STANDARD_NAMESPACE::detail::maybe_static_array< + index_type, size_t, dynamic_extent, 0>; +}; + +template +struct padded_extent { + static constexpr size_t padding_value = _PaddingValue; + using index_type = typename _Extents::index_type; + using extents_type = _Extents; + using static_array_type = typename static_array_type_for_padded_extent< + padding_value, _Extents, _ExtentToPadIdx, _Extents::rank()>::type; + + static constexpr auto static_value() { return static_array_type::static_value(0); } + + MDSPAN_INLINE_FUNCTION + static constexpr static_array_type + init_padding(const _Extents &exts) { + if constexpr ((_Extents::rank() > 1) && (padding_value == dynamic_extent)) { + return {exts.extent(_ExtentToPadIdx)}; + } else { + return init_padding(exts, padding_value); + } + } + + MDSPAN_INLINE_FUNCTION static constexpr static_array_type + init_padding([[maybe_unused]] const _Extents &exts, + [[maybe_unused]] index_type pv) { + if constexpr (_Extents::rank() > 1) { + return {find_next_multiple(pv, + exts.extent(_ExtentToPadIdx))}; + } else { + return {}; + } + } + + template + MDSPAN_INLINE_FUNCTION static constexpr static_array_type + init_padding([[maybe_unused]] const _Mapping &other_mapping, + std::integral_constant) { + if constexpr (_Extents::rank() > 1) { + return {other_mapping.stride(_PaddingStrideIdx)}; + } else { + return {}; + } + } +}; +} // namespace detail + +template +template +class layout_left_padded::mapping { +public: + static constexpr size_t padding_value = PaddingValue; + + using extents_type = Extents; + using index_type = typename extents_type::index_type; + using size_type = typename extents_type::size_type; + using rank_type = typename extents_type::rank_type; + using layout_type = layout_left_padded; + +#ifndef MDSPAN_INTERNAL_TEST +private: +#endif // MDSPAN_INTERNAL_TEST + + static constexpr rank_type padded_stride_idx = detail::layout_padded_constants::padded_stride_idx; + static constexpr rank_type extent_to_pad_idx = detail::layout_padded_constants::extent_to_pad_idx; + + static_assert((padding_value != 0) + || (extents_type::static_extent(extent_to_pad_idx) == 0) + || (extents_type::static_extent(extent_to_pad_idx) == dynamic_extent), + "out of bounds access for rank 0"); + + using padded_stride_type = detail::padded_extent< padding_value, extents_type, extent_to_pad_idx >; + + static constexpr size_t static_padding_stride = padded_stride_type::static_value(); + + typename padded_stride_type::static_array_type padded_stride = {}; + extents_type exts = {}; + + constexpr index_type compute_offset(std::index_sequence<>) const { + return 0; + } + + template + constexpr index_type compute_offset(std::index_sequence, + IndexOffset index_offset) const { + return index_offset; + } + + template + constexpr index_type compute_offset(std::index_sequence, + IndexOffsets... index_offsets) const { + index_type indices[] = {static_cast(index_offsets)...}; + // self-recursive fold trick from + // https://github.com/llvm/llvm-project/blob/96e1914aa2e6d8966acbfbe2f4d184201f1aa318/libcxx/include/mdspan/layout_left.h#L144 + index_type res = 0; + ((res = indices[extents_type::rank() - 1 - Ranks] + + ((extents_type::rank() - 1 - Ranks) == extent_to_pad_idx + ? padded_stride.value(0) + : exts.extent(extents_type::rank() - 1 - Ranks)) * + res), + ...); + return res; + } + +public: +#if !MDSPAN_HAS_CXX_20 + MDSPAN_INLINE_FUNCTION_DEFAULTED + constexpr mapping() + : mapping(extents_type{}) + {} +#else + MDSPAN_INLINE_FUNCTION_DEFAULTED + constexpr mapping() + requires(static_padding_stride != dynamic_extent) = default; + + MDSPAN_INLINE_FUNCTION + constexpr mapping() + requires(static_padding_stride == dynamic_extent) + : mapping(extents_type{}) + {} +#endif + + MDSPAN_INLINE_FUNCTION_DEFAULTED constexpr mapping(const mapping&) noexcept = default; + MDSPAN_INLINE_FUNCTION_DEFAULTED mapping& operator=(const mapping&) noexcept = default; + + /** + * Initializes the mapping with the given extents. + * + * \param ext the given extents + */ + MDSPAN_INLINE_FUNCTION + constexpr mapping(const extents_type& ext) + : padded_stride(padded_stride_type::init_padding(ext)), exts(ext) + {} + + /** + * Initializes the mapping with the given extents and the specified padding value. + * + * This overload participates in overload resolution only if `is_convertible_v` + * is `true` and `is_nothrow_constructible_v` is `true` + * + * \param ext the given extents + * \param padding_value the padding value + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Size, + /* requires */ ( + std::is_convertible_v<_Size, index_type> + && std::is_nothrow_constructible_v + ) + ) + MDSPAN_INLINE_FUNCTION + constexpr mapping(const extents_type &ext, _Size dynamic_padding_value) + : padded_stride(padded_stride_type::init_padding(ext, dynamic_padding_value)), exts(ext) + { + assert((padding_value == dynamic_extent) || (static_cast(padding_value) == static_cast(dynamic_padding_value))); + } + + /** + * Converting constructor from `layout_left::mapping`. + * + * This overload participates in overload resolution only if `is_constructible_v` is true. + * If `OtherExtents::rank() > 1` then one of `padding_value`, `static_extent(0)`, or `OtherExtents::static_extent(0)` must be `dynamic_extent`; + * otherwise, `OtherExtents::static_extent(0)` must be equal to the least multiple of `padding_value` greater than or equal to `extents_type::static_extent(0)` + */ + MDSPAN_TEMPLATE_REQUIRES( + class _OtherExtents, + /* requires */ ( + std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((!std::is_convertible_v<_OtherExtents, extents_type>)) + constexpr mapping(const layout_left::mapping<_OtherExtents> &other_mapping) + : padded_stride(padded_stride_type::init_padding(other_mapping, std::integral_constant{})), + exts(other_mapping.extents()) + { + static_assert((_OtherExtents::rank() > 1) || (static_padding_stride != dynamic_extent) || (_OtherExtents::static_extent(extent_to_pad_idx) != dynamic_extent) + || (static_padding_stride == _OtherExtents::static_extent(extent_to_pad_idx))); + } + + /** + * Converting constructor from `layout_stride::mapping`. + * + * This overload participates in overload resolution only if `is_constructible_v` is true + */ + MDSPAN_TEMPLATE_REQUIRES( + class _OtherExtents, + /* requires */ ( + std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((extents_type::rank() > 0)) + constexpr mapping(const layout_stride::mapping<_OtherExtents> &other_mapping) + : padded_stride(padded_stride_type::init_padding(other_mapping, std::integral_constant{})), + exts(other_mapping.extents()) + { + } + + /** + * Converting constructor from `layout_left_padded::mapping`. + * + * This overload participates in overload resolution only if `is_constructible_v` is true. + * Either `padding_value` or `OtherPaddingStride` must be `std::dynamic_extent`, or `padding_value == OtherPaddingStride`. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_left_padded_mapping<_Mapping>::value + && std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((extents_type::rank() > 1 && (padding_value == dynamic_extent || _Mapping::padding_value == dynamic_extent))) + constexpr + mapping(const _Mapping &other_mapping) + : padded_stride(padded_stride_type::init_padding(other_mapping, std::integral_constant{})), + exts(other_mapping.extents()) + { + static_assert(padding_value == dynamic_extent || + _Mapping::padding_value == dynamic_extent || + padding_value == _Mapping::padding_value); + } + + /** + * Converting constructor from `layout_right_padded::mapping`. + * + * This overload participates in overload resolution only if `extents_type::rank()` is 0 or 1 and `is_constructible_v` is `true`. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_right_padded_mapping<_Mapping>::value + && extents_type::rank() <= 1 + && std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((!std::is_convertible_v)) + constexpr + mapping(const _Mapping &other_mapping) noexcept + : padded_stride(padded_stride_type::init_padding(other_mapping.extents(), other_mapping.extents().extent(extent_to_pad_idx))), + exts(other_mapping.extents()) + {} + + constexpr const extents_type &extents() const noexcept + { + return exts; + } + + constexpr std::array + strides() const noexcept + { + if constexpr ( extents_type::rank() == 0 ) { + return {}; + } else if constexpr ( extents_type::rank() == 1 ) { + return {1}; + } else { + index_type value = 1; + std::array s{}; + s[extent_to_pad_idx] = value; + value *= padded_stride.value(0); + for (rank_type r = extent_to_pad_idx + 1; r < extents_type::rank() - 1; ++r) + { + s[r] = value; + value *= exts.extent(r); + } + s[extents_type::rank() - 1] = value; + return s; + } + } + + constexpr index_type + required_span_size() const noexcept + { + if constexpr ( extents_type::rank() == 0 ) { + return 1; + } else if constexpr ( extents_type::rank() == 1 ) { + return exts.extent(0); + } else { + index_type value = padded_stride.value(0); + for (rank_type r = 1; r < extents_type::rank(); ++r) { + value *= exts.extent(r); + } + return value; + } + } + + /** + * Return the mapping given the provided indices per rank. + * + * This overload participates in overload resolution only if: + * - `sizeof...(Indices) == extents_type::rank()`, + * - `(is_convertible_v && ...) is true`, and + * - (is_nothrow_constructible_v && ...) is true. + */ + MDSPAN_TEMPLATE_REQUIRES( + class... _Indices, + /* requires */ ( + sizeof...(_Indices) == extents_type::rank() && + (::MDSPAN_IMPL_STANDARD_NAMESPACE::detail::are_valid_indices()) + ) + ) + constexpr size_t operator()(_Indices... idxs) const noexcept + { + return compute_offset(std::index_sequence_for<_Indices...>{}, idxs...); + } + + static constexpr bool is_always_unique() noexcept { return true; } + static constexpr bool is_always_exhaustive() noexcept + { + return (extents_type::rank() <= rank_type(1)) + || (extents_type::static_extent(extent_to_pad_idx) != dynamic_extent + && extents_type::static_extent(extent_to_pad_idx) == padded_stride_type::static_value()); + } + static constexpr bool is_always_strided() noexcept { return true; } + + static constexpr bool is_unique() noexcept { return true; } + constexpr bool is_exhaustive() const noexcept + { + return (extents_type::rank() < 2) + || (exts.extent(extent_to_pad_idx) == padded_stride.value(0)); + } + static constexpr bool is_strided() noexcept { return true; } + + constexpr index_type stride(rank_type r) const noexcept + { + assert(r < extents_type::rank()); + if(r == 0) return index_type(1); + + index_type value = padded_stride.value(0); + for (rank_type k = 1; k < r; k++) value *= exts.extent(k); + + return value; + } + + /** + * Equality operator between `layout_left_padded`s + * + * This overload only participates in overload resolution if `OtherExtents::rank() == extents_type::rank()`. + * + * \note There is currently a difference from p2642r2, where this function is specified as taking + * `layout_left_padded< padding_value >::mapping< Extents>`. However, this makes `padding_value` non-deducible. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_left_padded_mapping<_Mapping>::value + && (_Mapping::extents_type::rank() == extents_type::rank()) + ) + ) + friend constexpr bool operator==(const mapping &left, const _Mapping &right) noexcept + { + // Workaround for some compilers not short-circuiting properly with compile-time checks + // i.e. we can't access stride(_padding_stride_idx) of a rank 0 mapping + bool strides_equal = true; + if constexpr (extents_type::rank() > rank_type(1)) + { + strides_equal = left.stride(padded_stride_idx) == right.stride(padded_stride_idx); + } + return (left.extents() == right.extents()) && strides_equal; + } + +#if !MDSPAN_HAS_CXX_20 + /** + * Inequality operator between `layout_left_padded`s + * + * This overload only participates in overload resolution if `OtherExtents::rank() == extents_type::rank()`. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_left_padded_mapping<_Mapping>::value + && (_Mapping::extents_type::rank() == extents_type::rank()) + ) + ) + friend constexpr bool operator!=(const mapping &left, const _Mapping &right) noexcept + { + return !(left == right); + } +#endif +}; + +template +template +class layout_right_padded::mapping { +public: + static constexpr size_t padding_value = PaddingValue; + + using extents_type = Extents; + using index_type = typename extents_type::index_type; + using size_type = typename extents_type::size_type; + using rank_type = typename extents_type::rank_type; + using layout_type = layout_right_padded; + +#ifndef MDSPAN_INTERNAL_TEST + private: +#endif // MDSPAN_INTERNAL_TEST + + static constexpr rank_type padded_stride_idx = detail::layout_padded_constants::padded_stride_idx; + static constexpr rank_type extent_to_pad_idx = detail::layout_padded_constants::extent_to_pad_idx; + + static_assert((padding_value != 0) + || (extents_type::static_extent(extent_to_pad_idx) == 0) + || (extents_type::static_extent(extent_to_pad_idx) == dynamic_extent), + "if padding stride is 0, static_extent(extent-to-pad-rank) must also be 0 or dynamic_extent"); + + using padded_stride_type = detail::padded_extent< padding_value, extents_type, extent_to_pad_idx >; + static constexpr size_t static_padding_stride = padded_stride_type::static_value(); + + typename padded_stride_type::static_array_type padded_stride = {}; + extents_type exts = {}; + + constexpr index_type compute_offset(std::index_sequence<>) const { + return 0; + } + + template + constexpr index_type compute_offset(std::index_sequence, + IndexOffset index_offset) const { + return index_offset; + } + + template + constexpr index_type compute_offset(std::index_sequence, + IndexOffsets... index_offsets) const { + // self-recursive fold trick from + // https://github.com/llvm/llvm-project/blob/4d9771741d40cc9cfcccb6b033f43689d36b705a/libcxx/include/mdspan/layout_right.h#L141 + index_type res = 0; + ((res = static_cast(index_offsets) + + (Ranks == extent_to_pad_idx ? padded_stride.value(0) + : exts.extent(Ranks)) * + res), + ...); + return res; + } + +public: +#if !MDSPAN_HAS_CXX_20 + MDSPAN_INLINE_FUNCTION_DEFAULTED + constexpr mapping() + : mapping(extents_type{}) + {} +#else + MDSPAN_INLINE_FUNCTION_DEFAULTED + constexpr mapping() + requires(static_padding_stride != dynamic_extent) = default; + + MDSPAN_INLINE_FUNCTION + constexpr mapping() + requires(static_padding_stride == dynamic_extent) + : mapping(extents_type{}) + {} +#endif + + MDSPAN_INLINE_FUNCTION_DEFAULTED constexpr mapping(const mapping&) noexcept = default; + MDSPAN_INLINE_FUNCTION_DEFAULTED mapping& operator=(const mapping&) noexcept = default; + + /** + * Initializes the mapping with the given extents. + * + * \param ext the given extents + */ + MDSPAN_INLINE_FUNCTION + constexpr mapping(const extents_type &ext) + : padded_stride(padded_stride_type::init_padding(ext)), exts(ext) {} + + /** + * Initializes the mapping with the given extents and the specified padding value. + * + * This overload participates in overload resolution only if `is_convertible_v` + * is `true` and `is_nothrow_constructible_v` is `true` + * + * \param ext the given extents + * \param padding_value the padding value + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Size, + /* requires */ ( + std::is_convertible_v<_Size, index_type> + && std::is_nothrow_constructible_v + ) + ) + MDSPAN_INLINE_FUNCTION + constexpr mapping(const extents_type &ext, _Size dynamic_padding_value) + : padded_stride(padded_stride_type::init_padding(ext, static_cast(dynamic_padding_value))), + exts(ext) { + assert((padding_value == dynamic_extent) || + (static_cast(padding_value) == static_cast(dynamic_padding_value))); + } + + /** + * Converting constructor from `layout_right::mapping`. + * + * This overload participates in overload resolution only if `is_constructible_v` is true. + * If `OtherExtents::rank() > 1` then one of `padding_value`, `static_extent(0)`, or `OtherExtents::static_extent(0)` must be `dynamic_extent`; + * otherwise, `OtherExtents::static_extent(0)` must be equal to the least multiple of `padding_value` greater than or equal to `extents_type::static_extent(0)` + */ + MDSPAN_TEMPLATE_REQUIRES( + class _OtherExtents, + /* requires */ ( + std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((!std::is_convertible_v<_OtherExtents, extents_type>)) + constexpr mapping(const layout_right::mapping<_OtherExtents> &other_mapping) + : padded_stride(padded_stride_type::init_padding(other_mapping, std::integral_constant{})), + exts(other_mapping.extents()) + { + static_assert((_OtherExtents::rank() > 1) || (padded_stride_type::static_value() != dynamic_extent) || (_OtherExtents::static_extent(extent_to_pad_idx) != dynamic_extent) + || (padded_stride_type::static_value() == _OtherExtents::static_extent(extent_to_pad_idx))); + } + + /** + * Converting constructor from `layout_stride::mapping`. + * + * This overload participates in overload resolution only if `is_constructible_v` is true + */ + MDSPAN_TEMPLATE_REQUIRES( + class _OtherExtents, + /* requires */ ( + std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((extents_type::rank() > 0)) + constexpr mapping(const layout_stride::mapping<_OtherExtents> &other_mapping) + : padded_stride(padded_stride_type::init_padding(other_mapping, std::integral_constant{})), + exts(other_mapping.extents()) + {} + + /** + * Converting constructor from `layout_right_padded::mapping`. + * + * This overload participates in overload resolution only if `is_constructible_v` is true. + * Either `padding_value` or `OtherPaddingStride` must be `std::dynamic_extent`, or `padding_value == OtherPaddingStride`. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_right_padded_mapping<_Mapping>::value + && std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((extents_type::rank() > 1 && + (padding_value == dynamic_extent || + _Mapping::padding_value == dynamic_extent))) + constexpr mapping(const _Mapping &other_mapping) + : padded_stride(padded_stride_type::init_padding(other_mapping, std::integral_constant{})), + exts(other_mapping.extents()) + { + static_assert(padding_value == dynamic_extent || + _Mapping::padding_value == dynamic_extent || + padding_value == _Mapping::padding_value); + } + + /** + * Converting constructor from `layout_left_padded::mapping`. + * + * This overload participates in overload resolution only if `extents_type::rank()` is 0 or 1 and `is_constructible_v` is `true`. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_left_padded_mapping<_Mapping>::value + && extents_type::rank() <= 1 + && std::is_constructible_v + ) + ) + MDSPAN_CONDITIONAL_EXPLICIT((!std::is_convertible_v)) + constexpr mapping(const _Mapping &other_mapping) noexcept + : padded_stride(padded_stride_type::init_padding(other_mapping.extents(), other_mapping.extents().extent(extent_to_pad_idx))), + exts(other_mapping.extents()) + {} + + constexpr const extents_type &extents() const noexcept + { + return exts; + } + + constexpr std::array + strides() const noexcept + { + if constexpr ( extents_type::rank() == 0 ) { + return {}; + } else if constexpr ( extents_type::rank() == 1 ) { + return {1}; + } else { + index_type value = 1; + std::array s{}; + s[extent_to_pad_idx] = value; + value *= padded_stride.value(0); + for (rank_type r = extent_to_pad_idx - 1; r > 0; --r) + { + s[r] = value; + value *= exts.extent(r); + } + s[0] = value; + return s; + } + } + + constexpr index_type + required_span_size() const noexcept + { + if constexpr ( extents_type::rank() == 0 ) { + return 1; + } else if constexpr ( extents_type::rank() == 1 ) { + return exts.extent(0); + } else { + index_type value = 1; + for (rank_type r = 0; r < extent_to_pad_idx; ++r) + { + value *= exts.extent(r); + } + return value * padded_stride.value(0); + } + } + + /** + * Return the mapping given the provided indices per rank. + * + * This overload participates in overload resolution only if: + * - `sizeof...(Indices) == extents_type::rank()`, + * - `(is_convertible_v && ...) is true`, and + * - (is_nothrow_constructible_v && ...) is true. + */ + MDSPAN_TEMPLATE_REQUIRES( + class... _Indices, + /* requires */ ( + sizeof...(_Indices) == extents_type::rank() && + (::MDSPAN_IMPL_STANDARD_NAMESPACE::detail::are_valid_indices()) + ) + ) + constexpr size_t operator()(_Indices... idxs) const noexcept + { + return compute_offset(std::index_sequence_for<_Indices...>{}, idxs...); + } + + static constexpr bool is_always_unique() noexcept { return true; } + static constexpr bool is_always_exhaustive() noexcept + { + return (extents_type::rank() <= rank_type(1)) + || (extents_type::static_extent(extent_to_pad_idx) != dynamic_extent + && extents_type::static_extent(extent_to_pad_idx) == padded_stride_type::static_value()); + } + static constexpr bool is_always_strided() noexcept { return true; } + + static constexpr bool is_unique() noexcept { return true; } + constexpr bool is_exhaustive() const noexcept + { + return (extents_type::rank() < 2) + || (exts.extent(extent_to_pad_idx) == padded_stride.value(0)); + } + static constexpr bool is_strided() noexcept { return true; } + + constexpr index_type stride(rank_type r) const noexcept + { + assert(r < extents_type::rank()); + if(r == extents_type::rank() - 1) return index_type(1); + + index_type value = padded_stride.value(0); + for (rank_type k = extents_type::rank() - 2; k > r; k--) value *= exts.extent(k); + + return value; + } + + /** + * Equality operator between `layout_right_padded`s + * + * This overload only participates in overload resolution if `OtherExtents::rank() == extents_type::rank()`. + * + * \note There is currently a difference from p2642r2, where this function is specified as taking + * `layout_right_padded< padding_value >::mapping< Extents>`. However, this makes `padding_value` non-deducible. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_right_padded_mapping<_Mapping>::value + && (_Mapping::extents_type::rank() == extents_type::rank()) + ) + ) + friend constexpr bool operator==(const mapping &left, const _Mapping &right) noexcept + { + // Workaround for some compilers not short-circuiting properly with compile-time checks + // i.e. we can't access stride(_padding_stride_idx) of a rank 0 mapping + bool strides_equal = true; + if constexpr (extents_type::rank() > rank_type(1)) + { + strides_equal = left.stride(padded_stride_idx) == right.stride(padded_stride_idx); + } + return (left.extents() == right.extents()) && strides_equal; + } + +#if !MDSPAN_HAS_CXX_20 + /** + * Inequality operator between `layout_right_padded`s + * + * This overload only participates in overload resolution if `OtherExtents::rank() == extents_type::rank()`. + */ + MDSPAN_TEMPLATE_REQUIRES( + class _Mapping, + /* requires */ ( + detail::is_layout_right_padded_mapping<_Mapping>::value + && (_Mapping::extents_type::rank() == extents_type::rank()) + ) + ) + friend constexpr bool operator!=(const mapping &left, const _Mapping &right) noexcept + { + return !(left == right); + } +#endif +}; +} +} diff --git a/lib/kokkos/tpls/mdspan/include/experimental/__p2642_bits/layout_padded_fwd.hpp b/lib/kokkos/tpls/mdspan/include/experimental/__p2642_bits/layout_padded_fwd.hpp new file mode 100644 index 0000000000..945f091a2d --- /dev/null +++ b/lib/kokkos/tpls/mdspan/include/experimental/__p2642_bits/layout_padded_fwd.hpp @@ -0,0 +1,117 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER +#pragma once + +#include +#include "../__p0009_bits/dynamic_extent.hpp" + +namespace MDSPAN_IMPL_STANDARD_NAMESPACE { +namespace MDSPAN_IMPL_PROPOSED_NAMESPACE { + +template +struct layout_left_padded { + template + class mapping; +}; + +template +struct layout_right_padded { + template + class mapping; +}; + +namespace detail { +// The layout_padded_constants structs are only useful if rank > 1, otherwise they may wrap +template +struct layout_padded_constants; + +template +struct layout_padded_constants, _ExtentsType> +{ + using rank_type = typename _ExtentsType::rank_type; + static constexpr rank_type padded_stride_idx = 1; + static constexpr rank_type extent_to_pad_idx = 0; +}; + +template +struct layout_padded_constants, _ExtentsType> +{ + using rank_type = typename _ExtentsType::rank_type; + static constexpr rank_type padded_stride_idx = _ExtentsType::rank() - 2; + static constexpr rank_type extent_to_pad_idx = _ExtentsType::rank() - 1; +}; + +template +struct is_layout_left_padded : std::false_type {}; + +template +struct is_layout_left_padded> : std::true_type {}; + +template +struct is_layout_left_padded_mapping : std::false_type {}; + +template +struct is_layout_left_padded_mapping<_Mapping, + std::enable_if_t::template mapping>::value>> + : std::true_type {}; + +template +struct is_layout_right_padded : std::false_type {}; + +template +struct is_layout_right_padded> : std::true_type {}; + +template +struct is_layout_right_padded_mapping : std::false_type {}; + +template +struct is_layout_right_padded_mapping<_Mapping, + std::enable_if_t::template mapping>::value>> + : std::true_type {}; + +template +constexpr void check_padded_layout_converting_constructor_mandates() +{ + if constexpr (_LayoutExtentsType::rank() > 1) { + using extents_type = typename _PaddedLayoutMappingType::extents_type; + constexpr auto padding_value = _PaddedLayoutMappingType::padding_value; + constexpr auto idx = layout_padded_constants::extent_to_pad_idx; + if constexpr ((_LayoutExtentsType::static_extent(idx) != dynamic_extent) && + (extents_type::static_extent(idx) != dynamic_extent) && + (padding_value != dynamic_extent)) { + if constexpr (padding_value == 0) { + static_assert(_LayoutExtentsType::static_extent(idx) == 0); + } else { + static_assert( + _LayoutExtentsType::static_extent(idx) % padding_value == 0); + } + } + } +} + +template +constexpr void check_padded_layout_converting_constructor_preconditions([[maybe_unused]] const _OtherMapping &other_mapping) { + if constexpr (_ExtentsType::rank() > 1) { + constexpr auto padded_stride_idx = + layout_padded_constants::padded_stride_idx; + constexpr auto extent_to_pad_idx = layout_padded_constants::extent_to_pad_idx; + assert(other_mapping.stride(padded_stride_idx) == other_mapping.extents().extent(extent_to_pad_idx)); + } +} +} +} +} diff --git a/lib/kokkos/tpls/mdspan/include/mdspan/mdspan.hpp b/lib/kokkos/tpls/mdspan/include/mdspan/mdspan.hpp index b440873526..ac72a1a4e6 100644 --- a/lib/kokkos/tpls/mdspan/include/mdspan/mdspan.hpp +++ b/lib/kokkos/tpls/mdspan/include/mdspan/mdspan.hpp @@ -35,6 +35,7 @@ #include "../experimental/__p0009_bits/layout_right.hpp" #include "../experimental/__p0009_bits/macros.hpp" #if MDSPAN_HAS_CXX_17 +#include "../experimental/__p2642_bits/layout_padded.hpp" #include "../experimental/__p2630_bits/submdspan.hpp" #endif diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index 4a158cb31f..66501a74e9 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -16,8 +16,10 @@ parser = ArgumentParser(prog='Install.py', description="LAMMPS library build wrapper script") # settings +# Note: must also adjust check for supported API versions in +# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y -version = "2.8.3" +version = "2.9.1" mode = "static" # help message @@ -46,7 +48,9 @@ checksums = { \ '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \ '2.8.2' : '599092b6a0aa6fff992612537ad98994', \ '2.8.3' : '76d23cd394eba9e6530316ed1184e219', \ + '2.8.4' : '9f59c4f9bda86fe5bef19543c295a981', \ '2.9.0' : '661eabeebee05cf84bbf9dc23d7d5f46', \ + '2.9.1' : 'c3b2d31479c1e9ce211719d40e9efbd7', \ } # parse and process arguments diff --git a/potentials/HGa.msmeam b/potentials/HGa.msmeam index 9f01501c16..1f84d0f8a5 100644 --- a/potentials/HGa.msmeam +++ b/potentials/HGa.msmeam @@ -1,29 +1,29 @@ bkgd_dyn = 1 emb_lin_neg = 1 -augt1=0 -ialloy=1 -rc = 5.9 +augt1=0 +ialloy=1 +rc = 5.9 #H -attrac(1,1)=0.460 -repuls(1,1)=0.460 +attrac(1,1)=0.460 +repuls(1,1)=0.460 Cmin(1,1,1)=1.3 # PuMS -Cmax(1,1,1)= 2.80 +Cmax(1,1,1)= 2.80 nn2(1,1)=1 #Ga rho0(2) = 0.6 -attrac(2,2)=0.097 -repuls(2,2)=0.097 +attrac(2,2)=0.097 +repuls(2,2)=0.097 nn2(2,2)=1 #HGa -attrac(1,2)=0.300 -repuls(1,2)=0.300 -lattce(1,2)=l12 -re(1,2)=3.19 -delta(1,2)=-0.48 -alpha(1,2)=6.6 -Cmin(1,1,2)=2.0 -Cmin(2,1,2)= 2.0 -Cmin(1,2,1)=2.0 +attrac(1,2)=0.300 +repuls(1,2)=0.300 +lattce(1,2)=l12 +re(1,2)=3.19 +delta(1,2)=-0.48 +alpha(1,2)=6.6 +Cmin(1,1,2)=2.0 +Cmin(2,1,2)= 2.0 +Cmin(1,2,1)=2.0 Cmin(2,2,1) = 1.4 Cmin(1,2,2) = 1.4 Cmin(1,1,2) = 1.4 diff --git a/potentials/Nb.uf3 b/potentials/Nb.uf3 new file mode 100644 index 0000000000..5f1cdb6f63 --- /dev/null +++ b/potentials/Nb.uf3 @@ -0,0 +1,136 @@ +#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION: +2B Nb Nb 0 3 nk +8.0 31 +0.001 0.001 0.001 0.001 0.33429166666666665 0.66758333333333331 1.000875 1.3341666666666665 1.6674583333333333 2.00075 2.3340416666666663 2.6673333333333331 3.0006249999999999 3.3339166666666666 3.667208333333333 4.0004999999999997 4.3337916666666665 4.6670833333333333 5.000375 5.3336666666666668 5.6669583333333335 6.0002500000000003 6.3335416666666671 6.6668333333333338 7.0001249999999997 7.3334166666666665 7.6667083333333332 8 8 8 8 +27 +79.140244588519465 79.140244588519465 55.85833391113556 36.597903318706138 21.358952811231141 12.290000872768841 1.9593931914091953 -0.65697974623243804 -0.85177956270573463 -0.68929688239869991 -0.46787243412973262 -0.27624655899523165 -0.11912921944351409 -0.056302369393035338 -0.0049812809608429064 0.0085637634684603507 0.0034716161454604712 -0.0058751075573311978 -0.005453415412748467 -0.0015123194244718201 0.0011577919587182201 0.001583772506713282 -0.00049823976100720228 -0.0013902809146717273 0 0 0 +# +#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION: +3B Nb Nb Nb 0 3 nk +8.0 4.0 4.0 23 15 15 +0.001 0.001 0.001 0.001 0.50093749999999992 1.000875 1.5008124999999999 2.00075 2.5006874999999997 3.0006249999999999 3.5005624999999996 4.0004999999999997 4.5004375000000003 5.000375 5.5003124999999997 6.0002500000000003 6.5001875 7.0001249999999997 7.5000625000000003 8 8 8 8 +0.001 0.001 0.001 0.001 0.50087499999999996 1.00075 1.5006249999999999 2.0005000000000002 2.500375 3.0002499999999999 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--git a/potentials/README b/potentials/README index 2cb4a383c5..e6b5ef1bbe 100644 --- a/potentials/README +++ b/potentials/README @@ -87,6 +87,7 @@ adp ADP angular dependent potential airebo AI-REBO potentials bop.table BOP potential, tabulated form cdeam concentration-dependent EAM +cgdna potential files for styles in the CG-DNA package comb COMB potential comb3 COMB3 potential eam embedded atom method (EAM) single element, DYNAMO funcfl format @@ -118,4 +119,5 @@ sw Stillinger-Weber potential tersoff Tersoff potential tersoff.mod modified Tersoff potential tersoff.zbl Tersoff with ZBL core +uf3 UF3 potential vashishta Vashishta 2-body and 3-body potential diff --git a/potentials/Ta_coeff.pod b/potentials/Ta_coeff.pod index 5222e9e600..ab5e5fd43a 100644 --- a/potentials/Ta_coeff.pod +++ b/potentials/Ta_coeff.pod @@ -1,33 +1,33 @@ -POD_coefficients: 32 --4.44242 -4.10219 -2.36987 -3.92184 --0.83796 --0.79457 --0.26230 --21.24294 --15.38460 --38.44056 -8.29872 --42.54514 -2.79976 -3.76109 -5.23499 -0.04878 -2.96006 -0.09101 --0.19257 --0.24326 --0.16735 -0.53738 -0.02236 --0.00154 -0.02488 --0.00565 -0.07672 --0.05894 --0.05604 --0.12664 -0.11723 -0.00262 +model_coefficients: 32 0 0 +-4.45745 +29.40034 +-13.69439 +-0.32907 +-0.14786 +-1.35221 +-0.59315 +-26.30409 +-33.37233 +162.42473 +144.67248 +-149.50021 +1.78603 +2.49026 +-11.04768 +-11.14333 +12.40537 +0.48284 +0.39345 +-2.25812 +-1.38908 +1.31551 +0.02974 +-0.05094 +-0.21177 +0.12127 +0.23170 +0.02426 +-0.15305 +-0.10803 +0.25628 +0.01291 diff --git a/potentials/Ta_param.pod b/potentials/Ta_param.pod index 888dcb1b34..f5dbaf9254 100644 --- a/potentials/Ta_param.pod +++ b/potentials/Ta_param.pod @@ -1,4 +1,3 @@ -# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 # chemical element symbols species Ta @@ -11,28 +10,37 @@ rin 1.0 # outer cut-off radius rcut 5.0 +# use only for enviroment-adaptive potentials +number_of_environment_clusters 1 + +# principal_components of local descriptors +number_of_principal_components 2 + # polynomial degrees for radial basis functions bessel_polynomial_degree 3 inverse_polynomial_degree 6 -# one-body potential -onebody 1 - # two-body linear POD potential twobody_number_radial_basis_functions 6 # three-body linear POD potential threebody_number_radial_basis_functions 5 -threebody_number_angular_basis_functions 5 +threebody_angular_degree 4 -# four-body linear SNAP potential -fourbody_snap_twojmax 0 +# four-body linear POD potential +fourbody_number_radial_basis_functions 0 +fourbody_angular_degree 0 -# quadratic POD potential -quadratic_pod_potential 0 +# five-body linear POD potential +fivebody_number_radial_basis_functions 0 +fivebody_angular_degree 0 + +# six-body linear POD potential +sixbody_number_radial_basis_functions 0 +sixbody_angular_degree 0 + +# seven-body linear POD potential +sevenbody_number_radial_basis_functions 0 +sevenbody_angular_degree 0 -# Add the following basename to the name of output files -basename_for_output_files Ta -# number of digits after the decimal point -precision_for_pod_coefficients 5 diff --git a/potentials/oxdna2_lj.cgdna b/potentials/oxdna2_lj.cgdna new file mode 100644 index 0000000000..15c82f52c6 --- /dev/null +++ b/potentials/oxdna2_lj.cgdna @@ -0,0 +1,11 @@ +# DATE: 2024-04-21 UNITS: lj CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk CITATION: Snodin, Randisi, Mosayebi, Šulc et. al., J Chem Phys, 142, 23 (2015) +# +* fene 2.0 0.25 0.7564 +* * excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +* * stk 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +* * hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +1 4 hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +2 3 hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +* * xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +* * coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +* * dh 0.815 diff --git a/potentials/oxdna2_real.cgdna b/potentials/oxdna2_real.cgdna new file mode 100644 index 0000000000..fa42412f2b --- /dev/null +++ b/potentials/oxdna2_real.cgdna @@ -0,0 +1,11 @@ +# DATE: 2024-04-26 UNITS: real CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk +# +* fene 11.92337812042065 2.1295 6.4430152 +* * excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +* * stk 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +* * hbond 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +1 4 hbond 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +2 3 hbond 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +* * xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +* * coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 40.0 3.116592653589793 +* * dh 0.815 diff --git a/potentials/oxdna_lj.cgdna b/potentials/oxdna_lj.cgdna new file mode 100644 index 0000000000..e737d68e15 --- /dev/null +++ b/potentials/oxdna_lj.cgdna @@ -0,0 +1,10 @@ +# DATE: 2024-04-21 UNITS: lj CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk CITATION: Ouldridge, Louis, and Doye, J Chem Phys, 134, 8 (2011) +# +* fene 2.0 0.25 0.7525 +* * excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +* * stk 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +* * hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +1 4 hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +2 3 hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +* * xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +* * coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 diff --git a/potentials/oxdna_real.cgdna b/potentials/oxdna_real.cgdna new file mode 100644 index 0000000000..d687cbe1f4 --- /dev/null +++ b/potentials/oxdna_real.cgdna @@ -0,0 +1,10 @@ +# DATE: 2024-04-26 UNITS: real CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk +# +* fene 11.92337812042065 2.1295 6.409795 +* * excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +* * stk 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +* * hbond 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +1 4 hbond 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +2 3 hbond 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +* * xstk 3.902852174 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +* * coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 -0.65 2.0 -0.65 diff --git a/potentials/oxrna2_lj.cgdna b/potentials/oxrna2_lj.cgdna new file mode 100644 index 0000000000..f4e7c59dbb --- /dev/null +++ b/potentials/oxrna2_lj.cgdna @@ -0,0 +1,12 @@ +# DATE: 2024-04-19 UNITS: lj CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk CITATION: Šulc, Romano, Ouldridge, Rovigatti, Doye, Louis, J Chem Phys, 140, 23 (2014) +# +* fene 2.0 0.25 0.761070781051 +* * excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +* * stk 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +* * hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +1 4 hbond 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +2 3 hbond 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +3 4 hbond 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +* * xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +* * coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +* * dh 1.02455 diff --git a/potentials/oxrna2_real.cgdna b/potentials/oxrna2_real.cgdna new file mode 100644 index 0000000000..10a8d8a8b5 --- /dev/null +++ b/potentials/oxrna2_real.cgdna @@ -0,0 +1,12 @@ +# DATE: 2024-04-26 UNITS: real CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk +# +* fene 11.92337812042065 2.1295 6.482800913 +* * excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +* * stk 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +* * hbond 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +1 4 hbond 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +2 3 hbond 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +3 4 hbond 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +* * xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +* * coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +* * dh 1.02455 diff --git a/python/lammps/core.py b/python/lammps/core.py index 28b384d6ba..8966a77440 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -269,6 +269,9 @@ class lammps(object): self.lib.lammps_extract_global_datatype.restype = c_int self.lib.lammps_extract_compute.argtypes = [c_void_p, c_char_p, c_int, c_int] + self.lib.lammps_map_atom.argtypes = [c_void_p, c_void_p] + self.lib.lammps_map_atom.restype = c_int + self.lib.lammps_get_thermo.argtypes = [c_void_p, c_char_p] self.lib.lammps_get_thermo.restype = c_double @@ -376,12 +379,16 @@ class lammps(object): narg = 0 cargs = None if cmdargs is not None: - cmdargs.insert(0,"lammps") - narg = len(cmdargs) - for i in range(narg): - if type(cmdargs[i]) is str: - cmdargs[i] = cmdargs[i].encode() - cargs = (c_char_p*(narg+1))(*cmdargs) + myargs = ["lammps".encode()] + narg = len(cmdargs) + 1 + for arg in cmdargs: + if type(arg) is str: + myargs.append(arg.encode()) + elif type(arg) is bytes: + myargs.append(arg) + else: + raise TypeError('Unsupported cmdargs type ', type(arg)) + cargs = (c_char_p*(narg+1))(*myargs) cargs[narg] = None self.lib.lammps_open.argtypes = [c_int, c_char_p*(narg+1), MPI_Comm, c_void_p] else: @@ -397,12 +404,16 @@ class lammps(object): self.comm = self.MPI.COMM_WORLD self.opened = 1 if cmdargs is not None: - cmdargs.insert(0,"lammps") - narg = len(cmdargs) - for i in range(narg): - if type(cmdargs[i]) is str: - cmdargs[i] = cmdargs[i].encode() - cargs = (c_char_p*(narg+1))(*cmdargs) + myargs = ["lammps".encode()] + narg = len(cmdargs) + 1 + for arg in cmdargs: + if type(arg) is str: + myargs.append(arg.encode()) + elif type(arg) is bytes: + myargs.append(arg) + else: + raise TypeError('Unsupported cmdargs type ', type(arg)) + cargs = (c_char_p*(narg+1))(*myargs) cargs[narg] = None self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*(narg+1), c_void_p] self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None)) @@ -880,11 +891,13 @@ class lammps(object): # set length of vector for items that are not a scalar vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3, 'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3, - 'special_lj':4, 'special_coul':4 } + 'special_lj':4, 'special_coul':4, 'procgrid':3 } if name in vec_dict: veclen = vec_dict[name] elif name == 'respa_dt': veclen = self.extract_global('respa_levels',LAMMPS_INT) + elif name == 'sametag': + veclen = self.extract_setting('nall') else: veclen = 1 @@ -918,6 +931,24 @@ class lammps(object): else: return target_type(ptr[0]) return None + # ------------------------------------------------------------------------- + # map global atom ID to local atom index + + def map_atom(self, id): + """Map a global atom ID (aka tag) to the local atom index + + This is a wrapper around the :cpp:func:`lammps_map_atom` + function of the C-library interface. + + :param id: atom ID + :type id: int + :return: local index + :rtype: int + """ + + tag = self.c_tagint(id) + return self.lib.lammps_map_atom(self.lmp, pointer(tag)) + # ------------------------------------------------------------------------- # extract per-atom info datatype @@ -1078,15 +1109,23 @@ class lammps(object): def extract_fix(self,fid,fstyle,ftype,nrow=0,ncol=0): """Retrieve data from a LAMMPS fix - This is a wrapper around the :cpp:func:`lammps_extract_fix` - function of the C-library interface. - This function returns ``None`` if either the fix id is not - recognized, or an invalid combination of :ref:`fstyle ` - and :ref:`ftype ` constants is used. The - names and functionality of the constants are the same as for - the corresponding C-library function. For requests to return - a scalar or a size, the value is returned, also when accessing - global vectors or arrays, otherwise a pointer. + This is a wrapper around the :cpp:func:`lammps_extract_fix` function + of the C-library interface. This function returns ``None`` if + either the fix id is not recognized, or an invalid combination of + :ref:`fstyle ` and :ref:`ftype + ` constants is used. The names and functionality + of the constants are the same as for the corresponding C-library + function. For requests to return a scalar or a size, the value is + returned, also when accessing global vectors or arrays, otherwise a + pointer. + + .. note:: + + When requesting global data, the fix data can only be accessed + one item at a time without access to the whole vector or array. + Thus this function will always return a scalar. To access vector + or array elements the "nrow" and "ncol" arguments need to be set + accordingly (they default to 0). :param fid: fix ID :type fid: string diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py index a29853d16a..91042c43c8 100644 --- a/python/lammps/numpy_wrapper.py +++ b/python/lammps/numpy_wrapper.py @@ -203,6 +203,13 @@ class numpy_wrapper: It behaves the same as the original method, but returns NumPy arrays instead of ``ctypes`` pointers. + .. note:: + + When requesting global data, the fix data can only be accessed one + item at a time without access to the whole vector or array. Thus this + function will always return a scalar. To access vector or array elements + the "nrow" and "ncol" arguments need to be set accordingly (they default to 0). + :param fid: fix ID :type fid: string :param fstyle: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants` diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py index c693b7d565..96384255c2 100644 --- a/python/lammps/pylammps.py +++ b/python/lammps/pylammps.py @@ -192,11 +192,23 @@ class Atom(object): @property def mass(self): """ - Return the atom mass + Return the atom mass as a per-atom property. + This returns either the per-type mass or the per-atom + mass (AKA 'rmass') depending on what is available with + preference for the per-atom mass. + + .. versionchanged:: 17Apr2024 + + Support both per-type and per-atom masses. With + per-type return "mass[type[i]]" else return "rmass[i]". + Per-atom mass is preferred if available. :type: float """ - return self.get("mass", self.index) + if self._pylmp.lmp.extract_setting('rmass_flag'): + return self.get("rmass", self.index) + else: + return self.get("mass", self.type) @property def radius(self): @@ -532,6 +544,18 @@ class PyLammps(object): """ self._cmd_history = [] + + def append_cmd_history(self, cmd): + """ + Commands will be added to the command history but not executed. + + Add `commands` only to the command history, but do not execute them, so that you can + conveniently create Lammps input files, using + :py:meth:`PyLammps.write_script()`. + """ + self._cmd_history.append(cmd) + + def command(self, cmd): """ Execute LAMMPS command @@ -772,18 +796,16 @@ class PyLammps(object): comm = {} comm['nprocs'] = self.lmp.extract_setting("world_size") comm['nthreads'] = self.lmp.extract_setting("nthreads") + comm['proc_grid'] = comm['procgrid'] = self.lmp.extract_global("procgrid") + idx = self.lmp.extract_setting("comm_style") + comm['comm_style'] = ('brick', 'tiled')[idx] + idx = self.lmp.extract_setting("comm_style") + comm['comm_layout'] = ('uniform', 'nonuniform', 'irregular')[idx] + comm['ghost_velocity'] = self.lmp.extract_setting("ghost_velocity") == 1 for line in output: if line.startswith("MPI library"): comm['mpi_version'] = line.split(':')[1].strip() - elif line.startswith("Comm style"): - parts = self._split_values(line) - comm['comm_style'] = self._get_pair(parts[0])[1] - comm['comm_layout'] = self._get_pair(parts[1])[1] - elif line.startswith("Processor grid"): - comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')] - elif line.startswith("Communicate velocities for ghost atoms"): - comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes") return comm def _parse_element_list(self, output): diff --git a/src/.gitignore b/src/.gitignore index 88bb80fdc5..e5923d0149 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -109,6 +109,8 @@ /pair_pod.cpp /pair_pod.h +/eapod.cpp +/eapod.h /fitpod_command.cpp /fitpod_command.h /mlpod.cpp @@ -169,6 +171,17 @@ /rann_*.cpp /rann_*.h +/pair_uf3.cpp +/pair_uf3.h +/uf3_bspline_basis2.cpp +/uf3_bspline_basis2.h +/uf3_bspline_basis3.cpp +/uf3_bspline_basis3.h +/uf3_pair_bspline.cpp +/uf3_pair_bspline.h +/uf3_triplet_bspline.cpp +/uf3_triplet_bspline.h + /compute_test_nbl.cpp /compute_test_nbl.h /pair_multi_lucy.cpp @@ -236,6 +249,14 @@ /compute_grid.h /compute_grid_local.cpp /compute_grid_local.h +/compute_pod_atom.cpp +/compute_pod_atom.h +/compute_pod_global.cpp +/compute_pod_global.h +/compute_pod_local.cpp +/compute_pod_local.h +/compute_podd_atom.cpp +/compute_podd_atom.h /compute_sna_atom.cpp /compute_sna_atom.h /compute_snad_atom.cpp @@ -463,6 +484,8 @@ /angle_cosine_shift_exp.h /angle_cosine_squared.cpp /angle_cosine_squared.h +/angle_cosine_squared_restricted.cpp +/angle_cosine_squared_restricted.h /angle_cross.cpp /angle_cross.h /angle_dipole.cpp @@ -675,12 +698,16 @@ /compute_viscosity_cos.h /compute_voronoi_atom.cpp /compute_voronoi_atom.h +/constants_oxdna.cpp +/constants_oxdna.h /dihedral_charmm.cpp /dihedral_charmm.h /dihedral_class2.cpp /dihedral_class2.h /dihedral_cosine_shift_exp.cpp /dihedral_cosine_shift_exp.h +/dihedral_cosine_squared_restricted.cpp +/dihedral_cosine_squared_restricted.h /dihedral_fourier.cpp /dihedral_fourier.h /dihedral_harmonic.cpp @@ -1357,6 +1384,8 @@ /pair_oxrna2_*.cpp /pair_oxrna2_*.h /mf_oxdna.h +/pair_pedone.cpp +/pair_pedone.h /pair_peri.cpp /pair_peri.h /pair_peri_eps.cpp @@ -1698,6 +1727,8 @@ /pair_dpd.h /pair_dpd_tstat.cpp /pair_dpd_tstat.h +/pair_dpd_coul_slater_long.cpp +/pair_dpd_coul_slater_long.h /pair_dpd_ext.cpp /pair_dpd_ext.h /pair_dpd_ext_tstat.cpp diff --git a/src/ASPHERE/pair_ylz.cpp b/src/ASPHERE/pair_ylz.cpp index a678712619..833dc8e3e4 100644 --- a/src/ASPHERE/pair_ylz.cpp +++ b/src/ASPHERE/pair_ylz.cpp @@ -300,6 +300,7 @@ double PairYLZ::init_one(int i, int j) zeta[j][i] = zeta[i][j]; mu[j][i] = mu[i][j]; beta[j][i] = beta[i][j]; + cut[j][i] = cut[i][j]; return cut[i][j]; } @@ -409,7 +410,7 @@ void PairYLZ::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) - fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][i], sigma[i][i], cut[i][j], + fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][j], sigma[i][j], cut[i][j], zeta[i][j], mu[i][j], beta[i][j]); } diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 7a1dbaa0f0..4a34f31f54 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -99,7 +99,7 @@ int BodyNparticle::unpack_border_body(AtomVecBody::Bonus *bonus, double *buf) } /* ---------------------------------------------------------------------- - populate bonus data structure with data file values + populate bonus data structure with data file values for one body ------------------------------------------------------------------------- */ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble, diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 6a94f68a8e..5de0654d25 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -155,7 +155,7 @@ int BodyRoundedPolygon::unpack_border_body(AtomVecBody::Bonus *bonus, } /* ---------------------------------------------------------------------- - populate bonus data structure with data file values + populate bonus data structure with data file values for one body ------------------------------------------------------------------------- */ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 991f52cac5..f34a212087 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -99,10 +99,9 @@ int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus) { int nvertices = bonus->ivalue[0]; int nedges = bonus->ivalue[1]; - //int nfaces = bonus->ivalue[2]; if (nvertices == 1) return 0; else if (nvertices == 2) return 1; - return nedges; //(nvertices+nfaces-2); // Euler formula: V-E+F=2 + return nedges; } /* ---------------------------------------------------------------------- */ @@ -116,6 +115,9 @@ double *BodyRoundedPolyhedron::edges(AtomVecBody::Bonus *bonus) int BodyRoundedPolyhedron::nfaces(AtomVecBody::Bonus *bonus) { + int nvertices = bonus->ivalue[0]; + if (nvertices < 3) return 0; + return bonus->ivalue[2]; } @@ -185,7 +187,7 @@ int BodyRoundedPolyhedron::unpack_border_body(AtomVecBody::Bonus *bonus, double } /* ---------------------------------------------------------------------- - populate bonus data structure with data file values + populate bonus data structure with data file values for one body ------------------------------------------------------------------------- */ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble, diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 432f1d5c9c..2293f56a98 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -415,17 +415,14 @@ void PairBodyRoundedPolygon::init_style() if (!avec) error->all(FLERR,"Pair body/rounded/polygon requires atom style body"); if (strcmp(avec->bptr->style,"rounded/polygon") != 0) - error->all(FLERR,"Pair body/rounded/polygon requires " - "body style rounded/polygon"); + error->all(FLERR,"Pair body/rounded/polygon requires body style rounded/polygon"); bptr = dynamic_cast(avec->bptr); if (force->newton_pair == 0) - error->all(FLERR,"Pair style body/rounded/polygon requires " - "newton pair on"); + error->all(FLERR,"Pair style body/rounded/polygon requires newton pair on"); if (comm->ghost_velocity == 0) - error->all(FLERR,"Pair body/rounded/polygon requires " - "ghost atoms store velocity"); + error->all(FLERR,"Pair body/rounded/polygon requires ghost atoms store velocity"); neighbor->add_request(this); @@ -463,27 +460,24 @@ void PairBodyRoundedPolygon::init_style() for (i = 1; i <= ntypes; i++) maxerad[i] = merad[i] = 0; - int ipour; - for (ipour = 0; ipour < modify->nfix; ipour++) - if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; - if (ipour == modify->nfix) ipour = -1; + Fix *fixpour = nullptr; + auto pours = modify->get_fix_by_style("^pour"); + if (pours.size() > 0) fixpour = pours[0]; + + Fix *fixdep = nullptr; + auto deps = modify->get_fix_by_style("^deposit"); + if (deps.size() > 0) fixdep = deps[0]; - int idep; - for (idep = 0; idep < modify->nfix; idep++) - if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; - if (idep == modify->nfix) idep = -1; for (i = 1; i <= ntypes; i++) { merad[i] = 0.0; - if (ipour >= 0) { + if (fixpour) { itype = i; - merad[i] = - *((double *) modify->fix[ipour]->extract("radius",itype)); + merad[i] = *((double *) fixpour->extract("radius",itype)); } - if (idep >= 0) { + if (fixdep) { itype = i; - merad[i] = - *((double *) modify->fix[idep]->extract("radius",itype)); + merad[i] = *((double *) fixdep->extract("radius",itype)); } } @@ -570,8 +564,7 @@ void PairBodyRoundedPolygon::body2space(int i) } if ((body_num_edges > 0) && (edge_ends == nullptr)) - error->one(FLERR,"Inconsistent edge data for body of atom {}", - atom->tag[i]); + error->one(FLERR,"Inconsistent edge data for body of atom {}", atom->tag[i]); for (int m = 0; m < body_num_edges; m++) { edge[nedge][0] = static_cast(edge_ends[2*m+0]); diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 82660df1e0..ed83dc49e2 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -222,8 +222,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) // sphere-sphere interaction if (npi == 1 && npj == 1) { - sphere_against_sphere(i, j, itype, jtype, delx, dely, delz, - rsq, v, f, evflag); + sphere_against_sphere(i, j, itype, jtype, delx, dely, delz, rsq, v, f, evflag); continue; } @@ -391,20 +390,16 @@ void PairBodyRoundedPolyhedron::coeff(int narg, char **arg) void PairBodyRoundedPolyhedron::init_style() { avec = dynamic_cast(atom->style_match("body")); - if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires " - "atom style body"); + if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body"); if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0) - error->all(FLERR,"Pair body/rounded/polyhedron requires " - "body style rounded/polyhedron"); + error->all(FLERR,"Pair body/rounded/polyhedron requires body style rounded/polyhedron"); bptr = dynamic_cast(avec->bptr); if (force->newton_pair == 0) - error->all(FLERR,"Pair style body/rounded/polyhedron requires " - "newton pair on"); + error->all(FLERR,"Pair style body/rounded/polyhedron requires newton pair on"); if (comm->ghost_velocity == 0) - error->all(FLERR,"Pair body/rounded/polyhedron requires " - "ghost atoms store velocity"); + error->all(FLERR,"Pair body/rounded/polyhedron requires ghost atoms store velocity"); neighbor->add_request(this); @@ -446,27 +441,23 @@ void PairBodyRoundedPolyhedron::init_style() for (i = 1; i <= ntypes; i++) maxerad[i] = merad[i] = 0; - int ipour; - for (ipour = 0; ipour < modify->nfix; ipour++) - if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; - if (ipour == modify->nfix) ipour = -1; + Fix *fixpour = nullptr; + auto pours = modify->get_fix_by_style("^pour"); + if (pours.size() > 0) fixpour = pours[0]; - int idep; - for (idep = 0; idep < modify->nfix; idep++) - if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; - if (idep == modify->nfix) idep = -1; + Fix *fixdep = nullptr; + auto deps = modify->get_fix_by_style("^deposit"); + if (deps.size() > 0) fixdep = deps[0]; for (i = 1; i <= ntypes; i++) { merad[i] = 0.0; - if (ipour >= 0) { + if (fixpour) { itype = i; - merad[i] = - *((double *) modify->fix[ipour]->extract("radius",itype)); + merad[i] = *((double *) fixpour->extract("radius",itype)); } - if (idep >= 0) { + if (fixdep) { itype = i; - merad[i] = - *((double *) modify->fix[idep]->extract("radius",itype)); + merad[i] = *((double *) fixdep->extract("radius",itype)); } } @@ -558,8 +549,7 @@ void PairBodyRoundedPolyhedron::body2space(int i) } if ((body_num_edges > 0) && (edge_ends == nullptr)) - error->one(FLERR,"Inconsistent edge data for body of atom {}", - atom->tag[i]); + error->one(FLERR,"Inconsistent edge data for body of atom {}", atom->tag[i]); for (int m = 0; m < body_num_edges; m++) { edge[nedge][0] = static_cast(edge_ends[2*m+0]); @@ -585,8 +575,7 @@ void PairBodyRoundedPolyhedron::body2space(int i) } if ((body_num_faces > 0) && (face_pts == nullptr)) - error->one(FLERR,"Inconsistent face data for body of atom {}", - atom->tag[i]); + error->one(FLERR,"Inconsistent face data for body of atom {}", atom->tag[i]); for (int m = 0; m < body_num_faces; m++) { for (int k = 0; k < MAX_FACE_SIZE; k++) diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp index f1482d4203..e8521df32a 100644 --- a/src/BPM/bond_bpm.cpp +++ b/src/BPM/bond_bpm.cpp @@ -14,6 +14,7 @@ #include "bond_bpm.h" #include "atom.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" @@ -30,6 +31,19 @@ using namespace LAMMPS_NS; +static const char cite_bpm[] = + "BPM bond style: doi:10.1039/D3SM01373A\n\n" + "@Article{Clemmer2024,\n" + " author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},\n" + " title = {A soft departure from jamming: the compaction of deformable\n" + " granular matter under high pressures},\n" + " journal = {Soft Matter},\n" + " year = 2024,\n" + " volume = 20,\n" + " number = 8,\n" + " pages = {1702--1718}\n" + "}\n\n"; + /* ---------------------------------------------------------------------- */ BondBPM::BondBPM(LAMMPS *_lmp) : @@ -55,6 +69,8 @@ BondBPM::BondBPM(LAMMPS *_lmp) : id_fix_dummy2 = utils::strdup("BPM_DUMMY2"); modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy2)); + + if (lmp->citeme) lmp->citeme->add(cite_bpm); } /* ---------------------------------------------------------------------- */ @@ -336,19 +352,32 @@ void BondBPM::process_broken(int i, int j) { if (!break_flag) error->one(FLERR, "BPM bond broke with break no option"); - if (fix_store_local) { - for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j); - fix_store_local->add_data(output_data, i, j); + int nlocal = atom->nlocal; + if (fix_store_local) { + // If newton off, bond can break on two procs so only record if proc owns lower tag + // (BPM bond styles should sort so i -> atom with lower tag) + if (force->newton_bond || (i < nlocal)) { + for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j); + fix_store_local->add_data(output_data, i, j); + } } - if (fix_update_special_bonds) fix_update_special_bonds->add_broken_bond(i, j); + if (fix_update_special_bonds) { + // If this processor owns two copies of the bond (i.e. if the domain is periodic and 1 proc thick), + // skip instance where larger tag (j) owned + int check = 1; + if (i >= nlocal) { + int imap = atom->map(atom->tag[i]); + if (imap < nlocal) check = 0; + } + if (check) fix_update_special_bonds->add_broken_bond(i, j); + } // Manually search and remove from atom arrays // need to remove in case special bonds arrays rebuilt - int m, n; - int nlocal = atom->nlocal; + int m, n; tagint *tag = atom->tag; tagint **bond_atom = atom->bond_atom; int **bond_type = atom->bond_type; diff --git a/src/BPM/compute_nbond_atom.cpp b/src/BPM/compute_nbond_atom.cpp index 4f0fc4c3f0..85ef6f3fce 100644 --- a/src/BPM/compute_nbond_atom.cpp +++ b/src/BPM/compute_nbond_atom.cpp @@ -65,14 +65,13 @@ void ComputeNBondAtom::compute_peratom() tagint **bond_atom = atom->bond_atom; int **bond_type = atom->bond_type; - int ntotal = nlocal; - if (force->newton) ntotal += atom->nghost; - // set local nbond array int i, j, k; int *num_bond = atom->num_bond; int newton_bond = force->newton_bond; + int ntotal = nlocal; + if (newton_bond) ntotal += atom->nghost; for (i = 0; i < ntotal; i++) nbond[i] = 0; for (i = 0; i < nlocal; i++) { @@ -88,7 +87,7 @@ void ComputeNBondAtom::compute_peratom() } // communicate ghost nbond between neighbor procs - if (force->newton) comm->reverse_comm(this); + if (newton_bond) comm->reverse_comm(this); // zero nbond of atoms not in group // only do this after comm since ghost contributions must be included diff --git a/src/BPM/fix_update_special_bonds.cpp b/src/BPM/fix_update_special_bonds.cpp index cdc72ee987..1b408d6d4b 100644 --- a/src/BPM/fix_update_special_bonds.cpp +++ b/src/BPM/fix_update_special_bonds.cpp @@ -100,6 +100,7 @@ void FixUpdateSpecialBonds::pre_exchange() n1 = nspecial[i][0]; for (m = 0; m < n1; m++) if (slist[m] == tagj) break; + if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj); for (; m < n1 - 1; m++) slist[m] = slist[m + 1]; nspecial[i][0]--; nspecial[i][1] = nspecial[i][2] = nspecial[i][0]; @@ -110,6 +111,7 @@ void FixUpdateSpecialBonds::pre_exchange() n1 = nspecial[j][0]; for (m = 0; m < n1; m++) if (slist[m] == tagi) break; + if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj); for (; m < n1 - 1; m++) slist[m] = slist[m + 1]; nspecial[j][0]--; nspecial[j][1] = nspecial[j][2] = nspecial[j][0]; diff --git a/src/CG-DNA/Install.sh b/src/CG-DNA/Install.sh index 3c65fac787..a979ded2d5 100755 --- a/src/CG-DNA/Install.sh +++ b/src/CG-DNA/Install.sh @@ -43,6 +43,8 @@ fi # list of files with dependcies +action constants_oxdna.cpp +action constants_oxdna.h action atom_vec_oxdna.cpp action atom_vec_oxdna.h action bond_oxdna_fene.cpp bond_fene.h diff --git a/src/CG-DNA/atom_vec_oxdna.cpp b/src/CG-DNA/atom_vec_oxdna.cpp index d7aa7a3d01..38f78f94bf 100644 --- a/src/CG-DNA/atom_vec_oxdna.cpp +++ b/src/CG-DNA/atom_vec_oxdna.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "atom_vec_oxdna.h" +#include "constants_oxdna.h" #include "atom.h" #include "error.h" @@ -45,6 +46,9 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp) if (!force->newton_bond) error->warning(FLERR, "Write_data command requires newton on to preserve 3'->5' bond polarity"); + + // initialize oxDNA units + ConstantsOxdna constants(lmp); } /* ---------------------------------------------------------------------- diff --git a/src/CG-DNA/bond_oxdna2_fene.cpp b/src/CG-DNA/bond_oxdna2_fene.cpp index ace0742963..73ad827d72 100644 --- a/src/CG-DNA/bond_oxdna2_fene.cpp +++ b/src/CG-DNA/bond_oxdna2_fene.cpp @@ -15,6 +15,7 @@ ------------------------------------------------------------------------- */ #include "bond_oxdna2_fene.h" +#include "constants_oxdna.h" using namespace LAMMPS_NS; @@ -24,8 +25,8 @@ using namespace LAMMPS_NS; void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], double r[3]) const { - constexpr double d_cs_x = -0.34; - constexpr double d_cs_y = +0.3408; + double d_cs_x = ConstantsOxdna::get_d_cs_x(); + double d_cs_y = ConstantsOxdna::get_d_cs_y(); r[0] = d_cs_x * e1[0] + d_cs_y * e2[0]; r[1] = d_cs_x * e1[1] + d_cs_y * e2[1]; diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index 780b71e44c..f5edee9a05 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -18,10 +18,12 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "memory.h" #include "neighbor.h" +#include "potential_file_reader.h" #include "update.h" #include "math_extra.h" @@ -49,7 +51,7 @@ BondOxdnaFene::~BondOxdnaFene() void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3], double /*e3*/[3], double r[3]) const { - constexpr double d_cs = -0.4; + double d_cs = ConstantsOxdna::get_d_cs(); r[0] = d_cs * e1[0]; r[1] = d_cs * e1[1]; @@ -165,6 +167,7 @@ void BondOxdnaFene::compute(int eflag, int vflag) int nlocal = atom->nlocal; int newton_bond = force->newton_bond; + const double rlogarg_min = 0.2; ebond = 0.0; ev_init(eflag, vflag); @@ -217,14 +220,38 @@ void BondOxdnaFene::compute(int eflag, int vflag) Deltasq = Delta[type] * Delta[type]; rlogarg = 1.0 - rr0sq / Deltasq; - // if r -> Delta, then rlogarg < 0.0 which is an error - // issue a warning and reset rlogarg = epsilon - // if r > 2*Delta something serious is wrong, abort + // energy + if (eflag) { + ebond = -0.5 * k[type] * log(rlogarg); + } - if (rlogarg < 0.1) { + // switching to capped force for r-r0 -> Delta at + // r > r_max = r0 + Delta*sqrt(1-rlogarg) OR + // r < r_min = r0 - Delta*sqrt(1-rlogarg) + if (rlogarg < rlogarg_min) { + // issue warning, reset rlogarg and rr0 to cap force error->warning(FLERR, "FENE bond too long: {} {} {} {}", update->ntimestep, atom->tag[a], atom->tag[b], r); - rlogarg = 0.1; + rlogarg = rlogarg_min; + + // if overstretched F(r)=F(r_max)=F_max, E(r)=E(r_max)+F_max*(r-r_max) + if (r > r0[type]) { + rr0 = Delta[type]*sqrt(1.0-rlogarg); + // energy + if (eflag) { + ebond = -0.5 * k[type] * log(rlogarg) + k[type] * sqrt(1.0-rlogarg) / rlogarg / Delta[type] * + (r - r0[type] - Delta[type] * sqrt(1.0-rlogarg)); + } + } + // if overcompressed F(r)=F(r_min)=F_max, E(r)=E(r_min)+F_max*(r_min-r) + else if (r < r0[type]) { + rr0 = -Delta[type]*sqrt(1.0-rlogarg); + // energy + if (eflag) { + ebond = -0.5 * k[type] * log(rlogarg) + k[type] * sqrt(1.0-rlogarg) / rlogarg / Delta[type] * + (r0[type] - Delta[type] * sqrt(1.0-rlogarg) - r); + } + } } fbond = -k[type] * rr0 / rlogarg / Deltasq / r; @@ -232,10 +259,6 @@ void BondOxdnaFene::compute(int eflag, int vflag) delf[1] = delr[1] * fbond; delf[2] = delr[2] * fbond; - // energy - - if (eflag) { ebond = -0.5 * k[type] * log(rlogarg); } - // apply force and torque to each of 2 atoms if (newton_bond || a < nlocal) { @@ -295,15 +318,51 @@ void BondOxdnaFene::allocate() void BondOxdnaFene::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene"); + if (narg != 2 && narg != 4) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene"); if (!allocated) allocate(); int ilo, ihi; utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); - double k_one = utils::numeric(FLERR, arg[1], false, lmp); - double Delta_one = utils::numeric(FLERR, arg[2], false, lmp); - double r0_one = utils::numeric(FLERR, arg[3], false, lmp); + double k_one; + double Delta_one; + double r0_one; + + if (narg == 4) { + k_one = utils::numeric(FLERR, arg[1], false, lmp); + Delta_one = utils::numeric(FLERR, arg[2], false, lmp); + r0_one = utils::numeric(FLERR, arg[3], false, lmp); + } else { + if (comm->me == 0) { // read values from potential file + PotentialFileReader reader(lmp, arg[1], "oxdna potential", " (fene)"); + char * line; + std::string iloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && potential_name == "fene") { + k_one = values.next_double(); + Delta_one = values.next_double(); + r0_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (potential_name != "fene")) + error->one(FLERR, "No corresponding fene potential found in file {} for bond type {}", + arg[1], arg[0]); + } + + MPI_Bcast(&k_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&Delta_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&r0_one, 1, MPI_DOUBLE, 0, world); + } int count = 0; diff --git a/src/CG-DNA/bond_oxrna2_fene.cpp b/src/CG-DNA/bond_oxrna2_fene.cpp index 5d28f744a8..4faa95ef6f 100644 --- a/src/CG-DNA/bond_oxrna2_fene.cpp +++ b/src/CG-DNA/bond_oxrna2_fene.cpp @@ -16,6 +16,8 @@ #include "bond_oxrna2_fene.h" +#include "constants_oxdna.h" + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -25,8 +27,8 @@ using namespace LAMMPS_NS; void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], double r[3]) const { - constexpr double d_cs_x = -0.4; - constexpr double d_cs_z = +0.2; + double d_cs_x = ConstantsOxdna::get_d_cs(); + double d_cs_z = ConstantsOxdna::get_d_cs_z(); r[0] = d_cs_x * e1[0] + d_cs_z * e3[0]; r[1] = d_cs_x * e1[1] + d_cs_z * e3[1]; diff --git a/src/CG-DNA/constants_oxdna.cpp b/src/CG-DNA/constants_oxdna.cpp new file mode 100644 index 0000000000..3de3b9e57a --- /dev/null +++ b/src/CG-DNA/constants_oxdna.cpp @@ -0,0 +1,71 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Oliver Henrich (University of Strathclyde, Glasgow) + Kierran Falloon (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +#include "constants_oxdna.h" + +#include "update.h" + +namespace LAMMPS_NS { + +ConstantsOxdna::ConstantsOxdna(class LAMMPS *lmp) : Pointers(lmp) +{ + // set oxDNA units + units = update->unit_style; + real_flag = utils::strmatch(units.c_str(), "^real"); + if (real_flag) set_real_units(); +} + +// default to lj units +// oxDNA 1 parameters +double ConstantsOxdna::d_cs = -0.4; +double ConstantsOxdna::d_cst = +0.34; +double ConstantsOxdna::d_chb = +0.4; +double ConstantsOxdna::d_cb = +0.4; +// oxDNA 2 parameters +double ConstantsOxdna::d_cs_x = -0.34; +double ConstantsOxdna::d_cs_y = +0.3408; +double ConstantsOxdna::lambda_dh_one_prefactor = +0.3616455075438555; // = C1 +double ConstantsOxdna::qeff_dh_pf_one_prefactor = +0.08173808693529228; // = C2 +// oxRNA 2 parameters +double ConstantsOxdna::d_cs_z = +0.2; +double ConstantsOxdna::d_cst_x_3p = +0.4; +double ConstantsOxdna::d_cst_y_3p = +0.1; +double ConstantsOxdna::d_cst_x_5p = +0.124906078525; +double ConstantsOxdna::d_cst_y_5p = -0.00866274917473; + +void ConstantsOxdna::set_real_units() +{ + // oxDNA 1 parameters in real units + d_cs = -3.4072; + d_cst = +2.89612; + d_chb = +3.4072; + d_cb = +3.4072; + // oxDNA 2 parameters in real units + d_cs_x = -2.89612; + d_cs_y = +2.9029344; + lambda_dh_one_prefactor = +0.05624154892; // = C1 * 8.518 * sqrt(k_B/4.142e-20) + qeff_dh_pf_one_prefactor = +4.15079634587587; // = C2 * 5.961689060210325 * 8.518 + // oxRNA 2 parameters in real units + // d_cs_x = -3.4072 = d_cs for RNA + d_cs_z = +1.7036; + d_cst_x_3p = +3.4072; + d_cst_y_3p = +0.8518; + d_cst_x_5p = +1.063949977; + d_cst_y_5p = -0.07378929747; +}; + +} // namespace LAMMPS_NS diff --git a/src/CG-DNA/constants_oxdna.h b/src/CG-DNA/constants_oxdna.h new file mode 100644 index 0000000000..3ebcc47aff --- /dev/null +++ b/src/CG-DNA/constants_oxdna.h @@ -0,0 +1,65 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef CONSTANTS_OXDNA_H +#define CONSTANTS_OXDNA_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class ConstantsOxdna : protected Pointers { + public: + ConstantsOxdna(class LAMMPS *lmp); + virtual ~ConstantsOxdna(){}; + + // oxDNA 1 getters + static double get_d_cs() { return d_cs; } + static double get_d_cst() { return d_cst; } + static double get_d_chb() { return d_chb; } + static double get_d_cb() { return d_cb; } + + // oxDNA 2 getters + static double get_d_cs_x() { return d_cs_x; } + static double get_d_cs_y() { return d_cs_y; } + static double get_lambda_dh_one_prefactor() { return lambda_dh_one_prefactor; } + static double get_qeff_dh_pf_one_prefactor() { return qeff_dh_pf_one_prefactor; } + + // oxRNA 2 getters + static double get_d_cs_z() { return d_cs_z; } + static double get_d_cst_x_3p() { return d_cst_x_3p; } + static double get_d_cst_y_3p() { return d_cst_y_3p; } + static double get_d_cst_x_5p() { return d_cst_x_5p; } + static double get_d_cst_y_5p() { return d_cst_y_5p; } + + private: + std::string units; + bool real_flag; + void set_real_units(); + + // oxDNA 1 parameters + static double d_cs, d_cst, d_chb, d_cb; + + // oxDNA 2 parameters + static double d_cs_x, d_cs_y; + static double lambda_dh_one_prefactor, qeff_dh_pf_one_prefactor; + + // oxRNA 2 parameters + static double d_cs_z; + static double d_cst_x_3p, d_cst_y_3p; + static double d_cst_x_5p, d_cst_y_5p; +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/CG-DNA/pair_oxdna2_coaxstk.cpp b/src/CG-DNA/pair_oxdna2_coaxstk.cpp index 527020076c..a0f7c9e7e5 100644 --- a/src/CG-DNA/pair_oxdna2_coaxstk.cpp +++ b/src/CG-DNA/pair_oxdna2_coaxstk.cpp @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -26,6 +27,7 @@ #include "memory.h" #include "mf_oxdna.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -40,6 +42,7 @@ PairOxdna2Coaxstk::PairOxdna2Coaxstk(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; } /* ---------------------------------------------------------------------- */ @@ -112,7 +115,8 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag) double cosphi3; // distances COM-backbone site, COM-stacking site - double d_cs=-0.4, d_cst=+0.34; + double d_cs = ConstantsOxdna::get_d_cs(); + double d_cst = ConstantsOxdna::get_d_cst(); // vectors COM-backbone site, COM-stacking site in lab frame double ra_cs[3],ra_cst[3]; double rb_cs[3],rb_cst[3]; @@ -556,7 +560,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg) { int count; - if (narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk"); + if (narg != 3 && narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -583,30 +587,105 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg) double AA_cxst1_one, BB_cxst1_one; - k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp); - cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp); - cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp); - cut_cxst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); - cut_cxst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); + if (narg == 21) { + k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp); + cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp); + cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp); + cut_cxst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); + cut_cxst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); - a_cxst1_one = utils::numeric(FLERR,arg[7],false,lmp); - theta_cxst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); - dtheta_cxst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); + a_cxst1_one = utils::numeric(FLERR,arg[7],false,lmp); + theta_cxst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); + dtheta_cxst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); - a_cxst4_one = utils::numeric(FLERR,arg[10],false,lmp); - theta_cxst4_0_one = utils::numeric(FLERR,arg[11],false,lmp); - dtheta_cxst4_ast_one = utils::numeric(FLERR,arg[12],false,lmp); + a_cxst4_one = utils::numeric(FLERR,arg[10],false,lmp); + theta_cxst4_0_one = utils::numeric(FLERR,arg[11],false,lmp); + dtheta_cxst4_ast_one = utils::numeric(FLERR,arg[12],false,lmp); - a_cxst5_one = utils::numeric(FLERR,arg[13],false,lmp); - theta_cxst5_0_one = utils::numeric(FLERR,arg[14],false,lmp); - dtheta_cxst5_ast_one = utils::numeric(FLERR,arg[15],false,lmp); + a_cxst5_one = utils::numeric(FLERR,arg[13],false,lmp); + theta_cxst5_0_one = utils::numeric(FLERR,arg[14],false,lmp); + dtheta_cxst5_ast_one = utils::numeric(FLERR,arg[15],false,lmp); - a_cxst6_one = utils::numeric(FLERR,arg[16],false,lmp); - theta_cxst6_0_one = utils::numeric(FLERR,arg[17],false,lmp); - dtheta_cxst6_ast_one = utils::numeric(FLERR,arg[18],false,lmp); + a_cxst6_one = utils::numeric(FLERR,arg[16],false,lmp); + theta_cxst6_0_one = utils::numeric(FLERR,arg[17],false,lmp); + dtheta_cxst6_ast_one = utils::numeric(FLERR,arg[18],false,lmp); - AA_cxst1_one = utils::numeric(FLERR,arg[19],false,lmp); - BB_cxst1_one = utils::numeric(FLERR,arg[20],false,lmp); + AA_cxst1_one = utils::numeric(FLERR,arg[19],false,lmp); + BB_cxst1_one = utils::numeric(FLERR,arg[20],false,lmp); + } else { + if (comm->me == 0) { // read values from potential file + PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (coaxstk)"); + char * line; + std::string iloc, jloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "coaxstk") { + k_cxst_one = values.next_double(); + cut_cxst_0_one = values.next_double(); + cut_cxst_c_one = values.next_double(); + cut_cxst_lo_one = values.next_double(); + cut_cxst_hi_one = values.next_double(); + + a_cxst1_one = values.next_double(); + theta_cxst1_0_one = values.next_double(); + dtheta_cxst1_ast_one = values.next_double(); + + a_cxst4_one = values.next_double(); + theta_cxst4_0_one = values.next_double(); + dtheta_cxst4_ast_one = values.next_double(); + + a_cxst5_one = values.next_double(); + theta_cxst5_0_one = values.next_double(); + dtheta_cxst5_ast_one = values.next_double(); + + a_cxst6_one = values.next_double(); + theta_cxst6_0_one = values.next_double(); + dtheta_cxst6_ast_one = values.next_double(); + + AA_cxst1_one = values.next_double(); + BB_cxst1_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA2 potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "coaxstk")) + error->one(FLERR, "No corresponding coaxstk potential found in file {} for pair type {} {}", + arg[2], arg[0], arg[1]); + } + + MPI_Bcast(&k_cxst_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_c_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_lo_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_hi_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst1_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst1_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst4_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst4_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst4_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst5_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst5_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst5_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst6_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst6_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst6_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&AA_cxst1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&BB_cxst1_one, 1, MPI_DOUBLE, 0, world); + } b_cxst_lo_one = 0.25 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one)/ (0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) - diff --git a/src/CG-DNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp index a8114c84d7..5c0c32b2d9 100644 --- a/src/CG-DNA/pair_oxdna2_dh.cpp +++ b/src/CG-DNA/pair_oxdna2_dh.cpp @@ -19,11 +19,13 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_extra.h" #include "memory.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -36,6 +38,7 @@ PairOxdna2Dh::PairOxdna2Dh(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; } /* ---------------------------------------------------------------------- */ @@ -65,7 +68,8 @@ PairOxdna2Dh::~PairOxdna2Dh() void PairOxdna2Dh::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], double r[3]) { - double d_cs_x=-0.34, d_cs_y=+0.3408; + double d_cs_x = ConstantsOxdna::get_d_cs_x(); + double d_cs_y = ConstantsOxdna::get_d_cs_y(); r[0] = d_cs_x*e1[0] + d_cs_y*e2[0]; r[1] = d_cs_x*e1[1] + d_cs_y*e2[1]; @@ -302,7 +306,32 @@ void PairOxdna2Dh::coeff(int narg, char **arg) T = utils::numeric(FLERR,arg[2],false,lmp); rhos_dh_one = utils::numeric(FLERR,arg[3],false,lmp); - qeff_dh_one = utils::numeric(FLERR,arg[4],false,lmp); + + if (utils::strmatch(arg[4], "^[a-zA-Z0-9_]*\\.cgdna$")) { // if last arg is a potential file + if (comm->me == 0) { // read value from potential file + PotentialFileReader reader(lmp, arg[4], "oxdna potential", " (dh)"); + char * line; + std::string iloc, jloc, potential_name; + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "dh") { + qeff_dh_one = values.next_double(); + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA2 potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "dh")) + error->one(FLERR, "No corresponding dh potential found in file {} for pair type {} {}", + arg[4], arg[0], arg[1]); + } + MPI_Bcast(&qeff_dh_one, 1, MPI_DOUBLE, 0, world); + } else qeff_dh_one = utils::numeric(FLERR,arg[4],false,lmp); // else, it is effective charge double lambda_dh_one, kappa_dh_one, qeff_dh_pf_one; double b_dh_one, cut_dh_ast_one, cut_dh_c_one; @@ -314,7 +343,8 @@ void PairOxdna2Dh::coeff(int narg, char **arg) The numerical factor is the Debye length in s.u. lambda(T = 300 K = 0.1) = sqrt(eps_0 * eps_r * k_B * T/(2 * N_A * e^2 * 1000 mol/m^3)) - * 1/oxDNA_energy_unit + * 1/oxDNA_length_unit for LJ units, or; + * [(8.518 * sqrt(k_B / 4.142e-20))/oxDNA_length_unit] for real units (see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).) We use @@ -327,7 +357,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg) oxDNA_length_unit = 8.518e-10 m */ - lambda_dh_one = 0.3616455075438555*sqrt(T/0.1/rhos_dh_one); + lambda_dh_one = ConstantsOxdna::get_lambda_dh_one_prefactor()*sqrt(T/0.1/rhos_dh_one); kappa_dh_one = 1.0/lambda_dh_one; // prefactor in DH interaction containing qeff^2 @@ -336,14 +366,15 @@ void PairOxdna2Dh::coeff(int narg, char **arg) NOTE: The numerical factor is qeff_dh_pf = e^2/(4 * pi * eps_0 * eps_r) - * 1/(oxDNA_energy_unit * oxDNA_length_unit) + * 1/(oxDNA_energy_unit * oxDNA_length_unit) for LJ units, or; + * [(~5.96169* 8.518)/(oxDNA_energy_unit * oxDNA_length_unit)] for real units (see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).) In addition to the above units we use oxDNA_energy_unit = 4.142e-20 J */ - qeff_dh_pf_one = 0.08173808693529228*qeff_dh_one*qeff_dh_one; + qeff_dh_pf_one = ConstantsOxdna::get_qeff_dh_pf_one_prefactor()*qeff_dh_one*qeff_dh_one; // smoothing parameters - determined through continuity and differentiability diff --git a/src/CG-DNA/pair_oxdna2_excv.cpp b/src/CG-DNA/pair_oxdna2_excv.cpp index f0f9ca904e..2b047dae8e 100644 --- a/src/CG-DNA/pair_oxdna2_excv.cpp +++ b/src/CG-DNA/pair_oxdna2_excv.cpp @@ -14,6 +14,7 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "constants_oxdna.h" #include "pair_oxdna2_excv.h" using namespace LAMMPS_NS; @@ -24,7 +25,9 @@ using namespace LAMMPS_NS; void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], double rs[3], double rb[3]) { - double d_cs_x = -0.34, d_cs_y = +0.3408, d_cb = +0.4; + double d_cs_x = ConstantsOxdna::get_d_cs_x(); + double d_cs_y = ConstantsOxdna::get_d_cs_y(); + double d_cb = ConstantsOxdna::get_d_cb(); rs[0] = d_cs_x * e1[0] + d_cs_y * e2[0]; rs[1] = d_cs_x * e1[1] + d_cs_y * e2[1]; diff --git a/src/CG-DNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp index 679bfbf18d..d00e9fedf8 100644 --- a/src/CG-DNA/pair_oxdna_coaxstk.cpp +++ b/src/CG-DNA/pair_oxdna_coaxstk.cpp @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -26,6 +27,7 @@ #include "memory.h" #include "mf_oxdna.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -40,6 +42,7 @@ PairOxdnaCoaxstk::PairOxdnaCoaxstk(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; } /* ---------------------------------------------------------------------- */ @@ -123,7 +126,8 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag) double dcdrax,dcdray,dcdraz; // distances COM-backbone site, COM-stacking site - double d_cs=-0.4, d_cst=+0.34; + double d_cs = ConstantsOxdna::get_d_cs(); + double d_cst = ConstantsOxdna::get_d_cst(); // vectors COM-backbone site, COM-stacking site in lab frame double ra_cs[3],ra_cst[3]; double rb_cs[3],rb_cst[3]; @@ -690,7 +694,7 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg) { int count; - if (narg != 23) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk"); + if (narg != 3 && narg != 23) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -718,32 +722,111 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg) double a_cxst3p_one, cosphi_cxst3p_ast_one, b_cxst3p_one, cosphi_cxst3p_c_one; double a_cxst4p_one, cosphi_cxst4p_ast_one, b_cxst4p_one, cosphi_cxst4p_c_one; - k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp); - cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp); - cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp); - cut_cxst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); - cut_cxst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); + if (narg == 23) { + k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp); + cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp); + cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp); + cut_cxst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); + cut_cxst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); - a_cxst1_one = utils::numeric(FLERR,arg[7],false,lmp); - theta_cxst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); - dtheta_cxst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); + a_cxst1_one = utils::numeric(FLERR,arg[7],false,lmp); + theta_cxst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); + dtheta_cxst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); - a_cxst4_one = utils::numeric(FLERR,arg[10],false,lmp); - theta_cxst4_0_one = utils::numeric(FLERR,arg[11],false,lmp); - dtheta_cxst4_ast_one = utils::numeric(FLERR,arg[12],false,lmp); + a_cxst4_one = utils::numeric(FLERR,arg[10],false,lmp); + theta_cxst4_0_one = utils::numeric(FLERR,arg[11],false,lmp); + dtheta_cxst4_ast_one = utils::numeric(FLERR,arg[12],false,lmp); - a_cxst5_one = utils::numeric(FLERR,arg[13],false,lmp); - theta_cxst5_0_one = utils::numeric(FLERR,arg[14],false,lmp); - dtheta_cxst5_ast_one = utils::numeric(FLERR,arg[15],false,lmp); + a_cxst5_one = utils::numeric(FLERR,arg[13],false,lmp); + theta_cxst5_0_one = utils::numeric(FLERR,arg[14],false,lmp); + dtheta_cxst5_ast_one = utils::numeric(FLERR,arg[15],false,lmp); - a_cxst6_one = utils::numeric(FLERR,arg[16],false,lmp); - theta_cxst6_0_one = utils::numeric(FLERR,arg[17],false,lmp); - dtheta_cxst6_ast_one = utils::numeric(FLERR,arg[18],false,lmp); + a_cxst6_one = utils::numeric(FLERR,arg[16],false,lmp); + theta_cxst6_0_one = utils::numeric(FLERR,arg[17],false,lmp); + dtheta_cxst6_ast_one = utils::numeric(FLERR,arg[18],false,lmp); - a_cxst3p_one = utils::numeric(FLERR,arg[19],false,lmp); - cosphi_cxst3p_ast_one = utils::numeric(FLERR,arg[20],false,lmp); - a_cxst4p_one = utils::numeric(FLERR,arg[21],false,lmp); - cosphi_cxst4p_ast_one = utils::numeric(FLERR,arg[22],false,lmp); + a_cxst3p_one = utils::numeric(FLERR,arg[19],false,lmp); + cosphi_cxst3p_ast_one = utils::numeric(FLERR,arg[20],false,lmp); + a_cxst4p_one = utils::numeric(FLERR,arg[21],false,lmp); + cosphi_cxst4p_ast_one = utils::numeric(FLERR,arg[22],false,lmp); + } else { + if (comm->me == 0) { // read values from potential file + PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (coaxstk)"); + char * line; + std::string iloc, jloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "coaxstk") { + k_cxst_one = values.next_double(); + cut_cxst_0_one = values.next_double(); + cut_cxst_c_one = values.next_double(); + cut_cxst_lo_one = values.next_double(); + cut_cxst_hi_one = values.next_double(); + + a_cxst1_one = values.next_double(); + theta_cxst1_0_one = values.next_double(); + dtheta_cxst1_ast_one = values.next_double(); + + a_cxst4_one = values.next_double(); + theta_cxst4_0_one = values.next_double(); + dtheta_cxst4_ast_one = values.next_double(); + + a_cxst5_one = values.next_double(); + theta_cxst5_0_one = values.next_double(); + dtheta_cxst5_ast_one = values.next_double(); + + a_cxst6_one = values.next_double(); + theta_cxst6_0_one = values.next_double(); + dtheta_cxst6_ast_one = values.next_double(); + + a_cxst3p_one = values.next_double(); + cosphi_cxst3p_ast_one = values.next_double(); + a_cxst4p_one = values.next_double(); + cosphi_cxst4p_ast_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "coaxstk")) + error->one(FLERR, "No corresponding coaxstk potential found in file {} for pair type {} {}", + arg[2], arg[0], arg[1]); + } + + MPI_Bcast(&k_cxst_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_c_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_lo_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_cxst_hi_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst1_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst1_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst4_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst4_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst4_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst5_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst5_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst5_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst6_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_cxst6_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_cxst6_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_cxst3p_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cosphi_cxst3p_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_cxst4p_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cosphi_cxst4p_ast_one, 1, MPI_DOUBLE, 0, world); + } b_cxst_lo_one = 0.25 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one)/ (0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) - diff --git a/src/CG-DNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp index 254b8e18d8..3e92512f4d 100644 --- a/src/CG-DNA/pair_oxdna_excv.cpp +++ b/src/CG-DNA/pair_oxdna_excv.cpp @@ -20,12 +20,14 @@ #include "atom.h" #include "atom_vec_ellipsoid.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_extra.h" #include "memory.h" #include "mf_oxdna.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -42,6 +44,7 @@ PairOxdnaExcv::PairOxdnaExcv(LAMMPS *lmp) : Pair(lmp) // set comm size needed by this Pair comm_forward = 9; + trim_flag = 0; } /* ---------------------------------------------------------------------- */ @@ -96,7 +99,8 @@ PairOxdnaExcv::~PairOxdnaExcv() void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3], double /*e3*/[3], double rs[3], double rb[3]) { - double d_cs=-0.4, d_cb=+0.4; + double d_cs = ConstantsOxdna::get_d_cs(); + double d_cb = ConstantsOxdna::get_d_cb(); rs[0] = d_cs*e1[0]; rs[1] = d_cs*e1[1]; @@ -499,7 +503,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg) { int count; - if (narg != 11) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv"); + if (narg != 3 && narg != 11) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -517,11 +521,74 @@ void PairOxdnaExcv::coeff(int narg, char **arg) double epsilon_bb_one, sigma_bb_one; double cut_bb_ast_one, cut_bb_c_one, b_bb_one; - // Excluded volume interaction - // LJ parameters - epsilon_ss_one = utils::numeric(FLERR,arg[2],false,lmp); - sigma_ss_one = utils::numeric(FLERR,arg[3],false,lmp); - cut_ss_ast_one = utils::numeric(FLERR,arg[4],false,lmp); + if (narg == 11) { + // Excluded volume interaction + // LJ parameters + epsilon_ss_one = utils::numeric(FLERR,arg[2],false,lmp); + sigma_ss_one = utils::numeric(FLERR,arg[3],false,lmp); + cut_ss_ast_one = utils::numeric(FLERR,arg[4],false,lmp); + + // LJ parameters + epsilon_sb_one = utils::numeric(FLERR,arg[5],false,lmp); + sigma_sb_one = utils::numeric(FLERR,arg[6],false,lmp); + cut_sb_ast_one = utils::numeric(FLERR,arg[7],false,lmp); + + // LJ parameters + epsilon_bb_one = utils::numeric(FLERR,arg[8],false,lmp); + sigma_bb_one = utils::numeric(FLERR,arg[9],false,lmp); + cut_bb_ast_one = utils::numeric(FLERR,arg[10],false,lmp); + } else { + if (comm->me == 0) { + PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (excv)"); + char * line; + std::string iloc, jloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "excv") { + // Excluded volume interaction + // LJ parameters + epsilon_ss_one = values.next_double(); + sigma_ss_one = values.next_double(); + cut_ss_ast_one = values.next_double(); + + // LJ parameters + epsilon_sb_one = values.next_double(); + sigma_sb_one = values.next_double(); + cut_sb_ast_one = values.next_double(); + + // LJ parameters + epsilon_bb_one = values.next_double(); + sigma_bb_one = values.next_double(); + cut_bb_ast_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "excv")) + error->one(FLERR, "No corresponding excv potential found in file {} for pair type {} {}", + arg[2], arg[0], arg[1]); + } + + MPI_Bcast(&epsilon_ss_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma_ss_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_ss_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&epsilon_sb_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma_sb_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_sb_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&epsilon_bb_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma_bb_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_bb_ast_one, 1, MPI_DOUBLE, 0, world); + } // smoothing - determined through continuity and differentiability b_ss_one = 4.0/sigma_ss_one @@ -549,11 +616,6 @@ void PairOxdnaExcv::coeff(int narg, char **arg) count = 0; - // LJ parameters - epsilon_sb_one = utils::numeric(FLERR,arg[5],false,lmp); - sigma_sb_one = utils::numeric(FLERR,arg[6],false,lmp); - cut_sb_ast_one = utils::numeric(FLERR,arg[7],false,lmp); - // smoothing - determined through continuity and differentiability b_sb_one = 4.0/sigma_sb_one *(6.0*pow(sigma_sb_one/cut_sb_ast_one,7)-12.0*pow(sigma_sb_one/cut_sb_ast_one,13)) @@ -580,11 +642,6 @@ void PairOxdnaExcv::coeff(int narg, char **arg) count = 0; - // LJ parameters - epsilon_bb_one = utils::numeric(FLERR,arg[8],false,lmp); - sigma_bb_one = utils::numeric(FLERR,arg[9],false,lmp); - cut_bb_ast_one = utils::numeric(FLERR,arg[10],false,lmp); - // smoothing - determined through continuity and differentiability b_bb_one = 4.0/sigma_bb_one *(6.0*pow(sigma_bb_one/cut_bb_ast_one,7)-12.0*pow(sigma_bb_one/cut_bb_ast_one,13)) diff --git a/src/CG-DNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp index 5b121a9113..ba82aeef83 100644 --- a/src/CG-DNA/pair_oxdna_hbond.cpp +++ b/src/CG-DNA/pair_oxdna_hbond.cpp @@ -19,12 +19,14 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_extra.h" #include "memory.h" #include "mf_oxdna.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -38,6 +40,7 @@ PairOxdnaHbond::PairOxdnaHbond(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; // sequence-specific base-pairing strength // A:0 C:1 G:2 T:3, 5'- [i][j] -3' @@ -144,7 +147,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag) double theta8,t8dir[3],cost8; // distance COM-hbonding site - double d_chb=+0.4; + double d_chb = ConstantsOxdna::get_d_chb(); // vectors COM-h-bonding site in lab frame double ra_chb[3],rb_chb[3]; // Cartesian unit vectors in lab frame @@ -633,7 +636,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) { int count; - if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond"); + if (narg != 4 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,imod4,jmod4; @@ -670,36 +673,125 @@ void PairOxdnaHbond::coeff(int narg, char **arg) if (strcmp(arg[2],"seqav") == 0) seqdepflag = 0; if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1; - epsilon_hb_one = utils::numeric(FLERR,arg[3],false,lmp); - a_hb_one = utils::numeric(FLERR,arg[4],false,lmp); - cut_hb_0_one = utils::numeric(FLERR,arg[5],false,lmp); - cut_hb_c_one = utils::numeric(FLERR,arg[6],false,lmp); - cut_hb_lo_one = utils::numeric(FLERR,arg[7],false,lmp); - cut_hb_hi_one = utils::numeric(FLERR,arg[8],false,lmp); + if (narg == 27) { + epsilon_hb_one = utils::numeric(FLERR,arg[3],false,lmp); + a_hb_one = utils::numeric(FLERR,arg[4],false,lmp); + cut_hb_0_one = utils::numeric(FLERR,arg[5],false,lmp); + cut_hb_c_one = utils::numeric(FLERR,arg[6],false,lmp); + cut_hb_lo_one = utils::numeric(FLERR,arg[7],false,lmp); + cut_hb_hi_one = utils::numeric(FLERR,arg[8],false,lmp); - a_hb1_one = utils::numeric(FLERR,arg[9],false,lmp); - theta_hb1_0_one = utils::numeric(FLERR,arg[10],false,lmp); - dtheta_hb1_ast_one = utils::numeric(FLERR,arg[11],false,lmp); + a_hb1_one = utils::numeric(FLERR,arg[9],false,lmp); + theta_hb1_0_one = utils::numeric(FLERR,arg[10],false,lmp); + dtheta_hb1_ast_one = utils::numeric(FLERR,arg[11],false,lmp); - a_hb2_one = utils::numeric(FLERR,arg[12],false,lmp); - theta_hb2_0_one = utils::numeric(FLERR,arg[13],false,lmp); - dtheta_hb2_ast_one = utils::numeric(FLERR,arg[14],false,lmp); + a_hb2_one = utils::numeric(FLERR,arg[12],false,lmp); + theta_hb2_0_one = utils::numeric(FLERR,arg[13],false,lmp); + dtheta_hb2_ast_one = utils::numeric(FLERR,arg[14],false,lmp); - a_hb3_one = utils::numeric(FLERR,arg[15],false,lmp); - theta_hb3_0_one = utils::numeric(FLERR,arg[16],false,lmp); - dtheta_hb3_ast_one = utils::numeric(FLERR,arg[17],false,lmp); + a_hb3_one = utils::numeric(FLERR,arg[15],false,lmp); + theta_hb3_0_one = utils::numeric(FLERR,arg[16],false,lmp); + dtheta_hb3_ast_one = utils::numeric(FLERR,arg[17],false,lmp); - a_hb4_one = utils::numeric(FLERR,arg[18],false,lmp); - theta_hb4_0_one = utils::numeric(FLERR,arg[19],false,lmp); - dtheta_hb4_ast_one = utils::numeric(FLERR,arg[20],false,lmp); + a_hb4_one = utils::numeric(FLERR,arg[18],false,lmp); + theta_hb4_0_one = utils::numeric(FLERR,arg[19],false,lmp); + dtheta_hb4_ast_one = utils::numeric(FLERR,arg[20],false,lmp); - a_hb7_one = utils::numeric(FLERR,arg[21],false,lmp); - theta_hb7_0_one = utils::numeric(FLERR,arg[22],false,lmp); - dtheta_hb7_ast_one = utils::numeric(FLERR,arg[23],false,lmp); + a_hb7_one = utils::numeric(FLERR,arg[21],false,lmp); + theta_hb7_0_one = utils::numeric(FLERR,arg[22],false,lmp); + dtheta_hb7_ast_one = utils::numeric(FLERR,arg[23],false,lmp); + + a_hb8_one = utils::numeric(FLERR,arg[24],false,lmp); + theta_hb8_0_one = utils::numeric(FLERR,arg[25],false,lmp); + dtheta_hb8_ast_one = utils::numeric(FLERR,arg[26],false,lmp); + } else { // read values from potential file + if (comm->me == 0) { + PotentialFileReader reader(lmp, arg[3], "oxdna potential", " (hbond)"); + char * line; + std::string iloc, jloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "hbond") { + + epsilon_hb_one = values.next_double(); + a_hb_one = values.next_double(); + cut_hb_0_one = values.next_double(); + cut_hb_c_one = values.next_double(); + cut_hb_lo_one = values.next_double(); + cut_hb_hi_one = values.next_double(); + + a_hb1_one = values.next_double(); + theta_hb1_0_one = values.next_double(); + dtheta_hb1_ast_one = values.next_double(); + + a_hb2_one = values.next_double(); + theta_hb2_0_one = values.next_double(); + dtheta_hb2_ast_one = values.next_double(); + + a_hb3_one = values.next_double(); + theta_hb3_0_one = values.next_double(); + dtheta_hb3_ast_one = values.next_double(); + + a_hb4_one = values.next_double(); + theta_hb4_0_one = values.next_double(); + dtheta_hb4_ast_one = values.next_double(); + + a_hb7_one = values.next_double(); + theta_hb7_0_one = values.next_double(); + dtheta_hb7_ast_one = values.next_double(); + + a_hb8_one = values.next_double(); + theta_hb8_0_one = values.next_double(); + dtheta_hb8_ast_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "hbond")) + error->one(FLERR, "No corresponding hbond potential found in file {} for pair type {} {}", + arg[3], arg[0], arg[1]); + } + + MPI_Bcast(&epsilon_hb_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_hb_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_hb_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_hb_c_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_hb_lo_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_hb_hi_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_hb1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_hb1_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_hb1_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_hb2_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_hb2_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_hb2_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_hb3_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_hb3_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_hb3_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_hb4_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_hb4_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_hb4_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_hb7_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_hb7_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_hb7_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_hb8_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_hb8_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_hb8_ast_one, 1, MPI_DOUBLE, 0, world); + } - a_hb8_one = utils::numeric(FLERR,arg[24],false,lmp); - theta_hb8_0_one = utils::numeric(FLERR,arg[25],false,lmp); - dtheta_hb8_ast_one = utils::numeric(FLERR,arg[26],false,lmp); b_hb_lo_one = 2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))* 2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))* diff --git a/src/CG-DNA/pair_oxdna_stk.cpp b/src/CG-DNA/pair_oxdna_stk.cpp index 1ef779dbd9..301782d212 100644 --- a/src/CG-DNA/pair_oxdna_stk.cpp +++ b/src/CG-DNA/pair_oxdna_stk.cpp @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_extra.h" @@ -26,6 +27,7 @@ #include "mf_oxdna.h" #include "neighbor.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -39,6 +41,7 @@ PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; // sequence-specific stacking strength // A:0 C:1 G:2 T:3, 3'- [i][j] -5' @@ -222,7 +225,8 @@ void PairOxdnaStk::compute(int eflag, int vflag) double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3]; // distances COM-backbone site, COM-stacking site - double d_cs=-0.4, d_cst=+0.34; + double d_cs = ConstantsOxdna::get_d_cs(); + double d_cst = ConstantsOxdna::get_d_cst(); // vectors COM-backbone site, COM-stacking site in lab frame double ra_cs[3],ra_cst[3]; double rb_cs[3],rb_cst[3]; @@ -774,7 +778,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) { int count; - if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); + if (narg != 7 && narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,imod4,jmod4; @@ -811,25 +815,91 @@ void PairOxdnaStk::coeff(int narg, char **arg) kappa_st_one = utils::numeric(FLERR,arg[5],false,lmp); epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T); - a_st_one = utils::numeric(FLERR,arg[6],false,lmp); - cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp); - cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp); - cut_st_lo_one = utils::numeric(FLERR,arg[9],false,lmp); - cut_st_hi_one = utils::numeric(FLERR,arg[10],false,lmp); + if (narg == 24) { // values are listed in input + a_st_one = utils::numeric(FLERR,arg[6],false,lmp); + cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp); + cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp); + cut_st_lo_one = utils::numeric(FLERR,arg[9],false,lmp); + cut_st_hi_one = utils::numeric(FLERR,arg[10],false,lmp); - a_st4_one = utils::numeric(FLERR,arg[11],false,lmp); - theta_st4_0_one = utils::numeric(FLERR,arg[12],false,lmp); - dtheta_st4_ast_one = utils::numeric(FLERR,arg[13],false,lmp); - a_st5_one = utils::numeric(FLERR,arg[14],false,lmp); - theta_st5_0_one = utils::numeric(FLERR,arg[15],false,lmp); - dtheta_st5_ast_one = utils::numeric(FLERR,arg[16],false,lmp); - a_st6_one = utils::numeric(FLERR,arg[17],false,lmp); - theta_st6_0_one = utils::numeric(FLERR,arg[18],false,lmp); - dtheta_st6_ast_one = utils::numeric(FLERR,arg[19],false,lmp); - a_st1_one = utils::numeric(FLERR,arg[20],false,lmp); - cosphi_st1_ast_one = utils::numeric(FLERR,arg[21],false,lmp); - a_st2_one = utils::numeric(FLERR,arg[22],false,lmp); - cosphi_st2_ast_one = utils::numeric(FLERR,arg[23],false,lmp); + a_st4_one = utils::numeric(FLERR,arg[11],false,lmp); + theta_st4_0_one = utils::numeric(FLERR,arg[12],false,lmp); + dtheta_st4_ast_one = utils::numeric(FLERR,arg[13],false,lmp); + a_st5_one = utils::numeric(FLERR,arg[14],false,lmp); + theta_st5_0_one = utils::numeric(FLERR,arg[15],false,lmp); + dtheta_st5_ast_one = utils::numeric(FLERR,arg[16],false,lmp); + a_st6_one = utils::numeric(FLERR,arg[17],false,lmp); + theta_st6_0_one = utils::numeric(FLERR,arg[18],false,lmp); + dtheta_st6_ast_one = utils::numeric(FLERR,arg[19],false,lmp); + a_st1_one = utils::numeric(FLERR,arg[20],false,lmp); + cosphi_st1_ast_one = utils::numeric(FLERR,arg[21],false,lmp); + a_st2_one = utils::numeric(FLERR,arg[22],false,lmp); + cosphi_st2_ast_one = utils::numeric(FLERR,arg[23],false,lmp); + } else { // read values from potential file + if (comm->me == 0) { + PotentialFileReader reader(lmp, arg[6], "oxdna potential", " (stk)"); + char * line; + std::string iloc, jloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "stk") { + + a_st_one = values.next_double(); + cut_st_0_one = values.next_double(); + cut_st_c_one = values.next_double(); + cut_st_lo_one = values.next_double(); + cut_st_hi_one = values.next_double(); + + a_st4_one = values.next_double(); + theta_st4_0_one = values.next_double(); + dtheta_st4_ast_one = values.next_double(); + a_st5_one = values.next_double(); + theta_st5_0_one = values.next_double(); + dtheta_st5_ast_one = values.next_double(); + a_st6_one = values.next_double(); + theta_st6_0_one = values.next_double(); + dtheta_st6_ast_one = values.next_double(); + a_st1_one = values.next_double(); + cosphi_st1_ast_one = values.next_double(); + a_st2_one = values.next_double(); + cosphi_st2_ast_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "stk")) + error->one(FLERR, "No corresponding stk potential found in file {} for pair type {} {}", + arg[4], arg[0], arg[1]); + } + + MPI_Bcast(&a_st_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_c_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_lo_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_hi_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_st4_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_st4_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_st4_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_st5_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_st5_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_st5_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_st6_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_st6_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_st6_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_st1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cosphi_st1_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_st2_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cosphi_st2_ast_one, 1, MPI_DOUBLE, 0, world); + } b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* diff --git a/src/CG-DNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp index 6ef6091889..646c0f7216 100644 --- a/src/CG-DNA/pair_oxdna_xstk.cpp +++ b/src/CG-DNA/pair_oxdna_xstk.cpp @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -26,6 +27,7 @@ #include "memory.h" #include "mf_oxdna.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -40,6 +42,7 @@ PairOxdnaXstk::PairOxdnaXstk(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; } /* ---------------------------------------------------------------------- */ @@ -121,7 +124,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag) double theta8,theta8p,t8dir[3],cost8; // distance COM-h-bonding site - double d_chb=+0.4; + double d_chb = ConstantsOxdna::get_d_chb(); // vectors COM-h-bonding site in lab frame double ra_chb[3],rb_chb[3]; // Cartesian unit vectors in lab frame @@ -630,7 +633,7 @@ void PairOxdnaXstk::coeff(int narg, char **arg) { int count; - if (narg != 25) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); + if (narg != 3 && narg != 25) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -661,35 +664,120 @@ void PairOxdnaXstk::coeff(int narg, char **arg) double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one; double b_xst8_one, dtheta_xst8_c_one; - k_xst_one = utils::numeric(FLERR,arg[2],false,lmp); - cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp); - cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp); - cut_xst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); - cut_xst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); + if (narg == 25) { + k_xst_one = utils::numeric(FLERR,arg[2],false,lmp); + cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp); + cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp); + cut_xst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); + cut_xst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); - a_xst1_one = utils::numeric(FLERR,arg[7],false,lmp); - theta_xst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); - dtheta_xst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); + a_xst1_one = utils::numeric(FLERR,arg[7],false,lmp); + theta_xst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); + dtheta_xst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); - a_xst2_one = utils::numeric(FLERR,arg[10],false,lmp); - theta_xst2_0_one = utils::numeric(FLERR,arg[11],false,lmp); - dtheta_xst2_ast_one = utils::numeric(FLERR,arg[12],false,lmp); + a_xst2_one = utils::numeric(FLERR,arg[10],false,lmp); + theta_xst2_0_one = utils::numeric(FLERR,arg[11],false,lmp); + dtheta_xst2_ast_one = utils::numeric(FLERR,arg[12],false,lmp); - a_xst3_one = utils::numeric(FLERR,arg[13],false,lmp); - theta_xst3_0_one = utils::numeric(FLERR,arg[14],false,lmp); - dtheta_xst3_ast_one = utils::numeric(FLERR,arg[15],false,lmp); + a_xst3_one = utils::numeric(FLERR,arg[13],false,lmp); + theta_xst3_0_one = utils::numeric(FLERR,arg[14],false,lmp); + dtheta_xst3_ast_one = utils::numeric(FLERR,arg[15],false,lmp); - a_xst4_one = utils::numeric(FLERR,arg[16],false,lmp); - theta_xst4_0_one = utils::numeric(FLERR,arg[17],false,lmp); - dtheta_xst4_ast_one = utils::numeric(FLERR,arg[18],false,lmp); + a_xst4_one = utils::numeric(FLERR,arg[16],false,lmp); + theta_xst4_0_one = utils::numeric(FLERR,arg[17],false,lmp); + dtheta_xst4_ast_one = utils::numeric(FLERR,arg[18],false,lmp); - a_xst7_one = utils::numeric(FLERR,arg[19],false,lmp); - theta_xst7_0_one = utils::numeric(FLERR,arg[20],false,lmp); - dtheta_xst7_ast_one = utils::numeric(FLERR,arg[21],false,lmp); + a_xst7_one = utils::numeric(FLERR,arg[19],false,lmp); + theta_xst7_0_one = utils::numeric(FLERR,arg[20],false,lmp); + dtheta_xst7_ast_one = utils::numeric(FLERR,arg[21],false,lmp); - a_xst8_one = utils::numeric(FLERR,arg[22],false,lmp); - theta_xst8_0_one = utils::numeric(FLERR,arg[23],false,lmp); - dtheta_xst8_ast_one = utils::numeric(FLERR,arg[24],false,lmp); + a_xst8_one = utils::numeric(FLERR,arg[22],false,lmp); + theta_xst8_0_one = utils::numeric(FLERR,arg[23],false,lmp); + dtheta_xst8_ast_one = utils::numeric(FLERR,arg[24],false,lmp); + } else { + if (comm->me == 0) { + PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (xstk)"); + char * line; + std::string iloc, jloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "xstk") { + k_xst_one = values.next_double(); + cut_xst_0_one = values.next_double(); + cut_xst_c_one = values.next_double(); + cut_xst_lo_one = values.next_double(); + cut_xst_hi_one = values.next_double(); + + a_xst1_one = values.next_double(); + theta_xst1_0_one = values.next_double(); + dtheta_xst1_ast_one = values.next_double(); + + a_xst2_one = values.next_double(); + theta_xst2_0_one = values.next_double(); + dtheta_xst2_ast_one = values.next_double(); + + a_xst3_one = values.next_double(); + theta_xst3_0_one = values.next_double(); + dtheta_xst3_ast_one = values.next_double(); + + a_xst4_one = values.next_double(); + theta_xst4_0_one = values.next_double(); + dtheta_xst4_ast_one = values.next_double(); + + a_xst7_one = values.next_double(); + theta_xst7_0_one = values.next_double(); + dtheta_xst7_ast_one = values.next_double(); + + a_xst8_one = values.next_double(); + theta_xst8_0_one = values.next_double(); + dtheta_xst8_ast_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "xstk")) + error->one(FLERR, "No corresponding xstk potential found in file {} for pair type {} {}", + arg[2], arg[0], arg[1]); + } + + MPI_Bcast(&k_xst_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_c_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_lo_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_hi_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst1_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst1_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst2_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst2_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst2_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst3_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst3_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst3_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst4_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst4_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst4_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst7_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst7_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst7_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst8_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst8_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst8_ast_one, 1, MPI_DOUBLE, 0, world); + } b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/ diff --git a/src/CG-DNA/pair_oxrna2_dh.cpp b/src/CG-DNA/pair_oxrna2_dh.cpp index eceda90768..1495e1f2ee 100644 --- a/src/CG-DNA/pair_oxrna2_dh.cpp +++ b/src/CG-DNA/pair_oxrna2_dh.cpp @@ -16,6 +16,8 @@ #include "pair_oxrna2_dh.h" +#include "constants_oxdna.h" + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -24,7 +26,8 @@ using namespace LAMMPS_NS; void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], double r[3]) { - double d_cs_x = -0.4, d_cs_z = +0.2; + double d_cs_x = ConstantsOxdna::get_d_cs(); + double d_cs_z = ConstantsOxdna::get_d_cs_z(); r[0] = d_cs_x * e1[0] + d_cs_z * e3[0]; r[1] = d_cs_x * e1[1] + d_cs_z * e3[1]; diff --git a/src/CG-DNA/pair_oxrna2_excv.cpp b/src/CG-DNA/pair_oxrna2_excv.cpp index a49497ef5a..7dda4f9434 100644 --- a/src/CG-DNA/pair_oxrna2_excv.cpp +++ b/src/CG-DNA/pair_oxrna2_excv.cpp @@ -17,6 +17,8 @@ #include "pair_oxrna2_excv.h" +#include "constants_oxdna.h" + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -25,7 +27,9 @@ using namespace LAMMPS_NS; void PairOxrna2Excv::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], double rs[3], double rb[3]) { - double d_cs_x=-0.4, d_cs_z=+0.2, d_cb=+0.4; + double d_cs_x = ConstantsOxdna::get_d_cs(); + double d_cs_z = ConstantsOxdna::get_d_cs_z(); + double d_cb = ConstantsOxdna::get_d_cb(); rs[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; rs[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; diff --git a/src/CG-DNA/pair_oxrna2_hbond.cpp b/src/CG-DNA/pair_oxrna2_hbond.cpp index 14ecc6c659..0c4ffcb4f7 100644 --- a/src/CG-DNA/pair_oxrna2_hbond.cpp +++ b/src/CG-DNA/pair_oxrna2_hbond.cpp @@ -24,6 +24,7 @@ PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; // sequence-specific base-pairing strength // A:0 C:1 G:2 U:3, 5'- [i][j] -3' diff --git a/src/CG-DNA/pair_oxrna2_stk.cpp b/src/CG-DNA/pair_oxrna2_stk.cpp index f56aa572e8..423235b46a 100644 --- a/src/CG-DNA/pair_oxrna2_stk.cpp +++ b/src/CG-DNA/pair_oxrna2_stk.cpp @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -27,6 +28,7 @@ #include "mf_oxdna.h" #include "neighbor.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -41,6 +43,7 @@ PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; // sequence-specific stacking strength // A:0 C:1 G:2 U:3, 3'- [i][j] -5' @@ -232,9 +235,12 @@ void PairOxrna2Stk::compute(int eflag, int vflag) double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3]; // distances COM-backbone site, COM-3' and COM-5' stacking site - double d_cs_x=-0.4, d_cs_z=+0.2; - double d_cst_x_3p=+0.4, d_cst_y_3p=+0.1; - double d_cst_x_5p=+0.124906078525, d_cst_y_5p=-0.00866274917473; + double d_cs_x = ConstantsOxdna::get_d_cs(); + double d_cs_z = ConstantsOxdna::get_d_cs_z(); + double d_cst_x_3p = ConstantsOxdna::get_d_cst_x_3p(); + double d_cst_y_3p = ConstantsOxdna::get_d_cst_y_3p(); + double d_cst_x_5p = ConstantsOxdna::get_d_cst_x_5p(); + double d_cst_y_5p = ConstantsOxdna::get_d_cst_y_5p(); // 3' and p5' auxiliary vectors double d3p_x=-0.462510,d3p_y=-0.528218,d3p_z=+0.712089; @@ -841,7 +847,7 @@ void PairOxrna2Stk::coeff(int narg, char **arg) { int count; - if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk"); + if (narg != 7 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -881,30 +887,106 @@ void PairOxrna2Stk::coeff(int narg, char **arg) kappa_st_one = utils::numeric(FLERR,arg[5],false,lmp); epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T); - a_st_one = utils::numeric(FLERR,arg[6],false,lmp); - cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp); - cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp); - cut_st_lo_one = utils::numeric(FLERR,arg[9],false,lmp); - cut_st_hi_one = utils::numeric(FLERR,arg[10],false,lmp); + if (narg == 27) { + a_st_one = utils::numeric(FLERR,arg[6],false,lmp); + cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp); + cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp); + cut_st_lo_one = utils::numeric(FLERR,arg[9],false,lmp); + cut_st_hi_one = utils::numeric(FLERR,arg[10],false,lmp); - a_st5_one = utils::numeric(FLERR,arg[11],false,lmp); - theta_st5_0_one = utils::numeric(FLERR,arg[12],false,lmp); - dtheta_st5_ast_one = utils::numeric(FLERR,arg[13],false,lmp); - a_st6_one = utils::numeric(FLERR,arg[14],false,lmp); - theta_st6_0_one = utils::numeric(FLERR,arg[15],false,lmp); - dtheta_st6_ast_one = utils::numeric(FLERR,arg[16],false,lmp); + a_st5_one = utils::numeric(FLERR,arg[11],false,lmp); + theta_st5_0_one = utils::numeric(FLERR,arg[12],false,lmp); + dtheta_st5_ast_one = utils::numeric(FLERR,arg[13],false,lmp); + a_st6_one = utils::numeric(FLERR,arg[14],false,lmp); + theta_st6_0_one = utils::numeric(FLERR,arg[15],false,lmp); + dtheta_st6_ast_one = utils::numeric(FLERR,arg[16],false,lmp); - a_st9_one = utils::numeric(FLERR,arg[17],false,lmp); - theta_st9_0_one = utils::numeric(FLERR,arg[18],false,lmp); - dtheta_st9_ast_one = utils::numeric(FLERR,arg[19],false,lmp); - a_st10_one = utils::numeric(FLERR,arg[20],false,lmp); - theta_st10_0_one = utils::numeric(FLERR,arg[21],false,lmp); - dtheta_st10_ast_one = utils::numeric(FLERR,arg[22],false,lmp); + a_st9_one = utils::numeric(FLERR,arg[17],false,lmp); + theta_st9_0_one = utils::numeric(FLERR,arg[18],false,lmp); + dtheta_st9_ast_one = utils::numeric(FLERR,arg[19],false,lmp); + a_st10_one = utils::numeric(FLERR,arg[20],false,lmp); + theta_st10_0_one = utils::numeric(FLERR,arg[21],false,lmp); + dtheta_st10_ast_one = utils::numeric(FLERR,arg[22],false,lmp); - a_st1_one = utils::numeric(FLERR,arg[23],false,lmp); - cosphi_st1_ast_one = utils::numeric(FLERR,arg[24],false,lmp); - a_st2_one = utils::numeric(FLERR,arg[25],false,lmp); - cosphi_st2_ast_one = utils::numeric(FLERR,arg[26],false,lmp); + a_st1_one = utils::numeric(FLERR,arg[23],false,lmp); + cosphi_st1_ast_one = utils::numeric(FLERR,arg[24],false,lmp); + a_st2_one = utils::numeric(FLERR,arg[25],false,lmp); + cosphi_st2_ast_one = utils::numeric(FLERR,arg[26],false,lmp); + } else { // read values from potential file + if (comm->me == 0) { + PotentialFileReader reader(lmp, arg[6], "oxdna potential", " (stk)"); + char * line; + std::string iloc, jloc, potential_name; + + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "stk") { + + a_st_one = values.next_double(); + cut_st_0_one = values.next_double(); + cut_st_c_one = values.next_double(); + cut_st_lo_one = values.next_double(); + cut_st_hi_one = values.next_double(); + + a_st5_one = values.next_double(); + theta_st5_0_one = values.next_double(); + dtheta_st5_ast_one = values.next_double(); + a_st6_one = values.next_double(); + theta_st6_0_one = values.next_double(); + dtheta_st6_ast_one = values.next_double(); + + a_st9_one = values.next_double(); + theta_st9_0_one = values.next_double(); + dtheta_st9_ast_one = values.next_double(); + a_st10_one = values.next_double(); + theta_st10_0_one = values.next_double(); + dtheta_st10_ast_one = values.next_double(); + + a_st1_one = values.next_double(); + cosphi_st1_ast_one = values.next_double(); + a_st2_one = values.next_double(); + cosphi_st2_ast_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "stk")) + error->one(FLERR, "No corresponding stk potential found in file {} for pair type {} {}", + arg[4], arg[0], arg[1]); + } + + MPI_Bcast(&a_st_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_c_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_lo_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_st_hi_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_st5_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_st5_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_st5_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_st6_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_st6_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_st6_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_st9_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_st9_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_st9_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_st10_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_st10_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_st10_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_st1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cosphi_st1_ast_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&a_st2_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cosphi_st2_ast_one, 1, MPI_DOUBLE, 0, world); + } b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* diff --git a/src/CG-DNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp index e28b6573bf..ee7ca141f8 100644 --- a/src/CG-DNA/pair_oxrna2_xstk.cpp +++ b/src/CG-DNA/pair_oxrna2_xstk.cpp @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "constants_oxdna.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -26,6 +27,7 @@ #include "memory.h" #include "mf_oxdna.h" #include "neigh_list.h" +#include "potential_file_reader.h" #include #include @@ -40,6 +42,7 @@ PairOxrna2Xstk::PairOxrna2Xstk(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + trim_flag = 0; } /* ---------------------------------------------------------------------- */ @@ -115,7 +118,7 @@ void PairOxrna2Xstk::compute(int eflag, int vflag) double theta8,theta8p,t8dir[3],cost8; // distance COM-h-bonding site - double d_chb=+0.4; + double d_chb = ConstantsOxdna::get_d_chb(); // vectors COM-h-bonding site in lab frame double ra_chb[3],rb_chb[3]; @@ -580,7 +583,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg) { int count; - if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk"); + if (narg != 3 && narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -608,32 +611,108 @@ void PairOxrna2Xstk::coeff(int narg, char **arg) double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one; double b_xst8_one, dtheta_xst8_c_one; - k_xst_one = utils::numeric(FLERR,arg[2],false,lmp); - cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp); - cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp); - cut_xst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); - cut_xst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); + if (narg == 22) { + k_xst_one = utils::numeric(FLERR,arg[2],false,lmp); + cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp); + cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp); + cut_xst_lo_one = utils::numeric(FLERR,arg[5],false,lmp); + cut_xst_hi_one = utils::numeric(FLERR,arg[6],false,lmp); - a_xst1_one = utils::numeric(FLERR,arg[7],false,lmp); - theta_xst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); - dtheta_xst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); + a_xst1_one = utils::numeric(FLERR,arg[7],false,lmp); + theta_xst1_0_one = utils::numeric(FLERR,arg[8],false,lmp); + dtheta_xst1_ast_one = utils::numeric(FLERR,arg[9],false,lmp); - a_xst2_one = utils::numeric(FLERR,arg[10],false,lmp); - theta_xst2_0_one = utils::numeric(FLERR,arg[11],false,lmp); - dtheta_xst2_ast_one = utils::numeric(FLERR,arg[12],false,lmp); + a_xst2_one = utils::numeric(FLERR,arg[10],false,lmp); + theta_xst2_0_one = utils::numeric(FLERR,arg[11],false,lmp); + dtheta_xst2_ast_one = utils::numeric(FLERR,arg[12],false,lmp); - a_xst3_one = utils::numeric(FLERR,arg[13],false,lmp); - theta_xst3_0_one = utils::numeric(FLERR,arg[14],false,lmp); - dtheta_xst3_ast_one = utils::numeric(FLERR,arg[15],false,lmp); + a_xst3_one = utils::numeric(FLERR,arg[13],false,lmp); + theta_xst3_0_one = utils::numeric(FLERR,arg[14],false,lmp); + dtheta_xst3_ast_one = utils::numeric(FLERR,arg[15],false,lmp); - a_xst7_one = utils::numeric(FLERR,arg[16],false,lmp); - theta_xst7_0_one = utils::numeric(FLERR,arg[17],false,lmp); - dtheta_xst7_ast_one = utils::numeric(FLERR,arg[18],false,lmp); + a_xst7_one = utils::numeric(FLERR,arg[16],false,lmp); + theta_xst7_0_one = utils::numeric(FLERR,arg[17],false,lmp); + dtheta_xst7_ast_one = utils::numeric(FLERR,arg[18],false,lmp); - a_xst8_one = utils::numeric(FLERR,arg[19],false,lmp); - theta_xst8_0_one = utils::numeric(FLERR,arg[20],false,lmp); - dtheta_xst8_ast_one = utils::numeric(FLERR,arg[21],false,lmp); + a_xst8_one = utils::numeric(FLERR,arg[19],false,lmp); + theta_xst8_0_one = utils::numeric(FLERR,arg[20],false,lmp); + dtheta_xst8_ast_one = utils::numeric(FLERR,arg[21],false,lmp); + } else { + if (comm->me == 0) { + PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (xstk)"); + char * line; + std::string iloc, jloc, potential_name; + while ((line = reader.next_line())) { + try { + ValueTokenizer values(line); + iloc = values.next_string(); + jloc = values.next_string(); + potential_name = values.next_string(); + if (iloc == arg[0] && jloc == arg[1] && potential_name == "xstk") { + k_xst_one = values.next_double(); + cut_xst_0_one = values.next_double(); + cut_xst_c_one = values.next_double(); + cut_xst_lo_one = values.next_double(); + cut_xst_hi_one = values.next_double(); + + a_xst1_one = values.next_double(); + theta_xst1_0_one = values.next_double(); + dtheta_xst1_ast_one = values.next_double(); + + a_xst2_one = values.next_double(); + theta_xst2_0_one = values.next_double(); + dtheta_xst2_ast_one = values.next_double(); + + a_xst3_one = values.next_double(); + theta_xst3_0_one = values.next_double(); + dtheta_xst3_ast_one = values.next_double(); + + a_xst7_one = values.next_double(); + theta_xst7_0_one = values.next_double(); + dtheta_xst7_ast_one = values.next_double(); + + a_xst8_one = values.next_double(); + theta_xst8_0_one = values.next_double(); + dtheta_xst8_ast_one = values.next_double(); + + break; + } else continue; + } catch (std::exception &e) { + error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what()); + } + } + if ((iloc != arg[0]) || (jloc != arg[1]) || (potential_name != "xstk")) + error->one(FLERR, "No corresponding xstk potential found in file {} for pair type {} {}", + arg[2], arg[0], arg[1]); + } + + MPI_Bcast(&k_xst_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_c_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_lo_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_xst_hi_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst1_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst1_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst1_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst2_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst2_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst2_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst3_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst3_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst3_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst7_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst7_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst7_ast_one, 1, MPI_DOUBLE, 0, world); + + MPI_Bcast(&a_xst8_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta_xst8_0_one, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&dtheta_xst8_ast_one, 1, MPI_DOUBLE, 0, world); + } b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/ (0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) - diff --git a/src/COLVARS/ndx_group.cpp b/src/COLVARS/ndx_group.cpp deleted file mode 100644 index 4170a9ea70..0000000000 --- a/src/COLVARS/ndx_group.cpp +++ /dev/null @@ -1,199 +0,0 @@ -// clang-format off -// -*- c++ -*- - -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - LAMMPS development team: developers@lammps.org - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing author: Axel Kohlmeyer (Temple U) -------------------------------------------------------------------------- */ - -#include "ndx_group.h" - -#include "atom.h" -#include "comm.h" -#include "error.h" -#include "group.h" -#include "tokenizer.h" - -using namespace LAMMPS_NS; -static constexpr int BUFLEN = 4096; - -// read file until next section "name" or any next section if name == "" - -static std::string find_section(FILE *fp, const std::string &name) -{ - char linebuf[BUFLEN]; - - std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$"; - if (!name.empty()) - pattern = fmt::format("^\\s*\\[\\s+{}\\s+\\]\\s*$",name); - - fgets(linebuf,BUFLEN,fp); - while (!feof(fp)) { - if (utils::strmatch(linebuf,pattern)) - return Tokenizer(linebuf).as_vector()[1]; - fgets(linebuf,BUFLEN,fp); - } - return ""; -} - -static std::vector read_section(FILE *fp, std::string &name) -{ - char linebuf[BUFLEN]; - std::vector tagbuf; - std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$"; - - while (fgets(linebuf,BUFLEN,fp)) { - // start of new section. we are done, update "name" - if (utils::strmatch(linebuf,pattern)) { - name = Tokenizer(linebuf).as_vector()[1]; - return tagbuf; - } - ValueTokenizer values(linebuf); - while (values.has_next()) - tagbuf.push_back(values.next_tagint()); - } - // set empty name to indicate end of file - name = ""; - return tagbuf; -} - -/* ---------------------------------------------------------------------- */ - -void Ndx2Group::command(int narg, char **arg) -{ - int len; - bigint num; - FILE *fp; - std::string name, next; - - if (narg < 1) error->all(FLERR,"Illegal ndx2group command"); - if (atom->tag_enable == 0) - error->all(FLERR,"Must have atom IDs for ndx2group command"); - if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Must have an atom map for ndx2group command"); - if (comm->me == 0) { - fp = fopen(arg[0], "r"); - if (fp == nullptr) - error->one(FLERR,"Cannot open index file for reading: {}", - utils::getsyserror()); - utils::logmesg(lmp,"Reading groups from index file {}:\n",arg[0]); - } - - if (narg == 1) { // restore all groups - - if (comm->me == 0) { - name = find_section(fp,""); - while (!name.empty()) { - - // skip over group "all", which is called "System" in gromacs - if (name == "System") { - name = find_section(fp,""); - continue; - } - - utils::logmesg(lmp," Processing group '{}'\n",name); - len = name.size()+1; - MPI_Bcast(&len,1,MPI_INT,0,world); - if (len > 1) { - MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world); - - // read tags for atoms in group and broadcast - std::vector tags = read_section(fp,next); - num = tags.size(); - MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world); - create(name,tags); - name = next; - } - } - len = -1; - MPI_Bcast(&len,1,MPI_INT,0,world); - - } else { - - while (true) { - MPI_Bcast(&len,1,MPI_INT,0,world); - if (len < 0) break; - if (len > 1) { - char *buf = new char[len]; - MPI_Bcast(buf,len,MPI_CHAR,0,world); - MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - tagint *tbuf = new tagint[num]; - MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world); - create(buf,std::vector(tbuf,tbuf+num)); - delete[] buf; - delete[] tbuf; - } - } - } - - } else { // restore selected groups - - for (int idx=1; idx < narg; ++idx) { - if (comm->me == 0) { - - // find named section, search from beginning of file - rewind(fp); - name = find_section(fp,arg[idx]); - utils::logmesg(lmp," {} group '{}'\n", name.size() - ? "Processing" : "Skipping",arg[idx]); - len = name.size()+1; - MPI_Bcast(&len,1,MPI_INT,0,world); - if (len > 1) { - MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world); - - // read tags for atoms in group and broadcast - std::vector tags = read_section(fp,next); - num = tags.size(); - MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world); - create(name,tags); - name = next; - } - } else { - MPI_Bcast(&len,1,MPI_INT,0,world); - if (len > 1) { - char *buf = new char[len]; - MPI_Bcast(buf,len,MPI_CHAR,0,world); - MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - tagint *tbuf = new tagint[num]; - MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world); - create(buf,std::vector(tbuf,tbuf+num)); - delete[] buf; - delete[] tbuf; - } - } - } - } - if (comm->me == 0) fclose(fp); -} - -/* ---------------------------------------------------------------------- */ - -void Ndx2Group::create(const std::string &name, const std::vector &tags) -{ - // wipe out all members if the group exists. gid==0 is group "all" - int gid = group->find(name); - if (gid > 0) group->assign(name + " clear"); - - // map from global to local - const int nlocal = atom->nlocal; - int *flags = (int *)calloc(nlocal,sizeof(int)); - for (bigint i=0; i < (int)tags.size(); ++i) { - const int id = atom->map(tags[i]); - if (id < nlocal && id >= 0) flags[id] = 1; - } - group->create(name,flags); - free(flags); -} diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index 3b25ad4e17..7412df118f 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -15,8 +15,10 @@ #include "atom.h" #include "citeme.h" +#include "domain.h" #include "error.h" #include "force.h" +#include "memory.h" #include "pair.h" #include "pair_hybrid.h" @@ -50,6 +52,8 @@ AtomVecDielectric::AtomVecDielectric(LAMMPS *_lmp) : AtomVec(_lmp) atom->molecule_flag = atom->q_flag = atom->mu_flag = 1; atom->dielectric_flag = 1; + mu_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -187,6 +191,58 @@ void AtomVecDielectric::data_atom_post(int ilocal) mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]); } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on dipole moment mu +------------------------------------------------------------------------- */ + +void AtomVecDielectric::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + for (int i = nlocal_previous; i < nlocal; i++) + domain->general_to_restricted_vector(mu[i]); +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on dipole momemt mu which has 4 values per atom +------------------------------------------------------------------------- */ + +void AtomVecDielectric::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(mu_hold,nlocal,3,"atomvec:mu_hold"); + for (int i = 0; i < nlocal; i++) { + memcpy(&mu_hold[i],&mu[i],3*sizeof(double)); + domain->restricted_to_general_vector(mu[i]); + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on dipole moment mu which has 4 values per atom +------------------------------------------------------------------------- */ + +void AtomVecDielectric::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!mu_hold) return; + + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) + memcpy(&mu[i],&mu_hold[i],3*sizeof(double)); + memory->destroy(mu_hold); + mu_hold = nullptr; +} + /* ---------------------------------------------------------------------- initialize other atom quantities after AtomVec::unpack_restart() ------------------------------------------------------------------------- */ diff --git a/src/DIELECTRIC/atom_vec_dielectric.h b/src/DIELECTRIC/atom_vec_dielectric.h index 28bf7abb33..71aba900f8 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.h +++ b/src/DIELECTRIC/atom_vec_dielectric.h @@ -35,6 +35,10 @@ class AtomVecDielectric : virtual public AtomVec { void grow_pointers() override; void create_atom_post(int) override; void data_atom_post(int) override; + void read_data_general_to_restricted(int, int) override; + void write_data_restricted_to_general() override; + void write_data_restore_restricted() override; + void unpack_restart_init(int) override; int property_atom(const std::string &) override; void pack_property_atom(int, double *, int, int) override; @@ -48,6 +52,8 @@ class AtomVecDielectric : virtual public AtomVec { double **mu; double *area, *ed, *em, *epsilon, *curvature, *q_scaled; + + double **mu_hold; }; } // namespace LAMMPS_NS diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 3f160787b2..470dfc77ef 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -14,6 +14,8 @@ #include "atom_vec_dipole.h" #include "atom.h" +#include "domain.h" +#include "memory.h" #include @@ -28,6 +30,8 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp) atom->q_flag = atom->mu_flag = 1; + mu_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -68,3 +72,55 @@ void AtomVecDipole::data_atom_post(int ilocal) double *mu_one = mu[ilocal]; mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]); } + +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on dipole moment mu +------------------------------------------------------------------------- */ + +void AtomVecDipole::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + for (int i = nlocal_previous; i < nlocal; i++) + domain->general_to_restricted_vector(mu[i]); +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on dipole momemt mu which has 4 values per atom +------------------------------------------------------------------------- */ + +void AtomVecDipole::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(mu_hold,nlocal,3,"atomvec:mu_hold"); + for (int i = 0; i < nlocal; i++) { + memcpy(&mu_hold[i],&mu[i],3*sizeof(double)); + domain->restricted_to_general_vector(mu[i]); + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on dipole moment mu which has 4 values per atom +------------------------------------------------------------------------- */ + +void AtomVecDipole::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!mu_hold) return; + + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) + memcpy(&mu[i],&mu_hold[i],3*sizeof(double)); + memory->destroy(mu_hold); + mu_hold = nullptr; +} diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h index d2f5746462..0b46195263 100644 --- a/src/DIPOLE/atom_vec_dipole.h +++ b/src/DIPOLE/atom_vec_dipole.h @@ -30,9 +30,13 @@ class AtomVecDipole : virtual public AtomVec { void grow_pointers() override; void data_atom_post(int) override; + void read_data_general_to_restricted(int, int) override; + void write_data_restricted_to_general() override; + void write_data_restore_restricted() override; protected: double **mu; + double **mu_hold; }; } // namespace LAMMPS_NS diff --git a/src/DPD-BASIC/Install.sh b/src/DPD-BASIC/Install.sh new file mode 100755 index 0000000000..7371e2fad6 --- /dev/null +++ b/src/DPD-BASIC/Install.sh @@ -0,0 +1,39 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# list of files with optional dependcies +action pair_dpd_coul_slater_long.cpp pppm.cpp +action pair_dpd_coul_slater_long.h pppm.h +action pair_dpd.cpp +action pair_dpd_ext.cpp +action pair_dpd_ext.h +action pair_dpd_ext_tstat.cpp +action pair_dpd_ext_tstat.h +action pair_dpd.h +action pair_dpd_tstat.cpp +action pair_dpd_tstat.h diff --git a/src/DPD-BASIC/pair_dpd_coul_slater_long.cpp b/src/DPD-BASIC/pair_dpd_coul_slater_long.cpp new file mode 100644 index 0000000000..c4af283a9e --- /dev/null +++ b/src/DPD-BASIC/pair_dpd_coul_slater_long.cpp @@ -0,0 +1,544 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Eddy BARRAUD (IFPEN/Sorbonne) +------------------------------------------------------------------------- */ + +#include "pair_dpd_coul_slater_long.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" + +#include "ewald_const.h" +#include "kspace.h" + +#include +#include + +using namespace LAMMPS_NS; +using namespace EwaldConst; + +static constexpr double EPSILON = 1.0e-10; + +/* ---------------------------------------------------------------------- */ + +PairDPDCoulSlaterLong::PairDPDCoulSlaterLong(LAMMPS *lmp) : + Pair(lmp), cut_dpd(nullptr), cut_dpdsq(nullptr), cut_slatersq(nullptr), + a0(nullptr), gamma(nullptr), sigma(nullptr), random(nullptr) +{ + writedata = 1; + ewaldflag = pppmflag = 1; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDCoulSlaterLong::~PairDPDCoulSlaterLong() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut_dpd); + memory->destroy(cut_dpdsq); + memory->destroy(cut_slatersq); + + memory->destroy(cut); + memory->destroy(a0); + memory->destroy(gamma); + memory->destroy(sigma); + } + + if (random) delete random; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double r2inv,forcedpd,forcecoul,factor_coul; + double grij,expm2,prefactor,t,erfc; + double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt; + int *ilist,*jlist,*numneigh,**firstneigh; + double slater_term; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + + double *q = atom->q; + double *special_coul = force->special_coul; + double qqrd2e = force->qqrd2e; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + factor_sqrt = special_sqrt[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + // forces if below maximum cutoff + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (evflag) evdwl = ecoul = 0.0; + + // apply DPD force if distance below DPD cutoff + if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) { + rinv = 1.0/r; + delvx = vxtmp - v[j][0]; + delvy = vytmp - v[j][1]; + delvz = vztmp - v[j][2]; + dot = delx*delvx + dely*delvy + delz*delvz; + wd = 1.0 - r/cut_dpd[itype][jtype]; + randnum = random->gaussian(); + + // conservative force = a0 * wd + // drag force = -gamma * wd^2 * (delx dot delv) / r + // random force = sigma * wd * rnd * dtinvsqrt; + // random force must be scaled by sqrt(factor_dpd) + + forcedpd = a0[itype][jtype]*wd; + forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv; + forcedpd *= factor_dpd; + forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt; + forcedpd *= rinv; + + if (eflag) { + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd; + evdwl *= factor_dpd; + } + + } else forcedpd = 0.0; + + // apply Slater electrostatic force if distance below Slater cutoff + // and the two species are charged + if (rsq < cut_slatersq[itype][jtype]){ + r2inv = 1.0/rsq; + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda))); + prefactor = qqrd2e * qtmp*q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term); + forcecoul *= r2inv; + + if (eflag) { + ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda)); + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda)); + } + + } else forcecoul = 0.0; + + fpair = forcedpd + forcecoul; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::allocate() +{ + int i,j; + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(cut_dpd,n+1,n+1,"pair:cut_dpd"); + memory->create(cut_dpdsq,n+1,n+1,"pair:cut_dpdsq"); + memory->create(cut_slatersq,n+1,n+1,"pair:cut_slatersq"); + memory->create(a0,n+1,n+1,"pair:a0"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + for (i = 0; i <= atom->ntypes; i++) + for (j = 0; j <= atom->ntypes; j++) + sigma[i][j] = gamma[i][j] = 0.0; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::settings(int narg, char **arg) +{ + // params : T cut_dpd seed lambda cut_coul + if (narg != 5) error->all(FLERR,"Illegal pair_style command"); + + temperature = utils::numeric(FLERR,arg[0],false,lmp); + cut_global = utils::numeric(FLERR,arg[1],false,lmp); + seed = utils::inumeric(FLERR,arg[2],false,lmp); + lamda = utils::numeric(FLERR,arg[3],false,lmp); + cut_coul = utils::numeric(FLERR,arg[4],false,lmp); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) + error->all(FLERR,"Invalid random seed {} for pair_style dpd/coul/slater/long command", seed); + delete random; + random = new RanMars(lmp,seed + comm->me); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_dpd[i][j] = MAX(cut_global,cut_coul); + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double a0_one = utils::numeric(FLERR,arg[2],false,lmp); + double gamma_one = utils::numeric(FLERR,arg[3],false,lmp); + + double cut_one = cut_global; + double cut_two = 0.0; + + if (narg > 4) { + bool do_slater = utils::logical(FLERR,arg[4],false,lmp); + if (do_slater) cut_two = cut_coul; + } + + if (narg > 5) cut_one = utils::numeric(FLERR,arg[5],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + gamma[i][j] = gamma_one; + cut_dpd[i][j] = cut_one; + cut_slatersq[i][j] = cut_two * cut_two; + cut[i][j] = MAX(cut_one, cut_two); + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair dpd requires ghost atoms store velocity"); + if (!atom->q_flag) + error->all(FLERR,"Pair style coul/slater/long requires atom attribute q"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) + error->warning(FLERR, "Pair dpd needs newton pair on for momentum conservation"); + + neighbor->add_request(this); + + // precompute random force scaling factors + + for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]); + + + // ensure use of KSpace long-range solver, set g_ewald + + if (force->kspace == nullptr) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + return the maximum cutoff between Slater or DPD cutoff if charged + return the DPD cutoff for uncharged +------------------------------------------------------------------------- */ + +double PairDPDCoulSlaterLong::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]); + + cut_dpdsq[i][j] = cut_dpd[i][j] * cut_dpd[i][j]; + + a0[j][i] = a0[i][j]; + gamma[j][i] = gamma[i][j]; + sigma[j][i] = sigma[i][j]; + cut_dpd[j][i] = cut_dpd[i][j]; + cut[j][i] = cut[i][j]; + cut_dpdsq[j][i] = cut_dpdsq[i][j]; + cut_slatersq[j][i] = cut_slatersq[i][j]; + + return MAX(cut_dpd[i][j], sqrt(cut_slatersq[i][j])); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&cut_dpd[i][j],sizeof(double),1,fp); + fwrite(&cut_slatersq[i][j],sizeof(double),1,fp); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_dpd[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_slatersq[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_dpd[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_slatersq[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::write_restart_settings(FILE *fp) +{ + fwrite(&temperature,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&lamda,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&temperature,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&lamda,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g\n",i,a0[i][i],gamma[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLong::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %s %g\n",i,j,a0[i][j],gamma[i][j], + (cut_slatersq[i][j] == 0.0) ? "yes" : "no", cut_dpd[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDCoulSlaterLong::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wd,phi; + double r2inv,grij,expm2,t,erfc,prefactor; + double slater_term; + double forcecoul,phicoul; + + double energy = 0.0; + fforce = 0.0; + + r = sqrt(rsq); + + // compute DPD force and energy + if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) { + rinv = 1.0/r; + wd = 1.0 - r/cut_dpd[itype][jtype]; + fforce += a0[itype][jtype]*wd * factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd; + energy += factor_dpd*phi; + } + + // compute Slater coulombic force and energy + if (atom->q[i]*atom->q[j] != 0.0 && rsq < cut_slatersq[itype][jtype]) { + r2inv = 1.0/rsq; + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda))); + prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + fforce += forcecoul * r2inv; + phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda)); + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + energy += phicoul; + } + + return energy; +} + +void *PairDPDCoulSlaterLong::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + if (strcmp(str,"lamda") == 0) return (void *) &lamda; + dim = 2; + if (strcmp(str,"a0") == 0) return (void *) a0; + if (strcmp(str,"gamma") == 0) return (void *) gamma; + return nullptr; +} diff --git a/src/DPD-BASIC/pair_dpd_coul_slater_long.h b/src/DPD-BASIC/pair_dpd_coul_slater_long.h new file mode 100644 index 0000000000..99498b4a95 --- /dev/null +++ b/src/DPD-BASIC/pair_dpd_coul_slater_long.h @@ -0,0 +1,64 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(dpd/coul/slater/long,PairDPDCoulSlaterLong); +// clang-format on +#else + +#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_H +#define LMP_PAIR_DPD_COUL_SLATER_LONG_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairDPDCoulSlaterLong : public Pair { + public: + PairDPDCoulSlaterLong(class LAMMPS *); + ~PairDPDCoulSlaterLong() override; + void compute(int, int) override; + void settings(int, char **) override; + void coeff(int, char **) override; + void init_style() override; + double init_one(int, int) override; + void write_restart(FILE *) override; + void read_restart(FILE *) override; + void write_restart_settings(FILE *) override; + void read_restart_settings(FILE *) override; + void write_data(FILE *) override; + void write_data_all(FILE *) override; + double single(int, int, int, int, double, double, double, double &) override; + void *extract(const char *, int &) override; + + protected: + double cut_global, temperature; + double special_sqrt[4]; + int seed; + double **cut; + double **cut_dpd, **cut_dpdsq, **cut_slatersq; + double **a0, **gamma; + double **sigma; + class RanMars *random; + double cut_coul; + double lamda; + double g_ewald; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/DRUDE/compute_temp_drude.cpp b/src/DRUDE/compute_temp_drude.cpp index 535808580e..0bf276924a 100644 --- a/src/DRUDE/compute_temp_drude.cpp +++ b/src/DRUDE/compute_temp_drude.cpp @@ -64,7 +64,7 @@ ComputeTempDrude::~ComputeTempDrude() void ComputeTempDrude::init() { // Fix drude already checks that there is only one fix drude instance - auto &fixes = modify->get_fix_by_style("drude"); + auto &fixes = modify->get_fix_by_style("^drude$"); if (fixes.size() == 0) error->all(FLERR, "compute temp/drude requires fix drude"); fix_drude = dynamic_cast(fixes[0]); diff --git a/src/DRUDE/fix_drude.cpp b/src/DRUDE/fix_drude.cpp index 6aaa4f1a74..6c0c84861a 100644 --- a/src/DRUDE/fix_drude.cpp +++ b/src/DRUDE/fix_drude.cpp @@ -82,7 +82,7 @@ FixDrude::~FixDrude() void FixDrude::init() { - if (modify->get_fix_by_style("drude").size() > 1) error->all(FLERR,"More than one fix drude"); + if (modify->get_fix_by_style("^drude$").size() > 1) error->all(FLERR,"More than one fix drude"); if (!rebuildflag) rebuild_special(); } diff --git a/src/DRUDE/fix_drude_transform.cpp b/src/DRUDE/fix_drude_transform.cpp index 88877ef70d..ad92740116 100644 --- a/src/DRUDE/fix_drude_transform.cpp +++ b/src/DRUDE/fix_drude_transform.cpp @@ -53,7 +53,7 @@ void FixDrudeTransform::init() std::string substyle = "direct"; if (inverse) substyle = "inverse"; - auto fixes = modify->get_fix_by_style("^drude"); + auto fixes = modify->get_fix_by_style("^drude$"); if (fixes.size() > 0) fix_drude = dynamic_cast(fixes[0]); if (!fix_drude) error->all(FLERR, "fix drude/transform/{} requires fix drude", substyle); diff --git a/src/DRUDE/fix_tgnh_drude.cpp b/src/DRUDE/fix_tgnh_drude.cpp index c067bf7adf..e15e865ce8 100644 --- a/src/DRUDE/fix_tgnh_drude.cpp +++ b/src/DRUDE/fix_tgnh_drude.cpp @@ -516,7 +516,7 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) : // find fix drude - auto fdrude = modify->get_fix_by_style("^drude"); + auto fdrude = modify->get_fix_by_style("^drude$"); if (fdrude.size() < 1) error->all(FLERR, "Fix {} requires fix drude", style); fix_drude = dynamic_cast(fdrude[0]); if (!fix_drude) error->all(FLERR, "Fix {} requires fix drude", style); diff --git a/src/Depend.sh b/src/Depend.sh index 3df1347e67..e55b100975 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -116,6 +116,7 @@ if (test $1 = "KSPACE") then depend CG-SPICA depend CORESHELL depend DIELECTRIC + depend DPD-BASIC depend GPU depend KOKKOS depend OPT @@ -184,6 +185,10 @@ if (test $1 = "ML-PACE") then depend KOKKOS fi +if (test $1 = "ML-POD") then + depend KOKKOS +fi + if (test $1 = "ML-SNAP") then depend ML-IAP depend KOKKOS diff --git a/src/EFF/fix_nh_eff.cpp b/src/EFF/fix_nh_eff.cpp index a569932000..6e8e2c68fa 100644 --- a/src/EFF/fix_nh_eff.cpp +++ b/src/EFF/fix_nh_eff.cpp @@ -16,7 +16,6 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ - #include "fix_nh_eff.h" #include "atom.h" @@ -62,7 +61,7 @@ void FixNHEff::nve_v() if (mask[i] & groupbit) { if (abs(spin[i])==1) { dtfm = dtf / mass[type[i]]; - ervel[i] = dtfm * erforce[i] / mefactor; + ervel[i] += dtfm * erforce[i] / mefactor; } } } @@ -79,15 +78,26 @@ void FixNHEff::nve_x() FixNH::nve_x(); double *eradius = atom->eradius; + double *erforce = atom->erforce; double *ervel = atom->ervel; + double *mass = atom->mass; + int *type = atom->type; int *spin = atom->spin; int *mask = atom->mask; int nlocal = atom->nlocal; if (igroup == atom->firstgroup) nlocal = atom->nfirst; + double mefactor = domain->dimension/4.0; + double dtfm; + for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - if (abs(spin[i])==1) eradius[i] += dtv * ervel[i]; + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + if (abs(spin[i])==1) { + ervel[i] += dtfm * erforce[i] / mefactor; + eradius[i] += dtv * ervel[i]; + } + } } /* ---------------------------------------------------------------------- diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index 18e65b2baf..48d0dfdb7c 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -922,20 +922,20 @@ void FixElectrodeConp::update_charges() a = ele_ele_interaction(q_local); r = add_nlocalele(b, a); } else { - r = add_nlocalele(r, scale_vector(alpha, y)); + r = add_nlocalele(r, scale_vector(alpha, std::move(y))); } auto p = constraint_projection(r); double dot_new = dot_nlocalele(r, p); - d = add_nlocalele(p, scale_vector(dot_new / dot_old, d)); + d = add_nlocalele(std::move(p), scale_vector(dot_new / dot_old, d)); delta = dot_nlocalele(r, d); dot_old = dot_new; } - recompute_potential(b, q_local); + recompute_potential(std::move(b), q_local); if ((delta > cg_threshold) && (comm->me == 0)) error->warning(FLERR, "CG threshold not reached"); } else { error->all(FLERR, "This algorithm is not implemented, yet"); } - set_charges(q_local); + set_charges(std::move(q_local)); update_time += MPI_Wtime() - start; } diff --git a/src/COLVARS/group_ndx.cpp b/src/EXTRA-COMMAND/group_ndx.cpp similarity index 59% rename from src/COLVARS/group_ndx.cpp rename to src/EXTRA-COMMAND/group_ndx.cpp index 05a50a1596..1dc0d3af97 100644 --- a/src/COLVARS/group_ndx.cpp +++ b/src/EXTRA-COMMAND/group_ndx.cpp @@ -1,4 +1,3 @@ -// clang-format off // -*- c++ -*- /* ---------------------------------------------------------------------- @@ -34,12 +33,15 @@ using namespace LAMMPS_NS; static int cmptagint(const void *p1, const void *p2) { - const tagint i1 = * static_cast(p1); - const tagint i2 = * static_cast(p2); - if (i1 == i2) return 0; + const tagint i1 = *static_cast(p1); + const tagint i2 = *static_cast(p2); + if (i1 == i2) + return 0; else { - if (i1 < i2) return -1; - else return 1; + if (i1 < i2) + return -1; + else + return 1; } } @@ -49,27 +51,24 @@ void Group2Ndx::command(int narg, char **arg) { FILE *fp = nullptr; - if (narg < 1) error->all(FLERR,"Illegal group2ndx command"); + if (narg < 1) utils::missing_cmd_args(FLERR, "group2ndx", error); - if (atom->tag_enable == 0) - error->all(FLERR,"Must have atom IDs for group2ndx command"); + if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for group2ndx command"); if (comm->me == 0) { fp = fopen(arg[0], "w"); if (fp == nullptr) - error->one(FLERR,"Cannot open index file for writing: {}", utils::getsyserror()); - utils::logmesg(lmp,"Writing groups to index file {}:\n",arg[0]); + error->one(FLERR, "Cannot open index file for writing: {}", utils::getsyserror()); + utils::logmesg(lmp, "Writing groups to index file {}:\n", arg[0]); } - if (narg == 1) { // write out all groups - for (int i=0; i < group->ngroup; ++i) { - write_group(fp,i); - } - } else { // write only selected groups - for (int i=1; i < narg; ++i) { + if (narg == 1) { // write out all groups + for (int i = 0; i < group->ngroup; ++i) { write_group(fp, i); } + } else { // write only selected groups + for (int i = 1; i < narg; ++i) { int gid = group->find(arg[i]); if (gid < 0) error->all(FLERR, "Non-existing group requested"); - write_group(fp,gid); + write_group(fp, gid); } } @@ -85,22 +84,26 @@ void Group2Ndx::write_group(FILE *fp, int gid) bigint gcount = group->count(gid); int lnum, width, cols; + if (utils::strmatch(group->names[gid], "\\s+")) { + if (fp) utils::logmesg(lmp, " skipping group {}...done", group->names[gid]); + return; + } if (fp) { - utils::logmesg(lmp," writing group {}...",group->names[gid]); + utils::logmesg(lmp, " writing group {}...", group->names[gid]); // the "all" group in LAMMPS is called "System" in Gromacs if (gid == 0) { fputs("[ System ]\n", fp); } else { - fmt::print(fp,"[ {} ]\n", group->names[gid]); + fmt::print(fp, "[ {} ]\n", group->names[gid]); } - width = log10((double) atom->natoms)+2; + width = log10((double) atom->natoms) + 2; cols = 80 / width; } if (gcount > 0) { - const int * const mask = atom->mask; - const tagint * const tag = atom->tag; + const int *const mask = atom->mask; + const tagint *const tag = atom->tag; const int groupbit = group->bitmask[gid]; const int nlocal = atom->nlocal; int i; @@ -111,45 +114,45 @@ void Group2Ndx::write_group(FILE *fp, int gid) for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) sendlist[lnum++] = tag[i]; - int nrecv=0; + int nrecv = 0; bigint allrecv; if (comm->me == 0) { MPI_Status status; MPI_Request request; - for (i=0; i < lnum; i++) - recvlist[i] = sendlist[i]; + for (i = 0; i < lnum; i++) recvlist[i] = sendlist[i]; allrecv = lnum; - for (i=1; i < comm->nprocs; ++i) { - MPI_Irecv(recvlist+allrecv,gcount-allrecv,MPI_LMP_TAGINT,i,0, world,&request); - MPI_Send(&nrecv,0,MPI_INT,i,0,world); // block rank "i" until we are ready to receive - MPI_Wait(&request,&status); - MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv); + for (i = 1; i < comm->nprocs; ++i) { + MPI_Irecv(recvlist + allrecv, gcount - allrecv, MPI_LMP_TAGINT, i, 0, world, &request); + // block rank "i" until we are ready to receive + MPI_Send(&nrecv, 0, MPI_INT, i, 0, world); + MPI_Wait(&request, &status); + MPI_Get_count(&status, MPI_LMP_TAGINT, &nrecv); allrecv += nrecv; } // sort received list - qsort((void *)recvlist, allrecv, sizeof(tagint), cmptagint); + qsort((void *) recvlist, allrecv, sizeof(tagint), cmptagint); } else { - MPI_Recv(&nrecv,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE); - MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world); + MPI_Recv(&nrecv, 0, MPI_INT, 0, 0, world, MPI_STATUS_IGNORE); + MPI_Rsend(sendlist, lnum, MPI_LMP_TAGINT, 0, 0, world); } - delete [] sendlist; + delete[] sendlist; } if (fp) { int i, j; - for (i=0, j=0; i < gcount; ++i) { - fmt::print(fp,"{:>{}}",recvlist[i],width); + for (i = 0, j = 0; i < gcount; ++i) { + fmt::print(fp, "{:>{}}", recvlist[i], width); ++j; if (j == cols) { - fputs("\n",fp); + fputs("\n", fp); j = 0; } } - if (j > 0) fputs("\n",fp); - utils::logmesg(lmp,"done\n"); + if (j > 0) fputs("\n", fp); + utils::logmesg(lmp, "done\n"); } if (gcount > 0) delete[] recvlist; } diff --git a/src/COLVARS/group_ndx.h b/src/EXTRA-COMMAND/group_ndx.h similarity index 100% rename from src/COLVARS/group_ndx.h rename to src/EXTRA-COMMAND/group_ndx.h diff --git a/src/EXTRA-COMMAND/ndx_group.cpp b/src/EXTRA-COMMAND/ndx_group.cpp new file mode 100644 index 0000000000..c5b0d3cf8a --- /dev/null +++ b/src/EXTRA-COMMAND/ndx_group.cpp @@ -0,0 +1,220 @@ +// -*- c++ -*- + +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "ndx_group.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "group.h" +#include "tokenizer.h" + +using namespace LAMMPS_NS; +static constexpr int BUFLEN = 4096; + +// read file until next section "name" or any next section if name == "" + +static std::string find_section(FILE *fp, const std::string &name) +{ + char linebuf[BUFLEN]; + + fgets(linebuf, BUFLEN, fp); + while (!feof(fp)) { + if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) { + auto words = Tokenizer(linebuf).as_vector(); + if (words.size() != 3) + throw TokenizerException("Invalid group name in index file", + utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+"))); + if (name.empty() || (name == words[1])) return words[1]; + } + fgets(linebuf, BUFLEN, fp); + } + return ""; +} + +static std::vector read_section(FILE *fp, std::string &name) +{ + char linebuf[BUFLEN]; + std::vector tagbuf; + + while (fgets(linebuf, BUFLEN, fp)) { + // start of new section. we are done, update "name" + if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) { + auto words = Tokenizer(linebuf).as_vector(); + if (words.size() != 3) + throw TokenizerException("Invalid group name in index file", + utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+"))); + name = words[1]; + return tagbuf; + } + ValueTokenizer values(linebuf); + while (values.has_next()) tagbuf.push_back(values.next_tagint()); + } + // set empty name to indicate end of file + name = ""; + return tagbuf; +} + +/* ---------------------------------------------------------------------- */ + +void Ndx2Group::command(int narg, char **arg) +{ + int len; + bigint num; + FILE *fp; + std::string name, next; + + if (narg < 1) utils::missing_cmd_args(FLERR, "ndx2group", error); + if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for ndx2group command"); + if (atom->map_style == Atom::MAP_NONE) + error->all(FLERR, "Must have an atom map for ndx2group command"); + if (comm->me == 0) { + fp = fopen(arg[0], "r"); + if (fp == nullptr) + error->one(FLERR, "Cannot open index file for reading: {}", utils::getsyserror()); + utils::logmesg(lmp, "Reading groups from index file {}:\n", arg[0]); + } + + if (narg == 1) { // restore all groups + + if (comm->me == 0) { + try { + name = find_section(fp, ""); + } catch (std::exception &e) { + error->one(FLERR, e.what()); + } + + while (!name.empty()) { + // skip over group "all", which is called "System" in gromacs + if (name == "System") { + try { + name = find_section(fp, ""); + } catch (std::exception &e) { + error->one(FLERR, e.what()); + } + continue; + } + + utils::logmesg(lmp, " Processing group '{}'\n", name); + len = name.size() + 1; + MPI_Bcast(&len, 1, MPI_INT, 0, world); + if (len > 1) { + MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world); + + // read tags for atoms in group and broadcast + std::vector tags; + try { + tags = read_section(fp, next); + } catch (std::exception &e) { + error->one(FLERR, e.what()); + } + num = tags.size(); + MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world); + MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world); + create(name, tags); + name = next; + } + } + len = -1; + MPI_Bcast(&len, 1, MPI_INT, 0, world); + + } else { + + while (true) { + MPI_Bcast(&len, 1, MPI_INT, 0, world); + if (len < 0) break; + if (len > 1) { + char *buf = new char[len]; + MPI_Bcast(buf, len, MPI_CHAR, 0, world); + MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world); + tagint *tbuf = new tagint[num]; + MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world); + create(buf, std::vector(tbuf, tbuf + num)); + delete[] buf; + delete[] tbuf; + } + } + } + + } else { // restore selected groups + + for (int idx = 1; idx < narg; ++idx) { + if (comm->me == 0) { + + // find named section, search from beginning of file + rewind(fp); + try { + name = find_section(fp, arg[idx]); + } catch (std::exception &e) { + error->one(FLERR, e.what()); + } + utils::logmesg(lmp, " {} group '{}'\n", name.size() ? "Processing" : "Skipping", arg[idx]); + len = name.size() + 1; + MPI_Bcast(&len, 1, MPI_INT, 0, world); + if (len > 1) { + MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world); + + // read tags for atoms in group and broadcast + std::vector tags; + try { + tags = read_section(fp, next); + } catch (std::exception &e) { + error->one(FLERR, e.what()); + } + num = tags.size(); + MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world); + MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world); + create(name, tags); + name = next; + } + } else { + MPI_Bcast(&len, 1, MPI_INT, 0, world); + if (len > 1) { + char *buf = new char[len]; + MPI_Bcast(buf, len, MPI_CHAR, 0, world); + MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world); + tagint *tbuf = new tagint[num]; + MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world); + create(buf, std::vector(tbuf, tbuf + num)); + delete[] buf; + delete[] tbuf; + } + } + } + } + if (comm->me == 0) fclose(fp); +} + +/* ---------------------------------------------------------------------- */ + +void Ndx2Group::create(const std::string &name, const std::vector &tags) +{ + // wipe out all members if the group exists. gid==0 is group "all" + int gid = group->find(name); + if (gid > 0) group->assign(name + " clear"); + + // map from global to local + const int nlocal = atom->nlocal; + int *flags = (int *) calloc(nlocal, sizeof(int)); + for (bigint i = 0; i < (int) tags.size(); ++i) { + const int id = atom->map(tags[i]); + if (id < nlocal && id >= 0) flags[id] = 1; + } + group->create(name, flags); + free(flags); +} diff --git a/src/COLVARS/ndx_group.h b/src/EXTRA-COMMAND/ndx_group.h similarity index 100% rename from src/COLVARS/ndx_group.h rename to src/EXTRA-COMMAND/ndx_group.h diff --git a/src/EXTRA-COMPUTE/compute_adf.cpp b/src/EXTRA-COMPUTE/compute_adf.cpp index 35ff8bfd33..20b1749fa9 100644 --- a/src/EXTRA-COMPUTE/compute_adf.cpp +++ b/src/EXTRA-COMPUTE/compute_adf.cpp @@ -34,32 +34,27 @@ #include using namespace LAMMPS_NS; -using namespace MathConst; +using MathConst::MY_PI; +using MathConst::RAD2DEG; -enum{DEGREE, RADIAN, COSINE}; +enum { DEGREE, RADIAN, COSINE }; /* ---------------------------------------------------------------------- compute angular distribution functions for I, J, K atoms ---------------------------------------------------------------------- */ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg), - ilo(nullptr), ihi(nullptr), jlo(nullptr), jhi(nullptr), klo(nullptr), khi(nullptr), - hist(nullptr), histall(nullptr), - rcutinnerj(nullptr), rcutinnerk(nullptr), - rcutouterj(nullptr), rcutouterk(nullptr), - list(nullptr), - iatomcount(nullptr), iatomcountall(nullptr), iatomflag(nullptr), - maxjatom(nullptr), maxkatom(nullptr), - numjatom(nullptr), numkatom(nullptr), - neighjatom(nullptr),neighkatom(nullptr), - jatomflag(nullptr), katomflag(nullptr), - maxjkatom(nullptr), numjkatom(nullptr), - neighjkatom(nullptr), bothjkatom(nullptr), delrjkatom(nullptr) + Compute(lmp, narg, arg), ilo(nullptr), ihi(nullptr), jlo(nullptr), jhi(nullptr), klo(nullptr), + khi(nullptr), hist(nullptr), histall(nullptr), rcutinnerj(nullptr), rcutinnerk(nullptr), + rcutouterj(nullptr), rcutouterk(nullptr), list(nullptr), iatomcount(nullptr), + iatomcountall(nullptr), iatomflag(nullptr), maxjatom(nullptr), maxkatom(nullptr), + numjatom(nullptr), numkatom(nullptr), neighjatom(nullptr), neighkatom(nullptr), + jatomflag(nullptr), katomflag(nullptr), maxjkatom(nullptr), numjkatom(nullptr), + neighjkatom(nullptr), bothjkatom(nullptr), delrjkatom(nullptr) { int nargsperadf = 7; - if (narg < 4 ) error->all(FLERR,"Illegal compute adf command"); + if (narg < 4) utils::missing_cmd_args(FLERR, "compute adf", error); array_flag = 1; extarray = 0; @@ -89,17 +84,16 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg+1],"degree") == 0) ordinate_style = DEGREE; else if (strcmp(arg[iarg+1],"radian") == 0) ordinate_style = RADIAN; else if (strcmp(arg[iarg+1],"cosine") == 0) ordinate_style = COSINE; - else error->all(FLERR,"Illegal compute adf command"); + else error->all(FLERR,"Unknown compute adf ordinate flag {}",arg[iarg+1]); iarg += 2; - } else error->all(FLERR,"Illegal compute adf command"); + } else error->all(FLERR,"Unknown compute adf keyword {}", arg[iarg]); } // triplewise args if (!nargtriple) ntriples = 1; else { - if (nargtriple % nargsperadf) - error->all(FLERR,"Illegal compute adf command"); + if (nargtriple % nargsperadf) error->all(FLERR,"Illegal compute adf command"); ntriples = nargtriple/nargsperadf; } @@ -107,12 +101,9 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : size_array_cols = 1 + 2*ntriples; int ntypes = atom->ntypes; - memory->create(iatomflag,ntriples,ntypes+1, - "adf:iatomflag"); - memory->create(jatomflag,ntriples,ntypes+1, - "adf:jatomflag"); - memory->create(katomflag,ntriples,ntypes+1, - "adf:katomflag"); + memory->create(iatomflag,ntriples,ntypes+1,"adf:iatomflag"); + memory->create(jatomflag,ntriples,ntypes+1,"adf:jatomflag"); + memory->create(katomflag,ntriples,ntypes+1,"adf:katomflag"); ilo = new int[ntriples]; ihi = new int[ntriples]; @@ -134,14 +125,14 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : klo[0] = 1; khi[0] = ntypes; } else { cutflag = 1; + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Compute adf with custom cutoffs requires neighbor style 'bin' or 'nsq'"); iarg = 4; for (int m = 0; m < ntriples; m++) { utils::bounds(FLERR,arg[iarg],1,atom->ntypes,ilo[m],ihi[m],error); utils::bounds(FLERR,arg[iarg+1],1,atom->ntypes,jlo[m],jhi[m],error); utils::bounds(FLERR,arg[iarg+2],1,atom->ntypes,klo[m],khi[m],error); - if (ilo[m] > ihi[m] || - jlo[m] > jhi[m] || - klo[m] > khi[m]) + if ((ilo[m] > ihi[m]) || (jlo[m] > jhi[m]) || (klo[m] > khi[m])) error->all(FLERR,"Illegal compute adf command"); rcutinnerj[m] = utils::numeric(FLERR,arg[iarg+3],false,lmp); rcutouterj[m] = utils::numeric(FLERR,arg[iarg+4],false,lmp); @@ -221,8 +212,6 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : memory->create(bothjkatom[m],maxjkatom[m],"adf:bothjkatom"); memory->create(delrjkatom[m],maxjkatom[m],4,"adf:delrjkatom"); } - - rad2deg = 180.0 / MY_PI; } /* ---------------------------------------------------------------------- */ @@ -230,47 +219,47 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : ComputeADF::~ComputeADF() { memory->destroy(iatomflag); - delete [] ilo; - delete [] ihi; - delete [] jlo; - delete [] jhi; - delete [] klo; - delete [] khi; - delete [] iatomcount; - delete [] iatomcountall; + delete[] ilo; + delete[] ihi; + delete[] jlo; + delete[] jhi; + delete[] klo; + delete[] khi; + delete[] iatomcount; + delete[] iatomcountall; memory->destroy(hist); memory->destroy(histall); memory->destroy(array); memory->destroy(jatomflag); - delete [] rcutinnerj; - delete [] rcutouterj; - delete [] maxjatom; - delete [] numjatom; + delete[] rcutinnerj; + delete[] rcutouterj; + delete[] maxjatom; + delete[] numjatom; for (int m = 0; m < ntriples; m++) memory->destroy(neighjatom[m]); - delete [] neighjatom; + delete[] neighjatom; memory->destroy(katomflag); - delete [] rcutinnerk; - delete [] rcutouterk; - delete [] maxkatom; - delete [] numkatom; + delete[] rcutinnerk; + delete[] rcutouterk; + delete[] maxkatom; + delete[] numkatom; for (int m = 0; m < ntriples; m++) memory->destroy(neighkatom[m]); - delete [] neighkatom; + delete[] neighkatom; - delete [] maxjkatom; - delete [] numjkatom; + delete[] maxjkatom; + delete[] numjkatom; for (int m = 0; m < ntriples; m++) memory->destroy(neighjkatom[m]); - delete [] neighjkatom; + delete[] neighjkatom; for (int m = 0; m < ntriples; m++) memory->destroy(bothjkatom[m]); - delete [] bothjkatom; + delete[] bothjkatom; for (int m = 0; m < ntriples; m++) memory->destroy(delrjkatom[m]); - delete [] delrjkatom; + delete[] delrjkatom; } /* ---------------------------------------------------------------------- */ @@ -282,8 +271,7 @@ void ComputeADF::init() if (!cutflag) { if (!force->pair) - error->all(FLERR,"Compute adf requires a pair style be defined " - "or an outer cutoff specified"); + error->all(FLERR,"Compute adf requires a pair style be defined or an outer cutoff specified"); rcutinnerj[0] = 0.0; rcutinnerk[0] = 0.0; rcutouterj[0] = force->pair->cutforce; @@ -298,7 +286,7 @@ void ComputeADF::init() // specify mycutneigh if force cutoff too small or non-existent - if (!(force->pair) || maxouter > force->pair->cutforce) { + if (!(force->pair) || (maxouter > force->pair->cutforce)) { double skin = neighbor->skin; mycutneigh = maxouter + skin; if (mycutneigh > comm->cutghostuser) @@ -310,7 +298,7 @@ void ComputeADF::init() int x0; if (ordinate_style == DEGREE) { - deltax = MY_PI / nbin * rad2deg; + deltax = MY_PI / nbin * RAD2DEG; deltaxinv = nbin / MY_PI; x0 = 0.0; @@ -337,7 +325,11 @@ void ComputeADF::init() // than maxouter apart, just like a normal neighbor list does auto req = neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); - if (mycutneigh > 0.0) req->set_cutoff(mycutneigh); + if (mycutneigh > 0.0) { + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Compute adf with custom cutoffs requires neighbor style 'bin' or 'nsq'"); + req->set_cutoff(mycutneigh); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-COMPUTE/compute_adf.h b/src/EXTRA-COMPUTE/compute_adf.h index 5f30995aa2..f1f95d325e 100644 --- a/src/EXTRA-COMPUTE/compute_adf.h +++ b/src/EXTRA-COMPUTE/compute_adf.h @@ -59,7 +59,6 @@ class ComputeADF : public Compute { int **bothjkatom; // 1 if atom is in both jatom and katom lists double ***delrjkatom; // list of 4-vectors: delx, dely, delx, and 1/r - double rad2deg; // conversion factor from radians to degrees int ordinate_style; // DEGREE, RADIAN, or COSINE int cutflag; // 1 if at least one outer cutoff specified }; diff --git a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp index 89011e7177..b3b920fef3 100644 --- a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp @@ -33,7 +33,7 @@ #include using namespace LAMMPS_NS; -using namespace MathConst; +using MathConst::MY_PI; /* ---------------------------------------------------------------------- */ @@ -108,6 +108,9 @@ void ComputeAveSphereAtom::init() else volume = MY_PI * cutsq; + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Compute ave/sphere/atom requires neighbor style 'bin' or 'nsq'"); + // need an occasional full neighbor list auto req = neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); diff --git a/src/EXTRA-COMPUTE/compute_composition_atom.cpp b/src/EXTRA-COMPUTE/compute_composition_atom.cpp index 47483f760b..d36cb96028 100644 --- a/src/EXTRA-COMPUTE/compute_composition_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_composition_atom.cpp @@ -102,6 +102,9 @@ void ComputeCompositionAtom::init() cutsq = cutoff * cutoff; + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Compute composition/atom requires neighbor style 'bin' or 'nsq'"); + // need an occasional full neighbor list auto req = neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); diff --git a/src/EXTRA-COMPUTE/compute_efield_wolf_atom.cpp b/src/EXTRA-COMPUTE/compute_efield_wolf_atom.cpp index ba5a16d52b..ceb16de2ec 100644 --- a/src/EXTRA-COMPUTE/compute_efield_wolf_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_efield_wolf_atom.cpp @@ -92,7 +92,11 @@ void ComputeEfieldWolfAtom::init() if (atom->mu_flag && (comm->me == 0)) error->warning(FLERR, "Compute efield/wolf/atom does not support per-atom dipoles"); - // need an occasional full neighbor list + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Compute efield/wolf/atom requires neighbor style 'bin' or 'nsq'"); + + // request an occasional full neighbor list + auto req = neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); if (cutoff_flag) req->set_cutoff(cutoff); diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp index 622ea839be..b8946b3647 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp @@ -386,7 +386,7 @@ void ComputeStressCartesian::compute_array() if (tag[i] > tag[j]) { if ((tag[i] + tag[j]) % 2 == 0) continue; } else if (tag[i] < tag[j]) { - if ((tag[i] < tag[j]) % 2 == 1) continue; + if ((tag[i] + tag[j]) % 2 == 1) continue; } } diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp index ee8f5e554a..b8d21d2a4f 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp @@ -89,7 +89,7 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : Compute( error->all(FLERR, "Plane for compute stress/mop is out of bounds"); } - if (pos < (domain->boxlo[dir] + domain->prd_half[dir])) { + if (pos < (domain->boxlo[dir] + domain->prd_half[dir])) { pos1 = pos + domain->prd[dir]; } else { pos1 = pos - domain->prd[dir]; @@ -146,14 +146,14 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : Compute( // Error checks: - // 3D only - - if (domain->dimension != 3) error->all(FLERR, "Compute stress/mop requires a 3d system"); - // orthogonal simulation box if (domain->triclinic != 0) error->all(FLERR, "Compute stress/mop is incompatible with triclinic simulation box"); + // 2D and pressure calculation in the Z coordinate + if (domain->dimension == 2 && dir == Z) + error->all(FLERR, "Compute stress/mop is incompatible with Z in 2d system"); + // Initialize some variables values_local = values_global = vector = nullptr; @@ -210,10 +210,14 @@ void ComputeStressMop::init() // Plane area - area = 1; - int i; - for (i = 0; i < 3; i++) { - if (i != dir) area = area * domain->prd[i]; + if (domain->dimension == 3) { + area = 1; + int i; + for (i = 0; i < 3; i++) { + if (i != dir) area = area * domain->prd[i]; + } + } else { + area = (dir == X) ? domain->prd[1] : domain->prd[0]; } // Timestep Value @@ -404,6 +408,7 @@ void ComputeStressMop::compute_pairs() xj[0] = atom->x[j][0]; xj[1] = atom->x[j][1]; xj[2] = atom->x[j][2]; + delx = xi[0] - xj[0]; dely = xi[1] - xj[1]; delz = xi[2] - xj[2]; @@ -420,7 +425,7 @@ void ComputeStressMop::compute_pairs() values_local[m + 1] += fpair * (xi[1] - xj[1]) / area * nktv2p; values_local[m + 2] += fpair * (xi[2] - xj[2]) / area * nktv2p; } else if (((xi[dir] < pos) && (xj[dir] > pos)) || - ((xi[dir] < pos1) && (xj[dir] > pos1))) { + ((xi[dir] < pos1) && (xj[dir] > pos1))) { pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair); values_local[m] -= fpair * (xi[0] - xj[0]) / area * nktv2p; values_local[m + 1] -= fpair * (xi[1] - xj[1]) / area * nktv2p; diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp index 676b0f5796..ca2d095fd9 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp @@ -133,8 +133,8 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a // 3D only - if (domain->dimension < 3) - error->all(FLERR, "Compute stress/mop/profile incompatible with simulation dimension"); + if (domain->dimension == 2 && dir == Z) + error->all(FLERR, "Compute stress/mop/profile incompatible with Z in 2d system"); // orthogonal simulation box @@ -198,11 +198,14 @@ void ComputeStressMopProfile::init() ftm2v = force->ftm2v; // plane area - - area = 1; - int i; - for (i = 0; i < 3; i++) { - if (i != dir) area = area * domain->prd[i]; + if (domain->dimension == 3) { + area = 1; + int i; + for (i = 0; i < 3; i++) { + if (i != dir) area = area * domain->prd[i]; + } + } else { + area = (dir == X) ? domain->prd[1] : domain->prd[0]; } // timestep Value diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp index 798bdcb391..3119a470dc 100644 --- a/src/EXTRA-DUMP/dump_xtc.cpp +++ b/src/EXTRA-DUMP/dump_xtc.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Naveen Michaud-Agrawal (Johns Hopkins U) - open-source XDR routines from + Open Source XDR based I/O routines from Frans van Hoesel (https://www.rug.nl/staff/f.h.j.van.hoesel/) are included in this file Axel Kohlmeyer (Temple U) @@ -35,27 +35,29 @@ #include "output.h" #include "update.h" +#include "xdr_compat.h" + #include #include #include using namespace LAMMPS_NS; -#define EPS 1e-5 -#define XTC_MAGIC 1995 +static constexpr double EPS = 1.0e-5; +static constexpr int XTC_MAGIC = 1995; #define MYMIN(a,b) ((a) < (b) ? (a) : (b)) #define MYMAX(a,b) ((a) > (b) ? (a) : (b)) -int xdropen(XDR *, const char *, const char *); -int xdrclose(XDR *); -void xdrfreebuf(); -int xdr3dfcoord(XDR *, float *, int *, float *); +static int xdropen(XDR *, const char *, const char *); +static int xdrclose(XDR *); +static void xdrfreebuf(); +static int xdr3dfcoord(XDR *, float *, int *, float *); /* ---------------------------------------------------------------------- */ -DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg), - coords(nullptr) +DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) + : Dump(lmp, narg, arg), coords(nullptr), xd(nullptr) { if (narg != 5) error->all(FLERR,"Illegal dump xtc command"); if (binary || compressed || multifile || multiproc) @@ -68,6 +70,7 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg), flush_flag = 0; unwrap_flag = 0; precision = 1000.0; + xd = new XDR; // allocate global array for atom coords @@ -105,9 +108,10 @@ DumpXTC::~DumpXTC() memory->destroy(coords); if (me == 0) { - xdrclose(&xd); + xdrclose(xd); xdrfreebuf(); } + delete xd; } /* ---------------------------------------------------------------------- */ @@ -150,7 +154,8 @@ void DumpXTC::openfile() fp = nullptr; if (me == 0) - if (xdropen(&xd,filename,"w") == 0) error->one(FLERR,"Cannot open dump file"); + if (xdropen(xd,filename,"w") == 0) + error->one(FLERR,"Cannot open XTC format dump file {}: {}", filename, utils::getsyserror()); } /* ---------------------------------------------------------------------- */ @@ -176,11 +181,11 @@ void DumpXTC::write_header(bigint nbig) if (me != 0) return; int tmp = XTC_MAGIC; - xdr_int(&xd,&tmp); - xdr_int(&xd,&n); - xdr_int(&xd,&ntimestep); + xdr_int(xd,&tmp); + xdr_int(xd,&n); + xdr_int(xd,&ntimestep); float time_value = ntimestep * tfactor * update->dt; - xdr_float(&xd,&time_value); + xdr_float(xd,&time_value); // cell basis vectors if (domain->triclinic) { @@ -192,18 +197,18 @@ void DumpXTC::write_header(bigint nbig) float xz = sfactor * domain->xz; float yz = sfactor * domain->yz; - xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero); - xdr_float(&xd,&xy ); xdr_float(&xd,&ydim); xdr_float(&xd,&zero); - xdr_float(&xd,&xz ); xdr_float(&xd,&yz ); xdr_float(&xd,&zdim); + xdr_float(xd,&xdim); xdr_float(xd,&zero); xdr_float(xd,&zero); + xdr_float(xd,&xy ); xdr_float(xd,&ydim); xdr_float(xd,&zero); + xdr_float(xd,&xz ); xdr_float(xd,&yz ); xdr_float(xd,&zdim); } else { float zero = 0.0; float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]); float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]); float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]); - xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero); - xdr_float(&xd,&zero); xdr_float(&xd,&ydim); xdr_float(&xd,&zero); - xdr_float(&xd,&zero); xdr_float(&xd,&zero); xdr_float(&xd,&zdim); + xdr_float(xd,&xdim); xdr_float(xd,&zero); xdr_float(xd,&zero); + xdr_float(xd,&zero); xdr_float(xd,&ydim); xdr_float(xd,&zero); + xdr_float(xd,&zero); xdr_float(xd,&zero); xdr_float(xd,&zdim); } } @@ -328,7 +333,7 @@ double DumpXTC::memory_usage() void DumpXTC::write_frame() { - xdr3dfcoord(&xd,coords,&natoms,&precision); + xdr3dfcoord(xd,coords,&natoms,&precision); } // ---------------------------------------------------------------------- @@ -406,7 +411,7 @@ static int magicints[] = { | | xdropen - open xdr file | - | This versions differs from xdrstdio_create, because I need to know + | This version differs from xdrstdio_create, because I need to know | the state of the file (read or write) so I can use xdr3dfcoord | in eigther read or write mode, and the file descriptor | so I can close the file (something xdr_destroy doesn't do). @@ -1048,7 +1053,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) } if (buf[1] != 0) buf[0]++; xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */ - return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0])); + return errval * (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0])); } else { /* xdrs is open for reading */ @@ -1129,7 +1134,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) if (xdr_int(xdrs, &(buf[0])) == 0) return 0; - if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0) + if (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]) == 0) return 0; buf[0] = buf[1] = buf[2] = 0; diff --git a/src/EXTRA-DUMP/dump_xtc.h b/src/EXTRA-DUMP/dump_xtc.h index 74147be06b..0a27cc67dd 100644 --- a/src/EXTRA-DUMP/dump_xtc.h +++ b/src/EXTRA-DUMP/dump_xtc.h @@ -21,8 +21,8 @@ DumpStyle(xtc,DumpXTC); #define LMP_DUMP_XTC_H #include "dump.h" -#include "xdr_compat.h" +struct XDR; namespace LAMMPS_NS { class DumpXTC : public Dump { @@ -37,7 +37,7 @@ class DumpXTC : public Dump { float precision; // user-adjustable precision setting float *coords; double sfactor, tfactor; // scaling factors for positions and time unit - XDR xd; + XDR *xd; void init_style() override; int modify_param(int, char **) override; diff --git a/src/EXTRA-DUMP/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp index e29bbe8334..3caa38663c 100644 --- a/src/EXTRA-DUMP/xdr_compat.cpp +++ b/src/EXTRA-DUMP/xdr_compat.cpp @@ -1,54 +1,63 @@ -// clang-format off #include "xdr_compat.h" + #include #include -/* This file is needed for systems, that do not provide XDR support - * in their system libraries. It was written for windows, but will - * most probably work on other platforms too. better make sure you - * test that the xtc files produced are ok before using it. +/* + * This file contains an implementation of the Sun External Data Representation (XDR) + * routines. They have been adapted specifically for the use with the LAMMPS xtc dump + * style to produce compressed trajectory files in the Gromacs XTC format. * - * It is also needed on BG/L and Cray XT3/XT4 as we don't have - * XDR support in the lightweight kernel runtimes either. + * The XDR sources are avaiable under the BSD 3-clause license for example in + * the MIT Kerberos 5 distribution with the following copyright notice and license. * - * This file contains the definitions for Sun External Data - * Representation (XDR) headers and routines. + * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC * - * Although the rest of LAMPPS is GPL, you can copy and use the XDR - * routines in any way you want as long as you obey Sun's license: + * Copyright (c) 2010, Oracle America, Inc. * - * Sun RPC is a product of Sun Microsystems, Inc. and is provided for - * unrestricted use provided that this legend is included on all tape - * media and as a part of the software program in whole or part. Users - * may copy or modify Sun RPC without charge, but are not authorized - * to license or distribute it to anyone else except as part of a product or - * program developed by the user. + * All rights reserved. * - * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE - * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR - * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE. + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: * - * Sun RPC is provided with no support and without any obligation on the - * part of Sun Microsystems, Inc. to assist in its use, correction, - * modification or enhancement. + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. * - * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE - * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC - * OR ANY PART THEREOF. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in + * the documentation and/or other materials provided with the + * distribution. * - * In no event will Sun Microsystems, Inc. be liable for any lost revenue - * or profits or other special, indirect and consequential damages, even if - * Sun has been advised of the possibility of such damages. + * * Neither the name of the "Oracle America, Inc." nor the names of + * its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. * - * Sun Microsystems, Inc. - * 2550 Garcia Avenue - * Mountain View, California 94043 + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS + * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED + * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A + * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifdef __cplusplus extern "C" { #endif +#ifndef FALSE +#define FALSE (0) +#endif +#ifndef TRUE +#define TRUE (1) +#endif + +#define BYTES_PER_XDR_UNIT (4) + /* * for unit alignment */ @@ -58,19 +67,18 @@ static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x) { xdr_uint32_t y; int i; - char *px=(char *)&x; - char *py=(char *)&y; + char *px = (char *) &x; + char *py = (char *) &y; - for (i=0;i<4;i++) - py[i]=px[3-i]; + for (i = 0; i < 4; i++) py[i] = px[3 - i]; return y; } static xdr_uint32_t xdr_htonl(xdr_uint32_t x) { - short s=0x0F00; - if (*((char *)&s)==(char)0x0F) { + short s = 0x0F00; + if (*((char *) &s) == (char) 0x0F) { /* bigendian, do nothing */ return x; } else { @@ -81,8 +89,8 @@ static xdr_uint32_t xdr_htonl(xdr_uint32_t x) static xdr_uint32_t xdr_ntohl(xdr_uint32_t x) { - short s=0x0F00; - if (*((char *)&s)==(char)0x0F) { + short s = 0x0F00; + if (*((char *) &s) == (char) 0x0F) { /* bigendian, do nothing */ return x; } else { @@ -91,221 +99,39 @@ static xdr_uint32_t xdr_ntohl(xdr_uint32_t x) } } - -/* - * Free a data structure using XDR - * Not a filter, but a convenient utility nonetheless - */ -void -xdr_free (xdrproc_t proc, char *objp) -{ - XDR x; - - x.x_op = XDR_FREE; - (*proc) (&x, objp); -} - -/* - * XDR nothing - */ -bool_t -xdr_void (void) -{ - return TRUE; -} - /* * XDR integers */ -bool_t -xdr_int (XDR *xdrs, int *ip) +bool_t xdr_int(XDR *xdrs, int *ip) { xdr_int32_t l; - switch (xdrs->x_op) - { + switch (xdrs->x_op) { + case XDR_ENCODE: l = (xdr_int32_t) (*ip); - return xdr_putint32 (xdrs, &l); + return xdr_putint32(xdrs, &l); + break; case XDR_DECODE: - if (!xdr_getint32 (xdrs, &l)) - { - return FALSE; - } + if (!xdr_getint32(xdrs, &l)) return FALSE; *ip = (int) l; + return TRUE; + break; case XDR_FREE: return TRUE; + break; } return FALSE; } - -/* - * XDR unsigned integers - */ -bool_t -xdr_u_int (XDR *xdrs, unsigned int *up) -{ - xdr_uint32_t l; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - l = (xdr_uint32_t) (*up); - return xdr_putuint32 (xdrs, &l); - - case XDR_DECODE: - if (!xdr_getuint32 (xdrs, &l)) - { - return FALSE; - } - *up = (unsigned int) l; - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - - - -/* - * XDR short integers - */ -bool_t -xdr_short (XDR *xdrs, short *sp) -{ - xdr_int32_t l; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - l = (xdr_int32_t) *sp; - return xdr_putint32 (xdrs, &l); - - case XDR_DECODE: - if (!xdr_getint32 (xdrs, &l)) - { - return FALSE; - } - *sp = (short) l; - return TRUE; - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - -/* - * XDR unsigned short integers - */ -bool_t -xdr_u_short (XDR *xdrs, unsigned short *usp) -{ - xdr_uint32_t l; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - l = (xdr_uint32_t) *usp; - return xdr_putuint32 (xdrs, &l); - - case XDR_DECODE: - if (!xdr_getuint32 (xdrs, &l)) - { - return FALSE; - } - *usp = (unsigned short) l; - return TRUE; - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - -/* - * XDR a char - */ -bool_t -xdr_char (XDR *xdrs, char *cp) -{ - int i; - - i = (*cp); - if (!xdr_int (xdrs, &i)) - { - return FALSE; - } - *cp = i; - return TRUE; -} - -/* - * XDR an unsigned char - */ -bool_t -xdr_u_char (XDR *xdrs, unsigned char *cp) -{ - unsigned int u; - - u = (*cp); - if (!xdr_u_int (xdrs, &u)) - { - return FALSE; - } - *cp = u; - return TRUE; -} - -/* - * XDR booleans - */ -bool_t -xdr_bool (XDR *xdrs, int *bp) -{ -#define XDR_FALSE ((xdr_int32_t) 0) -#define XDR_TRUE ((xdr_int32_t) 1) - - xdr_int32_t lb; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - lb = *bp ? XDR_TRUE : XDR_FALSE; - return xdr_putint32 (xdrs, &lb); - - case XDR_DECODE: - if (!xdr_getint32 (xdrs, &lb)) - { - return FALSE; - } - *bp = (lb == XDR_FALSE) ? FALSE : TRUE; - return TRUE; - - case XDR_FREE: - return TRUE; - } - return FALSE; -#undef XDR_FALSE -#undef XDR_TRUE -} - - - /* * XDR opaque data * Allows the specification of a fixed size sequence of opaque bytes. * cp points to the opaque object and cnt gives the byte length. */ -bool_t -xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt) +bool_t xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt) { unsigned int rndup; static char crud[BYTES_PER_XDR_UNIT]; @@ -313,219 +139,61 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt) /* * if no data we are done */ - if (cnt == 0) - return TRUE; + if (cnt == 0) return TRUE; /* * round byte count to full xdr units */ rndup = cnt % BYTES_PER_XDR_UNIT; - if (rndup > 0) - rndup = BYTES_PER_XDR_UNIT - rndup; - - switch (xdrs->x_op) - { - case XDR_DECODE: - if (!xdr_getbytes (xdrs, cp, cnt)) - { - return FALSE; - } - if (rndup == 0) - return TRUE; - return xdr_getbytes (xdrs, (char *)crud, rndup); - - case XDR_ENCODE: - if (!xdr_putbytes (xdrs, cp, cnt)) - { - return FALSE; - } - if (rndup == 0) - return TRUE; - return xdr_putbytes (xdrs, xdr_zero, rndup); - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - -/* - * XDR null terminated ASCII strings - * xdr_string deals with "C strings" - arrays of bytes that are - * terminated by a nullptr character. The parameter cpp references a - * pointer to storage; If the pointer is null, then the necessary - * storage is allocated. The last parameter is the max allowed length - * of the string as specified by a protocol. - */ -bool_t -xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize) -{ - char *sp = *cpp; /* sp is the actual string pointer */ - unsigned int size = 0; - unsigned int nodesize = 0; - - /* - * first deal with the length since xdr strings are counted-strings - */ - switch (xdrs->x_op) - { - case XDR_FREE: - if (sp == nullptr) - { - return TRUE; /* already free */ - } - /* fall through... */ - case XDR_ENCODE: - if (sp == nullptr) - return FALSE; - size = strlen (sp); - break; - case XDR_DECODE: - break; - } - - if (!xdr_u_int (xdrs, &size)) - { - return FALSE; - } - if (size > maxsize) - { - return FALSE; - } - nodesize = size + 1; - - /* - * now deal with the actual bytes - */ - switch (xdrs->x_op) - { - case XDR_DECODE: - if (nodesize == 0) - { - return TRUE; - } - if (sp == nullptr) - *cpp = sp = (char *) malloc (nodesize); - if (sp == nullptr) - { - (void) fputs ("xdr_string: out of memory\n", stderr); - return FALSE; - } - sp[size] = 0; - /* fall into ... */ - - case XDR_ENCODE: - return xdr_opaque (xdrs, sp, size); - - case XDR_FREE: - free (sp); - *cpp = nullptr; - return TRUE; - } - return FALSE; -} - - - -/* Floating-point stuff */ - -bool_t -xdr_float(XDR *xdrs, float *fp) -{ - xdr_int32_t tmp; - - switch (xdrs->x_op) { - - case XDR_ENCODE: - tmp = *(xdr_int32_t *)fp; - return (xdr_putint32(xdrs, &tmp)); - - break; - - case XDR_DECODE: - if (xdr_getint32(xdrs, &tmp)) { - *(xdr_int32_t *)fp = tmp; - return (TRUE); - } - - break; - - case XDR_FREE: - return (TRUE); - } - return (FALSE); -} - - -bool_t -xdr_double(XDR *xdrs, double *dp) -{ - - /* Windows and some other systems dont define double-precision - * word order in the header files, so unfortunately we have - * to calculate it! - */ - static int LSW=-1; /* Least significant fp word */ - int *ip; - xdr_int32_t tmp[2]; - - if (LSW<0) { - double x=0.987654321; /* Just a number */ - - /* Possible representations in IEEE double precision: - * (S=small endian, B=big endian) - * - * Byte order, Word order, Hex - * S S b8 56 0e 3c dd 9a ef 3f - * B S 3c 0e 56 b8 3f ef 9a dd - * S B dd 9a ef 3f b8 56 0e 3c - * B B 3f ef 9a dd 3c 0e 56 b8 - */ - - unsigned char ix = *((char *)&x); - - if (ix==0xdd || ix==0x3f) - LSW=1; /* Big endian word order */ - else if (ix==0xb8 || ix==0x3c) - LSW=0; /* Small endian word order */ - else { /* Catch strange errors */ - printf("Error when detecting floating-point word order.\n" - "Do you have a non-IEEE system?\n" - "If possible, use the XDR libraries provided with your system,\n" - "instead of the Gromacs fallback XDR source.\n"); - exit(0); - } - } + if (rndup > 0) rndup = BYTES_PER_XDR_UNIT - rndup; switch (xdrs->x_op) { - case XDR_ENCODE: - ip = (int *)dp; - tmp[0] = ip[!LSW]; - tmp[1] = ip[LSW]; - return (xdr_putint32(xdrs, tmp) && - xdr_putint32(xdrs, tmp+1)); + case XDR_DECODE: + if (!xdr_getbytes(xdrs, cp, cnt)) { return FALSE; } + if (rndup == 0) return TRUE; + return xdr_getbytes(xdrs, (char *) crud, rndup); + break; - break; + case XDR_ENCODE: + if (!xdr_putbytes(xdrs, cp, cnt)) { return FALSE; } + if (rndup == 0) return TRUE; + return xdr_putbytes(xdrs, xdr_zero, rndup); + break; - case XDR_DECODE: - ip = (int *)dp; - if (xdr_getint32(xdrs, tmp+!LSW) && - xdr_getint32(xdrs, tmp+LSW)) { - ip[0] = tmp[0]; - ip[1] = tmp[1]; - return (TRUE); - } - - break; - - case XDR_FREE: - return (TRUE); + case XDR_FREE: + return TRUE; + break; } - return (FALSE); + return FALSE; } +/* Floating-point stuff */ + +bool_t xdr_float(XDR *xdrs, float *fp) +{ + xdr_int32_t tmp; + + switch (xdrs->x_op) { + + case XDR_ENCODE: + tmp = *(xdr_int32_t *) fp; + return (xdr_putint32(xdrs, &tmp)); + break; + + case XDR_DECODE: + if (xdr_getint32(xdrs, &tmp)) { + *(xdr_int32_t *) fp = tmp; + return TRUE; + } + break; + + case XDR_FREE: + return TRUE; + break; + } + return FALSE; +} /* Array routines */ @@ -539,55 +207,37 @@ xdr_double(XDR *xdrs, double *dp) * > elemsize: size of each element * > xdr_elem: routine to XDR each element */ -bool_t -xdr_vector (XDR *xdrs, char *basep, unsigned int nelem, - unsigned int elemsize, xdrproc_t xdr_elem) +bool_t xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, unsigned int elemsize, + xdrproc_t xdr_elem) { -#define LASTUNSIGNED ((unsigned int)0-1) +#define LASTUNSIGNED ((unsigned int) 0 - 1) unsigned int i; char *elptr; elptr = basep; - for (i = 0; i < nelem; i++) - { - if (!(*xdr_elem) (xdrs, elptr, LASTUNSIGNED)) - { - return FALSE; - } - elptr += elemsize; - } + for (i = 0; i < nelem; i++) { + if (!(*xdr_elem)(xdrs, elptr, LASTUNSIGNED)) { return FALSE; } + elptr += elemsize; + } return TRUE; #undef LASTUNSIGNED } - - -static bool_t xdrstdio_getbytes (XDR *, char *, unsigned int); -static bool_t xdrstdio_putbytes (XDR *, char *, unsigned int); -static unsigned int xdrstdio_getpos (XDR *); -static bool_t xdrstdio_setpos (XDR *, unsigned int); -static xdr_int32_t *xdrstdio_inline (XDR *, int); -static void xdrstdio_destroy (XDR *); -static bool_t xdrstdio_getint32 (XDR *, xdr_int32_t *); -static bool_t xdrstdio_putint32 (XDR *, xdr_int32_t *); -static bool_t xdrstdio_getuint32 (XDR *, xdr_uint32_t *); -static bool_t xdrstdio_putuint32 (XDR *, xdr_uint32_t *); +static bool_t xdrstdio_getbytes(XDR *, char *, unsigned int); +static bool_t xdrstdio_putbytes(XDR *, char *, unsigned int); +static void xdrstdio_destroy(XDR *); +static bool_t xdrstdio_getint32(XDR *, xdr_int32_t *); +static bool_t xdrstdio_putint32(XDR *, xdr_int32_t *); /* * Ops vector for stdio type XDR */ -static const struct xdr_ops xdrstdio_ops = -{ - xdrstdio_getbytes, /* deserialize counted bytes */ - xdrstdio_putbytes, /* serialize counted bytes */ - xdrstdio_getpos, /* get offset in the stream */ - xdrstdio_setpos, /* set offset in the stream */ - xdrstdio_inline, /* prime stream for inline macros */ - xdrstdio_destroy, /* destroy stream */ - xdrstdio_getint32, /* deserialize a int */ - xdrstdio_putint32, /* serialize a int */ - xdrstdio_getuint32, /* deserialize a int */ - xdrstdio_putuint32 /* serialize a int */ +static const struct xdr_ops xdrstdio_ops = { + xdrstdio_getbytes, /* deserialize counted bytes */ + xdrstdio_putbytes, /* serialize counted bytes */ + xdrstdio_destroy, /* destroy stream */ + xdrstdio_getint32, /* deserialize a int */ + xdrstdio_putint32, /* serialize a int */ }; /* @@ -595,8 +245,7 @@ static const struct xdr_ops xdrstdio_ops = * Sets the xdr stream handle xdrs for use on the stream file. * Operation flag is set to op. */ -void -xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op) +void xdrstdio_create(XDR *xdrs, FILE *file, enum xdr_op op) { xdrs->x_op = op; /* We have to add the const since the `struct xdr_ops' in `struct XDR' @@ -611,104 +260,42 @@ xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op) * Destroy a stdio xdr stream. * Cleans up the xdr stream handle xdrs previously set up by xdrstdio_create. */ -static void -xdrstdio_destroy (XDR *xdrs) +static void xdrstdio_destroy(XDR *xdrs) { - (void) fflush ((FILE *) xdrs->x_private); + (void) fflush((FILE *) xdrs->x_private); /* xx should we close the file ?? */ } - -static bool_t -xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len) +static bool_t xdrstdio_getbytes(XDR *xdrs, char *addr, unsigned int len) { - if ((len != 0) && (fread (addr, (int) len, 1, - (FILE *) xdrs->x_private) != 1)) - return FALSE; + if ((len != 0) && (fread(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE; return TRUE; } -static bool_t -xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len) +static bool_t xdrstdio_putbytes(XDR *xdrs, char *addr, unsigned int len) { - if ((len != 0) && (fwrite (addr, (int) len, 1, - (FILE *) xdrs->x_private) != 1)) - return FALSE; + if ((len != 0) && (fwrite(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE; return TRUE; } -static unsigned int -xdrstdio_getpos (XDR *xdrs) -{ - return (unsigned int) ftell ((FILE *) xdrs->x_private); -} - -static bool_t -xdrstdio_setpos (XDR *xdrs, unsigned int pos) -{ - return fseek ((FILE *) xdrs->x_private, (xdr_int32_t) pos, 0) < 0 ? FALSE : TRUE; -} - -static xdr_int32_t * -xdrstdio_inline (XDR * /*xdrs*/, int /*len*/) -{ - /* - * Must do some work to implement this: must ensure - * enough data in the underlying stdio buffer, - * that the buffer is aligned so that we can indirect through a - * long *, and stuff this pointer in xdrs->x_buf. Doing - * a fread or fwrite to a scratch buffer would defeat - * most of the gains to be had here and require storage - * management on this buffer, so we don't do this. - */ - return nullptr; -} - -static bool_t -xdrstdio_getint32 (XDR *xdrs, xdr_int32_t *ip) +static bool_t xdrstdio_getint32(XDR *xdrs, xdr_int32_t *ip) { xdr_int32_t mycopy; - if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; - *ip = xdr_ntohl (mycopy); + if (fread((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; + *ip = xdr_ntohl(mycopy); return TRUE; } -static bool_t -xdrstdio_putint32 (XDR *xdrs, xdr_int32_t *ip) +static bool_t xdrstdio_putint32(XDR *xdrs, xdr_int32_t *ip) { - xdr_int32_t mycopy = xdr_htonl (*ip); + xdr_int32_t mycopy = xdr_htonl(*ip); ip = &mycopy; - if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; + if (fwrite((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; return TRUE; } -static bool_t -xdrstdio_getuint32 (XDR *xdrs, xdr_uint32_t *ip) -{ - xdr_uint32_t mycopy; - - if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; - *ip = xdr_ntohl (mycopy); - return TRUE; -} - -static bool_t -xdrstdio_putuint32 (XDR *xdrs, xdr_uint32_t *ip) -{ - xdr_uint32_t mycopy = xdr_htonl (*ip); - - ip = &mycopy; - if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; - return TRUE; -} - #ifdef __cplusplus } #endif - diff --git a/src/EXTRA-DUMP/xdr_compat.h b/src/EXTRA-DUMP/xdr_compat.h index 55dc22e9f9..d600a4a404 100644 --- a/src/EXTRA-DUMP/xdr_compat.h +++ b/src/EXTRA-DUMP/xdr_compat.h @@ -1,7 +1,7 @@ #ifndef LMP_XDR_COMPAT_H #define LMP_XDR_COMPAT_H -#include +#include #include #ifdef __cplusplus @@ -9,47 +9,53 @@ extern "C" { #endif /* - * This file is needed for systems, that do not provide XDR support - * in their system libraries. It was written for windows, but will - * most probably work on other platforms too. better make sure you - * test that the xtc files produced are ok before using it. + * This file contains the definitions for Sun External Data Representation (XDR). + * They have been adapted specifically for the use with the LAMMPS xtc dump style + * to produce compressed trajectory files in the Gromacs XTC format. * - * It is also needed on BG/L, BG/P and Cray XT3/XT4/XT5 as we don't - * have XDR support in the lightweight kernel runtimes either. + * The XDR sources are avaiable under the BSD 3-clause license for example in + * the MIT Kerberos 5 distribution with the following copyright notice and license. * - * This file contains the definitions for Sun External Data - * Representation (XDR) headers and routines. + * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC * - * Although the rest of LAMPPS is GPL, you can copy and use the XDR - * routines in any way you want as long as you obey Sun's license: - * Sun RPC is a product of Sun Microsystems, Inc. and is provided for - * unrestricted use provided that this legend is included on all tape - * media and as a part of the software program in whole or part. Users - * may copy or modify Sun RPC without charge, but are not authorized - * to license or distribute it to anyone else except as part of a product or - * program developed by the user. + * Copyright (c) 2010, Oracle America, Inc. * - * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE - * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR - * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE. + * All rights reserved. * - * Sun RPC is provided with no support and without any obligation on the - * part of Sun Microsystems, Inc. to assist in its use, correction, - * modification or enhancement. + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: * - * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE - * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC - * OR ANY PART THEREOF. + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. * - * In no event will Sun Microsystems, Inc. be liable for any lost revenue - * or profits or other special, indirect and consequential damages, even if - * Sun has been advised of the possibility of such damages. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in + * the documentation and/or other materials provided with the + * distribution. * - * Sun Microsystems, Inc. - * 2550 Garcia Avenue - * Mountain View, California 94043 + * * Neither the name of the "Oracle America, Inc." nor the names of + * its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS + * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED + * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A + * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ +/* compatibility typedefs */ +typedef int bool_t; + +typedef int32_t xdr_int32_t; +typedef uint32_t xdr_uint32_t; + /* * Xdr operations. XDR_ENCODE causes the type to be encoded into the * stream. XDR_DECODE causes the type to be extracted from the stream. @@ -57,44 +63,8 @@ extern "C" { * XDR_DECODE request. */ -typedef int bool_t; - -#if defined(_WIN32) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || \ - defined(__OpenBSD__) || defined(__NetBSD__) || (defined(__linux__) && !defined(__GLIBC_MINOR__)) -typedef char *caddr_t; -typedef unsigned int u_int; -#endif - -/* - * Aninteger type that is 32 bits wide. Check if int, - * long or short is 32 bits and die if none of them is :-) - */ -#if (INT_MAX == 2147483647) -typedef int xdr_int32_t; -typedef unsigned int xdr_uint32_t; -#elif (LONG_MAX == 2147483647L) -typedef long xdr_int32_t; -typedef unsigned long xdr_uint32_t; -#elif (SHRT_MAX == 2147483647) -typedef short xdr_int32_t; -typedef unsigned short xdr_uint32_t; -#else -#error ERROR: No 32 bit wide integer type found! -#endif - enum xdr_op { XDR_ENCODE = 0, XDR_DECODE = 1, XDR_FREE = 2 }; -#ifndef FALSE -#define FALSE (0) -#endif -#ifndef TRUE -#define TRUE (1) -#endif - -#define BYTES_PER_XDR_UNIT (4) -/* Macro to round up to units of 4. */ -#define XDR_RNDUP(x) (((x) + BYTES_PER_XDR_UNIT - 1) & ~(BYTES_PER_XDR_UNIT - 1)) - /* * The XDR handle. * Contains operation which is being applied to the stream, @@ -113,26 +83,16 @@ struct XDR { }; struct xdr_ops { + /* get some bytes from XDR stream */ bool_t (*x_getbytes)(XDR *__xdrs, char *__addr, unsigned int __len); - /* get some bytes from " */ + /* put some bytes to XDR stream */ bool_t (*x_putbytes)(XDR *__xdrs, char *__addr, unsigned int __len); - /* put some bytes to " */ - unsigned int (*x_getpostn)(XDR *__xdrs); - /* returns bytes off from beginning */ - bool_t (*x_setpostn)(XDR *__xdrs, unsigned int __pos); - /* lets you reposition the stream */ - xdr_int32_t *(*x_inline)(XDR *__xdrs, int __len); - /* buf quick ptr to buffered data */ - void (*x_destroy)(XDR *__xdrs); /* free privates of this xdr_stream */ + void (*x_destroy)(XDR *__xdrs); + /* get a int from XDR stream */ bool_t (*x_getint32)(XDR *__xdrs, xdr_int32_t *__ip); - /* get a int from underlying stream */ + /* put a int to XDR stream */ bool_t (*x_putint32)(XDR *__xdrs, xdr_int32_t *__ip); - /* put a int to " */ - bool_t (*x_getuint32)(XDR *__xdrs, xdr_uint32_t *__ip); - /* get a unsigned int from underlying stream */ - bool_t (*x_putuint32)(XDR *__xdrs, xdr_uint32_t *__ip); - /* put a int to " */ }; /* @@ -151,53 +111,25 @@ typedef bool_t (*xdrproc_t)(XDR *, void *, ...); * * XDR *xdrs; * xdr_int32_t *int32p; - * long *longp; - * char *addr; * unsigned int len; - * unsigned int pos; */ #define xdr_getint32(xdrs, int32p) (*(xdrs)->x_ops->x_getint32)(xdrs, int32p) - #define xdr_putint32(xdrs, int32p) (*(xdrs)->x_ops->x_putint32)(xdrs, int32p) - -#define xdr_getuint32(xdrs, uint32p) (*(xdrs)->x_ops->x_getuint32)(xdrs, uint32p) - -#define xdr_putuint32(xdrs, uint32p) (*(xdrs)->x_ops->x_putuint32)(xdrs, uint32p) - #define xdr_getbytes(xdrs, addr, len) (*(xdrs)->x_ops->x_getbytes)(xdrs, addr, len) - #define xdr_putbytes(xdrs, addr, len) (*(xdrs)->x_ops->x_putbytes)(xdrs, addr, len) - -#define xdr_getpos(xdrs) (*(xdrs)->x_ops->x_getpostn)(xdrs) - -#define xdr_setpos(xdrs, pos) (*(xdrs)->x_ops->x_setpostn)(xdrs, pos) - -#define xdr_inline(xdrs, len) (*(xdrs)->x_ops->x_inline)(xdrs, len) - #define xdr_destroy(xdrs) \ do { \ if ((xdrs)->x_ops->x_destroy) (*(xdrs)->x_ops->x_destroy)(xdrs); \ } while (0) extern bool_t xdr_int(XDR *__xdrs, int *__ip); -extern bool_t xdr_u_int(XDR *__xdrs, unsigned int *__ip); -extern bool_t xdr_short(XDR *__xdrs, short *__ip); -extern bool_t xdr_u_short(XDR *__xdrs, unsigned short *__ip); -extern bool_t xdr_bool(XDR *__xdrs, int *__bp); extern bool_t xdr_opaque(XDR *__xdrs, char *__cp, unsigned int __cnt); -extern bool_t xdr_string(XDR *__xdrs, char **__cpp, unsigned int __maxsize); -extern bool_t xdr_char(XDR *__xdrs, char *__cp); -extern bool_t xdr_u_char(XDR *__xdrs, unsigned char *__cp); extern bool_t xdr_vector(XDR *__xdrs, char *__basep, unsigned int __nelem, unsigned int __elemsize, xdrproc_t __xdr_elem); extern bool_t xdr_float(XDR *__xdrs, float *__fp); -extern bool_t xdr_double(XDR *__xdrs, double *__dp); extern void xdrstdio_create(XDR *__xdrs, FILE *__file, enum xdr_op __xop); -/* free memory buffers for xdr */ -extern void xdr_free(xdrproc_t __proc, char *__objp); - #ifdef __cplusplus } #endif diff --git a/src/EXTRA-FIX/fix_ave_correlate_long.cpp b/src/EXTRA-FIX/fix_ave_correlate_long.cpp index fc1760b353..7c80365c57 100644 --- a/src/EXTRA-FIX/fix_ave_correlate_long.cpp +++ b/src/EXTRA-FIX/fix_ave_correlate_long.cpp @@ -454,6 +454,8 @@ void FixAveCorrelateLong::end_of_step() scalar = val.val.f->compute_vector(val.argindex-1); // evaluate equal-style or vector-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori } else if (val.which == ArgInfo::VARIABLE) { if (val.argindex == 0) @@ -462,7 +464,7 @@ void FixAveCorrelateLong::end_of_step() double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); int index = val.argindex; - if (nvec < index) scalar = 0.0; + if (index > nvec) scalar = 0.0; else scalar = varvec[index-1]; } } diff --git a/src/EXTRA-FIX/fix_deform_pressure.cpp b/src/EXTRA-FIX/fix_deform_pressure.cpp index ffa3f11d92..e93def4926 100644 --- a/src/EXTRA-FIX/fix_deform_pressure.cpp +++ b/src/EXTRA-FIX/fix_deform_pressure.cpp @@ -110,6 +110,11 @@ FixDeformPressure::FixDeformPressure(LAMMPS *lmp, int narg, char **arg) : } set_extra[index].pgain = utils::numeric(FLERR, arg[iarg + 3], false, lmp); i += 4; + } else if (strcmp(arg[iarg + 1], "erate/rescale") == 0) { + if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix deform/pressure erate/rescale", error); + set[index].style = ERATERS; + set[index].rate = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + i += 3; } else error->all(FLERR, "Illegal fix deform/pressure command: {}", arg[iarg + 1]); } else if (strcmp(arg[iarg], "box") == 0) { @@ -424,16 +429,29 @@ void FixDeformPressure::init() if (!pressure) error->all(FLERR, "Pressure ID {} for fix deform/pressure does not exist", id_press); } + + // if yz [3] changes and will cause box flip, then xy [5] cannot be changing + // this is b/c the flips would induce continuous changes in xz + // in order to keep the edge vectors of the flipped shape matrix + // an integer combination of the edge vectors of the unflipped shape matrix + // error if style PRESSURE/ERATEER for yz, can't calculate if box flip occurs + + if (set[3].style && set[5].style) { + if (flipflag && set[3].style == PRESSURE) + error->all(FLERR, "Fix {} cannot use yz pressure with xy", style); + if (flipflag && set[3].style == ERATERS) + error->all(FLERR, "Fix {} cannot use yz erate/rescale with xy", style); + } } /* ---------------------------------------------------------------------- - compute T,P if needed before integrator starts + compute T,P before integrator starts ------------------------------------------------------------------------- */ void FixDeformPressure::setup(int /*vflag*/) { - // trigger virial computation on next timestep - if (pressure_flag) pressure->addstep(update->ntimestep+1); + // trigger virial computation, if needed, on next timestep + if (pressure_flag) pressure->addstep(update->ntimestep + 1); } /* ---------------------------------------------------------------------- */ @@ -446,7 +464,20 @@ void FixDeformPressure::end_of_step() // set new box size for strain-based dims - if (strain_flag) FixDeform::apply_strain(); + if (strain_flag) { + FixDeform::apply_strain(); + + for (int i = 3; i < 6; i++) { + if (set[i].style == ERATERS) { + double L = domain->zprd; + if (i == 5) L = domain->yprd; + + h_rate[i] = set[i].rate * L; + set_extra[i].cumulative_shift += update->dt * h_rate[i]; + set[i].tilt_target = set[i].tilt_start + set_extra[i].cumulative_shift; + } + } + } // set new box size for pressure-based dims @@ -479,12 +510,33 @@ void FixDeformPressure::end_of_step() for (int i = 0; i < 3; i++) { set_extra[i].prior_pressure = pressure->vector[i]; set_extra[i].prior_rate = ((set[i].hi_target - set[i].lo_target) / - (domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt; + domain->prd[i] - 1.0) / update->dt; } } if (varflag) modify->addstep_compute(update->ntimestep + nevery); + // If tilting while evolving linear dimension, sum remapping effects + // otherwise, update_domain() will inaccurately use the current + // linear dimension to apply prior remappings + + for (int i = 3; i < 6; i++) { + int idenom = 0; + if (i == 3) idenom = 1; + if (set[i].style && (set_box.style || set[idenom].style) && domain->periodicity[idenom]) { + // Add prior remappings. If the box remaps this timestep, don't + // add it yet so update_domain() will first detect the remapping + set[i].tilt_target += set_extra[i].cumulative_remap; + + // Update remapping for next timestep + double prd = set[idenom].hi_target - set[idenom].lo_target; + double prdinv = 1.0 / prd; + if (set[i].tilt_target * prdinv < -0.5) + set_extra[i].cumulative_remap += prd; + if (set[i].tilt_target * prdinv > 0.5) + set_extra[i].cumulative_remap -= prd; + } + } FixDeform::update_domain(); @@ -502,7 +554,7 @@ void FixDeformPressure::apply_pressure() { // If variable pressure, calculate current target for (int i = 0; i < 6; i++) - if (set[i].style == PRESSURE) + if (set[i].style == PRESSURE || set[i].style == PMEAN) if (set_extra[i].pvar_flag) set_extra[i].ptarget = input->variable->compute_equal(set_extra[i].pvar); @@ -556,26 +608,24 @@ void FixDeformPressure::apply_pressure() h_ratelo[i] = -0.5 * h_rate[i]; - double offset = 0.5 * (domain->boxhi[i] - domain->boxlo[i]) * (1.0 + update->dt * h_rate[i]); - set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - offset; - set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + offset; + double shift = domain->prd[i] * update->dt * h_rate[i]; + set_extra[i].cumulative_shift += shift; + set[i].lo_target = set[i].lo_start - 0.5 * set_extra[i].cumulative_shift; + set[i].hi_target = set[i].hi_start + 0.5 * set_extra[i].cumulative_shift; } for (int i = 3; i < 6; i++) { if (set[i].style != PRESSURE) continue; - double L, tilt, pcurrent; + double L, pcurrent; if (i == 3) { L = domain->zprd; - tilt = domain->yz; pcurrent = tensor[5]; } else if (i == 4) { L = domain->zprd; - tilt = domain->xz + update->dt; pcurrent = tensor[4]; } else { L = domain->yprd; - tilt = domain->xy; pcurrent = tensor[3]; } @@ -592,7 +642,8 @@ void FixDeformPressure::apply_pressure() if (fabs(h_rate[i]) > max_h_rate) h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]); - set[i].tilt_target = tilt + update->dt * h_rate[i]; + set_extra[i].cumulative_shift += update->dt * h_rate[i]; + set[i].tilt_target = set[i].tilt_start + set_extra[i].cumulative_shift; } } @@ -629,9 +680,9 @@ void FixDeformPressure::apply_volume() double dt = update->dt; double e1i = set_extra[i].prior_rate; double e2i = set_extra[fixed].prior_rate; - double L1i = domain->boxhi[i] - domain->boxlo[i]; - double L2i = domain->boxhi[fixed] - domain->boxlo[fixed]; - double L3i = domain->boxhi[dynamic1] - domain->boxlo[dynamic1]; + double L1i = domain->prd[i]; + double L2i = domain->prd[fixed]; + double L3i = domain->prd[dynamic1]; double L3 = (set[dynamic1].hi_target - set[dynamic1].lo_target); double Vi = L1i * L2i * L3i; double V = L3 * L1i * L2i; @@ -680,7 +731,7 @@ void FixDeformPressure::apply_volume() } } - h_rate[i] = (2.0 * shift / (domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt; + h_rate[i] = (2.0 * shift / domain->prd[i] - 1.0) / update->dt; h_ratelo[i] = -0.5 * h_rate[i]; set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; @@ -742,7 +793,7 @@ void FixDeformPressure::apply_box() set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; // Recalculate h_rate - h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0; + h_rate[i] = (set[i].hi_target - set[i].lo_target) / domain->prd[i] - 1.0; h_rate[i] /= update->dt; h_ratelo[i] = -0.5 * h_rate[i]; } @@ -767,15 +818,21 @@ void FixDeformPressure::apply_box() if (fabs(v_rate) > max_h_rate) v_rate = max_h_rate * v_rate / fabs(v_rate); - set_extra[6].cumulative_strain += update->dt * v_rate; - scale = (1.0 + set_extra[6].cumulative_strain); for (i = 0; i < 3; i++) { - shift = 0.5 * (set[i].hi_target - set[i].lo_target) * scale; - set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; - set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; + shift = (set[i].hi_target - set[i].lo_target) * update->dt * v_rate; + set_extra[6].cumulative_vshift[i] += shift; + + if (set[i].style == NONE) { + // Overwrite default targets of current length + set[i].lo_target = set[i].lo_start; + set[i].hi_target = set[i].hi_start; + } + + set[i].lo_target -= 0.5 * set_extra[6].cumulative_vshift[i]; + set[i].hi_target += 0.5 * set_extra[6].cumulative_vshift[i]; // Recalculate h_rate - h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0; + h_rate[i] = (set[i].hi_target - set[i].lo_target) / domain->prd[i] - 1.0; h_rate[i] /= update->dt; h_ratelo[i] = -0.5 * h_rate[i]; } @@ -789,7 +846,7 @@ void FixDeformPressure::apply_box() void FixDeformPressure::write_restart(FILE *fp) { if (comm->me == 0) { - int size = 9 * sizeof(double) + 7 * sizeof(Set) + 7 * sizeof(SetExtra); + int size = 7 * sizeof(Set) + 7 * sizeof(SetExtra); fwrite(&size, sizeof(int), 1, fp); fwrite(set, sizeof(Set), 6, fp); fwrite(&set_box, sizeof(Set), 1, fp); @@ -804,22 +861,16 @@ void FixDeformPressure::write_restart(FILE *fp) void FixDeformPressure::restart(char *buf) { int n = 0; - auto list = (double *) buf; - for (int i = 0; i < 6; i++) - h_rate[i] = list[n++]; - for (int i = 0; i < 3; i++) - h_ratelo[i] = list[n++]; - - n = n * sizeof(double); int samestyle = 1; - Set *set_restart = (Set *) &buf[n]; + Set *set_restart = (Set *) buf; for (int i = 0; i < 6; ++i) { // restore data from initial state set[i].lo_initial = set_restart[i].lo_initial; set[i].hi_initial = set_restart[i].hi_initial; set[i].vol_initial = set_restart[i].vol_initial; set[i].tilt_initial = set_restart[i].tilt_initial; - // check if style settings are consistent (should do the whole set?) + + // check if style settings are consistent if (set[i].style != set_restart[i].style) samestyle = 0; if (set[i].substyle != set_restart[i].substyle) @@ -843,7 +894,6 @@ void FixDeformPressure::restart(char *buf) set_extra[i].saved = set_extra_restart[i].saved; set_extra[i].prior_rate = set_extra_restart[i].prior_rate; set_extra[i].prior_pressure = set_extra_restart[i].prior_pressure; - set_extra[i].cumulative_strain = set_extra_restart[i].cumulative_strain; } } diff --git a/src/EXTRA-FIX/fix_deform_pressure.h b/src/EXTRA-FIX/fix_deform_pressure.h index 5a0d844bad..7ce69b9bc5 100644 --- a/src/EXTRA-FIX/fix_deform_pressure.h +++ b/src/EXTRA-FIX/fix_deform_pressure.h @@ -51,7 +51,9 @@ class FixDeformPressure : public FixDeform { struct SetExtra { double ptarget, pgain; double prior_pressure, prior_rate; - double cumulative_strain; + double cumulative_shift; + double cumulative_vshift[3]; + double cumulative_remap; int saved; char *pstr; int pvar, pvar_flag; diff --git a/src/EXTRA-FIX/fix_nonaffine_displacement.cpp b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp index 06702c408b..b651d5dc5e 100644 --- a/src/EXTRA-FIX/fix_nonaffine_displacement.cpp +++ b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp @@ -46,6 +46,8 @@ enum { TYPE, RADIUS, CUSTOM }; enum { INTEGRATED, D2MIN }; enum { FIXED, OFFSET, UPDATE }; +static constexpr double EPSILON = 1.0e-15; + static const char cite_nonaffine_d2min[] = "@article{PhysRevE.57.7192,\n" " title = {Dynamics of viscoplastic deformation in amorphous solids},\n" @@ -65,28 +67,33 @@ static const char cite_nonaffine_d2min[] = /* ---------------------------------------------------------------------- */ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), id_fix(nullptr), X(nullptr), Y(nullptr), F(nullptr), norm(nullptr) + Fix(lmp, narg, arg), id_fix(nullptr), fix(nullptr), D2min(nullptr), X(nullptr), Y(nullptr), + F(nullptr), norm(nullptr), singular(nullptr) { - if (narg < 4) error->all(FLERR,"Illegal fix nonaffine/displacement command"); + if (narg < 4) utils::missing_cmd_args(FLERR,"fix nonaffine/displacement", error); nevery = utils::inumeric(FLERR, arg[3], false, lmp); if (nevery <= 0) error->all(FLERR,"Illegal nevery value {} in fix nonaffine/displacement", nevery); reference_timestep = update_timestep = offset_timestep = -1; + z_min = 0; + int iarg = 4; if (strcmp(arg[iarg], "integrated") == 0) { nad_style = INTEGRATED; - nevery = 1; iarg += 1; } else if (strcmp(arg[iarg], "d2min") == 0) { - if (iarg + 1 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command"); + if (iarg + 1 > narg) utils::missing_cmd_args(FLERR,"fix nonaffine/displacement d2min", error); nad_style = D2MIN; if (strcmp(arg[iarg + 1], "type") == 0) { cut_style = TYPE; } else if (strcmp(arg[iarg + 1], "radius") == 0) { cut_style = RADIUS; } else if (strcmp(arg[iarg + 1], "custom") == 0) { - if (iarg + 2 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command"); + if (iarg + 2 > narg) + utils::missing_cmd_args(FLERR,"fix nonaffine/displacement custom", error); + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Fix nonaffine/displacement with custom cutoff requires neighbor style 'bin' or 'nsq'"); cut_style = CUSTOM; cutoff_custom = utils::numeric(FLERR, arg[iarg + 2], false, lmp); cutsq_custom = cutoff_custom * cutoff_custom; @@ -97,7 +104,7 @@ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char * iarg += 2; } else error->all(FLERR,"Illegal nonaffine displacement style {} in fix nonaffine/displacement", arg[iarg]); - if (iarg + 2 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR,"fix nonaffine/displacement", error); if (strcmp(arg[iarg], "fixed") == 0) { reference_style = FIXED; reference_timestep = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); @@ -106,7 +113,7 @@ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char * } else if (strcmp(arg[iarg], "update") == 0) { reference_style = UPDATE; update_timestep = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); - if (update_timestep < 0) + if (update_timestep <= 0) error->all(FLERR, "Illegal update timestep {} in fix nonaffine/displacement", arg[iarg + 1]); } else if (strcmp(arg[iarg], "offset") == 0) { reference_style = OFFSET; @@ -114,14 +121,21 @@ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char * if ((offset_timestep <= 0) || (offset_timestep > nevery)) error->all(FLERR, "Illegal offset timestep {} in fix nonaffine/displacement", arg[iarg + 1]); } else error->all(FLERR,"Illegal reference style {} in fix nonaffine/displacement", arg[iarg]); + iarg += 2; + + while (iarg < narg) { + if (strcmp(arg[iarg], "z/min") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR,"fix nonaffine/displacement", error); + z_min = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + if (z_min < 0) error->all(FLERR, "Minimum coordination must be positive"); + iarg += 2; + } else error->all(FLERR,"Illegal keyword {} in fix nonaffine/displacement", arg[iarg]); + } if (nad_style == D2MIN) if (cut_style == RADIUS && (!atom->radius_flag)) error->all(FLERR, "Fix nonaffine/displacement radius style requires atom attribute radius"); - if (nad_style == INTEGRATED && reference_style == OFFSET) - error->all(FLERR, "Fix nonaffine/displacement cannot use the integrated style with an offset reference state"); - peratom_flag = 1; peratom_freq = nevery; nmax = -1; @@ -151,8 +165,11 @@ FixNonaffineDisplacement::~FixNonaffineDisplacement() memory->destroy(Y); memory->destroy(F); memory->destroy(norm); - memory->destroy(array_atom); + memory->destroy(singular); + memory->destroy(D2min); } + + memory->destroy(array_atom); } /* ---------------------------------------------------------------------- */ @@ -176,12 +193,7 @@ void FixNonaffineDisplacement::post_constructor() id_fix = utils::strdup(id + std::string("_FIX_PA")); fix = dynamic_cast(modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 {} 1", id_fix, group->names[igroup], ghost_status))); - if (nad_style == INTEGRATED) - array_atom = fix->astore; - - if (nad_style == D2MIN) - grow_arrays(atom->nmax); - + grow_arrays(atom->nmax); for (int i = 0; i < atom->nlocal; i++) for (int j = 0; j < 3; j++) array_atom[i][j] = 0.0; } @@ -207,6 +219,9 @@ void FixNonaffineDisplacement::init() } else { auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); if (cut_style == CUSTOM) { + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Fix nonaffine/displacement with custom cutoff requires neighbor style 'bin' or 'nsq'"); + double skin = neighbor->skin; mycutneigh = cutoff_custom + skin; @@ -246,6 +261,15 @@ void FixNonaffineDisplacement::post_force(int /*vflag*/) if (reference_saved && (!update->setupflag)) { if (nad_style == INTEGRATED) { integrate_velocity(); + if ((update->ntimestep % nevery) == 0) { + if (atom->nmax > nmax) + grow_arrays(atom->nmax); + + double **x_nonaffine = fix->astore; + for (int i = 0; i < atom->nlocal; i++) + for (int m = 0; m < 3; m++) + array_atom[i][m] = x_nonaffine[i][m]; + } } else { if ((update->ntimestep % nevery) == 0) calculate_D2Min(); } @@ -292,11 +316,12 @@ void FixNonaffineDisplacement::integrate_velocity() int *mask = atom->mask; int nlocal = atom->nlocal; + double **x_nonaffine = fix->astore; for (int m = 0; m < 3; m++) { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { - array_atom[i][m] += dtv * v[i][m]; + x_nonaffine[i][m] += dtv * v[i][m]; } } } @@ -307,6 +332,7 @@ void FixNonaffineDisplacement::integrate_velocity() void FixNonaffineDisplacement::save_reference_state() { double **x = atom->x; + double **x0 = fix->astore; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -315,13 +341,13 @@ void FixNonaffineDisplacement::save_reference_state() if (nad_style == D2MIN) { for (int m = 0; m < 3; m++) { for (int i = 0; i < nall; i++) { - if (mask[i] & groupbit) array_atom[i][m] = x[i][m]; + if (mask[i] & groupbit) x0[i][m] = x[i][m]; } } } else { for (int m = 0; m < 3; m++) { for (int i = 0; i < nall; i++) { - if (mask[i] & groupbit) array_atom[i][m] = 0.0; + if (mask[i] & groupbit) x0[i][m] = 0.0; } } } @@ -359,7 +385,7 @@ void FixNonaffineDisplacement::calculate_D2Min() int *ilist, *jlist, *numneigh, **firstneigh; double **x = atom->x; - double **x0 = array_atom; + double **x0 = fix->astore; double *radius = atom->radius; int *type = atom->type; int *mask = atom->mask; @@ -384,7 +410,8 @@ void FixNonaffineDisplacement::calculate_D2Min() } } norm[i] = 0; - array_atom[i][0] = 0; + singular[i] = 0; + D2min[i] = 0; } // First loop through neighbors @@ -460,14 +487,29 @@ void FixNonaffineDisplacement::calculate_D2Min() } if (dim == 3) { - invert3(Y_tmp, Y_inv); + denom = det3(Y_tmp); + if (fabs(denom) < EPSILON) { + singular[i] = 1; + for (j = 0; j < 3; j++) + for (k = 0; k < 3; k++) + Y_inv[j][k] = 0.0; + } else { + invert3(Y_tmp, Y_inv); + } } else { denom = Y_tmp[0][0] * Y_tmp[1][1] - Y_tmp[0][1] * Y_tmp[1][0]; - if (denom != 0.0) denom = 1.0 / denom; - Y_inv[0][0] = Y_tmp[1][1] * denom; - Y_inv[0][1] = -Y_tmp[0][1] * denom; - Y_inv[1][0] = -Y_tmp[1][0] * denom; - Y_inv[1][1] = Y_tmp[0][0] * denom; + if (fabs(denom) < EPSILON) { + singular[i] = 1; + for (j = 0; j < 2; j++) + for (k = 0; k < 2; k++) + Y_inv[j][k] = 0.0; + } else { + denom = 1.0 / denom; + Y_inv[0][0] = Y_tmp[1][1] * denom; + Y_inv[0][1] = -Y_tmp[0][1] * denom; + Y_inv[1][0] = -Y_tmp[1][0] * denom; + Y_inv[1][1] = Y_tmp[0][0] * denom; + } } times3(X_tmp, Y_inv, F_tmp); @@ -525,7 +567,7 @@ void FixNonaffineDisplacement::calculate_D2Min() } sub3(r, temp, temp); - array_atom[i][0] += lensq3(temp); + D2min[i] += lensq3(temp); norm[i] += 1; if (newton_pair || j < nlocal) { @@ -536,7 +578,7 @@ void FixNonaffineDisplacement::calculate_D2Min() } sub3(r, temp, temp); - array_atom[j][0] += lensq3(temp); + D2min[j] += lensq3(temp); norm[j] += 1; } } @@ -548,11 +590,16 @@ void FixNonaffineDisplacement::calculate_D2Min() for (i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; - if (norm[i] != 0) - array_atom[i][0] /= norm[i]; - else + if (norm[i] < z_min || singular[i] == 1) { + if (norm[i] >= z_min) + error->warning(FLERR, "Singular matrix detected for atom {}, defaulting output to zero", atom->tag[i]); array_atom[i][0] = 0.0; - array_atom[i][0] = sqrt(array_atom[i][0]); + array_atom[i][1] = 0.0; + array_atom[i][2] = 0.0; + continue; + } + + D2min[i] /= norm[i]; for (j = 0; j < 3; j++) for (k = 0; k < 3; k++) @@ -572,6 +619,7 @@ void FixNonaffineDisplacement::calculate_D2Min() edev = sqrt(0.5 * j2); + array_atom[i][0] = sqrt(D2min[i]); array_atom[i][1] = evol; array_atom[i][2] = edev; } @@ -594,7 +642,7 @@ int FixNonaffineDisplacement::pack_reverse_comm(int n, int first, double *buf) } } } else { - buf[m++] = array_atom[i][0]; + buf[m++] = D2min[i]; buf[m++] = ubuf(norm[i]).d; } } @@ -618,7 +666,7 @@ void FixNonaffineDisplacement::unpack_reverse_comm(int n, int *list, double *buf } } } else { - array_atom[j][0] += buf[m++]; + D2min[j] += buf[m++]; norm[j] += (int) ubuf(buf[m++]).i; } } @@ -724,12 +772,20 @@ void FixNonaffineDisplacement::minimum_image0(double *delta) void FixNonaffineDisplacement::grow_arrays(int nmax_new) { nmax = nmax_new; - memory->destroy(X); - memory->destroy(Y); - memory->destroy(F); - memory->destroy(norm); - memory->create(X, nmax, 3, 3, "fix_nonaffine_displacement:X"); - memory->create(Y, nmax, 3, 3, "fix_nonaffine_displacement:Y"); - memory->create(F, nmax, 3, 3, "fix_nonaffine_displacement:F"); - memory->create(norm, nmax, "fix_nonaffine_displacement:norm"); + memory->destroy(array_atom); + memory->create(array_atom, nmax, 3, "fix_nonaffine_displacement:array_atom"); + if (nad_style == D2MIN) { + memory->destroy(X); + memory->destroy(Y); + memory->destroy(F); + memory->destroy(D2min); + memory->destroy(norm); + memory->destroy(singular); + memory->create(X, nmax, 3, 3, "fix_nonaffine_displacement:X"); + memory->create(Y, nmax, 3, 3, "fix_nonaffine_displacement:Y"); + memory->create(F, nmax, 3, 3, "fix_nonaffine_displacement:F"); + memory->create(D2min, nmax, "fix_nonaffine_displacement:D2min"); + memory->create(norm, nmax, "fix_nonaffine_displacement:norm"); + memory->create(singular, nmax, "fix_nonaffine_displacement:singular"); + } } diff --git a/src/EXTRA-FIX/fix_nonaffine_displacement.h b/src/EXTRA-FIX/fix_nonaffine_displacement.h index 3341ab1834..b0e9c464ca 100644 --- a/src/EXTRA-FIX/fix_nonaffine_displacement.h +++ b/src/EXTRA-FIX/fix_nonaffine_displacement.h @@ -48,16 +48,15 @@ class FixNonaffineDisplacement : public Fix { int nmax, comm_flag; int nad_style, cut_style; int reference_style, offset_timestep, reference_timestep, update_timestep; - int reference_saved; + int reference_saved, z_min; double cutoff_custom, cutsq_custom, mycutneigh; double xprd0, yprd0, zprd0, xprd0_half, yprd0_half, zprd0_half, xy0, xz0, yz0; - double ***X, ***Y, ***F; - int *norm; + double *D2min, ***X, ***Y, ***F; + int *norm, *singular; class NeighList *list; // half neighbor list - void integrate_velocity(); void calculate_D2Min(); void save_reference_state(); diff --git a/src/EXTRA-FIX/fix_spring_rg.cpp b/src/EXTRA-FIX/fix_spring_rg.cpp index 46afa905b3..3207f92a8d 100644 --- a/src/EXTRA-FIX/fix_spring_rg.cpp +++ b/src/EXTRA-FIX/fix_spring_rg.cpp @@ -46,6 +46,7 @@ FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) : restart_global = 1; scalar_flag = 1; + extscalar = 0; restart_global = 1; dynamic_group_allow = 1; respa_level_support = 1; diff --git a/src/EXTRA-FIX/fix_ttm_mod.cpp b/src/EXTRA-FIX/fix_ttm_mod.cpp index 79af414f0a..335acdd853 100644 --- a/src/EXTRA-FIX/fix_ttm_mod.cpp +++ b/src/EXTRA-FIX/fix_ttm_mod.cpp @@ -486,12 +486,12 @@ void FixTTMMod::read_parameters(const std::string &filename) reader.next_line(); intensity = reader.next_values(1).next_double(); - // coordinate of 1st surface in x-direction (in box units) - constant + // coordinate of 1st surface in x-direction (electron grid units) - constant reader.next_line(); surface_l = reader.next_values(1).next_int(); - // coordinate of 2nd surface in x-direction (in box units) - constant + // coordinate of 2nd surface in x-direction (electron grid units) - constant reader.next_line(); surface_r = reader.next_values(1).next_int(); diff --git a/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp new file mode 100644 index 0000000000..2da31ef893 --- /dev/null +++ b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp @@ -0,0 +1,298 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "angle_cosine_squared_restricted.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neighbor.h" + +#include + +using namespace LAMMPS_NS; +using MathConst::DEG2RAD; +using MathConst::RAD2DEG; + +/* ---------------------------------------------------------------------- */ + +AngleCosineSquaredRestricted::AngleCosineSquaredRestricted(LAMMPS *_lmp) : Angle(_lmp) +{ + k = nullptr; + theta0 = nullptr; + born_matrix_enable = 1; +} + +/* ---------------------------------------------------------------------- */ + +AngleCosineSquaredRestricted::~AngleCosineSquaredRestricted() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(theta0); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineSquaredRestricted::compute(int eflag, int vflag) +{ + int i1, i2, i3, n, type; + double delx1, dely1, delz1, delx2, dely2, delz2; + double eangle, f1[3], f3[3]; + double tk, rsq1, rsq2, r1, r2, c, a, a11, a12, a22; + + eangle = 0.0; + ev_init(eflag, vflag); + + double **x = atom->x; + double **f = atom->f; + int **anglelist = neighbor->anglelist; + int nanglelist = neighbor->nanglelist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nanglelist; n++) { + i1 = anglelist[n][0]; + i2 = anglelist[n][1]; + i3 = anglelist[n][2]; + type = anglelist[n][3]; + + // 1st bond + + delx1 = x[i1][0] - x[i2][0]; + dely1 = x[i1][1] - x[i2][1]; + delz1 = x[i1][2] - x[i2][2]; + + rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1; + r1 = sqrt(rsq1); + + // 2nd bond + + delx2 = x[i3][0] - x[i2][0]; + dely2 = x[i3][1] - x[i2][1]; + delz2 = x[i3][2] - x[i2][2]; + + rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2; + r2 = sqrt(rsq2); + + // angle (cos and sin) + + c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; + c /= r1 * r2; + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + // force & energy + + double sq_sin = 1.0 - c * c; + double c0 = cos(theta0[type]); + + tk = k[type] * (c - c0) * (1.0 - c * c0) / (sq_sin * sq_sin); + + if (eflag) eangle = k[type] * (c - c0) * (c - c0) / sq_sin; + + a = 2.0 * tk; + a11 = a * c / rsq1; + a12 = -a / (r1 * r2); + a22 = a * c / rsq2; + + f1[0] = a11 * delx1 + a12 * delx2; + f1[1] = a11 * dely1 + a12 * dely2; + f1[2] = a11 * delz1 + a12 * delz2; + f3[0] = a22 * delx2 + a12 * delx1; + f3[1] = a22 * dely2 + a12 * dely1; + f3[2] = a22 * delz2 + a12 * delz1; + + // apply force to each of 3 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= f1[0] + f3[0]; + f[i2][1] -= f1[1] + f3[1]; + f[i2][2] -= f1[2] + f3[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (evflag) + ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2, + delz2); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineSquaredRestricted::allocate() +{ + allocated = 1; + const int np1 = atom->nangletypes + 1; + + memory->create(k, np1, "angle:k"); + memory->create(theta0, np1, "angle:theta0"); + + memory->create(setflag, np1, "angle:setflag"); + for (int i = 1; i < np1; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void AngleCosineSquaredRestricted::coeff(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients"); + if (!allocated) allocate(); + + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error); + + double k_one = utils::numeric(FLERR, arg[1], false, lmp); + double theta0_one = utils::numeric(FLERR, arg[2], false, lmp); + + // convert theta0 from degrees to radians + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = k_one; + theta0[i] = DEG2RAD * theta0_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); +} + +/* ---------------------------------------------------------------------- */ + +double AngleCosineSquaredRestricted::equilibrium_angle(int i) +{ + return theta0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void AngleCosineSquaredRestricted::write_restart(FILE *fp) +{ + fwrite(&k[1], sizeof(double), atom->nangletypes, fp); + fwrite(&theta0[1], sizeof(double), atom->nangletypes, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void AngleCosineSquaredRestricted::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + utils::sfread(FLERR, &k[1], sizeof(double), atom->nangletypes, fp, nullptr, error); + utils::sfread(FLERR, &theta0[1], sizeof(double), atom->nangletypes, fp, nullptr, error); + } + MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&theta0[1], atom->nangletypes, MPI_DOUBLE, 0, world); + + for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void AngleCosineSquaredRestricted::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nangletypes; i++) + fprintf(fp, "%d %g %g\n", i, k[i], RAD2DEG * theta0[i]); +} + +/* ---------------------------------------------------------------------- */ + +double AngleCosineSquaredRestricted::single(int type, int i1, int i2, int i3) +{ + double **x = atom->x; + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1, dely1, delz1); + double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2, dely2, delz2); + double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); + + double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; + c /= r1 * r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + double sq_sin = 1.0 - c * c; + double dcostheta = c - cos(theta0[type]); + double tk = k[type] * dcostheta / sq_sin; + return tk * dcostheta; +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineSquaredRestricted::born_matrix(int type, int i1, int i2, int i3, double &du, + double &du2) +{ + double **x = atom->x; + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1, dely1, delz1); + double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2, dely2, delz2); + double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); + + double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; + c /= r1 * r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + double c0 = cos(theta0[type]); + double sq_sin = 1.0 - c * c; + + du = 2 * k[type] * (c - c0) * (1.0 - c * c0) / (sq_sin * sq_sin); + + double numerator = 2.0 * c0 * c * c * c - 3.0 * (c0 * c0 + 1) * c * c + 6 * c0 * c - c0 * c0 - 1; + double denominator = sq_sin * sq_sin * sq_sin; + + du2 = 2 * k[type] * numerator / denominator; +} diff --git a/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.h b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.h new file mode 100644 index 0000000000..674252b7d0 --- /dev/null +++ b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.h @@ -0,0 +1,49 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ANGLE_CLASS +// clang-format off +AngleStyle(cosine/squared/restricted,AngleCosineSquaredRestricted); +// clang-format on +#else + +#ifndef LMP_ANGLE_COSINE_SQUARED_RESTRICTED_H +#define LMP_ANGLE_COSINE_SQUARED_RESTRICTED_H + +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleCosineSquaredRestricted : public Angle { + public: + AngleCosineSquaredRestricted(class LAMMPS *); + ~AngleCosineSquaredRestricted() override; + void compute(int, int) override; + void coeff(int, char **) override; + double equilibrium_angle(int) override; + void write_restart(FILE *) override; + void read_restart(FILE *) override; + void write_data(FILE *) override; + double single(int, int, int, int) override; + void born_matrix(int type, int i1, int i2, int i3, double &du, double &du2) override; + + protected: + double *k, *theta0; + + void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp b/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp new file mode 100644 index 0000000000..5b2feb6897 --- /dev/null +++ b/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp @@ -0,0 +1,395 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "dihedral_cosine_squared_restricted.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neighbor.h" + +#include + +using namespace LAMMPS_NS; +using MathConst::DEG2RAD; +using MathConst::RAD2DEG; + +static constexpr double TOLERANCE = 0.05; +static constexpr double SMALL = 0.001; + +/* ---------------------------------------------------------------------- */ + +DihedralCosineSquaredRestricted::DihedralCosineSquaredRestricted(LAMMPS *_lmp) : + Dihedral(_lmp), k(nullptr), phi0(nullptr) +{ + writedata = 1; + born_matrix_enable = 1; +} + +/* ---------------------------------------------------------------------- */ + +DihedralCosineSquaredRestricted::~DihedralCosineSquaredRestricted() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(phi0); + } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralCosineSquaredRestricted::compute(int eflag, int vflag) +{ + int i1, i2, i3, i4, n, type; + double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm; + double edihedral, f1[3], f2[3], f3[3], f4[3]; + double sb1, sb2, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2; + double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2; + double c2mag, sc1, sc2, s1, s12, c, pd, a, a11, a22; + double a33, a12, a13, a23, sx2, sy2, sz2; + double s2, sin2; + + edihedral = 0.0; + ev_init(eflag, vflag); + + double **x = atom->x; + double **f = atom->f; + int **dihedrallist = neighbor->dihedrallist; + int ndihedrallist = neighbor->ndihedrallist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < ndihedrallist; n++) { + i1 = dihedrallist[n][0]; + i2 = dihedrallist[n][1]; + i3 = dihedrallist[n][2]; + i4 = dihedrallist[n][3]; + type = dihedrallist[n][4]; + + // 1st bond + + vb1x = x[i1][0] - x[i2][0]; + vb1y = x[i1][1] - x[i2][1]; + vb1z = x[i1][2] - x[i2][2]; + + // 2nd bond + + vb2x = x[i3][0] - x[i2][0]; + vb2y = x[i3][1] - x[i2][1]; + vb2z = x[i3][2] - x[i2][2]; + + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + + // 3rd bond + + vb3x = x[i4][0] - x[i3][0]; + vb3y = x[i4][1] - x[i3][1]; + vb3z = x[i4][2] - x[i3][2]; + + // c0 calculation + + sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z); + sb2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z); + sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z); + + rb1 = sqrt(sb1); + rb3 = sqrt(sb3); + + c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3; + + // 1st and 2nd angle + + b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z; + b1mag = sqrt(b1mag2); + b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z; + b2mag = sqrt(b2mag2); + b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z; + b3mag = sqrt(b3mag2); + + ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z; + r12c1 = 1.0 / (b1mag * b2mag); + c1mag = ctmp * r12c1; + + ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z; + r12c2 = 1.0 / (b2mag * b3mag); + c2mag = ctmp * r12c2; + + // cos and sin of 2 angles and final c + + sin2 = MAX(1.0 - c1mag * c1mag, 0.0); + sc1 = sqrt(sin2); + if (sc1 < SMALL) sc1 = SMALL; + sc1 = 1.0 / sc1; + + sin2 = MAX(1.0 - c2mag * c2mag, 0.0); + sc2 = sqrt(sin2); + if (sc2 < SMALL) sc2 = SMALL; + sc2 = 1.0 / sc2; + + s1 = sc1 * sc1; + s2 = sc2 * sc2; + s12 = sc1 * sc2; + c = (c0 + c1mag * c2mag) * s12; + + // error check + + if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + // force & energy + + double p0 = cos(phi0[type]); + double sq_sin = 1.0 - c * c; + + pd = 2 * k[type] * (c - p0) * (1.0 - c * p0) / (sq_sin * sq_sin); + + if (eflag) edihedral = k[type] * (c - p0) * (c - p0) / sq_sin; + + a = pd; + c = c * a; + s12 = s12 * a; + a11 = c * sb1 * s1; + a22 = -sb2 * (2.0 * c0 * s12 - c * (s1 + s2)); + a33 = c * sb3 * s2; + a12 = -r12c1 * (c1mag * c * s1 + c2mag * s12); + a13 = -rb1 * rb3 * s12; + a23 = r12c2 * (c2mag * c * s2 + c1mag * s12); + + sx2 = a12 * vb1x + a22 * vb2x + a23 * vb3x; + sy2 = a12 * vb1y + a22 * vb2y + a23 * vb3y; + sz2 = a12 * vb1z + a22 * vb2z + a23 * vb3z; + + f1[0] = a11 * vb1x + a12 * vb2x + a13 * vb3x; + f1[1] = a11 * vb1y + a12 * vb2y + a13 * vb3y; + f1[2] = a11 * vb1z + a12 * vb2z + a13 * vb3z; + + f2[0] = -sx2 - f1[0]; + f2[1] = -sy2 - f1[1]; + f2[2] = -sz2 - f1[2]; + + f4[0] = a13 * vb1x + a23 * vb2x + a33 * vb3x; + f4[1] = a13 * vb1y + a23 * vb2y + a33 * vb3y; + f4[2] = a13 * vb1z + a23 * vb2z + a33 * vb3z; + + f3[0] = sx2 - f4[0]; + f3[1] = sy2 - f4[1]; + f3[2] = sz2 - f4[2]; + + // apply force to each of 4 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] += f2[0]; + f[i2][1] += f2[1]; + f[i2][2] += f2[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (newton_bond || i4 < nlocal) { + f[i4][0] += f4[0]; + f[i4][1] += f4[1]; + f[i4][2] += f4[2]; + } + + if (evflag) + ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x, + vb2y, vb2z, vb3x, vb3y, vb3z); + } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralCosineSquaredRestricted::allocate() +{ + allocated = 1; + const int np1 = atom->ndihedraltypes + 1; + + memory->create(k, np1, "dihedral:k"); + memory->create(phi0, np1, "dihedral:phi0"); + + memory->create(setflag, np1, "dihedral:setflag"); + for (int i = 1; i < np1; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +------------------------------------------------------------------------- */ + +void DihedralCosineSquaredRestricted::coeff(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (!allocated) allocate(); + + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error); + + double k_one = utils::numeric(FLERR, arg[1], false, lmp); + double phi0_one = utils::numeric(FLERR, arg[2], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = k_one; + phi0[i] = DEG2RAD * phi0_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void DihedralCosineSquaredRestricted::write_restart(FILE *fp) +{ + fwrite(&k[1], sizeof(double), atom->ndihedraltypes, fp); + fwrite(&phi0[1], sizeof(double), atom->ndihedraltypes, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void DihedralCosineSquaredRestricted::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + utils::sfread(FLERR, &k[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error); + utils::sfread(FLERR, &phi0[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error); + } + MPI_Bcast(&k[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&phi0[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world); + + for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralCosineSquaredRestricted::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp, "%d %g %g\n", i, k[i], RAD2DEG * phi0[i]); +} + +/* ---------------------------------------------------------------------- */ + +void DihedralCosineSquaredRestricted::born_matrix(int nd, int i1, int i2, int i3, int i4, + double &du, double &du2) +{ + double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm; + double sb1, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2; + double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2; + double c2mag, sc1, sc2, s12, c; + double sin2; + + double **x = atom->x; + int **dihedrallist = neighbor->dihedrallist; + + int type = dihedrallist[nd][4]; + + // 1st bond + vb1x = x[i1][0] - x[i2][0]; + vb1y = x[i1][1] - x[i2][1]; + vb1z = x[i1][2] - x[i2][2]; + + // 2nd bond + vb2x = x[i3][0] - x[i2][0]; + vb2y = x[i3][1] - x[i2][1]; + vb2z = x[i3][2] - x[i2][2]; + + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + + // 3rd bond + vb3x = x[i4][0] - x[i3][0]; + vb3y = x[i4][1] - x[i3][1]; + vb3z = x[i4][2] - x[i3][2]; + + // c0 calculation + sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z); + sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z); + + rb1 = sqrt(sb1); + rb3 = sqrt(sb3); + + c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3; + + // 1st and 2nd angle + b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z; + b1mag = sqrt(b1mag2); + b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z; + b2mag = sqrt(b2mag2); + b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z; + b3mag = sqrt(b3mag2); + + ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z; + r12c1 = 1.0 / (b1mag * b2mag); + c1mag = ctmp * r12c1; + + ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z; + r12c2 = 1.0 / (b2mag * b3mag); + c2mag = ctmp * r12c2; + + // cos and sin of 2 angles and final c + sin2 = MAX(1.0 - c1mag * c1mag, 0.0); + sc1 = sqrt(sin2); + if (sc1 < SMALL) sc1 = SMALL; + sc1 = 1.0 / sc1; + + sin2 = MAX(1.0 - c2mag * c2mag, 0.0); + sc2 = sqrt(sin2); + if (sc2 < SMALL) sc2 = SMALL; + sc2 = 1.0 / sc2; + + s12 = sc1 * sc2; + c = (c0 + c1mag * c2mag) * s12; + + // error check + if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + double p0 = cos(phi0[type]); + double sq_sin = 1.0 - c * c; + + du = 2 * k[type] * (c - p0) * (1.0 - c * p0) / (sq_sin * sq_sin); + + double numerator = 2.0 * p0 * c * c * c - 3.0 * (p0 * p0 + 1) * c * c + 6 * p0 * c - p0 * p0 - 1; + double denominator = sq_sin * sq_sin * sq_sin; + + du2 = 2 * k[type] * numerator / denominator; +} diff --git a/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.h b/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.h new file mode 100644 index 0000000000..b9e2e1d9d8 --- /dev/null +++ b/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef DIHEDRAL_CLASS +// clang-format off +DihedralStyle(cosine/squared/restricted,DihedralCosineSquaredRestricted); +// clang-format on +#else + +#ifndef LMP_DIHEDRAL_COSINE_SQUARED_RESTRICTED_H +#define LMP_DIHEDRAL_COSINE_SQUARED_RESTRICTED_H + +#include "dihedral.h" + +namespace LAMMPS_NS { + +class DihedralCosineSquaredRestricted : public Dihedral { + public: + DihedralCosineSquaredRestricted(class LAMMPS *); + ~DihedralCosineSquaredRestricted() override; + void compute(int, int) override; + void coeff(int, char **) override; + void write_restart(FILE *) override; + void read_restart(FILE *) override; + void write_data(FILE *) override; + void born_matrix(int, int, int, int, int, double &, double &) override; + + protected: + double *k, *phi0; + + void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/EXTRA-PAIR/pair_coul_slater_long.cpp b/src/EXTRA-PAIR/pair_coul_slater_long.cpp index 65906f73b5..09926f6533 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_long.cpp +++ b/src/EXTRA-PAIR/pair_coul_slater_long.cpp @@ -39,7 +39,6 @@ using namespace EwaldConst; PairCoulSlaterLong::PairCoulSlaterLong(LAMMPS *lmp) : Pair(lmp) { ewaldflag = pppmflag = 1; - qdist = 0.0; } /* ---------------------------------------------------------------------- */ @@ -232,7 +231,7 @@ void PairCoulSlaterLong::init_style() double PairCoulSlaterLong::init_one(int i, int j) { scale[j][i] = scale[i][j]; - return cut_coul+2.0*qdist; + return cut_coul; } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_coul_slater_long.h b/src/EXTRA-PAIR/pair_coul_slater_long.h index ef1742ece1..04e0bfe35b 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_long.h +++ b/src/EXTRA-PAIR/pair_coul_slater_long.h @@ -41,9 +41,7 @@ class PairCoulSlaterLong : public Pair { void *extract(const char *, int &) override; protected: - double cut_coul, cut_coulsq, qdist; - double lamda; - double g_ewald; + double cut_coul, cut_coulsq, lamda, g_ewald; double **scale; virtual void allocate(); diff --git a/src/EXTRA-PAIR/pair_pedone.cpp b/src/EXTRA-PAIR/pair_pedone.cpp new file mode 100644 index 0000000000..9b8ce451d9 --- /dev/null +++ b/src/EXTRA-PAIR/pair_pedone.cpp @@ -0,0 +1,389 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_pedone.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" + +#include +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairPedone::PairPedone(LAMMPS *lmp) : + Pair(lmp), cut(nullptr), d0(nullptr), alpha(nullptr), r0(nullptr), c0(nullptr), + pedone1(nullptr), pedone2(nullptr), offset(nullptr) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairPedone::~PairPedone() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(c0); + memory->destroy(d0); + memory->destroy(alpha); + memory->destroy(r0); + memory->destroy(pedone1); + memory->destroy(pedone2); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairPedone::compute(int eflag, int vflag) +{ + int i, j, ii, jj, inum, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; + double rsq, r, r2inv, r6inv, dr, dexp, factor_lj; + int *ilist, *jlist, *numneigh, **firstneigh; + + evdwl = 0.0; + ev_init(eflag, vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + + pedone2[itype][jtype] * r6inv * r6inv * r2inv; + fpair *= factor_lj; + + f[i][0] += delx * fpair; + f[i][1] += dely * fpair; + f[i][2] += delz * fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx * fpair; + f[j][1] -= dely * fpair; + f[j][2] -= delz * fpair; + } + + if (eflag) { + evdwl = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) + c0[itype][jtype] * r6inv * r6inv - + offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairPedone::allocate() +{ + allocated = 1; + int np1 = atom->ntypes + 1; + + memory->create(setflag, np1, np1, "pair:setflag"); + for (int i = 1; i < np1; i++) + for (int j = i; j < np1; j++) setflag[i][j] = 0; + + memory->create(cutsq, np1, np1, "pair:cutsq"); + + memory->create(cut, np1, np1, "pair:cut"); + memory->create(c0, np1, np1, "pair:c0"); + memory->create(d0, np1, np1, "pair:d0"); + memory->create(alpha, np1, np1, "pair:alpha"); + memory->create(r0, np1, np1, "pair:r0"); + memory->create(pedone1, np1, np1, "pair:pedone1"); + memory->create(pedone2, np1, np1, "pair:pedone2"); + memory->create(offset, np1, np1, "pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairPedone::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); + + cut_global = utils::numeric(FLERR, arg[0], false, lmp); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairPedone::coeff(int narg, char **arg) +{ + if (narg < 6 || narg > 7) error->all(FLERR, "Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); + + double d0_one = utils::numeric(FLERR, arg[2], false, lmp); + double alpha_one = utils::numeric(FLERR, arg[3], false, lmp); + double r0_one = utils::numeric(FLERR, arg[4], false, lmp); + double c0_one = utils::numeric(FLERR, arg[5], false, lmp); + + double cut_one = cut_global; + if (narg == 7) cut_one = utils::numeric(FLERR, arg[6], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { + c0[i][j] = c0_one; + d0[i][j] = d0_one; + alpha[i][j] = alpha_one; + r0[i][j] = r0_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairPedone::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + + pedone1[i][j] = 2.0 * d0[i][j] * alpha[i][j]; + pedone2[i][j] = 12.0 * c0[i][j]; + + if (offset_flag) { + double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); + offset[i][j] = + d0[i][j] * (exp(2.0 * alpha_dr) - 2.0 * exp(alpha_dr)) - c0[i][j] / pow(cut[i][j], 12.0); + } else + offset[i][j] = 0.0; + + c0[j][i] = c0[i][j]; + d0[j][i] = d0[i][j]; + alpha[j][i] = alpha[i][j]; + r0[j][i] = r0[i][j]; + pedone1[j][i] = pedone1[i][j]; + pedone2[j][i] = pedone2[i][j]; + offset[j][i] = offset[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairPedone::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i, j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1, fp); + if (setflag[i][j]) { + fwrite(&c0[i][j], sizeof(double), 1, fp); + fwrite(&d0[i][j], sizeof(double), 1, fp); + fwrite(&alpha[i][j], sizeof(double), 1, fp); + fwrite(&r0[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairPedone::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i, j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR, &c0[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &d0[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &alpha[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &r0[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); + } + MPI_Bcast(&c0[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&d0[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&alpha[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairPedone::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&offset_flag, sizeof(int), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairPedone::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error); + utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); + } + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairPedone::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp, "%d %g %g %g %g\n", i, d0[i][i], alpha[i][i], r0[i][i], c0[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairPedone::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp, "%d %d %g %g %g %g %g\n", i, j, d0[i][j], alpha[i][j], r0[i][j], c0[i][j], + cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairPedone::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) +{ + double r, dr, dexp, phi, r2inv, r6inv; + + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + fforce = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + + pedone2[itype][jtype] * r6inv * r6inv * r2inv; + fforce *= factor_lj; + + phi = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) + c0[itype][jtype] * r6inv * r6inv - + offset[itype][jtype]; + return factor_lj * phi; +} + +/* ---------------------------------------------------------------------- */ + +void *PairPedone::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str, "c0") == 0) return (void *) c0; + if (strcmp(str, "d0") == 0) return (void *) d0; + if (strcmp(str, "r0") == 0) return (void *) r0; + if (strcmp(str, "alpha") == 0) return (void *) alpha; + return nullptr; +} diff --git a/src/EXTRA-PAIR/pair_pedone.h b/src/EXTRA-PAIR/pair_pedone.h new file mode 100644 index 0000000000..a54f50a6b3 --- /dev/null +++ b/src/EXTRA-PAIR/pair_pedone.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(pedone,PairPedone); +// clang-format on +#else + +#ifndef LMP_PAIR_PEDONE_H +#define LMP_PAIR_PEDONE_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairPedone : public Pair { + public: + PairPedone(class LAMMPS *); + ~PairPedone() override; + void compute(int, int) override; + + void settings(int, char **) override; + void coeff(int, char **) override; + double init_one(int, int) override; + void write_restart(FILE *) override; + void read_restart(FILE *) override; + void write_restart_settings(FILE *) override; + void read_restart_settings(FILE *) override; + void write_data(FILE *) override; + void write_data_all(FILE *) override; + double single(int, int, int, int, double, double, double, double &) override; + void *extract(const char *, int &) override; + + protected: + double cut_global; + double **cut; + double **d0, **alpha, **r0, **c0; + double **pedone1, **pedone2; + double **offset; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/FEP/fix_adapt_fep.cpp b/src/FEP/fix_adapt_fep.cpp index e0c5868e96..d343c16aae 100644 --- a/src/FEP/fix_adapt_fep.cpp +++ b/src/FEP/fix_adapt_fep.cpp @@ -91,10 +91,22 @@ FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) : adapt[nadapt].which = PAIR; adapt[nadapt].pstyle = utils::strdup(arg[iarg+1]); adapt[nadapt].pparam = utils::strdup(arg[iarg+2]); - utils::bounds(FLERR,arg[iarg+3],1,atom->ntypes, - adapt[nadapt].ilo,adapt[nadapt].ihi,error); - utils::bounds(FLERR,arg[iarg+4],1,atom->ntypes, - adapt[nadapt].jlo,adapt[nadapt].jhi,error); + utils::bounds_typelabel(FLERR, arg[iarg+3], 1, atom->ntypes, + adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::ATOM); + utils::bounds_typelabel(FLERR, arg[iarg+4], 1, atom->ntypes, + adapt[nadapt].jlo, adapt[nadapt].jhi, lmp, Atom::ATOM); + + // switch i,j if i > j, if wildcards were not used + + if ( (adapt[nadapt].ilo == adapt[nadapt].ihi) && + (adapt[nadapt].jlo == adapt[nadapt].jhi) && + (adapt[nadapt].ilo > adapt[nadapt].jlo) ) { + adapt[nadapt].jlo = adapt[nadapt].ihi; + adapt[nadapt].ilo = adapt[nadapt].jhi; + adapt[nadapt].ihi = adapt[nadapt].ilo; + adapt[nadapt].jhi = adapt[nadapt].jlo; + } + if (utils::strmatch(arg[iarg+5],"^v_")) { adapt[nadapt].var = utils::strdup(arg[iarg+5]+2); } else error->all(FLERR,"Illegal fix adapt/fep command"); @@ -118,8 +130,8 @@ FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) : adapt[nadapt].aparam = CHARGE; chgflag = 1; } else error->all(FLERR,"Illegal fix adapt/fep command"); - utils::bounds(FLERR,arg[iarg+2],1,atom->ntypes, - adapt[nadapt].ilo,adapt[nadapt].ihi,error); + utils::bounds_typelabel(FLERR, arg[iarg+2], 1, atom->ntypes, + adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::ATOM); if (utils::strmatch(arg[iarg+3],"^v_")) { adapt[nadapt].var = utils::strdup(arg[iarg+3]+2); } else error->all(FLERR,"Illegal fix adapt/fep command"); diff --git a/src/GPU/pair_dpd_coul_slater_long_gpu.cpp b/src/GPU/pair_dpd_coul_slater_long_gpu.cpp new file mode 100644 index 0000000000..1acd95b30c --- /dev/null +++ b/src/GPU/pair_dpd_coul_slater_long_gpu.cpp @@ -0,0 +1,474 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Eddy BARRAUD (IFPEN/Sorbonne) +------------------------------------------------------------------------- */ + +#include "pair_dpd_coul_slater_long_gpu.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "gpu_extra.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "suffix.h" +#include "update.h" + +#include "ewald_const.h" +#include "kspace.h" + +#include +#include + +using namespace LAMMPS_NS; +using namespace EwaldConst; + +// External functions from cuda library for atom decomposition + +int dpd_coul_slater_long_gpu_init(const int ntypes, double **cutsq, double **host_a0, + double **host_gamma, double **host_sigma, double **host_cut_dpd, + double **host_cut_dpdsq, double **host_cut_slatersq, + double *special_lj, const int inum, const int nall, + const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double *host_special_coul, const double qqrd2e, + const double g_ewald, const double lamda); +void dpd_coul_slater_long_gpu_clear(); +int **dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, double *sublo, + double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double **host_v, const double dtinvsqrt, + const int seed, const int timestep, double *boxlo, + double *prd); +void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, tagint *tag, + double **host_v, const double dtinvsqrt, const int seed, + const int timestep, const int nlocal, double *boxlo, + double *prd); + +void dpd_coul_slater_long_gpu_get_extra_data(double *host_q); + +double dpd_coul_slater_long_gpu_bytes(); + +static constexpr double EPSILON = 1.0e-10; + +//#define _USE_UNIFORM_SARU_LCG +//#define _USE_UNIFORM_SARU_TEA8 +//#define _USE_GAUSSIAN_SARU_LCG + +#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && \ + !defined(_USE_GAUSSIAN_SARU_LCG) +#define _USE_UNIFORM_SARU_LCG +#endif + +// References: +// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128. +// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201. +// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19 + +#define LCGA 0x4beb5d59 // Full period 32 bit LCG +#define LCGC 0x2600e1f7 +#define oWeylPeriod 0xda879add // Prime period 3666320093 +#define oWeylOffset 0x8009d14b +#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */ + +// specifically implemented for steps = 1; high = 1.0; low = -1.0 +// returns uniformly distributed random numbers u in [-1.0;1.0] +// using the inherent LCG, then multiply u with sqrt(3) to "match" +// with a normal random distribution. +// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12) +// Curly brackets to make variables local to the scope. +#ifdef _USE_UNIFORM_SARU_LCG +#define numtyp double +#define SQRT3 (numtyp) 1.7320508075688772935274463 +#define saru(seed1, seed2, seed, timestep, randnum) \ + { \ + unsigned int seed3 = seed + timestep; \ + seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \ + seed2 += (seed1 >> 4) ^ (seed3 >> 15); \ + seed1 ^= (seed2 << 9) + (seed3 << 8); \ + seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \ + seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \ + seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \ + seed2 += seed1 * seed3; \ + seed1 += seed3 ^ (seed2 >> 2); \ + seed2 ^= ((signed int) seed2) >> 17; \ + unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \ + unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8); \ + state = state + (wstate * (wstate ^ 0xdddf97f5)); \ + wstate = 0xABCB96F7 + (wstate >> 1); \ + state = LCGA * state + LCGC; \ + wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \ + unsigned int v = (state ^ (state >> 26)) + wstate; \ + unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \ + randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0); \ + } +#endif + +// specifically implemented for steps = 1; high = 1.0; low = -1.0 +// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8 +// then multiply u with sqrt(3) to "match" with a normal random distribution +// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12) +#ifdef _USE_UNIFORM_SARU_TEA8 +#define numtyp double +#define SQRT3 (numtyp) 1.7320508075688772935274463 +#define k0 0xA341316C +#define k1 0xC8013EA4 +#define k2 0xAD90777D +#define k3 0x7E95761E +#define delta 0x9e3779b9 +#define rounds 8 +#define saru(seed1, seed2, seed, timestep, randnum) \ + { \ + unsigned int seed3 = seed + timestep; \ + seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \ + seed2 += (seed1 >> 4) ^ (seed3 >> 15); \ + seed1 ^= (seed2 << 9) + (seed3 << 8); \ + seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \ + seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \ + seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \ + seed2 += seed1 * seed3; \ + seed1 += seed3 ^ (seed2 >> 2); \ + seed2 ^= ((signed int) seed2) >> 17; \ + unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \ + unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8); \ + state = state + (wstate * (wstate ^ 0xdddf97f5)); \ + wstate = 0xABCB96F7 + (wstate >> 1); \ + unsigned int sum = 0; \ + for (int i = 0; i < rounds; i++) { \ + sum += delta; \ + state += ((wstate << 4) + k0) ^ (wstate + sum) ^ ((wstate >> 5) + k1); \ + wstate += ((state << 4) + k2) ^ (state + sum) ^ ((state >> 5) + k3); \ + } \ + unsigned int v = (state ^ (state >> 26)) + wstate; \ + unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \ + randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0); \ + } +#endif + +// specifically implemented for steps = 1; high = 1.0; low = -1.0 +// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0], +// and uses the polar method (Marsaglia's) to transform to a normal random value +// This is used to compared with CPU DPD using RandMars::gaussian() +#ifdef _USE_GAUSSIAN_SARU_LCG +#define numtyp double +#define saru(seed1, seed2, seed, timestep, randnum) \ + { \ + unsigned int seed3 = seed + timestep; \ + seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \ + seed2 += (seed1 >> 4) ^ (seed3 >> 15); \ + seed1 ^= (seed2 << 9) + (seed3 << 8); \ + seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \ + seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \ + seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \ + seed2 += seed1 * seed3; \ + seed1 += seed3 ^ (seed2 >> 2); \ + seed2 ^= ((signed int) seed2) >> 17; \ + unsigned int state = 0x12345678; \ + unsigned int wstate = 12345678; \ + state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \ + wstate = (state + seed2) ^ (((signed int) state) >> 8); \ + state = state + (wstate * (wstate ^ 0xdddf97f5)); \ + wstate = 0xABCB96F7 + (wstate >> 1); \ + unsigned int v, s; \ + numtyp r1, r2, rsq; \ + while (1) { \ + state = LCGA * state + LCGC; \ + wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \ + v = (state ^ (state >> 26)) + wstate; \ + s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \ + r1 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0; \ + state = LCGA * state + LCGC; \ + wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \ + v = (state ^ (state >> 26)) + wstate; \ + s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \ + r2 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0; \ + rsq = r1 * r1 + r2 * r2; \ + if (rsq < (numtyp) 1.0) break; \ + } \ + numtyp fac = sqrt((numtyp) -2.0 * log(rsq) / rsq); \ + randnum = r2 * fac; \ + } +#endif + +/* ---------------------------------------------------------------------- */ + +PairDPDCoulSlaterLongGPU::PairDPDCoulSlaterLongGPU(LAMMPS *lmp) : PairDPDCoulSlaterLong(lmp), gpu_mode(GPU_FORCE) +{ + respa_enable = 0; + reinitflag = 0; + cpu_time = 0.0; + suffix_flag |= Suffix::GPU; + GPU_EXTRA::gpu_ready(lmp->modify, lmp->error); +} + +/* ---------------------------------------------------------------------- + free all arrays +------------------------------------------------------------------------- */ + +PairDPDCoulSlaterLongGPU::~PairDPDCoulSlaterLongGPU() +{ + dpd_coul_slater_long_gpu_clear(); +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLongGPU::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + + int nall = atom->nlocal + atom->nghost; + int inum, host_start; + + double dtinvsqrt = 1.0 / sqrt(update->dt); + + bool success = true; + int *ilist, *numneigh, **firstneigh; + + double *q = atom->q; + dpd_coul_slater_long_gpu_get_extra_data(q); + + if (gpu_mode != GPU_FORCE) { + double sublo[3], subhi[3]; + if (domain->triclinic == 0) { + sublo[0] = domain->sublo[0]; + sublo[1] = domain->sublo[1]; + sublo[2] = domain->sublo[2]; + subhi[0] = domain->subhi[0]; + subhi[1] = domain->subhi[1]; + subhi[2] = domain->subhi[2]; + } else { + domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi); + } + inum = atom->nlocal; + firstneigh = dpd_coul_slater_long_gpu_compute_n( + neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial, + atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, + cpu_time, success, atom->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd); + } else { + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + dpd_coul_slater_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, + eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->tag, + atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo, + domain->prd); + } + if (!success) error->one(FLERR, "Insufficient memory on accelerator"); + + if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0) + neighbor->build_topology(); + if (host_start < inum) { + cpu_time = platform::walltime(); + cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh); + cpu_time = platform::walltime() - cpu_time; + } +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLongGPU::init_style() +{ + + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair dpd requires ghost atoms store velocity"); + if (!atom->q_flag) + error->all(FLERR,"Pair style coul/slater/long requires atom attribute q"); + // ensure use of KSpace long-range solver, set g_ewald + if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; + + // Repeat cutsq calculation because done after call to init_style + double maxcut = -1.0; + double mcut; + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + mcut = init_one(i, j); + mcut *= mcut; + if (mcut > maxcut) maxcut = mcut; + cutsq[i][j] = cutsq[j][i] = mcut; + } else + cutsq[i][j] = cutsq[j][i] = 0.0; + } + } + double cell_size = sqrt(maxcut) + neighbor->skin; + + int maxspecial = 0; + if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial; + int mnf = 5e-2 * neighbor->oneatom; + int success = + dpd_coul_slater_long_gpu_init(atom->ntypes + 1, cutsq, a0, gamma, sigma, + cut_dpd, cut_dpdsq, cut_slatersq, force->special_lj, atom->nlocal, + atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen, + force->special_coul, force->qqrd2e, g_ewald, lamda); + GPU_EXTRA::check_flag(success, error, world); + + if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL); + +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDCoulSlaterLongGPU::memory_usage() +{ + double bytes = Pair::memory_usage(); + return bytes + dpd_coul_slater_long_gpu_bytes(); +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDCoulSlaterLongGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) +{ + int i, j, ii, jj, jnum, itype, jtype; + double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair; + double vxtmp, vytmp, vztmp, delvx, delvy, delvz; + double r2inv,forcedpd,forcecoul,factor_coul; + double grij,expm2,prefactor,t,erfc; + double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt; + int *jlist; + double slater_term; + + tagint itag, jtag; + + double *q = atom->q; + double *special_coul = force->special_coul; + double qqrd2e = force->qqrd2e; + + evdwl = 0.0; + ecoul = 0.0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + tagint *tag = atom->tag; + double *special_lj = force->special_lj; + double dtinvsqrt = 1.0 / sqrt(update->dt); + int timestep = (int) update->ntimestep; + + // loop over neighbors of my atoms + + for (ii = start; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + itag = tag[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + factor_sqrt = special_sqrt[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + jtype = type[j]; + jtag = tag[j]; + + // forces if below maximum cutoff + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (evflag) evdwl = ecoul = 0.0; + // apply DPD force if distance below DPD cutoff + if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON ) { + rinv = 1.0 / r; + delvx = vxtmp - v[j][0]; + delvy = vytmp - v[j][1]; + delvz = vztmp - v[j][2]; + dot = delx * delvx + dely * delvy + delz * delvz; + wd = 1.0 - r / cut[itype][jtype]; + + unsigned int tag1 = itag, tag2 = jtag; + if (tag1 > tag2) { + tag1 = jtag; + tag2 = itag; + } + + randnum = 0.0; + saru(tag1, tag2, seed, timestep, randnum); + + // conservative force = a0 * wd + // drag force = -gamma * wd^2 * (delx dot delv) / r + // random force = sigma * wd * rnd * dtinvsqrt; + forcedpd = a0[itype][jtype]*wd; + forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv; + forcedpd *= factor_dpd; + forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt; + forcedpd *= rinv; + + if (eflag) { + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd; + evdwl *= factor_dpd; + } + + } else forcedpd = 0.0; + + // apply Slater electrostatic force if distance below Slater cutoff + // and the two species are charged + if (rsq < cut_slatersq[itype][jtype]){ + r2inv = 1.0/rsq; + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda))); + prefactor = qqrd2e * qtmp*q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term); + forcecoul *= r2inv; + + if (eflag) { + ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda)); + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda)); + } + + } else forcecoul = 0.0; + + fpair = forcedpd + forcecoul; + + f[i][0] += delx * fpair; + f[i][1] += dely * fpair; + f[i][2] += delz * fpair; + + if (evflag) ev_tally_full(i, evdwl, ecoul, fpair, delx, dely, delz); + } + } + } +} diff --git a/src/GPU/pair_dpd_coul_slater_long_gpu.h b/src/GPU/pair_dpd_coul_slater_long_gpu.h new file mode 100644 index 0000000000..5903391d4d --- /dev/null +++ b/src/GPU/pair_dpd_coul_slater_long_gpu.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(dpd/coul/slater/long/gpu,PairDPDCoulSlaterLongGPU); +// clang-format on +#else + +#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H +#define LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H + +#include "pair_dpd_coul_slater_long.h" + +namespace LAMMPS_NS { + +class PairDPDCoulSlaterLongGPU : public PairDPDCoulSlaterLong { + public: + PairDPDCoulSlaterLongGPU(LAMMPS *lmp); + ~PairDPDCoulSlaterLongGPU() override; + void cpu_compute(int, int, int, int, int *, int *, int **); + void compute(int, int) override; + void init_style() override; + double memory_usage() override; + + enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH }; + + private: + int gpu_mode; + double cpu_time; +}; + +} // namespace LAMMPS_NS +#endif +#endif diff --git a/src/GPU/pair_sph_heatconduction_gpu.cpp b/src/GPU/pair_sph_heatconduction_gpu.cpp index a81de53c91..ba68c5fcc5 100644 --- a/src/GPU/pair_sph_heatconduction_gpu.cpp +++ b/src/GPU/pair_sph_heatconduction_gpu.cpp @@ -113,7 +113,7 @@ void PairSPHHeatConductionGPU::compute(int eflag, int vflag) neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, - cpu_time, success, atom->v); + cpu_time, success, atom->vest); } else { inum = list->inum; ilist = list->ilist; @@ -122,7 +122,7 @@ void PairSPHHeatConductionGPU::compute(int eflag, int vflag) sph_heatconduction_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, - atom->tag, atom->v); + atom->tag, atom->vest); } if (!success) error->one(FLERR, "Insufficient memory on accelerator"); diff --git a/src/GPU/pair_sph_lj_gpu.cpp b/src/GPU/pair_sph_lj_gpu.cpp index 46d7b38073..d503a26335 100644 --- a/src/GPU/pair_sph_lj_gpu.cpp +++ b/src/GPU/pair_sph_lj_gpu.cpp @@ -114,7 +114,7 @@ void PairSPHLJGPU::compute(int eflag, int vflag) neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, - cpu_time, success, atom->v); + cpu_time, success, atom->vest); } else { inum = list->inum; ilist = list->ilist; @@ -123,7 +123,7 @@ void PairSPHLJGPU::compute(int eflag, int vflag) sph_lj_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, - atom->tag, atom->v); + atom->tag, atom->vest); } if (!success) error->one(FLERR, "Insufficient memory on accelerator"); @@ -136,21 +136,21 @@ void PairSPHLJGPU::compute(int eflag, int vflag) int nlocal = atom->nlocal; if (acc_float) { auto drhoE_ptr = (float *)drhoE_pinned; - int idx = 0; - for (int i = 0; i < nlocal; i++) { - drho[i] = drhoE_ptr[idx]; - desph[i] = drhoE_ptr[idx+1]; - idx += 2; - } + for (int i = 0; i < nlocal; i++) + drho[i] += drhoE_ptr[i]; + + drhoE_ptr += nlocal; + for (int i = 0; i < nlocal; i++) + desph[i] += drhoE_ptr[i]; } else { auto drhoE_ptr = (double *)drhoE_pinned; - int idx = 0; - for (int i = 0; i < nlocal; i++) { - drho[i] = drhoE_ptr[idx]; - desph[i] = drhoE_ptr[idx+1]; - idx += 2; - } + for (int i = 0; i < nlocal; i++) + drho[i] += drhoE_ptr[i]; + + drhoE_ptr += nlocal; + for (int i = 0; i < nlocal; i++) + desph[i] += drhoE_ptr[i]; } if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0) diff --git a/src/GPU/pair_sph_taitwater_gpu.cpp b/src/GPU/pair_sph_taitwater_gpu.cpp index 6f2762c144..23252cea8a 100644 --- a/src/GPU/pair_sph_taitwater_gpu.cpp +++ b/src/GPU/pair_sph_taitwater_gpu.cpp @@ -18,6 +18,7 @@ #include "pair_sph_taitwater_gpu.h" #include "atom.h" +#include "comm.h" #include "domain.h" #include "error.h" #include "force.h" @@ -85,6 +86,25 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag) { ev_init(eflag, vflag); + // check consistency of pair coefficients + + if (first) { + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 1; i <= atom->ntypes; i++) { + if (cutsq[i][j] > 1.e-32) { + if (!setflag[i][i] || !setflag[j][j]) { + if (comm->me == 0) { + printf( + "SPH particle types %d and %d interact with cutoff=%g, but not all of their single particle properties are set.\n", + i, j, sqrt(cutsq[i][j])); + } + } + } + } + } + first = 0; + } + int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -110,7 +130,7 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag) firstneigh = sph_taitwater_gpu_compute_n( neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, - cpu_time, success, atom->v); + cpu_time, success, atom->vest); } else { inum = list->inum; ilist = list->ilist; @@ -118,7 +138,7 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag) firstneigh = list->firstneigh; sph_taitwater_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, - atom->tag, atom->v); + atom->tag, atom->vest); } if (!success) error->one(FLERR, "Insufficient memory on accelerator"); @@ -131,21 +151,21 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag) int nlocal = atom->nlocal; if (acc_float) { auto drhoE_ptr = (float *)drhoE_pinned; - int idx = 0; - for (int i = 0; i < nlocal; i++) { - drho[i] = drhoE_ptr[idx]; - desph[i] = drhoE_ptr[idx+1]; - idx += 2; - } + for (int i = 0; i < nlocal; i++) + drho[i] += drhoE_ptr[i]; + + drhoE_ptr += nlocal; + for (int i = 0; i < nlocal; i++) + desph[i] += drhoE_ptr[i]; } else { auto drhoE_ptr = (double *)drhoE_pinned; - int idx = 0; - for (int i = 0; i < nlocal; i++) { - drho[i] = drhoE_ptr[idx]; - desph[i] = drhoE_ptr[idx+1]; - idx += 2; - } + for (int i = 0; i < nlocal; i++) + drho[i] += drhoE_ptr[i]; + + drhoE_ptr += nlocal; + for (int i = 0; i < nlocal; i++) + desph[i] += drhoE_ptr[i]; } if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0) diff --git a/src/GRANULAR/fix_heat_flow.cpp b/src/GRANULAR/fix_heat_flow.cpp index b7643c2c24..be8d93839f 100644 --- a/src/GRANULAR/fix_heat_flow.cpp +++ b/src/GRANULAR/fix_heat_flow.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "update.h" @@ -127,7 +128,7 @@ void FixHeatFlow::final_integrate() if (igroup == atom->firstgroup) nlocal = atom->nfirst; // add ghost contributions to heatflow if first instance of fix - if (first_flag) comm->reverse_comm(this); + if (force->newton_pair && first_flag) comm->reverse_comm(this); if (rmass) { for (int i = 0; i < nlocal; i++) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index cc5f0567e8..a4e76aa87a 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -59,6 +59,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : if (lmp->kokkos) error->all(FLERR, "Cannot yet use fix pour with the KOKKOS package"); scalar_flag = 1; + extscalar = 0; time_depend = 1; if (!atom->radius_flag || !atom->rmass_flag) @@ -702,7 +703,7 @@ void FixPour::pre_exchange() // rebuild atom map if (atom->map_style != Atom::MAP_NONE) { - if (success) atom->map_init(); + atom->map_init(); atom->map_set(); } diff --git a/src/GRANULAR/gran_sub_mod_damping.cpp b/src/GRANULAR/gran_sub_mod_damping.cpp index 4386ed71fc..1745f6addf 100644 --- a/src/GRANULAR/gran_sub_mod_damping.cpp +++ b/src/GRANULAR/gran_sub_mod_damping.cpp @@ -16,16 +16,23 @@ #include "gran_sub_mod_normal.h" #include "granular_model.h" #include "math_special.h" +#include "math_const.h" + +#include #include using namespace LAMMPS_NS; using namespace Granular_NS; +using namespace MathConst; using MathSpecial::cube; using MathSpecial::powint; using MathSpecial::square; +static constexpr double TWOROOTFIVEBYSIX = 1.82574185835055380345; // 2/sqrt(5/6) +static constexpr double ROOTTHREEBYTWO = 1.22474487139158894067; // sqrt(3/2) + /* ---------------------------------------------------------------------- Default damping model ------------------------------------------------------------------------- */ @@ -141,3 +148,38 @@ double GranSubModDampingTsuji::calculate_forces() damp_prefactor = damp * sqrt(sqrt1); return -damp_prefactor * gm->vnnr; } + +/* ---------------------------------------------------------------------- + Coefficient of restitution damping +------------------------------------------------------------------------- */ + +GranSubModDampingCoeffRestitution::GranSubModDampingCoeffRestitution(GranularModel *gm, LAMMPS *lmp) : + GranSubModDamping(gm, lmp) +{ + allow_cohesion = 0; +} + +void GranSubModDampingCoeffRestitution::init() +{ + // Calculate prefactor, assume Hertzian as default + double cor = gm->normal_model->get_damp(); + double logcor = log(cor); + if (gm->normal_model->name == "hooke") { + damp = -2 * logcor / sqrt(MY_PI * MY_PI + logcor * logcor); + } else { + damp = -ROOTTHREEBYTWO * TWOROOTFIVEBYSIX * logcor; + damp /= sqrt(MY_PI * MY_PI + logcor * logcor); + } +} + +double GranSubModDampingCoeffRestitution::calculate_forces() +{ + // in case argument <= 0 due to precision issues + double sqrt1; + if (gm->delta > 0.0) + sqrt1 = MAX(0.0, gm->meff * gm->Fnormal / gm->delta); + else + sqrt1 = 0.0; + damp_prefactor = damp * sqrt(sqrt1); + return -damp_prefactor * gm->vnnr; +} diff --git a/src/GRANULAR/gran_sub_mod_damping.h b/src/GRANULAR/gran_sub_mod_damping.h index db5bb43ca5..c931e385cc 100644 --- a/src/GRANULAR/gran_sub_mod_damping.h +++ b/src/GRANULAR/gran_sub_mod_damping.h @@ -18,6 +18,7 @@ GranSubModStyle(velocity,GranSubModDampingVelocity,DAMPING); GranSubModStyle(mass_velocity,GranSubModDampingMassVelocity,DAMPING); GranSubModStyle(viscoelastic,GranSubModDampingViscoelastic,DAMPING); GranSubModStyle(tsuji,GranSubModDampingTsuji,DAMPING); +GranSubModStyle(coeff_restitution,GranSubModDampingCoeffRestitution,DAMPING); // clang-format on #else @@ -84,6 +85,17 @@ namespace Granular_NS { double calculate_forces() override; }; + /* ---------------------------------------------------------------------- */ + + class GranSubModDampingCoeffRestitution : public GranSubModDamping { + public: + GranSubModDampingCoeffRestitution(class GranularModel *, class LAMMPS *); + void init() override; + double calculate_forces() override; + }; + + /* ---------------------------------------------------------------------- */ + } // namespace Granular_NS } // namespace LAMMPS_NS diff --git a/src/GRANULAR/gran_sub_mod_normal.h b/src/GRANULAR/gran_sub_mod_normal.h index 6f2f3aabbe..c1ed36b6e1 100644 --- a/src/GRANULAR/gran_sub_mod_normal.h +++ b/src/GRANULAR/gran_sub_mod_normal.h @@ -38,7 +38,7 @@ namespace Granular_NS { virtual double calculate_contact_radius(); virtual double calculate_forces() = 0; - double get_cohesive_flag() const { return cohesive_flag; } + int get_cohesive_flag() const { return cohesive_flag; } double get_damp() const { return damp; } double get_emod() const { return Emod; } double get_fncrit() const { return Fncrit; } @@ -49,6 +49,7 @@ namespace Granular_NS { protected: double damp; // argument historically needed by damping + // typically (but not always) equals eta_n0 double Emod, poiss; double Fncrit; int material_properties, cohesive_flag; diff --git a/src/GRANULAR/granular_model.cpp b/src/GRANULAR/granular_model.cpp index 6de147b34a..9764ec42e9 100644 --- a/src/GRANULAR/granular_model.cpp +++ b/src/GRANULAR/granular_model.cpp @@ -32,6 +32,7 @@ #include #include +#include using namespace LAMMPS_NS; using namespace Granular_NS; @@ -215,9 +216,15 @@ int GranularModel::define_classic_model(char **arg, int iarg, int narg) // manually parse coeffs normal_model->coeffs[0] = kn; normal_model->coeffs[1] = gamman; - tangential_model->coeffs[0] = kt; - tangential_model->coeffs[1] = gammat / gamman; - tangential_model->coeffs[2] = xmu; + + if (tangential_model->num_coeffs == 2) { + tangential_model->coeffs[0] = gammat / gamman; + tangential_model->coeffs[1] = xmu; + } else { + tangential_model->coeffs[0] = kt; + tangential_model->coeffs[1] = gammat / gamman; + tangential_model->coeffs[2] = xmu; + } normal_model->coeffs_to_local(); tangential_model->coeffs_to_local(); @@ -333,11 +340,11 @@ void GranularModel::read_restart(FILE *fp) utils::sfread(FLERR, &num_char, sizeof(int), 1, fp, nullptr, error); MPI_Bcast(&num_char, 1, MPI_INT, 0, world); - std::string model_name (num_char, ' '); + std::string model_name(num_char, ' '); if (comm->me == 0) utils::sfread(FLERR, const_cast(model_name.data()), sizeof(char),num_char, fp, nullptr, error); MPI_Bcast(const_cast(model_name.data()), num_char, MPI_CHAR, 0, world); - construct_sub_model(model_name, (SubModelType) i); + construct_sub_model(std::move(model_name), (SubModelType) i); if (comm->me == 0) utils::sfread(FLERR, &num_coeff, sizeof(int), 1, fp, nullptr, error); diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index d5179a19b7..cb19a8c025 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -769,7 +769,7 @@ double PairGranular::single(int i, int j, int itype, int jtype, // apply forces & torques // Calculate normal component, normalized by r - fforce = model->Fnormal * model->rinv; + fforce = model->Fntot * model->rinv; // set single_extra quantities svector[0] = model->fs[0]; diff --git a/src/INTEL/fix_nh_intel.cpp b/src/INTEL/fix_nh_intel.cpp index 5455576a1c..8de52835e2 100644 --- a/src/INTEL/fix_nh_intel.cpp +++ b/src/INTEL/fix_nh_intel.cpp @@ -26,6 +26,7 @@ #include "memory.h" #include "modify.h" #include "neighbor.h" +#include "respa.h" #include "update.h" #include @@ -335,8 +336,13 @@ void FixNHIntel::reset_dt() // If using respa, then remap is performed in innermost level - if (utils::strmatch(update->integrate_style,"^respa")) + if (utils::strmatch(update->integrate_style,"^respa")) { + auto respa_ptr = dynamic_cast(update->integrate); + if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style); + nlevels_respa = respa_ptr->nlevels; + step_respa = respa_ptr->step; dto = 0.5*step_respa[0]; + } if (pstat_flag) pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain); diff --git a/src/INTEL/npair_skip_intel.cpp b/src/INTEL/npair_skip_intel.cpp index 3596237746..9353a6f520 100644 --- a/src/INTEL/npair_skip_intel.cpp +++ b/src/INTEL/npair_skip_intel.cpp @@ -74,9 +74,13 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, const int nlocal = atom->nlocal; const int e_nall = nlocal + atom->nghost; const int * _noalias const type = atom->type; + const tagint * _noalias const molecule = atom->molecule; + int * _noalias const ilist = list->ilist; int * _noalias const numneigh = list->numneigh; int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT + const int molskip = list->molskip; + const int * _noalias const ilist_skip = list->listskip->ilist; const int * _noalias const numneigh_skip = list->listskip->numneigh; const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT @@ -110,7 +114,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, for (int ii = ifrom; ii < ito; ii++) { const int i = ilist_skip[ii]; const int itype = type[i]; - if (iskip[itype]) continue; + if (!molskip && iskip[itype]) continue; int n = 0; int *neighptr = ipage.vget(); @@ -142,7 +146,11 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, for (int jj = 0; jj < jnum; jj++) { const int joriginal = jlist[jj]; const int j = joriginal & NEIGHMASK; - if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal; + if (!molskip && ijskip[itype][type[j]]) continue; + if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; + if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; + + neighptr[n++] = joriginal; } } @@ -269,9 +277,13 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, const int e_nall = nlocal + atom->nghost; const ATOM_T * _noalias const x = buffers->get_x(); const int * _noalias const type = atom->type; + const tagint * _noalias const molecule = atom->molecule; + int * _noalias const ilist = list->ilist; int * _noalias const numneigh = list->numneigh; int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT + const int molskip = list->molskip; + const int * _noalias const ilist_skip = list->listskip->ilist; const int * _noalias const numneigh_skip = list->listskip->numneigh; const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT @@ -306,7 +318,7 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, for (int ii = ifrom; ii < ito; ii++) { const int i = ilist_skip[ii]; const int itype = type[i]; - if (iskip[itype]) continue; + if (!molskip && iskip[itype]) continue; const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -370,7 +382,9 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, const int j = joriginal & NEIGHMASK; int addme = 1; - if (ijskip[itype][type[j]]) addme = 0; + if (!molskip && ijskip[itype][type[j]]) addme = 0; + if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) addme = 0; + if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) addme = 0; // trim to shorter cutoff diff --git a/src/INTEL/pair_eam_intel.cpp b/src/INTEL/pair_eam_intel.cpp index bd78c3239d..a7fd6af408 100644 --- a/src/INTEL/pair_eam_intel.cpp +++ b/src/INTEL/pair_eam_intel.cpp @@ -234,7 +234,6 @@ void PairEAMIntel::eval(const int offload, const int vflag, const int istride = fc.rhor_istride(); const int jstride = fc.rhor_jstride(); const int fstride = fc.frho_stride(); - { #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD) *timer_compute = MIC_Wtime(); @@ -565,12 +564,10 @@ void PairEAMIntel::eval(const int offload, const int vflag, } else rhoip = rhojp; const flt_t z2p = (z2r_spline_t[joff].a*p + - z2r_spline_t[joff].b)*p + - z2r_spline_t[joff].c; + z2r_spline_t[joff].b)*p + z2r_spline_t[joff].c; const flt_t z2 = ((z2r_spline_t[joff].d*p + z2r_spline_t[joff].e)*p + - z2r_spline_t[joff].f)*p + - z2r_spline_t[joff].g; + z2r_spline_t[joff].f)*p + z2r_spline_t[joff].g; const flt_t recip = (flt_t)1.0/r; const flt_t phi = z2*recip; @@ -849,4 +846,3 @@ void PairEAMIntel::unpack_forward_comm(int n, int first, double *buf, last = first + n; for (i = first; i < last; i++) fp_f[i] = buf[m++]; } - diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 75949c35d8..aa920981e2 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -86,6 +86,8 @@ action bond_fene_kokkos.cpp bond_fene.cpp action bond_fene_kokkos.h bond_fene.h action bond_harmonic_kokkos.cpp bond_harmonic.cpp action bond_harmonic_kokkos.h bond_harmonic.h +action bond_hybrid_kokkos.cpp bond_hybrid.cpp +action bond_hybrid_kokkos.h bond_hybrid.h action comm_kokkos.cpp action comm_kokkos.h action comm_tiled_kokkos.cpp @@ -356,6 +358,8 @@ action pair_multi_lucy_rx_kokkos.cpp pair_multi_lucy_rx.cpp action pair_multi_lucy_rx_kokkos.h pair_multi_lucy_rx.h action pair_pace_extrapolation_kokkos.cpp pair_pace_extrapolation.cpp action pair_pace_extrapolation_kokkos.h pair_pace_extrapolation.h +action pair_pod_kokkos.cpp pair_pod.cpp +action pair_pod_kokkos.h pair_pod.h action pair_pace_kokkos.cpp pair_pace.cpp action pair_pace_kokkos.h pair_pace.h action pair_reaxff_kokkos.cpp pair_reaxff.cpp @@ -363,6 +367,8 @@ action pair_reaxff_kokkos.h pair_reaxff.h action pair_snap_kokkos_impl.h pair_snap.cpp action pair_snap_kokkos.cpp pair_snap.cpp action pair_snap_kokkos.h pair_snap.h +action pair_soft_kokkos.cpp +action pair_soft_kokkos.h action pair_sw_kokkos.cpp pair_sw.cpp action pair_sw_kokkos.h pair_sw.h action pair_table_kokkos.cpp diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index b1a066f165..6707deddd5 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -31,9 +31,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp), -mapBinner(1, 0.0, 1.0), // no default constructor, these values are not used -mapSorter(d_tag_sorted, 0, 1, mapBinner, true) +AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp) { avecKK = nullptr; diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index 652e6c2191..8501af2a24 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -88,8 +88,25 @@ class AtomKokkos : public Atom { DAT::tdual_int_1d k_map_array; dual_hash_type k_map_hash; - DAT::t_tagint_1d d_tag_sorted; - DAT::t_int_1d d_i_sorted; + struct KeyValue { + int i; + bigint tag; + }; + + typedef Kokkos::View t_keyvalue_1d; + t_keyvalue_1d d_sorted; + + struct MyComp { + KOKKOS_FUNCTION + bool operator()(const KeyValue& a, const KeyValue& b) const + { + if (a.tag < b.tag) + return true; + if (b.tag < a.tag) + return false; + return a.i < b.i; + } + }; typedef Kokkos::DualView tdual_tagint_2; typedef tdual_tagint_2::t_dev t_tagint_2; @@ -101,11 +118,6 @@ class AtomKokkos : public Atom { DAT::t_tagint_scalar d_tag_min,d_tag_max; HAT::t_tagint_scalar h_tag_min,h_tag_max; - using MapKeyViewType = decltype(d_tag_sorted); - using BinOpMap = Kokkos::BinOp1D; - BinOpMap mapBinner; - Kokkos::BinSort mapSorter; - class AtomVecKokkos* avecKK; // map lookup function inlined for efficiency @@ -156,7 +168,7 @@ class AtomKokkos : public Atom { virtual void grow(unsigned int mask); int add_custom(const char *, int, int, int border = 0) override; void remove_custom(int, int, int) override; - virtual void deallocate_topology(); + void deallocate_topology() override; void map_set_device(); void map_set_host(); diff --git a/src/KOKKOS/atom_map_kokkos.cpp b/src/KOKKOS/atom_map_kokkos.cpp index 8203e1e6a2..2c4c58ee19 100644 --- a/src/KOKKOS/atom_map_kokkos.cpp +++ b/src/KOKKOS/atom_map_kokkos.cpp @@ -190,128 +190,64 @@ void AtomKokkos::map_set_device() atomKK->sync(Device, TAG_MASK); + int map_style_array = (map_style == MAP_ARRAY); + auto d_tag = atomKK->k_tag.d_view; auto d_sametag = k_sametag.d_view; - // sort by tag - int nmax = atom->nmax; - int realloc_flag = 0; - if (!d_tag_sorted.data() || (int)d_tag_sorted.extent(0) < nmax) { - MemKK::realloc_kokkos(d_tag_sorted,"atom:tag_sorted",nmax); - MemKK::realloc_kokkos(d_i_sorted,"atom:i_sorted",nmax); - realloc_flag = 1; - } + // sort by tag then local id - h_tag_min() = MAXTAGINT; - h_tag_max() = 0; + if (!d_sorted.data() || (int)d_sorted.extent(0) < nmax) + MemKK::realloc_kokkos(d_sorted,"atom:sorted",nmax); - Kokkos::deep_copy(d_tag_min_max,h_tag_min_max); - - auto l_tag_sorted = d_tag_sorted; - auto l_i_sorted = d_i_sorted; - auto l_tag_min = d_tag_min; - auto l_tag_max = d_tag_max; - int map_style_array = (map_style == MAP_ARRAY); + auto l_sorted = Kokkos::subview(d_sorted,std::make_pair(0,nall)); Kokkos::parallel_for(nall, LAMMPS_LAMBDA(int i) { - l_i_sorted(i) = i; - tagint tag_i = d_tag(i); - l_tag_sorted(i) = tag_i; - Kokkos::atomic_min(&l_tag_min(),tag_i); - Kokkos::atomic_max(&l_tag_max(),tag_i); + l_sorted(i).i = i; + l_sorted(i).tag = d_tag(i); }); - Kokkos::deep_copy(h_tag_min_max,d_tag_min_max); - - tagint min = h_tag_min(); - tagint max = h_tag_max(); - - using MapKeyViewType = decltype(d_tag_sorted); - using BinOpMap = Kokkos::BinOp1D; - - mapBinner = BinOpMap(nall, min, max); - - if (realloc_flag) { - mapSorter = Kokkos::BinSort(d_tag_sorted, 0, nall, mapBinner, true); - MemKK::realloc_kokkos(mapSorter.bin_count_atomic,"Kokkos::SortImpl::BinSortFunctor::bin_count",nmax+1); - Kokkos::deep_copy(mapSorter.bin_count_atomic,0); - mapSorter.bin_count_const = mapSorter.bin_count_atomic; - MemKK::realloc_kokkos(mapSorter.bin_offsets,"Kokkos::SortImpl::BinSortFunctor::bin_offsets",nmax+1); - MemKK::realloc_kokkos(mapSorter.sort_order,"Kokkos::SortImpl::BinSortFunctor::sort_order",nmax); - } else { - Kokkos::deep_copy(mapSorter.bin_count_atomic,0); - mapSorter.bin_op = mapBinner; - mapSorter.range_begin = 0; - mapSorter.range_end = nall; - } - - mapSorter.create_permute_vector(LMPDeviceType()); - mapSorter.sort(LMPDeviceType(), d_tag_sorted, 0, nall); - mapSorter.sort(LMPDeviceType(), d_i_sorted, 0, nall); + Kokkos::sort(LMPDeviceType(),l_sorted,MyComp{}); auto d_map_array = k_map_array.d_view; auto d_map_hash = k_map_hash.d_view; - d_map_hash.clear(); + if (!map_style_array) + d_map_hash.clear(); auto d_error_flag = k_error_flag.d_view; Kokkos::deep_copy(d_error_flag,0); - // for each tag find: - // neighboring atoms with closest local id for sametag // atom with smallest local id for atom map Kokkos::parallel_for(nall, LAMMPS_LAMBDA(int ii) { - const int i = l_i_sorted(ii); - const tagint tag_i = l_tag_sorted(ii); - int i_min = i; - int i_closest = MAXSMALLINT; + const int i = l_sorted(ii).i; + const tagint tag_i = l_sorted(ii).tag; - // search atoms with same tag in the forward direction + // sametag + tagint tag_j = -1; int jj = ii+1; - int closest_flag = 0; + if (jj < nall) tag_j = l_sorted(jj).tag; - while (jj < nall) { - const tagint tag_j = l_tag_sorted(jj); - if (tag_j != tag_i) break; - const int j = l_i_sorted(jj); - i_min = MIN(i_min,j); - if (j > i) { - i_closest = MIN(i_closest,j); - closest_flag = 1; - } - jj++; - } + if (tag_j == tag_i) + d_sametag(i) = l_sorted(jj).i; + else + d_sametag(i) = -1; - // search atoms with same tag in the reverse direction + // atom map + tag_j = -1; jj = ii-1; + if (jj >= 0) tag_j = l_sorted(jj).tag; - while (jj >= 0) { - const tagint tag_j = l_tag_sorted(jj); - if (tag_j != tag_i) break; - const int j = l_i_sorted(jj); - i_min = MIN(i_min,j); - if (j > i) { - i_closest = MIN(i_closest,j); - closest_flag = 1; - } - jj--; - } - - if (!closest_flag) - i_closest = -1; - - d_sametag(i) = i_closest; - - if (i == i_min) { + if (tag_j != tag_i) { if (map_style_array) - d_map_array(tag_i) = i_min; + d_map_array(tag_i) = i; else { - auto insert_result = d_map_hash.insert(tag_i, i_min); + auto insert_result = d_map_hash.insert(tag_i, i); if (insert_result.failed()) d_error_flag() = 1; } } diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index eeecc385b0..2cf113ec00 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -34,6 +34,8 @@ using namespace LAMMPS_NS; template BondClass2Kokkos::BondClass2Kokkos(LAMMPS *lmp) : BondClass2(lmp) { + kokkosable = 1; + atomKK = (AtomKokkos *) atom; neighborKK = (NeighborKokkos *) neighbor; execution_space = ExecutionSpaceFromDevice::space; @@ -122,12 +124,12 @@ void BondClass2Kokkos::compute(int eflag_in, int vflag_in) if (eflag_atom) { k_eatom.template modify(); - k_eatom.template sync(); + k_eatom.sync_host(); } if (vflag_atom) { k_vatom.template modify(); - k_vatom.template sync(); + k_vatom.sync_host(); } copymode = 0; @@ -227,13 +229,13 @@ void BondClass2Kokkos::coeff(int narg, char **arg) k_r0.h_view[i] = r0[i]; } - k_k2.template modify(); + k_k2.modify_host(); k_k2.template sync(); - k_k3.template modify(); + k_k3.modify_host(); k_k3.template sync(); - k_k4.template modify(); + k_k4.modify_host(); k_k4.template sync(); - k_r0.template modify(); + k_r0.modify_host(); k_r0.template sync(); } @@ -264,13 +266,13 @@ void BondClass2Kokkos::read_restart(FILE *fp) k_r0.h_view[i] = r0[i]; } - k_k2.template modify(); + k_k2.modify_host(); k_k2.template sync(); - k_k3.template modify(); + k_k3.modify_host(); k_k3.template sync(); - k_k4.template modify(); + k_k4.modify_host(); k_k4.template sync(); - k_r0.template modify(); + k_r0.modify_host(); k_r0.template sync(); } diff --git a/src/KOKKOS/bond_class2_kokkos.h b/src/KOKKOS/bond_class2_kokkos.h index 0eb3c4d39a..1056bf021d 100644 --- a/src/KOKKOS/bond_class2_kokkos.h +++ b/src/KOKKOS/bond_class2_kokkos.h @@ -59,6 +59,10 @@ class BondClass2Kokkos : public BondClass2 { const F_FLOAT &ebond, const F_FLOAT &fbond, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const; + typedef typename KKDevice::value KKDeviceType; + Kokkos::DualView k_eatom; + Kokkos::DualView k_vatom; + protected: class NeighborKokkos *neighborKK; @@ -67,9 +71,6 @@ class BondClass2Kokkos : public BondClass2 { typename Kokkos::View::value,Kokkos::MemoryTraits > f; typename AT::t_int_2d bondlist; - typedef typename KKDevice::value KKDeviceType; - Kokkos::DualView k_eatom; - Kokkos::DualView k_vatom; Kokkos::View > d_eatom; Kokkos::View > d_vatom; diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index a6bbb1edde..a056f35fde 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -37,6 +37,8 @@ using MathConst::MY_CUBEROOT2; template BondFENEKokkos::BondFENEKokkos(LAMMPS *lmp) : BondFENE(lmp) { + kokkosable = 1; + atomKK = (AtomKokkos *) atom; neighborKK = (NeighborKokkos *) neighbor; execution_space = ExecutionSpaceFromDevice::space; @@ -135,12 +137,12 @@ void BondFENEKokkos::compute(int eflag_in, int vflag_in) if (eflag_atom) { k_eatom.template modify(); - k_eatom.template sync(); + k_eatom.sync_host(); } if (vflag_atom) { k_vatom.template modify(); - k_vatom.template sync(); + k_vatom.sync_host(); } copymode = 0; @@ -267,10 +269,10 @@ void BondFENEKokkos::coeff(int narg, char **arg) k_sigma.h_view[i] = sigma[i]; } - k_k.template modify(); - k_r0.template modify(); - k_epsilon.template modify(); - k_sigma.template modify(); + k_k.modify_host(); + k_r0.modify_host(); + k_epsilon.modify_host(); + k_sigma.modify_host(); } @@ -291,10 +293,10 @@ void BondFENEKokkos::read_restart(FILE *fp) k_sigma.h_view[i] = sigma[i]; } - k_k.template modify(); - k_r0.template modify(); - k_epsilon.template modify(); - k_sigma.template modify(); + k_k.modify_host(); + k_r0.modify_host(); + k_epsilon.modify_host(); + k_sigma.modify_host(); } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/bond_fene_kokkos.h b/src/KOKKOS/bond_fene_kokkos.h index 18f8d87b6a..450490d6a9 100644 --- a/src/KOKKOS/bond_fene_kokkos.h +++ b/src/KOKKOS/bond_fene_kokkos.h @@ -58,6 +58,9 @@ class BondFENEKokkos : public BondFENE { const F_FLOAT &ebond, const F_FLOAT &fbond, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const; + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + protected: class NeighborKokkos *neighborKK; @@ -66,8 +69,6 @@ class BondFENEKokkos : public BondFENE { typename ArrayTypes::t_f_array f; typename ArrayTypes::t_int_2d bondlist; - DAT::tdual_efloat_1d k_eatom; - DAT::tdual_virial_array k_vatom; typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 7dcdf24c66..7e12400c9b 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -34,6 +34,8 @@ using namespace LAMMPS_NS; template BondHarmonicKokkos::BondHarmonicKokkos(LAMMPS *lmp) : BondHarmonic(lmp) { + kokkosable = 1; + atomKK = (AtomKokkos *) atom; neighborKK = (NeighborKokkos *) neighbor; execution_space = ExecutionSpaceFromDevice::space; @@ -65,23 +67,20 @@ void BondHarmonicKokkos::compute(int eflag_in, int vflag_in) // reallocate per-atom arrays if necessary if (eflag_atom) { - //if(k_eatom.extent(0)destroy_kokkos(k_eatom,eatom); memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom"); d_eatom = k_eatom.template view(); - //} + } else Kokkos::deep_copy(d_eatom,0.0); } if (vflag_atom) { - //if(k_vatom.extent(0)destroy_kokkos(k_vatom,vatom); memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"improper:vatom"); d_vatom = k_vatom.template view(); - //} + } else Kokkos::deep_copy(d_vatom,0.0); } -// if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); -// else atomKK->modified(execution_space,F_MASK); - x = atomKK->k_x.template view(); f = atomKK->k_f.template view(); neighborKK->k_bondlist.template sync(); @@ -122,12 +121,12 @@ void BondHarmonicKokkos::compute(int eflag_in, int vflag_in) if (eflag_atom) { k_eatom.template modify(); - k_eatom.template sync(); + k_eatom.sync_host(); } if (vflag_atom) { k_vatom.template modify(); - k_vatom.template sync(); + k_vatom.sync_host(); } copymode = 0; @@ -214,8 +213,8 @@ void BondHarmonicKokkos::coeff(int narg, char **arg) k_r0.h_view[i] = r0[i]; } - k_k.template modify(); - k_r0.template modify(); + k_k.modify_host(); + k_r0.modify_host(); k_k.template sync(); k_r0.template sync(); } @@ -241,8 +240,8 @@ void BondHarmonicKokkos::read_restart(FILE *fp) k_r0.h_view[i] = r0[i]; } - k_k.template modify(); - k_r0.template modify(); + k_k.modify_host(); + k_r0.modify_host(); k_k.template sync(); k_r0.template sync(); } diff --git a/src/KOKKOS/bond_harmonic_kokkos.h b/src/KOKKOS/bond_harmonic_kokkos.h index 837e669b98..b613dbc310 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.h +++ b/src/KOKKOS/bond_harmonic_kokkos.h @@ -37,6 +37,7 @@ class BondHarmonicKokkos : public BondHarmonic { public: typedef DeviceType device_type; typedef EV_FLOAT value_type; + typedef ArrayTypes AT; BondHarmonicKokkos(class LAMMPS *); ~BondHarmonicKokkos() override; @@ -62,7 +63,6 @@ class BondHarmonicKokkos : public BondHarmonic { class NeighborKokkos *neighborKK; - typedef ArrayTypes AT; typename AT::t_x_array_randomread x; typename Kokkos::View::value,Kokkos::MemoryTraits > f; typename AT::t_int_2d bondlist; diff --git a/src/KOKKOS/bond_hybrid_kokkos.cpp b/src/KOKKOS/bond_hybrid_kokkos.cpp new file mode 100644 index 0000000000..d63ebccac6 --- /dev/null +++ b/src/KOKKOS/bond_hybrid_kokkos.cpp @@ -0,0 +1,215 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "bond_hybrid_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "memory_kokkos.h" +#include "neighbor_kokkos.h" + +#include + +using namespace LAMMPS_NS; + +#define EXTRA 1000 + +/* ---------------------------------------------------------------------- */ + +BondHybridKokkos::BondHybridKokkos(LAMMPS *lmp) : BondHybrid(lmp) +{ + kokkosable = 1; + + atomKK = (AtomKokkos *) atom; + neighborKK = (NeighborKokkos *) neighbor; + + execution_space = Device; + + datamask_read = EMPTY_MASK; + datamask_modify = EMPTY_MASK; +} + +/* ---------------------------------------------------------------------- */ + +BondHybridKokkos::~BondHybridKokkos() +{ + deallocate(); +} + +/* ---------------------------------------------------------------------- */ + +void BondHybridKokkos::compute(int eflag, int vflag) +{ + // save ptrs to original bondlist + + int nbondlist_orig = neighbor->nbondlist; + neighborKK->k_bondlist.sync_device(); + auto k_bondlist_orig = neighborKK->k_bondlist; + auto d_bondlist_orig = k_bondlist_orig.d_view; + auto d_nbondlist = k_nbondlist.d_view; + auto h_nbondlist = k_nbondlist.h_view; + + // if this is re-neighbor step, create sub-style bondlists + // nbondlist[] = length of each sub-style list + // realloc sub-style bondlist if necessary + // load sub-style bondlist with 3 values from original bondlist + + if (neighbor->ago == 0) { + Kokkos::deep_copy(d_nbondlist,0); + + k_map.sync_device(); + auto d_map = k_map.d_view; + + Kokkos::parallel_for(nbondlist_orig,LAMMPS_LAMBDA(int i) { + const int m = d_map[d_bondlist_orig(i,2)]; + if (m >= 0) Kokkos::atomic_increment(&d_nbondlist[m]); + }); + + k_nbondlist.modify_device(); + k_nbondlist.sync_host(); + + maxbond_all = 0; + for (int m = 0; m < nstyles; m++) + if (h_nbondlist[m] > maxbond_all) + maxbond_all = h_nbondlist[m] + EXTRA; + + if (k_bondlist.d_view.extent(1) < maxbond_all) + MemKK::realloc_kokkos(k_bondlist, "bond_hybrid:bondlist", nstyles, maxbond_all, 3); + auto d_bondlist = k_bondlist.d_view; + + Kokkos::deep_copy(d_nbondlist,0); + + Kokkos::parallel_for(nbondlist_orig,LAMMPS_LAMBDA(int i) { + const int m = d_map[d_bondlist_orig(i,2)]; + if (m < 0) return; + const int n = Kokkos::atomic_fetch_add(&d_nbondlist[m],1); + d_bondlist(m,n,0) = d_bondlist_orig(i,0); + d_bondlist(m,n,1) = d_bondlist_orig(i,1); + d_bondlist(m,n,2) = d_bondlist_orig(i,2); + }); + } + + // call each sub-style's compute function + // set neighbor->bondlist to sub-style bondlist before call + // accumulate sub-style global/peratom energy/virial in hybrid + + ev_init(eflag, vflag); + + k_nbondlist.modify_device(); + k_nbondlist.sync_host(); + + for (int m = 0; m < nstyles; m++) { + neighbor->nbondlist = h_nbondlist[m]; + auto k_bondlist_m = Kokkos::subview(k_bondlist,m,Kokkos::ALL,Kokkos::ALL); + k_bondlist_m.modify_device(); + neighborKK->k_bondlist = k_bondlist_m; + + auto style = styles[m]; + atomKK->sync(style->execution_space,style->datamask_read); + style->compute(eflag, vflag); + atomKK->modified(style->execution_space,style->datamask_modify); + + if (eflag_global) energy += style->energy; + if (vflag_global) + for (int n = 0; n < 6; n++) virial[n] += style->virial[n]; + + if (eflag_atom) { + int n = atom->nlocal; + if (force->newton_bond) n += atom->nghost; + double *eatom_substyle = styles[m]->eatom; + for (int i = 0; i < n; i++) eatom[i] += eatom_substyle[i]; + } + if (vflag_atom) { + int n = atom->nlocal; + if (force->newton_bond) n += atom->nghost; + double **vatom_substyle = styles[m]->vatom; + for (int i = 0; i < n; i++) + for (int j = 0; j < 6; j++) vatom[i][j] += vatom_substyle[i][j]; + } + } + + // restore ptrs to original bondlist + + neighbor->nbondlist = nbondlist_orig; + neighborKK->k_bondlist = k_bondlist_orig; +} + +/* ---------------------------------------------------------------------- */ + +void BondHybridKokkos::allocate() +{ + allocated = 1; + int n = atom->nbondtypes; + + memoryKK->create_kokkos(k_map, map, n + 1, "bond:map"); + memory->create(setflag, n + 1, "bond:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; + + k_nbondlist = DAT::tdual_int_1d("bond:nbondlist", nstyles); +} + +/* ---------------------------------------------------------------------- */ + +void BondHybridKokkos::deallocate() +{ + if (!allocated) return; + + allocated = 0; + + memory->destroy(setflag); + memoryKK->destroy_kokkos(k_map,map); +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +---------------------------------------------------------------------- */ + +void BondHybridKokkos::coeff(int narg, char **arg) +{ + BondHybrid::coeff(narg,arg); + + k_map.modify_host(); +} + +/* ---------------------------------------------------------------------- */ + +void BondHybridKokkos::init_style() +{ + BondHybrid::init_style(); + + for (int m = 0; m < nstyles; m++) { + if (!styles[m]->kokkosable) + error->all(FLERR,"Must use only Kokkos-enabled bond styles with bond_style hybrid/kk"); + + if (styles[m]->execution_space == Host) + lmp->kokkos->allow_overlap = 0; + } +} + +/* ---------------------------------------------------------------------- + memory usage +------------------------------------------------------------------------- */ + +double BondHybridKokkos::memory_usage() +{ + double bytes = (double) maxeatom * sizeof(double); + bytes += (double) maxvatom * 6 * sizeof(double); + for (int m = 0; m < nstyles; m++) bytes += (double) maxbond_all * 3 * sizeof(int); + for (int m = 0; m < nstyles; m++) + if (styles[m]) bytes += styles[m]->memory_usage(); + return bytes; +} diff --git a/src/KOKKOS/bond_hybrid_kokkos.h b/src/KOKKOS/bond_hybrid_kokkos.h new file mode 100644 index 0000000000..217beaca5f --- /dev/null +++ b/src/KOKKOS/bond_hybrid_kokkos.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BOND_CLASS +// clang-format off +BondStyle(hybrid/kk,BondHybridKokkos); +BondStyle(hybrid/kk/device,BondHybridKokkos); +BondStyle(hybrid/kk/host,BondHybridKokkos); +// clang-format on +#else + +// clang-format off +#ifndef LMP_BOND_HYBRID_KOKKOS_H +#define LMP_BOND_HYBRID_KOKKOS_H + +#include "bond_hybrid.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +class BondHybridKokkos : public BondHybrid { + friend class Force; + + public: + BondHybridKokkos(class LAMMPS *); + ~BondHybridKokkos() override; + void compute(int, int) override; + void coeff(int, char **) override; + void init_style() override; + double memory_usage() override; + + private: + int maxbond_all; + + class NeighborKokkos *neighborKK; + + DAT::tdual_int_1d k_map; // which style each bond type points to + DAT::tdual_int_1d k_nbondlist; // # of bonds in sub-style bondlists + DAT::tdual_int_3d k_bondlist; // bondlist for each sub-style + + void allocate() override; + void deallocate() override; +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 2425857d61..8f821c3036 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -880,15 +880,8 @@ void CommKokkos::exchange_device() // sort exchange_sendlist - auto d_exchange_sendlist = k_exchange_sendlist.view(); - using KeyViewType = decltype(d_exchange_sendlist); - using BinOp = Kokkos::BinOp1D; - - BinOp binner(count, 0, nlocal); - Kokkos::BinSort Sorter(d_exchange_sendlist, 0, count, binner, true); - Sorter.create_permute_vector(DeviceType()); - Sorter.sort(DeviceType(), d_exchange_sendlist, 0, count); - + auto d_exchange_sendlist = Kokkos::subview(k_exchange_sendlist.view(),std::make_pair(0,count)); + Kokkos::sort(DeviceType(), d_exchange_sendlist); k_exchange_sendlist.sync(); // when atom is deleted, fill it in with last atom diff --git a/src/KOKKOS/domain_kokkos.cpp b/src/KOKKOS/domain_kokkos.cpp index aecc12cd12..d0865c6afb 100644 --- a/src/KOKKOS/domain_kokkos.cpp +++ b/src/KOKKOS/domain_kokkos.cpp @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; -static constexpr double BIG = 1.0e20; +static constexpr double BIG = 1.0e20; /* ---------------------------------------------------------------------- */ @@ -80,6 +80,11 @@ public: void DomainKokkos::reset_box() { // perform shrink-wrapping + + // nothing to do for empty systems + + if (atom->natoms == 0) return; + // compute extent of atoms on this proc // for triclinic, this is done in lamda space diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index 5caed42f43..202d46e788 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -39,8 +39,11 @@ FFT3dKokkos::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int Pointers(lmp) { int nthreads = lmp->kokkos->nthreads; + +#if defined(LMP_KOKKOS_GPU) int ngpus = lmp->kokkos->ngpus; ExecutionSpace execution_space = ExecutionSpaceFromDevice::space; +#endif #if defined(FFT_KOKKOS_MKL) if (ngpus > 0 && execution_space == Device) diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index cc4e00819f..7f0eb5c105 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -143,12 +143,13 @@ typedef Kokkos::DefaultExecutionSpace LMPDeviceType; typedef Kokkos::HostSpace::execution_space LMPHostType; -// Need to use Cuda UVM memory space for Host execution space +// If unified memory, need to use device memory space for host execution space template class KKDevice { -public: -#if defined(KOKKOS_ENABLE_CUDA) && defined(KOKKOS_ENABLE_CUDA_UVM) + public: +#if ((defined(KOKKOS_ENABLE_CUDA) && defined(KOKKOS_ENABLE_CUDA_UVM)) || \ + (defined(KOKKOS_ENABLE_HIP) && defined(KOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY))) typedef Kokkos::Device value; #else typedef Kokkos::Device value; @@ -1407,6 +1408,7 @@ typedef SNAComplex SNAcomplex; #endif #define LAMMPS_LAMBDA KOKKOS_LAMBDA +#define LAMMPS_CLASS_LAMBDA KOKKOS_CLASS_LAMBDA #if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) #define LAMMPS_DEVICE_FUNCTION __device__ diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 88b0445dc8..4e3debaacb 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -138,9 +138,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairBuckKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT r6inv = r2inv*r2inv*r2inv; const F_FLOAT r = sqrt(rsq); @@ -157,9 +155,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairBuckKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT r6inv = r2inv*r2inv*r2inv; const F_FLOAT r = sqrt(rsq); diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index 84d43bcec8..353998a950 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -31,9 +31,7 @@ PairHybridKokkos::PairHybridKokkos(LAMMPS *lmp) : PairHybrid(lmp) kokkosable = 1; atomKK = (AtomKokkos *) atom; - // prevent overlapping host/device computation, which isn't - // yet supported by pair_hybrid_kokkos - execution_space = Device; + execution_space = Device; datamask_read = EMPTY_MASK; datamask_modify = EMPTY_MASK; diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 87324b49b9..c4bd603041 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -952,6 +952,8 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, std::enable_if_t<(NEIGHFLAG&P static int atoms_per_team = 0; #if defined(LMP_KOKKOS_GPU) + static int teamsize_max_for = 0; + static int teamsize_max_reduce = 0; static int lastcall = -1; if (!vectorsize || lastcall < fpair->lmp->neighbor->lastcall) { lastcall = fpair->lmp->update->ntimestep; @@ -966,7 +968,6 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, std::enable_if_t<(NEIGHFLAG&P vectorsize = MIN(vectorsize,max_vectorsize); - int teamsize_max_for,teamsize_max_reduce; if (fpair->atom->ntypes > MAX_TYPES_STACKPARAMS) { PairComputeFunctor ff(fpair,list); GetMaxTeamSize(ff, inum, teamsize_max_for, teamsize_max_reduce); @@ -974,12 +975,12 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, std::enable_if_t<(NEIGHFLAG&P PairComputeFunctor ff(fpair,list); GetMaxTeamSize(ff, inum, teamsize_max_for, teamsize_max_reduce); } - - int teamsize_max = teamsize_max_for; - if (fpair->eflag || fpair->vflag) - teamsize_max = teamsize_max_reduce; - atoms_per_team = teamsize_max/vectorsize; } + + int teamsize_max = teamsize_max_for; + if (fpair->eflag || fpair->vflag) + teamsize_max = teamsize_max_reduce; + atoms_per_team = teamsize_max/vectorsize; #else vectorsize = 1; atoms_per_team = 1; @@ -1020,7 +1021,7 @@ template EV_FLOAT pair_compute (PairStyle* fpair, NeighListKokkos* list) { EV_FLOAT ev; if (fpair->neighflag == FULL) { - if (utils::strmatch(fpair->lmp->force->pair_style,"^hybrid/overlay")) { + if (utils::strmatch(fpair->lmp->force->pair_style,"^hybrid")) { fpair->fuse_force_clear_flag = 0; ev = pair_compute_neighlist (fpair,list); } else { diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 7d2db17440..de4d3b9df8 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -155,10 +155,8 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJClass2CoulCutKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, - const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, + const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT rinv = sqrt(r2inv); const F_FLOAT r3inv = r2inv*rinv; @@ -178,9 +176,9 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJClass2CoulCutKokkos:: -compute_fcoul(const F_FLOAT& rsq, const int& /*i*/, const int&j, - const int& /*itype*/, const int& /*jtype*/, - const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const { +compute_fcoul(const F_FLOAT &rsq, const int &/*i*/, const int &j, + const int &/*itype*/, const int &/*jtype*/, + const F_FLOAT &factor_coul, const F_FLOAT &qtmp) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT rinv = sqrt(r2inv); F_FLOAT forcecoul; diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index b5d55a023a..04dc746f09 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -160,10 +160,8 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJClass2CoulLongKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, - const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, + const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT rinv = sqrt(r2inv); const F_FLOAT r3inv = r2inv*rinv; @@ -183,9 +181,9 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJClass2CoulLongKokkos:: -compute_fcoul(const F_FLOAT& rsq, const int& /*i*/, const int&j, - const int& /*itype*/, const int& /*jtype*/, - const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const { +compute_fcoul(const F_FLOAT &rsq, const int &/*i*/, const int &j, + const int &/*itype*/, const int &/*jtype*/, + const F_FLOAT &factor_coul, const F_FLOAT &qtmp) const { if (Specialisation::DoTable && rsq > tabinnersq) { union_int_float_t rsq_lookup; rsq_lookup.f = rsq; diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index 9ee1b93bd8..47bd3fc108 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -139,9 +139,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJClass2Kokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT rinv = sqrt(r2inv); const F_FLOAT r3inv = r2inv*rinv; @@ -159,9 +157,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJClass2Kokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT rinv = sqrt(r2inv); const F_FLOAT r3inv = r2inv*rinv; diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 566d74088c..ccc56a707d 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -133,9 +133,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJCutKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT r6inv = r2inv*r2inv*r2inv; @@ -150,9 +148,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJCutKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT r6inv = r2inv*r2inv*r2inv; diff --git a/src/KOKKOS/pair_lj_spica_kokkos.cpp b/src/KOKKOS/pair_lj_spica_kokkos.cpp index a6a31b31a2..1f6cccf073 100644 --- a/src/KOKKOS/pair_lj_spica_kokkos.cpp +++ b/src/KOKKOS/pair_lj_spica_kokkos.cpp @@ -138,39 +138,13 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJSPICAKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const int ljt = (STACKPARAMS?m_params[itype][jtype].lj_type:params(itype,jtype).lj_type); const F_FLOAT lj_1 = (STACKPARAMS?m_params[itype][jtype].lj1:params(itype,jtype).lj1); const F_FLOAT lj_2 = (STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2); - /*if (ljt == LJ12_4) { - - const F_FLOAT r4inv=r2inv*r2inv; - return r4inv*(lj_1*r4inv*r4inv - lj_2) * r2inv; - - } else if (ljt == LJ9_6) { - - const F_FLOAT r3inv = r2inv*sqrt(r2inv); - const F_FLOAT r6inv = r3inv*r3inv; - return r6inv*(lj_1*r3inv - lj_2) * r2inv; - - } else if (ljt == LJ12_6) { - - const double r6inv = r2inv*r2inv*r2inv; - return r6inv*(lj_1*r6inv - lj_2) * r2inv; - - } else if (ljt == LJ12_5) { - - const F_FLOAT r5inv = r2inv*r2inv*sqrt(r2inv); - const F_FLOAT r7inv = r5inv*r2inv; - return r5inv*(lj_1*r7inv - lj_2) * r2inv; - - } - if (ljt!=LJ12_4 && ljt!=LJ9_6 && ljt!=LJ12_6 && ljt!=LJ12_5) return 0.0;*/ const F_FLOAT r4inv=r2inv*r2inv; const F_FLOAT r6inv=r2inv*r4inv; const F_FLOAT a = ljt==LJ12_4?r4inv:(ljt==LJ12_5?r4inv*sqrt(r2inv):r6inv); @@ -182,9 +156,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairLJSPICAKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r2inv = 1.0/rsq; const int ljt = (STACKPARAMS?m_params[itype][jtype].lj_type:params(itype,jtype).lj_type); diff --git a/src/KOKKOS/pair_meam_kokkos.h b/src/KOKKOS/pair_meam_kokkos.h index 66b5700a72..82f48aa997 100644 --- a/src/KOKKOS/pair_meam_kokkos.h +++ b/src/KOKKOS/pair_meam_kokkos.h @@ -13,9 +13,6 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(meam/c/kk,PairMEAMKokkos); -PairStyle(meam/c/kk/device,PairMEAMKokkos); -PairStyle(meam/c/kk/host,PairMEAMKokkos); PairStyle(meam/kk,PairMEAMKokkos); PairStyle(meam/kk/device,PairMEAMKokkos); PairStyle(meam/kk/host,PairMEAMKokkos); diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index f0a5415d60..581311a965 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -140,9 +140,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairMorseKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT rr = sqrt(rsq); const F_FLOAT r0 = STACKPARAMS ? m_params[itype][jtype].r0 : params(itype,jtype).r0; const F_FLOAT d0 = STACKPARAMS ? m_params[itype][jtype].d0 : params(itype,jtype).d0; @@ -162,9 +160,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairMorseKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT rr = sqrt(rsq); const F_FLOAT r0 = STACKPARAMS ? m_params[itype][jtype].r0 : params(itype,jtype).r0; const F_FLOAT d0 = STACKPARAMS ? m_params[itype][jtype].d0 : params(itype,jtype).d0; diff --git a/src/KOKKOS/pair_pod_kokkos.cpp b/src/KOKKOS/pair_pod_kokkos.cpp new file mode 100644 index 0000000000..b0cab5a1df --- /dev/null +++ b/src/KOKKOS/pair_pod_kokkos.cpp @@ -0,0 +1,1852 @@ +// clang-format off +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + aE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Ngoc Cuong Nguyen (MIT) +------------------------------------------------------------------------- */ + +#include "pair_pod_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "math_const.h" +#include "memory_kokkos.h" +#include "neighbor_kokkos.h" +#include "neigh_request.h" + +#include +#include + +#include "eapod.h" + +using namespace LAMMPS_NS; +using namespace MathConst; +using MathSpecial::powint; + +enum{FS,FS_SHIFTEDSCALED}; + +/* ---------------------------------------------------------------------- */ + +template +PairPODKokkos::PairPODKokkos(LAMMPS *lmp) : PairPOD(lmp) +{ + respa_enable = 0; + + kokkosable = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = EMPTY_MASK; + datamask_modify = EMPTY_MASK; + + ni = 0; + nimax = 0; + nij = 0; + nijmax = 0; + atomBlockSize = 2048; + nAtomBlocks = 0; + timing = 0; + for (int i=0; i<100; i++) comptime[i] = 0; + + host_flag = (execution_space == Host); +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +template +PairPODKokkos::~PairPODKokkos() +{ + if (copymode) return; + + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +template +void PairPODKokkos::init_style() +{ + if (host_flag) { + if (lmp->kokkos->nthreads > 1) + error->all(FLERR,"Pair style pod/kk can currently only run on a single " + "CPU thread"); + + PairPOD::init_style(); + return; + } + + if (atom->tag_enable == 0) error->all(FLERR, "Pair style POD requires atom IDs"); + if (force->newton_pair == 0) error->all(FLERR, "Pair style POD requires newton pair on"); + + neighflag = lmp->kokkos->neighflag; + + auto request = neighbor->add_request(this, NeighConst::REQ_FULL); + request->set_kokkos_host(std::is_same_v && + !std::is_same_v); + request->set_kokkos_device(std::is_same_v); + if (neighflag == FULL) + error->all(FLERR,"Must use half neighbor list style with pair pace/kk"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +template +double PairPODKokkos::init_one(int i, int j) +{ + double cutone = PairPOD::init_one(i,j); + + k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone; + k_cutsq.template modify(); + + return cutone; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +template +void PairPODKokkos::coeff(int narg, char **arg) +{ + if (narg < 5) utils::missing_cmd_args(FLERR, "pair_coeff", error); + + PairPOD::coeff(narg,arg); // create a PairPOD object + + copy_from_pod_class(PairPOD::fastpodptr); // copy parameters and arrays from pod class + + int n = atom->ntypes + 1; + MemKK::realloc_kokkos(d_map, "pair_pod:map", n); + + MemKK::realloc_kokkos(k_cutsq, "pair_pod:cutsq", n, n); + d_cutsq = k_cutsq.template view(); + + MemKK::realloc_kokkos(k_scale, "pair_pod:scale", n, n); + d_scale = k_scale.template view(); + + // Set up element lists + + auto h_map = Kokkos::create_mirror_view(d_map); + + for (int i = 1; i <= atom->ntypes; i++) + h_map(i) = map[i]; + + Kokkos::deep_copy(d_map,h_map); +} + +/* ---------------------------------------------------------------------- */ + +template +void PairPODKokkos::allocate() +{ + PairPOD::allocate(); +} + +template +struct FindMaxNumNeighs { + typedef DeviceType device_type; + NeighListKokkos k_list; + + FindMaxNumNeighs(NeighListKokkos* nl): k_list(*nl) {} + ~FindMaxNumNeighs() {k_list.copymode = 1;} + + KOKKOS_INLINE_FUNCTION + void operator() (const int& ii, int& max_neighs) const { + const int i = k_list.d_ilist[ii]; + const int num_neighs = k_list.d_numneigh[i]; + if (max_neighs +void PairPODKokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + if (neighflag == FULL) no_virial_fdotr_compute = 1; + + ev_init(eflag,vflag,0); + + // reallocate per-atom arrays if necessary + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); + d_eatom = k_eatom.view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom"); + d_vatom = k_vatom.view(); + } + + copymode = 1; + int newton_pair = force->newton_pair; + if (newton_pair == false) + error->all(FLERR,"PairPODKokkos requires 'newton on'"); + + atomKK->sync(execution_space,X_MASK|F_MASK|TYPE_MASK); + x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + type = atomKK->k_type.view(); + + maxneigh = 0; + if (host_flag) { + inum = list->inum; + d_numneigh = typename ArrayTypes::t_int_1d("pair_pod:numneigh",inum); + for (int i=0; inumneigh[i]; + d_ilist = typename ArrayTypes::t_int_1d("pair_pod:ilist",inum); + for (int i=0; iilist[i]; + + int maxn = 0; + for (int i=0; inumneigh[i]) maxn = list->numneigh[i]; + MemoryKokkos::realloc_kokkos(d_neighbors,"neighlist:neighbors",inum,maxn); + for (int i=0; iilist[i]; + int m = list->numneigh[gi]; + if (maxneighfirstneigh[gi][l]; + } + } + } + else { + NeighListKokkos* k_list = static_cast*>(list); + d_numneigh = k_list->d_numneigh; + d_neighbors = k_list->d_neighbors; + d_ilist = k_list->d_ilist; + inum = list->inum; + int maxneighs; + Kokkos::parallel_reduce("PairPODKokkos::find_max_neighs",inum, FindMaxNumNeighs(k_list), Kokkos::Max(maxneighs)); + maxneigh = maxneighs; + } + + auto begin = std::chrono::high_resolution_clock::now(); + auto end = std::chrono::high_resolution_clock::now(); + + // determine the number of atom blocks and divide atoms into blocks + nAtomBlocks = calculateNumberOfIntervals(inum, atomBlockSize); + if (nAtomBlocks > 100) nAtomBlocks = 100; + divideInterval(atomBlocks, inum, nAtomBlocks); + + int nmax = 0; + for (int block=0; block(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + // obtain the neighbors within rcut + NeighborList(rij, numij, typeai, idxi, ai, aj, ti, tj, rcutsq, gi1, ni); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[1] += std::chrono::duration_cast(end-begin).count()/1e6; + + // compute atomic energy and force for the current atom block + begin = std::chrono::high_resolution_clock::now(); + blockatom_energyforce(ei, fij, ni, nij); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[2] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + // tally atomic energy to global energy + tallyenergy(ei, gi1, ni); + + // tally atomic force to global force + tallyforce(fij, ai, aj, nij); + + // tally atomic stress + if (vflag) { + tallystress(fij, rij, ai, aj, nij); + } + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[3] += std::chrono::duration_cast(end-begin).count()/1e6; + + //savedatafordebugging(); + } + + if (vflag_fdotr) pair_virial_fdotr_compute(this); + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + } + + atomKK->modified(execution_space,F_MASK); + + copymode = 0; +} + +template +void PairPODKokkos::copy_from_pod_class(EAPOD *podptr) +{ + nelements = podptr->nelements; // number of elements + onebody = podptr->onebody; // one-body descriptors + besseldegree = podptr->besseldegree; // degree of Bessel functions + inversedegree = podptr->inversedegree; // degree of inverse functions + nbesselpars = podptr->nbesselpars; // number of Bessel parameters + nCoeffPerElement = podptr->nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters) + ns = podptr->ns; // number of snapshots for radial basis functions + nl1 = podptr->nl1; // number of one-body descriptors + nl2 = podptr->nl2; // number of two-body descriptors + nl3 = podptr->nl3; // number of three-body descriptors + nl4 = podptr->nl4; // number of four-body descriptors + nl23 = podptr->nl23; // number of two-body x three-body descriptors + nl33 = podptr->nl33; // number of three-body x three-body descriptors + nl34 = podptr->nl34; // number of three-body x four-body descriptors + nl44 = podptr->nl44; // number of four-body x four-body descriptors + nl = podptr->nl; // number of local descriptors + nrbf2 = podptr->nrbf2; + nrbf3 = podptr->nrbf3; + nrbf4 = podptr->nrbf4; + nrbfmax = podptr->nrbfmax; // number of radial basis functions + nabf3 = podptr->nabf3; // number of three-body angular basis functions + nabf4 = podptr->nabf4; // number of four-body angular basis functions + K3 = podptr->K3; // number of three-body monomials + K4 = podptr->K4; // number of four-body monomials + Q4 = podptr->Q4; // number of four-body monomial coefficients + nClusters = podptr->nClusters; // number of environment clusters + nComponents = podptr->nComponents; // number of principal components + Mdesc = podptr->Mdesc; // number of base descriptors + + rin = podptr->rin; + rcut = podptr->rcut; + rmax = rcut - rin; + + MemKK::realloc_kokkos(besselparams, "pair_pod:besselparams", 3); + auto h_besselparams = Kokkos::create_mirror_view(besselparams); + h_besselparams[0] = podptr->besselparams[0]; + h_besselparams[1] = podptr->besselparams[1]; + h_besselparams[2] = podptr->besselparams[2]; + Kokkos::deep_copy(besselparams, h_besselparams); + + MemKK::realloc_kokkos(elemindex, "pair_pod:elemindex", nelements*nelements); + auto h_elemindex = Kokkos::create_mirror_view(elemindex); + for (int i=0; ielemindex[i]; + Kokkos::deep_copy(elemindex, h_elemindex); + + MemKK::realloc_kokkos(Phi, "pair_pod:Phi", ns*ns); + auto h_Phi = Kokkos::create_mirror_view(Phi); + for (int i=0; iPhi[i]; + Kokkos::deep_copy(Phi, h_Phi); + + MemKK::realloc_kokkos(coefficients, "pair_pod:coefficients", nCoeffPerElement * nelements); + auto h_coefficients = Kokkos::create_mirror_view(coefficients); + for (int i=0; icoeff[i]; + Kokkos::deep_copy(coefficients, h_coefficients); + + if (nClusters > 1) { + MemKK::realloc_kokkos(Proj, "pair_pod:Proj", Mdesc * nComponents * nelements); + auto h_Proj = Kokkos::create_mirror_view(Proj); + for (int i=0; iProj[i]; + Kokkos::deep_copy(Proj, h_Proj); + + MemKK::realloc_kokkos(Centroids, "pair_pod:Centroids", nClusters * nComponents * nelements); + auto h_Centroids = Kokkos::create_mirror_view(Centroids); + for (int i=0; iCentroids[i]; + Kokkos::deep_copy(Centroids, h_Centroids); + } + + MemKK::realloc_kokkos(pn3, "pair_pod:pn3", nabf3+1); // array stores the number of monomials for each degree + MemKK::realloc_kokkos(pq3, "pair_pod:pq3", K3*2); // array needed for the recursive computation of the angular basis functions + MemKK::realloc_kokkos(pc3, "pair_pod:pc3", K3); // array needed for the computation of the three-body descriptors + MemKK::realloc_kokkos(pa4, "pair_pod:pa4", nabf4+1); // this array is a subset of the array {0, 1, 4, 10, 19, 29, 47, 74, 89, 119, 155, 209, 230, 275, 335, 425, 533, 561, 624, 714, 849, 949, 1129, 1345} + MemKK::realloc_kokkos(pb4, "pair_pod:pb4", Q4*3); // array stores the indices of the monomials needed for the computation of the angular basis functions + MemKK::realloc_kokkos(pc4, "pair_pod:pc4", Q4); // array of monomial coefficients needed for the computation of the four-body descriptors + + auto h_pn3 = Kokkos::create_mirror_view(pn3); + for (int i=0; ipn3[i]; + Kokkos::deep_copy(pn3, h_pn3); + + auto h_pq3 = Kokkos::create_mirror_view(pq3); + for (int i = 0; i < K3*2; i++) h_pq3[i] = podptr->pq3[i]; + Kokkos::deep_copy(pq3, h_pq3); + + auto h_pc3 = Kokkos::create_mirror_view(pc3); + for (int i = 0; i < K3; i++) h_pc3[i] = podptr->pc3[i]; + Kokkos::deep_copy(pc3, h_pc3); + + auto h_pa4 = Kokkos::create_mirror_view(pa4); + for (int i = 0; i < nabf4+1; i++) h_pa4[i] = podptr->pa4[i]; + Kokkos::deep_copy(pa4, h_pa4); + + auto h_pb4 = Kokkos::create_mirror_view(pb4); + for (int i = 0; i < Q4*3; i++) h_pb4[i] = podptr->pb4[i]; + Kokkos::deep_copy(pb4, h_pb4); + + auto h_pc4 = Kokkos::create_mirror_view(pc4); + for (int i = 0; i < Q4; i++) h_pc4[i] = podptr->pc4[i]; + Kokkos::deep_copy(pc4, h_pc4); + + MemKK::realloc_kokkos(ind33l, "pair_pod:ind33l", nl33); + MemKK::realloc_kokkos(ind33r, "pair_pod:ind33r", nl33); + MemKK::realloc_kokkos(ind34l, "pair_pod:ind34l", nl34); + MemKK::realloc_kokkos(ind34r, "pair_pod:ind34r", nl34); + MemKK::realloc_kokkos(ind44l, "pair_pod:ind44l", nl44); + MemKK::realloc_kokkos(ind44r, "pair_pod:ind44r", nl44); + + auto h_ind33l = Kokkos::create_mirror_view(ind33l); + for (int i = 0; i < nl33; i++) h_ind33l[i] = podptr->ind33l[i]; + Kokkos::deep_copy(ind33l, h_ind33l); + + auto h_ind33r = Kokkos::create_mirror_view(ind33r); + for (int i = 0; i < nl33; i++) h_ind33r[i] = podptr->ind33r[i]; + Kokkos::deep_copy(ind33r, h_ind33r); + + auto h_ind34l = Kokkos::create_mirror_view(ind34l); + for (int i = 0; i < nl34; i++) h_ind34l[i] = podptr->ind34l[i]; + Kokkos::deep_copy(ind34l, h_ind34l); + + auto h_ind34r = Kokkos::create_mirror_view(ind34r); + for (int i = 0; i < nl34; i++) h_ind34r[i] = podptr->ind34r[i]; + Kokkos::deep_copy(ind34r, h_ind34r); + + auto h_ind44l = Kokkos::create_mirror_view(ind44l); + for (int i = 0; i < nl44; i++) h_ind44l[i] = podptr->ind44l[i]; + Kokkos::deep_copy(ind44l, h_ind44l); + + auto h_ind44r = Kokkos::create_mirror_view(ind44r); + for (int i = 0; i < nl44; i++) h_ind44r[i] = podptr->ind44r[i]; + Kokkos::deep_copy(ind44r, h_ind44r); +} + +template +void PairPODKokkos::divideInterval(int *intervals, int N, int M) +{ + int intervalSize = N / M; // Basic size of each interval + int remainder = N % M; // Remainder to distribute + intervals[0] = 1; // Start of the first interval + for (int i = 1; i <= M; i++) { + intervals[i] = intervals[i - 1] + intervalSize + (remainder > 0 ? 1 : 0); + if (remainder > 0) { + remainder--; + } + } +} + +template +int PairPODKokkos::calculateNumberOfIntervals(int N, int intervalSize) +{ + int M = N / intervalSize; + if (N % intervalSize != 0) { + M++; // Add an additional interval to cover the remainder + } + + return M; +} + +template +void PairPODKokkos::grow_atoms(int Ni) +{ + if (Ni > nimax) { + nimax = Ni; + MemKK::realloc_kokkos(numij, "pair_pod:numij", nimax+1); + MemKK::realloc_kokkos(ei, "pair_pod:ei", nimax); + MemKK::realloc_kokkos(typeai, "pair_pod:typeai", nimax); + int n = nimax * nelements * K3 * nrbfmax; + MemKK::realloc_kokkos(sumU, "pair_pod:sumU", n); + MemKK::realloc_kokkos(forcecoeff, "pair_pod:forcecoeff", n); + MemKK::realloc_kokkos(bd, "pair_pod:bd", nimax * Mdesc); + MemKK::realloc_kokkos(cb, "pair_pod:cb", nimax * Mdesc); + if (nClusters > 1)MemKK::realloc_kokkos(pd, "pair_pod:pd", nimax * (1 + nComponents + 3*nClusters)); + Kokkos::deep_copy(numij, 0); + } +} + +template +void PairPODKokkos::grow_pairs(int Nij) +{ + if (Nij > nijmax) { + nijmax = Nij; + MemKK::realloc_kokkos(rij, "pair_pod:r_ij", 3 * nijmax); + MemKK::realloc_kokkos(fij, "pair_pod:f_ij", 3 * nijmax); + MemKK::realloc_kokkos(idxi, "pair_pod:idxi", nijmax); + MemKK::realloc_kokkos(ai, "pair_pod:ai", nijmax); + MemKK::realloc_kokkos(aj, "pair_pod:aj", nijmax); + MemKK::realloc_kokkos(ti, "pair_pod:ti", nijmax); + MemKK::realloc_kokkos(tj, "pair_pod:tj", nijmax); + MemKK::realloc_kokkos(rbf, "pair_pod:rbf", nijmax * nrbfmax); + MemKK::realloc_kokkos(rbfx, "pair_pod:rbfx", nijmax * nrbfmax); + MemKK::realloc_kokkos(rbfy, "pair_pod:rbfy", nijmax * nrbfmax); + MemKK::realloc_kokkos(rbfz, "pair_pod:rbfz", nijmax * nrbfmax); + int kmax = (K3 > ns) ? K3 : ns; + MemKK::realloc_kokkos(abf, "pair_pod:abf", nijmax * kmax); + MemKK::realloc_kokkos(abfx, "pair_pod:abfx", nijmax * kmax); + MemKK::realloc_kokkos(abfy, "pair_pod:abfy", nijmax * kmax); + MemKK::realloc_kokkos(abfz, "pair_pod:abfz", nijmax * kmax); + } +} + +template +int PairPODKokkos::NeighborCount(t_pod_1i l_numij, double l_rcutsq, int gi1, int Ni) +{ + // create local shadow views for KOKKOS_LAMBDA to pass them into parallel_for + auto l_ilist = d_ilist; + auto l_x = x; + auto l_numneigh = d_numneigh; + auto l_neighbors = d_neighbors; + + // compute number of pairs for each atom i + Kokkos::parallel_for("NeighborCount", Kokkos::TeamPolicy<>(Ni, Kokkos::AUTO), KOKKOS_LAMBDA(const Kokkos::TeamPolicy<>::member_type& team) { + int i = team.league_rank(); + int gi = l_ilist(gi1 + i); + double xi0 = l_x(gi, 0); + double xi1 = l_x(gi, 1); + double xi2 = l_x(gi, 2); + int jnum = l_numneigh(gi); + int ncount = 0; + Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team,jnum), + [&] (const int jj, int& count) { + int j = l_neighbors(gi,jj); + j &= NEIGHMASK; + double delx = xi0 - l_x(j,0); + double dely = xi1 - l_x(j,1); + double delz = xi2 - l_x(j,2); + double rsq = delx*delx + dely*dely + delz*delz; + if (rsq < l_rcutsq) count++; + },ncount); + + l_numij(i+1) = ncount; + }); + + // accumalative sum + Kokkos::parallel_scan("InclusivePrefixSum", Ni + 1, KOKKOS_LAMBDA(int i, int& update, const bool final) { + if (i > 0) { + update += l_numij(i); + if (final) { + l_numij(i) = update; + } + } + }); + + int total_neighbors = 0; + Kokkos::deep_copy(Kokkos::View(&total_neighbors), Kokkos::subview(l_numij, Ni)); + + return total_neighbors; +} + +template +void PairPODKokkos::NeighborList(t_pod_1d l_rij, t_pod_1i l_numij, t_pod_1i l_typeai, + t_pod_1i l_idxi, t_pod_1i l_ai, t_pod_1i l_aj, t_pod_1i l_ti, t_pod_1i l_tj, double l_rcutsq, int gi1, int Ni) +{ + // create local shadow views for KOKKOS_LAMBDA to pass them into parallel_for + auto l_ilist = d_ilist; + auto l_x = x; + auto l_numneigh = d_numneigh; + auto l_neighbors = d_neighbors; + auto l_map = d_map; + auto l_type = type; + + Kokkos::parallel_for("NeighborList", Kokkos::TeamPolicy<>(Ni, Kokkos::AUTO), KOKKOS_LAMBDA(const Kokkos::TeamPolicy<>::member_type& team) { + int i = team.league_rank(); + int gi = l_ilist(gi1 + i); + double xi0 = l_x(gi, 0); + double xi1 = l_x(gi, 1); + double xi2 = l_x(gi, 2); + int itype = l_map(l_type(gi)) + 1; //map[atomtypes[gi]] + 1; + l_typeai(i) = itype; + int jnum = l_numneigh(gi); + int nij0 = l_numij(i); + Kokkos::parallel_scan(Kokkos::TeamThreadRange(team,jnum), + [&] (const int jj, int& offset, bool final) { + int gj = l_neighbors(gi,jj); + gj &= NEIGHMASK; + double delx = l_x(gj,0) - xi0; + double dely = l_x(gj,1) - xi1; + double delz = l_x(gj,2) - xi2; + double rsq = delx*delx + dely*dely + delz*delz; + if (rsq >= l_rcutsq) return; + if (final) { + int nij1 = nij0 + offset; + l_rij(nij1 * 3 + 0) = delx; + l_rij(nij1 * 3 + 1) = dely; + l_rij(nij1 * 3 + 2) = delz; + l_idxi(nij1) = i; + l_ai(nij1) = gi; + l_aj(nij1) = gj; + l_ti(nij1) = itype; + l_tj(nij1) = l_map(l_type(gj)) + 1; //map[atomtypes[gj)) + 1; + } + offset++; + }); + }); +} + +template +void PairPODKokkos::radialbasis(t_pod_1d rbft, t_pod_1d rbftx, t_pod_1d rbfty, t_pod_1d rbftz, + t_pod_1d l_rij, t_pod_1d l_besselparams, double l_rin, double l_rmax, int l_besseldegree, + int l_inversedegree, int l_nbesselpars, int Nij) +{ + Kokkos::parallel_for("ComputeRadialBasis", Nij, KOKKOS_LAMBDA(int n) { + double xij1 = l_rij(0+3*n); + double xij2 = l_rij(1+3*n); + double xij3 = l_rij(2+3*n); + + double dij = sqrt(xij1*xij1 + xij2*xij2 + xij3*xij3); + double dr1 = xij1/dij; + double dr2 = xij2/dij; + double dr3 = xij3/dij; + + double r = dij - l_rin; + double y = r/l_rmax; + double y2 = y*y; + + double y3 = 1.0 - y2*y; + double y4 = y3*y3 + 1e-6; + double y5 = sqrt(y4); + double y6 = exp(-1.0/y5); + double y7 = y4*sqrt(y4); + + // Calculate the final cutoff function as y6/exp(-1) + double fcut = y6/exp(-1.0); + + // Calculate the derivative of the final cutoff function + double dfcut = ((3.0/(l_rmax*exp(-1.0)))*(y2)*y6*(y*y2 - 1.0))/y7; + + // Calculate fcut/r, fcut/r^2, and dfcut/r + double f1 = fcut/r; + double f2 = f1/r; + double df1 = dfcut/r; + + double alpha = l_besselparams(0); + double t1 = (1.0-exp(-alpha)); + double t2 = exp(-alpha*r/l_rmax); + double x0 = (1.0 - t2)/t1; + double dx0 = (alpha/l_rmax)*t2/t1; + + alpha = l_besselparams(1); + t1 = (1.0-exp(-alpha)); + t2 = exp(-alpha*r/l_rmax); + double x1 = (1.0 - t2)/t1; + double dx1 = (alpha/l_rmax)*t2/t1; + + alpha = l_besselparams(2); + t1 = (1.0-exp(-alpha)); + t2 = exp(-alpha*r/l_rmax); + double x2 = (1.0 - t2)/t1; + double dx2 = (alpha/l_rmax)*t2/t1; + + for (int i=0; i +void PairPODKokkos::matrixMultiply(t_pod_1d a, t_pod_1d b, t_pod_1d c, int r1, int c1, int c2) +{ + Kokkos::parallel_for("MatrixMultiply", r1 * c2, KOKKOS_LAMBDA(int idx) { + int j = idx / r1; // Calculate column index + int i = idx % r1; // Calculate row index + double sum = 0.0; + for (int k = 0; k < c1; ++k) { + sum += a(i + r1*k) * b(k + c1*j); // Manually calculate the 1D index + } + c(i + r1*j) = sum; // Manually calculate the 1D index for c + }); +} + +template +void PairPODKokkos::angularbasis(t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, + t_pod_1d l_rij, t_pod_1i l_pq3, int l_K3, int N) +{ + Kokkos::parallel_for("AngularBasis", N, KOKKOS_LAMBDA(int j) { + double x = l_rij(j*3 + 0); + double y = l_rij(j*3 + 1); + double z = l_rij(j*3 + 2); + + double xx = x*x; + double yy = y*y; + double zz = z*z; + double xy = x*y; + double xz = x*z; + double yz = y*z; + + double dij = sqrt(xx + yy + zz); + const double u = x / dij; + const double v = y / dij; + const double w = z / dij; + + double dij3 = dij * dij * dij; + const double dudx = (yy + zz) / dij3; + const double dudy = -xy / dij3; + const double dudz = -xz / dij3; + + const double dvdx = -xy / dij3; + const double dvdy = (xx + zz) / dij3; + const double dvdz = -yz / dij3; + + const double dwdx = -xz / dij3; + const double dwdy = -yz / dij3; + const double dwdz = (xx + yy) / dij3; + + int idxa = j; + l_abf(idxa) = 1.0; + l_abfx(idxa) = 0.0; + l_abfy(idxa) = 0.0; + l_abfz(idxa) = 0.0; + + // Loop over all angular basis functions + for (int n=1; n +void PairPODKokkos::radialangularsum(t_pod_1d l_sumU, t_pod_1d l_rbf, t_pod_1d l_abf, t_pod_1i l_tj, + t_pod_1i l_numij, const int l_nelements, const int l_nrbf3, const int l_K3, const int Ni, const int Nij) +{ + int totalIterations = l_nrbf3 * l_K3 * Ni; + if (l_nelements==1) { + Kokkos::parallel_for("RadialAngularSum", totalIterations, KOKKOS_LAMBDA(int idx) { + int k = idx % l_K3; + int temp = idx / l_K3; + int m = temp % l_nrbf3; + int i = temp / l_nrbf3; + int kmi = k + l_K3*m + l_K3*l_nrbf3*i; + + int start = l_numij(i); + int nj = l_numij(i+1)-start; + double sum=0.0; + for (int j=0; j +void PairPODKokkos::twobodydesc(t_pod_1d d2, t_pod_1d l_rbf, t_pod_1i l_idxi, t_pod_1i l_tj, + int l_nrbf2, const int Ni, const int Nij) +{ + int totalIterations = l_nrbf2 * Nij; + Kokkos::parallel_for("twobodydesc", totalIterations, KOKKOS_LAMBDA(int idx) { + int n = idx / l_nrbf2; // pair index + int m = idx % l_nrbf2; // rbd index + int i2 = n + Nij * m; // Index of the radial basis function for atom n and RBF m + Kokkos::atomic_add(&d2(l_idxi(n) + Ni * (m + l_nrbf2 * (l_tj(n) - 1))), l_rbf(i2)); // Add the radial basis function to the corresponding descriptor + }); +} + +template +void PairPODKokkos::twobody_forces(t_pod_1d fij, t_pod_1d cb2, t_pod_1d l_rbfx, t_pod_1d l_rbfy, + t_pod_1d l_rbfz, t_pod_1i l_idxi, t_pod_1i l_tj, int l_nrbf2, const int Ni, const int Nij) +{ + int totalIterations = l_nrbf2 * Nij; + Kokkos::parallel_for("twobody_forces", totalIterations, KOKKOS_LAMBDA(int idx) { + int n = idx / l_nrbf2; // pair index + int m = idx % l_nrbf2; // rbd index + int i2 = n + Nij * m; // Index of the radial basis function for atom n and RBF m + int i1 = 3*n; + double c = cb2(l_idxi(n) + Ni*m + Ni*l_nrbf2*(l_tj(n) - 1)); + Kokkos::atomic_add(&fij(0 + i1), c*l_rbfx(i2)); // Add the derivative with respect to x to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(1 + i1), c*l_rbfy(i2)); // Add the derivative with respect to y to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(2 + i1), c*l_rbfz(i2)); // Add the derivative with respect to z to the corresponding descriptor derivative + }); +} + +template +void PairPODKokkos::threebodydesc(t_pod_1d d3, t_pod_1d l_sumU, t_pod_1i l_pc3, t_pod_1i l_pn3, + int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, const int Ni) +{ + int totalIterations = l_nrbf3 * Ni; + Kokkos::parallel_for("ThreeBodyDesc", totalIterations, KOKKOS_LAMBDA(int idx) { + int m = idx % l_nrbf3; + int i = idx / l_nrbf3; + int nmi = l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3*i; + for (int p = 0; p < l_nabf3; p++) { + int n1 = l_pn3(p); + int n2 = l_pn3(p + 1); + int nn = n2 - n1; + int ipm = i + Ni * (p + l_nabf3 * m); + int k = 0; + for (int i1 = 0; i1 < l_nelements; i1++) { + for (int i2 = i1; i2 < l_nelements; i2++) { + double tmp=0; + for (int q = 0; q < nn; q++) { + tmp += l_pc3(n1 + q) * l_sumU(i1 + l_nelements * (n1 + q) + nmi) * l_sumU(i2 + l_nelements * (n1 + q) + nmi); + } + d3(ipm + totalIterations * l_nabf3 * k) = tmp; + k += 1; + } + } + } + }); +} + +template +void PairPODKokkos::threebody_forces(t_pod_1d fij, t_pod_1d cb3, t_pod_1d l_rbf, t_pod_1d l_rbfx, + t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, + t_pod_1d l_sumU, t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pc3, t_pod_1i l_pn3, t_pod_1i l_elemindex, + int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, int Ni, int Nij) +{ + int totalIterations = l_nrbf3 * Nij; + if (l_nelements==1) { + Kokkos::parallel_for("threebody_forces1", totalIterations, KOKKOS_LAMBDA(int idx) { + int j = idx / l_nrbf3; // Calculate j using integer division + int m = idx % l_nrbf3; // Calculate m using modulo operation + int idxR = j + Nij * m; // Pre-compute the index for rbf + double rbfBase = l_rbf(idxR); + double rbfxBase = l_rbfx(idxR); + double rbfyBase = l_rbfy(idxR); + double rbfzBase = l_rbfz(idxR); + double fx = 0; + double fy = 0; + double fz = 0; + for (int p = 0; p < l_nabf3; p++) { + double c3 = 2.0 * cb3(l_idxi(j) + Ni*p + Ni*l_nabf3*m); + int n1 = l_pn3(p); + int nn = l_pn3(p + 1) - n1; + int idxU = l_K3 * m + l_K3*l_nrbf3*l_idxi(j); + for (int q = 0; q < nn; q++) { + int idxNQ = n1 + q; // Combine n1 and q into a single index for pc3 and sumU + double f = c3 * l_pc3(idxNQ) * l_sumU(idxNQ + idxU); + int idxA = j + Nij*idxNQ; // Pre-compute the index for abf + double abfA = l_abf(idxA); + + // Use the pre-computed indices to update dd3 + fx += f * (l_abfx(idxA) * rbfBase + rbfxBase * abfA); + fy += f * (l_abfy(idxA) * rbfBase + rbfyBase * abfA); + fz += f * (l_abfz(idxA) * rbfBase + rbfzBase * abfA); + } + } + int ii = 3 * j; // Pre-compute the base index for dd3 + Kokkos::atomic_add(&fij(0 + ii), fx); // Add the derivative with respect to x to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(1 + ii), fy); // Add the derivative with respect to y to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(2 + ii), fz); // Add the derivative with respect to z to the corresponding descriptor derivative + }); + } + else { + int N3 = Ni * l_nabf3 * l_nrbf3; + Kokkos::parallel_for("threebody_forces2", totalIterations, KOKKOS_LAMBDA(int idx) { + int j = idx / l_nrbf3; // Derive the original j value + int m = idx % l_nrbf3; // Derive the original m value + int i2 = l_tj(j) - 1; + int idxK = l_nelements * l_K3 * m + l_nelements*l_K3*l_nrbf3*l_idxi(j); + int idxR = j + Nij * m; // Pre-compute the index for rbf + double rbfBase = l_rbf(idxR); + double rbfxBase = l_rbfx(idxR); + double rbfyBase = l_rbfy(idxR); + double rbfzBase = l_rbfz(idxR); + double fx = 0; + double fy = 0; + double fz = 0; + for (int p = 0; p < l_nabf3; p++) { + int n1 = l_pn3(p); + int nn = l_pn3(p + 1) - n1; + int jmp = l_idxi(j) + Ni*(p + l_nabf3*m); + for (int i1 = 0; i1 < l_nelements; i1++) { + double c3 = (i1 == i2) ? 2.0 : 1.0; + c3 = c3 * cb3(jmp + N3*l_elemindex(i2 + l_nelements * i1)); + for (int q = 0; q < nn; q++) { + int idxNQ = n1 + q; // Combine n1 and q into a single index + int idxA = j + Nij*idxNQ; // Pre-compute the index for abf + double abfA = l_abf(idxA); + double f = c3 * l_pc3(idxNQ) * l_sumU(i1 + l_nelements * idxNQ + idxK); + fx += f * (l_abfx(idxA) * rbfBase + rbfxBase * abfA); + fy += f * (l_abfy(idxA) * rbfBase + rbfyBase * abfA); + fz += f * (l_abfz(idxA) * rbfBase + rbfzBase * abfA); + } + } + } + int ii = 3 * j; // Pre-compute the base index for dd3 + Kokkos::atomic_add(&fij(0 + ii), fx); // Add the derivative with respect to x to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(1 + ii), fy); // Add the derivative with respect to y to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(2 + ii), fz); // Add the derivative with respect to z to the corresponding descriptor derivative + }); + } +} + +template +void PairPODKokkos::threebody_forcecoeff(t_pod_1d fb3, t_pod_1d cb3, + t_pod_1d l_sumU, t_pod_1i l_pc3, t_pod_1i l_pn3, t_pod_1i l_elemindex, + int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, int Ni) +{ + int totalIterations = l_nrbf3 * Ni; + if (l_nelements==1) { + Kokkos::parallel_for("threebody_forcecoeff1", totalIterations, KOKKOS_LAMBDA(int idx) { + int i = idx / l_nrbf3; // Calculate j using integer division + int m = idx % l_nrbf3; // Calculate m using modulo operation + for (int p = 0; p < l_nabf3; p++) { + double c3 = 2.0 * cb3(i + Ni*p + Ni*l_nabf3*m); + int n1 = l_pn3(p); + int nn = l_pn3(p + 1) - n1; + int idxU = l_K3 * m + l_K3*l_nrbf3*i; + for (int q = 0; q < nn; q++) { + int idxNQ = n1 + q; // Combine n1 and q into a single index for pc3 and sumU + fb3(idxNQ + idxU) += c3 * l_pc3(idxNQ) * l_sumU(idxNQ + idxU); + } + } + }); + } + else { + int N3 = Ni * l_nabf3 * l_nrbf3; + Kokkos::parallel_for("threebody_forcecoeff2", totalIterations, KOKKOS_LAMBDA(int idx) { + int i = idx / l_nrbf3; // Derive the original j value + int m = idx % l_nrbf3; // Derive the original m value + for (int p = 0; p < l_nabf3; p++) { + int n1 = l_pn3(p); + int nn = l_pn3(p + 1) - n1; + int jmp = i + Ni*(p + l_nabf3*m); + for (int q = 0; q < nn; q++) { + int k = n1 + q; // Combine n1 and q into a single index + int idxU = l_nelements * k + l_nelements * l_K3 * m + l_nelements*l_K3*l_nrbf3*i; + for (int i1 = 0; i1 < l_nelements; i1++) { + double tm = l_pc3[k] * l_sumU[i1 + idxU]; + for (int i2 = i1; i2 < l_nelements; i2++) { + int em = l_elemindex[i2 + l_nelements * i1]; + double t1 = tm * cb3[jmp + N3*em]; // Ni * nabf3 * nrbf3 * nelements*(nelements+1)/2 + fb3[i2 + idxU] += t1; // K3*nrbf3*Ni + fb3[i1 + idxU] += l_pc3[k] * cb3[jmp + N3*em] * l_sumU[i2 + idxU]; + } + } + } + } + }); + } +} + +template +void PairPODKokkos::fourbodydesc(t_pod_1d d4, t_pod_1d l_sumU, t_pod_1i l_pa4, t_pod_1i l_pb4, + t_pod_1i l_pc4, int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni) +{ + int totalIterations = l_nrbf4 * Ni; + Kokkos::parallel_for("fourbodydesc", totalIterations, KOKKOS_LAMBDA(int idx) { + int m = idx % l_nrbf4; + int i = idx / l_nrbf4; + int idxU = l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3 * i; + for (int p = 0; p < l_nabf4; p++) { + int n1 = l_pa4(p); + int n2 = l_pa4(p + 1); + int nn = n2 - n1; + int k = 0; + for (int i1 = 0; i1 < l_nelements; i1++) { + for (int i2 = i1; i2 < l_nelements; i2++) { + for (int i3 = i2; i3 < l_nelements; i3++) { + double tmp = 0.0; + for (int q = 0; q < nn; q++) { + int c = l_pc4(n1 + q); + int j1 = l_pb4(n1 + q); + int j2 = l_pb4(n1 + q + l_Q4); + int j3 = l_pb4(n1 + q + 2 * l_Q4); + tmp += c * l_sumU(idxU + i1 + l_nelements * j1) * l_sumU(idxU + i2 + l_nelements * j2) * l_sumU(idxU + i3 + l_nelements * j3); + } + int kk = p + l_nabf4 * m + l_nabf4 * l_nrbf4 * k; + d4(i + Ni * kk) = tmp; + k += 1; + } + } + } + } + }); +} + +template +void PairPODKokkos::fourbody_forces(t_pod_1d fij, t_pod_1d cb4, t_pod_1d l_rbf, t_pod_1d l_rbfx, + t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, + t_pod_1d l_sumU, t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, + int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni, int Nij) +{ + int totalIterations = l_nrbf4 * Nij; + if (l_nelements==1) { + Kokkos::parallel_for("fourbody_forces1", totalIterations, KOKKOS_LAMBDA(int idx) { + int j = idx / l_nrbf4; // Derive the original j value + int m = idx % l_nrbf4; // Derive the original m value + int idxU = l_K3 * m + l_K3*l_nrbf3*l_idxi(j); + int baseIdxJ = j + Nij * m; // Pre-compute the index for rbf + double rbfBase = l_rbf(baseIdxJ); + double rbfxBase = l_rbfx(baseIdxJ); + double rbfyBase = l_rbfy(baseIdxJ); + double rbfzBase = l_rbfz(baseIdxJ); + double fx = 0; + double fy = 0; + double fz = 0; + for (int p = 0; p < l_nabf4; p++) { + int n1 = l_pa4(p); + int n2 = l_pa4(p + 1); + int nn = n2 - n1; + double c4 = cb4(l_idxi(j) + Ni*p + Ni*l_nabf4*m); + for (int q = 0; q < nn; q++) { + int idxNQ = n1 + q; // Combine n1 and q into a single index + double c = c4 * l_pc4[idxNQ]; + int j1 = l_pb4(idxNQ); + int j2 = l_pb4(idxNQ + l_Q4); + int j3 = l_pb4(idxNQ + 2 * l_Q4); + double c1 = l_sumU(idxU + j1); + double c2 = l_sumU(idxU + j2); + double c3 = l_sumU(idxU + j3); + double t12 = c * c1 * c2; + double t13 = c * c1 * c3; + double t23 = c * c2 * c3; + + // Pre-calculate commonly used indices + int baseIdxJ3 = j + Nij * j3; // Common index for j3 terms + int baseIdxJ2 = j + Nij * j2; // Common index for j2 terms + int baseIdxJ1 = j + Nij * j1; // Common index for j1 terms + + // Temporary variables to store repeated calculations + double abfBaseJ1 = l_abf(baseIdxJ1); + double abfBaseJ2 = l_abf(baseIdxJ2); + double abfBaseJ3 = l_abf(baseIdxJ3); + // Update dd4 using pre-computed indices + fx += t12 * (l_abfx(baseIdxJ3) * rbfBase + rbfxBase * abfBaseJ3) + + t13 * (l_abfx(baseIdxJ2) * rbfBase + rbfxBase * abfBaseJ2) + + t23 * (l_abfx(baseIdxJ1) * rbfBase + rbfxBase * abfBaseJ1); + fy += t12 * (l_abfy(baseIdxJ3) * rbfBase + rbfyBase * abfBaseJ3) + + t13 * (l_abfy(baseIdxJ2) * rbfBase + rbfyBase * abfBaseJ2) + + t23 * (l_abfy(baseIdxJ1) * rbfBase + rbfyBase * abfBaseJ1); + fz += t12 * (l_abfz(baseIdxJ3) * rbfBase + rbfzBase * abfBaseJ3) + + t13 * (l_abfz(baseIdxJ2) * rbfBase + rbfzBase * abfBaseJ2) + + t23 * (l_abfz(baseIdxJ1) * rbfBase + rbfzBase * abfBaseJ1); + } + } + int ii = 3 * j; // Pre-compute the base index for dd3 + Kokkos::atomic_add(&fij(0 + ii), fx); // Add the derivative with respect to x to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(1 + ii), fy); // Add the derivative with respect to y to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(2 + ii), fz); // Add the derivative with respect to z to the corresponding descriptor derivative + }); + } + else { + int N3 = Ni * l_nabf4 * l_nrbf4; + Kokkos::parallel_for("fourbody_forces2", totalIterations, KOKKOS_LAMBDA(int idx) { + int j = idx / l_nrbf4; // Derive the original j value + int m = idx % l_nrbf4; // Derive the original m value + int idxM = j + Nij * m; + double rbfM = l_rbf(idxM); + double rbfxM = l_rbfx(idxM); + double rbfyM = l_rbfy(idxM); + double rbfzM = l_rbfz(idxM); + int typej = l_tj(j) - 1; + double fx = 0; + double fy = 0; + double fz = 0; + for (int p = 0; p < l_nabf4; p++) { + int n1 = l_pa4(p); + int n2 = l_pa4(p + 1); + int nn = n2 - n1; + int jpm = l_idxi(j) + Ni*p + Ni*l_nabf4*m; + int k = 0; + for (int i1 = 0; i1 < l_nelements; i1++) { + for (int i2 = i1; i2 < l_nelements; i2++) { + for (int i3 = i2; i3 < l_nelements; i3++) { + for (int q = 0; q < nn; q++) { + double c = l_pc4(n1 + q) * cb4(jpm + N3*k); + int j1 = l_pb4(n1 + q); + int j2 = l_pb4(n1 + q + l_Q4); + int j3 = l_pb4(n1 + q + 2 * l_Q4); + + int idx1 = i1 + l_nelements * j1 + l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3 * l_idxi(j); + int idx2 = i2 + l_nelements * j2 + l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3 * l_idxi(j); + int idx3 = i3 + l_nelements * j3 + l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3 * l_idxi(j); + double c1 = l_sumU(idx1); + double c2 = l_sumU(idx2 ); + double c3 = l_sumU(idx3); + double t12 = c*(c1 * c2); + double t13 = c*(c1 * c3); + double t23 = c*(c2 * c3); + + int idxJ3 = j + Nij * j3; + int idxJ2 = j + Nij * j2; + int idxJ1 = j + Nij * j1; + double abfJ1 = l_abf(idxJ1); + double abfJ2 = l_abf(idxJ2); + double abfJ3 = l_abf(idxJ3); + double abfxJ1 = l_abfx(idxJ1); + double abfxJ2 = l_abfx(idxJ2); + double abfxJ3 = l_abfx(idxJ3); + double abfyJ1 = l_abfy(idxJ1); + double abfyJ2 = l_abfy(idxJ2); + double abfyJ3 = l_abfy(idxJ3); + double abfzJ1 = l_abfz(idxJ1); + double abfzJ2 = l_abfz(idxJ2); + double abfzJ3 = l_abfz(idxJ3); + + // Compute contributions for each condition + if (typej == i3) { + fx += t12 * (abfxJ3 * rbfM + rbfxM * abfJ3); + fy += t12 * (abfyJ3 * rbfM + rbfyM * abfJ3); + fz += t12 * (abfzJ3 * rbfM + rbfzM * abfJ3); + } + if (typej == i2) { + fx += t13 * (abfxJ2 * rbfM + rbfxM * abfJ2); + fy += t13 * (abfyJ2 * rbfM + rbfyM * abfJ2); + fz += t13 * (abfzJ2 * rbfM + rbfzM * abfJ2); + } + if (typej == i1) { + fx += t23 * (abfxJ1 * rbfM + rbfxM * abfJ1); + fy += t23 * (abfyJ1 * rbfM + rbfyM * abfJ1); + fz += t23 * (abfzJ1 * rbfM + rbfzM * abfJ1); + } + } + k += 1; + } + } + } + } + int ii = 3 * j; // Pre-compute the base index for dd3 + Kokkos::atomic_add(&fij(0 + ii), fx); // Add the derivative with respect to x to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(1 + ii), fy); // Add the derivative with respect to y to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(2 + ii), fz); // Add the derivative with respect to z to the corresponding descriptor derivative + }); + } +} + +template +void PairPODKokkos::fourbody_forcecoeff(t_pod_1d fb4, t_pod_1d cb4, + t_pod_1d l_sumU, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, int l_nelements, + int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni) +{ + int totalIterations = l_nrbf4 * Ni; + if (l_nelements==1) { + Kokkos::parallel_for("fourbody_forcecoeff1", totalIterations, KOKKOS_LAMBDA(int idx) { + int i = idx / l_nrbf4; // Derive the original j value + int m = idx % l_nrbf4; // Derive the original m value + int idxU = l_K3 * m + l_K3*l_nrbf3*i; + for (int p = 0; p < l_nabf4; p++) { + int n1 = l_pa4(p); + int n2 = l_pa4(p + 1); + int nn = n2 - n1; + double c4 = cb4(i + Ni*p + Ni*l_nabf4*m); + for (int q = 0; q < nn; q++) { + int idxNQ = n1 + q; // Combine n1 and q into a single index + double c = c4 * l_pc4[idxNQ]; + int j1 = idxU + l_pb4(idxNQ); + int j2 = idxU + l_pb4(idxNQ + l_Q4); + int j3 = idxU + l_pb4(idxNQ + 2 * l_Q4); + double c1 = l_sumU(j1); + double c2 = l_sumU(j2); + double c3 = l_sumU(j3); + fb4[j3] += c * c1 * c2; + fb4[j2] += c * c1 * c3; + fb4[j1] += c * c2 * c3; + } + } + }); + } + else { + int N3 = Ni * l_nabf4 * l_nrbf4; + Kokkos::parallel_for("fourbody_forcecoeff2", totalIterations, KOKKOS_LAMBDA(int idx) { + int i = idx / l_nrbf4; // Derive the original j value + int m = idx % l_nrbf4; // Derive the original m value + for (int p = 0; p < l_nabf4; p++) { + int n1 = l_pa4(p); + int n2 = l_pa4(p + 1); + int nn = n2 - n1; + int jpm = i + Ni*p + Ni*l_nabf4*m; + for (int q = 0; q < nn; q++) { + double c = l_pc4(n1 + q); + int j1 = l_pb4(n1 + q); + int j2 = l_pb4(n1 + q + l_Q4); + int j3 = l_pb4(n1 + q + 2 * l_Q4); + int idx1 = l_nelements * j1 + l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3 * i; + int idx2 = l_nelements * j2 + l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3 * i; + int idx3 = l_nelements * j3 + l_nelements * l_K3 * m + l_nelements * l_K3 * l_nrbf3 * i; + int k = 0; + for (int i1 = 0; i1 < l_nelements; i1++) { + double c1 = l_sumU[idx1 + i1]; + for (int i2 = i1; i2 < l_nelements; i2++) { + double c2 = l_sumU[idx2 + i2]; + for (int i3 = i2; i3 < l_nelements; i3++) { + double c3 = l_sumU[idx3 + i3]; + double c4 = c * cb4[jpm + N3*k]; + fb4[idx3 + i3] += c4*(c1 * c2); + fb4[idx2 + i2] += c4*(c1 * c3); + fb4[idx1 + i1] += c4*(c2 * c3); + k += 1; + } + } + } + } + } + }); + } +} + +template +void PairPODKokkos::allbody_forces(t_pod_1d fij, t_pod_1d l_forcecoeff, t_pod_1d l_rbf, t_pod_1d l_rbfx, + t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, + t_pod_1i l_idxi, t_pod_1i l_tj, int l_nelements, int l_nrbf3, int l_K3, int Nij) +{ + int totalIterations = l_nrbf3 * Nij; + Kokkos::parallel_for("allbody_forces", totalIterations, KOKKOS_LAMBDA(int idx) { + int j = idx / l_nrbf3; // Calculate j using integer division + int m = idx % l_nrbf3; // Calculate m using modulo operation + int i2 = l_tj(j) - 1; + int idxR = j + Nij * m; // Pre-compute the index for rbf + double rbfBase = l_rbf(idxR); + double rbfxBase = l_rbfx(idxR); + double rbfyBase = l_rbfy(idxR); + double rbfzBase = l_rbfz(idxR); + double fx = 0; + double fy = 0; + double fz = 0; + for (int k = 0; k < l_K3; k++) { + int idxU = l_nelements * k + l_nelements * l_K3 * m + l_nelements*l_K3*l_nrbf3*l_idxi[j]; + double fc = l_forcecoeff[i2 + idxU]; + int idxA = j + Nij*k; // Pre-compute the index for abf + double abfA = l_abf[idxA]; + double abfxA = l_abfx[idxA]; + double abfyA = l_abfy[idxA]; + double abfzA = l_abfz[idxA]; + fx += fc * (abfxA * rbfBase + rbfxBase * abfA); // K3*nrbf3*Nij + fy += fc * (abfyA * rbfBase + rbfyBase * abfA); + fz += fc * (abfzA * rbfBase + rbfzBase * abfA); + } + int ii = 3 * j; // Pre-compute the base index for dd3 + Kokkos::atomic_add(&fij(0 + ii), fx); // Add the derivative with respect to x to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(1 + ii), fy); // Add the derivative with respect to y to the corresponding descriptor derivative + Kokkos::atomic_add(&fij(2 + ii), fz); // Add the derivative with respect to z to the corresponding descriptor derivative + }); +} + +template +void PairPODKokkos::crossdesc(t_pod_1d d12, t_pod_1d d1, t_pod_1d d2, t_pod_1i ind1, t_pod_1i ind2, int n12, int Ni) +{ + int totalIterations = n12 * Ni; + Kokkos::parallel_for("crossdesc", totalIterations, KOKKOS_LAMBDA(int idx) { + int n = idx % Ni; + int i = idx / Ni; + + d12(n + Ni * i) = d1(n + Ni * ind1(i)) * d2(n + Ni * ind2(i)); + }); +} + +template +void PairPODKokkos::crossdesc_reduction(t_pod_1d cb1, t_pod_1d cb2, t_pod_1d c12, t_pod_1d d1, + t_pod_1d d2, t_pod_1i ind1, t_pod_1i ind2, int n12, int Ni) +{ + int totalIterations = n12 * Ni; + Kokkos::parallel_for("crossdesc_reduction", totalIterations, KOKKOS_LAMBDA(int idx) { + int n = idx % Ni; // Ni + int m = idx / Ni; // n12 + int k1 = ind1(m); // dd1 + int k2 = ind2(m); // dd2 + int m1 = n + Ni * k1; // d1 + int m2 = n + Ni * k2; // d2 + double c = c12(n + Ni * m); + Kokkos::atomic_add(&cb1(m1), c * d2(m2)); + Kokkos::atomic_add(&cb2(m2), c * d1(m1)); + }); +} + +template +void PairPODKokkos::set_array_to_zero(t_pod_1d a, int N) +{ + Kokkos::parallel_for("initialize_array", N, KOKKOS_LAMBDA(int i) { + a(i) = 0.0; + }); +} + +template +void PairPODKokkos::blockatom_base_descriptors(t_pod_1d bd, int Ni, int Nij) +{ + auto begin = std::chrono::high_resolution_clock::now(); + auto end = std::chrono::high_resolution_clock::now(); + + auto d2 = Kokkos::subview(bd, std::make_pair(0, Ni * nl2)); + auto d3 = Kokkos::subview(bd, std::make_pair(Ni * nl2, Ni * (nl2 + nl3))); + auto d4 = Kokkos::subview(bd, std::make_pair(Ni * (nl2 + nl3), Ni * (nl2 + nl3 + nl4))); + auto d33 = Kokkos::subview(bd, std::make_pair(Ni * (nl2 + nl3 + nl4), Ni * (nl2 + nl3 + nl4 + nl33))); + auto d34 = Kokkos::subview(bd, std::make_pair(Ni * (nl2 + nl3 + nl4 + nl33), Ni * (nl2 + nl3 + nl4 + nl33 + nl34))); + auto d44 = Kokkos::subview(bd, std::make_pair(Ni * (nl2 + nl3 + nl4 + nl33 + nl34), Ni * (nl2 + nl3 + nl4 + nl33 + nl34 + nl44))); + + begin = std::chrono::high_resolution_clock::now(); + radialbasis(abf, abfx, abfy, abfz, rij, besselparams, rin, rmax, + besseldegree, inversedegree, nbesselpars, Nij); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[10] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + matrixMultiply(abf, Phi, rbf, Nij, ns, nrbfmax); + matrixMultiply(abfx, Phi, rbfx, Nij, ns, nrbfmax); + matrixMultiply(abfy, Phi, rbfy, Nij, ns, nrbfmax); + matrixMultiply(abfz, Phi, rbfz, Nij, ns, nrbfmax); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[11] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + set_array_to_zero(d2, Ni*nl2); + twobodydesc(d2, rbf, idxi, tj, nrbf2, Ni, Nij); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[12] += std::chrono::duration_cast(end-begin).count()/1e6; + + if ((nl3 > 0) && (Nij>1)) { + begin = std::chrono::high_resolution_clock::now(); + angularbasis(abf, abfx, abfy, abfz, rij, pq3, K3, Nij); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[13] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + set_array_to_zero(sumU, nelements * nrbf3 * K3 * Ni); + radialangularsum(sumU, rbf, abf, tj, numij, nelements, nrbf3, K3, Ni, Nij); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[14] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + //set_array_to_zero(d3, Ni*nl3); + threebodydesc(d3, sumU, pc3, pn3, nelements, nrbf3, nabf3, K3, Ni); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[15] += std::chrono::duration_cast(end-begin).count()/1e6; + } + + if ((nl4 > 0) && (Nij>2)) { + begin = std::chrono::high_resolution_clock::now(); + //set_array_to_zero(d4, Ni*nl4); + fourbodydesc(d4, sumU, pa4, pb4, pc4, nelements, nrbf3, nrbf4, nabf4, K3, Q4, Ni); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[16] += std::chrono::duration_cast(end-begin).count()/1e6; + } + + if ((nl33>0) && (Nij>3)) { + begin = std::chrono::high_resolution_clock::now(); + crossdesc(d33, d3, d3, ind33l, ind33r, nl33, Ni); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[17] += std::chrono::duration_cast(end-begin).count()/1e6; + } + + if ((nl34>0) && (Nij>4)) { + begin = std::chrono::high_resolution_clock::now(); + crossdesc(d34, d3, d4, ind34l, ind34r, nl34, Ni); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[18] += std::chrono::duration_cast(end-begin).count()/1e6; + } + + if ((nl44>0) && (Nij>5)) { + begin = std::chrono::high_resolution_clock::now(); + crossdesc(d44, d4, d4, ind44l, ind44r, nl44, Ni); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[19] += std::chrono::duration_cast(end-begin).count()/1e6; + } +} + +template +void PairPODKokkos::blockatom_base_coefficients(t_pod_1d ei, t_pod_1d cb, t_pod_1d B, int Ni) +{ + auto cefs = coefficients; + auto tyai = typeai; + int nDes = Mdesc; + int nCoeff = nCoeffPerElement; + + Kokkos::parallel_for("atomic_energies", Ni, KOKKOS_LAMBDA(int n) { + int nc = nCoeff*(tyai[n]-1); + ei[n] = cefs[0 + nc]; + for (int m=0; m +void PairPODKokkos::blockatom_environment_descriptors(t_pod_1d ei, t_pod_1d cb, t_pod_1d B, int Ni) +{ + auto P = Kokkos::subview(pd, std::make_pair(0, Ni * nClusters)); + auto cp = Kokkos::subview(pd, std::make_pair(Ni * nClusters, 2 * Ni * nClusters)); + auto D = Kokkos::subview(pd, std::make_pair(2 * Ni * nClusters, 3 * Ni * nClusters)); + auto pca = Kokkos::subview(pd, std::make_pair(3 * Ni * nClusters, 3 * Ni * nClusters + Ni * nComponents)); + auto sumD = Kokkos::subview(pd, std::make_pair(3 * Ni * nClusters + Ni * nComponents, 3 * Ni * nClusters + Ni * nComponents + Ni)); + + auto proj = Proj; + auto cent = Centroids; + auto cefs = coefficients; + auto tyai = typeai; + + int nCom = nComponents; + int nCls = nClusters; + int nDes = Mdesc; + int nCoeff = nCoeffPerElement; + + int totalIterations = Ni*nCom; + Kokkos::parallel_for("pca", totalIterations, KOKKOS_LAMBDA(int idx) { + int i = idx % Ni; + int k = idx / Ni; + double sum = 0.0; + int typei = tyai[i]-1; + for (int m = 0; m < nDes; m++) { + sum += proj[k + nCom*m + nCom*nDes*typei] * B[i + Ni*m]; + } + pca[i + Ni*k] = sum; + }); + + totalIterations = Ni*nCls; + Kokkos::parallel_for("inverse_square_distances", totalIterations, KOKKOS_LAMBDA(int idx) { + int i = idx % Ni; + int j = idx / Ni; + int typei = tyai[i]-1; + double sum = 1e-20; + for (int k = 0; k < nCom; k++) { + double c = cent[k + j * nCom + nCls*nCom*typei]; + double p = pca[i + Ni*k]; + sum += (p - c) * (p - c); + } + D[i + Ni*j] = 1.0 / sum; + }); + + Kokkos::parallel_for("Probabilities", Ni, KOKKOS_LAMBDA(int i) { + double sum = 0; + for (int j = 0; j < nCls; j++) sum += D[i + Ni*j]; + sumD[i] = sum; + for (int j = 0; j < nCls; j++) P[i + Ni*j] = D[i + Ni*j]/sum; + }); + + Kokkos::parallel_for("atomic_energies", Ni, KOKKOS_LAMBDA(int n) { + int nc = nCoeff*(tyai[n]-1); + ei[n] = cefs[0 + nc]; + for (int k = 0; k +void PairPODKokkos::blockatom_energyforce(t_pod_1d l_ei, t_pod_1d l_fij, int Ni, int Nij) +{ + auto begin = std::chrono::high_resolution_clock::now(); + auto end = std::chrono::high_resolution_clock::now(); + + // calculate base descriptors and their derivatives with respect to atom coordinates + begin = std::chrono::high_resolution_clock::now(); + blockatom_base_descriptors(bd, Ni, Nij); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[4] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + if (nClusters > 1) { + blockatom_environment_descriptors(l_ei, cb, bd, Ni); + } + else { + blockatom_base_coefficients(l_ei, cb, bd, Ni); + } + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[5] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + auto d3 = Kokkos::subview(bd, std::make_pair(Ni * nl2, Ni * (nl2 + nl3))); + auto d4 = Kokkos::subview(bd, std::make_pair(Ni * (nl2 + nl3), Ni * (nl2 + nl3 + nl4))); + auto cb2 = Kokkos::subview(cb, std::make_pair(0, Ni * nl2)); + auto cb3 = Kokkos::subview(cb, std::make_pair(Ni * nl2, Ni * (nl2 + nl3))); + auto cb4 = Kokkos::subview(cb, std::make_pair(Ni * (nl2 + nl3), Ni * (nl2 + nl3 + nl4))); + auto cb33 = Kokkos::subview(cb, std::make_pair(Ni * (nl2 + nl3 + nl4), Ni * (nl2 + nl3 + nl4 + nl33))); + auto cb34 = Kokkos::subview(cb, std::make_pair(Ni * (nl2 + nl3 + nl4 + nl33), Ni * (nl2 + nl3 + nl4 + nl33 + nl34))); + auto cb44 = Kokkos::subview(cb, std::make_pair(Ni * (nl2 + nl3 + nl4 + nl33 + nl34), Ni * (nl2 + nl3 + nl4 + nl33 + nl34 + nl44))); + + if ((nl33>0) && (Nij>3)) { + crossdesc_reduction(cb3, cb3, cb33, d3, d3, ind33l, ind33r, nl33, Ni); + } + if ((nl34>0) && (Nij>4)) { + crossdesc_reduction(cb3, cb4, cb34, d3, d4, ind34l, ind34r, nl34, Ni); + } + if ((nl44>0) && (Nij>5)) { + crossdesc_reduction(cb4, cb4, cb44, d4, d4, ind44l, ind44r, nl44, Ni); + } + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[6] += std::chrono::duration_cast(end-begin).count()/1e6; + + begin = std::chrono::high_resolution_clock::now(); + set_array_to_zero(l_fij, 3*Nij); + if ((nl2 > 0) && (Nij>0)) twobody_forces(l_fij, cb2, rbfx, rbfy, rbfz, idxi, tj, nrbf2, Ni, Nij); + Kokkos::fence(); + end = std::chrono::high_resolution_clock::now(); + comptime[7] += std::chrono::duration_cast(end-begin).count()/1e6; + + set_array_to_zero(forcecoeff, nelements * nrbf3 * K3 * Ni); + if ((nl3 > 0) && (Nij>1)) threebody_forcecoeff(forcecoeff, cb3, sumU, + pc3, pn3, elemindex, nelements, nrbf3, nabf3, K3, Ni); + if ((nl4 > 0) && (Nij>2)) fourbody_forcecoeff(forcecoeff, cb4, sumU, + pa4, pb4, pc4, nelements, nrbf3, nrbf4, nabf4, K3, Q4, Ni); + if ((nl3 > 0) && (Nij>1)) allbody_forces(l_fij, forcecoeff, rbf, rbfx, rbfy, rbfz, abf, abfx, abfy, abfz, + idxi, tj, nelements, nrbf3, K3, Nij); +} + +template +void PairPODKokkos::tallyforce(t_pod_1d l_fij, t_pod_1i l_ai, t_pod_1i l_aj, int Nij) +{ + auto l_f = f; + Kokkos::parallel_for("TallyForce", Nij, KOKKOS_LAMBDA(int n) { + int im = l_ai(n); + int jm = l_aj(n); + int n3 = 3*n; + double fx = l_fij(n3 + 0); + double fy = l_fij(n3 + 1); + double fz = l_fij(n3 + 2); + Kokkos::atomic_add(&l_f(im, 0), fx); + Kokkos::atomic_add(&l_f(im, 1), fy); + Kokkos::atomic_add(&l_f(im, 2), fz); + Kokkos::atomic_sub(&l_f(jm, 0), fx); + Kokkos::atomic_sub(&l_f(jm, 1), fy); + Kokkos::atomic_sub(&l_f(jm, 2), fz); + }); +} + +template +void PairPODKokkos::tallyenergy(t_pod_1d l_ei, int istart, int Ni) +{ + auto l_eatom = d_eatom; + + // For global energy tally + if (eflag_global) { + double local_eng_vdwl = 0.0; + Kokkos::parallel_reduce("GlobalEnergyTally", Ni, KOKKOS_LAMBDA(int k, E_FLOAT& update) { + update += l_ei(k); + }, local_eng_vdwl); + + // Update global energy on the host after the parallel region + eng_vdwl += local_eng_vdwl; + } + + // For per-atom energy tally + if (eflag_atom) { + Kokkos::parallel_for("PerAtomEnergyTally", Ni, KOKKOS_LAMBDA(int k) { + l_eatom(istart + k) += l_ei(k); + }); + } +} + +template +void PairPODKokkos::tallystress(t_pod_1d l_fij, t_pod_1d l_rij, t_pod_1i l_ai, t_pod_1i l_aj, int Nij) +{ + auto l_vatom = d_vatom; + + if (vflag_global) { + for (int j=0; j<3; j++) { + F_FLOAT sum = 0.0; + Kokkos::parallel_reduce("GlobalStressTally", Nij, KOKKOS_LAMBDA(int k, F_FLOAT& update) { + int k3 = 3*k; + update += l_rij(j + k3) * l_fij(j + k3); + }, sum); + virial[j] -= sum; + } + + F_FLOAT sum = 0.0; + Kokkos::parallel_reduce("GlobalStressTally", Nij, KOKKOS_LAMBDA(int k, F_FLOAT& update) { + int k3 = 3*k; + update += l_rij(k3) * l_fij(1 + k3); + }, sum); + virial[3] -= sum; + + sum = 0.0; + Kokkos::parallel_reduce("GlobalStressTally", Nij, KOKKOS_LAMBDA(int k, F_FLOAT& update) { + int k3 = 3*k; + update += l_rij(k3) * l_fij(2 + k3); + }, sum); + virial[4] -= sum; + + sum = 0.0; + Kokkos::parallel_reduce("GlobalStressTally", Nij, KOKKOS_LAMBDA(int k, F_FLOAT& update) { + int k3 = 3*k; + update += l_rij(1+k3) * l_fij(2+k3); + }, sum); + virial[5] -= sum; + } + + if (vflag_atom) { + Kokkos::parallel_for("PerAtomStressTally", Nij, KOKKOS_LAMBDA(int k) { + int i = l_ai(k); + int j = l_aj(k); + int k3 = 3*k; + double v_local[6]; + v_local[0] = -l_rij(k3) * l_fij(k3 + 0); + v_local[1] = -l_rij(k3 + 1) * l_fij(k3 + 1); + v_local[2] = -l_rij(k3 + 2) * l_fij(k3 + 2); + v_local[3] = -l_rij(k3 + 0) * l_fij(k3 + 1); + v_local[4] = -l_rij(k3 + 0) * l_fij(k3 + 2); + v_local[5] = -l_rij(k3 + 1) * l_fij(k3 + 2); + + for (int d = 0; d < 6; ++d) { + Kokkos::atomic_add(&l_vatom(i, d), 0.5 * v_local[d]); + } + + for (int d = 0; d < 6; ++d) { + Kokkos::atomic_add(&l_vatom(j, d), 0.5 * v_local[d]); + } + + }); + } +} + +template +void PairPODKokkos::savematrix2binfile(std::string filename, t_pod_1d d_A, int nrows, int ncols) +{ + auto A = Kokkos::create_mirror_view(d_A); + Kokkos::deep_copy(A, d_A); + + FILE *fp = fopen(filename.c_str(), "wb"); + double sz[2]; + sz[0] = (double) nrows; + sz[1] = (double) ncols; + fwrite( reinterpret_cast( sz ), sizeof(double) * (2), 1, fp); + fwrite( reinterpret_cast( A.data() ), sizeof(double) * (nrows*ncols), 1, fp); + fclose(fp); +} + +template +void PairPODKokkos::saveintmatrix2binfile(std::string filename, t_pod_1i d_A, int nrows, int ncols) +{ + auto A = Kokkos::create_mirror_view(d_A); + Kokkos::deep_copy(A, d_A); + + FILE *fp = fopen(filename.c_str(), "wb"); + int sz[2]; + sz[0] = nrows; + sz[1] = ncols; + fwrite( reinterpret_cast( sz ), sizeof(int) * (2), 1, fp); + fwrite( reinterpret_cast( A.data() ), sizeof(int) * (nrows*ncols), 1, fp); + fclose(fp); +} + +template +void PairPODKokkos::savedatafordebugging() +{ + saveintmatrix2binfile("podkktypeai.bin", typeai, ni, 1); + saveintmatrix2binfile("podkknumij.bin", numij, ni+1, 1); + saveintmatrix2binfile("podkkai.bin", ai, nij, 1); + saveintmatrix2binfile("podkkaj.bin", aj, nij, 1); + saveintmatrix2binfile("podkkti.bin", ti, nij, 1); + saveintmatrix2binfile("podkktj.bin", tj, nij, 1); + saveintmatrix2binfile("podkkidxi.bin", idxi, nij, 1); + savematrix2binfile("podkkrbf.bin", rbf, nrbfmax, nij); + savematrix2binfile("podkkrbfx.bin", rbfx, nrbfmax, nij); + savematrix2binfile("podkkrbfy.bin", rbfy, nrbfmax, nij); + savematrix2binfile("podkkrbfz.bin", rbfz, nrbfmax, nij); + int kmax = (K3 > ns) ? K3 : ns; + savematrix2binfile("podkkabf.bin", abf, kmax, nij); + savematrix2binfile("podkkabfx.bin", abfx, kmax, nij); + savematrix2binfile("podkkabfy.bin", abfy, kmax, nij); + savematrix2binfile("podkkabfz.bin", abfz, kmax, nij); + savematrix2binfile("podkkbd.bin", bd, ni, Mdesc); + savematrix2binfile("podkksumU.bin", sumU, nelements * K3 * nrbfmax, ni); + savematrix2binfile("podkkrij.bin", rij, 3, nij); + savematrix2binfile("podkkfij.bin", fij, 3, nij); + savematrix2binfile("podkkei.bin", ei, ni, 1); + + error->all(FLERR, "Save data and stop the run for debugging"); +} + +/* ---------------------------------------------------------------------- + memory usage of arrays +------------------------------------------------------------------------- */ + +template +double PairPODKokkos::memory_usage() +{ + double bytes = 0; + + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class PairPODKokkos; +#ifdef LMP_KOKKOS_GPU +template class PairPODKokkos; +#endif +} diff --git a/src/KOKKOS/pair_pod_kokkos.h b/src/KOKKOS/pair_pod_kokkos.h new file mode 100644 index 0000000000..4763261029 --- /dev/null +++ b/src/KOKKOS/pair_pod_kokkos.h @@ -0,0 +1,226 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(pod/kk,PairPODKokkos); +PairStyle(pod/kk/device,PairPODKokkos); +PairStyle(pod/kk/host,PairPODKokkos); +// clang-format on +#else + +// clang-format off +#ifndef LMP_PAIR_POD_KOKKOS_H +#define LMP_PAIR_POD_KOKKOS_H + +#include "pair_pod.h" +#include "kokkos_type.h" +#include "pair_kokkos.h" + +namespace LAMMPS_NS { + +template +class PairPODKokkos : public PairPOD { + public: + typedef DeviceType device_type; + typedef ArrayTypes AT; + + PairPODKokkos(class LAMMPS *); + ~PairPODKokkos() override; + + void compute(int, int) override; + void coeff(int, char **) override; + void init_style() override; + double init_one(int, int) override; + + int inum, maxneigh; + int host_flag; + + int eflag, vflag; + int neighflag; + + typename AT::t_neighbors_2d d_neighbors; + typename AT::t_int_1d d_ilist; + typename AT::t_int_1d d_numneigh; + + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; + + typename AT::t_x_array_randomread x; + typename AT::t_f_array f; + typename AT::t_int_1d_randomread type; + + typedef Kokkos::DualView tdual_fparams; + tdual_fparams k_cutsq, k_scale; + typedef Kokkos::View t_fparams; + t_fparams d_cutsq, d_scale; + typename AT::t_int_1d d_map; + + friend void pair_virial_fdotr_compute(PairPODKokkos*); + + void grow(int, int); + void copy_from_pod_class(EAPOD *podptr); + void divideInterval(int *intervals, int N, int M); + int calculateNumberOfIntervals(int N, int intervalSize); + void grow_atoms(int Ni); + void grow_pairs(int Nij); + + void allocate() override; + double memory_usage() override; + + typedef Kokkos::View t_pod_1i; + typedef Kokkos::View t_pod_1d; +// typedef Kokkos::View t_pod_2i; +// typedef Kokkos::View t_pod_2d; +// typedef Kokkos::View t_pod_3d3; + + int atomBlockSize; // size of each atom block + int nAtomBlocks; // number of atoms blocks + int atomBlocks[101]; // atom blocks + double comptime[100]; + int timing; + + int ni; // number of atoms i in the current atom block + int nij; // number of pairs (i,j) in the current atom block + int nimax; // maximum number of atoms i + int nijmax; // maximum number of pairs (i,j) + + int nelements; // number of elements + int onebody; // one-body descriptors + int besseldegree; // degree of Bessel functions + int inversedegree; // degree of inverse functions + int nbesselpars; // number of Bessel parameters + int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters) + int ns; // number of snapshots for radial basis functions + int nl1, nl2, nl3, nl4, nl23, nl33, nl34, nl44, nl; // number of local descriptors + int nrbf2, nrbf3, nrbf4, nrbfmax; // number of radial basis functions + int nabf3, nabf4; // number of angular basis functions + int K3, K4, Q4; // number of monomials + + // environmental variables + int nClusters; // number of environment clusters + int nComponents; // number of principal components + int Mdesc; // number of base descriptors + + double rin; // inner cut-off radius + double rcut; // outer cut-off radius + double rmax; // rcut - rin + double rcutsq; + + t_pod_1d rij; // (xj - xi) for all pairs (I, J) + t_pod_1d fij; // force for all pairs (I, J) + t_pod_1d ei; // energy for each atom I + t_pod_1i typeai; // types of atoms I only + t_pod_1i numij; // number of pairs (I, J) for each atom I + t_pod_1i idxi; // storing linear indices of atom I for all pairs (I, J) + t_pod_1i ai; // IDs of atoms I for all pairs (I, J) + t_pod_1i aj; // IDs of atoms J for all pairs (I, J) + t_pod_1i ti; // types of atoms I for all pairs (I, J) + t_pod_1i tj; // types of atoms J for all pairs (I, J) + + t_pod_1d besselparams; + t_pod_1d Phi; // eigenvectors matrix ns x ns + t_pod_1d rbf; // radial basis functions nij x nrbfmax + t_pod_1d rbfx; // x-derivatives of radial basis functions nij x nrbfmax + t_pod_1d rbfy; // y-derivatives of radial basis functions nij x nrbfmax + t_pod_1d rbfz; // z-derivatives of radial basis functions nij x nrbfmax + t_pod_1d abf; // angular basis functions nij x K3 + t_pod_1d abfx; // x-derivatives of angular basis functions nij x K3 + t_pod_1d abfy; // y-derivatives of angular basis functions nij x K3 + t_pod_1d abfz; // z-derivatives of angular basis functions nij x K3 + t_pod_1d sumU; // sum of radial basis functions ni x K3 x nrbfmax x nelements + t_pod_1d forcecoeff; // force coefficients ni x K3 x nrbfmax x nelements + t_pod_1d Proj; // PCA Projection matrix + t_pod_1d Centroids; // centroids of the clusters + t_pod_1d bd; // base descriptors ni x Mdesc + t_pod_1d cb; // force coefficients for base descriptors ni x Mdesc + t_pod_1d pd; // environment probability descriptors ni x (1 + nComponents + 3*nClusters) + t_pod_1d coefficients; // coefficients nCoeffPerElement x nelements + t_pod_1i pq3, pn3, pc3; // arrays to compute 3-body angular basis functions + t_pod_1i pa4, pb4, pc4; // arrays to compute 4-body angular basis functions + t_pod_1i ind33l, ind33r; // nl33 + t_pod_1i ind34l, ind34r; // nl34 + t_pod_1i ind44l, ind44r; // nl44 + t_pod_1i elemindex; + + void set_array_to_zero(t_pod_1d a, int N); + + int NeighborCount(t_pod_1i, double, int, int); + + void NeighborList(t_pod_1d l_rij, t_pod_1i l_numij, t_pod_1i l_typeai, t_pod_1i l_idxi, + t_pod_1i l_ai, t_pod_1i l_aj, t_pod_1i l_ti, t_pod_1i l_tj, double l_rcutsq, int gi1, int Ni); + + void radialbasis(t_pod_1d rbft, t_pod_1d rbftx, t_pod_1d rbfty, t_pod_1d rbftz, + t_pod_1d rij, t_pod_1d l_besselparams, double l_rin, double l_rmax, int l_besseldegree, + int l_inversedegree, int l_nbesselpars, int Nij); + + void matrixMultiply(t_pod_1d a, t_pod_1d b, t_pod_1d c, int r1, int c1, int c2); + + void angularbasis(t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, + t_pod_1d l_rij, t_pod_1i l_pq3, int l_K3, int N); + + void radialangularsum(t_pod_1d l_sumU, t_pod_1d l_rbf, t_pod_1d l_abf, t_pod_1i l_tj, + t_pod_1i l_numij, const int l_nelements, const int l_nrbf3, const int l_K3, const int Ni, const int Nij); + + void twobodydesc(t_pod_1d d2, t_pod_1d l_rbf, t_pod_1i l_idxi, t_pod_1i l_tj, int l_nrbf2, const int Ni, const int Nij); + + void threebodydesc(t_pod_1d d3, t_pod_1d l_sumU, t_pod_1i l_pc3, t_pod_1i l_pn3, + int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, const int Ni); + + void fourbodydesc(t_pod_1d d4, t_pod_1d l_sumU, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, + int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni); + + void crossdesc(t_pod_1d d12, t_pod_1d d1, t_pod_1d d2, t_pod_1i ind1, t_pod_1i ind2, int n12, int Ni); + + void crossdesc_reduction(t_pod_1d cb1, t_pod_1d cb2, t_pod_1d c12, t_pod_1d d1, + t_pod_1d d2, t_pod_1i ind1, t_pod_1i ind2, int n12, int Ni); + void blockatom_base_descriptors(t_pod_1d bd, int Ni, int Nij); + void blockatom_base_coefficients(t_pod_1d ei, t_pod_1d cb, t_pod_1d B, int Ni); + void blockatom_environment_descriptors(t_pod_1d ei, t_pod_1d cb, t_pod_1d B, int Ni); + + void twobody_forces(t_pod_1d fij, t_pod_1d cb2, t_pod_1d l_rbfx, t_pod_1d l_rbfy, t_pod_1d l_rbfz, + t_pod_1i l_idxi, t_pod_1i l_tj, int l_nrbf2, const int Ni, const int Nij); + void threebody_forces(t_pod_1d fij, t_pod_1d cb3, t_pod_1d l_rbf, t_pod_1d l_rbfx, + t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, + t_pod_1d l_sumU, t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pc3, t_pod_1i l_pn3, t_pod_1i l_elemindex, + int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, int Ni, int Nij); + void fourbody_forces(t_pod_1d fij, t_pod_1d cb4, t_pod_1d l_rbf, t_pod_1d l_rbfx, t_pod_1d l_rbfy, + t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, t_pod_1d l_sumU, + t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, + int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni, int Nij); + + void threebody_forcecoeff(t_pod_1d fb3, t_pod_1d cb3, t_pod_1d l_sumU, t_pod_1i l_pc3, + t_pod_1i l_pn3, t_pod_1i l_elemindex, int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, int Ni); + + void fourbody_forcecoeff(t_pod_1d fb4, t_pod_1d cb4, t_pod_1d l_sumU, t_pod_1i l_pa4, + t_pod_1i l_pb4, t_pod_1i l_pc4, int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni); + + void allbody_forces(t_pod_1d fij, t_pod_1d l_forcecoeff, t_pod_1d l_rbf, t_pod_1d l_rbfx, + t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, + t_pod_1i l_idxi, t_pod_1i l_tj, int l_nelements, int l_nrbf3, int l_K3, int Nij); + + void blockatom_energyforce(t_pod_1d l_ei, t_pod_1d l_fij, int Ni, int Nij); + void tallyenergy(t_pod_1d l_ei, int istart, int Ni); + void tallyforce(t_pod_1d l_fij, t_pod_1i l_ai, t_pod_1i l_aj, int Nij); + void tallystress(t_pod_1d l_fij, t_pod_1d l_rij, t_pod_1i l_ai, t_pod_1i l_aj, int Nij); + + void savematrix2binfile(std::string filename, t_pod_1d d_A, int nrows, int ncols); + void saveintmatrix2binfile(std::string filename, t_pod_1i d_A, int nrows, int ncols); + void savedatafordebugging(); +}; +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/KOKKOS/pair_soft_kokkos.cpp b/src/KOKKOS/pair_soft_kokkos.cpp new file mode 100644 index 0000000000..5df926e4d2 --- /dev/null +++ b/src/KOKKOS/pair_soft_kokkos.cpp @@ -0,0 +1,252 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_soft_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "math_const.h" +#include "memory_kokkos.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +template +PairSoftKokkos::PairSoftKokkos(LAMMPS *lmp) : PairSoft(lmp) +{ + respa_enable = 0; + + kokkosable = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +PairSoftKokkos::~PairSoftKokkos() +{ + if (copymode) return; + + if (allocated) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->destroy_kokkos(k_cutsq,cutsq); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void PairSoftKokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + if (neighflag == FULL) no_virial_fdotr_compute = 1; + + ev_init(eflag,vflag,0); + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); + d_eatom = k_eatom.view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom"); + d_vatom = k_vatom.view(); + } + + atomKK->sync(execution_space,datamask_read); + k_cutsq.template sync(); + k_params.template sync(); + if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); + else atomKK->modified(execution_space,F_MASK); + + x = atomKK->k_x.view(); + c_x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + type = atomKK->k_type.view(); + nlocal = atom->nlocal; + nall = atom->nlocal + atom->nghost; + newton_pair = force->newton_pair; + special_lj[0] = force->special_lj[0]; + special_lj[1] = force->special_lj[1]; + special_lj[2] = force->special_lj[2]; + special_lj[3] = force->special_lj[3]; + + // loop over neighbors of my atoms + + copymode = 1; + + EV_FLOAT ev = pair_compute,void >(this,(NeighListKokkos*)list); + + if (eflag_global) eng_vdwl += ev.evdwl; + if (vflag_global) { + virial[0] += ev.v[0]; + virial[1] += ev.v[1]; + virial[2] += ev.v[2]; + virial[3] += ev.v[3]; + virial[4] += ev.v[4]; + virial[5] += ev.v[5]; + } + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + } + + if (vflag_fdotr) pair_virial_fdotr_compute(this); + + copymode = 0; +} + +template +template +KOKKOS_INLINE_FUNCTION +F_FLOAT PairSoftKokkos:: +compute_fpair(const F_FLOAT& rsq, const int &, const int &, const int& itype, const int& jtype) const { + const F_FLOAT r = sqrt(rsq); + const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut; + const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor; + const F_FLOAT arg = MY_PI*r/cut_ij; + + F_FLOAT fpair = 0.0; + if (r > 0.0) fpair = prefactor_ij * sin(arg) * MY_PI/cut_ij/r; + + return fpair; +} + +template +template +KOKKOS_INLINE_FUNCTION +F_FLOAT PairSoftKokkos:: +compute_evdwl(const F_FLOAT& rsq, const int &, const int &, const int& itype, const int& jtype) const { + const F_FLOAT r = sqrt(rsq); + const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut; + const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor; + const F_FLOAT arg = MY_PI*r/cut_ij; + + return prefactor_ij*(1.0+cos(arg)); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +template +void PairSoftKokkos::allocate() +{ + PairSoft::allocate(); + + int n = atom->ntypes; + memory->destroy(cutsq); + memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq"); + d_cutsq = k_cutsq.template view(); + k_params = Kokkos::DualView("PairSoft::params",n+1,n+1); + params = k_params.template view(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +template +void PairSoftKokkos::settings(int narg, char **arg) +{ + if (narg > 2) error->all(FLERR,"Illegal pair_style command"); + + PairSoft::settings(1,arg); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +template +void PairSoftKokkos::init_style() +{ + PairSoft::init_style(); + + // error if rRESPA with inner levels + + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { + int respa = 0; + if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + if (respa) + error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle"); + } + + // adjust neighbor list request for KOKKOS + + neighflag = lmp->kokkos->neighflag; + auto request = neighbor->find_request(this); + request->set_kokkos_host(std::is_same_v && + !std::is_same_v); + request->set_kokkos_device(std::is_same_v); + if (neighflag == FULL) request->enable_full(); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +template +double PairSoftKokkos::init_one(int i, int j) +{ + double cutone = PairSoft::init_one(i,j); + + k_params.h_view(i,j).prefactor = prefactor[i][j]; + k_params.h_view(i,j).cut = cutone; + k_params.h_view(i,j).cutsq = cutone*cutone; + k_params.h_view(j,i) = k_params.h_view(i,j); + if (i(); + k_params.template modify(); + + return cutone; +} + +namespace LAMMPS_NS { +template class PairSoftKokkos; +#ifdef LMP_KOKKOS_GPU +template class PairSoftKokkos; +#endif +} + diff --git a/src/KOKKOS/pair_soft_kokkos.h b/src/KOKKOS/pair_soft_kokkos.h new file mode 100644 index 0000000000..060d760937 --- /dev/null +++ b/src/KOKKOS/pair_soft_kokkos.h @@ -0,0 +1,114 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(soft/kk,PairSoftKokkos); +PairStyle(soft/kk/device,PairSoftKokkos); +PairStyle(soft/kk/host,PairSoftKokkos); +// clang-format on +#else + +// clang-format off +#ifndef LMP_PAIR_SOFT_KOKKOS_H +#define LMP_PAIR_SOFT_KOKKOS_H + +#include "pair_kokkos.h" +#include "pair_soft.h" +#include "neigh_list_kokkos.h" + +namespace LAMMPS_NS { + +template +class PairSoftKokkos : public PairSoft { + public: + enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF}; + enum {COUL_FLAG=0}; + typedef DeviceType device_type; + typedef ArrayTypes AT; + PairSoftKokkos(class LAMMPS *); + ~PairSoftKokkos() override; + + void compute(int, int) override; + + void settings(int, char **) override; + void init_style() override; + double init_one(int, int) override; + + struct params_soft{ + KOKKOS_INLINE_FUNCTION + params_soft() {cutsq=0,cut=0,prefactor=0;}; + KOKKOS_INLINE_FUNCTION + params_soft(int /*i*/) {cutsq=0,cut=0,prefactor=0;}; + F_FLOAT cutsq,cut,prefactor; + }; + + protected: + template + KOKKOS_INLINE_FUNCTION + F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const; + + template + KOKKOS_INLINE_FUNCTION + F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const; + + template + KOKKOS_INLINE_FUNCTION + F_FLOAT compute_ecoul(const F_FLOAT& /*rsq*/, const int& /*i*/, const int& /*j*/, + const int& /*itype*/, const int& /*jtype*/) const { return 0; } + + Kokkos::DualView k_params; + typename Kokkos::DualView::t_dev_const_um params; + params_soft m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 12 atom types + F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; + typename AT::t_x_array_randomread x; + typename AT::t_x_array c_x; + typename AT::t_f_array f; + typename AT::t_int_1d_randomread type; + + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; + + int newton_pair; + double special_lj[4]; + + typename AT::tdual_ffloat_2d k_cutsq; + typename AT::t_ffloat_2d d_cutsq; + + int neighflag; + int nlocal,nall,eflag,vflag; + + void allocate() override; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend EV_FLOAT pair_compute_neighlist(PairSoftKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist(PairSoftKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist(PairSoftKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist(PairSoftKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute(PairSoftKokkos*,NeighListKokkos*); + friend void pair_virial_fdotr_compute(PairSoftKokkos*); +}; + +} + +#endif +#endif + diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 99d01be4a5..fc38cdf19a 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -202,9 +202,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairTableKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { union_int_float_t rsq_lookup; double fpair; const int tidx = d_table_const.tabindex(itype,jtype); @@ -236,9 +234,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairTableKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { double evdwl; union_int_float_t rsq_lookup; const int tidx = d_table_const.tabindex(itype,jtype); diff --git a/src/KOKKOS/pair_uf3_kokkos.cpp b/src/KOKKOS/pair_uf3_kokkos.cpp new file mode 100644 index 0000000000..4a3bcc164b --- /dev/null +++ b/src/KOKKOS/pair_uf3_kokkos.cpp @@ -0,0 +1,1661 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Ajinkya Hire (Univ. of Florida), + Hendrik Kraß (Univ. of Constance), + Matthias Rupp (Luxembourg Institute of Science and Technology), + Richard Hennig (Univ of Florida) +---------------------------------------------------------------------- */ + +#include "pair_uf3.h" +#include "pair_uf3_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "kokkos_type.h" +#include "math_const.h" +#include "math_special_kokkos.h" +#include "memory.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair_kokkos.h" +#include "text_file_reader.h" + +#include +#include +#include + +using namespace LAMMPS_NS; +using namespace MathConst; +using MathSpecialKokkos::cube; +using MathSpecialKokkos::square; + +template PairUF3Kokkos::PairUF3Kokkos(LAMMPS *lmp) : PairUF3(lmp) +{ + respa_enable = 0; + + //kokkosable = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | F_MASK | TAG_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; + +} + +template PairUF3Kokkos::~PairUF3Kokkos() +{ + if (!copymode) { + memoryKK->destroy_kokkos(k_eatom, eatom); //destory eatom from host, set it to nullptr + //Also set k_eatom to empty View + memoryKK->destroy_kokkos(k_vatom, vatom); + memoryKK->destroy_kokkos(k_cutsq,cutsq); + destroy_3d(k_cut_3b,cut_3b); + destroy_4d(k_min_cut_3b,min_cut_3b); + eatom = NULL; + vatom = NULL; + cvatom = NULL; + } +} + +template +template +void PairUF3Kokkos::destroy_3d(TYPE data, typename TYPE::value_type*** &array) +{ + if (array == nullptr) return; + data = TYPE(); + memory->sfree(array); + array = nullptr; +} + +template +template +void PairUF3Kokkos::destroy_4d(TYPE data, typename TYPE::value_type**** &array) +{ + if (array == nullptr) return; + data = TYPE(); + memory->sfree(array); + array = nullptr; +} + +/* ---------------------------------------------------------------------- + * global settings + * ---------------------------------------------------------------------- */ + +template void PairUF3Kokkos::settings(int narg, char **arg) +{ + PairUF3::settings(narg, arg); + //1. Determines whether the simulation is 2-body or 2 and 3-body + //2. Set nbody_flag, num_of_elements, pot_3b +} + +/* ---------------------------------------------------------------------- + * set coeffs for one or more type pairs + * ---------------------------------------------------------------------- */ +template void PairUF3Kokkos::coeff(int narg, char **arg) +{ + PairUF3::coeff(narg,arg); + //Also calls allocate internally + //Grows arrays to the right dimensions --> setflag, cutsq, cut, knot_spacing_type_2b, + //knot_spacing_2b, n2b_knots_array_size, n2b_coeff_array_size, setflag_3b, + //cut_3b, cut_3b_list, min_cut_3b, knot_spacing_type_3b, knot_spacing_3b, + //tot_interaction_count_3b, map_3b, n3b_knots_array_size, n3b_coeff_array_size, + //neighshort + // + //Also reads the pot_files_internally + +} + +template +void PairUF3Kokkos::allocate() +{ + if (!allocated) PairUF3::allocate(); + int n = atom->ntypes; + memory->destroy(cutsq); //Why are we destroying cutsq? cutsq is allocated when + //PairUF3::coeff or PairUF3::allocate is called; in the next step when k_cutsq + //is created cutsq is set to point to the host array of k_cutsq + //memory->destroy(cut_3b); + + memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq"); + d_cutsq = k_cutsq.template view(); //assignment; get the device + //view of k_cutsq and assign it to d_cutsq; in the header file we just + //decleared d_cutsq's type + memoryKK->create_kokkos(k_cut_3b,n+1,n+1,n+1,"threebody:cut"); + memoryKK->create_kokkos(k_min_cut_3b,n+1,n+1,n+1,3,"threebody:cut"); + d_cut_3b = k_cut_3b.template view(); + d_min_cut_3b = k_min_cut_3b.template view(); +} + + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +template void PairUF3Kokkos::init_style() +{ + + PairUF3::init_style(); + + neighflag = lmp->kokkos->neighflag; + + auto request = neighbor->find_request(this); + request->set_kokkos_host(std::is_same::value && + !std::is_same::value); + request->set_kokkos_device(std::is_same::value); + + request->enable_full(); + request->enable_ghost(); +} + +/* ---------------------------------------------------------------------- + init list sets the pointer to full neighbour list requested in previous function +------------------------------------------------------------------------- */ + +template +void PairUF3Kokkos::init_list(int /*id*/, class NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ +template double PairUF3Kokkos::init_one(int i, int j) +{ + double cutone = PairUF3::init_one(i, j); + + if (!coefficients_created) create_coefficients(); + + k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone; //Update the k_cutsq's + //host memory + k_cutsq.template modify(); //Record that k_cutsq's host memory has + //been modified + + return cutone; +} + +template void PairUF3Kokkos::create_coefficients() +{ + const int num_of_elements = atom->ntypes; + coefficients_created = 1; + + if (pot_3b) { + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + for (int k = 1; k < num_of_elements + 1; k++) { + k_cut_3b.h_view(i,j,k) = cut_3b[i][j][k]; + + // Notice the order of min_cut_3b[i][j][k] + //In min_cut_3b[i][j][k], + //min_cut_3b[i][j][k][0] is the knot_vector along jk, + //min_cut_3b[i][j][k][1] is the knot_vector along ik, + //min_cut_3b[i][j][k][2] is the knot_vector along ij, + //see pair_uf3.cpp for more details + k_min_cut_3b.h_view(i,j,k,0) = min_cut_3b[i][j][k][0]; + k_min_cut_3b.h_view(i,j,k,1) = min_cut_3b[i][j][k][1]; + k_min_cut_3b.h_view(i,j,k,2) = min_cut_3b[i][j][k][2]; + } + } + } + k_cut_3b.template modify(); + k_min_cut_3b.template modify(); + } + + //No allocation on device for --> setflag, cut, knot_spacing_type_2b, + //n2b_knot, n2b_coeff, n2b_knot[i], n2b_coeff[i], setflag_3b, cut_3b, + //cut_3b_list, min_cut_3b, knot_spacing_type_3b, cut_3b_list, n3b_knot_matrix, + //neighshort + + //UFBS2b and UFBS3b are array of objects. Bad idea to use kokkos view(array) + //for it + create_2b_coefficients(); + if (pot_3b) create_3b_coefficients(); + +} + +template void PairUF3Kokkos::create_2b_coefficients() +{ + const int num_of_elements = atom->ntypes; + + // Setup interaction pair map + //TODO: Instead of using map2b and map3b use simple indexing + Kokkos::realloc(map2b, num_of_elements + 1, num_of_elements + 1); + auto map2b_view = Kokkos::create_mirror(map2b); + + int interaction_count = 0; + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = i; j < num_of_elements + 1; j++) { + map2b_view(i, j) = interaction_count; + map2b_view(j, i) = interaction_count++; + } + } + Kokkos::deep_copy(map2b, map2b_view); + + // Count max knots for array size + + int max_knots = max_num_knots_2b; + + // Copy coefficients to view + + Kokkos::realloc(d_coefficients_2b, interaction_count, max_knots - 4); + auto d_coefficients_2b_view = Kokkos::create_mirror(d_coefficients_2b); + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = i; j < num_of_elements + 1; j++) { + for (int k = 0; k < max_num_coeff_2b; k++) { + d_coefficients_2b_view(map2b_view(i, j), k) = n2b_coeff_array[i][j][k]; + } + } + } + Kokkos::deep_copy(d_coefficients_2b, d_coefficients_2b_view); + + // Copy knots from array to view + + Kokkos::realloc(d_n2b_knot, interaction_count, max_knots); + Kokkos::realloc(d_n2b_knot_spacings, interaction_count); + auto d_n2b_knot_view = Kokkos::create_mirror(d_n2b_knot); + auto d_n2b_knot_spacings_view = Kokkos::create_mirror(d_n2b_knot_spacings); + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = i; j < num_of_elements + 1; j++) { + for (int k = 0; k < max_num_knots_2b; k++) { + d_n2b_knot_view(map2b_view(i, j), k) = n2b_knots_array[i][j][k]; + } + d_n2b_knot_spacings_view(map2b_view(i, j)) = n2b_knots_array[i][j][4] - n2b_knots_array[i][j][3]; + } + } + + Kokkos::deep_copy(d_n2b_knot, d_n2b_knot_view); + Kokkos::deep_copy(d_n2b_knot_spacings, d_n2b_knot_spacings_view); + // Set spline constants + + Kokkos::realloc(constants_2b, interaction_count, max_knots - 4); + auto constants_2b_view = Kokkos::create_mirror(constants_2b); + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = i; j < num_of_elements + 1; j++) { + for (int l = 0; l < n2b_knots_array_size[i][j] - 4; l++) { + //n2b_knot[i][j].size() - 4; l++) { + auto c = get_constants(&n2b_knots_array[i][j][l], n2b_coeff_array[i][j][l]); + for (int k = 0; k < 16; k++) + constants_2b_view(map2b_view(i, j), l, k) = (std::isinf(c[k]) || std::isnan(c[k])) ? 0 + : c[k]; + } + } + } + Kokkos::deep_copy(constants_2b, constants_2b_view); + + Kokkos::realloc(dnconstants_2b, interaction_count, max_knots - 5); + auto dnconstants_2b_view = Kokkos::create_mirror(dnconstants_2b); + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = i; j < num_of_elements + 1; j++) { + for (int l = 0; l < n2b_knots_array_size[i][j] - 5; l++) { + double dntemp4 = 3 / (n2b_knots_array[i][j][l + 4] - n2b_knots_array[i][j][l + 1]); + double coeff = (n2b_coeff_array[i][j][l + 1] - n2b_coeff_array[i][j][l]) * dntemp4; + auto c = get_dnconstants(&n2b_knots_array[i][j][l + 1], coeff); + for (int k = 0; k < 9; k++) + dnconstants_2b_view(map2b_view(i, j), l, k) = + (std::isinf(c[k]) || std::isnan(c[k])) ? 0 : c[k]; + } + } + } + Kokkos::deep_copy(dnconstants_2b, dnconstants_2b_view); +} + +template void PairUF3Kokkos::create_3b_coefficients() +{ + const int num_of_elements = atom->ntypes; + // Init interaction map for 3B + + Kokkos::realloc(map3b, num_of_elements + 1, num_of_elements + 1, num_of_elements + 1); + auto map3b_view = Kokkos::create_mirror(map3b); + + int interaction_count = 0; + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + for (int k = 1; k < num_of_elements + 1; k++) { + map3b_view(i, j, k) = interaction_count; + interaction_count++; + } + } + } + Kokkos::deep_copy(map3b, map3b_view); + + // Count max knots for view + + int max_knots = max_num_knots_3b; + //In n3b_knot_matrix[i][j][k], + //n3b_knot_matrix[i][j][k][0] is the knot_vector along jk, + //n3b_knot_matrix[i][j][k][1] is the knot_vector along ik, + //n3b_knot_matrix[i][j][k][2] is the knot_vector along ij, + //see pair_uf3.cpp for more details + + + // Init knot matrix view + + Kokkos::realloc(d_n3b_knot_matrix, interaction_count, 3, max_knots); + Kokkos::realloc(d_n3b_knot_matrix_spacings, interaction_count, 3); + auto d_n3b_knot_matrix_view = Kokkos::create_mirror(d_n3b_knot_matrix); + auto d_n3b_knot_matrix_spacings_view = Kokkos::create_mirror(d_n3b_knot_matrix_spacings); + + for (int i = 1; i < num_of_elements + 1; i++) + for (int j = 1; j < num_of_elements + 1; j++) + for (int k = 1; k < num_of_elements + 1; k++) { + for (int m = 0; m < n3b_knots_array_size[map_3b[i][j][k]][0]; m++) + d_n3b_knot_matrix_view(map3b_view(i, j, k), 0, m) = + n3b_knots_array[map_3b[i][j][k]][0][m]; + for (int m = 0; m < n3b_knots_array_size[map_3b[i][j][k]][1]; m++) + d_n3b_knot_matrix_view(map3b_view(i, j, k), 1, m) = + n3b_knots_array[map_3b[i][j][k]][1][m]; + for (int m = 0; m < n3b_knots_array_size[map_3b[i][j][k]][2]; m++) + d_n3b_knot_matrix_view(map3b_view(i, j, k), 2, m) = + n3b_knots_array[map_3b[i][j][k]][2][m]; + + d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),2) = + n3b_knots_array[map_3b[i][j][k]][2][4] - n3b_knots_array[map_3b[i][j][k]][2][3]; + + d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),1) = + n3b_knots_array[map_3b[i][j][k]][1][4] - n3b_knots_array[map_3b[i][j][k]][1][3]; + + d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),0) = + n3b_knots_array[map_3b[i][j][k]][0][4] - n3b_knots_array[map_3b[i][j][k]][0][3]; + } + Kokkos::deep_copy(d_n3b_knot_matrix, d_n3b_knot_matrix_view); + Kokkos::deep_copy(d_n3b_knot_matrix_spacings, d_n3b_knot_matrix_spacings_view); + + // Set knots spacings + + Kokkos::realloc(d_n3b_knot_spacings, interaction_count, 3); + auto d_n3b_knot_spacings_view = Kokkos::create_mirror(d_n3b_knot_spacings); + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + for (int k = 1; k < num_of_elements + 1; k++) { + d_n3b_knot_spacings_view(map3b_view(i, j, k), 0) = + 1 / (n3b_knots_array[map_3b[i][j][k]][0][5] - n3b_knots_array[map_3b[i][j][k]][0][4]); + + d_n3b_knot_spacings_view(map3b_view(i, j, k), 1) = + 1 / (n3b_knots_array[map_3b[i][j][k]][1][5] - n3b_knots_array[map_3b[i][j][k]][1][4]); + + d_n3b_knot_spacings_view(map3b_view(i, j, k), 2) = + 1 / (n3b_knots_array[map_3b[i][j][k]][2][5] - n3b_knots_array[map_3b[i][j][k]][2][4]); + } + } + } + Kokkos::deep_copy(d_n3b_knot_spacings, d_n3b_knot_spacings_view); + + // Copy coefficients + + Kokkos::realloc(d_coefficients_3b, interaction_count, max_knots - 4, max_knots - 4, + max_knots - 4); + auto d_coefficients_3b_view = Kokkos::create_mirror(d_coefficients_3b); + + for (int n = 1; n < num_of_elements + 1; n++) { + for (int m = 1; m < num_of_elements + 1; m++) { + for (int o = 1; o < num_of_elements + 1; o++) { + for (int i = 0; i < n3b_coeff_array_size[map_3b[n][m][o]][0]; i++) { + for (int j = 0; j < n3b_coeff_array_size[map_3b[n][m][o]][1]; j++) { + for (int k = 0; k < n3b_coeff_array_size[map_3b[n][m][o]][2]; k++) { + d_coefficients_3b_view(map3b_view(n, m, o), i, j, k) = + n3b_coeff_array[map_3b[n][m][o]][i][j][k]; + } + } + } + } + } + } + Kokkos::deep_copy(d_coefficients_3b, d_coefficients_3b_view); + // + // Create derivative coefficients + + // TODO: Shrink size + Kokkos::realloc(d_dncoefficients_3b, interaction_count, 3, max_knots - 4, max_knots - 4, + max_knots - 4); + auto d_dncoefficients_3b_view = Kokkos::create_mirror(d_dncoefficients_3b); + + //Notice the order for d_dncoefficients_3b_view(map3b_view(n, m, o), X, i, j, k) + //d_dncoefficients_3b_view(map3b_view(n, m, o), 2, i, j, k) --> coeff for rjk + //d_dncoefficients_3b_view(map3b_view(n, m, o), 1, i, j, k) --> coeff for rik + //d_dncoefficients_3b_view(map3b_view(n, m, o), 0, i, j, k) --> coeff for rij + // + //This is because- + //In n3b_knot_matrix[i][j][k], + //n3b_knot_matrix[i][j][k][0] is the knot_vector along jk, + //n3b_knot_matrix[i][j][k][1] is the knot_vector along ik, + //n3b_knot_matrix[i][j][k][2] is the knot_vector along ij, + //see pair_uf3.cpp for more details + + for (int n = 1; n < num_of_elements + 1; n++) { + for (int m = 1; m < num_of_elements + 1; m++) { + for (int o = 1; o < num_of_elements + 1; o++) { + int coeff_dim1 = n3b_coeff_array_size[map_3b[n][m][o]][0]; + int coeff_dim2 = n3b_coeff_array_size[map_3b[n][m][o]][1]; + int coeff_dim3 = n3b_coeff_array_size[map_3b[n][m][o]][2]; + for (int i = 0; i < coeff_dim1; i++) { + for (int j = 0; j < coeff_dim2; j++) { + for (int k = 0; k < coeff_dim3; k++) { + F_FLOAT dntemp4 = + 3 / (n3b_knots_array[map_3b[n][m][o]][0][k + 4] - n3b_knots_array[map_3b[n][m][o]][0][k + 1]); + + d_dncoefficients_3b_view(map3b_view(n, m, o), 2, i, j, k) = + (n3b_coeff_array[map_3b[n][m][o]][i][j][k + 1] - n3b_coeff_array[map_3b[n][m][o]][i][j][k]) * dntemp4; + } + } + } + + for (int i = 0; i < coeff_dim1; i++) { + std::vector> dncoeff_vect2; + for (int j = 0; j < coeff_dim2; j++) { + F_FLOAT dntemp4 = + 3 / (n3b_knots_array[map_3b[n][m][o]][1][j + 4] - n3b_knots_array[map_3b[n][m][o]][1][j + 1]); + + std::vector dncoeff_vect; + for (int k = 0; k < coeff_dim3; k++) { + d_dncoefficients_3b_view(map3b_view(n, m, o), 1, i, j, k) = + (n3b_coeff_array[map_3b[n][m][o]][i][j + 1][k] - n3b_coeff_array[map_3b[n][m][o]][i][j][k]) * dntemp4; + } + } + } + + for (int i = 0; i < coeff_dim1; i++) { + F_FLOAT dntemp4 = + 3 / (n3b_knots_array[map_3b[n][m][o]][2][i + 4] - n3b_knots_array[map_3b[n][m][o]][2][i + 1]); + for (int j = 0; j < coeff_dim2; j++) { + for (int k = 0; k < coeff_dim3; k++) { + d_dncoefficients_3b_view(map3b_view(n, m, o), 0, i, j, k) = + (n3b_coeff_array[map_3b[n][m][o]][i + 1][j][k] - n3b_coeff_array[map_3b[n][m][o]][i][j][k]) * dntemp4; + } + } + } + } + } + } + Kokkos::deep_copy(d_dncoefficients_3b, d_dncoefficients_3b_view); + + // Set spline constants + + Kokkos::realloc(constants_3b, interaction_count, 3, max_knots - 4); + auto constants_3b_view = Kokkos::create_mirror(constants_3b); + + //In n3b_knot_matrix[i][j][k], + //n3b_knot_matrix[i][j][k][0] is the knot_vector along jk, + //n3b_knot_matrix[i][j][k][1] is the knot_vector along ik, + //n3b_knot_matrix[i][j][k][2] is the knot_vector along ij, + //see pair_uf3.cpp for more details + for (int n = 1; n < num_of_elements + 1; n++) { + for (int m = 1; m < num_of_elements + 1; m++) { + for (int o = 1; o < num_of_elements + 1; o++) { + for (int l = 0; l < n3b_knots_array_size[map_3b[n][m][o]][2] - 4; l++) { + auto c = get_constants(&n3b_knots_array[map_3b[n][m][o]][2][l], 1); + for (int k = 0; k < 16; k++) + constants_3b_view(map3b_view(n, m, o), 0, l, k) = + (std::isinf(c[k]) || std::isnan(c[k])) ? 0 : c[k]; + } + for (int l = 0; l < n3b_knots_array_size[map_3b[n][m][o]][1] - 4; l++) { + auto c = get_constants(&n3b_knots_array[map_3b[n][m][o]][1][l], 1); + for (int k = 0; k < 16; k++) + constants_3b_view(map3b_view(n, m, o), 1, l, k) = + (std::isinf(c[k]) || std::isnan(c[k])) ? 0 : c[k]; + } + for (int l = 0; l < n3b_knots_array_size[map_3b[n][m][o]][0] -4; l++) { + auto c = get_constants(&n3b_knots_array[map_3b[n][m][o]][0][l], 1); + for (int k = 0; k < 16; k++) + constants_3b_view(map3b_view(n, m, o), 2, l, k) = + (std::isinf(c[k]) || std::isnan(c[k])) ? 0 : c[k]; + } + } + } + } + Kokkos::deep_copy(constants_3b, constants_3b_view); + + Kokkos::realloc(dnconstants_3b, interaction_count, 3, max_knots - 6); + auto dnconstants_3b_view = Kokkos::create_mirror(dnconstants_3b); + + for (int n = 1; n < num_of_elements + 1; n++) { + for (int m = 1; m < num_of_elements + 1; m++) { + for (int o = 1; o < num_of_elements + 1; o++) { + for (int l = 1; l < n3b_knots_array_size[map_3b[n][m][o]][2] - 5; l++) { + auto c = get_dnconstants(&n3b_knots_array[map_3b[n][m][o]][2][l], 1); + for (int k = 0; k < 9; k++) + dnconstants_3b_view(map3b_view(n, m, o), 0, l - 1, k) = + (std::isinf(c[k]) || std::isnan(c[k])) ? 0 : c[k]; + } + for (int l = 1; l < n3b_knots_array_size[map_3b[n][m][o]][1] - 5; l++) { + auto c = get_dnconstants(&n3b_knots_array[map_3b[n][m][o]][1][l], 1); + for (int k = 0; k < 9; k++) + dnconstants_3b_view(map3b_view(n, m, o), 1, l - 1, k) = + (std::isinf(c[k]) || std::isnan(c[k])) ? 0 : c[k]; + } + for (int l = 1; l < n3b_knots_array_size[map_3b[n][m][o]][0] - 5; l++) { + auto c = get_dnconstants(&n3b_knots_array[map_3b[n][m][o]][0][l], 1); + for (int k = 0; k < 9; k++) + dnconstants_3b_view(map3b_view(n, m, o), 2, l - 1, k) = + (std::isinf(c[k]) || std::isnan(c[k])) ? 0 : c[k]; + } + } + } + } + Kokkos::deep_copy(dnconstants_3b, dnconstants_3b_view); +} + +template +template +KOKKOS_INLINE_FUNCTION void PairUF3Kokkos::twobody(const int itype, const int jtype, + const F_FLOAT r, F_FLOAT &evdwl, + F_FLOAT &fpair) const +{ + + // Find knot starting position + int interaction_id = map2b(itype, jtype); + int start_index = 3; + while (r > d_n2b_knot(interaction_id, start_index + 1)) start_index++; + //int start_index = 3+(int)((r-d_n2b_knot(interaction_id,0))/d_n2b_knot_spacings(interaction_id)); + + F_FLOAT r_values[4]; + r_values[0] = 1; + r_values[1] = r; + r_values[2] = r_values[1] * r_values[1]; + + if (EVFLAG) { + r_values[3] = r_values[2] * r_values[1]; + // Calculate energy + evdwl = constants_2b(interaction_id, start_index, 0); + evdwl += r_values[1] * constants_2b(interaction_id, start_index, 1); + evdwl += r_values[2] * constants_2b(interaction_id, start_index, 2); + evdwl += r_values[3] * constants_2b(interaction_id, start_index, 3); + evdwl += constants_2b(interaction_id, start_index - 1, 4); + evdwl += r_values[1] * constants_2b(interaction_id, start_index - 1, 5); + evdwl += r_values[2] * constants_2b(interaction_id, start_index - 1, 6); + evdwl += r_values[3] * constants_2b(interaction_id, start_index - 1, 7); + evdwl += constants_2b(interaction_id, start_index - 2, 8); + evdwl += r_values[1] * constants_2b(interaction_id, start_index - 2, 9); + evdwl += r_values[2] * constants_2b(interaction_id, start_index - 2, 10); + evdwl += r_values[3] * constants_2b(interaction_id, start_index - 2, 11); + evdwl += constants_2b(interaction_id, start_index - 3, 12); + evdwl += r_values[1] * constants_2b(interaction_id, start_index - 3, 13); + evdwl += r_values[2] * constants_2b(interaction_id, start_index - 3, 14); + evdwl += r_values[3] * constants_2b(interaction_id, start_index - 3, 15); + } + + // Calculate force + fpair = dnconstants_2b(interaction_id, start_index - 1, 0); + fpair += r_values[1] * dnconstants_2b(interaction_id, start_index - 1, 1); + fpair += r_values[2] * dnconstants_2b(interaction_id, start_index - 1, 2); + fpair += dnconstants_2b(interaction_id, start_index - 2, 3); + fpair += r_values[1] * dnconstants_2b(interaction_id, start_index - 2, 4); + fpair += r_values[2] * dnconstants_2b(interaction_id, start_index - 2, 5); + fpair += dnconstants_2b(interaction_id, start_index - 3, 6); + fpair += r_values[1] * dnconstants_2b(interaction_id, start_index - 3, 7); + fpair += r_values[2] * dnconstants_2b(interaction_id, start_index - 3, 8); +} + +template +template +KOKKOS_INLINE_FUNCTION void PairUF3Kokkos::threebody( + const int itype, const int jtype, const int ktype, const F_FLOAT value_rij, + const F_FLOAT value_rik, const F_FLOAT value_rjk, F_FLOAT &evdwl, F_FLOAT (&fforce)[3]) const +{ + evdwl = 0; + fforce[0] = 0; + fforce[1] = 0; + fforce[2] = 0; + + F_FLOAT evals[3][4]; + F_FLOAT dnevals[3][4]; + int start_indices[3]; + F_FLOAT r[3] = {value_rij, value_rik, value_rjk}; + int interaction_id = map3b(itype, jtype, ktype); + + auto coefficients = + Kokkos::subview(d_coefficients_3b, interaction_id, Kokkos::ALL, Kokkos::ALL, Kokkos::ALL); + auto dncoefficients = Kokkos::subview(d_dncoefficients_3b, interaction_id, Kokkos::ALL, + Kokkos::ALL, Kokkos::ALL, Kokkos::ALL); + //Notice the 2-d in d_n3b_knot_matrix + // + //In d_n3b_knot_matrix[i][j][k], + //d_n3b_knot_matrix[i][j][k][0] is the knot_vector along jk, + //d_n3b_knot_matrix[i][j][k][1] is the knot_vector along ik, + //d_n3b_knot_matrix[i][j][k][2] is the knot_vector along ij, + // + //and r[0] = rij, r[1] = rik and r[2] = rjk + //see n3b_knot_matrix and pair_uf3.cpp for more details + for (int d = 0; d < 3; d++) { + start_indices[d] = 3; + while (r[d] > d_n3b_knot_matrix(interaction_id, 2-d, start_indices[d] + 1)) start_indices[d]++; + //start_indices[d] = 3+(int)((r[d]-d_n3b_knot_matrix(interaction_id, 2-d, 0))/d_n3b_knot_matrix_spacings(interaction_id, 2-d)); + + F_FLOAT r_values[4]; + r_values[0] = 1; + r_values[1] = r[d]; + r_values[2] = r_values[1] * r_values[1]; + + r_values[3] = r_values[2] * r_values[1]; + + // Calculate energy + evals[d][0] = constants_3b(interaction_id, d, start_indices[d], 0); + evals[d][0] += r_values[1] * constants_3b(interaction_id, d, start_indices[d], 1); + evals[d][0] += r_values[2] * constants_3b(interaction_id, d, start_indices[d], 2); + evals[d][0] += r_values[3] * constants_3b(interaction_id, d, start_indices[d], 3); + evals[d][1] = constants_3b(interaction_id, d, start_indices[d] - 1, 4); + evals[d][1] += r_values[1] * constants_3b(interaction_id, d, start_indices[d] - 1, 5); + evals[d][1] += r_values[2] * constants_3b(interaction_id, d, start_indices[d] - 1, 6); + evals[d][1] += r_values[3] * constants_3b(interaction_id, d, start_indices[d] - 1, 7); + evals[d][2] = constants_3b(interaction_id, d, start_indices[d] - 2, 8); + evals[d][2] += r_values[1] * constants_3b(interaction_id, d, start_indices[d] - 2, 9); + evals[d][2] += r_values[2] * constants_3b(interaction_id, d, start_indices[d] - 2, 10); + evals[d][2] += r_values[3] * constants_3b(interaction_id, d, start_indices[d] - 2, 11); + evals[d][3] = constants_3b(interaction_id, d, start_indices[d] - 3, 12); + evals[d][3] += r_values[1] * constants_3b(interaction_id, d, start_indices[d] - 3, 13); + evals[d][3] += r_values[2] * constants_3b(interaction_id, d, start_indices[d] - 3, 14); + evals[d][3] += r_values[3] * constants_3b(interaction_id, d, start_indices[d] - 3, 15); + + dnevals[d][0] = dnconstants_3b(interaction_id, d, start_indices[d] - 1, 0); + dnevals[d][0] += r_values[1] * dnconstants_3b(interaction_id, d, start_indices[d] - 1, 1); + dnevals[d][0] += r_values[2] * dnconstants_3b(interaction_id, d, start_indices[d] - 1, 2); + dnevals[d][1] = dnconstants_3b(interaction_id, d, start_indices[d] - 2, 3); + dnevals[d][1] += r_values[1] * dnconstants_3b(interaction_id, d, start_indices[d] - 2, 4); + dnevals[d][1] += r_values[2] * dnconstants_3b(interaction_id, d, start_indices[d] - 2, 5); + dnevals[d][2] = dnconstants_3b(interaction_id, d, start_indices[d] - 3, 6); + dnevals[d][2] += r_values[1] * dnconstants_3b(interaction_id, d, start_indices[d] - 3, 7); + dnevals[d][2] += r_values[2] * dnconstants_3b(interaction_id, d, start_indices[d] - 3, 8); + dnevals[d][3] = 0; + } + + if (EVFLAG) { + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + evdwl += coefficients(start_indices[0] - i, start_indices[1] - j, start_indices[2] - k) * + evals[0][i] * evals[1][j] * evals[2][k]; + } + } + } + } + + for (int i = 0; i < 3; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + fforce[0] += dncoefficients(0, start_indices[0] - 3 + i, start_indices[1] - 3 + j, + start_indices[2] - 3 + k) * + dnevals[0][2 - i] * evals[1][3 - j] * evals[2][3 - k]; + } + } + } + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 3; j++) { + for (int k = 0; k < 4; k++) { + fforce[1] += dncoefficients(1, start_indices[0] - 3 + i, start_indices[1] - 3 + j, + start_indices[2] - 3 + k) * + evals[0][3 - i] * dnevals[1][2 - j] * evals[2][3 - k]; + } + } + } + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 3; k++) { + fforce[2] += dncoefficients(2, start_indices[0] - 3 + i, start_indices[1] - 3 + j, + start_indices[2] - 3 + k) * + evals[0][3 - i] * evals[1][3 - j] * dnevals[2][2 - k]; + } + } + } +} + +template void PairUF3Kokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + if (neighflag == FULL) no_virial_fdotr_compute = 1; + + ev_init(eflag, vflag, 0); + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom, eatom); + memoryKK->create_kokkos(k_eatom, eatom, maxeatom, "pair:eatom"); + d_eatom = k_eatom.view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom, vatom); + memoryKK->create_kokkos(k_vatom, vatom, maxvatom, "pair:vatom"); + d_vatom = k_vatom.view(); + } + + atomKK->sync(execution_space, datamask_read); + if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); + else atomKK->modified(execution_space,F_MASK); + + x = atomKK->k_x.template view(); + f = atomKK->k_f.template view(); + tag = atomKK->k_tag.template view(); + type = atomKK->k_type.template view(); + nlocal = atom->nlocal; + newton_pair = force->newton_pair; + nall = atom->nlocal + atom->nghost; + k_cutsq.template sync(); //Sync the device memory of k_cutsq with + //the array from the host memory; this updates d_cutsq also + k_cut_3b.template sync(); + k_min_cut_3b.template sync(); + + inum = list->inum; + const int ignum = inum + list->gnum; + NeighListKokkos *k_list = static_cast *>(list); + d_ilist = k_list->d_ilist; + d_numneigh = k_list->d_numneigh; + d_neighbors = k_list->d_neighbors; + + copymode = 1; + + escatter = ScatterEType(d_eatom); + fscatter = ScatterFType(f); + vscatter = ScatterVType(d_vatom); + //cvscatter = ScatterCVType(d_cvatom); + + EV_FLOAT ev; + EV_FLOAT ev_all; + + // build short neighbor list + + int max_neighs = d_neighbors.extent(1); + + if (((int)d_neighbors_short.extent(1) != max_neighs) || + ((int)d_neighbors_short.extent(0) != ignum)) { + d_neighbors_short = Kokkos::View("UF3::neighbors_short", ignum, max_neighs); + } + if (d_numneigh_short.extent(0) != ignum) + d_numneigh_short = Kokkos::View("UF3::numneighs_short", ignum); + Kokkos::parallel_for( + Kokkos::RangePolicy(0, ignum), *this); + + // loop over neighbor list of my atoms + + if (evflag) { + Kokkos::parallel_reduce( + Kokkos::RangePolicy>(0, inum), *this, ev); + } + else{ + Kokkos::parallel_for( + Kokkos::RangePolicy>(0, inum), *this); + } + ev_all += ev; + + Kokkos::Experimental::contribute(d_eatom, escatter); + Kokkos::Experimental::contribute(d_vatom, vscatter); + //Kokkos::Experimental::contribute(d_cvatom, cvscatter); + Kokkos::Experimental::contribute(f, fscatter); + + if (eflag_global) eng_vdwl += ev_all.evdwl; + if (vflag_global) { + virial[0] += ev_all.v[0]; + virial[1] += ev_all.v[1]; + virial[2] += ev_all.v[2]; + virial[3] += ev_all.v[3]; + virial[4] += ev_all.v[4]; + virial[5] += ev_all.v[5]; + } + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + } + + if (cvflag_atom) { + //k_cvatom.template modify(); + //k_cvatom.template sync(); + } + + if (vflag_fdotr) pair_virial_fdotr_compute(this); + + copymode = 0; +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION void PairUF3Kokkos::operator()(TagPairUF3ComputeShortNeigh, + const int &ii) const +{ + const int i = d_ilist[ii]; + const X_FLOAT xtmp = x(i, 0); + const X_FLOAT ytmp = x(i, 1); + const X_FLOAT ztmp = x(i, 2); + + const int jnum = d_numneigh[i]; + int inside = 0; + for (int jj = 0; jj < jnum; jj++) { + int j = d_neighbors(i, jj); + j &= NEIGHMASK; + + const X_FLOAT delx = xtmp - x(j, 0); + const X_FLOAT dely = ytmp - x(j, 1); + const X_FLOAT delz = ztmp - x(j, 2); + const F_FLOAT rsq = delx * delx + dely * dely + delz * delz; + + const int itype = type[i]; + const int jtype = type[j]; + + if (rsq <= d_cutsq(itype, jtype)) { + d_neighbors_short(i, inside) = j; + inside++; + } + } + d_numneigh_short(i) = inside; +} + +/* ---------------------------------------------------------------------- */ + +template +template +KOKKOS_INLINE_FUNCTION void +PairUF3Kokkos::operator()(TagPairUF3ComputeFullA, const int &ii, + EV_FLOAT &ev) const +{ + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = vscatter.access(); + auto a_f = fscatter.access(); + auto a_cvatom = cvscatter.access(); + + F_FLOAT del_rji[3], del_rki[3], del_rkj[3], triangle_eval[3]; + F_FLOAT fij[3], fik[3], fjk[3]; + F_FLOAT fji[3], fki[3], fkj[3]; + F_FLOAT Fj[3], Fk[3]; + F_FLOAT evdwl = 0, evdwl3 = 0; + F_FLOAT fpair = 0; + + const int i = d_ilist[ii]; + const int itype = type[i]; + const X_FLOAT xtmp = x(i, 0); + const X_FLOAT ytmp = x(i, 1); + const X_FLOAT ztmp = x(i, 2); + + // two-body interactions + + const int jnum = d_numneigh_short[i]; + + F_FLOAT fxtmpi = 0.0; + F_FLOAT fytmpi = 0.0; + F_FLOAT fztmpi = 0.0; + + for (int jj = 0; jj < jnum; jj++) { + int j = d_neighbors_short(i, jj); + j &= NEIGHMASK; + const int jtype = type[j]; + + const X_FLOAT delx = xtmp - x(j, 0); + const X_FLOAT dely = ytmp - x(j, 1); + const X_FLOAT delz = ztmp - x(j, 2); + const F_FLOAT rsq = delx * delx + dely * dely + delz * delz; + + if (rsq >= d_cutsq(itype, jtype)) continue; + + const F_FLOAT rij = sqrt(rsq); + this->template twobody(itype, jtype, rij, evdwl, fpair); + + fpair = -fpair / rij; + + fxtmpi += delx * fpair; + fytmpi += dely * fpair; + fztmpi += delz * fpair; + a_f(j, 0) -= delx * fpair; + a_f(j, 1) -= dely * fpair; + a_f(j, 2) -= delz * fpair; + + if (EVFLAG) { + if (eflag) ev.evdwl += evdwl; + if (vflag_either || eflag_atom) + this->template ev_tally(ev, i, j, evdwl, fpair, delx, dely, delz); + } + } + + // 3-body interaction + // jth atom + const int jnumm1 = jnum - 1; + for (int jj = 0; jj < jnumm1; jj++) { + int j = d_neighbors_short(i, jj); + j &= NEIGHMASK; + const int jtype = type[j]; + del_rji[0] = x(j, 0) - xtmp; + del_rji[1] = x(j, 1) - ytmp; + del_rji[2] = x(j, 2) - ztmp; + F_FLOAT rij = sqrt(del_rji[0] * del_rji[0] + del_rji[1] * del_rji[1] + del_rji[2] * del_rji[2]); + + F_FLOAT fxtmpj = 0.0; + F_FLOAT fytmpj = 0.0; + F_FLOAT fztmpj = 0.0; + + for (int kk = jj + 1; kk < jnum; kk++) { + int k = d_neighbors_short(i, kk); + k &= NEIGHMASK; + const int ktype = type[k]; + + // Notice the order of d_min_cut_3b[i][j][k] + //In d_min_cut_3b[i][j][k], + //d_min_cut_3b[i][j][k][0] is the knot_vector along jk, + //d_min_cut_3b[i][j][k][1] is the knot_vector along ik, + //d_min_cut_3b[i][j][k][2] is the knot_vector along ij, + //see pair_uf3.cpp for more details + if (rij < d_min_cut_3b(itype, jtype, ktype, 2)) continue; + if (rij > d_cut_3b(itype, jtype, ktype)) continue; + + del_rki[0] = x(k, 0) - xtmp; + del_rki[1] = x(k, 1) - ytmp; + del_rki[2] = x(k, 2) - ztmp; + F_FLOAT rik = + sqrt(del_rki[0] * del_rki[0] + del_rki[1] * del_rki[1] + del_rki[2] * del_rki[2]); + + if (rik < d_min_cut_3b(itype, jtype, ktype, 1)) continue; + if (rik > d_cut_3b(itype, ktype, jtype)) continue; + + del_rkj[0] = x(k, 0) - x(j, 0); + del_rkj[1] = x(k, 1) - x(j, 1); + del_rkj[2] = x(k, 2) - x(j, 2); + F_FLOAT rjk = + sqrt(del_rkj[0] * del_rkj[0] + del_rkj[1] * del_rkj[1] + del_rkj[2] * del_rkj[2]); + if (rjk < d_min_cut_3b(itype, jtype, ktype, 0)) continue; + this->template threebody(itype, jtype, ktype, rij, rik, rjk, evdwl3, triangle_eval); + + fij[0] = *(triangle_eval + 0) * (del_rji[0] / rij); + fji[0] = -fij[0]; + fik[0] = *(triangle_eval + 1) * (del_rki[0] / rik); + fki[0] = -fik[0]; + fjk[0] = *(triangle_eval + 2) * (del_rkj[0] / rjk); + fkj[0] = -fjk[0]; + + fij[1] = *(triangle_eval + 0) * (del_rji[1] / rij); + fji[1] = -fij[1]; + fik[1] = *(triangle_eval + 1) * (del_rki[1] / rik); + fki[1] = -fik[1]; + fjk[1] = *(triangle_eval + 2) * (del_rkj[1] / rjk); + fkj[1] = -fjk[1]; + + fij[2] = *(triangle_eval + 0) * (del_rji[2] / rij); + fji[2] = -fij[2]; + fik[2] = *(triangle_eval + 1) * (del_rki[2] / rik); + fki[2] = -fik[2]; + fjk[2] = *(triangle_eval + 2) * (del_rkj[2] / rjk); + fkj[2] = -fjk[2]; + + Fj[0] = fji[0] + fjk[0]; + Fj[1] = fji[1] + fjk[1]; + Fj[2] = fji[2] + fjk[2]; + + Fk[0] = fki[0] + fkj[0]; + Fk[1] = fki[1] + fkj[1]; + Fk[2] = fki[2] + fkj[2]; + + fxtmpi += (fij[0] + fik[0]); + fytmpi += (fij[1] + fik[1]); + fztmpi += (fij[2] + fik[2]); + fxtmpj += Fj[0]; + fytmpj += Fj[1]; + fztmpj += Fj[2]; + a_f(k, 0) += Fk[0]; + a_f(k, 1) += Fk[1]; + a_f(k, 2) += Fk[2]; + + if (EVFLAG) { + if (eflag) { ev.evdwl += evdwl3; } + if (vflag_either || eflag_atom) { + this->template ev_tally3(ev, i, j, k, evdwl3, 0.0, Fj, Fk, del_rji, del_rki); + if (cvflag_atom) { + + F_FLOAT ric[3]; + ric[0] = THIRD * (-del_rji[0] - del_rki[0]); + ric[1] = THIRD * (-del_rji[1] - del_rki[1]); + ric[2] = THIRD * (-del_rji[2] - del_rki[2]); + a_cvatom(i, 0) += ric[0] * (-Fj[0] - Fk[0]); + a_cvatom(i, 1) += ric[1] * (-Fj[1] - Fk[1]); + a_cvatom(i, 2) += ric[2] * (-Fj[2] - Fk[2]); + a_cvatom(i, 3) += ric[0] * (-Fj[1] - Fk[1]); + a_cvatom(i, 4) += ric[0] * (-Fj[2] - Fk[2]); + a_cvatom(i, 5) += ric[1] * (-Fj[2] - Fk[2]); + a_cvatom(i, 6) += ric[1] * (-Fj[0] - Fk[0]); + a_cvatom(i, 7) += ric[2] * (-Fj[0] - Fk[0]); + a_cvatom(i, 8) += ric[2] * (-Fj[1] - Fk[1]); + + double rjc[3]; + rjc[0] = THIRD * (del_rji[0] - del_rkj[0]); + rjc[1] = THIRD * (del_rji[1] - del_rkj[1]); + rjc[2] = THIRD * (del_rji[2] - del_rkj[2]); + + a_cvatom(j, 0) += rjc[0] * Fj[0]; + a_cvatom(j, 1) += rjc[1] * Fj[1]; + a_cvatom(j, 2) += rjc[2] * Fj[2]; + a_cvatom(j, 3) += rjc[0] * Fj[1]; + a_cvatom(j, 4) += rjc[0] * Fj[2]; + a_cvatom(j, 5) += rjc[1] * Fj[2]; + a_cvatom(j, 6) += rjc[1] * Fj[0]; + a_cvatom(j, 7) += rjc[2] * Fj[0]; + a_cvatom(j, 8) += rjc[2] * Fj[1]; + + double rkc[3]; + rkc[0] = THIRD * (del_rki[0] + del_rkj[0]); + rkc[1] = THIRD * (del_rki[1] + del_rkj[1]); + rkc[2] = THIRD * (del_rki[2] + del_rkj[2]); + + a_cvatom(k, 0) += rkc[0] * Fk[0]; + a_cvatom(k, 1) += rkc[1] * Fk[1]; + a_cvatom(k, 2) += rkc[2] * Fk[2]; + a_cvatom(k, 3) += rkc[0] * Fk[1]; + a_cvatom(k, 4) += rkc[0] * Fk[2]; + a_cvatom(k, 5) += rkc[1] * Fk[2]; + a_cvatom(k, 6) += rkc[1] * Fk[0]; + a_cvatom(k, 7) += rkc[2] * Fk[0]; + a_cvatom(k, 8) += rkc[2] * Fk[1]; + } + } + } + } + a_f(j, 0) += fxtmpj; + a_f(j, 1) += fytmpj; + a_f(j, 2) += fztmpj; + } + + a_f(i, 0) += fxtmpi; + a_f(i, 1) += fytmpi; + a_f(i, 2) += fztmpi; +} + +template +template +KOKKOS_INLINE_FUNCTION void +PairUF3Kokkos::operator()(TagPairUF3ComputeFullA, + const int &ii) const +{ + EV_FLOAT ev; + this->template operator()(TagPairUF3ComputeFullA(), ii, ev); +} + +/* ---------------------------------------------------------------------- */ + +template +template +KOKKOS_INLINE_FUNCTION void +PairUF3Kokkos::ev_tally(EV_FLOAT &ev, const int &i, const int &j, const F_FLOAT &epair, + const F_FLOAT &fpair, const F_FLOAT &delx, const F_FLOAT &dely, + const F_FLOAT &delz) const +{ + + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, + // and neither for Serial + + auto a_eatom = escatter.access(); + auto a_vatom = vscatter.access(); + auto a_cvatom = cvscatter.access(); + + if (eflag_atom) { + const E_FLOAT epairhalf = 0.5 * epair; + a_eatom[i] += epairhalf; + a_eatom[j] += epairhalf; + } + + if (vflag_either) { + const E_FLOAT v0 = delx * delx * fpair; + const E_FLOAT v1 = dely * dely * fpair; + const E_FLOAT v2 = delz * delz * fpair; + const E_FLOAT v3 = delx * dely * fpair; + const E_FLOAT v4 = delx * delz * fpair; + const E_FLOAT v5 = dely * delz * fpair; + + if (vflag_global) { + ev.v[0] += v0; + ev.v[1] += v1; + ev.v[2] += v2; + ev.v[3] += v3; + ev.v[4] += v4; + ev.v[5] += v5; + } + + if (vflag_atom) { + a_vatom(i, 0) += 0.5 * v0; + a_vatom(i, 1) += 0.5 * v1; + a_vatom(i, 2) += 0.5 * v2; + a_vatom(i, 3) += 0.5 * v3; + a_vatom(i, 4) += 0.5 * v4; + a_vatom(i, 5) += 0.5 * v5; + + a_vatom(j, 0) += 0.5 * v0; + a_vatom(j, 1) += 0.5 * v1; + a_vatom(j, 2) += 0.5 * v2; + a_vatom(j, 3) += 0.5 * v3; + a_vatom(j, 4) += 0.5 * v4; + a_vatom(j, 5) += 0.5 * v5; + } + + if (cvflag_atom) { + a_cvatom(i, 0) += 0.5 * v0; + a_cvatom(i, 1) += 0.5 * v1; + a_cvatom(i, 2) += 0.5 * v2; + a_cvatom(i, 3) += 0.5 * v3; + a_cvatom(i, 4) += 0.5 * v4; + a_cvatom(i, 5) += 0.5 * v5; + a_cvatom(i, 6) += 0.5 * v3; + a_cvatom(i, 7) += 0.5 * v4; + a_cvatom(i, 8) += 0.5 * v5; + a_cvatom(j, 0) += 0.5 * v0; + a_cvatom(j, 1) += 0.5 * v1; + a_cvatom(j, 2) += 0.5 * v2; + a_cvatom(j, 3) += 0.5 * v3; + a_cvatom(j, 4) += 0.5 * v4; + a_cvatom(j, 5) += 0.5 * v5; + a_cvatom(j, 6) += 0.5 * v3; + a_cvatom(j, 7) += 0.5 * v4; + a_cvatom(j, 8) += 0.5 * v5; + } + } +} + +/* ---------------------------------------------------------------------- + tally eng_vdwl and virial into global and per-atom accumulators + called by SW and hbond potentials, newton_pair is always on + virial = riFi + rjFj + rkFk = (rj-ri) Fj + (rk-ri) Fk = drji*fj + drki*fk + ------------------------------------------------------------------------- */ + +template +template +KOKKOS_INLINE_FUNCTION void +PairUF3Kokkos::ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k, + const F_FLOAT &evdwl, const F_FLOAT &ecoul, F_FLOAT *fj, + F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const +{ + F_FLOAT epairthird, v[6]; + + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, + // and neither for Serial + + auto a_eatom = escatter.access(); + auto a_vatom = vscatter.access(); + + if (eflag_atom) { + epairthird = THIRD * (evdwl + ecoul); + a_eatom[i] += epairthird; + a_eatom[j] += epairthird; + a_eatom[k] += epairthird; + } + + if (vflag_either) { + v[0] = drji[0] * fj[0] + drki[0] * fk[0]; + v[1] = drji[1] * fj[1] + drki[1] * fk[1]; + v[2] = drji[2] * fj[2] + drki[2] * fk[2]; + v[3] = drji[0] * fj[1] + drki[0] * fk[1]; + v[4] = drji[0] * fj[2] + drki[0] * fk[2]; + v[5] = drji[1] * fj[2] + drki[1] * fk[2]; + + if (vflag_global) { + ev.v[0] += v[0]; + ev.v[1] += v[1]; + ev.v[2] += v[2]; + ev.v[3] += v[3]; + ev.v[4] += v[4]; + ev.v[5] += v[5]; + } + + if (vflag_atom) { + a_vatom(i, 0) += THIRD * v[0]; + a_vatom(i, 1) += THIRD * v[1]; + a_vatom(i, 2) += THIRD * v[2]; + a_vatom(i, 3) += THIRD * v[3]; + a_vatom(i, 4) += THIRD * v[4]; + a_vatom(i, 5) += THIRD * v[5]; + + a_vatom(j, 0) += THIRD * v[0]; + a_vatom(j, 1) += THIRD * v[1]; + a_vatom(j, 2) += THIRD * v[2]; + a_vatom(j, 3) += THIRD * v[3]; + a_vatom(j, 4) += THIRD * v[4]; + a_vatom(j, 5) += THIRD * v[5]; + + a_vatom(k, 0) += THIRD * v[0]; + a_vatom(k, 1) += THIRD * v[1]; + a_vatom(k, 2) += THIRD * v[2]; + a_vatom(k, 3) += THIRD * v[3]; + a_vatom(k, 4) += THIRD * v[4]; + a_vatom(k, 5) += THIRD * v[5]; + } + } +} + +/* ---------------------------------------------------------------------- + tally eng_vdwl and virial into global and per-atom accumulators + called by SW and hbond potentials, newton_pair is always on + virial = riFi + rjFj + rkFk = (rj-ri) Fj + (rk-ri) Fk = drji*fj + drki*fk + ------------------------------------------------------------------------- */ + +template +template +void PairUF3Kokkos::copy_2d(V &d, T **h, int m, int n) +{ + Kokkos::View tmp("pair::tmp", m, n); //Create tmp view(array) on + //device memory + + //auto h_view = Kokkos::create_mirror_view(tmp); + auto h_view = Kokkos::create_mirror(tmp); //Create a mirror of the device + //view(array) tmp, as deep_copy is only possible for mirror views + + for (int i = 0; i < m; i++) { + for (int j = 0; j < n; j++) { + h_view(i, j) = h[i][j]; //fill mirror + } + //views with data from normal array 'h' which always lives on host memory + } + + Kokkos::deep_copy(tmp, h_view); //Deepcopy data from h_view(host) to tmp(device) + + d = tmp; +} + +template +template +void PairUF3Kokkos::copy_3d(V &d, T ***h, int m, int n, int o) +{ + Kokkos::View tmp("pair::tmp", m, n, o); //Create tmp view(array) on + //device memory + + //auto h_view = Kokkos::create_mirror_view(tmp); //create_mirror always copies + //the data. create_mirror_view only copies data if the host cannot access the + //data + auto h_view = Kokkos::create_mirror(tmp); //Create a mirror of the device + //view(array) tmp, as deep_copy is only possible for mirror views + for (int i = 0; i < m; i++) { + for (int j = 0; j < n; j++) { + for (int k = 0; k < o; k++) { h_view(i, j, k) = h[i][j][k]; } //fill mirror + //views with data from normal array 'h' which always lives on host memory + } + } + + Kokkos::deep_copy(tmp, h_view); //Deepcopy data from h_view(host) to tmp(device) + + d = tmp; +} + +template +std::vector PairUF3Kokkos::get_constants(double *knots, double coefficient) +{ + + std::vector constants(16); + + constants[0] = coefficient * + (-cube(knots[0]) / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + constants[1] = coefficient * + (3 * square(knots[0]) / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + constants[2] = coefficient * + (-3 * knots[0] / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + constants[3] = coefficient * + (1 / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + constants[4] = coefficient * + (square(knots[1]) * knots[4] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) + + square(knots[0]) * knots[2] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) + + knots[0] * knots[1] * knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + constants[5] = coefficient * + (-square(knots[1]) / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) - + 2 * knots[1] * knots[4] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) - + square(knots[0]) / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) - + 2 * knots[0] * knots[2] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) - + knots[0] * knots[1] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) - + knots[0] * knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) - + knots[1] * knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + constants[6] = coefficient * + (2 * knots[1] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) + + knots[4] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) + + 2 * knots[0] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) + + knots[2] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) + + knots[0] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) + + knots[1] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) + + knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + constants[7] = coefficient * + (-1 / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) - + 1 / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) - + 1 / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + constants[8] = coefficient * + (-knots[0] * square(knots[3]) / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) - + knots[1] * knots[3] * knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[2] * square(knots[4]) / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + constants[9] = coefficient * + (2 * knots[0] * knots[3] / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) + + square(knots[3]) / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) + + knots[1] * knots[3] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + knots[1] * knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + knots[3] * knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + 2 * knots[2] * knots[4] / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4])) + + square(knots[4]) / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + constants[10] = coefficient * + (-knots[0] / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) - + 2 * knots[3] / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) - + knots[1] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[3] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[2] / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4])) - + 2 * knots[4] / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + constants[11] = coefficient * + (1 / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) + + 1 / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + 1 / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + constants[12] = coefficient * + (cube(knots[4]) / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + constants[13] = coefficient * + (-3 * square(knots[4]) / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + constants[14] = coefficient * + (3 * knots[4] / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + constants[15] = coefficient * + (-1 / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + + return constants; +} + +template +std::vector PairUF3Kokkos::get_dnconstants(double *knots, double coefficient) +{ + std::vector constants(9); + + constants[0] = coefficient * + (square(knots[0]) / + (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2])); + constants[1] = coefficient * + (-2 * knots[0] / + (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2])); + constants[2] = coefficient * + (1 / (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2])); + constants[3] = coefficient * + (-knots[1] * knots[3] / + (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) - + knots[0] * knots[2] / + (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2]))); + constants[4] = coefficient * + (knots[1] / + (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) + + knots[3] / + (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) + + knots[0] / + (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])) + + knots[2] / + (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2]))); + constants[5] = coefficient * + (-1 / (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) - + 1 / (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2]))); + constants[6] = coefficient * + (square(knots[3]) / + (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3]))); + constants[7] = coefficient * + (-2 * knots[3] / + (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3]))); + constants[8] = coefficient * + (1 / (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3]))); + + return constants; +} + +template +double PairUF3Kokkos::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) +{ + double value = 0.0; + double r = sqrt(rsq); + int interaction_id = map2b(itype, jtype); + int start_index = 3; + while (r > d_n2b_knot(interaction_id, start_index + 1)) start_index++; + + if (r < d_cutsq(itype, jtype)) { + F_FLOAT r_values[4]; + r_values[0] = 1; + r_values[1] = r; + r_values[2] = r_values[1] * r_values[1]; + r_values[3] = r_values[2] * r_values[1]; + + // Calculate energy + value = constants_2b(interaction_id, start_index, 0); + value += r_values[1] * constants_2b(interaction_id, start_index, 1); + value += r_values[2] * constants_2b(interaction_id, start_index, 2); + value += r_values[3] * constants_2b(interaction_id, start_index, 3); + value += constants_2b(interaction_id, start_index - 1, 4); + value += r_values[1] * constants_2b(interaction_id, start_index - 1, 5); + value += r_values[2] * constants_2b(interaction_id, start_index - 1, 6); + value += r_values[3] * constants_2b(interaction_id, start_index - 1, 7); + value += constants_2b(interaction_id, start_index - 2, 8); + value += r_values[1] * constants_2b(interaction_id, start_index - 2, 9); + value += r_values[2] * constants_2b(interaction_id, start_index - 2, 10); + value += r_values[3] * constants_2b(interaction_id, start_index - 2, 11); + value += constants_2b(interaction_id, start_index - 3, 12); + value += r_values[1] * constants_2b(interaction_id, start_index - 3, 13); + value += r_values[2] * constants_2b(interaction_id, start_index - 3, 14); + value += r_values[3] * constants_2b(interaction_id, start_index - 3, 15); + + // Calculate force + fforce = dnconstants_2b(interaction_id, start_index - 1, 0); + fforce += r_values[1] * dnconstants_2b(interaction_id, start_index - 1, 1); + fforce += r_values[2] * dnconstants_2b(interaction_id, start_index - 1, 2); + fforce += dnconstants_2b(interaction_id, start_index - 2, 3); + fforce += r_values[1] * dnconstants_2b(interaction_id, start_index - 2, 4); + fforce += r_values[2] * dnconstants_2b(interaction_id, start_index - 2, 5); + fforce += dnconstants_2b(interaction_id, start_index - 3, 6); + fforce += r_values[1] * dnconstants_2b(interaction_id, start_index - 3, 7); + fforce += r_values[2] * dnconstants_2b(interaction_id, start_index - 3, 8); + } + + return factor_lj * value; +} + +namespace LAMMPS_NS { +template class PairUF3Kokkos; +#ifdef KOKKOS_ENABLE_CUDA +template class PairUF3Kokkos; +#endif +} // namespace LAMMPS_NS diff --git a/src/KOKKOS/pair_uf3_kokkos.h b/src/KOKKOS/pair_uf3_kokkos.h new file mode 100644 index 0000000000..15c2832da1 --- /dev/null +++ b/src/KOKKOS/pair_uf3_kokkos.h @@ -0,0 +1,187 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Ajinkya Hire (Univ. of Florida), + Hendrik Kraß (Univ. of Constance), + Matthias Rupp (Luxembourg Institute of Science and Technology), + Richard Hennig (Univ of Florida) +---------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(uf3/kk,PairUF3Kokkos) +PairStyle(uf3/kk/device,PairUF3Kokkos) +// clang-format on +#else + +#ifndef LMP_PAIR_UF3_KOKKOS_H +#define LMP_PAIR_UF3_KOKKOS_H + +#include "kokkos.h" +#include "pair_kokkos.h" +#include "pair_uf3.h" + +template struct TagPairUF3ComputeFullA {}; +struct TagPairUF3ComputeShortNeigh {}; + +namespace LAMMPS_NS { + +template class PairUF3Kokkos : public PairUF3 { + public: + PairUF3Kokkos(class LAMMPS *); + ~PairUF3Kokkos() override; + void compute(int, int) override; + void settings(int, char **) override; + void coeff(int, char **) override; + void allocate(); + void init_style() override; + void init_list(int, class NeighList *) override; // needed for ptr to full neigh list + double init_one(int, int) override; // needed for cutoff radius for neighbour list + double single(int, int, int, int, double, double, double, double &) override; + + template void copy_2d(V &d, T **h, int m, int n); + template void copy_3d(V &d, T ***h, int m, int n, int o); + + template + KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA, const int &, + EV_FLOAT &) const; + + template + KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA, + const int &) const; + + KOKKOS_INLINE_FUNCTION + void operator()(TagPairUF3ComputeShortNeigh, const int &) const; + + enum { EnabledNeighFlags = FULL }; + enum { COUL_FLAG = 0 }; + typedef DeviceType device_type; + typedef ArrayTypes AT; + typedef EV_FLOAT value_type; + + protected: + typename AT::tdual_ffloat_2d k_cutsq;//Create a DualView, defination of tdual_ffloat_2d in kokkos_type.h + typename AT::t_ffloat_2d d_cutsq; //t_ffloat_2d = t_dev ==> Creates a new View d_cutsq + //the type of d_cutsq is decided by the Device(not host) type for the DualView k_cutsq + //Meaning the memory location of d_cutsq is the same as the Device(not host) memory location of + //k_cutsq + typedef Kokkos::DualView tdual_ffloat_3d; + typedef Kokkos::DualView tdual_ffloat_4d; + tdual_ffloat_3d k_cut_3b; + tdual_ffloat_4d k_min_cut_3b; + typename tdual_ffloat_3d::t_dev d_cut_3b; + typename tdual_ffloat_4d::t_dev d_min_cut_3b; + template void destroy_3d(TYPE data, typename TYPE::value_type*** &array); + template void destroy_4d(TYPE data, typename TYPE::value_type**** &array); + Kokkos::View /*d_cutsq,*/ d_cut_3b_list; + //Kokkos::View d_cut_3b; + + Kokkos::View d_coefficients_2b; + Kokkos::View d_dncoefficients_2b; + Kokkos::View d_n2b_knot; + Kokkos::View d_n2b_knot_spacings; + Kokkos::View map2b; + Kokkos::View constants; + Kokkos::View dnconstants; + Kokkos::View d_n3b_knot_matrix; + Kokkos::View d_coefficients_3b; + Kokkos::View d_dncoefficients_3b; + Kokkos::View d_n3b_knot_spacings; + Kokkos::View d_n3b_knot_matrix_spacings; + Kokkos::View map3b; + + Kokkos::View constants_2b; + Kokkos::View dnconstants_2b; + Kokkos::View constants_3b; + Kokkos::View dnconstants_3b; + + std::vector get_constants(double *knots, double coefficient); + std::vector get_dnconstants(double *knots, double coefficient); + + int coefficients_created = 0; + void create_coefficients(); + void create_3b_coefficients(); + void create_2b_coefficients(); + std::vector get_coefficients(const double *knots, const double coefficient) const; + std::vector get_dncoefficients(const double *knots, const double coefficient) const; + + template + void twobody(const int itype, const int jtype, const F_FLOAT r, F_FLOAT &evdwl, + F_FLOAT &fpair) const; + template + void threebody(const int itype, const int jtype, const int ktype, const F_FLOAT value_rij, + const F_FLOAT value_rik, const F_FLOAT value_rjk, F_FLOAT &evdwl3, + F_FLOAT (&fforce)[3]) const; + + template + KOKKOS_INLINE_FUNCTION void + ev_tally(EV_FLOAT &ev, const int &i, const int &j, const F_FLOAT &epair, const F_FLOAT &fpair, + const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const; + + template + KOKKOS_INLINE_FUNCTION void ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k, + const F_FLOAT &evdwl, const F_FLOAT &ecoul, F_FLOAT *fj, + F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const; + + typename AT::t_x_array_randomread x; + typename AT::t_f_array f; + typename AT::t_tagint_1d tag; + typename AT::t_int_1d_randomread type; + + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; + + using ScatterFType = Kokkos::Experimental::ScatterView; + ScatterFType fscatter; + using ScatterVType = Kokkos::Experimental::ScatterView; + ScatterVType vscatter; + using ScatterCVType = Kokkos::Experimental::ScatterView; + ScatterCVType cvscatter; + using ScatterEType = Kokkos::Experimental::ScatterView; + ScatterEType escatter; + + typename AT::t_neighbors_2d d_neighbors; + typename AT::t_int_1d_randomread d_ilist; + typename AT::t_int_1d_randomread d_numneigh; + + int neighflag, newton_pair; + int nlocal, nall, eflag, vflag; + + int inum; + Kokkos::View d_neighbors_short; + Kokkos::View d_numneigh_short; + + friend void pair_virial_fdotr_compute(PairUF3Kokkos *); +}; + +KOKKOS_INLINE_FUNCTION int min(int i, int j) +{ + return i < j ? i : j; +} +KOKKOS_INLINE_FUNCTION int max(int i, int j) +{ + return i > j ? i : j; +} + +} // namespace LAMMPS_NS + +#endif +#endif + diff --git a/src/KOKKOS/pair_yukawa_colloid_kokkos.cpp b/src/KOKKOS/pair_yukawa_colloid_kokkos.cpp index 9303e0d435..1457e3439d 100644 --- a/src/KOKKOS/pair_yukawa_colloid_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_colloid_kokkos.cpp @@ -216,10 +216,8 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairYukawaColloidKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, - const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &i, const int &j, + const int &itype, const int &jtype) const { const F_FLOAT radi = radius[i]; const F_FLOAT radj = radius[j]; const F_FLOAT rr = sqrt(rsq); @@ -242,10 +240,8 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairYukawaColloidKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, - const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &i, const int &j, + const int &itype, const int &jtype) const { const F_FLOAT radi = radius[i]; const F_FLOAT radj = radius[j]; const F_FLOAT rr = sqrt(rsq); diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index e51170e195..fda40c14b6 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -215,10 +215,8 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairYukawaKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, - const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT &rsq, const int &, const int &, + const int &itype, const int &jtype) const { const F_FLOAT rr = sqrt(rsq); // Fetch the params either off the stack or from some mapped memory? const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].a @@ -241,10 +239,8 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairYukawaKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, - const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, + const int &itype, const int &jtype) const { const F_FLOAT rr = sqrt(rsq); const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].a : params(itype,jtype).a; diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index e2467ebe95..a91a6642e8 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -184,9 +184,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairZBLKokkos:: -compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_fpair(const F_FLOAT& rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r = sqrt(rsq); F_FLOAT fpair = dzbldr(r, itype, jtype); @@ -205,9 +203,7 @@ template template KOKKOS_INLINE_FUNCTION F_FLOAT PairZBLKokkos:: -compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { - (void) i; - (void) j; +compute_evdwl(const F_FLOAT &rsq, const int &, const int &, const int &itype, const int &jtype) const { const F_FLOAT r = sqrt(rsq); F_FLOAT evdwl = e_zbl(r, itype, jtype); evdwl += d_sw5(itype,jtype); diff --git a/src/MACHDYN/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp index 760dd963eb..820527503c 100644 --- a/src/MACHDYN/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -25,6 +25,8 @@ #include "atom_vec_smd.h" #include "atom.h" +#include "domain.h" +#include "memory.h" #include @@ -57,6 +59,8 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp) atom->damage_flag = 1; atom->eff_plastic_strain_rate_flag = 1; + x0_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -156,6 +160,13 @@ void AtomVecSMD::create_atom_post(int ilocal) void AtomVecSMD::data_atom_post(int ilocal) { esph[ilocal] = 0.0; + + // x and x0 are in Atoms section of data file + // reset x0 b/c x may have been modified in Atom::data_atoms() + // for PBC, shift, etc + // this means no need for read_data_general_to_restricted() method + // to rotate x0 for general triclinic + x0[ilocal][0] = x[ilocal][0]; x0[ilocal][1] = x[ilocal][1]; x0[ilocal][2] = x[ilocal][2]; @@ -177,3 +188,40 @@ void AtomVecSMD::data_atom_post(int ilocal) smd_data_9[ilocal][4] = 1.0; // yy smd_data_9[ilocal][8] = 1.0; // zz } + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on original coords x0 +------------------------------------------------------------------------- */ + +void AtomVecSMD::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(x0_hold,nlocal,3,"atomvec:x0_hold"); + if (nlocal) memcpy(&x0_hold[0][0],&x0[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_coords(x0[i]); + +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on original coords x0 +------------------------------------------------------------------------- */ + +void AtomVecSMD::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!x0_hold) return; + + int nlocal = atom->nlocal; + memcpy(&x0[0][0],&x0_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(x0_hold); + x0_hold = nullptr; +} diff --git a/src/MACHDYN/atom_vec_smd.h b/src/MACHDYN/atom_vec_smd.h index 6ca7f08b4d..47117c0b90 100644 --- a/src/MACHDYN/atom_vec_smd.h +++ b/src/MACHDYN/atom_vec_smd.h @@ -43,12 +43,16 @@ class AtomVecSMD : virtual public AtomVec { void force_clear(int, size_t) override; void create_atom_post(int) override; void data_atom_post(int) override; + void write_data_restricted_to_general() override; + void write_data_restore_restricted() override; private: tagint *molecule; double *esph, *desph, *vfrac, *rmass, *radius, *contact_radius; double *eff_plastic_strain, *eff_plastic_strain_rate, *damage; double **x0, **smd_data_9, **smd_stress, **vest; + + double **x0_hold; }; } // namespace LAMMPS_NS diff --git a/src/MAKE/MACHINES/Makefile.elcapitan_kokkos b/src/MAKE/MACHINES/Makefile.elcapitan_kokkos new file mode 100644 index 0000000000..64d55ebc86 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.elcapitan_kokkos @@ -0,0 +1,124 @@ +# elcapitan_kokkos = KOKKOS/HIP, AMD MI300A APU, Cray MPICH, hipcc compiler, hipFFT + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = hipcc +CCFLAGS = -g -O3 -DNDEBUG -DKOKKOS_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS -DKOKKOS_ENABLE_IMPL_HIP_UNIFIED_MEMORY -DKOKKOS_ENABLE_ROCTHRUST +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = hipcc +LINKFLAGS = -g -O3 +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared +KOKKOS_DEVICES = HIP +KOKKOS_ARCH = AMD_GFX942 + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 3.5 of the manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 3.4 of the manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I${MPICH_DIR}/include +MPI_PATH = +MPI_LIB = -L${MPICH_DIR}/lib -lmpi -L${CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa + +# FFT library +# see discussion in Section 3.5.2 of manual +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +MY_HIP_EXE = $(shell which hipcc) +MY_HIP_PATH = $(dir ${MY_HIP_EXE}) + +FFT_INC = -DFFT_KOKKOS_HIPFFT +FFT_PATH = +FFT_LIB = -L${MY_HIP_PATH}../lib -lhipfft + +# JPEG and/or PNG library +# see discussion in Section 3.5.4 of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@ + $(SIZE) $@ + +# Library targets + +$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS) + @rm -f ../$(ARLIB) + $(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ) + @rm -f $(ARLIB) + @ln -s ../$(ARLIB) $(ARLIB) + +$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + @rm -f $(SHLIB) + @ln -s ../$(SHLIB) $(SHLIB) + +# Compilation rules + +%.o:%.cpp + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.frontier_kokkos b/src/MAKE/MACHINES/Makefile.frontier_kokkos index b58a3d871c..470f2e1449 100644 --- a/src/MAKE/MACHINES/Makefile.frontier_kokkos +++ b/src/MAKE/MACHINES/Makefile.frontier_kokkos @@ -7,7 +7,7 @@ SHELL = /bin/sh # specify flags and libraries needed for your compiler CC = hipcc -CCFLAGS = -g -O3 -munsafe-fp-atomics -DNDEBUG -DKOKKOS_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS +CCFLAGS = -g -O3 -munsafe-fp-atomics -DNDEBUG -DKOKKOS_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS -DKOKKOS_ENABLE_ROCTHRUST SHFLAGS = -fPIC DEPFLAGS = -M @@ -20,7 +20,7 @@ ARCHIVE = ar ARFLAGS = -rc SHLIBFLAGS = -shared KOKKOS_DEVICES = HIP -KOKKOS_ARCH = Vega90A,Zen3 +KOKKOS_ARCH = AMD_GFX90A,ZEN3 # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 669a5cadbb..e4a0155ab9 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -148,6 +148,8 @@ void PairEAM::compute(int eflag, int vflag) evdwl = 0.0; ev_init(eflag,vflag); + int beyond_rhomax = 0; + // grow energy and fp arrays if necessary // need to be atom->nmax in length @@ -237,7 +239,10 @@ void PairEAM::compute(int eflag, int vflag) fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; if (eflag) { phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; - if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); + if (rho[i] > rhomax) { + phi += fp[i] * (rho[i]-rhomax); + beyond_rhomax = 1; + } phi *= scale[type[i]][type[i]]; if (eflag_global) eng_vdwl += phi; if (eflag_atom) eatom[i] += phi; @@ -322,6 +327,16 @@ void PairEAM::compute(int eflag, int vflag) } } + if (eflag && (!exceeded_rhomax)) { + MPI_Allreduce(&beyond_rhomax, &exceeded_rhomax, 1, MPI_INT, MPI_SUM, world); + if (exceeded_rhomax) { + if (comm->me == 0) + error->warning(FLERR, + "A per-atom density exceeded rhomax of EAM potential table - " + "a linear extrapolation to the energy was made"); + } + } + if (vflag_fdotr) virial_fdotr_compute(); } @@ -424,6 +439,8 @@ void PairEAM::init_style() neighbor->add_request(this); embedstep = -1; + + exceeded_rhomax = 0; } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 67bbde570d..24221a07ce 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -68,6 +68,9 @@ class PairEAM : public Pair { double **scale; bigint embedstep; // timestep, the embedding term was computed + int exceeded_rhomax; // global flag for whether rho[i] has exceeded rhomax + // on a step energy is computed - 0 = no, 1 = yes + // per-atom arrays double *rho, *fp; diff --git a/src/MANYBODY/pair_rebomos.cpp b/src/MANYBODY/pair_rebomos.cpp index a84469f212..0941ca0a3a 100644 --- a/src/MANYBODY/pair_rebomos.cpp +++ b/src/MANYBODY/pair_rebomos.cpp @@ -54,7 +54,9 @@ static constexpr int PGDELTA = 1; /* ---------------------------------------------------------------------- */ -PairREBOMoS::PairREBOMoS(LAMMPS *lmp) : Pair(lmp) +PairREBOMoS::PairREBOMoS(LAMMPS *lmp) : + Pair(lmp), lj1(nullptr), lj2(nullptr), lj3(nullptr), lj4(nullptr), ipage(nullptr), + REBO_numneigh(nullptr), REBO_firstneigh(nullptr), nM(nullptr), nS(nullptr) { single_enable = 0; restartinfo = 0; @@ -63,12 +65,9 @@ PairREBOMoS::PairREBOMoS(LAMMPS *lmp) : Pair(lmp) manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; + cut3rebo = 0.0; maxlocal = 0; - REBO_numneigh = nullptr; - REBO_firstneigh = nullptr; - ipage = nullptr; pgsize = oneatom = 0; - nM = nS = nullptr; } // clang-format off diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 18b642967c..74d1ae1871 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -250,6 +250,7 @@ void PairSW::settings(int narg, char ** arg) // pair_coeff * * and can enable the single function. one_coeff = skip_threebody_flag ? 0 : 1; single_enable = skip_threebody_flag ? 1 : 0; + manybody_flag = skip_threebody_flag ? 0 : 1; iarg += 2; } else error->all(FLERR, "Illegal pair_style sw keyword: {}", arg[iarg]); } diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 6fe0ac98b7..8807de18ad 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -171,7 +171,7 @@ void FixAtomSwap::options(int narg, char **arg) while (iarg < narg) { if (isalpha(arg[iarg][0])) break; if (nswaptypes >= atom->ntypes) error->all(FLERR, "Illegal fix atom/swap command"); - type_list[nswaptypes] = utils::numeric(FLERR, arg[iarg], false, lmp); + type_list[nswaptypes] = utils::expand_type_int(FLERR, arg[iarg], Atom::ATOM, lmp); nswaptypes++; iarg++; } diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index bb3e725c96..94ec5a89bb 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -46,8 +46,8 @@ FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) : MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - if (nevery <= 0) error->all(FLERR,"Illegal fix bond/break command"); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + if (nevery <= 0) error->all(FLERR, "Illegal fix bond/break command"); force_reneighbor = 1; next_reneighbor = -1; @@ -56,8 +56,8 @@ FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) : global_freq = 1; extvector = 0; - btype = utils::inumeric(FLERR,arg[4],false,lmp); - cutoff = utils::numeric(FLERR,arg[5],false,lmp); + btype = utils::expand_type_int(FLERR, arg[4], Atom::BOND, lmp); + cutoff = utils::numeric(FLERR, arg[5], false, lmp); if (btype < 1 || btype > atom->nbondtypes) error->all(FLERR,"Invalid bond type in fix bond/break command"); diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 8922bde55f..589625cc16 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -59,10 +59,10 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) : global_freq = 1; extvector = 0; - iatomtype = utils::inumeric(FLERR,arg[4],false,lmp); - jatomtype = utils::inumeric(FLERR,arg[5],false,lmp); + iatomtype = utils::expand_type_int(FLERR, arg[4], Atom::ATOM, lmp); + jatomtype = utils::expand_type_int(FLERR, arg[5], Atom::ATOM, lmp); double cutoff = utils::numeric(FLERR,arg[6],false,lmp); - btype = utils::inumeric(FLERR,arg[7],false,lmp); + btype = utils::expand_type_int(FLERR, arg[7], Atom::BOND, lmp); if (iatomtype < 1 || iatomtype > atom->ntypes || jatomtype < 1 || jatomtype > atom->ntypes) @@ -92,49 +92,49 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"iparam") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command"); - imaxbond = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - inewtype = utils::inumeric(FLERR,arg[iarg+2],false,lmp); + imaxbond = utils::inumeric(FLERR, arg[iarg+1], false, lmp); + inewtype = utils::expand_type_int(FLERR, arg[iarg+2], Atom::ATOM, lmp); if (imaxbond < 0) error->all(FLERR,"Illegal fix bond/create command"); if (inewtype < 1 || inewtype > atom->ntypes) error->all(FLERR,"Invalid atom type in fix bond/create command"); iarg += 3; } else if (strcmp(arg[iarg],"jparam") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command"); - jmaxbond = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - jnewtype = utils::inumeric(FLERR,arg[iarg+2],false,lmp); + jmaxbond = utils::inumeric(FLERR, arg[iarg+1], false, lmp); + jnewtype = utils::expand_type_int(FLERR, arg[iarg+2], Atom::ATOM, lmp); if (jmaxbond < 0) error->all(FLERR,"Illegal fix bond/create command"); if (jnewtype < 1 || jnewtype > atom->ntypes) error->all(FLERR,"Invalid atom type in fix bond/create command"); iarg += 3; } else if (strcmp(arg[iarg],"prob") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command"); - fraction = utils::numeric(FLERR,arg[iarg+1],false,lmp); - seed = utils::inumeric(FLERR,arg[iarg+2],false,lmp); + fraction = utils::numeric(FLERR, arg[iarg+1], false, lmp); + seed = utils::inumeric(FLERR, arg[iarg+2], false, lmp); if (fraction < 0.0 || fraction > 1.0) error->all(FLERR,"Illegal fix bond/create command"); if (seed <= 0) error->all(FLERR,"Illegal fix bond/create command"); iarg += 3; } else if (strcmp(arg[iarg],"atype") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command"); - atype = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + atype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ANGLE, lmp); if (atype < 0) error->all(FLERR,"Illegal fix bond/create command"); iarg += 2; } else if (strcmp(arg[iarg],"dtype") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command"); - dtype = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + dtype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::DIHEDRAL, lmp); if (dtype < 0) error->all(FLERR,"Illegal fix bond/create command"); iarg += 2; } else if (strcmp(arg[iarg],"itype") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command"); - itype = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + itype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::IMPROPER, lmp); if (itype < 0) error->all(FLERR,"Illegal fix bond/create command"); iarg += 2; } else if (strcmp(arg[iarg],"aconstrain") == 0 && strcmp(style,"bond/create/angle") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create/angle command"); - amin = utils::numeric(FLERR,arg[iarg+1],false,lmp); - amax = utils::inumeric(FLERR,arg[iarg+2],false,lmp); + amin = utils::numeric(FLERR, arg[iarg+1], false, lmp); + amax = utils::inumeric(FLERR, arg[iarg+2], false, lmp); if (amin >= amax) error->all(FLERR,"Illegal fix bond/create/angle command"); if (amin < 0 || amin > 180) @@ -1430,4 +1430,3 @@ double FixBondCreate::memory_usage() bytes += (double)nmax * sizeof(double); return bytes; } - diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 4358513095..cd035781c8 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -97,8 +97,8 @@ FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) : energy_stored = 0; // necessary to specify the free ion types - cation_type = utils::inumeric(FLERR, arg[3], false, lmp); - anion_type = utils::inumeric(FLERR, arg[4], false, lmp); + cation_type = utils::expand_type_int(FLERR, arg[3], Atom::ATOM, lmp); + anion_type = utils::expand_type_int(FLERR, arg[4], Atom::ATOM, lmp); // set defaults and read optional arguments options(narg - 5, &arg[5]); @@ -1398,11 +1398,11 @@ void FixChargeRegulation::options(int narg, char **arg) { iarg += 2; } else if (strcmp(arg[iarg], "acid_type") == 0) { if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge/regulation command"); - acid_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + acid_type = utils::expand_type_int(FLERR, arg[iarg + 1], Atom::ATOM, lmp); iarg += 2; } else if (strcmp(arg[iarg], "base_type") == 0) { if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge/regulation command"); - base_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + base_type = utils::expand_type_int(FLERR, arg[iarg + 1], Atom::ATOM, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pH") == 0) { if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge/regulation command"); diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index bd7e46b3d1..e0f1cd243b 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -94,22 +94,22 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) : // required args - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - nexchanges = utils::inumeric(FLERR,arg[4],false,lmp); - nmcmoves = utils::inumeric(FLERR,arg[5],false,lmp); - ngcmc_type = utils::inumeric(FLERR,arg[6],false,lmp); - seed = utils::inumeric(FLERR,arg[7],false,lmp); - reservoir_temperature = utils::numeric(FLERR,arg[8],false,lmp); - chemical_potential = utils::numeric(FLERR,arg[9],false,lmp); - displace = utils::numeric(FLERR,arg[10],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + nexchanges = utils::inumeric(FLERR, arg[4], false, lmp); + nmcmoves = utils::inumeric(FLERR, arg[5], false, lmp); + ngcmc_type = utils::expand_type_int(FLERR, arg[6], Atom::ATOM, lmp); + seed = utils::inumeric(FLERR, arg[7], false, lmp); + reservoir_temperature = utils::numeric(FLERR, arg[8], false, lmp); + chemical_potential = utils::numeric(FLERR, arg[9], false, lmp); + displace = utils::numeric(FLERR, arg[10], false, lmp); - if (nevery <= 0) error->all(FLERR,"Illegal fix gcmc command"); - if (nexchanges < 0) error->all(FLERR,"Illegal fix gcmc command"); - if (nmcmoves < 0) error->all(FLERR,"Illegal fix gcmc command"); - if (seed <= 0) error->all(FLERR,"Illegal fix gcmc command"); + if (nevery <= 0) error->all(FLERR, "Illegal fix gcmc command"); + if (nexchanges < 0) error->all(FLERR, "Illegal fix gcmc command"); + if (nmcmoves < 0) error->all(FLERR, "Illegal fix gcmc command"); + if (seed <= 0) error->all(FLERR, "Illegal fix gcmc command"); if (reservoir_temperature < 0.0) - error->all(FLERR,"Illegal fix gcmc command"); - if (displace < 0.0) error->all(FLERR,"Illegal fix gcmc command"); + error->all(FLERR, "Illegal fix gcmc command"); + if (displace < 0.0) error->all(FLERR, "Illegal fix gcmc command"); // read options from end of input line @@ -359,7 +359,7 @@ void FixGCMC::options(int narg, char **arg) ngrouptypesmax*sizeof(char *), "fix_gcmc:grouptypestrings"); } - grouptypes[ngrouptypes] = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + grouptypes[ngrouptypes] = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ATOM, lmp); grouptypestrings[ngrouptypes] = utils::strdup(arg[iarg+2]); ngrouptypes++; iarg += 3; @@ -2233,7 +2233,8 @@ void FixGCMC::attempt_molecule_insertion_full() } /* ---------------------------------------------------------------------- - compute particle's interaction energy with the rest of the system + compute particle's interaction energy with the rest of the system by + looping over all atoms in the sub-domain including ghosts. ------------------------------------------------------------------------- */ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord) diff --git a/src/MC/fix_mol_swap.cpp b/src/MC/fix_mol_swap.cpp index f496d4a9c5..de408df204 100644 --- a/src/MC/fix_mol_swap.cpp +++ b/src/MC/fix_mol_swap.cpp @@ -56,10 +56,10 @@ FixMolSwap::FixMolSwap(LAMMPS *lmp, int narg, char **arg) : // parse args - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - ncycles = utils::inumeric(FLERR,arg[4],false,lmp); - itype = utils::inumeric(FLERR,arg[5],false,lmp); - jtype = utils::inumeric(FLERR,arg[6],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + ncycles = utils::inumeric(FLERR, arg[4], false, lmp); + itype = utils::expand_type_int(FLERR, arg[5], Atom::ATOM, lmp); + jtype = utils::expand_type_int(FLERR, arg[6], Atom::ATOM, lmp); seed = utils::inumeric(FLERR,arg[7],false,lmp); double temperature = utils::numeric(FLERR,arg[8],false,lmp); diff --git a/src/MC/fix_sgcmc.cpp b/src/MC/fix_sgcmc.cpp index ae0e69d77e..77ead0479f 100644 --- a/src/MC/fix_sgcmc.cpp +++ b/src/MC/fix_sgcmc.cpp @@ -253,11 +253,9 @@ void FixSemiGrandCanonicalMC::init() error->all(FLERR, "Can not run fix sgcmc with naive total energy calculation " "and more than one MPI process."); - // Create a compute that will provide the total energy of the system. + // Get reference to a compute that will provide the total energy of the system. // This is needed by computeTotalEnergy(). - char* id_pe = (char*)"thermo_pe"; - int ipe = modify->find_compute(id_pe); - compute_pe = modify->compute[ipe]; + compute_pe = modify->get_compute_by_id("thermo_pe"); } interactionRadius = force->pair->cutforce; if (comm->me == 0) utils::logmesg(lmp, " SGC - Interaction radius: {}\n", interactionRadius); @@ -373,8 +371,7 @@ void FixSemiGrandCanonicalMC::doMC() // Use a random number to choose the new species if there are three or more atom types. newSpecies = (int)(localRandom->uniform() * (atom->ntypes-1)) + 1; if (newSpecies >= oldSpecies) newSpecies++; - } - else { + } else { // If there are only two atom types, then the decision is clear. newSpecies = (oldSpecies == 1) ? 2 : 1; } @@ -394,8 +391,7 @@ void FixSemiGrandCanonicalMC::doMC() if (serialMode && kappa != 0.0) { for (int i = 2; i <= atom->ntypes; i++) dm += (deltamu[i] + kappa / atom->natoms * (2.0 * speciesCounts[i] + deltaN[i])) * deltaN[i]; - } - else { + } else { for (int i = 2; i <= atom->ntypes; i++) dm += deltamu[i] * deltaN[i]; } @@ -436,8 +432,7 @@ void FixSemiGrandCanonicalMC::doMC() // Update global species counters. for (int i = 1; i <= atom->ntypes; i++) speciesCounts[i] += deltaNGlobal[i]; - } - else if (serialMode) { + } else if (serialMode) { // Update the local species counters. for (int i = 1; i <= atom->ntypes; i++) speciesCounts[i] += deltaN[i]; @@ -450,8 +445,7 @@ void FixSemiGrandCanonicalMC::doMC() else flipAtomGeneric(selectedAtom, oldSpecies, newSpecies); nAcceptedSwapsLocal++; - } - else { + } else { nRejectedSwapsLocal++; } diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 9871dc8f60..2c76050430 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -77,11 +77,11 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) : // required args - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - ninsertions = utils::inumeric(FLERR,arg[4],false,lmp); - nwidom_type = utils::inumeric(FLERR,arg[5],false,lmp); - seed = utils::inumeric(FLERR,arg[6],false,lmp); - insertion_temperature = utils::numeric(FLERR,arg[7],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + ninsertions = utils::inumeric(FLERR, arg[4], false, lmp); + nwidom_type = utils::expand_type_int(FLERR, arg[5], Atom::ATOM, lmp); + seed = utils::inumeric(FLERR, arg[6], false, lmp); + insertion_temperature = utils::numeric(FLERR, arg[7], false, lmp); if (nevery <= 0) error->all(FLERR,"Invalid fix widom every argument: {}", nevery); if (ninsertions < 0) error->all(FLERR,"Invalid fix widom insertions argument: {}", ninsertions); @@ -973,7 +973,8 @@ void FixWidom::attempt_molecule_insertion_full() } /* ---------------------------------------------------------------------- - compute particle's interaction energy with the rest of the system + compute particle's interaction energy with the rest of the system by + looping over all atoms in the sub-domain including ghosts. ------------------------------------------------------------------------- */ double FixWidom::energy(int i, int itype, tagint imolecule, double *coord) diff --git a/src/MDI/mdi_engine.cpp b/src/MDI/mdi_engine.cpp index 6d7c604fa6..4f69e814f5 100644 --- a/src/MDI/mdi_engine.cpp +++ b/src/MDI/mdi_engine.cpp @@ -695,7 +695,7 @@ void MDIEngine::mdi_md() if (strcmp(mdicmd, "EXIT") == 0) return; // run one step at a time forever - // driver triggers exit with @ command other than @COORDS,@FORCES,@ENDSTEP + // driver triggers exit with @ command other than @COORDS,@FORCES,@ENDSTEP,@ update->integrate->setup(1); @@ -711,7 +711,7 @@ void MDIEngine::mdi_md() update->integrate->run(1); if (strcmp(mdicmd, "@COORDS") != 0 && strcmp(mdicmd, "@FORCES") != 0 && - strcmp(mdicmd, "@ENDSTEP") != 0) + strcmp(mdicmd, "@ENDSTEP") != 0 && strcmp(mdicmd, "@") != 0) break; } diff --git a/src/MEAM/meam_force.cpp b/src/MEAM/meam_force.cpp index 1ee8b5e468..6fc3fd762f 100644 --- a/src/MEAM/meam_force.cpp +++ b/src/MEAM/meam_force.cpp @@ -65,11 +65,11 @@ void MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, double rhoa2mj,drhoa2mj,rhoa2mi,drhoa2mi; double rhoa3mj, drhoa3mj, rhoa3mi, drhoa3mi; double arg1i1m, arg1j1m, arg1i2m, arg1j2m, arg1i3m, arg1j3m, arg3i3m, arg3j3m; - double drho1mdr1, drho1mdr2, drho1mds1, drho1mds2; + double drho1mdr1, drho1mdr2; double drho1mdrm1[3], drho1mdrm2[3]; - double drho2mdr1, drho2mdr2, drho2mds1, drho2mds2; + double drho2mdr1, drho2mdr2; double drho2mdrm1[3], drho2mdrm2[3]; - double drho3mdr1, drho3mdr2, drho3mds1, drho3mds2; + double drho3mdr1, drho3mdr2; double drho3mdrm1[3], drho3mdrm2[3]; third = 1.0 / 3.0; @@ -528,16 +528,12 @@ void MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, if (msmeamflag) { - drho1mds1 = a1 * rhoa1mj * arg1i1m; - drho1mds2 = a1 * rhoa1mi * arg1j1m; - drho2mds1 = a2 * rhoa2mj * arg1i2m - 2.0 / 3.0 * arho2mb[i] * rhoa2mj; - drho2mds2 = a2 * rhoa2mi * arg1j2m - 2.0 / 3.0 * arho2mb[j] * rhoa2mi; - drho3mds1 = a3 * rhoa3mj * arg1i3m - a3a * rhoa3mj * arg3i3m; - drho3mds2 = a3 * rhoa3mi * arg1j3m - a3a * rhoa3mi * arg3j3m; - drho1mds1 *= -1; - drho1mds2 *= -1; - drho3mds1 *= -1; - drho3mds2 *= -1; + const double drho1mds1 = -a1 * rhoa1mj * arg1i1m; + const double drho1mds2 = -a1 * rhoa1mi * arg1j1m; + const double drho2mds1 = a2 * rhoa2mj * arg1i2m - 2.0 / 3.0 * arho2mb[i] * rhoa2mj; + const double drho2mds2 = a2 * rhoa2mi * arg1j2m - 2.0 / 3.0 * arho2mb[j] * rhoa2mi; + const double drho3mds1 = -a3 * rhoa3mj * arg1i3m + a3a * rhoa3mj * arg3i3m; + const double drho3mds2 = -a3 * rhoa3mi * arg1j3m + a3a * rhoa3mi * arg3j3m; t1i = 1.0; t2i = 1.0; @@ -560,13 +556,6 @@ void MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, * ((drho1ds2 - drho1mds2) + (drho2ds2 - drho2mds2) + (drho3ds2 - drho3mds2)); } else { - drho1mds1 = 0.0; - drho1mds2 = 0.0; - drho2mds1 = 0.0; - drho2mds2 = 0.0; - drho3mds1 = 0.0; - drho3mds2 = 0.0; - if (ialloy == 1) { a1i = fdiv_zero(rhoa0j, tsq_ave[i][0]); diff --git a/src/MEAM/meam_setup_global.cpp b/src/MEAM/meam_setup_global.cpp index 4afffb4b02..1487a53b2e 100644 --- a/src/MEAM/meam_setup_global.cpp +++ b/src/MEAM/meam_setup_global.cpp @@ -123,4 +123,7 @@ void MEAM::meam_setup_global(int nelt, lattice_t *lat, int *ielement, double * / // for trimer, zigzag, line refernece structure, sungkwang setall2d(stheta_meam, 1.0); // stheta = sin(theta/2*pi/180) where theta is 180, so 1.0 setall2d(ctheta_meam, 0.0); // stheta = cos(theta/2*pi/180) where theta is 180, so 0 + + if (msmeamflag) ialloy = 1; + } diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index 6159c452b0..d9d2b53885 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -206,7 +206,12 @@ void PairMEAM::coeff(int narg, char **arg) // check for presence of first meam file std::string lib_file = utils::get_potential_file_path(arg[2]); - if (lib_file.empty()) error->all(FLERR, "Cannot open MEAM library file {}", lib_file); + if (lib_file.empty()) { + if (msmeamflag) + error->all(FLERR, "Cannot open MS-MEAM library file {}", lib_file); + else + error->all(FLERR, "Cannot open MEAM library file {}", lib_file); + } // find meam parameter file in arguments: // first word that is a file or "NULL" after the MEAM library file @@ -226,7 +231,12 @@ void PairMEAM::coeff(int narg, char **arg) break; } } - if (paridx < 0) error->all(FLERR, "No MEAM parameter file in pair coefficients"); + if (paridx < 0) { + if (msmeamflag) + error->all(FLERR, "No MS-MEAM parameter file in pair coefficients"); + else + error->all(FLERR, "No MEAM parameter file in pair coefficients"); + } if ((narg - paridx - 1) != atom->ntypes) error->all(FLERR, "Incorrect args for pair style {} coefficients", myname); diff --git a/src/MEAM/pair_meam.h b/src/MEAM/pair_meam.h index a89714bfa9..3d50ca9368 100644 --- a/src/MEAM/pair_meam.h +++ b/src/MEAM/pair_meam.h @@ -14,7 +14,6 @@ #ifdef PAIR_CLASS // clang-format off PairStyle(meam,PairMEAM); -PairStyle(meam/c,PairMEAM); // clang-format on #else diff --git a/src/MISC/fix_ipi.cpp b/src/MISC/fix_ipi.cpp index 30a6fe893d..87668b9192 100644 --- a/src/MISC/fix_ipi.cpp +++ b/src/MISC/fix_ipi.cpp @@ -48,6 +48,7 @@ using namespace FixConst; #ifndef _WIN32 #include #include +#include #include #include #include @@ -78,7 +79,7 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro error: pointer to a LAMMPS Error object */ { - int ai_err; + int ai_err,flagNagle; #ifdef _WIN32 error->one(FLERR, "i-PI socket implementation requires UNIX environment"); @@ -100,6 +101,11 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol); if (sockfd < 0) error->one(FLERR, "Error creating socket for fix ipi"); + // set TCP_NODELAY=1 to disable Nagle's algorithm as it slows down the small transactions for i-PI + flagNagle = 1; + int result_TCP = setsockopt(sockfd, IPPROTO_TCP, TCP_NODELAY, (char *)&flagNagle, sizeof(int)); + if (result_TCP < 0) { perror("Error setting TCP_NODELAY"); } + // makes connection if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0) error->one(FLERR, "Error opening INET socket: wrong port or server unreachable"); @@ -363,11 +369,31 @@ void FixIPI::initial_integrate(int /*vflag*/) // has to be be done before invoking Irregular::migrate_atoms() // since it requires atoms be inside simulation box + // folds atomic coordinates close to the origin if (domain->triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); domain->reset_box(); if (domain->triclinic) domain->lamda2x(atom->nlocal); + // ensures continuity of trajectories relative to the + // snapshot at neighbor list creation, minimizing the + // number of neighbor list updates + auto xhold = neighbor->get_xhold(); + if (xhold != NULL) { // don't wrap if xhold is not used in the NL + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + auto delx = x[i][0] - xhold[i][0]; + auto dely = x[i][1] - xhold[i][1]; + auto delz = x[i][2] - xhold[i][2]; + + domain->minimum_image(delx, dely, delz); + + x[i][0] = xhold[i][0] + delx; + x[i][1] = xhold[i][1] + dely; + x[i][2] = xhold[i][2] + delz; + } + } + } // move atoms to new processors via irregular() // only needed if migrate_check() says an atom moves to far if (domain->triclinic) domain->x2lamda(atom->nlocal); @@ -452,6 +478,7 @@ void FixIPI::final_integrate() retstr[0]=0; if (master) { + // check for new messages while (true) { readbuffer(ipisock, header, MSGLEN, error); header[MSGLEN]=0; @@ -464,6 +491,7 @@ void FixIPI::final_integrate() error->one(FLERR, "Got EXIT message from i-PI. Now leaving!"); if (strcmp(header,"GETFORCE ") == 0) { + // return force and energy data writebuffer(ipisock,"FORCEREADY ",MSGLEN, error); writebuffer(ipisock,(char*) &pot,8, error); writebuffer(ipisock,(char*) &nat,4, error); @@ -478,5 +506,3 @@ void FixIPI::final_integrate() hasdata=0; } - - diff --git a/src/ML-IAP/Install.sh b/src/ML-IAP/Install.sh index 18812c6026..38e3b574c2 100755 --- a/src/ML-IAP/Install.sh +++ b/src/ML-IAP/Install.sh @@ -40,6 +40,20 @@ for file in *.cpp *.h; do test -f ${file} && action $file done +# Edit makefile for ace descriptors if ML-PACE is available +if (test $1 = 1 || test $1 = 2) then + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*-DMLIAP_ACE[^ \t]* //g' ../Makefile.package + if (test -e ../compute_pace.h) then + sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_ACE |' ../Makefile.package + else + rm -f ../mliap_descriptor_ace.cpp ../mliap_descriptor_ace.h + fi + else + rm -f ../mliap_descriptor_ace.cpp ../mliap_descriptor_ace.h + fi +fi + # Install cython pyx file only if also Python is available action mliap_model_python_couple.pyx python_impl.cpp action mliap_unified_couple.pyx python_impl.cpp @@ -69,6 +83,10 @@ elif (test $1 = 0) then rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h \ ../mliap_unified_couple.cpp ../mliap_unified_couple.h sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*-DMLIAP_ACE[^ \t]* //g' ../Makefile.package + fi + rm -f ../mliap_descriptor_ace.cpp ../mliap_descriptor_ace.h elif (test $1 = 2) then if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then diff --git a/src/ML-IAP/compute_mliap.cpp b/src/ML-IAP/compute_mliap.cpp index 0ee35ea080..0f87e2b13f 100644 --- a/src/ML-IAP/compute_mliap.cpp +++ b/src/ML-IAP/compute_mliap.cpp @@ -21,6 +21,9 @@ #include "mliap_data.h" #include "mliap_descriptor_snap.h" #include "mliap_descriptor_so3.h" +#ifdef MLIAP_ACE +#include "mliap_descriptor_ace.h" +#endif #include "mliap_model_linear.h" #include "mliap_model_quadratic.h" #ifdef MLIAP_PYTHON @@ -34,7 +37,6 @@ #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "neigh_list.h" #include "pair.h" #include "update.h" @@ -89,13 +91,23 @@ ComputeMLIAP::ComputeMLIAP(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) error->all(FLERR,"Illegal compute mliap command"); if (strcmp(arg[iarg+1],"sna") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal compute mliap command"); + if (lmp->kokkos) error->all(FLERR,"Cannot (yet) use KOKKOS package with SNAP descriptors"); descriptor = new MLIAPDescriptorSNAP(lmp,arg[iarg+2]); iarg += 3; } else if (strcmp(arg[iarg+1],"so3") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command"); descriptor = new MLIAPDescriptorSO3(lmp,arg[iarg+2]); iarg += 3; - } else error->all(FLERR,"Illegal compute mliap command"); + } +#ifdef MLIAP_ACE + else if (strcmp(arg[iarg+1],"ace") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command"); + if (lmp->kokkos) error->all(FLERR,"Cannot (yet) use KOKKOS package with ACE descriptors"); + descriptor = new MLIAPDescriptorACE(lmp,arg[iarg+2]); + iarg += 3; + } +#endif + else error->all(FLERR,"Illegal compute mliap command"); descriptorflag = 1; } else if (strcmp(arg[iarg],"gradgradflag") == 0) { if (iarg+1 > narg) error->all(FLERR,"Illegal compute mliap command"); diff --git a/src/ML-IAP/mliap_data.cpp b/src/ML-IAP/mliap_data.cpp index b40fefd3ba..5d847ee25e 100644 --- a/src/ML-IAP/mliap_data.cpp +++ b/src/ML-IAP/mliap_data.cpp @@ -31,9 +31,9 @@ MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in, class MLIAPM Pointers(lmp), f(nullptr), gradforce(nullptr), betas(nullptr), descriptors(nullptr), eatoms(nullptr), gamma(nullptr), gamma_row_index(nullptr), gamma_col_index(nullptr), egradient(nullptr), - numneighs(nullptr), iatoms(nullptr), ielems(nullptr), pair_i(nullptr), jatoms(nullptr), - jelems(nullptr), elems(nullptr), rij(nullptr), graddesc(nullptr), model(nullptr), - descriptor(nullptr), list(nullptr) + numneighs(nullptr), iatoms(nullptr), ielems(nullptr), itypes(nullptr), pair_i(nullptr), + jatoms(nullptr), jelems(nullptr), elems(nullptr), lmp_firstneigh(nullptr), rij(nullptr), + graddesc(nullptr), model(nullptr), descriptor(nullptr), list(nullptr) { gradgradflag = gradgradflag_in; map = map_in; @@ -84,8 +84,10 @@ MLIAPData::~MLIAPData() memory->destroy(iatoms); memory->destroy(pair_i); memory->destroy(ielems); + memory->destroy(itypes); memory->destroy(numneighs); memory->destroy(jatoms); + memory->destroy(lmp_firstneigh); memory->destroy(jelems); memory->destroy(elems); memory->destroy(rij); @@ -183,6 +185,7 @@ void MLIAPData::generate_neighdata(NeighList *list_in, int eflag_in, int vflag_i int jtype = type[j]; const int jelem = map[jtype]; + lmp_firstneigh[ii][jj] = firstneigh[i][jj]; if (rsq < descriptor->cutsq[ielem][jelem]) { pair_i[ij] = i; jatoms[ij] = j; @@ -196,6 +199,7 @@ void MLIAPData::generate_neighdata(NeighList *list_in, int eflag_in, int vflag_i } iatoms[ii] = i; ielems[ii] = ielem; + itypes[ii] = itype; numneighs[ii] = ninside; npairs += ninside; } @@ -222,6 +226,7 @@ void MLIAPData::grow_neigharrays() if (natomneigh_max < natomneigh) { memory->grow(iatoms, natomneigh, "MLIAPData:iatoms"); memory->grow(ielems, natomneigh, "MLIAPData:ielems"); + memory->grow(itypes, natomneigh, "MLIAPData:itypes"); memory->grow(numneighs, natomneigh, "MLIAPData:numneighs"); natomneigh_max = natomneigh; } @@ -265,6 +270,7 @@ void MLIAPData::grow_neigharrays() if (nneigh_max < nneigh) { memory->grow(pair_i, nneigh, "MLIAPData:pair_i"); memory->grow(jatoms, nneigh, "MLIAPData:jatoms"); + memory->grow(lmp_firstneigh, natomneigh, nneigh, "MLIAPData:lmp_firstneigh"); memory->grow(jelems, nneigh, "MLIAPData:jelems"); memory->grow(rij, nneigh, 3, "MLIAPData:rij"); if (gradgradflag == 0) memory->grow(graddesc, nneigh, ndescriptors, 3, "MLIAPData:graddesc"); @@ -292,12 +298,14 @@ double MLIAPData::memory_usage() bytes += (double) natomneigh_max * sizeof(int); // iatoms bytes += (double) natomneigh_max * sizeof(int); // ielems + bytes += (double) natomneigh_max * sizeof(int); // itypes bytes += (double) natomneigh_max * sizeof(int); // numneighs - bytes += (double) nneigh_max * sizeof(int); // pair_i - bytes += (double) nneigh_max * sizeof(int); // jatoms - bytes += (double) nneigh_max * sizeof(int); // jelems - bytes += (double) nneigh_max * 3 * sizeof(double); // rij" + bytes += (double) nneigh_max * sizeof(int); // pair_i + bytes += (double) nneigh_max * sizeof(int); // jatoms + bytes += (double) nneigh_max * sizeof(int); // jelems + bytes += (double) nneigh_max * natomneigh_max * sizeof(int); // lmp_firstneigh + bytes += (double) nneigh_max * 3 * sizeof(double); // rij" if (gradgradflag == 0) bytes += (double) nneigh_max * ndescriptors * 3 * sizeof(double); // graddesc diff --git a/src/ML-IAP/mliap_data.h b/src/ML-IAP/mliap_data.h index 9746b4da5e..3c27040bb8 100644 --- a/src/ML-IAP/mliap_data.h +++ b/src/ML-IAP/mliap_data.h @@ -58,8 +58,8 @@ class MLIAPData : protected Pointers { // data structures for mliap neighbor list // only neighbors strictly inside descriptor cutoff - int ntotal; // total number of owned and ghost atoms on this proc - int nlistatoms; // current number of atoms in local atom lists + int ntotal; // total number of owned and ghost atoms on this proc + int nlistatoms; // current number of atoms in local atom lists int nlocal; int nlistatoms_max; // allocated size of descriptor array int natomneigh; // current number of atoms and ghosts in atom neighbor arrays @@ -67,12 +67,14 @@ class MLIAPData : protected Pointers { int *numneighs; // neighbors count for each atom int *iatoms; // index of each atom int *ielems; // element of each atom + int *itypes; // LAMMPS type of each atom for external evaluators int nneigh_max; // number of ij neighbors allocated int npairs; // number of ij neighbor pairs int *pair_i; // index of each i atom for each ij pair int *jatoms; // index of each neighbor int *jelems; // element of each neighbor int *elems; // element of each atom in or not in the neighborlist + int **lmp_firstneigh; // copy of list->firstneigh for external evaluators double **rij; // distance vector of each neighbor double ***graddesc; // descriptor gradient w.r.t. each neighbor int eflag; // indicates if energy is needed diff --git a/src/ML-IAP/mliap_descriptor.h b/src/ML-IAP/mliap_descriptor.h index 7f05c6804a..6d66356960 100644 --- a/src/ML-IAP/mliap_descriptor.h +++ b/src/ML-IAP/mliap_descriptor.h @@ -31,6 +31,7 @@ class MLIAPDescriptor : virtual protected Pointers { int ndescriptors; // number of descriptors int nelements; // # of unique elements + int allocated_elements; // is the element array allocated char **elements; // names of unique elements double **cutsq; // nelem x nelem rcutsq values double **cutghost; // cutoff for each ghost pair diff --git a/src/ML-IAP/mliap_descriptor_ace.cpp b/src/ML-IAP/mliap_descriptor_ace.cpp new file mode 100644 index 0000000000..fd059b822b --- /dev/null +++ b/src/ML-IAP/mliap_descriptor_ace.cpp @@ -0,0 +1,386 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Goff (SNL) +------------------------------------------------------------------------- */ +#ifdef MLIAP_ACE + +#include "mliap_descriptor_ace.h" + +#include "ace-evaluator/ace_abstract_basis.h" +#include "ace-evaluator/ace_c_basis.h" +#include "ace-evaluator/ace_evaluator.h" +#include "ace-evaluator/ace_types.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" +#include "mliap_data.h" +#include "neigh_list.h" +#include "pair_mliap.h" +#include "tokenizer.h" + +#include +#include + +namespace LAMMPS_NS { +struct ACE_ML_impl { + ACE_ML_impl() : basis_set(nullptr), ace(nullptr) {} + ~ACE_ML_impl() + { + delete basis_set; + delete ace; + } + ACECTildeBasisSet *basis_set; + ACECTildeEvaluator *ace; +}; +} // namespace LAMMPS_NS + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +MLIAPDescriptorACE::MLIAPDescriptorACE(LAMMPS *_lmp, char *yacefilename) : + Pointers(_lmp), MLIAPDescriptor(_lmp) +{ + + acemlimpl = new ACE_ML_impl; + allocated_elements = 0; + //read in file with CG coefficients or c_tilde coefficients + ctilde_file = yacefilename; + delete acemlimpl->basis_set; + acemlimpl->basis_set = new ACECTildeBasisSet(ctilde_file); + nelements = acemlimpl->basis_set->nelements; + int tot_num = 0; + for (int mu = 0; mu < nelements; mu++) { + if (max_num < acemlimpl->basis_set->total_basis_size_rank1[mu] + + acemlimpl->basis_set->total_basis_size[mu]) { + max_num = acemlimpl->basis_set->total_basis_size_rank1[mu] + + acemlimpl->basis_set->total_basis_size[mu]; + } + tot_num += acemlimpl->basis_set->total_basis_size_rank1[mu] + + acemlimpl->basis_set->total_basis_size[mu]; + } + + ndescriptors = max_num; + nelements = acemlimpl->basis_set->nelements; + + memory->destroy(cutsq); + + if (allocated_elements) { + for (int iielem = 0; iielem < nelements; iielem++) delete[] elements[iielem]; + delete[] elements; + allocated_elements = 0; + } else if (not allocated_elements) { + elements = new char *[nelements]; + for (int iielem = 0; iielem < nelements; iielem++) { + elements[iielem] = utils::strdup(acemlimpl->basis_set->elements_name[iielem]); + } + allocated_elements = 1; + } + + memory->create(cutsq, nelements + 1, nelements + 1, "mliap/descriptor/ace:cutsq"); + float icmax = 0.0; + float icuti, icutj; + for (int mui = 0; mui < acemlimpl->basis_set->nelements; mui++) { + icuti = acemlimpl->basis_set->radial_functions->cut(mui, mui); + if (icuti > icmax) icmax = icuti; + for (int muj = mui + 1; muj < acemlimpl->basis_set->nelements; muj++) { + icutj = acemlimpl->basis_set->radial_functions->cut(mui, muj); + if (icutj > icmax) icmax = icutj; + } + } + float cutmax = 0.0; + float cuti, cutj; + float cutfac = 1.0; + for (int mui = 0; mui < acemlimpl->basis_set->nelements; mui++) { + cuti = acemlimpl->basis_set->radial_functions->cut(mui, mui); + if (cuti > cutmax) cutmax = cuti; + + cutsq[mui][mui] = ((2 * cuti * cutfac) * (2 * cuti * cutfac)); + for (int muj = mui + 1; muj < nelements; muj++) { + cutj = acemlimpl->basis_set->radial_functions->cut(mui, muj); + cutsq[mui][muj] = cutsq[muj][mui] = ((2 * cuti * cutfac) * (2 * cutj * cutfac)); + } + } +} + +void MLIAPDescriptorACE::allocate() {} + +/* ---------------------------------------------------------------------- */ + +MLIAPDescriptorACE::~MLIAPDescriptorACE() +{ + delete acemlimpl; +} + +/* ---------------------------------------------------------------------- + compute descriptors for each atom + ---------------------------------------------------------------------- */ + +void MLIAPDescriptorACE::compute_descriptors(class MLIAPData *data) +{ + int max_jnum = -1; + int nei = 0; + int jtmp = 0; + for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) { + jtmp = data->numneighs[iitmp]; + nei = nei + jtmp; + if (jtmp > max_jnum) { max_jnum = jtmp; } + } + + for (int ii = 0; ii < data->nlistatoms; ii++) { + const int i = data->iatoms[ii]; + const int jnum = data->numneighs[ii]; + + delete acemlimpl->ace; + acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set); + acemlimpl->ace->compute_projections = 1; + acemlimpl->ace->compute_b_grad = 1; + + acemlimpl->ace->element_type_mapping.init(nelements + 1); + for (int ik = 1; ik <= nelements; ik++) { + for (int mu = 0; mu < nelements; mu++) { + if (mu != -1) { + if (mu == ik - 1) { acemlimpl->ace->element_type_mapping(ik) = mu; } + } + } + } + + acemlimpl->ace->resize_neighbours_cache(jnum); + acemlimpl->ace->compute_atom(i, atom->x, atom->type, data->numneighs[ii], + data->lmp_firstneigh[ii]); + for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) { + data->descriptors[ii][icoeff] = acemlimpl->ace->projections(icoeff); + } + } +} + +/* ---------------------------------------------------------------------- + compute forces for each atom + ---------------------------------------------------------------------- */ + +void MLIAPDescriptorACE::compute_forces(class MLIAPData *data) +{ + double fij[3]; + double **f = atom->f; + int ij = 0; + + int max_jnum = -1; + int nei = 0; + int jtmp = 0; + for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) { + jtmp = data->numneighs[iitmp]; + nei = nei + jtmp; + if (jtmp > max_jnum) { max_jnum = jtmp; } + } + + // BEGIN force loop + for (int ii = 0; ii < data->nlistatoms; ii++) { + const int i = data->iatoms[ii]; + delete acemlimpl->ace; + acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set); + acemlimpl->ace->compute_projections = 1; + acemlimpl->ace->compute_b_grad = 1; + acemlimpl->ace->element_type_mapping.init(nelements + 1); + for (int ik = 1; ik <= nelements; ik++) { + for (int mu = 0; mu < acemlimpl->basis_set->nelements; mu++) { + if (mu != -1) { + if (mu == ik - 1) { acemlimpl->ace->element_type_mapping(ik) = mu; } + } + } + } + + const int jnum = data->numneighs[ii]; + acemlimpl->ace->resize_neighbours_cache(jnum); + acemlimpl->ace->compute_atom(i, atom->x, atom->type, data->numneighs[ii], + data->lmp_firstneigh[ii]); + int ij0 = ij; + int ninside = 0; + for (int jj = 0; jj < jnum; jj++) { + ninside++; + ij++; + } + + ij = ij0; + const int *const jlist = data->lmp_firstneigh[ii]; + double **x = atom->x; + const double xtmp = x[i][0]; + const double ytmp = x[i][1]; + const double ztmp = x[i][2]; + + for (int jj = 0; jj < jnum; jj++) { + const int j = jlist[jj]; + for (int idim = 0; idim < 3; idim++) { fij[idim] = 0.0; } + for (int iicoeff = 0; iicoeff < ndescriptors; iicoeff++) { + DOUBLE_TYPE fx_dB = + acemlimpl->ace->neighbours_dB(iicoeff, jj, 0) * data->betas[ii][iicoeff]; + DOUBLE_TYPE fy_dB = + acemlimpl->ace->neighbours_dB(iicoeff, jj, 1) * data->betas[ii][iicoeff]; + DOUBLE_TYPE fz_dB = + acemlimpl->ace->neighbours_dB(iicoeff, jj, 2) * data->betas[ii][iicoeff]; + // add force contribution from each descriptor + fij[0] += fx_dB; + fij[1] += fy_dB; + fij[2] += fz_dB; + f[i][0] += fx_dB; + f[i][1] += fy_dB; + f[i][2] += fz_dB; + f[j][0] -= fx_dB; + f[j][1] -= fy_dB; + f[j][2] -= fz_dB; + } + const double delx = x[j][0] - xtmp; + const double dely = x[j][1] - ytmp; + const double delz = x[j][2] - ztmp; + double rij_tmp[3] = {delx, dely, delz}; + if (data->vflag) data->pairmliap->v_tally(i, j, fij, rij_tmp); + ij++; + } + } +} + +/* ---------------------------------------------------------------------- + calculate gradients of forces w.r.t. parameters + ---------------------------------------------------------------------- */ + +void MLIAPDescriptorACE::compute_force_gradients(class MLIAPData *data) +{ + int ij = 0; + + int max_jnum = -1; + int nei = 0; + int jtmp = 0; + for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) { + jtmp = data->numneighs[iitmp]; + nei = nei + jtmp; + if (jtmp > max_jnum) { max_jnum = jtmp; } + } + + for (int ii = 0; ii < data->nlistatoms; ii++) { + const int i = data->iatoms[ii]; + delete acemlimpl->ace; + acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set); + acemlimpl->ace->compute_projections = 1; + acemlimpl->ace->compute_b_grad = 1; + + acemlimpl->ace->element_type_mapping.init(nelements + 1); + for (int ik = 1; ik <= nelements; ik++) { + for (int mu = 0; mu < acemlimpl->basis_set->nelements; mu++) { + if (mu != -1) { + if (mu == ik - 1) { acemlimpl->ace->element_type_mapping(ik) = mu; } + } + } + } + + const int jnum = data->numneighs[ii]; + const int *const jlist = data->lmp_firstneigh[ii]; + acemlimpl->ace->resize_neighbours_cache(jnum); + acemlimpl->ace->compute_atom(i, atom->x, atom->type, data->numneighs[ii], + data->lmp_firstneigh[ii]); + for (int jj = 0; jj < jnum; jj++) { + const int j = jlist[jj]; + for (int inz = 0; inz < data->gamma_nnz; inz++) { + const int l = data->gamma_row_index[ii][inz]; + const int k = data->gamma_col_index[ii][inz]; + DOUBLE_TYPE fx_dB = acemlimpl->ace->neighbours_dB(k, jj, 0); + DOUBLE_TYPE fy_dB = acemlimpl->ace->neighbours_dB(k, jj, 1); + DOUBLE_TYPE fz_dB = acemlimpl->ace->neighbours_dB(k, jj, 2); + data->gradforce[i][l] += data->gamma[ii][inz] * fx_dB; + data->gradforce[i][l + data->yoffset] += data->gamma[ii][inz] * fy_dB; + data->gradforce[i][l + data->zoffset] += data->gamma[ii][inz] * fz_dB; + data->gradforce[j][l] -= data->gamma[ii][inz] * fx_dB; + data->gradforce[j][l + data->yoffset] -= data->gamma[ii][inz] * fy_dB; + data->gradforce[j][l + data->zoffset] -= data->gamma[ii][inz] * fz_dB; + } + ij++; + } + } +} + +/* ---------------------------------------------------------------------- + compute descriptor gradients for each neighbor atom + ---------------------------------------------------------------------- */ + +void MLIAPDescriptorACE::compute_descriptor_gradients(class MLIAPData *data) +{ + int ij = 0; + int max_jnum = -1; + int nei = 0; + int jtmp = 0; + for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) { + jtmp = data->numneighs[iitmp]; + nei = nei + jtmp; + if (jtmp > max_jnum) { max_jnum = jtmp; } + } + for (int ii = 0; ii < data->nlistatoms; ii++) { + const int i = data->iatoms[ii]; + delete acemlimpl->ace; + acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set); + acemlimpl->ace->compute_projections = 1; + acemlimpl->ace->compute_b_grad = 1; + + acemlimpl->ace->element_type_mapping.init(nelements + 1); + for (int ik = 1; ik <= nelements; ik++) { + for (int mu = 0; mu < acemlimpl->basis_set->nelements; mu++) { + if (mu != -1) { + if (mu == ik - 1) { acemlimpl->ace->element_type_mapping(ik) = mu; } + } + } + } + + const int jnum = data->numneighs[ii]; + acemlimpl->ace->resize_neighbours_cache(jnum); + acemlimpl->ace->compute_atom(i, atom->x, atom->type, data->numneighs[ii], + data->lmp_firstneigh[ii]); + int ij0 = ij; + int ninside = 0; + for (int jj = 0; jj < jnum; jj++) { + ninside++; + ij++; + } + + ij = ij0; + for (int jj = 0; jj < data->numneighs[ii]; jj++) { + for (int iicoeff = 0; iicoeff < ndescriptors; iicoeff++) { + DOUBLE_TYPE fx_dB = acemlimpl->ace->neighbours_dB(iicoeff, jj, 0); + DOUBLE_TYPE fy_dB = acemlimpl->ace->neighbours_dB(iicoeff, jj, 1); + DOUBLE_TYPE fz_dB = acemlimpl->ace->neighbours_dB(iicoeff, jj, 2); + // Accumulate dB_k^i/dRi, dB_k^i/dRj + data->graddesc[ij][iicoeff][0] = fx_dB; + data->graddesc[ij][iicoeff][1] = fy_dB; + data->graddesc[ij][iicoeff][2] = fz_dB; + } + ij++; + } + } +} + +void MLIAPDescriptorACE::init() {} + +/* ---------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + memory usage +------------------------------------------------------------------------- */ + +double MLIAPDescriptorACE::memory_usage() +{ + double bytes = MLIAPDescriptor::memory_usage(); + + return bytes; +} + +#endif diff --git a/src/ML-IAP/mliap_descriptor_ace.h b/src/ML-IAP/mliap_descriptor_ace.h new file mode 100644 index 0000000000..116a154acb --- /dev/null +++ b/src/ML-IAP/mliap_descriptor_ace.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_MLIAP_DESCRIPTOR_ACE_H +#define LMP_MLIAP_DESCRIPTOR_ACE_H + +#include "mliap_descriptor.h" + +namespace LAMMPS_NS { + +class MLIAPDescriptorACE : public MLIAPDescriptor { + public: + MLIAPDescriptorACE(LAMMPS *, char *); + ~MLIAPDescriptorACE() override; + void compute_descriptors(class MLIAPData *) override; + void compute_forces(class MLIAPData *) override; + void compute_force_gradients(class MLIAPData *) override; + void compute_descriptor_gradients(class MLIAPData *) override; + void init() override; + double memory_usage() override; + + double rcutfac; + int allocated = 0; + int max_num = 0; + char *ctilde_file; + + protected: + virtual void allocate(); + int natoms, nmax, size_peratom, lastcol; + int ncoeff, nvalues, nperdim, yoffset, zoffset; + int ndims_peratom, ndims_force, ndims_virial; + int n_r1, n_rp; + int chemflag; + int bikflag, bik_rows, dgradflag, dgrad_rows; + double cutmax; + struct ACE_ML_impl *acemlimpl; +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/ML-IAP/mliap_unified.cpp b/src/ML-IAP/mliap_unified.cpp index 7697204e44..3f0d0b2a8f 100644 --- a/src/ML-IAP/mliap_unified.cpp +++ b/src/ML-IAP/mliap_unified.cpp @@ -246,7 +246,6 @@ void LAMMPS_NS::update_pair_energy(MLIAPData *data, double *eij) { double e_total = 0.0; const auto nlistatoms = data->nlistatoms; - const auto nlocal = data->nlocal; for (int ii = 0; ii < nlistatoms; ii++) data->eatoms[ii] = 0; for (int ii = 0; ii < data->npairs; ii++) { @@ -268,7 +267,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPData *data, double *fij) { //Bugfix: need to account for Null atoms in local atoms //const auto nlistatoms = data->nlistatoms; - const auto nlocal = data->nlocal; double **f = data->f; for (int ii = 0; ii < data->npairs; ii++) { int ii3 = ii * 3; diff --git a/src/ML-IAP/pair_mliap.cpp b/src/ML-IAP/pair_mliap.cpp index 66e8b848cd..8585fffadb 100644 --- a/src/ML-IAP/pair_mliap.cpp +++ b/src/ML-IAP/pair_mliap.cpp @@ -21,6 +21,9 @@ #include "mliap_data.h" #include "mliap_descriptor_snap.h" #include "mliap_descriptor_so3.h" +#ifdef MLIAP_ACE +#include "mliap_descriptor_ace.h" +#endif #include "mliap_model_linear.h" #include "mliap_model_nn.h" #include "mliap_model_quadratic.h" @@ -181,8 +184,16 @@ void PairMLIAP::settings(int narg, char ** arg) if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "pair_style mliap descriptor so3", error); descriptor = new MLIAPDescriptorSO3(lmp,arg[iarg+2]); iarg += 3; - - } else error->all(FLERR,"Illegal pair_style mliap command"); + } +#ifdef MLIAP_ACE + else if (strcmp(arg[iarg+1],"ace") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command"); + if (lmp->kokkos) error->all(FLERR,"Cannot (yet) use KOKKOS package with ACE descriptors"); + descriptor = new MLIAPDescriptorACE(lmp,arg[iarg+2]); + iarg += 3; + } +#endif + else error->all(FLERR,"Illegal pair_style mliap command"); } else if (strcmp(arg[iarg], "unified") == 0) { #ifdef MLIAP_PYTHON if (model != nullptr) error->all(FLERR,"Illegal multiple pair_style mliap model definitions"); diff --git a/src/ML-PACE/pair_pace.h b/src/ML-PACE/pair_pace.h index 9b5d2c5480..5cff7045fa 100644 --- a/src/ML-PACE/pair_pace.h +++ b/src/ML-PACE/pair_pace.h @@ -52,7 +52,7 @@ class PairPACE : public Pair { protected: struct ACEImpl *aceimpl; - int nmax_corerep = 0; + int nmax_corerep; virtual void allocate(); double *corerep_factor; //per-atom core-rep factor (= 1 - fcut) diff --git a/src/ML-PACE/pair_pace_extrapolation.h b/src/ML-PACE/pair_pace_extrapolation.h index 440d999029..e01fdd2329 100644 --- a/src/ML-PACE/pair_pace_extrapolation.h +++ b/src/ML-PACE/pair_pace_extrapolation.h @@ -46,15 +46,15 @@ class PairPACEExtrapolation : public Pair { protected: struct ACEALImpl *aceimpl; - int nmax = 0, nmax_corerep = 0; + int nmax, nmax_corerep; virtual void allocate(); std::vector element_names; // list of elements (used by dump pace/extrapolation) - double *extrapolation_grade_gamma = nullptr; //per-atom gamma value - double *corerep_factor = nullptr; //per-atom core-rep factor (= 1 - fcut) + double *extrapolation_grade_gamma; //per-atom gamma value + double *corerep_factor; //per-atom core-rep factor (= 1 - fcut) - int flag_compute_extrapolation_grade = 0; - int flag_corerep_factor = 0; + int flag_compute_extrapolation_grade; + int flag_corerep_factor; double **scale; diff --git a/src/ML-POD/compute_pod_atom.cpp b/src/ML-POD/compute_pod_atom.cpp new file mode 100644 index 0000000000..dde7dc7ef7 --- /dev/null +++ b/src/ML-POD/compute_pod_atom.cpp @@ -0,0 +1,277 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_pod_atom.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include + +#include "eapod.h" + +using namespace LAMMPS_NS; + +enum { SCALAR, VECTOR, ARRAY }; + +ComputePODAtom::ComputePODAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), list(nullptr), podptr(nullptr), pod(nullptr), tmpmem(nullptr), + rij(nullptr), elements(nullptr), map(nullptr) +{ + int nargmin = 6; + + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); + if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors"); + + std::string pod_file = std::string(arg[3]); // pod input file + std::string coeff_file = std::string(arg[4]); // coefficient input file + podptr = new EAPOD(lmp, pod_file, coeff_file); + + int ntypes = atom->ntypes; + memory->create(map, ntypes + 1, "compute_pod_global:map"); + map_element2type(narg - 5, arg + 5, podptr->nelements); + + cutmax = podptr->rcut; + + nmax = 0; + nijmax = 0; + pod = nullptr; + elements = nullptr; + + size_peratom_cols = podptr->Mdesc * podptr->nClusters; + peratom_flag = 1; +} + +/* ---------------------------------------------------------------------- */ + +ComputePODAtom::~ComputePODAtom() +{ + memory->destroy(map); + memory->destroy(pod); + delete podptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODAtom::init() +{ + if (force->pair == nullptr) + error->all(FLERR,"Compute pod requires a pair style be defined"); + + if (cutmax > force->pair->cutforce) + error->all(FLERR,"Compute pod cutoff is longer than pairwise cutoff"); + + // need an occasional full neighbor list + + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); + + if (modify->get_compute_by_style("pod").size() > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute pod"); +} + + +/* ---------------------------------------------------------------------- */ + +void ComputePODAtom::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODAtom::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow pod array if necessary + + if (atom->natoms > nmax) { + memory->destroy(pod); + nmax = atom->natoms; + int numdesc = podptr->Mdesc * podptr->nClusters; + memory->create(pod, nmax, numdesc,"sna/atom:sna"); + array_atom = pod; + } + + for (int i = 0; i < atom->natoms; i++) + for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++) { + pod[i][icoeff] = 0.0; + } + + // invoke full neighbor list (will copy or build if necessary) + + neighbor->build_one(list); + + double **x = atom->x; + int **firstneigh = list->firstneigh; + int *numneigh = list->numneigh; + int *type = atom->type; + int *ilist = list->ilist; + int inum = list->inum; + int nClusters = podptr->nClusters; + int Mdesc = podptr->Mdesc; + double rcutsq = podptr->rcut*podptr->rcut; + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + int jnum = numneigh[i]; + + // allocate temporary memory + if (nijmax < jnum) { + nijmax = MAX(nijmax, jnum); + podptr->free_temp_memory(); + podptr->allocate_temp_memory(nijmax); + } + + rij = &podptr->tmpmem[0]; + tmpmem = &podptr->tmpmem[3*nijmax]; + ai = &podptr->tmpint[0]; + aj = &podptr->tmpint[nijmax]; + ti = &podptr->tmpint[2*nijmax]; + tj = &podptr->tmpint[3*nijmax]; + + // get neighbor list for atom i + lammpsNeighborList(x, firstneigh, atom->tag, type, numneigh, rcutsq, i); + + if (nij > 0) { + // peratom base descriptors + double *bd = &podptr->bd[0]; + double *bdd = &podptr->bdd[0]; + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); + + if (nClusters>1) { + // peratom env descriptors + double *pd = &podptr->pd[0]; + double *pdd = &podptr->pdd[0]; + podptr->peratomenvironment_descriptors(pd, pdd, bd, bdd, tmpmem, ti[0] - 1, nij); + for (int k = 0; k < nClusters; k++) + for (int m = 0; m < Mdesc; m++) { + int mk = m + Mdesc*k; + pod[i][mk] = pd[k]*bd[m]; + // for (int n=0; n 1e-20) { + rij[nij * 3 + 0] = delx; + rij[nij * 3 + 1] = dely; + rij[nij * 3 + 2] = delz; + ai[nij] = atomid[gi]-1; + aj[nij] = atomid[gj]-1; + ti[nij] = itype; + tj[nij] = map[atomtypes[gj]] + 1; + nij++; + } + } +} + +void ComputePODAtom::map_element2type(int narg, char **arg, int nelements) +{ + int i,j; + const int ntypes = atom->ntypes; + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if "NULL" + // nelements = # of unique elements + // elements = list of element names + + if (narg != ntypes) + error->all(FLERR, "Number of element to type mappings does not match number of atom types"); + + if (elements) { + for (i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + } + elements = new char*[ntypes]; + for (i = 0; i < ntypes; i++) elements[i] = nullptr; + + nelements = 0; + map[0] = -1; + for (i = 1; i <= narg; i++) { + std::string entry = arg[i-1]; + if (entry == "NULL") { + map[i] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (entry == elements[j]) break; + map[i] = j; + if (j == nelements) { + elements[j] = utils::strdup(entry); + nelements++; + } + } +} diff --git a/src/ML-POD/compute_pod_atom.h b/src/ML-POD/compute_pod_atom.h new file mode 100644 index 0000000000..d2f8a9b993 --- /dev/null +++ b/src/ML-POD/compute_pod_atom.h @@ -0,0 +1,61 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(pod/atom,ComputePODAtom); +// clang-format on +#else + +#ifndef LMP_COMPUTE_POD_ATOM_H +#define LMP_COMPUTE_POD_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePODAtom : public Compute { + public: + ComputePODAtom(class LAMMPS *, int, char **); + ~ComputePODAtom() override; + void init() override; + void init_list(int, class NeighList *) override; + void compute_peratom() override; + double memory_usage() override; + void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, + int *numneigh, double rcutsq, int i); + void map_element2type(int narg, char **arg, int nelements); + + private: + class NeighList *list; + class EAPOD *podptr; + double **pod; + double cutmax; + int nmax; + int nij; + int nijmax; + + double *tmpmem; // temporary memory + double *rij; // (xj - xi) for all pairs (I, J) + char **elements; + int *map; + int *ai; // IDs of atoms I for all pairs (I, J) + int *aj; // IDs of atoms J for all pairs (I, J) + int *ti; // types of atoms I for all pairs (I, J) + int *tj; // types of atoms J for all pairs (I, J) +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-POD/compute_pod_global.cpp b/src/ML-POD/compute_pod_global.cpp new file mode 100644 index 0000000000..14b70a5a90 --- /dev/null +++ b/src/ML-POD/compute_pod_global.cpp @@ -0,0 +1,283 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_pod_global.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include + +#include "eapod.h" + +using namespace LAMMPS_NS; + +enum { SCALAR, VECTOR, ARRAY }; + +ComputePODGlobal::ComputePODGlobal(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), list(nullptr), podptr(nullptr), pod(nullptr), tmpmem(nullptr), + rij(nullptr), elements(nullptr), map(nullptr), ai(nullptr), aj(nullptr), ti(nullptr), + tj(nullptr) +{ + array_flag = 1; + extarray = 0; + + int nargmin = 6; + + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); + if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors"); + + std::string pod_file = std::string(arg[3]); // pod input file + std::string coeff_file = std::string(arg[4]); // coefficient input file + podptr = new EAPOD(lmp, pod_file, coeff_file); + + int ntypes = atom->ntypes; + memory->create(map, ntypes + 1, "compute_pod_global:map"); + map_element2type(narg - 5, arg + 5, podptr->nelements); + + size_array_rows = 1 + 3*atom->natoms; + size_array_cols = podptr->nCoeffAll; + cutmax = podptr->rcut; + + nijmax = 0; + pod = nullptr; + elements = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +ComputePODGlobal::~ComputePODGlobal() +{ + memory->destroy(map); + memory->destroy(pod); + delete podptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODGlobal::init() +{ + if (force->pair == nullptr) + error->all(FLERR,"Compute pod requires a pair style be defined"); + + if (cutmax > force->pair->cutforce) + error->all(FLERR,"Compute pod cutoff is longer than pairwise cutoff"); + + // need an occasional full neighbor list + + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); + + if (modify->get_compute_by_style("pod").size() > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute pod"); + + // allocate memory for global array + memory->create(pod,size_array_rows,size_array_cols, + "compute_pod_global:pod"); + array = pod; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODGlobal::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODGlobal::compute_array() +{ + // int ntotal = atom->nlocal + atom->nghost; + invoked_peratom = update->ntimestep; + + // clear global array + + for (int irow = 0; irow < size_array_rows; irow++) + for (int icoeff = 0; icoeff < size_array_cols; icoeff++) + pod[irow][icoeff] = 0.0; + + // invoke full neighbor list (will copy or build if necessary) + + neighbor->build_one(list); + + double **x = atom->x; + int **firstneigh = list->firstneigh; + int *numneigh = list->numneigh; + int *type = atom->type; + int *ilist = list->ilist; + int inum = list->inum; + int nClusters = podptr->nClusters; + int Mdesc = podptr->Mdesc; + int nCoeffPerElement = podptr->nCoeffPerElement; + + double rcutsq = podptr->rcut*podptr->rcut; + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + int jnum = numneigh[i]; + + // allocate temporary memory + if (nijmax < jnum) { + nijmax = MAX(nijmax, jnum); + podptr->free_temp_memory(); + podptr->allocate_temp_memory(nijmax); + } + + rij = &podptr->tmpmem[0]; + tmpmem = &podptr->tmpmem[3*nijmax]; + ai = &podptr->tmpint[0]; + aj = &podptr->tmpint[nijmax]; + ti = &podptr->tmpint[2*nijmax]; + tj = &podptr->tmpint[3*nijmax]; + + // get neighbor list for atom i + lammpsNeighborList(x, firstneigh, atom->tag, type, numneigh, rcutsq, i); + + if (nij > 0) { + // peratom base descriptors + double *bd = &podptr->bd[0]; + double *bdd = &podptr->bdd[0]; + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); + + pod[0][nCoeffPerElement*(ti[0]-1)] += 1.0; // one-body descriptor + + if (nClusters>1) { + // peratom env descriptors + double *pd = &podptr->pd[0]; + double *pdd = &podptr->pdd[0]; + podptr->peratomenvironment_descriptors(pd, pdd, bd, bdd, tmpmem, ti[0] - 1, nij); + + for (int j = 0; j < nClusters; j++) { + for (int m=0; m 1e-20) { + rij[nij * 3 + 0] = delx; + rij[nij * 3 + 1] = dely; + rij[nij * 3 + 2] = delz; + ai[nij] = atomid[gi]-1; + aj[nij] = atomid[gj]-1; + ti[nij] = itype; + tj[nij] = map[atomtypes[gj]] + 1; + nij++; + } + } +} + +void ComputePODGlobal::map_element2type(int narg, char **arg, int nelements) +{ + int i,j; + const int ntypes = atom->ntypes; + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if "NULL" + // nelements = # of unique elements + // elements = list of element names + + if (narg != ntypes) + error->all(FLERR, "Number of element to type mappings does not match number of atom types"); + + if (elements) { + for (i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + } + elements = new char*[ntypes]; + for (i = 0; i < ntypes; i++) elements[i] = nullptr; + + nelements = 0; + map[0] = -1; + for (i = 1; i <= narg; i++) { + std::string entry = arg[i-1]; + if (entry == "NULL") { + map[i] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (entry == elements[j]) break; + map[i] = j; + if (j == nelements) { + elements[j] = utils::strdup(entry); + nelements++; + } + } +} diff --git a/src/ML-POD/compute_pod_global.h b/src/ML-POD/compute_pod_global.h new file mode 100644 index 0000000000..b637be59d9 --- /dev/null +++ b/src/ML-POD/compute_pod_global.h @@ -0,0 +1,60 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(pod/global,ComputePODGlobal); +// clang-format on +#else + +#ifndef LMP_COMPUTE_POD_GLOBAL_H +#define LMP_COMPUTE_POD_GLOBAL_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePODGlobal : public Compute { + public: + ComputePODGlobal(class LAMMPS *, int, char **); + ~ComputePODGlobal() override; + void init() override; + void init_list(int, class NeighList *) override; + void compute_array() override; + double memory_usage() override; + void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, + int *numneigh, double rcutsq, int i); + void map_element2type(int narg, char **arg, int nelements); + + private: + class NeighList *list; + class EAPOD *podptr; + double **pod; + double cutmax; + int nij; + int nijmax; + + double *tmpmem; // temporary memory + double *rij; // (xj - xi) for all pairs (I, J) + char **elements; + int *map; + int *ai; // IDs of atoms I for all pairs (I, J) + int *aj; // IDs of atoms J for all pairs (I, J) + int *ti; // types of atoms I for all pairs (I, J) + int *tj; // types of atoms J for all pairs (I, J) +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-POD/compute_pod_local.cpp b/src/ML-POD/compute_pod_local.cpp new file mode 100644 index 0000000000..2d2c89fd4d --- /dev/null +++ b/src/ML-POD/compute_pod_local.cpp @@ -0,0 +1,280 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_pod_local.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include + +#include "eapod.h" + +using namespace LAMMPS_NS; + +enum { SCALAR, VECTOR, ARRAY }; + +ComputePODLocal::ComputePODLocal(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), list(nullptr), podptr(nullptr), pod(nullptr), tmpmem(nullptr), + rij(nullptr), elements(nullptr), map(nullptr), ai(nullptr), aj(nullptr), ti(nullptr), + tj(nullptr) +{ + array_flag = 1; + extarray = 0; + + int nargmin = 6; + + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); + if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors"); + + std::string pod_file = std::string(arg[3]); // pod input file + std::string coeff_file = std::string(arg[4]); // coefficient input file + podptr = new EAPOD(lmp, pod_file, coeff_file); + + int ntypes = atom->ntypes; + memory->create(map, ntypes + 1, "compute_pod_local:map"); + + map_element2type(narg - 5, arg + 5, podptr->nelements); + + int numdesc = podptr->Mdesc * podptr->nClusters; + size_array_rows = 1 + 3*atom->natoms; + size_array_cols = atom->natoms*numdesc; + cutmax = podptr->rcut; + + nijmax = 0; + pod = nullptr; + elements = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +ComputePODLocal::~ComputePODLocal() +{ + memory->destroy(map); + memory->destroy(pod); + delete podptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODLocal::init() +{ + if (force->pair == nullptr) + error->all(FLERR,"Compute pod requires a pair style be defined"); + + if (cutmax > force->pair->cutforce) + error->all(FLERR,"Compute pod cutoff is longer than pairwise cutoff"); + + // need an occasional full neighbor list + + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); + + if (modify->get_compute_by_style("pod").size() > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute pod"); + + // allocate memory for global array + memory->create(pod,size_array_rows,size_array_cols, + "compute_pod_local:pod"); + array = pod; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODLocal::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODLocal::compute_array() +{ + // int ntotal = atom->nlocal + atom->nghost; + invoked_peratom = update->ntimestep; + + // clear global array + + for (int irow = 0; irow < size_array_rows; irow++) + for (int icoeff = 0; icoeff < size_array_cols; icoeff++) + pod[irow][icoeff] = 0.0; + + // invoke full neighbor list (will copy or build if necessary) + + neighbor->build_one(list); + + double **x = atom->x; + int **firstneigh = list->firstneigh; + int *numneigh = list->numneigh; + int *type = atom->type; + int *ilist = list->ilist; + int inum = list->inum; + int nClusters = podptr->nClusters; + int Mdesc = podptr->Mdesc; + + double rcutsq = podptr->rcut*podptr->rcut; + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + int jnum = numneigh[i]; + + // allocate temporary memory + if (nijmax < jnum) { + nijmax = MAX(nijmax, jnum); + podptr->free_temp_memory(); + podptr->allocate_temp_memory(nijmax); + } + + rij = &podptr->tmpmem[0]; + tmpmem = &podptr->tmpmem[3*nijmax]; + ai = &podptr->tmpint[0]; + aj = &podptr->tmpint[nijmax]; + ti = &podptr->tmpint[2*nijmax]; + tj = &podptr->tmpint[3*nijmax]; + + // get neighbor list for atom i + lammpsNeighborList(x, firstneigh, atom->tag, type, numneigh, rcutsq, i); + + if (nij > 0) { + // peratom base descriptors + double *bd = &podptr->bd[0]; + double *bdd = &podptr->bdd[0]; + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); + + if (nClusters>1) { + // peratom env descriptors + double *pd = &podptr->pd[0]; + double *pdd = &podptr->pdd[0]; + podptr->peratomenvironment_descriptors(pd, pdd, bd, bdd, tmpmem, ti[0] - 1, nij); + for (int k = 0; k < nClusters; k++) + for (int m = 0; m < Mdesc; m++) { + int imk = m + Mdesc*k + Mdesc*nClusters*i; + pod[0][imk] = pd[k]*bd[m]; + for (int n=0; n 1e-20) { + rij[nij * 3 + 0] = delx; + rij[nij * 3 + 1] = dely; + rij[nij * 3 + 2] = delz; + ai[nij] = atomid[gi]-1; + aj[nij] = atomid[gj]-1; + ti[nij] = itype; + tj[nij] = map[atomtypes[gj]] + 1; + nij++; + } + } +} + +void ComputePODLocal::map_element2type(int narg, char **arg, int nelements) +{ + int i,j; + const int ntypes = atom->ntypes; + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if "NULL" + // nelements = # of unique elements + // elements = list of element names + + if (narg != ntypes) + error->all(FLERR, "Number of element to type mappings does not match number of atom types"); + + if (elements) { + for (i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + } + elements = new char*[ntypes]; + for (i = 0; i < ntypes; i++) elements[i] = nullptr; + + nelements = 0; + map[0] = -1; + for (i = 1; i <= narg; i++) { + std::string entry = arg[i-1]; + if (entry == "NULL") { + map[i] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (entry == elements[j]) break; + map[i] = j; + if (j == nelements) { + elements[j] = utils::strdup(entry); + nelements++; + } + } +} diff --git a/src/ML-POD/compute_pod_local.h b/src/ML-POD/compute_pod_local.h new file mode 100644 index 0000000000..3d8137271a --- /dev/null +++ b/src/ML-POD/compute_pod_local.h @@ -0,0 +1,60 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(pod/local,ComputePODLocal); +// clang-format on +#else + +#ifndef LMP_COMPUTE_POD_LOCAL_H +#define LMP_COMPUTE_POD_LOCAL_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePODLocal : public Compute { + public: + ComputePODLocal(class LAMMPS *, int, char **); + ~ComputePODLocal() override; + void init() override; + void init_list(int, class NeighList *) override; + void compute_array() override; + double memory_usage() override; + void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, + int *numneigh, double rcutsq, int i); + void map_element2type(int narg, char **arg, int nelements); + + private: + class NeighList *list; + class EAPOD *podptr; + double **pod; + double cutmax; + int nij; + int nijmax; + + double *tmpmem; // temporary memory + double *rij; // (xj - xi) for all pairs (I, J) + char **elements; + int *map; + int *ai; // IDs of atoms I for all pairs (I, J) + int *aj; // IDs of atoms J for all pairs (I, J) + int *ti; // types of atoms I for all pairs (I, J) + int *tj; // types of atoms J for all pairs (I, J) +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-POD/compute_podd_atom.cpp b/src/ML-POD/compute_podd_atom.cpp new file mode 100644 index 0000000000..4ab6e23393 --- /dev/null +++ b/src/ML-POD/compute_podd_atom.cpp @@ -0,0 +1,282 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_podd_atom.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include + +#include "eapod.h" + +using namespace LAMMPS_NS; + +enum { SCALAR, VECTOR, ARRAY }; + +ComputePODDAtom::ComputePODDAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), list(nullptr), podptr(nullptr), pod(nullptr), tmpmem(nullptr), + rij(nullptr), elements(nullptr), map(nullptr), ai(nullptr), aj(nullptr), ti(nullptr), + tj(nullptr) +{ + int nargmin = 6; + + if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style); + if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors"); + + std::string pod_file = std::string(arg[3]); // pod input file + std::string coeff_file = std::string(arg[4]); // coefficient input file + podptr = new EAPOD(lmp, pod_file, coeff_file); + + int ntypes = atom->ntypes; + memory->create(map, ntypes + 1, "compute_pod_global:map"); + map_element2type(narg - 5, arg + 5, podptr->nelements); + + cutmax = podptr->rcut; + + nmax = 0; + nijmax = 0; + pod = nullptr; + elements = nullptr; + + if (((((MAXBIGINT*3.0)*atom->natoms)*podptr->nClusters)*podptr->Mdesc) > (MAXSMALLINT*1.0)) + error->all(FLERR, "Per-atom data too large"); + size_peratom_cols = 3 * atom->natoms * podptr->Mdesc * podptr->nClusters; + peratom_flag = 1; +} + +/* ---------------------------------------------------------------------- */ + +ComputePODDAtom::~ComputePODDAtom() +{ + memory->destroy(map); + memory->destroy(pod); + delete podptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODDAtom::init() +{ + if (force->pair == nullptr) + error->all(FLERR,"Compute pod requires a pair style be defined"); + + if (cutmax > force->pair->cutforce) + error->all(FLERR,"Compute pod cutoff is longer than pairwise cutoff"); + + // need an occasional full neighbor list + + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); + + if (modify->get_compute_by_style("pod").size() > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute pod"); +} + + +/* ---------------------------------------------------------------------- */ + +void ComputePODDAtom::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePODDAtom::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow pod array if necessary + + if (atom->natoms > nmax) { + memory->destroy(pod); + nmax = atom->natoms; + if (((((MAXBIGINT*3.0)*atom->natoms)*podptr->nClusters)*podptr->Mdesc) > (MAXSMALLINT*1.0)) + error->all(FLERR, "Per-atom data too large"); + int numdesc = 3 * atom->natoms * podptr->Mdesc * podptr->nClusters; + memory->create(pod, nmax, numdesc,"podd/atom:pod"); + array_atom = pod; + } + + for (int i = 0; i < atom->natoms; i++) + for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++) { + pod[i][icoeff] = 0.0; + } + + // invoke full neighbor list (will copy or build if necessary) + + neighbor->build_one(list); + + double **x = atom->x; + int **firstneigh = list->firstneigh; + int *numneigh = list->numneigh; + int *type = atom->type; + int *ilist = list->ilist; + int inum = list->inum; + int nClusters = podptr->nClusters; + int Mdesc = podptr->Mdesc; + double rcutsq = podptr->rcut*podptr->rcut; + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + int jnum = numneigh[i]; + + // allocate temporary memory + if (nijmax < jnum) { + nijmax = MAX(nijmax, jnum); + podptr->free_temp_memory(); + podptr->allocate_temp_memory(nijmax); + } + + rij = &podptr->tmpmem[0]; + tmpmem = &podptr->tmpmem[3*nijmax]; + ai = &podptr->tmpint[0]; + aj = &podptr->tmpint[nijmax]; + ti = &podptr->tmpint[2*nijmax]; + tj = &podptr->tmpint[3*nijmax]; + + // get neighbor list for atom i + lammpsNeighborList(x, firstneigh, atom->tag, type, numneigh, rcutsq, i); + + if (nij > 0) { + // peratom base descriptors + double *bd = &podptr->bd[0]; + double *bdd = &podptr->bdd[0]; + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); + + if (nClusters>1) { + // peratom env descriptors + double *pd = &podptr->pd[0]; + double *pdd = &podptr->pdd[0]; + podptr->peratomenvironment_descriptors(pd, pdd, bd, bdd, tmpmem, ti[0] - 1, nij); + for (int n=0; n 1e-20) { + rij[nij * 3 + 0] = delx; + rij[nij * 3 + 1] = dely; + rij[nij * 3 + 2] = delz; + ai[nij] = atomid[gi]-1; + aj[nij] = atomid[gj]-1; + ti[nij] = itype; + tj[nij] = map[atomtypes[gj]] + 1; + nij++; + } + } +} + +void ComputePODDAtom::map_element2type(int narg, char **arg, int nelements) +{ + int i,j; + const int ntypes = atom->ntypes; + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if "NULL" + // nelements = # of unique elements + // elements = list of element names + + if (narg != ntypes) + error->all(FLERR, "Number of element to type mappings does not match number of atom types"); + + if (elements) { + for (i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + } + elements = new char*[ntypes]; + for (i = 0; i < ntypes; i++) elements[i] = nullptr; + + nelements = 0; + map[0] = -1; + for (i = 1; i <= narg; i++) { + std::string entry = arg[i-1]; + if (entry == "NULL") { + map[i] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (entry == elements[j]) break; + map[i] = j; + if (j == nelements) { + elements[j] = utils::strdup(entry); + nelements++; + } + } +} diff --git a/src/ML-POD/compute_podd_atom.h b/src/ML-POD/compute_podd_atom.h new file mode 100644 index 0000000000..60802803ce --- /dev/null +++ b/src/ML-POD/compute_podd_atom.h @@ -0,0 +1,61 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(podd/atom,ComputePODDAtom); +// clang-format on +#else + +#ifndef LMP_COMPUTE_PODD_ATOM_H +#define LMP_COMPUTE_PODD_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePODDAtom : public Compute { + public: + ComputePODDAtom(class LAMMPS *, int, char **); + ~ComputePODDAtom() override; + void init() override; + void init_list(int, class NeighList *) override; + void compute_peratom() override; + double memory_usage() override; + void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, + int *numneigh, double rcutsq, int i); + void map_element2type(int narg, char **arg, int nelements); + + private: + class NeighList *list; + class EAPOD *podptr; + double **pod; + double cutmax; + int nmax; + int nij; + int nijmax; + + double *tmpmem; // temporary memory + double *rij; // (xj - xi) for all pairs (I, J) + char **elements; + int *map; + int *ai; // IDs of atoms I for all pairs (I, J) + int *aj; // IDs of atoms J for all pairs (I, J) + int *ti; // types of atoms I for all pairs (I, J) + int *tj; // types of atoms J for all pairs (I, J) +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-POD/eapod.cpp b/src/ML-POD/eapod.cpp new file mode 100644 index 0000000000..11dace1f28 --- /dev/null +++ b/src/ML-POD/eapod.cpp @@ -0,0 +1,4733 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ngoc Cuong Nguyen (MIT) +------------------------------------------------------------------------- */ + +// LAMMPS header files + +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "tokenizer.h" + +#include + +// header file. Moved down here to avoid polluting other headers with its defines +#include "eapod.h" + +using namespace LAMMPS_NS; +using MathConst::MY_PI; +using MathSpecial::cube; +using MathSpecial::powint; + +static constexpr int MAXLINE=1024; + +// constructor +EAPOD::EAPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file) : + Pointers(_lmp), elemindex(nullptr), Phi(nullptr), Lambda(nullptr), coeff(nullptr), + tmpmem(nullptr), Proj(nullptr), Centroids(nullptr), bd(nullptr), bdd(nullptr), pd(nullptr), + pdd(nullptr), pn3(nullptr), pq3(nullptr), pc3(nullptr), pq4(nullptr), pa4(nullptr), + pb4(nullptr), pc4(nullptr), tmpint(nullptr), ind23(nullptr), ind32(nullptr), ind33(nullptr), + ind34(nullptr), ind43(nullptr), ind44(nullptr), ind33l(nullptr), ind33r(nullptr), + ind34l(nullptr), ind34r(nullptr), ind44l(nullptr), ind44r(nullptr) +{ + rin = 0.5; + rcut = 5.0; + nClusters = 1; + nComponents = 1; + nelements = 1; + onebody = 1; + besseldegree = 4; + inversedegree = 8; + nbesselpars = 3; + true4BodyDesc = 1; + ns = nbesselpars*besseldegree + inversedegree; + Njmax = 100; + nrbf2 = 8; + nrbf3 = 6; + nrbf4 = 4; + nabf3 = 5; + nabf4 = 3; + nrbf23 = 0; + nabf23 = 0; + nrbf33 = 0; + nabf33 = 0; + nrbf34 = 0; + nabf34 = 0; + nabf43 = 0; + nrbf44 = 0; + nabf44 = 0; + P3 = 4; + P4 = 3; + P23 = 0; + P33 = 0; + P34 = 0; + P44 = 0; + pdegree[0] = besseldegree; + pdegree[1] = inversedegree; + pbc[0] = 1; + pbc[1] = 1; + pbc[2] = 1; + besselparams[0] = 1e-3; + besselparams[1] = 2.0; + besselparams[2] = 4.0; + + // read pod input file to podstruct + read_pod_file(pod_file); + + if (coeff_file != "") { + read_model_coeff_file(coeff_file); + } +} + +// destructor +EAPOD::~EAPOD() +{ + memory->destroy(elemindex); + memory->destroy(Phi); + memory->destroy(Lambda); + memory->destroy(Proj); + memory->destroy(Centroids); + memory->destroy(bd); + memory->destroy(bdd); + memory->destroy(pd); + memory->destroy(pdd); + memory->destroy(coeff); + memory->destroy(tmpmem); + memory->destroy(tmpint); + memory->destroy(pn3); + memory->destroy(pq3); + memory->destroy(pc3); + memory->destroy(pa4); + memory->destroy(pb4); + memory->destroy(pc4); + memory->destroy(pq4); + memory->destroy(ind23); + memory->destroy(ind32); + memory->destroy(ind33); + memory->destroy(ind34); + memory->destroy(ind43); + memory->destroy(ind44); + memory->destroy(ind33l); + memory->destroy(ind34l); + memory->destroy(ind44l); + memory->destroy(ind33r); + memory->destroy(ind34r); + memory->destroy(ind44r); +} + +void EAPOD::read_pod_file(std::string pod_file) +{ + std::string podfilename = pod_file; + FILE *fppod; + if (comm->me == 0) { + + fppod = utils::open_potential(podfilename,lmp,nullptr); + if (fppod == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", + podfilename, utils::getsyserror()); + } + + // loop through lines of POD file and parse keywords + + char line[MAXLINE],*ptr; + int eof = 0; + + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fppod); + if (ptr == nullptr) { + eof = 1; + fclose(fppod); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + auto keywd = words[0]; + + if (keywd == "species") { + nelements = words.size()-1; + for (int ielem = 1; ielem <= nelements; ielem++) { + species.push_back(words[ielem]); + } + } + + if (keywd == "pbc") { + if (words.size() != 4) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + pbc[0] = utils::inumeric(FLERR,words[1],false,lmp); + pbc[1] = utils::inumeric(FLERR,words[2],false,lmp); + pbc[2] = utils::inumeric(FLERR,words[3],false,lmp); + } + + if ((keywd != "#") && (keywd != "species") && (keywd != "pbc")) { + + if (words.size() != 2) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + + if (keywd == "rin") rin = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "rcut") rcut = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "number_of_environment_clusters") + nClusters = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "number_of_principal_components") + nComponents = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_polynomial_degree") + besseldegree = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "inverse_polynomial_degree") + inversedegree = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "onebody") onebody = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "twobody_number_radial_basis_functions") + nrbf2 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_number_radial_basis_functions") + nrbf3 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_angular_degree") + P3 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_number_radial_basis_functions") + nrbf4 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_angular_degree") + P4 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fivebody_number_radial_basis_functions") + nrbf33 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fivebody_angular_degree") + P33 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "sixbody_number_radial_basis_functions") + nrbf34 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "sixbody_angular_degree") + P34 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "sevenbody_number_radial_basis_functions") + nrbf44 = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "sevenbody_angular_degree") + P44 = utils::inumeric(FLERR,words[1],false,lmp); + } + } + if (nrbf3 < nrbf4) error->all(FLERR,"number of four-body radial basis functions must be equal or less than number of three-body radial basis functions"); + if (nrbf4 < nrbf33) error->all(FLERR,"number of five-body radial basis functions must be equal or less than number of four-body radial basis functions"); + if (nrbf4 < nrbf34) error->all(FLERR,"number of six-body radial basis functions must be equal or less than number of four-body radial basis functions"); + if (nrbf4 < nrbf44) error->all(FLERR,"number of seven-body radial basis functions must be equal or less than number of four-body radial basis functions"); + nrbfmax = (nrbf2 < nrbf3) ? nrbf3 : nrbf2; + nrbfmax = (nrbfmax < nrbf4) ? nrbf4 : nrbfmax; + nrbfmax = (nrbfmax < nrbf33) ? nrbf33 : nrbfmax; + nrbfmax = (nrbfmax < nrbf34) ? nrbf34 : nrbfmax; + nrbfmax = (nrbfmax < nrbf44) ? nrbf44 : nrbfmax; + + if (P3 < P4) error->all(FLERR,"four-body angular degree must be equal or less than three-body angular degree"); + if (P4 < P33) error->all(FLERR,"five-body angular degree must be equal or less than four-body angular degree"); + if (P4 < P34) error->all(FLERR,"six-body angular degree must be equal or less than four-body angular degree"); + if (P4 < P44) error->all(FLERR,"seven-body angular degree must be equal or less than four-body angular degree"); + + if (P3 > 12) error->all(FLERR,"three-body angular degree must be equal or less than 12"); + if (P4 > 6) error->all(FLERR,"four-body angular degree must be equal or less than 6"); + + int Ne = nelements; + memory->create(elemindex, Ne*Ne, "elemindex"); + int k = 0; + for (int i1 = 0; i1create(ind23, n23, "ind23"); + memory->create(ind32, n32, "ind32"); + memory->create(ind33, n33, "ind33"); + memory->create(ind34, n34, "ind34"); + memory->create(ind43, n43, "ind43"); + memory->create(ind44, n44, "ind44"); + + indexmap3(ind23, 1, nrbf23, Ne, 1, nrbf2); + indexmap3(ind32, nabf23, nrbf23, Ne*(Ne+1)/2, nabf3, nrbf3); + indexmap3(ind33, nabf33, nrbf33, Ne*(Ne+1)/2, nabf3, nrbf3); + indexmap3(ind34, nabf34, nrbf34, Ne*(Ne+1)/2, nabf3, nrbf3); + indexmap3(ind43, nabf43, nrbf34, Ne*(Ne+1)*(Ne+2)/6, nabf4, nrbf4); + indexmap3(ind44, nabf44, nrbf44, Ne*(Ne+1)*(Ne+2)/6, nabf4, nrbf4); + + nld33 = 0; + nld34 = 0; + nld44 = 0; + int nebf3 = Ne*(Ne+1)/2; + int nebf4 = Ne*(Ne+1)*(Ne+2)/6; + int dabf3[] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}; + int dabf4[] = {0, 1, 2, 2, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6}; + if (nrbf33>0) { + nld33 = crossindices(dabf3, nabf3, nrbf3, nebf3, dabf3, nabf3, nrbf3, nebf3, P33, nrbf33); + memory->create(ind33l, nld33, "ind33l"); + memory->create(ind33r, nld33, "ind33r"); + crossindices(ind33l, ind33r, dabf3, nabf3, nrbf3, nebf3, dabf3, nabf3, nrbf3, nebf3, P33, nrbf33); + } + if (nrbf34>0) { + nld34 = crossindices(dabf3, nabf3, nrbf3, nebf3, dabf4, nabf4, nrbf4, nebf4, P34, nrbf34); + memory->create(ind34l, nld34, "ind34l"); + memory->create(ind34r, nld34, "ind34r"); + crossindices(ind34l, ind34r, dabf3, nabf3, nrbf3, nebf3, dabf4, nabf4, nrbf4, nebf4, P34, nrbf34); + } + if (nrbf44>0) { + nld44 = crossindices(dabf4, nabf4, nrbf4, nebf4, dabf4, nabf4, nrbf4, nebf4, P44, nrbf44); + memory->create(ind44l, nld44, "ind44l"); + memory->create(ind44r, nld44, "ind44r"); + crossindices(ind44l, ind44r, dabf4, nabf4, nrbf4, nebf4, dabf4, nabf4, nrbf4, nebf4, P44, nrbf44); + } + ngd33 = nld33*Ne; + ngd34 = nld34*Ne; + ngd44 = nld44*Ne; + nl33 = nld33; + nl34 = nld34; + nl44 = nld44; + nd33 = ngd33; + nd34 = ngd34; + nd44 = ngd44; + + Mdesc = nl2 + nl3 + nl4 + nl23 + nl33 + nl34 + nl44; + nl = nl1 + nl2 + nl3 + nl4 + nl23 + nl33 + nl34 + nl44; + nd = nd1 + nd2 + nd3 + nd4 + nd23 + nd33 + nd34 + nd44; + nCoeffPerElement = nl1 + Mdesc*nClusters; + nCoeffAll = nCoeffPerElement*nelements; + + allocate_temp_memory(Njmax); + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of POD Potentials ****************\n"); + utils::logmesg(lmp, "species: "); + for (int i=0; ime == 0) { + + fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); + if (fpcoeff == nullptr) + error->one(FLERR,"Cannot open model coefficient file {}: ", coefffilename, utils::getsyserror()); + } + + // check format for first line of file + + char line[MAXLINE],*ptr; + int eof = 0; + int nwords = 0; + while (nwords == 0) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // strip comment, skip line if blank + nwords = utils::count_words(utils::trim_comment(line)); + } + + if (nwords != 4) + error->all(FLERR,"Incorrect format in POD coefficient file"); + + // strip single and double quotes from words + + int ncoeffall, nprojall, ncentall; + std::string tmp_str; + try { + ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f"); + tmp_str = words.next_string(); + ncoeffall = words.next_int(); + nprojall = words.next_int(); + ncentall = words.next_int(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); + } + + // loop over single block of coefficients and insert values in coeff + + memory->create(coeff, ncoeffall, "pod:pod_coeff"); + + for (int icoeff = 0; icoeff < ncoeffall; icoeff++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) error->all(FLERR,"Incorrect format in model coefficient file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer cff(utils::trim_comment(line)); + if (cff.count() != 1) error->all(FLERR,"Incorrect format in model coefficient file"); + + coeff[icoeff] = cff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in model coefficient file: {}", e.what()); + } + } + + memory->create(Proj, nprojall, "pod:pca_proj"); + + for (int iproj = 0; iproj < nprojall; iproj++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) error->all(FLERR,"Incorrect format in model coefficient file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer cff(utils::trim_comment(line)); + if (cff.count() != 1) error->all(FLERR,"Incorrect format in model coefficient file"); + + Proj[iproj] = cff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in model coefficient file: {}", e.what()); + } + } + + memory->create(Centroids, ncentall, "pod:pca_cent"); + + for (int icent = 0; icent < ncentall; icent++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) error->all(FLERR,"Incorrect format in model coefficient file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer cff(utils::trim_comment(line)); + if (cff.count() != 1) error->all(FLERR,"Incorrect format in model coefficient file"); + + Centroids[icent] = cff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in model coefficient file: {}", e.what()); + } + } + + if (comm->me == 0) { + if (!eof) fclose(fpcoeff); + } + + + if (ncoeffall != nCoeffAll) + error->all(FLERR,"number of coefficients in the coefficient file is not correct"); + + if (nClusters > 1) { + if (nprojall != nComponents*Mdesc*nelements) + error->all(FLERR,"number of coefficients in the projection file is not correct"); + + if (ncentall != nComponents*nClusters*nelements) + error->all(FLERR,"number of coefficients in the projection file is not correct"); + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of Model Coefficients ****************\n"); + utils::logmesg(lmp, "total number of coefficients for POD potential: {}\n", ncoeffall); + utils::logmesg(lmp, "total number of elements for PCA projection matrix: {}\n", nprojall); + utils::logmesg(lmp, "total number of elements for PCA centroids: {}\n", ncentall); + utils::logmesg(lmp, "**************** End of Model Coefficients ****************\n\n"); + } +} + +int EAPOD::read_coeff_file(std::string coeff_file) +{ + std::string coefffilename = coeff_file; + FILE *fpcoeff; + if (comm->me == 0) { + + fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); + if (fpcoeff == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", + coefffilename, utils::getsyserror()); + } + + // check format for first line of file + + char line[MAXLINE],*ptr; + int eof = 0; + int nwords = 0; + while (nwords == 0) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + nwords = utils::count_words(utils::trim_comment(line)); + } + + if (nwords != 2) + error->all(FLERR,"Incorrect format in POD coefficient file"); + + // strip single and double quotes from words + + int ncoeffall; + std::string tmp_str; + try { + ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f"); + tmp_str = words.next_string(); + ncoeffall = words.next_int(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); + } + + // loop over single block of coefficients and insert values in coeff + + memory->create(coeff, ncoeffall, "pod:pod_coeff"); + + for (int icoeff = 0; icoeff < ncoeffall; icoeff++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) + error->all(FLERR,"Incorrect format in POD coefficient file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer cff(utils::trim_comment(line)); + if (cff.count() != 1) + error->all(FLERR,"Incorrect format in POD coefficient file"); + + coeff[icoeff] = cff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); + } + } + + if (comm->me == 0) { + if (!eof) fclose(fpcoeff); + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of POD Coefficients ****************\n"); + utils::logmesg(lmp, "total number of coefficients for POD potential: {}\n", ncoeffall); + utils::logmesg(lmp, "**************** End of POD Coefficients ****************\n\n"); + } + + return ncoeffall; +} + +// funcion to read the projection matrix from file. +int EAPOD::read_projection_matrix(std::string proj_file) +{ + std::string projfilename = proj_file; + FILE *fpproj; + if (comm->me == 0) { + + fpproj = utils::open_potential(projfilename,lmp,nullptr); + if (fpproj == nullptr) + error->one(FLERR,"Cannot open PCA projection matrix file {}: ", + projfilename, utils::getsyserror()); + } + + // check format for first line of file + + char line[MAXLINE],*ptr; + int eof = 0; + int nwords = 0; + while (nwords == 0) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpproj); + if (ptr == nullptr) { + eof = 1; + fclose(fpproj); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + nwords = utils::count_words(utils::trim_comment(line)); + } + + if (nwords != 2) + error->all(FLERR,"Incorrect format in PCA projection matrix file"); + + // strip single and double quotes from words + + int nprojall; + std::string tmp_str; + try { + ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f"); + tmp_str = words.next_string(); + nprojall = words.next_int(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in PCA projection matrix file: {}", e.what()); + } + + // loop over single block of coefficients and insert values in coeff + + memory->create(Proj, nprojall, "pod:pca_proj"); + + for (int iproj = 0; iproj < nprojall; iproj++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpproj); + if (ptr == nullptr) { + eof = 1; + fclose(fpproj); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) + error->all(FLERR,"Incorrect format in PCA projection matrix file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer cff(utils::trim_comment(line)); + if (cff.count() != 1) + error->all(FLERR,"Incorrect format in PCA projection matrix file"); + + Proj[iproj] = cff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in PCA projection matrix file: {}", e.what()); + } + } + if (comm->me == 0) { + if (!eof) fclose(fpproj); + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of PCA projection matrix ****************\n"); + utils::logmesg(lmp, "total number of elements for PCA projection matrix: {}\n", nprojall); + utils::logmesg(lmp, "**************** End of PCA projection matrix ****************\n\n"); + } + + return nprojall; +} + +// read Centroids from file +int EAPOD::read_centroids(std::string centroids_file) +{ + std::string centfilename = centroids_file; + FILE *fpcent; + if (comm->me == 0) { + + fpcent = utils::open_potential(centfilename,lmp,nullptr); + if (fpcent == nullptr) + error->one(FLERR,"Cannot open PCA centroids file {}: ", + centfilename, utils::getsyserror()); + } + + // check format for first line of file + + char line[MAXLINE],*ptr; + int eof = 0; + int nwords = 0; + while (nwords == 0) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcent); + if (ptr == nullptr) { + eof = 1; + fclose(fpcent); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + nwords = utils::count_words(utils::trim_comment(line)); + } + + if (nwords != 2) + error->all(FLERR,"Incorrect format in PCA centroids file"); + + // strip single and double quotes from words + + int ncentall; + std::string tmp_str; + try { + ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f"); + tmp_str = words.next_string(); + ncentall = words.next_int(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in PCA centroids file: {}", e.what()); + } + + // loop over single block of coefficients and insert values in coeff + + memory->create(Centroids, ncentall, "pod:pca_cent"); + + for (int icent = 0; icent < ncentall; icent++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcent); + if (ptr == nullptr) { + eof = 1; + fclose(fpcent); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) + error->all(FLERR,"Incorrect format in PCA centroids file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer cff(utils::trim_comment(line)); + if (cff.count() != 1) + error->all(FLERR,"Incorrect format in PCA centroids file"); + + Centroids[icent] = cff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in PCA centroids file: {}", e.what()); + } + } + if (comm->me == 0) { + if (!eof) fclose(fpcent); + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of PCA centroids ****************\n"); + utils::logmesg(lmp, "total number of elements for PCA centroids: {}\n", ncentall); + utils::logmesg(lmp, "**************** End of PCA centroids ****************\n\n"); + } + + return ncentall; +} + + +void EAPOD::peratombase_descriptors(double *bd1, double *bdd1, double *rij, double *temp, + int *tj, int Nj) +{ + for (int i=0; i0) && (Nj>0)) { + twobodydescderiv(d2, dd2, rbf, rbfx, rbfy, rbfz, tj, Nj); + } + + if ((nl3 > 0) && (Nj>1)) { + double *abf = &temp[4*n1 + n5 + 4*n2]; // Nj*K3 + double *abfx = &temp[4*n1 + n5 + 4*n2 + n4]; // Nj*K3 + double *abfy = &temp[4*n1 + n5 + 4*n2 + 2*n4]; // Nj*K3 + double *abfz = &temp[4*n1 + n5 + 4*n2 + 3*n4]; // Nj*K3 + double *tm = &temp[4*n1 + n5 + 4*n2 + 4*n4]; // 4*K3 + + angularbasis(abf, abfx, abfy, abfz, rij, tm, pq3, Nj, K3); + + radialangularbasis(sumU, U, Ux, Uy, Uz, rbf, rbfx, rbfy, rbfz, + abf, abfx, abfy, abfz, tj, Nj, K3, nrbf3, nelements); + + threebodydesc(d3, sumU); + threebodydescderiv(dd3, sumU, Ux, Uy, Uz, tj, Nj); + + if ((nl23>0) && (Nj>2)) { + fourbodydesc23(d23, d2, d3); + fourbodydescderiv23(dd23, d2, d3, dd2, dd3, 3*Nj); + } + + if ((nl33>0) && (Nj>3)) { + crossdesc(d33, d3, d3, ind33l, ind33r, nl33); + crossdescderiv(dd33, d3, d3, dd3, dd3, ind33l, ind33r, nl33, 3*Nj); + } + + if ((nl4 > 0) && (Nj>2)) { + if (K4 < K3) { + for (int m=0; m0) && (Nj>4)) { + crossdesc(d34, d3, d4, ind34l, ind34r, nl34); + crossdescderiv(dd34, d3, d4, dd3, dd4, ind34l, ind34r, nl34, 3*Nj); + } + + if ((nl44>0) && (Nj>5)) { + crossdesc(d44, d4, d4, ind44l, ind44r, nl44); + crossdescderiv(dd44, d4, d4, dd4, dd4, ind44l, ind44r, nl44, 3*Nj); + } + } + } +} + +double EAPOD::peratombase_coefficients(double *cb, double *bd, int *ti) +{ + int nc = nCoeffPerElement*(ti[0]-1); + + double ei = coeff[0 + nc]; + for (int m=0; m0) && (Nj>0)) { + twobodydesc(d2, rbf, tj, Nj); + } + + if ((nl3 > 0) && (Nj>1)) { + double *abf = &temp[4*n1 + n5 + 4*n2]; // Nj*K3 + double *abfx = &temp[4*n1 + n5 + 4*n2 + n4]; // Nj*K3 + double *abfy = &temp[4*n1 + n5 + 4*n2 + 2*n4]; // Nj*K3 + double *abfz = &temp[4*n1 + n5 + 4*n2 + 3*n4]; // Nj*K3 + double *tm = &temp[4*n1 + n5 + 4*n2 + 4*n4]; // 4*K3 + + angularbasis(abf, abfx, abfy, abfz, rij, tm, pq3, Nj, K3); + + radialangularbasis(sumU, U, Ux, Uy, Uz, rbf, rbfx, rbfy, rbfz, + abf, abfx, abfy, abfz, tj, Nj, K3, nrbf3, nelements); + + threebodydesc(d3, sumU); + + if ((nl23>0) && (Nj>2)) { + fourbodydesc23(d23, d2, d3); + } + + if ((nl33>0) && (Nj>3)) { + crossdesc(d33, d3, d3, ind33l, ind33r, nl33); + } + + if ((nl4 > 0) && (Nj>2)) { + fourbodydesc(d4, sumU); + + if ((nl34>0) && (Nj>4)) { + crossdesc(d34, d3, d4, ind34l, ind34r, nl34); + } + + if ((nl44>0) && (Nj>5)) { + crossdesc(d44, d4, d4, ind44l, ind44r, nl44); + } + } + } + + double *cb = &bdd[0]; + if (nClusters > 1) { + e += peratom_environment_descriptors(cb, bd, &temp[4*n1 + n5 + 4*n2], ti); + } + else { + e += peratombase_coefficients(cb, bd, ti); + } + + double *cb2 = &cb[0]; // nl3 + double *cb3 = &cb[nl2]; // nl3 + double *cb4 = &cb[(nl2 + nl3)]; // nl4 + double *cb33 = &cb[(nl2 + nl3 + nl4)]; // nl33 + double *cb34 = &cb[(nl2 + nl3 + nl4 + nl33)]; // nl34 + double *cb44 = &cb[(nl2 + nl3 + nl4 + nl33 + nl34)]; // nl44 + + if ((nl33>0) && (Nj>3)) { + crossdesc_reduction(cb3, cb3, cb33, d3, d3, ind33l, ind33r, nl33); + } + if ((nl34>0) && (Nj>4)) { + crossdesc_reduction(cb3, cb4, cb34, d3, d4, ind34l, ind34r, nl34); + } + if ((nl44>0) && (Nj>5)) { + crossdesc_reduction(cb4, cb4, cb44, d4, d4, ind44l, ind44r, nl44); + } + + if ((nl2 > 0) && (Nj>0)) twobody_forces(fij, cb2, rbfx, rbfy, rbfz, tj, Nj); + + // Initialize forcecoeff to zero + double *forcecoeff = &cb[(nl2 + nl3 + nl4)]; // nl33 + std::fill(forcecoeff, forcecoeff + nelements * K3 * nrbf3, 0.0); + if ((nl3 > 0) && (Nj>1)) threebody_forcecoeff(forcecoeff, cb3, sumU); + if ((nl4 > 0) && (Nj>2)) fourbody_forcecoeff(forcecoeff, cb4, sumU); + if ((nl3 > 0) && (Nj>1)) allbody_forces(fij, forcecoeff, Ux, Uy, Uz, tj, Nj); + + return e; +} + +double EAPOD::peratomenergyforce(double *fij, double *rij, double *temp, + int *ti, int *tj, int Nj) +{ + if (Nj==0) { + return coeff[nCoeffPerElement*(ti[0]-1)]; + } + + int N = 3*Nj; + for (int n=0; n 1) { // multi-environment descriptors + // calculate multi-environment descriptors and their derivatives with respect to atom coordinates + peratomenvironment_descriptors(pd, pdd, bd, bdd, temp, ti[0] - 1, Nj); + + for (int j = 0; jNjmax) { + Njmax = Nj; + free_temp_memory(); + allocate_temp_memory(Njmax); + } + + double *rij = &tmpmem[0]; // 3*Nj + double *fij = &tmpmem[3*Nj]; // 3*Nj + int *ai = &tmpint[0]; // Nj + int *aj = &tmpint[Nj]; // Nj + int *ti = &tmpint[2*Nj]; // Nj + int *tj = &tmpint[3*Nj]; // Nj + + myneighbors(rij, x, ai, aj, ti, tj, jlist, pairnumsum, atomtype, alist, i); + + etot += peratomenergyforce(fij, rij, &tmpmem[6*Nj], ti, tj, Nj); + + tallyforce(force, fij, ai, aj, Nj); + } + } + + return etot; +} + +void EAPOD::base_descriptors(double *basedesc, double *x, + int *atomtype, int *alist, int *jlist, int *pairnumsum, int natom) +{ + for (int i=0; i0) { + // reallocate temporary memory + if (Nj>Njmax) { + Njmax = Nj; + free_temp_memory(); + allocate_temp_memory(Njmax); + if (comm->me == 0) utils::logmesg(lmp, "reallocate temporary memory with Njmax = %d ...\n", Njmax); + } + + double *rij = &tmpmem[0]; // 3*Nj + int *ai = &tmpint[0]; // Nj + int *aj = &tmpint[Nj]; // Nj + int *ti = &tmpint[2*Nj]; // Nj + int *tj = &tmpint[3*Nj]; // Nj + + myneighbors(rij, x, ai, aj, ti, tj, jlist, pairnumsum, atomtype, alist, i); + + // many-body descriptors + peratombase_descriptors(bd, bdd, rij, &tmpmem[3*Nj], tj, Nj); + + for (int m=0; m0) { + gd[nCoeffPerElement*(atomtype[i]-1)] += 1.0; + } + + if (Nj>0) { + // reallocate temporary memory + if (Nj>Njmax) { + Njmax = Nj; + free_temp_memory(); + allocate_temp_memory(Njmax); + if (comm->me == 0) utils::logmesg(lmp, "reallocate temporary memory with Njmax = %d ...\n", Njmax); + } + + double *rij = &tmpmem[0]; // 3*Nj + int *ai = &tmpint[0]; // Nj + int *aj = &tmpint[Nj]; // Nj + int *ti = &tmpint[2*Nj]; // Nj + int *tj = &tmpint[3*Nj]; // Nj + + myneighbors(rij, x, ai, aj, ti, tj, jlist, pairnumsum, atomtype, alist, i); + + // many-body descriptors + peratombase_descriptors(bd, bdd, rij, &tmpmem[3*Nj], tj, Nj); + + for (int m=0; m0) { + gd[nCoeffPerElement*(atomtype[i]-1)] += 1.0; + } + + if (Nj>0) { + // reallocate temporary memory + if (Nj>Njmax) { + Njmax = Nj; + free_temp_memory(); + allocate_temp_memory(Njmax); + if (comm->me == 0) utils::logmesg(lmp, "reallocate temporary memory with Njmax = %d ...\n", Njmax); + } + + double *rij = &tmpmem[0]; // 3*Nj + int *ai = &tmpint[0]; // Nj + int *aj = &tmpint[Nj]; // Nj + int *ti = &tmpint[2*Nj]; // Nj + int *tj = &tmpint[3*Nj]; // Nj + + myneighbors(rij, x, ai, aj, ti, tj, jlist, pairnumsum, atomtype, alist, i); + + // many-body descriptors + peratombase_descriptors(bd, bdd, rij, &tmpmem[3*Nj], tj, Nj); + + // calculate multi-environment descriptors and their derivatives with respect to atom coordinates + peratomenvironment_descriptors(pd, pdd, bd, bdd, tmpmem, ti[0] - 1, Nj); + + for (int j = 0; j < nClusters; j++) { + probdesc[i + natom*(j)] = pd[j]; + for (int m=0; mcreate(coeff, nc, "coeff"); + + // Copy the coefficients + for (int n=0; ncreate(xij, N, "eapod:xij"); + memory->create(S, N*ns, "eapod:S"); + memory->create(Q, N*ns, "eapod:Q"); + memory->create(A, ns*ns, "eapod:A"); + memory->create(work, ns*ns, "eapod:work"); + memory->create(b, ns, "eapod:ns"); + + // Generate the xij array + for (int i=0; i= max(1,3*N-1) + int info = 1; // = 0: successful exit + //double work[ns*ns]; + char chv = 'V'; + char chu = 'U'; + DSYEV(&chv, &chu, &ns, A, &ns, b, work, &lwork, &info); + + // Order eigenvalues and eigenvectors from largest to smallest + for (int j=0; jdestroy(xij); + memory->destroy(S); + memory->destroy(A); + memory->destroy(work); + memory->destroy(b); + memory->destroy(Q); +} + +/** + * @brief Initialize the two-body coefficients. + * + * @param None + */ +void EAPOD::init2body() +{ + // Set the degree of the Bessel function and the inverse distance function + pdegree[0] = besseldegree; + pdegree[1] = inversedegree; + + // Compute the total number of snapshots + ns = nbesselpars * pdegree[0] + pdegree[1]; + + // Allocate memory for the eigenvectors and eigenvalues + memory->create(Phi, ns * ns, "Phi"); + memory->create(Lambda, ns, "Lambda"); + + // Perform eigenvalue decomposition of the snapshots matrix S and store the eigenvectors and eigenvalues + eigenvaluedecomposition(Phi, Lambda, 2000); +} + +/** + * @brief Initialize arrays for the three-body descriptors. + * + * @param Pa3 The degree of the angular basis functions of the three-body descriptors. + */ +void EAPOD::init3body(int Pa3) +{ + // Define the number of monomials for each degree + int npa[] = {0, 1, 4, 10, 20, 35, 56, 84, 120, 165, 220, 286, 364, 455}; + + // Set the number of coefficients, the number of basis functions, and the degree of the Bessel function + nabf3 = Pa3+1; // Number of angular basis functions + K3 = npa[nabf3]; // number of monimials + P3 = nabf3-1; // the degree of angular basis functions of the three-body descriptors + + // Allocate memory for the coefficients, the basis functions, and the cutoff function + memory->create(pn3, nabf3+1, "pn3"); // array stores the number of monomials for each degree + memory->create(pq3, K3*2, "pq3"); // array needed for the recursive computation of the angular basis functions + memory->create(pc3, K3, "pc3"); // array needed for the computation of the three-body descriptors + + // Initialize the arrays + init3bodyarray(pn3, pq3, pc3, nabf3-1); +} + +/** + * @brief Initialize arrays for the four-body descriptors. + * + * @param Pa4 The degree of the angular basis functions of the four-body descriptors. + */ +void EAPOD::init4body(int Pa4) +{ + // Define the number of monomials for each degree + int npa[] = {0, 1, 4, 10, 20, 35, 56, 84, 120, 165, 220, 286, 364, 455}; + + // Define the number of angular basis functions for each degree + int nb[] = {1, 2, 4, 7, 11, 16, 23}; + + // Define the number of terms needed to compute angular basis functions + int ns[] = {0, 1, 4, 10, 19, 29, 47, 74, 89, 119, 155, 209, 230, 275, 335, 425, 533, 561, 624, 714, 849, 949, 1129, 1345}; + + // Set the degree of the angular basis functions of the four-body descriptors + P4 = Pa4; + + // Set the number of monomials for the angular basis functions of the four-body descriptors + K4 = npa[Pa4+1]; + + // Allocate memory for the output arrays + int *pn4, *tm4; + memory->create(pn4, Pa4+2, "pn4"); // array stores the number of monomials for each degree + memory->create(pq4, K4*2, "pq4"); // array needed for the recursive computation of the angular basis functions + memory->create(tm4, K4, "tm4"); + + // Initialize the arrays + init3bodyarray(pn4, pq4, tm4, Pa4); + + // Set the number of angular basis functions for the four-body descriptors + nabf4 = nb[Pa4]; + + // the size of the array pc4 + Q4 = ns[nabf4]; + + // Allocate memory for the coefficients, the basis functions, and the cutoff function + memory->create(pa4, nabf4+1, "pa4"); // this array is a subset of the array ns + memory->create(pb4, Q4*3, "pb4"); // array stores the indices of the monomials needed for the computation of the angular basis functions + memory->create(pc4, Q4, "pc4"); // array of monomial coefficients needed for the computation of the four-body descriptors + + // Initialize the arrays + init4bodyarray(pa4, pb4, pc4, Pa4); + + // Deallocate memory + memory->destroy(pn4); + memory->destroy(tm4); +} + + +/** + * @brief Estimate the amount of memory needed for the computation. + * + * @param Nj Number of neighboring atoms. + * @return int The estimated amount of memory needed. + */ +int EAPOD::estimate_temp_memory(int Nj) +{ + // Determine the maximum number of radial basis functions and angular basis functions + int Kmax = (K3 > K4) ? K3 : K4; + int nrbf34 = (nrbf3 > nrbf4) ? nrbf3 : nrbf4; + int nrbfmax = (nrbf2 > nrbf34) ? nrbf2 : nrbf34; + int Knrbf34 = (K3*nrbf3 > K4*nrbf4) ? K3*nrbf3 : K4*nrbf4; + + // Determine the maximum number of local descriptors + int nld = (nl23 > nl33) ? nl23 : nl33; + nld = (nld > nl34) ? nld : nl34; + nld = (nld > nl44) ? nld : nl44; + + // rij, fij, and d2, dd2, d3, dd3, d4, dd4 + int nmax1 = 6*Nj + nl2 + 3*Nj*nl2 + nl3 + 3*Nj*nl3 + nl4 + 3*Nj*nl4 + nld + 3*Nj*nld; + + // U, Ux, Uy, Uz + int nmax2 = 4*Nj*Knrbf34; + + // sumU and cU + int nmax3 = 2*nelements*Knrbf34; + + // rbf, rbfx, rbfy, rbfz + int nmax4 = 4*Nj*nrbfmax; + + // rbft, rbfxt, rbfyt, rbfzt + int nmax5 = 4*Nj*ns; + + // abf, abfx, abfy, abfz + int nmax6 = 4*(Nj+1)*Kmax; + + // Determine the maximum amount of memory needed for U, Ux, Uy, Uz, sumU, cU, rbf, rbfx, rbfy, rbfz, abf, abfx, abfy, abfz + int nmax7 = (nmax5 > nmax6) ? nmax5 : nmax6; + int nmax8 = nmax2 + nmax3 + nmax4 + nmax7; + + // Determine the total amount of memory needed for all double memory + ndblmem = (nmax1 + nmax8); + + int nmax9 = 6*Nj + nComponents + nClusters + nClusters*nComponents + 2*nClusters*Mdesc + nClusters*nClusters; + if (ndblmem < nmax9) ndblmem = nmax9; + + // Determine the total amount of memory needed for all integer memory + nintmem = 4*Nj; + + // Return the estimated amount of memory needed + return ndblmem; +} + +void EAPOD::allocate_temp_memory(int Nj) +{ + estimate_temp_memory(Nj); + memory->create(tmpmem, ndblmem, "tmpmem"); + memory->create(tmpint, nintmem, "tmpint"); + memory->create(bd, Mdesc, "bdd"); + memory->create(bdd, 3*Nj*Mdesc, "bdd"); + memory->create(pd, nClusters, "bdd"); + memory->create(pdd, 3*Nj*nClusters, "bdd"); +} + +void EAPOD::free_temp_memory() +{ + memory->destroy(tmpmem); + memory->destroy(tmpint); + memory->destroy(bd); + memory->destroy(bdd); + memory->destroy(pd); + memory->destroy(pdd); +} + +/** + * @brief Map a 3D index to a 1D index. + * + * @param indx The 1D index array. + * @param n1 The size of the first dimension. + * @param n2 The size of the second dimension. + * @param n3 The size of the third dimension. + * @param N1 The stride of the first dimension. + * @param N2 The stride of the second dimension. + * @return int The total number of elements in the 1D index array. + */ +int EAPOD::indexmap3(int *indx, int n1, int n2, int n3, int N1, int N2) +{ + int k = 0; + for (int i3=0; i3= m1) && (i2 >= i1) && (a1 + a2 <= dabf12) && (j1+j2 < nrbf12)) { + n += 1; + } + } + } + + return n; +} + +/** + * @brief Calculate the number of cross descriptors between two sets of descriptors and store the indices in two arrays. + * + * @param ind1 Pointer to the array of indices of the first set of descriptors. + * @param ind2 Pointer to the array of indices of the second set of descriptors. + * @param dabf1 Pointer to the array of degrees of angular basis functions of the first set of descriptors. + * @param nabf1 Number of angular basis functions in the first set of descriptors. + * @param nrbf1 Number of radial basis functions in the first set of descriptors. + * @param nebf1 Number of element interactions in the first set of descriptors. + * @param dabf2 Pointer to the array of degrees of angular basis functions of the second set of descriptors. + * @param nabf2 Number of angular basis functions in the second set of descriptors. + * @param nrbf2 Number of radial basis functions in the second set of descriptors. + * @param nebf2 Number of element interactions in the second set descriptors. + * @param dabf12 degree of angular basis functions for the cross descriptors + * @param nrbf12 number of radial basis functions for the cross descriptors + * @return int The number of cross descriptors between two sets of descriptors. + */ +int EAPOD::crossindices(int *ind1, int *ind2, int *dabf1, int nabf1, int nrbf1, int nebf1, + int *dabf2, int nabf2, int nrbf2, int nebf2, int dabf12, int nrbf12) +{ + int n = 0; + + // Loop over the first set of descriptors + for (int i1=0; i1= m1) && (i2 >= i1) && (a1 + a2 <= dabf12) && (j1+j2 < nrbf12)) { + ind1[n] = n1; + ind2[n] = n2; + n += 1; + } + } + } + + return n; +} + +void EAPOD::scalarproduct(double *d, double c, int N) +{ + for (int n=0; n species; + + double rin; + double rcut; + int true4BodyDesc; + + int nelements; // number of elements + int pbc[3]; + int *elemindex; + + int onebody; // one-body descriptors + int besseldegree; + int inversedegree; + int pdegree[2]; + int nbesselpars; + int timing; + double comptime[20]; + double besselparams[3]; + double *Phi; // eigenvectors + double *Lambda; // eigenvalues + double *coeff; // coefficients + //double *newcoeff ; // coefficients + double *tmpmem; + + // environmental variables + int nClusters; // number of environment clusters + int nComponents; // number of principal components + //int nNeighbors; // numbe of neighbors + int Mdesc; // number of base descriptors + + double *Proj; // PCA Projection matrix + double *Centroids; // centroids of the clusters + double *bd; // base descriptors + double *bdd; // derivatives of the base descriptors with respect to the atomic positions + double *pd; // multi-environment descriptors + double * + pdd; // derivative of the multi-environment descriptors with respect to the atomic positions + + int nproj; // number of elements in projection matrix (nComponents * Mdesc * nelements) + int ncentroids; // number of centroids (nComponents * nClusters * nelements) + + int Njmax; + int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters) + int nCoeffAll; // number of coefficients for all elements = (nl1 + Mdesc*nClusters)*nelements + int ncoeff; // number of coefficients in the input file + int ns; // number of snapshots for radial basis functions + int nd1, nd2, nd3, nd4, nd5, nd6, nd7, nd; // number of global descriptors + int nl1, nl2, nl3, nl4, nl5, nl6, nl7, nl; // number of local descriptors + int nrbf2, nrbf3, nrbf4, nrbfmax; // number of radial basis functions + int nabf3, nabf4; // number of angular basis functions + int P3, P4; // angular polynomial degrees + int K3, K4, Q4; // number of monomials + int *pn3, *pq3, *pc3; // arrays to compute 3-body angular basis functions + int *pq4, *pa4, *pb4, *pc4; // arrays to compute 3-body angular basis functions + int *tmpint; + int nintmem; // number of integers in tmpint array + int ndblmem; // number of doubles in tmpmem array + + // four-body descriptors + int *ind23, *ind32, nrbf23, nabf23, P23, n23, n32, nl23, nd23; + + // five-body descriptors + int *ind33, nrbf33, nabf33, P33, n33, nl33, nd33; + + // six-body descriptors + int *ind34, *ind43, nrbf34, nabf34, nabf43, P34, n34, n43, nl34, nd34; + + // seven-body descriptors + int *ind44, nrbf44, nabf44, P44, n44, nl44, nd44; + + int nld33, nld34, nld44, ngd33, ngd34, ngd44; + int *ind33l, *ind33r, *ind34l, *ind34r, *ind44l, *ind44r; + + EAPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file); + + EAPOD(LAMMPS *lmp) : Pointers(lmp){}; + ~EAPOD() override; + + void read_pod_file(std::string pod_file); + void read_model_coeff_file(std::string coeff_file); + int read_coeff_file(std::string coeff_file); + int read_projection_matrix(std::string proj_file); + int read_centroids(std::string centroids_file); + + int estimate_temp_memory(int Nj); + void free_temp_memory(); + void allocate_temp_memory(int Nj); + + //void mknewcoeff(); + + void mknewcoeff(double *c, int nc); + + void twobodydesc(double *d2, double *rbf, int *tj, int N); + void twobodydescderiv(double *d2, double *dd2, double *rbf, double *rbfx, double *rbfy, + double *rbfz, int *tj, int N); + void twobody_forces(double *fij, double *cb2, double *rbfx, double *rbfy, double *rbfz, int *tj, + int Nj); + + void threebodydesc(double *d3, double *sumU); + void threebodydescderiv(double *dd3, double *sumU, double *Ux, double *Uy, double *Uz, + int *atomtype, int N); + void threebody_forcecoeff(double *fb3, double *cb3, double *sumU); + + void fourbodydesc(double *d4, double *sumU); + void fourbodydescderiv(double *d4, double *dd4, double *sumU, double *Ux, double *Uy, double *Uz, + int *atomtype, int N); + void fourbody_forcecoeff(double *fb4, double *cb4, double *sumU); + + void allbody_forces(double *fij, double *forcecoeff, double *rbf, double *rbfx, double *rbfy, + double *rbfz, double *abf, double *abfx, double *abfy, double *abfz, int *tj, + int Nj); + void allbody_forces(double *fij, double *forcecoeff, double *Ux, double *Uy, double *Uz, int *tj, + int Nj); + + void descriptors(double *gd, double *gdd, double *basedesc, double *probdesc, double *x, + int *atomtype, int *alist, int *jlist, int *pairnumsum, int natom); + + void descriptors(double *gd, double *gdd, double *basedesc, double *x, int *atomtype, int *alist, + int *jlist, int *pairnumsum, int natom); + + void peratombase_descriptors(double *bd, double *bdd, double *rij, double *temp, int *tj, int Nj); + double peratombase_coefficients(double *cb, double *bd, int *ti); + double peratom_environment_descriptors(double *cb, double *bd, double *tm, int *ti); + + void peratomenvironment_descriptors(double *P, double *dP_dR, double *B, double *dB_dR, + double *tmp, int elem, int nNeighbors); + + void base_descriptors(double *basedesc, double *x, int *atomtype, int *alist, int *jlist, + int *pairnumsum, int natom); + + void descriptors(double *basedesc, double *probdesc, double *x, int *atomtype, int *alist, + int *jlist, int *pairnumsum, int natom); + + double peratomenergyforce(double *fij, double *rij, double *temp, int *ti, int *tj, int Nj); + double peratomenergyforce2(double *fij, double *rij, double *temp, int *ti, int *tj, int Nj); + + double energyforce(double *force, double *x, int *atomtype, int *alist, int *jlist, + int *pairnumsum, int natom); + + void tallyforce(double *force, double *fij, int *ai, int *aj, int N); + + void fourbodydesc23(double *d23, double *d2, double *d3); + void fourbodydescderiv23(double *dd23, double *d2, double *d3, double *dd2, double *dd3, int N); + + void crossdesc(double *d12, double *d1, double *d2, int *ind1, int *ind2, int n12); + void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2, int *ind1, + int *ind2, int n12, int N); + void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, double *d2, int *ind1, + int *ind2, int n12); +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/ML-POD/fitpod_command.cpp b/src/ML-POD/fitpod_command.cpp index ef39962e0b..ba7ffeba3a 100644 --- a/src/ML-POD/fitpod_command.cpp +++ b/src/ML-POD/fitpod_command.cpp @@ -17,8 +17,6 @@ #include "fitpod_command.h" -#include "mlpod.h" - #include "comm.h" #include "error.h" #include "math_special.h" @@ -28,7 +26,11 @@ #include #include #include -#include +#include +#include +#include + +#include "eapod.h" using namespace LAMMPS_NS; using MathSpecial::powint; @@ -36,106 +38,245 @@ using MathSpecial::powint; static constexpr int MAXLINE = 1024; static constexpr double SMALL = 1.0e-10; -FitPOD::FitPOD(LAMMPS *_lmp) : Command(_lmp), podptr(nullptr) +FitPOD::datastruct::datastruct() : + file_format("extxyz"), file_extension("xyz"), filenametag("pod"), group_weight_type("global"), + lattice(nullptr), energy(nullptr), stress(nullptr), position(nullptr), force(nullptr), + atomtype(nullptr), we(nullptr), wf(nullptr), + fitting_weights{100.0, 1.0, 0.0, 1, 1, 0, 0, 1, 1, 1, 1, 1e-10} { + training = 1; + normalizeenergy = 1; + training_analysis = 1; + test_analysis = 1; + training_calculation = 0; + test_calculation = 0; + randomize = 1; + precision = 8; + fraction = 1.0; +} + +void FitPOD::datastruct::copydatainfo(datastruct &data) const +{ + data.data_path = data_path; + data.file_format = file_format; + data.file_extension = file_extension; + data.data_files = data_files; + data.filenametag = filenametag; + data.filenames = filenames; + data.training_analysis = training_analysis; + data.test_analysis = test_analysis; + data.training_calculation = training_calculation; + data.test_calculation = test_calculation; + data.fraction = fraction; + data.randomize = randomize; + data.precision = precision; + data.training = training; + data.normalizeenergy = normalizeenergy; + for (int i = 0; i < 12; i++) data.fitting_weights[i] = fitting_weights[i]; + data.we_map = we_map; + data.wf_map = wf_map; +} + +FitPOD::neighborstruct::neighborstruct() : + alist(nullptr), pairnum(nullptr), pairnum_cumsum(nullptr), pairlist(nullptr), y(nullptr) +{ + natom_max = 0; + sze = 0; + sza = 0; + szy = 0; + szp = 0; +} + +FitPOD::descriptorstruct::descriptorstruct() : + bd(nullptr), pd(nullptr), gd(nullptr), gdd(nullptr), A(nullptr), b(nullptr), c(nullptr) +{ + szd = 0; + nCoeffAll = 0; + nClusters = 0; +} + +FitPOD::FitPOD(LAMMPS *_lmp) : Command(_lmp), fastpodptr(nullptr) +{ + save_descriptors = 0; + compute_descriptors = 0; } void FitPOD::command(int narg, char **arg) { if (narg < 2) utils::missing_cmd_args(FLERR, "fitpod", error); - std::string pod_file = std::string(arg[0]); // pod input file - std::string data_file = std::string(arg[1]); // data input file - std::string coeff_file; // coefficient input file + std::string pod_file = std::string(arg[0]); // pod input file + std::string data_file = std::string(arg[1]); // data input file + std::string coeff_file, proj_file, cent_file; // coefficient input files if (narg > 2) - coeff_file = std::string(arg[2]); // coefficient input file + coeff_file = std::string(arg[2]); // coefficient input file else coeff_file = ""; - podptr = new MLPOD(lmp, pod_file, coeff_file); - read_data_files(data_file, podptr->pod.species); + fastpodptr = new EAPOD(lmp, pod_file, coeff_file); - if ((int) traindata.data_path.size() > 1) - allocate_memory(traindata); - else if ((int) testdata.data_path.size() > 1) - allocate_memory(testdata); + desc.nCoeffAll = fastpodptr->nCoeffAll; + desc.nClusters = fastpodptr->nClusters; + read_data_files(data_file, fastpodptr->species); - // get POD coefficients from an input file + estimate_memory_neighborstruct(traindata, fastpodptr->pbc, fastpodptr->rcut, + fastpodptr->nelements); + estimate_memory_neighborstruct(testdata, fastpodptr->pbc, fastpodptr->rcut, + fastpodptr->nelements); + if (desc.nClusters > 1) + estimate_memory_neighborstruct(envdata, fastpodptr->pbc, fastpodptr->rcut, + fastpodptr->nelements); + allocate_memory_neighborstruct(); + estimate_memory_fastpod(traindata); + estimate_memory_fastpod(testdata); + allocate_memory_descriptorstruct(fastpodptr->nCoeffAll); - if (coeff_file != "") podArrayCopy(desc.c, podptr->pod.coeff, podptr->pod.nd); + if (coeff_file != "") podArrayCopy(desc.c, fastpodptr->coeff, fastpodptr->nCoeffAll); - // compute POD coefficients using least-squares method + if (((int) envdata.data_path.size() > 1) && (desc.nClusters > 1)) { + environment_cluster_calculation(envdata); + memory->destroy(envdata.lattice); + memory->destroy(envdata.energy); + memory->destroy(envdata.stress); + memory->destroy(envdata.position); + memory->destroy(envdata.force); + memory->destroy(envdata.atomtype); + memory->destroy(envdata.we); + memory->destroy(envdata.wf); + } - least_squares_fit(traindata); + if (compute_descriptors == 0) { - // calculate errors for the training data set + // compute POD coefficients using least-squares method + if (coeff_file == "") { + least_squares_fit(traindata); - if ((traindata.training_analysis) && ((int) traindata.data_path.size() > 1) ) - error_analysis(traindata, desc.c); + if (comm->me == 0) { // save coefficients into a text file + std::string filename = traindata.filenametag + "_coefficients" + ".pod"; + FILE *fp = fopen(filename.c_str(), "w"); - // calculate errors for the test data set + int nCoeffAll = desc.nCoeffAll; + int n1 = 0, n2 = 0; + if (((int) envdata.data_path.size() > 1) && (desc.nClusters > 1)) { + n1 = fastpodptr->nComponents * fastpodptr->Mdesc * fastpodptr->nelements; + n2 = fastpodptr->nComponents * fastpodptr->nClusters * fastpodptr->nelements; + } - if ((testdata.test_analysis) && ((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path)) - error_analysis(testdata, desc.c); + fmt::print(fp, "model_coefficients: {} {} {}\n", nCoeffAll, n1, n2); + for (int count = 0; count < nCoeffAll; count++) { + fmt::print(fp, "{:<10.{}f}\n", desc.c[count], traindata.precision); + } + for (int count = 0; count < n1; count++) { + fmt::print(fp, "{:<10.{}f}\n", fastpodptr->Proj[count], 14); + } + for (int count = 0; count < n2; count++) { + fmt::print(fp, "{:<10.{}f}\n", fastpodptr->Centroids[count], 14); + } + fclose(fp); + } + } - // calculate energy and force for the training data set + // calculate errors for the training data set - if ((traindata.training_calculation) && ((int) traindata.data_path.size() > 1) ) - energyforce_calculation(traindata, desc.c); + if ((traindata.training_analysis) && ((int) traindata.data_path.size() > 1)) + error_analysis(traindata, desc.c); - // calculate energy and force for the test data set + //error->all(FLERR, "stop after error_analysis"); - if ((testdata.test_calculation) && ((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path) ) - energyforce_calculation(testdata, desc.c); + // calculate energy and force for the training data set + + if ((traindata.training_calculation) && ((int) traindata.data_path.size() > 1)) + energyforce_calculation(traindata); + + if (!((testdata.data_path == traindata.data_path) && (testdata.fraction == 1.0) && + (traindata.fraction == 1.0))) { + // calculate errors for the test data set + + if ((testdata.test_analysis) && ((int) testdata.data_path.size() > 1) && + (testdata.fraction > 0)) { + error_analysis(testdata, desc.c); + } + + // calculate energy and force for the test data set + + if ((testdata.test_analysis) && (testdata.test_calculation) && + ((int) testdata.data_path.size() > 1) && (testdata.fraction > 0)) + energyforce_calculation(testdata); + + // deallocate testing data + + if ((int) testdata.data_path.size() > 1 && (testdata.test_analysis) && + (testdata.fraction > 0)) { + memory->destroy(testdata.lattice); + memory->destroy(testdata.energy); + memory->destroy(testdata.stress); + memory->destroy(testdata.position); + memory->destroy(testdata.force); + memory->destroy(testdata.atomtype); + memory->destroy(testdata.we); + memory->destroy(testdata.wf); + } + } + } else if (compute_descriptors > 0) { + // compute and save POD descriptors + descriptors_calculation(traindata); + + if (!((testdata.data_path == traindata.data_path) && (testdata.fraction == 1.0))) { + if ((int) testdata.data_path.size() > 1) { + descriptors_calculation(testdata); + memory->destroy(testdata.lattice); + memory->destroy(testdata.energy); + memory->destroy(testdata.stress); + memory->destroy(testdata.position); + memory->destroy(testdata.force); + memory->destroy(testdata.atomtype); + memory->destroy(testdata.we); + memory->destroy(testdata.wf); + } + } + } // deallocate training data - if ((int) traindata.data_path.size() > 1){ + if ((int) traindata.data_path.size() > 1) { memory->destroy(traindata.lattice); memory->destroy(traindata.energy); memory->destroy(traindata.stress); memory->destroy(traindata.position); memory->destroy(traindata.force); memory->destroy(traindata.atomtype); - } - - // deallocate testing data - - if ((int) testdata.data_path.size() > 1 && (testdata.data_path != traindata.data_path)){ - memory->destroy(testdata.lattice); - memory->destroy(testdata.energy); - memory->destroy(testdata.stress); - memory->destroy(testdata.position); - memory->destroy(testdata.force); - memory->destroy(testdata.atomtype); + memory->destroy(traindata.we); + memory->destroy(traindata.wf); } // deallocate descriptors - memory->destroy(desc.gd); - memory->destroy(desc.gdd); memory->destroy(desc.A); memory->destroy(desc.b); memory->destroy(desc.c); - memory->destroy(desc.tmpint); - - // deallocate neighbor data + memory->destroy(desc.bd); + memory->destroy(desc.pd); + memory->destroy(desc.gd); + memory->destroy(desc.gdd); + // // deallocate neighbor data memory->destroy(nb.alist); memory->destroy(nb.pairnum); memory->destroy(nb.pairnum_cumsum); memory->destroy(nb.pairlist); memory->destroy(nb.y); - delete podptr; + + delete fastpodptr; } -/* ---------------------------------------------------------------------- */ - int FitPOD::read_data_file(double *fitting_weights, std::string &file_format, - std::string &file_extension, std::string &test_path, - std::string &training_path, std::string &filenametag, - const std::string &data_file) + std::string &file_extension, std::string &env_path, + std::string &test_path, std::string &training_path, + std::string &filenametag, const std::string &data_file, + std::string &group_weight_type, + std::unordered_map &we_map, + std::unordered_map &wf_map) { int precision = 8; @@ -143,60 +284,75 @@ int FitPOD::read_data_file(double *fitting_weights, std::string &file_format, FILE *fpdata; if (comm->me == 0) { - fpdata = utils::open_potential(datafilename,lmp,nullptr); + fpdata = utils::open_potential(datafilename, lmp, nullptr); if (fpdata == nullptr) - error->one(FLERR,"Cannot open training data file {}: ", datafilename, utils::getsyserror()); + error->one(FLERR, "Cannot open training data file {}: ", datafilename, utils::getsyserror()); } // loop through lines of training data file and parse keywords - char line[MAXLINE] = {'\0'}; - char *ptr; + char line[MAXLINE], *ptr; int eof = 0; while (true) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fpdata); + ptr = fgets(line, MAXLINE, fpdata); if (ptr == nullptr) { eof = 1; fclose(fpdata); } } - MPI_Bcast(&eof,1,MPI_INT,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); if (eof) break; - MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + MPI_Bcast(line, MAXLINE, MPI_CHAR, 0, world); // words = ptrs to all words in line // strip single and double quotes from words std::vector words; try { - words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + words = Tokenizer(utils::trim_comment(line), "\"' \t\n\r\f").as_vector(); } catch (TokenizerException &) { // ignore } if (words.size() == 0) continue; - const auto &keywd = words[0]; + auto keywd = words[0]; - if (words.size() != 2) - error->one(FLERR,"Improper POD file.", utils::getsyserror()); + if (words.size() != 2) error->one(FLERR, "Improper POD data file.", utils::getsyserror()); // settings for fitting weights - if (keywd == "fitting_weight_energy") fitting_weights[0] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fitting_weight_force") fitting_weights[1] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fitting_weight_stress") fitting_weights[2] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "error_analysis_for_training_data_set") fitting_weights[3] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "error_analysis_for_test_data_set") fitting_weights[4] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "energy_force_calculation_for_training_data_set") fitting_weights[5] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "energy_force_calculation_for_test_data_set") fitting_weights[6] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fraction_training_data_set") fitting_weights[7] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fraction_test_data_set") fitting_weights[8] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "randomize_training_data_set") fitting_weights[9] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "randomize_test_data_set") fitting_weights[10] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fitting_regularization_parameter") fitting_weights[11] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "precision_for_pod_coefficients") precision = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fitting_weight_energy") + fitting_weights[0] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "fitting_weight_force") + fitting_weights[1] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "fitting_weight_stress") + fitting_weights[2] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "error_analysis_for_training_data_set") + fitting_weights[3] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "error_analysis_for_test_data_set") + fitting_weights[4] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "energy_force_calculation_for_training_data_set") + fitting_weights[5] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "energy_force_calculation_for_test_data_set") + fitting_weights[6] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "fraction_training_data_set") + fitting_weights[7] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "fraction_test_data_set") + fitting_weights[8] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "randomize_training_data_set") + fitting_weights[9] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "randomize_test_data_set") + fitting_weights[10] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "fitting_regularization_parameter") + fitting_weights[11] = utils::numeric(FLERR, words[1], false, lmp); + if (keywd == "precision_for_pod_coefficients") + precision = utils::inumeric(FLERR, words[1], false, lmp); + if (keywd == "save_pod_descriptors") + save_descriptors = utils::inumeric(FLERR, words[1], false, lmp); + if (keywd == "compute_pod_descriptors") + compute_descriptors = utils::inumeric(FLERR, words[1], false, lmp); // other settings @@ -204,7 +360,59 @@ int FitPOD::read_data_file(double *fitting_weights, std::string &file_format, if (keywd == "file_extension") file_extension = words[1]; if (keywd == "path_to_training_data_set") training_path = words[1]; if (keywd == "path_to_test_data_set") test_path = words[1]; + if (keywd == "path_to_environment_configuration_set") env_path = words[1]; if (keywd == "basename_for_output_files") filenametag = words[1]; + + // group weight table + if (keywd == "group_weights") group_weight_type = words[1]; + if (std::strcmp(group_weight_type.c_str(), "table") == 0) { + // Read the table as a hash map. + // Get next line. + if (comm->me == 0) { + ptr = fgets(line, MAXLINE, fpdata); + if (ptr == nullptr) { + eof = 1; + fclose(fpdata); + } + } + MPI_Bcast(&eof, 1, MPI_INT, 0, world); + if (eof) break; + MPI_Bcast(line, MAXLINE, MPI_CHAR, 0, world); + // Tokenize. + try { + words = Tokenizer(utils::trim_comment(line), "\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + int numwords = words.size(); + + // Loop over group table entries. + while (numwords == 3) { + + // Insert in map. + we_map[words[0]] = utils::numeric(FLERR, words[1], false, lmp); + wf_map[words[0]] = utils::numeric(FLERR, words[2], false, lmp); + + // Get next line. + if (comm->me == 0) { + ptr = fgets(line, MAXLINE, fpdata); + if (ptr == nullptr) { + eof = 1; + fclose(fpdata); + } + } + MPI_Bcast(&eof, 1, MPI_INT, 0, world); + if (eof) break; + MPI_Bcast(line, MAXLINE, MPI_CHAR, 0, world); + // Tokenize. + try { + words = Tokenizer(utils::trim_comment(line), "\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + numwords = words.size(); + } + } } if (comm->me == 0) { @@ -213,6 +421,8 @@ int FitPOD::read_data_file(double *fitting_weights, std::string &file_format, utils::logmesg(lmp, "file extension: {}\n", file_extension); utils::logmesg(lmp, "path to training data set: {}\n", training_path); utils::logmesg(lmp, "path to test data set: {}\n", test_path); + utils::logmesg(lmp, "path to environment configuration set: {}\n", env_path); + utils::logmesg(lmp, "basename for output files: {}\n", filenametag); utils::logmesg(lmp, "training fraction: {}\n", fitting_weights[7]); utils::logmesg(lmp, "test fraction: {}\n", fitting_weights[8]); utils::logmesg(lmp, "randomize training data set: {}\n", fitting_weights[9]); @@ -224,36 +434,40 @@ int FitPOD::read_data_file(double *fitting_weights, std::string &file_format, utils::logmesg(lmp, "fitting weight for energy: {}\n", fitting_weights[0]); utils::logmesg(lmp, "fitting weight for force: {}\n", fitting_weights[1]); utils::logmesg(lmp, "fitting weight for stress: {}\n", fitting_weights[2]); - utils::logmesg(lmp, "fitting regularization parameter: {}\n", fitting_weights[11]); + utils::logmesg(lmp, "save pod descriptors: {}\n", save_descriptors); + utils::logmesg(lmp, "compute pod descriptors: {}\n", compute_descriptors); utils::logmesg(lmp, "**************** End of Data File ****************\n"); } return precision; } -void FitPOD::get_exyz_files(std::vector& files, const std::string &datapath, - const std::string &extension) +void FitPOD::get_exyz_files(std::vector &files, std::vector &group_names, + const std::string &datapath, const std::string &extension) { auto allfiles = platform::list_directory(datapath); std::sort(allfiles.begin(), allfiles.end()); for (const auto &fname : allfiles) { - if (utils::strmatch(fname, fmt::format(".*\\.{}$", extension))) + if (utils::strmatch(fname, fmt::format(".*\\.{}$", extension))) { files.push_back(datapath + platform::filepathsep + fname); + int start_pos_erase = fname.find(extension) - 1; + std::string substr = fname.substr(0, start_pos_erase); + group_names.push_back(substr); + } } } -int FitPOD::get_number_atom_exyz(std::vector& num_atom, int& num_atom_sum, std::string file) +int FitPOD::get_number_atom_exyz(std::vector &num_atom, int &num_atom_sum, std::string file) { std::string filename = std::move(file); FILE *fp; if (comm->me == 0) { - fp = utils::open_potential(filename,lmp,nullptr); + fp = utils::open_potential(filename, lmp, nullptr); if (fp == nullptr) - error->one(FLERR,"Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); + error->one(FLERR, "Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); } - char line[MAXLINE] = {'\0'}; - char *ptr; + char line[MAXLINE], *ptr; int eof = 0; int num_configs = 0; num_atom_sum = 0; @@ -262,22 +476,22 @@ int FitPOD::get_number_atom_exyz(std::vector& num_atom, int& num_atom_sum, while (true) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); + ptr = fgets(line, MAXLINE, fp); if (ptr == nullptr) { eof = 1; fclose(fp); } } - MPI_Bcast(&eof,1,MPI_INT,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); if (eof) break; - MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + MPI_Bcast(line, MAXLINE, MPI_CHAR, 0, world); // words = ptrs to all words in line // strip single and double quotes from words std::vector words; try { - words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + words = Tokenizer(utils::trim_comment(line), "\"' \t\n\r\f").as_vector(); } catch (TokenizerException &) { // ignore } @@ -286,7 +500,7 @@ int FitPOD::get_number_atom_exyz(std::vector& num_atom, int& num_atom_sum, int natom; if (words.size() == 1) { - natom = utils::inumeric(FLERR,words[0],false,lmp); + natom = utils::inumeric(FLERR, words[0], false, lmp); num_atom.push_back(natom); num_configs += 1; num_atom_sum += natom; @@ -295,38 +509,38 @@ int FitPOD::get_number_atom_exyz(std::vector& num_atom, int& num_atom_sum, return num_configs; } -int FitPOD::get_number_atoms(std::vector& num_atom, std::vector &num_atom_sum, std::vector& num_config, std::vector training_files) +int FitPOD::get_number_atoms(std::vector &num_atom, std::vector &num_atom_sum, + std::vector &num_config, std::vector training_files) { - int nfiles = training_files.size(); // number of files + int nfiles = training_files.size(); // number of files int d, n; - for (int i=0; i species) +void FitPOD::read_exyz_file(double *lattice, double *stress, double *energy, double *we, double *wf, + double *pos, double *forces, int *atomtype, std::string file, + std::vector species, double we_group, double wf_group) { std::string filename = std::move(file); FILE *fp; if (comm->me == 0) { - fp = utils::open_potential(filename,lmp,nullptr); + fp = utils::open_potential(filename, lmp, nullptr); if (fp == nullptr) - error->one(FLERR,"Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); + error->one(FLERR, "Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); } - char line[MAXLINE] = {'\0'}; - char *ptr; + char line[MAXLINE], *ptr; int eof = 0; int cfi = 0; int nat = 0; @@ -336,34 +550,36 @@ void FitPOD::read_exyz_file(double *lattice, double *stress, double *energy, dou while (true) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); + ptr = fgets(line, MAXLINE, fp); if (ptr == nullptr) { eof = 1; fclose(fp); } } - MPI_Bcast(&eof,1,MPI_INT,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); if (eof) break; - MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + MPI_Bcast(line, MAXLINE, MPI_CHAR, 0, world); // words = ptrs to all words in line // strip single and double quotes from words std::vector words; try { - words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + words = Tokenizer(utils::trim_comment(line), "\"' \t\n\r\f").as_vector(); } catch (TokenizerException &) { // ignore } if (words.size() == 0) continue; - ValueTokenizer text(utils::trim_comment(line),"\"' \t\n\r\f"); + ValueTokenizer text(utils::trim_comment(line), "\"' \t\n\r\f"); if (text.contains("attice")) { // find the word containing "lattice" - auto it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("attice") != std::string::npos; }); + auto it = std::find_if(words.begin(), words.end(), [](const std::string &str) { + return str.find("attice") != std::string::npos; + }); // get index of element from iterator @@ -374,65 +590,77 @@ void FitPOD::read_exyz_file(double *lattice, double *stress, double *energy, dou // lattice numbers start at index + 1 for (int k = 0; k < 9; k++) { - lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp); + lattice[k + 9 * cfi] = utils::numeric(FLERR, words[index + 1 + k], false, lmp); } } else { // lattice numbers start at index + 2 for (int k = 0; k < 9; k++) { - lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp); + lattice[k + 9 * cfi] = utils::numeric(FLERR, words[index + 2 + k], false, lmp); } } - // find the word containing "energy" + if (compute_descriptors == 0) { - it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("nergy") != std::string::npos; }); + // find the word containing "energy" - // get index of element from iterator + it = std::find_if(words.begin(), words.end(), [](const std::string &str) { + return str.find("nergy") != std::string::npos; + }); - index = std::distance(words.begin(), it); + // get index of element from iterator - if (words[index].find("=") != std::string::npos) { + index = std::distance(words.begin(), it); - // energy is after "=" inside this string + if (words[index].find("=") != std::string::npos) { - std::size_t found = words[index].find("="); - energy[cfi] = utils::numeric(FLERR,words[index].substr(found+1),false,lmp); - } else { + // energy is after "=" inside this string - // energy is at index + 2 + std::size_t found = words[index].find("="); + energy[cfi] = utils::numeric(FLERR, words[index].substr(found + 1), false, lmp); + } else { - energy[cfi] = utils::numeric(FLERR,words[index+2],false,lmp); + // energy is at index + 2 - } - - // find the word containing "stress" - - it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("tress") != std::string::npos; }); - - // get index of element from iterator - - index = std::distance(words.begin(), it); - - if (words[index].find("=") != std::string::npos) { - - // stress numbers start at index + 1 - - for (int k = 0; k < 9; k++) { - stress[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp); + energy[cfi] = utils::numeric(FLERR, words[index + 2], false, lmp); } - } else { - // lattice numbers start at index + 2 + // find the word containing "stress" - for (int k = 0; k < 9; k++) { - stress[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp); + it = std::find_if(words.begin(), words.end(), [](const std::string &str) { + return str.find("tress") != std::string::npos; + }); + + // get index of element from iterator + + index = std::distance(words.begin(), it); + + if (index < std::distance(words.begin(), words.end())) { + if (words[index].find("=") != std::string::npos) { + + // stress numbers start at index + 1 + + for (int k = 0; k < 9; k++) { + stress[k + 9 * cfi] = utils::numeric(FLERR, words[index + 1 + k], false, lmp); + } + } else { + + // lattice numbers start at index + 2 + + for (int k = 0; k < 9; k++) { + stress[k + 9 * cfi] = utils::numeric(FLERR, words[index + 2 + k], false, lmp); + } + } } } + // set fitting weights for this config + + we[cfi] = we_group; + wf[cfi] = wf_group; + cfi += 1; - } // loop over atoms @@ -440,37 +668,43 @@ void FitPOD::read_exyz_file(double *lattice, double *stress, double *energy, dou else if (words.size() > 1) { for (int ii = 0; ii < ns; ii++) - if (species[ii] == words[0]) - atomtype[nat] = ii+1; + if (species[ii] == words[0]) atomtype[nat] = ii + 1; - for (int k = 0; k < 6; k++) { - if (k <= 2) pos[k + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp); - if (k > 2 ) forces[k-3 + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp); + if (compute_descriptors > 0) { + for (int k = 0; k < 3; k++) + pos[k + 3 * nat] = utils::numeric(FLERR, words[1 + k], false, lmp); + } else { + for (int k = 0; k < 6; k++) { + if (k <= 2) pos[k + 3 * nat] = utils::numeric(FLERR, words[1 + k], false, lmp); + if (k > 2) forces[k - 3 + 3 * nat] = utils::numeric(FLERR, words[1 + k], false, lmp); + } } + nat += 1; } } } -void FitPOD::get_data(datastruct &data, const std::vector& species) +void FitPOD::get_data(datastruct &data, const std::vector &species) { - get_exyz_files(data.data_files, data.data_path, data.file_extension); - data.num_atom_sum = get_number_atoms(data.num_atom, data.num_atom_each_file, data.num_config, data.data_files); + get_exyz_files(data.data_files, data.group_names, data.data_path, data.file_extension); + data.num_atom_sum = + get_number_atoms(data.num_atom, data.num_atom_each_file, data.num_config, data.data_files); data.num_config_sum = data.num_atom.size(); size_t maxname = 9; - for (const auto &fname : data.data_files) maxname = MAX(maxname,fname.size()); - maxname -= data.data_path.size()+1; - const std::string sepline(maxname+46, '-'); + for (const auto &fname : data.data_files) maxname = MAX(maxname, fname.size()); + maxname -= data.data_path.size() + 1; + const std::string sepline(maxname + 46, '-'); if (comm->me == 0) - utils::logmesg(lmp, "{}\n {:^{}} | number of configurations | number of atoms\n{}\n", - sepline, "data file", maxname, sepline); + utils::logmesg(lmp, "{}\n {:^{}} | number of configurations | number of atoms\n{}\n", sepline, + "data file", maxname, sepline); int i = 0; for (const auto &fname : data.data_files) { - std::string filename = fname.substr(data.data_path.size()+1); + std::string filename = fname.substr(data.data_path.size() + 1); data.filenames.push_back(filename); if (comm->me == 0) - utils::logmesg(lmp, " {:<{}} | {:>10} | {:>8}\n", - filename, maxname, data.num_config[i], data.num_atom_each_file[i]); + utils::logmesg(lmp, " {:<{}} | {:>10} | {:>8}\n", filename, maxname, + data.num_config[i], data.num_atom_each_file[i]); ++i; } if (comm->me == 0) { @@ -480,24 +714,44 @@ void FitPOD::get_data(datastruct &data, const std::vector& species) utils::logmesg(lmp, "number of atoms in all files: {}\n", data.num_atom_sum); } - if (data.data_files.size() < 1) error->all(FLERR, "Cannot fit potential without data files"); + if (data.data_files.size() < 1) + error->all(FLERR, + "Cannot fit potential without data files. The data paths may not be valid. Please " + "check the data paths in the POD data file."); int n = data.num_config_sum; - memory->create(data.lattice, 9*n, "fitpod:lattice"); - memory->create(data.stress, 9*n, "fitpod:stress"); + memory->create(data.lattice, 9 * n, "fitpod:lattice"); + memory->create(data.stress, 9 * n, "fitpod:stress"); memory->create(data.energy, n, "fitpod:energy"); + // Group weights have same size as energy. + memory->create(data.we, n, "fitpod:we"); + memory->create(data.wf, n, "fitpod:wf"); + n = data.num_atom_sum; - memory->create(data.position, 3*n, "fitpod:position"); - memory->create(data.force, 3*n, "fitpod:force"); + memory->create(data.position, 3 * n, "fitpod:position"); + memory->create(data.force, 3 * n, "fitpod:force"); memory->create(data.atomtype, n, "fitpod:atomtype"); - int nfiles = data.data_files.size(); // number of files + double we_group, wf_group; // group weights + int nfiles = data.data_files.size(); // number of files int nconfigs = 0; int natoms = 0; - for (int i=0; i& species) int len = data.num_atom.size(); data.num_atom_min = podArrayMin(&data.num_atom[0], len); data.num_atom_max = podArrayMax(&data.num_atom[0], len); - data.num_atom_cumsum.resize(len+1); - podCumsum(&data.num_atom_cumsum[0], &data.num_atom[0], len+1); + data.num_atom_cumsum.resize(len + 1); + podCumsum(&data.num_atom_cumsum[0], &data.num_atom[0], len + 1); - data.num_config_cumsum.resize(nfiles+1); - podCumsum(&data.num_config_cumsum[0], &data.num_config[0], nfiles+1); + data.num_config_cumsum.resize(nfiles + 1); + podCumsum(&data.num_config_cumsum[0], &data.num_config[0], nfiles + 1); // convert all structures to triclinic system constexpr int DIM = 3; - double Qmat[DIM*DIM]; - for (int ci=0; ci FitPOD::linspace(int start_in, int end_in, int num_in) int elm; if (num == 0) { return linspaced; } - if (num == 1) - { + if (num == 1) { elm = (int) std::round(start); linspaced.push_back(elm); return linspaced; @@ -559,8 +812,7 @@ std::vector FitPOD::linspace(int start_in, int end_in, int num_in) double delta = (end - start) / (num - 1); - for(int i=0; i < num-1; ++i) - { + for (int i = 0; i < num - 1; ++i) { elm = (int) std::round(start + delta * i); linspaced.push_back(elm); } @@ -576,15 +828,14 @@ std::vector FitPOD::shuffle(int start_in, int end_in, int num_in) int sz = end_in - start_in + 1; std::vector myvector(sz); - for (int i = 0; i shuffle_vec(num_in); - for (int i = 0; i FitPOD::select(int n, double fraction, int randomize) { std::vector selected; - int m = (int) std::round(n*fraction); + int m = (int) std::round(n * fraction); m = MAX(m, 1); - selected = (randomize==1) ? shuffle(1, n, m) : linspace(1, n, m); + selected = (randomize == 1) ? shuffle(1, n, m) : linspace(1, n, m); return selected; } @@ -607,28 +858,30 @@ void FitPOD::select_data(datastruct &newdata, const datastruct &data) int randomize = data.randomize; if (comm->me == 0) { - if (randomize==1) - utils::logmesg(lmp, "Select {} fraction of the data set at random using shuffle\n", data.fraction); + if (randomize == 1) + utils::logmesg(lmp, "Select {} fraction of the data set at random using shuffle\n", + data.fraction); else - utils::logmesg(lmp, "Select {} fraction of the data set deterministically using linspace\n", data.fraction); + utils::logmesg(lmp, "Select {} fraction of the data set deterministically using linspace\n", + data.fraction); } - int nfiles = data.data_files.size(); // number of files + int nfiles = data.data_files.size(); // number of files std::vector> selected(nfiles); newdata.num_config.resize(nfiles); - newdata.num_config_cumsum.resize(nfiles+1); + newdata.num_config_cumsum.resize(nfiles + 1); newdata.num_atom_each_file.resize(nfiles); for (int file = 0; file < nfiles; file++) { int nconfigs = data.num_config[file]; selected[file] = select(nconfigs, fraction, randomize); - int ns = (int) selected[file].size(); // number of selected configurations + int ns = (int) selected[file].size(); // number of selected configurations newdata.num_config[file] = ns; int num_atom_sum = 0; - for (int ii=0; ii < ns; ii++) { // loop over each selected configuration in a file - int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; + for (int ii = 0; ii < ns; ii++) { // loop over each selected configuration in a file + int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; int natom = data.num_atom[ci]; newdata.num_atom.push_back(natom); num_atom_sum += natom; @@ -638,27 +891,31 @@ void FitPOD::select_data(datastruct &newdata, const datastruct &data) int len = newdata.num_atom.size(); newdata.num_atom_min = podArrayMin(&newdata.num_atom[0], len); newdata.num_atom_max = podArrayMax(&newdata.num_atom[0], len); - newdata.num_atom_cumsum.resize(len+1); - podCumsum(&newdata.num_atom_cumsum[0], &newdata.num_atom[0], len+1); + newdata.num_atom_cumsum.resize(len + 1); + podCumsum(&newdata.num_atom_cumsum[0], &newdata.num_atom[0], len + 1); newdata.num_atom_sum = newdata.num_atom_cumsum[len]; - podCumsum(&newdata.num_config_cumsum[0], &newdata.num_config[0], nfiles+1); + podCumsum(&newdata.num_config_cumsum[0], &newdata.num_config[0], nfiles + 1); newdata.num_config_sum = newdata.num_atom.size(); - int n = data.num_config_sum; - memory->create(newdata.lattice, 9*n, "fitpod:newdata_lattice"); - memory->create(newdata.stress, 9*n, "fitpod:newdata_stress"); + int n = newdata.num_config_sum; + memory->create(newdata.lattice, 9 * n, "fitpod:newdata_lattice"); + memory->create(newdata.stress, 9 * n, "fitpod:newdata_stress"); memory->create(newdata.energy, n, "fitpod:newdata_energy"); - n = data.num_atom_sum; - memory->create(newdata.position, 3*n, "fitpod:newdata_position"); - memory->create(newdata.force, 3*n, "fitpod:newdata_force"); + // Group weights have same size as energy. + memory->create(newdata.we, n, "fitpod:we"); + memory->create(newdata.wf, n, "fitpod:wf"); + + n = newdata.num_atom_sum; + memory->create(newdata.position, 3 * n, "fitpod:newdata_position"); + memory->create(newdata.force, 3 * n, "fitpod:newdata_force"); memory->create(newdata.atomtype, n, "fitpod:newdata_atomtype"); int cn = 0; int dim = 3; for (int file = 0; file < nfiles; file++) { - int ns = (int) selected[file].size(); // number of selected configurations - for (int ii=0; ii < ns; ii++) { // loop over each selected configuration in a file - int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; + int ns = (int) selected[file].size(); // number of selected configurations + for (int ii = 0; ii < ns; ii++) { // loop over each selected configuration in a file + int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; int natom = data.num_atom[ci]; int natom_cumsum = data.num_atom_cumsum[ci]; @@ -666,23 +923,27 @@ void FitPOD::select_data(datastruct &newdata, const datastruct &data) int natomnew_cumsum = newdata.num_atom_cumsum[cn]; if (natom != natomnew) - error->all(FLERR,"number of atoms in the new data set must be the same as that in the old data set."); + error->all( + FLERR, + "number of atoms in the new data set must be the same as that in the old data set."); int *atomtype = &data.atomtype[natom_cumsum]; - double *position = &data.position[dim*natom_cumsum]; - double *force = &data.force[dim*natom_cumsum]; + double *position = &data.position[dim * natom_cumsum]; + double *force = &data.force[dim * natom_cumsum]; newdata.energy[cn] = data.energy[ci]; - for (int j=0; j<9; j++) { - newdata.stress[j+9*cn] = data.stress[j+9*ci]; - newdata.lattice[j+9*cn] = data.lattice[j+9*ci]; + newdata.we[cn] = data.we[ci]; + newdata.wf[cn] = data.wf[ci]; + for (int j = 0; j < 9; j++) { + newdata.stress[j + 9 * cn] = data.stress[j + 9 * ci]; + newdata.lattice[j + 9 * cn] = data.lattice[j + 9 * ci]; } - for (int na=0; name == 0) - utils::logmesg(lmp, "{:-<{}}\n {:^{}} | # configs (selected) | # atoms (selected) " + utils::logmesg(lmp, + "{:-<{}}\n {:^{}} | # configs (selected) | # atoms (selected) " "| # configs (original) | # atoms (original)\n{:-<{}}\n", - "", maxname+90, "data_file", maxname, "", maxname+90); - for (int i=0; i< (int) newdata.data_files.size(); i++) { - std::string filename = newdata.data_files[i].substr(newdata.data_path.size()+1,newdata.data_files[i].size()); + "", maxname + 90, "data_file", maxname, "", maxname + 90); + for (int i = 0; i < (int) newdata.data_files.size(); i++) { + std::string filename = + newdata.data_files[i].substr(newdata.data_path.size() + 1, newdata.data_files[i].size()); newdata.filenames.emplace_back(filename.c_str()); if (comm->me == 0) - utils::logmesg(lmp, " {:<{}} | {:>8} | {:>8} | {:>8} | {:>8}\n", - newdata.filenames[i], maxname, newdata.num_config[i], newdata.num_atom_each_file[i], - data.num_config[i], data.num_atom_each_file[i]); + utils::logmesg( + lmp, " {:<{}} | {:>8} | {:>8} | {:>8} | {:>8}\n", + newdata.filenames[i], maxname, newdata.num_config[i], newdata.num_atom_each_file[i], + data.num_config[i], data.num_atom_each_file[i]); } if (comm->me == 0) { - utils::logmesg(lmp, "{:-<{}}\nnumber of files: {}\n", "", maxname+90, newdata.data_files.size()); - utils::logmesg(lmp, "number of configurations in all files (selected and original): {} and {}\n", newdata.num_config_sum, data.num_config_sum); - utils::logmesg(lmp, "number of atoms in all files (selected and original: {} and {}\n", newdata.num_atom_sum, data.num_atom_sum); + utils::logmesg(lmp, "{:-<{}}\nnumber of files: {}\n", "", maxname + 90, + newdata.data_files.size()); + utils::logmesg(lmp, + "number of configurations in all files (selected and original): {} and {}\n", + newdata.num_config_sum, data.num_config_sum); + utils::logmesg(lmp, "number of atoms in all files (selected and original: {} and {}\n", + newdata.num_atom_sum, data.num_atom_sum); } } -void FitPOD::read_data_files(const std::string& data_file, const std::vector& species) +void FitPOD::read_data_files(const std::string &data_file, const std::vector &species) { datastruct data; // read data input file to datastruct - data.precision = read_data_file(data.fitting_weights, data.file_format, data.file_extension, - testdata.data_path, data.data_path, data.filenametag, data_file); + data.precision = + read_data_file(data.fitting_weights, data.file_format, data.file_extension, envdata.data_path, + testdata.data_path, data.data_path, data.filenametag, data_file, + data.group_weight_type, data.we_map, data.wf_map); data.training_analysis = (int) data.fitting_weights[3]; data.test_analysis = (int) data.fitting_weights[4]; @@ -737,7 +1007,7 @@ void FitPOD::read_data_files(const std::string& data_file, const std::vector 1) get_data(traindata, species); else - error->all(FLERR,"data set is not found"); + error->all(FLERR, "data set is not found"); if (comm->me == 0) utils::logmesg(lmp, "**************** End of Training Data Set ****************\n"); } else { @@ -746,7 +1016,7 @@ void FitPOD::read_data_files(const std::string& data_file, const std::vector 1) get_data(data, species); else - error->all(FLERR,"data set is not found"); + error->all(FLERR, "data set is not found"); if (comm->me == 0) utils::logmesg(lmp, "**************** End of Training Data Set ****************\n"); @@ -764,80 +1034,127 @@ void FitPOD::read_data_files(const std::string& data_file, const std::vectordestroy(data.atomtype); } - if (((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path)) { + testdata.fraction = traindata.fitting_weights[8]; + testdata.test_analysis = traindata.test_analysis; + testdata.filenametag = traindata.filenametag; + + if (((int) envdata.data_path.size() > 1) && (desc.nClusters > 1)) { + envdata.filenametag = traindata.filenametag; + envdata.file_format = traindata.file_format; + envdata.file_extension = traindata.file_extension; + int tmp = compute_descriptors; + compute_descriptors = 1; + if (comm->me == 0) + utils::logmesg(lmp, + "**************** Begin of Environment Configuration Set ****************\n"); + get_data(envdata, species); + if (comm->me == 0) + utils::logmesg(lmp, + "**************** End of Environment Configuration Set ****************\n"); + compute_descriptors = tmp; + } + + if ((testdata.data_path == traindata.data_path) && (testdata.fraction == 1.0) && + (traindata.fraction == 1.0)) { + testdata.data_path = traindata.data_path; + } else if (((int) testdata.data_path.size() > 1) && (testdata.fraction > 0) && + (testdata.test_analysis)) { testdata.training = 0; testdata.file_format = traindata.file_format; testdata.file_extension = traindata.file_extension; testdata.training_analysis = traindata.training_analysis; - testdata.test_analysis = traindata.test_analysis; testdata.training_calculation = traindata.training_calculation; testdata.test_calculation = traindata.test_calculation; - testdata.fraction = traindata.fitting_weights[8]; testdata.randomize = (int) traindata.fitting_weights[10]; - if (comm->me == 0) - utils::logmesg(lmp, "**************** Begin of Test Data Set ****************\n"); - get_data(testdata, species); - if (comm->me == 0) - utils::logmesg(lmp, "**************** End of Test Data Set ****************\n"); - } - else { + + if (testdata.fraction >= 1.0) { + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Test Data Set ****************\n"); + get_data(testdata, species); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Test Data Set ****************\n"); + } else { + datastruct datatm; + testdata.copydatainfo(datatm); + + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Test Data Set ****************\n"); + get_data(datatm, species); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Test Data Set ****************\n"); + + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Select Test Data Set ****************\n"); + select_data(testdata, datatm); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Select Test Data Set ****************\n"); + + memory->destroy(datatm.lattice); + memory->destroy(datatm.energy); + memory->destroy(datatm.stress); + memory->destroy(datatm.position); + memory->destroy(datatm.force); + memory->destroy(datatm.atomtype); + } + } else { testdata.data_path = traindata.data_path; } } -int FitPOD::latticecoords(double *y, int *alist, double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx) +int FitPOD::latticecoords(double *y, int *alist, double *x, double *a1, double *a2, double *a3, + double rcut, int *pbc, int nx) { - int m=0, n=0, p=0; - if (pbc[0] == 1) m = (int) ceil(rcut/a1[0]); - if (pbc[1] == 1) n = (int) ceil(rcut/a2[1]); - if (pbc[2] == 1) p = (int) ceil(rcut/a3[2]); + int m = 0, n = 0, p = 0; + if (pbc[0] == 1) m = (int) ceil(rcut / a1[0]); + if (pbc[1] == 1) n = (int) ceil(rcut / a2[1]); + if (pbc[2] == 1) p = (int) ceil(rcut / a3[2]); // index for the center lattice - int ind = m + (2*m+1)*(n) + (2*m+1)*(2*n+1)*(p); + int ind = m + (2 * m + 1) * (n) + (2 * m + 1) * (2 * n + 1) * (p); // number of lattices - int nl = (2*m+1)*(2*n+1)*(2*p+1); + int nl = (2 * m + 1) * (2 * n + 1) * (2 * p + 1); - for (int j=0; j<3*nx; j++) - y[j] = x[j]; + for (int j = 0; j < 3 * nx; j++) y[j] = x[j]; int q = nx; - for (int i = 0; i < (2*p+1); i++) - for (int j = 0; j < (2*n+1); j++) - for (int k = 0; k < (2*m+1); k++) { - int ii = k + (2*m+1)*j + (2*m+1)*(2*n+1)*i; + for (int i = 0; i < (2 * p + 1); i++) + for (int j = 0; j < (2 * n + 1); j++) + for (int k = 0; k < (2 * m + 1); k++) { + int ii = k + (2 * m + 1) * j + (2 * m + 1) * (2 * n + 1) * i; if (ii != ind) { - double x0 = a1[0]*(k - m) + a2[0]*(j - n) + a3[0]*(i - p); - double x1 = a1[1]*(k - m) + a2[1]*(j - n) + a3[1]*(i - p); - double x2 = a1[2]*(k - m) + a2[2]*(j - n) + a3[2]*(i - p); - for (int jj=0; jj SMALL) && (rijsq <= rcutsq)) { + for (int j = 0; j < N; j++) { + double *rj = &r[dim * j]; + double rijsq = (ri[0] - rj[0]) * (ri[0] - rj[0]) + (ri[1] - rj[1]) * (ri[1] - rj[1]) + + (ri[2] - rj[2]) * ((ri[2] - rj[2])); + if ((rijsq > SMALL) && (rijsq <= rcutsq)) { inc += 1; neighlist[k] = j; k += 1; @@ -848,320 +1165,413 @@ int FitPOD::podneighborlist(int *neighlist, int *numneigh, double *r, double rcu return k; } -int FitPOD::podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, int *numneighsum, - double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx) +int FitPOD::podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, + int *numneighsum, double *x, double *a1, double *a2, double *a3, + double rcut, int *pbc, int nx) { - double rcutsq = rcut*rcut; + double rcutsq = rcut * rcut; int dim = 3, nl = 0, nn = 0; // number of lattices nl = latticecoords(y, alist, x, a1, a2, a3, rcut, pbc, nx); - int N = nx*nl; + int N = nx * nl; // total number of neighbors nn = podneighborlist(neighlist, numneigh, y, rcutsq, nx, N, dim); - podCumsum(numneighsum, numneigh, nx+1); + podCumsum(numneighsum, numneigh, nx + 1); return nn; } -void FitPOD::allocate_memory(const datastruct &data) +void FitPOD::estimate_memory_neighborstruct(const datastruct &data, int *pbc, double rcut, + int nelements) { - int nd = podptr->pod.nd; - memory->create(desc.gd, nd, "fitpod:desc_gd"); - memory->create(desc.A, nd*nd, "fitpod:desc_A"); - memory->create(desc.b, nd, "fitpod:desc_b"); - memory->create(desc.c, nd, "fitpod:desc_c"); - podArraySetValue(desc.A, 0.0, nd*nd); - podArraySetValue(desc.b, 0.0, nd); - podArraySetValue(desc.c, 0.0, nd); - int dim = 3; int natom_max = data.num_atom_max; - int nd1 = podptr->pod.nd1; - int nd2 = podptr->pod.nd2; - int nd3 = podptr->pod.nd3; - int nd4 = podptr->pod.nd4; - int nelements = podptr->pod.nelements; - int nbesselpars = podptr->pod.nbesselpars; - int nrbf2 = podptr->pod.nbf2; - int nabf3 = podptr->pod.nabf3; - int nrbf3 = podptr->pod.nrbf3; - int *pdegree2 = podptr->pod.twobody; - int *pdegree3 = podptr->pod.threebody; - int *pbc = podptr->pod.pbc; - double rcut = podptr->pod.rcut; + int m = 0, n = 0, p = 0, nl = 0, ny = 0, na = 0, np = 0; - int Nj=0, Nij=0; - int m=0, n=0, p=0, nl=0, ny=0, na=0, np=0; - - for (int ci=0; ci<(int) data.num_atom.size(); ci++) - { + for (int ci = 0; ci < (int) data.num_atom.size(); ci++) { int natom = data.num_atom[ci]; - double *lattice = &data.lattice[9*ci]; + double *lattice = &data.lattice[9 * ci]; double *a1 = &lattice[0]; double *a2 = &lattice[3]; double *a3 = &lattice[6]; - if (pbc[0] == 1) m = (int) ceil(rcut/a1[0]); - if (pbc[1] == 1) n = (int) ceil(rcut/a2[1]); - if (pbc[2] == 1) p = (int) ceil(rcut/a3[2]); + if (pbc[0] == 1) m = (int) ceil(rcut / a1[0]); + if (pbc[1] == 1) n = (int) ceil(rcut / a2[1]); + if (pbc[2] == 1) p = (int) ceil(rcut / a3[2]); // number of lattices - nl = (2*m+1)*(2*n+1)*(2*p+1); - ny = MAX(ny,dim*natom*nl); - na = MAX(na, natom*nl); - np = MAX(np, natom*natom*nl); + nl = (2 * m + 1) * (2 * n + 1) * (2 * p + 1); + ny = MAX(ny, dim * natom * nl); + na = MAX(na, natom * nl); + np = MAX(np, natom * natom * nl); } - memory->create(nb.y, ny, "fitpod:nb_y"); - memory->create(nb.alist, na, "fitpod:nb_alist"); - memory->create(nb.pairnum, natom_max, "fitpod:nb_pairnum"); - memory->create(nb.pairnum_cumsum, natom_max+1, "fitpod:nb_pairnum_cumsum"); - memory->create(nb.pairlist, np, "fitpod:nb_pairlist"); + nb.natom_max = MAX(nb.natom_max, natom_max); + nb.sze = nelements * nelements; + nb.sza = MAX(nb.sza, na); + nb.szy = MAX(nb.szy, ny); + nb.szp = MAX(nb.szp, np); +} - nb.natom_max = natom_max; - nb.sze = nelements*nelements; - nb.sza = na; - nb.szy = ny; - nb.szp = np; +void FitPOD::allocate_memory_neighborstruct() +{ + memory->create(nb.y, nb.szy, "fitpod:nb_y"); + memory->create(nb.alist, nb.sza, "fitpod:nb_alist"); + memory->create(nb.pairnum, nb.natom_max, "fitpod:nb_pairnum"); + memory->create(nb.pairnum_cumsum, nb.natom_max + 1, "fitpod:nb_pairnum_cumsum"); + memory->create(nb.pairlist, nb.szp, "fitpod:nb_pairlist"); +} - if (comm->me == 0) - utils::logmesg(lmp,"**************** Begin of Memory Allocation ****************\n"); - - int szd = 0, szi=0, szsnap=0; - for (int ci=0; ci<(int) data.num_atom.size(); ci++) - { - int natom = data.num_atom[ci]; - int natom_cumsum = data.num_atom_cumsum[ci]; - double *x = &data.position[dim*natom_cumsum]; - double *lattice = &data.lattice[9*ci]; - double *a1 = &lattice[0]; - double *a2 = &lattice[3]; - double *a3 = &lattice[6]; - - Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, x, a1, a2, a3, rcut, pbc, natom); - - int ns2 = pdegree2[0]*nbesselpars + pdegree2[1]; - int ns3 = pdegree3[0]*nbesselpars + pdegree3[1]; - - int szd1 = 3*Nij+ (1+dim)*Nij*MAX(nrbf2+ns2,nrbf3+ns3) + (nabf3+1)*7; - int szi1 = 6*Nij + 2*natom+1 + (Nj-1)*Nj; - szd = MAX(szd, szd1); - szi = MAX(szi, szi1); - - if (podptr->sna.twojmax>0) { - szd1 = 0; - szd1 += Nij*dim; // rij - szd1 += MAX(2*podptr->sna.idxu_max*Nij, 2*podptr->sna.idxz_max*podptr->sna.ndoubles*natom); // (Ur, Ui) and (Zr, Zi) - szd1 += 2*podptr->sna.idxu_max*dim*Nij; // dUr, dUi - szd1 += MAX(podptr->sna.idxb_max*podptr->sna.ntriples*dim*Nij, 2*podptr->sna.idxu_max*podptr->sna.nelements*natom); // dblist and (Utotr, Utoti) - szsnap = MAX(szsnap, szd1); - } - } - - szd = MAX(szsnap, szd); - szd = MAX(natom_max*(nd1+nd2+nd3+nd4) + szd, dim*natom_max*(nd-nd1-nd2-nd3-nd4)); - szd = dim*natom_max*(nd1+nd2+nd3+nd4) + szd; - - // gdd includes linear descriptors derivatives, quadratic descriptors derivatives and temporary memory - - memory->create(desc.gdd, szd, "fitpod:desc_gdd"); - memory->create(desc.tmpint, szi, "fitpod:desc_tmpint"); - desc.szd = szd; - desc.szi = szi; +void FitPOD::allocate_memory_descriptorstruct(int nCoeffAll) +{ + memory->create(desc.bd, nb.natom_max * fastpodptr->Mdesc, "fitpod:desc_ld"); + memory->create(desc.pd, nb.natom_max * fastpodptr->nClusters, "fitpod:desc_ld"); + memory->create(desc.gd, nCoeffAll, "fitpod:desc_gd"); + memory->create(desc.A, nCoeffAll * nCoeffAll, "fitpod:desc_A"); + memory->create(desc.b, nCoeffAll, "fitpod:desc_b"); + memory->create(desc.c, nCoeffAll, "fitpod:desc_c"); + memory->create(desc.gdd, desc.szd, "fitpod:desc_gdd"); + podArraySetValue(desc.A, 0.0, nCoeffAll * nCoeffAll); + podArraySetValue(desc.b, 0.0, nCoeffAll); + podArraySetValue(desc.c, 0.0, nCoeffAll); if (comm->me == 0) { - utils::logmesg(lmp, "maximum number of atoms in periodic domain: {}\n", natom_max); + utils::logmesg(lmp, "**************** Begin of Memory Allocation ****************\n"); + utils::logmesg(lmp, "maximum number of atoms in periodic domain: {}\n", nb.natom_max); utils::logmesg(lmp, "maximum number of atoms in extended domain: {}\n", nb.sza); utils::logmesg(lmp, "maximum number of neighbors in extended domain: {}\n", nb.szp); - utils::logmesg(lmp, "size of double memory: {}\n", szd); - utils::logmesg(lmp, "size of int memory: {}\n", szi); - utils::logmesg(lmp, "size of descriptor matrix: {} x {}\n", nd, nd); + utils::logmesg(lmp, "size of double memory: {}\n", desc.szd); + utils::logmesg(lmp, "size of descriptor matrix: {} x {}\n", nCoeffAll, nCoeffAll); utils::logmesg(lmp, "**************** End of Memory Allocation ****************\n"); } } -void FitPOD::linear_descriptors(const datastruct &data, int ci) +void FitPOD::estimate_memory_fastpod(const datastruct &data) { int dim = 3; - int nd1 = podptr->pod.nd1; - int nd2 = podptr->pod.nd2; - int nd3 = podptr->pod.nd3; - int nd4 = podptr->pod.nd4; - int nd1234 = nd1+nd2+nd3+nd4; - int *pbc = podptr->pod.pbc; - double rcut = podptr->pod.rcut; + int *pbc = fastpodptr->pbc; + double rcut = fastpodptr->rcut; + + int Nij = 0, Nijmax = 0; + for (int ci = 0; ci < (int) data.num_atom.size(); ci++) { + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + double *x = &data.position[dim * natom_cumsum]; + double *lattice = &data.lattice[9 * ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + + Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, x, a1, a2, + a3, rcut, pbc, natom); + Nijmax = MAX(Nijmax, Nij); + } + + desc.szd = MAX(desc.szd, 3 * Nijmax * fastpodptr->nCoeffAll); +} + +void FitPOD::local_descriptors_fastpod(const datastruct &data, int ci) +{ + int dim = 3; + int *pbc = fastpodptr->pbc; + double rcut = fastpodptr->rcut; int natom = data.num_atom[ci]; int natom_cumsum = data.num_atom_cumsum[ci]; int *atomtype = &data.atomtype[natom_cumsum]; - double *position = &data.position[dim*natom_cumsum]; - double *lattice = &data.lattice[9*ci]; + double *position = &data.position[dim * natom_cumsum]; + double *lattice = &data.lattice[9 * ci]; double *a1 = &lattice[0]; double *a2 = &lattice[3]; double *a3 = &lattice[6]; // neighbor list - int Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, - position, a1, a2, a3, rcut, pbc, natom); - - int *tmpint = &desc.tmpint[0]; - double *tmpmem = &desc.gdd[dim*natom*nd1234+natom*nd1234]; - podptr->linear_descriptors(desc.gd, desc.gdd, nb.y, tmpmem, atomtype, nb.alist, - nb.pairlist, nb.pairnum, nb.pairnum_cumsum, tmpint, natom, Nij); + podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, position, a1, a2, + a3, rcut, pbc, natom); + if (desc.nClusters > 1) { + fastpodptr->descriptors(desc.gd, desc.gdd, desc.bd, desc.pd, nb.y, atomtype, nb.alist, + nb.pairlist, nb.pairnum_cumsum, natom); + } else { + fastpodptr->descriptors(desc.gd, desc.gdd, desc.bd, nb.y, atomtype, nb.alist, nb.pairlist, + nb.pairnum_cumsum, natom); + } } -void FitPOD::quadratic_descriptors(const datastruct &data, int ci) +void FitPOD::base_descriptors_fastpod(const datastruct &data, int ci) { int dim = 3; + int *pbc = fastpodptr->pbc; + double rcut = fastpodptr->rcut; + int natom = data.num_atom[ci]; - int nd1 = podptr->pod.nd1; - int nd2 = podptr->pod.nd2; - int nd3 = podptr->pod.nd3; - int nd4 = podptr->pod.nd4; - int nd22 = podptr->pod.nd22; - int nd23 = podptr->pod.nd23; - int nd24 = podptr->pod.nd24; - int nd33 = podptr->pod.nd33; - int nd34 = podptr->pod.nd34; - int nd44 = podptr->pod.nd44; - int nd123 = nd1+nd2+nd3; - int nd1234 = nd1+nd2+nd3+nd4; + int natom_cumsum = data.num_atom_cumsum[ci]; + int *atomtype = &data.atomtype[natom_cumsum]; + double *position = &data.position[dim * natom_cumsum]; + double *lattice = &data.lattice[9 * ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; - double *fatom2 = &desc.gdd[dim*natom*(nd1)]; - double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; - double *fatom4 = &desc.gdd[dim*natom*(nd123)]; + // neighbor list + podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, position, a1, a2, + a3, rcut, pbc, natom); - // global descriptors for four-body quadratic22 potential - - if (nd22 > 0) { - int nq2 = podptr->pod.quadratic22[0]*podptr->pod.nc2; - podptr->quadratic_descriptors(&desc.gd[nd1234], &desc.gdd[dim*natom*nd1234], - &desc.gd[nd1], fatom2, nq2, dim*natom); - } - - // global descriptors for four-body quadratic23 potential - - if (nd23 > 0) { - int nq2 = podptr->pod.quadratic23[0]*podptr->pod.nc2; - int nq3 = podptr->pod.quadratic23[1]*podptr->pod.nc3; - podptr->quadratic_descriptors(&desc.gd[nd1234+nd22], &desc.gdd[dim*natom*(nd1234+nd22)], - &desc.gd[nd1], &desc.gd[nd1+nd2], fatom2, fatom3, nq2, nq3, dim*natom); - } - - // global descriptors for five-body quadratic24 potential - - if (nd24 > 0) { - int nq2 = podptr->pod.quadratic24[0]*podptr->pod.nc2; - int nq4 = podptr->pod.quadratic24[1]*podptr->pod.nc4; - podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23], &desc.gdd[dim*natom*(nd1234+nd22+nd23)], - &desc.gd[nd1], &desc.gd[nd1+nd2+nd3], fatom2, fatom4, nq2, nq4, dim*natom); - } - - // global descriptors for five-body quadratic33 potential - - if (nd33 > 0) { - int nq3 = podptr->pod.quadratic33[0]*podptr->pod.nc3; - podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24)], - &desc.gd[nd1+nd2], fatom3, nq3, dim*natom); - } - - // global descriptors for six-body quadratic34 potential - - if (nd34 > 0) { - int nq3 = podptr->pod.quadratic34[0]*podptr->pod.nc3; - int nq4 = podptr->pod.quadratic34[1]*podptr->pod.nc4; - podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24+nd33], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24+nd33)], - &desc.gd[nd1+nd2], &desc.gd[nd1+nd2+nd3], fatom3, fatom4, nq3, nq4, dim*natom); - } - - // global descriptors for seven-body quadratic44 potential - - if (nd44 > 0) { - int nq4 = podptr->pod.quadratic44[0]*podptr->pod.nc4; - podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24+nd33+nd34], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24+nd33+nd34)], - &desc.gd[nd1+nd2+nd3], fatom4, nq4, dim*natom); - } - - // normalize quadratic descriptors - - for (int i=0; i<(nd22+nd23+nd24+nd33+nd34+nd44); i++) - desc.gd[nd1234+i] = desc.gd[nd1234+i]/(natom); - - for (int i=0; ibase_descriptors(desc.bd, nb.y, atomtype, nb.alist, nb.pairlist, nb.pairnum_cumsum, + natom); } -void FitPOD::cubic_descriptors(const datastruct &data, int ci) +void FitPOD::descriptors_calculation(const datastruct &data) { - int dim = 3; - int natom = data.num_atom[ci]; - int nd1 = podptr->pod.nd1; - int nd2 = podptr->pod.nd2; - int nd3 = podptr->pod.nd3; - int nd4 = podptr->pod.nd4; - int nd22 = podptr->pod.nd22; - int nd23 = podptr->pod.nd23; - int nd24 = podptr->pod.nd24; - int nd33 = podptr->pod.nd33; - int nd34 = podptr->pod.nd34; - int nd44 = podptr->pod.nd44; - int nd234 = podptr->pod.nd234; - int nd333 = podptr->pod.nd333; - int nd444 = podptr->pod.nd444; - int nd123 = nd1+nd2+nd3; - int nd1234 = nd1+nd2+nd3+nd4; + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin Calculating Descriptors ****************\n"); - // global descriptors for seven-body cubic234 potential - if (nd234 > 0) { - int nq2 = podptr->pod.cubic234[0]*podptr->pod.nc2; - int nq3 = podptr->pod.cubic234[1]*podptr->pod.nc3; - int nq4 = podptr->pod.cubic234[2]*podptr->pod.nc4; - int np3 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44; - double *eatom2 = &desc.gd[nd1]; - double *eatom3 = &desc.gd[nd1+nd2]; - double *eatom4 = &desc.gd[nd123]; - double *fatom2 = &desc.gdd[dim*natom*(nd1)]; - double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; - double *fatom4 = &desc.gdd[dim*natom*(nd123)]; - podptr->cubic_descriptors(&desc.gd[np3], &desc.gdd[dim*natom*np3], - eatom2, eatom3, eatom4, fatom2, fatom3, fatom4, nq2, nq3, nq4, dim*natom); + // loop over each configuration in the training data set + + double sz[2]; + for (int ci = 0; ci < (int) data.num_atom.size(); ci++) { + + if ((ci % 100) == 0) { + if (comm->me == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci + 1); + } + + if ((ci % comm->nprocs) == comm->me) { + + // compute local POD descriptors + local_descriptors_fastpod(data, ci); + + std::string filename0 = + data.data_path + "/basedescriptors_config" + std::to_string(ci + 1) + ".bin"; + FILE *fp0 = fopen(filename0.c_str(), "wb"); + sz[0] = (double) data.num_atom[ci]; + sz[1] = (double) fastpodptr->Mdesc; + fwrite(reinterpret_cast(sz), sizeof(double) * (2), 1, fp0); + fwrite(reinterpret_cast(desc.bd), + sizeof(double) * (data.num_atom[ci] * fastpodptr->Mdesc), 1, fp0); + fclose(fp0); + + if (desc.nClusters > 1) { + std::string filename1 = + data.data_path + "/environmentdescriptors_config" + std::to_string(ci + 1) + ".bin"; + FILE *fp1 = fopen(filename1.c_str(), "wb"); + sz[0] = (double) data.num_atom[ci]; + sz[1] = (double) fastpodptr->nClusters; + fwrite(reinterpret_cast(sz), sizeof(double) * (2), 1, fp1); + fwrite(reinterpret_cast(desc.pd), + sizeof(double) * (data.num_atom[ci] * fastpodptr->nClusters), 1, fp1); + fclose(fp1); + } + + std::string filename = + data.data_path + "/globaldescriptors_config" + std::to_string(ci + 1) + ".bin"; + FILE *fp = fopen(filename.c_str(), "wb"); + + sz[0] = (double) data.num_atom[ci]; + sz[1] = (double) desc.nCoeffAll; + fwrite(reinterpret_cast(sz), sizeof(double) * (2), 1, fp); + fwrite(reinterpret_cast(desc.gd), sizeof(double) * (desc.nCoeffAll), 1, fp); + if (compute_descriptors == 2) { + fwrite(reinterpret_cast(desc.gdd), + sizeof(double) * (3 * data.num_atom[ci] * desc.nCoeffAll), 1, fp); + } + fclose(fp); + } } - // global descriptors for seven-body cubic333 potential + if (comm->me == 0) + utils::logmesg(lmp, "**************** End Calculating Descriptors ****************\n"); +} - if (nd333 > 0) { - int nq3 = podptr->pod.cubic333[0]*podptr->pod.nc3; - int np3 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234; - double *eatom3 = &desc.gd[nd1+nd2]; - double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; - podptr->cubic_descriptors(&desc.gd[np3], &desc.gdd[dim*natom*np3], - eatom3, fatom3, nq3, dim*natom); +void FitPOD::environment_cluster_calculation(const datastruct &data) +{ + if (comm->me == 0) + utils::logmesg( + lmp, "**************** Begin Calculating Environment Descriptor Matrix ****************\n"); + + int nComponents = fastpodptr->nComponents; + int Mdesc = fastpodptr->Mdesc; + int nClusters = fastpodptr->nClusters; + int nelements = fastpodptr->nelements; + memory->create(fastpodptr->Centroids, nClusters * nComponents * nelements, "fitpod:centroids"); + memory->create(fastpodptr->Proj, Mdesc * nComponents * nelements, "fitpod:P"); + + int nAtoms = 0; + int nTotalAtoms = 0; + for (int ci = 0; ci < (int) data.num_atom.size(); ci++) { + if ((ci % comm->nprocs) == comm->me) nAtoms += data.num_atom[ci]; + nTotalAtoms += data.num_atom[ci]; } - // global descriptors for ten-body cubic444 potential + double *basedescmatrix; + double *pca; + double *A; + double *work; + double *b; + double *Lambda; + int *clusterSizes; + int *assignments; + int *nElemAtoms; + int *nElemAtomsCumSum; + int *nElemAtomsCount; - if (nd444 > 0) { - int nq4 = podptr->pod.cubic444[0]*podptr->pod.nc4; - int np4 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333; - double *eatom4 = &desc.gd[nd123]; - double *fatom4 = &desc.gdd[dim*natom*(nd123)]; - podptr->cubic_descriptors(&desc.gd[np4], &desc.gdd[dim*natom*(np4)], - eatom4, fatom4, nq4, dim*natom); + memory->create(basedescmatrix, nAtoms * Mdesc, "fitpod:basedescmatrix"); + memory->create(pca, nAtoms * nComponents, "fitpod:pca"); + memory->create(A, Mdesc * Mdesc, "fitpod:A"); + memory->create(work, Mdesc * Mdesc, "fitpod:work"); + memory->create(b, Mdesc, "fitpod:b"); + memory->create(Lambda, Mdesc * nelements, "fitpod:Lambda"); + memory->create(clusterSizes, nClusters * nelements, "fitpod:clusterSizes"); + memory->create(assignments, nAtoms, "fitpod:assignments"); + memory->create(nElemAtoms, nelements, "fitpod:nElemAtoms"); + memory->create(nElemAtomsCumSum, 1 + nelements, "fitpod:nElemAtomsCumSum"); + memory->create(nElemAtomsCount, nelements, "fitpod:nElemAtomsCount"); + + char chn = 'N'; + char cht = 'T'; + char chv = 'V'; + char chu = 'U'; + double alpha = 1.0, beta = 0.0; + + for (int elem = 0; elem < nelements; elem++) { + nElemAtoms[elem] = 0; // number of atoms for this element + } + for (int ci = 0; ci < (int) data.num_atom.size(); ci++) { + if ((ci % comm->nprocs) == comm->me) { + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + int *atomtype = &data.atomtype[natom_cumsum]; + for (int n = 0; n < natom; n++) nElemAtoms[atomtype[n] - 1] += 1; + } } - // normalize cubic descriptors - int nd = podptr->pod.nd; - for (int i=(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); ime == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci + 1); + } + + if ((ci % comm->nprocs) == comm->me) { + base_descriptors_fastpod(data, ci); + + // basedescmatrix is a Mdesc x nAtoms matrix + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + int *atomtype = &data.atomtype[natom_cumsum]; + for (int n = 0; n < natom; n++) { + int elem = atomtype[n] - 1; // offset by 1 to match the element index in the C++ code + nElemAtomsCount[elem] += 1; + int k = nElemAtomsCumSum[elem] + nElemAtomsCount[elem] - 1; + for (int m = 0; m < Mdesc; m++) basedescmatrix[m + Mdesc * k] = desc.bd[n + natom * (m)]; + } + } + } + + int save = 0; + for (int elem = 0; elem < nelements; elem++) { // loop over each element + nAtoms = nElemAtoms[elem]; + nTotalAtoms = nAtoms; + MPI_Allreduce(MPI_IN_PLACE, &nTotalAtoms, 1, MPI_INT, MPI_SUM, world); + + double *descmatrix = &basedescmatrix[Mdesc * nElemAtomsCumSum[elem]]; + double *Proj = &fastpodptr->Proj[nComponents * Mdesc * elem]; + double *centroids = &fastpodptr->Centroids[nComponents * nClusters * elem]; + + // Calculate covariance matrix A = basedescmatrix*basedescmatrix'. A is a Mdesc x Mdesc matrix + DGEMM(&chn, &cht, &Mdesc, &Mdesc, &nAtoms, &alpha, descmatrix, &Mdesc, descmatrix, &Mdesc, + &beta, A, &Mdesc); + MPI_Allreduce(MPI_IN_PLACE, A, Mdesc * Mdesc, MPI_DOUBLE, MPI_SUM, world); + + //if (comm->me == 0) print_matrix("A", Mdesc, Mdesc, A, Mdesc); + + if ((comm->me == 0) && (save == 1)) + savematrix2binfile(data.filenametag + "_covariance_matrix_elem" + std::to_string(elem + 1) + + ".bin", + A, Mdesc, Mdesc); + + // Calculate eigenvalues and eigenvectors of A + int lwork = Mdesc * Mdesc; // the length of the array work, lwork >= max(1,3*N-1) + int info = 1; // = 0: successful exit + + DSYEV(&chv, &chu, &Mdesc, A, &Mdesc, b, work, &lwork, &info); + + // order eigenvalues and eigenvectors from largest to smallest + for (int i = 0; i < Mdesc; i++) Lambda[(Mdesc - i - 1)] = b[i]; + + // P is a nComponents x Mdesc matrix + for (int j = 0; j < nComponents; j++) + for (int i = 0; i < Mdesc; i++) + Proj[j + nComponents * i] = + A[i + Mdesc * (Mdesc - j - 1)] * sqrt(fabs(b[(Mdesc - j - 1)] / Lambda[0])); + + // Calculate principal compoment analysis matrix pca = P*descmatrix. pca is a nComponents x nAtoms matrix + DGEMM(&chn, &chn, &nComponents, &nAtoms, &Mdesc, &alpha, Proj, &nComponents, descmatrix, &Mdesc, + &beta, pca, &nComponents); + + // initialize centroids + for (int i = 0; i < nClusters * nComponents; i++) centroids[i] = 0.0; + for (int i = 0; i < nAtoms; i++) { + int m = (i * nClusters) / nAtoms; + for (int j = 0; j < nComponents; j++) + centroids[j + nComponents * m] += pca[j + nComponents * i]; + } + + MPI_Allreduce(MPI_IN_PLACE, centroids, nClusters * nComponents, MPI_DOUBLE, MPI_SUM, world); + double fac = ((double) nClusters) / ((double) nTotalAtoms); + for (int i = 0; i < nClusters * nComponents; i++) centroids[i] = centroids[i] * fac; + + // Calculate centroids using k-means clustering + int max_iter = 100; + KmeansClustering(pca, centroids, assignments, clusterSizes, nAtoms, nClusters, nComponents, + max_iter); + + if (save == 1) { + if (comm->me == 0) { + savematrix2binfile(data.filenametag + "_eigenvector_matrix_elem" + + std::to_string(elem + 1) + ".bin", + A, Mdesc, Mdesc); + savematrix2binfile(data.filenametag + "_eigenvalues_elem" + std::to_string(elem + 1) + + ".bin", + b, Mdesc, 1); + } + savematrix2binfile(data.filenametag + "_desc_matrix_elem" + std::to_string(elem + 1) + + "_proc" + std::to_string(comm->me + 1) + ".bin", + descmatrix, Mdesc, nAtoms); + savematrix2binfile(data.filenametag + "_pca_matrix_elem" + std::to_string(elem + 1) + + "_proc" + std::to_string(comm->me + 1) + ".bin", + pca, nComponents, nAtoms); + saveintmatrix2binfile(data.filenametag + "_cluster_assignments_elem" + + std::to_string(elem + 1) + "_proc" + std::to_string(comm->me + 1) + + ".bin", + assignments, nAtoms, 1); + } + } + + memory->destroy(basedescmatrix); + memory->destroy(pca); + memory->destroy(A); + memory->destroy(work); + memory->destroy(b); + memory->destroy(clusterSizes); + memory->destroy(Lambda); + memory->destroy(assignments); + memory->destroy(nElemAtoms); + memory->destroy(nElemAtomsCumSum); + memory->destroy(nElemAtomsCount); + + if (comm->me == 0) + utils::logmesg( + lmp, "**************** End Calculating Environment Descriptor Matrix ****************\n"); } void FitPOD::least_squares_matrix(const datastruct &data, int ci) @@ -1169,26 +1579,26 @@ void FitPOD::least_squares_matrix(const datastruct &data, int ci) int dim = 3; int natom = data.num_atom[ci]; int natom_cumsum = data.num_atom_cumsum[ci]; - int nd = podptr->pod.nd; - int nforce = dim*natom; + int nCoeffAll = desc.nCoeffAll; + int nforce = dim * natom; // compute energy weight and force weight double normconst = 1.0; - if (data.normalizeenergy==1) normconst = 1.0/natom; - double we = data.fitting_weights[0]; - double wf = data.fitting_weights[1]; - double we2 = (we*we)*(normconst*normconst); - double wf2 = (wf*wf); + if (data.normalizeenergy == 1) normconst = 1.0 / natom; + double we = data.we[ci]; + double wf = data.wf[ci]; + double we2 = (we * we) * (normconst * normconst); + double wf2 = (wf * wf); // get energy and force from the training data set double energy = data.energy[ci]; - double *force = &data.force[dim*natom_cumsum]; + double *force = &data.force[dim * natom_cumsum]; // least-square matrix for all descriptors: A = A + (we*we)*(gd^T * gd) - podKron(desc.A, desc.gd, desc.gd, we2, nd, nd); + podKron(desc.A, desc.gd, desc.gd, we2, nCoeffAll, nCoeffAll); // least-square matrix for all descriptors derivatives: A = A + (wf*wf) * (gdd^T * gdd) @@ -1196,18 +1606,17 @@ void FitPOD::least_squares_matrix(const datastruct &data, int ci) char chn = 'N'; double one = 1.0; int inc1 = 1; - DGEMM(&cht, &chn, &nd, &nd, &nforce, &wf2, desc.gdd, &nforce, desc.gdd, &nforce, &one, desc.A, &nd); + DGEMM(&cht, &chn, &nCoeffAll, &nCoeffAll, &nforce, &wf2, desc.gdd, &nforce, desc.gdd, &nforce, + &one, desc.A, &nCoeffAll); // least-square vector for all descriptors: b = b + (we*we*energy)*gd - double wee = we2*energy; - for (int i = 0; i< nd; i++) - desc.b[i] += wee*desc.gd[i]; + double wee = we2 * energy; + for (int i = 0; i < nCoeffAll; i++) desc.b[i] += wee * desc.gd[i]; // least-square vector for all descriptors derivatives: b = b + (wf*wf) * (gdd^T * f) - DGEMV(&cht, &nforce, &nd, &wf2, desc.gdd, &nforce, force, &inc1, &one, desc.b, &inc1); - + DGEMV(&cht, &nforce, &nCoeffAll, &wf2, desc.gdd, &nforce, force, &inc1, &one, desc.b, &inc1); } void FitPOD::least_squares_fit(const datastruct &data) @@ -1217,26 +1626,28 @@ void FitPOD::least_squares_fit(const datastruct &data) // loop over each configuration in the training data set - for (int ci=0; ci < (int) data.num_atom.size(); ci++) { + for (int ci = 0; ci < (int) data.num_atom.size(); ci++) { - if ((ci % 100)==0) { - if (comm->me == 0) - utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + if ((ci % 100) == 0) { + if (comm->me == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci + 1); } if ((ci % comm->nprocs) == comm->me) { // compute linear POD descriptors + local_descriptors_fastpod(data, ci); - linear_descriptors(data, ci); - - // compute quadratic POD descriptors - - quadratic_descriptors(data, ci); - - // compute cubic POD descriptors - - cubic_descriptors(data, ci); + if (save_descriptors > 0) { + std::string filename = + data.data_path + "/descriptors_config" + std::to_string(ci + 1) + ".bin"; + FILE *fp = fopen(filename.c_str(), "wb"); + fwrite(reinterpret_cast(desc.gd), sizeof(double) * (desc.nCoeffAll), 1, fp); + if (save_descriptors == 2) { + fwrite(reinterpret_cast(desc.gdd), + sizeof(double) * (3 * data.num_atom[ci] * desc.nCoeffAll), 1, fp); + } + fclose(fp); + } // assemble the least-squares linear system @@ -1244,172 +1655,159 @@ void FitPOD::least_squares_fit(const datastruct &data) } } - int nd = podptr->pod.nd; + int nCoeffAll = desc.nCoeffAll; - MPI_Allreduce(MPI_IN_PLACE, desc.b, nd, MPI_DOUBLE, MPI_SUM, world); - MPI_Allreduce(MPI_IN_PLACE, desc.A, nd*nd, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, desc.b, nCoeffAll, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, desc.A, nCoeffAll * nCoeffAll, MPI_DOUBLE, MPI_SUM, world); if (comm->me == 0) { // symmetrize A - for (int i = 0; i fabs(desc.b[i])) ? maxb : fabs(desc.b[i]); - - maxb = 1.0/maxb; - for (int i = 0; ime == 0) { // save coefficients into a text file - std::string filename = data.filenametag + "_coefficients" + ".pod"; - FILE *fp = fopen(filename.c_str(), "w"); - - fmt::print(fp, "POD_coefficients: {}\n", nd); - for (int count = 0; count < nd; count++) { - fmt::print(fp, "{:<10.{}f}\n", desc.c[count], data.precision); - } - fclose(fp); - utils::logmesg(lmp, "**************** End of Least-Squares Fitting ****************\n"); - } + // update coefficients in POD class to compute energy and force + fastpodptr->mknewcoeff(desc.c, nCoeffAll); } -double FitPOD::energyforce_calculation(double *force, double *coeff, const datastruct &data, int ci) +double latticevolume(double *lattice) +{ + double *v1 = &lattice[0]; + double *v2 = &lattice[3]; + double *v3 = &lattice[6]; + + double b0 = v1[1] * v2[2] - v1[2] * v2[1]; + double b1 = v1[2] * v2[0] - v1[0] * v2[2]; + double b2 = v1[0] * v2[1] - v1[1] * v2[0]; + + return (b0 * v3[0] + b1 * v3[1] + b2 * v3[2]); +} + +double FitPOD::energyforce_calculation_fastpod(double *force, const datastruct &data, int ci) { int dim = 3; - int *pbc = podptr->pod.pbc; - double rcut = podptr->pod.rcut; - int nd1234 = podptr->pod.nd1 + podptr->pod.nd2 + podptr->pod.nd3 + podptr->pod.nd4; + int *pbc = fastpodptr->pbc; + double rcut = fastpodptr->rcut; int natom = data.num_atom[ci]; int natom_cumsum2 = data.num_atom_cumsum[ci]; int *atomtype = &data.atomtype[natom_cumsum2]; - double *position = &data.position[dim*natom_cumsum2]; - double *lattice = &data.lattice[9*ci]; + double *position = &data.position[dim * natom_cumsum2]; + double *lattice = &data.lattice[9 * ci]; double *a1 = &lattice[0]; double *a2 = &lattice[3]; double *a3 = &lattice[6]; - // neighbor list + podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, position, a1, a2, + a3, rcut, pbc, natom); - int Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, - position, a1, a2, a3, rcut, pbc, natom); - - double *tmpmem = &desc.gdd[0]; - int *tmpint = &desc.tmpint[0]; - double *rij = &tmpmem[0]; // 3*Nij - int *ai = &tmpint[0]; // Nij - int *aj = &tmpint[Nij]; // Nij - int *ti = &tmpint[2*Nij]; // Nij - int *tj = &tmpint[3*Nij]; // Nij - int *idxi = &tmpint[4*Nij]; // Nij - podptr->podNeighPairs(rij, nb.y, idxi, ai, aj, ti, tj, nb.pairnum_cumsum, atomtype, nb.pairlist, nb.alist, natom); - - double *effectivecoeff = &tmpmem[3*Nij]; // 3*Nij - podArraySetValue(effectivecoeff, 0.0, nd1234); - - double energy = podptr->energyforce_calculation(force, coeff, effectivecoeff, desc.gd, rij, - &tmpmem[3*Nij+nd1234], nb.pairnum_cumsum, atomtype, idxi, ai, aj, ti, tj, natom, Nij); + double energy = fastpodptr->energyforce(force, nb.y, atomtype, nb.alist, nb.pairlist, + nb.pairnum_cumsum, natom); return energy; } void FitPOD::print_analysis(const datastruct &data, double *outarray, double *errors) { - int nfiles = data.data_files.size(); // number of files + int nfiles = data.data_files.size(); // number of files int lm = 10; - for (int i = 0; i < nfiles; i++) - lm = MAX(lm, (int) data.filenames[i].size()); + for (int i = 0; i < nfiles; i++) lm = MAX(lm, (int) data.filenames[i].size()); lm = lm + 2; - std::string filename_errors = fmt::format("{}_{}_errors.pod", data.filenametag, data.training ? "training" : "test"); - std::string filename_analysis = fmt::format("{}_{}_analysis.pod", data.filenametag, data.training ? "training" : "test"); + std::string filename_errors = + fmt::format("{}_{}_errors.pod", data.filenametag, data.training ? "training" : "test"); + std::string filename_analysis = + fmt::format("{}_{}_analysis.pod", data.filenametag, data.training ? "training" : "test"); FILE *fp_errors = nullptr; FILE *fp_analysis = nullptr; fp_errors = fopen(filename_errors.c_str(), "w"); fp_analysis = fopen(filename_analysis.c_str(), "w"); - std::string mystr = fmt::format("**************** Begin of Error Analysis for the {} Data Set ****************\n", - data.training ? "Training" : "Test"); + std::string mystr = + fmt::format("**************** Begin of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); utils::logmesg(lmp, mystr); fmt::print(fp_errors, mystr); - std::string sa(lm+80,'-'); + std::string sa(lm + 80, '-'); sa += '\n'; - std::string sb = fmt::format(" {:^{}} | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force\n", - "File", lm); + std::string sb = fmt::format( + " {:^{}} | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force\n", + "File", lm); utils::logmesg(lmp, sa + sb + sa); fmt::print(fp_errors, sa + sb + sa); - int ci=0, m=8, nc=0, nf=0; + int ci = 0, m = 8, nc = 0, nf = 0; for (int file = 0; file < nfiles; file++) { fmt::print(fp_analysis, "# {}\n", data.filenames[file]); - fmt::print(fp_analysis, " config # atoms energy DFT energy energy error " + fmt::print(fp_analysis, + " config # atoms volume energy DFT energy energy error " " force DFT force force error\n"); int nforceall = 0; int nconfigs = data.num_config[file]; nc += nconfigs; - for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file - fmt::print(fp_analysis, "{:6} {:8} ", outarray[m*ci], outarray[1 + m*ci]); - for(int count = 2; count < m; count ++) - fmt::print(fp_analysis, "{:<15.10} ", outarray[count + m*ci]); + for (int ii = 0; ii < nconfigs; ii++) { // loop over each configuration in a file + fmt::print(fp_analysis, "{:6} {:8} ", outarray[m * ci], outarray[1 + m * ci]); + + double vol = latticevolume(&data.lattice[9 * ci]); + fmt::print(fp_analysis, "{:<15.10} ", vol); + + for (int count = 2; count < m; count++) + fmt::print(fp_analysis, "{:<15.10} ", outarray[count + m * ci]); fmt::print(fp_analysis, "\n"); - nforceall += 3*data.num_atom[ci]; + nforceall += 3 * data.num_atom[ci]; ci += 1; } nf += nforceall; - int q = file+1; - auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", - data.filenames[file], lm, nconfigs, nforceall/3, - errors[0 + 4*q], errors[1 + 4*q], errors[2 + 4*q], errors[3 + 4*q]); + int q = file + 1; + auto s = + fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + data.filenames[file], lm, nconfigs, nforceall / 3, errors[0 + 4 * q], + errors[1 + 4 * q], errors[2 + 4 * q], errors[3 + 4 * q]); utils::logmesg(lmp, s); fmt::print(fp_errors, s); } utils::logmesg(lmp, sa); fmt::print(fp_errors, sa); - auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", - "All files", lm, nc, nf/3, errors[0], errors[1], errors[2], errors[3]); + auto s = + fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + "All files", lm, nc, nf / 3, errors[0], errors[1], errors[2], errors[3]); utils::logmesg(lmp, s + sa); fmt::print(fp_errors, "{}", s + sa); - mystr = fmt::format("**************** End of Error Analysis for the {} Data Set ****************\n", - data.training ? "Training" : "Test"); + mystr = + fmt::format("**************** End of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); utils::logmesg(lmp, mystr); fmt::print(fp_errors, mystr); @@ -1421,87 +1819,64 @@ void FitPOD::print_analysis(const datastruct &data, double *outarray, double *er void FitPOD::error_analysis(const datastruct &data, double *coeff) { int dim = 3; + int nCoeffAll = desc.nCoeffAll; double energy; - std::vector force(dim*data.num_atom_max); + std::vector force(dim * data.num_atom_max); - int nfiles = data.data_files.size(); // number of files - int num_configs = data.num_atom.size(); // number of configurations in all files + int nfiles = data.data_files.size(); // number of files + int num_configs = data.num_atom.size(); // number of configurations in all files int m = 8; - std::vector outarray(m*num_configs); - for (int i=0; i outarray(m * num_configs); + for (int i = 0; i < m * num_configs; i++) outarray[i] = 0.0; std::vector ssrarray(num_configs); - for (int i=0; i errors(4*(nfiles+1)); - for (int i=0; i<4*(nfiles+1); i++) - errors[i] = 0.0; + std::vector errors(4 * (nfiles + 1)); + for (int i = 0; i < 4 * (nfiles + 1); i++) errors[i] = 0.0; - int nd1 = podptr->pod.nd1; - int nd2 = podptr->pod.nd2; - int nd3 = podptr->pod.nd3; - int nd4 = podptr->pod.nd4; - int nd22 = podptr->pod.nd22; - int nd23 = podptr->pod.nd23; - int nd24 = podptr->pod.nd24; - int nd33 = podptr->pod.nd33; - int nd34 = podptr->pod.nd34; - int nd44 = podptr->pod.nd44; - int nd1234 = nd1+nd2+nd3+nd4; - int nd = podptr->pod.nd; - - std::vector newcoeff(nd); - for (int j=0; j newcoeff(nCoeffAll); + for (int j = 0; j < nCoeffAll; j++) newcoeff[j] = coeff[j]; if (comm->me == 0) utils::logmesg(lmp, "**************** Begin of Error Calculation ****************\n"); - int ci = 0; // configuration counter - for (int file = 0; file < nfiles; file++) { // loop over each file in the training data set + int ci = 0; // configuration counter + for (int file = 0; file < nfiles; file++) { // loop over each file in the training data set int nconfigs = data.num_config[file]; - for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file + for (int ii = 0; ii < nconfigs; ii++) { // loop over each configuration in a file - if ((ci % 100)==0) { - if (comm->me == 0) - utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + if ((ci % 100) == 0) { + if (comm->me == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci + 1); } if ((ci % comm->nprocs) == comm->me) { int natom = data.num_atom[ci]; - int nforce = dim*natom; + int nforce = dim * natom; - for (int j=nd1234; j<(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); j++) - newcoeff[j] = coeff[j]/(natom); - - for (int j=(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); jme == 0) { utils::logmesg(lmp, "**************** End of Error Calculation ****************\n"); @@ -1562,40 +1938,39 @@ void FitPOD::error_analysis(const datastruct &data, double *coeff) } } -void FitPOD::energyforce_calculation(const datastruct &data, double *coeff) +void FitPOD::energyforce_calculation(const datastruct &data) { int dim = 3; double energy; - std::vector force(1+dim*data.num_atom_max); + std::vector force(1 + dim * data.num_atom_max); - int nfiles = data.data_files.size(); // number of files + int nfiles = data.data_files.size(); // number of files if (comm->me == 0) utils::logmesg(lmp, "**************** Begin of Energy/Force Calculation ****************\n"); - int ci = 0; // configuration counter - for (int file = 0; file < nfiles; file++) { // loop over each file in the data set + int ci = 0; // configuration counter + for (int file = 0; file < nfiles; file++) { // loop over each file in the data set int nconfigs = data.num_config[file]; - for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file - if ((ci % 100)==0) { - if (comm->me == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + for (int ii = 0; ii < nconfigs; ii++) { // loop over each configuration in a file + if ((ci % 100) == 0) { + if (comm->me == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci + 1); } int natom = data.num_atom[ci]; - int nforce = dim*natom; + int nforce = dim * natom; if ((ci % comm->nprocs) == comm->me) { - energy = energyforce_calculation(force.data()+1, coeff, data, ci); + energy = energyforce_calculation_fastpod(force.data() + 1, data, ci); // save energy and force into a binary file - force[0] = energy; - std::string filename = "energyforce_config" + std::to_string(ci+1) + ".bin"; + std::string filename = "energyforce_config" + std::to_string(ci + 1) + ".bin"; FILE *fp = fopen(filename.c_str(), "wb"); - fwrite( reinterpret_cast( force.data() ), sizeof(double) * (1 + nforce), 1, fp); + fwrite(reinterpret_cast(force.data()), sizeof(double) * (1 + nforce), 1, fp); fclose(fp); } @@ -1606,136 +1981,88 @@ void FitPOD::energyforce_calculation(const datastruct &data, double *coeff) utils::logmesg(lmp, "**************** End of Energy/Force Calculation ****************\n"); } -void FitPOD::print_matrix(const char *desc, int m, int n, double **a, int /*lda*/ ) +void FitPOD::podArrayFill(int *output, int start, int length) { - int i, j; - printf( "\n %s\n", desc ); - - for( i = 0; i < m; i++ ) - { - for( j = 0; j < n; j++ ) printf( " %6.12f", a[j][i] ); - printf( "\n" ); - } -} - -void FitPOD::print_matrix(const char *desc, int m, int n, double *a, int lda ) -{ - int i, j; - printf( "\n %s\n", desc ); - - for( i = 0; i < m; i++ ) - { - for( j = 0; j < n; j++ ) printf( " %6.12f", a[i+j*lda] ); - printf( "\n" ); - } -} - -void FitPOD::print_matrix(const char *desc, int m, int n, int *a, int lda) -{ - int i, j; - printf( "\n %s\n", desc ); - - for( i = 0; i < m; i++ ) - { - for( j = 0; j < n; j++ ) printf( " %d", a[i+j*lda] ); - printf( "\n" ); - } -} - -void FitPOD::podArrayFill(int* output, int start, int length) -{ - for (int j = 0; j < length; ++j) - output[j] = start + j; + for (int j = 0; j < length; ++j) output[j] = start + j; } double FitPOD::podArraySum(double *a, int n) { double e = a[0]; - for (int i=1; ib) - b = a[i]; + for (int i = 1; i < n; i++) + if (a[i] > b) b = a[i]; return b; } int FitPOD::podArrayMin(int *a, int n) { int b = a[0]; - for (int i=1; ib) - b = a[i]; + for (int i = 1; i < n; i++) + if (a[i] > b) b = a[i]; return b; } void FitPOD::podKron(double *C, double *A, double *B, double alpha, int M1, int M2) { - int M = M1*M2; - for (int idx=0; idx(sz), sizeof(double) * (2), 1, fp); + fwrite(reinterpret_cast(A), sizeof(double) * (nrows * ncols), 1, fp); + fclose(fp); +} + +void FitPOD::saveintmatrix2binfile(std::string filename, int *A, int nrows, int ncols) +{ + FILE *fp = fopen(filename.c_str(), "wb"); + int sz[2]; + sz[0] = nrows; + sz[1] = ncols; + fwrite(reinterpret_cast(sz), sizeof(int) * (2), 1, fp); + fwrite(reinterpret_cast(A), sizeof(int) * (nrows * ncols), 1, fp); + fclose(fp); +} + +void FitPOD::savedata2textfile(std::string filename, std::string text, double *A, int n, int m, + int dim) +{ + if (comm->me == 0) { + int precision = 15; + FILE *fp = fopen(filename.c_str(), "w"); + if (dim == 1) { + fmt::print(fp, text, n); + for (int i = 0; i < n; i++) fmt::print(fp, "{:<10.{}f} \n", A[i], precision); + } else if (dim == 2) { + fmt::print(fp, text, n); + fmt::print(fp, "{} \n", m); + for (int j = 0; j < n; j++) { + for (int i = 0; i < m; i++) fmt::print(fp, "{:<10.{}f} ", A[j + i * n], precision); + fmt::print(fp, " \n"); + } + } + fclose(fp); + } } diff --git a/src/ML-POD/fitpod_command.h b/src/ML-POD/fitpod_command.h index b359130240..b961ddc224 100644 --- a/src/ML-POD/fitpod_command.h +++ b/src/ML-POD/fitpod_command.h @@ -21,6 +21,7 @@ CommandStyle(fitpod,FitPOD); #define LMP_FITPOD_COMMAND_H #include "command.h" +#include namespace LAMMPS_NS { @@ -31,12 +32,17 @@ class FitPOD : public Command { private: struct datastruct { - std::string file_format = "extxyz"; - std::string file_extension = "xyz"; + datastruct(); + void copydatainfo(datastruct &data) const; + + std::string file_format; + std::string file_extension; std::string data_path; - std::vector data_files; + std::vector data_files; // sorted file names + std::vector group_names; // sorted group names std::vector filenames; - std::string filenametag = "pod"; + std::string filenametag; + std::string group_weight_type; std::vector num_atom; std::vector num_atom_cumsum; @@ -54,49 +60,35 @@ class FitPOD : public Command { double *position; double *force; int *atomtype; + // Group weights will have same size as energy. + double *we; + double *wf; - int training = 1; - int normalizeenergy = 1; - int training_analysis = 1; - int test_analysis = 1; - int training_calculation = 0; - int test_calculation = 0; - int randomize = 1; - int precision = 8; - double fraction = 1.0; + int training; + int normalizeenergy; + int training_analysis; + int test_analysis; + int training_calculation; + int test_calculation; + int randomize; + int precision; + double fraction; - double fitting_weights[12] = {100.0, 1.0, 0.0, 1, 1, 0, 0, 1, 1, 1, 1, 1e-10}; + std::unordered_map we_map; + std::unordered_map wf_map; - void copydatainfo(datastruct &data) const - { - data.data_path = data_path; - data.file_format = file_format; - data.file_extension = file_extension; - data.data_files = data_files; - data.filenametag = filenametag; - data.filenames = filenames; - data.training_analysis = training_analysis; - data.test_analysis = test_analysis; - data.training_calculation = training_calculation; - data.test_calculation = test_calculation; - data.fraction = fraction; - data.randomize = randomize; - data.precision = precision; - data.training = training; - data.normalizeenergy = normalizeenergy; - for (int i = 0; i < 12; i++) data.fitting_weights[i] = fitting_weights[i]; - } + double fitting_weights[12]; }; struct neighborstruct { + neighborstruct(); + int *alist; int *pairnum; int *pairnum_cumsum; int *pairlist; double *y; - int natom; - int nalist; int natom_max; int sze; int sza; @@ -105,27 +97,30 @@ class FitPOD : public Command { }; struct descriptorstruct { + descriptorstruct(); + + double *bd; // base descriptors + double *pd; // multi-environment descriptors (probabilities) double *gd; // global descriptors double *gdd; // derivatives of global descriptors and peratom descriptors double *A; // least-square matrix for all descriptors double *b; // least-square vector for all descriptors double *c; // coefficents of descriptors - int *tmpint; int szd; - int szi; + int nCoeffAll; // number of global descriptors + int nClusters; // number of environment clusters }; + int save_descriptors; + int compute_descriptors; datastruct traindata; datastruct testdata; + datastruct envdata; descriptorstruct desc; neighborstruct nb; - class MLPOD *podptr; + class EAPOD *fastpodptr; // functions for collecting/collating arrays - - void print_matrix(const char *desc, int m, int n, int *a, int lda); - void print_matrix(const char *desc, int m, int n, double *a, int lda); - void print_matrix(const char *desc, int m, int n, double **a, int lda); void podCumsum(int *output, int *input, int length); double podArrayNorm(double *a, int n); double podArrayErrorNorm(double *a, double *b, int n); @@ -144,23 +139,40 @@ class FitPOD : public Command { void matrix33_multiplication(double *xrot, double *Rmat, double *x, int natom); void matrix33_inverse(double *invA, double *A1, double *A2, double *A3); + double squareDistance(const double *a, const double *b, int DIMENSIONS); + void assignPointsToClusters(double *points, double *centroids, int *assignments, + int *clusterSizes, int NUM_POINTS, int NUM_CLUSTERS, int DIMENSION); + void updateCentroids(double *points, double *centroids, int *assignments, int *clusterSizes, + int NUM_POINTS, int NUM_CLUSTERS, int DIMENSIONS); + void KmeansClustering(double *points, double *centroids, int *assignments, int *clusterSizes, + int NUM_POINTS, int NUM_CLUSTERS, int DIMENSIONS, int MAX_ITER); + + void savedata2textfile(std::string filename, std::string text, double *A, int n, int m, int dim); + void savematrix2binfile(std::string filename, double *A, int nrows, int ncols); + void saveintmatrix2binfile(std::string filename, int *A, int nrows, int ncols); + // functions for reading input files and fitting int read_data_file(double *fitting_weights, std::string &file_format, std::string &file_extension, - std::string &test_path, std::string &training_path, std::string &filenametag, - const std::string &data_file); - void get_exyz_files(std::vector &, const std::string &, const std::string &); + std::string &env_path, std::string &test_path, std::string &training_path, + std::string &filenametag, const std::string &data_file, + std::string &group_weight_type, + std::unordered_map &we_map, + std::unordered_map &wf_map); + void get_exyz_files(std::vector &, std::vector &, const std::string &, + const std::string &); int get_number_atom_exyz(std::vector &num_atom, int &num_atom_sum, std::string file); int get_number_atoms(std::vector &num_atom, std::vector &num_atom_sum, std::vector &num_config, std::vector training_files); - void read_exyz_file(double *lattice, double *stress, double *energy, double *pos, double *forces, - int *atomtype, std::string file, std::vector species); - void get_data(datastruct &data, const std::vector& species); + void read_exyz_file(double *lattice, double *stress, double *energy, double *we, double *wf, + double *pos, double *forces, int *atomtype, std::string file, + std::vector species, double we_group, double wf_group); + void get_data(datastruct &data, const std::vector &species); std::vector linspace(int start_in, int end_in, int num_in); std::vector shuffle(int start_in, int end_in, int num_in); std::vector select(int n, double fraction, int randomize); void select_data(datastruct &newdata, const datastruct &data); - void read_data_files(const std::string& data_file, const std::vector& species); + void read_data_files(const std::string &data_file, const std::vector &species); int latticecoords(double *y, int *alist, double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx); int podneighborlist(int *neighlist, int *numneigh, double *r, double rcutsq, int nx, int N, @@ -168,19 +180,21 @@ class FitPOD : public Command { int podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, int *numneighsum, double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx); - void allocate_memory(const datastruct &data); - void linear_descriptors(const datastruct &data, int ci); - void quadratic_descriptors(const datastruct &data, int ci); - void cubic_descriptors(const datastruct &data, int ci); + void estimate_memory_neighborstruct(const datastruct &data, int *pbc, double rcut, int nelements); + void allocate_memory_neighborstruct(); + void allocate_memory_descriptorstruct(int nd); + void estimate_memory_fastpod(const datastruct &data); + void local_descriptors_fastpod(const datastruct &data, int ci); + void base_descriptors_fastpod(const datastruct &data, int ci); void least_squares_matrix(const datastruct &data, int ci); void least_squares_fit(const datastruct &data); + void descriptors_calculation(const datastruct &data); + void environment_cluster_calculation(const datastruct &data); void print_analysis(const datastruct &data, double *outarray, double *errors); void error_analysis(const datastruct &data, double *coeff); - double energyforce_calculation(double *force, double *coeff, const datastruct &data, int ci); - void energyforce_calculation(const datastruct &data, double *coeff); + double energyforce_calculation_fastpod(double *force, const datastruct &data, int ci); + void energyforce_calculation(const datastruct &data); }; - } // namespace LAMMPS_NS - #endif #endif diff --git a/src/ML-POD/mlpod.cpp b/src/ML-POD/mlpod.cpp deleted file mode 100644 index 088b9abadc..0000000000 --- a/src/ML-POD/mlpod.cpp +++ /dev/null @@ -1,3714 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ Sandia National Laboratories - LAMMPS development team: developers@lammps.org - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) -------------------------------------------------------------------------- */ - -// POD header file - -#include "mlpod.h" - -// LAMMPS header files - -#include "comm.h" -#include "error.h" -#include "math_const.h" -#include "math_special.h" -#include "memory.h" -#include "tokenizer.h" - -#include - -using namespace LAMMPS_NS; -using MathConst::MY_PI; -using MathSpecial::cube; -using MathSpecial::powint; - -static constexpr int MAXLINE = 1024; - -MLPOD::podstruct::podstruct() : - twobody{4, 8, 6}, threebody{4, 8, 5, 4}, fourbody{0, 0, 0, 0}, pbc(nullptr), - elemindex(nullptr), quadratic22{0, 0}, quadratic23{0, 0}, quadratic24{0, 0}, quadratic33{0, 0}, - quadratic34{0, 0}, quadratic44{0, 0}, cubic234{0, 0, 0}, cubic333{0, 0, 0}, cubic444{0, 0, 0}, - besselparams(nullptr), coeff(nullptr), Phi2(nullptr), Phi3(nullptr), Phi4(nullptr), - Lambda2(nullptr), Lambda3(nullptr), Lambda4(nullptr), - snapelementradius{0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5}, - snapelementweight{1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0} -{ - snaptwojmax = 0; - snapchemflag = 0; - snaprfac0 = 0.99363; -} - -MLPOD::podstruct::~podstruct() -{ - delete[] pbc; - delete[] elemindex; - delete[] besselparams; -} - -MLPOD::MLPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file) : - Pointers(_lmp) -{ - // read pod input file to podstruct - - read_pod(pod_file); - - // read pod coefficient file to podstruct - - if (coeff_file != "") read_coeff_file(coeff_file); - - if (pod.snaptwojmax > 0) InitSnap(); -} - -MLPOD::~MLPOD() -{ - // deallocate pod arrays - - memory->destroy(pod.coeff); - if (pod.ns2 > 0) { - memory->destroy(pod.Phi2); - memory->destroy(pod.Lambda2); - } - if (pod.ns3 > 0) { - memory->destroy(pod.Phi3); - memory->destroy(pod.Lambda3); - } - if (pod.ns4 > 0) { - memory->destroy(pod.Phi4); - memory->destroy(pod.Lambda4); - } - - // deallocate snap arrays if used - - if (pod.snaptwojmax > 0) { - memory->destroy(sna.map); - memory->destroy(sna.idx_max); - memory->destroy(sna.idxz); - memory->destroy(sna.idxb); - memory->destroy(sna.idxb_block); - memory->destroy(sna.idxu_block); - memory->destroy(sna.idxz_block); - memory->destroy(sna.idxcg_block); - memory->destroy(sna.rootpqarray); - memory->destroy(sna.cglist); - memory->destroy(sna.fac); - memory->destroy(sna.bzero); - memory->destroy(sna.wjelem); - memory->destroy(sna.radelem); - memory->destroy(sna.rcutsq); - } -} - -// clang-format off - -void MLPOD::podMatMul(double *c, double *a, double *b, int r1, int c1, int c2) -{ - int i, j, k; - - for(j = 0; j < c2; j++) - for(i = 0; i < r1; i++) - c[i + r1*j] = 0.0; - - for(j = 0; j < c2; j++) - for(i = 0; i < r1; i++) - for(k = 0; k < c1; k++) - c[i + r1*j] += a[i + r1*k] * b[k + c1*j]; -} - -void MLPOD::podArrayFill(int* output, int start, int length) -{ - for (int j = 0; j < length; ++j) - output[j] = start + j; -} - -void MLPOD::podArraySetValue(double *y, double a, int n) -{ - for (int i=0; icreate(xij, N, "pod:xij"); - memory->create(S, N*ns, "pod:S"); - memory->create(Q, N*ns, "pod:Q"); - memory->create(A, ns*ns, "pod:A"); - memory->create(b, ns, "pod:ns"); - - for (int i=0; i= max(1,3*N-1) - int info = 1; // = 0: successful exit - std::vector work(lwork); - DSYEV(&chv, &chu, &ns, A, &ns, b, work.data(), &lwork, &info); - - // order eigenvalues and eigenvectors from largest to smallest - - for (int j=0; jdestroy(xij); - memory->destroy(S); - memory->destroy(A); - memory->destroy(b); - memory->destroy(Q); -} - -void MLPOD::read_pod(const std::string &pod_file) -{ - pod.nbesselpars = 3; - delete[] pod.besselparams; - pod.besselparams = new double[3]; - delete[] pod.pbc; - pod.pbc = new int[3]; - - pod.besselparams[0] = 0.0; - pod.besselparams[1] = 2.0; - pod.besselparams[2] = 4.0; - - pod.nelements = 0; - pod.onebody = 1; - pod.besseldegree = 3; - pod.inversedegree = 6; - pod.quadraticpod = 0; - pod.rin = 0.5; - pod.rcut = 4.6; - - pod.snaptwojmax = 0; - pod.snapchemflag = 0; - pod.snaprfac0 = 0.99363; - - sna.twojmax = 0; - sna.ntypes = 0; - - std::string podfilename = pod_file; - FILE *fppod; - if (comm->me == 0) { - - fppod = utils::open_potential(podfilename,lmp,nullptr); - if (fppod == nullptr) - error->one(FLERR,"Cannot open POD coefficient file {}: ", - podfilename, utils::getsyserror()); - } - - // loop through lines of POD file and parse keywords - - char line[MAXLINE] = {'\0'}; - char *ptr; - int eof = 0; - while (true) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fppod); - if (ptr == nullptr) { - eof = 1; - fclose(fppod); - } - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); - - // words = ptrs to all words in line - // strip single and double quotes from words - - std::vector words; - try { - words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); - } catch (TokenizerException &) { - // ignore - } - - if (words.size() == 0) continue; - - const auto &keywd = words[0]; - - if (keywd == "species") { - pod.nelements = words.size()-1; - for (int ielem = 1; ielem <= pod.nelements; ielem++) { - pod.species.push_back(words[ielem]); - } - } - - if (keywd == "pbc") { - if (words.size() != 4) - error->one(FLERR,"Improper POD file.", utils::getsyserror()); - pod.pbc[0] = utils::inumeric(FLERR,words[1],false,lmp); - pod.pbc[1] = utils::inumeric(FLERR,words[2],false,lmp); - pod.pbc[2] = utils::inumeric(FLERR,words[3],false,lmp); - } - - if ((keywd != "#") && (keywd != "species") && (keywd != "pbc")) { - - if (words.size() != 2) - error->one(FLERR,"Improper POD file.", utils::getsyserror()); - - if (keywd == "rin") pod.rin = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "rcut") pod.rcut = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "bessel_scaling_parameter1") - pod.besselparams[0] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "bessel_scaling_parameter2") - pod.besselparams[1] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "bessel_scaling_parameter3") - pod.besselparams[2] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "bessel_polynomial_degree") - pod.besseldegree = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "inverse_polynomial_degree") - pod.inversedegree = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "onebody") pod.onebody = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "twobody_bessel_polynomial_degree") - pod.twobody[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "twobody_inverse_polynomial_degree") - pod.twobody[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "twobody_number_radial_basis_functions") - pod.twobody[2] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "threebody_bessel_polynomial_degree") - pod.threebody[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "threebody_inverse_polynomial_degree") - pod.threebody[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "threebody_number_radial_basis_functions") - pod.threebody[2] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "threebody_number_angular_basis_functions") - pod.threebody[3] = utils::inumeric(FLERR,words[1],false,lmp)-1; - if (keywd == "fourbody_bessel_polynomial_degree") - pod.fourbody[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_inverse_polynomial_degree") - pod.fourbody[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_number_radial_basis_functions") - pod.fourbody[2] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_twojmax") - pod.snaptwojmax = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_chemflag") - pod.snapchemflag = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_rfac0") - pod.snaprfac0 = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_neighbor_weight1") - pod.snapelementweight[0] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_neighbor_weight2") - pod.snapelementweight[1] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_neighbor_weight3") - pod.snapelementweight[2] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_neighbor_weight4") - pod.snapelementweight[3] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "fourbody_snap_neighbor_weight5") - pod.snapelementweight[4] = utils::numeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic_pod_potential") - pod.quadraticpod = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic22_number_twobody_basis_functions") - pod.quadratic22[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic22_number_twobody_basis_functions") - pod.quadratic22[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic23_number_twobody_basis_functions") - pod.quadratic23[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic23_number_threebody_basis_functions") - pod.quadratic23[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic24_number_twobody_basis_functions") - pod.quadratic24[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic24_number_fourbody_basis_functions") - pod.quadratic24[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic33_number_threebody_basis_functions") - pod.quadratic33[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic33_number_threebody_basis_functions") - pod.quadratic33[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic34_number_threebody_basis_functions") - pod.quadratic34[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic34_number_fourbody_basis_functions") - pod.quadratic34[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic44_number_fourbody_basis_functions") - pod.quadratic44[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "quadratic44_number_fourbody_basis_functions") - pod.quadratic44[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "cubic234_number_twobody_basis_functions") - pod.cubic234[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "cubic234_number_threebody_basis_functions") - pod.cubic234[1] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "cubic234_number_fourbody_basis_functions") - pod.cubic234[2] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "cubic333_number_threebody_basis_functions") - pod.cubic333[0] = utils::inumeric(FLERR,words[1],false,lmp); - if (keywd == "cubic444_number_fourbody_basis_functions") - pod.cubic444[0] = utils::inumeric(FLERR,words[1],false,lmp); - } - } - - pod.twobody[0] = pod.besseldegree; - pod.twobody[1] = pod.inversedegree; - pod.threebody[0] = pod.besseldegree; - pod.threebody[1] = pod.inversedegree; - - // number of snapshots - - pod.ns2 = pod.nbesselpars*pod.twobody[0] + pod.twobody[1]; - pod.ns3 = pod.nbesselpars*pod.threebody[0] + pod.threebody[1]; - pod.ns4 = pod.nbesselpars*pod.fourbody[0] + pod.fourbody[1]; - - for (int i = 0; i < pod.nbesselpars; i++) - if (fabs(pod.besselparams[i]) < 1e-3) pod.besselparams[i] = 1e-3; - - // allocate memory for eigenvectors and eigenvalues - - if (pod.ns2 > 0) { - memory->create(pod.Phi2, pod.ns2*pod.ns2, "pod:pod_Phi2"); - memory->create(pod.Lambda2, pod.ns2, "pod:pod_Lambda2"); - } - if (pod.ns3 > 0) { - memory->create(pod.Phi3, pod.ns3*pod.ns3, "pod:pod_Phi3"); - memory->create(pod.Lambda3, pod.ns3, "pod:pod_Lambda3"); - } - if (pod.ns4 > 0) { - memory->create(pod.Phi4, pod.ns4*pod.ns4, "pod:pod_Phi4"); - memory->create(pod.Lambda4, pod.ns4, "pod:pod_Lambda4"); - } - - if (pod.ns2 > 0) { - podeigenvaluedecomposition(pod.Phi2, pod.Lambda2, pod.besselparams, pod.rin, pod.rcut, - pod.twobody[0], pod.twobody[1], pod.nbesselpars, 2000); - -// /* Print eigenvalues */ -// print_matrix( "Eigenvalues for two-body potential:", 1, pod.ns2, pod.Lambda2, 1 ); -// -// /* Print eigenvectors */ -// print_matrix( "Eigenvectors for two-body potential:", pod.ns2, pod.ns2, pod.Phi2, pod.ns2); - } - if (pod.ns3 > 0) { - podeigenvaluedecomposition(pod.Phi3, pod.Lambda3, pod.besselparams, pod.rin, pod.rcut, - pod.threebody[0], pod.threebody[1], pod.nbesselpars, 2000); - } - if (pod.ns4 > 0) { - podeigenvaluedecomposition(pod.Phi4, pod.Lambda4, pod.besselparams, pod.rin, pod.rcut, - pod.fourbody[0], pod.fourbody[1], pod.nbesselpars, 2000); - } - - // number of chemical combinations - - pod.nc2 = pod.nelements*(pod.nelements+1)/2; - pod.nc3 = pod.nelements*pod.nelements*(pod.nelements+1)/2; - pod.nc4 = pod.snapchemflag ? pod.nelements*pod.nelements*pod.nelements*pod.nelements : pod.nelements; - - // number of basis functions and descriptors for one-body potential - - if (pod.onebody==1) { - pod.nbf1 = 1; - pod.nd1 = pod.nelements; - } else { - pod.nbf1 = 0; - pod.nd1 = 0; - } - - // number of basis functions and descriptors for two-body potential - - pod.nbf2 = pod.twobody[2]; - pod.nd2 = pod.nbf2*pod.nc2; - - // number of basis functions and descriptors for three-body potential - - pod.nrbf3 = pod.threebody[2]; - pod.nabf3 = pod.threebody[3]; - pod.nbf3 = pod.nrbf3*(1 + pod.nabf3); - pod.nd3 = pod.nbf3*pod.nc3; - - // number of basis functions and descriptors for four-body potential - - int twojmax = pod.snaptwojmax; - int idxb_count = 0; - if (twojmax > 0) { - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) - if (j >= j1) idxb_count++; - } - pod.nbf4 = idxb_count; - pod.nd4 = pod.nbf4*pod.nc4; - - if (pod.quadraticpod==1) { - pod.quadratic23[0] = pod.nbf2; - pod.quadratic23[1] = pod.nbf3; - } - - pod.quadratic22[0] = MIN(pod.quadratic22[0], pod.nbf2); - pod.quadratic22[1] = MIN(pod.quadratic22[1], pod.nbf2); - pod.quadratic23[0] = MIN(pod.quadratic23[0], pod.nbf2); - pod.quadratic23[1] = MIN(pod.quadratic23[1], pod.nbf3); - pod.quadratic24[0] = MIN(pod.quadratic24[0], pod.nbf2); - pod.quadratic24[1] = MIN(pod.quadratic24[1], pod.nbf4); - pod.quadratic33[0] = MIN(pod.quadratic33[0], pod.nbf3); - pod.quadratic33[1] = MIN(pod.quadratic33[1], pod.nbf3); - pod.quadratic34[0] = MIN(pod.quadratic34[0], pod.nbf3); - pod.quadratic34[1] = MIN(pod.quadratic34[1], pod.nbf4); - pod.quadratic44[0] = MIN(pod.quadratic44[0], pod.nbf4); - pod.quadratic44[1] = MIN(pod.quadratic44[1], pod.nbf4); - - pod.cubic234[0] = MIN(pod.cubic234[0], pod.nbf2); - pod.cubic234[1] = MIN(pod.cubic234[1], pod.nbf3); - pod.cubic234[2] = MIN(pod.cubic234[2], pod.nbf4); - pod.cubic333[0] = MIN(pod.cubic333[0], pod.nbf3); - pod.cubic333[1] = MIN(pod.cubic333[0], pod.nbf3); - pod.cubic333[2] = MIN(pod.cubic333[0], pod.nbf3); - pod.cubic444[0] = MIN(pod.cubic444[0], pod.nbf4); - pod.cubic444[1] = MIN(pod.cubic444[0], pod.nbf4); - pod.cubic444[2] = MIN(pod.cubic444[0], pod.nbf4); - - // number of descriptors for quadratic POD potentials - - pod.nd22 = pod.quadratic22[0]*pod.quadratic22[1]*pod.nc2*pod.nc2; - pod.nd23 = pod.quadratic23[0]*pod.quadratic23[1]*pod.nc2*pod.nc3; - pod.nd24 = pod.quadratic24[0]*pod.quadratic24[1]*pod.nc2*pod.nc4; - pod.nd33 = pod.quadratic33[0]*pod.quadratic33[1]*pod.nc3*pod.nc3; - pod.nd34 = pod.quadratic34[0]*pod.quadratic34[1]*pod.nc3*pod.nc4; - pod.nd44 = pod.quadratic44[0]*pod.quadratic44[1]*pod.nc4*pod.nc4; - - int nq; - nq = pod.quadratic22[0]*pod.nc2; pod.nd22 = nq*(nq+1)/2; - nq = pod.quadratic33[0]*pod.nc3; pod.nd33 = nq*(nq+1)/2; - nq = pod.quadratic44[0]*pod.nc4; pod.nd44 = nq*(nq+1)/2; - - // number of descriptors for cubic POD potentials - - pod.nd234 = pod.cubic234[0]*pod.cubic234[1]*pod.cubic234[2]*pod.nc2*pod.nc3*pod.nc4; - nq = pod.cubic333[0]*pod.nc3; pod.nd333 = nq*(nq+1)*(nq+2)/6; - nq = pod.cubic444[0]*pod.nc4; pod.nd444 = nq*(nq+1)*(nq+2)/6; - - // total number of descriptors for all POD potentials - - pod.nd = pod.nd1 + pod.nd2 + pod.nd3 + pod.nd4 + pod.nd22 + pod.nd23 + pod.nd24 + - pod.nd33 + pod.nd34 + pod.nd44 + pod.nd234 + pod.nd333 + pod.nd444; - pod.nd1234 = pod.nd1 + pod.nd2 + pod.nd3 + pod.nd4; - - int nelements = pod.nelements; - delete[] pod.elemindex; - pod.elemindex = new int[nelements*nelements]; - - int k = 1; - for (int i=0; i < nelements; i++) { - for (int j=i; j < nelements; j++) { - pod.elemindex[i + nelements*j] = k; - pod.elemindex[j + nelements*i] = k; - k += 1; - } - } - - if (comm->me == 0) { - utils::logmesg(lmp, "**************** Begin of POD Potentials ****************\n"); - utils::logmesg(lmp, "species: "); - for (int i=0; ime == 0) { - - fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); - if (fpcoeff == nullptr) - error->one(FLERR,"Cannot open POD coefficient file {}: ", - coefffilename, utils::getsyserror()); - } - - // check format for first line of file - - char line[MAXLINE] = {'\0'}; - char *ptr; - int eof = 0; - int nwords = 0; - while (nwords == 0) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fpcoeff); - if (ptr == nullptr) { - eof = 1; - fclose(fpcoeff); - } - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); - - // strip comment, skip line if blank - - nwords = utils::count_words(utils::trim_comment(line)); - } - - if (nwords != 2) - error->all(FLERR,"Incorrect format in POD coefficient file"); - - // strip single and double quotes from words - - int ncoeffall; - std::string tmp_str; - try { - ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f"); - tmp_str = words.next_string(); - ncoeffall = words.next_int(); - } catch (TokenizerException &e) { - error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); - } - - // loop over single block of coefficients and insert values in pod.coeff - - memory->create(pod.coeff, ncoeffall, "pod:pod_coeff"); - - for (int icoeff = 0; icoeff < ncoeffall; icoeff++) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fpcoeff); - if (ptr == nullptr) { - eof = 1; - fclose(fpcoeff); - } - } - - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) - error->all(FLERR,"Incorrect format in POD coefficient file"); - MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); - - try { - ValueTokenizer coeff(utils::trim_comment(line)); - if (coeff.count() != 1) - error->all(FLERR,"Incorrect format in POD coefficient file"); - - pod.coeff[icoeff] = coeff.next_double(); - } catch (TokenizerException &e) { - error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); - } - } - if (comm->me == 0) { - if (!eof) fclose(fpcoeff); - } -} - -/*********************************************************************************************************/ - -void MLPOD::linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, - int *atomtype, int *alist, int *pairlist, int * /*pairnum*/, - int *pairnumsum, int *tmpint, int natom, int Nij) -{ - int dim = 3; - int nelements = pod.nelements; - int nbesselpars = pod.nbesselpars; - int nrbf2 = pod.nbf2; - int nabf3 = pod.nabf3; - int nrbf3 = pod.nrbf3; - int nd1 = pod.nd1; - int nd2 = pod.nd2; - int nd3 = pod.nd3; - int nd4 = pod.nd4; - int nd1234 = nd1+nd2+nd3+nd4; - int *pdegree2 = pod.twobody; - int *elemindex = pod.elemindex; - double rin = pod.rin; - double rcut = pod.rcut; - double *Phi2 = pod.Phi2; - double *besselparams = pod.besselparams; - - double *fatom1 = &efatom[0]; - double *fatom2 = &efatom[dim*natom*(nd1)]; - double *fatom3 = &efatom[dim*natom*(nd1+nd2)]; - double *fatom4 = &efatom[dim*natom*(nd1+nd2+nd3)]; - double *eatom1 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)]; - double *eatom2 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*nd1]; - double *eatom3 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*(nd1+nd2)]; - double *eatom4 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*(nd1+nd2+nd3)]; - - podArraySetValue(fatom1, 0.0, (1+dim)*natom*(nd1+nd2+nd3+nd4)); - - double *rij = &tmpmem[0]; // 3*Nij - int *ai = &tmpint[0]; // Nij - int *aj = &tmpint[Nij]; // Nij - int *ti = &tmpint[2*Nij]; // Nij - int *tj = &tmpint[3*Nij]; // Nij - podNeighPairs(rij, y, ai, aj, ti, tj, pairlist, pairnumsum, atomtype, - alist, natom, dim); - - // peratom descriptors for one-body, two-body, and three-body linear potentials - - poddesc(eatom1, fatom1, eatom2, fatom2, eatom3, fatom3, rij, Phi2, besselparams, - &tmpmem[3*Nij], rin, rcut, pairnumsum, atomtype, ai, aj, ti, tj, elemindex, pdegree2, - nbesselpars, nrbf2, nrbf3, nabf3, nelements, Nij, natom); - - if (pod.snaptwojmax > 0) - snapdesc(eatom4, fatom4, rij, &tmpmem[3*Nij], atomtype, ai, aj, ti, tj, natom, Nij); - - // global descriptors for one-body, two-body, three-body, and four-bodt linear potentials - - podArraySetValue(tmpmem, 1.0, natom); - - char cht = 'T'; - double one = 1.0, zero = 0.0; - int inc1 = 1; - DGEMV(&cht, &natom, &nd1234, &one, eatom1, &natom, tmpmem, &inc1, &zero, gd, &inc1); -} - -void MLPOD::quadratic_descriptors(double* d23, double *dd23, double* d2, double *d3, double* dd2, double *dd3, - int M2, int M3, int N) -{ - for (int m3 = 0; m3 0) energy += quadratic_coefficients(c2, d2, coeff22, pod.quadratic22, nc2); - - // calculate energy for quadratic23 potential - - if (nd23 > 0) energy += quadratic_coefficients(c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); - - // calculate energy for quadratic24 potential - - if (nd24 > 0) energy += quadratic_coefficients(c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); - - // calculate energy for quadratic33 potential - - if (nd33 > 0) energy += quadratic_coefficients(c3, d3, coeff33, pod.quadratic33, nc3); - - // calculate energy for quadratic34 potential - - if (nd34 > 0) energy += quadratic_coefficients(c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); - - // calculate energy for quadratic44 potential - - if (nd44 > 0) energy += quadratic_coefficients(c4, d4, coeff44, pod.quadratic44, nc4); - - // calculate energy for cubic234 potential - - if (nd234 > 0) energy += cubic_coefficients(c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); - - // calculate energy for cubic333 potential - - if (nd333 > 0) energy += cubic_coefficients(c3, d3, coeff333, pod.cubic333, nc3); - - // calculate energy for cubic444 potential - - if (nd444 > 0) energy += cubic_coefficients(c4, d4, coeff444, pod.cubic444, nc4); - - // calculate effective POD coefficients - - for (int i=0; i< nd1234; i++) c1[i] += coeff[i]; - - // calculate force = gdd * c1 - - char chn = 'N'; - double one = 1.0, zero = 0.0; - int inc1 = 1; - DGEMV(&chn, &nforce, &nd1234, &one, gdd, &nforce, c1, &inc1, &zero, force, &inc1); - - return energy; -} - -double MLPOD::energyforce_calculation(double *force, double *gd, double *gdd, double *coeff, double *y, - int *atomtype, int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, int natom, int Nij) -{ - int dim = 3; - int nd1234 = pod.nd1+pod.nd2+pod.nd3+pod.nd4; - double *tmpmem = &gdd[dim*natom*nd1234+natom*nd1234]; - - // calculate POD and SNAP descriptors and their derivatives - - linear_descriptors(gd, gdd, y, tmpmem, atomtype, alist, - pairlist, pairnum, pairnumsum, tmpint, natom, Nij); - - // calculate energy and force - - double energy = 0.0; - energy = calculate_energyforce(force, gd, gdd, coeff, &gdd[dim*natom*nd1234], natom); - - return energy; -} - -void MLPOD::podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, - int *pairlist, int *pairnumsum, int *atomtype, int *alist, int inum, int dim) -{ - for (int ii=0; ii j) - ik = lk + s; - k = aj[ik]; // atom k - typek = tj[ik] - 1; - xik1 = yij[0+dim*ik]; // xk - xi - xik2 = yij[1+dim*ik]; // xk - xi - xik3 = yij[2+dim*ik]; // xk - xi - riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; - rik = sqrt(riksq); - - xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; - costhe = xdot/(rij*rik); - costhe = costhe > 1.0 ? 1.0 : costhe; - costhe = costhe < -1.0 ? -1.0 : costhe; - xdot = costhe*(rij*rik); - - sinthe = sqrt(1.0 - costhe*costhe); - sinthe = sinthe > 1e-12 ? sinthe : 1e-12; - theta = acos(costhe); - dtheta = -1.0/sinthe; - - tm1 = 1.0/(rij*rijsq*rik); - tm2 = 1.0/(rij*riksq*rik); - dct1 = (xik1*rijsq - xij1*xdot)*tm1; - dct2 = (xik2*rijsq - xij2*xdot)*tm1; - dct3 = (xik3*rijsq - xij3*xdot)*tm1; - dct4 = (xij1*riksq - xik1*xdot)*tm2; - dct5 = (xij2*riksq - xik2*xdot)*tm2; - dct6 = (xij3*riksq - xik3*xdot)*tm2; - - for (int p=0; p = j1) idxb_count++; - - int idxb_max = idxb_count; - idx_max[2] = idxb_max; - - idxb_count = 0; - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) - if (j >= j1) { - idxb[idxb_count*3 + 0] = j1; - idxb[idxb_count*3 + 1] = j2; - idxb[idxb_count*3 + 2] = j; - idxb_count++; - } - - idxb_count = 0; - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - if (j >= j1) { - idxb_block[j + j2*jdim + j1*jdim*jdim] = idxb_count; - idxb_count++; - } - } - - // index list for zlist - - int idxz_count = 0; - - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) - for (int mb = 0; 2*mb <= j; mb++) - for (int ma = 0; ma <= j; ma++) - idxz_count++; - - int idxz_max = idxz_count; - idx_max[3] = idxz_max; - - idxz_count = 0; - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - idxz_block[j + j2*jdim + j1*jdim*jdim] = idxz_count; - - for (int mb = 0; 2*mb <= j; mb++) - for (int ma = 0; ma <= j; ma++) { - - idxz[idxz_count*10 + 0] = j1; - idxz[idxz_count*10 + 1] = j2; - idxz[idxz_count*10 + 2] = j; - idxz[idxz_count*10 + 3] = MAX(0, (2 * ma - j - j2 + j1) / 2); - idxz[idxz_count*10 + 4] = (2 * ma - j - (2 * idxz[idxz_count*10 + 3] - j1) + j2) / 2; - idxz[idxz_count*10 + 5] = MIN(j1, (2 * ma - j + j2 + j1) / 2) - idxz[idxz_count*10 + 3] + 1; - idxz[idxz_count*10 + 6] = MAX(0, (2 * mb - j - j2 + j1) / 2); - idxz[idxz_count*10 + 7] = (2 * mb - j - (2 * idxz[idxz_count*10 + 6] - j1) + j2) / 2; - idxz[idxz_count*10 + 8] = MIN(j1, (2 * mb - j + j2 + j1) / 2) - idxz[idxz_count*10 + 6] + 1; - - const int jju = idxu_block[j] + (j+1)*mb + ma; - idxz[idxz_count*10 + 9] = jju; - - idxz_count++; - } - } -}; - -void snapInitRootpqArray(double *rootpqarray, int twojmax) -{ - int jdim = twojmax + 1; - for (int p = 1; p <= twojmax; p++) - for (int q = 1; q <= twojmax; q++) - rootpqarray[p*jdim + q] = sqrt(((double) p)/q); -}; - -double snapDeltacg(double *factorial, int j1, int j2, int j) -{ - double sfaccg = factorial[(j1 + j2 + j) / 2 + 1]; - return sqrt(factorial[(j1 + j2 - j) / 2] * - factorial[(j1 - j2 + j) / 2] * - factorial[(-j1 + j2 + j) / 2] / sfaccg); -}; - -void snapInitClebschGordan(double *cglist, double *factorial, int twojmax) -{ - double sum,dcg,sfaccg; - int m, aa2, bb2, cc2; - int ifac; - - int idxcg_count = 0; - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - for (int m1 = 0; m1 <= j1; m1++) { - aa2 = 2 * m1 - j1; - - for (int m2 = 0; m2 <= j2; m2++) { - - bb2 = 2 * m2 - j2; - m = (aa2 + bb2 + j) / 2; - - if(m < 0 || m > j) { - cglist[idxcg_count] = 0.0; - idxcg_count++; - continue; - } - - sum = 0.0; - - for (int z = MAX(0, MAX(-(j - j2 + aa2) - / 2, -(j - j1 - bb2) / 2)); - z <= MIN((j1 + j2 - j) / 2, - MIN((j1 - aa2) / 2, (j2 + bb2) / 2)); - z++) { - ifac = z % 2 ? -1 : 1; - sum += ifac / - (factorial[z] * - factorial[(j1 + j2 - j) / 2 - z] * - factorial[(j1 - aa2) / 2 - z] * - factorial[(j2 + bb2) / 2 - z] * - factorial[(j - j2 + aa2) / 2 + z] * - factorial[(j - j1 - bb2) / 2 + z]); - } - - cc2 = 2 * m - j; - dcg = snapDeltacg(factorial, j1, j2, j); - sfaccg = sqrt(factorial[(j1 + aa2) / 2] * - factorial[(j1 - aa2) / 2] * - factorial[(j2 + bb2) / 2] * - factorial[(j2 - bb2) / 2] * - factorial[(j + cc2) / 2] * - factorial[(j - cc2) / 2] * - (j + 1)); - - cglist[idxcg_count] = sum * dcg * sfaccg; - idxcg_count++; - } - } - } -} - -void snapInitSna(double *rootpqarray, double *cglist, double *factorial, int *idx_max, int *idxz, - int *idxz_block, int *idxb, int *idxb_block, int *idxu_block, int *idxcg_block, int twojmax) -{ - snapBuildIndexList(idx_max, idxz, idxz_block, idxb, - idxb_block, idxu_block, idxcg_block, twojmax); - - snapInitRootpqArray(rootpqarray, twojmax); - snapInitClebschGordan(cglist, factorial, twojmax); -} - -void MLPOD::snapSetup(int twojmax, int ntypes) -{ - sna.twojmax = twojmax; - sna.ntypes = ntypes; - - int jdim = twojmax + 1; - int jdimpq = twojmax + 2; - - memory->create(sna.map, ntypes+1, "pod:sna_map"); - memory->create(sna.idxcg_block, jdim*jdim*jdim, "pod:sna_idxcg_block"); - memory->create(sna.idxz_block, jdim*jdim*jdim, "pod:sna_idxz_block"); - memory->create(sna.idxb_block, jdim*jdim*jdim, "pod:sna_idxb_block"); - memory->create(sna.idxu_block, jdim, "pod:sna_idxu_block"); - memory->create(sna.idx_max, 5, "pod:sna_idx_max"); - - int idxb_count = 0; - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) - if (j >= j1) idxb_count++; - - int idxz_count = 0; - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) - for (int mb = 0; 2*mb <= j; mb++) - for (int ma = 0; ma <= j; ma++) - idxz_count++; - - int idxcg_count = 0; - for(int j1 = 0; j1 <= twojmax; j1++) - for(int j2 = 0; j2 <= j1; j2++) - for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - for (int m1 = 0; m1 <= j1; m1++) - for (int m2 = 0; m2 <= j2; m2++) - idxcg_count++; - } - - memory->create(sna.idxz, idxz_count*10, "pod:sna_idxz"); - memory->create(sna.idxb, idxb_count*3, "pod:sna_idxb"); - memory->create(sna.rcutsq, (ntypes+1)*(ntypes+1), "pod:sna_rcutsq"); - memory->create(sna.radelem, ntypes+1, "pod:sna_radelem"); - memory->create(sna.wjelem, ntypes+1, "pod:sna_wjelem"); - memory->create(sna.rootpqarray, jdimpq*jdimpq, "pod:sna_rootpqarray"); - memory->create(sna.cglist, idxcg_count, "pod:sna_cglist"); - memory->create(sna.bzero, jdim, "pod:sna_bzero"); - memory->create(sna.fac, 168, "pod:sna_fac"); - - for (int i=0; i rcutij) { - sfac = 0.0; - dsfac = 0.0; - } - else { - double rcutfac0 = MY_PI / (rcutij - rmin0); - sfac = 0.5 * (cos((r - rmin0) * rcutfac0) + 1.0); - dsfac = -0.5 * sin((r - rmin0) * rcutfac0) * rcutfac0; - } - } - sfac *= wjelem[tj[ij]]; - dsfac *= wjelem[tj[ij]]; - - double r0inv, dr0invdr; - double a_r, a_i, b_r, b_i; - double da_r[3], da_i[3], db_r[3], db_i[3]; - double dz0[3], dr0inv[3]; - double rootpq; - int jdim = twojmax + 1; - - r0inv = 1.0 / sqrt(r * r + z0 * z0); - a_r = r0inv * z0; - a_i = -r0inv * z; - b_r = r0inv * y; - b_i = -r0inv * x; - - dr0invdr = -cube(r0inv) * (r + z0 * dz0dr); - - dr0inv[0] = dr0invdr * ux; - dr0inv[1] = dr0invdr * uy; - dr0inv[2] = dr0invdr * uz; - - dz0[0] = dz0dr * ux; - dz0[1] = dz0dr * uy; - dz0[2] = dz0dr * uz; - - for (int k = 0; k < 3; k++) { - da_r[k] = dz0[k] * r0inv + z0 * dr0inv[k]; - da_i[k] = -z * dr0inv[k]; - } - da_i[2] += -r0inv; - - for (int k = 0; k < 3; k++) { - db_r[k] = y * dr0inv[k]; - db_i[k] = -x * dr0inv[k]; - } - db_i[0] += -r0inv; - db_r[1] += r0inv; - - Sr[ij+0*ijnum] = 1.0; - Si[ij+0*ijnum] = 0.0; - Srx[ij+0*ijnum] = 0.0; - Six[ij+0*ijnum] = 0.0; - Sry[ij+0*ijnum] = 0.0; - Siy[ij+0*ijnum] = 0.0; - Srz[ij+0*ijnum] = 0.0; - Siz[ij+0*ijnum] = 0.0; - for (int j = 1; j <= twojmax; j++) { - int jju = idxu_block[j]; - int jjup = idxu_block[j-1]; - - // fill in left side of matrix layer from previous layer - - for (int mb = 0; 2*mb <= j; mb++) { - Sr[ij+jju*ijnum] = 0.0; - Si[ij+jju*ijnum] = 0.0; - Srx[ij+jju*ijnum] = 0.0; - Six[ij+jju*ijnum] = 0.0; - Sry[ij+jju*ijnum] = 0.0; - Siy[ij+jju*ijnum] = 0.0; - Srz[ij+jju*ijnum] = 0.0; - Siz[ij+jju*ijnum] = 0.0; - for (int ma = 0; ma < j; ma++) { - rootpq = rootpqarray[(j - ma)*jdim + (j - mb)]; - int njju = ij+jju*ijnum; - int njju1 = ij+(jju+1)*ijnum; - int njjup = ij+jjup*ijnum; - double u_r = Sr[njjup]; - double u_i = Si[njjup]; - double ux_r = Srx[njjup]; - double ux_i = Six[njjup]; - double uy_r = Sry[njjup]; - double uy_i = Siy[njjup]; - double uz_r = Srz[njjup]; - double uz_i = Siz[njjup]; - - Sr[njju] += rootpq * (a_r * u_r + a_i * u_i); - Si[njju] += rootpq * (a_r * u_i - a_i * u_r); - Srx[njju] += rootpq * (da_r[0] * u_r + da_i[0] * u_i + a_r * ux_r + a_i * ux_i); - Six[njju] += rootpq * (da_r[0] * u_i - da_i[0] * u_r + a_r * ux_i - a_i * ux_r); - Sry[njju] += rootpq * (da_r[1] * u_r + da_i[1] * u_i + a_r * uy_r + a_i * uy_i); - Siy[njju] += rootpq * (da_r[1] * u_i - da_i[1] * u_r + a_r * uy_i - a_i * uy_r); - Srz[njju] += rootpq * (da_r[2] * u_r + da_i[2] * u_i + a_r * uz_r + a_i * uz_i); - Siz[njju] += rootpq * (da_r[2] * u_i - da_i[2] * u_r + a_r * uz_i - a_i * uz_r); - - rootpq = rootpqarray[(ma + 1)*jdim + (j - mb)]; - Sr[njju1] = -rootpq * (b_r * u_r + b_i * u_i); - Si[njju1] = -rootpq * (b_r * u_i - b_i * u_r); - Srx[njju1] = -rootpq * (db_r[0] * u_r + db_i[0] * u_i + b_r * ux_r + b_i * ux_i); - Six[njju1] = -rootpq * (db_r[0] * u_i - db_i[0] * u_r + b_r * ux_i - b_i * ux_r); - Sry[njju1] = -rootpq * (db_r[1] * u_r + db_i[1] * u_i + b_r * uy_r + b_i * uy_i); - Siy[njju1] = -rootpq * (db_r[1] * u_i - db_i[1] * u_r + b_r * uy_i - b_i * uy_r); - Srz[njju1] = -rootpq * (db_r[2] * u_r + db_i[2] * u_i + b_r * uz_r + b_i * uz_i); - Siz[njju1] = -rootpq * (db_r[2] * u_i - db_i[2] * u_r + b_r * uz_i - b_i * uz_r); - jju++; - jjup++; - } - jju++; - } - - jju = idxu_block[j]; - jjup = jju+(j+1)*(j+1)-1; - int mbpar = 1; - for (int mb = 0; 2*mb <= j; mb++) { - int mapar = mbpar; - for (int ma = 0; ma <= j; ma++) { - int njju = ij+jju*ijnum; - int njjup = ij+jjup*ijnum; - if (mapar == 1) { - Sr[njjup] = Sr[njju]; - Si[njjup] = -Si[njju]; - if (j%2==1 && mb==(j/2)) { - Srx[njjup] = Srx[njju]; - Six[njjup] = -Six[njju]; - Sry[njjup] = Sry[njju]; - Siy[njjup] = -Siy[njju]; - Srz[njjup] = Srz[njju]; - Siz[njjup] = -Siz[njju]; - } - } else { - Sr[njjup] = -Sr[njju]; - Si[njjup] = Si[njju]; - if (j%2==1 && mb==(j/2)) { - Srx[njjup] = -Srx[njju]; - Six[njjup] = Six[njju]; - Sry[njjup] = -Sry[njju]; - Siy[njjup] = Siy[njju]; - Srz[njjup] = -Srz[njju]; - Siz[njjup] = Siz[njju]; - } - } - mapar = -mapar; - jju++; - jjup--; - } - mbpar = -mbpar; - } - } - - for (int j = 0; j <= twojmax; j++) { - int jju = idxu_block[j]; - for (int mb = 0; 2*mb <= j; mb++) - for (int ma = 0; ma <= j; ma++) { - int ijk = ij+jju*ijnum; - Srx[ijk] = dsfac * Sr[ijk] * ux + sfac * Srx[ijk]; - Six[ijk] = dsfac * Si[ijk] * ux + sfac * Six[ijk]; - Sry[ijk] = dsfac * Sr[ijk] * uy + sfac * Sry[ijk]; - Siy[ijk] = dsfac * Si[ijk] * uy + sfac * Siy[ijk]; - Srz[ijk] = dsfac * Sr[ijk] * uz + sfac * Srz[ijk]; - Siz[ijk] = dsfac * Si[ijk] * uz + sfac * Siz[ijk]; - jju++; - } - } - - for (int k=0; k 1e-20) { - rij[ninside*3 + 0] = delx; - rij[ninside*3 + 1] = dely; - rij[ninside*3 + 2] = delz; - idxi[ninside] = ii; - ai[ninside] = gi; - aj[ninside] = gj; - ti[ninside] = itype; - tj[ninside] = atomtype[gj]; - ninside++; - pairnumsum[ii+1] += 1; - } - } - } - - pairnumsum[0] = 0; - for (int ii=0; ii j) - ik = lk + s; - typek = tj[ik] - 1; - xik1 = yij[0+dim*ik]; // xk - xi - xik2 = yij[1+dim*ik]; // xk - xi - xik3 = yij[2+dim*ik]; // xk - xi s - riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; - rik = sqrt(riksq); - - xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; - costhe = xdot/(rij*rik); - costhe = costhe > 1.0 ? 1.0 : costhe; - costhe = costhe < -1.0 ? -1.0 : costhe; - theta = acos(costhe); - - for (int p=0; p rcutij) { - sfac = 0.0; - } - else { - double rcutfac0 = MY_PI / (rcutij - rmin0); - sfac = 0.5 * (cos((r - rmin0) * rcutfac0) + 1.0); - } - } - sfac *= wjelem[tj[ij]]; - - double r0inv; - double a_r, a_i, b_r, b_i; - double rootpq; - int jdim = twojmax + 1; - - r0inv = 1.0 / sqrt(r * r + z0 * z0); - a_r = r0inv * z0; - a_i = -r0inv * z; - b_r = r0inv * y; - b_i = -r0inv * x; - - Sr[ij+0*ijnum] = 1.0; - Si[ij+0*ijnum] = 0.0; - for (int j = 1; j <= twojmax; j++) { - int jju = idxu_block[j]; - int jjup = idxu_block[j-1]; - - // fill in left side of matrix layer from previous layer - - for (int mb = 0; 2*mb <= j; mb++) { - Sr[ij+jju*ijnum] = 0.0; - Si[ij+jju*ijnum] = 0.0; - for (int ma = 0; ma < j; ma++) { - rootpq = rootpqarray[(j - ma)*jdim + (j - mb)]; - int njju = ij+jju*ijnum; - int njju1 = ij+(jju+1)*ijnum; - int njjup = ij+jjup*ijnum; - double u_r = Sr[njjup]; - double u_i = Si[njjup]; - - Sr[njju] += rootpq * (a_r * u_r + a_i * u_i); - Si[njju] += rootpq * (a_r * u_i - a_i * u_r); - - rootpq = rootpqarray[(ma + 1)*jdim + (j - mb)]; - Sr[njju1] = -rootpq * (b_r * u_r + b_i * u_i); - Si[njju1] = -rootpq * (b_r * u_i - b_i * u_r); - jju++; - jjup++; - } - jju++; - } - - jju = idxu_block[j]; - jjup = jju+(j+1)*(j+1)-1; - int mbpar = 1; - for (int mb = 0; 2*mb <= j; mb++) { - int mapar = mbpar; - for (int ma = 0; ma <= j; ma++) { - int njju = ij+jju*ijnum; - int njjup = ij+jjup*ijnum; - if (mapar == 1) { - Sr[njjup] = Sr[njju]; - Si[njjup] = -Si[njju]; - } else { - Sr[njjup] = -Sr[njju]; - Si[njjup] = Si[njju]; - } - mapar = -mapar; - jju++; - jjup--; - } - mbpar = -mbpar; - } - } - - for (int k=0; k 0) - snapdesc_ij(eatom4, rij, tmpmem, atomtype, idxi, ti, tj, natom, Nij); - - // global descriptors for one-body, two-body, three-body, and four-bodt linear potentials - - podArraySetValue(tmpmem, 1.0, natom); - - char cht = 'T'; - double one = 1.0; - int inc1 = 1; - DGEMV(&cht, &natom, &nd1234, &one, eatom1, &natom, tmpmem, &inc1, &one, gd, &inc1); -} - -double MLPOD::calculate_energy(double *effectivecoeff, double *gd, double *coeff) -{ - int nd1 = pod.nd1; - int nd2 = pod.nd2; - int nd3 = pod.nd3; - int nd4 = pod.nd4; - int nd1234 = nd1+nd2+nd3+nd4; - int nd22 = pod.nd22; - int nd23 = pod.nd23; - int nd24 = pod.nd24; - int nd33 = pod.nd33; - int nd34 = pod.nd34; - int nd44 = pod.nd44; - int nd234 = pod.nd234; - int nd333 = pod.nd333; - int nd444 = pod.nd444; - int nc2 = pod.nc2; - int nc3 = pod.nc3; - int nc4 = pod.nc4; - - // two-body, three-body, and four-body descriptors - - double *d2 = &gd[nd1]; - double *d3 = &gd[nd1+nd2]; - double *d4 = &gd[nd1+nd2+nd3]; - - // quadratic and cubic POD coefficients - - double *coeff22 = &coeff[nd1234]; - double *coeff23 = &coeff[nd1234+nd22]; - double *coeff24 = &coeff[nd1234+nd22+nd23]; - double *coeff33 = &coeff[nd1234+nd22+nd23+nd24]; - double *coeff34 = &coeff[nd1234+nd22+nd23+nd24+nd33]; - double *coeff44 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34]; - double *coeff234 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44]; - double *coeff333 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234]; - double *coeff444 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333]; - - // calculate energy for linear potentials - - double energy = 0.0; - for (int i=0; i< nd1234; i++) { - effectivecoeff[i] = 0.0; - energy += coeff[i]*gd[i]; - } - - // effective POD coefficients for calculating force - - double *c2 = &effectivecoeff[nd1]; - double *c3 = &effectivecoeff[nd1+nd2]; - double *c4 = &effectivecoeff[nd1+nd2+nd3]; - - // calculate energy for quadratic22 potential - - if (nd22 > 0) energy += quadratic_coefficients(c2, d2, coeff22, pod.quadratic22, nc2); - - // calculate energy for quadratic23 potential - - if (nd23 > 0) energy += quadratic_coefficients(c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); - - // calculate energy for quadratic24 potential - - if (nd24 > 0) energy += quadratic_coefficients(c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); - - // calculate energy for quadratic33 potential - - if (nd33 > 0) energy += quadratic_coefficients(c3, d3, coeff33, pod.quadratic33, nc3); - - // calculate energy for quadratic34 potential - - if (nd34 > 0) energy += quadratic_coefficients(c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); - - // calculate energy for quadratic44 potential - - if (nd44 > 0) energy += quadratic_coefficients(c4, d4, coeff44, pod.quadratic44, nc4); - - // calculate energy for cubic234 potential - - if (nd234 > 0) energy += cubic_coefficients(c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); - - // calculate energy for cubic333 potential - - if (nd333 > 0) energy += cubic_coefficients(c3, d3, coeff333, pod.cubic333, nc3); - - // calculate energy for cubic444 potential - - if (nd444 > 0) energy += cubic_coefficients(c4, d4, coeff444, pod.cubic444, nc4); - - // calculate effective POD coefficients - - for (int i=0; i< nd1234; i++) effectivecoeff[i] += coeff[i]; - - return energy; -} - -double MLPOD::calculate_energy(double *energycoeff, double *forcecoeff, double *gd, - double *gdall, double *coeff) -{ - int nd1 = pod.nd1; - int nd2 = pod.nd2; - int nd3 = pod.nd3; - int nd4 = pod.nd4; - int nd1234 = nd1+nd2+nd3+nd4; - int nd22 = pod.nd22; - int nd23 = pod.nd23; - int nd24 = pod.nd24; - int nd33 = pod.nd33; - int nd34 = pod.nd34; - int nd44 = pod.nd44; - int nd234 = pod.nd234; - int nd333 = pod.nd333; - int nd444 = pod.nd444; - int nc2 = pod.nc2; - int nc3 = pod.nc3; - int nc4 = pod.nc4; - - // quadratic and cubic POD coefficients - - double *coeff22 = &coeff[nd1234]; - double *coeff23 = &coeff[nd1234+nd22]; - double *coeff24 = &coeff[nd1234+nd22+nd23]; - double *coeff33 = &coeff[nd1234+nd22+nd23+nd24]; - double *coeff34 = &coeff[nd1234+nd22+nd23+nd24+nd33]; - double *coeff44 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34]; - double *coeff234 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44]; - double *coeff333 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234]; - double *coeff444 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333]; - - // sum global descriptors over all MPI ranks - - MPI_Allreduce(gd, gdall, nd1234, MPI_DOUBLE, MPI_SUM, world); - - for (int i=0; i< nd1234; i++) { - energycoeff[i] = 0.0; - forcecoeff[i] = 0.0; - } - - // effective POD coefficients for calculating force - - double *c2 = &forcecoeff[nd1]; - double *c3 = &forcecoeff[nd1+nd2]; - double *c4 = &forcecoeff[nd1+nd2+nd3]; - - // effective POD coefficients for calculating energy - - double *ce2 = &energycoeff[nd1]; - double *ce3 = &energycoeff[nd1+nd2]; - double *ce4 = &energycoeff[nd1+nd2+nd3]; - - // two-body, three-body, and four-body descriptors - - double *d2 = &gdall[nd1]; - double *d3 = &gdall[nd1+nd2]; - double *d4 = &gdall[nd1+nd2+nd3]; - - // calculate energy for quadratic22 potential - - if (nd22 > 0) quadratic_coefficients(ce2, c2, d2, coeff22, pod.quadratic22, nc2); - - // calculate energy for quadratic23 potential - - if (nd23 > 0) quadratic_coefficients(ce2, ce3, c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); - - // calculate energy for quadratic24 potential - - if (nd24 > 0) quadratic_coefficients(ce2, ce4, c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); - - // calculate energy for quadratic33 potential - - if (nd33 > 0) quadratic_coefficients(ce3, c3, d3, coeff33, pod.quadratic33, nc3); - - // calculate energy for quadratic34 potential - - if (nd34 > 0) quadratic_coefficients(ce3, ce4, c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); - - // calculate energy for quadratic44 potential - - if (nd44 > 0) quadratic_coefficients(ce4, c4, d4, coeff44, pod.quadratic44, nc4); - - // calculate energy for cubic234 potential - - if (nd234 > 0) cubic_coefficients(ce2, ce3, ce4, c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); - - // calculate energy for cubic333 potential - - if (nd333 > 0) cubic_coefficients(ce3, c3, d3, coeff333, pod.cubic333, nc3); - - // calculate energy for cubic444 potential - - if (nd444 > 0) cubic_coefficients(ce4, c4, d4, coeff444, pod.cubic444, nc4); - - // calculate effective POD coefficients - - for (int i=0; i< nd1234; i++) { - energycoeff[i] += coeff[i]; - forcecoeff[i] += coeff[i]; - } - - // calculate energy - - double energy = 0.0; - for (int i=0; i< nd1234; i++) - energy += energycoeff[i]*gd[i]; - - return energy; -} - -void MLPOD::pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, - int *tj, int *elemindex, int nelements, int nbf, int /*natom*/, int N) -{ - int nelements2 = nelements*(nelements+1)/2; - for (int n=0; n j) - ik = lk + s; - k = aj[ik]; // atom k - typek = tj[ik] - 1; - xik1 = yij[0+dim*ik]; // xk - xi - xik2 = yij[1+dim*ik]; // xk - xi - xik3 = yij[2+dim*ik]; // xk - xi s - riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; - rik = sqrt(riksq); - - xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; - costhe = xdot/(rij*rik); - costhe = costhe > 1.0 ? 1.0 : costhe; - costhe = costhe < -1.0 ? -1.0 : costhe; - xdot = costhe*(rij*rik); - - sinthe = sqrt(1.0 - costhe*costhe); - sinthe = sinthe > 1e-12 ? sinthe : 1e-12; - theta = acos(costhe); - dtheta = -1.0/sinthe; - - tm1 = 1.0/(rij*rijsq*rik); - tm2 = 1.0/(rij*riksq*rik); - dct1 = (xik1*rijsq - xij1*xdot)*tm1; - dct2 = (xik2*rijsq - xij2*xdot)*tm1; - dct3 = (xik3*rijsq - xij3*xdot)*tm1; - dct4 = (xij1*riksq - xik1*xdot)*tm2; - dct5 = (xij2*riksq - xik2*xdot)*tm2; - dct6 = (xij3*riksq - xik3*xdot)*tm2; - - for (int p=0; p 0) - pod4body_force(force, rij, coeff4, tmpmem, atomtype, idxi, ai, aj, ti, tj, natom, Nij); -} - -double MLPOD::energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff, double *gd, double *rij, - double *tmpmem, int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij) -{ - int nd1234 = pod.nd1+pod.nd2+pod.nd3+pod.nd4; - double *eatom = &tmpmem[0]; - - podArraySetValue(gd, 0.0, nd1234); - linear_descriptors_ij(gd, eatom, rij, &tmpmem[natom*nd1234], pairnumsum, atomtype, idxi, ti, tj, natom, Nij); - - // Need to do MPI_Allreduce on gd for parallel - - double energy = calculate_energy(effectivecoeff, gd, podcoeff); - - podArraySetValue(force, 0.0, 3*natom); - - calculate_force(force, effectivecoeff, rij, tmpmem, pairnumsum, atomtype, idxi, ai, aj, ti, tj, natom, Nij); - - return energy; -} - - -void MLPOD::pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, int *ti, - int *tj, int *elemindex, int nelements, int nbf, int /*natom*/, int N) -{ - int nelements2 = nelements*(nelements+1)/2; - for (int n=0; n j) - ik = lk + s; - k = aj[ik]; // atom k - typek = tj[ik] - 1; - xik1 = yij[0+dim*ik]; // xk - xi - xik2 = yij[1+dim*ik]; // xk - xi - xik3 = yij[2+dim*ik]; // xk - xi s - riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; - rik = sqrt(riksq); - - xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; - costhe = xdot/(rij*rik); - costhe = costhe > 1.0 ? 1.0 : costhe; - costhe = costhe < -1.0 ? -1.0 : costhe; - xdot = costhe*(rij*rik); - - sinthe = pow(1.0 - costhe*costhe, 0.5); - sinthe = sinthe > 1e-12 ? sinthe : 1e-12; - theta = acos(costhe); - dtheta = -1.0/sinthe; - - tm1 = 1.0/(rij*rijsq*rik); - tm2 = 1.0/(rij*riksq*rik); - dct1 = (xik1*rijsq - xij1*xdot)*tm1; - dct2 = (xik2*rijsq - xij2*xdot)*tm1; - dct3 = (xik3*rijsq - xij3*xdot)*tm1; - dct4 = (xij1*riksq - xik1*xdot)*tm2; - dct5 = (xij2*riksq - xik2*xdot)*tm2; - dct6 = (xij3*riksq - xik3*xdot)*tm2; - - for (int p=0; p 0) - pod4body_force(force, rij, coeff4, tmpmem, atomtype, idxi, ai, aj, ti, tj, natom, Nij); -} diff --git a/src/ML-POD/mlpod.h b/src/ML-POD/mlpod.h deleted file mode 100644 index 54e75988be..0000000000 --- a/src/ML-POD/mlpod.h +++ /dev/null @@ -1,308 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ Sandia National Laboratories - LAMMPS development team: developers@lammps.org - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifndef LMP_MLPOD_H -#define LMP_MLPOD_H - -#include "pointers.h" - -#define DDOT ddot_ -#define DGEMV dgemv_ -#define DGEMM dgemm_ -#define DGETRF dgetrf_ -#define DGETRI dgetri_ -#define DSYEV dsyev_ -#define DPOSV dposv_ - -extern "C" { -double DDOT(int *, double *, int *, double *, int *); -void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *, - int *); -void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *, - double *, double *, int *); -void DGETRF(int *, int *, double *, int *, int *, int *); -void DGETRI(int *, double *, int *, int *, double *, int *, int *); -void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *); -void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *); -} - -namespace LAMMPS_NS { - -class MLPOD : protected Pointers { - - private: - // functions for reading input files - - void read_pod(const std::string &pod_file); - void read_coeff_file(const std::string &coeff_file); - - // functions for calculating/collating POD descriptors/coefficients for energies - - void podradialbasis(double *rbf, double *drbf, double *xij, double *besselparams, double rin, - double rmax, int besseldegree, int inversedegree, int nbesselpars, int N); - void pod1body(double *eatom, double *fatom, int *atomtype, int nelements, int natom); - void podtally2b(double *eatom, double *fatom, double *eij, double *fij, int *ai, int *aj, int *ti, - int *tj, int *elemindex, int nelements, int nbf, int natom, int N); - void pod3body(double *eatom, double *fatom, double *rij, double *e2ij, double *f2ij, - double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, - int nrbf, int nabf, int nelements, int natom, int Nij); - void poddesc(double *eatom1, double *fatom1, double *eatom2, double *fatom2, double *eatom3, - double *fatom3, double *rij, double *Phi, double *besselparams, double *tmpmem, - double rin, double rcut, int *pairnumsum, int *atomtype, int *ai, int *aj, int *ti, - int *tj, int *elemindex, int *pdegree, int nbesselpars, int nrbf2, int nrbf3, - int nabf, int nelements, int Nij, int natom); - double quadratic_coefficients(double *c2, double *c3, double *d2, double *d3, double *coeff23, - int *quadratic, int nc2, int nc3); - double quadratic_coefficients(double *c3, double *d3, double *coeff33, int *quadratic, int nc3); - double cubic_coefficients(double *c2, double *c3, double *c4, double *d2, double *d3, double *d4, - double *coeff234, int *cubic, int nc2, int nc3, int nc4); - double cubic_coefficients(double *c3, double *d3, double *coeff333, int *cubic, int nc3); - double quadratic_coefficients(double *ce2, double *ce3, double *c2, double *c3, double *d2, - double *d3, double *coeff23, int *quadratic, int nc2, int nc3); - double quadratic_coefficients(double *ce3, double *c3, double *d3, double *coeff33, - int *quadratic, int nc3); - double cubic_coefficients(double *ce2, double *ce3, double *ce4, double *c2, double *c3, - double *c4, double *d2, double *d3, double *d4, double *coeff234, - int *cubic, int nc2, int nc3, int nc4); - double cubic_coefficients(double *ce3, double *c3, double *d3, double *coeff333, int *cubic, - int nc3); - - // functions for calculating/collating SNAP descriptors/coefficients for energies - - void snapSetup(int twojmax, int ntypes); - void InitSnap(); - void snapComputeUlist(double *Sr, double *Si, double *dSr, double *dSi, double *rootpqarray, - double *rij, double *wjelem, double *radelem, double rmin0, double rfac0, - double rcutfac, int *idxu_block, int *ti, int *tj, int twojmax, - int idxu_max, int ijnum, int switch_flag); - void snapZeroUarraytot2(double *Stotr, double *Stoti, double wself, int *idxu_block, int *type, - int *map, int *ai, int wselfall_flag, int chemflag, int idxu_max, - int nelements, int twojmax, int inum); - void snapAddUarraytot(double *Stotr, double *Stoti, double *Sr, double *Si, int *map, int *ai, - int *tj, int idxu_max, int inum, int ijnum, int chemflag); - void snapComputeZi2(double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, - double *cglist, int *idxz, int *idxu_block, int *idxcg_block, int twojmax, - int idxu_max, int idxz_max, int nelements, int bnorm_flag, int inum); - void snapComputeBi1(double *blist, double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, - int *idxb, int *idxu_block, int *idxz_block, int twojmax, int idxb_max, - int idxu_max, int idxz_max, int nelements, int inum); - void snapComputeDbidrj(double *dblist, double *zlist_r, double *zlist_i, double *dulist_r, - double *dulist_i, int *idxb, int *idxu_block, int *idxz_block, int *map, - int *ai, int *tj, int twojmax, int idxb_max, int idxu_max, int idxz_max, - int nelements, int bnorm_flag, int chemflag, int inum, int ijnum); - void snapdesc(double *blist, double *bd, double *rij, double *tmpmem, int *atomtype, int *ai, - int *aj, int *ti, int *tj, int natom, int Nij); - - // functions for calculating/collating POD descriptors/coefficients for forces - - void podradialbasis(double *rbf, double *xij, double *besselparams, double rin, double rmax, - int besseldegree, int inversedegree, int nbesselpars, int N); - void pod1body(double *eatom, int *atomtype, int nelements, int natom); - void podtally2b(double *eatom, double *eij, int *ai, int *ti, int *tj, int *elemindex, - int nelements, int nbf, int natom, int N); - void pod3body(double *eatom, double *yij, double *e2ij, double *tmpmem, int *elemindex, - int *pairnumsum, int *ai, int *ti, int *tj, int nrbf, int nabf, int nelements, - int natom, int Nij); - void poddesc_ij(double *eatom1, double *eatom2, double *eatom3, double *rij, double *Phi, - double *besselparams, double *tmpmem, double rin, double rcut, int *pairnumsum, - int *atomtype, int *ai, int *ti, int *tj, int *elemindex, int *pdegree, - int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, - int natom); - void snapComputeUij(double *Sr, double *Si, double *rootpqarray, double *rij, double *wjelem, - double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, - int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); - void snapdesc_ij(double *blist, double *rij, double *tmpmem, int *atomtype, int *ai, int *ti, - int *tj, int natom, int Nij); - void pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, - int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); - void pod3body_force(double *force, double *yij, double *e2ij, double *f2ij, double *coeff3, - double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, - int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); - void snapTallyForce(double *force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, - int ijnum, int ncoeff, int ntype); - void pod4body_force(double *force, double *rij, double *coeff4, double *tmpmem, int *atomtype, - int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); - void pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, int *ti, - int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); - void pod3body_force(double **force, double *yij, double *e2ij, double *f2ij, double *coeff3, - double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, - int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); - void snapTallyForce(double **force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, - int ijnum, int ncoeff, int ntype); - void pod4body_force(double **force, double *rij, double *coeff4, double *tmpmem, int *atomtype, - int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); - - // eigenproblem functions - - void podeigenvaluedecomposition(double *Phi, double *Lambda, double *besselparams, double rin, - double rcut, int besseldegree, int inversedegree, int nbesselpars, - int N); - - public: - MLPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file); - - MLPOD(LAMMPS *lmp) : Pointers(lmp){}; - ~MLPOD() override; - - struct podstruct { - podstruct(); - virtual ~podstruct(); - - std::vector species; - int twobody[3]; - int threebody[4]; - int fourbody[4]; - int *pbc; - int *elemindex; - - int quadratic22[2]; - int quadratic23[2]; - int quadratic24[2]; - int quadratic33[2]; - int quadratic34[2]; - int quadratic44[2]; - int cubic234[3]; - int cubic333[3]; - int cubic444[3]; - int nelements; - int onebody; - int besseldegree; - int inversedegree; - - int quadraticpod; - - double rin; - double rcut; - double *besselparams; - double *coeff; - double *Phi2, *Phi3, *Phi4, *Lambda2, *Lambda3, *Lambda4; - - // variables declaring number of snapshots, descriptors, and combinations - - int nbesselpars = 3; - int ns2, ns3, - ns4; // number of snapshots for radial basis functions for linear POD potentials - int nc2, nc3, nc4; // number of chemical combinations for linear POD potentials - int nbf1, nbf2, nbf3, nbf4; // number of basis functions for linear POD potentials - int nd1, nd2, nd3, nd4; // number of descriptors for linear POD potentials - int nd22, nd23, nd24, nd33, nd34, nd44; // number of descriptors for quadratic POD potentials - int nd234, nd333, nd444; // number of descriptors for cubic POD potentials - int nrbf3, nabf3, nrbf4, nabf4; - int nd, nd1234; - - int snaptwojmax; // also used to tell if SNAP is used when allocating/deallocating - int snapchemflag; - double snaprfac0; - double snapelementradius[10]; - double snapelementweight[10]; - }; - - struct snastruct { - int twojmax; - int ncoeff; - int idxb_max; - int idxu_max; - int idxz_max; - int idxcg_max; - int ntypes; - int nelements; - int ndoubles; // number of multi-element pairs - int ntriples; // number of multi-element triplets - int bnormflag; - int chemflag; - int switchflag; - int bzeroflag; - int wselfallflag; - - double wself; - double rmin0; - double rfac0; - double rcutfac; - double rcutmax; - - int *map; // map types to [0,nelements) - int *idx_max; - int *idxz; - int *idxz_block; - int *idxb; - int *idxb_block; - int *idxu_block; - int *idxcg_block; - - double *rcutsq; - double *radelem; - double *wjelem; - double *bzero; - double *fac; - double *rootpqarray; - double *cglist; - }; - - podstruct pod; - snastruct sna; - - // functions for collecting/collating arrays - - void podMatMul(double *c, double *a, double *b, int r1, int c1, int c2); - void podArraySetValue(double *y, double a, int n); - void podArrayCopy(double *y, double *x, int n); - void podArrayFill(int *output, int start, int length); - - // functions for calculating energy and force descriptors - - void podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, int *pairlist, - int *pairnumsum, int *atomtype, int *alist, int inum, int dim); - void linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, int *atomtype, - int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, - int natom, int Nij); - void quadratic_descriptors(double *d23, double *dd23, double *d2, double *d3, double *dd2, - double *dd3, int M2, int M3, int N); - void quadratic_descriptors(double *d33, double *dd33, double *d3, double *dd3, int M3, int N); - void cubic_descriptors(double *d234, double *dd234, double *d2, double *d3, double *d4, - double *dd2, double *dd3, double *dd4, int M2, int M3, int M4, int N); - void cubic_descriptors(double *d333, double *Dd333, double *d3, double *Dd3, int M3, int N); - double calculate_energyforce(double *force, double *gd, double *gdd, double *coeff, double *tmp, - int natom); - double energyforce_calculation(double *f, double *gd, double *gdd, double *coeff, double *y, - int *atomtype, int *alist, int *pairlist, int *pairnum, - int *pairnumsum, int *tmpint, int natom, int Nij); - - // functions for calculating energies and forces - - void podNeighPairs(double *rij, double *x, int *idxi, int *ai, int *aj, int *ti, int *tj, - int *pairnumsum, int *atomtype, int *jlist, int *alist, int inum); - int lammpsNeighPairs(double *rij, double **x, double rcutsq, int *idxi, int *ai, int *aj, int *ti, - int *tj, int *pairnumsum, int *atomtype, int *numneigh, int *ilist, - int **jlist, int inum); - void linear_descriptors_ij(double *gd, double *eatom, double *rij, double *tmpmem, - int *pairnumsum, int *atomtype, int *ai, int *ti, int *tj, int natom, - int Nij); - double calculate_energy(double *effectivecoeff, double *gd, double *coeff); - double calculate_energy(double *energycoeff, double *forcecoeff, double *gd, double *gdall, - double *coeff); - void calculate_force(double *force, double *effectivecoeff, double *rij, double *tmpmem, - int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, - int *tj, int natom, int Nij); - void calculate_force(double **force, double *effectivecoeff, double *rij, double *tmpmem, - int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, - int *tj, int natom, int Nij); - double energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff, - double *gd, double *rij, double *tmpmem, int *pairnumsum, - int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, - int natom, int Nij); - -}; - -} // namespace LAMMPS_NS - -#endif diff --git a/src/ML-POD/pair_pod.cpp b/src/ML-POD/pair_pod.cpp index d106b11a18..ee70d39df4 100644 --- a/src/ML-POD/pair_pod.cpp +++ b/src/ML-POD/pair_pod.cpp @@ -17,53 +17,137 @@ #include "pair_pod.h" -#include "mlpod.h" - #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" +#include "math_const.h" +#include "math_special.h" #include "memory.h" #include "neigh_list.h" #include "neighbor.h" +#include "tokenizer.h" + +#include +#include +#include + +#include "eapod.h" using namespace LAMMPS_NS; +using MathConst::MY_PI; +using MathSpecial::powint; + +#define MAXLINE 1024 /* ---------------------------------------------------------------------- */ -PairPOD::PairPOD(LAMMPS *lmp) : - Pair(lmp), gd(nullptr), gdall(nullptr), podcoeff(nullptr), newpodcoeff(nullptr), - energycoeff(nullptr), forcecoeff(nullptr), podptr(nullptr), tmpmem(nullptr), typeai(nullptr), - numneighsum(nullptr), rij(nullptr), idxi(nullptr), ai(nullptr), aj(nullptr), ti(nullptr), - tj(nullptr) +PairPOD::PairPOD(LAMMPS *lmp) : Pair(lmp), fastpodptr(nullptr) { single_enable = 0; restartinfo = 0; one_coeff = 1; manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - peratom_warn = true; + peratom_warn = false; - dim = 3; - nablockmax = 0; + ni = 0; + nimax = 0; nij = 0; nijmax = 0; - szd = 0; + atomBlockSize = 10; + nAtomBlocks = 0; + + rij = nullptr; + fij = nullptr; + ei = nullptr; + typeai = nullptr; + numij = nullptr; + idxi = nullptr; + ai = nullptr; + aj = nullptr; + ti = nullptr; + tj = nullptr; + Phi = nullptr; + rbf = nullptr; + rbfx = nullptr; + rbfy = nullptr; + rbfz = nullptr; + abf = nullptr; + abfx = nullptr; + abfy = nullptr; + abfz = nullptr; + sumU = nullptr; + forcecoeff = nullptr; + Centroids = nullptr; + Proj = nullptr; + bd = nullptr; + cb = nullptr; + bdd = nullptr; + pd = nullptr; + pdd = nullptr; + coefficients = nullptr; + pn3 = nullptr; + pc3 = nullptr; + pa4 = nullptr; + pb4 = nullptr; + pc4 = nullptr; + ind33l = nullptr; + ind33r = nullptr; + ind34l = nullptr; + ind34r = nullptr; + ind44l = nullptr; + ind44r = nullptr; + elemindex = nullptr; } /* ---------------------------------------------------------------------- */ PairPOD::~PairPOD() { - free_tempmemory(); - memory->destroy(podcoeff); - memory->destroy(newpodcoeff); - memory->destroy(gd); - memory->destroy(gdall); - memory->destroy(energycoeff); + memory->destroy(rij); + memory->destroy(fij); + memory->destroy(ei); + memory->destroy(typeai); + memory->destroy(numij); + memory->destroy(idxi); + memory->destroy(ai); + memory->destroy(aj); + memory->destroy(ti); + memory->destroy(tj); + memory->destroy(Phi); + memory->destroy(rbf); + memory->destroy(rbfx); + memory->destroy(rbfy); + memory->destroy(rbfz); + memory->destroy(abf); + memory->destroy(abfx); + memory->destroy(abfy); + memory->destroy(abfz); + memory->destroy(sumU); memory->destroy(forcecoeff); + memory->destroy(Centroids); + memory->destroy(Proj); + memory->destroy(bd); + memory->destroy(cb); + memory->destroy(bdd); + memory->destroy(pd); + memory->destroy(pdd); + memory->destroy(coefficients); + memory->destroy(pn3); + memory->destroy(pc3); + memory->destroy(pa4); + memory->destroy(pb4); + memory->destroy(pc4); + memory->destroy(ind33l); + memory->destroy(ind33r); + memory->destroy(ind34l); + memory->destroy(ind34r); + memory->destroy(ind44l); + memory->destroy(ind44r); + memory->destroy(elemindex); - delete podptr; + delete fastpodptr; if (allocated) { memory->destroy(setflag); @@ -75,14 +159,14 @@ void PairPOD::compute(int eflag, int vflag) { ev_init(eflag, vflag); - // we must enforce using F dot r, since we have no energy or stress tally calls. - vflag_fdotr = 1; - - if (peratom_warn && (vflag_atom || eflag_atom)) { - peratom_warn = false; - if (comm->me == 0) - error->warning(FLERR, "Pair style pod does not support per-atom energies or stresses"); - } +// // we must enforce using F dot r, since we have no energy or stress tally calls. +// vflag_fdotr = 1; +// +// if (peratom_warn && (vflag_atom || eflag_atom)) { +// peratom_warn = false; +// if (comm->me == 0) +// error->warning(FLERR, "Pair style pod does not support per-atom energies or stresses"); +// } double **x = atom->x; double **f = atom->f; @@ -91,65 +175,92 @@ void PairPOD::compute(int eflag, int vflag) int *type = atom->type; int *ilist = list->ilist; int inum = list->inum; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; - // initialize global descriptors to zero - - int nd1234 = podptr->pod.nd1234; - podptr->podArraySetValue(gd, 0.0, nd1234); + double rcutsq = rcut*rcut; + double evdwl = 0.0; + int blockMode = 0; + if (blockMode==0) { for (int ii = 0; ii < inum; ii++) { int i = ilist[ii]; int jnum = numneigh[i]; // allocate temporary memory - if (nijmax < jnum) { nijmax = MAX(nijmax, jnum); - nablockmax = 1; - free_tempmemory(); - estimate_tempmemory(); - allocate_tempmemory(); + fastpodptr->free_temp_memory(); + fastpodptr->allocate_temp_memory(nijmax); } - // get neighbor pairs for atom i + double *rij1 = &fastpodptr->tmpmem[0]; + double *fij1 = &fastpodptr->tmpmem[3*nijmax]; + double *tmp = &fastpodptr->tmpmem[6*nijmax]; + int *ai1 = &fastpodptr->tmpint[0]; + int *aj1 = &fastpodptr->tmpint[nijmax]; + int *ti1 = &fastpodptr->tmpint[2*nijmax]; + int *tj1 = &fastpodptr->tmpint[3*nijmax]; + lammpsNeighborList(rij1, ai1, aj1, ti1, tj1, x, firstneigh, type, map, numneigh, rcutsq, i); - lammpsNeighPairs(x, firstneigh, type, map, numneigh, i); + evdwl = fastpodptr->peratomenergyforce2(fij1, rij1, tmp, ti1, tj1, nij); - // compute global POD descriptors for atom i + // tally atomic energy to global energy + ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0); - podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nd1234], numneighsum, typeai, idxi, ti, - tj, 1, nij); + // tally atomic force to global force + tallyforce(f, fij1, ai1, aj1, nij); + + // tally atomic stress + if (vflag) { + for (int jj = 0; jj < nij; jj++) { + int j = aj1[jj]; + ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0, + fij1[0 + 3*jj],fij1[1 + 3*jj],fij1[2 + 3*jj], + -rij1[0 + 3*jj], -rij1[1 + 3*jj], -rij1[2 + 3*jj]); + } + } } + } + else if (blockMode == 1) { + // determine the number of atom blocks and divide atoms into blocks + nAtomBlocks = calculateNumberOfIntervals(inum, atomBlockSize); + if (nAtomBlocks > 100) nAtomBlocks = 100; + divideInterval(atomBlocks, inum, nAtomBlocks); - int nd22 = podptr->pod.nd22; - int nd23 = podptr->pod.nd23; - int nd24 = podptr->pod.nd24; - int nd33 = podptr->pod.nd33; - int nd34 = podptr->pod.nd34; - int nd44 = podptr->pod.nd44; - int nd = podptr->pod.nd; - bigint natom = atom->natoms; + int nmax = 0; + for (int block =0; blockcalculate_energy(energycoeff, forcecoeff, gd, gdall, newpodcoeff); + // get neighbor list for atoms i in the current atom block + NeighborList(x, firstneigh, type, map, ilist, numneigh, rcutsq, gi1); - for (int ii = 0; ii < inum; ii++) { - int i = ilist[ii]; + // compute atomic energy and force for the current atom block + blockatomenergyforce(ei, fij, ni, nij); - // get neighbor pairs for atom i + // tally atomic energy to global energy + tallyenergy(ei, gi1, ni); - lammpsNeighPairs(x, firstneigh, type, map, numneigh, i); + // tally atomic force to global force + tallyforce(f, fij, ai, aj, nij); - // compute atomic force for atom i + // tally atomic stress + if (vflag) tallystress(fij, rij, ai, aj, nlocal, nij); - podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum, typeai, idxi, ai, aj, ti, tj, - 1, nij); + //savedatafordebugging(); + } } if (vflag_fdotr) virial_fdotr_compute(); @@ -179,34 +290,23 @@ void PairPOD::coeff(int narg, char **arg) map = new int[np1]; allocated = 1; - if (narg < 4) utils::missing_cmd_args(FLERR, "pair_coeff", error); - map_element2type(narg - 4, arg + 4); + if (narg < 5) utils::missing_cmd_args(FLERR, "pair_coeff", error); std::string pod_file = std::string(arg[2]); // pod input file std::string coeff_file = std::string(arg[3]); // coefficient input file + map_element2type(narg - 4, arg + 4); - delete podptr; - podptr = new MLPOD(lmp, pod_file, coeff_file); + delete fastpodptr; + fastpodptr = new EAPOD(lmp, pod_file, coeff_file); - if (coeff_file != "") { - memory->destroy(podcoeff); - memory->destroy(newpodcoeff); - memory->destroy(energycoeff); - memory->destroy(forcecoeff); - memory->destroy(gd); - memory->destroy(gdall); - memory->create(podcoeff, podptr->pod.nd, "pair:podcoeff"); - memory->create(newpodcoeff, podptr->pod.nd, "pair:newpodcoeff"); - memory->create(energycoeff, podptr->pod.nd1234, "pair:energycoeff"); - memory->create(forcecoeff, podptr->pod.nd1234, "pair:forcecoeff"); - memory->create(gd, podptr->pod.nd1234, "pair:gd"); - memory->create(gdall, podptr->pod.nd1234, "pair:gdall"); - podptr->podArrayCopy(podcoeff, podptr->pod.coeff, podptr->pod.nd); - podptr->podArrayCopy(newpodcoeff, podptr->pod.coeff, podptr->pod.nd); - } + copy_data_from_pod_class(); + rcut = fastpodptr->rcut; + + memory->destroy(fastpodptr->tmpmem); + memory->destroy(fastpodptr->tmpint); for (int ii = 0; ii < np1; ii++) - for (int jj = 0; jj < np1; jj++) cutsq[ii][jj] = podptr->pod.rcut * podptr->pod.rcut; + for (int jj = 0; jj < np1; jj++) cutsq[ii][jj] = fastpodptr->rcut * fastpodptr->rcut; } /* ---------------------------------------------------------------------- @@ -222,7 +322,7 @@ void PairPOD::init_style() neighbor->add_request(this, NeighConst::REQ_FULL); // reset flag to print warning about per-atom energies or stresses - peratom_warn = true; + peratom_warn = false; } /* ---------------------------------------------------------------------- @@ -232,7 +332,16 @@ void PairPOD::init_style() double PairPOD::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); - return podptr->pod.rcut; + + double rcut = 0.0; + rcut = fastpodptr->rcut; + + return rcut; +} + +void PairPOD::allocate() +{ + allocated = 1; } /* ---------------------------------------------------------------------- @@ -245,67 +354,14 @@ double PairPOD::memory_usage() return bytes; } -void PairPOD::free_tempmemory() +void PairPOD::lammpsNeighborList(double *rij1, int *ai1, int *aj1, int *ti1, int *tj1, + double **x, int **firstneigh, int *atomtypes, int *map, + int *numneigh, double rcutsq, int gi) { - memory->destroy(rij); - memory->destroy(idxi); - memory->destroy(ai); - memory->destroy(aj); - memory->destroy(ti); - memory->destroy(tj); - memory->destroy(numneighsum); - memory->destroy(typeai); - memory->destroy(tmpmem); -} - -void PairPOD::allocate_tempmemory() -{ - memory->create(rij, dim * nijmax, "pair:rij"); - memory->create(idxi, nijmax, "pair:idxi"); - memory->create(ai, nijmax, "pair:ai"); - memory->create(aj, nijmax, "pair:aj"); - memory->create(ti, nijmax, "pair:ti"); - memory->create(tj, nijmax, "pair:tj"); - memory->create(numneighsum, nablockmax + 1, "pair:numneighsum"); - memory->create(typeai, nablockmax, "pair:typeai"); - memory->create(tmpmem, szd, "pair:tmpmem"); -} - -void PairPOD::estimate_tempmemory() -{ - int nrbf2 = podptr->pod.nbf2; - int nabf3 = podptr->pod.nabf3; - int nrbf3 = podptr->pod.nrbf3; - int ns2 = podptr->pod.ns2; - int ns3 = podptr->pod.ns3; - - szd = dim * nijmax + (1 + dim) * nijmax * MAX(nrbf2 + ns2, nrbf3 + ns3) + (nabf3 + 1) * 7; - int szsnap = 0; - if (podptr->sna.twojmax > 0) { - szsnap += nijmax * dim; - szsnap += MAX(2 * podptr->sna.idxu_max * nijmax, - 2 * podptr->sna.idxz_max * podptr->sna.ndoubles * - nablockmax); // (Ur, Ui) and (Zr, Zi) - szsnap += 2 * podptr->sna.idxu_max * dim * nijmax; // dUr, dUi - szsnap += MAX(podptr->sna.idxb_max * podptr->sna.ntriples * dim * nijmax, - 2 * podptr->sna.idxu_max * podptr->sna.nelements * - nablockmax); // dblist and (Utotr, Utoti) - } - - szd = MAX(szsnap, szd); - szd = nablockmax * (podptr->pod.nd1234) + szd; -} - -void PairPOD::lammpsNeighPairs(double **x, int **firstneigh, int *atomtypes, int *map, - int *numneigh, int gi) -{ - - double rcutsq = podptr->pod.rcut * podptr->pod.rcut; - nij = 0; int itype = map[atomtypes[gi]] + 1; + ti1[nij] = itype; int m = numneigh[gi]; - typeai[0] = itype; for (int l = 0; l < m; l++) { // loop over each atom around atom i int gj = firstneigh[gi][l]; // atom j double delx = x[gj][0] - x[gi][0]; // xj - xi @@ -313,18 +369,1778 @@ void PairPOD::lammpsNeighPairs(double **x, int **firstneigh, int *atomtypes, int double delz = x[gj][2] - x[gi][2]; // xj - xi double rsq = delx * delx + dely * dely + delz * delz; if (rsq < rcutsq && rsq > 1e-20) { - rij[nij * 3 + 0] = delx; - rij[nij * 3 + 1] = dely; - rij[nij * 3 + 2] = delz; - idxi[nij] = 0; - ai[nij] = gi; - aj[nij] = gj; - ti[nij] = itype; - tj[nij] = map[atomtypes[gj]] + 1; + rij1[nij * 3 + 0] = delx; + rij1[nij * 3 + 1] = dely; + rij1[nij * 3 + 2] = delz; + ai1[nij] = gi; + aj1[nij] = gj; + ti1[nij] = itype; + tj1[nij] = map[atomtypes[gj]] + 1; nij++; } } - - numneighsum[0] = 0; - numneighsum[1] = nij; +} + +void PairPOD::NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq, int gi1) +{ + for (int i=0; i 1e-20) n++; + } + numij[1+i] = n; + } +} + +int PairPOD::numberOfNeighbors() +{ + int n = 0; + for (int i=1; i<=ni; i++) { + n += numij[i]; + numij[i] += numij[i-1]; + } + return n; +} + +void PairPOD::NeighborList(double **x, int **firstneigh, int *atomtypes, int *map, + int *ilist, int *numneigh, double rcutsq, int gi1) +{ + for (int i=0; i 1e-20) { + int nij1 = nij0 + k; + rij[nij1 * 3 + 0] = delx; + rij[nij1 * 3 + 1] = dely; + rij[nij1 * 3 + 2] = delz; + idxi[nij1] = i; + ai[nij1] = gi; + aj[nij1] = gj; + ti[nij1] = itype; + tj[nij1] = map[atomtypes[gj]] + 1; + k++; + } + } + } +} + +void PairPOD::tallyforce(double **force, double *fij, int *ai, int *aj, int N) +{ + for (int n=0; nnelements; // number of elements + onebody = fastpodptr->onebody; // one-body descriptors + besseldegree = fastpodptr->besseldegree; // degree of Bessel functions + inversedegree = fastpodptr->inversedegree; // degree of inverse functions + nbesselpars = fastpodptr->nbesselpars; // number of Bessel parameters + nCoeffPerElement = fastpodptr->nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters) + ns = fastpodptr->ns; // number of snapshots for radial basis functions + nl1 = fastpodptr->nl1; // number of one-body descriptors + nl2 = fastpodptr->nl2; // number of two-body descriptors + nl3 = fastpodptr->nl3; // number of three-body descriptors + nl4 = fastpodptr->nl4; // number of four-body descriptors + nl23 = fastpodptr->nl23; // number of two-body x three-body descriptors + nl33 = fastpodptr->nl33; // number of three-body x three-body descriptors + nl34 = fastpodptr->nl34; // number of three-body x four-body descriptors + nl44 = fastpodptr->nl44; // number of four-body x four-body descriptors + nl = fastpodptr->nl; // number of local descriptors + nrbf2 = fastpodptr->nrbf2; + nrbf3 = fastpodptr->nrbf3; + nrbf4 = fastpodptr->nrbf4; + nrbfmax = fastpodptr->nrbfmax; // number of radial basis functions + nabf3 = fastpodptr->nabf3; // number of three-body angular basis functions + nabf4 = fastpodptr->nabf4; // number of four-body angular basis functions + K3 = fastpodptr->K3; // number of three-body monomials + K4 = fastpodptr->K4; // number of four-body monomials + Q4 = fastpodptr->Q4; // number of four-body monomial coefficients + nClusters = fastpodptr->nClusters; // number of environment clusters + nComponents = fastpodptr->nComponents; // number of principal components + Mdesc = fastpodptr->Mdesc; // number of base descriptors + + rin = fastpodptr->rin; + rcut = fastpodptr->rcut; + rmax = rcut - rin; + besselparams[0] = fastpodptr->besselparams[0]; + besselparams[1] = fastpodptr->besselparams[1]; + besselparams[2] = fastpodptr->besselparams[2]; + + memory->create(abftm, 4*K3, "abftm"); + memory->create(elemindex, nelements*nelements, "elemindex"); + for (int i=0; ielemindex[i]; + + memory->create(Phi, ns * ns, "pair_pod:Phi"); + for (int i=0; iPhi[i]; + + memory->create(coefficients, nCoeffPerElement * nelements, "pair_pod:coefficients"); + for (int i=0; icoeff[i]; + + if (nClusters > 1) { + memory->create(Proj, Mdesc * nComponents * nelements, "pair_pod:Proj"); + for (int i=0; iProj[i]; + + memory->create(Centroids, nClusters * nComponents * nelements, "pair_pod:Centroids"); + for (int i=0; iCentroids[i]; + } + + memory->create(pn3, nabf3+1, "pn3"); // array stores the number of monomials for each degree + memory->create(pq3, K3*2, "pq3"); // array needed for the recursive computation of the angular basis functions + memory->create(pc3, K3, "pc3"); // array needed for the computation of the three-body descriptors + memory->create(pa4, nabf4+1, "pa4"); // this array is a subset of the array {0, 1, 4, 10, 19, 29, 47, 74, 89, 119, 155, 209, 230, 275, 335, 425, 533, 561, 624, 714, 849, 949, 1129, 1345} + memory->create(pb4, Q4*3, "pb4"); // array stores the indices of the monomials needed for the computation of the angular basis functions + memory->create(pc4, Q4, "pc4"); // array of monomial coefficients needed for the computation of the four-body descriptors + for (int i=0; ipn3[i]; + for (int i=0; ipc3[i]; + for (int i=0; ipq3[i]; + for (int i=0; ipa4[i]; + for (int i=0; ipb4[i]; + for (int i=0; ipc4[i]; + + memory->create(ind33l, nl33, "pair_pod:ind33l"); + memory->create(ind33r, nl33, "pair_pod:ind33r"); + memory->create(ind34l, nl34, "pair_pod:ind34l"); + memory->create(ind34r, nl34, "pair_pod:ind34r"); + memory->create(ind44l, nl44, "pair_pod:ind44l"); + memory->create(ind44r, nl44, "pair_pod:ind44r"); + for (int i=0; iind33l[i]; + for (int i=0; iind33r[i]; + for (int i=0; iind34l[i]; + for (int i=0; iind34r[i]; + for (int i=0; iind44l[i]; + for (int i=0; iind44r[i]; +} + +void PairPOD::grow_atoms(int Ni) +{ + if (Ni > nimax) { + memory->destroy(ei); + memory->destroy(typeai); + memory->destroy(numij); + memory->destroy(sumU); + memory->destroy(forcecoeff); + memory->destroy(bd); + memory->destroy(cb); + memory->destroy(pd); + nimax = Ni; + memory->create(ei, nimax, "pair_pod:ei"); + memory->create(typeai, nimax, "pair_pod:typeai"); + memory->create(numij, nimax+1, "pair_pod:typeai"); + int n = nimax * nelements * K3 * nrbfmax; + memory->create(sumU, n , "pair_pod:sumU"); + memory->create(forcecoeff, n , "pair_pod:forcecoeff"); + memory->create(bd, nimax * Mdesc, "pair_pod:bd"); + memory->create(cb, nimax * Mdesc, "pair_pod:bd"); + if (nClusters > 1) memory->create(pd, nimax * (1 + nComponents + 3*nClusters), "pair_pod:pd"); + + for (int i=0; i<=nimax; i++) numij[i] = 0; + } +} + +void PairPOD::grow_pairs(int Nij) +{ + if (Nij > nijmax) { + memory->destroy(rij); + memory->destroy(fij); + memory->destroy(idxi); + memory->destroy(ai); + memory->destroy(aj); + memory->destroy(ti); + memory->destroy(tj); + memory->destroy(rbf); + memory->destroy(rbfx); + memory->destroy(rbfy); + memory->destroy(rbfz); + memory->destroy(abf); + memory->destroy(abfx); + memory->destroy(abfy); + memory->destroy(abfz); + nijmax = Nij; + memory->create(rij, 3 * nijmax, "pair_pod:r_ij"); + memory->create(fij, 3 * nijmax, "pair_pod:f_ij"); + memory->create(idxi, nijmax, "pair_pod:idxi"); + memory->create(ai, nijmax, "pair_pod:ai"); + memory->create(aj, nijmax, "pair_pod:aj"); + memory->create(ti, nijmax, "pair_pod:ti"); + memory->create(tj, nijmax, "pair_pod:tj"); + memory->create(rbf, nijmax * nrbfmax, "pair_pod:rbf"); + memory->create(rbfx, nijmax * nrbfmax, "pair_pod:rbfx"); + memory->create(rbfy, nijmax * nrbfmax, "pair_pod:rbfy"); + memory->create(rbfz, nijmax * nrbfmax, "pair_pod:rbfz"); + int kmax = (K3 > ns) ? K3 : ns; + memory->create(abf, nijmax * kmax, "pair_pod:abf"); + memory->create(abfx, nijmax * kmax, "pair_pod:abfx"); + memory->create(abfy, nijmax * kmax, "pair_pod:abfy"); + memory->create(abfz, nijmax * kmax, "pair_pod:abfz"); + } +} + +void PairPOD::divideInterval(int *intervals, int N, int M) +{ + int intervalSize = N / M; // Basic size of each interval + int remainder = N % M; // Remainder to distribute + intervals[0] = 1; // Start of the first interval + for (int i = 1; i <= M; i++) { + intervals[i] = intervals[i - 1] + intervalSize + (remainder > 0 ? 1 : 0); + if (remainder > 0) { + remainder--; + } + } +} + +int PairPOD::calculateNumberOfIntervals(int N, int intervalSize) +{ + int M = N / intervalSize; + if (N % intervalSize != 0) { + M++; // Add an additional interval to cover the remainder + } + + return M; +} + +void PairPOD::radialbasis(double *rbft, double *rbftx, double *rbfty, double *rbftz, double *rij, int Nij) +{ + // Loop over all neighboring atoms + for (int n=0; n0) && (Nij>0)) { + twobodydesc(d2, Ni, Nij); + } + + if ((nl3 > 0) && (Nij>1)) { + angularbasis(abftm, &abftm[K3], &abftm[2*K3], &abftm[3*K3], Nij); + radialangularsum2(Ni); + threebodydesc(d3, Ni); + + if ((nl33>0) && (Nij>3)) { + crossdesc(d33, d3, d3, ind33l, ind33r, nl33, Ni); + } + + if ((nl4 > 0) && (Nij>2)) { + if (K4 < K3) { + fourbodydesc(d4, Ni); + } + + if ((nl34>0) && (Nij>4)) { + crossdesc(d34, d3, d4, ind34l, ind34r, nl34, Ni); + } + + if ((nl44>0) && (Nij>5)) { + crossdesc(d44, d4, d4, ind44l, ind44r, nl44, Ni); + } + } + } +} + +void PairPOD::blockatombase_descriptors(double *bd1, double *bdd1, int Ni, int Nij) +{ + for (int i=0; i0) && (Nij>0)) { + twobodydescderiv(d2, dd2, Ni, Nij); + } + + if ((nl3 > 0) && (Nij>1)) { + angularbasis(abftm, &abftm[K3], &abftm[2*K3], &abftm[3*K3], Nij); + radialangularsum2(Ni); + + threebodydesc(d3, Ni); + threebodydescderiv(dd3, Nij); + + if ((nl33>0) && (Nij>3)) { + crossdesc(d33, d3, d3, ind33l, ind33r, nl33, Ni); + crossdescderiv(dd33, d3, d3, dd3, dd3, ind33l, ind33r, idxi, nl33, Ni, Nij); + } + + if ((nl4 > 0) && (Nij>2)) { + if (K4 < K3) { + fourbodydesc(d4, Ni); + fourbodydescderiv(dd4, Nij); + } + + if ((nl34>0) && (Nij>4)) { + crossdesc(d34, d3, d4, ind34l, ind34r, nl34, Ni); + crossdescderiv(dd34, d3, d4, dd3, dd4, ind34l, ind34r, idxi, nl34, Ni, Nij); + } + + if ((nl44>0) && (Nij>5)) { + crossdesc(d44, d4, d4, ind44l, ind44r, nl44, Ni); + crossdescderiv(dd44, d4, d4, dd4, dd4, ind44l, ind44r, idxi, nl44, Ni, Nij); + } + } + } +} + +void PairPOD::blockatom_base_coefficients(double *ei, double *cb, double *B, int Ni) +{ + double *cefs = &coefficients[0]; + int *tyai = &typeai[0]; + + int nDes = Mdesc; + int nCoeff = nCoeffPerElement; + + for (int n=0; n 1) { + blockatom_environment_descriptors(ei, cb, bd, Ni); + } + else { + blockatom_base_coefficients(ei, cb, bd, Ni); + } +} + +void PairPOD::blockatom_forces(double *fij, int Ni, int Nij) +{ + + int nld = nl2 + nl3 + nl4; + for (int i=0; i<3*Nij*nld; i++) bdd[i] = 0.0; + + double *dd2 = &bdd[0]; // 3*Nj*nl2 + double *dd3 = &bdd[3*Nij*nl2]; // 3*Nj*nl3 + double *dd4 = &bdd[3*Nij*(nl2+nl3)]; // 3*Nj*nl4 + + if ((nl2 > 0) && (Nij>0)) twobodydescderiv(dd2, Nij); + if ((nl3 > 0) && (Nij>1)) threebodydescderiv(dd3, Nij); + if ((nl4 > 0) && (Nij>2)) fourbodydescderiv(dd4, Nij); + + double *d3 = &bd[Ni*nl2]; // nl3 + double *d4 = &bd[Ni*(nl2 + nl3)]; // nl4 + //double *cb2 = &cb[0]; // nl2 + double *cb3 = &cb[Ni*nl2]; // nl3 + double *cb4 = &cb[Ni*(nl2 + nl3)]; // nl4 + double *cb33 = &cb[Ni*(nl2 + nl3 + nl4)]; // nl33 + double *cb34 = &cb[Ni*(nl2 + nl3 + nl4 + nl33)]; // nl34 + double *cb44 = &cb[Ni*(nl2 + nl3 + nl4 + nl33 + nl34)]; // nl44 + + if (nl33>0) crossdesc_reduction(cb3, cb3, cb33, d3, d3, ind33l, ind33r, nl33, Ni); + + if (nl34>0) crossdesc_reduction(cb3, cb4, cb34, d3, d4, ind34l, ind34r, nl34, Ni); + + if (nl44>0) crossdesc_reduction(cb4, cb4, cb44, d4, d4, ind44l, ind44r, nl44, Ni); + + int N3 = 3*Nij; + for (int n=0; n 1) { + blockatom_environment_descriptors(ei, cb, bd, Ni); + } + else { + blockatom_base_coefficients(ei, cb, bd, Ni); + } + + double *d3 = &bd[Ni*nl2]; // nl3 + double *d4 = &bd[Ni*(nl2 + nl3)]; // nl4 + double *cb2 = &cb[0]; // nl3 + double *cb3 = &cb[Ni*nl2]; // nl3 + double *cb4 = &cb[Ni*(nl2 + nl3)]; // nl4 + double *cb33 = &cb[Ni*(nl2 + nl3 + nl4)]; // nl33 + double *cb34 = &cb[Ni*(nl2 + nl3 + nl4 + nl33)]; // nl34 + double *cb44 = &cb[Ni*(nl2 + nl3 + nl4 + nl33 + nl34)]; // nl44 + + if ((nl33>0) && (Nij>3)) { + crossdesc_reduction(cb3, cb3, cb33, d3, d3, ind33l, ind33r, nl33, Ni); + } + if ((nl34>0) && (Nij>4)) { + crossdesc_reduction(cb3, cb4, cb34, d3, d4, ind34l, ind34r, nl34, Ni); + } + if ((nl44>0) && (Nij>5)) { + crossdesc_reduction(cb4, cb4, cb44, d4, d4, ind44l, ind44r, nl44, Ni); + } + + for (int n=0; n<3*Nij; n++) fij[n] = 0; + if ((nl2 > 0) && (Nij>0)) twobody_forces(fij, cb2, Ni, Nij); + + // Initialize forcecoeff to zero + std::fill(forcecoeff, forcecoeff + Ni * nelements * K3 * nrbf3, 0.0); + if ((nl3 > 0) && (Nij>1)) threebody_forcecoeff(forcecoeff, cb3, Ni); + if ((nl4 > 0) && (Nij>2)) fourbody_forcecoeff(forcecoeff, cb4, Ni); + if ((nl3 > 0) && (Nij>1)) allbody_forces(fij, forcecoeff, Nij); +} + +void PairPOD::blockatomenergyforce(double *ei, double *fij, int Ni, int Nij) +{ + blockatom_energyforce(ei, fij, Ni, Nij); +} + +void PairPOD::savematrix2binfile(std::string filename, double *A, int nrows, int ncols) +{ + FILE *fp = fopen(filename.c_str(), "wb"); + double sz[2]; + sz[0] = (double) nrows; + sz[1] = (double) ncols; + fwrite( reinterpret_cast( sz ), sizeof(double) * (2), 1, fp); + fwrite( reinterpret_cast( A ), sizeof(double) * (nrows*ncols), 1, fp); + fclose(fp); +} + +void PairPOD::saveintmatrix2binfile(std::string filename, int *A, int nrows, int ncols) +{ + FILE *fp = fopen(filename.c_str(), "wb"); + int sz[2]; + sz[0] = nrows; + sz[1] = ncols; + fwrite( reinterpret_cast( sz ), sizeof(int) * (2), 1, fp); + fwrite( reinterpret_cast( A ), sizeof(int) * (nrows*ncols), 1, fp); + fclose(fp); +} + +void PairPOD::savedatafordebugging() +{ + saveintmatrix2binfile("podtypeai.bin", typeai, ni, 1); + saveintmatrix2binfile("podnumij.bin", numij, ni+1, 1); + saveintmatrix2binfile("podai.bin", ai, nij, 1); + saveintmatrix2binfile("podaj.bin", aj, nij, 1); + saveintmatrix2binfile("podti.bin", ti, nij, 1); + saveintmatrix2binfile("podtj.bin", tj, nij, 1); + saveintmatrix2binfile("podidxi.bin", idxi, nij, 1); + savematrix2binfile("podrbf.bin", rbf, nrbfmax, nij); + savematrix2binfile("podrbfx.bin", rbfx, nrbfmax, nij); + savematrix2binfile("podrbfy.bin", rbfy, nrbfmax, nij); + savematrix2binfile("podrbfz.bin", rbfz, nrbfmax, nij); + int kmax = (K3 > ns) ? K3 : ns; + savematrix2binfile("podabf.bin", abf, kmax, nij); + savematrix2binfile("podabfx.bin", abfx, kmax, nij); + savematrix2binfile("podabfy.bin", abfy, kmax, nij); + savematrix2binfile("podabfz.bin", abfz, kmax, nij); + savematrix2binfile("podbdd.bin", bdd, 3*nij, Mdesc); + savematrix2binfile("podbd.bin", bd, ni, Mdesc); + savematrix2binfile("podsumU.bin", sumU, nelements * K3 * nrbfmax, ni); + savematrix2binfile("podrij.bin", rij, 3, nij); + savematrix2binfile("podfij.bin", fij, 3, nij); + savematrix2binfile("podei.bin", ei, ni, 1); + error->all(FLERR, "Save data and stop the run for debugging"); } diff --git a/src/ML-POD/pair_pod.h b/src/ML-POD/pair_pod.h index 62b6e99f3b..fe1b9ab024 100644 --- a/src/ML-POD/pair_pod.h +++ b/src/ML-POD/pair_pod.h @@ -36,41 +36,135 @@ class PairPOD : public Pair { double init_one(int, int) override; double memory_usage() override; - int dim; // typically 3 + void lammpsNeighborList(double *rij1, int *ai1, int *aj1, int *ti1, int *tj1, double **x, + int **firstneigh, int *atomtype, int *map, int *numneigh, double rcutsq, + int i); + void NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq, + int i1); + void NeighborList(double **x, int **firstneigh, int *atomtype, int *map, int *ilist, + int *numneigh, double rcutsq, int i1); + void tallyenergy(double *ei, int istart, int Ni); + void tallystress(double *fij, double *rij, int *ai, int *aj, int nlocal, int N); + void tallyforce(double **force, double *fij, int *ai, int *aj, int N); + void divideInterval(int *intervals, int N, int M); + int calculateNumberOfIntervals(int N, int intervalSize); + int numberOfNeighbors(); - double *gd; // global linear descriptors - double *gdall; // global linear descriptors summed over all MPI ranks - double *podcoeff; // POD coefficients - double *newpodcoeff; // normalized POD coefficients - double *energycoeff; // energy coefficients - double *forcecoeff; // force coefficients + void copy_data_from_pod_class(); + void radialbasis(double *rbft, double *rbftx, double *rbfty, double *rbftz, double *rij, int Nij); + void orthogonalradialbasis(int Nij); + void angularbasis(double *tm, double *tmu, double *tmv, double *tmw, int N); + void radialangularsum(int Ni, int Nij); + void radialangularsum2(int Ni); + void twobodydesc(double *d2, int Ni, int Nij); + void twobodydescderiv(double *dd2, int Nij); + void twobodydescderiv(double *d2, double *dd2, int Ni, int Nij); + void threebodydesc(double *d3, int Ni); + void threebodydescderiv(double *dd3, int Nij); + void extractsumU(int Ni); + void fourbodydesc(double *d4, int Ni); + void fourbodydescderiv(double *dd4, int Nij); + void crossdesc(double *d12, double *d1, double *d2, int *ind1, int *ind2, int n12, int Ni); + void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2, int *ind1, + int *ind2, int *idxi, int n12, int Ni, int Nij); + void blockatombase_descriptors(double *bd1, double *bdd1, int Ni, int Nij); + void blockatomenergyforce(double *ei, double *fij, int Ni, int Nij); - void estimate_tempmemory(); - void free_tempmemory(); - void allocate_tempmemory(); + void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, double *d2, int *ind1, + int *ind2, int n12, int Ni); + void blockatom_base_descriptors(double *bd1, int Ni, int Nij); + void blockatom_base_coefficients(double *ei, double *cb, double *B, int Ni); + void blockatom_environment_descriptors(double *ei, double *cb, double *B, int Ni); + void blockatom_energyforce(double *ei, double *fij, int Ni, int Nij); + void blockatom_energies(double *ei, int Ni, int Nij); + void blockatom_forces(double *fij, int Ni, int Nij); - void lammpsNeighPairs(double **x, int **firstneigh, int *atomtype, int *map, int *numneigh, - int i); + void twobody_forces(double *fij, double *cb2, int Ni, int Nij); + void threebody_forces(double *fij, double *cb3, int Ni, int Nij); + void fourbody_forces(double *fij, double *cb4, int Ni, int Nij); + + void threebody_forcecoeff(double *fb3, double *cb3, int Ni); + void fourbody_forcecoeff(double *fb4, double *cb4, int Ni); + void allbody_forces(double *fij, double *forcecoeff, int Nij); + + void savematrix2binfile(std::string filename, double *A, int nrows, int ncols); + void saveintmatrix2binfile(std::string filename, int *A, int nrows, int ncols); + void savedatafordebugging(); protected: - int nablockmax; // maximum number of atoms per computation block - int nij; // number of atom pairs - int nijmax; // maximum number of atom pairs - int szd; // size of tmpmem + class EAPOD *fastpodptr; + virtual void allocate(); + void grow_atoms(int Ni); + void grow_pairs(int Nij); - class MLPOD *podptr; + int atomBlockSize; // size of each atom block + int nAtomBlocks; // number of atoms blocks + int atomBlocks[101]; // atom blocks - // temporary arrays for computation blocks + int ni; // total number of atoms i + int nij; // total number of pairs (i,j) + int nimax; // maximum number of atoms i + int nijmax; // maximum number of pairs (i,j) - double *tmpmem; // temporary memory - int *typeai; // types of atoms I only - int *numneighsum; // cumulative sum for an array of numbers of neighbors - double *rij; // (xj - xi) for all pairs (I, J) - int *idxi; // storing linear indices for all pairs (I, J) - int *ai; // IDs of atoms I for all pairs (I, J) - int *aj; // IDs of atoms J for all pairs (I, J) - int *ti; // types of atoms I for all pairs (I, J) - int *tj; // types of atoms J for all pairs (I, J) + int nelements; // number of elements + int onebody; // one-body descriptors + int besseldegree; // degree of Bessel functions + int inversedegree; // degree of inverse functions + int nbesselpars; // number of Bessel parameters + int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters) + int ns; // number of snapshots for radial basis functions + int nl1, nl2, nl3, nl4, nl23, nl33, nl34, nl44, nl; // number of local descriptors + int nrbf2, nrbf3, nrbf4, nrbfmax; // number of radial basis functions + int nabf3, nabf4; // number of angular basis functions + int K3, K4, Q4; // number of monomials + + // environmental variables + int nClusters; // number of environment clusters + int nComponents; // number of principal components + int Mdesc; // number of base descriptors + + double rin; // inner cut-off radius + double rcut; // outer cut-off radius + double rmax; // rcut - rin + + double *rij; // (xj - xi) for all pairs (I, J) + double *fij; // force for all pairs (I, J) + double *ei; // energy for each atom I + int *typeai; // types of atoms I only + int *numij; // number of pairs (I, J) for each atom I + int *idxi; // storing linear indices of atom I for all pairs (I, J) + int *ai; // IDs of atoms I for all pairs (I, J) + int *aj; // IDs of atoms J for all pairs (I, J) + int *ti; // types of atoms I for all pairs (I, J) + int *tj; // types of atoms J for all pairs (I, J) + + double besselparams[3]; + double *Phi; // eigenvectors matrix ns x ns + double *rbf; // radial basis functions nij x nrbfmax + double *rbfx; // x-derivatives of radial basis functions nij x nrbfmax + double *rbfy; // y-derivatives of radial basis functions nij x nrbfmax + double *rbfz; // z-derivatives of radial basis functions nij x nrbfmax + double *abf; // angular basis functions nij x K3 + double *abfx; // x-derivatives of angular basis functions nij x K3 + double *abfy; // y-derivatives of angular basis functions nij x K3 + double *abfz; // z-derivatives of angular basis functions nij x K3 + double *abftm; // angular basis functions 4 x K3 + double *sumU; // sum of radial basis functions ni x K3 x nrbfmax x nelements + double *forcecoeff; // force coefficients ni x K3 x nrbfmax x nelements + double *Proj; // PCA Projection matrix + double *Centroids; // centroids of the clusters + double *bd; // base descriptors ni x Mdesc + double *cb; // force coefficients for base descriptors ni x Mdesc + double *pd; // environment probability descriptors ni x nClusters + double *bdd; // base descriptors derivatives 3 x nij x Mdesc + double *pdd; // environment probability descriptors derivatives 3 x nij x nClusters + double *coefficients; // coefficients nCoeffPerElement x nelements + int *pq3, *pn3, *pc3; // arrays to compute 3-body angular basis functions + int *pa4, *pb4, *pc4; // arrays to compute 4-body angular basis functions + int *ind33l, *ind33r; // nl33 + int *ind34l, *ind34r; // nl34 + int *ind44l, *ind44r; // nl44 + int *elemindex; bool peratom_warn; // print warning about missing per-atom energies or stresses }; diff --git a/src/ML-UF3/pair_uf3.cpp b/src/ML-UF3/pair_uf3.cpp new file mode 100644 index 0000000000..a952403287 --- /dev/null +++ b/src/ML-UF3/pair_uf3.cpp @@ -0,0 +1,1957 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Ajinkya Hire (Univ. of Florida), + Hendrik Kraß (Univ. of Constance), + Matthias Rupp (Luxembourg Institute of Science and Technology), + Richard Hennig (Univ of Florida) +---------------------------------------------------------------------- */ + +#include "pair_uf3.h" + +#include "uf3_bspline_basis2.h" +#include "uf3_bspline_basis3.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "text_file_reader.h" + +#include +#include + +using namespace LAMMPS_NS; +using MathConst::THIRD; + +/* ---------------------------------------------------------------------- */ + +PairUF3::PairUF3(LAMMPS *lmp) : + Pair(lmp), setflag_3b(nullptr), knot_spacing_type_2b(nullptr), knot_spacing_type_3b(nullptr), + cut(nullptr), cut_3b(nullptr), cut_3b_list(nullptr), min_cut_3b(nullptr), + knot_spacing_2b(nullptr), knot_spacing_3b(nullptr), n2b_knots_array(nullptr), + n2b_coeff_array(nullptr), n2b_knots_array_size(nullptr), n2b_coeff_array_size(nullptr), + cached_constants_2b(nullptr), cached_constants_2b_deri(nullptr), map_3b(nullptr), + n3b_knots_array(nullptr), n3b_coeff_array(nullptr), n3b_knots_array_size(nullptr), + n3b_coeff_array_size(nullptr), coeff_for_der_jk(nullptr), coeff_for_der_ik(nullptr), + coeff_for_der_ij(nullptr), cached_constants_3b(nullptr), cached_constants_3b_deri(nullptr), + neighshort(nullptr), get_starting_index_2b(nullptr), get_starting_index_3b(nullptr) +{ + single_enable = 1; // 1 if single() routine exists + one_coeff = 1; // 1 if allows only one coeff * * call + restartinfo = 0; // 1 if pair style writes restart info + maxshort = 20; + centroidstressflag = CENTROID_AVAIL; + manybody_flag = 1; + bsplines_created = 0; + pot_3b = false; + nbody_flag = 3; + max_num_knots_2b = 0; + max_num_coeff_2b = 0; + max_num_knots_3b = 0; + max_num_coeff_3b = 0; + tot_interaction_count_3b = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairUF3::~PairUF3() +{ + if (copymode) return; + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + memory->destroy(knot_spacing_type_2b); + memory->destroy(knot_spacing_2b); + memory->destroy(n2b_knots_array_size); + memory->destroy(n2b_coeff_array_size); + memory->destroy(n2b_knots_array); + memory->destroy(n2b_coeff_array); + memory->destroy(cached_constants_2b); + memory->destroy(cached_constants_2b_deri); + + if (pot_3b) { + memory->destroy(setflag_3b); + memory->destroy(cut_3b); + memory->destroy(cut_3b_list); + memory->destroy(min_cut_3b); + memory->destroy(neighshort); + memory->destroy(knot_spacing_type_3b); + memory->destroy(knot_spacing_3b); + memory->destroy(map_3b); + memory->destroy(n3b_knots_array_size); + memory->destroy(n3b_coeff_array_size); + memory->destroy(n3b_knots_array); + memory->destroy(n3b_coeff_array); + memory->destroy(coeff_for_der_jk); + memory->destroy(coeff_for_der_ik); + memory->destroy(coeff_for_der_ij); + memory->destroy(cached_constants_3b); + memory->destroy(cached_constants_3b_deri); + } + } +} + +/* ---------------------------------------------------------------------- + * global settings + * ---------------------------------------------------------------------- */ + +void PairUF3::settings(int narg, char **arg) +{ + + if (narg != 1) + error->all(FLERR, + "Invalid number of arguments for pair_style uf3" + " Are you using a 2-body or 2 & 3-body UF potential?"); + nbody_flag = utils::numeric(FLERR, arg[0], true, lmp); + const int num_of_elements = atom->ntypes; + if (nbody_flag == 2) { + pot_3b = false; + manybody_flag = 0; + } else if (nbody_flag == 3) { + pot_3b = true; + single_enable = 0; + } else + error->all(FLERR, "Pair style uf3 not (yet) implemented for {}-body terms", nbody_flag); +} + +/* ---------------------------------------------------------------------- + * set coeffs for one or more type pairs + * ---------------------------------------------------------------------- */ +void PairUF3::coeff(int narg, char **arg) +{ + if (narg != 3 + atom->ntypes) + error->all(FLERR, "Invalid number of arguments uf3 in pair coeffs."); + + if (!allocated) allocate(); + + map_element2type(narg - 3, arg + 3, false); + + if (comm->me == 0) uf3_read_unified_pot_file(arg[2]); + communicate(); +} + +void PairUF3::allocate() +{ + allocated = 1; + const int num_of_elements = atom->ntypes; + + map = new int[num_of_elements + 1]; //No need to delete map as ~Pair deletes map + + // Contains info about wether UF potential were found for type i and j + memory->create(setflag, num_of_elements + 1, num_of_elements + 1, "pair:setflag"); + + // Contains info about 2-body cutoff distance for type i and j + // cutsq is the global variable + // Even though we are making cutsq don't manually change the default values + // Lammps take care of setting the value + memory->create(cutsq, num_of_elements + 1, num_of_elements + 1, "pair:cutsq"); + // cut is specific to this pair style. We will set the values in cut + memory->create(cut, num_of_elements + 1, num_of_elements + 1, "pair:cut"); + //Contains info about type of knot_spacing--> 0 = uniform knot spacing (default) + //1 = non-uniform knot spacing + memory->create(knot_spacing_type_2b, num_of_elements + 1, num_of_elements + 1, + "pair:knot_spacing_type_2b"); + memory->create(knot_spacing_2b, num_of_elements + 1, num_of_elements + 1, "pair:knot_spacing_2b"); + + //Contains size of 2b knots vectors and 2b coeff matrices + memory->create(n2b_knots_array_size, num_of_elements + 1, num_of_elements + 1, + "pair:n2b_knots_array_size"); + memory->create(n2b_coeff_array_size, num_of_elements + 1, num_of_elements + 1, + "pair:n2b_coeff_array_size"); + + if (pot_3b) { + // Contains info about wether UF potential were found for type i, j and k + memory->create(setflag_3b, num_of_elements + 1, num_of_elements + 1, num_of_elements + 1, + "pair:setflag_3b"); + // Contains info about 3-body cutoff distance for type i, j and k + memory->create(cut_3b, num_of_elements + 1, num_of_elements + 1, num_of_elements + 1, + "pair:cut_3b"); + // Contains info about 3-body cutoff distance for type i, j and k + // for constructing 3-body list + memory->create(cut_3b_list, num_of_elements + 1, num_of_elements + 1, "pair:cut_3b_list"); + // Contains info about minimum 3-body cutoff distance for type i, j and k + memory->create(min_cut_3b, num_of_elements + 1, num_of_elements + 1, num_of_elements + 1, 3, + "pair:min_cut_3b"); + //Contains info about type of knot_spacing--> 0 = uniform knot spacing (default) + //1 = non-uniform knot spacing + memory->create(knot_spacing_type_3b, num_of_elements + 1, num_of_elements + 1, + num_of_elements + 1, "pair:knot_spacing_type_3b"); + memory->create(knot_spacing_3b, num_of_elements + 1, num_of_elements + 1, num_of_elements + 1, + 3, "pair:knot_spacing_3b"); + + tot_interaction_count_3b = 0; + //conatins map of I-J-K interaction + memory->create(map_3b, num_of_elements + 1, num_of_elements + 1, num_of_elements + 1, + "pair:map_3b"); + + // setting cut_3b, setflag = 0 and map_3b + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + cut_3b_list[i][j] = 0; + setflag[i][j] = 0; + n2b_coeff_array_size[i][j] = 0; + n2b_knots_array_size[i][j] = 0; + + for (int k = 1; k < num_of_elements + 1; k++) { + cut_3b[i][j][k] = 0; + min_cut_3b[i][j][k][0] = 0; + min_cut_3b[i][j][k][1] = 0; + min_cut_3b[i][j][k][2] = 0; + + setflag_3b[i][j][k] = 0; + + map_3b[i][j][k] = tot_interaction_count_3b; + tot_interaction_count_3b++; + } + } + } + + //contains sizes of 3b knots vectors and 3b coeff matrices + memory->create(n3b_knots_array_size, tot_interaction_count_3b, 3, "pair:n3b_knots_array_size"); + memory->create(n3b_coeff_array_size, tot_interaction_count_3b, 3, "pair:n3b_coeff_array_size"); + for (int i = 0; i < tot_interaction_count_3b; i++) { + n3b_coeff_array_size[i][0] = 0; + n3b_coeff_array_size[i][1] = 0; + n3b_coeff_array_size[i][2] = 0; + + n3b_knots_array_size[i][0] = 0; + n3b_knots_array_size[i][1] = 0; + n3b_knots_array_size[i][2] = 0; + } + + memory->create(neighshort, maxshort, "pair:neighshort"); + } +} + +void PairUF3::uf3_read_unified_pot_file(char *potf_name) +{ + //Go through the entire file and get the sizes of knot vectors and + //coeff vectors/matrices + // + //Create arrays + // + //Go through the file again and read the knots and coefficients + // + + const int num_of_elements = atom->ntypes; + + //if (true) { + FILE *fp = utils::open_potential(potf_name, lmp, nullptr); + if (!fp) + error->all(FLERR, "Cannot open UF3 potential file {}: {}", potf_name, utils::getsyserror()); + + TextFileReader txtfilereader(fp, "UF3:POTFP"); + txtfilereader.ignore_comments = false; + + //while loop over the entire file, find blocks starting with #UF3 POT + //if block found read the very next line to determine 2B or 3B block + //if 2B read the knot vector and coeff vector size + //if 3B read the knot vectors and coeff matrix size + int line_counter = 1; + char *line; + while ((line = txtfilereader.next_line(1))) { + Tokenizer line_token(line); + + //Detect start of a block + if (line_token.contains("#UF3 POT")) { + //Block start detected + if (line_token.contains("UNITS:") == 0) + error->all(FLERR, + "UF3: {} file does not contain the 'UNITS:' metadata in " + "the header", + potf_name); + + //Read the 2nd line of the block + std::string temp_line = txtfilereader.next_line(1); + line_counter++; + ValueTokenizer fp2nd_line(temp_line); + + std::string nbody_on_file = fp2nd_line.next_string(); + if (nbody_on_file == "2B") { + //2B block + if (fp2nd_line.count() != 6) + error->all(FLERR, + "UF3: Expected 6 words on line {} of {} file but found {} word/s", + line_counter, potf_name, fp2nd_line.count()); + + //get the elements + std::string element1 = fp2nd_line.next_string(); + std::string element2 = fp2nd_line.next_string(); + int itype = 0; + int jtype = 0; + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element1) { + itype = i; + break; + } + } + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element2) { + jtype = i; + break; + } + } + + if ((itype != 0) && (jtype != 0)) { + //Trailing and leading trim check + int leading_trim = fp2nd_line.next_int(); + int trailing_trim = fp2nd_line.next_int(); + if (leading_trim != 0) + error->all(FLERR, + "UF3: Current implementation is throughly tested only " + "for leading_trim=0"); + if (trailing_trim != 3) + error->all(FLERR, + "UF3: Current implementation is throughly tested only " + "for trailing_trim=3"); + + //read next line, should contain cutoff and size of knot vector + temp_line = txtfilereader.next_line(1); + line_counter++; + ValueTokenizer fp3rd_line(temp_line); + if (fp3rd_line.count() != 2) + error->all(FLERR, + "UF3: Expected only 2 words on 3rd line => " + "Rij_CUTOFF NUM_OF_KNOTS. Found {} word/s", + fp3rd_line.count()); + + //cut is used in init_one which is called by pair.cpp at line 267 + //where the return of init_one is squared + cut[itype][jtype] = fp3rd_line.next_double(); + cut[jtype][itype] = cut[itype][jtype]; + + int num_knots_2b = fp3rd_line.next_int(); + n2b_knots_array_size[itype][jtype] = num_knots_2b; + n2b_knots_array_size[jtype][itype] = num_knots_2b; + max_num_knots_2b = std::max(max_num_knots_2b, num_knots_2b); + + //skip next line + txtfilereader.skip_line(); + line_counter++; + + //read number of coeff + temp_line = txtfilereader.next_line(1); + line_counter++; + ValueTokenizer fp5th_line(temp_line); + + int num_coeff_2b = fp5th_line.next_int(); + if (num_coeff_2b <= 0) + error->all(FLERR, + "UF3: 0 or negative number found for num_coeff_2b" + " on line {} of the potential file", + line_counter); + n2b_coeff_array_size[itype][jtype] = num_coeff_2b; + n2b_coeff_array_size[jtype][itype] = num_coeff_2b; + max_num_coeff_2b = std::max(max_num_coeff_2b, num_coeff_2b); + } + } else if ((nbody_on_file == "3B") && (pot_3b)) { + //3B block + if (fp2nd_line.count() != 7) + error->all(FLERR, + "UF3: Expected 7 words on line {} of {} file" + "but found {} word/s", + line_counter, potf_name, fp2nd_line.count()); + + if (nbody_on_file == "3B") { + //get the elements + std::string element1 = fp2nd_line.next_string(); + std::string element2 = fp2nd_line.next_string(); + std::string element3 = fp2nd_line.next_string(); + int itype = 0; + int jtype = 0; + int ktype = 0; + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element1) { + itype = i; + break; + } + } + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element2) { + jtype = i; + break; + } + } + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element3) { + ktype = i; + break; + } + } + + if ((itype != 0) && (jtype != 0) && (ktype != 0)) { + //Trailing and leading trim check + int leading_trim = fp2nd_line.next_int(); + int trailing_trim = fp2nd_line.next_int(); + if (leading_trim != 0) + error->all(FLERR, + "UF3: Current implementation is throughly tested " + "only for leading_trim=0"); + if (trailing_trim != 3) + error->all(FLERR, + "UF3: Current implementation is throughly tested " + "only for trailing_trim=3"); + + //read next line, should contain cutoffs and size of knot vectors + temp_line = txtfilereader.next_line(6); + line_counter++; + ValueTokenizer fp3rd_line(temp_line); + + if (fp3rd_line.count() != 6) + error->all(FLERR, + "UF3: Expected only 6 numbers on 3rd line => " + "Rjk_CUTOFF Rik_CUTOFF Rij_CUTOFF NUM_OF_KNOTS_JK " + "NUM_OF_KNOTS_IK NUM_OF_KNOTS_IJ Found {} number/s", + fp3rd_line.count()); + + double cut3b_rjk = fp3rd_line.next_double(); + double cut3b_rij = fp3rd_line.next_double(); + double cut3b_rik = fp3rd_line.next_double(); + + if (cut3b_rij != cut3b_rik) + error->all(FLERR, + "UF3: rij!=rik for {}-{}-{}. " + "Current implementation only works for rij=rik", + element1, element2, element3); + + if (2 * cut3b_rik != cut3b_rjk) + error->all(FLERR, + "UF3: 2rij=2rik!=rik for {}-{}-{}. " + "Current implementation only works for 2rij=2rik!=rik", + element1, element2, element3); + + cut_3b_list[itype][jtype] = std::max(cut3b_rij, cut_3b_list[itype][jtype]); + cut_3b_list[itype][ktype] = std::max(cut_3b_list[itype][ktype], cut3b_rik); + + cut_3b[itype][jtype][ktype] = cut3b_rij; + cut_3b[itype][ktype][jtype] = cut3b_rik; + + int num_knots_3b_jk = fp3rd_line.next_int(); + int num_knots_3b_ik = fp3rd_line.next_int(); + int num_knots_3b_ij = fp3rd_line.next_int(); + + n3b_knots_array_size[map_3b[itype][jtype][ktype]][0] = num_knots_3b_jk; + n3b_knots_array_size[map_3b[itype][jtype][ktype]][1] = num_knots_3b_ik; + n3b_knots_array_size[map_3b[itype][jtype][ktype]][2] = num_knots_3b_ij; + + n3b_knots_array_size[map_3b[itype][ktype][jtype]][0] = num_knots_3b_jk; + n3b_knots_array_size[map_3b[itype][ktype][jtype]][1] = num_knots_3b_ij; + n3b_knots_array_size[map_3b[itype][ktype][jtype]][2] = num_knots_3b_ik; + + max_num_knots_3b = std::max(max_num_knots_3b, num_knots_3b_jk); + max_num_knots_3b = std::max(max_num_knots_3b, num_knots_3b_ik); + max_num_knots_3b = std::max(max_num_knots_3b, num_knots_3b_ij); + + //skip next 3 line + txtfilereader.skip_line(); + line_counter++; + txtfilereader.skip_line(); + line_counter++; + txtfilereader.skip_line(); + line_counter++; + + //read number of coeff + temp_line = txtfilereader.next_line(3); + line_counter++; + ValueTokenizer fp7th_line(temp_line); + + if (fp7th_line.count() != 3) + error->all(FLERR, + "UF3: Expected 3 numbers on 7th line => " + "SHAPE_OF_COEFF_MATRIX[I][J][K] found {} numbers", + fp7th_line.count()); + + int coeff_matrix_dim1 = fp7th_line.next_int(); + int coeff_matrix_dim2 = fp7th_line.next_int(); + int coeff_matrix_dim3 = fp7th_line.next_int(); + + n3b_coeff_array_size[map_3b[itype][jtype][ktype]][0] = coeff_matrix_dim1; + n3b_coeff_array_size[map_3b[itype][jtype][ktype]][1] = coeff_matrix_dim2; + n3b_coeff_array_size[map_3b[itype][jtype][ktype]][2] = coeff_matrix_dim3; + + n3b_coeff_array_size[map_3b[itype][ktype][jtype]][0] = coeff_matrix_dim2; + n3b_coeff_array_size[map_3b[itype][ktype][jtype]][1] = coeff_matrix_dim1; + n3b_coeff_array_size[map_3b[itype][ktype][jtype]][2] = coeff_matrix_dim3; + + max_num_coeff_3b = std::max(max_num_coeff_3b, coeff_matrix_dim1); + max_num_coeff_3b = std::max(max_num_coeff_3b, coeff_matrix_dim2); + max_num_coeff_3b = std::max(max_num_coeff_3b, coeff_matrix_dim3); + } + } + } else { + if (!((nbody_on_file == "3B") && (!pot_3b))) + error->all(FLERR, "UF3: Expected either '2B' or '3B' word on line {} of {} file", + line_counter, potf_name); + } + } //if of #UF3 POT + line_counter++; + } // while + + //Create knot and coeff arrays + if (max_num_knots_2b <= 0) + error->all(FLERR, + "UF3: Error reading the size of 2B knot vector\n" + "Possibly no 2B UF3 potential block detected in {} file", + potf_name); + memory->destroy(n2b_knots_array); + memory->create(n2b_knots_array, num_of_elements + 1, num_of_elements + 1, max_num_knots_2b, + "pair:n2b_knots_array"); + + if (max_num_coeff_2b <= 0) + error->all(FLERR, + "UF3: Error reading the size of 2B coeff vector\n" + "Possibly no 2B UF3 potential block detected in {} file", + potf_name); + + memory->destroy(n2b_coeff_array); + memory->create(n2b_coeff_array, num_of_elements + 1, num_of_elements + 1, max_num_coeff_2b, + "pair:n2b_coeff_array"); + + if (pot_3b) { + if (max_num_knots_3b <= 0) + error->all(FLERR, + "UF3: Error reading the size of 3B knot vector\n" + "Possibly no 3B UF3 potential block detected in {} file", + potf_name); + memory->destroy(n3b_knots_array); + memory->create(n3b_knots_array, tot_interaction_count_3b, 3, max_num_knots_3b, + "pair:n3b_knots_array"); + + if (max_num_coeff_3b <= 0) + error->all(FLERR, + "UF3: Error reading the size of 3B coeff matrices\n" + "Possibly no 3B UF3 potential block detected in {} file", + potf_name); + memory->destroy(n3b_coeff_array); + memory->create(n3b_coeff_array, tot_interaction_count_3b, max_num_coeff_3b, max_num_coeff_3b, + max_num_coeff_3b, "pair:n3b_coeff_array"); + } + + //Go back to the begning of the file + txtfilereader.rewind(); + + //Go through the file again and fill knot and coeff arrays + //while loop to read the data + while ((line = txtfilereader.next_line(1))) { + Tokenizer line_token(line); + + //Detect start of a block + if (line_token.contains("#UF3 POT")) { + //Block start detected + //Read the 2nd line of the block + std::string temp_line = txtfilereader.next_line(1); + ValueTokenizer fp2nd_line(temp_line); + std::string nbody_on_file = fp2nd_line.next_string(); + + if (nbody_on_file == "2B") { + //get the elements + std::string element1 = fp2nd_line.next_string(); + std::string element2 = fp2nd_line.next_string(); + int itype = 0; + int jtype = 0; + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element1) { + itype = i; + break; + } + } + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element2) { + jtype = i; + break; + } + } + + //skip the next two tokens + fp2nd_line.skip(2); + + //uk or nk? + std::string knot_type = fp2nd_line.next_string(); + if (knot_type == "uk") { + knot_spacing_type_2b[itype][jtype] = 0; + knot_spacing_type_2b[jtype][itype] = 0; + } else if (knot_type == "nk") { + knot_spacing_type_2b[itype][jtype] = 1; + knot_spacing_type_2b[jtype][itype] = 1; + } else + error->all(FLERR, + "UF3: Expected either 'uk'(uniform-knots) or 'nk'(non-uniform knots). " + "Found {} on the 2nd line of {}-{} interaction block", + knot_type, element1, element2); + + if ((itype != 0) && (jtype != 0)) { + //skip line containing info of cutoff and knot vect size + txtfilereader.skip_line(); + + int num_knots_2b = n2b_knots_array_size[itype][jtype]; + + temp_line = txtfilereader.next_line(num_knots_2b); + ValueTokenizer fp4th_line(temp_line); + + if (fp4th_line.count() != num_knots_2b) + error->all(FLERR, + "UF3: Error reading the 2B potential block for {}-{}\n" + "Expected {} numbers on 4th line of the block but found {} numbers", + element1, element2, num_knots_2b, fp4th_line.count()); + + for (int k = 0; k < num_knots_2b; k++) { + n2b_knots_array[itype][jtype][k] = fp4th_line.next_double(); + n2b_knots_array[jtype][itype][k] = n2b_knots_array[itype][jtype][k]; + } + + knot_spacing_2b[itype][jtype] = + n2b_knots_array[itype][jtype][4] - n2b_knots_array[itype][jtype][3]; + knot_spacing_2b[jtype][itype] = knot_spacing_2b[itype][jtype]; + + //skip next line + txtfilereader.skip_line(); + + int num_of_coeff_2b = n2b_coeff_array_size[itype][jtype]; + + temp_line = txtfilereader.next_line(num_of_coeff_2b); + ValueTokenizer fp6th_line(temp_line); + + if (fp6th_line.count() != num_of_coeff_2b) + error->all(FLERR, + "UF3: Error reading the 2B potential block for {}-{}\n" + "Expected {} numbers on 6th line of the block but found {} numbers", + element1, element2, num_of_coeff_2b, fp6th_line.count()); + + for (int k = 0; k < num_of_coeff_2b; k++) { + n2b_coeff_array[itype][jtype][k] = fp6th_line.next_double(); + n2b_coeff_array[jtype][itype][k] = n2b_coeff_array[itype][jtype][k]; + } + + if (num_knots_2b != num_of_coeff_2b + 4) + error->all(FLERR, + "UF3: {}-{} interaction block has incorrect knot and " + "coeff data nknots (={}) != ncoeffs (={}) + 3 + 1", + element1, element2, num_knots_2b, num_of_coeff_2b); + + setflag[itype][jtype] = 1; + setflag[jtype][itype] = 1; + } + } + + if ((nbody_on_file == "3B") && (pot_3b)) { + //get the elements + std::string element1 = fp2nd_line.next_string(); + std::string element2 = fp2nd_line.next_string(); + std::string element3 = fp2nd_line.next_string(); + int itype = 0; + int jtype = 0; + int ktype = 0; + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element1) { + itype = i; + break; + } + } + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element2) { + jtype = i; + break; + } + } + for (int i = 1; i < num_of_elements + 1; i++) { + if (std::string(elements[map[i]]) == element3) { + ktype = i; + break; + } + } + + //skip the next two tokens + fp2nd_line.skip(2); + + //uk or nk? + std::string knot_type = fp2nd_line.next_string(); + if (knot_type == "uk") { + knot_spacing_type_3b[itype][jtype][ktype] = 0; + knot_spacing_type_3b[itype][ktype][jtype] = 0; + } else if (knot_type == "nk") { + knot_spacing_type_3b[itype][jtype][ktype] = 1; + knot_spacing_type_3b[itype][ktype][jtype] = 1; + } else + error->all(FLERR, + "UF3: Expected either 'uk'(uniform-knots) or 'nk'(non-uniform knots) " + "Found {} on the 2nd line of {}-{}-{} interaction block", + knot_type, element1, element2, element3); + + if ((itype != 0) && (jtype != 0) && (ktype != 0)) { + //skip line containing info of cutoffs and knot vector sizes + txtfilereader.skip_line(); + + int num_knots_3b_jk = n3b_knots_array_size[map_3b[itype][jtype][ktype]][0]; + int num_knots_3b_ik = n3b_knots_array_size[map_3b[itype][jtype][ktype]][1]; + int num_knots_3b_ij = n3b_knots_array_size[map_3b[itype][jtype][ktype]][2]; + + temp_line = txtfilereader.next_line(num_knots_3b_jk); + ValueTokenizer fp4th_line(temp_line); + if (fp4th_line.count() != num_knots_3b_jk) + error->all(FLERR, + "UF3: Error reading the 3B potential block for {}-{}-{}\n" + "Expected {} numbers on 4th line of the block but found {} " + "numbers", + element1, element2, element3, num_knots_3b_jk, fp4th_line.count()); + + for (int i = 0; i < num_knots_3b_jk; i++) { + n3b_knots_array[map_3b[itype][jtype][ktype]][0][i] = fp4th_line.next_double(); + n3b_knots_array[map_3b[itype][ktype][jtype]][0][i] = + n3b_knots_array[map_3b[itype][jtype][ktype]][0][i]; + } + + min_cut_3b[itype][jtype][ktype][0] = n3b_knots_array[map_3b[itype][jtype][ktype]][0][0]; + min_cut_3b[itype][ktype][jtype][0] = n3b_knots_array[map_3b[itype][ktype][jtype]][0][0]; + + knot_spacing_3b[itype][jtype][ktype][0] = + n3b_knots_array[map_3b[itype][jtype][ktype]][0][4] - + n3b_knots_array[map_3b[itype][jtype][ktype]][0][3]; + knot_spacing_3b[itype][ktype][jtype][0] = knot_spacing_3b[itype][jtype][ktype][0]; + + temp_line = txtfilereader.next_line(num_knots_3b_ik); + ValueTokenizer fp5th_line(temp_line); + if (fp5th_line.count() != num_knots_3b_ik) + error->all(FLERR, + "UF3: Error reading the 3B potential block for {}-{}-{}\n" + "Expected {} numbers on 5th line of the block but found {} " + "numbers", + element1, element2, element3, num_knots_3b_ik, fp5th_line.count()); + + for (int i = 0; i < num_knots_3b_ik; i++) { + n3b_knots_array[map_3b[itype][jtype][ktype]][1][i] = fp5th_line.next_double(); + n3b_knots_array[map_3b[itype][ktype][jtype]][2][i] = + n3b_knots_array[map_3b[itype][jtype][ktype]][1][i]; + } + + min_cut_3b[itype][jtype][ktype][1] = n3b_knots_array[map_3b[itype][jtype][ktype]][1][0]; + min_cut_3b[itype][ktype][jtype][2] = n3b_knots_array[map_3b[itype][ktype][jtype]][2][0]; + + knot_spacing_3b[itype][jtype][ktype][1] = + n3b_knots_array[map_3b[itype][jtype][ktype]][1][4] - + n3b_knots_array[map_3b[itype][jtype][ktype]][1][3]; + knot_spacing_3b[itype][ktype][jtype][2] = knot_spacing_3b[itype][jtype][ktype][1]; + + temp_line = txtfilereader.next_line(num_knots_3b_ij); + ValueTokenizer fp6th_line(temp_line); + if (fp6th_line.count() != num_knots_3b_ij) + error->all(FLERR, + "UF3: Error reading the 3B potential block for {}-{}-{}\n" + "Expected {} numbers on 6th line of the block but found {} " + "numbers", + element1, element2, element3, num_knots_3b_ij, fp6th_line.count()); + + for (int i = 0; i < num_knots_3b_ij; i++) { + n3b_knots_array[map_3b[itype][jtype][ktype]][2][i] = fp6th_line.next_double(); + n3b_knots_array[map_3b[itype][ktype][jtype]][1][i] = + n3b_knots_array[map_3b[itype][jtype][ktype]][2][i]; + } + + min_cut_3b[itype][jtype][ktype][2] = n3b_knots_array[map_3b[itype][jtype][ktype]][2][0]; + min_cut_3b[itype][ktype][jtype][1] = n3b_knots_array[map_3b[itype][ktype][jtype]][1][0]; + + knot_spacing_3b[itype][jtype][ktype][2] = + n3b_knots_array[map_3b[itype][jtype][ktype]][2][4] - + n3b_knots_array[map_3b[itype][jtype][ktype]][2][3]; + knot_spacing_3b[itype][ktype][jtype][1] = knot_spacing_3b[itype][jtype][ktype][2]; + + //skip next line + txtfilereader.skip_line(); + + int coeff_matrix_dim1 = n3b_coeff_array_size[map_3b[itype][jtype][ktype]][0]; + int coeff_matrix_dim2 = n3b_coeff_array_size[map_3b[itype][jtype][ktype]][1]; + int coeff_matrix_dim3 = n3b_coeff_array_size[map_3b[itype][jtype][ktype]][2]; + + if (num_knots_3b_jk != coeff_matrix_dim3 + 3 + 1) + error->all(FLERR, + "UF3: {}-{}-{} interaction block has incorrect knot " + "(NUM_OF_KNOTS_JK) and coeff (coeff_matrix_dim3) data " + "nknots!=ncoeffs + 3 + 1", + element1, element2, element3); + + if (num_knots_3b_ik != coeff_matrix_dim2 + 3 + 1) + error->all(FLERR, + "UF3: {}-{}-{} interaction block has incorrect knot " + "(NUM_OF_KNOTS_IK) and coeff (coeff_matrix_dim2) data " + "nknots!=ncoeffs + 3 + 1", + element1, element2, element3); + + if (num_knots_3b_ij != coeff_matrix_dim1 + 3 + 1) + error->all(FLERR, + "UF3: {}-{}-{} interaction block has incorrect knot " + "(NUM_OF_KNOTS_IJ) and coeff (coeff_matrix_dim1) data " + "nknots!=ncoeffs + 3 + 1", + element1, element2, element3); + + int coeff_matrix_elements_len = coeff_matrix_dim3; + int key1 = map_3b[itype][jtype][ktype]; + int key2 = map_3b[itype][ktype][jtype]; + + int line_count = 0; + for (int i = 0; i < coeff_matrix_dim1; i++) { + for (int j = 0; j < coeff_matrix_dim2; j++) { + temp_line = txtfilereader.next_line(coeff_matrix_elements_len); + ValueTokenizer coeff_line(temp_line); + if (coeff_line.count() != coeff_matrix_elements_len) + error->all(FLERR, + "UF3: Error reading 3B potential block for {}-{}-{}\n" + "Expected {} numbers on {}th line of the block but found {} " + "numbers", + element1, element2, element3, coeff_matrix_elements_len, line_count + 8, + coeff_line.count()); + + for (int k = 0; k < coeff_matrix_dim3; k++) { + n3b_coeff_array[key1][i][j][k] = coeff_line.next_double(); + } + line_count += 1; + } + } + + for (int i = 0; i < coeff_matrix_dim1; i++) { + for (int j = 0; j < coeff_matrix_dim2; j++) { + for (int k = 0; k < coeff_matrix_dim3; k++) { + n3b_coeff_array[key2][j][i][k] = n3b_coeff_array[key1][i][j][k]; + } + } + } + + setflag_3b[itype][jtype][ktype] = 1; + setflag_3b[itype][ktype][jtype] = 1; + } + } + } // if #UF3 POT + } //while + fclose(fp); + + //Set interaction of atom types of the same elements + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + if (setflag[i][j] != 1) { + //i-j interaction not set + + //maybe i-j is mapped to some other atom type interaction? + int i_mapped_to = map[i] + 1; //+1 as map starts from 0 + int j_mapped_to = map[j] + 1; //+1 as map starts from 0 + + if ((i_mapped_to == i) && (j_mapped_to == j)) + //i-j is not mapped to some other atom type ie interaction is missing on file + error->all(FLERR, + "UF3: Potential for interaction {}-{} ie {}-{} not found " + "in {} file", + i, j, elements[i_mapped_to - 1], elements[j_mapped_to - 1], potf_name); + + cut[i][j] = cut[i_mapped_to][j_mapped_to]; + + n2b_knots_array_size[i][j] = n2b_knots_array_size[i_mapped_to][j_mapped_to]; + n2b_coeff_array_size[i][j] = n2b_coeff_array_size[i_mapped_to][j_mapped_to]; + + knot_spacing_type_2b[i][j] = knot_spacing_type_2b[i_mapped_to][j_mapped_to]; + knot_spacing_2b[i][j] = knot_spacing_2b[i_mapped_to][j_mapped_to]; + + for (int knot_no = 0; knot_no < max_num_knots_2b; knot_no++) + n2b_knots_array[i][j][knot_no] = n2b_knots_array[i_mapped_to][j_mapped_to][knot_no]; + + for (int coeff_no = 0; coeff_no < max_num_coeff_2b; coeff_no++) + n2b_coeff_array[i][j][coeff_no] = n2b_coeff_array[i_mapped_to][j_mapped_to][coeff_no]; + + setflag[i][j] = 1; + } + } + } + + if (pot_3b) { + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + //for (int k = j; k < num_of_elements + 1; k++) { + for (int k = 1; k < num_of_elements + 1; k++) { + if (setflag_3b[i][j][k] != 1) { + //i-j-k interaction not set + + //maybe i-j-k is mapped to some other atom type interaction? + int i_mapped_to = map[i] + 1; //+1 as map starts from 0 + int j_mapped_to = map[j] + 1; //+1 as map starts from 0 + int k_mapped_to = map[k] + 1; //+1 as map starts from 0 + + if ((i_mapped_to == i) && (j_mapped_to == j) && (k_mapped_to == k)) + error->all(FLERR, + "UF3: Potential for interaction {}-{}-{} ie {}-{}-{} " + " not found in {} file", + i, j, k, elements[i_mapped_to - 1], elements[j_mapped_to - 1], + elements[k_mapped_to - 1], potf_name); + if (setflag_3b[i_mapped_to][j_mapped_to][k_mapped_to] != 1) + error->all(FLERR, + "UF3: Interaction {}-{}-{} was mapped to {}-{}-{}, but " + "potential interaction for {}-{}-{} was not found in " + "{} file", + i, j, k, i_mapped_to, j_mapped_to, k_mapped_to, i_mapped_to, j_mapped_to, + k_mapped_to, potf_name); + + cut_3b_list[i][j] = std::max(cut_3b_list[i_mapped_to][j_mapped_to], cut_3b_list[i][j]); + + cut_3b[i][j][k] = cut_3b[i_mapped_to][j_mapped_to][k_mapped_to]; + + knot_spacing_type_3b[i][j][k] = + knot_spacing_type_3b[i_mapped_to][j_mapped_to][k_mapped_to]; + knot_spacing_3b[i][j][k][0] = knot_spacing_3b[i_mapped_to][j_mapped_to][k_mapped_to][0]; + knot_spacing_3b[i][j][k][1] = knot_spacing_3b[i_mapped_to][j_mapped_to][k_mapped_to][1]; + knot_spacing_3b[i][j][k][2] = knot_spacing_3b[i_mapped_to][j_mapped_to][k_mapped_to][2]; + + int key = map_3b[i][j][k]; + int mapped_to_key = map_3b[i_mapped_to][j_mapped_to][k_mapped_to]; + + n3b_knots_array_size[key][0] = n3b_knots_array_size[mapped_to_key][0]; + n3b_knots_array_size[key][1] = n3b_knots_array_size[mapped_to_key][1]; + n3b_knots_array_size[key][2] = n3b_knots_array_size[mapped_to_key][2]; + + n3b_coeff_array_size[key][0] = n3b_coeff_array_size[mapped_to_key][0]; + n3b_coeff_array_size[key][1] = n3b_coeff_array_size[mapped_to_key][1]; + n3b_coeff_array_size[key][2] = n3b_coeff_array_size[mapped_to_key][2]; + + min_cut_3b[i][j][k][0] = min_cut_3b[i_mapped_to][j_mapped_to][k_mapped_to][0]; + + min_cut_3b[i][j][k][1] = min_cut_3b[i_mapped_to][j_mapped_to][k_mapped_to][1]; + + min_cut_3b[i][j][k][2] = min_cut_3b[i_mapped_to][j_mapped_to][k_mapped_to][2]; + + for (int knot_no = 0; knot_no < n3b_knots_array_size[key][0]; knot_no++) + n3b_knots_array[key][0][knot_no] = n3b_knots_array[mapped_to_key][0][knot_no]; + + for (int knot_no = 0; knot_no < n3b_knots_array_size[key][1]; knot_no++) + n3b_knots_array[key][1][knot_no] = n3b_knots_array[mapped_to_key][1][knot_no]; + + for (int knot_no = 0; knot_no < n3b_knots_array_size[key][2]; knot_no++) + n3b_knots_array[key][2][knot_no] = n3b_knots_array[mapped_to_key][2][knot_no]; + + for (int coeff1 = 0; coeff1 < n3b_coeff_array_size[key][0]; coeff1++) + for (int coeff2 = 0; coeff2 < n3b_coeff_array_size[key][1]; coeff2++) + for (int coeff3 = 0; coeff3 < n3b_coeff_array_size[key][2]; coeff3++) + n3b_coeff_array[key][coeff1][coeff2][coeff3] = + n3b_coeff_array[mapped_to_key][coeff1][coeff2][coeff3]; + setflag_3b[i][j][k] = 1; + } + } + } + } + } +} + +//Broadcast data read from potential file to all processors +void PairUF3::communicate() +{ + const int num_of_elements = atom->ntypes; + MPI_Bcast(&cut[0][0], (num_of_elements + 1) * (num_of_elements + 1), MPI_DOUBLE, 0, world); + + MPI_Bcast(&n2b_knots_array_size[0][0], (num_of_elements + 1) * (num_of_elements + 1), MPI_INT, 0, + world); + MPI_Bcast(&n2b_coeff_array_size[0][0], (num_of_elements + 1) * (num_of_elements + 1), MPI_INT, 0, + world); + + MPI_Bcast(&max_num_knots_2b, 1, MPI_INT, 0, world); + MPI_Bcast(&max_num_coeff_2b, 1, MPI_INT, 0, world); + + if (pot_3b) { + MPI_Bcast(&cut_3b_list[0][0], (num_of_elements + 1) * (num_of_elements + 1), MPI_DOUBLE, 0, + world); + + MPI_Bcast(&cut_3b[0][0][0], + (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1), MPI_DOUBLE, 0, + world); + + MPI_Bcast(&n3b_knots_array_size[0][0], tot_interaction_count_3b * 3, MPI_INT, 0, world); + MPI_Bcast(&n3b_coeff_array_size[0][0], tot_interaction_count_3b * 3, MPI_INT, 0, world); + + MPI_Bcast(&max_num_knots_3b, 1, MPI_INT, 0, world); + MPI_Bcast(&max_num_coeff_3b, 1, MPI_INT, 0, world); + } + + if (comm->me != 0) { + memory->destroy(n2b_knots_array); + memory->destroy(n2b_coeff_array); + + memory->create(n2b_knots_array, num_of_elements + 1, num_of_elements + 1, max_num_knots_2b, + "pair:n2b_knots_array"); + memory->create(n2b_coeff_array, num_of_elements + 1, num_of_elements + 1, max_num_coeff_2b, + "pair:n2b_coeff_array"); + if (pot_3b) { + memory->destroy(n3b_knots_array); + memory->destroy(n3b_coeff_array); + + memory->create(n3b_knots_array, tot_interaction_count_3b, 3, max_num_knots_3b, + "pair:n3b_knots_array"); + + memory->create(n3b_coeff_array, tot_interaction_count_3b, max_num_coeff_3b, max_num_coeff_3b, + max_num_coeff_3b, "pair:n3b_coeff_array"); + } + } + + MPI_Bcast(&knot_spacing_type_2b[0][0], (num_of_elements + 1) * (num_of_elements + 1), MPI_INT, 0, + world); + + MPI_Bcast(&knot_spacing_2b[0][0], (num_of_elements + 1) * (num_of_elements + 1), MPI_DOUBLE, 0, + world); + + MPI_Bcast(&n2b_knots_array[0][0][0], + (num_of_elements + 1) * (num_of_elements + 1) * max_num_knots_2b, MPI_DOUBLE, 0, world); + MPI_Bcast(&n2b_coeff_array[0][0][0], + (num_of_elements + 1) * (num_of_elements + 1) * max_num_coeff_2b, MPI_DOUBLE, 0, world); + + MPI_Bcast(&setflag[0][0], (num_of_elements + 1) * (num_of_elements + 1), MPI_INT, 0, world); + + if (pot_3b) { + MPI_Bcast(&knot_spacing_type_3b[0][0][0], + (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1), MPI_INT, 0, + world); + + MPI_Bcast(&knot_spacing_3b[0][0][0][0], + (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * 3, MPI_DOUBLE, + 0, world); + MPI_Bcast(&n3b_knots_array[0][0][0], tot_interaction_count_3b * 3 * max_num_knots_3b, + MPI_DOUBLE, 0, world); + MPI_Bcast(&n3b_coeff_array[0][0][0][0], + tot_interaction_count_3b * max_num_coeff_3b * max_num_coeff_3b * max_num_coeff_3b, + MPI_DOUBLE, 0, world); + MPI_Bcast(&setflag_3b[0][0][0], + (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1), MPI_INT, 0, + world); + MPI_Bcast(&min_cut_3b[0][0][0][0], + (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * 3, MPI_DOUBLE, + 0, world); + } +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ +void PairUF3::init_style() +{ + if (force->newton_pair == 0) error->all(FLERR, "UF3: Pair style requires newton pair on"); + // request a default neighbor list + neighbor->add_request(this, NeighConst::REQ_FULL); +} + +/* ---------------------------------------------------------------------- + init list sets the pointer to full neighbour list requested in previous function +------------------------------------------------------------------------- */ + +void PairUF3::init_list(int /*id*/, class NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ +double PairUF3::init_one(int i /*i*/, int /*j*/ j) +{ + + if (!bsplines_created) create_bsplines(); + + //init_one is called by pair.cpp at line 267 where it is squred + //at line 268 + return cut[i][j]; +} + +void PairUF3::create_bsplines() +{ + const int num_of_elements = atom->ntypes; + bsplines_created = 1; + int spacing_type = knot_spacing_type_2b[1][1]; + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + if (setflag[i][j] != 1) + error->all(FLERR, + "UF3: Not all 2-body UF potentials are set, " + "missing potential for {}-{} interaction", + i, j); + /*if (spacing_type != knot_spacing_type_2b[i][j]) + error->all(FLERR, + "UF3: In the current version the knot spacing type, " + "for all interactions needs to be same. For {}-{} " + "i.e. {}-{} interaction expected {}, but found {}", + i,j,elements[map[i]],elements[map[j]],spacing_type, + knot_spacing_type_2b[i][j]);*/ + } + } + if (pot_3b) { + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + for (int k = 1; k < num_of_elements + 1; k++) { + if (setflag_3b[i][j][k] != 1) + error->all(FLERR, + "UF3: Not all 3-body UF potentials are set, " + "missing potential for {}-{}-{} interaction", + i, j, k); + if (spacing_type != knot_spacing_type_3b[i][j][k]) + error->all(FLERR, + "UF3: In the current version the knot spacing type, " + "for all interactions needs to be same. For {}-{}-{} " + "i.e. {}-{}-{} interaction expected{}, but found {}", + i, j, k, elements[map[i]], elements[map[j]], elements[map[k]], spacing_type, + knot_spacing_type_3b[i][j][k]); + } + } + } + } + + if (spacing_type) { + get_starting_index_2b = &PairUF3::get_starting_index_nonuniform_2b; + if (pot_3b) get_starting_index_3b = &PairUF3::get_starting_index_nonuniform_3b; + } else { + get_starting_index_2b = &PairUF3::get_starting_index_uniform_2b; + if (pot_3b) get_starting_index_3b = &PairUF3::get_starting_index_uniform_3b; + } + + create_cached_constants_2b(); + if (pot_3b) create_cached_constants_3b(); +} + +int PairUF3::get_starting_index_uniform_2b(int i, int j, double r) +{ + return 3 + (int) ((r - n2b_knots_array[i][j][0]) / (knot_spacing_2b[i][j])); +} + +int PairUF3::get_starting_index_uniform_3b(int i, int j, int k, double r, int knot_dim) +{ + return 3 + + (int) (((r - n3b_knots_array[map_3b[i][j][k]][knot_dim][0]) / + knot_spacing_3b[i][j][k][knot_dim])); +} + +int PairUF3::get_starting_index_nonuniform_2b(int i, int j, double r) +{ + for (int l = 3; l < n2b_knots_array_size[i][j] - 1; ++l) { + if ((n2b_knots_array[i][j][l] <= r) && (r < n2b_knots_array[i][j][l + 1])) return l; + } + return -1; +} + +int PairUF3::get_starting_index_nonuniform_3b(int i, int j, int k, double r, int knot_dim) +{ + for (int l = 3; l < n3b_knots_array_size[map_3b[i][j][k]][knot_dim] - 1; ++l) { + if ((n3b_knots_array[map_3b[i][j][k]][knot_dim][l] <= r) && + (r < n3b_knots_array[map_3b[i][j][k]][knot_dim][l + 1])) + return l; + } + return -1; +} + +void PairUF3::create_cached_constants_2b() +{ + const int num_of_elements = atom->ntypes; + memory->destroy(cached_constants_2b); + memory->destroy(cached_constants_2b_deri); + memory->create(cached_constants_2b, num_of_elements + 1, num_of_elements + 1, max_num_coeff_2b, + 16, "pair:cached_constants_2b"); + + memory->create(cached_constants_2b_deri, num_of_elements + 1, num_of_elements + 1, + max_num_coeff_2b - 1, 9, "pair:cached_constants_2b_deri"); + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + for (int l = 0; l < n2b_coeff_array_size[i][j]; l++) { + uf3_bspline_basis3 bspline_basis(lmp, &n2b_knots_array[i][j][l], n2b_coeff_array[i][j][l]); + for (int cc = 0; cc < 16; cc++) { + cached_constants_2b[i][j][l][cc] = bspline_basis.constants[cc]; + } + } + } + } + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + //initialize coeff and knots for derivative + //double* knots_for_deri = new double[n2b_knots_array_size[i][j]-2]; + double *knots_for_deri = nullptr; + memory->create(knots_for_deri, n2b_knots_array_size[i][j] - 2, "pair:knots_for_deri"); + + for (int l = 1; l < n2b_knots_array_size[i][j] - 1; l++) + knots_for_deri[l - 1] = n2b_knots_array[i][j][l]; + + //double* coeff_for_deri = new double[n2b_coeff_array_size[i][j]-1]; + double *coeff_for_deri = nullptr; + memory->create(coeff_for_deri, n2b_coeff_array_size[i][j] - 1, "pair:coeff_for_deri"); + for (int l = 0; l < n2b_coeff_array_size[i][j] - 1; l++) { + double dntemp = 3 / (n2b_knots_array[i][j][l + 4] - n2b_knots_array[i][j][l + 1]); + coeff_for_deri[l] = (n2b_coeff_array[i][j][l + 1] - n2b_coeff_array[i][j][l]) * dntemp; + } + + for (int l = 0; l < n2b_coeff_array_size[i][j] - 1; l++) { + uf3_bspline_basis2 bspline_basis_deri(lmp, &knots_for_deri[l], coeff_for_deri[l]); + for (int cc = 0; cc < 9; cc++) { + cached_constants_2b_deri[i][j][l][cc] = bspline_basis_deri.constants[cc]; + } + } + memory->destroy(knots_for_deri); + memory->destroy(coeff_for_deri); + //delete[] knots_for_deri; + //delete[] coeff_for_deri; + } + } +} + +void PairUF3::create_cached_constants_3b() +{ + const int num_of_elements = atom->ntypes; + memory->destroy(coeff_for_der_jk); + memory->destroy(coeff_for_der_ik); + memory->destroy(coeff_for_der_ij); + memory->destroy(cached_constants_3b); + memory->destroy(cached_constants_3b_deri); + + memory->create(coeff_for_der_jk, tot_interaction_count_3b, max_num_coeff_3b, max_num_coeff_3b, + max_num_coeff_3b, "pair:coeff_for_der_jk"); + + memory->create(coeff_for_der_ik, tot_interaction_count_3b, max_num_coeff_3b, max_num_coeff_3b, + max_num_coeff_3b, "pair:coeff_for_der_ik"); + + memory->create(coeff_for_der_ij, tot_interaction_count_3b, max_num_coeff_3b, max_num_coeff_3b, + max_num_coeff_3b, "pair:coeff_for_der_ij"); + + memory->create(cached_constants_3b, tot_interaction_count_3b, 3, max_num_coeff_3b, 16, + "pair:cached_constants_3b"); + + memory->create(cached_constants_3b_deri, tot_interaction_count_3b, 3, max_num_coeff_3b - 1, 9, + "pair:cached_constants_3b_deri"); + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + for (int k = 1; k < num_of_elements + 1; k++) { + int map_to = map_3b[i][j][k]; + + for (int l = 0; l < n3b_knots_array_size[map_to][2] - 4; l++) { + uf3_bspline_basis3 bspline_basis_ij(lmp, &n3b_knots_array[map_to][2][l], 1); + for (int cc = 0; cc < 16; cc++) + cached_constants_3b[map_to][0][l][cc] = bspline_basis_ij.constants[cc]; + } + + for (int l = 0; l < n3b_knots_array_size[map_to][1] - 4; l++) { + uf3_bspline_basis3 bspline_basis_ik(lmp, &n3b_knots_array[map_to][1][l], 1); + for (int cc = 0; cc < 16; cc++) + cached_constants_3b[map_to][1][l][cc] = bspline_basis_ik.constants[cc]; + } + + for (int l = 0; l < n3b_knots_array_size[map_to][0] - 4; l++) { + uf3_bspline_basis3 bspline_basis_jk(lmp, &n3b_knots_array[map_to][0][l], 1); + for (int cc = 0; cc < 16; cc++) + cached_constants_3b[map_to][2][l][cc] = bspline_basis_jk.constants[cc]; + } + } + } + } + + for (int i = 1; i < num_of_elements + 1; i++) { + for (int j = 1; j < num_of_elements + 1; j++) { + for (int k = 1; k < num_of_elements + 1; k++) { + int map_to = map_3b[i][j][k]; + double **knots_for_der = nullptr; //new double*[3]; + + //n3b_knots_array_size[map_to][0] for jk knot vector --> always largest + memory->create(knots_for_der, 3, n3b_knots_array_size[map_to][0] - 1, "pair:knots_for_der"); + + //--deri_basis_jk + for (int l = 1; l < n3b_knots_array_size[map_to][0] - 1; l++) + knots_for_der[0][l - 1] = n3b_knots_array[map_to][0][l]; + + for (int l = 0; l < n3b_coeff_array_size[map_to][0]; l++) { + for (int m = 0; m < n3b_coeff_array_size[map_to][1]; m++) { + for (int n = 0; n < n3b_coeff_array_size[map_to][2] - 1; n++) { + double dntemp = + 3 / (n3b_knots_array[map_to][0][n + 4] - n3b_knots_array[map_to][0][n + 1]); + coeff_for_der_jk[map_to][l][m][n] = + ((n3b_coeff_array[map_to][l][m][n + 1] - n3b_coeff_array[map_to][l][m][n]) * + dntemp); + } + } + } + + //--deri_basis_ik + for (int l = 1; l < n3b_knots_array_size[map_to][1] - 1; l++) + knots_for_der[1][l - 1] = n3b_knots_array[map_to][1][l]; + + for (int l = 0; l < n3b_coeff_array_size[map_to][0]; l++) { + for (int m = 0; m < n3b_coeff_array_size[map_to][1] - 1; m++) { + double dntemp = + 3 / (n3b_knots_array[map_to][1][m + 4] - n3b_knots_array[map_to][1][m + 1]); + for (int n = 0; n < n3b_coeff_array_size[map_to][2]; n++) { + coeff_for_der_ik[map_to][l][m][n] = + ((n3b_coeff_array[map_to][l][m + 1][n] - n3b_coeff_array[map_to][l][m][n]) * + dntemp); + } + } + } + + //--deri_basis_ij + for (int l = 1; l < n3b_knots_array_size[map_to][2] - 1; l++) + knots_for_der[2][l - 1] = n3b_knots_array[map_to][2][l]; + + for (int l = 0; l < n3b_coeff_array_size[map_to][0] - 1; l++) { + double dntemp = + 3 / (n3b_knots_array[map_to][2][l + 4] - n3b_knots_array[map_to][2][l + 1]); + for (int m = 0; m < n3b_coeff_array_size[map_to][1]; m++) { + for (int n = 0; n < n3b_coeff_array_size[map_to][2]; n++) { + coeff_for_der_ij[map_to][l][m][n] = + ((n3b_coeff_array[map_to][l + 1][m][n] - n3b_coeff_array[map_to][l][m][n]) * + dntemp); + } + } + } + + for (int l = 0; l < n3b_coeff_array_size[map_to][0] - 1; l++) { + uf3_bspline_basis2 bspline_basis_deri_ij(lmp, &knots_for_der[2][l], 1); + for (int cc = 0; cc < 9; cc++) { + cached_constants_3b_deri[map_to][0][l][cc] = bspline_basis_deri_ij.constants[cc]; + } + } + + for (int l = 0; l < n3b_coeff_array_size[map_to][1] - 1; l++) { + uf3_bspline_basis2 bspline_basis_deri_ik(lmp, &knots_for_der[1][l], 1); + for (int cc = 0; cc < 9; cc++) { + cached_constants_3b_deri[map_to][1][l][cc] = bspline_basis_deri_ik.constants[cc]; + } + } + + for (int l = 0; l < n3b_coeff_array_size[map_to][2] - 1; l++) { + uf3_bspline_basis2 bspline_basis_deri_jk(lmp, &knots_for_der[0][l], 1); + for (int cc = 0; cc < 9; cc++) { + cached_constants_3b_deri[map_to][2][l][cc] = bspline_basis_deri_jk.constants[cc]; + } + } + + memory->destroy(knots_for_der); + } + } + } +} + +void PairUF3::compute(int eflag, int vflag) +{ + int i, j, k, ii, jj, kk, inum, jnum, itype, jtype, ktype; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair, fx, fy, fz; + double del_rji[3], del_rki[3], del_rkj[3]; + double fij[3], fik[3], fjk[3]; + double fji[3], fki[3], fkj[3]; + double Fi[3], Fj[3], Fk[3]; + double rsq, rij, rik, rjk; + double rij_sq, rik_sq, rjk_sq; + int *ilist, *jlist, *numneigh, **firstneigh; + + ev_init(eflag, vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + evdwl = 0; + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + int numshort = 0; + for (jj = 0; jj < jnum; jj++) { + fx = 0; + fy = 0; + fz = 0; + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + + rsq = delx * delx + dely * dely + delz * delz; + jtype = type[j]; + if (rsq < cutsq[itype][jtype]) { + rij = sqrt(rsq); + + if (pot_3b) { + if (rij <= cut_3b_list[itype][jtype]) { + neighshort[numshort] = j; + if (numshort >= maxshort - 1) { + maxshort += maxshort / 2; + memory->grow(neighshort, maxshort, "pair:neighshort"); + } + numshort = numshort + 1; + } + } + + int knot_start_index = (this->*get_starting_index_2b)(itype, jtype, rij); + + double force_2b = cached_constants_2b_deri[itype][jtype][knot_start_index - 1][0]; + force_2b += rij * cached_constants_2b_deri[itype][jtype][knot_start_index - 1][1]; + force_2b += rsq * cached_constants_2b_deri[itype][jtype][knot_start_index - 1][2]; + force_2b += cached_constants_2b_deri[itype][jtype][knot_start_index - 2][3]; + force_2b += rij * cached_constants_2b_deri[itype][jtype][knot_start_index - 2][4]; + force_2b += rsq * cached_constants_2b_deri[itype][jtype][knot_start_index - 2][5]; + force_2b += cached_constants_2b_deri[itype][jtype][knot_start_index - 3][6]; + force_2b += rij * cached_constants_2b_deri[itype][jtype][knot_start_index - 3][7]; + force_2b += rsq * cached_constants_2b_deri[itype][jtype][knot_start_index - 3][8]; + + fpair = -1 * force_2b / rij; + + fx = delx * fpair; + fy = dely * fpair; + fz = delz * fpair; + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + + if (eflag) { + double rth = rsq * rij; + evdwl = cached_constants_2b[itype][jtype][knot_start_index][0]; + evdwl += rij * cached_constants_2b[itype][jtype][knot_start_index][1]; + evdwl += rsq * cached_constants_2b[itype][jtype][knot_start_index][2]; + evdwl += rth * cached_constants_2b[itype][jtype][knot_start_index][3]; + evdwl += cached_constants_2b[itype][jtype][knot_start_index - 1][4]; + evdwl += rij * cached_constants_2b[itype][jtype][knot_start_index - 1][5]; + evdwl += rsq * cached_constants_2b[itype][jtype][knot_start_index - 1][6]; + evdwl += rth * cached_constants_2b[itype][jtype][knot_start_index - 1][7]; + evdwl += cached_constants_2b[itype][jtype][knot_start_index - 2][8]; + evdwl += rij * cached_constants_2b[itype][jtype][knot_start_index - 2][9]; + evdwl += rsq * cached_constants_2b[itype][jtype][knot_start_index - 2][10]; + evdwl += rth * cached_constants_2b[itype][jtype][knot_start_index - 2][11]; + evdwl += cached_constants_2b[itype][jtype][knot_start_index - 3][12]; + evdwl += rij * cached_constants_2b[itype][jtype][knot_start_index - 3][13]; + evdwl += rsq * cached_constants_2b[itype][jtype][knot_start_index - 3][14]; + evdwl += rth * cached_constants_2b[itype][jtype][knot_start_index - 3][15]; + }; + + if (evflag) { + ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fx, fy, fz, delx, dely, delz); + + // Centroid Stress + if (vflag_either && cvflag_atom) { + double v[6]; + + v[0] = delx * fx; + v[1] = dely * fy; + v[2] = delz * fz; + v[3] = delx * fy; + v[4] = delx * fz; + v[5] = dely * fz; + + cvatom[i][0] += 0.5 * v[0]; + cvatom[i][1] += 0.5 * v[1]; + cvatom[i][2] += 0.5 * v[2]; + cvatom[i][3] += 0.5 * v[3]; + cvatom[i][4] += 0.5 * v[4]; + cvatom[i][5] += 0.5 * v[5]; + cvatom[i][6] += 0.5 * v[3]; + cvatom[i][7] += 0.5 * v[4]; + cvatom[i][8] += 0.5 * v[5]; + + cvatom[j][0] += 0.5 * v[0]; + cvatom[j][1] += 0.5 * v[1]; + cvatom[j][2] += 0.5 * v[2]; + cvatom[j][3] += 0.5 * v[3]; + cvatom[j][4] += 0.5 * v[4]; + cvatom[j][5] += 0.5 * v[5]; + cvatom[j][6] += 0.5 * v[3]; + cvatom[j][7] += 0.5 * v[4]; + cvatom[j][8] += 0.5 * v[5]; + } + } + } + } + + // 3-body interaction + // jth atom + jnum = numshort - 1; + for (jj = 0; jj < jnum; jj++) { + fij[0] = fji[0] = 0; + fij[1] = fji[1] = 0; + fij[2] = fji[2] = 0; + j = neighshort[jj]; + jtype = type[j]; + del_rji[0] = x[j][0] - xtmp; + del_rji[1] = x[j][1] - ytmp; + del_rji[2] = x[j][2] - ztmp; + rij_sq = (del_rji[0] * del_rji[0]) + (del_rji[1] * del_rji[1]) + (del_rji[2] * del_rji[2]); + rij = sqrt(rij_sq); + + // kth atom + for (kk = jj + 1; kk < numshort; kk++) { + + fik[0] = fki[0] = 0; + fik[1] = fki[1] = 0; + fik[2] = fki[2] = 0; + + fjk[0] = fkj[0] = 0; + fjk[1] = fkj[1] = 0; + fjk[2] = fkj[2] = 0; + + k = neighshort[kk]; + ktype = type[k]; + del_rki[0] = x[k][0] - xtmp; + del_rki[1] = x[k][1] - ytmp; + del_rki[2] = x[k][2] - ztmp; + rik_sq = (del_rki[0] * del_rki[0]) + (del_rki[1] * del_rki[1]) + (del_rki[2] * del_rki[2]); + rik = sqrt(rik_sq); + + if ((rij <= cut_3b[itype][jtype][ktype]) && (rik <= cut_3b[itype][ktype][jtype]) && + (rij >= min_cut_3b[itype][jtype][ktype][2]) && + (rik >= min_cut_3b[itype][jtype][ktype][1])) { + + del_rkj[0] = x[k][0] - x[j][0]; + del_rkj[1] = x[k][1] - x[j][1]; + del_rkj[2] = x[k][2] - x[j][2]; + + rjk_sq = + (del_rkj[0] * del_rkj[0]) + (del_rkj[1] * del_rkj[1]) + (del_rkj[2] * del_rkj[2]); + rjk = sqrt(rjk_sq); + + if (rjk >= min_cut_3b[itype][jtype][ktype][0]) { + double rij_th = rij * rij_sq; + double rik_th = rik * rik_sq; + double rjk_th = rjk * rjk_sq; + + int map_to = map_3b[itype][jtype][ktype]; + int knot_start_index_ij = (this->*get_starting_index_3b)(itype, jtype, ktype, rij, 2); + int knot_start_index_ik = (this->*get_starting_index_3b)(itype, jtype, ktype, rik, 1); + int knot_start_index_jk = (this->*get_starting_index_3b)(itype, jtype, ktype, rjk, 0); + double basis_ij[4]; + double basis_ik[4]; + double basis_jk[4]; + double basis_ij_der[3]; + double basis_ik_der[3]; + double basis_jk_der[3]; + + //--------------basis_ij + basis_ij[0] = cached_constants_3b[map_to][0][knot_start_index_ij - 3][12]; + basis_ij[0] += rij * cached_constants_3b[map_to][0][knot_start_index_ij - 3][13]; + basis_ij[0] += rij_sq * cached_constants_3b[map_to][0][knot_start_index_ij - 3][14]; + basis_ij[0] += rij_th * cached_constants_3b[map_to][0][knot_start_index_ij - 3][15]; + + basis_ij[1] = cached_constants_3b[map_to][0][knot_start_index_ij - 2][8]; + basis_ij[1] += rij * cached_constants_3b[map_to][0][knot_start_index_ij - 2][9]; + basis_ij[1] += rij_sq * cached_constants_3b[map_to][0][knot_start_index_ij - 2][10]; + basis_ij[1] += rij_th * cached_constants_3b[map_to][0][knot_start_index_ij - 2][11]; + + basis_ij[2] = cached_constants_3b[map_to][0][knot_start_index_ij - 1][4]; + basis_ij[2] += rij * cached_constants_3b[map_to][0][knot_start_index_ij - 1][5]; + basis_ij[2] += rij_sq * cached_constants_3b[map_to][0][knot_start_index_ij - 1][6]; + basis_ij[2] += rij_th * cached_constants_3b[map_to][0][knot_start_index_ij - 1][7]; + + basis_ij[3] = cached_constants_3b[map_to][0][knot_start_index_ij][0]; + basis_ij[3] += rij * cached_constants_3b[map_to][0][knot_start_index_ij][1]; + basis_ij[3] += rij_sq * cached_constants_3b[map_to][0][knot_start_index_ij][2]; + basis_ij[3] += rij_th * cached_constants_3b[map_to][0][knot_start_index_ij][3]; + + //--------------basis_ik + basis_ik[0] = cached_constants_3b[map_to][1][knot_start_index_ik - 3][12]; + basis_ik[0] += rik * cached_constants_3b[map_to][1][knot_start_index_ik - 3][13]; + basis_ik[0] += rik_sq * cached_constants_3b[map_to][1][knot_start_index_ik - 3][14]; + basis_ik[0] += rik_th * cached_constants_3b[map_to][1][knot_start_index_ik - 3][15]; + + basis_ik[1] = cached_constants_3b[map_to][1][knot_start_index_ik - 2][8]; + basis_ik[1] += rik * cached_constants_3b[map_to][1][knot_start_index_ik - 2][9]; + basis_ik[1] += rik_sq * cached_constants_3b[map_to][1][knot_start_index_ik - 2][10]; + basis_ik[1] += rik_th * cached_constants_3b[map_to][1][knot_start_index_ik - 2][11]; + + basis_ik[2] = cached_constants_3b[map_to][1][knot_start_index_ik - 1][4]; + basis_ik[2] += rik * cached_constants_3b[map_to][1][knot_start_index_ik - 1][5]; + basis_ik[2] += rik_sq * cached_constants_3b[map_to][1][knot_start_index_ik - 1][6]; + basis_ik[2] += rik_th * cached_constants_3b[map_to][1][knot_start_index_ik - 1][7]; + + basis_ik[3] = cached_constants_3b[map_to][1][knot_start_index_ik][0]; + basis_ik[3] += rik * cached_constants_3b[map_to][1][knot_start_index_ik][1]; + basis_ik[3] += rik_sq * cached_constants_3b[map_to][1][knot_start_index_ik][2]; + basis_ik[3] += rik_th * cached_constants_3b[map_to][1][knot_start_index_ik][3]; + + //--------------basis_jk + basis_jk[0] = cached_constants_3b[map_to][2][knot_start_index_jk - 3][12]; + basis_jk[0] += rjk * cached_constants_3b[map_to][2][knot_start_index_jk - 3][13]; + basis_jk[0] += rjk_sq * cached_constants_3b[map_to][2][knot_start_index_jk - 3][14]; + basis_jk[0] += rjk_th * cached_constants_3b[map_to][2][knot_start_index_jk - 3][15]; + + basis_jk[1] = cached_constants_3b[map_to][2][knot_start_index_jk - 2][8]; + basis_jk[1] += rjk * cached_constants_3b[map_to][2][knot_start_index_jk - 2][9]; + basis_jk[1] += rjk_sq * cached_constants_3b[map_to][2][knot_start_index_jk - 2][10]; + basis_jk[1] += rjk_th * cached_constants_3b[map_to][2][knot_start_index_jk - 2][11]; + + basis_jk[2] = cached_constants_3b[map_to][2][knot_start_index_jk - 1][4]; + basis_jk[2] += rjk * cached_constants_3b[map_to][2][knot_start_index_jk - 1][5]; + basis_jk[2] += rjk_sq * cached_constants_3b[map_to][2][knot_start_index_jk - 1][6]; + basis_jk[2] += rjk_th * cached_constants_3b[map_to][2][knot_start_index_jk - 1][7]; + + basis_jk[3] = cached_constants_3b[map_to][2][knot_start_index_jk][0]; + basis_jk[3] += rjk * cached_constants_3b[map_to][2][knot_start_index_jk][1]; + basis_jk[3] += rjk_sq * cached_constants_3b[map_to][2][knot_start_index_jk][2]; + basis_jk[3] += rjk_th * cached_constants_3b[map_to][2][knot_start_index_jk][3]; + + //----------------basis_ij_der + basis_ij_der[0] = cached_constants_3b_deri[map_to][0][knot_start_index_ij - 3][6]; + basis_ij_der[0] += + rij * cached_constants_3b_deri[map_to][0][knot_start_index_ij - 3][7]; + basis_ij_der[0] += + rij_sq * cached_constants_3b_deri[map_to][0][knot_start_index_ij - 3][8]; + + basis_ij_der[1] = cached_constants_3b_deri[map_to][0][knot_start_index_ij - 2][3]; + basis_ij_der[1] += + rij * cached_constants_3b_deri[map_to][0][knot_start_index_ij - 2][4]; + basis_ij_der[1] += + rij_sq * cached_constants_3b_deri[map_to][0][knot_start_index_ij - 2][5]; + + basis_ij_der[2] = cached_constants_3b_deri[map_to][0][knot_start_index_ij - 1][0]; + basis_ij_der[2] += + rij * cached_constants_3b_deri[map_to][0][knot_start_index_ij - 1][1]; + basis_ij_der[2] += + rij_sq * cached_constants_3b_deri[map_to][0][knot_start_index_ij - 1][2]; + + //----------------basis_ik_der + basis_ik_der[0] = cached_constants_3b_deri[map_to][1][knot_start_index_ik - 3][6]; + basis_ik_der[0] += + rik * cached_constants_3b_deri[map_to][1][knot_start_index_ik - 3][7]; + basis_ik_der[0] += + rik_sq * cached_constants_3b_deri[map_to][1][knot_start_index_ik - 3][8]; + + basis_ik_der[1] = cached_constants_3b_deri[map_to][1][knot_start_index_ik - 2][3]; + basis_ik_der[1] += + rik * cached_constants_3b_deri[map_to][1][knot_start_index_ik - 2][4]; + basis_ik_der[1] += + rik_sq * cached_constants_3b_deri[map_to][1][knot_start_index_ik - 2][5]; + + basis_ik_der[2] = cached_constants_3b_deri[map_to][1][knot_start_index_ik - 1][0]; + basis_ik_der[2] += + rik * cached_constants_3b_deri[map_to][1][knot_start_index_ik - 1][1]; + basis_ik_der[2] += + rik_sq * cached_constants_3b_deri[map_to][1][knot_start_index_ik - 1][2]; + + //----------------basis_jk_der + basis_jk_der[0] = cached_constants_3b_deri[map_to][2][knot_start_index_jk - 3][6]; + basis_jk_der[0] += + rjk * cached_constants_3b_deri[map_to][2][knot_start_index_jk - 3][7]; + basis_jk_der[0] += + rjk_sq * cached_constants_3b_deri[map_to][2][knot_start_index_jk - 3][8]; + + basis_jk_der[1] = cached_constants_3b_deri[map_to][2][knot_start_index_jk - 2][3]; + basis_jk_der[1] += + rjk * cached_constants_3b_deri[map_to][2][knot_start_index_jk - 2][4]; + basis_jk_der[1] += + rjk_sq * cached_constants_3b_deri[map_to][2][knot_start_index_jk - 2][5]; + + basis_jk_der[2] = cached_constants_3b_deri[map_to][2][knot_start_index_jk - 1][0]; + basis_jk_der[2] += + rjk * cached_constants_3b_deri[map_to][2][knot_start_index_jk - 1][1]; + basis_jk_der[2] += + rjk_sq * cached_constants_3b_deri[map_to][2][knot_start_index_jk - 1][2]; + + double triangle_eval[4] = {0, 0, 0, 0}; + + int iknot_ij = knot_start_index_ij - 3; + int iknot_ik = knot_start_index_ik - 3; + int iknot_jk = knot_start_index_jk - 3; + + for (int l = 0; l < 3; l++) { + const double basis_ij_der_i = basis_ij_der[l]; + for (int m = 0; m < 4; m++) { + const double factor = basis_ij_der_i * basis_ik[m]; + const double *slice = + &coeff_for_der_ij[map_to][iknot_ij + l][iknot_ik + m][iknot_jk]; + double tmp[4]; + tmp[0] = slice[0] * basis_jk[0]; + tmp[1] = slice[1] * basis_jk[1]; + tmp[2] = slice[2] * basis_jk[2]; + tmp[3] = slice[3] * basis_jk[3]; + double sum = tmp[0] + tmp[1] + tmp[2] + tmp[3]; + triangle_eval[1] += factor * sum; + } + } + + for (int l = 0; l < 4; l++) { + const double basis_ij_i = basis_ij[l]; + for (int m = 0; m < 3; m++) { + const double factor = basis_ij_i * basis_ik_der[m]; + const double *slice = + &coeff_for_der_ik[map_to][iknot_ij + l][iknot_ik + m][iknot_jk]; + double tmp[4]; + tmp[0] = slice[0] * basis_jk[0]; + tmp[1] = slice[1] * basis_jk[1]; + tmp[2] = slice[2] * basis_jk[2]; + tmp[3] = slice[3] * basis_jk[3]; + double sum = tmp[0] + tmp[1] + tmp[2] + tmp[3]; + triangle_eval[2] += factor * sum; + } + } + + for (int l = 0; l < 4; l++) { + const double basis_ij_i = basis_ij[l]; + for (int m = 0; m < 4; m++) { + const double factor = basis_ij_i * basis_ik[m]; + const double *slice = + &coeff_for_der_jk[map_to][iknot_ij + l][iknot_ik + m][iknot_jk]; + double tmp[3]; + tmp[0] = slice[0] * basis_jk_der[0]; + tmp[1] = slice[1] * basis_jk_der[1]; + tmp[2] = slice[2] * basis_jk_der[2]; + double sum = tmp[0] + tmp[1] + tmp[2]; + triangle_eval[3] += factor * sum; + } + } + + fij[0] = *(triangle_eval + 1) * (del_rji[0] / rij); + fji[0] = -fij[0]; + fik[0] = *(triangle_eval + 2) * (del_rki[0] / rik); + fki[0] = -fik[0]; + fjk[0] = *(triangle_eval + 3) * (del_rkj[0] / rjk); + fkj[0] = -fjk[0]; + + fij[1] = *(triangle_eval + 1) * (del_rji[1] / rij); + fji[1] = -fij[1]; + fik[1] = *(triangle_eval + 2) * (del_rki[1] / rik); + fki[1] = -fik[1]; + fjk[1] = *(triangle_eval + 3) * (del_rkj[1] / rjk); + fkj[1] = -fjk[1]; + + fij[2] = *(triangle_eval + 1) * (del_rji[2] / rij); + fji[2] = -fij[2]; + fik[2] = *(triangle_eval + 2) * (del_rki[2] / rik); + fki[2] = -fik[2]; + fjk[2] = *(triangle_eval + 3) * (del_rkj[2] / rjk); + fkj[2] = -fjk[2]; + + Fi[0] = fij[0] + fik[0]; + Fi[1] = fij[1] + fik[1]; + Fi[2] = fij[2] + fik[2]; + f[i][0] += Fi[0]; + f[i][1] += Fi[1]; + f[i][2] += Fi[2]; + + Fj[0] = fji[0] + fjk[0]; + Fj[1] = fji[1] + fjk[1]; + Fj[2] = fji[2] + fjk[2]; + f[j][0] += Fj[0]; + f[j][1] += Fj[1]; + f[j][2] += Fj[2]; + + Fk[0] = fki[0] + fkj[0]; + Fk[1] = fki[1] + fkj[1]; + Fk[2] = fki[2] + fkj[2]; + f[k][0] += Fk[0]; + f[k][1] += Fk[1]; + f[k][2] += Fk[2]; + + if (eflag) { + for (int l = 0; l < 4; l++) { + const double basis_ij_i = basis_ij[l]; + for (int m = 0; m < 4; m++) { + const double factor = basis_ij_i * basis_ik[m]; + const double *slice = + &n3b_coeff_array[map_to][iknot_ij + l][iknot_ik + m][iknot_jk]; + double tmp[4]; + tmp[0] = slice[0] * basis_jk[0]; + tmp[1] = slice[1] * basis_jk[1]; + tmp[2] = slice[2] * basis_jk[2]; + tmp[3] = slice[3] * basis_jk[3]; + double sum = tmp[0] + tmp[1] + tmp[2] + tmp[3]; + triangle_eval[0] += factor * sum; + } + } + evdwl = *triangle_eval; + } + + if (evflag) { + ev_tally3(i, j, k, evdwl, 0, Fj, Fk, del_rji, del_rki); + // Centroid stress 3-body term + if (vflag_either && cvflag_atom) { + double ric[3]; + ric[0] = THIRD * (-del_rji[0] - del_rki[0]); + ric[1] = THIRD * (-del_rji[1] - del_rki[1]); + ric[2] = THIRD * (-del_rji[2] - del_rki[2]); + + cvatom[i][0] += ric[0] * Fi[0]; + cvatom[i][1] += ric[1] * Fi[1]; + cvatom[i][2] += ric[2] * Fi[2]; + cvatom[i][3] += ric[0] * Fi[1]; + cvatom[i][4] += ric[0] * Fi[2]; + cvatom[i][5] += ric[1] * Fi[2]; + cvatom[i][6] += ric[1] * Fi[0]; + cvatom[i][7] += ric[2] * Fi[0]; + cvatom[i][8] += ric[2] * Fi[1]; + + double rjc[3]; + rjc[0] = THIRD * (del_rji[0] - del_rkj[0]); + rjc[1] = THIRD * (del_rji[1] - del_rkj[1]); + rjc[2] = THIRD * (del_rji[2] - del_rkj[2]); + + cvatom[j][0] += rjc[0] * Fj[0]; + cvatom[j][1] += rjc[1] * Fj[1]; + cvatom[j][2] += rjc[2] * Fj[2]; + cvatom[j][3] += rjc[0] * Fj[1]; + cvatom[j][4] += rjc[0] * Fj[2]; + cvatom[j][5] += rjc[1] * Fj[2]; + cvatom[j][6] += rjc[1] * Fj[0]; + cvatom[j][7] += rjc[2] * Fj[0]; + cvatom[j][8] += rjc[2] * Fj[1]; + + double rkc[3]; + rkc[0] = THIRD * (del_rki[0] + del_rkj[0]); + rkc[1] = THIRD * (del_rki[1] + del_rkj[1]); + rkc[2] = THIRD * (del_rki[2] + del_rkj[2]); + + cvatom[k][0] += rkc[0] * Fk[0]; + cvatom[k][1] += rkc[1] * Fk[1]; + cvatom[k][2] += rkc[2] * Fk[2]; + cvatom[k][3] += rkc[0] * Fk[1]; + cvatom[k][4] += rkc[0] * Fk[2]; + cvatom[k][5] += rkc[1] * Fk[2]; + cvatom[k][6] += rkc[1] * Fk[0]; + cvatom[k][7] += rkc[2] * Fk[0]; + cvatom[k][8] += rkc[2] * Fk[1]; + } + } + } + } + } + } + } + if (vflag_fdotr) virial_fdotr_compute(); +} + +double PairUF3::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) +{ + double value = 0.0; + double r = sqrt(rsq); + + if (r < cut[itype][jtype]) { + int knot_start_index = (this->*get_starting_index_2b)(itype, jtype, r); + + double force_2b = cached_constants_2b_deri[itype][jtype][knot_start_index - 1][0]; + force_2b += r * cached_constants_2b_deri[itype][jtype][knot_start_index - 1][1]; + force_2b += rsq * cached_constants_2b_deri[itype][jtype][knot_start_index - 1][2]; + force_2b += cached_constants_2b_deri[itype][jtype][knot_start_index - 2][3]; + force_2b += r * cached_constants_2b_deri[itype][jtype][knot_start_index - 2][4]; + force_2b += rsq * cached_constants_2b_deri[itype][jtype][knot_start_index - 2][5]; + force_2b += cached_constants_2b_deri[itype][jtype][knot_start_index - 3][6]; + force_2b += r * cached_constants_2b_deri[itype][jtype][knot_start_index - 3][7]; + force_2b += rsq * cached_constants_2b_deri[itype][jtype][knot_start_index - 3][8]; + fforce = factor_lj * force_2b; + + double rth = rsq * r; + value = cached_constants_2b[itype][jtype][knot_start_index][0]; + value += r * cached_constants_2b[itype][jtype][knot_start_index][1]; + value += rsq * cached_constants_2b[itype][jtype][knot_start_index][2]; + value += rth * cached_constants_2b[itype][jtype][knot_start_index][3]; + value += cached_constants_2b[itype][jtype][knot_start_index - 1][4]; + value += r * cached_constants_2b[itype][jtype][knot_start_index - 1][5]; + value += rsq * cached_constants_2b[itype][jtype][knot_start_index - 1][6]; + value += rth * cached_constants_2b[itype][jtype][knot_start_index - 1][7]; + value += cached_constants_2b[itype][jtype][knot_start_index - 2][8]; + value += r * cached_constants_2b[itype][jtype][knot_start_index - 2][9]; + value += rsq * cached_constants_2b[itype][jtype][knot_start_index - 2][10]; + value += rth * cached_constants_2b[itype][jtype][knot_start_index - 2][11]; + value += cached_constants_2b[itype][jtype][knot_start_index - 3][12]; + value += r * cached_constants_2b[itype][jtype][knot_start_index - 3][13]; + value += rsq * cached_constants_2b[itype][jtype][knot_start_index - 3][14]; + value += rth * cached_constants_2b[itype][jtype][knot_start_index - 3][15]; + } + + return factor_lj * value; +} + +double PairUF3::memory_usage() +{ + const int num_of_elements = atom->ntypes; + double bytes = Pair::memory_usage(); + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(int); //***setflag_3b + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(int); //knot_spacing_type_2b + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(int); //knot_spacing_type_3b + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * sizeof(double); //cut + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(double); //***cut_3b + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * sizeof(double); //cut_3b_list + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * 3 * + sizeof(double); //min_cut_3b + + bytes += + (double) (num_of_elements + 1) * (num_of_elements + 1) * sizeof(double); //knot_spacing_2b + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(double); //knot_spacing_3b + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * max_num_knots_2b * + sizeof(double); //n2b_knots_array + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * max_num_coeff_2b * + sizeof(double); //n2b_coeff_array + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(int); //n2b_knots_array_size + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(int); //n2b_coeff_array_size + + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * max_num_coeff_2b * 16 * + sizeof(double); //cached_constants_2b, + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * (max_num_coeff_2b - 1) * 9 * + sizeof(double); //cached_constants_2b_deri + + if (pot_3b) { + bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * (num_of_elements + 1) * + sizeof(int); //map_3b + + bytes += (double) tot_interaction_count_3b * 3 * max_num_knots_3b * + sizeof(double); //n3b_knots_array + bytes += (double) tot_interaction_count_3b * max_num_coeff_3b * max_num_coeff_3b * + max_num_coeff_3b * sizeof(double); //n3b_coeff_array + + bytes += (double) tot_interaction_count_3b * 3 * sizeof(int); //n3b_knots_array_size + bytes += (double) tot_interaction_count_3b * 3 * sizeof(int); //n3b_coeff_array_size + + bytes += (double) tot_interaction_count_3b * max_num_coeff_3b * max_num_coeff_3b * + max_num_coeff_3b * 3 * + sizeof(double); //coeff_for_der_jk coeff_for_der_ik coeff_for_der_ij + + bytes += (double) tot_interaction_count_3b * 3 * max_num_coeff_3b * 16 * + sizeof(double); //cached_constants_3b + bytes += (double) tot_interaction_count_3b * 3 * (max_num_coeff_3b - 1) * 16 * + sizeof(double); //cached_constants_3b_deri + } + + bytes += (double) maxshort * sizeof(int); //neighshort + + bytes += (double) 6 * sizeof(int); //maxshort, bsplines_created, nbody_flag, + //max_num_knots_2b, max_num_coeff_2b, + //max_num_knots_3b, max_num_coeff_3b + bytes += (double) 1 * sizeof(bool); //pot_3b + + return bytes; +} diff --git a/src/ML-UF3/pair_uf3.h b/src/ML-UF3/pair_uf3.h new file mode 100644 index 0000000000..58a951c4c2 --- /dev/null +++ b/src/ML-UF3/pair_uf3.h @@ -0,0 +1,94 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Ajinkya Hire (Univ. of Florida), + Hendrik Kraß (Univ. of Constance), + Matthias Rupp (Luxembourg Institute of Science and Technology), + Richard Hennig (Univ of Florida) +---------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(uf3,PairUF3); +// clang-format on +#else + +#ifndef LMP_PAIR_UF3_H +#define LMP_PAIR_UF3_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairUF3 : public Pair { + public: + PairUF3(class LAMMPS *); + ~PairUF3() override; + void compute(int, int) override; + void settings(int, char **) override; + void coeff(int, char **) override; + void init_style() override; + void init_list(int, class NeighList *) override; // needed for ptr to full neigh list + double init_one(int, int) override; // needed for cutoff radius for neighbour list + double single(int, int, int, int, double, double, double, double &) override; + double memory_usage() override; + + protected: + int ***setflag_3b, **knot_spacing_type_2b, ***knot_spacing_type_3b; + double **cut, ***cut_3b, **cut_3b_list, ****min_cut_3b; + double **knot_spacing_2b, ****knot_spacing_3b; + + double ***n2b_knots_array, ***n2b_coeff_array; + int **n2b_knots_array_size, **n2b_coeff_array_size; + double ****cached_constants_2b, ****cached_constants_2b_deri; + + int ***map_3b; + double ***n3b_knots_array, ****n3b_coeff_array; + int **n3b_knots_array_size, **n3b_coeff_array_size; + double ****coeff_for_der_jk, ****coeff_for_der_ik, ****coeff_for_der_ij; + double ****cached_constants_3b, ****cached_constants_3b_deri; + + int *neighshort, maxshort; // short neighbor list array for 3body interaction + + void uf3_read_unified_pot_file(char *potf_name); + void communicate(); + int bsplines_created; + bool pot_3b; + + virtual void allocate(); + void create_bsplines(); + void create_cached_constants_2b(); + void create_cached_constants_3b(); + + int get_starting_index_uniform_2b(int i, int j, double r); + int get_starting_index_uniform_3b(int i, int j, int k, double r, int knot_dim); + + int get_starting_index_nonuniform_2b(int i, int j, double r); + int get_starting_index_nonuniform_3b(int i, int j, int k, double r, int knot_dim); + + int (PairUF3::*get_starting_index_2b)(int i, int j, double r); + int (PairUF3::*get_starting_index_3b)(int i, int j, int k, double r, int knot_dim); + + int nbody_flag; + int max_num_knots_2b; + int max_num_coeff_2b; + int max_num_knots_3b; + int max_num_coeff_3b; + int tot_interaction_count_3b; +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-UF3/uf3_bspline_basis2.cpp b/src/ML-UF3/uf3_bspline_basis2.cpp new file mode 100644 index 0000000000..bb73e07970 --- /dev/null +++ b/src/ML-UF3/uf3_bspline_basis2.cpp @@ -0,0 +1,111 @@ +// clang-format off +/* ---------------------------------------------------------------------- + lammps - large-scale atomic/molecular massively parallel simulator + https://www.lammps.org/, sandia national laboratories + lammps development team: developers@lammps.org + + copyright (2003) sandia corporation. under the terms of contract + de-ac04-94al85000 with sandia corporation, the u.s. government retains + certain rights in this software. this software is distributed under + the gnu general public license. + + see the readme file in the top-level lammps directory. +------------------------------------------------------------------------- */ + +#include "uf3_bspline_basis2.h" + +#include "math_special.h" + +using namespace LAMMPS_NS; +using MathSpecial::square; + +// Constructor +// Initializes coefficients and knots +// Requires [knots] to have length 4 +uf3_bspline_basis2::uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient) +{ + lmp = ulmp; + + double c0, c1, c2; + + c0 = coefficient + * (square(knots[0]) + / (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2])); + c1 = coefficient * + (-2.0 * knots[0] / + (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2])); + c2 = coefficient * + (1.0 / (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2])); + //constants.push_back(c0); + //constants.push_back(c1); + //constants.push_back(c2); + constants[0] = c0; + constants[1] = c1; + constants[2] = c2; + c0 = coefficient * + (-knots[1] * knots[3] / + (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) - + knots[0] * knots[2] / + (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2]))); + c1 = coefficient * + (knots[1] / + (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) + + knots[3] / + (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) + + knots[0] / + (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])) + + knots[2] / + (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2]))); + c2 = coefficient * + (-1.0 / (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) - + 1.0 / (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2]))); + //constants.push_back(c0); + //constants.push_back(c1); + //constants.push_back(c2); + constants[3] = c0; + constants[4] = c1; + constants[5] = c2; + c0 = coefficient * + (square(knots[3]) / + (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3]))); + c1 = coefficient * + (-2.0 * knots[3] / + (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3]))); + c2 = coefficient * + (1.0 / (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3]))); + //constants.push_back(c0); + //constants.push_back(c1); + //constants.push_back(c2); + constants[6] = c0; + constants[7] = c1; + constants[8] = c2; +} + +uf3_bspline_basis2::~uf3_bspline_basis2() {} + +// Evaluate outer-left part of spline +double uf3_bspline_basis2::eval0(double rsq, double r) +{ + return rsq * constants[2] + r * constants[1] + constants[0]; +} + +// Evaluate center-left part of spline +double uf3_bspline_basis2::eval1(double rsq, double r) +{ + return rsq * constants[5] + r * constants[4] + constants[3]; +} + +// Evaluate center-right part of spline +double uf3_bspline_basis2::eval2(double rsq, double r) +{ + return rsq * constants[8] + r * constants[7] + constants[6]; +} + +double uf3_bspline_basis2::memory_usage() +{ + double bytes = 0; + + bytes += (double)9*sizeof(double); + + return bytes; +} diff --git a/src/ML-UF3/uf3_bspline_basis2.h b/src/ML-UF3/uf3_bspline_basis2.h new file mode 100644 index 0000000000..b577e0c92a --- /dev/null +++ b/src/ML-UF3/uf3_bspline_basis2.h @@ -0,0 +1,41 @@ +// clang-format off +/* ---------------------------------------------------------------------- + lammps - large-scale atomic/molecular massively parallel simulator + https://www.lammps.org/, sandia national laboratories + lammps development team: developers@lammps.org + + copyright (2003) sandia corporation. under the terms of contract + de-ac04-94al85000 with sandia corporation, the u.s. government retains + certain rights in this software. this software is distributed under + the gnu general public license. + + see the readme file in the top-level lammps directory. +------------------------------------------------------------------------- */ +#include "pointers.h" + +#include + +#ifndef UF3_BSPLINE_BASIS2_H +#define UF3_BSPLINE_BASIS2_H + +namespace LAMMPS_NS { + +class uf3_bspline_basis2 { + private: + LAMMPS *lmp; + //std::vector constants; + + public: + uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient); + ~uf3_bspline_basis2(); + //std::vector constants; + double constants[9] = {}; + double eval0(double, double); + double eval1(double, double); + double eval2(double, double); + + double memory_usage(); +}; + +} // namespace LAMMPS_NS +#endif diff --git a/src/ML-UF3/uf3_bspline_basis3.cpp b/src/ML-UF3/uf3_bspline_basis3.cpp new file mode 100644 index 0000000000..b2c7aa2acb --- /dev/null +++ b/src/ML-UF3/uf3_bspline_basis3.cpp @@ -0,0 +1,355 @@ +// clang-format off +/* ---------------------------------------------------------------------- + lammps - large-scale atomic/molecular massively parallel simulator + https://www.lammps.org/, sandia national laboratories + lammps development team: developers@lammps.org + + copyright (2003) sandia corporation. under the terms of contract + de-ac04-94al85000 with sandia corporation, the u.s. government retains + certain rights in this software. this software is distributed under + the gnu general public license. + + see the readme file in the top-level lammps directory. +------------------------------------------------------------------------- */ + +#include "uf3_bspline_basis3.h" + +#include "math_special.h" + +using namespace LAMMPS_NS; +using MathSpecial::cube; +using MathSpecial::square; + +// Constructor +// Initializes coefficients and knots +// [knots] needs to have length 4 +uf3_bspline_basis3::uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient) +{ + lmp = ulmp; + + double c0, c1, c2, c3; + + c0 = coefficient * + (-cube(knots[0]) / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + c1 = coefficient * + (3.0 * square(knots[0]) / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + c2 = coefficient * + (-3.0 * knots[0] / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + c3 = coefficient * + (1.0 / + (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] - + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[3])); + //constants.push_back(c0); + //constants.push_back(c1); + //constants.push_back(c2); + //constants.push_back(c3); + constants[0] = c0; + constants[1] = c1; + constants[2] = c2; + constants[3] = c3; + c0 = coefficient * + (square(knots[1]) * knots[4] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) + + square(knots[0]) * knots[2] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) + + knots[0] * knots[1] * knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + c1 = coefficient * + (-square(knots[1]) / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) - + 2.0 * knots[1] * knots[4] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) - + square(knots[0]) / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) - + 2.0 * knots[0] * knots[2] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) - + knots[0] * knots[1] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) - + knots[0] * knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) - + knots[1] * knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + c2 = coefficient * + (2.0 * knots[1] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) + + knots[4] / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) + + 2.0 * knots[0] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) + + knots[2] / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) + + knots[0] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) + + knots[1] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3])) + + knots[3] / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + c3 = coefficient * + (-1.0 / + (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + knots[2] * knots[3] * knots[4]) - + 1.0 / + (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] + + knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] - + knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] - + knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) - + 1.0 / + (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] + + knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] + + square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] - + knots[1] * square(knots[3]) + knots[2] * square(knots[3]))); + //constants.push_back(c0); + //constants.push_back(c1); + //constants.push_back(c2); + //constants.push_back(c3); + constants[4] = c0; + constants[5] = c1; + constants[6] = c2; + constants[7] = c3; + c0 = coefficient * + (-knots[0] * square(knots[3]) / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) - + knots[1] * knots[3] * knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[2] * square(knots[4]) / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + c1 = coefficient * + (2.0 * knots[0] * knots[3] / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) + + square(knots[3]) / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) + + knots[1] * knots[3] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + knots[1] * knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + knots[3] * knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + 2.0 * knots[2] * knots[4] / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4])) + + square(knots[4]) / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + c2 = coefficient * + (-knots[0] / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) - + 2.0 * knots[3] / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) - + knots[1] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[3] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[4] / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) - + knots[2] / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4])) - + 2.0 * knots[4] / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + c3 = coefficient * + (1.0 / + (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] + + knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) + + knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) - + knots[2] * square(knots[3]) + cube(knots[3])) + + 1.0 / + (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] + + knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] - + knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] - + knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) + + 1.0 / + (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] + + knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] + + square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] - + knots[2] * square(knots[4]) + knots[3] * square(knots[4]))); + //constants.push_back(c0); + //constants.push_back(c1); + //constants.push_back(c2); + //constants.push_back(c3); + constants[8] = c0; + constants[9] = c1; + constants[10] = c2; + constants[11] = c3; + c0 = coefficient * + (cube(knots[4]) / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + c1 = coefficient * + (-3.0 * square(knots[4]) / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + c2 = coefficient * + (3.0 * knots[4] / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + c3 = coefficient * + (-1.0 / + (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] + + knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) + + knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) + + cube(knots[4]))); + //constants.push_back(c0); + //constants.push_back(c1); + //constants.push_back(c2); + //constants.push_back(c3); + constants[12] = c0; + constants[13] = c1; + constants[14] = c2; + constants[15] = c3; +} + +uf3_bspline_basis3::~uf3_bspline_basis3() {} + +// Evaluate outer-left part of spline +double uf3_bspline_basis3::eval0(double rth, double rsq, double r) +{ + return rth * constants[3] + rsq * constants[2] + r * constants[1] + constants[0]; +} + +// Evaluate center-left part of spline +double uf3_bspline_basis3::eval1(double rth, double rsq, double r) +{ + return rth * constants[7] + rsq * constants[6] + r * constants[5] + constants[4]; +} + +// Evaluate center-right part of spline +double uf3_bspline_basis3::eval2(double rth, double rsq, double r) +{ + return rth * constants[11] + rsq * constants[10] + r * constants[9] + constants[8]; +} + +// Evaluate outer-right part of spline +double uf3_bspline_basis3::eval3(double rth, double rsq, double r) +{ + return rth * constants[15] + rsq * constants[14] + r * constants[13] + constants[12]; +} + +double uf3_bspline_basis3::memory_usage() +{ + double bytes = 0; + + bytes += (double)16*sizeof(double); + + return bytes; +} diff --git a/src/ML-UF3/uf3_bspline_basis3.h b/src/ML-UF3/uf3_bspline_basis3.h new file mode 100644 index 0000000000..70e1bbd2aa --- /dev/null +++ b/src/ML-UF3/uf3_bspline_basis3.h @@ -0,0 +1,42 @@ +// clang-format off +/* ---------------------------------------------------------------------- + lammps - large-scale atomic/molecular massively parallel simulator + https://www.lammps.org/, sandia national laboratories + lammps development team: developers@lammps.org + + copyright (2003) sandia corporation. under the terms of contract + de-ac04-94al85000 with sandia corporation, the u.s. government retains + certain rights in this software. this software is distributed under + the gnu general public license. + + see the readme file in the top-level lammps directory. +------------------------------------------------------------------------- */ + +#include "pointers.h" + +#include + +#ifndef UF3_BSPLINE_BASIS3_H +#define UF3_BSPLINE_BASIS3_H + +namespace LAMMPS_NS { + +class uf3_bspline_basis3 { + private: + LAMMPS *lmp; + //std::vector constants; + + public: + uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient); + ~uf3_bspline_basis3(); + double constants[16] = {}; + double eval0(double, double, double); + double eval1(double, double, double); + double eval2(double, double, double); + double eval3(double, double, double); + + double memory_usage(); +}; + +} // namespace LAMMPS_NS +#endif diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index cb4cb8cadc..bc220da30e 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -970,7 +970,8 @@ void FixCMAP::read_data_section(char * /*keyword*/, int /*n*/, char *buf, atom5 = values.next_tagint(); if (values.has_next()) throw TokenizerException("too many items",line); } catch (std::exception &e) { - error->all(FLERR,"Incorrect format of CMAP section: {}", e.what()); + error->all(FLERR,"Incorrect format of CMAP section in data file: {}{}", + e.what(), utils::errorurl(2)); } atom1 += id_offset; diff --git a/src/Makefile b/src/Makefile index b9f1bcbdef..805b950112 100644 --- a/src/Makefile +++ b/src/Makefile @@ -74,6 +74,7 @@ PACKAGE = \ dpd-smooth \ drude \ eff \ + extra-command \ extra-compute \ extra-dump \ extra-fix \ @@ -104,6 +105,7 @@ PACKAGE = \ ml-quip \ ml-rann \ ml-snap \ + ml-uf3 \ mofff \ molfile \ netcdf \ @@ -167,6 +169,7 @@ PACKMOST = \ dpd-smooth \ drude \ eff \ + extra-command \ extra-compute \ extra-dump \ extra-fix \ diff --git a/src/OPENMP/angle_cosine_squared_omp.cpp b/src/OPENMP/angle_cosine_squared_omp.cpp index 9b849c62a3..f70e167d36 100644 --- a/src/OPENMP/angle_cosine_squared_omp.cpp +++ b/src/OPENMP/angle_cosine_squared_omp.cpp @@ -16,14 +16,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "angle_cosine_squared_omp.h" -#include + #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" +#include + +#include "omp_compat.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/OPENMP/angle_cosine_squared_restricted_omp.cpp b/src/OPENMP/angle_cosine_squared_restricted_omp.cpp new file mode 100644 index 0000000000..80960653b4 --- /dev/null +++ b/src/OPENMP/angle_cosine_squared_restricted_omp.cpp @@ -0,0 +1,170 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "angle_cosine_squared_restricted_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" + +#include + +#include "omp_compat.h" +#include "suffix.h" +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +AngleCosineSquaredRestrictedOMP::AngleCosineSquaredRestrictedOMP(class LAMMPS *lmp) + : AngleCosineSquaredRestricted(lmp), ThrOMP(lmp,THR_ANGLE) +{ + suffix_flag |= Suffix::OMP; +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineSquaredRestrictedOMP::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + const int inum = neighbor->nanglelist; + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr); + + if (inum > 0) { + if (evflag) { + if (eflag) { + if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr); + else eval<1,1,0>(ifrom, ito, thr); + } else { + if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr); + else eval<1,0,0>(ifrom, ito, thr); + } + } else { + if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr); + else eval<0,0,0>(ifrom, ito, thr); + } + } + thr->timer(Timer::BOND); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void AngleCosineSquaredRestrictedOMP::eval(int nfrom, int nto, ThrData * const thr) +{ + int i1,i2,i3,n,type; + double delx1,dely1,delz1,delx2,dely2,delz2; + double eangle,f1[3],f3[3]; + double tk,rsq1,rsq2,r1,r2,c,a,a11,a12,a22; + + const auto * _noalias const x = (dbl3_t *) atom->x[0]; + auto * _noalias const f = (dbl3_t *) thr->get_f()[0]; + const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0]; + const int nlocal = atom->nlocal; + eangle = 0.0; + + for (n = nfrom; n < nto; n++) { + i1 = anglelist[n].a; + i2 = anglelist[n].b; + i3 = anglelist[n].c; + type = anglelist[n].t; + + // 1st bond + + delx1 = x[i1].x - x[i2].x; + dely1 = x[i1].y - x[i2].y; + delz1 = x[i1].z - x[i2].z; + + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + // 2nd bond + + delx2 = x[i3].x - x[i2].x; + dely2 = x[i3].y - x[i2].y; + delz2 = x[i3].z - x[i2].z; + + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); + + // angle (cos and sin) + + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + // force & energy + + double sq_sin = 1.0 - c * c; + double c0 = cos(theta0[type]); + + tk = k[type] * (c - c0) * (1.0 - c * c0) / (sq_sin * sq_sin); + + if (EFLAG) eangle = k[type] * (c - c0) * (c - c0) / sq_sin; + + a = 2.0 * tk; + a11 = a*c / rsq1; + a12 = -a / (r1*r2); + a22 = a*c / rsq2; + + f1[0] = a11*delx1 + a12*delx2; + f1[1] = a11*dely1 + a12*dely2; + f1[2] = a11*delz1 + a12*delz2; + f3[0] = a22*delx2 + a12*delx1; + f3[1] = a22*dely2 + a12*dely1; + f3[2] = a22*delz2 + a12*delz1; + + // apply force to each of 3 atoms + + if (NEWTON_BOND || i1 < nlocal) { + f[i1].x += f1[0]; + f[i1].y += f1[1]; + f[i1].z += f1[2]; + } + + if (NEWTON_BOND || i2 < nlocal) { + f[i2].x -= f1[0] + f3[0]; + f[i2].y -= f1[1] + f3[1]; + f[i2].z -= f1[2] + f3[2]; + } + + if (NEWTON_BOND || i3 < nlocal) { + f[i3].x += f3[0]; + f[i3].y += f3[1]; + f[i3].z += f3[2]; + } + + if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3, + delx1,dely1,delz1,delx2,dely2,delz2,thr); + } +} diff --git a/src/OPENMP/angle_cosine_squared_restricted_omp.h b/src/OPENMP/angle_cosine_squared_restricted_omp.h new file mode 100644 index 0000000000..b2ad545230 --- /dev/null +++ b/src/OPENMP/angle_cosine_squared_restricted_omp.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef ANGLE_CLASS +// clang-format off +AngleStyle(cosine/squared/restricted/omp,AngleCosineSquaredRestrictedOMP); +// clang-format on +#else + +#ifndef LMP_ANGLE_COSINE_SQUARED_RESTRICTED_OMP_H +#define LMP_ANGLE_COSINE_SQUARED_RESTRICTED_OMP_H + +#include "angle_cosine_squared_restricted.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class AngleCosineSquaredRestrictedOMP : public AngleCosineSquaredRestricted, public ThrOMP { + + public: + AngleCosineSquaredRestrictedOMP(class LAMMPS *lmp); + void compute(int, int) override; + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/OPENMP/fix_omp.cpp b/src/OPENMP/fix_omp.cpp index 3a249bad82..59f0e9d534 100644 --- a/src/OPENMP/fix_omp.cpp +++ b/src/OPENMP/fix_omp.cpp @@ -161,12 +161,15 @@ void FixOMP::init() { // OPENMP package cannot be used with atom_style template if (atom->molecular == Atom::TEMPLATE) - error->all(FLERR,"OPENMP package does not (yet) work with " - "atom_style template"); + error->all(FLERR,"OPENMP package does not (yet) work with atom_style template"); // adjust number of data objects when the number of OpenMP // threads has been changed somehow const int nthreads = comm->nthreads; +#if defined(_OPENMP) + // make certain threads are initialized correctly. avoids segfaults with LAMMPS-GUI + if (nthreads != omp_get_max_threads()) omp_set_num_threads(nthreads); +#endif if (_nthr != nthreads) { if (comm->me == 0) utils::logmesg(lmp,"Re-init OPENMP for {} OpenMP thread(s)\n", nthreads); @@ -212,7 +215,7 @@ void FixOMP::init() // kspace_split < 0 : master partition, does not do kspace // kspace_split > 0 : slave partition, only does kspace - if (strstr(update->integrate_style,"verlet/split") != nullptr) { + if (utils::strmatch(update->integrate_style, "^verlet/split")) { if (universe->iworld == 0) kspace_split = -1; else kspace_split = 1; } else { @@ -226,7 +229,13 @@ void FixOMP::init() check_hybrid = 0; \ if (force->name) { \ if ( (strcmp(force->name ## _style,"hybrid") == 0) || \ - (strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \ + (strcmp(force->name ## _style,"hybrid/overlay") == 0) || \ + (strcmp(force->name ## _style,"hybrid/scaled") == 0) || \ + (strcmp(force->name ## _style,"hybrid/molecular") == 0) || \ + (strcmp(force->name ## _style,"hybrid/omp") == 0) || \ + (strcmp(force->name ## _style,"hybrid/overlay/omp") == 0) || \ + (strcmp(force->name ## _style,"hybrid/scaled/omp") == 0) || \ + (strcmp(force->name ## _style,"hybrid/molecular/omp") == 0) ) \ check_hybrid=1; \ if (force->name->suffix_flag & Suffix::OMP) { \ last_force_name = (const char *) #name; \ diff --git a/src/OPENMP/npair_skip_omp.h b/src/OPENMP/npair_skip_omp.h index 937304ad3f..ddfdb9f055 100644 --- a/src/OPENMP/npair_skip_omp.h +++ b/src/OPENMP/npair_skip_omp.h @@ -19,14 +19,12 @@ NPairStyle(skip/omp, NPairSkip, - NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NPairStyle(skip/half/respa/omp, NPairSkipRespa, - NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NPairStyle(skip/half/size/omp, @@ -36,32 +34,27 @@ NPairStyle(skip/half/size/omp, NPairStyle(skip/size/off2on/omp, NPairSkipSizeOff2on, - NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD | + NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NPairStyle(skip/size/off2on/oneside/omp, NPairSkipSizeOff2onOneside, - NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | - NP_ORTHO | NP_TRI | NP_OMP); + NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NPairStyle(skip/ghost/omp, NPairSkip, - NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST); NPairStyle(skip/trim/omp, NPairSkipTrim, - NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NPairStyle(skip/trim/half/respa/omp, NPairSkipTrimRespa, - NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NPairStyle(skip/trim/half/size/omp, @@ -71,20 +64,17 @@ NPairStyle(skip/trim/half/size/omp, NPairStyle(skip/trim/size/off2on/omp, NPairSkipTrimSizeOff2on, - NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD | + NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NPairStyle(skip/trim/size/off2on/oneside/omp, NPairSkipTrimSizeOff2onOneside, - NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | - NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); + NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NPairStyle(skip/trim/ghost/omp, NPairSkipTrim, - NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST); // clang-format off #endif diff --git a/src/OPENMP/pair_eam_omp.cpp b/src/OPENMP/pair_eam_omp.cpp index e99fbedbb7..c530f383df 100644 --- a/src/OPENMP/pair_eam_omp.cpp +++ b/src/OPENMP/pair_eam_omp.cpp @@ -17,6 +17,7 @@ #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" #include "neigh_list.h" @@ -45,6 +46,7 @@ void PairEAMOMP::compute(int eflag, int vflag) const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; const int inum = list->inum; + int beyond_rhomax = 0; // grow energy and fp arrays if necessary // need to be atom->nmax in length @@ -60,7 +62,7 @@ void PairEAMOMP::compute(int eflag, int vflag) } #if defined(_OPENMP) -#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) reduction(+:beyond_rhomax) #endif { int ifrom, ito, tid; @@ -77,24 +79,34 @@ void PairEAMOMP::compute(int eflag, int vflag) if (evflag) { if (eflag) { - if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr); - else eval<1,1,0>(ifrom, ito, thr); + if (force->newton_pair) eval<1,1,1>(ifrom, ito, &beyond_rhomax, thr); + else eval<1,1,0>(ifrom, ito, &beyond_rhomax, thr); } else { - if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr); - else eval<1,0,0>(ifrom, ito, thr); + if (force->newton_pair) eval<1,0,1>(ifrom, ito, &beyond_rhomax, thr); + else eval<1,0,0>(ifrom, ito, &beyond_rhomax, thr); } } else { - if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr); - else eval<0,0,0>(ifrom, ito, thr); + if (force->newton_pair) eval<0,0,1>(ifrom, ito, &beyond_rhomax, thr); + else eval<0,0,0>(ifrom, ito, &beyond_rhomax, thr); } thr->timer(Timer::PAIR); reduce_thr(this, eflag, vflag, thr); } // end of omp parallel region + + if (eflag && (!exceeded_rhomax)) { + MPI_Allreduce(&beyond_rhomax, &exceeded_rhomax, 1, MPI_INT, MPI_SUM, world); + if (exceeded_rhomax) { + if (comm->me == 0) + error->warning(FLERR, + "A per-atom density exceeded rhomax of EAM potential table - " + "a linear extrapolation to the energy was made"); + } + } } template -void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) +void PairEAMOMP::eval(int iifrom, int iito, int *beyond_rhomax, ThrData * const thr) { int i,j,ii,jj,m,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; @@ -203,7 +215,10 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; if (EFLAG) { phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; - if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); + if (rho[i] > rhomax) { + phi += fp[i] * (rho[i]-rhomax); + *beyond_rhomax = 1; + } e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, scale[type[i]][type[i]]*phi, 0.0, thr); } } diff --git a/src/OPENMP/pair_eam_omp.h b/src/OPENMP/pair_eam_omp.h index 1be24fc18a..e801e52762 100644 --- a/src/OPENMP/pair_eam_omp.h +++ b/src/OPENMP/pair_eam_omp.h @@ -39,7 +39,7 @@ class PairEAMOMP : public PairEAM, public ThrOMP { private: template - void eval(int iifrom, int iito, ThrData *const thr); + void eval(int iifrom, int iito, int *beyond_rhomax, ThrData *const thr); }; } // namespace LAMMPS_NS diff --git a/src/OPENMP/pair_pedone_omp.cpp b/src/OPENMP/pair_pedone_omp.cpp new file mode 100644 index 0000000000..140816bfe4 --- /dev/null +++ b/src/OPENMP/pair_pedone_omp.cpp @@ -0,0 +1,169 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_pedone_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairPedoneOMP::PairPedoneOMP(LAMMPS *lmp) : PairPedone(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairPedoneOMP::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + const int inum = list->inum; + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + if (evflag) { + if (eflag) { + if (force->newton_pair) + eval<1, 1, 1>(ifrom, ito, thr); + else + eval<1, 1, 0>(ifrom, ito, thr); + } else { + if (force->newton_pair) + eval<1, 0, 1>(ifrom, ito, thr); + else + eval<1, 0, 0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) + eval<0, 0, 1>(ifrom, ito, thr); + else + eval<0, 0, 0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairPedoneOMP::eval(int iifrom, int iito, ThrData *const thr) +{ + int i, j, ii, jj, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; + double rsq, r, r2inv, r6inv, dr, dexp, factor_lj; + int *ilist, *jlist, *numneigh, **firstneigh; + + evdwl = 0.0; + + const auto *_noalias const x = (dbl3_t *) atom->x[0]; + auto *_noalias const f = (dbl3_t *) thr->get_f()[0]; + const int *_noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double *_noalias const special_lj = force->special_lj; + double fxtmp, fytmp, fztmp; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp = fytmp = fztmp = 0.0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx * delx + dely * dely + delz * delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + + pedone2[itype][jtype] * r6inv * r6inv * r2inv; + fpair *= factor_lj; + + fxtmp += delx * fpair; + fytmp += dely * fpair; + fztmp += delz * fpair; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= delx * fpair; + f[j].y -= dely * fpair; + f[j].z -= delz * fpair; + } + + if (EFLAG) { + evdwl = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) + c0[itype][jtype] * r6inv * r6inv - + offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (EVFLAG) + ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, 0.0, fpair, delx, dely, delz, thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairPedoneOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairPedone::memory_usage(); + + return bytes; +} diff --git a/src/OPENMP/pair_pedone_omp.h b/src/OPENMP/pair_pedone_omp.h new file mode 100644 index 0000000000..8c23e86fcd --- /dev/null +++ b/src/OPENMP/pair_pedone_omp.h @@ -0,0 +1,48 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(pedone/omp,PairPedoneOMP); +// clang-format on +#else + +#ifndef LMP_PAIR_PEDONE_OMP_H +#define LMP_PAIR_PEDONE_OMP_H + +#include "pair_pedone.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairPedoneOMP : public PairPedone, public ThrOMP { + + public: + PairPedoneOMP(class LAMMPS *); + + void compute(int, int) override; + double memory_usage() override; + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index 0560b0693a..96afff4ee5 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -23,6 +23,7 @@ #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" #include "neigh_list.h" @@ -118,6 +119,7 @@ template void PairEAMOpt::eval() int ntypes = atom->ntypes; int ntypes2 = ntypes * ntypes; + int beyond_rhomax = 0; auto *_noalias fast_alpha = (fast_alpha_t *) malloc((size_t) ntypes2 * (nr + 1) * sizeof(fast_alpha_t)); @@ -251,7 +253,10 @@ template void PairEAMOpt::eval() fp[i] = (coeff[0] * p + coeff[1]) * p + coeff[2]; if (EFLAG) { double phi = ((coeff[3] * p + coeff[4]) * p + coeff[5]) * p + coeff[6]; - if (rho[i] > rhomax) phi += fp[i] * (rho[i] - rhomax); + if (rho[i] > rhomax) { + phi += fp[i] * (rho[i] - rhomax); + beyond_rhomax = 1; + } phi *= scale[type[i]][type[i]]; if (eflag_global) eng_vdwl += phi; if (eflag_atom) eatom[i] += phi; @@ -361,5 +366,15 @@ template void PairEAMOpt::eval() free(fast_gamma); fast_gamma = nullptr; + if (EFLAG && (!exceeded_rhomax)) { + MPI_Allreduce(&beyond_rhomax, &exceeded_rhomax, 1, MPI_INT, MPI_SUM, world); + if (exceeded_rhomax) { + if (comm->me == 0) + error->warning(FLERR, + "A per-atom density exceeded rhomax of EAM potential table - " + "a linear extrapolation to the energy was made"); + } + } + if (vflag_fdotr) virial_fdotr_compute(); } diff --git a/src/PLUMED/fix_plumed.cpp b/src/PLUMED/fix_plumed.cpp index ad7f4f3995..2bf56acbbf 100644 --- a/src/PLUMED/fix_plumed.cpp +++ b/src/PLUMED/fix_plumed.cpp @@ -77,9 +77,9 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) : int api_version=0; p->cmd("getApiVersion",&api_version); - if ((api_version < 5) || (api_version > 9)) + if ((api_version < 5) || (api_version > 10)) error->all(FLERR,"Incompatible API version for PLUMED in fix plumed. " - "Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x are tested and supported."); + "Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x, 2.9.x are tested and supported."); #if !defined(MPI_STUBS) // If the -partition option is activated then enable @@ -205,6 +205,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) : double dt=update->dt; p->cmd("setTimestep",&dt); + extscalar = 1; scalar_flag = 1; energy_global_flag = virial_global_flag = 1; thermo_energy = thermo_virial = 1; diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 411bdfb60b..47ad3d260f 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -74,6 +74,9 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) : if ((nevery <= 0) || (cutoff <= 0.0) || (tolerance <= 0.0) || (maxiter <= 0)) error->all(FLERR,"Illegal fix qeq command"); + // must have charges + if (!atom->q_flag) error->all(FLERR, "Fix {} requires atom attribute q", style); + alpha = 0.20; swa = 0.0; swb = cutoff; diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 6987732048..2e653b9226 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -55,29 +55,53 @@ void FixQEqShielded::init() neighbor->add_request(this, NeighConst::REQ_FULL); - int ntypes = atom->ntypes; + const int ntypes = atom->ntypes; memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding"); init_shielding(); - int i; - for (i = 1; i <= ntypes; i++) { - if (gamma[i] == 0.0) error->all(FLERR, "Invalid param file for fix qeq/shielded"); + // check if valid parameters for all atom types in the fix group are provided + const int *type = atom->type; + const int *mask = atom->mask; + int tmp = 0, tmp_all = 0; + for (int i = 0; i < nlocal; ++i) { + if (mask[i] & groupbit) { + if (gamma[type[i]] == 0.0) + tmp = type[i]; + } } + MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world); + if (tmp_all) + error->all(FLERR, "Invalid QEq parameters for atom type {} provided", tmp_all); } /* ---------------------------------------------------------------------- */ void FixQEqShielded::extract_reax() { - Pair *pair = force->pair_match("^reax..", 0); - if (pair == nullptr) error->all(FLERR, "No pair reaxff for fix qeq/shielded"); - int tmp; + const int nlocal = atom->nlocal; + const int *mask = atom->mask; + const int *type = atom->type; + + Pair *pair = force->pair_match("^reaxff", 0); + if (pair == nullptr) error->all(FLERR, "No reaxff pair style for fix qeq/shielded"); + int tmp, tmp_all; chi = (double *) pair->extract("chi", tmp); eta = (double *) pair->extract("eta", tmp); gamma = (double *) pair->extract("gamma", tmp); - if (chi == nullptr || eta == nullptr || gamma == nullptr) - error->all(FLERR, "Fix qeq/shielded could not extract params from pair reaxff"); + if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr)) + error->all(FLERR, "Fix qeq/shielded could not extract all QEq parameters from pair reaxff"); + + tmp = tmp_all = 0; + for (int i = 0; i < nlocal; ++i) { + if (mask[i] & groupbit) { + if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0)) + tmp = type[i]; + } + } + MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world); + if (tmp_all) + error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all); } // clang-format off diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp index ab561de0a7..7e935fd6cd 100644 --- a/src/REAXFF/fix_qeq_reaxff.cpp +++ b/src/REAXFF/fix_qeq_reaxff.cpp @@ -141,7 +141,7 @@ FixQEqReaxFF::FixQEqReaxFF(LAMMPS *lmp, int narg, char **arg) : // perform initial allocation of atom-based arrays // register with Atom class - reaxff = dynamic_cast(force->pair_match("^reax..",0)); + reaxff = dynamic_cast(force->pair_match("^reaxff",0)); s_hist = t_hist = nullptr; atom->add_callback(Atom::GROW); @@ -205,23 +205,43 @@ int FixQEqReaxFF::setmask() void FixQEqReaxFF::pertype_parameters(char *arg) { + const int nlocal = atom->nlocal; + const int *mask = atom->mask; + const int *type = atom->type; + if (utils::strmatch(arg,"^reaxff")) { reaxflag = 1; Pair *pair = force->pair_match("^reaxff",0); if (!pair) error->all(FLERR,"No reaxff pair style for fix qeq/reaxff"); - int tmp; + int tmp, tmp_all; chi = (double *) pair->extract("chi",tmp); eta = (double *) pair->extract("eta",tmp); gamma = (double *) pair->extract("gamma",tmp); - if (chi == nullptr || eta == nullptr || gamma == nullptr) - error->all(FLERR, "Fix qeq/reaxff could not extract params from pair reaxff"); + if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr)) + error->all(FLERR, "Fix qeq/reaxff could not extract all QEq parameters from pair reaxff"); + tmp = tmp_all = 0; + for (int i = 0; i < nlocal; ++i) { + if (mask[i] & groupbit) { + if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0)) + tmp = type[i]; + } + } + MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world); + if (tmp_all) + error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all); return; + } else if (utils::strmatch(arg,"^reax/c")) { + error->all(FLERR, "Fix qeq/reaxff keyword 'reax/c' is obsolete; please use 'reaxff'"); + } else if (platform::file_is_readable(arg)) { + ; // arg is readable file. will read below + } else { + error->all(FLERR, "Unknown fix qeq/reaxff keyword {}", arg); } reaxflag = 0; - const int ntypes = atom->ntypes; + const int ntypes = atom->ntypes; memory->create(chi,ntypes+1,"qeq/reaxff:chi"); memory->create(eta,ntypes+1,"qeq/reaxff:eta"); memory->create(gamma,ntypes+1,"qeq/reaxff:gamma"); diff --git a/src/REAXFF/fix_reaxff_species.cpp b/src/REAXFF/fix_reaxff_species.cpp index 8fa06cafb3..0183d2670b 100644 --- a/src/REAXFF/fix_reaxff_species.cpp +++ b/src/REAXFF/fix_reaxff_species.cpp @@ -65,7 +65,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), Name(nullptr), MolName(nullptr), NMol(nullptr), nd(nullptr), MolType(nullptr), molmap(nullptr), mark(nullptr), Mol2Spec(nullptr), clusterID(nullptr), x0(nullptr), BOCut(nullptr), fp(nullptr), pos(nullptr), fdel(nullptr), delete_Tcount(nullptr), - ele(nullptr), eletype(nullptr), filepos(nullptr), filedel(nullptr) + filepos(nullptr), filedel(nullptr) { if (narg < 7) utils::missing_cmd_args(FLERR, "fix reaxff/species", error); @@ -84,6 +84,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : nvalid = -1; ntypes = atom->ntypes; + eletype.resize(ntypes); + ueletype.resize(ntypes); + ele2uele.resize(ntypes); nevery = utils::inumeric(FLERR, arg[3], false, lmp); nrepeat = utils::inumeric(FLERR, arg[4], false, lmp); @@ -156,8 +159,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : for (int j = 1; j < np1; j++) BOCut[i][j] = bo_cut; // optional args - eletype = nullptr; - ele = filepos = filedel = nullptr; + filepos = filedel = nullptr; eleflag = posflag = padflag = 0; delflag = specieslistflag = masslimitflag = 0; delete_Nlimit = delete_Nsteps = 0; @@ -191,14 +193,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : if (iarg + ntypes + 1 > narg) utils::missing_cmd_args(FLERR, "fix reaxff/species element", error); - eletype = (char **) malloc(ntypes * sizeof(char *)); - int len; - for (int i = 0; i < ntypes; i++) { - len = strlen(arg[iarg + 1 + i]) + 1; - eletype[i] = (char *) malloc(len * sizeof(char)); - strcpy(eletype[i], arg[iarg + 1 + i]); - } - eleflag = 1; + for (int i = 0; i < ntypes; i++) + eletype[i] = arg[iarg + 1 + i]; + GetUniqueElements(); iarg += ntypes + 1; // delete species @@ -285,14 +282,6 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Unknown fix reaxff/species keyword: {}", arg[iarg]); } - if (!eleflag) { - memory->create(ele, ntypes + 1, "reaxff/species:ele"); - ele[0] = 'C'; - if (ntypes > 1) ele[1] = 'H'; - if (ntypes > 2) ele[2] = 'O'; - if (ntypes > 3) ele[3] = 'N'; - } - if (delflag && specieslistflag && masslimitflag) error->all(FLERR, "Incompatible combination fix reaxff/species command options"); @@ -312,7 +301,6 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : FixReaxFFSpecies::~FixReaxFFSpecies() { - memory->destroy(ele); memory->destroy(BOCut); memory->destroy(clusterID); memory->destroy(x0); @@ -358,7 +346,14 @@ int FixReaxFFSpecies::setmask() void FixReaxFFSpecies::setup(int /*vflag*/) { ntotal = static_cast(atom->natoms); - if (Name == nullptr) memory->create(Name, ntypes, "reaxff/species:Name"); + + if (!eleflag) { + for (int i = 0; i < ntypes; i++) + eletype[i] = reaxff->eletype[i+1]; + GetUniqueElements(); + } + memory->destroy(Name); + memory->create(Name, nutypes, "reaxff/species:Name"); post_integrate(); } @@ -648,14 +643,14 @@ void FixReaxFFSpecies::FindSpecies(int Nmole, int &Nspec) memory->destroy(MolName); MolName = nullptr; - memory->create(MolName, Nmole * (ntypes + 1), "reaxff/species:MolName"); + memory->create(MolName, Nmole * (nutypes + 1), "reaxff/species:MolName"); memory->destroy(NMol); NMol = nullptr; memory->create(NMol, Nmole, "reaxff/species:NMol"); for (m = 0; m < Nmole; m++) NMol[m] = 1; - memory->create(Nameall, ntypes, "reaxff/species:Nameall"); + memory->create(Nameall, nutypes, "reaxff/species:Nameall"); memory->create(NMolall, Nmole, "reaxff/species:NMolall"); memory->destroy(Mol2Spec); @@ -664,12 +659,12 @@ void FixReaxFFSpecies::FindSpecies(int Nmole, int &Nspec) for (m = 0; m < Nmole; m++) Mol2Spec[m] = -1; for (m = 1, Nspec = 0; m <= Nmole; m++) { - for (n = 0; n < ntypes; n++) Name[n] = 0; + for (n = 0; n < nutypes; n++) Name[n] = 0; for (n = 0, flag_mol = 0; n < nlocal; n++) { if (!(mask[n] & groupbit)) continue; cid = nint(clusterID[n]); if (cid == m) { - itype = atom->type[n] - 1; + itype = ele2uele[atom->type[n] - 1]; Name[itype]++; flag_mol = 1; } @@ -677,15 +672,15 @@ void FixReaxFFSpecies::FindSpecies(int Nmole, int &Nspec) MPI_Allreduce(&flag_mol, &flag_tmp, 1, MPI_INT, MPI_MAX, world); flag_mol = flag_tmp; - MPI_Allreduce(Name, Nameall, ntypes, MPI_INT, MPI_SUM, world); - for (n = 0; n < ntypes; n++) Name[n] = Nameall[n]; + MPI_Allreduce(Name, Nameall, nutypes, MPI_INT, MPI_SUM, world); + for (n = 0; n < nutypes; n++) Name[n] = Nameall[n]; if (flag_mol == 1) { flag_identity = 1; for (k = 0; k < Nspec; k++) { flag_spec = 0; - for (l = 0; l < ntypes; l++) - if (MolName[ntypes * k + l] != Name[l]) flag_spec = 1; + for (l = 0; l < nutypes; l++) + if (MolName[nutypes * k + l] != Name[l]) flag_spec = 1; if (flag_spec == 0) { NMol[k]++; Mol2Spec[m - 1] = k; @@ -693,7 +688,7 @@ void FixReaxFFSpecies::FindSpecies(int Nmole, int &Nspec) flag_identity *= flag_spec; } if (Nspec == 0 || flag_identity == 1) { - for (l = 0; l < ntypes; l++) MolName[ntypes * Nspec + l] = Name[l]; + for (l = 0; l < nutypes; l++) MolName[nutypes * Nspec + l] = Name[l]; Mol2Spec[m - 1] = Nspec; Nspec++; } @@ -708,24 +703,24 @@ void FixReaxFFSpecies::FindSpecies(int Nmole, int &Nspec) memory->destroy(MolType); MolType = nullptr; - memory->create(MolType, Nspec * (ntypes + 2), "reaxff/species:MolType"); + memory->create(MolType, Nspec * (nutypes + 2), "reaxff/species:MolType"); } /* ---------------------------------------------------------------------- */ -int FixReaxFFSpecies::CheckExistence(int id, int ntypes) +int FixReaxFFSpecies::CheckExistence(int id, int nutypes) { int i, j, molid, flag; for (i = 0; i < Nmoltype; i++) { flag = 0; - for (j = 0; j < ntypes; j++) { - molid = MolType[ntypes * i + j]; - if (molid != MolName[ntypes * id + j]) flag = 1; + for (j = 0; j < nutypes; j++) { + molid = MolType[nutypes * i + j]; + if (molid != MolName[nutypes * id + j]) flag = 1; } if (flag == 0) return i; } - for (i = 0; i < ntypes; i++) MolType[ntypes * Nmoltype + i] = MolName[ntypes * id + i]; + for (i = 0; i < nutypes; i++) MolType[nutypes * Nmoltype + i] = MolName[nutypes * id + i]; Nmoltype++; return Nmoltype - 1; @@ -733,6 +728,50 @@ int FixReaxFFSpecies::CheckExistence(int id, int ntypes) /* ---------------------------------------------------------------------- */ +void FixReaxFFSpecies::GetUniqueElements() +{ + eleflag = 1; + + // get unique 'element' labels + + nutypes = 0; + int skipflag; + for (int i = 0; i < ntypes; i++) { + skipflag = 0; + for (int j = 0; j < nutypes; j++) + if (eletype[i] == ueletype[j]) { + skipflag = 1; + break; + } + if (skipflag) continue; + ueletype[nutypes++] = eletype[i]; + } + + // reorder CHON, if necessary + + int incr = 0; + std::vector CHON = {"C", "H", "O", "N"}; + for (auto it = CHON.begin(); it != CHON.end(); ++it) + for (int j = incr; j < nutypes; j++) { + if (ueletype[j] == *it) { + ueletype.erase(ueletype.begin() + j); + ueletype.insert(ueletype.begin() + incr++, *it); + break; + } + } + + // map user input to unique list + + for (int i = 0; i < ntypes; i++) + for (int j = 0; j < nutypes; j++) + if (eletype[i] == ueletype[j]) { + ele2uele[i] = j; + break; + } +} + +/* ---------------------------------------------------------------------- */ + void FixReaxFFSpecies::WriteFormulas(int Nmole, int Nspec) { int i, j, itemp; @@ -742,17 +781,14 @@ void FixReaxFFSpecies::WriteFormulas(int Nmole, int Nspec) Nmoltype = 0; - for (i = 0; i < Nspec; i++) nd[i] = CheckExistence(i, ntypes); + for (i = 0; i < Nspec; i++) nd[i] = CheckExistence(i, nutypes); for (i = 0; i < Nmoltype; i++) { std::string molname; - for (j = 0; j < ntypes; j++) { - itemp = MolType[ntypes * i + j]; + for (j = 0; j < nutypes; j++) { + itemp = MolType[nutypes * i + j]; if (itemp != 0) { - if (eletype) - molname += eletype[j]; - else - molname += ele[j]; + molname += ueletype[j]; if (itemp != 1) molname += std::to_string(itemp); } } @@ -810,20 +846,20 @@ void FixReaxFFSpecies::WritePos(int Nmole, int Nspec) } Nameall = nullptr; - memory->create(Nameall, ntypes, "reaxff/species:Nameall"); + memory->create(Nameall, nutypes, "reaxff/species:Nameall"); for (m = 1; m <= Nmole; m++) { count = 0; avq = 0.0; for (n = 0; n < 3; n++) avx[n] = 0.0; - for (n = 0; n < ntypes; n++) Name[n] = 0; + for (n = 0; n < nutypes; n++) Name[n] = 0; for (i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; cid = nint(clusterID[i]); if (cid == m) { - itype = atom->type[i] - 1; + itype = ele2uele[atom->type[i] - 1]; Name[itype]++; count++; avq += spec_atom[i][0]; @@ -850,17 +886,14 @@ void FixReaxFFSpecies::WritePos(int Nmole, int Nspec) MPI_Reduce(&count, &count_tmp, 1, MPI_INT, MPI_SUM, 0, world); count = count_tmp; - MPI_Reduce(Name, Nameall, ntypes, MPI_INT, MPI_SUM, 0, world); - for (n = 0; n < ntypes; n++) Name[n] = Nameall[n]; + MPI_Reduce(Name, Nameall, nutypes, MPI_INT, MPI_SUM, 0, world); + for (n = 0; n < nutypes; n++) Name[n] = Nameall[n]; if (comm->me == 0) { fprintf(pos, "%d\t%d\t", m, count); - for (n = 0; n < ntypes; n++) { + for (n = 0; n < nutypes; n++) { if (Name[n] != 0) { - if (eletype) - fprintf(pos, "%s", eletype[n]); - else - fprintf(pos, "%c", ele[n]); + fprintf(pos, "%s", ueletype[n].c_str()); if (Name[n] != 1) fprintf(pos, "%d", Name[n]); } } @@ -912,7 +945,7 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec) for (i = 0; i < nlocal; i++) mark[i] = 0; Nameall = nullptr; - memory->create(Nameall, ntypes, "reaxff/species:Nameall"); + memory->create(Nameall, nutypes, "reaxff/species:Nameall"); int ndelcomm; if (masslimitflag) @@ -944,13 +977,13 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec) if (this_delete_Tcount == headroom) break; m = molrange[mm]; localmass = totalmass = count = nmarklist = 0; - for (n = 0; n < ntypes; n++) Name[n] = 0; + for (n = 0; n < nutypes; n++) Name[n] = 0; for (i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; cid = nint(clusterID[i]); if (cid == m) { - itype = atom->type[i] - 1; + itype = ele2uele[atom->type[i] - 1]; Name[itype]++; count++; marklist[nmarklist++] = i; @@ -961,18 +994,15 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec) MPI_Allreduce(&count, &count_tmp, 1, MPI_INT, MPI_SUM, world); count = count_tmp; - MPI_Allreduce(Name, Nameall, ntypes, MPI_INT, MPI_SUM, world); - for (n = 0; n < ntypes; n++) Name[n] = Nameall[n]; + MPI_Allreduce(Name, Nameall, nutypes, MPI_INT, MPI_SUM, world); + for (n = 0; n < nutypes; n++) Name[n] = Nameall[n]; MPI_Allreduce(&localmass, &totalmass, 1, MPI_DOUBLE, MPI_SUM, world); species_str = ""; - for (j = 0; j < ntypes; j++) { + for (j = 0; j < nutypes; j++) { if (Name[j] != 0) { - if (eletype) - species_str += eletype[j]; - else - species_str += ele[j]; + species_str += ueletype[j]; if (Name[j] != 1) species_str += fmt::format("{}", Name[j]); } } @@ -1034,13 +1064,10 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec) printflag = 1; } fprintf(fdel, " %g ", deletecount[m]); - for (j = 0; j < ntypes; j++) { - int itemp = MolName[ntypes * m + j]; + for (j = 0; j < nutypes; j++) { + int itemp = MolName[nutypes * m + j]; if (itemp != 0) { - if (eletype) - fprintf(fdel, "%s", eletype[j]); - else - fprintf(fdel, "%c", ele[j]); + fprintf(fdel, "%s", ueletype[j].c_str()); if (itemp != 1) fprintf(fdel, "%d", itemp); } } diff --git a/src/REAXFF/fix_reaxff_species.h b/src/REAXFF/fix_reaxff_species.h index 8fcbb131a9..b9afc5466a 100644 --- a/src/REAXFF/fix_reaxff_species.h +++ b/src/REAXFF/fix_reaxff_species.h @@ -43,7 +43,7 @@ class FixReaxFFSpecies : public Fix { double compute_vector(int) override; protected: - int nmax, nlocal, ntypes, ntotal; + int nmax, nlocal, ntypes, nutypes, ntotal; int nrepeat, nfreq, posfreq, compressed, ndelspec; int Nmoltype, vector_nmole, vector_nspec; int *Name, *MolName, *NMol, *nd, *MolType, *molmap, *mark; @@ -62,7 +62,10 @@ class FixReaxFFSpecies : public Fix { int delete_Nsteps, *delete_Tcount; double massmin, massmax; int singlepos_opened, multipos_opened, del_opened; - char *ele, **eletype, *filepos, *filedel; + char *filepos, *filedel; + std::vector ele2uele; // for element eletype[i], ele2uele[i] stores index of unique element + std::vector eletype; // list of ReaxFF elements of length ntypes + std::vector ueletype; // list of unique elements, of quantity nutypes void Output_ReaxFF_Bonds(bigint, FILE *); AtomCoord chAnchor(AtomCoord, AtomCoord); @@ -72,6 +75,7 @@ class FixReaxFFSpecies : public Fix { void WriteFormulas(int, int); void DeleteSpecies(int, int); int CheckExistence(int, int); + void GetUniqueElements(); int nint(const double &); int pack_forward_comm(int, int *, double *, int, int *) override; diff --git a/src/REAXFF/pair_reaxff.cpp b/src/REAXFF/pair_reaxff.cpp index 1867aec81b..b9f4f6c838 100644 --- a/src/REAXFF/pair_reaxff.cpp +++ b/src/REAXFF/pair_reaxff.cpp @@ -297,14 +297,17 @@ void PairReaxFF::coeff(int nargs, char **args) } int n = atom->ntypes; + eletype.resize(n+1); // pair_coeff element map - for (int i = 3; i < nargs; i++) + for (int i = 3; i < nargs; i++) { + eletype[i-2] = args[i]; for (int j = 0; j < nreax_types; j++) if (utils::lowercase(args[i]) == utils::lowercase(api->system->reax_param.sbp[j].name)) { map[i-2] = j; itmp ++; } + } // error check if (itmp != n) @@ -691,24 +694,28 @@ void *PairReaxFF::extract(const char *str, int &dim) { dim = 1; if (strcmp(str,"chi") == 0 && chi) { + chi[0] = 0.0; for (int i = 1; i <= atom->ntypes; i++) if (map[i] >= 0) chi[i] = api->system->reax_param.sbp[map[i]].chi; else chi[i] = 0.0; return (void *) chi; } if (strcmp(str,"eta") == 0 && eta) { + eta[0] = 0.0; for (int i = 1; i <= atom->ntypes; i++) if (map[i] >= 0) eta[i] = api->system->reax_param.sbp[map[i]].eta; else eta[i] = 0.0; return (void *) eta; } if (strcmp(str,"gamma") == 0 && gamma) { + gamma[0] = 0.0; for (int i = 1; i <= atom->ntypes; i++) if (map[i] >= 0) gamma[i] = api->system->reax_param.sbp[map[i]].gamma; else gamma[i] = 0.0; return (void *) gamma; } if (strcmp(str,"bcut_acks2") == 0 && bcut_acks2) { + bcut_acks2[0] = 0.0; for (int i = 1; i <= atom->ntypes; i++) if (map[i] >= 0) bcut_acks2[i] = api->system->reax_param.sbp[map[i]].bcut_acks2; else bcut_acks2[i] = 0.0; diff --git a/src/REAXFF/pair_reaxff.h b/src/REAXFF/pair_reaxff.h index 594e7e502d..7bd2c6efe1 100644 --- a/src/REAXFF/pair_reaxff.h +++ b/src/REAXFF/pair_reaxff.h @@ -53,6 +53,7 @@ class PairReaxFF : public Pair { int fixbond_flag, fixspecies_flag; int **tmpid; double **tmpbo, **tmpr; + std::vector eletype; ReaxFF::API *api; typedef double rvec[3]; diff --git a/src/REAXFF/reaxff_ffield.cpp b/src/REAXFF/reaxff_ffield.cpp index b941d7d0f0..7dfa2ee1cb 100644 --- a/src/REAXFF/reaxff_ffield.cpp +++ b/src/REAXFF/reaxff_ffield.cpp @@ -39,6 +39,7 @@ using LAMMPS_NS::utils::open_potential; using LAMMPS_NS::utils::getsyserror; +using LAMMPS_NS::utils::strmatch; using LAMMPS_NS::utils::uppercase; using LAMMPS_NS::EOFException; using LAMMPS_NS::ValueTokenizer; @@ -71,7 +72,7 @@ namespace ReaxFF { filename, lineno, want, values.count())) if (control->me == 0) { - FILE *fp = LAMMPS_NS::utils::open_potential(filename, lmp, nullptr); + FILE *fp = open_potential(filename, lmp, nullptr); if (!fp) error->one(FLERR,"The ReaxFF parameter file {} cannot be opened: {}", filename, getsyserror()); @@ -81,9 +82,11 @@ namespace ReaxFF { try { int i,j,k,l,m,n,lineno = 0; - // skip header comment line + // check if header comment line is present - reader.skip_line(); + auto line = reader.next_line(); + if (strmatch(line, "^\\s*[0-9]+\\s+!.*general parameters.*")) + THROW_ERROR("First line of ReaxFF potential file must be a comment or empty"); ++lineno; // set some defaults diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp index c6886fbed7..c24984f152 100644 --- a/src/REPLICA/fix_pimd_langevin.cpp +++ b/src/REPLICA/fix_pimd_langevin.cpp @@ -47,10 +47,10 @@ using namespace LAMMPS_NS; using namespace FixConst; -using MathConst::MY_PI; using MathConst::MY_2PI; -using MathConst::THIRD; +using MathConst::MY_PI; using MathConst::MY_SQRT2; +using MathConst::THIRD; using MathSpecial::powint; enum { PIMD, NMPIMD }; @@ -475,11 +475,13 @@ void FixPIMDLangevin::init() c_pe = modify->get_compute_by_id(id_pe); if (!c_pe) - error->universe_all(FLERR, fmt::format("Could not find fix {} potential energy compute ID {}", style, id_pe)); + error->universe_all( + FLERR, fmt::format("Could not find fix {} potential energy compute ID {}", style, id_pe)); c_press = modify->get_compute_by_id(id_press); if (!c_press) - error->universe_all(FLERR, fmt::format("Could not find fix {} pressure compute ID {}", style, id_press)); + error->universe_all( + FLERR, fmt::format("Could not find fix {} pressure compute ID {}", style, id_press)); t_prim = t_vir = t_cv = p_prim = p_vir = p_cv = p_md = 0.0; } @@ -667,27 +669,26 @@ void FixPIMDLangevin::post_force(int /*flag*/) imageint *image = atom->image; tagint *tag = atom->tag; - if (method == NMPIMD) { - if (atom->nmax > maxunwrap) reallocate_x_unwrap(); - if (atom->nmax > maxxc) reallocate_xc(); - for (int i = 0; i < nlocal; i++) { - x_unwrap[i][0] = x[i][0]; - x_unwrap[i][1] = x[i][1]; - x_unwrap[i][2] = x[i][2]; - } - if (mapflag) { - for (int i = 0; i < nlocal; i++) { domain->unmap(x_unwrap[i], image[i]); } - } - for (int i = 0; i < nlocal; i++) { - xc[i][0] = xcall[3 * (tag[i] - 1) + 0]; - xc[i][1] = xcall[3 * (tag[i] - 1) + 1]; - xc[i][2] = xcall[3 * (tag[i] - 1) + 2]; - } - - compute_vir(); - compute_cvir(); - compute_t_vir(); + if (atom->nmax > maxunwrap) reallocate_x_unwrap(); + if (atom->nmax > maxxc) reallocate_xc(); + for (int i = 0; i < nlocal; i++) { + x_unwrap[i][0] = x[i][0]; + x_unwrap[i][1] = x[i][1]; + x_unwrap[i][2] = x[i][2]; } + if (mapflag) { + for (int i = 0; i < nlocal; i++) { domain->unmap(x_unwrap[i], image[i]); } + } + for (int i = 0; i < nlocal; i++) { + xc[i][0] = xcall[3 * (tag[i] - 1) + 0]; + xc[i][1] = xcall[3 * (tag[i] - 1) + 1]; + xc[i][2] = xcall[3 * (tag[i] - 1) + 2]; + } + + compute_vir(); + compute_xf_vir(); + compute_cvir(); + compute_t_vir(); if (method == PIMD) { if (mapflag) { @@ -696,6 +697,7 @@ void FixPIMDLangevin::post_force(int /*flag*/) inter_replica_comm(x); spring_force(); compute_spring_energy(); + compute_t_prim(); if (mapflag) { for (int i = 0; i < nlocal; i++) { domain->unmap_inv(x[i], image[i]); } } @@ -741,7 +743,7 @@ void FixPIMDLangevin::collect_xc() } } - const double sqrtnp = sqrt((double)np); + const double sqrtnp = sqrt((double) np); for (int i = 0; i < nlocal; i++) { xcall[3 * (tag[i] - 1) + 0] = x[i][0] / sqrtnp; xcall[3 * (tag[i] - 1) + 1] = x[i][1] / sqrtnp; @@ -1048,8 +1050,8 @@ void FixPIMDLangevin::langevin_init() c2_k[i] = sqrt(1.0 - c1_k[i] * c1_k[i]); } for (int i = 0; i < np; i++) { - out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i, - _omega_k[i], tau_k[i], c1_k[i], c2_k[i]); + out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i, _omega_k[i], tau_k[i], + c1_k[i], c2_k[i]); } } else if (method == PIMD) { for (int i = 0; i < np; i++) { @@ -1111,7 +1113,7 @@ void FixPIMDLangevin::nmpimd_init() } // Set up eigenvectors for degenerated modes - const double sqrtnp = sqrt((double)np); + const double sqrtnp = sqrt((double) np); for (int j = 0; j < np; j++) { for (int i = 1; i < int(np / 2) + 1; i++) { M_x2xp[i][j] = MY_SQRT2 * cos(MY_2PI * double(i) * double(j) / double(np)) / sqrtnp; @@ -1364,7 +1366,23 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr) void FixPIMDLangevin::remove_com_motion() { - if (universe->iworld == 0) { + if (method == NMPIMD) { + if (universe->iworld == 0) { + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (dynamic) masstotal = group->mass(igroup); + double vcm[3]; + group->vcm(igroup, masstotal, vcm); + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + v[i][0] -= vcm[0]; + v[i][1] -= vcm[1]; + v[i][2] -= vcm[2]; + } + } + } + } else if (method == PIMD) { double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -1378,24 +1396,34 @@ void FixPIMDLangevin::remove_com_motion() v[i][2] -= vcm[2]; } } + } else { + error->all(FLERR, "Unknown method for fix pimd/langevin. Only nmpimd and pimd are supported!"); } } /* ---------------------------------------------------------------------- */ +void FixPIMDLangevin::compute_xf_vir() +{ + int nlocal = atom->nlocal; + double xf = 0.0; + vir_ = 0.0; + for (int i = 0; i < nlocal; i++) { + for (int j = 0; j < 3; j++) { xf += x_unwrap[i][j] * atom->f[i][j]; } + } + MPI_Allreduce(&xf, &vir_, 1, MPI_DOUBLE, MPI_SUM, universe->uworld); +} + +/* ---------------------------------------------------------------------- */ + void FixPIMDLangevin::compute_cvir() { int nlocal = atom->nlocal; - double xf = 0.0; double xcf = 0.0; - vir_ = centroid_vir = 0.0; + centroid_vir = 0.0; for (int i = 0; i < nlocal; i++) { - for (int j = 0; j < 3; j++) { - xf += x_unwrap[i][j] * atom->f[i][j]; - xcf += (x_unwrap[i][j] - xc[i][j]) * atom->f[i][j]; - } + for (int j = 0; j < 3; j++) { xcf += (x_unwrap[i][j] - xc[i][j]) * atom->f[i][j]; } } - MPI_Allreduce(&xf, &vir_, 1, MPI_DOUBLE, MPI_SUM, universe->uworld); MPI_Allreduce(&xcf, ¢roid_vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld); if (pstyle == ANISO) { for (int i = 0; i < 6; i++) c_vir_tensor[i] = 0.0; @@ -1553,11 +1581,19 @@ void FixPIMDLangevin::compute_p_prim() void FixPIMDLangevin::compute_p_cv() { double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd); - if (universe->iworld == 0) { - p_cv = THIRD * inv_volume * ((2.0 * ke_bead - centroid_vir) * force->nktv2p + vir) / np; - } p_md = THIRD * inv_volume * (totke + vir); - MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld); + if (method == NMPIMD) { + if (universe->iworld == 0) { + p_cv = THIRD * inv_volume * ((2.0 * ke_bead - centroid_vir) * force->nktv2p + vir) / np; + } + MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld); + } else if (method == PIMD) { + p_cv = THIRD * inv_volume * ((2.0 * totke / np - centroid_vir) * force->nktv2p + vir) / np; + } else { + error->universe_all( + FLERR, + "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!"); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h index 0f21b908b0..869281243f 100644 --- a/src/REPLICA/fix_pimd_langevin.h +++ b/src/REPLICA/fix_pimd_langevin.h @@ -176,6 +176,7 @@ class FixPIMDLangevin : public Fix { void compute_p_prim(); void compute_p_cv(); // centroid-virial pressure estimator void compute_vir(); + void compute_xf_vir(); void compute_cvir(); void compute_totenthalpy(); diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index d9144a9489..4023f2c0b3 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -198,7 +198,7 @@ void NEB::run() if (me == 0) color = 0; else - color = 1; + color = MPI_UNDEFINED; MPI_Comm_split(uworld, color, 0, &roots); auto fixes = modify->get_fix_by_style("^neb$"); @@ -608,17 +608,20 @@ void NEB::open(char *file) void NEB::print_status() { double fnorm2 = sqrt(update->minimize->fnorm_sqr()); - double fmaxreplica; - MPI_Allreduce(&fnorm2, &fmaxreplica, 1, MPI_DOUBLE, MPI_MAX, roots); double fnorminf = update->minimize->fnorm_inf(); - double fmaxatom; - MPI_Allreduce(&fnorminf, &fmaxatom, 1, MPI_DOUBLE, MPI_MAX, roots); + double fmaxreplica = 0.0; + double fmaxatom = 0.0; - if (print_mode == VERBOSE) { - freplica = new double[nreplica]; - MPI_Allgather(&fnorm2, 1, MPI_DOUBLE, &freplica[0], 1, MPI_DOUBLE, roots); - fmaxatomInRepl = new double[nreplica]; - MPI_Allgather(&fnorminf, 1, MPI_DOUBLE, &fmaxatomInRepl[0], 1, MPI_DOUBLE, roots); + if (me == 0) { + MPI_Allreduce(&fnorm2, &fmaxreplica, 1, MPI_DOUBLE, MPI_MAX, roots); + MPI_Allreduce(&fnorminf, &fmaxatom, 1, MPI_DOUBLE, MPI_MAX, roots); + + if (print_mode == VERBOSE) { + freplica = new double[nreplica]; + MPI_Allgather(&fnorm2, 1, MPI_DOUBLE, &freplica[0], 1, MPI_DOUBLE, roots); + fmaxatomInRepl = new double[nreplica]; + MPI_Allgather(&fnorminf, 1, MPI_DOUBLE, &fmaxatomInRepl[0], 1, MPI_DOUBLE, roots); + } } double one[7]; @@ -703,7 +706,7 @@ void NEB::print_status() fflush(universe->ulogfile); } } - if (print_mode == VERBOSE) { + if ((me == 0) && (print_mode == VERBOSE)) { delete[] freplica; delete[] fmaxatomInRepl; } diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 7a63c52220..f4b82e1fd2 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -1234,11 +1234,6 @@ void FixRigid::enforce2d() angmom[ibody][1] = 0.0; omega[ibody][0] = 0.0; omega[ibody][1] = 0.0; - if (langflag && langextra) { - langextra[ibody][2] = 0.0; - langextra[ibody][3] = 0.0; - langextra[ibody][4] = 0.0; - } } } @@ -1958,6 +1953,8 @@ void FixRigid::setup_bodies_static() // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia + // request that jacobi3() return them in ascending order, + /// so that in 2d last evector is z-axis // evectors and exzy_space = 3 evectors = principal axes of rigid body int ierror; @@ -1972,7 +1969,7 @@ void FixRigid::setup_bodies_static() tensor[0][2] = tensor[2][0] = all[ibody][4]; tensor[0][1] = tensor[1][0] = all[ibody][5]; - ierror = MathEigen::jacobi3(tensor,inertia[ibody],evectors); + ierror = MathEigen::jacobi3(tensor,inertia[ibody],evectors,1); if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for rigid body"); @@ -1986,6 +1983,22 @@ void FixRigid::setup_bodies_static() ez_space[ibody][1] = evectors[1][2]; ez_space[ibody][2] = evectors[2][2]; + // for 2d, ensure that evector along z axis is last + // necessary so that quaternion is a simple rotation around +z axis + // or a 180 degree rotation for a -z axis + // otherwise richardson() method for a body with a tiny evalue (near-linear) + // may not preserve the correct z-aligned quat and associated evectors + // over time due to round-off accumulation + + if (domain->dimension == 2) { + if (fabs(ez_space[ibody][0]) > EPSILON || fabs(ez_space[ibody][1]) > EPSILON) { + std::swap(inertia[ibody][1],inertia[ibody][2]); + std::swap(ey_space[ibody][0],ez_space[ibody][0]); + std::swap(ey_space[ibody][1],ez_space[ibody][1]); + std::swap(ey_space[ibody][2],ez_space[ibody][2]); + } + } + // if any principal moment < scaled EPSILON, set to 0.0 double max; diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 9e185a4de2..0bfd8032c5 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -1110,11 +1110,6 @@ void FixRigidSmall::enforce2d() b->angmom[1] = 0.0; b->omega[0] = 0.0; b->omega[1] = 0.0; - if (langflag && langextra) { - langextra[ibody][2] = 0.0; - langextra[ibody][3] = 0.0; - langextra[ibody][4] = 0.0; - } } } @@ -2102,6 +2097,8 @@ void FixRigidSmall::setup_bodies_static() // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia + // request that jacobi3() returns them in ascending order, + // so that in 2d last evector is z-axis // evectors and exzy_space = 3 evectors = principal axes of rigid body int ierror; @@ -2118,7 +2115,7 @@ void FixRigidSmall::setup_bodies_static() tensor[0][1] = tensor[1][0] = itensor[ibody][5]; inertia = body[ibody].inertia; - ierror = MathEigen::jacobi3(tensor,inertia,evectors); + ierror = MathEigen::jacobi3(tensor,inertia,evectors,1); if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for rigid body"); ex = body[ibody].ex_space; @@ -2134,6 +2131,22 @@ void FixRigidSmall::setup_bodies_static() ez[1] = evectors[1][2]; ez[2] = evectors[2][2]; + // for 2d, ensure that evector along z axis is last + // necessary so that quaternion is a simple rotation around +z axis + // or a 180 degree rotation for a -z axis + // otherwise richardson() method for a body with a tiny evalue (near-linear) + // may not preserve the correct z-aligned quat and associated evectors + // over time due to round-off accumulation + + if (domain->dimension == 2) { + if (fabs(ez[0]) > EPSILON || fabs(ez[1]) > EPSILON) { + std::swap(inertia[1],inertia[2]); + std::swap(ey[0],ez[0]); + std::swap(ey[1],ez[1]); + std::swap(ey[2],ez[2]); + } + } + // if any principal moment < scaled EPSILON, set to 0.0 double max; @@ -2156,11 +2169,12 @@ void FixRigidSmall::setup_bodies_static() // convert geometric center position to principal axis coordinates // xcm is wrapped, but xgc is not initially + xcm = body[ibody].xcm; xgc = body[ibody].xgc; double delta[3]; MathExtra::sub3(xgc,xcm,delta); - domain->minimum_image(delta); + domain->minimum_image_big(delta); MathExtra::transpose_matvec(ex,ey,ez,delta,body[ibody].xgc_body); MathExtra::add3(xcm,delta,xgc); } diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 73c29d86bd..ac71ea01a6 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -63,6 +63,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) : create_attribute = 1; dof_flag = 1; scalar_flag = 1; + extscalar = 1; stores_ids = 1; centroidstressflag = CENTROID_AVAIL; next_output = -1; @@ -371,7 +372,9 @@ void FixShake::init() // if rRESPA, find associated fix that must exist // could have changed locations in fix list since created // set ptrs to rRESPA variables + // set respa to 0 if verlet is used and to 1 otherwise + respa = 0; fix_respa = nullptr; if (utils::strmatch(update->integrate_style,"^respa")) { if (update->whichflag > 0) { @@ -379,10 +382,12 @@ void FixShake::init() if (fixes.size() > 0) fix_respa = dynamic_cast(fixes.front()); else error->all(FLERR,"Run style respa did not create fix RESPA"); } - auto respa_style = dynamic_cast(update->integrate); - nlevels_respa = respa_style->nlevels; - loop_respa = respa_style->loop; - step_respa = respa_style->step; + auto respa_ptr = dynamic_cast(update->integrate); + if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style); + respa = 1; + nlevels_respa = respa_ptr->nlevels; + loop_respa = respa_ptr->loop; + step_respa = respa_ptr->step; } // set equilibrium bond distances @@ -473,18 +478,22 @@ void FixShake::setup(int vflag) next_output = (ntimestep/output_every)*output_every + output_every; } else next_output = -1; - // set respa to 0 if verlet is used and to 1 otherwise - - if (utils::strmatch(update->integrate_style,"^verlet")) - respa = 0; - else - respa = 1; - if (!respa) { dtv = update->dt; dtfsq = 0.5 * update->dt * update->dt * force->ftm2v; if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v; } else { + auto respa_ptr = dynamic_cast(update->integrate); + if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style); + if (update->whichflag > 0) { + auto fixes = modify->get_fix_by_style("^RESPA"); + if (fixes.size() > 0) fix_respa = dynamic_cast(fixes.front()); + else error->all(FLERR,"Run style respa did not create fix RESPA"); + } + respa = 1; + nlevels_respa = respa_ptr->nlevels; + loop_respa = respa_ptr->loop; + step_respa = respa_ptr->step; dtv = step_respa[0]; dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v; dtf_inner = dtf_innerhalf; @@ -3123,7 +3132,14 @@ void FixShake::reset_dt() dtv = update->dt; if (rattle) dtfsq = 0.5 * update->dt * update->dt * force->ftm2v; else dtfsq = update->dt * update->dt * force->ftm2v; + respa = 0; } else { + auto respa_ptr = dynamic_cast(update->integrate); + if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style); + respa = 1; + nlevels_respa = respa_ptr->nlevels; + loop_respa = respa_ptr->loop; + step_respa = respa_ptr->step; dtv = step_respa[0]; dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v; if (rattle) dtf_inner = dtf_innerhalf; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 9a7e4c6aac..f941ddc990 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -1,5 +1,4 @@ /* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories LAMMPS development team: developers@lammps.org @@ -10,7 +9,6 @@ the GNU General Public License. See the README file in the top-level LAMMPS directory. - ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ @@ -26,6 +24,8 @@ #include "atom_vec_spin.h" #include "atom.h" +#include "domain.h" +#include "memory.h" #include #include @@ -42,6 +42,8 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp) atom->sp_flag = 1; + sp_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -100,3 +102,55 @@ void AtomVecSpin::data_atom_post(int ilocal) sp_one[1] *= norm; sp_one[2] *= norm; } + +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on spin vector sp +------------------------------------------------------------------------- */ + +void AtomVecSpin::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + for (int i = nlocal_previous; i < nlocal; i++) + domain->general_to_restricted_vector(sp[i]); +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on spin vector sp which has 4 values per atom +------------------------------------------------------------------------- */ + +void AtomVecSpin::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(sp_hold,nlocal,3,"atomvec:sp_hold"); + for (int i = 0; i < nlocal; i++) { + memcpy(&sp_hold[i],&sp[i],3*sizeof(double)); + domain->restricted_to_general_vector(sp[i]); + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on spin vector sp which has 4 values per atom +------------------------------------------------------------------------- */ + +void AtomVecSpin::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!sp_hold) return; + + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) + memcpy(&sp[i],&sp_hold[i],3*sizeof(double)); + memory->destroy(sp_hold); + sp_hold = nullptr; +} diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h index bf11d5856e..7a2f890086 100644 --- a/src/SPIN/atom_vec_spin.h +++ b/src/SPIN/atom_vec_spin.h @@ -31,9 +31,13 @@ class AtomVecSpin : virtual public AtomVec { void grow_pointers() override; void force_clear(int, size_t) override; void data_atom_post(int) override; + void read_data_general_to_restricted(int, int) override; + void write_data_restricted_to_general() override; + void write_data_restore_restricted() override; protected: double **sp, **fm, **fm_long; + double **sp_hold; }; } // namespace LAMMPS_NS diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 1c92d284f0..fc5e223e75 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -215,9 +215,8 @@ void ComputeSpin::compute_vector() tempnum += tx*tx+ty*ty+tz*tz; tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2]; countsp++; - } + } else error->all(FLERR,"Compute compute/spin requires atom/spin style"); } - else error->all(FLERR,"Compute compute/spin requires atom/spin style"); } MPI_Allreduce(mag,magtot,4,MPI_DOUBLE,MPI_SUM,world); diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index ca4ad4a85c..4aa6ebf559 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -126,6 +126,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) : if (maxedge > 0) { vector_flag = 1; + extvector = 0; size_vector = maxedge+1; memory->create(edge,maxedge+1,"voronoi/atom:edge"); memory->create(sendvector,maxedge+1,"voronoi/atom:sendvector"); diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index e79776b0d2..0c61970a1f 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -270,7 +270,7 @@ void AngleHybrid::coeff(int narg, char **arg) else if (strcmp(arg[1], "bb") == 0) error->all(FLERR, "BondBond coeff for hybrid angle has invalid format"); else - error->all(FLERR, "Angle coeff for hybrid has invalid style"); + error->all(FLERR, "Expected hybrid sub-style instead of {} in angle_coeff command", arg[1]); } // move 1st arg to 2nd arg diff --git a/src/atom.cpp b/src/atom.cpp index 085ca88b4e..799a256e31 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -50,6 +50,7 @@ using namespace MathConst; static constexpr int DELTA = 1; static constexpr double EPSILON = 1.0e-6; +static constexpr double EPS_ZCOORD = 1.0e-12; /* ---------------------------------------------------------------------- one instance per AtomVec style in style_atom.h @@ -1039,12 +1040,13 @@ void Atom::deallocate_topology() /* ---------------------------------------------------------------------- unpack N lines from Atom section of data file - call style-specific routine to parse line + call atom-style specific method to parse each line + triclinic_general = 1 if data file defines a general triclinic box ------------------------------------------------------------------------- */ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, int type_offset, int shiftflag, double *shift, - int labelflag, int *ilabel) + int labelflag, int *ilabel, int triclinic_general) { int xptr,iptr; imageint imagedata; @@ -1055,6 +1057,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, auto location = "Atoms section of data file"; // use the first line to detect and validate the number of words/tokens per line + next = strchr(buf,'\n'); if (!next) error->all(FLERR, "Missing data in {}", location); *next = '\0'; @@ -1068,13 +1071,16 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, } if ((nwords != avec->size_data_atom) && (nwords != avec->size_data_atom + 3)) - error->all(FLERR,"Incorrect format in {}: {}", location, utils::trim(buf)); + error->all(FLERR,"Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); *next = '\n'; + // set bounds for my proc // if periodic and I am lo/hi proc, adjust bounds by EPSILON // ensures all data atoms will be owned even with round-off + int dimension = domain->dimension; int triclinic = domain->triclinic; double epsilon[3]; @@ -1145,18 +1151,27 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, *next = '\0'; auto values = Tokenizer(buf).as_vector(); int nvalues = values.size(); - if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) { - // skip over empty or comment lines + + // skip comment lines + + if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) { + + // check that line has correct # of words + } else if ((nvalues < nwords) || ((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) { - error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); + + // extract the atom coords and image flags (if they exist) + } else { int imx = 0, imy = 0, imz = 0; if (imageflag) { imx = utils::inumeric(FLERR,values[iptr],false,lmp); imy = utils::inumeric(FLERR,values[iptr+1],false,lmp); imz = utils::inumeric(FLERR,values[iptr+2],false,lmp); - if ((domain->dimension == 2) && (imz != 0)) + if ((dimension == 2) && (imz != 0)) error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems"); if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; } if ((!domain->yperiodic) && (imy != 0)) { reset_image_flag[1] = true; imy = 0; } @@ -1169,13 +1184,35 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, xdata[0] = utils::numeric(FLERR,values[xptr],false,lmp); xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp); xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp); + + // for 2d simulation: + // check if z coord is within EPS_ZCOORD of zero and set to zero + + if (dimension == 2) { + if (fabs(xdata[2]) > EPS_ZCOORD) + error->all(FLERR,"Read_data atom z coord is non-zero for 2d simulation"); + xdata[2] = 0.0; + } + + // convert atom coords from general to restricted triclinic + // so can decide which proc owns the atom + + if (triclinic_general) domain->general_to_restricted_coords(xdata); + + // apply shift if requested by read_data command + if (shiftflag) { xdata[0] += shift[0]; xdata[1] += shift[1]; xdata[2] += shift[2]; } + // map atom into simulation box for periodic dimensions + domain->remap(xdata,imagedata); + + // determine if this proc owns the atom + if (triclinic) { domain->x2lamda(xdata,lamda); coord = lamda; @@ -1184,6 +1221,9 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, if (coord[0] >= sublo[0] && coord[0] < subhi[0] && coord[1] >= sublo[1] && coord[1] < subhi[1] && coord[2] >= sublo[2] && coord[2] < subhi[2]) { + + // atom-style specific method parses single line + avec->data_atom(xdata,imagedata,values,typestr); typestr = utils::utf8_subst(typestr); if (id_offset) tag[nlocal-1] += id_offset; @@ -1223,8 +1263,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, /* ---------------------------------------------------------------------- unpack N lines from Velocity section of data file check that atom IDs are > 0 and <= map_tag_max - call style-specific routine to parse line -------------------------------------------------------------------------- */ + call style-specific routine to parse line- +------------------------------------------------------------------------ */ void Atom::data_vels(int n, char *buf, tagint id_offset) { @@ -1243,7 +1283,8 @@ void Atom::data_vels(int n, char *buf, tagint id_offset) if (values.size() == 0) { // skip over empty or comment lines } else if ((int)values.size() != avec->size_data_vel) { - error->all(FLERR, "Incorrect velocity format in data file: {}", utils::trim(buf)); + error->all(FLERR, "Incorrect format in Velocities section of data file: {}{}", + utils::trim(buf), utils::errorurl(2)); } else { tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset; if (tagdata <= 0 || tagdata > map_tag_max) @@ -1287,7 +1328,9 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Bonds line is: number(ignored), bond type, atomID 1, atomID 2 if (nwords > 0) { - if (nwords != 4) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 4) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1378,7 +1421,9 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Angles line is: number(ignored), angle type, atomID 1, atomID 2, atomID 3 if (nwords > 0) { - if (nwords != 5) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 5) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1485,7 +1530,9 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Dihedrals line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4 if (nwords > 0) { - if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 6) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1611,7 +1658,9 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Impropers line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4 if (nwords > 0) { - if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 6) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1727,7 +1776,8 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset) if (values.size() == 0) { // skip over empty or comment lines } else if ((int)values.size() != avec_bonus->size_data_bonus) { - error->all(FLERR, "Incorrect bonus data format in data file: {}", utils::trim(buf)); + error->all(FLERR, "Incorrect format in Bonus section of data file: {}{}", + utils::trim(buf), utils::errorurl(2)); } else { tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset; if (tagdata <= 0 || tagdata > map_tag_max) @@ -1944,18 +1994,14 @@ void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg) if (mass == nullptr) error->all(file,line, "Cannot set per-type atom mass for atom style {}", atom_style); - char *typestr = utils::expand_type(file, line, arg[0], Atom::ATOM, lmp); - const std::string str = typestr ? typestr : arg[0]; - delete[] typestr; - int lo, hi; - utils::bounds(file, line, str, 1, ntypes, lo, hi, error); + utils::bounds_typelabel(file, line, arg[0], 1, ntypes, lo, hi, lmp, Atom::ATOM); if ((lo < 1) || (hi > ntypes)) - error->all(file, line, "Invalid atom type {} for atom mass", str); + error->all(file, line, "Invalid atom type {} for atom mass", arg[0]); const double value = utils::numeric(FLERR, arg[1], false, lmp); if (value <= 0.0) - error->all(file, line, "Invalid atom mass value {} for type {}", value, str); + error->all(file, line, "Invalid atom mass value {} for type {}", value, arg[0]); for (int itype = lo; itype <= hi; itype++) { mass[itype] = value; diff --git a/src/atom.h b/src/atom.h index f238b2d5b1..195c1b2cf9 100644 --- a/src/atom.h +++ b/src/atom.h @@ -327,9 +327,9 @@ class Atom : protected Pointers { int parse_data(const char *); - void deallocate_topology(); + virtual void deallocate_topology(); - void data_atoms(int, char *, tagint, tagint, int, int, double *, int, int *); + void data_atoms(int, char *, tagint, tagint, int, int, double *, int, int *, int); void data_vels(int, char *, tagint); void data_bonds(int, char *, int *, tagint, int, int, int *); void data_angles(int, char *, int *, tagint, int, int, int *); diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 8ea1d145eb..60526adcf2 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -68,6 +68,9 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp) image = nullptr; x = v = f = nullptr; + x_hold = nullptr; + v_hold = omega_hold = angmom_hold = nullptr; + threads = nullptr; } @@ -1684,7 +1687,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vectorgeneral_to_restricted_vector(array[i]); + } + } + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + create "hold" copy of original restricted data to restore after data file is written + parent class only operates on x and data from Velocities section of data file + child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc +------------------------------------------------------------------------- */ + +void AtomVec::write_data_restricted_to_general() +{ + int datatype, cols; + void *pdata; + + int nlocal = atom->nlocal; + + memory->create(x_hold,nlocal,3,"atomvec:x_hold"); + if (nlocal) memcpy(&x_hold[0][0],&x[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_coords(x[i]); + + double **omega = atom->omega; + double **angmom = atom->angmom; + + for (int n = 1; n < ndata_vel; n++) { + pdata = mdata_vel.pdata[n]; + datatype = mdata_vel.datatype[n]; + cols = mdata_vel.cols[n]; + + // operate on v, omega, angmom + // no other write_data Velocities fields are Nx3 double arrays + + if (datatype == Atom::DOUBLE) { + if (cols == 3) { + double **array = *((double ***) pdata); + + if (array == v) { + memory->create(v_hold,nlocal,3,"atomvec:v_hold"); + if (nlocal) memcpy(&v_hold[0][0],&v[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(v[i]); + } else if (array == omega) { + memory->create(omega_hold,nlocal,3,"atomvec:omega_hold"); + if (nlocal) memcpy(&omega_hold[0][0],&omega[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(omega[i]); + } else if (array == angmom) { + memory->create(angmom_hold,nlocal,3,"atomvec:angmom_hold"); + if (nlocal) memcpy(&angmom_hold[0][0],&angmom[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(angmom[i]); + } + } + } + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class only operates on x and data from Velocities section of data file + child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc +------------------------------------------------------------------------- */ + +void AtomVec::write_data_restore_restricted() +{ + int nlocal = atom->nlocal; + + if (x_hold) { + memcpy(&x[0][0],&x_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(x_hold); + x_hold = nullptr; + } + + // operate on v, omega, angmom + // no other write_data Velocities fields are Nx3 double arrays + + if (v_hold) { + memcpy(&v[0][0],&v_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(v_hold); + v_hold = nullptr; + } + + if (omega_hold) { + memcpy(&atom->omega[0][0],&omega_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(omega_hold); + omega_hold = nullptr; + } + + if (angmom_hold) { + memcpy(&atom->angmom[0][0],&angmom_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(angmom_hold); + angmom_hold = nullptr; + } +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/atom_vec.h b/src/atom_vec.h index a4db054752..2342964797 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -123,7 +123,8 @@ class AtomVec : protected Pointers { virtual void create_atom(int, double *); virtual void create_atom_post(int) {} - virtual void data_atom(double *, imageint, const std::vector &, std::string &); + virtual void data_atom(double *, imageint, const std::vector &, + std::string &); virtual void data_atom_post(int) {} virtual void data_atom_bonus(int, const std::vector &) {} virtual void data_body(int, int, int, int *, double *) {} @@ -151,6 +152,10 @@ class AtomVec : protected Pointers { virtual int pack_data_bonus(double *, int) { return 0; } virtual void write_data_bonus(FILE *, int, double *, int) {} + virtual void read_data_general_to_restricted(int, int); + virtual void write_data_restricted_to_general(); + virtual void write_data_restore_restricted(); + virtual int property_atom(const std::string &) { return -1; } virtual void pack_property_atom(int, double *, int, int) {} @@ -168,6 +173,11 @@ class AtomVec : protected Pointers { imageint *image; double **x, **v, **f; + // copies of original unrotated fields for write_data for general triclinic + + double **x_hold; + double **v_hold, **omega_hold, **angmom_hold; + // standard list of peratom fields always operated on by different methods // common to all styles, so not listed in field strings diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 538e9783df..5ff84d6b1f 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -16,8 +16,10 @@ #include "atom.h" #include "body.h" +#include "domain.h" #include "error.h" #include "fix.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "my_pool_chunk.h" @@ -595,6 +597,15 @@ void AtomVecBody::pack_data_pre(int ilocal) body[ilocal] = 1; } +/* ---------------------------------------------------------------------- + unmodify values packed by AtomVec::pack_data() +------------------------------------------------------------------------- */ + +void AtomVecBody::pack_data_post(int ilocal) +{ + body[ilocal] = body_flag; +} + /* ---------------------------------------------------------------------- pack bonus body info for writing to data file if buf is nullptr, just return buffer size @@ -629,12 +640,80 @@ void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/) } /* ---------------------------------------------------------------------- - unmodify values packed by AtomVec::pack_data() + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on body quaternion ------------------------------------------------------------------------- */ -void AtomVecBody::pack_data_post(int ilocal) +void AtomVecBody::read_data_general_to_restricted(int nlocal_previous, int nlocal) { - body[ilocal] = body_flag; + int j; + + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + // quat_g2r = quat that rotates from general to restricted triclinic + // quat_new = body quat converted to restricted triclinic + + double quat_g2r[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r); + + for (int i = nlocal_previous; i < nlocal; i++) { + if (body[i] < 0) continue; + j = body[i]; + MathExtra::quatquat(quat_g2r,bonus[j].quat,quat_new); + bonus[j].quat[0] = quat_new[0]; + bonus[j].quat[1] = quat_new[1]; + bonus[j].quat[2] = quat_new[2]; + bonus[j].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on body quaternion +------------------------------------------------------------------------- */ + +void AtomVecBody::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(quat_hold[i],bonus[i].quat,4*sizeof(double)); + + // quat_r2g = quat that rotates from restricted to general triclinic + // quat_new = ellipsoid quat converted to general triclinic + + double quat_r2g[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g); + + for (int i = 0; i < nlocal_bonus; i++) { + MathExtra::quatquat(quat_r2g,bonus[i].quat,quat_new); + bonus[i].quat[0] = quat_new[0]; + bonus[i].quat[1] = quat_new[1]; + bonus[i].quat[2] = quat_new[2]; + bonus[i].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on body quaternion +------------------------------------------------------------------------- */ + +void AtomVecBody::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(bonus[i].quat,quat_hold[i],4*sizeof(double)); + + memory->destroy(quat_hold); + quat_hold = nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index e02fd3bbb0..5c7ed73d21 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -66,6 +66,10 @@ class AtomVecBody : public AtomVec { int pack_data_bonus(double *, int) override; void write_data_bonus(FILE *, int, double *, int) override; + void read_data_general_to_restricted(int, int) override; + void write_data_restricted_to_general() override; + void write_data_restore_restricted() override; + // methods used by other classes to query/set body info double radius_body(int, int, int *, double *); @@ -77,6 +81,7 @@ class AtomVecBody : public AtomVec { int *body; double *rmass, *radius; double **angmom; + double **quat_hold; int nghost_bonus, nmax_bonus; int intdoubleratio; // sizeof(double) / sizeof(int) @@ -87,7 +92,6 @@ class AtomVecBody : public AtomVec { void grow_bonus(); void copy_bonus_all(int, int); - // check(int); }; } // namespace LAMMPS_NS diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 3eaa927384..417c3cf5fa 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -18,6 +18,7 @@ #include "atom_vec_ellipsoid.h" #include "atom.h" +#include "domain.h" #include "error.h" #include "fix.h" #include "math_const.h" @@ -535,6 +536,83 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag } } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on ellipsoid quaternion +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + int j; + + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + // quat_g2r = quat that rotates from general to restricted triclinic + // quat_new = ellipsoid quat converted to restricted triclinic + + double quat_g2r[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r); + + for (int i = nlocal_previous; i < nlocal; i++) { + if (ellipsoid[i] < 0) continue; + j = ellipsoid[i]; + MathExtra::quatquat(quat_g2r,bonus[j].quat,quat_new); + bonus[j].quat[0] = quat_new[0]; + bonus[j].quat[1] = quat_new[1]; + bonus[j].quat[2] = quat_new[2]; + bonus[j].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on ellipsoid quaternion +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(quat_hold[i],bonus[i].quat,4*sizeof(double)); + + // quat_r2g = quat that rotates from restricted to general triclinic + // quat_new = ellipsoid quat converted to general triclinic + + double quat_r2g[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g); + + for (int i = 0; i < nlocal_bonus; i++) { + MathExtra::quatquat(quat_r2g,bonus[i].quat,quat_new); + bonus[i].quat[0] = quat_new[0]; + bonus[i].quat[1] = quat_new[1]; + bonus[i].quat[2] = quat_new[2]; + bonus[i].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on ellipsoid quaternion +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(bonus[i].quat,quat_hold[i],4*sizeof(double)); + + memory->destroy(quat_hold); + quat_hold = nullptr; +} + /* ---------------------------------------------------------------------- set shape values in bonus data for particle I oriented aligned with xyz axes diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 6e06d773fc..5b0d878c84 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -59,6 +59,10 @@ class AtomVecEllipsoid : public AtomVec { int pack_data_bonus(double *, int) override; void write_data_bonus(FILE *, int, double *, int) override; + void read_data_general_to_restricted(int, int) override; + void write_data_restricted_to_general() override; + void write_data_restore_restricted() override; + // unique to AtomVecEllipsoid void set_shape(int, double, double, double); @@ -69,6 +73,7 @@ class AtomVecEllipsoid : public AtomVec { int *ellipsoid; double *rmass; double **angmom; + double **quat_hold; int nghost_bonus, nmax_bonus; int ellipsoid_flag; diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index cd747d0862..6ec4836770 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -351,6 +351,35 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector &values) double y1 = utils::numeric(FLERR, values[ivalue++], true, lmp); double x2 = utils::numeric(FLERR, values[ivalue++], true, lmp); double y2 = utils::numeric(FLERR, values[ivalue++], true, lmp); + + // convert x1/y1 and x2/y2 from general to restricted triclniic + // x is already restricted triclinic + + double coords[3]; + + if (domain->triclinic_general) { + coords[0] = x1; coords[1] = y1; coords[2] = 0.0; + domain->general_to_restricted_coords(coords); + x1 = coords[0]; y1 = coords[1]; + coords[0] = x2; coords[1] = y2; coords[2] = 0.0; + domain->general_to_restricted_coords(coords); + x2 = coords[0]; y2 = coords[1]; + } + + // remap end points to be near x + // necessary if atom x was remapped into periodic box + + coords[0] = x1; coords[1] = y1; coords[2] = 0.0; + domain->remap_near(coords,x[m]); + x1 = coords[0]; y1 = coords[1]; + coords[0] = x2; coords[1] = y2; coords[2] = 0.0; + domain->remap_near(coords,x[m]); + x2 = coords[0]; y2 = coords[1]; + + // calculate length and theta + // error if segment center is not within EPSILON of atom x + // reset atom x to center point + double dx = x2 - x1; double dy = y2 - y1; double length = sqrt(dx * dx + dy * dy); @@ -477,8 +506,14 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) int i, j; double length, theta; double xc, yc, x1, x2, y1, y2; + double coords[3]; + + int triclinic_general = domain->triclinic_general; + + double **x_bonus; + if (triclinic_general) x_bonus = x_hold; + else x_bonus = x; - double **x = atom->x; tagint *tag = atom->tag; int nlocal = atom->nlocal; @@ -490,8 +525,9 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) j = line[i]; length = bonus[j].length; theta = bonus[j].theta; - xc = x[i][0]; - yc = x[i][1]; + + xc = x_bonus[i][0]; + yc = x_bonus[i][1]; x1 = xc - 0.5 * cos(theta) * length; y1 = yc - 0.5 * sin(theta) * length; x2 = xc + 0.5 * cos(theta) * length; @@ -500,6 +536,20 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) buf[m++] = y1; buf[m++] = x2; buf[m++] = y2; + + // if triclinic_general: + // rotate 4 buf values from restricted to general triclinic + // output by write_data_bonus() as x1/y1 and x2/y2 + + if (triclinic_general) { + coords[0] = buf[m-4]; coords[1] = buf[m-3]; coords[2] = 0.0; + domain->restricted_to_general_coords(coords); + buf[m-4] = coords[0]; buf[m-3] = coords[1]; + coords[0] = buf[m-2]; coords[1] = buf[m-1]; coords[2] = 0.0; + domain->restricted_to_general_coords(coords); + buf[m-2] = coords[0]; buf[m-1] = coords[1]; + } + } else m += size_data_bonus; } diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h index 740c541916..0f5e5800f5 100644 --- a/src/atom_vec_line.h +++ b/src/atom_vec_line.h @@ -76,7 +76,6 @@ class AtomVecLine : public AtomVec { void grow_bonus(); void copy_bonus_all(int, int); - // void consistency_check(int, char *); }; } // namespace LAMMPS_NS diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 205e94d792..888ed954fc 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -507,7 +507,25 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector &values) MathExtra::sub3(c3, c1, c3mc1); double size = MAX(MathExtra::len3(c2mc1), MathExtra::len3(c3mc1)); + // convert c1,c2,c3 from general to restricted triclniic + // x is already restricted triclinic + + if (domain->triclinic_general) { + domain->general_to_restricted_coords(c1); + domain->general_to_restricted_coords(c2); + domain->general_to_restricted_coords(c3); + } + + // remap corner points to be near x + // necessary if atom x was remapped into periodic box + + domain->remap_near(c1,x[m]); + domain->remap_near(c2,x[m]); + domain->remap_near(c3,x[m]); + // centroid = 1/3 of sum of vertices + // error if centroid is not within EPSILON of atom x + // reset atom x to centroid double centroid[3]; centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0; @@ -705,7 +723,12 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) double dc1[3], dc2[3], dc3[3]; double p[3][3]; - double **x = atom->x; + int triclinic_general = domain->triclinic_general; + + double **x_bonus; + if (triclinic_general) x_bonus = x_hold; + else x_bonus = x; + tagint *tag = atom->tag; int nlocal = atom->nlocal; @@ -719,9 +742,10 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) MathExtra::matvec(p, bonus[j].c1, dc1); MathExtra::matvec(p, bonus[j].c2, dc2); MathExtra::matvec(p, bonus[j].c3, dc3); - xc = x[i][0]; - yc = x[i][1]; - zc = x[i][2]; + + xc = x_bonus[i][0]; + yc = x_bonus[i][1]; + zc = x_bonus[i][2]; buf[m++] = xc + dc1[0]; buf[m++] = yc + dc1[1]; buf[m++] = zc + dc1[2]; @@ -731,6 +755,17 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) buf[m++] = xc + dc3[0]; buf[m++] = yc + dc3[1]; buf[m++] = zc + dc3[2]; + + // if triclinic_general: + // rotate 9 buf values from restricted to general triclinic + // output by write_data_bonus() as c1,c2,c3 + + if (triclinic_general) { + domain->restricted_to_general_coords(&buf[m-9]); + domain->restricted_to_general_coords(&buf[m-6]); + domain->restricted_to_general_coords(&buf[m-3]); + } + } else m += size_data_bonus; } diff --git a/src/bond.cpp b/src/bond.cpp index 943784427a..b414ddbdca 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -63,8 +63,7 @@ Bond::Bond(LAMMPS *_lmp) : Pointers(_lmp) execution_space = Host; datamask_read = ALL_MASK; datamask_modify = ALL_MASK; - - copymode = 0; + copymode = kokkosable = 0; } /* ---------------------------------------------------------------------- */ diff --git a/src/bond.h b/src/bond.h index be6d737597..f52204662c 100644 --- a/src/bond.h +++ b/src/bond.h @@ -49,7 +49,7 @@ class Bond : protected Pointers { ExecutionSpace execution_space; unsigned int datamask_read, datamask_modify; - int copymode; + int copymode, kokkosable; Bond(class LAMMPS *); ~Bond() override; diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 401358dda0..7df4f31455 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -51,14 +51,7 @@ BondHybrid::~BondHybrid() delete[] svector; - if (allocated) { - memory->destroy(setflag); - memory->destroy(map); - delete[] nbondlist; - delete[] maxbond; - for (int i = 0; i < nstyles; i++) memory->destroy(bondlist[i]); - delete[] bondlist; - } + deallocate(); } /* ---------------------------------------------------------------------- */ @@ -166,6 +159,22 @@ void BondHybrid::allocate() for (int m = 0; m < nstyles; m++) bondlist[m] = nullptr; } +/* ---------------------------------------------------------------------- */ + +void BondHybrid::deallocate() +{ + if (!allocated) return; + + allocated = 0; + + memory->destroy(setflag); + memory->destroy(map); + delete[] nbondlist; + delete[] maxbond; + for (int i = 0; i < nstyles; i++) memory->destroy(bondlist[i]); + delete[] bondlist; +} + /* ---------------------------------------------------------------------- create one bond style for each arg in list ------------------------------------------------------------------------- */ @@ -186,15 +195,7 @@ void BondHybrid::settings(int narg, char **arg) has_quartic = -1; } - if (allocated) { - memory->destroy(setflag); - memory->destroy(map); - delete[] nbondlist; - delete[] maxbond; - for (i = 0; i < nstyles; i++) memory->destroy(bondlist[i]); - delete[] bondlist; - } - allocated = 0; + deallocate(); // allocate list of sub-styles @@ -305,7 +306,7 @@ void BondHybrid::coeff(int narg, char **arg) if (strcmp(arg[1], "none") == 0) none = 1; else - error->all(FLERR, "Bond coeff for hybrid has invalid style"); + error->all(FLERR, "Expected hybrid sub-style instead of {} in bond_coeff command", arg[1]); } // move 1st arg to 2nd arg @@ -400,7 +401,7 @@ void BondHybrid::read_restart(FILE *fp) keywords[m] = new char[n]; if (me == 0) utils::sfread(FLERR, keywords[m], sizeof(char), n, fp, nullptr, error); MPI_Bcast(keywords[m], n, MPI_CHAR, 0, world); - styles[m] = force->new_bond(keywords[m], 0, dummy); + styles[m] = force->new_bond(keywords[m], 1, dummy); styles[m]->read_restart_settings(fp); } } diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index df1437c038..d2496b8297 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -44,14 +44,15 @@ class BondHybrid : public Bond { double single(int, double, int, int, double &) override; double memory_usage() override; - private: + protected: int *map; // which style each bond type points to int has_quartic; // which style, if any is a quartic bond style int *nbondlist; // # of bonds in sub-style bondlists int *maxbond; // max # of bonds sub-style lists can store int ***bondlist; // bondlist for each sub-style - void allocate(); + virtual void allocate(); + virtual void deallocate(); void flags(); virtual void init_svector(); diff --git a/src/comm.cpp b/src/comm.cpp index 1293dd3d6d..02999fd541 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -420,6 +420,7 @@ void Comm::set_processors(int narg, char **arg) error->all(FLERR,"Specified processors != physical processors"); int iarg = 3; + numa_nodes = 2; while (iarg < narg) { if (strcmp(arg[iarg],"grid") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal processors command"); @@ -514,6 +515,12 @@ void Comm::set_processors(int narg, char **arg) outfile = utils::strdup(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"numa_nodes") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal processors command"); + numa_nodes = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if (numa_nodes < 1) numa_nodes = 2; + iarg += 2; + } else error->all(FLERR,"Illegal processors command"); } @@ -565,7 +572,7 @@ void Comm::set_proc_grid(int outflag) otherflag,other_style,other_procgrid,other_coregrid); } else if (gridflag == NUMA) { - pmap->numa_grid(nprocs,user_procgrid,procgrid,coregrid); + pmap->numa_grid(numa_nodes,nprocs,user_procgrid,procgrid,coregrid); } else if (gridflag == CUSTOM) { pmap->custom_grid(customfile,nprocs,user_procgrid,procgrid); diff --git a/src/comm.h b/src/comm.h index 5d803c1afa..fde4c3b81f 100644 --- a/src/comm.h +++ b/src/comm.h @@ -146,6 +146,7 @@ class Comm : protected Pointers { char xyz[4]; // xyz mapping of procs to 3d grid char *customfile; // file with custom proc map char *outfile; // proc grid/map output file + int numa_nodes; // Number of numa domains per socket for 3d grid int otherflag; // 1 if this partition dependent on another int other_style; // style of dependency diff --git a/src/compute.cpp b/src/compute.cpp index a12373fd51..d703cbfe6a 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -59,6 +59,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : // set child class defaults scalar_flag = vector_flag = array_flag = 0; + extscalar = extvector = extarray = -1; peratom_flag = local_flag = pergrid_flag = 0; size_vector_variable = size_array_rows_variable = 0; @@ -116,6 +117,16 @@ void Compute::init_flags() initialized_flag = 1; invoked_scalar = invoked_vector = invoked_array = -1; invoked_peratom = invoked_local = -1; + + if (scalar_flag && (extscalar < 0)) + error->all(FLERR, "Must set 'extscalar' when setting 'scalar_flag' for compute {}. " + "Contact the developer.", style); + if (vector_flag && (extvector < 0) && !extlist) + error->all(FLERR, "Must set 'extvector' or 'extlist' when setting 'vector_flag' for compute {}. " + "Contact the developer.", style); + if (array_flag && (extarray < 0)) + error->all(FLERR, "Must set 'extarray' when setting 'array_flag' for compute {}. " + "Contact the developer.", style); } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_count_type.cpp b/src/compute_count_type.cpp index d430b23e11..7b1651b61c 100644 --- a/src/compute_count_type.cpp +++ b/src/compute_count_type.cpp @@ -62,24 +62,24 @@ ComputeCountType::ComputeCountType(LAMMPS *lmp, int narg, char **arg) : if (mode == ATOM) { vector_flag = 1; size_vector = atom->ntypes; - extvector = 1; + extvector = 0; } else if (mode == BOND) { scalar_flag = vector_flag = 1; size_vector = atom->nbondtypes; - extscalar = 1; - extvector = 1; + extscalar = 0; + extvector = 0; } else if (mode == ANGLE) { vector_flag = 1; size_vector = atom->nangletypes; - extvector = 1; + extvector = 0; } else if (mode == DIHEDRAL) { vector_flag = 1; size_vector = atom->ndihedraltypes; - extvector = 1; + extvector = 0; } else if (mode == IMPROPER) { vector_flag = 1; size_vector = atom->nimpropertypes; - extvector = 1; + extvector = 0; } // output vector diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 17fe450fe5..372bebbfc7 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -46,7 +46,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : hist(nullptr), histall(nullptr), typecount(nullptr), icount(nullptr), jcount(nullptr), duplicates(nullptr) { - if (narg < 4) error->all(FLERR,"Illegal compute rdf command"); + if (narg < 4) utils::missing_cmd_args(FLERR,"compute rdf", error); array_flag = 1; extarray = 0; @@ -67,12 +67,14 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"cutoff") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal compute rdf command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"compute rdf cutoff", error); + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Compute rdf with custom cutoff requires neighbor style 'bin' or 'nsq'"); cutoff_user = utils::numeric(FLERR,arg[iarg+1],false,lmp); if (cutoff_user <= 0.0) cutflag = 0; else cutflag = 1; iarg += 2; - } else error->all(FLERR,"Illegal compute rdf command"); + } else error->all(FLERR,"Unknown compute rdf keyword {}", arg[iarg]); } // pairwise args @@ -94,16 +96,26 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : jlo = new int[npairs]; jhi = new int[npairs]; - if (nargpair == 0) { + if (!nargpair) { ilo[0] = 1; ihi[0] = ntypes; jlo[0] = 1; jhi[0] = ntypes; } else { iarg = 4; for (int ipair = 0; ipair < npairs; ipair++) { - utils::bounds(FLERR,arg[iarg],1,atom->ntypes,ilo[ipair],ihi[ipair],error); - utils::bounds(FLERR,arg[iarg+1],1,atom->ntypes,jlo[ipair],jhi[ipair],error); - if (ilo[ipair] > ihi[ipair] || jlo[ipair] > jhi[ipair]) - error->all(FLERR,"Illegal compute rdf command"); + utils::bounds_typelabel(FLERR, arg[iarg], 1, atom->ntypes, ilo[ipair], ihi[ipair], lmp, Atom::ATOM); + utils::bounds_typelabel(FLERR, arg[iarg+1], 1, atom->ntypes, jlo[ipair], jhi[ipair], lmp, Atom::ATOM); + + // switch i,j if i > j, if wildcards were not used + + if ( (ilo[ipair] == ihi[ipair]) && + (jlo[ipair] == jhi[ipair]) && + (ilo[ipair] > jlo[ipair]) ) { + jlo[ipair] = ihi[ipair]; + ilo[ipair] = jhi[ipair]; + ihi[ipair] = ilo[ipair]; + jhi[ipair] = jlo[ipair]; + } + iarg += 2; } } @@ -139,17 +151,17 @@ ComputeRDF::~ComputeRDF() { memory->destroy(rdfpair); memory->destroy(nrdfpair); - delete [] ilo; - delete [] ihi; - delete [] jlo; - delete [] jhi; + delete[] ilo; + delete[] ihi; + delete[] jlo; + delete[] jhi; memory->destroy(hist); memory->destroy(histall); memory->destroy(array); - delete [] typecount; - delete [] icount; - delete [] jcount; - delete [] duplicates; + delete[] typecount; + delete[] icount; + delete[] jcount; + delete[] duplicates; } /* ---------------------------------------------------------------------- */ @@ -158,8 +170,7 @@ void ComputeRDF::init() { if (!force->pair && !cutflag) - error->all(FLERR,"Compute rdf requires a pair style be defined " - "or cutoff specified"); + error->all(FLERR,"Compute rdf requires a pair style or an explicit cutoff"); if (cutflag) { double skin = neighbor->skin; @@ -205,7 +216,11 @@ void ComputeRDF::init() // than cutoff_user apart, just like a normal neighbor list does auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); - if (cutflag) req->set_cutoff(mycutneigh); + if (cutflag) { + if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) + error->all(FLERR, "Compute rdf with custom cutoff requires neighbor style 'bin' or 'nsq'"); + req->set_cutoff(mycutneigh); + } } /* ---------------------------------------------------------------------- */ @@ -254,7 +269,7 @@ void ComputeRDF::init_norm() for (i = 0; i < npairs; i++) jcount[i] = scratch[i]; MPI_Allreduce(duplicates,scratch,npairs,MPI_INT,MPI_SUM,world); for (i = 0; i < npairs; i++) duplicates[i] = scratch[i]; - delete [] scratch; + delete[] scratch; } /* ---------------------------------------------------------------------- */ diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 578ce999f5..d6c402f721 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -54,6 +54,8 @@ static constexpr double INV_P_CONST = 0.7548777; static constexpr double INV_SQ_P_CONST = 0.5698403; static constexpr int DEFAULT_MAXTRY = 1000; +#define EPS_ZCOORD 1.0e-12 + enum { BOX, REGION, SINGLE, RANDOM, MESH }; enum { ATOM, MOLECULE }; enum { COUNT, INSERT, INSERT_SELECTED }; @@ -89,7 +91,7 @@ void CreateAtoms::command(int narg, char **arg) // parse arguments if (narg < 2) utils::missing_cmd_args(FLERR, "create_atoms", error); - ntype = utils::inumeric(FLERR, arg[0], false, lmp); + ntype = utils::expand_type_int(FLERR, arg[0], Atom::ATOM, lmp); const char *meshfile; int iarg; @@ -111,6 +113,8 @@ void CreateAtoms::command(int narg, char **arg) xone[0] = utils::numeric(FLERR, arg[2], false, lmp); xone[1] = utils::numeric(FLERR, arg[3], false, lmp); xone[2] = utils::numeric(FLERR, arg[4], false, lmp); + if (domain->dimension == 2 && xone[2] != 0.0) + error->all(FLERR,"Create_atoms single for 2d simulation requires z coord = 0.0"); iarg = 5; } else if (strcmp(arg[1], "random") == 0) { style = RANDOM; @@ -152,9 +156,10 @@ void CreateAtoms::command(int narg, char **arg) overlapflag = 0; maxtry = DEFAULT_MAXTRY; radscale = 1.0; - radthresh = domain->lattice->xlattice; mesh_style = BISECTION; + radthresh = 1.0; mesh_density = 1.0; + nbasis = domain->lattice->nbasis; basistype = new int[nbasis]; for (int i = 0; i < nbasis; i++) basistype[i] = ntype; @@ -163,7 +168,7 @@ void CreateAtoms::command(int narg, char **arg) if (strcmp(arg[iarg], "basis") == 0) { if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "create_atoms basis", error); int ibasis = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); - int itype = utils::inumeric(FLERR, arg[iarg + 2], false, lmp); + int itype = utils::expand_type_int(FLERR, arg[iarg + 2], Atom::ATOM, lmp); if (ibasis <= 0 || ibasis > nbasis || itype <= 0 || itype > atom->ntypes) error->all(FLERR, "Out of range basis setting '{} {}' in create_atoms command", ibasis, itype); @@ -311,6 +316,7 @@ void CreateAtoms::command(int narg, char **arg) onemol->compute_center(); ranmol = new RanMars(lmp, molseed + comm->me); + memory->create(xmol, onemol->natoms, 3, "create_atoms:xmol"); } if (style == MESH) { @@ -355,19 +361,28 @@ void CreateAtoms::command(int narg, char **arg) } } - // demand non-none lattice be defined for BOX and REGION - // else setup scaling for SINGLE and RANDOM - // could use domain->lattice->lattice2box() to do conversion of - // lattice to box, but not consistent with other uses of units=lattice - // triclinic remapping occurs in add_single() + // require non-none lattice be defined for BOX or REGION styles if ((style == BOX) || (style == REGION)) { if (nbasis == 0) error->all(FLERR, "Cannot create atoms with undefined lattice"); - } else if (scaleflag == 1) { + } + + // apply scaling factor for styles that use distance-dependent factors + + if (scaleflag) { + if (style == SINGLE) { xone[0] *= domain->lattice->xlattice; xone[1] *= domain->lattice->ylattice; xone[2] *= domain->lattice->zlattice; - overlap *= domain->lattice->xlattice; + } else if (style == RANDOM) { + if (overlapflag) overlap *= domain->lattice->xlattice; + } else if (style == MESH) { + if (mesh_style == BISECTION) { + radthresh *= domain->lattice->xlattice; + } else if (mesh_style == QUASIRANDOM) { + mesh_density /= (domain->lattice->xlattice * domain->lattice->xlattice); + } + } } // set bounds for my proc in sublo[3] & subhi[3] @@ -453,7 +468,7 @@ void CreateAtoms::command(int narg, char **arg) atom->nghost = 0; atom->avec->clear_bonus(); - // add atoms/molecules in one of 3 ways + // add atoms/molecules with appropriate add() method bigint natoms_previous = atom->natoms; int nlocal_previous = atom->nlocal; @@ -637,6 +652,7 @@ void CreateAtoms::command(int narg, char **arg) delete[] xstr; delete[] ystr; delete[] zstr; + if (mode == MOLECULE) memory->destroy(xmol); // for MOLECULE mode: // create special bond lists for molecular systems, @@ -700,7 +716,8 @@ void CreateAtoms::add_single() if (mode == ATOM) { atom->avec->create_atom(ntype, xone); } else { - add_molecule(xone); + get_xmol(xone); + add_molecule(); } } } @@ -711,14 +728,13 @@ void CreateAtoms::add_single() void CreateAtoms::add_random() { - double xlo, ylo, zlo, xhi, yhi, zhi, zmid; + double xlo, ylo, zlo, xhi, yhi, zhi; double delx, dely, delz, distsq, odistsq; double lamda[3], *coord; double *boxlo, *boxhi; if (overlapflag) { double odist = overlap; - if (mode == MOLECULE) odist += onemol->molradius; odistsq = odist * odist; } @@ -730,7 +746,6 @@ void CreateAtoms::add_random() for (int ii = 0; ii < 30; ii++) random->uniform(); // bounding box for atom creation - // in real units, even if triclinic // only limit bbox by region if its bboxflag is set (interior region) if (triclinic == 0) { @@ -740,7 +755,6 @@ void CreateAtoms::add_random() yhi = domain->boxhi[1]; zlo = domain->boxlo[2]; zhi = domain->boxhi[2]; - zmid = zlo + 0.5 * (zhi - zlo); } else { xlo = domain->boxlo_bound[0]; xhi = domain->boxhi_bound[0]; @@ -748,7 +762,6 @@ void CreateAtoms::add_random() yhi = domain->boxhi_bound[1]; zlo = domain->boxlo_bound[2]; zhi = domain->boxhi_bound[2]; - zmid = zlo + 0.5 * (zhi - zlo); boxlo = domain->boxlo_lamda; boxhi = domain->boxhi_lamda; } @@ -784,7 +797,7 @@ void CreateAtoms::add_random() xone[0] = xlo + random->uniform() * (xhi - xlo); xone[1] = ylo + random->uniform() * (yhi - ylo); xone[2] = zlo + random->uniform() * (zhi - zlo); - if (domain->dimension == 2) xone[2] = zmid; + if (domain->dimension == 2) xone[2] = 0.0; if (region && (region->match(xone[0], xone[1], xone[2]) == 0)) continue; if (varflag && vartest(xone) == 0) continue; @@ -802,25 +815,43 @@ void CreateAtoms::add_random() // check for overlap of new atom/mol with all other atoms // including prior insertions // minimum_image() needed to account for distances across PBC - // new molecule only checks its center pt against others - // odistsq is expanded for mode=MOLECULE to account for molecule size if (overlapflag) { double **x = atom->x; int nlocal = atom->nlocal; int reject = 0; - for (int i = 0; i < nlocal; i++) { - delx = xone[0] - x[i][0]; - dely = xone[1] - x[i][1]; - delz = xone[2] - x[i][2]; - domain->minimum_image(delx, dely, delz); - distsq = delx * delx + dely * dely + delz * delz; - if (distsq < odistsq) { - reject = 1; - break; + if (mode == ATOM) { + for (int i = 0; i < nlocal; i++) { + delx = xone[0] - x[i][0]; + dely = xone[1] - x[i][1]; + delz = xone[2] - x[i][2]; + domain->minimum_image(delx, dely, delz); + distsq = delx * delx + dely * dely + delz * delz; + if (distsq < odistsq) { + reject = 1; + break; + } + } + } else { + if (comm->me == 0) get_xmol(xone); + MPI_Bcast(&xmol[0][0], onemol->natoms*3, MPI_DOUBLE, 0, world); + + for (int i = 0; i < nlocal; i++) { + for (int j = 0; j < onemol->natoms; j++) { + delx = xmol[j][0] - x[i][0]; + dely = xmol[j][1] - x[i][1]; + delz = xmol[j][2] - x[i][2]; + domain->minimum_image(delx, dely, delz); + distsq = delx * delx + dely * dely + delz * delz; + if (distsq < odistsq) { + reject = 1; + break; + } + } } } + int reject_any; MPI_Allreduce(&reject, &reject_any, 1, MPI_INT, MPI_MAX, world); if (reject_any) continue; @@ -847,7 +878,11 @@ void CreateAtoms::add_random() if (mode == ATOM) { atom->avec->create_atom(ntype, xone); } else { - add_molecule(xone); + + // atomic coordinates calculated above for overlap check + + if (!overlapflag) get_xmol(xone); + add_molecule(); } } } @@ -1168,6 +1203,14 @@ void CreateAtoms::add_mesh(const char *filename) void CreateAtoms::add_lattice() { + // add atoms on general triclinic lattice if Domain has setting for it + // verify lattice was defined with triclinic/general option + + if (!domain->triclinic_general && domain->lattice->is_general_triclinic()) + error->all(FLERR,"Create_atoms for non general triclinic box cannot use triclinic/general lattice"); + if (domain->triclinic_general && !domain->lattice->is_general_triclinic()) + error->all(FLERR,"Create_atoms for general triclinic box requires triclinic/general lattice"); + // convert 8 corners of my subdomain from box coords to lattice coords // for orthogonal, use corner pts of my subbox // for triclinic, use bounding box of my subbox @@ -1185,7 +1228,7 @@ void CreateAtoms::add_lattice() } else domain->bbox(domain->sublo_lamda, domain->subhi_lamda, bboxlo, bboxhi); - // narrow down the subbox by the bounding box of the given region, if available. + // narrow down the subbox by the bounding box of the given region, if available // for small regions in large boxes, this can result in a significant speedup if ((style == REGION) && region->bboxflag) { @@ -1209,16 +1252,55 @@ void CreateAtoms::add_lattice() xmin = ymin = zmin = BIG; xmax = ymax = zmax = -BIG; - // convert to lattice coordinates and set bounding box + // convert 8 corner points of bounding box to lattice coordinates + // compute new bounding box (xyz min/max) in lattice coords + // for orthogonal or restricted triclinic, use 8 corner points of bbox lo/hi - domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + if (!domain->triclinic_general) { + domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + + // for general triclinic, convert 8 corner points of bbox to general triclinic coords + // new set of 8 points is no longer an orthogonal bounding box + // instead invoke lattice->bbox() on each of 8 points + + } else if (domain->triclinic_general) { + double point[3]; + + point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + + point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + + point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + + point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2]; + domain->restricted_to_general_coords(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + } // ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox // overlap = any part of a unit cell (face,edge,pt) in common with my subbox @@ -1228,6 +1310,7 @@ void CreateAtoms::add_lattice() // decrement lo, increment hi to avoid round-off issues in lattice->bbox(), // which can lead to missing atoms in rare cases // extra decrement of lo if min < 0, since static_cast(-1.5) = -1 + // for 2d simulation, klo = khi = 0 so just one plane of atoms ilo = static_cast(xmin) - 1; jlo = static_cast(ymin) - 1; @@ -1240,6 +1323,8 @@ void CreateAtoms::add_lattice() if (ymin < 0.0) jlo--; if (zmin < 0.0) klo--; + if (domain->dimension == 2) klo = khi = 0; + // count lattice sites on each proc nlatt_overflow = 0; @@ -1305,6 +1390,8 @@ void CreateAtoms::loop_lattice(int action) { int i, j, k, m; + int dimension = domain->dimension; + int triclinic_general = domain->triclinic_general; const double *const *const basis = domain->lattice->basis; nlatt = 0; @@ -1324,6 +1411,19 @@ void CreateAtoms::loop_lattice(int action) domain->lattice->lattice2box(x[0], x[1], x[2]); + // convert from general to restricted triclinic coords + // for 2d simulation: + // check if z coord is within EPS_ZCOORD of zero and set to zero + + if (triclinic_general) { + domain->general_to_restricted_coords(x); + if (dimension == 2) { + if (fabs(x[2]) > EPS_ZCOORD) + error->all(FLERR,"Create_atoms atom z coord is non-zero for 2d simulation"); + x[2] = 0.0; + } + } + // if a region was specified, test if atom is in it if (style == REGION) @@ -1353,7 +1453,8 @@ void CreateAtoms::loop_lattice(int action) if (mode == ATOM) { atom->avec->create_atom(basistype[m], x); } else { - add_molecule(x); + get_xmol(x); + add_molecule(); } } else if (action == COUNT) { if (nlatt == MAXSMALLINT) nlatt_overflow = 1; @@ -1361,7 +1462,8 @@ void CreateAtoms::loop_lattice(int action) if (mode == ATOM) { atom->avec->create_atom(basistype[m], x); } else { - add_molecule(x); + get_xmol(x); + add_molecule(); } } @@ -1376,7 +1478,7 @@ void CreateAtoms::loop_lattice(int action) add a molecule with its center at center ------------------------------------------------------------------------- */ -void CreateAtoms::add_molecule(double *center) +void CreateAtoms::get_xmol(double *center) { double r[3], rotmat[3][3]; @@ -1399,22 +1501,34 @@ void CreateAtoms::add_molecule(double *center) MathExtra::quat_to_mat(quatone, rotmat); - // create atoms in molecule with atom ID = 0 and mol ID = 0 - // IDs are reset in caller after all molecules created by all procs - // pass add_molecule_atom an offset of 0 since don't know - // max tag of atoms in previous molecules at this point // onemol->quat_external is used by atom->add_moleclue_atom() onemol->quat_external = quatone; - int n, natoms = onemol->natoms; + int natoms = onemol->natoms; double xnew[3]; for (int m = 0; m < natoms; m++) { MathExtra::matvec(rotmat, onemol->dx[m], xnew); MathExtra::add3(xnew, center, xnew); - atom->avec->create_atom(ntype + onemol->type[m], xnew); - n = atom->nlocal - 1; - atom->add_molecule_atom(onemol, m, n, 0); + for (int i = 0; i < 3; i++) + xmol[m][i] = xnew[i]; + } +} + +/* ---------------------------------------------------------------------- + add a molecule with atom coordinates from xmol +------------------------------------------------------------------------- */ + +void CreateAtoms::add_molecule() +{ + // create atoms in molecule with atom ID = 0 and mol ID = 0 + // IDs are reset in caller after all molecules created by all procs + // pass add_molecule_atom an offset of 0 since don't know + // max tag of atoms in previous molecules at this point + + for (int m = 0; m < onemol->natoms; m++) { + atom->avec->create_atom(ntype + onemol->type[m], xmol[m]); + atom->add_molecule_atom(onemol, m, atom->nlocal - 1, 0); } } diff --git a/src/create_atoms.h b/src/create_atoms.h index ae6f1b9d33..f839e3f0df 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -40,7 +40,7 @@ class CreateAtoms : public Command { bigint nsubset; double subsetfrac; int *basistype; - double xone[3], quatone[4]; + double xone[3], quatone[4], **xmol; double radthresh, radscale, mesh_density; int varflag, vvar, xvar, yvar, zvar; @@ -71,7 +71,8 @@ class CreateAtoms : public Command { int add_quasirandom(const double[3][3], tagint); void add_lattice(); void loop_lattice(int); - void add_molecule(double *); + void get_xmol(double *); + void add_molecule(); int vartest(double *); // evaluate a variable with new atom position }; diff --git a/src/create_box.cpp b/src/create_box.cpp index 02aa63acf0..8a74ffd7bd 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -19,6 +19,7 @@ #include "domain.h" #include "error.h" #include "force.h" +#include "lattice.h" #include "region.h" #include "region_prism.h" #include "update.h" @@ -45,40 +46,117 @@ void CreateBox::command(int narg, char **arg) // region check - auto region = domain->get_region_by_id(arg[1]); - if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]); - if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box"); + Region *region = nullptr; + int triclinic_general = 0; - region->init(); + if (strcmp(arg[1],"NULL") == 0) triclinic_general = 1; + else { + region = domain->get_region_by_id(arg[1]); + if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]); + if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box"); + region->init(); + } - // if region not prism: - // setup orthogonal domain - // set simulation domain from region extent - // if region is prism: - // seutp triclinic domain - // set simulation domain params from prism params + // setup simulation box + // 3 options: orthogonal, restricted triclinic, general triclinic - if (strcmp(region->style, "prism") != 0) { - domain->triclinic = 0; - domain->boxlo[0] = region->extent_xlo; - domain->boxhi[0] = region->extent_xhi; - domain->boxlo[1] = region->extent_ylo; - domain->boxhi[1] = region->extent_yhi; - domain->boxlo[2] = region->extent_zlo; - domain->boxhi[2] = region->extent_zhi; + int iarg = 2; - } else { - domain->triclinic = 1; - auto prism = dynamic_cast(region); - domain->boxlo[0] = prism->xlo; - domain->boxhi[0] = prism->xhi; - domain->boxlo[1] = prism->ylo; - domain->boxhi[1] = prism->yhi; - domain->boxlo[2] = prism->zlo; - domain->boxhi[2] = prism->zhi; - domain->xy = prism->xy; - domain->xz = prism->xz; - domain->yz = prism->yz; + if (region) { + + // region is not prism + // setup orthogonal box + // set simulation domain from region extent + + if (strcmp(region->style, "prism") != 0) { + domain->triclinic = 0; + domain->boxlo[0] = region->extent_xlo; + domain->boxhi[0] = region->extent_xhi; + domain->boxlo[1] = region->extent_ylo; + domain->boxhi[1] = region->extent_yhi; + domain->boxlo[2] = region->extent_zlo; + domain->boxhi[2] = region->extent_zhi; + + // region is prism + // seutp restricted triclinic box + // set simulation domain from prism params + + } else { + domain->triclinic = 1; + auto prism = dynamic_cast(region); + domain->boxlo[0] = prism->xlo; + domain->boxhi[0] = prism->xhi; + domain->boxlo[1] = prism->ylo; + domain->boxhi[1] = prism->yhi; + domain->boxlo[2] = prism->zlo; + domain->boxhi[2] = prism->zhi; + domain->xy = prism->xy; + domain->xz = prism->xz; + domain->yz = prism->yz; + } + + if (domain->dimension == 2) { + if (domain->boxlo[2] >= 0.0 || domain->boxhi[2] <= 0.0) + error->all(FLERR,"Create_box region zlo/zhi for 2d simulation must straddle 0.0"); + } + + // setup general triclinic box (with no region) + // read next box extent arguments to create ABC edge vectors + origin + // define_general_triclinic() converts + // ABC edge vectors + origin to restricted triclinic + + } else if (triclinic_general) { + if (!domain->lattice->is_general_triclinic()) + error->all(FLERR,"Create_box for general triclinic requires triclnic/general lattice"); + + if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error); + + double alo = utils::numeric(FLERR, arg[iarg + 0], false, lmp); + double ahi = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + double blo = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + double bhi = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + double clo = utils::numeric(FLERR, arg[iarg + 4], false, lmp); + double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp); + iarg += 6; + + if (domain->dimension == 2) + if (clo != -0.5 || chi != 0.5) + error->all(FLERR,"Create_box for general triclinic requires clo = -0.5 and chi = 0.5"); + + // use lattice2box() to generate origin and ABC vectors + // origin = abc lo + // ABC vectors = hi in one dim - origin + + double avec[3],bvec[3],cvec[3],origin[3]; + double px,py,pz; + + px = alo; py = blo; pz = clo; + domain->lattice->lattice2box(px,py,pz); + origin[0] = px; + origin[1] = py; + origin[2] = pz; + + px = ahi; py = blo; pz = clo; + domain->lattice->lattice2box(px,py,pz); + avec[0] = px - origin[0]; + avec[1] = py - origin[1]; + avec[2] = pz - origin[2]; + + px = alo; py = bhi; pz = clo; + domain->lattice->lattice2box(px,py,pz); + bvec[0] = px - origin[0]; + bvec[1] = py - origin[1]; + bvec[2] = pz - origin[2]; + + px = alo; py = blo; pz = chi; + domain->lattice->lattice2box(px,py,pz); + cvec[0] = px - origin[0]; + cvec[1] = py - origin[1]; + cvec[2] = pz - origin[2]; + + // define general triclinic box within Domain class + + domain->define_general_triclinic(avec,bvec,cvec,origin); } // if molecular, zero out topology info @@ -104,7 +182,6 @@ void CreateBox::command(int narg, char **arg) // process optional args that can overwrite default settings - int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg], "bond/types") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box bond/type", error); @@ -166,7 +243,7 @@ void CreateBox::command(int narg, char **arg) error->all(FLERR, "Unknown create_box keyword: {}", arg[iarg]); } - // problem setup using info from header + // setup the simulation box and initial system // deallocate/grow ensures any extra settings are used for topology arrays // necessary in case no create_atoms is performed diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 6e14964a35..6f887a33e6 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -22,6 +22,7 @@ #include "comm.h" #include "domain.h" #include "error.h" +#include "fix_bond_history.h" #include "force.h" #include "group.h" #include "input.h" @@ -754,6 +755,10 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr) int nlocal = daptr->atom->nlocal; + // find instances of bond history to delete data + auto histories = daptr->modify->get_fix_by_style("BOND_HISTORY"); + int n_histories = histories.size(); + // cbuf = list of N deleted atom IDs from other proc, put them in hash hash->clear(); @@ -771,6 +776,11 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr) if (hash->find(bond_atom[i][m]) != hash->end()) { bond_type[i][m] = bond_type[i][n - 1]; bond_atom[i][m] = bond_atom[i][n - 1]; + if (n_histories > 0) + for (auto &ihistory: histories) { + dynamic_cast(ihistory)->shift_history(i,m,n-1); + dynamic_cast(ihistory)->delete_history(i,n-1); + } n--; } else m++; diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index 1f8fe71bff..056851bec1 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -85,19 +85,37 @@ void DeleteBonds::command(int narg, char **arg) if (narg < 3) error->all(FLERR,"Illegal delete_bonds command"); int n = -1; - if (style == ATOM) n = atom->ntypes; - if (style == BOND) n = atom->nbondtypes; - if (style == ANGLE) n = atom->nangletypes; - if (style == DIHEDRAL) n = atom->ndihedraltypes; - if (style == IMPROPER) n = atom->nimpropertypes; + char *typestr = nullptr; + if (style == ATOM) { + n = atom->ntypes; + typestr = utils::expand_type(FLERR, arg[2], Atom::ATOM, lmp); + } + if (style == BOND) { + n = atom->nbondtypes; + typestr = utils::expand_type(FLERR, arg[2], Atom::BOND, lmp); + } + if (style == ANGLE) { + n = atom->nangletypes; + typestr = utils::expand_type(FLERR, arg[2], Atom::ANGLE, lmp); + } + if (style == DIHEDRAL) { + n = atom->ndihedraltypes; + typestr = utils::expand_type(FLERR, arg[2], Atom::DIHEDRAL, lmp); + } + if (style == IMPROPER) { + n = atom->nimpropertypes; + typestr = utils::expand_type(FLERR, arg[2], Atom::IMPROPER, lmp); + } tlist = new int[n+1]; for (int i = 0; i <= n; i++) tlist[i] = 0; int nlo,nhi; - utils::bounds(FLERR,arg[2],0,n,nlo,nhi,error); + if (typestr) nlo = nhi = utils::inumeric(FLERR, typestr, false, lmp); + else utils::bounds(FLERR, arg[2], 0, n, nlo, nhi, error); for (int i = nlo; i <= nhi; i++) tlist[i] = 1; iarg++; + delete[] typestr; } // grab optional keywords diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 9da4df1f68..4ee0ffdad9 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -277,7 +277,8 @@ void DihedralHybrid::coeff(int narg, char **arg) else if (strcmp(arg[1], "bb13") == 0) error->all(FLERR, "BondBond13 coeff for hybrid dihedral has invalid format"); else - error->all(FLERR, "Dihedral coeff for hybrid has invalid style"); + error->all(FLERR, "Expected hybrid sub-style instead of {} in dihedral_coeff command", + arg[1]); } // move 1st arg to 2nd arg diff --git a/src/domain.cpp b/src/domain.cpp index 7513d384e2..db7533f21a 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -28,6 +28,7 @@ #include "force.h" #include "kspace.h" #include "lattice.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "molecule.h" @@ -41,6 +42,7 @@ #include using namespace LAMMPS_NS; +using namespace MathExtra; static constexpr double BIG = 1.0e20; static constexpr double SMALL = 1.0e-4; @@ -80,7 +82,7 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp) minylo = minyhi = 0.0; minzlo = minzhi = 0.0; - triclinic = 0; + triclinic = triclinic_general = 0; boxlo[0] = boxlo[1] = boxlo[2] = -0.5; boxhi[0] = boxhi[1] = boxhi[2] = 0.5; @@ -287,6 +289,30 @@ void Domain::set_global_box() boxhi_bound[1] = MAX(boxhi[1],boxhi[1]+yz); boxhi_bound[2] = boxhi[2]; } + + // update general triclinic box if defined + // reset general tri ABC edge vectors from restricted tri box + + if (triclinic_general) { + double aprime[3],bprime[3],cprime[3]; + + // A'B'C' = edge vectors of restricted triclinic box + + aprime[0] = boxhi[0] - boxlo[0]; + aprime[1] = aprime[2] = 0.0; + bprime[0] = xy; + bprime[1] = boxhi[1] - boxlo[1]; + bprime[2] = 0.0; + cprime[0] = xz; + cprime[1] = yz; + cprime[2] = boxhi[2] - boxlo[2]; + + // transform restricted A'B'C' to general triclinic ABC + + MathExtra::matvec(rotate_r2g,aprime,avec); + MathExtra::matvec(rotate_r2g,bprime,bvec); + MathExtra::matvec(rotate_r2g,cprime,cvec); + } } /* ---------------------------------------------------------------------- @@ -515,6 +541,220 @@ void Domain::reset_box() } } +/* ---------------------------------------------------------------------- + define and store a general triclinic simulation box + 3 edge vectors of box = avec/bvec/cvec caller + origin of edge vectors = origin_caller = lower left corner of box + create mapping to restricted triclinic box + set boxlo[3], boxhi[3] and 3 tilt factors + create rotation matrices for general <--> restricted transformations +------------------------------------------------------------------------- */ + +void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, + double *cvec_caller, double *origin_caller) +{ + if (triclinic || triclinic_general) + error->all(FLERR,"General triclinic box edge vectors are already set"); + + triclinic = triclinic_general = 1; + + avec[0] = avec_caller[0]; + avec[1] = avec_caller[1]; + avec[2] = avec_caller[2]; + + bvec[0] = bvec_caller[0]; + bvec[1] = bvec_caller[1]; + bvec[2] = bvec_caller[2]; + + cvec[0] = cvec_caller[0]; + cvec[1] = cvec_caller[1]; + cvec[2] = cvec_caller[2]; + + // error check on cvec for 2d systems + + if (dimension == 2 && (cvec[0] != 0.0 || cvec[1] != 0.0)) + error->all(FLERR,"General triclinic box edge vector C invalid for 2d system"); + + // rotate_g2r = rotation matrix from general to restricted triclnic + // rotate_r2g = rotation matrix from restricted to general triclnic + + double aprime[3],bprime[3],cprime[3]; + general_to_restricted_rotation(avec,bvec,cvec,rotate_g2r,aprime,bprime,cprime); + MathExtra::transpose3(rotate_g2r,rotate_r2g); + + // set restricted triclinic boxlo, boxhi, and tilt factors + + boxlo[0] = origin_caller[0]; + boxlo[1] = origin_caller[1]; + boxlo[2] = origin_caller[2]; + + boxhi[0] = boxlo[0] + aprime[0]; + boxhi[1] = boxlo[1] + bprime[1]; + boxhi[2] = boxlo[2] + cprime[2]; + + xy = bprime[0]; + xz = cprime[0]; + yz = cprime[1]; +} + +/* ---------------------------------------------------------------------- + compute rotation matrix to transform from general to restricted triclinic + ABC = 3 general triclinic edge vectors + rotmat = rotation matrix + A`B`C` = 3 restricited triclinic edge vectors +------------------------------------------------------------------------- */ + +void Domain::general_to_restricted_rotation(double *a, double *b, double *c, + double rotmat[3][3], + double *aprime, double *bprime, double *cprime) +{ + // error checks + // A,B,C cannot be co-planar + // A x B must point in C direction (right-handed) + + double abcross[3]; + MathExtra::cross3(a,b,abcross); + double dot = MathExtra::dot3(abcross,c); + if (dot == 0.0) + error->all(FLERR,"General triclinic edge vectors are co-planar"); + if (dot < 0.0) + error->all(FLERR,"General triclinic edge vectors must be right-handed"); + + // quat1 = convert A into A' along +x-axis + // rot1 = unit vector to rotate A around + // theta1 = angle of rotation calculated from + // A dot xunit = Ax = |A| cos(theta1) + + double rot1[3],quat1[4]; + double xaxis[3] = {1.0, 0.0, 0.0}; + + double alen = MathExtra::len3(a); + MathExtra::cross3(a,xaxis,rot1); + MathExtra::norm3(rot1); + double theta1 = acos(a[0]/alen); + MathExtra::axisangle_to_quat(rot1,theta1,quat1); + + // rotmat1 = rotation matrix associated with quat1 + + double rotmat1[3][3]; + MathExtra::quat_to_mat(quat1,rotmat1); + + // B1 = rotation of B by quat1 rotation matrix + + double b1[3]; + MathExtra::matvec(rotmat1,b,b1); + + // quat2 = rotation to convert B1 into B' in xy plane + // Byz1 = projection of B1 into yz plane + // +xaxis = unit vector to rotate B1 around + // theta2 = angle of rotation calculated from + // Byz1 dot yunit = B1y = |Byz1| cos(theta2) + // theta2 via acos() is positive (0 to PI) + // positive is valid if B1z < 0.0 else flip sign of theta2 + + double byzvec1[3],quat2[4]; + MathExtra::copy3(b1,byzvec1); + byzvec1[0] = 0.0; + double byzvec1_len = MathExtra::len3(byzvec1); + double theta2 = acos(b1[1]/byzvec1_len); + if (b1[2] > 0.0) theta2 = -theta2; + MathExtra::axisangle_to_quat(xaxis,theta2,quat2); + + // quat_single = rotation via single quat = quat2 * quat1 + // quat_r2g = rotation from restricted to general + // rotmat = general to restricted rotation matrix + + double quat_single[4]; + MathExtra::quatquat(quat2,quat1,quat_single); + MathExtra::quat_to_mat(quat_single,rotmat); + + // rotate general ABC to restricted triclinic A'B'C' + + MathExtra::matvec(rotmat,a,aprime); + MathExtra::matvec(rotmat,b,bprime); + MathExtra::matvec(rotmat,c,cprime); +} + +/* ---------------------------------------------------------------------- + transform atom coords from general triclinic to restricted triclinic +------------------------------------------------------------------------- */ + +void Domain::general_to_restricted_coords(double *x) +{ + double xshift[3],xnew[3]; + + xshift[0] = x[0] - boxlo[0]; + xshift[1] = x[1] - boxlo[1]; + xshift[2] = x[2] - boxlo[2]; + MathExtra::matvec(rotate_g2r,xshift,xnew); + x[0] = xnew[0] + boxlo[0]; + x[1] = xnew[1] + boxlo[1]; + x[2] = xnew[2] + boxlo[2]; +} + +/* ---------------------------------------------------------------------- + transform atom coords from restricted triclinic to general triclinic +------------------------------------------------------------------------- */ + +void Domain::restricted_to_general_coords(double *x) +{ + double xshift[3],xnew[3]; + + xshift[0] = x[0] - boxlo[0]; + xshift[1] = x[1] - boxlo[1]; + xshift[2] = x[2] - boxlo[2]; + MathExtra::matvec(rotate_r2g,xshift,xnew); + x[0] = xnew[0] + boxlo[0]; + x[1] = xnew[1] + boxlo[1]; + x[2] = xnew[2] + boxlo[2]; +} + +void Domain::restricted_to_general_coords(double *x, double *xnew) +{ + double xshift[3]; + + xshift[0] = x[0] - boxlo[0]; + xshift[1] = x[1] - boxlo[1]; + xshift[2] = x[2] - boxlo[2]; + MathExtra::matvec(rotate_r2g,xshift,xnew); + xnew[0] += boxlo[0]; + xnew[1] += boxlo[1]; + xnew[2] += boxlo[2]; +} + +/* ---------------------------------------------------------------------- + transform atom vector from general triclinic to restricted triclinic +------------------------------------------------------------------------- */ + +void Domain::general_to_restricted_vector(double *v) +{ + double vnew[3]; + + MathExtra::matvec(rotate_g2r,v,vnew); + v[0] = vnew[0]; + v[1] = vnew[1]; + v[2] = vnew[2]; +} + +/* ---------------------------------------------------------------------- + transform atom vector from restricted triclinic to general triclinic +------------------------------------------------------------------------- */ + +void Domain::restricted_to_general_vector(double *v) +{ + double vnew[3]; + + MathExtra::matvec(rotate_r2g,v,vnew); + v[0] = vnew[0]; + v[1] = vnew[1]; + v[2] = vnew[2]; +} + +void Domain::restricted_to_general_vector(double *v, double *vnew) +{ + MathExtra::matvec(rotate_r2g,v,vnew); +} + /* ---------------------------------------------------------------------- enforce PBC and modify box image flags for each atom called every reneighboring and by other commands that change atoms @@ -675,9 +915,7 @@ int Domain::inside(double* x) lamda[1] < lo[1] || lamda[1] >= hi[1] || lamda[2] < lo[2] || lamda[2] >= hi[2]) return 0; else return 1; - } - } /* ---------------------------------------------------------------------- @@ -712,7 +950,6 @@ int Domain::inside_nonperiodic(double* x) if (!zperiodic && (lamda[2] < lo[2] || lamda[2] >= hi[2])) return 0; return 1; } - } /* ---------------------------------------------------------------------- @@ -973,6 +1210,9 @@ void Domain::subbox_too_small_check(double thresh) changed "if" to "while" to enable distance to far-away ghost atom returned by atom->map() to be wrapped back into box could be problem for looking up atom IDs when cutoff > boxsize + should be used for most cases where the difference in the image count + is small (usually 0 or 1) + use minimum_image_big() when a large difference between image counts is expected ------------------------------------------------------------------------- */ static constexpr double MAXIMGCOUNT = 16; @@ -1045,6 +1285,72 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) const } } +/* ---------------------------------------------------------------------- + minimum image convention in periodic dimensions + use 1/2 of box size as test + for triclinic, also add/subtract tilt factors in other dims as needed + allow multiple box lengths to enable distance to + far-away ghost atom returned by atom->map() to be wrapped back into box + could be problem for looking up atom IDs when cutoff > boxsize + this should be used when there is a large image count difference possible + this applies for example to fix rigid/small +------------------------------------------------------------------------- */ + +void Domain::minimum_image_big(double &dx, double &dy, double &dz) const +{ + if (triclinic == 0) { + if (xperiodic) { + double dfactor = dx/xprd + 0.5; + if (dx < 0) dfactor -= 1.0; + if (dfactor > MAXSMALLINT) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); + dx -= xprd * static_cast(dfactor); + } + if (yperiodic) { + double dfactor = dy/yprd + 0.5; + if (dy < 0) dfactor -= 1.0; + if (dfactor > MAXSMALLINT) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); + dy -= yprd * static_cast(dfactor); + } + if (zperiodic) { + double dfactor = dz/zprd + 0.5; + if (dz < 0) dfactor -= 1.0; + if (dfactor > MAXSMALLINT) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); + dz -= zprd * static_cast(dfactor); + } + + } else { + if (zperiodic) { + double dfactor = dz/zprd + 0.5; + if (dz < 0) dfactor -= 1.0; + if (dfactor > MAXSMALLINT) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); + int factor = static_cast(dfactor); + dz -= zprd * factor; + dy -= yz * factor; + dx -= xz * factor; + } + if (yperiodic) { + double dfactor = dy/yprd + 0.5; + if (dy < 0) dfactor -= 1.0; + if (dfactor > MAXSMALLINT) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); + int factor = static_cast(dfactor); + dy -= yprd * factor; + dx -= xy * factor; + } + if (xperiodic) { + double dfactor = dx/xprd + 0.5; + if (dx < 0) dfactor -= 1.0; + if (dfactor > MAXSMALLINT) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); + dx -= xprd * static_cast(dfactor); + } + } +} + /* ---------------------------------------------------------------------- return local index of atom J or any of its images that is closest to atom I if J is not a valid index like -1, just return it @@ -1117,7 +1423,7 @@ int Domain::closest_image(const double * const pos, int j) /* ---------------------------------------------------------------------- find and return Xj image = periodic image of Xj that is closest to Xi for triclinic, add/subtract tilt factors in other dims as needed - called by ServerMD class and LammpsInterface in lib/atc. + called by ServerMD class and LammpsInterface in lib/atc ------------------------------------------------------------------------- */ void Domain::closest_image(const double * const xi, const double * const xj, double * const xjimage) diff --git a/src/domain.h b/src/domain.h index ab054f1b50..6479bd8d44 100644 --- a/src/domain.h +++ b/src/domain.h @@ -39,7 +39,8 @@ class Domain : protected Pointers { // 2 = shrink-wrap non-periodic // 3 = shrink-wrap non-per w/ min - int triclinic; // 0 = orthog box, 1 = triclinic + int triclinic; // 0 = orthog box, 1 = triclinic (restricted or general) + int triclinic_general; // 1 if general <-> restricted tri mapping is stored, 0 if not // orthogonal box @@ -48,8 +49,8 @@ class Domain : protected Pointers { double prd[3]; // array form of dimensions double prd_half[3]; // array form of half dimensions - // triclinic box - // xyzprd,xyzprd_half and prd,prd_half = same as if untilted + // restricted triclinic box + // xyz prd,xyz prd_half and prd,prd_half = same as if not tilted double prd_lamda[3]; // lamda box = (1,1,1) double prd_half_lamda[3]; // lamda half box = (0.5,0.5,0.5) @@ -58,14 +59,14 @@ class Domain : protected Pointers { double boxlo[3], boxhi[3]; - // triclinic box - // boxlo/hi = same as if untilted + // restricted triclinic box + // boxlo/hi = same as if not tilted double boxlo_lamda[3], boxhi_lamda[3]; // lamda box = (0,1) double boxlo_bound[3], boxhi_bound[3]; // bounding box of tilted domain double corners[8][3]; // 8 corner points - // orthogonal box & triclinic box + // orthogonal box & restricted triclinic box double minxlo, minxhi; // minimum size of global box double minylo, minyhi; // when shrink-wrapping @@ -75,18 +76,27 @@ class Domain : protected Pointers { double sublo[3], subhi[3]; // sub-box bounds on this proc - // triclinic box + // restricted triclinic box // sublo/hi = undefined double sublo_lamda[3], subhi_lamda[3]; // bounds of subbox in lamda - // triclinic box + // restricted triclinic box double xy, xz, yz; // 3 tilt factors double h[6], h_inv[6]; // shape matrix in Voigt ordering // Voigt = xx,yy,zz,yz,xz,xy double h_rate[6], h_ratelo[3]; // rate of box size/shape change + // general triclinic box + // boxlo = lower left corner + + double avec[3], bvec[3], cvec[3]; // ABC edge vectors of general triclinic box + double rotate_g2r[3][3]; // rotation matrix from general --> restricted tri + double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri + + // box flags + int box_change; // 1 if any of next 3 flags are set, else 0 int box_change_size; // 1 if box size changes, 0 if not int box_change_shape; // 1 if box shape changes, 0 if not @@ -119,6 +129,8 @@ class Domain : protected Pointers { void subbox_too_small_check(double); void minimum_image(double &, double &, double &) const; void minimum_image(double *delta) const { minimum_image(delta[0], delta[1], delta[2]); } + void minimum_image_big(double &, double &, double &) const; + void minimum_image_big(double *delta) const { minimum_image_big(delta[0], delta[1], delta[2]); } int closest_image(int, int); int closest_image(const double *const, int); void closest_image(const double *const, const double *const, double *const); @@ -131,6 +143,17 @@ class Domain : protected Pointers { void image_flip(int, int, int); int ownatom(int, double *, imageint *, int); + void define_general_triclinic(double *, double *, double *, double *); + void general_to_restricted_rotation(double *, double *, double *, + double [3][3], + double *, double *, double *); + void general_to_restricted_coords(double *); + void restricted_to_general_coords(double *); + void restricted_to_general_coords(double *, double *); + void general_to_restricted_vector(double *); + void restricted_to_general_vector(double *); + void restricted_to_general_vector(double *, double *x); + void set_lattice(int, char **); void add_region(int, char **); void delete_region(Region *); diff --git a/src/dump.h b/src/dump.h index 43baf96ccf..e5711af7a7 100644 --- a/src/dump.h +++ b/src/dump.h @@ -107,7 +107,7 @@ class Dump : protected Pointers { char *format_int_user; char *format_bigint_user; char **format_column_user; - enum { INT, DOUBLE, STRING, BIGINT }; + enum { INT, DOUBLE, STRING, STRING2, BIGINT }; std::map key2col; std::vector keyword_user; diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index fb3f58042c..dfacf8f2da 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -36,6 +36,7 @@ DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : scale_flag = 1; image_flag = 0; + triclinic_general = 0; buffer_allow = 1; buffer_flag = 1; format_default = nullptr; @@ -92,25 +93,46 @@ void DumpAtom::init_style() if (binary && domain->triclinic == 0) header_choice = &DumpAtom::header_binary; + else if (binary && triclinic_general == 1) + header_choice = &DumpAtom::header_binary_triclinic_general; else if (binary && domain->triclinic == 1) header_choice = &DumpAtom::header_binary_triclinic; else if (!binary && domain->triclinic == 0) header_choice = &DumpAtom::header_item; + else if (!binary && triclinic_general == 1) + header_choice = &DumpAtom::header_item_triclinic_general; else if (!binary && domain->triclinic == 1) header_choice = &DumpAtom::header_item_triclinic; - if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0) - pack_choice = &DumpAtom::pack_scale_noimage; - else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0) - pack_choice = &DumpAtom::pack_scale_image; - else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1) - pack_choice = &DumpAtom::pack_scale_noimage_triclinic; - else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1) - pack_choice = &DumpAtom::pack_scale_image_triclinic; - else if (scale_flag == 0 && image_flag == 0) - pack_choice = &DumpAtom::pack_noscale_noimage; - else if (scale_flag == 0 && image_flag == 1) - pack_choice = &DumpAtom::pack_noscale_image; + if (scale_flag == 0) { + if (image_flag == 0) { + if (triclinic_general == 1) { + pack_choice = &DumpAtom::pack_noscale_noimage_triclinic_general; + } else { + pack_choice = &DumpAtom::pack_noscale_noimage; + } + } else if (image_flag == 1) { + if (triclinic_general == 1) { + pack_choice = &DumpAtom::pack_noscale_image_triclinic_general; + } else { + pack_choice = &DumpAtom::pack_noscale_image; + } + } + } else if (scale_flag == 1) { + if (image_flag == 0) { + if (domain->triclinic == 0) { + pack_choice = &DumpAtom::pack_scale_noimage; + } else { + pack_choice = &DumpAtom::pack_scale_noimage_triclinic; + } + } else if (image_flag == 1) { + if (domain->triclinic == 0) { + pack_choice = &DumpAtom::pack_scale_image; + } else { + pack_choice = &DumpAtom::pack_scale_image_triclinic; + } + } + } if (image_flag == 0) convert_choice = &DumpAtom::convert_noimage; else convert_choice = &DumpAtom::convert_image; @@ -134,12 +156,24 @@ int DumpAtom::modify_param(int narg, char **arg) scale_flag = utils::logical(FLERR,arg[1],false,lmp); for (auto &item : keyword_user) item.clear(); return 2; - } else if (strcmp(arg[0],"image") == 0) { + } + + if (strcmp(arg[0],"image") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); image_flag = utils::logical(FLERR,arg[1],false,lmp); for (auto &item : keyword_user) item.clear(); return 2; } + + if (strcmp(arg[0],"triclinic/general") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + triclinic_general = utils::logical(FLERR,arg[1],false,lmp); + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Dump_modify triclinic/general cannot be used " + "if simulation box is not general triclinic"); + return 2; + } + return 0; } @@ -306,6 +340,31 @@ void DumpAtom::header_binary_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpAtom::header_binary_triclinic_general(bigint ndump) +{ + header_format_binary(); + + fwrite(&update->ntimestep,sizeof(bigint),1,fp); + fwrite(&ndump,sizeof(bigint),1,fp); + int triclinic_general_flag = 2; + fwrite(&triclinic_general_flag,sizeof(int),1,fp); + fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); + fwrite(domain->avec,3*sizeof(double),1,fp); + fwrite(domain->bvec,3*sizeof(double),1,fp); + fwrite(domain->cvec,3*sizeof(double),1,fp); + fwrite(domain->boxlo,3*sizeof(double),1,fp); + fwrite(&size_one,sizeof(int),1,fp); + + header_unit_style_binary(); + header_time_binary(); + header_columns_binary(); + + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- */ + void DumpAtom::header_item(bigint ndump) { if (unit_flag && !unit_count) { @@ -348,6 +407,30 @@ void DumpAtom::header_item_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpAtom::header_item_triclinic_general(bigint ndump) +{ + if (unit_flag && !unit_count) { + ++unit_count; + fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style); + } + if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); + + fmt::print(fp,"ITEM: TIMESTEP\n{}\nITEM: NUMBER OF ATOMS\n{}\n", update->ntimestep, ndump); + + fmt::print(fp,"ITEM: BOX BOUNDS abc origin {}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n", + boundstr, + domain->avec[0],domain->avec[1],domain->avec[2],domain->boxlo[0], + domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->boxlo[1], + domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->boxlo[2]); + + fmt::print(fp,"ITEM: ATOMS {}\n",columns); +} + +/* ---------------------------------------------------------------------- */ + void DumpAtom::pack_scale_image(tagint *ids) { int m,n; @@ -406,6 +489,59 @@ void DumpAtom::pack_scale_noimage(tagint *ids) } } +/* ---------------------------------------------------------------------- */ + +void DumpAtom::pack_noscale_image(tagint *ids) +{ + int m,n; + + tagint *tag = atom->tag; + int *type = atom->type; + imageint *image = atom->image; + int *mask = atom->mask; + double **x = atom->x; + int nlocal = atom->nlocal; + + m = n = 0; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + buf[m++] = tag[i]; + buf[m++] = type[i]; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = (image[i] & IMGMASK) - IMGMAX; + buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; + buf[m++] = (image[i] >> IMG2BITS) - IMGMAX; + if (ids) ids[n++] = tag[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtom::pack_noscale_noimage(tagint *ids) +{ + int m,n; + + tagint *tag = atom->tag; + int *type = atom->type; + int *mask = atom->mask; + double **x = atom->x; + int nlocal = atom->nlocal; + + m = n = 0; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + buf[m++] = tag[i]; + buf[m++] = type[i]; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + if (ids) ids[n++] = tag[i]; + } +} + + /* ---------------------------------------------------------------------- */ void DumpAtom::pack_scale_image_triclinic(tagint *ids) @@ -466,7 +602,7 @@ void DumpAtom::pack_scale_noimage_triclinic(tagint *ids) /* ---------------------------------------------------------------------- */ -void DumpAtom::pack_noscale_image(tagint *ids) +void DumpAtom::pack_noscale_image_triclinic_general(tagint *ids) { int m,n; @@ -477,14 +613,17 @@ void DumpAtom::pack_noscale_image(tagint *ids) double **x = atom->x; int nlocal = atom->nlocal; + double xtri[3]; + m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; - buf[m++] = x[i][0]; - buf[m++] = x[i][1]; - buf[m++] = x[i][2]; + domain->restricted_to_general_coords(x[i],xtri); + buf[m++] = xtri[0]; + buf[m++] = xtri[1]; + buf[m++] = xtri[2]; buf[m++] = (image[i] & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMG2BITS) - IMGMAX; @@ -494,7 +633,7 @@ void DumpAtom::pack_noscale_image(tagint *ids) /* ---------------------------------------------------------------------- */ -void DumpAtom::pack_noscale_noimage(tagint *ids) +void DumpAtom::pack_noscale_noimage_triclinic_general(tagint *ids) { int m,n; @@ -504,14 +643,17 @@ void DumpAtom::pack_noscale_noimage(tagint *ids) double **x = atom->x; int nlocal = atom->nlocal; + double xtri[3]; + m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; - buf[m++] = x[i][0]; - buf[m++] = x[i][1]; - buf[m++] = x[i][2]; + domain->restricted_to_general_coords(x[i],xtri); + buf[m++] = xtri[0]; + buf[m++] = xtri[1]; + buf[m++] = xtri[2]; if (ids) ids[n++] = tag[i]; } } diff --git a/src/dump_atom.h b/src/dump_atom.h index e28b390520..0b0d3a4f05 100644 --- a/src/dump_atom.h +++ b/src/dump_atom.h @@ -33,8 +33,9 @@ class DumpAtom : public Dump { const int ENDIAN = 0x0001; protected: - int scale_flag; // 1 if atom coords are scaled, 0 if no - int image_flag; // 1 if append box count to atom coords, 0 if no + int scale_flag; // 1 if atom coords are scaled, 0 if no + int image_flag; // 1 if append box count to atom coords, 0 if no + int triclinic_general; // 1 if output box & coords for general triclinic, 0 if no std::string columns; // column labels @@ -57,8 +58,10 @@ class DumpAtom : public Dump { FnPtrHeader header_choice; // ptr to write header functions void header_binary(bigint); void header_binary_triclinic(bigint); + void header_binary_triclinic_general(bigint); void header_item(bigint); void header_item_triclinic(bigint); + void header_item_triclinic_general(bigint); typedef void (DumpAtom::*FnPtrPack)(tagint *); FnPtrPack pack_choice; // ptr to pack functions @@ -68,6 +71,8 @@ class DumpAtom : public Dump { void pack_noscale_noimage(tagint *); void pack_scale_image_triclinic(tagint *); void pack_scale_noimage_triclinic(tagint *); + void pack_noscale_image_triclinic_general(tagint *); + void pack_noscale_noimage_triclinic_general(tagint *); typedef int (DumpAtom::*FnPtrConvert)(int, double *); FnPtrConvert convert_choice; // ptr to convert data functions diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index e9935b774f..abdc46c55a 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -23,6 +23,7 @@ #include "fix_store_atom.h" #include "group.h" #include "input.h" +#include "label_map.h" #include "memory.h" #include "modify.h" #include "region.h" @@ -34,9 +35,9 @@ using namespace LAMMPS_NS; // customize by adding keyword -// also customize compute_atom_property.cpp +// also customize compute_property_atom.cpp -enum{ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS, +enum{ID,MOL,PROC,PROCP1,TYPE,TYPELABEL,ELEMENT,MASS, X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI, XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI, IX,IY,IZ, @@ -88,6 +89,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : buffer_allow = 1; buffer_flag = 1; + triclinic_general = 0; nthresh = 0; nthreshlast = 0; @@ -139,6 +141,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : if (vtype[i] == Dump::INT) cols += "%d "; else if (vtype[i] == Dump::DOUBLE) cols += "%g "; else if (vtype[i] == Dump::STRING) cols += "%s "; + else if (vtype[i] == Dump::STRING2) cols += "%s "; else if (vtype[i] == Dump::BIGINT) cols += BIGINT_FORMAT " "; vformat[i] = nullptr; } @@ -237,7 +240,7 @@ DumpCustom::~DumpCustom() void DumpCustom::init_style() { - // assemble ITEMS: column string from defaults and user values + // assemble ITEMS column string from defaults and user values delete[] columns; std::string combined; @@ -290,14 +293,18 @@ void DumpCustom::init_style() domain->boundary_string(boundstr); - // setup function ptrs + // setup function ptrs for writing header and file format if (binary && domain->triclinic == 0) header_choice = &DumpCustom::header_binary; + else if (binary && triclinic_general == 1) + header_choice = &DumpCustom::header_binary_triclinic_general; else if (binary && domain->triclinic == 1) header_choice = &DumpCustom::header_binary_triclinic; else if (!binary && domain->triclinic == 0) header_choice = &DumpCustom::header_item; + else if (!binary && triclinic_general == 1) + header_choice = &DumpCustom::header_item_triclinic_general; else if (!binary && domain->triclinic == 1) header_choice = &DumpCustom::header_item_triclinic; @@ -305,6 +312,128 @@ void DumpCustom::init_style() else if (buffer_flag == 1) write_choice = &DumpCustom::write_string; else write_choice = &DumpCustom::write_lines; + // triclinic_general can be toggled by dump_modify before or between runs + // change any affected pack_choice function ptrs + + if (triclinic_general == 0) { + for (int n = 0; n < size_one; n++) { + if (pack_choice[n] == &DumpCustom::pack_x_triclinic_general) + pack_choice[n] = &DumpCustom::pack_x; + else if (pack_choice[n] == &DumpCustom::pack_y_triclinic_general) + pack_choice[n] = &DumpCustom::pack_y; + else if (pack_choice[n] == &DumpCustom::pack_z_triclinic_general) + pack_choice[n] = &DumpCustom::pack_z; + else if (pack_choice[n] == &DumpCustom::pack_xu_triclinic_general) { + if (domain->triclinic) pack_choice[n] = &DumpCustom::pack_xu_triclinic; + else pack_choice[n] = &DumpCustom::pack_xu; + } else if (pack_choice[n] == &DumpCustom::pack_yu_triclinic_general) { + if (domain->triclinic) pack_choice[n] = &DumpCustom::pack_yu_triclinic; + else pack_choice[n] = &DumpCustom::pack_yu; + } else if (pack_choice[n] == &DumpCustom::pack_zu_triclinic_general) { + if (domain->triclinic) pack_choice[n] = &DumpCustom::pack_zu_triclinic; + else pack_choice[n] = &DumpCustom::pack_zu; + } + + else if (pack_choice[n] == &DumpCustom::pack_vx_triclinic_general) + pack_choice[n] = &DumpCustom::pack_vx; + else if (pack_choice[n] == &DumpCustom::pack_vy_triclinic_general) + pack_choice[n] = &DumpCustom::pack_vy; + else if (pack_choice[n] == &DumpCustom::pack_vz_triclinic_general) + pack_choice[n] = &DumpCustom::pack_vz; + else if (pack_choice[n] == &DumpCustom::pack_fx_triclinic_general) + pack_choice[n] = &DumpCustom::pack_fx; + else if (pack_choice[n] == &DumpCustom::pack_fy_triclinic_general) + pack_choice[n] = &DumpCustom::pack_fy; + else if (pack_choice[n] == &DumpCustom::pack_fz_triclinic_general) + pack_choice[n] = &DumpCustom::pack_fz; + + else if (pack_choice[n] == &DumpCustom::pack_mux_triclinic_general) + pack_choice[n] = &DumpCustom::pack_mux; + else if (pack_choice[n] == &DumpCustom::pack_muy_triclinic_general) + pack_choice[n] = &DumpCustom::pack_muy; + else if (pack_choice[n] == &DumpCustom::pack_muz_triclinic_general) + pack_choice[n] = &DumpCustom::pack_muz; + + else if (pack_choice[n] == &DumpCustom::pack_omegax_triclinic_general) + pack_choice[n] = &DumpCustom::pack_omegax; + else if (pack_choice[n] == &DumpCustom::pack_omegay_triclinic_general) + pack_choice[n] = &DumpCustom::pack_omegay; + else if (pack_choice[n] == &DumpCustom::pack_omegaz_triclinic_general) + pack_choice[n] = &DumpCustom::pack_omegaz; + else if (pack_choice[n] == &DumpCustom::pack_angmomx_triclinic_general) + pack_choice[n] = &DumpCustom::pack_angmomx; + else if (pack_choice[n] == &DumpCustom::pack_angmomy_triclinic_general) + pack_choice[n] = &DumpCustom::pack_angmomy; + else if (pack_choice[n] == &DumpCustom::pack_angmomz_triclinic_general) + pack_choice[n] = &DumpCustom::pack_angmomz; + else if (pack_choice[n] == &DumpCustom::pack_tqx_triclinic_general) + pack_choice[n] = &DumpCustom::pack_tqx; + else if (pack_choice[n] == &DumpCustom::pack_tqy_triclinic_general) + pack_choice[n] = &DumpCustom::pack_tqy; + else if (pack_choice[n] == &DumpCustom::pack_tqz_triclinic_general) + pack_choice[n] = &DumpCustom::pack_tqz; + } + } + + if (triclinic_general == 1) { + for (int n = 0; n < size_one; n++) { + if (pack_choice[n] == &DumpCustom::pack_x) + pack_choice[n] = &DumpCustom::pack_x_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_y) + pack_choice[n] = &DumpCustom::pack_y_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_z) + pack_choice[n] = &DumpCustom::pack_z_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_xu || + pack_choice[n] == &DumpCustom::pack_xu_triclinic) + pack_choice[n] = &DumpCustom::pack_xu_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_yu || + pack_choice[n] == &DumpCustom::pack_yu_triclinic) + pack_choice[n] = &DumpCustom::pack_yu_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_zu || + pack_choice[n] == &DumpCustom::pack_zu_triclinic) + pack_choice[n] = &DumpCustom::pack_zu_triclinic_general; + + else if (pack_choice[n] == &DumpCustom::pack_vx) + pack_choice[n] = &DumpCustom::pack_vx_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_vy) + pack_choice[n] = &DumpCustom::pack_vy_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_vz) + pack_choice[n] = &DumpCustom::pack_vz_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_fx) + pack_choice[n] = &DumpCustom::pack_fx_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_fy) + pack_choice[n] = &DumpCustom::pack_fy_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_fz) + pack_choice[n] = &DumpCustom::pack_fz_triclinic_general; + + else if (pack_choice[n] == &DumpCustom::pack_mux) + pack_choice[n] = &DumpCustom::pack_mux_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_muy) + pack_choice[n] = &DumpCustom::pack_muy_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_muz) + pack_choice[n] = &DumpCustom::pack_muz_triclinic_general; + + else if (pack_choice[n] == &DumpCustom::pack_omegax) + pack_choice[n] = &DumpCustom::pack_omegax_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_omegay) + pack_choice[n] = &DumpCustom::pack_omegay_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_omegaz) + pack_choice[n] = &DumpCustom::pack_omegaz_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_angmomx) + pack_choice[n] = &DumpCustom::pack_angmomx_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_angmomy) + pack_choice[n] = &DumpCustom::pack_angmomy_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_angmomz) + pack_choice[n] = &DumpCustom::pack_angmomz_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_tqx) + pack_choice[n] = &DumpCustom::pack_tqx_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_tqy) + pack_choice[n] = &DumpCustom::pack_tqy_triclinic_general; + else if (pack_choice[n] == &DumpCustom::pack_tqz) + pack_choice[n] = &DumpCustom::pack_tqz_triclinic_general; + } + } + // find current ptr for each compute,fix,variable and custom atom property // check that fix frequency is acceptable @@ -489,6 +618,31 @@ void DumpCustom::header_binary_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpCustom::header_binary_triclinic_general(bigint ndump) +{ + header_format_binary(); + + fwrite(&update->ntimestep,sizeof(bigint),1,fp); + fwrite(&ndump,sizeof(bigint),1,fp); + int triclinic_general_flag = 2; + fwrite(&triclinic_general_flag,sizeof(int),1,fp); + fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); + fwrite(domain->avec,3*sizeof(double),1,fp); + fwrite(domain->bvec,3*sizeof(double),1,fp); + fwrite(domain->cvec,3*sizeof(double),1,fp); + fwrite(domain->boxlo,3*sizeof(double),1,fp); + fwrite(&nfield,sizeof(int),1,fp); + + header_unit_style_binary(); + header_time_binary(); + header_columns_binary(); + + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::header_item(bigint ndump) { if (unit_flag && !unit_count) { @@ -535,6 +689,30 @@ void DumpCustom::header_item_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpCustom::header_item_triclinic_general(bigint ndump) +{ + if (unit_flag && !unit_count) { + ++unit_count; + fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style); + } + if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); + + fmt::print(fp,"ITEM: TIMESTEP\n{}\nITEM: NUMBER OF ATOMS\n{}\n", update->ntimestep, ndump); + + fmt::print(fp,"ITEM: BOX BOUNDS abc origin {}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n", + boundstr, + domain->avec[0],domain->avec[1],domain->avec[2],domain->boxlo[0], + domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->boxlo[1], + domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->boxlo[2]); + + fmt::print(fp,"ITEM: ATOMS {}\n",columns); +} + +/* ---------------------------------------------------------------------- */ + int DumpCustom::count() { int i; @@ -641,7 +819,12 @@ int DumpCustom::count() for (i = 0; i < nlocal; i++) dchoose[i] = type[i]; ptr = dchoose; nstride = 1; - } else if (thresh_array[ithresh] == ELEMENT) { + } else if (thresh_array[ithresh] == TYPELABEL) { // dead code? + int *type = atom->type; + for (i = 0; i < nlocal; i++) dchoose[i] = type[i]; + ptr = dchoose; + nstride = 1; + } else if (thresh_array[ithresh] == ELEMENT) { // dead code? int *type = atom->type; for (i = 0; i < nlocal; i++) dchoose[i] = type[i]; ptr = dchoose; @@ -1181,6 +1364,8 @@ int DumpCustom::convert_string(int n, double *mybuf) offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]); else if (vtype[j] == Dump::STRING) offset += sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::STRING2) + offset += sprintf(&sbuf[offset],vformat[j],atom->lmap->typelabel[(int) mybuf[m]-1].c_str()); else if (vtype[j] == Dump::BIGINT) offset += sprintf(&sbuf[offset],vformat[j], static_cast (mybuf[m])); @@ -1229,6 +1414,8 @@ void DumpCustom::write_lines(int n, double *mybuf) else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]); else if (vtype[j] == Dump::STRING) fprintf(fp,vformat[j],typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::STRING2) + fprintf(fp,vformat[j],atom->lmap->typelabel[(int) mybuf[m]-1].c_str()); else if (vtype[j] == Dump::BIGINT) fprintf(fp,vformat[j],static_cast (mybuf[m])); m++; @@ -1269,6 +1456,9 @@ int DumpCustom::parse_fields(int narg, char **arg) } else if (strcmp(arg[iarg],"element") == 0) { pack_choice[iarg] = &DumpCustom::pack_type; vtype[iarg] = Dump::STRING; + } else if (strcmp(arg[iarg],"typelabel") == 0) { + pack_choice[iarg] = &DumpCustom::pack_type; + vtype[iarg] = Dump::STRING2; } else if (strcmp(arg[iarg],"mass") == 0) { pack_choice[iarg] = &DumpCustom::pack_mass; vtype[iarg] = Dump::DOUBLE; @@ -1318,6 +1508,7 @@ int DumpCustom::parse_fields(int narg, char **arg) if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zsu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_zsu; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"ix") == 0) { pack_choice[iarg] = &DumpCustom::pack_ix; vtype[iarg] = Dump::INT; @@ -1352,6 +1543,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_q; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"mux") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1398,6 +1590,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_omegaz; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"angmomx") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1413,6 +1606,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_angmomz; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"tqx") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1680,6 +1874,15 @@ int DumpCustom::modify_param(int narg, char **arg) return 2; } + if (strcmp(arg[0],"triclinic/general") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + triclinic_general = utils::logical(FLERR,arg[1],false,lmp); + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Dump_modify triclinic/general cannot be used " + "if simulation box is not general triclinic"); + return 2; + } + if (strcmp(arg[0],"format") == 0) { if (narg < 2) utils::missing_cmd_args(FLERR, "dump_modify format", error); @@ -2259,6 +2462,48 @@ void DumpCustom::pack_z(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_x_triclinic_general(int n) +{ + double **x = atom->x; + double xtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(x[clist[i]],xtri); + buf[n] = xtri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_y_triclinic_general(int n) +{ + double **x = atom->x; + double xtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(x[clist[i]],xtri); + buf[n] = xtri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_z_triclinic_general(int n) +{ + double **x = atom->x; + double xtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(x[clist[i]],xtri); + buf[n] = xtri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_xs(int n) { double **x = atom->x; @@ -2465,6 +2710,84 @@ void DumpCustom::pack_zu_triclinic(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_xu_triclinic_general(int n) +{ + int j; + double **x = atom->x; + imageint *image = atom->image; + + double *h = domain->h; + double xu[3]; + int xbox,ybox,zbox; + + for (int i = 0; i < nchoose; i++) { + j = clist[i]; + xbox = (image[j] & IMGMASK) - IMGMAX; + ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (image[j] >> IMG2BITS) - IMGMAX; + xu[0] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; + xu[1] = x[j][1] + h[1]*ybox + h[3]*zbox; + xu[2] = x[j][2] + h[2]*zbox; + domain->restricted_to_general_coords(xu); + buf[n] = xu[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_yu_triclinic_general(int n) +{ + int j; + double **x = atom->x; + imageint *image = atom->image; + + double *h = domain->h; + double xu[3]; + int xbox,ybox,zbox; + + for (int i = 0; i < nchoose; i++) { + j = clist[i]; + xbox = (image[j] & IMGMASK) - IMGMAX; + ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (image[j] >> IMG2BITS) - IMGMAX; + xu[0] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; + xu[1] = x[j][1] + h[1]*ybox + h[3]*zbox; + xu[2] = x[j][2] + h[2]*zbox; + domain->restricted_to_general_coords(xu); + buf[n] = xu[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_zu_triclinic_general(int n) +{ + int j; + double **x = atom->x; + imageint *image = atom->image; + + double *h = domain->h; + double xu[3]; + int xbox,ybox,zbox; + + for (int i = 0; i < nchoose; i++) { + j = clist[i]; + xbox = (image[j] & IMGMASK) - IMGMAX; + ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (image[j] >> IMG2BITS) - IMGMAX; + xu[0] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; + xu[1] = x[j][1] + h[1]*ybox + h[3]*zbox; + xu[2] = x[j][2] + h[2]*zbox; + domain->restricted_to_general_coords(xu); + buf[n] = xu[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_xsu(int n) { int j; @@ -2647,6 +2970,48 @@ void DumpCustom::pack_vz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_vx_triclinic_general(int n) +{ + double **v = atom->v; + double vtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(v[clist[i]],vtri); + buf[n] = vtri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_vy_triclinic_general(int n) +{ + double **v = atom->v; + double vtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(v[clist[i]],vtri); + buf[n] = vtri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_vz_triclinic_general(int n) +{ + double **v = atom->v; + double vtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(v[clist[i]],vtri); + buf[n] = vtri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_fx(int n) { double **f = atom->f; @@ -2683,6 +3048,48 @@ void DumpCustom::pack_fz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_fx_triclinic_general(int n) +{ + double **f = atom->f; + double ftri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(f[clist[i]],ftri); + buf[n] = ftri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_fy_triclinic_general(int n) +{ + double **f = atom->f; + double ftri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(f[clist[i]],ftri); + buf[n] = ftri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_fz_triclinic_general(int n) +{ + double **f = atom->f; + double ftri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(f[clist[i]],ftri); + buf[n] = ftri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_q(int n) { double *q = atom->q; @@ -2743,6 +3150,48 @@ void DumpCustom::pack_mu(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_mux_triclinic_general(int n) +{ + double **mu = atom->mu; + double mutri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(mu[clist[i]],mutri); + buf[n] = mutri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_muy_triclinic_general(int n) +{ + double **mu = atom->mu; + double mutri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(mu[clist[i]],mutri); + buf[n] = mutri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_muz_triclinic_general(int n) +{ + double **mu = atom->mu; + double mutri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(mu[clist[i]],mutri); + buf[n] = mutri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_radius(int n) { double *radius = atom->radius; @@ -2803,6 +3252,48 @@ void DumpCustom::pack_omegaz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_omegax_triclinic_general(int n) +{ + double **omega = atom->omega; + double omegatri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(omega[clist[i]],omegatri); + buf[n] = omegatri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_omegay_triclinic_general(int n) +{ + double **omega = atom->omega; + double omegatri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(omega[clist[i]],omegatri); + buf[n] = omegatri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_omegaz_triclinic_general(int n) +{ + double **omega = atom->omega; + double omegatri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(omega[clist[i]],omegatri); + buf[n] = omegatri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_angmomx(int n) { double **angmom = atom->angmom; @@ -2839,6 +3330,48 @@ void DumpCustom::pack_angmomz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_angmomx_triclinic_general(int n) +{ + double **angmom = atom->angmom; + double angmomtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); + buf[n] = angmomtri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_angmomy_triclinic_general(int n) +{ + double **angmom = atom->angmom; + double angmomtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); + buf[n] = angmomtri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_angmomz_triclinic_general(int n) +{ + double **angmom = atom->angmom; + double angmomtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); + buf[n] = angmomtri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_tqx(int n) { double **torque = atom->torque; @@ -2872,3 +3405,45 @@ void DumpCustom::pack_tqz(int n) n += size_one; } } + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_tqx_triclinic_general(int n) +{ + double **torque = atom->torque; + double tqtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(torque[clist[i]],tqtri); + buf[n] = tqtri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_tqy_triclinic_general(int n) +{ + double **torque = atom->torque; + double tqtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(torque[clist[i]],tqtri); + buf[n] = tqtri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_tqz_triclinic_general(int n) +{ + double **torque = atom->torque; + double tqtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(torque[clist[i]],tqtri); + buf[n] = tqtri[2]; + n += size_one; + } +} diff --git a/src/dump_custom.h b/src/dump_custom.h index b600bd60b8..6b4ca88b0b 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -36,6 +36,7 @@ class DumpCustom : public Dump { protected: int nevery; // dump frequency for output char *idregion; // region ID, nullptr if no region + int triclinic_general; // 1 if output box & per-atom info for general triclinic int nthresh; // # of defined thresholds int nthreshlast; // # of defined thresholds with value = LAST @@ -124,8 +125,10 @@ class DumpCustom : public Dump { FnPtrHeader header_choice; // ptr to write header functions void header_binary(bigint); void header_binary_triclinic(bigint); + void header_binary_triclinic_general(bigint); void header_item(bigint); void header_item_triclinic(bigint); + void header_item_triclinic_general(bigint); typedef void (DumpCustom::*FnPtrWrite)(int, double *); FnPtrWrite write_choice; // ptr to write data functions @@ -153,24 +156,34 @@ class DumpCustom : public Dump { void pack_x(int); void pack_y(int); void pack_z(int); + void pack_x_triclinic_general(int); + void pack_y_triclinic_general(int); + void pack_z_triclinic_general(int); + void pack_xs(int); void pack_ys(int); void pack_zs(int); void pack_xs_triclinic(int); void pack_ys_triclinic(int); void pack_zs_triclinic(int); + void pack_xu(int); void pack_yu(int); void pack_zu(int); void pack_xu_triclinic(int); void pack_yu_triclinic(int); void pack_zu_triclinic(int); + void pack_xu_triclinic_general(int); + void pack_yu_triclinic_general(int); + void pack_zu_triclinic_general(int); + void pack_xsu(int); void pack_ysu(int); void pack_zsu(int); void pack_xsu_triclinic(int); void pack_ysu_triclinic(int); void pack_zsu_triclinic(int); + void pack_ix(int); void pack_iy(int); void pack_iz(int); @@ -178,26 +191,50 @@ class DumpCustom : public Dump { void pack_vx(int); void pack_vy(int); void pack_vz(int); + void pack_vx_triclinic_general(int); + void pack_vy_triclinic_general(int); + void pack_vz_triclinic_general(int); + void pack_fx(int); void pack_fy(int); void pack_fz(int); + void pack_fx_triclinic_general(int); + void pack_fy_triclinic_general(int); + void pack_fz_triclinic_general(int); + void pack_q(int); + void pack_mux(int); void pack_muy(int); void pack_muz(int); void pack_mu(int); + void pack_mux_triclinic_general(int); + void pack_muy_triclinic_general(int); + void pack_muz_triclinic_general(int); + void pack_radius(int); void pack_diameter(int); void pack_omegax(int); void pack_omegay(int); void pack_omegaz(int); + void pack_omegax_triclinic_general(int); + void pack_omegay_triclinic_general(int); + void pack_omegaz_triclinic_general(int); + void pack_angmomx(int); void pack_angmomy(int); void pack_angmomz(int); + void pack_angmomx_triclinic_general(int); + void pack_angmomy_triclinic_general(int); + void pack_angmomz_triclinic_general(int); + void pack_tqx(int); void pack_tqy(int); void pack_tqz(int); + void pack_tqx_triclinic_general(int); + void pack_tqy_triclinic_general(int); + void pack_tqz_triclinic_general(int); }; } // namespace LAMMPS_NS diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index f7ab77b2bf..018fa754d7 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "error.h" +#include "label_map.h" #include "memory.h" #include "update.h" @@ -122,6 +123,32 @@ int DumpXYZ::modify_param(int narg, char **arg) return ntypes+1; } + if (strcmp(arg[0],"types") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + + if (typenames) { + for (int i = 1; i <= ntypes; i++) + delete [] typenames[i]; + + delete [] typenames; + typenames = nullptr; + } + + if (strcmp(arg[1],"numeric") == 0) { + return 2; + } else if (strcmp(arg[1],"labels") == 0) { + if (!atom->labelmapflag) + error->all(FLERR, "Label map must be defined when using 'types labels'"); + } else error->all(FLERR, "Illegal option for dump_modify 'types' keyword"); + + typenames = new char*[ntypes+1]; + for (int itype = 1; itype <= ntypes; itype++) { + typenames[itype] = utils::strdup(atom->lmap->typelabel[itype-1]); + } + + return 2; + } + return 0; } diff --git a/src/fix.cpp b/src/fix.cpp index 754948fdd1..8678706347 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -81,6 +81,7 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) : diam_flag = 0; scalar_flag = vector_flag = array_flag = 0; + extscalar = extvector = extarray = -1; peratom_flag = local_flag = pergrid_flag = 0; global_freq = local_freq = peratom_freq = pergrid_freq = -1; size_vector_variable = size_array_rows_variable = 0; @@ -119,13 +120,28 @@ Fix::~Fix() { if (copymode) return; - delete [] id; - delete [] style; + delete[] id; + delete[] style; memory->destroy(eatom); memory->destroy(vatom); memory->destroy(cvatom); } +/* ---------------------------------------------------------------------- */ + +void Fix::init_flags() +{ + if (scalar_flag && (extscalar < 0)) + error->all(FLERR, "Must set 'extscalar' when setting 'scalar_flag' for fix {}. " + "Contact the developer.", style); + if (vector_flag && (extvector < 0) && !extlist) + error->all(FLERR, "Must set 'extvector' or 'extlist' when setting 'vector_flag' for fix {}. " + "Contact the developer.", style); + if (array_flag && (extarray < 0)) + error->all(FLERR, "Must set 'extarray' when setting 'array_flag' for fix {}. " + "Contact the developer.", style); +} + /* ---------------------------------------------------------------------- process params common to all fixes here if unknown param, call modify_param specific to the fix @@ -133,36 +149,37 @@ Fix::~Fix() void Fix::modify_params(int narg, char **arg) { - if (narg == 0) error->all(FLERR,"Illegal fix_modify command"); + if (narg == 0) utils::missing_cmd_args(FLERR, "fix_modify", error); int iarg = 0; while (iarg < narg) { if (strcmp(arg[iarg],"dynamic/dof") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify dynamic/dof", error); dynamic = utils::logical(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"energy") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify energy", error); thermo_energy = utils::logical(FLERR,arg[iarg+1],false,lmp); if (thermo_energy && !energy_global_flag && !energy_peratom_flag) error->all(FLERR,"Fix {} {} does not support fix_modify energy command", id, style); iarg += 2; } else if (strcmp(arg[iarg],"virial") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify virial", error); thermo_virial = utils::logical(FLERR,arg[iarg+1],false,lmp); if (thermo_virial && !virial_global_flag && !virial_peratom_flag) error->all(FLERR,"Fix {} {} does not support fix_modify virial command", id, style); iarg += 2; } else if (strcmp(arg[iarg],"respa") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command"); - if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify respa", error); + if (!respa_level_support) error->all(FLERR,"Illegal fix_modify respa command"); int lvl = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if (lvl < 0) error->all(FLERR,"Illegal fix_modify command"); + if (lvl < 0) error->all(FLERR,"Illegal fix_modify respa command"); respa_level = lvl-1; iarg += 2; } else { int n = modify_param(narg-iarg,&arg[iarg]); - if (n == 0) error->all(FLERR,"Illegal fix_modify command"); + if (n == 0) + error->all(FLERR,"Fix {} {} does not support fix_modify {} command", id, style, arg[iarg]); iarg += n; } } diff --git a/src/fix.h b/src/fix.h index ca0a1ef84b..594fbb51bf 100644 --- a/src/fix.h +++ b/src/fix.h @@ -145,6 +145,7 @@ class Fix : protected Pointers { virtual void post_constructor() {} virtual void init() {} + void init_flags(); virtual void init_list(int, class NeighList *) {} virtual void setup(int) {} virtual void setup_pre_exchange() {} diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 2a10b9d603..cad157f2be 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -99,10 +99,22 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : adapt[nadapt].pair = nullptr; adapt[nadapt].pstyle = utils::strdup(arg[iarg+1]); adapt[nadapt].pparam = utils::strdup(arg[iarg+2]); - utils::bounds(FLERR,arg[iarg+3],1,atom->ntypes, - adapt[nadapt].ilo,adapt[nadapt].ihi,error); - utils::bounds(FLERR,arg[iarg+4],1,atom->ntypes, - adapt[nadapt].jlo,adapt[nadapt].jhi,error); + utils::bounds_typelabel(FLERR, arg[iarg+3], 1, atom->ntypes, + adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::ATOM); + utils::bounds_typelabel(FLERR, arg[iarg+4], 1, atom->ntypes, + adapt[nadapt].jlo, adapt[nadapt].jhi, lmp, Atom::ATOM); + + // switch i,j if i > j, if wildcards were not used + + if ( (adapt[nadapt].ilo == adapt[nadapt].ihi) && + (adapt[nadapt].jlo == adapt[nadapt].jhi) && + (adapt[nadapt].ilo > adapt[nadapt].jlo) ) { + adapt[nadapt].jlo = adapt[nadapt].ihi; + adapt[nadapt].ilo = adapt[nadapt].jhi; + adapt[nadapt].ihi = adapt[nadapt].ilo; + adapt[nadapt].jhi = adapt[nadapt].jlo; + } + if (utils::strmatch(arg[iarg+5],"^v_")) { adapt[nadapt].var = utils::strdup(arg[iarg+5]+2); } else error->all(FLERR,"Argument #{} must be variable not {}", iarg+6, arg[iarg+5]); @@ -114,8 +126,8 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : adapt[nadapt].bond = nullptr; adapt[nadapt].bstyle = utils::strdup(arg[iarg+1]); adapt[nadapt].bparam = utils::strdup(arg[iarg+2]); - utils::bounds(FLERR,arg[iarg+3],1,atom->nbondtypes, - adapt[nadapt].ilo,adapt[nadapt].ihi,error); + utils::bounds_typelabel(FLERR, arg[iarg+3], 1, atom->nbondtypes, + adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::BOND); if (utils::strmatch(arg[iarg+4],"^v_")) { adapt[nadapt].var = utils::strdup(arg[iarg+4]+2); } else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]); @@ -127,8 +139,8 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : adapt[nadapt].angle = nullptr; adapt[nadapt].astyle = utils::strdup(arg[iarg+1]); adapt[nadapt].aparam = utils::strdup(arg[iarg+2]); - utils::bounds(FLERR,arg[iarg+3],1,atom->nangletypes, - adapt[nadapt].ilo,adapt[nadapt].ihi,error); + utils::bounds_typelabel(FLERR, arg[iarg+3], 1, atom->nangletypes, + adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::ANGLE); if (utils::strmatch(arg[iarg+4],"^v_")) { adapt[nadapt].var = utils::strdup(arg[iarg+4]+2); } else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]); diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index a0d25cf2c7..9382b6d38e 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -193,10 +193,12 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; - } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk file", error); + } else if ((strcmp(arg[iarg],"file") == 0) || (strcmp(arg[iarg],"append") == 0)) { + if (iarg+2 > narg) + utils::missing_cmd_args(FLERR, std::string("fix ave/chunk ")+arg[iarg], error); if (comm->me == 0) { - fp = fopen(arg[iarg+1],"w"); + if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w"); + else fp = fopen(arg[iarg+1],"a"); if (fp == nullptr) error->one(FLERR, "Cannot open fix ave/chunk file {}: {}", arg[iarg+1], utils::getsyserror()); diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index d506e17761..08cd673122 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -97,7 +97,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : while (iarg < nargnew) { if (strcmp(arg[iarg],"type") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate type", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate type", error); if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO; else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER; else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER; @@ -107,21 +107,21 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : else error->all(FLERR,"Unknown fix ave/correlate type: {}"); iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate ave", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate ave", error); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; else error->all(FLERR,"Unknown fix ave/correlate ave mode: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"start") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate start", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate start", error); startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"prefactor") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate prefactor", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate prefactor", error); prefactor = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate file", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate file", error); if (comm->me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) @@ -133,17 +133,17 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : overwrite = 1; iarg += 1; } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title1", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate title1", error); delete[] title1; title1 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title2", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate title2", error); delete[] title2; title2 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title3", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate title3", error); delete[] title3; title3 = utils::strdup(arg[iarg+1]); iarg += 2; @@ -414,6 +414,8 @@ void FixAveCorrelate::end_of_step() scalar = val.val.f->compute_vector(val.argindex-1); // evaluate equal-style or vector-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori } else if (val.which == ArgInfo::VARIABLE) { if (val.argindex == 0) @@ -422,7 +424,7 @@ void FixAveCorrelate::end_of_step() double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); int index = val.argindex; - if (nvec < index) scalar = 0.0; + if (index > nvec) scalar = 0.0; else scalar = varvec[index-1]; } } diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index a92efcdacd..9b384e60fa 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -207,7 +207,8 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : if (val.val.v < 0) error->all(FLERR,"Variable name {} for {} does not exist", val.id, mycmd); // variables only produce one kind of output - if (input->variable->equalstyle(val.val.v)) kindglobal = 1; + if (input->variable->equalstyle(val.val.v) || input->variable->vectorstyle(val.val.v)) + kindglobal = 1; else if (input->variable->atomstyle(val.val.v)) kindperatom = 1; else error->all(FLERR,"{} variable {} is incompatible style", mycmd, val.id); } @@ -600,6 +601,8 @@ void FixAveHisto::end_of_step() } // evaluate equal-style or vector-style or atom-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori } else if (val.which == ArgInfo::VARIABLE) { if (kind == GLOBAL && mode == SCALAR) { @@ -607,7 +610,7 @@ void FixAveHisto::end_of_step() else { double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); - if (nvec < j) bin_one(0.0); + if (j > nvec) bin_one(0.0); else bin_one(varvec[j-1]); } @@ -839,10 +842,12 @@ void FixAveHisto::options(int iarg, int narg, char **arg) auto mycmd = fmt::format("fix {}", style); while (iarg < narg) { - if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " file", error); + if ((strcmp(arg[iarg],"file") == 0) || (strcmp(arg[iarg],"append") == 0)) { + if (iarg+2 > narg) + utils::missing_cmd_args(FLERR, std::string("fix ave/histo ")+arg[iarg], error); if (comm->me == 0) { - fp = fopen(arg[iarg+1],"w"); + if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w"); + else fp = fopen(arg[iarg+1],"a"); if (fp == nullptr) error->one(FLERR, "Cannot open fix ave/histo file {}: {}", arg[iarg+1], utils::getsyserror()); diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 7a5458bd3d..cccfc86d59 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -113,256 +113,256 @@ void FixAveHistoWeight::end_of_step() double weight = 0.0; double *weights = nullptr; int stride = 0; - auto &val = values[1]; - int j = val.argindex; + auto &val1 = values[1]; + int j = val1.argindex; // atom attributes - if (val.which == ArgInfo::X) { + if (val1.which == ArgInfo::X) { weights = &atom->x[0][j]; stride = 3; - } else if (val.which == ArgInfo::V) { + } else if (val1.which == ArgInfo::V) { weights = &atom->v[0][j]; stride = 3; bin_atoms(&atom->v[0][j],3); - } else if (val.which == ArgInfo::F) { + } else if (val1.which == ArgInfo::F) { weights = &atom->f[0][j]; stride = 3; } // invoke compute if not previously invoked - if (val.which == ArgInfo::COMPUTE) { + if (val1.which == ArgInfo::COMPUTE) { if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { - val.val.c->compute_scalar(); - val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val1.val.c->compute_scalar(); + val1.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - weight = val.val.c->scalar; + weight = val1.val.c->scalar; } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val1.val.c->compute_vector(); + val1.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - weight = val.val.c->vector[j-1]; + weight = val1.val.c->vector[j-1]; } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val1.val.c->compute_vector(); + val1.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - weights = val.val.c->vector; + weights = val1.val.c->vector; stride = 1; } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { - val.val.c->compute_array(); - val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val1.val.c->compute_array(); + val1.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - if (val.val.c->array) weights = &val.val.c->array[0][j-1]; - stride = val.val.c->size_array_cols; + if (val1.val.c->array) weights = &val1.val.c->array[0][j-1]; + stride = val1.val.c->size_array_cols; } } else if (kind == PERATOM) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { - val.val.c->compute_peratom(); - val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val1.val.c->compute_peratom(); + val1.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) { - weights = val.val.c->vector_atom; + weights = val1.val.c->vector_atom; stride = 1; - } else if (val.val.c->array_atom) { - weights = &val.val.c->array_atom[0][j-1]; - stride = val.val.c->size_peratom_cols; + } else if (val1.val.c->array_atom) { + weights = &val1.val.c->array_atom[0][j-1]; + stride = val1.val.c->size_peratom_cols; } } else if (kind == LOCAL) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { - val.val.c->compute_local(); - val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val1.val.c->compute_local(); + val1.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (j == 0) { - weights = val.val.c->vector_local; + weights = val1.val.c->vector_local; stride = 1; - } else if (val.val.c->array_local) { - weights = &val.val.c->array_local[0][j-1]; - stride = val.val.c->size_local_cols; + } else if (val1.val.c->array_local) { + weights = &val1.val.c->array_local[0][j-1]; + stride = val1.val.c->size_local_cols; } } // access fix fields, guaranteed to be ready - } else if (val.which == ArgInfo::FIX) { + } else if (val1.which == ArgInfo::FIX) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) weight = val.val.f->compute_scalar(); - else weight = val.val.f->compute_vector(j-1); + if (j == 0) weight = val1.val.f->compute_scalar(); + else weight = val1.val.f->compute_vector(j-1); } else if (kind == GLOBAL && mode == VECTOR) { error->all(FLERR,"Fix ave/histo/weight option not yet supported"); // NOTE: need to allocate local storage if (j == 0) { - int n = val.val.f->size_vector; - for (int i = 0; i < n; i++) weights[n] = val.val.f->compute_vector(i); + int n = val1.val.f->size_vector; + for (int i = 0; i < n; i++) weights[n] = val1.val.f->compute_vector(i); } else { - int n = val.val.f->size_vector; - for (int i = 0; i < n; i++) weights[n] = val.val.f->compute_array(i,j-1); + int n = val1.val.f->size_vector; + for (int i = 0; i < n; i++) weights[n] = val1.val.f->compute_array(i,j-1); } } else if (kind == PERATOM) { if (j == 0) { - weights = val.val.f->vector_atom; + weights = val1.val.f->vector_atom; stride = 1; - } else if (val.val.f->array_atom) { - weights = &val.val.f->array_atom[0][j-1]; - stride = val.val.f->size_peratom_cols; + } else if (val1.val.f->array_atom) { + weights = &val1.val.f->array_atom[0][j-1]; + stride = val1.val.f->size_peratom_cols; } } else if (kind == LOCAL) { if (j == 0) { - weights = val.val.f->vector_local; + weights = val1.val.f->vector_local; stride = 1; - } else if (val.val.f->array_local) { - weights = &val.val.f->array_local[0][j-1]; - stride = val.val.f->size_local_cols; + } else if (val1.val.f->array_local) { + weights = &val1.val.f->array_local[0][j-1]; + stride = val1.val.f->size_local_cols; } } // evaluate equal-style variable - } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL) { - weight = input->variable->compute_equal(val.val.v); + } else if (val1.which == ArgInfo::VARIABLE && kind == GLOBAL) { + weight = input->variable->compute_equal(val1.val.v); - } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val1.which == ArgInfo::VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } - input->variable->compute_atom(val.val.v,igroup,vector,1,0); + input->variable->compute_atom(val1.val.v,igroup,vector,1,0); weights = vector; stride = 1; } // bin values using weights, values are 1st value (i = 0) - val = values[0]; - j = val.argindex; + auto &val0 = values[0]; + j = val0.argindex; // atom attributes - if (val.which == ArgInfo::X && weights != nullptr) + if (val0.which == ArgInfo::X && weights != nullptr) bin_atoms_weights(&atom->x[0][j],3,weights,stride); - else if (val.which == ArgInfo::V && weights != nullptr) + else if (val0.which == ArgInfo::V && weights != nullptr) bin_atoms_weights(&atom->v[0][j],3,weights,stride); - else if (val.which == ArgInfo::F && weights != nullptr) + else if (val0.which == ArgInfo::F && weights != nullptr) bin_atoms_weights(&atom->f[0][j],3,weights,stride); // invoke compute if not previously invoked - if (val.which == ArgInfo::COMPUTE) { + if (val0.which == ArgInfo::COMPUTE) { if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { - val.val.c->compute_scalar(); - val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val0.val.c->compute_scalar(); + val0.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - bin_one_weights(val.val.c->scalar,weight); + bin_one_weights(val0.val.c->scalar,weight); } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val0.val.c->compute_vector(); + val0.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_one_weights(val.val.c->vector[j-1],weight); + bin_one_weights(val0.val.c->vector[j-1],weight); } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val0.val.c->compute_vector(); + val0.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_vector_weights(val.val.c->size_vector,val.val.c->vector,1, + bin_vector_weights(val0.val.c->size_vector,val0.val.c->vector,1, weights,stride); } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { - val.val.c->compute_array(); - val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val0.val.c->compute_array(); + val0.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - if (val.val.c->array) - bin_vector_weights(val.val.c->size_array_rows,&val.val.c->array[0][j-1], - val.val.c->size_array_cols,weights,stride); + if (val0.val.c->array) + bin_vector_weights(val0.val.c->size_array_rows,&val0.val.c->array[0][j-1], + val0.val.c->size_array_cols,weights,stride); } } else if (kind == PERATOM) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { - val.val.c->compute_peratom(); - val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val0.val.c->compute_peratom(); + val0.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) - bin_atoms_weights(val.val.c->vector_atom,1,weights, stride); - else if (val.val.c->array_atom) - bin_atoms_weights(&val.val.c->array_atom[0][j-1], - val.val.c->size_peratom_cols,weights,stride); + bin_atoms_weights(val0.val.c->vector_atom,1,weights, stride); + else if (val0.val.c->array_atom) + bin_atoms_weights(&val0.val.c->array_atom[0][j-1], + val0.val.c->size_peratom_cols,weights,stride); } else if (kind == LOCAL) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { - val.val.c->compute_local(); - val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val0.val.c->compute_local(); + val0.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (j == 0) - bin_vector_weights(val.val.c->size_local_rows, - val.val.c->vector_local,1,weights,stride); - else if (val.val.c->array_local) - bin_vector_weights(val.val.c->size_local_rows, - &val.val.c->array_local[0][j-1], - val.val.c->size_local_cols,weights,stride); + bin_vector_weights(val0.val.c->size_local_rows, + val0.val.c->vector_local,1,weights,stride); + else if (val0.val.c->array_local) + bin_vector_weights(val0.val.c->size_local_rows, + &val0.val.c->array_local[0][j-1], + val0.val.c->size_local_cols,weights,stride); } // access fix fields, guaranteed to be ready - } else if (val.which == ArgInfo::FIX) { + } else if (val0.which == ArgInfo::FIX) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) bin_one_weights(val.val.f->compute_scalar(),weight); - else bin_one_weights(val.val.f->compute_vector(j-1),weight); + if (j == 0) bin_one_weights(val0.val.f->compute_scalar(),weight); + else bin_one_weights(val0.val.f->compute_vector(j-1),weight); } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - int n = val.val.f->size_vector; + int n = val0.val.f->size_vector; for (int i = 0; i < n; i++) - bin_one_weights(val.val.f->compute_vector(i),weights[i*stride]); + bin_one_weights(val0.val.f->compute_vector(i),weights[i*stride]); } else { - int n = val.val.f->size_vector; + int n = val0.val.f->size_vector; for (int i = 0; i < n; i++) - bin_one_weights(val.val.f->compute_array(i,j-1),weights[i*stride]); + bin_one_weights(val0.val.f->compute_array(i,j-1),weights[i*stride]); } } else if (kind == PERATOM) { if (j == 0) - bin_atoms_weights(val.val.f->vector_atom,1,weights,stride); - else if (val.val.f->array_atom) - bin_atoms_weights(&val.val.f->array_atom[0][j-1],val.val.f->size_peratom_cols, + bin_atoms_weights(val0.val.f->vector_atom,1,weights,stride); + else if (val0.val.f->array_atom) + bin_atoms_weights(&val0.val.f->array_atom[0][j-1],val0.val.f->size_peratom_cols, weights,stride); } else if (kind == LOCAL) { - if (j == 0) bin_vector_weights(val.val.f->size_local_rows,val.val.f->vector_local,1, + if (j == 0) bin_vector_weights(val0.val.f->size_local_rows,val0.val.f->vector_local,1, weights,stride); - else if (val.val.f->array_local) - bin_vector_weights(val.val.f->size_local_rows,&val.val.f->array_local[0][j-1], - val.val.f->size_local_cols,weights,stride); + else if (val0.val.f->array_local) + bin_vector_weights(val0.val.f->size_local_rows,&val0.val.f->array_local[0][j-1], + val0.val.f->size_local_cols,weights,stride); } // evaluate equal-style variable - } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL) { - bin_one_weights(input->variable->compute_equal(val.val.v),weight); + } else if (val0.which == ArgInfo::VARIABLE && kind == GLOBAL) { + bin_one_weights(input->variable->compute_equal(val0.val.v),weight); - } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val0.which == ArgInfo::VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } - input->variable->compute_atom(val.val.v,igroup,vector,1,0); + input->variable->compute_atom(val0.val.v,igroup,vector,1,0); bin_atoms_weights(vector,1,weights,stride); } diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index f6ba0ad0e6..417e0fd97a 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -178,7 +178,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) : if (val.argindex && (val.val.f->array_flag == 0)) error->all(FLERR,"Fix ave/time fix {} does not calculate an array", val.id); if (val.argindex && (val.val.f->size_array_rows_variable)) - error->all(FLERR,"Fix ave/time fix {} array cannot be variable length", val.id); + error->all(FLERR,"Fix ave/time fix {} array cannot have variable row length", val.id); if (val.argindex && (val.argindex > val.val.f->size_array_cols)) error->all(FLERR,"Fix ave/time fix {} array is accessed out-of-range", val.id); if (nevery % val.val.f->global_freq) @@ -562,7 +562,8 @@ void FixAveTime::invoke_scalar(bigint ntimestep) scalar = val.val.f->compute_vector(val.argindex-1); // evaluate equal-style or vector-style variable - // ensure no out-of-range access to vector-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori } else if (val.which == ArgInfo::VARIABLE) { if (val.argindex == 0) @@ -570,7 +571,7 @@ void FixAveTime::invoke_scalar(bigint ntimestep) else { double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); - if (nvec < val.argindex) scalar = 0.0; + if (val.argindex > nvec) scalar = 0.0; else scalar = varvec[val.argindex-1]; } } @@ -1033,41 +1034,44 @@ void FixAveTime::options(int iarg, int narg, char **arg) // optional args while (iarg < narg) { - if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if ((strcmp(arg[iarg],"file") == 0) || (strcmp(arg[iarg],"append") == 0)) { + if (iarg+2 > narg) + utils::missing_cmd_args(FLERR, std::string("fix ave/time ")+arg[iarg], error); yaml_flag = utils::strmatch(arg[iarg+1],"\\.[yY][aA]?[mM][lL]$"); if (comm->me == 0) { - fp = fopen(arg[iarg+1],"w"); + if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w"); + else fp = fopen(arg[iarg+1],"a"); if (fp == nullptr) error->one(FLERR,"Cannot open fix ave/time file {}: {}", arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time ave", error); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW; - else error->all(FLERR,"Illegal fix ave/time command"); + else error->all(FLERR,"Unknown fix ave/time ave keyword {}", arg[iarg+1]); if (ave == WINDOW) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix ave/time ave window", error); nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp); - if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/time command"); + if (nwindow <= 0) + error->all(FLERR,"Illegal fix ave/time ave window argument {}; must be > 0", nwindow); } iarg += 2; if (ave == WINDOW) iarg++; } else if (strcmp(arg[iarg],"start") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time start", error); startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"mode") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time mode", error); if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR; else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR; - else error->all(FLERR,"Illegal fix ave/time command"); + else error->all(FLERR,"Unknown fix ave/time mode {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"off") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time off", error); memory->grow(offlist,noff+1,"ave/time:offlist"); offlist[noff++] = utils::inumeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; @@ -1075,27 +1079,27 @@ void FixAveTime::options(int iarg, int narg, char **arg) overwrite = 1; iarg += 1; } else if (strcmp(arg[iarg],"format") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time format", error); delete[] format_user; format_user = utils::strdup(arg[iarg+1]); format = format_user; iarg += 2; } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time title1", error); delete[] title1; title1 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time title2", error); delete[] title2; title2 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time title3", error); delete[] title3; title3 = utils::strdup(arg[iarg+1]); iarg += 2; - } else error->all(FLERR,"Unknown fix ave/time command option {}", arg[iarg]); + } else error->all(FLERR,"Unknown fix ave/time keyword {}", arg[iarg]); } } diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index 23a56c0a9d..2a32e96106 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -61,20 +61,36 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) : if (nevery < 0) error->all(FLERR,"Illegal fix balance command"); thresh = utils::numeric(FLERR,arg[4],false,lmp); - if (strcmp(arg[5],"shift") == 0) lbstyle = SHIFT; - else if (strcmp(arg[5],"rcb") == 0) lbstyle = BISECTION; - else error->all(FLERR,"Illegal fix balance command"); + reportonly = 0; + if (strcmp(arg[5],"shift") == 0) { + lbstyle = SHIFT; + } else if (strcmp(arg[5],"rcb") == 0) { + lbstyle = BISECTION; + } else if (strcmp(arg[5],"report") == 0) { + lbstyle = SHIFT; + reportonly = 1; + } else error->all(FLERR,"Unknown fix balance style {}", arg[5]); int iarg = 5; if (lbstyle == SHIFT) { - if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix balance shift", error); - bstr = arg[iarg+1]; - if (bstr.size() > Balance::BSTR_SIZE) error->all(FLERR,"Illegal fix balance shift command"); - nitermax = utils::inumeric(FLERR,arg[iarg+2],false,lmp); - if (nitermax <= 0) error->all(FLERR,"Illegal fix balance command"); - stopthresh = utils::numeric(FLERR,arg[iarg+3],false,lmp); - if (stopthresh < 1.0) error->all(FLERR,"Illegal fix balance command"); - iarg += 4; + if (reportonly) { + if (dimension == 2) + bstr = "xy"; + else + bstr = "xyz"; + nitermax = 5; + stopthresh = 1.1; + iarg++; + } else { + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix balance shift", error); + bstr = arg[iarg+1]; + if (bstr.size() > Balance::BSTR_SIZE) error->all(FLERR,"Illegal fix balance shift command"); + nitermax = utils::inumeric(FLERR,arg[iarg+2],false,lmp); + if (nitermax <= 0) error->all(FLERR,"Illegal fix balance command"); + stopthresh = utils::numeric(FLERR,arg[iarg+3],false,lmp); + if (stopthresh < 1.0) error->all(FLERR,"Illegal fix balance command"); + iarg += 4; + } } else if (lbstyle == BISECTION) { iarg++; @@ -175,7 +191,7 @@ void FixBalance::setup(int /*vflag*/) void FixBalance::setup_pre_exchange() { // do not allow rebalancing twice on same timestep - // even if wanted to, can mess up elapsed time in ImbalanceTime + // even if you wanted to, it can mess up elapsed time in ImbalanceTime if (update->ntimestep == lastbalance) return; lastbalance = update->ntimestep; @@ -195,6 +211,7 @@ void FixBalance::setup_pre_exchange() balance->set_weights(); imbnow = balance->imbalance_factor(maxloadperproc); + if (imbnow > thresh) rebalance(); // next timestep to rebalance @@ -263,6 +280,13 @@ void FixBalance::pre_neighbor() void FixBalance::rebalance() { + // return immediately if only reporting of the imbalance is requested + + if (reportonly) { + imbprev = imbfinal = imbnow; + return; + } + imbprev = imbnow; // invoke balancer and reset comm->uniform flag diff --git a/src/fix_balance.h b/src/fix_balance.h index 964357a634..a319710ac6 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -45,6 +45,7 @@ class FixBalance : public Fix { std::string bstr; int wtflag; // 1 for weighted balancing int sortflag; // 1 for sorting comm messages + int reportonly; // 1 if skipping rebalancing and only computing imbalance double imbnow; // current imbalance factor double imbprev; // imbalance factor before last rebalancing diff --git a/src/fix_bond_history.h b/src/fix_bond_history.h index fafcf52bd9..e19deee82f 100644 --- a/src/fix_bond_history.h +++ b/src/fix_bond_history.h @@ -44,6 +44,7 @@ class FixBondHistory : public Fix { void update_atom_value(int, int, int, double); double get_atom_value(int, int, int); + int get_ndata() const { return ndata; } // methods to reorder/delete elements of atom->bond_atom void delete_history(int, int); diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index bb27faeaa8..135d7176e6 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -63,7 +63,7 @@ irregular(nullptr), set(nullptr) int nskip; if (utils::strmatch(style, "^deform/pressure")) { child_parameters.insert("box"); - child_styles.insert({{"pressure", 4}, {"pressure/mean", 4}, {"volume", 2}}); + child_styles.insert({{"pressure", 4}, {"pressure/mean", 4}, {"erate/rescale", 3}, {"volume", 2}}); } // set defaults diff --git a/src/fix_deform.h b/src/fix_deform.h index b133729444..c524c2fe6c 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -29,7 +29,7 @@ class FixDeform : public Fix { int remapflag; // whether x,v are remapped across PBC int dimflag[6]; // which dims are deformed - enum { NONE, FINAL, DELTA, SCALE, VEL, ERATE, TRATE, VOLUME, WIGGLE, VARIABLE, PRESSURE, PMEAN }; + enum { NONE, FINAL, DELTA, SCALE, VEL, ERATE, TRATE, VOLUME, WIGGLE, VARIABLE, PRESSURE, PMEAN, ERATERS }; enum { ONE_FROM_ONE, ONE_FROM_TWO, TWO_FROM_ONE }; FixDeform(class LAMMPS *, int, char **); diff --git a/src/fix_deposit.cpp b/src/fix_deposit.cpp index d8ea665149..d6630bcbf0 100644 --- a/src/fix_deposit.cpp +++ b/src/fix_deposit.cpp @@ -54,15 +54,16 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) : if (narg < 7) error->all(FLERR,"Illegal fix deposit command"); scalar_flag = 1; + extscalar = 0; restart_global = 1; time_depend = 1; // required args - ninsert = utils::inumeric(FLERR,arg[3],false,lmp); - ntype = utils::inumeric(FLERR,arg[4],false,lmp); - nfreq = utils::inumeric(FLERR,arg[5],false,lmp); - seed = utils::inumeric(FLERR,arg[6],false,lmp); + ninsert = utils::inumeric(FLERR, arg[3], false, lmp); + ntype = utils::expand_type_int(FLERR, arg[4], Atom::ATOM, lmp); + nfreq = utils::inumeric(FLERR, arg[5], false, lmp); + seed = utils::inumeric(FLERR, arg[6], false, lmp); if (seed <= 0) error->all(FLERR,"Illegal fix deposit command"); @@ -629,7 +630,7 @@ void FixDeposit::pre_exchange() // rebuild atom map if (atom->map_style != Atom::MAP_NONE) { - if (success) atom->map_init(); + atom->map_init(); atom->map_set(); } diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index 9adb337dd6..a8b14940f4 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -23,6 +22,7 @@ #include "error.h" #include "input.h" #include "lattice.h" +#include "math_extra.h" #include "modify.h" #include "respa.h" #include "update.h" @@ -34,14 +34,14 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{NONE,SPHERE,CYLINDER,PLANE}; -enum{INSIDE,OUTSIDE}; +enum { NONE, SPHERE, CYLINDER, PLANE, CONE }; +enum { INSIDE, OUTSIDE }; /* ---------------------------------------------------------------------- */ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - xstr(nullptr), ystr(nullptr), zstr(nullptr), rstr(nullptr), pstr(nullptr) + Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), rstr(nullptr), pstr(nullptr), + rlostr(nullptr), rhistr(nullptr), lostr(nullptr), histr(nullptr) { if (narg < 4) utils::missing_cmd_args(FLERR, "fix indent", error); @@ -55,22 +55,20 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : respa_level_support = 1; ilevel_respa = 0; - k = utils::numeric(FLERR,arg[3],false,lmp); - k3 = k/3.0; + k = utils::numeric(FLERR, arg[3], false, lmp); + if (k < 0.0) error->all(FLERR, "Illegal fix indent force constant: {}", k); + k3 = k / 3.0; - // read options from end of input line + // read geometry of indenter and optional args - options(narg-4,&arg[4]); + int iarg = geometry(narg - 4, &arg[4]) + 4; + options(narg - iarg, &arg[iarg]); // setup scaling - double xscale,yscale,zscale; - if (scaleflag) { - xscale = domain->lattice->xlattice; - yscale = domain->lattice->ylattice; - zscale = domain->lattice->zlattice; - } - else xscale = yscale = zscale = 1.0; + const double xscale{scaleflag ? domain->lattice->xlattice : 1.0}; + const double yscale{scaleflag ? domain->lattice->ylattice : 1.0}; + const double zscale{scaleflag ? domain->lattice->zlattice : 1.0}; // apply scaling factors to geometry @@ -79,14 +77,43 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : if (!ystr) yvalue *= yscale; if (!zstr) zvalue *= zscale; if (!rstr) rvalue *= xscale; + + } else if (istyle == CONE) { + if (!xstr) xvalue *= xscale; + if (!ystr) yvalue *= yscale; + if (!zstr) zvalue *= zscale; + + double scaling_factor = 1.0; + switch (cdim) { + case 0: + scaling_factor = xscale; + break; + case 1: + scaling_factor = yscale; + break; + case 2: + scaling_factor = zscale; + break; + } + + if (!rlostr) rlovalue *= scaling_factor; + if (!rhistr) rhivalue *= scaling_factor; + if (!lostr) lovalue *= scaling_factor; + if (!histr) hivalue *= scaling_factor; + } else if (istyle == PLANE) { - if (cdim == 0 && !pstr) pvalue *= xscale; - else if (cdim == 1 && !pstr) pvalue *= yscale; - else if (cdim == 2 && !pstr) pvalue *= zscale; - } else error->all(FLERR,"Unknown fix indent keyword: {}", istyle); + if (cdim == 0 && !pstr) + pvalue *= xscale; + else if (cdim == 1 && !pstr) + pvalue *= yscale; + else if (cdim == 2 && !pstr) + pvalue *= zscale; + + } else + error->all(FLERR, "Unknown fix indent keyword: {}", istyle); varflag = 0; - if (xstr || ystr || zstr || rstr || pstr) varflag = 1; + if (xstr || ystr || zstr || rstr || pstr || rlostr || rhistr || lostr || histr) varflag = 1; indenter_flag = 0; indenter[0] = indenter[1] = indenter[2] = indenter[3] = 0.0; @@ -96,11 +123,15 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : FixIndent::~FixIndent() { - delete [] xstr; - delete [] ystr; - delete [] zstr; - delete [] rstr; - delete [] pstr; + delete[] xstr; + delete[] ystr; + delete[] zstr; + delete[] rstr; + delete[] pstr; + delete[] rlostr; + delete[] rhistr; + delete[] lostr; + delete[] histr; } /* ---------------------------------------------------------------------- */ @@ -120,43 +151,62 @@ void FixIndent::init() { if (xstr) { xvar = input->variable->find(xstr); - if (xvar < 0) - error->all(FLERR,"Variable {} for fix indent does not exist", xstr); + if (xvar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", xstr); if (!input->variable->equalstyle(xvar)) - error->all(FLERR,"Variable {} for fix indent is invalid style", xstr); + error->all(FLERR, "Variable {} for fix indent is invalid style", xstr); } if (ystr) { yvar = input->variable->find(ystr); - if (yvar < 0) - error->all(FLERR,"Variable {} for fix indent does not exist", ystr); + if (yvar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", ystr); if (!input->variable->equalstyle(yvar)) - error->all(FLERR,"Variable {} for fix indent is invalid style", ystr); + error->all(FLERR, "Variable {} for fix indent is invalid style", ystr); } if (zstr) { zvar = input->variable->find(zstr); - if (zvar < 0) - error->all(FLERR,"Variable {} for fix indent does not exist", zstr); + if (zvar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", zstr); if (!input->variable->equalstyle(zvar)) - error->all(FLERR,"Variable {} for fix indent is invalid style", zstr); + error->all(FLERR, "Variable {} for fix indent is invalid style", zstr); } if (rstr) { rvar = input->variable->find(rstr); - if (rvar < 0) - error->all(FLERR,"Variable {} for fix indent does not exist", rstr); + if (rvar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", rstr); if (!input->variable->equalstyle(rvar)) - error->all(FLERR,"Variable {} for fix indent is invalid style", rstr); + error->all(FLERR, "Variable {} for fix indent is invalid style", rstr); } if (pstr) { pvar = input->variable->find(pstr); - if (pvar < 0) - error->all(FLERR,"Variable {} for fix indent does not exist", pstr); + if (pvar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", pstr); if (!input->variable->equalstyle(pvar)) - error->all(FLERR,"Variable {} for fix indent is invalid style", pstr); + error->all(FLERR, "Variable {} for fix indent is invalid style", pstr); + } + if (rlostr) { + rlovar = input->variable->find(rlostr); + if (rlovar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", rlostr); + if (!input->variable->equalstyle(rlovar)) + error->all(FLERR, "Variable {} for fix indent is invalid style", rlostr); + } + if (rhistr) { + rhivar = input->variable->find(rhistr); + if (rhivar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", rhistr); + if (!input->variable->equalstyle(rhivar)) + error->all(FLERR, "Variable {} for fix indent is invalid style", rhistr); + } + if (lostr) { + lovar = input->variable->find(lostr); + if (lovar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", lostr); + if (!input->variable->equalstyle(lovar)) + error->all(FLERR, "Variable {} for fix indent is invalid style", lostr); + } + if (histr) { + hivar = input->variable->find(histr); + if (hivar < 0) error->all(FLERR, "Variable {} for fix indent does not exist", histr); + if (!input->variable->equalstyle(hivar)) + error->all(FLERR, "Variable {} for fix indent is invalid style", histr); } - if (utils::strmatch(update->integrate_style,"^respa")) { - ilevel_respa = (dynamic_cast(update->integrate))->nlevels-1; - if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); + if (utils::strmatch(update->integrate_style, "^respa")) { + ilevel_respa = (dynamic_cast(update->integrate))->nlevels - 1; + if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa); } } @@ -164,11 +214,11 @@ void FixIndent::init() void FixIndent::setup(int vflag) { - if (utils::strmatch(update->integrate_style,"^verlet")) + if (utils::strmatch(update->integrate_style, "^verlet")) post_force(vflag); else { (dynamic_cast(update->integrate))->copy_flevel_f(ilevel_respa); - post_force_respa(vflag,ilevel_respa,0); + post_force_respa(vflag, ilevel_respa, 0); (dynamic_cast(update->integrate))->copy_f_flevel(ilevel_respa); } } @@ -192,61 +242,59 @@ void FixIndent::post_force(int /*vflag*/) indenter_flag = 0; indenter[0] = indenter[1] = indenter[2] = indenter[3] = 0.0; + // ctr = current indenter centerz + + double ctr[3] = {xvalue, yvalue, zvalue}; + if (xstr) ctr[0] = input->variable->compute_equal(xvar); + if (ystr) ctr[1] = input->variable->compute_equal(yvar); + if (zstr) ctr[2] = input->variable->compute_equal(zvar); + + double **x = atom->x; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + double delx, dely, delz, r, dr, fmag, fx, fy, fz; + // spherical indenter if (istyle == SPHERE) { - // ctr = current indenter center - // remap into periodic box + // remap indenter center into periodic box - double ctr[3]; - if (xstr) ctr[0] = input->variable->compute_equal(xvar); - else ctr[0] = xvalue; - if (ystr) ctr[1] = input->variable->compute_equal(yvar); - else ctr[1] = yvalue; - if (zstr) ctr[2] = input->variable->compute_equal(zvar); - else ctr[2] = zvalue; domain->remap(ctr); - double radius; - if (rstr) radius = input->variable->compute_equal(rvar); - else radius = rvalue; - - double **x = atom->x; - double **f = atom->f; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - double delx,dely,delz,r,dr,fmag,fx,fy,fz; + double radius = rstr ? input->variable->compute_equal(rvar) : rvalue; + if (radius < 0.0) error->all(FLERR, "Illegal fix indent sphere radius: {}", radius); for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { delx = x[i][0] - ctr[0]; dely = x[i][1] - ctr[1]; delz = x[i][2] - ctr[2]; - domain->minimum_image(delx,dely,delz); - r = sqrt(delx*delx + dely*dely + delz*delz); + domain->minimum_image(delx, dely, delz); + r = sqrt(delx * delx + dely * dely + delz * delz); if (side == OUTSIDE) { dr = r - radius; - fmag = k*dr*dr; + fmag = k * dr * dr; } else { dr = radius - r; - fmag = -k*dr*dr; + fmag = -k * dr * dr; } if (dr >= 0.0) continue; - fx = delx*fmag/r; - fy = dely*fmag/r; - fz = delz*fmag/r; + fx = delx * fmag / r; + fy = dely * fmag / r; + fz = delz * fmag / r; f[i][0] += fx; f[i][1] += fy; f[i][2] += fz; - indenter[0] -= k3 * dr*dr*dr; + indenter[0] -= k3 * dr * dr * dr; indenter[1] -= fx; indenter[2] -= fy; indenter[3] -= fz; } - // cylindrical indenter + // cylindrical indenter } else if (istyle == CYLINDER) { @@ -254,101 +302,120 @@ void FixIndent::post_force(int /*vflag*/) // remap into periodic box // 3rd coord is just near box for remap(), since isn't used - double ctr[3]; - if (cdim == 0) { - ctr[0] = domain->boxlo[0]; - if (ystr) ctr[1] = input->variable->compute_equal(yvar); - else ctr[1] = yvalue; - if (zstr) ctr[2] = input->variable->compute_equal(zvar); - else ctr[2] = zvalue; - } else if (cdim == 1) { - if (xstr) ctr[0] = input->variable->compute_equal(xvar); - else ctr[0] = xvalue; - ctr[1] = domain->boxlo[1]; - if (zstr) ctr[2] = input->variable->compute_equal(zvar); - else ctr[2] = zvalue; - } else { - if (xstr) ctr[0] = input->variable->compute_equal(xvar); - else ctr[0] = xvalue; - if (ystr) ctr[1] = input->variable->compute_equal(yvar); - else ctr[1] = yvalue; - ctr[2] = domain->boxlo[2]; - } + ctr[cdim] = domain->boxlo[cdim]; domain->remap(ctr); - double radius; - if (rstr) radius = input->variable->compute_equal(rvar); - else radius = rvalue; - - double **x = atom->x; - double **f = atom->f; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - double delx,dely,delz,r,dr,fmag,fx,fy,fz; + double radius{rstr ? input->variable->compute_equal(rvar) : rvalue}; + if (radius < 0.0) error->all(FLERR, "Illegal fix indent cylinder radius: {}", radius); for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - if (cdim == 0) { - delx = 0; - dely = x[i][1] - ctr[1]; - delz = x[i][2] - ctr[2]; - } else if (cdim == 1) { - delx = x[i][0] - ctr[0]; - dely = 0; - delz = x[i][2] - ctr[2]; - } else { - delx = x[i][0] - ctr[0]; - dely = x[i][1] - ctr[1]; - delz = 0; - } - domain->minimum_image(delx,dely,delz); - r = sqrt(delx*delx + dely*dely + delz*delz); + double del[3] = {x[i][0] - ctr[0], x[i][1] - ctr[1], x[i][2] - ctr[2]}; + del[cdim] = 0; + domain->minimum_image(del[0], del[1], del[2]); + r = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); if (side == OUTSIDE) { dr = r - radius; - fmag = k*dr*dr; + fmag = k * dr * dr; } else { dr = radius - r; - fmag = -k*dr*dr; + fmag = -k * dr * dr; } if (dr >= 0.0) continue; - fx = delx*fmag/r; - fy = dely*fmag/r; - fz = delz*fmag/r; + fx = del[0] * fmag / r; + fy = del[1] * fmag / r; + fz = del[2] * fmag / r; f[i][0] += fx; f[i][1] += fy; f[i][2] += fz; - indenter[0] -= k3 * dr*dr*dr; + indenter[0] -= k3 * dr * dr * dr; indenter[1] -= fx; indenter[2] -= fy; indenter[3] -= fz; } - // planar indenter + // conical indenter + + } else if (istyle == CONE) { + + double radiuslo{rlostr ? input->variable->compute_equal(rlovar) : rlovalue}; + if (radiuslo < 0.0) error->all(FLERR, "Illegal fix indent cone lower radius: {}", radiuslo); + double radiushi{rhistr ? input->variable->compute_equal(rhivar) : rhivalue}; + if (radiushi < 0.0) error->all(FLERR, "Illegal fix indent cone high radius: {}", radiushi); + + double initial_lo{lostr ? input->variable->compute_equal(lovar) : lovalue}; + double initial_hi{histr ? input->variable->compute_equal(hivar) : hivalue}; + + ctr[cdim] = 0.5 * (initial_hi + initial_lo); + + domain->remap(ctr); + + double hi = ctr[cdim] + 0.5 * (initial_hi - initial_lo); + double lo = ctr[cdim] - 0.5 * (initial_hi - initial_lo); + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + delx = x[i][0] - ctr[0]; + dely = x[i][1] - ctr[1]; + delz = x[i][2] - ctr[2]; + domain->minimum_image(delx, dely, delz); + + double x0[3] = {delx + ctr[0], dely + ctr[1], delz + ctr[2]}; + r = sqrt(delx * delx + dely * dely + delz * delz); + + // check if particle is inside or outside the cone + + bool point_inside_cone = PointInsideCone(cdim, ctr, lo, hi, radiuslo, radiushi, x0); + + if (side == INSIDE && point_inside_cone) continue; + if (side == OUTSIDE && !point_inside_cone) continue; + + // find the distance between the point and the cone + + if (point_inside_cone) { + DistanceInteriorPoint(cdim, ctr, lo, hi, radiuslo, radiushi, x0[0], x0[1], x0[2]); + } else { + DistanceExteriorPoint(cdim, ctr, lo, hi, radiuslo, radiushi, x0[0], x0[1], x0[2]); + } + + // compute the force from the center of the cone + // this is different from how it is done in fix wall/region + + dr = sqrt(x0[0] * x0[0] + x0[1] * x0[1] + x0[2] * x0[2]); + + int force_sign = {point_inside_cone ? 1 : -1}; + fmag = force_sign * k * dr * dr; + + fx = delx * fmag / r; + fy = dely * fmag / r; + fz = delz * fmag / r; + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + indenter[0] -= k3 * dr * dr * dr; + indenter[1] -= fx; + indenter[2] -= fy; + indenter[3] -= fz; + } + } + + // planar indenter } else { // plane = current plane position - double plane; - if (pstr) plane = input->variable->compute_equal(pvar); - else plane = pvalue; - - double **x = atom->x; - double **f = atom->f; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - double dr,fatom; + double plane{pstr ? input->variable->compute_equal(pvar) : pvalue}; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { dr = planeside * (plane - x[i][cdim]); if (dr >= 0.0) continue; - fatom = -planeside * k*dr*dr; - f[i][cdim] += fatom; - indenter[0] -= k3 * dr*dr*dr; - indenter[cdim+1] -= fatom; + fmag = -planeside * k * dr * dr; + f[i][cdim] += fmag; + indenter[0] -= k3 * dr * dr * dr; + indenter[cdim + 1] -= fmag; } } @@ -378,7 +445,7 @@ double FixIndent::compute_scalar() // only sum across procs one time if (indenter_flag == 0) { - MPI_Allreduce(indenter,indenter_all,4,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(indenter, indenter_all, 4, MPI_DOUBLE, MPI_SUM, world); indenter_flag = 1; } return indenter_all[0]; @@ -393,113 +460,406 @@ double FixIndent::compute_vector(int n) // only sum across procs one time if (indenter_flag == 0) { - MPI_Allreduce(indenter,indenter_all,4,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(indenter, indenter_all, 4, MPI_DOUBLE, MPI_SUM, world); indenter_flag = 1; } - return indenter_all[n+1]; + return indenter_all[n + 1]; } /* ---------------------------------------------------------------------- - parse optional parameters at end of input line + parse input args for geometry of indenter ------------------------------------------------------------------------- */ -void FixIndent::options(int narg, char **arg) +int FixIndent::geometry(int narg, char **arg) { if (narg < 0) utils::missing_cmd_args(FLERR, "fix indent", error); istyle = NONE; xstr = ystr = zstr = rstr = pstr = nullptr; xvalue = yvalue = zvalue = rvalue = pvalue = 0.0; + + // sphere + + if (strcmp(arg[0], "sphere") == 0) { + if (istyle != NONE) error->all(FLERR, "Fix indent requires a single geometry keyword"); + if (5 > narg) utils::missing_cmd_args(FLERR, "fix indent sphere", error); + + if (utils::strmatch(arg[1], "^v_")) { + xstr = utils::strdup(arg[1] + 2); + } else + xvalue = utils::numeric(FLERR, arg[1], false, lmp); + if (utils::strmatch(arg[2], "^v_")) { + ystr = utils::strdup(arg[2] + 2); + } else + yvalue = utils::numeric(FLERR, arg[2], false, lmp); + if (utils::strmatch(arg[3], "^v_")) { + zstr = utils::strdup(arg[3] + 2); + } else + zvalue = utils::numeric(FLERR, arg[3], false, lmp); + if (utils::strmatch(arg[4], "^v_")) { + rstr = utils::strdup(arg[4] + 2); + } else + rvalue = utils::numeric(FLERR, arg[4], false, lmp); + + istyle = SPHERE; + return 5; + } + + // cylinder + + if (strcmp(arg[0], "cylinder") == 0) { + if (istyle != NONE) error->all(FLERR, "Fix indent requires a single geometry keyword"); + if (5 > narg) utils::missing_cmd_args(FLERR, "fix indent cylinder", error); + + if (strcmp(arg[1], "x") == 0) { + cdim = 0; + if (utils::strmatch(arg[2], "^v_")) { + ystr = utils::strdup(arg[2] + 2); + } else + yvalue = utils::numeric(FLERR, arg[2], false, lmp); + if (utils::strmatch(arg[3], "^v_")) { + zstr = utils::strdup(arg[3] + 2); + } else + zvalue = utils::numeric(FLERR, arg[3], false, lmp); + } else if (strcmp(arg[1], "y") == 0) { + cdim = 1; + if (utils::strmatch(arg[2], "^v_")) { + xstr = utils::strdup(arg[2] + 2); + } else + xvalue = utils::numeric(FLERR, arg[2], false, lmp); + if (utils::strmatch(arg[3], "^v_")) { + zstr = utils::strdup(arg[3] + 2); + } else + zvalue = utils::numeric(FLERR, arg[3], false, lmp); + } else if (strcmp(arg[1], "z") == 0) { + cdim = 2; + if (utils::strmatch(arg[2], "^v_")) { + xstr = utils::strdup(arg[2] + 2); + } else + xvalue = utils::numeric(FLERR, arg[2], false, lmp); + if (utils::strmatch(arg[3], "^v_")) { + ystr = utils::strdup(arg[3] + 2); + } else + yvalue = utils::numeric(FLERR, arg[3], false, lmp); + } else + error->all(FLERR, "Unknown fix indent cylinder argument: {}", arg[1]); + + if (utils::strmatch(arg[4], "^v_")) { + rstr = utils::strdup(arg[4] + 2); + } else + rvalue = utils::numeric(FLERR, arg[4], false, lmp); + + istyle = CYLINDER; + return 5; + } + + // cone + + if (strcmp(arg[0], "cone") == 0) { + if (istyle != NONE) error->all(FLERR, "Fix indent requires a single geometry keyword"); + if (8 > narg) utils::missing_cmd_args(FLERR, "fix indent cone", error); + + if (strcmp(arg[1], "x") == 0) { + cdim = 0; + if (utils::strmatch(arg[2], "^v_")) { + ystr = utils::strdup(arg[2] + 2); + } else + yvalue = utils::numeric(FLERR, arg[2], false, lmp); + if (utils::strmatch(arg[3], "^v_")) { + zstr = utils::strdup(arg[3] + 2); + } else + zvalue = utils::numeric(FLERR, arg[3], false, lmp); + + } else if (strcmp(arg[1], "y") == 0) { + cdim = 1; + if (utils::strmatch(arg[2], "^v_")) { + xstr = utils::strdup(arg[2] + 2); + } else + xvalue = utils::numeric(FLERR, arg[2], false, lmp); + if (utils::strmatch(arg[3], "^v_")) { + zstr = utils::strdup(arg[3] + 2); + } else + zvalue = utils::numeric(FLERR, arg[3], false, lmp); + + } else if (strcmp(arg[1], "z") == 0) { + cdim = 2; + if (utils::strmatch(arg[2], "^v_")) { + xstr = utils::strdup(arg[2] + 2); + } else + xvalue = utils::numeric(FLERR, arg[2], false, lmp); + if (utils::strmatch(arg[3], "^v_")) { + ystr = utils::strdup(arg[3] + 2); + } else + yvalue = utils::numeric(FLERR, arg[3], false, lmp); + + } else + error->all(FLERR, "Unknown fix indent cone argument: {}", arg[1]); + + if (utils::strmatch(arg[4], "^v_")) { + rlostr = utils::strdup(arg[4] + 2); + } else + rlovalue = utils::numeric(FLERR, arg[4], false, lmp); + if (utils::strmatch(arg[5], "^v_")) { + rhistr = utils::strdup(arg[5] + 2); + } else + rhivalue = utils::numeric(FLERR, arg[5], false, lmp); + if (utils::strmatch(arg[6], "^v_")) { + lostr = utils::strdup(arg[6] + 2); + } else + lovalue = utils::numeric(FLERR, arg[6], false, lmp); + if (utils::strmatch(arg[7], "^v_")) { + histr = utils::strdup(arg[7] + 2); + } else + hivalue = utils::numeric(FLERR, arg[7], false, lmp); + + istyle = CONE; + return 8; + } + + // plane + + if (strcmp(arg[0], "plane") == 0) { + if (istyle != NONE) error->all(FLERR, "Fix indent requires a single geometry keyword"); + if (4 > narg) utils::missing_cmd_args(FLERR, "fix indent plane", error); + if (strcmp(arg[1], "x") == 0) + cdim = 0; + else if (strcmp(arg[1], "y") == 0) + cdim = 1; + else if (strcmp(arg[1], "z") == 0) + cdim = 2; + else + error->all(FLERR, "Unknown fix indent plane argument: {}", arg[1]); + + if (utils::strmatch(arg[2], "^v_")) { + pstr = utils::strdup(arg[2] + 2); + } else + pvalue = utils::numeric(FLERR, arg[2], false, lmp); + + if (strcmp(arg[3], "lo") == 0) + planeside = -1; + else if (strcmp(arg[3], "hi") == 0) + planeside = 1; + else + error->all(FLERR, "Unknown fix indent plane argument: {}", arg[3]); + istyle = PLANE; + return 4; + } + + // invalid istyle arg + + error->all(FLERR, "Unknown fix indent argument: {}", arg[0]); + + return 0; +} + +/* ---------------------------------------------------------------------- + parse optional input args +------------------------------------------------------------------------- */ + +void FixIndent::options(int narg, char **arg) +{ scaleflag = 1; side = OUTSIDE; int iarg = 0; + while (iarg < narg) { - if (strcmp(arg[iarg],"sphere") == 0) { - if (iarg+5 > narg) utils::missing_cmd_args(FLERR, "fix indent sphere", error); - - if (utils::strmatch(arg[iarg+1],"^v_")) { - xstr = utils::strdup(arg[iarg+1]+2); - } else xvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp); - if (utils::strmatch(arg[iarg+2],"^v_")) { - ystr = utils::strdup(arg[iarg+2]+2); - } else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); - if (utils::strmatch(arg[iarg+3],"^v_")) { - zstr = utils::strdup(arg[iarg+3]+2); - } else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp); - if (utils::strmatch(arg[iarg+4],"^v_")) { - rstr = utils::strdup(arg[iarg+4]+2); - } else rvalue = utils::numeric(FLERR,arg[iarg+4],false,lmp); - - istyle = SPHERE; - iarg += 5; - - } else if (strcmp(arg[iarg],"cylinder") == 0) { - if (iarg+5 > narg) utils::missing_cmd_args(FLERR, "fix indent cylinder", error); - - if (strcmp(arg[iarg+1],"x") == 0) { - cdim = 0; - if (utils::strmatch(arg[iarg+2],"^v_")) { - ystr = utils::strdup(arg[iarg+2]+2); - } else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); - if (utils::strmatch(arg[iarg+3],"^v_")) { - zstr = utils::strdup(arg[iarg+3]+2); - } else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp); - } else if (strcmp(arg[iarg+1],"y") == 0) { - cdim = 1; - if (utils::strmatch(arg[iarg+2],"^v_")) { - xstr = utils::strdup(arg[iarg+2]+2); - } else xvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); - if (utils::strmatch(arg[iarg+3],"^v_")) { - zstr = utils::strdup(arg[iarg+3]+2); - } else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp); - } else if (strcmp(arg[iarg+1],"z") == 0) { - cdim = 2; - if (utils::strmatch(arg[iarg+2],"^v_")) { - xstr = utils::strdup(arg[iarg+2]+2); - } else xvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); - if (utils::strmatch(arg[iarg+3],"^v_")) { - ystr = utils::strdup(arg[iarg+3]+2); - } else yvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp); - } else error->all(FLERR,"Unknown fix indent cylinder argument: {}", arg[iarg+1]); - - if (utils::strmatch(arg[iarg+4],"^v_")) { - rstr = utils::strdup(arg[iarg+4]+2); - } else rvalue = utils::numeric(FLERR,arg[iarg+4],false,lmp); - - istyle = CYLINDER; - iarg += 5; - - } else if (strcmp(arg[iarg],"plane") == 0) { - if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix indent plane", error); - if (strcmp(arg[iarg+1],"x") == 0) cdim = 0; - else if (strcmp(arg[iarg+1],"y") == 0) cdim = 1; - else if (strcmp(arg[iarg+1],"z") == 0) cdim = 2; - else error->all(FLERR,"Unknown fix indent plane argument: {}", arg[iarg+1]); - - if (utils::strmatch(arg[iarg+2],"^v_")) { - pstr = utils::strdup(arg[iarg+2]+2); - } else pvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); - - if (strcmp(arg[iarg+3],"lo") == 0) planeside = -1; - else if (strcmp(arg[iarg+3],"hi") == 0) planeside = 1; - else error->all(FLERR,"Unknown fix indent plane argument: {}", arg[iarg+3]); - istyle = PLANE; - iarg += 4; - - } else if (strcmp(arg[iarg],"units") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix indent units", error); - if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; - else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; - else error->all(FLERR,"Unknown fix indent units argument: {}", arg[iarg+1]); + if (strcmp(arg[iarg], "units") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix indent units", error); + if (strcmp(arg[iarg + 1], "box") == 0) + scaleflag = 0; + else if (strcmp(arg[iarg + 1], "lattice") == 0) + scaleflag = 1; + else + error->all(FLERR, "Unknown fix indent units argument: {}", arg[iarg + 1]); iarg += 2; - } else if (strcmp(arg[iarg],"side") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix indent side", error); - if (strcmp(arg[iarg+1],"in") == 0) side = INSIDE; - else if (strcmp(arg[iarg+1],"out") == 0) side = OUTSIDE; - else error->all(FLERR,"Unknown fix indent side argument: {}", arg[iarg+1]); + } else if (strcmp(arg[iarg], "side") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix indent side", error); + if (strcmp(arg[iarg + 1], "in") == 0) + side = INSIDE; + else if (strcmp(arg[iarg + 1], "out") == 0) + side = OUTSIDE; + else + error->all(FLERR, "Unknown fix indent side argument: {}", arg[iarg + 1]); iarg += 2; - } else error->all(FLERR,"Unknown fix indent argument: {}", arg[iarg]); + + } else + error->all(FLERR, "Unknown fix indent argument: {}", arg[iarg]); } } + +/* ---------------------------------------------------------------------- + determines if a point is inside (true) or outside (false) of a cone +------------------------------------------------------------------------- */ + +bool FixIndent::PointInsideCone(int dir, double *center, double lo, double hi, double rlo, + double rhi, double *x) +{ + if ((x[dir] > hi) || (x[dir] < lo)) return false; + + double del[3] = {x[0] - center[0], x[1] - center[1], x[2] - center[2]}; + del[dir] = 0.0; + + double dist = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); + double currentradius = rlo + (x[dir] - lo) * (rhi - rlo) / (hi - lo); + + if (dist > currentradius) return false; + + return true; +} + +/* ---------------------------------------------------------------------- + distance between an exterior point and a cone +------------------------------------------------------------------------- */ + +void FixIndent::DistanceExteriorPoint(int dir, double *center, double lo, double hi, double rlo, + double rhi, double &x, double &y, double &z) +{ + double xp[3], nearest[3], corner1[3], corner2[3]; + double point[3] = {x, y, z}; + double del[3] = {x - center[0], y - center[1], z - center[2]}; + + del[dir] = 0.0; + double r = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); + + corner1[0] = center[0] + del[0] * rlo / r; + corner1[1] = center[1] + del[1] * rlo / r; + corner1[2] = center[2] + del[2] * rlo / r; + corner1[dir] = lo; + + corner2[0] = center[0] + del[0] * rhi / r; + corner2[1] = center[1] + del[1] * rhi / r; + corner2[2] = center[2] + del[2] * rhi / r; + corner2[dir] = hi; + + double corner3[3] = {center[0], center[1], center[2]}; + corner3[dir] = lo; + + double corner4[3] = {center[0], center[1], center[2]}; + corner4[dir] = hi; + + // initialize distance to a big number + + double distsq = 1.0e20; + + // check the first triangle + + point_on_line_segment(corner1, corner2, point, xp); + distsq = closest(point, xp, nearest, distsq); + + // check the second triangle + + point_on_line_segment(corner1, corner3, point, xp); + distsq = closest(point, xp, nearest, distsq); + + // check the third triangle + + point_on_line_segment(corner2, corner4, point, xp); + distsq = closest(point, xp, nearest, distsq); + + x -= nearest[0]; + y -= nearest[1]; + z -= nearest[2]; + + return; +} + +/* ---------------------------------------------------------------------- + distance between an interior point and a cone +------------------------------------------------------------------------- */ + +void FixIndent::DistanceInteriorPoint(int dir, double *center, double lo, double hi, double rlo, + double rhi, double &x, double &y, double &z) +{ + double r, dist_disk, dist_surf; + double surflo[3], surfhi[3], xs[3]; + double initial_point[3] = {x, y, z}; + double point[3] = {0.0, 0.0, 0.0}; + + // initial check with the two disks + + if ((initial_point[dir] - lo) < (hi - initial_point[dir])) { + dist_disk = (initial_point[dir] - lo) * (initial_point[dir] - lo); + point[dir] = initial_point[dir] - lo; + } else { + dist_disk = (hi - initial_point[dir]) * (hi - initial_point[dir]); + point[dir] = initial_point[dir] - hi; + } + + // check with the points in the conical surface + + double del[3] = {x - center[0], y - center[1], z - center[2]}; + del[dir] = 0.0; + r = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); + + surflo[0] = center[0] + del[0] * rlo / r; + surflo[1] = center[1] + del[1] * rlo / r; + surflo[2] = center[2] + del[2] * rlo / r; + surflo[dir] = lo; + + surfhi[0] = center[0] + del[0] * rhi / r; + surfhi[1] = center[1] + del[1] * rhi / r; + surfhi[2] = center[2] + del[2] * rhi / r; + surfhi[dir] = hi; + + point_on_line_segment(surflo, surfhi, initial_point, xs); + + double dx[3] = {initial_point[0] - xs[0], initial_point[1] - xs[1], initial_point[2] - xs[2]}; + dist_surf = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2]; + if (dist_surf < dist_disk) { + x = dx[0]; + y = dx[1]; + z = dx[2]; + } else { + x = point[0]; + y = point[1]; + z = point[2]; + } + + return; +} + +/* ---------------------------------------------------------------------- + helper function extracted from region.cpp +------------------------------------------------------------------------- */ + +void FixIndent::point_on_line_segment(double *a, double *b, double *c, double *d) +{ + double ba[3], ca[3]; + + MathExtra::sub3(b, a, ba); + MathExtra::sub3(c, a, ca); + double t = MathExtra::dot3(ca, ba) / MathExtra::dot3(ba, ba); + if (t <= 0.0) { + d[0] = a[0]; + d[1] = a[1]; + d[2] = a[2]; + } else if (t >= 1.0) { + d[0] = b[0]; + d[1] = b[1]; + d[2] = b[2]; + } else { + d[0] = a[0] + t * ba[0]; + d[1] = a[1] + t * ba[1]; + d[2] = a[2] + t * ba[2]; + } +} + +/* ---------------------------------------------------------------------- + helper function extracted from region_cone.cpp +------------------------------------------------------------------------- */ + +double FixIndent::closest(double *x, double *near, double *nearest, double dsq) +{ + double dx = x[0] - near[0]; + double dy = x[1] - near[1]; + double dz = x[2] - near[2]; + double rsq = dx * dx + dy * dy + dz * dz; + if (rsq >= dsq) return dsq; + + nearest[0] = near[0]; + nearest[1] = near[1]; + nearest[2] = near[2]; + return rsq; +} diff --git a/src/fix_indent.h b/src/fix_indent.h index 527e9ec277..37e1623df9 100644 --- a/src/fix_indent.h +++ b/src/fix_indent.h @@ -49,7 +49,24 @@ class FixIndent : public Fix { int cdim, varflag; int ilevel_respa; + char *rlostr, *rhistr, *lostr, *histr; + int rlovar, rhivar, lovar, hivar; + double rlovalue, rhivalue, lovalue, hivalue; + + // methods for argument parsing + + int geometry(int, char **); void options(int, char **); + + // methods for conical indenter + + bool PointInsideCone(int, double *, double, double, double, double, double *); + void DistanceExteriorPoint(int, double *, double, double, double, double, + double &, double &, double &); + void DistanceInteriorPoint(int, double *, double, double, double, double, + double &, double &, double &); + void point_on_line_segment(double *, double *, double *, double *); + double closest(double *, double *, double *, double); }; } // namespace LAMMPS_NS diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index a7536800cb..f2ad246611 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -53,7 +53,7 @@ enum{ISO,ANISO,TRICLINIC}; ---------------------------------------------------------------------- */ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), id_dilate(nullptr), irregular(nullptr), id_temp(nullptr), + Fix(lmp, narg, arg), id_dilate(nullptr), irregular(nullptr), step_respa(nullptr), id_temp(nullptr), id_press(nullptr), eta(nullptr), eta_dot(nullptr), eta_dotdot(nullptr), eta_mass(nullptr), etap(nullptr), etap_dot(nullptr), etap_dotdot(nullptr), etap_mass(nullptr) { @@ -712,8 +712,10 @@ void FixNH::init() else kspace_flag = 0; if (utils::strmatch(update->integrate_style,"^respa")) { - nlevels_respa = (dynamic_cast(update->integrate))->nlevels; - step_respa = (dynamic_cast(update->integrate))->step; + auto respa_ptr = dynamic_cast(update->integrate); + if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style); + nlevels_respa = respa_ptr->nlevels; + step_respa = respa_ptr->step; dto = 0.5*step_respa[0]; } @@ -1692,8 +1694,13 @@ void FixNH::reset_dt() // If using respa, then remap is performed in innermost level - if (utils::strmatch(update->integrate_style,"^respa")) + if (utils::strmatch(update->integrate_style,"^respa")) { + auto respa_ptr = dynamic_cast(update->integrate); + if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style); + nlevels_respa = respa_ptr->nlevels; + step_respa = respa_ptr->step; dto = 0.5*step_respa[0]; + } if (pstat_flag) pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain); diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 023b9355cd..ccef03c3ae 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,6 +13,7 @@ #include "fix_print.h" +#include "comm.h" #include "error.h" #include "input.h" #include "memory.h" @@ -29,24 +29,22 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - fp(nullptr), text(nullptr), copy(nullptr), work(nullptr), var_print(nullptr) + Fix(lmp, narg, arg), fp(nullptr), text(nullptr), copy(nullptr), work(nullptr), + var_print(nullptr) { - if (narg < 5) error->all(FLERR,"Illegal fix print command"); - if (utils::strmatch(arg[3],"^v_")) { - var_print = utils::strdup(arg[3]+2); + if (narg < 5) utils::missing_cmd_args(FLERR, "fix print", error); + if (utils::strmatch(arg[3], "^v_")) { + var_print = utils::strdup(arg[3] + 2); nevery = 1; } else { - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - if (nevery <= 0) error->all(FLERR,"Illegal fix print command"); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + if (nevery <= 0) error->all(FLERR, "Illegal fix print nevery value {}; must be > 0", nevery); } - MPI_Comm_rank(world,&me); - text = utils::strdup(arg[4]); - int n = strlen(text)+1; - copy = (char *) memory->smalloc(n*sizeof(char),"fix/print:copy"); - work = (char *) memory->smalloc(n*sizeof(char),"fix/print:work"); + int n = strlen(text) + 1; + copy = (char *) memory->smalloc(n * sizeof(char), "fix/print:copy"); + work = (char *) memory->smalloc(n * sizeof(char), "fix/print:work"); maxcopy = maxwork = n; // parse optional args @@ -57,48 +55,54 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) : int iarg = 5; while (iarg < narg) { - if (strcmp(arg[iarg],"file") == 0 || strcmp(arg[iarg],"append") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix print command"); - if (me == 0) { - if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w"); - else fp = fopen(arg[iarg+1],"a"); + if ((strcmp(arg[iarg], "file") == 0) || (strcmp(arg[iarg], "append") == 0)) { + if (iarg + 2 > narg) + utils::missing_cmd_args(FLERR, std::string("fix print ") + arg[iarg], error); + if (comm->me == 0) { + if (strcmp(arg[iarg], "file") == 0) + fp = fopen(arg[iarg + 1], "w"); + else + fp = fopen(arg[iarg + 1], "a"); if (fp == nullptr) - error->one(FLERR,"Cannot open fix print file {}: {}", - arg[iarg+1], utils::getsyserror()); + error->one(FLERR, "Cannot open fix print file {}: {}", arg[iarg + 1], + utils::getsyserror()); } iarg += 2; - } else if (strcmp(arg[iarg],"screen") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix print command"); - screenflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "screen") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix print screen", error); + screenflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"title") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix print command"); - delete [] title; - title = utils::strdup(arg[iarg+1]); + } else if (strcmp(arg[iarg], "title") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix print title", error); + delete[] title; + title = utils::strdup(arg[iarg + 1]); iarg += 2; - } else error->all(FLERR,"Illegal fix print command"); + } else + error->all(FLERR, "Unknown fix print keyword: {}", arg[iarg]); } // print file comment line - if (fp && me == 0) { - if (title) fprintf(fp,"%s\n",title); - else fprintf(fp,"# Fix print output for fix %s\n",id); + if (fp && (comm->me == 0)) { + if (title) + fprintf(fp, "%s\n", title); + else + fprintf(fp, "# Fix print output for fix %s\n", id); } - delete [] title; + delete[] title; } /* ---------------------------------------------------------------------- */ FixPrint::~FixPrint() { - delete [] text; - delete [] var_print; + delete[] text; + delete[] var_print; memory->sfree(copy); memory->sfree(work); - if (fp && me == 0) fclose(fp); + if (fp && (comm->me == 0)) fclose(fp); } /* ---------------------------------------------------------------------- */ @@ -117,16 +121,16 @@ void FixPrint::init() if (var_print) { ivar_print = input->variable->find(var_print); if (ivar_print < 0) - error->all(FLERR,"Variable name for fix print timestep does not exist"); + error->all(FLERR, "Variable {} for fix print timestep does not exist", var_print); if (!input->variable->equalstyle(ivar_print)) - error->all(FLERR,"Variable for fix print timestep is invalid style"); - next_print = static_cast - (input->variable->compute_equal(ivar_print)); + error->all(FLERR, "Variable {} for fix print timestep is invalid style", var_print); + next_print = static_cast(input->variable->compute_equal(ivar_print)); if (next_print <= update->ntimestep) - error->all(FLERR,"Fix print timestep variable returned a bad timestep"); + error->all(FLERR, "Fix print timestep variable {} returned a bad timestep: {}", var_print, + next_print); } else { if (update->ntimestep % nevery) - next_print = (update->ntimestep/nevery)*nevery + nevery; + next_print = (update->ntimestep / nevery) * nevery + nevery; else next_print = update->ntimestep; } @@ -158,24 +162,23 @@ void FixPrint::end_of_step() modify->clearstep_compute(); - strncpy(copy,text,maxcopy); - input->substitute(copy,work,maxcopy,maxwork,0); + strncpy(copy, text, maxcopy); + input->substitute(copy, work, maxcopy, maxwork, 0); if (var_print) { - next_print = static_cast - (input->variable->compute_equal(ivar_print)); + next_print = static_cast(input->variable->compute_equal(ivar_print)); if (next_print <= update->ntimestep) - error->all(FLERR,"Fix print timestep variable returned a bad timestep"); + error->all(FLERR, "Fix print timestep variable returned a bad timestep: {}", next_print); } else { - next_print = (update->ntimestep/nevery)*nevery + nevery; + next_print = (update->ntimestep / nevery) * nevery + nevery; } modify->addstep_compute(next_print); - if (me == 0) { - if (screenflag) utils::logmesg(lmp,std::string(copy) + "\n"); + if (comm->me == 0) { + if (screenflag) utils::logmesg(lmp, std::string(copy) + "\n"); if (fp) { - fmt::print(fp,"{}\n",copy); + fmt::print(fp, "{}\n", copy); fflush(fp); } } diff --git a/src/fix_print.h b/src/fix_print.h index 48eda897b5..9e699e22ba 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -34,7 +34,7 @@ class FixPrint : public Fix { void end_of_step() override; private: - int me, screenflag; + int screenflag; FILE *fp; char *text, *copy, *work; int maxcopy, maxwork; diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index de96b5c39d..2cbdb44ab0 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -328,8 +328,9 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint try { ValueTokenizer values(buf); if ((int) values.count() != values_peratom + 1) - error->all(FLERR, "Incorrect format in {} section of data file: {} expected {} and got {}", - keyword, buf, values_peratom + 1, values.count()); + error->all(FLERR, "Incorrect format in {} section of data file: {}\n" + "expected {} parameters and got {}{}", keyword, utils::trim(buf), + values_peratom + 1, values.count(), utils::errorurl(2)); itag = values.next_tagint() + id_offset; if (itag <= 0 || itag > map_tag_max) diff --git a/src/group.cpp b/src/group.cpp index a586c33ed9..baf9f377ff 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -229,12 +229,16 @@ void Group::assign(int narg, char **arg) else error->all(FLERR,"Illegal group command"); tagint bound1,bound2; - bound1 = utils::tnumeric(FLERR,arg[3],false,lmp); + if (category == TYPE) + bound1 = (tagint) utils::expand_type_int(FLERR, arg[3], Atom::ATOM, lmp); + else bound1 = utils::tnumeric(FLERR, arg[3], false, lmp); bound2 = -1; if (condition == BETWEEN) { if (narg != 5) error->all(FLERR,"Illegal group command"); - bound2 = utils::tnumeric(FLERR,arg[4],false,lmp); + if (category == TYPE) + bound2 = (tagint) utils::expand_type_int(FLERR, arg[4], Atom::ATOM, lmp); + else bound2 = utils::tnumeric(FLERR, arg[4], false, lmp); } else if (narg != 4) error->all(FLERR,"Illegal group command"); int *attribute = nullptr; @@ -304,26 +308,34 @@ void Group::assign(int narg, char **arg) else if (category == MOLECULE) tattribute = atom->molecule; else if (category == ID) tattribute = atom->tag; + char *typestr = nullptr; tagint start,stop,delta; for (int iarg = 2; iarg < narg; iarg++) { delta = 1; - try { - ValueTokenizer values(arg[iarg],":"); - start = values.next_tagint(); - if (utils::strmatch(arg[iarg],"^-?\\d+$")) { - stop = start; - } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+$")) { - stop = values.next_tagint(); - } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+:\\d+$")) { - stop = values.next_tagint(); - delta = values.next_tagint(); - } else throw TokenizerException("Syntax error",""); - } catch (TokenizerException &e) { - error->all(FLERR,"Incorrect range string '{}': {}",arg[iarg],e.what()); + if (category == TYPE) { + delete[] typestr; + typestr = utils::expand_type(FLERR, arg[iarg], Atom::ATOM, lmp); + if (typestr) stop = start = utils::tnumeric(FLERR, typestr, false, lmp); + } + if (typestr == nullptr) { + try { + ValueTokenizer values(arg[iarg],":"); + start = values.next_tagint(); + if (utils::strmatch(arg[iarg],"^-?\\d+$")) { + stop = start; + } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+$")) { + stop = values.next_tagint(); + } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+:\\d+$")) { + stop = values.next_tagint(); + delta = values.next_tagint(); + } else throw TokenizerException("Syntax error",""); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect range string '{}': {}",arg[iarg],e.what()); + } + if (delta < 1) + error->all(FLERR,"Illegal range increment value"); } - if (delta < 1) - error->all(FLERR,"Illegal range increment value"); // add to group if attribute matches value or sequence @@ -337,6 +349,8 @@ void Group::assign(int narg, char **arg) (tattribute[i]-start) % delta == 0) mask[i] |= bit; } } + + delete[] typestr; } // style = variable diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 505488cce6..a847b7bc95 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -269,7 +269,8 @@ void ImproperHybrid::coeff(int narg, char **arg) else if (strcmp(arg[1], "aa") == 0) error->all(FLERR, "AngleAngle coeff for hybrid improper has invalid format"); else - error->all(FLERR, "Improper coeff for hybrid has invalid style"); + error->all(FLERR, "Expected hybrid sub-style instead of {} in improper_coeff command", + arg[1]); } // move 1st arg to 2nd arg diff --git a/src/info.cpp b/src/info.cpp index 2b87452d72..43409fca67 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -110,12 +110,6 @@ static const int STYLES = ATOM_STYLES | INTEGRATE_STYLES | MINIMIZE_STYLES using namespace LAMMPS_NS; -// must match enumerator in variable.h -static const char *varstyles[] = { - "index", "loop", "world", "universe", "uloop", "string", "getenv", - "file", "atomfile", "format", "equal", "atom", "vector", "python", - "timer", "internal", "(unknown)"}; - static const char *mapstyles[] = { "none", "array", "hash", "yes" }; static const char *commstyles[] = { "brick", "tiled" }; @@ -1401,7 +1395,7 @@ std::string Info::get_variable_info(int num) { std::string text; int ndata = 1; text = fmt::format("Variable[{:3d}]: {:16} style = {:16} def =", num, - std::string(names[num]) + ',', std::string(varstyles[style[num]]) + ','); + std::string(names[num]) + ',', Variable::varstyles[style[num]] + ','); if (style[num] == Variable::INTERNAL) { text += fmt::format("{:.8}\n",input->variable->dvalue[num]); return text; diff --git a/src/input.cpp b/src/input.cpp index c9a3cf5f52..826b1821d5 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -888,6 +888,7 @@ void Input::clear() lmp->destroy(); lmp->create(); lmp->post_create(); + variable->clear_in_progress(); } /* ---------------------------------------------------------------------- */ diff --git a/src/label_map.cpp b/src/label_map.cpp index 67b1ae480d..52bf3f92f2 100644 --- a/src/label_map.cpp +++ b/src/label_map.cpp @@ -14,6 +14,7 @@ #include "label_map.h" #include "atom.h" +#include "citeme.h" #include "comm.h" #include "error.h" #include "force.h" @@ -22,6 +23,19 @@ using namespace LAMMPS_NS; +static const char cite_type_label_framework[] = + "Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419\n\n" + "@Article{Gissinger24,\n" + " author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi," + " Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},\n" + " title = {Type Label Framework for Bonded Force Fields in LAMMPS},\n" + " journal = {J. Phys. Chem. B},\n" + " year = 2024,\n" + " volume = 128,\n" + " number = 13,\n" + " pages = {3282–-3297}\n" + "}\n\n"; + /* ---------------------------------------------------------------------- */ LabelMap::LabelMap(LAMMPS *_lmp, int _natomtypes, int _nbondtypes, int _nangletypes, @@ -30,6 +44,8 @@ LabelMap::LabelMap(LAMMPS *_lmp, int _natomtypes, int _nbondtypes, int _nanglety natomtypes(_natomtypes), nbondtypes(_nbondtypes), nangletypes(_nangletypes), ndihedraltypes(_ndihedraltypes), nimpropertypes(_nimpropertypes) { + if (lmp->citeme) lmp->citeme->add(cite_type_label_framework); + lmap2lmap.atom = lmap2lmap.bond = lmap2lmap.angle = lmap2lmap.dihedral = lmap2lmap.improper = nullptr; reset_type_labels(); diff --git a/src/label_map.h b/src/label_map.h index a96fcc255c..eeab3aeae8 100644 --- a/src/label_map.h +++ b/src/label_map.h @@ -22,6 +22,8 @@ namespace LAMMPS_NS { class LabelMap : protected Pointers { friend class AtomVec; + friend class DumpCustom; + friend class DumpXYZ; friend class ReadData; public: diff --git a/src/lattice.cpp b/src/lattice.cpp index fa50a9ea94..e84bd87876 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -17,6 +17,7 @@ #include "comm.h" #include "domain.h" #include "error.h" +#include "math_extra.h" #include "memory.h" #include "update.h" @@ -24,6 +25,7 @@ #include using namespace LAMMPS_NS; +using namespace MathExtra; static constexpr double BIG = 1.0e30; @@ -138,6 +140,9 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // process optional args + triclinic_general = 0; + oriented = 0; + int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg],"origin") == 0) { @@ -186,6 +191,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) a1[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); a1[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); iarg += 4; + } else if (strcmp(arg[iarg],"a2") == 0) { if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "lattice a2", error); if (style != CUSTOM) @@ -221,6 +227,11 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) error->all(FLERR, "Invalid lattice basis argument: {}", z); add_basis(x,y,z); iarg += 4; + + } else if (strcmp(arg[iarg],"triclinic/general") == 0) { + triclinic_general = 1; + iarg++; + } else error->all(FLERR,"Unknown lattice keyword: {}", arg[iarg]); } @@ -229,24 +240,54 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (nbasis == 0) error->all(FLERR,"No basis atoms in lattice"); if (!orthogonal()) error->all(FLERR,"Lattice orient vectors are not orthogonal"); - if (!right_handed()) + if (!right_handed_orientation()) error->all(FLERR,"Lattice orient vectors are not right-handed"); if (collinear()) error->all(FLERR,"Lattice primitive vectors are collinear"); + // requirements for 2d system + if (dimension == 2) { if (origin[2] != 0.0) error->all(FLERR, - "Lattice settings are not compatible with 2d simulation"); + "Lattice origin z coord must be 0.0 for 2d simulation"); + if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0) + error->all(FLERR, + "Lattice a1/a2/a3 vectors are not compatible with 2d simulation"); if (orientx[2] != 0 || orienty[2] != 0 || orientz[0] != 0 || orientz[1] != 0) error->all(FLERR, - "Lattice settings are not compatible with 2d simulation"); - if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0) - error->all(FLERR, - "Lattice settings are not compatible with 2d simulation"); + "Lattice orient vectors are not compatible with 2d simulation"); + for (int i = 0; i < nbasis; i++) + if (basis[i][2] != 0.0) + error->all(FLERR,"Lattice basis atom z coords must be zero for 2d simulation"); } + // additional requirements for a general triclinic lattice + // a123 prime are used to compute lattice spacings + + if (triclinic_general) { + if (style != CUSTOM) + error->all(FLERR,"Lattice triclinic/general must be style = CUSTOM"); + if (origin[0] != 0.0 || origin[1] != 0.0 || origin[2] != 0.0) + error->all(FLERR,"Lattice triclinic/general must have default origin"); + int oriented = 0; + if (orientx[0] != 1 || orientx[1] != 0 || orientx[2] != 0) oriented = 1; + if (orienty[0] != 0 || orienty[1] != 1 || orienty[2] != 0) oriented = 1; + if (orientz[0] != 0 || orientz[1] != 0 || orientz[2] != 1) oriented = 1; + if (oriented) + error->all(FLERR,"Lattice triclinic/general must have default orientation"); + if (dimension == 2 && (a3[0] != 0.0 || a3[1] != 0.0 || a3[2] != 1.0)) + error->all(FLERR,"Lattice triclinic/general a3 vector for a 2d simulation must be (0,0,1)"); + if (!right_handed_primitive()) + error->all(FLERR,"Lattice triclinic/general a1,a2,a3 must be right-handed"); + + double rotmat[3][3]; + domain->general_to_restricted_rotation(a1,a2,a3,rotmat,a1_prime,a2_prime,a3_prime); + } + + // user-defined lattice spacings must all be positive + if (spaceflag) { if (xlattice <= 0.0 || ylattice <= 0.0 || zlattice <= 0.0) error->all(FLERR,"Lattice spacings are invalid"); @@ -254,18 +295,20 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // reset scale for LJ units (input scale is rho*) // scale = (Nbasis/(Vprimitive * rho*)) ^ (1/dim) + // use fabs() in case a1,a2,a3 are not right-handed for general triclinic if (strcmp(update->unit_style,"lj") == 0) { double vec[3]; - cross(a2,a3,vec); - double volume = dot(a1,vec); + MathExtra::cross3(a2,a3,vec); + double volume = fabs(MathExtra::dot3(a1,vec)); scale = pow(nbasis/volume/scale,1.0/dimension); } // initialize lattice <-> box transformation matrices - setup_transform(); + setup_transform(a1,a2,a3); + // automatic calculation of lattice spacings // convert 8 corners of primitive unit cell from lattice coords to box coords // min to max = bounding box around the pts in box space // xlattice,ylattice,zlattice = extent of bbox in box space @@ -278,6 +321,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) xmax = ymax = zmax = -BIG; xlattice = ylattice = zlattice = 0.0; + // for general triclinic, bounding box is around unit cell + // in restricted triclinic orientation, NOT general + // this enables lattice spacings to be used for other commands (e.g. region) + // after create_box and create_atoms create the restricted triclnic system + // reset transform used by bbox() to be based on rotated a123 prime vectors + + if (triclinic_general) setup_transform(a1_prime,a2_prime,a3_prime); + bbox(0,0.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,1.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,0.0,1.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); @@ -287,10 +338,16 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) bbox(0,0.0,1.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,1.0,1.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax); + // restore original general triclinic a123 transform + + if (triclinic_general) setup_transform(a1,a2,a3); + xlattice = xmax - xmin; ylattice = ymax - ymin; zlattice = zmax - zmin; + // user-defined lattice spacings + } else { xlattice *= scale; ylattice *= scale; @@ -311,6 +368,17 @@ Lattice::~Lattice() memory->destroy(basis); } +/* ---------------------------------------------------------------------- + return 1 if lattice is for a general triclinic simulation box + queried by create_box and create_atoms +------------------------------------------------------------------------- */ + +int Lattice::is_general_triclinic() +{ + if (triclinic_general) return 1; + return 0; +} + /* ---------------------------------------------------------------------- check if 3 orientation vectors are mutually orthogonal ------------------------------------------------------------------------- */ @@ -331,7 +399,7 @@ int Lattice::orthogonal() x cross y must be in same direction as z ------------------------------------------------------------------------- */ -int Lattice::right_handed() +int Lattice::right_handed_orientation() { int xy0 = orientx[1]*orienty[2] - orientx[2]*orienty[1]; int xy1 = orientx[2]*orienty[0] - orientx[0]*orienty[2]; @@ -340,19 +408,33 @@ int Lattice::right_handed() return 1; } +/* ---------------------------------------------------------------------- + check righthandedness of a1,a2,a3 primitive vectors + x cross y must be in same direction as z +------------------------------------------------------------------------- */ + +int Lattice::right_handed_primitive() +{ + double vec[3]; + MathExtra::cross3(a1,a2,vec); + if (MathExtra::dot3(vec,a3) <= 0.0) return 0; + return 1; +} + /* ---------------------------------------------------------------------- check collinearity of each pair of primitive vectors + also checks if any primitive vector is zero-length ------------------------------------------------------------------------- */ int Lattice::collinear() { double vec[3]; - cross(a1,a2,vec); - if (dot(vec,vec) == 0.0) return 1; - cross(a2,a3,vec); - if (dot(vec,vec) == 0.0) return 1; - cross(a1,a3,vec); - if (dot(vec,vec) == 0.0) return 1; + MathExtra::cross3(a1,a2,vec); + if (MathExtra::len3(vec) == 0.0) return 1; + MathExtra::cross3(a2,a3,vec); + if (MathExtra::len3(vec) == 0.0) return 1; + MathExtra::cross3(a1,a3,vec); + if (MathExtra::len3(vec) == 0.0) return 1; return 0; } @@ -360,21 +442,21 @@ int Lattice::collinear() initialize lattice <-> box transformation matrices ------------------------------------------------------------------------- */ -void Lattice::setup_transform() +void Lattice::setup_transform(double *a, double *b, double *c) { double length; // primitive = 3x3 matrix with primitive vectors as columns - primitive[0][0] = a1[0]; - primitive[1][0] = a1[1]; - primitive[2][0] = a1[2]; - primitive[0][1] = a2[0]; - primitive[1][1] = a2[1]; - primitive[2][1] = a2[2]; - primitive[0][2] = a3[0]; - primitive[1][2] = a3[1]; - primitive[2][2] = a3[2]; + primitive[0][0] = a[0]; + primitive[1][0] = a[1]; + primitive[2][0] = a[2]; + primitive[0][1] = b[0]; + primitive[1][1] = b[1]; + primitive[2][1] = b[2]; + primitive[0][2] = c[0]; + primitive[1][2] = c[1]; + primitive[2][2] = c[2]; // priminv = inverse of primitive @@ -532,28 +614,9 @@ void Lattice::add_basis(double x, double y, double z) } /* ---------------------------------------------------------------------- - return x dot y -------------------------------------------------------------------------- */ - -double Lattice::dot(double *x, double *y) -{ - return x[0]*y[0] + x[1]*y[1] + x[2]*y[2]; -} - -/* ---------------------------------------------------------------------- - z = x cross y -------------------------------------------------------------------------- */ - -void Lattice::cross(double *x, double *y, double *z) -{ - z[0] = x[1]*y[2] - x[2]*y[1]; - z[1] = x[2]*y[0] - x[0]*y[2]; - z[2] = x[0]*y[1] - x[1]*y[0]; -} - -/* ---------------------------------------------------------------------- - convert x,y,z from lattice coords to box coords (flag = 0) or vice versa - use new point to expand bounding box (min to max) + convert x,y,z from lattice coords to box coords (flag = 0) + or from box coords to lattice coords (flag = 1) + either way, use new point to expand bounding box (min to max) ------------------------------------------------------------------------- */ void Lattice::bbox(int flag, double x, double y, double z, diff --git a/src/lattice.h b/src/lattice.h index 5b98f580b7..b5eca8c13a 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -35,23 +35,31 @@ class Lattice : protected Pointers { void box2lattice(double &, double &, double &); void bbox(int, double, double, double, double &, double &, double &, double &, double &, double &); + int is_general_triclinic(); private: + int triclinic_general; // 1 if general triclinic, else 0 + int oriented; // 1 if non-default orient xyz, else 0 double scale; double origin[3]; // lattice origin int orientx[3]; // lattice orientation vecs int orienty[3]; // orientx = what lattice dir lies int orientz[3]; // along x dim in box - double primitive[3][3]; // lattice <-> box transform matrices + double primitive[3][3]; // lattice <-> box transformation matrices double priminv[3][3]; double rotaterow[3][3]; double rotatecol[3][3]; + double a1_prime[3]; // a123 rotated to restricted triclinic orientation + double a2_prime[3]; + double a3_prime[3]; + int orthogonal(); - int right_handed(); + int right_handed_orientation(); + int right_handed_primitive(); int collinear(); - void setup_transform(); + void setup_transform(double *, double *, double *); void add_basis(double, double, double); double dot(double *, double *); void cross(double *, double *, double *); diff --git a/src/library.cpp b/src/library.cpp index fcf0f6a631..bb58762563 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -527,7 +527,7 @@ void lammps_file(void *handle, const char *filename) BEGIN_CAPTURE { if (lmp->update->whichflag != 0) - lmp->error->all(FLERR, "Library error: issuing LAMMPS commands during a run is not allowed"); + lmp->error->all(FLERR, "Issuing LAMMPS commands during a run is not allowed"); else lmp->input->file(filename); } @@ -564,8 +564,7 @@ char *lammps_command(void *handle, const char *cmd) BEGIN_CAPTURE { if (lmp->update->whichflag != 0) - lmp->error->all(FLERR,"Library error: issuing LAMMPS commands " - "during a run is not allowed."); + lmp->error->all(FLERR, "Issuing LAMMPS command during a run is not allowed."); else result = lmp->input->one(cmd); } @@ -641,7 +640,7 @@ void lammps_commands_string(void *handle, const char *str) BEGIN_CAPTURE { if (lmp->update->whichflag != 0) { - lmp->error->all(FLERR,"Library error: issuing LAMMPS command during run"); + lmp->error->all(FLERR, "Issuing LAMMPS commands during a run is not allowed"); } std::size_t cursor = 0; @@ -949,9 +948,9 @@ void lammps_extract_box(void *handle, double *boxlo, double *boxhi, BEGIN_CAPTURE { // do nothing if box does not yet exist - if ((lmp->domain->box_exist == 0) - && (lmp->comm->me == 0)) { - lmp->error->warning(FLERR,"Calling lammps_extract_box without a box"); + if (lmp->domain->box_exist == 0) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR, "Call to lammps_extract_box() without a box ignored"); return; } @@ -1011,12 +1010,12 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi, BEGIN_CAPTURE { if (lmp->atom->natoms > 0) - lmp->error->all(FLERR,"Calling lammps_reset_box not supported when atoms exist"); + lmp->error->all(FLERR, "Calling lammps_reset_box() not supported when atoms exist"); // warn and do nothing if no box exists if (lmp->domain->box_exist == 0) { if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Ignoring call to lammps_reset_box without a box"); + lmp->error->warning(FLERR,"Call to lammps_reset_box() without a box ignored"); return; } @@ -1199,14 +1198,31 @@ internally by the :doc:`Fortran interface ` and are not likely to be us * - triclinic - 1 if the the simulation box is triclinic, 0 if orthogonal. See :doc:`change_box`. + +**Communication status** + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Keyword + - Description / Return value * - universe_rank - MPI rank on LAMMPS' universe communicator (0 <= universe_rank < universe_size) * - universe_size - Number of ranks on LAMMPS' universe communicator (world_size <= universe_size) * - world_rank - - MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size) + - MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size, aka comm->me) * - world_size - - Number of ranks on LAMMPS' world communicator + - Number of ranks on LAMMPS' world communicator (aka comm->nprocs) + * - comm_style + - communication style (0 = BRICK, 1 = TILED) + * - comm_layout + - communication layout (0 = LAYOUT_UNIFORM, 1 = LAYOUT_NONUNIFORM, 2 = LAYOUT_TILED) + * - comm_mode + - communication mode (0 = SINGLE, 1 = MULTI, 2 = MULTIOLD) + * - ghost_velocity + - whether velocities are communicated for ghost atoms (0 = no, 1 = yes) .. _extract_system_sizes: @@ -1311,6 +1327,10 @@ int lammps_extract_setting(void *handle, const char *keyword) if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me; if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs; if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads; + if (strcmp(keyword,"comm_style") == 0) return lmp->comm->style; + if (strcmp(keyword,"comm_layout") == 0) return lmp->comm->layout; + if (strcmp(keyword,"comm_mode") == 0) return lmp->comm->mode; + if (strcmp(keyword,"ghost_velocity") == 0) return lmp->comm->ghost_velocity; if (strcmp(keyword,"nlocal") == 0) return lmp->atom->nlocal; if (strcmp(keyword,"nghost") == 0) return lmp->atom->nghost; @@ -1387,6 +1407,7 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name) if (strcmp(name,"xy") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"xz") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"yz") == 0) return LAMMPS_DOUBLE; + if (strcmp(name,"procgrid") == 0) return LAMMPS_INT; if (strcmp(name,"natoms") == 0) return LAMMPS_BIGINT; if (strcmp(name,"nbonds") == 0) return LAMMPS_BIGINT; @@ -1400,6 +1421,16 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name) if (strcmp(name,"special_lj") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"special_coul") == 0) return LAMMPS_DOUBLE; + if (strcmp(name,"map_style") == 0) return LAMMPS_INT; +#if defined(LAMMPS_BIGBIG) + if (strcmp(name,"map_tag_max") == 0) return LAMMPS_BIGINT; +#else + if (strcmp(name,"map_tag_max") == 0) return LAMMPS_INT; +#endif + if (strcmp(name,"sametag") == 0) return LAMMPS_INT; + if (strcmp(name,"sortfreq") == 0) return LAMMPS_INT; + if (strcmp(name,"nextsort") == 0) return LAMMPS_BIGINT; + if (strcmp(name,"q_flag") == 0) return LAMMPS_INT; if (strcmp(name,"units") == 0) return LAMMPS_STRING; @@ -1595,6 +1626,10 @@ report the "native" data type. The following tables are provided: - double - 1 - triclinic tilt factor. See :doc:`Howto_triclinic`. + * - procgrid + - int + - 3 + - processor count assigned to each dimension of 3d grid. See :doc:`processors`. .. _extract_system_settings: @@ -1652,6 +1687,26 @@ report the "native" data type. The following tables are provided: - double - 4 - special :doc:`pair weighting factors ` for Coulomb interactions (first element is always 1.0) + * - map_style + - int + - 1 + - :doc:`atom map setting `: 0 = none, 1 = array, 2 = hash, 3 = yes + * - map_tag_max + - bigint or int + - 1 + - largest atom ID that can be mapped to a local index (bigint only with -DLAMMPS_BIGBIG) + * - sametag + - int + - nlocal+nghost + - index of next local atom with the same ID in ascending order. -1 signals end. + * - sortfreq + - int + - 1 + - frequency of atom sorting. 0 means sorting is off. + * - nextsort + - bigint + - 1 + - timestep when atoms are sorted next * - q_flag - int - 1 @@ -1832,6 +1887,9 @@ void *lammps_extract_global(void *handle, const char *name) if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy; if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz; if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz; + if (((lmp->comm->layout == Comm::LAYOUT_UNIFORM) || + (lmp->comm->layout == Comm::LAYOUT_NONUNIFORM)) && (strcmp(name,"procgrid") == 0)) + return (void *) &lmp->comm->procgrid; if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms; if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes; @@ -1847,6 +1905,12 @@ void *lammps_extract_global(void *handle, const char *name) if (strcmp(name,"q_flag") == 0) return (void *) &lmp->atom->q_flag; + if (strcmp(name,"map_style") == 0) return (void *) &lmp->atom->map_style; + if (strcmp(name,"map_tag_max") == 0) return (void *) &lmp->atom->map_tag_max; + if (strcmp(name,"sametag") == 0) return (void *) lmp->atom->sametag; + if (strcmp(name,"sortfreq") == 0) return (void *) &lmp->atom->sortfreq; + if (strcmp(name,"nextsort") == 0) return (void *) &lmp->atom->nextsort; + // global constants defined by units if (strcmp(name,"boltz") == 0) return (void *) &lmp->force->boltz; @@ -1874,6 +1938,37 @@ void *lammps_extract_global(void *handle, const char *name) /* ---------------------------------------------------------------------- */ +/** Map global atom ID to local atom index + * +\verbatim embed:rst + +.. versionadded:: 27June2024 + +This function returns an integer that corresponds to the local atom +index for an atom with the global atom ID *id*. The atom ID is passed +as a void pointer so that it can use the same interface for either a +32-bit or 64-bit tagint. The size of the tagint can be determined +using :cpp:func:`lammps_extract_setting`. + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance + * \param id void pointer to the atom ID (of data type tagint, i.e. 32-bit or 64-bit integer) + * \return local atom index or -1 if the atom is not found or no map exists + * */ + +int lammps_map_atom(void *handle, const void *id) +{ + auto lmp = (LAMMPS *) handle; + auto tag = (const tagint *) id; + if (lmp->atom->map_style > Atom::MAP_NONE) + return lmp->atom->map(*tag); + else + return -1; +} + +/* ---------------------------------------------------------------------- */ + /** Get data type of a LAMMPS per-atom property * \verbatim embed:rst @@ -2137,7 +2232,8 @@ available. .. code-block:: c - double *dptr = (double *) lammps_extract_fix(handle,name,0,1,0,0); + double *dptr = (double *) lammps_extract_fix(handle, name, + LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, 0); double value = *dptr; lammps_free((void *)dptr); @@ -2324,7 +2420,7 @@ use to avoid a memory leak. Example: .. code-block:: c - double *dptr = (double *) lammps_extract_variable(handle,name,NULL); + double *dptr = (double *) lammps_extract_variable(handle, name, NULL); double value = *dptr; lammps_free((void *)dptr); @@ -2335,16 +2431,25 @@ content will not be updated in case the variable is re-evaluated. To avoid a memory leak, this pointer needs to be freed after use in the calling program. -For *vector*\ -style variables, the returned pointer is to actual LAMMPS data. -The pointer should not be deallocated. Its length depends on the variable, -compute, or fix data used to construct the *vector*\ -style variable. -This length can be fetched by calling this function with *group* set to the -constant "LMP_SIZE_VECTOR", which returns a ``void *`` pointer that can be -dereferenced to an integer that is the length of the vector. This pointer -needs to be deallocated when finished with it to avoid memory leaks. +For *vector*\ -style variables, the returned pointer points to actual +LAMMPS data and thus it should **not** be deallocated. Its length +depends on the variable, compute, or fix data used to construct the +*vector*\ -style variable. This length can be fetched by calling this +function with *group* set to a non-NULL pointer (NULL returns the vector). +In that case it will return the vector length as an allocated int +pointer cast to a ``void *`` pointer. That pointer can be recast and +dereferenced to an integer yielding the length of the vector. This pointer +must be deallocated when finished with it to avoid memory leaks. Example: + +.. code-block:: c + + double *vectvals = (double *) lammps_extract_variable(handle, name, NULL); + int *intptr = (int *) lammps_extract_variable(handle, name, 1); + int vectlen = *intptr; + lammps_free((void *)intptr); For other variable styles the returned pointer needs to be cast to -a char pointer. It should not be deallocated. +a char pointer and it should **not** be deallocated. Example: .. code-block:: c @@ -2356,7 +2461,7 @@ a char pointer. It should not be deallocated. LAMMPS cannot easily check if it is valid to access the data referenced by the variables (e.g., computes, fixes, or thermodynamic info), so it may fail with an error. The caller has to make certain - that the data are extracted only when it safe to evaluate the variable + that the data is extracted only when it safe to evaluate the variable and thus an error or crash are avoided. \endverbatim @@ -2391,7 +2496,7 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group) } else if (lmp->input->variable->vectorstyle(ivar)) { double *values = nullptr; int nvector = lmp->input->variable->compute_vector(ivar, &values); - if (group != nullptr && strcmp(group,"LMP_SIZE_VECTOR") == 0) { + if (group) { int* nvecptr = (int *) malloc(sizeof(int)); *nvecptr = nvector; return (void *) nvecptr; @@ -2628,7 +2733,14 @@ x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`); *natoms*), as queried by :cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined and consecutive. + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -2649,8 +2761,7 @@ This function is not compatible with ``-DLAMMPS_BIGBIG``. Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ -void lammps_gather_atoms(void *handle, const char *name, int type, int count, - void *data) +void lammps_gather_atoms(void *handle, const char *name, int type, int count, void *data) { auto lmp = (LAMMPS *) handle; @@ -2670,8 +2781,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count, flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_gather_atoms"); + lmp->error->all(FLERR,"lammps_gather_atoms(): Atom-IDs must exist and be consecutive"); return; } @@ -2679,8 +2789,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count, void *vptr = lmp->atom->extract(name); if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name"); + lmp->error->all(FLERR, "lammps_gather_atoms(): unknown property {}", name); return; } @@ -2755,8 +2864,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count, MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world); lmp->memory->destroy(copy); } else { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_atoms: unsupported data type"); + lmp->error->all(FLERR,"lammps_gather_atoms(): unsupported data type"); return; } #endif @@ -2784,10 +2892,17 @@ groups total, but not in order by atom ID (e.g., if *name* is *x* and *count* is 3, then *data* might be something like x[10][0], x[10][1], x[10][2], x[2][0], x[2][1], x[2][2], x[4][0], :math:`\dots`); *data* must be pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as -queried by :cpp:func:`lammps_get_natoms`, -:cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. +queried by :cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, +or :cpp:func:`lammps_extract_setting`. -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined. + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -2827,8 +2942,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type, if (lmp->atom->tag_enable == 0) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_gather_atoms"); + lmp->error->all(FLERR,"lammps_gather_atoms_concat(): Atom-IDs must exist"); return; } @@ -2836,8 +2950,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type, void *vptr = lmp->atom->extract(name); if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name"); + lmp->error->all(FLERR,"lammps_gather_atoms_concat(): unknown property {}", name); return; } @@ -2857,10 +2970,6 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type, if ((count == 1) || imgunpack) vector = (int *) vptr; else array = (int **) vptr; - int *copy; - lmp->memory->create(copy,count*natoms,"lib/gather:copy"); - for (i = 0; i < count*natoms; i++) copy[i] = 0; - int nlocal = lmp->atom->nlocal; if (count == 1) { @@ -2868,11 +2977,13 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type, displs[0] = 0; for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1]; - MPI_Allgatherv(vector,nlocal,MPI_INT,data,recvcounts,displs, - MPI_INT,lmp->world); + MPI_Allgatherv(vector,nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world); } else if (imgunpack) { - lmp->memory->create(copy,count*nlocal,"lib/gather:copy"); + int *copy; + lmp->memory->create(copy,count*natoms,"lib/gather:copy"); + for (i = 0; i < count*natoms; i++) copy[i] = 0; + offset = 0; for (i = 0; i < nlocal; i++) { const int image = vector[i]; @@ -2885,8 +2996,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type, displs[0] = 0; for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1]; - MPI_Allgatherv(copy,count*nlocal,MPI_INT, - data,recvcounts,displs,MPI_INT,lmp->world); + MPI_Allgatherv(copy,count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world); lmp->memory->destroy(copy); } else { @@ -2895,8 +3005,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type, displs[0] = 0; for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1]; - MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT, - data,recvcounts,displs,MPI_INT,lmp->world); + MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world); } } else { @@ -2912,8 +3021,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type, displs[0] = 0; for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1]; - MPI_Allgatherv(vector,nlocal,MPI_DOUBLE,data,recvcounts,displs, - MPI_DOUBLE,lmp->world); + MPI_Allgatherv(vector,nlocal,MPI_DOUBLE,data,recvcounts,displs,MPI_DOUBLE,lmp->world); } else { int n = count*nlocal; @@ -2951,7 +3059,14 @@ x[100][2], x[57][0], x[57][1], x[57][2], x[210][0], :math:`\dots`); *data* must be pre-allocated by the caller to length (*count* :math:`\times` *ndata*). -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined and an :doc:`atom map must be enabled ` + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -2997,16 +3112,13 @@ void lammps_gather_atoms_subset(void *handle, const char *name, int type, if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_gather_atoms_subset: atoms must have mappable ids"); + lmp->error->all(FLERR,"lammps_gather_atoms_subset(): Atom-IDs must exist and be mapped"); return; } void *vptr = lmp->atom->extract(name); if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_atoms_subset: " - "unknown property name"); + lmp->error->all(FLERR,"lammps_gather_atoms_subset(): unknown property {}", name); return; } @@ -3114,7 +3226,15 @@ atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*). -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined, must be consecutive, and an + :doc:`atom map must be enabled ` + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -3156,8 +3276,8 @@ void lammps_scatter_atoms(void *handle, const char *name, int type, int count, if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms: ids must exist, be consecutive, and be mapped"); + lmp->error->all(FLERR,"lammps_scatter_atoms(): " + "Atom-IDs must exist, be consecutive, and be mapped"); return; } @@ -3165,16 +3285,10 @@ void lammps_scatter_atoms(void *handle, const char *name, int type, int count, void *vptr = lmp->atom->extract(name); if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR, - "lammps_scatter_atoms: unknown property name"); + lmp->error->all(FLERR, "lammps_scatter_atoms(): unknown property {}", name); return; } - // copy = Natom length vector of per-atom values - // use atom ID to insert each atom's values into copy - // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID - if (type == 0) { int *vector = nullptr; int **array = nullptr; @@ -3252,7 +3366,14 @@ to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2], x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would be {1, 100, 57}. -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined and an :doc:`atom map must be enabled ` + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -3309,23 +3430,16 @@ void lammps_scatter_atoms_subset(void *handle, const char *name, int type, if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset: atoms must have mapped ids"); + lmp->error->all(FLERR,"lammps_scatter_atoms_subset(): Atom-IDs must exist and be mapped"); return; } void *vptr = lmp->atom->extract(name); if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR, - "lammps_scatter_atoms_subset: unknown property name"); + lmp->error->all(FLERR, "lammps_scatter_atoms_subset(): unknown property {}", name); return; } - // copy = Natom length vector of per-atom values - // use atom ID to insert each atom's values into copy - // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID - if (type == 0) { int *vector = nullptr; int **array = nullptr; @@ -3861,7 +3975,14 @@ The *data* array will be ordered in groups of *count* values, sorted by atom ID This function will return an error if fix or compute data are requested and the fix or compute ID given does not have per-atom data. -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined and must be consecutive. + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -3911,7 +4032,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da BEGIN_CAPTURE { #if defined(LAMMPS_BIGBIG) - lmp->error->all(FLERR,"Library function lammps_gather not compatible with -DLAMMPS_BIGBIG"); + lmp->error->all(FLERR, "Library function lammps_gather() is not compatible with -DLAMMPS_BIGBIG"); #else int i,j,offset,ltype; @@ -3922,8 +4043,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_gather"); + lmp->error->all(FLERR,"lammps_gather(): Atom-IDs must exist, and be consecutive"); return; } @@ -3933,28 +4053,25 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da // fix if (vptr==nullptr && utils::strmatch(name,"^f_")) { + const char *fixid = name+2; - auto fix = lmp->modify->get_fix_by_id(&name[2]); + auto fix = lmp->modify->get_fix_by_id(fixid); if (!fix) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: unknown fix id"); + lmp->error->all(FLERR,"lammps_gather(): unknown fix id {}", fixid); return; } if (fix->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: fix does not return peratom data"); + lmp->error->all(FLERR,"lammps_gather(): fix {} does not return peratom data", fixid); return; } if ((count > 1) && (fix->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: count != values peratom for fix"); + lmp->error->all(FLERR,"lammps_gather: count != values peratom for fix {}", fixid); return; } if (lmp->update->ntimestep % fix->peratom_freq) { - if (lmp->comm->me == 0) - lmp->error->all(FLERR,"lammps_gather: fix not computed at compatible time"); + lmp->error->all(FLERR,"lammps_gather: fix {} not computed at compatible time", fixid); return; } @@ -3965,22 +4082,19 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da // compute if (vptr==nullptr && utils::strmatch(name,"^c_")) { - - auto compute = lmp->modify->get_compute_by_id(&name[2]); + const char *compid = name+2; + auto compute = lmp->modify->get_compute_by_id(compid); if (!compute) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: unknown compute id"); + lmp->error->all(FLERR,"lammps_gather(): unknown compute id {}", compid); return; } if (compute->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: compute does not return peratom data"); + lmp->error->all(FLERR,"lammps_gather(): compute {} does not return peratom data", compid); return; } if ((count > 1) && (compute->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: count != values peratom for compute"); + lmp->error->all(FLERR,"lammps_gather(): count != values peratom for compute {}", compid); return; } @@ -3996,28 +4110,26 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { int idx,icol; - if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); - else idx = lmp->atom->find_custom(&name[3],ltype,icol); + const char *propid; + if (utils::strmatch(name,"^[id]_")) propid = name+2; + else propid = name+3; + idx = lmp->atom->find_custom(propid,ltype,icol); if (idx < 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: unknown property/atom id"); + lmp->error->all(FLERR,"lammps_gather(): unknown property/atom id {}", propid); return; } if (ltype != type) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom type"); + lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom type for {}", propid); return; } if ((count == 1) && (icol != 0)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom count for {}", propid); return; } if ((count > 1) && (icol != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom count for {}", propid); return; } @@ -4033,8 +4145,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da // no match if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: undefined property name"); + lmp->error->all(FLERR,"lammps_gather(): undefined property {}", name); return; } @@ -4134,7 +4245,14 @@ pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as quer :cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined. + + The total number of atoms must be less than 2147483647 (max 32-bit signed int). \endverbatim * @@ -4185,8 +4303,8 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, BEGIN_CAPTURE { #if defined(LAMMPS_BIGBIG) - lmp->error->all(FLERR,"Library function lammps_gather_concat" - " not compatible with -DLAMMPS_BIGBIG"); + lmp->error->all(FLERR,"Library function lammps_gather_concat()" + " is not compatible with -DLAMMPS_BIGBIG"); #else int i,offset,ltype; @@ -4196,8 +4314,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, if (lmp->atom->tag_enable == 0) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_gather_concat"); + lmp->error->all(FLERR,"lammps_gather_concat(): atom-IDs must exist"); return; } @@ -4207,27 +4324,24 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, // fix if (vptr==nullptr && utils::strmatch(name,"^f_")) { - - auto fix = lmp->modify->get_fix_by_id(&name[2]); + const char *fixid = name+2; + auto fix = lmp->modify->get_fix_by_id(fixid); if (!fix) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: unknown fix id"); + lmp->error->all(FLERR,"lammps_gather_concat(): unknown fix id {}", fixid); return; } if (fix->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: fix does not return peratom data"); + lmp->error->all(FLERR,"lammps_gather_concat(): fix {} does not return peratom data", fixid); return; } if ((count > 1) && (fix->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for fix"); + lmp->error->all(FLERR,"lammps_gather_concat(): count != values peratom for fix {}", fixid); return; } if (lmp->update->ntimestep % fix->peratom_freq) { - if (lmp->comm->me == 0) - lmp->error->all(FLERR,"lammps_gather_concat: fix not computed at compatible time"); + lmp->error->all(FLERR,"lammps_gather_concat(): fix {} not computed at compatible time", + fixid); return; } @@ -4239,21 +4353,21 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, if (vptr==nullptr && utils::strmatch(name,"^c_")) { - auto compute = lmp->modify->get_compute_by_id(&name[2]); + const char *compid = name + 2; + auto compute = lmp->modify->get_compute_by_id(compid); if (!compute) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: unknown compute id"); + lmp->error->all(FLERR,"lammps_gather_concat(): unknown compute id {}", compid); return; } if (compute->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: compute does not return peratom data"); + lmp->error->all(FLERR,"lammps_gather_concat(): compute {} does not return peratom data", + compid); return; } if ((count > 1) && (compute->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for compute"); + lmp->error->all(FLERR,"lammps_gather_concat(): count != values peratom for compute {}", + compid); return; } @@ -4269,28 +4383,26 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, if ((vptr==nullptr) && utils::strmatch(name,"^[id]2?_")) { int idx,icol; - if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); - else idx = lmp->atom->find_custom(&name[3],ltype,icol); + const char *propid; + if (utils::strmatch(name,"^[id]_")) propid = name + 2; + else propid = name + 3; + idx = lmp->atom->find_custom(propid,ltype,icol); if (idx < 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: unknown property/atom id"); + lmp->error->all(FLERR,"lammps_gather_concat(): unknown property/atom id {}", propid); return; } if (ltype != type) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom type"); + lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} type", propid); return; } if ((count == 1) && (icol != 0)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} count", propid); return; } if ((count > 1) && (icol != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} count", propid); return; } @@ -4306,8 +4418,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, // no match if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_concat: undefined property name"); + lmp->error->all(FLERR,"lammps_gather_concat(): undefined property {}", name); return; } @@ -4328,10 +4439,6 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, if ((count == 1) || imgunpack) vector = (int *) vptr; else array = (int **) vptr; - int *copy; - lmp->memory->create(copy,count*natoms,"lib/gather:copy"); - for (i = 0; i < count*natoms; i++) copy[i] = 0; - int nlocal = lmp->atom->nlocal; if (count == 1) { @@ -4343,7 +4450,10 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, MPI_INT,lmp->world); } else if (imgunpack) { - lmp->memory->create(copy,count*nlocal,"lib/gather:copy"); + int *copy; + lmp->memory->create(copy,count*natoms,"lib/gather:copy"); + for (i = 0; i < count*natoms; i++) copy[i] = 0; + offset = 0; for (i = 0; i < nlocal; i++) { const int image = vector[i]; @@ -4356,8 +4466,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, displs[0] = 0; for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1]; - MPI_Allgatherv(copy,count*nlocal,MPI_INT, - data,recvcounts,displs,MPI_INT,lmp->world); + MPI_Allgatherv(copy,count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world); lmp->memory->destroy(copy); } else { @@ -4366,8 +4475,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count, displs[0] = 0; for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1]; - MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT, - data,recvcounts,displs,MPI_INT,lmp->world); + MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world); } } else { @@ -4420,7 +4528,14 @@ look like {x[100][0], x[100][1], x[100][2], x[57][0], x[57][1], x[57][2], x[210] :math:`\dots`}); *ids* must be provided by the user with length *ndata*, and *data* must be pre-allocated by the caller to length (*count*\ :math:`{}\times{}`\ *ndata*). -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined and an :doc:`atom map must be enabled ` + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -4486,8 +4601,7 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count, if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_gather_subset"); + lmp->error->all (FLERR,"lammps_gather_subset(): atom IDs must be enabled and mapped"); return; } @@ -4496,26 +4610,24 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count, // fix if (vptr==nullptr && utils::strmatch(name,"^f_")) { + const char *fixid = name + 2; - auto fix = lmp->modify->get_fix_by_id(&name[2]); + auto fix = lmp->modify->get_fix_by_id(fixid); if (!fix) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: unknown fix id"); + lmp->error->all(FLERR,"lammps_gather_subset(): unknown fix id {}", fixid); return; } if (fix->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: fix does not return peratom data"); + lmp->error->all(FLERR,"lammps_gather_subset(): fix {} does not return peratom data", fixid); return; } if ((count > 1) && (fix->size_peratom_cols != count)) { - lmp->error->warning(FLERR,"lammps_gather_subset: count != values peratom for fix"); + lmp->error->all(FLERR,"lammps_gather_subset(): count != values peratom for fix {}", fixid); return; } if (lmp->update->ntimestep % fix->peratom_freq) { - if (lmp->comm->me == 0) - lmp->error->all(FLERR,"lammps_gather_subset: fix not computed at compatible time"); + lmp->error->all(FLERR,"lammps_gather_subset(): fix {} not computed at compatible time", fixid); return; } @@ -4526,22 +4638,21 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count, // compute if (vptr==nullptr && utils::strmatch(name,"^c_")) { - - auto compute = lmp->modify->get_compute_by_id(&name[2]); + const char *compid = name + 2; + auto compute = lmp->modify->get_compute_by_id(compid); if (!compute) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: unknown compute id"); + lmp->error->all(FLERR,"lammps_gather_subset(): unknown compute id {}", compid); return; } if (compute->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: compute does not return peratom data"); + lmp->error->all(FLERR,"lammps_gather_subset(): compute {} does not return peratom data", + compid); return; } if ((count > 1) && (compute->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: count != values peratom for compute"); + lmp->error->all(FLERR,"lammps_gather_subset(): count != values peratom for compute {}", + compid); return; } @@ -4557,28 +4668,26 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count, if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { int idx,icol; - if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); - else idx = lmp->atom->find_custom(&name[3],ltype,icol); + const char *propid; + if (utils::strmatch(name,"^[id]_")) propid = name + 2; + else propid = name + 3; + idx = lmp->atom->find_custom(propid,ltype,icol); if (idx < 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: unknown property/atom id"); + lmp->error->all(FLERR,"lammps_gather_subset(): unknown property/atom id {}", propid); return; } if (ltype != type) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom type"); + lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} type", propid); return; } if (count == 1 && icol != 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} count", propid); return; } if (count > 1 && icol != count) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} count", propid); return; } @@ -4594,8 +4703,7 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count, // no match if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather_subset: undefined property name"); + lmp->error->all(FLERR,"lammps_gather_subset(): undefined property {}", name); return; } @@ -4703,7 +4811,15 @@ The *data* array needs to be ordered in groups of *count* values, sorted by atom *name* is *x* and *count* = 3, then *data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*). -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined, must be consecutive, and an + :doc:`atom map must be enabled ` + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -4766,8 +4882,7 @@ void lammps_scatter(void *handle, const char *name, int type, int count, if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_scatter"); + lmp->error->all(FLERR,"lammps_scatter(): atom IDs must be defined, consecutive, and mapped"); return; } @@ -4777,22 +4892,19 @@ void lammps_scatter(void *handle, const char *name, int type, int count, // fix if (vptr==nullptr && utils::strmatch(name,"^f_")) { - - auto fix = lmp->modify->get_fix_by_id(&name[2]); + const char *fixid = name + 2; + auto fix = lmp->modify->get_fix_by_id(fixid); if (!fix) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: unknown fix id"); + lmp->error->all(FLERR,"lammps_scatter(): unknown fix id {}", fixid); return; } if (fix->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: fix does not return peratom data"); + lmp->error->all(FLERR,"lammps_scatter(): fix {} does not return peratom data", fixid); return; } if ((count > 1) && (fix->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: count != values peratom for fix"); + lmp->error->all(FLERR,"lammps_scatter(): count != values peratom for fix {}", fixid); return; } @@ -4803,22 +4915,19 @@ void lammps_scatter(void *handle, const char *name, int type, int count, // compute if (vptr==nullptr && utils::strmatch(name,"^c_")) { - - auto compute = lmp->modify->get_compute_by_id(&name[2]); + const char *compid = name + 2; + auto compute = lmp->modify->get_compute_by_id(compid); if (!compute) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: unknown compute id"); + lmp->error->all(FLERR,"lammps_scatter(): unknown compute id {}",compid); return; } if (compute->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: compute does not return peratom data"); + lmp->error->all(FLERR,"lammps_scatter(): compute {} does not return peratom data", compid); return; } if ((count > 1) && (compute->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: count != values peratom for compute"); + lmp->error->all(FLERR,"lammps_scatter(): count != values peratom for compute {}", compid); return; } @@ -4834,28 +4943,26 @@ void lammps_scatter(void *handle, const char *name, int type, int count, if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { int idx,icol; - if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); - else idx = lmp->atom->find_custom(&name[3],ltype,icol); + const char *propid; + if (utils::strmatch(name,"^[id]_")) propid = name + 2; + else propid = name + 3; + idx = lmp->atom->find_custom(propid,ltype,icol); if (idx < 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: unknown property/atom id"); + lmp->error->all(FLERR,"lammps_scatter(): unknown property/atom id {}", propid); return; } if (ltype != type) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom type"); + lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} type", propid); return; } if (count == 1 && icol != 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} count", propid); return; } if (count > 1 && icol != count) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} count", propid); return; } @@ -4871,15 +4978,10 @@ void lammps_scatter(void *handle, const char *name, int type, int count, // no match if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter: unknown property name"); + lmp->error->all(FLERR,"lammps_scatter(): unknown property {}", name); return; } - // copy = Natom length vector of per-atom values - // use atom ID to insert each atom's values into copy - // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID - if (type == 0) { int *vector = nullptr; int **array = nullptr; @@ -4957,7 +5059,14 @@ to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2], x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would be {1, 100, 57}. -This function is not compatible with ``-DLAMMPS_BIGBIG``. +.. admonition:: Restrictions + :class: warning + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + Atom IDs must be defined and an :doc:`atom map must be enabled ` + + The total number of atoms must not be more than 2147483647 (max 32-bit signed int). \endverbatim * @@ -4998,8 +5107,8 @@ This function is not compatible with ``-DLAMMPS_BIGBIG``. loop over Ndata, if I own atom ID, set its values from data ------------------------------------------------------------------------- */ -void lammps_scatter_subset(void *handle, const char *name,int type, int count, - int ndata, int *ids, void *data) +void lammps_scatter_subset(void *handle, const char *name,int type, int count, int ndata, + int *ids, void *data) { auto lmp = (LAMMPS *) handle; @@ -5020,8 +5129,7 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count, if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (flag) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset"); + lmp->error->all(FLERR,"lammps_scatter_subset(): atom-IDs must be defined and mapped"); return; } @@ -5030,22 +5138,19 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count, // fix if (vptr==nullptr && utils::strmatch(name,"^f_")) { - - auto fix = lmp->modify->get_fix_by_id(&name[2]); + const char *fixid = name + 2; + auto fix = lmp->modify->get_fix_by_id(fixid); if (!fix) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: unknown fix id"); + lmp->error->all(FLERR,"lammps_scatter_subset(): unknown fix id {}", fixid); return; } if (fix->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: fix does not return peratom data"); + lmp->error->all(FLERR,"lammps_scatter_subset(): fix {} does not return peratom data", fixid); return; } if ((count > 1) && (fix->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: count != values peratom for fix"); + lmp->error->all(FLERR,"lammps_scatter_subset(): count != values peratom for fix {}", fixid); return; } @@ -5056,22 +5161,21 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count, // compute if (vptr==nullptr && utils::strmatch(name,"^c_")) { - - auto compute = lmp->modify->get_compute_by_id(&name[2]); + const char *compid = name + 2; + auto compute = lmp->modify->get_compute_by_id(compid); if (!compute) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: unknown compute id"); + lmp->error->all(FLERR,"lammps_scatter_subset(): unknown compute id {}", compid); return; } if (compute->peratom_flag == 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: compute does not return peratom data"); + lmp->error->all(FLERR,"lammps_scatter_subset(): compute {} does not return peratom data", + compid); return; } if ((count > 1) && (compute->size_peratom_cols != count)) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: count != values peratom for compute"); + lmp->error->all(FLERR,"lammps_scatter_subset(): count != values peratom for compute {}", + compid); return; } @@ -5087,28 +5191,26 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count, if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { int idx,icol; - if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); - else idx = lmp->atom->find_custom(&name[3],ltype,icol); + const char *propid; + if (utils::strmatch(name,"^[id]_")) propid = name + 2; + else propid = name + 3; + idx = lmp->atom->find_custom(propid,ltype,icol); if (idx < 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: unknown property/atom id"); + lmp->error->all(FLERR,"lammps_scatter_subset(): unknown property/atom id {}", propid); return; } if (ltype != type) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_subset: mismatch property/atom type"); + lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} type", propid); return; } if (count == 1 && icol != 0) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} count", propid); return; } if (count > 1 && icol != count) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count"); + lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} count", propid); return; } @@ -5124,16 +5226,10 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count, // no match if (vptr == nullptr) { - if (lmp->comm->me == 0) - lmp->error->warning(FLERR,"lammps_scatter_atoms_subset: " - "unknown property name"); + lmp->error->all(FLERR,"lammps_scatter_subset(): unknown property {}", name); return; } - // copy = Natom length vector of per-atom values - // use atom ID to insert each atom's values into copy - // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID - if (type == 0) { int *vector = nullptr; int **array = nullptr; @@ -5269,7 +5365,7 @@ int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type, // error if box does not exist or tags not defined int flag = 0; - std::string msg("Failure in lammps_create_atoms: "); + std::string msg("Failure in lammps_create_atoms(): "); if (lmp->domain->box_exist == 0) { flag = 1; msg += "trying to create atoms before before simulation box is defined"; @@ -5280,7 +5376,7 @@ int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type, } if (flag) { - if (lmp->comm->me == 0) lmp->error->warning(FLERR,msg); + lmp->error->all(FLERR, msg); return -1; } @@ -5490,7 +5586,8 @@ int lammps_neighlist_num_elements(void *handle, int idx) { * \param[out] numneigh number of neighbors of atom iatom or 0 * \param[out] neighbors pointer to array of neighbor atom local indices or NULL */ -void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom, int *numneigh, int **neighbors) { +void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom, + int *numneigh, int **neighbors) { auto lmp = (LAMMPS *) handle; Neighbor * neighbor = lmp->neighbor; *iatom = -1; @@ -5777,9 +5874,7 @@ otherwise 0. * \param setting string with the name of the specific setting * \return 1 if available, 0 if not. */ -int lammps_config_accelerator(const char *package, - const char *category, - const char *setting) +int lammps_config_accelerator(const char *package, const char *category, const char *setting) { return Info::has_accelerator_feature(package,category,setting) ? 1 : 0; } @@ -5901,8 +5996,7 @@ int lammps_style_count(void *handle, const char *category) { * \param buf_size size of the provided string buffer * \return 1 if successful, otherwise 0 */ -int lammps_style_name(void *handle, const char *category, int idx, - char *buffer, int buf_size) { +int lammps_style_name(void *handle, const char *category, int idx, char *buffer, int buf_size) { auto lmp = (LAMMPS *) handle; Info info(lmp); auto styles = info.get_available_styles(category); diff --git a/src/library.h b/src/library.h index 10cac6741a..fa4a3bd0a5 100644 --- a/src/library.h +++ b/src/library.h @@ -162,6 +162,8 @@ int lammps_extract_setting(void *handle, const char *keyword); int lammps_extract_global_datatype(void *handle, const char *name); void *lammps_extract_global(void *handle, const char *name); +int lammps_map_atom(void *handle, const void *id); + /* ---------------------------------------------------------------------- * Library functions to read or modify per-atom data in LAMMPS * ---------------------------------------------------------------------- */ @@ -173,9 +175,9 @@ void *lammps_extract_atom(void *handle, const char *name); * Library functions to access data from computes, fixes, variables in LAMMPS * ---------------------------------------------------------------------- */ -void *lammps_extract_compute(void *handle, const char *, int, int); -void *lammps_extract_fix(void *handle, const char *, int, int, int, int); -void *lammps_extract_variable(void *handle, const char *, const char *); +void *lammps_extract_compute(void *handle, const char *id, int style, int type); +void *lammps_extract_fix(void *handle, const char *id, int style, int type, int nrow, int ncol); +void *lammps_extract_variable(void *handle, const char *name, const char *group); int lammps_extract_variable_datatype(void *handle, const char *name); int lammps_set_variable(void *handle, const char *name, const char *str); int lammps_set_string_variable(void *handle, const char *name, const char *str); diff --git a/src/lmprestart.h b/src/lmprestart.h index e5e1da7edf..40abcf4fe2 100644 --- a/src/lmprestart.h +++ b/src/lmprestart.h @@ -37,7 +37,8 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL, - NELLIPSOIDS,NLINES,NTRIS,NBODIES,ATIME,ATIMESTEP,LABELMAP}; + NELLIPSOIDS,NLINES,NTRIS,NBODIES,ATIME,ATIMESTEP,LABELMAP, + TRICLINIC_GENERAL,ROTATE_G2R}; #define LB_FACTOR 1.1 diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index 65c3fa806a..c79a61f84a 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -31,7 +31,7 @@ using namespace MathEigen; typedef Jacobi Jacobi_v1; typedef Jacobi Jacobi_v2; -int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) +int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort) { // make copy of const matrix @@ -44,7 +44,15 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v1 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS); + int ierror = 1; + if (sort == -1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS); + else if (sort == 0) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::DO_NOT_SORT); + else if (sort == 1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVALS); + + if (ierror) return ierror; // transpose the evec matrix @@ -54,7 +62,7 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) return ierror; } -int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) +int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort) { // make copy of const matrix @@ -67,7 +75,15 @@ int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v2 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS); + int ierror = 1; + if (sort == -1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS); + else if (sort == 0) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::DO_NOT_SORT); + else if (sort == 1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_INCREASING_EVALS); + + if (ierror) return ierror; // transpose the evec matrix diff --git a/src/math_eigen.h b/src/math_eigen.h index 9f2431e14a..c7a3853767 100644 --- a/src/math_eigen.h +++ b/src/math_eigen.h @@ -22,13 +22,14 @@ namespace MathEigen { * \param mat the 3x3 matrix you wish to diagonalize * \param eval store the eigenvalues here * \param evec store the eigenvectors here... + * \param sort order eigenvalues and -vectors (-1 decreasing (default), 1 increasing, 0 unsorted) * \return 0 if eigenvalue calculation converged, 1 if it failed */ -int jacobi3(double const *const *mat, double *eval, double **evec); +int jacobi3(double const *const *mat, double *eval, double **evec, int sort = -1); /** \overload */ -int jacobi3(double const mat[3][3], double *eval, double evec[3][3]); +int jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort = -1); } // namespace MathEigen diff --git a/src/math_extra.cpp b/src/math_extra.cpp index 83e548f79f..a36600d970 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -362,6 +362,29 @@ void exyz_to_q(double *ex, double *ey, double *ez, double *q) qnormalize(q); } +/* ---------------------------------------------------------------------- + create unit quaternion from a rotation matrix + just a wrapper on exyz_to_q() + ex,ey,ez are columns of a rotation matrix +------------------------------------------------------------------------- */ + +void mat_to_quat(double mat[3][3], double *q) +{ + double ex[3],ey[3],ez[3]; + + ex[0] = mat[0][0]; + ex[1] = mat[1][0]; + ex[2] = mat[2][0]; + ey[0] = mat[0][1]; + ey[1] = mat[1][1]; + ey[2] = mat[2][1]; + ez[0] = mat[0][2]; + ez[1] = mat[1][2]; + ez[2] = mat[2][2]; + + MathExtra::exyz_to_q(ex,ey,ez,q); +} + /* ---------------------------------------------------------------------- compute space-frame ex,ey,ez from current quaternion q ex,ey,ez = space-frame coords of 1st,2nd,3rd principal axis @@ -417,6 +440,7 @@ void quat_to_mat(const double *quat, double mat[3][3]) /* ---------------------------------------------------------------------- compute rotation matrix from quaternion conjugate quat = [w i j k] + similar logic to quat_to_mat() ------------------------------------------------------------------------- */ void quat_to_mat_trans(const double *quat, double mat[3][3]) @@ -647,5 +671,4 @@ void tribbox(double *h, double radius, double *dist) /* ---------------------------------------------------------------------- */ - } diff --git a/src/math_extra.h b/src/math_extra.h index 1efacea463..52d1d838ff 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -47,6 +47,7 @@ inline void cross3(const double *v1, const double *v2, double *ans); inline void zeromat3(double m[3][3]); inline void zeromat3(double **m); +inline void transpose3(const double m[3][3], double ans[3][3]); inline void col2mat(const double *ex, const double *ey, const double *ez, double m[3][3]); inline double det3(const double mat[3][3]); @@ -99,6 +100,7 @@ void angmom_to_omega(double *m, double *ex, double *ey, double *ez, double *idia void omega_to_angmom(double *w, double *ex, double *ey, double *ez, double *idiag, double *m); void mq_to_omega(double *m, double *q, double *moments, double *w); void exyz_to_q(double *ex, double *ey, double *ez, double *q); +void mat_to_quat(double mat[3][3], double *quat); void q_to_exyz(double *q, double *ex, double *ey, double *ez); void quat_to_mat(const double *quat, double mat[3][3]); void quat_to_mat_trans(const double *quat, double mat[3][3]); @@ -763,6 +765,21 @@ inline void MathExtra::zeromat3(double **m) m[2][0] = m[2][1] = m[2][2] = 0.0; } +// transpose a matrix + +inline void MathExtra::transpose3(const double m[3][3], double ans[3][3]) +{ + ans[0][0] = m[0][0]; + ans[0][1] = m[1][0]; + ans[0][2] = m[2][0]; + ans[1][0] = m[0][1]; + ans[1][1] = m[1][1]; + ans[1][2] = m[2][1]; + ans[2][0] = m[0][2]; + ans[2][1] = m[1][2]; + ans[2][2] = m[2][2]; +} + // add two matrices inline void MathExtra::plus3(const double m[3][3], double **m2, double **ans) diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index d33b7579b9..5dc3d6568b 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -686,7 +686,7 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha) // choosing the initial alpha that we'll use // rough estimate that'll decrease energy to 1/10 - alpha_init = 0.1*fabs(eoriginal)/fdothall; + alpha_init = MAX(EPS_QUAD, 0.1*fabs(eoriginal)/fdothall); // initialize aplha to 0.0 diff --git a/src/modify.cpp b/src/modify.cpp index ba04c5969a..1a9c056027 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -188,6 +188,8 @@ void Modify::init() // since any of them may be invoked by initial thermo // do not clear out invocation times stored within a compute, // b/c some may be holdovers from previous run, like for ave fixes + // perform check whether extscalar, extvector, and extarray have been + // set when scalar_flag, vector_flag, or array_flag are true. for (i = 0; i < ncompute; i++) { compute[i]->init(); @@ -200,8 +202,13 @@ void Modify::init() // used to b/c temperature computes called fix->dof() in their init, // and fix rigid required its own init before its dof() could be called, // but computes now do their DOF in setup() + // perform check whether extscalar, extvector, and extarray have been + // set when scalar_flag, vector_flag, or array_flag are true. - for (i = 0; i < nfix; i++) fix[i]->init(); + for (i = 0; i < nfix; i++) { + fix[i]->init(); + fix[i]->init_flags(); + } // set global flag if any fix has its restart_pbc flag set diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 4bdd58eead..878ee98917 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -148,6 +148,7 @@ void NeighList::post_constructor(NeighRequest *nq) copy = nq->copy; trim = nq->trim; id = nq->id; + molskip = nq->molskip; if (nq->copy) { listcopy = neighbor->lists[nq->copylist]; @@ -157,14 +158,16 @@ void NeighList::post_constructor(NeighRequest *nq) if (nq->skip) { listskip = neighbor->lists[nq->skiplist]; - int ntypes = atom->ntypes; - iskip = new int[ntypes+1]; - memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip"); - int i,j; - for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i]; - for (i = 1; i <= ntypes; i++) - for (j = 1; j <= ntypes; j++) - ijskip[i][j] = nq->ijskip[i][j]; + if (!molskip) { + int ntypes = atom->ntypes; + iskip = new int[ntypes+1]; + memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip"); + int i,j; + for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i]; + for (i = 1; i <= ntypes; i++) + for (j = 1; j <= ntypes; j++) + ijskip[i][j] = nq->ijskip[i][j]; + } } if (nq->halffull) diff --git a/src/neigh_list.h b/src/neigh_list.h index 01e9a1c6a7..4c592772ad 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -46,6 +46,7 @@ class NeighList : protected Pointers { int kk2cpu; // 1 if this list is copied from Kokkos to CPU int copymode; // 1 if this is a Kokkos on-device copy int id; // copied from neighbor list request + int molskip; // 1/2 if this is an intra-/inter-molecular skip list // data structs to store neighbor pairs I,J and associated values diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp index 280b5c54ae..77e71c6860 100644 --- a/src/neigh_request.cpp +++ b/src/neigh_request.cpp @@ -76,6 +76,7 @@ NeighRequest::NeighRequest(LAMMPS *_lmp) : Pointers(_lmp) skip = 0; iskip = nullptr; ijskip = nullptr; + molskip = REGULAR; // only set when command = 1; @@ -183,6 +184,8 @@ int NeighRequest::identical(NeighRequest *other) int NeighRequest::same_skip(NeighRequest *other) { + if (molskip != other->molskip) return 0; + const int ntypes = atom->ntypes; int same = 1; @@ -307,6 +310,12 @@ void NeighRequest::set_skip(int *_iskip, int **_ijskip) ijskip = _ijskip; } +void NeighRequest::set_molskip(int _molskip) +{ + skip = 1; + molskip = _molskip; +} + void NeighRequest::enable_full() { half = 0; diff --git a/src/neigh_request.h b/src/neigh_request.h index fa57922c93..caa9e05ad6 100644 --- a/src/neigh_request.h +++ b/src/neigh_request.h @@ -29,6 +29,9 @@ class NeighRequest : protected Pointers { friend class NPairSkipTrimIntel; friend class FixIntel; + public: + enum { REGULAR, INTRA, INTER }; + protected: void *requestor; // class that made request int requestor_instance; // instance of that class (only Fix, Compute, Pair) @@ -88,6 +91,7 @@ class NeighRequest : protected Pointers { int skip; // 1 if this list skips atom types from another list int *iskip; // iskip[i] if atoms of type I are not in list int **ijskip; // ijskip[i][j] if pairs of type I,J are not in list + int molskip; // 0 reqular list, 1 keep only intra-molecular entries, 2 keep inter-molecular // command_style only set if command = 1 // allows print_pair_info() to access command name @@ -137,6 +141,7 @@ class NeighRequest : protected Pointers { void set_kokkos_device(int); void set_kokkos_host(int); void set_skip(int *, int **); + void set_molskip(int); void enable_full(); void enable_ghost(); void enable_intel(); diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 662494ea7b..59ddf87698 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -427,6 +427,9 @@ void Neighbor::init() } } } else { + if (!force->pair) + error->all(FLERR, "Cannot use collection/interval command without defining a pairstyle"); + if (force->pair->finitecutflag) { finite_cut_flag = 1; // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs @@ -1797,10 +1800,17 @@ void Neighbor::print_pairwise_info() else out += fmt::format(", half/full from ({})",rq->halffulllist+1); } else if (rq->skip) { - if (rq->trim) - out += fmt::format(", skip trim from ({})",rq->skiplist+1); - else - out += fmt::format(", skip from ({})",rq->skiplist+1); + if (rq->molskip) { + if (rq->trim) + out += fmt::format(", molskip trim from ({})",rq->skiplist+1); + else + out += fmt::format(", molskip from ({})",rq->skiplist+1); + } else { + if (rq->trim) + out += fmt::format(", skip trim from ({})",rq->skiplist+1); + else + out += fmt::format(", skip from ({})",rq->skiplist+1); + } } out += "\n"; @@ -2381,7 +2391,7 @@ int Neighbor::check_distance() dely = x[i][1] - xhold[i][1]; delz = x[i][2] - xhold[i][2]; rsq = delx*delx + dely*dely + delz*delz; - if (rsq > deltasq) flag = 1; + if (rsq > deltasq) { flag = 1; break; } } int flagall; @@ -2973,6 +2983,14 @@ bigint Neighbor::get_nneigh_half() return nneighhalf; } +/* ---------------------------------------------------------------------- + return the pointer containing the last positions stored by the NL builder +------------------------------------------------------------------------- */ +double **Neighbor::get_xhold() +{ + return xhold; +} + /* ---------------------------------------------------------------------- add pair of atoms to bondlist array will only persist until the next neighbor build diff --git a/src/neighbor.h b/src/neighbor.h index 4807e90393..8533fe5efa 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -175,6 +175,7 @@ class Neighbor : protected Pointers { double memory_usage(); bigint last_setup_bins; // step of last neighbor::setup_bins() call + double **get_xhold(); // access the latest-computed neighbor list positions protected: int me, nprocs; diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 6afb43bc16..75802567b7 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -17,6 +17,7 @@ #include "error.h" #include "my_page.h" #include "neigh_list.h" +#include "neigh_request.h" using namespace LAMMPS_NS; @@ -41,11 +42,13 @@ void NPairSkipTemp::build(NeighList *list) int *type = atom->type; int nlocal = atom->nlocal; + tagint *molecule = atom->molecule; int *ilist = list->ilist; int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; MyPage *ipage = list->ipage; + int molskip = list->molskip; int *ilist_skip = list->listskip->ilist; int *numneigh_skip = list->listskip->numneigh; @@ -71,7 +74,8 @@ void NPairSkipTemp::build(NeighList *list) for (ii = 0; ii < num_skip; ii++) { i = ilist_skip[ii]; itype = type[i]; - if (iskip[itype]) continue; + + if (!molskip && iskip[itype]) continue; if (TRIM) { xtmp = x[i][0]; @@ -90,7 +94,9 @@ void NPairSkipTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (ijskip[itype][type[j]]) continue; + if (!molskip && ijskip[itype][type[j]]) continue; + if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; + if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; if (TRIM) { delx = xtmp - x[j][0]; diff --git a/src/npair_skip.h b/src/npair_skip.h index cb0d201555..72e86d3a3e 100644 --- a/src/npair_skip.h +++ b/src/npair_skip.h @@ -30,7 +30,8 @@ NPairStyle(skip/ghost, typedef NPairSkipTemp<0> NPairSkipSize; NPairStyle(skip/half/size, NPairSkipSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI); typedef NPairSkipTemp<1> NPairSkipTrim; @@ -50,7 +51,8 @@ NPairStyle(skip/ghost/trim, typedef NPairSkipTemp<1> NPairSkipTrimSize; NPairStyle(skip/trim/half/size, NPairSkipTrimSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM); // clang-format on diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 4c3dda91eb..211aa6142a 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -18,6 +18,7 @@ #include "error.h" #include "my_page.h" #include "neigh_list.h" +#include "neigh_request.h" using namespace LAMMPS_NS; @@ -39,11 +40,13 @@ void NPairSkipRespaTemp::build(NeighList *list) int *neighptr, *jlist, *neighptr_inner, *neighptr_middle; int *type = atom->type; + tagint *molecule = atom->molecule; int *ilist = list->ilist; int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; MyPage *ipage = list->ipage; + int molskip = list->molskip; int *ilist_skip = list->listskip->ilist; int *numneigh_skip = list->listskip->numneigh; @@ -90,7 +93,7 @@ void NPairSkipRespaTemp::build(NeighList *list) for (ii = 0; ii < inum_skip; ii++) { i = ilist_skip[ii]; itype = type[i]; - if (iskip[itype]) continue; + if (!molskip && iskip[itype]) continue; if (TRIM) { xtmp = x[i][0]; @@ -114,7 +117,9 @@ void NPairSkipRespaTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (ijskip[itype][type[j]]) continue; + if (!molskip && ijskip[itype][type[j]]) continue; + if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; + if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; if (TRIM) { delx = xtmp - x[j][0]; @@ -135,7 +140,9 @@ void NPairSkipRespaTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (ijskip[itype][type[j]]) continue; + if (!molskip && ijskip[itype][type[j]]) continue; + if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; + if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; if (TRIM) { delx = xtmp - x[j][0]; @@ -157,7 +164,9 @@ void NPairSkipRespaTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (ijskip[itype][type[j]]) continue; + if (!molskip && ijskip[itype][type[j]]) continue; + if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; + if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; if (TRIM) { delx = xtmp - x[j][0]; diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 298fc26fd0..2c86b252ea 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -56,6 +56,9 @@ void PairDeprecated::settings(int, char **) utils::logmesg(lmp, "\nPair style 'mesont/tpm' has been removed from LAMMPS. " "Please use pair style 'mesocnt' instead\n\n"); + } else if (utils::strmatch(my_style, "^meam/c")) { + if (lmp->comm->me == 0) + utils::logmesg(lmp, "\nPair style 'meam/c' has been renamed to 'meam'\n\n"); } error->all(FLERR, "This pair style is no longer available"); } diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h index 1a705c9051..8db8b3541d 100644 --- a/src/pair_deprecated.h +++ b/src/pair_deprecated.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS // clang-format off PairStyle(DEPRECATED,PairDeprecated); +PairStyle(meam/c,PairDeprecated); PairStyle(reax,PairDeprecated); PairStyle(reax/c,PairDeprecated); PairStyle(mesont/tpm,PairDeprecated); diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index f05a201e33..09f233a4f6 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -321,11 +321,12 @@ void PairHybrid::settings(int narg, char **arg) iarg = 0; nstyles = 0; + const std::string mystyle = force->pair_style; while (iarg < narg) { if (utils::strmatch(arg[iarg],"^hybrid")) - error->all(FLERR,"Pair style hybrid cannot have hybrid as a sub-style"); + error->all(FLERR,"Pair style {} cannot have hybrid as a sub-style", mystyle); if (strcmp(arg[iarg],"none") == 0) - error->all(FLERR,"Pair style hybrid cannot have none as a sub-style"); + error->all(FLERR,"Pair style {} cannot have none as a sub-style", mystyle); styles[nstyles] = force->new_pair(arg[iarg],1,dummy); keywords[nstyles] = force->store_style(arg[iarg],0); @@ -345,6 +346,9 @@ void PairHybrid::settings(int narg, char **arg) nstyles++; } + if (utils::strmatch(mystyle,"^hybrid/molecular") && (nstyles != 2)) + error->all(FLERR, "Pair style {} must have exactly two sub-styles", mystyle); + delete[] cutmax_style; cutmax_style = new double[nstyles]; memset(cutmax_style, 0, nstyles*sizeof(double)); @@ -394,8 +398,7 @@ void PairHybrid::flags() for (m = 0; m < nstyles; m++) { if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward); if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse); - if (styles[m]) comm_reverse_off = MAX(comm_reverse_off, - styles[m]->comm_reverse_off); + if (styles[m]) comm_reverse_off = MAX(comm_reverse_off,styles[m]->comm_reverse_off); } // single_enable = 1 if all sub-styles are set @@ -521,8 +524,10 @@ void PairHybrid::coeff(int narg, char **arg) int none = 0; if (m == nstyles) { - if (strcmp(arg[2],"none") == 0) none = 1; - else error->all(FLERR,"Pair coeff for hybrid has invalid style: {}", arg[2]); + if (strcmp(arg[2],"none") == 0) + none = 1; + else + error->all(FLERR,"Expected hybrid sub-style instead of {} in pair_coeff command", arg[2]); } // move 1st/2nd args to 2nd/3rd args diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index d3a7693f9b..b59cc82cb4 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS // clang-format off PairStyle(hybrid,PairHybrid); +PairStyle(hybrid/omp,PairHybrid); // clang-format on #else diff --git a/src/pair_hybrid_molecular.cpp b/src/pair_hybrid_molecular.cpp new file mode 100644 index 0000000000..67b654da61 --- /dev/null +++ b/src/pair_hybrid_molecular.cpp @@ -0,0 +1,162 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_hybrid_molecular.h" + +#include "atom.h" +#include "error.h" +#include "neigh_request.h" +#include "neighbor.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairHybridMolecular::PairHybridMolecular(LAMMPS *lmp) : PairHybridOverlay(lmp) {} + +/* ---------------------------------------------------------------------- + modify neighbor list requests +------------------------------------------------------------------------- */ + +void PairHybridMolecular::init_style() +{ + if (!atom->molecule_flag) + error->all(FLERR, "Pair style hybrid/molecular requires atom attribute molecule"); + if (manybody_flag) + error->all(FLERR, "Pair style hybrid/molecular is not compatible with manybody potentials"); + + PairHybridOverlay::init_style(); + + // modify neighbor list requests + + bool first = true; + for (auto &request : neighbor->get_pair_requests()) { + if (first) { + request->set_molskip(NeighRequest::INTRA); + first = false; + } else { + request->set_molskip(NeighRequest::INTER); + } + } + born_matrix_enable = 0; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairHybridMolecular::init_one(int i, int j) +{ + // if I,J is not set explicitly: + // perform mixing only if I,I sub-style = J,J sub-style + // plus I,I and J,J need the same number of substyles + + if (setflag[i][j] == 0) { + if (nmap[i][i] != nmap[j][j]) + error->one(FLERR,"All pair coeffs are not set"); + int num = 0; + for (int k = 0; k < nmap[i][i]; ++k) { + for (int l = 0; l < nmap[j][j]; ++l) { + if (map[i][i][k] == map[j][j][l]) { + map[i][j][num] = map[i][i][k]; + ++num; + nmap[i][j] = num; + } + } + } + if (nmap[i][i] != nmap[i][j]) + error->one(FLERR,"All pair coeffs are not set"); + } + nmap[j][i] = nmap[i][j]; + + // call init/mixing for all sub-styles of I,J + // set cutsq in sub-style just as Pair::init() does via call to init_one() + // set cutghost for I,J and J,I just as sub-style does + // sum tail corrections for I,J + // return max cutoff of all sub-styles assigned to I,J + // if no sub-styles assigned to I,J (pair_coeff none), cutmax = 0.0 returned + + double cutmax = 0.0; + cutghost[i][j] = cutghost[j][i] = 0.0; + if (tail_flag) etail_ij = ptail_ij = 0.0; + + for (int k = 0; k < nmap[i][j]; k++) { + map[j][i][k] = map[i][j][k]; + double cut = styles[map[i][j][k]]->init_one(i,j); + if (styles[map[i][j][k]]->did_mix) did_mix = true; + styles[map[i][j][k]]->cutsq[i][j] = styles[map[i][j][k]]->cutsq[j][i] = cut*cut; + if (styles[map[i][j][k]]->ghostneigh) + cutghost[i][j] = cutghost[j][i] = MAX(cutghost[i][j],styles[map[i][j][k]]->cutghost[i][j]); + if (tail_flag) { + etail_ij += styles[map[i][j][k]]->etail_ij; + ptail_ij += styles[map[i][j][k]]->ptail_ij; + } + cutmax = MAX(cutmax,cut); + + int istyle; + for (istyle = 0; istyle < nstyles; istyle++) + if (styles[istyle] == styles[map[i][j][k]]) break; + + if (styles[istyle]->trim_flag) { + + if (cut > cutmax_style[istyle]) { + cutmax_style[istyle] = cut; + + for (auto &request : neighbor->get_pair_requests()) { + if (styles[istyle] == request->get_requestor()) { + request->set_cutoff(cutmax_style[istyle]); + break; + } + } + } + } + } + return cutmax; +} + +/* ---------------------------------------------------------------------- + call sub-style to compute single interaction + error if sub-style does not support single() call + since overlay could have multiple sub-styles, sum results explicitly +------------------------------------------------------------------------- */ + +double PairHybridMolecular::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &fforce) +{ + if (nmap[itype][jtype] == 0) + error->one(FLERR,"Invoked pair single() on sub-style none"); + + double fone; + fforce = 0.0; + double esum = 0.0; + if (nmap[itype][jtype] == 2) { + int m = 0; + if (atom->molecule[i] != atom->molecule[j]) m = 1; + const int mystyle = map[itype][jtype][m]; + if (rsq < styles[mystyle]->cutsq[itype][jtype]) { + if (styles[mystyle]->single_enable == 0) + error->one(FLERR,"Pair hybrid/molecular sub-style {} does not support single() call", + keywords[mystyle]); + + if ((special_lj[mystyle] != nullptr) || (special_coul[mystyle] != nullptr)) + error->one(FLERR,"Pair hybrid/molecular single() calls do not support per sub-style " + "special bond values"); + + esum += styles[mystyle]->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fone); + fforce += fone; + } + } + + if (single_extra) copy_svector(itype,jtype); + return esum; +} diff --git a/src/pair_hybrid_molecular.h b/src/pair_hybrid_molecular.h new file mode 100644 index 0000000000..92f8bdc198 --- /dev/null +++ b/src/pair_hybrid_molecular.h @@ -0,0 +1,41 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(hybrid/molecular,PairHybridMolecular); +PairStyle(hybrid/molecular/omp,PairHybridMolecular); +// clang-format on +#else + +#ifndef LMP_PAIR_HYBRID_MOLECULAR_H +#define LMP_PAIR_HYBRID_MOLECULAR_H + +#include "pair_hybrid_overlay.h" + +namespace LAMMPS_NS { + +class PairHybridMolecular : public PairHybridOverlay { + public: + PairHybridMolecular(class LAMMPS *); + + void init_style() override; + double init_one(int, int) override; + + double single(int, int, int, int, double, double, double, double &) override; +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 118403d345..4211d0e5cb 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -59,8 +59,10 @@ void PairHybridOverlay::coeff(int narg, char **arg) int none = 0; if (m == nstyles) { - if (strcmp(arg[2],"none") == 0) none = 1; - else error->all(FLERR,"Pair coeff for hybrid has invalid style: {}", arg[2]); + if (strcmp(arg[2],"none") == 0) + none = 1; + else + error->all(FLERR,"Expected hybrid sub-style instead of {} in pair_coeff command", arg[2]); } // move 1st/2nd args to 2nd/3rd args diff --git a/src/pair_hybrid_overlay.h b/src/pair_hybrid_overlay.h index ea0babbde5..f0e85b859f 100644 --- a/src/pair_hybrid_overlay.h +++ b/src/pair_hybrid_overlay.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS // clang-format off PairStyle(hybrid/overlay,PairHybridOverlay); +PairStyle(hybrid/overlay/omp,PairHybridOverlay); // clang-format on #else diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 69ff037e4a..e897c784c7 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -516,7 +516,7 @@ void PairHybridScaled::coeff(int narg, char **arg) if (strcmp(arg[2], "none") == 0) none = 1; else - error->all(FLERR, "Pair coeff for hybrid has invalid style: {}", arg[2]); + error->all(FLERR, "Expected hybrid sub-style instead of {} in pair_coeff command", arg[2]); } // move 1st/2nd args to 2nd/3rd args diff --git a/src/pair_hybrid_scaled.h b/src/pair_hybrid_scaled.h index 64fd938822..2af5b61f8d 100644 --- a/src/pair_hybrid_scaled.h +++ b/src/pair_hybrid_scaled.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS // clang-format off PairStyle(hybrid/scaled,PairHybridScaled); +PairStyle(hybrid/scaled/omp,PairHybridScaled); // clang-format on #else diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 66c4c1f9cd..cba6c742ab 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -39,6 +39,8 @@ PairSoft::PairSoft(LAMMPS *lmp) : Pair(lmp) PairSoft::~PairSoft() { + if (copymode) return; + if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); diff --git a/src/pair_soft.h b/src/pair_soft.h index 8fd1654609..d011b16322 100644 --- a/src/pair_soft.h +++ b/src/pair_soft.h @@ -49,7 +49,7 @@ class PairSoft : public Pair { double **prefactor; double **cut; - void allocate(); + virtual void allocate(); }; } // namespace LAMMPS_NS diff --git a/src/platform.cpp b/src/platform.cpp index b324bd0b5c..7cc4815f51 100644 --- a/src/platform.cpp +++ b/src/platform.cpp @@ -248,13 +248,10 @@ std::string platform::os_info() buf = "Windows 11 22H2"; } else if (build == "22631") { buf = "Windows 11 23H2"; + } else if (build == "26100") { + buf = "Windows 11 24H2"; } else { - const char *entry = "ProductName"; - RegGetValue(HKEY_LOCAL_MACHINE, subkey, entry, RRF_RT_REG_SZ, nullptr, &value, - (LPDWORD) &value_length); - // enforce zero termination - value[1023] = '\0'; - buf = value; + buf = "Windows Build " + build; } DWORD fullversion, majorv, minorv, buildv = 0; fullversion = GetVersion(); diff --git a/src/procmap.cpp b/src/procmap.cpp index 71e1cf5a6b..b520354f53 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -150,13 +150,9 @@ void ProcMap::twolevel_grid(int nprocs, int *user_procgrid, int *procgrid, auto-detects NUMA sockets within a multi-core node ------------------------------------------------------------------------- */ -void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid, - int *numagrid) +void ProcMap::numa_grid(int numa_nodes, int nprocs, int *user_procgrid, + int *procgrid, int *numagrid) { - // hardwire this for now - - int numa_nodes = 1; - // get names of all nodes int name_length; @@ -181,6 +177,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid, } procs_per_node = name_map.begin()->second; procs_per_numa = procs_per_node / numa_nodes; + if (procs_per_numa < 1) procs_per_numa = 1; delete [] node_names; @@ -192,6 +189,24 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid, user_procgrid[2] > 1) error->all(FLERR,"Could not create numa grid of processors"); + // factorization for the grid of NUMA nodes + + int node_count = nprocs / procs_per_numa; + + int **nodefactors; + int nodepossible = factor(node_count,nullptr); + memory->create(nodefactors,nodepossible,3,"procmap:nodefactors"); + nodepossible = factor(node_count,nodefactors); + + if (domain->dimension == 2) + nodepossible = cull_2d(nodepossible,nodefactors,3); + nodepossible = cull_user(nodepossible,nodefactors,3,user_procgrid); + + if (nodepossible == 0) + error->all(FLERR,"Could not create numa grid of processors"); + + best_factors(nodepossible,nodefactors,nodegrid,1,1,1); + // user settings for the factorization per numa node // currently not user settable // if user specifies 1 for a proc grid dimension, @@ -204,6 +219,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid, if (user_procgrid[1] == 1) user_numagrid[1] = 1; if (user_procgrid[2] == 1) user_numagrid[2] = 1; + // perform NUMA node factorization using subdomain sizes // initial factorization within NUMA node int **numafactors; @@ -218,38 +234,6 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid, if (numapossible == 0) error->all(FLERR,"Could not create numa grid of processors"); - best_factors(numapossible,numafactors,numagrid,1,1,1); - - // user_nodegrid = implied user constraints on nodes - - int user_nodegrid[3]; - user_nodegrid[0] = user_procgrid[0] / numagrid[0]; - user_nodegrid[1] = user_procgrid[1] / numagrid[1]; - user_nodegrid[2] = user_procgrid[2] / numagrid[2]; - - // factorization for the grid of NUMA nodes - - int node_count = nprocs / procs_per_numa; - - int **nodefactors; - int nodepossible = factor(node_count,nullptr); - memory->create(nodefactors,nodepossible,3,"procmap:nodefactors"); - nodepossible = factor(node_count,nodefactors); - - if (domain->dimension == 2) - nodepossible = cull_2d(nodepossible,nodefactors,3); - nodepossible = cull_user(nodepossible,nodefactors,3,user_nodegrid); - - if (nodepossible == 0) - error->all(FLERR,"Could not create numa grid of processors"); - - best_factors(nodepossible,nodefactors,nodegrid, - numagrid[0],numagrid[1],numagrid[2]); - - // repeat NUMA node factorization using subdomain sizes - // refines the factorization if the user specified the node layout - // NOTE: this will not re-enforce user-procgrid constraint will it? - best_factors(numapossible,numafactors,numagrid, nodegrid[0],nodegrid[1],nodegrid[2]); @@ -270,6 +254,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid, procgrid[0] = nodegrid[0] * numagrid[0]; procgrid[1] = nodegrid[1] * numagrid[1]; procgrid[2] = nodegrid[2] * numagrid[2]; + } /* ---------------------------------------------------------------------- diff --git a/src/procmap.h b/src/procmap.h index 06867837c6..2731aec984 100644 --- a/src/procmap.h +++ b/src/procmap.h @@ -24,7 +24,7 @@ class ProcMap : protected Pointers { void onelevel_grid(int, int *, int *, int, int, int *, int *); void twolevel_grid(int, int *, int *, int, int *, int *, int, int, int *, int *); - void numa_grid(int, int *, int *, int *); + void numa_grid(int, int, int *, int *, int *); void custom_grid(char *, int, int *, int *); void cart_map(int, int *, int *, int[3][2], int ***); void cart_map(int, int *, int, int *, int *, int[3][2], int ***); diff --git a/src/read_data.cpp b/src/read_data.cpp index 657369d5d0..d83456e985 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -479,6 +479,9 @@ void ReadData::command(int narg, char **arg) bondflag = angleflag = dihedralflag = improperflag = 0; ellipsoidflag = lineflag = triflag = bodyflag = 0; + xloxhi_flag = yloyhi_flag = zlozhi_flag = tilt_flag = 0; + avec_flag = bvec_flag = cvec_flag = abc_origin_flag = 0; + // values in this data file natoms = 0; @@ -488,7 +491,15 @@ void ReadData::command(int narg, char **arg) boxlo[0] = boxlo[1] = boxlo[2] = -0.5; boxhi[0] = boxhi[1] = boxhi[2] = 0.5; - triclinic = 0; + xy = xz = yz = 0.0; + + avec[0] = bvec[1] = cvec[2] = 1.0; + avec[1] = avec[2] = 0.0; + bvec[0] = bvec[2] = 0.0; + cvec[0] = cvec[1] = 0.0; + abc_origin[0] = abc_origin[1] = abc_origin[2] = 0.0; + if (domain->dimension == 2) abc_origin[2] = -0.5; + keyword[0] = '\0'; nlocal_previous = atom->nlocal; @@ -508,6 +519,30 @@ void ReadData::command(int narg, char **arg) header(firstpass); + // check if simulation box specified consistently + + if (!avec_flag && !bvec_flag && !cvec_flag && !abc_origin_flag) { + triclinic = triclinic_general = 0; + if (tilt_flag) triclinic = 1; + } else { + if (xloxhi_flag || yloyhi_flag || zlozhi_flag || tilt_flag) + error->all(FLERR,"Read_data header cannot specify simulation box lo/hi/tilt and ABC vectors"); + triclinic = triclinic_general = 1; + } + + // check if simulation box specified correctly for 2d + + if (domain->dimension == 2) { + if (triclinic_general == 0) { + if (boxlo[2] >= 0.0 || boxhi[2] <= 0.0) + error->all(FLERR,"Read_data zlo/zhi for 2d simulation must straddle 0.0"); + } else if (triclinic_general == 1) { + if (cvec[0] != 0.0 || cvec[1] != 0.0 || cvec[2] != 1.0 || abc_origin[2] != -0.5) + error->all(FLERR,"Read_data cvec and/or abc_origin is invalid for " + "2d simulation with general triclinic box"); + } + } + // problem setup using info from header // only done once, if firstpass and first data file // apply extra settings before grow(), even if no topology in file @@ -536,31 +571,80 @@ void ReadData::command(int narg, char **arg) n = static_cast(nbig); atom->avec->grow(n); - domain->boxlo[0] = boxlo[0]; - domain->boxhi[0] = boxhi[0]; - domain->boxlo[1] = boxlo[1]; - domain->boxhi[1] = boxhi[1]; - domain->boxlo[2] = boxlo[2]; - domain->boxhi[2] = boxhi[2]; + // setup simulation box + // 3 options: orthogonal, restricted triclinic, general triclinic - if (triclinic) { - domain->triclinic = 1; - domain->xy = xy; - domain->xz = xz; - domain->yz = yz; + if (!triclinic_general) { + + // orthogonal or restricted triclinic box + + domain->boxlo[0] = boxlo[0]; + domain->boxhi[0] = boxhi[0]; + domain->boxlo[1] = boxlo[1]; + domain->boxhi[1] = boxhi[1]; + domain->boxlo[2] = boxlo[2]; + domain->boxhi[2] = boxhi[2]; + + // restricted triclinic box + + if (triclinic) { + domain->triclinic = 1; + domain->xy = xy; + domain->xz = xz; + domain->yz = yz; + } + + // general triclinic box + // define_general_triclinic() converts + // ABC edge vectors + abc_origin to restricted triclinic + + } else if (triclinic_general) { + domain->define_general_triclinic(avec,bvec,cvec,abc_origin); } - - domain->print_box(" "); - domain->set_initial_box(); - domain->set_global_box(); - comm->set_proc_grid(); - domain->set_local_box(); } // change simulation box to be union of existing box and new box + shift // only done if firstpass and not first data file if (firstpass && addflag != NONE) { + + // general triclinic + // first data file must also be general triclinic + // avec,bvec,vec and origin must match first data file + // shift not allowed + + if (triclinic_general) { + if (!domain->triclinic_general) + error->all(FLERR,"Read_data subsequent file cannot switch to general triclinic"); + int errflag = 0; + if (avec[0] != domain->avec[0] || avec[1] != domain->avec[1] || avec[2] != domain->avec[2]) + errflag = 1; + if (bvec[0] != domain->bvec[0] || bvec[1] != domain->bvec[1] || bvec[2] != domain->bvec[2]) + errflag = 1; + if (cvec[0] != domain->cvec[0] || cvec[1] != domain->cvec[1] || cvec[2] != domain->cvec[2]) + errflag = 1; + if (abc_origin[0] != domain->boxlo[0] || abc_origin[1] != domain->boxlo[1] || + abc_origin[2] != domain->boxlo[2]) + errflag = 1; + if (errflag) + error->all(FLERR,"Read_data subsequent file ABC vectors must be same as first file"); + if (shift[0] != 0.0 || shift[1] != 0.0 || shift[2] != 0.0) + error->all(FLERR,"Read_data subsequent file with ABC vectors cannot define shift"); + + // restricted triclinic + // tilt factors must match first data file + + } else if (triclinic) { + if (!domain->triclinic || domain->triclinic_general) + error->all(FLERR,"Read_data subsequent file cannot switch to restricted triclinic"); + if (xy != domain->xy || xz != domain->xz || yz != domain->yz) + error->all(FLERR,"Read_data subsequent file tilt factors must be same as first file"); + + } else { + if (domain->triclinic) + error->all(FLERR,"Read_data subsequent file cannot switch to orthogonal"); + } + double oldboxlo[3] = {domain->boxlo[0], domain->boxlo[1], domain->boxlo[2]}; double oldboxhi[3] = {domain->boxhi[0], domain->boxhi[1], domain->boxhi[2]}; domain->boxlo[0] = MIN(domain->boxlo[0], boxlo[0] + shift[0]); @@ -570,7 +654,9 @@ void ReadData::command(int narg, char **arg) domain->boxlo[2] = MIN(domain->boxlo[2], boxlo[2] + shift[2]); domain->boxhi[2] = MAX(domain->boxhi[2], boxhi[2] + shift[2]); - // check of box has changed. If yes, warn about non-zero image flags + // check if box has changed + // if yes, warn about non-zero image flags + if ((oldboxlo[0] != domain->boxlo[0]) || (oldboxlo[1] != domain->boxlo[1]) || (oldboxlo[2] != domain->boxlo[2]) || (oldboxhi[0] != domain->boxhi[0]) || (oldboxhi[1] != domain->boxhi[1]) || (oldboxhi[2] != domain->boxhi[2])) { @@ -586,21 +672,18 @@ void ReadData::command(int narg, char **arg) int flag_all; MPI_Allreduce(&iflag, &flag_all, 1, MPI_INT, MPI_SUM, world); if ((flag_all > 0) && (comm->me == 0)) - error->warning(FLERR, "Non-zero image flags with growing box leads to bad coordinates"); + error->warning(FLERR, "Non-zero image flags with growing box can produce bad coordinates"); } - - // NOTE: not sure what to do about tilt value in subsequent data files - //if (triclinic) { - // domain->xy = xy; domain->xz = xz; domain->yz = yz; - // } - - domain->print_box(" "); - domain->set_initial_box(); - domain->set_global_box(); - comm->set_proc_grid(); - domain->set_local_box(); } + // setup simulation box and paritioning in Domain and Comm classes + + domain->print_box(" "); + domain->set_initial_box(); + domain->set_global_box(); + comm->set_proc_grid(); + domain->set_local_box(); + // allocate space for type label map if (firstpass) { @@ -608,8 +691,10 @@ void ReadData::command(int narg, char **arg) lmap = new LabelMap(lmp, ntypes, nbondtypes, nangletypes, ndihedraltypes, nimpropertypes); } + // ------------------------------------------------------------------------------------- + // rest of data file is Sections + // read in any order, except where error checks // customize for new sections - // read rest of file in free format while (strlen(keyword)) { @@ -980,6 +1065,12 @@ void ReadData::command(int narg, char **arg) atom->avec->grow(atom->nmax); } + // if general triclinic, perform general to restricted rotation operation + // on any quantities read from data file which require it + + if (triclinic_general) + atom->avec->read_data_general_to_restricted(nlocal_previous, atom->nlocal); + // init per-atom fix/compute/variable values for created atoms atom->data_fix_compute_variable(nlocal_previous, atom->nlocal); @@ -1140,7 +1231,8 @@ void ReadData::header(int firstpass) // initialize type counts by the "extra" numbers so they get counted // in case the corresponding "types" line is missing and thus the extra - // value will not be processed. + // value will not be processed + if (addflag == NONE) { atom->ntypes = extra_atom_types; atom->nbondtypes = extra_bond_types; @@ -1156,6 +1248,7 @@ void ReadData::header(int firstpass) if (eof == nullptr) error->one(FLERR, "Unexpected end of data file"); // check for units keyword in first line and print warning on mismatch + auto units = Tokenizer(utils::strfind(line, "units = \\w+")).as_vector(); if (units.size() > 2) { if (units[2] != update->unit_style) @@ -1278,7 +1371,7 @@ void ReadData::header(int firstpass) else if (firstpass) atom->nimpropers += nimpropers; - // Atom class type settings are only set by first data file + // Atom class type settings are only set by first data file } else if (utils::strmatch(line, "^\\s*\\d+\\s+atom\\s+types\\s")) { ntypes = utils::inumeric(FLERR, words[0], false, lmp); @@ -1300,11 +1393,10 @@ void ReadData::header(int firstpass) nimpropertypes = utils::inumeric(FLERR, words[0], false, lmp); if (addflag == NONE) atom->nimpropertypes = nimpropertypes + extra_improper_types; - // these settings only used by first data file - // also, these are obsolescent. we parse them to maintain backward - // compatibility, but the recommended way is to set them via keywords - // in the LAMMPS input file. In case these flags are set in both, - // the input and the data file, we use the larger of the two. + // these settings only used by first data file + // NOTE: these are now obsolete, we parse them to maintain backward compatibility + // the recommended way is to set them via command keywords in the input script + // if these flags are set both ways, the larger of the two values is used } else if (strstr(line, "extra bond per atom")) { if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp); @@ -1322,27 +1414,54 @@ void ReadData::header(int firstpass) if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp); force->special_extra = MAX(force->special_extra, extra_flag_value); - // local copy of box info - // so can treat differently for first vs subsequent data files + // local copy of box info + // so can treat differently for first vs subsequent data files } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi\\s")) { + xloxhi_flag = 1; boxlo[0] = utils::numeric(FLERR, words[0], false, lmp); boxhi[0] = utils::numeric(FLERR, words[1], false, lmp); } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi\\s")) { + yloyhi_flag = 1; boxlo[1] = utils::numeric(FLERR, words[0], false, lmp); boxhi[1] = utils::numeric(FLERR, words[1], false, lmp); } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi\\s")) { + zlozhi_flag = 1; boxlo[2] = utils::numeric(FLERR, words[0], false, lmp); boxhi[2] = utils::numeric(FLERR, words[1], false, lmp); } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+xy\\s+xz\\s+yz\\s")) { - triclinic = 1; + tilt_flag = 1; xy = utils::numeric(FLERR, words[0], false, lmp); xz = utils::numeric(FLERR, words[1], false, lmp); yz = utils::numeric(FLERR, words[2], false, lmp); + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\avec\\s")) { + avec_flag = 1; + avec[0] = utils::numeric(FLERR, words[0], false, lmp); + avec[1] = utils::numeric(FLERR, words[1], false, lmp); + avec[2] = utils::numeric(FLERR, words[2], false, lmp); + + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\bvec\\s")) { + bvec_flag = 1; + bvec[0] = utils::numeric(FLERR, words[0], false, lmp); + bvec[1] = utils::numeric(FLERR, words[1], false, lmp); + bvec[2] = utils::numeric(FLERR, words[2], false, lmp); + + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\cvec\\s")) { + cvec_flag = 1; + cvec[0] = utils::numeric(FLERR, words[0], false, lmp); + cvec[1] = utils::numeric(FLERR, words[1], false, lmp); + cvec[2] = utils::numeric(FLERR, words[2], false, lmp); + + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\abc\\s+origin\\s")) { + abc_origin_flag = 1; + abc_origin[0] = utils::numeric(FLERR, words[0], false, lmp); + abc_origin[1] = utils::numeric(FLERR, words[1], false, lmp); + abc_origin[2] = utils::numeric(FLERR, words[2], false, lmp); + } else break; } @@ -1360,7 +1479,8 @@ void ReadData::header(int firstpass) // check that exiting string is a valid section keyword parse_keyword(1); - if (!is_data_section(keyword)) error->all(FLERR, "Unknown identifier in data file: {}", keyword); + if (!is_data_section(keyword)) + error->all(FLERR, "Unknown identifier in data file: {}{}", keyword, utils::errorurl(1)); // error checks on header values // must be consistent with atom style and other header values @@ -1407,8 +1527,8 @@ void ReadData::atoms() if (eof) error->all(FLERR, "Unexpected end of data file"); if (tlabelflag && !lmap->is_complete(Atom::ATOM)) error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label"); - atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, shiftflag, shift, tlabelflag, - lmap->lmap2lmap.atom); + atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, + shiftflag, shift, tlabelflag, lmap->lmap2lmap.atom, triclinic_general); nread += nchunk; } diff --git a/src/read_data.h b/src/read_data.h index e97f225997..008283251c 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -59,11 +59,16 @@ class ReadData : public Command { class LabelMap *lmap; - // box info + // box info read from file + + int triclinic, triclinic_general; + int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag; + int avec_flag, bvec_flag, cvec_flag, abc_origin_flag; double boxlo[3], boxhi[3]; double xy, xz, yz; - int triclinic; + double avec[3], bvec[3], cvec[3]; + double abc_origin[3]; // optional args diff --git a/src/read_restart.cpp b/src/read_restart.cpp index c538702728..ee46d57fc3 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -28,6 +28,7 @@ #include "improper.h" #include "irregular.h" #include "label_map.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "pair.h" @@ -783,6 +784,12 @@ void ReadRestart::header() } else if (flag == YZ) { domain->yz = read_double(); + } else if (flag == TRICLINIC_GENERAL) { + domain->triclinic_general = read_int(); + } else if (flag == ROTATE_G2R) { + read_double_vec(9,&domain->rotate_g2r[0][0]); + MathExtra::transpose3(domain->rotate_g2r,domain->rotate_r2g); + } else if (flag == SPECIAL_LJ) { read_int(); read_double_vec(3,&force->special_lj[1]); diff --git a/src/reader_native.cpp b/src/reader_native.cpp index ae59ca6805..4dac65e3cb 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -289,7 +289,7 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, labelline = line + strlen("ITEM: ATOMS "); } - Tokenizer tokens(labelline); + Tokenizer tokens(std::move(labelline)); std::map labels; nwords = 0; diff --git a/src/replicate.cpp b/src/replicate.cpp index b27304a2a0..15c477faa6 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -12,6 +12,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: + Chris Knight (ANL) for bbox option + Jake Gissinger (Stevens Institute of Technology) for bond/periodic option +------------------------------------------------------------------------- */ + #include "replicate.h" #include "accelerator_kokkos.h" @@ -20,29 +26,34 @@ #include "comm.h" #include "domain.h" #include "error.h" +#include "label_map.h" #include "memory.h" #include "special.h" -#include "label_map.h" #include using namespace LAMMPS_NS; static constexpr double LB_FACTOR = 1.1; -static constexpr double EPSILON = 1.0e-6; +static constexpr double EPSILON = 1.0e-6; /* ---------------------------------------------------------------------- */ -Replicate::Replicate(LAMMPS *lmp) : Command(lmp) {} +Replicate::Replicate(LAMMPS *lmp) : Command(lmp), old(nullptr), old_x(nullptr), old_tag(nullptr) +{ + bbox_flag = 0; + bond_flag = 0; +} /* ---------------------------------------------------------------------- */ void Replicate::command(int narg, char **arg) { - int i,j,m,n; + int i,n; if (domain->box_exist == 0) error->all(FLERR,"Replicate command before simulation box is defined"); + if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command"); int me = comm->me; @@ -63,13 +74,27 @@ void Replicate::command(int narg, char **arg) "Please use replicate multiple times", nx, ny, nz, nrepbig); int nrep = (int) nrepbig; + allnrep[0] = nx; + allnrep[1] = ny; + allnrep[2] = nz; if (me == 0) utils::logmesg(lmp, "Replication is creating a {}x{}x{} = {} times larger system...\n", nx, ny, nz, nrep); - int bbox_flag = 0; - if (narg == 4) - if (strcmp(arg[3],"bbox") == 0) bbox_flag = 1; + // optional keywords + + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"bbox") == 0) { + bbox_flag = 1; + iarg++; + } else if (strcmp(arg[iarg],"bond/periodic") == 0) { + bond_flag = 1; + iarg++; + } else error->all(FLERR,"Illegal replicate command"); + } + + if (bond_flag) bbox_flag = 1; // error and warning checks @@ -85,16 +110,16 @@ void Replicate::command(int narg, char **arg) } if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store) - error->all(FLERR,"Cannot replicate with fixes that store atom quantities"); + error->all(FLERR,"Cannot replicate with fixes that store per-atom quantities"); // record wall time for atom replication MPI_Barrier(world); double time1 = platform::walltime(); - // maxtag = largest atom tag across all existing atoms + // maxtag = original largest atom tag across all existing atoms - tagint maxtag = 0; + maxtag = 0; if (atom->tag_enable) { for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag); tagint maxtag_all; @@ -104,7 +129,7 @@ void Replicate::command(int narg, char **arg) // maxmol = largest molecule tag across all existing atoms - tagint maxmol = 0; + maxmol = 0; if (atom->molecule_flag) { for (i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol); tagint maxmol_all; @@ -112,10 +137,16 @@ void Replicate::command(int narg, char **arg) maxmol = maxmol_all; } - // check image flags maximum extent + // reset image flags to zero for bond/periodic option + + if (bond_flag) + for (i=0; inlocal; ++i) + atom->image[i] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + + // _imagelo/hi = maximum extent of image flags in each dimension // only efficient small image flags compared to new system - int _imagelo[3], _imagehi[3]; _imagelo[0] = 0; _imagelo[1] = 0; _imagelo[2] = 0; @@ -123,7 +154,7 @@ void Replicate::command(int narg, char **arg) _imagehi[1] = 0; _imagehi[2] = 0; - if (bbox_flag) { + if (bbox_flag || bond_flag) { for (i=0; inlocal; ++i) { imageint image = atom->image[i]; @@ -145,14 +176,14 @@ void Replicate::command(int narg, char **arg) } // unmap existing atoms via image flags + // no-op for bond/periodic option for (i = 0; i < atom->nlocal; i++) domain->unmap(atom->x[i],atom->image[i]); // communication buffer for all my atom's info // max_size = largest buffer needed by any proc - // must do before new Atom class created, - // since size_restart() uses atom->nlocal + // must do before new Atom class created, since size_restart() uses atom->nlocal int max_size; int send_size = atom->avec->size_restart(); @@ -165,7 +196,7 @@ void Replicate::command(int narg, char **arg) // atom = new replicated atom class // also set atomKK for Kokkos version of Atom class - Atom *old = atom; + old = atom; atomKK = nullptr; if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp); else atom = new Atom(lmp); @@ -204,7 +235,7 @@ void Replicate::command(int narg, char **arg) nrep*old->nimpropers < 0 || nrep*old->nimpropers >= MAXBIGINT) error->all(FLERR,"Replicated system is too big"); - // assign atom and topology counts in new class from old one + // assign atom and topology counts in new Atom class from old Atom class atom->natoms = old->natoms * nrep; atom->nbonds = old->nbonds * nrep; @@ -246,14 +277,18 @@ void Replicate::command(int narg, char **arg) // store old simulation box int triclinic = domain->triclinic; - double old_xprd = domain->xprd; - double old_yprd = domain->yprd; - double old_zprd = domain->zprd; - double old_xy = domain->xy; - double old_xz = domain->xz; - double old_yz = domain->yz; + old_xprd = domain->xprd; + old_yprd = domain->yprd; + old_zprd = domain->zprd; + for (i = 0; i < 3; i++) { + old_prd_half[i] = domain->prd_half[i]; + old_center[i] = 0.5*(domain->boxlo[i]+domain->boxhi[i]); + } + old_xy = domain->xy; + old_xz = domain->xz; + old_yz = domain->yz; - // setup new simulation box + // define new simulation box domain->boxhi[0] = domain->boxlo[0] + nx*old_xprd; domain->boxhi[1] = domain->boxlo[1] + ny*old_yprd; @@ -264,15 +299,14 @@ void Replicate::command(int narg, char **arg) domain->yz *= nz; } - // new problem setup using new box boundaries + // setup of new system using new atom counts and new box boundaries + // allocate atom arrays to size N, rounded up by AtomVec->DELTA if (nprocs == 1) n = static_cast (atom->natoms); else n = static_cast (LB_FACTOR * atom->natoms / nprocs); atom->allocate_type_arrays(); - // allocate atom arrays to size N, rounded up by AtomVec->DELTA - bigint nbig = n; nbig = atom->avec->roundup(nbig); n = static_cast (nbig); @@ -346,420 +380,13 @@ void Replicate::command(int narg, char **arg) } } - // loop over all procs - // if this iteration of loop is me: - // pack my unmapped atom data into buf - // bcast it to all other procs - // performs 3d replicate loop with while loop over atoms in buf - // x = new replicated position, remapped into simulation box - // unpack atom into new atom class from buf if I own it - // adjust tag, mol #, coord, topology info as needed + // use one of two algorithms for replication - AtomVec *old_avec = old->avec; - AtomVec *avec = atom->avec; - - int ix,iy,iz; - tagint atom_offset,mol_offset; - imageint image; - double x[3],lamda[3]; - double *coord; - int tag_enable = atom->tag_enable; - - if (bbox_flag) { - - // allgather size of buf on each proc - - n = 0; - for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]); - - int * size_buf_rnk; - memory->create(size_buf_rnk, nprocs, "replicate:size_buf_rnk"); - - MPI_Allgather(&n, 1, MPI_INT, size_buf_rnk, 1, MPI_INT, world); - - // size of buf_all - - int size_buf_all = 0; - MPI_Allreduce(&n, &size_buf_all, 1, MPI_INT, MPI_SUM, world); - - if (me == 0) { - auto mesg = fmt::format(" bounding box image = ({} {} {}) " - "to ({} {} {})\n", - _imagelo[0],_imagelo[1],_imagelo[2], - _imagehi[0],_imagehi[1],_imagehi[2]); - mesg += fmt::format(" bounding box extra memory = {:.2f} MB\n", - (double)size_buf_all*sizeof(double)/1024/1024); - utils::logmesg(lmp,mesg); - } - - // rnk offsets - - int *disp_buf_rnk; - memory->create(disp_buf_rnk, nprocs, "replicate:disp_buf_rnk"); - disp_buf_rnk[0] = 0; - for (i = 1; i < nprocs; i++) - disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1]; - - // allgather buf_all - - double * buf_all; - memory->create(buf_all, size_buf_all, "replicate:buf_all"); - - MPI_Allgatherv(buf,n,MPI_DOUBLE,buf_all,size_buf_rnk,disp_buf_rnk, - MPI_DOUBLE,world); - - // bounding box of original unwrapped system - - double _orig_lo[3], _orig_hi[3]; - if (triclinic) { - _orig_lo[0] = domain->boxlo[0] + - _imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz; - _orig_lo[1] = domain->boxlo[1] + - _imagelo[1] * old_yprd + _imagelo[2] * old_yz; - _orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd; - - _orig_hi[0] = domain->boxlo[0] + - (_imagehi[0]+1) * old_xprd + - (_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz; - _orig_hi[1] = domain->boxlo[1] + - (_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz; - _orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd; - } else { - _orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd; - _orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd; - _orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd; - - _orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd; - _orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd; - _orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd; - } - - double _lo[3], _hi[3]; - - int num_replicas_added = 0; - - for (ix = 0; ix < nx; ix++) { - for (iy = 0; iy < ny; iy++) { - for (iz = 0; iz < nz; iz++) { - - // domain->remap() overwrites coordinates, so always recompute here - - if (triclinic) { - _lo[0] = _orig_lo[0] + ix * old_xprd + iy * old_xy + iz * old_xz; - _hi[0] = _orig_hi[0] + ix * old_xprd + iy * old_xy + iz * old_xz; - - _lo[1] = _orig_lo[1] + iy * old_yprd + iz * old_yz; - _hi[1] = _orig_hi[1] + iy * old_yprd + iz * old_yz; - - _lo[2] = _orig_lo[2] + iz * old_zprd; - _hi[2] = _orig_hi[2] + iz * old_zprd; - } else { - _lo[0] = _orig_lo[0] + ix * old_xprd; - _hi[0] = _orig_hi[0] + ix * old_xprd; - - _lo[1] = _orig_lo[1] + iy * old_yprd; - _hi[1] = _orig_hi[1] + iy * old_yprd; - - _lo[2] = _orig_lo[2] + iz * old_zprd; - _hi[2] = _orig_hi[2] + iz * old_zprd; - } - - // test if bounding box of shifted replica overlaps sub-domain of proc - // if not, then skip testing atoms - - int xoverlap = 1; - int yoverlap = 1; - int zoverlap = 1; - if (triclinic) { - double _llo[3]; - domain->x2lamda(_lo,_llo); - double _lhi[3]; - domain->x2lamda(_hi,_lhi); - - if (_llo[0] > (subhi[0] - EPSILON) - || _lhi[0] < (sublo[0] + EPSILON) ) xoverlap = 0; - if (_llo[1] > (subhi[1] - EPSILON) - || _lhi[1] < (sublo[1] + EPSILON) ) yoverlap = 0; - if (_llo[2] > (subhi[2] - EPSILON) - || _lhi[2] < (sublo[2] + EPSILON) ) zoverlap = 0; - } else { - if (_lo[0] > (subhi[0] - EPSILON) - || _hi[0] < (sublo[0] + EPSILON) ) xoverlap = 0; - if (_lo[1] > (subhi[1] - EPSILON) - || _hi[1] < (sublo[1] + EPSILON) ) yoverlap = 0; - if (_lo[2] > (subhi[2] - EPSILON) - || _hi[2] < (sublo[2] + EPSILON) ) zoverlap = 0; - } - - int overlap = 0; - if (xoverlap && yoverlap && zoverlap) overlap = 1; - - // if no overlap, test if bounding box wrapped back into new system - - if (!overlap) { - - // wrap back into cell - - imageint imagelo = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - domain->remap(&(_lo[0]), imagelo); - int xboxlo = (imagelo & IMGMASK) - IMGMAX; - int yboxlo = (imagelo >> IMGBITS & IMGMASK) - IMGMAX; - int zboxlo = (imagelo >> IMG2BITS) - IMGMAX; - - imageint imagehi = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - domain->remap(&(_hi[0]), imagehi); - int xboxhi = (imagehi & IMGMASK) - IMGMAX; - int yboxhi = (imagehi >> IMGBITS & IMGMASK) - IMGMAX; - int zboxhi = (imagehi >> IMG2BITS) - IMGMAX; - - if (triclinic) { - double _llo[3]; - _llo[0] = _lo[0]; _llo[1] = _lo[1]; _llo[2] = _lo[2]; - domain->x2lamda(_llo,_lo); - - double _lhi[3]; - _lhi[0] = _hi[0]; _lhi[1] = _hi[1]; _lhi[2] = _hi[2]; - domain->x2lamda(_lhi,_hi); - } - - // test all fragments for any overlap; ok to include false positives - - int _xoverlap1 = 0; - int _xoverlap2 = 0; - if (!xoverlap) { - if (xboxlo < 0) { - _xoverlap1 = 1; - if (_lo[0] > (subhi[0] - EPSILON)) _xoverlap1 = 0; - } - - if (xboxhi > 0) { - _xoverlap2 = 1; - if (_hi[0] < (sublo[0] + EPSILON)) _xoverlap2 = 0; - } - - if (_xoverlap1 || _xoverlap2) xoverlap = 1; - } - - int _yoverlap1 = 0; - int _yoverlap2 = 0; - if (!yoverlap) { - if (yboxlo < 0) { - _yoverlap1 = 1; - if (_lo[1] > (subhi[1] - EPSILON)) _yoverlap1 = 0; - } - - if (yboxhi > 0) { - _yoverlap2 = 1; - if (_hi[1] < (sublo[1] + EPSILON)) _yoverlap2 = 0; - } - - if (_yoverlap1 || _yoverlap2) yoverlap = 1; - } - - - int _zoverlap1 = 0; - int _zoverlap2 = 0; - if (!zoverlap) { - if (zboxlo < 0) { - _zoverlap1 = 1; - if (_lo[2] > (subhi[2] - EPSILON)) _zoverlap1 = 0; - } - - if (zboxhi > 0) { - _zoverlap2 = 1; - if (_hi[2] < (sublo[2] + EPSILON)) _zoverlap2 = 0; - } - - if (_zoverlap1 || _zoverlap2) zoverlap = 1; - } - - // does either fragment overlap w/ sub-domain - - if (xoverlap && yoverlap && zoverlap) overlap = 1; - } - - // while loop over one proc's atom list - - if (overlap) { - num_replicas_added++; - - m = 0; - while (m < size_buf_all) { - image = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - if (triclinic == 0) { - x[0] = buf_all[m+1] + ix*old_xprd; - x[1] = buf_all[m+2] + iy*old_yprd; - x[2] = buf_all[m+3] + iz*old_zprd; - } else { - x[0] = buf_all[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz; - x[1] = buf_all[m+2] + iy*old_yprd + iz*old_yz; - x[2] = buf_all[m+3] + iz*old_zprd; - } - domain->remap(x,image); - if (triclinic) { - domain->x2lamda(x,lamda); - coord = lamda; - } else coord = x; - - if (coord[0] >= sublo[0] && coord[0] < subhi[0] && - coord[1] >= sublo[1] && coord[1] < subhi[1] && - coord[2] >= sublo[2] && coord[2] < subhi[2]) { - - m += avec->unpack_restart(&buf_all[m]); - - i = atom->nlocal - 1; - if (tag_enable) - atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag; - else atom_offset = 0; - mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol; - - atom->x[i][0] = x[0]; - atom->x[i][1] = x[1]; - atom->x[i][2] = x[2]; - - atom->tag[i] += atom_offset; - atom->image[i] = image; - - if (atom->molecular != Atom::ATOMIC) { - if (atom->molecule[i] > 0) - atom->molecule[i] += mol_offset; - if (atom->molecular == Atom::MOLECULAR) { - if (atom->avec->bonds_allow) - for (j = 0; j < atom->num_bond[i]; j++) - atom->bond_atom[i][j] += atom_offset; - if (atom->avec->angles_allow) - for (j = 0; j < atom->num_angle[i]; j++) { - atom->angle_atom1[i][j] += atom_offset; - atom->angle_atom2[i][j] += atom_offset; - atom->angle_atom3[i][j] += atom_offset; - } - if (atom->avec->dihedrals_allow) - for (j = 0; j < atom->num_dihedral[i]; j++) { - atom->dihedral_atom1[i][j] += atom_offset; - atom->dihedral_atom2[i][j] += atom_offset; - atom->dihedral_atom3[i][j] += atom_offset; - atom->dihedral_atom4[i][j] += atom_offset; - } - if (atom->avec->impropers_allow) - for (j = 0; j < atom->num_improper[i]; j++) { - atom->improper_atom1[i][j] += atom_offset; - atom->improper_atom2[i][j] += atom_offset; - atom->improper_atom3[i][j] += atom_offset; - atom->improper_atom4[i][j] += atom_offset; - } - } - } - } else m += static_cast (buf_all[m]); - } - } // if (overlap) - - } - } - } - - memory->destroy(size_buf_rnk); - memory->destroy(disp_buf_rnk); - memory->destroy(buf_all); - - int sum = 0; - MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world); - double avg = (double) sum / nprocs; - if (me == 0) - utils::logmesg(lmp," average # of replicas added to proc = {:.2f} out " - "of {} ({:.2f}%)\n",avg,nx*ny*nz,avg/(nx*ny*nz)*100.0); + if (!bbox_flag) { + replicate_by_proc(nx,ny,nz,sublo,subhi,buf); } else { - - for (int iproc = 0; iproc < nprocs; iproc++) { - if (me == iproc) { - n = 0; - for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]); - } - MPI_Bcast(&n,1,MPI_INT,iproc,world); - MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world); - - for (ix = 0; ix < nx; ix++) { - for (iy = 0; iy < ny; iy++) { - for (iz = 0; iz < nz; iz++) { - - // while loop over one proc's atom list - - m = 0; - while (m < n) { - image = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - if (triclinic == 0) { - x[0] = buf[m+1] + ix*old_xprd; - x[1] = buf[m+2] + iy*old_yprd; - x[2] = buf[m+3] + iz*old_zprd; - } else { - x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz; - x[1] = buf[m+2] + iy*old_yprd + iz*old_yz; - x[2] = buf[m+3] + iz*old_zprd; - } - domain->remap(x,image); - if (triclinic) { - domain->x2lamda(x,lamda); - coord = lamda; - } else coord = x; - - if (coord[0] >= sublo[0] && coord[0] < subhi[0] && - coord[1] >= sublo[1] && coord[1] < subhi[1] && - coord[2] >= sublo[2] && coord[2] < subhi[2]) { - - m += avec->unpack_restart(&buf[m]); - - i = atom->nlocal - 1; - if (tag_enable) - atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag; - else atom_offset = 0; - mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol; - - atom->x[i][0] = x[0]; - atom->x[i][1] = x[1]; - atom->x[i][2] = x[2]; - - atom->tag[i] += atom_offset; - atom->image[i] = image; - - if (atom->molecular != Atom::ATOMIC) { - if (atom->molecule[i] > 0) - atom->molecule[i] += mol_offset; - if (atom->molecular == Atom::MOLECULAR) { - if (atom->avec->bonds_allow) - for (j = 0; j < atom->num_bond[i]; j++) - atom->bond_atom[i][j] += atom_offset; - if (atom->avec->angles_allow) - for (j = 0; j < atom->num_angle[i]; j++) { - atom->angle_atom1[i][j] += atom_offset; - atom->angle_atom2[i][j] += atom_offset; - atom->angle_atom3[i][j] += atom_offset; - } - if (atom->avec->dihedrals_allow) - for (j = 0; j < atom->num_dihedral[i]; j++) { - atom->dihedral_atom1[i][j] += atom_offset; - atom->dihedral_atom2[i][j] += atom_offset; - atom->dihedral_atom3[i][j] += atom_offset; - atom->dihedral_atom4[i][j] += atom_offset; - } - if (atom->avec->impropers_allow) - for (j = 0; j < atom->num_improper[i]; j++) { - atom->improper_atom1[i][j] += atom_offset; - atom->improper_atom2[i][j] += atom_offset; - atom->improper_atom3[i][j] += atom_offset; - atom->improper_atom4[i][j] += atom_offset; - } - } - } - } else m += static_cast (buf[m]); - } - } - } - } - } - } // if (bbox_flag) + replicate_by_bbox(nx,ny,nz,sublo,subhi,buf); + } // free communication buffer and old atom class @@ -821,3 +448,533 @@ void Replicate::command(int narg, char **arg) if (me == 0) utils::logmesg(lmp," replicate CPU = {:.3f} seconds\n",platform::walltime()-time1); } + +/* ---------------------------------------------------------------------- + simple replication algorithm, suitable for small proc count + loop over procs, then over replication factors + check each atom to see if in my subdomain +------------------------------------------------------------------------- */ + +void Replicate::replicate_by_proc(int nx, int ny, int nz, + double *sublo, double *subhi, double *buf) +{ + int i,j,m,n; + int ix,iy,iz; + + int me = comm->me; + int nprocs = comm->nprocs; + int triclinic = domain->triclinic; + int tag_enable = atom->tag_enable; + + AtomVec *old_avec = old->avec; + AtomVec *avec = atom->avec; + + tagint atom_offset,mol_offset; + imageint image; + double x[3],lamda[3]; + double *coord; + + // loop over all procs + // if this iteration of loop is me: + // pack my unmapped atom data into buf + // bcast it to all other procs + + for (int iproc = 0; iproc < nprocs; iproc++) { + if (me == iproc) { + n = 0; + for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]); + } + MPI_Bcast(&n,1,MPI_INT,iproc,world); + MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world); + + for (ix = 0; ix < nx; ix++) { + for (iy = 0; iy < ny; iy++) { + for (iz = 0; iz < nz; iz++) { + + // while loop over one proc's atom list + // x = new replicated position, remapped into new simulation box + // if atom is within my new subdomain, unpack it into new atom class + // adjust tag, mol #, coord, topology info as needed + + m = 0; + while (m < n) { + image = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + if (triclinic == 0) { + x[0] = buf[m+1] + ix*old_xprd; + x[1] = buf[m+2] + iy*old_yprd; + x[2] = buf[m+3] + iz*old_zprd; + } else { + x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz; + x[1] = buf[m+2] + iy*old_yprd + iz*old_yz; + x[2] = buf[m+3] + iz*old_zprd; + } + domain->remap(x,image); + if (triclinic) { + domain->x2lamda(x,lamda); + coord = lamda; + } else coord = x; + + if (coord[0] >= sublo[0] && coord[0] < subhi[0] && + coord[1] >= sublo[1] && coord[1] < subhi[1] && + coord[2] >= sublo[2] && coord[2] < subhi[2]) { + + m += avec->unpack_restart(&buf[m]); + + i = atom->nlocal - 1; + if (tag_enable) atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag; + else atom_offset = 0; + mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol; + + atom->x[i][0] = x[0]; + atom->x[i][1] = x[1]; + atom->x[i][2] = x[2]; + + atom->tag[i] += atom_offset; + atom->image[i] = image; + + if (atom->molecular != Atom::ATOMIC) { + if (atom->molecule[i] > 0) + atom->molecule[i] += mol_offset; + if (atom->molecular == Atom::MOLECULAR) { + if (atom->avec->bonds_allow) + for (j = 0; j < atom->num_bond[i]; j++) + atom->bond_atom[i][j] += atom_offset; + if (atom->avec->angles_allow) + for (j = 0; j < atom->num_angle[i]; j++) { + atom->angle_atom1[i][j] += atom_offset; + atom->angle_atom2[i][j] += atom_offset; + atom->angle_atom3[i][j] += atom_offset; + } + if (atom->avec->dihedrals_allow) + for (j = 0; j < atom->num_dihedral[i]; j++) { + atom->dihedral_atom1[i][j] += atom_offset; + atom->dihedral_atom2[i][j] += atom_offset; + atom->dihedral_atom3[i][j] += atom_offset; + atom->dihedral_atom4[i][j] += atom_offset; + } + if (atom->avec->impropers_allow) + for (j = 0; j < atom->num_improper[i]; j++) { + atom->improper_atom1[i][j] += atom_offset; + atom->improper_atom2[i][j] += atom_offset; + atom->improper_atom3[i][j] += atom_offset; + atom->improper_atom4[i][j] += atom_offset; + } + } + } + } else m += static_cast (buf[m]); + } + } + } + } + } +} + +/* ---------------------------------------------------------------------- + more complex replication algorithm + uses bounding box of each proc's subdomain to avoid checking individual atoms + faster for large processor counts + required for bond/periodic option +------------------------------------------------------------------------- */ + +void Replicate::replicate_by_bbox(int nx, int ny, int nz, + double *sublo, double *subhi, double *buf) +{ + int i,j,m,n; + int ix,iy,iz; + + int me = comm->me; + int nprocs = comm->nprocs; + int triclinic = domain->triclinic; + int tag_enable = atom->tag_enable; + + AtomVec *old_avec = old->avec; + AtomVec *avec = atom->avec; + + tagint atom_offset,mol_offset,atom0tag; + imageint image; + double x[3],lamda[3]; + double *coord; + + // allgather size of buf on each proc + + n = 0; + for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]); + + int * size_buf_rnk; + memory->create(size_buf_rnk, nprocs, "replicate:size_buf_rnk"); + + MPI_Allgather(&n, 1, MPI_INT, size_buf_rnk, 1, MPI_INT, world); + + // size of buf_all + + int size_buf_all = 0; + MPI_Allreduce(&n, &size_buf_all, 1, MPI_INT, MPI_SUM, world); + + if (me == 0) { + auto mesg = fmt::format(" bounding box image = ({} {} {}) " + "to ({} {} {})\n", + _imagelo[0],_imagelo[1],_imagelo[2], + _imagehi[0],_imagehi[1],_imagehi[2]); + mesg += fmt::format(" bounding box extra memory = {:.2f} MB\n", + (double)size_buf_all*sizeof(double)/1024/1024); + utils::logmesg(lmp,mesg); + } + + // rnk offsets + + int *disp_buf_rnk; + memory->create(disp_buf_rnk, nprocs, "replicate:disp_buf_rnk"); + disp_buf_rnk[0] = 0; + for (i = 1; i < nprocs; i++) + disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1]; + + // allgather buf_all + + double *buf_all; + memory->create(buf_all, size_buf_all, "replicate:buf_all"); + + MPI_Allgatherv(buf,n,MPI_DOUBLE,buf_all,size_buf_rnk,disp_buf_rnk, + MPI_DOUBLE,world); + + // bounding box of original unwrapped system + + double _orig_lo[3], _orig_hi[3]; + if (triclinic) { + _orig_lo[0] = domain->boxlo[0] + + _imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz; + _orig_lo[1] = domain->boxlo[1] + + _imagelo[1] * old_yprd + _imagelo[2] * old_yz; + _orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd; + + _orig_hi[0] = domain->boxlo[0] + + (_imagehi[0]+1) * old_xprd + + (_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz; + _orig_hi[1] = domain->boxlo[1] + + (_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz; + _orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd; + } else { + _orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd; + _orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd; + _orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd; + + _orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd; + _orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd; + _orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd; + } + + double _lo[3], _hi[3]; + + int num_replicas_added = 0; + + // if bond/periodic option + // store old_x and old_tag for the entire original system + + if (bond_flag) { + memory->create(old_x,old->natoms,3,"replicate:old_x"); + memory->create(old_tag,old->natoms,"replicate:old_tag"); + + i = m = 0; + while (m < size_buf_all) { + old_x[i][0] = buf_all[m+1]; + old_x[i][1] = buf_all[m+2]; + old_x[i][2] = buf_all[m+3]; + old_tag[i] = (tagint) ubuf(buf_all[m+4]).i; + old_map.insert({old_tag[i],i}); + m += static_cast (buf_all[m]); + i++; + } + } + + // replication loop + + for (ix = 0; ix < nx; ix++) { + for (iy = 0; iy < ny; iy++) { + for (iz = 0; iz < nz; iz++) { + + thisrep[0] = ix; + thisrep[1] = iy; + thisrep[2] = iz; + + // domain->remap() overwrites coordinates, so always recompute here + + if (triclinic) { + _lo[0] = _orig_lo[0] + ix * old_xprd + iy * old_xy + iz * old_xz; + _hi[0] = _orig_hi[0] + ix * old_xprd + iy * old_xy + iz * old_xz; + + _lo[1] = _orig_lo[1] + iy * old_yprd + iz * old_yz; + _hi[1] = _orig_hi[1] + iy * old_yprd + iz * old_yz; + + _lo[2] = _orig_lo[2] + iz * old_zprd; + _hi[2] = _orig_hi[2] + iz * old_zprd; + } else { + _lo[0] = _orig_lo[0] + ix * old_xprd; + _hi[0] = _orig_hi[0] + ix * old_xprd; + + _lo[1] = _orig_lo[1] + iy * old_yprd; + _hi[1] = _orig_hi[1] + iy * old_yprd; + + _lo[2] = _orig_lo[2] + iz * old_zprd; + _hi[2] = _orig_hi[2] + iz * old_zprd; + } + + // test if bounding box of shifted replica overlaps sub-domain of proc + // if not, then can skip testing of any individual atoms + + int xoverlap = 1; + int yoverlap = 1; + int zoverlap = 1; + if (triclinic) { + double _llo[3]; + domain->x2lamda(_lo,_llo); + double _lhi[3]; + domain->x2lamda(_hi,_lhi); + + if (_llo[0] > (subhi[0] - EPSILON) + || _lhi[0] < (sublo[0] + EPSILON) ) xoverlap = 0; + if (_llo[1] > (subhi[1] - EPSILON) + || _lhi[1] < (sublo[1] + EPSILON) ) yoverlap = 0; + if (_llo[2] > (subhi[2] - EPSILON) + || _lhi[2] < (sublo[2] + EPSILON) ) zoverlap = 0; + } else { + if (_lo[0] > (subhi[0] - EPSILON) + || _hi[0] < (sublo[0] + EPSILON) ) xoverlap = 0; + if (_lo[1] > (subhi[1] - EPSILON) + || _hi[1] < (sublo[1] + EPSILON) ) yoverlap = 0; + if (_lo[2] > (subhi[2] - EPSILON) + || _hi[2] < (sublo[2] + EPSILON) ) zoverlap = 0; + } + + int overlap = 0; + if (xoverlap && yoverlap && zoverlap) overlap = 1; + + // if no overlap, test if bounding box wrapped back into new system + + if (!overlap) { + + // wrap back into cell + + imageint imagelo = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + domain->remap(&(_lo[0]), imagelo); + int xboxlo = (imagelo & IMGMASK) - IMGMAX; + int yboxlo = (imagelo >> IMGBITS & IMGMASK) - IMGMAX; + int zboxlo = (imagelo >> IMG2BITS) - IMGMAX; + + imageint imagehi = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + domain->remap(&(_hi[0]), imagehi); + int xboxhi = (imagehi & IMGMASK) - IMGMAX; + int yboxhi = (imagehi >> IMGBITS & IMGMASK) - IMGMAX; + int zboxhi = (imagehi >> IMG2BITS) - IMGMAX; + + if (triclinic) { + double _llo[3]; + _llo[0] = _lo[0]; _llo[1] = _lo[1]; _llo[2] = _lo[2]; + domain->x2lamda(_llo,_lo); + + double _lhi[3]; + _lhi[0] = _hi[0]; _lhi[1] = _hi[1]; _lhi[2] = _hi[2]; + domain->x2lamda(_lhi,_hi); + } + + // test all fragments for any overlap; ok to include false positives + + int _xoverlap1 = 0; + int _xoverlap2 = 0; + if (!xoverlap) { + if (xboxlo < 0) { + _xoverlap1 = 1; + if (_lo[0] > (subhi[0] - EPSILON)) _xoverlap1 = 0; + } + + if (xboxhi > 0) { + _xoverlap2 = 1; + if (_hi[0] < (sublo[0] + EPSILON)) _xoverlap2 = 0; + } + + if (_xoverlap1 || _xoverlap2) xoverlap = 1; + } + + int _yoverlap1 = 0; + int _yoverlap2 = 0; + if (!yoverlap) { + if (yboxlo < 0) { + _yoverlap1 = 1; + if (_lo[1] > (subhi[1] - EPSILON)) _yoverlap1 = 0; + } + + if (yboxhi > 0) { + _yoverlap2 = 1; + if (_hi[1] < (sublo[1] + EPSILON)) _yoverlap2 = 0; + } + + if (_yoverlap1 || _yoverlap2) yoverlap = 1; + } + + + int _zoverlap1 = 0; + int _zoverlap2 = 0; + if (!zoverlap) { + if (zboxlo < 0) { + _zoverlap1 = 1; + if (_lo[2] > (subhi[2] - EPSILON)) _zoverlap1 = 0; + } + + if (zboxhi > 0) { + _zoverlap2 = 1; + if (_hi[2] < (sublo[2] + EPSILON)) _zoverlap2 = 0; + } + + if (_zoverlap1 || _zoverlap2) zoverlap = 1; + } + + // does either fragment overlap w/ sub-domain + + if (xoverlap && yoverlap && zoverlap) overlap = 1; + } + + // while loop over one proc's atom list + + if (overlap) { + num_replicas_added++; + + m = 0; + while (m < size_buf_all) { + image = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + if (triclinic == 0) { + x[0] = buf_all[m+1] + ix*old_xprd; + x[1] = buf_all[m+2] + iy*old_yprd; + x[2] = buf_all[m+3] + iz*old_zprd; + } else { + x[0] = buf_all[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz; + x[1] = buf_all[m+2] + iy*old_yprd + iz*old_yz; + x[2] = buf_all[m+3] + iz*old_zprd; + } + domain->remap(x,image); + if (triclinic) { + domain->x2lamda(x,lamda); + coord = lamda; + } else coord = x; + + if (coord[0] >= sublo[0] && coord[0] < subhi[0] && + coord[1] >= sublo[1] && coord[1] < subhi[1] && + coord[2] >= sublo[2] && coord[2] < subhi[2]) { + + m += avec->unpack_restart(&buf_all[m]); + + i = atom->nlocal - 1; + if (tag_enable) + atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag; + else atom_offset = 0; + mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol; + + atom->x[i][0] = x[0]; + atom->x[i][1] = x[1]; + atom->x[i][2] = x[2]; + + atom0tag = atom->tag[i]; + atom->tag[i] += atom_offset; + atom->image[i] = image; + + if (atom->molecular != Atom::ATOMIC) { + if (atom->molecule[i] > 0) + atom->molecule[i] += mol_offset; + if (atom->molecular == Atom::MOLECULAR) { + if (atom->avec->bonds_allow) + for (j = 0; j < atom->num_bond[i]; j++) { + if (bond_flag) + newtag(atom0tag,atom->bond_atom[i][j]); + else atom->bond_atom[i][j] += atom_offset; + } + if (atom->avec->angles_allow) + for (j = 0; j < atom->num_angle[i]; j++) { + if (bond_flag) { + newtag(atom0tag,atom->angle_atom1[i][j]); + newtag(atom0tag,atom->angle_atom2[i][j]); + newtag(atom0tag,atom->angle_atom3[i][j]); + } else { + atom->angle_atom1[i][j] += atom_offset; + atom->angle_atom2[i][j] += atom_offset; + atom->angle_atom3[i][j] += atom_offset; + } + } + if (atom->avec->dihedrals_allow) + for (j = 0; j < atom->num_dihedral[i]; j++) { + if (bond_flag) { + newtag(atom0tag,atom->dihedral_atom1[i][j]); + newtag(atom0tag,atom->dihedral_atom2[i][j]); + newtag(atom0tag,atom->dihedral_atom3[i][j]); + newtag(atom0tag,atom->dihedral_atom4[i][j]); + } else { + atom->dihedral_atom1[i][j] += atom_offset; + atom->dihedral_atom2[i][j] += atom_offset; + atom->dihedral_atom3[i][j] += atom_offset; + atom->dihedral_atom4[i][j] += atom_offset; + } + } + if (atom->avec->impropers_allow) + for (j = 0; j < atom->num_improper[i]; j++) { + if (bond_flag) { + newtag(atom0tag,atom->improper_atom1[i][j]); + newtag(atom0tag,atom->improper_atom2[i][j]); + newtag(atom0tag,atom->improper_atom3[i][j]); + newtag(atom0tag,atom->improper_atom4[i][j]); + } else { + atom->improper_atom1[i][j] += atom_offset; + atom->improper_atom2[i][j] += atom_offset; + atom->improper_atom3[i][j] += atom_offset; + atom->improper_atom4[i][j] += atom_offset; + } + } + } + } + } else m += static_cast (buf_all[m]); + } + } + } + } + } + + memory->destroy(size_buf_rnk); + memory->destroy(disp_buf_rnk); + memory->destroy(buf_all); + if (bond_flag) { + memory->destroy(old_x); + memory->destroy(old_tag); + } + + int sum = 0; + MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world); + double avg = (double) sum / nprocs; + if (me == 0) + utils::logmesg(lmp," average # of replicas added to proc = {:.2f} out " + "of {} ({:.2f}%)\n",avg,nx*ny*nz,avg/(nx*ny*nz)*100.0); +} + +/* ---------------------------------------------------------------------- + find new tag for atom 'atom2bond' bonded to atom 'atom0' + for bond/periodic option + useful for periodic loops or inconsistent image flags + reassign bond if > old boxlength / 2 +------------------------------------------------------------------------- */ + +void Replicate::newtag(tagint atom0tag, tagint &tag2bond) { + double del; + int repshift,rep2bond[3]; + int atom0 = old_map.find(atom0tag)->second; + int atom2bond = old_map.find(tag2bond)->second; + for (int i = 0; i < 3; i++) { + del = fabs(old_x[atom0][i] - old_x[atom2bond][i]); + if (del > old_prd_half[i]) { + if (old_x[atom0][i] > old_center[i]) repshift = 1; + else repshift = -1; + } else repshift = 0; + rep2bond[i] = thisrep[i] + repshift; + if (rep2bond[i] >= allnrep[i]) rep2bond[i] = 0; + if (rep2bond[i] < 0) rep2bond[i] = allnrep[i]-1; + } + tag2bond = (tag2bond + rep2bond[2]*allnrep[1]*allnrep[0]*maxtag + + rep2bond[1]*allnrep[0]*maxtag + rep2bond[0]*maxtag); +} diff --git a/src/replicate.h b/src/replicate.h index 8d71ba6584..defb35d1c6 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -22,12 +22,37 @@ CommandStyle(replicate,Replicate); #include "command.h" +#include + namespace LAMMPS_NS { class Replicate : public Command { public: Replicate(class LAMMPS *); void command(int, char **) override; + +private: + int bbox_flag, bond_flag; + + class Atom *old; + + double old_xprd, old_yprd, old_zprd; + double old_xy, old_xz, old_yz; + + int _imagelo[3], _imagehi[3]; + + double **old_x; + double old_prd_half[3], old_center[3]; + tagint *old_tag; + tagint maxtag, maxmol; + int thisrep[3], allnrep[3]; + + std::unordered_map old_map; + + void replicate_by_proc(int, int, int, double *, double *, double *); + void replicate_by_bbox(int, int, int, double *, double *, double *); + + void newtag(tagint, tagint &); }; } // namespace LAMMPS_NS diff --git a/src/set.cpp b/src/set.cpp index cee769a573..73e218db0f 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -90,22 +90,16 @@ void Set::command(int narg, char **arg) if (strcmp(arg[iarg],"type") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set type", error); - if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1); - else { - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp); - ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; - } + if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1], 1); + else ivalue = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ATOM, lmp); set(TYPE); iarg += 2; } else if (strcmp(arg[iarg],"type/fraction") == 0) { if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "set type/fraction", error); - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp); - newtype = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; - fraction = utils::numeric(FLERR,arg[iarg+2],false,lmp); - ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp); + newtype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ATOM, lmp); + fraction = utils::numeric(FLERR, arg[iarg+2], false, lmp); + ivalue = utils::inumeric(FLERR, arg[iarg+3], false, lmp); if (newtype <= 0 || newtype > atom->ntypes) error->all(FLERR,"Invalid type value {} in set type/fraction command", newtype); if (fraction < 0.0 || fraction > 1.0) @@ -117,11 +111,9 @@ void Set::command(int narg, char **arg) } else if (strcmp(arg[iarg],"type/ratio") == 0) { if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "set type/ratio", error); - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp); - newtype = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; - fraction = utils::numeric(FLERR,arg[iarg+2],false,lmp); - ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp); + newtype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ATOM, lmp); + fraction = utils::numeric(FLERR, arg[iarg+2], false, lmp); + ivalue = utils::inumeric(FLERR, arg[iarg+3], false, lmp); if (newtype <= 0 || newtype > atom->ntypes) error->all(FLERR,"Invalid type value {} in set type/ratio command", newtype); if (fraction < 0.0 || fraction > 1.0) @@ -133,11 +125,9 @@ void Set::command(int narg, char **arg) } else if (strcmp(arg[iarg],"type/subset") == 0) { if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "set type/subset", error); - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp); - newtype = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; - nsubset = utils::bnumeric(FLERR,arg[iarg+2],false,lmp); - ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp); + newtype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ATOM, lmp); + nsubset = utils::bnumeric(FLERR, arg[iarg+2], false, lmp); + ivalue = utils::inumeric(FLERR, arg[iarg+3], false, lmp); if (newtype <= 0 || newtype > atom->ntypes) error->all(FLERR,"Invalid type value {} in set type/subset command", newtype); if (nsubset < 0) @@ -485,9 +475,7 @@ void Set::command(int narg, char **arg) } else if (strcmp(arg[iarg],"bond") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set bond", error); - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::BOND,lmp); - ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; + ivalue = utils::expand_type_int(FLERR, arg[iarg+1], Atom::BOND, lmp); if (atom->avec->bonds_allow == 0) error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style()); if (ivalue <= 0 || ivalue > atom->nbondtypes) @@ -497,9 +485,7 @@ void Set::command(int narg, char **arg) } else if (strcmp(arg[iarg],"angle") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set angle", error); - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ANGLE,lmp); - ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; + ivalue = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ANGLE, lmp); if (atom->avec->angles_allow == 0) error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style()); if (ivalue <= 0 || ivalue > atom->nangletypes) @@ -509,9 +495,7 @@ void Set::command(int narg, char **arg) } else if (strcmp(arg[iarg],"dihedral") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set dihedral", error); - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::DIHEDRAL,lmp); - ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; + ivalue = utils::expand_type_int(FLERR, arg[iarg+1], Atom::DIHEDRAL, lmp); if (atom->avec->dihedrals_allow == 0) error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style()); if (ivalue <= 0 || ivalue > atom->ndihedraltypes) @@ -521,9 +505,7 @@ void Set::command(int narg, char **arg) } else if (strcmp(arg[iarg],"improper") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set improper", error); - char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::IMPROPER,lmp); - ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp); - delete[] typestr; + ivalue = utils::expand_type_int(FLERR, arg[iarg+1], Atom::IMPROPER, lmp); if (atom->avec->impropers_allow == 0) error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style()); if (ivalue <= 0 || ivalue > atom->nimpropertypes) @@ -758,11 +740,7 @@ void Set::selection(int n) else select[i] = 0; } else if (style == TYPE_SELECT) { - if (char *typestr = utils::expand_type(FLERR,id,Atom::ATOM,lmp)) { - delete[] id; - id = typestr; - } - utils::bounds(FLERR,id,1,atom->ntypes,nlo,nhi,error); + utils::bounds_typelabel(FLERR,id,1,atom->ntypes,nlo,nhi,lmp,Atom::ATOM); int *type = atom->type; for (int i = 0; i < n; i++) diff --git a/src/thermo.cpp b/src/thermo.cpp index efc5f984fc..892de240b2 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -34,6 +34,7 @@ #include "kspace.h" #include "lattice.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "neighbor.h" @@ -51,20 +52,22 @@ using namespace LAMMPS_NS; using namespace MathConst; +using namespace MathExtra; // CUSTOMIZATION: add a new keyword by adding it to this list: -// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain, -// part, timeremain +// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain, part, timeremain // atoms, temp, press, pe, ke, etotal // evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail // enthalpy, ecouple, econserve -// vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz +// vol, density, lx, ly, lz, +// xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz +// avecx, avecy, avecz, bvecx, bvecy, bvecz, cvecx, cvecy, cvecz, // xlat, ylat, zlat -// bonds, angles, dihedrals, impropers -// pxx, pyy, pzz, pxy, pxz, pyz -// fmax, fnorm, nbuild, ndanger // cella, cellb, cellc, cellalpha, cellbeta, cellgamma +// pxx, pyy, pzz, pxy, pxz, pyz +// bonds, angles, dihedrals, impropers +// fmax, fnorm, nbuild, ndanger // CUSTOMIZATION: add a new thermo style by adding a constant to the enumerator, // define a new string constant with the keywords and provide default formats. @@ -110,6 +113,7 @@ Thermo::Thermo(LAMMPS *_lmp, int narg, char **arg) : lostflag = lostbond = Thermo::ERROR; lostbefore = warnbefore = 0; flushflag = 0; + triclinic_general = 0; firststep = 0; ntimestep = -1; nline = -1; @@ -571,6 +575,14 @@ void Thermo::modify_params(int narg, char **arg) iarg += 2; + } else if (strcmp(arg[iarg],"triclinic/general") == 0) { + if (iarg + 2 > narg) error->all(FLERR,"Illegal thermo_modify command"); + triclinic_general = utils::logical(FLERR,arg[iarg+1],false,lmp); + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Thermo_modify triclinic/general cannot be used " + "if simulation box is not general triclinic"); + iarg += 2; + } else if (strcmp(arg[iarg], "lost") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "thermo_modify lost", error); if (strcmp(arg[iarg + 1], "ignore") == 0) @@ -905,6 +917,7 @@ void Thermo::parse_fields(const std::string &str) addfield("Volume", &Thermo::compute_vol, FLOAT); } else if (word == "density") { addfield("Density", &Thermo::compute_density, FLOAT); + } else if (word == "lx") { addfield("Lx", &Thermo::compute_lx, FLOAT); } else if (word == "ly") { @@ -932,6 +945,25 @@ void Thermo::parse_fields(const std::string &str) } else if (word == "yz") { addfield("Yz", &Thermo::compute_yz, FLOAT); + } else if (word == "avecx") { + addfield("Avecx", &Thermo::compute_avecx, FLOAT); + } else if (word == "avecy") { + addfield("Avecy", &Thermo::compute_avecy, FLOAT); + } else if (word == "avecz") { + addfield("Avecz", &Thermo::compute_avecz, FLOAT); + } else if (word == "bvecx") { + addfield("Bvecx", &Thermo::compute_bvecx, FLOAT); + } else if (word == "bvecy") { + addfield("Bvecy", &Thermo::compute_bvecy, FLOAT); + } else if (word == "bvecz") { + addfield("Bvecz", &Thermo::compute_bvecz, FLOAT); + } else if (word == "cvecx") { + addfield("Cvecx", &Thermo::compute_cvecx, FLOAT); + } else if (word == "cvecy") { + addfield("Cvecy", &Thermo::compute_cvecy, FLOAT); + } else if (word == "cvecz") { + addfield("Cvecz", &Thermo::compute_cvecz, FLOAT); + } else if (word == "xlat") { addfield("Xlat", &Thermo::compute_xlat, FLOAT); } else if (word == "ylat") { @@ -939,44 +971,6 @@ void Thermo::parse_fields(const std::string &str) } else if (word == "zlat") { addfield("Zlat", &Thermo::compute_zlat, FLOAT); - } else if (word == "bonds") { - addfield("Bonds", &Thermo::compute_bonds, BIGINT); - } else if (word == "angles") { - addfield("Angles", &Thermo::compute_angles, BIGINT); - } else if (word == "dihedrals") { - addfield("Diheds", &Thermo::compute_dihedrals, BIGINT); - } else if (word == "impropers") { - addfield("Impros", &Thermo::compute_impropers, BIGINT); - - } else if (word == "pxx") { - addfield("Pxx", &Thermo::compute_pxx, FLOAT); - index_press_vector = add_compute(id_press, VECTOR); - } else if (word == "pyy") { - addfield("Pyy", &Thermo::compute_pyy, FLOAT); - index_press_vector = add_compute(id_press, VECTOR); - } else if (word == "pzz") { - addfield("Pzz", &Thermo::compute_pzz, FLOAT); - index_press_vector = add_compute(id_press, VECTOR); - } else if (word == "pxy") { - addfield("Pxy", &Thermo::compute_pxy, FLOAT); - index_press_vector = add_compute(id_press, VECTOR); - } else if (word == "pxz") { - addfield("Pxz", &Thermo::compute_pxz, FLOAT); - index_press_vector = add_compute(id_press, VECTOR); - } else if (word == "pyz") { - addfield("Pyz", &Thermo::compute_pyz, FLOAT); - index_press_vector = add_compute(id_press, VECTOR); - - } else if (word == "fmax") { - addfield("Fmax", &Thermo::compute_fmax, FLOAT); - } else if (word == "fnorm") { - addfield("Fnorm", &Thermo::compute_fnorm, FLOAT); - - } else if (word == "nbuild") { - addfield("Nbuild", &Thermo::compute_nbuild, BIGINT); - } else if (word == "ndanger") { - addfield("Ndanger", &Thermo::compute_ndanger, BIGINT); - } else if (word == "cella") { addfield("Cella", &Thermo::compute_cella, FLOAT); } else if (word == "cellb") { @@ -990,6 +984,56 @@ void Thermo::parse_fields(const std::string &str) } else if (word == "cellgamma") { addfield("CellGamma", &Thermo::compute_cellgamma, FLOAT); + } else if (word == "pxx") { + if (triclinic_general) + addfield("Pxx", &Thermo::compute_pxx_triclinic_general, FLOAT); + else addfield("Pxx", &Thermo::compute_pxx, FLOAT); + index_press_vector = add_compute(id_press, VECTOR); + } else if (word == "pyy") { + if (triclinic_general) + addfield("Pyy", &Thermo::compute_pyy_triclinic_general, FLOAT); + else addfield("Pyy", &Thermo::compute_pyy, FLOAT); + index_press_vector = add_compute(id_press, VECTOR); + } else if (word == "pzz") { + if (triclinic_general) + addfield("Pzz", &Thermo::compute_pzz_triclinic_general, FLOAT); + else addfield("Pzz", &Thermo::compute_pzz, FLOAT); + index_press_vector = add_compute(id_press, VECTOR); + } else if (word == "pxy") { + if (triclinic_general) + addfield("Pxy", &Thermo::compute_pxy_triclinic_general, FLOAT); + else addfield("Pxy", &Thermo::compute_pxy, FLOAT); + index_press_vector = add_compute(id_press, VECTOR); + } else if (word == "pxz") { + if (triclinic_general) + addfield("Pxz", &Thermo::compute_pxz_triclinic_general, FLOAT); + else addfield("Pxz", &Thermo::compute_pxz, FLOAT); + index_press_vector = add_compute(id_press, VECTOR); + } else if (word == "pyz") { + if (triclinic_general) + addfield("Pyz", &Thermo::compute_pyz_triclinic_general, FLOAT); + addfield("Pyz", &Thermo::compute_pyz, FLOAT); + index_press_vector = add_compute(id_press, VECTOR); + + } else if (word == "bonds") { + addfield("Bonds", &Thermo::compute_bonds, BIGINT); + } else if (word == "angles") { + addfield("Angles", &Thermo::compute_angles, BIGINT); + } else if (word == "dihedrals") { + addfield("Diheds", &Thermo::compute_dihedrals, BIGINT); + } else if (word == "impropers") { + addfield("Impros", &Thermo::compute_impropers, BIGINT); + + } else if (word == "fmax") { + addfield("Fmax", &Thermo::compute_fmax, FLOAT); + } else if (word == "fnorm") { + addfield("Fnorm", &Thermo::compute_fnorm, FLOAT); + + } else if (word == "nbuild") { + addfield("Nbuild", &Thermo::compute_nbuild, BIGINT); + } else if (word == "ndanger") { + addfield("Ndanger", &Thermo::compute_ndanger, BIGINT); + // compute value = c_ID, fix value = f_ID, variable value = v_ID // count trailing [] and store int arguments @@ -1197,6 +1241,17 @@ void Thermo::check_press_vector(const std::string &keyword) if (!(pressure->invoked_flag & Compute::INVOKED_VECTOR)) { pressure->compute_vector(); pressure->invoked_flag |= Compute::INVOKED_VECTOR; + + // store 3x3 matrix form of symmetric pressure tensor for use in triclinic_general() + + if (triclinic_general) { + press_tensor[0][0] = pressure->vector[0]; + press_tensor[1][1] = pressure->vector[1]; + press_tensor[2][2] = pressure->vector[2]; + press_tensor[0][1] = press_tensor[1][0] = pressure->vector[3]; + press_tensor[0][2] = press_tensor[2][0] = pressure->vector[4]; + press_tensor[1][2] = press_tensor[2][1] = pressure->vector[5]; + } } } @@ -1282,22 +1337,6 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer) compute_atoms(); dvalue = bivalue; - } else if (word == "bonds") { - compute_bonds(); - dvalue = bivalue; - - } else if (word == "angles") { - compute_angles(); - dvalue = bivalue; - - } else if (word == "dihedrals") { - compute_dihedrals(); - dvalue = bivalue; - - } else if (word == "impropers") { - compute_impropers(); - dvalue = bivalue; - } else if (word == "temp") { check_temp(word); compute_temp(); @@ -1378,6 +1417,7 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer) compute_vol(); else if (word == "density") compute_density(); + else if (word == "lx") compute_lx(); else if (word == "ly") @@ -1405,6 +1445,25 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer) else if (word == "yz") compute_yz(); + else if (word == "avecx") + compute_avecx(); + else if (word == "avecy") + compute_avecy(); + else if (word == "avecz") + compute_avecz(); + else if (word == "bvecx") + compute_bvecx(); + else if (word == "bvecy") + compute_bvecy(); + else if (word == "bvecz") + compute_bvecz(); + else if (word == "cvecx") + compute_cvecx(); + else if (word == "cvecy") + compute_cvecy(); + else if (word == "cvecz") + compute_cvecz(); + else if (word == "xlat") compute_xlat(); else if (word == "ylat") @@ -1412,44 +1471,6 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer) else if (word == "zlat") compute_zlat(); - else if (word == "pxx") { - check_press_vector(word); - compute_pxx(); - - } else if (word == "pyy") { - check_press_vector(word); - compute_pyy(); - - } else if (word == "pzz") { - check_press_vector(word); - compute_pzz(); - - } else if (word == "pxy") { - check_press_vector(word); - compute_pxy(); - - } else if (word == "pxz") { - check_press_vector(word); - compute_pxz(); - - } else if (word == "pyz") { - check_press_vector(word); - compute_pyz(); - } - - else if (word == "fmax") - compute_fmax(); - else if (word == "fnorm") - compute_fnorm(); - - else if (word == "nbuild") { - compute_nbuild(); - dvalue = bivalue; - } else if (word == "ndanger") { - compute_ndanger(); - dvalue = bivalue; - } - else if (word == "cella") compute_cella(); else if (word == "cellb") @@ -1463,6 +1484,65 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer) else if (word == "cellgamma") compute_cellgamma(); + else if (word == "pxx") { + check_press_vector(word); + if (triclinic_general) compute_pxx_triclinic_general(); + else compute_pxx(); + + } else if (word == "pyy") { + check_press_vector(word); + if (triclinic_general) compute_pyy_triclinic_general(); + else compute_pyy(); + + } else if (word == "pzz") { + check_press_vector(word); + if (triclinic_general) compute_pzz_triclinic_general(); + else compute_pzz(); + + } else if (word == "pxy") { + check_press_vector(word); + if (triclinic_general) compute_pxy_triclinic_general(); + else compute_pxy(); + + } else if (word == "pxz") { + check_press_vector(word); + if (triclinic_general) compute_pxz_triclinic_general(); + else compute_pxz(); + + } else if (word == "pyz") { + check_press_vector(word); + if (triclinic_general) compute_pyz_triclinic_general(); + else compute_pyz(); + + } else if (word == "bonds") { + compute_bonds(); + dvalue = bivalue; + + } else if (word == "angles") { + compute_angles(); + dvalue = bivalue; + + } else if (word == "dihedrals") { + compute_dihedrals(); + dvalue = bivalue; + + } else if (word == "impropers") { + compute_impropers(); + dvalue = bivalue; + + } else if (word == "fmax") + compute_fmax(); + else if (word == "fnorm") + compute_fnorm(); + + else if (word == "nbuild") { + compute_nbuild(); + dvalue = bivalue; + } else if (word == "ndanger") { + compute_ndanger(); + dvalue = bivalue; + } + else return 1; @@ -1490,9 +1570,8 @@ void Thermo::compute_compute() if (normflag && compute->extscalar) dvalue /= natoms; } else if (compute_which[m] == VECTOR) { if (compute->size_vector_variable && argindex1[ifield] > compute->size_vector) - dvalue = 0.0; - else - dvalue = compute->vector[argindex1[ifield] - 1]; + error->all(FLERR, "Thermo compute vector is accessed out-of-range"); + dvalue = compute->vector[argindex1[ifield] - 1]; if (normflag) { if (compute->extvector == 0) return; @@ -1503,9 +1582,8 @@ void Thermo::compute_compute() } } else { if (compute->size_array_rows_variable && argindex1[ifield] > compute->size_array_rows) - dvalue = 0.0; - else - dvalue = compute->array[argindex1[ifield] - 1][argindex2[ifield] - 1]; + error->all(FLERR, "Thermo compute array is accessed out-of-range"); + dvalue = compute->array[argindex1[ifield] - 1][argindex2[ifield] - 1]; if (normflag && compute->extarray) dvalue /= natoms; } } @@ -1521,7 +1599,12 @@ void Thermo::compute_fix() dvalue = fix->compute_scalar(); if (normflag && fix->extscalar) dvalue /= natoms; } else if (argindex2[ifield] == 0) { - dvalue = fix->compute_vector(argindex1[ifield] - 1); + + // if index exceeds variable vector length, use a zero value + // this can be useful if vector length is not known a priori + + if (fix->size_vector_variable && argindex1[ifield] > fix->size_vector) dvalue = 0.0; + else dvalue = fix->compute_vector(argindex1[ifield] - 1); if (normflag) { if (fix->extvector == 0) return; @@ -1531,7 +1614,12 @@ void Thermo::compute_fix() dvalue /= natoms; } } else { - dvalue = fix->compute_array(argindex1[ifield] - 1, argindex2[ifield] - 1); + + // if index exceeds variable array rows, use a zero value + // this can be useful if array size is not known a priori + + if (fix->size_array_rows_variable && argindex1[ifield] > fix->size_array_rows) dvalue = 0.0; + else dvalue = fix->compute_array(argindex1[ifield] - 1, argindex2[ifield] - 1); if (normflag && fix->extarray) dvalue /= natoms; } } @@ -1542,15 +1630,17 @@ void Thermo::compute_variable() { int iarg = argindex1[ifield]; + // evaluate equal-style or vector-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori + if (iarg == 0) dvalue = input->variable->compute_equal(variables[field2index[ifield]]); else { double *varvec; int nvec = input->variable->compute_vector(variables[field2index[ifield]], &varvec); - if (nvec < iarg) - dvalue = 0.0; - else - dvalue = varvec[iarg - 1]; + if (iarg > nvec) dvalue = 0.0; + else dvalue = varvec[iarg - 1]; } } @@ -1728,23 +1818,6 @@ void Thermo::compute_etotal() /* ---------------------------------------------------------------------- */ -void Thermo::compute_ecouple() -{ - dvalue = modify->energy_couple(); -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_econserve() -{ - compute_etotal(); - double dvalue_etotal = dvalue; - compute_ecouple(); - dvalue += dvalue_etotal; -} - -/* ---------------------------------------------------------------------- */ - void Thermo::compute_evdwl() { double tmp = 0.0; @@ -1892,6 +1965,23 @@ void Thermo::compute_enthalpy() /* ---------------------------------------------------------------------- */ +void Thermo::compute_ecouple() +{ + dvalue = modify->energy_couple(); +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_econserve() +{ + compute_etotal(); + double dvalue_etotal = dvalue; + compute_ecouple(); + dvalue += dvalue_etotal; +} + +/* ---------------------------------------------------------------------- */ + void Thermo::compute_vol() { if (domain->dimension == 3) @@ -1995,6 +2085,85 @@ void Thermo::compute_yz() /* ---------------------------------------------------------------------- */ +void Thermo::compute_avecx() +{ + if (!domain->triclinic) dvalue = domain->xprd; + else if (triclinic_general) dvalue = domain->avec[0]; + else dvalue = domain->xprd; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_avecy() +{ + if (!domain->triclinic) dvalue = 0.0; + else if (triclinic_general) dvalue = domain->avec[1]; + else dvalue = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_avecz() +{ + if (!domain->triclinic) dvalue = 0.0; + else if (triclinic_general) dvalue = domain->avec[2]; + else dvalue = 0.0; +} +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_bvecx() +{ + if (!domain->triclinic) dvalue = 0.0; + else if (triclinic_general) dvalue = domain->bvec[0]; + else dvalue = domain->xy; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_bvecy() +{ + if (!domain->triclinic) dvalue = domain->yprd; + else if (triclinic_general) dvalue = domain->bvec[1]; + else dvalue = domain->yprd; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_bvecz() +{ + if (!domain->triclinic) dvalue = 0.0; + else if (triclinic_general) dvalue = domain->bvec[2]; + else dvalue = 0.0; +} +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_cvecx() +{ + if (!domain->triclinic) dvalue = 0.0; + else if (triclinic_general) dvalue = domain->cvec[0]; + else dvalue = domain->xz; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_cvecy() +{ + if (!domain->triclinic) dvalue = 0.0; + else if (triclinic_general) dvalue = domain->cvec[1]; + else dvalue = domain->yz; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_cvecz() +{ + if (!domain->triclinic) dvalue = domain->zprd; + else if (triclinic_general) dvalue = domain->cvec[2]; + else dvalue = domain->zprd; +} + +/* ---------------------------------------------------------------------- */ + void Thermo::compute_xlat() { dvalue = domain->lattice->xlattice; @@ -2016,122 +2185,6 @@ void Thermo::compute_zlat() /* ---------------------------------------------------------------------- */ -void Thermo::compute_bonds() -{ - bivalue = atom->nbonds; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_angles() -{ - bivalue = atom->nangles; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_dihedrals() -{ - bivalue = atom->ndihedrals; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_impropers() -{ - bivalue = atom->nimpropers; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_pxx() -{ - dvalue = pressure->vector[0]; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_pyy() -{ - dvalue = pressure->vector[1]; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_pzz() -{ - dvalue = pressure->vector[2]; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_pxy() -{ - dvalue = pressure->vector[3]; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_pxz() -{ - dvalue = pressure->vector[4]; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_pyz() -{ - dvalue = pressure->vector[5]; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_fmax() -{ - double **f = atom->f; - int nlocal = atom->nlocal; - - double max = 0.0; - for (int i = 0; i < nlocal; i++) { - max = MAX(max, fabs(f[i][0])); - max = MAX(max, fabs(f[i][1])); - max = MAX(max, fabs(f[i][2])); - } - double maxall; - MPI_Allreduce(&max, &maxall, 1, MPI_DOUBLE, MPI_MAX, world); - dvalue = maxall; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_fnorm() -{ - double **f = atom->f; - int nlocal = atom->nlocal; - - double dot = 0.0; - for (int i = 0; i < nlocal; i++) dot += f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2]; - double dotall; - MPI_Allreduce(&dot, &dotall, 1, MPI_DOUBLE, MPI_SUM, world); - dvalue = sqrt(dotall); -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_nbuild() -{ - bivalue = neighbor->ncalls; -} - -/* ---------------------------------------------------------------------- */ - -void Thermo::compute_ndanger() -{ - bivalue = neighbor->ndanger; -} - -/* ---------------------------------------------------------------------- */ - void Thermo::compute_cella() { dvalue = domain->xprd; @@ -2209,3 +2262,179 @@ void Thermo::compute_cellgamma() dvalue = acos(cosgamma) * 180.0 / MY_PI; } } + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxx() +{ + dvalue = pressure->vector[0]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pyy() +{ + dvalue = pressure->vector[1]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pzz() +{ + dvalue = pressure->vector[2]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxy() +{ + dvalue = pressure->vector[3]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxz() +{ + dvalue = pressure->vector[4]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pyz() +{ + dvalue = pressure->vector[5]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxx_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[0][0]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pyy_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[1][1]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pzz_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[2][2]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxy_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[0][1]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxz_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[0][2]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pyz_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[1][2]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_bonds() +{ + bivalue = atom->nbonds; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_angles() +{ + bivalue = atom->nangles; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_dihedrals() +{ + bivalue = atom->ndihedrals; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_impropers() +{ + bivalue = atom->nimpropers; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_fmax() +{ + double **f = atom->f; + int nlocal = atom->nlocal; + + double max = 0.0; + for (int i = 0; i < nlocal; i++) { + max = MAX(max, fabs(f[i][0])); + max = MAX(max, fabs(f[i][1])); + max = MAX(max, fabs(f[i][2])); + } + double maxall; + MPI_Allreduce(&max, &maxall, 1, MPI_DOUBLE, MPI_MAX, world); + dvalue = maxall; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_fnorm() +{ + double **f = atom->f; + int nlocal = atom->nlocal; + + double dot = 0.0; + for (int i = 0; i < nlocal; i++) dot += f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2]; + double dotall; + MPI_Allreduce(&dot, &dotall, 1, MPI_DOUBLE, MPI_SUM, world); + dvalue = sqrt(dotall); +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_nbuild() +{ + bivalue = neighbor->ncalls; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_ndanger() +{ + bivalue = neighbor->ndanger; +} diff --git a/src/thermo.h b/src/thermo.h index ad1e1c440d..4d18c3be7e 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -57,6 +57,8 @@ class Thermo : protected Pointers { private: int nfield, nfield_initial; int *vtype; + int triclinic_general; // set by thermo_modify + std::string line; std::vector keyword, format, format_column_user, keyword_user; std::string format_line_user, format_float_user, format_int_user, format_bigint_user; @@ -81,6 +83,7 @@ class Thermo : protected Pointers { std::string image_fname; // data used by routines that compute single values + int ivalue; // integer value to print double dvalue; // double value to print bigint bivalue; // big integer value to print @@ -93,8 +96,10 @@ class Thermo : protected Pointers { // index = where they are in computes list // id = ID of Compute objects // Compute * = ptrs to the Compute objects + int index_temp, index_press_scalar, index_press_vector, index_pe; class Compute *temperature, *pressure, *pe; + double press_tensor[3][3]; int ncompute; // # of Compute objects called by thermo char **id_compute; // their IDs @@ -171,6 +176,7 @@ class Thermo : protected Pointers { void compute_vol(); void compute_density(); + void compute_lx(); void compute_ly(); void compute_lz(); @@ -186,14 +192,26 @@ class Thermo : protected Pointers { void compute_xz(); void compute_yz(); + void compute_avecx(); + void compute_avecy(); + void compute_avecz(); + void compute_bvecx(); + void compute_bvecy(); + void compute_bvecz(); + void compute_cvecx(); + void compute_cvecy(); + void compute_cvecz(); + void compute_xlat(); void compute_ylat(); void compute_zlat(); - void compute_bonds(); - void compute_angles(); - void compute_dihedrals(); - void compute_impropers(); + void compute_cella(); + void compute_cellb(); + void compute_cellc(); + void compute_cellalpha(); + void compute_cellbeta(); + void compute_cellgamma(); void compute_pxx(); void compute_pyy(); @@ -202,18 +220,24 @@ class Thermo : protected Pointers { void compute_pyz(); void compute_pxz(); + void compute_pxx_triclinic_general(); + void compute_pyy_triclinic_general(); + void compute_pzz_triclinic_general(); + void compute_pxy_triclinic_general(); + void compute_pxz_triclinic_general(); + void compute_pyz_triclinic_general(); + + void compute_bonds(); + void compute_angles(); + void compute_dihedrals(); + void compute_impropers(); + void compute_fmax(); void compute_fnorm(); void compute_nbuild(); void compute_ndanger(); - void compute_cella(); - void compute_cellb(); - void compute_cellc(); - void compute_cellalpha(); - void compute_cellbeta(); - void compute_cellgamma(); }; } // namespace LAMMPS_NS diff --git a/src/timer.cpp b/src/timer.cpp index 288ac28f43..c6f6401799 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -28,8 +28,8 @@ Timer::Timer(LAMMPS *_lmp) : Pointers(_lmp) { _level = NORMAL; _sync = OFF; - _timeout = -1; - _s_timeout = -1; + _timeout = -1.0; + _s_timeout = -1.0; _checkfreq = 10; _nextcheck = -1; this->_stamp(RESET); @@ -251,7 +251,7 @@ void Timer::modify_params(int narg, char **arg) // format timeout setting std::string timeout = "off"; - if (_timeout >= 0) { + if (_timeout >= 0.0) { std::tm tv = fmt::gmtime((std::time_t) _timeout); timeout = fmt::format("{:02d}:{:%M:%S}", tv.tm_yday * 24 + tv.tm_hour, tv); } diff --git a/src/timer.h b/src/timer.h index f7efa5ac64..371a895d1f 100644 --- a/src/timer.h +++ b/src/timer.h @@ -110,12 +110,12 @@ class Timer : protected Pointers { double previous_cpu; double previous_wall; double timeout_start; - int _level; // level of detail: off=0,loop=1,normal=2,full=3 - int _sync; // if nonzero, synchronize tasks before setting the timer - int _timeout; // max allowed wall time in seconds. infinity if negative - int _s_timeout; // copy of timeout for restoring after a forced timeout - int _checkfreq; // frequency of timeout checking - int _nextcheck; // loop number of next timeout check + double _timeout; // max allowed wall time in seconds. infinity if negative + double _s_timeout; // copy of timeout for restoring after a forced timeout + int _level; // level of detail: off=0,loop=1,normal=2,full=3 + int _sync; // if nonzero, synchronize tasks before setting the timer + int _checkfreq; // frequency of timeout checking + int _nextcheck; // loop number of next timeout check // update one specific timer array void _stamp(enum ttype); diff --git a/src/update.cpp b/src/update.cpp index 13ff7c872a..c9e57f9621 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -328,7 +328,8 @@ void Update::create_integrate(int narg, char **arg, int trysuffix) delete[] integrate_style; delete integrate; - integrate_style = nullptr; + // temporarily assign the style name without suffix (for error messages during creation) + integrate_style = utils::strdup(arg[0]); integrate = nullptr; int sflag; @@ -349,6 +350,7 @@ void Update::create_integrate(int narg, char **arg, int trysuffix) else if ((sflag == 3) && lmp->non_pair_suffix()) estyle += lmp->non_pair_suffix(); } + delete[] integrate_style; integrate_style = utils::strdup(estyle); } @@ -398,11 +400,10 @@ void Update::create_minimize(int narg, char **arg, int trysuffix) delete[] minimize_style; delete minimize; - minimize_style = nullptr; + // temporarily assign the style name without suffix (for error messages during creation) + minimize_style = utils::strdup(arg[0]); minimize = nullptr; - // temporarily assign the style name without suffix (for error messages during creation) - minimize_style = arg[0]; int sflag; new_minimize(arg[0], narg - 1, &arg[1], trysuffix, sflag); @@ -417,6 +418,7 @@ void Update::create_minimize(int narg, char **arg, int trysuffix) else if ((sflag == 3) && lmp->non_pair_suffix()) estyle += lmp->non_pair_suffix(); } + delete[] minimize_style; minimize_style = utils::strdup(estyle); } diff --git a/src/utils.cpp b/src/utils.cpp index 8aa33e14e6..87c46c47ab 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -17,6 +17,7 @@ #include "atom.h" #include "comm.h" #include "compute.h" +#include "domain.h" #include "error.h" #include "fix.h" #include "fmt/chrono.h" @@ -604,7 +605,7 @@ void utils::bounds(const char *file, int line, const std::string &str, { nlo = nhi = -1; - // check for illegal charcters + // check for illegal characters size_t found = str.find_first_not_of("*-0123456789"); if (found != std::string::npos) { if (error) error->all(file, line, "Invalid range string: {}", str); @@ -647,7 +648,39 @@ template void utils::bounds<>(const char *, int, const std::string &, bigint, bigint, long &, long &, Error *); template void utils::bounds<>(const char *, int, const std::string &, bigint, bigint, long long &, long long &, Error *); + // clang-format on +/* ---------------------------------------------------------------------- + wrapper for utils::bounds() that accepts type label input +------------------------------------------------------------------------- */ + +template +void utils::bounds_typelabel(const char *file, int line, const std::string &str, bigint nmin, + bigint nmax, TYPE &nlo, TYPE &nhi, LAMMPS *lmp, int mode) +{ + nlo = nhi = -1; + + // cannot check for typelabels without a LAMMPS instance or a box + if (!lmp || !lmp->domain->box_exist) + utils::bounds(file, line, str, nmin, nmax, nlo, nhi, nullptr); + + char *typestr = nullptr; + if ((typestr = utils::expand_type(FLERR, str, mode, lmp))) + nlo = nhi = utils::inumeric(FLERR, typestr, false, lmp); + + delete[] typestr; + if (nlo > -1) + return; + else + utils::bounds(file, line, str, nmin, nmax, nlo, nhi, lmp->error); +} + +template void utils::bounds_typelabel<>(const char *, int, const std::string &, bigint, bigint, + int &, int &, LAMMPS *, int); +template void utils::bounds_typelabel<>(const char *, int, const std::string &, bigint, bigint, + long &, long &, LAMMPS *, int); +template void utils::bounds_typelabel<>(const char *, int, const std::string &, bigint, bigint, + long long &, long long &, LAMMPS *, int); /* ------------------------------------------------------------------------- Expand list of arguments in arg to earg if arg contains wildcards @@ -915,6 +948,21 @@ char *utils::expand_type(const char *file, int line, const std::string &str, int return nullptr; } +/* ------------------------------------------------------------------------- + Expand type string to integer-valued numeric type from labelmap. + Not guaranteed to return a valid type. + For example, type <= 0 or type > Ntypes is checked in calling routine. +------------------------------------------------------------------------- */ + +int utils::expand_type_int(const char *file, int line, const std::string &str, int mode, + LAMMPS *lmp) +{ + char *typestr = expand_type(file, line, str, mode, lmp); + int out = inumeric(file, line, typestr ? typestr : str, false, lmp); + delete[] typestr; + return out; +} + /* ---------------------------------------------------------------------- Check grid reference for valid Compute or Fix which produces per-grid data errstr = name of calling command used if error is generated @@ -1629,7 +1677,7 @@ double utils::timespec2seconds(const std::string ×pec) try { for (i = 0; i < 3; i++) { if (!values.has_next()) break; - vals[i] = values.next_int(); + vals[i] = values.next_double(); } } catch (TokenizerException &) { return -1.0; diff --git a/src/utils.h b/src/utils.h index 335016831d..3b85824a68 100644 --- a/src/utils.h +++ b/src/utils.h @@ -331,6 +331,32 @@ namespace utils { void bounds(const char *file, int line, const std::string &str, bigint nmin, bigint nmax, TYPE &nlo, TYPE &nhi, Error *error); + /*! Same as utils::bounds(), but string may be a typelabel + * +\verbatim embed:rst + +.. versionadded:: 27June2024 + +This functions adds the following case to :cpp:func:`utils::bounds() `: + + - a single type label, typestr: nlo = nhi = label2type(typestr) + +\endverbatim + + * \param file name of source file for error message + * \param line line number in source file for error message + * \param str string to be processed + * \param nmin smallest possible lower bound + * \param nmax largest allowed upper bound + * \param nlo lower bound + * \param nhi upper bound + * \param lmp pointer to top-level LAMMPS class instance + * \param mode select labelmap using constants from Atom class */ + + template + void bounds_typelabel(const char *file, int line, const std::string &str, bigint nmin, + bigint nmax, TYPE &nlo, TYPE &nhi, LAMMPS *lmp, int mode); + /*! Expand list of arguments when containing fix/compute wildcards * * This function searches the list of arguments in *arg* for strings @@ -379,6 +405,12 @@ namespace utils { char *expand_type(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp); + /*! Expand type label string into its equivalent integer-valued numeric type + * + * This function has the same arguments as expand_type() but returns an integer value */ + + int expand_type_int(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp); + /*! Check grid reference for valid Compute or Fix which produces per-grid data * * This function checks if a command argument in the input script @@ -399,8 +431,8 @@ namespace utils { * \return index which column of data is referenced (0 for vec, 1-N for array) * \return ArgINFO::COMPUTE or FIX or UNKNOWN or NONE */ - int check_grid_reference(char *errstr, char *ref, int nevery, - char *&id, int &igrid, int &idata, int &index, LAMMPS *lmp); + int check_grid_reference(char *errstr, char *ref, int nevery, char *&id, int &igrid, int &idata, + int &index, LAMMPS *lmp); /*! Parse grid reference into 3 sub-strings * @@ -482,7 +514,7 @@ or the *-suffix/-sf* command line flag and return correspondingly modified strin std::string strip_style_suffix(const std::string &style, LAMMPS *lmp); -/*! Check if a string will likely have UTF-8 encoded characters + /*! Check if a string will likely have UTF-8 encoded characters * * UTF-8 uses the 7-bit standard ASCII table for the first 127 characters and * all other characters are encoded as multiple bytes. For the multi-byte diff --git a/src/variable.cpp b/src/variable.cpp index 8124d9c4a1..823a68a506 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -34,15 +34,18 @@ #include "random_mars.h" #include "region.h" #include "thermo.h" +#include "timer.h" #include "tokenizer.h" #include "universe.h" #include "update.h" #include "fmt/ranges.h" +#include #include #include #include +#include #include using namespace LAMMPS_NS; @@ -54,6 +57,12 @@ static constexpr int MAXLINE = 256; static constexpr int CHUNK = 1024; static constexpr int MAXFUNCARG = 6; +// must match enumerator in variable.h +const std::vector Variable::varstyles = { + "index", "loop", "world", "universe", "uloop", "string", "getenv", + "file", "atomfile", "format", "equal", "atom", "vector", "python", + "timer", "internal", "(unknown)"}; + static inline double MYROUND(double a) { return ((a - floor(a)) >= 0.5) ? ceil(a) : floor(a); } enum{ARG,OP}; @@ -73,7 +82,7 @@ enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY, // customize by adding a special function -enum{SUM,XMIN,XMAX,AVE,TRAP,SLOPE}; +enum{SUM,XMIN,XMAX,AVE,TRAP,SLOPE,SORT,RSORT,NOVECTOR}; static constexpr double BIG = 1.0e20; @@ -369,7 +378,8 @@ void Variable::set(int narg, char **arg) data[nvar][0] = new char[MAXLINE]; reader[nvar] = new VarReader(lmp,arg[0],arg[2],SCALARFILE); int flag = reader[nvar]->read_scalar(data[nvar][0]); - if (flag) error->all(FLERR,"File variable could not read value"); + if (flag) + error->all(FLERR,"File variable {} could not read value from {}", arg[0], arg[2]); // ATOMFILE for numbers // which = 1st value @@ -387,7 +397,8 @@ void Variable::set(int narg, char **arg) data[nvar][0] = nullptr; reader[nvar] = new VarReader(lmp,arg[0],arg[2],ATOMFILE); int flag = reader[nvar]->read_peratom(); - if (flag) error->all(FLERR,"Atomfile variable could not read values"); + if (flag) + error->all(FLERR,"Atomfile variable {} could not read values from {}", arg[0], arg[2]); // FORMAT // num = 3, which = 1st value @@ -869,6 +880,17 @@ void Variable::purge_atomfile() if (style[i] == ATOMFILE) remove(i); } +/* ---------------------------------------------------------------------- + called by "clear" command to reset all "in_progress" state variables + to avoid spurious "variable has circular dependency" issues +------------------------------------------------------------------------- */ + +void Variable::clear_in_progress() +{ + for (int i = 0; i < nvar; ++i) + eval_in_progress[i] = 0; +} + /* ---------------------------------------------------------------------- called by python command in input script simply pass input script line args to Python class @@ -1225,7 +1247,6 @@ int Variable::compute_vector(int ivar, double **result) int nlen = size_tree_vector(tree); if (nlen == 0) print_var_error(FLERR,"Vector-style variable has zero length",ivar); - if (nlen < 0) print_var_error(FLERR,"Inconsistent lengths in vector-style variable",ivar); @@ -1535,9 +1556,6 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->vector_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (index1 > compute->size_vector && - compute->size_vector_variable == 0) - print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -1546,10 +1564,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->invoked_flag |= Compute::INVOKED_VECTOR; } - if (compute->size_vector_variable && - index1 > compute->size_vector) value1 = 0.0; - else value1 = compute->vector[index1-1]; - argstack[nargstack++] = value1; + // wait to check index1 until after compute invocation + // to allow for computes with size_vector_variable == 1 + + if (index1 > compute->size_vector) + print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0); + + value1 = compute->vector[index1-1]; + argstack[nargstack++] = value1; // c_ID[i][j] = scalar from global array @@ -1557,9 +1579,6 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->array_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (index1 > compute->size_array_rows && - compute->size_array_rows_variable == 0) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); if (index2 > compute->size_array_cols) print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); if (!compute->is_initialized()) @@ -1570,9 +1589,13 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->invoked_flag |= Compute::INVOKED_ARRAY; } - if (compute->size_array_rows_variable && - index1 > compute->size_array_rows) value1 = 0.0; - else value1 = compute->array[index1-1][index2-1]; + // wait to check index1 until after compute invocation + // to allow for computes with size_array_rows_variable == 1 + + if (index1 > compute->size_array_rows) + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + + value1 = compute->array[index1-1][index2-1]; argstack[nargstack++] = value1; // C_ID[i] = scalar element of per-atom vector, note uppercase "C" @@ -1634,8 +1657,6 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->vector_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (compute->size_vector == 0) - print_var_error(FLERR,"Variable formula compute vector is zero length",ivar); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -1644,6 +1665,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->invoked_flag |= Compute::INVOKED_VECTOR; } + // wait to check vector size until after compute invocation + // to allow for computes with size_vector_variable == 1 + + if (compute->size_vector == 0) + print_var_error(FLERR,"Variable formula compute vector is zero length",ivar); + auto newtree = new Tree(); newtree->type = VECTORARRAY; newtree->array = compute->vector; @@ -1657,18 +1684,22 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->array_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (compute->size_array_rows == 0) - print_var_error(FLERR,"Variable formula compute array is zero length",ivar); - if (index1 > compute->size_array_cols) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); + if (index1 > compute->size_array_cols) + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) { compute->compute_array(); compute->invoked_flag |= Compute::INVOKED_ARRAY; } + // wait to check row count until after compute invocation + // to allow for computes with size_array_rows_variable == 1 + + if (compute->size_array_rows == 0) + print_var_error(FLERR,"Variable formula compute array has zero rows",ivar); + auto newtree = new Tree(); newtree->type = VECTORARRAY; newtree->array = &compute->array[0][index1-1]; @@ -1798,13 +1829,16 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->vector_flag) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); - if (index1 > fix->size_vector && - fix->size_vector_variable == 0) + if (index1 > fix->size_vector && fix->size_vector_variable == 0) print_var_error(FLERR,"Variable formula fix vector is accessed out-of-range",ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); - value1 = fix->compute_vector(index1-1); + // if index exceeds variable vector length, use a zero value + // this can be useful if vector length is not known a priori + + if (fix->size_vector_variable && index1 > fix->size_vector) value1 = 0.0; + else value1 = fix->compute_vector(index1-1); argstack[nargstack++] = value1; // f_ID[i][j] = scalar from global array @@ -1813,15 +1847,18 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->array_flag) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); - if (index1 > fix->size_array_rows && - fix->size_array_rows_variable == 0) + if (index1 > fix->size_array_rows && fix->size_array_rows_variable == 0) print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); if (index2 > fix->size_array_cols) print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); - value1 = fix->compute_array(index1-1,index2-1); + // if index exceeds variable array rows, use a zero value + // this can be useful if array size is not known a priori + + if (fix->size_array_rows_variable && index1 > fix->size_array_rows) value1 = 0.0; + else value1 = fix->compute_array(index1-1,index2-1); argstack[nargstack++] = value1; // F_ID[i] = scalar element of per-atom vector, note uppercase "F" @@ -2262,7 +2299,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (math_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar)); else if (group_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar)); - else if (special_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar)); + else if (special_function(std::string(word),contents,tree,treestack,ntreestack,argstack,nargstack,ivar,str,i,ptr)); else if (feature_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar)); else print_var_error(FLERR,fmt::format("Invalid math/group/special/feature function '{}()' " "in variable formula", word),ivar); @@ -4240,36 +4277,39 @@ Region *Variable::region_function(char *id, int ivar) return 0 if not a match, 1 if successfully processed customize by adding a special function: sum(x),min(x),max(x),ave(x),trap(x),slope(x), - gmask(x),rmask(x),grmask(x,y),next(x),is_file(x),is_ox(x), - extract_setting(x),label2type(x,y),is_typelabel(x,y) + gmask(x),rmask(x),grmask(x,y),next(x),is_file(x),is_os(x), + extract_setting(x),label2type(x,y),is_tpelabel(x,y) + is_timeout() ------------------------------------------------------------------------- */ -int Variable::special_function(char *word, char *contents, Tree **tree, Tree **treestack, - int &ntreestack, double *argstack, int &nargstack, int ivar) +// to simplify finding matches and assigning constants for functions operating on vectors + +static const std::unordered_map special_function_map = { + {"sum", SUM}, {"min", XMIN}, {"max", XMAX}, {"ave", AVE}, {"trap", TRAP}, {"slope", SLOPE}, + {"sort", SORT}, {"rsort", RSORT}, {"gmask", NOVECTOR}, {"rmask", NOVECTOR}, {"grmask", NOVECTOR}, + {"next", NOVECTOR}, {"is_file", NOVECTOR}, {"is_os", NOVECTOR}, {"extract_setting", NOVECTOR}, + {"label2type", NOVECTOR}, {"is_typelabel", NOVECTOR}, {"is_timeout", NOVECTOR} }; + +int Variable::special_function(const std::string &word, char *contents, Tree **tree, + Tree **treestack, int &ntreestack, double *argstack, + int &nargstack, int ivar, char *str, int &istr, char *&ptr) { double sx,sxx; double value,sy,sxy; - // word is not a match to any special function - - if (strcmp(word,"sum") != 0 && strcmp(word,"min") && strcmp(word,"max") != 0 && - strcmp(word,"ave") != 0 && strcmp(word,"trap") != 0 && strcmp(word,"slope") != 0 && - strcmp(word,"gmask") != 0 && strcmp(word,"rmask") != 0 && strcmp(word,"grmask") != 0 && - strcmp(word,"next") != 0 && strcmp(word,"is_file") != 0 && strcmp(word,"is_os") != 0 && - strcmp(word,"extract_setting") != 0 && strcmp(word,"label2type") != 0 && - strcmp(word,"is_typelabel") != 0) - return 0; + // return if "word" is not a match to any special function + if (special_function_map.find(word) == special_function_map.end()) return 0; // process label2type() separately b/c its label arg can have commas in it - if (strcmp(word,"label2type") == 0 || strcmp(word,"is_typelabel") == 0) { + if ((word == "label2type") || (word == "is_typelabel")) { if (!atom->labelmapflag) print_var_error(FLERR,fmt::format("Cannot use {}() function without a labelmap",word),ivar); std::string contents_copy(contents); auto pos = contents_copy.find_first_of(','); if (pos == std::string::npos) { - if (strcmp(word,"label2type") == 0) { + if (word == "label2type") { print_var_error(FLERR, fmt::format("Invalid label2type({}) function in variable formula", contents_copy), ivar); } else { @@ -4296,7 +4336,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t print_var_error(FLERR, fmt::format("Invalid kind {} in {}() in variable", kind, word),ivar); } - if (strcmp(word,"label2type") == 0) { + if (word == "label2type") { if (value == -1) print_var_error(FLERR, fmt::format("Invalid {} type label {} in label2type() in variable", kind, typestr), ivar); @@ -4323,22 +4363,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t char *args[MAXFUNCARG]; int narg = parse_args(contents,args); - // special functions that operate on global vectors + // special functions that operate on global vectors are NOT mapped to NOVECTOR - if (strcmp(word,"sum") == 0 || strcmp(word,"min") == 0 || - strcmp(word,"max") == 0 || strcmp(word,"ave") == 0 || - strcmp(word,"trap") == 0 || strcmp(word,"slope") == 0) { - - int method = 0; - if (strcmp(word,"sum") == 0) method = SUM; - else if (strcmp(word,"min") == 0) method = XMIN; - else if (strcmp(word,"max") == 0) method = XMAX; - else if (strcmp(word,"ave") == 0) method = AVE; - else if (strcmp(word,"trap") == 0) method = TRAP; - else if (strcmp(word,"slope") == 0) method = SLOPE; + int method = special_function_map.find(word)->second; + if (method != NOVECTOR) { if (narg != 1) - print_var_error(FLERR,"Invalid special function in variable formula",ivar); + print_var_error(FLERR,fmt::format("Invalid special function {}() in variable formula", word),ivar); Compute *compute = nullptr; Fix *fix = nullptr; @@ -4456,6 +4487,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t if (method == SLOPE) sx = sxx = sy = sxy = 0.0; else if (method == XMIN) value = BIG; else if (method == XMAX) value = -BIG; + std::vector unsorted; if (compute) { double *vec; @@ -4464,6 +4496,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t else vec = nullptr; } else vec = compute->vector; + if ((method == SORT) || (method == RSORT)) unsorted.reserve(nvec); int j = 0; for (int i = 0; i < nvec; i++) { if (method == SUM) value += vec[j]; @@ -4471,6 +4504,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t else if (method == XMAX) value = MAX(value,vec[j]); else if (method == AVE) value += vec[j]; else if (method == TRAP) value += vec[j]; + else if ((method == SORT) || (method == RSORT)) unsorted.push_back(vec[j]); else if (method == SLOPE) { sx += (double)i; sy += vec[j]; @@ -4492,6 +4526,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t else if (method == XMAX) value = MAX(value,one); else if (method == AVE) value += one; else if (method == TRAP) value += one; + else if ((method == SORT) || (method == RSORT)) unsorted.push_back(one); else if (method == SLOPE) { sx += (double)i; sy += one; @@ -4517,6 +4552,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t else if (method == XMAX) value = MAX(value,one); else if (method == AVE) value += one; else if (method == TRAP) value += one; + else if ((method == SORT) || (method == RSORT)) unsorted.push_back(one); else if (method == SLOPE) { sx += (double) i; sy += one; @@ -4536,18 +4572,55 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t else value = BIG; } - // save value in tree or on argstack + if ((method == SORT) || (method == RSORT)) { + if (method == SORT) std::sort(unsorted.begin(), unsorted.end(), std::less()); + if (method == RSORT) std::sort(unsorted.begin(), unsorted.end(), std::greater()); - if (tree) { - auto newtree = new Tree(); - newtree->type = VALUE; - newtree->value = value; - treestack[ntreestack++] = newtree; - } else argstack[nargstack++] = value; + if (tree) { + double *newvec; + memory->create(newvec,nvec,"variable:values"); + for (int m = 0; m < nvec; m++) + newvec[m] = unsorted[m]; + + auto newtree = new Tree(); + newtree->type = VECTORARRAY; + newtree->array = newvec; + newtree->nvector = nvec; + newtree->nstride = 1; + newtree->selfalloc = 1; + treestack[ntreestack++] = newtree; + + } else { + + // process one pair of trailing brackets + // point istr beyond last bracket + // nbracket = # of bracket pairs + // index = int inside each bracket pair, vector index + + if (str[istr] == '[') { + ptr = &str[istr]; + int index = int_between_brackets(ptr,1); + if (index > nvec) + print_var_error(FLERR, fmt::format("index {} exceeds vector size of {}\n", index, nvec),ivar); + istr = ptr-str+1; + argstack[nargstack++] = unsorted[index-1]; + } + } + } else { + + // save value in tree or on argstack + + if (tree) { + auto newtree = new Tree(); + newtree->type = VALUE; + newtree->value = value; + treestack[ntreestack++] = newtree; + } else argstack[nargstack++] = value; + } // mask special functions - } else if (strcmp(word,"gmask") == 0) { + } else if (word == "gmask") { if (tree == nullptr) print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar); if (narg != 1) @@ -4562,7 +4635,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t newtree->ivalue = group->bitmask[igroup]; treestack[ntreestack++] = newtree; - } else if (strcmp(word,"rmask") == 0) { + } else if (word == "rmask") { if (tree == nullptr) print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar); if (narg != 1) @@ -4576,7 +4649,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t newtree->region = region; treestack[ntreestack++] = newtree; - } else if (strcmp(word,"grmask") == 0) { + } else if (word == "grmask") { if (tree == nullptr) print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar); if (narg != 2) @@ -4596,7 +4669,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t // special function for file-style or atomfile-style variables - } else if (strcmp(word,"next") == 0) { + } else if (word == "next") { if (narg != 1) print_var_error(FLERR,"Invalid special function in variable formula",ivar); @@ -4647,7 +4720,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t } else print_var_error(FLERR,"Invalid variable style in special function next",ivar); - } else if (strcmp(word,"is_file") == 0) { + } else if (word == "is_file") { if (narg != 1) print_var_error(FLERR,"Invalid is_file() function in variable formula",ivar); @@ -4664,7 +4737,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t treestack[ntreestack++] = newtree; } else argstack[nargstack++] = value; - } else if (strcmp(word,"is_os") == 0) { + } else if (word == "is_os") { if (narg != 1) print_var_error(FLERR,"Invalid is_os() function in variable formula",ivar); value = utils::strmatch(platform::os_info(), args[0]) ? 1.0 : 0.0; @@ -4677,7 +4750,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t treestack[ntreestack++] = newtree; } else argstack[nargstack++] = value; - } else if (strcmp(word,"extract_setting") == 0) { + } else if (word == "extract_setting") { if (narg != 1) print_var_error(FLERR,"Invalid extract_setting() function in variable formula",ivar); value = lammps_extract_setting(lmp, args[0]); @@ -4694,6 +4767,21 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t newtree->value = value; treestack[ntreestack++] = newtree; } else argstack[nargstack++] = value; + + } else if (word == "is_timeout") { + if ((narg != 1) || (std::string(args[0]).size() != 0)) + print_var_error(FLERR,"Invalid is_timeout() function in variable formula",ivar); + value = timer->is_timeout() ? 1.0 : 0.0; + + // save value in tree or on argstack + + if (tree) { + auto newtree = new Tree(); + newtree->type = VALUE; + newtree->value = value; + treestack[ntreestack++] = newtree; + } else argstack[nargstack++] = value; + } // delete stored args @@ -5398,7 +5486,8 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) : if (me == 0) { fp = fopen(file,"r"); if (fp == nullptr) - error->one(FLERR,"Cannot open file variable file {}: {}", file, utils::getsyserror()); + error->one(FLERR,"Cannot open {} variable {} file {}: {}", (style == Variable::ATOMFILE) + ? "atomfile" : "file", name, file, utils::getsyserror()); } // if atomfile-style variable, must store per-atom values read from file @@ -5456,14 +5545,12 @@ int VarReader::read_scalar(char *str) while (true) { ptr = fgets(str,MAXLINE,fp); if (!ptr) { n=0; break; } // end of file - ptr[strcspn(ptr,"#")] = '\0'; // strip comment - ptr += strspn(ptr," \t\n\r\f"); // strip leading whitespace - ptr[strcspn(ptr," \t\n\r\f")] = '\0'; // strip trailing whitespace - n = strlen(ptr) + 1; + auto line = utils::trim(utils::trim_comment(str)); + n = line.size() + 1; if (n == 1) continue; // skip if blank line + memcpy(str, line.c_str(), n); break; } - if (n > 0) memmove(str,ptr,n); // move trimmed string back } MPI_Bcast(&n,1,MPI_INT,0,world); if (n == 0) return 1; @@ -5479,9 +5566,9 @@ int VarReader::read_scalar(char *str) int VarReader::read_peratom() { - int i,m,n,nchunk,eof; + int i,m,nchunk,eof; tagint tag; - char *ptr,*next; + char *ptr; double value; // set all per-atom values to 0.0 @@ -5495,24 +5582,22 @@ int VarReader::read_peratom() // read one string from file, convert to Nlines char str[MAXLINE]; + bigint nlines = 0; if (me == 0) { while (true) { ptr = fgets(str,MAXLINE,fp); - if (!ptr) { n=0; break; } // end of file - ptr[strcspn(ptr,"#")] = '\0'; // strip comment - ptr += strspn(ptr," \t\n\r\f"); // strip leading whitespace - ptr[strcspn(ptr," \t\n\r\f")] = '\0'; // strip trailing whitespace - n = strlen(ptr) + 1; - if (n == 1) continue; // skip if blank line + if (!ptr) { nlines = 0; break; } // end of file + Tokenizer words(utils::trim(utils::trim_comment(str))); + if (words.count() == 0) continue; // skip if blank or comment line + if (words.count() != 1) + error->one(FLERR, "Expected 1 token but found {} when parsing {}", words.count(), str); + nlines = utils::bnumeric(FLERR,words.next(),true,lmp); break; } - memmove(str,ptr,n); // move trimmed string back } + MPI_Bcast(&nlines,1,MPI_LMP_BIGINT,0,world); + if (nlines == 0) return 1; - MPI_Bcast(&n,1,MPI_INT,0,world); - if (n == 0) return 1; - MPI_Bcast(str,n,MPI_CHAR,0,world); - bigint nlines = utils::bnumeric(FLERR,str,false,lmp); tagint map_tag_max = atom->map_tag_max; bigint nread = 0; @@ -5521,24 +5606,22 @@ int VarReader::read_peratom() eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) return 1; - char *buf = buffer; - for (i = 0; i < nchunk; i++) { - next = strchr(buf,'\n'); - *next = '\0'; + for (const auto &line : utils::split_lines(buffer)) { try { - ValueTokenizer words(buf); + ValueTokenizer words(utils::trim_comment(utils::trim(line))); + if (words.count() == 0) continue; // skip comment or empty lines + if (words.count() != 2) + throw TokenizerException(fmt::format("expected 2 tokens but found {}", words.count()), ""); tag = words.next_bigint(); value = words.next_double(); + ++nread; } catch (TokenizerException &e) { - error->all(FLERR,"Invalid atomfile line '{}': {}",buf,e.what()); + error->all(FLERR,"Invalid atomfile line '{}': {}", line, e.what()); } if ((tag <= 0) || (tag > map_tag_max)) error->all(FLERR,"Invalid atom ID {} in variable file", tag); if ((m = atom->map(tag)) >= 0) vstore[m] = value; - buf = next + 1; } - - nread += nchunk; } return 0; diff --git a/src/variable.h b/src/variable.h index 8acfa5bcc7..6aeba848a8 100644 --- a/src/variable.h +++ b/src/variable.h @@ -35,6 +35,7 @@ class Variable : protected Pointers { void set_arrays(int); void python_command(int, char **); void purge_atomfile(); + void clear_in_progress(); int equalstyle(int); int atomstyle(int); @@ -56,7 +57,7 @@ class Variable : protected Pointers { int nvar; // # of defined variables char **names; // name of each variable - // must match "varstyles" array in info.cpp + // must match "varstyles" array in variables.cpp, UNKNOWN must be last. enum { INDEX, LOOP, @@ -73,9 +74,11 @@ class Variable : protected Pointers { VECTOR, PYTHON, TIMER, - INTERNAL + INTERNAL, + UNKNOWN }; static constexpr int VALUELENGTH = 64; + static const std::vector varstyles; private: int me; @@ -141,7 +144,8 @@ class Variable : protected Pointers { int math_function(char *, char *, Tree **, Tree **, int &, double *, int &, int); int group_function(char *, char *, Tree **, Tree **, int &, double *, int &, int); Region *region_function(char *, int); - int special_function(char *, char *, Tree **, Tree **, int &, double *, int &, int); + int special_function(const std::string &, char *, Tree **, Tree **, int &, double *, int &, + int, char *, int &, char *&); int feature_function(char *, char *, Tree **, Tree **, int &, double *, int &, int); void peratom2global(int, char *, double *, int, tagint, Tree **, Tree **, int &, double *, int &); void custom2global(int *, double *, int, tagint, Tree **, Tree **, int &, double *, int &); diff --git a/src/version.h b/src/version.h index 76ede29b68..eb26209afb 100644 --- a/src/version.h +++ b/src/version.h @@ -1,2 +1 @@ -#define LAMMPS_VERSION "7 Feb 2024" -#define LAMMPS_UPDATE "Development" +#define LAMMPS_VERSION "27 Jun 2024" diff --git a/src/write_data.cpp b/src/write_data.cpp index 5454edab44..bc6f1773d4 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -72,8 +72,12 @@ void WriteData::command(int narg, char **arg) pairflag = II; coeffflag = 1; fixflag = 1; + triclinic_general = 0; lmapflag = 1; - // store current (default) setting since we may change it. + + // store current (default) setting since we may change it + + int domain_triclinic_general = domain->triclinic_general; int types_style = atom->types_style; int noinit = 0; @@ -94,6 +98,9 @@ void WriteData::command(int narg, char **arg) } else if (strcmp(arg[iarg],"nofix") == 0) { fixflag = 0; iarg++; + } else if (strcmp(arg[iarg],"triclinic/general") == 0) { + triclinic_general = 1; + iarg++; } else if (strcmp(arg[iarg],"nolabelmap") == 0) { lmapflag = 0; iarg++; @@ -106,6 +113,14 @@ void WriteData::command(int narg, char **arg) } else error->all(FLERR,"Unknown write_data keyword: {}", arg[iarg]); } + // temporarily disable domain->triclinic_general if output not requested + + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Write_data triclinic/general for system " + "that is not general triclinic"); + if (!triclinic_general && domain->triclinic_general) + domain->triclinic_general = 0; + // init entire system since comm->exchange is done // comm::init needs neighbor::init needs pair::init needs kspace::init, etc // exception is when called by -r command-line switch @@ -135,7 +150,10 @@ void WriteData::command(int narg, char **arg) } write(file); - // restore saved setting + + // restore saved settings + + domain->triclinic_general = domain_triclinic_general; atom->types_style = types_style; } @@ -204,6 +222,11 @@ void WriteData::write(const std::string &file) if (coeffflag) force_fields(); } + // if general triclinic output: + // reset internal per-atom data that needs rotation + + if (domain->triclinic_general) atom->avec->write_data_restricted_to_general(); + // per atom info in Atoms and Velocities sections // must not write velocities without tags since we cannot read them back @@ -239,6 +262,11 @@ void WriteData::write(const std::string &file) if (ifix->wd_section) for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m); + // if general triclinic output: + // restore internal per-atom data that was rotated + + if (domain->triclinic_general) atom->avec->write_data_restore_restricted(); + // close data file if (me == 0) fclose(fp); @@ -294,15 +322,24 @@ void WriteData::header() for (int m = 0; m < ifix->wd_header; m++) ifix->write_data_header(fp,m); - // box info + // box info: orthogonal, restricted triclinic, or general triclinic (if requested) - auto box = fmt::format("\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n", - domain->boxlo[0],domain->boxhi[0], - domain->boxlo[1],domain->boxhi[1], - domain->boxlo[2],domain->boxhi[2]); - if (domain->triclinic) - box += fmt::format("{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz); - fputs(box.c_str(),fp); + if (!domain->triclinic_general) { + fmt::print(fp,"\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n", + domain->boxlo[0],domain->boxhi[0], + domain->boxlo[1],domain->boxhi[1], + domain->boxlo[2],domain->boxhi[2]); + if (domain->triclinic) + fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz); + + } else if (domain->triclinic_general) { + fmt::print(fp,"\n{} {} {} avec\n{} {} {} bvec\n{} {} {} cvec\n", + domain->avec[0],domain->avec[1],domain->avec[2], + domain->bvec[0],domain->bvec[1],domain->bvec[2], + domain->cvec[0],domain->cvec[1],domain->cvec[2]); + fmt::print(fp,"{} {} {} abc origin\n", + domain->boxlo[0],domain->boxlo[1],domain->boxlo[2]); + } } /* ---------------------------------------------------------------------- diff --git a/src/write_data.h b/src/write_data.h index f0df9b0c5f..ebaa97ffc0 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -35,6 +35,7 @@ class WriteData : public Command { int pairflag; int coeffflag; int fixflag; + int triclinic_general; int lmapflag; FILE *fp; bigint nbonds_local, nbonds; diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 89dd48e0ba..8cd7dec88e 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -45,11 +45,16 @@ void WriteDump::command(int narg, char **arg) // create the Dump instance // create dump command line with extra required args + // work around "fix not computed at compatible times" errors. + + int dumpfreq = MAX(1, update->nsteps); + dumpfreq += update->ntimestep % dumpfreq; + auto dumpargs = new char *[modindex + 2]; - dumpargs[0] = (char *) "WRITE_DUMP"; // dump id - dumpargs[1] = arg[0]; // group - dumpargs[2] = arg[1]; // dump style - dumpargs[3] = utils::strdup(std::to_string(MAX(update->ntimestep, 1))); // dump frequency + dumpargs[0] = (char *) "WRITE_DUMP"; // dump id + dumpargs[1] = arg[0]; // group + dumpargs[2] = arg[1]; // dump style + dumpargs[3] = utils::strdup(std::to_string(dumpfreq)); // dump frequency for (int i = 2; i < modindex; ++i) dumpargs[i + 2] = arg[i]; diff --git a/src/write_restart.cpp b/src/write_restart.cpp index ad279c14f6..a2022deeb9 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -448,6 +448,10 @@ void WriteRestart::header() write_double(XZ,domain->xz); write_double(YZ,domain->yz); + write_int(TRICLINIC_GENERAL,domain->triclinic_general); + if (domain->triclinic_general) + write_double_vec(ROTATE_G2R,9,&domain->rotate_g2r[0][0]); + write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]); write_double_vec(SPECIAL_COUL,3,&force->special_coul[1]); diff --git a/tools/binary2txt.cpp b/tools/binary2txt.cpp index b77614a8fc..2369057324 100644 --- a/tools/binary2txt.cpp +++ b/tools/binary2txt.cpp @@ -60,6 +60,7 @@ int main(int narg, char **arg) bigint ntimestep, natoms; int size_one, nchunk, triclinic; double xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz; + double ax, ay, az, bx, by, bz, cx, cy, cz, abcx, abcy, abcz; int boundary[3][2]; char boundstr[9]; @@ -133,17 +134,39 @@ int main(int narg, char **arg) fread(&natoms, sizeof(bigint), 1, fp); fread(&triclinic, sizeof(int), 1, fp); fread(&boundary[0][0], 6 * sizeof(int), 1, fp); - fread(&xlo, sizeof(double), 1, fp); - fread(&xhi, sizeof(double), 1, fp); - fread(&ylo, sizeof(double), 1, fp); - fread(&yhi, sizeof(double), 1, fp); - fread(&zlo, sizeof(double), 1, fp); - fread(&zhi, sizeof(double), 1, fp); - if (triclinic) { + + if (triclinic == 0) { + fread(&xlo, sizeof(double), 1, fp); + fread(&xhi, sizeof(double), 1, fp); + fread(&ylo, sizeof(double), 1, fp); + fread(&yhi, sizeof(double), 1, fp); + fread(&zlo, sizeof(double), 1, fp); + fread(&zhi, sizeof(double), 1, fp); + } else if (triclinic == 1) { + fread(&xlo, sizeof(double), 1, fp); + fread(&xhi, sizeof(double), 1, fp); + fread(&ylo, sizeof(double), 1, fp); + fread(&yhi, sizeof(double), 1, fp); + fread(&zlo, sizeof(double), 1, fp); + fread(&zhi, sizeof(double), 1, fp); fread(&xy, sizeof(double), 1, fp); fread(&xz, sizeof(double), 1, fp); fread(&yz, sizeof(double), 1, fp); + } else if (triclinic == 2) { + fread(&ax, sizeof(double), 1, fp); + fread(&ay, sizeof(double), 1, fp); + fread(&az, sizeof(double), 1, fp); + fread(&bx, sizeof(double), 1, fp); + fread(&by, sizeof(double), 1, fp); + fread(&bz, sizeof(double), 1, fp); + fread(&cx, sizeof(double), 1, fp); + fread(&cy, sizeof(double), 1, fp); + fread(&cz, sizeof(double), 1, fp); + fread(&abcx, sizeof(double), 1, fp); + fread(&abcy, sizeof(double), 1, fp); + fread(&abcz, sizeof(double), 1, fp); } + fread(&size_one, sizeof(int), 1, fp); if (magic_string && revision > 0x0001) { @@ -201,16 +224,21 @@ int main(int narg, char **arg) } boundstr[8] = '\0'; - if (!triclinic) { + if (triclinic == 0) { fprintf(fptxt, "ITEM: BOX BOUNDS %s\n", boundstr); fprintf(fptxt, "%-1.16e %-1.16e\n", xlo, xhi); fprintf(fptxt, "%-1.16e %-1.16e\n", ylo, yhi); fprintf(fptxt, "%-1.16e %-1.16e\n", zlo, zhi); - } else { + } else if (triclinic == 1) { fprintf(fptxt, "ITEM: BOX BOUNDS xy xz yz %s\n", boundstr); fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", xlo, xhi, xy); fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", ylo, yhi, xz); fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", zlo, zhi, yz); + } else if (triclinic == 2) { + fprintf(fptxt, "ITEM: BOX BOUNDS abc origin %s\n", boundstr); + fprintf(fptxt, "%-1.16e %-1.16e %-1.16e %-1.16e\n", ax, ay, az, abcx); + fprintf(fptxt, "%-1.16e %-1.16e %-1.16e %-1.16e\n", bx, by, bz, abcy); + fprintf(fptxt, "%-1.16e %-1.16e %-1.16e %-1.16e\n", cx, cy, cz, abcz); } if (columns) diff --git a/tools/fep/fep.py b/tools/fep/fep.py index c7656c5ef5..cdcf3f10c6 100755 --- a/tools/fep/fep.py +++ b/tools/fep/fep.py @@ -2,23 +2,40 @@ # fep.py - calculate free energy from compute fep results import sys +from argparse import ArgumentParser import math -if len(sys.argv) < 2: - print("Free Energy Perturbation") - print("usage: fep.py temperature < out.fep") - sys.exit() +def compute_fep(): -rt = 0.008314 / 4.184 * float(sys.argv[1]) # in kcal/mol + parser = ArgumentParser(description='A python script to calculate free energy from compute fep results') -v = 1.0 -sum = 0.0 -for line in sys.stdin: - if line.startswith("#"): - continue - tok = line.split() - if len(tok) == 4: - v = float(tok[3]) - sum += math.log(float(tok[2]) / v) + parser.add_argument("units", help="unit system can be lj, real or si") + parser.add_argument("Temperature", type=float, help="The temperature of the system") + parser.add_argument("InputFile", help="The name of the file with the data from compute fep.") + + args = parser.parse_args() + + r_value = {'lj': 1.0, 'real': 0.0019872036, 'si': 8.31446} + + if args.units in r_value: + rt = r_value[args.units] * args.Temperature + else: + sys.exit("The provided units keyword is not valid") + + v = 1.0 + mysum = 0.0 + + with open(args.InputFile, "r") as input_file: + for line in input_file: + if line.startswith("#"): + continue + tok = line.split() + if len(tok) == 4: + v = float(tok[3]) + mysum += math.log(float(tok[2]) / v) + + print(-rt * mysum) + +if __name__ == "__main__": + compute_fep() -print(-rt * sum) diff --git a/tools/i-pi/.vimrc b/tools/i-pi/.vimrc deleted file mode 100644 index fd7d41af27..0000000000 --- a/tools/i-pi/.vimrc +++ /dev/null @@ -1,4 +0,0 @@ -set tabstop=3 -set softtabstop=3 -set shiftwidth=3 -set expandtab diff --git a/tools/i-pi/MANIFEST.in b/tools/i-pi/MANIFEST.in deleted file mode 100644 index 9561fb1061..0000000000 --- a/tools/i-pi/MANIFEST.in +++ /dev/null @@ -1 +0,0 @@ -include README.rst diff --git a/tools/i-pi/README.md b/tools/i-pi/README.md new file mode 100644 index 0000000000..2c522a08bd --- /dev/null +++ b/tools/i-pi/README.md @@ -0,0 +1,18 @@ +This folder used to contain a bundled version of [i-PI](https://ipi-code.org) +but the bundled version was removed in 06/2024. + +i-PI is available via PyPI using the pip package manager at: +https://pypi.org/project/ipi/ + +Here are the commands to set up a virtual environment and +install i-PI into it with all its dependencies. + +``` sh +python -m venv ipienv +source ipienv/bin/activate +pip install --upgrade pip +pip install ipi +``` + +For further information and other methods of installing i-PI, +please consult the [i-PI home page](https://ipi-code.org). diff --git a/tools/i-pi/README.rst b/tools/i-pi/README.rst deleted file mode 100644 index 8d10b343f8..0000000000 --- a/tools/i-pi/README.rst +++ /dev/null @@ -1,49 +0,0 @@ -i-PI V1.0 -- LAMMPS -------------------- - -A Python interface for ab initio path integral molecular dynamics simulations. -i-PI is composed of a Python server (i-pi itself, that does not need to be -compiled but only requires a relatively recent version of Python and Numpy) -that propagates the (path integral) dynamics of the nuclei, and of an external -code that acts as client and computes the electronic energy and forces. - -This is typically a patched version of an electronic structure code, but a -simple self-contained Fortran driver that implements Lennard-Jones and -Silveira-Goldman potentials is included for test purposes. - -This folder contains a stripped-down version to be used with LAMMPS, and might -not contain all the features of the latest version. Please see -[http://epfl-cosmo.github.io/gle4md/index.html?page=ipi] or -[http://github.com/i-pi/i-pi] to obtain an up-to-date version. - - -Quick Installation and Test ---------------------------- - -Follow these instruction to test i-PI. These assume to be run from a Linux -environment, with a recent version of Python, Numpy and gfortran, and that -the terminal is initially in the i-pi package directory (the directory -containing this file). - -* Generate the driver code - -:: - -$ cd driver -$ make -$ cd .. - -* Run one of the examples - -This will first start the wrapper in the background, redirecting the output on -a log file, then run a couple of instances of the driver code and then follow -the progress of the wrapper by monitoring the log file:: - -$ cd examples/tutorial/tutorial-1/ -$ ../../../i-pi tutorial-1.xml > log & -$ ../../../drivers/driver.x -h localhost -p 31415 -m sg -o 15 & -$ ../../../drivers/driver.x -h localhost -p 31415 -m sg -o 15 & -$ tail -f log - -The monitoring can be interrupted with ``CTRL+C`` when the run has finished (5000 steps) - diff --git a/tools/i-pi/drivers/LJ.f90 b/tools/i-pi/drivers/LJ.f90 deleted file mode 100644 index 8341c64be7..0000000000 --- a/tools/i-pi/drivers/LJ.f90 +++ /dev/null @@ -1,215 +0,0 @@ -! This performs the calculations necessary to run a Lennard-Jones (LJ) -! simulation. -! -! Copyright (C) 2013, Joshua More and Michele Ceriotti -! -! Permission is hereby granted, free of charge, to any person obtaining -! a copy of this software and associated documentation files (the -! "Software"), to deal in the Software without restriction, including -! without limitation the rights to use, copy, modify, merge, publish, -! distribute, sublicense, and/or sell copies of the Software, and to -! permit persons to whom the Software is furnished to do so, subject to -! the following conditions: -! -! The above copyright notice and this permission notice shall be included -! in all copies or substantial portions of the Software. -! -! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -! EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -! MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. -! IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY -! CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -! TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE -! SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -! -! -! This contains the functions that calculate the potential, forces and -! virial tensor of a single-component LJ system. -! Includes functions which calculate the long-range correction terms for a -! simulation with a sharp nearest-neighbour cut-off. -! -! Functions: -! LJ_functions: Calculates the LJ pair potential and the magnitude of the -! forces acting on a pair of atoms. -! LJ_fij: Calculates the LJ pair potential and force vector for the -! interaction of a pair of atoms. -! LJ_longrange: Calculates the long range correction to the potential -! and virial. -! LJ_getall: Calculates the potential and virial of the system and the -! forces acting on all the atoms. - - MODULE LJ - USE DISTANCE - IMPLICIT NONE - - DOUBLE PRECISION, PARAMETER :: four_tau_by_3 = 8.3775804095727811d0 - - CONTAINS - - SUBROUTINE LJ_functions(sigma, eps, r, pot, force) - ! Calculates the magnitude of the LJ force and potential between - ! a pair of atoms at a given distance from each other. - ! - ! Args: - ! sigma: The LJ distance parameter. - ! eps: The LJ energy parameter. - ! r: The separation of the atoms. - ! pot: The LJ interaction potential. - ! force: The magnitude of the LJ force. - - DOUBLE PRECISION, INTENT(IN) :: sigma - DOUBLE PRECISION, INTENT(IN) :: eps - DOUBLE PRECISION, INTENT(IN) :: r - DOUBLE PRECISION, INTENT(OUT) :: pot - DOUBLE PRECISION, INTENT(OUT) :: force - - DOUBLE PRECISION sigma_by_r6 - - sigma_by_r6 = sigma/r - sigma_by_r6 = sigma_by_r6*sigma_by_r6*sigma_by_r6 - sigma_by_r6 = sigma_by_r6*sigma_by_r6 - - pot = 4*eps*(sigma_by_r6*(sigma_by_r6 - 1)) - force = 24*eps*(sigma_by_r6*(2*sigma_by_r6 - 1)/r) - - END SUBROUTINE - - SUBROUTINE LJ_fij(sigma, eps, rij, r, pot, fij) - ! This calculates the LJ potential energy and the magnitude and - ! direction of the force acting on a pair of atoms. - ! - ! Args: - ! sigma: The LJ distance parameter. - ! eps: The LJ energy parameter. - ! rij: The vector joining the two atoms. - ! r: The separation of the two atoms. - ! pot: The LJ interaction potential. - ! fij: The LJ force vector. - - DOUBLE PRECISION, INTENT(IN) :: sigma - DOUBLE PRECISION, INTENT(IN) :: eps - DOUBLE PRECISION, DIMENSION(3), INTENT(IN) :: rij - DOUBLE PRECISION, INTENT(IN) :: r - DOUBLE PRECISION, INTENT(OUT) :: pot - DOUBLE PRECISION, DIMENSION(3), INTENT(OUT) :: fij - - DOUBLE PRECISION f_tot - - CALL LJ_functions(sigma, eps, r, pot, f_tot) - fij = f_tot*rij/r - - END SUBROUTINE - - SUBROUTINE LJ_longrange(rc, sigma, eps, natoms, volume, pot_lr, vir_lr) - ! Calculates the long range correction to the total potential and - ! virial pressure. - ! - ! Uses the tail correction for a sharp cut-off, with no smoothing - ! function, as derived in Martyna and Hughes, Journal of Chemical - ! Physics, 110, 3275, (1999). - ! - ! Args: - ! rc: The cut-off radius. - ! sigma: The LJ distance parameter. - ! eps: The LJ energy parameter. - ! natoms: The number of atoms in the system. - ! volume: The volume of the system box. - ! pot_lr: The tail correction to the LJ interaction potential. - ! vir_lr: The tail correction to the LJ virial pressure. - - DOUBLE PRECISION, INTENT(IN) :: rc - DOUBLE PRECISION, INTENT(IN) :: sigma - DOUBLE PRECISION, INTENT(IN) :: eps - INTEGER, INTENT(IN) :: natoms - DOUBLE PRECISION, INTENT(IN) :: volume - DOUBLE PRECISION, INTENT(OUT) :: pot_lr - DOUBLE PRECISION, INTENT(OUT) :: vir_lr - - DOUBLE PRECISION sbyr, s3byr3, s6byr3, s6byr6, prefactor - - sbyr = sigma/rc - s3byr3 = sbyr*sbyr*sbyr - s6byr6 = s3byr3*s3byr3 - prefactor = four_tau_by_3*natoms*natoms*eps/volume - prefactor = prefactor*s3byr3*sigma*sigma*sigma - - pot_lr = prefactor*(s6byr6/3-1) - vir_lr = prefactor*(s6byr6-1) + pot_lr - - END SUBROUTINE - - SUBROUTINE LJ_getall(rc, sigma, eps, natoms, atoms, cell_h, cell_ih, index_list, n_list, pot, forces, virial) - ! Calculates the LJ potential energy and virial and the forces - ! acting on all the atoms. - ! - ! Args: - ! rc: The cut-off radius. - ! sigma: The LJ distance parameter. - ! eps: The LJ energy parameter. - ! natoms: The number of atoms in the system. - ! atoms: A vector holding all the atom positions. - ! cell_h: The simulation box cell vector matrix. - ! cell_ih: The inverse of the simulation box cell vector matrix. - ! index_list: A array giving the last index of n_list that - ! gives the neighbours of a given atom. - ! n_list: An array giving the indices of the atoms that neighbour - ! the atom determined by index_list. - ! pot: The total potential energy of the system. - ! forces: An array giving the forces acting on all the atoms. - ! virial: The virial tensor, not divided by the volume. - - DOUBLE PRECISION, INTENT(IN) :: rc - DOUBLE PRECISION, INTENT(IN) :: sigma - DOUBLE PRECISION, INTENT(IN) :: eps - INTEGER, INTENT(IN) :: natoms - DOUBLE PRECISION, DIMENSION(natoms,3), INTENT(IN) :: atoms - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_h - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_ih - INTEGER, DIMENSION(natoms), INTENT(IN) :: index_list - INTEGER, DIMENSION(natoms*(natoms-1)/2), INTENT(IN) :: n_list - DOUBLE PRECISION, INTENT(OUT) :: pot - DOUBLE PRECISION, DIMENSION(natoms,3), INTENT(OUT) :: forces - DOUBLE PRECISION, DIMENSION(3,3), INTENT(OUT) :: virial - - INTEGER i, j, k, l, start - DOUBLE PRECISION, DIMENSION(3) :: fij, rij - DOUBLE PRECISION r2, pot_ij, pot_lr, vir_lr, volume - - forces = 0.0d0 - pot = 0.0d0 - virial = 0.0d0 - - start = 1 - - DO i = 1, natoms - 1 - ! Only loops over the neighbour list, not all the atoms. - DO j = start, index_list(i) - CALL vector_separation(cell_h, cell_ih, atoms(i,:), atoms(n_list(j),:), rij, r2) - IF (r2 < rc*rc) THEN ! Only calculates contributions between neighbouring particles. - CALL LJ_fij(sigma, eps, rij, sqrt(r2), pot_ij, fij) - - forces(i,:) = forces(i,:) + fij - forces(n_list(j),:) = forces(n_list(j),:) - fij - pot = pot + pot_ij - DO k = 1, 3 - DO l = k, 3 - ! Only the upper triangular elements calculated. - virial(k,l) = virial(k,l) + fij(k)*rij(l) - ENDDO - ENDDO - ENDIF - ENDDO - start = index_list(i) + 1 - ENDDO - - ! Assuming an upper-triangular vector matrix for the simulation box. - volume = cell_h(1,1)*cell_h(2,2)*cell_h(3,3) - CALL LJ_longrange(rc, sigma, eps, natoms, volume, pot_lr, vir_lr) - pot = pot + pot_lr - DO k = 1, 3 - virial(k,k) = virial(k,k) + vir_lr - ENDDO - - END SUBROUTINE - - END MODULE diff --git a/tools/i-pi/drivers/Makefile b/tools/i-pi/drivers/Makefile deleted file mode 100644 index ed0336f689..0000000000 --- a/tools/i-pi/drivers/Makefile +++ /dev/null @@ -1,42 +0,0 @@ -# Makefile for the driver tests -# -# Permission is hereby granted, free of charge, to any person obtaining -# a copy of this software and associated documentation files (the -# "Software"), to deal in the Software without restriction, including -# without limitation the rights to use, copy, modify, merge, publish, -# distribute, sublicense, and/or sell copies of the Software, and to -# permit persons to whom the Software is furnished to do so, subject to -# the following conditions: -# -# The above copyright notice and this permission notice shall be included -# in all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. -# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY -# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE -# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - -.PHONY: all - -SOURCES=$(shell ls *.f90) -MODULES=distance.f90 LJ.f90 SG.f90 -OBJECTS=$(SOURCES:.f90=.o) sockets.o -all: modules sockets.o driver.x - -modules: $(MODULES) - gfortran -O3 -c $(MODULES) - -sockets.o: sockets.c - gcc -c -o sockets.o sockets.c - -driver.x: $(OBJECTS) - gfortran -O3 -o driver.x $(OBJECTS) - -%.o: %.f90 - gfortran -O3 -c $< - -clean: - rm *.o *.mod *.x diff --git a/tools/i-pi/drivers/README b/tools/i-pi/drivers/README deleted file mode 100644 index 563cbce9ce..0000000000 --- a/tools/i-pi/drivers/README +++ /dev/null @@ -1,14 +0,0 @@ - -- Driver code directory -- - - * This gives simple test driver codes. - - * Files: - - LJ.f90: Calculates the Lennard-Jones potential/forces/virial. - - SG.f90: Calculates the Silvera-Goldman potential/forces/virial. - - distance.f90: Deals with calculating the separation between atoms and - the neighbour list calculation. - - sockets.c: Contains the functions to create the client socket and read from - and write to it. - - driver.f90: Socket interface for the driver codes. - - Makefile: A makefile that which compiles all the fortran code as - necessary. diff --git a/tools/i-pi/drivers/SG.f90 b/tools/i-pi/drivers/SG.f90 deleted file mode 100644 index bb243b3469..0000000000 --- a/tools/i-pi/drivers/SG.f90 +++ /dev/null @@ -1,283 +0,0 @@ -! This performs the calculations necessary to run a simulation using a -! Silvera-Goldman (SG) potential for para-hydrogen. See I. Silvera and V. -! Goldman, J. Chem. Phys., 69, 4209 (1978). -! -! Copyright (C) 2013, Joshua More and Michele Ceriotti -! -! Permission is hereby granted, free of charge, to any person obtaining -! a copy of this software and associated documentation files (the -! "Software"), to deal in the Software without restriction, including -! without limitation the rights to use, copy, modify, merge, publish, -! distribute, sublicense, and/or sell copies of the Software, and to -! permit persons to whom the Software is furnished to do so, subject to -! the following conditions: -! -! The above copyright notice and this permission notice shall be included -! in all copies or substantial portions of the Software. -! -! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -! EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -! MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. -! IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY -! CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -! TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE -! SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -! -! -! This contains the functions that calculate the potential, forces and -! virial tensor of liquid para-hydrogen -! Includes functions which calculate the long-range correction terms for a -! simulation with a sharp nearest-neighbour cut-off. -! -! Functions: -! f_c: Calculates the damping function for the dispersive interactions -! at short range. -! exp_func: Calculates the short range repulsive part of the SG potential. -! SG_functions: Calculates the SG pair potential and the magnitude of the -! forces acting on a pair of atoms. -! SG_fij: Calculates the SG pair potential and force vector for the -! interaction of a pair of atoms. -! SG_longrange: Calculates the long range correction to the potential -! and virial. -! SG_getall: Calculates the potential and virial of the system and the -! forces acting on all the atoms. - - MODULE SG - USE DISTANCE - IMPLICIT NONE - - ! Parameters of the SG potential. This potential is of the form: - ! V(r) = exp(alpha - beta*r - delta*r**2) - - ! (C_6/r**6 + C_8/r**8 - C_9/r**9 + C_10/r**10)*f_c(r) - ! where f_c(r) = exp(-(rc_exp/r - 1)**2) if r <= rc_exp - ! = 1 otherwise - DOUBLE PRECISION, PARAMETER :: tau = 6.2831853071795862d0 !If you don't know why I used this name, you're not a real nerd - DOUBLE PRECISION, PARAMETER :: alpha = 1.713d0 - DOUBLE PRECISION, PARAMETER :: beta = 1.5671d0 - DOUBLE PRECISION, PARAMETER :: delta = 0.00993d0 - DOUBLE PRECISION, PARAMETER :: delta_diff = delta*2.0d0 - DOUBLE PRECISION, PARAMETER :: rc_exp = 8.32d0 - DOUBLE PRECISION, PARAMETER :: C_6 = 12.14d0 - DOUBLE PRECISION, PARAMETER :: C_8 = 215.2d0 - DOUBLE PRECISION, PARAMETER :: C_9 = 143.1d0 - DOUBLE PRECISION, PARAMETER :: C_10 = 4813.9d0 - DOUBLE PRECISION, PARAMETER :: C_6_diff = C_6*6d0 - DOUBLE PRECISION, PARAMETER :: C_8_diff = C_8*8d0 - DOUBLE PRECISION, PARAMETER :: C_9_diff = C_9*9d0 - DOUBLE PRECISION, PARAMETER :: C_10_diff = C_10*10d0 - DOUBLE PRECISION, PARAMETER :: C_6_int = C_6/3d0 - DOUBLE PRECISION, PARAMETER :: C_8_int = C_8/5d0 - DOUBLE PRECISION, PARAMETER :: C_9_int = C_9/6d0 - DOUBLE PRECISION, PARAMETER :: C_10_int = C_10/7d0 - - CONTAINS - - SUBROUTINE f_c(r, long_range, long_range_diff) - ! Calculates the damping function for the dispersive interactions - ! at short range. - ! - ! Args: - ! r: The separation of the atoms. - ! long_range: The value of the damping function. - ! long_range_diff: The differential of the damping function - ! with respect to r. - - DOUBLE PRECISION, INTENT(IN) :: r - DOUBLE PRECISION, INTENT(OUT) :: long_range - DOUBLE PRECISION, INTENT(OUT) :: long_range_diff - - DOUBLE PRECISION dist_frac - - IF (r > rc_exp) THEN - long_range = 1.0d0 - long_range_diff = 0.0d0 - ELSE - dist_frac = rc_exp/r - 1.0d0 - long_range = dexp(-(dist_frac)**2) - long_range_diff = 2.0d0*dist_frac*rc_exp*long_range/(r*r) - END IF - - END SUBROUTINE - - SUBROUTINE exp_func(r, pot, force) - ! Calculates the repulsive part of the SG force and potential - ! between a pair of atoms at a given distance from each other. - ! - ! Args: - ! r: The separation of the atoms. - ! pot: The repulsive part of the potential energy. - ! force: The magnitude of the repulsive part of the force. - - DOUBLE PRECISION, INTENT(IN) :: r - DOUBLE PRECISION, INTENT(OUT) :: pot - DOUBLE PRECISION, INTENT(OUT) :: force - - pot = dexp(alpha - r*(beta + delta*r)) - force = (beta + delta_diff*r)*pot - - END SUBROUTINE - - SUBROUTINE SG_functions(r, pot, force) - ! Calculates the magnitude of the SG force and potential between - ! a pair of atoms at a given distance from each other. - ! - ! Args: - ! r: The separation of the atoms. - ! pot: The SG interaction potential. - ! force: The magnitude of the SG force. - - DOUBLE PRECISION, INTENT(IN) :: r - DOUBLE PRECISION, INTENT(OUT) :: pot - DOUBLE PRECISION, INTENT(OUT) :: force - - DOUBLE PRECISION long_range, long_range_diff, disp, disp_diff, exp_pot, exp_force - DOUBLE PRECISION onr3, onr6, onr9, onr10 - - onr3 = 1/(r*r*r) - onr6 = onr3*onr3 - onr9 = onr6*onr3 - onr10 = onr9/r - - CALL exp_func(r, exp_pot, exp_force) - CALL f_c(r, long_range, long_range_diff) - - disp = -(C_6*onr6 + C_8*onr9*r - C_9*onr9 + C_10*onr10) - disp_diff = (C_6_diff*onr6/r + C_8_diff*onr9 - C_9_diff*onr10 + C_10_diff*onr10/r) - - pot = exp_pot + disp*long_range - force = exp_force - disp_diff*long_range - disp*long_range_diff - - END SUBROUTINE - - SUBROUTINE SG_fij(rij, r, pot, fij) - ! This calculates the SG potential energy and the magnitude and - ! direction of the force acting on a pair of atoms. - ! - ! Args: - ! rij: The vector joining the two atoms. - ! r: The separation of the two atoms. - ! pot: The SG interaction potential. - ! fij: The SG force vector. - - DOUBLE PRECISION, DIMENSION(3), INTENT(IN) :: rij - DOUBLE PRECISION, INTENT(IN) :: r - DOUBLE PRECISION, INTENT(OUT) :: pot - DOUBLE PRECISION, DIMENSION(3), INTENT(OUT) :: fij - - DOUBLE PRECISION f_tot - - CALL SG_functions(r, pot, f_tot) - fij = f_tot*rij/r - - END SUBROUTINE - - SUBROUTINE SG_longrange(rc, natoms, volume, pot_lr, vir_lr) - ! Calculates the long range correction to the total potential and - ! virial pressure. - ! - ! Uses the tail correction for a sharp cut-off, with no smoothing - ! function, as derived in Martyna and Hughes, Journal of Chemical - ! Physics, 110, 3275, (1999). - ! - ! Note that we will assume that rc > rc_exp, and that - ! exp(alpha - beta*rc - delta*rc**2) << 0, so we can neglect the - ! contribution of the repulsive potential and the dispersion - ! damping function in the long range correction terms. - ! - ! Args: - ! rc: The cut-off radius. - ! natoms: The number of atoms in the system. - ! volume: The volume of the system box. - ! pot_lr: The tail correction to the SG interaction potential. - ! vir_lr: The tail correction to the SG virial pressure. - - DOUBLE PRECISION, INTENT(IN) :: rc - INTEGER, INTENT(IN) :: natoms - DOUBLE PRECISION, INTENT(IN) :: volume - DOUBLE PRECISION, INTENT(OUT) :: pot_lr - DOUBLE PRECISION, INTENT(OUT) :: vir_lr - - DOUBLE PRECISION onr3, onr5, onr6, onr7, prefactor - - onr3 = 1/(rc*rc*rc) - onr6 = onr3*onr3 - onr5 = onr6*rc - onr7 = onr6/rc - prefactor = tau*natoms*natoms/volume - - pot_lr = prefactor*(-C_6_int*onr3 - C_8_int*onr5 + C_9_int*onr6 - C_10_int*onr7) - vir_lr = prefactor*(-C_6*onr3 - C_8*onr5 + C_9*onr6 - C_10*onr7)/3 + pot_lr - - END SUBROUTINE - - SUBROUTINE SG_getall(rc, natoms, atoms, cell_h, cell_ih, index_list, n_list, pot, forces, virial) - ! Calculates the SG potential energy and virial and the forces - ! acting on all the atoms. - ! - ! Args: - ! rc: The cut-off radius. - ! natoms: The number of atoms in the system. - ! atoms: A vector holding all the atom positions. - ! cell_h: The simulation box cell vector matrix. - ! cell_ih: The inverse of the simulation box cell vector matrix. - ! index_list: A array giving the last index of n_list that - ! gives the neighbours of a given atom. - ! n_list: An array giving the indices of the atoms that neighbour - ! the atom determined by index_list. - ! pot: The total potential energy of the system. - ! forces: An array giving the forces acting on all the atoms. - ! virial: The virial tensor, not divided by the volume. - - DOUBLE PRECISION, INTENT(IN) :: rc - INTEGER, INTENT(IN) :: natoms - DOUBLE PRECISION, DIMENSION(natoms,3), INTENT(IN) :: atoms - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_h - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_ih - INTEGER, DIMENSION(natoms), INTENT(IN) :: index_list - INTEGER, DIMENSION(natoms*(natoms-1)/2), INTENT(IN) :: n_list - DOUBLE PRECISION, INTENT(OUT) :: pot - DOUBLE PRECISION, DIMENSION(natoms,3), INTENT(OUT) :: forces - DOUBLE PRECISION, DIMENSION(3,3), INTENT(OUT) :: virial - - INTEGER i, j, k, l, start - DOUBLE PRECISION, DIMENSION(3) :: fij, rij - DOUBLE PRECISION r2, pot_ij, pot_lr, vir_lr, volume - - forces = 0.0d0 - pot = 0.0d0 - virial = 0.0d0 - - start = 1 - - DO i = 1, natoms - 1 - ! Only loops over the neighbour list, not all the atoms. - DO j = start, index_list(i) - CALL vector_separation(cell_h, cell_ih, atoms(i,:), atoms(n_list(j),:), rij, r2) - IF (r2 < rc*rc) THEN ! Only calculates contributions between neighbouring particles. - CALL SG_fij(rij, sqrt(r2), pot_ij, fij) - - forces(i,:) = forces(i,:) + fij - forces(n_list(j),:) = forces(n_list(j),:) - fij - pot = pot + pot_ij - DO k = 1, 3 - DO l = k, 3 - ! Only the upper triangular elements calculated. - virial(k,l) = virial(k,l) + fij(k)*rij(l) - ENDDO - ENDDO - ENDIF - ENDDO - start = index_list(i) + 1 - ENDDO - - ! Assuming an upper-triangular vector matrix for the simulation box. - volume = cell_h(1,1)*cell_h(2,2)*cell_h(3,3) - CALL SG_longrange(rc, natoms, volume, pot_lr, vir_lr) - pot = pot + pot_lr - DO k = 1, 3 - virial(k,k) = virial(k,k) + vir_lr - ENDDO - - END SUBROUTINE - - END MODULE diff --git a/tools/i-pi/drivers/distance.f90 b/tools/i-pi/drivers/distance.f90 deleted file mode 100644 index aa9cde3217..0000000000 --- a/tools/i-pi/drivers/distance.f90 +++ /dev/null @@ -1,174 +0,0 @@ -! This contains the algorithms needed to calculate the distance between atoms. -! -! Copyright (C) 2013, Joshua More and Michele Ceriotti -! -! Permission is hereby granted, free of charge, to any person obtaining a copy -! of this software and associated documentation files (the "Software"), to deal -! in the Software without restriction, including without limitation the rights -! to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -! copies of the Software, and to permit persons to whom the Software is -! furnished to do so, subject to the following conditions: - -! The above copyright notice and this permission notice shall be included in -! all copies or substantial portions of the Software. - -! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -! IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -! FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -! AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -! LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -! OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -! THE SOFTWARE. -! -! Functions: -! vector_separation: Calculates the vector separating two atoms. -! separation: Calculates the square distance between two vectors. -! nearest_neighbours: Generates arrays to calculate the pairs of atoms within -! a certain radius of each other. - - MODULE DISTANCE - IMPLICIT NONE - - CONTAINS - - SUBROUTINE vector_separation(cell_h, cell_ih, ri, rj, rij, r2) - ! Calculates the vector separating two atoms. - ! - ! Note that minimum image convention is used, so only the image of - ! atom j that is the shortest distance from atom i is considered. - ! - ! Also note that while this may not work if the simulation - ! box is highly skewed from orthorhombic, as - ! in this case it is possible to return a distance less than the - ! nearest neighbour distance. However, this will not be of - ! importance unless the cut-off radius is more than half the - ! width of the shortest face-face distance of the simulation box, - ! which should never be the case. - ! - ! Args: - ! cell_h: The simulation box cell vector matrix. - ! cell_ih: The inverse of the simulation box cell vector matrix. - ! ri: The position vector of atom i. - ! rj: The position vector of atom j - ! rij: The vector separating atoms i and j. - ! r2: The square of the distance between atoms i and j. - - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_h - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_ih - DOUBLE PRECISION, DIMENSION(3), INTENT(IN) :: ri - DOUBLE PRECISION, DIMENSION(3), INTENT(IN) :: rj - DOUBLE PRECISION, DIMENSION(3), INTENT(OUT) :: rij - DOUBLE PRECISION, INTENT(OUT) :: r2 - - INTEGER k - DOUBLE PRECISION, DIMENSION(3) :: sij - ! The separation in a basis where the simulation box - ! is a unit cube. - - sij = matmul(cell_ih, ri - rj) - DO k = 1, 3 - ! Finds the smallest separation of all the images of atom i and j - sij(k) = sij(k) - dnint(sij(k)) - ENDDO - rij = matmul(cell_h, sij) - r2 = dot_product(rij,rij) - - END SUBROUTINE - - SUBROUTINE separation(cell_h, cell_ih, ri, rj, r2) - ! Calculates the squared distance between two position vectors. - ! - ! Note that minimum image convention is used, so only the image of - ! atom j that is the shortest distance from atom i is considered. - ! - ! Also note that while this may not work if the simulation - ! box is highly skewed from orthorhombic, as - ! in this case it is possible to return a distance less than the - ! nearest neighbour distance. However, this will not be of - ! importance unless the cut-off radius is more than half the - ! width of the shortest face-face distance of the simulation box, - ! which should never be the case. - ! - ! Args: - ! cell_h: The simulation box cell vector matrix. - ! cell_ih: The inverse of the simulation box cell vector matrix. - ! ri: The position vector of atom i. - ! rj: The position vector of atom j - ! r2: The square of the distance between atoms i and j. - - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_h - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_ih - DOUBLE PRECISION, DIMENSION(3), INTENT(IN) :: ri - DOUBLE PRECISION, DIMENSION(3), INTENT(IN) :: rj - DOUBLE PRECISION, INTENT(OUT) :: r2 - - INTEGER k - ! The separation in a basis where the simulation box - ! is a unit cube. - DOUBLE PRECISION, DIMENSION(3) :: sij - DOUBLE PRECISION, DIMENSION(3) :: rij - - sij = matmul(cell_ih, ri - rj) - DO k = 1, 3 - ! Finds the smallest separation of all the images of atom i and j - sij(k) = sij(k) - dnint(sij(k)) - ENDDO - rij = matmul(cell_h, sij) - r2 = dot_product(rij, rij) - - END SUBROUTINE - - SUBROUTINE nearest_neighbours(rn, natoms, atoms, cell_h, cell_ih, index_list, n_list) - ! Creates a list of all the pairs of atoms that are closer together - ! than a certain distance. - ! - ! This takes all the positions, and calculates which ones are - ! shorter than the distance rn. This creates two vectors, index_list - ! and n_list. index_list(i) gives the last index of n_list that - ! corresponds to a neighbour of atom i. - ! - ! - ! Args: - ! rn: The nearest neighbour list cut-off parameter. This should - ! be larger than the potential cut-off radius. - ! natoms: The number of atoms in the system. - ! atoms: A vector holding all the atom positions. - ! cell_h: The simulation box cell vector matrix. - ! cell_ih: The inverse of the simulation box cell vector matrix. - ! index_list: A array giving the last index of n_list that - ! gives the neighbours of a given atom. Essentially keeps - ! track of how many atoms neighbour a given atom. - ! n_list: An array giving the indices of the atoms that neighbour - ! the atom determined by index_list. Essentially keeps track - ! of which atoms neighbour a given atom. - - DOUBLE PRECISION, INTENT(IN) :: rn - INTEGER, INTENT(IN) :: natoms - DOUBLE PRECISION, DIMENSION(:,:), INTENT(IN) :: atoms - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_h - DOUBLE PRECISION, DIMENSION(3,3), INTENT(IN) :: cell_ih - INTEGER, DIMENSION(natoms), INTENT(OUT) :: index_list - INTEGER, DIMENSION(natoms*(natoms-1)/2), INTENT(OUT) :: n_list - - INTEGER :: i, j - DOUBLE PRECISION r2 - - index_list(1) = 0 - - DO i = 1, natoms - 1 - DO j = i + 1, natoms - CALL separation(cell_h, cell_ih, atoms(i,:), atoms(j,:), r2) - IF (r2 < rn*rn) THEN - ! We have found an atom that neighbours atom i, so the - ! i-th index of index_list is incremented by one, and a new - ! entry is added to n_list. - index_list(i) = index_list(i) + 1 - n_list(index_list(i)) = j - ENDIF - ENDDO - index_list(i+1) = index_list(i) - ENDDO - - END SUBROUTINE - - END MODULE diff --git a/tools/i-pi/drivers/driver.f90 b/tools/i-pi/drivers/driver.f90 deleted file mode 100644 index 646f1e9add..0000000000 --- a/tools/i-pi/drivers/driver.f90 +++ /dev/null @@ -1,309 +0,0 @@ -! The main program which runs our driver test case potentials -! -! Copyright (C) 2013, Joshua More and Michele Ceriotti -! -! Permission is hereby granted, free of charge, to any person obtaining -! a copy of this software and associated documentation files (the -! "Software"), to deal in the Software without restriction, including -! without limitation the rights to use, copy, modify, merge, publish, -! distribute, sublicense, and/or sell copies of the Software, and to -! permit persons to whom the Software is furnished to do so, subject to -! the following conditions: -! -! The above copyright notice and this permission notice shall be included -! in all copies or substantial portions of the Software. -! -! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -! EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -! MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. -! IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY -! CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -! TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE -! SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -! -! -! Currently the potentials implemented are the Lennard-Jones -! potential, the Silvera-Goldman para-hydrogen potential and -! the ideal gas (i.e. no interaction at all) - - PROGRAM DRIVER - USE LJ - USE SG - IMPLICIT NONE - - ! SOCKET VARIABLES - INTEGER, PARAMETER :: MSGLEN=12 ! length of the headers of the driver/wrapper communication protocol - INTEGER socket, inet, port ! socket ID & address of the server - CHARACTER*1024 :: host - - ! COMMAND LINE PARSING - CHARACTER*1024 :: cmdbuffer, vops - INTEGER ccmd, vstyle - LOGICAL verbose - INTEGER commas(4), par_count ! stores the index of commas in the parameter string - DOUBLE PRECISION vpars(4) ! array to store the parameters of the potential - - ! SOCKET COMMUNICATION BUFFERS - CHARACTER*12 :: header - LOGICAL :: isinit=.false., hasdata=.false. - INTEGER cbuf - CHARACTER*2048 :: initbuffer ! it's unlikely a string this large will ever be passed... - DOUBLE PRECISION, ALLOCATABLE :: msgbuffer(:) - - ! PARAMETERS OF THE SYSTEM (CELL, ATOM POSITIONS, ...) - DOUBLE PRECISION sigma, eps, rc, rn, ks ! potential parameters - INTEGER nat - DOUBLE PRECISION pot - DOUBLE PRECISION, ALLOCATABLE :: atoms(:,:), forces(:,:) - DOUBLE PRECISION cell_h(3,3), cell_ih(3,3), virial(3,3) - DOUBLE PRECISION volume - - ! NEIGHBOUR LIST ARRAYS - INTEGER, DIMENSION(:), ALLOCATABLE :: n_list, index_list - DOUBLE PRECISION init_volume, init_rc ! needed to correctly adjust the cut-off radius for variable cell dynamics - DOUBLE PRECISION, ALLOCATABLE :: last_atoms(:,:) ! Holds the positions when the neighbour list is created - DOUBLE PRECISION displacement ! Tracks how far each atom has moved since the last call of nearest_neighbours - - INTEGER i - - ! parse the command line parameters - ! initialize defaults - ccmd = 0 - inet = 1 - host = "localhost"//achar(0) - port = 31415 - verbose = .false. - par_count = 0 - vstyle = -1 - - DO i = 1, IARGC() - CALL GETARG(i, cmdbuffer) - IF (cmdbuffer == "-u") THEN ! flag for unix socket - inet = 0 - ccmd = 0 - ELSEIF (cmdbuffer == "-h") THEN ! read the hostname - ccmd = 1 - ELSEIF (cmdbuffer == "-p") THEN ! reads the port number - ccmd = 2 - ELSEIF (cmdbuffer == "-m") THEN ! reads the style of the potential function - ccmd = 3 - ELSEIF (cmdbuffer == "-o") THEN ! reads the parameters - ccmd = 4 - ELSEIF (cmdbuffer == "-v") THEN ! flag for verbose standard output - verbose = .true. - ELSE - IF (ccmd == 0) THEN - WRITE(*,*) " Unrecognized command line argument", ccmd - WRITE(*,*) " SYNTAX: driver.x [-u] -h hostname -p port -m [gas|lj|sg|harm] -o 'comma_separated_parameters' [-v] " - WRITE(*,*) "" - WRITE(*,*) " For LJ potential use -o sigma,epsilon,cutoff " - WRITE(*,*) " For SG potential use -o cutoff " - WRITE(*,*) " For 1D harmonic oscillator use -o k " - WRITE(*,*) " For the ideal gas, no options needed! " - CALL EXIT(-1) - ENDIF - IF (ccmd == 1) THEN - host = trim(cmdbuffer)//achar(0) - ELSEIF (ccmd == 2) THEN - READ(cmdbuffer,*) port - ELSEIF (ccmd == 3) THEN - IF (trim(cmdbuffer) == "lj") THEN - vstyle = 1 - ELSEIF (trim(cmdbuffer) == "sg") THEN - vstyle = 2 - ELSEIF (trim(cmdbuffer) == "harm") THEN - vstyle = 3 - ELSEIF (trim(cmdbuffer) == "gas") THEN - vstyle = 0 ! ideal gas - ELSE - WRITE(*,*) " Unrecognized potential type ", trim(cmdbuffer) - WRITE(*,*) " Use -m [gas|lj|sg|harm] " - CALL EXIT(-1) - ENDIF - ELSEIF (ccmd == 4) THEN - par_count = 1 - commas(1) = 0 - DO WHILE (index(cmdbuffer(commas(par_count)+1:), ',') > 0) - commas(par_count + 1) = index(cmdbuffer(commas(par_count)+1:), ',') + commas(par_count) - READ(cmdbuffer(commas(par_count)+1:commas(par_count + 1)-1),*) vpars(par_count) - par_count = par_count + 1 - ENDDO - READ(cmdbuffer(commas(par_count)+1:),*) vpars(par_count) - ENDIF - ccmd = 0 - ENDIF - ENDDO - - IF (vstyle == -1) THEN - WRITE(*,*) " Error, type of potential not specified." - WRITE(*,*) " SYNTAX: driver.x [-u] -h hostname -p port -m [gas|lj|sg|harm] -o 'comma_separated_parameters' [-v] " - WRITE(*,*) "" - WRITE(*,*) " For LJ potential use -o sigma,epsilon,cutoff " - WRITE(*,*) " For SG potential use -o cutoff " - WRITE(*,*) " For the ideal gas, no options needed! " - CALL EXIT(-1) - ELSEIF (vstyle == 0) THEN - IF (par_count /= 0) THEN - WRITE(*,*) "Error: no initialization string needed for ideal gas." - CALL EXIT(-1) - ENDIF - isinit = .true. - ELSEIF (vstyle == 1) THEN - IF (par_count /= 3) THEN - WRITE(*,*) "Error: parameters not initialized correctly." - WRITE(*,*) "For LJ potential use -o sigma,epsilon,cutoff " - CALL EXIT(-1) ! Note that if initialization from the wrapper is implemented this exit should be removed. - ENDIF - sigma = vpars(1) - eps = vpars(2) - rc = vpars(3) - rn = rc*1.2 - isinit = .true. - ELSEIF (vstyle == 2) THEN - IF (par_count /= 1) THEN - WRITE(*,*) "Error: parameters not initialized correctly." - WRITE(*,*) "For SG potential use -o cutoff " - CALL EXIT(-1) ! Note that if initialization from the wrapper is implemented this exit should be removed. - ENDIF - rc = vpars(1) - rn = rc*1.2 - isinit = .true. - ELSEIF (vstyle == 3) THEN - IF (par_count /= 1) THEN - WRITE(*,*) "Error: parameters not initialized correctly." - WRITE(*,*) "For 1D harmonic potential use -o k " - CALL EXIT(-1) ! Note that if initialization from the wrapper is implemented this exit should be removed. - ENDIF - ks = vpars(1) - isinit = .true. - ENDIF - - IF (verbose) THEN - WRITE(*,*) " DRIVER - Connecting to host ", trim(host) - IF (inet > 0) THEN - WRITE(*,*) " on port ", port, " using an internet socket." - ELSE - WRITE(*,*) " using an UNIX socket." - ENDIF - ENDIF - - ! Calls the interface to the C sockets to open a communication channel - CALL open_socket(socket, inet, port, host) - nat = -1 - DO WHILE (.true.) ! Loops forever (or until the wrapper ends!) - - ! Reads from the socket one message header - CALL readbuffer(socket, header, MSGLEN) - IF (verbose) WRITE(*,*) " Message from server: ", trim(header) - - IF (trim(header) == "STATUS") THEN - ! The wrapper is inquiring on what we are doing - IF (.not. isinit) THEN - CALL writebuffer(socket,"NEEDINIT ",MSGLEN) ! Signals that we need initialization data - ELSEIF (hasdata) THEN - CALL writebuffer(socket,"HAVEDATA ",MSGLEN) ! Signals that we are done computing and can return forces - ELSE - CALL writebuffer(socket,"READY ",MSGLEN) ! We are idling and eager to compute something - ENDIF - ELSEIF (trim(header) == "INIT") THEN ! The driver is kindly providing a string for initialization - CALL readbuffer(socket, cbuf, 4) - CALL readbuffer(socket, initbuffer, cbuf) - IF (verbose) WRITE(*,*) " Initializing system from wrapper, using ", trim(initbuffer) - isinit=.true. ! We actually do nothing with this string, thanks anyway. Could be used to pass some information (e.g. the input parameters, or the index of the replica, from the driver - ELSEIF (trim(header) == "POSDATA") THEN ! The driver is sending the positions of the atoms. Here is where we do the calculation! - - ! Parses the flow of data from the socket - CALL readbuffer(socket, cell_h, 9*8) ! Cell matrix - CALL readbuffer(socket, cell_ih, 9*8) ! Inverse of the cell matrix (so we don't have to invert it every time here) - - ! The wrapper uses atomic units for everything, and row major storage. - ! At this stage one should take care that everything is converted in the - ! units and storage mode used in the driver. - cell_h = transpose(cell_h) - cell_ih = transpose(cell_ih) - ! We assume an upper triangular cell-vector matrix - volume = cell_h(1,1)*cell_h(2,2)*cell_h(3,3) - - CALL readbuffer(socket, cbuf, 4) ! The number of atoms in the cell - IF (nat < 0) THEN ! Assumes that the number of atoms does not change throughout a simulation, so only does this once - nat = cbuf - IF (verbose) WRITE(*,*) " Allocating buffer and data arrays, with ", nat, " atoms" - ALLOCATE(msgbuffer(3*nat)) - ALLOCATE(atoms(nat,3)) - ALLOCATE(forces(nat,3)) - ENDIF - - CALL readbuffer(socket, msgbuffer, nat*3*8) - DO i = 1, nat - atoms(i,:) = msgbuffer(3*(i-1)+1:3*i) - ENDDO - - IF (vstyle == 0) THEN ! ideal gas, so no calculation done - pot = 0 - forces = 0 - virial = 0 - ELSEIF (vstyle == 3) THEN ! 1D harmonic potential, so only uses the first position variable - pot = 0.5*ks*atoms(1,1)**2 - forces = 0 - forces(1,1) = -ks*atoms(1,1) - virial = 0 - virial(1,1) = forces(1,1)*atoms(1,1) - ELSE - IF ((allocated(n_list) .neqv. .true.)) THEN - IF (verbose) WRITE(*,*) " Allocating neighbour lists." - ALLOCATE(n_list(nat*(nat-1)/2)) - ALLOCATE(index_list(nat)) - ALLOCATE(last_atoms(nat,3)) - CALL nearest_neighbours(rn, nat, atoms, cell_h, cell_ih, index_list, n_list) - last_atoms = atoms - init_volume = volume - init_rc = rc - ENDIF - - ! Checking to see if we need to re-calculate the neighbour list - rc = init_rc*(volume/init_volume)**(1.0/3.0) - DO i = 1, nat - CALL separation(cell_h, cell_ih, atoms(i,:), last_atoms(i,:), displacement) - ! Note that displacement is the square of the distance moved by atom i since the last time the neighbour list was created. - IF (4*displacement > (rn-rc)*(rn-rc)) THEN - IF (verbose) WRITE(*,*) " Recalculating neighbour lists" - CALL nearest_neighbours(rn, nat, atoms, cell_h, cell_ih, index_list, n_list) - last_atoms = atoms - rn = 1.2*rc - EXIT - ENDIF - ENDDO - - IF (vstyle == 1) THEN - CALL LJ_getall(rc, sigma, eps, nat, atoms, cell_h, cell_ih, index_list, n_list, pot, forces, virial) - ELSEIF (vstyle == 2) THEN - CALL SG_getall(rc, nat, atoms, cell_h, cell_ih, index_list, n_list, pot, forces, virial) - ENDIF - IF (verbose) WRITE(*,*) " Calculated energy is ", pot - ENDIF - hasdata = .true. ! Signal that we have data ready to be passed back to the wrapper - ELSEIF (trim(header) == "GETFORCE") THEN ! The driver calculation is finished, it's time to send the results back to the wrapper - - ! Data must be re-formatted (and units converted) in the units and shapes used in the wrapper - DO i = 1, nat - msgbuffer(3*(i-1)+1:3*i) = forces(i,:) - ENDDO - virial = transpose(virial) - - CALL writebuffer(socket,"FORCEREADY ",MSGLEN) - CALL writebuffer(socket,pot,8) ! Writing the potential - CALL writebuffer(socket,nat,4) ! Writing the number of atoms - CALL writebuffer(socket,msgbuffer,3*nat*8) ! Writing the forces - CALL writebuffer(socket,virial,9*8) ! Writing the virial tensor, NOT divided by the volume - cbuf = 7 ! Size of the "extras" string - CALL writebuffer(socket,cbuf,4) ! This would write out the "extras" string, but in this case we only use a dummy string. - CALL writebuffer(socket,"nothing",7) - - hasdata = .false. - ELSE - WRITE(*,*) " Unexpected header ", header - CALL EXIT(-1) - ENDIF - ENDDO - IF (nat > 0) DEALLOCATE(atoms, forces, msgbuffer) - END PROGRAM diff --git a/tools/i-pi/drivers/sockets.c b/tools/i-pi/drivers/sockets.c deleted file mode 100644 index 6fda1b64ec..0000000000 --- a/tools/i-pi/drivers/sockets.c +++ /dev/null @@ -1,147 +0,0 @@ -/* A minimal wrapper for socket communication. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -Permission is hereby granted, free of charge, to any person obtaining -a copy of this software and associated documentation files (the -"Software"), to deal in the Software without restriction, including -without limitation the rights to use, copy, modify, merge, publish, -distribute, sublicense, and/or sell copies of the Software, and to -permit persons to whom the Software is furnished to do so, subject to -the following conditions: - -The above copyright notice and this permission notice shall be included -in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. -IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY -CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE -SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - -Contains both the functions that transmit data to the socket and read the data -back out again once finished, and the function which opens the socket initially. -Can be linked to a FORTRAN code that does not support sockets natively. - -Functions: - error: Prints an error message and then exits. - open_socket_: Opens a socket with the required host server, socket type and - port number. - write_buffer_: Writes a string to the socket. - read_buffer_: Reads data from the socket. -*/ - -#include -#include -#include -#include -#include -#include -#include -#include -#include - -void error(const char *msg) -// Prints an error message and then exits. -{ perror(msg); exit(-1); } - -void open_socket_(int *psockfd, int* inet, int* port, char* host) -/* Opens a socket. - -Note that fortran passes an extra argument for the string length, but this is -ignored here for C compatibility. - -Args: - psockfd: The id of the socket that will be created. - inet: An integer that determines whether the socket will be an inet or unix - domain socket. Gives unix if 0, inet otherwise. - port: The port number for the socket to be created. Low numbers are often - reserved for important channels, so use of numbers of 4 or more digits is - recommended. - host: The name of the host server. -*/ - -{ - int sockfd, portno, n; - struct hostent *server; - - struct sockaddr * psock; int ssock; - - if (*inet>0) - { // creates an internet socket - struct sockaddr_in serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); - sockfd = socket(AF_INET, SOCK_STREAM, 0); - if (sockfd < 0) error("Error opening socket"); - - server = gethostbyname(host); - if (server == NULL) - { - fprintf(stderr, "Error opening socket: no such host %s \n", host); - exit(-1); - } - - bzero((char *) &serv_addr, sizeof(serv_addr)); - serv_addr.sin_family = AF_INET; - bcopy((char *)server->h_addr, (char *)&serv_addr.sin_addr.s_addr, server->h_length); - serv_addr.sin_port = htons(*port); - if (connect(sockfd, psock, ssock) < 0) error("Error opening socket: wrong host address, or broken connection"); - } - else - { // creates a unix socket - struct sockaddr_un serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); - sockfd = socket(AF_UNIX, SOCK_STREAM, 0); - bzero((char *) &serv_addr, sizeof(serv_addr)); - serv_addr.sun_family = AF_UNIX; - strcpy(serv_addr.sun_path, "/tmp/ipi_"); - strcpy(serv_addr.sun_path+9, host); - if (connect(sockfd, psock, ssock) < 0) error("Error opening socket: wrong host address, or broken connection"); - } - - *psockfd=sockfd; -} - -void writebuffer_(int *psockfd, char *data, int* plen) -/* Writes to a socket. - -Args: - psockfd: The id of the socket that will be written to. - data: The data to be written to the socket. - plen: The length of the data in bytes. -*/ - -{ - int n; - int sockfd=*psockfd; - int len=*plen; - - n = write(sockfd,data,len); - if (n < 0) error("Error writing to socket: server has quit or connection broke"); -} - - -void readbuffer_(int *psockfd, char *data, int* plen) -/* Reads from a socket. - -Args: - psockfd: The id of the socket that will be read from. - data: The storage array for data read from the socket. - plen: The length of the data in bytes. -*/ - -{ - int n, nr; - int sockfd=*psockfd; - int len=*plen; - - n = nr = read(sockfd,data,len); - - while (nr>0 && n. - -.PHONY: all clean graphene h2o-piglet_2 h2o-piglet_4 h2o-piglet_8 h2o-rpc h2o-pimd -all: graphene h2o-piglet_2 h2o-piglet_4 h2o-piglet_8 h2o-rpc h2o-pimd - -LAMMPS:=../../../../../src/lmp_ubuntu -IPI:=../../../i-pi - -define run_lammps - for i in `seq 1 $1`; do \ - $(LAMMPS) < $2 & \ - done; -endef --include make.in - -graphene: - cd graphene; $(IPI) input.xml & \ - sleep 20; \ - $(call run_lammps,4,in.kappa.Graphene) \ - wait - -h2o-piglet_2: - cd h2o-piglet.2; $(IPI) input.xml & sleep 5; \ - $(call run_lammps,2,in.water) \ - wait - -h2o-piglet_4: - cd h2o-piglet.4; $(IPI) input.xml & sleep 5; \ - $(call run_lammps,4,in.water) \ - wait - -h2o-piglet_8: - cd h2o-piglet.8; $(IPI) input.xml & sleep 5; \ - $(call run_lammps,4,in.water) \ - wait - -h2o-pimd: - cd h2o-pimd; $(IPI) input.xml & sleep 5; \ - $(call run_lammps,4,in.water) \ - wait - -h2o-rpc: - cd h2o-pimd-rpc; $(IPI) input.xml & sleep 5; \ - $(call run_lammps,4,in.water_shortrange) \ - $(call run_lammps,1,in.water_longrange) \ - wait - -clean: - rm -f */gle_lammps.* */RESTART */EXIT */log.lammps; \ - cd h2o-pimd; \ - rm -f RESTART EXIT log.lammps no_rpc.*; cd ..; \ - cd h2o-pimd-rpc; \ - rm -f RESTART EXIT log.lammps rpc.*; cd ..; \ - cd graphene; \ - rm -f graph.* RESTART EXIT log.lammps graphene.lammpstraj nohup.out; cd .. diff --git a/tools/i-pi/examples/lammps/README b/tools/i-pi/examples/lammps/README deleted file mode 100644 index 0bb5a74fa6..0000000000 --- a/tools/i-pi/examples/lammps/README +++ /dev/null @@ -1,70 +0,0 @@ - -- Examples of i-PI working with LAMMPS -- - - -- Example with Tersoff graphene potential -- - - Uses the Tersoff parameters of Lindsay and Broido PRB 81, 205441 (2010) - to run a short simulation of graphene with the LAMMPS MD code. - - -- Example with the q-TIP4P-F water potential -- - - * This gives an example of water with the q-TIP4P-F potential - of Scott Habershon, Thomas E. Markland and David E. Manolopoulos, - J. Chem. Phys., 131, 024501, (2009). - - * State point: (N, V, T) = (216 water molecules, 43737 a_0**3, 298 K) - - * This demonstrates the convergence of the kinetic and potential energy - using the ring polymer contraction (RPC) method of Thomas E. Markland and - David E. Manolopoulos, J. Chem. Phys. 129, 024105, (2008), and - the PIGLET method of Michele Ceriotti and - David Manolopoulos, Phys. Rev. Lett., 109, 100604, (2012). - - -** Run the examples automatically: - - * First, it is necessary to patch and compile LAMMPS, and create a make.in - file containing the path to the executable and i-pi, e.g. - -LAMMPS:=~/bin/lmp_serial -IPI:=~/bin/i-pi - - * The runs can be done automatically using the Makefile provided. The make - targets are self-explanatory. To run the RPC example, for instance, just type: - -$ make h2o-rpc - - * To clean up output files: - -$ make clean - - -** Run the examples manually: - - * Go back to the example directory and run - -$ python path/i-pi input.xml - - the wrapper will start and sit waiting on the UDS /tmp/ipi. - - * Open a separate terminal and run the LAMMPS driver code using: - -$ path/lammps/src/lmp_serial < in.water - - For the RPC run, instead use: - -$ path/lammps/src/lmp_serial < in.water_longrange -$ path/lammps/src/lmp_serial < in.water_shortrange - - You can run multiple instances of the code; it is so fast that parallel - scaling won't be appreciable. - - * If your system does not support Unix domain sockets, just set in input.xml - port_no - - To make the client socket connect, the in.water file should - be changed so that it has the line: - - fix 1 all driver hostname port_no - - where hostname is the address the socket is binding to; either graphene, piglet_2, - piglet_4, piglet_8, rpc_long, rpc_short or no_rpc depending on the run. diff --git a/tools/i-pi/examples/lammps/h2o-piglet.2/data.water b/tools/i-pi/examples/lammps/h2o-piglet.2/data.water deleted file mode 100644 index 13c75e9933..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.2/data.water +++ /dev/null @@ -1,1331 +0,0 @@ -LAMMPS Description - - 648 atoms - 432 bonds - 216 angles - - 2 atom types - 1 bond types - 1 angle types - - 0 35.233 xlo xhi - 0 35.233 ylo yhi - 0 35.233 zlo zhi - -Masses - - 1 15.9994 - 2 1.0080 - -Bond Coeffs - - 1 1.78 0.2708585 -0.327738785 0.231328959 - -Angle Coeffs - - 1 0.0700 107.400000 - -Atoms - - 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 - 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 - 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 - 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000 - 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 - 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 - 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 - 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 - 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 - 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 - 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 - 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 - 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 - 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 - 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 - 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176 1 527 526 528 - 177 1 530 529 531 - 178 1 533 532 534 - 179 1 536 535 537 - 180 1 539 538 540 - 181 1 542 541 543 - 182 1 545 544 546 - 183 1 548 547 549 - 184 1 551 550 552 - 185 1 554 553 555 - 186 1 557 556 558 - 187 1 560 559 561 - 188 1 563 562 564 - 189 1 566 565 567 - 190 1 569 568 570 - 191 1 572 571 573 - 192 1 575 574 576 - 193 1 578 577 579 - 194 1 581 580 582 - 195 1 584 583 585 - 196 1 587 586 588 - 197 1 590 589 591 - 198 1 593 592 594 - 199 1 596 595 597 - 200 1 599 598 600 - 201 1 602 601 603 - 202 1 605 604 606 - 203 1 608 607 609 - 204 1 611 610 612 - 205 1 614 613 615 - 206 1 617 616 618 - 207 1 620 619 621 - 208 1 623 622 624 - 209 1 626 625 627 - 210 1 629 628 630 - 211 1 632 631 633 - 212 1 635 634 636 - 213 1 638 637 639 - 214 1 641 640 642 - 215 1 644 643 645 - 216 1 647 646 648 diff --git a/tools/i-pi/examples/lammps/h2o-piglet.2/in.water b/tools/i-pi/examples/lammps/h2o-piglet.2/in.water deleted file mode 100644 index e810a02a75..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.2/in.water +++ /dev/null @@ -1,32 +0,0 @@ -units electron -atom_style full - -#pair_style lj/cut/coul/long 17.01 -pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 -#bond_style harmonic -bond_style class2 -angle_style harmonic -#kspace_style pppm 0.0001 -kspace_style pppm/tip4p 0.0001 - -read_data data.water -pair_coeff * * 0 0 -pair_coeff 1 1 0.000295147 5.96946 - -neighbor 2.0 bin - -timestep 0.00025 - -#velocity all create 298.0 2345187 - -#thermo_style multi -#thermo 1 - -#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 -#fix 1 all nve -fix 1 all ipi piglet_2 32344 unix - -#dump 1 all xyz 25 dump.xyz - -run 100000000 - diff --git a/tools/i-pi/examples/lammps/h2o-piglet.2/input.xml b/tools/i-pi/examples/lammps/h2o-piglet.2/input.xml deleted file mode 100644 index 1dff8eb519..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.2/input.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - water_298K.pdb - 298 - - - [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] - positions - - 500000 - 32344 - - -

piglet_2
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-6.447837508760e+1, -3.768899601800e+2, 3.002298898960e+2, -3.200807605760e+1, -9.321443096220e+1, 1.456848407112e+5, 2.242472021306e-6, -1.291218519198e+3, 2.139711935710e+0, -2.608106016078e+2, -8.237240093440e+1, -3.067013601100e+3, 5.531363469240e+0, -3.766729941280e+2, 2.242476256184e-6, 1.456018646376e+5 -] - - - - - 0.1 - 298 - - diff --git a/tools/i-pi/examples/lammps/h2o-piglet.2/water_298K.pdb b/tools/i-pi/examples/lammps/h2o-piglet.2/water_298K.pdb deleted file mode 100644 index e8509c868e..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.2/water_298K.pdb +++ /dev/null @@ -1,650 +0,0 @@ -CRYST 35.233 35.233 35.233 90.00 90.00 90.00 P 1 1 -ATOM 1 O 1 1 3.846 5.672 1.323 0.00 0.00 0 -ATOM 2 H 1 1 2.979 7.054 0.857 0.00 0.00 0 -ATOM 3 H 1 1 5.525 5.697 0.451 0.00 0.00 0 -ATOM 4 O 1 1 34.557 34.341 3.078 0.00 0.00 0 -ATOM 5 H 1 1 33.722 34.689 4.840 0.00 0.00 0 -ATOM 6 H 1 1 36.029 33.220 3.711 0.00 0.00 0 -ATOM 7 O 1 1 5.591 1.963 13.477 0.00 0.00 0 -ATOM 8 H 1 1 7.265 1.864 13.851 0.00 0.00 0 -ATOM 9 H 1 1 5.009 3.555 13.916 0.00 0.00 0 -ATOM 10 O 1 1 1.060 2.061 21.718 0.00 0.00 0 -ATOM 11 H 1 1 0.757 0.261 21.820 0.00 0.00 0 -ATOM 12 H 1 1 0.213 3.013 23.047 0.00 0.00 0 -ATOM 13 O 1 1 1.200 1.337 29.006 0.00 0.00 0 -ATOM 14 H 1 1 0.818 1.884 30.732 0.00 0.00 0 -ATOM 15 H 1 1 2.883 1.825 29.011 0.00 0.00 0 -ATOM 16 O 1 1 1.331 1.386 34.306 0.00 0.00 0 -ATOM 17 H 1 1 2.392 2.898 34.846 0.00 0.00 0 -ATOM 18 H 1 1 0.814 0.532 35.836 0.00 0.00 0 -ATOM 19 O 1 1 31.451 10.201 0.726 0.00 0.00 0 -ATOM 20 H 1 1 32.282 10.877 -0.750 0.00 0.00 0 -ATOM 21 H 1 1 30.920 11.594 1.677 0.00 0.00 0 -ATOM 22 O 1 1 0.836 10.808 4.298 0.00 0.00 0 -ATOM 23 H 1 1 0.305 10.643 2.793 0.00 0.00 0 -ATOM 24 H 1 1 -0.356 10.334 5.524 0.00 0.00 0 -ATOM 25 O 1 1 34.381 5.979 9.194 0.00 0.00 0 -ATOM 26 H 1 1 33.616 7.673 8.857 0.00 0.00 0 -ATOM 27 H 1 1 35.115 5.260 7.618 0.00 0.00 0 -ATOM 28 O 1 1 33.212 6.480 24.278 0.00 0.00 0 -ATOM 29 H 1 1 31.624 6.908 23.521 0.00 0.00 0 -ATOM 30 H 1 1 32.544 4.990 24.982 0.00 0.00 0 -ATOM 31 O 1 1 1.992 9.002 26.863 0.00 0.00 0 -ATOM 32 H 1 1 1.856 10.175 25.579 0.00 0.00 0 -ATOM 33 H 1 1 0.519 8.099 26.386 0.00 0.00 0 -ATOM 34 O 1 1 2.054 8.660 32.515 0.00 0.00 0 -ATOM 35 H 1 1 2.167 8.727 30.494 0.00 0.00 0 -ATOM 36 H 1 1 2.374 10.513 33.038 0.00 0.00 0 -ATOM 37 O 1 1 3.402 16.639 3.008 0.00 0.00 0 -ATOM 38 H 1 1 4.127 15.872 4.446 0.00 0.00 0 -ATOM 39 H 1 1 2.905 18.339 3.160 0.00 0.00 0 -ATOM 40 O 1 1 4.222 15.444 8.072 0.00 0.00 0 -ATOM 41 H 1 1 5.211 16.756 8.299 0.00 0.00 0 -ATOM 42 H 1 1 2.560 15.492 8.860 0.00 0.00 0 -ATOM 43 O 1 1 2.831 9.246 16.488 0.00 0.00 0 -ATOM 44 H 1 1 2.869 8.023 18.050 0.00 0.00 0 -ATOM 45 H 1 1 3.960 8.467 15.154 0.00 0.00 0 -ATOM 46 O 1 1 5.563 6.003 20.907 0.00 0.00 0 -ATOM 47 H 1 1 4.653 4.638 21.480 0.00 0.00 0 -ATOM 48 H 1 1 6.405 6.208 22.529 0.00 0.00 0 -ATOM 49 O 1 1 2.087 13.370 22.913 0.00 0.00 0 -ATOM 50 H 1 1 2.832 14.804 23.422 0.00 0.00 0 -ATOM 51 H 1 1 1.434 13.509 21.196 0.00 0.00 0 -ATOM 52 O 1 1 3.369 17.886 25.109 0.00 0.00 0 -ATOM 53 H 1 1 3.655 17.200 26.766 0.00 0.00 0 -ATOM 54 H 1 1 4.772 18.977 24.500 0.00 0.00 0 -ATOM 55 O 1 1 34.764 20.803 0.948 0.00 0.00 0 -ATOM 56 H 1 1 35.210 21.267 2.816 0.00 0.00 0 -ATOM 57 H 1 1 35.962 21.726 0.131 0.00 0.00 0 -ATOM 58 O 1 1 2.836 24.178 15.229 0.00 0.00 0 -ATOM 59 H 1 1 2.795 22.346 14.876 0.00 0.00 0 -ATOM 60 H 1 1 2.414 24.115 17.130 0.00 0.00 0 -ATOM 61 O 1 1 33.000 24.481 15.230 0.00 0.00 0 -ATOM 62 H 1 1 34.640 24.804 15.013 0.00 0.00 0 -ATOM 63 H 1 1 32.401 25.764 14.295 0.00 0.00 0 -ATOM 64 O 1 1 0.404 26.779 23.400 0.00 0.00 0 -ATOM 65 H 1 1 1.353 27.248 24.987 0.00 0.00 0 -ATOM 66 H 1 1 1.546 28.050 22.317 0.00 0.00 0 -ATOM 67 O 1 1 34.222 21.380 25.418 0.00 0.00 0 -ATOM 68 H 1 1 35.669 20.151 25.317 0.00 0.00 0 -ATOM 69 H 1 1 32.960 21.180 23.992 0.00 0.00 0 -ATOM 70 O 1 1 33.259 17.438 32.480 0.00 0.00 0 -ATOM 71 H 1 1 33.314 18.782 33.883 0.00 0.00 0 -ATOM 72 H 1 1 32.743 18.181 30.871 0.00 0.00 0 -ATOM 73 O 1 1 4.463 21.979 3.936 0.00 0.00 0 -ATOM 74 H 1 1 5.856 23.084 3.400 0.00 0.00 0 -ATOM 75 H 1 1 3.986 22.180 5.602 0.00 0.00 0 -ATOM 76 O 1 1 6.258 25.851 8.520 0.00 0.00 0 -ATOM 77 H 1 1 5.767 27.693 8.476 0.00 0.00 0 -ATOM 78 H 1 1 7.202 25.506 10.186 0.00 0.00 0 -ATOM 79 O 1 1 0.601 29.737 12.747 0.00 0.00 0 -ATOM 80 H 1 1 -0.685 30.842 12.350 0.00 0.00 0 -ATOM 81 H 1 1 1.336 30.716 14.031 0.00 0.00 0 -ATOM 82 O 1 1 7.563 28.191 24.333 0.00 0.00 0 -ATOM 83 H 1 1 9.201 28.828 24.684 0.00 0.00 0 -ATOM 84 H 1 1 7.381 27.621 22.799 0.00 0.00 0 -ATOM 85 O 1 1 3.653 27.109 27.772 0.00 0.00 0 -ATOM 86 H 1 1 5.126 27.015 26.772 0.00 0.00 0 -ATOM 87 H 1 1 3.031 28.756 27.698 0.00 0.00 0 -ATOM 88 O 1 1 2.596 23.991 32.476 0.00 0.00 0 -ATOM 89 H 1 1 2.879 24.791 30.859 0.00 0.00 0 -ATOM 90 H 1 1 4.003 22.913 32.701 0.00 0.00 0 -ATOM 91 O 1 1 3.083 31.317 3.644 0.00 0.00 0 -ATOM 92 H 1 1 4.133 30.589 2.539 0.00 0.00 0 -ATOM 93 H 1 1 4.218 32.173 5.037 0.00 0.00 0 -ATOM 94 O 1 1 4.661 30.555 9.368 0.00 0.00 0 -ATOM 95 H 1 1 3.184 29.843 10.132 0.00 0.00 0 -ATOM 96 H 1 1 4.358 32.448 9.126 0.00 0.00 0 -ATOM 97 O 1 1 3.465 32.537 15.778 0.00 0.00 0 -ATOM 98 H 1 1 5.072 31.819 15.903 0.00 0.00 0 -ATOM 99 H 1 1 4.055 34.257 15.284 0.00 0.00 0 -ATOM 100 O 1 1 4.215 29.153 20.317 0.00 0.00 0 -ATOM 101 H 1 1 3.658 30.176 18.842 0.00 0.00 0 -ATOM 102 H 1 1 4.959 30.291 21.449 0.00 0.00 0 -ATOM 103 O 1 1 1.126 31.333 28.768 0.00 0.00 0 -ATOM 104 H 1 1 2.395 31.124 29.925 0.00 0.00 0 -ATOM 105 H 1 1 0.768 33.092 28.898 0.00 0.00 0 -ATOM 106 O 1 1 4.881 32.616 32.302 0.00 0.00 0 -ATOM 107 H 1 1 6.588 32.911 31.725 0.00 0.00 0 -ATOM 108 H 1 1 4.486 34.037 33.249 0.00 0.00 0 -ATOM 109 O 1 1 8.962 5.556 0.151 0.00 0.00 0 -ATOM 110 H 1 1 9.652 6.991 0.859 0.00 0.00 0 -ATOM 111 H 1 1 9.173 4.477 1.645 0.00 0.00 0 -ATOM 112 O 1 1 1.833 3.518 5.679 0.00 0.00 0 -ATOM 113 H 1 1 2.889 2.731 6.788 0.00 0.00 0 -ATOM 114 H 1 1 2.789 4.187 4.147 0.00 0.00 0 -ATOM 115 O 1 1 10.510 34.726 13.073 0.00 0.00 0 -ATOM 116 H 1 1 11.920 34.118 11.919 0.00 0.00 0 -ATOM 117 H 1 1 11.295 34.968 14.741 0.00 0.00 0 -ATOM 118 O 1 1 7.212 0.042 22.454 0.00 0.00 0 -ATOM 119 H 1 1 6.924 0.470 24.172 0.00 0.00 0 -ATOM 120 H 1 1 8.319 1.228 21.653 0.00 0.00 0 -ATOM 121 O 1 1 6.365 2.010 27.544 0.00 0.00 0 -ATOM 122 H 1 1 5.954 3.585 26.852 0.00 0.00 0 -ATOM 123 H 1 1 7.758 2.549 28.696 0.00 0.00 0 -ATOM 124 O 1 1 10.833 3.140 30.787 0.00 0.00 0 -ATOM 125 H 1 1 12.697 2.975 30.867 0.00 0.00 0 -ATOM 126 H 1 1 10.389 3.700 32.404 0.00 0.00 0 -ATOM 127 O 1 1 8.684 9.342 3.912 0.00 0.00 0 -ATOM 128 H 1 1 6.985 9.256 4.773 0.00 0.00 0 -ATOM 129 H 1 1 8.684 10.809 3.011 0.00 0.00 0 -ATOM 130 O 1 1 4.873 9.919 7.707 0.00 0.00 0 -ATOM 131 H 1 1 3.698 9.771 6.194 0.00 0.00 0 -ATOM 132 H 1 1 5.047 11.961 7.624 0.00 0.00 0 -ATOM 133 O 1 1 10.031 5.018 9.699 0.00 0.00 0 -ATOM 134 H 1 1 9.675 3.382 10.340 0.00 0.00 0 -ATOM 135 H 1 1 9.132 5.987 10.825 0.00 0.00 0 -ATOM 136 O 1 1 11.246 3.918 21.929 0.00 0.00 0 -ATOM 137 H 1 1 12.614 2.770 22.341 0.00 0.00 0 -ATOM 138 H 1 1 12.073 5.686 21.497 0.00 0.00 0 -ATOM 139 O 1 1 6.825 7.164 25.708 0.00 0.00 0 -ATOM 140 H 1 1 8.036 8.374 25.980 0.00 0.00 0 -ATOM 141 H 1 1 5.206 7.900 25.891 0.00 0.00 0 -ATOM 142 O 1 1 10.171 12.811 0.295 0.00 0.00 0 -ATOM 143 H 1 1 10.033 12.818 -1.609 0.00 0.00 0 -ATOM 144 H 1 1 9.880 14.492 0.480 0.00 0.00 0 -ATOM 145 O 1 1 8.190 17.402 1.253 0.00 0.00 0 -ATOM 146 H 1 1 9.472 18.531 1.253 0.00 0.00 0 -ATOM 147 H 1 1 6.351 17.817 1.568 0.00 0.00 0 -ATOM 148 O 1 1 11.233 16.188 8.299 0.00 0.00 0 -ATOM 149 H 1 1 10.291 17.689 8.166 0.00 0.00 0 -ATOM 150 H 1 1 12.768 17.123 8.733 0.00 0.00 0 -ATOM 151 O 1 1 6.386 8.002 12.846 0.00 0.00 0 -ATOM 152 H 1 1 7.701 8.896 13.655 0.00 0.00 0 -ATOM 153 H 1 1 5.591 8.877 11.519 0.00 0.00 0 -ATOM 154 O 1 1 8.184 10.419 18.848 0.00 0.00 0 -ATOM 155 H 1 1 9.498 9.434 19.905 0.00 0.00 0 -ATOM 156 H 1 1 6.882 9.027 18.948 0.00 0.00 0 -ATOM 157 O 1 1 10.806 14.431 21.328 0.00 0.00 0 -ATOM 158 H 1 1 9.177 13.531 20.670 0.00 0.00 0 -ATOM 159 H 1 1 11.344 15.696 20.448 0.00 0.00 0 -ATOM 160 O 1 1 9.237 13.928 30.341 0.00 0.00 0 -ATOM 161 H 1 1 10.779 14.839 30.522 0.00 0.00 0 -ATOM 162 H 1 1 9.965 13.192 28.899 0.00 0.00 0 -ATOM 163 O 1 1 10.918 21.707 1.864 0.00 0.00 0 -ATOM 164 H 1 1 10.280 23.449 2.279 0.00 0.00 0 -ATOM 165 H 1 1 12.708 21.456 1.749 0.00 0.00 0 -ATOM 166 O 1 1 9.353 16.125 13.927 0.00 0.00 0 -ATOM 167 H 1 1 9.938 17.594 14.618 0.00 0.00 0 -ATOM 168 H 1 1 9.518 16.360 12.244 0.00 0.00 0 -ATOM 169 O 1 1 10.371 11.107 14.268 0.00 0.00 0 -ATOM 170 H 1 1 9.644 10.406 15.859 0.00 0.00 0 -ATOM 171 H 1 1 9.434 12.523 14.117 0.00 0.00 0 -ATOM 172 O 1 1 3.351 22.769 20.196 0.00 0.00 0 -ATOM 173 H 1 1 2.055 23.686 21.503 0.00 0.00 0 -ATOM 174 H 1 1 2.452 21.401 19.413 0.00 0.00 0 -ATOM 175 O 1 1 6.836 21.329 23.199 0.00 0.00 0 -ATOM 176 H 1 1 8.249 20.848 22.320 0.00 0.00 0 -ATOM 177 H 1 1 5.668 21.841 21.886 0.00 0.00 0 -ATOM 178 O 1 1 4.604 15.649 30.043 0.00 0.00 0 -ATOM 179 H 1 1 6.453 15.217 30.207 0.00 0.00 0 -ATOM 180 H 1 1 3.822 14.762 31.562 0.00 0.00 0 -ATOM 181 O 1 1 7.125 19.976 9.421 0.00 0.00 0 -ATOM 182 H 1 1 5.918 20.453 10.730 0.00 0.00 0 -ATOM 183 H 1 1 8.099 21.496 9.491 0.00 0.00 0 -ATOM 184 O 1 1 9.063 25.912 13.186 0.00 0.00 0 -ATOM 185 H 1 1 10.350 26.572 12.367 0.00 0.00 0 -ATOM 186 H 1 1 9.680 24.367 13.697 0.00 0.00 0 -ATOM 187 O 1 1 8.022 22.343 17.042 0.00 0.00 0 -ATOM 188 H 1 1 9.144 23.367 18.074 0.00 0.00 0 -ATOM 189 H 1 1 6.562 23.462 16.852 0.00 0.00 0 -ATOM 190 O 1 1 10.762 26.285 19.963 0.00 0.00 0 -ATOM 191 H 1 1 11.036 27.966 20.538 0.00 0.00 0 -ATOM 192 H 1 1 11.078 25.401 21.456 0.00 0.00 0 -ATOM 193 O 1 1 9.158 22.902 28.391 0.00 0.00 0 -ATOM 194 H 1 1 8.219 23.528 27.085 0.00 0.00 0 -ATOM 195 H 1 1 8.089 21.760 29.509 0.00 0.00 0 -ATOM 196 O 1 1 6.219 20.158 31.921 0.00 0.00 0 -ATOM 197 H 1 1 5.635 18.511 31.161 0.00 0.00 0 -ATOM 198 H 1 1 7.530 19.624 33.071 0.00 0.00 0 -ATOM 199 O 1 1 11.191 31.509 2.617 0.00 0.00 0 -ATOM 200 H 1 1 10.460 32.214 4.108 0.00 0.00 0 -ATOM 201 H 1 1 13.176 31.751 2.577 0.00 0.00 0 -ATOM 202 O 1 1 4.748 0.055 8.605 0.00 0.00 0 -ATOM 203 H 1 1 5.380 0.517 10.183 0.00 0.00 0 -ATOM 204 H 1 1 6.050 -0.306 7.480 0.00 0.00 0 -ATOM 205 O 1 1 8.695 30.809 15.731 0.00 0.00 0 -ATOM 206 H 1 1 9.189 32.103 14.495 0.00 0.00 0 -ATOM 207 H 1 1 8.447 29.069 14.868 0.00 0.00 0 -ATOM 208 O 1 1 10.128 31.402 20.766 0.00 0.00 0 -ATOM 209 H 1 1 9.456 30.905 19.155 0.00 0.00 0 -ATOM 210 H 1 1 9.020 32.731 21.415 0.00 0.00 0 -ATOM 211 O 1 1 12.238 30.162 25.837 0.00 0.00 0 -ATOM 212 H 1 1 11.418 30.908 27.110 0.00 0.00 0 -ATOM 213 H 1 1 12.396 31.331 24.678 0.00 0.00 0 -ATOM 214 O 1 1 10.395 32.537 30.624 0.00 0.00 0 -ATOM 215 H 1 1 11.042 34.339 30.751 0.00 0.00 0 -ATOM 216 H 1 1 11.378 31.486 31.538 0.00 0.00 0 -ATOM 217 O 1 1 10.438 3.626 5.087 0.00 0.00 0 -ATOM 218 H 1 1 12.435 4.082 5.136 0.00 0.00 0 -ATOM 219 H 1 1 9.822 4.284 6.681 0.00 0.00 0 -ATOM 220 O 1 1 14.762 3.401 13.776 0.00 0.00 0 -ATOM 221 H 1 1 16.518 3.824 13.376 0.00 0.00 0 -ATOM 222 H 1 1 13.752 4.757 12.964 0.00 0.00 0 -ATOM 223 O 1 1 12.382 1.012 17.643 0.00 0.00 0 -ATOM 224 H 1 1 13.346 1.997 16.444 0.00 0.00 0 -ATOM 225 H 1 1 11.931 2.133 18.998 0.00 0.00 0 -ATOM 226 O 1 1 15.278 1.293 24.559 0.00 0.00 0 -ATOM 227 H 1 1 16.071 0.946 26.365 0.00 0.00 0 -ATOM 228 H 1 1 15.794 0.199 23.499 0.00 0.00 0 -ATOM 229 O 1 1 22.226 31.627 24.712 0.00 0.00 0 -ATOM 230 H 1 1 23.338 32.595 23.876 0.00 0.00 0 -ATOM 231 H 1 1 22.161 30.053 24.132 0.00 0.00 0 -ATOM 232 O 1 1 15.640 1.847 32.717 0.00 0.00 0 -ATOM 233 H 1 1 17.488 2.473 31.874 0.00 0.00 0 -ATOM 234 H 1 1 16.403 0.869 34.267 0.00 0.00 0 -ATOM 235 O 1 1 14.858 10.199 2.754 0.00 0.00 0 -ATOM 236 H 1 1 13.360 10.712 2.282 0.00 0.00 0 -ATOM 237 H 1 1 14.560 9.316 4.559 0.00 0.00 0 -ATOM 238 O 1 1 15.717 8.469 10.739 0.00 0.00 0 -ATOM 239 H 1 1 17.323 9.581 10.875 0.00 0.00 0 -ATOM 240 H 1 1 14.574 9.631 10.221 0.00 0.00 0 -ATOM 241 O 1 1 15.248 10.398 16.525 0.00 0.00 0 -ATOM 242 H 1 1 16.324 9.181 16.149 0.00 0.00 0 -ATOM 243 H 1 1 14.172 10.488 15.098 0.00 0.00 0 -ATOM 244 O 1 1 13.226 8.438 20.801 0.00 0.00 0 -ATOM 245 H 1 1 14.043 8.996 19.295 0.00 0.00 0 -ATOM 246 H 1 1 14.661 7.802 22.093 0.00 0.00 0 -ATOM 247 O 1 1 10.173 10.961 25.875 0.00 0.00 0 -ATOM 248 H 1 1 11.477 10.223 26.940 0.00 0.00 0 -ATOM 249 H 1 1 11.269 10.738 24.343 0.00 0.00 0 -ATOM 250 O 1 1 12.792 7.737 29.173 0.00 0.00 0 -ATOM 251 H 1 1 12.199 6.038 29.475 0.00 0.00 0 -ATOM 252 H 1 1 14.427 7.450 29.617 0.00 0.00 0 -ATOM 253 O 1 1 15.180 19.498 3.578 0.00 0.00 0 -ATOM 254 H 1 1 14.883 17.596 4.080 0.00 0.00 0 -ATOM 255 H 1 1 16.754 19.579 2.626 0.00 0.00 0 -ATOM 256 O 1 1 12.517 11.093 7.701 0.00 0.00 0 -ATOM 257 H 1 1 12.224 12.778 7.555 0.00 0.00 0 -ATOM 258 H 1 1 11.150 10.393 7.057 0.00 0.00 0 -ATOM 259 O 1 1 16.266 16.271 10.758 0.00 0.00 0 -ATOM 260 H 1 1 16.507 15.795 12.768 0.00 0.00 0 -ATOM 261 H 1 1 17.725 16.977 10.292 0.00 0.00 0 -ATOM 262 O 1 1 14.069 18.399 18.897 0.00 0.00 0 -ATOM 263 H 1 1 15.513 17.523 18.155 0.00 0.00 0 -ATOM 264 H 1 1 14.958 18.709 20.673 0.00 0.00 0 -ATOM 265 O 1 1 14.099 15.480 25.510 0.00 0.00 0 -ATOM 266 H 1 1 13.698 16.872 26.938 0.00 0.00 0 -ATOM 267 H 1 1 12.567 15.379 24.444 0.00 0.00 0 -ATOM 268 O 1 1 13.309 17.574 30.292 0.00 0.00 0 -ATOM 269 H 1 1 14.937 16.934 30.810 0.00 0.00 0 -ATOM 270 H 1 1 13.969 19.494 30.012 0.00 0.00 0 -ATOM 271 O 1 1 18.371 23.257 0.925 0.00 0.00 0 -ATOM 272 H 1 1 19.479 23.480 2.321 0.00 0.00 0 -ATOM 273 H 1 1 19.087 24.325 -0.369 0.00 0.00 0 -ATOM 274 O 1 1 12.100 21.730 11.355 0.00 0.00 0 -ATOM 275 H 1 1 13.141 22.287 12.743 0.00 0.00 0 -ATOM 276 H 1 1 13.467 22.236 10.244 0.00 0.00 0 -ATOM 277 O 1 1 12.163 23.290 23.597 0.00 0.00 0 -ATOM 278 H 1 1 11.324 22.736 24.949 0.00 0.00 0 -ATOM 279 H 1 1 13.882 22.872 23.840 0.00 0.00 0 -ATOM 280 O 1 1 20.173 26.761 22.628 0.00 0.00 0 -ATOM 281 H 1 1 20.206 26.532 20.792 0.00 0.00 0 -ATOM 282 H 1 1 21.556 25.742 23.389 0.00 0.00 0 -ATOM 283 O 1 1 16.701 21.165 22.605 0.00 0.00 0 -ATOM 284 H 1 1 18.028 20.686 23.848 0.00 0.00 0 -ATOM 285 H 1 1 17.104 22.866 21.949 0.00 0.00 0 -ATOM 286 O 1 1 11.391 26.461 33.705 0.00 0.00 0 -ATOM 287 H 1 1 9.841 27.192 34.048 0.00 0.00 0 -ATOM 288 H 1 1 11.776 25.540 35.243 0.00 0.00 0 -ATOM 289 O 1 1 9.898 25.989 4.553 0.00 0.00 0 -ATOM 290 H 1 1 8.902 26.131 6.039 0.00 0.00 0 -ATOM 291 H 1 1 10.287 27.806 4.376 0.00 0.00 0 -ATOM 292 O 1 1 14.308 26.960 10.877 0.00 0.00 0 -ATOM 293 H 1 1 15.302 27.405 12.173 0.00 0.00 0 -ATOM 294 H 1 1 15.463 26.151 9.633 0.00 0.00 0 -ATOM 295 O 1 1 13.433 22.960 16.904 0.00 0.00 0 -ATOM 296 H 1 1 13.409 24.131 18.132 0.00 0.00 0 -ATOM 297 H 1 1 13.624 21.191 17.520 0.00 0.00 0 -ATOM 298 O 1 1 16.409 26.768 26.875 0.00 0.00 0 -ATOM 299 H 1 1 17.590 26.987 25.431 0.00 0.00 0 -ATOM 300 H 1 1 14.751 27.703 26.230 0.00 0.00 0 -ATOM 301 O 1 1 14.405 22.733 29.892 0.00 0.00 0 -ATOM 302 H 1 1 15.423 23.079 28.494 0.00 0.00 0 -ATOM 303 H 1 1 12.826 23.259 29.416 0.00 0.00 0 -ATOM 304 O 1 1 6.905 29.408 0.749 0.00 0.00 0 -ATOM 305 H 1 1 8.428 30.483 1.567 0.00 0.00 0 -ATOM 306 H 1 1 6.353 30.814 -0.444 0.00 0.00 0 -ATOM 307 O 1 1 9.189 34.159 6.509 0.00 0.00 0 -ATOM 308 H 1 1 10.198 34.193 8.002 0.00 0.00 0 -ATOM 309 H 1 1 9.890 35.692 5.785 0.00 0.00 0 -ATOM 310 O 1 1 14.256 32.316 9.369 0.00 0.00 0 -ATOM 311 H 1 1 15.733 32.867 9.486 0.00 0.00 0 -ATOM 312 H 1 1 14.754 30.670 10.090 0.00 0.00 0 -ATOM 313 O 1 1 14.714 30.841 16.516 0.00 0.00 0 -ATOM 314 H 1 1 13.748 29.551 17.279 0.00 0.00 0 -ATOM 315 H 1 1 13.218 31.933 16.614 0.00 0.00 0 -ATOM 316 O 1 1 18.409 33.641 20.611 0.00 0.00 0 -ATOM 317 H 1 1 19.601 32.274 21.115 0.00 0.00 0 -ATOM 318 H 1 1 17.360 32.655 19.518 0.00 0.00 0 -ATOM 319 O 1 1 16.062 28.638 32.207 0.00 0.00 0 -ATOM 320 H 1 1 14.648 27.958 33.253 0.00 0.00 0 -ATOM 321 H 1 1 15.752 28.014 30.522 0.00 0.00 0 -ATOM 322 O 1 1 16.200 30.895 1.473 0.00 0.00 0 -ATOM 323 H 1 1 16.626 29.968 -0.130 0.00 0.00 0 -ATOM 324 H 1 1 17.167 29.833 2.927 0.00 0.00 0 -ATOM 325 O 1 1 20.278 3.529 6.048 0.00 0.00 0 -ATOM 326 H 1 1 20.977 3.611 4.575 0.00 0.00 0 -ATOM 327 H 1 1 21.312 4.513 7.251 0.00 0.00 0 -ATOM 328 O 1 1 23.079 5.778 10.408 0.00 0.00 0 -ATOM 329 H 1 1 24.650 6.259 10.838 0.00 0.00 0 -ATOM 330 H 1 1 22.342 7.609 10.178 0.00 0.00 0 -ATOM 331 O 1 1 19.581 2.031 12.110 0.00 0.00 0 -ATOM 332 H 1 1 19.039 1.082 10.440 0.00 0.00 0 -ATOM 333 H 1 1 21.141 2.991 11.851 0.00 0.00 0 -ATOM 334 O 1 1 22.005 3.223 23.178 0.00 0.00 0 -ATOM 335 H 1 1 21.429 4.090 24.554 0.00 0.00 0 -ATOM 336 H 1 1 20.654 1.791 22.711 0.00 0.00 0 -ATOM 337 O 1 1 16.630 6.422 23.792 0.00 0.00 0 -ATOM 338 H 1 1 16.219 4.804 24.406 0.00 0.00 0 -ATOM 339 H 1 1 17.066 7.128 25.282 0.00 0.00 0 -ATOM 340 O 1 1 21.676 5.564 28.158 0.00 0.00 0 -ATOM 341 H 1 1 20.658 6.717 29.185 0.00 0.00 0 -ATOM 342 H 1 1 23.413 5.828 28.996 0.00 0.00 0 -ATOM 343 O 1 1 15.257 5.265 5.626 0.00 0.00 0 -ATOM 344 H 1 1 16.914 4.519 5.490 0.00 0.00 0 -ATOM 345 H 1 1 15.144 6.150 6.972 0.00 0.00 0 -ATOM 346 O 1 1 20.137 11.082 10.437 0.00 0.00 0 -ATOM 347 H 1 1 20.021 10.947 8.733 0.00 0.00 0 -ATOM 348 H 1 1 21.025 12.555 10.853 0.00 0.00 0 -ATOM 349 O 1 1 23.089 14.627 12.437 0.00 0.00 0 -ATOM 350 H 1 1 24.716 15.254 12.736 0.00 0.00 0 -ATOM 351 H 1 1 23.284 13.228 13.653 0.00 0.00 0 -ATOM 352 O 1 1 24.083 12.649 22.566 0.00 0.00 0 -ATOM 353 H 1 1 22.397 12.663 23.042 0.00 0.00 0 -ATOM 354 H 1 1 24.901 13.851 23.565 0.00 0.00 0 -ATOM 355 O 1 1 17.865 7.909 30.036 0.00 0.00 0 -ATOM 356 H 1 1 17.509 8.045 31.982 0.00 0.00 0 -ATOM 357 H 1 1 18.078 9.582 29.318 0.00 0.00 0 -ATOM 358 O 1 1 18.824 8.486 0.104 0.00 0.00 0 -ATOM 359 H 1 1 19.997 10.191 -0.057 0.00 0.00 0 -ATOM 360 H 1 1 17.077 8.998 0.779 0.00 0.00 0 -ATOM 361 O 1 1 20.122 9.143 5.343 0.00 0.00 0 -ATOM 362 H 1 1 19.373 8.819 3.821 0.00 0.00 0 -ATOM 363 H 1 1 21.998 8.776 5.128 0.00 0.00 0 -ATOM 364 O 1 1 16.413 14.459 5.855 0.00 0.00 0 -ATOM 365 H 1 1 15.536 13.007 5.239 0.00 0.00 0 -ATOM 366 H 1 1 16.006 14.725 7.737 0.00 0.00 0 -ATOM 367 O 1 1 17.561 15.066 15.654 0.00 0.00 0 -ATOM 368 H 1 1 17.575 13.398 16.055 0.00 0.00 0 -ATOM 369 H 1 1 18.978 15.828 16.400 0.00 0.00 0 -ATOM 370 O 1 1 26.374 17.047 24.817 0.00 0.00 0 -ATOM 371 H 1 1 27.983 17.098 25.632 0.00 0.00 0 -ATOM 372 H 1 1 25.629 18.751 24.919 0.00 0.00 0 -ATOM 373 O 1 1 19.784 12.960 28.706 0.00 0.00 0 -ATOM 374 H 1 1 21.662 13.055 28.871 0.00 0.00 0 -ATOM 375 H 1 1 19.545 14.070 27.143 0.00 0.00 0 -ATOM 376 O 1 1 17.891 16.733 32.499 0.00 0.00 0 -ATOM 377 H 1 1 18.327 15.240 31.277 0.00 0.00 0 -ATOM 378 H 1 1 18.633 18.335 31.693 0.00 0.00 0 -ATOM 379 O 1 1 23.733 23.024 1.663 0.00 0.00 0 -ATOM 380 H 1 1 24.800 24.052 2.776 0.00 0.00 0 -ATOM 381 H 1 1 24.693 22.618 0.198 0.00 0.00 0 -ATOM 382 O 1 1 20.789 18.440 9.443 0.00 0.00 0 -ATOM 383 H 1 1 20.766 17.257 7.881 0.00 0.00 0 -ATOM 384 H 1 1 21.896 17.345 10.385 0.00 0.00 0 -ATOM 385 O 1 1 21.574 17.493 17.838 0.00 0.00 0 -ATOM 386 H 1 1 20.597 18.955 17.218 0.00 0.00 0 -ATOM 387 H 1 1 22.538 16.874 16.251 0.00 0.00 0 -ATOM 388 O 1 1 19.168 14.748 24.131 0.00 0.00 0 -ATOM 389 H 1 1 19.711 16.390 23.712 0.00 0.00 0 -ATOM 390 H 1 1 17.429 14.695 24.403 0.00 0.00 0 -ATOM 391 O 1 1 22.149 20.198 24.977 0.00 0.00 0 -ATOM 392 H 1 1 21.639 20.924 26.486 0.00 0.00 0 -ATOM 393 H 1 1 22.656 21.657 24.411 0.00 0.00 0 -ATOM 394 O 1 1 20.565 20.792 29.600 0.00 0.00 0 -ATOM 395 H 1 1 22.264 20.409 30.214 0.00 0.00 0 -ATOM 396 H 1 1 20.548 22.408 30.597 0.00 0.00 0 -ATOM 397 O 1 1 20.802 26.547 9.615 0.00 0.00 0 -ATOM 398 H 1 1 20.099 27.984 8.338 0.00 0.00 0 -ATOM 399 H 1 1 21.277 27.539 11.325 0.00 0.00 0 -ATOM 400 O 1 1 16.283 23.589 7.779 0.00 0.00 0 -ATOM 401 H 1 1 16.093 21.973 6.712 0.00 0.00 0 -ATOM 402 H 1 1 17.901 22.971 8.154 0.00 0.00 0 -ATOM 403 O 1 1 18.469 29.798 13.568 0.00 0.00 0 -ATOM 404 H 1 1 19.712 31.216 13.506 0.00 0.00 0 -ATOM 405 H 1 1 16.872 30.343 14.396 0.00 0.00 0 -ATOM 406 O 1 1 18.790 21.712 16.060 0.00 0.00 0 -ATOM 407 H 1 1 19.878 23.090 16.485 0.00 0.00 0 -ATOM 408 H 1 1 17.201 22.326 15.819 0.00 0.00 0 -ATOM 409 O 1 1 21.747 26.084 16.349 0.00 0.00 0 -ATOM 410 H 1 1 20.783 27.021 15.300 0.00 0.00 0 -ATOM 411 H 1 1 22.705 27.328 17.206 0.00 0.00 0 -ATOM 412 O 1 1 20.769 26.211 32.050 0.00 0.00 0 -ATOM 413 H 1 1 21.488 27.404 33.328 0.00 0.00 0 -ATOM 414 H 1 1 18.989 26.710 32.145 0.00 0.00 0 -ATOM 415 O 1 1 19.820 29.181 5.559 0.00 0.00 0 -ATOM 416 H 1 1 20.991 29.509 4.109 0.00 0.00 0 -ATOM 417 H 1 1 19.431 31.018 6.221 0.00 0.00 0 -ATOM 418 O 1 1 19.240 33.867 7.993 0.00 0.00 0 -ATOM 419 H 1 1 19.107 35.039 6.604 0.00 0.00 0 -ATOM 420 H 1 1 20.697 33.671 9.063 0.00 0.00 0 -ATOM 421 O 1 1 22.511 34.976 15.793 0.00 0.00 0 -ATOM 422 H 1 1 23.716 36.163 16.603 0.00 0.00 0 -ATOM 423 H 1 1 21.699 36.150 14.467 0.00 0.00 0 -ATOM 424 O 1 1 22.622 30.284 19.069 0.00 0.00 0 -ATOM 425 H 1 1 22.049 31.351 17.725 0.00 0.00 0 -ATOM 426 H 1 1 24.411 30.773 19.576 0.00 0.00 0 -ATOM 427 O 1 1 18.639 33.611 28.369 0.00 0.00 0 -ATOM 428 H 1 1 18.226 32.159 29.103 0.00 0.00 0 -ATOM 429 H 1 1 19.906 33.008 27.158 0.00 0.00 0 -ATOM 430 O 1 1 22.520 1.325 31.926 0.00 0.00 0 -ATOM 431 H 1 1 22.803 2.668 30.796 0.00 0.00 0 -ATOM 432 H 1 1 21.045 0.425 31.122 0.00 0.00 0 -ATOM 433 O 1 1 21.754 3.789 1.159 0.00 0.00 0 -ATOM 434 H 1 1 22.085 2.785 -0.180 0.00 0.00 0 -ATOM 435 H 1 1 20.850 5.175 0.610 0.00 0.00 0 -ATOM 436 O 1 1 28.457 5.539 12.133 0.00 0.00 0 -ATOM 437 H 1 1 29.489 4.390 11.182 0.00 0.00 0 -ATOM 438 H 1 1 29.161 7.131 12.587 0.00 0.00 0 -ATOM 439 O 1 1 22.495 5.966 17.324 0.00 0.00 0 -ATOM 440 H 1 1 24.377 5.379 17.393 0.00 0.00 0 -ATOM 441 H 1 1 21.906 5.491 18.857 0.00 0.00 0 -ATOM 442 O 1 1 28.128 3.304 22.287 0.00 0.00 0 -ATOM 443 H 1 1 28.123 2.999 20.491 0.00 0.00 0 -ATOM 444 H 1 1 26.533 3.355 22.876 0.00 0.00 0 -ATOM 445 O 1 1 28.378 10.455 27.266 0.00 0.00 0 -ATOM 446 H 1 1 30.019 10.292 28.051 0.00 0.00 0 -ATOM 447 H 1 1 28.635 10.039 25.463 0.00 0.00 0 -ATOM 448 O 1 1 27.031 8.353 34.806 0.00 0.00 0 -ATOM 449 H 1 1 26.116 9.984 34.571 0.00 0.00 0 -ATOM 450 H 1 1 28.685 8.951 34.739 0.00 0.00 0 -ATOM 451 O 1 1 24.951 8.160 4.454 0.00 0.00 0 -ATOM 452 H 1 1 25.930 9.616 5.160 0.00 0.00 0 -ATOM 453 H 1 1 25.947 7.994 2.724 0.00 0.00 0 -ATOM 454 O 1 1 26.937 12.436 6.869 0.00 0.00 0 -ATOM 455 H 1 1 25.492 13.284 6.708 0.00 0.00 0 -ATOM 456 H 1 1 27.689 13.332 8.266 0.00 0.00 0 -ATOM 457 O 1 1 23.365 11.214 16.933 0.00 0.00 0 -ATOM 458 H 1 1 22.247 9.744 16.789 0.00 0.00 0 -ATOM 459 H 1 1 23.264 12.035 18.539 0.00 0.00 0 -ATOM 460 O 1 1 28.321 8.759 22.158 0.00 0.00 0 -ATOM 461 H 1 1 27.662 6.895 22.482 0.00 0.00 0 -ATOM 462 H 1 1 26.971 9.710 21.902 0.00 0.00 0 -ATOM 463 O 1 1 27.071 6.109 29.555 0.00 0.00 0 -ATOM 464 H 1 1 27.591 7.663 28.857 0.00 0.00 0 -ATOM 465 H 1 1 27.304 6.320 31.261 0.00 0.00 0 -ATOM 466 O 1 1 22.474 11.704 34.640 0.00 0.00 0 -ATOM 467 H 1 1 22.752 13.304 35.584 0.00 0.00 0 -ATOM 468 H 1 1 22.840 12.090 33.030 0.00 0.00 0 -ATOM 469 O 1 1 21.656 14.971 5.615 0.00 0.00 0 -ATOM 470 H 1 1 21.690 15.860 3.977 0.00 0.00 0 -ATOM 471 H 1 1 19.964 14.225 5.774 0.00 0.00 0 -ATOM 472 O 1 1 28.539 21.492 9.820 0.00 0.00 0 -ATOM 473 H 1 1 27.288 22.181 8.688 0.00 0.00 0 -ATOM 474 H 1 1 28.065 22.420 11.602 0.00 0.00 0 -ATOM 475 O 1 1 28.364 16.020 11.109 0.00 0.00 0 -ATOM 476 H 1 1 30.033 16.649 12.089 0.00 0.00 0 -ATOM 477 H 1 1 28.456 17.440 10.082 0.00 0.00 0 -ATOM 478 O 1 1 0.054 13.686 18.103 0.00 0.00 0 -ATOM 479 H 1 1 -1.714 12.928 18.841 0.00 0.00 0 -ATOM 480 H 1 1 1.008 12.429 17.383 0.00 0.00 0 -ATOM 481 O 1 1 24.636 12.894 29.957 0.00 0.00 0 -ATOM 482 H 1 1 25.906 13.914 31.183 0.00 0.00 0 -ATOM 483 H 1 1 25.641 11.609 29.162 0.00 0.00 0 -ATOM 484 O 1 1 21.548 17.250 0.749 0.00 0.00 0 -ATOM 485 H 1 1 21.843 19.026 0.905 0.00 0.00 0 -ATOM 486 H 1 1 20.385 16.716 -0.697 0.00 0.00 0 -ATOM 487 O 1 1 26.095 27.274 4.520 0.00 0.00 0 -ATOM 488 H 1 1 27.889 26.458 4.505 0.00 0.00 0 -ATOM 489 H 1 1 25.648 26.970 6.165 0.00 0.00 0 -ATOM 490 O 1 1 23.610 22.515 8.008 0.00 0.00 0 -ATOM 491 H 1 1 22.653 21.187 8.739 0.00 0.00 0 -ATOM 492 H 1 1 22.286 24.095 8.444 0.00 0.00 0 -ATOM 493 O 1 1 27.355 18.929 18.180 0.00 0.00 0 -ATOM 494 H 1 1 27.200 20.349 17.155 0.00 0.00 0 -ATOM 495 H 1 1 25.579 18.322 18.770 0.00 0.00 0 -ATOM 496 O 1 1 26.765 23.633 14.444 0.00 0.00 0 -ATOM 497 H 1 1 27.441 25.298 13.651 0.00 0.00 0 -ATOM 498 H 1 1 25.086 24.256 14.749 0.00 0.00 0 -ATOM 499 O 1 1 31.478 20.769 20.986 0.00 0.00 0 -ATOM 500 H 1 1 30.440 22.509 21.135 0.00 0.00 0 -ATOM 501 H 1 1 30.567 19.656 20.043 0.00 0.00 0 -ATOM 502 O 1 1 24.812 20.412 32.668 0.00 0.00 0 -ATOM 503 H 1 1 26.242 21.478 31.874 0.00 0.00 0 -ATOM 504 H 1 1 25.787 19.023 33.158 0.00 0.00 0 -ATOM 505 O 1 1 22.105 29.076 0.928 0.00 0.00 0 -ATOM 506 H 1 1 23.296 27.923 1.739 0.00 0.00 0 -ATOM 507 H 1 1 22.623 30.994 0.882 0.00 0.00 0 -ATOM 508 O 1 1 29.572 31.256 8.626 0.00 0.00 0 -ATOM 509 H 1 1 30.795 30.203 7.736 0.00 0.00 0 -ATOM 510 H 1 1 28.277 31.519 7.260 0.00 0.00 0 -ATOM 511 O 1 1 31.817 34.843 18.283 0.00 0.00 0 -ATOM 512 H 1 1 32.438 34.389 16.474 0.00 0.00 0 -ATOM 513 H 1 1 32.743 36.422 18.341 0.00 0.00 0 -ATOM 514 O 1 1 27.915 25.601 19.033 0.00 0.00 0 -ATOM 515 H 1 1 29.358 26.561 19.190 0.00 0.00 0 -ATOM 516 H 1 1 28.148 24.429 17.530 0.00 0.00 0 -ATOM 517 O 1 1 24.548 24.654 24.025 0.00 0.00 0 -ATOM 518 H 1 1 25.528 25.635 22.824 0.00 0.00 0 -ATOM 519 H 1 1 25.300 25.200 25.645 0.00 0.00 0 -ATOM 520 O 1 1 28.540 22.922 30.370 0.00 0.00 0 -ATOM 521 H 1 1 27.414 24.096 29.781 0.00 0.00 0 -ATOM 522 H 1 1 29.674 23.914 31.873 0.00 0.00 0 -ATOM 523 O 1 1 24.969 33.623 1.014 0.00 0.00 0 -ATOM 524 H 1 1 26.521 33.058 1.518 0.00 0.00 0 -ATOM 525 H 1 1 24.990 34.322 -0.683 0.00 0.00 0 -ATOM 526 O 1 1 23.075 32.171 11.324 0.00 0.00 0 -ATOM 527 H 1 1 23.316 32.775 13.097 0.00 0.00 0 -ATOM 528 H 1 1 24.460 33.203 10.662 0.00 0.00 0 -ATOM 529 O 1 1 27.497 2.736 17.224 0.00 0.00 0 -ATOM 530 H 1 1 28.397 3.415 15.715 0.00 0.00 0 -ATOM 531 H 1 1 28.234 1.233 17.412 0.00 0.00 0 -ATOM 532 O 1 1 26.369 33.060 22.077 0.00 0.00 0 -ATOM 533 H 1 1 26.170 34.746 22.264 0.00 0.00 0 -ATOM 534 H 1 1 27.592 32.404 23.321 0.00 0.00 0 -ATOM 535 O 1 1 30.221 30.950 25.843 0.00 0.00 0 -ATOM 536 H 1 1 30.305 29.038 26.208 0.00 0.00 0 -ATOM 537 H 1 1 30.363 31.979 27.414 0.00 0.00 0 -ATOM 538 O 1 1 24.973 26.732 28.607 0.00 0.00 0 -ATOM 539 H 1 1 25.385 28.369 29.248 0.00 0.00 0 -ATOM 540 H 1 1 23.330 26.597 29.234 0.00 0.00 0 -ATOM 541 O 1 1 32.165 4.857 2.258 0.00 0.00 0 -ATOM 542 H 1 1 32.417 6.195 1.157 0.00 0.00 0 -ATOM 543 H 1 1 32.615 3.727 1.112 0.00 0.00 0 -ATOM 544 O 1 1 28.067 3.533 5.217 0.00 0.00 0 -ATOM 545 H 1 1 26.960 4.447 4.158 0.00 0.00 0 -ATOM 546 H 1 1 29.875 3.863 4.448 0.00 0.00 0 -ATOM 547 O 1 1 33.279 2.782 13.028 0.00 0.00 0 -ATOM 548 H 1 1 33.708 3.955 11.817 0.00 0.00 0 -ATOM 549 H 1 1 33.656 3.545 14.631 0.00 0.00 0 -ATOM 550 O 1 1 34.278 4.944 17.492 0.00 0.00 0 -ATOM 551 H 1 1 33.438 6.563 17.876 0.00 0.00 0 -ATOM 552 H 1 1 34.906 4.452 18.995 0.00 0.00 0 -ATOM 553 O 1 1 32.363 1.908 26.092 0.00 0.00 0 -ATOM 554 H 1 1 31.941 1.683 24.268 0.00 0.00 0 -ATOM 555 H 1 1 33.850 1.390 26.904 0.00 0.00 0 -ATOM 556 O 1 1 27.982 0.418 28.241 0.00 0.00 0 -ATOM 557 H 1 1 27.516 2.080 28.309 0.00 0.00 0 -ATOM 558 H 1 1 29.593 0.176 27.299 0.00 0.00 0 -ATOM 559 O 1 1 28.845 14.672 2.724 0.00 0.00 0 -ATOM 560 H 1 1 27.963 13.930 4.139 0.00 0.00 0 -ATOM 561 H 1 1 30.386 15.714 3.379 0.00 0.00 0 -ATOM 562 O 1 1 28.083 10.618 14.298 0.00 0.00 0 -ATOM 563 H 1 1 28.623 12.160 13.293 0.00 0.00 0 -ATOM 564 H 1 1 26.486 11.015 15.379 0.00 0.00 0 -ATOM 565 O 1 1 33.867 10.545 13.306 0.00 0.00 0 -ATOM 566 H 1 1 35.165 9.612 13.810 0.00 0.00 0 -ATOM 567 H 1 1 33.615 10.270 11.513 0.00 0.00 0 -ATOM 568 O 1 1 31.790 9.696 18.223 0.00 0.00 0 -ATOM 569 H 1 1 30.484 9.334 19.421 0.00 0.00 0 -ATOM 570 H 1 1 30.834 10.096 16.929 0.00 0.00 0 -ATOM 571 O 1 1 30.141 15.006 21.532 0.00 0.00 0 -ATOM 572 H 1 1 28.565 15.594 22.099 0.00 0.00 0 -ATOM 573 H 1 1 30.942 14.253 23.077 0.00 0.00 0 -ATOM 574 O 1 1 32.798 10.732 30.680 0.00 0.00 0 -ATOM 575 H 1 1 34.073 9.528 30.799 0.00 0.00 0 -ATOM 576 H 1 1 32.991 11.512 28.983 0.00 0.00 0 -ATOM 577 O 1 1 33.652 16.265 5.086 0.00 0.00 0 -ATOM 578 H 1 1 35.399 16.239 4.730 0.00 0.00 0 -ATOM 579 H 1 1 33.503 17.939 5.631 0.00 0.00 0 -ATOM 580 O 1 1 31.947 10.799 7.943 0.00 0.00 0 -ATOM 581 H 1 1 29.894 10.549 7.619 0.00 0.00 0 -ATOM 582 H 1 1 32.271 12.414 7.075 0.00 0.00 0 -ATOM 583 O 1 1 0.329 15.516 11.746 0.00 0.00 0 -ATOM 584 H 1 1 -0.446 14.249 12.939 0.00 0.00 0 -ATOM 585 H 1 1 -0.685 17.018 11.935 0.00 0.00 0 -ATOM 586 O 1 1 4.262 19.165 14.308 0.00 0.00 0 -ATOM 587 H 1 1 3.579 17.691 14.920 0.00 0.00 0 -ATOM 588 H 1 1 5.723 19.183 15.204 0.00 0.00 0 -ATOM 589 O 1 1 32.995 13.546 25.948 0.00 0.00 0 -ATOM 590 H 1 1 32.167 15.060 26.787 0.00 0.00 0 -ATOM 591 H 1 1 34.425 13.800 25.007 0.00 0.00 0 -ATOM 592 O 1 1 1.773 13.524 34.037 0.00 0.00 0 -ATOM 593 H 1 1 0.227 14.409 33.446 0.00 0.00 0 -ATOM 594 H 1 1 2.167 14.670 35.511 0.00 0.00 0 -ATOM 595 O 1 1 33.029 20.529 7.247 0.00 0.00 0 -ATOM 596 H 1 1 34.388 21.414 8.003 0.00 0.00 0 -ATOM 597 H 1 1 31.451 20.831 8.182 0.00 0.00 0 -ATOM 598 O 1 1 2.037 24.250 10.251 0.00 0.00 0 -ATOM 599 H 1 1 3.743 25.008 9.876 0.00 0.00 0 -ATOM 600 H 1 1 1.894 25.043 11.903 0.00 0.00 0 -ATOM 601 O 1 1 32.753 19.259 13.976 0.00 0.00 0 -ATOM 602 H 1 1 32.792 20.886 13.792 0.00 0.00 0 -ATOM 603 H 1 1 34.334 18.799 14.976 0.00 0.00 0 -ATOM 604 O 1 1 0.396 18.673 18.699 0.00 0.00 0 -ATOM 605 H 1 1 -1.211 18.950 19.127 0.00 0.00 0 -ATOM 606 H 1 1 0.469 16.977 18.436 0.00 0.00 0 -ATOM 607 O 1 1 30.855 18.370 27.959 0.00 0.00 0 -ATOM 608 H 1 1 29.759 19.681 28.690 0.00 0.00 0 -ATOM 609 H 1 1 32.103 19.477 26.763 0.00 0.00 0 -ATOM 610 O 1 1 27.723 15.992 33.091 0.00 0.00 0 -ATOM 611 H 1 1 29.390 16.423 32.192 0.00 0.00 0 -ATOM 612 H 1 1 27.801 15.859 34.804 0.00 0.00 0 -ATOM 613 O 1 1 31.068 27.895 3.348 0.00 0.00 0 -ATOM 614 H 1 1 32.517 27.825 4.610 0.00 0.00 0 -ATOM 615 H 1 1 31.529 29.459 2.324 0.00 0.00 0 -ATOM 616 O 1 1 35.039 28.008 6.663 0.00 0.00 0 -ATOM 617 H 1 1 35.966 26.934 7.683 0.00 0.00 0 -ATOM 618 H 1 1 36.055 28.336 5.336 0.00 0.00 0 -ATOM 619 O 1 1 29.356 28.196 13.025 0.00 0.00 0 -ATOM 620 H 1 1 29.210 29.335 14.589 0.00 0.00 0 -ATOM 621 H 1 1 28.874 29.629 11.867 0.00 0.00 0 -ATOM 622 O 1 1 32.386 28.434 18.961 0.00 0.00 0 -ATOM 623 H 1 1 33.368 28.574 20.411 0.00 0.00 0 -ATOM 624 H 1 1 33.410 27.406 17.949 0.00 0.00 0 -ATOM 625 O 1 1 30.898 25.390 25.799 0.00 0.00 0 -ATOM 626 H 1 1 32.369 25.913 24.580 0.00 0.00 0 -ATOM 627 H 1 1 31.317 24.075 27.029 0.00 0.00 0 -ATOM 628 O 1 1 32.259 25.611 33.104 0.00 0.00 0 -ATOM 629 H 1 1 32.238 25.736 34.806 0.00 0.00 0 -ATOM 630 H 1 1 33.920 25.042 32.775 0.00 0.00 0 -ATOM 631 O 1 1 30.290 32.645 1.341 0.00 0.00 0 -ATOM 632 H 1 1 29.949 32.793 -0.430 0.00 0.00 0 -ATOM 633 H 1 1 31.762 33.340 1.847 0.00 0.00 0 -ATOM 634 O 1 1 25.536 34.235 6.469 0.00 0.00 0 -ATOM 635 H 1 1 25.716 36.059 6.651 0.00 0.00 0 -ATOM 636 H 1 1 25.283 33.866 4.895 0.00 0.00 0 -ATOM 637 O 1 1 31.674 33.161 13.106 0.00 0.00 0 -ATOM 638 H 1 1 31.793 34.863 13.281 0.00 0.00 0 -ATOM 639 H 1 1 30.425 32.928 11.783 0.00 0.00 0 -ATOM 640 O 1 1 33.844 32.668 22.296 0.00 0.00 0 -ATOM 641 H 1 1 32.750 32.234 23.524 0.00 0.00 0 -ATOM 642 H 1 1 32.917 32.875 20.736 0.00 0.00 0 -ATOM 643 O 1 1 31.603 30.542 30.805 0.00 0.00 0 -ATOM 644 H 1 1 33.451 30.804 30.468 0.00 0.00 0 -ATOM 645 H 1 1 31.575 28.816 31.756 0.00 0.00 0 -ATOM 646 O 1 1 26.295 31.235 30.599 0.00 0.00 0 -ATOM 647 H 1 1 27.834 30.515 30.607 0.00 0.00 0 -ATOM 648 H 1 1 26.362 32.920 29.856 0.00 0.00 0 -END diff --git a/tools/i-pi/examples/lammps/h2o-piglet.4/data.water b/tools/i-pi/examples/lammps/h2o-piglet.4/data.water deleted file mode 100644 index 13c75e9933..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.4/data.water +++ /dev/null @@ -1,1331 +0,0 @@ -LAMMPS Description - - 648 atoms - 432 bonds - 216 angles - - 2 atom types - 1 bond types - 1 angle types - - 0 35.233 xlo xhi - 0 35.233 ylo yhi - 0 35.233 zlo zhi - -Masses - - 1 15.9994 - 2 1.0080 - -Bond Coeffs - - 1 1.78 0.2708585 -0.327738785 0.231328959 - -Angle Coeffs - - 1 0.0700 107.400000 - -Atoms - - 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 - 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 - 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 - 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000 - 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 - 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 - 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 - 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 - 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 - 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 - 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 - 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 - 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 - 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 - 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 - 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001 - 17 6 2 0.5564 2.39200001 2.89799999 34.84600000 - 18 6 2 0.5564 0.81400000 0.53200001 35.83600000 - 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999 - 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000 - 21 7 2 0.5564 30.91999999 11.59399999 1.67700000 - 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000 - 23 8 2 0.5564 0.30500000 10.64300001 2.79300000 - 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000 - 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000 - 26 9 2 0.5564 33.61600000 7.67300000 8.85700000 - 27 9 2 0.5564 35.11500000 5.25999999 7.61800001 - 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999 - 29 10 2 0.5564 31.62400000 6.90800001 23.52100001 - 30 10 2 0.5564 32.54400000 4.99000000 24.98200000 - 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000 - 32 11 2 0.5564 1.85600000 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612 - 205 1 614 613 615 - 206 1 617 616 618 - 207 1 620 619 621 - 208 1 623 622 624 - 209 1 626 625 627 - 210 1 629 628 630 - 211 1 632 631 633 - 212 1 635 634 636 - 213 1 638 637 639 - 214 1 641 640 642 - 215 1 644 643 645 - 216 1 647 646 648 diff --git a/tools/i-pi/examples/lammps/h2o-piglet.4/in.water b/tools/i-pi/examples/lammps/h2o-piglet.4/in.water deleted file mode 100644 index c43fe7c15c..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.4/in.water +++ /dev/null @@ -1,32 +0,0 @@ -units electron -atom_style full - -#pair_style lj/cut/coul/long 17.01 -pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 -#bond_style harmonic -bond_style class2 -angle_style harmonic -#kspace_style pppm 0.0001 -kspace_style pppm/tip4p 0.0001 - -read_data data.water -pair_coeff * * 0 0 -pair_coeff 1 1 0.000295147 5.96946 - -neighbor 2.0 bin - -timestep 0.00025 - -#velocity all create 298.0 2345187 - -#thermo_style multi -#thermo 1 - -#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 -#fix 1 all nve -fix 1 all ipi piglet_4 32343 unix - -#dump 1 all xyz 25 dump.xyz - -run 100000000 - diff --git a/tools/i-pi/examples/lammps/h2o-piglet.4/input.xml b/tools/i-pi/examples/lammps/h2o-piglet.4/input.xml deleted file mode 100644 index af3b01a1d3..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.4/input.xml +++ /dev/null @@ -1,40 +0,0 @@ - - - water_298K.pdb - 298 - - - [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] - positions - - 500000 - 32343 - - -
piglet_4
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-ATOM 2 H 1 1 2.979 7.054 0.857 0.00 0.00 0 -ATOM 3 H 1 1 5.525 5.697 0.451 0.00 0.00 0 -ATOM 4 O 1 1 34.557 34.341 3.078 0.00 0.00 0 -ATOM 5 H 1 1 33.722 34.689 4.840 0.00 0.00 0 -ATOM 6 H 1 1 36.029 33.220 3.711 0.00 0.00 0 -ATOM 7 O 1 1 5.591 1.963 13.477 0.00 0.00 0 -ATOM 8 H 1 1 7.265 1.864 13.851 0.00 0.00 0 -ATOM 9 H 1 1 5.009 3.555 13.916 0.00 0.00 0 -ATOM 10 O 1 1 1.060 2.061 21.718 0.00 0.00 0 -ATOM 11 H 1 1 0.757 0.261 21.820 0.00 0.00 0 -ATOM 12 H 1 1 0.213 3.013 23.047 0.00 0.00 0 -ATOM 13 O 1 1 1.200 1.337 29.006 0.00 0.00 0 -ATOM 14 H 1 1 0.818 1.884 30.732 0.00 0.00 0 -ATOM 15 H 1 1 2.883 1.825 29.011 0.00 0.00 0 -ATOM 16 O 1 1 1.331 1.386 34.306 0.00 0.00 0 -ATOM 17 H 1 1 2.392 2.898 34.846 0.00 0.00 0 -ATOM 18 H 1 1 0.814 0.532 35.836 0.00 0.00 0 -ATOM 19 O 1 1 31.451 10.201 0.726 0.00 0.00 0 -ATOM 20 H 1 1 32.282 10.877 -0.750 0.00 0.00 0 -ATOM 21 H 1 1 30.920 11.594 1.677 0.00 0.00 0 -ATOM 22 O 1 1 0.836 10.808 4.298 0.00 0.00 0 -ATOM 23 H 1 1 0.305 10.643 2.793 0.00 0.00 0 -ATOM 24 H 1 1 -0.356 10.334 5.524 0.00 0.00 0 -ATOM 25 O 1 1 34.381 5.979 9.194 0.00 0.00 0 -ATOM 26 H 1 1 33.616 7.673 8.857 0.00 0.00 0 -ATOM 27 H 1 1 35.115 5.260 7.618 0.00 0.00 0 -ATOM 28 O 1 1 33.212 6.480 24.278 0.00 0.00 0 -ATOM 29 H 1 1 31.624 6.908 23.521 0.00 0.00 0 -ATOM 30 H 1 1 32.544 4.990 24.982 0.00 0.00 0 -ATOM 31 O 1 1 1.992 9.002 26.863 0.00 0.00 0 -ATOM 32 H 1 1 1.856 10.175 25.579 0.00 0.00 0 -ATOM 33 H 1 1 0.519 8.099 26.386 0.00 0.00 0 -ATOM 34 O 1 1 2.054 8.660 32.515 0.00 0.00 0 -ATOM 35 H 1 1 2.167 8.727 30.494 0.00 0.00 0 -ATOM 36 H 1 1 2.374 10.513 33.038 0.00 0.00 0 -ATOM 37 O 1 1 3.402 16.639 3.008 0.00 0.00 0 -ATOM 38 H 1 1 4.127 15.872 4.446 0.00 0.00 0 -ATOM 39 H 1 1 2.905 18.339 3.160 0.00 0.00 0 -ATOM 40 O 1 1 4.222 15.444 8.072 0.00 0.00 0 -ATOM 41 H 1 1 5.211 16.756 8.299 0.00 0.00 0 -ATOM 42 H 1 1 2.560 15.492 8.860 0.00 0.00 0 -ATOM 43 O 1 1 2.831 9.246 16.488 0.00 0.00 0 -ATOM 44 H 1 1 2.869 8.023 18.050 0.00 0.00 0 -ATOM 45 H 1 1 3.960 8.467 15.154 0.00 0.00 0 -ATOM 46 O 1 1 5.563 6.003 20.907 0.00 0.00 0 -ATOM 47 H 1 1 4.653 4.638 21.480 0.00 0.00 0 -ATOM 48 H 1 1 6.405 6.208 22.529 0.00 0.00 0 -ATOM 49 O 1 1 2.087 13.370 22.913 0.00 0.00 0 -ATOM 50 H 1 1 2.832 14.804 23.422 0.00 0.00 0 -ATOM 51 H 1 1 1.434 13.509 21.196 0.00 0.00 0 -ATOM 52 O 1 1 3.369 17.886 25.109 0.00 0.00 0 -ATOM 53 H 1 1 3.655 17.200 26.766 0.00 0.00 0 -ATOM 54 H 1 1 4.772 18.977 24.500 0.00 0.00 0 -ATOM 55 O 1 1 34.764 20.803 0.948 0.00 0.00 0 -ATOM 56 H 1 1 35.210 21.267 2.816 0.00 0.00 0 -ATOM 57 H 1 1 35.962 21.726 0.131 0.00 0.00 0 -ATOM 58 O 1 1 2.836 24.178 15.229 0.00 0.00 0 -ATOM 59 H 1 1 2.795 22.346 14.876 0.00 0.00 0 -ATOM 60 H 1 1 2.414 24.115 17.130 0.00 0.00 0 -ATOM 61 O 1 1 33.000 24.481 15.230 0.00 0.00 0 -ATOM 62 H 1 1 34.640 24.804 15.013 0.00 0.00 0 -ATOM 63 H 1 1 32.401 25.764 14.295 0.00 0.00 0 -ATOM 64 O 1 1 0.404 26.779 23.400 0.00 0.00 0 -ATOM 65 H 1 1 1.353 27.248 24.987 0.00 0.00 0 -ATOM 66 H 1 1 1.546 28.050 22.317 0.00 0.00 0 -ATOM 67 O 1 1 34.222 21.380 25.418 0.00 0.00 0 -ATOM 68 H 1 1 35.669 20.151 25.317 0.00 0.00 0 -ATOM 69 H 1 1 32.960 21.180 23.992 0.00 0.00 0 -ATOM 70 O 1 1 33.259 17.438 32.480 0.00 0.00 0 -ATOM 71 H 1 1 33.314 18.782 33.883 0.00 0.00 0 -ATOM 72 H 1 1 32.743 18.181 30.871 0.00 0.00 0 -ATOM 73 O 1 1 4.463 21.979 3.936 0.00 0.00 0 -ATOM 74 H 1 1 5.856 23.084 3.400 0.00 0.00 0 -ATOM 75 H 1 1 3.986 22.180 5.602 0.00 0.00 0 -ATOM 76 O 1 1 6.258 25.851 8.520 0.00 0.00 0 -ATOM 77 H 1 1 5.767 27.693 8.476 0.00 0.00 0 -ATOM 78 H 1 1 7.202 25.506 10.186 0.00 0.00 0 -ATOM 79 O 1 1 0.601 29.737 12.747 0.00 0.00 0 -ATOM 80 H 1 1 -0.685 30.842 12.350 0.00 0.00 0 -ATOM 81 H 1 1 1.336 30.716 14.031 0.00 0.00 0 -ATOM 82 O 1 1 7.563 28.191 24.333 0.00 0.00 0 -ATOM 83 H 1 1 9.201 28.828 24.684 0.00 0.00 0 -ATOM 84 H 1 1 7.381 27.621 22.799 0.00 0.00 0 -ATOM 85 O 1 1 3.653 27.109 27.772 0.00 0.00 0 -ATOM 86 H 1 1 5.126 27.015 26.772 0.00 0.00 0 -ATOM 87 H 1 1 3.031 28.756 27.698 0.00 0.00 0 -ATOM 88 O 1 1 2.596 23.991 32.476 0.00 0.00 0 -ATOM 89 H 1 1 2.879 24.791 30.859 0.00 0.00 0 -ATOM 90 H 1 1 4.003 22.913 32.701 0.00 0.00 0 -ATOM 91 O 1 1 3.083 31.317 3.644 0.00 0.00 0 -ATOM 92 H 1 1 4.133 30.589 2.539 0.00 0.00 0 -ATOM 93 H 1 1 4.218 32.173 5.037 0.00 0.00 0 -ATOM 94 O 1 1 4.661 30.555 9.368 0.00 0.00 0 -ATOM 95 H 1 1 3.184 29.843 10.132 0.00 0.00 0 -ATOM 96 H 1 1 4.358 32.448 9.126 0.00 0.00 0 -ATOM 97 O 1 1 3.465 32.537 15.778 0.00 0.00 0 -ATOM 98 H 1 1 5.072 31.819 15.903 0.00 0.00 0 -ATOM 99 H 1 1 4.055 34.257 15.284 0.00 0.00 0 -ATOM 100 O 1 1 4.215 29.153 20.317 0.00 0.00 0 -ATOM 101 H 1 1 3.658 30.176 18.842 0.00 0.00 0 -ATOM 102 H 1 1 4.959 30.291 21.449 0.00 0.00 0 -ATOM 103 O 1 1 1.126 31.333 28.768 0.00 0.00 0 -ATOM 104 H 1 1 2.395 31.124 29.925 0.00 0.00 0 -ATOM 105 H 1 1 0.768 33.092 28.898 0.00 0.00 0 -ATOM 106 O 1 1 4.881 32.616 32.302 0.00 0.00 0 -ATOM 107 H 1 1 6.588 32.911 31.725 0.00 0.00 0 -ATOM 108 H 1 1 4.486 34.037 33.249 0.00 0.00 0 -ATOM 109 O 1 1 8.962 5.556 0.151 0.00 0.00 0 -ATOM 110 H 1 1 9.652 6.991 0.859 0.00 0.00 0 -ATOM 111 H 1 1 9.173 4.477 1.645 0.00 0.00 0 -ATOM 112 O 1 1 1.833 3.518 5.679 0.00 0.00 0 -ATOM 113 H 1 1 2.889 2.731 6.788 0.00 0.00 0 -ATOM 114 H 1 1 2.789 4.187 4.147 0.00 0.00 0 -ATOM 115 O 1 1 10.510 34.726 13.073 0.00 0.00 0 -ATOM 116 H 1 1 11.920 34.118 11.919 0.00 0.00 0 -ATOM 117 H 1 1 11.295 34.968 14.741 0.00 0.00 0 -ATOM 118 O 1 1 7.212 0.042 22.454 0.00 0.00 0 -ATOM 119 H 1 1 6.924 0.470 24.172 0.00 0.00 0 -ATOM 120 H 1 1 8.319 1.228 21.653 0.00 0.00 0 -ATOM 121 O 1 1 6.365 2.010 27.544 0.00 0.00 0 -ATOM 122 H 1 1 5.954 3.585 26.852 0.00 0.00 0 -ATOM 123 H 1 1 7.758 2.549 28.696 0.00 0.00 0 -ATOM 124 O 1 1 10.833 3.140 30.787 0.00 0.00 0 -ATOM 125 H 1 1 12.697 2.975 30.867 0.00 0.00 0 -ATOM 126 H 1 1 10.389 3.700 32.404 0.00 0.00 0 -ATOM 127 O 1 1 8.684 9.342 3.912 0.00 0.00 0 -ATOM 128 H 1 1 6.985 9.256 4.773 0.00 0.00 0 -ATOM 129 H 1 1 8.684 10.809 3.011 0.00 0.00 0 -ATOM 130 O 1 1 4.873 9.919 7.707 0.00 0.00 0 -ATOM 131 H 1 1 3.698 9.771 6.194 0.00 0.00 0 -ATOM 132 H 1 1 5.047 11.961 7.624 0.00 0.00 0 -ATOM 133 O 1 1 10.031 5.018 9.699 0.00 0.00 0 -ATOM 134 H 1 1 9.675 3.382 10.340 0.00 0.00 0 -ATOM 135 H 1 1 9.132 5.987 10.825 0.00 0.00 0 -ATOM 136 O 1 1 11.246 3.918 21.929 0.00 0.00 0 -ATOM 137 H 1 1 12.614 2.770 22.341 0.00 0.00 0 -ATOM 138 H 1 1 12.073 5.686 21.497 0.00 0.00 0 -ATOM 139 O 1 1 6.825 7.164 25.708 0.00 0.00 0 -ATOM 140 H 1 1 8.036 8.374 25.980 0.00 0.00 0 -ATOM 141 H 1 1 5.206 7.900 25.891 0.00 0.00 0 -ATOM 142 O 1 1 10.171 12.811 0.295 0.00 0.00 0 -ATOM 143 H 1 1 10.033 12.818 -1.609 0.00 0.00 0 -ATOM 144 H 1 1 9.880 14.492 0.480 0.00 0.00 0 -ATOM 145 O 1 1 8.190 17.402 1.253 0.00 0.00 0 -ATOM 146 H 1 1 9.472 18.531 1.253 0.00 0.00 0 -ATOM 147 H 1 1 6.351 17.817 1.568 0.00 0.00 0 -ATOM 148 O 1 1 11.233 16.188 8.299 0.00 0.00 0 -ATOM 149 H 1 1 10.291 17.689 8.166 0.00 0.00 0 -ATOM 150 H 1 1 12.768 17.123 8.733 0.00 0.00 0 -ATOM 151 O 1 1 6.386 8.002 12.846 0.00 0.00 0 -ATOM 152 H 1 1 7.701 8.896 13.655 0.00 0.00 0 -ATOM 153 H 1 1 5.591 8.877 11.519 0.00 0.00 0 -ATOM 154 O 1 1 8.184 10.419 18.848 0.00 0.00 0 -ATOM 155 H 1 1 9.498 9.434 19.905 0.00 0.00 0 -ATOM 156 H 1 1 6.882 9.027 18.948 0.00 0.00 0 -ATOM 157 O 1 1 10.806 14.431 21.328 0.00 0.00 0 -ATOM 158 H 1 1 9.177 13.531 20.670 0.00 0.00 0 -ATOM 159 H 1 1 11.344 15.696 20.448 0.00 0.00 0 -ATOM 160 O 1 1 9.237 13.928 30.341 0.00 0.00 0 -ATOM 161 H 1 1 10.779 14.839 30.522 0.00 0.00 0 -ATOM 162 H 1 1 9.965 13.192 28.899 0.00 0.00 0 -ATOM 163 O 1 1 10.918 21.707 1.864 0.00 0.00 0 -ATOM 164 H 1 1 10.280 23.449 2.279 0.00 0.00 0 -ATOM 165 H 1 1 12.708 21.456 1.749 0.00 0.00 0 -ATOM 166 O 1 1 9.353 16.125 13.927 0.00 0.00 0 -ATOM 167 H 1 1 9.938 17.594 14.618 0.00 0.00 0 -ATOM 168 H 1 1 9.518 16.360 12.244 0.00 0.00 0 -ATOM 169 O 1 1 10.371 11.107 14.268 0.00 0.00 0 -ATOM 170 H 1 1 9.644 10.406 15.859 0.00 0.00 0 -ATOM 171 H 1 1 9.434 12.523 14.117 0.00 0.00 0 -ATOM 172 O 1 1 3.351 22.769 20.196 0.00 0.00 0 -ATOM 173 H 1 1 2.055 23.686 21.503 0.00 0.00 0 -ATOM 174 H 1 1 2.452 21.401 19.413 0.00 0.00 0 -ATOM 175 O 1 1 6.836 21.329 23.199 0.00 0.00 0 -ATOM 176 H 1 1 8.249 20.848 22.320 0.00 0.00 0 -ATOM 177 H 1 1 5.668 21.841 21.886 0.00 0.00 0 -ATOM 178 O 1 1 4.604 15.649 30.043 0.00 0.00 0 -ATOM 179 H 1 1 6.453 15.217 30.207 0.00 0.00 0 -ATOM 180 H 1 1 3.822 14.762 31.562 0.00 0.00 0 -ATOM 181 O 1 1 7.125 19.976 9.421 0.00 0.00 0 -ATOM 182 H 1 1 5.918 20.453 10.730 0.00 0.00 0 -ATOM 183 H 1 1 8.099 21.496 9.491 0.00 0.00 0 -ATOM 184 O 1 1 9.063 25.912 13.186 0.00 0.00 0 -ATOM 185 H 1 1 10.350 26.572 12.367 0.00 0.00 0 -ATOM 186 H 1 1 9.680 24.367 13.697 0.00 0.00 0 -ATOM 187 O 1 1 8.022 22.343 17.042 0.00 0.00 0 -ATOM 188 H 1 1 9.144 23.367 18.074 0.00 0.00 0 -ATOM 189 H 1 1 6.562 23.462 16.852 0.00 0.00 0 -ATOM 190 O 1 1 10.762 26.285 19.963 0.00 0.00 0 -ATOM 191 H 1 1 11.036 27.966 20.538 0.00 0.00 0 -ATOM 192 H 1 1 11.078 25.401 21.456 0.00 0.00 0 -ATOM 193 O 1 1 9.158 22.902 28.391 0.00 0.00 0 -ATOM 194 H 1 1 8.219 23.528 27.085 0.00 0.00 0 -ATOM 195 H 1 1 8.089 21.760 29.509 0.00 0.00 0 -ATOM 196 O 1 1 6.219 20.158 31.921 0.00 0.00 0 -ATOM 197 H 1 1 5.635 18.511 31.161 0.00 0.00 0 -ATOM 198 H 1 1 7.530 19.624 33.071 0.00 0.00 0 -ATOM 199 O 1 1 11.191 31.509 2.617 0.00 0.00 0 -ATOM 200 H 1 1 10.460 32.214 4.108 0.00 0.00 0 -ATOM 201 H 1 1 13.176 31.751 2.577 0.00 0.00 0 -ATOM 202 O 1 1 4.748 0.055 8.605 0.00 0.00 0 -ATOM 203 H 1 1 5.380 0.517 10.183 0.00 0.00 0 -ATOM 204 H 1 1 6.050 -0.306 7.480 0.00 0.00 0 -ATOM 205 O 1 1 8.695 30.809 15.731 0.00 0.00 0 -ATOM 206 H 1 1 9.189 32.103 14.495 0.00 0.00 0 -ATOM 207 H 1 1 8.447 29.069 14.868 0.00 0.00 0 -ATOM 208 O 1 1 10.128 31.402 20.766 0.00 0.00 0 -ATOM 209 H 1 1 9.456 30.905 19.155 0.00 0.00 0 -ATOM 210 H 1 1 9.020 32.731 21.415 0.00 0.00 0 -ATOM 211 O 1 1 12.238 30.162 25.837 0.00 0.00 0 -ATOM 212 H 1 1 11.418 30.908 27.110 0.00 0.00 0 -ATOM 213 H 1 1 12.396 31.331 24.678 0.00 0.00 0 -ATOM 214 O 1 1 10.395 32.537 30.624 0.00 0.00 0 -ATOM 215 H 1 1 11.042 34.339 30.751 0.00 0.00 0 -ATOM 216 H 1 1 11.378 31.486 31.538 0.00 0.00 0 -ATOM 217 O 1 1 10.438 3.626 5.087 0.00 0.00 0 -ATOM 218 H 1 1 12.435 4.082 5.136 0.00 0.00 0 -ATOM 219 H 1 1 9.822 4.284 6.681 0.00 0.00 0 -ATOM 220 O 1 1 14.762 3.401 13.776 0.00 0.00 0 -ATOM 221 H 1 1 16.518 3.824 13.376 0.00 0.00 0 -ATOM 222 H 1 1 13.752 4.757 12.964 0.00 0.00 0 -ATOM 223 O 1 1 12.382 1.012 17.643 0.00 0.00 0 -ATOM 224 H 1 1 13.346 1.997 16.444 0.00 0.00 0 -ATOM 225 H 1 1 11.931 2.133 18.998 0.00 0.00 0 -ATOM 226 O 1 1 15.278 1.293 24.559 0.00 0.00 0 -ATOM 227 H 1 1 16.071 0.946 26.365 0.00 0.00 0 -ATOM 228 H 1 1 15.794 0.199 23.499 0.00 0.00 0 -ATOM 229 O 1 1 22.226 31.627 24.712 0.00 0.00 0 -ATOM 230 H 1 1 23.338 32.595 23.876 0.00 0.00 0 -ATOM 231 H 1 1 22.161 30.053 24.132 0.00 0.00 0 -ATOM 232 O 1 1 15.640 1.847 32.717 0.00 0.00 0 -ATOM 233 H 1 1 17.488 2.473 31.874 0.00 0.00 0 -ATOM 234 H 1 1 16.403 0.869 34.267 0.00 0.00 0 -ATOM 235 O 1 1 14.858 10.199 2.754 0.00 0.00 0 -ATOM 236 H 1 1 13.360 10.712 2.282 0.00 0.00 0 -ATOM 237 H 1 1 14.560 9.316 4.559 0.00 0.00 0 -ATOM 238 O 1 1 15.717 8.469 10.739 0.00 0.00 0 -ATOM 239 H 1 1 17.323 9.581 10.875 0.00 0.00 0 -ATOM 240 H 1 1 14.574 9.631 10.221 0.00 0.00 0 -ATOM 241 O 1 1 15.248 10.398 16.525 0.00 0.00 0 -ATOM 242 H 1 1 16.324 9.181 16.149 0.00 0.00 0 -ATOM 243 H 1 1 14.172 10.488 15.098 0.00 0.00 0 -ATOM 244 O 1 1 13.226 8.438 20.801 0.00 0.00 0 -ATOM 245 H 1 1 14.043 8.996 19.295 0.00 0.00 0 -ATOM 246 H 1 1 14.661 7.802 22.093 0.00 0.00 0 -ATOM 247 O 1 1 10.173 10.961 25.875 0.00 0.00 0 -ATOM 248 H 1 1 11.477 10.223 26.940 0.00 0.00 0 -ATOM 249 H 1 1 11.269 10.738 24.343 0.00 0.00 0 -ATOM 250 O 1 1 12.792 7.737 29.173 0.00 0.00 0 -ATOM 251 H 1 1 12.199 6.038 29.475 0.00 0.00 0 -ATOM 252 H 1 1 14.427 7.450 29.617 0.00 0.00 0 -ATOM 253 O 1 1 15.180 19.498 3.578 0.00 0.00 0 -ATOM 254 H 1 1 14.883 17.596 4.080 0.00 0.00 0 -ATOM 255 H 1 1 16.754 19.579 2.626 0.00 0.00 0 -ATOM 256 O 1 1 12.517 11.093 7.701 0.00 0.00 0 -ATOM 257 H 1 1 12.224 12.778 7.555 0.00 0.00 0 -ATOM 258 H 1 1 11.150 10.393 7.057 0.00 0.00 0 -ATOM 259 O 1 1 16.266 16.271 10.758 0.00 0.00 0 -ATOM 260 H 1 1 16.507 15.795 12.768 0.00 0.00 0 -ATOM 261 H 1 1 17.725 16.977 10.292 0.00 0.00 0 -ATOM 262 O 1 1 14.069 18.399 18.897 0.00 0.00 0 -ATOM 263 H 1 1 15.513 17.523 18.155 0.00 0.00 0 -ATOM 264 H 1 1 14.958 18.709 20.673 0.00 0.00 0 -ATOM 265 O 1 1 14.099 15.480 25.510 0.00 0.00 0 -ATOM 266 H 1 1 13.698 16.872 26.938 0.00 0.00 0 -ATOM 267 H 1 1 12.567 15.379 24.444 0.00 0.00 0 -ATOM 268 O 1 1 13.309 17.574 30.292 0.00 0.00 0 -ATOM 269 H 1 1 14.937 16.934 30.810 0.00 0.00 0 -ATOM 270 H 1 1 13.969 19.494 30.012 0.00 0.00 0 -ATOM 271 O 1 1 18.371 23.257 0.925 0.00 0.00 0 -ATOM 272 H 1 1 19.479 23.480 2.321 0.00 0.00 0 -ATOM 273 H 1 1 19.087 24.325 -0.369 0.00 0.00 0 -ATOM 274 O 1 1 12.100 21.730 11.355 0.00 0.00 0 -ATOM 275 H 1 1 13.141 22.287 12.743 0.00 0.00 0 -ATOM 276 H 1 1 13.467 22.236 10.244 0.00 0.00 0 -ATOM 277 O 1 1 12.163 23.290 23.597 0.00 0.00 0 -ATOM 278 H 1 1 11.324 22.736 24.949 0.00 0.00 0 -ATOM 279 H 1 1 13.882 22.872 23.840 0.00 0.00 0 -ATOM 280 O 1 1 20.173 26.761 22.628 0.00 0.00 0 -ATOM 281 H 1 1 20.206 26.532 20.792 0.00 0.00 0 -ATOM 282 H 1 1 21.556 25.742 23.389 0.00 0.00 0 -ATOM 283 O 1 1 16.701 21.165 22.605 0.00 0.00 0 -ATOM 284 H 1 1 18.028 20.686 23.848 0.00 0.00 0 -ATOM 285 H 1 1 17.104 22.866 21.949 0.00 0.00 0 -ATOM 286 O 1 1 11.391 26.461 33.705 0.00 0.00 0 -ATOM 287 H 1 1 9.841 27.192 34.048 0.00 0.00 0 -ATOM 288 H 1 1 11.776 25.540 35.243 0.00 0.00 0 -ATOM 289 O 1 1 9.898 25.989 4.553 0.00 0.00 0 -ATOM 290 H 1 1 8.902 26.131 6.039 0.00 0.00 0 -ATOM 291 H 1 1 10.287 27.806 4.376 0.00 0.00 0 -ATOM 292 O 1 1 14.308 26.960 10.877 0.00 0.00 0 -ATOM 293 H 1 1 15.302 27.405 12.173 0.00 0.00 0 -ATOM 294 H 1 1 15.463 26.151 9.633 0.00 0.00 0 -ATOM 295 O 1 1 13.433 22.960 16.904 0.00 0.00 0 -ATOM 296 H 1 1 13.409 24.131 18.132 0.00 0.00 0 -ATOM 297 H 1 1 13.624 21.191 17.520 0.00 0.00 0 -ATOM 298 O 1 1 16.409 26.768 26.875 0.00 0.00 0 -ATOM 299 H 1 1 17.590 26.987 25.431 0.00 0.00 0 -ATOM 300 H 1 1 14.751 27.703 26.230 0.00 0.00 0 -ATOM 301 O 1 1 14.405 22.733 29.892 0.00 0.00 0 -ATOM 302 H 1 1 15.423 23.079 28.494 0.00 0.00 0 -ATOM 303 H 1 1 12.826 23.259 29.416 0.00 0.00 0 -ATOM 304 O 1 1 6.905 29.408 0.749 0.00 0.00 0 -ATOM 305 H 1 1 8.428 30.483 1.567 0.00 0.00 0 -ATOM 306 H 1 1 6.353 30.814 -0.444 0.00 0.00 0 -ATOM 307 O 1 1 9.189 34.159 6.509 0.00 0.00 0 -ATOM 308 H 1 1 10.198 34.193 8.002 0.00 0.00 0 -ATOM 309 H 1 1 9.890 35.692 5.785 0.00 0.00 0 -ATOM 310 O 1 1 14.256 32.316 9.369 0.00 0.00 0 -ATOM 311 H 1 1 15.733 32.867 9.486 0.00 0.00 0 -ATOM 312 H 1 1 14.754 30.670 10.090 0.00 0.00 0 -ATOM 313 O 1 1 14.714 30.841 16.516 0.00 0.00 0 -ATOM 314 H 1 1 13.748 29.551 17.279 0.00 0.00 0 -ATOM 315 H 1 1 13.218 31.933 16.614 0.00 0.00 0 -ATOM 316 O 1 1 18.409 33.641 20.611 0.00 0.00 0 -ATOM 317 H 1 1 19.601 32.274 21.115 0.00 0.00 0 -ATOM 318 H 1 1 17.360 32.655 19.518 0.00 0.00 0 -ATOM 319 O 1 1 16.062 28.638 32.207 0.00 0.00 0 -ATOM 320 H 1 1 14.648 27.958 33.253 0.00 0.00 0 -ATOM 321 H 1 1 15.752 28.014 30.522 0.00 0.00 0 -ATOM 322 O 1 1 16.200 30.895 1.473 0.00 0.00 0 -ATOM 323 H 1 1 16.626 29.968 -0.130 0.00 0.00 0 -ATOM 324 H 1 1 17.167 29.833 2.927 0.00 0.00 0 -ATOM 325 O 1 1 20.278 3.529 6.048 0.00 0.00 0 -ATOM 326 H 1 1 20.977 3.611 4.575 0.00 0.00 0 -ATOM 327 H 1 1 21.312 4.513 7.251 0.00 0.00 0 -ATOM 328 O 1 1 23.079 5.778 10.408 0.00 0.00 0 -ATOM 329 H 1 1 24.650 6.259 10.838 0.00 0.00 0 -ATOM 330 H 1 1 22.342 7.609 10.178 0.00 0.00 0 -ATOM 331 O 1 1 19.581 2.031 12.110 0.00 0.00 0 -ATOM 332 H 1 1 19.039 1.082 10.440 0.00 0.00 0 -ATOM 333 H 1 1 21.141 2.991 11.851 0.00 0.00 0 -ATOM 334 O 1 1 22.005 3.223 23.178 0.00 0.00 0 -ATOM 335 H 1 1 21.429 4.090 24.554 0.00 0.00 0 -ATOM 336 H 1 1 20.654 1.791 22.711 0.00 0.00 0 -ATOM 337 O 1 1 16.630 6.422 23.792 0.00 0.00 0 -ATOM 338 H 1 1 16.219 4.804 24.406 0.00 0.00 0 -ATOM 339 H 1 1 17.066 7.128 25.282 0.00 0.00 0 -ATOM 340 O 1 1 21.676 5.564 28.158 0.00 0.00 0 -ATOM 341 H 1 1 20.658 6.717 29.185 0.00 0.00 0 -ATOM 342 H 1 1 23.413 5.828 28.996 0.00 0.00 0 -ATOM 343 O 1 1 15.257 5.265 5.626 0.00 0.00 0 -ATOM 344 H 1 1 16.914 4.519 5.490 0.00 0.00 0 -ATOM 345 H 1 1 15.144 6.150 6.972 0.00 0.00 0 -ATOM 346 O 1 1 20.137 11.082 10.437 0.00 0.00 0 -ATOM 347 H 1 1 20.021 10.947 8.733 0.00 0.00 0 -ATOM 348 H 1 1 21.025 12.555 10.853 0.00 0.00 0 -ATOM 349 O 1 1 23.089 14.627 12.437 0.00 0.00 0 -ATOM 350 H 1 1 24.716 15.254 12.736 0.00 0.00 0 -ATOM 351 H 1 1 23.284 13.228 13.653 0.00 0.00 0 -ATOM 352 O 1 1 24.083 12.649 22.566 0.00 0.00 0 -ATOM 353 H 1 1 22.397 12.663 23.042 0.00 0.00 0 -ATOM 354 H 1 1 24.901 13.851 23.565 0.00 0.00 0 -ATOM 355 O 1 1 17.865 7.909 30.036 0.00 0.00 0 -ATOM 356 H 1 1 17.509 8.045 31.982 0.00 0.00 0 -ATOM 357 H 1 1 18.078 9.582 29.318 0.00 0.00 0 -ATOM 358 O 1 1 18.824 8.486 0.104 0.00 0.00 0 -ATOM 359 H 1 1 19.997 10.191 -0.057 0.00 0.00 0 -ATOM 360 H 1 1 17.077 8.998 0.779 0.00 0.00 0 -ATOM 361 O 1 1 20.122 9.143 5.343 0.00 0.00 0 -ATOM 362 H 1 1 19.373 8.819 3.821 0.00 0.00 0 -ATOM 363 H 1 1 21.998 8.776 5.128 0.00 0.00 0 -ATOM 364 O 1 1 16.413 14.459 5.855 0.00 0.00 0 -ATOM 365 H 1 1 15.536 13.007 5.239 0.00 0.00 0 -ATOM 366 H 1 1 16.006 14.725 7.737 0.00 0.00 0 -ATOM 367 O 1 1 17.561 15.066 15.654 0.00 0.00 0 -ATOM 368 H 1 1 17.575 13.398 16.055 0.00 0.00 0 -ATOM 369 H 1 1 18.978 15.828 16.400 0.00 0.00 0 -ATOM 370 O 1 1 26.374 17.047 24.817 0.00 0.00 0 -ATOM 371 H 1 1 27.983 17.098 25.632 0.00 0.00 0 -ATOM 372 H 1 1 25.629 18.751 24.919 0.00 0.00 0 -ATOM 373 O 1 1 19.784 12.960 28.706 0.00 0.00 0 -ATOM 374 H 1 1 21.662 13.055 28.871 0.00 0.00 0 -ATOM 375 H 1 1 19.545 14.070 27.143 0.00 0.00 0 -ATOM 376 O 1 1 17.891 16.733 32.499 0.00 0.00 0 -ATOM 377 H 1 1 18.327 15.240 31.277 0.00 0.00 0 -ATOM 378 H 1 1 18.633 18.335 31.693 0.00 0.00 0 -ATOM 379 O 1 1 23.733 23.024 1.663 0.00 0.00 0 -ATOM 380 H 1 1 24.800 24.052 2.776 0.00 0.00 0 -ATOM 381 H 1 1 24.693 22.618 0.198 0.00 0.00 0 -ATOM 382 O 1 1 20.789 18.440 9.443 0.00 0.00 0 -ATOM 383 H 1 1 20.766 17.257 7.881 0.00 0.00 0 -ATOM 384 H 1 1 21.896 17.345 10.385 0.00 0.00 0 -ATOM 385 O 1 1 21.574 17.493 17.838 0.00 0.00 0 -ATOM 386 H 1 1 20.597 18.955 17.218 0.00 0.00 0 -ATOM 387 H 1 1 22.538 16.874 16.251 0.00 0.00 0 -ATOM 388 O 1 1 19.168 14.748 24.131 0.00 0.00 0 -ATOM 389 H 1 1 19.711 16.390 23.712 0.00 0.00 0 -ATOM 390 H 1 1 17.429 14.695 24.403 0.00 0.00 0 -ATOM 391 O 1 1 22.149 20.198 24.977 0.00 0.00 0 -ATOM 392 H 1 1 21.639 20.924 26.486 0.00 0.00 0 -ATOM 393 H 1 1 22.656 21.657 24.411 0.00 0.00 0 -ATOM 394 O 1 1 20.565 20.792 29.600 0.00 0.00 0 -ATOM 395 H 1 1 22.264 20.409 30.214 0.00 0.00 0 -ATOM 396 H 1 1 20.548 22.408 30.597 0.00 0.00 0 -ATOM 397 O 1 1 20.802 26.547 9.615 0.00 0.00 0 -ATOM 398 H 1 1 20.099 27.984 8.338 0.00 0.00 0 -ATOM 399 H 1 1 21.277 27.539 11.325 0.00 0.00 0 -ATOM 400 O 1 1 16.283 23.589 7.779 0.00 0.00 0 -ATOM 401 H 1 1 16.093 21.973 6.712 0.00 0.00 0 -ATOM 402 H 1 1 17.901 22.971 8.154 0.00 0.00 0 -ATOM 403 O 1 1 18.469 29.798 13.568 0.00 0.00 0 -ATOM 404 H 1 1 19.712 31.216 13.506 0.00 0.00 0 -ATOM 405 H 1 1 16.872 30.343 14.396 0.00 0.00 0 -ATOM 406 O 1 1 18.790 21.712 16.060 0.00 0.00 0 -ATOM 407 H 1 1 19.878 23.090 16.485 0.00 0.00 0 -ATOM 408 H 1 1 17.201 22.326 15.819 0.00 0.00 0 -ATOM 409 O 1 1 21.747 26.084 16.349 0.00 0.00 0 -ATOM 410 H 1 1 20.783 27.021 15.300 0.00 0.00 0 -ATOM 411 H 1 1 22.705 27.328 17.206 0.00 0.00 0 -ATOM 412 O 1 1 20.769 26.211 32.050 0.00 0.00 0 -ATOM 413 H 1 1 21.488 27.404 33.328 0.00 0.00 0 -ATOM 414 H 1 1 18.989 26.710 32.145 0.00 0.00 0 -ATOM 415 O 1 1 19.820 29.181 5.559 0.00 0.00 0 -ATOM 416 H 1 1 20.991 29.509 4.109 0.00 0.00 0 -ATOM 417 H 1 1 19.431 31.018 6.221 0.00 0.00 0 -ATOM 418 O 1 1 19.240 33.867 7.993 0.00 0.00 0 -ATOM 419 H 1 1 19.107 35.039 6.604 0.00 0.00 0 -ATOM 420 H 1 1 20.697 33.671 9.063 0.00 0.00 0 -ATOM 421 O 1 1 22.511 34.976 15.793 0.00 0.00 0 -ATOM 422 H 1 1 23.716 36.163 16.603 0.00 0.00 0 -ATOM 423 H 1 1 21.699 36.150 14.467 0.00 0.00 0 -ATOM 424 O 1 1 22.622 30.284 19.069 0.00 0.00 0 -ATOM 425 H 1 1 22.049 31.351 17.725 0.00 0.00 0 -ATOM 426 H 1 1 24.411 30.773 19.576 0.00 0.00 0 -ATOM 427 O 1 1 18.639 33.611 28.369 0.00 0.00 0 -ATOM 428 H 1 1 18.226 32.159 29.103 0.00 0.00 0 -ATOM 429 H 1 1 19.906 33.008 27.158 0.00 0.00 0 -ATOM 430 O 1 1 22.520 1.325 31.926 0.00 0.00 0 -ATOM 431 H 1 1 22.803 2.668 30.796 0.00 0.00 0 -ATOM 432 H 1 1 21.045 0.425 31.122 0.00 0.00 0 -ATOM 433 O 1 1 21.754 3.789 1.159 0.00 0.00 0 -ATOM 434 H 1 1 22.085 2.785 -0.180 0.00 0.00 0 -ATOM 435 H 1 1 20.850 5.175 0.610 0.00 0.00 0 -ATOM 436 O 1 1 28.457 5.539 12.133 0.00 0.00 0 -ATOM 437 H 1 1 29.489 4.390 11.182 0.00 0.00 0 -ATOM 438 H 1 1 29.161 7.131 12.587 0.00 0.00 0 -ATOM 439 O 1 1 22.495 5.966 17.324 0.00 0.00 0 -ATOM 440 H 1 1 24.377 5.379 17.393 0.00 0.00 0 -ATOM 441 H 1 1 21.906 5.491 18.857 0.00 0.00 0 -ATOM 442 O 1 1 28.128 3.304 22.287 0.00 0.00 0 -ATOM 443 H 1 1 28.123 2.999 20.491 0.00 0.00 0 -ATOM 444 H 1 1 26.533 3.355 22.876 0.00 0.00 0 -ATOM 445 O 1 1 28.378 10.455 27.266 0.00 0.00 0 -ATOM 446 H 1 1 30.019 10.292 28.051 0.00 0.00 0 -ATOM 447 H 1 1 28.635 10.039 25.463 0.00 0.00 0 -ATOM 448 O 1 1 27.031 8.353 34.806 0.00 0.00 0 -ATOM 449 H 1 1 26.116 9.984 34.571 0.00 0.00 0 -ATOM 450 H 1 1 28.685 8.951 34.739 0.00 0.00 0 -ATOM 451 O 1 1 24.951 8.160 4.454 0.00 0.00 0 -ATOM 452 H 1 1 25.930 9.616 5.160 0.00 0.00 0 -ATOM 453 H 1 1 25.947 7.994 2.724 0.00 0.00 0 -ATOM 454 O 1 1 26.937 12.436 6.869 0.00 0.00 0 -ATOM 455 H 1 1 25.492 13.284 6.708 0.00 0.00 0 -ATOM 456 H 1 1 27.689 13.332 8.266 0.00 0.00 0 -ATOM 457 O 1 1 23.365 11.214 16.933 0.00 0.00 0 -ATOM 458 H 1 1 22.247 9.744 16.789 0.00 0.00 0 -ATOM 459 H 1 1 23.264 12.035 18.539 0.00 0.00 0 -ATOM 460 O 1 1 28.321 8.759 22.158 0.00 0.00 0 -ATOM 461 H 1 1 27.662 6.895 22.482 0.00 0.00 0 -ATOM 462 H 1 1 26.971 9.710 21.902 0.00 0.00 0 -ATOM 463 O 1 1 27.071 6.109 29.555 0.00 0.00 0 -ATOM 464 H 1 1 27.591 7.663 28.857 0.00 0.00 0 -ATOM 465 H 1 1 27.304 6.320 31.261 0.00 0.00 0 -ATOM 466 O 1 1 22.474 11.704 34.640 0.00 0.00 0 -ATOM 467 H 1 1 22.752 13.304 35.584 0.00 0.00 0 -ATOM 468 H 1 1 22.840 12.090 33.030 0.00 0.00 0 -ATOM 469 O 1 1 21.656 14.971 5.615 0.00 0.00 0 -ATOM 470 H 1 1 21.690 15.860 3.977 0.00 0.00 0 -ATOM 471 H 1 1 19.964 14.225 5.774 0.00 0.00 0 -ATOM 472 O 1 1 28.539 21.492 9.820 0.00 0.00 0 -ATOM 473 H 1 1 27.288 22.181 8.688 0.00 0.00 0 -ATOM 474 H 1 1 28.065 22.420 11.602 0.00 0.00 0 -ATOM 475 O 1 1 28.364 16.020 11.109 0.00 0.00 0 -ATOM 476 H 1 1 30.033 16.649 12.089 0.00 0.00 0 -ATOM 477 H 1 1 28.456 17.440 10.082 0.00 0.00 0 -ATOM 478 O 1 1 0.054 13.686 18.103 0.00 0.00 0 -ATOM 479 H 1 1 -1.714 12.928 18.841 0.00 0.00 0 -ATOM 480 H 1 1 1.008 12.429 17.383 0.00 0.00 0 -ATOM 481 O 1 1 24.636 12.894 29.957 0.00 0.00 0 -ATOM 482 H 1 1 25.906 13.914 31.183 0.00 0.00 0 -ATOM 483 H 1 1 25.641 11.609 29.162 0.00 0.00 0 -ATOM 484 O 1 1 21.548 17.250 0.749 0.00 0.00 0 -ATOM 485 H 1 1 21.843 19.026 0.905 0.00 0.00 0 -ATOM 486 H 1 1 20.385 16.716 -0.697 0.00 0.00 0 -ATOM 487 O 1 1 26.095 27.274 4.520 0.00 0.00 0 -ATOM 488 H 1 1 27.889 26.458 4.505 0.00 0.00 0 -ATOM 489 H 1 1 25.648 26.970 6.165 0.00 0.00 0 -ATOM 490 O 1 1 23.610 22.515 8.008 0.00 0.00 0 -ATOM 491 H 1 1 22.653 21.187 8.739 0.00 0.00 0 -ATOM 492 H 1 1 22.286 24.095 8.444 0.00 0.00 0 -ATOM 493 O 1 1 27.355 18.929 18.180 0.00 0.00 0 -ATOM 494 H 1 1 27.200 20.349 17.155 0.00 0.00 0 -ATOM 495 H 1 1 25.579 18.322 18.770 0.00 0.00 0 -ATOM 496 O 1 1 26.765 23.633 14.444 0.00 0.00 0 -ATOM 497 H 1 1 27.441 25.298 13.651 0.00 0.00 0 -ATOM 498 H 1 1 25.086 24.256 14.749 0.00 0.00 0 -ATOM 499 O 1 1 31.478 20.769 20.986 0.00 0.00 0 -ATOM 500 H 1 1 30.440 22.509 21.135 0.00 0.00 0 -ATOM 501 H 1 1 30.567 19.656 20.043 0.00 0.00 0 -ATOM 502 O 1 1 24.812 20.412 32.668 0.00 0.00 0 -ATOM 503 H 1 1 26.242 21.478 31.874 0.00 0.00 0 -ATOM 504 H 1 1 25.787 19.023 33.158 0.00 0.00 0 -ATOM 505 O 1 1 22.105 29.076 0.928 0.00 0.00 0 -ATOM 506 H 1 1 23.296 27.923 1.739 0.00 0.00 0 -ATOM 507 H 1 1 22.623 30.994 0.882 0.00 0.00 0 -ATOM 508 O 1 1 29.572 31.256 8.626 0.00 0.00 0 -ATOM 509 H 1 1 30.795 30.203 7.736 0.00 0.00 0 -ATOM 510 H 1 1 28.277 31.519 7.260 0.00 0.00 0 -ATOM 511 O 1 1 31.817 34.843 18.283 0.00 0.00 0 -ATOM 512 H 1 1 32.438 34.389 16.474 0.00 0.00 0 -ATOM 513 H 1 1 32.743 36.422 18.341 0.00 0.00 0 -ATOM 514 O 1 1 27.915 25.601 19.033 0.00 0.00 0 -ATOM 515 H 1 1 29.358 26.561 19.190 0.00 0.00 0 -ATOM 516 H 1 1 28.148 24.429 17.530 0.00 0.00 0 -ATOM 517 O 1 1 24.548 24.654 24.025 0.00 0.00 0 -ATOM 518 H 1 1 25.528 25.635 22.824 0.00 0.00 0 -ATOM 519 H 1 1 25.300 25.200 25.645 0.00 0.00 0 -ATOM 520 O 1 1 28.540 22.922 30.370 0.00 0.00 0 -ATOM 521 H 1 1 27.414 24.096 29.781 0.00 0.00 0 -ATOM 522 H 1 1 29.674 23.914 31.873 0.00 0.00 0 -ATOM 523 O 1 1 24.969 33.623 1.014 0.00 0.00 0 -ATOM 524 H 1 1 26.521 33.058 1.518 0.00 0.00 0 -ATOM 525 H 1 1 24.990 34.322 -0.683 0.00 0.00 0 -ATOM 526 O 1 1 23.075 32.171 11.324 0.00 0.00 0 -ATOM 527 H 1 1 23.316 32.775 13.097 0.00 0.00 0 -ATOM 528 H 1 1 24.460 33.203 10.662 0.00 0.00 0 -ATOM 529 O 1 1 27.497 2.736 17.224 0.00 0.00 0 -ATOM 530 H 1 1 28.397 3.415 15.715 0.00 0.00 0 -ATOM 531 H 1 1 28.234 1.233 17.412 0.00 0.00 0 -ATOM 532 O 1 1 26.369 33.060 22.077 0.00 0.00 0 -ATOM 533 H 1 1 26.170 34.746 22.264 0.00 0.00 0 -ATOM 534 H 1 1 27.592 32.404 23.321 0.00 0.00 0 -ATOM 535 O 1 1 30.221 30.950 25.843 0.00 0.00 0 -ATOM 536 H 1 1 30.305 29.038 26.208 0.00 0.00 0 -ATOM 537 H 1 1 30.363 31.979 27.414 0.00 0.00 0 -ATOM 538 O 1 1 24.973 26.732 28.607 0.00 0.00 0 -ATOM 539 H 1 1 25.385 28.369 29.248 0.00 0.00 0 -ATOM 540 H 1 1 23.330 26.597 29.234 0.00 0.00 0 -ATOM 541 O 1 1 32.165 4.857 2.258 0.00 0.00 0 -ATOM 542 H 1 1 32.417 6.195 1.157 0.00 0.00 0 -ATOM 543 H 1 1 32.615 3.727 1.112 0.00 0.00 0 -ATOM 544 O 1 1 28.067 3.533 5.217 0.00 0.00 0 -ATOM 545 H 1 1 26.960 4.447 4.158 0.00 0.00 0 -ATOM 546 H 1 1 29.875 3.863 4.448 0.00 0.00 0 -ATOM 547 O 1 1 33.279 2.782 13.028 0.00 0.00 0 -ATOM 548 H 1 1 33.708 3.955 11.817 0.00 0.00 0 -ATOM 549 H 1 1 33.656 3.545 14.631 0.00 0.00 0 -ATOM 550 O 1 1 34.278 4.944 17.492 0.00 0.00 0 -ATOM 551 H 1 1 33.438 6.563 17.876 0.00 0.00 0 -ATOM 552 H 1 1 34.906 4.452 18.995 0.00 0.00 0 -ATOM 553 O 1 1 32.363 1.908 26.092 0.00 0.00 0 -ATOM 554 H 1 1 31.941 1.683 24.268 0.00 0.00 0 -ATOM 555 H 1 1 33.850 1.390 26.904 0.00 0.00 0 -ATOM 556 O 1 1 27.982 0.418 28.241 0.00 0.00 0 -ATOM 557 H 1 1 27.516 2.080 28.309 0.00 0.00 0 -ATOM 558 H 1 1 29.593 0.176 27.299 0.00 0.00 0 -ATOM 559 O 1 1 28.845 14.672 2.724 0.00 0.00 0 -ATOM 560 H 1 1 27.963 13.930 4.139 0.00 0.00 0 -ATOM 561 H 1 1 30.386 15.714 3.379 0.00 0.00 0 -ATOM 562 O 1 1 28.083 10.618 14.298 0.00 0.00 0 -ATOM 563 H 1 1 28.623 12.160 13.293 0.00 0.00 0 -ATOM 564 H 1 1 26.486 11.015 15.379 0.00 0.00 0 -ATOM 565 O 1 1 33.867 10.545 13.306 0.00 0.00 0 -ATOM 566 H 1 1 35.165 9.612 13.810 0.00 0.00 0 -ATOM 567 H 1 1 33.615 10.270 11.513 0.00 0.00 0 -ATOM 568 O 1 1 31.790 9.696 18.223 0.00 0.00 0 -ATOM 569 H 1 1 30.484 9.334 19.421 0.00 0.00 0 -ATOM 570 H 1 1 30.834 10.096 16.929 0.00 0.00 0 -ATOM 571 O 1 1 30.141 15.006 21.532 0.00 0.00 0 -ATOM 572 H 1 1 28.565 15.594 22.099 0.00 0.00 0 -ATOM 573 H 1 1 30.942 14.253 23.077 0.00 0.00 0 -ATOM 574 O 1 1 32.798 10.732 30.680 0.00 0.00 0 -ATOM 575 H 1 1 34.073 9.528 30.799 0.00 0.00 0 -ATOM 576 H 1 1 32.991 11.512 28.983 0.00 0.00 0 -ATOM 577 O 1 1 33.652 16.265 5.086 0.00 0.00 0 -ATOM 578 H 1 1 35.399 16.239 4.730 0.00 0.00 0 -ATOM 579 H 1 1 33.503 17.939 5.631 0.00 0.00 0 -ATOM 580 O 1 1 31.947 10.799 7.943 0.00 0.00 0 -ATOM 581 H 1 1 29.894 10.549 7.619 0.00 0.00 0 -ATOM 582 H 1 1 32.271 12.414 7.075 0.00 0.00 0 -ATOM 583 O 1 1 0.329 15.516 11.746 0.00 0.00 0 -ATOM 584 H 1 1 -0.446 14.249 12.939 0.00 0.00 0 -ATOM 585 H 1 1 -0.685 17.018 11.935 0.00 0.00 0 -ATOM 586 O 1 1 4.262 19.165 14.308 0.00 0.00 0 -ATOM 587 H 1 1 3.579 17.691 14.920 0.00 0.00 0 -ATOM 588 H 1 1 5.723 19.183 15.204 0.00 0.00 0 -ATOM 589 O 1 1 32.995 13.546 25.948 0.00 0.00 0 -ATOM 590 H 1 1 32.167 15.060 26.787 0.00 0.00 0 -ATOM 591 H 1 1 34.425 13.800 25.007 0.00 0.00 0 -ATOM 592 O 1 1 1.773 13.524 34.037 0.00 0.00 0 -ATOM 593 H 1 1 0.227 14.409 33.446 0.00 0.00 0 -ATOM 594 H 1 1 2.167 14.670 35.511 0.00 0.00 0 -ATOM 595 O 1 1 33.029 20.529 7.247 0.00 0.00 0 -ATOM 596 H 1 1 34.388 21.414 8.003 0.00 0.00 0 -ATOM 597 H 1 1 31.451 20.831 8.182 0.00 0.00 0 -ATOM 598 O 1 1 2.037 24.250 10.251 0.00 0.00 0 -ATOM 599 H 1 1 3.743 25.008 9.876 0.00 0.00 0 -ATOM 600 H 1 1 1.894 25.043 11.903 0.00 0.00 0 -ATOM 601 O 1 1 32.753 19.259 13.976 0.00 0.00 0 -ATOM 602 H 1 1 32.792 20.886 13.792 0.00 0.00 0 -ATOM 603 H 1 1 34.334 18.799 14.976 0.00 0.00 0 -ATOM 604 O 1 1 0.396 18.673 18.699 0.00 0.00 0 -ATOM 605 H 1 1 -1.211 18.950 19.127 0.00 0.00 0 -ATOM 606 H 1 1 0.469 16.977 18.436 0.00 0.00 0 -ATOM 607 O 1 1 30.855 18.370 27.959 0.00 0.00 0 -ATOM 608 H 1 1 29.759 19.681 28.690 0.00 0.00 0 -ATOM 609 H 1 1 32.103 19.477 26.763 0.00 0.00 0 -ATOM 610 O 1 1 27.723 15.992 33.091 0.00 0.00 0 -ATOM 611 H 1 1 29.390 16.423 32.192 0.00 0.00 0 -ATOM 612 H 1 1 27.801 15.859 34.804 0.00 0.00 0 -ATOM 613 O 1 1 31.068 27.895 3.348 0.00 0.00 0 -ATOM 614 H 1 1 32.517 27.825 4.610 0.00 0.00 0 -ATOM 615 H 1 1 31.529 29.459 2.324 0.00 0.00 0 -ATOM 616 O 1 1 35.039 28.008 6.663 0.00 0.00 0 -ATOM 617 H 1 1 35.966 26.934 7.683 0.00 0.00 0 -ATOM 618 H 1 1 36.055 28.336 5.336 0.00 0.00 0 -ATOM 619 O 1 1 29.356 28.196 13.025 0.00 0.00 0 -ATOM 620 H 1 1 29.210 29.335 14.589 0.00 0.00 0 -ATOM 621 H 1 1 28.874 29.629 11.867 0.00 0.00 0 -ATOM 622 O 1 1 32.386 28.434 18.961 0.00 0.00 0 -ATOM 623 H 1 1 33.368 28.574 20.411 0.00 0.00 0 -ATOM 624 H 1 1 33.410 27.406 17.949 0.00 0.00 0 -ATOM 625 O 1 1 30.898 25.390 25.799 0.00 0.00 0 -ATOM 626 H 1 1 32.369 25.913 24.580 0.00 0.00 0 -ATOM 627 H 1 1 31.317 24.075 27.029 0.00 0.00 0 -ATOM 628 O 1 1 32.259 25.611 33.104 0.00 0.00 0 -ATOM 629 H 1 1 32.238 25.736 34.806 0.00 0.00 0 -ATOM 630 H 1 1 33.920 25.042 32.775 0.00 0.00 0 -ATOM 631 O 1 1 30.290 32.645 1.341 0.00 0.00 0 -ATOM 632 H 1 1 29.949 32.793 -0.430 0.00 0.00 0 -ATOM 633 H 1 1 31.762 33.340 1.847 0.00 0.00 0 -ATOM 634 O 1 1 25.536 34.235 6.469 0.00 0.00 0 -ATOM 635 H 1 1 25.716 36.059 6.651 0.00 0.00 0 -ATOM 636 H 1 1 25.283 33.866 4.895 0.00 0.00 0 -ATOM 637 O 1 1 31.674 33.161 13.106 0.00 0.00 0 -ATOM 638 H 1 1 31.793 34.863 13.281 0.00 0.00 0 -ATOM 639 H 1 1 30.425 32.928 11.783 0.00 0.00 0 -ATOM 640 O 1 1 33.844 32.668 22.296 0.00 0.00 0 -ATOM 641 H 1 1 32.750 32.234 23.524 0.00 0.00 0 -ATOM 642 H 1 1 32.917 32.875 20.736 0.00 0.00 0 -ATOM 643 O 1 1 31.603 30.542 30.805 0.00 0.00 0 -ATOM 644 H 1 1 33.451 30.804 30.468 0.00 0.00 0 -ATOM 645 H 1 1 31.575 28.816 31.756 0.00 0.00 0 -ATOM 646 O 1 1 26.295 31.235 30.599 0.00 0.00 0 -ATOM 647 H 1 1 27.834 30.515 30.607 0.00 0.00 0 -ATOM 648 H 1 1 26.362 32.920 29.856 0.00 0.00 0 -END diff --git a/tools/i-pi/examples/lammps/h2o-piglet.8/data.water b/tools/i-pi/examples/lammps/h2o-piglet.8/data.water deleted file mode 100644 index 13c75e9933..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.8/data.water +++ /dev/null @@ -1,1331 +0,0 @@ -LAMMPS Description - - 648 atoms - 432 bonds - 216 angles - - 2 atom types - 1 bond types - 1 angle types - - 0 35.233 xlo xhi - 0 35.233 ylo yhi - 0 35.233 zlo zhi - -Masses - - 1 15.9994 - 2 1.0080 - -Bond Coeffs - - 1 1.78 0.2708585 -0.327738785 0.231328959 - -Angle Coeffs - - 1 0.0700 107.400000 - -Atoms - - 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 - 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 - 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 - 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000 - 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 - 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 - 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 - 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 - 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 - 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 - 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 - 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 - 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 - 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 - 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 - 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001 - 17 6 2 0.5564 2.39200001 2.89799999 34.84600000 - 18 6 2 0.5564 0.81400000 0.53200001 35.83600000 - 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999 - 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000 - 21 7 2 0.5564 30.91999999 11.59399999 1.67700000 - 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000 - 23 8 2 0.5564 0.30500000 10.64300001 2.79300000 - 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000 - 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000 - 26 9 2 0.5564 33.61600000 7.67300000 8.85700000 - 27 9 2 0.5564 35.11500000 5.25999999 7.61800001 - 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999 - 29 10 2 0.5564 31.62400000 6.90800001 23.52100001 - 30 10 2 0.5564 32.54400000 4.99000000 24.98200000 - 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000 - 32 11 2 0.5564 1.85600000 10.17500000 25.57899999 - 33 11 2 0.5564 0.51900000 8.09899999 26.38599999 - 34 12 1 -1.1128 2.05400000 8.66000000 32.51499999 - 35 12 2 0.5564 2.16699999 8.72700000 30.49400000 - 36 12 2 0.5564 2.37400001 10.51300000 33.03799999 - 37 13 1 -1.1128 3.40200000 16.63900001 3.00800000 - 38 13 2 0.5564 4.12700001 15.87200001 4.44600001 - 39 13 2 0.5564 2.90500001 18.33899999 3.15999999 - 40 14 1 -1.1128 4.22200000 15.44400000 8.07200000 - 41 14 2 0.5564 5.21100000 16.75600000 8.29900001 - 42 14 2 0.5564 2.56000000 15.49200001 8.86000000 - 43 15 1 -1.1128 2.83100000 9.24599999 16.48800000 - 44 15 2 0.5564 2.86900001 8.02300001 18.05000000 - 45 15 2 0.5564 3.96000000 8.46700001 15.15400000 - 46 16 1 -1.1128 5.56300000 6.00300000 20.90700000 - 47 16 2 0.5564 4.65300000 4.63800000 21.48000000 - 48 16 2 0.5564 6.40500000 6.20800000 22.52899999 - 49 17 1 -1.1128 2.08700001 13.37000000 22.91299999 - 50 17 2 0.5564 2.83200000 14.80400001 23.42200000 - 51 17 2 0.5564 1.43400000 13.50900000 21.19599999 - 52 18 1 -1.1128 3.36900000 17.88600000 25.10900001 - 53 18 2 0.5564 3.65500000 17.20000000 26.76599999 - 54 18 2 0.5564 4.77200001 18.97699999 24.49999999 - 55 19 1 -1.1128 34.76400000 20.80300000 0.94800001 - 56 19 2 0.5564 35.20999999 21.26700001 2.81599999 - 57 19 2 0.5564 35.96200001 21.72599999 0.13099999 - 58 20 1 -1.1128 2.83600000 24.17799999 15.22900000 - 59 20 2 0.5564 2.79500000 22.34599999 14.87600001 - 60 20 2 0.5564 2.41399999 24.11500000 17.13000001 - 61 21 1 -1.1128 33.00000000 24.48100000 15.23000000 - 62 21 2 0.5564 34.63999999 24.80400001 15.01299999 - 63 21 2 0.5564 32.40100000 25.76400000 14.29500001 - 64 22 1 -1.1128 0.40399999 26.77900001 23.39999999 - 65 22 2 0.5564 1.35300001 27.24800000 24.98700001 - 66 22 2 0.5564 1.54600001 28.05000000 22.31700001 - 67 23 1 -1.1128 34.22200000 21.38000000 25.41799999 - 68 23 2 0.5564 35.66899999 20.15100000 25.31700001 - 69 23 2 0.5564 32.96000000 21.18000000 23.99200000 - 70 24 1 -1.1128 33.25900000 17.43800000 32.48000000 - 71 24 2 0.5564 33.31399999 18.78200000 33.88300001 - 72 24 2 0.5564 32.74300001 18.18100001 30.87100000 - 73 25 1 -1.1128 4.46300000 21.97900000 3.93600000 - 74 25 2 0.5564 5.85600000 23.08400001 3.39999999 - 75 25 2 0.5564 3.98600000 22.18000000 5.60200000 - 76 26 1 -1.1128 6.25800000 25.85100001 8.52000000 - 77 26 2 0.5564 5.76700000 27.69300001 8.47600000 - 78 26 2 0.5564 7.20200001 25.50600000 10.18600000 - 79 27 1 -1.1128 0.60099999 29.73699999 12.74700001 - 80 27 2 0.5564 -0.68500000 30.84200000 12.34999999 - 81 27 2 0.5564 1.33600000 30.71600000 14.03099999 - 82 28 1 -1.1128 7.56300000 28.19100001 24.33300000 - 83 28 2 0.5564 9.20100000 28.82800000 24.68400000 - 84 28 2 0.5564 7.38100001 27.62100000 22.79900000 - 85 29 1 -1.1128 3.65300000 27.10900001 27.77200001 - 86 29 2 0.5564 5.12600000 27.01500000 26.77200001 - 87 29 2 0.5564 3.03099999 28.75600000 27.69800000 - 88 30 1 -1.1128 2.59600001 23.99100001 32.47600000 - 89 30 2 0.5564 2.87900000 24.79099999 30.85899999 - 90 30 2 0.5564 4.00300000 22.91299999 32.70099999 - 91 31 1 -1.1128 3.08300000 31.31700001 3.64399999 - 92 31 2 0.5564 4.13300000 30.58900001 2.53900001 - 93 31 2 0.5564 4.21800000 32.17300001 5.03700001 - 94 32 1 -1.1128 4.66100001 30.55500000 9.36799999 - 95 32 2 0.5564 3.18400001 29.84300000 10.13200000 - 96 32 2 0.5564 4.35800000 32.44800000 9.12600000 - 97 33 1 -1.1128 3.46499999 32.53700000 15.77800000 - 98 33 2 0.5564 5.07200000 31.81899999 15.90300000 - 99 33 2 0.5564 4.05500001 34.25699999 15.28400000 - 100 34 1 -1.1128 4.21500000 29.15299999 20.31700001 - 101 34 2 0.5564 3.65799999 30.17600000 18.84200000 - 102 34 2 0.5564 4.95899999 30.29100000 21.44900001 - 103 35 1 -1.1128 1.12600000 31.33300000 28.76800001 - 104 35 2 0.5564 2.39500000 31.12399999 29.92500000 - 105 35 2 0.5564 0.76800001 33.09199999 28.89799999 - 106 36 1 -1.1128 4.88100000 32.61600000 32.30200000 - 107 36 2 0.5564 6.58800000 32.91100000 31.72500001 - 108 36 2 0.5564 4.48599999 34.03700001 33.24900001 - 109 37 1 -1.1128 8.96200001 5.55600000 0.15100000 - 110 37 2 0.5564 9.65200000 6.99100001 0.85899999 - 111 37 2 0.5564 9.17300001 4.47700000 1.64500000 - 112 38 1 -1.1128 1.83300001 3.51799999 5.67900001 - 113 38 2 0.5564 2.88900000 2.73100000 6.78800000 - 114 38 2 0.5564 2.78900000 4.18700000 4.14700000 - 115 39 1 -1.1128 10.51000001 34.72599999 13.07300001 - 116 39 2 0.5564 11.91999999 34.11800000 11.91900001 - 117 39 2 0.5564 11.29500001 34.96800000 14.74100000 - 118 40 1 -1.1128 7.21200000 0.04199999 22.45399999 - 119 40 2 0.5564 6.92400000 0.47000000 24.17200000 - 120 40 2 0.5564 8.31900000 1.22799999 21.65300000 - 121 41 1 -1.1128 6.36500000 2.01000000 27.54400000 - 122 41 2 0.5564 5.95400000 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-pair_coeff * * 0 0 -pair_coeff 1 1 0.000295147 5.96946 - -neighbor 2.0 bin - -timestep 0.00025 - -#velocity all create 298.0 2345187 - -#thermo_style multi -#thermo 1 - -#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 -#fix 1 all nve -fix 1 all ipi piglet_8 32342 unix - -#dump 1 all xyz 25 dump.xyz - -run 100000000 - diff --git a/tools/i-pi/examples/lammps/h2o-piglet.8/input.xml b/tools/i-pi/examples/lammps/h2o-piglet.8/input.xml deleted file mode 100644 index ace4d7f3de..0000000000 --- a/tools/i-pi/examples/lammps/h2o-piglet.8/input.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - water_298K.pdb - 298 - - - [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] - positions - - 500000 - 32342 - - -
piglet_8
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21.718 0.00 0.00 0 -ATOM 11 H 1 1 0.757 0.261 21.820 0.00 0.00 0 -ATOM 12 H 1 1 0.213 3.013 23.047 0.00 0.00 0 -ATOM 13 O 1 1 1.200 1.337 29.006 0.00 0.00 0 -ATOM 14 H 1 1 0.818 1.884 30.732 0.00 0.00 0 -ATOM 15 H 1 1 2.883 1.825 29.011 0.00 0.00 0 -ATOM 16 O 1 1 1.331 1.386 34.306 0.00 0.00 0 -ATOM 17 H 1 1 2.392 2.898 34.846 0.00 0.00 0 -ATOM 18 H 1 1 0.814 0.532 35.836 0.00 0.00 0 -ATOM 19 O 1 1 31.451 10.201 0.726 0.00 0.00 0 -ATOM 20 H 1 1 32.282 10.877 -0.750 0.00 0.00 0 -ATOM 21 H 1 1 30.920 11.594 1.677 0.00 0.00 0 -ATOM 22 O 1 1 0.836 10.808 4.298 0.00 0.00 0 -ATOM 23 H 1 1 0.305 10.643 2.793 0.00 0.00 0 -ATOM 24 H 1 1 -0.356 10.334 5.524 0.00 0.00 0 -ATOM 25 O 1 1 34.381 5.979 9.194 0.00 0.00 0 -ATOM 26 H 1 1 33.616 7.673 8.857 0.00 0.00 0 -ATOM 27 H 1 1 35.115 5.260 7.618 0.00 0.00 0 -ATOM 28 O 1 1 33.212 6.480 24.278 0.00 0.00 0 -ATOM 29 H 1 1 31.624 6.908 23.521 0.00 0.00 0 -ATOM 30 H 1 1 32.544 4.990 24.982 0.00 0.00 0 -ATOM 31 O 1 1 1.992 9.002 26.863 0.00 0.00 0 -ATOM 32 H 1 1 1.856 10.175 25.579 0.00 0.00 0 -ATOM 33 H 1 1 0.519 8.099 26.386 0.00 0.00 0 -ATOM 34 O 1 1 2.054 8.660 32.515 0.00 0.00 0 -ATOM 35 H 1 1 2.167 8.727 30.494 0.00 0.00 0 -ATOM 36 H 1 1 2.374 10.513 33.038 0.00 0.00 0 -ATOM 37 O 1 1 3.402 16.639 3.008 0.00 0.00 0 -ATOM 38 H 1 1 4.127 15.872 4.446 0.00 0.00 0 -ATOM 39 H 1 1 2.905 18.339 3.160 0.00 0.00 0 -ATOM 40 O 1 1 4.222 15.444 8.072 0.00 0.00 0 -ATOM 41 H 1 1 5.211 16.756 8.299 0.00 0.00 0 -ATOM 42 H 1 1 2.560 15.492 8.860 0.00 0.00 0 -ATOM 43 O 1 1 2.831 9.246 16.488 0.00 0.00 0 -ATOM 44 H 1 1 2.869 8.023 18.050 0.00 0.00 0 -ATOM 45 H 1 1 3.960 8.467 15.154 0.00 0.00 0 -ATOM 46 O 1 1 5.563 6.003 20.907 0.00 0.00 0 -ATOM 47 H 1 1 4.653 4.638 21.480 0.00 0.00 0 -ATOM 48 H 1 1 6.405 6.208 22.529 0.00 0.00 0 -ATOM 49 O 1 1 2.087 13.370 22.913 0.00 0.00 0 -ATOM 50 H 1 1 2.832 14.804 23.422 0.00 0.00 0 -ATOM 51 H 1 1 1.434 13.509 21.196 0.00 0.00 0 -ATOM 52 O 1 1 3.369 17.886 25.109 0.00 0.00 0 -ATOM 53 H 1 1 3.655 17.200 26.766 0.00 0.00 0 -ATOM 54 H 1 1 4.772 18.977 24.500 0.00 0.00 0 -ATOM 55 O 1 1 34.764 20.803 0.948 0.00 0.00 0 -ATOM 56 H 1 1 35.210 21.267 2.816 0.00 0.00 0 -ATOM 57 H 1 1 35.962 21.726 0.131 0.00 0.00 0 -ATOM 58 O 1 1 2.836 24.178 15.229 0.00 0.00 0 -ATOM 59 H 1 1 2.795 22.346 14.876 0.00 0.00 0 -ATOM 60 H 1 1 2.414 24.115 17.130 0.00 0.00 0 -ATOM 61 O 1 1 33.000 24.481 15.230 0.00 0.00 0 -ATOM 62 H 1 1 34.640 24.804 15.013 0.00 0.00 0 -ATOM 63 H 1 1 32.401 25.764 14.295 0.00 0.00 0 -ATOM 64 O 1 1 0.404 26.779 23.400 0.00 0.00 0 -ATOM 65 H 1 1 1.353 27.248 24.987 0.00 0.00 0 -ATOM 66 H 1 1 1.546 28.050 22.317 0.00 0.00 0 -ATOM 67 O 1 1 34.222 21.380 25.418 0.00 0.00 0 -ATOM 68 H 1 1 35.669 20.151 25.317 0.00 0.00 0 -ATOM 69 H 1 1 32.960 21.180 23.992 0.00 0.00 0 -ATOM 70 O 1 1 33.259 17.438 32.480 0.00 0.00 0 -ATOM 71 H 1 1 33.314 18.782 33.883 0.00 0.00 0 -ATOM 72 H 1 1 32.743 18.181 30.871 0.00 0.00 0 -ATOM 73 O 1 1 4.463 21.979 3.936 0.00 0.00 0 -ATOM 74 H 1 1 5.856 23.084 3.400 0.00 0.00 0 -ATOM 75 H 1 1 3.986 22.180 5.602 0.00 0.00 0 -ATOM 76 O 1 1 6.258 25.851 8.520 0.00 0.00 0 -ATOM 77 H 1 1 5.767 27.693 8.476 0.00 0.00 0 -ATOM 78 H 1 1 7.202 25.506 10.186 0.00 0.00 0 -ATOM 79 O 1 1 0.601 29.737 12.747 0.00 0.00 0 -ATOM 80 H 1 1 -0.685 30.842 12.350 0.00 0.00 0 -ATOM 81 H 1 1 1.336 30.716 14.031 0.00 0.00 0 -ATOM 82 O 1 1 7.563 28.191 24.333 0.00 0.00 0 -ATOM 83 H 1 1 9.201 28.828 24.684 0.00 0.00 0 -ATOM 84 H 1 1 7.381 27.621 22.799 0.00 0.00 0 -ATOM 85 O 1 1 3.653 27.109 27.772 0.00 0.00 0 -ATOM 86 H 1 1 5.126 27.015 26.772 0.00 0.00 0 -ATOM 87 H 1 1 3.031 28.756 27.698 0.00 0.00 0 -ATOM 88 O 1 1 2.596 23.991 32.476 0.00 0.00 0 -ATOM 89 H 1 1 2.879 24.791 30.859 0.00 0.00 0 -ATOM 90 H 1 1 4.003 22.913 32.701 0.00 0.00 0 -ATOM 91 O 1 1 3.083 31.317 3.644 0.00 0.00 0 -ATOM 92 H 1 1 4.133 30.589 2.539 0.00 0.00 0 -ATOM 93 H 1 1 4.218 32.173 5.037 0.00 0.00 0 -ATOM 94 O 1 1 4.661 30.555 9.368 0.00 0.00 0 -ATOM 95 H 1 1 3.184 29.843 10.132 0.00 0.00 0 -ATOM 96 H 1 1 4.358 32.448 9.126 0.00 0.00 0 -ATOM 97 O 1 1 3.465 32.537 15.778 0.00 0.00 0 -ATOM 98 H 1 1 5.072 31.819 15.903 0.00 0.00 0 -ATOM 99 H 1 1 4.055 34.257 15.284 0.00 0.00 0 -ATOM 100 O 1 1 4.215 29.153 20.317 0.00 0.00 0 -ATOM 101 H 1 1 3.658 30.176 18.842 0.00 0.00 0 -ATOM 102 H 1 1 4.959 30.291 21.449 0.00 0.00 0 -ATOM 103 O 1 1 1.126 31.333 28.768 0.00 0.00 0 -ATOM 104 H 1 1 2.395 31.124 29.925 0.00 0.00 0 -ATOM 105 H 1 1 0.768 33.092 28.898 0.00 0.00 0 -ATOM 106 O 1 1 4.881 32.616 32.302 0.00 0.00 0 -ATOM 107 H 1 1 6.588 32.911 31.725 0.00 0.00 0 -ATOM 108 H 1 1 4.486 34.037 33.249 0.00 0.00 0 -ATOM 109 O 1 1 8.962 5.556 0.151 0.00 0.00 0 -ATOM 110 H 1 1 9.652 6.991 0.859 0.00 0.00 0 -ATOM 111 H 1 1 9.173 4.477 1.645 0.00 0.00 0 -ATOM 112 O 1 1 1.833 3.518 5.679 0.00 0.00 0 -ATOM 113 H 1 1 2.889 2.731 6.788 0.00 0.00 0 -ATOM 114 H 1 1 2.789 4.187 4.147 0.00 0.00 0 -ATOM 115 O 1 1 10.510 34.726 13.073 0.00 0.00 0 -ATOM 116 H 1 1 11.920 34.118 11.919 0.00 0.00 0 -ATOM 117 H 1 1 11.295 34.968 14.741 0.00 0.00 0 -ATOM 118 O 1 1 7.212 0.042 22.454 0.00 0.00 0 -ATOM 119 H 1 1 6.924 0.470 24.172 0.00 0.00 0 -ATOM 120 H 1 1 8.319 1.228 21.653 0.00 0.00 0 -ATOM 121 O 1 1 6.365 2.010 27.544 0.00 0.00 0 -ATOM 122 H 1 1 5.954 3.585 26.852 0.00 0.00 0 -ATOM 123 H 1 1 7.758 2.549 28.696 0.00 0.00 0 -ATOM 124 O 1 1 10.833 3.140 30.787 0.00 0.00 0 -ATOM 125 H 1 1 12.697 2.975 30.867 0.00 0.00 0 -ATOM 126 H 1 1 10.389 3.700 32.404 0.00 0.00 0 -ATOM 127 O 1 1 8.684 9.342 3.912 0.00 0.00 0 -ATOM 128 H 1 1 6.985 9.256 4.773 0.00 0.00 0 -ATOM 129 H 1 1 8.684 10.809 3.011 0.00 0.00 0 -ATOM 130 O 1 1 4.873 9.919 7.707 0.00 0.00 0 -ATOM 131 H 1 1 3.698 9.771 6.194 0.00 0.00 0 -ATOM 132 H 1 1 5.047 11.961 7.624 0.00 0.00 0 -ATOM 133 O 1 1 10.031 5.018 9.699 0.00 0.00 0 -ATOM 134 H 1 1 9.675 3.382 10.340 0.00 0.00 0 -ATOM 135 H 1 1 9.132 5.987 10.825 0.00 0.00 0 -ATOM 136 O 1 1 11.246 3.918 21.929 0.00 0.00 0 -ATOM 137 H 1 1 12.614 2.770 22.341 0.00 0.00 0 -ATOM 138 H 1 1 12.073 5.686 21.497 0.00 0.00 0 -ATOM 139 O 1 1 6.825 7.164 25.708 0.00 0.00 0 -ATOM 140 H 1 1 8.036 8.374 25.980 0.00 0.00 0 -ATOM 141 H 1 1 5.206 7.900 25.891 0.00 0.00 0 -ATOM 142 O 1 1 10.171 12.811 0.295 0.00 0.00 0 -ATOM 143 H 1 1 10.033 12.818 -1.609 0.00 0.00 0 -ATOM 144 H 1 1 9.880 14.492 0.480 0.00 0.00 0 -ATOM 145 O 1 1 8.190 17.402 1.253 0.00 0.00 0 -ATOM 146 H 1 1 9.472 18.531 1.253 0.00 0.00 0 -ATOM 147 H 1 1 6.351 17.817 1.568 0.00 0.00 0 -ATOM 148 O 1 1 11.233 16.188 8.299 0.00 0.00 0 -ATOM 149 H 1 1 10.291 17.689 8.166 0.00 0.00 0 -ATOM 150 H 1 1 12.768 17.123 8.733 0.00 0.00 0 -ATOM 151 O 1 1 6.386 8.002 12.846 0.00 0.00 0 -ATOM 152 H 1 1 7.701 8.896 13.655 0.00 0.00 0 -ATOM 153 H 1 1 5.591 8.877 11.519 0.00 0.00 0 -ATOM 154 O 1 1 8.184 10.419 18.848 0.00 0.00 0 -ATOM 155 H 1 1 9.498 9.434 19.905 0.00 0.00 0 -ATOM 156 H 1 1 6.882 9.027 18.948 0.00 0.00 0 -ATOM 157 O 1 1 10.806 14.431 21.328 0.00 0.00 0 -ATOM 158 H 1 1 9.177 13.531 20.670 0.00 0.00 0 -ATOM 159 H 1 1 11.344 15.696 20.448 0.00 0.00 0 -ATOM 160 O 1 1 9.237 13.928 30.341 0.00 0.00 0 -ATOM 161 H 1 1 10.779 14.839 30.522 0.00 0.00 0 -ATOM 162 H 1 1 9.965 13.192 28.899 0.00 0.00 0 -ATOM 163 O 1 1 10.918 21.707 1.864 0.00 0.00 0 -ATOM 164 H 1 1 10.280 23.449 2.279 0.00 0.00 0 -ATOM 165 H 1 1 12.708 21.456 1.749 0.00 0.00 0 -ATOM 166 O 1 1 9.353 16.125 13.927 0.00 0.00 0 -ATOM 167 H 1 1 9.938 17.594 14.618 0.00 0.00 0 -ATOM 168 H 1 1 9.518 16.360 12.244 0.00 0.00 0 -ATOM 169 O 1 1 10.371 11.107 14.268 0.00 0.00 0 -ATOM 170 H 1 1 9.644 10.406 15.859 0.00 0.00 0 -ATOM 171 H 1 1 9.434 12.523 14.117 0.00 0.00 0 -ATOM 172 O 1 1 3.351 22.769 20.196 0.00 0.00 0 -ATOM 173 H 1 1 2.055 23.686 21.503 0.00 0.00 0 -ATOM 174 H 1 1 2.452 21.401 19.413 0.00 0.00 0 -ATOM 175 O 1 1 6.836 21.329 23.199 0.00 0.00 0 -ATOM 176 H 1 1 8.249 20.848 22.320 0.00 0.00 0 -ATOM 177 H 1 1 5.668 21.841 21.886 0.00 0.00 0 -ATOM 178 O 1 1 4.604 15.649 30.043 0.00 0.00 0 -ATOM 179 H 1 1 6.453 15.217 30.207 0.00 0.00 0 -ATOM 180 H 1 1 3.822 14.762 31.562 0.00 0.00 0 -ATOM 181 O 1 1 7.125 19.976 9.421 0.00 0.00 0 -ATOM 182 H 1 1 5.918 20.453 10.730 0.00 0.00 0 -ATOM 183 H 1 1 8.099 21.496 9.491 0.00 0.00 0 -ATOM 184 O 1 1 9.063 25.912 13.186 0.00 0.00 0 -ATOM 185 H 1 1 10.350 26.572 12.367 0.00 0.00 0 -ATOM 186 H 1 1 9.680 24.367 13.697 0.00 0.00 0 -ATOM 187 O 1 1 8.022 22.343 17.042 0.00 0.00 0 -ATOM 188 H 1 1 9.144 23.367 18.074 0.00 0.00 0 -ATOM 189 H 1 1 6.562 23.462 16.852 0.00 0.00 0 -ATOM 190 O 1 1 10.762 26.285 19.963 0.00 0.00 0 -ATOM 191 H 1 1 11.036 27.966 20.538 0.00 0.00 0 -ATOM 192 H 1 1 11.078 25.401 21.456 0.00 0.00 0 -ATOM 193 O 1 1 9.158 22.902 28.391 0.00 0.00 0 -ATOM 194 H 1 1 8.219 23.528 27.085 0.00 0.00 0 -ATOM 195 H 1 1 8.089 21.760 29.509 0.00 0.00 0 -ATOM 196 O 1 1 6.219 20.158 31.921 0.00 0.00 0 -ATOM 197 H 1 1 5.635 18.511 31.161 0.00 0.00 0 -ATOM 198 H 1 1 7.530 19.624 33.071 0.00 0.00 0 -ATOM 199 O 1 1 11.191 31.509 2.617 0.00 0.00 0 -ATOM 200 H 1 1 10.460 32.214 4.108 0.00 0.00 0 -ATOM 201 H 1 1 13.176 31.751 2.577 0.00 0.00 0 -ATOM 202 O 1 1 4.748 0.055 8.605 0.00 0.00 0 -ATOM 203 H 1 1 5.380 0.517 10.183 0.00 0.00 0 -ATOM 204 H 1 1 6.050 -0.306 7.480 0.00 0.00 0 -ATOM 205 O 1 1 8.695 30.809 15.731 0.00 0.00 0 -ATOM 206 H 1 1 9.189 32.103 14.495 0.00 0.00 0 -ATOM 207 H 1 1 8.447 29.069 14.868 0.00 0.00 0 -ATOM 208 O 1 1 10.128 31.402 20.766 0.00 0.00 0 -ATOM 209 H 1 1 9.456 30.905 19.155 0.00 0.00 0 -ATOM 210 H 1 1 9.020 32.731 21.415 0.00 0.00 0 -ATOM 211 O 1 1 12.238 30.162 25.837 0.00 0.00 0 -ATOM 212 H 1 1 11.418 30.908 27.110 0.00 0.00 0 -ATOM 213 H 1 1 12.396 31.331 24.678 0.00 0.00 0 -ATOM 214 O 1 1 10.395 32.537 30.624 0.00 0.00 0 -ATOM 215 H 1 1 11.042 34.339 30.751 0.00 0.00 0 -ATOM 216 H 1 1 11.378 31.486 31.538 0.00 0.00 0 -ATOM 217 O 1 1 10.438 3.626 5.087 0.00 0.00 0 -ATOM 218 H 1 1 12.435 4.082 5.136 0.00 0.00 0 -ATOM 219 H 1 1 9.822 4.284 6.681 0.00 0.00 0 -ATOM 220 O 1 1 14.762 3.401 13.776 0.00 0.00 0 -ATOM 221 H 1 1 16.518 3.824 13.376 0.00 0.00 0 -ATOM 222 H 1 1 13.752 4.757 12.964 0.00 0.00 0 -ATOM 223 O 1 1 12.382 1.012 17.643 0.00 0.00 0 -ATOM 224 H 1 1 13.346 1.997 16.444 0.00 0.00 0 -ATOM 225 H 1 1 11.931 2.133 18.998 0.00 0.00 0 -ATOM 226 O 1 1 15.278 1.293 24.559 0.00 0.00 0 -ATOM 227 H 1 1 16.071 0.946 26.365 0.00 0.00 0 -ATOM 228 H 1 1 15.794 0.199 23.499 0.00 0.00 0 -ATOM 229 O 1 1 22.226 31.627 24.712 0.00 0.00 0 -ATOM 230 H 1 1 23.338 32.595 23.876 0.00 0.00 0 -ATOM 231 H 1 1 22.161 30.053 24.132 0.00 0.00 0 -ATOM 232 O 1 1 15.640 1.847 32.717 0.00 0.00 0 -ATOM 233 H 1 1 17.488 2.473 31.874 0.00 0.00 0 -ATOM 234 H 1 1 16.403 0.869 34.267 0.00 0.00 0 -ATOM 235 O 1 1 14.858 10.199 2.754 0.00 0.00 0 -ATOM 236 H 1 1 13.360 10.712 2.282 0.00 0.00 0 -ATOM 237 H 1 1 14.560 9.316 4.559 0.00 0.00 0 -ATOM 238 O 1 1 15.717 8.469 10.739 0.00 0.00 0 -ATOM 239 H 1 1 17.323 9.581 10.875 0.00 0.00 0 -ATOM 240 H 1 1 14.574 9.631 10.221 0.00 0.00 0 -ATOM 241 O 1 1 15.248 10.398 16.525 0.00 0.00 0 -ATOM 242 H 1 1 16.324 9.181 16.149 0.00 0.00 0 -ATOM 243 H 1 1 14.172 10.488 15.098 0.00 0.00 0 -ATOM 244 O 1 1 13.226 8.438 20.801 0.00 0.00 0 -ATOM 245 H 1 1 14.043 8.996 19.295 0.00 0.00 0 -ATOM 246 H 1 1 14.661 7.802 22.093 0.00 0.00 0 -ATOM 247 O 1 1 10.173 10.961 25.875 0.00 0.00 0 -ATOM 248 H 1 1 11.477 10.223 26.940 0.00 0.00 0 -ATOM 249 H 1 1 11.269 10.738 24.343 0.00 0.00 0 -ATOM 250 O 1 1 12.792 7.737 29.173 0.00 0.00 0 -ATOM 251 H 1 1 12.199 6.038 29.475 0.00 0.00 0 -ATOM 252 H 1 1 14.427 7.450 29.617 0.00 0.00 0 -ATOM 253 O 1 1 15.180 19.498 3.578 0.00 0.00 0 -ATOM 254 H 1 1 14.883 17.596 4.080 0.00 0.00 0 -ATOM 255 H 1 1 16.754 19.579 2.626 0.00 0.00 0 -ATOM 256 O 1 1 12.517 11.093 7.701 0.00 0.00 0 -ATOM 257 H 1 1 12.224 12.778 7.555 0.00 0.00 0 -ATOM 258 H 1 1 11.150 10.393 7.057 0.00 0.00 0 -ATOM 259 O 1 1 16.266 16.271 10.758 0.00 0.00 0 -ATOM 260 H 1 1 16.507 15.795 12.768 0.00 0.00 0 -ATOM 261 H 1 1 17.725 16.977 10.292 0.00 0.00 0 -ATOM 262 O 1 1 14.069 18.399 18.897 0.00 0.00 0 -ATOM 263 H 1 1 15.513 17.523 18.155 0.00 0.00 0 -ATOM 264 H 1 1 14.958 18.709 20.673 0.00 0.00 0 -ATOM 265 O 1 1 14.099 15.480 25.510 0.00 0.00 0 -ATOM 266 H 1 1 13.698 16.872 26.938 0.00 0.00 0 -ATOM 267 H 1 1 12.567 15.379 24.444 0.00 0.00 0 -ATOM 268 O 1 1 13.309 17.574 30.292 0.00 0.00 0 -ATOM 269 H 1 1 14.937 16.934 30.810 0.00 0.00 0 -ATOM 270 H 1 1 13.969 19.494 30.012 0.00 0.00 0 -ATOM 271 O 1 1 18.371 23.257 0.925 0.00 0.00 0 -ATOM 272 H 1 1 19.479 23.480 2.321 0.00 0.00 0 -ATOM 273 H 1 1 19.087 24.325 -0.369 0.00 0.00 0 -ATOM 274 O 1 1 12.100 21.730 11.355 0.00 0.00 0 -ATOM 275 H 1 1 13.141 22.287 12.743 0.00 0.00 0 -ATOM 276 H 1 1 13.467 22.236 10.244 0.00 0.00 0 -ATOM 277 O 1 1 12.163 23.290 23.597 0.00 0.00 0 -ATOM 278 H 1 1 11.324 22.736 24.949 0.00 0.00 0 -ATOM 279 H 1 1 13.882 22.872 23.840 0.00 0.00 0 -ATOM 280 O 1 1 20.173 26.761 22.628 0.00 0.00 0 -ATOM 281 H 1 1 20.206 26.532 20.792 0.00 0.00 0 -ATOM 282 H 1 1 21.556 25.742 23.389 0.00 0.00 0 -ATOM 283 O 1 1 16.701 21.165 22.605 0.00 0.00 0 -ATOM 284 H 1 1 18.028 20.686 23.848 0.00 0.00 0 -ATOM 285 H 1 1 17.104 22.866 21.949 0.00 0.00 0 -ATOM 286 O 1 1 11.391 26.461 33.705 0.00 0.00 0 -ATOM 287 H 1 1 9.841 27.192 34.048 0.00 0.00 0 -ATOM 288 H 1 1 11.776 25.540 35.243 0.00 0.00 0 -ATOM 289 O 1 1 9.898 25.989 4.553 0.00 0.00 0 -ATOM 290 H 1 1 8.902 26.131 6.039 0.00 0.00 0 -ATOM 291 H 1 1 10.287 27.806 4.376 0.00 0.00 0 -ATOM 292 O 1 1 14.308 26.960 10.877 0.00 0.00 0 -ATOM 293 H 1 1 15.302 27.405 12.173 0.00 0.00 0 -ATOM 294 H 1 1 15.463 26.151 9.633 0.00 0.00 0 -ATOM 295 O 1 1 13.433 22.960 16.904 0.00 0.00 0 -ATOM 296 H 1 1 13.409 24.131 18.132 0.00 0.00 0 -ATOM 297 H 1 1 13.624 21.191 17.520 0.00 0.00 0 -ATOM 298 O 1 1 16.409 26.768 26.875 0.00 0.00 0 -ATOM 299 H 1 1 17.590 26.987 25.431 0.00 0.00 0 -ATOM 300 H 1 1 14.751 27.703 26.230 0.00 0.00 0 -ATOM 301 O 1 1 14.405 22.733 29.892 0.00 0.00 0 -ATOM 302 H 1 1 15.423 23.079 28.494 0.00 0.00 0 -ATOM 303 H 1 1 12.826 23.259 29.416 0.00 0.00 0 -ATOM 304 O 1 1 6.905 29.408 0.749 0.00 0.00 0 -ATOM 305 H 1 1 8.428 30.483 1.567 0.00 0.00 0 -ATOM 306 H 1 1 6.353 30.814 -0.444 0.00 0.00 0 -ATOM 307 O 1 1 9.189 34.159 6.509 0.00 0.00 0 -ATOM 308 H 1 1 10.198 34.193 8.002 0.00 0.00 0 -ATOM 309 H 1 1 9.890 35.692 5.785 0.00 0.00 0 -ATOM 310 O 1 1 14.256 32.316 9.369 0.00 0.00 0 -ATOM 311 H 1 1 15.733 32.867 9.486 0.00 0.00 0 -ATOM 312 H 1 1 14.754 30.670 10.090 0.00 0.00 0 -ATOM 313 O 1 1 14.714 30.841 16.516 0.00 0.00 0 -ATOM 314 H 1 1 13.748 29.551 17.279 0.00 0.00 0 -ATOM 315 H 1 1 13.218 31.933 16.614 0.00 0.00 0 -ATOM 316 O 1 1 18.409 33.641 20.611 0.00 0.00 0 -ATOM 317 H 1 1 19.601 32.274 21.115 0.00 0.00 0 -ATOM 318 H 1 1 17.360 32.655 19.518 0.00 0.00 0 -ATOM 319 O 1 1 16.062 28.638 32.207 0.00 0.00 0 -ATOM 320 H 1 1 14.648 27.958 33.253 0.00 0.00 0 -ATOM 321 H 1 1 15.752 28.014 30.522 0.00 0.00 0 -ATOM 322 O 1 1 16.200 30.895 1.473 0.00 0.00 0 -ATOM 323 H 1 1 16.626 29.968 -0.130 0.00 0.00 0 -ATOM 324 H 1 1 17.167 29.833 2.927 0.00 0.00 0 -ATOM 325 O 1 1 20.278 3.529 6.048 0.00 0.00 0 -ATOM 326 H 1 1 20.977 3.611 4.575 0.00 0.00 0 -ATOM 327 H 1 1 21.312 4.513 7.251 0.00 0.00 0 -ATOM 328 O 1 1 23.079 5.778 10.408 0.00 0.00 0 -ATOM 329 H 1 1 24.650 6.259 10.838 0.00 0.00 0 -ATOM 330 H 1 1 22.342 7.609 10.178 0.00 0.00 0 -ATOM 331 O 1 1 19.581 2.031 12.110 0.00 0.00 0 -ATOM 332 H 1 1 19.039 1.082 10.440 0.00 0.00 0 -ATOM 333 H 1 1 21.141 2.991 11.851 0.00 0.00 0 -ATOM 334 O 1 1 22.005 3.223 23.178 0.00 0.00 0 -ATOM 335 H 1 1 21.429 4.090 24.554 0.00 0.00 0 -ATOM 336 H 1 1 20.654 1.791 22.711 0.00 0.00 0 -ATOM 337 O 1 1 16.630 6.422 23.792 0.00 0.00 0 -ATOM 338 H 1 1 16.219 4.804 24.406 0.00 0.00 0 -ATOM 339 H 1 1 17.066 7.128 25.282 0.00 0.00 0 -ATOM 340 O 1 1 21.676 5.564 28.158 0.00 0.00 0 -ATOM 341 H 1 1 20.658 6.717 29.185 0.00 0.00 0 -ATOM 342 H 1 1 23.413 5.828 28.996 0.00 0.00 0 -ATOM 343 O 1 1 15.257 5.265 5.626 0.00 0.00 0 -ATOM 344 H 1 1 16.914 4.519 5.490 0.00 0.00 0 -ATOM 345 H 1 1 15.144 6.150 6.972 0.00 0.00 0 -ATOM 346 O 1 1 20.137 11.082 10.437 0.00 0.00 0 -ATOM 347 H 1 1 20.021 10.947 8.733 0.00 0.00 0 -ATOM 348 H 1 1 21.025 12.555 10.853 0.00 0.00 0 -ATOM 349 O 1 1 23.089 14.627 12.437 0.00 0.00 0 -ATOM 350 H 1 1 24.716 15.254 12.736 0.00 0.00 0 -ATOM 351 H 1 1 23.284 13.228 13.653 0.00 0.00 0 -ATOM 352 O 1 1 24.083 12.649 22.566 0.00 0.00 0 -ATOM 353 H 1 1 22.397 12.663 23.042 0.00 0.00 0 -ATOM 354 H 1 1 24.901 13.851 23.565 0.00 0.00 0 -ATOM 355 O 1 1 17.865 7.909 30.036 0.00 0.00 0 -ATOM 356 H 1 1 17.509 8.045 31.982 0.00 0.00 0 -ATOM 357 H 1 1 18.078 9.582 29.318 0.00 0.00 0 -ATOM 358 O 1 1 18.824 8.486 0.104 0.00 0.00 0 -ATOM 359 H 1 1 19.997 10.191 -0.057 0.00 0.00 0 -ATOM 360 H 1 1 17.077 8.998 0.779 0.00 0.00 0 -ATOM 361 O 1 1 20.122 9.143 5.343 0.00 0.00 0 -ATOM 362 H 1 1 19.373 8.819 3.821 0.00 0.00 0 -ATOM 363 H 1 1 21.998 8.776 5.128 0.00 0.00 0 -ATOM 364 O 1 1 16.413 14.459 5.855 0.00 0.00 0 -ATOM 365 H 1 1 15.536 13.007 5.239 0.00 0.00 0 -ATOM 366 H 1 1 16.006 14.725 7.737 0.00 0.00 0 -ATOM 367 O 1 1 17.561 15.066 15.654 0.00 0.00 0 -ATOM 368 H 1 1 17.575 13.398 16.055 0.00 0.00 0 -ATOM 369 H 1 1 18.978 15.828 16.400 0.00 0.00 0 -ATOM 370 O 1 1 26.374 17.047 24.817 0.00 0.00 0 -ATOM 371 H 1 1 27.983 17.098 25.632 0.00 0.00 0 -ATOM 372 H 1 1 25.629 18.751 24.919 0.00 0.00 0 -ATOM 373 O 1 1 19.784 12.960 28.706 0.00 0.00 0 -ATOM 374 H 1 1 21.662 13.055 28.871 0.00 0.00 0 -ATOM 375 H 1 1 19.545 14.070 27.143 0.00 0.00 0 -ATOM 376 O 1 1 17.891 16.733 32.499 0.00 0.00 0 -ATOM 377 H 1 1 18.327 15.240 31.277 0.00 0.00 0 -ATOM 378 H 1 1 18.633 18.335 31.693 0.00 0.00 0 -ATOM 379 O 1 1 23.733 23.024 1.663 0.00 0.00 0 -ATOM 380 H 1 1 24.800 24.052 2.776 0.00 0.00 0 -ATOM 381 H 1 1 24.693 22.618 0.198 0.00 0.00 0 -ATOM 382 O 1 1 20.789 18.440 9.443 0.00 0.00 0 -ATOM 383 H 1 1 20.766 17.257 7.881 0.00 0.00 0 -ATOM 384 H 1 1 21.896 17.345 10.385 0.00 0.00 0 -ATOM 385 O 1 1 21.574 17.493 17.838 0.00 0.00 0 -ATOM 386 H 1 1 20.597 18.955 17.218 0.00 0.00 0 -ATOM 387 H 1 1 22.538 16.874 16.251 0.00 0.00 0 -ATOM 388 O 1 1 19.168 14.748 24.131 0.00 0.00 0 -ATOM 389 H 1 1 19.711 16.390 23.712 0.00 0.00 0 -ATOM 390 H 1 1 17.429 14.695 24.403 0.00 0.00 0 -ATOM 391 O 1 1 22.149 20.198 24.977 0.00 0.00 0 -ATOM 392 H 1 1 21.639 20.924 26.486 0.00 0.00 0 -ATOM 393 H 1 1 22.656 21.657 24.411 0.00 0.00 0 -ATOM 394 O 1 1 20.565 20.792 29.600 0.00 0.00 0 -ATOM 395 H 1 1 22.264 20.409 30.214 0.00 0.00 0 -ATOM 396 H 1 1 20.548 22.408 30.597 0.00 0.00 0 -ATOM 397 O 1 1 20.802 26.547 9.615 0.00 0.00 0 -ATOM 398 H 1 1 20.099 27.984 8.338 0.00 0.00 0 -ATOM 399 H 1 1 21.277 27.539 11.325 0.00 0.00 0 -ATOM 400 O 1 1 16.283 23.589 7.779 0.00 0.00 0 -ATOM 401 H 1 1 16.093 21.973 6.712 0.00 0.00 0 -ATOM 402 H 1 1 17.901 22.971 8.154 0.00 0.00 0 -ATOM 403 O 1 1 18.469 29.798 13.568 0.00 0.00 0 -ATOM 404 H 1 1 19.712 31.216 13.506 0.00 0.00 0 -ATOM 405 H 1 1 16.872 30.343 14.396 0.00 0.00 0 -ATOM 406 O 1 1 18.790 21.712 16.060 0.00 0.00 0 -ATOM 407 H 1 1 19.878 23.090 16.485 0.00 0.00 0 -ATOM 408 H 1 1 17.201 22.326 15.819 0.00 0.00 0 -ATOM 409 O 1 1 21.747 26.084 16.349 0.00 0.00 0 -ATOM 410 H 1 1 20.783 27.021 15.300 0.00 0.00 0 -ATOM 411 H 1 1 22.705 27.328 17.206 0.00 0.00 0 -ATOM 412 O 1 1 20.769 26.211 32.050 0.00 0.00 0 -ATOM 413 H 1 1 21.488 27.404 33.328 0.00 0.00 0 -ATOM 414 H 1 1 18.989 26.710 32.145 0.00 0.00 0 -ATOM 415 O 1 1 19.820 29.181 5.559 0.00 0.00 0 -ATOM 416 H 1 1 20.991 29.509 4.109 0.00 0.00 0 -ATOM 417 H 1 1 19.431 31.018 6.221 0.00 0.00 0 -ATOM 418 O 1 1 19.240 33.867 7.993 0.00 0.00 0 -ATOM 419 H 1 1 19.107 35.039 6.604 0.00 0.00 0 -ATOM 420 H 1 1 20.697 33.671 9.063 0.00 0.00 0 -ATOM 421 O 1 1 22.511 34.976 15.793 0.00 0.00 0 -ATOM 422 H 1 1 23.716 36.163 16.603 0.00 0.00 0 -ATOM 423 H 1 1 21.699 36.150 14.467 0.00 0.00 0 -ATOM 424 O 1 1 22.622 30.284 19.069 0.00 0.00 0 -ATOM 425 H 1 1 22.049 31.351 17.725 0.00 0.00 0 -ATOM 426 H 1 1 24.411 30.773 19.576 0.00 0.00 0 -ATOM 427 O 1 1 18.639 33.611 28.369 0.00 0.00 0 -ATOM 428 H 1 1 18.226 32.159 29.103 0.00 0.00 0 -ATOM 429 H 1 1 19.906 33.008 27.158 0.00 0.00 0 -ATOM 430 O 1 1 22.520 1.325 31.926 0.00 0.00 0 -ATOM 431 H 1 1 22.803 2.668 30.796 0.00 0.00 0 -ATOM 432 H 1 1 21.045 0.425 31.122 0.00 0.00 0 -ATOM 433 O 1 1 21.754 3.789 1.159 0.00 0.00 0 -ATOM 434 H 1 1 22.085 2.785 -0.180 0.00 0.00 0 -ATOM 435 H 1 1 20.850 5.175 0.610 0.00 0.00 0 -ATOM 436 O 1 1 28.457 5.539 12.133 0.00 0.00 0 -ATOM 437 H 1 1 29.489 4.390 11.182 0.00 0.00 0 -ATOM 438 H 1 1 29.161 7.131 12.587 0.00 0.00 0 -ATOM 439 O 1 1 22.495 5.966 17.324 0.00 0.00 0 -ATOM 440 H 1 1 24.377 5.379 17.393 0.00 0.00 0 -ATOM 441 H 1 1 21.906 5.491 18.857 0.00 0.00 0 -ATOM 442 O 1 1 28.128 3.304 22.287 0.00 0.00 0 -ATOM 443 H 1 1 28.123 2.999 20.491 0.00 0.00 0 -ATOM 444 H 1 1 26.533 3.355 22.876 0.00 0.00 0 -ATOM 445 O 1 1 28.378 10.455 27.266 0.00 0.00 0 -ATOM 446 H 1 1 30.019 10.292 28.051 0.00 0.00 0 -ATOM 447 H 1 1 28.635 10.039 25.463 0.00 0.00 0 -ATOM 448 O 1 1 27.031 8.353 34.806 0.00 0.00 0 -ATOM 449 H 1 1 26.116 9.984 34.571 0.00 0.00 0 -ATOM 450 H 1 1 28.685 8.951 34.739 0.00 0.00 0 -ATOM 451 O 1 1 24.951 8.160 4.454 0.00 0.00 0 -ATOM 452 H 1 1 25.930 9.616 5.160 0.00 0.00 0 -ATOM 453 H 1 1 25.947 7.994 2.724 0.00 0.00 0 -ATOM 454 O 1 1 26.937 12.436 6.869 0.00 0.00 0 -ATOM 455 H 1 1 25.492 13.284 6.708 0.00 0.00 0 -ATOM 456 H 1 1 27.689 13.332 8.266 0.00 0.00 0 -ATOM 457 O 1 1 23.365 11.214 16.933 0.00 0.00 0 -ATOM 458 H 1 1 22.247 9.744 16.789 0.00 0.00 0 -ATOM 459 H 1 1 23.264 12.035 18.539 0.00 0.00 0 -ATOM 460 O 1 1 28.321 8.759 22.158 0.00 0.00 0 -ATOM 461 H 1 1 27.662 6.895 22.482 0.00 0.00 0 -ATOM 462 H 1 1 26.971 9.710 21.902 0.00 0.00 0 -ATOM 463 O 1 1 27.071 6.109 29.555 0.00 0.00 0 -ATOM 464 H 1 1 27.591 7.663 28.857 0.00 0.00 0 -ATOM 465 H 1 1 27.304 6.320 31.261 0.00 0.00 0 -ATOM 466 O 1 1 22.474 11.704 34.640 0.00 0.00 0 -ATOM 467 H 1 1 22.752 13.304 35.584 0.00 0.00 0 -ATOM 468 H 1 1 22.840 12.090 33.030 0.00 0.00 0 -ATOM 469 O 1 1 21.656 14.971 5.615 0.00 0.00 0 -ATOM 470 H 1 1 21.690 15.860 3.977 0.00 0.00 0 -ATOM 471 H 1 1 19.964 14.225 5.774 0.00 0.00 0 -ATOM 472 O 1 1 28.539 21.492 9.820 0.00 0.00 0 -ATOM 473 H 1 1 27.288 22.181 8.688 0.00 0.00 0 -ATOM 474 H 1 1 28.065 22.420 11.602 0.00 0.00 0 -ATOM 475 O 1 1 28.364 16.020 11.109 0.00 0.00 0 -ATOM 476 H 1 1 30.033 16.649 12.089 0.00 0.00 0 -ATOM 477 H 1 1 28.456 17.440 10.082 0.00 0.00 0 -ATOM 478 O 1 1 0.054 13.686 18.103 0.00 0.00 0 -ATOM 479 H 1 1 -1.714 12.928 18.841 0.00 0.00 0 -ATOM 480 H 1 1 1.008 12.429 17.383 0.00 0.00 0 -ATOM 481 O 1 1 24.636 12.894 29.957 0.00 0.00 0 -ATOM 482 H 1 1 25.906 13.914 31.183 0.00 0.00 0 -ATOM 483 H 1 1 25.641 11.609 29.162 0.00 0.00 0 -ATOM 484 O 1 1 21.548 17.250 0.749 0.00 0.00 0 -ATOM 485 H 1 1 21.843 19.026 0.905 0.00 0.00 0 -ATOM 486 H 1 1 20.385 16.716 -0.697 0.00 0.00 0 -ATOM 487 O 1 1 26.095 27.274 4.520 0.00 0.00 0 -ATOM 488 H 1 1 27.889 26.458 4.505 0.00 0.00 0 -ATOM 489 H 1 1 25.648 26.970 6.165 0.00 0.00 0 -ATOM 490 O 1 1 23.610 22.515 8.008 0.00 0.00 0 -ATOM 491 H 1 1 22.653 21.187 8.739 0.00 0.00 0 -ATOM 492 H 1 1 22.286 24.095 8.444 0.00 0.00 0 -ATOM 493 O 1 1 27.355 18.929 18.180 0.00 0.00 0 -ATOM 494 H 1 1 27.200 20.349 17.155 0.00 0.00 0 -ATOM 495 H 1 1 25.579 18.322 18.770 0.00 0.00 0 -ATOM 496 O 1 1 26.765 23.633 14.444 0.00 0.00 0 -ATOM 497 H 1 1 27.441 25.298 13.651 0.00 0.00 0 -ATOM 498 H 1 1 25.086 24.256 14.749 0.00 0.00 0 -ATOM 499 O 1 1 31.478 20.769 20.986 0.00 0.00 0 -ATOM 500 H 1 1 30.440 22.509 21.135 0.00 0.00 0 -ATOM 501 H 1 1 30.567 19.656 20.043 0.00 0.00 0 -ATOM 502 O 1 1 24.812 20.412 32.668 0.00 0.00 0 -ATOM 503 H 1 1 26.242 21.478 31.874 0.00 0.00 0 -ATOM 504 H 1 1 25.787 19.023 33.158 0.00 0.00 0 -ATOM 505 O 1 1 22.105 29.076 0.928 0.00 0.00 0 -ATOM 506 H 1 1 23.296 27.923 1.739 0.00 0.00 0 -ATOM 507 H 1 1 22.623 30.994 0.882 0.00 0.00 0 -ATOM 508 O 1 1 29.572 31.256 8.626 0.00 0.00 0 -ATOM 509 H 1 1 30.795 30.203 7.736 0.00 0.00 0 -ATOM 510 H 1 1 28.277 31.519 7.260 0.00 0.00 0 -ATOM 511 O 1 1 31.817 34.843 18.283 0.00 0.00 0 -ATOM 512 H 1 1 32.438 34.389 16.474 0.00 0.00 0 -ATOM 513 H 1 1 32.743 36.422 18.341 0.00 0.00 0 -ATOM 514 O 1 1 27.915 25.601 19.033 0.00 0.00 0 -ATOM 515 H 1 1 29.358 26.561 19.190 0.00 0.00 0 -ATOM 516 H 1 1 28.148 24.429 17.530 0.00 0.00 0 -ATOM 517 O 1 1 24.548 24.654 24.025 0.00 0.00 0 -ATOM 518 H 1 1 25.528 25.635 22.824 0.00 0.00 0 -ATOM 519 H 1 1 25.300 25.200 25.645 0.00 0.00 0 -ATOM 520 O 1 1 28.540 22.922 30.370 0.00 0.00 0 -ATOM 521 H 1 1 27.414 24.096 29.781 0.00 0.00 0 -ATOM 522 H 1 1 29.674 23.914 31.873 0.00 0.00 0 -ATOM 523 O 1 1 24.969 33.623 1.014 0.00 0.00 0 -ATOM 524 H 1 1 26.521 33.058 1.518 0.00 0.00 0 -ATOM 525 H 1 1 24.990 34.322 -0.683 0.00 0.00 0 -ATOM 526 O 1 1 23.075 32.171 11.324 0.00 0.00 0 -ATOM 527 H 1 1 23.316 32.775 13.097 0.00 0.00 0 -ATOM 528 H 1 1 24.460 33.203 10.662 0.00 0.00 0 -ATOM 529 O 1 1 27.497 2.736 17.224 0.00 0.00 0 -ATOM 530 H 1 1 28.397 3.415 15.715 0.00 0.00 0 -ATOM 531 H 1 1 28.234 1.233 17.412 0.00 0.00 0 -ATOM 532 O 1 1 26.369 33.060 22.077 0.00 0.00 0 -ATOM 533 H 1 1 26.170 34.746 22.264 0.00 0.00 0 -ATOM 534 H 1 1 27.592 32.404 23.321 0.00 0.00 0 -ATOM 535 O 1 1 30.221 30.950 25.843 0.00 0.00 0 -ATOM 536 H 1 1 30.305 29.038 26.208 0.00 0.00 0 -ATOM 537 H 1 1 30.363 31.979 27.414 0.00 0.00 0 -ATOM 538 O 1 1 24.973 26.732 28.607 0.00 0.00 0 -ATOM 539 H 1 1 25.385 28.369 29.248 0.00 0.00 0 -ATOM 540 H 1 1 23.330 26.597 29.234 0.00 0.00 0 -ATOM 541 O 1 1 32.165 4.857 2.258 0.00 0.00 0 -ATOM 542 H 1 1 32.417 6.195 1.157 0.00 0.00 0 -ATOM 543 H 1 1 32.615 3.727 1.112 0.00 0.00 0 -ATOM 544 O 1 1 28.067 3.533 5.217 0.00 0.00 0 -ATOM 545 H 1 1 26.960 4.447 4.158 0.00 0.00 0 -ATOM 546 H 1 1 29.875 3.863 4.448 0.00 0.00 0 -ATOM 547 O 1 1 33.279 2.782 13.028 0.00 0.00 0 -ATOM 548 H 1 1 33.708 3.955 11.817 0.00 0.00 0 -ATOM 549 H 1 1 33.656 3.545 14.631 0.00 0.00 0 -ATOM 550 O 1 1 34.278 4.944 17.492 0.00 0.00 0 -ATOM 551 H 1 1 33.438 6.563 17.876 0.00 0.00 0 -ATOM 552 H 1 1 34.906 4.452 18.995 0.00 0.00 0 -ATOM 553 O 1 1 32.363 1.908 26.092 0.00 0.00 0 -ATOM 554 H 1 1 31.941 1.683 24.268 0.00 0.00 0 -ATOM 555 H 1 1 33.850 1.390 26.904 0.00 0.00 0 -ATOM 556 O 1 1 27.982 0.418 28.241 0.00 0.00 0 -ATOM 557 H 1 1 27.516 2.080 28.309 0.00 0.00 0 -ATOM 558 H 1 1 29.593 0.176 27.299 0.00 0.00 0 -ATOM 559 O 1 1 28.845 14.672 2.724 0.00 0.00 0 -ATOM 560 H 1 1 27.963 13.930 4.139 0.00 0.00 0 -ATOM 561 H 1 1 30.386 15.714 3.379 0.00 0.00 0 -ATOM 562 O 1 1 28.083 10.618 14.298 0.00 0.00 0 -ATOM 563 H 1 1 28.623 12.160 13.293 0.00 0.00 0 -ATOM 564 H 1 1 26.486 11.015 15.379 0.00 0.00 0 -ATOM 565 O 1 1 33.867 10.545 13.306 0.00 0.00 0 -ATOM 566 H 1 1 35.165 9.612 13.810 0.00 0.00 0 -ATOM 567 H 1 1 33.615 10.270 11.513 0.00 0.00 0 -ATOM 568 O 1 1 31.790 9.696 18.223 0.00 0.00 0 -ATOM 569 H 1 1 30.484 9.334 19.421 0.00 0.00 0 -ATOM 570 H 1 1 30.834 10.096 16.929 0.00 0.00 0 -ATOM 571 O 1 1 30.141 15.006 21.532 0.00 0.00 0 -ATOM 572 H 1 1 28.565 15.594 22.099 0.00 0.00 0 -ATOM 573 H 1 1 30.942 14.253 23.077 0.00 0.00 0 -ATOM 574 O 1 1 32.798 10.732 30.680 0.00 0.00 0 -ATOM 575 H 1 1 34.073 9.528 30.799 0.00 0.00 0 -ATOM 576 H 1 1 32.991 11.512 28.983 0.00 0.00 0 -ATOM 577 O 1 1 33.652 16.265 5.086 0.00 0.00 0 -ATOM 578 H 1 1 35.399 16.239 4.730 0.00 0.00 0 -ATOM 579 H 1 1 33.503 17.939 5.631 0.00 0.00 0 -ATOM 580 O 1 1 31.947 10.799 7.943 0.00 0.00 0 -ATOM 581 H 1 1 29.894 10.549 7.619 0.00 0.00 0 -ATOM 582 H 1 1 32.271 12.414 7.075 0.00 0.00 0 -ATOM 583 O 1 1 0.329 15.516 11.746 0.00 0.00 0 -ATOM 584 H 1 1 -0.446 14.249 12.939 0.00 0.00 0 -ATOM 585 H 1 1 -0.685 17.018 11.935 0.00 0.00 0 -ATOM 586 O 1 1 4.262 19.165 14.308 0.00 0.00 0 -ATOM 587 H 1 1 3.579 17.691 14.920 0.00 0.00 0 -ATOM 588 H 1 1 5.723 19.183 15.204 0.00 0.00 0 -ATOM 589 O 1 1 32.995 13.546 25.948 0.00 0.00 0 -ATOM 590 H 1 1 32.167 15.060 26.787 0.00 0.00 0 -ATOM 591 H 1 1 34.425 13.800 25.007 0.00 0.00 0 -ATOM 592 O 1 1 1.773 13.524 34.037 0.00 0.00 0 -ATOM 593 H 1 1 0.227 14.409 33.446 0.00 0.00 0 -ATOM 594 H 1 1 2.167 14.670 35.511 0.00 0.00 0 -ATOM 595 O 1 1 33.029 20.529 7.247 0.00 0.00 0 -ATOM 596 H 1 1 34.388 21.414 8.003 0.00 0.00 0 -ATOM 597 H 1 1 31.451 20.831 8.182 0.00 0.00 0 -ATOM 598 O 1 1 2.037 24.250 10.251 0.00 0.00 0 -ATOM 599 H 1 1 3.743 25.008 9.876 0.00 0.00 0 -ATOM 600 H 1 1 1.894 25.043 11.903 0.00 0.00 0 -ATOM 601 O 1 1 32.753 19.259 13.976 0.00 0.00 0 -ATOM 602 H 1 1 32.792 20.886 13.792 0.00 0.00 0 -ATOM 603 H 1 1 34.334 18.799 14.976 0.00 0.00 0 -ATOM 604 O 1 1 0.396 18.673 18.699 0.00 0.00 0 -ATOM 605 H 1 1 -1.211 18.950 19.127 0.00 0.00 0 -ATOM 606 H 1 1 0.469 16.977 18.436 0.00 0.00 0 -ATOM 607 O 1 1 30.855 18.370 27.959 0.00 0.00 0 -ATOM 608 H 1 1 29.759 19.681 28.690 0.00 0.00 0 -ATOM 609 H 1 1 32.103 19.477 26.763 0.00 0.00 0 -ATOM 610 O 1 1 27.723 15.992 33.091 0.00 0.00 0 -ATOM 611 H 1 1 29.390 16.423 32.192 0.00 0.00 0 -ATOM 612 H 1 1 27.801 15.859 34.804 0.00 0.00 0 -ATOM 613 O 1 1 31.068 27.895 3.348 0.00 0.00 0 -ATOM 614 H 1 1 32.517 27.825 4.610 0.00 0.00 0 -ATOM 615 H 1 1 31.529 29.459 2.324 0.00 0.00 0 -ATOM 616 O 1 1 35.039 28.008 6.663 0.00 0.00 0 -ATOM 617 H 1 1 35.966 26.934 7.683 0.00 0.00 0 -ATOM 618 H 1 1 36.055 28.336 5.336 0.00 0.00 0 -ATOM 619 O 1 1 29.356 28.196 13.025 0.00 0.00 0 -ATOM 620 H 1 1 29.210 29.335 14.589 0.00 0.00 0 -ATOM 621 H 1 1 28.874 29.629 11.867 0.00 0.00 0 -ATOM 622 O 1 1 32.386 28.434 18.961 0.00 0.00 0 -ATOM 623 H 1 1 33.368 28.574 20.411 0.00 0.00 0 -ATOM 624 H 1 1 33.410 27.406 17.949 0.00 0.00 0 -ATOM 625 O 1 1 30.898 25.390 25.799 0.00 0.00 0 -ATOM 626 H 1 1 32.369 25.913 24.580 0.00 0.00 0 -ATOM 627 H 1 1 31.317 24.075 27.029 0.00 0.00 0 -ATOM 628 O 1 1 32.259 25.611 33.104 0.00 0.00 0 -ATOM 629 H 1 1 32.238 25.736 34.806 0.00 0.00 0 -ATOM 630 H 1 1 33.920 25.042 32.775 0.00 0.00 0 -ATOM 631 O 1 1 30.290 32.645 1.341 0.00 0.00 0 -ATOM 632 H 1 1 29.949 32.793 -0.430 0.00 0.00 0 -ATOM 633 H 1 1 31.762 33.340 1.847 0.00 0.00 0 -ATOM 634 O 1 1 25.536 34.235 6.469 0.00 0.00 0 -ATOM 635 H 1 1 25.716 36.059 6.651 0.00 0.00 0 -ATOM 636 H 1 1 25.283 33.866 4.895 0.00 0.00 0 -ATOM 637 O 1 1 31.674 33.161 13.106 0.00 0.00 0 -ATOM 638 H 1 1 31.793 34.863 13.281 0.00 0.00 0 -ATOM 639 H 1 1 30.425 32.928 11.783 0.00 0.00 0 -ATOM 640 O 1 1 33.844 32.668 22.296 0.00 0.00 0 -ATOM 641 H 1 1 32.750 32.234 23.524 0.00 0.00 0 -ATOM 642 H 1 1 32.917 32.875 20.736 0.00 0.00 0 -ATOM 643 O 1 1 31.603 30.542 30.805 0.00 0.00 0 -ATOM 644 H 1 1 33.451 30.804 30.468 0.00 0.00 0 -ATOM 645 H 1 1 31.575 28.816 31.756 0.00 0.00 0 -ATOM 646 O 1 1 26.295 31.235 30.599 0.00 0.00 0 -ATOM 647 H 1 1 27.834 30.515 30.607 0.00 0.00 0 -ATOM 648 H 1 1 26.362 32.920 29.856 0.00 0.00 0 -END diff --git a/tools/i-pi/examples/lammps/h2o-pimd-rpc/data.water_longrange b/tools/i-pi/examples/lammps/h2o-pimd-rpc/data.water_longrange deleted file mode 100644 index a08e2d741e..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd-rpc/data.water_longrange +++ /dev/null @@ -1,1331 +0,0 @@ -LAMMPS Description - - 648 atoms - 432 bonds - 216 angles - - 2 atom types - 1 bond types - 1 angle types - - 0 35.233 xlo xhi - 0 35.233 ylo yhi - 0 35.233 zlo zhi - -Masses - - 1 15.9994 - 2 1.0080 - -Bond Coeffs - - 1 0 1.78 - -Angle Coeffs - - 1 0 107.400000 - -Atoms - - 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 - 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 - 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 - 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000 - 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 - 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 - 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 - 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 - 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 - 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 - 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 - 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 - 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 - 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 - 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 - 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001 - 17 6 2 0.5564 2.39200001 2.89799999 34.84600000 - 18 6 2 0.5564 0.81400000 0.53200001 35.83600000 - 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999 - 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000 - 21 7 2 0.5564 30.91999999 11.59399999 1.67700000 - 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000 - 23 8 2 0.5564 0.30500000 10.64300001 2.79300000 - 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000 - 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000 - 26 9 2 0.5564 33.61600000 7.67300000 8.85700000 - 27 9 2 0.5564 35.11500000 5.25999999 7.61800001 - 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999 - 29 10 2 0.5564 31.62400000 6.90800001 23.52100001 - 30 10 2 0.5564 32.54400000 4.99000000 24.98200000 - 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000 - 32 11 2 0.5564 1.85600000 10.17500000 25.57899999 - 33 11 2 0.5564 0.51900000 8.09899999 26.38599999 - 34 12 1 -1.1128 2.05400000 8.66000000 32.51499999 - 35 12 2 0.5564 2.16699999 8.72700000 30.49400000 - 36 12 2 0.5564 2.37400001 10.51300000 33.03799999 - 37 13 1 -1.1128 3.40200000 16.63900001 3.00800000 - 38 13 2 0.5564 4.12700001 15.87200001 4.44600001 - 39 13 2 0.5564 2.90500001 18.33899999 3.15999999 - 40 14 1 -1.1128 4.22200000 15.44400000 8.07200000 - 41 14 2 0.5564 5.21100000 16.75600000 8.29900001 - 42 14 2 0.5564 2.56000000 15.49200001 8.86000000 - 43 15 1 -1.1128 2.83100000 9.24599999 16.48800000 - 44 15 2 0.5564 2.86900001 8.02300001 18.05000000 - 45 15 2 0.5564 3.96000000 8.46700001 15.15400000 - 46 16 1 -1.1128 5.56300000 6.00300000 20.90700000 - 47 16 2 0.5564 4.65300000 4.63800000 21.48000000 - 48 16 2 0.5564 6.40500000 6.20800000 22.52899999 - 49 17 1 -1.1128 2.08700001 13.37000000 22.91299999 - 50 17 2 0.5564 2.83200000 14.80400001 23.42200000 - 51 17 2 0.5564 1.43400000 13.50900000 21.19599999 - 52 18 1 -1.1128 3.36900000 17.88600000 25.10900001 - 53 18 2 0.5564 3.65500000 17.20000000 26.76599999 - 54 18 2 0.5564 4.77200001 18.97699999 24.49999999 - 55 19 1 -1.1128 34.76400000 20.80300000 0.94800001 - 56 19 2 0.5564 35.20999999 21.26700001 2.81599999 - 57 19 2 0.5564 35.96200001 21.72599999 0.13099999 - 58 20 1 -1.1128 2.83600000 24.17799999 15.22900000 - 59 20 2 0.5564 2.79500000 22.34599999 14.87600001 - 60 20 2 0.5564 2.41399999 24.11500000 17.13000001 - 61 21 1 -1.1128 33.00000000 24.48100000 15.23000000 - 62 21 2 0.5564 34.63999999 24.80400001 15.01299999 - 63 21 2 0.5564 32.40100000 25.76400000 14.29500001 - 64 22 1 -1.1128 0.40399999 26.77900001 23.39999999 - 65 22 2 0.5564 1.35300001 27.24800000 24.98700001 - 66 22 2 0.5564 1.54600001 28.05000000 22.31700001 - 67 23 1 -1.1128 34.22200000 21.38000000 25.41799999 - 68 23 2 0.5564 35.66899999 20.15100000 25.31700001 - 69 23 2 0.5564 32.96000000 21.18000000 23.99200000 - 70 24 1 -1.1128 33.25900000 17.43800000 32.48000000 - 71 24 2 0.5564 33.31399999 18.78200000 33.88300001 - 72 24 2 0.5564 32.74300001 18.18100001 30.87100000 - 73 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193 1 578 577 579 - 194 1 581 580 582 - 195 1 584 583 585 - 196 1 587 586 588 - 197 1 590 589 591 - 198 1 593 592 594 - 199 1 596 595 597 - 200 1 599 598 600 - 201 1 602 601 603 - 202 1 605 604 606 - 203 1 608 607 609 - 204 1 611 610 612 - 205 1 614 613 615 - 206 1 617 616 618 - 207 1 620 619 621 - 208 1 623 622 624 - 209 1 626 625 627 - 210 1 629 628 630 - 211 1 632 631 633 - 212 1 635 634 636 - 213 1 638 637 639 - 214 1 641 640 642 - 215 1 644 643 645 - 216 1 647 646 648 diff --git a/tools/i-pi/examples/lammps/h2o-pimd-rpc/in.water_longrange b/tools/i-pi/examples/lammps/h2o-pimd-rpc/in.water_longrange deleted file mode 100644 index 0e0e09a5b8..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd-rpc/in.water_longrange +++ /dev/null @@ -1,33 +0,0 @@ -units electron -atom_style full - -#pair_style lj/cut/coul/long 17.01 -pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 -bond_style harmonic -#bond_style class2 -angle_style harmonic -#kspace_style pppm 0.0001 -kspace_style pppm/tip4p 0.0001 - -read_data data.water_longrange -pair_coeff * * 0 0 -pair_coeff 1 1 0.000295147 5.96946 - -neighbor 2.0 bin -neigh_modify delay 0 every 1 check yes - -timestep 0.00025 - -#velocity all create 298.0 2345187 - -#thermo_style multi -#thermo 1 - -#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 -#fix 1 all nve -fix 1 all ipi rpc_long 32347 unix - -#dump 1 all xyz 25 dump.xyz - -run 100000000 - diff --git a/tools/i-pi/examples/lammps/h2o-pimd-rpc/in.water_shortrange b/tools/i-pi/examples/lammps/h2o-pimd-rpc/in.water_shortrange deleted file mode 100644 index 6df6d16ee2..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd-rpc/in.water_shortrange +++ /dev/null @@ -1,34 +0,0 @@ -units electron -atom_style full - -pair_style lj/cut 0.51 -#pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 -#bond_style harmonic -bond_style class2 -angle_style harmonic -#kspace_style pppm 0.0001 -#kspace_style pppm/tip4p 0.0001 - -read_data data.water_shortrange -pair_coeff * * 0 0.1 -#pair_coeff 1 1 0.000295147 5.96946 - -#atom_modify sort 1 3.00 -neighbor 2.0 bin -neigh_modify delay 0 every 1 check yes - -timestep 0.00025 - -#velocity all create 298.0 2345187 - -#thermo_style multi -#thermo 1 - -#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 -#fix 1 all nve -fix 1 all ipi rpc_short 32346 unix - -#dump 1 all xyz 25 dump.xyz - -run 100000000 - diff --git a/tools/i-pi/examples/lammps/h2o-pimd-rpc/input.xml b/tools/i-pi/examples/lammps/h2o-pimd-rpc/input.xml deleted file mode 100644 index fc7596d097..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd-rpc/input.xml +++ /dev/null @@ -1,27 +0,0 @@ - - - water_298K.pdb - 298 - - - [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] - positions - - 500000 - 32346 - - -
rpc_short
- - -
rpc_long
- - - - - 25 - - 0.25 - 298 - - diff --git a/tools/i-pi/examples/lammps/h2o-pimd-rpc/water_298K.pdb b/tools/i-pi/examples/lammps/h2o-pimd-rpc/water_298K.pdb deleted file mode 100644 index e8509c868e..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd-rpc/water_298K.pdb +++ /dev/null @@ -1,650 +0,0 @@ -CRYST 35.233 35.233 35.233 90.00 90.00 90.00 P 1 1 -ATOM 1 O 1 1 3.846 5.672 1.323 0.00 0.00 0 -ATOM 2 H 1 1 2.979 7.054 0.857 0.00 0.00 0 -ATOM 3 H 1 1 5.525 5.697 0.451 0.00 0.00 0 -ATOM 4 O 1 1 34.557 34.341 3.078 0.00 0.00 0 -ATOM 5 H 1 1 33.722 34.689 4.840 0.00 0.00 0 -ATOM 6 H 1 1 36.029 33.220 3.711 0.00 0.00 0 -ATOM 7 O 1 1 5.591 1.963 13.477 0.00 0.00 0 -ATOM 8 H 1 1 7.265 1.864 13.851 0.00 0.00 0 -ATOM 9 H 1 1 5.009 3.555 13.916 0.00 0.00 0 -ATOM 10 O 1 1 1.060 2.061 21.718 0.00 0.00 0 -ATOM 11 H 1 1 0.757 0.261 21.820 0.00 0.00 0 -ATOM 12 H 1 1 0.213 3.013 23.047 0.00 0.00 0 -ATOM 13 O 1 1 1.200 1.337 29.006 0.00 0.00 0 -ATOM 14 H 1 1 0.818 1.884 30.732 0.00 0.00 0 -ATOM 15 H 1 1 2.883 1.825 29.011 0.00 0.00 0 -ATOM 16 O 1 1 1.331 1.386 34.306 0.00 0.00 0 -ATOM 17 H 1 1 2.392 2.898 34.846 0.00 0.00 0 -ATOM 18 H 1 1 0.814 0.532 35.836 0.00 0.00 0 -ATOM 19 O 1 1 31.451 10.201 0.726 0.00 0.00 0 -ATOM 20 H 1 1 32.282 10.877 -0.750 0.00 0.00 0 -ATOM 21 H 1 1 30.920 11.594 1.677 0.00 0.00 0 -ATOM 22 O 1 1 0.836 10.808 4.298 0.00 0.00 0 -ATOM 23 H 1 1 0.305 10.643 2.793 0.00 0.00 0 -ATOM 24 H 1 1 -0.356 10.334 5.524 0.00 0.00 0 -ATOM 25 O 1 1 34.381 5.979 9.194 0.00 0.00 0 -ATOM 26 H 1 1 33.616 7.673 8.857 0.00 0.00 0 -ATOM 27 H 1 1 35.115 5.260 7.618 0.00 0.00 0 -ATOM 28 O 1 1 33.212 6.480 24.278 0.00 0.00 0 -ATOM 29 H 1 1 31.624 6.908 23.521 0.00 0.00 0 -ATOM 30 H 1 1 32.544 4.990 24.982 0.00 0.00 0 -ATOM 31 O 1 1 1.992 9.002 26.863 0.00 0.00 0 -ATOM 32 H 1 1 1.856 10.175 25.579 0.00 0.00 0 -ATOM 33 H 1 1 0.519 8.099 26.386 0.00 0.00 0 -ATOM 34 O 1 1 2.054 8.660 32.515 0.00 0.00 0 -ATOM 35 H 1 1 2.167 8.727 30.494 0.00 0.00 0 -ATOM 36 H 1 1 2.374 10.513 33.038 0.00 0.00 0 -ATOM 37 O 1 1 3.402 16.639 3.008 0.00 0.00 0 -ATOM 38 H 1 1 4.127 15.872 4.446 0.00 0.00 0 -ATOM 39 H 1 1 2.905 18.339 3.160 0.00 0.00 0 -ATOM 40 O 1 1 4.222 15.444 8.072 0.00 0.00 0 -ATOM 41 H 1 1 5.211 16.756 8.299 0.00 0.00 0 -ATOM 42 H 1 1 2.560 15.492 8.860 0.00 0.00 0 -ATOM 43 O 1 1 2.831 9.246 16.488 0.00 0.00 0 -ATOM 44 H 1 1 2.869 8.023 18.050 0.00 0.00 0 -ATOM 45 H 1 1 3.960 8.467 15.154 0.00 0.00 0 -ATOM 46 O 1 1 5.563 6.003 20.907 0.00 0.00 0 -ATOM 47 H 1 1 4.653 4.638 21.480 0.00 0.00 0 -ATOM 48 H 1 1 6.405 6.208 22.529 0.00 0.00 0 -ATOM 49 O 1 1 2.087 13.370 22.913 0.00 0.00 0 -ATOM 50 H 1 1 2.832 14.804 23.422 0.00 0.00 0 -ATOM 51 H 1 1 1.434 13.509 21.196 0.00 0.00 0 -ATOM 52 O 1 1 3.369 17.886 25.109 0.00 0.00 0 -ATOM 53 H 1 1 3.655 17.200 26.766 0.00 0.00 0 -ATOM 54 H 1 1 4.772 18.977 24.500 0.00 0.00 0 -ATOM 55 O 1 1 34.764 20.803 0.948 0.00 0.00 0 -ATOM 56 H 1 1 35.210 21.267 2.816 0.00 0.00 0 -ATOM 57 H 1 1 35.962 21.726 0.131 0.00 0.00 0 -ATOM 58 O 1 1 2.836 24.178 15.229 0.00 0.00 0 -ATOM 59 H 1 1 2.795 22.346 14.876 0.00 0.00 0 -ATOM 60 H 1 1 2.414 24.115 17.130 0.00 0.00 0 -ATOM 61 O 1 1 33.000 24.481 15.230 0.00 0.00 0 -ATOM 62 H 1 1 34.640 24.804 15.013 0.00 0.00 0 -ATOM 63 H 1 1 32.401 25.764 14.295 0.00 0.00 0 -ATOM 64 O 1 1 0.404 26.779 23.400 0.00 0.00 0 -ATOM 65 H 1 1 1.353 27.248 24.987 0.00 0.00 0 -ATOM 66 H 1 1 1.546 28.050 22.317 0.00 0.00 0 -ATOM 67 O 1 1 34.222 21.380 25.418 0.00 0.00 0 -ATOM 68 H 1 1 35.669 20.151 25.317 0.00 0.00 0 -ATOM 69 H 1 1 32.960 21.180 23.992 0.00 0.00 0 -ATOM 70 O 1 1 33.259 17.438 32.480 0.00 0.00 0 -ATOM 71 H 1 1 33.314 18.782 33.883 0.00 0.00 0 -ATOM 72 H 1 1 32.743 18.181 30.871 0.00 0.00 0 -ATOM 73 O 1 1 4.463 21.979 3.936 0.00 0.00 0 -ATOM 74 H 1 1 5.856 23.084 3.400 0.00 0.00 0 -ATOM 75 H 1 1 3.986 22.180 5.602 0.00 0.00 0 -ATOM 76 O 1 1 6.258 25.851 8.520 0.00 0.00 0 -ATOM 77 H 1 1 5.767 27.693 8.476 0.00 0.00 0 -ATOM 78 H 1 1 7.202 25.506 10.186 0.00 0.00 0 -ATOM 79 O 1 1 0.601 29.737 12.747 0.00 0.00 0 -ATOM 80 H 1 1 -0.685 30.842 12.350 0.00 0.00 0 -ATOM 81 H 1 1 1.336 30.716 14.031 0.00 0.00 0 -ATOM 82 O 1 1 7.563 28.191 24.333 0.00 0.00 0 -ATOM 83 H 1 1 9.201 28.828 24.684 0.00 0.00 0 -ATOM 84 H 1 1 7.381 27.621 22.799 0.00 0.00 0 -ATOM 85 O 1 1 3.653 27.109 27.772 0.00 0.00 0 -ATOM 86 H 1 1 5.126 27.015 26.772 0.00 0.00 0 -ATOM 87 H 1 1 3.031 28.756 27.698 0.00 0.00 0 -ATOM 88 O 1 1 2.596 23.991 32.476 0.00 0.00 0 -ATOM 89 H 1 1 2.879 24.791 30.859 0.00 0.00 0 -ATOM 90 H 1 1 4.003 22.913 32.701 0.00 0.00 0 -ATOM 91 O 1 1 3.083 31.317 3.644 0.00 0.00 0 -ATOM 92 H 1 1 4.133 30.589 2.539 0.00 0.00 0 -ATOM 93 H 1 1 4.218 32.173 5.037 0.00 0.00 0 -ATOM 94 O 1 1 4.661 30.555 9.368 0.00 0.00 0 -ATOM 95 H 1 1 3.184 29.843 10.132 0.00 0.00 0 -ATOM 96 H 1 1 4.358 32.448 9.126 0.00 0.00 0 -ATOM 97 O 1 1 3.465 32.537 15.778 0.00 0.00 0 -ATOM 98 H 1 1 5.072 31.819 15.903 0.00 0.00 0 -ATOM 99 H 1 1 4.055 34.257 15.284 0.00 0.00 0 -ATOM 100 O 1 1 4.215 29.153 20.317 0.00 0.00 0 -ATOM 101 H 1 1 3.658 30.176 18.842 0.00 0.00 0 -ATOM 102 H 1 1 4.959 30.291 21.449 0.00 0.00 0 -ATOM 103 O 1 1 1.126 31.333 28.768 0.00 0.00 0 -ATOM 104 H 1 1 2.395 31.124 29.925 0.00 0.00 0 -ATOM 105 H 1 1 0.768 33.092 28.898 0.00 0.00 0 -ATOM 106 O 1 1 4.881 32.616 32.302 0.00 0.00 0 -ATOM 107 H 1 1 6.588 32.911 31.725 0.00 0.00 0 -ATOM 108 H 1 1 4.486 34.037 33.249 0.00 0.00 0 -ATOM 109 O 1 1 8.962 5.556 0.151 0.00 0.00 0 -ATOM 110 H 1 1 9.652 6.991 0.859 0.00 0.00 0 -ATOM 111 H 1 1 9.173 4.477 1.645 0.00 0.00 0 -ATOM 112 O 1 1 1.833 3.518 5.679 0.00 0.00 0 -ATOM 113 H 1 1 2.889 2.731 6.788 0.00 0.00 0 -ATOM 114 H 1 1 2.789 4.187 4.147 0.00 0.00 0 -ATOM 115 O 1 1 10.510 34.726 13.073 0.00 0.00 0 -ATOM 116 H 1 1 11.920 34.118 11.919 0.00 0.00 0 -ATOM 117 H 1 1 11.295 34.968 14.741 0.00 0.00 0 -ATOM 118 O 1 1 7.212 0.042 22.454 0.00 0.00 0 -ATOM 119 H 1 1 6.924 0.470 24.172 0.00 0.00 0 -ATOM 120 H 1 1 8.319 1.228 21.653 0.00 0.00 0 -ATOM 121 O 1 1 6.365 2.010 27.544 0.00 0.00 0 -ATOM 122 H 1 1 5.954 3.585 26.852 0.00 0.00 0 -ATOM 123 H 1 1 7.758 2.549 28.696 0.00 0.00 0 -ATOM 124 O 1 1 10.833 3.140 30.787 0.00 0.00 0 -ATOM 125 H 1 1 12.697 2.975 30.867 0.00 0.00 0 -ATOM 126 H 1 1 10.389 3.700 32.404 0.00 0.00 0 -ATOM 127 O 1 1 8.684 9.342 3.912 0.00 0.00 0 -ATOM 128 H 1 1 6.985 9.256 4.773 0.00 0.00 0 -ATOM 129 H 1 1 8.684 10.809 3.011 0.00 0.00 0 -ATOM 130 O 1 1 4.873 9.919 7.707 0.00 0.00 0 -ATOM 131 H 1 1 3.698 9.771 6.194 0.00 0.00 0 -ATOM 132 H 1 1 5.047 11.961 7.624 0.00 0.00 0 -ATOM 133 O 1 1 10.031 5.018 9.699 0.00 0.00 0 -ATOM 134 H 1 1 9.675 3.382 10.340 0.00 0.00 0 -ATOM 135 H 1 1 9.132 5.987 10.825 0.00 0.00 0 -ATOM 136 O 1 1 11.246 3.918 21.929 0.00 0.00 0 -ATOM 137 H 1 1 12.614 2.770 22.341 0.00 0.00 0 -ATOM 138 H 1 1 12.073 5.686 21.497 0.00 0.00 0 -ATOM 139 O 1 1 6.825 7.164 25.708 0.00 0.00 0 -ATOM 140 H 1 1 8.036 8.374 25.980 0.00 0.00 0 -ATOM 141 H 1 1 5.206 7.900 25.891 0.00 0.00 0 -ATOM 142 O 1 1 10.171 12.811 0.295 0.00 0.00 0 -ATOM 143 H 1 1 10.033 12.818 -1.609 0.00 0.00 0 -ATOM 144 H 1 1 9.880 14.492 0.480 0.00 0.00 0 -ATOM 145 O 1 1 8.190 17.402 1.253 0.00 0.00 0 -ATOM 146 H 1 1 9.472 18.531 1.253 0.00 0.00 0 -ATOM 147 H 1 1 6.351 17.817 1.568 0.00 0.00 0 -ATOM 148 O 1 1 11.233 16.188 8.299 0.00 0.00 0 -ATOM 149 H 1 1 10.291 17.689 8.166 0.00 0.00 0 -ATOM 150 H 1 1 12.768 17.123 8.733 0.00 0.00 0 -ATOM 151 O 1 1 6.386 8.002 12.846 0.00 0.00 0 -ATOM 152 H 1 1 7.701 8.896 13.655 0.00 0.00 0 -ATOM 153 H 1 1 5.591 8.877 11.519 0.00 0.00 0 -ATOM 154 O 1 1 8.184 10.419 18.848 0.00 0.00 0 -ATOM 155 H 1 1 9.498 9.434 19.905 0.00 0.00 0 -ATOM 156 H 1 1 6.882 9.027 18.948 0.00 0.00 0 -ATOM 157 O 1 1 10.806 14.431 21.328 0.00 0.00 0 -ATOM 158 H 1 1 9.177 13.531 20.670 0.00 0.00 0 -ATOM 159 H 1 1 11.344 15.696 20.448 0.00 0.00 0 -ATOM 160 O 1 1 9.237 13.928 30.341 0.00 0.00 0 -ATOM 161 H 1 1 10.779 14.839 30.522 0.00 0.00 0 -ATOM 162 H 1 1 9.965 13.192 28.899 0.00 0.00 0 -ATOM 163 O 1 1 10.918 21.707 1.864 0.00 0.00 0 -ATOM 164 H 1 1 10.280 23.449 2.279 0.00 0.00 0 -ATOM 165 H 1 1 12.708 21.456 1.749 0.00 0.00 0 -ATOM 166 O 1 1 9.353 16.125 13.927 0.00 0.00 0 -ATOM 167 H 1 1 9.938 17.594 14.618 0.00 0.00 0 -ATOM 168 H 1 1 9.518 16.360 12.244 0.00 0.00 0 -ATOM 169 O 1 1 10.371 11.107 14.268 0.00 0.00 0 -ATOM 170 H 1 1 9.644 10.406 15.859 0.00 0.00 0 -ATOM 171 H 1 1 9.434 12.523 14.117 0.00 0.00 0 -ATOM 172 O 1 1 3.351 22.769 20.196 0.00 0.00 0 -ATOM 173 H 1 1 2.055 23.686 21.503 0.00 0.00 0 -ATOM 174 H 1 1 2.452 21.401 19.413 0.00 0.00 0 -ATOM 175 O 1 1 6.836 21.329 23.199 0.00 0.00 0 -ATOM 176 H 1 1 8.249 20.848 22.320 0.00 0.00 0 -ATOM 177 H 1 1 5.668 21.841 21.886 0.00 0.00 0 -ATOM 178 O 1 1 4.604 15.649 30.043 0.00 0.00 0 -ATOM 179 H 1 1 6.453 15.217 30.207 0.00 0.00 0 -ATOM 180 H 1 1 3.822 14.762 31.562 0.00 0.00 0 -ATOM 181 O 1 1 7.125 19.976 9.421 0.00 0.00 0 -ATOM 182 H 1 1 5.918 20.453 10.730 0.00 0.00 0 -ATOM 183 H 1 1 8.099 21.496 9.491 0.00 0.00 0 -ATOM 184 O 1 1 9.063 25.912 13.186 0.00 0.00 0 -ATOM 185 H 1 1 10.350 26.572 12.367 0.00 0.00 0 -ATOM 186 H 1 1 9.680 24.367 13.697 0.00 0.00 0 -ATOM 187 O 1 1 8.022 22.343 17.042 0.00 0.00 0 -ATOM 188 H 1 1 9.144 23.367 18.074 0.00 0.00 0 -ATOM 189 H 1 1 6.562 23.462 16.852 0.00 0.00 0 -ATOM 190 O 1 1 10.762 26.285 19.963 0.00 0.00 0 -ATOM 191 H 1 1 11.036 27.966 20.538 0.00 0.00 0 -ATOM 192 H 1 1 11.078 25.401 21.456 0.00 0.00 0 -ATOM 193 O 1 1 9.158 22.902 28.391 0.00 0.00 0 -ATOM 194 H 1 1 8.219 23.528 27.085 0.00 0.00 0 -ATOM 195 H 1 1 8.089 21.760 29.509 0.00 0.00 0 -ATOM 196 O 1 1 6.219 20.158 31.921 0.00 0.00 0 -ATOM 197 H 1 1 5.635 18.511 31.161 0.00 0.00 0 -ATOM 198 H 1 1 7.530 19.624 33.071 0.00 0.00 0 -ATOM 199 O 1 1 11.191 31.509 2.617 0.00 0.00 0 -ATOM 200 H 1 1 10.460 32.214 4.108 0.00 0.00 0 -ATOM 201 H 1 1 13.176 31.751 2.577 0.00 0.00 0 -ATOM 202 O 1 1 4.748 0.055 8.605 0.00 0.00 0 -ATOM 203 H 1 1 5.380 0.517 10.183 0.00 0.00 0 -ATOM 204 H 1 1 6.050 -0.306 7.480 0.00 0.00 0 -ATOM 205 O 1 1 8.695 30.809 15.731 0.00 0.00 0 -ATOM 206 H 1 1 9.189 32.103 14.495 0.00 0.00 0 -ATOM 207 H 1 1 8.447 29.069 14.868 0.00 0.00 0 -ATOM 208 O 1 1 10.128 31.402 20.766 0.00 0.00 0 -ATOM 209 H 1 1 9.456 30.905 19.155 0.00 0.00 0 -ATOM 210 H 1 1 9.020 32.731 21.415 0.00 0.00 0 -ATOM 211 O 1 1 12.238 30.162 25.837 0.00 0.00 0 -ATOM 212 H 1 1 11.418 30.908 27.110 0.00 0.00 0 -ATOM 213 H 1 1 12.396 31.331 24.678 0.00 0.00 0 -ATOM 214 O 1 1 10.395 32.537 30.624 0.00 0.00 0 -ATOM 215 H 1 1 11.042 34.339 30.751 0.00 0.00 0 -ATOM 216 H 1 1 11.378 31.486 31.538 0.00 0.00 0 -ATOM 217 O 1 1 10.438 3.626 5.087 0.00 0.00 0 -ATOM 218 H 1 1 12.435 4.082 5.136 0.00 0.00 0 -ATOM 219 H 1 1 9.822 4.284 6.681 0.00 0.00 0 -ATOM 220 O 1 1 14.762 3.401 13.776 0.00 0.00 0 -ATOM 221 H 1 1 16.518 3.824 13.376 0.00 0.00 0 -ATOM 222 H 1 1 13.752 4.757 12.964 0.00 0.00 0 -ATOM 223 O 1 1 12.382 1.012 17.643 0.00 0.00 0 -ATOM 224 H 1 1 13.346 1.997 16.444 0.00 0.00 0 -ATOM 225 H 1 1 11.931 2.133 18.998 0.00 0.00 0 -ATOM 226 O 1 1 15.278 1.293 24.559 0.00 0.00 0 -ATOM 227 H 1 1 16.071 0.946 26.365 0.00 0.00 0 -ATOM 228 H 1 1 15.794 0.199 23.499 0.00 0.00 0 -ATOM 229 O 1 1 22.226 31.627 24.712 0.00 0.00 0 -ATOM 230 H 1 1 23.338 32.595 23.876 0.00 0.00 0 -ATOM 231 H 1 1 22.161 30.053 24.132 0.00 0.00 0 -ATOM 232 O 1 1 15.640 1.847 32.717 0.00 0.00 0 -ATOM 233 H 1 1 17.488 2.473 31.874 0.00 0.00 0 -ATOM 234 H 1 1 16.403 0.869 34.267 0.00 0.00 0 -ATOM 235 O 1 1 14.858 10.199 2.754 0.00 0.00 0 -ATOM 236 H 1 1 13.360 10.712 2.282 0.00 0.00 0 -ATOM 237 H 1 1 14.560 9.316 4.559 0.00 0.00 0 -ATOM 238 O 1 1 15.717 8.469 10.739 0.00 0.00 0 -ATOM 239 H 1 1 17.323 9.581 10.875 0.00 0.00 0 -ATOM 240 H 1 1 14.574 9.631 10.221 0.00 0.00 0 -ATOM 241 O 1 1 15.248 10.398 16.525 0.00 0.00 0 -ATOM 242 H 1 1 16.324 9.181 16.149 0.00 0.00 0 -ATOM 243 H 1 1 14.172 10.488 15.098 0.00 0.00 0 -ATOM 244 O 1 1 13.226 8.438 20.801 0.00 0.00 0 -ATOM 245 H 1 1 14.043 8.996 19.295 0.00 0.00 0 -ATOM 246 H 1 1 14.661 7.802 22.093 0.00 0.00 0 -ATOM 247 O 1 1 10.173 10.961 25.875 0.00 0.00 0 -ATOM 248 H 1 1 11.477 10.223 26.940 0.00 0.00 0 -ATOM 249 H 1 1 11.269 10.738 24.343 0.00 0.00 0 -ATOM 250 O 1 1 12.792 7.737 29.173 0.00 0.00 0 -ATOM 251 H 1 1 12.199 6.038 29.475 0.00 0.00 0 -ATOM 252 H 1 1 14.427 7.450 29.617 0.00 0.00 0 -ATOM 253 O 1 1 15.180 19.498 3.578 0.00 0.00 0 -ATOM 254 H 1 1 14.883 17.596 4.080 0.00 0.00 0 -ATOM 255 H 1 1 16.754 19.579 2.626 0.00 0.00 0 -ATOM 256 O 1 1 12.517 11.093 7.701 0.00 0.00 0 -ATOM 257 H 1 1 12.224 12.778 7.555 0.00 0.00 0 -ATOM 258 H 1 1 11.150 10.393 7.057 0.00 0.00 0 -ATOM 259 O 1 1 16.266 16.271 10.758 0.00 0.00 0 -ATOM 260 H 1 1 16.507 15.795 12.768 0.00 0.00 0 -ATOM 261 H 1 1 17.725 16.977 10.292 0.00 0.00 0 -ATOM 262 O 1 1 14.069 18.399 18.897 0.00 0.00 0 -ATOM 263 H 1 1 15.513 17.523 18.155 0.00 0.00 0 -ATOM 264 H 1 1 14.958 18.709 20.673 0.00 0.00 0 -ATOM 265 O 1 1 14.099 15.480 25.510 0.00 0.00 0 -ATOM 266 H 1 1 13.698 16.872 26.938 0.00 0.00 0 -ATOM 267 H 1 1 12.567 15.379 24.444 0.00 0.00 0 -ATOM 268 O 1 1 13.309 17.574 30.292 0.00 0.00 0 -ATOM 269 H 1 1 14.937 16.934 30.810 0.00 0.00 0 -ATOM 270 H 1 1 13.969 19.494 30.012 0.00 0.00 0 -ATOM 271 O 1 1 18.371 23.257 0.925 0.00 0.00 0 -ATOM 272 H 1 1 19.479 23.480 2.321 0.00 0.00 0 -ATOM 273 H 1 1 19.087 24.325 -0.369 0.00 0.00 0 -ATOM 274 O 1 1 12.100 21.730 11.355 0.00 0.00 0 -ATOM 275 H 1 1 13.141 22.287 12.743 0.00 0.00 0 -ATOM 276 H 1 1 13.467 22.236 10.244 0.00 0.00 0 -ATOM 277 O 1 1 12.163 23.290 23.597 0.00 0.00 0 -ATOM 278 H 1 1 11.324 22.736 24.949 0.00 0.00 0 -ATOM 279 H 1 1 13.882 22.872 23.840 0.00 0.00 0 -ATOM 280 O 1 1 20.173 26.761 22.628 0.00 0.00 0 -ATOM 281 H 1 1 20.206 26.532 20.792 0.00 0.00 0 -ATOM 282 H 1 1 21.556 25.742 23.389 0.00 0.00 0 -ATOM 283 O 1 1 16.701 21.165 22.605 0.00 0.00 0 -ATOM 284 H 1 1 18.028 20.686 23.848 0.00 0.00 0 -ATOM 285 H 1 1 17.104 22.866 21.949 0.00 0.00 0 -ATOM 286 O 1 1 11.391 26.461 33.705 0.00 0.00 0 -ATOM 287 H 1 1 9.841 27.192 34.048 0.00 0.00 0 -ATOM 288 H 1 1 11.776 25.540 35.243 0.00 0.00 0 -ATOM 289 O 1 1 9.898 25.989 4.553 0.00 0.00 0 -ATOM 290 H 1 1 8.902 26.131 6.039 0.00 0.00 0 -ATOM 291 H 1 1 10.287 27.806 4.376 0.00 0.00 0 -ATOM 292 O 1 1 14.308 26.960 10.877 0.00 0.00 0 -ATOM 293 H 1 1 15.302 27.405 12.173 0.00 0.00 0 -ATOM 294 H 1 1 15.463 26.151 9.633 0.00 0.00 0 -ATOM 295 O 1 1 13.433 22.960 16.904 0.00 0.00 0 -ATOM 296 H 1 1 13.409 24.131 18.132 0.00 0.00 0 -ATOM 297 H 1 1 13.624 21.191 17.520 0.00 0.00 0 -ATOM 298 O 1 1 16.409 26.768 26.875 0.00 0.00 0 -ATOM 299 H 1 1 17.590 26.987 25.431 0.00 0.00 0 -ATOM 300 H 1 1 14.751 27.703 26.230 0.00 0.00 0 -ATOM 301 O 1 1 14.405 22.733 29.892 0.00 0.00 0 -ATOM 302 H 1 1 15.423 23.079 28.494 0.00 0.00 0 -ATOM 303 H 1 1 12.826 23.259 29.416 0.00 0.00 0 -ATOM 304 O 1 1 6.905 29.408 0.749 0.00 0.00 0 -ATOM 305 H 1 1 8.428 30.483 1.567 0.00 0.00 0 -ATOM 306 H 1 1 6.353 30.814 -0.444 0.00 0.00 0 -ATOM 307 O 1 1 9.189 34.159 6.509 0.00 0.00 0 -ATOM 308 H 1 1 10.198 34.193 8.002 0.00 0.00 0 -ATOM 309 H 1 1 9.890 35.692 5.785 0.00 0.00 0 -ATOM 310 O 1 1 14.256 32.316 9.369 0.00 0.00 0 -ATOM 311 H 1 1 15.733 32.867 9.486 0.00 0.00 0 -ATOM 312 H 1 1 14.754 30.670 10.090 0.00 0.00 0 -ATOM 313 O 1 1 14.714 30.841 16.516 0.00 0.00 0 -ATOM 314 H 1 1 13.748 29.551 17.279 0.00 0.00 0 -ATOM 315 H 1 1 13.218 31.933 16.614 0.00 0.00 0 -ATOM 316 O 1 1 18.409 33.641 20.611 0.00 0.00 0 -ATOM 317 H 1 1 19.601 32.274 21.115 0.00 0.00 0 -ATOM 318 H 1 1 17.360 32.655 19.518 0.00 0.00 0 -ATOM 319 O 1 1 16.062 28.638 32.207 0.00 0.00 0 -ATOM 320 H 1 1 14.648 27.958 33.253 0.00 0.00 0 -ATOM 321 H 1 1 15.752 28.014 30.522 0.00 0.00 0 -ATOM 322 O 1 1 16.200 30.895 1.473 0.00 0.00 0 -ATOM 323 H 1 1 16.626 29.968 -0.130 0.00 0.00 0 -ATOM 324 H 1 1 17.167 29.833 2.927 0.00 0.00 0 -ATOM 325 O 1 1 20.278 3.529 6.048 0.00 0.00 0 -ATOM 326 H 1 1 20.977 3.611 4.575 0.00 0.00 0 -ATOM 327 H 1 1 21.312 4.513 7.251 0.00 0.00 0 -ATOM 328 O 1 1 23.079 5.778 10.408 0.00 0.00 0 -ATOM 329 H 1 1 24.650 6.259 10.838 0.00 0.00 0 -ATOM 330 H 1 1 22.342 7.609 10.178 0.00 0.00 0 -ATOM 331 O 1 1 19.581 2.031 12.110 0.00 0.00 0 -ATOM 332 H 1 1 19.039 1.082 10.440 0.00 0.00 0 -ATOM 333 H 1 1 21.141 2.991 11.851 0.00 0.00 0 -ATOM 334 O 1 1 22.005 3.223 23.178 0.00 0.00 0 -ATOM 335 H 1 1 21.429 4.090 24.554 0.00 0.00 0 -ATOM 336 H 1 1 20.654 1.791 22.711 0.00 0.00 0 -ATOM 337 O 1 1 16.630 6.422 23.792 0.00 0.00 0 -ATOM 338 H 1 1 16.219 4.804 24.406 0.00 0.00 0 -ATOM 339 H 1 1 17.066 7.128 25.282 0.00 0.00 0 -ATOM 340 O 1 1 21.676 5.564 28.158 0.00 0.00 0 -ATOM 341 H 1 1 20.658 6.717 29.185 0.00 0.00 0 -ATOM 342 H 1 1 23.413 5.828 28.996 0.00 0.00 0 -ATOM 343 O 1 1 15.257 5.265 5.626 0.00 0.00 0 -ATOM 344 H 1 1 16.914 4.519 5.490 0.00 0.00 0 -ATOM 345 H 1 1 15.144 6.150 6.972 0.00 0.00 0 -ATOM 346 O 1 1 20.137 11.082 10.437 0.00 0.00 0 -ATOM 347 H 1 1 20.021 10.947 8.733 0.00 0.00 0 -ATOM 348 H 1 1 21.025 12.555 10.853 0.00 0.00 0 -ATOM 349 O 1 1 23.089 14.627 12.437 0.00 0.00 0 -ATOM 350 H 1 1 24.716 15.254 12.736 0.00 0.00 0 -ATOM 351 H 1 1 23.284 13.228 13.653 0.00 0.00 0 -ATOM 352 O 1 1 24.083 12.649 22.566 0.00 0.00 0 -ATOM 353 H 1 1 22.397 12.663 23.042 0.00 0.00 0 -ATOM 354 H 1 1 24.901 13.851 23.565 0.00 0.00 0 -ATOM 355 O 1 1 17.865 7.909 30.036 0.00 0.00 0 -ATOM 356 H 1 1 17.509 8.045 31.982 0.00 0.00 0 -ATOM 357 H 1 1 18.078 9.582 29.318 0.00 0.00 0 -ATOM 358 O 1 1 18.824 8.486 0.104 0.00 0.00 0 -ATOM 359 H 1 1 19.997 10.191 -0.057 0.00 0.00 0 -ATOM 360 H 1 1 17.077 8.998 0.779 0.00 0.00 0 -ATOM 361 O 1 1 20.122 9.143 5.343 0.00 0.00 0 -ATOM 362 H 1 1 19.373 8.819 3.821 0.00 0.00 0 -ATOM 363 H 1 1 21.998 8.776 5.128 0.00 0.00 0 -ATOM 364 O 1 1 16.413 14.459 5.855 0.00 0.00 0 -ATOM 365 H 1 1 15.536 13.007 5.239 0.00 0.00 0 -ATOM 366 H 1 1 16.006 14.725 7.737 0.00 0.00 0 -ATOM 367 O 1 1 17.561 15.066 15.654 0.00 0.00 0 -ATOM 368 H 1 1 17.575 13.398 16.055 0.00 0.00 0 -ATOM 369 H 1 1 18.978 15.828 16.400 0.00 0.00 0 -ATOM 370 O 1 1 26.374 17.047 24.817 0.00 0.00 0 -ATOM 371 H 1 1 27.983 17.098 25.632 0.00 0.00 0 -ATOM 372 H 1 1 25.629 18.751 24.919 0.00 0.00 0 -ATOM 373 O 1 1 19.784 12.960 28.706 0.00 0.00 0 -ATOM 374 H 1 1 21.662 13.055 28.871 0.00 0.00 0 -ATOM 375 H 1 1 19.545 14.070 27.143 0.00 0.00 0 -ATOM 376 O 1 1 17.891 16.733 32.499 0.00 0.00 0 -ATOM 377 H 1 1 18.327 15.240 31.277 0.00 0.00 0 -ATOM 378 H 1 1 18.633 18.335 31.693 0.00 0.00 0 -ATOM 379 O 1 1 23.733 23.024 1.663 0.00 0.00 0 -ATOM 380 H 1 1 24.800 24.052 2.776 0.00 0.00 0 -ATOM 381 H 1 1 24.693 22.618 0.198 0.00 0.00 0 -ATOM 382 O 1 1 20.789 18.440 9.443 0.00 0.00 0 -ATOM 383 H 1 1 20.766 17.257 7.881 0.00 0.00 0 -ATOM 384 H 1 1 21.896 17.345 10.385 0.00 0.00 0 -ATOM 385 O 1 1 21.574 17.493 17.838 0.00 0.00 0 -ATOM 386 H 1 1 20.597 18.955 17.218 0.00 0.00 0 -ATOM 387 H 1 1 22.538 16.874 16.251 0.00 0.00 0 -ATOM 388 O 1 1 19.168 14.748 24.131 0.00 0.00 0 -ATOM 389 H 1 1 19.711 16.390 23.712 0.00 0.00 0 -ATOM 390 H 1 1 17.429 14.695 24.403 0.00 0.00 0 -ATOM 391 O 1 1 22.149 20.198 24.977 0.00 0.00 0 -ATOM 392 H 1 1 21.639 20.924 26.486 0.00 0.00 0 -ATOM 393 H 1 1 22.656 21.657 24.411 0.00 0.00 0 -ATOM 394 O 1 1 20.565 20.792 29.600 0.00 0.00 0 -ATOM 395 H 1 1 22.264 20.409 30.214 0.00 0.00 0 -ATOM 396 H 1 1 20.548 22.408 30.597 0.00 0.00 0 -ATOM 397 O 1 1 20.802 26.547 9.615 0.00 0.00 0 -ATOM 398 H 1 1 20.099 27.984 8.338 0.00 0.00 0 -ATOM 399 H 1 1 21.277 27.539 11.325 0.00 0.00 0 -ATOM 400 O 1 1 16.283 23.589 7.779 0.00 0.00 0 -ATOM 401 H 1 1 16.093 21.973 6.712 0.00 0.00 0 -ATOM 402 H 1 1 17.901 22.971 8.154 0.00 0.00 0 -ATOM 403 O 1 1 18.469 29.798 13.568 0.00 0.00 0 -ATOM 404 H 1 1 19.712 31.216 13.506 0.00 0.00 0 -ATOM 405 H 1 1 16.872 30.343 14.396 0.00 0.00 0 -ATOM 406 O 1 1 18.790 21.712 16.060 0.00 0.00 0 -ATOM 407 H 1 1 19.878 23.090 16.485 0.00 0.00 0 -ATOM 408 H 1 1 17.201 22.326 15.819 0.00 0.00 0 -ATOM 409 O 1 1 21.747 26.084 16.349 0.00 0.00 0 -ATOM 410 H 1 1 20.783 27.021 15.300 0.00 0.00 0 -ATOM 411 H 1 1 22.705 27.328 17.206 0.00 0.00 0 -ATOM 412 O 1 1 20.769 26.211 32.050 0.00 0.00 0 -ATOM 413 H 1 1 21.488 27.404 33.328 0.00 0.00 0 -ATOM 414 H 1 1 18.989 26.710 32.145 0.00 0.00 0 -ATOM 415 O 1 1 19.820 29.181 5.559 0.00 0.00 0 -ATOM 416 H 1 1 20.991 29.509 4.109 0.00 0.00 0 -ATOM 417 H 1 1 19.431 31.018 6.221 0.00 0.00 0 -ATOM 418 O 1 1 19.240 33.867 7.993 0.00 0.00 0 -ATOM 419 H 1 1 19.107 35.039 6.604 0.00 0.00 0 -ATOM 420 H 1 1 20.697 33.671 9.063 0.00 0.00 0 -ATOM 421 O 1 1 22.511 34.976 15.793 0.00 0.00 0 -ATOM 422 H 1 1 23.716 36.163 16.603 0.00 0.00 0 -ATOM 423 H 1 1 21.699 36.150 14.467 0.00 0.00 0 -ATOM 424 O 1 1 22.622 30.284 19.069 0.00 0.00 0 -ATOM 425 H 1 1 22.049 31.351 17.725 0.00 0.00 0 -ATOM 426 H 1 1 24.411 30.773 19.576 0.00 0.00 0 -ATOM 427 O 1 1 18.639 33.611 28.369 0.00 0.00 0 -ATOM 428 H 1 1 18.226 32.159 29.103 0.00 0.00 0 -ATOM 429 H 1 1 19.906 33.008 27.158 0.00 0.00 0 -ATOM 430 O 1 1 22.520 1.325 31.926 0.00 0.00 0 -ATOM 431 H 1 1 22.803 2.668 30.796 0.00 0.00 0 -ATOM 432 H 1 1 21.045 0.425 31.122 0.00 0.00 0 -ATOM 433 O 1 1 21.754 3.789 1.159 0.00 0.00 0 -ATOM 434 H 1 1 22.085 2.785 -0.180 0.00 0.00 0 -ATOM 435 H 1 1 20.850 5.175 0.610 0.00 0.00 0 -ATOM 436 O 1 1 28.457 5.539 12.133 0.00 0.00 0 -ATOM 437 H 1 1 29.489 4.390 11.182 0.00 0.00 0 -ATOM 438 H 1 1 29.161 7.131 12.587 0.00 0.00 0 -ATOM 439 O 1 1 22.495 5.966 17.324 0.00 0.00 0 -ATOM 440 H 1 1 24.377 5.379 17.393 0.00 0.00 0 -ATOM 441 H 1 1 21.906 5.491 18.857 0.00 0.00 0 -ATOM 442 O 1 1 28.128 3.304 22.287 0.00 0.00 0 -ATOM 443 H 1 1 28.123 2.999 20.491 0.00 0.00 0 -ATOM 444 H 1 1 26.533 3.355 22.876 0.00 0.00 0 -ATOM 445 O 1 1 28.378 10.455 27.266 0.00 0.00 0 -ATOM 446 H 1 1 30.019 10.292 28.051 0.00 0.00 0 -ATOM 447 H 1 1 28.635 10.039 25.463 0.00 0.00 0 -ATOM 448 O 1 1 27.031 8.353 34.806 0.00 0.00 0 -ATOM 449 H 1 1 26.116 9.984 34.571 0.00 0.00 0 -ATOM 450 H 1 1 28.685 8.951 34.739 0.00 0.00 0 -ATOM 451 O 1 1 24.951 8.160 4.454 0.00 0.00 0 -ATOM 452 H 1 1 25.930 9.616 5.160 0.00 0.00 0 -ATOM 453 H 1 1 25.947 7.994 2.724 0.00 0.00 0 -ATOM 454 O 1 1 26.937 12.436 6.869 0.00 0.00 0 -ATOM 455 H 1 1 25.492 13.284 6.708 0.00 0.00 0 -ATOM 456 H 1 1 27.689 13.332 8.266 0.00 0.00 0 -ATOM 457 O 1 1 23.365 11.214 16.933 0.00 0.00 0 -ATOM 458 H 1 1 22.247 9.744 16.789 0.00 0.00 0 -ATOM 459 H 1 1 23.264 12.035 18.539 0.00 0.00 0 -ATOM 460 O 1 1 28.321 8.759 22.158 0.00 0.00 0 -ATOM 461 H 1 1 27.662 6.895 22.482 0.00 0.00 0 -ATOM 462 H 1 1 26.971 9.710 21.902 0.00 0.00 0 -ATOM 463 O 1 1 27.071 6.109 29.555 0.00 0.00 0 -ATOM 464 H 1 1 27.591 7.663 28.857 0.00 0.00 0 -ATOM 465 H 1 1 27.304 6.320 31.261 0.00 0.00 0 -ATOM 466 O 1 1 22.474 11.704 34.640 0.00 0.00 0 -ATOM 467 H 1 1 22.752 13.304 35.584 0.00 0.00 0 -ATOM 468 H 1 1 22.840 12.090 33.030 0.00 0.00 0 -ATOM 469 O 1 1 21.656 14.971 5.615 0.00 0.00 0 -ATOM 470 H 1 1 21.690 15.860 3.977 0.00 0.00 0 -ATOM 471 H 1 1 19.964 14.225 5.774 0.00 0.00 0 -ATOM 472 O 1 1 28.539 21.492 9.820 0.00 0.00 0 -ATOM 473 H 1 1 27.288 22.181 8.688 0.00 0.00 0 -ATOM 474 H 1 1 28.065 22.420 11.602 0.00 0.00 0 -ATOM 475 O 1 1 28.364 16.020 11.109 0.00 0.00 0 -ATOM 476 H 1 1 30.033 16.649 12.089 0.00 0.00 0 -ATOM 477 H 1 1 28.456 17.440 10.082 0.00 0.00 0 -ATOM 478 O 1 1 0.054 13.686 18.103 0.00 0.00 0 -ATOM 479 H 1 1 -1.714 12.928 18.841 0.00 0.00 0 -ATOM 480 H 1 1 1.008 12.429 17.383 0.00 0.00 0 -ATOM 481 O 1 1 24.636 12.894 29.957 0.00 0.00 0 -ATOM 482 H 1 1 25.906 13.914 31.183 0.00 0.00 0 -ATOM 483 H 1 1 25.641 11.609 29.162 0.00 0.00 0 -ATOM 484 O 1 1 21.548 17.250 0.749 0.00 0.00 0 -ATOM 485 H 1 1 21.843 19.026 0.905 0.00 0.00 0 -ATOM 486 H 1 1 20.385 16.716 -0.697 0.00 0.00 0 -ATOM 487 O 1 1 26.095 27.274 4.520 0.00 0.00 0 -ATOM 488 H 1 1 27.889 26.458 4.505 0.00 0.00 0 -ATOM 489 H 1 1 25.648 26.970 6.165 0.00 0.00 0 -ATOM 490 O 1 1 23.610 22.515 8.008 0.00 0.00 0 -ATOM 491 H 1 1 22.653 21.187 8.739 0.00 0.00 0 -ATOM 492 H 1 1 22.286 24.095 8.444 0.00 0.00 0 -ATOM 493 O 1 1 27.355 18.929 18.180 0.00 0.00 0 -ATOM 494 H 1 1 27.200 20.349 17.155 0.00 0.00 0 -ATOM 495 H 1 1 25.579 18.322 18.770 0.00 0.00 0 -ATOM 496 O 1 1 26.765 23.633 14.444 0.00 0.00 0 -ATOM 497 H 1 1 27.441 25.298 13.651 0.00 0.00 0 -ATOM 498 H 1 1 25.086 24.256 14.749 0.00 0.00 0 -ATOM 499 O 1 1 31.478 20.769 20.986 0.00 0.00 0 -ATOM 500 H 1 1 30.440 22.509 21.135 0.00 0.00 0 -ATOM 501 H 1 1 30.567 19.656 20.043 0.00 0.00 0 -ATOM 502 O 1 1 24.812 20.412 32.668 0.00 0.00 0 -ATOM 503 H 1 1 26.242 21.478 31.874 0.00 0.00 0 -ATOM 504 H 1 1 25.787 19.023 33.158 0.00 0.00 0 -ATOM 505 O 1 1 22.105 29.076 0.928 0.00 0.00 0 -ATOM 506 H 1 1 23.296 27.923 1.739 0.00 0.00 0 -ATOM 507 H 1 1 22.623 30.994 0.882 0.00 0.00 0 -ATOM 508 O 1 1 29.572 31.256 8.626 0.00 0.00 0 -ATOM 509 H 1 1 30.795 30.203 7.736 0.00 0.00 0 -ATOM 510 H 1 1 28.277 31.519 7.260 0.00 0.00 0 -ATOM 511 O 1 1 31.817 34.843 18.283 0.00 0.00 0 -ATOM 512 H 1 1 32.438 34.389 16.474 0.00 0.00 0 -ATOM 513 H 1 1 32.743 36.422 18.341 0.00 0.00 0 -ATOM 514 O 1 1 27.915 25.601 19.033 0.00 0.00 0 -ATOM 515 H 1 1 29.358 26.561 19.190 0.00 0.00 0 -ATOM 516 H 1 1 28.148 24.429 17.530 0.00 0.00 0 -ATOM 517 O 1 1 24.548 24.654 24.025 0.00 0.00 0 -ATOM 518 H 1 1 25.528 25.635 22.824 0.00 0.00 0 -ATOM 519 H 1 1 25.300 25.200 25.645 0.00 0.00 0 -ATOM 520 O 1 1 28.540 22.922 30.370 0.00 0.00 0 -ATOM 521 H 1 1 27.414 24.096 29.781 0.00 0.00 0 -ATOM 522 H 1 1 29.674 23.914 31.873 0.00 0.00 0 -ATOM 523 O 1 1 24.969 33.623 1.014 0.00 0.00 0 -ATOM 524 H 1 1 26.521 33.058 1.518 0.00 0.00 0 -ATOM 525 H 1 1 24.990 34.322 -0.683 0.00 0.00 0 -ATOM 526 O 1 1 23.075 32.171 11.324 0.00 0.00 0 -ATOM 527 H 1 1 23.316 32.775 13.097 0.00 0.00 0 -ATOM 528 H 1 1 24.460 33.203 10.662 0.00 0.00 0 -ATOM 529 O 1 1 27.497 2.736 17.224 0.00 0.00 0 -ATOM 530 H 1 1 28.397 3.415 15.715 0.00 0.00 0 -ATOM 531 H 1 1 28.234 1.233 17.412 0.00 0.00 0 -ATOM 532 O 1 1 26.369 33.060 22.077 0.00 0.00 0 -ATOM 533 H 1 1 26.170 34.746 22.264 0.00 0.00 0 -ATOM 534 H 1 1 27.592 32.404 23.321 0.00 0.00 0 -ATOM 535 O 1 1 30.221 30.950 25.843 0.00 0.00 0 -ATOM 536 H 1 1 30.305 29.038 26.208 0.00 0.00 0 -ATOM 537 H 1 1 30.363 31.979 27.414 0.00 0.00 0 -ATOM 538 O 1 1 24.973 26.732 28.607 0.00 0.00 0 -ATOM 539 H 1 1 25.385 28.369 29.248 0.00 0.00 0 -ATOM 540 H 1 1 23.330 26.597 29.234 0.00 0.00 0 -ATOM 541 O 1 1 32.165 4.857 2.258 0.00 0.00 0 -ATOM 542 H 1 1 32.417 6.195 1.157 0.00 0.00 0 -ATOM 543 H 1 1 32.615 3.727 1.112 0.00 0.00 0 -ATOM 544 O 1 1 28.067 3.533 5.217 0.00 0.00 0 -ATOM 545 H 1 1 26.960 4.447 4.158 0.00 0.00 0 -ATOM 546 H 1 1 29.875 3.863 4.448 0.00 0.00 0 -ATOM 547 O 1 1 33.279 2.782 13.028 0.00 0.00 0 -ATOM 548 H 1 1 33.708 3.955 11.817 0.00 0.00 0 -ATOM 549 H 1 1 33.656 3.545 14.631 0.00 0.00 0 -ATOM 550 O 1 1 34.278 4.944 17.492 0.00 0.00 0 -ATOM 551 H 1 1 33.438 6.563 17.876 0.00 0.00 0 -ATOM 552 H 1 1 34.906 4.452 18.995 0.00 0.00 0 -ATOM 553 O 1 1 32.363 1.908 26.092 0.00 0.00 0 -ATOM 554 H 1 1 31.941 1.683 24.268 0.00 0.00 0 -ATOM 555 H 1 1 33.850 1.390 26.904 0.00 0.00 0 -ATOM 556 O 1 1 27.982 0.418 28.241 0.00 0.00 0 -ATOM 557 H 1 1 27.516 2.080 28.309 0.00 0.00 0 -ATOM 558 H 1 1 29.593 0.176 27.299 0.00 0.00 0 -ATOM 559 O 1 1 28.845 14.672 2.724 0.00 0.00 0 -ATOM 560 H 1 1 27.963 13.930 4.139 0.00 0.00 0 -ATOM 561 H 1 1 30.386 15.714 3.379 0.00 0.00 0 -ATOM 562 O 1 1 28.083 10.618 14.298 0.00 0.00 0 -ATOM 563 H 1 1 28.623 12.160 13.293 0.00 0.00 0 -ATOM 564 H 1 1 26.486 11.015 15.379 0.00 0.00 0 -ATOM 565 O 1 1 33.867 10.545 13.306 0.00 0.00 0 -ATOM 566 H 1 1 35.165 9.612 13.810 0.00 0.00 0 -ATOM 567 H 1 1 33.615 10.270 11.513 0.00 0.00 0 -ATOM 568 O 1 1 31.790 9.696 18.223 0.00 0.00 0 -ATOM 569 H 1 1 30.484 9.334 19.421 0.00 0.00 0 -ATOM 570 H 1 1 30.834 10.096 16.929 0.00 0.00 0 -ATOM 571 O 1 1 30.141 15.006 21.532 0.00 0.00 0 -ATOM 572 H 1 1 28.565 15.594 22.099 0.00 0.00 0 -ATOM 573 H 1 1 30.942 14.253 23.077 0.00 0.00 0 -ATOM 574 O 1 1 32.798 10.732 30.680 0.00 0.00 0 -ATOM 575 H 1 1 34.073 9.528 30.799 0.00 0.00 0 -ATOM 576 H 1 1 32.991 11.512 28.983 0.00 0.00 0 -ATOM 577 O 1 1 33.652 16.265 5.086 0.00 0.00 0 -ATOM 578 H 1 1 35.399 16.239 4.730 0.00 0.00 0 -ATOM 579 H 1 1 33.503 17.939 5.631 0.00 0.00 0 -ATOM 580 O 1 1 31.947 10.799 7.943 0.00 0.00 0 -ATOM 581 H 1 1 29.894 10.549 7.619 0.00 0.00 0 -ATOM 582 H 1 1 32.271 12.414 7.075 0.00 0.00 0 -ATOM 583 O 1 1 0.329 15.516 11.746 0.00 0.00 0 -ATOM 584 H 1 1 -0.446 14.249 12.939 0.00 0.00 0 -ATOM 585 H 1 1 -0.685 17.018 11.935 0.00 0.00 0 -ATOM 586 O 1 1 4.262 19.165 14.308 0.00 0.00 0 -ATOM 587 H 1 1 3.579 17.691 14.920 0.00 0.00 0 -ATOM 588 H 1 1 5.723 19.183 15.204 0.00 0.00 0 -ATOM 589 O 1 1 32.995 13.546 25.948 0.00 0.00 0 -ATOM 590 H 1 1 32.167 15.060 26.787 0.00 0.00 0 -ATOM 591 H 1 1 34.425 13.800 25.007 0.00 0.00 0 -ATOM 592 O 1 1 1.773 13.524 34.037 0.00 0.00 0 -ATOM 593 H 1 1 0.227 14.409 33.446 0.00 0.00 0 -ATOM 594 H 1 1 2.167 14.670 35.511 0.00 0.00 0 -ATOM 595 O 1 1 33.029 20.529 7.247 0.00 0.00 0 -ATOM 596 H 1 1 34.388 21.414 8.003 0.00 0.00 0 -ATOM 597 H 1 1 31.451 20.831 8.182 0.00 0.00 0 -ATOM 598 O 1 1 2.037 24.250 10.251 0.00 0.00 0 -ATOM 599 H 1 1 3.743 25.008 9.876 0.00 0.00 0 -ATOM 600 H 1 1 1.894 25.043 11.903 0.00 0.00 0 -ATOM 601 O 1 1 32.753 19.259 13.976 0.00 0.00 0 -ATOM 602 H 1 1 32.792 20.886 13.792 0.00 0.00 0 -ATOM 603 H 1 1 34.334 18.799 14.976 0.00 0.00 0 -ATOM 604 O 1 1 0.396 18.673 18.699 0.00 0.00 0 -ATOM 605 H 1 1 -1.211 18.950 19.127 0.00 0.00 0 -ATOM 606 H 1 1 0.469 16.977 18.436 0.00 0.00 0 -ATOM 607 O 1 1 30.855 18.370 27.959 0.00 0.00 0 -ATOM 608 H 1 1 29.759 19.681 28.690 0.00 0.00 0 -ATOM 609 H 1 1 32.103 19.477 26.763 0.00 0.00 0 -ATOM 610 O 1 1 27.723 15.992 33.091 0.00 0.00 0 -ATOM 611 H 1 1 29.390 16.423 32.192 0.00 0.00 0 -ATOM 612 H 1 1 27.801 15.859 34.804 0.00 0.00 0 -ATOM 613 O 1 1 31.068 27.895 3.348 0.00 0.00 0 -ATOM 614 H 1 1 32.517 27.825 4.610 0.00 0.00 0 -ATOM 615 H 1 1 31.529 29.459 2.324 0.00 0.00 0 -ATOM 616 O 1 1 35.039 28.008 6.663 0.00 0.00 0 -ATOM 617 H 1 1 35.966 26.934 7.683 0.00 0.00 0 -ATOM 618 H 1 1 36.055 28.336 5.336 0.00 0.00 0 -ATOM 619 O 1 1 29.356 28.196 13.025 0.00 0.00 0 -ATOM 620 H 1 1 29.210 29.335 14.589 0.00 0.00 0 -ATOM 621 H 1 1 28.874 29.629 11.867 0.00 0.00 0 -ATOM 622 O 1 1 32.386 28.434 18.961 0.00 0.00 0 -ATOM 623 H 1 1 33.368 28.574 20.411 0.00 0.00 0 -ATOM 624 H 1 1 33.410 27.406 17.949 0.00 0.00 0 -ATOM 625 O 1 1 30.898 25.390 25.799 0.00 0.00 0 -ATOM 626 H 1 1 32.369 25.913 24.580 0.00 0.00 0 -ATOM 627 H 1 1 31.317 24.075 27.029 0.00 0.00 0 -ATOM 628 O 1 1 32.259 25.611 33.104 0.00 0.00 0 -ATOM 629 H 1 1 32.238 25.736 34.806 0.00 0.00 0 -ATOM 630 H 1 1 33.920 25.042 32.775 0.00 0.00 0 -ATOM 631 O 1 1 30.290 32.645 1.341 0.00 0.00 0 -ATOM 632 H 1 1 29.949 32.793 -0.430 0.00 0.00 0 -ATOM 633 H 1 1 31.762 33.340 1.847 0.00 0.00 0 -ATOM 634 O 1 1 25.536 34.235 6.469 0.00 0.00 0 -ATOM 635 H 1 1 25.716 36.059 6.651 0.00 0.00 0 -ATOM 636 H 1 1 25.283 33.866 4.895 0.00 0.00 0 -ATOM 637 O 1 1 31.674 33.161 13.106 0.00 0.00 0 -ATOM 638 H 1 1 31.793 34.863 13.281 0.00 0.00 0 -ATOM 639 H 1 1 30.425 32.928 11.783 0.00 0.00 0 -ATOM 640 O 1 1 33.844 32.668 22.296 0.00 0.00 0 -ATOM 641 H 1 1 32.750 32.234 23.524 0.00 0.00 0 -ATOM 642 H 1 1 32.917 32.875 20.736 0.00 0.00 0 -ATOM 643 O 1 1 31.603 30.542 30.805 0.00 0.00 0 -ATOM 644 H 1 1 33.451 30.804 30.468 0.00 0.00 0 -ATOM 645 H 1 1 31.575 28.816 31.756 0.00 0.00 0 -ATOM 646 O 1 1 26.295 31.235 30.599 0.00 0.00 0 -ATOM 647 H 1 1 27.834 30.515 30.607 0.00 0.00 0 -ATOM 648 H 1 1 26.362 32.920 29.856 0.00 0.00 0 -END diff --git a/tools/i-pi/examples/lammps/h2o-pimd/data.water b/tools/i-pi/examples/lammps/h2o-pimd/data.water deleted file mode 100644 index 13c75e9933..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd/data.water +++ /dev/null @@ -1,1331 +0,0 @@ -LAMMPS Description - - 648 atoms - 432 bonds - 216 angles - - 2 atom types - 1 bond types - 1 angle types - - 0 35.233 xlo xhi - 0 35.233 ylo yhi - 0 35.233 zlo zhi - -Masses - - 1 15.9994 - 2 1.0080 - -Bond Coeffs - - 1 1.78 0.2708585 -0.327738785 0.231328959 - -Angle Coeffs - - 1 0.0700 107.400000 - -Atoms - - 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 - 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 - 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 - 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000 - 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 - 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 - 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 - 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 - 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 - 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 - 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 - 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 - 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 - 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 - 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 - 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001 - 17 6 2 0.5564 2.39200001 2.89799999 34.84600000 - 18 6 2 0.5564 0.81400000 0.53200001 35.83600000 - 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999 - 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000 - 21 7 2 0.5564 30.91999999 11.59399999 1.67700000 - 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000 - 23 8 2 0.5564 0.30500000 10.64300001 2.79300000 - 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000 - 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000 - 26 9 2 0.5564 33.61600000 7.67300000 8.85700000 - 27 9 2 0.5564 35.11500000 5.25999999 7.61800001 - 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999 - 29 10 2 0.5564 31.62400000 6.90800001 23.52100001 - 30 10 2 0.5564 32.54400000 4.99000000 24.98200000 - 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000 - 32 11 2 0.5564 1.85600000 10.17500000 25.57899999 - 33 11 2 0.5564 0.51900000 8.09899999 26.38599999 - 34 12 1 -1.1128 2.05400000 8.66000000 32.51499999 - 35 12 2 0.5564 2.16699999 8.72700000 30.49400000 - 36 12 2 0.5564 2.37400001 10.51300000 33.03799999 - 37 13 1 -1.1128 3.40200000 16.63900001 3.00800000 - 38 13 2 0.5564 4.12700001 15.87200001 4.44600001 - 39 13 2 0.5564 2.90500001 18.33899999 3.15999999 - 40 14 1 -1.1128 4.22200000 15.44400000 8.07200000 - 41 14 2 0.5564 5.21100000 16.75600000 8.29900001 - 42 14 2 0.5564 2.56000000 15.49200001 8.86000000 - 43 15 1 -1.1128 2.83100000 9.24599999 16.48800000 - 44 15 2 0.5564 2.86900001 8.02300001 18.05000000 - 45 15 2 0.5564 3.96000000 8.46700001 15.15400000 - 46 16 1 -1.1128 5.56300000 6.00300000 20.90700000 - 47 16 2 0.5564 4.65300000 4.63800000 21.48000000 - 48 16 2 0.5564 6.40500000 6.20800000 22.52899999 - 49 17 1 -1.1128 2.08700001 13.37000000 22.91299999 - 50 17 2 0.5564 2.83200000 14.80400001 23.42200000 - 51 17 2 0.5564 1.43400000 13.50900000 21.19599999 - 52 18 1 -1.1128 3.36900000 17.88600000 25.10900001 - 53 18 2 0.5564 3.65500000 17.20000000 26.76599999 - 54 18 2 0.5564 4.77200001 18.97699999 24.49999999 - 55 19 1 -1.1128 34.76400000 20.80300000 0.94800001 - 56 19 2 0.5564 35.20999999 21.26700001 2.81599999 - 57 19 2 0.5564 35.96200001 21.72599999 0.13099999 - 58 20 1 -1.1128 2.83600000 24.17799999 15.22900000 - 59 20 2 0.5564 2.79500000 22.34599999 14.87600001 - 60 20 2 0.5564 2.41399999 24.11500000 17.13000001 - 61 21 1 -1.1128 33.00000000 24.48100000 15.23000000 - 62 21 2 0.5564 34.63999999 24.80400001 15.01299999 - 63 21 2 0.5564 32.40100000 25.76400000 14.29500001 - 64 22 1 -1.1128 0.40399999 26.77900001 23.39999999 - 65 22 2 0.5564 1.35300001 27.24800000 24.98700001 - 66 22 2 0.5564 1.54600001 28.05000000 22.31700001 - 67 23 1 -1.1128 34.22200000 21.38000000 25.41799999 - 68 23 2 0.5564 35.66899999 20.15100000 25.31700001 - 69 23 2 0.5564 32.96000000 21.18000000 23.99200000 - 70 24 1 -1.1128 33.25900000 17.43800000 32.48000000 - 71 24 2 0.5564 33.31399999 18.78200000 33.88300001 - 72 24 2 0.5564 32.74300001 18.18100001 30.87100000 - 73 25 1 -1.1128 4.46300000 21.97900000 3.93600000 - 74 25 2 0.5564 5.85600000 23.08400001 3.39999999 - 75 25 2 0.5564 3.98600000 22.18000000 5.60200000 - 76 26 1 -1.1128 6.25800000 25.85100001 8.52000000 - 77 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b/tools/i-pi/examples/lammps/h2o-pimd/in.water deleted file mode 100644 index d1d9048cc8..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd/in.water +++ /dev/null @@ -1,32 +0,0 @@ -units electron -atom_style full - -#pair_style lj/cut/coul/long 17.01 -pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 -#bond_style harmonic -bond_style class2 -angle_style harmonic -#kspace_style pppm 0.0001 -kspace_style pppm/tip4p 0.0001 - -read_data data.water -pair_coeff * * 0 0 -pair_coeff 1 1 0.000295147 5.96946 - -neighbor 2.0 bin - -timestep 0.00025 - -#velocity all create 298.0 2345187 - -#thermo_style multi -#thermo 1 - -#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 -#fix 1 all nve -fix 1 all ipi no_rpc 32345 unix - -#dump 1 all xyz 25 dump.xyz - -run 100000000 - diff --git a/tools/i-pi/examples/lammps/h2o-pimd/input.xml b/tools/i-pi/examples/lammps/h2o-pimd/input.xml deleted file mode 100644 index 36bcd38d2e..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd/input.xml +++ /dev/null @@ -1,24 +0,0 @@ - - - water_298K.pdb - 298 - - - [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] - positions - - 500000 - 32345 - - -
no_rpc
- - - - - 25 - - 0.25 - 298 - - diff --git a/tools/i-pi/examples/lammps/h2o-pimd/water_298K.pdb b/tools/i-pi/examples/lammps/h2o-pimd/water_298K.pdb deleted file mode 100644 index e8509c868e..0000000000 --- a/tools/i-pi/examples/lammps/h2o-pimd/water_298K.pdb +++ /dev/null @@ -1,650 +0,0 @@ -CRYST 35.233 35.233 35.233 90.00 90.00 90.00 P 1 1 -ATOM 1 O 1 1 3.846 5.672 1.323 0.00 0.00 0 -ATOM 2 H 1 1 2.979 7.054 0.857 0.00 0.00 0 -ATOM 3 H 1 1 5.525 5.697 0.451 0.00 0.00 0 -ATOM 4 O 1 1 34.557 34.341 3.078 0.00 0.00 0 -ATOM 5 H 1 1 33.722 34.689 4.840 0.00 0.00 0 -ATOM 6 H 1 1 36.029 33.220 3.711 0.00 0.00 0 -ATOM 7 O 1 1 5.591 1.963 13.477 0.00 0.00 0 -ATOM 8 H 1 1 7.265 1.864 13.851 0.00 0.00 0 -ATOM 9 H 1 1 5.009 3.555 13.916 0.00 0.00 0 -ATOM 10 O 1 1 1.060 2.061 21.718 0.00 0.00 0 -ATOM 11 H 1 1 0.757 0.261 21.820 0.00 0.00 0 -ATOM 12 H 1 1 0.213 3.013 23.047 0.00 0.00 0 -ATOM 13 O 1 1 1.200 1.337 29.006 0.00 0.00 0 -ATOM 14 H 1 1 0.818 1.884 30.732 0.00 0.00 0 -ATOM 15 H 1 1 2.883 1.825 29.011 0.00 0.00 0 -ATOM 16 O 1 1 1.331 1.386 34.306 0.00 0.00 0 -ATOM 17 H 1 1 2.392 2.898 34.846 0.00 0.00 0 -ATOM 18 H 1 1 0.814 0.532 35.836 0.00 0.00 0 -ATOM 19 O 1 1 31.451 10.201 0.726 0.00 0.00 0 -ATOM 20 H 1 1 32.282 10.877 -0.750 0.00 0.00 0 -ATOM 21 H 1 1 30.920 11.594 1.677 0.00 0.00 0 -ATOM 22 O 1 1 0.836 10.808 4.298 0.00 0.00 0 -ATOM 23 H 1 1 0.305 10.643 2.793 0.00 0.00 0 -ATOM 24 H 1 1 -0.356 10.334 5.524 0.00 0.00 0 -ATOM 25 O 1 1 34.381 5.979 9.194 0.00 0.00 0 -ATOM 26 H 1 1 33.616 7.673 8.857 0.00 0.00 0 -ATOM 27 H 1 1 35.115 5.260 7.618 0.00 0.00 0 -ATOM 28 O 1 1 33.212 6.480 24.278 0.00 0.00 0 -ATOM 29 H 1 1 31.624 6.908 23.521 0.00 0.00 0 -ATOM 30 H 1 1 32.544 4.990 24.982 0.00 0.00 0 -ATOM 31 O 1 1 1.992 9.002 26.863 0.00 0.00 0 -ATOM 32 H 1 1 1.856 10.175 25.579 0.00 0.00 0 -ATOM 33 H 1 1 0.519 8.099 26.386 0.00 0.00 0 -ATOM 34 O 1 1 2.054 8.660 32.515 0.00 0.00 0 -ATOM 35 H 1 1 2.167 8.727 30.494 0.00 0.00 0 -ATOM 36 H 1 1 2.374 10.513 33.038 0.00 0.00 0 -ATOM 37 O 1 1 3.402 16.639 3.008 0.00 0.00 0 -ATOM 38 H 1 1 4.127 15.872 4.446 0.00 0.00 0 -ATOM 39 H 1 1 2.905 18.339 3.160 0.00 0.00 0 -ATOM 40 O 1 1 4.222 15.444 8.072 0.00 0.00 0 -ATOM 41 H 1 1 5.211 16.756 8.299 0.00 0.00 0 -ATOM 42 H 1 1 2.560 15.492 8.860 0.00 0.00 0 -ATOM 43 O 1 1 2.831 9.246 16.488 0.00 0.00 0 -ATOM 44 H 1 1 2.869 8.023 18.050 0.00 0.00 0 -ATOM 45 H 1 1 3.960 8.467 15.154 0.00 0.00 0 -ATOM 46 O 1 1 5.563 6.003 20.907 0.00 0.00 0 -ATOM 47 H 1 1 4.653 4.638 21.480 0.00 0.00 0 -ATOM 48 H 1 1 6.405 6.208 22.529 0.00 0.00 0 -ATOM 49 O 1 1 2.087 13.370 22.913 0.00 0.00 0 -ATOM 50 H 1 1 2.832 14.804 23.422 0.00 0.00 0 -ATOM 51 H 1 1 1.434 13.509 21.196 0.00 0.00 0 -ATOM 52 O 1 1 3.369 17.886 25.109 0.00 0.00 0 -ATOM 53 H 1 1 3.655 17.200 26.766 0.00 0.00 0 -ATOM 54 H 1 1 4.772 18.977 24.500 0.00 0.00 0 -ATOM 55 O 1 1 34.764 20.803 0.948 0.00 0.00 0 -ATOM 56 H 1 1 35.210 21.267 2.816 0.00 0.00 0 -ATOM 57 H 1 1 35.962 21.726 0.131 0.00 0.00 0 -ATOM 58 O 1 1 2.836 24.178 15.229 0.00 0.00 0 -ATOM 59 H 1 1 2.795 22.346 14.876 0.00 0.00 0 -ATOM 60 H 1 1 2.414 24.115 17.130 0.00 0.00 0 -ATOM 61 O 1 1 33.000 24.481 15.230 0.00 0.00 0 -ATOM 62 H 1 1 34.640 24.804 15.013 0.00 0.00 0 -ATOM 63 H 1 1 32.401 25.764 14.295 0.00 0.00 0 -ATOM 64 O 1 1 0.404 26.779 23.400 0.00 0.00 0 -ATOM 65 H 1 1 1.353 27.248 24.987 0.00 0.00 0 -ATOM 66 H 1 1 1.546 28.050 22.317 0.00 0.00 0 -ATOM 67 O 1 1 34.222 21.380 25.418 0.00 0.00 0 -ATOM 68 H 1 1 35.669 20.151 25.317 0.00 0.00 0 -ATOM 69 H 1 1 32.960 21.180 23.992 0.00 0.00 0 -ATOM 70 O 1 1 33.259 17.438 32.480 0.00 0.00 0 -ATOM 71 H 1 1 33.314 18.782 33.883 0.00 0.00 0 -ATOM 72 H 1 1 32.743 18.181 30.871 0.00 0.00 0 -ATOM 73 O 1 1 4.463 21.979 3.936 0.00 0.00 0 -ATOM 74 H 1 1 5.856 23.084 3.400 0.00 0.00 0 -ATOM 75 H 1 1 3.986 22.180 5.602 0.00 0.00 0 -ATOM 76 O 1 1 6.258 25.851 8.520 0.00 0.00 0 -ATOM 77 H 1 1 5.767 27.693 8.476 0.00 0.00 0 -ATOM 78 H 1 1 7.202 25.506 10.186 0.00 0.00 0 -ATOM 79 O 1 1 0.601 29.737 12.747 0.00 0.00 0 -ATOM 80 H 1 1 -0.685 30.842 12.350 0.00 0.00 0 -ATOM 81 H 1 1 1.336 30.716 14.031 0.00 0.00 0 -ATOM 82 O 1 1 7.563 28.191 24.333 0.00 0.00 0 -ATOM 83 H 1 1 9.201 28.828 24.684 0.00 0.00 0 -ATOM 84 H 1 1 7.381 27.621 22.799 0.00 0.00 0 -ATOM 85 O 1 1 3.653 27.109 27.772 0.00 0.00 0 -ATOM 86 H 1 1 5.126 27.015 26.772 0.00 0.00 0 -ATOM 87 H 1 1 3.031 28.756 27.698 0.00 0.00 0 -ATOM 88 O 1 1 2.596 23.991 32.476 0.00 0.00 0 -ATOM 89 H 1 1 2.879 24.791 30.859 0.00 0.00 0 -ATOM 90 H 1 1 4.003 22.913 32.701 0.00 0.00 0 -ATOM 91 O 1 1 3.083 31.317 3.644 0.00 0.00 0 -ATOM 92 H 1 1 4.133 30.589 2.539 0.00 0.00 0 -ATOM 93 H 1 1 4.218 32.173 5.037 0.00 0.00 0 -ATOM 94 O 1 1 4.661 30.555 9.368 0.00 0.00 0 -ATOM 95 H 1 1 3.184 29.843 10.132 0.00 0.00 0 -ATOM 96 H 1 1 4.358 32.448 9.126 0.00 0.00 0 -ATOM 97 O 1 1 3.465 32.537 15.778 0.00 0.00 0 -ATOM 98 H 1 1 5.072 31.819 15.903 0.00 0.00 0 -ATOM 99 H 1 1 4.055 34.257 15.284 0.00 0.00 0 -ATOM 100 O 1 1 4.215 29.153 20.317 0.00 0.00 0 -ATOM 101 H 1 1 3.658 30.176 18.842 0.00 0.00 0 -ATOM 102 H 1 1 4.959 30.291 21.449 0.00 0.00 0 -ATOM 103 O 1 1 1.126 31.333 28.768 0.00 0.00 0 -ATOM 104 H 1 1 2.395 31.124 29.925 0.00 0.00 0 -ATOM 105 H 1 1 0.768 33.092 28.898 0.00 0.00 0 -ATOM 106 O 1 1 4.881 32.616 32.302 0.00 0.00 0 -ATOM 107 H 1 1 6.588 32.911 31.725 0.00 0.00 0 -ATOM 108 H 1 1 4.486 34.037 33.249 0.00 0.00 0 -ATOM 109 O 1 1 8.962 5.556 0.151 0.00 0.00 0 -ATOM 110 H 1 1 9.652 6.991 0.859 0.00 0.00 0 -ATOM 111 H 1 1 9.173 4.477 1.645 0.00 0.00 0 -ATOM 112 O 1 1 1.833 3.518 5.679 0.00 0.00 0 -ATOM 113 H 1 1 2.889 2.731 6.788 0.00 0.00 0 -ATOM 114 H 1 1 2.789 4.187 4.147 0.00 0.00 0 -ATOM 115 O 1 1 10.510 34.726 13.073 0.00 0.00 0 -ATOM 116 H 1 1 11.920 34.118 11.919 0.00 0.00 0 -ATOM 117 H 1 1 11.295 34.968 14.741 0.00 0.00 0 -ATOM 118 O 1 1 7.212 0.042 22.454 0.00 0.00 0 -ATOM 119 H 1 1 6.924 0.470 24.172 0.00 0.00 0 -ATOM 120 H 1 1 8.319 1.228 21.653 0.00 0.00 0 -ATOM 121 O 1 1 6.365 2.010 27.544 0.00 0.00 0 -ATOM 122 H 1 1 5.954 3.585 26.852 0.00 0.00 0 -ATOM 123 H 1 1 7.758 2.549 28.696 0.00 0.00 0 -ATOM 124 O 1 1 10.833 3.140 30.787 0.00 0.00 0 -ATOM 125 H 1 1 12.697 2.975 30.867 0.00 0.00 0 -ATOM 126 H 1 1 10.389 3.700 32.404 0.00 0.00 0 -ATOM 127 O 1 1 8.684 9.342 3.912 0.00 0.00 0 -ATOM 128 H 1 1 6.985 9.256 4.773 0.00 0.00 0 -ATOM 129 H 1 1 8.684 10.809 3.011 0.00 0.00 0 -ATOM 130 O 1 1 4.873 9.919 7.707 0.00 0.00 0 -ATOM 131 H 1 1 3.698 9.771 6.194 0.00 0.00 0 -ATOM 132 H 1 1 5.047 11.961 7.624 0.00 0.00 0 -ATOM 133 O 1 1 10.031 5.018 9.699 0.00 0.00 0 -ATOM 134 H 1 1 9.675 3.382 10.340 0.00 0.00 0 -ATOM 135 H 1 1 9.132 5.987 10.825 0.00 0.00 0 -ATOM 136 O 1 1 11.246 3.918 21.929 0.00 0.00 0 -ATOM 137 H 1 1 12.614 2.770 22.341 0.00 0.00 0 -ATOM 138 H 1 1 12.073 5.686 21.497 0.00 0.00 0 -ATOM 139 O 1 1 6.825 7.164 25.708 0.00 0.00 0 -ATOM 140 H 1 1 8.036 8.374 25.980 0.00 0.00 0 -ATOM 141 H 1 1 5.206 7.900 25.891 0.00 0.00 0 -ATOM 142 O 1 1 10.171 12.811 0.295 0.00 0.00 0 -ATOM 143 H 1 1 10.033 12.818 -1.609 0.00 0.00 0 -ATOM 144 H 1 1 9.880 14.492 0.480 0.00 0.00 0 -ATOM 145 O 1 1 8.190 17.402 1.253 0.00 0.00 0 -ATOM 146 H 1 1 9.472 18.531 1.253 0.00 0.00 0 -ATOM 147 H 1 1 6.351 17.817 1.568 0.00 0.00 0 -ATOM 148 O 1 1 11.233 16.188 8.299 0.00 0.00 0 -ATOM 149 H 1 1 10.291 17.689 8.166 0.00 0.00 0 -ATOM 150 H 1 1 12.768 17.123 8.733 0.00 0.00 0 -ATOM 151 O 1 1 6.386 8.002 12.846 0.00 0.00 0 -ATOM 152 H 1 1 7.701 8.896 13.655 0.00 0.00 0 -ATOM 153 H 1 1 5.591 8.877 11.519 0.00 0.00 0 -ATOM 154 O 1 1 8.184 10.419 18.848 0.00 0.00 0 -ATOM 155 H 1 1 9.498 9.434 19.905 0.00 0.00 0 -ATOM 156 H 1 1 6.882 9.027 18.948 0.00 0.00 0 -ATOM 157 O 1 1 10.806 14.431 21.328 0.00 0.00 0 -ATOM 158 H 1 1 9.177 13.531 20.670 0.00 0.00 0 -ATOM 159 H 1 1 11.344 15.696 20.448 0.00 0.00 0 -ATOM 160 O 1 1 9.237 13.928 30.341 0.00 0.00 0 -ATOM 161 H 1 1 10.779 14.839 30.522 0.00 0.00 0 -ATOM 162 H 1 1 9.965 13.192 28.899 0.00 0.00 0 -ATOM 163 O 1 1 10.918 21.707 1.864 0.00 0.00 0 -ATOM 164 H 1 1 10.280 23.449 2.279 0.00 0.00 0 -ATOM 165 H 1 1 12.708 21.456 1.749 0.00 0.00 0 -ATOM 166 O 1 1 9.353 16.125 13.927 0.00 0.00 0 -ATOM 167 H 1 1 9.938 17.594 14.618 0.00 0.00 0 -ATOM 168 H 1 1 9.518 16.360 12.244 0.00 0.00 0 -ATOM 169 O 1 1 10.371 11.107 14.268 0.00 0.00 0 -ATOM 170 H 1 1 9.644 10.406 15.859 0.00 0.00 0 -ATOM 171 H 1 1 9.434 12.523 14.117 0.00 0.00 0 -ATOM 172 O 1 1 3.351 22.769 20.196 0.00 0.00 0 -ATOM 173 H 1 1 2.055 23.686 21.503 0.00 0.00 0 -ATOM 174 H 1 1 2.452 21.401 19.413 0.00 0.00 0 -ATOM 175 O 1 1 6.836 21.329 23.199 0.00 0.00 0 -ATOM 176 H 1 1 8.249 20.848 22.320 0.00 0.00 0 -ATOM 177 H 1 1 5.668 21.841 21.886 0.00 0.00 0 -ATOM 178 O 1 1 4.604 15.649 30.043 0.00 0.00 0 -ATOM 179 H 1 1 6.453 15.217 30.207 0.00 0.00 0 -ATOM 180 H 1 1 3.822 14.762 31.562 0.00 0.00 0 -ATOM 181 O 1 1 7.125 19.976 9.421 0.00 0.00 0 -ATOM 182 H 1 1 5.918 20.453 10.730 0.00 0.00 0 -ATOM 183 H 1 1 8.099 21.496 9.491 0.00 0.00 0 -ATOM 184 O 1 1 9.063 25.912 13.186 0.00 0.00 0 -ATOM 185 H 1 1 10.350 26.572 12.367 0.00 0.00 0 -ATOM 186 H 1 1 9.680 24.367 13.697 0.00 0.00 0 -ATOM 187 O 1 1 8.022 22.343 17.042 0.00 0.00 0 -ATOM 188 H 1 1 9.144 23.367 18.074 0.00 0.00 0 -ATOM 189 H 1 1 6.562 23.462 16.852 0.00 0.00 0 -ATOM 190 O 1 1 10.762 26.285 19.963 0.00 0.00 0 -ATOM 191 H 1 1 11.036 27.966 20.538 0.00 0.00 0 -ATOM 192 H 1 1 11.078 25.401 21.456 0.00 0.00 0 -ATOM 193 O 1 1 9.158 22.902 28.391 0.00 0.00 0 -ATOM 194 H 1 1 8.219 23.528 27.085 0.00 0.00 0 -ATOM 195 H 1 1 8.089 21.760 29.509 0.00 0.00 0 -ATOM 196 O 1 1 6.219 20.158 31.921 0.00 0.00 0 -ATOM 197 H 1 1 5.635 18.511 31.161 0.00 0.00 0 -ATOM 198 H 1 1 7.530 19.624 33.071 0.00 0.00 0 -ATOM 199 O 1 1 11.191 31.509 2.617 0.00 0.00 0 -ATOM 200 H 1 1 10.460 32.214 4.108 0.00 0.00 0 -ATOM 201 H 1 1 13.176 31.751 2.577 0.00 0.00 0 -ATOM 202 O 1 1 4.748 0.055 8.605 0.00 0.00 0 -ATOM 203 H 1 1 5.380 0.517 10.183 0.00 0.00 0 -ATOM 204 H 1 1 6.050 -0.306 7.480 0.00 0.00 0 -ATOM 205 O 1 1 8.695 30.809 15.731 0.00 0.00 0 -ATOM 206 H 1 1 9.189 32.103 14.495 0.00 0.00 0 -ATOM 207 H 1 1 8.447 29.069 14.868 0.00 0.00 0 -ATOM 208 O 1 1 10.128 31.402 20.766 0.00 0.00 0 -ATOM 209 H 1 1 9.456 30.905 19.155 0.00 0.00 0 -ATOM 210 H 1 1 9.020 32.731 21.415 0.00 0.00 0 -ATOM 211 O 1 1 12.238 30.162 25.837 0.00 0.00 0 -ATOM 212 H 1 1 11.418 30.908 27.110 0.00 0.00 0 -ATOM 213 H 1 1 12.396 31.331 24.678 0.00 0.00 0 -ATOM 214 O 1 1 10.395 32.537 30.624 0.00 0.00 0 -ATOM 215 H 1 1 11.042 34.339 30.751 0.00 0.00 0 -ATOM 216 H 1 1 11.378 31.486 31.538 0.00 0.00 0 -ATOM 217 O 1 1 10.438 3.626 5.087 0.00 0.00 0 -ATOM 218 H 1 1 12.435 4.082 5.136 0.00 0.00 0 -ATOM 219 H 1 1 9.822 4.284 6.681 0.00 0.00 0 -ATOM 220 O 1 1 14.762 3.401 13.776 0.00 0.00 0 -ATOM 221 H 1 1 16.518 3.824 13.376 0.00 0.00 0 -ATOM 222 H 1 1 13.752 4.757 12.964 0.00 0.00 0 -ATOM 223 O 1 1 12.382 1.012 17.643 0.00 0.00 0 -ATOM 224 H 1 1 13.346 1.997 16.444 0.00 0.00 0 -ATOM 225 H 1 1 11.931 2.133 18.998 0.00 0.00 0 -ATOM 226 O 1 1 15.278 1.293 24.559 0.00 0.00 0 -ATOM 227 H 1 1 16.071 0.946 26.365 0.00 0.00 0 -ATOM 228 H 1 1 15.794 0.199 23.499 0.00 0.00 0 -ATOM 229 O 1 1 22.226 31.627 24.712 0.00 0.00 0 -ATOM 230 H 1 1 23.338 32.595 23.876 0.00 0.00 0 -ATOM 231 H 1 1 22.161 30.053 24.132 0.00 0.00 0 -ATOM 232 O 1 1 15.640 1.847 32.717 0.00 0.00 0 -ATOM 233 H 1 1 17.488 2.473 31.874 0.00 0.00 0 -ATOM 234 H 1 1 16.403 0.869 34.267 0.00 0.00 0 -ATOM 235 O 1 1 14.858 10.199 2.754 0.00 0.00 0 -ATOM 236 H 1 1 13.360 10.712 2.282 0.00 0.00 0 -ATOM 237 H 1 1 14.560 9.316 4.559 0.00 0.00 0 -ATOM 238 O 1 1 15.717 8.469 10.739 0.00 0.00 0 -ATOM 239 H 1 1 17.323 9.581 10.875 0.00 0.00 0 -ATOM 240 H 1 1 14.574 9.631 10.221 0.00 0.00 0 -ATOM 241 O 1 1 15.248 10.398 16.525 0.00 0.00 0 -ATOM 242 H 1 1 16.324 9.181 16.149 0.00 0.00 0 -ATOM 243 H 1 1 14.172 10.488 15.098 0.00 0.00 0 -ATOM 244 O 1 1 13.226 8.438 20.801 0.00 0.00 0 -ATOM 245 H 1 1 14.043 8.996 19.295 0.00 0.00 0 -ATOM 246 H 1 1 14.661 7.802 22.093 0.00 0.00 0 -ATOM 247 O 1 1 10.173 10.961 25.875 0.00 0.00 0 -ATOM 248 H 1 1 11.477 10.223 26.940 0.00 0.00 0 -ATOM 249 H 1 1 11.269 10.738 24.343 0.00 0.00 0 -ATOM 250 O 1 1 12.792 7.737 29.173 0.00 0.00 0 -ATOM 251 H 1 1 12.199 6.038 29.475 0.00 0.00 0 -ATOM 252 H 1 1 14.427 7.450 29.617 0.00 0.00 0 -ATOM 253 O 1 1 15.180 19.498 3.578 0.00 0.00 0 -ATOM 254 H 1 1 14.883 17.596 4.080 0.00 0.00 0 -ATOM 255 H 1 1 16.754 19.579 2.626 0.00 0.00 0 -ATOM 256 O 1 1 12.517 11.093 7.701 0.00 0.00 0 -ATOM 257 H 1 1 12.224 12.778 7.555 0.00 0.00 0 -ATOM 258 H 1 1 11.150 10.393 7.057 0.00 0.00 0 -ATOM 259 O 1 1 16.266 16.271 10.758 0.00 0.00 0 -ATOM 260 H 1 1 16.507 15.795 12.768 0.00 0.00 0 -ATOM 261 H 1 1 17.725 16.977 10.292 0.00 0.00 0 -ATOM 262 O 1 1 14.069 18.399 18.897 0.00 0.00 0 -ATOM 263 H 1 1 15.513 17.523 18.155 0.00 0.00 0 -ATOM 264 H 1 1 14.958 18.709 20.673 0.00 0.00 0 -ATOM 265 O 1 1 14.099 15.480 25.510 0.00 0.00 0 -ATOM 266 H 1 1 13.698 16.872 26.938 0.00 0.00 0 -ATOM 267 H 1 1 12.567 15.379 24.444 0.00 0.00 0 -ATOM 268 O 1 1 13.309 17.574 30.292 0.00 0.00 0 -ATOM 269 H 1 1 14.937 16.934 30.810 0.00 0.00 0 -ATOM 270 H 1 1 13.969 19.494 30.012 0.00 0.00 0 -ATOM 271 O 1 1 18.371 23.257 0.925 0.00 0.00 0 -ATOM 272 H 1 1 19.479 23.480 2.321 0.00 0.00 0 -ATOM 273 H 1 1 19.087 24.325 -0.369 0.00 0.00 0 -ATOM 274 O 1 1 12.100 21.730 11.355 0.00 0.00 0 -ATOM 275 H 1 1 13.141 22.287 12.743 0.00 0.00 0 -ATOM 276 H 1 1 13.467 22.236 10.244 0.00 0.00 0 -ATOM 277 O 1 1 12.163 23.290 23.597 0.00 0.00 0 -ATOM 278 H 1 1 11.324 22.736 24.949 0.00 0.00 0 -ATOM 279 H 1 1 13.882 22.872 23.840 0.00 0.00 0 -ATOM 280 O 1 1 20.173 26.761 22.628 0.00 0.00 0 -ATOM 281 H 1 1 20.206 26.532 20.792 0.00 0.00 0 -ATOM 282 H 1 1 21.556 25.742 23.389 0.00 0.00 0 -ATOM 283 O 1 1 16.701 21.165 22.605 0.00 0.00 0 -ATOM 284 H 1 1 18.028 20.686 23.848 0.00 0.00 0 -ATOM 285 H 1 1 17.104 22.866 21.949 0.00 0.00 0 -ATOM 286 O 1 1 11.391 26.461 33.705 0.00 0.00 0 -ATOM 287 H 1 1 9.841 27.192 34.048 0.00 0.00 0 -ATOM 288 H 1 1 11.776 25.540 35.243 0.00 0.00 0 -ATOM 289 O 1 1 9.898 25.989 4.553 0.00 0.00 0 -ATOM 290 H 1 1 8.902 26.131 6.039 0.00 0.00 0 -ATOM 291 H 1 1 10.287 27.806 4.376 0.00 0.00 0 -ATOM 292 O 1 1 14.308 26.960 10.877 0.00 0.00 0 -ATOM 293 H 1 1 15.302 27.405 12.173 0.00 0.00 0 -ATOM 294 H 1 1 15.463 26.151 9.633 0.00 0.00 0 -ATOM 295 O 1 1 13.433 22.960 16.904 0.00 0.00 0 -ATOM 296 H 1 1 13.409 24.131 18.132 0.00 0.00 0 -ATOM 297 H 1 1 13.624 21.191 17.520 0.00 0.00 0 -ATOM 298 O 1 1 16.409 26.768 26.875 0.00 0.00 0 -ATOM 299 H 1 1 17.590 26.987 25.431 0.00 0.00 0 -ATOM 300 H 1 1 14.751 27.703 26.230 0.00 0.00 0 -ATOM 301 O 1 1 14.405 22.733 29.892 0.00 0.00 0 -ATOM 302 H 1 1 15.423 23.079 28.494 0.00 0.00 0 -ATOM 303 H 1 1 12.826 23.259 29.416 0.00 0.00 0 -ATOM 304 O 1 1 6.905 29.408 0.749 0.00 0.00 0 -ATOM 305 H 1 1 8.428 30.483 1.567 0.00 0.00 0 -ATOM 306 H 1 1 6.353 30.814 -0.444 0.00 0.00 0 -ATOM 307 O 1 1 9.189 34.159 6.509 0.00 0.00 0 -ATOM 308 H 1 1 10.198 34.193 8.002 0.00 0.00 0 -ATOM 309 H 1 1 9.890 35.692 5.785 0.00 0.00 0 -ATOM 310 O 1 1 14.256 32.316 9.369 0.00 0.00 0 -ATOM 311 H 1 1 15.733 32.867 9.486 0.00 0.00 0 -ATOM 312 H 1 1 14.754 30.670 10.090 0.00 0.00 0 -ATOM 313 O 1 1 14.714 30.841 16.516 0.00 0.00 0 -ATOM 314 H 1 1 13.748 29.551 17.279 0.00 0.00 0 -ATOM 315 H 1 1 13.218 31.933 16.614 0.00 0.00 0 -ATOM 316 O 1 1 18.409 33.641 20.611 0.00 0.00 0 -ATOM 317 H 1 1 19.601 32.274 21.115 0.00 0.00 0 -ATOM 318 H 1 1 17.360 32.655 19.518 0.00 0.00 0 -ATOM 319 O 1 1 16.062 28.638 32.207 0.00 0.00 0 -ATOM 320 H 1 1 14.648 27.958 33.253 0.00 0.00 0 -ATOM 321 H 1 1 15.752 28.014 30.522 0.00 0.00 0 -ATOM 322 O 1 1 16.200 30.895 1.473 0.00 0.00 0 -ATOM 323 H 1 1 16.626 29.968 -0.130 0.00 0.00 0 -ATOM 324 H 1 1 17.167 29.833 2.927 0.00 0.00 0 -ATOM 325 O 1 1 20.278 3.529 6.048 0.00 0.00 0 -ATOM 326 H 1 1 20.977 3.611 4.575 0.00 0.00 0 -ATOM 327 H 1 1 21.312 4.513 7.251 0.00 0.00 0 -ATOM 328 O 1 1 23.079 5.778 10.408 0.00 0.00 0 -ATOM 329 H 1 1 24.650 6.259 10.838 0.00 0.00 0 -ATOM 330 H 1 1 22.342 7.609 10.178 0.00 0.00 0 -ATOM 331 O 1 1 19.581 2.031 12.110 0.00 0.00 0 -ATOM 332 H 1 1 19.039 1.082 10.440 0.00 0.00 0 -ATOM 333 H 1 1 21.141 2.991 11.851 0.00 0.00 0 -ATOM 334 O 1 1 22.005 3.223 23.178 0.00 0.00 0 -ATOM 335 H 1 1 21.429 4.090 24.554 0.00 0.00 0 -ATOM 336 H 1 1 20.654 1.791 22.711 0.00 0.00 0 -ATOM 337 O 1 1 16.630 6.422 23.792 0.00 0.00 0 -ATOM 338 H 1 1 16.219 4.804 24.406 0.00 0.00 0 -ATOM 339 H 1 1 17.066 7.128 25.282 0.00 0.00 0 -ATOM 340 O 1 1 21.676 5.564 28.158 0.00 0.00 0 -ATOM 341 H 1 1 20.658 6.717 29.185 0.00 0.00 0 -ATOM 342 H 1 1 23.413 5.828 28.996 0.00 0.00 0 -ATOM 343 O 1 1 15.257 5.265 5.626 0.00 0.00 0 -ATOM 344 H 1 1 16.914 4.519 5.490 0.00 0.00 0 -ATOM 345 H 1 1 15.144 6.150 6.972 0.00 0.00 0 -ATOM 346 O 1 1 20.137 11.082 10.437 0.00 0.00 0 -ATOM 347 H 1 1 20.021 10.947 8.733 0.00 0.00 0 -ATOM 348 H 1 1 21.025 12.555 10.853 0.00 0.00 0 -ATOM 349 O 1 1 23.089 14.627 12.437 0.00 0.00 0 -ATOM 350 H 1 1 24.716 15.254 12.736 0.00 0.00 0 -ATOM 351 H 1 1 23.284 13.228 13.653 0.00 0.00 0 -ATOM 352 O 1 1 24.083 12.649 22.566 0.00 0.00 0 -ATOM 353 H 1 1 22.397 12.663 23.042 0.00 0.00 0 -ATOM 354 H 1 1 24.901 13.851 23.565 0.00 0.00 0 -ATOM 355 O 1 1 17.865 7.909 30.036 0.00 0.00 0 -ATOM 356 H 1 1 17.509 8.045 31.982 0.00 0.00 0 -ATOM 357 H 1 1 18.078 9.582 29.318 0.00 0.00 0 -ATOM 358 O 1 1 18.824 8.486 0.104 0.00 0.00 0 -ATOM 359 H 1 1 19.997 10.191 -0.057 0.00 0.00 0 -ATOM 360 H 1 1 17.077 8.998 0.779 0.00 0.00 0 -ATOM 361 O 1 1 20.122 9.143 5.343 0.00 0.00 0 -ATOM 362 H 1 1 19.373 8.819 3.821 0.00 0.00 0 -ATOM 363 H 1 1 21.998 8.776 5.128 0.00 0.00 0 -ATOM 364 O 1 1 16.413 14.459 5.855 0.00 0.00 0 -ATOM 365 H 1 1 15.536 13.007 5.239 0.00 0.00 0 -ATOM 366 H 1 1 16.006 14.725 7.737 0.00 0.00 0 -ATOM 367 O 1 1 17.561 15.066 15.654 0.00 0.00 0 -ATOM 368 H 1 1 17.575 13.398 16.055 0.00 0.00 0 -ATOM 369 H 1 1 18.978 15.828 16.400 0.00 0.00 0 -ATOM 370 O 1 1 26.374 17.047 24.817 0.00 0.00 0 -ATOM 371 H 1 1 27.983 17.098 25.632 0.00 0.00 0 -ATOM 372 H 1 1 25.629 18.751 24.919 0.00 0.00 0 -ATOM 373 O 1 1 19.784 12.960 28.706 0.00 0.00 0 -ATOM 374 H 1 1 21.662 13.055 28.871 0.00 0.00 0 -ATOM 375 H 1 1 19.545 14.070 27.143 0.00 0.00 0 -ATOM 376 O 1 1 17.891 16.733 32.499 0.00 0.00 0 -ATOM 377 H 1 1 18.327 15.240 31.277 0.00 0.00 0 -ATOM 378 H 1 1 18.633 18.335 31.693 0.00 0.00 0 -ATOM 379 O 1 1 23.733 23.024 1.663 0.00 0.00 0 -ATOM 380 H 1 1 24.800 24.052 2.776 0.00 0.00 0 -ATOM 381 H 1 1 24.693 22.618 0.198 0.00 0.00 0 -ATOM 382 O 1 1 20.789 18.440 9.443 0.00 0.00 0 -ATOM 383 H 1 1 20.766 17.257 7.881 0.00 0.00 0 -ATOM 384 H 1 1 21.896 17.345 10.385 0.00 0.00 0 -ATOM 385 O 1 1 21.574 17.493 17.838 0.00 0.00 0 -ATOM 386 H 1 1 20.597 18.955 17.218 0.00 0.00 0 -ATOM 387 H 1 1 22.538 16.874 16.251 0.00 0.00 0 -ATOM 388 O 1 1 19.168 14.748 24.131 0.00 0.00 0 -ATOM 389 H 1 1 19.711 16.390 23.712 0.00 0.00 0 -ATOM 390 H 1 1 17.429 14.695 24.403 0.00 0.00 0 -ATOM 391 O 1 1 22.149 20.198 24.977 0.00 0.00 0 -ATOM 392 H 1 1 21.639 20.924 26.486 0.00 0.00 0 -ATOM 393 H 1 1 22.656 21.657 24.411 0.00 0.00 0 -ATOM 394 O 1 1 20.565 20.792 29.600 0.00 0.00 0 -ATOM 395 H 1 1 22.264 20.409 30.214 0.00 0.00 0 -ATOM 396 H 1 1 20.548 22.408 30.597 0.00 0.00 0 -ATOM 397 O 1 1 20.802 26.547 9.615 0.00 0.00 0 -ATOM 398 H 1 1 20.099 27.984 8.338 0.00 0.00 0 -ATOM 399 H 1 1 21.277 27.539 11.325 0.00 0.00 0 -ATOM 400 O 1 1 16.283 23.589 7.779 0.00 0.00 0 -ATOM 401 H 1 1 16.093 21.973 6.712 0.00 0.00 0 -ATOM 402 H 1 1 17.901 22.971 8.154 0.00 0.00 0 -ATOM 403 O 1 1 18.469 29.798 13.568 0.00 0.00 0 -ATOM 404 H 1 1 19.712 31.216 13.506 0.00 0.00 0 -ATOM 405 H 1 1 16.872 30.343 14.396 0.00 0.00 0 -ATOM 406 O 1 1 18.790 21.712 16.060 0.00 0.00 0 -ATOM 407 H 1 1 19.878 23.090 16.485 0.00 0.00 0 -ATOM 408 H 1 1 17.201 22.326 15.819 0.00 0.00 0 -ATOM 409 O 1 1 21.747 26.084 16.349 0.00 0.00 0 -ATOM 410 H 1 1 20.783 27.021 15.300 0.00 0.00 0 -ATOM 411 H 1 1 22.705 27.328 17.206 0.00 0.00 0 -ATOM 412 O 1 1 20.769 26.211 32.050 0.00 0.00 0 -ATOM 413 H 1 1 21.488 27.404 33.328 0.00 0.00 0 -ATOM 414 H 1 1 18.989 26.710 32.145 0.00 0.00 0 -ATOM 415 O 1 1 19.820 29.181 5.559 0.00 0.00 0 -ATOM 416 H 1 1 20.991 29.509 4.109 0.00 0.00 0 -ATOM 417 H 1 1 19.431 31.018 6.221 0.00 0.00 0 -ATOM 418 O 1 1 19.240 33.867 7.993 0.00 0.00 0 -ATOM 419 H 1 1 19.107 35.039 6.604 0.00 0.00 0 -ATOM 420 H 1 1 20.697 33.671 9.063 0.00 0.00 0 -ATOM 421 O 1 1 22.511 34.976 15.793 0.00 0.00 0 -ATOM 422 H 1 1 23.716 36.163 16.603 0.00 0.00 0 -ATOM 423 H 1 1 21.699 36.150 14.467 0.00 0.00 0 -ATOM 424 O 1 1 22.622 30.284 19.069 0.00 0.00 0 -ATOM 425 H 1 1 22.049 31.351 17.725 0.00 0.00 0 -ATOM 426 H 1 1 24.411 30.773 19.576 0.00 0.00 0 -ATOM 427 O 1 1 18.639 33.611 28.369 0.00 0.00 0 -ATOM 428 H 1 1 18.226 32.159 29.103 0.00 0.00 0 -ATOM 429 H 1 1 19.906 33.008 27.158 0.00 0.00 0 -ATOM 430 O 1 1 22.520 1.325 31.926 0.00 0.00 0 -ATOM 431 H 1 1 22.803 2.668 30.796 0.00 0.00 0 -ATOM 432 H 1 1 21.045 0.425 31.122 0.00 0.00 0 -ATOM 433 O 1 1 21.754 3.789 1.159 0.00 0.00 0 -ATOM 434 H 1 1 22.085 2.785 -0.180 0.00 0.00 0 -ATOM 435 H 1 1 20.850 5.175 0.610 0.00 0.00 0 -ATOM 436 O 1 1 28.457 5.539 12.133 0.00 0.00 0 -ATOM 437 H 1 1 29.489 4.390 11.182 0.00 0.00 0 -ATOM 438 H 1 1 29.161 7.131 12.587 0.00 0.00 0 -ATOM 439 O 1 1 22.495 5.966 17.324 0.00 0.00 0 -ATOM 440 H 1 1 24.377 5.379 17.393 0.00 0.00 0 -ATOM 441 H 1 1 21.906 5.491 18.857 0.00 0.00 0 -ATOM 442 O 1 1 28.128 3.304 22.287 0.00 0.00 0 -ATOM 443 H 1 1 28.123 2.999 20.491 0.00 0.00 0 -ATOM 444 H 1 1 26.533 3.355 22.876 0.00 0.00 0 -ATOM 445 O 1 1 28.378 10.455 27.266 0.00 0.00 0 -ATOM 446 H 1 1 30.019 10.292 28.051 0.00 0.00 0 -ATOM 447 H 1 1 28.635 10.039 25.463 0.00 0.00 0 -ATOM 448 O 1 1 27.031 8.353 34.806 0.00 0.00 0 -ATOM 449 H 1 1 26.116 9.984 34.571 0.00 0.00 0 -ATOM 450 H 1 1 28.685 8.951 34.739 0.00 0.00 0 -ATOM 451 O 1 1 24.951 8.160 4.454 0.00 0.00 0 -ATOM 452 H 1 1 25.930 9.616 5.160 0.00 0.00 0 -ATOM 453 H 1 1 25.947 7.994 2.724 0.00 0.00 0 -ATOM 454 O 1 1 26.937 12.436 6.869 0.00 0.00 0 -ATOM 455 H 1 1 25.492 13.284 6.708 0.00 0.00 0 -ATOM 456 H 1 1 27.689 13.332 8.266 0.00 0.00 0 -ATOM 457 O 1 1 23.365 11.214 16.933 0.00 0.00 0 -ATOM 458 H 1 1 22.247 9.744 16.789 0.00 0.00 0 -ATOM 459 H 1 1 23.264 12.035 18.539 0.00 0.00 0 -ATOM 460 O 1 1 28.321 8.759 22.158 0.00 0.00 0 -ATOM 461 H 1 1 27.662 6.895 22.482 0.00 0.00 0 -ATOM 462 H 1 1 26.971 9.710 21.902 0.00 0.00 0 -ATOM 463 O 1 1 27.071 6.109 29.555 0.00 0.00 0 -ATOM 464 H 1 1 27.591 7.663 28.857 0.00 0.00 0 -ATOM 465 H 1 1 27.304 6.320 31.261 0.00 0.00 0 -ATOM 466 O 1 1 22.474 11.704 34.640 0.00 0.00 0 -ATOM 467 H 1 1 22.752 13.304 35.584 0.00 0.00 0 -ATOM 468 H 1 1 22.840 12.090 33.030 0.00 0.00 0 -ATOM 469 O 1 1 21.656 14.971 5.615 0.00 0.00 0 -ATOM 470 H 1 1 21.690 15.860 3.977 0.00 0.00 0 -ATOM 471 H 1 1 19.964 14.225 5.774 0.00 0.00 0 -ATOM 472 O 1 1 28.539 21.492 9.820 0.00 0.00 0 -ATOM 473 H 1 1 27.288 22.181 8.688 0.00 0.00 0 -ATOM 474 H 1 1 28.065 22.420 11.602 0.00 0.00 0 -ATOM 475 O 1 1 28.364 16.020 11.109 0.00 0.00 0 -ATOM 476 H 1 1 30.033 16.649 12.089 0.00 0.00 0 -ATOM 477 H 1 1 28.456 17.440 10.082 0.00 0.00 0 -ATOM 478 O 1 1 0.054 13.686 18.103 0.00 0.00 0 -ATOM 479 H 1 1 -1.714 12.928 18.841 0.00 0.00 0 -ATOM 480 H 1 1 1.008 12.429 17.383 0.00 0.00 0 -ATOM 481 O 1 1 24.636 12.894 29.957 0.00 0.00 0 -ATOM 482 H 1 1 25.906 13.914 31.183 0.00 0.00 0 -ATOM 483 H 1 1 25.641 11.609 29.162 0.00 0.00 0 -ATOM 484 O 1 1 21.548 17.250 0.749 0.00 0.00 0 -ATOM 485 H 1 1 21.843 19.026 0.905 0.00 0.00 0 -ATOM 486 H 1 1 20.385 16.716 -0.697 0.00 0.00 0 -ATOM 487 O 1 1 26.095 27.274 4.520 0.00 0.00 0 -ATOM 488 H 1 1 27.889 26.458 4.505 0.00 0.00 0 -ATOM 489 H 1 1 25.648 26.970 6.165 0.00 0.00 0 -ATOM 490 O 1 1 23.610 22.515 8.008 0.00 0.00 0 -ATOM 491 H 1 1 22.653 21.187 8.739 0.00 0.00 0 -ATOM 492 H 1 1 22.286 24.095 8.444 0.00 0.00 0 -ATOM 493 O 1 1 27.355 18.929 18.180 0.00 0.00 0 -ATOM 494 H 1 1 27.200 20.349 17.155 0.00 0.00 0 -ATOM 495 H 1 1 25.579 18.322 18.770 0.00 0.00 0 -ATOM 496 O 1 1 26.765 23.633 14.444 0.00 0.00 0 -ATOM 497 H 1 1 27.441 25.298 13.651 0.00 0.00 0 -ATOM 498 H 1 1 25.086 24.256 14.749 0.00 0.00 0 -ATOM 499 O 1 1 31.478 20.769 20.986 0.00 0.00 0 -ATOM 500 H 1 1 30.440 22.509 21.135 0.00 0.00 0 -ATOM 501 H 1 1 30.567 19.656 20.043 0.00 0.00 0 -ATOM 502 O 1 1 24.812 20.412 32.668 0.00 0.00 0 -ATOM 503 H 1 1 26.242 21.478 31.874 0.00 0.00 0 -ATOM 504 H 1 1 25.787 19.023 33.158 0.00 0.00 0 -ATOM 505 O 1 1 22.105 29.076 0.928 0.00 0.00 0 -ATOM 506 H 1 1 23.296 27.923 1.739 0.00 0.00 0 -ATOM 507 H 1 1 22.623 30.994 0.882 0.00 0.00 0 -ATOM 508 O 1 1 29.572 31.256 8.626 0.00 0.00 0 -ATOM 509 H 1 1 30.795 30.203 7.736 0.00 0.00 0 -ATOM 510 H 1 1 28.277 31.519 7.260 0.00 0.00 0 -ATOM 511 O 1 1 31.817 34.843 18.283 0.00 0.00 0 -ATOM 512 H 1 1 32.438 34.389 16.474 0.00 0.00 0 -ATOM 513 H 1 1 32.743 36.422 18.341 0.00 0.00 0 -ATOM 514 O 1 1 27.915 25.601 19.033 0.00 0.00 0 -ATOM 515 H 1 1 29.358 26.561 19.190 0.00 0.00 0 -ATOM 516 H 1 1 28.148 24.429 17.530 0.00 0.00 0 -ATOM 517 O 1 1 24.548 24.654 24.025 0.00 0.00 0 -ATOM 518 H 1 1 25.528 25.635 22.824 0.00 0.00 0 -ATOM 519 H 1 1 25.300 25.200 25.645 0.00 0.00 0 -ATOM 520 O 1 1 28.540 22.922 30.370 0.00 0.00 0 -ATOM 521 H 1 1 27.414 24.096 29.781 0.00 0.00 0 -ATOM 522 H 1 1 29.674 23.914 31.873 0.00 0.00 0 -ATOM 523 O 1 1 24.969 33.623 1.014 0.00 0.00 0 -ATOM 524 H 1 1 26.521 33.058 1.518 0.00 0.00 0 -ATOM 525 H 1 1 24.990 34.322 -0.683 0.00 0.00 0 -ATOM 526 O 1 1 23.075 32.171 11.324 0.00 0.00 0 -ATOM 527 H 1 1 23.316 32.775 13.097 0.00 0.00 0 -ATOM 528 H 1 1 24.460 33.203 10.662 0.00 0.00 0 -ATOM 529 O 1 1 27.497 2.736 17.224 0.00 0.00 0 -ATOM 530 H 1 1 28.397 3.415 15.715 0.00 0.00 0 -ATOM 531 H 1 1 28.234 1.233 17.412 0.00 0.00 0 -ATOM 532 O 1 1 26.369 33.060 22.077 0.00 0.00 0 -ATOM 533 H 1 1 26.170 34.746 22.264 0.00 0.00 0 -ATOM 534 H 1 1 27.592 32.404 23.321 0.00 0.00 0 -ATOM 535 O 1 1 30.221 30.950 25.843 0.00 0.00 0 -ATOM 536 H 1 1 30.305 29.038 26.208 0.00 0.00 0 -ATOM 537 H 1 1 30.363 31.979 27.414 0.00 0.00 0 -ATOM 538 O 1 1 24.973 26.732 28.607 0.00 0.00 0 -ATOM 539 H 1 1 25.385 28.369 29.248 0.00 0.00 0 -ATOM 540 H 1 1 23.330 26.597 29.234 0.00 0.00 0 -ATOM 541 O 1 1 32.165 4.857 2.258 0.00 0.00 0 -ATOM 542 H 1 1 32.417 6.195 1.157 0.00 0.00 0 -ATOM 543 H 1 1 32.615 3.727 1.112 0.00 0.00 0 -ATOM 544 O 1 1 28.067 3.533 5.217 0.00 0.00 0 -ATOM 545 H 1 1 26.960 4.447 4.158 0.00 0.00 0 -ATOM 546 H 1 1 29.875 3.863 4.448 0.00 0.00 0 -ATOM 547 O 1 1 33.279 2.782 13.028 0.00 0.00 0 -ATOM 548 H 1 1 33.708 3.955 11.817 0.00 0.00 0 -ATOM 549 H 1 1 33.656 3.545 14.631 0.00 0.00 0 -ATOM 550 O 1 1 34.278 4.944 17.492 0.00 0.00 0 -ATOM 551 H 1 1 33.438 6.563 17.876 0.00 0.00 0 -ATOM 552 H 1 1 34.906 4.452 18.995 0.00 0.00 0 -ATOM 553 O 1 1 32.363 1.908 26.092 0.00 0.00 0 -ATOM 554 H 1 1 31.941 1.683 24.268 0.00 0.00 0 -ATOM 555 H 1 1 33.850 1.390 26.904 0.00 0.00 0 -ATOM 556 O 1 1 27.982 0.418 28.241 0.00 0.00 0 -ATOM 557 H 1 1 27.516 2.080 28.309 0.00 0.00 0 -ATOM 558 H 1 1 29.593 0.176 27.299 0.00 0.00 0 -ATOM 559 O 1 1 28.845 14.672 2.724 0.00 0.00 0 -ATOM 560 H 1 1 27.963 13.930 4.139 0.00 0.00 0 -ATOM 561 H 1 1 30.386 15.714 3.379 0.00 0.00 0 -ATOM 562 O 1 1 28.083 10.618 14.298 0.00 0.00 0 -ATOM 563 H 1 1 28.623 12.160 13.293 0.00 0.00 0 -ATOM 564 H 1 1 26.486 11.015 15.379 0.00 0.00 0 -ATOM 565 O 1 1 33.867 10.545 13.306 0.00 0.00 0 -ATOM 566 H 1 1 35.165 9.612 13.810 0.00 0.00 0 -ATOM 567 H 1 1 33.615 10.270 11.513 0.00 0.00 0 -ATOM 568 O 1 1 31.790 9.696 18.223 0.00 0.00 0 -ATOM 569 H 1 1 30.484 9.334 19.421 0.00 0.00 0 -ATOM 570 H 1 1 30.834 10.096 16.929 0.00 0.00 0 -ATOM 571 O 1 1 30.141 15.006 21.532 0.00 0.00 0 -ATOM 572 H 1 1 28.565 15.594 22.099 0.00 0.00 0 -ATOM 573 H 1 1 30.942 14.253 23.077 0.00 0.00 0 -ATOM 574 O 1 1 32.798 10.732 30.680 0.00 0.00 0 -ATOM 575 H 1 1 34.073 9.528 30.799 0.00 0.00 0 -ATOM 576 H 1 1 32.991 11.512 28.983 0.00 0.00 0 -ATOM 577 O 1 1 33.652 16.265 5.086 0.00 0.00 0 -ATOM 578 H 1 1 35.399 16.239 4.730 0.00 0.00 0 -ATOM 579 H 1 1 33.503 17.939 5.631 0.00 0.00 0 -ATOM 580 O 1 1 31.947 10.799 7.943 0.00 0.00 0 -ATOM 581 H 1 1 29.894 10.549 7.619 0.00 0.00 0 -ATOM 582 H 1 1 32.271 12.414 7.075 0.00 0.00 0 -ATOM 583 O 1 1 0.329 15.516 11.746 0.00 0.00 0 -ATOM 584 H 1 1 -0.446 14.249 12.939 0.00 0.00 0 -ATOM 585 H 1 1 -0.685 17.018 11.935 0.00 0.00 0 -ATOM 586 O 1 1 4.262 19.165 14.308 0.00 0.00 0 -ATOM 587 H 1 1 3.579 17.691 14.920 0.00 0.00 0 -ATOM 588 H 1 1 5.723 19.183 15.204 0.00 0.00 0 -ATOM 589 O 1 1 32.995 13.546 25.948 0.00 0.00 0 -ATOM 590 H 1 1 32.167 15.060 26.787 0.00 0.00 0 -ATOM 591 H 1 1 34.425 13.800 25.007 0.00 0.00 0 -ATOM 592 O 1 1 1.773 13.524 34.037 0.00 0.00 0 -ATOM 593 H 1 1 0.227 14.409 33.446 0.00 0.00 0 -ATOM 594 H 1 1 2.167 14.670 35.511 0.00 0.00 0 -ATOM 595 O 1 1 33.029 20.529 7.247 0.00 0.00 0 -ATOM 596 H 1 1 34.388 21.414 8.003 0.00 0.00 0 -ATOM 597 H 1 1 31.451 20.831 8.182 0.00 0.00 0 -ATOM 598 O 1 1 2.037 24.250 10.251 0.00 0.00 0 -ATOM 599 H 1 1 3.743 25.008 9.876 0.00 0.00 0 -ATOM 600 H 1 1 1.894 25.043 11.903 0.00 0.00 0 -ATOM 601 O 1 1 32.753 19.259 13.976 0.00 0.00 0 -ATOM 602 H 1 1 32.792 20.886 13.792 0.00 0.00 0 -ATOM 603 H 1 1 34.334 18.799 14.976 0.00 0.00 0 -ATOM 604 O 1 1 0.396 18.673 18.699 0.00 0.00 0 -ATOM 605 H 1 1 -1.211 18.950 19.127 0.00 0.00 0 -ATOM 606 H 1 1 0.469 16.977 18.436 0.00 0.00 0 -ATOM 607 O 1 1 30.855 18.370 27.959 0.00 0.00 0 -ATOM 608 H 1 1 29.759 19.681 28.690 0.00 0.00 0 -ATOM 609 H 1 1 32.103 19.477 26.763 0.00 0.00 0 -ATOM 610 O 1 1 27.723 15.992 33.091 0.00 0.00 0 -ATOM 611 H 1 1 29.390 16.423 32.192 0.00 0.00 0 -ATOM 612 H 1 1 27.801 15.859 34.804 0.00 0.00 0 -ATOM 613 O 1 1 31.068 27.895 3.348 0.00 0.00 0 -ATOM 614 H 1 1 32.517 27.825 4.610 0.00 0.00 0 -ATOM 615 H 1 1 31.529 29.459 2.324 0.00 0.00 0 -ATOM 616 O 1 1 35.039 28.008 6.663 0.00 0.00 0 -ATOM 617 H 1 1 35.966 26.934 7.683 0.00 0.00 0 -ATOM 618 H 1 1 36.055 28.336 5.336 0.00 0.00 0 -ATOM 619 O 1 1 29.356 28.196 13.025 0.00 0.00 0 -ATOM 620 H 1 1 29.210 29.335 14.589 0.00 0.00 0 -ATOM 621 H 1 1 28.874 29.629 11.867 0.00 0.00 0 -ATOM 622 O 1 1 32.386 28.434 18.961 0.00 0.00 0 -ATOM 623 H 1 1 33.368 28.574 20.411 0.00 0.00 0 -ATOM 624 H 1 1 33.410 27.406 17.949 0.00 0.00 0 -ATOM 625 O 1 1 30.898 25.390 25.799 0.00 0.00 0 -ATOM 626 H 1 1 32.369 25.913 24.580 0.00 0.00 0 -ATOM 627 H 1 1 31.317 24.075 27.029 0.00 0.00 0 -ATOM 628 O 1 1 32.259 25.611 33.104 0.00 0.00 0 -ATOM 629 H 1 1 32.238 25.736 34.806 0.00 0.00 0 -ATOM 630 H 1 1 33.920 25.042 32.775 0.00 0.00 0 -ATOM 631 O 1 1 30.290 32.645 1.341 0.00 0.00 0 -ATOM 632 H 1 1 29.949 32.793 -0.430 0.00 0.00 0 -ATOM 633 H 1 1 31.762 33.340 1.847 0.00 0.00 0 -ATOM 634 O 1 1 25.536 34.235 6.469 0.00 0.00 0 -ATOM 635 H 1 1 25.716 36.059 6.651 0.00 0.00 0 -ATOM 636 H 1 1 25.283 33.866 4.895 0.00 0.00 0 -ATOM 637 O 1 1 31.674 33.161 13.106 0.00 0.00 0 -ATOM 638 H 1 1 31.793 34.863 13.281 0.00 0.00 0 -ATOM 639 H 1 1 30.425 32.928 11.783 0.00 0.00 0 -ATOM 640 O 1 1 33.844 32.668 22.296 0.00 0.00 0 -ATOM 641 H 1 1 32.750 32.234 23.524 0.00 0.00 0 -ATOM 642 H 1 1 32.917 32.875 20.736 0.00 0.00 0 -ATOM 643 O 1 1 31.603 30.542 30.805 0.00 0.00 0 -ATOM 644 H 1 1 33.451 30.804 30.468 0.00 0.00 0 -ATOM 645 H 1 1 31.575 28.816 31.756 0.00 0.00 0 -ATOM 646 O 1 1 26.295 31.235 30.599 0.00 0.00 0 -ATOM 647 H 1 1 27.834 30.515 30.607 0.00 0.00 0 -ATOM 648 H 1 1 26.362 32.920 29.856 0.00 0.00 0 -END diff --git a/tools/i-pi/examples/tutorial/README b/tools/i-pi/examples/tutorial/README deleted file mode 100644 index 3062659bd0..0000000000 --- a/tools/i-pi/examples/tutorial/README +++ /dev/null @@ -1,6 +0,0 @@ - -- Example with the rudimentary PH2 code -- - - * This gives an example of para-H2 with the isotropic Silvera-Goldman - pair potential, as discussed in the tutorial section of the user manual. - Please refer to this section for more detailed instructions - on how to run this example. diff --git a/tools/i-pi/examples/tutorial/tutorial-1/our_ref.pdb b/tools/i-pi/examples/tutorial/tutorial-1/our_ref.pdb deleted file mode 100755 index fbeba1afc9..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-1/our_ref.pdb +++ /dev/null @@ -1,111 +0,0 @@ -TITLE Traj: positions{angstrom} Step: 0 Bead: 1 -CRYST1 17.847 17.847 17.847 90.00 90.00 90.00 P 1 1 -ATOM 1 H2 1 1 0.147 0.132 0.114 0.00 0.00 0 -ATOM 2 H2 1 1 -0.125 2.943 3.188 0.00 0.00 0 -ATOM 3 H2 1 1 3.042 2.937 0.107 0.00 0.00 0 -ATOM 4 H2 1 1 2.976 -0.148 2.960 0.00 0.00 0 -ATOM 5 H2 1 1 -0.229 -0.030 5.923 0.00 0.00 0 -ATOM 6 H2 1 1 0.094 2.999 8.915 0.00 0.00 0 -ATOM 7 H2 1 1 2.954 2.895 5.910 0.00 0.00 0 -ATOM 8 H2 1 1 2.892 -0.155 8.870 0.00 0.00 0 -ATOM 9 H2 1 1 -0.048 0.087 11.901 0.00 0.00 0 -ATOM 10 H2 1 1 0.017 2.947 14.955 0.00 0.00 0 -ATOM 11 H2 1 1 2.979 2.989 11.875 0.00 0.00 0 -ATOM 12 H2 1 1 2.976 0.114 14.794 0.00 0.00 0 -ATOM 13 H2 1 1 -0.053 5.852 -0.165 0.00 0.00 0 -ATOM 14 H2 1 1 0.006 8.858 3.040 0.00 0.00 0 -ATOM 15 H2 1 1 3.041 8.951 -0.096 0.00 0.00 0 -ATOM 16 H2 1 1 3.007 5.879 2.876 0.00 0.00 0 -ATOM 17 H2 1 1 0.057 5.910 6.036 0.00 0.00 0 -ATOM 18 H2 1 1 -0.097 8.867 8.804 0.00 0.00 0 -ATOM 19 H2 1 1 2.832 8.766 5.719 0.00 0.00 0 -ATOM 20 H2 1 1 3.148 5.956 8.964 0.00 0.00 0 -ATOM 21 H2 1 1 0.031 5.974 11.932 0.00 0.00 0 -ATOM 22 H2 1 1 0.124 8.972 14.723 0.00 0.00 0 -ATOM 23 H2 1 1 2.998 8.861 11.952 0.00 0.00 0 -ATOM 24 H2 1 1 2.971 5.943 14.914 0.00 0.00 0 -ATOM 25 H2 1 1 0.009 11.770 0.089 0.00 0.00 0 -ATOM 26 H2 1 1 0.015 14.931 2.992 0.00 0.00 0 -ATOM 27 H2 1 1 2.924 14.889 0.062 0.00 0.00 0 -ATOM 28 H2 1 1 2.832 11.918 3.162 0.00 0.00 0 -ATOM 29 H2 1 1 -0.097 11.885 6.105 0.00 0.00 0 -ATOM 30 H2 1 1 0.169 14.731 8.889 0.00 0.00 0 -ATOM 31 H2 1 1 2.877 14.750 5.921 0.00 0.00 0 -ATOM 32 H2 1 1 3.078 12.038 8.936 0.00 0.00 0 -ATOM 33 H2 1 1 0.019 12.011 11.885 0.00 0.00 0 -ATOM 34 H2 1 1 0.139 14.848 14.841 0.00 0.00 0 -ATOM 35 H2 1 1 2.904 14.835 12.020 0.00 0.00 0 -ATOM 36 H2 1 1 3.083 12.013 14.942 0.00 0.00 0 -ATOM 37 H2 1 1 6.042 0.051 -0.122 0.00 0.00 0 -ATOM 38 H2 1 1 5.911 2.957 2.811 0.00 0.00 0 -ATOM 39 H2 1 1 8.949 3.111 0.013 0.00 0.00 0 -ATOM 40 H2 1 1 8.991 -0.010 2.794 0.00 0.00 0 -ATOM 41 H2 1 1 6.061 0.042 6.018 0.00 0.00 0 -ATOM 42 H2 1 1 6.156 3.002 8.708 0.00 0.00 0 -ATOM 43 H2 1 1 8.922 3.069 5.909 0.00 0.00 0 -ATOM 44 H2 1 1 8.988 0.132 9.006 0.00 0.00 0 -ATOM 45 H2 1 1 5.916 0.157 11.936 0.00 0.00 0 -ATOM 46 H2 1 1 6.011 2.841 14.909 0.00 0.00 0 -ATOM 47 H2 1 1 8.974 2.990 11.906 0.00 0.00 0 -ATOM 48 H2 1 1 8.946 -0.012 14.762 0.00 0.00 0 -ATOM 49 H2 1 1 5.871 5.856 -0.119 0.00 0.00 0 -ATOM 50 H2 1 1 6.164 8.843 3.017 0.00 0.00 0 -ATOM 51 H2 1 1 9.193 8.762 0.076 0.00 0.00 0 -ATOM 52 H2 1 1 8.834 5.965 2.835 0.00 0.00 0 -ATOM 53 H2 1 1 5.987 6.003 5.941 0.00 0.00 0 -ATOM 54 H2 1 1 5.977 8.974 8.839 0.00 0.00 0 -ATOM 55 H2 1 1 9.025 8.846 6.022 0.00 0.00 0 -ATOM 56 H2 1 1 8.848 5.694 9.143 0.00 0.00 0 -ATOM 57 H2 1 1 5.924 6.032 11.865 0.00 0.00 0 -ATOM 58 H2 1 1 6.019 8.827 14.866 0.00 0.00 0 -ATOM 59 H2 1 1 8.835 9.076 11.941 0.00 0.00 0 -ATOM 60 H2 1 1 8.891 6.039 14.895 0.00 0.00 0 -ATOM 61 H2 1 1 5.856 11.998 0.105 0.00 0.00 0 -ATOM 62 H2 1 1 5.828 14.783 2.903 0.00 0.00 0 -ATOM 63 H2 1 1 8.942 14.899 -0.042 0.00 0.00 0 -ATOM 64 H2 1 1 8.930 11.966 3.015 0.00 0.00 0 -ATOM 65 H2 1 1 6.073 11.865 5.912 0.00 0.00 0 -ATOM 66 H2 1 1 6.031 14.891 8.979 0.00 0.00 0 -ATOM 67 H2 1 1 8.972 14.858 5.883 0.00 0.00 0 -ATOM 68 H2 1 1 8.957 11.835 8.967 0.00 0.00 0 -ATOM 69 H2 1 1 5.966 11.882 12.044 0.00 0.00 0 -ATOM 70 H2 1 1 5.947 14.705 14.774 0.00 0.00 0 -ATOM 71 H2 1 1 8.876 14.853 11.951 0.00 0.00 0 -ATOM 72 H2 1 1 8.992 11.917 14.929 0.00 0.00 0 -ATOM 73 H2 1 1 11.946 0.088 -0.028 0.00 0.00 0 -ATOM 74 H2 1 1 11.829 3.081 3.117 0.00 0.00 0 -ATOM 75 H2 1 1 15.004 3.033 -0.008 0.00 0.00 0 -ATOM 76 H2 1 1 14.828 0.120 3.029 0.00 0.00 0 -ATOM 77 H2 1 1 11.906 0.017 5.995 0.00 0.00 0 -ATOM 78 H2 1 1 11.873 2.916 9.016 0.00 0.00 0 -ATOM 79 H2 1 1 14.907 3.062 5.960 0.00 0.00 0 -ATOM 80 H2 1 1 14.948 -0.122 8.864 0.00 0.00 0 -ATOM 81 H2 1 1 11.869 -0.118 11.930 0.00 0.00 0 -ATOM 82 H2 1 1 11.932 2.863 14.979 0.00 0.00 0 -ATOM 83 H2 1 1 14.835 2.976 12.018 0.00 0.00 0 -ATOM 84 H2 1 1 14.852 -0.218 14.783 0.00 0.00 0 -ATOM 85 H2 1 1 11.892 5.990 0.058 0.00 0.00 0 -ATOM 86 H2 1 1 11.816 8.684 2.936 0.00 0.00 0 -ATOM 87 H2 1 1 14.958 8.876 -0.055 0.00 0.00 0 -ATOM 88 H2 1 1 14.840 6.061 2.916 0.00 0.00 0 -ATOM 89 H2 1 1 11.911 5.971 5.726 0.00 0.00 0 -ATOM 90 H2 1 1 11.921 8.947 8.915 0.00 0.00 0 -ATOM 91 H2 1 1 15.032 8.972 5.831 0.00 0.00 0 -ATOM 92 H2 1 1 14.699 5.889 8.931 0.00 0.00 0 -ATOM 93 H2 1 1 11.765 5.844 11.846 0.00 0.00 0 -ATOM 94 H2 1 1 11.983 8.755 14.933 0.00 0.00 0 -ATOM 95 H2 1 1 14.840 8.926 11.947 0.00 0.00 0 -ATOM 96 H2 1 1 14.976 5.712 14.771 0.00 0.00 0 -ATOM 97 H2 1 1 11.824 11.871 -0.007 0.00 0.00 0 -ATOM 98 H2 1 1 11.894 14.840 2.771 0.00 0.00 0 -ATOM 99 H2 1 1 15.039 14.928 0.021 0.00 0.00 0 -ATOM 100 H2 1 1 14.876 11.851 2.910 0.00 0.00 0 -ATOM 101 H2 1 1 11.785 11.934 6.071 0.00 0.00 0 -ATOM 102 H2 1 1 11.937 14.681 8.929 0.00 0.00 0 -ATOM 103 H2 1 1 14.935 14.902 5.873 0.00 0.00 0 -ATOM 104 H2 1 1 14.882 11.944 9.007 0.00 0.00 0 -ATOM 105 H2 1 1 11.941 11.956 11.877 0.00 0.00 0 -ATOM 106 H2 1 1 11.791 14.900 14.955 0.00 0.00 0 -ATOM 107 H2 1 1 14.838 14.947 11.831 0.00 0.00 0 -ATOM 108 H2 1 1 14.891 12.005 15.050 0.00 0.00 0 -END diff --git a/tools/i-pi/examples/tutorial/tutorial-1/our_ref.xyz b/tools/i-pi/examples/tutorial/tutorial-1/our_ref.xyz deleted file mode 100644 index 46ecc5b5d9..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-1/our_ref.xyz +++ /dev/null @@ -1,110 +0,0 @@ -108 -# CELL(abcABC): 17.8469984966 17.8469984966 17.8469984966 90.00000 90.00000 90.00000 Traj: positions Step: 0 Bead: 0 -H2 0.147000137166 0.132000079971 0.114000117173 -H2 -0.125000123837 2.94299788633 3.18800164278 -H2 3.04200165055 2.93700230854 0.107000161039 -H2 2.97599737714 -0.147999752916 2.96000035008 -H2 -0.228999850096 -0.0300000085539 5.92297467609 -H2 0.0939998645211 2.99900071046 8.91499553915 -H2 2.95399948052 2.89500151338 5.91000983444 -H2 2.8920010786 -0.155000238227 8.8700154763 -H2 -0.0480000242697 0.0869999083873 11.900983782 -H2 0.0169999766244 2.94699846603 14.9550242141 -H2 2.97899781192 2.98899926119 11.875001181 -H2 2.97599737714 0.114000117173 14.7939955891 -H2 -0.0529997434675 5.85201201223 -0.165000099964 -H2 0.00600002287786 8.85800315363 3.04000136069 -H2 3.04100150562 8.95097958943 -0.0960001543749 -H2 3.00700186988 5.87900004994 2.87599875977 -H2 0.0569997939979 5.91000983444 6.03600692814 -H2 -0.0969997701246 8.8669991662 8.80397416049 -H2 2.83199767476 8.76597923681 5.71897686163 -H2 3.14800113748 5.95599533399 8.96399734879 -H2 0.0309999947276 5.97398735913 11.9319935665 -H2 0.12399997891 8.97198792467 14.7229800075 -H2 2.99800056553 8.86101946373 11.9519964651 -H2 2.97100194428 5.94297757463 14.9140129803 -H2 0.00899998139907 11.7700124225 0.0890001982411 -H2 0.0150000042769 14.9309995688 2.99199969597 -H2 2.92400042449 14.8889828983 0.0619999894552 -H2 2.83199767476 11.9180232882 3.16199787469 -H2 -0.0969997701246 11.8850026303 6.10501163633 -H2 0.169000150494 14.7310235011 8.88901293814 -H2 2.8769989047 14.7500209629 5.92101672041 -H2 3.07800157614 12.0379877617 8.93600387439 -H2 0.0190000018896 12.010999724 11.8850026303 -H2 0.139000036105 14.8480245822 14.8409865253 -H2 2.90399752595 14.8350068229 12.0199957365 -H2 3.08300230078 12.0130105974 14.9420064547 -H2 6.04198663062 0.050999982791 -0.122000218234 -H2 5.91101527114 2.9569999153 2.81099992306 -H2 8.94902163375 3.11100106696 0.0129999790117 -H2 8.9909853865 -0.0100000204905 2.79399745931 -H2 6.06098409246 0.0420000013919 6.018014903 -H2 6.15602431937 3.00200114524 8.7079814146 -H2 8.92198067832 3.0690002718 5.90900439774 -H2 8.98802199413 0.132000079971 9.00601401927 -H2 5.91598953692 0.156999998903 11.9360153133 -H2 6.01097684611 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b/tools/i-pi/examples/tutorial/tutorial-1/tutorial-1.xml deleted file mode 100755 index 713953fe46..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-1/tutorial-1.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - our_ref.pdb - 25 - - - [step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}] - [atom_f{piconewton}(atom=0;bead=0)] - positions{angstrom} - - - 5000 - - -
localhost
- 31415 - - - - - 25 - - 1 - 25 - - diff --git a/tools/i-pi/examples/tutorial/tutorial-2/tutorial-1_RESTART b/tools/i-pi/examples/tutorial/tutorial-2/tutorial-1_RESTART deleted file mode 100755 index 30912ef04a..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-2/tutorial-1_RESTART +++ /dev/null @@ -1,736 +0,0 @@ - - 5000 - - - [ -1.83955900e+00, -2.24073938e+00, -1.08250020e+00, -5.70795599e-01, 7.32627980e+00, - 7.19210265e+00, -3.30615234e-01, 3.98119438e+00, 1.51691432e+00, 2.52717260e+00, - -1.27666806e+00, 4.73413388e+00, 1.12126184e+00, 1.26764230e+00, 1.02704916e+01, - 1.29998780e+00, 3.73413588e+00, 1.61919862e+01, 5.88202729e+00, 8.04850032e+00, - 1.24311326e+01, 1.02078708e+01, 1.86360455e+00, 1.64012625e+01, 1.17619062e+00, - 4.24983476e-01, 2.55535965e+01, 1.65002846e-01, 5.34507262e+00, 2.73617602e+01, - 6.62641741e+00, 5.73764066e+00, 2.33893339e+01, 6.10026934e+00, 2.56958142e+00, - 2.92780910e+01, 2.01269291e+00, 8.69979574e+00, -6.33324249e-01, 1.14898211e+00, - 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- - [ 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, 3.67494322e+03, - 3.67494322e+03, 3.67494322e+03, 3.67494322e+03 ] - - - [ H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2, H2, H2, - H2, H2, H2 ] - - - 100000 - - [ 3.37259417e+01, 2.06511833e-15, 2.06511833e-15, 0.00000000e+00, 3.37259417e+01, - 2.06511833e-15, 0.00000000e+00, 0.00000000e+00, 3.37259417e+01 ] - - - - 31415 - - - - - [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, - kinetic_cv{kelvin}, pressure_cv{megapascal}, volume ] - - [ atom_f{piconewton}(atom=0;bead=0) ] - positions{angstrom} - - - - - [ 2687888409, 4059721984, 529212847, 1944050140, 549951740, - 753730274, 4256902940, 3644633819, 1619935418, 2926854959, - 3845596702, 3377185214, 672656208, 1522275289, 2252162595, - 3840064745, 4027492069, 3675681571, 2579879846, 1816332499, - 4032401752, 1911816378, 303445975, 1468438718, 4013747657, - 1340600813, 2333908485, 2694837801, 4170600699, 2510847348, - 3039951471, 3744192067, 1926386446, 1272375545, 1414207521, - 66179398, 4083890893, 4151044133, 576437212, 1676792606, - 434309634, 1907904212, 552501071, 2721977900, 1774218030, - 2379944892, 895572049, 964207007, 855123501, 322370220, - 2071560835, 311075834, 2622627631, 3049706185, 2343013325, - 68709345, 1862864050, 3480897554, 1688711674, 3849088037, - 2335410691, 2553458415, 3853338058, 2210199727, 2794071459, - 2398176951, 3934057850, 1698758425, 1011318686, 1806201471, - 1034736815, 3855360847, 835665231, 2475925733, 233924796, - 3024757758, 2198530484, 3673044703, 1249768122, 3962863565, - 3357863236, 2995035040, 307264231, 726406611, 2449569067, - 2105792248, 2511154863, 1776943467, 1288186977, 1069459630, - 4142069906, 2662399901, 2976669074, 3587203732, 2374529826, - 1425481845, 228954896, 829104572, 3792121363, 2155121068, - 4012537920, 4004560763, 1828234324, 523136808, 212778594, - 2400962328, 2941249333, 941934455, 1185399473, 1989697055, - 3876270640, 2356595322, 2240658826, 1455744954, 1294764103, - 197281598, 3596260716, 1784450322, 4229237399, 2625160461, - 3437563840, 99534139, 4231199313, 4186457231, 1356327267, - 11955050, 694326214, 3281619587, 1501920361, 4047724237, - 254407815, 1209336385, 2469757968, 3247917043, 467877924, - 714928015, 1424369871, 2112691093, 961450464, 1302826015, - 1508195287, 2682046824, 1166405749, 130758490, 669915191, - 3325468865, 2863429703, 99481154, 2455859519, 3512819878, - 2058734245, 713709489, 92681358, 1270820689, 2875258344, - 4089059727, 2319856617, 3246994482, 2375401460, 3526989769, - 2037481502, 1523778672, 4277357577, 3378312673, 1761280988, - 385602812, 2806072191, 263793228, 3893867788, 1122562696, - 3292179677, 196613098, 1412940405, 437753556, 2089537898, - 3093827021, 2543771523, 2707596589, 4247024898, 423016972, - 1950202748, 619404510, 1524092033, 2603783903, 1668886628, - 1610491330, 203643004, 378998824, 3077420296, 1135622483, - 1741156718, 4043803158, 134627695, 3826076900, 2236198903, - 1299249975, 1841801847, 1664600294, 3214378313, 4189671272, - 3480243241, 2314880827, 726164864, 1258895459, 1021877225, - 57278710, 2540601428, 2729779922, 1740214549, 1640865107, - 1355185385, 2109593488, 2195506700, 672372257, 2178115007, - 1875949822, 1689867492, 385658740, 2445406785, 271863064, - 988127097, 1025468932, 2359419817, 30505704, 3740615491, - 302654725, 68322970, 3937476624, 1133164597, 2115798914, - 320399345, 783710429, 2653212426, 3534685928, 1799928422, - 3374564924, 140092188, 2838741355, 118331603, 3274090979, - 2536288199, 424964681, 2624886533, 930882804, 2205394448, - 2184146172, 676812400, 3846276446, 3664199786, 1428020191, - 174713762, 1742043028, 1988587715, 250315220, 3460710952, - 518855886, 3301263820, 3376830340, 1924596217, 3991359611, - 4018324691, 2736101407, 3348220756, 4134954748, 1014806456, - 811815211, 2969949177, 1648717003, 1095340695, 3941199066, - 1442177871, 2118024477, 3440070762, 2652513624, 2449760687, - 3263443330, 2902806218, 3234417117, 1849567332, 947381041, - 3667048364, 951549915, 3479164436, 3858250612, 331400252, - 2281345388, 2762215954, 3082365401, 683228175, 3454398927, - 970279118, 2070406438, 3049304524, 1693733059, 175159517, - 1769171565, 2762326718, 2494712358, 1596534753, 696283870, - 2018059673, 92137961, 494184422, 392011733, 1385029818, - 934252405, 333359117, 3764822796, 1330799844, 1968964095, - 1099463842, 3602247127, 2198538609, 99239880, 3666952197, - 1538751175, 687515492, 1759850188, 1784319556, 219306934, - 3607066683, 3549791334, 1244006176, 3168276190, 2506130029, - 934365798, 4125460139, 2267772610, 4123099235, 3145641762, - 2282867996, 947174487, 2735752579, 1153570283, 1214198797, - 3843855592, 226542409, 1556151146, 2140750114, 173612017, - 3793649149, 513160329, 1696259753, 2196908248, 4236321655, - 3978054768, 3076169778, 1237756707, 794294503, 2478806329, - 3270485108, 21511829, 3648378180, 2173244083, 390728983, - 1613278496, 245589104, 1871555825, 840092166, 2005126608, - 2086709055, 346538249, 755528088, 4150217063, 1800593080, - 2996189003, 223378615, 26641502, 1408725657, 1055486622, - 2783260926, 2418422845, 1425876347, 2681749907, 689577833, - 2439224882, 1119191698, 3284738598, 3248369824, 2184806341, - 3827067703, 1403375638, 2039560728, 2026930258, 1439858255, - 3646642925, 357706083, 801162144, 200302113, 843383109, - 3953988752, 803642989, 133507707, 1890262095, 2010928680, - 153102298, 62155903, 277159866, 3184049271, 3470490419, - 1263803797, 1744789719, 291191777, 2104793752, 3710673355, - 690715888, 3985842110, 2609560703, 850539005, 86744360, - 1737104979, 1863808169, 1774594416, 295814460, 349948339, - 2998856642, 2965669633, 1901828086, 3978738887, 1547972061, - 3099911135, 2005717380, 567557764, 4005749125, 2160875982, - 3708061218, 71131479, 4020136758, 2494015768, 1649237263, - 3904477723, 398737933, 1060721700, 1863476301, 370356512, - 3071414126, 2579819024, 1413367122, 2902740002, 111597792, - 3291486874, 2640531015, 3168695648, 2512654909, 3959449531, - 2099836667, 1724339088, 1513859793, 1867797563, 72940112, - 150365030, 2695841664, 1822792143, 1313669546, 2967322181, - 520611643, 353667991, 2717535171, 3765848346, 388428102, - 1356267895, 3512676772, 370279636, 3846898162, 230096495, - 1637173159, 611261822, 1005164736, 269482378, 3515088803, - 3384787851, 219854487, 3527128574, 1621986556, 2351564858, - 1464556636, 3969432414, 4241153635, 3481875215, 2028710485, - 2552303669, 398357876, 502240174, 2783848798, 3029135000, - 3389310739, 2505116094, 142532114, 3164584552, 2476051612, - 3402430270, 3909441351, 3427500434, 334653597, 3680534388, - 994471388, 3554495285, 1194116172, 2229772907, 1080120321, - 764714490, 2033099135, 14870392, 1699063853, 4063486208, - 1292743360, 2032090912, 72238972, 161094465, 1452285444, - 2672671278, 1692937611, 1323803845, 3240748400, 4018998180, - 747254077, 236045767, 3239449578, 983232024, 3337514013, - 1251769771, 3333700522, 410670915, 987407435, 2475716801, - 2872258033, 4098868775, 1252507952, 3804640001, 1349395704, - 3776831082, 2921973556, 4089719272, 2209056770, 4132418611, - 1349045766, 1096167788, 946557058, 2742739413, 675697683, - 981116951, 3762459934, 735892043, 2820765771, 3285067216, - 2160644040, 3791763118, 3326789900, 4049571064, 2680776632, - 3569204094, 65929649, 3389067210, 3597945585, 1844146738, - 2700511765, 329482853, 1760204187, 923334769, 4064120545, - 3501525441, 185277522, 1241941790, 3591317416, 417403194, - 1300287444, 568015210, 1937417620, 1293297106, 1132926831, - 2866724791, 3257502829, 2947848120, 3895316838, 522557077, - 3227142004, 3090084150, 1099385887, 281296826, 1305525858, - 4048212751, 1083053479, 1851665893, 2417839863, 1623516667, - 3571192609, 3711731288, 2688150423, 1385750380, 3001410324, - 3992036671, 438613795, 1675062808, 126103207, 3806023665, - 3378609204, 3872710810, 3254661971, 3271656093, 2954958773, - 2955771203, 943499290, 1783244758, 27256593, 2736330207, - 2854314347, 1414980118, 3499653814, 2716003330, 1906739972, - 2097871403, 833490830, 860249641, 1359898654, 681385897, - 768010275, 1337229341, 2176361026, 1243749829, 2535464086, - 3587794549, 257320265, 1799338138, 2326145708 ] - - 12345 - 432 - -8.30560467e-01 - - - 0 - - - 250 - - 250 - - - 1.03353433e+03 - 2.24648494e-02 - - 4.13413730e+01 - 7.91703800e-05 - - diff --git a/tools/i-pi/examples/tutorial/tutorial-2/tutorial-2b.xml b/tools/i-pi/examples/tutorial/tutorial-2/tutorial-2b.xml deleted file mode 100755 index d90bbc3e34..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-2/tutorial-2b.xml +++ /dev/null @@ -1,33 +0,0 @@ - - - tutorial-1_RESTART - - - [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}, pressure_cv{megapascal}, volume ] - [atom_f{piconewton}(atom=0;bead=0)] - positions{angstrom} - - - 100000 - 31415 - - -
localhost
- 31415 - - - - - - 250 - - 250 - - - 25 - - 1 - 25 - 0 - - diff --git a/tools/i-pi/examples/tutorial/tutorial-3/our_ref.pdb b/tools/i-pi/examples/tutorial/tutorial-3/our_ref.pdb deleted file mode 100755 index 4734f80613..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-3/our_ref.pdb +++ /dev/null @@ -1,174 +0,0 @@ -CRYST1 39.115 39.115 39.115 90.00 90.00 90.00 P 1 1 -ATOM 1 H2 1 1 0.000 0.000 0.000 0.00 0.00 0 -ATOM 2 H2 1 1 5.582 5.582 0.000 0.00 0.00 0 -ATOM 3 H2 1 1 5.582 0.000 5.582 0.00 0.00 0 -ATOM 4 H2 1 1 0.000 5.582 5.582 0.00 0.00 0 -ATOM 5 H2 1 1 0.000 0.000 11.165 0.00 0.00 0 -ATOM 6 H2 1 1 5.582 5.582 11.165 0.00 0.00 0 -ATOM 7 H2 1 1 5.582 0.000 16.747 0.00 0.00 0 -ATOM 8 H2 1 1 0.000 5.582 16.747 0.00 0.00 0 -ATOM 9 H2 1 1 0.000 0.000 22.330 0.00 0.00 0 -ATOM 10 H2 1 1 5.582 5.582 22.330 0.00 0.00 0 -ATOM 11 H2 1 1 5.582 0.000 27.912 0.00 0.00 0 -ATOM 12 H2 1 1 0.000 5.582 27.912 0.00 0.00 0 -ATOM 13 H2 1 1 0.000 0.000 33.495 0.00 0.00 0 -ATOM 14 H2 1 1 5.582 5.582 33.495 0.00 0.00 0 -ATOM 15 H2 1 1 0.000 11.165 0.000 0.00 0.00 0 -ATOM 16 H2 1 1 5.582 16.747 0.000 0.00 0.00 0 -ATOM 17 H2 1 1 5.582 11.165 5.582 0.00 0.00 0 -ATOM 18 H2 1 1 0.000 16.747 5.582 0.00 0.00 0 -ATOM 19 H2 1 1 0.000 11.165 11.165 0.00 0.00 0 -ATOM 20 H2 1 1 5.582 16.747 11.165 0.00 0.00 0 -ATOM 21 H2 1 1 5.582 11.165 16.747 0.00 0.00 0 -ATOM 22 H2 1 1 0.000 16.747 16.747 0.00 0.00 0 -ATOM 23 H2 1 1 0.000 11.165 22.330 0.00 0.00 0 -ATOM 24 H2 1 1 5.582 16.747 22.330 0.00 0.00 0 -ATOM 25 H2 1 1 5.582 11.165 27.912 0.00 0.00 0 -ATOM 26 H2 1 1 0.000 16.747 27.912 0.00 0.00 0 -ATOM 27 H2 1 1 0.000 11.165 33.495 0.00 0.00 0 -ATOM 28 H2 1 1 5.582 16.747 33.495 0.00 0.00 0 -ATOM 29 H2 1 1 0.000 22.330 0.000 0.00 0.00 0 -ATOM 30 H2 1 1 5.582 27.912 0.000 0.00 0.00 0 -ATOM 31 H2 1 1 5.582 22.330 5.582 0.00 0.00 0 -ATOM 32 H2 1 1 0.000 27.912 5.582 0.00 0.00 0 -ATOM 33 H2 1 1 0.000 22.330 11.165 0.00 0.00 0 -ATOM 34 H2 1 1 5.582 27.912 11.165 0.00 0.00 0 -ATOM 35 H2 1 1 5.582 22.330 16.747 0.00 0.00 0 -ATOM 36 H2 1 1 0.000 27.912 16.747 0.00 0.00 0 -ATOM 37 H2 1 1 0.000 22.330 22.330 0.00 0.00 0 -ATOM 38 H2 1 1 5.582 27.912 22.330 0.00 0.00 0 -ATOM 39 H2 1 1 5.582 22.330 27.912 0.00 0.00 0 -ATOM 40 H2 1 1 0.000 27.912 27.912 0.00 0.00 0 -ATOM 41 H2 1 1 0.000 22.330 33.495 0.00 0.00 0 -ATOM 42 H2 1 1 5.582 27.912 33.495 0.00 0.00 0 -ATOM 43 H2 1 1 0.000 33.495 0.000 0.00 0.00 0 -ATOM 44 H2 1 1 5.582 33.495 5.582 0.00 0.00 0 -ATOM 45 H2 1 1 0.000 33.495 11.165 0.00 0.00 0 -ATOM 46 H2 1 1 5.582 33.495 16.747 0.00 0.00 0 -ATOM 47 H2 1 1 0.000 33.495 22.330 0.00 0.00 0 -ATOM 48 H2 1 1 5.582 33.495 27.912 0.00 0.00 0 -ATOM 49 H2 1 1 0.000 33.495 33.495 0.00 0.00 0 -ATOM 50 H2 1 1 11.165 0.000 0.000 0.00 0.00 0 -ATOM 51 H2 1 1 16.747 5.582 0.000 0.00 0.00 0 -ATOM 52 H2 1 1 16.747 0.000 5.582 0.00 0.00 0 -ATOM 53 H2 1 1 11.165 5.582 5.582 0.00 0.00 0 -ATOM 54 H2 1 1 11.165 0.000 11.165 0.00 0.00 0 -ATOM 55 H2 1 1 16.747 5.582 11.165 0.00 0.00 0 -ATOM 56 H2 1 1 16.747 0.000 16.747 0.00 0.00 0 -ATOM 57 H2 1 1 11.165 5.582 16.747 0.00 0.00 0 -ATOM 58 H2 1 1 11.165 0.000 22.330 0.00 0.00 0 -ATOM 59 H2 1 1 16.747 5.582 22.330 0.00 0.00 0 -ATOM 60 H2 1 1 16.747 0.000 27.912 0.00 0.00 0 -ATOM 61 H2 1 1 11.165 5.582 27.912 0.00 0.00 0 -ATOM 62 H2 1 1 11.165 0.000 33.495 0.00 0.00 0 -ATOM 63 H2 1 1 16.747 5.582 33.495 0.00 0.00 0 -ATOM 64 H2 1 1 11.165 11.165 0.000 0.00 0.00 0 -ATOM 65 H2 1 1 16.747 16.747 0.000 0.00 0.00 0 -ATOM 66 H2 1 1 16.747 11.165 5.582 0.00 0.00 0 -ATOM 67 H2 1 1 11.165 16.747 5.582 0.00 0.00 0 -ATOM 68 H2 1 1 11.165 11.165 11.165 0.00 0.00 0 -ATOM 69 H2 1 1 16.747 16.747 11.165 0.00 0.00 0 -ATOM 70 H2 1 1 16.747 11.165 16.747 0.00 0.00 0 -ATOM 71 H2 1 1 11.165 16.747 16.747 0.00 0.00 0 -ATOM 72 H2 1 1 11.165 11.165 22.330 0.00 0.00 0 -ATOM 73 H2 1 1 16.747 16.747 22.330 0.00 0.00 0 -ATOM 74 H2 1 1 16.747 11.165 27.912 0.00 0.00 0 -ATOM 75 H2 1 1 11.165 16.747 27.912 0.00 0.00 0 -ATOM 76 H2 1 1 11.165 11.165 33.495 0.00 0.00 0 -ATOM 77 H2 1 1 16.747 16.747 33.495 0.00 0.00 0 -ATOM 78 H2 1 1 11.165 22.330 0.000 0.00 0.00 0 -ATOM 79 H2 1 1 16.747 27.912 0.000 0.00 0.00 0 -ATOM 80 H2 1 1 16.747 22.330 5.582 0.00 0.00 0 -ATOM 81 H2 1 1 11.165 27.912 5.582 0.00 0.00 0 -ATOM 82 H2 1 1 11.165 22.330 11.165 0.00 0.00 0 -ATOM 83 H2 1 1 16.747 27.912 11.165 0.00 0.00 0 -ATOM 84 H2 1 1 16.747 22.330 16.747 0.00 0.00 0 -ATOM 85 H2 1 1 11.165 27.912 16.747 0.00 0.00 0 -ATOM 86 H2 1 1 11.165 22.330 22.330 0.00 0.00 0 -ATOM 87 H2 1 1 16.747 27.912 22.330 0.00 0.00 0 -ATOM 88 H2 1 1 16.747 22.330 27.912 0.00 0.00 0 -ATOM 89 H2 1 1 11.165 27.912 27.912 0.00 0.00 0 -ATOM 90 H2 1 1 11.165 22.330 33.495 0.00 0.00 0 -ATOM 91 H2 1 1 16.747 27.912 33.495 0.00 0.00 0 -ATOM 92 H2 1 1 11.165 33.495 0.000 0.00 0.00 0 -ATOM 93 H2 1 1 16.747 33.495 5.582 0.00 0.00 0 -ATOM 94 H2 1 1 11.165 33.495 11.165 0.00 0.00 0 -ATOM 95 H2 1 1 16.747 33.495 16.747 0.00 0.00 0 -ATOM 96 H2 1 1 11.165 33.495 22.330 0.00 0.00 0 -ATOM 97 H2 1 1 16.747 33.495 27.912 0.00 0.00 0 -ATOM 98 H2 1 1 11.165 33.495 33.495 0.00 0.00 0 -ATOM 99 H2 1 1 22.330 0.000 0.000 0.00 0.00 0 -ATOM 100 H2 1 1 27.912 5.582 0.000 0.00 0.00 0 -ATOM 101 H2 1 1 27.912 0.000 5.582 0.00 0.00 0 -ATOM 102 H2 1 1 22.330 5.582 5.582 0.00 0.00 0 -ATOM 103 H2 1 1 22.330 0.000 11.165 0.00 0.00 0 -ATOM 104 H2 1 1 27.912 5.582 11.165 0.00 0.00 0 -ATOM 105 H2 1 1 27.912 0.000 16.747 0.00 0.00 0 -ATOM 106 H2 1 1 22.330 5.582 16.747 0.00 0.00 0 -ATOM 107 H2 1 1 22.330 0.000 22.330 0.00 0.00 0 -ATOM 108 H2 1 1 27.912 5.582 22.330 0.00 0.00 0 -ATOM 109 H2 1 1 27.912 0.000 27.912 0.00 0.00 0 -ATOM 110 H2 1 1 22.330 5.582 27.912 0.00 0.00 0 -ATOM 111 H2 1 1 22.330 0.000 33.495 0.00 0.00 0 -ATOM 112 H2 1 1 27.912 5.582 33.495 0.00 0.00 0 -ATOM 113 H2 1 1 22.330 11.165 0.000 0.00 0.00 0 -ATOM 114 H2 1 1 27.912 16.747 0.000 0.00 0.00 0 -ATOM 115 H2 1 1 27.912 11.165 5.582 0.00 0.00 0 -ATOM 116 H2 1 1 22.330 16.747 5.582 0.00 0.00 0 -ATOM 117 H2 1 1 22.330 11.165 11.165 0.00 0.00 0 -ATOM 118 H2 1 1 27.912 16.747 11.165 0.00 0.00 0 -ATOM 119 H2 1 1 27.912 11.165 16.747 0.00 0.00 0 -ATOM 120 H2 1 1 22.330 16.747 16.747 0.00 0.00 0 -ATOM 121 H2 1 1 22.330 11.165 22.330 0.00 0.00 0 -ATOM 122 H2 1 1 27.912 16.747 22.330 0.00 0.00 0 -ATOM 123 H2 1 1 27.912 11.165 27.912 0.00 0.00 0 -ATOM 124 H2 1 1 22.330 16.747 27.912 0.00 0.00 0 -ATOM 125 H2 1 1 22.330 11.165 33.495 0.00 0.00 0 -ATOM 126 H2 1 1 27.912 16.747 33.495 0.00 0.00 0 -ATOM 127 H2 1 1 22.330 22.330 0.000 0.00 0.00 0 -ATOM 128 H2 1 1 27.912 27.912 0.000 0.00 0.00 0 -ATOM 129 H2 1 1 27.912 22.330 5.582 0.00 0.00 0 -ATOM 130 H2 1 1 22.330 27.912 5.582 0.00 0.00 0 -ATOM 131 H2 1 1 22.330 22.330 11.165 0.00 0.00 0 -ATOM 132 H2 1 1 27.912 27.912 11.165 0.00 0.00 0 -ATOM 133 H2 1 1 27.912 22.330 16.747 0.00 0.00 0 -ATOM 134 H2 1 1 22.330 27.912 16.747 0.00 0.00 0 -ATOM 135 H2 1 1 22.330 22.330 22.330 0.00 0.00 0 -ATOM 136 H2 1 1 27.912 27.912 22.330 0.00 0.00 0 -ATOM 137 H2 1 1 27.912 22.330 27.912 0.00 0.00 0 -ATOM 138 H2 1 1 22.330 27.912 27.912 0.00 0.00 0 -ATOM 139 H2 1 1 22.330 22.330 33.495 0.00 0.00 0 -ATOM 140 H2 1 1 27.912 27.912 33.495 0.00 0.00 0 -ATOM 141 H2 1 1 22.330 33.495 0.000 0.00 0.00 0 -ATOM 142 H2 1 1 27.912 33.495 5.582 0.00 0.00 0 -ATOM 143 H2 1 1 22.330 33.495 11.165 0.00 0.00 0 -ATOM 144 H2 1 1 27.912 33.495 16.747 0.00 0.00 0 -ATOM 145 H2 1 1 22.330 33.495 22.330 0.00 0.00 0 -ATOM 146 H2 1 1 27.912 33.495 27.912 0.00 0.00 0 -ATOM 147 H2 1 1 22.330 33.495 33.495 0.00 0.00 0 -ATOM 148 H2 1 1 33.495 0.000 0.000 0.00 0.00 0 -ATOM 149 H2 1 1 33.495 5.582 5.582 0.00 0.00 0 -ATOM 150 H2 1 1 33.495 0.000 11.165 0.00 0.00 0 -ATOM 151 H2 1 1 33.495 5.582 16.747 0.00 0.00 0 -ATOM 152 H2 1 1 33.495 0.000 22.330 0.00 0.00 0 -ATOM 153 H2 1 1 33.495 5.582 27.912 0.00 0.00 0 -ATOM 154 H2 1 1 33.495 0.000 33.495 0.00 0.00 0 -ATOM 155 H2 1 1 33.495 11.165 0.000 0.00 0.00 0 -ATOM 156 H2 1 1 33.495 16.747 5.582 0.00 0.00 0 -ATOM 157 H2 1 1 33.495 11.165 11.165 0.00 0.00 0 -ATOM 158 H2 1 1 33.495 16.747 16.747 0.00 0.00 0 -ATOM 159 H2 1 1 33.495 11.165 22.330 0.00 0.00 0 -ATOM 160 H2 1 1 33.495 16.747 27.912 0.00 0.00 0 -ATOM 161 H2 1 1 33.495 11.165 33.495 0.00 0.00 0 -ATOM 162 H2 1 1 33.495 22.330 0.000 0.00 0.00 0 -ATOM 163 H2 1 1 33.495 27.912 5.582 0.00 0.00 0 -ATOM 164 H2 1 1 33.495 22.330 11.165 0.00 0.00 0 -ATOM 165 H2 1 1 33.495 27.912 16.747 0.00 0.00 0 -ATOM 166 H2 1 1 33.495 22.330 22.330 0.00 0.00 0 -ATOM 167 H2 1 1 33.495 27.912 27.912 0.00 0.00 0 -ATOM 168 H2 1 1 33.495 22.330 33.495 0.00 0.00 0 -ATOM 169 H2 1 1 33.495 33.495 0.000 0.00 0.00 0 -ATOM 170 H2 1 1 33.495 33.495 11.165 0.00 0.00 0 -ATOM 171 H2 1 1 33.495 33.495 22.330 0.00 0.00 0 -ATOM 172 H2 1 1 33.495 33.495 33.495 0.00 0.00 0 -END diff --git a/tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_npt.xml b/tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_npt.xml deleted file mode 100755 index 2392797e01..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_npt.xml +++ /dev/null @@ -1,31 +0,0 @@ - - - tutorial-3_RESTART - - - [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}, pressure_cv{megapascal}, volume ] - positions{angstrom} - - - ??? - - -
localhost
- 31415 - - - - - - ??? - - ??? - - - ??? - - ??? - 25 - 0 - - diff --git a/tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_nvt.xml b/tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_nvt.xml deleted file mode 100755 index 7a333be0f1..0000000000 --- a/tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_nvt.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - our_ref.pdb - ??? - - - [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}, pressure_cv{megapascal} ] - positions{angstrom} - - - ??? - - -
localhost
- 31415 - - - - - ??? - - ??? - 25 - - diff --git a/tools/i-pi/i-pi b/tools/i-pi/i-pi deleted file mode 100755 index fa6a1ae623..0000000000 --- a/tools/i-pi/i-pi +++ /dev/null @@ -1,60 +0,0 @@ -#!/usr/bin/python - -"""Main script from which the simulation is run. - -Deals with creation of the simulation object, reading the input file and -initialising the system. - -Run using: - i-pi input_file.xml - -Where 'input_file.xml' should be replaced by the name of the xml input file from -which the system data will be read. For a description of how the input file -should be formatted, see the reference manual. - -Functions: - main: Runs the simulation. -""" - -import sys -from ipi.engine import simulation -from ipi.inputs.simulation import InputSimulation -from ipi.utils.io.io_xml import * -from ipi.utils.messages import banner, help, verbosity - -def main(file_name): - """Runs the simulation. - - Will run automatically when the module is used as a script. - """ - - ifile = open(file_name,"r") - xmlrestart = xml_parse_file(ifile) # Parses the file. - ifile.close() - - simrestart = InputSimulation() - # Checks the input and partitions it appropriately. - simrestart.parse(xmlrestart.fields[0][1]) - # Here we must do this manually; from here on everything should be automated by the messages classes - if simrestart.verbosity.fetch() != "quiet" : - banner() - print " # i-pi starting from input file: ", file_name - if simrestart.verbosity.fetch() != "quiet" and simrestart.verbosity.fetch() != "low" : - print " --- begin input file content --- " - ifile = open(file_name,"r") - for line in ifile.readlines(): - print line, - ifile.close() - print " --- end input file content --- " - - simul = simrestart.fetch() # Creates the appropriate simulation object. - simul.run() - - del simul - -#This is what is run if the file is run as a script. -if __name__ == '__main__': - if (len(sys.argv) != 2): - help() - else: - main(sys.argv[1]) diff --git a/tools/i-pi/ipi/README b/tools/i-pi/ipi/README deleted file mode 100644 index a775b2066e..0000000000 --- a/tools/i-pi/ipi/README +++ /dev/null @@ -1,14 +0,0 @@ - -- Source code directory -- - - * This is the main source directory. - - * Files: - - i-pi: Runs the simulation. - - * Directories: - - engine: Holds the modules containing the objects used during the - simulation. - - interfaces: Holds the modules containing the socket interface code. - - utils: Holds the modules containing utility functions. - - inputs: Holds the modules that deals with reading the input and the - restart mechanism. diff --git a/tools/i-pi/ipi/__init__.py b/tools/i-pi/ipi/__init__.py deleted file mode 100644 index 0ed5b4dbf5..0000000000 --- a/tools/i-pi/ipi/__init__.py +++ /dev/null @@ -1 +0,0 @@ -__all__ = ["engine", "inputs", "interfaces", "utils"] diff --git a/tools/i-pi/ipi/engine/README b/tools/i-pi/ipi/engine/README deleted file mode 100644 index 0ce3661b35..0000000000 --- a/tools/i-pi/ipi/engine/README +++ /dev/null @@ -1,18 +0,0 @@ - -- Engine code directory -- - - * This is the directory containing all the major class definitions. - - * Files: - - atoms.py: Deals with classical simulations. - - barostats.py: Deals with constant pressure simulations. - - beads.py: Deals with quantum simulations. - - cell.py: Deals with the simulation box. - - ensembles.py: Deals with the different ensembles. - - forces.py: Deals with creating the jobs to send to the driver code. - - initializer.py: Deals with initialization of the simulation. - - normalmodes.py: Deals with the normal mode transformations. - - outputs.py: Deals with the output files. - - properties.py: Deals with calculating all the output properties. - - simulation.py: Deals with all the top level information, such as - input/output. - - thermostats.py: Deals with constant temperature simulations. diff --git a/tools/i-pi/ipi/engine/__init__.py b/tools/i-pi/ipi/engine/__init__.py deleted file mode 100644 index 609556a5e0..0000000000 --- a/tools/i-pi/ipi/engine/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -__all__ = ["atoms", "cell", "simulation", "forces", "ensembles", "properties", - "thermostats", "barostats", "beads", "outputs", "normalmodes", - "initializer" ] diff --git a/tools/i-pi/ipi/engine/atoms.py b/tools/i-pi/ipi/engine/atoms.py deleted file mode 100644 index 9e6e2752f6..0000000000 --- a/tools/i-pi/ipi/engine/atoms.py +++ /dev/null @@ -1,269 +0,0 @@ -"""Contains the classes which deal with the atoms. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Used for holding information about the atoms, including their positions, masses -momenta and kinetic energy. Has separate classes for accessing the global -arrays of atoms and for individual atoms. - -Classes: - Atom: Class with methods dealing with individual atoms. - Atoms: Class with methods dealing with all the atoms. -""" - -__all__ = ['Atoms', 'Atom'] - -import numpy as np -from ipi.utils.depend import * -from ipi.utils import units - -class Atom(dobject): - """Represent an atom, with position, velocity, mass and related properties. - - This is actually only an interface to the Atoms class, i.e. only stores - views of the large arrays which contain all the coordinates. - - Attributes: - kin: The kinetic energy of the atom. - kstress: The contribution of the atom to the kinetic stress tensor. - - Depend objects: - p: The three components of the momentum of the atom. - q: The three components of the position of the atom. - m: The mass of the atom. - name: The name of the atom. - m3: An array of 3 elements with each element being the mass of the atom. - Used when each degree of freedom needs to be divided by the mass. - """ - - def __init__(self, system, index): - """Initializes Atom. - - Args: - system: An Atoms object containing the required atom. - index: An integer giving the index of the required atom in the atoms - list. Note that indices start from 0. - """ - - dset(self,"p",system.p[3*index:3*index+3]) - dset(self,"q",system.q[3*index:3*index+3]) - dset(self,"m",system.m[index:index+1]) - dset(self,"name",system.names[index:index+1]) - dset(self,"m3",system.m3[3*index:3*index+3]) - - @property - def kin(self): - """Calculates the contribution of the atom to the kinetic energy.""" - - return np.dot(self.p,self.p)/(2.0*self.m) - - @property - def kstress(self): - """Calculates the contribution of the atom to the kinetic stress - tensor. - """ - - p = depstrip(self.p) - ks = numpy.zeros((3,3),float) - for i in range(3): - for j in range(i,3): - ks[i,j] = p[i]*p[j] - return ks/self.m - - -class Atoms(dobject): - """Storage for the atoms' positions, masses and velocities. - - Everything is stored as 3*n sized contiguous arrays, - and a convenience-access is provided through a list of Atom objects. - - Attributes: - natoms: The number of atoms. - - Depend objects: - p: An array giving the components of the atom positions. - q: An array giving the components of the atom momenta. - m: An array giving the atom masses. - names: An array giving the atom names. - m3: An array of 3*n elements where each element of m has been copied - three times. Used when each degree of freedom needs to be divided - by the mass. - M: The total mass of all the atoms. - kin: The total kinetic energy of the atoms. Depends on p and m3. - kstress: The contribution of the atoms to the kinetic stress tensor. - Depends on px, py, pz and m. - qx: An array giving the x components of the positions. - qy: An array giving the y components of the positions. - qz: An array giving the z components of the positions. - px: An array giving the x components of the momenta. - py: An array giving the y components of the momenta. - pz: An array giving the z components of the momenta. - """ - - - def __init__(self, natoms, _prebind=None): - """Initializes Atoms. - - Each replica and the centroid coordinate are all held as Atoms objects, - and so slices of the global position and momentum arrays must be used in - the initialization so that they always agree with each other. - - Args: - natoms: An integer giving the number of atoms. - _prebind: An optional tuple of four elements; a depend_array of length - 3*natoms for the positions, another for the momenta, a depend_array - of length natoms for the masses and another for the names. - """ - - self.natoms = natoms - - if _prebind is None: - dset(self,"q",depend_array(name="q",value=np.zeros(3*natoms, float))) - dset(self,"p",depend_array(name="p",value=np.zeros(3*natoms, float))) - dset(self,"m",depend_array(name="m",value=np.zeros(natoms, float))) - dset(self,"names", - depend_array(name="names",value=np.zeros(natoms, np.dtype('|S6')))) - else: - dset(self,"q",_prebind[0]) - dset(self,"p",_prebind[1]) - dset(self,"m",_prebind[2]) - dset(self,"names",_prebind[3]) - - self.px = self.p[0:3*natoms:3] - self.py = self.p[1:3*natoms:3] - self.pz = self.p[2:3*natoms:3] - self.qx = self.q[0:3*natoms:3] - self.qy = self.q[1:3*natoms:3] - self.qz = self.q[2:3*natoms:3] - - dset(self,"m3", - depend_array(name="m3",value=np.zeros(3*natoms, float),func=self.mtom3, - dependencies=[dget(self,"m")])) - - dset(self,"M", - depend_value(name="M",func=self.get_msum, - dependencies=[dget(self,"m")]) ) - dset(self,"kin", - depend_value(name="kin",func=self.get_kin, - dependencies=[dget(self,"p"),dget(self,"m3")]) ) - dset(self,"kstress", - depend_value(name="kstress",func=self.get_kstress, - dependencies=[dget(self,"px"),dget(self,"py"),dget(self,"pz"),dget(self,"m")]) ) - - def copy(self): - """Creates a new Atoms object. - - Returns: - An Atoms object with the same q, p, m and names arrays as the original. - """ - - newat = Atoms(self.natoms) - newat.q[:] = self.q - newat.p[:] = self.p - newat.m[:] = self.m - newat.names[:] = self.names - return newat - - def __len__(self): - """Length function. - - This is called whenever the standard function len(atoms) is used. - - Returns: - The number of atoms. - """ - - return self.natoms - - def __getitem__(self,index): - """Overwrites standard getting function. - - This is called whenever the standard function atoms[index] is used. - Returns an Atom object with the appropriate position and momenta arrays. - Note that they are dynamically generated each time an Atom needs to be - accessed, as this reduces the number of depend objects that need to be - held at any one time. - - Args: - index: The index of the atom to be accessed. - - Returns: - The atom given by the index. - """ - - return Atom(self,index) - - def __setitem__(self,index,value): - """Overwrites standard setting function. - - This is called whenever the standard function atoms[index]=value is used. - Changes the position and momenta of the appropriate slice of the global - position and momentum arrays to those given by value. - Note that they are dynamically generated each time an Atom needs to be - accessed, as this reduces the number of depend objects that need to be - held at any one time. - - Args: - index: The atom to be changed. - value: The Atom object that holds the new values. - """ - - pat = Atom(self,index) - pat.p = value.p - pat.q = value.q - pat.m = value.m - pat.name = value.name - - def get_msum(self): - """Calculates the total mass.""" - - return self.m.sum() - - def mtom3(self): - """Returns a 3*n mass array. - - Returns: - An array of 3*n elements where each element of m has been copied - three times. Used when each degree of freedom needs to be divided - by the mass. - """ - - m3 = np.zeros(3*self.natoms,float) - m3[0:3*self.natoms:3] = self.m - m3[1:3*self.natoms:3] = m3[0:3*self.natoms:3] - m3[2:3*self.natoms:3] = m3[0:3*self.natoms:3] - return m3 - - def get_kin(self): - """Calculates the total kinetic energy of the system.""" - - p = depstrip(self.p) - return 0.5*np.dot(p,p/depstrip(self.m3)) - - def get_kstress(self): - """Calculates the total contribution of the atoms to the kinetic stress - tensor -- not volume-scaled - """ - - ks = np.zeros((3,3),float) - ks[0,0] = np.dot(self.px,self.px/self.m) - ks[1,1] = np.dot(self.py,self.py/self.m) - ks[2,2] = np.dot(self.pz,self.pz/self.m) - ks[0,1] = np.dot(self.px,self.py/self.m) - ks[0,2] = np.dot(self.px,self.pz/self.m) - ks[1,2] = np.dot(self.py,self.pz/self.m) - return ks diff --git a/tools/i-pi/ipi/engine/barostats.py b/tools/i-pi/ipi/engine/barostats.py deleted file mode 100644 index b65e62746c..0000000000 --- a/tools/i-pi/ipi/engine/barostats.py +++ /dev/null @@ -1,450 +0,0 @@ -"""Contains the classes that deal with constant pressure dynamics. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Contains the algorithms which propagate the position and momenta steps in the -constant pressure ensemble. Holds the properties directly related to -these ensembles, such as the internal and external pressure and stress. - -Classes: - Barostat: Base barostat class with the generic methods and attributes. - BaroBZP: Generates dynamics with a stochastic barostat -- see - Ceriotti, More, Manolopoulos, Comp. Phys. Comm. 2013 for - implementation details. -""" - -# NB: this file also contains a 'BaroMHT' class, that follows more closely the -# Martyna, Hughes, Tuckerman implementation of a PIMD barostat. However it is so -# close to the BZP implementation that we disabled it for the sake of simplicity -# BaroMHT: Generates dynamics according to the method of G. Martyna, A. -# Hughes and M. Tuckerman, J. Chem. Phys., 110, 3275. - -__all__ = ['Barostat', 'BaroBZP'] - -import numpy as np -from ipi.utils.depend import * -from ipi.utils.units import * -from ipi.utils.mathtools import eigensystem_ut3x3, invert_ut3x3, exp_ut3x3, det_ut3x3 -from ipi.inputs.thermostats import InputThermo -from ipi.engine.thermostats import Thermostat - -class Barostat(dobject): - """Base barostat class. - - Gives the standard methods and attributes needed in all the barostat classes. - - Attributes: - beads: A beads object giving the atoms positions - cell: A cell object giving the system box. - forces: A forces object giving the virial and the forces acting on - each bead. - nm: An object to do the normal mode transformation. - thermostat: A thermostat coupled to the barostat degrees of freedom. - mdof: The number of atomic degrees of freedom - - Depend objects: - dt: The time step used in the algorithms. Depends on the simulation dt. - temp: The (classical) simulation temperature. Higher than the physical - temperature by a factor of the number of beads. - tau: The timescale associated with the piston - pext: The external pressure - ebaro: The conserved quantity associated with the barostat. - pot: The potential energy associated with the barostat. - kstress: The system kinetic stress tensor. - stress: The system stress tensor. - press: The system pressure. - """ - - def __init__(self, dt=None, temp=None, pext=None, tau=None, ebaro=None, thermostat=None): - """Initializes base barostat class. - - Note that the external stress and the external pressure are synchronized. - This makes most sense going from the stress to the pressure, but if you - must go in the other direction the stress is assumed to be isotropic. - - Args: - dt: Optional float giving the time step for the algorithms. Defaults - to the simulation dt. - temp: Optional float giving the temperature for the thermostat. - Defaults to the simulation temp. - pext: Optional float giving the external pressure. - tau: Optional float giving the time scale associated with the barostat. - ebaro: Optional float giving the conserved quantity already stored - in the barostat initially. Used on restart. - thermostat: The thermostat connected to the barostat degree of freedom. - """ - - dset(self,"dt",depend_value(name='dt')) - if not dt is None: - self.dt = dt - else: self.dt = 1.0 - - dset(self, "temp", depend_value(name="temp")) - if not temp is None: - self.temp = temp - else: self.temp = 1.0 - - dset(self,"tau",depend_value(name='tau')) - if not tau is None: - self.tau = tau - else: self.tau = 1.0 - - dset(self,"pext",depend_value(name='pext')) - if not pext is None: - self.pext = pext - else: self.pext = 0.0 - - dset(self,"ebaro",depend_value(name='ebaro')) - if not ebaro is None: - self.ebaro = ebaro - else: self.ebaro = 0.0 - - if thermostat is None: - thermostat = Thermostat() - self.thermostat = thermostat - - # pipes timestep and temperature to the thermostat - deppipe(self,"dt", self.thermostat, "dt") - deppipe(self, "temp", self.thermostat,"temp") - - - def bind(self, beads, nm, cell, forces, prng=None, fixdof=None): - """Binds beads, cell and forces to the barostat. - - This takes a beads object, a cell object and a forcefield object and - makes them members of the barostat. It also then creates the objects that - will hold the data needed in the barostat algorithms and the dependency - network. - - Args: - beads: The beads object from which the bead positions are taken. - nm: The normal modes propagator object - cell: The cell object from which the system box is taken. - forces: The forcefield object from which the force and virial are - taken. - prng: The parent PRNG to bind the thermostat to - fixdof: The number of blocked degrees of freedom. - """ - - self.beads = beads - self.cell = cell - self.forces = forces - self.nm = nm - - dset(self,"pot", - depend_value(name='pot', func=self.get_pot, - dependencies=[ dget(cell,"V"), dget(self,"pext") ])) - dset(self,"kstress", - depend_value(name='kstress', func=self.get_kstress, - dependencies=[ dget(beads,"q"), dget(beads,"qc"), dget(beads,"pc"), dget(forces,"f") ])) - dset(self,"stress", - depend_value(name='stress', func=self.get_stress, - dependencies=[ dget(self,"kstress"), dget(cell,"V"), dget(forces,"vir") ])) - dset(self,"press", - depend_value(name='press', func=self.get_press, - dependencies=[ dget(self,"stress") ])) - - if fixdof is None: - self.mdof = float(self.beads.natoms)*3.0 - else: - self.mdof = float(self.beads.natoms)*3.0 - float(fixdof) - - def get_pot(self): - """Calculates the elastic strain energy of the cell.""" - - # NOTE: since there are nbeads replicas of the unit cell, the enthalpy contains a nbeads factor - return self.cell.V*self.pext*self.beads.nbeads - - def get_kstress(self): - """Calculates the quantum centroid virial kinetic stress tensor - estimator. - """ - - kst = np.zeros((3,3),float) - q = depstrip(self.beads.q) - qc = depstrip(self.beads.qc) - pc = depstrip(self.beads.pc) - m = depstrip(self.beads.m) - na3 = 3*self.beads.natoms - fall = depstrip(self.forces.f) - - for b in range(self.beads.nbeads): - for i in range(3): - for j in range(i,3): - kst[i,j] -= np.dot(q[b,i:na3:3] - qc[i:na3:3], - fall[b,j:na3:3]) - - # NOTE: In order to have a well-defined conserved quantity, the Nf kT term in the - # diagonal stress estimator must be taken from the centroid kinetic energy. - for i in range(3): - kst[i,i] += np.dot(pc[i:na3:3],pc[i:na3:3]/m) *self.beads.nbeads - - return kst - - def get_stress(self): - """Calculates the internal stress tensor.""" - - return (self.kstress + self.forces.vir)/self.cell.V - - def get_press(self): - """Calculates the internal pressure.""" - - return np.trace(self.stress)/3.0 - - def pstep(self): - """Dummy momenta propagator step.""" - - pass - - def qcstep(self): - """Dummy centroid position propagator step.""" - - pass - - -class BaroBZP(Barostat): - """Bussi-Zykova-Parrinello barostat class. - - Just extends the standard class adding finite-dt propagators for the barostat - velocities, positions, piston. - - Depend objects: - p: The momentum associated with the volume degree of freedom. - m: The mass associated with the volume degree of freedom. - """ - - def __init__(self, dt=None, temp=None, pext=None, tau=None, ebaro=None, thermostat=None, p=None): - """Initializes BZP barostat. - - Args: - dt: Optional float giving the time step for the algorithms. Defaults - to the simulation dt. - temp: Optional float giving the temperature for the thermostat. - Defaults to the simulation temp. - pext: Optional float giving the external pressure. - tau: Optional float giving the time scale associated with the barostat. - ebaro: Optional float giving the conserved quantity already stored - in the barostat initially. Used on restart. - thermostat: The thermostat connected to the barostat degree of freedom. - p: Optional initial volume conjugate momentum. Defaults to 0. - """ - - - super(BaroBZP, self).__init__(dt, temp, pext, tau, ebaro, thermostat) - - dset(self,"p", depend_array(name='p', value=np.atleast_1d(0.0))) - - if not p is None: - self.p = np.asarray([p]) - else: - self.p = 0.0 - - def bind(self, beads, nm, cell, forces, prng=None, fixdof=None): - """Binds beads, cell and forces to the barostat. - - This takes a beads object, a cell object and a forcefield object and - makes them members of the barostat. It also then creates the objects that - will hold the data needed in the barostat algorithms and the dependency - network. - - Args: - beads: The beads object from which the bead positions are taken. - nm: The normal modes propagator object - cell: The cell object from which the system box is taken. - forces: The forcefield object from which the force and virial are - taken. - prng: The parent PRNG to bind the thermostat to - fixdof: The number of blocked degrees of freedom. - """ - - super(BaroBZP, self).bind(beads, nm, cell, forces, prng, fixdof) - - # obtain the thermostat mass from the given time constant - # note that the barostat temperature is nbeads times the physical T - dset(self,"m", depend_array(name='m', value=np.atleast_1d(0.0), - func=(lambda:np.asarray([self.tau**2*3*self.beads.natoms*Constants.kb*self.temp])), - dependencies=[ dget(self,"tau"), dget(self,"temp") ] )) - - # binds the thermostat to the piston degrees of freedom - self.thermostat.bind(pm=[ self.p, self.m ], prng=prng) - - dset(self,"kin",depend_value(name='kin', - func=(lambda:0.5*self.p[0]**2/self.m[0]), - dependencies= [dget(self,"p"), dget(self,"m")] ) ) - - # the barostat energy must be computed from bits & pieces (overwrite the default) - dset(self, "ebaro", depend_value(name='ebaro', func=self.get_ebaro, - dependencies=[ dget(self, "kin"), dget(self, "pot"), - dget(self.cell, "V"), dget(self, "temp"), - dget(self.thermostat,"ethermo")] )) - - def get_ebaro(self): - """Calculates the barostat conserved quantity.""" - - return self.thermostat.ethermo + self.kin + self.pot - np.log(self.cell.V)*Constants.kb*self.temp - - - def pstep(self): - """Propagates the momenta for half a time step.""" - - dthalf = self.dt*0.5 - dthalf2 = dthalf**2 - dthalf3 = dthalf**3/3.0 - - # This differs from the BZP thermostat in that it uses just one kT in the propagator. - # This leads to an ensemble equaivalent to Martyna-Hughes-Tuckermann for both fixed and moving COM - # Anyway, it is a small correction so whatever. - self.p += dthalf*3.0*( self.cell.V* ( self.press - self.beads.nbeads*self.pext ) + - Constants.kb*self.temp ) - - fc = np.sum(depstrip(self.forces.f),0)/self.beads.nbeads - m = depstrip(self.beads.m3)[0] - pc = depstrip(self.beads.pc) - - # I am not 100% sure, but these higher-order terms come from integrating the pressure virial term, - # so they should need to be multiplied by nbeads to be consistent with the equations of motion in the PI context - # again, these are tiny tiny terms so whatever. - self.p += (dthalf2*np.dot(pc,fc/m) + dthalf3*np.dot(fc,fc/m)) * self.beads.nbeads - - self.beads.p += depstrip(self.forces.f)*dthalf - - def qcstep(self): - """Propagates the centroid position and momentum and the volume.""" - - v = self.p[0]/self.m[0] - expq, expp = (np.exp(v*self.dt), np.exp(-v*self.dt)) - - m = depstrip(self.beads.m3)[0] - - self.nm.qnm[0,:] *= expq - self.nm.qnm[0,:] += ((expq-expp)/(2.0*v))* (depstrip(self.nm.pnm)[0,:]/m) - self.nm.pnm[0,:] *= expp - - self.cell.h *= expq - - -class BaroMHT(Barostat): - """Martyna-Hughes-Tuckerman barostat class. - - Just extends the standard class adding finite-dt propagators for the barostat - velocities, positions, piston. - - Depend objects: - p: The momentum associated with the volume degree of freedom. - m: The mass associated with the volume degree of freedom. - """ - - def __init__(self, dt=None, temp=None, pext=None, tau=None, ebaro=None, thermostat=None, p=None): - """Initializes MHT barostat. - - Args: - dt: Optional float giving the time step for the algorithms. Defaults - to the simulation dt. - temp: Optional float giving the temperature for the thermostat. - Defaults to the simulation temp. - pext: Optional float giving the external pressure. - tau: Optional float giving the time scale associated with the barostat. - ebaro: Optional float giving the conserved quantity already stored - in the barostat initially. Used on restart. - thermostat: The thermostat connected to the barostat degree of freedom. - p: Optional initial volume conjugate momentum. Defaults to 0. - """ - - super(BaroMHT, self).__init__(dt, temp, pext, tau, ebaro, thermostat) - - dset(self,"p", depend_array(name='p', value=np.atleast_1d(0.0))) - - if not p is None: - self.p = np.asarray([p]) - else: - self.p = 0.0 - - def bind(self, beads, nm, cell, forces, prng=None, fixdof=None): - """Binds beads, cell and forces to the barostat. - - This takes a beads object, a cell object and a forcefield object and - makes them members of the barostat. It also then creates the objects that - will hold the data needed in the barostat algorithms and the dependency - network. - - Args: - beads: The beads object from which the bead positions are taken. - nm: The normal modes propagator object - cell: The cell object from which the system box is taken. - forces: The forcefield object from which the force and virial are - taken. - prng: The parent PRNG to bind the thermostat to - fixdof: The number of blocked degrees of freedom. - """ - - super(BaroMHT, self).bind(beads, nm, cell, forces, prng, fixdof) - - # obtain the thermostat mass from the given time constant - # note that the barostat temperature is nbeads times the physical T - dset(self,"m", depend_array(name='m', value=np.atleast_1d(0.0), - func=(lambda:np.asarray([self.tau**2*3*self.beads.natoms*Constants.kb*self.temp])), - dependencies=[ dget(self,"tau"), dget(self,"temp") ] )) - - # binds the thermostat to the piston degrees of freedom - self.thermostat.bind(pm=[ self.p, self.m ], prng=prng) - - dset(self,"kin",depend_value(name='kin', - func=(lambda:0.5*self.p[0]**2/self.m[0]), - dependencies=[dget(self,"p"), dget(self,"m")] ) ) - - # the barostat energy must be computed from bits & pieces (overwrite the default) - dset(self, "ebaro", depend_value(name='ebaro', func=self.get_ebaro, - dependencies=[ dget(self, "kin"), dget(self, "pot"), - dget(self.cell, "V"), dget(self, "temp"), - dget(self.thermostat,"ethermo")])) - - def get_ebaro(self): - """Calculates the barostat conserved quantity.""" - - return self.thermostat.ethermo + self.kin + self.pot - - def pstep(self): - """Propagates the momenta for half a time step.""" - - dthalf = self.dt*0.5 - dthalf2 = dthalf**2 - dthalf3 = dthalf**3/3.0 - - fc = np.sum(depstrip(self.forces.f),0)/float(self.beads.nbeads) - m = depstrip(self.beads.m3)[0] - pc = depstrip(self.beads.pc) - - self.p += dthalf*3.0*( self.cell.V* ( self.press - self.beads.nbeads*self.pext ) + - float(self.beads.nbeads)/self.mdof*np.dot(pc,pc/m) ) - - self.beads.p += depstrip(self.forces.f)*dthalf - - def qcstep(self): - """Propagates the centroid position and momentum and the volume.""" - - v = self.p[0]/self.m[0] - adof = (1 + 3.0/self.mdof) - expq, expp = (np.exp(v*self.dt), np.exp( -v*self.dt * adof ) ) - - m = depstrip(self.beads.m3)[0] - - self.nm.qnm[0,:] *= expq - self.nm.qnm[0,:] += ((expq-expp)/(v*(1+adof)) * - (depstrip(self.nm.pnm)[0,:])/m) - self.nm.pnm[0,:] *= expp - - self.cell.h *= expq diff --git a/tools/i-pi/ipi/engine/beads.py b/tools/i-pi/ipi/engine/beads.py deleted file mode 100644 index 1a20574522..0000000000 --- a/tools/i-pi/ipi/engine/beads.py +++ /dev/null @@ -1,323 +0,0 @@ -"""Contains the classes which deal with all the beads. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Used for holding information about the beads, including their positions, masses -momenta and kinetic energy. Has different objects for the position and normal -mode representations, and has a special centroid atoms object for when the -centroid coordinate is required. - -Classes: - Beads: Class with methods dealing with all the beads. -""" - -__all__ = ['Beads'] - -import numpy as np -from ipi.utils.depend import * -from ipi.engine.atoms import Atoms -from ipi.utils import units - -class Beads(dobject): - """Storage for the beads positions and velocities. - - Everything is stored as (nbeads,3*natoms) sized contiguous arrays, - and a convenience-access to each replica of the system is provided through a - list of Atoms objects. Contains arrays of both the normal mode representation - and the position representation, and various sized arrays for the atom - labels and masses. Also contains the potential and force between - neighbouring replicas. - - Attributes: - natoms: The number of atoms. - nbeads: The number of beads. - _blist: A list of Atoms objects for each replica of the system. Each - replica is assumed to have the same mass and atom label. - centroid: An atoms object giving the centroid coordinate of the beads. - - Depend objects: - names: An array giving the atom names. - m: An array giving the atom masses. - m3: An array giving the mass associated with each degree of freedom. - sm3: An array giving the square root of m3. - q: An array giving all the bead positions. - p: An array giving all the bead momenta. - qc: An array giving the centroid positions. Depends on qnm. - pc: An array giving the centroid momenta. Depends on pnm. - vpath: The spring potential between the beads, divided by omegan**2. - Depends on q. - fpath: The spring force between the beads, divided by omegan**2. - Depends on q. - kins: A list of the kinetic energy of each replica. - kin: The total kinetic energy of the system. Note that this is not the - same as the estimate of the kinetic energy of the system, which is - contained in the properties module. - kstress: The total kinetic stress tensor for the system. - rg: An array giving the radius of gyration of each atom. - """ - - def __init__(self, natoms, nbeads): - """Initializes Beads. - - Args: - natoms: Number of atoms. - nbeads: Number of beads. - """ - - self.resize(natoms, nbeads) - - def resize(self, natoms, nbeads): - """Creates all the data arrays needed in the simulation. - - Effectively initializes the whole Beads object, according to the - specified number of atoms and beads. Is also used, as the name suggests, - to resize the data to a new number of beads when this is necessary, for - example in initialization from a simulation with a different number of - beads. - - Also creates, or recreates, the dependency network, as this requires - the data arrays to be created for it to work. - - Args: - natoms: The number of atoms. - nbeads: The number of beads. - """ - - self.natoms = natoms - self.nbeads = nbeads - - dset(self,"names", - depend_array(name="names",value=np.zeros(natoms, np.dtype('|S6'))) ) - - # atom masses, and mass-related arrays - dset(self,"m",depend_array(name="m",value=np.zeros(natoms, float)) ) # this is the prototype mass array (just one independent of bead n) - dset(self,"m3", - depend_array(name="m3",value=np.zeros((nbeads,3*natoms), float), # this is m conveniently replicated to be (nb,3*nat) - func=self.mtom3, dependencies=[dget(self,"m")])) - dset(self,"sm3", - depend_array(name="sm3",value=np.zeros((nbeads,3*natoms), float), # this is just the square root of m3 - func=self.m3tosm3, dependencies=[dget(self,"m3")])) - - # positions and momenta. bead representation, base storage used everywhere - dset(self,"q", - depend_array(name="q",value=np.zeros((nbeads,3*natoms), float)) ) - dset(self,"p", - depend_array(name="p",value=np.zeros((nbeads,3*natoms), float)) ) - - # position and momentum of the centroid - dset(self,"qc", - depend_array(name="qc",value=np.zeros(3*natoms, float), - func=self.get_qc, dependencies=[dget(self,"q")] ) ) - dset(self,"pc", - depend_array(name="pc",value=np.zeros(3*natoms, float), - func=self.get_pc, dependencies=[dget(self,"p")] ) ) - - # create proxies to access the centroid and the individual beads as Atoms objects - self.centroid = Atoms(natoms, _prebind=(self.qc, self.pc, self.m, self.names)) - self._blist = [Atoms(natoms, _prebind=( self.q[i,:], self.p[i,:], self.m, self.names )) for i in range(nbeads) ] - - # path springs potential and force - dset(self,"vpath", - depend_value(name="vpath", func=self.get_vpath, - dependencies=[dget(self,"q")])) - dset(self,"fpath", - depend_array(name="fpath", value=np.zeros((nbeads,3*natoms), float), - func=self.get_fpath, dependencies=[dget(self,"q")])) - - # kinetic energies of thhe beads, and total (classical) kinetic stress tensor - dset(self,"kins", - depend_array(name="kins",value=np.zeros(nbeads, float), - func=self.kin_gather, - dependencies=[dget(b,"kin") for b in self._blist])) - dset(self,"kin", - depend_value(name="kin", func=self.get_kin, - dependencies=[dget(self,"kins")])) - dset(self,"kstress", - depend_array(name="kstress",value=np.zeros((3,3), float), - func=self.get_kstress, - dependencies=[dget(b,"kstress") for b in self._blist])) - - def copy(self): - """Creates a new beads object from the original. - - Returns: - A Beads object with the same q, p, m and names arrays as the original. - """ - - newbd = Beads(self.natoms, self.nbeads) - newbd.q[:] = self.q - newbd.p[:] = self.p - newbd.m[:] = self.m - newbd.names[:] = self.names - return newbd - - - def m3tosm3(self): - """Takes the mass array and returns the square rooted mass array.""" - - return np.sqrt(depstrip(self.m3)) - - def mtom3(self): - """Takes the mass array for each bead and returns one with an element - for each degree of freedom. - - Returns: - An array of size (nbeads,3*natoms), with each element corresponding - to the mass associated with the appropriate degree of freedom in q. - """ - - m3 = np.zeros((self.nbeads,3*self.natoms),float) - m3[:,0:3*self.natoms:3] = self.m - m3[:,1:3*self.natoms:3] = m3[:,0:3*self.natoms:3] - m3[:,2:3*self.natoms:3] = m3[:,0:3*self.natoms:3] - return m3 - - def get_qc(self): - """Gets the centroid coordinates.""" - - return np.dot(np.ones(self.nbeads,float),depstrip(self.q))/float(self.nbeads) - - def get_pc(self): - """Gets the centroid momenta.""" - - return np.dot(np.ones(self.nbeads,float),depstrip(self.p))/float(self.nbeads) - - def kin_gather(self): - """Gets the kinetic energy for all the replicas. - - Returns: - A list of the kinetic energy for each system. - """ - - return np.array([b.kin for b in self._blist]) - - def get_kin(self): - """Gets the total kinetic energy of all the replicas. - - Note that this does not correspond to the total kinetic energy estimate - for the system. - - Returns: - The sum of the kinetic energy of each replica. - """ - - return self.kins.sum() - - def get_kstress(self): - """Calculates the total kinetic stress tensor of all the replicas. - - Note that this does not correspond to the quantum kinetic stress tensor - estimate for the system. - - Returns: - The sum of the kinetic stress tensor of each replica. - """ - - ks = np.zeros((3,3),float) - for b in range(self.nbeads): - ks += self[b].kstress - return ks - - def get_vpath(self): - """Calculates the spring potential between the replicas. - - Note that this is actually the harmonic potential without being - multiplied by the factor omegan**2, which is only available in the - ensemble as the temperature is required to calculate it. - """ - - epath = 0.0 - q = depstrip(self.q) - m = depstrip(self.m3)[0] - for b in range(self.nbeads): - if b > 0: - dq = q[b,:] - q[b-1,:] - else: - dq = q[b,:] - q[self.nbeads-1,:] - epath += np.dot(dq, m*dq) - return epath*0.5 - - def get_fpath(self): - """Calculates the spring force between the replicas. - - Note that this is actually the harmonic force without being - multiplied by the factor omegan**2, which is only available in the - ensemble as the temperature is required to calculate it. - """ - - nbeads = self.nbeads - natoms = self.natoms - f = np.zeros((nbeads,3*natoms),float) - - q = depstrip(self.q) - m = depstrip(self.m3)[0] - for b in range(nbeads): - if b > 0: - dq = q[b,:] - q[b-1,:] - else: - dq = q[b,:] - q[self.nbeads-1,:] - dq *= m - f[b] -= dq - if b > 0: - f[b-1] += dq - else: - f[nbeads-1] += dq - return f - - # A set of functions to access individual beads as Atoms objects - def __len__(self): - """Length function. - - This is called whenever the standard function len(beads) is used. - - Returns: - The number of beads. - """ - - return self.nbeads - - def __getitem__(self,index): - """Overwrites standard getting function. - - This is called whenever the standard function beads[index] is used. - Returns an Atoms object with the appropriate position and momenta arrays. - - Args: - index: The index of the replica of the system to be accessed. - - Returns: - The replica of the system given by the index. - """ - - return self._blist[index] - - def __setitem__(self,index,value): - """Overwrites standard setting function. - - This is called whenever the standard function beads[index]=value is used. - Changes the position and momenta of the appropriate slice of the global - position and momentum arrays to those given by value. - - Args: - index: The replica of the system to be changed. - value: The Atoms object that holds the new values. - """ - - self._blist[index].p[:] = value.p - self._blist[index].q[:] = value.q - self._blist[index].m[:] = value.m - self._blist[index].names[:] = value.names diff --git a/tools/i-pi/ipi/engine/cell.py b/tools/i-pi/ipi/engine/cell.py deleted file mode 100644 index f800773a23..0000000000 --- a/tools/i-pi/ipi/engine/cell.py +++ /dev/null @@ -1,140 +0,0 @@ -"""Contains the classes which deal with the system box. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Used for implementing the minimum image convention. - -Classes: - Cell: Base cell class with the generic methods and attributes. -""" - -__all__ = ['Cell'] - -import numpy as np -from ipi.utils.depend import * -from ipi.utils.mathtools import * -from ipi.utils import units - - -class Cell(dobject): - """Base class to represent the simulation cell in a periodic system. - - This class has the base attributes required for either flexible or - isotropic cell dynamics. Uses an upper triangular lattice vector matrix to - represent the cell. - - Depend objects: - h: An array giving the lattice vector matrix. - ih: An array giving the inverse of the lattice vector matrix. - V: The volume of the cell. - """ - - def __init__(self, h=None): - """Initializes base cell class. - - Args: - h: Optional array giving the initial lattice vector matrix. The - reference cell matrix is set equal to this. Must be an upper - triangular 3*3 matrix. Defaults to a 3*3 zeroes matrix. - """ - - if h is None: - #h = np.identity(3,float) - h = np.zeros((3,3), float) - dset(self,"h",depend_array(name = 'h', value = h) ) - - dset(self,"ih", - depend_array(name = "ih", value = np.zeros((3,3),float), - func=self.get_ih, dependencies=[dget(self,"h")]) ) - dset(self,"V", - depend_value(name = 'V', func=self.get_volume, - dependencies=[dget(self,"h")]) ) - - def get_ih(self): - """Inverts the lattice vector matrix.""" - - return invert_ut3x3(self.h) - - def get_volume(self): - """Calculates the volume of the system box.""" - - return det_ut3x3(self.h) - - def apply_pbc(self, atom): - """Uses the minimum image convention to return a particle to the - unit cell. - - Args: - atom: An Atom object. - - Returns: - An array giving the position of the image that is inside the - system box. - """ - - s = np.dot(self.ih,atom.q) - - - for i in range(3): - s[i] = s[i] - round(s[i]) - - return np.dot(self.h,s) - - def array_pbc(self, pos): - """Uses the minimum image convention to return a list of particles to the - unit cell. - - Args: - atom: An Atom object. - - Returns: - An array giving the position of the image that is inside the - system box. - """ - - s = depstrip(pos).copy() - s.shape = (len(pos)/3,3) - - s = np.dot(depstrip(self.ih),s.T) - s = s - np.round(s) - - s = np.dot(depstrip(self.h),s).T - - pos[:] = s.reshape((len(s)*3)) - - def minimum_distance(self, atom1, atom2): - """Takes two atoms and tries to find the smallest vector between two - images. - - This is only rigorously accurate in the case of a cubic cell, - but gives the correct results as long as the cut-off radius is defined - as smaller than the smallest width between parallel faces even for - triclinic cells. - - Args: - atom1: An Atom object. - atom2: An Atom object. - - Returns: - An array giving the minimum distance between the positions of atoms - atom1 and atom2 in the minimum image convention. - """ - - s = np.dot(self.ih,atom1.q-atom2.q) - for i in range(3): - s[i] -= round(s[i]) - return np.dot(self.h, s) diff --git a/tools/i-pi/ipi/engine/ensembles.py b/tools/i-pi/ipi/engine/ensembles.py deleted file mode 100644 index 23d88e436b..0000000000 --- a/tools/i-pi/ipi/engine/ensembles.py +++ /dev/null @@ -1,565 +0,0 @@ -"""Contains the classes that deal with the different dynamics required in -different types of ensembles. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Holds the algorithms required for normal mode propagators, and the objects to -do the constant temperature and pressure algorithms. Also calculates the -appropriate conserved energy quantity for the ensemble of choice. - -Classes: - Ensemble: Base ensemble class with generic methods and attributes. - NVEEnsemble: Deals with constant energy dynamics. - NVTEnsemble: Deals with constant temperature dynamics. - NPTEnsemble: Deals with constant pressure dynamics. - ReplayEnsemble: Takes a trajectory, and simply sets the atom positions to - match it, rather than doing dynamics. In this way new properties can - be calculated on an old simulation, without having to rerun it from - scratch. -""" - -__all__ = ['Ensemble', 'NVEEnsemble', 'NVTEnsemble', 'NPTEnsemble', 'ReplayEnsemble'] - -import numpy as np -import time - -from ipi.utils.depend import * -from ipi.utils import units -from ipi.utils.softexit import softexit -from ipi.utils.io.io_xyz import read_xyz -from ipi.utils.io.io_pdb import read_pdb -from ipi.utils.io.io_xml import xml_parse_file -from ipi.utils.units import Constants, unit_to_internal -from ipi.inputs.thermostats import InputThermo -from ipi.inputs.barostats import InputBaro -from ipi.engine.thermostats import * -from ipi.engine.barostats import * - - -class Ensemble(dobject): - """Base ensemble class. - - Gives the standard methods and attributes needed in all the - ensemble classes. - - Attributes: - beads: A beads object giving the atoms positions. - cell: A cell object giving the system box. - forces: A forces object giving the virial and the forces acting on - each bead. - prng: A random number generator object. - nm: An object which does the normal modes transformation. - fixcom: A boolean which decides whether the centre of mass - motion will be constrained or not. - - Depend objects: - econs: The conserved energy quantity appropriate to the given - ensemble. Depends on the various energy terms which make it up, - which are different depending on the ensemble. - temp: The system temperature. - dt: The timestep for the algorithms. - ntemp: The simulation temperature. Will be nbeads times higher than - the system temperature as PIMD calculations are done at this - effective classical temperature. - """ - - def __init__(self, dt, temp, fixcom=False): - """Initializes Ensemble. - - Args: - dt: The timestep of the simulation algorithms. - temp: The temperature. - fixcom: An optional boolean which decides whether the centre of mass - motion will be constrained or not. Defaults to False. - """ - - dset(self, "econs", depend_value(name='econs', func=self.get_econs)) - dset(self, "temp", depend_value(name='temp', value=temp)) - dset(self, "dt", depend_value(name='dt', value=dt)) - self.fixcom = fixcom - - - def bind(self, beads, nm, cell, bforce, prng): - """Binds beads, cell, bforce and prng to the ensemble. - - This takes a beads object, a cell object, a forcefield object and a - random number generator object and makes them members of the ensemble. - It also then creates the objects that will hold the data needed in the - ensemble algorithms and the dependency network. Note that the conserved - quantity is defined in the init, but as each ensemble has a different - conserved quantity the dependencies are defined in bind. - - Args: - beads: The beads object from which the bead positions are taken. - nm: A normal modes object used to do the normal modes transformation. - cell: The cell object from which the system box is taken. - bforce: The forcefield object from which the force and virial are - taken. - prng: The random number generator object which controls random number - generation. - """ - - # store local references to the different bits of the simulation - self.beads = beads - self.cell = cell - self.forces = bforce - self.prng = prng - self.nm = nm - - # n times the temperature - dset(self,"ntemp", depend_value(name='ntemp',func=self.get_ntemp, - dependencies=[dget(self,"temp")])) - - # dependencies of the conserved quantity - dget(self,"econs").add_dependency(dget(self.beads, "kin")) - dget(self,"econs").add_dependency(dget(self.forces, "pot")) - dget(self,"econs").add_dependency(dget(self.beads, "vpath")) - - - def get_ntemp(self): - """Returns the PI simulation temperature (P times the physical T).""" - - return self.temp*self.beads.nbeads - - - def pstep(self): - """Dummy momenta propagator which does nothing.""" - - pass - - def qcstep(self): - """Dummy centroid position propagator which does nothing.""" - - pass - - def step(self): - """Dummy simulation time step which does nothing.""" - - pass - - def get_econs(self): - """Calculates the conserved energy quantity for constant energy - ensembles. - """ - - return self.beads.vpath*self.nm.omegan2 + self.nm.kin + self.forces.pot - - -class NVEEnsemble(Ensemble): - """Ensemble object for constant energy simulations. - - Has the relevant conserved quantity and normal mode propagator for the - constant energy ensemble. Note that a temperature of some kind must be - defined so that the spring potential can be calculated. - - Attributes: - ptime: The time taken in updating the velocities. - qtime: The time taken in updating the positions. - ttime: The time taken in applying the thermostat steps. - - Depend objects: - econs: Conserved energy quantity. Depends on the bead kinetic and - potential energy, and the spring potential energy. - """ - - def __init__(self, dt, temp, fixcom=False): - """Initializes NVEEnsemble. - - Args: - dt: The simulation timestep. - temp: The system temperature. - fixcom: An optional boolean which decides whether the centre of mass - motion will be constrained or not. Defaults to False. - """ - - super(NVEEnsemble,self).__init__(dt=dt,temp=temp, fixcom=fixcom) - - def rmcom(self): - """This removes the centre of mass contribution to the kinetic energy. - - Calculates the centre of mass momenta, then removes the mass weighted - contribution from each atom. If the ensemble defines a thermostat, then - the contribution to the conserved quantity due to this subtraction is - added to the thermostat heat energy, as it is assumed that the centre of - mass motion is due to the thermostat. - - If there is a choice of thermostats, the thermostat - connected to the centroid is chosen. - """ - - if (self.fixcom): - pcom = np.zeros(3,float); - - na3 = self.beads.natoms*3 - nb = self.beads.nbeads - p = depstrip(self.beads.p) - m = depstrip(self.beads.m3)[:,0:na3:3] - M = self.beads[0].M - - for i in range(3): - pcom[i] = p[:,i:na3:3].sum() - - if hasattr(self,"thermostat"): - if hasattr(self.thermostat, "_thermos"): - self.thermostat._thermos[0].ethermo += np.dot(pcom,pcom)/(2.0*M*nb) - else: - self.thermostat.ethermo += np.dot(pcom,pcom)/(2.0*M*nb) - - # subtracts COM _velocity_ - pcom *= 1.0/(nb*M) - for i in range(3): - self.beads.p[:,i:na3:3] -= m*pcom[i] - - def pstep(self): - """Velocity Verlet momenta propagator.""" - - self.beads.p += depstrip(self.forces.f)*(self.dt*0.5) - - def qcstep(self): - """Velocity Verlet centroid position propagator.""" - - self.nm.qnm[0,:] += depstrip(self.nm.pnm)[0,:]/depstrip(self.beads.m3)[0]*self.dt - - def step(self): - """Does one simulation time step.""" - - self.ptime = -time.time() - self.pstep() - self.ptime += time.time() - - self.qtime = -time.time() - self.qcstep() - - self.nm.free_qstep() - self.qtime += time.time() - - self.ptime -= time.time() - self.pstep() - self.ptime += time.time() - - self.ttime = -time.time() - self.rmcom() - self.ttime += time.time() - - -class NVTEnsemble(NVEEnsemble): - """Ensemble object for constant temperature simulations. - - Has the relevant conserved quantity and normal mode propagator for the - constant temperature ensemble. Contains a thermostat object containing the - algorithms to keep the temperature constant. - - Attributes: - thermostat: A thermostat object to keep the temperature constant. - - Depend objects: - econs: Conserved energy quantity. Depends on the bead kinetic and - potential energy, the spring potential energy and the heat - transferred to the thermostat. - """ - - def __init__(self, dt, temp, thermostat=None, fixcom=False): - """Initializes NVTEnsemble. - - Args: - dt: The simulation timestep. - temp: The system temperature. - thermostat: A thermostat object to keep the temperature constant. - Defaults to Thermostat() - fixcom: An optional boolean which decides whether the centre of mass - motion will be constrained or not. Defaults to False. - """ - - super(NVTEnsemble,self).__init__(dt=dt,temp=temp, fixcom=fixcom) - - if thermostat is None: - self.thermostat = Thermostat() - else: - self.thermostat = thermostat - - def bind(self, beads, nm, cell, bforce, prng): - """Binds beads, cell, bforce and prng to the ensemble. - - This takes a beads object, a cell object, a forcefield object and a - random number generator object and makes them members of the ensemble. - It also then creates the objects that will hold the data needed in the - ensemble algorithms and the dependency network. Also note that the - thermostat timestep and temperature are defined relative to the system - temperature, and the the thermostat temperature is held at the - higher simulation temperature, as is appropriate. - - Args: - beads: The beads object from which the bead positions are taken. - nm: A normal modes object used to do the normal modes transformation. - cell: The cell object from which the system box is taken. - bforce: The forcefield object from which the force and virial are - taken. - prng: The random number generator object which controls random number - generation. - """ - - super(NVTEnsemble,self).bind(beads, nm, cell, bforce, prng) - fixdof = None - if self.fixcom: - fixdof = 3 - - # first makes sure that the thermostat has the correct temperature, then proceed with binding it. - deppipe(self,"ntemp", self.thermostat,"temp") - deppipe(self,"dt", self.thermostat, "dt") - - #decides whether the thermostat will work in the normal mode or - #the bead representation. - if isinstance(self.thermostat,ThermoNMGLE) or isinstance(self.thermostat,ThermoNMGLEG) or isinstance(self.thermostat,ThermoPILE_L) or isinstance(self.thermostat,ThermoPILE_G): - self.thermostat.bind(nm=self.nm,prng=prng,fixdof=fixdof ) - else: - self.thermostat.bind(beads=self.beads,prng=prng, fixdof=fixdof) - - dget(self,"econs").add_dependency(dget(self.thermostat, "ethermo")) - - def step(self): - """Does one simulation time step.""" - - self.ttime = -time.time() - self.thermostat.step() - self.rmcom() - self.ttime += time.time() - - self.ptime = -time.time() - self.pstep() - self.ptime += time.time() - - self.qtime = -time.time() - self.qcstep() - self.nm.free_qstep() - self.qtime += time.time() - - self.ptime -= time.time() - self.pstep() - self.ptime += time.time() - - self.ttime -= time.time() - self.thermostat.step() - self.rmcom() - self.ttime += time.time() - - def get_econs(self): - """Calculates the conserved energy quantity for constant temperature - ensemble. - """ - - return NVEEnsemble.get_econs(self) + self.thermostat.ethermo - - -class NPTEnsemble(NVTEnsemble): - """Ensemble object for constant pressure simulations. - - Has the relevant conserved quantity and normal mode propagator for the - constant pressure ensemble. Contains a thermostat object containing the - algorithms to keep the temperature constant, and a barostat to keep the - pressure constant. - - Attributes: - barostat: A barostat object to keep the pressure constant. - - Depend objects: - econs: Conserved energy quantity. Depends on the bead and cell kinetic - and potential energy, the spring potential energy, the heat - transferred to the beads and cell thermostat, the temperature and - the cell volume. - pext: External pressure. - """ - - def __init__(self, dt, temp, pext, thermostat=None, barostat=None, fixcom=False): - """Initializes NPTEnsemble. - - Args: - dt: The simulation timestep. - temp: The system temperature. - pext: The external pressure. - thermostat: A thermostat object to keep the temperature constant. - Defaults to Thermostat(). - barostat: A barostat object to keep the pressure constant. - Defaults to Barostat(). - fixcom: An optional boolean which decides whether the centre of mass - motion will be constrained or not. Defaults to False. - """ - - super(NPTEnsemble,self).__init__(dt, temp, thermostat, fixcom=fixcom) - if barostat == None: - self.barostat = Barostat() - else: - self.barostat = barostat - - dset(self,"pext",depend_value(name='pext')) - if not pext is None: - self.pext = pext - else: self.pext = 0.0 - - - def bind(self, beads, nm, cell, bforce, prng): - """Binds beads, cell, bforce and prng to the ensemble. - - This takes a beads object, a cell object, a forcefield object and a - random number generator object and makes them members of the ensemble. - It also then creates the objects that will hold the data needed in the - ensemble algorithms and the dependency network. Also note that the cell - thermostat timesteps and temperatures are defined relative to the system - temperature, and the the thermostat temperatures are held at the - higher simulation temperature, as is appropriate. - - Args: - beads: The beads object from which the bead positions are taken. - nm: A normal modes object used to do the normal modes transformation. - cell: The cell object from which the system box is taken. - bforce: The forcefield object from which the force and virial are - taken. - prng: The random number generator object which controls random number - generation. - """ - - - fixdof = None - if self.fixcom: - fixdof = 3 - - super(NPTEnsemble,self).bind(beads, nm, cell, bforce, prng) - self.barostat.bind(beads, nm, cell, bforce, prng=prng, fixdof=fixdof) - - - deppipe(self,"ntemp", self.barostat, "temp") - deppipe(self,"dt", self.barostat, "dt") - deppipe(self,"pext", self.barostat, "pext") - dget(self,"econs").add_dependency(dget(self.barostat, "ebaro")) - - def get_econs(self): - """Calculates the conserved energy quantity for the constant pressure - ensemble. - """ - - return NVTEnsemble.get_econs(self) + self.barostat.ebaro - - def step(self): - """NPT time step. - - Note that the barostat only propagates the centroid coordinates. If this - approximation is made a centroid virial pressure and stress estimator can - be defined, so this gives the best statistical convergence. This is - allowed as the normal mode propagation is approximately unaffected - by volume fluctuations as long as the system box is much larger than - the radius of gyration of the ring polymers. - """ - - self.ttime = -time.time() - self.thermostat.step() - self.barostat.thermostat.step() - self.rmcom() - self.ttime += time.time() - - self.ptime = -time.time() - self.barostat.pstep() - self.ptime += time.time() - - self.qtime = -time.time() - self.barostat.qcstep() - self.nm.free_qstep() - self.qtime += time.time() - - self.ptime -= time.time() - self.barostat.pstep() - self.ptime += time.time() - - self.ttime -= time.time() - self.barostat.thermostat.step() - self.thermostat.step() - self.rmcom() - self.ttime += time.time() - - -class ReplayEnsemble(Ensemble): - """Ensemble object that just loads snapshots from an external file in sequence. - - Has the relevant conserved quantity and normal mode propagator for the - constant energy ensemble. Note that a temperature of some kind must be - defined so that the spring potential can be calculated. - - Attributes: - intraj: The input trajectory file. - ptime: The time taken in updating the velocities. - qtime: The time taken in updating the positions. - ttime: The time taken in applying the thermostat steps. - - Depend objects: - econs: Conserved energy quantity. Depends on the bead kinetic and - potential energy, and the spring potential energy. - """ - - def __init__(self, dt, temp, fixcom=False, intraj=None): - """Initializes ReplayEnsemble. - - Args: - dt: The simulation timestep. - temp: The system temperature. - fixcom: An optional boolean which decides whether the centre of mass - motion will be constrained or not. Defaults to False. - intraj: The input trajectory file. - """ - - super(ReplayEnsemble,self).__init__(dt=dt,temp=temp,fixcom=fixcom) - if intraj == None: - raise ValueError("Must provide an initialized InitFile object to read trajectory from") - self.intraj = intraj - if intraj.mode == "manual": - raise ValueError("Replay can only read from PDB or XYZ files -- or a single frame from a CHK file") - self.rfile = open(self.intraj.value,"r") - - def step(self): - """Does one simulation time step.""" - - self.ptime = self.ttime = 0 - self.qtime = -time.time() - - try: - if (self.intraj.mode == "xyz"): - for b in self.beads: - myatoms = read_xyz(self.rfile) - myatoms.q *= unit_to_internal("length",self.intraj.units,1.0) - b.q[:] = myatoms.q - elif (self.intraj.mode == "pdb"): - for b in self.beads: - myatoms, mycell = read_pdb(self.rfile) - myatoms.q *= unit_to_internal("length",self.intraj.units,1.0) - mycell.h *= unit_to_internal("length",self.intraj.units,1.0) - b.q[:] = myatoms.q - self.cell.h[:] = mycell.h - elif (self.intraj.mode == "chk" or self.intraj.mode == "checkpoint"): - # reads configuration from a checkpoint file - xmlchk = xml_parse_file(self.rfile) # Parses the file. - - from ipi.inputs.simulation import InputSimulation - simchk = InputSimulation() - simchk.parse(xmlchk.fields[0][1]) - mycell = simchk.cell.fetch() - mybeads = simchk.beads.fetch() - self.cell.h[:] = mycell.h - self.beads.q[:] = mybeads.q - softexit.trigger(" # Read single checkpoint") - except EOFError: - softexit.trigger(" # Finished reading re-run trajectory") - - self.qtime += time.time() - - diff --git a/tools/i-pi/ipi/engine/forces.py b/tools/i-pi/ipi/engine/forces.py deleted file mode 100644 index 5e3dabf8db..0000000000 --- a/tools/i-pi/ipi/engine/forces.py +++ /dev/null @@ -1,781 +0,0 @@ -"""Contains the classes that connect the driver to the python code. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Communicates with the driver code, obtaining the force, virial and potential. -Deals with creating the jobs that will be sent to the driver, and -returning the results to the python code. - -Classes: - ForceField: Base forcefield class with the generic methods and attributes. - FFSocket: Deals with a single replica of the system - ForceBeads: Deals with the parallelization of the force calculation over - different beads. - Forces: Deals with the parallelizatoin of the force calculation over - different forcefields. -""" - -__all__ = ['ForceField', 'ForceBeads', 'Forces', 'FFSocket'] - -import numpy as np -import time -from ipi.utils.softexit import softexit -from ipi.utils.messages import verbosity, warning -from ipi.utils.depend import * -from ipi.utils.nmtransform import nm_rescale -from ipi.interfaces.sockets import InterfaceSocket -from ipi.engine.beads import Beads - -class ForceField(dobject): - """Base forcefield class. - - Gives the standard methods and quantities needed in all the forcefield - classes. - - Attributes: - atoms: An Atoms object containing all the atom positions. - cell: A Cell object containing the system box. - - Depend objects: - ufvx: A list of the form [pot, f, vir]. These quantities are calculated - all at one time by the driver, so are collected together. Each separate - object is then taken from the list. Depends on the atom positions and - the system box. - extra: A string containing some formatted output returned by the client. Depends on ufvx. - pot: A float giving the potential energy of the system. Depends on ufvx. - f: An array containing all the components of the force. Depends on ufvx. - fx: A slice of f containing only the x components of the forces. - fy: A slice of f containing only the y components of the forces. - fz: A slice of f containing only the z components of the forces. - vir: An array containing the components of the virial tensor in upper - triangular form, not divided by the volume. Depends on ufvx. - """ - - def __init__(self): - """Initializes ForceField.""" - - # ufvx is a list [ u, f, vir, extra ] which stores the results of the force - #calculation - dset(self,"ufvx", depend_value(name="ufvx", func=self.get_all)) - - def copy(self): - """Creates a deep copy without the bound objects. - - Used in ForceBeads to create a ForceField for each replica of the system. - - Returns: - A ForceField object without atoms or cell attributes. - """ - - return type(self)(self.nbeads, self.weight) - - def bind(self, atoms, cell): - """Binds atoms and cell to the forcefield. - - This takes an atoms object and a cell object and makes them members of - the forcefield. It also then creates the objects that will hold the data - that the driver returns and the dependency network. - - Args: - atoms: The Atoms object from which the atom positions are taken. - cell: The Cell object from which the system box is taken. - """ - - # stores a reference to the atoms and cell we are computing forces for - self.atoms = atoms - self.cell = cell - - # ufv depends on the atomic positions and on the cell - dget(self,"ufvx").add_dependency(dget(self.atoms,"q")) - dget(self,"ufvx").add_dependency(dget(self.cell,"h")) - - # potential and virial are to be extracted very simply from ufv - dset(self,"pot", - depend_value(name="pot", func=self.get_pot, - dependencies=[dget(self,"ufvx")])) - - dset(self,"vir", - depend_array(name="vir", value=np.zeros((3,3),float),func=self.get_vir, - dependencies=[dget(self,"ufvx")])) - - # NB: the force requires a bit more work, to define shortcuts to xyz - # slices without calculating the force at this point. - fbase = np.zeros(atoms.natoms*3, float) - dset(self,"f", - depend_array(name="f", value=fbase, func=self.get_f, - dependencies=[dget(self,"ufvx")])) - - dset(self,"extra", - depend_value(name="extra", func=self.get_extra, - dependencies=[dget(self,"ufvx")])) - - dset(self,"fx", depend_array(name="fx", value=fbase[0:3*atoms.natoms:3])) - dset(self,"fy", depend_array(name="fy", value=fbase[1:3*atoms.natoms:3])) - dset(self,"fz", depend_array(name="fz", value=fbase[2:3*atoms.natoms:3])) - depcopy(self,"f", self,"fx") - depcopy(self,"f", self,"fy") - depcopy(self,"f", self,"fz") - - def queue(self): - """Dummy queueing method.""" - - pass - - def stop(self): - """Dummy queueing method.""" - - pass - - def run(self): - """Dummy queueing method.""" - - pass - - def get_all(self): - """Dummy driver routine. - - Returns: - A list of the form [potential, force, virial] where the potential - and all components of the force and virial have been set to zero. - """ - - return [0.0, np.zeros(3*self.atoms.natoms), np.zeros((3,3),float), ""] - - def get_pot(self): - """Calls get_all routine of forcefield to update potential. - - Returns: - Potential energy. - """ - - return self.ufvx[0] - - def get_f(self): - """Calls get_all routine of forcefield to update force. - - Returns: - An array containing all the components of the force. - """ - - return depstrip(self.ufvx[1]) - - def get_vir(self): - """Calls get_all routine of forcefield to update virial. - - Returns: - An array containing the virial in upper triangular form, not divided - by the volume. - """ - - vir = depstrip(self.ufvx[2]) - vir[1,0] = 0.0 - vir[2,0:2] = 0.0 - return vir - - def get_extra(self): - """Calls get_all routine of forcefield to update potential. - - Returns: - A string containing all formatted additional output that the - client might have produced. - """ - - return self.ufvx[3] - - -class FFSocket(ForceField): - """Interface between the PIMD code and the socket for a single replica. - - Deals with an individual replica of the system, obtaining the potential - force and virial appropriate to this system. Deals with the distribution of - jobs to the interface. - - Attributes: - parameters: A dictionary of the parameters used by the driver. Of the - form {'name': value}. - socket: The interface object which contains the socket through which - communication between the forcefield and the driver is done. - request: During the force calculation step this holds a dictionary - containing the relevant data for determining the progress of the step. - Of the form {'atoms': atoms, 'cell': cell, 'pars': parameters, - 'status': status, 'result': result, 'id': bead id, - 'start': starting time}. - """ - - def __init__(self, pars=None, interface=None): - """Initializes FFSocket. - - Args: - pars: Optional dictionary, giving the parameters needed by the driver. - interface: Optional Interface object, which contains the socket. - """ - - # a socket to the communication library is created or linked - super(FFSocket,self).__init__() - if interface is None: - self.socket = InterfaceSocket() - else: - self.socket = interface - - if pars is None: - self.pars = {} - else: - self.pars = pars - self.request = None - - def bind(self, atoms, cell): - """Pass on the binding request from ForceBeads. - - Also makes sure to set the socket's softexit. - - Args: - atoms: Atoms object from which the bead positions are taken. - cell: Cell object from which the system box is taken. - """ - - super(FFSocket,self).bind(atoms, cell) - - def copy(self): - """Creates a deep copy without the bound objects. - - Used in ForceBeads to create a FFSocket for each replica of the system. - - Returns: - A FFSocket object without atoms or cell attributes. - """ - - # does not copy the bound objects - # (i.e., the returned forcefield must be bound before use) - return type(self)(self.pars, self.socket) - - def get_all(self): - """Driver routine. - - When one of the force, potential or virial are called, this sends the - atoms and cell to the driver through the interface, requesting that the - driver does the calculation. This then waits until the driver is finished, - and then returns the ufvx list. - - Returns: - A list of the form [potential, force, virial, extra]. - """ - - # this is converting the distribution library requests into [ u, f, v ] lists - if self.request is None: - self.request = self.socket.queue(self.atoms, self.cell, pars=self.pars, reqid=-1) - while self.request["status"] != "Done": - if self.request["status"] == "Exit": - break - time.sleep(self.socket.latency) - if self.request["status"] == "Exit": - softexit.trigger(" @Force: Requested returned a Exit status") - - # data has been collected, so the request can be released and a slot - #freed up for new calculations - self.socket.release(self.request) - result = self.request["result"] - self.request = None - - return result - - def queue(self, reqid=-1): - """Sends the job to the interface queue directly. - - Allows the ForceBeads object to ask for the ufvx list of each replica - directly without going through the get_all function. This allows - all the jobs to be sent at once, allowing them to be parallelized. - - Args: - reqid: An optional integer that indentifies requests of the same type, - e.g. the bead index. - """ - - if self.request is None and dget(self,"ufvx").tainted(): - self.request = self.socket.queue(self.atoms, self.cell, pars=self.pars, reqid=reqid) - - def run(self): - """Makes the socket start looking for driver codes. - - Tells the interface code to start the thread that looks for - connection from the driver codes in a loop. Until this point no - jobs can be queued. - """ - - if not self.socket.started(): - self.socket.start_thread() - - def stop(self): - """Makes the socket stop looking for driver codes. - - Tells the interface code to stop the thread that looks for - connection from the driver codes in a loop. After this point no - jobs can be queued. - """ - - if self.socket.started(): - self.socket.end_thread() - - -class ForceBeads(dobject): - """Class that gathers the forces for each replica together. - - Deals with splitting the bead representation into - separate replicas, and collecting the data from each replica. - - Attributes: - natoms: An integer giving the number of atoms. - nbeads: An integer giving the number of beads. - f_model: A model used to create the forcefield objects for each replica - of the system. - _forces: A list of the forcefield objects for all the replicas. - weight: A float that will be used to weight the contribution of this - forcefield to the total force. - - Depend objects: - f: An array containing the components of the force. Depends on each - replica's ufvx list. - pots: A list containing the potential energy for each system replica. - Depends on each replica's ufvx list. - virs: A list containing the virial tensor for each system replica. - Depends on each replica's ufvx list. - pot: The sum of the potential energy of the replicas. - vir: The sum of the virial tensor of the replicas. - extras: Strings containing some formatted output returned by the client. - Depends on each replica's ufvx list. - """ - - def __init__(self, model, nbeads=0, weight=1.0): - """Initializes ForceBeads - - Args: - model: A model to be used to create the forcefield objects for all - the replicas of the system. - nbeads: The number of replicas. - weight: A relative weight to be given to the values obtained with this - forcefield. When the contribution of all the forcefields is - combined to give a total force, the contribution of this forcefield - will be weighted by this factor. - """ - - self.f_model = model - self.nbeads = nbeads - self.weight = weight - - def copy(self): - """Creates a deep copy without the bound objects. - - Used so that we can create multiple Forces objects from the same - Forcebeads model, without binding a particular ForceBeads object twice. - - Returns: - A ForceBeads object without beads or cell attributes. - """ - - # does not copy the bound objects (i.e., the returned forcefield must be bound before use) - return type(self)(self.f_model, self.nbeads, self.weight) - - - def bind(self, beads, cell): - """Binds beads, cell and force to the forcefield. - - Takes the beads, cell objects and makes them members of the forcefield. - Also takes the force object and copies it once for each replica of the - system, then binds each replica to one of the copies so that the force - calculation can be parallelized. Creates the objects that will - hold the data that the driver returns and the dependency network. - - Args: - beads: Beads object from which the bead positions are taken. - cell: Cell object from which the system box is taken. - """ - - # stores a copy of the number of atoms and of beads - #!TODO! make them read-only properties - self.natoms = beads.natoms - if (self.nbeads != beads.nbeads): - raise ValueError("Binding together a Beads and a ForceBeads objects with different numbers of beads") - - # creates an array of force objects, which are bound to the beads - #and the cell - self._forces = []; - for b in range(self.nbeads): - new_force = self.f_model.copy() - new_force.bind(beads[b], cell) - self._forces.append(new_force) - - # f is a big array which assembles the forces on individual beads - dset(self,"f", - depend_array(name="f",value=np.zeros((self.nbeads,3*self.natoms)), - func=self.f_gather, - dependencies=[dget(self._forces[b],"f") for b in range(self.nbeads)])) - - # collection of pots and virs from individual beads - dset(self,"pots", - depend_array(name="pots", value=np.zeros(self.nbeads,float), - func=self.pot_gather, - dependencies=[dget(self._forces[b],"pot") for b in range(self.nbeads)])) - dset(self,"virs", - depend_array(name="virs", value=np.zeros((self.nbeads,3,3),float), - func=self.vir_gather, - dependencies=[dget(self._forces[b],"vir") for b in range(self.nbeads)])) - dset(self,"extras", - depend_value(name="extras", value=np.zeros(self.nbeads,float), - func=self.extra_gather, - dependencies=[dget(self._forces[b],"extra") for b in range(self.nbeads)])) - - # total potential and total virial - dset(self,"pot", - depend_value(name="pot", func=(lambda: self.pots.sum()), - dependencies=[dget(self,"pots")])) - dset(self,"vir", - depend_array(name="vir", func=self.get_vir, value=np.zeros((3,3)), - dependencies=[dget(self,"virs")])) - - def run(self): - """Makes the socket start looking for driver codes. - - Tells the interface code to start the thread that looks for - connection from the driver codes in a loop. Until this point no - jobs can be queued. - """ - - for b in range(self.nbeads): - self._forces[b].run() - - def stop(self): - """Makes the socket stop looking for driver codes. - - Tells the interface code to stop the thread that looks for - connection from the driver codes in a loop. After this point no - jobs can be queued. - """ - - for b in range(self.nbeads): - self._forces[b].stop() - - def queue(self): - """Submits all the required force calculations to the interface.""" - - # this should be called in functions which access u,v,f for ALL the beads, - # before accessing them. it is basically pre-queueing so that the - # distributed-computing magic can work - for b in range(self.nbeads): - self._forces[b].queue(reqid=b) - - def pot_gather(self): - """Obtains the potential energy for each replica. - - Returns: - A list of the potential energy of each replica of the system. - """ - - self.queue() - return np.array([b.pot for b in self._forces], float) - - def extra_gather(self): - """Obtains the potential energy for each replica. - - Returns: - A list of the potential energy of each replica of the system. - """ - - self.queue() - return [b.extra for b in self._forces] - - def vir_gather(self): - """Obtains the virial for each replica. - - Returns: - A list of the virial of each replica of the system. - """ - - self.queue() - return np.array([b.vir for b in self._forces], float) - - def f_gather(self): - """Obtains the force vector for each replica. - - Returns: - An array with all the components of the force. Row i gives the force - array for replica i of the system. - """ - - newf = np.zeros((self.nbeads,3*self.natoms),float) - - self.queue() - for b in range(self.nbeads): - newf[b] = depstrip(self._forces[b].f) - - return newf - - #serial -# for b in range(self.nbeads): newf[b]=self._forces[b].f - # threaded -# bthreads=[] -# print "starting threads" -# for b in range(self.nbeads): -# thread=threading.Thread(target=self._getbead, args=(b,newf,)) -# thread.start() -# bthreads.append(thread) - -# print "waiting threads" -# for b in range(self.nbeads): bthreads[b].join() -# print "threads joined in" - - def get_vir(self): - """Sums the virial of each replica. - - Not the actual system virial, as it has not been divided by either the - number of beads or the cell volume. - - Returns: - Virial sum. - """ - - vir = np.zeros((3,3)) - for v in depstrip(self.virs): - vir += v - return vir - - def __len__(self): - """Length function. - - This is called whenever the standard function len(forcebeads) is used. - - Returns: - The number of beads. - """ - - return self.nbeads - - def __getitem__(self,index): - """Overwrites standard getting function. - - This is called whenever the standard function forcebeads[index] is used. - Returns the force on bead index. - - Args: - index: The index of the replica of the system to be accessed. - - Returns: - The forces acting on the replica of the system given by the index. - """ - - return self._forces[index] - - -class Forces(dobject): - """Class that gathers all the forces together. - - Collects many forcefield instances and parallelizes getting the forces - in a PIMD environment. - - Attributes: - natoms: An integer giving the number of atoms. - nbeads: An integer giving the number of beads. - nforces: An integer giving the number of ForceBeads objects. - mforces: A list of all the forcefield objects. - mbeads: A list of all the beads objects. Some of these may be contracted - ring polymers, with a smaller number of beads than of the simulation. - mweights: A list of the weights of all the forcefields. - mrpc: A list of the objects containing the functions required to - contract the ring polymers of the different forcefields. - - Depend objects: - f: An array containing the components of the force. Depends on each - replica's ufvx list. - pots: A list containing the potential energy for each system replica. - Depends on each replica's ufvx list. - virs: A list containing the virial tensor for each system replica. - Depends on each replica's ufvx list. - extras: A list containing the "extra" strings for each replica. - pot: The sum of the potential energy of the replicas. - vir: The sum of the virial tensor of the replicas. - """ - - def bind(self, beads, cell, flist): - - self.natoms = beads.natoms - self.nbeads = beads.nbeads - self.nforces = len(flist) - - # flist should be a list of tuples containing ( "name", forcebeads) - self.mforces = [] - self.mbeads = [] - self.mweights = [] - self.mrpc = [] - - # a "function factory" to generate functions to automatically update - #contracted paths - def make_rpc(rpc, beads): - return lambda: rpc.b1tob2(depstrip(beads.q)) - - # creates new force objects, possibly acting on contracted path - #representations - for (ftype, fbeads) in flist: - - # creates an automatically-updated contracted beads object - newb = fbeads.nbeads - newforce = fbeads.copy() - newweight = fbeads.weight - - # if the number of beads for this force component is unspecified, - #assume full force evaluation - if newb == 0: - newb = beads.nbeads - newforce.nbeads = newb - - newbeads = Beads(beads.natoms, newb) - newrpc = nm_rescale(beads.nbeads, newb) - - dget(newbeads,"q")._func = make_rpc(newrpc, beads) - for b in newbeads: - # must update also indirect access to the beads coordinates - dget(b,"q")._func = dget(newbeads,"q")._func - - # makes newbeads.q depend from beads.q - dget(beads,"q").add_dependant(dget(newbeads,"q")) - - #now we create a new forcebeads which is bound to newbeads! - newforce.bind(newbeads, cell) - - #adds information we will later need to the appropriate lists. - self.mweights.append(newweight) - self.mbeads.append(newbeads) - self.mforces.append(newforce) - self.mrpc.append(newrpc) - - #now must expose an interface that gives overall forces - dset(self,"f", - depend_array(name="f",value=np.zeros((self.nbeads,3*self.natoms)), - func=self.f_combine, - dependencies=[dget(ff, "f") for ff in self.mforces] ) ) - - # collection of pots and virs from individual ff objects - dset(self,"pots", - depend_array(name="pots", value=np.zeros(self.nbeads,float), - func=self.pot_combine, - dependencies=[dget(ff, "pots") for ff in self.mforces]) ) - - # must take care of the virials! - dset(self,"virs", - depend_array(name="virs", value=np.zeros((self.nbeads,3,3),float), - func=self.vir_combine, - dependencies=[dget(ff, "virs") for ff in self.mforces]) ) - - dset(self,"extras", - depend_value(name="extras", value=np.zeros(self.nbeads,float), - func=self.extra_combine, - dependencies=[dget(ff, "extras") for ff in self.mforces])) - - # total potential and total virial - dset(self,"pot", - depend_value(name="pot", func=(lambda: self.pots.sum()), - dependencies=[dget(self,"pots")])) - dset(self,"vir", - depend_array(name="vir", func=self.get_vir, value=np.zeros((3,3)), - dependencies=[dget(self,"virs")])) - - def run(self): - """Makes the socket start looking for driver codes. - - Tells the interface code to start the thread that looks for - connection from the driver codes in a loop. Until this point no - jobs can be queued. - """ - - for ff in self.mforces: - ff.run() - - def stop(self): - """Makes the socket stop looking for driver codes. - - Tells the interface code to stop the thread that looks for - connection from the driver codes in a loop. After this point no - jobs can be queued. - """ - - for ff in self.mforces: - ff.stop() - - def queue(self): - """Submits all the required force calculations to the forcefields.""" - - for ff in self.mforces: - ff.queue() - - def get_vir(self): - """Sums the virial of each forcefield. - - Not the actual system virial. - - Returns: - Virial sum. - """ - - vir = np.zeros((3,3)) - for v in depstrip(self.virs): - vir += v - return vir - - def f_combine(self): - """Obtains the total force vector.""" - - self.queue() - rf = np.zeros((self.nbeads,3*self.natoms),float) - for k in range(self.nforces): - # "expand" to the total number of beads the forces from the - #contracted one - rf += self.mweights[k]*self.mrpc[k].b2tob1(depstrip(self.mforces[k].f)) - return rf - - def pot_combine(self): - """Obtains the potential energy for each forcefield.""" - - self.queue() - rp = np.zeros(self.nbeads,float) - for k in range(self.nforces): - # "expand" to the total number of beads the potentials from the - #contracted one - rp += self.mweights[k]*self.mrpc[k].b2tob1(self.mforces[k].pots) - return rp - - def extra_combine(self): - """Obtains the potential energy for each forcefield.""" - - self.queue() - rp = [ "" for b in range(self.nbeads) ] - for k in range(self.nforces): - # "expand" to the total number of beads the potentials from the - #contracted one - for b in range(self.nbeads): - rp[b] += self.mforces[k].extras[b] - return rp - - def vir_combine(self): - """Obtains the virial tensor for each forcefield.""" - - self.queue() - rp = np.zeros((self.nbeads,3,3),float) - for k in range(self.nforces): - virs = depstrip(self.mforces[k].virs) - # "expand" to the total number of beads the virials from the - #contracted one, element by element - for i in range(3): - for j in range(3): - rp[:,i,j] += self.mweights[k]*self.mrpc[k].b2tob1(virs[:,i,j]) - return rp diff --git a/tools/i-pi/ipi/engine/initializer.py b/tools/i-pi/ipi/engine/initializer.py deleted file mode 100644 index fd9bcfb9fa..0000000000 --- a/tools/i-pi/ipi/engine/initializer.py +++ /dev/null @@ -1,549 +0,0 @@ -"""Contains the classes that are used to initialize data in the simulation. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -These classes can either be used to restart a simulation with some different -data or used to start a calculation. Any data given in these classes will -overwrite data given elsewhere. - -Classes: - Initializer: Holds the functions that are required to initialize objects in - the code. Data can be initialized from a file, or according to a - particular parameter. An example of the former would be initializing - the configurations from a xyz file, an example of the latter would be - initializing the velocities according to the physical temperature. - InitBase: Simple class that reads data from a string or file. - InitIndexed: The same as init base, but can also optionally hold - information about which atom or bead to initialize from. - -Functions: - init_xyz: Reads beads data from a xyz file. - init_pdb: Reads beads and cell data from a pdb file. - init_chk: Reads beads, cell and thermostat data from a checkpoint file. - init_beads: Initializes a beads object from an Initializer object. - init_vector: Initializes a vector from an Initializer object. - set_vector: Initializes a vector from another vector. -""" - -import numpy as np - -from ipi.engine.beads import Beads -from ipi.engine.cell import Cell -from ipi.engine.normalmodes import NormalModes -from ipi.engine.ensembles import Ensemble -from ipi.utils.io.io_xyz import read_xyz -from ipi.utils.io.io_pdb import read_pdb -from ipi.utils.io.io_xml import xml_parse_file -from ipi.utils.depend import dobject -from ipi.utils.units import Constants, unit_to_internal -from ipi.utils.nmtransform import nm_rescale -from ipi.utils.messages import verbosity, warning, info - -__all__ = ['Initializer', 'InitBase', 'InitIndexed'] - -class InitBase(dobject): - """Base class for initializer objects. - - Attributes: - value: A duck-typed stored value. - mode: A string that determines how the value is to be interpreted. - units: A string giving which unit the value is in. - """ - - def __init__(self, value="", mode="", units="", **others): - """Initializes InitFile. - - Args: - value: A string which specifies what value to initialize the - simulation property to. - mode: A string specifying what style of initialization should be - used to read the data. - units: A string giving which unit the value is in. - """ - - self.value = value - self.mode = mode - self.units = units - - for (o, v) in others.items(): - self.__dict__[o] = v - - -class InitIndexed(InitBase): - """Class to initialize objects which can be set for a particular bead. - - Attributes: - index: Which atom to initialize the value of. - bead: Which bead to initialize the value of. - """ - - def __init__(self, value="", mode="", units="", index=-1, bead=-1): - """Initializes InitFile. - - Args: - value: A string which specifies what value to initialize the - simulation property to. - mode: A string specifying what style of initialization should be - used to read the data. - units: A string giving which unit the value is in. - index: Which atom to initialize the value of. - bead: Which bead to initialize the value of. - """ - - super(InitIndexed,self).__init__(value=value, mode=mode, units=units, index=index, bead=bead) - - -def init_xyz(filename): - """Reads an xyz file and returns the data contained in it. - - Args: - filename: A string giving the name of the xyz file to be read from. - - Returns: - A list of Atoms objects as read from each frame of the xyz file. - """ - - rfile = open(filename,"r") - ratoms = [] - while True: - #while loop, so that more than one configuration can be given - #so multiple beads can be initialized at once. - try: - myatoms = read_xyz(rfile) - except EOFError: - break - ratoms.append(myatoms) - return ratoms - -def init_pdb(filename): - """Reads an pdb file and returns the data contained in it. - - Args: - filename: A string giving the name of the pdb file to be read from. - - Returns: - A list of Atoms objects as read from each frame of the pdb file, and - a Cell object as read from the final pdb frame. - """ - - rfile = open(filename,"r") - ratoms = [] - while True: - #while loop, so that more than one configuration can be given - #so multiple beads can be initialized at once. - try: - myatoms, rcell = read_pdb(rfile) - except EOFError: - break - ratoms.append(myatoms) - return ( ratoms, rcell ) # if multiple frames, the last cell is returned - -def init_chk(filename): - """Reads an checkpoint file and returns the data contained in it. - - Args: - filename: A string giving the name of the checkpoint file to be read from. - - Returns: - A Beads object, Cell object and Thermostat object as read from the - checkpoint file. - """ - - # reads configuration from a checkpoint file - rfile = open(filename,"r") - xmlchk = xml_parse_file(rfile) # Parses the file. - - from ipi.inputs.simulation import InputSimulation - simchk = InputSimulation() - simchk.parse(xmlchk.fields[0][1]) - rcell = simchk.cell.fetch() - rbeads = simchk.beads.fetch() - rthermo = simchk.ensemble.thermostat.fetch() - - return (rbeads, rcell, rthermo) - -def init_beads(iif, nbeads): - """A file to initialize a beads object from an appropriate initializer - object. - - Args: - iif: An Initializer object which has information on the bead positions. - nbeads: The number of beads. - - Raises: - ValueError: If called using an Initializer object with a 'manual' mode. - """ - - mode = iif.mode; value = iif.value - if mode == "xyz" or mode == "pdb": - if mode == "xyz": ratoms = init_xyz(value) - if mode == "pdb": ratoms = init_pdb(value)[0] - rbeads = Beads(ratoms[0].natoms,len(ratoms)) - for i in range(len(ratoms)): rbeads[i] = ratoms[i] - elif mode == "chk": - rbeads = init_chk(value)[0] - elif mode == "manual": - raise ValueError("Cannot initialize manually a whole beads object.") - - return rbeads - -def init_vector(iif, nbeads, momenta=False): - """A file to initialize a vector from an appropriate initializer - object. - - Args: - iif: An Initializer object specifying the value of a vector. - nbeads: The number of beads. - momenta: If bead momenta rather than positions are being initialized - from a checkpoint file, this is set to True. - """ - - mode = iif.mode; value = iif.value - if mode == "xyz" or mode == "pdb": - rq = init_beads(iif, nbeads).q - elif mode == "chk": - if momenta: rq = init_beads(iif, nbeads).p - else: rq = init_beads(iif, nbeads).q - elif mode == "manual": - rq = value - - # determines the size of the input data - if mode == "manual": - if iif.bead >= 0: # if there is a bead specifier then we return a single bead slice - nbeads = 1 - natoms = len(rq)/nbeads/3 - rq.shape = (nbeads,3*natoms) - - return rq - -def set_vector(iif, dq, rq): - """A file to initialize a vector from an another vector. - - If the first dimension is different, i.e. the two vectors correspond - to a different number of beads, then the ring polymer contraction/expansion - is used to rescale the original vector to the one used in the simulation, - as described in the paper T. E. Markland and D. E. Manolopoulos, J. Chem. - Phys. 129, 024105, (2008). - - Args: - iif: An Initializer object specifying the value of a vector. - dq: The vector to be initialized. - rq: The vector to initialize from. - """ - - (nbeads, natoms) = rq.shape; natoms /= 3 - (dbeads, datoms) = dq.shape; datoms /= 3 - - # Check that indices make sense - if iif.index < 0 and natoms != datoms: - raise ValueError("Initialization tries to mix up structures with different atom numbers.") - if iif.index >= datoms: - raise ValueError("Cannot initialize single atom as atom index %d is larger than the number of atoms" % iif.index) - if iif.bead >= dbeads: - raise ValueError("Cannot initialize single bead as bead index %d is larger than the number of beads" % iif.bead) - - if iif.bead < 0: # we are initializing the path - res = nm_rescale(nbeads,dbeads) # path rescaler - if nbeads != dbeads: - info(" # Initialize is rescaling from %5d beads to %5d beads" % (nbeads, dbeads), verbosity.low) - if iif.index < 0: - dq[:] = res.b1tob2(rq) - else: # we are initializing a specific atom - dq[:,3*iif.index:3*(iif.index+1)] = res.b1tob2(rq) - else: # we are initializing a specific bead - if iif.index < 0: - dq[iif.bead] = rq - else: - dq[iif.bead,3*iif.index:3*(iif.index+1)] = rq - -class Initializer(dobject): - """Class that deals with the initialization of data. - - This can either be used to initialize the atom positions and the cell data - from a file, or to initialize them from a beads, atoms or cell object. - - Currently, we use a ring polymer contraction scheme to create a new beads - object from one given in initialize if they have different numbers of beads, - as described in the paper T. E. Markland and D. E. Manolopoulos, J. Chem. - Phys. 129, 024105, (2008). If the new beads object has more beads than - the beads object it was initialized from, we set the higher ring polymer - normal modes to zero. - - Attributes: - queue: A list of things to initialize. Each member of the list is a tuple - of the form ('type', 'object'), where 'type' specifies what kind of - initialization is being done, and 'object' gives the data to - initialize it from. - """ - - def __init__(self, nbeads=0, queue=None): - """Initializes Initializer. - - Arguments: - nbeads: The number of beads that we need in the simulation. Not - necessarily the same as the number of beads of the objects we are - initializing the data from. - queue: A list of things to initialize. Each member of the list is a - tuple of the form ('type', 'object'), where 'type' specifies what - kind of initialization is being done, and 'object' gives the data to - initialize it from. - """ - - self.nbeads = nbeads - - if queue is None: - self.queue = [] - else: - self.queue = queue - - def init_stage1(self, simul): - """Initializes the simulation -- first stage. - - Takes a simulation object, and uses all the data in the initialization - queue to fill up the beads and cell data needed to run the simulation. - - Args: - simul: A simulation object to be initialized. - - Raises: - ValueError: Raised if there is a problem with the initialization, - if something that should have been has not been, or if the objects - that have been specified are not compatible with each other. - """ - - if simul.beads.nbeads == 0: - fpos = fmom = fmass = flab = fcell = False # we don't have an explicitly defined beads object yet - else: - fpos = fmom = fmass = flab = fcell = True - - for (k,v) in self.queue: - info(" # Initializer (stage 1) parsing " + str(k) + " object.", verbosity.high) - - if k == "cell": - if fcell : - warning("Overwriting previous cell parameters", verbosity.medium) - if v.mode == "pdb": - rh = init_pdb(v.value)[1].h - elif v.mode == "chk": - rh = init_chk(v.value)[1].h - else: - rh = v.value.reshape((3,3)) - rh *= unit_to_internal("length",v.units,1.0) - - simul.cell.h = rh - if simul.cell.V == 0.0: - ValueError("Cell provided has zero volume") - - fcell = True - elif k == "masses": - if simul.beads.nbeads == 0: - raise ValueError("Cannot initialize the masses before the size of the system is known") - if fmass: - warning("Overwriting previous atomic masses", verbosity.medium) - if v.mode == "manual": - rm = v.value - else: - rm = init_beads(v, self.nbeads).m - rm *= unit_to_internal("mass",v.units,1.0) - - if v.bead < 0: # we are initializing the path - if (fmom and fmass): - warning("Rescaling momenta to make up for changed mass", verbosity.medium) - simul.beads.p /= simul.beads.sm3 # go to mass-scaled momenta, that are mass-invariant - if v.index < 0: - simul.beads.m = rm - else: # we are initializing a specific atom - simul.beads.m[v.index:v.index+1] = rm - if (fmom and fmass): # finishes correcting the momenta - simul.beads.p *= simul.beads.sm3 # back to normal momenta - else: - raise ValueError("Cannot change the mass of a single bead") - fmass = True - - elif k == "labels": - if simul.beads.nbeads == 0: - raise ValueError("Cannot initialize the labels before the size of the system is known") - if flab: - warning("Overwriting previous atomic labels", verbosity.medium) - if v.mode == "manual": - rn = v.value - else: - rn = init_beads(v, self.nbeads).names - - if v.bead < 0: # we are initializing the path - if v.index < 0: - simul.beads.names = rn - else: # we are initializing a specific atom - simul.beads.names[v.index:v.index+1] = rn - else: - raise ValueError("Cannot change the label of a single bead") - flab = True - - elif k == "positions": - if fpos: - warning("Overwriting previous atomic positions", verbosity.medium) - # read the atomic positions as a vector - rq = init_vector(v, self.nbeads) - rq *= unit_to_internal("length",v.units,1.0) - (nbeads, natoms) = rq.shape; natoms /= 3 - - # check if we must initialize the simulation beads - if simul.beads.nbeads == 0: - if v.index >= 0: - raise ValueError("Cannot initialize single atoms before the size of the system is known") - simul.beads.resize(natoms,self.nbeads) - - set_vector(v, simul.beads.q, rq) - fpos = True - - elif (k == "velocities" or k == "momenta") and v.mode == "thermal" : # intercept here thermal initialization, so we don't need to check further down - if fmom: - warning("Overwriting previous atomic momenta", verbosity.medium) - if simul.beads.natoms == 0: - raise ValueError("Cannot initialize momenta before the size of the system is known.") - if not fmass: - raise ValueError("Trying to resample velocities before having masses.") - - rtemp = v.value * unit_to_internal("temperature",v.units,1.0) - if rtemp <= 0: - warning("Using the simulation temperature to resample velocities", verbosity.low) - rtemp = simul.ensemble.temp - else: - info(" # Resampling velocities at temperature %s %s" % (v.value, v.units), verbosity.low) - - # pull together a mock initialization to get NM masses right - #without too much code duplication - if v.bead >= 0: - raise ValueError("Cannot thermalize a single bead") - if v.index >= 0: - rnatoms = 1 - else: - rnatoms = simul.beads.natoms - rbeads = Beads(rnatoms, simul.beads.nbeads) - if v.index < 0: - rbeads.m[:] = simul.beads.m - else: - rbeads.m[:] = simul.beads.m[v.index] - rnm = NormalModes(mode=simul.nm.mode, transform_method=simul.nm.transform_method, freqs=simul.nm.nm_freqs) - rens = Ensemble(dt=simul.ensemble.dt, temp=simul.ensemble.temp) - rnm.bind(rbeads,rens) - # then we exploit the sync magic to do a complicated initialization - # in the NM representation - # with (possibly) shifted-frequencies NM - rnm.pnm = simul.prng.gvec((rbeads.nbeads,3*rbeads.natoms))*np.sqrt(rnm.dynm3)*np.sqrt(rbeads.nbeads*rtemp*Constants.kb) - - if v.index < 0: - simul.beads.p = rbeads.p - else: - simul.beads.p[:,3*v.index:3*(v.index+1)] = rbeads.p - fmom = True - - elif k == "momenta": - if fmom: - warning("Overwriting previous atomic momenta", verbosity.medium) - # read the atomic momenta as a vector - rp = init_vector(v, self.nbeads, momenta = True) - rp *= unit_to_internal("momentum",v.units,1.0) - (nbeads, natoms) = rp.shape; natoms /= 3 - - # checks if we must initialize the simulation beads - if simul.beads.nbeads == 0: - if v.index >= 0 : - raise ValueError("Cannot initialize single atoms before the size of the system is known") - simul.beads.resize(natoms,self.nbeads) - - rp *= np.sqrt(self.nbeads/nbeads) - set_vector(v, simul.beads.p, rp) - fmom = True - - elif k == "velocities": - if fmom: - warning("Overwriting previous atomic momenta", verbosity.medium) - # read the atomic velocities as a vector - rv = init_vector(v, self.nbeads) - rv *= unit_to_internal("velocity",v.units,1.0) - (nbeads, natoms) = rv.shape; natoms /= 3 - - # checks if we must initialize the simulation beads - if simul.beads.nbeads == 0 or not fmass: - ValueError("Cannot initialize velocities before the masses of the atoms are known") - simul.beads.resize(natoms,self.nbeads) - - warning("Initializing from velocities uses the previously defined masses -- not the masses inferred from the file -- to build momenta", verbosity.low) - if v.index >= 0: - rv *= simul.beads.m[v.index] - elif v.bead >= 0: - rv *= simul.beads.m3[0] - else: - rv *= simul.beads.m3 - rv *= np.sqrt(self.nbeads/nbeads) - set_vector(v, simul.beads.p, rv) - fmom = True - elif k == "thermostat": pass # thermostats must be initialized in a second stage - - if simul.beads.natoms == 0: - raise ValueError("Initializer could not initialize the atomic positions") - if simul.cell.V == 0: - raise ValueError("Initializer could not initialize the cell") - for i in range(simul.beads.natoms): - if simul.beads.m[i] <= 0: - raise ValueError("Initializer could not initialize the masses") - if simul.beads.names[i] == "": - raise ValueError("Initializer could not initialize the atom labels") - if not fmom: - warning("Momenta not specified in initialize. Will start with zero velocity if they are not specified in beads.", verbosity.low) - - def init_stage2(self, simul): - """Initializes the simulation -- second stage. - - Takes a simulation object which has been fully generated, - and restarts additional information such as the thermostat internal state. - - Args: - simul: A simulation object to be initialized. - - Raises: - ValueError: Raised if there is a problem with the initialization, - if something that should have been has not been, or if the objects - that have been specified are not compatible with each other. - """ - - for (k,v) in self.queue: - info(" # Initializer (stage 2) parsing " + str(k) + " object.", verbosity.high) - - if k == "gle": - # read thermostat parameters from file - if not ( hasattr(simul.ensemble, "thermostat") ): - raise ValueError("Ensemble does not have a thermostat to initialize") - if not ( hasattr(simul.ensemble.thermostat, "s") ): - raise ValueError("There is nothing to initialize in non-GLE thermostats") - ssimul = simul.ensemble.thermostat.s - if v.mode == "manual": - sinput = v.value.copy() - if (sinput.size() != ssimul.size() ): - raise ValueError("Size mismatch in thermostat initialization data") - sinput.shape = ssimul.shape - elif v.mode == "chk": - rthermo = init_chk(v.value)[2] - if not hasattr(rthermo,"s"): - raise ValueError("Checkpoint file does not contain usable thermostat data") - sinput = rthermo.s.copy() - if sinput.shape != ssimul.shape : - raise ValueError("Shape mismatch in thermostat initialization data") - - # if all the preliminary checks are good, we can initialize the s's - ssimul[:] = sinput diff --git a/tools/i-pi/ipi/engine/normalmodes.py b/tools/i-pi/ipi/engine/normalmodes.py deleted file mode 100644 index 38566736f7..0000000000 --- a/tools/i-pi/ipi/engine/normalmodes.py +++ /dev/null @@ -1,400 +0,0 @@ -"""Contains the classes that deal with the normal mode representation. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Deals with the normal mode transformation, including the complications -introduced by PA-CMD when the bead masses are rescaled. Also deals with -the change in the dynamics introduced by this mass-scaling, and has its -own functions to calculate the kinetic energy, and the exact propagator -in the normal mode representation under the ring polymer Hamiltonian. - -Classes: - NormalModes: Deals with the normal mode transformation in RPMD and PA-CMD. -""" - -import numpy as np -from ipi.utils.depend import * -from ipi.utils import units -from ipi.utils import nmtransform -from ipi.utils.messages import verbosity, warning, info - -__all__ = [ "NormalModes" ] - -class NormalModes(dobject): - """ A helper class to manipulate the path NM. - - Normal-modes transformation, determination of path frequencies, - dynamical mass matrix change, etc. - - Attributes: - natoms: The number of atoms. - nbeads: The number of beads. - beads: The beads object for which the normal mode transformation should - be done. - ensemble: The ensemble object, specifying the temperature to hold the - system to. - transform: A nm_trans object that contains the functions that are - required for the normal mode transformation. - - Depend objects: - mode: A string specifying how the bead masses are chosen. - transform_method: A string specifying how to do the normal mode - transformation. - nm_freqs: An array that specifies how the normal mode frequencies - of the ring polymers are to be calculated, and thus how the - bead masses should be chosen. - qnm: The bead positions in the normal mode representation. Depends on - beads.q. - pnm: The bead momenta in the normal mode representation. Depends on - beads.p. - omegan: The effective vibrational frequency for the interaction - between the replicas. Depends on the simulation temperature. - omegan2: omegan**2. - omegak: The normal mode frequencies for the free ring polymer. - Depends on omegan. - prop_pq: An array holding the exact normal mode propagator for the - free ring polymer, using mass scaled coordinates. - See J. Chem. Phys. 133, 124101 (2010). Depends on the bead masses - and the timestep. - nm_factor: An array of dynamical mass factors associated with each of - the normal modes. Depends on nm_freqs and mode. - dynm3: An array that gives the dynamical masses of individual atoms in the - normal modes representation. Depends on nm_factor and beads.m3. - dynomegak: The scaled vibrational frequencies. Depends on nm_factor and - omegak. - kins: A list of the kinetic energy for each normal mode, as - calculated in the normal mode representation, using the - dynamical mass factors. Depends on beads.sm3, beads.p and nm_factor. - kin: The total kinetic energy, as calculated in the normal mode - representation, using the dynamical mass factors. - kstress: The kinetic stress tensor, as calculated in the normal mode - representation, using the dynamical mass factors. Depends on - beads.sm3, beads.p and nm_factor. - """ - - def __init__(self, mode="rpmd", transform_method="fft", freqs=None): - """Initializes NormalModes. - - Sets the options for the normal mode transform. - - Args: - mode: A string specifying how to calculate the bead masses. - transform_method: A string specifying how to do the normal mode - transformation. - freqs: A list of data used to calculate the dynamical mass factors. - """ - - if freqs is None: - freqs = [] - dset(self,"mode", depend_value(name='mode', value=mode)) - dset(self,"transform_method", - depend_value(name='transform_method', value=transform_method)) - dset(self,"nm_freqs", - depend_array(name="nm_freqs",value=np.asarray(freqs, float) ) ) - - def bind(self, beads, ensemble): - """ Initializes the normal modes object and binds to beads and ensemble. - - Do all the work down here as we need a full-formed necklace and ensemble - to know how this should be done. - - Args: - beads: A beads object to be bound. - ensemble: An ensemble object to be bound. - """ - - self.nbeads = beads.nbeads - self.natoms = beads.natoms - - # stores a reference to the bound beads and ensemble objects - self.beads = beads - self.ensemble = ensemble - - # sets up what's necessary to perform nm transformation. - if self.transform_method == "fft": - self.transform = nmtransform.nm_fft(nbeads=self.nbeads, natoms=self.natoms) - elif self.transform_method == "matrix": - self.transform = nmtransform.nm_trans(nbeads=self.nbeads) - - # creates arrays to store normal modes representation of the path. - # must do a lot of piping to create "ex post" a synchronization between the beads and the nm - sync_q = synchronizer() - sync_p = synchronizer() - dset(self,"qnm", - depend_array(name="qnm", - value=np.zeros((self.nbeads,3*self.natoms), float), - func={"q": (lambda : self.transform.b2nm(depstrip(self.beads.q)) ) }, - synchro=sync_q ) ) - dset(self,"pnm", - depend_array(name="pnm", - value=np.zeros((self.nbeads,3*self.natoms), float), - func={"p": (lambda : self.transform.b2nm(depstrip(self.beads.p)) ) }, - synchro=sync_p ) ) - - # must overwrite the functions - dget(self.beads, "q")._func = { "qnm": (lambda : self.transform.nm2b(depstrip(self.qnm)) ) } - dget(self.beads, "p")._func = { "pnm": (lambda : self.transform.nm2b(depstrip(self.pnm)) ) } - dget(self.beads, "q").add_synchro(sync_q) - dget(self.beads, "p").add_synchro(sync_p) - - # also within the "atomic" interface to beads - for b in range(self.nbeads): - dget(self.beads._blist[b],"q")._func = { "qnm": (lambda : self.transform.nm2b(depstrip(self.qnm)) ) } - dget(self.beads._blist[b],"p")._func = { "pnm": (lambda : self.transform.nm2b(depstrip(self.pnm)) ) } - dget(self.beads._blist[b],"q").add_synchro(sync_q) - dget(self.beads._blist[b],"p").add_synchro(sync_p) - - - # finally, we mark the beads as those containing the set positions - dget(self.beads, "q").update_man() - dget(self.beads, "p").update_man() - - # create path-frequencies related properties - dset(self,"omegan", - depend_value(name='omegan', func=self.get_omegan, - dependencies=[dget(self.ensemble,"temp")]) ) - dset(self,"omegan2", depend_value(name='omegan2',func=self.get_omegan2, - dependencies=[dget(self,"omegan")]) ) - dset(self,"omegak", depend_array(name='omegak', - value=np.zeros(self.beads.nbeads,float), - func=self.get_omegak, dependencies=[dget(self,"omegan")]) ) - - # sets up "dynamical" masses -- mass-scalings to give the correct RPMD/CMD dynamics - dset(self,"nm_factor", depend_array(name="nmm", - value=np.zeros(self.nbeads, float), func=self.get_nmm, - dependencies=[dget(self,"nm_freqs"), dget(self,"mode") ]) ) - dset(self,"dynm3", depend_array(name="dm3", - value=np.zeros((self.nbeads,3*self.natoms), float),func=self.get_dynm3, - dependencies=[dget(self,"nm_factor"), dget(self.beads, "m3")] ) ) - dset(self,"dynomegak", depend_array(name="dynomegak", - value=np.zeros(self.nbeads, float), func=self.get_dynwk, - dependencies=[dget(self,"nm_factor"), dget(self,"omegak") ]) ) - - dset(self,"prop_pq", - depend_array(name='prop_pq',value=np.zeros((self.beads.nbeads,2,2)), - func=self.get_prop_pq, - dependencies=[dget(self,"omegak"), dget(self,"nm_factor"), dget(self.ensemble,"dt")]) ) - - # if the mass matrix is not the RPMD one, the MD kinetic energy can't be - # obtained in the bead representation because the masses are all mixed up - dset(self,"kins", - depend_array(name="kins",value=np.zeros(self.nbeads, float), - func=self.get_kins, - dependencies=[dget(self,"pnm"), dget(self.beads,"sm3"), dget(self, "nm_factor") ] )) - dset(self,"kin", - depend_value(name="kin", func=self.get_kin, - dependencies=[dget(self,"kins")] )) - dset(self,"kstress", - depend_array(name="kstress",value=np.zeros((3,3), float), - func=self.get_kstress, - dependencies=[dget(self,"pnm"), dget(self.beads,"sm3"), dget(self, "nm_factor") ] )) - - def get_omegan(self): - """Returns the effective vibrational frequency for the interaction - between replicas. - """ - - return self.ensemble.temp*self.nbeads*units.Constants.kb/units.Constants.hbar - - def get_omegan2(self): - """Returns omegan**2.""" - - return self.omegan**2 - - def get_omegak(self): - """Gets the normal mode frequencies. - - Returns: - A list of the normal mode frequencies for the free ring polymer. - The first element is the centroid frequency (0.0). - """ - - return 2*self.omegan*np.array([np.sin(k*np.pi/self.nbeads) for k in range(self.nbeads)]) - - def get_dynwk(self): - """Gets the dynamical normal mode frequencies. - - Returns: - A list of the scaled normal mode frequencies for the free ring polymer. - The first element is the centroid frequency (0.0). - """ - - return self.omegak/np.sqrt(self.nm_factor) - - def get_prop_pq(self): - """Gets the normal mode propagator matrix. - - Note the special treatment for the centroid normal mode, which is - propagated using the standard velocity Verlet algorithm as required. - Note that both the normal mode positions and momenta are propagated - using this matrix. - - Returns: - An array of the form (nbeads, 2, 2). Each 2*2 array prop_pq[i,:,:] - gives the exact propagator for the i-th normal mode of the - ring polymer. - """ - - dt = self.ensemble.dt - pqk = np.zeros((self.nbeads,2,2), float) - pqk[0] = np.array([[1,0], [dt,1]]) - - for b in range(1, self.nbeads): - sk = np.sqrt(self.nm_factor[b]) # NOTE THAT THE PROPAGATOR USES MASS-SCALED MOMENTA! - - dtomegak = self.omegak[b]*dt/sk - c = np.cos(dtomegak) - s = np.sin(dtomegak) - pqk[b,0,0] = c - pqk[b,1,1] = c - pqk[b,0,1] = -s*self.omegak[b]*sk - pqk[b,1,0] = s/(self.omegak[b]*sk) - - return pqk - - def get_nmm(self): - """Returns dynamical mass factors, i.e. the scaling of normal mode - masses that determine the path dynamics (but not statics).""" - - # also checks that the frequencies and the mode given in init are - # consistent with the beads and ensemble - - dmf = np.zeros(self.nbeads,float) - dmf[:] = 1.0 - if self.mode == "rpmd": - if len(self.nm_freqs) > 0: - warning("nm.frequencies will be ignored for RPMD mode.", verbosity.low) - elif self.mode == "manual": - if len(self.nm_freqs) != self.nbeads-1: - raise ValueError("Manual path mode requires (nbeads-1) frequencies, one for each internal mode of the path.") - for b in range(1, self.nbeads): - sk = self.omegak[b]/self.nm_freqs[b-1] - dmf[b] = sk**2 - elif self.mode == "pa-cmd": - if len(self.nm_freqs) > 1: - warning("Only the first element in nm.frequencies will be considered for PA-CMD mode.", verbosity.low) - if len(self.nm_freqs) == 0: - raise ValueError("PA-CMD mode requires the target frequency of all the internal modes.") - for b in range(1, self.nbeads): - sk = self.omegak[b]/self.nm_freqs[0] - info(" ".join(["NM FACTOR", str(b), str(sk), str(self.omegak[b]), str(self.nm_freqs[0])]), verbosity.medium) - dmf[b] = sk**2 - elif self.mode == "wmax-cmd": - if len(self.nm_freqs) > 2: - warning("Only the first two element in nm.frequencies will be considered for WMAX-CMD mode.", verbosity.low) - if len(self.nm_freqs) < 2: - raise ValueError("WMAX-CMD mode requires [wmax, wtarget]. The normal modes will be scaled such that the first internal mode is at frequency wtarget and all the normal modes coincide at frequency wmax.") - wmax = self.nm_freqs[0] - wt = self.nm_freqs[1] - for b in range(1, self.nbeads): - sk = 1.0/np.sqrt((wt)**2*(1+(wmax/self.omegak[1])**2)/(wmax**2+(self.omegak[b])**2)) - dmf[b] = sk**2 - - return dmf - - def get_dynm3(self): - """Returns an array with the dynamical masses of individual atoms in the normal modes representation.""" - - dm3 = np.zeros(self.beads.m3.shape,float) - for b in range(self.nbeads): - dm3[b] = self.beads.m3[b]*self.nm_factor[b] - - return dm3 - - def free_qstep(self): - """Exact normal mode propagator for the free ring polymer. - - Note that the propagator works in mass scaled coordinates, so that the - propagator matrix can be determined independently from the particular - atom masses, and so the same propagator will work for all the atoms in - the system. All the ring polymers are propagated at the same time by a - matrix multiplication. - - Also note that the centroid coordinate is propagated in qcstep, so is - not altered here. - """ - - if self.nbeads == 1: - pass - else: - pq = np.zeros((2,self.natoms*3),float) - sm = depstrip(self.beads.sm3)[0] - prop_pq = depstrip(self.prop_pq) - for k in range(1,self.nbeads): - pq[0,:] = depstrip(self.pnm)[k]/sm - pq[1,:] = depstrip(self.qnm)[k]*sm - pq = np.dot(prop_pq[k],pq) - self.qnm[k] = pq[1,:]/sm - self.pnm[k] = pq[0,:]*sm - - def get_kins(self): - """Gets the MD kinetic energy for all the normal modes. - - Returns: - A list of the kinetic energy for each NM. - """ - - kmd = np.zeros(self.nbeads,float) - sm = depstrip(self.beads.sm3[0]) - pnm = depstrip(self.pnm) - nmf = depstrip(self.nm_factor) - - # computes the MD ke in the normal modes representation, to properly account for CMD mass scaling - for b in range(self.nbeads): - sp = pnm[b]/sm # mass-scaled momentum of b-th NM - kmd[b] = np.dot(sp,sp)*0.5/nmf[b] # include the partially adiabatic CMD mass scaling - - return kmd - - def get_kin(self): - """Gets the total MD kinetic energy. - - Note that this does not correspond to the quantum kinetic energy estimate - for the system. - - Returns: - The sum of the kinetic energy of each NM in the path. - """ - - return self.kins.sum() - - def get_kstress(self): - """Calculates the total MD kinetic stress tensor. - - Note that this does not correspond to the quantum kinetic stress tensor - estimate for the system. - - Returns: - The sum of the MD kinetic stress tensor contributions from each NM. - """ - - kmd = np.zeros((3,3),float) - sm = depstrip(self.beads.sm3[0]) - pnm = depstrip(self.pnm) - nmf = depstrip(self.nm_factor) - - for b in range(self.nbeads): - sp = pnm[b]/sm # mass-scaled momentum of b-th NM - - for i in range(3): - for j in range(3): - # computes the outer product of the p of various normal modes - # singling out Cartesian components to build the tensor - # also takes care of the possibility of having non-RPMD masses - kmd[i,j] += np.dot(sp[i:3*self.natoms:3],sp[j:3*self.natoms:3])/nmf[b] - - return kmd diff --git a/tools/i-pi/ipi/engine/outputs.py b/tools/i-pi/ipi/engine/outputs.py deleted file mode 100644 index 7d6e7587b5..0000000000 --- a/tools/i-pi/ipi/engine/outputs.py +++ /dev/null @@ -1,378 +0,0 @@ -"""Classes to deal with output of simulation data. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Holds classes to deal with the output of different properties, trajectories -and the restart files. - -Classes: - PropertyOutput: Deals with outputting properties. - TrajectoryOutput: Deals with outputting trajectories. - CheckpointOutput: Deals with outputting restart files. -""" - -import os -import numpy as np -import ipi.inputs.simulation -from ipi.utils.depend import * -from ipi.utils.io.io_xml import * -from ipi.engine.properties import getkey - -__all__ = [ 'PropertyOutput', 'TrajectoryOutput', 'CheckpointOutput' ] - -class PropertyOutput(dobject): - """Class dealing with outputting a set of properties to file. - - Does not do any calculation, just manages opening a file, getting data - from a Properties object and outputting with the desired stride. - - Attributes: - filename: The name of the file to output to. - outlist: A list of the properties to be output. - stride: The number of steps that should be taken between outputting the - data to file. - flush: How often we should flush to disk. - nout: Number of steps since data was last flushed. - out: The output stream on which to output the properties. - simul: The simulation object to get the data to be output from. - """ - - - def __init__(self, filename="out", stride=1, flush=1, outlist=None): - """Initializes a property output stream opening the corresponding - file name. - - Also writes out headers. - - Args: - filename: A string giving the name of the file to be output to. - stride: An integer giving how many steps should be taken between - outputting the data to file. - flush: Number of writes to file between flushing data. - outlist: A list of all the properties that should be output. - """ - - if outlist is None: - outlist = np.zeros(0,np.dtype('|S1024')) - self.filename = filename - self.outlist = np.asarray(outlist,np.dtype('|S1024')) - self.stride = stride - self.flush = flush - self.nout = 0 - self.out = None - - def bind(self, simul): - """Binds output proxy to simulation object. - - Args: - simul: A simulation object to be bound. - """ - - self.simul = simul - - # Checks as soon as possible if some asked-for properties are - # missing or misspelled - for what in self.outlist: - key = getkey(what) - if not key in self.simul.properties.property_dict.keys(): - print "Computable properties list: ", self.simul.properties.property_dict.keys() - raise KeyError(key + " is not a recognized property") - - self.open_stream() - - def open_stream(self): - """Opens the output stream.""" - - try: - self.out = open(self.filename, "a") - except: - raise ValueError("Could not open file " + self.filename + " for output") - - # print nice header if information is available on the properties - if (self.simul.step == 0) : - icol = 1 - for what in self.outlist: - ohead = "# " - key = getkey(what) - prop = self.simul.properties.property_dict[key] - - if "size" in prop and prop["size"] > 1: - ohead += "cols. %3d-%-3d" % ( icol, icol+prop["size"] - 1 ) - icol += prop["size"] - else: - ohead += "column %3d " % ( icol ) - icol += 1 - ohead += " --> %s " % (what) - if "help" in prop: - ohead += ": " + prop["help"] - self.out.write(ohead + "\n") - - def close_stream(): - """Closes the output stream.""" - - self.out.close() - - def write(self): - """Outputs the required properties of the system. - - Note that properties are outputted using the same format as for the - output to the xml checkpoint files, as specified in io_xml. - - Raises: - KeyError: Raised if one of the properties specified in the output list - are not contained in the property_dict member of properties. - """ - - if not (self.simul.step + 1) % self.stride == 0: - return - self.out.write(" ") - for what in self.outlist: - try: - quantity = self.simul.properties[what] - except KeyError: - raise KeyError(what + " is not a recognized property") - if not hasattr(quantity,"__len__") : - self.out.write(write_type(float, quantity) + " ") - else: - for el in quantity: - self.out.write(write_type(float, el) + " ") - - self.out.write("\n") - - self.nout += 1 - if self.flush > 0 and self.nout >= self.flush : - self.out.flush() - os.fsync(self.out) # we REALLY want to print out! pretty please OS let us do it. - self.nout = 0 - - -class TrajectoryOutput(dobject): - """Class dealing with outputting atom-based properties as a - trajectory file. - - Does not do any calculation, just manages opening a file, getting data - from a Trajectories object and outputting with the desired stride. - - Attributes: - filename: The (base) name of the file to output to. - format: The format of the trajectory file to be created. - what: The trajectory that needs to be output. - stride: The number of steps that should be taken between outputting the - data to file. - out: The output stream on which to output the trajectories. - flush: How often we should flush to disk. - nout: Number of steps since data was last flushed. - ibead: Index of the replica to print the trajectory of. - cell_units: The units that the cell parameters are given in. - simul: The simulation object to get the data to be output from. - """ - - def __init__(self, filename="out", stride=1, flush=1, what="", format="xyz", cell_units="atomic_unit", ibead=-1): - """ Initializes a property output stream opening the corresponding - file name. - - Also writes out headers. - - Args: - filename: A string giving the name of the file to be output to. - stride: An integer giving how many steps should be taken between - outputting the data to file. - flush: How often we should flush to disk - what: A string specifying what trajectory should be output. - format: A string specifying the type of trajectory file to be created. - cell_units: A string specifying the units that the cell parameters are - given in. - ibead: If positive, prints out only the selected bead. If negative, prints out one file per bead. - """ - - self.filename = filename - self.what = what - self.stride = stride - self.flush = flush - self.ibead = ibead - self.format = format - self.cell_units = cell_units - self.out = None - self.nout = 0 - - def bind(self, simul): - """Binds output proxy to simulation object. - - Args: - simul: A simulation object to be bound. - """ - - self.simul = simul - - # Checks as soon as possible if some asked-for trajs are missing or misspelled - key = getkey(self.what) - if not key in self.simul.trajs.traj_dict.keys(): - print "Computable trajectories list: ", self.simul.trajs.traj_dict.keys() - raise KeyError(key + " is not a recognized output trajectory") - - self.open_stream() - - def open_stream(self): - """Opens the output stream(s).""" - - if getkey(self.what) in [ "positions", "velocities", "forces", "extras" ]: - # must write out trajectories for each bead, so must create b streams - self.out = [] - for b in range(self.simul.beads.nbeads): - # zero-padded bead number - padb = ( ("%0" + str(int(1 + np.floor(np.log(self.simul.beads.nbeads)/np.log(10)))) + "d") % (b) ) - try: - if (self.ibead < 0 or self.ibead == b): - if getkey(self.what) == "extras": - self.out.append(open(self.filename + "_" + padb, "a")) - else: - self.out.append(open(self.filename + "_" + padb + "." + self.format, "a")) - else: - self.out.append(None) # creates null outputs if a - # single bead output is chosen - except: - raise ValueError("Could not open file " + self.filename + "_" + padb + "." + self.format + " for output") - else: - try: - self.out = ( open(self.filename + "." + self.format, "a") ) - except: - raise ValueError("Could not open file " + self.filename + "." + self.format + " for output") - - def close_stream(): - """Closes the output stream.""" - - if hasattr(self.out, "__getitem__"): - for o in self.out: - o.close() - else: - self.out.close() - - def write(self): - """Writes out the required trajectories.""" - - if not (self.simul.step + 1) % self.stride == 0: - return - - doflush = False - self.nout += 1 - if self.flush > 0 and self.nout >= self.flush : - doflush = True - self.nout = 0 - - # quick-and-dirty way to check if a trajectory is "global" or per-bead - # Checks to see if there is a list of files or just a single file. - if hasattr(self.out, "__getitem__"): - if self.ibead < 0: - for b in range(len(self.out)): - self.simul.trajs.print_traj(self.what, self.out[b], b, format=self.format, cell_units=self.cell_units, flush=doflush) - elif self.ibead < len(self.out): - self.simul.trajs.print_traj(self.what, self.out[self.ibead], self.ibead, format=self.format, cell_units=self.cell_units, flush=doflush) - else: - raise ValueError("Selected bead index " + str(self.ibead) + " does not exist for trajectory " + self.what) - else: - self.simul.trajs.print_traj(self.what, self.out, b=0, format=self.format, cell_units=self.cell_units, flush=doflush) - - -class CheckpointOutput(dobject): - """Class dealing with outputting checkpoints. - - Saves the complete status of the simulation at regular intervals. - - Attributes: - filename: The (base) name of the file to output to. - step: the number of times a checkpoint has been written out. - stride: The number of steps that should be taken between outputting the - data to file. - overwrite: If True, the checkpoint file is overwritten at each output. - If False, will output to 'filename_step'. Note that no check is done - on whether 'filename_step' exists already. - simul: The simulation object to get the data to be output from. - status: An input simulation object used to write out the checkpoint file. - """ - - - def __init__(self, filename="restart", stride=1000, overwrite=True, step=0): - """Initializes a checkpoint output proxy. - - Args: - filename: A string giving the name of the file to be output to. - stride: An integer giving how many steps should be taken between - outputting the data to file. - overwrite: If True, the checkpoint file is overwritten at each output. - If False, will output to 'filename_step'. Note that no check is done - on whether 'filename_step' exists already. - step: The number of checkpoint files that have been created so far. - """ - - self.filename = filename - self.step = step - self.stride = stride - self.overwrite = overwrite - - def bind(self, simul): - """Binds output proxy to simulation object. - - Args: - simul: A simulation object to be bound. - """ - - self.simul = simul - self.status = ipi.inputs.simulation.InputSimulation() - self.status.store(simul) - - def store(self): - """Stores the current simulation status. - - Used so that, if halfway through a step a kill signal is received, - we can output a checkpoint file corresponding to the beginning of the - current step, which is the last time that both the velocities and - positions would have been consistent. - """ - - self.status.store(self.simul) - - def write(self, store=True): - """Writes out the required trajectories. - - Used for both the checkpoint files and the soft-exit restart file. - We have slightly different behavior for these two different types of - checkpoint file, as the soft-exit files have their store() function - called automatically, and we do not want this to be updated as the - status of the simulation after a soft-exit call is unlikely to be in - a consistent state. On the other hand, the standard checkpoint files - are not automatically updated in this way, and we must manually store the - current state of the system before writing them. - - Args: - store: A boolean saying whether the state of the system should be - stored before writing the checkpoint file. - """ - - if not (self.simul.step + 1) % self.stride == 0: - return - - if self.overwrite: - filename = self.filename - else: - filename = self.filename + "_" + str(self.step) - - if store: - self.step += 1 # advances the step counter before saving, so next time the correct index will be loaded. - self.store() - check_file = open(filename, "w") - check_file.write(self.status.write(name="simulation")) - check_file.close() diff --git a/tools/i-pi/ipi/engine/properties.py b/tools/i-pi/ipi/engine/properties.py deleted file mode 100644 index 48b0c00ecc..0000000000 --- a/tools/i-pi/ipi/engine/properties.py +++ /dev/null @@ -1,1273 +0,0 @@ -"""Holds the class which computes important properties of the system, and -prepares them for output. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - Properties: This is the class that holds all the algorithms to calculate - the important properties that should be output. - Trajectories: This class deals with outputting all position data in the - appropriate format. - -Functions: - getkey: This function strips the units and argument list specification - from a string specifying an output parameter. - getall: This function gives the keyword, units and argument list - specification from a string specifying an output parameter. - help_latex: This returns a string that can be used in the manual to - specify the different available outputs. -""" - -__all__ = ['Properties', 'Trajectories', 'getkey', 'getall', 'help_latex'] - -import os -import numpy as np -from ipi.utils.messages import verbosity, info, warning -from ipi.utils.depend import * -from ipi.utils.units import Constants, unit_to_internal, unit_to_user -from ipi.utils.mathtools import logsumlog, h2abc_deg -from ipi.utils.io import * -from ipi.engine.atoms import * -from ipi.engine.cell import * -from ipi.engine.ensembles import * -from ipi.engine.forces import * - -def getkey(pstring): - """Strips units and argument lists from a property/trajectory keyword. - - Args: - pstring: The string input by the user that specifies an output, - which in general will specify units and argument lists. - - Returns: A string giving the keyword for the property, stripped of the - argument lists and units key words. - """ - - pa = pstring.find('(') - if pa < 0: - pa = len(pstring) - pu = pstring.find('{') - if pu < 0: - pu = len(pstring) - return pstring[0:min(pa,pu)].strip() - -def getall(pstring): - """Returns the keyword, units and argument list separately. - - Args: - pstring: The string input by the user that specifies an output, - which in general will specify units and argument lists. - - Returns: A tuple giving the keyword for the property, and its units - argument list and key word argument list. - """ - - unit = "" - arglist = () - kwarglist = {} - unstart = len(pstring) - argstart = unstart - - if '}' in pstring: - # the property has a user-defined unit - unstart = pstring.find('{') - unstop = pstring.find('}', unstart) - if unstop == -1: - raise ValueError("Incorrect format in units specification " + pstring) - unit = pstring[unstart+1:unstop] - if '(' in pstring: - # If the property has additional arguments - argstart = pstring.find('(') - argstop = pstring.find(')', argstart) - if argstop == -1: - raise ValueError("Incorrect format in argument list " + pstring) - - argstr = pstring[argstart:argstop+1] - arglist = io_xml.read_tuple(argstr, delims="()", split=";", arg_type=str) - for arg in arglist: - # If a keyword argument is used - equals = arg.find('=') - if equals >= 0: - kwarglist[arg[0:equals].strip()] = arg[equals+1:].strip() - arglist = tuple(a for a in arglist if not a == arg) - - pstring = pstring[0:min(unstart,argstart)].strip() # strips the arguments from pstring name - - return (pstring, unit, arglist, kwarglist) - -def help_latex(idict, standalone=True): - """Function to generate a LaTeX formatted file. - - Args: - idict: Either property_dict or traj_dict, to be used to - generate the help file. - standalone: A boolean giving whether the latex file produced will be a - stand-alone document, or will be intended as a section of a larger - document with cross-references between the different sections. - - Returns: - A LaTeX formatted string. - """ - - rstr = "" - if standalone: - #assumes that it is a stand-alone document, so must have document - #options. - rstr += r"\documentclass[12pt,fleqn]{report}" - rstr += r""" -\usepackage{etoolbox} -\usepackage{suffix} - -\newcommand{\ipiitem}[3]{% -\ifblank{#1}{}{\ifstrequal{#1}{\underline{}}{}{ -{\noindent\textbf{#1}:\rule{0.0pt}{1.05\baselineskip}\quad}}}% uses a strut to add a bit of vertical space -{#2}\parskip=0pt\par -\ifblank{#3}{}% -{ {\hfill\raggedleft\textit{\small #3}\par} } -} -""" - rstr += "\n\\begin{document}\n" - rstr += "The following are the different allowable outputs:\n\\par" - - for out in sorted(idict): - rstr += "\\ipiitem{" + out + "}" - if "longhelp" in idict[out]: - rstr += "{" + idict[out]['longhelp'] +"}" - else: - rstr += "{" + idict[out]['help'] +"}" - - #see if there are additional attributes to print out - xstr = "" - if "dimension" in idict[out] and idict[out]['dimension'] != "undefined": #doesn't print out dimension if not necessary. - xstr += "dimension: " + idict[out]['dimension'] + '; ' - if "size" in idict[out]: - xstr += "size: " + str(idict[out]['size']) +"; " - rstr += "{" + xstr + "}" - - if standalone: - #ends the created document if it is not part of a larger document - rstr += "\\end{document}" - - # Some escape characters are necessary for the proper latex formatting - rstr = rstr.replace('_', '\\_') - rstr = rstr.replace('\\\\_', '\\_') - rstr = rstr.replace('...', '\\ldots ') - rstr = rstr.replace('<', '$<$') - rstr = rstr.replace('>', '$>$') - rstr = rstr.replace('[', '$[$') - rstr = rstr.replace(']', '$]$') - - return rstr - - -class Properties(dobject): - """A proxy to compute and output properties of the system. - - Takes the fundamental properties calculated during the simulation, and - prepares them for output. It also contains simple algorithms to calculate - other properties not calculated during the simulation itself, so that - these can also be output. - - Attributes: - fd_delta: A float giving the size of the finite difference - parameter used in the Yamamoto kinetic energy estimator. Defaults - to _DEFAULT_FINDIFF. - _DEFAULT_FDERROR: A float giving the size of the minimum precision - allowed for the finite difference calculation in the Yamamoto kinetic - energy estimator. - _DEFAULT_MINFID: A float giving the maximum displacement in the Yamamoto - kinetic energy estimator. - dbeads: A dummy Beads object used in the Yamamoto kinetic energy - estimator. - dforces: A dummy Forces object used in the Yamamoto kinetic energy - estimator. - simul: The Simulation object containing the data to be output. - ensemble: An ensemble object giving the objects necessary for producing - the correct ensemble. - beads: A beads object giving the atoms positions. - nm: A normal modes object giving the normal mode representation. - cell: A cell object giving the system box. - forces: A forcefield object giving the force calculator for each - replica of the system. - property_dict: A dictionary containing all the properties that can be - output. - """ - - _DEFAULT_FINDIFF = 1e-5 - _DEFAULT_FDERROR = 1e-9 - _DEFAULT_MINFID = 1e-12 - - def __init__(self): - """Initializes Properties.""" - - self.property_dict = { - "step": { "dimension" : "number", - "help" : "The current simulation time step.", - 'func': (lambda: (1 + self.simul.step))}, - "time": { "dimension": "time", - "help": "The elapsed simulation time.", - 'func': (lambda: (1 + self.simul.step)*self.ensemble.dt)}, - "temperature": {"dimension": "temperature", - "help": "The current temperature, as obtained from the MD kinetic energy.", - "longhelp" : """The current temperature, as obtained from the MD kinetic energy of the (extended) - ring polymer. Takes a single, optional argument 'atom', which can be either an - atom label or an index (zero-based) to specify which species or individual atom - to output the temperature of. If not specified, all atoms are used and averaged.""", - 'func': self.get_temp }, - "density": { "dimension": "density", - "help": "The mass density of the physical system.", - 'func': (lambda: self.beads.m.sum()/self.cell.V)}, - "volume": { "dimension": "volume", - "help": "The volume of the cell box.", - 'func': (lambda: self.cell.V) }, - "cell_h": { "dimension" : "length", - "help": "The simulation cell as a matrix. Returns the 6 non-zero components in the form [xx, yy, zz, xy, xz, yz].", - "size": 6, - "func": (lambda: self.tensor2vec(self.cell.h))}, - "cell_abcABC": {"dimension" : "undefined", - "help": "The lengths of the cell vectors and the angles between them in degrees as a list of the form [a, b, c, A, B, C]", - "longhelp": """The lengths of the cell vectors and the angles between them in degrees as a list of the - form [a, b, c, A, B, C], where A is the angle between the sides of length b and c in degrees, and B and C - are defined similarly. Since the output mixes different units, a, b and c can only be output in bohr.""", - "size": 6, - 'func': (lambda: np.asarray(h2abc_deg(self.cell.h)))}, - "conserved": { "dimension": "energy", - "help": "The value of the conserved energy quantity per bead.", - 'func': (lambda: self.ensemble.econs/float(self.beads.nbeads))}, - "potential": { "dimension" : "energy", - "help": "The physical system potential energy.", - 'func': (lambda: self.forces.pot/self.beads.nbeads)}, - "spring": { "dimension" : "energy", - "help": "The total spring potential energy between the beads of all the ring polymers in the system.", - 'func': (lambda: self.beads.vpath*self.nm.omegan2/self.beads.nbeads)}, - "kinetic_md": {"dimension" : "energy", - "help": "The kinetic energy of the (extended) classical system.", - "longhelp" : """The kinetic energy of the (extended) classical system. Takes an argument 'atom', - which can be either an atom label or index (zero based) to specify which species to find the - kinetic energy of. If not specified, all atoms are used.""", - 'func': self.get_kinmd}, - "kinetic_cv": {"dimension" : "energy", - "help": "The centroid-virial quantum kinetic energy of the physical system.", - "longhelp": """The centroid-virial quantum kinetic energy of the physical system. - Takes an argument 'atom', which can be either an atom label or index (zero based) - to specify which species to find the kinetic energy of. If not specified, all atoms are used.""", - 'func': self.get_kincv}, - "kinetic_tens":{"dimension" : "energy", - "help" : "The centroid-virial quantum kinetic energy tensor of the physical system.", - "longhelp" : """The centroid-virial quantum kinetic energy tensor of the physical system. - Returns the 6 independent components in the form [xx, yy, zz, xy, xz, yz]. Takes an - argument 'atom', which can be either an atom label or index (zero based) to specify - which species to find the kinetic tensor components of. If not specified, all atoms are used.""", - "size" : 6, - "func" : self.get_ktens}, - "kinetic_ij": {"dimension" : "energy", - "help" : "The centroid-virial off-diagonal quantum kinetic energy tensor of the physical system.", - "longhelp" : """The centroid-virial off-diagonal quantum kinetic energy tensor of the physical system. - This computes the cross terms between atoms i and atom j, whose average is . - Returns the 6 independent components in the form [xx, yy, zz, xy, xz, yz]. Takes arguments 'i' and 'j', - which give the indices of the two desired atoms.""", - "size" : 6, - "func" : self.get_kij}, - "r_gyration": { "dimension" : "length", - "help" : "The average radius of gyration of the selected ring polymers.", - "longhelp" : """The average radius of gyration of the selected ring polymers. Takes an - argument 'atom', which can be either an atom label or index (zero based) to specify which - species to find the radius of gyration of. If not specified, all atoms are used and averaged.""", - "func": self.get_rg}, - "atom_x": { "dimension" : "length", - "help": "The position (x,y,z) of a particle given its index.", - "longhelp" : """The position (x,y,z) of a particle given its index. Takes arguments index - and bead (both zero based). If bead is not specified, refers to the centroid.""", - "size" : 3, - "func" : (lambda atom="", bead="-1": self.get_atom_vec(self.beads.q, atom=atom, bead=bead))}, - "atom_v": { "dimension" : "velocity", - "help": "The velocity (x,y,z) of a particle given its index.", - "longhelp": """The velocity (x,y,z) of a particle given its index. Takes arguments index - and bead (both zero based). If bead is not specified, refers to the centroid.""", - "size" : 3, - "func" : (lambda atom="", bead="-1": self.get_atom_vec(self.beads.p/self.beads.m3, atom=atom, bead=bead))}, - "atom_p": { "dimension" : "momentum", - "help": "The momentum (x,y,z) of a particle given its index.", - "longhelp": """The momentum (x,y,z) of a particle given its index. Takes arguments index - and bead (both zero based). If bead is not specified, refers to the centroid.""", - "size" : 3, - "func" : (lambda atom="", bead="-1": self.get_atom_vec(self.beads.p, atom=atom, bead=bead))}, - "atom_f": { "dimension" : "force", - "help": "The force (x,y,z) acting on a particle given its index.", - "longhelp": """The force (x,y,z) acting on a particle given its index. Takes arguments index - and bead (both zero based). If bead is not specified, refers to the centroid.""", - "size" : 3, - "func" : (lambda atom="", bead="-1": self.get_atom_vec(self.forces.f, atom=atom, bead=bead))}, - "stress_md": { "dimension": "pressure", - "size" : 6, - "help": "The total stress tensor of the (extended) classical system.", - "longhelp": """The total stress tensor of the (extended) classical system. Returns the 6 - independent components in the form [xx, yy, zz, xy, xz, yz].""", - "func": (lambda: self.tensor2vec((self.forces.vir + self.nm.kstress)/self.cell.V))}, - "pressure_md": {"dimension": "pressure", - "help": "The pressure of the (extended) classical system.", - "func": (lambda: np.trace((self.forces.vir + self.nm.kstress)/(3.0*self.cell.V)))}, - "kstress_md": {"dimension": "pressure", - "size" : 6, - "help": "The kinetic stress tensor of the (extended) classical system.", - "longhelp": """The kinetic stress tensor of the (extended) classical system. Returns the 6 - independent components in the form [xx, yy, zz, xy, xz, yz].""", - "func": (lambda: self.tensor2vec(self.nm.kstress/self.cell.V))}, - "virial_md": { "dimension": "pressure", - "size" : 6, - "help": "The virial tensor of the (extended) classical system.", - "longhelp": """The virial tensor of the (extended) classical system. Returns the 6 - independent components in the form [xx, yy, zz, xy, xz, yz].""", - "func": (lambda: self.tensor2vec(self.forces.vir/self.cell.V))}, - "stress_cv": { "dimension": "pressure", - "size" : 6, - "help": "The total quantum estimator for the stress tensor of the physical system.", - "longhelp": """The total quantum estimator for the stress tensor of the physical system. Returns the - 6 independent components in the form [xx, yy, zz, xy, xz, yz].""", - "func": (lambda: self.tensor2vec(self.forces.vir + self.kstress_cv())/(self.cell.V*self.beads.nbeads))}, - "pressure_cv": {"dimension": "pressure", - "help": "The quantum estimator for pressure of the physical system.", - "func": (lambda: np.trace(self.forces.vir + self.kstress_cv())/(3.0*self.cell.V*self.beads.nbeads))}, - "kstress_cv": {"dimension": "pressure", - "size" : 6, - "help": "The quantum estimator for the kinetic stress tensor of the physical system.", - "longhelp": """The quantum estimator for the kinetic stress tensor of the physical system. - Returns the 6 independent components in the form [xx, yy, zz, xy, xz, yz].""", - "func": (lambda: self.tensor2vec(self.kstress_cv()/(self.cell.V*self.beads.nbeads)))}, - "virial_cv": { "dimension": "pressure", - "size" : 6, - "help": "The quantum estimator for the virial stress tensor of the physical system.", - "longhelp": """The quantum estimator for the virial stress tensor of the physical system. - Returns the 6 independent components in the form [xx, yy, zz, xy, xz, yz].""", - "func": (lambda: self.tensor2vec(self.forces.vir/(self.cell.V*self.beads.nbeads)))}, - "displacedpath": { "dimension": "undefined", - "help": "The displaced path end-to-end distribution estimator", - "longhelp": """This is the estimator for the end-to-end distribution, that can be used to calculate the - particle momentum distribution as described in in L. Lin, J. A. Morrone, R. Car and M. Parrinello, - 105, 110602 (2010), Phys. Rev. Lett. Takes arguments 'ux', 'uy' and 'uz', which are the components of - the path opening vector. Also takes an argument 'atom', which can be either an atom label or index - (zero based) to specify which species to find the end-to-end distribution estimator for. If not - specified, all atoms are used. Note that one atom is computed at a time, and that each path opening - operation costs as much as a PIMD step. Returns the average over the selected atoms of the estimator of - exp(-U(u)) for each frame.""", - "func": self.get_linlin}, - "scaledcoords": { "dimension": "undefined", - "help" : "The scaled coordinates estimators that can be used to compute energy and heat capacity", - "longhelp": """Returns the estimators that are required to evaluate the scaled-coordinates estimators - for total energy and heat capacity, as described in T. M. Yamamoto, - J. Chem. Phys., 104101, 123 (2005). Returns eps_v and eps_v', as defined in that paper. - As the two estimators have a different dimensions, this can only be output in atomic units. - Takes one argument, 'fd_delta', which gives the value of the finite difference parameter used - - which defaults to """+ str(-self._DEFAULT_FINDIFF) + """. If the value of 'fd_delta' is negative, - then its magnitude will be reduced automatically by the code if the finite difference error - becomes too large.""", - 'func': self.get_yama_estimators, - "size": 2}, - "isotope_scfep": {"dimension": "undefined", - "size": 7, - 'func': self.get_isotope_yama, - "help": "The scaled-coordinates free energy perturbation scaled mass KE estimator.", - "longhelp" : """Returns the (many) terms needed to compute the scaled-coordinates free energy - perturbation scaled mass KE estimator (M. Ceriotti, T. Markland, J. Chem. Phys. 138, 014112 (2013)). - Takes two arguments, 'alpha' and 'atom', which give the - scaled mass parameter and the atom of interest respectively, and default to '1.0' and ''. The - 'atom' argument can either be the label of a particular kind of atom, or an index (zero based) - of a specific atom. This property computes, for each atom in the selection, an estimator for - the kinetic energy it would have had if it had the mass scaled by alpha. The 7 numbers output - are the average over the selected atoms of the log of the weights , the average of the - squares , the average of the un-weighted scaled-coordinates kinetic energies - and of the squares , the log sum of the weights LW=ln(sum(e**(-h))), the sum of the - re-weighted kinetic energies, stored as a log modulus and sign, LTW=ln(abs(sum(T_CV e**(-h)))) - STW=sign(sum(T_CV e**(-h))). In practice, the best estimate of the estimator can be computed - as [sum_i exp(LTW_i)*STW_i]/[sum_i exp(LW_i)]. The other terms can be used to compute diagnostics - for the statistical accuracy of the re-weighting process. Note that evaluating this estimator costs - as much as a PIMD step for each atom in the list. The elements that are output have different - units, so the output can be only in atomic units.""" }, - "isotope_tdfep": {"dimension" : "undefined", - "size" : 7, - 'func': self.get_isotope_thermo, - "help": "The thermodynamic free energy perturbation scaled mass KE estimator.", - "longhelp" : """Returns the (many) terms needed to compute the thermodynamic free energy - perturbation scaled mass KE estimator (M. Ceriotti, T. Markland, J. Chem. Phys. 138, 014112 (2013)). - Takes two arguments, 'alpha' and 'atom', which give the - scaled mass parameter and the atom of interest respectively, and default to '1.0' and ''. The - 'atom' argument can either be the label of a particular kind of atom, or an index (zero based) - of a specific atom. This property computes, for each atom in the selection, an estimator for - the kinetic energy it would have had if it had the mass scaled by alpha. The 7 numbers output - are the average over the selected atoms of the log of the weights , the average of the - squares , the average of the un-weighted scaled-coordinates kinetic energies - and of the squares , the log sum of the weights LW=ln(sum(e**(-h))), the sum of the - re-weighted kinetic energies, stored as a log modulus and sign, LTW=ln(abs(sum(T_CV e**(-h)))) - STW=sign(sum(T_CV e**(-h))). In practice, the best estimate of the estimator can be computed - as [sum_i exp(LTW_i)*STW_i]/[sum_i exp(LW_i)]. The other terms can be used to compute diagnostics - for the statistical accuracy of the re-weighting process. Evaluating this estimator is inexpensive, - but typically the statistical accuracy is worse than with the scaled coordinates estimator. - The elements that are output have different - units, so the output can be only in atomic units.""" } - } - - def bind(self, simul): - """Binds the necessary objects from the simulation to calculate the - required properties. - - Args: - simul: The Simulation object to be bound. - """ - - self.ensemble = simul.ensemble - self.beads = simul.beads - self.nm = simul.nm - self.cell = simul.cell - self.forces = simul.forces - self.simul = simul - # dummy beads and forcefield objects so that we can use scaled and - # displaced path estimators without changing the simulation bead - # coordinates - self.dbeads = simul.beads.copy() - self.dforces = Forces() - self.dforces.bind(self.dbeads, self.simul.cell, self.simul.flist) - - def __getitem__(self, key): - """Retrieves the item given by key. - - Note that if the key contains a string (arg1; arg2; ... ) - then it will pass the appropriate positional arguments to the - calculation function of the property. Note the brackets and - the semi-colon separators. If instead we have the syntax - (arg1=val1;arg2; ... ), then the keyword/value pair (arg1,val1) - will be added to the keyword argument list. The appropriate key word - arguments will then be passed to the calculation function instead. - - Similarly, if the key contains a string {unit}, then it will take - the string 'unit' and use it to define the units that the property - is output in. - - Args: - key: A string contained in property_dict. - - Returns: - The property labeled by the keyword key, along with its unit - keyword, and the argument lists for the function used to calculate - the property specified by the keyword key. - """ - - (key, unit, arglist, kwarglist) = getall(key) - pkey = self.property_dict[key] - - #pkey["func"](*arglist,**kwarglist) gives the value of the property - #in atomic units. unit_to_user() returns the value in the user - #specified units. - if "dimension" in pkey and unit != "": - return unit_to_user(pkey["dimension"], unit, pkey["func"](*arglist,**kwarglist)) - else: - return pkey["func"](*arglist,**kwarglist) - - def tensor2vec(self, tensor): - """Takes a 3*3 symmetric tensor and returns it as a 1D array, - containing the elements [xx, yy, zz, xy, xz, yz]. - """ - - return np.array([tensor[0,0], tensor[1,1], tensor[2,2], tensor[0,1], tensor[0,2], tensor[1,2]]) - - def get_atom_vec(self, prop_vec, atom="", bead="-1"): - """Gives a vector for one atom. - - Args: - prop_vec: An array from which to take the atomic vector from. - atom: The index of the atom for which the vector will - be output. - bead: The index of the replica of the atom for which the - vector will be output. If less than 0, then the centroid is used. - """ - - if atom == "": - raise IndexError("Must specify the index for atom_vec property") - atom = int(atom) - bead = int(bead) - if atom >= self.beads.natoms: - raise IndexError("Cannot output atom_vec property as atom index %d is larger than the number of atoms" % atom) - if bead >= self.beads.nbeads: - raise IndexError("Cannot output atom_vec property as bead index %d is larger than the number of beads" % bead) - - if bead < 0: - atom_vec = np.zeros(3) - for b in range(self.beads.nbeads): - atom_vec += prop_vec[b,3*atom:3*(atom+1)] - return atom_vec/float(self.beads.nbeads) - else: - return prop_vec[bead,3*atom:3*(atom+1)] - - def get_temp(self, atom=""): - """Calculates the MD kinetic temperature. - - Note that in the case that the centre of mass constraint there will be - 3 fewer degrees of freedom than without, so this has to be taken into - account when calculating the kinetic temperature. - - Args: - atom: If given, specifies the atom to give the temperature - for. If not, then the simulation temperature. - """ - - if self.ensemble.fixcom: - mdof = 3 - else: - mdof = 0 - - if atom == "": - # use the KE computed in the NM representation in order to avoid problems when mass scaling is used - kedof = self.get_kinmd()/(3*self.beads.natoms*self.beads.nbeads - mdof) - else: - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output temperature as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - ncount = 0 - for i in range(self.beads.natoms): - if (iatom == i or latom == self.beads.names[i]): - ncount += 1 - - if ncount == 0: - raise IndexError("Couldn't find an atom which matched the argument of temperature") - # "spreads" the COM removal correction evenly over all the atoms... - kedof = self.get_kinmd(atom)/ncount*(self.beads.natoms/(3.0*self.beads.natoms*self.beads.nbeads - mdof)) - - return kedof/(0.5*Constants.kb) - - def get_kincv(self, atom=""): - """Calculates the quantum centroid virial kinetic energy estimator. - - Args: - atom: If given, specifies the atom to give the kinetic energy - for. If not, the system kinetic energy is given. - """ - - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output kinetic energy as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - q = depstrip(self.beads.q) - qc = depstrip(self.beads.qc) - f = depstrip(self.forces.f) - - acv = 0.0 - ncount = 0 - for i in range(self.beads.natoms): - if (atom != "" and iatom != i and latom != self.beads.names[i]): - continue - - kcv = 0.0 - k = 3*i - for b in range(self.beads.nbeads): - kcv += (q[b,k] - qc[k])* f[b,k] + (q[b,k+1] - qc[k+1])* f[b,k+1] + (q[b,k+2] - qc[k+2])* f[b,k+2] - kcv *= -0.5/self.beads.nbeads - kcv += 1.5*Constants.kb*self.ensemble.temp - acv += kcv - ncount += 1 - - if ncount == 0: - warning("Couldn't find an atom which matched the argument of kinetic energy, setting to zero.", verbosity.medium) - - return acv - - def get_kinmd(self, atom=""): - """Calculates the classical kinetic energy of the simulation (p^2/2m) - - Args: - atom: If given, specifies the atom to give the kinetic energy - for. If not, the simulation kinetic energy is given. - """ - - if atom == "": - return self.nm.kin/self.beads.nbeads - else: - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output kinetic energy as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - pnm = depstrip(self.nm.pnm) - dm3 = depstrip(self.nm.dynm3) - kmd = 0.0 - ncount = 0 - for i in range(self.beads.natoms): - if (atom != "" and iatom != i and latom != self.beads.names[i]): - continue - k = 3*i - for b in range(self.beads.nbeads): - kmd += (pnm[b,k]**2 + pnm[b,k+1]**2 + pnm[b,k+2]**2)/(2.0*dm3[b,k]) - ncount += 1 - - if ncount == 0: - warning("Couldn't find an atom which matched the argument of kinetic energy, setting to zero.", verbosity.medium) - - return kmd/self.beads.nbeads - - def get_ktens(self, atom=""): - """Calculates the quantum centroid virial kinetic energy - TENSOR estimator. - - Args: - atom: The index of the atom for which the kinetic energy tensor - is to be output, or the index of the type of atoms for which - it should be output. - """ - - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output kinetic tensor as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - tkcv = np.zeros((6),float) - ncount = 0 - for i in range(self.beads.natoms): - if (atom != "" and iatom != i and latom != self.beads.names[i]): - continue - - tkcv += self.get_kij(str(i), str(i)) - ncount += 1 - - if ncount == 0: - warning("Couldn't find an atom which matched the argument of kinetic tensor, setting to zero.", verbosity.medium) - - return tkcv - - def get_kij(self, ni="0", nj="0"): - """Calculates the quantum centroid virial kinetic energy - TENSOR estimator for two possibly different atom indices. - - Args: - ni: The index of atom i. - nj: The index of atom j. - - Returns: - The contribution to the kinetic energy tensor estimator from - the interactions between atom i and atom j. - """ - - i = int(ni) - j = int(nj) - if i >= self.beads.natoms: - raise IndexError("Cannot output kinetic_ij as atom index %d is larger than the number of atoms" % i) - if j >= self.beads.natoms: - raise IndexError("Cannot output kinetic_ij as atom index %d is larger than the number of atoms" % j) - mi = self.beads.m[i] - mj = self.beads.m[j] - ai = 3*i - aj = 3*j - - q = depstrip(self.beads.q) - qc = depstrip(self.beads.qc) - f = depstrip(self.forces.f) - - # I implement this for the most general case. In practice T_ij = /(2sqrt(m_i m_j)) - kcv = np.zeros((6),float) - for b in range(self.beads.nbeads): - kcv[0] += mi*(q[b,ai] - qc[ai]) *f[b,aj] + mj*(q[b,aj] - qc[aj]) *f[b,ai] #Txx - kcv[1] += mi*(q[b,ai+1] - qc[ai+1])*f[b,aj+1] + mj*(q[b,aj+1] - qc[aj+1])*f[b,ai+1] #Tyy - kcv[2] += mi*(q[b,ai+2] - qc[ai+2])*f[b,aj+2] + mj*(q[b,aj+2] - qc[aj+2])*f[b,ai+2] #Tzz - kcv[3] += mi*(q[b,ai] - qc[ai])* f[b,aj+1] + mj*(q[b,aj+1] - qc[aj+1])*f[b,ai] #Txy - kcv[4] += mi*(q[b,ai] - qc[ai])* f[b,aj+2] + mj*(q[b,aj+2] - qc[aj+2])*f[b,ai] #Txz - kcv[5] += mi*(q[b,ai+1] - qc[ai+1])*f[b,aj+2] + mj*(q[b,aj+2] - qc[aj+2])*f[b,ai+1] #Tyz - - kcv *= -0.5/(self.beads.nbeads*2*np.sqrt(mi*mj)) - if i == j: - kcv[0:3] += 0.5*Constants.kb*self.ensemble.temp - - return kcv - - def get_rg(self, atom=""): - """Calculates the radius of gyration of the ring polymers. - - Args: - atom: If given, specifies the atom to give the gyration radius - for. If not, the system average gyration radius is given. - """ - - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output gyration radius as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - q = depstrip(self.beads.q) - qc = depstrip(self.beads.qc) - nat = self.beads.natoms - nb = self.beads.nbeads - rg_tot = 0.0 - ncount = 0 - for i in range(nat): - if (atom != "" and iatom != i and latom != self.beads.names[i]): - continue - - rg_at = 0.0 - for j in range(nb): - dq = q[j,3*i:3*(i+1)] - qc[3*i:3*(i+1)] - rg_at += np.dot(dq, dq) - ncount += 1 - rg_tot += np.sqrt(rg_at/float(nb)) - - if ncount == 0: - raise IndexError("Couldn't find an atom which matched the argument of r_gyration") - - return rg_tot/float(ncount) - - def kstress_cv(self): - """Calculates the quantum centroid virial kinetic stress tensor - estimator. - - Note that this is not divided by the volume or the number of beads. - - Returns: - A 3*3 tensor with all the components of the tensor. - """ - - kst = np.zeros((3,3),float) - q = depstrip(self.beads.q) - qc = depstrip(self.beads.qc) - pc = depstrip(self.beads.pc) - m = depstrip(self.beads.m) - fall = depstrip(self.forces.f) - na3 = 3*self.beads.natoms - - for b in range(self.beads.nbeads): - for i in range(3): - for j in range(i,3): - kst[i,j] -= np.dot(q[b,i:na3:3] - qc[i:na3:3], - fall[b,j:na3:3]) - - # return the CV estimator MULTIPLIED BY NBEADS -- again for consistency with the virial, kstress_MD, etc... - for i in range(3): - kst[i,i] += self.beads.nbeads * ( np.dot(pc[i:na3:3],pc[i:na3:3]/m) ) - - return kst - - def opening(self, bead): - """Path opening function, used in linlin momentum distribution - estimator. - - Args: - bead: The index of the bead to shift. - """ - - return bead/float(self.beads.nbeads) + 0.5*(1.0/self.beads.nbeads - 1) - - def get_linlin(self, ux="0", uy="0", uz="0", atom=""): - """Calculates the end-to-end distribution for a particular path opening - vector. - - Args: - ux: The x-component of the path opening vector. - uy: The y-component of the path opening vector. - uz: The z-component of the path opening vector. - atom: If given, specifies the atom to give the kinetic energy - for. If not, the simulation kinetic energy is given. - """ - - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output linlin estimator as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - beta = 1.0/(self.ensemble.temp*Constants.kb) - - u = np.array([float(ux), float(uy), float(uz)]) - u_size = np.dot(u,u) - q = depstrip(self.beads.q) - nat = self.beads.natoms - nb = self.beads.nbeads - nx_tot = 0.0 - ncount = 0 - for i in range(nat): - if (atom != "" and iatom != i and latom != self.beads.names[i]): - continue - - mass = self.beads.m[i] - self.dbeads.q[:] = q - for b in range(nb): - self.dbeads.q[b,3*i:3*(i+1)] += self.opening(b)*u - dV = self.dforces.pot - self.forces.pot - - n0 = np.exp(-mass*u_size/(2.0*beta*Constants.hbar**2)) - nx_tot += n0*np.exp(-dV*beta/float(self.beads.nbeads)) - ncount += 1 - - if ncount == 0: - raise IndexError("Couldn't find an atom which matched the argument of linlin") - - return nx_tot/float(ncount) - - def get_yama_estimators(self, fd_delta= - _DEFAULT_FINDIFF): - """Calculates the quantum scaled coordinate kinetic energy estimator. - - Uses a finite difference method to calculate the estimators - needed to calculate the energy and heat capacity of the system, as - shown in Takeshi M. Yamamoto, Journal of Chemical Physics, - 104101, 123 (2005). Returns both eps_v and eps_v' as defined in - the above article. Note that heat capacity is calculated as - beta**2*kboltzmann*( - **2 - ), and the - energy of the system as . - - Args: - fd_delta: the relative finite difference in temperature to apply in - computing finite-difference quantities. If it is negative, will be - scaled down automatically to avoid discontinuities in the potential. - """ - - dbeta = abs(float(fd_delta)) - beta = 1.0/(Constants.kb*self.ensemble.temp) - - qc = depstrip(self.beads.centroid.q) - q = depstrip(self.beads.q) - v0 = self.forces.pot/self.beads.nbeads - while True: - splus = np.sqrt(1.0 + dbeta) - sminus = np.sqrt(1.0 - dbeta) - - for b in range(self.beads.nbeads): - self.dbeads[b].q = qc*(1.0 - splus) + splus*q[b,:] - vplus = self.dforces.pot/self.beads.nbeads - - for b in range(self.beads.nbeads): - self.dbeads[b].q = qc*(1.0 - sminus) + sminus*q[b,:] - vminus = self.dforces.pot/self.beads.nbeads - - if (fd_delta < 0 and abs((vplus + vminus)/(v0*2) - 1.0) > self._DEFAULT_FDERROR and dbeta > self._DEFAULT_MINFID): - dbeta *= 0.5 - info("Reducing displacement in Yamamoto kinetic estimator", verbosity.low) - continue - else: - eps = ((1.0 + dbeta)*vplus - (1.0 - dbeta)*vminus)/(2*dbeta) - eps += 0.5*(3*self.beads.natoms)/beta - - eps_prime = ((1.0 + dbeta)*vplus + (1.0 - dbeta)*vminus - 2*v0)/(dbeta**2*beta) - eps_prime -= 0.5*(3*self.beads.natoms)/beta**2 - - break - - return np.asarray([eps, eps_prime]) - - def get_isotope_yama(self, alpha="1.0", atom=""): - """Gives the components of the yamamoto scaled-mass KE estimator - for a given atom index. - - Args: - alpha: m'/m the mass ratio - atom: the index of the atom to compute the isotope fractionation - pair for, or a label - - Returns: - a tuple from which one can reconstruct all that is needed to - compute the SMKEE, and its statistical accuracy: - (sum_deltah, sum_ke, log(sum(weights)), log(sum(weight*ke)), - sign(sum(weight*ke)) ) - """ - - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output scaled-mass kinetic energy estimator as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - alpha = float(alpha) - - atcv = 0.0 - atcv2 = 0.0 - alogr = 0.0 - alogr2 = 0.0 - law = 0.0 - lawke = 0.0 - sawke = 1.0 - ni = 0 - - # strips dependency control since we are not gonna change the true beads in what follows - q = depstrip(self.beads.q) - f = depstrip(self.forces.f) - qc = depstrip(self.beads.qc) - - for i in range(self.beads.natoms): - # selects only the atoms we care about - if (atom != "" and iatom != i and latom != self.beads.names[i]): - continue - - ni += 1 - - # arranges coordinate-scaled beads in a auxiliary beads object - self.dbeads.q[:] = q[:] - for b in range(self.beads.nbeads): - self.dbeads.q[b,3*i:3*(i+1)] = ( qc[3*i:3*(i+1)]+ - np.sqrt(1.0/alpha)*(q[b,3*i:3*(i+1)]-qc[3*i:3*(i+1)]) ) - - tcv = 0.0 - for b in range(self.beads.nbeads): - tcv += np.dot( (self.dbeads.q[b,3*i:3*(i+1)]-self.dbeads.qc[3*i:3*(i+1)]), - self.dforces.f[b,3*i:3*(i+1)] ) - tcv *= -0.5/self.beads.nbeads - tcv += 1.5*Constants.kb*self.simul.ensemble.temp - - logr = (self.dforces.pot-self.forces.pot)/(Constants.kb*self.simul.ensemble.temp*self.beads.nbeads) - - atcv += tcv - atcv2 += tcv*tcv - - alogr += logr - alogr2 += logr*logr; - - #accumulates log averages in a way which preserves accuracy - if (ni == 1): - law = -logr - else: - (law, drop) = logsumlog( (law,1.0), (-logr,1.0)) - - #here we need to take care of the sign of tcv, which might as well be - #negative... almost never but... - if (ni == 1): - lawke = -logr + np.log(abs(tcv)) - sawke = np.sign(tcv); - else: - (lawke, sawke) = logsumlog( (lawke, sawke), (-logr+np.log(abs(tcv)), np.sign(tcv)) ) - - if ni == 0: - raise IndexError("Couldn't find an atom which matched the argument of isotope_y") - - return np.asarray([alogr/ni, alogr2/ni, atcv/ni, atcv2/ni, law, lawke, sawke]) - - def get_isotope_thermo(self, alpha="1.0", atom=""): - """Gives the components of the thermodynamic scaled-mass KE - estimator for a given atom index. - - Args: - alpha: m'/m the mass ratio - atom: the index of the atom to compute the isotope fractionation - pair for, or a label - - Returns: - a tuple from which one can reconstruct all that is needed to - compute the SMKEE: - (sum_deltah, sum_ke, log(sum(weights)), log(sum(weight*ke)), - sign(sum(weight*ke)) ) - """ - - try: - #iatom gives the index of the atom to be studied - iatom = int(atom) - latom = "" - if iatom >= self.beads.natoms: - raise IndexError("Cannot output scaled-mass kinetic energy estimator as atom index %d is larger than the number of atoms" % iatom) - except ValueError: - #here 'atom' is a label rather than an index which is stored in latom - iatom = -1 - latom = atom - - alpha = float(alpha) - - atcv = 0.0 - alogr = 0.0 - atcv2 = 0.0 - alogr2 = 0.0 - law = 0.0 - lawke = 0.0 - sawke = 1.0 - ni = 0 - - # strips dependency control since we are not gonna change the true beads in what follows - q = depstrip(self.beads.q) - f = depstrip(self.forces.f) - qc = depstrip(self.beads.qc) - - for i in range(self.beads.natoms): - # selects only the atoms we care about - if (atom != "" and iatom != i and latom != self.beads.names[i]): - continue - - ni += 1 - - spr = 0.0 - for b in range(1,self.beads.nbeads): - for j in range(3*i,3*(i+1)): - spr += (q[b,j]-q[b-1,j])**2 - for j in range(3*i,3*(i+1)): - spr += (q[self.beads.nbeads-1,j]-q[0,j])**2 - - spr *= 0.5*self.beads.m[i]*self.nm.omegan2 - - # centroid virial contribution from atom i - tcv = 0.0 - for b in range(self.beads.nbeads): - tcv += np.dot( (q[b,3*i:3*(i+1)]-qc[3*i:3*(i+1)]), f[b,3*i:3*(i+1)]) - tcv *= -0.5/self.beads.nbeads - tcv += 1.5*Constants.kb*self.simul.ensemble.temp - - logr = (alpha-1)*spr/(Constants.kb*self.simul.ensemble.temp*self.beads.nbeads) - - atcv += tcv - atcv2 += tcv*tcv - alogr += logr - alogr2 += logr*logr - - #accumulates log averages in a way which preserves accuracy - if (ni == 1): - law = -logr - else: - (law, drop) = logsumlog( (law,1.0), (-logr,1.0)) - - #here we need to take care of the sign of tcv, which might as well be - #negative... almost never but... - if (ni == 1): - lawke = -logr + np.log(abs(tcv)) - sawke = np.sign(tcv) - else: - (lawke, sawke) = logsumlog( (lawke, sawke), (-logr+np.log(abs(tcv)), np.sign(tcv)) ) - - if ni == 0: - raise IndexError("Couldn't find an atom which matched the argument of isotope_y") - - return np.asarray([alogr/ni, alogr2/ni, atcv/ni, atcv2/ni, law, lawke, sawke]) - - -class Trajectories(dobject): - """A simple class to take care of output of trajectory data. - - Attributes: - simul: The simulation object from which the position data will be - obtained. - fatom: A dummy beads object used so that individual replica trajectories - can be output. - traj_dict: A dictionary containing all the trajectories that can be - output. - """ - - def __init__(self): - """Initializes a Trajectories object.""" - - self.traj_dict = { - # Note that here we want to return COPIES of the different arrays, so we make sure to make an operation in order not to return a reference. - "positions": { "dimension" : "length", - "help": "The atomic coordinate trajectories. Will print out one file per bead, unless the bead attribute is set by the user.", - 'func': (lambda : 1.0*self.simul.beads.q)}, - "velocities": {"dimension" : "velocity", - "help": "The velocity trajectories. Will print out one file per bead, unless the bead attribute is set by the user.", - 'func': (lambda : self.simul.beads.p/self.simul.beads.m3)}, - "momenta": {"dimension" : "momentum", - "help": "The momentum trajectories. Will print out one file per bead, unless the bead attribute is set by the user.", - 'func': (lambda : 1.0*self.simul.beads.p)}, - "forces": { "dimension" : "force", - "help": "The force trajectories. Will print out one file per bead, unless the bead attribute is set by the user.", - 'func': (lambda : 1.0*self.simul.forces.f)}, - "x_centroid": {"dimension" : "length", - "help": "The centroid coordinates.", - 'func': (lambda : 1.0*self.simul.beads.qc)}, - "v_centroid": {"dimension" : "velocity", - "help": "The centroid velocity.", - 'func': (lambda : self.simul.beads.pc/self.simul.beads.m3[0])}, - "p_centroid": {"dimension" : "momentum", - "help": "The centroid momentum.", - 'func': (lambda : 1.0*self.simul.beads.pc)}, - "f_centroid": {"dimension" : "force", - "help": "The force acting on the centroid.", - 'func': (lambda : np.sum(self.simul.forces.f,0)/float(self.simul.beads.nbeads))}, - "kinetic_cv": {"dimension" : "energy", - "help": "The centroid virial quantum kinetic energy estimator for each atom, resolved into Cartesian components [xx, yy, zz]", - 'func': self.get_akcv}, - "kinetic_od": {"dimension" : "energy", - "help": "The off diagonal elements of the centroid virial quantum kinetic energy tensor [xy, xz, yz]", - 'func': self.get_akcv_od}, - "r_gyration": {"dimension" : "length", - "help": "The radius of gyration of the ring polymer, for each atom and resolved into Cartesian components [xx, yy, zz]", - 'func': self.get_rg}, - "extras": { "help": """The additional data returned by the client code, printed verbatim. Will print - out one file per bead, unless the bead attribute is set by the user.""", - 'func': (lambda : self.simul.forces.extras)} - } - - - def bind(self, simul): - """ Binds to a simulation object to fetch atomic and force data. - - Args: - simul: The simulation object that will be managed by this Trajectories. - """ - - self.simul = simul - self.fatom = simul.beads[0].copy() - - def get_akcv(self): - """Calculates the contribution to the kinetic energy due to each degree - of freedom. - """ - - rv = np.zeros(self.simul.beads.natoms*3) - for b in range(self.simul.beads.nbeads): - rv[:] += (self.simul.beads.q[b]-self.simul.beads.qc)*self.simul.forces.f[b] - rv *= -0.5/self.simul.beads.nbeads - rv += 0.5*Constants.kb*self.simul.ensemble.temp - return rv - - def get_akcv_od(self): - """Calculates the "off-diagonal" contribution to the kinetic energy tensor - due to each atom. - """ - - rv = np.zeros((self.simul.beads.natoms,3)) - # helper arrays to make it more obvious what we are computing - dq = np.zeros((self.simul.beads.natoms,3)) - f = np.zeros((self.simul.beads.natoms,3)) - for b in range(self.simul.beads.nbeads): - dq[:] = (self.simul.beads.q[b]-self.simul.beads.qc).reshape((self.simul.beads.natoms,3)) - f[:] = self.simul.forces.f[b].reshape((self.simul.beads.natoms,3)) - rv[:,0] += dq[:,0]*f[:,1] + dq[:,1]*f[:,0] - rv[:,1] += dq[:,0]*f[:,2] + dq[:,2]*f[:,0] - rv[:,2] += dq[:,1]*f[:,2] + dq[:,2]*f[:,1] - rv *= 0.5 - rv *= -0.5/self.simul.beads.nbeads - - return rv.reshape(self.simul.beads.natoms*3) - - def get_rg(self): - """Calculates the radius of gyration of the ring polymers. - - Computes separately the x, y, z contributions so that the actual - gyration radius can be recovered as sqrt(rx^2+ry^2+rz^2). - """ - - q = depstrip(self.simul.beads.q) - qc = depstrip(self.simul.beads.qc) - nat = self.simul.beads.natoms - nb = self.simul.beads.nbeads - rg = np.zeros(3*nat) - for i in range(nb): - for j in range(nat): - dq = q[i,3*j:3*(j+1)] - qc[3*j:3*(j+1)] - rg[3*j:3*(j+1)] += dq*dq - return np.sqrt(rg/float(nb)) - - def __getitem__(self, key): - """Retrieves the item given by key. - - Note that if the key contains a string (arg1; arg2; ... ) - then it will pass the appropriate positional arguments to the - calculation function of the property. Note the brackets and - the semi-colon separators. If instead we have the syntax - (arg1=val1;arg2; ... ), then the keyword/value pair (arg1,val1) - will be added to the keyword argument list. The appropriate key word - arguments will then be passed to the calculation function instead. - - Similarly, if the key contains a string {unit}, then it will take - the string 'unit' and use it to define the units that the trajectory - is output in. - - Args: - key: A string contained in trajectory_dict. - - Returns: - The trajectory labeled by the keyword key, along with its unit - keyword, and the argument lists for the function used to calculate - the trajectory specified by the keyword key. - """ - - (key, unit, arglist, kwarglist) = getall(key) - pkey = self.traj_dict[key] - - #pkey["func"](*arglist,**kwarglist) gives the value of the trajectory - #in atomic units. unit_to_user() returns the value in the user - #specified units. - if "dimension" in pkey and unit != "": - return unit_to_user(pkey["dimension"], unit, 1.0) * pkey["func"](*arglist,**kwarglist) - else: - return pkey["func"](*arglist,**kwarglist) - - def print_traj(self, what, stream, b=0, format="pdb", cell_units="atomic_unit", flush=True): - """Prints out a frame of a trajectory for the specified quantity and bead. - - Args: - what: A string specifying what to print. - b: The bead index. Defaults to 0. - stream: A reference to the stream on which data will be printed. - format: The output file format. - cell_units: The units used to specify the cell parameters. - flush: A boolean which specifies whether to flush the output buffer - after each write to file or not. - """ - - cq = self[what] - if getkey(what) in [ "extras" ] : - stream.write(" #*EXTRAS*# Step: %10d Bead: %5d \n" % (self.simul.step+1, b) ) - stream.write(cq[b]) - stream.write("\n") - if flush : - stream.flush() - os.fsync(stream) - return - elif getkey(what) in [ "positions", "velocities", "forces" ] : - self.fatom.q[:] = cq[b] - else: - self.fatom.q[:] = cq - - fcell = Cell() - fcell.h = self.simul.cell.h*unit_to_user("length", cell_units, 1.0) - - if format == "pdb": - io_pdb.print_pdb(self.fatom, fcell, stream, title=("Traj: %s Step: %10d Bead: %5d " % (what, self.simul.step+1, b) ) ) - elif format == "xyz": - io_xyz.print_xyz(self.fatom, fcell, stream, title=("Traj: %s Step: %10d Bead: %5d " % (what, self.simul.step+1, b) ) ) - elif format == "bin": - io_binary.print_bin(self.fatom, fcell, stream, title=("Traj: %s Step: %10d Bead: %5d " % (what, self.simul.step+1, b) ) ) - if flush : - stream.flush() - os.fsync(stream) diff --git a/tools/i-pi/ipi/engine/simulation.py b/tools/i-pi/ipi/engine/simulation.py deleted file mode 100644 index b1483de576..0000000000 --- a/tools/i-pi/ipi/engine/simulation.py +++ /dev/null @@ -1,232 +0,0 @@ -"""Contains the class that deals with the running of the simulation and -outputting the results. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -The root class for the whole simulation. Contains references to all the top -level objects used in the simulation, and controls all the steps that are -not inherently system dependent, like the running of each time step, -choosing which properties to initialize, and which properties to output. - -Classes: - Simulation: Deals with running the simulation and outputting the results. -""" - -__all__ = ['Simulation'] - -import numpy as np -import os.path, sys, time -from ipi.utils.depend import * -from ipi.utils.units import * -from ipi.utils.prng import * -from ipi.utils.io import * -from ipi.utils.io.io_xml import * -from ipi.utils.messages import verbosity, info -from ipi.utils.softexit import softexit -from ipi.engine.atoms import * -from ipi.engine.cell import * -from ipi.engine.forces import Forces -from ipi.engine.beads import Beads -from ipi.engine.normalmodes import NormalModes -from ipi.engine.properties import Properties, Trajectories -from ipi.engine.outputs import CheckpointOutput - -class Simulation(dobject): - """Main simulation object. - - Contains all the references and the main dynamics loop. Also handles the - initialization and output. - - Attributes: - beads: A beads object giving the atom positions. - cell: A cell object giving the system box. - prng: A random number generator object. - flist: A list of forcefield objects giving different ways to partially - calculate the forces. - forces: A Forces object for calculating the total force for all the - replicas. - ensemble: An ensemble object giving the objects necessary for producing - the correct ensemble. - tsteps: The total number of steps. - ttime: The wall clock time (in seconds). - format: A string specifying both the format and the extension of traj - output. - outputs: A list of output objects that should be printed during the run - nm: A helper object dealing with normal modes transformation - properties: A property object for dealing with property output. - trajs: A trajectory object for dealing with trajectory output. - chk: A checkpoint object for dealing with checkpoint output. - rollback: If set to true, the state of the simulation at the start - of the step will be output to a restart file rather than - the current state of the simulation. This is because we cannot - restart from half way through a step, only from the beginning of a - step, so this is necessary for the trajectory to be continuous. - - Depend objects: - step: The current simulation step. - """ - - def __init__(self, beads, cell, forces, ensemble, prng, outputs, nm, init, step=0, tsteps=1000, ttime=0): - """Initializes Simulation class. - - Args: - beads: A beads object giving the atom positions. - cell: A cell object giving the system box. - forces: A forcefield object giving the force calculator for each - replica of the system. - ensemble: An ensemble object giving the objects necessary for - producing the correct ensemble. - prng: A random number object. - outputs: A list of output objects. - nm: A class dealing with path NM operations. - init: A class to deal with initializing the simulation object. - step: An optional integer giving the current simulation time step. - Defaults to 0. - tsteps: An optional integer giving the total number of steps. Defaults - to 1000. - ttime: The simulation running time. Used on restart, to keep a - cumulative total. - """ - - info(" # Initializing simulation object ", verbosity.low ) - self.prng = prng - self.ensemble = ensemble - self.beads = beads - self.cell = cell - self.nm = nm - - # initialize the configuration of the system - self.init = init - init.init_stage1(self) - - self.flist = forces - self.forces = Forces() - self.outputs = outputs - - dset(self, "step", depend_value(name="step", value=step)) - self.tsteps = tsteps - self.ttime = ttime - - self.properties = Properties() - self.trajs = Trajectories() - self.chk = None - self.rollback = True - - def bind(self): - """Calls the bind routines for all the objects in the simulation.""" - - # binds important computation engines - self.nm.bind(self.beads, self.ensemble) - self.forces.bind(self.beads, self.cell, self.flist) - self.ensemble.bind(self.beads, self.nm, self.cell, self.forces, self.prng) - self.init.init_stage2(self) - - # binds output management objects - self.properties.bind(self) - self.trajs.bind(self) - for o in self.outputs: - o.bind(self) - - self.chk = CheckpointOutput("RESTART", 1, True, 0) - self.chk.bind(self) - - # registers the softexit routine - softexit.register(self.softexit) - - def softexit(self): - """Deals with a soft exit request. - - Tries to ensure that a consistent restart checkpoint is - written out. - """ - - if self.step < self.tsteps: - self.step += 1 - if not self.rollback: - self.chk.store() - self.chk.write(store=False) - - self.forces.stop() - - def run(self): - """Runs the simulation. - - Does all the simulation steps, and outputs data to the appropriate files - when necessary. Also deals with starting and cleaning up the threads used - in the communication between the driver and the PIMD code. - """ - - self.forces.run() - - # prints initial configuration -- only if we are not restarting - if (self.step == 0): - self.step = -1 - for o in self.outputs: - o.write() - self.step = 0 - - steptime = 0.0 - simtime = time.time() - - cstep = 0 - tptime = 0.0 - tqtime = 0.0 - tttime = 0.0 - ttot = 0.0 - # main MD loop - for self.step in range(self.step,self.tsteps): - # stores the state before doing a step. - # this is a bit time-consuming but makes sure that we can honor soft - # exit requests without screwing the trajectory - - steptime = -time.time() - self.chk.store() - - self.ensemble.step() - - for o in self.outputs: - o.write() - - if os.path.exists("EXIT"): # soft-exit - self.rollback = False - softexit.trigger() - - steptime += time.time() - ttot += steptime - tptime += self.ensemble.ptime - tqtime += self.ensemble.qtime - tttime += self.ensemble.ttime - cstep += 1 - - if verbosity.high or (verbosity.medium and self.step%100 == 0) or (verbosity.low and self.step%1000 == 0): - info(" # Average timings at MD step % 7d. t/step: %10.5e [p: %10.5e q: %10.5e t: %10.5e]" % - ( self.step, ttot/cstep, tptime/cstep, tqtime/cstep, tttime/cstep ) ) - cstep = 0 - tptime = 0.0 - tqtime = 0.0 - tttime = 0.0 - ttot = 0.0 - info(" # MD diagnostics: V: %10.5e Kcv: %10.5e Ecns: %10.5e" % - (self.properties["potential"], self.properties["kinetic_cv"], self.properties["conserved"] ) ) - - if (self.ttime > 0 and time.time() - simtime > self.ttime): - info(" # Wall clock time expired! Bye bye!", verbosity.low ) - break - - info(" # Simulation ran successfully for the prescribed total_step! Bye bye!", verbosity.low ) - self.rollback = False - softexit.trigger() diff --git a/tools/i-pi/ipi/engine/thermostats.py b/tools/i-pi/ipi/engine/thermostats.py deleted file mode 100644 index 7941f55916..0000000000 --- a/tools/i-pi/ipi/engine/thermostats.py +++ /dev/null @@ -1,884 +0,0 @@ -"""Contains the classes that deal with constant temperature dynamics. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Contains the algorithms which propagate the thermostatting steps in the constant -temperature ensembles. Includes the new GLE thermostat, which can be used to -run PI+GLE dynamics, reducing the number of path integral beads required. - -Classes: - Thermostat: Base thermostat class with the generic methods and attributes. - ThermoLangevin: Holds the algorithms for a langevin thermostat. - ThermoPILE_L: Holds the algorithms for a path-integral langevin equation - thermostat, with a thermostat coupled directly to the - centroid coordinate of each bead. - ThermoPILE_G: Holds the algorithms for a path-integral langevin equation - thermostat, with a thermostat coupled to the kinetic energy for - the entire system. - ThermoSVR: Holds the algorithms for a stochastic velocity rescaling - thermostat. - ThermoGLE: Holds the algorithms for a generalized langevin equation - thermostat. - ThermoNMGLE: Holds the algorithms for a generalized langevin equation - thermostat in the normal mode representation. - ThermoNMGLEG: Holds the algorithms for a generalized langevin equation - thermostat in the normal mode representation, with kinetic energy as - well as potential energy sampling optimization. -""" - -__all__ = ['Thermostat', 'ThermoLangevin', 'ThermoPILE_L', 'ThermoPILE_G', - 'ThermoSVR', 'ThermoGLE', 'ThermoNMGLE', 'ThermoNMGLEG'] - -import numpy as np -from ipi.utils.depend import * -from ipi.utils.units import * -from ipi.utils.mathtools import matrix_exp, stab_cholesky, root_herm -from ipi.utils.prng import Random -from ipi.utils.messages import verbosity, warning, info -from ipi.engine.beads import Beads -from ipi.engine.normalmodes import NormalModes - -class Thermostat(dobject): - """Base thermostat class. - - Gives the standard methods and attributes needed in all the thermostat - classes. - - Attributes: - prng: A pseudo random number generator object. - ndof: The number of degrees of freedom that the thermostat will be - attached to. - - Depend objects: - dt: The time step used in the algorithms. Depends on the simulation dt. - temp: The simulation temperature. Higher than the system temperature by - a factor of the number of beads. Depends on the simulation temp. - ethermo: The total energy exchanged with the bath due to the thermostat. - p: The momentum vector that the thermostat is coupled to. Depends on the - beads p object. - m: The mass vector associated with p. Depends on the beads m object. - sm: The square root of the mass vector. - """ - - def __init__(self, temp = 1.0, dt = 1.0, ethermo=0.0): - """Initializes Thermostat. - - Args: - temp: The simulation temperature. Defaults to 1.0. - dt: The simulation time step. Defaults to 1.0. - ethermo: The initial heat energy transferred to the bath. - Defaults to 0.0. Will be non-zero if the thermostat is - initialized from a checkpoint file. - """ - - dset(self,"temp", depend_value(name='temp', value=temp)) - dset(self,"dt", depend_value(name='dt', value=dt)) - dset(self,"ethermo",depend_value(name='ethermo',value=ethermo)) - - def bind(self, beads=None, atoms=None, pm=None, prng=None, fixdof=None): - """Binds the appropriate degrees of freedom to the thermostat. - - This takes an object with degrees of freedom, and makes their momentum - and mass vectors members of the thermostat. It also then creates the - objects that will hold the data needed in the thermostat algorithms - and the dependency network. - - Args: - beads: An optional beads object to take the mass and momentum vectors - from. - atoms: An optional atoms object to take the mass and momentum vectors - from. - pm: An optional tuple containing a single momentum value and its - conjugate mass. - prng: An optional pseudo random number generator object. Defaults to - Random(). - fixdof: An optional integer which can specify the number of constraints - applied to the system. Defaults to zero. - - Raises: - TypeError: Raised if no appropriate degree of freedom or object - containing a momentum vector is specified for - the thermostat to couple to. - """ - - if prng is None: - warning("Initializing thermostat from standard random PRNG", verbosity.medium) - self.prng = Random() - else: - self.prng = prng - - if not beads is None: - dset(self,"p",beads.p.flatten()) - dset(self,"m",beads.m3.flatten()) - elif not atoms is None: - dset(self,"p",dget(atoms, "p")) - dset(self,"m",dget(atoms, "m3")) - elif not pm is None: - dset(self,"p",pm[0]) - dset(self,"m",pm[1]) - else: - raise TypeError("Thermostat.bind expects either Beads, Atoms, NormalModes, or a (p,m) tuple to bind to") - - if fixdof is None: - self.ndof = len(self.p) - else: - self.ndof = float(len(self.p) - fixdof) - - dset(self, "sm", - depend_array(name="sm", value=np.zeros(len(dget(self,"m"))), - func=self.get_sm, dependencies=[dget(self,"m")])) - - def get_sm(self): - """Retrieves the square root of the mass matrix. - - Returns: - A vector of the square root of the mass matrix with one value for - each degree of freedom. - """ - - return np.sqrt(self.m) - - def step(self): - """Dummy thermostat step.""" - - pass - - -class ThermoLangevin(Thermostat): - """Represents a langevin thermostat. - - Depend objects: - tau: Thermostat damping time scale. Larger values give a less strongly - coupled thermostat. - T: Coefficient of the diffusive contribution of the thermostat, i.e. the - drift back towards equilibrium. Depends on tau and the time step. - S: Coefficient of the stochastic contribution of the thermostat, i.e. - the uncorrelated Gaussian noise. Depends on T and the temperature. - """ - - def get_T(self): - """Calculates the coefficient of the overall drift of the velocities.""" - - return np.exp(-0.5*self.dt/self.tau) - - def get_S(self): - """Calculates the coefficient of the white noise.""" - - return np.sqrt(Constants.kb*self.temp*(1 - self.T**2)) - - def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0): - """Initializes ThermoLangevin. - - Args: - temp: The simulation temperature. Defaults to 1.0. - dt: The simulation time step. Defaults to 1.0. - tau: The thermostat damping timescale. Defaults to 1.0. - ethermo: The initial heat energy transferred to the bath. - Defaults to 0.0. Will be non-zero if the thermostat is - initialized from a checkpoint file. - """ - - super(ThermoLangevin,self).__init__(temp, dt, ethermo) - - dset(self,"tau",depend_value(value=tau,name='tau')) - dset(self,"T", - depend_value(name="T",func=self.get_T, - dependencies=[dget(self,"tau"), dget(self,"dt")])) - dset(self,"S", - depend_value(name="S",func=self.get_S, - dependencies=[dget(self,"temp"), dget(self,"T")])) - - def step(self): - """Updates the bound momentum vector with a langevin thermostat.""" - - p = depstrip(self.p).copy() - sm = depstrip(self.sm) - - p /= sm - - self.ethermo += np.dot(p,p)*0.5 - p *= self.T - p += self.S*self.prng.gvec(len(p)) - self.ethermo -= np.dot(p,p)*0.5 - - p *= sm - - self.p = p - - -class ThermoPILE_L(Thermostat): - """Represents a PILE thermostat with a local centroid thermostat. - - Attributes: - _thermos: The list of the different thermostats for all the ring polymer - normal modes. - nm: A normal modes object to attach the thermostat to. - prng: Random number generator used in the stochastic integration - algorithms. - - Depend objects: - tau: Centroid thermostat damping time scale. Larger values give a - less strongly coupled centroid thermostat. - tauk: Thermostat damping time scale for the non-centroid normal modes. - Depends on the ring polymer spring constant, and thus the simulation - temperature. - pilescale: A float used to reduce the intensity of the PILE thermostat if - required. - """ - - def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0, scale=1.0): - """Initializes ThermoPILE_L. - - Args: - temp: The simulation temperature. Defaults to 1.0. - dt: The simulation time step. Defaults to 1.0. - tau: The centroid thermostat damping timescale. Defaults to 1.0. - ethermo: The initial conserved energy quantity. Defaults to 0.0. Will - be non-zero if the thermostat is initialized from a checkpoint file. - scale: A float used to reduce the intensity of the PILE thermostat if - required. - - Raises: - TypeError: Raised if the thermostat is used with any object other than - a beads object, so that we make sure that the objects needed for the - normal mode transformation exist. - """ - - super(ThermoPILE_L,self).__init__(temp,dt,ethermo) - dset(self,"tau",depend_value(value=tau,name='tau')) - dset(self,"pilescale",depend_value(value=scale,name='pilescale')) - - def bind(self, nm=None, prng=None, bindcentroid=True, fixdof=None): - """Binds the appropriate degrees of freedom to the thermostat. - - This takes a beads object with degrees of freedom, and makes its momentum - and mass vectors members of the thermostat. It also then creates the - objects that will hold the data needed in the thermostat algorithms - and the dependency network. - - Gives the interface for both the PILE_L and PILE_G thermostats, which - only differ in their treatment of the centroid coordinate momenta. - - Args: - nm: An optional normal mode object to take the mass and momentum - vectors from. - prng: An optional pseudo random number generator object. Defaults to - Random(). - bindcentroid: An optional boolean which decides whether a Langevin - thermostat is attached to the centroid mode of each atom - separately, or the total kinetic energy. Defaults to True, which - gives a thermostat bound to each centroid momentum. - fixdof: An optional integer which can specify the number of constraints - applied to the system. Defaults to zero. - - Raises: - TypeError: Raised if no appropriate degree of freedom or object - containing a momentum vector is specified for - the thermostat to couple to. - """ - - if nm is None or not type(nm) is NormalModes: - raise TypeError("ThermoPILE_L.bind expects a NormalModes argument to bind to") - if prng is None: - self.prng = Random() - else: - self.prng = prng - - prev_ethermo = self.ethermo - - # creates a set of thermostats to be applied to individual normal modes - self._thermos = [ ThermoLangevin(temp=1, dt=1, tau=1) for b in range(nm.nbeads) ] - # optionally does not bind the centroid, so we can re-use all of this - # in the PILE_G case - if not bindcentroid: - self._thermos[0] = None - - self.nm = nm - - dset(self,"tauk", - depend_array(name="tauk", value=np.zeros(nm.nbeads-1,float), - func=self.get_tauk, dependencies=[dget(self,"pilescale"), dget(nm,"dynomegak")] ) ) - - # must pipe all the dependencies in such a way that values for the nm thermostats - # are automatically updated based on the "master" thermostat - def make_taugetter(k): - return lambda: self.tauk[k-1] - it = 0 - for t in self._thermos: - if t is None: - it += 1 - continue - if it > 0: - fixdof = None # only the centroid thermostat may have constraints - - # bind thermostat t to the it-th bead - t.bind(pm=(nm.pnm[it,:],nm.dynm3[it,:]),prng=self.prng, fixdof=fixdof) - # pipes temp and dt - deppipe(self,"temp", t, "temp") - deppipe(self,"dt", t, "dt") - - # for tau it is slightly more complex - if it == 0: - deppipe(self,"tau", t, "tau") - else: - # Here we manually connect _thermos[i].tau to tauk[i]. - # Simple and clear. - dget(t,"tau").add_dependency(dget(self,"tauk")) - dget(t,"tau")._func = make_taugetter(it) - dget(self,"ethermo").add_dependency(dget(t,"ethermo")) - it += 1 - - # since the ethermo will be "delegated" to the normal modes thermostats, - # one has to split - # any previously-stored value between the sub-thermostats - if bindcentroid: - for t in self._thermos: - t.ethermo = prev_ethermo/nm.nbeads - dget(self,"ethermo")._func = self.get_ethermo; - # if we are not binding the centroid just yet, this bit of the piping - # is delegated to the function which is actually calling this - - def get_tauk(self): - """Computes the thermostat damping time scale for the non-centroid - normal modes. - - Returns: - An array with the damping time scales for the non-centroid modes. - """ - - # Also include an optional scaling factor to reduce the intensity of NM thermostats - return np.array([ self.pilescale/(2*self.nm.dynomegak[k]) for k in range(1,len(self._thermos)) ]) - - def get_ethermo(self): - """Computes the total energy transferred to the heat bath for all the - thermostats. - """ - - et = 0.0; - for t in self._thermos: - et += t.ethermo - return et - - def step(self): - """Updates the bound momentum vector with a PILE thermostat.""" - - # super-cool! just loop over the thermostats! it's as easy as that! - for t in self._thermos: - t.step() - - -class ThermoSVR(Thermostat): - """Represents a stochastic velocity rescaling thermostat. - - Depend objects: - tau: Centroid thermostat damping time scale. Larger values give a - less strongly coupled centroid thermostat. - K: Scaling factor for the total kinetic energy. Depends on the - temperature. - et: Parameter determining the strength of the thermostat coupling. - Depends on tau and the time step. - """ - - def get_et(self): - """Calculates the damping term in the propagator.""" - - return np.exp(-0.5*self.dt/self.tau) - - def get_K(self): - """Calculates the average kinetic energy per degree of freedom.""" - - return Constants.kb*self.temp*0.5 - - def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0): - """Initializes ThermoSVR. - - Args: - temp: The simulation temperature. Defaults to 1.0. - dt: The simulation time step. Defaults to 1.0. - tau: The thermostat damping timescale. Defaults to 1.0. - ethermo: The initial conserved energy quantity. Defaults to 0.0. Will - be non-zero if the thermostat is initialized from a checkpoint file. - """ - - super(ThermoSVR,self).__init__(temp,dt,ethermo) - - dset(self,"tau",depend_value(value=tau,name='tau')) - dset(self,"et", - depend_value(name="et",func=self.get_et, - dependencies=[dget(self,"tau"), dget(self,"dt")])) - dset(self,"K", - depend_value(name="K",func=self.get_K, dependencies=[dget(self,"temp")])) - - def step(self): - """Updates the bound momentum vector with a stochastic velocity rescaling - thermostat. See G Bussi, D Donadio, M Parrinello, - Journal of Chemical Physics 126, 014101 (2007) - """ - - K = np.dot(depstrip(self.p),depstrip(self.p)/depstrip(self.m))*0.5 - - # rescaling is un-defined if the KE is zero - if K == 0.0: - return - - # gets the stochastic term (basically a Gamma distribution for the kinetic energy) - r1 = self.prng.g - if (self.ndof-1)%2 == 0: - rg = 2.0*self.prng.gamma((self.ndof-1)/2) - else: - rg = 2.0*self.prng.gamma((self.ndof-2)/2) + self.prng.g**2 - - alpha2 = self.et + self.K/K*(1 - self.et)*(r1**2 + rg) + 2.0*r1*np.sqrt(self.K/K*self.et*(1 - self.et)) - alpha = np.sqrt(alpha2) - if (r1 + np.sqrt(2*K/self.K*self.et/(1 - self.et))) < 0: - alpha *= -1 - - self.ethermo += K*(1 - alpha2) - self.p *= alpha - - -class ThermoPILE_G(ThermoPILE_L): - """Represents a PILE thermostat with a global centroid thermostat. - - Simply replaces the Langevin thermostat for the centroid normal mode with - a global velocity rescaling thermostat. - """ - - def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0, scale = 1.0): - """Initializes ThermoPILE_G. - - Args: - temp: The simulation temperature. Defaults to 1.0. - dt: The simulation time step. Defaults to 1.0. - tau: The centroid thermostat damping timescale. Defaults to 1.0. - ethermo: The initial conserved energy quantity. Defaults to 0.0. Will - be non-zero if the thermostat is initialized from a checkpoint file. - scale: A float used to reduce the intensity of the PILE thermostat if - required. - """ - - super(ThermoPILE_G,self).__init__(temp,dt,tau,ethermo) - dset(self,"pilescale",depend_value(value=scale,name='pilescale')) - - def bind(self, nm=None, prng=None, fixdof=None): - """Binds the appropriate degrees of freedom to the thermostat. - - This takes a beads object with degrees of freedom, and makes its momentum - and mass vectors members of the thermostat. It also then creates the - objects that will hold the data needed in the thermostat algorithms - and the dependency network. - - Uses the PILE_L bind interface, with bindcentroid set to false so we can - specify that thermostat separately, by binding a global - thermostat to the centroid mode. - - Args: - beads: An optional beads object to take the mass and momentum vectors - from. - prng: An optional pseudo random number generator object. Defaults to - Random(). - fixdof: An optional integer which can specify the number of constraints - applied to the system. Defaults to zero. - - """ - - # first binds as a local PILE, then substitutes the thermostat on the centroid - prev_ethermo = self.ethermo - super(ThermoPILE_G,self).bind(nm=nm,prng=prng,bindcentroid=False, fixdof=fixdof) - - #centroid thermostat - self._thermos[0] = ThermoSVR(temp=1, dt=1, tau=1) - - t = self._thermos[0] - t.bind(pm=(nm.pnm[0,:],nm.dynm3[0,:]),prng=self.prng, fixdof=fixdof) - deppipe(self,"temp", t, "temp") - deppipe(self,"dt", t, "dt") - deppipe(self,"tau", t, "tau") - dget(self,"ethermo").add_dependency(dget(t,"ethermo")) - - # splits any previous ethermo between the thermostats, and finishes to bind ethermo to the sum function - for t in self._thermos: - t.ethermo = prev_ethermo/nm.nbeads - dget(self,"ethermo")._func = self.get_ethermo; - - -class ThermoGLE(Thermostat): - """Represents a GLE thermostat. - - This is similar to a langevin thermostat, in that it uses Gaussian random - numbers to simulate a heat bath acting on the system, but simulates a - non-Markovian system by using a Markovian formulation in an extended phase - space. This allows for a much greater degree of flexibility, and this - thermostat, properly fitted, can give the an approximation to the correct - quantum ensemble even for a classical, 1-bead simulation. More reasonably, - using this thermostat allows for a far smaller number of replicas of the - system to be used, as the convergence of the properties - of the system is accelerated with respect to number of beads when PI+GLE - are used in combination. (See M. Ceriotti, D. E. Manolopoulos, M. Parinello, - J. Chem. Phys. 134, 084104 (2011)). - - Attributes: - ns: The number of auxiliary degrees of freedom. - s: An array holding all the momenta, including the ones for the - auxiliary degrees of freedom. - - Depend objects: - A: Drift matrix giving the damping time scales for all the different - degrees of freedom. - C: Static covariance matrix. - Satisfies A.C + C.transpose(A) = B.transpose(B), where B is the - diffusion matrix, giving the strength of the coupling of the system - with the heat bath, and thus the size of the stochastic - contribution of the thermostat. - T: Matrix for the diffusive contribution of the thermostat, i.e. the - drift back towards equilibrium. Depends on A and the time step. - S: Matrix for the stochastic contribution of the thermostat, i.e. - the uncorrelated Gaussian noise. Depends on C and T. - """ - - def get_T(self): - """Calculates the matrix for the overall drift of the velocities.""" - - return matrix_exp(-0.5*self.dt*self.A) - - def get_S(self): - """Calculates the matrix for the colored noise.""" - - SST = Constants.kb*(self.C - np.dot(self.T,np.dot(self.C,self.T.T))) - - # Uses a symmetric decomposition rather than Cholesky, since it is more stable - return root_herm(SST) - - def get_C(self): - """Calculates C from temp (if C is not set explicitly)""" - - rC = np.identity(self.ns + 1,float)*self.temp - return rC[:] - - def __init__(self, temp = 1.0, dt = 1.0, A = None, C = None, ethermo=0.0): - """Initializes ThermoGLE. - - Args: - temp: The simulation temperature. Defaults to 1.0. - dt: The simulation time step. Defaults to 1.0. - A: An optional matrix giving the drift matrix. Defaults to a single - value of 1.0. - C: An optional matrix giving the covariance matrix. Defaults to an - identity matrix times temperature with the same dimensions as the - total number of degrees of freedom in the system. - ethermo: The initial heat energy transferred to the bath. - Defaults to 0.0. Will be non-zero if the thermostat is - initialized from a checkpoint file. - """ - - super(ThermoGLE,self).__init__(temp,dt,ethermo) - - if A is None: - A = np.identity(1,float) - dset(self,"A",depend_value(value=A.copy(),name='A')) - - self.ns = len(self.A) - 1; - - # now, this is tricky. if C is taken from temp, then we want it to be updated - # as a depend of temp. Otherwise, we want it to be an independent beast. - if C is None: - C = np.identity(self.ns+1,float)*self.temp - dset(self,"C", - depend_value(name='C', func=self.get_C, - dependencies=[dget(self,"temp")])) - else: - dset(self,"C",depend_value(value=C.copy(),name='C')) - - dset(self,"T", - depend_value(name="T",func=self.get_T, - dependencies=[dget(self,"A"), dget(self,"dt")])) - dset(self,"S", - depend_value(name="S",func=self.get_S, - dependencies=[dget(self,"C"), dget(self,"T")])) - - self.s = np.zeros(0) - - def bind(self, beads=None, atoms=None, pm=None, prng=None, fixdof=None): - """Binds the appropriate degrees of freedom to the thermostat. - - This takes an object with degrees of freedom, and makes their momentum - and mass vectors members of the thermostat. It also then creates the - objects that will hold the data needed in the thermostat algorithms - and the dependency network. - - Args: - beads: An optional beads object to take the mass and momentum vectors - from. - atoms: An optional atoms object to take the mass and momentum vectors - from. - pm: An optional tuple containing a single momentum value and its - conjugate mass. - prng: An optional pseudo random number generator object. Defaults to - Random(). - fixdof: An optional integer which can specify the number of constraints - applied to the system. Defaults to zero. - - Raises: - TypeError: Raised if no appropriate degree of freedom or object - containing a momentum vector is specified for - the thermostat to couple to. - """ - - super(ThermoGLE,self).bind(beads,atoms,pm,prng,fixdof) - - # allocates, initializes or restarts an array of s's - if self.s.shape != (self.ns + 1, len(dget(self,"m"))): - if len(self.s) > 0: - warning("Mismatch in GLE s array size on restart, will reinitialize to free particle.", verbosity.low) - self.s = np.zeros((self.ns + 1, len(dget(self,"m")))) - - # Initializes the s vector in the free-particle limit - info(" GLE additional DOFs initialized to the free-particle limit.", verbosity.low) - SC = stab_cholesky(self.C*Constants.kb) - self.s[:] = np.dot(SC, self.prng.gvec(self.s.shape)) - else: - info("GLE additional DOFs initialized from input.", verbosity.medium) - - def step(self): - """Updates the bound momentum vector with a GLE thermostat""" - - p = depstrip(self.p).copy() - - self.s[0,:] = self.p/self.sm - - self.ethermo += np.dot(self.s[0],self.s[0])*0.5 - self.s[:] = np.dot(self.T,self.s) + np.dot(self.S,self.prng.gvec(self.s.shape)) - self.ethermo -= np.dot(self.s[0],self.s[0])*0.5 - - self.p = self.s[0]*self.sm - - -class ThermoNMGLE(Thermostat): - """Represents a 'normal-modes' GLE thermostat. - - An extension to the GLE thermostat which is applied in the - normal modes representation, and which allows to use a different - GLE for each normal mode - - Attributes: - ns: The number of auxiliary degrees of freedom. - nb: The number of beads. - s: An array holding all the momenta, including the ones for the - auxiliary degrees of freedom. - - Depend objects: - A: Drift matrix giving the damping time scales for all the different - degrees of freedom (must contain nb terms). - C: Static covariance matrix. - Satisfies A.C + C.transpose(A) = B.transpose(B), where B is the - diffusion matrix, giving the strength of the coupling of the system - with the heat bath, and thus the size of the stochastic - contribution of the thermostat. - """ - - def get_C(self): - """Calculates C from temp (if C is not set explicitly).""" - - rv = np.ndarray((self.nb, self.ns+1, self.ns+1), float) - for b in range(0,self.nb): - rv[b] = np.identity(self.ns + 1,float)*self.temp - return rv[:] - - def __init__(self, temp = 1.0, dt = 1.0, A = None, C = None, ethermo=0.0): - """Initializes ThermoGLE. - - Args: - temp: The simulation temperature. Defaults to 1.0. - dt: The simulation time step. Defaults to 1.0. - A: An optional matrix giving the drift matrix. Defaults to a single - value of 1.0. - C: An optional matrix giving the covariance matrix. Defaults to an - identity matrix times temperature with the same dimensions as the - total number of degrees of freedom in the system. - ethermo: The initial heat energy transferred to the bath. - Defaults to 0.0. Will be non-zero if the thermostat is - initialized from a checkpoint file. - """ - - super(ThermoNMGLE,self).__init__(temp,dt,ethermo) - - if A is None: - A = np.identity(1,float) - dset(self,"A",depend_value(value=A.copy(),name='A')) - - self.nb = len(self.A) - self.ns = len(self.A[0]) - 1; - - # now, this is tricky. if C is taken from temp, then we want it to be - # updated as a depend of temp. - # Otherwise, we want it to be an independent beast. - if C is None: - dset(self,"C",depend_value(name='C', func=self.get_C, dependencies=[dget(self,"temp")])) - else: - dset(self,"C",depend_value(value=C.copy(),name='C')) - - def bind(self, nm=None, prng=None, fixdof=None): - """Binds the appropriate degrees of freedom to the thermostat. - - This takes an object with degrees of freedom, and makes their momentum - and mass vectors members of the thermostat. It also then creates the - objects that will hold the data needed in the thermostat algorithms - and the dependency network. Actually, this specific thermostat requires - being called on a beads object. - - Args: - nm: An optional normal modes object to take the mass and momentum - vectors from. - prng: An optional pseudo random number generator object. Defaults to - Random(). - fixdof: An optional integer which can specify the number of constraints - applied to the system. Defaults to zero. - - Raises: - TypeError: Raised if no beads object is specified for - the thermostat to couple to. - """ - - if nm is None or not type(nm) is NormalModes: - raise TypeError("ThermoNMGLE.bind expects a NormalModes argument to bind to") - - if prng is None: - self.prng = Random() - else: - self.prng = prng - - if (nm.nbeads != self.nb): - raise IndexError("The parameters in nm_gle options correspond to a bead number "+str(self.nb)+ " which does not match the number of beads in the path" + str(nm.nbeads) ) - - # allocates, initializes or restarts an array of s's - if self.s.shape != (self.nb, self.ns + 1, nm.natoms *3) : - if len(self.s) > 0: - warning("Mismatch in GLE s array size on restart, will reinitialize to free particle.", verbosity.low) - self.s = np.zeros((self.nb, self.ns + 1, nm.natoms*3)) - - # Initializes the s vector in the free-particle limit - info(" GLE additional DOFs initialized to the free-particle limit.", verbosity.low) - for b in range(self.nb): - SC = stab_cholesky(self.C[b]*Constants.kb) - self.s[b] = np.dot(SC, self.prng.gvec(self.s[b].shape)) - else: - info("GLE additional DOFs initialized from input.", verbosity.medium) - - prev_ethermo = self.ethermo - - # creates a set of thermostats to be applied to individual normal modes - self._thermos = [ThermoGLE(temp=1, dt=1, A=self.A[b], C=self.C[b]) for b in range(self.nb)] - - # must pipe all the dependencies in such a way that values for the nm - # thermostats are automatically updated based on the "master" thermostat - def make_Agetter(k): - return lambda: self.A[k] - def make_Cgetter(k): - return lambda: self.C[k] - - it = 0 - for t in self._thermos: - t.s = self.s[it] # gets the s's as a slice of self.s - t.bind(pm=(nm.pnm[it,:],nm.dynm3[it,:]), prng=self.prng) # bind thermostat t to the it-th normal mode - - # pipes temp and dt - deppipe(self,"temp", t, "temp") - deppipe(self,"dt", t, "dt") - - # here we pipe the A and C of individual NM to the "master" arrays - dget(t,"A").add_dependency(dget(self,"A")) - dget(t,"A")._func = make_Agetter(it) - dget(t,"C").add_dependency(dget(self,"C")) - dget(t,"C")._func = make_Cgetter(it) - dget(self,"ethermo").add_dependency(dget(t,"ethermo")) - it += 1 - - # since the ethermo will be "delegated" to the normal modes thermostats, - # one has to split - # any previously-stored value between the sub-thermostats - for t in self._thermos: - t.ethermo = prev_ethermo/self.nb - - dget(self,"ethermo")._func = self.get_ethermo; - - def step(self): - """Updates the thermostat in NM representation by looping over the - individual DOFs. - """ - - for t in self._thermos: - t.step() - - def get_ethermo(self): - """Computes the total energy transferred to the heat bath for all the nm - thermostats. - """ - - et = 0.0; - for t in self._thermos: - et += t.ethermo - return et - - -class ThermoNMGLEG(ThermoNMGLE): - """Represents a 'normal-modes' GLE thermostat + SVR. - - An extension to the above NMGLE thermostat which also adds a stochastic velocity - rescaling to the centroid. - - Depend objects: - tau: Thermostat damping time scale. Larger values give a less strongly - coupled thermostat. - """ - - def __init__(self, temp = 1.0, dt = 1.0, A = None, C = None, tau=1.0, ethermo=0.0): - - super(ThermoNMGLEG,self).__init__(temp, dt, A, C, ethermo) - dset(self,"tau",depend_value(value=tau,name='tau')) - - def bind(self, nm=None, prng=None, fixdof=None): - """Binds the appropriate degrees of freedom to the thermostat. - - This takes an object with degrees of freedom, and makes their momentum - and mass vectors members of the thermostat. It also then creates the - objects that will hold the data needed in the thermostat algorithms - and the dependency network. Actually, this specific thermostat requires - being called on a beads object. - - Args: - nm: An optional normal modes object to take the mass and momentum - vectors from. - prng: An optional pseudo random number generator object. Defaults to - Random(). - fixdof: An optional integer which can specify the number of constraints - applied to the system. Defaults to zero. - """ - - super(ThermoNMGLEG,self).bind(nm, prng, fixdof) - - t = ThermoSVR(self.temp, self.dt, self.tau) - - t.bind(pm=(nm.pnm[0,:],nm.dynm3[0,:]), prng=self.prng) # bind global thermostat to centroid - - # pipes temp and dt - deppipe(self,"temp", t, "temp") - deppipe(self,"dt", t, "dt") - deppipe(self,"tau", t, "tau") - - dget(self,"ethermo").add_dependency(dget(t,"ethermo")) - self._thermos.append(t) - diff --git a/tools/i-pi/ipi/inputs/README b/tools/i-pi/ipi/inputs/README deleted file mode 100644 index 547884031d..0000000000 --- a/tools/i-pi/ipi/inputs/README +++ /dev/null @@ -1,24 +0,0 @@ - -- Input files directory -- - - * This is the directory containing the input classes. - - * Files: - - atoms.py: Creates objects that deal with classical simulations. - - barostats.py: Creates objects that deal with constant pressure and - stress simulations. - - beads.py: Creates objects that deal with quantum simulations. - - cell.py: Creates objects that deal with the simulation box. - - ensembles.py: Creates objects that deal with the different ensembles. - - forces.py: Creates objects that deal with the jobs to send to - the driver code. - - initializer.py: Creates the objects that deal with initializing the - simulation. - - interface.py: Creates objects that deal with socket creation. - - normalmodes.py: Creates the objects that deal with the normal mode - transformation. - - outputs.py: Creates objects that deal with output files. - - prng.py: Creates the objects that deal with random number generation. - - simulation.py: Creates objects that deal with all the top level - information, such as input/output. - - thermostats.py: Creates objects that deal with constant temperature - simulations. diff --git a/tools/i-pi/ipi/inputs/__init__.py b/tools/i-pi/ipi/inputs/__init__.py deleted file mode 100644 index 8e5fcd5089..0000000000 --- a/tools/i-pi/ipi/inputs/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -__all__ = [ 'barostats', 'cell', 'simulation', 'ensembles', 'thermostats', - 'interface', 'forces', 'atoms', 'beads', 'prng', 'outputs', - 'normalmodes', 'initializer'] diff --git a/tools/i-pi/ipi/inputs/atoms.py b/tools/i-pi/ipi/inputs/atoms.py deleted file mode 100644 index 4ae16bfdf5..0000000000 --- a/tools/i-pi/ipi/inputs/atoms.py +++ /dev/null @@ -1,121 +0,0 @@ -"""Deals with creating the atoms class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Generates an atoms class either from a set of positions and momenta. -This class is only used if no beads tag is present in the xml file. - -Classes: - InputAtoms: Deals with creating the Atoms object from a file, and - writing the checkpoints. -""" - -import numpy as np -from ipi.engine.atoms import * -from ipi.utils.inputvalue import * -from ipi.utils.depend import * -from ipi.utils.units import unit_to_internal - -__all__ = ['InputAtoms'] - -class InputAtoms(Input): - """Atoms input class. - - Handles generating the appropriate atoms class from the xml input file, - and generating the xml checkpoint tags and data from an instance of the - object. - - Attributes: - natoms: An optional integer giving the number of atoms. Defaults to 0. - q: An optional array giving the atom positions. Defaults to an empty - array with no elements. - p: An optional array giving the atom momenta. Defaults to an empty - array with no elements. - m: An optional array giving the atom masses. Defaults to an empty - array with no elements. - names: An optional array giving the atom names. Defaults to an empty - array with no elements - """ - - fields={ "natoms" : (InputValue, {"dtype" : int, - "default" : 0, - "help" : "The number of atoms." }), - "q" : (InputArray, {"dtype" : float, - "default" : input_default(factory=np.zeros, args=(0,)), - "help" : "The positions of the atoms, in the format [x1, y1, z1, x2, ... ].", - "dimension" : "length" }), - "p" : (InputArray, {"dtype" : float, - "default" : input_default(factory=np.zeros, args=(0,)), - "help" : "The momenta of the atoms, in the format [px1, py1, pz1, px2, ... ].", - "dimension" : "momentum" }), - "m" : (InputArray, {"dtype" : float, - "default" : input_default(factory=np.zeros, args=(0,)), - "help" : "The masses of the atoms, in the format [m1, m2, ... ].", - "dimension" : "mass" }), - "names" : (InputArray, {"dtype" : str, - "default" : input_default(factory=np.zeros, args=(0,), kwargs = {'dtype': np.dtype('|S6')}), - "help" : "The names of the atoms, in the format [name1, name2, ... ]." }) - } - - default_help = "Deals with a single replica of the system or classical simulations." - default_label = "ATOMS" - - def store(self, atoms): - """Takes an Atoms instance and stores a minimal representation of it. - - Args: - atoms: An Atoms object from which to initialize from. - filename: An optional string giving a filename to take the atom - positions from. Defaults to ''. - """ - - super(InputAtoms,self).store() - self.natoms.store(atoms.natoms) - self.q.store(depstrip(atoms.q)) - self.p.store(depstrip(atoms.p)) - self.m.store(depstrip(atoms.m)) - self.names.store(depstrip(atoms.names)) - - def fetch(self): - """Creates an atoms object. - - Returns: - An atoms object of the appropriate type and with the appropriate - properties given the attributes of the InputAtoms object. - """ - - super(InputAtoms,self).fetch() - atoms = Atoms(self.natoms.fetch()) - atoms.q = self.q.fetch() - atoms.p = self.p.fetch() - atoms.m = self.m.fetch() - atoms.names = self.names.fetch() - return atoms - - def write(self, name="", indent=""): - """Overloads Input write() function so that nothing is written if - no atoms are present. This occurs if the beads object has been specified, - so that the classical atoms object is not initialized. - - Returns: - A string giving the appropriate xml tags for the checkpoint file. - """ - - if self.natoms.fetch() > 0: - return super(InputAtoms,self).write(name=name,indent=indent) - else: - return "" diff --git a/tools/i-pi/ipi/inputs/barostats.py b/tools/i-pi/ipi/inputs/barostats.py deleted file mode 100644 index 84d0d83f43..0000000000 --- a/tools/i-pi/ipi/inputs/barostats.py +++ /dev/null @@ -1,107 +0,0 @@ -"""Deals with creating the barostat class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputBaro: Deals with creating the Barostat object from a file, and - writing the checkpoints. -""" - -import numpy as np -import ipi.engine.thermostats -from ipi.engine.barostats import * -from ipi.utils.inputvalue import * -from ipi.inputs.thermostats import * - -__all__ = ['InputBaro'] - -class InputBaro(Input): - """Barostat input class. - - Handles generating the appropriate barostat class from the xml input file, - and generating the xml checkpoint tags and data from an - instance of the object. - - Attributes: - mode: An optional string giving the type of barostat used. Defaults to - 'rigid'. - - Fields: - thermostat: A thermostat object giving the cell thermostat. - tau: The time constant associated with the dynamics of the piston. - p: The conjugate momentum to the volume degree of freedom. - """ - - attribs={ "mode": (InputAttribute, {"dtype" : str, - "default" : "dummy", - "help" : """The type of barostat. Currently, only a 'isotropic' barostat is implemented, that combines - ideas from the Bussi-Zykova-Parrinello barostat for classical MD with ideas from the - Martyna-Hughes-Tuckerman centroid barostat for PIMD; see Ceriotti, More, Manolopoulos, Comp. Phys. Comm. 2013 for - implementation details.""", - "options" : ["dummy", "isotropic"]}) } - fields={ "thermostat": (InputThermo, {"default" : input_default(factory=ipi.engine.thermostats.Thermostat), - "help" : "The thermostat for the cell. Keeps the cell velocity distribution at the correct temperature. Note that the 'pile_l', 'pile_g', 'nm_gle' and 'nm_gle_g' options will not work for this thermostat."}), - "tau": (InputValue, {"default" : 1.0, - "dtype" : float, - "dimension" : "time", - "help" : "The time constant associated with the dynamics of the piston."}), - "p": (InputArray, { "dtype" : float, - "default" : input_default(factory=np.zeros, args = (0,)), - "help" : "Momentum (or momenta) of the piston.", - "dimension" : "momentum" }) - } - - default_help = "Simulates an external pressure bath." - default_label = "BAROSTAT" - - def store(self, baro): - """Takes a barostat instance and stores a minimal representation of it. - - Args: - baro: A barostat object. - """ - - super(InputBaro,self).store(baro) - self.thermostat.store(baro.thermostat) - self.tau.store(baro.tau) - if type(baro) is BaroBZP: - self.mode.store("isotropic") - self.p.store(baro.p) - elif type(baro) is Barostat: - self.mode.store("dummy") - else: - raise TypeError("The type " + type(baro).__name__ + " is not a valid barostat type") - - - def fetch(self): - """Creates a barostat object. - - Returns: - A barostat object of the appropriate type and with the appropriate - thermostat given the attributes of the InputBaro object. - """ - - super(InputBaro,self).fetch() - if self.mode.fetch() == "isotropic": - baro = BaroBZP(thermostat=self.thermostat.fetch(), tau=self.tau.fetch()) - if self.p._explicit: baro.p = self.p.fetch() - elif self.mode.fetch() == "dummy": - baro = Barostat(thermostat=self.thermostat.fetch(), tau=self.tau.fetch()) - else: - raise ValueError(self.mode.fetch() + " is not a valid mode of barostat") - - return baro diff --git a/tools/i-pi/ipi/inputs/beads.py b/tools/i-pi/ipi/inputs/beads.py deleted file mode 100644 index d889563d92..0000000000 --- a/tools/i-pi/ipi/inputs/beads.py +++ /dev/null @@ -1,137 +0,0 @@ -"""Deals with creating the beads class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputBeads: Deals with creating the Beads object from a file, and - writing the checkpoints. -""" - -import numpy as np -from ipi.engine.beads import * -from ipi.engine.atoms import Atoms -from ipi.utils.inputvalue import * -from ipi.utils.depend import * -from ipi.utils.units import * -from ipi.inputs.atoms import * - -__all__ = ['InputBeads'] - -class InputBeads(Input): - """Beads input class. - - Handles generating the appropriate beads class from the xml input file, - and generating the xml checkpoint tags and data from an instance of the - object. - - Attributes: - nbeads: An optional integer giving the number of beads. Defaults to 0. - natoms: An optional integer giving the number of atoms. Defaults to 0. - - Fields: - q: An optional array giving the bead positions. Defaults to an empty - array with no elements. - p: An optional array giving the bead momenta. Defaults to an empty - array with no elements. - m: An optional array giving the bead masses. Defaults to an empty array - with no elements. - names: An optional array giving the bead names. Defaults to an empty - array with no elements. - """ - - attribs = { "natoms" : (InputAttribute, {"dtype" : int, "default" : 0, - "help" : "The number of atoms."}), - "nbeads" : (InputAttribute, {"dtype" : int, "default" : 0, - "help" : "The number of beads."}) - } - fields={ "q" : (InputArray, {"dtype" : float, - "default" : input_default(factory=np.zeros, args = (0,)), - "help" : "The positions of the beads. In an array of size [nbeads, 3*natoms].", - "dimension" : "length"}), - "p" : (InputArray, {"dtype" : float, - "default" : input_default(factory=np.zeros, args = (0,)), - "help" : "The momenta of the beads. In an array of size [nbeads, 3*natoms].", - "dimension" : "momentum"}), - "m" : (InputArray, {"dtype" : float, - "default" : input_default(factory=np.zeros, args = (0,)), - "help" : "The masses of the atoms, in the format [m1, m2, ... ].", - "dimension" : "mass"}), - "names" : (InputArray, {"dtype" : str, - "default" : input_default(factory=np.zeros, args=(0,), kwargs={'dtype': np.dtype('|S6')}), - "help" : "The names of the atoms, in the format [name1, name2, ... ]."}) } - - default_help = "Describes the bead configurations in a path integral simulation." - default_label = "BEADS" - - - def store(self, beads): - """Takes a Beads instance and stores a minimal representation of it. - - Args: - beads: A Beads object from which to initialize from. - """ - - super(InputBeads,self).store() - self.natoms.store(beads.natoms) - self.nbeads.store(beads.nbeads) - - self.q.store(depstrip(beads.q)) - self.p.store(depstrip(beads.p)) - self.m.store(depstrip(beads.m)) - self.names.store(depstrip(beads.names)) - - def fetch(self): - """Creates a beads object. - - Returns: - A beads object of the appropriate type and with the appropriate - properties given the attributes of the InputBeads object. - """ - - super(InputBeads,self).fetch() - beads = Beads(self.natoms.fetch(),self.nbeads.fetch()) - - # tries to fill up with as much data as available and valid - q = self.q.fetch() - if (q.shape == (beads.nbeads,3*beads.natoms)): - beads.q = q - elif (beads.nbeads == 1 and q.shape == (3*beads.natoms,)): - beads.q = q - elif len(q) != 0: - raise ValueError("Array shape mismatches for q in input.") - - p = self.p.fetch() - if (p.shape == (beads.nbeads,3*beads.natoms)): - beads.p = p - elif (beads.nbeads == 1 and p.shape == (3*beads.natoms,)): - beads.p = p - elif len(p) != 0: - raise ValueError("Array shape mismatches for p in input.") - - m = self.m.fetch() - if (m.shape == (beads.natoms,)): - beads.m = m - elif len(m) != 0: - raise ValueError("Array shape mismatches for m in input.") - - n = self.names.fetch() - if (n.shape == (beads.natoms,)): - beads.names = n - elif len(n) != 0: - raise ValueError("Array shape mismatches for names in input.") - - return beads diff --git a/tools/i-pi/ipi/inputs/cell.py b/tools/i-pi/ipi/inputs/cell.py deleted file mode 100644 index 9b316ef92f..0000000000 --- a/tools/i-pi/ipi/inputs/cell.py +++ /dev/null @@ -1,77 +0,0 @@ -"""Deals with creating the cell class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Generates an cell class from a cell vector. - -Classes: - InputCell: Deals with creating the Cell object from a file, and - writing the checkpoints. -""" - -import numpy as np -from copy import copy -from ipi.engine.cell import * -from ipi.utils.inputvalue import * -from ipi.utils.units import UnitMap -from ipi.utils.messages import verbosity, warning - -__all__ = [ 'InputCell' ] - -class InputCell(InputArray): - """Cell input class. - - Handles generating the appropriate cell class from the xml input file, - and generating the xml checkpoint tags and data from an instance of the - object. - """ - - attribs = copy(InputArray.attribs) - - default_help = "Deals with the cell parameters. Takes as array which can be used to initialize the cell vector matrix." - default_label = "CELL" - - def __init__(self, help=None, dimension=None, units=None, default=None, dtype=None): - """Initializes InputCell. - - Just calls the parent initialization function with appropriate arguments. - """ - - super(InputCell,self).__init__(dtype=float, dimension="length", default=default, help=help) - - def store(self, cell): - """Takes a Cell instance and stores of minimal representation of it. - - Args: - cell: A cell object. - """ - - super(InputCell,self).store(cell.h) - self.shape.store((3,3)) - - def fetch(self): - """Creates a cell object. - - Returns: - A cell object of the appropriate type and with the appropriate - properties given the attributes of the InputCell object. - """ - - h = super(InputCell,self).fetch() - h.shape = (3,3) - - return Cell(h=h) diff --git a/tools/i-pi/ipi/inputs/ensembles.py b/tools/i-pi/ipi/inputs/ensembles.py deleted file mode 100644 index 4a5519fff7..0000000000 --- a/tools/i-pi/ipi/inputs/ensembles.py +++ /dev/null @@ -1,185 +0,0 @@ -"""Deals with creating the ensembles class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputEnsemble: Deals with creating the Ensemble object from a file, and - writing the checkpoints. -""" - -import numpy as np -import ipi.engine.thermostats -import ipi.engine.initializer -import ipi.engine.barostats -from ipi.engine.ensembles import * -from ipi.utils.inputvalue import * -from ipi.inputs.barostats import * -from ipi.inputs.thermostats import * -from ipi.inputs.initializer import * -from ipi.utils.units import * - -__all__ = ['InputEnsemble'] - -class InputEnsemble(Input): - """Ensemble input class. - - Handles generating the appropriate ensemble class from the xml input file, - and generating the xml checkpoint tags and data from an instance of the - object. - - Attributes: - mode: An optional string giving the mode of ensemble to be simulated. - Defaults to 'unknown'. - - Fields: - thermostat: The thermostat to be used for constant temperature dynamics. - barostat: The barostat to be used for constant pressure or stress - dynamics. - timestep: An optional float giving the size of the timestep in atomic - units. Defaults to 1.0. - temperature: An optional float giving the temperature in Kelvin. Defaults - to 1.0. - pressure: An optional float giving the external pressure in atomic units. - Defaults to 1.0. - fixcom: An optional boolean which decides whether the centre of mass - motion will be constrained or not. Defaults to False. - replay_file: An optional string that gives an input file name to get - a trajectory to be re-run. - """ - - attribs={"mode" : (InputAttribute, {"dtype" : str, - "help" : "The ensemble that will be sampled during the simulation. 'replay' means that a simulation is restarted from a previous simulation.", - "options" : ['nve', 'nvt', 'npt', 'replay']}) } - fields={"thermostat" : (InputThermo, {"default" : input_default(factory=ipi.engine.thermostats.Thermostat), - "help" : "The thermostat for the atoms, keeps the atom velocity distribution at the correct temperature."} ), - "barostat" : (InputBaro, {"default" : input_default(factory=ipi.engine.barostats.Barostat), - "help" : InputBaro.default_help}), - "timestep": (InputValue, {"dtype" : float, - "default" : 1.0, - "help" : "The time step.", - "dimension" : "time"}), - "temperature" : (InputValue, {"dtype" : float, - "default" : 1.0, - "help" : "The temperature of the system.", - "dimension" : "temperature"}), - "pressure" : (InputValue, {"dtype" : float, - "default" : 1.0, - "help" : "The external pressure.", - "dimension" : "pressure"}), - "fixcom": (InputValue, {"dtype" : bool, - "default" : True, - "help" : "This describes whether the centre of mass of the particles is fixed."}), - "replay_file": (InputInitFile, {"default" : input_default(factory=ipi.engine.initializer.InitBase), - "help" : "This describes the location to read a trajectory file from."}) - } - - default_help = "Holds all the information that is ensemble specific, such as the temperature and the external pressure, and the thermostats and barostats that control it." - default_label = "ENSEMBLE" - - def store(self, ens): - """Takes an ensemble instance and stores a minimal representation of it. - - Args: - ens: An ensemble object. - """ - - super(InputEnsemble,self).store(ens) - if type(ens) is ReplayEnsemble: - self.mode.store("rerun") - tens = 0 - elif type(ens) is NVEEnsemble: - self.mode.store("nve") - tens = 1 - elif type(ens) is NVTEnsemble: - self.mode.store("nvt") - tens = 2 - elif type(ens) is NPTEnsemble: - self.mode.store("npt") - tens = 3 - - self.timestep.store(ens.dt) - self.temperature.store(ens.temp) - - if tens == 0: - self.replay_file.store(ens.intraj) - if tens > 1: - self.thermostat.store(ens.thermostat) - self.fixcom.store(ens.fixcom) - if tens > 2: - self.barostat.store(ens.barostat) - if tens == 3: - self.pressure.store(ens.pext) - - - def fetch(self): - """Creates an ensemble object. - - Returns: - An ensemble object of the appropriate mode and with the appropriate - objects given the attributes of the InputEnsemble object. - """ - - super(InputEnsemble,self).fetch() - - if self.mode.fetch() == "nve" : - ens = NVEEnsemble(dt=self.timestep.fetch(), - temp=self.temperature.fetch(), fixcom=self.fixcom.fetch()) - elif self.mode.fetch() == "nvt" : - ens = NVTEnsemble(dt=self.timestep.fetch(), - temp=self.temperature.fetch(), thermostat=self.thermostat.fetch(), fixcom=self.fixcom.fetch()) - elif self.mode.fetch() == "npt" : - ens = NPTEnsemble(dt=self.timestep.fetch(), - temp=self.temperature.fetch(), thermostat=self.thermostat.fetch(), fixcom=self.fixcom.fetch(), - pext=self.pressure.fetch(), barostat=self.barostat.fetch() ) - elif self.mode.fetch() == "replay": - ens = ReplayEnsemble(dt=self.timestep.fetch(), - temp=self.temperature.fetch(),fixcom=False,intraj=self.replay_file.fetch() ) - else: - raise ValueError("'" + self.mode.fetch() + "' is not a supported ensemble mode.") - - return ens - - def check(self): - """Function that deals with optional arguments. - - Makes sure that if the ensemble requires a thermostat or barostat that - they have been defined by the user and not given the default values. - """ - - super(InputEnsemble,self).check() - if self.mode.fetch() == "nvt": - if self.thermostat._explicit == False: - raise ValueError("No thermostat tag supplied for NVT simulation") - if self.mode.fetch() == "npt": - if self.thermostat._explicit == False: - raise ValueError("No thermostat tag supplied for NPT simulation") - if self.barostat._explicit == False: - raise ValueError("No barostat tag supplied for NPT simulation") - if self.barostat.thermostat._explicit == False: - raise ValueError("No thermostat tag supplied in barostat for NPT simulation") - - if self.timestep.fetch() <= 0: - raise ValueError("Non-positive timestep specified.") - if self.temperature.fetch() <= 0: - raise ValueError("Non-positive temperature specified.") - - if self.mode.fetch() == "npt": - if not self.pressure._explicit: - raise ValueError("Pressure should be supplied for constant pressure simulation") - if self.mode.fetch() == "npt" or self.mode.fetch() == "nvt": - if not self.temperature._explicit: - raise ValueError("Temperature should be supplied for constant temperature simulation") diff --git a/tools/i-pi/ipi/inputs/forces.py b/tools/i-pi/ipi/inputs/forces.py deleted file mode 100644 index d343e19e0f..0000000000 --- a/tools/i-pi/ipi/inputs/forces.py +++ /dev/null @@ -1,176 +0,0 @@ -"""Deals with creating the forcefield class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputForces: Deals with creating all the forcefield objects. - InputForceBeads: Base class to deal with one particular forcefield object. - InputFBSocket: Deals with creating a forcefield using sockets. -""" - -__all__ = ['InputForces', 'InputForceBeads', "InputFBSocket"] - -from copy import copy -from ipi.engine.forces import * -from ipi.inputs.interface import InputInterfaceSocket -from ipi.utils.inputvalue import * - -class InputForceBeads(Input): - """ForceBeads input class. - - Handles generating one instance of a particular forcefield class from the xml - input file, and generating the xml checkpoint tags and data from an - instance of the object. - - Attributes: - nbeads: The number of beads that the forcefield will be evaluated on. - weight: A scaling factor for the contribution from this forcefield. - """ - - attribs = { "nbeads" : ( InputAttribute, { "dtype" : int, - "default" : 0, - "help" : "If the forcefield is to be evaluated on a contracted ring polymer, this gives the number of beads that are used. If not specified, the forcefield will be evaluated on the full ring polymer." } ), - "weight" : ( InputAttribute, { "dtype" : float, - "default" : 1.0, - "help" : "A scaling factor for this forcefield, to be applied before adding the force calculated by this forcefield to the total force." } ) - } - - default_help = "Base class that deals with the assigning of force calculation jobs and collecting the data." - default_label = "FORCEBEADS" - - def store(self, forceb): - """Takes a ForceBeads instance and stores a minimal representation of it. - - Args: - forceb: A ForceBeads object. - """ - - Input.store(self,forceb) - self.nbeads.store(forceb.nbeads) - self.weight.store(forceb.weight) - - def fetch(self): - """Creates a ForceBeads object. - - Returns: - A ForceBeads object. - """ - - super(InputForceBeads,self).fetch() - - return ForceBeads(model=ForceField(), nbeads=self.nbeads.fetch(), weight=self.weight.fetch()) - - def check(self): - """Checks for optional parameters.""" - - super(InputForceBeads,self).check() - if self.nbeads.fetch() < 0: - raise ValueError("The forces must be evaluated over a positive number of beads.") - - -class InputFBSocket(InputForceBeads, InputInterfaceSocket): - """Creates a ForceBeads object with a socket interface. - - Handles generating one instance of a socket interface forcefield class. - Shares its attributes between InputForceBeads, which deals with creating the - forcefield, and InputInterfaceSocket, which deals with creating the socket - interface. - """ - - attribs = copy(InputInterfaceSocket.attribs) - attribs.update(InputForceBeads.attribs) - - default_help = "Deals with the assigning of force calculation jobs to different driver codes, and collecting the data, using a socket for the data communication." - default_label = "SOCKET" - - def store(self, forceb): - """Takes a ForceField instance and stores a minimal representation of it. - - Args: - forceb: A ForceBeads object with a FFSocket forcemodel object. - """ - - if (not type(forceb.f_model) is FFSocket): - raise TypeError("The type " + type(forceb.f_model).__name__ + " is not a valid socket forcefield") - - InputForceBeads.store(self,forceb) - InputInterfaceSocket.store(self,forceb.f_model.socket) - - def fetch(self): - """Creates a ForceBeads object. - - Returns: - A ForceBeads object with the correct socket parameters. - """ - - return ForceBeads(model=FFSocket( interface=InputInterfaceSocket.fetch(self) ),nbeads=self.nbeads.fetch(),weight=self.weight.fetch() ) - - def check(self): - """Deals with optional parameters.""" - - InputInterfaceSocket.check(self) - InputForceBeads.check(self) - - -class InputForces(Input): - """Deals with creating all the forcefield objects required in the - simulation. - - Dynamic fields: - socket: Socket object to create the server socket. - """ - - #At the moment only socket driver codes implemented, other types - #could be used in principle - dynamic = { "socket" : (InputFBSocket, { "help" : InputFBSocket.default_help } ) - } - - default_help = "Deals with creating all the necessary forcefield objects." - default_label = "FORCES" - - def fetch(self): - """Returns a list of the output objects included in this dynamic - container. - - Returns: - A list of tuples, with each tuple being of the form ('type', 'object'), - where 'type' is the type of forcefield, and 'object' is a - """ - - super(InputForces, self).fetch() - flist = [ (n, f.fetch()) for (n, f) in self.extra ] - - return flist - - def store(self, flist): - """Stores a list of the output objects, creating a sequence of - dynamic containers. - - Args: - flist: A list of tuples, with each tuple being of the form - ('type', 'object') where 'type' is the type of forcefield - and 'object' is a forcefield object of that type. - """ - - super(InputForces, self).store() - self.extra = [] - - for el in flist: - if el[0]=="socket": - iff = InputFBSocket() - iff.store(el[1]) - self.extra.append(("socket", iff)) diff --git a/tools/i-pi/ipi/inputs/initializer.py b/tools/i-pi/ipi/inputs/initializer.py deleted file mode 100644 index f78a617e2a..0000000000 --- a/tools/i-pi/ipi/inputs/initializer.py +++ /dev/null @@ -1,406 +0,0 @@ -"""Deals with creating the initiliazer class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputInitializer: Initializes the classes that initialize the simulation - data. - InputInitFile: Initializes the classes that initialize the simulation data - from a file. Rather than initializing one piece of data, everything that - can be initialized from that file will be. - InputInitPositions: Initializes the positions. - InputInitMomenta: Initializes the momenta. - InputInitVelocities: Initializes the velocities. - InputInitMasses: Initializes the masses. - InputInitLabels: Initializes the atom labels. - InputInitCell: Initializes the cell. - InputInitThermo: Initializes the thermostat. - InputInitBase: The base class for all Initializer objects. - InputInitIndexed: The class for all Initializer objects which can be called - to initialize data for a particular atom or bead. -""" - -import numpy as np -from copy import copy, deepcopy -import ipi.utils.mathtools as mt -import ipi.engine.initializer as ei -from ipi.utils.inputvalue import * -from ipi.inputs.beads import InputBeads -from ipi.inputs.cell import InputCell -from ipi.utils.io import io_xml -from ipi.utils.messages import verbosity, warning - -__all__ = ['InputInitializer', 'InputInitFile', 'InputInitPositions', 'InputInitMomenta', 'InputInitVelocities', 'InputInitMasses', 'InputInitLabels', 'InputInitCell', 'InputInitThermo'] - -class InputInitBase(InputValue): - """Base class to handle initialization. - - Attributes: - mode: The type of data to be initialized from. - _initclass: Which InputInit class to use to read the data. - _storageclass: Which data type to use to hold the data. - """ - - attribs = deepcopy(InputValue.attribs) - attribs["mode"] = (InputAttribute,{ "dtype" : str, "default": "other", "help": "The input data format. 'xyz' and 'pdb' stand for xyz and pdb input files respectively. 'chk' stands for initialization from a checkpoint file. 'manual' means that the value to initialize from is giving explicitly as a vector. 'thermal' means that the data is to be generated from a Maxwell-Boltzmann distribution at the given temperature.", "options": None } ) - - default_label = "INITBASE" - default_help = "This is the base class for initialization. Initializers for different aspects of the simulation can be inherit for it for the base methods." - - _initclass = ei.InitBase - _storageclass = float - - def __init__(self, help=None, default=None, dtype=None, options=None, dimension=None): - """Initializes InputInitFile. - - Just calls the parent initialize function with appropriate arguments. - """ - - super(InputInitBase,self).__init__(dtype=str, dimension=dimension, default=default, options=options, help=help) - - def store(self, ibase): - """Takes a InitBase instance and stores a minimal representation of it. - - Args: - ibase: An input base object. - """ - - if ibase.mode == "manual": - if hasattr(value, __len__): - value = io_xml.write_list(ibase.value) - else: # if it's a single value then just write the value - value = io_xml.write_type(self._storageclass, ibase.value) - else: # just store the value as a string - value = ibase.value - - super(InputInitBase,self).store(value, units=ibase.units) - - for k in self.attribs: # store additional attributes from the input class - self.__dict__[k].store(ibase.__dict__[k]) - - def getval(self): - """Calculates the value from the data supplied in the xml file. - - Either reads the string from the input file as an array of numbers, - or as a string specifying either a file name or a single value. - """ - - value = super(InputInitBase,self).fetch() - if self.mode.fetch() == "manual": - if '[' in value and ']' in value: # value appears to be a list - if self._storageclass is float: - value = io_xml.read_array(np.float, value) - else: - value = io_xml.read_list(value) - else: - value = io_xml.read_type(self._storageclass, value) - else: - value = str(value) # typically this will be a no-op - return value - - def fetch(self, initclass=None): - """Creates an input base object. - - Returns: - An input base object. - """ - - rdict = {} - for k in self.attribs: - rdict[k] = self.__dict__[k].fetch() - - if initclass is None: # allows for some flexibility in return class - initclass = self._initclass - - return initclass(value=self.getval(), **rdict) - - -class InputInitFile(InputInitBase): - """Class to handle initialization from a file.""" - - attribs = deepcopy(InputInitBase.attribs) - attribs["mode"][1]["default"] = "chk" - attribs["mode"][1]["options"] = ["xyz", "pdb", "chk"] - attribs["mode"][1]["help"] = "The input data format. 'xyz' and 'pdb' stand for xyz and pdb input files respectively. 'chk' stands for initialization from a checkpoint file." - - default_label = "INITFILE" - default_help = "This is the class to initialize from file." - - -class InputInitThermo(InputInitBase): - """Class to handle initialization of the thermostat.""" - - attribs = deepcopy(InputInitBase.attribs) - attribs["mode"][1]["default"] = "manual" - attribs["mode"][1]["options"] = ["chk", "manual"] - attribs["mode"][1]["help"] = "'chk' stands for initialization from a checkpoint file. 'manual' means that the value to initialize from is giving explicitly as a vector." - - default_label = "INITTHERMO" - default_help = "This is the class to initialize the thermostat (ethermo and fictitious momenta)." - - -class InputInitIndexed(InputInitBase): - """Class to handle initialization of properties which the value of each - bead and atom can be specified. - - Attributes: - index: Which atom to initialize the value of. - bead: Which bead to initialize the value of. - """ - - attribs = deepcopy(InputInitBase.attribs) - attribs["index"] = (InputAttribute,{ "dtype" : int, "default": -1, "help": "The index of the atom for which the value will be set. If a negative value is specified, then all atoms are assumed." } ) - attribs["bead"] = (InputAttribute,{ "dtype" : int, "default": -1, "help": "The index of the bead for which the value will be set. If a negative value is specified, then all beads are assumed." } ) - - default_label = "INITINDEXED" - default_help = "This is a helper class to initialize with an index." - - -class InputInitPositions(InputInitIndexed): - """Class to handle initialization of the positions.""" - - attribs = deepcopy(InputInitIndexed.attribs) - attribs["mode"][1]["default"] = "chk" - attribs["mode"][1]["options"] = ["manual", "xyz", "pdb", "chk"] - attribs["mode"][1]["help"] = "The input data format. 'xyz' and 'pdb' stand for xyz and pdb input files respectively. 'chk' stands for initialization from a checkpoint file. 'manual' means that the value to initialize from is giving explicitly as a vector." - - default_label = "INITPOSITIONS" - default_help = "This is the class to initialize positions." - _initclass = ei.InitIndexed - - -class InputInitMomenta(InputInitPositions): - """Class to handle initialization of the momenta.""" - - attribs = deepcopy(InputInitPositions.attribs) - attribs["mode"][1]["options"].append( "thermal" ) - attribs["mode"][1]["help"] = "The input data format. 'xyz' and 'pdb' stand for xyz and pdb input files respectively. 'chk' stands for initialization from a checkpoint file. 'manual' means that the value to initialize from is giving explicitly as a vector. 'thermal' means that the data is to be generated from a Maxwell-Boltzmann distribution at the given temperature." - - default_label = "INITMOMENTA" - default_help = "This is the class to initialize momenta." - - def fetch(self): - """Creates an momentum initializer object. - - Note that the momenta can be initialized by a single value, specifying - the temperature at which to thermalize the momenta. - """ - - if self.mode.fetch() == "thermal": - return self._initclass(value=float(InputValue.fetch(self)), mode=self.mode.fetch(), units=self.units.fetch(), index=self.index.fetch(), bead=self.bead.fetch()) - else: - return super(InputInitMomenta,self).fetch() - - -class InputInitVelocities(InputInitMomenta): - """Class to handle initialization of the velocities.""" - - attribs = deepcopy(InputInitMomenta.attribs) - - default_label = "INITVELOCITIES" - default_help = "This is the class to initialize velocities." - - -class InputInitMasses(InputInitPositions): - """Class to handle initialization of the masses.""" - - attribs = deepcopy(InputInitPositions.attribs) - - default_label = "INITMASSES" - default_help = "This is the class to initialize atomic masses." - - -class InputInitLabels(InputInitPositions): - """Class to handle initialization of the atom labels.""" - - attribs = deepcopy(InputInitPositions.attribs) - - default_label = "INITLABELS" - default_help = "This is the class to initialize atomic labels." - - _storageclass = str - - -class InputInitCell(InputInitBase): - """Class to handle initialization of the cell.""" - - attribs = deepcopy(InputInitBase.attribs) - attribs["mode"] = (InputAttribute, { "dtype" : str, - "default": "manual", - "options": ["manual", "pdb", "chk", "abc", "abcABC"], - "help" : "This decides whether the system box is created from a cell parameter matrix, or from the side lengths and angles between them. If 'mode' is 'manual', then 'cell' takes a 9-elements vector containing the cell matrix (row-major). If 'mode' is 'abcABC', then 'cell' takes an array of 6 floats, the first three being the length of the sides of the system parallelopiped, and the last three being the angles (in degrees) between those sides. Angle A corresponds to the angle between sides b and c, and so on for B and C. If mode is 'abc', then this is the same as for 'abcABC', but the cell is assumed to be orthorhombic. 'pdb' and 'chk' read the cell from a PDB or a checkpoint file, respectively."} ) - - default_label = "INITCELL" - default_help = "This is the class to initialize cell." - - def fetch(self): - """Creates a cell initializer object. - - Note that the cell can be initialized from the lengths of the sides and - the angles between them instead of by a vector, as specified by the - 'abc' or 'abcABC' modes. - """ - - mode = self.mode.fetch() - - ibase = super(InputInitCell,self).fetch() - if mode == "abc" or mode == "abcABC": - - h = io_xml.read_array(np.float, ibase.value) - - if mode == "abc": - if h.size != 3: - raise ValueError("If you are initializing cell from cell side lengths you must pass the 'cell' tag an array of 3 floats.") - else: - h = mt.abc2h(h[0], h[1], h[2], np.pi/2, np.pi/2, np.pi/2) - elif mode == "abcABC": - if h.size != 6: - raise ValueError("If you are initializing cell from cell side lengths and angles you must pass the 'cell' tag an array of 6 floats.") - else: - h = mt.abc2h(h[0], h[1], h[2], h[3]*np.pi/180.0, h[4]*np.pi/180.0, h[5]*np.pi/180.0) - - h.shape = (9,) - ibase.value = h - mode = "manual" - - if mode == "manual": - h = ibase.value - if h.size != 9: - raise ValueError("Cell objects must contain a 3x3 matrix describing the cell vectors.") - - if not (h[3] == 0.0 and h[6] == 0.0 and h[7] == 0.0): - warning("Cell vector matrix must be upper triangular, all elements below the diagonal being set to zero.", verbosity.low) - h[3] = h[6] = h[7] = 0 - ibase.value = h - - return self._initclass(value=ibase.value, mode=mode, units=self.units.fetch()) - - -class InputInitializer(Input): - """Input class to handle initialization. - - Attributes: - nbeads: The number of beads to be used in the simulation. - - Dynamic fields: - positions: An object to initialize the positions from. - velocities: An object to initialize the velocities from. - momenta: An object to initialize the momenta from. - cell: An object to initialize the cell from. - masses: An object to initialize the masses from. - labels: An object to initialize the labels from. - gle: An object to initialize the GLE matrices from. - file: A file from which to initialize multiple properties from. Anything - that can be initialized either directly or indirectly from this file - will be. - """ - - attribs = { "nbeads" : (InputAttribute, {"dtype" : int, - "help" : "The number of beads. Will override any provision from inside the initializer. A ring polymer contraction scheme is used to scale down the number of beads if required. If instead the number of beads is scaled up, higher normal modes will be initialized to zero."}) - } - - dynamic = { - "positions" : (InputInitPositions, { "help" : "Initializes atomic positions. Will take a 'units' attribute of dimension 'length'"}), - "velocities" : (InputInitVelocities, { "help" : "Initializes atomic velocities. Will take a 'units' attribute of dimension 'velocity'" }), - "momenta" : (InputInitMomenta, { "help" : "Initializes atomic momenta. Will take a 'units' attribute of dimension 'momentum'" }), - "masses" : (InputInitMasses, { "help" : "Initializes atomic masses. Will take a 'units' attribute of dimension 'mass'" }), - "labels" : (InputInitLabels, { "help" : "Initializes atomic labels" }), - "cell" : (InputInitCell, { "help" : "Initializes the configuration of the cell. Will take a 'units' attribute of dimension 'length'" }), - "file" : (InputInitFile, { "help" : "Initializes everything possible for the given mode. Will take a 'units' attribute of dimension 'length'. The unit conversion will only be applied to the positions and cell parameters." }), - "gle" : (InputInitThermo, { "help" : "Initializes the additional momenta in a GLE thermostat." }) - } - - default_help = "Specifies the number of beads, and how the system should be initialized." - default_label = "INITIALIZER" - - def write(self, name="", indent=""): - """Overloads Input write() function so that we never write out - InputInitializer to restart files. - - Returns: - An empty string. - """ - - return "" - - def store(self, ii): - """Takes a Initializer instance and stores a minimal representation of it. - - Args: - ii: An initializer object. - """ - - self.extra = [] - - for (k, el) in ii.queue: - if k == "positions" : - ip = InputInitPositions() - ip.store(el) - elif k == "velocities" : - ip = InputInitVelocities() - ip.store(el) - elif k == "momenta" : - ip = InputInitMomenta() - ip.store(el) - elif k == "masses" : - ip = InputInitMasses() - ip.store(el) - elif k == "labels" : - ip = InputInitLabels() - ip.store(el) - elif k == "cell" : - ip = InputInitCell() - ip.store(el) - elif k == "gle" : - ip = InputInitThermo() - ip.store(el) - self.extra.append((k, ip)) - - self.nbeads.store(ii.nbeads) - - def fetch(self): - """Creates an initializer object. - - Returns: - An initializer object. - """ - - super(InputInitializer,self).fetch() - - initlist = [] - for (k,v) in self.extra: - if v.mode.fetch() == "chk" and v.fetch(initclass=ei.InitIndexed).units != "": - raise ValueError("Cannot specify units for initialization from a checkpoint file - units should be defined _inside_ the file.") - if k == "file": - mode = v.mode.fetch() - if mode == "xyz" or mode == "manual" or mode == "pdb" or mode == "chk": - initlist.append( ( "positions", v.fetch(initclass=ei.InitIndexed) ) ) - if mode == "xyz" or mode == "pdb" or mode == "chk": - rm = v.fetch(initclass=ei.InitIndexed) - rm.units = "" - initlist.append( ( "masses", rm ) ) - initlist.append( ( "labels", v.fetch(initclass=ei.InitIndexed) ) ) - if mode == "pdb" or mode == "chk": - initlist.append( ( "cell", v.fetch(initclass=ei.InitIndexed) ) ) - if mode == "chk": - rm = v.fetch(initclass=ei.InitIndexed) - rm.units = "" - initlist.append( ( "momenta", rm ) ) - else: - initlist.append( (k, v.fetch()) ) - - return ei.Initializer(self.nbeads.fetch(), initlist ) diff --git a/tools/i-pi/ipi/inputs/interface.py b/tools/i-pi/ipi/inputs/interface.py deleted file mode 100644 index 2ff092a665..0000000000 --- a/tools/i-pi/ipi/inputs/interface.py +++ /dev/null @@ -1,125 +0,0 @@ -"""Deals with creating the interface between the wrapper and the socket. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputInterface: Deals with creating the Interface object from a file, and - writing the checkpoints. -""" - -__all__ = [ 'InputInterfaceSocket' ] - -import socket, select, threading, signal, string, os, time -import numpy as np -from ipi.utils.messages import verbosity, warning -from ipi.utils.inputvalue import * -from ipi.interfaces.sockets import * - - -class InputInterfaceSocket(Input): - """Interface input class. - - Handles generating the apporopriate interface class from the xml - input file, and generating the xml checkpoin tags and data from an - instance of the object. - - Attributes: - mode: A string giving the type of socket used. - pbc: A boolean giving whether the atom positions will be folded back - into the unit cell before being sent through the socket or not. - - Fields: - address: A string giving the host name. - port: An integer giving the port used by the socket. - slots: An integer giving the maximum allowed backlog of queued clients. - latency: A float giving the number of seconds that the interface waits - before updating the client list. - timeout: A float giving a number of seconds after which a calculation core - is considered dead. Defaults to zero, i.e. no timeout. - """ - - fields = {"address": (InputValue, {"dtype" : str, - "default" : "localhost", - "help" : "This gives the server address that the socket will run on." } ), - "port": (InputValue, {"dtype" : int, - "default" : 65535, - "help" : "This gives the port number that defines the socket."} ), - "slots": (InputValue, {"dtype" : int, - "default" : 4, - "help" : "This gives the number of client codes that can queue at any one time."} ), - "latency": (InputValue, {"dtype" : float, - "default" : 1e-3, - "help" : "This gives the number of seconds between each check for new clients."} ), - "timeout": (InputValue, {"dtype" : float, - "default" : 0.0, - "help" : "This gives the number of seconds before assuming a calculation has died. If 0 there is no timeout." } )} - attribs = { "mode": (InputAttribute, {"dtype" : str, - "options" : [ "unix", "inet" ], - "default" : "inet", - "help" : "Specifies whether the driver interface will listen onto a internet socket [inet] or onto a unix socket [unix]." } ), - "pbc": ( InputAttribute, { "dtype" : bool, - "default" : True, - "help" : "Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code." }) - } - - default_help = "Specifies the parameters for the socket interface." - default_label = "INTERFACE" - - def store(self, iface): - """Takes an Interface instance and stores a minimal representation of it. - - Args: - iface: An interface object. - """ - - super(InputInterfaceSocket,self).store(iface) - self.latency.store(iface.latency) - self.mode.store(iface.mode) - self.address.store(iface.address) - self.port.store(iface.port) - self.slots.store(iface.slots) - self.timeout.store(iface.timeout) - self.pbc.store(iface.dopbc) - - def fetch(self): - """Creates an InterfaceSocket object. - - Returns: - An interface object with the appropriate socket given the attributes - of the InputInterfaceSocket object. - """ - - super(InputInterfaceSocket,self).fetch() - return InterfaceSocket(address=self.address.fetch(), port=self.port.fetch(), - slots=self.slots.fetch(), mode=self.mode.fetch(), - latency=self.latency.fetch(), timeout=self.timeout.fetch(), dopbc=self.pbc.fetch()) - - def check(self): - """Function that deals with optional arguments.""" - - super(InputInterfaceSocket,self).check() - if self.port.fetch() < 1 or self.port.fetch() > 65535: - raise ValueError("Port number " + str(self.port.fetch()) + " out of acceptable range.") - elif self.port.fetch() < 1025: - warning("Low port number being used, this may interrupt important system processes.", verbosity.low) - - if self.slots.fetch() < 1 or self.slots.fetch() > 5: - raise ValueError("Slot number " + str(self.slots.fetch()) + " out of acceptable range.") - if self.latency.fetch() < 0: - raise ValueError("Negative latency parameter specified.") - if self.timeout.fetch() < 0.0: - raise ValueError("Negative timeout parameter specified.") diff --git a/tools/i-pi/ipi/inputs/normalmodes.py b/tools/i-pi/ipi/inputs/normalmodes.py deleted file mode 100644 index 0e46051049..0000000000 --- a/tools/i-pi/ipi/inputs/normalmodes.py +++ /dev/null @@ -1,84 +0,0 @@ -"""Deals with creating the normal mode representation arrays. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputNormalModes: Deals with creating the normal mode objects. -""" - -import numpy as np -from copy import copy -from ipi.engine.normalmodes import * -from ipi.utils.inputvalue import * -from ipi.utils.units import * - -__all__ = ['InputNormalModes'] - -class InputNormalModes(InputArray): - """ Storage class for NormalModes engine. - - Describes how normal-modes transformation and integration should be - performed. - - Attributes: - mode: Specifies the method by which the dynamical masses are created. - transform: Specifies whether the normal mode calculation will be - done using a FFT transform or a matrix multiplication. - """ - - attribs = copy(InputArray.attribs) - attribs["mode"] = (InputAttribute, {"dtype" : str, - "default" : "rpmd", - "help" : "Specifies the technique to be used to calculate the dynamical masses. 'rpmd' simply assigns the bead masses the physical mass. 'manual' sets all the normal mode frequencies except the centroid normal mode manually. 'pa-cmd' takes an argument giving the frequency to set all the non-centroid normal modes to. 'wmax-cmd' is similar to 'pa-cmd', except instead of taking one argument it takes two ([wmax,wtarget]). The lowest-lying normal mode will be set to wtarget for a free particle, and all the normal modes will coincide at frequency wmax. ", - "options" : ['pa-cmd', 'wmax-cmd', 'manual', 'rpmd']}) - attribs["transform"] = (InputValue,{"dtype" : str, - "default" : "fft", - "help" : "Specifies whether to calculate the normal mode transform using a fast Fourier transform or a matrix multiplication. For small numbers of beads the matrix multiplication may be faster.", - "options" : ['fft', 'matrix']}) - - default_help = "Deals with the normal mode transformations, including the adjustment of bead masses to give the desired ring polymer normal mode frequencies if appropriate. Takes as arguments frequencies, of which different numbers must be specified and which are used to scale the normal mode frequencies in different ways depending on which 'mode' is specified." - default_label = "NORMALMODES" - - def __init__(self, help=None, dimension=None, default=None, dtype=None): - """ Initializes InputNormalModes. - - Just calls the parent initialization function with appropriate arguments. - """ - - super(InputNormalModes,self).__init__(help=help, default=default, dtype=float, dimension="frequency") - - def store(self, nm): - """Takes a normal modes instance and stores a minimal representation - of it. - - Args: - nm: A normal modes object. - """ - - super(InputNormalModes,self).store(nm.nm_freqs) - self.mode.store(nm.mode) - self.transform.store(nm.transform_method) - - def fetch(self): - """Creates a normal modes object. - - Returns: - A normal modes object. - """ - - super(InputNormalModes,self).check() - return NormalModes(self.mode.fetch(), self.transform.fetch(), super(InputNormalModes,self).fetch() ) diff --git a/tools/i-pi/ipi/inputs/outputs.py b/tools/i-pi/ipi/inputs/outputs.py deleted file mode 100644 index 5141c79beb..0000000000 --- a/tools/i-pi/ipi/inputs/outputs.py +++ /dev/null @@ -1,323 +0,0 @@ -"""Deals with creating the output objects. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputOutputs: Creates a list of all the output objects. - InputProperties: Deals with property output. - InputTrajectory: Deals with trajectory output. - InputCheckpoint: Deals with restart file output. -""" -import numpy as np -from copy import copy -import ipi.engine.outputs -from ipi.utils.depend import * -from ipi.utils.inputvalue import * -from ipi.engine.properties import getkey - -__all__=['InputOutputs', 'InputProperties', 'InputTrajectory', - 'InputCheckpoint'] - -class InputProperties(InputArray): - """Simple input class to describe output for properties. - - Storage class for PropertyOutput. - - Attributes: - filename: The name of the file to output to. - stride: The number of steps that should be taken between outputting the - data to file. - flush: An integer describing how often the output streams are flushed, - so that it doesn't wait for the buffer to fill before outputting to - file. - """ - - default_help = """This class deals with the output of properties to one file. Between each property tag there should be an array of strings, each of which specifies one property to be output.""" - default_label = "PROPERTIES" - - attribs = copy(InputArray.attribs) - attribs["filename"] = (InputAttribute,{ "dtype" : str, "default": "out", - "help": "A string to specify the name of the file that is output. The file name is given by 'prefix'.'filename' + format_specifier. The format specifier may also include a number if multiple similar files are output."} ) - attribs["stride"] = (InputAttribute,{ "dtype" : int, "default": 1, - "help": "The number of steps between successive writes." } ) - attribs["flush"] = (InputAttribute, {"dtype" : int, "default" : 1, - "help" : "How often should streams be flushed. 1 means each time, zero means never." }) - - def __init__(self, help=None, default=None, dtype=None, dimension=None): - """Initializes InputProperties. - - Just calls the parent initialization function with appropriate arguments. - """ - - super(InputProperties,self).__init__(help=help, default=default, dtype=str, dimension=dimension) - - def fetch(self): - """Returns a PropertyOutput object.""" - - return ipi.engine.outputs.PropertyOutput(filename=self.filename.fetch(), - stride=self.stride.fetch(), flush=self.flush.fetch(), outlist=super(InputProperties,self).fetch()) - - def store(self, prop): - """Stores a PropertyOutput object.""" - - super(InputProperties,self).store(prop.outlist) - self.stride.store(prop.stride) - self.flush.store(prop.flush) - self.filename.store(prop.filename) - - def check(self): - """Checks for optional parameters.""" - - super(InputProperties,self).check() - if self.stride.fetch() < 0: - raise ValueError("The stride length for the properties file output must be positive.") - - -class InputTrajectory(InputValue): - """Simple input class to describe output for trajectories. - - Storage class for TrajectoryOutput. - - Attributes: - filename: The (base) name of the file to output to. - stride: The number of steps that should be taken between outputting the - data to file. - format: The format of the trajectory output file. - cell_units: The units that the cell parameters are given in. - bead: If the trajectory is a per-bead property, this can be used to - specify a single bead to output. If negative, it defaults to - the centroid. - flush: An integer describing how often the output streams are flushed, - so that it doesn't wait for the buffer to fill before outputting to - file. - """ - - default_help = """This class defines how one trajectory file should be output. Between each trajectory tag one string should be given, which specifies what data is to be output.""" - default_label = "TRAJECTORY" - - attribs = copy(InputValue.attribs) - attribs["filename"] = (InputAttribute,{ "dtype" : str, "default": "traj", - "help": "A string to specify the name of the file that is output. The file name is given by 'prefix'.'filename' + format_specifier. The format specifier may also include a number if multiple similar files are output."} ) - attribs["stride"] = (InputAttribute,{ "dtype" : int, "default": 1, - "help": "The number of steps between successive writes." } ) - attribs["format"] = (InputAttribute,{ "dtype" : str, "default": "xyz", - "help": "The output file format.", - "options": ['xyz', 'pdb'] } ) - attribs["cell_units"] = (InputAttribute,{ "dtype" : str, "default": "", - "help": "The units for the cell dimensions." } ) - attribs["bead"] = (InputAttribute,{ "dtype" : int, "default": -1, - "help": "Print out only the specified bead. A negative value means print all." } ) - attribs["flush"] = (InputAttribute, {"dtype" : int, "default" : 1, - "help" : "How often should streams be flushed. 1 means each time, zero means never." }) - - def __init__(self, help=None, default=None, dtype=None, dimension=None): - """Initializes InputTrajectory. - - Just calls the parent initialization function with appropriate arguments. - """ - - super(InputTrajectory,self).__init__(help=help, default=default, dtype=str, dimension=dimension) - - def fetch(self): - """Returns a TrajectoryOutput object.""" - - return ipi.engine.outputs.TrajectoryOutput(filename=self.filename.fetch(), stride=self.stride.fetch(), - flush=self.flush.fetch(), what=super(InputTrajectory,self).fetch(), - format=self.format.fetch(), cell_units=self.cell_units.fetch(), ibead=self.bead.fetch()) - - def store(self, traj): - """Stores a PropertyOutput object.""" - - super(InputTrajectory,self).store(traj.what) - self.stride.store(traj.stride) - self.flush.store(traj.flush) - self.filename.store(traj.filename) - self.format.store(traj.format) - self.cell_units.store(traj.cell_units) - self.bead.store(traj.ibead) - - def check(self): - """Checks for optional parameters.""" - - super(InputTrajectory,self).check() - if self.stride.fetch() < 0: - raise ValueError("The stride length for the trajectory file output must be positive.") - - -class InputCheckpoint(InputValue): - """Simple input class to describe output for properties. - - Storage class for CheckpointOutput. - - Attributes: - filename: The (base) name of the file to output to. - stride: The number of steps that should be taken between outputting the - data to file. - overwrite: whether checkpoints should be overwritten, or multiple - files output. - """ - - default_help = """This class defines how a checkpoint file should be output. Optionally, between the checkpoint tags, you can specify one integer giving the current step of the simulation. By default this integer will be zero.""" - default_label = "CHECKPOINT" - - attribs=copy(InputValue.attribs) - attribs["filename"] = (InputAttribute,{ "dtype" : str, "default": "restart", - "help": "A string to specify the name of the file that is output. The file name is given by 'prefix'.'filename' + format_specifier. The format specifier may also include a number if multiple similar files are output."} ) - attribs["stride"] = (InputAttribute,{ "dtype" : int, "default": 1, - "help": "The number of steps between successive writes." } ) - attribs["overwrite"] = (InputAttribute,{ "dtype" : bool, "default": True, - "help": "This specifies whether or not each consecutive checkpoint file will overwrite the old one."} ) - - def __init__(self, help=None, default=None, dtype=None, dimension=None): - """Initializes InputCheckpoint. - - Just calls the parent initialization function with appropriate arguments. - """ - - super(InputCheckpoint,self).__init__(help=help, default=default, dtype=int, dimension=dimension) - - def fetch(self): - """Returns a CheckpointOutput object.""" - - step = super(InputCheckpoint,self).fetch() - return ipi.engine.outputs.CheckpointOutput(self.filename.fetch(), self.stride.fetch(), self.overwrite.fetch(), step=step ) - - def parse(self, xml=None, text=""): - """Overwrites the standard parse function so that we can specify this tag - in the input without any data. - - We can use the syntax to do this - - Args: - xml: An xml node containing all the data for the parent tag. - text: The data to read the data from. Will be None if we have not - specified any data. - """ - - # just a quick hack to allow an empty element - try: - super(InputCheckpoint,self).parse(xml,text) - except: #TODO make this except a specific exception, not every one - self.value = 0 #This could hide actual errors, at least in theory. - - def store(self, chk): - """Stores a CheckpointOutput object.""" - - super(InputCheckpoint,self).store(chk.step) - self.stride.store(chk.stride) - self.filename.store(chk.filename) - self.overwrite.store(chk.overwrite) - - def check(self): - """Checks for optional parameters.""" - - super(InputCheckpoint,self).check() - if self.stride.fetch() < 0: - raise ValueError("The stride length for the checkpoint file output must be positive.") - - -class InputOutputs(Input): - """ List of outputs input class. - - An example of a dynamic input class: a variable number of tags might be - present, corresponding to different output requests. This allows for - instance to print multiple property outputs, with different content - and/or output frequency. - - Attributes: - prefix: A string that will be appended to all output files from this - simulation. - - Dynamic fields: - trajectory: Specifies a trajectory to be output - properties: Specifies some properties to be output. - checkpoint: Specifies a checkpoint file to be output. - """ - - attribs = { "prefix" : ( InputAttribute, { "dtype" : str, - "default" : "i-pi", - "help" : "A string that will be prepended to each output file name. The file name is given by 'prefix'.'filename' + format_specifier. The format specifier may also include a number if multiple similar files are output." }) - } - - dynamic = { "properties" : (InputProperties, { "help" : "Each of the properties tags specify how to create a file in which one or more properties are written, one line per frame. " } ), - "trajectory" : (InputTrajectory, { "help" : "Each of the trajectory tags specify how to create a trajectory file, containing a list of per-atom coordinate properties. " } ), - "checkpoint" : (InputCheckpoint, { "help" : "Each of the checkpoint tags specify how to create a checkpoint file, which can be used to restart a simulation. " } ), - } - - default_help = """This class defines how properties, trajectories and checkpoints should be output during the simulation. May contain zero, one or many instances of properties, trajectory or checkpoint tags, each giving instructions on how one output file should be created and managed.""" - default_label = "OUTPUTS" - - @classmethod - def make_default(cls): - """Used to make the default value of the outputs class for use when no - output is specified. - - Needed since this is a fairly complicated default, with many mutable - objects, and the default has to be generated by a function that does not - use any mutable objects as arguments. - """ - - return [ ipi.engine.outputs.PropertyOutput(filename="i-pi.md", stride=10, outlist=[ "time", "step", "conserved", "temperature", "potential", "kinetic_cv" ] ), - ipi.engine.outputs.TrajectoryOutput(filename="i-pi.pos", stride=100, what="positions", format="xyz"), - ipi.engine.outputs.CheckpointOutput(filename="i-pi.checkpoint", stride=1000, overwrite=True)] - - def fetch(self): - """Returns a list of the output objects included in this dynamic - container. - - Returns: - A list of tuples, with each tuple being of the form ('type', 'object') - where 'type' is the type of output object and 'object' is a particular - object of that type. - """ - - super(InputOutputs, self).fetch() - outlist = [ p.fetch() for (n, p) in self.extra ] - prefix = self.prefix.fetch() - if not prefix == "": - for p in outlist: - p.filename = prefix + "." + p.filename - - return outlist - - def store(self, plist): - """ Stores a list of the output objects, creating a sequence of - dynamic containers. - - Args: - plist: A list of tuples, with each tuple being of the form - ('type', 'object') where 'type' is the type of forcefield and - 'object' is a particular object of that type. - """ - - super(InputOutputs, self).store() - self.extra = [] - - self.prefix.store("") - for el in plist: - if (isinstance(el, ipi.engine.outputs.PropertyOutput)): - ip = InputProperties() - ip.store(el) - self.extra.append(("properties", ip)) - elif (isinstance(el, ipi.engine.outputs.TrajectoryOutput)): - ip = InputTrajectory() - ip.store(el) - self.extra.append(("trajectory", ip)) - elif (isinstance(el, ipi.engine.outputs.CheckpointOutput)): - ip = InputCheckpoint() - ip.store(el) - self.extra.append(("checkpoint", ip)) diff --git a/tools/i-pi/ipi/inputs/prng.py b/tools/i-pi/ipi/inputs/prng.py deleted file mode 100644 index e3464ca791..0000000000 --- a/tools/i-pi/ipi/inputs/prng.py +++ /dev/null @@ -1,101 +0,0 @@ -"""Deals with creating the random number generator. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Generates a random number generator either from a seed number, or from a -state vector. - -Classes: - InputRandom: Deals with creating the Random object from a file, and - writing the checkpoints. -""" - -__all__ = ['InputRandom'] - -import numpy as np -from ipi.utils.prng import * -from ipi.utils.inputvalue import * - -class InputRandom(Input): - """Random input class. - - Handles generating the appropriate random number class from the xml - input file, and generating the xml checkpoint tags and data from an - instance of the object. - - Attributes: - seed: An optional integer giving a seed to initialize the random number - generator from. Defaults to 123456. - state: An optional array giving the state of the random number generator. - Defaults to an empty array. - has_gauss: An optional integer giving whether there is a stored - Gaussian number or not. Defaults to 0. - gauss: An optional float giving the stored Gaussian number. Defaults to - 0.0. - set_pos: An optional integer giving the position in the state array - that is being read from. Defaults to 0. - """ - - fields = {"seed" : (InputValue, {"dtype" : int, - "default" : 123456, - "help" : "This is the seed number used to generate the initial state of the random number generator."}), - "state" : (InputArray, {"dtype" : np.uint, - "default" : input_default(factory=np.zeros, kwargs={'shape': (0,), 'dtype': np.uint}), - "help" : "Gives the state vector for the random number generator. Avoid directly modifying this unless you are very familiar with the inner workings of the algorithm used."}), - "has_gauss" : (InputValue, {"dtype" : int, - "default" : 0, - "help" : "Determines whether there is a stored gaussian number or not. A value of 0 means there is none stored."}), - "gauss" : (InputValue, {"dtype" : float, - "default" : 0.00, - "help" : "The stored Gaussian number." }), - "set_pos" : (InputValue, {"dtype" : int, - "default" : 0, - "help" : "Gives the position in the state array that the random number generator is reading from."})} - - default_help = "Deals with the pseudo-random number generator." - default_label = "PRNG" - - def store(self, prng): - """Takes a random number instance and stores a minimal - representation of it. - - Args: - prng: A random number object from which to initialize from. - """ - - super(InputRandom,self).store(prng) - self.seed.store(prng.seed) - gstate = prng.state - self.state.store(gstate[1]) - self.set_pos.store(gstate[2]) - self.has_gauss.store(gstate[3]) - self.gauss.store(gstate[4]) - - def fetch(self): - """Creates a random number object. - - Returns: - An random number object of the appropriate type and with the - appropriate properties given the attributes of the InputRandom - object. - """ - - super(InputRandom,self).fetch() - if not self.state._explicit: - return Random(seed=self.seed.fetch()) - else: - return Random(state=('MT19937',self.state.fetch(), self.set_pos.fetch(), self.has_gauss.fetch(), self.gauss.fetch() )) diff --git a/tools/i-pi/ipi/inputs/simulation.py b/tools/i-pi/ipi/inputs/simulation.py deleted file mode 100644 index d020547cd2..0000000000 --- a/tools/i-pi/ipi/inputs/simulation.py +++ /dev/null @@ -1,193 +0,0 @@ -"""Deals with creating the simulation class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - InputSimulation: Deals with creating the Simulation object from a file, and - writing the checkpoints. -""" - -__all__ = ['InputSimulation'] - -import numpy as np -import os.path, sys -import ipi.engine.simulation -from ipi.utils.depend import * -from ipi.utils.inputvalue import * -from ipi.utils.units import * -from ipi.utils.prng import * -from ipi.utils.io import * -from ipi.utils.io.io_xml import * -from ipi.utils.messages import verbosity -from ipi.inputs.forces import InputForces -from ipi.inputs.prng import InputRandom -from ipi.inputs.initializer import InputInitializer -from ipi.inputs.beads import InputBeads -from ipi.inputs.cell import InputCell -from ipi.inputs.ensembles import InputEnsemble -from ipi.inputs.outputs import InputOutputs -from ipi.inputs.normalmodes import InputNormalModes -from ipi.engine.normalmodes import NormalModes -from ipi.engine.atoms import Atoms -from ipi.engine.beads import Beads -from ipi.engine.cell import Cell -from ipi.engine.initializer import Initializer - -class InputSimulation(Input): - """Simulation input class. - - Handles generating the appropriate forcefield class from the xml input file, - and generating the xml checkpoint tags and data from an instance of the - object. - - Attributes: - verbosity: A string saying how much should be output to standard output. - - Fields: - force: A restart force instance. Used as a model for all the replicas. - ensemble: A restart ensemble instance. - beads: A restart beads instance. - normal_modes: Setup of normal mode integrator. - cell: A restart cell instance. - output: A list of the required outputs. - prng: A random number generator object. - step: An integer giving the current simulation step. Defaults to 0. - total_steps: The total number of steps. Defaults to 1000 - total_time: The wall clock time limit. Defaults to 0 (no limit). - initialize: An array of strings giving all the quantities that should - be output. - """ - - fields = { "forces" : (InputForces, { "help" : InputForces.default_help }), - "ensemble": (InputEnsemble, { "help" : InputEnsemble.default_help } ), - "prng" : (InputRandom, { "help" : InputRandom.default_help, - "default" : input_default(factory=Random)} ), - "initialize" : (InputInitializer, { "help" : InputInitializer.default_help, - "default" : input_default(factory=Initializer) } ), - "beads" : (InputBeads, { "help" : InputBeads.default_help, - "default" : input_default(factory=Beads, kwargs={'natoms': 0, 'nbeads': 0}) } ), - "normal_modes" : (InputNormalModes, { "help" : InputNormalModes.default_help, - "default" : input_default(factory=NormalModes, kwargs={'mode': "rpmd"}) } ), - "cell" : (InputCell, { "help" : InputCell.default_help, - "default" : input_default(factory=Cell) }), - "output" : (InputOutputs, { "help" : InputOutputs.default_help, - "default": input_default(factory=InputOutputs.make_default) }), - "step" : ( InputValue, { "dtype" : int, - "default" : 0, - "help" : "The current simulation time step." }), - "total_steps": ( InputValue, { "dtype" : int, - "default" : 1000, - "help" : "The total number of steps that will be done. If 'step' is equal to or greater than 'total_steps', then the simulation will finish." }), - "total_time" : ( InputValue, { "dtype" : float, - "default" : 0, - "help" : "The maximum wall clock time (in seconds)." }), - } - - attribs = { "verbosity" : (InputAttribute, { "dtype" : str, - "default" : "low", - "options" : [ "quiet", "low", "medium", "high", "debug" ], - "help" : "The level of output on stdout." - }) - } - - default_help = "This is the top level class that deals with the running of the simulation, including holding the simulation specific properties such as the time step and outputting the data." - default_label = "SIMULATION" - - def store(self, simul): - """Takes a simulation instance and stores a minimal representation of it. - - Args: - simul: A simulation object. - """ - - super(InputSimulation,self).store() - self.forces.store(simul.flist) - self.ensemble.store(simul.ensemble) - - self.beads.store(simul.beads) - - self.normal_modes.store(simul.nm) - self.cell.store(simul.cell) - self.prng.store(simul.prng) - self.step.store(simul.step) - self.total_steps.store(simul.tsteps) - self.total_time.store(simul.ttime) - self.output.store(simul.outputs) - - # this we pick from the messages class. kind of a "global" but it seems to - # be the best way to pass around the (global) information on the level of output. - if verbosity.debug: - self.verbosity.store("debug") - elif verbosity.high: - self.verbosity.store("high") - elif verbosity.medium: - self.verbosity.store("medium") - elif verbosity.low: - self.verbosity.store("low") - elif verbosity.quiet: - self.verbosity.store("quiet") - else: - raise ValueError("Invalid verbosity level") - - def fetch(self): - """Creates a simulation object. - - Returns: - A simulation object of the appropriate type and with the appropriate - properties and other objects given the attributes of the - InputSimulation object. - - Raises: - TypeError: Raised if one of the file types in the stride keyword - is incorrect. - """ - - super(InputSimulation,self).fetch() - - # small hack: initialize here the verbosity level -- we really assume to have - # just one simulation object - verbosity.level=self.verbosity.fetch() - - # this creates a simulation object which gathers all the little bits - #TODO use named arguments since this list is a bit too long... - rsim = ipi.engine.simulation.Simulation(self.beads.fetch(), self.cell.fetch(), - self.forces.fetch(), self.ensemble.fetch(), self.prng.fetch(), - self.output.fetch(), self.normal_modes.fetch(), - self.initialize.fetch(), self.step.fetch(), - tsteps=self.total_steps.fetch(), - ttime=self.total_time.fetch()) - - # this does all of the piping between the components of the simulation - rsim.bind() - - return rsim - - def check(self): - """Function that deals with optional arguments. - - Deals with the difference between classical and PI dynamics. If there is - no beads argument, the bead positions are generated from the atoms, with - the necklace being fixed at the atom position. Similarly, if no nbeads - argument is specified a classical simulation is done. - - Raises: - TypeError: Raised if no beads or atoms attribute is defined. - """ - - super(InputSimulation,self).check() - if self.total_steps.fetch() <= self.step.fetch(): - raise ValueError("Current step greater than total steps, no dynamics will be done.") diff --git a/tools/i-pi/ipi/inputs/thermostats.py b/tools/i-pi/ipi/inputs/thermostats.py deleted file mode 100644 index 5c1ec2d65b..0000000000 --- a/tools/i-pi/ipi/inputs/thermostats.py +++ /dev/null @@ -1,195 +0,0 @@ -"""Deals with creating the thermostats class. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Chooses between the different possible thermostat options and creates the -appropriate thermostat object, with suitable parameters. - -Classes: - InputThermo: Deals with creating the thermostat object from a file, and - writing the checkpoints. -""" - -__all__ = ['InputThermo'] - -import numpy as np -from ipi.utils.depend import * -from ipi.utils.inputvalue import * -from ipi.engine.thermostats import * - -class InputThermo(Input): - """Thermostat input class. - - Handles generating the appropriate thermostat class from the xml input file, - and generating the xml checkpoiunt tags and data from an instance of the - object. - - Attributes: - mode: An optional string giving the type of the thermostat used. Defaults - to 'langevin'. - - Fields: - ethermo: An optional float giving the amount of heat energy transferred - to the bath. Defaults to 0.0. - tau: An optional float giving the damping time scale. Defaults to 1.0. - pile_scale: Scaling for the PILE damping relative to the critical damping. - A: An optional array of floats giving the drift matrix. Defaults to 0.0. - C: An optional array of floats giving the static covariance matrix. - Defaults to 0.0. - s: An optional array of floats giving the additional momentum-scaled - momenta in GLE. Defaults to 0.0. - """ - - attribs = { "mode": (InputAttribute, { "dtype" : str, - "options" : [ "", "langevin", "svr", "pile_l", "pile_g", "gle", "nm_gle", "nm_gle_g" ], - "help" : "The style of thermostatting. 'langevin' specifies a white noise langevin equation to be attached to the cartesian representation of the momenta. 'svr' attaches a velocity rescaling thermostat to the cartesian representation of the momenta. Both 'pile_l' and 'pile_g' attaches a white noise langevin thermostat to the normal mode representation, with 'pile_l' attaching a local langevin thermostat to the centroid mode and 'pile_g' instead attaching a global velocity rescaling thermostat. 'gle' attaches a colored noise langevin thermostat to the cartesian representation of the momenta, 'nm_gle' attaches a colored noise langevin thermostat to the normal mode representation of the momenta and a langevin thermostat to the centroid and 'nm_gle_g' attaches a gle thermostat to the normal modes and a svr thermostat to the centroid." - }) } - fields = { "ethermo" : (InputValue, { "dtype" : float, - "default" : 0.0, - "help" : "The initial value of the thermostat energy. Used when the simulation is restarted to guarantee continuity of the conserved quantity.", - "dimension" : "energy" }), - "tau" : (InputValue, { "dtype" : float, - "default" : 0.0, - "help" : "The friction coefficient for white noise thermostats.", - "dimension" : "time" }), - "pile_scale" : (InputValue, { "dtype" : float, - "default" : 1.0, - "help" : "Scaling for the PILE damping relative to the critical damping."} ), - "A" : (InputArray, { "dtype" : float, - "default" : input_default(factory=np.zeros, args = (0,)), - "help" : "The friction matrix for GLE thermostats.", - "dimension" : "frequency" }), - "C" : (InputArray, { "dtype" : float, - "default" : input_default(factory=np.zeros, args = (0,)), - "help" : "The covariance matrix for GLE thermostats.", - "dimension" : "temperature" }), - "s" : (InputArray, { "dtype" : float, - "default" : input_default(factory=np.zeros, args = (0,)), - "help" : "Input values for the additional momenta in GLE.", - "dimension" : "ms-momentum" }) - } - - default_help = "Simulates an external heat bath to keep the velocity distribution at the correct temperature." - default_label = "THERMOSTATS" - - def store(self, thermo): - """Takes a thermostat instance and stores a minimal representation of it. - - Args: - thermo: A thermostat object. - - Raises: - TypeError: Raised if the thermostat is not a recognized type. - """ - - super(InputThermo,self).store(thermo) - if type(thermo) is ThermoLangevin: - self.mode.store("langevin") - self.tau.store(thermo.tau) - elif type(thermo) is ThermoSVR: - self.mode.store("svr") - self.tau.store(thermo.tau) - elif type(thermo) is ThermoPILE_L: - self.mode.store("pile_l") - self.tau.store(thermo.tau) - self.pile_scale.store(thermo.pilescale) - elif type(thermo) is ThermoPILE_G: - self.mode.store("pile_g") - self.tau.store(thermo.tau) - self.pile_scale.store(thermo.pilescale) - elif type(thermo) is ThermoGLE: - self.mode.store("gle") - self.A.store(thermo.A) - if dget(thermo,"C")._func is None: - self.C.store(thermo.C) - self.s.store(thermo.s) - elif type(thermo) is ThermoNMGLE: - self.mode.store("nm_gle") - self.A.store(thermo.A) - if dget(thermo,"C")._func is None: - self.C.store(thermo.C) - self.s.store(thermo.s) - elif type(thermo) is ThermoNMGLEG: - self.mode.store("nm_gle_g") - self.A.store(thermo.A) - self.tau.store(thermo.tau) - if dget(thermo,"C")._func is None: - self.C.store(thermo.C) - self.s.store(thermo.s) - elif type(thermo) is Thermostat: - self.mode.store("") - else: - raise TypeError("Unknown thermostat mode " + type(thermo).__name__) - self.ethermo.store(thermo.ethermo) - - def fetch(self): - """Creates a thermostat object. - - Returns: - A thermostat object of the appropriate type and with the appropriate - parameters given the attributes of the InputThermo object. - - Raises: - TypeError: Raised if the thermostat type is not a recognized option. - """ - - super(InputThermo,self).fetch() - if self.mode.fetch() == "langevin": - thermo = ThermoLangevin(tau=self.tau.fetch()) - elif self.mode.fetch() == "svr": - thermo = ThermoSVR(tau=self.tau.fetch()) - elif self.mode.fetch() == "pile_l": - thermo = ThermoPILE_L(tau=self.tau.fetch(), scale=self.pile_scale.fetch()) - elif self.mode.fetch() == "pile_g": - thermo = ThermoPILE_G(tau=self.tau.fetch(), scale=self.pile_scale.fetch()) - elif self.mode.fetch() == "gle": - rC = self.C.fetch() - if len(rC) == 0: - rC = None - thermo = ThermoGLE(A=self.A.fetch(),C=rC) - thermo.s = self.s.fetch() - elif self.mode.fetch() == "nm_gle": - rC = self.C.fetch() - if len(rC) == 0: - rC = None - thermo = ThermoNMGLE(A=self.A.fetch(),C=rC) - thermo.s = self.s.fetch() - elif self.mode.fetch() == "nm_gle_g": - rC = self.C.fetch() - if len(rC) == 0: - rC = None - thermo = ThermoNMGLEG(A=self.A.fetch(),C=rC, tau=self.tau.fetch()) - thermo.s = self.s.fetch() - elif self.mode.fetch() == "" : - thermo=Thermostat() - else: - raise TypeError("Invalid thermostat mode " + self.mode.fetch()) - - thermo.ethermo = self.ethermo.fetch() - - return thermo - - def check(self): - """Checks that the parameter arrays represents a valid thermostat.""" - - super(InputThermo,self).check() - - if self.mode.fetch() in ["langevin", "svr", "pile_l", "pile_g", "nm_gle_g"]: - if self.tau.fetch() <= 0: - raise ValueError("The thermostat friction coefficient must be set to a positive value") - if self.mode.fetch() in ["gle", "nm_gle", "nm_gle_g"]: - pass # PERHAPS DO CHECKS THAT MATRICES SATISFY REASONABLE CONDITIONS (POSITIVE-DEFINITENESS, ETC) diff --git a/tools/i-pi/ipi/interfaces/README b/tools/i-pi/ipi/interfaces/README deleted file mode 100644 index d5693d8f35..0000000000 --- a/tools/i-pi/ipi/interfaces/README +++ /dev/null @@ -1,8 +0,0 @@ - -- Interfaces between i-PI and the drivers -- - - * This is the directory containing the code that deals with the socket - interface. - - * Files: - - sockets.py: Deals with the driver communication and the wrapper socket - and threading interface. diff --git a/tools/i-pi/ipi/interfaces/__init__.py b/tools/i-pi/ipi/interfaces/__init__.py deleted file mode 100644 index 68af0572bf..0000000000 --- a/tools/i-pi/ipi/interfaces/__init__.py +++ /dev/null @@ -1 +0,0 @@ -__all__ = ["sockets"] diff --git a/tools/i-pi/ipi/interfaces/sockets.py b/tools/i-pi/ipi/interfaces/sockets.py deleted file mode 100644 index f946cf3149..0000000000 --- a/tools/i-pi/ipi/interfaces/sockets.py +++ /dev/null @@ -1,773 +0,0 @@ -"""Deals with the socket communication between the PIMD and driver code. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Deals with creating the socket, transmitting and receiving data, accepting and -removing different driver routines and the parallelization of the force -calculation. - -Classes: - Status: Simple class to keep track of the status, uses bitwise or to give - combinations of different status options. - DriverSocket: Class to deal with communication between a client and - the driver code. - InterfaceSocket: Host server class. Deals with distribution of all the jobs - between the different client servers. - -Functions: - Message: Sends a header string through the socket. - -Exceptions: - Disconnected: Raised if client has been disconnected. - InvalidStatus: Raised if client has the wrong status. Shouldn't have to be - used if the structure of the program is correct. -""" - -__all__ = ['InterfaceSocket'] - -import numpy as np -import sys, os -import socket, select, threading, signal, string, time -from ipi.utils.depend import depstrip -from ipi.utils.messages import verbosity, warning, info -from ipi.utils.softexit import softexit - - -HDRLEN = 12 -UPDATEFREQ = 10 -TIMEOUT = 5.0 -SERVERTIMEOUT = 2.0*TIMEOUT -NTIMEOUT = 10 - -def Message(mystr): - """Returns a header of standard length HDRLEN.""" - - return string.ljust(string.upper(mystr), HDRLEN) - - -class Disconnected(Exception): - """Disconnected: Raised if client has been disconnected.""" - - pass - -class InvalidSize(Exception): - """Disconnected: Raised if client returns forces with inconsistent number of atoms.""" - - pass - -class InvalidStatus(Exception): - """InvalidStatus: Raised if client has the wrong status. - - Shouldn't have to be used if the structure of the program is correct. - """ - - pass - -class Status: - """Simple class used to keep track of the status of the client. - - Uses bitwise or to give combinations of different status options. - i.e. Status.Up | Status.Ready would be understood to mean that the client - was connected and ready to receive the position and cell data. - - Attributes: - Disconnected: Flag for if the client has disconnected. - Up: Flag for if the client is running. - Ready: Flag for if the client has ready to receive position and cell data. - NeedsInit: Flag for if the client is ready to receive forcefield - parameters. - HasData: Flag for if the client is ready to send force data. - Busy: Flag for if the client is busy. - Timeout: Flag for if the connection has timed out. - """ - - Disconnected = 0 - Up = 1 - Ready = 2 - NeedsInit = 4 - HasData = 8 - Busy = 16 - Timeout = 32 - - -class DriverSocket(socket.socket): - """Deals with communication between the client and driver code. - - Deals with sending and receiving the data from the driver code. Keeps track - of the status of the driver. Initializes the driver forcefield, sends the - position and cell data, and receives the force data. - - Attributes: - _buf: A string buffer to hold the reply from the driver. - status: Keeps track of the status of the driver. - lastreq: The ID of the last request processed by the client. - locked: Flag to mark if the client has been working consistently on one image. - """ - - def __init__(self, socket): - """Initializes DriverSocket. - - Args: - socket: A socket through which the communication should be done. - """ - - super(DriverSocket,self).__init__(_sock=socket) - self._buf = np.zeros(0,np.byte) - self.peername = self.getpeername() - self.status = Status.Up - self.waitstatus = False - self.lastreq = None - self.locked = False - - def shutdown(self, how=socket.SHUT_RDWR): - - self.sendall(Message("exit")) - self.status = Status.Disconnected - super(DriverSocket,self).shutdown(how) - - def poll(self): - """Waits for driver status.""" - - self.status = Status.Disconnected # sets disconnected as failsafe status, in case _getstatus fails and exceptions are ignored upstream - self.status = self._getstatus() - - def _getstatus(self): - """Gets driver status. - - Returns: - An integer labelling the status via bitwise or of the relevant members - of Status. - """ - - if not self.waitstatus: - try: - readable, writable, errored = select.select([], [self], []) - if self in writable: - self.sendall(Message("status")) - self.waitstatus = True - except: - return Status.Disconnected - - try: - reply = self.recv(HDRLEN) - self.waitstatus = False # got status reply - except socket.timeout: - warning(" @SOCKET: Timeout in status recv!", verbosity.debug ) - return Status.Up | Status.Busy | Status.Timeout - except: - return Status.Disconnected - - if not len(reply) == HDRLEN: - return Status.Disconnected - elif reply == Message("ready"): - return Status.Up | Status.Ready - elif reply == Message("needinit"): - return Status.Up | Status.NeedsInit - elif reply == Message("havedata"): - return Status.Up | Status.HasData - else: - warning(" @SOCKET: Unrecognized reply: " + str(reply), verbosity.low ) - return Status.Up - - def recvall(self, dest): - """Gets the potential energy, force and virial from the driver. - - Args: - dest: Object to be read into. - - Raises: - Disconnected: Raised if client is disconnected. - - Returns: - The data read from the socket to be read into dest. - """ - - blen = dest.itemsize*dest.size - if (blen > len(self._buf)): - self._buf.resize(blen) - bpos = 0 - ntimeout = 0 - - while bpos < blen: - timeout = False - -# pre-2.5 version. - try: - bpart = "" - bpart = self.recv(blen - bpos) - if len(bpart) == 0: raise socket.timeout # There is a problem if this returns no data - self._buf[bpos:bpos + len(bpart)] = np.fromstring(bpart, np.byte) - except socket.timeout: - warning(" @SOCKET: Timeout in status recvall, trying again!", verbosity.low) - timeout = True - ntimeout += 1 - if ntimeout > NTIMEOUT: - warning(" @SOCKET: Couldn't receive within %5d attempts. Time to give up!" % (NTIMEOUT), verbosity.low) - raise Disconnected() - pass - if (not timeout and bpart == 0): - raise Disconnected() - bpos += len(bpart) - -# post-2.5 version: slightly more compact for modern python versions -# try: -# bpart = 1 -# bpart = self.recv_into(self._buf[bpos:], blen-bpos) -# except socket.timeout: -# print " @SOCKET: Timeout in status recvall, trying again!" -# timeout = True -# pass -# if (not timeout and bpart == 0): -# raise Disconnected() -# bpos += bpart -#TODO this Disconnected() exception currently just causes the program to hang. -#This should do something more graceful - - if np.isscalar(dest): - return np.fromstring(self._buf[0:blen], dest.dtype)[0] - else: - return np.fromstring(self._buf[0:blen], dest.dtype).reshape(dest.shape) - - def initialize(self, rid, pars): - """Sends the initialization string to the driver. - - Args: - rid: The index of the request, i.e. the replica that - the force calculation is for. - pars: The parameter string to be sent to the driver. - - Raises: - InvalidStatus: Raised if the status is not NeedsInit. - """ - - if self.status & Status.NeedsInit: - try: - self.sendall(Message("init")) - self.sendall(np.int32(rid)) - self.sendall(np.int32(len(pars))) - self.sendall(pars) - except: - self.poll() - return - else: - raise InvalidStatus("Status in init was " + self.status) - - def sendpos(self, pos, cell): - """Sends the position and cell data to the driver. - - Args: - pos: An array containing the atom positions. - cell: A cell object giving the system box. - - Raises: - InvalidStatus: Raised if the status is not Ready. - """ - - if (self.status & Status.Ready): - try: - self.sendall(Message("posdata")) - self.sendall(cell.h, 9*8) - self.sendall(cell.ih, 9*8) - self.sendall(np.int32(len(pos)/3)) - self.sendall(pos, len(pos)*8) - except: - self.poll() - return - else: - raise InvalidStatus("Status in sendpos was " + self.status) - - def getforce(self): - """Gets the potential energy, force and virial from the driver. - - Raises: - InvalidStatus: Raised if the status is not HasData. - Disconnected: Raised if the driver has disconnected. - - Returns: - A list of the form [potential, force, virial, extra]. - """ - - if (self.status & Status.HasData): - self.sendall(Message("getforce")); - reply = "" - while True: - try: - reply = self.recv(HDRLEN) - except socket.timeout: - warning(" @SOCKET: Timeout in getforce, trying again!", verbosity.low) - continue - if reply == Message("forceready"): - break - else: - warning(" @SOCKET: Unexpected getforce reply: %s" % (reply), verbosity.low) - if reply == "": - raise Disconnected() - else: - raise InvalidStatus("Status in getforce was " + self.status) - - mu = np.float64() - mu = self.recvall(mu) - - mlen = np.int32() - mlen = self.recvall(mlen) - mf = np.zeros(3*mlen,np.float64) - mf = self.recvall(mf) - - mvir = np.zeros((3,3),np.float64) - mvir = self.recvall(mvir) - - #! Machinery to return a string as an "extra" field. Comment if you are using a old patched driver that does not return anything! - mlen = np.int32() - mlen = self.recvall(mlen) - if mlen > 0 : - mxtra = np.zeros(mlen,np.character) - mxtra = self.recvall(mxtra) - mxtra = "".join(mxtra) - else: - mxtra = "" - - #!TODO must set up a machinery to intercept the "extra" return field - return [mu, mf, mvir, mxtra] - - -class InterfaceSocket(object): - """Host server class. - - Deals with distribution of all the jobs between the different client servers - and both initially and as clients either finish or are disconnected. - Deals with cleaning up after all calculations are done. Also deals with the - threading mechanism, and cleaning up if the interface is killed. - - Attributes: - address: A string giving the name of the host network. - port: An integer giving the port the socket will be using. - slots: An integer giving the maximum allowed backlog of queued clients. - mode: A string giving the type of socket used. - latency: A float giving the number of seconds the interface will wait - before updating the client list. - timeout: A float giving a timeout limit for considering a calculation dead - and dropping the connection. - dopbc: A boolean which decides whether or not to fold the bead positions - back into the unit cell before passing them to the client code. - server: The socket used for data transmition. - clients: A list of the driver clients connected to the server. - requests: A list of all the jobs required in the current PIMD step. - jobs: A list of all the jobs currently running. - _poll_thread: The thread the poll loop is running on. - _prev_kill: Holds the signals to be sent to clean up the main thread - when a kill signal is sent. - _poll_true: A boolean giving whether the thread is alive. - _poll_iter: An integer used to decide whether or not to check for - client connections. It is used as a counter, once it becomes higher - than the pre-defined number of steps between checks the socket will - update the list of clients and then be reset to zero. - """ - - def __init__(self, address="localhost", port=31415, slots=4, mode="unix", latency=1e-3, timeout=1.0, dopbc=True): - """Initializes interface. - - Args: - address: An optional string giving the name of the host server. - Defaults to 'localhost'. - port: An optional integer giving the port number. Defaults to 31415. - slots: An optional integer giving the maximum allowed backlog of - queueing clients. Defaults to 4. - mode: An optional string giving the type of socket. Defaults to 'unix'. - latency: An optional float giving the time in seconds the socket will - wait before updating the client list. Defaults to 1e-3. - timeout: Length of time waiting for data from a client before we assume - the connection is dead and disconnect the client. - dopbc: A boolean which decides whether or not to fold the bead positions - back into the unit cell before passing them to the client code. - - Raises: - NameError: Raised if mode is not 'unix' or 'inet'. - """ - - self.address = address - self.port = port - self.slots = slots - self.mode = mode - self.latency = latency - self.timeout = timeout - self.dopbc = dopbc - self._poll_thread = None - self._prev_kill = {} - self._poll_true = False - self._poll_iter = 0 - - def open(self): - """Creates a new socket. - - Used so that we can create a interface object without having to also - create the associated socket object. - """ - - if self.mode == "unix": - self.server = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM) - try: - self.server.bind("/tmp/ipi_" + self.address) - info("Created unix socket with address " + self.address, verbosity.medium) - except: - raise ValueError("Error opening unix socket. Check if a file " + ("/tmp/ipi_" + self.address) + " exists, and remove it if unused.") - - elif self.mode == "inet": - self.server = socket.socket(socket.AF_INET, socket.SOCK_STREAM) - self.server.bind((self.address,self.port)) - info("Created inet socket with address " + self.address + " and port number " + str(self.port), verbosity.medium) - else: - raise NameError("InterfaceSocket mode " + self.mode + " is not implemented (should be unix/inet)") - - self.server.listen(self.slots) - self.server.settimeout(SERVERTIMEOUT) - self.clients = [] - self.requests = [] - self.jobs = [] - - def close(self): - """Closes down the socket.""" - - info(" @SOCKET: Shutting down the driver interface.", verbosity.low ) - - for c in self.clients[:]: - if (c.status & Status.Up): - c.shutdown(socket.SHUT_RDWR) - - self.server.shutdown(socket.SHUT_RDWR) - self.server.close() - if self.mode == "unix": - os.unlink("/tmp/ipi_" + self.address) - - def queue(self, atoms, cell, pars=None, reqid=0): - """Adds a request. - - Note that the pars dictionary need to be sent as a string of a - standard format so that the initialization of the driver can be done. - - Args: - atoms: An Atoms object giving the atom positions. - cell: A Cell object giving the system box. - pars: An optional dictionary giving the parameters to be sent to the - driver for initialization. Defaults to {}. - reqid: An optional integer that identifies requests of the same type, - e.g. the bead index - - Returns: - A list giving the status of the request of the form {'atoms': Atoms - object giving the atom positions, 'cell': Cell object giving the - system box, 'pars': parameter string, 'result': holds the result as a - list once the computation is done, 'status': a string labelling the - status, 'id': the id of the request, usually the bead number, 'start': - the starting time for the calculation, used to check for timeouts.}. - """ - - par_str = " " - - if not pars is None: - for k,v in pars.items(): - par_str += k + " : " + str(v) + " , " - else: - par_str = " " - - # APPLY PBC -- this is useful for codes such as LAMMPS that don't do full PBC when computing distances - pbcpos = depstrip(atoms.q).copy() - if self.dopbc: - cell.array_pbc(pbcpos) - - newreq = {"pos": pbcpos, "cell": cell, "pars": par_str, - "result": None, "status": "Queued", "id": reqid, - "start": -1 } - - self.requests.append(newreq) - return newreq - - def release(self, request): - """Empties the list of requests once finished. - - Args: - request: A list of requests that are done. - """ - - if request in self.requests: - self.requests.remove(request) - - def pool_update(self): - """Deals with keeping the pool of client drivers up-to-date during a - force calculation step. - - Deals with maintaining the client list. Clients that have - disconnected are removed and their jobs removed from the list of - running jobs and new clients are connected to the server. - """ - - for c in self.clients[:]: - if not (c.status & Status.Up): - try: - warning(" @SOCKET: Client " + str(c.peername) +" died or got unresponsive(C). Removing from the list.", verbosity.low) - c.shutdown(socket.SHUT_RDWR) - c.close() - except: - pass - c.status = Status.Disconnected - self.clients.remove(c) - for [k,j] in self.jobs[:]: - if j is c: - self.jobs = [ w for w in self.jobs if not ( w[0] is k and w[1] is j ) ] # removes pair in a robust way - #self.jobs.remove([k,j]) - k["status"] = "Queued" - k["start"] = -1 - - keepsearch = True - while keepsearch: - readable, writable, errored = select.select([self.server], [], [], 0.0) - if self.server in readable: - client, address = self.server.accept() - client.settimeout(TIMEOUT) - driver = DriverSocket(client) - info(" @SOCKET: Client asked for connection from "+ str( address ) +". Now hand-shaking.", verbosity.low) - driver.poll() - if (driver.status | Status.Up): - self.clients.append(driver) - info(" @SOCKET: Handshaking was successful. Added to the client list.", verbosity.low) - else: - warning(" @SOCKET: Handshaking failed. Dropping connection.", verbosity.low) - client.shutdown(socket.SHUT_RDWR) - client.close() - else: - keepsearch = False - - def pool_distribute(self): - """Deals with keeping the list of jobs up-to-date during a force - calculation step. - - Deals with maintaining the jobs list. Gets data from drivers that have - finished their calculation and removes that job from the list of running - jobs, adds jobs to free clients and initializes the forcefields of new - clients. - """ - - for c in self.clients: - if c.status == Status.Disconnected : # client disconnected. force a pool_update - self._poll_iter = UPDATEFREQ - return - if not c.status & ( Status.Ready | Status.NeedsInit ): - c.poll() - - for [r,c] in self.jobs[:]: - if c.status & Status.HasData: - try: - r["result"] = c.getforce() - if len(r["result"][1]) != len(r["pos"]): - raise InvalidSize - except Disconnected: - c.status = Status.Disconnected - continue - except InvalidSize: - warning(" @SOCKET: Client returned an inconsistent number of forces. Will mark as disconnected and try to carry on.", verbosity.low) - c.status = Status.Disconnected - continue - except: - warning(" @SOCKET: Client got in a awkward state during getforce. Will mark as disconnected and try to carry on.", verbosity.low) - c.status = Status.Disconnected - continue - c.poll() - while c.status & Status.Busy: # waits, but check if we got stuck. - if self.timeout > 0 and r["start"] > 0 and time.time() - r["start"] > self.timeout: - warning(" @SOCKET: Timeout! HASDATA for bead " + str(r["id"]) + " has been running for " + str(time.time() - r["start"]) + " sec.", verbosity.low) - warning(" @SOCKET: Client " + str(c.peername) + " died or got unresponsive(A). Disconnecting.", verbosity.low) - try: - c.shutdown(socket.SHUT_RDWR) - except: - pass - c.close() - c.status = Status.Disconnected - continue - c.poll() - if not (c.status & Status.Up): - warning(" @SOCKET: Client died a horrible death while getting forces. Will try to cleanup.", verbosity.low) - continue - r["status"] = "Done" - c.lastreq = r["id"] # saves the ID of the request that the client has just processed - self.jobs = [ w for w in self.jobs if not ( w[0] is r and w[1] is c ) ] # removes pair in a robust way - - if self.timeout > 0 and c.status != Status.Disconnected and r["start"] > 0 and time.time() - r["start"] > self.timeout: - warning(" @SOCKET: Timeout! Request for bead " + str( r["id"]) + " has been running for " + str(time.time() - r["start"]) + " sec.", verbosity.low) - warning(" @SOCKET: Client " + str(c.peername) + " died or got unresponsive(B). Disconnecting.",verbosity.low) - try: - c.shutdown(socket.SHUT_RDWR) - except socket.error: - e = sys.exc_info() - warning(" @SOCKET: could not shut down cleanly the socket. %s: %s in file '%s' on line %d" % (e[0].__name__, e[1], os.path.basename(e[2].tb_frame.f_code.co_filename), e[2].tb_lineno), verbosity.low ) - c.close() - c.poll() - c.status = Status.Disconnected - - freec = self.clients[:] - for [r2, c] in self.jobs: - freec.remove(c) - - pendr = self.requests[:] - pendr = [ r for r in self.requests if r["status"] == "Queued" ] - - for fc in freec[:]: - matched = False - # first, makes sure that the client is REALLY free - if not (fc.status & Status.Up): - self.clients.remove(fc) # if fc is in freec it can't be associated with a job (we just checked for that above) - continue - if fc.status & Status.HasData: - continue - if not (fc.status & (Status.Ready | Status.NeedsInit | Status.Busy) ): - warning(" @SOCKET: Client " + str(fc.peername) + " is in an unexpected status " + str(fc.status) + " at (1). Will try to keep calm and carry on.", verbosity.low) - continue - for match_ids in ( "match", "none", "free", "any" ): - for r in pendr[:]: - if match_ids == "match" and not fc.lastreq is r["id"]: - continue - elif match_ids == "none" and not fc.lastreq is None: - continue - elif match_ids == "free" and fc.locked: - continue - - info(" @SOCKET: Assigning [%5s] request id %4s to client with last-id %4s (% 3d/% 3d : %s)" % (match_ids, str(r["id"]), str(fc.lastreq), self.clients.index(fc), len(self.clients), str(fc.peername) ), verbosity.high ) - - while fc.status & Status.Busy: - fc.poll() - if fc.status & Status.NeedsInit: - fc.initialize(r["id"], r["pars"]) - fc.poll() - while fc.status & Status.Busy: # waits for initialization to finish. hopefully this is fast - fc.poll() - if fc.status & Status.Ready: - fc.sendpos(r["pos"], r["cell"]) - r["status"] = "Running" - r["start"] = time.time() # sets start time for the request - fc.poll() - self.jobs.append([r,fc]) - fc.locked = (fc.lastreq is r["id"]) - matched = True - # removes r from the list of pending jobs - pendr = [nr for nr in pendr if (not nr is r)] - break - else: - warning(" @SOCKET: Client " + str(fc.peername) + " is in an unexpected status " + str(fc.status) + " at (2). Will try to keep calm and carry on.", verbosity.low) - if matched: - break # doesn't do a second (or third) round if it managed - # to assign the job - - def _kill_handler(self, signal, frame): - """Deals with handling a kill call gracefully. - - Prevents any of the threads becoming zombies, by intercepting a - kill signal using the standard python function signal.signal() and - then closing the socket and the spawned threads before closing the main - thread. Called when signals SIG_INT and SIG_TERM are received. - - Args: - signal: An integer giving the signal number of the signal received - from the socket. - frame: Current stack frame. - """ - - warning(" @SOCKET: Kill signal. Trying to make a clean exit.", verbosity.low) - self.end_thread() - - softexit.trigger(" @SOCKET: Kill signal received") - - try: - self.__del__() - except: - pass - if signal in self._prev_kill: - self._prev_kill[signal](signal, frame) - - def _poll_loop(self): - """The main thread loop. - - Runs until either the program finishes or a kill call is sent. Updates - the pool of clients every UPDATEFREQ loops and loops every latency - seconds until _poll_true becomes false. - """ - - info(" @SOCKET: Starting the polling thread main loop.", verbosity.low) - self._poll_iter = UPDATEFREQ - while self._poll_true: - time.sleep(self.latency) - # makes sure to remove the last dead client as soon as possible -- and to get clients if we are dry - if self._poll_iter >= UPDATEFREQ or len(self.clients)==0 or (len(self.clients) > 0 and not(self.clients[0].status & Status.Up)): - self.pool_update() - self._poll_iter = 0 - self._poll_iter += 1 - self.pool_distribute() - - if os.path.exists("EXIT"): # softexit - info(" @SOCKET: Soft exit request from file EXIT. Flushing job queue.", verbosity.low) - # releases all pending requests - for r in self.requests: - r["status"] = "Exit" - for c in self.clients: - try: - c.shutdown(socket.SHUT_RDWR) - c.close() - except: - pass - # flush it all down the drain - self.clients = [] - self.jobs = [] - self._poll_thread = None - - def started(self): - """Returns a boolean specifying whether the thread has started yet.""" - - return (not self._poll_thread is None) - - def start_thread(self): - """Spawns a new thread. - - Splits the main program into two threads, one that runs the polling loop - which updates the client list, and one which gets the data. Also sets up - the machinery to deal with a kill call, in the case of a Ctrl-C or - similar signal the signal is intercepted by the _kill_handler function, - which cleans up the spawned thread before closing the main thread. - - Raises: - NameError: Raised if the polling thread already exists. - """ - - self.open() - if not self._poll_thread is None: - raise NameError("Polling thread already started") - self._poll_thread = threading.Thread(target=self._poll_loop, name="poll_" + self.address) - self._poll_thread.daemon = True - self._prev_kill[signal.SIGINT] = signal.signal(signal.SIGINT, self._kill_handler) - self._prev_kill[signal.SIGTERM] = signal.signal(signal.SIGTERM, self._kill_handler) - self._poll_true = True - self._poll_thread.start() - - def end_thread(self): - """Closes the spawned thread. - - Deals with cleaning up the spawned thread cleanly. First sets - _poll_true to false to indicate that the poll_loop should be exited, then - closes the spawned thread and removes it. - """ - - self._poll_true = False - if not self._poll_thread is None: - self._poll_thread.join() - self._poll_thread = None - self.close() diff --git a/tools/i-pi/ipi/tests/README b/tools/i-pi/ipi/tests/README deleted file mode 100644 index 029c87a726..0000000000 --- a/tools/i-pi/ipi/tests/README +++ /dev/null @@ -1,9 +0,0 @@ - -- Nosetests directory -- - - * This is the directory containing the tests that can be run with nosetests. - - * Files: - - common.py: Common helper functions for use in the tests. - - datest.py: Tests the dependency utility and some of the numpy - facilities. - - test_*.py: The actual tests for at least some of the code basis. diff --git a/tools/i-pi/ipi/tests/common.py b/tools/i-pi/ipi/tests/common.py deleted file mode 100644 index 3ffea431a1..0000000000 --- a/tools/i-pi/ipi/tests/common.py +++ /dev/null @@ -1,96 +0,0 @@ -"""Common helper functions for running the tests. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Functions: - local: Returns local folder of the tests directory. - -Classes: - TestSimulation: Can be used to test that a particular simulation - will run properly, given an input file and a driver code. -""" - -import glob -import os -import subprocess -import shutil -import tempfile - -def local(file=None): - """Returns local folder of the tests directory. - - Args: - - file: Append file to the local folder - """ - if file: - return os.sep.join(__file__.split(os.sep)[:-1]+[file]) - else: - return os.sep.join(__file__.split(os.sep)[:-1]) - -class TestSimulation(object): - """Simple class used to test various aspects of the simulation. - - Can be used to run an example given the location of an xml - input file and the location of a suitable driver code. - - Attributes: - finput: The name of the xml input file - folder_input: A string giving the directory the input file is held in. - fdriver: The location of a driver code. - cwd: Current working directory. - tmpdir: A temporary directory to run the simulation in. - """ - - def __init__(self, input, driver): - """Initializes TestSimulation. - - Args: - input: The name of the xml input file. - driver: The location of the driver code. - """ - - self.finput = input - self.folder_input = os.sep.join(input.split(os.sep)[:-1]) - self.fdriver = driver - self.cwd = os.getcwd() - self.tmpdir = tempfile.mkdtemp() - - # Copy needed files to tmpdir - for src in glob.glob("%s/*"%self.folder_input): - shutil.copy(src, self.tmpdir) - - os.chdir(self.tmpdir) - - def __del__(self): - """Cleans the temporary directory once the simulation is over.""" - - os.chdir(self.cwd) - shutil.rmtree(self.tmpdir) - - def run(self): - """Runs the simulation.""" - - # Run driver - p = subprocess.Popen("echo running %s"%self.fdriver, shell=True) - - # Start simulation - # TODO - print subprocess.check_output("ls", shell=True) - print subprocess.check_output("pwd", shell=True) - - # wait for driver to finish - p.wait() diff --git a/tools/i-pi/ipi/tests/datest.py b/tools/i-pi/ipi/tests/datest.py deleted file mode 100644 index aa608691ef..0000000000 --- a/tools/i-pi/ipi/tests/datest.py +++ /dev/null @@ -1,56 +0,0 @@ -"""Short test scripts. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Used to test the depend array view mechanism. -""" - -import sys -sys.path.append("../") -sys.path.append("../../") - -import utils.depend as dp -import numpy as np - -print "## Creation test" -a = dp.depend_array(name="a",value=np.zeros((2,2),float)) -b = dp.depend_array(name="b",value=np.zeros((2,2),float)) - -print "## Slicing test" -c = a[0] -print type(c) - -print "## Addition test" -c = a + b -print type(c) - -print "## Increment test" -c = np.zeros((2,2)) -c += a -print type(c) - -print "## Dot test" -c = np.dot(a,b) -print type(c) - -rdot = np.dot -def fdot(a,b): - return rdot(a,b).view(np.ndarray) -#np.dot=fdot - -print "## Dot-f test" -c = np.dot(a,b) diff --git a/tools/i-pi/ipi/tests/test.pos_0.pdb b/tools/i-pi/ipi/tests/test.pos_0.pdb deleted file mode 100644 index 426c470192..0000000000 --- a/tools/i-pi/ipi/tests/test.pos_0.pdb +++ /dev/null @@ -1,10 +0,0 @@ -CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 -ATOM 1 O 1 1 0.000 1.000 2.000 0.00 0.00 0 -ATOM 2 H 1 1 3.000 4.000 5.000 0.00 0.00 0 -ATOM 3 H 1 1 6.000 7.000 8.000 0.00 0.00 0 -END -CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 -ATOM 1 O 1 1 0.000 2.000 4.000 0.00 0.00 0 -ATOM 2 H 1 1 6.000 8.000 10.000 0.00 0.00 0 -ATOM 3 H 1 1 12.000 14.000 16.000 0.00 0.00 0 -END diff --git a/tools/i-pi/ipi/tests/test.pos_0.xyz b/tools/i-pi/ipi/tests/test.pos_0.xyz deleted file mode 100644 index 05ae14da54..0000000000 --- a/tools/i-pi/ipi/tests/test.pos_0.xyz +++ /dev/null @@ -1,10 +0,0 @@ -3 -# CELL(abcABC): 1.00000 1.00000 1.00000 90.00000 90.00000 90.00000 - O 0.00000e+00 1.00000e+00 2.00000e+00 - H 3.00000e+00 4.00000e+00 5.00000e+00 - H 6.00000e+00 7.00000e+00 8.00000e+00 -3 -# CELL(abcABC): 1.00000 1.00000 1.00000 90.00000 90.00000 90.00000 - O 0.00000e+00 2.00000e+00 4.00000e+00 - H 6.00000e+00 8.00000e+00 1.00000e+01 - H 1.20000e+01 1.40000e+01 1.60000e+01 diff --git a/tools/i-pi/ipi/tests/test_contraction.py b/tools/i-pi/ipi/tests/test_contraction.py deleted file mode 100644 index ad9556fbea..0000000000 --- a/tools/i-pi/ipi/tests/test_contraction.py +++ /dev/null @@ -1,127 +0,0 @@ -"""Tests ring polymer contraction. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -""" - -import sys -sys.path.append("../") -sys.path.append("../../") - -from ipi.utils import nmtransform -import numpy as np -from numpy.testing import assert_almost_equal as assert_equals - -def check_up_and_down_scaling(n, q): - """Check if q expanding and then contracting a ring polymer is a no-op. - - Args: - n: The number of beads in the scaled ring polymer. - q: The original position array. - """ - - rescale = nmtransform.nm_rescale(q.shape[0], n) - print "Initial position of the beads:" - print q, q.shape, (q.shape[0], n) - - # rescale up to the n beads - beads_n = rescale.b1tob2(q) - print "Upscaled to %d beads:"%n - print beads_n, beads_n.shape - - beads_final = rescale.b2tob1(beads_n) - print "Final position of the beads:" - print beads_final - - assert_equals(q, beads_final) - return beads_n - -def check_rpc_consistency(n, q): - """Check if q expanding and then contracting a ring polymer is a no-op. - - Args: - n: The number of beads in the scaled ring polymer. - q: The original position array. - """ - - rescale1 = nmtransform.nm_rescale(q.shape[0], n) - rescale2 = nmtransform.nm_rescale(n,q.shape[0]) - - beads_n=rescale1.b1tob2(q) - beads_1=rescale1.b2tob1(beads_n) - beads_2=rescale2.b1tob2(beads_n) - - assert_equals(beads_1, beads_2) - -def check_centroid_pos(n, q): - """Check if expanding and then contracting a ring polymer - maintains the centroid. - - Args: - n: The number of beads in the scaled ring polymer. - q: The original position array. - """ - - beads_big = check_up_and_down_scaling(n, q) - rescale_big = nmtransform.mk_rs_matrix(n, 1) - rescale_q = nmtransform.mk_rs_matrix(q.shape[0], 1) - - centroid_big = np.dot(rescale_big, beads_big) - centroid_q = np.dot(rescale_q, q) - - assert_equals(centroid_q, centroid_big) - -numbers_to_check = range(10, 56, 9) -def test_1_to_n(): - """One bead tests.""" - - for n in numbers_to_check: - q = np.array([[0.0,0.0,0.0, 1.0,0.0,0.0]]) - yield check_up_and_down_scaling, n, q - yield check_rpc_consistency, n, q - yield check_centroid_pos, n, q - -def test_2_to_n(): - """Two bead tests.""" - - for n in numbers_to_check: - q = np.array([[0.0,0.0,0.0, 1.0,0.0,0.0], - [0.0,0.1,0.0, 1.0,0.1,0.0]]) - yield check_up_and_down_scaling, n, q - yield check_rpc_consistency, n, q - yield check_centroid_pos, n, q - -def test_3_to_n(): - """Three bead tests.""" - - for n in numbers_to_check: - q = np.array([[0.0, 0.0,0.0, 1.0, 0.0,0.0], - [0.0, 0.1,0.0, 1.0, 0.1,0.0], - [0.0,-0.1,0.0, 1.0,-0.1,0.0]]) - yield check_up_and_down_scaling, n, q - yield check_rpc_consistency, n, q - yield check_centroid_pos, n, q - -def test_4_to_n(): - """Four bead tests.""" - - for n in numbers_to_check: - q = np.array([[0.0, 0.0,0.0, 1.0, 0.0,0.0], - [0.0, 0.1,0.0, 1.0, 0.1,0.0], - [0.0, 0.2,0.0, 1.0, 0.2,0.0], - [0.0,-0.1,0.0, 1.0,-0.1,0.0]]) - yield check_up_and_down_scaling, n, q - yield check_rpc_consistency, n, q - yield check_centroid_pos, n, q diff --git a/tools/i-pi/ipi/tests/test_io.py b/tools/i-pi/ipi/tests/test_io.py deleted file mode 100644 index 53fad808f7..0000000000 --- a/tools/i-pi/ipi/tests/test_io.py +++ /dev/null @@ -1,96 +0,0 @@ -"""Deals with testing the io system. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -Note that this will only run if you have Python version 2.5 or later. -Otherwise, replace all the with statements with f = filestream. -""" - -import sys -sys.path.append("../") -sys.path.append("../../") - -import filecmp -import os, sys -import numpy as np -from numpy.testing import assert_equal -from common import local - -from ipi.engine.cell import Cell - -from ipi.utils.io import io_xyz -from ipi.utils.io import io_pdb - -pos = np.array([i for i in range(3*3)]) - -def test_read_xyz(): - """Tests that xyz files are read correctly.""" - - with open(local("test.pos_0.xyz"), "r") as f: - atoms = io_xyz.read_xyz(f) - assert(len(atoms) == 3) - assert_equal(pos, atoms.q) - -def test_iter_xyz(): - """Tests that xyz files with multiple frames are read correctly.""" - - with open(local("test.pos_0.xyz"), "r") as f: - for num, atoms in enumerate(io_xyz.iter_xyz(f)): - assert(len(atoms) == 3) - assert_equal(pos*(num+1), atoms.q) - -def test_read_pdb(): - """Tests that pdb files are read correctly.""" - - with open(local("test.pos_0.pdb"), "r") as f: - atoms, cell = io_pdb.read_pdb(f) - assert(len(atoms) == 3) - assert_equal(pos, atoms.q) - # TODO: test cell - -def test_iter_pdb(): - """Tests that pdb files with multiple frames are read correctly.""" - - with open(local("test.pos_0.pdb"), "r") as f: - for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)): - assert(len(atoms) == 3) - assert_equal(pos*(num+1), atoms.q) - -def test_print_pdb(): - """Tests that pdb files are printed correctly.""" - - with open(local("test.pos_0.pdb"), "r") as f: - with open(local("test.pos_1.xyz"), "w") as out: - for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)): - assert(len(atoms) == 3) - assert_equal(pos*(num+1), atoms.q) - io_xyz.print_xyz(atoms, Cell(h=np.identity(3, float)), filedesc=out) - - assert(filecmp.cmp(local("test.pos_0.xyz"), local("test.pos_1.xyz"))) - os.unlink(local("test.pos_1.xyz")) - -def test_print_xyz(): - """Tests that xyz files are printed correctly.""" - - with open(local("test.pos_0.pdb"), "r") as f: - with open(local("test.pos_1.pdb"), "w") as out: - for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)): - assert(len(atoms) == 3) - assert_equal(pos*(num+1), atoms.q) - io_pdb.print_pdb(atoms, Cell(h=np.identity(3, float)), filedesc=out) - - assert(filecmp.cmp(local("test.pos_0.pdb"), local("test.pos_1.pdb"))) - os.unlink(local("test.pos_1.pdb")) diff --git a/tools/i-pi/ipi/tests/test_runs.py b/tools/i-pi/ipi/tests/test_runs.py deleted file mode 100644 index 940f2c9ed9..0000000000 --- a/tools/i-pi/ipi/tests/test_runs.py +++ /dev/null @@ -1,24 +0,0 @@ -"""Tests that the Lennard-Jones test case works properly. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -""" - -from common import TestSimulation - -def test_lj_gas(): - ts = TestSimulation(input="../../test/lj/gas/input.xml", driver="../../drivers/driver.x") - ts.run() - # Test properties (e.g. latest positions/temperature etc) diff --git a/tools/i-pi/ipi/utils/README b/tools/i-pi/ipi/utils/README deleted file mode 100644 index edc629f081..0000000000 --- a/tools/i-pi/ipi/utils/README +++ /dev/null @@ -1,21 +0,0 @@ - -- Utility functions directory -- - - * This is the directory containing functions that are used in the other - modules in the code. - - * Files: - - depend.py: Deals with the dependency detection, value caching and - automatic updating of variables. - - inputvalue.py: Contains the base classes used in reading the xml - input file, and creating the restart file. - - mathtools.py: Contains the algorithms used in various parts of the code. - - messages.py: Contains the classes to generate info and warning messages - to standard output during the simulation. - - nmtransform.py: Contains the algorithms that deal with the normal mode - and ring polymer contraction transformations. - - prng.py: Deals with random number generation. - - softexit: Contains the classes to deal with calls for a soft exit. - - units.py: Holds atomic masses, fundamental constants, and unit conversions. - - * Directories: - - io: Holds the modules that deal with reading and outputting files. diff --git a/tools/i-pi/ipi/utils/__init__.py b/tools/i-pi/ipi/utils/__init__.py deleted file mode 100644 index 6fa5c8e00c..0000000000 --- a/tools/i-pi/ipi/utils/__init__.py +++ /dev/null @@ -1 +0,0 @@ -__all__ = ["depend", "units", "mathtools", "prng" , "inputvalue", 'nmtransform', 'messages', 'softexit'] diff --git a/tools/i-pi/ipi/utils/depend.py b/tools/i-pi/ipi/utils/depend.py deleted file mode 100644 index a4da91b47b..0000000000 --- a/tools/i-pi/ipi/utils/depend.py +++ /dev/null @@ -1,768 +0,0 @@ -"""Contains the classes that are used to define the dependency network. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -The classes defined in this module overload the standard __get__ and __set__ -routines of the numpy ndarray class and standard library object class so that -they automatically keep track of whether anything they depend on has been -altered, and so only recalculate their value when necessary. - -Basic quantities that depend on nothing else can be manually altered in the -usual way, all other quantities are updated automatically and cannot be changed -directly. - -The exceptions to this are synchronized properties, which are in effect -multiple basic quantities all related to each other, for example the bead and -normal mode representations of the positions and momenta. In this case any of -the representations can be set manually, and all the other representations -must keep in step. - -For a more detailed discussion, see the reference manual. - -Classes: - depend_base: Base depend class with the generic methods and attributes. - depend_value: Depend class for scalar objects. - depend_array: Depend class for arrays. - synchronizer: Class that holds the different objects that are related to each - other and keeps track of which property has been set manually. - dobject: An extension of the standard library object that overloads - __getattribute__ and __setattribute__, so that we can use the - standard syntax for setting and getting the depend object, - i.e. foo = value, not foo.set(value). - -Functions: - dget: Gets the dependencies of a depend object. - dset: Sets the dependencies of a depend object. - depstrip: Used on a depend_array object, to access its value without - needing the depend machinery, and so much more quickly. Must not be used - if the value of the array is to be changed. - depcopy: Copies the dependencies from one object to another - deppipe: Used to make two objects be synchronized to the same value. -""" - -__all__ = ['depend_base', 'depend_value', 'depend_array', 'synchronizer', - 'dobject', 'dget', 'dset', 'depstrip', 'depcopy', 'deppipe'] - -import numpy as np -from ipi.utils.messages import verbosity, warning - -class synchronizer(object): - """Class to implement synched objects. - - Holds the objects used to keep two or more objects in step with each other. - This is shared between all the synched objects. - - Attributes: - synched: A dictionary containing all the synched objects, of the form - {"name": depend object}. - manual: A string containing the name of the object being manually changed. - """ - - def __init__(self, deps=None): - """Initializes synchronizer. - - Args: - deps: Optional dictionary giving the synched objects of the form - {"name": depend object}. - """ - - if deps is None: - self.synced = dict() - else: - self.synced = deps - - self.manual = None - - -#TODO put some error checks in the init to make sure that the object is initialized from consistent synchro and func states -class depend_base(object): - """Base class for dependency handling. - - Builds the majority of the machinery required for the different depend - objects. Contains functions to add and remove dependencies, the tainting - mechanism by which information about which objects have been updated is - passed around the dependency network, and the manual and automatic update - functions to check that depend objects with functions are not manually - updated and that synchronized objects are kept in step with the one manually - changed. - - Attributes: - _tainted: An array containing one boolean, which is True if one of the - dependencies has been changed since the last time the value was - cached. - _func: A function name giving the method of calculating the value, - if required. None otherwise. - _name: The name of the depend base object. - _synchro: A synchronizer object to deal with synched objects, if - required. None otherwise. - _dependants: A list containing all objects dependent on the self. - """ - - def __init__(self, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None): - """Initializes depend_base. - - An unusual initialization routine, as it has to be able to deal with the - depend array mechanism for returning slices as new depend arrays. - - This is the reason for the penultimate if statement; it automatically - taints objects created from scratch but does nothing to slices which are - not tainted. - - Also, the last if statement makes sure that if a synchronized property is - sliced, this initialization routine does not automatically set it to the - manually updated property. - - Args: - name: A string giving the name of self. - tainted: An optional array containing one boolean which is True if one - of the dependencies has been changed. - func: An optional argument that can be specified either by a function - name, or for synchronized values a dictionary of the form - {"name": function name}; where "name" is one of the other - synched objects and function name is the name of a function to - get the object "name" from self. - synchro: An optional synchronizer object. - dependants: An optional list containing objects that depend on self. - dependencies: An optional list containing objects that self - depends upon. - """ - - self._dependants = [] - if tainted is None: - tainted = np.array([True],bool) - if dependants is None: - dependants = [] - if dependencies is None: - dependencies = [] - self._tainted = tainted - self._func = func - self._name = name - - self.add_synchro(synchro) - - for item in dependencies: - item.add_dependant(self, tainted) - - self._dependants = dependants - - # Don't taint self if the object is a primitive one. However, do propagate tainting to dependants if required. - if (tainted): - if self._func is None: - self.taint(taintme=False) - else: - self.taint(taintme=tainted) - - - def add_synchro(self, synchro=None): - """ Links depend object to a synchronizer. """ - - self._synchro = synchro - if not self._synchro is None and not self._name in self._synchro.synced: - self._synchro.synced[self._name] = self - self._synchro.manual = self._name - - - def add_dependant(self, newdep, tainted=True): - """Adds a dependant property. - - Args: - newdep: The depend object to be added to the dependency list. - tainted: A boolean that decides whether newdep should be tainted. - True by default. - """ - - self._dependants.append(newdep) - if tainted: - newdep.taint(taintme=True) - - def add_dependency(self, newdep, tainted=True): - """Adds a dependency. - - Args: - newdep: The depend object self now depends upon. - tainted: A boolean that decides whether self should - be tainted. True by default. - """ - - newdep._dependants.append(self) - if tainted: - self.taint(taintme=True) - - def taint(self,taintme=True): - """Recursively sets tainted flag on dependent objects. - - The main function dealing with the dependencies. Taints all objects - further down the dependency tree until either all objects have been - tainted, or it reaches only objects that have already been tainted. Note - that in the case of a dependency loop the initial setting of _tainted to - True prevents an infinite loop occurring. - - Also, in the case of a synchro object, the manually set quantity is not - tainted, as it is assumed that synchro objects only depend on each other. - - Args: - taintme: A boolean giving whether self should be tainted at the end. - True by default. - """ - - self._tainted[:] = True - for item in self._dependants: - if (not item._tainted[0]): - item.taint() - if not self._synchro is None: - for v in self._synchro.synced.values(): - if (not v._tainted[0]) and (not v is self): - v.taint(taintme=True) - self._tainted[:] = (taintme and (not self._name == self._synchro.manual)) - else: - self._tainted[:] = taintme - - def tainted(self): - """Returns tainted flag.""" - - return self._tainted[0] - - def update_auto(self): - """Automatic update routine. - - Updates the value when get has been called and self has been tainted. - """ - - if not self._synchro is None: - if (not self._name == self._synchro.manual): - self.set(self._func[self._synchro.manual](), manual=False) - else: - warning(self._name + " probably shouldn't be tainted (synchro)", verbosity.low) - elif not self._func is None: - self.set(self._func(), manual=False) - else: - warning(self._name + " probably shouldn't be tainted (value)", verbosity.low) - - def update_man(self): - """Manual update routine. - - Updates the value when the value has been manually set. Also raises an - exception if a calculated quantity has been manually set. Also starts the - tainting routine. - - Raises: - NameError: If a calculated quantity has been manually set. - """ - - if not self._synchro is None: - self._synchro.manual = self._name - for v in self._synchro.synced.values(): - v.taint(taintme=True) - self._tainted[:] = False - elif not self._func is None: - raise NameError("Cannot set manually the value of the automatically-computed property <" + self._name + ">") - else: - self.taint(taintme=False) - - def set(self, value, manual=False): - """Dummy setting routine.""" - - pass - - def get(self): - """Dummy getting routine.""" - - pass - -class depend_value(depend_base): - """Scalar class for dependency handling. - - Attributes: - _value: The value associated with self. - """ - - def __init__(self, name, value=None, synchro=None, func=None, dependants=None, dependencies=None, tainted=None): - """Initializes depend_value. - - Args: - name: A string giving the name of self. - value: The value of the object. Optional. - tainted: An optional array giving the tainted flag. Default is [True]. - func: An optional argument that can be specified either by a function - name, or for synchronized values a dictionary of the form - {"name": function name}; where "name" is one of the other - synched objects and function name is the name of a function to - get the object "name" from self. - synchro: An optional synchronizer object. - dependants: An optional list containing objects that depend on self. - dependencies: An optional list containing objects that self - depends upon. - """ - - self._value = value - super(depend_value,self).__init__(name, synchro, func, dependants, dependencies, tainted) - - def get(self): - """Returns value, after recalculating if necessary. - - Overwrites the standard method of getting value, so that value - is recalculated if tainted. - """ - - if self._tainted[0]: - self.update_auto() - self.taint(taintme=False) - - return self._value - - def __get__(self, instance, owner): - """Overwrites standard get function.""" - - return self.get() - - def set(self, value, manual=True): - """Alters value and taints dependencies. - - Overwrites the standard method of setting value, so that dependent - quantities are tainted, and so we check that computed quantities are not - manually updated. - """ - - self._value = value - self.taint(taintme=False) - if (manual): - self.update_man() - - def __set__(self, instance, value): - """Overwrites standard set function.""" - - self.set(value) - - -class depend_array(np.ndarray, depend_base): - """Array class for dependency handling. - - Differs from depend_value as arrays handle getting items in a different - way to scalar quantities, and as there needs to be support for slicing an - array. Initialisation is also done in a different way for ndarrays. - - Attributes: - _bval: The base deparray storage space. Equal to depstrip(self) unless - self is a slice. - """ - - def __new__(cls, value, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None, base=None): - """Creates a new array from a template. - - Called whenever a new instance of depend_array is created. Casts the - array base into an appropriate form before passing it to - __array_finalize__(). - - Args: - See __init__(). - """ - - obj = np.asarray(value).view(cls) - return obj - - def __init__(self, value, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None, base=None): - """Initializes depend_array. - - Note that this is only called when a new array is created by an - explicit constructor. - - Args: - name: A string giving the name of self. - value: The (numpy) array to serve as the memory base. - tainted: An optional array giving the tainted flag. Default is [True]. - func: An optional argument that can be specified either by a function - name, or for synchronized values a dictionary of the form - {"name": function name}; where "name" is one of the other - synched objects and function name is the name of a function to - get the object "name" from self. - synchro: An optional synchronizer object. - dependants: An optional list containing objects that depend on self. - dependencies: An optional list containing objects that self - depends upon. - """ - - super(depend_array,self).__init__(name, synchro, func, dependants, dependencies, tainted) - - if base is None: - self._bval = value - else: - self._bval = base - - def copy(self, order='C', maskna=None): - """Wrapper for numpy copy mechanism.""" - - # Sets a flag and hands control to the numpy copy - self._fcopy = True - return super(depend_array,self).copy(order) - - def __array_finalize__(self, obj): - """Deals with properly creating some arrays. - - In the case where a function acting on a depend array returns a ndarray, - this casts it into the correct form and gives it the - depend machinery for other methods to be able to act upon it. New - depend_arrays will next be passed to __init__ ()to be properly - initialized, but some ways of creating arrays do not call __new__() or - __init__(), so need to be initialized. - """ - - depend_base.__init__(self, name="") - - if type(obj) is depend_array: - # We are in a view cast or in new from template. Unfortunately - # there is no sure way to tell (or so it seems). Hence we need to - # handle special cases, and hope we are in a view cast otherwise. - if hasattr(obj,"_fcopy"): - del(obj._fcopy) # removes the "copy flag" - self._bval = depstrip(self) - else: - # Assumes we are in view cast, so copy over the attributes from the - # parent object. Typical case: when transpose is performed as a - # view. - super(depend_array,self).__init__(obj._name, obj._synchro, obj._func, obj._dependants, None, obj._tainted) - self._bval = obj._bval - else: - # Most likely we came here on the way to init. - # Just sets a defaults for safety - self._bval = depstrip(self) - - - def __array_prepare__(self, arr, context=None): - """Prepare output array for ufunc. - - Depending on the context we try to understand if we are doing an - in-place operation (in which case we want to keep the return value a - deparray) or we are generating a new array as a result of the ufunc. - In this case there is no way to know if dependencies should be copied, - so we strip and return a ndarray. - """ - - if context is None or len(context) < 2 or not type(context[0]) is np.ufunc: - # It is not clear what we should do. If in doubt, strip dependencies. - return np.ndarray.__array_prepare__(self.view(np.ndarray),arr.view(np.ndarray),context) - elif len(context[1]) > context[0].nin and context[0].nout > 0: - # We are being called by a ufunc with a output argument, which is being - # actually used. Most likely, something like an increment, - # so we pass on a deparray - return super(depend_array,self).__array_prepare__(arr,context) - else: - # Apparently we are generating a new array. - # We have no way of knowing its - # dependencies, so we'd better return a ndarray view! - return np.ndarray.__array_prepare__(self.view(np.ndarray),arr.view(np.ndarray),context) - - def __array_wrap__(self, arr, context=None): - """ Wraps up output array from ufunc. - - See docstring of __array_prepare__(). - """ - - if context is None or len(context) < 2 or not type(context[0]) is np.ufunc: - return np.ndarray.__array_wrap__(self.view(np.ndarray),arr.view(np.ndarray),context) - elif len(context[1]) > context[0].nin and context[0].nout > 0: - return super(depend_array,self).__array_wrap__(arr,context) - else: - return np.ndarray.__array_wrap__(self.view(np.ndarray),arr.view(np.ndarray),context) - - # whenever possible in compound operations just return a regular ndarray - __array_priority__ = -1.0 - - def reshape(self, newshape): - """Changes the shape of the base array. - - Args: - newshape: A tuple giving the desired shape of the new array. - - Returns: - A depend_array with the dimensions given by newshape. - """ - - return depend_array(depstrip(self).reshape(newshape), name=self._name, synchro=self._synchro, func=self._func, dependants=self._dependants, tainted=self._tainted, base=self._bval) - - def flatten(self): - """Makes the base array one dimensional. - - Returns: - A flattened array. - """ - - return self.reshape(self.size) - - @staticmethod - def __scalarindex(index, depth=1): - """Checks if an index points at a scalar value. - - Used so that looking up one item in an array returns a scalar, whereas - looking up a slice of the array returns a new array with the same - dependencies as the original, so that changing the slice also taints - the global array. - - Arguments: - index: the index to be checked. - depth: the rank of the array which is being accessed. Default value - is 1. - - Returns: - A logical stating whether a __get__ instruction based - on index would return a scalar. - """ - - if (np.isscalar(index) and depth <= 1): - return True - elif (isinstance(index, tuple) and len(index)==depth): - #if the index is a tuple check it does not contain slices - for i in index: - if not np.isscalar(i): return False - return True - return False - - def __getitem__(self,index): - """Returns value[index], after recalculating if necessary. - - Overwrites the standard method of getting value, so that value - is recalculated if tainted. Scalar slices are returned as an ndarray, - so without depend machinery. If you need a "scalar depend" which - behaves as a slice, just create a 1x1 matrix, e.g b=a(7,1:2) - - Args: - index: A slice variable giving the appropriate slice to be read. - """ - - if self._tainted[0]: - self.update_auto() - self.taint(taintme=False) - - if (self.__scalarindex(index, self.ndim)): - return depstrip(self)[index] - else: - return depend_array(depstrip(self)[index], name=self._name, synchro=self._synchro, func=self._func, dependants=self._dependants, tainted=self._tainted, base=self._bval) - - - def __getslice__(self,i,j): - """Overwrites standard get function.""" - - return self.__getitem__(slice(i,j,None)) - - def get(self): - """Alternative to standard get function.""" - - return self.__get__(slice(None,None,None)) - - def __get__(self, instance, owner): - """Overwrites standard get function.""" - - # It is worth duplicating this code that is also used in __getitem__ as this - # is called most of the time, and we avoid creating a load of copies pointing to the same depend_array - - if self._tainted[0]: - self.update_auto() - self.taint(taintme=False) - - return self - - def __setitem__(self,index,value,manual=True): - """Alters value[index] and taints dependencies. - - Overwrites the standard method of setting value, so that dependent - quantities are tainted, and so we check that computed quantities are not - manually updated. - - Args: - index: A slice variable giving the appropriate slice to be read. - value: The new value of the slice. - manual: Optional boolean giving whether the value has been changed - manually. True by default. - """ - - self.taint(taintme=False) - if manual: - depstrip(self)[index] = value - self.update_man() - elif index == slice(None,None,None): - self._bval[index] = value - else: - raise IndexError("Automatically computed arrays should span the whole parent") - - def __setslice__(self,i,j,value): - """Overwrites standard set function.""" - - return self.__setitem__(slice(i,j),value) - - def set(self, value, manual=True): - """Alterative to standard set function. - - Args: - See __setitem__(). - """ - - self.__setitem__(slice(None,None),value=value,manual=manual) - - def __set__(self, instance, value): - """Overwrites standard set function.""" - - self.__setitem__(slice(None,None),value=value) - - -# np.dot and other numpy.linalg functions have the nasty habit to -# view cast to generate the output. Since we don't want to pass on -# dependencies to the result of these functions, and we can't use -# the ufunc mechanism to demote the class type to ndarray, we must -# overwrite np.dot and other similar functions. -# BEGINS NUMPY FUNCTIONS OVERRIDE -# ** np.dot -__dp_dot = np.dot - -def dep_dot(da, db): - a=depstrip(da) - b=depstrip(db) - - return __dp_dot(da,db) - -np.dot = dep_dot -# ENDS NUMPY FUNCTIONS OVERRIDE - -def dget(obj,member): - """Takes an object and retrieves one of its attributes. - - Note that this is necessary as calling it in the standard way calls the - __get__() function of member. - - Args: - obj: A user defined class. - member: A string giving the name of an attribute of obj. - - Exceptions: - KeyError: If member is not an attribute of obj. - - Returns: - obj.member. - """ - - return obj.__dict__[member] - -def dset(obj,member,value,name=None): - """Takes an object and sets one of its attributes. - - Necessary for editing any depend object, and should be used for - initialising them as well, as often initialization occurs more than once, - with the second time effectively being an edit. - - Args: - obj: A user defined class. - member: A string giving the name of an attribute of obj. - value: The new value of member. - name: New name of member. - - Exceptions: - KeyError: If member is not an attribute of obj. - """ - - obj.__dict__[member] = value - if not name is None: - obj.__dict__[member]._name = name - -def depstrip(da): - """Removes dependencies from a depend_array. - - Takes a depend_array and returns its value as a ndarray, effectively - stripping the dependencies from the ndarray. This speeds up a lot of - calculations involving these arrays. Must only be used if the value of the - array is not going to be changed. - - Args: - deparray: A depend_array. - - Returns: - A ndarray with the same value as deparray. - """ - - if isinstance(da, depend_array): # only bother to strip dependencies if the array actually IS a depend_array - #if da._tainted[0]: - # print "!!! WARNING depstrip called on tainted array WARNING !!!!!" # I think we can safely assume that when we call depstrip the array has been cleared already but I am not 100% sure so better check - and in case raise the update - return da.view(np.ndarray) - else: - return da - -def deppipe(objfrom,memberfrom,objto,memberto): - """Synchronizes two depend objects. - - Takes two depend objects, and makes one of them depend on the other in such - a way that both keep the same value. Used for attributes such as temperature - that are used in many different modules, and so need different depend objects - in each, but which should all have the same value. - - Args: - objfrom: An object containing memberfrom. - memberfrom: The base depend object. - objto: An object containing memberto. - memberto: The depend object that should be equal to memberfrom. - """ - - dfrom = dget(objfrom,memberfrom) - dto = dget(objto,memberto) - dto._func = lambda : dfrom.get() - dto.add_dependency(dfrom) - -def depcopy(objfrom,memberfrom,objto,memberto): - """Copies the dependencies of one depend object to another. - - Args: - See deppipe. - """ - dfrom = dget(objfrom,memberfrom) - dto = dget(objto,memberto) - dto._dependants = dfrom._dependants - dto._synchro = dfrom._synchro - dto.add_synchro(dfrom._synchro) - dto._tainted = dfrom._tainted - dto._func = dfrom._func - if hasattr(dfrom,"_bval"): - dto._bval = dfrom._bval - - -class dobject(object): - """Class that allows standard notation to be used for depend objects.""" - - def __getattribute__(self, name): - """Overwrites standard __getattribute__(). - - This changes the standard __getattribute__() function of any class that - subclasses dobject such that depend objects are called with their own - __get__() function rather than the standard one. - """ - - value = object.__getattribute__(self, name) - if hasattr(value, '__get__'): - value = value.__get__(self, self.__class__) - return value - - def __setattr__(self, name, value): - """Overwrites standard __setattribute__(). - - This changes the standard __setattribute__() function of any class that - subclasses dobject such that depend objects are called with their own - __set__() function rather than the standard one. - """ - - try: - obj = object.__getattribute__(self, name) - except AttributeError: - pass - else: - if hasattr(obj, '__set__'): - return obj.__set__(self, value) - return object.__setattr__(self, name, value) diff --git a/tools/i-pi/ipi/utils/inputvalue.py b/tools/i-pi/ipi/utils/inputvalue.py deleted file mode 100644 index 35b2945910..0000000000 --- a/tools/i-pi/ipi/utils/inputvalue.py +++ /dev/null @@ -1,968 +0,0 @@ -"""Contains the classes that are used to write to and read from restart files. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -The classes defined in this module define the base functions which parse the -data in the restart files. Each restart object defined has a fields and an -attributes dictionary, which are filled with the tags and attributes that -are allowed to be present, along with their default values and data type. - -These are then filled with the data from the xml file when the program -is initialized, and are filled by the values calculated in the program which -are then output to the checkpoint file when a restart file is required. - -Also deals with checking for user input errors, of the form of misspelt tags, -bad data types, and failure to input required fields. - -Classes: - Input: Base input class. - InputAttribute: Input class for attribute data. - InputValue: Input class for scalar objects. - InputArray: Input class for arrays. - input_default: Class used to create mutable objects dynamically. -""" - -__all__ = ['Input', 'InputValue', 'InputAttribute', 'InputArray', 'input_default'] - -import numpy as np -from copy import copy -from ipi.utils.io.io_xml import * -from ipi.utils.units import unit_to_internal, unit_to_user - - - -class input_default(object): - """Contains information required to dynamically create objects - - Used so that we can define mutable default input values to various tags - without the usual trouble with having a class object that is also mutable, - namely that all members of that class share the same mutable object, so that - changing it for one instance of that class changes it for all others. It - does this by not holding the mutable default value, but instead the - information to create it, so that each instance of an input class can - have a separate instance of the default value. - - Attributes: - type: Either a class type or function call from which to create the - default object. - args: A tuple giving positional arguments to be passed to the function. - kwargs: A dictionary giving key word arguments to be passed to the - function. - """ - - def __init__(self, factory, args = None, kwargs = None): - """Initializes input_default. - - Args: - type: The class or function to be used to create the default object. - args: A tuple giving the arguments to be used to initialize - the default value. - kwargs: A dictionary giving the key word arguments to be used - to initialize the default value. - """ - - if args is None: - args = () - if kwargs is None: - kwargs = {} - # a default will be generated by factory(*args, **kwargs) - # *args unpacks the tuple, and is used for positional arguments - # **kwargs unpacks the dictionary, and is used for keyword arguments - self.factory = factory - self.args = args - self.kwargs = kwargs - - -class Input(object): - """Base class for input handling. - - Has the generic methods for dealing with the xml input file. Parses the input - data, outputs the output data, and deals with storing and returning the - data obtained during the simulation for the restart files. - - Attributes: - fields: A dictionary holding the possible tags contained within the - tags for this restart object, which are then turned into the objects - held by the object given by this restart object. The dictionary is - of the form: - {"tag name": ( Input_object, - {"default": default value, - "dtype": data type, - "options": list of available options, - "help": help string, - "dimension": dimensionality of data}), ... }. - dynamic: A dictionary holding the possible tags contained within the - tags for this restart object, which are then turned into the objects - held by the object given by this restart object. These are used for - tags that can be specified more than once. - The dictionary is of the form: - {"tag name": ( Input_object, - {"default": default value, - "dtype": data type, - "options": list of available options, - "help": help string, - "dimension": dimensionality of data}), ... }. - attribs: A dictionary holding the attribute data for the tag for this - restart object. The dictionary is of the form: - {"attribute name": ( Input_object, - {"default": default value, - "dtype": data type, - "options": list of available options, - "help": help string, - "dimension": dimensionality of data}), ... }. - extra: A list of tuples ( "name", Input_object ) that may be used to - extend the capabilities of the class, i.e. to hold several instances of - a field with the same name, or to hold variable numbers of elements. - default_help: The default help string. - _help: The help string of the object. Defaults to default_help. - _default: Optional default value. - _optional: A bool giving whether the field is a required field. - _explicit: A bool giving whether the field has been specified by the user. - _text: All text written between the tags of the object. - _label: A label to be used to identify the class in the latex user manual. - _defwrite: The string which would be output if the class has its default - value. - """ - - fields = {} - attribs = {} - dynamic = {} - - default_help = "Generic input value" - default_label = "" #used as a way to reference a particular class using - #hyperlinks - - def __init__(self, help=None, default=None): - """Initializes Input. - - Automatically adds all the fields and attribs names to the input object's - dictionary, then initializes all the appropriate input objects - as the corresponding values. - - Args: - help: A help string. - default: A default value. - """ - - # list of extended (dynamic) fields - self.extra = [] - - if help is None: - self._help = self.default_help - else: - self._help = help - - if isinstance(default,input_default): - #creates default dynamically if a suitable template is defined. - self._default = default.factory(*default.args, **default.kwargs) - else: - self._default = default - - self._optional = not (self._default is None) - - self._label = self.default_label - - #For each tag name in the fields and attribs dictionaries, - #creates and object of the type given, expanding the dictionary to give - #the arguments of the __init__() function, then adds it to the input - #object's dictionary. - for f, v in self.fields.iteritems(): - self.__dict__[f] = v[0](**v[1]) - - for a, v in self.attribs.iteritems(): - self.__dict__[a] = v[0](**v[1]) - - self.set_default() - - self._text = "" - - # stores what we would write out if the default was set - self._defwrite = "" - if not self._default is None: - self._defwrite = self.write(name="%%NAME%%") - - def set_default(self): - """Sets the default value of the object.""" - - if not self._default is None: - self.store(self._default) - elif not hasattr(self, 'value'): - self.value = None #Makes sure we don't get exceptions when we - #look for self.value - - self._explicit = False #Since the value was not set by the user - - def store(self, value=None): - """Dummy function for storing data.""" - - self._explicit = True - pass - - def fetch(self): - """Dummy function to retrieve data.""" - - self.check() - pass - - def check(self): - """Base function to check for input errors. - - Raises: - ValueError: Raised if the user does not specify a required field. - """ - - if not (self._explicit or self._optional): - raise ValueError("Uninitialized Input value of type " + type(self).__name__) - - def extend(self, name, xml): - """ Dynamically add elements to the 'extra' list. - - Picks from one of the templates in the self.dynamic dictionary, then - parses. - - Args: - name: The tag name of the dynamically stored tag. - xml: The xml_node object used to parse the data stored in the tags. - """ - - newfield = self.dynamic[name][0](**self.dynamic[name][1]) - newfield.parse(xml) - self.extra.append((name,newfield)) - - def write(self, name="", indent="", text="\n"): - """Writes data in xml file format. - - Writes the tag, attributes, data and closing tag appropriate to the - particular fields and attribs data. Writes in a recursive manner, so - that objects contained in the fields dictionary have their write function - called, so that their tags are written between the start and end tags - of this object, as is required for the xml format. - - This also adds an indent to the lower levels of the xml hierarchy, - so that it is easy to see which tags contain other tags. - - Args: - name: An optional string giving the tag name. Defaults to "". - indent: An optional string giving the string to be added to the start - of the line, so usually a number of tabs. Defaults to "". - text: Additional text to be output between the tags. - - Returns: - A string giving all the data contained in the fields and attribs - dictionaries, in the appropriate xml format. - """ - - rstr = indent + "<" + name; - for a in self.attribs: - # only write out attributes that are not defaults - # have a very simple way to check whether they actually add something: - # we compare with the string that would be output if the argument was set - # to its default - defstr = self.__dict__[a]._defwrite.replace("%%NAME%%",a) - outstr = self.__dict__[a].write(name=a) - if outstr != defstr: - rstr += " " + outstr - rstr += ">" - rstr += text - for f in self.fields: - #only write out fields that are not defaults - - defstr = self.__dict__[f]._defwrite.replace("%%NAME%%",f) - if defstr != self.__dict__[f].write(f): # here we must compute the write string twice not to be confused by indents. - rstr += self.__dict__[f].write(f, " " + indent) - - for (f,v) in self.extra: - # also write out extended (dynamic) fields if present - rstr += v.write(f, " " + indent) - - if text.find('\n') >= 0: - rstr += indent + "\n" - else: - rstr += "\n" - return rstr - - def parse(self, xml=None, text=""): - """Parses an xml file. - - Uses the xml_node class defined in io_xml to read all the information - contained within the root tags, and uses it to give values for the attribs - and fields data recursively. It does this by giving all the data between - the appropriate field tag to the appropriate field restart object as a - string, and the appropriate attribute data to the appropriate attribs - restart object as a string. These data are then parsed by these objects - until all the information is read, or an input error is found. - - Args: - xml: An xml_node object containing all the data for the parent - tag. - text: The data held between the start and end tags. - - Raises: - NameError: Raised if one of the tags in the xml input file is - incorrect. - ValueError: Raised if the user does not specify a required field. - """ - - # before starting, sets everything to its default -- if a default is set! - for a in self.attribs: - self.__dict__[a].set_default() - for f in self.fields: - self.__dict__[f].set_default() - - self.extra = [] - self._explicit = True - if xml is None: - self._text = text - else: - for a, v in xml.attribs.iteritems(): - if a in self.attribs: - self.__dict__[a].parse(text=v) - elif a == "_text": - pass - else: - raise NameError("Attribute name '" + a + "' is not a recognized property of '" + xml.name + "' objects") - - for (f, v) in xml.fields: #reads all field and dynamic data. - if f in self.fields: - self.__dict__[f].parse(xml=v) - elif f == "_text": - self._text = v - elif f in self.dynamic: - self.extend(f, v) - else: - raise NameError("Tag name '" + f + "' is not a recognized property of '" + xml.name + "' objects") - - #checks for missing arguments. - for a in self.attribs: - va = self.__dict__[a] - if not (va._explicit or va._optional): - raise ValueError("Attribute name '" + a + "' is mandatory and was not found in the input for the property " + xml.name) - for f in self.fields: - vf = self.__dict__[f] - if not (vf._explicit or vf._optional): - raise ValueError("Field name '" + f + "' is mandatory and was not found in the input for the property " + xml.name) - - def detail_str(self): - """Prints out the supplementary information about a particular input class. - - Used to print out the dimensions, default value, possible options and data - type of an input value to the LaTeX helf file. - """ - - xstr = "" - if hasattr(self, '_dimension') and self._dimension != "undefined": #gives dimension - xstr += "dimension: " + self._dimension + "; " - - if self._default != None and issubclass(self.__class__, InputAttribute): - #We only print out the default if it has a well defined value. - #For classes such as InputCell, self._default is not the value, - #instead it is an object that is stored to give the default value in - #self.value. For this reason we print out self.value at this stage, - #and not self._default - xstr += "default: " + self.pprint(self.value) + "; " - - if issubclass(self.__class__, InputAttribute): - #if possible, prints out the type of data that is being used - xstr += "data type: " + self.type_print(self.type) + "; " - - if hasattr(self, "_valid"): - if self._valid is not None: - xstr += "options: " #prints out valid options, if - for option in self._valid: #required. - xstr += "`" + str(option) + "', " - xstr = xstr.rstrip(", ") - xstr += "; " - return xstr - - def help_latex(self, name="", level=0, stop_level=None, standalone=True): - """Function to generate a LaTeX formatted help file. - - Args: - name: Name of the tag that has to be written out. - level: Current level of the hierarchy being considered. - stop_level: The depth to which information will be given. If not given, - will give all information. - standalone: A boolean giving whether the latex file produced will be a - stand-alone document, or will be intended as a section of a larger - document with cross-references between the different sections. - - Returns: - A LaTeX formatted string. - """ - - #stops when we've printed out the prerequisite number of levels - if (not stop_level is None and level > stop_level): - return "" - - rstr = "" - if level == 0: - if standalone: - #assumes that it is a stand-alone document, so must have - #document options. - rstr += r"\documentclass[12pt,fleqn]{report}" - rstr += r""" -\usepackage{etoolbox} -\usepackage{suffix} - -\newcommand{\ipiitem}[3]{% -\setul{1pt}{.4pt}\ifblank{#1}{}{\ifstrequal{#1}{\underline{\smash{}}}{}{ -{\noindent\textbf{#1}:\rule{0.0pt}{1.05\baselineskip}\quad}}}% uses a strut to add a bit of vertical space -{#2}\parskip=0pt\par -\ifblank{#3}{}% -{ {\hfill\raggedleft\textit{\small #3}\par} } -} - -\makeatletter -\newenvironment{ipifield}[4]{% - \ifblank{#1}{}{\vspace{0.5em}} - \noindent\parskip=0pt\begin{tabular}[t]{|p{1.0\linewidth}} - %cell without border - \multicolumn{1}{@{}p{1.0\linewidth}}{ - \ipiitem{\underline{\smash{#1}}}{#2}{} - \ifblank{#4}{ % - \ifblank{#3}{}{{\hfill\raggedleft\textit{\small #3}}\par}}{} } \vspace{-1em}\\ % - % cell with border - \ifblank{#4}{} % - { \ifblank{#3}{}{\vspace{-1em}{\hfill\raggedleft\textit{\small #3}}\par} % - {#4}\vspace{-1em}\\\hline } % negative vspace to undo the line break - \end{tabular} - \parskip=0pt\list{}{\listparindent 1.5em% - \leftmargin \listparindent - \rightmargin 0pt - \parsep 0pt - \itemsep 0pt - \topsep 0pt - }% - \item\relax - } - {\endlist} -\makeatother -""" - rstr += "\n\\begin{document}\n" - if self._label != "" and not standalone: - #assumes that it is part of a cross-referenced document, so only - #starts a new section. - rstr += "\\section{" + self._label + "}\n" - rstr += "\\label{" + self._label + "}\n" - - rstr += "\\begin{ipifield}{}%\n" - else: - if self._label != "" and not standalone: - rstr += "\\begin{ipifield}{\hyperref["+self._label+"]{"+name+"}}%\n" - else: - rstr += "\\begin{ipifield}{"+name+"}%\n" - - rstr += "{"+self._help+"}%\n" - - rstr += "{"+self.detail_str()+"}%\n" - - rstr += "{" - # Prints out the attributes - if len(self.attribs) != 0: - #don't print out units if not necessary - if len(self.attribs) == 1 and (("units" in self.attribs) and self._dimension == "undefined"): - pass - else: - for a in self.attribs: - #don't print out units if not necessary - if not (a == "units" and self._dimension == "undefined"): - rstr += "\\ipiitem{" + a + "}%\n{" + self.__dict__[a]._help + "}%\n{"+self.__dict__[a].detail_str()+"}%\n" #!!MUST ADD OTHER STUFF - rstr+="}\n" - - #As above, for the fields. Only prints out if we have not reached the - #user-specified limit. - if len(self.fields) != 0 and level != stop_level: - for f in self.fields: - rstr += self.__dict__[f].help_latex(name=f, level=level+1, stop_level=stop_level, standalone=standalone) - - if len(self.dynamic) != 0 and level != stop_level: - for f, v in self.dynamic.iteritems(): - dummy_obj = v[0](**v[1]) - rstr += dummy_obj.help_latex(name=f, level=level+1, stop_level=stop_level, standalone=standalone) - - rstr += "\\end{ipifield}\n" - if level == 0 and standalone: - #ends the created document if it is not part of a larger document - rstr += "\\end{document}" - - #Some escape characters are necessary for the proper latex formatting - rstr = rstr.replace('_', '\\_') - rstr = rstr.replace('\\\\_', '\\_') - rstr = rstr.replace('...', '\\ldots ') - rstr = rstr.replace('<', '$<$') - rstr = rstr.replace('>', '$>$') - - return rstr - - def pprint(self, default, indent="", latex = True): - """Function to convert arrays and other objects to human-readable strings. - - Args: - default: The object that needs to be converted to a string. - indent: The indent at the beginning of a line. - latex: A boolean giving whether the string will be latex-format. - - Returns: - A formatted string. - """ - - if type(default) is np.ndarray: - if default.shape == (0,): - return " [ ] " #proper treatment of empty arrays. - else: - #indents new lines for multi-D arrays properly - rstr = "\n" + indent + " " - rstr += str(default).replace("\n", "\n" + indent + " ") - if not latex: - rstr += "\n" + indent + " " - - return rstr - elif type(default) == str: - if latex: - return "`" + default + "'" #indicates that it is a string - else: - return " " + default + " " - elif default == []: - return " [ ] " - elif default == {}: - if latex: - return " \\{ \\} " #again, escape characters needed for latex - else: #formatting - return " { } " - else: - #in most cases standard formatting will do - return " " + str(default) + " " - - def type_print(self, dtype): - """Function to convert a data types to human-readable strings. - - Args: - dtype: A data type. - """ - - if dtype == bool: - return "boolean" - elif dtype == float or dtype == np.float64: - return "float" - elif dtype == int or dtype == np.uint64 or dtype == np.int64: - return "integer" - elif dtype == dict: - return "dictionary" - elif dtype == str: - return "string" - elif dtype == tuple: - return "tuple" - else: - raise TypeError("Unrecognized data type " + str(dtype)) - - def help_xml(self, name="", indent="", level=0, stop_level=None): - """Function to generate an xml formatted help file. - - Args: - name: A string giving the name of the root node. - indent: The indent at the beginning of a line. - level: Current level of the hierarchy being considered. - stop_level: The depth to which information will be given. If not given, - all information will be given - - Returns: - An xml formatted string. - """ - - #stops when we've printed out the prerequisite number of levels - if (not stop_level is None and level > stop_level): - return "" - - #these are booleans which tell us whether there are any attributes - #and fields to print out - show_attribs = (len(self.attribs) != 0) - show_fields = (not (len(self.fields) == 0 and len(self.dynamic) == 0)) and level != stop_level - - rstr = "" - rstr = indent + "<" + name; #prints tag name - for a in self.attribs: - if not (a == "units" and self._dimension == "undefined"): - #don't print out units if not necessary - rstr += " " + a + "=''" #prints attribute names - rstr += ">\n" - - #prints help string - rstr += indent + " " + self._help + " \n" - if show_attribs: - for a in self.attribs: - if not (a == "units" and self._dimension == "undefined"): - #information about tags is found in tags beginning with the name - #of the attribute - rstr += indent + " <" + a + "_help> " + self.__dict__[a]._help + " \n" - - #prints dimensionality of the object - if hasattr(self, '_dimension') and self._dimension != "undefined": - rstr += indent + " " + self._dimension + " \n" - - if self._default != None and issubclass(self.__class__, InputAttribute): - #We only print out the default if it has a well defined value. - #For classes such as InputCell, self._default is not the value, - #instead it is an object that is stored, putting the default value in - #self.value. For this reason we print out self.value at this stage, - #and not self._default - rstr += indent + " " + self.pprint(self.value, indent=indent, latex=False) + "\n" - if show_attribs: - for a in self.attribs: - if not (a == "units" and self._dimension == "undefined"): - if self.__dict__[a]._default is not None: - rstr += indent + " <" + a + "_default>" + self.pprint(self.__dict__[a]._default, indent=indent, latex=False) + "\n" - - #prints out valid options, if required. - if hasattr(self, "_valid"): - if self._valid is not None: - rstr += indent + " " + str(self._valid) + " \n" - if show_attribs: - for a in self.attribs: - if not (a == "units" and self._dimension == "undefined"): - if hasattr(self.__dict__[a], "_valid"): - if self.__dict__[a]._valid is not None: - rstr += indent + " <" + a + "_options> " + str(self.__dict__[a]._valid) + " \n" - - #if possible, prints out the type of data that is being used - if issubclass(self.__class__, InputAttribute): - rstr += indent + " " + self.type_print(self.type) + " \n" - if show_attribs: - for a in self.attribs: - if not (a == "units" and self._dimension == "undefined"): - rstr += indent + " <" + a + "_dtype> " + self.type_print(self.__dict__[a].type) + " \n" - - #repeats the above instructions for any fields or dynamic tags. - #these will only be printed if their level in the hierarchy is not above - #the user specified limit. - if show_fields: - for f in self.fields: - rstr += self.__dict__[f].help_xml(f, " " + indent, level+1, stop_level) - for f, v in self.dynamic.iteritems(): - #we must create the object manually, as dynamic objects are - #not automatically added to the input object's dictionary - dummy_obj = v[0](**v[1]) - rstr += dummy_obj.help_xml(f, " " + indent, level+1, stop_level) - - rstr += indent + "\n" - return rstr - - -class InputAttribute(Input): - """Class for handling attribute data. - - Has the methods for dealing with attribute data of the form: - ..., where data is just a value. Takes the data and - converts it to the required data_type, so that it can be used in the - simulation. - - Attributes: - type: Data type of the data. - value: Value of data. Also specifies data type if type is None. - _valid: An optional list of valid options. - """ - - def __init__(self, help=None, default=None, dtype=None, options=None): - """Initializes InputAttribute. - - Args: - help: A help string. - default: A default value. - dtype: An optional data type. Defaults to None. - options: An optional list of valid options. - """ - - if not dtype is None: - self.type = dtype - else: - raise TypeError("You must provide dtype") - - super(InputAttribute,self).__init__(help, default) - - if options is not None: - self._valid = options - if not default is None and not self._default in self._valid: - #This makes sure that the programmer has set the default value - #so that it is a valid value. - raise ValueError("Default value '" + str(self._default) + "' not in option list " + str(self._valid)+ "\n" + self._help) - else: - self._valid = None - - def parse(self, text=""): - """Reads the data for a single attribute value from an xml file. - - Args: - text: The data held between the start and end tags. - """ - - super(InputAttribute, self).parse(text=text) - - self.value = read_type(self.type, self._text) - - def store(self, value): - """Stores the input data. - - Args: - value: The raw data to be stored. - """ - super(InputAttribute,self).store(value) - self.value = value - - def fetch(self): - """Returns the stored data.""" - - super(InputAttribute,self).fetch() - return self.value - - def check(self): - """Function to check for input errors. - - Raises: - ValueError: Raised if the value chosen is not one of the valid options. - """ - - super(InputAttribute,self).check() - if not (self._valid is None or self.value in self._valid): - #This checks that the user has set the value to a valid value. - raise ValueError(str(self.value) + " is not a valid option (" + str(self._valid) + ")") - - def write(self, name=""): - """Writes data in xml file format. - - Writes the attribute data in the appropriate format. - - Args: - name: An optional string giving the attribute name. Defaults to "". - - Returns: - A string giving the stored value in the appropriate format. - """ - - return name + "='" + write_type(self.type, self.value) + "'" - - -class InputValue(InputAttribute): - """Scalar class for input handling. - - Has the methods for dealing with simple data tags of the form: - data , where data is just a value. Takes the data and - converts it to the required data_type, so that it can be used in the - simulation. - - Attributes: - units: The units that the input data is given in. - _dimension: The dimensionality of the data. - """ - - default_dimension = "undefined" - default_units = "" - - attribs= { "units" : ( InputAttribute, { "dtype" : str, "help" : "The units the input data is given in.", "default" : default_units } ) } - - def __init__(self, help=None, default=None, dtype=None, options=None, dimension=None): - """Initializes InputValue. - - Args: - help: A help string. - dimension: The dimensionality of the value. - default: A default value. - dtype: An optional data type. Defaults to None. - options: An optional list of valid options. - """ - - # a note on units handling: - # 1) units are only processed at parse/fetch time: - # internally EVERYTHING is in internal units - # 2) if one adds an explicit "units" attribute to a derived class, - # the internal units handling will be just ignored - if dimension is None: - self._dimension = self.default_dimension - else: - self._dimension = dimension - - super(InputValue,self).__init__(help, default, dtype, options) - - def store(self, value, units=""): - """Converts the data to the appropriate data type and units and stores it. - - Args: - value: The raw data to be stored. - units: Optional string giving the units that the data should be stored - in. - """ - - super(InputValue,self).store(value) - - if units != "": - self.units.store(units) #User can define in the code the units to be - #printed - - self.value = value - if self._dimension != "undefined": - self.value *= unit_to_user(self._dimension, units, 1.0) - - def fetch(self): - """Returns the stored data in the user defined units.""" - - super(InputValue,self).fetch() - - rval = self.value - if self._dimension != "undefined": - rval *= unit_to_internal(self._dimension, self.units.fetch(), 1.0) - return rval - - def write(self, name="", indent=""): - """Writes data in xml file format. - - Writes the data in the appropriate format between appropriate tags. - - Args: - name: An optional string giving the tag name. Defaults to "". - indent: An optional string giving the string to be added to the start - of the line, so usually a number of tabs. Defaults to "". - - Returns: - A string giving the stored value in the appropriate xml format. - """ - - return Input.write(self, name=name, indent=indent, text=write_type(self.type, self.value)) - - def parse(self, xml=None, text=""): - """Reads the data for a single value from an xml file. - - Args: - xml: An xml_node object containing the all the data for the parent - tag. - text: The data held between the start and end tags. - """ - - Input.parse(self, xml=xml, text=text) - self.value = read_type(self.type, self._text) - - -ELPERLINE = 5 -class InputArray(InputValue): - """Array class for input handling. - - Has the methods for dealing with simple data tags of the form: - data , where data is an array - of the form [data[0], data[1], ... , data[length]]. - - Takes the data and converts it to the required data type, - so that it can be used in the simulation. Also holds the shape of the array, - so that we can use a simple 1D list of data to specify a multi-dimensional - array. - - Attributes: - shape: The shape of the array. - """ - - attribs = copy(InputValue.attribs) - attribs["shape"] = (InputAttribute, {"dtype": tuple, "help": "The shape of the array.", "default": (0,)}) - - def __init__(self, help=None, default=None, dtype=None, dimension=None): - """Initializes InputArray. - - Args: - help: A help string. - dimension: The dimensionality of the value. - default: A default value. - dtype: An optional data type. Defaults to None. - """ - - super(InputArray,self).__init__(help, default, dtype, dimension=dimension) - - def store(self, value, units=""): - """Converts the data to the appropriate data type, shape and units and - stores it. - - Args: - value: The raw data to be stored. - units: Optional string giving the units that the data should be stored - in. - """ - - super(InputArray,self).store(value=np.array(value, dtype=self.type).flatten().copy(), units=units) - self.shape.store(value.shape) - - #if the shape is not specified, assume the array is linear. - if self.shape.fetch() == (0,): - self.shape.store((len(self.value),)) - - def fetch(self): - """Returns the stored data in the user defined units.""" - - value = super(InputArray,self).fetch() - - #if the shape is not specified, assume the array is linear. - if self.shape.fetch() == (0,): - value = np.resize(self.value,0).copy() - else: - value = self.value.reshape(self.shape.fetch()).copy() - - return value - - def write(self, name="", indent=""): - """Writes data in xml file format. - - Writes the data in the appropriate format between appropriate tags. Note - that only ELPERLINE values are printed on each line if there are more - than this in the array. If the values are floats, or another data type - with a fixed width of data output, then they are aligned in columns. - - Args: - name: An optional string giving the tag name. Defaults to "". - indent: An optional string giving the string to be added to the start - of the line, so usually a number of tabs. Defaults to "". - - Returns: - A string giving the stored value in the appropriate xml format. - """ - - rstr = "" - if (len(self.value) > ELPERLINE): - rstr += "\n" + indent + " [ " - else: - rstr += " [ " #inlines the array if it is small enough - - for i, v in enumerate(self.value): - if (len(self.value) > ELPERLINE and i > 0 and i%ELPERLINE == 0): - rstr += "\n" + indent + " " - rstr += write_type(self.type, v) + ", " - - rstr = rstr.rstrip(", ") #get rid of trailing commas - if (len(self.value) > ELPERLINE): - rstr += " ]\n" - else: - rstr += " ] " - - return Input.write(self, name=name, indent=indent, text=rstr) - - def parse(self, xml=None, text=""): - """Reads the data for an array from an xml file. - - Args: - xml: An xml_node object containing the all the data for the parent - tag. - text: The data held between the start and end tags. - """ - - Input.parse(self, xml=xml, text=text) - self.value = read_array(self.type, self._text) - - #if the shape is not specified, assume the array is linear. - if self.shape.fetch() == (0,): - self.shape.store((len(self.value),)) diff --git a/tools/i-pi/ipi/utils/io/README b/tools/i-pi/ipi/utils/io/README deleted file mode 100644 index d70ff09ddd..0000000000 --- a/tools/i-pi/ipi/utils/io/README +++ /dev/null @@ -1,12 +0,0 @@ - -- IO functions directory -- - - * This is the directory containing input/output functions. - - * Files: - - io_binary.py: Contains the functions to write output in binary format. - - io_pdb.py: Contains the functions to read pdb structure files and to - create pdb trajectory output files. - - io_xml.py: Contains the functions used to read the xml input file and - to format the restart output file. - - io_xyz.py: Contains the functions to read xyz structure files and to - create xyz trajectory output files. diff --git a/tools/i-pi/ipi/utils/io/__init__.py b/tools/i-pi/ipi/utils/io/__init__.py deleted file mode 100644 index 01615a0d57..0000000000 --- a/tools/i-pi/ipi/utils/io/__init__.py +++ /dev/null @@ -1 +0,0 @@ -__all__ = [ "io_xml", "io_pdb" , "io_xyz", "io_binary" ] diff --git a/tools/i-pi/ipi/utils/io/io_binary.py b/tools/i-pi/ipi/utils/io/io_binary.py deleted file mode 100644 index 6e8fbd8346..0000000000 --- a/tools/i-pi/ipi/utils/io/io_binary.py +++ /dev/null @@ -1,47 +0,0 @@ -"""Contains the functions used to print the trajectories and read input -configurations (or even full status dump) as unformatted binary. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Functions: - print_bin: Prints an atomic configuration. -""" - -__all__ = ['print_bin'] - -import os -import numpy as np -import math, sys -from ipi.utils.depend import depstrip - -def print_bin(atoms, cell, filedesc = sys.stdout, title=""): - """Prints the centroid configurations, into a binary file. - - Args: - beads: An atoms object giving the centroid positions. - cell: A cell object giving the system box. - filedesc: An open writable file object. Defaults to standard output. - title: This gives a string to be appended to the comment line. - """ - - buff = filedesc # .buffer - cell.h.tofile(buff) - nat = np.asarray([atoms.natoms]) - nat.tofile(buff) - atoms.names.tofile(buff) - atoms.q.tofile(buff) - diff --git a/tools/i-pi/ipi/utils/io/io_pdb.py b/tools/i-pi/ipi/utils/io/io_pdb.py deleted file mode 100644 index b3ce8fc202..0000000000 --- a/tools/i-pi/ipi/utils/io/io_pdb.py +++ /dev/null @@ -1,173 +0,0 @@ -"""Contains the functions used to print the trajectories and read input -configurations with pdb formatting. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Functions: - print_pdb_path: Prints all the bead configurations, and shows the ring - polymer connectivity. - print_pdb: Prints the centroid configurations. - read_pdb: Reads the cell parameters and atom configurations from a pdb file. -""" - -__all__ = ['print_pdb_path', 'print_pdb', 'read_pdb'] - -import numpy as np -import sys -import ipi.utils.mathtools as mt -from ipi.utils.depend import depstrip -from ipi.engine.cell import Cell -from ipi.engine.atoms import Atoms -from ipi.utils.units import * - -def print_pdb_path(beads, cell, filedesc = sys.stdout): - """Prints all the bead configurations, into a pdb formatted file. - - Prints the ring polymer springs as well as the bead positions using the - CONECT command. Also prints the cell parameters in standard pdb form. Note - that the angles are in degrees. - - Args: - beads: A beads object giving the bead positions. - cell: A cell object giving the system box. - filedesc: An open writable file object. Defaults to standard output. - """ - - a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h) - - z = 1 #What even is this parameter? - filedesc.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f%s%4i\n" % (a, b, c, alpha, beta, gamma, " P 1 ", z)) - - natoms = beads.natoms - nbeads = beads.nbeads - for j in range(nbeads): - for i in range(natoms): - qs = depstrip(beads.q) - lab = depstrip(beads.names) - filedesc.write("ATOM %5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2i\n" % (j*natoms+i+1, lab[i],' ',' 1',' ',1,' ', qs[j][3*i], qs[j][3*i+1], qs[j][3*i+2],0.0,0.0,' ',0)) - - if nbeads > 1: - for i in range(natoms): - filedesc.write("CONECT%5i%5i\n" % (i+1, (nbeads-1)*natoms+i+1)) - for j in range(nbeads-1): - for i in range(natoms): - filedesc.write("CONECT%5i%5i\n" % (j*natoms+i+1, (j+1)*natoms+i+1)) - - filedesc.write("END\n") - -def print_pdb(atoms, cell, filedesc = sys.stdout, title=""): - """Prints the atom configurations, into a pdb formatted file. - - Also prints the cell parameters in standard pdb form. Note - that the angles are in degrees. - - Args: - atoms: An atoms object giving the atom positions. - cell: A cell object giving the system box. - filedesc: An open writable file object. Defaults to standard output. - title: An optional string of max. 70 characters. - """ - - - if title != "" : - filedesc.write("TITLE %70s\n" % (title)) - - a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h) - - z = 1 - filedesc.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f%s%4i\n" % (a, b, c, alpha, beta, gamma, " P 1 ", z)) - - natoms = atoms.natoms - qs = depstrip(atoms.q) - lab = depstrip(atoms.names) - for i in range(natoms): - filedesc.write("ATOM %5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2i\n" % (i+1, lab[i], ' ', ' 1', ' ', 1, ' ', qs[3*i], qs[3*i+1], qs[3*i+2], 0.0, 0.0, ' ', 0)) - - filedesc.write("END\n") - -def read_pdb(filedesc): - """Takes a pdb-style file and creates an Atoms and Cell object. - - Args: - filedesc: An open readable file object from a pdb formatted file. - - Returns: - An Atoms object with the appropriate atom labels, masses and positions, - and a Cell object with the appropriate cell dimensions and an estimate - of a reasonable cell mass. - """ - - header = filedesc.readline() - if "TITLE" in header: header = filedesc.readline() # skip the comment field - if header == "": - raise EOFError("End of file or empty header in PDB file") - - a = float(header[6:15]) - b = float(header[15:24]) - c = float(header[24:33]) - alpha = float(header[33:40]) - beta = float(header[40:47]) - gamma = float(header[47:54]) - alpha *= np.pi/180.0 - beta *= np.pi/180.0 - gamma *= np.pi/180.0 - h = mt.abc2h(a, b, c, alpha, beta, gamma) - cell = Cell(h) - - natoms = 0 - body = filedesc.readline() - qatoms = [] - names = [] - masses = [] - while (body.strip() != "" and body.strip() != "END"): - natoms += 1 - name = body[12:16].strip() - names.append(name) - masses.append(Elements.mass(name)) - x = float(body[31:39]) - y = float(body[39:47]) - z = float(body[47:55]) - qatoms.append(x) - qatoms.append(y) - qatoms.append(z) - - body = filedesc.readline() - - atoms = Atoms(natoms) - atoms.q = np.asarray(qatoms) - atoms.names = np.asarray(names,dtype='|S4') - atoms.m = np.asarray(masses) - - return atoms, cell - -def iter_pdb(filedesc): - """Takes a pdb-style file and yields one Atoms, Cell tuple after another. - - Args: - filedesc: An open readable file object from a pdb formatted file. - - Returns: - Generator over the pdb trajectory, that yields - (Atoms, Cell) tuple with the appropriate atom labels, masses and positions. - """ - - try: - while 1: - atoms, cell = read_pdb(filedesc) - yield atoms, cell - except EOFError: - pass diff --git a/tools/i-pi/ipi/utils/io/io_xml.py b/tools/i-pi/ipi/utils/io/io_xml.py deleted file mode 100644 index 961a398848..0000000000 --- a/tools/i-pi/ipi/utils/io/io_xml.py +++ /dev/null @@ -1,520 +0,0 @@ -"""Contains the functions used to read the input file and print the checkpoint -files with xml formatting. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Functions: - xml_node: Class to handle a particular xml tag. - xml_handler: Class giving general xml data reading methods. - xml_parse_string: Parses a string made from a section of a xml input file. - xml_parse_file: Parses an entire xml input file. - read_type: Reads a string and outputs data of a specified type. - read_float: Reads a string and outputs a float. - read_int: Reads a string and outputs an integer. - read_bool: Reads a string and outputs a boolean. - read_list: Reads a string and outputs a list. - read_array: Reads a string and outputs an array. - read_tuple: Reads a string and outputs a tuple. - read_dict: Reads a string and outputs a dictionary. - write_type: Writes a string from data of a specified type. - write_list: Writes a string from a list. - write_tuple: Writes a string from a tuple. - write_float: Writes a string from a float. - write_bool: Writes a string from a boolean. - write_dict: Writes a string from a dictionary. -""" - -__all__ = ['xml_node', 'xml_handler', 'xml_parse_string', 'xml_parse_file', - 'read_type', 'read_float', 'read_int', 'read_bool', 'read_list', - 'read_array', 'read_tuple', 'read_dict', 'write_type', 'write_list', - 'write_tuple', 'write_float', 'write_bool', 'write_dict'] - -from xml.sax import parseString, parse -from xml.sax.handler import ContentHandler -import numpy as np -import string - -class xml_node(object): - """Class to handle a particular xml tag. - - Tags are generally written in the form - main_data . This class holds - tag_name, attrib_data and main_data separately so they can be used to - create the objects with the appropriate names and data. - - Attributes: - attribs: The attribute data for the tag. - fields: The rest of the data. - name: The tag name. - """ - - def __init__(self, attribs=None, name="", fields=None): - """Initializes xml_node. - - Args: - attribs: An optional dictionary giving attribute data. Defaults to {}. - fields: An optional dictionary holding all the data between the start - and end tags, including information about other nodes. - Defaults to {}. - name: An optional string giving the tag name. Defaults to ''. - """ - - if attribs is None: - attribs = {} - if fields is None: - fields = [] - - self.attribs = attribs - self.name = name - self.fields = fields - - -class xml_handler(ContentHandler): - """Class giving general xml_reading methods. - - Uses the standard python xml_reader to read the different kinds of data. - Keeps track of the heirarchial nature of an xml file by recording the level - of nesting, so that the correct data and attributes can be associated with - the correct tag name. - - Attributes: - root: An xml_node object for the root node. - open: The list of the tags that the parser is currently between the start - and end tags of. - level: The level of nesting that the parser is currently at. - buffer: A list of the data found between the tags at the different levels - of nesting. - """ - - def __init__(self): - """Initializes xml_handler.""" - - #root xml node with all the data - self.root = xml_node(name="root", fields=[]) - self.open = [self.root] - #current level of the hierarchy - self.level = 0 - #Holds all the data between each of the tags. - #If level = 1, then buffer[0] holds all the data collected between the - #root tags, and buffer[1] holds all the data collected between the - #first child tag. - self.buffer = [[""]] - - def startElement(self, name, attrs): - """Reads an opening tag. - - Adds the opening tag to the list of open tags, adds a new space in the - buffer, reads the appropriate attributes and adds a new level to the - hierarchy. - - Args: - name: The tag_name. - attrs: The attribute data. - """ - - #creates a new node - newnode = xml_node(attribs=dict((k,attrs[k]) for k in attrs.keys()), name=name, fields=[]) - #adds it to the list of open nodes - self.open.append(newnode) - #adds it to the list of fields of the parent tag - self.open[self.level].fields.append((name,newnode)) - #gets ready to read new data - self.buffer.append([""]) - self.level += 1 - - def characters(self, data): - """Reads data. - - Adds the data to the buffer of the current level of the hierarchy. - Data is read as a string, and needs to be converted to the required - type later. - - Args: - data: The data to be read. - """ - - self.buffer[self.level].append(data) - - def endElement(self, name): - """Reads a closing tag. - - Once all the data has been read, and the closing tag found, the buffer - is read into the appropriate field. - - Args: - name: The tag_name. - """ - - #all the text found between the tags stored in the appropriate xml_node - #object - self.buffer[self.level] = ''.join(self.buffer[self.level]) - self.open[self.level].fields.append(("_text" , self.buffer[self.level])) - #'closes' the xml_node object, as we are no longer within its tags, so - #there is no more data to be added to it. - #Note that the xml_node is still held within the parent tag, so we - #no longer require this xml node object. - self.buffer.pop(self.level) - self.open.pop(self.level) - self.level -= 1 - -def xml_parse_string(buf): - """Parses a string made from a section of a xml input file. - - Args: - buf: A string in correct xml format. - - Returns: - A xml_node for the root node of the file. - """ - - myhandle = xml_handler() - parseString(buf, myhandle) - return myhandle.root - -def xml_parse_file(stream): - """Parses an entire xml input file. - - Args: - stream: A string describing a xml formatted file. - - Returns: - A xml_node for the root node of the file. - """ - - myhandle = xml_handler() - parse(stream, myhandle) - return myhandle.root - -def read_type(type, data): - """Reads a string and outputs data of a specified type. - - Args: - type: The data type of the target container. - data: The string to be read in. - - Raises: - TypeError: Raised if it tries to read into a data type that has not been - implemented. - - Returns: - An object of type type. - """ - - if not type in readtype_funcs: - raise TypeError("Conversion not available for given type") - return type(readtype_funcs[type](data)) - -def read_float(data): - """Reads a string and outputs a float. - - Args: - data: The string to be read in. - - Raises: - ValueError: Raised if the input data is not of the correct format. - - Returns: - A float. - """ - - return float(data) - -def read_int(data): - """Reads a string and outputs a integer. - - Args: - data: The string to be read in. - - Raises: - ValueError: Raised if the input data is not of the correct format. - - Returns: - An integer. - """ - - return int(data) - -def read_bool(data): - """Reads a string and outputs a boolean. - - Takes a string of the form 'true' or 'false', and returns the appropriate - boolean. - - Args: - data: The string to be read in. - - Raises: - ValueError: Raised if the string is not 'true' or 'false'. - - Returns: - A boolean. - """ - - - if data.strip().upper() == "TRUE": - return True - elif data.strip().upper() == "FALSE": - return False - else: - raise ValueError(data + " does not represent a bool value") - -def read_list(data, delims="[]", split=",", strip=" \n\t'"): - """Reads a formatted string and outputs a list. - - The string must be formatted in the correct way. - The start character must be delimiters[0], the end character - must be delimiters[1] and each element must be split along - the character split. Characters at the beginning or - end of each element in strip are ignored. The standard list format is of the - form '[array[0], array[1],..., array[n]]', which is used for actual lists. - Other formats are used for tuples and dictionaries. - - Args: - data: The string to be read in. '[]' by default. - delims: A string of two characters giving the first and last character of - the list format. ',' by default. - split: The character between different elements of the list format. - strip: Characters to be removed from the beginning and end of each - element. ' \n\t' by default. - - Raises: - ValueError: Raised if the input data is not of the correct format. - - Returns: - A list of strings. - """ - - try: - begin = data.index(delims[0]) - end = data.index(delims[1]) - except ValueError: - raise ValueError("Error in list syntax: could not locate delimiters") - - rlist = data[begin+1:end].split(split) - for i in range(len(rlist)): - rlist[i] = rlist[i].strip(strip) - - # handles empty lists correctly - if len(rlist) == 1 and rlist[0] == "": - rlist = [] - - return rlist - -def read_array(dtype, data): - """Reads a formatted string and outputs an array. - - The format is as for standard python arrays, which is - [array[0], array[1], ... , array[n]]. Note the use of comma separators, and - the use of square brackets. - - Args: - data: The string to be read in. - dtype: The data type of the elements of the target array. - - Raises: - ValueError: Raised if the input data is not of the correct format. - - Returns: - An array of data type dtype. - """ - - rlist = read_list(data) - for i in range(len(rlist)): - rlist[i] = read_type(dtype,rlist[i]) - - return np.array(rlist, dtype) - -def read_tuple(data, delims="()", split=",", strip=" \n\t'", arg_type=int): - """Reads a formatted string and outputs a tuple. - - The format is as for standard python tuples, which is - (tuple[0], tuple[1], ... , tuple[n]). Note the comma - separators, and the use of brackets. - - Args: - data: The string to be read in. - delims: A string of two characters giving the first and last character of - the list format. ',' by default. - split: The character between different elements of the list format. - strip: Characters to be removed from the beginning and end of each - element. ' \n\t' by default. - arg_type: The strings in the input will be converted, and a tuple - of ar_type will be returned. - - Raises: - ValueError: Raised if the input data is not of the correct format. - - Returns: - A tuple of elements of the specified data type. - """ - - rlist = read_list(data, delims=delims, split=split, strip=strip) - return tuple([arg_type(i) for i in rlist]) - -def read_dict(data, delims="{}", split=",", key_split=":", strip=" \n\t"): - """Reads a formatted string and outputs a dictionary. - - The format is as for standard python dictionaries, which is - {keyword[0]: arg[0], keyword[1]: arg[1], ... , keyword[n]: arg[n]}. Note the - comma separators, and the use of curly brackets. - - Args: - data: The string to be read in. - delims: A string of two characters giving the first and last character of - the list format. ',' by default. - split: The character between different elements of the list format. - key_split: The character between the key word and the value. - strip: Characters to be removed from the beginning and end of each - element. ' \n\t' by default. - - Raises: - ValueError: Raised if the input data is not of the correct format. - - Returns: - A dictionary of strings. - """ - - rlist = read_list(data, delims=delims, split=split, strip=strip) - def mystrip(data): - return data.strip(strip) - rdict = {} - for s in rlist: - rtuple = map(mystrip,s.split(key_split)) - if not len(rtuple) == 2: - raise ValueError("Format for a key:value format is wrong for item " + s) - rdict[rtuple[0]] = rtuple[1] - - return rdict - -readtype_funcs = {np.ndarray: read_array, dict: read_dict, float: read_float, int: read_int, bool: read_bool, str: string.strip, tuple: read_tuple, np.uint : read_int} - -def write_type(type, data): - """Writes a formatted string from a value of a specified type. - - Args: - type: The data type of the value. - data: The value to be read in. - - Raises: - TypeError: Raised if it tries to write from a data type that has not been - implemented. - - Returns: - A formatted string. - """ - - if not type in writetype_funcs: - raise TypeError("Conversion not available for given type") - return writetype_funcs[type](data) - -def write_list(data, delims="[]"): - """Writes a formatted string from a list. - - The format of the output is as for a standard python list, - [list[0], list[1],..., list[n]]. Note the space after the commas, and the - use of square brackets. - - Args: - data: The value to be read in. - delims: An optional string of two characters giving the first and last - character to be printed. Defaults to "[]". - - Returns: - A formatted string. - """ - - rstr = delims[0] - - for v in data: - rstr += str(v) + ", " - - rstr = rstr.rstrip(", ") - rstr += delims[1] - return rstr - -def write_tuple(data): - """Writes a formatted string from a tuple. - - The format of the output is as for a standard python tuple, - (tuple[0], tuple[1],..., tuple[n]). Note the space after the commas, and the - use of brackets. - - Args: - data: The value to be read in. - - Returns: - A formatted string. - """ - - return write_list(data, delims="()") - -def write_float(data): - """Writes a formatted string from a float. - - Floats are printed out in exponential format, to 8 decimal places and - filling up any spaces under 16 not used with spaces. - - For example 1.0 --> ' 1.00000000e+00' - - Args: - data: The value to be read in. - - Returns: - A formatted string. - """ - - return "%16.8e" % (data) - -def write_bool(data): - """Writes a formatted string from a float. - - Booleans are printed as a string of either ' true' or 'false'. Note that - both are printed out as exactly 5 characters. - - Args: - data: The value to be read in. - - Returns: - A formatted string. - """ - - return "%5.5s" % (str(data)) - -def write_dict(data, delims="{}"): - """Writes a formatted string from a dictionary. - - The format of the output is as for a standard python dictionary, - {keyword[0]: arg[0], keyword[1]: arg[1],..., keyword[n]: arg[n]}. Note the - space after the commas, and the use of curly brackets. - - Args: - data: The value to be read in. - delims: An optional string of two characters giving the first and last - character to be printed. Defaults to "{}". - - Returns: - A formatted string. - """ - - rstr = delims[0] - for v in data: - rstr += str(v) + ": " + str(data[v]) + ", " - rstr = rstr.strip(", ") - rstr += delims[1] - return rstr - -writetype_funcs = {float: write_float, dict: write_dict, int: str, bool: write_bool, str: string.strip, tuple: write_tuple, np.uint : str} diff --git a/tools/i-pi/ipi/utils/io/io_xyz.py b/tools/i-pi/ipi/utils/io/io_xyz.py deleted file mode 100644 index e5fe3e93b7..0000000000 --- a/tools/i-pi/ipi/utils/io/io_xyz.py +++ /dev/null @@ -1,145 +0,0 @@ -"""Contains the functions used to print the trajectories and read input -configurations with xyz formatting. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Functions: - print_xyz_path: Prints all the bead configurations. - print_xyz: Prints the centroid configurations. - read_xyz: Reads the cell parameters and atom configurations from a xyz file. -""" - -__all__ = ['print_xyz_path', 'print_xyz', 'read_xyz', 'iter_xyz'] - -import numpy as np -import math, sys -import ipi.utils.mathtools as mt -from ipi.utils.depend import depstrip -from ipi.engine.atoms import Atoms -from ipi.utils.units import * - -def print_xyz_path(beads, cell, filedesc = sys.stdout): - """Prints all the bead configurations, into a xyz formatted file. - - Prints all the replicas for each time step separately, rather than all at - once. - - Args: - beads: A beads object giving the bead positions. - cell: A cell object giving the system box. - filedesc: An open writable file object. Defaults to standard output. - """ - - a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h) - - natoms = beads.natoms - nbeads = beads.nbeads - for j in range(nbeads): - filedesc.write("%d\n# bead: %d CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f \n" % (natoms, j, a, b, c, alpha, beta, gamma)) - for i in range(natoms): - qs = depstrip(beads.q) - lab = depstrip(beads.names) - filedesc.write("%8s %12.5e %12.5e %12.5e\n" % (lab[i], qs[j][3*i], qs[j][3*i+1], qs[j][3*i+2])) - -def print_xyz(atoms, cell, filedesc = sys.stdout, title=""): - """Prints the centroid configurations, into a xyz formatted file. - - Args: - atoms: An atoms object giving the centroid positions. - cell: A cell object giving the system box. - filedesc: An open writable file object. Defaults to standard output. - title: This gives a string to be appended to the comment line. - """ - - a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h) - - natoms = atoms.natoms - filedesc.write("%d\n# CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f %s\n" % ( natoms, a, b, c, alpha, beta, gamma, title)) - # direct access to avoid unnecessary slow-down - qs = depstrip(atoms.q) - lab = depstrip(atoms.names) - for i in range(natoms): - filedesc.write("%8s %12.5e %12.5e %12.5e\n" % (lab[i], qs[3*i], qs[3*i+1], qs[3*i+2])) - -def read_xyz(filedesc): - """Takes a xyz-style file and creates an Atoms object. - - Args: - filedesc: An open readable file object from a xyz formatted file. - - Returns: - An Atoms object with the appropriate atom labels, masses and positions. - """ - - natoms = filedesc.readline() - if natoms == "": - raise EOFError("The file descriptor hit EOF.") - natoms = int(natoms) - comment = filedesc.readline() - - qatoms = [] - names = [] - masses = [] - iat = 0 - while (iat < natoms): - body = filedesc.readline() - if body.strip() == "": - break - body = body.split() - name = body[0] - names.append(name) - masses.append(Elements.mass(name)) - x = float(body[1]) - y = float(body[2]) - z = float(body[3]) - qatoms.append(x) - qatoms.append(y) - qatoms.append(z) - iat += 1 - - if natoms != len(names): - raise ValueError("The number of atom records does not match the header of the xyz file.") - - atoms = Atoms(natoms) -# for i in range(natoms): -# nat = atoms[i] -# nat.q = qatoms[i] -# nat.name = names[i] -# nat.m = Elements.mass(names[i]) - atoms.q = np.asarray(qatoms) - atoms.names = np.asarray(names, dtype='|S4') - atoms.m = np.asarray(masses) - - return atoms - -def iter_xyz(filedesc): - """Takes a xyz-style file and yields one Atoms object after another. - - Args: - filedesc: An open readable file object from a xyz formatted file. - - Returns: - Generator over the xyz trajectory, that yields - Atoms objects with the appropriate atom labels, masses and positions. - """ - - try: - while 1: - atoms = read_xyz(filedesc) - yield atoms - except EOFError: - pass diff --git a/tools/i-pi/ipi/utils/mathtools.py b/tools/i-pi/ipi/utils/mathtools.py deleted file mode 100644 index 767feca53f..0000000000 --- a/tools/i-pi/ipi/utils/mathtools.py +++ /dev/null @@ -1,343 +0,0 @@ -"""Contains simple algorithms. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Functions: - matrix_exp: Computes the exponential of a square matrix via a Taylor series. - stab_cholesky: A numerically stable version of the Cholesky decomposition. - h2abc: Takes the representation of the system box in terms of an upper - triangular matrix of column vectors, and returns the representation in - terms of the lattice vector lengths and the angles between them - in radians. - h2abc_deg: Takes the representation of the system box in terms of an upper - triangular matrix of column vectors, and returns the representation in - terms of the lattice vector lengths and the angles between them in - degrees. - abc2h: Takes the representation of the system box in terms of the lattice - vector lengths and the angles between them, and returns the - representation in terms of an upper triangular lattice vector matrix. - invert_ut3x3: Inverts a 3*3 upper triangular matrix. - det_ut3x3(h): Finds the determinant of a 3*3 upper triangular matrix. - eigensystem_ut3x3: Finds the eigenvector matrix and eigenvalues of a 3*3 - upper triangular matrix - exp_ut3x3: Computes the exponential of a 3*3 upper triangular matrix. - root_herm: Computes the square root of a positive-definite hermitian - matrix. - logsumlog: Routine to accumulate the logarithm of a sum -""" - -__all__ = ['matrix_exp', 'stab_cholesky', 'h2abc', 'h2abc_deg', 'abc2h', - 'invert_ut3x3', 'det_ut3x3', 'eigensystem_ut3x3', 'exp_ut3x3', - 'root_herm', 'logsumlog' ] - -import numpy as np -import math -from ipi.utils.messages import verbosity, warning - -def logsumlog(lasa, lbsb): - """Computes log(|A+B|) and sign(A+B) given log(|A|), log(|B|), - sign(A), sign(B). - - Args: - lasa: (log(|A|), sign(A)) as a tuple - lbsb: (log(|B|), sign(B)) as a tuple - - Returns: - (log(|A+B|), sign(A+B)) as a tuple - """ - - (la,sa) = lasa - (lb,sb) = lbsb - - if (la > lb): - sr = sa - lr = la + np.log(1.0 + sb*np.exp(lb-la)) - else: - sr = sb - lr = lb + np.log(1.0 + sa*np.exp(la-lb)) - - return (lr,sr) - -def matrix_exp(M, ntaylor=15, nsquare=15): - """Computes the exponential of a square matrix via a Taylor series. - - Calculates the matrix exponential by first calculating exp(M/(2**nsquare)), - then squaring the result the appropriate number of times. - - Args: - M: Matrix to be exponentiated. - ntaylor: Optional integer giving the number of terms in the Taylor series. - Defaults to 15. - nsquare: Optional integer giving how many times the original matrix will - be halved. Defaults to 15. - - Returns: - The matrix exponential of M. - """ - - n = M.shape[1] - tc = np.zeros(ntaylor+1) - tc[0] = 1.0 - for i in range(ntaylor): - tc[i+1] = tc[i]/(i+1) - - SM = np.copy(M)/2.0**nsquare - - EM = np.identity(n,float)*tc[ntaylor] - for i in range(ntaylor-1,-1,-1): - EM = np.dot(SM,EM) - EM += np.identity(n)*tc[i] - - for i in range(nsquare): - EM = np.dot(EM,EM) - return EM - -def stab_cholesky(M): - """ A numerically stable version of the Cholesky decomposition. - - Used in the GLE implementation. Since many of the matrices used in this - algorithm have very large and very small numbers in at once, to handle a - wide range of frequencies, a naive algorithm can end up having to calculate - the square root of a negative number, which breaks the algorithm. This is - due to numerical precision errors turning a very tiny positive eigenvalue - into a tiny negative value. - - Instead of this, an LDU decomposition is used, and any small negative numbers - in the diagonal D matrix are assumed to be due to numerical precision errors, - and so are replaced with zero. - - Args: - M: The matrix to be decomposed. - """ - - n = M.shape[1] - D = np.zeros(n,float) - L = np.zeros(M.shape,float) - for i in range(n): - L[i,i] = 1. - for j in range(i): - L[i,j] = M[i,j] - for k in range(j): - L[i,j] -= L[i,k]*L[j,k]*D[k] - if (not D[j] == 0.0): - L[i,j] = L[i,j]/D[j] - D[i] = M[i,i] - for k in range(i): - D[i] -= L[i,k]*L[i,k]*D[k] - - S = np.zeros(M.shape,float) - for i in range(n): - if (D[i]>0): - D[i] = math.sqrt(D[i]) - else: - warning("Zeroing negative element in stab-cholesky decomposition: " + str(D[i]), verbosity.low) - D[i] = 0 - for j in range(i+1): - S[i,j] += L[i,j]*D[j] - return S - -def h2abc(h): - """Returns a description of the cell in terms of the length of the - lattice vectors and the angles between them in radians. - - Args: - h: Cell matrix in upper triangular column vector form. - - Returns: - A list containing the lattice vector lengths and the angles between them. - """ - - a = float(h[0,0]) - b = math.sqrt(h[0,1]**2 + h[1,1]**2) - c = math.sqrt(h[0,2]**2 + h[1,2]**2 + h[2,2]**2) - gamma = math.acos(h[0,1]/b) - beta = math.acos(h[0,2]/c) - alpha = math.acos(np.dot(h[:,1], h[:,2])/(b*c)) - - return a, b, c, alpha, beta, gamma - -def h2abc_deg(h): - """Returns a description of the cell in terms of the length of the - lattice vectors and the angles between them in degrees. - - Args: - h: Cell matrix in upper triangular column vector form. - - Returns: - A list containing the lattice vector lengths and the angles between them - in degrees. - """ - - (a, b, c, alpha, beta, gamma) = h2abc(h) - return a, b, c, alpha*180/math.pi, beta*180/math.pi, gamma*180/math.pi - -def abc2h(a, b, c, alpha, beta, gamma): - """Returns a lattice vector matrix given a description in terms of the - lattice vector lengths and the angles in between. - - Args: - a: First cell vector length. - b: Second cell vector length. - c: Third cell vector length. - alpha: Angle between sides b and c in radians. - beta: Angle between sides a and c in radians. - gamma: Angle between sides b and a in radians. - - Returns: - An array giving the lattice vector matrix in upper triangular form. - """ - - h = np.zeros((3,3) ,float) - h[0,0] = a - h[0,1] = b*math.cos(gamma) - h[0,2] = c*math.cos(beta) - h[1,1] = b*math.sin(gamma) - h[1,2] = (b*c*math.cos(alpha) - h[0,1]*h[0,2])/h[1,1] - h[2,2] = math.sqrt(c**2 - h[0,2]**2 - h[1,2]**2) - return h - -def invert_ut3x3(h): - """Inverts a 3*3 upper triangular matrix. - - Args: - h: An upper triangular 3*3 matrix. - - Returns: - The inverse matrix of h. - """ - - ih = np.zeros((3,3), float) - for i in range(3): - ih[i,i] = 1.0/h[i,i] - ih[0,1] = -ih[0,0]*h[0,1]*ih[1,1] - ih[1,2] = -ih[1,1]*h[1,2]*ih[2,2] - ih[0,2] = -ih[1,2]*h[0,1]*ih[0,0] - ih[0,0]*h[0,2]*ih[2,2] - return ih - -def eigensystem_ut3x3(p): - """Finds the eigenvector matrix of a 3*3 upper-triangular matrix. - - Args: - p: An upper triangular 3*3 matrix. - - Returns: - An array giving the 3 eigenvalues of p, and the eigenvector matrix of p. - """ - - eigp = np.zeros((3,3), float) - eigvals = np.zeros(3, float) - - for i in range(3): - eigp[i,i] = 1 - eigp[0,1] = -p[0,1]/(p[0,0] - p[1,1]) - eigp[1,2] = -p[1,2]/(p[1,1] - p[2,2]) - eigp[0,2] = -(p[0,1]*p[1,2] - p[0,2]*p[1,1] + p[0,2]*p[2,2])/((p[0,0] - p[2,2])*(p[2,2] - p[1,1])) - - for i in range(3): - eigvals[i] = p[i,i] - return eigp, eigvals - -def det_ut3x3(h): - """Calculates the determinant of a 3*3 upper triangular matrix. - - Note that the volume of the system box when the lattice vector matrix is - expressed as a 3*3 upper triangular matrix is given by the determinant of - this matrix. - - Args: - h: An upper triangular 3*3 matrix. - - Returns: - The determinant of h. - """ - - return h[0,0]*h[1,1]*h[2,2] - -MINSERIES=1e-8 -def exp_ut3x3(h): - """Computes the matrix exponential for a 3x3 upper-triangular matrix. - - Note that for 3*3 upper triangular matrices this is the best method, as - it is stable. This is terms which become unstable as the - denominator tends to zero are calculated via a Taylor series in this limit. - - Args: - h: An upper triangular 3*3 matrix. - - Returns: - The matrix exponential of h. - """ - eh = np.zeros((3,3), float) - e00 = math.exp(h[0,0]) - e11 = math.exp(h[1,1]) - e22 = math.exp(h[2,2]) - eh[0,0] = e00 - eh[1,1] = e11 - eh[2,2] = e22 - - if (abs((h[0,0] - h[1,1])/h[0,0])>MINSERIES): - r01 = (e00 - e11)/(h[0,0] - h[1,1]) - else: - r01 = e00*(1 + (h[0,0] - h[1,1])*(0.5 + (h[0,0] - h[1,1])/6.0)) - if (abs((h[1,1] - h[2,2])/h[1,1])>MINSERIES): - r12 = (e11 - e22)/(h[1,1] - h[2,2]) - else: - r12 = e11*(1 + (h[1,1] - h[2,2])*(0.5 + (h[1,1] - h[2,2])/6.0)) - if (abs((h[2,2] - h[0,0])/h[2,2])>MINSERIES): - r02 = (e22 - e00)/(h[2,2] - h[0,0]) - else: - r02 = e22*(1 + (h[2,2] - h[0,0])*(0.5 + (h[2,2] - h[0,0])/6.0)) - - eh[0,1] = h[0,1]*r01 - eh[1,2] = h[1,2]*r12 - - eh[0,2] = h[0,2]*r02 - if (abs((h[2,2] - h[0,0])/h[2,2])>MINSERIES): - eh[0,2] += h[0,1]*h[0,2]*(r01 - r12)/(h[0,0] - h[2,2]) - elif (abs((h[1,1] - h[0,0])/h[1,1])>MINSERIES): - eh[0,2] += h[0,1]*h[0,2]*(r12 - r02)/(h[1,1] - h[0,0]) - elif (abs((h[1,1]-h[2,2])/h[1,1])>MINSERIES): - eh[0,2] += h[0,1]*h[0,2]*(r02 - r01)/(h[2,2] - h[1,1]) - else: - eh[0,2] += h[0,1]*h[0,2]*e00/24.0*(12.0 + 4*(h[1,1] + h[2,2] - 2*h[0,0]) + (h[1,1] - h[0,0])*(h[2,2] - h[0,0])) - - return eh - -def root_herm(A): - """Gives the square root of a hermitian matrix with real eigenvalues. - - Args: - A: A Hermitian matrix. - - Returns: - A matrix such that itself matrix multiplied by its transpose gives the - original matrix. - """ - - if not (abs(A.T - A) < 1e-10).all(): - raise ValueError("Non-Hermitian matrix passed to root_herm function") - eigvals, eigvecs = np.linalg.eigh(A) - ndgrs = len(eigvals) - diag = np.zeros((ndgrs,ndgrs)) - for i in range(ndgrs): - if eigvals[i] >= 0: - diag[i,i] = math.sqrt(eigvals[i]) - else: - warning("Zeroing negative element in matrix square root: " + str(eigvals[i]), verbosity.low) - diag[i,i] = 0 - return np.dot(eigvecs, np.dot(diag, eigvecs.T)) - diff --git a/tools/i-pi/ipi/utils/messages.py b/tools/i-pi/ipi/utils/messages.py deleted file mode 100644 index 928eb537a3..0000000000 --- a/tools/i-pi/ipi/utils/messages.py +++ /dev/null @@ -1,155 +0,0 @@ -"""Utility functions for outputting messages, diagnostics and errors' - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - Verbosity: Concise class to check the selected level of output - -Functions: - banner: Prints the program welcome "screen" - help: Prints the input syntax help - info: Prints some information to standard output, depending on the level of verbosity - warning: Same as info, but with a "!W!" prefix and optionally printing a stack trace -""" - -import traceback, sys - -__all__ = ['Verbosity', 'verbosity',' help', 'banner', 'info', 'warning'] - - -VERB_QUIET = 0 -VERB_LOW = 1 -VERB_MEDIUM = 2 -VERB_HIGH = 3 -VERB_DEBUG = 4 - -class Verbosity(object): - """Class used to determine what to print to standard output. - - Attributes: - level: Determines what level of output to print. - """ - - level = "low" - - def __getattr__(self, name): - """Determines whether a certain verbosity level is - less than or greater than the stored value. - - Used to decide whether or not a certain info or warning string - should be output. - - Args: - name: The verbosity level at which the info/warning string - will be output. - """ - - if name is "quiet": - return self.level >= VERB_QUIET - elif name is "low": - return self.level >= VERB_LOW - elif name is "medium": - return self.level >= VERB_MEDIUM - elif name is "high": - return self.level >= VERB_HIGH - elif name is "debug": - return self.level >= VERB_DEBUG - - def __setattr__(self, name, value): - """Sets the verbosity level - - Args: - name: The name of what to set. Should always be 'level'. - value: The value to set the verbosity to. - - Raises: - ValueError: Raised if either the name or the level is not - a valid option. - """ - - if name == "level": - if value == "quiet": - level = VERB_QUIET - elif value == "low": - level = VERB_LOW - elif value == "medium": - level = VERB_MEDIUM - elif value == "high": - level = VERB_HIGH - elif value == "debug": - level = VERB_DEBUG - else: - raise ValueError("Invalid verbosity level " + str(value) + " specified.") - super(Verbosity,self).__setattr__("level", level) - - -verbosity = Verbosity() - -def help(): - """Prints out a help string.""" - - print """usage: %s input """%sys.argv[0] - -def banner(): - """Prints out a banner.""" - - print """ - ____ ____ ____ ____ -/ \ / \ / \ / \ -| ################################# | -\__#_/ \____/ \____/ \_#__/ - # _ _______ _____ # - # (_) |_ __ \|_ _| # v. 1.0 - # __ ______ | |__) | | | # - Y [ ||______|| ___/ | | # A Python interface for (ab initio) - 0 0 | | _| |_ _| |_ # (path integral) molecular dynamics. - # [___] |_____| |_____| # - __#_ ____ ____ _#__ -/ # \ / \ / \ / # \ -| ################################# | -\____/ \____/ \____/ \____/ - - """ - - -def info(text="", show=True ): - """Prints a warning message. - - Args: - text: The text of the information message. - show: A boolean describing whether or not the message should be - printed. - """ - - if not show: - return - print text - -def warning(text="", show=True): - """Prints a warning message. - - Args: - text: The text of the information message. - show: A boolean describing whether or not the message should be - printed. - """ - - if not show: - return - if verbosity.debug: - traceback.print_stack(file=sys.stdout) - print " !W! " + text diff --git a/tools/i-pi/ipi/utils/nmtransform.py b/tools/i-pi/ipi/utils/nmtransform.py deleted file mode 100644 index a8c258d522..0000000000 --- a/tools/i-pi/ipi/utils/nmtransform.py +++ /dev/null @@ -1,283 +0,0 @@ -"""Contains functions for doing the inverse and forward normal mode transforms. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - nm_trans: Uses matrix multiplication to do normal mode transformations. - nm_rescale: Uses matrix multiplication to do ring polymer contraction - or expansion. - nm_fft: Uses fast-Fourier transforms to do normal modes transformations. - -Functions: - mk_nm_matrix: Makes a matrix to transform between the normal mode and bead - representations. - mk_rs_matrix: Makes a matrix to transform between one number of beads and - another. Higher normal modes in the case of an expansion are set to zero. -""" - -__all__ = ['nm_trans', 'nm_rescale', 'nm_fft'] - -import numpy as np -from ipi.utils.messages import verbosity, info - -def mk_nm_matrix(nbeads): - """Gets the matrix that transforms from the bead representation - to the normal mode representation. - - If we return from this function a matrix C, then we transform between the - bead and normal mode representation using q_nm = C . q_b, q_b = C.T . q_nm - - Args: - nbeads: The number of beads. - """ - - b2nm = np.zeros((nbeads,nbeads)) - b2nm[0,:] = np.sqrt(1.0) - for j in range(nbeads): - for i in range(1, nbeads/2+1): - b2nm[i,j] = np.sqrt(2.0)*np.cos(2*np.pi*j*i/float(nbeads)) - for i in range(nbeads/2+1, nbeads): - b2nm[i,j] = np.sqrt(2.0)*np.sin(2*np.pi*j*i/float(nbeads)) - if (nbeads%2) == 0: - b2nm[nbeads/2,0:nbeads:2] = 1.0 - b2nm[nbeads/2,1:nbeads:2] = -1.0 - return b2nm/np.sqrt(nbeads) - -def mk_rs_matrix(nb1, nb2): - """Gets the matrix that transforms a path with nb1 beads into one with - nb2 beads. - - If we return from this function a matrix T, then we transform between the - system with nb1 bead and the system of nb2 beads using q_2 = T . q_1 - - Args: - nb1: The initial number of beads. - nb2: The final number of beads. - """ - - if (nb1 == nb2): - return np.identity(nb1,float) - elif (nb1 > nb2): - b1_nm = mk_nm_matrix(nb1) - nm_b2 = mk_nm_matrix(nb2).T - - #builds the "reduction" matrix that picks the normal modes we want to keep - b1_b2 = np.zeros((nb2, nb1), float) - b1_b2[0,0] = 1.0 - for i in range(1, nb2/2+1): - b1_b2[i,i] = 1.0 - b1_b2[nb2-i, nb1-i] = 1.0 - if (nb2 % 2 == 0): - #if we are contracting down to an even number of beads, then we have to - #pick just one of the last degenerate modes to match onto the single - #stiffest mode in the new path - b1_b2[nb2/2, nb1-nb2/2] = 0.0 - - rs_b1_b2 = np.dot(nm_b2, np.dot(b1_b2, b1_nm)) - return rs_b1_b2*np.sqrt(float(nb2)/float(nb1)) - else: - return mk_rs_matrix(nb2, nb1).T*(float(nb2)/float(nb1)) - - -class nm_trans: - """Helper class to perform beads <--> normal modes transformation. - - Attributes: - _b2nm: The matrix to transform between the bead and normal mode - representations. - _nm2b: The matrix to transform between the normal mode and bead - representations. - """ - - def __init__(self, nbeads): - """Initializes nm_trans. - - Args: - nbeads: The number of beads. - """ - - self._b2nm = mk_nm_matrix(nbeads) - self._nm2b = self._b2nm.T - - def b2nm(self, q): - """Transforms a matrix to the normal mode representation. - - Args: - q: A matrix with nbeads rows, in the bead representation. - """ - - return np.dot(self._b2nm,q) - - def nm2b(self, q): - """Transforms a matrix to the bead representation. - - Args: - q: A matrix with nbeads rows, in the normal mode representation. - """ - - return np.dot(self._nm2b,q) - - -class nm_rescale: - """Helper class to rescale a ring polymer between different number of beads. - - Attributes: - _b1tob2: The matrix to transform between a ring polymer with 'nbeads1' - beads and another with 'nbeads2' beads. - _b2tob1: The matrix to transform between a ring polymer with 'nbeads2' - beads and another with 'nbeads1' beads. - """ - - def __init__(self, nbeads1, nbeads2): - """Initializes nm_rescale. - - Args: - nbeads1: The initial number of beads. - nbeads2: The rescaled number of beads. - """ - - self._b1tob2 = mk_rs_matrix(nbeads1,nbeads2) - self._b2tob1 = self._b1tob2.T*(float(nbeads1)/float(nbeads2)) - - def b1tob2(self, q): - """Transforms a matrix from one value of beads to another. - - Args: - q: A matrix with nbeads1 rows, in the bead representation. - """ - - return np.dot(self._b1tob2,q) - - def b2tob1(self, q): - """Transforms a matrix from one value of beads to another. - - Args: - q: A matrix with nbeads2 rows, in the bead representation. - """ - - return np.dot(self._b2tob1,q) - - - -class nm_fft: - """Helper class to perform beads <--> normal modes transformation - using Fast Fourier transforms. - - Attributes: - fft: The fast-Fourier transform function to transform between the - bead and normal mode representations. - ifft: The inverse fast-Fourier transform function to transform - between the normal mode and bead representations. - qdummy: A matrix to hold a copy of the bead positions to transform - them to the normal mode representation. - qnmdummy: A matrix to hold a copy of the normal modes to transform - them to the bead representation. - nbeads: The number of beads. - natoms: The number of atoms. - """ - - def __init__(self, nbeads, natoms): - """Initializes nm_trans. - - Args: - nbeads: The number of beads. - natoms: The number of atoms. - """ - - self.nbeads = nbeads - self.natoms = natoms - try: - import pyfftw - info("Import of PyFFTW successful", verbosity.medium) - self.qdummy = pyfftw.n_byte_align_empty((nbeads, 3*natoms), 16, 'float32') - self.qnmdummy = pyfftw.n_byte_align_empty((nbeads//2+1, 3*natoms), 16, 'complex64') - self.fft = pyfftw.FFTW(self.qdummy, self.qnmdummy, axes=(0,), direction='FFTW_FORWARD') - self.ifft = pyfftw.FFTW(self.qnmdummy, self.qdummy, axes=(0,), direction='FFTW_BACKWARD') - except ImportError: #Uses standard numpy fft library if nothing better - #is available - info("Import of PyFFTW unsuccessful, using NumPy library instead", verbosity.medium) - self.qdummy = np.zeros((nbeads,3*natoms), dtype='float32') - self.qnmdummy = np.zeros((nbeads//2+1,3*natoms), dtype='complex64') - def dummy_fft(self): - self.qnmdummy = np.fft.rfft(self.qdummy, axis=0) - def dummy_ifft(self): - self.qdummy = np.fft.irfft(self.qnmdummy, n=self.nbeads, axis=0) - self.fft = lambda: dummy_fft(self) - self.ifft = lambda: dummy_ifft(self) - - def b2nm(self, q): - """Transforms a matrix to the normal mode representation. - - Args: - q: A matrix with nbeads rows and 3*natoms columns, - in the bead representation. - """ - - if self.nbeads == 1: - return q - self.qdummy[:] = q - self.fft() - if self.nbeads == 2: - return self.qnmdummy.real/np.sqrt(self.nbeads) - - nmodes = self.nbeads/2 - - self.qnmdummy /= np.sqrt(self.nbeads) - qnm = np.zeros(q.shape) - qnm[0,:] = self.qnmdummy[0,:].real - - if self.nbeads % 2 == 0: - self.qnmdummy[1:-1,:] *= np.sqrt(2) - (qnm[1:nmodes,:], qnm[self.nbeads:nmodes:-1,:]) = (self.qnmdummy[1:-1,:].real, self.qnmdummy[1:-1,:].imag) - qnm[nmodes,:] = self.qnmdummy[nmodes,:].real - else: - self.qnmdummy[1:,:] *= np.sqrt(2) - (qnm[1:nmodes+1,:], qnm[self.nbeads:nmodes:-1,:]) = (self.qnmdummy[1:,:].real, self.qnmdummy[1:,:].imag) - - return qnm - - def nm2b(self, qnm): - """Transforms a matrix to the bead representation. - - Args: - qnm: A matrix with nbeads rows and 3*natoms columns, - in the normal mode representation. - """ - - if self.nbeads == 1: - return qnm - if self.nbeads == 2: - self.qnmdummy[:] = qnm - self.ifft() - return self.qdummy*np.sqrt(self.nbeads) - - nmodes = self.nbeads/2 - odd = self.nbeads - 2*nmodes # 0 if even, 1 if odd - - qnm_complex = np.zeros((nmodes+1, len(qnm[0,:])), complex) - qnm_complex[0,:] = qnm[0,:] - if not odd: - (qnm_complex[1:-1,:].real, qnm_complex[1:-1,:].imag) = (qnm[1:nmodes,:], qnm[self.nbeads:nmodes:-1,:]) - qnm_complex[1:-1,:] /= np.sqrt(2) - qnm_complex[nmodes,:] = qnm[nmodes,:] - else: - (qnm_complex[1:,:].real, qnm_complex[1:,:].imag) = (qnm[1:nmodes+1,:], qnm[self.nbeads:nmodes:-1,:]) - qnm_complex[1:,:] /= np.sqrt(2) - - self.qnmdummy[:] = qnm_complex - self.ifft() - return self.qdummy*np.sqrt(self.nbeads) diff --git a/tools/i-pi/ipi/utils/prng.py b/tools/i-pi/ipi/utils/prng.py deleted file mode 100644 index b6d9e6d21d..0000000000 --- a/tools/i-pi/ipi/utils/prng.py +++ /dev/null @@ -1,129 +0,0 @@ -"""Contains the classes used to generate pseudo-random numbers. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Allows the user to specify a seed for the random number generator. -These are used in initialising the velocities and in stochastic thermostats. -The state of the random number generator is kept track of, so that the if the -simulation is restarted from a checkpoint, we will see the same dynamics as if -it had not been stopped. - -Classes: - Random: An interface between the numpy.random module and the user. -""" - -__all__ = ['Random'] - -import numpy as np -import math - -class Random(object): - """Class to interface with the standard pseudo-random number generator. - - Initializes the standard numpy pseudo-random number generator from a seed - at the beginning of the simulation, and keeps track of the state so that - it can be output to the checkpoint files throughout the simulation. - - Attributes: - rng: The random number generator to be used. - seed: The seed number to start the generator. - state: A tuple of five objects giving the current state of the random - number generator. The first is the type of random number generator, - here 'MT19937', the second is an array of 624 integers, the third - is the current position in the array that is being read from, the - fourth gives whether it has a gaussian random number stored, and - the fifth is this stored Gaussian random number, or else the last - Gaussian random number returned. - """ - - def __init__(self, seed=12345, state=None): - """Initializes Random. - - Args: - seed: An optional seed giving an integer to initialize the state with. - state: An optional state tuple to initialize the state with. - """ - - self.rng = np.random.mtrand.RandomState(seed=seed) - self.seed = seed - if state is None: - self.rng.seed(seed) - else: - self.state = state - - def get_state(self): - """Interface to the standard get_state() function.""" - - return self.rng.get_state() - - def set_state(self, value): - """Interface to the standard set_state() function. - - Should only be used with states generated from another similar random - number generator, such as one from a previous run. - """ - - return self.rng.set_state(value) - - state=property(get_state, set_state) - - @property - def u(self): - """Interface to the standard random_sample() function. - - Returns: - A pseudo-random number from a uniform distribution from 0-1. - """ - - return self.rng.random_sample() - - @property - def g(self): - """Interface to the standard standard_normal() function. - - Returns: - A pseudo-random number from a normal Gaussian distribution. - """ - - return self.rng.standard_normal() - - def gamma(self, k, theta=1.0): - """Interface to the standard gamma() function. - - Args: - k: Shape parameter for the gamma distribution. - theta: Mean of the distribution. - - Returns: - A random number from a gamma distribution with a shape k and a - mean value theta. - """ - - return self.rng.gamma(k,theta) - - def gvec(self, shape): - """Interface to the standard_normal array function. - - Args: - shape: The shape of the array to be returned. - - Returns: - An array with the required shape where each element is taken from - a normal Gaussian distribution. - """ - - return self.rng.standard_normal(shape) diff --git a/tools/i-pi/ipi/utils/softexit.py b/tools/i-pi/ipi/utils/softexit.py deleted file mode 100644 index 5d22d9de6b..0000000000 --- a/tools/i-pi/ipi/utils/softexit.py +++ /dev/null @@ -1,73 +0,0 @@ -"""Utility functions for killing the wrapper softly. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - Softexit: Concise class to manage cleaning up in case of an emergency exit. -""" - -import traceback, sys -from ipi.utils.messages import verbosity, warning - -__all__ = ['Softexit', 'softexit'] - - -class Softexit(object): - """Class to deal with stopping a simulation half way through. - - Holds the functions used to clean up a simulation that has been - stopped early, either because of a SIGTERM signal or because the - user has added an EXIT file to the directory in which it is - running. This will then properly shut down the socket interface, - and print out a RESTART file for the appropriate time step. - - Attributes: - flist: A list of functions used to close down the socket - interface. - """ - - def __init__(self): - """Initializes SoftExit.""" - - self.flist = [] - - def register(self, func): - """Adds another function to flist. - - Args: - func: The function to be added to flist. - """ - - self.flist.append(func) - - def trigger(self, message=""): - """Halts the simulation. - - Prints out a warning message, then runs all the exit functions in flist - before terminating the simulation. - - Args: - message: The message to output to standard output. - """ - - if message != "": - warning("Soft exit has been requested with message: '" + message + "'. Cleaning up.", verbosity.low) - for f in self.flist: - f() - sys.exit() - -softexit = Softexit() diff --git a/tools/i-pi/ipi/utils/units.py b/tools/i-pi/ipi/utils/units.py deleted file mode 100644 index 93d05ea0f8..0000000000 --- a/tools/i-pi/ipi/utils/units.py +++ /dev/null @@ -1,358 +0,0 @@ -"""Contains fundamental constants in atomic units. - -Copyright (C) 2013, Joshua More and Michele Ceriotti - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - - -Classes: - Constants: Class whose members are fundamental constants. - Elements: Class which contains the mass of different elements - Units: Class which contains the methods needed to transform - between different systems of units. -""" - -import re -from ipi.utils.messages import verbosity, info - -__all__ = ['Constants', 'Elements', 'unit_to_internal', 'unit_to_user'] - - -class Constants: - """Class whose members are fundamental constants. - - Attributes: - kb: Boltzmann constant. - hbar: Reduced Planck's constant. - amu: Atomic mass unit. - """ - - kb = 1.0 - hbar = 1.0 - amu = 1822.8885 - - -class Elements(dict): - """Class which contains the mass of different elements. - - Attributes: - mass_list: A dictionary containing the masses of different elements. - Has the form {"label": Mass in a.m.u.}. Note that the generic "X" - label is assumed to be an electron. - """ - - mass_list={ - "X" : 1.0000/Constants.amu, - "H" : 1.00794, - "D" : 2.0141, - "Z" : 1.382943, #an interpolated H-D atom, based on y=1/sqrt(m) scaling - "H2" : 2.0160, - "He" : 4.002602, - "Li" : 6.9410, - "Be" : 9.012182, - "B" : 10.811, - "C" : 12.0107, - "N" : 14.00674, - "O" : 15.9994, - "F" : 18.998403, - "Ne" : 20.1797, - "Na" : 22.989770, - "Mg" : 24.3050, - "Al" : 26.981538, - "Si" : 28.0855, - "P" : 30.973761, - "S" : 32.066, - "Cl" : 35.4527, - "Ar" : 39.9480, - "K" : 39.0983, - "Ca" : 40.078, - "Sc" : 44.955910, - "Ti" : 47.867, - "V" : 50.9415, - "Cr" : 51.9961, - "Mn" : 54.938049, - "Fe" : 55.845, - "Co" : 58.933200, - "Ni" : 58.6934, - "Cu" : 63.546, - "Zn" : 65.39, - "Ga" : 69.723, - "Ge" : 72.61, - "As" : 74.92160, - "Se" : 78.96, - "Br" : 79.904, - "Kr" : 83.80, - "Rb" : 85.4678, - "Sr" : 87.62, - "Y" : 88.90585, - "Zr" : 91.224, - "Nb" : 92.90638, - "Mo" : 95.94, - "Tc" : 98, - "Ru" : 101.07, - "Rh" : 102.90550, - "Pd" : 106.42, - "Ag" : 107.8682, - "Cd" : 112.411, - "In" : 114.818, - "Sn" : 118.710, - "Sb" : 121.760, - "Te" : 127.60, - "I" : 126.90447, - "Xe" : 131.29, - "Cs" : 132.90545, - "Ba" : 137.327, - "La" : 138.9055, - "Ce" : 140.166, - "Pr" : 140.90765, - "Nd" : 144.24, - "Pm" : 145, - "Sm" : 150.36, - "Eu" : 151.964, - "Gd" : 157.25, - "Tb" : 158.92534, - "Dy" : 162.50, - "Ho" : 164.93032, - "Er" : 167.26, - "Tm" : 168.93241, - "Yb" : 173.04, - "Lu" : 174.967, - "Hf" : 178.49, - "Ta" : 180.9479, - "W" : 183.84, - "Re" : 186.207, - "Os" : 190.23, - "Ir" : 192.217, - "Pt" : 195.078, - "Au" : 196.96655, - "Hg" : 200.59, - "Tl" : 204.3833, - "Pb" : 207.2, - "Bi" : 208.98038, - "Po" : 209, - "At" : 210, - "Rn" : 222, - "Fr" : 223, - "Ra" : 226, - "Ac" : 227, - "Th" : 232.0381, - "Pa" : 231.03588, - "U" : 238.0289, - "Np" : 237, - "Pu" : 244, - "Am" : 243, - "Cm" : 247, - "Bk" : 247, - "Cf" : 251, - "Es" : 252, - "Fm" : 257, - "Md" : 258, - "No" : 259, - "Lr" : 262, - "Rf" : 267, - "Db" : 268, - "Sg" : 269, - "Bh" : 270, - "Hs" : 269, - "Mt" : 278, - "Ds" : 281, - "Rg" : 280, - "Cn" : 285, - "Uut" : 286, - "Fl" : 289, - "Uup" : 288, - "Lv" : 293, - "Uus" : 294, - "Uuo" : 294 - } - - @classmethod - def mass(cls, label): - """Function to access the mass_list attribute. - - Note that this does not require an instance of the Elements class to be - created, as this is a class method. Therefore using Elements.mass(label) - will give the mass of the element with the atomic symbol given by label. - - Args: - label: The atomic symbol of the atom whose mass is required. - - Returns: - A float giving the mass of the atom with atomic symbol label. - """ - - try: - return cls.mass_list[label]*Constants.amu - except KeyError: - info("Unknown element given, you must specify the mass", verbosity.low) - return -1.0 - -# these are the conversion FROM the unit stated to internal (atomic) units -UnitMap = { - "undefined": { - "" : 1.00 - }, - "energy": { - "" : 1.00, - "atomic_unit" : 1.00, - "electronvolt" : 0.036749326, - "j/mol" : 0.00000038087989, - "cal/mol" : 0.0000015946679, - "kelvin" : 3.1668152e-06 - }, - "temperature": { - "" : 1.00, - "atomic_unit" : 1.00, - "kelvin" : 3.1668152e-06 - }, - "time": { - "" : 1.00, - "atomic_unit" : 1.00, - "second" : 4.1341373e+16 - }, - "frequency" : { # NB Internally, ANGULAR frequencies are used. - "" : 1.00, - "atomic_unit" : 1.00, - "inversecm" : 4.5563353e-06, - "hertz*rad" : 2.4188843e-17, - "hertz" : 1.5198298e-16 - }, - "ms-momentum" : { # TODO fill up units here (mass-scaled momentum) - "" : 1.00, - "atomic_unit" : 1.00 - }, - "length" : { - "" : 1.00, - "atomic_unit" : 1.00, - "angstrom" : 1.8897261, - "meter" : 1.8897261e+10 - }, - "volume" : { - "" : 1.00, - "atomic_unit" : 1.00, - "angstrom3" : 6.748334231, - }, - "velocity": { - "" : 1.00, - "atomic_unit" : 1.00, - "m/s" : 4.5710289e-7 - }, - "momentum": { - "" : 1.00, - "atomic_unit" : 1.00 - }, - "mass": { - "" : 1.00, - "atomic_unit" : 1.00, - "dalton" : 1.00*Constants.amu, - "electronmass" : 1.00 - }, - "pressure" : { - "" : 1.00, - "atomic_unit" : 1.00, - "bar" : 3.398827377e-9, - "atmosphere" : 3.44386184e-9, - "pascal" : 3.398827377e-14 - }, - "density" : { - "" : 1.00, - "atomic_unit" : 1.00, - "g/cm3" : 162.67263 - }, - "force" : { - "" : 1.00, - "atomic_unit" : 1.00, - "newton" : 12137805 - } - -} - -# a list of magnitude prefixes -UnitPrefix = { - "" : 1.0, - "yotta" : 1e24, "zetta" : 1e21, "exa" : 1e18, "peta" : 1e15, - "tera" : 1e12, "giga" : 1e9, "mega" : 1e6, "kilo" : 1e3, - "milli" : 1e-3, "micro" : 1e-6, "nano" : 1e-9, "pico" : 1e-12, - "femto" : 1e-15, "atto" : 1e-18, "zepto" : 1e-21, "yocto" : 1e-24 -} - -# builds a RE to match prefix and split out the base unit -UnitPrefixRE = "" -for key in UnitPrefix: - UnitPrefixRE = UnitPrefixRE + key + "|" -UnitPrefixRE = " *(" + UnitPrefixRE[1:] + ")(.*) *" -UnitPrefixRE = re.compile(UnitPrefixRE) - -######################################################################## -# Atomic units are used EVERYWHERE internally. In order to quickly # -# interface with any "outside" unit, we set up a simple conversion # -# library. # -######################################################################## - -def unit_to_internal(family, unit, number): - """Converts a number of given dimensions and units into internal units. - - Args: - family: The dimensionality of the number. - unit: The units 'number' is originally in. - number: The value of the parameter in the units 'unit'. - - Returns: - The number in internal units. - - Raises: - ValueError: Raised if the user specified units aren't given in the - UnitMap dictionary. - IndexError: Raised if the programmer specified dimensionality for the - parameter isn't in UnitMap. Shouldn't happen, for obvious reasons. - TypeError: Raised if the prefix is correct, but the base unit is not, in - the user specified unit string. - """ - - if not (family == "number" or family in UnitMap): - raise IndexError(family + " is an undefined units kind.") - if family == "number": - return number - - - if unit == "": - prefix = "" - base = "" - else: - m = UnitPrefixRE.match(unit); - if m is None: - raise ValueError("Unit " + unit + " is not structured with a prefix+base syntax.") - prefix = m.group(1) - base = m.group(2) - - if not prefix in UnitPrefix: - raise TypeError(prefix + " is not a valid unit prefix.") - if not base in UnitMap[family]: - raise TypeError(base + " is an undefined unit for kind " + family + ".") - - return number*UnitMap[family][base]*UnitPrefix[prefix] - -def unit_to_user(family, unit, number): - """Converts a number of given dimensions from internal to user units. - - Args: - family: The dimensionality of the number. - unit: The units 'number' should be changed to. - number: The value of the parameter in internal units. - - Returns: - The number in the user specified units - """ - - return number/unit_to_internal(family, unit, 1.0) diff --git a/tools/i-pi/licenses/license_GPL.txt b/tools/i-pi/licenses/license_GPL.txt deleted file mode 100644 index 10926e87f1..0000000000 --- a/tools/i-pi/licenses/license_GPL.txt +++ /dev/null @@ -1,675 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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But first, please read -. - diff --git a/tools/i-pi/licenses/license_MIT.txt b/tools/i-pi/licenses/license_MIT.txt deleted file mode 100644 index 3a85b00ea7..0000000000 --- a/tools/i-pi/licenses/license_MIT.txt +++ /dev/null @@ -1,21 +0,0 @@ - MIT license - Modern Style with sublicense - -Permission is hereby granted, free of charge, to any person obtaining -a copy of this software and associated documentation files (the -"Software"), to deal in the Software without restriction, including -without limitation the rights to use, copy, modify, merge, publish, -distribute, sublicense, and/or sell copies of the Software, and to -permit persons to whom the Software is furnished to do so, subject to -the following conditions: - -The above copyright notice and this permission notice shall be included -in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. -IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY -CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE -SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/tools/i-pi/manual.pdf b/tools/i-pi/manual.pdf deleted file mode 100644 index b4a239d43f..0000000000 Binary files a/tools/i-pi/manual.pdf and /dev/null differ diff --git a/tools/lammps-gui/CMakeLists.txt b/tools/lammps-gui/CMakeLists.txt index b1469794bb..951b350edb 100644 --- a/tools/lammps-gui/CMakeLists.txt +++ b/tools/lammps-gui/CMakeLists.txt @@ -250,7 +250,9 @@ if(APPLE) elseif(MSVC) install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR}) install(FILES $ TYPE BIN) - install(FILES $ TYPE BIN) + if(BUILD_SHARED_LIBS) + install(FILES $ TYPE BIN) + endif() install(FILES $ TYPE BIN) # find path to VC++ init batch file get_filename_component(VC_COMPILER_DIR "${CMAKE_CXX_COMPILER}" DIRECTORY) @@ -262,7 +264,9 @@ elseif(MSVC) elseif((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR}) install(FILES $ TYPE BIN) - install(FILES $ TYPE BIN) + if(BUILD_SHARED_LIBS) + install(FILES $ TYPE BIN) + endif() install(FILES $ TYPE BIN) add_custom_target(zip COMMAND sh -vx ${LAMMPS_DIR}/cmake/packaging/build_windows_cross_zip.sh ${CMAKE_INSTALL_PREFIX} diff --git a/tools/lammps-gui/lammpsgui.cpp b/tools/lammps-gui/lammpsgui.cpp index 4b0f7370dc..a78d891318 100644 --- a/tools/lammps-gui/lammpsgui.cpp +++ b/tools/lammps-gui/lammpsgui.cpp @@ -852,14 +852,19 @@ void LammpsGui::logupdate() } for (int i = 0; i < ncols; ++i) { - int datatype = *(int *)lammps.last_thermo("type", i); + int datatype = -1; double data = 0.0; - if (datatype == 0) // int - data = *(int *)lammps.last_thermo("data", i); - else if (datatype == 2) // double - data = *(double *)lammps.last_thermo("data", i); - else if (datatype == 4) // bigint - data = (double)*(int64_t *)lammps.last_thermo("data", i); + void *ptr = lammps.last_thermo("type", i); + if (ptr) datatype = *(int *)ptr; + ptr = lammps.last_thermo("data", i); + if (ptr) { + if (datatype == 0) // int + data = *(int *)ptr; + else if (datatype == 2) // double + data = *(double *)ptr; + else if (datatype == 4) // bigint + data = (double)*(int64_t *)ptr; + } chartwindow->add_data(step, data, i); } } diff --git a/tools/swig/lammps.i b/tools/swig/lammps.i index b0670b40a4..d350966c2a 100644 --- a/tools/swig/lammps.i +++ b/tools/swig/lammps.i @@ -125,6 +125,7 @@ extern int lammps_get_mpi_comm(void *handle); extern int lammps_extract_setting(void *handle, const char *keyword); extern int lammps_extract_global_datatype(void *handle, const char *name); extern void *lammps_extract_global(void *handle, const char *name); +extern int lammps_map_atom(void *handle, const void *id); extern int lammps_extract_atom_datatype(void *handle, const char *name); extern void *lammps_extract_atom(void *handle, const char *name); @@ -310,6 +311,7 @@ extern int lammps_get_mpi_comm(void *handle); extern int lammps_extract_setting(void *handle, const char *keyword); extern int lammps_extract_global_datatype(void *handle, const char *name); extern void *lammps_extract_global(void *handle, const char *name); +extern int lammps_map_atom(void *handle, const void *id); extern int lammps_extract_atom_datatype(void *handle, const char *name); extern void *lammps_extract_atom(void *handle, const char *name); diff --git a/tools/tinker/tinker2lmp.py b/tools/tinker/tinker2lmp.py index e3ae59748c..3cb9160119 100644 --- a/tools/tinker/tinker2lmp.py +++ b/tools/tinker/tinker2lmp.py @@ -923,7 +923,7 @@ for atom1,atom2,atom3 in alist: elif (c3,c2,c1) in ubdict: ublist.append((atom3,atom2,atom1)) -# create pitorslist = list of 6-body interactions +# create pitorsionlist = list of 6-body interactions # based on central bond, each bond atom is bonded to exactly 2 other atoms # avoid double counting by requiring atom1 < atom2 # NOTE: need more info on how to order the 6 atoms for Tinker to compute on @@ -962,7 +962,7 @@ for atom1 in id: pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6)) -# create bitorslist = list of 5-body interactions +# create bitorsionlist = list of 5-body interactions # generate topology via double loop over neighbors of central atom3 # additional double loop over bonds of atom2 and bonds of atom4 # avoid double counting the reverse bitorsion by use of btdict dictionary diff --git a/unittest/c-library/CMakeLists.txt b/unittest/c-library/CMakeLists.txt index 0ab216caf5..f5793a804e 100644 --- a/unittest/c-library/CMakeLists.txt +++ b/unittest/c-library/CMakeLists.txt @@ -18,6 +18,12 @@ target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=$ add_test(NAME LibraryProperties COMMAND test_library_properties) set_tests_properties(LibraryProperties PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") +add_executable(test_library_objects test_library_objects.cpp test_main.cpp) +target_link_libraries(test_library_objects PRIVATE lammps GTest::GMock) +target_compile_definitions(test_library_objects PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) +add_test(NAME LibraryObjects COMMAND test_library_objects) +set_tests_properties(LibraryObjects PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") + add_executable(test_library_scatter_gather test_library_scatter_gather.cpp test_main.cpp) target_link_libraries(test_library_scatter_gather PRIVATE lammps GTest::GMock) target_compile_definitions(test_library_scatter_gather PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) diff --git a/unittest/c-library/test_library_objects.cpp b/unittest/c-library/test_library_objects.cpp new file mode 100644 index 0000000000..d224c76225 --- /dev/null +++ b/unittest/c-library/test_library_objects.cpp @@ -0,0 +1,215 @@ +// unit tests for checking and changing simulation properties through the library interface + +#include "library.h" + +#include "atom.h" +#include "input.h" +#include "lammps.h" +#include "lmptype.h" +#include "platform.h" +#include "variable.h" + +#include + +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include "test_main.h" + +#define STRINGIFY(val) XSTR(val) +#define XSTR(val) #val + +using ::LAMMPS_NS::Atom; +using ::LAMMPS_NS::bigint; +using ::LAMMPS_NS::Input; +using ::LAMMPS_NS::tagint; +using ::LAMMPS_NS::Variable; +using ::testing::HasSubstr; +using ::testing::StartsWith; +using ::testing::StrEq; + +class LibraryObjects : public ::testing::Test { +protected: + void *lmp; + Variable *variable; + std::string INPUT_DIR = STRINGIFY(TEST_INPUT_FOLDER); + + LibraryObjects() = default; + ~LibraryObjects() override = default; + + void SetUp() override + { + const char *args[] = {"LAMMPS_test", "-log", "none", + "-echo", "screen", "-nocite", + "-var", "input_dir", STRINGIFY(TEST_INPUT_FOLDER), + nullptr}; + + char **argv = (char **)args; + int argc = (sizeof(args) / sizeof(char *)) - 1; + + ::testing::internal::CaptureStdout(); + lmp = lammps_open_no_mpi(argc, argv, nullptr); + variable = ((LAMMPS_NS::LAMMPS *)lmp)->input->variable; + std::string output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + EXPECT_THAT(output, StartsWith("LAMMPS (")); + } + + void TearDown() override + { + ::testing::internal::CaptureStdout(); + lammps_close(lmp); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(output, HasSubstr("Total wall time:")); + if (verbose) std::cout << output; + lmp = nullptr; + } +}; + +TEST_F(LibraryObjects, variables) +{ + FILE *fp = fopen("test_variable.file", "w"); + fputs("# test file for file style variable\n\n\none\n two \n\n" + "three # with comment\nfour ! with non-comment\n" + "# comments only\n five\n#END\n", + fp); + fclose(fp); + + ::testing::internal::CaptureStdout(); + lammps_command(lmp, "region box block 0 2 0 2 0 2"); + lammps_command(lmp, "create_box 1 box"); + lammps_command(lmp, "mass 1 3.0"); + lammps_command(lmp, "create_atoms 1 single 1.0 1.0 1.5"); + lammps_command(lmp, "create_atoms 1 single 0.2 0.1 0.1"); + lammps_command(lmp, "shell putenv TEST_VARIABLE=simpletest2"); + lammps_command(lmp, "shell putenv TEST_VARIABLE2=simpletest OTHER_VARIABLE=2"); + lammps_command(lmp, "variable one index 1 2 3 4"); + lammps_command(lmp, "variable two equal 1"); + lammps_command(lmp, "variable two equal 2"); + lammps_command(lmp, "variable three string four"); + lammps_command(lmp, "variable three string three"); + lammps_command(lmp, "variable four1 loop 4"); + lammps_command(lmp, "variable four2 loop 2 4"); + lammps_command(lmp, "variable five1 loop 100 pad"); + lammps_command(lmp, "variable five2 loop 10 200 pad"); + lammps_command(lmp, "variable six world one"); + lammps_command(lmp, "variable seven format two \"%5.2f\""); + lammps_command(lmp, "variable eight getenv TEST_VARIABLE2"); + lammps_command(lmp, "variable eight getenv XXX"); + lammps_command(lmp, "variable nine file test_variable.file"); + lammps_command(lmp, "variable ten internal 1.0"); + lammps_command(lmp, "variable ten internal 10.0"); + lammps_command(lmp, "variable ten1 universe 1 2 3 4"); + lammps_command(lmp, "variable ten2 uloop 4"); + lammps_command(lmp, "variable ten3 uloop 4 pad"); + lammps_command(lmp, "variable ten4 vector [0,1,2,3,5,7,11]"); + lammps_command(lmp, "variable ten5 vector [0.5,1.25]"); + lammps_command(lmp, "variable dummy index 0"); + lammps_command(lmp, "variable file equal is_file(MYFILE)"); + lammps_command(lmp, "variable iswin equal is_os(^Windows)"); + lammps_command(lmp, "variable islin equal is_os(^Linux)"); + std::string output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "unknown"), -1); + void *ptr = lammps_extract_variable(lmp, "unknown", NULL); + EXPECT_EQ(ptr, nullptr); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "one"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "one", NULL); + EXPECT_NE(ptr, nullptr); + EXPECT_THAT((char *)ptr, StrEq("1")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "two"), LMP_VAR_EQUAL); + ptr = lammps_extract_variable(lmp, "two", NULL); + EXPECT_NE(ptr, nullptr); + EXPECT_THAT(*(double *)ptr, 2.0); + lammps_free(ptr); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "three"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "three", NULL); + EXPECT_THAT((char *)ptr, StrEq("three")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "four1"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "four1", NULL); + EXPECT_THAT((char *)ptr, StrEq("1")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "four2"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "four2", NULL); + EXPECT_THAT((char *)ptr, StrEq("2")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "five1"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "five1", NULL); + EXPECT_THAT((char *)ptr, StrEq("001")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "five2"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "five2", NULL); + EXPECT_THAT((char *)ptr, StrEq("010")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "six"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "six", NULL); + EXPECT_THAT((char *)ptr, StrEq("one")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "seven"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "seven", NULL); + EXPECT_THAT((char *)ptr, StrEq(" 2.00")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "eight"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "eight", NULL); + EXPECT_THAT((char *)ptr, StrEq("")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "nine"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "nine", NULL); + EXPECT_THAT((char *)ptr, StrEq("one")); + + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "ten"), LMP_VAR_EQUAL); + ptr = lammps_extract_variable(lmp, "ten", NULL); + EXPECT_THAT(*(double *)ptr, 1.0); + lammps_free(ptr); + variable->internal_set(variable->find("ten"), 2.5); + ptr = lammps_extract_variable(lmp, "ten", NULL); + EXPECT_THAT(*(double *)ptr, 2.5); + lammps_free(ptr); + + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "ten1"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "ten1", NULL); + EXPECT_THAT((char *)ptr, StrEq("1")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "ten2"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "ten2", NULL); + EXPECT_THAT((char *)ptr, StrEq("1")); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "ten3"), LMP_VAR_STRING); + ptr = lammps_extract_variable(lmp, "ten3", NULL); + EXPECT_THAT((char *)ptr, StrEq("1")); + + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "ten4"), LMP_VAR_VECTOR); + ptr = lammps_extract_variable(lmp, "ten4", (const char *)1); + double *dptr = (double *)lammps_extract_variable(lmp, "ten4", NULL); + EXPECT_EQ((*(int *)ptr), 7); + lammps_free(ptr); + EXPECT_EQ(dptr[0], 0); + EXPECT_EQ(dptr[4], 5); + EXPECT_EQ(dptr[6], 11); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "ten5"), LMP_VAR_VECTOR); + ptr = lammps_extract_variable(lmp, "ten5", (const char *)1); + dptr = (double *)lammps_extract_variable(lmp, "ten5", NULL); + EXPECT_EQ((*(int *)ptr), 2); + lammps_free(ptr); + EXPECT_EQ(dptr[0], 0.5); + EXPECT_EQ(dptr[1], 1.25); + + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "iswin"), LMP_VAR_EQUAL); + EXPECT_EQ(lammps_extract_variable_datatype(lmp, "islin"), LMP_VAR_EQUAL); +#if defined(_WIN32) + ptr = lammps_extract_variable(lmp, "iswin", NULL); + EXPECT_THAT(*(double *)ptr, 1.0); + lammps_free(ptr); + ptr = lammps_extract_variable(lmp, "islin", NULL); + EXPECT_THAT(*(double *)ptr, 0.0); + lammps_free(ptr); +#elif defined(__linux__) + ptr = lammps_extract_variable(lmp, "iswin", NULL); + EXPECT_THAT(*(double *)ptr, 0.0); + lammps_free(ptr); + ptr = lammps_extract_variable(lmp, "islin", NULL); + EXPECT_THAT(*(double *)ptr, 1.0); + lammps_free(ptr); +#else + ptr = lammps_extract_variable(lmp, "iswin", NULL); + EXPECT_THAT(*(double *)ptr, 0.0); + lammps_free(ptr); + ptr = lammps_extract_variable(lmp, "islin", NULL); + EXPECT_THAT(*(double *)ptr, 0.0); + lammps_free(ptr); +#endif + + LAMMPS_NS::platform::unlink("test_variable.file"); +} diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index 4f5cd97d1f..804853194b 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -1,7 +1,9 @@ // unit tests for checking and changing simulation properties through the library interface -#include "lammps.h" #include "library.h" + +#include "atom.h" +#include "lammps.h" #include "lmptype.h" #include "platform.h" #include @@ -14,6 +16,7 @@ #define STRINGIFY(val) XSTR(val) #define XSTR(val) #val +using ::LAMMPS_NS::Atom; using ::LAMMPS_NS::bigint; using ::LAMMPS_NS::tagint; using ::LAMMPS_NS::platform::path_join; @@ -400,6 +403,68 @@ TEST_F(LibraryProperties, global) EXPECT_DOUBLE_EQ(special_coul[1], 1.0); EXPECT_DOUBLE_EQ(special_coul[2], 1.0); EXPECT_DOUBLE_EQ(special_coul[3], 1.0); + + EXPECT_EQ(lammps_extract_global_datatype(lmp, "map_style"), LAMMPS_INT); +#if defined(LAMMPS_BIGBIG) + EXPECT_EQ(lammps_extract_global_datatype(lmp, "map_tag_max"), LAMMPS_BIGINT); +#else + EXPECT_EQ(lammps_extract_global_datatype(lmp, "map_tag_max"), LAMMPS_INT); +#endif + EXPECT_EQ(lammps_extract_global_datatype(lmp, "sametag"), LAMMPS_INT); + EXPECT_EQ(lammps_extract_global_datatype(lmp, "sortfreq"), LAMMPS_INT); + EXPECT_EQ(lammps_extract_global_datatype(lmp, "nextsort"), LAMMPS_BIGINT); + int *sametag = (int *)lammps_extract_global(lmp, "sametag"); + int map_style = *(int *)lammps_extract_global(lmp, "map_style"); + EXPECT_EQ(map_style, Atom::MAP_ARRAY); + EXPECT_NE(sametag, nullptr); + + tagint *tags = (tagint *)lammps_extract_atom(lmp, "id"); + tagint sometags[] = {1, 5, 10, 15, 20}; + for (int i = 0; i < 5; ++i) { + int idx = lammps_map_atom(lmp, (const void *)&sometags[i]); + EXPECT_EQ(sometags[i], tags[idx]); + int nextidx = sametag[idx]; + if (nextidx >= 0) { + EXPECT_EQ(sometags[i], tags[nextidx]); + } + } + + if (!verbose) ::testing::internal::CaptureStdout(); + lammps_command(lmp, "clear"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + map_style = *(int *)lammps_extract_global(lmp, "map_style"); + EXPECT_EQ(map_style, Atom::MAP_NONE); + sametag = (int *)lammps_extract_global(lmp, "sametag"); + EXPECT_EQ(sametag, nullptr); + if (!verbose) ::testing::internal::CaptureStdout(); + lammps_command(lmp, "atom_modify map yes"); + lammps_command(lmp, "region box block 0 1 0 1 0 1"); + lammps_command(lmp, "create_box 1 box"); + lammps_command(lmp, "mass 1 1.0"); + lammps_command(lmp, "run 0 post no"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + map_style = *(int *)lammps_extract_global(lmp, "map_style"); + EXPECT_EQ(map_style, Atom::MAP_YES); + if (!verbose) ::testing::internal::CaptureStdout(); + lammps_command(lmp, "clear"); + lammps_command(lmp, "atom_modify map hash"); + lammps_command(lmp, "region box block 0 1 0 1 0 1"); + lammps_command(lmp, "create_box 1 box"); + lammps_command(lmp, "mass 1 1.0"); + lammps_command(lmp, "run 0 post no"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + map_style = *(int *)lammps_extract_global(lmp, "map_style"); + EXPECT_EQ(map_style, Atom::MAP_HASH); + if (!verbose) ::testing::internal::CaptureStdout(); + lammps_command(lmp, "clear"); + lammps_command(lmp, "atom_modify map array"); + lammps_command(lmp, "region box block 0 1 0 1 0 1"); + lammps_command(lmp, "create_box 1 box"); + lammps_command(lmp, "mass 1 1.0"); + lammps_command(lmp, "run 0 post no"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + map_style = *(int *)lammps_extract_global(lmp, "map_style"); + EXPECT_EQ(map_style, Atom::MAP_ARRAY); }; TEST_F(LibraryProperties, neighlist) diff --git a/unittest/commands/test_lattice_region.cpp b/unittest/commands/test_lattice_region.cpp index da36628b7f..6eac1f45df 100644 --- a/unittest/commands/test_lattice_region.cpp +++ b/unittest/commands/test_lattice_region.cpp @@ -322,7 +322,7 @@ TEST_F(LatticeRegionTest, lattice_sq) ASSERT_EQ(lattice->basis[0][1], 0.0); ASSERT_EQ(lattice->basis[0][2], 0.0); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice orient vectors are not compatible with 2d simulation.*", command("lattice sq 1.0 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1");); BEGIN_HIDE_OUTPUT(); @@ -463,13 +463,13 @@ TEST_F(LatticeRegionTest, lattice_custom) command("dimension 2"); END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: No basis atoms in lattice.*", command("lattice custom 1.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice origin z coord must be 0.0 for 2d simulation.*", command("lattice custom 1.0 origin 0.5 0.5 0.5 basis 0.0 0.0 0.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice a1/a2/a3 vectors are not compatible with 2d simulation.*", command("lattice custom 1.0 a1 1.0 1.0 1.0 basis 0.0 0.0 0.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice a1/a2/a3 vectors are not compatible with 2d simulation.*", command("lattice custom 1.0 a2 1.0 1.0 1.0 basis 0.0 0.0 0.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice a1/a2/a3 vectors are not compatible with 2d simulation.*", command("lattice custom 1.0 a3 1.0 1.0 1.0 basis 0.0 0.0 0.0");); } diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index c631b69528..1826263dea 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -157,6 +157,7 @@ TEST_F(VariableTest, CreateDelete) ASSERT_THAT(variable->retrieve("three"), StrEq("four")); ASSERT_THAT(variable->retrieve("four2"), StrEq("2")); ASSERT_THAT(variable->retrieve("five1"), StrEq("001")); + ASSERT_THAT(variable->retrieve("five2"), StrEq("010")); ASSERT_THAT(variable->retrieve("seven"), StrEq(" 2.00")); ASSERT_THAT(variable->retrieve("ten"), StrEq("1")); ASSERT_THAT(variable->retrieve("eight"), StrEq("")); @@ -216,7 +217,7 @@ TEST_F(VariableTest, CreateDelete) command("variable one internal 2");); TEST_FAILURE(".*ERROR: Cannot use atomfile-style variable unless an atom map exists.*", command("variable eleven atomfile test_variable.atomfile");); - TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", + TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable nine1 file test_variable.xxx.*", command("variable nine1 file test_variable.xxx");); TEST_FAILURE(".*ERROR: World variable count doesn't match # of partitions.*", command("variable ten10 world xxx xxx");); @@ -293,7 +294,7 @@ TEST_F(VariableTest, AtomicSystem) command("variable one atom x");); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", command("variable id vector f_press");); - TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", + TEST_FAILURE(".*ERROR on proc 0: Cannot open atomfile variable ten1 file test_variable.xxx.*", command("variable ten1 atomfile test_variable.xxx");); TEST_FAILURE(".*ERROR: Variable loop: has a circular dependency.*", variable->compute_equal("v_loop");); @@ -337,6 +338,13 @@ TEST_F(VariableTest, Expressions) command("variable vec1 vector \"[-2, 0, 1,2 ,3, 5 , 7\n]\""); command("variable vec2 vector v_vec1*0.5"); command("variable vec3 equal v_vec2[3]"); + command("variable vec4 vector '[1, 5, 2.5, -10, -5, 20, 120, 4, 3, 3]'"); + command("variable sort vector sort(v_vec4)"); + command("variable rsrt vector rsort(v_vec4)"); + command("variable max2 equal sort(v_vec4)[2]"); + command("variable rmax equal rsort(v_vec4)[1]"); + command("variable xxxl equal rsort(v_vec4)[11]"); + command("variable isrt vector sort(v_one)"); variable->set("dummy index 1 2"); END_HIDE_OUTPUT(); @@ -366,6 +374,10 @@ TEST_F(VariableTest, Expressions) EXPECT_THAT(variable->retrieve("vec1"), StrEq("[-2,0,1,2,3,5,7]")); EXPECT_THAT(variable->retrieve("vec2"), StrEq("[-1,0,0.5,1,1.5,2.5,3.5]")); ASSERT_DOUBLE_EQ(variable->compute_equal("v_vec3"), 0.5); + EXPECT_THAT(variable->retrieve("sort"), StrEq("[-10,-5,1,2.5,3,3,4,5,20,120]")); + EXPECT_THAT(variable->retrieve("rsrt"), StrEq("[120,20,5,4,3,3,2.5,1,-5,-10]")); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_max2"), -5); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_rmax"), 120); TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", command("print \"${six}\"");); @@ -377,6 +389,10 @@ TEST_F(VariableTest, Expressions) command("print \"${err2}\"");); TEST_FAILURE(".*ERROR on proc 0: Variable err3: Invalid power expression in variable formula.*", command("print \"${err3}\"");); + TEST_FAILURE(".*ERROR: Variable one: Mis-matched special function variable in variable formula.*", + command("print \"${isrt}\"");); + TEST_FAILURE(".*ERROR: Variable vec4: index 11 exceeds vector size of 10.*", + command("print \"${xxxl}\"");); } TEST_F(VariableTest, Functions) diff --git a/unittest/cplusplus/test_advanced_utils.cpp b/unittest/cplusplus/test_advanced_utils.cpp index 0453ef0143..1da9500b35 100644 --- a/unittest/cplusplus/test_advanced_utils.cpp +++ b/unittest/cplusplus/test_advanced_utils.cpp @@ -110,17 +110,33 @@ TEST_F(Advanced_utils, expand_args) { atomic_system(); BEGIN_CAPTURE_OUTPUT(); - command("compute temp all temp"); - command("variable temp vector c_temp"); - command("variable step equal step"); - command("variable pe equal pe"); - command("variable pe equal pe"); - command("variable epair equal epair"); - command("compute gofr all rdf 20 1 1 1 2"); - command("fix 1 all ave/time 1 1 1 v_step v_pe v_epair"); - command("fix 2 all nve"); - command("run 1 post no"); + try { + command("compute temp all temp"); + command("variable temp vector c_temp"); + command("variable step equal step"); + command("variable pe equal pe"); + command("variable pe equal pe"); + command("variable epair equal epair"); + command("compute gofr all rdf 20 1 1 1 2"); + command("fix 1 all ave/time 1 1 1 v_step v_pe v_epair"); + command("fix 2 all nve"); + command("run 1 post no"); + } catch (LAMMPSAbortException &ae) { + fprintf(stderr, "LAMMPS Error: %s\n", ae.what()); + exit(2); + } catch (LAMMPSException &e) { + fprintf(stderr, "LAMMPS Error: %s\n", e.what()); + exit(3); + } catch (fmt::format_error &fe) { + fprintf(stderr, "fmt::format_error: %s\n", fe.what()); + exit(4); + } catch (std::exception &e) { + fprintf(stderr, "General exception: %s\n", e.what()); + exit(5); + } + auto output = END_CAPTURE_OUTPUT(); + if (verbose) std::cout << output << std::endl; char **args, **earg; constexpr int oarg = 9; diff --git a/unittest/force-styles/check_tests.py b/unittest/force-styles/check_tests.py index df71640789..4dba8f9b9e 100755 --- a/unittest/force-styles/check_tests.py +++ b/unittest/force-styles/check_tests.py @@ -54,7 +54,7 @@ improper = {} kspace = {} pair = {} -style_pattern = re.compile("(.+)Style\((.+),(.+)\)") +style_pattern = re.compile("(.+)Style\\((.+),(.+)\\)") upper = re.compile("[A-Z]+") gpu = re.compile("(.+)/gpu$") intel = re.compile("(.+)/intel$") @@ -176,19 +176,19 @@ def check_tests(name,styles,yaml,search,skip=()): counter = 0 counter += check_tests('pair',pair,'*-pair-*.yaml', - '.*pair_style:\s*((\S+).*)?',skip=('meam','lj/sf')) + '.*pair_style:\\s*((\\S+).*)?',skip=('meam','lj/sf')) counter += check_tests('bond',bond,'bond-*.yaml', - '.*bond_style:\s*((\S+).*)?') + '.*bond_style:\\s*((\\S+).*)?') counter += check_tests('angle',angle,'angle-*.yaml', - '.*angle_style:\s*((\S+).*)?') + '.*angle_style:\\s*((\\S+).*)?') counter += check_tests('dihedral',dihedral,'dihedral-*.yaml', - '.*dihedral_style:\s*((\S+).*)?') + '.*dihedral_style:\\s*((\\S+).*)?') counter += check_tests('improper',improper,'improper-*.yaml', - '.*improper_style:\s*((\S+).*)?') + '.*improper_style:\\s*((\\S+).*)?') counter += check_tests('kspace',kspace,'kspace-*.yaml', - '.*kspace_style\s*((\S+).*)?') + '.*kspace_style\\s*((\\S+).*)?') counter += check_tests('fix',fix,'fix-*.yaml', - ' fix\s+((\S+)\s*)?') + ' fix\\s+((\\S+)\\s*)?') total = len(pair)+len(bond)+len(angle)+len(dihedral)+len(improper)+len(kspace)+len(fix) print(f"\nTotal tests missing: {counter} of {total}") diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index 010fabd6e2..6e823b32fc 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -138,8 +138,9 @@ LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton } command("run 0 post no"); + command("variable write_data_pair index ii"); command("write_restart " + cfg.basename + ".restart"); - command("write_data " + cfg.basename + ".data"); + command("write_data " + cfg.basename + ".data pair ${write_data_pair}"); command("write_coeff " + cfg.basename + "-coeffs.in"); return lmp; diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index 185d28089e..eb6b0b488d 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -138,8 +138,9 @@ LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton } command("run 0 post no"); + command("variable write_data_pair index ii"); command("write_restart " + cfg.basename + ".restart"); - command("write_data " + cfg.basename + ".data nofix"); + command("write_data " + cfg.basename + ".data nofix pair ${write_data_pair}"); command("write_coeff " + cfg.basename + "-coeffs.in"); return lmp; diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index efc37b9e03..060dd040c2 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -136,8 +136,9 @@ LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton } command("run 0 post no"); + command("variable write_data_pair index ii"); command("write_restart " + cfg.basename + ".restart"); - command("write_data " + cfg.basename + ".data"); + command("write_data " + cfg.basename + ".data pair ${write_data_pair}"); command("write_coeff " + cfg.basename + "-coeffs.in"); return lmp; diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index 2d2c2fa0b8..64c56f3602 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -36,6 +36,7 @@ #include "pair.h" #include "platform.h" #include "universe.h" +#include "update.h" #include "utils.h" #include "variable.h" @@ -61,7 +62,7 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg) delete lmp; } -LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool use_respa = false) +LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool use_respa = false) { LAMMPS *lmp; @@ -160,6 +161,13 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg, bool use_rmass, bool use for (auto &post_command : cfg.post_commands) command(post_command); + auto ifix = lmp->modify->get_fix_by_id("test"); + if (ifix && !utils::strmatch(ifix->style, "^move")) { + // must be set to trigger calling Fix::reset_dt() with timestep + lmp->update->first_update = 1; + // test validity of Fix::reset_dt(). With run_style respa there may be segfaults + command("timestep 0.25"); + } command("thermo 2"); command("run 4 post no start 0 stop 8"); } @@ -170,7 +178,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) { // initialize system geometry LAMMPS::argv args = {"FixIntegrate", "-log", "none", "-echo", "screen", "-nocite"}; - LAMMPS *lmp = init_lammps(args, config); + LAMMPS *lmp = init_lammps(args, config); if (!lmp) { std::cerr << "One or more prerequisite styles are not available " "in this LAMMPS configuration:\n"; @@ -190,33 +198,31 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // natoms writer.emit("natoms", natoms); - int ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + auto ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { std::cerr << "ERROR: no fix defined with fix ID 'test'\n"; exit(1); } else { - Fix *fix = lmp->modify->fix[ifix]; - // run_stress, if enabled - if (fix->thermo_virial) { - auto stress = fix->virial; + if (ifix->thermo_virial) { + auto stress = ifix->virial; block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0], stress[1], stress[2], stress[3], stress[4], stress[5]); writer.emit_block("run_stress", block); } // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); writer.emit("global_scalar", value); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; block = std::to_string(num); for (int i = 0; i < num; ++i) - block += fmt::format(" {}", fix->compute_vector(i)); + block += fmt::format(" {}", ifix->compute_vector(i)); writer.emit_block("global_vector", block); } } @@ -283,37 +289,36 @@ TEST(FixTimestep, plain) EXPECT_POSITIONS("run_pos (normal run, verlet)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (normal run, verlet)", lmp->atom, test_config.run_vel, epsilon); - int ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + auto ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, verlet)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (normal run, verlet)", ifix->virial, test_config.run_stress, epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), epsilon); } // check t_target for thermostats int dim = -1; - double *ptr = (double *)fix->extract("t_target", dim); + double *ptr = (double *)ifix->extract("t_target", dim); if ((ptr != nullptr) && (dim == 0)) { int ivar = lmp->input->variable->find("t_target"); if (ivar >= 0) { @@ -333,31 +338,30 @@ TEST(FixTimestep, plain) EXPECT_POSITIONS("run_pos (restart, verlet)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (restart, verlet)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, verlet)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (restart, verlet)", ifix->virial, test_config.run_stress, epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) @@ -372,31 +376,30 @@ TEST(FixTimestep, plain) EXPECT_POSITIONS("run_pos (rmass, verlet)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (rmass, verlet)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, verlet)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (rmass, verlet)", ifix->virial, test_config.run_stress, epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) @@ -406,9 +409,9 @@ TEST(FixTimestep, plain) // rigid fixes need work to test properly with r-RESPA. // fix nve/limit cannot work with r-RESPA - ifix = lmp->modify->find_fix("test"); - if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid") && - !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit")) { + ifix = lmp->modify->get_fix_by_id("test"); + if (ifix && !utils::strmatch(ifix->style, "^rigid") && + !utils::strmatch(ifix->style, "^nve/limit")) { if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -424,31 +427,30 @@ TEST(FixTimestep, plain) EXPECT_POSITIONS("run_pos (normal run, respa)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (normal run, respa)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, respa)", fix->virial, test_config.run_stress, - 1000 * epsilon); + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (normal run, respa)", ifix->virial, + test_config.run_stress, 1000 * epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) @@ -462,31 +464,30 @@ TEST(FixTimestep, plain) EXPECT_POSITIONS("run_pos (restart, respa)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (restart, respa)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, respa)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (restart, respa)", ifix->virial, test_config.run_stress, 1000 * epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) @@ -501,31 +502,30 @@ TEST(FixTimestep, plain) EXPECT_POSITIONS("run_pos (rmass, respa)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (rmass, respa)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, respa)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (rmass, respa)", ifix->virial, test_config.run_stress, 1000 * epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) @@ -551,7 +551,6 @@ TEST(FixTimestep, omp) LAMMPS::argv args = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; - ::testing::internal::CaptureStdout(); LAMMPS *lmp = init_lammps(args, test_config); std::string output = ::testing::internal::GetCapturedStdout(); @@ -584,37 +583,36 @@ TEST(FixTimestep, omp) EXPECT_POSITIONS("run_pos (normal run, verlet)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (normal run, verlet)", lmp->atom, test_config.run_vel, epsilon); - int ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + auto ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, verlet)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (normal run, verlet)", ifix->virial, test_config.run_stress, epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), epsilon); } // check t_target for thermostats int dim = -1; - double *ptr = (double *)fix->extract("t_target", dim); + double *ptr = (double *)ifix->extract("t_target", dim); if ((ptr != nullptr) && (dim == 0)) { int ivar = lmp->input->variable->find("t_target"); if (ivar >= 0) { @@ -634,31 +632,30 @@ TEST(FixTimestep, omp) EXPECT_POSITIONS("run_pos (restart, verlet)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (restart, verlet)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, verlet)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (restart, verlet)", ifix->virial, test_config.run_stress, epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) @@ -673,31 +670,30 @@ TEST(FixTimestep, omp) EXPECT_POSITIONS("run_pos (rmass, verlet)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (rmass, verlet)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, verlet)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (rmass, verlet)", ifix->virial, test_config.run_stress, epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) @@ -707,8 +703,8 @@ TEST(FixTimestep, omp) // rigid fixes need work to test properly with r-RESPA, // also, torque is not supported by respa/omp - ifix = lmp->modify->find_fix("test"); - if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid") && !lmp->atom->torque) { + ifix = lmp->modify->get_fix_by_id("test"); + if (ifix && !utils::strmatch(ifix->style, "^rigid") && !lmp->atom->torque) { if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); @@ -725,31 +721,30 @@ TEST(FixTimestep, omp) EXPECT_POSITIONS("run_pos (normal run, respa)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (normal run, respa)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, respa)", fix->virial, test_config.run_stress, - 1000 * epsilon); + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (normal run, respa)", ifix->virial, + test_config.run_stress, 1000 * epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) @@ -763,31 +758,30 @@ TEST(FixTimestep, omp) EXPECT_POSITIONS("run_pos (restart, respa)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (restart, respa)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, respa)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (restart, respa)", ifix->virial, test_config.run_stress, 1000 * epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) @@ -802,31 +796,30 @@ TEST(FixTimestep, omp) EXPECT_POSITIONS("run_pos (rmass, respa)", lmp->atom, test_config.run_pos, epsilon); EXPECT_VELOCITIES("run_vel (rmass, respa)", lmp->atom, test_config.run_vel, epsilon); - ifix = lmp->modify->find_fix("test"); - if (ifix < 0) { + ifix = lmp->modify->get_fix_by_id("test"); + if (!ifix) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { - Fix *fix = lmp->modify->fix[ifix]; - if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, respa)", fix->virial, test_config.run_stress, + if (ifix->thermo_virial) { + EXPECT_STRESS("run_stress (rmass, respa)", ifix->virial, test_config.run_stress, 1000 * epsilon); } stats.reset(); // global scalar - if (fix->scalar_flag) { - double value = fix->compute_scalar(); + if (ifix->scalar_flag) { + double value = ifix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector - if (fix->vector_flag) { - int num = fix->size_vector; + if (ifix->vector_flag) { + int num = ifix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) - EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), + EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index ba3618d3dc..c90d30c21a 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -138,8 +138,9 @@ LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton } command("run 0 post no"); + command("variable write_data_pair index ii"); command("write_restart " + cfg.basename + ".restart"); - command("write_data " + cfg.basename + ".data"); + command("write_data " + cfg.basename + ".data pair ${write_data_pair}"); command("write_coeff " + cfg.basename + "-coeffs.in"); return lmp; diff --git a/unittest/force-styles/tests/angle-cosine_squared_restricted.yaml b/unittest/force-styles/tests/angle-cosine_squared_restricted.yaml new file mode 100644 index 0000000000..400babb3c0 --- /dev/null +++ b/unittest/force-styles/tests/angle-cosine_squared_restricted.yaml @@ -0,0 +1,88 @@ +--- +lammps_version: 7 Feb 2024 +tags: +date_generated: Fri Mar 29 21:14:05 2024 +epsilon: 2.5e-13 +skip_tests: +prerequisites: ! | + atom full + angle cosine/squared/restricted +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +angle_style: cosine/squared/restricted +angle_coeff: ! | + 1 75.0 110.1 + 2 45.0 111.0 + 3 50.0 120.0 + 4 100.0 108.5 +equilibrium: 4 1.9216075064457567 1.9373154697137058 2.0943951023931953 1.8936822384138476 +extract: ! "" +natoms: 29 +init_energy: 43.16721849625078 +init_stress: ! |2- + 9.1896481583329006e+01 -9.9073798939810871e+01 7.1773173564818959e+00 1.0147556441011812e+02 -3.1614702670042060e+01 6.3320341995277474e-01 +init_forces: ! |2 + 1 5.4616646260609812e+01 6.4912761997628223e+00 -3.3960574186374622e+01 + 2 -1.1520735029225428e+00 -9.3280585589864415e+00 -7.5009000871307308e+00 + 3 -1.3676356546913162e+01 4.9291191335900074e+01 5.1495824934074705e+01 + 4 -1.7548953236977070e+01 -2.4649435647138144e+01 1.4994156277002995e+01 + 5 -4.7191706109161828e+01 -4.7108395361010651e+01 -2.3419810899443089e+01 + 6 5.4456046768792298e+01 -1.0628221895648938e+01 -4.4205117451573471e+01 + 7 -1.5479402058953555e+01 1.3800535101019676e+01 -3.3710945974014352e+00 + 8 -4.5010195114618039e+00 -1.9041823240486167e+01 1.0790072547105123e+02 + 9 -1.5817751557854660e+01 1.6558437937477478e+01 -4.5571617839569933e-01 + 10 4.9597370008417769e+00 4.0344934206635401e+01 -7.9652184287503914e+01 + 11 -1.9904147169399383e+01 -5.8247456312686090e+00 8.4471337004560691e+00 + 12 -1.0750141644440905e+01 -1.0959289684407434e+01 -9.7375245407417310e+00 + 13 3.0110873732763217e+00 7.6125328583508187e+00 -1.8728278765280493e-02 + 14 1.4804534890961024e+01 -9.4162987076082505e+00 -6.4475703726793121e+00 + 15 1.2405121083152171e+01 -6.1967835746148943e+00 1.8294821492807777e+01 + 16 3.1352949560138343e-01 1.1035513814862394e+01 6.5673781465816949e+00 + 17 1.4548484648501341e+00 -1.9813691528391315e+00 1.0691808580347990e+00 + 18 1.5557496930974857e-01 1.6257536594477804e+00 -6.5978344782819773e+00 + 19 -1.9049016835509454e+00 -2.3731208324249899e+00 2.8255706424396045e+00 + 20 1.7493267142411968e+00 7.4736717297720956e-01 3.7722638358423728e+00 + 21 3.3279741492378183e+00 4.1660737555188891e+00 -1.2450454543863602e+01 + 22 -5.9261551336076748e+00 -4.0404494135493199e+00 4.4014087371258892e+00 + 23 2.5981809843698564e+00 -1.2562434196956951e-01 8.0490458067377126e+00 + 24 -1.2888190495929852e+00 5.0097160214605641e+00 -2.9825927599219058e+00 + 25 -1.0338174598680057e+00 -3.4636797875161851e+00 5.6646346770669309e-01 + 26 2.3226365094609909e+00 -1.5460362339443785e+00 2.4161292922152127e+00 + 27 -2.8563709770508883e-01 2.3448568102582543e+00 -7.9873605851552354e-01 + 28 -6.2456251656312733e-01 -1.4020243449848773e+00 3.2568906896433880e-02 + 29 9.1019961426821616e-01 -9.4283246527337705e-01 7.6616715161908966e-01 +run_energy: 42.9022488368839 +run_stress: ! |2- + 9.0388148558231080e+01 -9.8306784914711429e+01 7.9186363564803592e+00 9.9981546403593825e+01 -3.2129110268269365e+01 -3.6431126570529515e-01 +run_forces: ! |2 + 1 5.3981820216746733e+01 6.9247252423091306e+00 -3.3185401895138106e+01 + 2 -1.1944338217682868e+00 -9.7346413974706021e+00 -7.8615437717021557e+00 + 3 -1.2688555593426315e+01 4.8769286528132106e+01 5.0839055814558762e+01 + 4 -1.7617326624105857e+01 -2.4269207832769677e+01 1.5260301967540304e+01 + 5 -4.7323547490196731e+01 -4.6894886975434055e+01 -2.3440133100826486e+01 + 6 5.4382423772065998e+01 -1.0696866841386006e+01 -4.4201170087829055e+01 + 7 -1.5492082837122805e+01 1.3818527237625043e+01 -3.3812483934830673e+00 + 8 -4.4634623862144078e+00 -1.9093779476665727e+01 1.0771575923879119e+02 + 9 -1.5843321387394678e+01 1.6589965876806524e+01 -4.4411228983080475e-01 + 10 5.0768945646127097e+00 4.0040817044035947e+01 -7.9450255761393905e+01 + 11 -1.9901406164815324e+01 -5.7840333581333585e+00 8.4316140350776880e+00 + 12 -1.0895919045638994e+01 -1.1165043741641941e+01 -9.2828865105939240e+00 + 13 2.9272358235905029e+00 7.4354786772387680e+00 1.0142661372278194e-01 + 14 1.4792360939950459e+01 -8.9353318022993182e+00 -6.3910772582380133e+00 + 15 1.2418288954456656e+01 -6.0153396231171570e+00 1.7743757855168997e+01 + 16 4.0781740822800217e-01 1.0963878023768416e+01 6.4917802461985135e+00 + 17 1.4332136710323162e+00 -1.9535475809980913e+00 1.0541332979772831e+00 + 18 1.4023773325248556e-01 1.4086440965467837e+00 -5.6940807148906991e+00 + 19 -1.6400859684012328e+00 -2.0475288381692676e+00 2.4445067235235367e+00 + 20 1.4998482351487472e+00 6.3888474162248376e-01 3.2495739913671629e+00 + 21 3.1432629198624089e+00 3.9072243542777101e+00 -1.1745189375890282e+01 + 22 -5.5777858442915553e+00 -3.7895069817029867e+00 4.1606823590513633e+00 + 23 2.4345229244291464e+00 -1.1771737257472337e-01 7.5845070168389190e+00 + 24 -1.1529613091971900e+00 4.4757566436680412e+00 -2.6619956178204864e+00 + 25 -9.1659948782954015e-01 -3.0936731063721679e+00 5.0626909884369264e-01 + 26 2.0695607970267300e+00 -1.3820835372958733e+00 2.1557265189767940e+00 + 27 -2.6669219302298908e-01 2.1720439184593126e+00 -7.3558544897318312e-01 + 28 -5.7634641435086742e-01 -1.2987031699370619e+00 2.8222187310339070e-02 + 29 8.4303860737385650e-01 -8.7334074852225052e-01 7.0736326166284402e-01 +... diff --git a/unittest/force-styles/tests/atomic-pair-pedone.yaml b/unittest/force-styles/tests/atomic-pair-pedone.yaml new file mode 100644 index 0000000000..ea97d9ee8c --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-pedone.yaml @@ -0,0 +1,112 @@ +--- +lammps_version: 7 Feb 2024 +tags: +date_generated: Tue Apr 9 07:44:34 2024 +epsilon: 7.5e-13 +skip_tests: +prerequisites: ! | + pair pedone + pair coul/dsf +pre_commands: ! | + echo screen + atom_modify map array + units metal + atom_style charge + lattice fcc 4.01 + region box block 0 2 0 2 0 2 + create_box 2 box + create_atoms 1 box + displace_atoms all random 0.1 0.1 0.1 623426 + mass 1 40.0 + mass 2 16.0 + set type 1 type/fraction 2 0.5 998877 + set type 1 charge 1.2 + set type 2 charge -1.2 + velocity all create 100 4534624 loop geom +post_commands: ! "" +input_file: in.empty +pair_style: hybrid/overlay pedone 8.0 coul/dsf 0.05 8.0 +pair_coeff: ! | + * * coul/dsf + 1 2 pedone 0.030211 2.241334 2.923245 5.0 +extract: ! | + c0 2 + d0 2 + r0 2 + alpha 2 +natoms: 32 +init_vdwl: -0.05846735245123568 +init_coul: -127.6163776098739 +init_stress: ! |- + -2.3766889264059056e+01 -4.4271670366067475e+01 -2.5180846524036202e+01 5.0038886969182466e+00 1.8669335074554186e-01 -5.7263597257471289e+01 +init_forces: ! |2 + 1 1.3068329866550368e+00 -3.2426393314368136e+00 -1.7090059822217059e+00 + 2 -8.3708962469663994e-01 8.0332716327131255e+00 3.3880696306892157e+00 + 3 1.0817171269316166e+00 6.9121377930223904e-01 6.1164739509900095e+00 + 4 -6.2705188270402727e+00 -8.8174699380428727e+00 -6.6683743935745587e+00 + 5 2.8006317273000447e-01 -1.4785785338160322e+00 2.1291363801130675e-01 + 6 -9.9407772093842439e-02 3.0597043453576771e+00 2.6317878547215199e+00 + 7 -3.0340486322792599e+00 1.3184658303824097e+00 3.6223571622028894e+00 + 8 5.0115915641263573e+00 -4.9677051620674799e+00 -6.1712277135681015e+00 + 9 -6.1985573132343514e+00 -2.9794836727762029e+00 -1.3747449204783135e+00 + 10 6.8202263133821162e-02 -8.8740995444094821e+00 -3.7669178307548044e+00 + 11 1.8229752044042762e+00 1.2148573816886858e+00 -4.4347407582895784e+00 + 12 -3.9294213238803009e+00 8.8686068238310583e+00 -1.5696200877040254e+00 + 13 4.6671449089488757e+00 -4.6189653076982848e+00 -1.3124536997564062e+00 + 14 4.5651421484368113e-02 -2.3521973378049634e+00 -1.6447916834323362e+00 + 15 2.0718235766251047e+00 -1.0016787355222116e+00 2.6102514913196893e+00 + 16 4.2906354719273310e+00 5.5091935314875675e+00 2.3081189742020186e-01 + 17 2.4088963659786491e+00 2.6695675589930521e+00 3.5122235738936918e+00 + 18 3.4512362576614999e+00 -4.1430347952161721e+00 4.2175118122911428e+00 + 19 -1.1172781222643726e+00 5.0374260939675146e+00 6.1287692774066489e+00 + 20 4.7466340882928550e+00 4.2198180415705018e+00 -8.2329099903756351e+00 + 21 4.9922952432844170e-01 -3.3643476589192347e+00 -3.4586600244054257e+00 + 22 1.9519912199733915e+00 2.3651493661604901e+00 1.9718930394593539e+00 + 23 3.2436581993388014e+00 9.2909318945485386e-01 4.6199095913337018e+00 + 24 -4.6577163797485408e+00 1.0944440231458034e-01 -3.9975755528276791e+00 + 25 -8.9409463869190198e+00 2.4726478248668329e+00 3.7066236847004816e+00 + 26 1.1745295461487557e+00 -6.0775548138182502e+00 3.9173262687577626e-01 + 27 2.1387234883139223e+00 -9.1458060453528878e-01 3.4582641764483730e+00 + 28 -5.4502482566484289e+00 3.4786802718788201e+00 2.2450528597292503e+00 + 29 -7.5667651846088226e+00 -1.4577149705984696e+00 -3.9568568740165220e+00 + 30 3.1230549128026425e-01 1.3068114717904746e+00 1.5378868153458369e+00 + 31 3.8386185003687259e+00 2.2553073046534435e+00 -1.3273631790345837e+00 + 32 3.6895374447617666e+00 7.5079155624842708e-01 -9.7729039239942395e-01 +run_vdwl: -0.05936305172833948 +run_coul: -127.68271387147016 +run_stress: ! |- + -2.3775085785175861e+01 -4.4287200358424037e+01 -2.5219014434426338e+01 5.0215354612619398e+00 1.6449805968891407e-01 -5.7274887432938485e+01 +run_forces: ! |2 + 1 1.2991722692082786e+00 -3.2346896741423627e+00 -1.7041329770094276e+00 + 2 -8.3577389730915552e-01 8.0381530163215924e+00 3.3923109270711151e+00 + 3 1.0835047785054042e+00 6.9319911007073187e-01 6.1150295417259430e+00 + 4 -6.2592674457409263e+00 -8.8205393549813724e+00 -6.6664974877688721e+00 + 5 2.8319324224275277e-01 -1.4769949542028844e+00 2.1366042708413130e-01 + 6 -1.0153594962155643e-01 3.0590371871661279e+00 2.6305719846785136e+00 + 7 -3.0312781169981404e+00 1.3253014477860192e+00 3.6137212324460495e+00 + 8 5.0065920194766118e+00 -4.9738538898220481e+00 -6.1680653045217282e+00 + 9 -6.1953589072633033e+00 -2.9840507476418630e+00 -1.3858506137213893e+00 + 10 7.2110931001166223e-02 -8.8715664120515498e+00 -3.7622114666042830e+00 + 11 1.8261227725248501e+00 1.2127884088947380e+00 -4.4352512345078896e+00 + 12 -3.9286782746032927e+00 8.8761060543305845e+00 -1.5679267227812392e+00 + 13 4.6639719242626425e+00 -4.6221575223138132e+00 -1.3189131763776332e+00 + 14 4.5202926162814835e-02 -2.3548742883712031e+00 -1.6491976796732051e+00 + 15 2.0720535642022995e+00 -1.0069819281480463e+00 2.6083600468918844e+00 + 16 4.2902983639126537e+00 5.5131718679546795e+00 2.3830711385553280e-01 + 17 2.4096838033622459e+00 2.6710791048618789e+00 3.5085731540934209e+00 + 18 3.4514062725618015e+00 -4.1373868590762886e+00 4.2169294048595312e+00 + 19 -1.1264411792212099e+00 5.0227271243385347e+00 6.1237583999889607e+00 + 20 4.7393545880453329e+00 4.2216825100295452e+00 -8.2318896574215081e+00 + 21 5.0316022185802045e-01 -3.3658905024666987e+00 -3.4562503451177298e+00 + 22 1.9368078287723918e+00 2.3534799016713426e+00 1.9729696376413666e+00 + 23 3.2400632484576661e+00 9.3259676426325444e-01 4.6157700185053541e+00 + 24 -4.6586992607556210e+00 1.1241261874328348e-01 -3.9896118917888690e+00 + 25 -8.9349626587186393e+00 2.4768648221903695e+00 3.7112080381606569e+00 + 26 1.1679346190142463e+00 -6.0828712249034158e+00 3.8801942263557465e-01 + 27 2.1417538088342263e+00 -9.0746081465677486e-01 3.4626716637488029e+00 + 28 -5.4328133673274284e+00 3.4793352823397115e+00 2.2408588660642268e+00 + 29 -7.5599171237192415e+00 -1.4574882072609379e+00 -3.9594670101361755e+00 + 30 3.1095531392911402e-01 1.2978745340983431e+00 1.5451191860370526e+00 + 31 3.8408681082369638e+00 2.2573010571848813e+00 -1.3280944539185844e+00 + 32 3.6805155767070339e+00 7.5369556779361924e-01 -9.7447904413958231e-01 +... diff --git a/unittest/force-styles/tests/dihedral-cosine_squared_restricted.yaml b/unittest/force-styles/tests/dihedral-cosine_squared_restricted.yaml new file mode 100644 index 0000000000..f67a093017 --- /dev/null +++ b/unittest/force-styles/tests/dihedral-cosine_squared_restricted.yaml @@ -0,0 +1,88 @@ +--- +lammps_version: 7 Feb 2024 +tags: +date_generated: Sat Apr 13 11:41:16 2024 +epsilon: 2.5e-13 +skip_tests: +prerequisites: ! | + atom full + dihedral cosine/squared/restricted +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +dihedral_style: cosine/squared/restricted +dihedral_coeff: ! | + 1 17.0 10.0 + 2 14.0 20.0 + 3 15.0 -10.0 + 4 12.0 0.0 + 5 11.0 45.0 +extract: ! "" +natoms: 29 +init_energy: 10643.96352037142 +init_stress: ! |2- + 8.2655807554971598e+03 6.2324906154519340e+03 -1.4498071370948830e+04 1.0953420376656040e+04 1.1057094124317168e+03 -8.3313158421382595e+03 +init_forces: ! |2 + 1 -2.9998360221989606e+03 1.5614240759467791e+03 -1.4993484270227148e+03 + 2 2.3464901141409141e+03 -1.2117018270409203e+03 1.1464619463537790e+03 + 3 -8.4367569419635300e+04 -8.8610214478341717e+04 1.3641091254798606e+04 + 4 -7.7728947837396186e+02 -1.1834661410404278e+03 6.2790819006201627e+02 + 5 1.9271341641256136e+03 -1.1638057759737167e+03 2.7159431719235641e+01 + 6 4.4134274351326589e+04 5.5926488430371595e+04 2.3644507487725932e+03 + 7 5.6253242167919998e+03 6.0326849037643433e+03 -9.8937413117578353e+02 + 8 1.5398571438042008e+05 1.4826543321068442e+05 -4.6786535127649200e+04 + 9 5.2872438366384667e+03 3.9367087924112984e+03 -2.1528982310842534e+03 + 10 -1.2076914217812811e+05 -1.1928499037053883e+05 3.1759537647021025e+04 + 11 -2.7869283077129630e+03 -2.7624462832092408e+03 2.3692905638286411e+03 + 12 -1.7137278451679694e+02 -4.0643861446907772e+02 -8.4482327773661689e+02 + 13 1.8033469195161777e+02 4.1452681735267817e+02 8.7002410666914204e+02 + 14 1.0785063285146067e+02 -1.5007679697175007e+02 -5.3363703034369962e+01 + 15 -1.2637123349071543e+02 4.2783038317466065e+01 -1.2928289731925594e+02 + 16 -1.3974766748247812e+03 -1.2440022591573602e+03 -3.1834363647575998e+02 + 17 -1.9838028936516241e+02 -1.6290672210557804e+02 -3.1954457727099452e+01 + 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +run_energy: 4829.55350497352 +run_stress: ! 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| @@ -14,65 +15,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356937318884e+03 -1.4496493315649691e+03 -3.6144360984224995e+03 8.4840626828644076e+02 2.0318336761611761e+02 -6.0622397707970140e+02 -global_scalar: 15.711521423178082 + -1.4245356937318909e+03 -1.4496493315649632e+03 -3.6144360984225123e+03 8.4840626828644361e+02 2.0318336761612773e+02 -6.0622397707969583e+02 +global_scalar: 15.711521423178084 run_pos: ! |2 - 1 -2.7899546863891400e-01 2.4731857340328229e+00 -1.7290667740242271e-01 - 2 3.0296221610264262e-01 2.9517129916957545e+00 -8.5798904387773245e-01 - 3 -6.9368802364134741e-01 1.2445115421754194e+00 -6.2281111198650418e-01 - 4 -1.5764879647103154e+00 1.4919714415841279e+00 -1.2492069414674623e+00 - 5 -8.9434512967429969e-01 9.3651699743511030e-01 4.0191726558261276e-01 - 6 2.9454439634451712e-01 2.2724545792544038e-01 -1.2845195053960268e+00 - 7 3.4049112903270051e-01 -9.4655678322458359e-03 -2.4634480020857055e+00 - 8 1.1644354555804874e+00 -4.8367776650961336e-01 -6.7663643940735863e-01 - 9 1.3781717822696469e+00 -2.5332509530010694e-01 2.6864954436590061e-01 - 10 2.0186368606041896e+00 -1.4285861423625796e+00 -9.6712491252780131e-01 - 11 1.7929137227577452e+00 -1.9875455388407426e+00 -1.8836565352266534e+00 - 12 3.0032775230399604e+00 -4.8983022415174027e-01 -1.6190248017343642e+00 - 13 4.0448964162125947e+00 -9.0213155122391020e-01 -1.6385398399479558e+00 - 14 2.6035151245015822e+00 -4.0874995493219213e-01 -2.6555999074786607e+00 - 15 2.9761196776172318e+00 5.6287237454108674e-01 -1.2442626196083388e+00 - 16 2.6517373021566168e+00 -2.3957035508393707e+00 3.3389262100692263e-02 - 17 2.2311114924744970e+00 -2.1018393228798513e+00 1.1496088522377543e+00 - 18 2.1390642573201784e+00 3.0164773560693781e+00 -3.5143984803853878e+00 - 19 1.5353246655146278e+00 2.6305911186316133e+00 -4.2455871034737074e+00 - 20 2.7649421538938390e+00 3.6818603528430849e+00 -3.9364115785985550e+00 - 21 4.9043112657298877e+00 -4.0774268210397882e+00 -3.6200836396129836e+00 - 22 4.3665322424283310e+00 -4.2075138112953594e+00 -4.4636587264885881e+00 - 23 5.7355405581985188e+00 -3.5789558641908918e+00 -3.8805763324089981e+00 - 24 2.0692780332810115e+00 3.1504920436416004e+00 3.1571131300668789e+00 - 25 1.3007297593169076e+00 3.2745259354179481e+00 2.5110163874103675e+00 - 26 2.5819416446099739e+00 4.0104903120756576e+00 3.2150249624526035e+00 + 1 -2.7899546863891755e-01 2.4731857340328198e+00 -1.7290667740241461e-01 + 2 3.0296221610263996e-01 2.9517129916957550e+00 -8.5798904387772190e-01 + 3 -6.9368802364134963e-01 1.2445115421754176e+00 -6.2281111198650141e-01 + 4 -1.5764879647103172e+00 1.4919714415841279e+00 -1.2492069414674598e+00 + 5 -8.9434512967430235e-01 9.3651699743510453e-01 4.0191726558261442e-01 + 6 2.9454439634451712e-01 2.2724545792544146e-01 -1.2845195053960266e+00 + 7 3.4049112903270240e-01 -9.4655678322404235e-03 -2.4634480020857055e+00 + 8 1.1644354555804877e+00 -4.8367776650961403e-01 -6.7663643940735962e-01 + 9 1.3781717822696455e+00 -2.5332509530011083e-01 2.6864954436590072e-01 + 10 2.0186368606041905e+00 -1.4285861423625785e+00 -9.6712491252780486e-01 + 11 1.7929137227577487e+00 -1.9875455388407386e+00 -1.8836565352266592e+00 + 12 3.0032775230399622e+00 -4.8983022415173583e-01 -1.6190248017343625e+00 + 13 4.0448964162125964e+00 -9.0213155122390454e-01 -1.6385398399479547e+00 + 14 2.6035151245015857e+00 -4.0874995493218413e-01 -2.6555999074786598e+00 + 15 2.9761196776172323e+00 5.6287237454109007e-01 -1.2442626196083335e+00 + 16 2.6517373021566182e+00 -2.3957035508393734e+00 3.3389262100686046e-02 + 17 2.2311114924744961e+00 -2.1018393228798584e+00 1.1496088522377494e+00 + 18 2.1390642573201792e+00 3.0164773560693803e+00 -3.5143984803853883e+00 + 19 1.5353246655146293e+00 2.6305911186316160e+00 -4.2455871034737100e+00 + 20 2.7649421538938399e+00 3.6818603528430875e+00 -3.9364115785985545e+00 + 21 4.9043112657298966e+00 -4.0774268210397882e+00 -3.6200836396129850e+00 + 22 4.3665322424283417e+00 -4.2075138112953612e+00 -4.4636587264885925e+00 + 23 5.7355405581985277e+00 -3.5789558641908901e+00 -3.8805763324089995e+00 + 24 2.0692780332810012e+00 3.1504920436415969e+00 3.1571131300668829e+00 + 25 1.3007297593168976e+00 3.2745259354179459e+00 2.5110163874103693e+00 + 26 2.5819416446099637e+00 4.0104903120756576e+00 3.2150249624526102e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! 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| @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 -global_scalar: 18.3405601674144 + -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 +global_scalar: 18.340560167414402 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00 - 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00 - 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00 - 22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00 - 23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 + 18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00 + 19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00 + 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 + 21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00 + 22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00 + 23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00 - 25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00 - 26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00 + 25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00 + 26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04 - 19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03 - 20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04 - 21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03 - 22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03 - 23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04 - 24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04 - 25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04 - 26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03 + 18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04 + 19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03 + 20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04 + 21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03 + 22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03 + 23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04 + 24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04 + 25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04 + 26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml index 304db9fd60..672bf8946c 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:11 2024 epsilon: 5e-12 skip_tests: prerequisites: ! | @@ -15,8 +16,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134788658e+01 -2.6907707565985344e+01 -6.0080860422268874e+00 -2.5620423972099733e+01 -1.3450224059983656e+01 -1.4947288487000705e+00 -global_scalar: 18.340560167414306 + -4.9200116134789653e+01 -2.6907707565986087e+01 -6.0080860422267843e+00 -2.5620423972100063e+01 -1.3450224059983270e+01 -1.4947288486998982e+00 +global_scalar: 18.340560167414335 run_pos: ! |2 1 -2.7993683669226854e-01 2.4726588069312836e+00 -1.7200860244148508e-01 2 3.0197083955402171e-01 2.9515239068888608e+00 -8.5689735572907555e-01 @@ -36,14 +37,14 @@ run_pos: ! |2 16 2.6517554244980301e+00 -2.3957110424978438e+00 3.2908335999177751e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 18 2.1392027588271310e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074566e+00 2.6286809834111740e+00 -4.2452547844370239e+00 + 19 1.5366124997074584e+00 2.6286809834111722e+00 -4.2452547844370230e+00 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 - 21 4.9036621347791245e+00 -4.0757648442838557e+00 -3.6192617654515900e+00 - 22 4.3655322291888465e+00 -4.2084949965552569e+00 -4.4622011117402334e+00 + 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515900e+00 + 22 4.3655322291888465e+00 -4.2084949965552578e+00 -4.4622011117402343e+00 23 5.7380414793463101e+00 -3.5841969195032686e+00 -3.8827839830470232e+00 24 2.0701314765323913e+00 3.1499370533342308e+00 3.1565324852522920e+00 - 25 1.3030170721374770e+00 3.2711173927682236e+00 2.5081940917429755e+00 - 26 2.5776230782480054e+00 4.0127347068243875e+00 3.2182355138709262e+00 + 25 1.3030170721374779e+00 3.2711173927682236e+00 2.5081940917429755e+00 + 26 2.5776230782480036e+00 4.0127347068243875e+00 3.2182355138709280e+00 27 -1.9613581876744357e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678509e+00 29 -1.3108232656499084e+00 -3.5992986322410765e+00 2.2680459788743512e+00 @@ -65,15 +66,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704681e-04 -3.1032459262907857e-04 8.1043030117346074e-04 - 19 8.5103884665345820e-04 -1.4572280596788108e-03 1.0163621287634073e-03 - 20 -6.5204659278590271e-04 4.3989037444289630e-04 4.9909839028508215e-04 - 21 -1.3888125881903852e-03 -3.1978049143082049e-04 1.1455681499836594e-03 - 22 -1.6084223477729513e-03 -1.5355394240820970e-03 1.4772010826232351e-03 - 23 2.6392672378803975e-04 -3.9375414431174569e-03 -3.6991583139727910e-04 - 24 8.6062827067889835e-04 -9.4179873474469346e-04 5.5396395550012518e-04 - 25 1.5933645477487516e-03 -2.2139156625681669e-03 -5.5078029695647542e-04 - 26 -1.5679561743998831e-03 3.5146224354726187e-04 2.4446924193334495e-03 + 18 3.6149625095704659e-04 -3.1032459262907825e-04 8.1043030117346085e-04 + 19 8.5103884665346059e-04 -1.4572280596788099e-03 1.0163621287634082e-03 + 20 -6.5204659278590227e-04 4.3989037444289446e-04 4.9909839028508150e-04 + 21 -1.3888125881903869e-03 -3.1978049143081757e-04 1.1455681499836596e-03 + 22 -1.6084223477729556e-03 -1.5355394240821013e-03 1.4772010826232407e-03 + 23 2.6392672378803953e-04 -3.9375414431174656e-03 -3.6991583139727423e-04 + 24 8.6062827067889998e-04 -9.4179873474469411e-04 5.5396395550012377e-04 + 25 1.5933645477487516e-03 -2.2139156625681634e-03 -5.5078029695647109e-04 + 26 -1.5679561743998922e-03 3.5146224354726068e-04 2.4446924193334543e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml index c80a70b428..16ba7c079d 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:11 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,38 +15,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 4.3578059172167876e+01 1.7275105166465000e+01 6.7372361276631054e+01 5.1985075049901745e+01 -2.0990677389800993e+01 -7.5321398101844359e+00 -global_scalar: 29.023636440847998 + 4.3578059175768836e+01 1.7275105168781163e+01 6.7372361277896715e+01 5.1985075050485008e+01 -2.0990677388216337e+01 -7.5321398110797180e+00 +global_scalar: 29.023636439584656 run_pos: ! |2 - 1 -6.3472039825517168e-01 3.0113983126282058e+00 -8.8148450172235826e-02 - 2 6.4798884173500326e-02 3.5870486860057795e+00 -9.1146271255434463e-01 - 3 -1.1328967478840362e+00 1.5344674077762583e+00 -6.2949567786977667e-01 - 4 -2.1941320441841130e+00 1.8319737599530370e+00 -1.3824693495474225e+00 - 5 -1.3741175247360697e+00 1.1637763350569887e+00 6.0220861483086097e-01 - 6 5.5368589242158706e-02 3.1209253712244411e-01 -1.4252606627467266e+00 - 7 1.1075313780270069e-01 2.8008314824797154e-02 -2.8425552056438050e+00 - 8 1.1011987966104080e+00 -5.4254536577068713e-01 -6.9472264392660854e-01 - 9 1.3580030945401020e+00 -2.6595138115345840e-01 4.4172536708297194e-01 - 10 2.1282964643831388e+00 -1.6781145595676907e+00 -1.0442216631471304e+00 - 11 1.8571593172391605e+00 -2.3497452731071471e+00 -2.1462323657665392e+00 - 12 3.3117732698469986e+00 -5.4913311816190635e-01 -1.8274356036322548e+00 - 13 4.5640183918453143e+00 -1.0445083545907554e+00 -1.8509716390298214e+00 - 14 2.8312769330518019e+00 -4.5135848464344086e-01 -3.0735173792331993e+00 - 15 3.2788434490964296e+00 7.1618295543695254e-01 -1.3765217601452289e+00 - 16 2.8895075000232158e+00 -2.8409365554010479e+00 1.5818504152554702e-01 - 17 2.3837073405559277e+00 -2.4882133308169232e+00 1.5000885103549333e+00 - 18 2.2738793194357232e+00 3.6743407122553755e+00 -4.1408965121163197e+00 - 19 1.6572750518209336e+00 3.2770314238152451e+00 -4.8886441786593569e+00 - 20 2.9120476452800226e+00 4.3568412675031851e+00 -4.5732834167769187e+00 - 21 5.6058485050774536e+00 -4.8495065176300871e+00 -4.2655497599953458e+00 - 22 5.0552709232982114e+00 -4.9851876752032496e+00 -5.1280564953560424e+00 - 23 6.4593933585948218e+00 -4.3461765105422652e+00 -4.5350231456236889e+00 - 24 2.1823354619125279e+00 3.8552931130470363e+00 3.8953804330431208e+00 - 25 1.3973696115403698e+00 3.9794119228484153e+00 3.2321313266194949e+00 - 26 2.7018361227965517e+00 4.7379517631305443e+00 3.9583193478092706e+00 - 27 -2.6559803075358257e+00 -5.1969823689078796e+00 2.6552621488555683e+00 - 28 -3.5927802460207046e+00 -4.7943885088602283e+00 2.0214142204095413e+00 - 29 -1.8739632618339108e+00 -4.2877858778713946e+00 2.8450749793919066e+00 + 1 -6.3472039825540794e-01 3.0113983126285611e+00 -8.8148450172186088e-02 + 2 6.4798884173342230e-02 3.5870486860061987e+00 -9.1146271255438371e-01 + 3 -1.1328967478843275e+00 1.5344674077764573e+00 -6.2949567786978555e-01 + 4 -2.1941320441845233e+00 1.8319737599532644e+00 -1.3824693495475202e+00 + 5 -1.3741175247363868e+00 1.1637763350571468e+00 6.0220861483099597e-01 + 6 5.5368589242003274e-02 3.1209253712249918e-01 -1.4252606627468261e+00 + 7 1.1075313780254881e-01 2.8008314824818470e-02 -2.8425552056440617e+00 + 8 1.1011987966103707e+00 -5.4254536577072621e-01 -6.9472264392662098e-01 + 9 1.3580030945400878e+00 -2.6595138115347083e-01 4.4172536708308918e-01 + 10 2.1282964643832170e+00 -1.6781145595678604e+00 -1.0442216631471855e+00 + 11 1.8571593172392049e+00 -2.3497452731073896e+00 -2.1462323657667168e+00 + 12 3.3117732698472082e+00 -5.4913311816195076e-01 -1.8274356036323969e+00 + 13 4.5640183918456607e+00 -1.0445083545908531e+00 -1.8509716390299671e+00 + 14 2.8312769330519618e+00 -4.5135848464346928e-01 -3.0735173792334827e+00 + 15 3.2788434490966321e+00 7.1618295543705379e-01 -1.3765217601453177e+00 + 16 2.8895075000233756e+00 -2.8409365554013446e+00 1.5818504152563229e-01 + 17 2.3837073405560343e+00 -2.4882133308171808e+00 1.5000885103551624e+00 + 18 2.2738793194332434e+00 3.6743407122541889e+00 -4.1408965121171795e+00 + 19 1.6572750518219337e+00 3.2770314238270633e+00 -4.8886441786700008e+00 + 20 2.9120476452894675e+00 4.3568412674987194e+00 -4.5732834167653644e+00 + 21 5.6058485051319096e+00 -4.8495065176594299e+00 -4.2655497599906971e+00 + 22 5.0552709232924169e+00 -4.9851876754509741e+00 -5.1280564952785888e+00 + 23 6.4593933583860359e+00 -4.3461765101804879e+00 -4.5350231457223327e+00 + 24 2.1823354618683570e+00 3.8552931130563355e+00 3.8953804330779889e+00 + 25 1.3973696115700545e+00 3.9794119229082359e+00 3.2321313265764022e+00 + 26 2.7018361229436465e+00 4.7379517630364116e+00 3.9583193477161114e+00 + 27 -2.6559803075362858e+00 -5.1969823689084436e+00 2.6552621488559236e+00 + 28 -3.5927802460212725e+00 -4.7943885088607452e+00 2.0214142204098309e+00 + 29 -1.8739632618342856e+00 -4.2877858778718556e+00 2.8450749793922920e+00 run_vel: ! |2 1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.0094600491564739e-04 -2.4312792027781263e-04 6.5542049134062323e-04 - 19 7.4731683462770076e-04 -1.2894119671278408e-03 8.4327024053533397e-04 - 20 -6.2333686369976551e-04 4.4115361641690044e-04 3.7135656431834220e-04 - 21 -1.1457423793218525e-03 -1.7337748161437940e-04 9.4510018429417686e-04 - 22 -1.3457150581639313e-03 -1.2816797357047471e-03 1.2470992250388096e-03 - 23 3.6277645415306518e-04 -3.4719859048227848e-03 -4.3796817853449118e-04 - 24 7.2410992462873655e-04 -7.6012809744767037e-04 4.3327155128124943e-04 - 25 1.3921349892629666e-03 -1.9207002802664867e-03 -5.7453335109528090e-04 - 26 -1.4901465947638008e-03 4.2012923457099966e-04 2.1578545404178418e-03 + 18 3.0094600492089644e-04 -2.4312792028464785e-04 6.5542049134054972e-04 + 19 7.4731683460624917e-04 -1.2894119671240515e-03 8.4327024053305281e-04 + 20 -6.2333686369944134e-04 4.4115361644063580e-04 3.7135656432041769e-04 + 21 -1.1457423794330429e-03 -1.7337748206069275e-04 9.4510018428907005e-04 + 22 -1.3457150585185161e-03 -1.2816797348700177e-03 1.2470992253076274e-03 + 23 3.6277645495226573e-04 -3.4719859038751704e-03 -4.3796817878355291e-04 + 24 7.2410992459670032e-04 -7.6012809759399148e-04 4.3327155120505761e-04 + 25 1.3921349891892136e-03 -1.9207002802470530e-03 -5.7453335098663809e-04 + 26 -1.4901465945625111e-03 4.2012923513626559e-04 2.1578545406129137e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml index 3894815950..80cc4865c0 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:11 2024 epsilon: 6.5e-13 skip_tests: prerequisites: ! | @@ -14,38 +15,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 2.7340318973870396e+01 4.7963870091858283e+00 6.8884396847592512e+01 2.9853310007358935e+01 -1.0857139901347722e+01 -5.1889756561454785e+00 -global_scalar: 9.77678786310451 + 2.7340318979717416e+01 4.7963870104375275e+00 6.8884396847589585e+01 2.9853310005453281e+01 -1.0857139898599751e+01 -5.1889756547311965e+00 +global_scalar: 9.776787862991728 run_pos: ! |2 - 1 -5.1121862036604515e-01 2.8134872171079977e+00 -4.8993015395518924e-02 - 2 1.4735952488047133e-01 3.3535825972277546e+00 -9.3694001270735150e-01 - 3 -9.8023793775378820e-01 1.4277788160410712e+00 -6.3283768722999234e-01 - 4 -1.9793617512974304e+00 1.7069097152779946e+00 -1.4449221382955635e+00 - 5 -1.2073406578712120e+00 1.0799834439081337e+00 6.9555923026692668e-01 - 6 1.3848116183742931e-01 2.8090381873852976e-01 -1.4910727029127884e+00 - 7 1.9062418946016990e-01 1.4366032742456625e-02 -3.0196292835199614e+00 - 8 1.1231015082845541e+00 -5.2094745136401599e-01 -7.0318517336042774e-01 - 9 1.3648756844511976e+00 -2.6143726919534771e-01 5.2247754752734465e-01 - 10 2.0900856844466578e+00 -1.5863783165912952e+00 -1.0801209545800976e+00 - 11 1.8348175253566659e+00 -2.2165258198419622e+00 -2.2686429310672072e+00 - 12 3.2042965133156098e+00 -5.2712831182449804e-01 -1.9248196297790088e+00 - 13 4.3832508188729271e+00 -9.9190674157019298e-01 -1.9502033172902991e+00 - 14 2.7519224412447691e+00 -4.3539271970391624e-01 -3.2687227073821310e+00 - 15 3.1732939937025400e+00 6.6003562890618639e-01 -1.4385076445934288e+00 - 16 2.8067449168447887e+00 -2.6773787170015133e+00 2.1667842294144180e-01 - 17 2.3305479923928516e+00 -2.3464414104884277e+00 1.6639254952584981e+00 - 18 2.2269920241232128e+00 3.4328783208254681e+00 -4.4342132514635013e+00 - 19 1.6145347679280793e+00 3.0386658278179439e+00 -5.1868156516245785e+00 - 20 2.8608613711028656e+00 4.1100452338287408e+00 -4.8694049549907970e+00 - 21 5.3613621396958795e+00 -4.5653056926475841e+00 -4.5681019697305372e+00 - 22 4.8144754754921184e+00 -4.6999404674483083e+00 -5.4362066556130868e+00 - 23 6.2091840278795729e+00 -4.0659479262420684e+00 -4.8393130641864568e+00 - 24 2.1433208912603074e+00 3.5960988832146015e+00 4.2399236066404100e+00 - 25 1.3636453973491918e+00 3.7192408266342980e+00 3.5723762826473990e+00 - 26 2.6593036729945752e+00 4.4718649490241678e+00 4.3032623333405660e+00 - 27 -2.4141791756398536e+00 -4.8879035738852403e+00 2.9097838637418292e+00 - 28 -3.2961505257539048e+00 -4.5101758871984199e+00 2.2261768979308005e+00 - 29 -1.6779316575994301e+00 -4.0348635219024889e+00 3.1144975929056571e+00 + 1 -5.1121862036689958e-01 2.8134872171089729e+00 -4.8993015395755179e-02 + 2 1.4735952487989756e-01 3.3535825972289093e+00 -9.3694001270719340e-01 + 3 -9.8023793775484513e-01 1.4277788160415970e+00 -6.3283768722997102e-01 + 4 -1.9793617512989155e+00 1.7069097152786199e+00 -1.4449221382951762e+00 + 5 -1.2073406578723613e+00 1.0799834439085494e+00 6.9555923026634758e-01 + 6 1.3848116183685821e-01 2.8090381873868608e-01 -1.4910727029123834e+00 + 7 1.9062418945961834e-01 1.4366032742524126e-02 -3.0196292835188681e+00 + 8 1.1231015082843996e+00 -5.2094745136412257e-01 -7.0318517336038155e-01 + 9 1.3648756844511478e+00 -2.6143726919537080e-01 5.2247754752684727e-01 + 10 2.0900856844469189e+00 -1.5863783165917535e+00 -1.0801209545798738e+00 + 11 1.8348175253568222e+00 -2.2165258198426265e+00 -2.2686429310664504e+00 + 12 3.2042965133163452e+00 -5.2712831182460818e-01 -1.9248196297784048e+00 + 13 4.3832508188741741e+00 -9.9190674157045855e-01 -1.9502033172896844e+00 + 14 2.7519224412453145e+00 -4.3539271970399618e-01 -3.2687227073809266e+00 + 15 3.1732939937032665e+00 6.6003562890646350e-01 -1.4385076445930487e+00 + 16 2.8067449168453553e+00 -2.6773787170023233e+00 2.1667842294107942e-01 + 17 2.3305479923932175e+00 -2.3464414104891320e+00 1.6639254952574838e+00 + 18 2.2269920241209178e+00 3.4328783208250382e+00 -4.4342132514621486e+00 + 19 1.6145347679293440e+00 3.0386658278306271e+00 -5.1868156516331227e+00 + 20 2.8608613711127191e+00 4.1100452338250122e+00 -4.8694049549767646e+00 + 21 5.3613621397513214e+00 -4.5653056926761684e+00 -4.5681019697231218e+00 + 22 4.8144754754873968e+00 -4.6999404677006380e+00 -5.4362066555318300e+00 + 23 6.2091840276731247e+00 -4.0659479258840996e+00 -4.8393130642860642e+00 + 24 2.1433208912158790e+00 3.5960988832250020e+00 4.2399236066734023e+00 + 25 1.3636453973794058e+00 3.7192408266942927e+00 3.5723762826011995e+00 + 26 2.6593036731433042e+00 4.4718649489304223e+00 4.3032623332423157e+00 + 27 -2.4141791756415234e+00 -4.8879035738867795e+00 2.9097838637402536e+00 + 28 -3.2961505257559520e+00 -4.5101758871998348e+00 2.2261768979295358e+00 + 29 -1.6779316576007828e+00 -4.0348635219037465e+00 3.1144975929039944e+00 run_vel: ! |2 1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.1638284997073272e-04 -2.6313163919070405e-04 6.1054395248656961e-04 - 19 7.6494647252307673e-04 -1.3190724749214326e-03 7.9947132612985723e-04 - 20 -6.1620104632513929e-04 4.2577138774295274e-04 3.2526261653548693e-04 - 21 -1.2063428871524097e-03 -2.2879409878999576e-04 8.9132836538734445e-04 - 22 -1.4151473871894464e-03 -1.3502255393198256e-03 1.1972773109437849e-03 - 23 3.1280366109607172e-04 -3.5563936893394407e-03 -4.9548546532774958e-04 - 24 7.5594375541558026e-04 -8.1321043994394464e-04 3.9340911295780739e-04 - 25 1.4373446731689036e-03 -1.9778020567486213e-03 -6.1842201918304478e-04 - 26 -1.4806168650325999e-03 3.7766934274110835e-04 2.1280924225288342e-03 + 18 3.1638284997600319e-04 -2.6313163919763335e-04 6.1054395248685519e-04 + 19 7.6494647250110288e-04 -1.3190724749175438e-03 7.9947132612783736e-04 + 20 -6.1620104632483571e-04 4.2577138776739548e-04 3.2526261653790590e-04 + 21 -1.2063428872614197e-03 -2.2879409923923591e-04 8.9132836537741717e-04 + 22 -1.4151473875545966e-03 -1.3502255384792933e-03 1.1972773112250280e-03 + 23 3.1280366189902534e-04 -3.5563936883846667e-03 -4.9548546556753227e-04 + 24 7.5594375538112746e-04 -8.1321044009394260e-04 3.9340911288157350e-04 + 25 1.4373446730968913e-03 -1.9778020567293151e-03 -6.1842201907436371e-04 + 26 -1.4806168648243687e-03 3.7766934332225264e-04 2.1280924227258073e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml index f5965e53ff..6757db5703 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:12 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,65 +14,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.6326314448663306e+03 -1.4727331978532295e+03 -3.8557370515932275e+03 5.5052891601644615e+02 4.7346742977310657e+02 -6.2035591882122355e+02 -global_scalar: 106.86683072474125 + -1.6326314448662429e+03 -1.4727331978532245e+03 -3.8557370515929042e+03 5.5052891601619581e+02 4.7346742977256520e+02 -6.2035591882208064e+02 +global_scalar: 106.86683072474244 run_pos: ! |2 - 1 -2.6314711410922875e-01 2.4664715027241684e+00 -1.7093568570875561e-01 - 2 3.1632911015968190e-01 2.9434731493852482e+00 -8.5432214735778889e-01 - 3 -6.7623447816593885e-01 1.2410822625695044e+00 -6.1935152269903870e-01 - 4 -1.5552134736906362e+00 1.4878541800991378e+00 -1.2440909745466859e+00 - 5 -8.7601967096402067e-01 9.3417436540572218e-01 4.0272031680440712e-01 - 6 3.0755837780638462e-01 2.2629147986241449e-01 -1.2791162680673960e+00 - 7 3.5322094628053069e-01 -1.0043890952307954e-02 -2.4548503163676365e+00 - 8 1.1736205127907979e+00 -4.8269091330540537e-01 -6.7273784266507608e-01 - 9 1.3865071239751696e+00 -2.5278331076620741e-01 2.6996653369766221e-01 - 10 2.0239883243193546e+00 -1.4252201368162511e+00 -9.6228264545891751e-01 - 11 1.7991233925769246e+00 -1.9828365722517098e+00 -1.8762366544355809e+00 - 12 3.0044710092992837e+00 -4.8928363303895761e-01 -1.6126944183951402e+00 - 13 4.0415308387392486e+00 -9.0061411581930262e-01 -1.6321139880363660e+00 - 14 2.6064005411338655e+00 -4.0859653026870735e-01 -2.6465043951812621e+00 - 15 2.9775904824773907e+00 5.6065407887877150e-01 -1.2391617757503752e+00 - 16 2.6542663248057963e+00 -2.3895844048756363e+00 3.5746598094128501e-02 - 17 2.2355490747046538e+00 -2.0962135127180099e+00 1.1489434027780590e+00 - 18 2.0921160979727347e+00 2.9872159674143273e+00 -3.4902339097026891e+00 - 19 1.4908686219092431e+00 2.6025398330908249e+00 -4.2194623779121834e+00 - 20 2.7154518806645740e+00 3.6506388357595867e+00 -3.9111287168645399e+00 - 21 4.8435638296030810e+00 -4.0881941921728835e+00 -3.5957796498833634e+00 - 22 4.3080557005367073e+00 -4.2177797604324549e+00 -4.4370935526124242e+00 - 23 5.6713237924930837e+00 -3.5912865024293716e+00 -3.8555915013182531e+00 - 24 2.0228224543345528e+00 3.1208125399081723e+00 3.1634860992076259e+00 - 25 1.2576132296055036e+00 3.2447174749294536e+00 2.5191319958251963e+00 - 26 2.5334951322488237e+00 3.9783477827941720e+00 3.2212409164234312e+00 - 27 -1.8488304998563332e+00 -4.2601261704683342e+00 2.0568476369354265e+00 - 28 -2.6026086128772454e+00 -3.9329047688996304e+00 1.5399898445636406e+00 - 29 -1.2195954744860957e+00 -3.5211468177700818e+00 2.2116264666073615e+00 + 1 -2.6314711410917102e-01 2.4664715027243860e+00 -1.7093568570953632e-01 + 2 3.1632911015962950e-01 2.9434731493852171e+00 -8.5432214735883338e-01 + 3 -6.7623447816593352e-01 1.2410822625695497e+00 -6.1935152269929450e-01 + 4 -1.5552134736907304e+00 1.4878541800989344e+00 -1.2440909745469027e+00 + 5 -8.7601967096385724e-01 9.3417436540614585e-01 4.0272031680429610e-01 + 6 3.0755837780630380e-01 2.2629147986222176e-01 -1.2791162680674191e+00 + 7 3.5322094628027934e-01 -1.0043890952942114e-02 -2.4548503163675806e+00 + 8 1.1736205127908210e+00 -4.8269091330536096e-01 -6.7273784266496328e-01 + 9 1.3865071239753313e+00 -2.5278331076580596e-01 2.6996653369765600e-01 + 10 2.0239883243193466e+00 -1.4252201368163044e+00 -9.6228264545858089e-01 + 11 1.7991233925767878e+00 -1.9828365722521095e+00 -1.8762366544350000e+00 + 12 3.0044710092991682e+00 -4.8928363303924272e-01 -1.6126944183953009e+00 + 13 4.0415308387391402e+00 -9.0061411581958151e-01 -1.6321139880365303e+00 + 14 2.6064005411335902e+00 -4.0859653026938592e-01 -2.6465043951813936e+00 + 15 2.9775904824773161e+00 5.6065407887862850e-01 -1.2391617757509259e+00 + 16 2.6542663248059526e+00 -2.3895844048753085e+00 3.5746598094734239e-02 + 17 2.2355490747049700e+00 -2.0962135127172692e+00 1.1489434027786212e+00 + 18 2.0921160979710356e+00 2.9872159674136229e+00 -3.4902339097027140e+00 + 19 1.4908686219074729e+00 2.6025398330897387e+00 -4.2194623779119471e+00 + 20 2.7154518806624317e+00 3.6506388357591026e+00 -3.9111287168648765e+00 + 21 4.8435638296045518e+00 -4.0881941921723524e+00 -3.5957796498832693e+00 + 22 4.3080557005379525e+00 -4.2177797604322951e+00 -4.4370935526121276e+00 + 23 5.6713237924942437e+00 -3.5912865024285043e+00 -3.8555915013185178e+00 + 24 2.0228224543350635e+00 3.1208125399084361e+00 3.1634860992076055e+00 + 25 1.2576132296057372e+00 3.2447174749292715e+00 2.5191319958254175e+00 + 26 2.5334951322489658e+00 3.9783477827946756e+00 3.2212409164231035e+00 + 27 -1.8488304998563332e+00 -4.2601261704683413e+00 2.0568476369354238e+00 + 28 -2.6026086128772454e+00 -3.9329047688996370e+00 1.5399898445636415e+00 + 29 -1.2195954744860957e+00 -3.5211468177700862e+00 2.2116264666073588e+00 run_vel: ! 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| @@ -13,38 +14,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -8.7531774769722489e+01 5.5811525017966304e+00 -5.5468297744356747e+01 -1.5316306343483370e+02 1.4641268097314367e+02 1.7263710089631324e+01 -global_scalar: 77.78983430293286 + -8.7531774640811420e+01 5.5811525750281774e+00 -5.5468297761715007e+01 -1.5316306336726905e+02 1.4641268095299071e+02 1.7263710083146290e+01 +global_scalar: 77.78983430422252 run_pos: ! |2 - 1 -4.6333219629007161e-01 2.7511450055070625e+00 -1.2865946102806269e-01 - 2 1.7937148390204793e-01 3.2800405238539234e+00 -8.8510337855738808e-01 - 3 -9.2104620265671233e-01 1.3941717929286011e+00 -6.2603796687145774e-01 - 4 -1.8960869879711328e+00 1.6675144043869761e+00 -1.3178544214440926e+00 - 5 -1.1426748052069362e+00 1.0535885915279550e+00 5.0562616550054784e-01 - 6 1.7070712623541162e-01 2.7107933832755826e-01 -1.3571701846607374e+00 - 7 2.2159329060539701e-01 1.0068698962042433e-02 -2.6593507556860114e+00 - 8 1.1315940381701060e+00 -5.1414408469809381e-01 -6.8596713849763802e-01 - 9 1.3675404538221994e+00 -2.6001531899016506e-01 3.5817751536664133e-01 - 10 2.0752698846777218e+00 -1.5574812996955254e+00 -1.0070795245589492e+00 - 11 1.8261547470632067e+00 -2.1745615463231482e+00 -2.0195839000288469e+00 - 12 3.1626236108721066e+00 -5.2019677375525752e-01 -1.7266801053747978e+00 - 13 4.3131602274134853e+00 -9.7533717592326674e-01 -1.7483045222380902e+00 - 14 2.7211536303664605e+00 -4.3036348628163701e-01 -2.8715539682060491e+00 - 15 3.1323683805788374e+00 6.4234915962457073e-01 -1.3123899007466848e+00 - 16 2.7746546569032322e+00 -2.6258578189755974e+00 9.7666596945726880e-02 - 17 2.3099360535750506e+00 -2.3017831004883886e+00 1.3305794265747686e+00 - 18 2.2091748314094701e+00 3.3564440703097080e+00 -3.8370878208998480e+00 - 19 1.5986312961639815e+00 2.9614993054417287e+00 -4.5778944294436021e+00 - 20 2.8405364052167421e+00 4.0335971973474170e+00 -4.2659151034329339e+00 - 21 5.2651527410670678e+00 -4.4761614286515128e+00 -3.9518304737634447e+00 - 22 4.7192922284117014e+00 -4.6119045765637390e+00 -4.8062296930647124e+00 - 23 6.1127575782518644e+00 -3.9811721108739997e+00 -4.2204729624242692e+00 - 24 2.1290800761933255e+00 3.5132841007593623e+00 3.5392070209389175e+00 - 25 1.3519459804490630e+00 3.6349473854278020e+00 2.8807586653452137e+00 - 26 2.6413474233716503e+00 4.3893648735951771e+00 3.6035699967293215e+00 - 27 -2.3204235087828389e+00 -4.7905434153250859e+00 2.3919287951691697e+00 - 28 -3.1811356909797261e+00 -4.4206486004501846e+00 1.8095625809312565e+00 - 29 -1.6019226098503827e+00 -3.9551927030786480e+00 2.5663248522869146e+00 + 1 -4.6333219629057343e-01 2.7511450055078264e+00 -1.2865946102794723e-01 + 2 1.7937148390171043e-01 3.2800405238548382e+00 -8.8510337855745913e-01 + 3 -9.2104620265733672e-01 1.3941717929290096e+00 -6.2603796687147195e-01 + 4 -1.8960869879720148e+00 1.6675144043874610e+00 -1.3178544214442827e+00 + 5 -1.1426748052076219e+00 1.0535885915282748e+00 5.0562616550083384e-01 + 6 1.7070712623507234e-01 2.7107933832768616e-01 -1.3571701846609390e+00 + 7 2.2159329060507194e-01 1.0068698962099276e-02 -2.6593507556865532e+00 + 8 1.1315940381700180e+00 -5.1414408469817374e-01 -6.8596713849766644e-01 + 9 1.3675404538221745e+00 -2.6001531899018637e-01 3.5817751536688647e-01 + 10 2.0752698846778816e+00 -1.5574812996958780e+00 -1.0070795245590576e+00 + 11 1.8261547470632973e+00 -2.1745615463236652e+00 -2.0195839000292208e+00 + 12 3.1626236108725436e+00 -5.2019677375534190e-01 -1.7266801053750953e+00 + 13 4.3131602274142278e+00 -9.7533717592347013e-01 -1.7483045222383922e+00 + 14 2.7211536303667962e+00 -4.3036348628169740e-01 -2.8715539682066451e+00 + 15 3.1323683805792637e+00 6.4234915962478567e-01 -1.3123899007468758e+00 + 16 2.7746546569035768e+00 -2.6258578189762343e+00 9.7666596945902739e-02 + 17 2.3099360535752709e+00 -2.3017831004889393e+00 1.3305794265752642e+00 + 18 2.2091748313982826e+00 3.3564440703034535e+00 -3.8370878209026742e+00 + 19 1.5986312961681257e+00 2.9614993054929961e+00 -4.5778944294898185e+00 + 20 2.8405364052584243e+00 4.0335971973267473e+00 -4.2659151033808254e+00 + 21 5.2651527413064194e+00 -4.4761614287784965e+00 -3.9518304737405883e+00 + 22 4.7192922283808425e+00 -4.6119045776644754e+00 -4.8062296927145907e+00 + 23 6.1127575773332410e+00 -3.9811721092729444e+00 -4.2204729628712050e+00 + 24 2.1290800759971340e+00 3.5132841007987228e+00 3.5392070210919400e+00 + 25 1.3519459805793055e+00 3.6349473856926782e+00 2.8807586651545414e+00 + 26 2.6413474240255201e+00 4.3893648731792023e+00 3.6035699963154144e+00 + 27 -2.3204235087838274e+00 -4.7905434153262867e+00 2.3919287951699459e+00 + 28 -3.1811356909809412e+00 -4.4206486004512886e+00 1.8095625809318783e+00 + 29 -1.6019226098511883e+00 -3.9551927030796277e+00 2.5663248522877335e+00 run_vel: ! |2 1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 @@ -63,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 7.2384391131466940e-04 -6.0015829212802722e-04 1.5957533238990559e-03 - 19 1.7583138222551384e-03 -3.0158245948490804e-03 2.0310435058142470e-03 - 20 -1.4153552732353322e-03 9.7835305930749246e-04 9.3881222516217474e-04 - 21 -2.7591188772323472e-03 -5.1180650802276303e-04 2.2758295071994400e-03 - 22 -3.2319732401280494e-03 -3.0809796427949646e-03 2.9861065768383484e-03 - 23 6.9767443123301817e-04 -8.1543313142268207e-03 -8.9929522742256325e-04 - 24 1.7345816999787505e-03 -1.8508160062822962e-03 1.0723416147087287e-03 - 25 3.2855417755407162e-03 -4.5284294762327620e-03 -1.2529299007822618e-03 - 26 -3.4004728795728936e-03 8.5952140737749613e-04 5.0505027847540665e-03 + 18 7.2384391137821785e-04 -6.0015829219183913e-04 1.5957533239005792e-03 + 19 1.7583138220942001e-03 -3.0158245949231362e-03 2.0310435058145879e-03 + 20 -1.4153552733289841e-03 9.7835305963750062e-04 9.3881222515317965e-04 + 21 -2.7591188784018856e-03 -5.1180651254767841e-04 2.2758295071625967e-03 + 22 -3.2319732438308327e-03 -3.0809796341686479e-03 2.9861065796802132e-03 + 23 6.9767443960831559e-04 -8.1543313047864312e-03 -8.9929523012053270e-04 + 24 1.7345816996818938e-03 -1.8508160077951139e-03 1.0723416139084840e-03 + 25 3.2855417748809557e-03 -4.5284294761711655e-03 -1.2529298997977286e-03 + 26 -3.4004728777299181e-03 8.5952141335802687e-04 5.0505027869618231e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml index b20d639fd4..0e8f18da7b 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:13 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,65 +15,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356938011610e+03 -1.4496493316650424e+03 -3.6144360982532016e+03 8.4840626794792252e+02 2.0318336802442886e+02 -6.0622397695978805e+02 -global_scalar: 15.711521423178128 + -1.4245356938011316e+03 -1.4496493316650758e+03 -3.6144360982530934e+03 8.4840626794790273e+02 2.0318336802433893e+02 -6.0622397695991208e+02 +global_scalar: 15.711521423178162 run_pos: ! |2 - 1 -2.7899546863905123e-01 2.4731857340327181e+00 -1.7290667740231969e-01 - 2 3.0296221610252227e-01 2.9517129916957194e+00 -8.5798904387756503e-01 - 3 -6.9368802364141247e-01 1.2445115421753310e+00 -6.2281111198650718e-01 - 4 -1.5764879647103560e+00 1.4919714415840475e+00 -1.2492069414674947e+00 - 5 -8.9434512967440649e-01 9.3651699743494377e-01 4.0191726558257690e-01 - 6 2.9454439634452678e-01 2.2724545792543693e-01 -1.2845195053960459e+00 - 7 3.4049112903278234e-01 -9.4655678321664549e-03 -2.4634480020857370e+00 - 8 1.1644354555804921e+00 -4.8367776650962330e-01 -6.7663643940738027e-01 - 9 1.3781717822695918e+00 -2.5332509530017322e-01 2.6864954436590494e-01 - 10 2.0186368606042460e+00 -1.4285861423625348e+00 -9.6712491252784183e-01 - 11 1.7929137227578726e+00 -1.9875455388406436e+00 -1.8836565352267429e+00 - 12 3.0032775230400142e+00 -4.8983022415161337e-01 -1.6190248017342870e+00 - 13 4.0448964162126639e+00 -9.0213155122374034e-01 -1.6385398399478515e+00 - 14 2.6035151245016883e+00 -4.0874995493201027e-01 -2.6555999074785985e+00 - 15 2.9761196776172243e+00 5.6287237454118566e-01 -1.2442626196081918e+00 - 16 2.6517373021566577e+00 -2.3957035508393689e+00 3.3389262100618433e-02 - 17 2.2311114924744668e+00 -2.1018393228799419e+00 1.1496088522376777e+00 - 18 2.1390642573199212e+00 3.0164773560692755e+00 -3.5143984803853900e+00 - 19 1.5353246655143720e+00 2.6305911186314508e+00 -4.2455871034736816e+00 - 20 2.7649421538935122e+00 3.6818603528430254e+00 -3.9364115785985936e+00 - 21 4.9043112657301942e+00 -4.0774268210396798e+00 -3.6200836396129796e+00 - 22 4.3665322424286144e+00 -4.2075138112953070e+00 -4.4636587264885614e+00 - 23 5.7355405581987764e+00 -3.5789558641907195e+00 -3.8805763324090350e+00 - 24 2.0692780332810026e+00 3.1504920436416008e+00 3.1571131300668833e+00 - 25 1.3007297593168636e+00 3.2745259354178766e+00 2.5110163874103986e+00 - 26 2.5819416446099002e+00 4.0104903120757012e+00 3.2150249624525742e+00 + 1 -2.7899546863904412e-01 2.4731857340327541e+00 -1.7290667740243348e-01 + 2 3.0296221610251317e-01 2.9517129916957181e+00 -8.5798904387771990e-01 + 3 -6.9368802364141358e-01 1.2445115421753392e+00 -6.2281111198654315e-01 + 4 -1.5764879647103740e+00 1.4919714415840188e+00 -1.2492069414675249e+00 + 5 -8.9434512967438362e-01 9.3651699743500849e-01 4.0191726558256402e-01 + 6 2.9454439634451368e-01 2.2724545792540876e-01 -1.2845195053960490e+00 + 7 3.4049112903274215e-01 -9.4655678322607961e-03 -2.4634480020857299e+00 + 8 1.1644354555804954e+00 -4.8367776650961680e-01 -6.7663643940736340e-01 + 9 1.3781717822696169e+00 -2.5332509530011327e-01 2.6864954436590560e-01 + 10 2.0186368606042455e+00 -1.4285861423625437e+00 -9.6712491252779242e-01 + 11 1.7929137227578522e+00 -1.9875455388407057e+00 -1.8836565352266585e+00 + 12 3.0032775230399977e+00 -4.8983022415165589e-01 -1.6190248017343138e+00 + 13 4.0448964162126479e+00 -9.0213155122378219e-01 -1.6385398399478794e+00 + 14 2.6035151245016470e+00 -4.0874995493211108e-01 -2.6555999074786221e+00 + 15 2.9761196776172136e+00 5.6287237454116579e-01 -1.2442626196082760e+00 + 16 2.6517373021566839e+00 -2.3957035508393223e+00 3.3389262100708361e-02 + 17 2.2311114924745179e+00 -2.1018393228798340e+00 1.1496088522377621e+00 + 18 2.1390642573196605e+00 3.0164773560691671e+00 -3.5143984803853927e+00 + 19 1.5353246655140995e+00 2.6305911186312847e+00 -4.2455871034736425e+00 + 20 2.7649421538931831e+00 3.6818603528429503e+00 -3.9364115785986438e+00 + 21 4.9043112657304171e+00 -4.0774268210395990e+00 -3.6200836396129659e+00 + 22 4.3665322424288018e+00 -4.2075138112952830e+00 -4.4636587264885161e+00 + 23 5.7355405581989505e+00 -3.5789558641905872e+00 -3.8805763324090754e+00 + 24 2.0692780332810834e+00 3.1504920436416377e+00 3.1571131300668784e+00 + 25 1.3007297593169014e+00 3.2745259354178451e+00 2.5110163874104305e+00 + 26 2.5819416446099250e+00 4.0104903120757749e+00 3.2150249624525231e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093289825841293e-04 2.6351122778450888e-04 -4.4905093064113717e-04 - 2 4.9594625316469964e-04 9.4561370489668111e-05 -5.4581359894048111e-04 - 3 3.3306085115754910e-04 2.3224943880673595e-04 -2.3659455671744723e-04 - 4 3.3692327392259764e-04 2.1926810694050300e-04 -2.4716631558861373e-04 - 5 3.3642542694184180e-04 4.1797578013266372e-04 -1.8011341766654800e-04 - 6 2.0926869754934492e-04 2.6449308951570887e-05 -1.0508938983871866e-04 - 7 1.4629043007908284e-04 -1.6873376665352296e-04 -6.8354048774366290e-05 - 8 1.5844101624224813e-04 3.7728761273997381e-05 -1.9162715667088780e-05 - 9 2.1299362072601532e-04 1.6917140529158732e-04 -6.3528165037833598e-05 - 10 5.4261629412260376e-05 -9.4655528376821362e-05 1.0511362869146115e-04 - 11 -3.2194160796493454e-05 -2.2025095264761673e-04 2.0300202946211041e-04 - 12 1.2640586304751833e-04 -2.9851080445664229e-04 -7.9476371818270762e-05 - 13 8.4523575162163329e-05 -4.0583135407329152e-04 -4.7551111331733064e-05 - 14 9.9954050381288400e-05 -4.2610816481298728e-04 -7.9255633594414740e-05 - 15 2.4417481119791087e-04 -2.3521002264675206e-04 -2.4875318161051227e-04 - 16 -9.0958138549618100e-06 3.7774817121146141e-06 2.4035199548835590e-04 - 17 5.7507224523608950e-05 2.2629217444844056e-04 2.0686920072686990e-04 - 18 2.9220264989358538e-04 -6.2478376436791018e-04 8.4222594596602778e-04 - 19 2.0572616567796829e-04 -5.0334424271721273e-04 8.4953929443210897e-04 - 20 4.1224811789512659e-04 -7.4115205416005016e-04 8.3678612337508636e-04 - 21 -1.0671858777656236e-03 -1.1531171045500116e-03 7.3720674900161585e-04 - 22 -1.1066511338291651e-03 -1.0433933757601002e-03 7.4544544325707912e-04 - 23 -9.7629260480938717e-04 -1.3100872491594619e-03 7.2687284219704522e-04 - 24 4.3308126651259090e-04 -6.6527658087322823e-04 8.4451298670663681e-04 - 25 4.4565811905441464e-04 -5.1298436273583472e-04 8.5878867884521526e-04 - 26 5.9865972692023459e-04 -7.6385263287079232e-04 8.4259943226842524e-04 + 1 4.7093289825842481e-04 2.6351122778449815e-04 -4.4905093064115029e-04 + 2 4.9594625316470614e-04 9.4561370489646928e-05 -5.4581359894049163e-04 + 3 3.3306085115755453e-04 2.3224943880673822e-04 -2.3659455671744877e-04 + 4 3.3692327392259862e-04 2.1926810694050856e-04 -2.4716631558860722e-04 + 5 3.3642542694185568e-04 4.1797578013267277e-04 -1.8011341766655748e-04 + 6 2.0926869754934175e-04 2.6449308951572771e-05 -1.0508938983871239e-04 + 7 1.4629043007906883e-04 -1.6873376665352220e-04 -6.8354048774347479e-05 + 8 1.5844101624224818e-04 3.7728761274000153e-05 -1.9162715667088122e-05 + 9 2.1299362072602399e-04 1.6917140529158875e-04 -6.3528165037844006e-05 + 10 5.4261629412255362e-05 -9.4655528376817648e-05 1.0511362869146607e-04 + 11 -3.2194160796507657e-05 -2.2025095264760857e-04 2.0300202946212778e-04 + 12 1.2640586304750909e-04 -2.9851080445665606e-04 -7.9476371818267184e-05 + 13 8.4523575162152420e-05 -4.0583135407330979e-04 -4.7551111331730963e-05 + 14 9.9954050381270538e-05 -4.2610816481300132e-04 -7.9255633594400035e-05 + 15 2.4417481119790729e-04 -2.3521002264677391e-04 -2.4875318161051720e-04 + 16 -9.0958138549606716e-06 3.7774817121242263e-06 2.4035199548835337e-04 + 17 5.7507224523620660e-05 2.2629217444845357e-04 2.0686920072685659e-04 + 18 2.9220264989356375e-04 -6.2478376436786377e-04 8.4222594596602756e-04 + 19 2.0572616567793704e-04 -5.0334424271716611e-04 8.4953929443210886e-04 + 20 4.1224811789511017e-04 -7.4115205415999053e-04 8.3678612337508690e-04 + 21 -1.0671858777656028e-03 -1.1531171045500558e-03 7.3720674900162051e-04 + 22 -1.1066511338291541e-03 -1.0433933757601397e-03 7.4544544325708389e-04 + 23 -9.7629260480935768e-04 -1.3100872491594961e-03 7.2687284219705075e-04 + 24 4.3308126651259366e-04 -6.6527658087323755e-04 8.4451298670663172e-04 + 25 4.4565811905440515e-04 -5.1298436273583775e-04 8.5878867884520984e-04 + 26 5.9865972692024294e-04 -7.6385263287079004e-04 8.4259943226842036e-04 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml index 839ac060a5..b0e52d3fea 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:13 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 -global_scalar: 18.340560167364448 + -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 +global_scalar: 18.340560165889197 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 - 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 - 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 - 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 - 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 - 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 - 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 - 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 - 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 + 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 + 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 + 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 + 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 + 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 + 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 + 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 + 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 + 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 - 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 - 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 - 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 - 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 - 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 - 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 - 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 - 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 + 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 + 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 + 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 + 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 + 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 + 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 + 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 + 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 + 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml index 854e8b4d45..0277d7991a 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:13 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,26 +15,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817467882767e+03 -1.4228425246441275e+03 -3.6087196200592489e+03 8.7407043142559303e+02 2.1665316510426268e+02 -6.0480791467747542e+02 -global_scalar: 4.531423038570333 + -1.3754817467882813e+03 -1.4228425246442055e+03 -3.6087196200592184e+03 8.7407043142559792e+02 2.1665316510417179e+02 -6.0480791467761571e+02 +global_scalar: 4.531423038570381 run_pos: ! |2 - 1 -2.7899546859706881e-01 2.4731857340427750e+00 -1.7290667720866193e-01 - 2 3.0296221616781649e-01 2.9517129917211218e+00 -8.5798904365338713e-01 - 3 -6.9368802362172777e-01 1.2445115422148878e+00 -6.2281111185285920e-01 - 4 -1.5764879646739900e+00 1.4919714416721197e+00 -1.2492069413381908e+00 - 5 -8.9434512967965252e-01 9.3651699743522254e-01 4.0191726569953845e-01 - 6 2.9454439635066831e-01 2.2724545796942719e-01 -1.2845195052894431e+00 - 7 3.4049112905319934e-01 -9.4655677384814507e-03 -2.4634480019885556e+00 - 8 1.1644354555589707e+00 -4.8367776651303718e-01 -6.7663643931662931e-01 - 9 1.3781717822376129e+00 -2.5332509534954067e-01 2.6864954447021949e-01 - 10 2.0186368605646337e+00 -1.4285861423742481e+00 -9.6712491246329535e-01 - 11 1.7929137227202196e+00 -1.9875455388073511e+00 -1.8836565351901273e+00 - 12 3.0032775230343667e+00 -4.8983022415922672e-01 -1.6190248016125368e+00 - 13 4.0448964161972993e+00 -9.0213155125590028e-01 -1.6385398398261621e+00 - 14 2.6035151245156412e+00 -4.0874995488520105e-01 -2.6555999073601511e+00 - 15 2.9761196776308623e+00 5.6287237451808192e-01 -1.2442626194415292e+00 - 16 2.6517373020764632e+00 -2.3957035509096389e+00 3.3389262134244646e-02 - 17 2.2311114923824555e+00 -2.1018393229880719e+00 1.1496088522768189e+00 + 1 -2.7899546859705771e-01 2.4731857340428069e+00 -1.7290667720877784e-01 + 2 3.0296221616781072e-01 2.9517129917211151e+00 -8.5798904365354312e-01 + 3 -6.9368802362172532e-01 1.2445115422148945e+00 -6.2281111185289584e-01 + 4 -1.5764879646740031e+00 1.4919714416720897e+00 -1.2492069413382207e+00 + 5 -8.9434512967962521e-01 9.3651699743528616e-01 4.0191726569952280e-01 + 6 2.9454439635065666e-01 2.2724545796939852e-01 -1.2845195052894454e+00 + 7 3.4049112905316026e-01 -9.4655677385761805e-03 -2.4634480019885459e+00 + 8 1.1644354555589742e+00 -4.8367776651303018e-01 -6.7663643931661244e-01 + 9 1.3781717822376380e+00 -2.5332509534948033e-01 2.6864954447021760e-01 + 10 2.0186368605646310e+00 -1.4285861423742554e+00 -9.6712491246324517e-01 + 11 1.7929137227201968e+00 -1.9875455388074099e+00 -1.8836565351900401e+00 + 12 3.0032775230343471e+00 -4.8983022415926980e-01 -1.6190248016125621e+00 + 13 4.0448964161972807e+00 -9.0213155125594269e-01 -1.6385398398261892e+00 + 14 2.6035151245155976e+00 -4.0874995488530264e-01 -2.6555999073601715e+00 + 15 2.9761196776308503e+00 5.6287237451805949e-01 -1.2442626194416131e+00 + 16 2.6517373020764849e+00 -2.3957035509095892e+00 3.3389262134333686e-02 + 17 2.2311114923825035e+00 -2.1018393229879604e+00 1.1496088522769004e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -47,23 +48,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226164550e-04 2.6351124312060223e-04 -4.4905063547613568e-04 - 2 4.9594635271876775e-04 9.4561409237174846e-05 -5.4581325723053790e-04 - 3 3.3306088119081919e-04 2.3224949911015709e-04 -2.3659435306899653e-04 - 4 3.3692332940285361e-04 2.1926824120528752e-04 -2.4716611858555457e-04 - 5 3.3642541894622217e-04 4.1797578053944250e-04 -1.8011323945926332e-04 - 6 2.0926870695908031e-04 2.6449376032433555e-05 -1.0508922741401509e-04 - 7 1.4629046128363305e-04 -1.6873362379725323e-04 -6.8353900724087087e-05 - 8 1.5844098346817862e-04 3.7728756087615553e-05 -1.9162577392847385e-05 - 9 2.1299357198252531e-04 1.6917133003967874e-04 -6.3528006071188683e-05 - 10 5.4261569071251603e-05 -9.4655546204709643e-05 1.0511372702289179e-04 - 11 -3.2194218121513917e-05 -2.2025090185605342e-04 2.0300208519291412e-04 - 12 1.2640585449265036e-04 -2.9851081600945991e-04 -7.9476186245599681e-05 - 13 8.4523551795123310e-05 -4.0583140303606936e-04 -4.7550925831962545e-05 - 14 9.9954071734181717e-05 -4.2610809338914382e-04 -7.9255453072696249e-05 - 15 2.4417483202631243e-04 -2.3521005781666407e-04 -2.4875292755154228e-04 - 16 -9.0959360838797421e-06 3.7773746063106756e-06 2.4035204669042973e-04 - 17 5.7507084250803101e-05 2.2629200960629499e-04 2.0686926033796699e-04 + 1 4.7093296226165618e-04 2.6351124312058857e-04 -4.4905063547614403e-04 + 2 4.9594635271877252e-04 9.4561409237151983e-05 -5.4581325723054321e-04 + 3 3.3306088119082413e-04 2.3224949911015692e-04 -2.3659435306899455e-04 + 4 3.3692332940285378e-04 2.1926824120529077e-04 -2.4716611858554389e-04 + 5 3.3642541894623611e-04 4.1797578053944765e-04 -1.8011323945926958e-04 + 6 2.0926870695907706e-04 2.6449376032434591e-05 -1.0508922741400673e-04 + 7 1.4629046128361865e-04 -1.6873362379725188e-04 -6.8353900724066446e-05 + 8 1.5844098346817927e-04 3.7728756087617390e-05 -1.9162577392845779e-05 + 9 2.1299357198253474e-04 1.6917133003967807e-04 -6.3528006071197993e-05 + 10 5.4261569071247645e-05 -9.4655546204705848e-05 1.0511372702289633e-04 + 11 -3.2194218121526927e-05 -2.2025090185604412e-04 2.0300208519293052e-04 + 12 1.2640585449264128e-04 -2.9851081600947238e-04 -7.9476186245595616e-05 + 13 8.4523551795112752e-05 -4.0583140303608579e-04 -4.7550925831960783e-05 + 14 9.9954071734163598e-05 -4.2610809338915548e-04 -7.9255453072680826e-05 + 15 2.4417483202630842e-04 -2.3521005781668527e-04 -2.4875292755154548e-04 + 16 -9.0959360838764895e-06 3.7773746063197473e-06 2.4035204669042547e-04 + 17 5.7507084250817169e-05 2.2629200960630572e-04 2.0686926033795233e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml index 664921b147..1a017f0a6c 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:14 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 -global_scalar: 0.5007318719663203 + -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 +global_scalar: 0.5007318719399354 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 - 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 - 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 - 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 - 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 - 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 - 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 - 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 - 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 + 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 + 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 + 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 + 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 + 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 + 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 + 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 + 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 + 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 - 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 - 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 - 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 - 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 - 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 - 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 - 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 - 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 + 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 + 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 + 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 + 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 + 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 + 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 + 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 + 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 + 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml index a49508ca15..f15e2a3c7f 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml @@ -1,7 +1,8 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 -epsilon: 5e-13 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:14 2024 +epsilon: 1e-12 skip_tests: prerequisites: ! | atom full @@ -13,26 +14,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3123962047757550e+03 -1.3675423591710460e+03 -3.5468492999583855e+03 7.8271738572396373e+02 2.6480486115495069e+02 -7.6950536863736306e+02 -global_scalar: 68.08659647423171 + -1.3123962047758187e+03 -1.3675423591720764e+03 -3.5468492999580299e+03 7.8271738572394452e+02 2.6480486115379637e+02 -7.6950536863892899e+02 +global_scalar: 68.08659647424867 run_pos: ! |2 - 1 -2.7802951913990959e-01 2.4737132264311215e+00 -1.7381271738602289e-01 - 2 3.0397800832473609e-01 2.9519031941431444e+00 -8.5908822750267100e-01 - 3 -6.9299720296404743e-01 1.2449766685866726e+00 -6.2329294828335358e-01 - 4 -1.5757894675975461e+00 1.4924105480974301e+00 -1.2497098747240374e+00 - 5 -8.9364750934418624e-01 9.3735293261000852e-01 4.0154813851989335e-01 - 6 2.9498813449175199e-01 2.2729986882976547e-01 -1.2847387164260673e+00 - 7 3.4080910885027837e-01 -9.8008218359699473e-03 -2.4635938021179546e+00 - 8 1.1647778042705452e+00 -4.8360070140706557e-01 -6.7668409924218165e-01 - 9 1.3786230528159027e+00 -2.5298559880150862e-01 2.6851325883861188e-01 - 10 2.0187712935465942e+00 -1.4287732348422091e+00 -9.6692440387148870e-01 - 11 1.7928755785831587e+00 -1.9879833661313322e+00 -1.8832605388690278e+00 - 12 3.0035558347419657e+00 -4.9042429038271507e-01 -1.6191927838346238e+00 - 13 4.0450911337530959e+00 -9.0293975523160919e-01 -1.6386440514135796e+00 - 14 2.6037405819194577e+00 -4.0959881564101863e-01 -2.6557674031621108e+00 - 15 2.9766330093335447e+00 5.6240461100771322e-01 -1.2447686007433758e+00 - 16 2.6517453810147344e+00 -2.3956939898026426e+00 3.3859750042781744e-02 - 17 2.2312525656149020e+00 -2.1013855689264771e+00 1.1500124166835219e+00 + 1 -2.7802951913978302e-01 2.4737132264315886e+00 -1.7381271738770820e-01 + 2 3.0397800832462774e-01 2.9519031941430738e+00 -8.5908822750493219e-01 + 3 -6.9299720296403144e-01 1.2449766685867643e+00 -6.2329294828390935e-01 + 4 -1.5757894675977402e+00 1.4924105480969891e+00 -1.2497098747245081e+00 + 5 -8.9364750934382919e-01 9.3735293261092456e-01 4.0154813851965188e-01 + 6 2.9498813449158368e-01 2.2729986882934847e-01 -1.2847387164261186e+00 + 7 3.4080910884973536e-01 -9.8008218373410172e-03 -2.4635938021178290e+00 + 8 1.1647778042705941e+00 -4.8360070140696521e-01 -6.7668409924193851e-01 + 9 1.3786230528162504e+00 -2.5298559880063631e-01 2.6851325883859889e-01 + 10 2.0187712935465760e+00 -1.4287732348423197e+00 -9.6692440387075651e-01 + 11 1.7928755785828601e+00 -1.9879833661321924e+00 -1.8832605388677695e+00 + 12 3.0035558347417104e+00 -4.9042429038332558e-01 -1.6191927838349707e+00 + 13 4.0450911337528455e+00 -9.0293975523220671e-01 -1.6386440514139291e+00 + 14 2.6037405819188639e+00 -4.0959881564248080e-01 -2.6557674031623937e+00 + 15 2.9766330093333795e+00 5.6240461100740513e-01 -1.2447686007445669e+00 + 16 2.6517453810150675e+00 -2.3956939898019254e+00 3.3859750044092363e-02 + 17 2.2312525656155877e+00 -2.1013855689248668e+00 1.1500124166847305e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -46,23 +47,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 1.8443993556501188e-03 1.0121779580014884e-03 -1.7361326034900006e-03 - 2 1.9401022924558343e-03 3.6428754787592733e-04 -2.1069540627804634e-03 - 3 1.3158623602983108e-03 8.9265747656461540e-04 -9.2144725682164657e-04 - 4 1.3306255280096089e-03 8.4281508655990054e-04 -9.6194026572564146e-04 - 5 1.3289682243410692e-03 1.6048237018834067e-03 -7.0511232123071470e-04 - 6 8.4113718611833661e-04 1.0389683283144290e-04 -4.1697370456873913e-04 - 7 5.9950574545626287e-04 -6.4437674895215604e-04 -2.7586696717582678e-04 - 8 6.4634547270651834e-04 1.4734228826522431e-04 -8.7540766366730972e-05 - 9 8.5561404484505246e-04 6.5123532540338036e-04 -2.5782947158524498e-04 - 10 2.4688038968480818e-04 -3.5995975344065565e-04 3.8912416843275122e-04 - 11 -8.4672359473208624e-05 -8.4134349031640394e-04 7.6463157764214873e-04 - 12 5.2321633256319569e-04 -1.1418047427480882e-03 -3.1842516233562688e-04 - 13 3.6258187754908603e-04 -1.5531581259494627e-03 -1.9590476904013767e-04 - 14 4.2166181631324117e-04 -1.6310415916630540e-03 -3.1740232809360453e-04 - 15 9.7471807923383321e-04 -8.9939841790992827e-04 -9.6757308853409824e-04 - 16 4.1534888649229478e-06 1.7705740202856454e-05 9.0753010117813394e-04 - 17 2.5969943716026096e-04 8.7075266710270492e-04 7.7887058799645239e-04 + 1 1.8443993556507550e-03 1.0121779580008364e-03 -1.7361326034906117e-03 + 2 1.9401022924561704e-03 3.6428754787474148e-04 -2.1069540627809144e-03 + 3 1.3158623602986111e-03 8.9265747656469769e-04 -9.2144725682167822e-04 + 4 1.3306255280096579e-03 8.4281508656016844e-04 -9.6194026572521364e-04 + 5 1.3289682243418409e-03 1.6048237018838117e-03 -7.0511232123120064e-04 + 6 8.4113718611817723e-04 1.0389683283156166e-04 -4.1697370456838980e-04 + 7 5.9950574545550414e-04 -6.4437674895204296e-04 -2.7586696717479603e-04 + 8 6.4634547270655271e-04 1.4734228826538870e-04 -8.7540766366732192e-05 + 9 8.5561404484556399e-04 6.5123532540342654e-04 -2.5782947158584915e-04 + 10 2.4688038968457540e-04 -3.5995975344040265e-04 3.8912416843293944e-04 + 11 -8.4672359473939376e-05 -8.4134349031586390e-04 7.6463157764299549e-04 + 12 5.2321633256271539e-04 -1.1418047427487572e-03 -3.1842516233546950e-04 + 13 3.6258187754852045e-04 -1.5531581259503574e-03 -1.9590476904008422e-04 + 14 4.2166181631227780e-04 -1.6310415916636891e-03 -3.1740232809282303e-04 + 15 9.7471807923364706e-04 -8.9939841791107037e-04 -9.6757308853435780e-04 + 16 4.1534888650543531e-06 1.7705740203412426e-05 9.0753010117785768e-04 + 17 2.5969943716097897e-04 8.7075266710338634e-04 7.7887058799558893e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml index 6068993094..dab3d52a04 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:15 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,8 +14,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4827261116680472e+02 -1.8411194349753309e+01 -1.0752762859308649e+02 -2.1814511477016276e+02 1.7027764307147623e+02 2.1058942244057214e+01 -global_scalar: 0.9532609554739606 + -1.4827261099624999e+02 -1.8411194282828326e+01 -1.0752762861573947e+02 -2.1814511471949461e+02 1.7027764305079162e+02 2.1058942246396320e+01 +global_scalar: 0.9532609552151339 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -33,15 +34,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1395635672981443e+00 3.0168023048492310e+00 -3.5136606977867388e+00 - 19 1.5374727853253387e+00 2.6272080572819609e+00 -4.2442423140467360e+00 - 20 2.7621434607990372e+00 3.6846842324743214e+00 -3.9366036441030396e+00 - 21 4.9022821625125470e+00 -4.0760572704380627e+00 -3.6181235130909242e+00 - 22 4.3639257458824501e+00 -4.2100277325126187e+00 -4.4607219430080747e+00 - 23 5.7383384133351401e+00 -3.5881799317362106e+00 -3.8831848688588710e+00 - 24 2.0709922902331592e+00 3.1490053461169678e+00 3.1570777020268803e+00 - 25 1.3046262534530633e+00 3.2688902575528282e+00 2.5076144141701078e+00 - 26 2.5760050685080813e+00 4.0131166912605272e+00 3.2207051913215210e+00 + 18 2.1395635672857165e+00 3.0168023048413781e+00 -3.5136606977888540e+00 + 19 1.5374727853296883e+00 2.6272080573369379e+00 -4.2442423140961818e+00 + 20 2.7621434608442974e+00 3.6846842324506923e+00 -3.9366036440451500e+00 + 21 4.9022821627727593e+00 -4.0760572705753884e+00 -3.6181235130648650e+00 + 22 4.3639257458473608e+00 -4.2100277337137149e+00 -4.4607219426242057e+00 + 23 5.7383384123314833e+00 -3.5881799299869201e+00 -3.8831848693467652e+00 + 24 2.0709922900187268e+00 3.1490053461587983e+00 3.1570777021928031e+00 + 25 1.3046262535950772e+00 3.2688902578410239e+00 2.5076144139609013e+00 + 26 2.5760050692220648e+00 4.0131166908053464e+00 3.2207051908683750e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -63,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 7.8522439440007537e-04 -6.6826115062653757e-04 1.7528441282153480e-03 - 19 1.8628941719211862e-03 -3.1840047051916367e-03 2.2062694140207390e-03 - 20 -1.4430972531298200e-03 9.7564145841628493e-04 1.0686492192569898e-03 - 21 -3.0047717246574385e-03 -6.6139343888744974e-04 2.4784169377340712e-03 - 22 -3.4980341571643784e-03 -3.3380963325931002e-03 3.2191613979274040e-03 - 23 5.9333930569297746e-04 -8.6231086219834968e-03 -8.2692040355627789e-04 - 24 1.8727912311097641e-03 -2.0349136820274911e-03 1.1951471753018509e-03 - 25 3.4887365958745920e-03 -4.8232966889391266e-03 -1.2263764490291313e-03 - 26 -3.4770258010749858e-03 7.8662050223200905e-04 5.3381090661352298e-03 + 18 7.8522439447394326e-04 -6.6826115070004464e-04 1.7528441282176825e-03 + 19 1.8628941717384645e-03 -3.1840047052822556e-03 2.2062694140226819e-03 + 20 -1.4430972532419690e-03 9.7564145880034414e-04 1.0686492192457362e-03 + 21 -3.0047717260078453e-03 -6.6139344410253201e-04 2.4784169376928207e-03 + 22 -3.4980341614361554e-03 -3.3380963226435131e-03 3.2191614012082861e-03 + 23 5.9333931535562748e-04 -8.6231086111150188e-03 -8.2692040667271425e-04 + 24 1.8727912307694413e-03 -2.0349136837727452e-03 1.1951471743788897e-03 + 25 3.4887365951187166e-03 -4.8232966888750181e-03 -1.2263764478999317e-03 + 26 -3.4770257989604671e-03 7.8662050913487318e-04 5.3381090686904524e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml index 02acb437d9..5af45ebc1b 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:15 2024 epsilon: 7.5e-13 skip_tests: prerequisites: ! | @@ -14,26 +15,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817466835989e+03 -1.4228425246166137e+03 -3.6087196201914348e+03 8.7407043149698916e+02 2.1665316519769885e+02 -6.0480791462033073e+02 -global_scalar: 4.531423038570297 + -1.3754817466835991e+03 -1.4228425246166084e+03 -3.6087196201914162e+03 8.7407043149699155e+02 2.1665316519769920e+02 -6.0480791462032153e+02 +global_scalar: 4.531423038570312 run_pos: ! |2 - 1 -2.7899546859693136e-01 2.4731857340428784e+00 -1.7290667720876285e-01 - 2 3.0296221616793728e-01 2.9517129917211546e+00 -8.5798904365355155e-01 - 3 -6.9368802362166204e-01 1.2445115422149751e+00 -6.2281111185285498e-01 - 4 -1.5764879646739487e+00 1.4919714416722010e+00 -1.2492069413381564e+00 - 5 -8.9434512967954416e-01 9.3651699743538730e-01 4.0191726569957442e-01 - 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894232e+00 - 7 3.4049112905311751e-01 -9.4655677385591108e-03 -2.4634480019885228e+00 - 8 1.1644354555589662e+00 -4.8367776651302724e-01 -6.7663643931660777e-01 - 9 1.3781717822376680e+00 -2.5332509534947545e-01 2.6864954447021416e-01 - 10 2.0186368605645764e+00 -1.4285861423742918e+00 -9.6712491246325605e-01 - 11 1.7929137227200918e+00 -1.9875455388074483e+00 -1.8836565351900385e+00 - 12 3.0032775230343125e+00 -4.8983022415935312e-01 -1.6190248016126132e+00 - 13 4.0448964161972283e+00 -9.0213155125606947e-01 -1.6385398398262669e+00 - 14 2.6035151245155355e+00 -4.0874995488538129e-01 -2.6555999073602123e+00 - 15 2.9761196776308694e+00 5.6287237451798222e-01 -1.2442626194416753e+00 - 16 2.6517373020764219e+00 -2.3957035509096407e+00 3.3389262134315700e-02 - 17 2.2311114923824857e+00 -2.1018393229879817e+00 1.1496088522768926e+00 + 1 -2.7899546859693225e-01 2.4731857340428771e+00 -1.7290667720876018e-01 + 2 3.0296221616793617e-01 2.9517129917211538e+00 -8.5798904365354822e-01 + 3 -6.9368802362166271e-01 1.2445115422149740e+00 -6.2281111185285387e-01 + 4 -1.5764879646739496e+00 1.4919714416722003e+00 -1.2492069413381550e+00 + 5 -8.9434512967954460e-01 9.3651699743538508e-01 4.0191726569957453e-01 + 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894227e+00 + 7 3.4049112905311785e-01 -9.4655677385578896e-03 -2.4634480019885232e+00 + 8 1.1644354555589664e+00 -4.8367776651302741e-01 -6.7663643931660822e-01 + 9 1.3781717822376678e+00 -2.5332509534947639e-01 2.6864954447021405e-01 + 10 2.0186368605645768e+00 -1.4285861423742912e+00 -9.6712491246325705e-01 + 11 1.7929137227200933e+00 -1.9875455388074468e+00 -1.8836565351900401e+00 + 12 3.0032775230343129e+00 -4.8983022415935129e-01 -1.6190248016126136e+00 + 13 4.0448964161972292e+00 -9.0213155125606781e-01 -1.6385398398262672e+00 + 14 2.6035151245155359e+00 -4.0874995488537874e-01 -2.6555999073602123e+00 + 15 2.9761196776308694e+00 5.6287237451798344e-01 -1.2442626194416739e+00 + 16 2.6517373020764223e+00 -2.3957035509096416e+00 3.3389262134313369e-02 + 17 2.2311114923824853e+00 -2.1018393229879830e+00 1.1496088522768906e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -47,23 +48,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226165759e-04 2.6351124312057290e-04 -4.4905063547614669e-04 - 2 4.9594635271877263e-04 9.4561409237138512e-05 -5.4581325723053421e-04 - 3 3.3306088119083101e-04 2.3224949911015481e-04 -2.3659435306900835e-04 - 4 3.3692332940286717e-04 2.1926824120529722e-04 -2.4716611858556465e-04 - 5 3.3642541894624077e-04 4.1797578053943724e-04 -1.8011323945929064e-04 - 6 2.0926870695908283e-04 2.6449376032441855e-05 -1.0508922741401397e-04 - 7 1.4629046128362884e-04 -1.6873362379723068e-04 -6.8353900724071325e-05 - 8 1.5844098346817943e-04 3.7728756087619084e-05 -1.9162577392849316e-05 - 9 2.1299357198253002e-04 1.6917133003966749e-04 -6.3528006071200284e-05 - 10 5.4261569071245856e-05 -9.4655546204698666e-05 1.0511372702289738e-04 - 11 -3.2194218121523431e-05 -2.2025090185602293e-04 2.0300208519292805e-04 - 12 1.2640585449263546e-04 -2.9851081600946745e-04 -7.9476186245575585e-05 - 13 8.4523551795102263e-05 -4.0583140303608199e-04 -4.7550925831931374e-05 - 14 9.9954071734163435e-05 -4.2610809338913835e-04 -7.9255453072661880e-05 - 15 2.4417483202629980e-04 -2.3521005781669047e-04 -2.4875292755152005e-04 - 16 -9.0959360838836724e-06 3.7773746063194780e-06 2.4035204669042463e-04 - 17 5.7507084250807628e-05 2.2629200960629336e-04 2.0686926033794547e-04 + 1 4.7093296226165726e-04 2.6351124312057366e-04 -4.4905063547614750e-04 + 2 4.9594635271877263e-04 9.4561409237139244e-05 -5.4581325723053519e-04 + 3 3.3306088119083079e-04 2.3224949911015511e-04 -2.3659435306900900e-04 + 4 3.3692332940286722e-04 2.1926824120529738e-04 -2.4716611858556574e-04 + 5 3.3642541894624012e-04 4.1797578053943767e-04 -1.8011323945929113e-04 + 6 2.0926870695908297e-04 2.6449376032441903e-05 -1.0508922741401427e-04 + 7 1.4629046128362941e-04 -1.6873362379723111e-04 -6.8353900724071745e-05 + 8 1.5844098346817935e-04 3.7728756087619165e-05 -1.9162577392849147e-05 + 9 2.1299357198252962e-04 1.6917133003966793e-04 -6.3528006071199972e-05 + 10 5.4261569071245965e-05 -9.4655546204698774e-05 1.0511372702289789e-04 + 11 -3.2194218121522970e-05 -2.2025090185602350e-04 2.0300208519292848e-04 + 12 1.2640585449263589e-04 -2.9851081600946756e-04 -7.9476186245575178e-05 + 13 8.4523551795102697e-05 -4.0583140303608210e-04 -4.7550925831930561e-05 + 14 9.9954071734164248e-05 -4.2610809338913878e-04 -7.9255453072661758e-05 + 15 2.4417483202630007e-04 -2.3521005781669015e-04 -2.4875292755151984e-04 + 16 -9.0959360838839976e-06 3.7773746063194848e-06 2.4035204669042588e-04 + 17 5.7507084250806896e-05 2.2629200960629374e-04 2.0686926033794661e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml index 92754f85f5..ed92a4e5a8 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:15 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 -global_scalar: 18.3405601674144 + -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 +global_scalar: 18.340560167414402 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00 - 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00 - 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00 - 22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00 - 23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 + 18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00 + 19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00 + 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 + 21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00 + 22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00 + 23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00 - 25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00 - 26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00 + 25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00 + 26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04 - 19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03 - 20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04 - 21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03 - 22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03 - 23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04 - 24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04 - 25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04 - 26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03 + 18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04 + 19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03 + 20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04 + 21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03 + 22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03 + 23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04 + 24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04 + 25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04 + 26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/manybody-pair-pod.yaml b/unittest/force-styles/tests/manybody-pair-pod.yaml index a0820d97dd..5dcd79d3f8 100644 --- a/unittest/force-styles/tests/manybody-pair-pod.yaml +++ b/unittest/force-styles/tests/manybody-pair-pod.yaml @@ -1,8 +1,8 @@ --- -lammps_version: 3 Nov 2022 -date_generated: Thu Dec 1 23:18:00 2022 +lammps_version: 17 Apr 2024 +date_generated: Wed May 22 23:39:15 2024 epsilon: 5e-11 -skip_tests: +skip_tests: kokkos_omp prerequisites: ! | pair pod pre_commands: ! | @@ -15,142 +15,142 @@ pair_coeff: ! | * * Ta_param.pod Ta_coeff.pod Ta Ta Ta Ta Ta Ta Ta Ta extract: ! "" natoms: 64 -init_vdwl: -528.2910264879091 +init_vdwl: -410.2384867313104 init_coul: 0 init_stress: ! |2- - 8.3402602596264614e+00 2.0643446850903056e+00 1.5678421067854520e+01 -2.9333918215385154e+01 1.1525924506418683e+02 -1.5484432052782759e+00 + 4.9022269500032161e+02 4.9376448227589816e+02 5.3401476248646236e+02 -4.6634637000407110e+01 2.2048539348045341e+02 7.5348803918588310e+00 init_forces: ! |2 - 1 -2.3392393040434762e+00 6.6115449678096514e+00 6.3527759473517156e+00 - 2 -6.2200179688845711e+00 -2.3262609632188291e+00 -5.8808304295691327e+00 - 3 5.9926007198108278e-01 1.1403349257840218e+00 -9.4165026520447437e-01 - 4 -4.3700401366848958e+00 6.7048502738679057e+00 3.5634847031773593e+00 - 5 -1.7470266510830950e+00 -2.2743594271203493e+00 2.4630591043738376e-01 - 6 2.7662435046081360e+00 7.4528086029205447e+00 1.6339061500227601e+00 - 7 -2.9166253939568025e+00 -2.4536749402602376e+00 2.3182705383557933e+00 - 8 2.8946709981057628e-01 1.5909888405138495e+00 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"" +input_file: in.manybody +pair_style: uf3 3 +pair_coeff: ! | + * * Nb.uf3 Nb Nb Nb Nb Nb Nb Nb Nb +extract: ! 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-2.0845605296052469e-01 + 62 -2.1181153169676303e+00 9.6226604332888710e-01 -5.7042120154066434e-01 + 63 2.2161829432347631e+00 -7.0548049758710407e-01 -1.3062673143062038e+00 + 64 2.1263589729936818e+00 1.8281740261598369e+00 5.2543331430537403e+00 +... diff --git a/unittest/force-styles/tests/mol-pair-dpd_coul_slater_long.yaml b/unittest/force-styles/tests/mol-pair-dpd_coul_slater_long.yaml new file mode 100644 index 0000000000..e75defbf16 --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-dpd_coul_slater_long.yaml @@ -0,0 +1,103 @@ +--- +lammps_version: 17 Apr 2024 +tags: +date_generated: Tue Jun 18 21:32:14 2024 +epsilon: 5e-13 +skip_tests: gpu intel kokkos_omp single +prerequisites: ! | + atom full + pair dpd/coul/slater/long + kspace ewald +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on + comm_modify vel yes +post_commands: ! | + kspace_style ewald 1.0e-6 + kspace_modify gewald 0.3 + kspace_modify compute no +input_file: in.fourmol +pair_style: dpd/coul/slater/long 100.0 8.0 11223344 1.0 8.0 +pair_coeff: ! | + * * 0.4 4.0 yes + 1 1 0.4 4.0 yes + 2 2 0.1 2.0 no + 2 4 0.1 1.0 + 3 3 0.4 3.2 yes + 4 4 0.3 3.1 yes + 5 5 0.3 3.1 yes +extract: ! | + cut_coul 0 + lamda 0 + a0 2 + gamma 2 +natoms: 29 +init_vdwl: 50.81607024833933 +init_coul: 246.30486150616926 +init_stress: ! |2- + 3.8847917252197334e+01 6.0909421169945198e+01 1.3177337627459440e+01 -2.5125674673037557e-01 -2.6831071031318483e+01 -1.5576430133730318e+01 +init_forces: ! |2 + 1 1.7431218673076398e+00 -3.3508607597652662e-01 -2.4777022847678101e+00 + 2 4.3303449895107429e+00 -4.7270196423904629e+00 8.9179383719117788e-01 + 3 -3.0026241136767506e-01 1.4898682537669559e+00 -2.9373470062765152e+00 + 4 5.2673340332969785e+00 -4.7092409943919726e+00 -1.4235077704192447e+00 + 5 -6.8022719083087080e-01 5.7354131392205714e+00 -3.4748110565769061e+00 + 6 -3.8215670358728731e+00 2.7445299161598462e+00 -2.7043379570240411e+00 + 7 -3.3428118289029851e+00 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1.0062759048570287e+00 + 28 2.3730888896530073e+00 -1.9664779055036602e-01 1.0051483653476245e+00 + 29 -4.0524559526880868e+00 -7.5547871426945932e+00 4.6302307547994435e+00 +... diff --git a/unittest/force-styles/tests/mol-pair-hybrid_molecular.yaml b/unittest/force-styles/tests/mol-pair-hybrid_molecular.yaml new file mode 100644 index 0000000000..6bdf3b679d --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-hybrid_molecular.yaml @@ -0,0 +1,100 @@ +--- +lammps_version: 17 Apr 2024 +tags: +date_generated: Sun Jun 9 11:41:13 2024 +epsilon: 1e-13 +skip_tests: +prerequisites: ! | + atom full + pair lj/cut + pair hybrid/molecular +pre_commands: ! "" +post_commands: ! | + pair_modify mix arithmetic + pair_modify shift yes +input_file: in.fourmol +pair_style: hybrid/molecular lj/cut 8.0 lj/cut 8.0 +pair_coeff: ! | + 1 1 lj/cut 1 0.02 2.5 + 2 2 lj/cut 1 0.005 1.0 + 2 4 lj/cut 1 0.005 0.5 + 3 3 lj/cut 1 0.02 3.2 + 4 4 lj/cut 1 0.015 3.1 + 5 5 lj/cut 1 0.015 3.1 + 1 1 lj/cut 2 0.02 2.5 + 2 2 lj/cut 2 0.005 1.0 + 2 4 lj/cut 2 0.005 0.5 + 3 3 lj/cut 2 0.02 3.2 + 4 4 lj/cut 2 0.015 3.1 + 5 5 lj/cut 2 0.015 3.1 +extract: ! "" +natoms: 29 +init_vdwl: 749.2470096189497 +init_coul: 0 +init_stress: ! |2- + 2.1793857186503237e+03 2.1988957679770601e+03 4.6653994738862348e+03 -7.5956544622684351e+02 2.4751393539193327e+01 6.6652061873806679e+02 +init_forces: ! |2 + 1 -2.3333390274530565e+01 2.6994567613591136e+02 3.3272827850621587e+02 + 2 1.5828554630423909e+02 1.3025008843536872e+02 -1.8629682358915150e+02 + 3 -1.3528903744071786e+02 -3.8704313350789641e+02 -1.4568978426110147e+02 + 4 -7.8711096705734178e+00 2.1350518625352004e+00 -5.5954532185292400e+00 + 5 -2.5176757267276137e+00 -4.0521510680612876e+00 1.2152704057983799e+01 + 6 -8.3190665562047559e+02 9.6394165349388811e+02 1.1509101492424440e+03 + 7 5.8203416066164465e+01 -3.3609013622052356e+02 -1.7179626006587687e+03 + 8 1.4451392646293456e+02 -1.0927476052490437e+02 3.9990594285329479e+02 + 9 7.9156945283109025e+01 8.5273009784086469e+01 3.5032175698457496e+02 + 10 5.3118875219106917e+02 -6.1040990846582008e+02 -1.8355872692632028e+02 + 11 -2.3530157265571860e+00 -5.9077640075588906e+00 -9.6590723956614433e+00 + 12 1.7527155197359406e+01 1.0633119514682473e+01 -7.9254397903886158e+00 + 13 8.0986409580712841e+00 -3.2098088269317300e+00 -1.4896399871387667e-01 + 14 -3.3852721291218524e+00 6.8636181224987947e-01 -8.7507190862837803e+00 + 15 -2.0454999188607306e-01 8.4846165523012136e+00 3.0131615419840623e+00 + 16 4.6326331471561195e+02 -3.3087730492363477e+02 -1.1893030175606582e+03 + 17 -4.5334322060634048e+02 3.1554297967975305e+02 1.2058423415744451e+03 + 18 -1.8862629870158503e-02 -3.3402022492930034e-02 3.1000492146377390e-02 + 19 3.1843079948447594e-04 -2.3918628211596124e-04 1.7427252652160224e-03 + 20 -9.9760831169755002e-04 -1.0209184785886856e-03 3.6910973051849135e-04 + 21 -7.1566158640374354e+01 -8.1615716383825756e+01 2.2589571940670788e+02 + 22 -1.0808840769631149e+02 -2.6193799449067580e+01 -1.6957912849816358e+02 + 23 1.7964463850759611e+02 1.0782102722442450e+02 -5.6305812731665995e+01 + 24 3.6591423637378952e+01 -2.1181597497621908e+02 1.1218307103182993e+02 + 25 -1.4851496072162067e+02 2.3907129270267117e+01 -1.2485640694398953e+02 + 26 1.1191134671510581e+02 1.8789783424990625e+02 1.2650143102803206e+01 + 27 5.1810412832328005e+01 -2.2705468907750404e+02 9.0849153441059272e+01 + 28 -1.8041315533250560e+02 7.7534079082878250e+01 -1.2206962452216493e+02 + 29 1.2861063251415737e+02 1.4952718246094852e+02 3.1216040111076957e+01 +run_vdwl: 719.4532389988315 +run_coul: 0 +run_stress: ! |2- + 2.1330157554553725e+03 2.1547730555430494e+03 4.3976512412988704e+03 -7.3873325485023713e+02 4.1743707190785464e+01 6.2788040986774649e+02 +run_forces: ! |2 + 1 -2.0299419744961813e+01 2.6686193379336868e+02 3.2358785871037435e+02 + 2 1.5298617928501707e+02 1.2596516341411086e+02 -1.7961292655320207e+02 + 3 -1.3353630670276331e+02 -3.7923748676909099e+02 -1.4291839777232488e+02 + 4 -7.8374717836014449e+00 2.1276610789788282e+00 -5.5845014473593917e+00 + 5 -2.5014258629959465e+00 -4.0250131424457543e+00 1.2103512372172734e+01 + 6 -8.0681466162480240e+02 9.2165651041424792e+02 1.0270802401119468e+03 + 7 5.5780302775854636e+01 -3.1117544157318952e+02 -1.5746997989226002e+03 + 8 1.3452983973683914e+02 -1.0064660034658647e+02 3.8851792520911863e+02 + 9 7.6746213900459239e+01 8.2501469902247337e+01 3.3944351209160595e+02 + 10 5.2128033526109800e+02 -5.9920098832868109e+02 -1.8126029871233905e+02 + 11 -2.3573118088794365e+00 -5.8616944553482799e+00 -9.6049808813641686e+00 + 12 1.7503975897697526e+01 1.0626930302269722e+01 -8.0603160114673926e+00 + 13 8.0530313324242382e+00 -3.1756495175042607e+00 -1.4618315691984204e-01 + 14 -3.3416065166863160e+00 6.6492606318663194e-01 -8.6345131440736740e+00 + 15 -2.2253843262483208e-01 8.5025661635305205e+00 3.0369735873547175e+00 + 16 4.3476329769010198e+02 -3.1171099668258080e+02 -1.1135222104230593e+03 + 17 -4.2469864617016134e+02 2.9615424659116553e+02 1.1302578406458213e+03 + 18 -1.8849988250623853e-02 -3.3371648038832503e-02 3.0986306282264790e-02 + 19 3.0940278115793517e-04 -2.4634536779368854e-04 1.7433360016754921e-03 + 20 -9.8648131231171901e-04 -1.0112587092668940e-03 3.6932949186791977e-04 + 21 -7.0490777148272102e+01 -7.9749189729874402e+01 2.2171013458550721e+02 + 22 -1.0638722739944252e+02 -2.5949513934649758e+01 -1.6645597092015180e+02 + 23 1.7686805727889882e+02 1.0571023691370021e+02 -5.5243362166860535e+01 + 24 3.8206035227327128e+01 -2.1022829679057401e+02 1.1260716393332925e+02 + 25 -1.4918888258035886e+02 2.3762162241718102e+01 -1.2549193847418989e+02 + 26 1.1097064525776705e+02 1.8645512086371158e+02 1.2861565481437628e+01 + 27 5.0800867695850577e+01 -2.2296598219372004e+02 8.8607407764830413e+01 + 28 -1.7694198509380672e+02 7.6029979926844575e+01 -1.1950523558040683e+02 + 29 1.2614900659680345e+02 1.4694257504728049e+02 3.0893400701043564e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-hybrid_molecular_lj_morse.yaml b/unittest/force-styles/tests/mol-pair-hybrid_molecular_lj_morse.yaml new file mode 100644 index 0000000000..17fb89dc4f --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-hybrid_molecular_lj_morse.yaml @@ -0,0 +1,119 @@ +--- +lammps_version: 17 Apr 2024 +tags: +date_generated: Sun Jun 9 11:41:13 2024 +epsilon: 1e-13 +skip_tests: +prerequisites: ! | + atom full + pair lj/cut + pair morse + pair hybrid/molecular +pre_commands: ! "" +post_commands: ! | + pair_modify mix arithmetic + pair_modify shift yes +input_file: in.fourmol +pair_style: hybrid/molecular lj/cut 8.0 morse 8.0 +pair_coeff: ! | + 1 1 lj/cut 0.02 2.5 + 1 2 lj/cut 0.01 1.75 + 1 3 lj/cut 0.02 2.85 + 1 4 lj/cut 0.01732050807568877293 2.8 + 1 5 lj/cut 0.01732050807568877293 2.8 + 2 2 lj/cut 0.005 1.0 + 2 3 lj/cut 0.01 2.1 + 2 4 lj/cut 0.005 0.5 + 2 5 lj/cut 0.00866025403784438646 2.05 + 3 3 lj/cut 0.02 3.2 + 3 4 lj/cut 0.01732050807568877293 3.15 + 3 5 lj/cut 0.01732050807568877293 3.15 + 4 4 lj/cut 0.015 3.1 + 4 5 lj/cut 0.015 3.1 + 5 5 lj/cut 0.015 3.1 + 1 1 morse 0.0202798941614106 2.78203488021395 2.725417159299 + 1 2 morse 0.0101167811264648 3.9793050302425 1.90749569018897 + 1 3 morse 0.0202934330695928 2.43948720203264 3.10711749999622 + 1 4 morse 0.0175731334238374 2.48316585521317 3.05258880102438 + 1 5 morse 0.0175731334238374 2.48316585521317 3.05258880102438 + 2 2 morse 0.00503064360487288 6.98433077606902 1.08960295117864 + 2 3 morse 0.0101296013842819 3.31380153807866 2.28919067558352 + 2 4 morse 0.00497405122588691 14.0508902925745 0.544416409093563 + 2 5 morse 0.00877114211614446 3.39491256196178 2.23466262511073 + 3 3 morse 0.0203039874239943 2.17204344301477 3.48881895084762 + 3 4 morse 0.0175825321440736 2.20660439192238 3.43428999287994 + 3 5 morse 0.0175825321440736 2.20660439192238 3.43428999287994 + 4 4 morse 0.0152259201379927 2.24227873774009 3.37976131582396 + 4 5 morse 0.0152259201379927 2.24227873774009 3.37976131582396 + 5 5 morse 0.0152259201379927 2.24227873774009 3.37976131582396 +extract: ! "" +natoms: 29 +init_vdwl: 642.2857035487534 +init_coul: 0 +init_stress: ! |2- + 1.5446101412530770e+03 1.7762864877230827e+03 4.3406629723991382e+03 -2.4168966825090698e+02 -4.2399281241000449e+02 1.0313398732648857e+03 +init_forces: ! |2 + 1 -2.3337658999820331e+01 2.6994849929388920e+02 3.3272731927204762e+02 + 2 1.5828475525620013e+02 1.3025198646645657e+02 -1.8629727921784635e+02 + 3 -1.3530883593401191e+02 -3.8702990176780906e+02 -1.4568955729804821e+02 + 4 -7.8720974048138279e+00 2.1357285334450031e+00 -5.5956697614574145e+00 + 5 -2.5179872246085657e+00 -4.0521698308193113e+00 1.2152426584580066e+01 + 6 -1.0627539753780246e+02 3.7096636535889553e+02 1.6577829288882351e+03 + 7 6.2545311732649182e+01 -3.3857732069504033e+02 -1.7085638850072914e+03 + 8 -5.8544805218664203e+02 4.8619364551174579e+02 -1.1637016110669298e+02 + 9 7.9157108381891348e+01 8.5271268694585373e+01 3.5031950365280102e+02 + 10 5.3119792393751504e+02 -6.1042010285634149e+02 -1.8355328074325874e+02 + 11 -2.3525975498215241e+00 -5.9087312467830966e+00 -9.6592450379633981e+00 + 12 1.7514418718210869e+01 1.0633490551535797e+01 -7.9269392455530774e+00 + 13 8.0989976759274995e+00 -3.2092537736156967e+00 -1.4857368826935238e-01 + 14 -3.3831155658252769e+00 6.8583230320825528e-01 -8.7521044176224088e+00 + 15 -2.0078689909299524e-01 8.4842702953333049e+00 3.0127255727602438e+00 + 16 4.6326713730462569e+02 -3.3088113342819690e+02 -1.1892994362776039e+03 + 17 -4.5333858978430715e+02 3.1553830929611308e+02 1.2058459850635415e+03 + 18 -2.0452760511035117e-02 -3.1643654311568722e-02 2.7038063904994043e-02 + 19 6.7683676563436612e-04 5.5257878746558435e-04 3.4368881128008698e-04 + 20 -7.2687428125721442e-04 -6.4369255876917293e-04 -7.3055429537143658e-05 + 21 -7.1559739956792001e+01 -8.1623086552077027e+01 2.2588907386171752e+02 + 22 -1.0808827580116072e+02 -2.6193999003846525e+01 -1.6957935616989226e+02 + 23 1.7964485683675787e+02 1.0782085824265097e+02 -5.6306005220676077e+01 + 24 3.6592705490564995e+01 -2.1181065162415683e+02 1.1218892889291895e+02 + 25 -1.4851386780240065e+02 2.3908077402265249e+01 -1.2485428291933182e+02 + 26 1.1191162087301427e+02 1.8789805761651786e+02 1.2650515090480996e+01 + 27 5.1805674347396028e+01 -2.2705907095144718e+02 9.0852216146745278e+01 + 28 -1.8041330407833553e+02 7.7533936594765862e+01 -1.2206953762508090e+02 + 29 1.2861029896870866e+02 1.4952683033680830e+02 3.1216382013473979e+01 +run_vdwl: 612.532027437114 +run_coul: 0 +run_stress: ! |2- + 1.5079612443981077e+03 1.7300922919292559e+03 4.0645404509935297e+03 -2.2501656863720930e+02 -3.8440649220519191e+02 9.6872117407090468e+02 +run_forces: ! |2 + 1 -2.0303664163328520e+01 2.6686344032747223e+02 3.2358595259116754e+02 + 2 1.5298537986232245e+02 1.2596704781215615e+02 -1.7961336269199933e+02 + 3 -1.3340899705451542e+02 -3.7937983996408559e+02 -1.4304731523709151e+02 + 4 -7.8384621494638589e+00 2.1283385602122546e+00 -5.5847156581558837e+00 + 5 -2.5017213737297879e+00 -4.0250398342732856e+00 1.2103221315331954e+01 + 6 -1.0069389067343234e+02 3.4070704568948952e+02 1.4995989516904360e+03 + 7 5.6637967265264535e+01 -3.0800622792471370e+02 -1.5506690902144287e+03 + 8 -5.6211472712331181e+02 4.6807109251305587e+02 -1.0712697415342610e+02 + 9 7.6069407842570087e+01 8.0619386602314336e+01 3.3418245682682038e+02 + 10 5.1153094792744940e+02 -5.8811350830044319e+02 -1.7678443640175220e+02 + 11 -2.3568347685072353e+00 -5.8621926046697821e+00 -9.6044928327397194e+00 + 12 1.7464493846680174e+01 1.0623724119993449e+01 -8.0428896399820058e+00 + 13 8.0533880511151636e+00 -3.1750913604087598e+00 -1.4579751155151741e-01 + 14 -3.3394709175794697e+00 6.6440083564233665e-01 -8.6358918170724337e+00 + 15 -2.1889102849274136e-01 8.5021207266300767e+00 3.0365920030191385e+00 + 16 4.3476429812120438e+02 -3.1171100998816553e+02 -1.1135203700101538e+03 + 17 -4.2469867717957146e+02 2.9615706504039451e+02 1.1302529422580635e+03 + 18 -2.0438484585882859e-02 -3.1629705308846789e-02 2.7018991453856001e-02 + 19 6.6852492737214141e-04 5.4625495751892833e-04 3.4152455215868423e-04 + 20 -7.1620896561888831e-04 -6.3500663583982407e-04 -7.1700429767679216e-05 + 21 -7.0484355349417541e+01 -7.9756579011007801e+01 2.2170349595393003e+02 + 22 -1.0638710558378827e+02 -2.5949713015442118e+01 -1.6645620880910886e+02 + 23 1.7686828769914484e+02 1.0571007956441812e+02 -5.5243556600722584e+01 + 24 3.8207315780355771e+01 -2.1022299522635379e+02 1.1261302962088173e+02 + 25 -1.4918780612527124e+02 2.3763111781582175e+01 -1.2548982817638399e+02 + 26 1.1097093258138914e+02 1.8645536456663984e+02 1.2861936841695268e+01 + 27 5.0796145560529055e+01 -2.2297034959629724e+02 8.8610475497234873e+01 + 28 -1.7694213444502824e+02 7.6029840540845129e+01 -1.1950515191029582e+02 + 29 1.2614865956603674e+02 1.4694220660200173e+02 3.0893738250707873e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-tip4p_long.yaml index 072642c471..9a67706c01 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_long.yaml @@ -2,7 +2,7 @@ lammps_version: 17 Feb 2022 tags: unstable date_generated: Fri Mar 18 22:17:36 2022 -epsilon: 5e-13 +epsilon: 1e-10 skip_tests: prerequisites: ! | atom full diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index c9f16f6a71..3a222dde5a 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -580,6 +580,37 @@ create_atoms 1 single & "Press" : 0.0} self.assertDictEqual(self.lmp.last_thermo(), ref) + def test_extract_setting(self): + self.assertEqual(self.lmp.extract_setting("dimension"), 3) + self.assertEqual(self.lmp.extract_setting("box_exist"), 0) + self.assertEqual(self.lmp.extract_setting("kokkos_active"), 0) + self.assertEqual(self.lmp.extract_setting("kokkos_nthreads"), 0) + self.assertEqual(self.lmp.extract_setting("kokkos_ngpus"), 0) + self.lmp.command("region box block -1 1 -2 2 -3 3") + self.lmp.command("create_box 1 box") + self.lmp.command("special_bonds lj 0.0 0.5 0.8 coul 0.1 0.5 1.0") + self.assertEqual(self.lmp.extract_setting("newton_bond"), 1) + self.assertEqual(self.lmp.extract_setting("newton_pair"), 1) + self.assertEqual(self.lmp.extract_setting("triclinic"), 0) + self.assertEqual(self.lmp.extract_setting("universe_rank"), 0) + self.assertEqual(self.lmp.extract_setting("universe_size"), 1) + self.assertEqual(self.lmp.extract_setting("world_rank"), 0) + self.assertEqual(self.lmp.extract_setting("world_size"), 1) + self.assertEqual(self.lmp.extract_setting("triclinic"), 0) + self.assertEqual(self.lmp.extract_setting("comm_style"), 0) + self.assertEqual(self.lmp.extract_setting("comm_layout"), 0) + self.assertEqual(self.lmp.extract_setting("comm_mode"), 0) + self.assertEqual(self.lmp.extract_setting("ghost_velocity"), 0) + self.lmp.command("comm_style tiled") + self.lmp.command("comm_modify vel yes") + self.lmp.command("mass 1 1.0") + self.lmp.command("run 0 post no") + self.lmp.command("balance 0.1 rcb") + self.assertEqual(self.lmp.extract_setting("comm_style"), 1) + self.assertEqual(self.lmp.extract_setting("comm_layout"), 2) + self.assertEqual(self.lmp.extract_setting("comm_mode"), 0) + self.assertEqual(self.lmp.extract_setting("ghost_velocity"), 1) + def test_extract_global(self): self.lmp.command("region box block -1 1 -2 2 -3 3") self.lmp.command("create_box 1 box") @@ -609,6 +640,10 @@ create_atoms 1 single & self.lmp.command("special_bonds lj/coul 0.0 1.0 1.0") self.assertEqual(self.lmp.extract_global("special_lj"), [1.0, 0.0, 1.0, 1.0]) self.assertEqual(self.lmp.extract_global("special_coul"), [1.0, 0.0, 1.0, 1.0]) + self.assertEqual(self.lmp.extract_global("map_style"), 0) + self.assertEqual(self.lmp.extract_global("map_tag_max"), -1) + self.assertEqual(self.lmp.extract_global("sortfreq"), 1000) + self.assertEqual(self.lmp.extract_global("nextsort"), 0) # set and initialize r-RESPA self.lmp.command("run_style respa 3 5 2 pair 2 kspace 3") @@ -624,6 +659,13 @@ create_atoms 1 single & self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0]) self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0]) + # processor grid + self.assertEqual(self.lmp.extract_global("procgrid"), [1,1,1]) + self.lmp.command("comm_style tiled") + self.lmp.command("run 0 post no") + self.lmp.command("balance 0.1 rcb") + self.assertEqual(self.lmp.extract_global("procgrid"), None) + def test_create_atoms(self): self.lmp.command("boundary f p m") self.lmp.command("region box block 0 10 0 10 0 10") @@ -660,6 +702,19 @@ create_atoms 1 single & self.assertEqual(vel[i][0:3],result[i][3]) self.assertEqual(self.lmp.decode_image_flags(img[i]), result[i][4]) + def test_map_atom(self): + self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) + self.lmp.command("newton on on") + self.lmp.file("in.fourmol") + self.lmp.command("run 4 post no") + sometags = [1, 10, 25, 29] + tags = self.lmp.extract_atom("id") + sametag = self.lmp.extract_global("sametag") + for mytag in sometags: + myidx = self.lmp.map_atom(mytag) + self.assertEqual(mytag, tags[myidx]) + if sametag[myidx] < 0: continue + self.assertEqual(mytag, tags[sametag[myidx]]) ############################## if __name__ == "__main__": diff --git a/unittest/python/python-pylammps.py b/unittest/python/python-pylammps.py index 9e691b1b8c..3a7f0dc9cf 100644 --- a/unittest/python/python-pylammps.py +++ b/unittest/python/python-pylammps.py @@ -119,6 +119,10 @@ class PythonPyLammps(unittest.TestCase): self.assertEqual(self.pylmp.communication.comm_style,'brick') self.assertEqual(self.pylmp.communication.comm_layout,'uniform') self.assertEqual(self.pylmp.communication.nprocs,1) + self.assertEqual(self.pylmp.communication.nthreads,1) + self.assertEqual(self.pylmp.communication.procgrid,[1,1,1]) + self.assertEqual(self.pylmp.communication.proc_grid,[1,1,1]) + self.assertEqual(self.pylmp.communication.ghost_velocity,0) self.assertEqual(len(self.pylmp.computes),3) self.assertEqual(self.pylmp.computes[0]['name'], 'thermo_temp') self.assertEqual(self.pylmp.computes[0]['style'], 'temp') @@ -137,6 +141,11 @@ class PythonPyLammps(unittest.TestCase): self.assertEqual(self.pylmp.fixes[0]['group'], 'all') self.pylmp.group('none','empty') self.assertEqual(len(self.pylmp.groups),2) + self.pylmp.comm_style('tiled') + self.pylmp.mass('*',1.0) + self.pylmp.run('0','post','no') + self.pylmp.balance(0.1,'rcb') + self.assertEqual(self.pylmp.communication.procgrid,None) if __name__ == "__main__": unittest.main() diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 58940f6600..c486d0cf3e 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -1061,6 +1061,16 @@ TEST(Utils, timespec2seconds_hhmmss) ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:10:45"), 7845.0); } +TEST(Utils, timespec2seconds_ssfraction) +{ + ASSERT_DOUBLE_EQ(utils::timespec2seconds("5.2"), 5.2); +} + +TEST(Utils, timespec2seconds_mmfraction) +{ + ASSERT_DOUBLE_EQ(utils::timespec2seconds("2.5:10"), 160.0); +} + TEST(Utils, timespec2seconds_invalid) { ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:aa:45"), -1.0);